YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|24375598, gi\|...
Organism:	Shewanella oneidensis MR-1
Length:	310 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|24375598, gi|....

Description	E-value	Query Range	Subject Range
gi\|114337265, gi... - gi\|71541872\|ref\|ZP_00663575.1\| Helix-turn-helix, Fis-type [Syntrophomonas wolfei str. Goettingen], g...	198.0	[0..2]	[303..333]
gi\|83590549, gi\|... - gi\|83590549\|ref\|YP_430558.1\| sigma-54 dependent trancsriptional regulator [Moorella thermoacetica AT...	194.0	[0..3]	[303..410]
gi\|20808135 - gi\|20808135\|ref\|NP_623306.1\| NtrC family Transcriptional regulator, ATPase domain [Thermoanaerobacte... gi\|20808135, gi\|... - gi\|20808135\|ref\|NP_623306.1\| transcriptional regulator [Thermoanaerobacter tengcongensis MB4], gi\|20...	193.0	[0..5]	[304..286]
gi\|77995063, gi\|... - gi\|78042948\|ref\|YP_360167.1\| putative sigma-54-dependent transcriptional regulator [Carboxydothermus...	191.0	[0..22]	[304..208]
gi\|39577000, gi\|... - gi\|42524790\|ref\|NP_970170.1\| response regulator of hydrogenase 3 activity (sensor HydH) [Bdellovibri...	191.0	[0..3]	[260..127]
gi\|91202504 - gi\|91202504\|emb\|CAJ72143.1\| strongly similar to sigma 54 response regulatory protein [Candidatus Kue...	188.0	[0..7]	[306..129]
gi\|158139343, gi... - gi\|158319144\|ref\|YP_001511651.1\| PAS modulated sigma54 specific transcriptional regulator [Alkaliphi...	188.0	[0..3]	[304..151]
gi\|89210675, gi\|... - gi\|89210675\|ref\|ZP_01189062.1\| PAS:Helix-turn-helix, Fis-type [Halothermothrix orenii H 168], gi\|891...	188.0	[0..3]	[306..246]
gi\|89894465, gi\|... - gi\|89894465\|ref\|YP_517952.1\| hypothetical protein DSY1719 [Desulfitobacterium hafniense Y51], gi\|893...	188.0	[0..2]	[303..379]

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Predicted Domain #1

Region A:
Residues: [1-310]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MYLKHFGLGQ APFSLTPNTG FFFGLSPHVE ALQVLQTALQ TGEGFIKVTG EVGTGKTLIC  60
   61 RKLINELPQG FHCAYLPNPY LTPAELRWAV ANELGLKYTS EIDQQQLTGL IQQQLLALST 120
  121 HGHAIVLVLD EAQALPDESL EALRLFTNLE TESRKLLQVV LFGQPELDER LKRQAFRQLR 180
  181 QRITFSYNLR PLTWDETDAY IRYRLAVAGH AGQALFSPKI TRKIAQASRG IPRLINILAH 240
  241 KALMLSFGEG ATQVRMSHLK GAICDTEDAS PTRVQKWSTY FAIAFMVFAV AMLALLLSGT 300
  301 NFLQWWGDGA

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	42.0
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