YRC Public Data Repository - Protein Structure Prediction

Protein:	YGEV_ECOLI
Organism:	Escherichia coli
Length:	592 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 YGEV_ECOLI.

Description	E-value	Query Range	Subject Range
gi\|215488170, gi... - gi\|215488170\|ref\|YP_002330601.1\| predicted DNA-binding transcriptional regulator [Escherichia coli O... gi\|227834686, gi... - gi\|227888417\|ref\|ZP_04006222.1\| sigma-54-dependent transcriptional regulator ygeV [Escherichia coli ... gi\|26109689, gi\|... - gi\|26249282\|ref\|NP_755322.1\| putative sigma-54-dependent transcriptional regulator ygeV [Escherichia...	410.0	[0..1]	[589..1]
gi\|110643018, gi... - gi\|110643018\|ref\|YP_670748.1\| sigma-54-dependent transcriptional regulator YgeV [Escherichia coli 53... gi\|191173229, gi... - gi\|75239214\|ref\|ZP_00723187.1\| COG3829: Transcriptional regulator containing PAS, AAA-type ATPase, a...	410.0	[0..1]	[589..1]
gi\|218366631, gi... - gi\|218559862\|ref\|YP_002392775.1\| putative DNA-binding transcriptional regulator [Escherichia coli S8... gi\|117625101, gi... - gi\|117625101\|ref\|YP_854089.1\| DNA-binding transcriptional regulator [Escherichia coli APEC O1], gi\|1... gi\|91073821, gi\|... - gi\|91212247\|ref\|YP_542233.1\| sigma-54-dependent transcriptional regulator ygeV [Escherichia coli UTI... gi\|226899528, gi... - gi\|237706488\|ref\|ZP_04536969.1\| sigma-54-dependent transcriptional regulator ygeV [Escherichia sp. 3...	410.0	[0..1]	[589..1]
gi\|73856905, gi\|... - gi\|74313428\|ref\|YP_311847.1\| putative transcriptional regulator [Shigella sonnei Ss046], gi\|73856905...	408.0	[0..1]	[589..1]
gi\|194424146, gi... - gi\|83587735\|ref\|ZP_00926362.1\| COG3829: Transcriptional regulator containing PAS, AAA-type ATPase, a... gi\|209920324, gi... - gi\|209920324\|ref\|YP_002294408.1\| putative transcriptional regulator [Escherichia coli SE11], gi\|2099... gi\|218555418, gi... - gi\|218555418\|ref\|YP_002388331.1\| putative DNA-binding transcriptional regulator [Escherichia coli IA... gi\|170018884, gi... - gi\|170018884\|ref\|YP_001723838.1\| PAS modulated sigma54 specific transcriptional regulator [Escherich... gi\|124502328, gi... - gi\|124526224\|ref\|ZP_01698229.1\| sigma54 specific transcriptional regulator, Fis family [Escherichia ... gi\|218353197, gi... - gi\|218696465\|ref\|YP_002404132.1\| putative DNA-binding transcriptional regulator [Escherichia coli 55... gi\|191165987, gi... - gi\|75230843\|ref\|ZP_00717301.1\| COG3829: Transcriptional regulator containing PAS, AAA-type ATPase, a... gi\|75212517, gi\|... - gi\|75212517\|ref\|ZP_00712541.1\| COG3829: Transcriptional regulator containing PAS, AAA-type ATPase, a... gi\|157068010, gi... - gi\|75196822\|ref\|ZP_00706892.1\| COG3829: Transcriptional regulator containing PAS, AAA-type ATPase, a...	408.0	[0..1]	[589..1]
gi\|168785714, gi... - gi\|189373965\|gb\|EDU92381.1\| sigma-54 dependent transcriptional regulator, Fis family [Escherichia co... gi\|254794821, gi... - gi\|254794821\|ref\|YP_003079658.1\| predicted DNA-binding transcriptional regulator [Escherichia coli O... gi\|189377653, gi... - gi\|189377653\|gb\|EDU96069.1\| sigma-54 dependent transcriptional regulator, Fis family [Escherichia co... gi\|195936486 - gi\|195936486\|ref\|ZP_03081868.1\| putative transcriptional regulator [Escherichia coli O157:H7 str. EC... gi\|208806656, gi... - gi\|208806656\|ref\|ZP_03248993.1\| sigma-54 dependent transcriptional regulator, Fis family [Escherichi... gi\|209760780, gi... - pir\|\|F91096 probable transcription regulator [imported] - Escherichia coli (strain O157:H7, substrai... gi\|189369255, gi... - gi\|189369255\|gb\|EDU87671.1\| sigma-54 dependent transcriptional regulator, Fis family [Escherichia co... gi\|168766861, gi... - gi\|189363731\|gb\|EDU82150.1\| sigma-54 dependent transcriptional regulator, Fis family [Escherichia co... gi\|15803406, gi\|... - gi\|15803406\|ref\|NP_289439.1\| putative transcriptional regulator [Escherichia coli O157:H7 EDL933], g... gi\|168775745, gi... - gi\|187768757\|gb\|EDU32601.1\| sigma-54 dependent transcriptional regulator, Fis family [Escherichia co... gi\|13363214, gi\|... - gi\|15832996\|ref\|NP_311769.1\| putative transcriptional regulator [Escherichia coli O157:H7], gi\|13363... gi\|189003206, gi... - gi\|189003206\|gb\|EDU72192.1\| sigma-54 dependent transcriptional regulator, Fis family [Escherichia co... gi\|168747654, gi... - gi\|188017865\|gb\|EDU55987.1\| sigma-54 dependent transcriptional regulator, Fis family [Escherichia co... gi\|189358384, gi... - gi\|189358384\|gb\|EDU76803.1\| sigma-54 dependent transcriptional regulator, Fis family [Escherichia co... gi\|13363214, gi\|... - gi\|15832996\|ref\|NP_311769.1\| putative transcriptional regulator [Escherichia coli O157:H7 str. Sakai... gi\|208735327, gi... - gi\|208814050\|ref\|ZP_03255379.1\| sigma-54 dependent transcriptional regulator, Fis family [Escherichi... gi\|208741266, gi... - gi\|208821143\|ref\|ZP_03261463.1\| sigma-54 dependent transcriptional regulator, Fis family [Escherichi... gi\|209162399, gi... - gi\|209400999\|ref\|YP_002272344.1\| sigma-54 dependent transcriptional regulator, Fis family [Escherich... gi\|217326894, gi... - gi\|217326894\|ref\|ZP_03442977.1\| sigma-54 dependent transcriptional regulator, Fis family [Escherichi...	407.0	[0..1]	[589..1]
gi\|193070552, gi... - gi\|75234598\|ref\|ZP_00718929.1\| COG3829: Transcriptional regulator containing PAS, AAA-type ATPase, a...	407.0	[0..1]	[589..1]
gi\|75258469, gi\|... - gi\|75258469\|ref\|ZP_00729891.1\| COG3829: Transcriptional regulator containing PAS, AAA-type ATPase, a...	406.0	[0..1]	[589..1]
gi\|157155317, gi... - gi\|75187586\|ref\|ZP_00700853.1\| COG3829: Transcriptional regulator containing PAS, AAA-type ATPase, a...	405.0	[0..1]	[589..1]
gi\|62182467, gi\|... - gi\|62182467\|ref\|YP_218884.1\| response regulator in two-component regulatory system with GlnL (EBP fa...	387.0	[0..119]	[590..13]

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Predicted Domain #1

Region A:
Residues: [1-118]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MELATTQSVL MQIQPTIQRF ARMLASVLQL EVEIVDENLC RVAGTGAYGK FLGRQLSGNS  60
   61 RLLRHVLETK TEKVVTQSRF DPLCEGCDSK ENCREKAFLG TPVILQDRCV GVISLIAV

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	22.0
Match:	1jbkA
Description:	ClpB
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
two-component response regulator activity	1.45919623810582	bayes_pls_golite062009
catalytic activity	1.37148167194523	bayes_pls_golite062009
binding	1.30574971150356	bayes_pls_golite062009
hydrolase activity	1.18053993810305	bayes_pls_golite062009
nucleic acid binding	0.900561861643259	bayes_pls_golite062009
transcription regulator activity	0.530058973650498	bayes_pls_golite062009
DNA binding	0.460315660888175	bayes_pls_golite062009
purine ribonucleotide binding	0.0324692870996578	bayes_pls_golite062009
ribonucleotide binding	0.0319901144782286	bayes_pls_golite062009
purine nucleotide binding	0.0199205367873159	bayes_pls_golite062009
nucleotide binding	0.00540039127746217	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [119-514]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 THEQQEHISD NLREFSDYVR HISTIFVSKL LEDQGPGDNI SKIFATMIDN MDQGVLVVDD  60
   61 ENRVQFVNQT ALKTLGVVQN NIIGKPIRFR PLTFESNFTH GHMQHIVSWD DKSELIIGQL 120
  121 HNIQGRQLFL MAFHQSHTSF SVANAPDEPH IEQLVGECRV MRQLKRLISR IAPSPSSVMV 180
  181 VGESGTGKEV VARAIHKLSG RRNKPFIAIN CAAIPEQLLE SELFGYVKGA FTGASANGKT 240
  241 GLIQAANTGT LFLDEIGDMP LMLQAKLLRA IEAREILPIG ASSPIQVDIR IISATNQNLA 300
  301 QFIAEGKFRE DLFYRLNVIP ITLPPLRERQ EDIELLVHYF LHLHTRRLGS VYPGIAPDVV 360
  361 EILRKHRWPG NLRELSNLME YLVNVVPSGE VIDSTL

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	83.522879
Match:	1ny5A
Description:	Crystal structure of sigm54 activator (AAA+ ATPase) in the inactive state
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
protein histidine kinase activity	2.35011582062573	bayes_pls_golite062009
two-component sensor activity	2.32303301074957	bayes_pls_golite062009
phosphotransferase activity, nitrogenous group as acceptor	2.28838869071567	bayes_pls_golite062009
two-component response regulator activity	1.45919623810582	bayes_pls_golite062009
catalytic activity	1.37148167194523	bayes_pls_golite062009
binding	1.30574971150356	bayes_pls_golite062009
hydrolase activity	1.18053993810305	bayes_pls_golite062009
nucleic acid binding	0.900561861643259	bayes_pls_golite062009
transcription regulator activity	0.530058973650498	bayes_pls_golite062009
DNA binding	0.460315660888175	bayes_pls_golite062009
purine ribonucleotide binding	0.0324692870996578	bayes_pls_golite062009
ribonucleotide binding	0.0319901144782286	bayes_pls_golite062009
purine nucleotide binding	0.0199205367873159	bayes_pls_golite062009
nucleotide binding	0.00540039127746217	bayes_pls_golite062009

Predicted Domain #3

Region A:
Residues: [515-592]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 LPPNLLNNGT TEQSDVTEVS EAHLSLDDAG GTALEEMEKQ MIREALSRHN SKKQVADELG  60
   61 IGIATLYRKI KKYELLNT

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	80.30103
Match:	1ojlA
Description:	Crystal structure of a sigma54-activator suggests the mechanism for the conformational switch necessary for sigma54 binding
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:

Predicted functions: