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SUPPLEMENT 1:
Table of protein sequences and associated NCBI accession numbers stored in the LRRdb. The 186 sequences
were manually separated and used to generate the LRR-based PSSMs which form the basis of the LRRfinder
application.
TLR Accession Length Species Name
1 Q15399 786aa Homo sapiens Toll-like receptor 1
1 ABO15772 796aa Tetraodon nigroviridis Toll-like receptor 1
1 AAW69368 812aa Takifugu rubripes TLR1
1 AAI63271 795aa Danio rerio Toll-like receptor 1
1 BAD67422 818aa Gallus gallus Toll-like receptor 1
1 XP_001138777 786aa Pan troglodytes PREDICTED: Toll-like receptor 1 isoform 1
1 XP_001088852 786aa Macaca mulatta PREDICTED: Toll-like receptor
1 NP_109607 795aa Mus musculus Toll-like receptor 1
1 ACB41373 789aa Canis lupus familiaris Toll-like receptor 1
1 NP_001026945 796aa Sus scrofa Toll-like receptor 1
1 XP_00149894 789aa Equus caballus PREDICTED: similar to toll-like receptor 1
1 NP_001039969 727aa Bos taurus Toll-like receptor 1
1 ABU86938 727aa Bos indicus Toll-like receptor 1
2 AAW69370 810aa Takifugu rubripes TLR2
2 ABD17347 790aa Ictalurus punctatus Toll-like receptor 2
2 O60603 784aa Homo sapiens Toll-like receptor 2
2 BAD01044 818aa Paralichthys olivaceus Toll-like receptor 2
2 NP_997977 788aa Danio rerio Toll-like receptor 2
2 NP_989609 793aa Gallus gallus Toll-like receptor 2
2 NP_001075265 784aa Equus caballus Toll-like receptor 2
2 NP_001005264 785aa Canis lupus familiaris Toll-like receptor 2
2 NP_001076250 784aa Oryctolagus cuniculus Toll-like receptor 2
2 XP_001155239 784aa Pan troglodytes PREDICTED: Toll-like receptor 2 isoform 1
2 AAD46477 503aa Cricetulus griseus Toll-like receptor precursor
2 NP_036035 784aa Mus musculus Toll-like receptor 2
2 NP_942064 784aa Rattus norvegicus Toll-like receptor 2
2 NP_998926 785aa Sus scrofa Toll-like receptor 2
2 ACB72731 784aa Giraffa camelopardalis Toll-like receptor 2
2 NP_776622 784aa Bos taurus Toll-like receptor 2
2 ABY90177 784aa Bos indicus Toll-like receptor 2
2 ABI58266 784aa Ovis aries Toll-like receptor 2
2 ACB72728 784aa Bison bison Toll-like receptor 2
2 ABC00775 784aa Bubalus bubalis Toll-like receptor 2
2 ABB97025 784aa Boselaphus tragocamelus Toll-like receptor 2
2 ABI31733 784aa Capra hircus Toll-like receptor 2
2 ACB72729 784aa Capris ibex Toll-like receptor 2
2 ACB72727 783aa Antidorcas marsupialis Toll-like receptor 2
2 ACB72730 783aa Damaliscus pygargus
phillipsi Toll-like receptor 2
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TLR Accession Length Species Name
2.1 Q9DD78 793aa Gallus gallus Toll-like receptor 2 type 1 precursor
2.1 XP_001182083 794aa Strongylocentrotus purpuratus
PREDICTED: similar to toll-like receptor 2.1
2.2 Q9DGB6 781aa Gallus gallus Toll-like receptor 2 type 2 precursor
3 NP_001011691 1011aa Gallus gallus Toll-like receptor 3
3 O15455 904aa Homo sapiens Toll-like receptor 3
3 AAW69373 894aa Takifugu rubripes TLR3
3 BAD01047 961aa Paralichthys olivaceus Toll-like receptor 3
3 AAX68425 913aa Onchorhynchus mykiss Toll-like receptor 3
3 ABD93872 905aa Ictalurus punctatus Toll-like receptor 3
3 NP_001013287 903aa Danio rerio Toll-like receptor 3
3 ABL11471 905aa Gobiocypris rarus Toll-like receptor 3
3 ABC86865 904aa Carassus auratus Toll-like receptor 3
3 ABC95781 905aa Loxodonta africana Toll-like receptor 3
3 NP_001075688 905aa Oryctolagus cuniculus Toll-like receptor 3
3 NP_001075267 904aa Equus caballus Toll-like receptor 3
3 NP_001090913 905aa Sus scrofa Toll-like receptor 3
3 NP_001073298 904aa Felis catus Toll-like receptor 3
3 ABG77523 904aa Boselaphus tragocamelus Toll-like receptor 3
3 ABF59103 904aa Bubalus bubalis Toll-like receptor 3
3 NP_001008664 904aa Bos taurus Toll-like receptor 3
3 ABN71666 904aa Bos indicus Toll-like receptor 3
3 ABD77101 905aa Cavia porcellus Toll-like receptor 3
3 NP_942086 905aa Rattus norvegicus Toll-like receptor 3
3 NP_569054 905aa Mus musculus Toll-like receptor 3
3 NP_001031762 904aa Macaca mulatta Toll-like receptor 3
3 XP_526756 904aa Pan troglodytes PREDICTED: Toll-like receptor 3 isoform 2
4 NP_001025864 843aa Gallus gallus Toll-like receptor 4
4 NP_001093239 843aa Equus caballus Toll-like receptor 4
4 AAF05316 839aa Homo sapiens Toll-like receptor 4
4 AAD41891 838aa Cricetulus griseus Toll-like receptor 4
4 NP_062051 835aa Rattus norvegicus Toll-like receptor 4
4 NP_067272 835aa Mus musculus Toll-like receptor 4
4 AAF05320 839aa Pan paniscus Toll-like receptor 4
4 AAM18616 828aa Pongo pygmaeus Toll-like receptor 4
4 AAM18617 837aa Gorilla gorilla Toll-like receptor 4
4 AAX63196 799aa Macaca mulatta Toll-like receptor 4
4 AAF07059 826aa Papio cynocephalus anubis Toll-like receptor 4
4 NP_001093239 843aa Oryctolagus cuniculus Toll-like receptor 4
4 NP_001002950 636aa Canis lupus familiaris Toll-like receptor 4
4 NP_001009223 833aa Felis catus Toll-like receptor 4
4 BAF76728 841aa Tursicps truncatus Toll-like receptor 4
4 NP_001106510 841aa Sus scrofa Toll-like receptor 4
4 ABB97024 841aa Boselaphus tragocamelus Toll-like receptor 4
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TLR Accession Length Species Name
4 AAZ38830 841aa Bison bison Toll-like receptor 4
4 ABY85152 841aa Bubalus bubalis Toll-like receptor 4
4 NP_776623 841aa Bos taurus Toll-like receptor 4
4 ABY85151 841aa Bos indicus Toll-like receptor 4 precursor
4b NP_997978 817aa Danio rerio Toll-like recptor 4b
5 NP_001019757 861aa Gallus gallus Toll-like receptor 5
5 O60602 858aa Homo sapiens Toll-like receptor 5
5 AAW69374 884aa Takifugu rubripes Toll-like receptor 5
5 NP_001118216 879aa Onchorhynchus mykiss Membrane toll-like receptor 5
5 XP_001512233 858aa Ornithorhynchus anatinus PREDICTED: similar to TLR5 protein
5 ACB41374 858aa Canis lupus familiaris Toll-like receptor 5
5 XP_001063885 859aa Rattus norvegicus PREDICTED: similar to toll-like receptor 5 precursor
5 ABD73995 859aa Mus musculus molossinus Toll-like receptor 5
5 XP_001099501 858aa Macaca mulatta PREDICTED: similar to toll-like receptor 5
5 NP_001116674 856aa Sus scrofa Toll-like receptor 5
5 ABC68311 858aa Bos taurus Toll-like receptor 5
5 ABU86930 858aa Bos indicus Toll-like receptor 5
6 NP_001007489 818aa Gallus gallus Toll-like receptor 6
6 Q9Y2C9 796aa Homo sapiens Toll-like receptor 6
6 XP_001498680 796aa Equus caballus PREDICTED: similar to toll-like receptor 6
6 AAZ52552 789aa Dasypus novemcinctus Toll-like receptor 6
6 ACB41375 794aa Canis lupus familiaris Toll-like receptor 6
6 XP_001089296 796aa Macaca mulatta Toll-like receptor 6
6 XP_001139197 796aa Pan troglodytes PREDICTED: Toll-like receptor 6 isoform 2
6 NP_997487 806aa Rattus norvegicus Toll-like receptor 6
6 NP_035734 806aa Mus musculus Toll-like receptor 6
6 NP_998925 796aa Sus scrofa Toll-like receptor 6
6 NP_001001159 793aa Bos taurus Toll-like receptor 6
7 NP_001120883 1054aa Xenopus tropicalis Toll-like receptor 7
7 Q9NYK1 1049aa Homo sapiens Toll-like receptor 7
7 AAW69375 1047aa Takifugu rubripes TLR7
7 XP_701101 1099aa Danio rerio PREDICTED: Toll-like receptor 7
7 NP_001011688 1059aa Gallus gallus Toll-like receptor 7
7 ABK51522 1047aa Anas platyrhynchos Toll-like receptor 7
7 ABC95782 1049aa Loxodonta africana Toll-like receptor 7
7 NP_001075240 1050aa Equus caballus Toll-like receptor 7
7 NP_001041589 1050aa Canis lupus familiaris Toll-like receptor 7
7 NP_001073602 1050aa Felis catus Toll-like receptor 7
7 XP_001095269 1049aa Macaca mulatta PRECICTED: Toll-like receptor 7
7 XP_528892 1057aa Pan troglodytes PREDICTED: Toll-like receptor 7
7 NP_001090903 1050aa Sus scrofa Toll-like receptor 7
7 ACA34988 1057aa Bison bonasus Toll-like receptor 7
7 ACA34989 1045aa Ovis aries Toll-like receptor 7
7 NP_001028933 1058aa Bos taurus Toll-like receptor 7
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TLR Accession Length Species Name
7 ABN71674 1058aa Bos indicus Toll-like receptor 7
7 NP_001091051 1050aa Rattus norvegicus Toll-like receptor 7
7 CAM14953 1050aa Mus musculus Toll-like receptor 7
8 AAW69376 1017aa Takifugu rubripes TLR8
8 Q9NR97 1041aa Homo sapiens Toll-like receptor 8
8 ABS28968 1026aa Loxodonta africana Toll-like receptor 8
8 NP_001104771 1038aa Equus caballus Toll-like receptor 8
8 ABS28967 1039aa Felis catus Toll-like receptor 8
8 ABM92444 1029aa Rattus norvegicus Toll-like receptor 8
8 NP_573475 1032aa Mus musculus Toll-like receptor 8
8 XP_001095602 1037aa Macaca mulatta PREDICTED: Toll-like receptor 8
8 XP_001134921 1038aa Pan troglodytes PREDICTED: Toll-like receptor 8 isofrom 1
8 NP_999352 1028aa Sus scrofa Toll-like receptor 8
8 ABQ52584 1033aa Bos taurus Toll-like receptor 8
8 ABN71684 1033aa Bos indicus Toll-like receptor 8
9 AAW69377 1045aa Takifugu rubripes TLR9
9 Q9NR96 1032aa Homo sapiens Toll-like receptor 9
9 BAE80691 1065aa Paralichthys olivaceus Toll-like receptor 9
9 AAI63628 1057aa Danio rerio Toll-like receptor 9
9 NP_001117125 1074aa Salmo salar Toll-like receptor 9
9 ACC93939 1074aa Onchorhynchus mykiss Toll-like receptor 9
9 ABY79218 1063aa Dentex tumifrons Toll-like receptor 9
9 ABY79217 1063aa Pagrus major Toll-like receptor 9
9 ABY97216 1063aa Acanthopagrus sclegelli Toll-like receptor 9
9 AAW81698 1063aa Sparus aurata Toll-like receptor 9
9 NP_001075259 1031aa Equus caballus Toll-like receptor 9
9 NP_001002998 1032aa Canis lupus familiaris Toll-like receptor 9
9 NP_001009285 1031aa Felis catus Toll-like receptor 9
9 AAX14714 1032aa Aotus nancymaae Toll-like receptor 9
9 XP_001090094 1055aa Macaca mulatta PREDICTED: Toll-like receptor 9
9 XP_001171324 1032aa Pan troglodytes PREDICTED: Toll-like receptor 9 isoform 3
9 NP_937764 1032aa Rattus norvegicus Toll-like receptor 9
9 NP_112455 1032aa Mus musculus Toll-like receptor 9
9 NP_999123 1030aa Sus scrofa Toll-like receptor 9
9 ACE88251 1029aa Capra hircus Toll-like receptor 9
9 ACE88254 1029aa Boselaphus tragocamelus Toll-like receptor 9
9 NP_001011555 1029aa Ovis aries Toll-like receptor 9
9 NP_898904 1029aa Bos taurus Toll-like receptor 9
10 XP_001512990 796aa Ornithorhynchus anatinus PREDICTED: Toll-like receptor 10
10 XP_001138106 811aa Pan troglodytes PREDICTED: Toll-like receptor 10 isoform 1
10 NP_001025705 811aa Sus scrofa Toll-like receptor 10
10 NP_001070386 812aa Bos taurus Toll-like receptor 10
10 ABU86948 812aa Bos indicus Toll-like receptor 10
10 Q9BXR5 811aa Homo sapiens Toll-like receptor 10
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TLR Accession Length Species Name
11 Q6R5P0 926aa Mus musculus Toll-like receptor 11
12 NP_001102152 904aa Rattus norvegicus Toll-like receptor 12
12 Q6QNU9 906aa Mus musculus Toll-like receptor 12
13 Q6R5N8 991aa Mus musculus Toll-like receptor 13
14 AAW69369 871aa Takifugu rubripes TLR14
15 ABB71177 868aa Gallus gallus Toll-like receptor 15
16 NP_001092324 804aa Gallus gallus Toll-like receptor 16
21 AAW69371 965aa Takifugu rubripes TLR21
21 CAQ13807 989aa Danio rerio Toll-like receptor 21
21 ABF74623 986aa Ictalurus punctatus Toll-like receptor 21
22 NP_001122147 947aa Danio rerio Toll-like receptor 22
22 AAW69372 950aa Takifugu rubripes TLR22
S5 AAW69378 641aa Takifugu rubripes TLRS5
S5 NP_001089098 651aa Xenopus laevis Soluble toll-like receptor 5
II NP_001117891 969aa Onchorhynchus mykiss Toll-like receptor II
a Q33E93 813aa Paralichthys olivaceus Toll-like receptor a
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SUPPLEMENT 2:
Screenshot of the form used to send data to the LRRfinder application. Default significance boundaries are set
for classification of LRRfinder results into significant (default E < 0.05) or insignificant (default 0.05 ≥ E < 0.2)
LRRs. LRRfinder is optimized for TLRs, thus TLR specific options have been included to search the input
sequence for LRR N-terminal, LRR C-terminal and TIR domains. This is achieved using simple character
matching of the separated domains from the LRRdb protein sequences.
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SUPPLEMENT 3:
Screenshot of LRRfinder categorized results for protein sequence ABY79215 from Acanthopagrus berda.
LRRfinder is based upon a database of LRRs from TLRs and so performs at its optimum level with TLR or
similar sequences. When compared against other applications which predict LRRs, LRRfinder is able to
identify several LRRs which are missed by these applications. For example, when entering the sequence for
ABY79215 into PFAM, LRRfinder identifies 3 LRRs not found by PFAM (LRRfinder amino acid start
positions 163, 332 and 500). Additionally, PFAM predicts an LRR with start position 120 (N.B.) which
LRRfinder shows to be misidentified using the LRRdb (see LRRfinder LRR with start position 118).
N.B. PFAM start positions are one place less than LRRfinder so LRRfinder start position would be amino
acid 121)
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SUPPLEMENT 4:
Figure A:
Screenshot of LRRfinder domain search results for protein sequence ABY79215 from Acanthopagrus berda.
Results show matches for all three domains for which LRRfinder provides search options as well as the
predicted signal and transmembrane regions calculated from the start and stop positions of the LRRCT, LRRNT
and TIR domains. The results table gives a prediction for each domain based on the average of all sequence
matches over 95%. Additionally it gives the sequences which were used for this calculation.
Figure B:
Screenshot of LRRfinder overlap results for protein sequence ABY79215 from Acanthopagrus berda. When
predicting potential LRRs overlapping of predicted frames often occurs. LRRfinder finds the optimum
prediction using the bit-score of each frame and takes the LRR with the highest bit-score into the general results
table. However, this overlap removal may result in gaps forming where an overlap may in fact be a true LRR.
This is accounted for by re-running this process whilst checking for overlaps which may fill gaps between LRRs
already identified and replacing them into the categorized results with the status “Replaced”. Additionally,
LRRfinder searches the final overlaps to find those in each cluster which are most likely to be mis-identified
overlaps and emboldens and underlines them.
Figure C:
Screenshot of LRRfinder graphical viewer for protein sequence ABY79215 from Acanthopagrus berda. When
sequences over ~900 amino acids are entered the graphical viewer halves the lengths in its creation to fit the
predictions into the window. The graphical viewer shows predicted LRRs and domains to provide the user with
a visual representation of the results.
A
B
C
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SUPPLEMENT 5:
Screenshot of the form used to send data to the LRRdb and sequence search application (Figure A). The
LRRfinder sequence database contains TLR sequences which may be useful when using LRRfinder or if the
user requires a number of TLR sequences for multiple alignment. The LRRdb search is used to query TLR
sequences which were separated for the creation of LRRfinder. The user may submit a query for a number of
TLRs (Figure C), species (Figure B), regions (Figure D) as well as a particular accession number or LRR HS
region following the 11 amino acid LxxLxLxxN/CxL consensus.
A
B C
D
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SUPPLEMENT 6:
Screenshot of LRRfinder sequence search results using the species query “Felis” (Figure A). It is possible to
obtain selected sequences in FASTA format (Figure B) or transfer a sequence into LRRfinder for analysis.
A
B
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SUPPLEMENT 7:
Screenshot of LRRdb search results using the accession query “ABY79216” for the species Acanthopagrus
schlegelii. The tabulated results display, in order of occurrence, the regions into which the sequence was
separated and their respective lengths. Several tables such as this may be displayed as results and a show/hide
toggle is used to compact these into a screen-friendly format.
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SUPPLEMENT 8:
Screenshot of LRRdb search results for LRR-HS region query “LTWISLIYNYE” identified as a database hit in
the previously mentioned LRRfinder analysis of protein ABY79215 from Acanthopagrus berda.. The tabulated
results display, in order of occurrence in the LRRdb, the matches to the query sequence in other species present
in the database.
