YRC Public Data Repository - Protein Structure Prediction

Protein:	SYH_YERPA
Organism:	Yersinia pestis Antiqua
Length:	424 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 SYH_YERPA.

Description	E-value	Query Range	Subject Range
gi\|22125253, gi\|... - gi\|22125253\|ref\|NP_668676.1\| histidyl-tRNA synthetase [Yersinia pestis KIM], gi\|21958124\|gb\|AAM84927...	5.0E-79	[1..424]	[1..424]
SYH_YERP3 - Histidine--tRNA ligase OS=Yersinia pseudotuberculosis serotype O:1b (strain IP 31758) GN=hisS PE=3 S...	1.0E-78	[1..424]	[1..424]
SYH_SALPA - Histidine--tRNA ligase OS=Salmonella paratyphi A (strain ATCC 9150 / SARB42) GN=hisS PE=3 SV=1 SYH_SALPK - Histidine--tRNA ligase OS=Salmonella paratyphi A (strain AKU_12601) GN=hisS PE=3 SV=1 SYH_SALPA - Histidine--tRNA ligase OS=Salmonella paratyphi A GN=hisS PE=3 SV=1	3.0E-78	[1..424]	[1..424]
gi\|16761437 - gi\|16761437\|ref\|NP_457054.1\| histidyl-tRNA synthetase [Salmonella enterica subsp. enterica serovar T... gi\|213425332 - gi\|213425332\|ref\|ZP_03358082.1\| histidyl-tRNA synthetase [Salmonella enterica subsp. enterica serova... gi\|213649664 - gi\|213649664\|ref\|ZP_03379717.1\| histidyl-tRNA synthetase [Salmonella enterica subsp. enterica serova... gi\|213861387 - gi\|213861387\|ref\|ZP_03385857.1\| histidyl-tRNA synthetase [Salmonella enterica subsp. enterica serova... gi\|214000624 - gi\|214000624\|ref\|ZP_03411359.1\| histidyl-tRNA synthetase [Salmonella enterica subsp. enterica serova... gi\|213028525 - gi\|213028525\|ref\|ZP_03342972.1\| histidyl-tRNA synthetase [Salmonella enterica subsp. enterica serova... gi\|213161949 - gi\|213161949\|ref\|ZP_03347659.1\| histidyl-tRNA synthetase [Salmonella enterica subsp. enterica serova... SYH_SALTI - Histidine--tRNA ligase OS=Salmonella typhi GN=hisS PE=3 SV=3 gi\|29136491, gi\|... - gi\|29140866\|ref\|NP_804208.1\| histidyl-tRNA synthetase [Salmonella enterica subsp. enterica serovar T... SYH_SALTI - Histidyl-tRNA synthetase OS=Salmonella typhi GN=hisS PE=3 SV=3	3.0E-78	[1..424]	[1..424]
gi\|24052934, gi\|... - gi\|24113843\|ref\|NP_708353.1\| histidyl-tRNA synthetase [Shigella flexneri 2a str. 301], gi\|24052934\|g... gi\|30063906, gi\|... - gi\|30063906\|ref\|NP_838077.1\| histidyl-tRNA synthetase [Shigella flexneri 2a str. 2457T], gi\|30042161... SYH_SHIFL - Histidine--tRNA ligase OS=Shigella flexneri GN=hisS PE=3 SV=3	3.0E-78	[1..424]	[1..424]
gi\|194470025, gi... - gi\|194470025\|ref\|ZP_03076009.1\| histidyl-tRNA synthetase [Salmonella enterica subsp. enterica serova... gi\|195630851, gi... - gi\|195630851\|gb\|EDX49443.1\| histidyl-tRNA synthetase [Salmonella enterica subsp. enterica serovar Ne... SYH_SALTY - Histidine--tRNA ligase OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) GN=hisS PE=1 ... gi\|199604382, gi... - gi\|200387284\|ref\|ZP_03213896.1\| histidyl-tRNA synthetase [Salmonella enterica subsp. enterica serova... SYH_SALTY - Histidyl-tRNA synthetase OS=Salmonella typhimurium GN=hisS PE=1 SV=4 gi\|197263278, gi... - gi\|197263278\|ref\|ZP_03163352.1\| histidyl-tRNA synthetase [Salmonella enterica subsp. enterica serova... gi\|167549458, gi... - gi\|205325473\|gb\|EDZ13312.1\| histidyl-tRNA synthetase [Salmonella enterica subsp. enterica serovar Sa... gi\|205333643, gi... - gi\|205333643\|gb\|EDZ20407.1\| histidyl-tRNA synthetase [Salmonella enterica subsp. enterica serovar Ke... gi\|167991830, gi... - gi\|205329927\|gb\|EDZ16691.1\| histidyl-tRNA synthetase [Salmonella enterica subsp. enterica serovar 4,... SYH_SALPB - Histidine--tRNA ligase OS=Salmonella paratyphi B (strain ATCC BAA-1250 / SPB7) GN=hisS PE=3 SV=1 lcl\|NC_016856.1_... - [gene=hisS] [protein=histidyl-tRNA synthetase] [protein_id=YP_005238620.1] [location=complement(2706... SYH_SALTY - Histidine--tRNA ligase OS=Salmonella typhimurium GN=hisS PE=1 SV=4 SYH_SALPB - Histidyl-tRNA synthetase OS=Salmonella paratyphi B (strain ATCC BAA-1250 / SPB7) GN=hisS PE=3 SV=1 SYH_SALPC - Histidine--tRNA ligase OS=Salmonella paratyphi C (strain RKS4594) GN=hisS PE=3 SV=1	3.0E-78	[1..424]	[1..424]
SYH_SHISS - Histidine--tRNA ligase OS=Shigella sonnei (strain Ss046) GN=hisS PE=3 SV=1	4.0E-78	[1..424]	[1..424]
SYH_PECAS - Histidine--tRNA ligase OS=Pectobacterium atrosepticum (strain SCRI 1043 / ATCC BAA-672) GN=hisS PE=3... SYH_ERWCT - Histidine--tRNA ligase OS=Erwinia carotovora subsp. atroseptica GN=hisS PE=3 SV=1	4.0E-78	[1..423]	[1..423]
SYH_SALCH - Histidyl-tRNA synthetase OS=Salmonella choleraesuis GN=hisS PE=3 SV=1 SYH_SALCH - Histidine--tRNA ligase OS=Salmonella choleraesuis (strain SC-B67) GN=hisS PE=3 SV=1 SYH_SALCH - Histidine--tRNA ligase OS=Salmonella choleraesuis GN=hisS PE=3 SV=1	6.0E-78	[1..424]	[1..424]
gi\|188017124, gi... - gi\|188017124\|gb\|EDU55246.1\| histidyl-tRNA synthetase [Escherichia coli O157:H7 str. EC4113], gi\|1687... SYH_ECOSM - Histidine--tRNA ligase OS=Escherichia coli (strain SMS-3-5 / SECEC) GN=hisS PE=3 SV=1 gi\|195936656 - gi\|195936656\|ref\|ZP_03082038.1\| histidyl-tRNA synthetase [Escherichia coli O157:H7 str. EC4024] gi\|208728409, gi... - gi\|208808608\|ref\|ZP_03250945.1\| histidyl-tRNA synthetase [Escherichia coli O157:H7 str. EC4206], gi\|... gi\|208813413, gi... - gi\|208813413\|ref\|ZP_03254742.1\| histidyl-tRNA synthetase [Escherichia coli O157:H7 str. EC4045], gi\|... gi\|208739907, gi... - gi\|208819784\|ref\|ZP_03260104.1\| histidyl-tRNA synthetase [Escherichia coli O157:H7 str. EC4042], gi\|... SYH_ECO5E - Histidine--tRNA ligase OS=Escherichia coli O157:H7 (strain EC4115 / EHEC) GN=hisS PE=3 SV=1 gi\|217319852, gi... - gi\|217327485\|ref\|ZP_03443568.1\| histidyl-tRNA synthetase [Escherichia coli O157:H7 str. TW14588], gi... SYH_ECO8A - Histidine--tRNA ligase OS=Escherichia coli O8 (strain IAI1) GN=hisS PE=3 SV=1 gi\|189356659, gi... - gi\|189356659\|gb\|EDU75078.1\| histidyl-tRNA synthetase [Escherichia coli O157:H7 str. EC4401], gi\|1687... gi\|168761124, gi... - gi\|189368474\|gb\|EDU86890.1\| histidyl-tRNA synthetase [Escherichia coli O157:H7 str. EC4501], gi\|1687... gi\|168768606, gi... - gi\|189362191\|gb\|EDU80610.1\| histidyl-tRNA synthetase [Escherichia coli O157:H7 str. EC4486], gi\|1687... gi\|187770705, gi... - gi\|187770705\|gb\|EDU34549.1\| histidyl-tRNA synthetase [Escherichia coli O157:H7 str. EC4196], gi\|1687... gi\|189003447, gi... - gi\|189003447\|gb\|EDU72433.1\| histidyl-tRNA synthetase [Escherichia coli O157:H7 str. EC4076], gi\|1687... gi\|189372265, gi... - gi\|189372265\|gb\|EDU90681.1\| histidyl-tRNA synthetase [Escherichia coli O157:H7 str. EC869], gi\|16878... gi\|189378621, gi... - gi\|189378621\|gb\|EDU97037.1\| histidyl-tRNA synthetase [Escherichia coli O157:H7 str. EC508], gi\|16879... SYH_ECODH - Histidine--tRNA ligase OS=Escherichia coli (strain K12 / DH10B) GN=hisS PE=3 SV=1 gi\|254794460, gi... - gi\|254794460\|ref\|YP_003079297.1\| histidyl tRNA synthetase [Escherichia coli O157:H7 str. TW14359], g... gi\|253974389, gi... - gi\|254162488\|ref\|YP_003045596.1\| histidyl-tRNA synthetase [Escherichia coli B str. REL606], gi\|25397... gi\|254289249, gi... - gi\|254289249\|ref\|YP_003054997.1\| histidyl-tRNA synthetase [Escherichia coli BL21(DE3)], gi\|253978556... gi\|242378112, gi... - gi\|251785839\|ref\|YP_003000143.1\| hypothetical protein B21_02368 [Escherichia coli BL21], gi\|24237811... SYH_ECOBW - Histidine--tRNA ligase OS=Escherichia coli (strain K12 / MC4100 / BW2952) GN=hisS PE=3 SV=1 gi\|237705024, gi... - gi\|237705024\|ref\|ZP_04535505.1\| histidyl-tRNA synthetase [Escherichia sp. 3_2_53FAA], gi\|226901390\|g... gi\|227835899, gi... - gi\|227887549\|ref\|ZP_04005354.1\| histidine--tRNA ligase [Escherichia coli 83972], gi\|227835899\|gb\|EEJ... EG10453 - histidyl tRNA synthetase / Histidine--tRNA ligase SYH_ECOL6 - Histidine--tRNA ligase OS=Escherichia coli O6 GN=hisS PE=3 SV=2 SYH_ECOLI - Histidyl-tRNA synthetase (EC 6.1.1.21) (Histidine--tRNA ligase) (HisRS) - Escherichia coli gi\|188488902, gi... - gi\|75515853\|ref\|ZP_00737988.1\| COG0124: Histidyl-tRNA synthetase [Escherichia coli 53638], gi\|188493... SYH_ECOL6 - Histidine--tRNA ligase OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) GN=hisS PE=3 S... SYH_ECO57 - Histidine--tRNA ligase OS=Escherichia coli O157:H7 GN=hisS PE=3 SV=2 EG10453 - histidyl tRNA synthetase / Histidine--tRNA ligase gi\|12516905, gi\|... - gi\|15803037\|ref\|NP_289067.1\| histidyl-tRNA synthetase [Escherichia coli O157:H7 EDL933], gi\|12516905... gi\|194437576, gi... - gi\|83586837\|ref\|ZP_00925468.1\| COG0124: Histidyl-tRNA synthetase [Escherichia coli 101-1], gi\|194437... SYH_ECO24 - Histidine--tRNA ligase OS=Escherichia coli O139:H28 (strain E24377A / ETEC) GN=hisS PE=3 SV=1 SYH_ECOHS - Histidine--tRNA ligase OS=Escherichia coli O9:H4 (strain HS) GN=hisS PE=3 SV=1 gi\|194414700, gi... - gi\|75211480\|ref\|ZP_00711570.1\| COG0124: Histidyl-tRNA synthetase [Escherichia coli B171], gi\|1944273... gi\|190902286, gi... - gi\|75229154\|ref\|ZP_00715726.1\| COG0124: Histidyl-tRNA synthetase [Escherichia coli B7A], gi\|19116768... gi\|193068437, gi... - gi\|75237740\|ref\|ZP_00721756.1\| COG0124: Histidyl-tRNA synthetase [Escherichia coli E110019], gi\|1930... gi\|75240461, gi\|... - gi\|75240461\|ref\|ZP_00724395.1\| COG0124: Histidyl-tRNA synthetase [Escherichia coli F11], gi\|19117262... gi\|75257938, gi\|... - gi\|75257938\|ref\|ZP_00729412.1\| COG0124: Histidyl-tRNA synthetase [Escherichia coli E22], gi\|19306407... SYH_ECO45 - Histidine--tRNA ligase OS=Escherichia coli O45:K1 (strain S88 / ExPEC) GN=hisS PE=3 SV=1 SYH_ECO81 - Histidine--tRNA ligase OS=Escherichia coli O81 (strain ED1a) GN=hisS PE=3 SV=1 SYH_ECO7I - Histidine--tRNA ligase OS=Escherichia coli O7:K1 (strain IAI39 / ExPEC) GN=hisS PE=3 SV=1 SYH_ECOK1 - Histidine--tRNA ligase OS=Escherichia coli O1:K1 / APEC GN=hisS PE=3 SV=1 gi\|124531248, gi... - gi\|124531248\|ref\|ZP_01701590.1\| histidyl-tRNA synthetase [Escherichia coli B], gi\|124498694\|gb\|EAY46... SYH_ECOLC - Histidine--tRNA ligase OS=Escherichia coli (strain ATCC 8739 / DSM 1576 / Crooks) GN=hisS PE=3 SV=1 gi\|1805574, gi\|8... - gi\|89109320\|ref\|AP_003100.1\| histidyl tRNA synthetase [Escherichia coli str. K-12 substr. W3110], gi... SYH_ECOUT - Histidine--tRNA ligase OS=Escherichia coli (strain UTI89 / UPEC) GN=hisS PE=3 SV=1 gi\|15832630, gi\|... - gi\|15832630\|ref\|NP_311403.1\| histidyl-tRNA synthetase [Escherichia coli O157:H7 str. Sakai], gi\|1336... SYH_ECOL5 - Histidine--tRNA ligase OS=Escherichia coli O6:K15:H31 (strain 536 / UPEC) GN=hisS PE=3 SV=1	7.0E-78	[1..424]	[1..424]

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Predicted Domain #1

Region A:
Residues: [1-424]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MAKNIQAIRG MNDYLPADTA IWQRIESILK QVLSGYGYSE IRMPIVEQTP LFKRAIGEVT  60
   61 DVVEKEMYTF DDRNGESLTL RPEGTAGCVR AGIEHGLLYN QEQRLWYIGP MFRYERPQKG 120
  121 RYRQFHQLGA EVFGLPGPDI DAELILLTAR WWRALGIFEH VKLELNSIGS LAARADYREA 180
  181 LVAFLEQHVE VLDEDCKRRM YSNPLRVLDS KNPDVQQLLD DAPKLSDYLD EESKQHFAGL 240
  241 CELLDKASIP YTVNERLVRG LDYYNRTVFE WVTHSLGAQG TVCAGGRYDG LVEQLGGRAT 300
  301 PAVGFAMGLE RLVLLVQAVN ADFQVPATVD AYVISSGEGA QSAAMLLAES LRDALPTLKI 360
  361 MTNYGGGNVK KQFTRADKWG ARVALMLGES EVAAQQVVVK DLRNGEQETL AQADVAARLA 420
  421 LMLG

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	79.39794
Match:	1kmmA
Description:	Histidyl-tRNA synthetase (HisRS), C-terminal domain; Histidyl-tRNA synthetase (HisRS)
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
ligase activity, forming aminoacyl-tRNA and related compounds	7.89468709683036	bayes_pls_golite062009
ligase activity, forming carbon-oxygen bonds	7.89468709683036	bayes_pls_golite062009
aminoacyl-tRNA ligase activity	7.88410036819636	bayes_pls_golite062009
ligase activity	6.92073480193262	bayes_pls_golite062009
histidine-tRNA ligase activity	5.91343220471745	bayes_pls_golite062009
phenylalanine-tRNA ligase activity	2.99105702052936	bayes_pls_golite062009
serine-tRNA ligase activity	2.46505535069103	bayes_pls_golite062009
glycine-tRNA ligase activity	2.29229136935761	bayes_pls_golite062009
threonine-tRNA ligase activity	2.18642354927	bayes_pls_golite062009
catalytic activity	1.99372273395202	bayes_pls_golite062009
alanine-tRNA ligase activity	1.82594054955281	bayes_pls_golite062009
lysine-tRNA ligase activity	1.72324031407565	bayes_pls_golite062009
binding	0.966824335333342	bayes_pls_golite062009
asparagine-tRNA ligase activity	0.921492123574877	bayes_pls_golite062009
transcription regulator activity	0.375542987753806	bayes_pls_golite062009
nucleic acid binding	0.281662799812287	bayes_pls_golite062009
protein binding	0.0804954454681041	bayes_pls_golite062009
DNA binding	0.0309732052586011	bayes_pls_golite062009
aspartate-tRNA ligase activity	0.00572514744734753	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: