YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|24374516, gi\|...
Organism:	Shewanella oneidensis MR-1
Length:	272 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|24374516, gi|....

Description	E-value	Query Range	Subject Range
gi\|160875134, gi... - gi\|160875134\|ref\|YP_001554450.1\| putative phage repressor [Shewanella baltica OS195], gi\|160860656\|g...	148.0	[0..7]	[267..1]
gi\|68544779, gi\|... - gi\|68544779\|ref\|ZP_00584383.1\| Helix-turn-helix motif:Peptidase S24, S26A and S26B [Shewanella balti...	148.0	[0..7]	[267..1]
gi\|91716618, gi\|... - gi\|91794616\|ref\|YP_564267.1\| transciptional regulator [Shewanella denitrificans OS217], gi\|91716618\|...	143.0	[0..12]	[267..4]
gi\|94417993, gi\|... - gi\|94417993\|ref\|ZP_01297809.1\| hypothetical protein PaerP_01000142 [Pseudomonas aeruginosa PA7], gi\|...	135.0	[0..8]	[267..1]
gi\|49081996 - gi\|49081996\|gb\|AAT50398.1\| PA0906 [synthetic construct]	133.0	[0..8]	[267..1]
gi\|218893125, gi... - gi\|218893125\|ref\|YP_002441994.1\| putative transcriptional regulator [Pseudomonas aeruginosa LESB58],... gi\|107100364 - gi\|107100364\|ref\|ZP_01364282.1\| hypothetical protein PaerPA_01001389 [Pseudomonas aeruginosa PACS2] gi\|9946808, gi\|1... - gi\|9946808\|gb\|AAG04295.1\|AE004525_3 probable transcriptional regulator [Pseudomonas aeruginosa PAO1]... gi\|11351998 - pir\|\|E83531 probable transcription regulator PA0906 [imported] - Pseudomonas aeruginosa (strain PAO1... gi\|116048830, gi... - gi\|53727399\|ref\|ZP_00138503.2\| COG2932: Predicted transcriptional regulator [Pseudomonas aeruginosa ... gi\|254239258, gi... - gi\|84316676\|ref\|ZP_00965148.1\| COG2932: Predicted transcriptional regulator [Pseudomonas aeruginosa ...	133.0	[0..8]	[267..1]
gi\|69951778, gi\|... - gi\|69951778\|ref\|ZP_00639418.1\| Helix-turn-helix motif:Peptidase S24, S26A and S26B [Shewanella frigi...	131.0	[0..7]	[267..1]
gi\|115589560, gi... - gi\|53727242\|ref\|ZP_00141067.2\| COG2932: Predicted transcriptional regulator [Pseudomonas aeruginosa ...	131.0	[0..1]	[271..1]

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Predicted Domain #1

Region A:
Residues: [1-171]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MNYDDPKKKV GRNIKRLRLK AGIKSQAALA ELCGWKSQSR VGNYEAGTRA VSAIDAETLA  60
   61 KVLNVTPAEI LYGENNKDDD FVSMPSAQYS SGPYEEEDPF QLFKPKQELQ NAEWHAGFEL 120
  121 WDGDTPLRDD EVALPFYREV ELAAGSGSTF VQENGGCKLR FAKSTLKKSR V

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	11.154902
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
chromatin binding	1.95349305901468	bayes_pls_golite062009
RNA polymerase II transcription factor activity	1.68628693197843	bayes_pls_golite062009
transcription regulator activity	1.53379254385616	bayes_pls_golite062009
sequence-specific DNA binding	1.5260010669675	bayes_pls_golite062009
nucleic acid binding	1.39112186102649	bayes_pls_golite062009
DNA binding	1.21399747785847	bayes_pls_golite062009
transcription activator activity	1.19708518304437	bayes_pls_golite062009
transcription repressor activity	1.1438331905924	bayes_pls_golite062009
binding	1.11663192519845	bayes_pls_golite062009
transcription factor activity	0.546420977042213	bayes_pls_golite062009
catalytic activity	0.401988496917198	bayes_pls_golite062009
protein binding	0.110960530780648	bayes_pls_golite062009
structure-specific DNA binding	0.0777655554748162	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [172-272]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 EPSNAACVTV SGNSMLPVLR HGTTVGVDTS KKSIIDGEMY AIDHDGMLRV KMLYRTPGGG  60
   61 IRIKSYNNDE FPDEFIPPEK ASDIKIIGWV FWWSVLNVWN N

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	13.30103
Match:	2ho0A
Description:	No description for 2ho0A was found.

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: