YRC Public Data Repository - Protein Structure Prediction

Protein:	SYV_ECOLI
Organism:	Escherichia coli
Length:	951 amino acids
Reference:	Drew K, et al. (2011) The proteome folding project: Proteome-scale prediction of structure and function. Genome Res. 2011 Sep 16

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Top Sequence Alignment Hits

Listed below are up to the top 10 sequence alignment matches, by species, for the PSI-BLAST search against the protein sequence for SYV_ECOLI.

Description	E-value	Query Range	Subject Range
gi\|238714082, gi... - gi\|77957034\|ref\|ZP_00821102.1\| COG0525: Valyl-tRNA synthetase [Yersinia bercovieri ATCC 43970], gi\|2...	944.0	[0..1]	[951..15]
SYV_YERPS - Valine--tRNA ligase OS=Yersinia pseudotuberculosis serotype I (strain IP32953) GN=valS PE=3 SV=1 gi\|153948685, gi... - gi\|77631524\|ref\|ZP_00794110.1\| COG0525: Valyl-tRNA synthetase [Yersinia pseudotuberculosis IP 31758]... SYV_YERPS - Valine--tRNA ligase OS=Yersinia pseudotuberculosis GN=valS PE=3 SV=1 gi\|186696917, gi... - gi\|186893891\|ref\|YP_001871003.1\| valyl-tRNA synthetase [Yersinia pseudotuberculosis PB1/+], gi\|18669...	944.0	[0..1]	[951..15]
gi\|94415871, gi\|... - gi\|94415871\|ref\|ZP_01295706.1\| hypothetical protein PaerP_01002441 [Pseudomonas aeruginosa PA7], gi\|...	942.0	[0..1]	[951..1]
SYV_SALCH - Valyl-tRNA synthetase OS=Salmonella choleraesuis GN=valS PE=3 SV=1 SYV_SALCH - Valine--tRNA ligase OS=Salmonella choleraesuis (strain SC-B67) GN=valS PE=3 SV=1 gi\|224470827, gi... - gi\|224586299\|ref\|YP_002640098.1\| valyl-tRNA synthetase [Salmonella enterica subsp. enterica serovar ... SYV_SALCH - Valine--tRNA ligase OS=Salmonella choleraesuis GN=valS PE=3 SV=1	942.0	[0..1]	[951..1]
gi\|77978582 - gi\|77978582\|ref\|ZP_00834009.1\| COG0525: Valyl-tRNA synthetase [Yersinia intermedia ATCC 29909]	942.0	[0..1]	[951..15]
gi\|238787641, gi... - gi\|77974071\|ref\|ZP_00829614.1\| COG0525: Valyl-tRNA synthetase [Yersinia frederiksenii ATCC 33641], g...	942.0	[0..1]	[951..15]
gi\|229695453, gi... - gi\|229839087\|ref\|ZP_04459246.1\| valyl-tRNA synthetase [Yersinia pestis biovar Orientalis str. PEXU2]... gi\|229700353, gi... - gi\|229896575\|ref\|ZP_04511742.1\| valyl-tRNA synthetase [Yersinia pestis Pestoides A], gi\|229700353\|gb... gi\|229687142, gi... - gi\|229899650\|ref\|ZP_04514791.1\| valyl-tRNA synthetase [Yersinia pestis biovar Orientalis str. India ... gi\|165991094, gi... - gi\|166010187\|ref\|ZP_02231085.1\| valyl-tRNA synthetase [Yersinia pestis biovar Antiqua str. E1979001]... gi\|165925800, gi... - gi\|165925800\|ref\|ZP_02221632.1\| valyl-tRNA synthetase [Yersinia pestis biovar Orientalis str. F19910... gi\|167398378, gi... - gi\|167398378\|ref\|ZP_02303902.1\| valyl-tRNA synthetase [Yersinia pestis biovar Antiqua str. UG05-0454... gi\|166204551, gi... - gi\|166214319\|ref\|ZP_02240354.1\| valyl-tRNA synthetase [Yersinia pestis biovar Antiqua str. B42003004... SYV_YERPE - Valine--tRNA ligase OS=Yersinia pestis GN=valS PE=3 SV=1 gi\|167423189, gi... - gi\|167423189\|ref\|ZP_02314942.1\| valyl-tRNA synthetase [Yersinia pestis biovar Mediaevalis str. K1973... gi\|167420487, gi... - gi\|167420487\|ref\|ZP_02312240.1\| valyl-tRNA synthetase [Yersinia pestis biovar Orientalis str. MG05-1... gi\|45440493, gi\|... - gi\|45440493\|ref\|NP_992032.1\| valyl-tRNA synthetase [Yersinia pestis biovar Microtus str. 91001], gi\|... gi\|22124656, gi\|... - gi\|22124656\|ref\|NP_668079.1\| valyl-tRNA synthetase [Yersinia pestis KIM], gi\|21957465\|gb\|AAM84330.1\|... gi\|108780848, gi... - gi\|108808935\|ref\|YP_652851.1\| valyl-tRNA synthetase [Yersinia pestis Antiqua], gi\|108780848\|gb\|ABG14... gi\|16123591, gi\|... - gi\|218930459\|ref\|YP_002348334.1\| valyl-tRNA synthetase [Yersinia pestis CO92], gi\|16123591\|ref\|NP_40... gi\|108774458, gi... - gi\|229901013\|ref\|ZP_04516137.1\| valyl-tRNA synthetase [Yersinia pestis Nepal516], gi\|229682352\|gb\|EE... gi\|149289152, gi... - gi\|153997515\|ref\|ZP_02022615.1\| valyl-tRNA synthetase [Yersinia pestis CA88-4125], gi\|149289152\|gb\|E... gi\|145600507, gi... - gi\|145600507\|ref\|YP_001164583.1\| valyl-tRNA synthetase [Yersinia pestis Pestoides F], gi\|145212203\|g... gi\|165915473, gi... - gi\|89102510\|ref\|ZP_01175138.1\| COG0525: Valyl-tRNA synthetase [Yersinia pestis biovar Orientalis str... gi\|162418871, gi... - gi\|77634908\|ref\|ZP_00797000.1\| COG0525: Valyl-tRNA synthetase [Yersinia pestis Angola], gi\|162418871...	941.0	[0..1]	[951..15]
SYV_PSEAE - Valyl-tRNA synthetase OS=Pseudomonas aeruginosa GN=valS PE=3 SV=1 SYV_PSEAE - Valine--tRNA ligase OS=Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) ...	940.0	[0..1]	[951..1]
SYV_SALTI - Valyl-tRNA synthetase OS=Salmonella typhi GN=valS PE=3 SV=1 gi\|29140394, gi\|... - gi\|29144755\|ref\|NP_808097.1\| valyl-tRNA synthetase [Salmonella enterica subsp. enterica serovar Typh... SYV_SALTI - Valine--tRNA ligase OS=Salmonella typhi GN=valS PE=3 SV=1 gi\|16763276 - gi\|16763276\|ref\|NP_458893.1\| valyl-tRNA synthetase [Salmonella enterica subsp. enterica serovar Typh... gi\|213650371 - gi\|213650371\|ref\|ZP_03380424.1\| valyl-tRNA synthetase [Salmonella enterica subsp. enterica serovar T... gi\|213427638 - gi\|213427638\|ref\|ZP_03360388.1\| valyl-tRNA synthetase [Salmonella enterica subsp. enterica serovar T...	940.0	[0..1]	[951..1]
gi\|107103354 - gi\|107103354\|ref\|ZP_01367272.1\| hypothetical protein PaerPA_01004423 [Pseudomonas aeruginosa PACS2]	939.0	[0..1]	[951..1]

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Predicted Domain #1

Region A:
Residues: [1-951]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MEKTYNPQDI EQPLYEHWEK QGYFKPNGDE SQESFCIMIP PPNVTGSLHM GHAFQQTIMD  60
   61 TMIRYQRMQG KNTLWQVGTD HAGIATQMVV ERKIAAEEGK TRHDYGREAF IDKIWEWKAE 120
  121 SGGTITRQMR RLGNSVDWER ERFTMDEGLS NAVKEVFVRL YKEDLIYRGK RLVNWDPKLR 180
  181 TAISDLEVEN RESKGSMWHI RYPLADGAKT ADGKDYLVVA TTRPETLLGD TGVAVNPEDP 240
  241 RYKDLIGKYV ILPLVNRRIP IVGDEHADME KGTGCVKITP AHDFNDYEVG KRHALPMINI 300
  301 LTFDGDIRES AQVFDTKGNE SDVYSSEIPA EFQKLERFAA RKAVVAAVDA LGLLEEIKPH 360
  361 DLTVPYGDRG GVVIEPMLTD QWYVRADVLA KPAVEAVENG DIQFVPKQYE NMYFSWMRDI 420
  421 QDWCISRQLW WGHRIPAWYD EAGNVYVGRN EDEVRKENNL GADVVLRQDE DVLDTWFSSA 480
  481 LWTFSTLGWP ENTDALRQFH PTSVMVSGFD IIFFWIARMI MMTMHFIKDE NGKPQVPFHT 540
  541 VYMTGLIRDD EGQKMSKSKG NVIDPLDMVD GISLPELLEK RTGNMMQPQL ADKIRKRTEK 600
  601 QFPNGIEPHG TDALRFTLAA LASTGRDINW DMKRLEGYRN FCNKLWNASR FVLMNTEGQD 660
  661 CGFNGGEMTL SLADRWILAE FNQTIKAYRE ALDSFRFDIA AGILYEFTWN QFCDWYLELT 720
  721 KPVMNGGTEA ELRGTRHTLV TVLEGLLRLA HPIIPFITET IWQRVKVLCG ITADTIMLQP 780
  781 FPQYDASQVD EAALADTEWL KQAIVAVRNI RAEMNIAPGK PLELLLRGCS ADAERRVNEN 840
  841 RGFLQTLARL ESITVLPADD KGPVSVTKII DGAELLIPMA GLINKEDELA RLAKEVAKIE 900
  901 GEISRIENKL ANEGFVARAP EAVIAKEREK LEGYAEAKAK LIEQQAVIAA L

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	1000.0
Match:	1gaxA
Description:	Valyl-tRNA synthetase (ValRS) C-terminal domain; Valyl-tRNA synthetase (ValRS)
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
ligase activity, forming aminoacyl-tRNA and related compounds	7.16276509815667	bayes_pls_golite062009
ligase activity, forming carbon-oxygen bonds	7.16276509815667	bayes_pls_golite062009
aminoacyl-tRNA ligase activity	7.13957775963187	bayes_pls_golite062009
valine-tRNA ligase activity	7.13767629265822	bayes_pls_golite062009
leucine-tRNA ligase activity	7.03538514482698	bayes_pls_golite062009
isoleucine-tRNA ligase activity	6.38633897147986	bayes_pls_golite062009
ligase activity	6.11211476973434	bayes_pls_golite062009
glutamate-tRNA ligase activity	2.63681738794687	bayes_pls_golite062009
methionine-tRNA ligase activity	2.56893064485672	bayes_pls_golite062009
catalytic activity	2.37674226834122	bayes_pls_golite062009
tyrosine-tRNA ligase activity	1.88984817882585	bayes_pls_golite062009
arginine-tRNA ligase activity	1.50161401062914	bayes_pls_golite062009
tryptophan-tRNA ligase activity	1.14187887833901	bayes_pls_golite062009
cysteine-tRNA ligase activity	0.844943947059557	bayes_pls_golite062009
transferase activity, transferring phosphorus-containing groups	0.625793556381714	bayes_pls_golite062009
binding	0.485102284225571	bayes_pls_golite062009
nucleic acid binding	0.449504767632354	bayes_pls_golite062009
nucleotidyltransferase activity	0.2293846471193	bayes_pls_golite062009
glutamine-tRNA ligase activity	0.118292082006187	bayes_pls_golite062009

TMHMM	2.0c	PSIPRED	v2.61
SignalP	3.0	COILS	1999
DISOPRED	v0.1	NCBI nr	06/2007
PSI-BLAST	2.2.18	FFAS	ffas03
PDB	06/2007	Pfam	22
HMMER	2.3.2

View Structure Prediction Details

Top Sequence Alignment Hits

Predicted functions: