Supplementary Data Set 1: Riboswitches in eubacteria sense ... · Msp-2-1 Bacteria Actinobacteria...

Supplementary Data Set 1:

Riboswitches in eubacteria sense the second messenger c-di-AMP

James W. Nelson, Narasimhan Sudarsan, Kazuhiro Furukawa, Zasha Weinberg, Joy X. Wang, Ronald R. Breaker

Note: the presentation of this supplementary data on novel RNA motifs follows the pattern of our presentation of previously found conserved RNA motifs.

Contents

1 c-di-AMP riboswitch 21.1 Taxa . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21.2 Notes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91.3 Gene contexts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91.4 Conserved domains . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68

Nature Chemical Biology: doi:10.1038/nchembio.1363

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1 c-di-AMP riboswitch

1.1 Taxa

The taxonomy of each organism containing a putative c-di-AMP riboswitchis listed, with abbreviations identifying each hit (e.g., “Eco-1-1” and “Eco-1-2”

might hypothetically represent two distinct RNAs in E. coli). The abbreviationswill be used to identify each individual c-di-AMP riboswitch in Section 1.3.

abbrev. of hits taxonomy of speciesCSo-1-1 Bacteria Acidobacteria Solibacteres Solibacterales Solibacteraceae Candidatus Solibacter usitatus Ellin6076Aco-1-1 Bacteria Actinobacteria Actinobacteridae Actinomycetales Actinomycineae Actinomycetaceae Actinomyces coleocanis DSM 15436Aod-1-1 Bacteria Actinobacteria Actinobacteridae Actinomycetales Actinomycineae Actinomycetaceae Actinomyces odontolyticus ATCC 17982Aod-2-1 Bacteria Actinobacteria Actinobacteridae Actinomycetales Actinomycineae Actinomycetaceae Actinomyces odontolyticus F0309Aur-1-1 to Aur-1-2 Bacteria Actinobacteria Actinobacteridae Actinomycetales Actinomycineae Actinomycetaceae Actinomyces urogenitalis DSM 15434Avi-1-1 Bacteria Actinobacteria Actinobacteridae Actinomycetales Actinomycineae Actinomycetaceae Actinomyces viscosus C505Cac-1-1 to Cac-1-3 Bacteria Actinobacteria Actinobacteridae Actinomycetales Catenulisporineae Catenulisporaceae Catenulispora acidiphila DSM 44928Cam-1-1 Bacteria Actinobacteria Actinobacteridae Actinomycetales Corynebacterineae Corynebacteriaceae Corynebacterium amycolatum SK46Cef-1-1 to Cef-1-2 Bacteria Actinobacteria Actinobacteridae Actinomycetales Corynebacterineae Corynebacteriaceae Corynebacterium efficiens YS-314Cge-1-1 to Cge-1-2 Bacteria Actinobacteria Actinobacteridae Actinomycetales Corynebacterineae Corynebacteriaceae Corynebacterium genitalium ATCC 33030Cgl-1-1 to Cgl-1-4 Bacteria Actinobacteria Actinobacteridae Actinomycetales Corynebacterineae Corynebacteriaceae Corynebacterium glutamicum ATCC 13032Cgl-2-1 to Cgl-2-2 Bacteria Actinobacteria Actinobacteridae Actinomycetales Corynebacterineae Corynebacteriaceae Corynebacterium glutamicum RCli-1-1 to Cli-1-2 Bacteria Actinobacteria Actinobacteridae Actinomycetales Corynebacterineae Corynebacteriaceae Corynebacterium lipophiloflavum DSM 44291Gbr-1-1 to Gbr-1-2 Bacteria Actinobacteria Actinobacteridae Actinomycetales Corynebacterineae Gordoniaceae Gordonia bronchialis DSM 43247Mgi-1-1 Bacteria Actinobacteria Actinobacteridae Actinomycetales Corynebacterineae Mycobacteriaceae Mycobacterium gilvum PYR-GCKMka-1-1 to Mka-1-2 Bacteria Actinobacteria Actinobacteridae Actinomycetales Corynebacterineae Mycobacteriaceae Mycobacterium kansasii ATCC 12478Mma-1-1 Bacteria Actinobacteria Actinobacteridae Actinomycetales Corynebacterineae Mycobacteriaceae Mycobacterium marinum MMpa-1-1 Bacteria Actinobacteria Actinobacteridae Actinomycetales Corynebacterineae Mycobacteriaceae Mycobacterium parascrofulaceum ATCC BAA-614Msm-1-1 Bacteria Actinobacteria Actinobacteridae Actinomycetales Corynebacterineae Mycobacteriaceae Mycobacterium smegmatis str. MC2 155Msp-1-1 Bacteria Actinobacteria Actinobacteridae Actinomycetales Corynebacterineae Mycobacteriaceae Mycobacterium sp. JLSMsp-2-1 Bacteria Actinobacteria Actinobacteridae Actinomycetales Corynebacterineae Mycobacteriaceae Mycobacterium sp. KMSMsp-3-1 Bacteria Actinobacteria Actinobacteridae Actinomycetales Corynebacterineae Mycobacteriaceae Mycobacterium sp. MCSMul-1-1 Bacteria Actinobacteria Actinobacteridae Actinomycetales Corynebacterineae Mycobacteriaceae Mycobacterium ulcerans Agy99Mva-1-1 Bacteria Actinobacteria Actinobacteridae Actinomycetales Corynebacterineae Mycobacteriaceae Mycobacterium vanbaalenii PYR-1Mab-1-1 Bacteria Actinobacteria Actinobacteridae Actinomycetales Corynebacterineae Mycobacteriaceae Mycobacterium Mycobacteriumabscessus Mycobacterium

abscessus ATCC 19977Mav-1-1 Bacteria Actinobacteria Actinobacteridae Actinomycetales Corynebacterineae Mycobacteriaceae Mycobacterium Mycobacteriumavium complex (MAC) My-

cobacterium avium 104Mav-2-1 Bacteria Actinobacteria Actinobacteridae Actinomycetales Corynebacterineae Mycobacteriaceae Mycobacterium Mycobacteriumavium complex (MAC) My-

cobacterium avium subsp. avium ATCC 25291Mav-3-1 Bacteria Actinobacteria Actinobacteridae Actinomycetales Corynebacterineae Mycobacteriaceae Mycobacterium Mycobacteriumavium complex (MAC) My-

cobacterium avium subsp. paratuberculosis K-10Min-1-1 Bacteria Actinobacteria Actinobacteridae Actinomycetales Corynebacterineae Mycobacteriaceae Mycobacterium Mycobacteriumavium complex (MAC) My-

cobacterium intracellulare ATCC 13950Mbo-1-1 Bacteria Actinobacteria Actinobacteridae Actinomycetales Corynebacterineae Mycobacteriaceae Mycobacterium Mycobacteriumtuberculosis complex My-

cobacterium bovis AF2122/97Mbo-2-1 Bacteria Actinobacteria Actinobacteridae Actinomycetales Corynebacterineae Mycobacteriaceae Mycobacterium Mycobacteriumtuberculosis complex My-

cobacterium bovis BCG str. Pasteur 1173P2Mbo-3-1 Bacteria Actinobacteria Actinobacteridae Actinomycetales Corynebacterineae Mycobacteriaceae Mycobacterium Mycobacteriumtuberculosis complex My-

cobacterium bovis BCG str. Tokyo 172Mtu-1-1 Bacteria Actinobacteria Actinobacteridae Actinomycetales Corynebacterineae Mycobacteriaceae Mycobacterium Mycobacteriumtuberculosis complex My-

cobacterium tuberculosis ’98-R604 INH-RIF-EM’Mtu-2-1 Bacteria Actinobacteria Actinobacteridae Actinomycetales Corynebacterineae Mycobacteriaceae Mycobacterium Mycobacteriumtuberculosis complex My-

cobacterium tuberculosis 02 1987Mtu-3-1 Bacteria Actinobacteria Actinobacteridae Actinomycetales Corynebacterineae Mycobacteriaceae Mycobacterium Mycobacteriumtuberculosis complex My-

cobacterium tuberculosis 210


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Mtu-4-1 Bacteria Actinobacteria Actinobacteridae Actinomycetales Corynebacterineae Mycobacteriaceae Mycobacterium Mycobacteriumtuberculosis complex My-

cobacterium tuberculosis 94 M4241AMtu-5-1 Bacteria Actinobacteria Actinobacteridae Actinomycetales Corynebacterineae Mycobacteriaceae Mycobacterium Mycobacteriumtuberculosis complex My-

cobacterium tuberculosis CMtu-6-1 Bacteria Actinobacteria Actinobacteridae Actinomycetales Corynebacterineae Mycobacteriaceae Mycobacterium Mycobacteriumtuberculosis complex My-

cobacterium tuberculosis CDC1551Mtu-7-1 Bacteria Actinobacteria Actinobacteridae Actinomycetales Corynebacterineae Mycobacteriaceae Mycobacterium Mycobacteriumtuberculosis complex My-

cobacterium tuberculosis CPHL AMtu-8-1 Bacteria Actinobacteria Actinobacteridae Actinomycetales Corynebacterineae Mycobacteriaceae Mycobacterium Mycobacteriumtuberculosis complex My-

cobacterium tuberculosis EAS054Mtu-9-1 Bacteria Actinobacteria Actinobacteridae Actinomycetales Corynebacterineae Mycobacteriaceae Mycobacterium Mycobacteriumtuberculosis complex My-

cobacterium tuberculosis F11Mtu-10-1 Bacteria Actinobacteria Actinobacteridae Actinomycetales Corynebacterineae Mycobacteriaceae Mycobacterium Mycobacteriumtuberculosis complex My-

cobacterium tuberculosis GM 1503Mtu-11-1 Bacteria Actinobacteria Actinobacteridae Actinomycetales Corynebacterineae Mycobacteriaceae Mycobacterium Mycobacteriumtuberculosis complex My-

cobacterium tuberculosis H37RaMtu-12-1 Bacteria Actinobacteria Actinobacteridae Actinomycetales Corynebacterineae Mycobacteriaceae Mycobacterium Mycobacteriumtuberculosis complex My-

cobacterium tuberculosis H37RvMtu-13-1 Bacteria Actinobacteria Actinobacteridae Actinomycetales Corynebacterineae Mycobacteriaceae Mycobacterium Mycobacteriumtuberculosis complex My-

cobacterium tuberculosis K85Mtu-14-1 Bacteria Actinobacteria Actinobacteridae Actinomycetales Corynebacterineae Mycobacteriaceae Mycobacterium Mycobacteriumtuberculosis complex My-

cobacterium tuberculosis KZN 1435Mtu-15-1 to Mtu-15-2 Bacteria Actinobacteria Actinobacteridae Actinomycetales Corynebacterineae Mycobacteriaceae Mycobacterium Mycobacteriumtuberculosis complex My-

cobacterium tuberculosis KZN 4207Mtu-16-1 Bacteria Actinobacteria Actinobacteridae Actinomycetales Corynebacterineae Mycobacteriaceae Mycobacterium Mycobacteriumtuberculosis complex My-

cobacterium tuberculosis KZN 605Mtu-17-1 Bacteria Actinobacteria Actinobacteridae Actinomycetales Corynebacterineae Mycobacteriaceae Mycobacterium Mycobacteriumtuberculosis complex My-

cobacterium tuberculosis KZN R506Mtu-18-1 Bacteria Actinobacteria Actinobacteridae Actinomycetales Corynebacterineae Mycobacteriaceae Mycobacterium Mycobacteriumtuberculosis complex My-

cobacterium tuberculosis KZN V2475Mtu-34-1 Bacteria Actinobacteria Actinobacteridae Actinomycetales Corynebacterineae Mycobacteriaceae Mycobacterium Mycobacteriumtuberculosis complex My-

cobacterium tuberculosis str. HaarlemMtu-19-1 Bacteria Actinobacteria Actinobacteridae Actinomycetales Corynebacterineae Mycobacteriaceae Mycobacterium Mycobacteriumtuberculosis complex My-

cobacterium tuberculosis SUMu001Mtu-20-1 Bacteria Actinobacteria Actinobacteridae Actinomycetales Corynebacterineae Mycobacteriaceae Mycobacterium Mycobacteriumtuberculosis complex My-









cobacterium tuberculosis SUMu010


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Mtu-29-1 Bacteria Actinobacteria Actinobacteridae Actinomycetales Corynebacterineae Mycobacteriaceae Mycobacterium Mycobacteriumtuberculosis complex My-



cobacterium tuberculosis T17Mtu-32-1 Bacteria Actinobacteria Actinobacteridae Actinomycetales Corynebacterineae Mycobacteriaceae Mycobacterium Mycobacteriumtuberculosis complex My-

cobacterium tuberculosis T46Mtu-33-1 Bacteria Actinobacteria Actinobacteridae Actinomycetales Corynebacterineae Mycobacteriaceae Mycobacterium Mycobacteriumtuberculosis complex My-

cobacterium tuberculosis T92Nfa-1-1 Bacteria Actinobacteria Actinobacteridae Actinomycetales Corynebacterineae Nocardiaceae Nocardia farcinica IFM 10152Req-1-1 to Req-1-2 Bacteria Actinobacteria Actinobacteridae Actinomycetales Corynebacterineae Nocardiaceae Rhodococcus equi ATCC 33707Rer-1-1 to Rer-1-2 Bacteria Actinobacteria Actinobacteridae Actinomycetales Corynebacterineae Nocardiaceae Rhodococcus erythropolis PR4Rer-2-1 to Rer-2-2 Bacteria Actinobacteria Actinobacteridae Actinomycetales Corynebacterineae Nocardiaceae Rhodococcus erythropolis SK121Rjo-1-1 to Rjo-1-3 Bacteria Actinobacteria Actinobacteridae Actinomycetales Corynebacterineae Nocardiaceae Rhodococcus jostii RHA1Rop-1-1 to Rop-1-2 Bacteria Actinobacteria Actinobacteridae Actinomycetales Corynebacterineae Nocardiaceae Rhodococcus opacus B4Tpa-1-1 Bacteria Actinobacteria Actinobacteridae Actinomycetales Corynebacterineae Tsukamurellaceae Tsukamurella paurometabola DSM 20162Ace-1-1 to Ace-1-2 Bacteria Actinobacteria Actinobacteridae Actinomycetales Frankineae Acidothermaceae Acidothermus cellulolyticus 11BFal-1-1 to Fal-1-5 Bacteria Actinobacteria Actinobacteridae Actinomycetales Frankineae Frankiaceae Frankia alni ACN14aFsp-1-1 to Fsp-1-5 Bacteria Actinobacteria Actinobacteridae Actinomycetales Frankineae Frankiaceae Frankia sp. CcI3Fsp-2-1 to Fsp-2-6 Bacteria Actinobacteria Actinobacteridae Actinomycetales Frankineae Frankiaceae Frankia sp. EAN1pecFsp-4-1 to Fsp-4-5 Bacteria Actinobacteria Actinobacteridae Actinomycetales Frankineae Frankiaceae Frankia sp. EuI1cFsp-3-1 to Fsp-3-8 Bacteria Actinobacteria Actinobacteridae Actinomycetales Frankineae Frankiaceae Frankia sp. EUN1fFsy-1-1 to Fsy-1-6 Bacteria Actinobacteria Actinobacteridae Actinomycetales Frankineae Frankiaceae Frankia symbiont of Datisca glomerataGob-1-1 to Gob-1-11 Bacteria Actinobacteria Actinobacteridae Actinomycetales Frankineae Geodermatophilaceae Geodermatophilus obscurus DSM 43160Nmu-1-1 to Nmu-1-3 Bacteria Actinobacteria Actinobacteridae Actinomycetales Frankineae Nakamurellaceae Nakamurella multipartita DSM 44233Sna-1-1 to Sna-1-4 Bacteria Actinobacteria Actinobacteridae Actinomycetales Glycomycineae Glycomycetaceae Stackebrandtia nassauensis DSM 44728Kra-1-1 to Kra-1-3 Bacteria Actinobacteria Actinobacteridae Actinomycetales Kineosporiineae Kineosporiaceae Kineococcus radiotolerans SRS30216Bca-1-1 Bacteria Actinobacteria Actinobacteridae Actinomycetales Micrococcineae Beutenbergiaceae Beutenbergia cavernae DSM 12333Cfl-1-1 Bacteria Actinobacteria Actinobacteridae Actinomycetales Micrococcineae Cellulomonadaceae Cellulomonas flavigena DSM 20109Dsp-1-1 to Dsp-1-3 Bacteria Actinobacteria Actinobacteridae Actinomycetales Micrococcineae Dermacoccaceae Dermacoccus sp. Ellin185Kse-1-1 to Kse-1-3 Bacteria Actinobacteria Actinobacteridae Actinomycetales Micrococcineae Dermacoccaceae Kytococcus sedentarius DSM 20547Jsp-1-1 Bacteria Actinobacteria Actinobacteridae Actinomycetales Micrococcineae Intrasporangiaceae Janibacter sp. HTCC2649Jde-1-1 to Jde-1-2 Bacteria Actinobacteria Actinobacteridae Actinomycetales Micrococcineae Jonesiaceae Jonesia denitrificans DSM 20603Aar-1-1 to Aar-1-2 Bacteria Actinobacteria Actinobacteridae Actinomycetales Micrococcineae Micrococcaceae Arthrobacter arilaitensis Re117Aau-1-1 to Aau-1-8 Bacteria Actinobacteria Actinobacteridae Actinomycetales Micrococcineae Micrococcaceae Arthrobacter aurescens TC1Ach-1-1 to Ach-1-5 Bacteria Actinobacteria Actinobacteridae Actinomycetales Micrococcineae Micrococcaceae Arthrobacter chlorophenolicus A6Asp-1-1 to Asp-1-5 Bacteria Actinobacteria Actinobacteridae Actinomycetales Micrococcineae Micrococcaceae Arthrobacter sp. FB24Krh-1-1 Bacteria Actinobacteria Actinobacteridae Actinomycetales Micrococcineae Micrococcaceae Kocuria rhizophila DC2201Rsa-1-1 to Rsa-1-3 Bacteria Actinobacteria Actinobacteridae Actinomycetales Micrococcineae Micrococcaceae Renibacterium salmoninarum ATCC 33209Rde-1-1 Bacteria Actinobacteria Actinobacteridae Actinomycetales Micrococcineae Micrococcaceae Rothia dentocariosa ATCC 17931Rde-2-1 Bacteria Actinobacteria Actinobacteridae Actinomycetales Micrococcineae Micrococcaceae Rothia dentocariosa M567Rmu-1-1 Bacteria Actinobacteria Actinobacteridae Actinomycetales Micrococcineae Micrococcaceae Rothia mucilaginosa ATCC 25296Rmu-2-1 Bacteria Actinobacteria Actinobacteridae Actinomycetales Micrococcineae Micrococcaceae Rothia mucilaginosa DY-18Xce-1-1 to Xce-1-2 Bacteria Actinobacteria Actinobacteridae Actinomycetales Micrococcineae Promicromonosporaceae Xylanimonas cellulosilytica DSM 15894Ske-1-1 Bacteria Actinobacteria Actinobacteridae Actinomycetales Micrococcineae Sanguibacteraceae Sanguibacter keddieii DSM 10542Mau-1-1 to Mau-1-5 Bacteria Actinobacteria Actinobacteridae Actinomycetales Micromonosporineae Micromonosporaceae Micromonospora aurantiaca ATCC 27029Msp-4-1 to Msp-4-4 Bacteria Actinobacteria Actinobacteridae Actinomycetales Micromonosporineae Micromonosporaceae Micromonospora sp. ATCC 39149Msp-5-1 to Msp-5-5 Bacteria Actinobacteria Actinobacteridae Actinomycetales Micromonosporineae Micromonosporaceae Micromonospora sp. L5Sar-1-1 to Sar-1-3 Bacteria Actinobacteria Actinobacteridae Actinomycetales Micromonosporineae Micromonosporaceae Salinispora arenicola CNS-205Str-1-1 to Str-1-2 Bacteria Actinobacteria Actinobacteridae Actinomycetales Micromonosporineae Micromonosporaceae Salinispora tropica CNB-440Kfl-1-1 to Kfl-1-2 Bacteria Actinobacteria Actinobacteridae Actinomycetales Propionibacterineae Nocardioidaceae Kribbella flavida DSM 17836Nsp-1-1 to Nsp-1-2 Bacteria Actinobacteria Actinobacteridae Actinomycetales Propionibacterineae Nocardioidaceae Nocardioides sp. JS614Ser-1-1 to Ser-1-2 Bacteria Actinobacteria Actinobacteridae Actinomycetales Pseudonocardineae Pseudonocardiaceae Saccharopolyspora erythraea NRRL 2338Tbi-1-1 Bacteria Actinobacteria Actinobacteridae Actinomycetales Pseudonocardineae Pseudonocardiaceae Thermobispora bispora DSM 43833Sal-1-1 to Sal-1-6 Bacteria Actinobacteria Actinobacteridae Actinomycetales Streptomycineae Streptomycetaceae Streptomyces albus J1074Sav-1-1 to Sav-1-8 Bacteria Actinobacteria Actinobacteridae Actinomycetales Streptomycineae Streptomycetaceae Streptomyces avermitilis MA-4680Scl-1-1 to Scl-1-5 Bacteria Actinobacteria Actinobacteridae Actinomycetales Streptomycineae Streptomycetaceae Streptomyces clavuligerus ATCC 27064Sco-1-1 to Sco-1-7 Bacteria Actinobacteria Actinobacteridae Actinomycetales Streptomycineae Streptomycetaceae Streptomyces coelicolor A3(2)Sfl-1-1 to Sfl-1-6 Bacteria Actinobacteria Actinobacteridae Actinomycetales Streptomycineae Streptomycetaceae Streptomyces flavogriseus ATCC 33331Sgh-1-1 to Sgh-1-7 Bacteria Actinobacteria Actinobacteridae Actinomycetales Streptomycineae Streptomycetaceae Streptomyces ghanaensis ATCC 14672Sgr-1-1 to Sgr-1-7 Bacteria Actinobacteria Actinobacteridae Actinomycetales Streptomycineae Streptomycetaceae Streptomyces griseoflavus Tu4000Sgr-2-1 to Sgr-2-7 Bacteria Actinobacteria Actinobacteridae Actinomycetales Streptomycineae Streptomycetaceae Streptomyces griseus subsp. griseus NBRC 13350


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Shy-1-1 to Shy-1-3 Bacteria Actinobacteria Actinobacteridae Actinomycetales Streptomycineae Streptomycetaceae Streptomyces hygroscopicus ATCC 53653Sli-1-1 to Sli-1-7 Bacteria Actinobacteria Actinobacteridae Actinomycetales Streptomycineae Streptomycetaceae Streptomyces lividans TK24Spr-1-1 to Spr-1-7 Bacteria Actinobacteria Actinobacteridae Actinomycetales Streptomycineae Streptomycetaceae Streptomyces pristinaespiralis ATCC 25486Sro-1-1 to Sro-1-7 Bacteria Actinobacteria Actinobacteridae Actinomycetales Streptomycineae Streptomycetaceae Streptomyces roseosporus NRRL 11379Sro-2-1 to Sro-2-7 Bacteria Actinobacteria Actinobacteridae Actinomycetales Streptomycineae Streptomycetaceae Streptomyces roseosporus NRRL 15998Ssc-1-1 to Ssc-1-7 Bacteria Actinobacteria Actinobacteridae Actinomycetales Streptomycineae Streptomycetaceae Streptomyces scabiei 87.22Ssp-1-1 to Ssp-1-7 Bacteria Actinobacteria Actinobacteridae Actinomycetales Streptomycineae Streptomycetaceae Streptomyces sp. ACT-1Ssp-2-1 to Ssp-2-6 Bacteria Actinobacteria Actinobacteridae Actinomycetales Streptomycineae Streptomycetaceae Streptomyces sp. ACTESsp-3-1 to Ssp-3-3 Bacteria Actinobacteria Actinobacteridae Actinomycetales Streptomycineae Streptomycetaceae Streptomyces sp. CSsp-7-1 to Ssp-7-5 Bacteria Actinobacteria Actinobacteridae Actinomycetales Streptomycineae Streptomycetaceae Streptomyces sp. e14Ssp-4-1 to Ssp-4-3 Bacteria Actinobacteria Actinobacteridae Actinomycetales Streptomycineae Streptomycetaceae Streptomyces sp. Mg1Ssp-5-1 to Ssp-5-5 Bacteria Actinobacteria Actinobacteridae Actinomycetales Streptomycineae Streptomycetaceae Streptomyces sp. SPB74Ssp-6-1 to Ssp-6-5 Bacteria Actinobacteria Actinobacteridae Actinomycetales Streptomycineae Streptomycetaceae Streptomyces sp. SPB78Ssv-1-1 to Ssv-1-7 Bacteria Actinobacteria Actinobacteridae Actinomycetales Streptomycineae Streptomycetaceae Streptomyces sviceus ATCC 29083Svi-1-1 to Svi-1-4 Bacteria Actinobacteria Actinobacteridae Actinomycetales Streptomycineae Streptomycetaceae Streptomyces violaceusniger Tu 4113Svi-2-1 to Svi-2-7 Bacteria Actinobacteria Actinobacteridae Actinomycetales Streptomycineae Streptomycetaceae Streptomyces viridochromogenes DSM 40736Sro-3-1 to Sro-3-6 Bacteria Actinobacteria Actinobacteridae Actinomycetales Streptosporangineae Streptosporangiaceae Streptosporangium roseum DSM 43021Tcu-1-1 to Tcu-1-5 Bacteria Actinobacteria Actinobacteridae Actinomycetales Streptosporangineae Thermomonosporaceae Thermomonospora curvata DSM 43183Cwo-1-1 to Cwo-1-9 Bacteria Actinobacteria Rubrobacteridae Solirubrobacterales Conexibacteraceae Conexibacter woesei DSM 14684Rca-1-1 Bacteria Chloroflexi Chloroflexales Chloroflexaceae Roseiflexus castenholzii DSM 13941Csp-1-1 Bacteria Cyanobacteria Chroococcales Cyanothece sp. ATCC 51142Csp-2-1 Bacteria Cyanobacteria Chroococcales Cyanothece sp. CCY0110Csp-3-1 to Csp-3-4 Bacteria Cyanobacteria Chroococcales Cyanothece sp. PCC 7424Csp-4-1 to Csp-4-2 Bacteria Cyanobacteria Chroococcales Cyanothece sp. PCC 7425Csp-5-1 to Csp-5-4 Bacteria Cyanobacteria Chroococcales Cyanothece sp. PCC 7822Csp-6-1 to Csp-6-2 Bacteria Cyanobacteria Chroococcales Cyanothece sp. PCC 8801Csp-7-1 to Csp-7-2 Bacteria Cyanobacteria Chroococcales Cyanothece sp. PCC 8802Mae-1-1 Bacteria Cyanobacteria Chroococcales Microcystis aeruginosa NIES-843Ssp-8-1 Bacteria Cyanobacteria Chroococcales Synechococcus sp. PCC 7002Ssp-9-1 Bacteria Cyanobacteria Chroococcales Synechocystis sp. PCC 6803’az-1-1 to ’az-1-2 Bacteria Cyanobacteria Nostocales Nostocaceae Anabaena ’Nostoc azollae’ 0708Ava-1-1 to Ava-1-4 Bacteria Cyanobacteria Nostocales Nostocaceae Anabaena variabilis ATCC 29413 (Anabaena flos-aquae UTEX 1444)Cra-1-1 Bacteria Cyanobacteria Nostocales Nostocaceae Cylindrospermopsis raciborskii CS-505Npu-1-1 to Npu-1-3 Bacteria Cyanobacteria Nostocales Nostocaceae Nostoc punctiforme PCC 73102 (Nostoc punctiforme ATCC 29133)Nsp-2-1 to Nsp-2-4 Bacteria Cyanobacteria Nostocales Nostocaceae Nostoc sp. PCC 7120Rbr-1-1 Bacteria Cyanobacteria Nostocales Nostocaceae Raphidiopsis brookii D9Asp-2-1 Bacteria Cyanobacteria Oscillatoriales Arthrospira sp. PCC 8005Ama-1-1 Bacteria Cyanobacteria Oscillatoriales Arthrospira Arthrospiramaxima Arthrospira maxima CS-328Apl-1-1 Bacteria Cyanobacteria Oscillatoriales Arthrospira Arthrospiraplatensis Arthrospira platensis str. ParacaLsp-1-1 to Lsp-1-2 Bacteria Cyanobacteria Oscillatoriales Lyngbya sp. PCC 8106Mch-1-1 Bacteria Cyanobacteria Oscillatoriales Microcoleus chthonoplastes PCC 7420Osp-1-1 Bacteria Cyanobacteria Oscillatoriales Oscillatoria sp. PCC 6506 (Oscillatoria sp. PCC 9029)Ter-1-1 Bacteria Cyanobacteria Oscillatoriales Trichodesmium erythraeum IMS101Aac-1-1 to Aac-1-3 Bacteria Firmicutes Bacillales Alicyclobacillaceae Alicyclobacillus acidocaldarius LAA1Aac-2-1 to Aac-2-4 Bacteria Firmicutes Bacillales Alicyclobacillaceae Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446Btu-1-1 to Btu-1-3 Bacteria Firmicutes Bacillales Alicyclobacillaceae Bacillus tusciae DSM 2912Bam-1-1 Bacteria Firmicutes Bacillales Bacillaceae Bacillus amyloliquefaciens DSM7Bam-2-1 Bacteria Firmicutes Bacillales Bacillaceae Bacillus amyloliquefaciens FZB42Bat-1-1 to Bat-1-2 Bacteria Firmicutes Bacillales Bacillaceae Bacillus atrophaeus 1942Bce-1-1 Bacteria Firmicutes Bacillales Bacillaceae Bacillus cellulosilyticus DSM 2522Bco-1-1 to Bco-1-2 Bacteria Firmicutes Bacillales Bacillaceae Bacillus coagulans 36D1Bha-1-1 Bacteria Firmicutes Bacillales Bacillaceae Bacillus halodurans C-125Bli-1-1 to Bli-1-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus licheniformis ATCC 14580 (DSM 13)Bme-1-1 to Bme-1-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus megaterium DSM319Bme-2-1 to Bme-2-5 Bacteria Firmicutes Bacillales Bacillaceae Bacillus megaterium QM B1551Bps-1-1 Bacteria Firmicutes Bacillales Bacillaceae Bacillus pseudofirmus OF4Bps-2-1 to Bps-2-5 Bacteria Firmicutes Bacillales Bacillaceae Bacillus pseudomycoides DSM 12442Bpu-1-1 to Bpu-1-2 Bacteria Firmicutes Bacillales Bacillaceae Bacillus pumilus ATCC 7061Bpu-2-1 to Bpu-2-2 Bacteria Firmicutes Bacillales Bacillaceae Bacillus pumilus SAFR-032Bsp-1-1 to Bsp-1-2 Bacteria Firmicutes Bacillales Bacillaceae Bacillus sp. B14905Bsp-3-1 Bacteria Firmicutes Bacillales Bacillaceae Bacillus sp. m3-13Bsp-2-1 to Bsp-2-6 Bacteria Firmicutes Bacillales Bacillaceae Bacillus sp. NRRL B-14911Bsu-1-1 to Bsu-1-3 Bacteria Firmicutes Bacillales Bacillaceae Bacillus subtilis subsp. spizizenii ATCC 6633Bsu-2-1 to Bsu-2-3 Bacteria Firmicutes Bacillales Bacillaceae Bacillus subtilis subsp. spizizenii str. W23Bsu-3-1 to Bsu-3-2 Bacteria Firmicutes Bacillales Bacillaceae Bacillus subtilis subsp. subtilis str. 168


6

Bsu-4-1 Bacteria Firmicutes Bacillales Bacillaceae Bacillus subtilis subsp. subtilis str. JH642Bsu-5-1 to Bsu-5-2 Bacteria Firmicutes Bacillales Bacillaceae Bacillus subtilis subsp. subtilis str. NCIB 3610Bsu-6-1 to Bsu-6-2 Bacteria Firmicutes Bacillales Bacillaceae Bacillus subtilis subsp. subtilis str. SMYBan-2-1 to Ban-2-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus anthracis str. ’Ames Ancestor’Ban-3-1 to Ban-3-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus anthracis str. A0174Ban-4-1 to Ban-4-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus anthracis str. A0193Ban-5-1 to Ban-5-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus anthracis str. A0248Ban-6-1 to Ban-6-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus anthracis str. A0389Ban-7-1 to Ban-7-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus anthracis str. A0442Ban-8-1 to Ban-8-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus anthracis str. A0465Ban-9-1 to Ban-9-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus anthracis str. A0488Ban-10-1 to Ban-10-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus anthracis str. A1055Ban-11-1 to Ban-11-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus anthracis str. A2012Ban-12-1 to Ban-12-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus anthracis str. AmesBan-13-1 to Ban-13-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus anthracis str. Australia 94Ban-14-1 to Ban-14-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus anthracis str. CDC 684Ban-15-1 to Ban-15-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus anthracis str. CNEVA-9066Ban-16-1 to Ban-16-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus anthracis str. Kruger BBan-17-1 to Ban-17-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus anthracis str. SterneBan-18-1 to Ban-18-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus anthracis str. VollumBan-19-1 to Ban-19-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus anthracis str. Western North America USA6153Ban-1-1 to Ban-1-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus anthracis Tsiankovskii-IBce-2-1 to Bce-2-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus cereus 03BB102Bce-3-1 to Bce-3-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus cereus 03BB108Bce-4-1 to Bce-4-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus cereus 172560WBce-5-1 to Bce-5-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus cereus 95/8201Bce-6-1 to Bce-6-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus cereus AH1134Bce-7-1 to Bce-7-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus cereus AH1271Bce-8-1 to Bce-8-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus cereus AH1272Bce-9-1 to Bce-9-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus cereus AH1273Bce-10-1 to Bce-10-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus cereus AH187Bce-11-1 to Bce-11-5 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus cereus AH603Bce-12-1 to Bce-12-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus cereus AH621Bce-13-1 to Bce-13-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus cereus AH676Bce-14-1 to Bce-14-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus cereus AH820Bce-15-1 to Bce-15-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus cereus ATCC 10876Bce-16-1 to Bce-16-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus cereus ATCC 10987Bce-17-1 to Bce-17-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus cereus ATCC 14579Bce-18-1 to Bce-18-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus cereus ATCC 4342Bce-19-1 to Bce-19-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus cereus B4264Bce-20-1 to Bce-20-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus cereus BDRD-Cer4Bce-21-1 to Bce-21-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus cereus BDRD-ST196Bce-22-1 to Bce-22-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus cereus BDRD-ST24Bce-23-1 to Bce-23-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus cereus BDRD-ST26Bce-24-1 to Bce-24-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus cereus BGSC 6E1Bce-44-1 to Bce-44-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus cereus biovar anthracis str. CIBce-25-1 to Bce-25-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus cereus E33LBce-26-1 to Bce-26-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus cereus F65185Bce-27-1 to Bce-27-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus cereus G9241Bce-28-1 to Bce-28-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus cereus G9842Bce-29-1 to Bce-29-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus cereus H3081.97Bce-45-1 to Bce-45-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus cereus m1293Bce-46-1 to Bce-46-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus cereus m1550Bce-30-1 to Bce-30-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus cereus MM3Bce-31-1 to Bce-31-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus cereus NVH0597-99Bce-32-1 to Bce-32-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus cereus Q1Bce-33-1 to Bce-33-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus cereus R309803Bce-34-1 to Bce-34-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus cereus Rock1-15Bce-35-1 to Bce-35-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus cereus Rock1-3Bce-36-1 to Bce-36-2 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus cereus Rock3-28Bce-37-1 to Bce-37-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus cereus Rock3-29Bce-38-1 to Bce-38-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus cereus Rock3-42Bce-39-1 to Bce-39-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus cereus Rock3-44Bce-40-1 to Bce-40-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus cereus Rock4-18Bce-41-1 to Bce-41-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus cereus Rock4-2


7

Bce-42-1 to Bce-42-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus cereus SJ1Bce-43-1 to Bce-43-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus cereus WBcy-1-1 to Bcy-1-3 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus cytotoxicus NVH 391-98Bmy-1-1 to Bmy-1-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus mycoides DSM 2048Bmy-2-1 to Bmy-2-5 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus mycoides Rock1-4Bmy-3-1 to Bmy-3-5 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus mycoides Rock3-17Bth-1-1 to Bth-1-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus thuringiensis BMB171Bth-2-1 to Bth-2-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus thuringiensis Bt407Bth-3-1 to Bth-3-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus thuringiensis IBL 200Bth-4-1 to Bth-4-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus thuringiensis IBL 4222Bth-5-1 to Bth-5-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus thuringiensis serovar andalousiensis BGSC 4AW1Bth-6-1 to Bth-6-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus thuringiensis serovar berliner ATCC 10792Bth-7-1 to Bth-7-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus thuringiensis serovar huazhongensis BGSC 4BD1Bth-8-1 to Bth-8-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus thuringiensis serovar israelensis ATCC 35646Bth-9-1 to Bth-9-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus thuringiensis serovar konkukian str. 97-27Bth-10-1 to Bth-10-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus thuringiensis serovar kurstaki str. T03a001Bth-11-1 to Bth-11-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus thuringiensis serovar monterrey BGSC 4AJ1Bth-12-1 to Bth-12-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus thuringiensis serovar pakistani str. T13001Bth-13-1 to Bth-13-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus thuringiensis serovar pondicheriensis BGSC 4BA1Bth-14-1 to Bth-14-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus thuringiensis serovar pulsiensis BGSC 4CC1Bth-15-1 to Bth-15-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus thuringiensis serovar sotto str. T04001Bth-16-1 to Bth-16-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus thuringiensis serovar thuringiensis str. T01001Bth-17-1 to Bth-17-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus thuringiensis serovar tochigiensis BGSC 4Y1Bth-18-1 to Bth-18-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus thuringiensis str. Al HakamBwe-1-1 to Bwe-1-4 Bacteria Firmicutes Bacillales Bacillaceae Bacillus Bacilluscereus group Bacillus weihenstephanensis KBAB4Gka-1-1 to Gka-1-2 Bacteria Firmicutes Bacillales Bacillaceae Geobacillus kaustophilus HTA426Gsp-1-1 Bacteria Firmicutes Bacillales Bacillaceae Geobacillus sp. C56-T3Gsp-2-1 Bacteria Firmicutes Bacillales Bacillaceae Geobacillus sp. Y4.1MC1Gsp-3-1 to Gsp-3-8 Bacteria Firmicutes Bacillales Bacillaceae Geobacillus sp. Y412MC10Gsp-4-1 Bacteria Firmicutes Bacillales Bacillaceae Geobacillus sp. Y412MC52Gsp-5-1 Bacteria Firmicutes Bacillales Bacillaceae Geobacillus sp. Y412MC61Gth-1-1 Bacteria Firmicutes Bacillales Bacillaceae Geobacillus thermoglucosidasius C56-YS93Lfu-1-1 to Lfu-1-2 Bacteria Firmicutes Bacillales Bacillaceae Lysinibacillus fusiformis ZC1Lsp-2-1 to Lsp-2-2 Bacteria Firmicutes Bacillales Bacillaceae Lysinibacillus sphaericus C3-41Oih-1-1 Bacteria Firmicutes Bacillales Bacillaceae Oceanobacillus iheyensis HTE831Esi-1-1 Bacteria Firmicutes Bacillales Bacillales Family XII. IncertaeSedis Exiguobacterium sibiricum 255-15Esp-1-1 Bacteria Firmicutes Bacillales Bacillales Family XII. IncertaeSedis Exiguobacterium sp. AT1bBbr-1-1 to Bbr-1-5 Bacteria Firmicutes Bacillales Paenibacillaceae Brevibacillus brevis NBRC 100599Pcu-1-1 to Pcu-1-7 Bacteria Firmicutes Bacillales Paenibacillaceae Paenibacillus curdlanolyticus YK9Pla-1-1 to Pla-1-3 Bacteria Firmicutes Bacillales Paenibacillaceae Paenibacillus larvae subsp. larvae BRL-230010Ppo-1-1 to Ppo-1-5 Bacteria Firmicutes Bacillales Paenibacillaceae Paenibacillus polymyxa E681Ppo-2-1 to Ppo-2-5 Bacteria Firmicutes Bacillales Paenibacillaceae Paenibacillus polymyxa SC2Psp-1-1 to Psp-1-7 Bacteria Firmicutes Bacillales Paenibacillaceae Paenibacillus sp. JDR-2Psp-2-1 to Psp-2-8 Bacteria Firmicutes Bacillales Paenibacillaceae Paenibacillus sp. oral taxon 786 str. D14Ath-1-1 to Ath-1-3 Bacteria Firmicutes Clostridia Clostridiales Anaerocellumgroup Anaerocellum thermophilum DSM 6725Bhy-1-1 Bacteria Firmicutes Clostridia Clostridiales Blautia hydrogenotrophica DSM 10507 (RuminococcusAor-1-1 Bacteria Firmicutes Clostridia Clostridiales Clostridiaceae Alkaliphilus oremlandii OhILAsCac-2-1 to Cac-2-2 Bacteria Firmicutes Clostridia Clostridiales Clostridiaceae Clostridium acetobutylicum ATCC 824Cas-1-1 Bacteria Firmicutes Clostridia Clostridiales Clostridiaceae Clostridium asparagiforme DSM 15981Cbe-1-1 to Cbe-1-2 Bacteria Firmicutes Clostridia Clostridiales Clostridiaceae Clostridium beijerinckii NCIMB 8052Cbo-1-1 Bacteria Firmicutes Clostridia Clostridiales Clostridiaceae Clostridium bolteae ATCC BAA-613Cbo-2-1 to Cbo-2-2 Bacteria Firmicutes Clostridia Clostridiales Clostridiaceae Clostridium botulinum A str. ATCC 19397Cbo-3-1 to Cbo-3-2 Bacteria Firmicutes Clostridia Clostridiales Clostridiaceae Clostridium botulinum A str. ATCC 3502Cbo-4-1 to Cbo-4-2 Bacteria Firmicutes Clostridia Clostridiales Clostridiaceae Clostridium botulinum A str. HallCbo-5-1 to Cbo-5-2 Bacteria Firmicutes Clostridia Clostridiales Clostridiaceae Clostridium botulinum A2 str. KyotoCbo-6-1 to Cbo-6-2 Bacteria Firmicutes Clostridia Clostridiales Clostridiaceae Clostridium botulinum A3 str. Loch MareeCbo-7-1 to Cbo-7-2 Bacteria Firmicutes Clostridia Clostridiales Clostridiaceae Clostridium botulinum B1 str. OkraCbo-8-1 to Cbo-8-2 Bacteria Firmicutes Clostridia Clostridiales Clostridiaceae Clostridium botulinum Ba4 str. 657Cbo-9-1 to Cbo-9-2 Bacteria Firmicutes Clostridia Clostridiales Clostridiaceae Clostridium botulinum BfCbo-10-1 Bacteria Firmicutes Clostridia Clostridiales Clostridiaceae Clostridium botulinum C str. EklundCbo-11-1 Bacteria Firmicutes Clostridia Clostridiales Clostridiaceae Clostridium botulinum D str. 1873Cbo-12-1 to Cbo-12-2 Bacteria Firmicutes Clostridia Clostridiales Clostridiaceae Clostridium botulinum F str. LangelandCbo-13-1 to Cbo-13-2 Bacteria Firmicutes Clostridia Clostridiales Clostridiaceae Clostridium botulinum NCTC 2916Cca-1-1 to Cca-1-3 Bacteria Firmicutes Clostridia Clostridiales Clostridiaceae Clostridium carboxidivorans P7Cce-1-1 to Cce-1-4 Bacteria Firmicutes Clostridia Clostridiales Clostridiaceae Clostridium cellulolyticum H10


8

Ckl-1-1 to Ckl-1-2 Bacteria Firmicutes Clostridia Clostridiales Clostridiaceae Clostridium kluyveri DSM 555Ckl-2-1 to Ckl-2-2 Bacteria Firmicutes Clostridia Clostridiales Clostridiaceae Clostridium kluyveri NBRC 12016Clj-1-1 to Clj-1-2 Bacteria Firmicutes Clostridia Clostridiales Clostridiaceae Clostridium ljungdahlii DSM 13528Cno-1-1 Bacteria Firmicutes Clostridia Clostridiales Clostridiaceae Clostridium novyi NTCpa-1-1 to Cpa-1-5 Bacteria Firmicutes Clostridia Clostridiales Clostridiaceae Clostridium papyrosolvens DSM 2782Cph-1-1 Bacteria Firmicutes Clostridia Clostridiales Clostridiaceae Clostridium phytofermentans ISDgCsp-8-1 Bacteria Firmicutes Clostridia Clostridiales Clostridiaceae Clostridium sp. M62/1Csp-9-1 to Csp-9-2 Bacteria Firmicutes Clostridia Clostridiales Clostridiaceae Clostridium sporogenes ATCC 15579Cte-1-1 to Cte-1-2 Bacteria Firmicutes Clostridia Clostridiales Clostridiaceae Clostridium tetani E88Cth-1-1 Bacteria Firmicutes Clostridia Clostridiales Clostridiaceae Clostridium thermocellum ATCC 27405Cth-2-1 Bacteria Firmicutes Clostridia Clostridiales Clostridiaceae Clostridium thermocellum DSM 2360Cth-3-1 Bacteria Firmicutes Clostridia Clostridiales Clostridiaceae Clostridium thermocellum JW20Cba-1-1 Bacteria Firmicutes Clostridia Clostridiales bacterium 1 7 47FAASth-1-1 to Sth-1-2 Bacteria Firmicutes Clostridia Clostridiales ClostridialesFamily XVIII. Incertae Sedis Symbiobacterium thermophilum IAM 14863Hmo-1-1 Bacteria Firmicutes Clostridia Clostridiales Heliobacteriaceae Heliobacterium modesticaldum Ice1CDe-1-1 Bacteria Firmicutes Clostridia Clostridiales Peptococcaceae Candidatus Desulforudis audaxviator MP104CDha-1-1 to Dha-1-4 Bacteria Firmicutes Clostridia Clostridiales Peptococcaceae Desulfitobacterium hafniense DCB-2Dha-2-1 to Dha-2-5 Bacteria Firmicutes Clostridia Clostridiales Peptococcaceae Desulfitobacterium hafniense Y51Dac-1-1 to Dac-1-3 Bacteria Firmicutes Clostridia Clostridiales Peptococcaceae Desulfotomaculum acetoxidans DSM 771Dre-1-1 to Dre-1-4 Bacteria Firmicutes Clostridia Clostridiales Peptococcaceae Desulfotomaculum reducens MI-1Pth-1-1 to Pth-1-5 Bacteria Firmicutes Clostridia Clostridiales Peptococcaceae Pelotomaculum thermopropionicum SITpo-1-1 to Tpo-1-3 Bacteria Firmicutes Clostridia Clostridiales Peptococcaceae Thermincola potens JRAce-2-1 to Ace-2-3 Bacteria Firmicutes Clostridia Clostridiales Ruminococcaceae Acetivibrio cellulolyticus CD2Swo-1-1 to Swo-1-2 Bacteria Firmicutes Clostridia Clostridiales Syntrophomonadaceae Syntrophomonas wolfei subsp. wolfei str. GoettingenSli-2-1 to Sli-2-2 Bacteria Firmicutes Clostridia Clostridiales Syntrophomonadaceae Syntrophothermus lipocalidus DSM 12680Afe-1-1 Bacteria Firmicutes Clostridia Clostridiales Veillonellaceae Acidaminococcus fermentans DSM 20731Asp-3-1 Bacteria Firmicutes Clostridia Clostridiales Veillonellaceae Acidaminococcus sp. D21Mmu-1-1 Bacteria Firmicutes Clostridia Clostridiales Veillonellaceae Mitsuokella multacida DSM 20544Ssp-10-1 Bacteria Firmicutes Clostridia Clostridiales Veillonellaceae Selenomonas sputigena ATCC 35185Tca-1-1 to Tca-1-4 Bacteria Firmicutes Clostridia Clostridiales Veillonellaceae Thermosinus carboxydivorans Nor1Hor-1-1 Bacteria Firmicutes Clostridia Halanaerobiales Halanaerobiaceae Halothermothrix orenii H 168Aar-2-1 to Aar-2-2 Bacteria Firmicutes Clostridia Halanaerobiales Halobacteroidaceae Acetohalobium arabaticum DSM 5501Nth-1-1 Bacteria Firmicutes Clostridia Natranaerobiales Natranaerobiaceae Natranaerobius thermophilus JW/NM-WN-LFCpa-2-1 to Cpa-2-3 Bacteria Firmicutes Clostridia Thermoanaerobacterales Thermoanaerobacteraceae Carboxydibrachium pacificum DSM 12653Chy-1-1 Bacteria Firmicutes Clostridia Thermoanaerobacterales Thermoanaerobacteraceae Carboxydothermus hydrogenoformans Z-2901Ade-1-1 to Ade-1-3 Bacteria Firmicutes Clostridia Thermoanaerobacterales Thermoanaerobacteraceae Moorella group Ammonifex degensii KC4Mth-1-1 to Mth-1-6 Bacteria Firmicutes Clostridia Thermoanaerobacterales Thermoanaerobacteraceae Moorella group Moorella thermoacetica ATCC 39073Tbr-1-1 to Tbr-1-3 Bacteria Firmicutes Clostridia Thermoanaerobacterales Thermoanaerobacteraceae Thermoanaerobacter brockii subsp. finnii Ako-1Tet-1-1 to Tet-1-3 Bacteria Firmicutes Clostridia Thermoanaerobacterales Thermoanaerobacteraceae Thermoanaerobacter ethanolicus CCSD1Tit-1-1 to Tit-1-3 Bacteria Firmicutes Clostridia Thermoanaerobacterales Thermoanaerobacteraceae Thermoanaerobacter italicus Ab9Tma-1-1 to Tma-1-3 Bacteria Firmicutes Clostridia Thermoanaerobacterales Thermoanaerobacteraceae Thermoanaerobacter mathranii subsp. mathranii str. A3Tps-1-1 to Tps-1-3 Bacteria Firmicutes Clostridia Thermoanaerobacterales Thermoanaerobacteraceae Thermoanaerobacter pseudethanolicus ATCC 33223Tsp-1-1 to Tsp-1-3 Bacteria Firmicutes Clostridia Thermoanaerobacterales Thermoanaerobacteraceae Thermoanaerobacter sp. X513Tsp-2-1 to Tsp-2-3 Bacteria Firmicutes Clostridia Thermoanaerobacterales Thermoanaerobacteraceae Thermoanaerobacter sp. X514Tsp-3-1 to Tsp-3-3 Bacteria Firmicutes Clostridia Thermoanaerobacterales Thermoanaerobacteraceae Thermoanaerobacter sp. X561Tte-1-1 to Tte-1-4 Bacteria Firmicutes Clostridia Thermoanaerobacterales Thermoanaerobacteraceae Thermoanaerobacter tengcongensis MB4Twi-1-1 to Twi-1-3 Bacteria Firmicutes Clostridia Thermoanaerobacterales Thermoanaerobacteraceae Thermoanaerobacter wiegelii Rt8.B1Cob-1-1 to Cob-1-3 Bacteria Firmicutes Clostridia Thermoanaerobacterales Thermoanaerobacterales Family III. Incertae Sedis Caldicellulosiruptor obsidiansis OB47Csa-1-1 to Csa-1-3 Bacteria Firmicutes Clostridia Thermoanaerobacterales Thermoanaerobacterales Family III. Incertae Sedis Caldicellulosiruptor saccharolyticus DSM 8903Tth-1-1 to Tth-1-5 Bacteria Firmicutes Clostridia Thermoanaerobacterales Thermoanaerobacterales Family III. Incertae Sedis Thermoanaerobacterium thermosaccharolyticum

DSM 571Toc-1-1 to Toc-1-3 Bacteria Firmicutes Clostridia Thermoanaerobacterales Thermoanaerobacterales Family III. Incertae Sedis Thermosediminibacter oceani DSM 16646Fmo-1-1 to Fmo-1-2 Bacteria Fusobacteria Fusobacteriales Fusobacteriaceae Fusobacterium mortiferum ATCC 9817Ful-1-1 Bacteria Fusobacteria Fusobacteriales Fusobacteriaceae Fusobacterium ulcerans ATCC 49185Fva-1-1 Bacteria Fusobacteria Fusobacteriales Fusobacteriaceae Fusobacterium varium ATCC 27725Dfr-1-1 Bacteria Proteobacteria Deltaproteobacteria Desulfovibrionales Desulfovibrionaceae Desulfovibrio fructosovorans JJDma-1-1 Bacteria Proteobacteria Deltaproteobacteria Desulfovibrionales Desulfovibrionaceae Desulfovibrio magneticus RS-1Dvu-1-1 Bacteria Proteobacteria Deltaproteobacteria Desulfovibrionales Desulfovibrionaceae Desulfovibrio vulgaris str. ’Miyazaki F’Gbe-1-1 Bacteria Proteobacteria Deltaproteobacteria Desulfuromonadales Geobacteraceae Geobacter bemidjiensis BemGsu-1-1 Bacteria Proteobacteria Deltaproteobacteria Desulfuromonadales Geobacteraceae Geobacter sulfurreducens PCAPpr-1-1 Bacteria Proteobacteria Deltaproteobacteria Desulfuromonadales Pelobacteraceae Pelobacter propionicus DSM 2379Sac-1-1 Bacteria Proteobacteria Deltaproteobacteria Syntrophobacterales Syntrophaceae Syntrophus aciditrophicus SBSfu-1-1 Bacteria Proteobacteria Deltaproteobacteria Syntrophobacterales Syntrophobacteraceae Syntrophobacter fumaroxidans MPOBTte-2-1 to Tte-2-2 Bacteria Thermobaculum terrenum ATCC BAA-798Ote-1-1 Bacteria Verrucomicrobia Opitutae Opitutales Opitutaceae Opitutus terrae PB90-1


9

Cfl-2-1 to Cfl-2-2 Bacteria Verrucomicrobia Spartobacteria Chthoniobacter flavus Ellin428bEl-1-1 to bEl-1-3 Bacteria Verrucomicrobia Verrucomicrobiae Verrucomicrobiales Verrucomicrobia subdivision 3 bacterium Ellin514Vsp-1-1 Bacteria Verrucomicrobia Verrucomicrobiae Verrucomicrobiales Verrucomicrobiaceae Verrucomicrobium spinosum DSM 4136env-1 to env-1927 environmental samples

1.2 Notes

Superscript numbers are used to annotate any c-di-AMP riboswitch that hasspecial characteristics (described below). These numeric annotations will be used

in Section 1.3. The meaning of the numbers are as follows.

1 Unclear homology. Some mutations in otherwise well conserved nucleotides. Ahomology search using Infernal with the single sequence and predicted sec-ondary structure as query revealed no homologs with similarly mutated corenucleotides. Therefore, this sequence might be a false positive.

2 Translated BLAST searches suggest that the immediately downstream gene is a

transglycosylase.

3 Alignment of P1 stem is unclear.

4 Several mutations in highly conserved nucleotides. Upstream of CHAP domain,TIGR02594. CHAP domains are proposed as amidases that include pepti-doglycan hydrolases.

1.3 Gene contexts

Each c-di-AMP riboswitch (indicated by “RNA→”) is listed.The surroundinggenes for each hit is given. Environmental sequences and some RefSeq entries lackgene annotations, and no genes are listed for such sequences. The direction of eachgene is indicated with an arrow (→), and each conserved domain in the gene iscolored. Conserved domains associated with more than one c-di-AMP riboswitchare assigned a color; other domains are gray. Information about these conserveddomains is given in Section 1.4.The accession number of the sequence containing

each c-di-AMP riboswitch is given. Accessions beginning with “NC ” or “NZ ” areRefSeq, while other accession refer to environmental samples. Nucleotide coordi-nates are given for the 5′ and 3′ boundaries of each. If the 5′ coordinate is greaterthan the 3′ coordinate, the RNA is present on the reverse-complement strand of thecontaining genomic DNA sequence. Each hit is denoted by an abbreviation (like“Eco-1-1”) that refers to a taxonomy given in Section 1.1. Superscript numbersrefer to annotations listed in Section 1.2

abbrev. Seq. accession 5′ at 3′ at genes

BacteriaRca-1-1 NC 009767.1 - 3059318 3059191 RNA→ STAS SulP like sulfate transporter (cd07042)→CSo-1-1 NC 008536.1 + 5838278 5838396 RNA→ hypo→ PotE (COG0531)→ hypo→ hypo→Tte-2-1 NC 013525.1 - 523792 523673 RNA→ COG1213 (COG1213)CDP-OH P transf (pfam01066)→ GlpA (COG0578)→ glycerol kin (TIGR01311)→

SapB (COG1285)→Tte-2-2 NC 013525.1 - 1446754 1446633 RNA→ hypo→ hypo→ COG1392 (COG1392)→

Bacteria ActinobacteriaKse-1-1 NC 013169.1 + 374355 374540 RNA→ Transglycosylase (pfam06737)→Mka-1-1 NZ ACBV01000022.1 + 53294 53509 RNA→ hypo→ ABC SMC barmotin (cd03278)→ ftsY (TIGR00064)→Dsp-1-1 NZ AEIQ01000069.1 + 35320 35494 RNA→ NLPC P60 (pfam00877)→Jde-1-1 NC 013174.1 - 2182203 2182026 RNA→ NLPC P60 (pfam00877)→Aar-1-1 NC 014550.1 + 624334 624526 RNA→ NLPC P60 (pfam00877)→Ach-1-1 NC 011886.1 + 2323600 2323793 RNA→ LysM (cd00118)NLPC P60 (pfam00877)→Aau-1-1 NC 008712.1 + 195264 195456 RNA→ NlpD (COG0739)→Cge-1-1 NZ ACLJ02000003.1 + 1090308 1090510 RNA→ Transglycosylase (pfam06737)DUF3235 (pfam11574)→


10

Rsa-1-1 NC 010168.1 + 416075 416276 RNA→ Peptidase M23 (pfam01551)→Aco-1-1 NZ ACFG01000004.1 + 273306 273470 RNA→ CHAP (pfam05257)→Kse-1-2 NC 013169.1 + 1583533 1583702 RNA→ NLPC P60 (pfam00877)→Kse-1-3 NC 013169.1 + 375700 375888 RNA→ COG3103 (COG3103)Transglycosylase (pfam06737)→ tRNA-Thr→Dsp-1-2 NZ AEIQ01000049.1 + 4244 4452 RNA→ hypo (cons)→Ach-1-2 NC 011886.1 + 1002071 1002305 RNA→ Peptidase M23 (pfam01551)→Cge-1-2 NZ ACLJ02000003.1 + 117297 117453 RNA→ NLPC P60 (pfam00877)→Fsp-1-1 NC 007777.1 + 5215277 5215495 RNA→ hypo→ Transglycosylase (pfam06737)→ DUF3151 (pfam11349)→ AdSS (cd03108)→Cli-1-1 NZ ACHJ01000034.1 + 68745 68932 RNA→ Transglycosylase (pfam06737)DUF3235 (pfam11574)→Asp-1-1 NC 008541.1 - 696516 696342 RNA→ LT GEWL (cd00254)→Ach-1-3 NC 011886.1 - 862845 862672 RNA→ LT GEWL (cd00254)→Mab-1-1 NC 010397.1 - 867920 867723 RNA→ Transglycosylase (pfam06737)→Asp-1-2 NC 008541.1 + 860245 860480 RNA→ Peptidase M23 (pfam01551)→Gbr-1-1 NC 013441.1 - 1287070 1286868 RNA→ Transglycosylase (pfam06737)→Ach-1-4 NC 011881.1 + 38364 38568 RNA→ NlpD (COG0739)→Rmu-2-1 NC 013715.1 + 275640 275817 RNA→ NLPC P60 (pfam00877)→Rmu-1-1 NZ ACVO01000015.1 + 38206 38383 RNA→ NLPC P60 (pfam00877)→Rde-2-1 NZ GL379574.1 - 1329324 1329156 RNA→ NLPC P60 (pfam00877)→Rde-1-1 NC 014643.1 - 606202 606034 RNA→ NLPC P60 (pfam00877)→Cwo-1-1 NC 013739.1 - 3702498 3702290 RNA→ RlpA (COG0797)→ PolY Pol IV kappa (cd03586)→ DSBA oxidoreductase→Cli-1-2 NZ ACHJ01000108.1 + 5155 5355 RNA→ NLPC P60 (pfam00877)→Krh-1-1 NC 010617.1 - 2079663 2079472 RNA→ NLPC P60 (pfam00877)→Fsp-4-1 NZ ADDL01000002.1 - 59510 59303 RNA→ Transglycosylase (pfam06737)→ DUF3151 (pfam11349)→Req-1-1 NZ ADNW01000053.1 + 7997 8233 RNA→ Transglycosylase (pfam06737)→Rsa-1-2 NC 010168.1 + 52561 52722 RNA→ LT GEWL (cd00254)→Kfl-1-1 NC 013729.1 - 663678 663498 RNA→ NLPC P60 (pfam00877)PG binding 1 (pfam01471)→Bca-1-1 NC 012669.1 + 982162 982348 RNA→ NLPC P60 (pfam00877)→Jsp-1-1 NZ AAMN01000005.1 + 105550 105725 RNA→ NLPC P60 (pfam00877)→Cef-1-1 NC 004369.1 - 944139 943978 RNA→ Transglycosylase (pfam06737)DUF3235 (pfam11574)→Dsp-1-3 NZ AEIQ01000033.1 - 18825 18654 RNA→ Transglycosylase (pfam06737)spore SleB (TIGR02869)→Cef-1-2 NC 004369.1 - 2209148 2208939 RNA→ NLPC P60 (pfam00877)→Aau-1-2 NC 008711.1 + 1078087 1078319 RNA→ Peptidase M23 (pfam01551)→Asp-1-3 NC 008541.1 - 2626115 2625921 RNA→ PRK13914 (PRK13914)→Asp-1-4 NC 008537.1 + 45780 45959 RNA→ hypo→Aau-1-3 NC 008712.1 - 172392 172198 RNA→ LysM (cd00118)NLPC P60 (pfam00877)→ hypo→Rsa-1-3 NC 010168.1 + 417439 417620 RNA→ NLPC P60 (pfam00877)→Asp-1-5 NC 008541.1 + 861427 861609 RNA→ NLPC P60 (pfam00877)→Ach-1-5 NC 011886.1 + 1003268 1003454 RNA→ NLPC P60 (pfam00877)→Aau-1-4 NC 008711.1 + 1079284 1079464 RNA→ NLPC P60 (pfam00877)→Aau-1-5 NC 008711.1 + 421172 421362 RNA→ NLPC P60 (pfam00877)→Aur-1-1 NZ ACFH01000040.1 - 12308 12144 RNA→ NLPC P60 (pfam00877)→Avi-1-1 NZ ACRE01000065.1 + 5692 5879 RNA→ NLPC P60 (pfam00877)→Jde-1-2 NC 013174.1 + 2602467 2602628 RNA→ NLPC P60 (pfam00877)→Aau-1-6 NC 008713.1 - 40519 40329 RNA→ Peptidase M23 (pfam01551)→Cam-1-1 NZ ABZU01000004.1 - 137451 137282 RNA→ NLPC P60 (pfam00877)→Gob-1-1 NC 013757.1 - 2953716 2953541 RNA→ peptidoglycan binding domain-containing protein→Fsy-1-1 NZ ADGT01000061.1 + 19396 19590 RNA→ NLPC P60 (pfam00877)→Cwo-1-2 NC 013739.1 + 4991555 4991703 RNA→ rlpA (TIGR00413)→Cgl-1-1 NC 006958.1 - 870104 869859 RNA→ Transglycosylase (pfam06737)DUF3235 (pfam11574)→Cgl-1-2 NC 003450.3 - 868633 868388 RNA→ Transglycosylase (pfam06737)DUF3235 (pfam11574)→Cgl-2-1 NC 009342.1 - 1033186 1032941 RNA→ ←hypo

Rer-1-1 NC 012490.1 + 5078932 5079165 RNA→ Transglycosylase (pfam06737)→


11

Rer-2-1 NZ ACNO01000001.1 + 154330 154563 RNA→ Transglycosylase (pfam06737)→Fsp-2-1 NC 009921.1 - 6974916 6974730 RNA→ NLPC P60 (pfam00877)→Fsy-1-2 NZ ADGT01000073.1 + 12472 12664 RNA→ Transglycosylase (pfam06737)→Aur-1-2 NZ ACFH01000040.1 - 13390 13211 RNA→ NLPC P60 (pfam00877)→Nmu-1-1 NC 013235.1 + 2571038 2571268 RNA→ LysM (cd00118)Transglycosylase (pfam06737)→ MFS (cd06174)→Ske-1-1 NC 013521.1 - 3426263 3426081 RNA→ NLPC P60 (pfam00877)→Fsp-4-2 NZ ADDL01000007.1 + 46211 46405 RNA→ NLPC P60 (pfam00877)→Fsp-1-2 NC 007777.1 - 331691 331497 RNA→ hypo→ NLPC P60 (pfam00877)→Fsp-3-1 NZ ADGX01000045.1 - 25967 25772 RNA→ NLPC P60 (pfam00877)→Fal-1-1 NC 008278.1 - 706607 706410 RNA→ NLPC P60 (pfam00877)→Fsp-2-2 NC 009921.1 + 7938179 7938374 RNA→ NLPC P60 (pfam00877)→Nsp-1-1 NC 008699.1 - 3328806 3328662 RNA→ NLPC P60 (pfam00877)→ hypo→ Peptidase M48 (pfam01435)→

2Fsp-3-2 NZ ADGX01000205.1 + 5169 5360 RNA→ ←hypo

Fsp-3-3 NZ ADGX01000020.1 + 81805 81995 RNA→Ser-1-1 NC 009142.1 - 627217 627035 RNA→ LysM (cd00118)Transglycosylase (pfam06737)→Aod-1-1 NZ AAYI02000004.1 - 369629 369478 RNA→ NLPC P60 (pfam00877)→ USP Like (cd00293)→Aod-2-1 NZ ACYT02000031.1 - 12948 12797 RNA→ NLPC P60 (pfam00877)→ USP Like (cd00293)→Kra-1-1 NC 009806.1 + 39841 40027 RNA→ NLPC P60 (pfam00877)→Kra-1-2 NC 009664.2 + 3388517 3388703 RNA→ NLPC P60 (pfam00877)→Xce-1-1 NC 013530.1 - 3159814 3159640 RNA→ NLPC P60 (pfam00877)→Fsp-4-3 NZ ADDL01000028.1 + 66850 67050 RNA→ SLT (pfam01464)PG binding 1 (pfam01471)→Fsp-1-3 NC 007777.1 - 3540575 3540388 RNA→ hypo→Fal-1-2 NC 008278.1 - 5337715 5337537 RNA→ ←hypoFsp-2-3 NC 009921.1 - 2985996 2985795 RNA→ Lys (pfam00062)PG binding 1 (pfam01471)→Fsp-3-4 NZ ADGX01000102.1 + 14032 14222 RNA→ Lys (pfam00062)PG binding 1 (pfam01471)→Fsy-1-3 NZ ADGT01000072.1 + 11242 11435 RNA→ NLPC P60 (pfam00877)→Scl-1-1 NZ CM000913.1 + 6180056 6180254 RNA→ Secreted peptidase→Nfa-1-1 NC 006361.1 - 5934987 5934824 RNA→ NLPC P60 (pfam00877)→ S4 (cd00165)→Mau-1-1 NC 014391.1 - 3766091 3765933 RNA→ LysM (cd00118)Transglycosylase (pfam06737)→Msp-5-1 NZ ADGV01000112.1 - 3544 3386 RNA→ LysM (cd00118)Transglycosylase (pfam06737)→Spr-1-1 NZ CM000950.1 - 6874949 6874762 RNA→ NLPC P60 (pfam00877)→Scl-1-2 NZ CM000913.1 + 707885 708071 RNA→ Hypothetical protein→ NLPC P60 (pfam00877)→Sav-1-1 NC 003155.4 - 8461822 8461635 RNA→ NLPC P60 (pfam00877)→ hypo→Svi-2-1 NZ GG657757.1 + 1286294 1286497 RNA→ NLPC P60 (pfam00877)→ hypo (cons)→Ssp-7-1 NZ GG753626.1 + 222641 222845 RNA→ NLPC P60 (pfam00877)→Ssc-1-1 NC 013929.1 - 8652422 8652220 RNA→ NLPC P60 (pfam00877)→ putative integral membrane protein→Sgr-1-1 NZ GG657758.1 - 6877859 6877666 RNA→ NLPC P60 (pfam00877)→Ssp-2-1 NZ ADFD01000007.1 + 312960 313147 RNA→ NLPC P60 (pfam00877)→Sro-2-1 NZ DS999644.1 + 458610 458795 RNA→ NLPC P60 (pfam00877)→Sro-1-1 NZ ABYX01000034.1 + 6865 7050 RNA→ NLPC P60 (pfam00877)→Sgr-2-1 NC 010572.1 - 7468334 7468148 RNA→ NLPC P60 (pfam00877)→Ssp-1-1 NZ ADFC01000022.1 + 74410 74596 RNA→ NLPC P60 (pfam00877)→Sgh-1-1 NZ DS999641.1 - 6701512 6701318 RNA→ NLPC P60 (pfam00877)→Ssv-1-1 NZ CM000951.1 + 1532317 1532520 RNA→ NLPC P60 (pfam00877)→Sal-1-1 NZ DS999645.1 + 555020 555216 RNA→ NLPC P60 (pfam00877)→Sfl-1-1 NZ ACZH01000005.1 - 130302 130115 RNA→ NLPC P60 (pfam00877)→Sco-1-1 NC 003888.3 + 1312466 1312677 RNA→ NLPC P60 (pfam00877)→Sli-1-1 NZ GG657756.1 - 7000706 7000495 RNA→ NLPC P60 (pfam00877)→Ssp-6-1 NZ GG657742.1 + 569050 569241 RNA→ NLPC P60 (pfam00877)→Ssp-5-1 NZ GG770539.1 - 6362085 6361894 RNA→ NLPC P60 (pfam00877)→Fsp-4-4 NZ ADDL01000014.1 + 127944 128132 RNA→ NLPC P60 (pfam00877)→Aau-1-7 NC 008711.1 - 834526 834352 RNA→ hypo→


12

Cgl-2-2 NC 009342.1 - 2284801 2284622 RNA→ NLPC P60 (pfam00877)→Cgl-1-3 NC 006958.1 - 2292461 2292282 RNA→ NLPC P60 (pfam00877)→Cgl-1-4 NC 003450.3 - 2320790 2320611 RNA→ NLPC P60 (pfam00877)→Kra-1-3 NC 009664.2 - 2709890 2709714 RNA→ Transglycosylase (pfam06737)→Ssp-6-2 NZ GG657742.1 + 6747412 6747607 RNA→ LysM (cd00118)Peptidase M23 (pfam01551)→Ssp-5-2 NZ GG770539.1 - 636246 636052 RNA→ LysM (cd00118)Peptidase M23 (pfam01551)→Aar-1-2 NC 014550.1 + 623012 623185 RNA→ Peptidase M23 (pfam01551)→Rop-1-1 NC 012522.1 - 5436229 5435992 RNA→ Transglycosylase (pfam06737)→Rjo-1-1 NC 008268.1 + 7516717 7516954 RNA→ Transglycosylase (pfam06737)→Rjo-1-2 NC 008268.1 - 5241716 5241479 RNA→ Transglycosylase (pfam06737)→Sav-1-2 NC 003155.4 - 2009809 2009626 RNA→ LysM (cd00118)Peptidase M23 (pfam01551)→Gbr-1-2 NC 013441.1 - 3265912 3265710 RNA→ NLPC P60 (pfam00877)→Cwo-1-3 NC 013739.1 - 1979963 1979811 RNA→ Peptidase M23 (pfam01551)→ hypo→Fsp-2-4 NC 009921.1 - 8014874 8014709 RNA→ Transglycosylase (pfam06737)→Mva-1-1 NC 008726.1 + 5402733 5402938 RNA→ Transglycosylase (pfam06737)→Mgi-1-1 NC 009338.1 - 1774758 1774551 RNA→ Transglycosylase (pfam06737)→Msm-1-1 NC 008596.1 + 5785367 5785567 RNA→ Transglycosylase (pfam06737)→Msp-3-1 NC 008146.1 + 4757545 4757741 RNA→ hypo→ Transglycosylase (pfam06737)→Msp-1-1 NC 009077.1 + 5106753 5106949 RNA→ Transglycosylase (pfam06737)→Msp-2-1 NC 008705.1 + 4796685 4796881 RNA→ Transglycosylase (pfam06737)→Mpa-1-1 NZ ADNV01000328.1 - 679 471 RNA→ Transglycosylase (pfam06737)→Mav-1-1 NC 008595.1 - 933546 933342 RNA→ Transglycosylase (pfam06737)→Mav-3-1 NC 002944.2 - 825810 825606 RNA→ Transglycosylase (pfam06737)→Mav-2-1 NZ ACFI01000032.1 - 188987 188781 RNA→ Transglycosylase (pfam06737)→Min-1-1 NZ ABIN01000324.1 + 17526 17728 RNA→ Transglycosylase (pfam06737)→Mbo-1-1 NC 002945.3 - 966221 966006 RNA→ Transglycosylase (pfam06737)→Mtu-9-1 NC 009565.1 - 969576 969361 RNA→ Transglycosylase (pfam06737)→Mtu-5-1 NZ CH482373.1 - 626844 626629 RNA→ Transglycosylase (pfam06737)→Mtu-6-1 NC 002755.2 - 965765 965550 RNA→ Transglycosylase (pfam06737)→Mtu-12-1 NC 000962.2 - 965761 965546 RNA→ Transglycosylase (pfam06737)→Mtu-34-1 NZ DS016976.1 - 627184 626969 RNA→ Transglycosylase (pfam06737)→Mbo-2-1 NC 008769.1 - 996212 995997 RNA→ Transglycosylase (pfam06737)→Mtu-11-1 NC 009525.1 - 967067 966852 RNA→ Transglycosylase (pfam06737)→Mtu-14-1 NC 012943.1 + 3446227 3446442 RNA→ Transglycosylase (pfam06737)→Mtu-16-1 NZ GG745507.1 + 3445639 3445854 RNA→ Transglycosylase (pfam06737)→Mtu-4-1 NZ DS985174.1 - 39462 39247 RNA→ Transglycosylase (pfam06737)→Mtu-2-1 NZ DS985182.1 - 220515 220300 RNA→ Transglycosylase (pfam06737)→Mtu-33-1 NZ DS985122.1 - 36984 36769 RNA→ Transglycosylase (pfam06737)→Mtu-8-1 NZ DS985165.1 - 41530 41315 RNA→ Transglycosylase (pfam06737)→Mtu-10-1 NZ DS986660.1 - 36976 36761 RNA→ (big gap) ←MoaE (cd00756)Mtu-31-1 NZ DS986677.1 - 294617 294402 RNA→ Transglycosylase (pfam06737)→Mbo-3-1 NC 012207.1 - 967929 967714 RNA→ Transglycosylase (pfam06737)→Mtu-32-1 NZ GG663490.1 - 340349 340134 RNA→ Transglycosylase (pfam06737)→Mtu-13-1 NZ GG663503.1 - 1447285 1447070 RNA→ Transglycosylase (pfam06737)→Mtu-15-1 NZ ABGL01000010.1 - 286954 286739 RNA→ (big gap) ←MoaE (cd00756)Mtu-1-1 NZ ABVM01000026.1 - 37292 37077 RNA→ Transglycosylase (pfam06737)→Mtu-15-2 NZ ACVS02000014.1 - 37988 37773 RNA→ Transglycosylase (pfam06737)→Mtu-18-1 NZ ACVT02000026.1 - 37246 37031 RNA→ Transglycosylase (pfam06737)→Mtu-17-1 NZ ACVU02000023.1 - 37929 37714 RNA→ Transglycosylase (pfam06737)→Mtu-3-1 NZ ADAB01000120.1 - 112636 112421 RNA→ Transglycosylase (pfam06737)→Mtu-19-1 NZ ADHQ01000026.1 - 35692 35477 RNA→ Transglycosylase (pfam06737)→Mtu-20-1 NZ ADHR01000167.1 + 2763 2978 RNA→ Transglycosylase (pfam06737)→


13

Mtu-21-1 NZ ADHS01000032.1 - 35385 35170 RNA→ Transglycosylase (pfam06737)→Mtu-22-1 NZ ADHT01000043.1 - 938 723 RNA→ Transglycosylase (pfam06737)→Mtu-23-1 NZ ADHU01000041.1 - 693 478 RNA→ Transglycosylase (pfam06737)→Mtu-24-1 NZ ADHV01000041.1 - 866 651 RNA→ Transglycosylase (pfam06737)→Mtu-25-1 NZ ADHW01000041.1 - 716 501 RNA→ Transglycosylase (pfam06737)→Mtu-26-1 NZ ADHX01000075.1 - 686 471 RNA→ Transglycosylase (pfam06737)→Mtu-27-1 NZ ADHY01000027.1 - 909 694 RNA→ Transglycosylase (pfam06737)→Mtu-28-1 NZ ADHZ01000024.1 - 827 612 RNA→ Transglycosylase (pfam06737)→Mtu-29-1 NZ ADIA01000030.1 - 786 571 RNA→ Transglycosylase (pfam06737)→Mtu-30-1 NZ ADIB01000064.1 - 779 564 RNA→ Transglycosylase (pfam06737)→Mtu-7-1 NZ GG663497.1 - 1430656 1430441 RNA→ Transglycosylase (pfam06737)→Mul-1-1 NC 008611.1 + 290986 291191 RNA→ Transglycosylase (pfam06737)→Mma-1-1 NC 010612.1 + 5717649 5717854 RNA→ Transglycosylase (pfam06737)→Mka-1-2 NZ ACBV01000079.1 + 26489 26702 RNA→ Transglycosylase (pfam06737)→Tcu-1-1 NC 013510.1 + 334115 334261 RNA→ hypo→Sav-1-3 NC 003155.4 + 8541480 8541692 RNA→ hypo→Tpa-1-1 NC 014158.1 - 2792088 2791934 RNA→ NLPC P60 (pfam00877)→ NLPC P60 (pfam00877)→ ACAD (cd00567)→ GT1 YqgM like (cd03801)→Cwo-1-4 NC 013739.1 - 225505 225353 RNA→ COG3409 (COG3409)PG binding 1 (pfam01471)→Nsp-1-2 NC 008699.1 + 1318686 1318852 RNA→ NLPC P60 (pfam00877)→Fsp-4-5 NZ ADDL01000002.1 - 61200 60899 RNA→ Transglycosylase (pfam06737)PG binding 1 (pfam01471)→Fsp-2-5 NC 009921.1 - 261009 260782 RNA→ Transglycosylase (pfam06737)→Fsp-3-5 NZ ADGX01000075.1 + 2506 2733 RNA→ Transglycosylase (pfam06737)→Cwo-1-5 NC 013739.1 + 1880282 1880416 RNA→ ←hypoGob-1-2 NC 013757.1 - 2029494 2029314 RNA→ LysM (cd00118)Transglycosylase (pfam06737)→Svi-2-2 NZ GG657757.1 + 7638537 7638720 RNA→ Peptidase M23 (pfam01551)→Sgh-1-2 NZ DS999641.1 - 985379 985194 RNA→ Peptidase M23 (pfam01551)→Ssv-1-2 NZ CM000951.1 + 8049184 8049371 RNA→ Peptidase M23 (pfam01551)→Sgr-1-2 NZ GG657758.1 - 861469 861281 RNA→ Peptidase M23 (pfam01551)→Sco-1-2 NC 003888.3 + 7530983 7531170 RNA→ LysM (cd00118)Peptidase M23 (pfam01551)→Sli-1-2 NZ GG657756.1 - 984681 984494 RNA→ LysM (cd00118)Peptidase M23 (pfam01551)→Ssc-1-2 NC 013929.1 - 1442543 1442360 RNA→ Peptidase M23 (pfam01551)→Cfl-1-1 NC 014151.1 + 842949 843166 RNA→ NLPC P60 (pfam00877)→Gob-1-3 NC 013757.1 + 2457806 2457990 RNA→ LysM (cd00118)S6PP C (pfam08472)→Kfl-1-2 NC 013729.1 + 2869448 2869642 RNA→ ManB (COG4124)→Ace-1-1 NC 008578.1 - 2373001 2372862 RNA→ hypo→ NLPC P60 (pfam00877)→Ssp-3-1 NZ GG657750.1 - 3200047 3199842 RNA→ LysM (cd00118)Transglycosylase (pfam06737)→Sgr-2-2 NC 010572.1 + 5189180 5189392 RNA→ LysM (cd00118)Transglycosylase (pfam06737)→Ssp-1-2 NZ ADFC01000023.1 - 93590 93378 RNA→ LysM (cd00118)Transglycosylase (pfam06737)→Sro-2-2 NZ DS999644.1 - 2839018 2838810 RNA→ LysM (cd00118)Transglycosylase (pfam06737)→Sro-1-2 NZ ABYX01000124.1 - 98371 98163 RNA→ LysM (cd00118)Transglycosylase (pfam06737)→Svi-2-3 NZ GG657757.1 - 5265636 5265433 RNA→ LysM (cd00118)COG3953 (COG3953)→Sal-1-2 NZ DS999645.1 - 6334080 6333879 RNA→ spore safA (TIGR02899)Peptidase M23 (pfam01551)→Sfl-1-2 NZ ACZH01000015.1 - 110892 110717 RNA→ LT GEWL (cd00254)XkdP (COG1652)→ hypo→ hypo (cons)→Ssp-2-2 NZ ADFD01000005.1 + 236240 236415 RNA→ LT GEWL (cd00254)→Spr-1-2 NZ CM000950.1 - 1850854 1850675 RNA→ LT GEWL (cd00254)→Ssv-1-3 NZ CM000951.1 - 5520186 5519994 RNA→ LT GEWL (cd00254)→Sav-1-4 NC 003155.4 - 5911909 5911724 RNA→ COG3953 (COG3953)→Ssp-7-2 NZ GG753626.1 - 3483695 3483482 RNA→ COG3953 (COG3953)→Ssc-1-3 NC 013929.1 + 4256366 4256605 RNA→ LT GEWL (cd00254)→Ssp-1-3 NZ ADFC01000046.1 + 31194 31375 RNA→ Peptidase M23 (pfam01551)→Sgr-2-3 NC 010572.1 - 1131803 1131622 RNA→ Peptidase M23 (pfam01551)→Sro-2-3 NZ DS999644.1 + 7138651 7138832 RNA→ Peptidase M23 (pfam01551)→


14

Sro-1-3 NZ ABYX01000248.1 + 29696 29877 RNA→ Peptidase M23 (pfam01551)→Sfl-1-3 NZ ACZH01000042.1 - 33182 33005 RNA→ Peptidase M23 (pfam01551)→Sgr-2-4 NC 010572.1 - 560039 559862 RNA→ LysM (cd00118)LT GEWL (cd00254)→Ssp-1-4 NZ ADFC01000001.1 + 181803 181980 RNA→ LysM (cd00118)LT GEWL (cd00254)→Sro-2-4 NZ DS999644.1 + 7575592 7575769 RNA→ LT GEWL (cd00254)→Sro-1-4 NZ ABYX01000274.1 + 5943 6120 RNA→ LysM (cd00118)LT GEWL (cd00254)→Ssp-2-3 NZ ADFD01000019.1 + 109933 110110 RNA→ Peptidase M23 (pfam01551)→Ssp-4-1 NZ DS570432.1 - 29927 29731 RNA→ ←hypo

Ssp-3-2 NZ GG657750.1 + 6590277 6590469 RNA→ Peptidase M23 (pfam01551)→Spr-1-3 NZ CM000950.1 - 746764 746585 RNA→ Peptidase M23 (pfam01551)→Sgr-1-3 NZ GG657758.1 + 3344228 3344419 RNA→ LT GEWL (cd00254)→Sgh-1-3 NZ DS999641.1 + 3335951 3336145 RNA→ LT GEWL (cd00254)→Sco-1-3 NC 003888.3 - 5004264 5004069 RNA→ LT GEWL (cd00254)→Sli-1-3 NZ GG657756.1 + 3436780 3436975 RNA→ LT GEWL (cd00254)→Sfl-1-4 NZ ACZH01000014.1 + 26663 26867 RNA→ LysM (cd00118)Transglycosylase (pfam06737)→Ssp-2-4 NZ ADFD01000021.1 - 84051 83851 RNA→ LysM (cd00118)Transglycosylase (pfam06737)→Fsp-2-6 NC 009921.1 - 263104 262867 RNA→ Transglycosylase (pfam06737)PG binding 1 (pfam01471)→Fal-1-3 NC 008278.1 + 7254791 7255014 RNA→ Transglycosylase (pfam06737)PG binding 1 (pfam01471)→Fsp-3-6 NZ ADGX01000020.1 + 77235 77413 RNA→ LT GEWL (cd00254)→Ssp-6-3 NZ GG657742.1 - 2837821 2837610 RNA→ LysM (cd00118)Transglycosylase (pfam06737)→Ssp-5-3 NZ GG770539.1 + 4221296 4221508 RNA→ LysM (cd00118)Transglycosylase (pfam06737)→Fsp-1-4 NC 007777.1 + 5213926 5214150 RNA→ hypo→ Transglycosylase (pfam06737)PG binding 1 (pfam01471)→Svi-1-1 NZ AEDI01000048.1 - 39489 39291 RNA→ LysM (cd00118)Transglycosylase (pfam06737)→Shy-1-1 NZ GG657754.1 + 6197278 6197475 RNA→ LysM (cd00118)Transglycosylase (pfam06737)→Sal-1-3 NZ DS999645.1 + 4476036 4476257 RNA→ LysM (cd00118)Transglycosylase (pfam06737)→Fsp-3-7 NZ ADGX01000075.1 + 245 479 RNA→ Transglycosylase (pfam06737)PG binding 1 (pfam01471)→Fsp-3-8 NZ ADGX01000037.1 + 68091 68326 RNA→Xce-1-2 NC 013530.1 - 3160971 3160806 RNA→ NLPC P60 (pfam00877)→Fsy-1-4 NZ ADGT01000073.1 + 11067 11230 RNA→ Transglycosylase (pfam06737)PG binding 1 (pfam01471)→Fsy-1-5 NZ ADGT01000016.1 + 47741 47907 RNA→ hypo→ LT GEWL (cd00254)→Fsp-1-5 NC 007777.1 + 5067440 5067603 RNA→ hypo→ Transglycosylase (pfam06737)→Fal-1-4 NC 008278.1 + 7087638 7087801 RNA→ ←hypo

Fsy-1-6 NZ ADGT01000092.1 + 4863 5025 RNA→ LT GEWL (cd00254)→ hypo→ transposase and inactivated derivatives-like protein→ hypo→Spr-1-4 NZ CM000950.1 + 4767063 4767317 RNA→ LysM (cd00118)Transglycosylase (pfam06737)→Sav-1-5 NC 003155.4 - 4374785 4374572 RNA→ LysM (cd00118)Transglycosylase (pfam06737)→Ssv-1-4 NZ CM000951.1 - 3942537 3942335 RNA→ LysM (cd00118)Transglycosylase (pfam06737)→Ssp-7-3 NZ GG753626.1 - 2255603 2255403 RNA→ LysM (cd00118)Transglycosylase (pfam06737)→Sgh-1-4 NZ DS999641.1 + 4644208 4644411 RNA→ LysM (cd00118)Transglycosylase (pfam06737)→Sco-1-4 NC 003888.3 - 3393027 3392826 RNA→ LysM (cd00118)Transglycosylase (pfam06737)→Sli-1-4 NZ GG657756.1 + 4920969 4921170 RNA→ LysM (cd00118)Transglycosylase (pfam06737)→Svi-2-4 NZ GG657757.1 - 3612322 3612121 RNA→ LysM (cd00118)Transglycosylase (pfam06737)→Ssc-1-4 NC 013929.1 + 6048614 6048847 RNA→ LysM (cd00118)Transglycosylase (pfam06737)→Sgr-1-4 NZ GG657758.1 + 4737271 4737475 RNA→ LysM (cd00118)Transglycosylase (pfam06737)→Scl-1-3 NZ CM000913.1 - 2623884 2623639 RNA→ LysM (cd00118)Transglycosylase (pfam06737)→ Hypothetical protein→ enolase (cd03313)→Ssp-4-2 NZ DS570414.1 + 22907 23108 RNA→ LysM (cd00118)Transglycosylase (pfam06737)→Gob-1-4 NC 013757.1 - 3705501 3705343 RNA→ Peptidase M23 (pfam01551)→Sro-3-1 NC 013595.1 + 8069439 8069566 RNA→ hypo→Gob-1-5 NC 013757.1 - 3504826 3504655 RNA→ Peptidase M48 (pfam01435)→Rop-1-2 NC 012522.1 - 895653 895496 RNA→ NLPC P60 (pfam00877)→Rjo-1-3 NC 008268.1 - 1199540 1199383 RNA→ NLPC P60 (pfam00877)→Rer-2-2 NZ ACNO01000026.1 - 118657 118486 RNA→ NLPC P60 (pfam00877)→Rer-1-2 NC 012490.1 - 3935534 3935363 RNA→ NLPC P60 (pfam00877)→


15

Req-1-2 NZ ADNW01000020.1 - 17828 17670 RNA→ NLPC P60 (pfam00877)→Gob-1-6 NC 013757.1 + 1873848 1874003 RNA→ ←hypo

Gob-1-7 NC 013757.1 + 3865079 3865220 RNA→ ←hypoGob-1-8 NC 013757.1 - 5081181 5081029 RNA→ NLPC P60 (pfam00877)→Cwo-1-6 NC 013739.1 - 5012209 5012059 RNA→ PG binding 1 (pfam01471)→Cwo-1-7 NC 013739.1 - 4509399 4509268 RNA→ hypo→Tcu-1-2 NC 013510.1 + 5079165 5079383 RNA→ NLPC P60 (pfam00877)→Shy-1-2 NZ GG657754.1 - 4918442 4918266 RNA→ Peptidase M23 (pfam01551)→Svi-1-2 NZ AEDI01000079.1 + 7236 7396 RNA→ Peptidase M23 (pfam01551)→Ssp-5-4 NZ GG770539.1 - 1393292 1393151 RNA→ Peptidase M23 (pfam01551)→ WHTH GntR (cd07377)→Ssp-6-4 NZ GG657742.1 + 5942248 5942390 RNA→ Peptidase M23 (pfam01551)→Scl-1-4 NZ CM000913.1 + 3687165 3687312 RNA→ Peptidase M23 (pfam01551)→Ssp-6-5 NZ GG657742.1 + 4033518 4033647 RNA→ Peptidase M23 (pfam01551)→Ssp-5-5 NZ GG770539.1 - 3229887 3229758 RNA→ Peptidase M23 (pfam01551)→Shy-1-3 NZ GG657754.1 - 3051050 3050897 RNA→ Peptidase M23 (pfam01551)→Ssp-2-5 NZ ADFD01000008.1 + 329434 329579 RNA→ Peptidase M23 (pfam01551)→Sgr-2-5 NC 010572.1 + 4570575 4570718 RNA→ Peptidase M23 (pfam01551)→Ssp-1-5 NZ ADFC01000076.1 - 12097 11954 RNA→ Peptidase M23 (pfam01551)→Sro-2-5 NZ DS999644.1 - 3531107 3530964 RNA→ Peptidase M23 (pfam01551)→Sro-1-5 NZ ABYX01000142.1 - 9410 9267 RNA→ Peptidase M23 (pfam01551)→Sfl-1-5 NZ ACZH01000009.1 - 19907 19764 RNA→ Peptidase M23 (pfam01551)→Sgh-1-5 NZ DS999641.1 + 4157018 4157161 RNA→ Peptidase M23 (pfam01551)→Sav-1-6 NC 003155.4 - 5051628 5051480 RNA→ Peptidase M23 (pfam01551)→Sgr-1-5 NZ GG657758.1 + 4278158 4278303 RNA→ Peptidase M23 (pfam01551)→Svi-2-5 NZ GG657757.1 - 4183349 4183202 RNA→ Peptidase M23 (pfam01551)→Ssc-1-5 NC 013929.1 + 5467031 5467183 RNA→ Peptidase M23 (pfam01551)→Ssv-1-5 NZ CM000951.1 - 4495651 4495503 RNA→ Peptidase M23 (pfam01551)→Spr-1-5 NZ CM000950.1 + 4206554 4206701 RNA→ Peptidase M23 (pfam01551)→Sal-1-4 NZ DS999645.1 + 3638500 3638627 RNA→ Peptidase M23 (pfam01551)→Ssp-7-4 NZ GG753626.1 - 2719541 2719393 RNA→ Peptidase M23 (pfam01551)→Sco-1-5 NC 003888.3 + 4507171 4507318 RNA→ Peptidase M23 (pfam01551)→Sli-1-5 NZ GG657756.1 - 3951781 3951634 RNA→ Peptidase M23 (pfam01551)→Sgh-1-6 NZ DS999641.1 - 2102567 2102411 RNA→ ←predicted protein

Sfl-1-6 NZ ACZH01000021.1 - 8225 8066 RNA→ Peptidase M23 (pfam01551)→Svi-1-3 NZ AEDI01000007.1 + 30956 31111 RNA→ Peptidase M23 (pfam01551)→Ssp-4-3 NZ DS570409.1 - 85108 84958 RNA→ Peptidase M23 (pfam01551)→Ssp-3-3 NZ GG657750.1 + 5890355 5890503 RNA→ Peptidase M23 (pfam01551)→Spr-1-6 NZ CM000950.1 - 2001553 2001400 RNA→ Peptidase M23 (pfam01551)→Sal-1-5 NZ DS999645.1 + 5621111 5621256 RNA→ Peptidase M23 (pfam01551)→Scl-1-5 NZ CM000913.1 + 5503292 5503444 RNA→ Peptidase M23 (pfam01551)→Ssv-1-6 NZ CM000951.1 + 6894100 6894249 RNA→ Peptidase M23 (pfam01551)→Sav-1-7 NC 003155.4 - 2949703 2949553 RNA→ Peptidase M23 (pfam01551)→Sco-1-6 NC 003888.3 + 6392151 6392306 RNA→ Peptidase M23 (pfam01551)→Sli-1-6 NZ GG657756.1 - 2118654 2118499 RNA→ Peptidase M23 (pfam01551)→Sro-2-6 NZ DS999644.1 + 6093697 6093855 RNA→ NlpD (COG0739)→Sro-1-6 NZ ABYX01000211.1 + 30112 30270 RNA→ Peptidase M23 (pfam01551)→Sgr-2-6 NC 010572.1 - 1986388 1986230 RNA→ Peptidase M23 (pfam01551)→Ssp-1-6 NZ ADFC01000007.1 + 112216 112374 RNA→ Peptidase M23 (pfam01551)→Ssp-7-5 NZ GG753626.1 + 4793896 4794049 RNA→ Peptidase M23 (pfam01551)→Sgr-1-6 NZ GG657758.1 - 2015316 2015162 RNA→ Peptidase M23 (pfam01551)→Svi-2-6 NZ GG657757.1 + 6571606 6571761 RNA→ Peptidase M23 (pfam01551)→Ssp-2-6 NZ ADFD01000005.1 + 111641 111798 RNA→ Peptidase M23 (pfam01551)→


16

Ssc-1-6 NC 013929.1 - 2742223 2742062 RNA→ Peptidase M23 (pfam01551)→Sna-1-1 NC 013947.1 - 6241858 6241709 RNA→ NLPC P60 (pfam00877)→Sro-3-2 NC 013595.1 - 8515563 8515425 RNA→ hypo→Sna-1-2 NC 013947.1 - 1512033 1511888 RNA→ NLPC P60 (pfam00877)SCRAP12 (SCRAP12)→Cac-1-1 NC 013131.1 - 9933837 9933646 RNA→ NLPC P60 (pfam00877)→Tcu-1-3 NC 013510.1 + 1558136 1558275 RNA→ CHAP (pfam05257)→Nmu-1-2 NC 013235.1 - 3567568 3567389 RNA→ NLPC P60 (pfam00877)→Msp-4-1 NZ GG657738.1 + 5527677 5527811 RNA→ Peptidase C39A (cd02549)→Cac-1-2 NC 013131.1 - 2145619 2145476 RNA→ LysM (cd00118)LT GEWL (cd00254)→Sco-1-7 NC 003888.3 - 5218364 5218190 RNA→ COG3883 (COG3883)NLPC P60 (pfam00877)→ integral membrane protein→Sli-1-7 NZ GG657756.1 + 3241046 3241220 RNA→ COG3883 (COG3883)NLPC P60 (pfam00877)→ integral membrane protein→Ser-1-2 NC 009142.1 + 1860924 1861066 RNA→ NLPC P60 (pfam00877)→Sro-3-3 NC 013595.1 + 10097004 10097145 RNA→ NLPC P60 (pfam00877)→Svi-2-7 NZ GG657757.1 - 5449303 5449139 RNA→ Smc (COG1196)NLPC P60 (pfam00877)→Gob-1-9 NC 013757.1 + 2241934 2242086 RNA→ LT GEWL (cd00254)→Gob-1-10 NC 013757.1 + 2463754 2463898 RNA→ surface antigen→ AdoMet MTases (cd02440)→Gob-1-11 NC 013757.1 - 147807 147659 RNA→ LT GEWL (cd00254)→Sar-1-1 NC 009953.1 - 603232 603113 RNA→ COG3883 (COG3883)→Msp-4-2 NZ GG657738.1 - 4050372 4050250 RNA→ SMC prok A (TIGR02169)→Mau-1-2 NC 014391.1 - 576716 576594 RNA→ COG4942 (COG4942)→Msp-5-2 NZ ADGV01000086.1 - 22668 22546 RNA→ COG4942 (COG4942)→Mau-1-3 NC 014391.1 + 5340148 5340269 RNA→ SMC prok B (TIGR02168)→Msp-5-3 NZ ADGV01000072.1 + 26925 27046 RNA→ SMC prok B (TIGR02168)→Msp-4-3 NZ GG657738.1 + 1841944 1842064 RNA→ hypo→Sar-1-2 NC 009953.1 + 4190719 4190841 RNA→ PspA (COG1842)→Str-1-1 NC 009380.1 + 3890467 3890589 RNA→ COG4942 (COG4942)→Ssv-1-7 NZ CM000951.1 - 5718528 5718366 RNA→ COG3883 (COG3883)NLPC P60 (pfam00877)→ integral membrane protein→Mau-1-4 NC 014391.1 + 116859 116990 RNA→ COG3883 (COG3883)NLPC P60 (pfam00877)SCRAP12 (SCRAP12)→Msp-5-4 NZ ADGV01000048.1 + 15370 15501 RNA→ COG3883 (COG3883)NLPC P60 (pfam00877)SCRAP12 (SCRAP12)→Msp-4-4 NZ GG657738.1 + 3602111 3602248 RNA→ NLPC P60 (pfam00877)SCRAP4 (SCRAP4)SCRAP41 (SCRAP41)→Sgh-1-7 NZ DS999641.1 + 3146018 3146183 RNA→ NLPC P60 (pfam00877)SMC prok B (TIGR02168)→ integral membrane protein→Sgr-1-7 NZ GG657758.1 + 3148905 3149072 RNA→ NLPC P60 (pfam00877)→Ace-1-2 NC 008578.1 + 1069188 1069309 RNA→ hypo→ NLPC P60 (pfam00877)SCRAP12 (SCRAP12)→ GT1 YqgM like (cd03801)→Sna-1-3 NC 013947.1 + 1209068 1209218 RNA→ SCRAP12 (SCRAP12)→ hypo→Svi-1-4 NZ AEDI01000143.1 + 6806 6984 RNA→ NLPC P60 (pfam00877)→Sal-1-6 NZ DS999645.1 + 2467477 2467620 RNA→ NLPC P60 (pfam00877)→ hypo (cons)→Sav-1-8 NC 003155.4 + 4296127 4296311 RNA→ COG3883 (COG3883)NLPC P60 (pfam00877)→ integral membrane protein→Ssc-1-7 NC 013929.1 + 4058249 4058414 RNA→ NLPC P60 (pfam00877)→Sro-2-7 NZ DS999644.1 - 4809228 4809070 RNA→ NLPC P60 (pfam00877)→Sro-1-7 NZ ABYX01000160.1 - 22121 21963 RNA→ NLPC P60 (pfam00877)→Ssp-1-7 NZ ADFC01000004.1 - 166795 166637 RNA→ NLPC P60 (pfam00877)→Sgr-2-7 NC 010572.1 + 3235835 3235993 RNA→ NLPC P60 (pfam00877)→

4Tbi-1-1 NC 014165.1 - 2028915 2028798 RNA→ TIGR02594 (TIGR02594)→Sro-3-4 NC 013595.1 + 2928686 2928835 RNA→ NLPC P60 (pfam00877)→Spr-1-7 NZ CM000950.1 + 3226598 3226751 RNA→ NLPC P60 (pfam00877)→Cac-1-3 NC 013131.1 - 1714637 1714413 RNA→ NLPC P60 (pfam00877)SCRAP12 (SCRAP12)→ hypo→Tcu-1-4 NC 013510.1 + 3559812 3560011 RNA→ hypo→Tcu-1-5 NC 013510.1 + 3560391 3560529 RNA→ TIGR02594 (TIGR02594)→ BSP (pfam04450)→ Peptidase M48 (pfam01435)→Sro-3-5 NC 013595.1 - 3605654 3605523 RNA→ TIGR02594 (TIGR02594)→Nmu-1-3 NC 013235.1 - 3564644 3564489 RNA→ NLPC P60 (pfam00877)→ MPP superfamily (cd00838)→ SRPBCC 2 (cd07819)→ ArsA (cd02035)→

hypo→ ROK glcA fam (TIGR00744)→Str-1-2 NC 009380.1 + 1922129 1922254 RNA→ Peptidase C39A (cd02549)→


17

Sar-1-3 NC 009953.1 + 1933327 1933452 RNA→ Peptidase C39A (cd02549)→Mau-1-5 NC 014391.1 + 2198111 2198244 RNA→ Peptidase C39A (cd02549)→Msp-5-5 NZ ADGV01000070.1 + 771 904 RNA→ Peptidase C39A (cd02549)→Sro-3-6 NC 013595.1 + 8853663 8853884 RNA→ NLPC P60 (pfam00877)→Sna-1-4 NC 013947.1 + 4287338 4287481 RNA→ COG3883 (COG3883)→Cwo-1-8 NC 013739.1 + 1875793 1875930 RNA→ hypo→Cwo-1-9 NC 013739.1 - 4866265 4866088 RNA→ Transglycosylase (pfam06737)spore SleB (TIGR02869)→Aau-1-8 NC 008711.1 + 4242478 4242640 RNA→ hypo→Fal-1-5 NC 008278.1 + 7256134 7256365 RNA→ Transglycosylase (pfam06737)→ DUF3151 (pfam11349)→ AdSS (cd03108)→

Bacteria CyanobacteriaCsp-5-1 NC 014501.1 + 1288806 1288965 RNA→ TM PBP2 (cd06261)→ TauA (COG0715)→ ABC NrtD SsuB transporters (cd03293)→Csp-3-1 NC 011729.1 + 707439 707598 RNA→ TM PBP2 (cd06261)→Mch-1-1 NZ DS989843.1 + 71013 71175 RNA→ ←hypoSsp-9-1 NC 000911.1 + 3422554 3422720 RNA→ P permease (cd01116)→Csp-1-1 NC 010546.1 - 62673 62528 RNA→ COG3932 (COG3932)→ HAD like (cd01427)→ SLC13 permease (cd01115)→ P permease (cd01116)→Csp-2-1 NZ AAXW01000019.1 + 19102 19247 RNA→ COG3932 (COG3932)→ HAD like (cd01427)→ SLC13 permease (cd01115)→ P permease (cd01116)→

COG2343 (COG2343)→Csp-6-1 NC 011726.1 + 2901195 2901340 RNA→ P permease (cd01116)→Csp-7-1 NC 013161.1 - 3362517 3362372 RNA→ P permease (cd01116)→Ama-1-1 NZ ABYK01000074.1 - 6858 6658 RNA→ hypo→ COG1357 (COG1357)→Asp-2-1 NZ ADDH01000020.1 - 62922 62722 RNA→ COG1357 (COG1357)→Apl-1-1 NZ ACSK01000962.1 - 1542 1341 RNA→ COG1357 (COG1357)→Osp-1-1 NZ CACA01000371.1 + 9533 9687 RNA→ hypo (cons)→Nsp-2-1 NC 003272.1 - 3675541 3675332 RNA→ hypo→ P permease (cd01116)→Cra-1-1 NZ ACYA01000064.1 + 31180 31307 RNA→ Usp (pfam00582)→ P permease (cd01116)→ PDZ serine protease (cd00987)→’az-1-1 NC 014248.1 + 4675293 4675419 RNA→ hypo→Rbr-1-1 NZ ACYB01000029.1 + 94485 94612 RNA→ Putative uncharacterized protein→ P permease (cd01116)→Ava-1-1 NC 007413.1 + 1072651 1072866 RNA→ hypo→Lsp-1-1 NZ AAVU01000012.1 + 6103 6312 RNA→ ←hypoNsp-2-2 NC 003272.1 + 5415292 5415495 RNA→ hypo→Ava-1-2 NC 007413.1 + 1722951 1723154 RNA→ hypo→Nsp-2-3 NC 003272.1 - 3677495 3677283 RNA→ hypo→Ava-1-3 NC 007413.1 + 1069081 1069294 RNA→ TM PBP2 (cd06261)→ TauA (COG0715)→ ABC NrtD SsuB transporters (cd03293)→’az-1-2 NC 014248.1 - 1388417 1388250 RNA→ GT1 Sucrose synthase (cd03800)→Ter-1-1 NC 008312.1 - 5425164 5424988 RNA→ hypo→Npu-1-2 NC 010628.1 - 1924316 1924113 RNA→ GT1 Sucrose synthase (cd03800)→Lsp-1-2 NZ AAVU01000078.1 - 10760 10604 RNA→ P permease (cd01116)→Nsp-2-4 NC 003272.1 + 4078682 4078821 RNA→ hypo→Ava-1-4 NC 007413.1 - 4238284 4238145 RNA→ GT1 Sucrose synthase (cd03800)→Csp-6-2 NC 011726.1 + 3841709 3841871 RNA→ TM PBP2 (cd06261)→ TauA (COG0715)→ ABC NrtD SsuB transporters (cd03293)→Csp-7-2 NC 013161.1 + 3816527 3816689 RNA→ TM PBP2 (cd06261)→ TauA (COG0715)→ ABC NrtD SsuB transporters (cd03293)→Mae-1-1 NC 010296.1 - 5450694 5450541 RNA→ P permease (cd01116)→ GT1 wbuB like (cd03794)→Csp-3-2 NC 011729.1 + 5815893 5816059 RNA→ hypo→Csp-5-2 NC 014501.1 + 855897 856061 RNA→ hypo→Npu-1-3 NC 010628.1 - 1617762 1617534 RNA→ RNA→ (big gap) Usp (pfam00582)→Npu-1-1 NC 010628.1 - 1615155 1615031 (shown above)Csp-4-1 NC 011884.1 + 5369027 5369212 RNA→ ArsB NhaD permease (cd00625)→Csp-3-3 NC 011729.1 + 5496169 5496340 RNA→ P permease (cd01116)→ COG3932 (COG3932)→ HisA (cd04732)→Csp-5-3 NC 014501.1 - 1647993 1647845 RNA→ P permease (cd01116)→ COG3932 (COG3932)→Csp-3-4 NC 011729.1 - 3786919 3786784 RNA→ HAD like (cd01427)→Csp-5-4 NC 014501.1 + 1496033 1496195 RNA→ hypo→


18

Csp-4-2 NC 011884.1 - 4373284 4373132 RNA→ USP Like (cd00293)→ GDE C (pfam06202)GDE N (pfam12439)→Ssp-8-1 NC 010474.1 - 21761 21609 RNA→ TM PBP2 (cd06261)→ TauA (COG0715)→ ABC NrtD SsuB transporters (cd03293)→

COG3932 (COG3932)→

Bacteria Firmicutes BacillalesPsp-1-1 NC 012914.1 - 125723 125577 RNA→ NLPC P60 (pfam00877)→Ppo-1-1 NC 014483.1 - 2765400 2765193 RNA→ LysM (cd00118)3D (pfam06725)→Ppo-2-1 NC 014622.1 - 3043596 3043387 RNA→ LysM (cd00118)3D (pfam06725)→Bsp-2-1 NZ AAOX01000003.1 + 202763 202892 RNA→ RNA→ GlnA (TIGR00653)→Bsp-2-2 NZ AAOX01000003.1 + 202935 203069 (shown above)

Esp-1-1 NC 012673.1 - 1228122 1227991 RNA→ hypo→ K+-transporting ATPase, F subunit→ KdpA (pfam03814)→ KdpB (COG2216)→KdpC (COG2156)→ USP OKCHK (cd01987)→ COG0702 (COG0702)→

Bpu-1-1 NZ ABRX01000003.1 - 303825 303703 RNA→ SDF (pfam00375)→Bpu-2-1 NC 009848.1 + 465466 465589 RNA→ SDF (pfam00375)→Bsu-2-1 NC 014479.1 + 489457 489577 RNA→ SDF (pfam00375)→ ABC DR subfamily A (cd03230)→ NosY (COG1277)→ YdbL→Bsu-1-1 NZ ADGS01000028.1 + 200212 200332 RNA→ SDF (pfam00375)→ ABC DR subfamily A (cd03230)→ NosY (COG1277)→ YdbL→Bli-1-1 NC 006270.3 + 542505 542636 RNA→ SDF (pfam00375)→ ABC DR subfamily A (cd03230)→ NosY (COG1277)→Bli-1-2 NC 006322.1 + 542311 542442 RNA→ SDF (pfam00375)→ ABC DR subfamily A (cd03230)→ NosY (COG1277)→Gsp-3-1 NC 013406.1 + 29842 30048 RNA→ COG3583 (COG3583)COG3584 (COG3584)→Bme-2-1 NC 014019.1 + 413626 413756 RNA→ SDF (pfam00375)→Bme-1-1 NC 014103.1 + 419660 419790 RNA→ SDF (pfam00375)→Bsp-2-3 NZ AAOX01000019.1 - 28604 28460 RNA→ 2a38 (TIGR00933)→Bps-1-1 NC 013791.1 - 1403154 1402993 RNA→ TrkA (COG0569)→ hypo→Ppo-1-2 NC 014483.1 + 1334052 1334213 RNA→ hypo→Ppo-2-2 NC 014622.1 + 1470092 1470254 RNA→ protein→Pcu-1-1 NZ AEDD01000002.1 - 464440 464278 RNA→ PotE (COG0531)→Gsp-3-2 NC 013406.1 - 6114504 6114369 RNA→ 2a38 (TIGR00933)→ TrkA (COG0569)→Psp-1-2 NC 012914.1 + 378328 378504 RNA→ PotE (COG0531)→Psp-2-1 NZ GG695986.1 - 35240 35079 RNA→ LysM (cd00118)3D (pfam06725)→Gsp-3-3 NC 013406.1 - 524540 524377 RNA→ hypo→Aac-2-1 NC 013205.1 + 1434100 1434230 RNA→ LysM (cd00118)spore SleB (TIGR02869)→Aac-1-1 NZ ACCS01000001.1 + 187377 187507 RNA→ LysM (cd00118)→Ppo-2-3 NC 014622.1 + 30270 30541 RNA→ COG3583 (COG3583)COG3584 (COG3584)→Bco-1-1 NZ AAWV02000001.1 + 2062949 2063087 RNA→ SDF (pfam00375)→Aac-1-2 NZ ACCS01000024.1 - 39030 38895 RNA→ Spr (COG0791)→Aac-2-2 NC 013205.1 - 1116290 1116155 RNA→ Spr (COG0791)→Ppo-1-3 NC 014483.1 + 30398 30670 RNA→ COG3583 (COG3583)COG3584 (COG3584)→Pcu-1-2 NZ AEDD01000014.1 + 56983 57151 RNA→ LysM (cd00118)3D (pfam06725)→Bbr-1-1 NC 012491.1 + 384110 384249 RNA→ ABC Pro Gly Bertaine (cd03294)→ TM PBP2 (cd06261)→ ProX (COG2113)OpuAC (pfam04069)→

hypo→Bbr-1-2 NC 012491.1 + 388729 388868 RNA→ hypo→Bsp-2-4 NZ AAOX01000003.1 - 202003 201868 RNA→ hypo→Lfu-1-1 NZ ADJR01000017.1 - 290379 290245 RNA→ hypo→ 2a38 (TIGR00933)→ TrkA (COG0569)→Lsp-2-1 NC 010382.1 + 3632467 3632599 RNA→ ←hypoBsp-1-1 NZ AAXV01000025.1 + 10447 10578 RNA→ 2a38 (TIGR00933)→ TrkA (COG0569)→Bsp-2-5 NZ AAOX01000002.1 + 156414 156543 RNA→ CBS pair 30 (cd04643)→Bbr-1-3 NC 012491.1 - 1043761 1043634 RNA→ NLPC P60 (pfam00877)→Gsp-3-4 NC 013406.1 - 4501653 4501533 RNA→ NLPC P60 (pfam00877)→Psp-2-2 NZ GG695975.1 + 171256 171378 RNA→ NLPC P60 (pfam00877)→Pcu-1-3 NZ AEDD01000010.1 + 208893 209041 RNA→ NLPC P60 (pfam00877)→Pcu-1-4 NZ AEDD01000010.1 + 208035 208185 RNA→ NLPC P60 (pfam00877)→Ppo-1-4 NC 014483.1 - 136184 136058 RNA→ NLPC P60 (pfam00877)→Ppo-2-4 NC 014622.1 - 137190 137064 RNA→ NLPC P60 (pfam00877)→ hypo→


19

Psp-2-3 NZ GG695996.1 - 18169 18044 RNA→ NLPC P60 (pfam00877)→Gsp-3-5 NC 013406.1 - 102955 102831 RNA→ NLPC P60 (pfam00877)→Psp-2-4 NZ GG695996.1 - 17281 17096 RNA→ NLPC P60 (pfam00877)→Psp-2-5 NZ GG695975.1 + 144945 145098 RNA→ 2a38 (TIGR00933)→ TrkA (COG0569)→ P permease (cd01116)→Bbr-1-4 NC 012491.1 + 3258655 3258805 RNA→ SCP bacterial (cd05379)→Bbr-1-5 NC 012491.1 - 613928 613778 RNA→ SCP bacterial (cd05379)→Psp-1-3 NC 012914.1 - 5534731 5534577 RNA→ 2a38 (TIGR00933)→ TrkA (COG0569)→ hypo→Oih-1-1 NC 004193.1 + 1706093 1706240 RNA→ TrkA (COG0569)→ 2a38 (TIGR00933)→ 2a38 (TIGR00933)→

COG3409 (COG3409)Peptidase M23 (pfam01551)→Bsp-3-1 NZ ACPC01000045.1 + 69202 69341 RNA→ TrkA (COG0569)→ 2a38 (TIGR00933)→Esi-1-1 NC 010556.1 - 2525920 2525775 RNA→ hypo→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Ppo-1-5 NC 014483.1 - 4222743 4222602 RNA→ 2a38 (TIGR00933)→Ppo-2-5 NC 014622.1 - 4569177 4569034 RNA→ 2a38 (TIGR00933)→ TrkA (COG0569)→Btu-1-1 NC 014098.1 - 2412166 2412008 RNA→ hypo→ DUF3055 (pfam11256)→Psp-2-6 NZ GG695972.1 + 72983 73156 RNA→ PotE (COG0531)→Bsu-3-1 NC 000964.3 + 3188199 3188337 RNA→ TrkA (COG0569)→ 2a38 (TIGR00933)→Bsu-5-1 NZ ABQL01000005.1 + 2168808 2168946 RNA→ TrkA (COG0569)→ 2a38 (TIGR00933)→Bsu-4-1 NZ ABQM01000009.1 + 12587 12725 RNA→ TrkA (COG0569)→ 2a38 (TIGR00933)→Bsu-6-1 NZ ABQN01000009.1 + 12594 12732 RNA→ TrkA (COG0569)→ 2a38 (TIGR00933)→Bsu-2-2 NC 014479.1 + 2974656 2974795 RNA→ TrkA (COG0569)→ 2a38 (TIGR00933)→Bsu-1-2 NZ ADGS01000020.1 + 9426 9565 RNA→ TrkA (COG0569)→ 2a38 (TIGR00933)→Bat-1-1 NC 014639.1 + 2619024 2619161 RNA→ TrkA (COG0569)→ 2a38 (TIGR00933)→Psp-1-5 NC 012914.1 + 27571 27771 RNA→ COG3583 (COG3583)COG3584 (COG3584)→Psp-2-7 NZ GG695988.1 - 71583 71380 RNA→ COG3583 (COG3583)COG3584 (COG3584)→Bce-1-1 NZ ADFH01000024.1 - 33401 33269 RNA→ TrkA (COG0569)→ 2a38 (TIGR00933)→Psp-1-6 NC 012914.1 - 6192035 6191906 RNA→ KamA (COG1509)→ Abhydrolase 3 (pfam07859)→Pcu-1-5 NZ AEDD01000002.1 - 474769 474639 RNA→ beta CA cladeD (cd03379)→ MFS (cd06174)→Psp-2-8 NZ GG695985.1 + 62952 63083 RNA→ KamA (COG1509)→Gsp-3-6 NC 013406.1 - 6352864 6352727 RNA→ PBPb (cd00134)→ TM PBP2 (cd06261)→ TM PBP2 (cd06261)→

ABC HisP GlnQ permeases (cd03262)→ NAT SF (cd04301)→ OAT like (cd00610)→ Ectoine synth (pfam06339)→ectoine ThpD (TIGR02408)→ COG4843 (COG4843)→

Bsp-1-2 NZ AAXV01000026.1 - 33584 33446 RNA→ PotE (COG0531)→Lsp-2-2 NC 010382.1 + 779377 779515 RNA→ PotE (COG0531)→Lfu-1-2 NZ ADJR01000021.1 + 14116 14254 RNA→ PotE (COG0531)→Pcu-1-6 NZ AEDD01000005.1 - 206961 206740 RNA→ COG3583 (COG3583)COG3584 (COG3584)→Pcu-1-7 NZ AEDD01000008.1 + 8970 9168 RNA→ 2a38 (TIGR00933)→ TrkA (COG0569)→ COG3263 (COG3263)→Psp-1-7 NC 012914.1 + 6859864 6860047 RNA→ RNA→ hypo→ hypo→Psp-1-4 NC 012914.1 + 6860170 6860344 (shown above)Aac-2-3 NC 013205.1 + 777901 778023 RNA→ MFS (cd06174)→Pla-1-1 NZ AARF01000285.1 - 7462 7308 RNA→ hypo→ hypo→ KdpA (pfam03814)→ potassium-transporting ATPase subunit A→Bha-1-1 NC 002570.2 + 632289 632433 RNA→ TrkA (COG0569)→ 2a38 (TIGR00933)→Pla-1-2 NZ AARF01000050.1 - 6267 6130 RNA→ NLPC P60 (pfam00877)Cu amine oxidN1 (pfam07833)→Gsp-5-1 NC 013411.1 + 1068303 1068435 RNA→ PotE (COG0531)→Gsp-4-1 NZ ACNM01000019.1 - 34866 34734 RNA→ PotE (COG0531)→Gsp-1-1 NC 014206.1 + 209132 209263 RNA→ PotE (COG0531)→Gka-1-1 NC 006510.1 + 224421 224552 RNA→ PotE (COG0531)→Gsp-2-1 NZ ACVM01000036.1 + 9487 9624 RNA→ PotE (COG0531)→Gth-1-1 NZ ADNQ01000008.1 - 100871 100734 RNA→ PotE (COG0531)→Gsp-3-7 NC 013406.1 + 525095 525252 RNA→ hypo→ hypo→Bme-2-3 NC 014019.1 - 3749552 3749418 RNA→ TrkA (COG0569)→ 2a38 (TIGR00933)→Bme-1-2 NC 014103.1 - 3754460 3754326 RNA→ TrkA (COG0569)→ 2a38 (TIGR00933)→Pla-1-3 NZ AARF01000314.1 - 964 755 RNA→ COG3583 (COG3583)→Bco-1-2 NZ AAWV02000001.1 - 912237 912100 RNA→ hypo→ PotE (COG0531)→


20

Btu-1-2 NC 014098.1 - 1971255 1971133 RNA→ hypo→Bme-2-4 NC 014019.1 - 3007759 3007626 RNA→ RNA→ (big gap) KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→

USP OKCHK (cd01987)→ CBS pair 30 (cd04643)→Bme-2-2 NC 014019.1 - 3007391 3007260 (shown above)

Gsp-3-8 NC 013406.1 + 6691969 6692154 RNA→ PotE (COG0531)→Bps-2-1 NZ ACMX01000030.1 + 57212 57349 RNA→ PotE (COG0531)→Bmy-2-1 NZ ACMV01000123.1 + 5700 5837 RNA→ PotE (COG0531)→Bmy-3-1 NZ ACMW01000041.1 + 5728 5865 RNA→ PotE (COG0531)→Bce-32-1 NC 011969.1 + 1856804 1856941 RNA→ PotE (COG0531)→Bce-10-1 NC 011658.1 + 1855356 1855493 RNA→ PotE (COG0531)→Bce-29-1 NZ ABDL02000004.1 + 314768 314905 RNA→ PotE (COG0531)→Bce-23-1 NZ ACMC01000044.1 + 58014 58151 RNA→ PotE (COG0531)→Bce-39-1 NZ ACML01000108.1 + 9658 9794 RNA→ PotE (COG0531)→Bce-26-1 NZ ACMO01000030.1 + 65366 65502 RNA→ PotE (COG0531)→Bth-3-1 NZ ACNK01000040.1 + 161017 161154 RNA→ PotE (COG0531)→Bce-36-1 NZ ACMI01000115.1 + 16661 16798 RNA→ PotE (COG0531)→Bce-19-1 NC 011725.1 + 1785230 1785367 RNA→ PotE (COG0531)→Bce-4-1 NZ ACLV01000038.1 + 68177 68314 RNA→ PotE (COG0531)→Bce-46-1 NZ ACMA01000037.1 + 3037 3174 RNA→ PotE (COG0531)→Bce-41-1 NZ ACMM01000136.1 + 63925 64062 RNA→ PotE (COG0531)→Bth-10-1 NZ ACND01000048.1 + 55519 55656 RNA→ PotE (COG0531)→Bce-35-1 NZ ACMG01000031.1 + 12183 12321 RNA→ PotE (COG0531)→Bce-37-1 NZ ACMJ01000037.1 + 12185 12323 RNA→ PotE (COG0531)→Bce-40-1 NZ ACMN01000036.1 + 12256 12394 RNA→Bce-33-1 NZ ACLY01000037.1 + 37660 37797 RNA→ PotE (COG0531)→Bce-17-1 NC 004722.1 + 1762538 1762675 RNA→ PotE (COG0531)→Bce-28-1 NC 011772.1 + 1739714 1739851 RNA→ PotE (COG0531)→Bth-1-1 NC 014171.1 + 1788194 1788331 RNA→ PotE (COG0531)→Bce-27-1 NZ AAEK01000005.1 - 2073 1936 RNA→ PotE (COG0531)→Bth-8-1 NZ AAJM01000456.1 + 1233 1370 RNA→ PotE (COG0531)→Bce-6-1 NZ ABDA02000005.1 - 114617 114480 RNA→ PotE (COG0531)→Bce-15-1 NZ ACLT01000044.1 + 68977 69114 RNA→ PotE (COG0531)→Bce-18-1 NZ ACLZ01000025.1 + 13807 13944 RNA→ PotE (COG0531)→Bce-22-1 NZ ACMB01000042.1 + 63402 63539 RNA→ PotE (COG0531)→Bce-20-1 NZ ACME01000038.1 + 148744 148881 RNA→ PotE (COG0531)→Bce-34-1 NZ ACMH01000043.1 + 308 445 RNA→ PotE (COG0531)→Bce-13-1 NZ ACMQ01000061.1 + 9335 9472 RNA→ PotE (COG0531)→Bth-17-1 NZ ACMY01000048.1 + 45777 45914 RNA→ PotE (COG0531)→Bth-2-1 NZ ACMZ01000039.1 + 297 434 RNA→ PotE (COG0531)→Bth-16-1 NZ ACNA01000041.1 + 210377 210514 RNA→ PotE (COG0531)→Bth-15-1 NZ ACNB01000065.1 + 69193 69330 RNA→ PotE (COG0531)→Bth-12-1 NZ ACNC01000068.1 + 8467 8604 RNA→ PotE (COG0531)→Bth-6-1 NZ ACNF01000047.1 + 10194 10331 RNA→ PotE (COG0531)→Bth-7-1 NZ ACNI01000037.1 + 225321 225458 RNA→ PotE (COG0531)→Bth-4-1 NZ ACNL01000060.1 + 301 438 RNA→ PotE (COG0531)→Bwe-1-1 NC 010184.1 + 1778979 1779116 RNA→ PotE (COG0531)→Bmy-1-1 NZ ACMU01000037.1 + 105992 106129 RNA→ PotE (COG0531)→Bce-12-1 NZ ACLX01000049.1 + 113190 113327 RNA→ PotE (COG0531)→Bce-8-1 NZ ACMS01000086.1 + 317 454 RNA→ PotE (COG0531)→Bce-9-1 NZ ACMT01000098.1 + 303 440 RNA→Bce-21-1 NZ ACMD01000069.1 + 61945 62082 RNA→ PotE (COG0531)→Bce-30-1 NZ ACLW01000047.1 + 210755 210892 RNA→ PotE (COG0531)→


21

Bce-16-1 NC 003909.8 + 1900022 1900159 RNA→ PotE (COG0531)→Ban-17-1 NC 005945.1 + 1768174 1768311 RNA→ PotE (COG0531)→ hypo→Ban-2-1 NC 007530.2 + 1768230 1768367 RNA→ (big gap) Bacillus HBL (pfam05791)→ Bacillus HBL (pfam05791)→Ban-14-1 NC 012581.1 - 2470987 2470850 RNA→ PotE (COG0531)→ amino acid permease→Ban-5-1 NC 012659.1 + 1768130 1768267 RNA→ (big gap) Bacillus HBL (pfam05791)→ Bacillus HBL (pfam05791)→Bce-44-1 NC 014335.1 + 1750012 1750149 RNA→ PotE (COG0531)→Ban-12-1 NC 003997.3 + 1768107 1768244 RNA→ potE pseudogene→Ban-11-1 NZ AAAC02000001.1 + 2253237 2253374 RNA→ PotE (COG0531)→ COG0531: Amino acid transporters→Ban-15-1 NZ AAEN01000016.1 + 67113 67250 RNA→ (big gap) Bacillus HBL (pfam05791)→ Bacillus HBL (pfam05791)→Ban-10-1 NZ AAEO01000025.2 + 335652 335789 RNA→ (big gap) Bacillus HBL (pfam05791)→ Bacillus HBL (pfam05791)→Ban-18-1 NZ AAEP01000035.1 + 339890 340027 RNA→ (big gap) Bacillus HBL (pfam05791)→ Bacillus HBL (pfam05791)→Ban-16-1 NZ AAEQ01000029.2 + 341285 341422 RNA→ (big gap) Bacillus HBL (pfam05791)→ Bacillus HBL (pfam05791)→Ban-19-1 NZ AAER01000023.2 + 328625 328762 RNA→ (big gap) Bacillus HBL (pfam05791)→ Bacillus HBL (pfam05791)→Ban-13-1 NZ AAES01000034.2 + 339657 339794 RNA→ (big gap) Bacillus HBL (pfam05791)→ Bacillus HBL (pfam05791)→Ban-1-1 NZ ABDN02000004.1 - 99487 99350 RNA→ (big gap) Bacillus HBL (pfam05791)→ Bacillus HBL (pfam05791)→Ban-9-1 NZ ABJC01000002.1 + 342843 342980 RNA→ (big gap) Bacillus HBL (pfam05791)→ Bacillus HBL (pfam05791)→Ban-4-1 NZ ABKF01000006.1 - 13331 13194 RNA→ (big gap) Bacillus HBL (pfam05791)→ Bacillus HBL (pfam05791)→Ban-7-1 NZ ABKG01000003.1 - 13019 12882 RNA→ (big gap) Bacillus HBL (pfam05791)→ Bacillus HBL (pfam05791)→Ban-6-1 NZ ABLB01000012.1 + 125062 125199 RNA→ (big gap) Bacillus HBL (pfam05791)→ Bacillus HBL (pfam05791)→Ban-8-1 NZ ABLH01000004.1 + 344355 344492 RNA→ (big gap) Bacillus HBL (pfam05791)→ Bacillus HBL (pfam05791)→Ban-3-1 NZ ABLT01000003.1 - 12827 12690 RNA→ (big gap) Bacillus HBL (pfam05791)→ Bacillus HBL (pfam05791)→Bce-38-1 NZ ACMK01000055.1 + 3217 3354 RNA→ PotE (COG0531)→Bce-7-1 NZ ACMR01000081.1 + 2324 2461 RNA→ PotE (COG0531)→Bth-14-1 NZ ACNJ01000041.1 + 18540 18677 RNA→ PotE (COG0531)→Bth-9-1 NC 005957.1 + 1806458 1806595 RNA→ amino acid permease, N-terminal→ PotE (COG0531)→ amino acid permease, C-terminal→Bce-25-1 NC 006274.1 + 1793583 1793720 RNA→ PotE (COG0531)→Bce-14-1 NC 011773.1 + 1824312 1824449 RNA→ PotE (COG0531)→Bth-18-1 NC 008600.1 + 1810265 1810402 RNA→ PotE (COG0531)→Bce-2-1 NC 012472.1 + 1804486 1804623 RNA→ PotE (COG0531)→Bce-43-1 NZ ABCZ02000003.1 - 13288 13151 RNA→ PotE (COG0531)→Bce-31-1 NZ ABDK02000017.1 - 26337 26200 RNA→ PotE (COG0531)→Bce-3-1 NZ ABDM02000007.1 - 11871 11734 RNA→ PotE (COG0531)→Bce-45-1 NZ ACLS01000056.1 + 2983 3120 RNA→ PotE (COG0531)→Bce-24-1 NZ ACLU01000045.1 + 3048 3185 RNA→ PotE (COG0531)→Bce-5-1 NZ ACMF01000038.1 + 59948 60085 RNA→ PotE (COG0531)→Bth-11-1 NZ ACNE01000039.1 + 16240 16377 RNA→ PotE (COG0531)→Bth-5-1 NZ ACNG01000055.1 + 35776 35913 RNA→ PotE (COG0531)→Bth-13-1 NZ ACNH01000034.1 + 106085 106222 RNA→ PotE (COG0531)→Bce-42-1 NZ ADFM01000057.1 + 309 446 RNA→Bce-11-1 NZ ACMP01000058.1 + 282 419 RNA→ PotE (COG0531)→Bme-1-3 NC 014103.1 - 1751995 1751860 RNA→ PotE (COG0531)→Bps-2-2 NZ ACMX01000058.1 + 190804 190936 RNA→ hypo→Bmy-2-2 NZ ACMV01000155.1 + 26519 26651 RNA→ hypo→Bmy-3-2 NZ ACMW01000073.1 + 41206 41338 RNA→ hypo→Bce-8-2 NZ ACMS01000155.1 + 13742 13875 RNA→ hypo→Bce-9-2 NZ ACMT01000149.1 + 13894 14027 RNA→ hypo→Bwe-1-2 NC 010184.1 + 3134677 3134810 RNA→ hypo→Bce-35-2 NZ ACMG01000054.1 + 136395 136526 RNA→ ←ubiE/COQ5 methyltransferaseBce-36-2 NZ ACMI01000143.1 + 2222 2353 RNA→ ←AdoMet MTases (cd02440)

Bce-37-2 NZ ACMJ01000056.1 + 2216 2347 RNA→ hypo→Bce-40-2 NZ ACMN01000057.1 + 100001 100132 RNA→ hypo→Bce-45-2 NZ ACLS01000079.1 + 101950 102080 RNA→ hypo→


22

Bce-18-2 NZ ACLZ01000052.1 + 93584 93715 RNA→ hypo→Bce-16-2 NC 003909.8 + 3159883 3160014 RNA→ hypo→Bce-32-2 NC 011969.1 + 3109066 3109197 RNA→ ←Collagen-like triple helix repeat proteinBce-10-2 NC 011658.1 + 3146816 3146947 RNA→ hypo→Bce-27-2 NZ AAEK01000001.1 - 145865 145734 RNA→ ←collagen-like triple helix repeat protein

Bce-29-2 NZ ABDL02000003.1 + 315923 316054 RNA→ hypo→Bce-23-2 NZ ACMC01000064.1 + 24617 24748 RNA→ hypo→Bth-17-2 NZ ACMY01000080.1 + 36952 37083 RNA→ ←Collagen-like triple helix repeat protein

Bce-12-2 NZ ACLX01000071.1 + 44757 44888 RNA→ ←Collagen-like triple helix repeat proteinBce-11-2 NZ ACMP01000084.1 + 19502 19633 RNA→ ←UPF0066 (pfam01980)

Bmy-1-2 NZ ACMU01000056.1 + 63812 63943 RNA→ ←UPF0066 (pfam01980)Bce-30-2 NZ ACLW01000070.1 + 28665 28796 RNA→ hypo→Bce-7-2 NZ ACMR01000143.1 + 12913 13044 RNA→Bce-21-2 NZ ACMD01000099.1 + 11580 11711 RNA→ hypo→Bce-28-2 NC 011772.1 + 3262817 3262949 RNA→ hypo→Bth-8-2 NZ AAJM01000259.1 - 5754 5622 RNA→ ←Collagen (pfam01391)

Bth-15-2 NZ ACNB01000107.1 + 13040 13172 RNA→ ←Collagen-like triple helix repeat proteinBth-4-2 NZ ACNL01000115.1 + 23773 23905 RNA→ hypo→Bth-3-2 NZ ACNK01000069.1 + 28244 28375 RNA→ hypo→Bce-17-2 NC 004722.1 + 3306600 3306731 RNA→ ←Collagen (pfam01391)Bce-19-2 NC 011725.1 + 3235195 3235326 RNA→ hypo→Bth-1-2 NC 014171.1 + 3232164 3232295 RNA→ hypo→Bce-6-2 NZ ABDA02000002.1 - 412291 412160 RNA→ hypo→Bce-15-2 NZ ACLT01000068.1 + 25331 25462 RNA→ hypo→Bce-4-2 NZ ACLV01000057.1 + 23342 23473 RNA→ hypo→Bce-46-2 NZ ACMA01000056.1 + 171692 171823 RNA→ hypo→Bce-22-2 NZ ACMB01000066.1 + 68608 68739 RNA→ hypo→Bce-20-2 NZ ACME01000057.1 + 102589 102720 RNA→ ←Collagen (pfam01391)Bce-34-2 NZ ACMH01000076.1 + 30676 30807 RNA→ hypo→Bce-41-2 NZ ACMM01000167.1 + 2156 2287 RNA→ hypo→Bce-26-2 NZ ACMO01000091.1 + 2174 2305 RNA→ hypo→Bce-13-2 NZ ACMQ01000143.1 + 2183 2314 RNA→ hypo→Bth-2-2 NZ ACMZ01000083.1 + 80357 80488 RNA→ hypo→Bth-16-2 NZ ACNA01000073.1 + 152350 152481 RNA→ hypo→Bth-12-2 NZ ACNC01000115.1 + 4710 4841 RNA→ hypo→Bth-10-2 NZ ACND01000096.1 + 29125 29256 RNA→ hypo→Bth-6-2 NZ ACNF01000076.1 + 14465 14596 RNA→ hypo→Bth-7-2 NZ ACNI01000071.1 + 116414 116545 RNA→ hypo→Bce-33-2 NZ ACLY01000058.1 + 63147 63278 RNA→ hypo→Bce-39-2 NZ ACML01000142.1 + 12657 12788 RNA→ hypo→Ban-17-2 NC 005945.1 + 3137592 3137724 RNA→ ←AdoMet MTases (cd02440)

Ban-2-2 NC 007530.2 + 3137026 3137158 RNA→ hypo→Bth-9-2 NC 005957.1 + 3215934 3216066 RNA→ ←AdoMet MTases (cd02440)Bce-25-2 NC 006274.1 + 3187266 3187398 RNA→ ←AdoMet MTases (cd02440)

Bce-14-2 NC 011773.1 + 3223700 3223832 RNA→ hypo→Bth-18-2 NC 008600.1 + 3219382 3219514 RNA→ ←AdoMet MTases (cd02440)Ban-14-2 NC 012581.1 - 1101730 1101598 RNA→ hypo→Bce-2-2 NC 012472.1 + 3222130 3222262 RNA→ hypo→Ban-5-2 NC 012659.1 + 3136926 3137058 RNA→ hypo→Bce-44-2 NC 014335.1 + 3117137 3117269 RNA→ ←AdoMet MTases (cd02440)Ban-12-2 NC 003997.3 + 3136899 3137031 RNA→ hypo→Ban-11-2 NZ AAAC02000001.1 + 3601526 3601658 RNA→ ←AdoMet MTases (cd02440)


23

Ban-15-2 NZ AAEN01000017.2 + 373036 373168 RNA→ hypo→Ban-10-2 NZ AAEO01000022.2 + 1095924 1096056 RNA→ hypo→Ban-18-2 NZ AAEP01000026.2 + 422710 422842 RNA→ hypo→Ban-16-2 NZ AAEQ01000035.2 - 96462 96330 RNA→ hypo→Ban-19-2 NZ AAER01000040.2 + 868193 868325 RNA→ hypo→Ban-13-2 NZ AAES01000035.1 + 1037402 1037534 RNA→ hypo→Bce-43-2 NZ ABCZ02000011.1 - 161401 161269 RNA→ hypo→Bce-31-2 NZ ABDK02000002.1 + 390238 390370 RNA→ ←AdoMet MTases (cd02440)

Bce-3-2 NZ ABDM02000001.1 + 460410 460542 RNA→ hypo→Ban-1-2 NZ ABDN02000001.1 - 307960 307828 RNA→ hypo→Ban-9-2 NZ ABJC01000001.2 + 878756 878888 RNA→ hypo→Ban-4-2 NZ ABKF01000001.1 + 371549 371681 RNA→ hypo→Ban-7-2 NZ ABKG01000001.1 + 878186 878318 RNA→ hypo→Ban-6-2 NZ ABLB01000002.1 + 371472 371604 RNA→ hypo→Ban-8-2 NZ ABLH01000001.1 + 371660 371792 RNA→ hypo→Ban-3-2 NZ ABLT01000002.1 + 371601 371733 RNA→ hypo→Bce-24-2 NZ ACLU01000076.1 + 10127 10259 RNA→ ←AdoMet MTases (cd02440)Bce-5-2 NZ ACMF01000057.1 + 30413 30545 RNA→ ←AdoMet MTases (cd02440)

Bce-38-2 NZ ACMK01000090.1 + 29368 29500 RNA→ ←AdoMet MTases (cd02440)

Bth-11-2 NZ ACNE01000092.1 + 56563 56695 RNA→ ←AdoMet MTases (cd02440)Bth-5-2 NZ ACNG01000076.1 + 36307 36439 RNA→ ←AdoMet MTases (cd02440)

Bth-13-2 NZ ACNH01000059.1 + 233173 233305 RNA→ ←AdoMet MTases (cd02440)

Bth-14-2 NZ ACNJ01000073.1 + 115433 115565 RNA→ ←AdoMet MTases (cd02440)Bce-42-2 NZ ADFM01000044.1 + 59470 59602 RNA→ hypo→Bcy-1-1 NC 009674.1 + 2226766 2226899 RNA→ hypo→Bsp-2-6 NZ AAOX01000019.1 + 14348 14476 RNA→ SDF (pfam00375)→Bmy-2-3 NZ ACMV01000122.1 + 4279 4409 RNA→ KdpA (pfam03814)→Bmy-3-3 NZ ACMW01000040.1 + 4383 4513 RNA→ KdpA (pfam03814)→Bps-2-3 NZ ACMX01000029.1 + 392426 392556 RNA→ KdpA (pfam03814)→Bce-39-3 NZ ACML01000064.1 + 2583 2717 RNA→ hypo→ hypo→Bcy-1-2 NC 009674.1 + 711911 712046 RNA→ hypo→ hypo→Bps-2-4 NZ ACMX01000017.1 + 9824 9960 RNA→ hypo→ hypo→Bmy-2-4 NZ ACMV01000048.1 + 9912 10048 RNA→ hypo→ hypo→Bmy-3-4 NZ ACMW01000021.1 + 9888 10024 RNA→ hypo→ hypo→Bce-45-3 NZ ACLS01000031.1 + 13711 13847 RNA→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Bce-16-3 NC 003909.8 + 838091 838227 RNA→ hypo→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Bce-17-3 NC 004722.1 + 738432 738568 RNA→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Ban-17-3 NC 005945.1 + 761309 761445 RNA→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Ban-2-3 NC 007530.2 + 761414 761550 RNA→ hypo→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Bth-9-3 NC 005957.1 + 752360 752496 RNA→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Bce-25-3 NC 006274.1 + 751375 751511 RNA→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Bce-28-3 NC 011772.1 + 739558 739694 RNA→ hypo→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Bce-19-3 NC 011725.1 + 770459 770595 RNA→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Bce-14-3 NC 011773.1 + 775502 775638 RNA→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Bth-18-3 NC 008600.1 + 781950 782086 RNA→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Ban-14-3 NC 012581.1 - 3477530 3477394 RNA→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Bce-2-3 NC 012472.1 + 750095 750231 RNA→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Ban-5-3 NC 012659.1 + 761314 761450 RNA→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Bce-44-3 NC 014335.1 + 726740 726876 RNA→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Bth-1-3 NC 014171.1 + 754562 754698 RNA→ hypo→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→Ban-12-3 NC 003997.3 + 761413 761549 RNA→ hypo→ K+-transporting ATPase subunit F→ KdpA (pfam03814)→ KdpB (COG2216)→

KdpC (COG2156)→ USP OKCHK (cd01987)→


24

Ban-11-3 NZ AAAC02000001.1 + 1263162 1263298 RNA→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Ban-15-3 NZ AAEN01000010.1 - 392176 392040 RNA→ hypo→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Ban-10-3 NZ AAEO01000033.2 - 432602 432466 RNA→ hypo→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Ban-18-3 NZ AAEP01000028.1 + 13203 13339 RNA→ hypo→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Ban-16-3 NZ AAEQ01000022.2 + 15765 15901 RNA→ hypo→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Ban-19-3 NZ AAER01000025.2 + 15270 15406 RNA→ hypo→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Ban-13-3 NZ AAES01000021.1 + 15279 15415 RNA→ hypo→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Bce-6-3 NZ ABDA02000001.1 + 441981 442117 RNA→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Bce-31-3 NZ ABDK02000001.1 - 461152 461016 RNA→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Bce-3-3 NZ ABDM02000017.1 + 15157 15293 RNA→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Ban-1-3 NZ ABDN02000019.1 + 14785 14921 RNA→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Ban-9-3 NZ ABJC01000027.1 + 16847 16983 RNA→ hypo→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Ban-4-3 NZ ABKF01000029.1 - 41420 41284 RNA→ hypo→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Ban-7-3 NZ ABKG01000021.1 - 58978 58842 RNA→ hypo→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Ban-6-3 NZ ABLB01000027.1 - 41243 41107 RNA→ hypo→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Ban-8-3 NZ ABLH01000028.1 + 15155 15291 RNA→ hypo→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Ban-3-3 NZ ABLT01000028.1 + 16313 16449 RNA→ hypo→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Bce-15-3 NZ ACLT01000023.1 + 10 146 RNA→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Bce-24-3 NZ ACLU01000025.1 + 13791 13927 RNA→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Bce-4-3 NZ ACLV01000024.1 + 13341 13477 RNA→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Bce-30-3 NZ ACLW01000025.1 + 13379 13515 RNA→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Bce-33-3 NZ ACLY01000020.1 + 14419 14555 RNA→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Bce-46-3 NZ ACMA01000018.1 + 13995 14131 RNA→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Bce-22-3 NZ ACMB01000019.1 + 14346 14482 RNA→ hypo→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Bce-20-3 NZ ACME01000017.1 + 13818 13954 RNA→ hypo→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Bce-5-3 NZ ACMF01000018.1 + 14224 14360 RNA→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Bce-35-3 NZ ACMG01000020.1 + 14524 14660 RNA→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Bce-34-3 NZ ACMH01000022.1 + 14262 14398 RNA→ hypo→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Bce-37-3 NZ ACMJ01000018.1 + 14427 14563 RNA→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Bce-38-3 NZ ACMK01000029.1 + 13793 13929 RNA→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Bce-41-3 NZ ACMM01000080.1 + 3937 4073 RNA→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Bce-40-3 NZ ACMN01000021.1 + 14075 14211 RNA→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Bce-26-3 NZ ACMO01000018.1 + 14353 14489 RNA→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Bce-13-3 NZ ACMQ01000026.1 + 13829 13965 RNA→ hypo→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ KdpD (COG2205)→

USP OKCHK (cd01987)→Bce-7-3 NZ ACMR01000042.1 + 13810 13946 RNA→ hypo→Bth-2-3 NZ ACMZ01000023.1 + 14261 14397 RNA→ hypo→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Bth-16-3 NZ ACNA01000025.1 + 14202 14338 RNA→ hypo→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Bth-15-3 NZ ACNB01000036.1 + 13506 13642 RNA→ hypo→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Bth-12-3 NZ ACNC01000031.1 + 14250 14386 RNA→ hypo→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Bth-10-3 NZ ACND01000025.1 + 14270 14406 RNA→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Bth-11-3 NZ ACNE01000018.1 + 13834 13970 RNA→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Bth-6-3 NZ ACNF01000025.1 + 14262 14398 RNA→ hypo→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Bth-5-3 NZ ACNG01000026.1 + 14319 14455 RNA→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Bth-13-3 NZ ACNH01000019.1 + 14224 14360 RNA→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Bth-7-3 NZ ACNI01000020.1 + 14346 14482 RNA→ hypo→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Bth-14-3 NZ ACNJ01000020.1 + 18987 19123 RNA→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Bth-3-3 NZ ACNK01000021.1 + 14264 14400 RNA→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Bth-4-3 NZ ACNL01000028.1 + 13582 13718 RNA→ hypo→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Bce-42-3 NZ ADFM01000064.1 + 11153 11289 RNA→Bce-43-3 NZ ABCZ02000021.1 + 15674 15810 RNA→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Bce-32-3 NC 011969.1 + 814641 814777 RNA→ hypo→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→


25

Bce-10-3 NC 011658.1 + 830121 830257 RNA→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Bce-29-3 NZ ABDL02000021.1 - 66564 66428 RNA→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Bce-18-3 NZ ACLZ01000016.1 + 14246 14382 RNA→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Bce-23-3 NZ ACMC01000023.1 + 14228 14364 RNA→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpB (COG2216)→ KdpC (COG2156)→

USP OKCHK (cd01987)→Bth-17-3 NZ ACMY01000026.1 + 13322 13458 RNA→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Bce-27-3 NZ AAEK01000002.1 + 19282 19418 RNA→ hypothetical protein protein→ KdpA (pfam03814)→Bce-11-3 NZ ACMP01000030.1 + 15076 15212 RNA→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Bwe-1-3 NC 010184.1 + 748444 748580 RNA→ hypo→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Bce-12-3 NZ ACLX01000031.1 + 13945 14081 RNA→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Bce-21-3 NZ ACMD01000040.1 + 13521 13657 RNA→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Bce-8-3 NZ ACMS01000048.1 + 14246 14382 RNA→Bce-9-3 NZ ACMT01000053.1 + 14761 14897 RNA→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Bmy-1-3 NZ ACMU01000020.1 + 14098 14234 RNA→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Bth-8-3 NZ AAJM01000133.1 - 9678 9543 RNA→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Bce-39-4 NZ ACML01000064.1 + 3714 3850 RNA→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Bcy-1-3 NC 009674.1 + 713121 713257 RNA→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Bmy-2-5 NZ ACMV01000048.1 + 11043 11177 RNA→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Bmy-3-5 NZ ACMW01000021.1 + 11019 11153 RNA→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Bps-2-5 NZ ACMX01000017.1 + 10955 11089 RNA→ KdpA (pfam03814)→ KdpB (COG2216)→ KdpC (COG2156)→ USP OKCHK (cd01987)→Bce-35-4 NZ ACMG01000020.1 + 13386 13525 RNA→ hypo→ hypo→ hypo→Bce-37-4 NZ ACMJ01000018.1 + 13290 13429 RNA→ hypo→ hypo→ hypo→Bce-40-4 NZ ACMN01000021.1 + 12938 13077 RNA→ hypo→ hypo→ hypo→Bce-7-4 NZ ACMR01000042.1 + 12674 12810 RNA→ hypo→ hypo→ hypo→Bce-33-4 NZ ACLY01000020.1 + 13283 13419 RNA→ hypo→ hypo→ hypo→Bth-14-4 NZ ACNJ01000020.1 + 17853 17988 RNA→ hypo→ hypo→ hypo→Bce-28-4 NC 011772.1 + 738423 738559 RNA→ hypo→ hypo→Bth-8-4 NZ AAJM01000133.1 - 10844 10708 RNA→ hypo→Bth-15-4 NZ ACNB01000036.1 + 12371 12507 RNA→ hypo→ hypo→Bth-4-4 NZ ACNL01000028.1 + 12447 12583 RNA→ hypo→ hypo→Bce-6-4 NZ ABDA02000001.1 + 440847 440983 RNA→ hypo→ hypo→Bce-15-4 NZ ACLT01000022.1 + 13129 13265 RNA→ hypo→ hypo→ hypo→Bce-4-4 NZ ACLV01000024.1 + 12207 12343 RNA→ hypo→ hypo→Bce-41-4 NZ ACMM01000080.1 + 2801 2937 RNA→ hypo→ hypo→Bce-26-4 NZ ACMO01000018.1 + 13219 13355 RNA→ hypo→ hypo→Bth-10-4 NZ ACND01000025.1 + 13136 13272 RNA→ hypo→ hypo→Bce-2-4 NC 012472.1 + 748960 749096 RNA→ hypo→ hypo→ hypo→Bce-12-4 NZ ACLX01000031.1 + 12807 12943 RNA→ hypo→ hypo→Bce-11-4 NZ ACMP01000030.1 + 13889 14025 RNA→ hypo→Bce-8-4 NZ ACMS01000048.1 + 13112 13248 RNA→ hypo→ hypo→ hypo→Bce-9-4 NZ ACMT01000053.1 + 13627 13763 RNA→ hypo→ hypo→ hypo→Bwe-1-4 NC 010184.1 + 747308 747443 RNA→ group-specific protein→ hypo→Bce-21-4 NZ ACMD01000040.1 + 12384 12520 RNA→ hypo→ hypo→Bmy-1-4 NZ ACMU01000020.1 + 12961 13097 RNA→ hypo→ hypo→Bth-17-4 NZ ACMY01000026.1 + 12186 12324 RNA→ hypo→ hypo→ hypo→Bce-10-4 NC 011658.1 + 828985 829123 RNA→ hypo→ hypo→ hypo→Bce-23-4 NZ ACMC01000023.1 + 13091 13229 RNA→ hypo→Ban-1-4 NZ ABDN02000019.1 + 13649 13785 RNA→ hypo→ hypo→Ban-17-4 NC 005945.1 + 760173 760309 RNA→ hypo→Ban-2-4 NC 007530.2 + 760278 760414 RNA→ hypo→ hypo→ hypo→Bth-9-4 NC 005957.1 + 751226 751362 RNA→ hypo→Bce-25-4 NC 006274.1 + 750239 750375 RNA→ group-specific protein→


26

Bce-14-4 NC 011773.1 + 774368 774504 RNA→ hypo→ hypo→ hypo→Bth-18-4 NC 008600.1 + 780814 780950 RNA→ ←hypo

Ban-14-4 NC 012581.1 - 3478666 3478530 RNA→ hypo→ hypo→ hypo→Ban-5-4 NC 012659.1 + 760178 760314 RNA→ hypo→ hypo→Bce-44-4 NC 014335.1 + 725604 725740 RNA→ hypo→Ban-12-4 NC 003997.3 + 760277 760413 RNA→ hypo→ hypo→ hypo→Ban-11-4 NZ AAAC02000001.1 + 1262026 1262162 RNA→ hypo→ hypo→Ban-15-4 NZ AAEN01000010.1 - 393312 393176 RNA→ hypo→ hypo→Ban-10-4 NZ AAEO01000033.2 - 433738 433602 RNA→ hypo→ hypo→Ban-18-4 NZ AAEP01000028.1 + 12067 12203 RNA→ hypo→ hypo→Ban-16-4 NZ AAEQ01000022.2 + 14629 14765 RNA→ hypo→ hypo→Ban-19-4 NZ AAER01000025.2 + 14134 14270 RNA→ hypo→ hypo→Ban-13-4 NZ AAES01000021.1 + 14143 14279 RNA→ hypo→ hypo→Bce-43-4 NZ ABCZ02000021.1 + 14540 14676 RNA→ hypo→ hypo→ hypo→Bce-31-4 NZ ABDK02000001.1 - 462288 462152 RNA→ hypo→ hypo→ hypo→Bce-3-4 NZ ABDM02000017.1 + 14021 14157 RNA→ hypo→ hypo→ hypo→Ban-9-4 NZ ABJC01000027.1 + 15711 15847 RNA→ hypo→ hypo→Ban-4-4 NZ ABKF01000029.1 - 42556 42420 RNA→ hypo→ hypo→Ban-7-4 NZ ABKG01000021.1 - 60114 59978 RNA→ hypo→ hypo→Ban-6-4 NZ ABLB01000027.1 - 42379 42243 RNA→ hypo→ hypo→Ban-8-4 NZ ABLH01000028.1 + 14019 14155 RNA→ hypo→ hypo→Ban-3-4 NZ ABLT01000028.1 + 15177 15313 RNA→ hypo→ hypo→Bce-24-4 NZ ACLU01000025.1 + 12655 12791 RNA→ hypo→ hypo→ hypo→Bce-5-4 NZ ACMF01000018.1 + 13090 13226 RNA→ hypo→ hypo→ hypo→Bce-38-4 NZ ACMK01000029.1 + 12657 12793 RNA→ hypo→ hypo→ hypo→Bth-11-4 NZ ACNE01000018.1 + 12698 12834 RNA→ hypo→ hypo→ hypo→Bth-5-4 NZ ACNG01000026.1 + 13184 13320 RNA→ hypo→ hypo→ hypo→Bth-13-4 NZ ACNH01000019.1 + 13090 13226 RNA→ hypo→ hypo→ hypo→Bce-42-4 NZ ADFM01000064.1 + 10021 10157 RNA→Bce-45-4 NZ ACLS01000031.1 + 12576 12712 RNA→ hypo→ hypo→Bce-16-4 NC 003909.8 + 836955 837091 RNA→ hypo→ hypo→ hypo→Bce-32-4 NC 011969.1 + 813505 813641 RNA→ hypo→Bce-29-4 NZ ABDL02000021.1 - 67700 67564 RNA→ hypo→ hypo→ hypo→Bce-27-4 NZ AAEK01000002.1 + 18146 18282 RNA→ hypothetical protein protein→ conserved hypothetical protein protein→ hypothetical protein protein→Bce-18-4 NZ ACLZ01000016.1 + 13110 13246 RNA→ hypo→ hypo→ hypo→Bce-17-4 NC 004722.1 + 737297 737433 RNA→ hypo→Bce-19-4 NC 011725.1 + 769324 769460 RNA→ hypo→ hypo→ hypo→Bce-46-4 NZ ACMA01000018.1 + 12860 12996 RNA→ hypo→ hypo→ hypo→Bce-20-4 NZ ACME01000017.1 + 12683 12819 RNA→ hypo→ hypo→ hypo→Bth-3-4 NZ ACNK01000021.1 + 13129 13265 RNA→ hypo→ hypo→ hypo→Bth-7-4 NZ ACNI01000020.1 + 13211 13347 RNA→ hypo→ hypo→Bth-1-4 NC 014171.1 + 753427 753563 RNA→ hypo→ hypo→Bce-22-4 NZ ACMB01000019.1 + 13211 13347 RNA→ hypo→ hypo→ hypo→Bce-34-4 NZ ACMH01000022.1 + 13127 13263 RNA→ hypo→ hypo→ hypo→Bce-13-4 NZ ACMQ01000026.1 + 12694 12830 RNA→ hypo→ hypo→ hypo→Bth-2-4 NZ ACMZ01000023.1 + 13126 13262 RNA→ hypo→ hypo→ hypo→Bth-16-4 NZ ACNA01000025.1 + 13067 13203 RNA→ hypo→ hypo→ hypo→Bth-12-4 NZ ACNC01000031.1 + 13115 13251 RNA→ hypo→ hypo→ hypo→Bth-6-4 NZ ACNF01000025.1 + 13127 13263 RNA→ hypo→ hypo→ hypo→Bce-30-4 NZ ACLW01000025.1 + 12247 12383 RNA→ hypo→ hypo→ hypo→Bce-11-5 NZ ACMP01000158.1 + 20652 20786 RNA→ LysP (COG0833)→ SapB (COG1285)→Bme-1-4 NC 014103.1 - 3935225 3935092 RNA→ PotE (COG0531)→


27

Bme-2-5 NC 014019.1 - 3934929 3934797 RNA→ PotE (COG0531)→Bli-1-3 NC 006270.3 + 525358 525490 RNA→ ←hypo

Bli-1-4 NC 006322.1 + 525164 525296 RNA→ PotE (COG0531)→Bam-2-1 NC 009725.1 + 454349 454483 RNA→ PotE (COG0531)→ Nudix Hydrolase (cd02883)→ TPP POX (cd02014)TPP PYR POX (cd07039)→Bam-1-1 NC 014551.1 + 441838 441975 RNA→ PotE (COG0531)→Bsu-2-3 NC 014479.1 + 472870 473005 RNA→ PotE (COG0531)→ Nudix Hydrolase (cd02883)→ TPP POX (cd02014)TPP PYR POX (cd07039)→

hypo→Bsu-1-3 NZ ADGS01000028.1 + 183624 183759 RNA→ PotE (COG0531)→ Nudix Hydrolase (cd02883)→ TPP POX (cd02014)TPP PYR POX (cd07039)→

hypo→Bsu-3-2 NC 000964.3 + 486098 486232 RNA→ PotE (COG0531)→ Nudix Hydrolase (cd02883)→ TPP POX (cd02014)TPP PYR POX (cd07039)→Bsu-5-2 NZ ABQL01000004.1 + 24679 24813 RNA→ PotE (COG0531)→ Nudix Hydrolase (cd02883)→ TPP POX (cd02014)TPP PYR POX (cd07039)→Bsu-6-2 NZ ABQN01000006.1 + 24681 24815 RNA→ PotE (COG0531)→ Nudix Hydrolase (cd02883)→ TPP POX (cd02014)TPP PYR POX (cd07039)→Bat-1-2 NC 014639.1 + 4122824 4122960 RNA→ PotE (COG0531)→ Nudix Hydrolase (cd02883)→ TPP POX (cd02014)TPP PYR POX (cd07039)→Bpu-2-2 NC 009848.1 + 448674 448809 RNA→ PotE (COG0531)→ TPP POX (cd02014)TPP PYR POX (cd07039)→Bpu-1-2 NZ ABRX01000003.1 - 320978 320840 RNA→ PotE (COG0531)→ TPP POX (cd02014)TPP PYR POX (cd07039)→Gka-1-2 NC 006510.1 - 3286120 3285971 RNA→ hypo→Aac-1-3 NZ ACCS01000001.1 + 175899 176022 RNA→ hypo→Aac-2-4 NC 013205.1 + 1422612 1422735 RNA→ hypo→Btu-1-3 NC 014098.1 - 1929875 1929736 RNA→ COG3584 (COG3584)→

Bacteria Firmicutes Clostridia

Swo-1-1 NC 008346.1 - 1984503 1984360 RNA→ ProX (COG2113)→ ABC NrtD SsuB transporters (cd03293)→ TM PBP2 (cd06261)→Cph-1-1 NC 010001.1 + 2073740 2073860 RNA→ KefB (COG0475)→ hypo→Tca-1-1 NZ AAWL01000001.1 - 57086 56955 RNA→ DUF2294 (pfam10057)→Mth-1-1 NC 007644.1 - 996336 996186 RNA→ hypo→Dac-1-1 NC 013216.1 - 3148769 3148645 RNA→ LysM (cd00118)NLPC P60 (pfam00877)→Hor-1-1 NC 011899.1 - 1255394 1255260 RNA→ TrkA (COG0569)→Dre-1-1 NC 009253.1 - 2967245 2967128 RNA→ LysM (cd00118)NLPC P60 (pfam00877)→Mth-1-2 NC 007644.1 + 1741465 1741642 RNA→ hypo→ SCP bacterial (cd05379)→Dha-1-1 NC 011830.1 + 831950 832087 RNA→ PBPb (cd00134)→ TM PBP2 (cd06261)→ TM PBP2 (cd06261)→

ABC HisP GlnQ permeases (cd03262)→Dha-2-1 NC 007907.1 + 891864 892001 RNA→ PBPb (cd00134)→ TM PBP2 (cd06261)→ TM PBP2 (cd06261)→

ABC HisP GlnQ permeases (cd03262)→Tca-1-2 NZ AAWL01000023.1 + 24495 24632 RNA→ COG3584 (COG3584)PG binding 1 (pfam01471)→Ace-2-1 NZ AEDB01000002.1 + 82865 82993 RNA→ COG3409 (COG3409)→Sth-1-1 NC 006177.1 - 606467 606337 RNA→ SCP bacterial (cd05379)→Sth-1-2 NC 006177.1 + 282023 282176 RNA→ NAD Gly3P dh N (pfam01210)Octopine DH (pfam02317)→

MM CoA mutase (cd00512)B12-binding (pfam02310)→ Asn Synthase B C (cd01991)AsnB (cd00712)→DUF1646 (pfam07854)→

Mth-1-3 NC 007644.1 + 1390422 1390601 RNA→ 2A0306 (TIGR00909)→Cce-1-1 NC 011898.1 + 2494674 2494833 RNA→ SH3 3 (pfam08239)NLPC P60 (pfam00877)→Cte-1-1 NC 004557.1 + 2711022 2711132 RNA→ spore SleB (TIGR02869)→

3Cac-2-1 NC 003030.1 + 3232093 3232206 RNA→ SleB (COG3773)→Cbo-3-1 NC 009495.1 + 3672557 3672668 RNA→ Hydrolase 2 (pfam07486)→Cbo-2-1 NC 009697.1 + 3648546 3648657 RNA→ Hydrolase 2 (pfam07486)→Cbo-4-1 NC 009698.1 + 3545655 3545766 RNA→ Hydrolase 2 (pfam07486)→Cbo-12-1 NC 009699.1 + 3775389 3775500 RNA→ Hydrolase 2 (pfam07486)→Cbo-7-1 NC 010516.1 + 3743610 3743721 RNA→ Hydrolase 2 (pfam07486)→ hypo→Cbo-6-1 NC 010520.1 + 3773124 3773235 RNA→ Hydrolase 2 (pfam07486)→Cbo-5-1 NC 012563.1 + 3940461 3940572 RNA→ Hydrolase 2 (pfam07486)→Cbo-13-1 NZ ABDO02000002.1 - 78563 78452 RNA→ Hydrolase 2 (pfam07486)→Csp-9-1 NZ ABKW02000002.1 - 114596 114485 RNA→ spore SleB (TIGR02869)→Cbo-8-1 NC 012658.1 + 3763473 3763584 RNA→ spore SleB (TIGR02869)→


28

Cbo-9-1 NZ ABDP01000003.1 - 78303 78192 RNA→ spore SleB (TIGR02869)→Ckl-1-1 NC 009706.1 - 279058 278936 RNA→ spore SleB (TIGR02869)→Ckl-2-1 NC 011837.1 - 279058 278936 RNA→ spore SleB (TIGR02869)→Clj-1-1 NC 014328.1 + 4402892 4403008 RNA→ spore SleB (TIGR02869)→Cca-1-1 NZ GG770677.1 - 13756 13638 RNA→ spore SleB (TIGR02869)→Toc-1-1 NC 014377.1 - 2122180 2122058 RNA→ RlpA (COG0797)→Tth-1-1 NC 014410.1 + 897300 897420 RNA→ 2a38 (TIGR00933)→ TrkA (COG0569)→Cba-1-1 NZ DS990263.1 - 259102 258959 RNA→ ←predicted protein

Cte-1-2 NC 004557.1 - 2209143 2209017 RNA→ NLPC P60 (pfam00877)→Asp-3-1 NZ ACGB01000042.1 + 15749 15868 RNA→ NLPC P60 (pfam00877)PG binding 1 (pfam01471)→ Radical SAM (cd01335)→Afe-1-1 NC 013740.1 + 950309 950421 RNA→ NLPC P60 (pfam00877)PG binding 1 (pfam01471)→Cbo-1-1 NZ ABCC02000015.1 + 37466 37607 RNA→ PutP (COG0591)→Cac-2-2 NC 003030.1 + 1374242 1374371 RNA→ LysM (cd00118)SleB (COG3773)→Cob-1-1 NC 014392.1 - 1836372 1836220 RNA→ SH3 3 (pfam08239)NLPC P60 (pfam00877)→Ath-1-1 NC 012034.1 - 2002004 2001853 RNA→ SH3 3 (pfam08239)SH3b (smart00287)NLPC P60 (pfam00877)→Mth-1-4 NC 007644.1 + 1412190 1412323 RNA→ GT1 TPS (cd03788)→ OtsB (COG1877)→ UGPase prokaryotic (cd02541)→Cpa-1-1 NZ ACXX01000020.1 - 84010 83892 RNA→ PBPb (cd00134)→ TM PBP2 (cd06261)→ ABC HisP GlnQ permeases (cd03262)→

Radical SAM (cd01335)→ NAT SF (cd04301)→ DUF970 (pfam06153)→Mmu-1-1 NZ ABWK02000017.1 + 232645 232797 RNA→ NLPC P60 (pfam00877)PG binding 1 (pfam01471)→Tca-1-3 NZ AAWL01000006.1 - 97038 96926 RNA→ NLPC P60 (pfam00877)PG binding 1 (pfam01471)→Csp-8-1 NZ ACFX02000020.1 + 19877 20033 RNA→ ABC OpuCA Osmoprotection (cd03295)→ OpuBC (COG1732)TM PBP2 (cd06261)→ hypo (cons)→Cas-1-1 NZ ACCJ01000509.1 - 2590 2431 RNA→ antiport nhaC (TIGR00931)→ NrdD (COG1328)→Tpo-1-1 NC 014152.1 - 1866482 1866355 RNA→ Radical SAM (cd01335)→Dha-1-2 NC 011830.1 - 2793973 2793847 RNA→ NLPC P60 (pfam00877)G5 (pfam07501)→Dha-2-2 NC 007907.1 - 1719294 1719168 RNA→ NLPC P60 (pfam00877)G5 (pfam07501)→Dha-1-3 NC 011830.1 - 1445445 1445329 RNA→ Radical SAM (cd01335)→ hypo→Dha-2-3 NC 007907.1 + 4597561 4597677 RNA→ Radical SAM (cd01335)→Aor-1-1 NC 009922.1 - 56231 56108 RNA→ NAT SF (cd04301)→Hmo-1-1 NC 010337.2 - 2489123 2488967 RNA→ LysM (cd00118)→Tca-1-4 NZ AAWL01000002.1 - 117854 117733 RNA→ COG3584 (COG3584)PG binding 1 (pfam01471)→Tpo-1-2 NC 014152.1 - 2210099 2209958 RNA→ LysM (cd00118)spore SleB (TIGR02869)→Swo-1-2 NC 008346.1 - 1297830 1297705 RNA→ Radical SAM (cd01335)→ hypo→CDe-1-1 NC 010424.1 + 1122624 1122753 RNA→ hypo→Sli-2-1 NC 014220.1 - 1495785 1495598 RNA→ Radical SAM (cd01335)→ Trans IPPS HT (cd00685)→ TatC (pfam00902)→Csa-1-1 NC 009437.1 + 1179814 1179969 RNA→ SH3 3 (pfam08239)NLPC P60 (pfam00877)→Pth-1-1 NC 009454.1 - 2706664 2706443 RNA→ LysM (cd00118)spore SleB (TIGR02869)→Tte-1-1 NC 003869.1 - 1853398 1853273 RNA→ PBP2 NikA DppA OppA like (cd00995)→ TM PBP2 (cd06261)→ TM PBP2 (cd06261)→

ABC NikE OppD transporters (cd03257)→ ABC NikE OppD transporters (cd03257)→Cpa-2-1 NZ DS999092.1 - 18207 18082 RNA→ hypo→ PBP2 NikA DppA OppA like (cd00995)→ TM PBP2 (cd06261)→Sli-2-2 NC 014220.1 - 662563 662435 RNA→ (big gap) ABC OpuCA Osmoprotection (cd03295)→ TM PBP2 (cd06261)→ TM PBP2 (cd06261)→

OpuBC (COG1732)→ GT1 Sucrose synthase (cd03800)→ S6PP (pfam05116)→Dre-1-2 NC 009253.1 - 2353806 2353673 RNA→ Radical SAM (cd01335)→Cpa-1-2 NZ ACXX01000078.1 + 74 236 RNA→ SH3 3 (pfam08239)NLPC P60 (pfam00877)→Nth-1-1 NC 010718.1 + 264352 264503 RNA→ HATPase c (cd00075)PAS (cd00130)HAMP (cd06225)HisKA (cd00082)→ REC (cd00156)→

REC (cd00156)TPR (cd00189)→ TrkA (COG0569)→ TrkA (COG0569)→ 2a38 (TIGR00933)→Pth-1-2 NC 009454.1 + 609965 610198 RNA→ Radical SAM (cd01335)→ GT1 Sucrose synthase (cd03800)→ S6PP (pfam05116)→Tpo-1-3 NC 014152.1 + 2541645 2541762 RNA→ PotE (COG0531)→ hypo→Chy-1-1 NC 007503.1 - 2221507 2221388 RNA→ Radical SAM (cd01335)→Dac-1-2 NC 013216.1 + 1136339 1136459 RNA→ PotE (COG0531)→Toc-1-2 NC 014377.1 + 225252 225415 RNA→ NAD Gly3P dh N (pfam01210)Octopine DH (pfam02317)→ B12-binding like (cd02065)Glm e (cd00245)→Toc-1-3 NC 014377.1 + 607996 608160 RNA→ Asn Synthase B C (cd01991)AsnB (cd00712)→Pth-1-3 NC 009454.1 + 2311730 2311887 RNA→ PotE (COG0531)→Dre-1-3 NC 009253.1 + 3033567 3033711 RNA→ LysM (cd00118)spore SleB (TIGR02869)→


29

Cca-1-2 NZ GG770678.1 + 339075 339199 RNA→ LysM (cd00118)spore SleB (TIGR02869)→Ath-1-2 NC 012034.1 + 2358849 2358988 RNA→ DRE TIM Re CS (cd07947)→Cob-1-2 NC 014392.1 + 2152302 2152443 RNA→ DRE TIM Re CS (cd07947)→Csa-1-2 NC 009437.1 - 819122 818982 RNA→ DRE TIM Re CS (cd07947)→Aar-2-1 NC 014378.1 - 1461208 1461045 RNA→ HATPase c (cd00075)PAS (cd00130)HAMP (cd06225)HisKA (cd00082)→ REC (cd00156)→

REC (cd00156)TPR (cd00189)→ TrkA (COG0569)→ TrkA (COG0569)→ 2a38 (TIGR00933)→Tth-1-2 NC 014410.1 + 725387 725495 RNA→ spore SleB (TIGR02869)NLPC P60 (pfam00877)→Tth-1-3 NC 014410.1 - 1619895 1619779 RNA→ LysM (cd00118)spore SleB (TIGR02869)→Tte-1-2 NC 003869.1 + 1020683 1020799 RNA→ LysM (cd00118)spore SleB (TIGR02869)→Twi-1-1 NZ ADXD01000013.1 - 23629 23515 RNA→ LysM (cd00118)spore SleB (TIGR02869)→Tsp-2-1 NC 010320.1 + 1463755 1463868 RNA→ LysM (cd00118)spore SleB (TIGR02869)→Tsp-1-1 NC 014538.1 - 1450628 1450515 RNA→ LysM (cd00118)spore SleB (TIGR02869)→Tsp-3-1 NZ ACXP02000002.1 + 100809 100922 RNA→ LysM (cd00118)spore SleB (TIGR02869)→Tet-1-1 NZ ACXY01000037.1 - 969 856 RNA→ LysM (cd00118)spore SleB (TIGR02869)→Tit-1-1 NC 013921.1 + 1033421 1033533 RNA→ LysM (cd00118)spore SleB (TIGR02869)→Tma-1-1 NC 014209.1 + 1058125 1058237 RNA→ LysM (cd00118)spore SleB (TIGR02869)→Tps-1-1 NC 010321.1 + 1051967 1052080 RNA→ LysM (cd00118)spore SleB (TIGR02869)→Tbr-1-1 NZ ACQZ01000024.1 - 8134 8021 RNA→ LysM (cd00118)spore SleB (TIGR02869)→Pth-1-4 NC 009454.1 + 82202 82409 RNA→ SCP bacterial (cd05379)→Dre-1-4 NC 009253.1 + 87018 87124 RNA→ SCP bacterial (cd05379)→Pth-1-5 NC 009454.1 + 1365197 1365337 RNA→ SCP bacterial (cd05379)→Cth-1-1 NC 009012.1 - 1397347 1397223 RNA→ DapB (COG0289)→Cth-3-1 NZ ABVG02000001.1 - 1590302 1590178 RNA→ DapB (COG0289)→Cth-2-1 NZ ACVX01000040.1 - 17818 17694 RNA→ DapB (COG0289)→Cce-1-2 NC 011898.1 - 2317680 2317545 RNA→ SH3 3 (pfam08239)NLPC P60 (pfam00877)→Cpa-1-3 NZ ACXX01000024.1 - 46955 46821 RNA→ SH3 3 (pfam08239)NLPC P60 (pfam00877)→Cpa-1-4 NZ ACXX01000040.1 - 14603 14473 RNA→ SH3 3 (pfam08239)NLPC P60 (pfam00877)→Cce-1-3 NC 011898.1 + 872458 872588 RNA→ SH3 3 (pfam08239)NLPC P60 (pfam00877)→Ace-2-2 NZ AEDB01000037.1 - 54060 53936 RNA→ DapB (COG0289)→Cbe-1-1 NC 009617.1 - 1710113 1709988 RNA→ NAT SF (cd04301)→Cbe-1-2 NC 009617.1 + 3440158 3440279 RNA→ DapB (COG0289)→Cca-1-3 NZ GG770678.1 + 58838 58959 RNA→ NAT SF (cd04301)→Cbo-8-2 NC 012658.1 - 1451435 1451322 RNA→ (big gap) WHTH GntR (cd07377)→ COG4194 (COG4194)→Cbo-13-2 NZ ABDO02000005.1 - 38611 38498 RNA→ putative cell wall hydrolase→ spore SleB (TIGR02869)→Cbo-9-2 NZ ABDP01000016.1 + 29548 29661 RNA→ LysM domain protein→ spore SleB (TIGR02869)→Cbo-7-2 NC 010516.1 - 1466872 1466759 RNA→ LysM (cd00118)spore SleB (TIGR02869)→Cbo-3-2 NC 009495.1 - 1445756 1445643 RNA→ LysM (cd00118)spore SleB (TIGR02869)→Cbo-2-2 NC 009697.1 - 1414376 1414263 RNA→ LysM (cd00118)spore SleB (TIGR02869)→Cbo-4-2 NC 009698.1 - 1414869 1414756 RNA→ LysM (cd00118)spore SleB (TIGR02869)→Cbo-6-2 NC 010520.1 - 1516022 1515909 RNA→ LysM (cd00118)spore SleB (TIGR02869)→Cbo-5-2 NC 012563.1 - 1553936 1553823 RNA→ LysM (cd00118)spore SleB (TIGR02869)→Cbo-12-2 NC 009699.1 - 1487033 1486919 RNA→ LysM (cd00118)spore SleB (TIGR02869)→Csp-9-2 NZ ABKW02000004.1 + 1917630 1917743 RNA→ LysM (cd00118)spore SleB (TIGR02869)→Ace-2-3 NZ AEDB01000021.1 + 54772 54886 RNA→ LysM (cd00118)spore SleB (TIGR02869)→Ade-1-1 NC 013385.1 - 1614491 1614336 RNA→ LysM (cd00118)spore SleB (TIGR02869)→ Fer (COG1141)→Tth-1-4 NC 014410.1 + 1135202 1135325 RNA→ SH3 3 (pfam08239)NLPC P60 (pfam00877)→Tps-1-2 NC 010321.1 - 1503496 1503374 RNA→ COG3103 (COG3103)SH3 3 (pfam08239)NLPC P60 (pfam00877)→Tsp-2-2 NC 010320.1 - 2154844 2154722 RNA→ COG3103 (COG3103)SH3 3 (pfam08239)NLPC P60 (pfam00877)→Tsp-1-2 NC 014538.1 + 799498 799620 RNA→ COG3103 (COG3103)SH3 3 (pfam08239)NLPC P60 (pfam00877)→Tbr-1-2 NZ ACQZ01000010.1 + 36376 36498 RNA→ COG3103 (COG3103)SH3 3 (pfam08239)NLPC P60 (pfam00877)→Tsp-3-2 NZ ACXP02000002.1 - 751939 751817 RNA→ COG3103 (COG3103)SH3 3 (pfam08239)NLPC P60 (pfam00877)→Tet-1-2 NZ ACXY01000004.1 - 30896 30774 RNA→ COG3103 (COG3103)SH3 3 (pfam08239)NLPC P60 (pfam00877)→


30

Twi-1-2 NZ ADXD01000039.1 - 3483 3359 RNA→ COG3103 (COG3103)NLPC P60 (pfam00877)→Tma-1-2 NC 014209.1 + 896815 896939 RNA→ COG3103 (COG3103)NLPC P60 (pfam00877)→Tit-1-2 NC 013921.1 + 882715 882840 RNA→ COG3103 (COG3103)NLPC P60 (pfam00877)→Tte-1-3 NC 003869.1 + 890822 890943 RNA→ COG3103 (COG3103)NLPC P60 (pfam00877)→ hypo→ UPF0236 (pfam06782)→Cpa-2-2 NZ DS999069.1 - 16149 16028 RNA→ hypo→ COG3103 (COG3103)NLPC P60 (pfam00877)→

BipA TypA C (cd03710)BipA TypA II (cd03691)TypA BipA (cd01891)→Mth-1-5 NC 007644.1 + 459168 459284 RNA→ hypo→Ade-1-2 NC 013385.1 - 672799 672660 RNA→ GT1 TPS (cd03788)→ OtsB (COG1877)→Ade-1-3 NC 013385.1 - 1413026 1412898 RNA→ Radical SAM (cd01335)→ RNaseH typeII bacteria HII like (cd07182)→ COG0792 (COG0792)→Dac-1-3 NC 013216.1 + 623354 623486 RNA→ Radical SAM (cd01335)→ Radical SAM (cd01335)→ NAT SF (cd04301)→Csa-1-3 NC 009437.1 + 237784 237925 RNA→ Radical SAM (cd01335)→Ath-1-3 NC 012034.1 - 2411366 2411228 RNA→ Radical SAM (cd01335)→Cob-1-3 NC 014392.1 - 2191619 2191481 RNA→ Radical SAM (cd01335)→ hypo→Tte-1-4 NC 003869.1 + 927264 927386 RNA→ NAD Gly3P dh N (pfam01210)Octopine DH (pfam02317)→ B12-binding like (cd02065)Glm e (cd00245)→Cpa-2-3 NZ DS999167.1 - 4255 4133 RNA→ (big gap) Glm e (cd00245)→Tps-1-3 NC 010321.1 - 1465886 1465763 RNA→ NAD Gly3P dh N (pfam01210)Octopine DH (pfam02317)→ B12-binding like (cd02065)Glm e (cd00245)→

Asn Synthase B C (cd01991)AsnB (cd00712)→Tsp-2-3 NC 010320.1 - 2119178 2119055 RNA→ NAD Gly3P dh N (pfam01210)Octopine DH (pfam02317)→ B12-binding like (cd02065)Glm e (cd00245)→

Asn Synthase B C (cd01991)AsnB (cd00712)→Tsp-1-3 NC 014538.1 + 835166 835289 RNA→ NAD Gly3P dh N (pfam01210)Octopine DH (pfam02317)→ B12-binding like (cd02065)Glm e (cd00245)→

Asn Synthase B C (cd01991)AsnB (cd00712)→Tit-1-3 NC 013921.1 + 919236 919359 RNA→ NAD Gly3P dh N (pfam01210)Octopine DH (pfam02317)→ B12-binding like (cd02065)Glm e (cd00245)→

Asn Synthase B C (cd01991)AsnB (cd00712)→Tma-1-3 NC 014209.1 + 936529 936652 RNA→ NAD Gly3P dh N (pfam01210)Octopine DH (pfam02317)→ B12-binding like (cd02065)Glm e (cd00245)→

Asn Synthase B C (cd01991)AsnB (cd00712)→Tbr-1-3 NZ ACQZ01000046.1 + 2568 2691 RNA→ NAD Gly3P dh N (pfam01210)Octopine DH (pfam02317)→ B12-binding like (cd02065)Glm e (cd00245)→

Asn Synthase B C (cd01991)AsnB (cd00712)→Tsp-3-3 NZ ACXP02000002.1 - 716271 716148 RNA→ NAD Gly3P dh N (pfam01210)Octopine DH (pfam02317)→ B12-binding like (cd02065)Glm e (cd00245)→

Asn Synthase B C (cd01991)AsnB (cd00712)→Tet-1-3 NZ ACXY01000021.1 - 35724 35601 RNA→ NAD Gly3P dh N (pfam01210)Octopine DH (pfam02317)→ B12-binding like (cd02065)Glm e (cd00245)→

AsnB (cd00712)→ Asn Synthase B C (cd01991)→Twi-1-3 NZ ADXD01000044.1 - 14513 14390 RNA→ NAD Gly3P dh N (pfam01210)Octopine DH (pfam02317)→ B12-binding like (cd02065)Glm e (cd00245)→

Asn Synthase B C (cd01991)AsnB (cd00712)→Tth-1-5 NC 014410.1 + 321193 321308 RNA→ Octopine DH (pfam02317)NAD binding 2 (pfam03446)→ B12-binding like (cd02065)→Cpa-1-5 NZ ACXX01000052.1 - 7037 6904 RNA→ DapB (COG0289)→Cce-1-4 NC 011898.1 + 597738 597872 RNA→ DapB (COG0289)→Aar-2-2 NC 014378.1 + 423440 423582 RNA→ 2a38 (TIGR00933)→ TrkA (COG0569)→ 2a38 (TIGR00933)→ TrkA (COG0569)→ SpoU (COG0566)→

hypo→Cno-1-1 NC 008593.1 - 667364 667243 RNA→ LysM (cd00118)spore SleB (TIGR02869)→Cbo-10-1 NZ ABDQ01000001.1 + 78235 78353 RNA→ LysM (cd00118)spore SleB (TIGR02869)→ spore pdaA (TIGR02884)→Cbo-11-1 NZ ACSJ01000007.1 + 1051454 1051572 RNA→ LysM (cd00118)spore SleB (TIGR02869)→Bhy-1-1 NZ ACBZ01000110.1 - 13226 13114 RNA→ PutP (COG0591)→Dha-2-4 NC 007907.1 - 5140252 5140122 RNA→ NLPC P60 (pfam00877)→Dha-2-5 NC 007907.1 - 2178000 2177873 RNA→ NLPC P60 (pfam00877)→Dha-1-4 NC 011830.1 - 3262203 3262078 RNA→ NLPC P60 (pfam00877)→Ssp-10-1 NZ ACKP02000012.1 + 97938 98098 RNA→ NLPC P60 (pfam00877)PG binding 1 (pfam01471)→Ckl-1-2 NC 009706.1 - 658084 657953 RNA→ LysM (cd00118)spore SleB (TIGR02869)→Ckl-2-2 NC 011837.1 - 658059 657928 RNA→ LysM (cd00118)spore SleB (TIGR02869)→Clj-1-2 NC 014328.1 - 498086 497958 RNA→ LysM (cd00118)→Mth-1-6 NC 007644.1 + 2197510 2197628 RNA→ hypo→ LysM (cd00118)NLPC P60 (pfam00877)→

Bacteria Fusobacteria

Fmo-1-1 NZ GG657909.1 - 510681 510552 RNA→ OpuBC (COG1732)TM PBP2 (cd06261)→ ABC OpuCA Osmoprotection (cd03295)→CBS pair CorC HlyC assoc (cd04590)→


31

Ful-1-1 NZ ACDH01000025.1 + 19980 20102 RNA→ HATPase c (cd00075)PAS (cd00130)HisKA (cd00082)→ REC (cd00156)→REC (cd00156)PEP TPR lipo (TIGR02917)→ USP OKCHK (cd01987)→

Fva-1-1 NZ GG696096.1 + 195998 196121 RNA→ HATPase c (cd00075)PAS (cd00130)HisKA (cd00082)→ REC (cd00156)→REC (cd00156)PEP TPR lipo (TIGR02917)→ USP OKCHK (cd01987)→

Fmo-1-2 NZ GG657908.1 - 649553 649423 RNA→ HATPase c (cd00075)HisKA (cd00082)→ REC (cd00156)TPR (cd00189)→ TrkA (COG0569)→TrkA (COG0569)→ 2a38 (TIGR00933)→ USP OKCHK (cd01987)→

Bacteria Proteobacteria

Ppr-1-1 NC 008609.1 - 648105 647962 RNA→ Kup (COG3158)→Gsu-1-1 NC 002939.4 + 2728260 2728388 RNA→ Kup (COG3158)→Gbe-1-1 NC 011146.1 - 643206 643086 RNA→ Kup (COG3158)→Sac-1-1 NC 007759.1 + 1919125 1919250 RNA→ 2a38 (TIGR00933)→ TrkA (COG0569)→Sfu-1-1 NC 008554.1 - 2207800 2207670 RNA→ Kup (COG3158)→Dma-1-1 NC 012796.1 + 5075826 5075951 RNA→ PotE (COG0531)→Dfr-1-1 NZ AECZ01000003.1 + 14312 14438 RNA→ PotE (COG0531)→Dvu-1-1 NC 011769.1 + 1194641 1194779 RNA→ Kup (COG3158)→

Bacteria VerrucomicrobiaCfl-2-1 NZ ABVL01000001.1 - 263114 262977 RNA→ ←hypo

bEl-1-1 NZ ABOX02000027.1 + 53580 53725 RNA→ USP Like (cd00293)PotE (COG0531)→Cfl-2-2 NZ ABVL01000001.1 + 37432 37595 RNA→ COG2268 (COG2268)→Ote-1-1 NC 010571.1 + 4322257 4322416 RNA→ Kup (COG3158)→Vsp-1-1 NZ ABIZ01000001.1 - 2172607 2172444 RNA→ ←hypo

bEl-1-2 NZ ABOX02000073.1 - 18503 18352 RNA→ Band 7 (pfam01145)→bEl-1-3 NZ ABOX02000005.1 - 18491 18336 RNA→ ←COG2159 (COG2159)

environmental

env-1 SRS024580 LANL scaffold 1779 + 39296 39516 RNA→ NLPC P60 (pfam00877)→env-2 SRS063193 LANL scaffold 58934 - 1482 1262 RNA→ NLPC P60 (pfam00877)→env-3 SRS013164 Baylor scaffold 25506 + 1096 1316 RNA→ metagenemark→ NLPC P60 (pfam00877)→env-4 SRS016037 WUGC scaffold 26104 + 830 1050 RNA→ NLPC P60 (pfam00877)→env-5 SRS018439 Baylor scaffold 60860 - 6170 5950 RNA→ NLPC P60 (pfam00877)→env-6 SRS019607 C2763683 + 6284 6504 RNA→ NLPC P60 (pfam00877)→env-7 SRS022077 Baylor scaffold 57405 - 1383 1163 RNA→ NLPC P60 (pfam00877)→env-8 SRS023958 C2069914 + 8917 9137 RNA→ metagenemark→env-9 SRS044373 C2917542 + 1095 1315 RNA→ NLPC P60 (pfam00877)→env-10 SRS055426 C3295941 + 1123 1346 RNA→ Spr (COG0791)→env-11 SRS019022 WUGC scaffold 14734 - 32779 32556 RNA→ NLPC P60 (pfam00877)→env-12 SRS019045 WUGC scaffold 41774 + 9834 10057 RNA→ NLPC P60 (pfam00877)→env-13 SRS051791 LANL scaffold 35536 + 147 373 RNA→ metagenemark→env-14 SRS024318 C3791864 + 201 429 RNA→ NLPC P60 (pfam00877)→env-15 SRS019022 C2648390 + 502 681 RNA→ metagenemark→env-16 SRS019045 C2739637 + 305 484 RNA→ NLPC P60 (pfam00877)→env-17 SRS016002 WUGC scaffold 47680 - 22183 22007 RNA→ NLPC P60 (pfam00877)→env-18 SRS019122 C5916309 - 312 136 RNA→ metagenemark→env-19 SRS019126 WUGC scaffold 41641 + 717 893 RNA→ NLPC P60 (pfam00877)→env-20 SRS019127 C1662896 - 312 136 RNA→ metagenemark→env-21 SRS015537 WUGC scaffold 20201 + 5422 5600 RNA→ NLPC P60 (pfam00877)→env-22 SRS015038 C1880224 + 245 424 RNA→env-23 SRS019974 C3348413 - 614 438 RNA→ metagenemark→env-24 SRS021496 Baylor scaffold 60604 - 858 682 RNA→ metagenemark→env-25 SRS022530 LANL scaffold 8446 - 61111 60935 RNA→ NLPC P60 (pfam00877)→env-26 SRS063288 LANL scaffold 62029 + 2205 2381 RNA→ metagenemark→


32

env-27 SRS018975 C1770276 + 73 252 RNA→ metagenemark→env-28 SRS057539 C2578428 - 195 17 RNA→env-29 SRS018971 C799760 + 7605 7783 RNA→ NLPC P60 (pfam00877)→env-30 SRS065278 C2347343 - 225 47 RNA→env-31 SRS018357 C3958007 + 1692 1870 RNA→ NLPC P60 (pfam00877)→env-32 SRS014470 WUGC scaffold 49198 + 2590 2768 RNA→ NLPC P60 (pfam00877)→env-33 SRS024637 LANL scaffold 27882 + 15136 15314 RNA→ NLPC P60 (pfam00877)→env-34 SRS018357 Baylor scaffold 3010 + 13564 13760 RNA→ NLPC P60 (pfam00877)→env-35 SRS015272 C3571063 - 2379 2183 RNA→ NLPC P60 (pfam00877)→env-36 SRS044486 C2260441 + 164 360 RNA→ metagenemark→env-37 TB03JUN2009E Contig 67 - 1585 1423 RNA→ PotE (COG0531)→env-38 TB18AUG2009E c24957 + 211 373 RNA→ hypo→env-39 LM15JUN2010E c3995 + 436 638 RNA→ hypo→env-40 LM15JUN2010E c1031 + 3283 3485 RNA→ hypo→env-41 DCrCPGB c308773 - 352 181 RNA→ hypo→env-42 JCVI SCAF 1101668135971 - 683 520 RNA→ predicted protein→env-43 JCVI SCAF 1096627459792 + 412 574 RNA→ predicted protein→env-44 JCVI SCAF 1096627462320 - 946 784 RNA→ predicted protein→env-45 FNTS GKKEVUV01CDI8C + 46 238 RNA→env-46 SwBSRL2 contig 8577908 - 1262 1071 RNA→ NLPC P60 (pfam00877)→env-47 FNTS067 GJ87FRN01B58SR + 9 200 RNA→env-48 LWFCAn GLO1YSU01DEYFP - 420 286 RNA→ hypo→ hypo→env-49 A2 c1 Cons24848 - 1024 882 RNA→ Sigma70 r4 (cd06171)SCRAP33 (SCRAP33)→env-50 LWFCAnN GO09JKT02GY96W - 257 103 RNA→env-51 SRS063932 LANL scaffold 62798 + 15 273 RNA→env-52 SRS013170 Baylor scaffold 46431 + 16222 16475 RNA→ Transglycosylase (pfam06737)DUF3235 (pfam11574)→env-53 SRS022149 C2805354 - 347 94 RNA→ ←metagenemark

env-54 SRS022536 LANL scaffold 24927 + 212 465 RNA→ Transglycosylase (pfam06737)→env-55 SRS023964 C2536665 - 635 382 RNA→ Transglycosylase (pfam06737)→env-56 SRS024649 C3627129 + 13 266 RNA→ Transglycosylase (pfam06737)→env-57 SRS043772 WUGC scaffold 29117 + 489 742 RNA→ Transglycosylase (pfam06737)→env-58 SRS047265 C1063981 - 511 258 RNA→ Transglycosylase (pfam06737)→env-59 SRS054430 LANL scaffold 15449 - 550 297 RNA→ Transglycosylase (pfam06737)→env-60 SRS019333 WUGC scaffold 5340 + 8 266 RNA→ Transglycosylase (pfam06737)→env-61 SRS012285 C2917260 - 650 392 RNA→ Transglycosylase (pfam06737)→env-62 SRS013836 C4734343 + 13 271 RNA→ Transglycosylase (pfam06737)→env-63 SRS015044 WUGC scaffold 69752 + 505 763 RNA→ Transglycosylase (pfam06737)→env-64 SRS015803 WUGC scaffold 20595 - 650 392 RNA→ Transglycosylase (pfam06737)→env-65 SRS015899 C1743853 + 13 271 RNA→env-66 SRS015989 WUGC scaffold 31022 - 608 350 RNA→ Transglycosylase (pfam06737)→env-67 SRS016043 WUGC scaffold 63415 - 311 53 RNA→env-68 SRS017511 C3502798 + 13 271 RNA→ Transglycosylase (pfam06737)→env-69 SRS018778 C1281177 - 6966 6708 RNA→ Transglycosylase (pfam06737)DUF3235 (pfam11574)→env-70 SRS018975 C1812339 + 327 585 RNA→ Transglycosylase (pfam06737)→env-71 SRS019128 C4361573 + 13 271 RNA→ Transglycosylase (pfam06737)→env-72 SRS019129 WUGC scaffold 26126 + 550 808 RNA→env-73 SRS019225 C1569121 + 7 265 RNA→ Transglycosylase (pfam06737)→env-74 SRS019906 C2229320 - 650 392 RNA→ Transglycosylase (pfam06737)→env-75 SRS020862 C915818 + 13 271 RNA→ Transglycosylase (pfam06737)→env-76 SRS022083 C1927916 + 13 271 RNA→ Transglycosylase (pfam06737)→env-77 SRS022725 C5794622 - 650 392 RNA→ Transglycosylase (pfam06737)→env-78 SRS024381 LANL scaffold 28199 + 2118 2376 RNA→ Transglycosylase (pfam06737)DUF3235 (pfam11574)→


33

env-79 SRS024447 C3937435 - 666 408 RNA→ Transglycosylase (pfam06737)→env-80 SRS024561 C2774130 - 677 419 RNA→ Transglycosylase (pfam06737)→env-81 SRS045313 C1348653 + 410 668 RNA→env-82 SRS047113 LANL scaffold 81317 - 650 392 RNA→ Transglycosylase (pfam06737)→env-83 SRS047634 LANL scaffold 129046 + 326 584 RNA→env-84 SRS052876 C2277494 - 345 87 RNA→ ←metagenemarkenv-85 SRS055378 LANL scaffold 92000 + 475 733 RNA→ Transglycosylase (pfam06737)→env-86 SRS063603 C4274592 - 653 395 RNA→ Transglycosylase (pfam06737)→env-87 SRS015574 WUGC scaffold 52694 + 13 272 RNA→ Transglycosylase (pfam06737)→env-88 SRS058808 LANL scaffold 73525 - 531 273 RNA→ Transglycosylase (pfam06737)→env-89 SRS015947 WUGC scaffold 17867 + 203 455 RNA→env-90 SRS054653 C2063486 - 649 397 RNA→ Transglycosylase (pfam06737)→env-91 DCrCPGB c125903 - 326 150 RNA→ ←hypo

env-92 A5 c1 Cons69507 + 273 489 RNA→ Transglycosylase (pfam06737)→env-93 FNTS067 GJ87FRN01A33JG + 22 205 RNA→ hypo→env-94 FNTS GKKEVUV01D9712 + 171 313 RNA→ hypo→

1env-95 LWAnN GIDYKCY01DRS5L - 297 165 RNA→ ←hypoenv-96 FNTS GKKEVUV01AVEL8 + 8 227 RNA→ hypo→env-97 DCrCPGB c202088 + 262 422 RNA→ hypo→env-98 FNTS GKKEVUV01C1S1C - 232 86 RNA→ ←hypoenv-99 DCrCPGB c94663 - 491 276 RNA→ Transglycosylase (pfam06737)→env-100 GBANfinal FHNL2OP04Y4F11 + 333 472 RNA→env-101 FNTS067 GKA24FP01ETDQ5 + 68 262 RNA→ ←hypoenv-102 botACOD GAKN62C01AE5XN + 80 223 RNA→ hypo→env-103 DCrCPGB c778734 + 8 151 RNA→env-104 BSRL3 Contig 408 + 20 167 RNA→ ←hypo

env-105 2034002239 + 142 279 RNA→env-106 FHA1B5K04X9303 - 223 88 RNA→ ←hypoenv-107 orpgwFw301 FCAY18007 x3 + 180 325 RNA→ PotE (COG0531)→env-108 ASMM170b GJFD58A01BVX9Q - 407 250 RNA→ hypo→env-109 FNTS GKKEVUV02JC03Z - 356 169 RNA→ hypo→env-110 GYO3UBL02FR7FY + 27 154 RNA→ ←hypo

env-111 FNTS GKKEVUV02IIL4U + 43 198 RNA→ hypo→env-112 FNTS GKKEVUV01DTQGY + 126 281 RNA→env-113 LWFCAnN GO09JKT01DTJ1T - 186 20 RNA→ ←hypo

env-114 P3 CLC Cons56251 + 683 856 RNA→ hypo→env-115 B3 all c Cons67908 + 3859 4032 RNA→ RlpA (COG0797)→env-116 Cons7577 - 413 240 RNA→ ←hypo

env-117 BMHBC 44149 + 190 320 RNA→env-118 P3 CLC Cons51948 + 266 424 RNA→ RlpA (COG0797)→env-119 GXP7IEG01CE9B5 - 449 308 RNA→ hypo→env-120 FNTS067 GKA24FP01EOJJA - 352 220 RNA→ hypo→env-121 FNTS067 GJ87FRN01CUWC0 + 43 183 RNA→ hypo→env-122 P3 CLC Cons147470 - 532 374 RNA→ hypo→env-123 PCEOT contig29826 - 40622 40477 RNA→ ProX (COG2113)→ ABC NrtD SsuB transporters (cd03293)→ TM PBP2 (cd06261)→env-124 A5 c1 Cons90918 + 283 520 RNA→env-125 A2 c1 Cons24363 - 493 307 RNA→ NLPC P60 (pfam00877)→env-126 AglaG GDN60OX02I3P1C + 197 400 RNA→ hypo→ hypo→env-127 SRB FXPBX6M01C6WVR - 246 92 RNA→env-128 LWAeNiSIP F6BA1ZZ02GISWL + 41 192 RNA→ hypo→env-129 B3 all c Cons106015 + 111 271 RNA→ K+-transporting ATPase, KdpF subunit→ KdpA (COG2060)→env-130 SwBSRL2 contig 857592 + 681 862 RNA→ hypo→


34

env-131 DCrCPGB c63140 - 391 199 RNA→ hypo→env-132 84915684 - 615 467 RNA→ LysM (cd00118)PG binding 1 (pfam01471)→env-133 orpgwFw301 FCAY4395 x1 - 475 331 RNA→ ←hypoenv-134 DCrCPGB c109592 + 188 369 RNA→ hypo→env-135 DCrCPGB c258528 + 12 209 RNA→ hypo→env-136 FIHLEPW02S8S6T - 254 79 RNA→env-137 ZhangC101043 1 + 156 312 RNA→ metagenemark→env-138 SRS022077 C2461149 + 34 211 RNA→ metagenemark→env-139 SRS011140 Baylor scaffold 11382 - 194 17 RNA→env-140 SRS013234 Baylor scaffold 29383 - 368 191 RNA→ metagenemark→env-141 SRS013705 Baylor scaffold 99601 + 1973 2150 RNA→ metagenemark→env-142 SRS014271 WUGC scaffold 39029 - 222 45 RNA→ metagenemark→env-143 SRS015762 C3622073 - 964 787 RNA→ NLPC P60 (pfam00877)→env-144 SRS019071 C5099437 + 109 286 RNA→ metagenemark→env-145 SRS022530 C2093255 - 411 234 RNA→ metagenemark→env-146 SRS023926 Baylor scaffold 69268 + 602 779 RNA→ NLPC P60 (pfam00877)→env-147 SRS042643 WUGC scaffold 395 + 338 515 RNA→ metagenemark→env-148 SRS047219 WUGC scaffold 16558 + 1161 1338 RNA→ NLPC P60 (pfam00877)→env-149 SRS048411 C6795882 + 75 252 RNA→ metagenemark→env-150 SRS055426 C3228047 + 75 252 RNA→ metagenemark→env-151 SRS057539 C2717759 + 625 802 RNA→ metagenemark→env-152 SRS024375 LANL scaffold 27309 + 462 639 RNA→ NLPC P60 (pfam00877)→env-153 SRS054687 LANL scaffold 28635 + 195 372 RNA→ metagenemark→env-154 SRS017209 Baylor scaffold 65833 + 6121 6298 RNA→ NLPC P60 (pfam00877)→env-155 SRS018145 Baylor scaffold 35051 + 60219 60396 RNA→ NLPC P60 (pfam00877)→env-156 SRS022719 LANL scaffold 65525 - 2038 1861 RNA→ NLPC P60 (pfam00877)→env-157 SRS024277 LANL scaffold 14307 + 96860 97037 RNA→ NLPC P60 (pfam00877)→env-158 SRS044662 LANL scaffold 9933 + 5852 6029 RNA→ NLPC P60 (pfam00877)→env-159 SRS049147 C4075627 + 76 253 RNA→ metagenemark→env-160 SRS050669 LANL scaffold 5821 - 25723 25546 RNA→ NLPC P60 (pfam00877)→env-161 SRS057692 LANL scaffold 58523 + 9522 9699 RNA→ NLPC P60 (pfam00877)→env-162 SRS016529 Baylor scaffold 246 + 195 372 RNA→ metagenemark→env-163 SRS014684 WUGC scaffold 13969 + 215 392 RNA→env-164 SRS024318 LANL scaffold 32095 + 3385 3562 RNA→ NLPC P60 (pfam00877)→env-165 SRS013825 C968173 - 350 172 RNA→ metagenemark→env-166 SRS013945 WUGC scaffold 3453 - 6313 6135 RNA→ NLPC P60 (pfam00877)→env-167 SRS013949 WUGC scaffold 59146 - 901 723 RNA→ NLPC P60 (pfam00877)→env-168 SRS015154 C755044 + 3446 3624 RNA→ NLPC P60 (pfam00877)→env-169 SRS015745 WUGC scaffold 9901 - 3530 3352 RNA→ NLPC P60 (pfam00877)→env-170 SRS015921 WUGC scaffold 3039 + 42921 43099 RNA→ NLPC P60 (pfam00877)→env-171 SRS016503 LANL scaffold 7478 - 6084 5906 RNA→ NLPC P60 (pfam00877)→env-172 SRS016533 Baylor scaffold 6400 - 2184 2006 RNA→ NLPC P60 (pfam00877)→env-173 SRS017013 Baylor scaffold 4457 + 4129 4307 RNA→ NLPC P60 (pfam00877)→env-174 SRS018359 Baylor scaffold 8241 + 15118 15296 RNA→env-175 SRS018971 WUGC scaffold 6116 - 221 43 RNA→env-176 SRS022079 C378359 + 334 512 RNA→env-177 SRS050029 WUGC scaffold 7885 + 5857 6035 RNA→ NLPC P60 (pfam00877)→env-178 SRS052874 LANL scaffold 15958 - 2257 2079 RNA→ NLPC P60 (pfam00877)→env-179 SRS056892 LANL scaffold 18636 + 617 795 RNA→ NLPC P60 (pfam00877)→env-180 SRS013942 C1232354 - 194 16 RNA→env-181 SRS047824 C2478141 - 590 412 RNA→ NLPC P60 (pfam00877)→env-182 SRS048719 C811145 - 435 258 RNA→ metagenemark→


35

env-183 SRS012279 C2613974 + 34 211 RNA→ metagenemark→env-184 SRS013818 C2670907 - 290 113 RNA→ metagenemark→env-185 SRS013879 WUGC scaffold 28618 + 1410 1587 RNA→ NLPC P60 (pfam00877)→env-186 SRS014124 C2549078 - 390 213 RNA→ metagenemark→env-187 SRS014888 WUGC scaffold 21430 + 524 701 RNA→ NLPC P60 (pfam00877)→env-188 SRS015395 WUGC scaffold 10096 - 313 136 RNA→ metagenemark→env-189 SRS015644 WUGC scaffold 29596 - 1033 856 RNA→ NLPC P60 (pfam00877)→env-190 SRS015797 C2621395 - 216 39 RNA→env-191 SRS016569 Baylor scaffold 17799 + 5044 5221 RNA→ NLPC P60 (pfam00877)→env-192 SRS019974 Baylor scaffold 25342 - 521 344 RNA→ metagenemark→env-193 SRS020856 Baylor scaffold 30119 + 13892 14069 RNA→ NLPC P60 (pfam00877)→env-194 SRS021496 Baylor scaffold 65632 + 833 1010 RNA→ metagenemark→env-195 SRS023617 Baylor scaffold 42575 - 1766 1589 RNA→ NLPC P60 (pfam00877)→env-196 SRS042131 WUGC scaffold 51096 - 180 3 RNA→env-197 SRS047210 C3287575 - 769 592 RNA→ NLPC P60 (pfam00877)→env-198 SRS057355 LANL scaffold 43281 - 940 763 RNA→ NLPC P60 (pfam00877)→env-199 SRS011243 Baylor scaffold 29686 - 798 621 RNA→ NLPC P60 (pfam00877)→env-200 SRS011306 Baylor scaffold 11633 + 109 286 RNA→ NLPC P60 (pfam00877)→env-201 SRS013502 C2174693 + 220 397 RNA→ metagenemark→env-202 SRS013947 WUGC scaffold 22409 + 991 1168 RNA→env-203 SRS014573 WUGC scaffold 9993 - 1868 1691 RNA→ NLPC P60 (pfam00877)→env-204 SRS015038 WUGC scaffold 3771 - 572 395 RNA→ metagenemark→env-205 SRS015059 WUGC scaffold 7014 + 61 238 RNA→ metagenemark→env-206 SRS015209 WUGC scaffold 6584 + 40722 40899 RNA→ NLPC P60 (pfam00877)→env-207 SRS015434 C5841884 - 459 282 RNA→ metagenemark→env-208 SRS015797 C2621487 + 583 760 RNA→env-209 SRS015893 WUGC scaffold 35302 - 180 3 RNA→env-210 SRS016002 WUGC scaffold 34932 - 1205 1028 RNA→ NLPC P60 (pfam00877)→env-211 SRS016086 WUGC scaffold 10294 - 2107 1930 RNA→ NLPC P60 (pfam00877)→env-212 SRS016319 WUGC scaffold 11816 + 313 490 RNA→env-213 SRS017439 Baylor scaffold 28239 - 459 282 RNA→ metagenemark→env-214 SRS017533 Baylor scaffold 24007 - 886 709 RNA→ NLPC P60 (pfam00877)→env-215 SRS018300 C3277728 + 113 290 RNA→ metagenemark→env-216 SRS019219 C2882948 - 480 303 RNA→ metagenemark→env-217 SRS019327 C2726790 - 528 351 RNA→ metagenemark→env-218 SRS021496 C2799947 - 316 139 RNA→ metagenemark→env-219 SRS022143 WUGC scaffold 7202 + 3151 3328 RNA→ NLPC P60 (pfam00877)→env-220 SRS024138 Baylor scaffold 29996 + 409 586 RNA→ NLPC P60 (pfam00877)→env-221 SRS042910 WUGC scaffold 35504 - 323 146 RNA→ metagenemark→env-222 SRS045715 C4769583 + 44 221 RNA→ metagenemark→env-223 SRS047824 WUGC scaffold 17083 + 1019 1196 RNA→ metagenemark→env-224 SRS056622 C2424588 - 320 143 RNA→ metagenemark→env-225 SRS058336 LANL scaffold 19516 + 65218 65395 RNA→ NLPC P60 (pfam00877)→env-226 SRS062544 C2773867 - 329 152 RNA→ metagenemark→env-227 SRS063193 LANL scaffold 46076 + 76 253 RNA→ metagenemark→env-228 SRS064423 LANL scaffold 66602 + 149 326 RNA→ metagenemark→env-229 SRS064774 LANL scaffold 48201 + 314 491 RNA→ NLPC P60 (pfam00877)→env-230 SRS063288 LANL scaffold 7861 + 945 1122 RNA→ NLPC P60 (pfam00877)→env-231 SRS063478 C527716 - 283 106 RNA→ metagenemark→env-232 SRS014689 WUGC scaffold 29411 - 1327 1150 RNA→ NLPC P60 (pfam00877)→env-233 SRS017120 Baylor scaffold 43397 + 5084 5261 RNA→env-234 SRS024637 LANL scaffold 4654 - 305 128 RNA→ metagenemark→


36

env-235 SRS043663 LANL scaffold 12679 + 4782 4959 RNA→ NLPC P60 (pfam00877)→env-236 SRS056323 LANL scaffold 14579 - 382 205 RNA→ metagenemark→env-237 SRS024081 LANL scaffold 47695 - 194 17 RNA→env-238 SRS016225 WUGC scaffold 17818 - 662 485 RNA→ Spr (COG0791)→env-239 SRS016342 C2889230 + 672 849 RNA→ metagenemark→env-240 SRS018739 C3659085 + 45 222 RNA→ NLPC P60 (pfam00877)→env-241 SRS065278 LANL scaffold 25050 - 966 789 RNA→ metagenemark→ NLPC P60 (pfam00877)→env-242 SRS013948 WUGC scaffold 14819 + 279 456 RNA→ metagenemark→env-243 SRS017808 Baylor scaffold 37815 - 1987 1810 RNA→ NLPC P60 (pfam00877)→env-244 SRS019122 C5904073 + 158 335 RNA→ NLPC P60 (pfam00877)→env-245 SRS019126 WUGC scaffold 24561 + 215 392 RNA→ NLPC P60 (pfam00877)→env-246 SRS018439 Baylor scaffold 49315 + 715 892 RNA→ metagenemark→env-247 SRS019027 C1961264 - 234 56 RNA→ metagenemark→env-248 SRS018591 WUGC scaffold 10300 + 3475 3652 RNA→env-249 SRS018791 WUGC scaffold 44408 + 1636 1813 RNA→env-250 SRS044373 WUGC scaffold 31275 - 180 3 RNA→env-251 SRS015158 WUGC scaffold 39161 + 786 950 RNA→ NLPC P60 (pfam00877)→env-252 SRS016575 C3745194 - 1329 1165 RNA→ NLPC P60 (pfam00877)→env-253 SRS020226 Baylor scaffold 20839 + 481 645 RNA→ NLPC P60 (pfam00877)→env-254 SRS024021 C1890870 - 274 110 RNA→env-255 SRS024289 LANL scaffold 13273 - 3450 3286 RNA→ NLPC P60 (pfam00877)→env-256 SRS024447 C3925644 + 39 203 RNA→ metagenemark→env-257 SRS015899 C1829138 - 535 371 RNA→ metagenemark→env-258 SRS011098 Baylor scaffold 48946 + 38 202 RNA→ NLPC P60 (pfam00877)→env-259 SRS011152 C4311195 + 38 202 RNA→ metagenemark→env-260 SRS011255 Baylor scaffold 64737 - 1916 1752 RNA→ NLPC P60 (pfam00877)→env-261 SRS011343 Baylor scaffold 33912 + 703 867 RNA→ metagenemark→env-262 SRS013170 Baylor scaffold 140525 + 39 203 RNA→ NLPC P60 (pfam00877)→env-263 SRS013533 PGA scaffold 42446 + 269 433 RNA→ metagenemark→env-264 SRS013723 Baylor scaffold 83426 - 6747 6583 RNA→ NLPC P60 (pfam00877)→env-265 SRS013836 C4786000 - 751 587 RNA→ NLPC P60 (pfam00877)→env-266 SRS013945 C1223075 - 544 380 RNA→ metagenemark→env-267 SRS013949 WUGC scaffold 61179 + 38 202 RNA→ NLPC P60 (pfam00877)→env-268 SRS014476 WUGC scaffold 35730 + 210 374 RNA→ metagenemark→env-269 SRS014578 WUGC scaffold 38785 - 1242 1078 RNA→ NLPC P60 (pfam00877)→env-270 SRS015044 WUGC scaffold 54177 - 519 355 RNA→ metagenemark→env-271 SRS015060 C1532175 - 413 249 RNA→ metagenemark→env-272 SRS015063 WUGC scaffold 12670 - 2394 2230 RNA→ NLPC P60 (pfam00877)→env-273 SRS015278 WUGC scaffold 6973 - 1812 1648 RNA→ NLPC P60 (pfam00877)→env-274 SRS015440 WUGC scaffold 25966 + 888 1052 RNA→ NLPC P60 (pfam00877)→env-275 SRS015470 C3286543 + 39 203 RNA→ metagenemark→env-276 SRS015574 C3316164 - 436 272 RNA→ metagenemark→env-277 SRS015755 C1679947 - 1227 1063 RNA→ NLPC P60 (pfam00877)→env-278 SRS015803 C2592664 + 39 203 RNA→ metagenemark→env-279 SRS015947 C1383587 - 539 375 RNA→ metagenemark→env-280 SRS016039 WUGC scaffold 16000 + 355 519 RNA→env-281 SRS016043 WUGC scaffold 46798 - 5566 5402 RNA→ NLPC P60 (pfam00877)→env-282 SRS016092 WUGC scaffold 14296 - 2325 2161 RNA→ NLPC P60 (pfam00877)→env-283 SRS016200 WUGC scaffold 47457 + 38 202 RNA→ NLPC P60 (pfam00877)→env-284 SRS016331 WUGC scaffold 35767 + 39 203 RNA→ NLPC P60 (pfam00877)→env-285 SRS016360 C2584971 - 525 361 RNA→ metagenemark→env-286 SRS016746 C2884349 + 38 202 RNA→


37

env-287 SRS017139 Baylor scaffold 108019 - 2326 2162 RNA→ NLPC P60 (pfam00877)→env-288 SRS017227 Baylor scaffold 50911 + 234 398 RNA→ NLPC P60 (pfam00877)→env-289 SRS017304 C2006177 + 482 646 RNA→ NLPC P60 (pfam00877)→env-290 SRS017445 Baylor scaffold 32717 - 1241 1077 RNA→ NLPC P60 (pfam00877)→env-291 SRS017511 C3489822 + 39 203 RNA→ metagenemark→env-292 SRS017533 C4091902 - 411 247 RNA→ metagenemark→env-293 SRS017814 Baylor scaffold 14769 - 995 831 RNA→ NLPC P60 (pfam00877)→env-294 SRS018157 C4761627 + 39 203 RNA→ metagenemark→env-295 SRS018337 C2360354 - 570 406 RNA→ metagenemark→env-296 SRS018394 C3996265 + 38 202 RNA→ metagenemark→env-297 SRS018573 WUGC scaffold 938 + 118 282 RNA→ NLPC P60 (pfam00877)→env-298 SRS018975 WUGC scaffold 39936 + 250 414 RNA→ NLPC P60 (pfam00877)→env-299 SRS019077 WUGC scaffold 67467 - 1241 1077 RNA→ NLPC P60 (pfam00877)→env-300 SRS019128 C4346713 + 38 202 RNA→ metagenemark→env-301 SRS019225 WUGC scaffold 9543 + 478 642 RNA→ NLPC P60 (pfam00877)→env-302 SRS019333 WUGC scaffold 24147 + 39 203 RNA→ NLPC P60 (pfam00877)→env-303 SRS019387 WUGC scaffold 33445 + 302 466 RNA→ NLPC P60 (pfam00877)→env-304 SRS019906 WUGC scaffold 35752 - 1798 1634 RNA→ NLPC P60 (pfam00877)→env-305 SRS019980 Baylor scaffold 59505 + 38 202 RNA→ NLPC P60 (pfam00877)→env-306 SRS020340 C2926245 + 39 203 RNA→ metagenemark→env-307 SRS021960 C2210932 - 512 348 RNA→ metagenemark→env-308 SRS022149 LANL scaffold 6049 - 345 181 RNA→ metagenemark→env-309 SRS023358 LANL scaffold 33765 - 232 68 RNA→ metagenemark→env-310 SRS023595 C7225597 - 1566 1402 RNA→ NLPC P60 (pfam00877)→env-311 SRS023964 Baylor scaffold 62906 - 2324 2160 RNA→ NLPC P60 (pfam00877)→env-312 SRS024144 C1811720 - 1647 1483 RNA→ NLPC P60 (pfam00877)→env-313 SRS024381 LANL scaffold 1787 + 609 773 RNA→ NLPC P60 (pfam00877)→env-314 SRS042984 LANL scaffold 28766 - 345 181 RNA→ metagenemark→env-315 SRS043018 WUGC scaffold 30095 - 690 526 RNA→ NLPC P60 (pfam00877)→env-316 SRS043755 C2348551 + 118 282 RNA→ metagenemark→env-317 SRS043772 C1721751 - 357 193 RNA→ metagenemark→env-318 SRS045197 C3508449 + 39 203 RNA→ metagenemark→env-319 SRS047100 WUGC scaffold 11017 + 8349 8513 RNA→ NLPC P60 (pfam00877)→env-320 SRS047113 C5403493 - 1197 1033 RNA→ NLPC P60 (pfam00877)→env-321 SRS047265 C1058021 - 446 282 RNA→ metagenemark→env-322 SRS049268 LANL scaffold 72827 + 40 204 RNA→ NLPC P60 (pfam00877)→env-323 SRS051244 C3462432 + 39 203 RNA→ NLPC P60 (pfam00877)→env-324 SRS051378 LANL scaffold 27731 + 357 521 RNA→ NLPC P60 (pfam00877)→env-325 SRS051930 C3238531 - 314 150 RNA→ metagenemark→env-326 SRS051941 LANL scaffold 71487 + 359 523 RNA→ metagenemark→env-327 SRS052876 C2272129 - 529 365 RNA→ metagenemark→env-328 SRS053584 LANL scaffold 29829 - 1307 1143 RNA→ NLPC P60 (pfam00877)→env-329 SRS054653 LANL scaffold 37283 + 488 652 RNA→ NLPC P60 (pfam00877)→env-330 SRS055378 C4072388 + 483 647 RNA→ metagenemark→env-331 SRS055401 LANL scaffold 32034 - 1402 1238 RNA→ NLPC P60 (pfam00877)→env-332 SRS058053 LANL scaffold 84014 - 1200 1036 RNA→ NLPC P60 (pfam00877)→env-333 SRS063603 LANL scaffold 1117 - 1910 1746 RNA→ NLPC P60 (pfam00877)→env-334 SRS063999 LANL scaffold 88754 + 455 619 RNA→ NLPC P60 (pfam00877)→env-335 SRS064449 LANL scaffold 62112 + 34 198 RNA→ NLPC P60 (pfam00877)→env-336 SRS064493 LANL scaffold 26196 - 2673 2509 RNA→ NLPC P60 (pfam00877)→env-337 SRS065099 LANL scaffold 5082 - 2478 2314 RNA→ NLPC P60 (pfam00877)→env-338 SRS075406 C831475 - 533 369 RNA→ metagenemark→


38

env-339 SRS022536 LANL scaffold 8207 - 1765 1602 RNA→ NLPC P60 (pfam00877)→env-340 SRS011126 Baylor scaffold 3699 + 34 197 RNA→ NLPC P60 (pfam00877)→env-341 SRS021477 Baylor scaffold 37481 + 477 640 RNA→ NLPC P60 (pfam00877)→env-342 SRS017025 Baylor scaffold 8760 + 490 653 RNA→ NLPC P60 (pfam00877)→env-343 SRS054430 C2091628 - 1955 1792 RNA→ NLPC P60 (pfam00877)→env-344 SRS015947 WUGC scaffold 9488 + 40 207 RNA→ metagenemark→env-345 SRS049318 C6466186 + 268 436 RNA→ metagenemark→env-346 SRS016342 Baylor scaffold 66296 - 292 144 RNA→ metagenemark→env-347 SRS019333 WUGC scaffold 24001 - 1119 950 RNA→ NLPC P60 (pfam00877)→env-348 SRS043676 WUGC scaffold 12314 + 481 650 RNA→ NLPC P60 (pfam00877)→env-349 SRS051378 LANL scaffold 17896 - 556 387 RNA→ metagenemark→env-350 SRS019028 WUGC scaffold 51341 + 251 420 RNA→ NLPC P60 (pfam00877)→env-351 SRS018665 WUGC scaffold 31461 - 1173 1004 RNA→ NLPC P60 (pfam00877)→env-352 SRS019128 C4352441 - 585 416 RNA→ metagenemark→env-353 SRS051244 LANL scaffold 9937 - 3367 3198 RNA→ NLPC P60 (pfam00877)→env-354 SRS022725 LANL scaffold 57487 + 165 334 RNA→ NLPC P60 (pfam00877)→env-355 SRS014690 WUGC scaffold 23157 + 159 328 RNA→ metagenemark→env-356 SRS018394 C3928288 - 389 220 RNA→ metagenemark→env-357 SRS019221 C286515 - 231 62 RNA→env-358 SRS014691 C2709904 - 463 294 RNA→ metagenemark→env-359 SRS018975 WUGC scaffold 32027 + 5069 5238 RNA→ NLPC P60 (pfam00877)→env-360 SRS058808 LANL scaffold 7436 - 18884 18715 RNA→ NLPC P60 (pfam00877)→env-361 SRS016501 C1553826 - 232 63 RNA→env-362 SRS016503 LANL scaffold 7412 + 350 519 RNA→ metagenemark→env-363 SRS016533 C486953 - 295 126 RNA→ metagenemark→env-364 SRS077738 LANL scaffold 5343 + 2438 2607 RNA→env-365 SRS015650 WUGC scaffold 1757 - 481 313 RNA→ metagenemark→env-366 SRS047265 C1050739 + 35 203 RNA→ metagenemark→env-367 SRS013533 PGA scaffold 16634 - 648 480 RNA→ metagenemark→env-368 SRS023964 C2510782 - 489 321 RNA→ metagenemark→env-369 SRS011098 Baylor scaffold 16866 + 40 209 RNA→ metagenemark→env-370 SRS055378 C4007087 - 230 62 RNA→env-371 SRS019073 C2508683 - 870 702 RNA→ NLPC P60 (pfam00877)→env-372 SRS011126 Baylor scaffold 65997 + 1664 1832 RNA→ NLPC P60 (pfam00877)→env-373 SRS011152 Baylor scaffold 30589 - 901 733 RNA→ NLPC P60 (pfam00877)→env-374 SRS015158 WUGC scaffold 35647 - 1073 905 RNA→ NLPC P60 (pfam00877)→env-375 SRS015755 WUGC scaffold 49684 + 644 812 RNA→ NLPC P60 (pfam00877)→env-376 SRS016088 C187340 + 98 266 RNA→ metagenemark→env-377 SRS016196 C482127 - 297 129 RNA→ metagenemark→env-378 SRS016200 WUGC scaffold 9505 - 250 82 RNA→ metagenemark→env-379 SRS016575 C3622900 - 493 325 RNA→ metagenemark→env-380 SRS017080 C1210979 - 901 733 RNA→ NLPC P60 (pfam00877)→env-381 SRS017139 Baylor scaffold 86254 - 3481 3313 RNA→ NLPC P60 (pfam00877)→env-382 SRS017445 Baylor scaffold 41969 + 158 326 RNA→ metagenemark→env-383 SRS021477 Baylor scaffold 38124 - 5712 5544 RNA→ NLPC P60 (pfam00877)→env-384 SRS024021 Baylor scaffold 11774 - 493 325 RNA→ metagenemark→env-385 SRS024355 C4204822 - 519 351 RNA→ metagenemark→env-386 SRS024637 C2362581 + 576 744 RNA→ metagenemark→env-387 SRS024649 LANL scaffold 7107 - 584 416 RNA→ metagenemark→env-388 SRS051930 C3175431 + 98 266 RNA→ metagenemark→env-389 SRS054653 LANL scaffold 15424 - 528 360 RNA→ metagenemark→env-390 SRS054776 C1588902 - 403 235 RNA→ metagenemark→


39

env-391 SRS064493 LANL scaffold 11737 - 2392 2224 RNA→ NLPC P60 (pfam00877)→env-392 SRS065099 LANL scaffold 94698 - 852 684 RNA→ NLPC P60 (pfam00877)→env-393 SRS011255 Baylor scaffold 52823 + 296 464 RNA→ NLPC P60 (pfam00877)→env-394 SRS012285 C2866467 - 403 235 RNA→ metagenemark→env-395 SRS013170 Baylor scaffold 102779 + 257 425 RNA→ metagenemark→env-396 SRS013252 Baylor scaffold 59311 + 443 611 RNA→ metagenemark→env-397 SRS013723 Baylor scaffold 93887 + 406 574 RNA→ NLPC P60 (pfam00877)→env-398 SRS013836 Baylor scaffold 28604 - 850 682 RNA→ metagenemark→ NLPC P60 (pfam00877)→env-399 SRS014476 WUGC scaffold 18365 + 40 208 RNA→ metagenemark→env-400 SRS014477 C1631286 - 852 684 RNA→ NLPC P60 (pfam00877)→env-401 SRS015274 C464466 + 77 245 RNA→ metagenemark→env-402 SRS015278 WUGC scaffold 17600 + 40 208 RNA→ NLPC P60 (pfam00877)→env-403 SRS015378 WUGC scaffold 3764 + 188 356 RNA→ NLPC P60 (pfam00877)→env-404 SRS015436 C1725737 - 483 315 RNA→ metagenemark→env-405 SRS015440 WUGC scaffold 58490 + 241 409 RNA→ metagenemark→env-406 SRS015899 WUGC scaffold 1938 + 616 784 RNA→env-407 SRS015921 C527678 - 489 321 RNA→ metagenemark→env-408 SRS015989 WUGC scaffold 23668 + 121 289 RNA→env-409 SRS016043 C2193660 - 585 417 RNA→ metagenemark→env-410 SRS016092 WUGC scaffold 3737 - 1027 859 RNA→ NLPC P60 (pfam00877)→env-411 SRS016349 C1022228 + 41 209 RNA→ metagenemark→env-412 SRS016360 Baylor scaffold 4334 + 845 1013 RNA→ metagenemark→env-413 SRS016746 Baylor scaffold 264 - 2146 1978 RNA→ NLPC P60 (pfam00877)→env-414 SRS017025 Baylor scaffold 4649 + 160 328 RNA→ metagenemark→env-415 SRS017304 Baylor scaffold 7891 + 223 391 RNA→ NLPC P60 (pfam00877)→env-416 SRS017511 C3436658 + 40 208 RNA→ metagenemark→env-417 SRS017533 C4088030 + 188 356 RNA→ metagenemark→env-418 SRS017691 C5396394 - 863 695 RNA→ NLPC P60 (pfam00877)→env-419 SRS018359 C1200774 - 294 126 RNA→ metagenemark→env-420 SRS019077 WUGC scaffold 45337 + 89 257 RNA→ NLPC P60 (pfam00877)→env-421 SRS019225 C1529788 + 40 208 RNA→ metagenemark→env-422 SRS019587 C1048848 - 529 361 RNA→ metagenemark→env-423 SRS019906 C2224822 + 40 208 RNA→ metagenemark→env-424 SRS020334 C2567594 + 146 314 RNA→env-425 SRS020340 Baylor scaffold 3834 + 334 502 RNA→ NLPC P60 (pfam00877)→env-426 SRS020862 C897366 - 424 256 RNA→ metagenemark→env-427 SRS022149 C2803984 - 585 417 RNA→ metagenemark→env-428 SRS023538 C1257386 + 43 211 RNA→ metagenemark→env-429 SRS023595 C7185599 + 40 208 RNA→ NLPC P60 (pfam00877)→env-430 SRS023987 C1178378 + 1172 1340 RNA→env-431 SRS024144 LANL scaffold 27349 - 2561 2393 RNA→ NLPC P60 (pfam00877)→env-432 SRS024381 LANL scaffold 27333 + 176 344 RNA→ metagenemark→env-433 SRS024447 C3881828 - 424 256 RNA→ metagenemark→env-434 SRS024561 C2793126 + 111 279 RNA→ NLPC P60 (pfam00877)→env-435 SRS042984 LANL scaffold 27330 + 334 502 RNA→ NLPC P60 (pfam00877)→env-436 SRS043755 WUGC scaffold 22115 + 73 241 RNA→ NLPC P60 (pfam00877)→env-437 SRS043772 WUGC scaffold 31805 + 256 424 RNA→ metagenemark→env-438 SRS045197 WUGC scaffold 21761 - 585 417 RNA→ metagenemark→env-439 SRS045313 C1357321 + 188 356 RNA→ NLPC P60 (pfam00877)→env-440 SRS047100 WUGC scaffold 3456 - 1559 1391 RNA→ NLPC P60 (pfam00877)→env-441 SRS051941 LANL scaffold 72646 - 340 172 RNA→ metagenemark→env-442 SRS055401 C2236337 + 14 182 RNA→ metagenemark→


40

env-443 SRS055450 C2031901 - 424 256 RNA→ metagenemark→env-444 SRS057022 C1984770 + 41 209 RNA→ metagenemark→env-445 SRS058053 LANL scaffold 38097 + 511 679 RNA→ metagenemark→env-446 SRS063603 C4153006 + 40 208 RNA→ metagenemark→env-447 SRS063999 LANL scaffold 14074 + 650 818 RNA→ NLPC P60 (pfam00877)→env-448 SRS064809 LANL scaffold 3092 + 407 575 RNA→ metagenemark→env-449 SRS065310 C1307757 - 424 256 RNA→ metagenemark→env-450 SRS075406 C829451 + 380 548 RNA→ metagenemark→env-451 SRS075410 LANL scaffold 4844 + 1085 1253 RNA→ NLPC P60 (pfam00877)→env-452 FNTS067 GJ87FRN01BCTM8 - 378 225 RNA→ hypo→env-453 P3 CLC Cons1600 + 1650 1838 RNA→ hypo→env-454 botACOD F64RS5002FOVPR - 159 16 RNA→env-455 DCrCPGB c176388 - 424 242 RNA→ hypo→env-456 sg4i contig14505 + 294 458 RNA→ RlpA (COG0797)→ hypo→env-457 DCrCPGB c542989 + 181 381 RNA→ ←hypo

env-458 FNTS GKKEVUV01A1DIF - 310 169 RNA→ hypo→env-459 FNTS GKKEVUV02HYBS6 + 63 304 RNA→ hypo→env-460 LWSO GLQAYWI01CTYJC - 193 61 RNA→env-461 botACOD F64RS5002GDG93 - 306 131 RNA→ hypo→env-462 B3 all c Cons176240 + 203 326 RNA→ ←hypoenv-463 FIHLEPW02SR58C + 66 258 RNA→ hypo→env-464 2034244254 + 358 496 RNA→env-465 FNTS067 GKA24FP01EOGC9 - 299 117 RNA→ ←hypoenv-466 2044540301 - 294 126 RNA→env-467 MA55A F65388E01CFDD3 + 56 184 RNA→env-468 ASMM170b GJFD58A01E09N8 + 109 236 RNA→ hypo→env-469 P3 CLC Cons139240 - 381 211 RNA→ ←hypo

env-470 P3 CLC Cons92917 + 538 709 RNA→ Transglycosylase (pfam06737)→env-471 Cons118179 - 498 327 RNA→ Transglycosylase (pfam06737)→env-472 P3 CLC Cons57123 - 386 215 RNA→ Transglycosylase (pfam06737)→env-473 Cons99633 - 547 376 RNA→ Transglycosylase (pfam06737)→env-474 Cons110895 + 680 852 RNA→ Transglycosylase (pfam06737)→env-475 DCrCPGB c814502 + 54 250 RNA→env-476 LWAnNiSIP F624WLL02FQ5NL + 41 165 RNA→ hypo→env-477 LWAnN F624WLL02FQ5NL + 41 165 RNA→ hypo→env-478 LWSO GLQAYWI01A6SW4 - 383 256 RNA→ hypo→env-479 LWFCAn GLQU6AQ01DER7O - 134 4 RNA→env-480 SRS017511 Baylor scaffold 90206 + 240 429 RNA→ metagenemark→env-481 soil XZS40993 g1 + 91 233 RNA→ Kup (COG3158)→env-482 A5 c1 Cons61080 - 256 47 RNA→env-483 SwRhRL2b contig 1690938 - 1295 1137 RNA→ hypo→env-484 MRS2a Contig 53286 + 110 252 RNA→env-485 MRS2a Contig 46378 + 110 252 RNA→env-486 MRS2a Contig 57407 + 110 252 RNA→env-487 MRS2a Contig 36736 + 110 252 RNA→env-488 MRS2a Contig 65762 + 110 252 RNA→env-489 MRS2a Contig 71879 + 110 252 RNA→env-490 MRS1b contig 8748267 - 791 649 RNA→ hypo→env-491 SwRhRL2b contig 2869770 - 2630 2477 RNA→ hypo→env-492 SRS013533 PGA scaffold 6402 - 1711 1526 RNA→ NLPC P60 (pfam00877)→ metagenemark→env-493 SRS013723 Baylor scaffold 98133 + 1394 1579 RNA→ metagenemark→env-494 SRS016331 C4140719 - 321 136 RNA→ metagenemark→


41

env-495 SRS016575 C3687005 - 414 229 RNA→ metagenemark→env-496 SRS017139 Baylor scaffold 25109 + 2279 2464 RNA→ metagenemark→env-497 SRS017691 Baylor scaffold 70311 + 1012 1197 RNA→env-498 SRS020226 C3417582 - 238 53 RNA→env-499 SRS023938 C2270105 - 300 115 RNA→ metagenemark→env-500 SRS051378 C1860885 + 702 887 RNA→ metagenemark→env-501 SRS013836 C4683527 + 229 414 RNA→env-502 SRS017227 Baylor scaffold 12437 + 9384 9569 RNA→ NLPC P60 (pfam00877)→env-503 SRS047113 C5400941 + 903 1088 RNA→env-504 SRS043018 C3855509 - 399 213 RNA→ metagenemark→env-505 SRS051941 LANL scaffold 75582 + 1282 1468 RNA→env-506 SRS016092 WUGC scaffold 14071 - 277 90 RNA→env-507 SRS065099 LANL scaffold 48996 - 396 209 RNA→ metagenemark→env-508 SRS018573 WUGC scaffold 15803 - 210 23 RNA→env-509 SRS019024 C912939 + 3 190 RNA→ metagenemark→env-510 SRS019221 C281677 + 38 225 RNA→env-511 SRS024144 LANL scaffold 22453 - 210 23 RNA→env-512 SRS064809 LANL scaffold 10667 + 450 637 RNA→ metagenemark→env-513 SRS017139 C3609389 - 310 123 RNA→env-514 SRS023938 Baylor scaffold 19654 + 2117 2304 RNA→ NLPC P60 (pfam00877)→env-515 SRS024355 LANL scaffold 53772 + 699 886 RNA→ NLPC P60 (pfam00877)→env-516 SRS047634 LANL scaffold 78229 + 644 831 RNA→env-517 SRS015060 WUGC scaffold 1446 + 380 567 RNA→ metagenemark→env-518 SRS015745 WUGC scaffold 4838 - 399 212 RNA→ metagenemark→env-519 SRS023538 Baylor scaffold 21549 + 3 190 RNA→ metagenemark→env-520 SRS013881 WUGC scaffold 3608 - 212 25 RNA→env-521 SRS013945 WUGC scaffold 17476 + 429 616 RNA→ metagenemark→env-522 SRS014473 C1104999 - 354 167 RNA→ metagenemark→env-523 SRS015044 WUGC scaffold 60523 + 443 630 RNA→ metagenemark→env-524 SRS015154 C734432 + 91 278 RNA→ metagenemark→env-525 SRS015803 C2561781 + 61 248 RNA→ metagenemark→env-526 SRS015895 WUGC scaffold 8273 + 418 605 RNA→env-527 SRS015921 WUGC scaffold 5142 + 2035 2222 RNA→ metagenemark→env-528 SRS016529 C3008873 + 17 204 RNA→env-529 SRS016600 C801105 - 280 93 RNA→env-530 SRS017533 C4027563 - 424 237 RNA→ metagenemark→env-531 SRS019029 C3221035 + 9 196 RNA→ metagenemark→env-532 SRS019129 WUGC scaffold 42288 - 351 164 RNA→ metagenemark→env-533 SRS019225 C1500295 + 60 247 RNA→env-534 SRS019333 WUGC scaffold 8033 - 555 368 RNA→ metagenemark→env-535 SRS021960 Baylor scaffold 1358 + 139 326 RNA→ metagenemark→env-536 SRS023987 C1174850 + 408 595 RNA→ metagenemark→env-537 SRS024021 Baylor scaffold 16504 - 388 201 RNA→ metagenemark→env-538 SRS024649 LANL scaffold 8802 + 149 336 RNA→ metagenemark→env-539 SRS043676 WUGC scaffold 19054 + 59 246 RNA→ metagenemark→ NLPC P60 (pfam00877)→env-540 SRS045313 C1308725 + 116 303 RNA→env-541 SRS048719 C802909 - 531 344 RNA→ metagenemark→env-542 SRS051930 C3088385 + 102 289 RNA→env-543 SRS055450 LANL scaffold 72191 - 352 165 RNA→ metagenemark→env-544 SRS056892 C1451957 - 352 165 RNA→ metagenemark→env-545 SRS058808 LANL scaffold 43291 + 8 195 RNA→ metagenemark→env-546 SRS063287 LANL scaffold 14386 + 606 793 RNA→


42

env-547 SRS049268 LANL scaffold 60870 - 350 178 RNA→ metagenemark→env-548 SRS049318 LANL scaffold 152253 - 788 616 RNA→ Spr (COG0791)→env-549 SRS013252 Baylor scaffold 58886 + 621 793 RNA→ metagenemark→env-550 SRS015215 WUGC scaffold 51213 + 297 469 RNA→ metagenemark→env-551 SRS016575 Baylor scaffold 56424 + 553 725 RNA→ metagenemark→env-552 SRS017304 C1967410 + 199 371 RNA→ metagenemark→env-553 SRS018665 C3643328 + 19 191 RNA→ metagenemark→env-554 SRS024087 LANL scaffold 64636 + 306 478 RNA→ metagenemark→env-555 SRS024144 C1736586 + 156 328 RNA→ metagenemark→env-556 SRS024561 C2793824 + 220 392 RNA→ metagenemark→env-557 SRS045197 C3521889 + 306 478 RNA→ metagenemark→env-558 SRS051244 C3445828 + 294 466 RNA→ metagenemark→env-559 SRS063932 C3898934 - 566 394 RNA→ metagenemark→env-560 SRS012285 C2948207 - 447 274 RNA→ metagenemark→env-561 SRS013950 C2063634 - 323 150 RNA→ metagenemark→env-562 SRS014476 WUGC scaffold 41428 + 476 649 RNA→ metagenemark→env-563 SRS014578 C2528240 - 354 181 RNA→ metagenemark→env-564 SRS016746 C2984344 - 406 233 RNA→ metagenemark→env-565 SRS019029 C3105866 - 315 142 RNA→ metagenemark→env-566 SRS019980 Baylor scaffold 55186 + 596 769 RNA→env-567 SRS020226 C3310258 - 292 119 RNA→env-568 SRS024649 C3602686 + 305 478 RNA→env-569 SRS047113 C5243061 - 416 243 RNA→ metagenemark→env-570 SRS063999 LANL scaffold 81143 + 305 478 RNA→ metagenemark→env-571 SRS022536 LANL scaffold 101034 + 477 649 RNA→ metagenemark→env-572 SRS023595 C6977796 - 225 53 RNA→env-573 SRS024355 C4216283 + 370 542 RNA→env-574 SRS065099 LANL scaffold 36079 + 329 501 RNA→ metagenemark→env-575 SRS011126 C4652129 + 305 477 RNA→ metagenemark→env-576 SRS013533 PGA scaffold 121249 - 556 384 RNA→ metagenemark→env-577 SRS017139 Baylor scaffold 97072 - 556 384 RNA→ metagenemark→env-578 SRS017691 C5389720 - 646 474 RNA→ metagenemark→env-579 SRS020340 C2954213 + 306 478 RNA→ metagenemark→env-580 SRS021477 Baylor scaffold 27748 + 472 644 RNA→ metagenemark→env-581 SRS022149 C2825348 - 535 363 RNA→ metagenemark→env-582 SRS042984 LANL scaffold 10621 + 306 478 RNA→ metagenemark→env-583 SRS055378 LANL scaffold 27249 - 901 729 RNA→ NLPC P60 (pfam00877)→env-584 SRS011343 Baylor scaffold 16274 - 551 379 RNA→ metagenemark→ metagenemark→env-585 SRS016043 C2079269 + 8 180 RNA→ metagenemark→env-586 SRS016200 WUGC scaffold 29523 - 285 113 RNA→env-587 SRS018337 C2356506 - 307 135 RNA→ metagenemark→env-588 SRS024289 LANL scaffold 54571 - 214 42 RNA→env-589 SRS043018 C3719998 - 358 186 RNA→ metagenemark→env-590 SRS016331 C4115711 + 118 290 RNA→ metagenemark→env-591 SRS023358 C3470451 - 265 82 RNA→env-592 SRS024447 C3766239 - 308 125 RNA→ metagenemark→env-593 SRS024649 LANL scaffold 29152 - 301 118 RNA→ metagenemark→env-594 SRS063932 C3819810 + 241 424 RNA→ metagenemark→env-595 SRS024381 LANL scaffold 49769 - 323 140 RNA→ metagenemark→env-596 SRS011255 Baylor scaffold 70812 + 272 455 RNA→ metagenemark→env-597 SRS015947 WUGC scaffold 20723 - 332 149 RNA→ metagenemark→env-598 SRS017304 Baylor scaffold 2045 - 253 70 RNA→


43

env-599 SRS023964 Baylor scaffold 64712 + 506 689 RNA→ NLPC P60 (pfam00877)→env-600 SRS024144 C1636082 + 86 269 RNA→env-601 SRS024289 LANL scaffold 10873 - 253 70 RNA→env-602 SRS011152 C4239618 + 154 333 RNA→env-603 SRS019128 C4259972 + 141 320 RNA→env-604 SRS011126 Baylor scaffold 49770 - 1230 1051 RNA→ NLPC P60 (pfam00877)→env-605 SRS011343 Baylor scaffold 53732 - 340 161 RNA→ metagenemark→env-606 SRS015899 WUGC scaffold 38450 - 2295 2116 RNA→ NLPC P60 (pfam00877)→env-607 SRS018975 WUGC scaffold 22289 + 1569 1748 RNA→ metagenemark→env-608 SRS021477 Baylor scaffold 74724 - 688 509 RNA→ metagenemark→env-609 SRS022083 Baylor scaffold 23066 + 418 597 RNA→ NLPC P60 (pfam00877)→env-610 SRS049268 LANL scaffold 72226 + 1008 1187 RNA→ NLPC P60 (pfam00877)→env-611 SRS075410 LANL scaffold 35142 + 19 198 RNA→ metagenemark→env-612 SRS015989 WUGC scaffold 25290 - 1251 1072 RNA→ NLPC P60 (pfam00877)→env-613 SRS016575 Baylor scaffold 43276 + 35 214 RNA→ NLPC P60 (pfam00877)→env-614 SRS017445 Baylor scaffold 65081 - 329 150 RNA→ metagenemark→env-615 SRS019333 C1290888 + 146 325 RNA→ NLPC P60 (pfam00877)→env-616 SRS013170 Baylor scaffold 127796 + 157 336 RNA→env-617 SRS013252 Baylor scaffold 5598 - 1114 935 RNA→ ←metagenemark

env-618 SRS015158 WUGC scaffold 45500 - 2280 2101 RNA→ NLPC P60 (pfam00877)→env-619 SRS015215 WUGC scaffold 14818 - 261 82 RNA→env-620 SRS017025 C1733568 - 336 157 RNA→ metagenemark→env-621 SRS018394 Baylor scaffold 56586 - 326 147 RNA→ metagenemark→env-622 SRS019591 WUGC scaffold 38018 + 138 317 RNA→ ←metagenemark

env-623 SRS019980 C2989225 + 338 517 RNA→ metagenemark→env-624 SRS023538 Baylor scaffold 6915 - 563 384 RNA→ metagenemark→env-625 SRS024021 Baylor scaffold 13669 - 269 90 RNA→env-626 SRS042984 LANL scaffold 2760 - 990 811 RNA→ NLPC P60 (pfam00877)→env-627 SRS043018 WUGC scaffold 2416 + 445 624 RNA→ NLPC P60 (pfam00877)→env-628 SRS051930 LANL scaffold 47253 + 141 320 RNA→ metagenemark→env-629 SRS054430 C2000770 - 259 80 RNA→env-630 SRS054653 LANL scaffold 16382 - 1438 1259 RNA→ NLPC P60 (pfam00877)→env-631 SRS063215 C2122849 + 55 234 RNA→env-632 SRS065310 LANL scaffold 14301 - 528 349 RNA→ metagenemark→env-633 SRS011098 Baylor scaffold 37389 - 328 149 RNA→ metagenemark→env-634 SRS016043 WUGC scaffold 65162 + 141 320 RNA→ NLPC P60 (pfam00877)→env-635 SRS016746 Baylor scaffold 11987 - 762 583 RNA→ ←metagenemarkenv-636 SRS021960 Baylor scaffold 12612 - 224 45 RNA→env-637 SRS015440 WUGC scaffold 56713 - 981 802 RNA→ NLPC P60 (pfam00877)→env-638 SRS015470 WUGC scaffold 13689 + 581 760 RNA→ NLPC P60 (pfam00877)→env-639 SRS013723 Baylor scaffold 71553 - 328 149 RNA→ metagenemark→env-640 SRS014476 WUGC scaffold 50424 - 689 510 RNA→ metagenemark→env-641 SRS019387 WUGC scaffold 31819 + 432 611 RNA→ metagenemark→env-642 SRS020862 Baylor scaffold 20647 - 319 143 RNA→ metagenemark→env-643 SRS011255 Baylor scaffold 8825 + 910 1102 RNA→ NLPC P60 (pfam00877)→env-644 SRS014578 WUGC scaffold 67519 + 631 819 RNA→ metagenemark→env-645 SRS015158 WUGC scaffold 47504 - 359 171 RNA→ metagenemark→env-646 SRS015215 WUGC scaffold 35434 - 311 123 RNA→ metagenemark→env-647 SRS015278 WUGC scaffold 39685 + 1184 1372 RNA→ NLPC P60 (pfam00877)→env-648 SRS016200 WUGC scaffold 5373 - 1061 873 RNA→ NLPC P60 (pfam00877)→env-649 SRS017445 Baylor scaffold 85759 - 1837 1649 RNA→ NLPC P60 (pfam00877)→env-650 SRS017691 Baylor scaffold 61477 - 1043 855 RNA→ NLPC P60 (pfam00877)→


44

env-651 SRS018573 WUGC scaffold 38867 + 2257 2445 RNA→ NLPC P60 (pfam00877)→env-652 SRS019225 WUGC scaffold 27460 + 1755 1943 RNA→ NLPC P60 (pfam00877)→env-653 SRS020340 Baylor scaffold 3364 - 498 310 RNA→ metagenemark→env-654 SRS024021 Baylor scaffold 31583 + 2299 2487 RNA→ NLPC P60 (pfam00877)→env-655 SRS024355 LANL scaffold 88985 + 2286 2474 RNA→ NLPC P60 (pfam00877)→env-656 SRS024649 LANL scaffold 8255 - 968 780 RNA→ NLPC P60 (pfam00877)→env-657 SRS043018 WUGC scaffold 4693 - 1059 871 RNA→ NLPC P60 (pfam00877)→env-658 SRS051941 LANL scaffold 9378 - 271 83 RNA→env-659 sg4i contig01119 + 1039 1320 RNA→ COG3583 (COG3583)COG3584 (COG3584)→env-660 PCEOT contig29431 - 1538 1389 RNA→ NLPC P60 (pfam00877)→ USP Like (cd00293)→env-661 A5 c1 Cons35033 + 3846 3982 RNA→ SCP bacterial (cd05379)→ GppA (COG0248)→env-662 FNTS GKKEVUV02H77IO + 53 248 RNA→ ←hypo

env-663 botACOD F64RS5002I09HE + 19 206 RNA→ Transglycosylase (pfam06737)→env-664 FNTS067 GJ87FRN01EC917 - 431 297 RNA→ hypo→env-665 A2 c1 Cons36493 - 630 468 RNA→ hypo→env-666 A2 c1 Cons28020 + 1065 1245 RNA→ XkdP (COG1652)Transglycosylase (pfam06737)→env-667 AglaG F499EG101EX9M5 + 268 465 RNA→env-668 P3 CLC Cons108979 + 1004 1202 RNA→ Transglycosylase (pfam06737)→env-669 DCrCPGB c344027 + 194 380 RNA→ hypo→env-670 84896692 - 848 725 RNA→ COG3584 (COG3584)→env-671 F10SI03100a Sequence0000005301 + 2867 2990 RNA→ hypo→env-672 FNTS067 GKA24FP01BDA5A + 40 215 RNA→ hypo→env-673 FNTS contig11525 - 190 15 RNA→env-674 FNTS067 contig01249 + 1348 1523 RNA→env-675 FNTS067 GJ87FRN01BXBSP + 236 413 RNA→ hypo→env-676 FNTS067 GJ87FRN01CFEML + 215 393 RNA→ hypo→env-677 AECF F4EK1NX01AL2J5 - 313 122 RNA→env-678 SRB contig20444 + 44 203 RNA→ hypo→env-679 SwiR contig06944 + 44 203 RNA→ hypo→env-680 botACOD F64RS5002F7CEO - 401 259 RNA→ hypo→env-681 SRB FXPBX6M01CU11H - 402 219 RNA→ hypo→env-682 botACOD GAKN62C01B4EAV - 293 124 RNA→ ←hypo

env-683 DCrCPGB c87524 + 222 418 RNA→ ←hypo

env-684 LWSO GLQAYWI02INLLE - 308 180 RNA→ hypo→env-685 LWSO GFMCQXZ02HHION - 156 41 RNA→env-686 SRS013252 Baylor scaffold 57399 + 142 319 RNA→ metagenemark→env-687 SRS024561 LANL scaffold 14919 - 499 322 RNA→ metagenemark→env-688 SRS055378 LANL scaffold 85191 + 144 321 RNA→ metagenemark→env-689 SRS011126 Baylor scaffold 39058 + 144 321 RNA→ metagenemark→env-690 SRS017691 Baylor scaffold 43706 - 562 385 RNA→ metagenemark→env-691 SRS021477 Baylor scaffold 57553 + 32 209 RNA→ metagenemark→env-692 SRS063603 LANL scaffold 88556 - 493 316 RNA→ metagenemark→env-693 SRS016575 Baylor scaffold 56896 + 119 296 RNA→ metagenemark→env-694 SRS049318 LANL scaffold 169281 - 442 264 RNA→ metagenemark→env-695 SRS013533 PGA scaffold 116872 - 227 50 RNA→env-696 SRS063932 LANL scaffold 89296 + 102 279 RNA→ metagenemark→env-697 SRS013836 C4748113 - 476 299 RNA→ metagenemark→env-698 SRS017139 Baylor scaffold 26025 - 545 368 RNA→ metagenemark→env-699 SRS023595 Baylor scaffold 24631 - 280 103 RNA→ ←metagenemark

env-700 SRS024355 C4227596 - 525 348 RNA→ metagenemark→env-701 SRS015574 WUGC scaffold 31372 + 7 184 RNA→ metagenemark→env-702 SRS012285 C2900466 - 489 312 RNA→ metagenemark→


45

env-703 SRS051930 C3089127 + 113 290 RNA→env-704 SRS011098 Baylor scaffold 41286 - 560 369 RNA→ metagenemark→env-705 SRS011152 Baylor scaffold 18181 + 838 1029 RNA→env-706 SRS011343 Baylor scaffold 28399 + 409 600 RNA→env-707 SRS012285 C2863773 - 366 175 RNA→ metagenemark→env-708 SRS015063 WUGC scaffold 47299 - 1307 1116 RNA→ NLPC P60 (pfam00877)→env-709 SRS015158 WUGC scaffold 44311 + 682 873 RNA→ metagenemark→env-710 SRS015440 WUGC scaffold 47844 - 392 201 RNA→ metagenemark→env-711 SRS015470 C3259183 + 165 356 RNA→env-712 SRS015899 WUGC scaffold 38450 - 3445 3254 RNA→ NLPC P60 (pfam00877)→env-713 SRS017025 C1751126 + 1006 1197 RNA→ metagenemark→env-714 SRS017445 Baylor scaffold 60863 + 569 760 RNA→ metagenemark→env-715 SRS018157 C4704289 + 210 401 RNA→env-716 SRS018975 WUGC scaffold 22289 + 409 600 RNA→ NLPC P60 (pfam00877)→env-717 SRS019077 WUGC scaffold 60399 + 1189 1380 RNA→ metagenemark→env-718 SRS019333 C1255211 + 7 198 RNA→ metagenemark→env-719 SRS019387 C1698667 - 258 67 RNA→env-720 SRS019591 WUGC scaffold 43085 - 572 381 RNA→ metagenemark→env-721 SRS019980 Baylor scaffold 48656 + 218 409 RNA→env-722 SRS022083 C1920564 + 129 320 RNA→ NLPC P60 (pfam00877)→env-723 SRS024289 LANL scaffold 59950 + 409 600 RNA→env-724 SRS054653 LANL scaffold 19557 + 1363 1554 RNA→ metagenemark→env-725 SRS065310 C1357737 - 290 99 RNA→env-726 SRS075410 C2953168 + 129 320 RNA→env-727 SRS015215 C2469918 + 211 402 RNA→env-728 SRS014476 WUGC scaffold 49230 - 574 386 RNA→ metagenemark→env-729 SRS015574 WUGC scaffold 27256 - 913 715 RNA→ NLPC P60 (pfam00877)→env-730 SRS023964 Baylor scaffold 65002 - 504 306 RNA→ metagenemark→env-731 SRS024289 LANL scaffold 67346 - 198 1 RNA→env-732 SRS015063 WUGC scaffold 37720 - 506 318 RNA→ metagenemark→env-733 SRS015158 WUGC scaffold 30850 - 340 152 RNA→ metagenemark→env-734 SRS017445 Baylor scaffold 43546 - 340 152 RNA→ metagenemark→env-735 SRS018337 Baylor scaffold 8332 - 319 131 RNA→env-736 SRS019225 WUGC scaffold 27460 + 528 716 RNA→ NLPC P60 (pfam00877)→env-737 SRS020340 Baylor scaffold 3364 - 1725 1537 RNA→ NLPC P60 (pfam00877)→env-738 SRS024021 Baylor scaffold 31583 + 1072 1260 RNA→ NLPC P60 (pfam00877)→env-739 SRS024355 LANL scaffold 88985 + 1059 1247 RNA→ NLPC P60 (pfam00877)→env-740 SRS024649 LANL scaffold 8255 - 2195 2007 RNA→ NLPC P60 (pfam00877)→env-741 SRS043018 WUGC scaffold 4693 - 2286 2098 RNA→ NLPC P60 (pfam00877)→env-742 SRS054653 LANL scaffold 38176 + 1564 1752 RNA→ NLPC P60 (pfam00877)→env-743 A5 c1 Cons66589 + 649 782 RNA→env-744 P3 CLC Cons38003 - 4047 3910 RNA→ ←hypoenv-745 LWFCAnN contig01461 - 373 223 RNA→ rlpA (TIGR00413)→env-746 comb1 contig42177 - 498 348 RNA→ RlpA (COG0797)→env-747 comb2 contig51632 - 498 348 RNA→ RlpA (COG0797)→env-748 2034282025 - 313 170 RNA→ hypo→env-749 P3 CLC Cons39435 - 263 122 RNA→ hypo→env-750 SRB FXPBX6M01DY0D0 + 34 177 RNA→ hypo→env-751 SRB FXPBX6M01DKD8X + 280 438 RNA→ hypo→env-752 2033984030 - 255 114 RNA→ ←hypoenv-753 A5 c1 Cons99328 - 623 486 RNA→ SCRAP12 (SCRAP12)→env-754 sg4i contig18357 + 8747 8895 RNA→ 2a38 (TIGR00933)→ TrkA (COG0569)→


46

env-755 2033462024 + 77 220 RNA→ hypo→env-756 SRB FXPBX6M01ADBKM + 145 264 RNA→ hypo→env-757 DCrCPGB c499973 + 53 215 RNA→env-758 soil XZS51199 y1 + 74 220 RNA→ ←PepN (COG0308)

env-759 DCrCPGB c625461 + 35 204 RNA→ hypo→env-760 LWFCAn GLQU6AQ01DPWR8 + 168 303 RNA→ hypo→env-761 B3 all c Cons108166 - 358 224 RNA→ ←hypo

env-762 botACOD GAKN62C01AX7LG - 148 24 RNA→env-763 LWFCAnN GO09JKT02JO199 + 193 330 RNA→env-764 topACOD F95O9CU01BIXQW + 103 249 RNA→env-765 botACOD F64RS5002GNKJN - 244 85 RNA→env-766 P3 CLC Cons51436 - 386 208 RNA→ hypo→env-767 DCrCPGB c157332 + 279 479 RNA→env-768 2015272387 + 660 784 RNA→env-769 ASLM20b GM71RDO02GKP8N - 288 153 RNA→env-770 LWAeNiSIP F6BA1ZZ02H90GP - 228 82 RNA→env-771 4463936.3.193565 + 150 295 RNA→env-772 botACOD F64RS5002G606Q - 270 89 RNA→ hypo→env-773 LWFCAn GLO1YSU01E3GKP + 194 349 RNA→env-774 ZhangC39687 1 - 147 9 RNA→env-775 SRS015209 WUGC scaffold 29276 + 75 227 RNA→ metagenemark→ NLPC P60 (pfam00877)→env-776 SRS015893 WUGC scaffold 30748 - 366 214 RNA→ metagenemark→env-777 SRS015941 WUGC scaffold 12219 - 579 427 RNA→ metagenemark→env-778 SRS018591 WUGC scaffold 12623 + 1917 2069 RNA→ NLPC P60 (pfam00877)→env-779 SRS020220 Baylor scaffold 42414 + 432 584 RNA→ metagenemark→env-780 SRS021954 Baylor scaffold 37794 - 534 382 RNA→ metagenemark→env-781 SRS051791 LANL scaffold 9526 + 778 930 RNA→ metagenemark→ Spr (COG0791)→env-782 SRS053854 LANL scaffold 37315 + 37 189 RNA→ NLPC P60 (pfam00877)→env-783 SRS024081 LANL scaffold 73922 + 719 871 RNA→env-784 SRS062544 LANL scaffold 21292 - 176 24 RNA→env-785 SRS017808 Baylor scaffold 12370 - 266 114 RNA→env-786 SRS024318 LANL scaffold 17843 + 896 1048 RNA→env-787 SRS013502 Baylor scaffold 25230 + 150 302 RNA→ metagenemark→env-788 SRS019327 WUGC scaffold 6021 - 274 122 RNA→env-789 SRS023557 Baylor scaffold 19080 - 280 128 RNA→env-790 SRS051791 LANL scaffold 53274 - 603 451 RNA→ metagenemark→env-791 SRS011140 Baylor scaffold 27818 + 253 405 RNA→env-792 SRS013234 C2951910 + 343 495 RNA→env-793 SRS013818 Baylor scaffold 7496 + 3755 3907 RNA→ NLPC P60 (pfam00877)→env-794 SRS014124 WUGC scaffold 17544 - 288 136 RNA→ ←metagenemarkenv-795 SRS015797 WUGC scaffold 29635 - 282 130 RNA→env-796 SRS016002 WUGC scaffold 62580 + 894 1046 RNA→env-797 SRS017808 Baylor scaffold 12930 - 266 114 RNA→env-798 SRS018145 Baylor scaffold 12476 + 2218 2370 RNA→ NLPC P60 (pfam00877)→env-799 SRS020220 Baylor scaffold 14170 + 4109 4261 RNA→ NLPC P60 (pfam00877)→env-800 SRS023958 Baylor scaffold 34307 + 781 933 RNA→ NLPC P60 (pfam00877)→env-801 SRS024441 LANL scaffold 9242 + 2280 2432 RNA→env-802 SRS024580 LANL scaffold 45034 + 438 590 RNA→env-803 SRS044662 LANL scaffold 1827 + 9417 9569 RNA→ metagenemark→env-804 SRS050244 LANL scaffold 42097 - 300 148 RNA→ metagenemark→env-805 SRS052227 LANL scaffold 21591 + 1378 1530 RNA→ metagenemark→env-806 SRS053854 LANL scaffold 37593 + 438 590 RNA→ metagenemark→


47

env-807 SRS057205 LANL scaffold 53439 + 709 861 RNA→env-808 SRS057355 C2296460 + 261 413 RNA→env-809 SRS057692 LANL scaffold 15653 - 288 136 RNA→ ←metagenemarkenv-810 SRS058336 LANL scaffold 56469 + 1647 1799 RNA→env-811 SRS062761 LANL scaffold 28752 - 274 122 RNA→env-812 SRS063193 LANL scaffold 25786 - 300 148 RNA→ metagenemark→env-813 SRS062540 C2314588 + 311 463 RNA→env-814 SRS015395 C2380068 + 434 586 RNA→env-815 SRS017713 C3331255 + 435 587 RNA→env-816 SRS018439 Baylor scaffold 14613 - 288 136 RNA→env-817 SRS019974 Baylor scaffold 38280 - 288 136 RNA→env-818 SRS022143 WUGC scaffold 49266 - 564 412 RNA→ metagenemark→env-819 SRS045127 LANL scaffold 29585 - 279 127 RNA→env-820 SRS049389 WUGC scaffold 44162 + 856 1008 RNA→env-821 SRS020334 Baylor scaffold 8632 + 1238 1390 RNA→env-822 SRS013946 C725710 + 420 571 RNA→ metagenemark→env-823 SRS014271 C2919516 + 776 927 RNA→ metagenemark→env-824 SRS017120 Baylor scaffold 21193 - 287 136 RNA→ metagenemark→env-825 SRS019026 WUGC scaffold 20761 - 204 53 RNA→env-826 SRS021496 Baylor scaffold 59252 + 186 337 RNA→ metagenemark→env-827 SRS024318 LANL scaffold 21591 - 291 140 RNA→ metagenemark→env-828 SRS014686 C870695 + 194 345 RNA→env-829 SRS015537 WUGC scaffold 12163 - 327 176 RNA→ metagenemark→env-830 SRS017713 Baylor scaffold 9740 + 1138 1289 RNA→ NLPC P60 (pfam00877)→env-831 SRS013234 Baylor scaffold 22689 + 1896 2047 RNA→ metagenemark→env-832 SRS015395 WUGC scaffold 10967 + 72 223 RNA→ metagenemark→env-833 SRS020220 Baylor scaffold 22748 - 274 123 RNA→ metagenemark→env-834 SRS020334 Baylor scaffold 17866 - 273 122 RNA→ metagenemark→env-835 SRS021954 Baylor scaffold 46848 + 422 573 RNA→env-836 SRS023557 Baylor scaffold 17159 - 271 120 RNA→ metagenemark→env-837 SRS044373 WUGC scaffold 50829 + 247 398 RNA→ metagenemark→env-838 SRS051791 LANL scaffold 10721 - 907 756 RNA→ NLPC P60 (pfam00877)→env-839 SRS053603 LANL scaffold 1191 - 728 577 RNA→ NLPC P60 (pfam00877)→env-840 SRS053854 LANL scaffold 41417 + 65 216 RNA→ NLPC P60 (pfam00877)→env-841 SRS054687 LANL scaffold 16303 - 287 136 RNA→ metagenemark→env-842 SRS015440 C2494351 + 134 285 RNA→env-843 SRS014578 WUGC scaffold 53219 - 458 307 RNA→ metagenemark→env-844 SRS012285 Baylor scaffold 58071 - 273 122 RNA→ metagenemark→env-845 SRS015215 C2518492 + 340 491 RNA→env-846 SRS015899 C1792485 - 279 128 RNA→ metagenemark→env-847 SRS017139 Baylor scaffold 85238 - 479 328 RNA→ metagenemark→env-848 SRS018394 C3939873 + 185 336 RNA→ metagenemark→env-849 SRS021477 Baylor scaffold 57953 - 467 316 RNA→ metagenemark→env-850 SRS023938 Baylor scaffold 65956 - 541 390 RNA→ metagenemark→env-851 SRS024087 C3433094 + 186 337 RNA→ metagenemark→env-852 SRS024289 LANL scaffold 46272 + 181 332 RNA→env-853 SRS016002 WUGC scaffold 36290 - 466 315 RNA→ metagenemark→env-854 SRS017209 Baylor scaffold 27434 + 42 193 RNA→env-855 SRS058336 C1987887 + 42 193 RNA→ metagenemark→env-856 SRS063288 LANL scaffold 22271 + 325 476 RNA→ metagenemark→env-857 SRS017439 C3822425 - 287 136 RNA→env-858 SRS016225 WUGC scaffold 25760 - 193 42 RNA→


48

env-859 SRS011140 Baylor scaffold 18521 - 287 136 RNA→ metagenemark→env-860 SRS013818 Baylor scaffold 5194 + 355 506 RNA→ metagenemark→env-861 SRS015644 C1835361 + 78 229 RNA→ metagenemark→env-862 SRS017808 Baylor scaffold 34240 - 279 128 RNA→ metagenemark→env-863 SRS022621 Baylor scaffold 65815 - 327 176 RNA→ metagenemark→env-864 SRS024138 Baylor scaffold 25058 + 423 574 RNA→ NLPC P60 (pfam00877)→env-865 SRS024441 LANL scaffold 11817 + 375 526 RNA→ NLPC P60 (pfam00877)→env-866 SRS047824 WUGC scaffold 29753 - 275 124 RNA→ metagenemark→env-867 SRS057205 LANL scaffold 31577 - 275 124 RNA→ metagenemark→env-868 SRS064774 LANL scaffold 43268 + 105 256 RNA→ metagenemark→env-869 SRS013164 Baylor scaffold 24313 + 655 806 RNA→ NLPC P60 (pfam00877)→env-870 SRS013502 Baylor scaffold 7917 - 354 203 RNA→ metagenemark→env-871 SRS015650 C1056356 + 185 336 RNA→env-872 SRS015797 WUGC scaffold 19932 - 306 155 RNA→ metagenemark→env-873 SRS016501 LANL scaffold 22572 + 282 433 RNA→ NLPC P60 (pfam00877)→env-874 SRS016529 Baylor scaffold 20250 + 3 154 RNA→ NLPC P60 (pfam00877)→env-875 SRS018145 Baylor scaffold 32385 + 894 1045 RNA→env-876 SRS018357 Baylor scaffold 9877 - 190 39 RNA→env-877 SRS018975 C1710263 - 230 79 RNA→env-878 SRS019028 WUGC scaffold 38358 + 203 354 RNA→ metagenemark→env-879 SRS019974 Baylor scaffold 50655 + 108 259 RNA→env-880 SRS023926 Baylor scaffold 6920 - 166 15 RNA→env-881 SRS023958 Baylor scaffold 35323 + 465 616 RNA→env-882 SRS024015 Baylor scaffold 16133 - 287 136 RNA→ metagenemark→env-883 SRS024081 LANL scaffold 20940 + 198 349 RNA→env-884 SRS043663 LANL scaffold 2520 + 762 913 RNA→env-885 SRS047210 WUGC scaffold 22611 + 168 319 RNA→env-886 SRS050628 C1823703 - 176 25 RNA→env-887 SRS051378 C1730183 - 241 90 RNA→env-888 SRS056622 LANL scaffold 30982 - 645 494 RNA→ ←metagenemark

env-889 SRS057692 LANL scaffold 25367 - 425 274 RNA→ metagenemark→env-890 SRS062540 LANL scaffold 60771 - 190 39 RNA→env-891 SRS022719 LANL scaffold 31065 - 5159 5008 RNA→ NLPC P60 (pfam00877)→env-892 SRS044662 LANL scaffold 7949 + 1298 1449 RNA→env-893 SRS049318 LANL scaffold 98673 - 255 103 RNA→env-894 SRS062544 C2872275 + 211 362 RNA→env-895 SRS013533 C5468474 + 25 176 RNA→ metagenemark→env-896 SRS018300 Baylor scaffold 21833 + 424 576 RNA→ metagenemark→env-897 SRS016037 WUGC scaffold 15710 + 2356 2508 RNA→ metagenemark→env-898 SRS024277 C2798980 + 403 555 RNA→env-899 SRS044373 WUGC scaffold 59225 - 370 218 RNA→ metagenemark→env-900 SRS013948 WUGC scaffold 18695 + 700 852 RNA→env-901 SRS015434 WUGC scaffold 45082 + 405 557 RNA→env-902 SRS019126 C2117330 + 235 387 RNA→env-903 SRS023926 Baylor scaffold 47759 + 4107 4259 RNA→env-904 SRS013946 C696373 + 216 375 RNA→env-905 SRS011243 Baylor scaffold 20835 - 252 96 RNA→env-906 SRS013502 Baylor scaffold 29185 - 281 125 RNA→ metagenemark→env-907 SRS014124 C2585666 - 478 322 RNA→ metagenemark→env-908 SRS014470 C3615294 - 227 71 RNA→env-909 SRS015272 C3517229 + 414 570 RNA→env-910 SRS015395 C2354882 - 473 317 RNA→ metagenemark→


49

env-911 SRS015537 C1232842 + 39 195 RNA→ metagenemark→env-912 SRS015644 C1841321 + 45 201 RNA→ metagenemark→env-913 SRS015941 C3434738 + 274 430 RNA→env-914 SRS016037 C1957702 - 393 237 RNA→ metagenemark→env-915 SRS016342 Baylor scaffold 62195 - 823 667 RNA→ NLPC P60 (pfam00877)→env-916 SRS016501 C1496219 - 295 139 RNA→ metagenemark→env-917 SRS016529 Baylor scaffold 18243 - 601 445 RNA→ metagenemark→env-918 SRS017533 C4069947 - 442 286 RNA→ metagenemark→env-919 SRS017713 C3345055 - 397 241 RNA→ metagenemark→env-920 SRS018591 WUGC scaffold 21510 + 39 195 RNA→ metagenemark→env-921 SRS018791 WUGC scaffold 32930 - 609 453 RNA→ metagenemark→env-922 SRS018969 C2854279 - 225 69 RNA→env-923 SRS019045 WUGC scaffold 14625 + 524 680 RNA→ NLPC P60 (pfam00877)→env-924 SRS019219 C2777913 + 157 313 RNA→env-925 SRS019974 Baylor scaffold 52506 + 8846 9002 RNA→ NLPC P60 (pfam00877)→env-926 SRS020334 Baylor scaffold 23089 + 360 516 RNA→env-927 SRS020856 Baylor scaffold 42082 + 1028 1184 RNA→ metagenemark→env-928 SRS021954 C2940521 - 265 109 RNA→env-929 SRS023557 C1745520 + 665 821 RNA→env-930 SRS023835 Baylor scaffold 21286 - 1308 1152 RNA→ NLPC P60 (pfam00877)→env-931 SRS024015 C3054091 + 360 516 RNA→ metagenemark→env-932 SRS024318 C3599134 - 227 71 RNA→env-933 SRS024637 C2378698 - 225 69 RNA→env-934 SRS042131 WUGC scaffold 20506 - 562 406 RNA→ metagenemark→env-935 SRS043663 C4067308 - 688 532 RNA→ NLPC P60 (pfam00877)→env-936 SRS044373 WUGC scaffold 14752 - 1899 1743 RNA→ NLPC P60 (pfam00877)→env-937 SRS044486 WUGC scaffold 33478 + 875 1031 RNA→ NLPC P60 (pfam00877)→env-938 SRS052227 LANL scaffold 5830 + 554 710 RNA→ metagenemark→env-939 SRS054687 C3488332 + 1040 1196 RNA→env-940 SRS055426 LANL scaffold 41547 + 296 452 RNA→ NLPC P60 (pfam00877)→env-941 SRS056323 C2451592 - 225 69 RNA→env-942 SRS057791 LANL scaffold 33580 - 1120 964 RNA→ NLPC P60 (pfam00877)→env-943 SRS062540 LANL scaffold 41185 - 827 671 RNA→ NLPC P60 (pfam00877)→env-944 SRS062761 LANL scaffold 47648 - 911 755 RNA→ NLPC P60 (pfam00877)→env-945 SRS063193 C2748229 + 142 298 RNA→ metagenemark→env-946 SRS077736 LANL scaffold 21822 - 601 445 RNA→ metagenemark→env-947 SRS015057 WUGC scaffold 7668 - 227 71 RNA→env-948 SRS018739 C3681075 - 823 667 RNA→ NLPC P60 (pfam00877)→env-949 SRS042643 WUGC scaffold 30220 - 367 211 RNA→env-950 SRS047824 WUGC scaffold 3677 - 227 71 RNA→env-951 SRS053603 LANL scaffold 68443 - 288 132 RNA→env-952 SRS013705 C3617702 - 306 150 RNA→env-953 SRS014573 C3618435 + 271 427 RNA→env-954 SRS015762 WUGC scaffold 47952 + 420 576 RNA→env-955 SRS016225 C3015932 + 2857 3013 RNA→env-956 SRS016569 Baylor scaffold 5132 - 227 71 RNA→env-957 SRS018439 Baylor scaffold 59388 + 601 757 RNA→ NLPC P60 (pfam00877)→env-958 SRS047219 WUGC scaffold 4171 - 225 69 RNA→env-959 SRS057205 C3467074 - 185 29 RNA→env-960 SRS062544 C3030826 + 1913 2069 RNA→ metagenemark→env-961 SRS063193 C2841153 - 293 137 RNA→env-962 SRS019607 WUGC scaffold 36887 - 2036 1880 RNA→ NLPC P60 (pfam00877)→


50

env-963 SRS012279 Baylor scaffold 66546 + 1968 2124 RNA→ NLPC P60 (pfam00877)→env-964 SRS015038 C1936743 - 1684 1528 RNA→ NLPC P60 (pfam00877)→env-965 SRS015209 WUGC scaffold 28219 - 7265 7109 RNA→ NLPC P60 (pfam00877)→env-966 SRS015941 C3470345 - 225 69 RNA→env-967 SRS018591 WUGC scaffold 10959 - 210 54 RNA→env-968 SRS020220 C3560517 + 376 532 RNA→env-969 SRS022077 C2543725 + 323 479 RNA→env-970 SRS024318 C3552213 - 198 42 RNA→env-971 SRS056323 C2617390 + 1102 1258 RNA→env-972 SRS056622 LANL scaffold 41741 - 291 135 RNA→env-973 AglaG F499EG101B36X5 - 520 359 RNA→ hypo→env-974 AglaG GBVDVLI01BZNOL - 295 137 RNA→ ←hypo

env-975 AglaG GDN60OX02G1PMR + 88 247 RNA→ hypo→env-976 AglaG contig04581 + 198 357 RNA→ NLPC P60 (pfam00877)→env-977 orpgwFw301 FCAY2397 y1 - 664 506 RNA→ COG2268 (COG2268)→env-978 botACOD GAKN62C01AWF5G + 182 342 RNA→env-979 MA55A contig03431 + 420 541 RNA→ DUF2294 (pfam10057)→ TrkA (COG0569)→ TrkA (COG0569)→env-980 DCrCPGB c84338 - 485 311 RNA→ LysM (cd00118)→env-981 A5 c1 Cons600 + 233 474 RNA→ hypo→env-982 A2 c1 Cons51467 + 226 467 RNA→ hypo→env-983 AglaG contig20244 + 56 235 RNA→ NLPC P60 (pfam00877)→env-984 AglaG F499EG101DVUTQ + 133 312 RNA→ ←hypo

env-985 FNTS067 GJ87FRN01B31JY + 57 207 RNA→ hypo→env-986 DHTCA2 GJDNVXK01D1FSF - 176 7 RNA→env-987 A5 c1 Cons11167 + 514 659 RNA→ Putative peptidoglycan-binding domain-containing protein→env-988 A5 c1 Cons3059 - 923 779 RNA→ Polysacc synt (pfam01943)→env-989 A2 c1 Cons29970 - 448 305 RNA→ PG binding 1 (pfam01471)→env-990 SRB FXPBX6M01CU949 + 138 283 RNA→ ←hypoenv-991 DCrCPGB c335144 - 302 103 RNA→ hypo→env-992 DCrCPGB c66544 + 161 442 RNA→ hypo→env-993 topACOD F95O9CU01EGPRB - 368 218 RNA→env-994 PRSSGFe2 Sequence0000015351 - 1387 1256 RNA→ COG3584 (COG3584)spore SleB (TIGR02869)→ Glo EDI BRP like (cd06587)→ hypo→env-995 A5 c1 Cons15732 + 211 391 RNA→ ←hypo

env-996 DCrCPGB c215890 + 55 250 RNA→ hypo→env-997 soil Contig23861 - 228 83 RNA→env-998 DCrCPGB c19686 - 634 493 RNA→ Peptidase M23 (pfam01551)→env-999 DCrCPGB c109887 + 105 243 RNA→ hypo→env-1000 A5 c1 Cons46125 + 486 654 RNA→ RlpA (COG0797)→env-1001 MA55A GIRCX1H02HJ4PH - 223 90 RNA→ ←hypoenv-1002 A2 c1 Cons32455 - 376 233 RNA→ hypo→env-1003 2033827214 - 481 327 RNA→ hypo→env-1004 A5 c1 Cons72861 + 266 417 RNA→ hypo→env-1005 DCrCPGB c374732 - 421 272 RNA→ PG binding 1 (pfam01471)→env-1006 Cons28689 + 66 271 RNA→ rlpA (TIGR00413)→env-1007 SRS014476 C3283569 - 208 54 RNA→env-1008 SRS013252 Baylor scaffold 60253 - 955 800 RNA→ NLPC P60 (pfam00877)→env-1009 SRS013533 C5390701 - 397 242 RNA→ metagenemark→env-1010 SRS015574 C3153713 - 180 25 RNA→env-1011 SRS016575 Baylor scaffold 54606 - 731 576 RNA→ NLPC P60 (pfam00877)→env-1012 SRS017139 Baylor scaffold 102317 - 934 779 RNA→ NLPC P60 (pfam00877)→env-1013 SRS017511 C3359116 + 107 262 RNA→env-1014 SRS017691 C4984448 + 105 260 RNA→


51

env-1015 SRS018975 C1815381 + 128 283 RNA→ NLPC P60 (pfam00877)→env-1016 SRS020340 C2959156 + 157 312 RNA→ NLPC P60 (pfam00877)→env-1017 SRS022536 C4402721 + 35 190 RNA→env-1018 SRS023595 C7130928 + 35 190 RNA→ metagenemark→env-1019 SRS024087 LANL scaffold 65177 + 480 635 RNA→env-1020 SRS024355 LANL scaffold 79071 - 232 77 RNA→env-1021 SRS024649 C3532660 - 283 128 RNA→env-1022 SRS047113 C5050169 - 230 75 RNA→env-1023 SRS051244 C3324876 + 77 232 RNA→env-1024 SRS065099 LANL scaffold 98603 - 932 777 RNA→ NLPC P60 (pfam00877)→env-1025 SRS051941 C4020472 + 112 267 RNA→ metagenemark→env-1026 84978035 + 697 828 RNA→env-1027 LWAnNN GHFF8UE02GX36V - 274 114 RNA→env-1028 SRB FXPBX6M01CVNKY - 383 227 RNA→env-1029 topACOD F95O9CU02HUDDQ + 188 357 RNA→ ←hypo

env-1030 A5 c1 Cons32246 + 3102 3244 RNA→ Peptidase M23 (pfam01551)→ Peptidase M23 (pfam01551)→env-1031 ASLM90b GJFDWOI02GR4EZ - 125 2 RNA→env-1032 FNTS GKKEVUV02IG46Z + 38 214 RNA→ hypo→env-1033 soil XZS12033 b1 + 312 480 RNA→ Transglycosylase (pfam06737)→env-1034 LWAnNN GHFF8UE02FT7AF + 224 413 RNA→ ←hypoenv-1035 LWSO NODE 1534 - 1139 956 RNA→ NLPC P60 (pfam00877)→env-1036 LWSO NODE 2113 + 669 867 RNA→ NLPC P60 (pfam00877)→env-1037 LWAeNNiSIP GDP3C2T02HXQON + 52 217 RNA→ hypo→env-1038 LWAnNN GDP3C2T02HXQON + 52 217 RNA→ hypo→env-1039 DCrCPGB c574318 - 353 219 RNA→ hypo→env-1040 A5 c1 Cons56200 + 357 506 RNA→ hypo→env-1041 DCrCPGB c186159 + 71 307 RNA→ hypo→env-1042 botACOD GAKN62C01ANGV8 + 65 205 RNA→ hypo→env-1043 A5 c1 Cons3357 - 536 370 RNA→ Transglycosylase (pfam06737)→env-1044 botACOD GAKN62C01D9NW9 + 51 216 RNA→ hypo→env-1045 A2 c1 Cons51004 + 277 459 RNA→ ←hypoenv-1046 A5 c1 Cons73662 + 378 560 RNA→ hypo→env-1047 DCrCPGB c812094 + 67 244 RNA→env-1048 SwRhRL3b contig 4197842 + 299 450 RNA→ hypo→env-1049 SwRhRL2b contig 3410220 + 183 334 RNA→ Amino acid transporters→env-1050 GXP7IEG01D15KU + 42 157 RNA→ Sodium/hydrogen exchanger family.→env-1051 PRSSGFe2 Sequence0000049075 - 534 405 RNA→ hypo→env-1052 PRSSGFe2 Sequence0000023899 + 219 351 RNA→ NLPC P60 (pfam00877)PG binding 1 (pfam01471)→env-1053 FNTS GKKEVUV01EDXUT + 76 233 RNA→ Transglycosylase (pfam06737)→env-1054 2031563704 + 246 371 RNA→ hypo→env-1055 LWSO2 GGWJX9X01EDPVT - 152 5 RNA→env-1056 2044686907 - 174 38 RNA→env-1057 DCrCPGB c306232 - 451 305 RNA→ hypo→env-1058 DCrCPGB c679332 - 299 172 RNA→ hypo→env-1059 GBANfinal FHNL2OP04YQQPN - 215 35 RNA→ hypo→env-1060 LWFCA GLZZ6Z001B21ZY - 282 120 RNA→ ←hypoenv-1061 LWFCA GLRXTHP02JTMLC - 472 310 RNA→ ←hypo

env-1062 LWFCA GLRXTHP02HS739 - 417 254 RNA→ ←hypoenv-1063 lwComb lwCombC18848 + 344 508 RNA→ hypo→env-1064 Cons46233 - 568 434 RNA→ hypo→env-1065 SRS011098 Baylor scaffold 30832 - 5963 5800 RNA→ NLPC P60 (pfam00877)→env-1066 SRS011126 C4691332 - 1648 1485 RNA→ NLPC P60 (pfam00877)→


52

env-1067 SRS011152 C4382521 - 465 302 RNA→ metagenemark→env-1068 SRS011255 Baylor scaffold 72789 + 2239 2402 RNA→ NLPC P60 (pfam00877)→env-1069 SRS013170 Baylor scaffold 26341 + 46682 46845 RNA→ NLPC P60 (pfam00877)→env-1070 SRS013252 C3680022 + 577 740 RNA→ NLPC P60 (pfam00877)→env-1071 SRS013533 PGA scaffold 79860 - 1992 1829 RNA→ NLPC P60 (pfam00877)→env-1072 SRS013836 C4788452 + 528 691 RNA→ metagenemark→env-1073 SRS013949 WUGC scaffold 21113 - 1269 1106 RNA→ NLPC P60 (pfam00877)→env-1074 SRS014476 C3466376 - 468 305 RNA→ metagenemark→env-1075 SRS014578 WUGC scaffold 46583 - 1748 1585 RNA→ NLPC P60 (pfam00877)→env-1076 SRS014894 WUGC scaffold 38821 + 2291 2454 RNA→ NLPC P60 (pfam00877)→env-1077 SRS015044 WUGC scaffold 71275 + 1459 1622 RNA→ metagenemark→env-1078 SRS015063 WUGC scaffold 30033 - 4054 3891 RNA→ NLPC P60 (pfam00877)→env-1079 SRS015158 WUGC scaffold 34226 - 5215 5052 RNA→ NLPC P60 (pfam00877)→env-1080 SRS015278 WUGC scaffold 15735 - 1029 866 RNA→ NLPC P60 (pfam00877)→env-1081 SRS015378 C1032108 - 472 309 RNA→ metagenemark→env-1082 SRS015440 WUGC scaffold 32244 + 4253 4416 RNA→ NLPC P60 (pfam00877)→env-1083 SRS015470 WUGC scaffold 59493 + 2345 2508 RNA→ NLPC P60 (pfam00877)→env-1084 SRS015574 C3425029 + 614 777 RNA→env-1085 SRS015650 WUGC scaffold 20122 + 390 553 RNA→ NLPC P60 (pfam00877)→env-1086 SRS015755 WUGC scaffold 8063 - 1581 1418 RNA→ NLPC P60 (pfam00877)→env-1087 SRS015803 WUGC scaffold 2978 - 3388 3225 RNA→ NLPC P60 (pfam00877)→env-1088 SRS015899 WUGC scaffold 43214 + 9955 10118 RNA→ NLPC P60 (pfam00877)→env-1089 SRS015989 WUGC scaffold 13289 - 3934 3771 RNA→ NLPC P60 (pfam00877)→env-1090 SRS016043 WUGC scaffold 64212 + 617 780 RNA→ metagenemark→env-1091 SRS016092 WUGC scaffold 32080 + 2088 2251 RNA→ NLPC P60 (pfam00877)→env-1092 SRS016200 WUGC scaffold 33802 + 1466 1629 RNA→ NLPC P60 (pfam00877)→env-1093 SRS016331 C4205400 - 602 439 RNA→ NLPC P60 (pfam00877)→env-1094 SRS016360 Baylor scaffold 63533 + 429 592 RNA→ metagenemark→env-1095 SRS016746 Baylor scaffold 5037 + 30673 30836 RNA→ NLPC P60 (pfam00877)→env-1096 SRS017025 Baylor scaffold 1020 - 655 492 RNA→ NLPC P60 (pfam00877)→env-1097 SRS017227 Baylor scaffold 23742 - 1434 1271 RNA→ NLPC P60 (pfam00877)→env-1098 SRS017304 C1972165 - 269 106 RNA→env-1099 SRS017445 Baylor scaffold 80704 + 1134 1297 RNA→ NLPC P60 (pfam00877)→env-1100 SRS017511 Baylor scaffold 93178 - 31128 30965 RNA→ NLPC P60 (pfam00877)→env-1101 SRS018157 Baylor scaffold 4558 - 2141 1978 RNA→ metagenemark→env-1102 SRS018394 Baylor scaffold 42748 + 1570 1733 RNA→ NLPC P60 (pfam00877)→env-1103 SRS018573 WUGC scaffold 38007 - 2473 2310 RNA→ NLPC P60 (pfam00877)→env-1104 SRS018665 C3792735 + 1459 1622 RNA→ metagenemark→env-1105 SRS018778 C1280955 - 462 299 RNA→ metagenemark→env-1106 SRS019077 WUGC scaffold 68058 - 2682 2519 RNA→ NLPC P60 (pfam00877)→env-1107 SRS019128 C4420576 + 1008 1171 RNA→ metagenemark→env-1108 SRS019225 C1600595 - 474 311 RNA→ metagenemark→env-1109 SRS019333 C1286004 + 775 938 RNA→env-1110 SRS019387 WUGC scaffold 22140 - 623 460 RNA→ metagenemark→env-1111 SRS019591 WUGC scaffold 31176 + 257 420 RNA→ metagenemark→env-1112 SRS019906 WUGC scaffold 52432 - 1369 1206 RNA→ NLPC P60 (pfam00877)DivIVA (pfam05103)→env-1113 SRS019980 C3049230 + 351 514 RNA→ NLPC P60 (pfam00877)→env-1114 SRS020340 C2955345 + 351 514 RNA→ metagenemark→env-1115 SRS021477 Baylor scaffold 65865 - 1554 1391 RNA→ NLPC P60 (pfam00877)→env-1116 SRS021960 Baylor scaffold 2449 - 561 398 RNA→ metagenemark→env-1117 SRS022149 C2685542 - 367 204 RNA→ metagenemark→env-1118 SRS022536 LANL scaffold 69944 - 1644 1481 RNA→ NLPC P60 (pfam00877)→


53

env-1119 SRS022725 LANL scaffold 9173 - 561 398 RNA→ metagenemark→env-1120 SRS023538 Baylor scaffold 17267 + 2589 2752 RNA→ metagenemark→env-1121 SRS023595 C7010996 + 218 381 RNA→env-1122 SRS023964 Baylor scaffold 66014 - 13016 12853 RNA→ NLPC P60 (pfam00877)→env-1123 SRS024021 Baylor scaffold 11455 + 6593 6756 RNA→ NLPC P60 (pfam00877)→env-1124 SRS024289 LANL scaffold 42941 + 1816 1979 RNA→ NLPC P60 (pfam00877)→env-1125 SRS024381 LANL scaffold 28277 - 4753 4590 RNA→ NLPC P60 (pfam00877)→env-1126 SRS024447 C3946289 - 455 292 RNA→ metagenemark→env-1127 SRS024649 C3649189 + 420 583 RNA→ metagenemark→env-1128 SRS042984 C4057433 + 390 553 RNA→ NLPC P60 (pfam00877)→env-1129 SRS043018 WUGC scaffold 53541 + 1933 2096 RNA→ NLPC P60 (pfam00877)→env-1130 SRS043755 C2370493 + 577 740 RNA→ metagenemark→env-1131 SRS043772 WUGC scaffold 20147 + 351 514 RNA→ metagenemark→env-1132 SRS045197 WUGC scaffold 54492 + 1620 1783 RNA→ NLPC P60 (pfam00877)→env-1133 SRS045313 C1328403 + 222 385 RNA→env-1134 SRS047100 WUGC scaffold 29617 + 575 738 RNA→ NLPC P60 (pfam00877)→env-1135 SRS047113 LANL scaffold 77949 - 1269 1106 RNA→ NLPC P60 (pfam00877)→env-1136 SRS047265 WUGC scaffold 21708 + 1458 1621 RNA→ NLPC P60 (pfam00877)→env-1137 SRS047634 C4427416 + 553 716 RNA→env-1138 SRS049268 LANL scaffold 16588 + 1462 1625 RNA→ NLPC P60 (pfam00877)→env-1139 SRS051244 C3397963 - 282 119 RNA→ metagenemark→env-1140 SRS051941 C4068888 - 466 303 RNA→ metagenemark→env-1141 SRS052604 C1789241 + 352 515 RNA→env-1142 SRS052876 C2120887 - 202 39 RNA→env-1143 SRS053584 C2093820 - 1269 1106 RNA→ NLPC P60 (pfam00877)→env-1144 SRS054430 C2083433 - 282 119 RNA→ metagenemark→env-1145 SRS054653 LANL scaffold 38508 - 1211 1048 RNA→ NLPC P60 (pfam00877)→env-1146 SRS054776 C1546144 - 226 63 RNA→env-1147 SRS055378 LANL scaffold 91193 + 1550 1713 RNA→ metagenemark→env-1148 SRS055401 C2347232 - 472 309 RNA→ metagenemark→env-1149 SRS058053 LANL scaffold 84471 - 1569 1406 RNA→ NLPC P60 (pfam00877)→env-1150 SRS058808 C2888121 - 448 285 RNA→ metagenemark→env-1151 SRS063215 C2273020 + 1583 1746 RNA→env-1152 SRS063603 C4204425 - 217 54 RNA→env-1153 SRS063999 LANL scaffold 90125 - 964 801 RNA→ NLPC P60 (pfam00877)→env-1154 SRS064449 LANL scaffold 56898 + 1774 1937 RNA→ NLPC P60 (pfam00877)→env-1155 SRS064493 LANL scaffold 13455 - 38145 37982 RNA→ NLPC P60 (pfam00877)→env-1156 SRS065099 LANL scaffold 51896 + 2767 2930 RNA→ NLPC P60 (pfam00877)→env-1157 SRS012285 Baylor scaffold 65460 - 4368 4205 RNA→ NLPC P60 (pfam00877)→env-1158 SRS017139 Baylor scaffold 106465 - 1152 989 RNA→ NLPC P60 (pfam00877)→env-1159 SRS020862 Baylor scaffold 19536 + 696 859 RNA→ NLPC P60 (pfam00877)→env-1160 SRS024355 C4298096 + 572 735 RNA→ NLPC P60 (pfam00877)→env-1161 2014181892 - 3305 3177 RNA→ STAS SulP like sulfate transporter (cd07042)→ hypo→env-1162 2015257038 - 742 614 RNA→ SUL1 (COG0659)→env-1163 Cons10394 - 2017 1891 RNA→ ←hypoenv-1164 LWAnNiSIP F624WLL02G837Q + 122 298 RNA→ ←hypoenv-1165 LWAnN F624WLL02G837Q + 122 298 RNA→ hypo→env-1166 MA55A F65388E01ADWI6 + 129 269 RNA→ hypo→env-1167 DCrCPGB c116605 - 508 359 RNA→ hypo→env-1168 B3 all c Cons79038 - 2479 2359 RNA→ PotE (COG0531)→ COG2317 (COG2317)→env-1169 B3 all c Cons69039 - 7551 7428 RNA→ PotE (COG0531)→ TonB family C-terminal domain→env-1170 2013518974 + 1346 1544 RNA→ GT1 Sucrose synthase (cd03800)→


54

env-1171 JCVI SCAF 1101668237584 - 1509 1372 RNA→ Band 7 (pfam01145)→env-1172 AglaG GDN60OX02FK2JA - 250 78 RNA→ hypo→env-1173 AglaG contig03525 - 377 205 RNA→ ←hypoenv-1174 P3 CLC Cons39857 - 440 262 RNA→ Spr (COG0791)→env-1175 Cons77943 - 580 402 RNA→ NLPC P60 (pfam00877)→env-1176 P3 CLC Cons62021 - 677 499 RNA→ NLPC P60 (pfam00877)→env-1177 Cons82607 + 331 511 RNA→ NLPC P60 (pfam00877)→ hypo→env-1178 botACOD GAKN62C01EBZN9 + 189 395 RNA→ hypo→env-1179 FNTS067 GJ87FRN01CRQH8 + 87 292 RNA→env-1180 soil Contig28625 + 644 787 RNA→env-1181 DCrCPGB c92986 + 260 449 RNA→ hypo→env-1182 ZhangC67531 1 + 25 178 RNA→env-1183 84802932 + 268 385 RNA→ COG1574 (COG1574)→env-1184 Cons36617 + 229 347 RNA→ Major Facilitator Superfamily.→ Urease gamma (cd00390)→ Urease alpha (cd00375)→env-1185 Cons46520 + 243 364 RNA→ hypo→env-1186 lwComb BCGO23446 y1 - 506 389 RNA→ hypo→env-1187 P3 CLC Cons46203 - 1398 1277 RNA→ Major Facilitator Superfamily.→env-1188 LWSO GLQAYWI01B1PDX + 107 226 RNA→env-1189 P3 CLC Cons99283 - 605 486 RNA→ hypo→env-1190 P3 CLC Cons26451 - 215 98 RNA→env-1191 2033943972 + 20 203 RNA→ SCRAP12 (SCRAP12)→env-1192 LWFCAnN GO09JKT02H9IGT + 60 183 RNA→env-1193 LWFCAnN GO09JKT02HE9E3 - 194 67 RNA→ ←hypoenv-1194 DCrCPGB c83580 - 517 375 RNA→ hypo→env-1195 A2 c1 Cons59355 + 437 590 RNA→ ←hypoenv-1196 84921157 - 567 453 RNA→env-1197 CABL01000002.1 - 184992 184868 RNA→ NLPC P60 (pfam00877)→env-1198 CABO01000018.1 - 113938 113814 RNA→ NLPC P60 (pfam00877)→env-1199 LWAnNNiSIP GDN60OX01AT0B2 + 77 201 RNA→env-1200 P3 CLC Cons121129 - 328 123 RNA→env-1201 Cons21290 + 639 839 RNA→ ←hypoenv-1202 P3 CLC Cons138640 + 299 499 RNA→ ←hypo

env-1203 Cons102170 + 420 623 RNA→ ←hypo

env-1204 Cons98616 + 555 761 RNA→ ←hypoenv-1205 P3 CLC Cons41513 + 1711 1912 RNA→env-1206 P3 CLC Cons40425 - 4385 4182 RNA→ NLPC P60 (pfam00877)→ PFK (cd00363)→ hypo→env-1207 DCrCPGB c93479 - 312 122 RNA→ hypo→env-1208 MA55A contig08214 - 906 785 RNA→ hypo→ SH3b (smart00287)NLPC P60 (pfam00877)→env-1209 2034317547 - 288 157 RNA→ hypo→env-1210 LWSO2 GGWJX9X01DZFLN + 166 296 RNA→ ←hypoenv-1211 topACOD F95O9CU02I57DD + 161 288 RNA→ ←hypo

env-1212 LWFCAnN GO09JKT01A3MHM - 262 110 RNA→env-1213 LWFCAnN GO09JKT01BIZB3 - 406 241 RNA→ hypo→env-1214 SRS023617 Baylor scaffold 32002 - 18013 17895 RNA→ NLPC P60 (pfam00877)PG binding 1 (pfam01471)→ AlaRS core (cd00673)→ DUF965 (pfam06135)→

UPF0081 (pfam03652)→ metagenemark→env-1215 SRS013705 Baylor scaffold 100192 - 2360 2242 RNA→ NLPC P60 (pfam00877)PG binding 1 (pfam01471)→ AlaRS core (cd00673)→env-1216 SRS014684 C3305953 - 825 707 RNA→ NLPC P60 (pfam00877)PG binding 1 (pfam01471)→env-1217 SRS014689 C1298343 + 173 291 RNA→ spore SleB (TIGR02869)→env-1218 SRS015893 C2391923 - 2330 2212 RNA→ NLPC P60 (pfam00877)PG binding 1 (pfam01471)→ AlaRS core (cd00673)→env-1219 SRS016319 C3879795 + 34 152 RNA→ spore SleB (TIGR02869)→env-1220 SRS018300 C3371206 + 1734 1852 RNA→ NLPC P60 (pfam00877)PG binding 1 (pfam01471)→ AlaRS core (cd00673)→env-1221 SRS019027 C1909293 - 266 148 RNA→


55

env-1222 SRS019894 WUGC scaffold 55300 + 1236 1354 RNA→ NLPC P60 (pfam00877)PG binding 1 (pfam01471)→ AlaS (COG0013)→env-1223 SRS042643 WUGC scaffold 35381 - 4395 4277 RNA→ NLPC P60 (pfam00877)PG binding 1 (pfam01471)→ AlaRS core (cd00673)→ AlaS (COG0013)→

DUF965 (pfam06135)→ UPF0081 (pfam03652)→env-1224 SRS047824 WUGC scaffold 28731 - 2677 2559 RNA→ NLPC P60 (pfam00877)PG binding 1 (pfam01471)→ AlaRS core (cd00673)→env-1225 SRS048411 C6936905 + 197 315 RNA→ spore SleB (TIGR02869)→env-1226 SRS053603 LANL scaffold 47177 - 4343 4225 RNA→ NLPC P60 (pfam00877)PG binding 1 (pfam01471)→ AlaRS core (cd00673)→ DUF965 (pfam06135)→

UPF0081 (pfam03652)→ metagenemark→env-1227 SRS053854 LANL scaffold 27495 + 1167 1285 RNA→ NLPC P60 (pfam00877)PG binding 1 (pfam01471)→ AlaRS core (cd00673)→env-1228 SRS064423 LANL scaffold 64160 + 4494 4612 RNA→ NLPC P60 (pfam00877)PG binding 1 (pfam01471)→ AlaRS core (cd00673)→env-1229 SRS065278 LANL scaffold 67692 + 1153 1271 RNA→ NLPC P60 (pfam00877)PG binding 1 (pfam01471)→ AlaRS core (cd00673)→env-1230 SRS014470 C3669014 + 161 279 RNA→ spore SleB (TIGR02869)→env-1231 SRS015057 C3386423 + 167 285 RNA→ spore SleB (TIGR02869)→env-1232 SRS015209 C1821649 - 731 613 RNA→ spore SleB (TIGR02869)→ NLPC P60 (pfam00877)→env-1233 SRS015762 C3648973 + 161 279 RNA→ NLPC P60 (pfam00877)PG binding 1 (pfam01471)→ AlaRS core (cd00673)→env-1234 SRS015941 C3530085 + 2240 2358 RNA→ NLPC P60 (pfam00877)PG binding 1 (pfam01471)→ AlaRS core (cd00673)→env-1235 SRS018591 WUGC scaffold 15083 - 6897 6779 RNA→ NLPC P60 (pfam00877)PG binding 1 (pfam01471)→ AlaRS core (cd00673)→ DUF965 (pfam06135)→

UPF0081 (pfam03652)→ metagenemark→env-1236 SRS018739 C3708389 - 252 134 RNA→env-1237 SRS018791 WUGC scaffold 29000 + 1184 1302 RNA→ NLPC P60 (pfam00877)PG binding 1 (pfam01471)→env-1238 SRS019026 WUGC scaffold 25345 - 423 305 RNA→ spore SleB (TIGR02869)→env-1239 SRS019219 WUGC scaffold 49408 - 16020 15902 RNA→ NLPC P60 (pfam00877)PG binding 1 (pfam01471)→ AlaRS core (cd00673)→ DUF965 (pfam06135)→

UPF0081 (pfam03652)→ metagenemark→env-1240 SRS020220 C3637923 + 1094 1212 RNA→ NLPC P60 (pfam00877)PG binding 1 (pfam01471)→ AlaS (COG0013)→env-1241 SRS020334 C2673943 + 2255 2373 RNA→ NLPC P60 (pfam00877)PG binding 1 (pfam01471)→ AlaRS core (cd00673)→env-1242 SRS022143 WUGC scaffold 7703 + 4450 4568 RNA→ NLPC P60 (pfam00877)PG binding 1 (pfam01471)→ AlaRS core (cd00673)→env-1243 SRS023352 LANL scaffold 54556 + 1629 1747 RNA→ NLPC P60 (pfam00877)PG binding 1 (pfam01471)→ AlaRS core (cd00673)→ DUF965 (pfam06135)→

UPF0081 (pfam03652)→ metagenemark→env-1244 SRS024015 Baylor scaffold 53301 - 750 632 RNA→ NLPC P60 (pfam00877)PG binding 1 (pfam01471)→env-1245 SRS024318 C3776381 - 1238 1120 RNA→ NLPC P60 (pfam00877)PG binding 1 (pfam01471)→ AlaS (COG0013)→env-1246 SRS045715 LANL scaffold 90772 + 1683 1801 RNA→ NLPC P60 (pfam00877)PG binding 1 (pfam01471)→ AlaRS core (cd00673)→ DUF965 (pfam06135)→

UPF0081 (pfam03652)→ metagenemark→env-1247 SRS047210 WUGC scaffold 62936 - 1775 1657 RNA→ NLPC P60 (pfam00877)PG binding 1 (pfam01471)→ AlaRS core (cd00673)→env-1248 SRS048791 LANL scaffold 48430 - 1769 1651 RNA→ NLPC P60 (pfam00877)PG binding 1 (pfam01471)→ AlaRS core (cd00673)→env-1249 SRS049147 C4102490 - 392 274 RNA→ spore SleB (TIGR02869)→env-1250 SRS050244 LANL scaffold 102683 + 1050 1168 RNA→ NLPC P60 (pfam00877)PG binding 1 (pfam01471)→ AlaRS core (cd00673)→env-1251 SRS051791 LANL scaffold 29277 - 6626 6508 RNA→ NLPC P60 (pfam00877)PG binding 1 (pfam01471)→ AlaRS core (cd00673)→ AlaS (COG0013)→

DUF965 (pfam06135)→ UPF0081 (pfam03652)→ metagenemark→env-1252 SRS056323 C2629029 + 590 708 RNA→ NLPC P60 (pfam00877)PG binding 1 (pfam01471)→ AlaRS core (cd00673)→env-1253 SRS056622 LANL scaffold 40322 - 2517 2399 RNA→ NLPC P60 (pfam00877)PG binding 1 (pfam01471)→ AlaRS core (cd00673)→env-1254 SRS057539 C2750461 - 4568 4450 RNA→ NLPC P60 (pfam00877)PG binding 1 (pfam01471)→ AlaRS core (cd00673)→ DUF965 (pfam06135)→

UPF0081 (pfam03652)→ metagenemark→env-1255 SRS057791 LANL scaffold 83664 + 2245 2363 RNA→ spore SleB (TIGR02869)→env-1256 MA55A GIRCX1H02HO3BM - 300 151 RNA→ ←ATZ TRZ like (cd01298)env-1257 2033320051 - 275 146 RNA→ hypo→env-1258 botACOD GAKN62C01ATHSV + 91 229 RNA→ hypo→env-1259 A2 c1 Cons7863 - 837 658 RNA→ NPCBM (pfam08305)→env-1260 A2 c1 Cons22897 + 264 442 RNA→ hypo→env-1261 botACOD FV90NF402HM4XV - 423 296 RNA→ T6PP (TIGR00685)→env-1262 2033903790 + 25 174 RNA→ hypo→env-1263 A5 c1 Cons78164 + 101 246 RNA→ LT GEWL (cd00254)SMC prok B (TIGR02168)SCRAP12 (SCRAP12)→env-1264 HCF12C 2 11838782 + 19 153 RNA→env-1265 HCF12C 149567 - 391 257 RNA→ PG binding 1 (pfam01471)→env-1266 GBANfinal FHNL2OP03RBV4H - 467 345 RNA→ KefB (COG0475)→env-1267 botACOD GAKN62C01DPZTB + 222 352 RNA→ 2a37 (TIGR00932)→


56

env-1268 topACOD FV90NF401E3F9X + 283 449 RNA→env-1269 A2 c1 Cons69909 + 478 610 RNA→env-1270 2016940393 - 762 636 RNA→ PotE (COG0531)→env-1271 LWSO GLQAYWI02FOIFL + 205 352 RNA→ hypo→env-1272 sg4i contig07094 - 342 152 RNA→env-1273 sgz454il contig08290 + 5487 5677 RNA→ ←hypoenv-1274 PBDCA2 FIDWTPW02PPHCF - 226 110 RNA→env-1275 PBDCA2 contig41210 + 504 635 RNA→ hypo→env-1276 DCrCPGB c147387 - 233 85 RNA→ hypo→env-1277 SwiR contig92918 + 335 479 RNA→env-1278 SRB FXPBX6M01CSLPE + 239 384 RNA→env-1279 FNTS067 GJ87FRN01CKBOS + 13 144 RNA→ ←hypo

env-1280 FIHLEPW02RRCFC + 56 182 RNA→env-1281 topACOD F95O9CU01EN1CC + 142 296 RNA→ ←hypoenv-1282 FNTS GKKEVUV01AFSHN - 345 213 RNA→ hypo→env-1283 DCrCPGB c588719 - 192 48 RNA→ hypo→env-1284 SwRhRL3b contig 1314943 + 2033 2203 RNA→ Band 7 (pfam01145)→env-1285 2044174472 - 280 98 RNA→env-1286 orpgwFw301 FCAY25544 y1 + 667 818 RNA→env-1287 Cons110556 - 668 533 RNA→ hypo→env-1288 botACOD F64RS5002GWOGN + 175 309 RNA→env-1289 A5 c1 Cons66684 - 629 501 RNA→ hypo→env-1290 FNTS067 GJ87FRN01BSW03 - 166 15 RNA→env-1291 sg4i contig00662 - 17856 17660 RNA→ NLPC P60 (pfam00877)→env-1292 DCrCPGB c443395 + 68 279 RNA→ Transglycosylase-like domain.→env-1293 FNTS067 GJ87FRN01BPOR6 - 455 263 RNA→ Transglycosylase (pfam06737)→env-1294 sg4i contig08811 - 2014 1868 RNA→ ABCC MRP Like (cd03228)→env-1295 sgz454il contig07405 - 16406 16261 RNA→ ABC OpuCA Osmoprotection (cd03295)→ TM PBP2 (cd06261)→ OpuBC (COG1732)→

MS channel (pfam00924)→env-1296 LWAnN GIDYKCY01BBJO8 + 66 195 RNA→env-1297 Cons2247 + 464 588 RNA→ hypo→env-1298 orpgwFw301 FCAY88126 b1 + 136 266 RNA→ hypo→env-1299 SwRhRL2b contig 3115889 - 588 454 RNA→ hypo→env-1300 sgz454il contig04680 - 3048 2889 RNA→ NLPC P60 (pfam00877)→env-1301 2044430032 + 339 454 RNA→env-1302 PBDCA2 FISUTAU01D4NV3 - 282 163 RNA→ hypo→env-1303 LVIA5G c00082 - 4806 4671 RNA→ 2a38 (TIGR00933)→ TrkA (COG0569)→env-1304 GBANfinal FHNL2OP04ZGMO1 + 99 230 RNA→env-1305 LVIA5G c00006 - 15377 15243 RNA→ hypo→env-1306 B3 all c Cons27049 + 183 341 RNA→ ←hypo

env-1307 MA55A contig08577 - 471 349 RNA→ SH3 3 (pfam08239)→env-1308 PRSSGFe2 Sequence0000001036 + 3206 3368 RNA→ PG binding 1 (pfam01471)→env-1309 A2 c1 Cons22957 - 832 665 RNA→ hypo→env-1310 sg4i contig00487 - 19394 19266 RNA→ NLPC P60 (pfam00877)→env-1311 sgz454il contig00200 + 8428 8556 RNA→ NLPC P60 (pfam00877)→env-1312 sg4i contig00665 + 3813 3956 RNA→ NLPC P60 (pfam00877)→env-1313 sgz454il contig08209 - 7969 7826 RNA→ NLPC P60 (pfam00877)→env-1314 DCrCPGB c415259 + 315 442 RNA→env-1315 2044115400 + 209 339 RNA→env-1316 2044088704 - 372 243 RNA→ hypo→env-1317 FHA1B5K04X4KAL + 160 304 RNA→ hypo→env-1318 BSRL3 Contig 28546 - 237 112 RNA→


57

env-1319 B3 all c Cons119611 - 420 295 RNA→ ←hypo

env-1320 A5 c1 Cons30106 + 5545 5682 RNA→ rlpA (TIGR00413)→env-1321 PRSSGFe2 Sequence0000017119 + 495 633 RNA→ PotE (COG0531)→env-1322 GBANfinal FHNL2OP04X1K0Y - 341 204 RNA→ hypo→env-1323 sg4i contig03433 + 430 569 RNA→ hypo→env-1324 MA55A contig00112 + 1068 1188 RNA→ COG3103 (COG3103)NLPC P60 (pfam00877)→env-1325 FNTS067 GJ87FRN01EUCFW + 22 173 RNA→ hypo→env-1326 Cons15790 + 200 330 RNA→ ←Pro isomerase (pfam00160)

env-1327 FNTS067 GKA24FP01BJMSA - 350 136 RNA→ hypo→ hypo→env-1328 FNTS GKKEVUV02GLDE8 + 116 274 RNA→ Transglycosylase (pfam06737)→env-1329 FNTS067 GJ87FRN01DJG3Y + 24 182 RNA→ ←hypoenv-1330 FNTS067 GJ87FRN01DX610 + 176 361 RNA→ ←hypo

env-1331 FNTS GKKEVUV01DGZ26 + 92 269 RNA→ Transglycosylase (pfam06737)→env-1332 FNTS GKKEVUV02JNS36 + 118 295 RNA→env-1333 FNTS GKKEVUV01BDW14 - 192 6 RNA→ ←hypo

env-1334 FNTS contig02925 - 531 347 RNA→ LysM (cd00118)→env-1335 FNTS GKKEVUV02IXRQX - 365 196 RNA→ Transglycosylase (pfam06737)→env-1336 FIHLEPW02QV9QB - 315 193 RNA→env-1337 2016859377 - 158 34 RNA→env-1338 DHTCA2 contig13941 + 154 304 RNA→env-1339 SRB FXPBX6M01A0PV1 + 95 252 RNA→ hypo→env-1340 TB03JUN2009E Contig 47264 - 505 356 RNA→ hypo→env-1341 LWAeNiSIP F6BA1ZZ02JDSA0 - 436 276 RNA→ Kup (COG3158)→env-1342 4463936.3.194048 + 10 167 RNA→ metagenemark→env-1343 FIHLEPW02SPX9P + 86 243 RNA→ ←hypoenv-1344 2034131602 - 407 274 RNA→ hypo→env-1345 LWSO GLQAYWI02GO8PT - 197 7 RNA→env-1346 lwComb BCHA37346 x1 - 146 18 RNA→env-1347 LWAnNiSIP F624WLL02G3TZM + 56 187 RNA→ hypo→env-1348 LWAnN F624WLL02G3TZM + 56 187 RNA→ hypo→env-1349 LWAnN GIDYKCY01EBE27 - 501 368 RNA→ ←hypoenv-1350 LWSO2 GGWJX9X02GYKRX - 271 139 RNA→env-1351 FIHLEPW02PV3HE + 152 305 RNA→ hypo→env-1352 2033804627 + 110 263 RNA→ hypo→env-1353 SRB FXPBX6M01AQ00Q + 29 181 RNA→ Kup (COG3158)→env-1354 LWSO2 GGWJX9X02GRRGO + 241 365 RNA→env-1355 FNTS067 GJ87FRN01AMWQQ + 354 525 RNA→env-1356 2044144818 - 275 129 RNA→ hypo→env-1357 LWFCAnN GO09JKT02G73RE - 320 196 RNA→ Kup (COG3158)→env-1358 A5 c1 Cons35499 + 440 578 RNA→ hypo→env-1359 soil XZS55206 x1 - 683 555 RNA→ STAS anti-anti-sigma factors (cd07043)→env-1360 2034089194 + 159 321 RNA→ hypo→env-1361 A5 c1 Cons60890 - 461 294 RNA→ hypo→env-1362 A2 c1 Cons44775 - 1362 1195 RNA→ NLPC P60 (pfam00877)→env-1363 XylAfBA GBURWN002C9UF2 - 348 173 RNA→ hypo→env-1364 LWSO NODE 4588 + 481 659 RNA→env-1365 LWSO NODE 2022 + 476 657 RNA→env-1366 2014741532 - 1035 913 RNA→ ←hypoenv-1367 ANASMECb 4085297 C9760 - 1035 913 RNA→ Kup (COG3158)→env-1368 BMHBC 1 1 newblercontig298342 - 280 154 RNA→env-1369 BMHBC 1 1 newblercontig298341 - 272 146 RNA→env-1370 FNTS GKKEVUV02HPG8W - 139 2 RNA→


58

env-1371 RUMENNODE 4366864 51500 - 99637 99522 RNA→ Glycosyltransferase GTB type (cd01635)Glyco tranf GTA type (cd00761)→ GT1 YqgM like (cd03801)→env-1372 DCrCPGB c71140 + 49 248 RNA→ hypo→env-1373 LWSO NODE 2021 + 603 809 RNA→ LysM (cd00118)Transglycosylase (pfam06737)→env-1374 2016869237 + 493 618 RNA→ hypo→env-1375 PRSSGFe2 Sequence0000011285 + 2201 2470 RNA→ COG3584 (COG3584)→env-1376 FNTS GKKEVUV02HQNLL + 68 208 RNA→ hypo→env-1377 B3 all c Cons62230 - 397 270 RNA→ ←hypo

env-1378 SwBSRL2 contig 2795282 - 190 11 RNA→env-1379 sgz454il contig05169 + 17753 17958 RNA→ KamA (COG1509)→env-1380 FNTS067 GKA24FP01CKNDR - 171 22 RNA→ ←hypo

env-1381 DCrCPGB c7334 + 684 833 RNA→ hypo→env-1382 FNTS067 GJ87FRN01BYJGA - 179 32 RNA→env-1383 DCrCPGB c46496 - 167 20 RNA→env-1384 LM15JUN2010E c408 - 6614 6489 RNA→ Universal stress protein family.→env-1385 LBLACPB2 contig00594 - 253 72 RNA→ ←hypo

env-1386 DCrCPGB c29150 + 51 205 RNA→ hypo→env-1387 DCrCPGB c36770 + 388 526 RNA→env-1388 DCrCPGB c662515 - 285 132 RNA→ ←hypo

env-1389 FNTS067 GKA24FP01C0SKA + 58 212 RNA→env-1390 DCrCPGB c7977 - 1241 1093 RNA→ hypo→env-1391 DCrCPGB c756 - 2294 2144 RNA→ hypo→env-1392 FNTS GKKEVUV02JFWU0 + 201 350 RNA→ ←hypo

env-1393 FNTS067 GKA24FP01AUUF6 + 8 162 RNA→ hypo→env-1394 FNTS067 GJ87FRN01AEPDM + 195 345 RNA→env-1395 DCrCPGB c477264 - 309 154 RNA→env-1396 DCrCPGB c58320 - 397 245 RNA→ hypo→env-1397 FNTS067 GJ87FRN01A2ZDO + 220 372 RNA→ ←hypo

env-1398 FNTS067 GJ87FRN01EDBL6 + 259 412 RNA→ ←hypoenv-1399 DCrCPGB c29947 + 175 325 RNA→ ←hypo

env-1400 FNTS067 GJ87FRN01BGWL2 + 280 431 RNA→ ←hypo

env-1401 2034211955 + 138 273 RNA→ RlpA (COG0797)→env-1402 MA55A contig01907 + 2069 2201 RNA→ SCP bacterial (cd05379)→env-1403 MA40A F51MHD001BULME - 186 27 RNA→env-1404 A5 c1 Cons29939 + 3526 3666 RNA→ hypo→env-1405 PBDCA2 FIDWTPW02RYU9D - 326 206 RNA→ hypo→env-1406 MA55A contig20485 + 241 361 RNA→ ←hypoenv-1407 MA40A F51MHD001DHJ67 - 233 123 RNA→ hypo→env-1408 BMHBC 86971 + 225 341 RNA→ LysM (cd00118)spore SleB (TIGR02869)→env-1409 BMHBC 2 4822178 + 51 167 RNA→env-1410 botACOD F64RS5002G7TGL - 291 146 RNA→ hypo→env-1411 A2 c1 Cons27975 + 1114 1266 RNA→env-1412 A5 c1 Cons11061 - 281 129 RNA→env-1413 DCrCPGB c683259 + 36 214 RNA→env-1414 DCrCPGB c38964 + 111 284 RNA→ GT1 Sucrose synthase (cd03800)→env-1415 FNTS GKKEVUV01C807Y - 207 69 RNA→env-1416 sg4i contig07016 + 284 433 RNA→ hypo→env-1417 Cons115629 - 259 91 RNA→env-1418 PRSSGFe2 Sequence0000000120 + 3654 3767 RNA→ spore SleB (TIGR02869)→env-1419 BMHBC 2 4598608 - 129 12 RNA→env-1420 BMHBC 2 6578405 - 129 12 RNA→env-1421 BMHBC 2 330660 - 123 6 RNA→env-1422 BMHBC 2 2149673 - 129 12 RNA→


59

env-1423 BMHBC 2 1568784 - 129 12 RNA→env-1424 BMHBC 2 3356847 + 3 120 RNA→env-1425 BMHBC 2 5895996 + 3 120 RNA→env-1426 BMHBC 2 915032 - 123 6 RNA→env-1427 BMHBC 2 5260138 + 3 120 RNA→env-1428 BMHBC 2 3991170 - 129 12 RNA→env-1429 BMHBC 2 7245253 - 129 12 RNA→env-1430 BMHBC 2 2769470 + 3 120 RNA→env-1431 MA40A GDRVJ9S01CB9HW left + 15 125 RNA→env-1432 DHTCA2 contig01041 + 1523 1645 RNA→ spore SleB (TIGR02869)→env-1433 GBSCECS77 GOYWCOZ02G6OAO - 316 167 RNA→ ←hypoenv-1434 GBSCECS77 GOYWCOZ02I7HY4 + 69 222 RNA→env-1435 GBSSS contig03630 - 1549 1397 RNA→ AdoMet MTases (cd02440)→env-1436 GBSCES77 Contig 253867 - 526 374 RNA→ hypo→env-1437 GBSCECS85 contig01164 - 1961 1808 RNA→ hypo→ Methyltransf 12 (pfam08242)→env-1438 MA55A contig00472 + 1705 1824 RNA→ ←hypo

env-1439 MA55A GIRCX1H01BA8KA + 141 261 RNA→env-1440 MA55A contig04245 + 1275 1394 RNA→ ←hypo

env-1441 sg4i contig15569 + 131090 131239 RNA→ ←hypo

env-1442 sgz454il contig00210 + 32136 32285 RNA→ ←hypoenv-1443 sg4i contig01098 + 4323 4474 RNA→ Radical SAM (cd01335)→env-1444 sgz454il contig08267 + 16355 16486 RNA→ Radical SAM (cd01335)→env-1445 PRSSGFe2 Sequence0000037123 - 642 511 RNA→ hypo→env-1446 Cons27796 - 610 440 RNA→ hypo→env-1447 AGSF01000752.1 - 28715 28516 RNA→ TM PBP2 (cd06261)→env-1448 AGSF01002837.1 + 611 810 RNA→ ntrB (TIGR01183)→env-1449 FNTS067 contig15923 - 218 58 RNA→env-1450 FNTS067 GKA24FP01DKZ81 - 164 5 RNA→env-1451 DCrCPGB c2664 + 1081 1285 RNA→ TM PBP2 (cd06261)→env-1452 FNTS067 GJ87FRN01C4H0P + 114 313 RNA→env-1453 LCrCPGB2 c41 - 695 496 RNA→ ntrB (TIGR01183)→env-1454 FNTS contig00756 - 734 530 RNA→ hypo→ ntrB (TIGR01183)→env-1455 DCrCPGB c26161 + 132 313 RNA→ GT1 Sucrose synthase (cd03800)→env-1456 AGSF01000210.1 - 4567 4428 RNA→ Na H Antiporter C (cd01988)Na H Exchanger (pfam00999)→ metagenemark→env-1457 AGSF01003928.1 - 498 359 RNA→ metagenemark→env-1458 FNTS067 GJ87FRN01CYAAG - 161 1 RNA→env-1459 DCrCPGB c9350 - 254 94 RNA→env-1460 DCrCPGB c22770 - 510 350 RNA→ hypo→env-1461 FNTS067 GKA24FP01CQJGX + 207 368 RNA→ ←hypoenv-1462 FNTS067 GKA24FP01AKCBR - 259 98 RNA→env-1463 DCrCPGB c6166 + 104 265 RNA→ TM PBP2 (cd06261)→env-1464 GX8B9KJ01AR7GF + 23 229 RNA→env-1465 TCCM contig00382 + 3292 3462 RNA→ hypo→env-1466 GYQO9XB02HO15S - 332 166 RNA→ hypo→env-1467 DCrCPGB c596400 - 188 33 RNA→env-1468 DCrCPGB c9945 + 553 803 RNA→ GT1 Sucrose synthase (cd03800)→env-1469 DCrCPGB c15963 + 553 731 RNA→env-1470 FNTS067 GJ87FRN01CU8P1 - 324 129 RNA→env-1471 LM29OCT2010E c19870 - 557 403 RNA→ ArsB (COG1055)→env-1472 LM29OCT2010E c32228 - 335 212 RNA→ hypo→env-1473 FNTS GKKEVUV01C826Y - 179 6 RNA→env-1474 DCrCPGB c4020 + 186 365 RNA→ hypo→ hypo→


60

env-1475 LM29OCT2010E c4479 - 834 650 RNA→ ntrB (TIGR01183)→env-1476 LM15JUN2010E c421 - 1137 953 RNA→ TM PBP2 (cd06261)→env-1477 MA40A contig25562 - 222 88 RNA→ ←hypoenv-1478 DCrCPGB c48758 - 170 4 RNA→env-1479 FNTS GKKEVUV01B8RZ0 + 126 291 RNA→ ←hypo

env-1480 FNTS GKKEVUV02GMOE2 - 482 306 RNA→ ←hypoenv-1481 BMHBC 58986 + 164 288 RNA→ ←hypo

env-1482 SRS024435 C3045921 + 38 210 RNA→ metagenemark→env-1483 SRS052697 C3168331 + 92 265 RNA→ metagenemark→env-1484 scaffold65472 2 MH0012 + 1779 1942 RNA→ hypo→env-1485 SRS019161 C2486274 - 493 330 RNA→ metagenemark→env-1486 C4819751 1 MH0014 + 1390 1553 RNA→ hypo→env-1487 scaffold11737 2 MH0054 - 3109 2946 RNA→ PotE (COG0531)→env-1488 scaffold96202 3 O2.UC-19 + 376 539 RNA→ hypo→env-1489 SRS014235 WUGC scaffold 30238 - 690 527 RNA→ metagenemark→ metagenemark→env-1490 SRS019685 C8232567 - 239 76 RNA→env-1491 BAAU01002440.1 - 157 39 RNA→env-1492 scaffold27619 10 MH0057 + 232 351 RNA→ NLPC P60 (pfam00877)PG binding 1 (pfam01471)→env-1493 scaffold1938 1 MH0083 - 2927 2808 RNA→ NLPC P60 (pfam00877)PG binding 1 (pfam01471)→env-1494 scaffold8253 2 O2.UC-17 + 2210 2329 RNA→ NLPC P60 (pfam00877)PG binding 1 (pfam01471)→env-1495 scaffold35769 2 O2.UC-21 - 2626 2507 RNA→ NLPC P60 (pfam00877)PG binding 1 (pfam01471)→env-1496 scaffold67271 2 O2.UC-24 + 264 383 RNA→ NLPC P60 (pfam00877)PG binding 1 (pfam01471)→env-1497 scaffold40642 3 V1.CD-1 + 8985 9104 RNA→ NLPC P60 (pfam00877)PG binding 1 (pfam01471)→env-1498 scaffold1609 1 V1.CD-9 - 13239 13120 RNA→ NLPC P60 (pfam00877)PG binding 1 (pfam01471)→env-1499 SRS014313 C2627331 + 38 157 RNA→ PG binding 1 (pfam01471)→env-1500 SRS014683 WUGC scaffold 26644 - 17282 17163 RNA→ NLPC P60 (pfam00877)PG binding 1 (pfam01471)→ Radical SAM (cd01335)→

HTH ARAC (smart00342)AraC binding (pfam02311)→env-1501 SRS015217 WUGC scaffold 35192 + 15766 15885 RNA→ NLPC P60 (pfam00877)PG binding 1 (pfam01471)→env-1502 SRS015264 WUGC scaffold 65914 - 997 878 RNA→ PG binding 1 (pfam01471)→env-1503 SRS016495 C1934669 - 1094 975 RNA→ NLPC P60 (pfam00877)PG binding 1 (pfam01471)→ PflX (COG1313)→env-1504 SRS019030 C1541851 - 250 131 RNA→ metagenemark→env-1505 SRS023346 C1111346 - 2935 2816 RNA→ NLPC P60 (pfam00877)PG binding 1 (pfam01471)→ Radical SAM (cd01335)→

HTH ARAC (smart00342)AraC binding (pfam02311)→env-1506 SRS050299 LANL scaffold 31732 + 667 786 RNA→ NLPC P60 (pfam00877)PG binding 1 (pfam01471)→ Radical SAM (cd01335)→env-1507 SRS051882 C2562621 - 1078 959 RNA→ NLPC P60 (pfam00877)PG binding 1 (pfam01471)→env-1508 SRS052027 C1907608 + 9701 9820 RNA→ NLPC P60 (pfam00877)PG binding 1 (pfam01471)→ Radical SAM (cd01335)→env-1509 SRS058723 C6751357 + 363 482 RNA→ PG binding 1 (pfam01471)→env-1510 BAAV01001889.1 - 290 178 RNA→ hypo→env-1511 scaffold65211 3 V1.UC-13 - 230 118 RNA→ hypo→env-1512 2033630181 + 214 387 RNA→ hypo→env-1513 botACOD GAKN62C01BBRUJ - 276 151 RNA→ hypo→env-1514 FNTS067 GJ87FRN01AEJ4H + 156 310 RNA→ hypo→env-1515 FNTS contig01979 + 222 378 RNA→ hypo→env-1516 FNTS067 GJ87FRN01CDEM0 - 326 173 RNA→ hypo→env-1517 FNTS GKKEVUV01BQDNW - 166 3 RNA→env-1518 FNTS contig04155 + 104 245 RNA→ NLPC P60 (pfam00877)→env-1519 FNTS067 contig00468 + 1393 1534 RNA→ NLPC P60 (pfam00877)→env-1520 FNTS GKKEVUV02G0C2Q + 79 219 RNA→ hypo→env-1521 DCrCPGB c824472 - 241 101 RNA→env-1522 FNTS067 GJ87FRN01AG8OO - 314 174 RNA→ hypo→env-1523 FNTS067 GKA24FP01AT9T9 + 310 451 RNA→ hypo→env-1524 FNTS067 GJ87FRN01C2QXR + 236 377 RNA→ hypo→env-1525 FNTS GKKEVUV01CIL2W + 60 195 RNA→ ←hypo


61

env-1526 FNTS067 GKA24FP01BAOCG + 140 275 RNA→ hypo→env-1527 FNTS067 GKA24FP01C1Y16 - 163 30 RNA→env-1528 FNTS067 GKA24FP01EVTF5 - 170 18 RNA→ hypo→env-1529 PRSSGFe2 Sequence0000049712 + 633 746 RNA→ PG binding 1 (pfam01471)→env-1530 PRSSGFe2 Sequence0000031906 + 351 472 RNA→ ←hypo

env-1531 ACOFG987 F36MELC01D9K1S + 41 154 RNA→ PG binding 1 (pfam01471)→env-1532 ASLM90b GN81PCX02HEE0E - 311 147 RNA→ hypo→env-1533 topACOD FV90NF401BDSQI - 299 155 RNA→env-1534 topACOD F95O9CU02GWX61 + 65 209 RNA→ hypo→ hypo→env-1535 FNTS067 GJ87FRN01A7W5D - 260 104 RNA→ hypo→env-1536 scaffold877 2 O2.UC-18 + 628 767 RNA→ hypo→env-1537 scaffold41962 1 V1.CD-12 + 124 267 RNA→ Na Pro sym (TIGR02121)→env-1538 FNTS GKKEVUV02HXHWN + 93 249 RNA→ hypo→env-1539 DCrCPGB c198499 - 183 38 RNA→ ←hypoenv-1540 A5 c1 Cons78508 - 1140 981 RNA→ hypo→env-1541 GBANfinal FHNL2OP03QM4MF - 424 257 RNA→ spore SleB (TIGR02869)→env-1542 FNTS GKKEVUV01BGYQK + 41 194 RNA→ hypo→env-1543 FNTS GKKEVUV02J6L1I + 151 318 RNA→ ←hypo

env-1544 P3 CLC Cons136658 + 333 489 RNA→ hypo→env-1545 ZhangC60857 1 - 164 28 RNA→env-1546 A2 c1 Cons15230 + 214 364 RNA→ hypo→ hypo→env-1547 botACOD FV90NF402I4N1Z - 255 126 RNA→ hypo→env-1548 A5 c1 Cons9234 + 589 736 RNA→ ←hypoenv-1549 FNTS067 GKA24FP01C0NGA - 150 2 RNA→env-1550 P3 CLC Cons16885 + 534 662 RNA→ hypo→env-1551 FNTS067 GJ87FRN01AFO6F - 169 37 RNA→ ←hypo

env-1552 A5 c1 Cons101191 - 322 185 RNA→ hypo→env-1553 A5 c1 Cons84081 - 875 738 RNA→ rlpA (TIGR00413)→env-1554 B3 all c Cons79562 - 4995 4859 RNA→ rlpA (TIGR00413)→env-1555 A5 c1 Cons811 - 482 346 RNA→ hypo→env-1556 ASMM170b GM97KZC01BGF2Y + 146 291 RNA→env-1557 A5 c1 Cons32245 - 1167 1019 RNA→ Peptidase M23 (pfam01551)→env-1558 A5 c1 Cons30632 + 1947 2098 RNA→ ←hypo

env-1559 A5 c1 Cons105912 + 623 774 RNA→ hypo→env-1560 2033473052 - 155 2 RNA→env-1561 A5 c1 Cons79188 + 1332 1478 RNA→env-1562 botACOD GAKN62C01CU8HH - 304 167 RNA→ hypo→env-1563 A5 c1 Cons66383 + 321 472 RNA→ hypo→env-1564 A5 c1 Cons54154 + 493 644 RNA→ PG binding 1 (pfam01471)→ SCAD SBCAD (cd01158)→env-1565 HCF12C 121183 - 199 54 RNA→env-1566 LWFCA GLZZ6Z001CM8GC + 130 251 RNA→env-1567 BDMC2 contig15757 - 3602 3474 RNA→ KdpA (pfam03814)→ KdpB (COG2216)→env-1568 BDMC2 contig12827 - 169 41 RNA→ ←hypoenv-1569 BDMC2 contig10162 + 195 323 RNA→ ←hypo

env-1570 BDMC2 contig16269 + 1072 1199 RNA→ KdpA (pfam03814)→env-1571 LWFCAn GLO1YSU01C5GAR + 25 148 RNA→ hypo→env-1572 PCEOT FS8BFFD02D0PER + 257 390 RNA→ ←hypo

env-1573 2033268912 - 301 182 RNA→env-1574 TB18AUG2009H c634 + 1923 2049 RNA→ LT GEWL (cd00254)→env-1575 PBDCA2 contig36377 - 253 117 RNA→env-1576 TB03JUN2009H c3815 - 408 284 RNA→ hypo→env-1577 TB18AUG2009H c391 + 3379 3503 RNA→ PotE (COG0531)→


62

env-1578 P3 CLC Cons70997 + 10 162 RNA→ SCRAP12 (SCRAP12)→env-1579 botACOD contig00127 - 467 306 RNA→ hypo→env-1580 FNTS067 GKA24FP01A60B8 - 156 15 RNA→env-1581 LWAnN GIDYKCY01DNJUG - 380 205 RNA→ hypo→env-1582 ZhangC97707 1 - 128 7 RNA→env-1583 topACOD F95O9CU02GFT4U + 126 278 RNA→ hypo→env-1584 botACOD F64RS5002HIV2E - 195 18 RNA→env-1585 A5 c1 Cons80636 + 360 525 RNA→ NLPC P60 (pfam00877)→env-1586 LWAnNiSIP F624WLL02JG5ED + 23 203 RNA→ hypo→env-1587 LWAnN F624WLL02JG5ED + 23 203 RNA→ hypo→env-1588 2033869581 + 48 189 RNA→env-1589 FNTS GKKEVUV01BGN9V + 86 236 RNA→ hypo→env-1590 FNTS067 GJ87FRN01APKP2 + 150 303 RNA→ ←hypo

env-1591 FNTS067 GJ87FRN01EVLT4 - 459 306 RNA→ hypo→env-1592 ATED1026 F5B15RW01D17EH + 23 154 RNA→ ←hypo

env-1593 A2 c1 Cons71496 - 683 563 RNA→ hypo→env-1594 FNTS067 GKA24FP01CUS1H - 362 223 RNA→ hypo→env-1595 botACOD FV90NF402JMDHD - 192 10 RNA→env-1596 FNTS067 GKA24FP01D42WS + 230 378 RNA→ ←hypo

env-1597 FNTS GKKEVUV02GNRGD + 156 327 RNA→ ←hypoenv-1598 FNTS067 contig08514 - 231 79 RNA→ hypo→env-1599 FNTS067 GKA24FP01D8SSX - 374 222 RNA→ ←hypo

env-1600 FNTS contig11351 - 276 124 RNA→ ←hypoenv-1601 FNTS067 GKA24FP01CVJCP - 217 74 RNA→env-1602 FNTS067 GJ87FRN01DU9AJ - 430 288 RNA→env-1603 FNTS067 GKA24FP01BTLUG - 180 36 RNA→ ←hypo

env-1604 FNTS GKKEVUV01AP07X - 192 57 RNA→ hypo→env-1605 FNTS GKKEVUV02JK9MO - 252 101 RNA→ ←hypoenv-1606 FNTS067 contig14953 + 246 396 RNA→ ←hypo

env-1607 DCrCPGB c409885 - 338 188 RNA→ hypo→env-1608 FNTS067 GJ87FRN01CDQM5 + 155 320 RNA→ hypo→env-1609 FNTS067 GJ87FRN01DGL2K - 163 10 RNA→ ←hypo

env-1610 FNTS067 GJ87FRN01AJ182 - 410 260 RNA→ ←hypo

env-1611 FNTS067 GJ87FRN01CQ66H - 184 33 RNA→env-1612 FNTS GKKEVUV02GOHXE + 76 227 RNA→ ←hypo

env-1613 FNTS067 GKA24FP01AW2K0 + 168 315 RNA→ hypo→env-1614 DCrCPGB c39214 - 204 55 RNA→ ←hypoenv-1615 FNTS067 GJ87FRN01BVU6T + 182 328 RNA→ ←hypo

env-1616 FNTS067 GJ87FRN01B6AFD + 121 268 RNA→ ←hypoenv-1617 FNTS067 GJ87FRN01CJSDE + 152 298 RNA→ ←hypoenv-1618 FNTS067 contig07444 + 241 394 RNA→ ←hypo

env-1619 FNTS067 GKA24FP01CSDHJ + 70 193 RNA→env-1620 FNTS067 GJ87FRN01E7NWB + 41 165 RNA→env-1621 FNTS067 GJ87FRN01B2WMM - 497 366 RNA→ hypo→env-1622 botACOD GAKN62C01EMJ66 + 216 339 RNA→env-1623 FNTS GKKEVUV01EAB0J + 105 229 RNA→ hypo→env-1624 GBANfinal contig10109 + 339 463 RNA→ hypo→env-1625 topACOD FV90NF401D03CG - 415 282 RNA→ hypo→env-1626 GBANfinal contig07350 + 1887 2013 RNA→ NLPC P60 (pfam00877)SCRAP12 (SCRAP12)→env-1627 topACOD F95O9CU01ATG7J + 150 272 RNA→ hypo→env-1628 ATED1026 F5B15RW02I6Z4B - 234 79 RNA→ hypo→env-1629 orpgwFw301 FCAY69047 y2 + 525 676 RNA→


63

env-1630 topACOD FV90NF401BVJ7P - 544 401 RNA→ hypo→env-1631 botACOD F64RS5002GGA88 + 135 280 RNA→ hypo→env-1632 botACOD FV90NF402HM6TP + 352 478 RNA→env-1633 topACOD FV90NF401BCX0P + 70 238 RNA→ ←hypo

env-1634 topACOD FV90NF401CPW51 + 321 449 RNA→env-1635 topACOD FV90NF401EKATU + 227 344 RNA→ hypo→env-1636 botACOD GAKN62C01ERZPH - 404 225 RNA→ hypo→env-1637 A5 c1 Cons6647 + 477 641 RNA→ hypo→env-1638 FIHLEPW02RHXF9 - 292 121 RNA→env-1639 ZhangC85567 1 - 161 34 RNA→env-1640 B3 all c Cons1482 - 1981 1857 RNA→ PotE (COG0531)→env-1641 MA55A contig06982 + 502 625 RNA→ LysM (cd00118)spore SleB (TIGR02869)→env-1642 GBSCES77 Contig 26114 - 3575 3423 RNA→ SH3 3 (pfam08239)NLPC P60 (pfam00877)→env-1643 GBSCES77 Contig 8175 - 3575 3423 RNA→ SH3 3 (pfam08239)NLPC P60 (pfam00877)→env-1644 GBSCES77 Contig 35262 + 1671 1823 RNA→ SH3 3 (pfam08239)NLPC P60 (pfam00877)→env-1645 GBSCES77 Contig 17349 + 1671 1823 RNA→ SH3 3 (pfam08239)NLPC P60 (pfam00877)→env-1646 GBSCES77 Contig 21592 - 3575 3423 RNA→ SH3 3 (pfam08239)NLPC P60 (pfam00877)→env-1647 GBSCES77 Contig 42605 + 1671 1823 RNA→ SH3 3 (pfam08239)NLPC P60 (pfam00877)→env-1648 GBSCES77 Contig 12703 - 3575 3423 RNA→ SH3 3 (pfam08239)NLPC P60 (pfam00877)→env-1649 GBSCES77 Contig 49722 - 2899 2747 RNA→ SH3 3 (pfam08239)NLPC P60 (pfam00877)→env-1650 GBSCES77 Contig 46771 - 3575 3423 RNA→ SH3 3 (pfam08239)NLPC P60 (pfam00877)→env-1651 GBSCES77 Contig 30844 - 3575 3423 RNA→ SH3 3 (pfam08239)NLPC P60 (pfam00877)→env-1652 GBSCES77 Contig 38860 - 2899 2747 RNA→ SH3 3 (pfam08239)NLPC P60 (pfam00877)→env-1653 GBSCES77 Contig 3868 + 1671 1823 RNA→ SH3 3 (pfam08239)NLPC P60 (pfam00877)→env-1654 GBSCECS77 GOYWCOZ02GQJQA - 186 33 RNA→env-1655 B3 all c Cons153896 + 292 411 RNA→ hypo→env-1656 B3 all c Cons125342 - 572 448 RNA→ hypo→env-1657 PRSSGFe2 Sequence0000011878 - 2723 2590 RNA→ ←hypoenv-1658 MA55A contig06585 - 815 682 RNA→ GT1 TPS (cd03788)→env-1659 BMHBC 112515 + 1414 1532 RNA→ NLPC P60 (pfam00877)PG binding 1 (pfam01471)→env-1660 sg4i contig00549 - 5574 5383 RNA→ COG3583 (COG3583)COG3584 (COG3584)→env-1661 SRS014235 C3165856 + 125 239 RNA→env-1662 SRS019685 C8183105 - 176 62 RNA→env-1663 WHOKRE c15778 - 240 108 RNA→ ←hypoenv-1664 ASLM90b GN81PCX02HKPEF + 226 356 RNA→env-1665 sg4i contig00392 - 32342 32223 RNA→ COG1213 (COG1213)CDP-OH P transf (pfam01066)→ GlpA (COG0578)→ glycerol kin (TIGR01311)→env-1666 sg4i contig00329 + 20073 20194 RNA→ hypo→env-1667 HCF12C 184572 + 20 140 RNA→ PG binding 1 (pfam01471)→env-1668 C5340313 1 MH0009 + 214 366 RNA→ NLPC P60 (pfam00877)PG binding 1 (pfam01471)→env-1669 scaffold599 16 MH0012 - 4779 4627 RNA→ NLPC P60 (pfam00877)PG binding 1 (pfam01471)→env-1670 scaffold10855 6 MH0032 + 358 510 RNA→ hypo→env-1671 scaffold68683 4 MH0053 - 1829 1673 RNA→ ←hypoenv-1672 scaffold55908 3 O2.UC-13 + 363 519 RNA→ NLPC P60 (pfam00877)PG binding 1 (pfam01471)→env-1673 MA55A F65388E01AIJGN - 418 304 RNA→ spore SleB (TIGR02869)→env-1674 scaffold41642 3 V1.UC-17 - 1142 993 RNA→ spore SleB (TIGR02869)NLPC P60 (pfam00877)→env-1675 scaffold35474 2 MH0080 + 2385 2534 RNA→ spore SleB (TIGR02869)NLPC P60 (pfam00877)→env-1676 scaffold6374 3 O2.UC-14 + 24919 25068 RNA→ spore SleB (TIGR02869)NLPC P60 (pfam00877)→env-1677 SRS012902 C539052 - 921 772 RNA→ spore SleB (TIGR02869)NLPC P60 (pfam00877)→env-1678 SRS024435 C2891372 + 15 164 RNA→ metagenemark→env-1679 SRS013950 C2036886 + 105 242 RNA→ ←metagenemarkenv-1680 SRS024561 C2753526 - 440 292 RNA→ PG binding 1 (pfam01471)→env-1681 SRS011255 C2392861 - 329 181 RNA→ ←metagenemark


64

env-1682 scaffold56712 3 V1.UC-15 - 415 296 RNA→ ABC ATPase (cd00267)→env-1683 SRS015133 C3235461 - 230 114 RNA→env-1684 scaffold3764 4 O2.UC-18 + 354 489 RNA→env-1685 SRS011302 C3366930 + 976 1090 RNA→ metagenemark→env-1686 RUMENNODE 2646218 1 - 14626 14516 RNA→ PutP (COG0591)→env-1687 RUMENNODE 2646218 1 - 15764 15647 RNA→ metagenemark→env-1688 PRSSGFe2 Sequence0000008498 + 129 249 RNA→ hypo→ GH18 CFLE spore hydrolase (cd02874)→env-1689 FNTS GKKEVUV02FSSKP - 169 39 RNA→ hypo→env-1690 2034199851 - 223 87 RNA→ hypo→env-1691 SRB FXPBX6M01DBXBK + 16 153 RNA→ Spr (COG0791)→env-1692 FNTS GKKEVUV02ISDUE - 144 13 RNA→env-1693 FNTS GKKEVUV02IU9MQ + 87 221 RNA→ hypo→env-1694 FNTS067 GKA24FP01EKR06 + 44 182 RNA→ ←hypo

env-1695 A5 c1 Cons73938 + 443 582 RNA→ hypo→ hypo→env-1696 A5 c1 Cons50195 + 1339 1472 RNA→ hypo→ hypo→env-1697 B3 all c Cons86421 + 1288 1429 RNA→ hypo→env-1698 A5 c1 Cons32350 - 346 205 RNA→ hypo→env-1699 Cons17769 + 216 357 RNA→ hypo→env-1700 botACOD GAKN62C01B3YOZ - 313 172 RNA→ hypo→env-1701 A5 c1 Cons66054 - 723 580 RNA→ hypo→env-1702 A5 c1 Cons32144 - 2320 2193 RNA→ hypo→env-1703 A5 c1 Cons32314 + 664 790 RNA→ hypo→env-1704 2034056076 + 240 381 RNA→env-1705 P3 CLC Cons15276 + 513 646 RNA→ hypo→env-1706 A5 c1 Cons52149 - 433 296 RNA→ hypo→env-1707 FNTS GKKEVUV01DA3V9 + 55 191 RNA→env-1708 2033478947 - 148 18 RNA→env-1709 2033445982 - 291 156 RNA→ hypo→env-1710 A2 c1 Cons8220 - 212 71 RNA→env-1711 topACOD F95O9CU02F0O34 - 279 144 RNA→ hypo→env-1712 MA40A GDRVJ9S02IJFIN left - 300 182 RNA→ hypo→ hypo→env-1713 MA55A F65388E02JCVTP + 5 122 RNA→ hypo→env-1714 PCEOT contig02308 - 11974 11849 RNA→ Radical SAM (cd01335)→env-1715 PCEOT contig01505 + 3499 3622 RNA→ Radical SAM (cd01335)→env-1716 PCEOT contig01441 + 469 590 RNA→ Radical SAM (cd01335)→env-1717 PRSSGFe2 Sequence0000051097 - 838 647 RNA→ SH3 3 (pfam08239)NLPC P60 (pfam00877)→env-1718 PBDCA2 GBB5CE401BOMWD right + 64 243 RNA→ hypo→env-1719 CLOF F4EQGSL01DNK6X + 239 425 RNA→env-1720 scaffold13266 1 V1.CD-11 - 4381 4252 RNA→ OpuBC (COG1732)TM PBP2 (cd06261)→ ABC OpuCA Osmoprotection (cd03295)→

CBS pair CorC HlyC assoc (cd04590)→env-1721 CAM READ 0099440109 - 197 73 RNA→env-1722 CAM READ 0099670315 + 156 280 RNA→ ←metagenemarkenv-1723 CAM READ 0099792629 + 249 373 RNA→env-1724 CAM READ 0100047117 - 348 224 RNA→ ABC ATPase (cd00267)→env-1725 4444164.3.03501 - 6731 6607 RNA→ ABC MJ0796 Lo1CDE FtsE (cd03255)→ CBS pair ABC OpuCA assoc2 (cd04583)→

OpuBB (COG1174)→ OpuBB (COG1174)OpuBC (COG1732)→env-1726 4444164.3.06668 + 1167 1291 RNA→env-1727 4444165.3.01418 - 1525 1401 RNA→ ABC OpuCA Osmoprotection (cd03295)→env-1728 4444165.3.56577 + 270 395 RNA→env-1729 CAM READ 0099579157 - 213 89 RNA→env-1730 CAM READ 0100051943 - 460 336 RNA→env-1731 4444164.3.11558 + 379 503 RNA→env-1732 CAM READ 0099860477 + 303 428 RNA→


65

env-1733 scaffold60855 1 V1.CD-11 + 10306 10436 RNA→ HATPase c (cd00075)HisKA (cd00082)→env-1734 4444165.3.07861 + 1754 1884 RNA→ metagenemark→env-1735 4444164.3.06833 - 1563 1436 RNA→ KdpD (pfam02702)→env-1736 CAM READ 0099621053 + 301 429 RNA→env-1737 4444165.3.13299 + 1062 1189 RNA→ OpuBB (COG1174)→env-1738 CAM READ 0099942719 + 74 199 RNA→env-1739 4444164.3.48393 - 336 211 RNA→ metagenemark→env-1740 CAM READ 0099567587 - 242 118 RNA→env-1741 CAM READ 0099778655 - 264 138 RNA→ ←metagenemarkenv-1742 4444164.3.50505 + 118 244 RNA→env-1743 4444165.3.29609 - 3277 3151 RNA→ metagenemark→ PAS (cd00130)HAMP (cd06225)→ HisKA (cd00082)→env-1744 PBDCA2 contig21384 - 695 545 RNA→ LysM (cd00118)spore SleB (TIGR02869)→env-1745 PRSSGFe2 Sequence0000001278 + 9445 9566 RNA→ NLPC P60 (pfam00877)PG binding 1 (pfam01471)→env-1746 BMHBC 133015 - 152 18 RNA→ ←hypoenv-1747 MA40A contig11243 + 36 149 RNA→ hypo→ LysM (cd00118)Peptidase M23 (pfam01551)→env-1748 PRSSGFe2 Sequence0000015855 - 1966 1816 RNA→ citrate synt like 1 2 (cd06113)→env-1749 MA55A contig03486 + 210 335 RNA→ ←hypoenv-1750 PBDCA2 GBB5CE401CPP2R left + 158 289 RNA→env-1751 LWFCA GLZZ6Z001CB8KR + 7 139 RNA→ ←hypo

env-1752 LWFCA GLZZ6Z001EIF6P + 107 242 RNA→env-1753 2016935643 - 206 71 RNA→env-1754 PBDCA2 FISUTAU01CFO0Q - 398 253 RNA→ PG binding 1 (pfam01471)→env-1755 LWAnN GIDYKCY01ESFAZ - 185 55 RNA→env-1756 FNTS GKKEVUV02JSR0S + 6 134 RNA→env-1757 taComm3 FFOP7019 x1 + 310 433 RNA→env-1758 PRSSGFe2 Sequence0000003322 + 5413 5528 RNA→ Radical SAM (cd01335)→env-1759 MA55A contig03336 + 18 145 RNA→ MS channel (pfam00924)→env-1760 PRSSGFe2 Sequence0000004191 + 1065 1195 RNA→ PotE (COG0531)→env-1761 BMHBC 2646 + 258 390 RNA→ Amino acid permease.→env-1762 PRSSGFe2 Sequence0000004191 + 3542 3682 RNA→ Kup (COG3158)→ hypo→env-1763 BMHBC 84036 - 2809 2677 RNA→ Kup (COG3158)→ Kup (COG3158)→env-1764 LWFCAnN GO09JKT02FJX8Q - 298 175 RNA→env-1765 PCEOT F164E7T01DT07C + 75 198 RNA→env-1766 LWFCAn GLO1YSU01DCKQE - 263 141 RNA→ hypo→env-1767 LWFCAnN GO09JKT02JKMQB + 126 249 RNA→env-1768 LWFCA contig05684 - 446 321 RNA→ Kup (COG3158)→env-1769 LWFCAn GLO1YSU01ATNSX + 152 277 RNA→ ←hypoenv-1770 comb1 contig05278 - 1690 1565 RNA→ Kup (COG3158)→ Kup (COG3158)→env-1771 comb2 contig05476 - 1690 1565 RNA→ Kup (COG3158)→ Kup (COG3158)→env-1772 LWFCA GLZZ6Z001CAT4P - 262 148 RNA→ ←hypoenv-1773 LWFCAn GLQU6AQ01BOSVR - 219 98 RNA→ ←hypo

env-1774 LWFCA GLZZ6Z001DC19P + 100 224 RNA→ ←hypoenv-1775 LWSO GLQAYWI02GBVO9 - 192 68 RNA→ hypo→env-1776 LWSO2 GGWJX9X02GBDHL - 239 113 RNA→env-1777 LWSO GLQAYWI02JVR7V + 97 221 RNA→ hypo→env-1778 LWSO GLQAYWI02FXOCM - 255 130 RNA→ ←hypoenv-1779 LWSO GLQAYWI02HUKWD + 135 260 RNA→ hypo→env-1780 lwComb BCGO36405 x1 - 359 231 RNA→env-1781 LWSO GFMCQXZ02F8CA2 - 360 235 RNA→ Kup (COG3158)→env-1782 LWSO2 GGBSFTI02H7086 - 166 37 RNA→env-1783 LWSO GLQAYWI02HMTM1 + 140 267 RNA→env-1784 2031582183 + 760 883 RNA→ hypo→


66

env-1785 GXP7IEG01ED91V + 27 146 RNA→env-1786 lwComb BHFI11741 g1 + 317 432 RNA→ Amino acid transporters→env-1787 2014738123 - 353 233 RNA→env-1788 ANASMECb 4085297 C6351 - 353 233 RNA→ hypo→env-1789 PBDCA2 contig40830 - 6262 6143 RNA→ DapB (COG0289)→env-1790 PBDCA2 FISUTAU01DLVYI + 138 255 RNA→env-1791 PBDCA2 GBB5CE401ELM9Z right - 247 130 RNA→env-1792 FNTS GKKEVUV02H0DON - 298 141 RNA→ hypo→env-1793 FNTS067 GJ87FRN01AEVGH + 142 289 RNA→ ←hypoenv-1794 DCrCPGB c94539 + 99 247 RNA→ hypo→env-1795 FNTS067 GJ87FRN01E4CGQ - 179 23 RNA→ ←hypoenv-1796 FNTS067 GJ87FRN01ETKKF - 294 141 RNA→ ←hypo

env-1797 FNTS067 GJ87FRN01C3HA9 + 182 340 RNA→ hypo→env-1798 FNTS067 GKA24FP01BOY9V - 269 114 RNA→ ←hypoenv-1799 DCrCPGB c59396 + 254 414 RNA→ hypo→env-1800 DCrCPGB c245916 + 187 347 RNA→ ←hypo

env-1801 FNTS067 GJ87FRN01CGQEZ - 323 166 RNA→ hypo→env-1802 FNTS GKKEVUV01B3SJA + 131 287 RNA→ hypo→env-1803 DCrCPGB c740967 + 82 235 RNA→env-1804 FNTS067 GKA24FP01DSGH5 + 94 249 RNA→ ←hypoenv-1805 MA55A contig00235 + 2580 2726 RNA→ Radical SAM (cd01335)→ DRE TIM Re CS (cd07947)→env-1806 BMHBC 209013 + 5510 5627 RNA→ citrate synt like 1 2 (cd06113)→env-1807 BMHBC 164527 - 989 860 RNA→ DapB (COG0289)→env-1808 MA55A contig05039 + 429 548 RNA→ DapB (COG0289)→env-1809 MA55A contig00617 - 163 40 RNA→ ←hypoenv-1810 MA55A contig01245 - 3842 3719 RNA→ ←hypo

env-1812 MA55A contig00306 + 406 519 RNA→ RNA→ NAD Gly3P dh N (pfam01210)Octopine DH (pfam02317)→B12-binding like (cd02065)Glm e (cd00245)→

env-1811 MA55A contig00306 + 651 766 (shown above)

env-1813 PCEOT contig07517 + 427 550 RNA→env-1814 PCEOT FUV4KOQ02DJ37P + 33 148 RNA→env-1815 PBDCA2 FISUTAU01D56Z1 - 188 66 RNA→env-1816 PBDCA2 contig20376 + 213 433 RNA→env-1817 PBDCA2 GBB5CE401CLDFS - 380 248 RNA→ hypo→env-1818 taComm3 FNHH6463 x1 + 347 497 RNA→ hypo→env-1819 PCEOT FUV4KOQ02DVXIX + 123 251 RNA→env-1820 CLOF F4EQGSL02HP8EW + 51 188 RNA→env-1821 PRSSGFe2 Sequence0000000003 - 8621 8515 RNA→ LysM (cd00118)Peptidase M23 (pfam01551)SCRAP27 (SCRAP27)→env-1822 PRSSGFe2 Sequence0000000788 - 4300 4192 RNA→ LysM (cd00118)Peptidase M23 (pfam01551)SCRAP27 (SCRAP27)→env-1823 SWWA GD6QK7J02JIRHS - 168 32 RNA→env-1824 GBANfinal FHNL2OP03RYWR2 - 178 47 RNA→env-1825 MA55A F65388E01EHGW8 - 309 191 RNA→env-1826 PBDCA2 FUFP3941 b1 + 484 621 RNA→env-1827 PRSSGFe2 Sequence0000000450 + 15399 15517 RNA→ Radical SAM (cd01335)→env-1828 NCBI READ 1113288988894 + 512 650 RNA→env-1829 ASHM260b GM9OZ8V02GS7QI + 38 177 RNA→env-1830 ASHM485B GQ8TDHF02HUPO7 + 15 152 RNA→env-1831 ASMM170b GM97KZC01AU7PE - 238 100 RNA→env-1832 ASMM170b GJFD58A01BXR2B + 166 304 RNA→ ←hypo

env-1833 ASLM90b GJFDWOI02IBSEK + 37 175 RNA→env-1834 ASMM170b GM97KZC01AEJY2 - 298 162 RNA→env-1835 MA55A GIRCX1H01ASZ9P - 235 102 RNA→ ←hypo


67

env-1836 GBSCES77W Contig 162479 + 71 213 RNA→ Radical SAM (cd01335)→env-1837 GBSCES77 Contig 4139 - 953 812 RNA→ DRE TIM Re CS (cd07947)→env-1838 GBSCES77 Contig 31227 - 953 812 RNA→ DRE TIM Re CS (cd07947)→env-1839 GBSCES77 Contig 13026 - 951 810 RNA→ DRE TIM Re CS (cd07947)→env-1840 GBSCES77 Contig 47045 - 949 808 RNA→ DRE TIM Re CS (cd07947)→env-1841 GBSCES77 Contig 8513 - 957 816 RNA→ DRE TIM Re CS (cd07947)→env-1842 GBSCES77 Contig 26554 - 957 816 RNA→ DRE TIM Re CS (cd07947)→env-1843 GBSCES77 Contig 35576 - 955 814 RNA→ DRE TIM Re CS (cd07947)→env-1844 GBSCES77 Contig 42756 + 8863 9004 RNA→ DRE TIM Re CS (cd07947)→env-1845 GBSCES77 Contig 17774 - 955 814 RNA→ DRE TIM Re CS (cd07947)→env-1846 GBSCES77 Contig 21809 - 951 810 RNA→ DRE TIM Re CS (cd07947)→env-1847 GBSCES77W Contig 197714 - 766 625 RNA→ DRE TIM Re CS (cd07947)→env-1848 taComm3 C1507 + 3219 3412 RNA→ SCP bacterial (cd05379)→env-1849 taComm3 C3767 - 1291 1124 RNA→ LysM (cd00118)spore SleB (TIGR02869)→env-1850 MA55A contig03673 + 1481 1589 RNA→ spore SleB (TIGR02869)NLPC P60 (pfam00877)→env-1851 MA55A contig03868 - 555 447 RNA→ spore SleB (TIGR02869)NLPC P60 (pfam00877)→env-1852 MA55A contig02110 - 2346 2231 RNA→ LysM (cd00118)spore SleB (TIGR02869)→env-1853 taComm3 C7943 + 803 998 RNA→ SCP bacterial (cd05379)→env-1854 taComm3 C13323 - 4222 4024 RNA→ SCP bacterial (cd05379)→env-1855 PBDCA2 GBB5CE401AKJL9 right - 290 75 RNA→env-1856 PBDCA2 GBB5CE401C4H0F left + 15 267 RNA→env-1857 PRSSGFe2 Sequence0000038392 + 24 158 RNA→ SH3 3 (pfam08239)NLPC P60 (pfam00877)→env-1858 PRSSGFe2 Sequence0000011540 + 1932 2055 RNA→ SH3 3 (pfam08239)NLPC P60 (pfam00877)→env-1859 PRSSGFe2 Sequence0000003600 + 4052 4186 RNA→ COG3807 (COG3807)NLPC P60 (pfam00877)→env-1860 PRSSGFe2 Sequence0000000611 + 2114 2243 RNA→ SH3 3 (pfam08239)NLPC P60 (pfam00877)→env-1861 MA40A contig04558 - 636 522 RNA→ dapB (TIGR00036)→env-1862 DHTCA2 contig00511 - 329 209 RNA→ hypo→env-1863 MA55A F65388E02JGKFB + 4 117 RNA→ LysM (cd00118)→env-1864 PRSSGFe2 Sequence0000045043 - 962 848 RNA→ LysM (cd00118)spore SleB (TIGR02869)→env-1865 PRSSGFe2 Sequence0000006939 - 944 826 RNA→ LysM (cd00118)spore SleB (TIGR02869)→env-1866 BMHBC 68847 - 486 360 RNA→ LysM (cd00118)→env-1867 MA40A F51MHD001DL178 - 448 328 RNA→ spore SleB (TIGR02869)→env-1868 MA55A contig00162 - 21551 21429 RNA→ SH3 3 (pfam08239)NLPC P60 (pfam00877)→env-1869 MA55A contig17526 - 404 287 RNA→ glutamate 2,3-aminomutase (EC 5.4.3.-)→env-1870 ACQI01003513.1 + 1064 1232 RNA→ hypo→env-1871 MA55A contig17130 + 55 172 RNA→ NAD binding 2 (pfam03446)→env-1872 GBSCES77 Contig 202324 + 188 329 RNA→ Radical SAM (cd01335)→env-1873 MA55A contig02249 + 783 903 RNA→ NAD Gly3P dh N (pfam01210)Octopine DH (pfam02317)→ B12-binding like (cd02065)→env-1874 DHTCA2 contig00255 - 9268 9142 RNA→ hypo→ Radical SAM (cd01335)→ NAT SF (cd04301)→env-1875 PBDCA2 FISUTAU01DHSMI - 422 299 RNA→ hypo→ dapB (TIGR00036)→env-1876 PRSSGFe2 Sequence0000051260 - 280 147 RNA→env-1877 PBDCA2 FISUTAU01AJ3K0 - 174 41 RNA→env-1878 PRSSGFe2 Sequence0000001628 - 6757 6627 RNA→ citrate synt like 1 2 (cd06113)→env-1879 MA40A F51MHD001EHDN7 + 277 392 RNA→env-1880 MA40A contig21162 + 216 326 RNA→ hypo→env-1881 MA40A F51MHD001A1B78 + 49 171 RNA→ hypo→env-1882 PBDCA2 FISUTAU01BT9YN - 430 309 RNA→ hypo→env-1883 GBANfinal FHNL2OP04YVQ7V - 208 72 RNA→env-1884 GXP7IEG01AS3UK - 308 181 RNA→ hypo→env-1885 GSLSAS GLMUJHB01B0XRS - 384 193 RNA→ hypo→env-1886 PBDCA2 contig26680 + 3 154 RNA→ spore SleB (TIGR02869)→env-1887 FGTW GHRKC7402GXT8Z - 148 31 RNA→


68

env-1888 FNTS067 GJ87FRN01ELE6B - 345 193 RNA→ hypo→env-1889 FNTS GKKEVUV01CV8HF - 274 144 RNA→ ←hypo

env-1890 FNTS GKKEVUV02ITFGJ + 133 286 RNA→ hypo→env-1891 FNTS067 GKA24FP01AUSAJ + 164 320 RNA→ ←hypo

env-1892 A5 c1 Cons19078 - 481 321 RNA→ PG binding 1 (pfam01471)→env-1893 CLOF F4EQGSL02GX2L5 + 17 196 RNA→env-1894 ZhangC47025 1 + 29 169 RNA→env-1895 PRSSGFe2 Sequence0000009261 - 3496 3363 RNA→ NLPC P60 (pfam00877)→env-1896 DHTCA2 contig00282 + 7543 7668 RNA→ hypo→ NLPC P60 (pfam00877)G5 (pfam07501)→env-1897 MA55A GIRCX1H02GDR1C - 359 247 RNA→ ←hypo

env-1898 FNTS067 GJ87FRN01C9I6V - 322 159 RNA→ ←hypoenv-1899 DCrCPGB c145738 - 298 149 RNA→ ←hypo

env-1900 sg4i contig05188 - 283 138 RNA→ hypo→env-1901 SRS013705 C3887545 + 154 311 RNA→ NLPC P60 (pfam00877)PG binding 1 (pfam01471)→env-1902 SRS018739 C3593918 + 93 250 RNA→ PG binding 1 (pfam01471)→env-1903 SRS062544 C2881241 + 148 307 RNA→ metagenemark→env-1904 SRS015574 C3245202 + 160 320 RNA→env-1905 SRS016575 C3742974 - 1149 989 RNA→ NLPC P60 (pfam00877)PG binding 1 (pfam01471)→env-1906 SRS024649 C3515671 + 141 301 RNA→env-1907 SRS042984 LANL scaffold 80428 - 356 221 RNA→ PG binding 1 (pfam01471)→env-1908 SRS013950 C2097384 + 17 177 RNA→ PG binding 1 (pfam01471)→env-1909 SRS024087 C3425131 + 221 381 RNA→env-1910 SRS049318 LANL scaffold 121275 + 421 581 RNA→ PG binding 1 (pfam01471)→env-1911 SRS017227 C5157056 + 81 241 RNA→ PG binding 1 (pfam01471)→env-1912 MA40A F51MHD002FIHAI + 74 184 RNA→ hypo→env-1913 BMHBC 148853 - 152 34 RNA→env-1914 A2 c1 Cons23359 + 788 944 RNA→ LT GEWL (cd00254)→env-1915 FNTS GKKEVUV01EEYO3 + 189 376 RNA→env-1916 botACOD F64RS5002J45UR + 130 343 RNA→ hypo→env-1917 MA55A GIRCX1H02HDK9H + 199 317 RNA→ LysM (cd00118)→env-1918 A5 c1 Cons22326 - 398 228 RNA→ ←hypoenv-1919 PBDCA2 contig30466 - 240 77 RNA→ hypo→env-1920 SRS015057 WUGC scaffold 50505 + 533 680 RNA→ NLPC P60 (pfam00877)PG binding 1 (pfam01471)→env-1921 SRS016342 C2773147 + 169 316 RNA→env-1922 SRS024318 LANL scaffold 18569 + 3377 3524 RNA→ NLPC P60 (pfam00877)PG binding 1 (pfam01471)→env-1923 SRS044486 C2253307 - 807 660 RNA→ NLPC P60 (pfam00877)PG binding 1 (pfam01471)→env-1924 SRS048411 C6837332 - 302 155 RNA→ metagenemark→ metagenemark→env-1925 2014735928 + 154 276 RNA→ hypo→ hypo→env-1926 ANASMECb 4085297 C4156 + 154 276 RNA→ hypo→ hypo→env-1927 A5 c1 Cons39249 - 771 604 RNA→ Lipoproteins→

1.4 Conserved domains

Conserved domains found in protein-coding genes listed in Section 1.3 are listed,with the first sentence in their description from the Conserved Domain Database.Conserved domains associated with more than one c-di-AMP riboswitch are as-

signed a color, while others are shown in gray. The number in parentheses is thenumber of occurrences of the given gene.


69

cd00075 (6) Histidine kinase-like ATPases; This family includes several ATP-binding pro-

teins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90,

phytochrome-like ATPases and DNA mismatch repair proteinscd00082 (7) Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A

dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually

these domains contain a conserved His residue and are activated via trans-autophosphorylation

by the catalytic domain of the histidine kinase.

cd00118 (101) Lysin domain, found in a variety of enzymes involved in bacterial cell wall

degradation.cd00130 (5) PAS domain; PAS motifs appear in archaea, eubacteria and eukarya.

cd00134 (4) Bacterial periplasmic transport systems use membrane-bound complexes and

substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a

wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions.

cd00156 (9) Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR,

NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain

receives the signal from the sensor partner in a two-component systems; contains a phosphoac-

ceptor site that is phosphorylated by histidine kinase homologs; usually found N-terminal to a

DNA binding effector domain; forms homodimerscd00165 (1) S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated

by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins,

ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional

similarity between these three protein classes.cd00189 (3) Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-

[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE]cd00245 (13) Coenzyme B12-dependent glutamate mutase epsilon subunit-like family; contains

proteins similar to Clostridium cochlearium glutamate mutase (Glm) and Streptomyces tendae

Tu901 NikV.cd00254 (25) Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain.

cd00267 (2) ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC trans-

porters are a large family of proteins involved in the transport of a wide variety of different

compounds, like sugars, ions, peptides, and more complex organic molecules.cd00293 (5) Usp: Universal stress protein family.cd00363 (1) Phosphofructokinase, a key regulatory enzyme in glycolysis, catalyzes the phospho-

rylation of fructose-6-phosphate to fructose-1,6-biphosphate.cd00375 (1) Urease alpha-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes

the hydrolysis of urea to form ammonia and carbon dioxide.cd00390 (1) Urease gamma-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes

the hydrolysis of urea to form ammonia and carbon dioxide.

cd00512 (1) Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM)-like

family; contains proteins similar to MCM, and the large subunit of Streptomyces coenzyme

B12-dependent isobutyryl-CoA mutase (ICM).cd00567 (1) Acyl-CoA dehydrogenase.

cd00610 (1) Acetyl ornithine aminotransferase family.cd00625 (1) Anion permease ArsB/NhaD.

cd00673 (25) Alanyl-tRNA synthetase (AlaRS) class II core catalytic domain.cd00685 (1) Trans-Isoprenyl Diphosphate Synthases, head-to-tail.

cd00712 (11) Glutamine amidotransferases class-II (GATase) asparagine synthase B type.

cd00756 (2) MoaE family.

cd00761 (1) Glycosyltransferase family A (GT-A) includes diverse families of glycosyl trans-

ferases with a common GT-A type structural fold.cd00838 (1) metallophosphatase superfamily, metallophosphatase domain.

cd00987 (1) PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are

oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis.cd00995 (2) The substrate-binding domain of an ABC-type nickel/oligopeptide-like import

system contains the type 2 periplasmic binding fold.

cd01115 (2) Permease SLC13 (solute carrier 13).

cd01116 (13) Permease P (pink-eyed dilution).cd01158 (1) Short chain acyl-CoA dehydrogenases and eukaryotic short/branched chain acyl-

CoA dehydrogenases.cd01298 (1) TRZ/ATZ family contains enzymes from the atrazine degradation pathway and

related hydrolases.

cd01335 (31) Radical SAM superfamily.

cd01427 (3) Haloacid dehalogenase-like hydrolases.cd01635 (1) Glycosyltransferases catalyze the transfer of sugar moieties from activated donor

molecules to specific acceptor molecules, forming glycosidic bonds.

cd01891 (1) TypA (tyrosine phosphorylated protein A)/BipA subfamily.

cd01987 (87) USP domain is located between the N-terminal sensor domain and C-terminal

catalytic domain of this Osmosensitive K+ channel histidine kinase family.

cd01988 (1) The C-terminal domain of a subfamily of Na+ /H+ antiporter existed in bacteria

and archea .cd01991 (11) The C-terminal domain of Asparagine Synthase B.

cd02014 (9) Thiamine pyrophosphate (TPP) family, Pyruvate oxidase (POX) subfamily, TPP-

binding module; composed of proteins similar to Lactobacillus plantarum POX, which plays a

key role in controlling acetate production under aerobic conditions.

cd02035 (1) ArsA ATPase functionas as an efflux pump located on the inner membrane of the

cell.

cd02065 (14) B12 binding domain (B12-BD).cd02440 (17) S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase),

class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a

substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy).cd02541 (1) Prokaryotic UGPase catalyses the synthesis of UDP-glucose.

cd02549 (5) A sub-family of peptidase family C39.

cd02874 (1) Cortical fragment-lytic enzyme (CFLE) is a peptidoglycan hydrolase involved in

bacterial endospore germination.cd02883 (7) Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life,

and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X.cd03108 (2) Adenylosuccinate synthetase (AdSS) catalyzes the first step in the de novo biosyn-

thesis of AMP.

cd03228 (1) The MRP (Mutidrug Resistance Protein)-like transporters are involved in drug,

peptide, and lipid export.

cd03230 (4) This family of ATP-binding proteins belongs to a multisubunit transporter involved

in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity.

cd03255 (1) This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific

ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of

liporoteins from the cytoplasmic membrane (LolCDE).


70

cd03257 (2) The ABC transporter subfamily specific for the transport of dipeptides, oligopep-

tides (OppD), and nickel (NikDE).cd03262 (4) HisP and GlnQ are the ATP-binding components of the bacterial periplasmic

histidine and glutamine permeases, repectively.cd03278 (1) Barmotin is a tight junction-associated protein expressed in rat epithelial cells

which is thought to have an important regulatory role in tight junction barrier function.

cd03293 (7) NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate

and sulfonate transport systems, respectively.

cd03294 (1) This family comprises the glycine betaine/L-proline ATP binding subunit in bac-

teria and its equivalents in archaea.cd03295 (6) OpuCA is a the ATP binding component of a bacterial solute transporter that

serves a protective role to cells growing in a hyperosmolar environment.cd03313 (1) Enolase: Enolases are homodimeric enzymes that catalyse the reversible dehydration

of 2-phospho-D-glycerate to phosphoenolpyruvate as part of the glycolytic and gluconeogenesis

pathways.cd03379 (1) Carbonic anhydrases (CA) are zinc-containing enzymes that catalyze the reversible

hydration of carbon dioxide in a two-step mechanism in which the nucleophilic attack of a

zinc-bound hydroxide ion on carbon dioxide is followed by the regeneration of an active site by

ionization of the zinc-bound water molecule and removal of a proton from the active site.cd03586 (1) DNA Polymerase IV/Kappa.cd03691 (1) BipA TypA II: domain II of BipA (also called TypA) having homology to domain

II of the elongation factors (EFs) EF-G and EF-Tu.

cd03710 (1) BipA TypA C: a C-terminal portion of BipA or TypA having homology to the C

terminal domains of the elongation factors EF-G and EF-2.

cd03788 (3) Trehalose-6-Phosphate Synthase (TPS) is a glycosyltransferase that catalyses

the synthesis of alpha,alpha-1,1-trehalose-6-phosphate from glucose-6-phosphate using a UDP-

glucose donor.

cd03794 (1) This family is most closely related to the GT1 family of glycosyltransferases.cd03800 (9) This family is most closely related to the GT1 family of glycosyltransferases.

cd03801 (3) This family is most closely related to the GT1 family of glycosyltransferases and

named after YqgM in Bacillus licheniformis about which little is known.

cd04301 (7) N-Acyltransferase superfamily: Various enzymes that characteristically catalyze

the transfer of an acyl group to a substrate.cd04583 (1) This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair)

domains in association with the ABC transporter OpuCA.cd04590 (2) This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair)

domains associated with the CorC HlyC domain.

cd04643 (2) The CBS domain, named after human CBS, is a small domain originally identified

in cystathionine beta-synthase and is subsequently found in a wide range of different proteins.cd04732 (1) HisA.

cd05379 (12) SCP bacterial: SCP-like extracellular protein domain, as found in bacteria and

archaea.cd06113 (3) Citrate synthase (CS) catalyzes the condensation of acetyl coenzyme A (AcCoA)

and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the oxidative

citric acid cycle (TCA or Krebs cycle).cd06171 (1) Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains

found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors

(SFs).

cd06174 (3) The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary

transporters that includes uniporters, symporters, and antiporters.cd06225 (3) Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase

(HAMP) domain.

cd06261 (29) Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-

dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs.cd06587 (1) This domain superfamily is found in a variety of structurally related metallopro-

teins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance

proteins.cd07039 (9) Pyrimidine (PYR) binding domain of POX.

cd07042 (2) Sulphate Transporter and Anti-Sigma factor antagonist domain of SulP-like sulfate

transporters, plays a role in the function and regulation of the transport activity, proposed

general NTP binding function.

cd07043 (1) Sulphate Transporter and Anti-Sigma factor antagonist) domain of anti-anti-sigma

factors, key regulators of anti-sigma factors by phosphorylation.

cd07182 (1) bacterial Ribonuclease HII-like.

cd07377 (2) Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of

transcriptional regulators.cd07819 (1) Ligand-binding SRPBCC domain of an uncharacterized subfamily of proteins.

cd07947 (15) Clostridium kluyveri Re-citrate synthase and related proteins, catalytic TIM barrel

domain.

COG0013 (5) Alanyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]COG0248 (1) Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion trans-

port and metabolism]COG0289 (10) Dihydrodipicolinate reductase [Amino acid transport and metabolism]COG0308 (1) Aminopeptidase N [Amino acid transport and metabolism]

COG0475 (2) Kef-type K+ transport systems, membrane components [Inorganic ion transport

and metabolism]COG0531 (113) Amino acid transporters [Amino acid transport and metabolism]COG0566 (1) rRNA methylases [Translation, ribosomal structure and biogenesis]

COG0569 (36) K+ transport systems, NAD-binding component [Inorganic ion transport and

metabolism]COG0578 (2) Glycerol-3-phosphate dehydrogenase [Energy production and conversion]

COG0591 (3) Na+/proline symporter [Amino acid transport and metabolism / General function

prediction only]COG0659 (1) Sulfate permease and related transporters (MFS superfamily) [Inorganic ion

transport and metabolism]

COG0702 (1) Predicted nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis,

outer membrane / Carbohydrate transport and metabolism]COG0715 (5) ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic compo-

nents [Inorganic ion transport and metabolism]COG0739 (3) Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis,

outer membrane]

COG0791 (8) Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope bio-

genesis, outer membrane]

COG0792 (1) Predicted endonuclease distantly related to archaeal Holliday junction resolvase

[DNA replication, recombination, and repair]


71

COG0797 (9) Lipoproteins [Cell envelope biogenesis, outer membrane]

COG0833 (1) Amino acid transporters [Amino acid transport and metabolism]

COG1055 (1) Na+/H+ antiporter NhaD and related arsenite permeases [Inorganic ion transport

and metabolism]COG1141 (1) Ferredoxin [Energy production and conversion]COG1174 (3) ABC-type proline/glycine betaine transport systems, permease component [Amino

acid transport and metabolism]

COG1196 (1) Chromosome segregation ATPases [Cell division and chromosome partitioning]

COG1213 (2) Predicted sugar nucleotidyltransferases [Cell envelope biogenesis, outer membrane]COG1277 (4) ABC-type transport system involved in multi-copper enzyme maturation, perme-

ase component [General function prediction only]

COG1285 (2) Uncharacterized membrane protein [Function unknown]

COG1313 (1) Uncharacterized Fe-S protein PflX, homolog of pyruvate formate lyase activating

proteins [General function prediction only]COG1328 (1) Oxygen-sensitive ribonucleoside-triphosphate reductase [Nucleotide transport and

metabolism]COG1357 (3) Pentapeptide repeats containing protein [Function unknown]

COG1392 (1) Phosphate transport regulator (distant homolog of PhoU) [Inorganic ion transport

and metabolism]

COG1509 (3) Lysine 2,3-aminomutase [Amino acid transport and metabolism]COG1574 (1) Predicted metal-dependent hydrolase with the TIM-barrel fold [General function

prediction only]COG1652 (2) Uncharacterized protein containing LysM domain [Function unknown]COG1732 (6) Periplasmic glycine betaine/choline-binding (lipo)protein of an ABC-type trans-

port system (osmoprotectant binding protein) [Cell envelope biogenesis, outer membrane]

COG1842 (1) Phage shock protein A (IM30), suppresses sigma54-dependent transcription

[Transcription / Signal transduction mechanisms]COG1877 (2) Trehalose-6-phosphatase [Carbohydrate transport and metabolism]COG2060 (1) K+-transporting ATPase, A chain [Inorganic ion transport and metabolism]

COG2113 (3) ABC-type proline/glycine betaine transport systems, periplasmic components

[Amino acid transport and metabolism]

COG2156 (86) K+-transporting ATPase, c chain [Inorganic ion transport and metabolism]COG2159 (1) Predicted metal-dependent hydrolase of the TIM-barrel fold [General function

prediction only]

COG2205 (1) Osmosensitive K+ channel histidine kinase [Signal transduction mechanisms]

COG2216 (88) High-affinity K+ transport system, ATPase chain B [Inorganic ion transport

and metabolism]COG2268 (2) Uncharacterized protein conserved in bacteria [Function unknown]COG2317 (1) Zn-dependent carboxypeptidase [Amino acid transport and metabolism]COG2343 (1) Uncharacterized protein conserved in bacteria [Function unknown]COG3103 (13) SH3 domain protein [Signal transduction mechanisms]COG3158 (20) K+ transporter [Inorganic ion transport and metabolism]

COG3263 (1) NhaP-type Na+/H+ and K+/H+ antiporters with a unique C-terminal domain

[Inorganic ion transport and metabolism]COG3409 (3) Putative peptidoglycan-binding domain-containing protein [Cell envelope biogen-

esis, outer membrane]COG3583 (9) Uncharacterized protein conserved in bacteria [Function unknown]

COG3584 (14) Uncharacterized protein conserved in bacteria [Function unknown]

COG3773 (2) Cell wall hydrolyses involved in spore germination [Cell envelope biogenesis, outer

membrane]


COG3883 (8) Uncharacterized protein conserved in bacteria [Function unknown]COG3932 (5) Uncharacterized ABC-type transport system, permease components [General

function prediction only]COG3953 (3) SLT domain proteins [General function prediction only]

COG4124 (1) Beta-mannanase [Carbohydrate transport and metabolism]COG4194 (1) Predicted membrane protein [General function prediction only]


COG4942 (3) Membrane-bound metallopeptidase [Cell division and chromosome partitioning]pfam00062 (2) C-type lysozyme/alpha-lactalbumin family.

pfam00160 (1) Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD.

pfam00375 (10) Sodium:dicarboxylate symporter family.pfam00582 (2) Universal stress protein family.

pfam00877 (575) NlpC/P60 family.

pfam00902 (1) Sec-independent protein translocase protein (TatC).pfam00924 (2) Mechanosensitive ion channel.

pfam00999 (1) Sodium/hydrogen exchanger family.pfam01066 (2) CDP-alcohol phosphatidyltransferase.pfam01145 (3) SPFH domain / Band 7 family.

pfam01210 (14) NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus.pfam01391 (3) Collagen triple helix repeat (20 copies).pfam01435 (3) Peptidase family M48.

pfam01464 (1) Transglycosylase SLT domain.pfam01471 (95) Putative peptidoglycan binding domain.pfam01551 (79) Peptidase family M23.

pfam01943 (1) Polysaccharide biosynthesis protein.pfam01980 (2) Uncharacterized protein family UPF0066.pfam02310 (1) B12 binding domain.

pfam02311 (2) AraC-like ligand binding domain.pfam02317 (15) NAD/NADP octopine/nopaline dehydrogenase, alpha-helical domain.

pfam02702 (1) Osmosensitive K+ channel His kinase sensor domain.pfam03446 (2) NAD binding domain of 6-phosphogluconate dehydrogenase.

pfam03652 (9) Uncharacterized protein family (UPF0081).

pfam03814 (93) Potassium-transporting ATPase A subunit.pfam04069 (1) Substrate binding domain of ABC-type glycine betaine transport system.

pfam04450 (1) Plant Basic Secretory Protein.

pfam05103 (1) DivIVA protein.pfam05116 (2) Sucrose-6F-phosphate phosphohydrolase.

pfam05257 (2) CHAP domain.pfam05791 (30) Bacillus haemolytic enterotoxin (HBL).pfam06135 (9) Bacterial protein of unknown function (DUF965).

pfam06153 (1) Protein of unknown function (DUF970).pfam06202 (1) Amylo-alpha-1,6-glucosidase.

pfam06339 (1) Ectoine synthase.

pfam06725 (4) 3D domain.pfam06737 (160) Transglycosylase-like domain.

pfam06782 (1) Uncharacterized protein family (UPF0236).

pfam07486 (8) Cell Wall Hydrolase.pfam07501 (3) G5 domain.

pfam07833 (1) Copper amine oxidase N-terminal domain.

pfam07854 (1) Protein of unknown function (DUF1646).


72

pfam07859 (1) alpha/beta hydrolase fold.

pfam08239 (34) Bacterial SH3 domain.

pfam08242 (1) Methyltransferase domain.pfam08305 (1) NPCBM/NEW2 domain.

pfam08472 (1) Sucrose-6-phosphate phosphohydrolase C-terminal.pfam10057 (2) Uncharacterized conserved protein (DUF2294).pfam11256 (1) Protein of unknown function (DUF3055).

pfam11349 (3) Protein of unknown function (DUF3151).pfam11574 (8) Protein of unknown function (DUF3235).pfam12439 (1) Glycogen debranching enzyme N terminal.

PRK13914 (1) invasion associated secreted endopeptidase; ProvisionalSCRAP12 (11) Self-Cleaving Ribozyme Associated Protein number 12

SCRAP27 (2) Self-Cleaving Ribozyme Associated Protein number 27

SCRAP33 (1) Self-Cleaving Ribozyme Associated Protein number 33SCRAP4 (1) Self-Cleaving Ribozyme Associated Protein number 4

SCRAP41 (1) Self-Cleaving Ribozyme Associated Protein number 41

smart00287 (2) Bacterial SH3 domain homologues.smart00342 (2) helix turn helix, arabinose operon control protein.

TIGR00036 (2) dihydrodipicolinate reductase.

TIGR00064 (1) signal recognition particle-docking protein FtsY.

TIGR00413 (6) rare lipoprotein A.

TIGR00653 (1) glutamine synthetase, type I.

TIGR00685 (1) trehalose-phosphatase.TIGR00744 (1) ROK family protein (putative glucokinase).

TIGR00909 (1) amino acid transporter.TIGR00931 (1) Na+/H+ antiporter NhaC.TIGR00932 (1) transporter, monovalent cation:proton antiporter-2 (CPA2) family.

TIGR00933 (32) potassium uptake protein, TrkH family.TIGR01183 (4) nitrate ABC transporter, permease protein.TIGR01311 (2) glycerol kinase.

TIGR02121 (1) sodium/proline symporter.TIGR02168 (4) chromosome segregation protein SMC, common bacterial type.

TIGR02169 (1) chromosome segregation protein SMC, primarily archaeal type.

TIGR02408 (1) ectoine hydroxylase.TIGR02594 (3) conserved hypothetical protein TIGR02594.

TIGR02869 (73) spore cortex-lytic enzyme.

TIGR02884 (1) delta-lactam-biosynthetic de-N-acetylase.TIGR02899 (1) spore coat assembly protein SafA.

TIGR02917 (2) putative PEP-CTERM system TPR-repeat lipoprotein.


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