YRC Public Data Repository - Protein Structure Prediction

Protein:	SYV_YERPE
Organism:	Yersinia pestis
Length:	965 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_YERPE.

Description	E-value	Query Range	Subject Range
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...	0.0	[1..965]	[1..965]
gi\|238714082, gi... - gi\|77957034\|ref\|ZP_00821102.1\| COG0525: Valyl-tRNA synthetase [Yersinia bercovieri ATCC 43970], gi\|2...	0.0	[1..965]	[1..965]
gi\|238787641, gi... - gi\|77974071\|ref\|ZP_00829614.1\| COG0525: Valyl-tRNA synthetase [Yersinia frederiksenii ATCC 33641], g...	0.0	[1..965]	[1..965]
gi\|77978582 - gi\|77978582\|ref\|ZP_00834009.1\| COG0525: Valyl-tRNA synthetase [Yersinia intermedia ATCC 29909]	0.0	[1..965]	[1..965]
SYV_PHOLL - Valyl-tRNA synthetase OS=Photorhabdus luminescens subsp. laumondii GN=valS PE=3 SV=1 SYV_PHOLL - Valine--tRNA ligase OS=Photorhabdus luminescens subsp. laumondii (strain DSM 15139 / CIP 105565 / TT...	0.0	[1..965]	[1..965]
gi\|94415871, gi\|... - gi\|94415871\|ref\|ZP_01295706.1\| hypothetical protein PaerP_01002441 [Pseudomonas aeruginosa PA7], gi\|...	0.0	[15..965]	[1..950]
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) ...	0.0	[15..965]	[1..950]
gi\|116051862, gi... - gi\|32038982\|ref\|ZP_00137254.1\| COG0525: Valyl-tRNA synthetase [Pseudomonas aeruginosa UCBPP-PA14], g...	0.0	[15..965]	[1..950]
gi\|107103354 - gi\|107103354\|ref\|ZP_01367272.1\| hypothetical protein PaerPA_01004423 [Pseudomonas aeruginosa PACS2]	0.0	[15..965]	[1..950]
gi\|194547723, gi... - gi\|84319398\|ref\|ZP_00967795.1\| COG0525: Valyl-tRNA synthetase [Pseudomonas aeruginosa C3719], gi\|254...	0.0	[15..965]	[1..950]

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Predicted Domain #1

Region A:
Residues: [1-965]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MENTPSHINK TEPSLDKTYS PQEIEQPLYE HWEKQGYFKP NGDTSKESYC IMIPPPNVTG  60
   61 SLHMGHAFQQ TIMDTLIRYQ RMQGKNTLWQ AGTDHAGIAT QMVVERKIAA EEGKTRHDYG 120
  121 RDAFIDKIWE WKGESGGTIT RQMRRLGNSV DWERERFTMD EGLSNAVKEV FVRLHKEDLI 180
  181 YRGKRLVNWD PKLRTAISDL EVENRESKGS MWHLRYPLAD GAKTAEGKDY LVVATTRPET 240
  241 VLGDTGVAVN PEDPRYKDLI GKEVILPLVG RRIPILGDEH ADMEKGTGCV KITPAHDFND 300
  301 YEVGKRHALP MINILTFDGD IRSEAEVFDT HGEATDAFSN AIPAQFQGLE RFAARKAVVA 360
  361 EFEKLGLLEE VKPHDLTVPY GDRGGVVIEP MLTDQWYVHT APLAKVAIEA VENGEIQFVP 420
  421 KQYENMYYSW MRDIQDWCIS RQLWWGHRIP AWYDEQGNVY VGRDEAEVRR DNNLGAEVAL 480
  481 RQDEDVLDTW FSSGLWTFST LGWPEQTDAL KTFHPTSVVV SGFDIIFFWI ARMIMLTMHF 540
  541 MKDENGKPQV PFKTVYMTGL IRDDEGQKMS KSKGNVIDPL DMVDGISLEA LLEKRTGNMM 600
  601 QPQLAEKIRK RTEKQFPNGI EPHGTDALRF TLAALASTGR DINWDMKRLE GYRNFCNKLW 660
  661 NASRFVLMNT EGQDCGQNGG EMVLSLADRW ILAEFNQTIK AYREAMDTYR FDLAAGILYE 720
  721 FTWNQFCDWY LELTKPVMNS GSEAELRGTR HTLIQVLEAL LRLAHPIIPY ITETIWQRVK 780
  781 NLKGITADTI MLQPFPEYDA SQVDEQALSD LEWIKQTIIA VRNIRAEMNI APGKPLEVML 840
  841 RGANAQAQRR VLENQSFIQS LARLSSLTLL AEGDKGPVSV TKLVEGAEVL IPMAGLIDKA 900
  901 TELDRLAKEV AKLDAEIERI EGKLGNEGFV ARAPEAVVAK ERERLAACAE AKQKLIEQQA 960
  961 TIAAL

[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
mRNA binding	2.82524485163416E-5	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: