YRC Public Data Repository - Protein Structure Prediction

Protein:	YDJF_ECOLI
Organism:	Escherichia coli
Length:	252 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 YDJF_ECOLI.

Description	E-value	Query Range	Subject Range
gi\|77978684, gi\|... - gi\|77978684\|ref\|ZP_00834110.1\| COG1349: Transcriptional regulators of sugar metabolism [Yersinia int...	214.0	[0..1]	[250..1]
gi\|255054070, gi... - gi\|255054070\|ref\|ZP_05306318.1\| transcriptional regulator, DeoR family [Pectobacterium wasabiae WPP1... gi\|253690290, gi... - gi\|253690290\|ref\|YP_003019480.1\| transcriptional regulator, DeoR family [Pectobacterium carotovorum ... gi\|50123057, gi\|... - gi\|50123057\|ref\|YP_052224.1\| DNA-binding transcriptional repressor GlpR [Pectobacterium atrosepticum...	212.0	[0..1]	[250..1]
gi\|207858762, gi... - gi\|207858762\|ref\|YP_002245413.1\| DNA-binding transcriptional repressor GlpR [Salmonella enterica sub... gi\|199604473, gi... - gi\|200387375\|ref\|ZP_03213987.1\| glycerol-3-phosphate regulon repressor [Salmonella enterica subsp. e... gi\|205354854, gi... - gi\|205354854\|ref\|YP_002228655.1\| DNA-binding transcriptional repressor GlpR [Salmonella enterica sub... gi\|197240099, gi... - gi\|197261844\|ref\|ZP_03161918.1\| glycerol-3-phosphate regulon repressor [Salmonella enterica subsp. e... gi\|197939339, gi... - gi\|198244823\|ref\|YP_002217481.1\| glycerol-3-phosphate regulon repressor [Salmonella enterica subsp. ... gi\|194459298, gi... - gi\|194472934\|ref\|ZP_03078918.1\| glycerol-3-phosphate regulon repressor [Salmonella enterica subsp. e... gi\|197214979, gi... - gi\|197251276\|ref\|YP_002148446.1\| glycerol-3-phosphate regulon repressor [Salmonella enterica subsp. ... lcl\|NC_016856.1_... - [gene=glpR] [protein=DNA-binding transcriptional repressor GlpR] [protein_id=YP_005239728.1] [locati... gi\|194446805, gi... - gi\|194446805\|ref\|YP_002042768.1\| glycerol-3-phosphate regulon repressor [Salmonella enterica subsp. ... gi\|194408128, gi... - gi\|194449824\|ref\|YP_002047547.1\| DNA-binding transcriptional repressor GlpR [Salmonella enterica sub... gi\|238910475 - gi\|238910475\|ref\|ZP_04654312.1\| DNA-binding transcriptional repressor GlpR [Salmonella enterica subs... gi\|16422082, gi\|... - gi\|16766810\|ref\|NP_462425.1\| DNA-binding transcriptional repressor GlpR [Salmonella typhimurium LT2]... gi\|168465204, gi... - gi\|195632411\|gb\|EDX50895.1\| glycerol-3-phosphate regulon repressor [Salmonella enterica subsp. enter... gi\|168818662, gi... - gi\|205344365\|gb\|EDZ31129.1\| glycerol-3-phosphate regulon repressor [Salmonella enterica subsp. enter... gi\|205333122, gi... - gi\|205333122\|gb\|EDZ19886.1\| glycerol-3-phosphate regulon repressor [Salmonella enterica subsp. enter... gi\|168241667, gi... - gi\|205339067\|gb\|EDZ25831.1\| glycerol-3-phosphate regulon repressor [Salmonella enterica subsp. enter... gi\|167549268, gi... - gi\|205325648\|gb\|EDZ13487.1\| glycerol-3-phosphate regulon repressor [Salmonella enterica subsp. enter... gi\|167990730, gi... - gi\|205330718\|gb\|EDZ17482.1\| glycerol-3-phosphate regulon repressor [Salmonella enterica subsp. enter... gi\|161365925, gi... - gi\|161616561\|ref\|YP_001590526.1\| DNA-binding transcriptional repressor GlpR [Salmonella enterica sub...	212.0	[0..1]	[250..1]
gi\|62182024, gi\|... - gi\|62182024\|ref\|YP_218441.1\| DNA-binding transcriptional repressor GlpR [Salmonella enterica subsp. ...	212.0	[0..1]	[250..1]
gi\|115514811, gi... - gi\|117625687\|ref\|YP_859010.1\| DNA-binding transcriptional repressor GlpR [Escherichia coli APEC O1],...	212.0	[0..1]	[250..13]
gi\|191171550, gi... - gi\|191171550\|ref\|ZP_03033098.1\| glycerol-3-phosphate regulon repressor [Escherichia coli F11], gi\|19... gi\|215266775, gi... - gi\|215488703\|ref\|YP_002331134.1\| DNA-binding transcriptional repressor GlpR [Escherichia coli O127:H... gi\|218367248, gi... - gi\|218560479\|ref\|YP_002393392.1\| DNA-binding transcriptional repressor GlpR [Escherichia coli S88], ... gi\|218429262, gi... - gi\|218691698\|ref\|YP_002399910.1\| DNA-binding transcriptional repressor GlpR [Escherichia coli ED1a],... gi\|227883557, gi... - gi\|227883557\|ref\|ZP_04001362.1\| DNA-binding transcriptional repressor GlpR [Escherichia coli 83972],... gi\|110345247, gi... - gi\|110643655\|ref\|YP_671385.1\| DNA-binding transcriptional repressor GlpR [Escherichia coli 536], gi\|...	211.0	[0..1]	[250..1]
gi\|91191480, gi\|... - gi\|91223394\|ref\|ZP_01258659.1\| transcriptional regulator, DeoR family protein [Vibrio alginolyticus ...	211.0	[0..1]	[250..1]
gi\|75241487 - gi\|75241487\|ref\|ZP_00725332.1\| COG1349: Transcriptional regulators of sugar metabolism [Escherichia ...	211.0	[0..1]	[250..13]
gi\|254229357, gi... - gi\|75855918\|ref\|ZP_00763557.1\| COG1349: Transcriptional regulators of sugar metabolism [Vibrio sp. E...	211.0	[0..1]	[250..1]
gi\|110616805, gi... - gi\|110807257\|ref\|YP_690777.1\| DNA-binding transcriptional repressor GlpR [Shigella flexneri 5 str. 8... gi\|238860967, gi... - gi\|238902516\|ref\|YP_002928312.1\| DNA-binding transcriptional repressor [Escherichia coli BW2952], gi... gi\|253322792, gi... - gi\|253771748\|ref\|YP_003034579.1\| transcriptional regulator, DeoR family [Escherichia coli BL21(DE3)]... gi\|226839096, gi... - gi\|254038590\|ref\|ZP_04872646.1\| glycerol-3-phosphate regulon repressor [Escherichia sp. 1_1_43], gi\|... gi\|606358\|gb\|AAA... - CG Site No. 688 [Escherichia coli], DNA-binding transcriptional repressor [Escherichia coli K12], DN... gi\|73857500, gi\|... - gi\|74314023\|ref\|YP_312442.1\| DNA-binding transcriptional repressor GlpR [Shigella sonnei Ss046], gi\|... gi\|170683823, gi... - gi\|170683823\|ref\|YP_001745670.1\| glycerol-3-phosphate regulon repressor [Escherichia coli SMS-3-5], ... gi\|82778762, gi\|... - gi\|82778762\|ref\|YP_405111.1\| DNA-binding transcriptional repressor GlpR [Shigella dysenteriae Sd197]... gi\|169890773, gi... - gi\|170082938\|ref\|YP_001732258.1\| DNA-binding transcriptional repressor [Escherichia coli str. K-12 s... gi\|192957880, gi... - gi\|75237024\|ref\|ZP_00721080.1\| COG1349: Transcriptional regulators of sugar metabolism [Escherichia ... gi\|209920880, gi... - gi\|209920880\|ref\|YP_002294964.1\| DNA-binding transcriptional repressor GlpR [Escherichia coli SE11],... gi\|193061762, gi... - gi\|75260289\|ref\|ZP_00731557.1\| COG1349: Transcriptional regulators of sugar metabolism [Escherichia ... gi\|194431129, gi... - gi\|194431129\|ref\|ZP_03063422.1\| glycerol-3-phosphate regulon repressor [Shigella dysenteriae 1012], ... gi\|218697105, gi... - gi\|218697105\|ref\|YP_002404772.1\| DNA-binding transcriptional repressor GlpR [Escherichia coli 55989]... gi\|218362739, gi... - gi\|218555971\|ref\|YP_002388884.1\| DNA-binding transcriptional repressor GlpR [Escherichia coli IAI1],... gi\|81247190, gi\|... - gi\|82545779\|ref\|YP_409726.1\| DNA-binding transcriptional repressor GlpR [Shigella boydii Sb227], gi\|... gi\|218707013, gi... - gi\|218707013\|ref\|YP_002414532.1\| DNA-binding transcriptional repressor GlpR [Escherichia coli UMN026... gi\|89110588, gi\|... - gi\|89110588\|ref\|AP_004368.1\| DNA-binding transcriptional repressor [Escherichia coli str. K-12 subst... gi\|218372153, gi... - gi\|218702167\|ref\|YP_002409796.1\| DNA-binding transcriptional repressor GlpR [Escherichia coli IAI39]... GLPR_ECOLI - Glycerol-3-phosphate regulon repressor - Escherichia coli GLPR_SHIFL - Glycerol-3-phosphate regulon repressor OS=Shigella flexneri GN=glpR PE=3 SV=1 gi\|24053898, gi\|... - gi\|24114688\|ref\|NP_709198.1\| DNA-binding transcriptional repressor GlpR [Shigella flexneri 2a str. 3... gi\|75211789, gi\|... - gi\|75211789\|ref\|ZP_00711853.1\| COG1349: Transcriptional regulators of sugar metabolism [Escherichia ... gi\|75229568, gi\|... - gi\|75229568\|ref\|ZP_00716111.1\| COG1349: Transcriptional regulators of sugar metabolism [Escherichia ... gi\|30043556, gi\|... - gi\|30065294\|ref\|NP_839465.1\| DNA-binding transcriptional repressor GlpR [Shigella flexneri 2a str. 2... gi\|187731240, gi... - gi\|75179956\|ref\|ZP_00699943.1\| COG1349: Transcriptional regulators of sugar metabolism [Shigella boy... gi\|1789829, gi\|1... - gi\|1789829\|gb\|AAC76448.1\| DNA-binding transcriptional repressor [Escherichia coli str. K-12 substr. ... gi\|157080914, gi... - gi\|75188196\|ref\|ZP_00701463.1\| COG1349: Transcriptional regulators of sugar metabolism [Escherichia ...	211.0	[0..1]	[250..1]

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Predicted Domain #1

Region A:
Residues: [1-65]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MAAKDRIQAI KQMVANDKKV TVSNLSGIFQ VTEETIRRDL EKLEDEGFLT RTYGGAVLNT  60
   61 AMLTE

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	6.69897
Match:	1i1gA
Description:	LprA
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
transcription regulator activity	3.98990675336286	bayes_pls_golite062009
DNA binding	3.4273272886116	bayes_pls_golite062009
nucleic acid binding	3.38054693035398	bayes_pls_golite062009
transcription factor activity	2.80110428028438	bayes_pls_golite062009
binding	2.18911933843505	bayes_pls_golite062009
transcription activator activity	0.53294679084865	bayes_pls_golite062009
sequence-specific DNA binding	0.53285802828572	bayes_pls_golite062009
transcription repressor activity	0.513853050429619	bayes_pls_golite062009
protein binding	0.035220363090062	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [66-252]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NIHFYKRASS FYEEKQLIAR KALPFIDNKT TMAADSSSTV MELLKLLQDR SGLTLLTNSA  60
   61 EAIHVLAQSE IKVVSTGGEL NKNTLSLQGR ITKEIIRRYH VDIMVMSCKG LDINSGALDS 120
  121 NEAEAEIKKT MIRQATEVAL LVDHSKFDRK AFVQLADFSH INYIITDKSP GAEWIAFCKD 180
  181 NNIQLVW

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	25.30103
Match:	1oozA
Description:	Deletion mutant of SUCCINYL-COA:3-KETOACID COA TRANSFERASE FROM PIG HEART
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
catalytic activity	1.68776709414398	bayes_pls_golite062009
nucleic acid binding	0.965520574888216	bayes_pls_golite062009
transcription regulator activity	0.769423781192988	bayes_pls_golite062009
DNA binding	0.223734115868557	bayes_pls_golite062009
binding	0.199466104892993	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:

Predicted functions: