YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|238901834, gi...
Organism:	Escherichia coli BW2952
Length:	876 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 gi|238901834, gi....

Description	E-value	Query Range	Subject Range
gi\|75241640, gi\|... - gi\|75241640\|ref\|ZP_00725477.1\| COG0013: Alanyl-tRNA synthetase [Escherichia coli F11], gi\|191171366\|...	1274.0	[0..1]	[876..1]
gi\|227888232, gi... - gi\|227888232\|ref\|ZP_04006037.1\| alanyl-tRNA synthetase [Escherichia coli 83972], gi\|227834501\|gb\|EEJ... SYA_ECOHS - Alanine--tRNA ligase OS=Escherichia coli O9:H4 (strain HS) GN=alaS PE=3 SV=1 gi\|218428383, gi... - gi\|218690819\|ref\|YP_002399031.1\| alanyl-tRNA synthetase [Escherichia coli ED1a], gi\|218428383\|emb\|CA...	1260.0	[0..1]	[876..1]
SYA_ECOL5 - Alanine--tRNA ligase OS=Escherichia coli O6:K15:H31 (strain 536 / UPEC) GN=alaS PE=3 SV=1	1260.0	[0..1]	[876..1]
SYA_SHISS - Alanine--tRNA ligase OS=Shigella sonnei (strain Ss046) GN=alaS PE=3 SV=1 gi\|209920136, gi... - gi\|209920136\|ref\|YP_002294220.1\| alanyl-tRNA synthetase [Escherichia coli SE11], gi\|209913395\|dbj\|BA... gi\|75256897, gi\|... - gi\|75256897\|ref\|ZP_00728473.1\| COG0013: Alanyl-tRNA synthetase [Escherichia coli E22], gi\|193065058\|... gi\|193069650, gi... - gi\|75235710\|ref\|ZP_00719884.1\| COG0013: Alanyl-tRNA synthetase [Escherichia coli E110019], gi\|193069... gi\|218555239, gi... - gi\|218555239\|ref\|YP_002388152.1\| alanyl-tRNA synthetase [Escherichia coli IAI1], gi\|218362007\|emb\|CA... gi\|218353020, gi... - gi\|218696288\|ref\|YP_002403955.1\| alanyl-tRNA synthetase [Escherichia coli 55989], gi\|218353020\|emb\|C... gi\|75229772, gi\|... - gi\|75229772\|ref\|ZP_00716302.1\| COG0013: Alanyl-tRNA synthetase [Escherichia coli B7A], gi\|191167095\|... gi\|194427866, gi... - gi\|75210896\|ref\|ZP_00711020.1\| COG0013: Alanyl-tRNA synthetase [Escherichia coli B171], gi\|194427866... SYA_ECO24 - Alanine--tRNA ligase OS=Escherichia coli O139:H28 (strain E24377A / ETEC) GN=alaS PE=3 SV=1	1260.0	[0..1]	[876..1]
gi\|218366454, gi... - gi\|218559685\|ref\|YP_002392598.1\| alanyl-tRNA synthetase [Escherichia coli S88], gi\|218366454\|emb\|CAR... SYA_ECOK1 - Alanine--tRNA ligase OS=Escherichia coli O1:K1 / APEC GN=alaS PE=3 SV=1 gi\|237706683, gi... - gi\|237706683\|ref\|ZP_04537164.1\| alanyl-tRNA synthetase [Escherichia sp. 3_2_53FAA], gi\|226899723\|gb\|... SYA_ECOUT - Alanine--tRNA ligase OS=Escherichia coli (strain UTI89 / UPEC) GN=alaS PE=3 SV=1	1259.0	[0..1]	[876..1]
gi\|56480163, gi\|... - gi\|56480163\|ref\|NP_708505.2\| alanyl-tRNA synthetase [Shigella flexneri 2a str. 301], gi\|56383714\|gb\|... SYA_SHIF8 - Alanine--tRNA ligase OS=Shigella flexneri serotype 5b (strain 8401) GN=alaS PE=3 SV=1 SYA_SHIFL - Alanine--tRNA ligase OS=Shigella flexneri GN=alaS PE=3 SV=1 gi\|30064057, gi\|... - gi\|30064057\|ref\|NP_838228.1\| alanyl-tRNA synthetase [Shigella flexneri 2a str. 2457T], gi\|30042313\|g...	1259.0	[0..1]	[876..1]
SYA_SHIBS - Alanine--tRNA ligase OS=Shigella boydii serotype 4 (strain Sb227) GN=alaS PE=3 SV=1	1258.0	[0..1]	[876..1]
SYA_SHIDS - Alanine--tRNA ligase OS=Shigella dysenteriae serotype 1 (strain Sd197) GN=alaS PE=3 SV=1	1258.0	[0..1]	[876..1]
SYA_SHIB3 - Alanine--tRNA ligase OS=Shigella boydii serotype 18 (strain CDC 3083-94 / BS512) GN=alaS PE=3 SV=1	1258.0	[0..1]	[876..1]
gi\|15832808, gi\|... - gi\|15832808\|ref\|NP_311581.1\| alanyl-tRNA synthetase [Escherichia coli O157:H7 str. Sakai], gi\|133630... gi\|168774775, gi... - gi\|187769613\|gb\|EDU33457.1\| alanyl-tRNA synthetase [Escherichia coli O157:H7 str. EC4196], gi\|168774... gi\|189003197, gi... - gi\|189003197\|gb\|EDU72183.1\| alanyl-tRNA synthetase [Escherichia coli O157:H7 str. EC4076], gi\|168778... gi\|189377449, gi... - gi\|189377449\|gb\|EDU95865.1\| alanyl-tRNA synthetase [Escherichia coli O157:H7 str. EC508], gi\|1688002... gi\|25293071 - pir\|\|B91073 alanyl-tRNA synthetase [imported] - Escherichia coli (strain O157:H7, substrain RIMD 050... gi\|195938445 - gi\|195938445\|ref\|ZP_03083827.1\| alanyl-tRNA synthetase [Escherichia coli O157:H7 str. EC4024] gi\|208805868, gi... - gi\|208805868\|ref\|ZP_03248205.1\| alanyl-tRNA synthetase [Escherichia coli O157:H7 str. EC4206], gi\|20... gi\|208735038, gi... - gi\|208813761\|ref\|ZP_03255090.1\| alanyl-tRNA synthetase [Escherichia coli O157:H7 str. EC4045], gi\|20... gi\|208738409, gi... - gi\|208818286\|ref\|ZP_03258606.1\| alanyl-tRNA synthetase [Escherichia coli O157:H7 str. EC4042], gi\|20... gi\|209160191, gi... - gi\|209398791\|ref\|YP_002272160.1\| alanyl-tRNA synthetase [Escherichia coli O157:H7 str. EC4115], gi\|2... gi\|168749982, gi... - gi\|188015823\|gb\|EDU53945.1\| alanyl-tRNA synthetase [Escherichia coli O157:H7 str. EC4113], gi\|168749... gi\|189357241, gi... - gi\|189357241\|gb\|EDU75660.1\| alanyl-tRNA synthetase [Escherichia coli O157:H7 str. EC4401], gi\|168755... gi\|189366853, gi... - gi\|189366853\|gb\|EDU85269.1\| alanyl-tRNA synthetase [Escherichia coli O157:H7 str. EC4501], gi\|168762... SYA_ECO57 - Alanine--tRNA ligase OS=Escherichia coli O157:H7 GN=alaS PE=3 SV=2 gi\|189362083, gi... - gi\|189362083\|gb\|EDU80502.1\| alanyl-tRNA synthetase [Escherichia coli O157:H7 str. EC4486], gi\|168768... gi\|83569947, gi\|... - gi\|83569947\|ref\|ZP_00921395.1\| COG0013: Alanyl-tRNA synthetase [Shigella dysenteriae 1012], gi\|19443... gi\|217327497, gi... - gi\|217327497\|ref\|ZP_03443580.1\| alanyl-tRNA synthetase [Escherichia coli O157:H7 str. TW14588], gi\|2... gi\|254594038, gi... - gi\|254794638\|ref\|YP_003079475.1\| alanyl-tRNA synthetase [Escherichia coli O157:H7 str. TW14359], gi\|...	1258.0	[0..1]	[876..1]

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Predicted Domain #1

Region A:
Residues: [1-465]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSKSTAEIRQ AFLDFFHSKG HQVVASSSLV PHNDPTLLFT NAGMNQFKDV FLGLDKRNYS  60
   61 RATTSQRCVR AGGKHNDLEN VGYTARHHTF FEMLGNFSFG DYFKHDAIQF AWELLTSEKW 120
  121 FALPKERLWV TVYESDDEAY EIWEKEVGIP RERIIRIGDN KGAPYASDNF WQMGDTGPCG 180
  181 PCTEIFYDHG DHIWGGPPGS PEEDGDRYIE IWNIVFMQFN RQADGTMEPL PKPSVDTGMG 240
  241 LERIAAVLQH VNSNYDIDLF RTLIQAVAKV TGATDLSNKS LRVIADHIRS CAFLIADGVM 300
  301 PSNENRGYVL RRIIRRAVRH GNMLGAKETF FYKLVGPLID VMGSAGEDLK RQQAQVEQVL 360
  361 KTEEEQFART LERGLALLDE ELAKLSGDTL DGETAFRLYD TYGFPVDLTA DVCRERNIKV 420
  421 DEAGFEAAME EQRRRAREAS GFGADYNAMI RVDSASEFKG YDHLE

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	1000.0
Match:	1riqA
Description:	The crystal structure of the catalytic fragment of the alanyl-tRNA synthetase
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
alanine-tRNA ligase activity	6.00693881794242	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
lysine-tRNA ligase activity	1.72324031407565	bayes_pls_golite062009
histidine-tRNA ligase activity	1.72215103383322	bayes_pls_golite062009
transcription regulator activity	1.47976803533584	bayes_pls_golite062009
nucleic acid binding	1.30216701059664	bayes_pls_golite062009
DNA binding	1.1862497958336	bayes_pls_golite062009
binding	1.11470390774037	bayes_pls_golite062009
asparagine-tRNA ligase activity	0.921492123574877	bayes_pls_golite062009
transcription repressor activity	0.80781620905336	bayes_pls_golite062009
transcription factor activity	0.566858624145031	bayes_pls_golite062009
RNA binding	0.0221706730298825	bayes_pls_golite062009
aspartate-tRNA ligase activity	0.00572514744734753	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [466-781]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 LNGKVTALFV DGKAVDAINA GQEAVVVLDQ TPFYAESGGQ VGDKGELKGA NFSFAVEDTQ  60
   61 KYGQAIGHIG KLAAGSLKVG DAVQADVDEA RRARIRLNHS ATHLMHAALR QVLGTHVSQK 120
  121 GSLVNDKVLR FDFSHNEAMK PEEIRAVEDL VNTQIRRNLP IETNIMDLEA AKAKGAMALF 180
  181 GEKYDERVRV LSMGDFSTEL CGGTHASRTG DIGLFRIISE SGTAAGVRRI EAVTGEGAIA 240
  241 TVHADSDRLS EVAHLLKGDS NNLADKVRSV LERTRQLEKE LQQLKEQAAA QESANLSSKA 300
  301 IDVNGVKLLV SELSGV

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	49.045757
Match:	1qf6A
Description:	Threonyl-tRNA synthetase (ThrRS), C-terminal domain; Threonyl-tRNA synthetase (ThrRS), N-terminal 'additional' domain; Threonyl-tRNA synthetase (ThrRS), second 'additional' domain; Threonyl-tRNA synthetase (ThrRS)
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
ligase activity, forming aminoacyl-tRNA and related compounds	7.43002999363006	bayes_pls_golite062009
ligase activity, forming carbon-oxygen bonds	7.43002999363006	bayes_pls_golite062009
aminoacyl-tRNA ligase activity	7.41942428925617	bayes_pls_golite062009
ligase activity	6.32830458335651	bayes_pls_golite062009
alanine-tRNA ligase activity	5.71383204545219	bayes_pls_golite062009
phenylalanine-tRNA ligase activity	2.36340232855305	bayes_pls_golite062009
catalytic activity	1.99372273395202	bayes_pls_golite062009
threonine-tRNA ligase activity	1.80163029560755	bayes_pls_golite062009
serine-tRNA ligase activity	1.77810600842868	bayes_pls_golite062009
glycine-tRNA ligase activity	1.73190731100586	bayes_pls_golite062009
lysine-tRNA ligase activity	1.56431758015114	bayes_pls_golite062009
histidine-tRNA ligase activity	1.30665379023529	bayes_pls_golite062009
binding	0.904147650999471	bayes_pls_golite062009
transcription regulator activity	0.819460789497064	bayes_pls_golite062009
nucleic acid binding	0.776772138477575	bayes_pls_golite062009
asparagine-tRNA ligase activity	0.619194216414817	bayes_pls_golite062009
DNA binding	0.586146825669637	bayes_pls_golite062009
transcription repressor activity	0.236808757312849	bayes_pls_golite062009

Predicted Domain #3

Region A:
Residues: [782-876]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 EPKMLRTMVD DLKNQLGSTI IVLATVVEGK VSLIAGVSKD VTDRVKAGEL IGMVAQQVGG  60
   61 KGGGRPDMAQ AGGTDAAALP AALASVKGWV SAKLQ

[Run NCBI BLAST on this sequence.]

Detection Method:	Pfam
Confidence:	21.769551
Match:	PF02272.10
Description:	No description for PF02272.10 was found.

Shown below are all of our structure predictions for this domain.
Click here to view only most confident match.

		MCM Score	GO Score	GO Term	SCOP Match	SCOP Description
View	Download	0.513	0.157	translation	d.58.7	RNA-binding domain, RBD
View	Download	0.552	0.024	nucleic acid binding	d.51.1	Eukaryotic type KH-domain (KH-domain type I)
View	Download	0.587	N/A	N/A	a.112.1	Description not found.
View	Download	0.531	N/A	N/A	d.51.1	Eukaryotic type KH-domain (KH-domain type I)
View	Download	0.511	N/A	N/A	d.58.11	EF-G/eEF-2 domains III and V

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:

Predicted functions: