YRC Public Data Repository - Protein Structure Prediction

Protein:	SYD_ECOLI
Organism:	Escherichia coli
Length:	590 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 SYD_ECOLI.

Description	E-value	Query Range	Subject Range
gi\|126509582, gi... - gi\|153819872\|ref\|ZP_01972539.1\| aspartyl-tRNA synthetase [Vibrio cholerae NCTC 8457], gi\|126509582\|g... SYD_VIBCM - Aspartate--tRNA ligase OS=Vibrio cholerae serotype O1 (strain M66-2) GN=aspS PE=3 SV=1 gi\|229505240, gi... - gi\|229505240\|ref\|ZP_04394750.1\| aspartyl-tRNA synthetase [Vibrio cholerae BX 330286], gi\|229357463\|g... gi\|229511090, gi... - gi\|229511090\|ref\|ZP_04400569.1\| aspartyl-tRNA synthetase [Vibrio cholerae B33], gi\|229351055\|gb\|EEO1... gi\|229518210, gi... - gi\|229518210\|ref\|ZP_04407654.1\| aspartyl-tRNA synthetase [Vibrio cholerae RC9], gi\|229344925\|gb\|EEO0... gi\|229370914, gi... - gi\|229608259\|ref\|YP_002878907.1\| aspartyl-tRNA synthetase [Vibrio cholerae MJ-1236], gi\|229370914\|gb... gi\|254843998, gi... - gi\|254848293\|ref\|ZP_05237643.1\| aspartyl-tRNA synthetase [Vibrio cholerae MO10], gi\|254843998\|gb\|EET... gi\|255745577\|ref... - aspartyl-tRNA synthetase [Vibrio cholera CIRS 101] gi\|262158349\|ref... - aspartyl-tRNA synthetase [Vibrio cholerae INDRE 91/1] SYD_VIBCH - Aspartate--tRNA ligase OS=Vibrio cholerae GN=aspS PE=3 SV=1 SYD_VIBCH - Aspartate--tRNA ligase OS=Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) GN=a... SYD_VIBC3 - Aspartate--tRNA ligase OS=Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O39... gi\|262170162\|ref... - aspartyl-tRNA synthetase [Vibrio cholerae RC27]	677.0	[0..1]	[589..1]
SYD_VIBVY - Aspartate--tRNA ligase OS=Vibrio vulnificus (strain YJ016) GN=aspS PE=3 SV=1	675.0	[0..1]	[590..1]
gi\|191172971, gi... - gi\|191172971\|ref\|ZP_03034505.1\| aspartyl-tRNA synthetase [Escherichia coli F11], gi\|190906682\|gb\|EDV... SYD_ECO45 - Aspartate--tRNA ligase OS=Escherichia coli O45:K1 (strain S88 / ExPEC) GN=aspS PE=3 SV=1 SYD_ECOL6 - Aspartate--tRNA ligase OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) GN=aspS PE=3 S... SYD_ECOK1 - Aspartate--tRNA ligase OS=Escherichia coli O1:K1 / APEC GN=aspS PE=3 SV=1 SYD_ECOL5 - Aspartate--tRNA ligase OS=Escherichia coli O6:K15:H31 (strain 536 / UPEC) GN=aspS PE=3 SV=1 gi\|227885706, gi... - gi\|227885706\|ref\|ZP_04003511.1\| aspartyl-tRNA synthetase [Escherichia coli 83972], gi\|227837279\|gb\|E... SYD_ECOUT - Aspartate--tRNA ligase OS=Escherichia coli (strain UTI89 / UPEC) GN=aspS PE=3 SV=1 SYD_ECO81 - Aspartate--tRNA ligase OS=Escherichia coli O81 (strain ED1a) GN=aspS PE=3 SV=1 SYD_ECOL6 - Aspartate--tRNA ligase OS=Escherichia coli O6 GN=aspS PE=3 SV=1 gi\|237705820, gi... - gi\|237705820\|ref\|ZP_04536301.1\| aspartyl-tRNA synthetase [Escherichia sp. 3_2_53FAA], gi\|226900577\|g...	675.0	[0..1]	[590..1]
SYD_VIBVU - Aspartate--tRNA ligase OS=Vibrio vulnificus (strain CMCP6) GN=aspS PE=3 SV=1 SYD_VIBVU - Aspartate--tRNA ligase OS=Vibrio vulnificus GN=aspS PE=3 SV=1	675.0	[0..1]	[590..1]
gi\|13362044, gi\|... - gi\|15831830\|ref\|NP_310603.1\| aspartyl-tRNA synthetase [Escherichia coli O157:H7 str. Sakai], gi\|1336... gi\|25293010, gi\|... - pir\|\|H90950 aspartate tRNA synthetase [imported] - Escherichia coli (strain O157:H7, substrain RIMD... gi\|217318181, gi... - gi\|217328834\|ref\|ZP_03444915.1\| aspartyl-tRNA synthetase [Escherichia coli O157:H7 str. TW14588], gi... SYD_ECO57 - Aspartate--tRNA ligase OS=Escherichia coli O157:H7 GN=aspS PE=3 SV=1 gi\|189367330, gi... - gi\|189367330\|gb\|EDU85746.1\| aspartyl-tRNA synthetase [Escherichia coli O157:H7 str. EC4501], gi\|1687...	674.0	[0..1]	[590..1]
gi\|191168067, gi... - gi\|191168067\|ref\|ZP_03029866.1\| aspartyl-tRNA synthetase [Escherichia coli B7A], gi\|190901865\|gb\|EDV... SYD_SHIB3 - Aspartate--tRNA ligase OS=Shigella boydii serotype 18 (strain CDC 3083-94 / BS512) GN=aspS PE=3 SV=1 SYD_ECOSM - Aspartate--tRNA ligase OS=Escherichia coli (strain SMS-3-5 / SECEC) GN=aspS PE=3 SV=1 SYD_SHIBS - Aspartate--tRNA ligase OS=Shigella boydii serotype 4 (strain Sb227) GN=aspS PE=3 SV=1 SYD_ECOLC - Aspartate--tRNA ligase OS=Escherichia coli (strain ATCC 8739 / DSM 1576 / Crooks) GN=aspS PE=3 SV=1 gi\|260844209\|ref... - aspartyl-tRNA synthetase [Escherichia coli O103:H2 str. 12009] gi\|260868401\|ref... - aspartyl-tRNA synthetase [Escherichia coli O111:H- str. 11128] gi\|293410178\|ref... - aspartyl-tRNA synthetase [Escherichia coli B354] gi\|256017930\|ref... - aspartyl-tRNA synthetase [Shigella sp. D9] SYD_ECO24 - Aspartate--tRNA ligase OS=Escherichia coli O139:H28 (strain E24377A / ETEC) GN=aspS PE=3 SV=1 gi\|293446253\|ref... - aspartyl-tRNA synthetase [Escherichia coli B088] gi\|195182928 - gi\|195182928\|dbj\|BAG66496.1\| aspartate tRNA synthetase [Escherichia coli O111:H-] SYD_ECOLU - Aspartate--tRNA ligase OS=Escherichia coli O17:K52:H18 (strain UMN026 / ExPEC) GN=aspS PE=3 SV=1 SYD_ECO55 - Aspartate--tRNA ligase OS=Escherichia coli (strain 55989 / EAEC) GN=aspS PE=3 SV=1 SYD_ECO8A - Aspartate--tRNA ligase OS=Escherichia coli O8 (strain IAI1) GN=aspS PE=3 SV=1 SYD_ECOSE - Aspartate--tRNA ligase OS=Escherichia coli (strain SE11) GN=aspS PE=3 SV=1 gi\|124498812, gi... - gi\|124531073\|ref\|ZP_01701458.1\| aspartyl-tRNA synthetase [Escherichia coli B], gi\|124498812\|gb\|EAY46... gi\|194417812, gi... - gi\|194433940\|ref\|ZP_03066212.1\| aspartyl-tRNA synthetase [Shigella dysenteriae 1012], gi\|194417812\|g... gi\|194412286, gi... - gi\|194429644\|ref\|ZP_03062162.1\| aspartyl-tRNA synthetase [Escherichia coli B171], gi\|194412286\|gb\|ED... gi\|193069878, gi... - gi\|193069878\|ref\|ZP_03050827.1\| aspartyl-tRNA synthetase [Escherichia coli E110019], gi\|192956778\|gb... gi\|260855806\|ref... - aspartyl-tRNA synthetase [Escherichia coli O26:H11 str. 11368] gi\|193066060, gi... - gi\|193066060\|ref\|ZP_03047117.1\| aspartyl-tRNA synthetase [Escherichia coli E22], gi\|192926297\|gb\|EDV...	673.0	[0..1]	[590..1]
SYD_SHIF8 - Aspartate--tRNA ligase OS=Shigella flexneri serotype 5b (strain 8401) GN=aspS PE=3 SV=1	673.0	[0..1]	[590..1]
SYD_SHIDS - Aspartate--tRNA ligase OS=Shigella dysenteriae serotype 1 (strain Sd197) GN=aspS PE=3 SV=1	672.0	[0..1]	[590..1]
SYD_SHIFL - Aspartate--tRNA ligase OS=Shigella flexneri GN=aspS PE=3 SV=2 gi\|24113215, gi\|... - gi\|24113215\|ref\|NP_707725.1\| aspartyl-tRNA synthetase [Shigella flexneri 2a str. 301], gi\|24052211\|g...	672.0	[0..1]	[590..1]
SYD_SHISS - Aspartate--tRNA ligase OS=Shigella sonnei (strain Ss046) GN=aspS PE=3 SV=1	672.0	[0..1]	[590..1]

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Predicted Domain #1

Region A:
Residues: [1-590]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MRTEYCGQLR LSHVGQQVTL CGWVNRRRDL GSLIFIDMRD REGIVQVFFD PDRADALKLA  60
   61 SELRNEFCIQ VTGTVRARDE KNINRDMATG EIEVLASSLT IINRADVLPL DSNHVNTEEA 120
  121 RLKYRYLDLR RPEMAQRLKT RAKITSLVRR FMDDHGFLDI ETPMLTKATP EGARDYLVPS 180
  181 RVHKGKFYAL PQSPQLFKQL LMMSGFDRYY QIVKCFRDED LRADRQPEFT QIDVETSFMT 240
  241 APQVREVMEA LVRHLWLEVK GVDLGDFPVM TFAEAERRYG SDKPDLRNPM ELTDVADLLK 300
  301 SVEFAVFAGP ANDPKGRVAA LRVPGGASLT RKQIDEYGNF VKIYGAKGLA YIKVNERAKG 360
  361 LEGINSPVAK FLNAEIIEDI LDRTAAQDGD MIFFGADNKK IVADAMGALR LKVGKDLGLT 420
  421 DESKWAPLWV IDFPMFEDDG EGGLTAMHHP FTSPKDMTAA ELKAAPENAV ANAYDMVING 480
  481 YEVGGGSVRI HNGDMQQTVF GILGINEEEQ REKFGFLLDA LKYGTPPHAG LAFGLDRLTM 540
  541 LLTGTDNIRD VIAFPKTTAA ACLMTEAPSF ANPTALAELS IQVVKKAENN

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	1000.0
Match:	1eqrA
Description:	Aspartyl-tRNA synthetase (AspRS); Prokaryotic AspRS, insert domain
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
aspartate-tRNA ligase activity	8.05810581952961	bayes_pls_golite062009
ligase activity, forming aminoacyl-tRNA and related compounds	6.64101149584905	bayes_pls_golite062009
ligase activity, forming carbon-oxygen bonds	6.64101149584905	bayes_pls_golite062009
aminoacyl-tRNA ligase activity	6.63037793576826	bayes_pls_golite062009
ligase activity	5.42788458660958	bayes_pls_golite062009
phenylalanine-tRNA ligase activity	2.99105702052936	bayes_pls_golite062009
structural constituent of ribosome	2.43759174701552	bayes_pls_golite062009
glycine-tRNA ligase activity	2.29229136935761	bayes_pls_golite062009
threonine-tRNA ligase activity	2.18642354927	bayes_pls_golite062009
structural molecule activity	2.08258913217268	bayes_pls_golite062009
serine-tRNA ligase activity	2.07594942154162	bayes_pls_golite062009
alanine-tRNA ligase activity	1.82594054955281	bayes_pls_golite062009
lysine-tRNA ligase activity	1.72324031407565	bayes_pls_golite062009
histidine-tRNA ligase activity	1.72215103383322	bayes_pls_golite062009
catalytic activity	1.32566224382655	bayes_pls_golite062009
translation initiation factor activity	0.96756670903925	bayes_pls_golite062009
asparagine-tRNA ligase activity	0.921492123574877	bayes_pls_golite062009
binding	0.311307565529325	bayes_pls_golite062009
single-stranded DNA binding	0.19668406318255	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: