YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|33151874, gi\|...
Organism:	Haemophilus ducreyi 35000HP
Length:	297 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|33151874, gi|....

Description	E-value	Query Range	Subject Range
gi\|91191158, gi\|... - gi\|91224247\|ref\|ZP_01259510.1\| putative transcription regulator protein [Vibrio alginolyticus 12G01]...	295.0	[0..6]	[297..7]
gi\|28900071, gi\|... - gi\|28900071\|ref\|NP_799726.1\| putative transcription regulator protein [Vibrio parahaemolyticus RIMD ... gi\|28808354 - gi\|28808354\|dbj\|BAC61559.1\| putative transcription regulator protein [Vibrio parahaemolyticus RIMD 2...	295.0	[0..6]	[297..7]
gi\|116185384, gi... - gi\|75856032\|ref\|ZP_00763668.1\| COG0583: Transcriptional regulator [Vibrio sp. Ex25], gi\|254227935\|re...	293.0	[0..6]	[297..7]
gi\|27367995, gi\|... - gi\|27367995\|ref\|NP_763522.1\| transcriptional regulator [Vibrio vulnificus CMCP6], gi\|27359568\|gb\|AAO...	288.0	[0..3]	[295..5]
gi\|37200667, gi\|... - gi\|37676126\|ref\|NP_936522.1\| transcriptional regulator [Vibrio vulnificus YJ016], gi\|37200667\|dbj\|BA...	287.0	[0..3]	[295..5]
gi\|114045851, gi... - gi\|78689367\|ref\|ZP_00854030.1\| transcriptional regulator, LysR family [Shewanella sp. MR-7], gi\|7851...	285.0	[0..1]	[292..1]
SO0369 - transcriptional regulator LysR family gi\|24345816, gi\|... - gi\|24371967\|ref\|NP_716009.1\| LysR family transcriptional regulator [Shewanella oneidensis MR-1], gi\|...	283.0	[0..3]	[293..4]
gi\|117614564, gi... - gi\|78685922\|ref\|ZP_00850696.1\| transcriptional regulator, LysR family [Shewanella sp. ANA-3], gi\|785...	283.0	[0..3]	[292..4]
gi\|82406257, gi\|... - gi\|82495665\|ref\|ZP_00881239.1\| transcriptional regulator, LysR family [Shewanella sp. MR-4], gi\|8240...	280.0	[0..1]	[291..1]
gi\|87118407, gi\|... - gi\|87118407\|ref\|ZP_01074306.1\| putative transcription regulator protein [Marinomonas sp. MED121], gi...	279.0	[0..3]	[297..4]

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Predicted Domain #1

Region A:
Residues: [1-87]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MNIRDLEYLI ALADYKHFRR AADACNVSQP TLSGQIRKLE NELGTILLER TSRKVLFTQA  60
   61 GLTLVEQAKA VLREVKILKE MASNQGK

[Run NCBI BLAST on this sequence.]

Detection Method:	FFAS03
Confidence:	4.43
Match:	1ixcA
Description:	LysR-type regulatory protein CbnR
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
transcription regulator activity	3.67519658226073	bayes_pls_golite062009
DNA binding	3.1229077545522	bayes_pls_golite062009
nucleic acid binding	3.10431747895367	bayes_pls_golite062009
transcription factor activity	2.49694475728018	bayes_pls_golite062009
binding	2.03697617454396	bayes_pls_golite062009
transcription activator activity	0.293284204935948	bayes_pls_golite062009
sequence-specific DNA binding	0.266645609122554	bayes_pls_golite062009
transcription repressor activity	0.259857063944388	bayes_pls_golite062009
protein binding	0.00796693091603284	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [88-297]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 EMSGPLHVGI IPTLGPYLLP FALPALKSAF PELDLYIYEL QTSQLIDQLE AGQLDCGILA  60
   61 LVKESEPFIE IPIFNEEMLL AVPKQHEWAK QSSLTINALK DKELLFLDDG HCLRTQTLDY 120
  121 CLSVGAKEST HFKATNLETL RNMVATNAGM SLVPELAAKQ NANIHYLTFE NPQPYRAIGL 180
  181 IYRPGSPLRI RYERLAKEVA YIMTKEGKNE

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	36.0
Match:	1i6aA
Description:	Hydrogen peroxide-inducible genes LysR-type activator OxyR, regulatory domain
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
transcription regulator activity	2.06846313752146	bayes_pls_golite062009
transcription factor activity	1.54776226622667	bayes_pls_golite062009
DNA binding	1.53867658911479	bayes_pls_golite062009
nucleic acid binding	1.45471488657915	bayes_pls_golite062009
binding	1.29220115989941	bayes_pls_golite062009
catalytic activity	1.04475291968158	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: