YRC Public Data Repository - Protein Structure Prediction

Protein:	YDCN_ECOLI
Organism:	Escherichia coli
Length:	178 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 YDCN_ECOLI.

Description	E-value	Query Range	Subject Range
gi\|78365654, gi\|... - gi\|78365654\|ref\|ZP_00835939.1\| Helix-turn-helix motif:Cupin region [Shewanella sp. PV-4], gi\|7836219...	124.0	[0..6]	[175..1]
SO1265 - transcriptional regulator putative gi\|24372846, gi\|... - gi\|24372846\|ref\|NP_716888.1\| transcriptional regulator, putative [Shewanella oneidensis MR-1], gi\|24...	123.0	[0..6]	[175..1]
gi\|95113300, gi\|... - gi\|95113300\|emb\|CAK18028.1\| putative transcriptional regulator [Pseudomonas entomophila L48], gi\|104... gi\|95113300 - gi\|95113300\|emb\|CAK18028.1\| putative transcriptional regulator [Pseudomonas entomophila L48]	123.0	[0..6]	[175..1]
gi\|68544420, gi\|... - gi\|68544420\|ref\|ZP_00584069.1\| Helix-turn-helix motif [Shewanella baltica OS155], gi\|68517873\|gb\|EAN... gi\|160859837, gi... - gi\|160874315\|ref\|YP_001553631.1\| XRE family transcriptional regulator [Shewanella baltica OS195], gi... gi\|151364315, gi... - gi\|152999697\|ref\|YP_001365378.1\| cupin 2 domain-containing protein [Shewanella baltica OS185], gi\|15... gi\|149116513, gi... - gi\|217974352\|ref\|YP_002359103.1\| transcriptional regulator, XRE family [Shewanella baltica OS223], g...	122.0	[0..6]	[175..1]
tr\|E4RCV5\|E4RCV5... - Cro/CI family transcriptional regulator OS=Pseudomonas putida (strain BIRD-1) GN=PPUBIRD1_5062 PE=4 ... tr\|I7BAY6\|I7BAY6... - Cro/CI family transcriptional regulator OS=Pseudomonas putida (strain DOT-T1E) GN=T1E_2779 PE=4 SV=1 gi\|26991944, gi\|... - gi\|26991944\|ref\|NP_747369.1\| Cro/CI family transcriptional regulator [Pseudomonas putida KT2440], gi...	122.0	[0..6]	[175..1]
gi\|82721877, gi\|... - gi\|82740773\|ref\|ZP_00903508.1\| Helix-turn-helix motif [Shewanella sp. W3-18-1], gi\|82721877\|gb\|EAP56... gi\|145563884, gi... - gi\|77816289\|ref\|ZP_00815487.1\| Helix-turn-helix motif [Shewanella putrefaciens CN-32], gi\|77808745\|g...	122.0	[0..6]	[175..1]
gi\|78692270, gi\|... - gi\|78692270\|ref\|ZP_00856824.1\| Helix-turn-helix motif [Shewanella sp. MR-7], gi\|78508326\|gb\|EAP21794... gi\|117921538, gi... - gi\|78686613\|ref\|ZP_00851378.1\| Helix-turn-helix motif [Shewanella sp. ANA-3], gi\|78505627\|gb\|EAP1915... gi\|82404079, gi\|... - gi\|82497917\|ref\|ZP_00883439.1\| Helix-turn-helix motif [Shewanella sp. MR-4], gi\|82404079\|gb\|EAP44778...	120.0	[0..1]	[175..24]
gi\|49081740 - gi\|49081740\|gb\|AAT50270.1\| PA5301 [synthetic construct]	120.0	[0..6]	[175..1]
gi\|148550378, gi... - gi\|82739390\|ref\|ZP_00902194.1\| Helix-turn-helix motif [Pseudomonas putida F1], gi\|82713513\|gb\|EAP486...	120.0	[0..7]	[175..19]
gi\|68347618, gi\|... - gi\|70733319\|ref\|YP_263093.1\| DNA-binding protein [Pseudomonas fluorescens Pf-5], gi\|68347618\|gb\|AAY9...	119.0	[0..6]	[175..1]

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Predicted Domain #1

Region A:
Residues: [1-178]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MENLARFLST TLKQLRQQRG WSLSRLAEAT GVSKAMLGQI ERNESSPTVA TLWKIATGLN  60
   61 VPFSTFISPP QSATPSVYDP QQQAMVITSL FPYDPQLCFE HFSIQMASGA ISESTPHEKG 120
  121 VIEHVVVIDG QLDLCVDGEW QTLNCGEGVR FAADVTHIYR NGGEQTVHFH SLIHYPRS

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	18.69897
Match:	1y9qA
Description:	Crystal Structure of HTH_3 family Transcriptional Regulator from Vibrio cholerae
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
catalytic activity	0.77242843392921	bayes_pls_golite062009
transcription regulator activity	0.707930119310256	bayes_pls_golite062009
nucleic acid binding	0.437474993266492	bayes_pls_golite062009
RNA polymerase II transcription factor activity	0.29966985317584	bayes_pls_golite062009
DNA binding	0.241621391797808	bayes_pls_golite062009
binding	0.206341280654185	bayes_pls_golite062009
sequence-specific DNA binding	0.20324889750334	bayes_pls_golite062009
transcription repressor activity	0.0485771867742395	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: