Psf HTML PilG

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ts from PredictProtein for predict_h31294 file:///C:/Documents%20and%20Settings/MSaleem/My%20Doc

9 09/02/20

ret store# default: single protein sequence description=PilGMAKNGGFSLF AKKEKRFIFE GRHSASDKLV NGEVSAFTEE EARKKLAKRG IRPLQITRVK TSSKRKITQE DITVFTRQLS TMIKAGLP

PROSITE motif search (A Bairoch; P Bucher and K Hofmann)

TOP - BOTTOM - ProSite

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Pattern-ID: CAMP_PHOSPHO_SITEPS00004PDOC00004

Pattern-DE: cAMP- and cGMP-dependent protein kinase phosphorylation sitePattern: [RK]{2}.[ST]

65 RKIT272 RKGT

Pattern-ID: PKC_PHOSPHO_SITEPS00005PDOC00005

Pattern-DE: Protein kinase C phosphorylation sitePattern: [ST].[RK]

26 SDK62 SSK250 SIK

Pattern-ID: CK2_PHOSPHO_SITEPS00006PDOC00006Pattern-DE: Casein kinase II phosphorylation sitePattern: [ST].{2}[DE]

24 SASD38 TEEE68 TQED104 SMTE152 SLLD217 TVMD345 SIGE352 SLDD

Pattern-ID: TYR_PHOSPHO_SITEPS00007PDOC00007

Pattern-DE: Tyrosine kinase phosphorylation sitePattern: [RK].{2,3}[DE].{2,3}Y

131 KYFDRFY

Pattern-ID:MYRISTYLPS00008PDOC00008

Pattern-DE: N-myristoylation sitePattern: G[^EDRKHPFYW].{2}[STAGCN][^P]

119 GSSLSR148 GVLESL302 GAAGNL323 GLSMTS329 GMRATE388 GLVIGT

Pattern-ID: T2SP_FPS00874PDOC00682

Pattern-DE: Bacterial type II secretion system protein F signaturePattern: [KRQ][LIVMA].{2}[SAIV][LIVM].[TY]P.{2}[LIVM].{3}[STAGV].{6}[LMY].{3}[LIVMF]{2}P

170 KVKTALTYPVSVIAVAIGLVFVMMIFVLP

SEG low-complexity regions (J C Wootton & S Federhen)

TOP - BOTTOM - SEG

prot (#) default: single protein sequence description=pilg /home/phd/server/work/predict_h31294


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prot (#) default: single protein sequence description=pilg /home/phd/server/work/predict_h31294/home/phd/server/work/predict_h31294.segNormGcg Length: 410 11-Jul-99 Check: 2818 ..

1 MAKNGGFSLF AKKEKRFIFE GRHSASDKLV NGEVSAFTEE EARKKLAKRG

51 IRPLQITRVK TSSKRKITQE DITVFTRQLS TMIKAGLPLM QAFEIVARGH

101 GNPSMTEMLM EIRGEVEQGS SLSRAFSNHP KYFDRFYCNL VAAGETGGVL

151 ESLLDKLAIY KEKTQAIRKK VKTALTYPVS VIAVAIGLVF VMMIFVLPAF

201 KEVYANMGAE LPALTQTVMD MSDFFVSYGW MVLIALGFAI YGFLKLKARS

251 IKIQRRMDAI LLRMPIFGDI VRKGTIARWG RTTATLIAAG VPLVDVLDST

301 AGAAGNLIYE EATREIRTRV IQGLSMTSGM RATELFPNMM LQMSSIGEES

351 GSLDDMLNKA AEFYEDEVDN AVGRLSAMME PxxxxxxxxxxxxxxxAMYL

401 PLFNLGNVVA

ProDom domain search (E Sonnhammer, Corpet, Gouzy, D Kahn)

TOP - BOTTOM - ProDom - MView

Identities computed with respect to: (query) protColored by: consensus/70% and property

HSP processing: ranked

25 [ . .prot (#) default: single protein... score P(N) N 100.0% ASDKLVNGEVSAFTEEEAR

1 PD034811 p2000.1 (2) Q51105(1) Q5707... 540 5.4e-71 1 99.1% -------------------2 PD001695 p2000.1 (56) GSPF(15) PILC(... 238 1.7e-36 2 44.9% AKGKKVKGQLEADSEREAR3 PD002882 p2000.1 (29) GSPF(8) PILC(2... 208 1.8e-22 1 47.6% -------------------4 PD006803 p2000.1 (12) HOFC(2) // PR... 184 8.1e-19 1 66.7% -------------------5 PD190313 p2000.1 (2) O84574(1) Q9Z78... 167 6.1e-16 1 27.5% -------------------

6 PD039976 p2000.1 (4) CMG2(1) O06667(... 101 6.5e-14 3 22.8% -------------------7 PD096544 p2000.1 (1) GSPF_XANCP // G... 91 7.9e-06 1 31.4% -------------------8 PD096546 p2000.1 (1) HOFC_HAEIN // P... 64 8.9e-05 2 28.0% -------------------9 PD007713 p2000.1 (9) // PROTEIN CONS... 67 0.00010 2 19.3% -------------------consensus/100% ...................consensus/90% ...................

consensus/80%consensus/70%

--- ------------------------------------------------------------------ Again: these results were obtained based on the domain data---- base collected by Daniel Kahn and his coworkers in Toulouse.------ PLEASE quote:--- F Corpet, J Gouzy, D Kahn (1998). The ProDom database--- of protein domain families. Nucleic Ac Res 26:323-326.------ The general WWW page is on:---- ------------------------------------------ http://www.toulouse.inra.fr/prodom.html---- ------------------------------------------

--- For WWW graphic interfaces to PRODOM, in particular for your--- protein family, follow the following links (each line is ONE--- single link for your protein!!):---http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom1=PD034811 ==> multiple alignment,http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom2=PD034811 ==> graphical output of


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http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom1=PD001695 ==> multiple alignment,http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom2=PD001695 ==> graphical output ofhttp://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom1=PD002882 ==> multiple alignment,http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom2=PD002882 ==> graphical output ofhttp://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom1=PD006803 ==> multiple alignment,http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom2=PD006803 ==> graphical output of

http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom1=PD190313 ==> multiple alignment,http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom2=PD190313 ==> graphical output ofhttp://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom1=PD039976 ==> multiple alignment,http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom2=PD039976 ==> graphical output ofhttp://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom1=PD096544 ==> multiple alignment,http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom2=PD096544 ==> graphical output ofhttp://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom1=PD096546 ==> multiple alignment,http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom2=PD096546 ==> graphical output ofhttp://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom1=PD007713 ==> multiple alignment,http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom2=PD007713 ==> graphical output of------ NOTE: if you want to use the link, make sure the entire line--- is pasted as URL into your browser!------ END of PRODOM--- ------------------------------------------------------------

PSI-BLAST alignment header

--- --------------------------------------------------------------- PSI-BLAST multiple sequence alignment--- ------------------------------------------------------------------ PSI-BLAST ALIGNMENT HEADER: ABBREVIATIONS FOR SUMMARY--- SEQLENGTH : 410--- ID : identifier of aligned (homologous) protein--- LSEQ2 : length of aligned sequence

--- IDE : percentage of pairwise sequence identity--- SIM : percentage of similarity--- LALI : number of residues aligned--- LGAP : number of residues in all indels

--- BSCORE : blast score (bits)--- BEXPECT : blast expectation value--- OMIM : OMIM (Online Mendelian Inheritance in Man) ID--- PROTEIN : one-line description of aligned protein--- '!' : indicates lower scoring alignment that is combined--- with the higher scoring adjacent one------ PSI-BLAST ALIGNMENT HEADER: SUMMARY

ID LSEQ2 IDE SIM LALI LGAP BSCORE BEXPECT PROTEINtrembl|Q57076|Q57076 410 95 95 410 0 388 e-107 PilG.trembl|Q9JR97|Q9JR97 410 96 96 410 0 388 e-107 Pilus-assembly protein (Ptrembl|Q51105|Q51105 410 95 95 410 0 387 e-106 PilG.trembl|Q888U1|Q888U1 405 40 63 398 4 360 2e-98 Type IV pilus biogenesistrembl|Q8P670|Q8P670 418 43 63 395 5 353 3e-96 Fimbrial assembly proteintrembl|O54482|O54482 413 37 62 397 5 351 1e-95 Type IV pilus assembly pr

trembl|Q8PHK9|Q8PHK9 418 41 63 398 5 350 3e-95 Fimbrial assembly proteintrembl|Q9PAI0|Q9PAI0 490 42 62 392 5 348 6e-95 Fimbrial assembly proteinswiss|P45793|TAPC_AERHY 413 38 62 397 5 348 7e-95 Type IV pilus assembly prtrembl|Q9ZEL5|Q9ZEL5 405 42 64 398 4 347 2e-94 PilC protein.trembl|Q82WR6|Q82WR6 406 52 69 395 3 347 2e-94 Bacterial type II secretitrembl|Q9F669|Q9F669 383 41 65 379 3 347 2e-94 Pilin biogenesis proteintrembl|Q87AA5|Q87AA5 420 42 62 392 5 345 6e-94 Fimbrial assembly proteintrembl|Q8EJP7|Q8EJP7 423 40 61 396 5 345 7e-94 Type IV pilus biogenesisswiss|P22609|PILC_PSEAE 374 45 67 368 3 344 1e-93 Type 4 fimbrial assemblytrembl|Q8XVK4|Q8XVK4 421 48 69 392 1 343 3e-93 Probable fimbrial assembltrembl|Q87TD5|Q87TD5 405 26 48 395 11 339 3e-92 General secretion pathwayswiss|P31705|GSPF_ERWCA 408 28 50 395 14 339 6e-92 General secretion pathwayswiss|P45780|GSPF_VIBCH 406 26 50 395 12 338 7e-92 General secretion pathwaytrembl|Q8DDT2|Q8DDT2 405 26 50 395 11 336 5e-91 Type II secretory pathwayswiss|P31743|GSPF_AERHY 388 27 49 376 11 334 2e-90 General secretion pathway


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trembl|CAD77776|CAD77776 479 27 52 340 32 228 9e-59 Type IV fimbrial assemblytrembl|Q8XX09|Q8XX09 400 22 40 374 9 228 1e-58 Putative GSPF-related tratrembl|Q9WXU9|Q9WXU9 399 24 47 388 9 227 2e-58 General secretion pathwaytrembl|O67317|O67317 394 25 46 383 14 224 2e-57 Fimbrial assembly proteintrembl|Q83EZ9|Q83EZ9 351 30 55 346 0 223 4e-57 Type IV-A pilus assemblytrembl|Q82V46|Q82V46 406 21 42 392 13 222 1e-56 Bacterial type II secreti

trembl|AAP77714|AAP77714 414 24 47 373 10 219 7e-56 Hypothetical protein.trembl|CAD79205|CAD79205 387 24 47 343 2 218 1e-55 General secretion pathwaytrembl|Q89HH1|Q89HH1 403 24 45 361 10 217 2e-55 Bll6020 protein.trembl|AAP87276|AAP87276 393 18 43 390 6 212 7e-54 CtsF.trembl|AAP87275|AAP87275 392 18 43 390 6 211 1e-53 CtsF.trembl|Q8XTG2|Q8XTG2 395 22 45 390 5 211 2e-53 Probable general secretiotrembl|Q9I0G2|Q9I0G2 395 22 44 391 5 210 4e-53 Probable type II secretiotrembl|Q8XSK5|Q8XSK5 397 20 40 392 6 209 5e-53 Putative general secretiotrembl|AAP95988|AAP95988 397 24 47 395 4 203 3e-51 Protein transport proteintrembl|Q988A9|Q988A9 405 20 41 392 13 201 2e-50 General secretion proteintrembl|Q8RHE3|Q8RHE3 346 22 49 344 1 199 7e-50 General secretion pathwaytrembl|P74465|P74465 298 31 58 264 0 195 7e-49 Pilin biogenesis protein.trembl|Q9CPF7|Q9CPF7 380 24 49 370 13 195 8e-49 HofC.trembl|EAA24563|EAA24563 346 22 48 344 1 194 2e-48 General secretion pathwaytrembl|Q818L1|Q818L1 345 15 40 342 5 194 2e-48 ComG operon protein 2.trembl|Q894E5|Q894E5 351 21 45 343 6 192 1e-47 Putative general secretiotrembl|Q81LZ2|Q81LZ2 343 15 39 338 5 183 4e-45 ComG operon protein 2.trembl|Q8DMJ7|Q8DMJ7 233 33 57 230 1 176 4e-43 PilC protein.trembl|Q92C08|Q92C08 343 16 39 340 10 173 4e-42 ComGB protein.trembl|Q8CP29|Q8CP29 355 14 36 323 5 171 1e-41 DNA transport machinery p

trembl|Q8Y7D7|Q8Y7D7 343 15 38 340 10 165 7e-40 ComGB protein.

trembl|Q8XJB7|Q8XJB7 339 18 41 326 10 164 2e-39 Probable fimbrial assembltrembl|Q8VQ72|Q8VQ72 322 14 36 318 9 160 3e-38 Late competence protein Cswiss|Q9K920|CMGB_BACHD 323 19 41 322 7 159 8e-38 ComG operon protein 2 homtrembl|CAD77260|CAD77260 346 17 41 293 14 151 2e-35 General secretion pathwayswiss|P25954|CMGB_BACSU 323 16 39 323 5 143 4e-33 ComG operon protein 2.trembl|Q93I66|Q93I66 341 16 40 306 12 131 2e-29 CofI.trembl|Q9CDT9|Q9CDT9 357 16 38 326 23 128 1e-28 Competence protein ComGB.trembl|Q8E7J4|Q8E7J4 363 15 35 309 21 125 1e-27 Hypothetical protein.trembl|Q8E235|Q8E235 282 15 36 278 17 125 1e-27 Competence protein CglB.swiss|P29487|TCPE_VIBCH 340 16 37 286 12 123 5e-27 Toxin coregulated pilus btrembl|AAK20793|AAK20793 340 16 37 286 12 123 5e-27 Toxin-coregulated pilus btrembl|Q9ZF71|Q9ZF71 186 37 50 162 0 121 2e-26 PilC (Fragment).trembl|Q833B9|Q833B9 348 17 37 329 19 121 2e-26 Competence protein.trembl|Q99TV1|Q99TV1 356 14 40 343 5 119 5e-26 Hypothetical protein SAV1trembl|Q8CXD8|Q8CXD8 346 15 40 337 10 116 5e-25 DNA transport machinery ptrembl|Q47071|Q47071 352 21 41 289 30 115 9e-25 BFPE.

trembl|Q47021|Q47021 179 26 48 149 1 114 2e-24 Hypothetical protein.trembl|Q47020|Q47020 276 22 43 150 1 114 2e-24 Hypothetical protein.trembl|Q8DS50|Q8DS50 282 15 32 280 17 114 3e-24 Putative ABC transporter

trembl|O06667|O06667 282 18 35 280 17 113 6e-24 Putative ABC transportertrembl|Q9R726|Q9R726 156 28 50 146 10 112 8e-24 XpsF (Fragment).trembl|O86278|O86278 348 16 37 326 24 112 1e-23 Orf348 protein.trembl|Q83Z76|Q83Z76 324 17 41 289 12 110 4e-23 CfcI.trembl|Q8P2Y0|Q8P2Y0 363 15 38 326 19 108 2e-22 Putative competence protetrembl|Q9A1T8|Q9A1T8 282 16 38 281 17 106 5e-22 Putative competence protetrembl|Q879Q5|Q879Q5 282 16 38 281 17 106 5e-22 Putative competence protetrembl|Q8K8V9|Q8K8V9 344 15 38 326 19 106 7e-22 Putative ABC transportertrembl|Q8DMJ6|Q8DMJ6 166 29 50 134 10 105 2e-21 PilC protein.trembl|P74464|P74464 165 29 48 134 9 104 2e-21 General secretion pathwaytrembl|CAD75879|CAD75879 357 13 32 234 12 104 3e-21 Probable type IV pilus astrembl|AAP84206|AAP84206 359 18 36 260 17 103 4e-21 PilR2.trembl|O85194|O85194 290 17 36 286 17 100 4e-20 Competence protein (Competrembl|Q8DN87|Q8DN87 363 17 36 333 25 100 4e-20 Competence protein.trembl|Q841M8|Q841M8 113 32 58 106 0 98 2e-19 Hypothetical protein (Fratrembl|CAD75878|CAD75878 362 20 44 141 2 92 1e-17 Probable type IV pilin bitrembl|Q9XD72|Q9XD72 126 23 49 126 0 91 2e-17 LspF (Fragment).trembl|Q88V36|Q88V36 349 14 33 329 29 70 4e-11 ComG operon protein 2.trembl|Q93AE7|Q93AE7 366 16 38 271 17 68 2e-10 Integral membrane proteintrembl|Q93D63|Q93D63 365 16 38 270 18 62 1e-08 PilR.

trembl|Q9F537|Q9F537 369 15 36 285 21 58 1e-07 PilR protein.trembl|O07376|O07376 365 15 33 261 20 58 3e-07 Integral membrane proteintrembl|AAP86096|AAP86096 346 19 36 245 25 55 1e-06 Putative component of typtrembl|Q9ZIV0|Q9ZIV0 361 17 35 264 16 54 2e-06 PilR (Putative membrane ptrembl|EAA02065|EAA02065 250 14 34 234 25 46 0.001 EbiP618 (Fragment).trembl|Q8KR26|Q8KR26 369 13 34 250 18 39 0.10 Integral membrane protein---


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--- PSI-BLAST ALIGNMENT

MAXHOM alignment header

--- ------------------------------------------------------------

--- MAXHOM multiple sequence alignment--- ------------------------------------------------------------------ MAXHOM ALIGNMENT HEADER: ABBREVIATIONS FOR SUMMARY--- ID : identifier of aligned (homologous) protein--- STRID : PDB identifier (only for known structures)--- IDE : percentage of pairwise sequence identity

--- WSIM : percentage of weighted similarity--- LALI : number of residues aligned--- NGAP : number of insertions and deletions (indels)--- LGAP : number of residues in all indels--- LSEQ2 : length of aligned sequence--- ACCNUM : SwissProt accession number--- OMIM : OMIM (Online Mendelian Inheritance in Man) ID--- NAME : one-line description of aligned protein---

--- MAXHOM ALIGNMENT HEADER: SUMMARYID STRID IDE WSIM LALI NGAP LGAP LSEQ2 ACCNUM NAMEpilc_pseae 46 63 398 2 4 406 P22609 FIMBRIAL ASSEMBLY PROTEINpilc_vibch 41 56 394 2 5 408 Q9X4G9 pilC).tapc_aerhy 40 56 408 2 5 413 P45793 TYPE IV PILUS ASSEMBLY PRpilc_psepu 33 51 399 2 3 401 P36641 FIMBRIAL ASSEMBLY PROTEINgspf_pseae 32 47 384 2 11 405 Q00513 GENERAL SECRETION PATHWAYgspf_erwca 31 47 385 2 13 408 P31705 OUTF).gspf_ecoli 31 46 385 2 5 398 P41441 PROTEIN HOFF).gspf_aerhy 31 45 370 3 13 388 P31743 GENERAL SECRETION PATHWAYgspf_xancp 30 42 379 3 12 390 P31744 GENERAL SECRETION PATHWAY

gspf_vibch 28 44 385 2 11 406 P45780 EPSF).gspf_klepn 28 42 365 3 26 381 P15745 PULF).gspf_erwch 28 41 383 4 15 404 P31704 OUTF).hofc_ecoli 28 38 395 2 2 400 P36646 PROTEIN TRANSPORT PROTEIN

hofc_haein 27 38 393 5 14 406 P44621 PROTEIN TRANSPORT PROTEIN------ MAXHOM ALIGNMENT: IN MSF FORMAT

------ Version of database searched for alignment:--- SWISS-PROT release 41 (02/2003) with 122 564 proteins---

MAXHOM alignment

TOP - BOTTOM - MaxHom - MView

Identities computed with respect to: (1) predict_h3120Colored by: consensus/70% and property

1 [ . . . . : .1 predict_h3120 100.0% MAKNGGFSLFAKKEKRFIFEGRHSASDKLVNGEVSAFTEEEARKKLAKRGIRPLQITRVKTSSKRKIT2 pilc_pseae 45.9% ----------ALKTSVFIWEGTDKKGAK-VKGELTGQNPMLVKAHLRKQGINPLKVRKKGISlgKKVK3 pilc_vibch 41.0% --------------KNYRWKG-INSNGKKVSGQMLAISEIEVRDKLKDQHIQIKKLKKGSVSLLARLT4 tapc_aerhy 39.6% MATLTQKQNAPKKVFAFRWSGVNRKGQK-VSGELQADSINTVKAELRKQGVNVTKVSKKssKGGAKIK5 pilc_psepu 33.0% ---------MNPSIRLYAWQG-TNADGLAVSGQMAGRSPAYVRAGLLRQGILVARLRPAGRAWrkRRE6 gspf_pseae 31.2% ------------------------PSGRQQKGVLEADSARQVRQLLRERQLAPLDVKPTRTREqrGLS7 gspf_erwca 31.1% ------------------------AQGKKCRGTQEADSARQARQLLRERGLVPLSVDENrlRRKIRLS8 gspf_ecoli 30.8% -----------------------TQDGQKLQGIIDANDERQARLRLREEGLFLLDIRPQKSSgrPRIS


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9 gspf_aerhy 29.8% -------------------------------------SARQVRQQLREQGLTPLEVNETTEKAkrGAS10 gspf_xancp 29.1% ----------------------------MLDGQMEAANDAEVALRLQEQGHLPVETRLATGEnkKPFD11 gspf_vibch 28.8% ------------------------AKGRHKKGVIEGDNARQVRQRLKEQSLVPMEVVETQVKakRGIS12 gspf_klepn 26.9% ------------------------EQGKPRRGVQQADSARHARQLLREKGWLALDIDPAAGGGrrRTS13 gspf_erwch 28.4% -----------------------NAQGKKSQGMQEADSARHARQLLREKGLVPVKIEEQRGEarSHRI14 hofc_ecoli 28.2% -------------SKQLWRWHGITGDGNAQDGMLWAESRTLLLMALQQQMVTPLSLKRIAINS-AQWR15 hofc_haein 27.0% -------------TKKLFYYQASNPLNQKQKGSIIADTKQQAHFQLISRGLTHIKLQQ-NWQFGAKPK

consensus/100% .....................................s...hh..L.pp.h..hph...t.t......consensus/90% ..............................pG...u.s...st..L.ppth..hplp..t.t...thpconsensus/80% ...............tsp..pG...utsttps+.hLpcpulhshclp.tthp.ttthpconsensus/70% ...........ttsp..pG.htApotpps+ttLpcpGlhslclp.tphptttphp

COILS prediction (A Lupas)

TOP - BOTTOM - COILS

--- COILS HEADER: SUMMARY

COILS version 2.2: R.B. Russell, A.N. Lupas, 1999using MTIDK matrix.

weights: a,d=2.5 and b,c,e,f,g=1.0

For the threshold of 5 ( probability > 0.5):>prot

window size = 14 14 residues in coiled coil domainwindow size = 21 0 residues in coiled coil domainwindow size = 28 0 residues in coiled coil domain

. : . : . : . : . 5seq MAKNGGFSLFAKKEKRFIFEGRHSASDKLVNGEVSAFTEEEARKKLAKRGframe-14 aabcdefaabcdefabcdefgabcdefgabcdefaabcdefgabcdefggframe-21 aabcdefabcdefgabcdefgabcdefgabcdefgaabcdefgabcdefgframe-28 abcdefgabcdefgabcdefgabcdefgabcdefgabcdefgabcdefggprob-14 --------------------------------------------------prob-21 --------------------------------------------------

prob-28 --------------------------------------------------. : . : . : . : . 10

seq IRPLQITRVKTSSKRKITQEDITVFTRQLSTMIKAGLPLMQAFEIVARGHframe-14 abcdefgabcdefgabcdefgabcdefgabcdefgefgabcdefgabcdeframe-21 abcdefgabcdefgabcdefgabcdefgabcdefgabcdefgefabcdefframe-28 abcdefgabcdefgabcdefgabcdefgabcdefgabcdefgababcdefprob-14 --------------------------------------------------prob-21 --------------------------------------------------prob-28 --------------------------------------------------

. : . : . : . : . 15seq GNPSMTEMLMEIRGEVEQGSSLSRAFSNHPKYFDRFYCNLVAAGETGGVLframe-14 fabcabcdefgabcdefgdefabcdefgabcdefgdefgabcabcdefgaframe-21 gabcabcdefgabcdefgabcdefgdefgbcdabcdefgabcabcdefgaframe-28 gabcdefgabcdefgabcdefgabcdefgefgabcdefgabcabcdefgaprob-14 -------------------------------------------------9

prob-21 -------------------------------------------------2prob-28 -------------------------------------------------1. : . : . : . : . 20

seq ESLLDKLAIYKEKTQAIRKKVKTALTYPVSVIAVAIGLVFVMMIFVLPAFframe-14 bcdefgabcdefgdefgefgefggfggefgaabcdefgabcdeabcabcdframe-21 bcdefgabcdefgabcdefgdefgefgefgefgcdefgaabcdefgabcdframe-28 bcdefgabcdefgabcdefgabcdefgefgefgdefgfgabcdefgabcdprob-14 9999999999999-------------------------------------prob-21 22222222222222222222------------------------------prob-28 111111111111111111111111111-----------------------

. : . : . : . : . 25seq KEVYANMGAELPALTQTVMDMSDFFVSYGWMVLIALGFAIYGFLKLKARSframe-14 efgabcdefgabcdefgabcdefgefgdefgeabcabcdeabcdefgabcframe-21 efgabcdefgabcdefgabcdefgabcdefgeaababcdefgabcdefgaframe-28 efgabcdefgabcdefgabcdefgabcdefgabcdabcdefgabcdefga


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prob-14 --------------------------------------------------prob-21 --------------------------------------------------prob-28 --------------------------------------------------

. : . : . : . : . 30seq IKIQRRMDAILLRMPIFGDIVRKGTIARWGRTTATLIAAGVPLVDVLDSTframe-14 defgefgbcdefggbcdefgabcdeabcdefgabcdefgefgaabcdefg

frame-21 bcdefgabcdefggbcdefgabcdefgcdefgabcabcdefgaabcdefgframe-28 bcdefgabcdefgabcdefgabcdefgcdefgabcabcdefgaabcdefgprob-14 --------------------------------------------------prob-21 --------------------------------------------------prob-28 --------------------------------------------------

. : . : . : . : . 35seq AGAAGNLIYEEATREIRTRVIQGLSMTSGMRATELFPNMMLQMSSIGEESframe-14 abcdefgeabcdefgabcdefgcdefgefgdabcdabcdefgabcabcdeframe-21 abcdefgabcdefgbcdefgabcdefgeabcdefgabcabcdefgabcdeframe-28 abcdefgabcdefgabcdefgbcdefgfabcabcdefgabcdabcdefgaprob-14 --------------------------------------------------prob-21 --------------------------------------------------prob-28 --------------------------------------------------

. : . : . : . : . 40seq GSLDDMLNKAAEFYEDEVDNAVGRLSAMMEPIIIVILGLVIGTLLVAMYLframe-14 fgabcdefgaabcdefgabcdefgabcdefgdeabcdefgabcdefgdefframe-21 fgaabcdefgabcdefgabcdefgabcdefgdefgabcdefgcdefgefgframe-28 bcdefgabcdefgabcdefgdefgabcdefgabcdefgdefgefgdefgeprob-14 --------------------------------------------------prob-21 --------------------------------------------------

prob-28 --------------------------------------------------

. : . : . : . : . 45seq PLFNLGNVVAframe-14 gabcdefgggframe-21 gabcdefgfgframe-28 fgdefgdefgprob-14 ----------prob-21 ----------prob-28 ----------// End

PHD information about accuracy

***************************************************************************** ** PHD: Profile fed neural network systems from HeiDelberg ** ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ** ** Prediction of: ** secondary structure, by PHDsec ** solvent accessibility, by PHDacc ** and helical transmembrane regions, by PHDhtm ** ** Author: ** Burkhard Rost *

* EMBL, 69012 Heidelberg, Germany *

* Internet: [email protected] ** ** All rights reserved. ** ****************************************************************************** ** The network systems are described in: ** ** PHDsec: B Rost & C Sander: JMB, 1993, 232, 584-599. ** B Rost & C Sander: Proteins, 1994, 19, 55-72. ** PHDacc: B Rost & C Sander: Proteins, 1994, 20, 216-226. ** PHDhtm: B Rost et al.: Prot. Science, 1995, 4, 521-533. ** *****************************************************************************


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PHD predictions

TOP - BOTTOM - PHD

PHD predictions for predict_h31294

Different levels of data:

PHD brief1.

PHD normal2.

PHDhtm summary

NHTM=4

PHDhtm detected 4 membrane helices for the best model.The second best model contained 3 helices.

TOP=inPHDhtm predicted the topology in, i.e. the first loop region is in (Note: this prediction may be

problematic when the sequence you sent starts or ends with a region predicted in a membrane helix!)

Reliability of best model=1 (0 is low, 9 is high)

Zscore for best model=0.920

Difference of positive charges (K+R) inside - outside=-8.931 (the higher the value, the more reliable)

Reliability of topology prediction =8 (0 is low, 9 is high)

Details of the strength of each predicted membrane helix:

(sorted by strength, strongest first)

N HTM Total score Best HTM c-N

1 0.7866 0.9100 380 - 401

2 0.8267 0.8913 177 - 197

3 0.8657 0.8808 224 - 244

4 0.8765 0.6006 269 - 290

Overview over transmembrane segments:

Positions Segments Explain

1- 176 i1 inside region 1

177- 197 M1 membrane helix 1

198- 223 o1 outside region 1

224- 244 M2 membrane helix 2245- 268 i2 inside region 2


291- 379 o2 outside region 2


402- 410 i3 inside region 3


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Residue composition for your protein:

%A: 9.8 %C: 0.2 %D: 3.4 %E: 6.6 %F: 5.1

%G: 7.8 %H: 0.7 %I: 7.6 %K: 6.1 %L: 10.2

%M: 5.6 %N: 2.9 %P: 2.9 %Q: 2.4 %R: 6.1

%S: 6.1 %T: 5.8 %V: 7.6 %W: 0.5 %Y: 2.4

AA : amino acid sequence

pH_sec: 'probability' for assigning helix (1=high, 0=low)

pL_sec: 'probability' for assigning neither helix, nor strand (1=high,

0=low)

PHD_htm: PHD predicted membrane helix: M=helical transmembrane region,

blank=non-membrane

PHD = PHD: Profile network prediction HeiDelbergPHDrhtm: refined PHD prediction: M=helical transmembrane region,

blank=non-membrane

PiMohtm: PHD prediction of membrane topology: T=helical transmembrane region,

i=inside of membrane, o=outside of membrane

pT_htm: 'probability' for assigning transmembrane helix

pN_htm: 'probability' for assigning globular region

PHD results (brief)

....,....1....,....2....,....3....,....4....,....5....,....6....,....7....,....8....,..AA MAKNGGFSLFAKKEKRFIFEGRHSASDKLVNGEVSAFTEEEARKKLAKRGIRPLQITRVKTSSKRKITQEDITVFTRQLSTMIKAGLPHD_htmPiMohtm iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii

PHD results (normal)

....,....1....,....2....,....3....,....4....,....5....,....6....,....7....,....8....,..AA MAKNGGFSLFAKKEKRFIFEGRHSASDKLVNGEVSAFTEEEARKKLAKRGIRPLQITRVKTSSKRKITQEDITVFTRQLSTMIKAGLPHD_htmPHDrhtmPiMohtm iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii


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Ambivalent Sequence Predictor(Malin Young, Kent Kirshenbaum,

Stefan Highsmith)

TOP - BOTTOM - ASP

Ambivalent Sequence Predictor (ASP v1.0) mmy

PROF predictions

TOP - BOTTOM - PROF

Bottom - Summary - Details - PredictProtein

PROF predictions for query

Contents:

SYNOPSIS of prediction for query

secondary structure class1.

secondary structure composition2.

surface/core ratio3.

HEADER information

about protein1.

about alignment2.residue composition3.

about method used4.

please quote5.

copyright & contact6.

abbreviations used7.

BODY with predictions

Different levels of data:

PROF normal1.

PROF detail2.

SYNOPSIS of prediction for query

PROFsec summary overall your protein can be classified as:

mixed given the following classes:


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%M: 5.6 %N: 2.9 %P: 2.9 %Q: 2.4 %R: 6.1

%S: 6.1 %T: 5.8 %V: 7.6 %W: 0.5 %Y: 2.4

About the PROF methods used:

prof_fpar acc=/home/phd/server/pub/prof/net/PROFboth_best.par

prof_nnet acc=6

Please quote:

PROF: B Rost & C Sander (1993) J Mol Biol, 232:584-5991.

PROFhtm: B Rost, P Fariselli & R Casadio (1996) Prot Science, 7:1704-17182.

Copyright & Contact:

Burkhard Rost, CUBIC NYC / LION Heidelberg

Email: [email protected]

WWW: http://cubic.bioc.columbia.edu

Fax: +1-212-305 3773

ABBREVIATIONS used:

AA : amino acid sequence

OBS_sec: observed secondary structure: H=helix, E=extended (sheet),

blank=other (loop)

PROF_sec: PROF predicted secondary structure: H=helix, E=extended

(sheet), blank=other (loop)

PROF = PROF: Profile network prediction HeiDelberg

Rel_sec: reliability index for PROFsec prediction (0=low to 9=high)

Note: for the brief presentation strong predictions marked by

'*'

SUB_sec: subset of the PROFsec prediction, for all residues with an

expected average accuracy > 82% (tables in header)

NOTE: for this subset the following symbols are used:

L: is loop (for which above ' ' is used)

.: means that no prediction is made for this residue, as the

reliability is: Rel < 5

pH_sec: 'probability' for assigning helix (1=high, 0=low)

pE_sec: 'probability' for assigning strand (1=high, 0=low)

pL_sec: 'probability' for assigning neither helix, nor strand (1=high,0=low)

O_2_acc: observerd relative solvent accessibility (acc) in 2 states: b

= 0-16%, e = 16-100%.

P_2_acc: PROF predicted relative solvent accessibility (acc) in 2

states: b = 0-16%, e = 16-100%.

O_3_acc: observerd relative solvent accessibility (acc) in 3 states: b

= 0-9%, i = 9-36%, e = 36-100%.


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PROF results (detail)

....,....1....,....2....,....3....,....4....,....5....,....6....,....7....,....8....,..AA MAKNGGFSLFAKKEKRFIFEGRHSASDKLVNGEVSAFTEEEARKKLAKRGIRPLQITRVKTSSKRKITQEDITVFTRQLSTMIKAGLpH_sec ...... ..........

pH_sec ........ ..............pH_sec .. ......... ...............pH_sec ... .......... ................pH_sec .... .......... ................pH_sec .......... .......... ................pH_sec .......... ........... ... ................pH_sec ................ ... ............ ........ ................. pH_sec ......................... .............. ......... .................

---------------------------------------------------------------------------------------pE_secpE_secpE_sec . ...pE_sec . .... ....pE_sec .. . ....... .....pE_sec ....... ......... ......pE_sec .. ....... ......... ........pE_sec ....... . ......... .......... ......... ...pE_sec ......................... ........... ..................

---------------------------------------------------------------------------------------pL_sec .

pL_sec . . .. . ..

pL_sec . .. .. . ..pL_sec .... ... . .... .. ...pL_sec ..... ... .. .... ..... ...pL_sec ...... ..... .. ..... .......... ...pL_sec ...... .. . .......... ... ..... ........... ....pL_sec ........ ........................... ....... ............. ....pL_sec ....................................... ......................... .....

---------------------------------------------------------------------------------------OBS_accOBS_accOBS_accOBS_accOBS_accOBS_accOBS_accOBS_acc

OBS_acc---------------------------------------------------------------------------------------

PROF_acc . ... . ..

PROF_acc . .... . . .. ...PROF_acc . ..... . . . . .. ... . .PROF_acc . . .. . ...... . . . . . . . . ....... ... .PROF_acc . . .. .. . . . ...... . . . . ... . .... . . .......... ... . PROF_acc . .. .. .. . . ........ . . . ..... ... .... . . .......... .... . . . PROF_acc . .. .. .. . . .......... . . ..... ... .... . . ............... . . .. PROF_acc . .. .. ...... .......... . . ..... ... ...... . ............... . . .. .PROF_acc . .. .. ...... .......... . . ..... ... ...... . ............... . . .. .

---------------------------------------------------------------------------------------

Top - Summary - Details - PredictProtein

GLOBE prediction of globularity

------ GLOBE: prediction of protein globularity


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------ nexp = 172 (number of predicted exposed residues)--- nfit = 163 (number of expected exposed residues--- diff = 9.00 (difference nexp-nfit)--- =====> your protein appears as compact, as a globular domain---

------ GLOBE: further explanations preliminaryily in:--- http://www.columbia.edu/~rost/Papers/98globe.html------ END of GLOBE

END of results for file predict_h31294

Quotes for methods

PredictProtein:PredicProtein: B Rost (1996) Methods in Enzymology, 266:525-539Author: B Rost

Contact: [email protected]

Url: http://cubic.bioc.columbia.edu

Version: 1.99.08

Description: PredictProtein is the acronym for all prediction programs run.

1.

ProSite:K Hofmann , P Bucher, L Falquet, A Bairoch:: The PROSITE database, its status in 1999. Nucleic Acids

Res, 27, 215-219, 1999

Author: Kay Hofmann, Philip Bucher, and Amos Bairoch (SIB, Geneva, Switzerland)

Contact: [email protected]: http://www.expasy.ch/prosite/

Version: 99.07

Description: PROSITE is a database of functional motifs. ScanProsite, finds all functional motifs in your

sequence that are annotated in the ProSite db

2.

SEG:J C Wootton, and S Federhen:: Analysis of compositionally biased regions in sequence databases. Methods

in Enzymology, 266, 554-571, 1996

Author: John C Wootton and Scott Federhen (NCBI, Washington)


Url: http://trex.musc.edu/manuals/unix/seg.html

Version: 1994

Description: SEG divides sequences into regions of low-, and high-complexity. Low-complexity regionstypically correspond to 'simple sequences' or 'compositionally-biased' regions

3.

ProDom:F Corpet, F Servant, J Gouzy, and D Kahn:: ProDom and ProDom-CG: tools for protein domain analysis

and whole genome comparisons. Nucleic Acids Res, 28, 267-269, 2000

Author: Florence Corpet, Florence Servant, Jerome Gouzy, and Daniel Kahn


Url: http://protein.toulouse.inra.fr/prodom.html

Version: 2000.1

Description: ProDom is a database of putative protein domains. The database is searched with BLAST

for domains corresponding to your protein

4.


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MaxHom:C Sander, and R Schneider::Database of Homology-Derived Structures and the Structural Meaning of

Sequence Alignment. Proteins, 9, 56-68, 1991

Author: Reinhard Schneider (LION, Boston) and Chris Sander (Millenium, Boston)


Url: local

Version: 1.99.04

Description: MaxHom is a dynamic multiple sequence alignment program which finds similar sequences

in a database.

5.

MView:N P Brown, C Leroy, and C Sander:: MView: A Web compatible database search or multiple alignment

viewer. Bioinformatics, 14, 380-381, 1998

Author: Nigel Brown


Url: http://mathbio.nimr.mrc.ac.uk/~nbrown/mview/

Copyright: Copyright (C) Nigel P. Brown, 1997-1998. All rights reserved.

Version: 1.40.2

Description: MView is a program converting multiple sequence alignments into fancy HTML formatted

output

6.

PHD:B Rost:: PHD: predicting one-dimensional protein structure by profile based neural networks. Methods in

Enzymology, 266, 525-539, 1996

Author: Burkhard Rost (CUBIC, Columbia Univ, New York)


Url: http://cubic.bioc.columbia.edu/predictprotein

Version: 1.96

Description: PHD is a suite of programs predicting 1D structure (secondary structure, solvent

accessibility) from multiple sequence alignments

7.

PHDhtm:B Rost, P Fariselli & R Casadio (1996) Protein Science, 7:1704-1718Author: B Rost


Url: http://cubic.bioc.columbia.eduVersion: 1.96

Description: PHDhtm predicts the location and topology of transmembrane helices from multiple

sequence alignments.

8.

PROF:B Rost:: PROF: predicting one-dimensional protein structure by profile based neural networks.

unpublished, 2000

Author: Burkhard Rost (CUBIC, Columbia Univ, New York)



Version: 2000_04

Description: Improved version of PHD: Profile-based neural network prediction of protein structure

9.

PROFsec:B Rost (2000) in submissionAuthor: B Rost



Version: 2000_04

Description: PROFsec predicts secondary structure from multiple sequence alignments.

10.

PROFacc:B Rost (2000) in submissionAuthor: B Rost



11.


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Version: 2000_04

Description: PROFacc predicts per residue solvent accessibility from multiple sequence alignments.

GLOBE:B Rost::Short yeast ORFs: expressed protein or not? unpublished, 2000Author: Burkhard Rost (CUBIC, Columbia Univ, New York)



Version: 1.98.05

Description: GLOBE predicts the globularity of a protein

12.

COILS:A Lupas:: Prediction and Analysis of Coiled-Coil Structures. Methods in Enzymology, 266, 513-525, 1996

Author: Andrei Lupas (Max Planck Institute, Tuebingen, Germany)


Url: local

Version: 1999_2.2

Description: COILS finds coiled-coil regions in your protein

13.

ASP: Young et al.:: Protein Science(1999) 8:1752-64.Author: Malin Young (Sandia National Laboratory), Kent Kirshenbaum(Caltech), and Stefan Highsmith

Contact: [email protected]; [email protected]; [email protected]

Version: 1.0

Description: ASP finds regions that are most likely to behave as switches in proteins known to exhibit

this behavior

14.

Links: TOP

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