YRC Public Data Repository - Protein Structure Prediction

Protein:	ISM1
Organism:	Saccharomyces cerevisiae
Length:	1002 amino acids
Reference:	Malmström L, et al. (2007) Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PLoS Biol 5(4): e76. doi:10.1371/journal.pbio.0050076

[What does the above image mean?]

[Show Ginzu Version Information]

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 ISM1.

Description	E-value	Query Range	Subject Range
gi\|227837909, gi... - gi\|227885080\|ref\|ZP_04002885.1\| isoleucyl-tRNA synthetase [Escherichia coli 83972], gi\|227837909\|gb\|... SYI_ECOL6 - Isoleucine--tRNA ligase OS=Escherichia coli O6 GN=ileS PE=3 SV=1 SYI_ECOL6 - Isoleucine--tRNA ligase OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) GN=ileS PE=3 ... SYI_ECO81 - Isoleucine--tRNA ligase OS=Escherichia coli O81 (strain ED1a) GN=ileS PE=3 SV=1	0.0	[24..997]	[3..928]
SYI_HAEIN - (P43824) Isoleucyl-tRNA synthetase (EC 6.1.1.5) (Isoleucine--tRNA ligase) (IleRS)	0.0	[24..997]	[4..931]
gi\|168781723, gi... - gi\|189000725\|gb\|EDU69711.1\| isoleucyl-tRNA synthetase [Escherichia coli O157:H7 str. EC4076], gi\|168... gi\|168776942, gi... - gi\|187767722\|gb\|EDU31566.1\| isoleucyl-tRNA synthetase [Escherichia coli O157:H7 str. EC4196], gi\|168... gi\|168766714, gi... - gi\|189364054\|gb\|EDU82473.1\| isoleucyl-tRNA synthetase [Escherichia coli O157:H7 str. EC4486], gi\|168... gi\|189356087, gi... - gi\|189356087\|gb\|EDU74506.1\| isoleucyl-tRNA synthetase [Escherichia coli O157:H7 str. EC4401], gi\|168... gi\|208729279, gi... - gi\|208809478\|ref\|ZP_03251815.1\| isoleucyl-tRNA synthetase [Escherichia coli O157:H7 str. EC4206], gi... gi\|195937699 - gi\|195937699\|ref\|ZP_03083081.1\| isoleucyl-tRNA synthetase [Escherichia coli O157:H7 str. EC4024] gi\|189375994, gi... - gi\|189375994\|gb\|EDU94410.1\| isoleucyl-tRNA synthetase [Escherichia coli O157:H7 str. EC508], gi\|1688... gi\|168785077, gi... - gi\|189375026\|gb\|EDU93442.1\| isoleucyl-tRNA synthetase [Escherichia coli O157:H7 str. EC869], gi\|1687... gi\|188014298, gi... - gi\|188014298\|gb\|EDU52420.1\| isoleucyl-tRNA synthetase [Escherichia coli O157:H7 str. EC4113], gi\|168... gi\|254791161, gi... - gi\|254791161\|ref\|YP_003075998.1\| isoleucyl-tRNA synthetase [Escherichia coli O157:H7 str. TW14359], ... gi\|217320687, gi... - gi\|217324466\|ref\|ZP_03440550.1\| isoleucyl-tRNA synthetase [Escherichia coli O157:H7 str. TW14588], g... SYI_ECO5E - Isoleucine--tRNA ligase OS=Escherichia coli O157:H7 (strain EC4115 / EHEC) GN=ileS PE=3 SV=1 SYI_ECO57 - Isoleucine--tRNA ligase OS=Escherichia coli O157:H7 GN=ileS PE=3 SV=1 gi\|208738402, gi... - gi\|208818279\|ref\|ZP_03258599.1\| isoleucyl-tRNA synthetase [Escherichia coli O157:H7 str. EC4042], gi... gi\|209748718, gi... - pir\|\|D85483 isoleucine tRNA synthetase [imported] - Escherichia coli (strain O157:H7, substrain EDL... gi\|208812638, gi... - gi\|208812638\|ref\|ZP_03253967.1\| isoleucyl-tRNA synthetase [Escherichia coli O157:H7 str. EC4045], gi... gi\|12512709, gi\|... - gi\|15799708\|ref\|NP_285720.1\| isoleucyl-tRNA synthetase [Escherichia coli O157:H7 EDL933], gi\|1251270... gi\|15829283, gi\|... - gi\|15829283\|ref\|NP_308056.1\| isoleucyl-tRNA synthetase [Escherichia coli O157:H7 str. Sakai], gi\|133...	0.0	[24..997]	[3..928]
SYI_ECO55 - Isoleucine--tRNA ligase OS=Escherichia coli (strain 55989 / EAEC) GN=ileS PE=3 SV=1 gi\|89106910, gi\|... - gi\|89106910\|ref\|AP_000690.1\| isoleucyl-tRNA synthetase [Escherichia coli str. K-12 substr. W3110], g... SYI_ECODH - Isoleucine--tRNA ligase OS=Escherichia coli (strain K12 / DH10B) GN=ileS PE=3 SV=1 SYI_ECOSE - Isoleucine--tRNA ligase OS=Escherichia coli (strain SE11) GN=ileS PE=3 SV=1 SYI_ECO8A - Isoleucine--tRNA ligase OS=Escherichia coli O8 (strain IAI1) GN=ileS PE=3 SV=1 gi\|193070965, gi... - gi\|75234163\|ref\|ZP_00718567.1\| COG0060: Isoleucyl-tRNA synthetase [Escherichia coli E110019], gi\|193... gi\|193066215, gi... - gi\|75255681\|ref\|ZP_00727447.1\| COG0060: Isoleucyl-tRNA synthetase [Escherichia coli E22], gi\|1930662... gi\|190901059, gi... - gi\|75227856\|ref\|ZP_00714566.1\| COG0060: Isoleucyl-tRNA synthetase [Escherichia coli B7A], gi\|1911688... EG10492 - isoleucyl-tRNA synthetase / Isoleucine--tRNA ligase SYI_ECOLI - Isoleucyl-tRNA synthetase (EC 6.1.1.5) (Isoleucine--tRNA ligase) (IleRS) - Escherichia coli EG10492 - isoleucyl-tRNA synthetase / Isoleucine--tRNA ligase SYI_ECOBW - Isoleucine--tRNA ligase OS=Escherichia coli (strain K12 / MC4100 / BW2952) GN=ileS PE=3 SV=1 SYI_SHISS - Isoleucine--tRNA ligase OS=Shigella sonnei (strain Ss046) GN=ileS PE=3 SV=1	0.0	[24..997]	[3..928]
SYI_YERPE - Isoleucine--tRNA ligase OS=Yersinia pestis GN=ileS PE=3 SV=1 SYI_YERPP - Isoleucine--tRNA ligase OS=Yersinia pestis (strain Pestoides F) GN=ileS PE=3 SV=1 gi\|45443437, gi\|... - gi\|45443437\|ref\|NP_994976.1\| isoleucyl-tRNA synthetase [Yersinia pestis biovar Microtus str. 91001],... gi\|22127574, gi\|... - gi\|22127574\|ref\|NP_670997.1\| isoleucyl-tRNA synthetase [Yersinia pestis KIM], gi\|21960680\|gb\|AAM8724... gi\|115346283, gi... - gi\|218927672\|ref\|YP_002345547.1\| isoleucyl-tRNA synthetase [Yersinia pestis CO92], gi\|16120804\|ref\|N... SYI_YERPS - Isoleucine--tRNA ligase OS=Yersinia pseudotuberculosis serotype I (strain IP32953) GN=ileS PE=3 SV=1 SYI_YERPS - Isoleucine--tRNA ligase OS=Yersinia pseudotuberculosis GN=ileS PE=3 SV=1 gi\|229836943, gi... - gi\|229836943\|ref\|ZP_04457108.1\| isoleucyl-tRNA synthetase [Yersinia pestis Pestoides A], gi\|22970588... SYI_YERPB - Isoleucine--tRNA ligase OS=Yersinia pseudotuberculosis serotype IB (strain PB1/+) GN=ileS PE=3 SV=1 gi\|229840362, gi... - gi\|229840362\|ref\|ZP_04460521.1\| isoleucyl-tRNA synthetase [Yersinia pestis biovar Orientalis str. PE... gi\|229690752, gi... - gi\|229842442\|ref\|ZP_04462597.1\| isoleucyl-tRNA synthetase [Yersinia pestis biovar Orientalis str. In... gi\|150260489, gi... - gi\|150260489\|ref\|ZP_01917217.1\| isoleucyl-tRNA synthetase [Yersinia pestis CA88-4125], gi\|149289897\|... gi\|165927280, gi... - gi\|165927280\|ref\|ZP_02223112.1\| isoleucyl-tRNA synthetase [Yersinia pestis biovar Orientalis str. F1... gi\|165992280, gi... - gi\|166008941\|ref\|ZP_02229839.1\| isoleucyl-tRNA synthetase [Yersinia pestis biovar Antiqua str. E1979... gi\|166206681, gi... - gi\|166211935\|ref\|ZP_02237970.1\| isoleucyl-tRNA synthetase [Yersinia pestis biovar Antiqua str. B4200... gi\|165914198, gi... - gi\|89102802\|ref\|ZP_01175411.1\| COG0060: Isoleucyl-tRNA synthetase [Yersinia pestis biovar Orientalis... gi\|167401654, gi... - gi\|167401654\|ref\|ZP_02307148.1\| isoleucyl-tRNA synthetase [Yersinia pestis biovar Antiqua str. UG05-... gi\|166962702, gi... - gi\|167418708\|ref\|ZP_02310461.1\| isoleucyl-tRNA synthetase [Yersinia pestis biovar Orientalis str. MG... gi\|167054982, gi... - gi\|167426059\|ref\|ZP_02317812.1\| isoleucyl-tRNA synthetase [Yersinia pestis biovar Mediaevalis str. K... gi\|167469838 - gi\|167469838\|ref\|ZP_02334542.1\| isoleucyl-tRNA synthetase [Yersinia pestis FV-1] SYI_YERPY - Isoleucine--tRNA ligase OS=Yersinia pseudotuberculosis serotype O:3 (strain YPIII) GN=ileS PE=3 SV=1 SYI_YERPA - Isoleucine--tRNA ligase OS=Yersinia pestis bv. Antiqua (strain Antiqua) GN=ileS PE=3 SV=1 SYI_YERPN - Isoleucine--tRNA ligase OS=Yersinia pestis bv. Antiqua (strain Nepal516) GN=ileS PE=3 SV=1 SYI_YERPG - Isoleucine--tRNA ligase OS=Yersinia pestis bv. Antiqua (strain Angola) GN=ileS PE=3 SV=1	0.0	[24..997]	[3..928]
SYI_SHIFL - Isoleucine--tRNA ligase OS=Shigella flexneri GN=ileS PE=3 SV=1 gi\|24050221, gi\|... - gi\|24111471\|ref\|NP_705981.1\| isoleucyl-tRNA synthetase [Shigella flexneri 2a str. 301], gi\|24050221\|...	0.0	[24..997]	[3..928]
gi\|30061594, gi\|... - gi\|30061594\|ref\|NP_835765.1\| isoleucyl-tRNA synthetase [Shigella flexneri 2a str. 2457T], gi\|3003983...	0.0	[24..997]	[3..928]
SYI_PASMU - Isoleucine--tRNA ligase OS=Pasteurella multocida (strain Pm70) GN=ileS PE=3 SV=1 SYI_PASMU - Isoleucyl-tRNA synthetase OS=Pasteurella multocida GN=ileS PE=3 SV=1	0.0	[24..998]	[4..923]
SYI_SALTY - Isoleucyl-tRNA synthetase OS=Salmonella typhimurium GN=ileS PE=3 SV=1 lcl\|NC_016856.1_... - [gene=ileS] [protein=isoleucyl-tRNA synthetase] [protein_id=YP_005235688.1] [location=53855..56689] SYI_SALTY - Isoleucine--tRNA ligase OS=Salmonella typhimurium GN=ileS PE=3 SV=1 SYI_SALTY - Isoleucine--tRNA ligase OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) GN=ileS PE=3...	0.0	[24..997]	[3..934]
gi\|29140590, gi\|... - gi\|29140590\|ref\|NP_803932.1\| isoleucyl-tRNA synthetase [Salmonella enterica subsp. enterica serovar ... SYI_SALTI - Isoleucyl-tRNA synthetase OS=Salmonella typhi GN=ileS PE=3 SV=1 gi\|16759040 - gi\|16759040\|ref\|NP_454657.1\| isoleucyl-tRNA synthetase [Salmonella enterica subsp. enterica serovar ... SYI_SALTI - Isoleucine--tRNA ligase OS=Salmonella typhi GN=ileS PE=3 SV=1	0.0	[24..997]	[3..934]

Back

Predicted Domain #1

Region A: Residues: [1-34]	1 11 21 31 41 51 \| \| \| \| \| \| 1 MKRSRLVPQH IFSIISKRYL AKHAYQKTLN LPKT [Run NCBI BLAST on this sequence.]
Region B: Residues: [736-767]	1 11 21 31 41 51 \| \| \| \| \| \| 1 LLSNLQKSQD FNLLPIEQLR RVDQYTLYKI NE [Run NCBI BLAST on this sequence.]
Region C: Residues: [793-828]	1 11 21 31 41 51 \| \| \| \| \| \| 1 NNELSAFYFD ISKDILYSNQ ISSLARRQVQ TTLVHI [Run NCBI BLAST on this sequence.]
Region D: Residues: [875-885]	1 11 21 31 41 51 \| \| \| \| \| \| 1 DSNTEIVTSF E [Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	2460.0
Match:	1ffyA_
Description:	Isoleucyl-tRNA synthetase (IleRS)
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
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
leucine-tRNA ligase activity	2.62601062778624	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

Predicted Domain #2

Region A: Residues: [35-87]	1 11 21 31 41 51 \| \| \| \| \| \| 1 KFPNRSNLEI TLRELIPKSS QLVYKEQLRD FFEEFSKLNT TDEKLEFIKE KLF [Run NCBI BLAST on this sequence.]
Region B: Residues: [99-127]	1 11 21 31 41 51 \| \| \| \| \| \| 1 ELHLGHALNK ILKDIINRYQ LSQGKYIFY [Run NCBI BLAST on this sequence.]
Region C: Residues: [174-187]	1 11 21 31 41 51 \| \| \| \| \| \| 1 QRETFQHFAI LTDW [Run NCBI BLAST on this sequence.]
Region D: Residues: [658-735]	1 11 21 31 41 51 \| \| \| \| \| \| 1 HGFTLDENGL KMSKSVGNTI SPEAIIRGDE NLGLPALGVD GLRYLIAQSN FTTDIVAGPT 60 61 VMKHVGEALK KVRLTFRY [Run NCBI BLAST on this sequence.]
Region E: Residues: [768-792]	1 11 21 31 41 51 \| \| \| \| \| \| 1 LLETTREHYQ KYNFSKVLIT LQYHL [Run NCBI BLAST on this sequence.]
Region F: Residues: [829-874]	1 11 21 31 41 51 \| \| \| \| \| \| 1 LNAYRAILAP ILPVMVQEVW KYIPEGWLQG QEHIDINPMR GKWPFL [Run NCBI BLAST on this sequence.]
Region G: Residues: [886-1002]	1 11 21 31 41 51 \| \| \| \| \| \| 1 NFELKILKQF QEEFKRLSLE EGVTKTTHSH VTIFTKHHLP FSSDELCDIL QSSAVDILQM 60 61 DDNNNSLPTI ELGSGINVQI LVERSKRHNC PRCWKANSAE EDKLCDRCKE AVDHLMS [Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	2460.0
Match:	1ffyA_
Description:	Isoleucyl-tRNA synthetase (IleRS)
Matching Structure (courtesy of the PDB):

Predicted Domain #3

Region A: Residues: [88-98]	1 11 21 31 41 51 \| \| \| \| \| \| 1 ILHDGPPYAN G [Run NCBI BLAST on this sequence.]
Region B: Residues: [128-173]	1 11 21 31 41 51 \| \| \| \| \| \| 1 KPGWDCHGLP IEIKALKDLS AQQIESISPL KIRSMALKHA QKAIKR [Run NCBI BLAST on this sequence.]
Region C: Residues: [188-219]	1 11 21 31 41 51 \| \| \| \| \| \| 1 ETPYLTMDKD YEINQLNIFK EMYERGLIKR QN [Run NCBI BLAST on this sequence.]
Region D: Residues: [473-657]	1 11 21 31 41 51 \| \| \| \| \| \| 1 QWFADLHDVK NLALESISRV KFCPKRGYSR LSSFMKSRNE WCISRQRSWG IPILSFYKKS 60 61 EPDSVLMNSE ILAHAIEKIK QKGINAWFND KDNDMKEWLP EKYHDVAHEY CRSQDTMDVW 120 121 FDSGSSWSVI KDFYEKSLKL SKLPSPLYQV CLEGSDQHRG WFQSSLLTKV ASSNVPVAPY 180 181 EEVIT [Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	2460.0
Match:	1ffyA_
Description:	Isoleucyl-tRNA synthetase (IleRS)
Matching Structure (courtesy of the PDB):

Predicted Domain #4

Region A:
Residues: [220-472]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KPVYWGTETR TALAEGELEY NENHKSIAAY VKFPLEKKSQ MDLCKKLGIT NNLPIYCLIW  60
   61 TSTPWTLLSN RAICFNQDFS YSLLRLNSEL ILVETGSIDK LGLTTNSFET IKQFQGTHLN 120
  121 GLYYQNLLVD DKVGRPLLHG AHVTSGTGTG LVHTAPGHGQ DDYLIGIQNG LEIYSPVDHQ 180
  181 GRYQLNELPQ SVRSIVRDEG DLTKGRQVLD AETAKIILCK LSDLNLLYKS HEYTHSYPYD 240
  241 WRSKKPVIIR ATP

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	2460.0
Match:	1ffyA_
Description:	Isoleucyl-tRNA synthetase (IleRS)
Matching Structure (courtesy of the PDB):

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: