YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|24349382, gi\|...
Organism:	Shewanella oneidensis MR-1
Length:	237 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|24349382, gi|....

Description	E-value	Query Range	Subject Range
gi\|88912059, gi\|... - gi\|88931788\|ref\|ZP_01137481.1\| Carbamoyl-phosphate synthase L chain, ATP-binding [Acidothermus cellu...	174.0	[0..2]	[234..230]
gi\|55737450, gi\|... - gi\|55821465\|ref\|YP_139907.1\| RNA polymerase sigma factor RpoD [Streptococcus thermophilus LMG 18311]... gi\|55737450 - gb\|AAV61092.1\| DNA directed RNA polymerase sigma 42 protein [Streptococcus thermophilus LMG 18311]	174.0	[0..1]	[234..120]
gi\|55739378, gi\|... - gi\|55823393\|ref\|YP_141834.1\| RNA polymerase sigma factor RpoD [Streptococcus thermophilus CNRZ1066],... gi\|116101464, gi... - gi\|62527015\|ref\|ZP_00388317.1\| COG0568: DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)... gi\|55739378 - gb\|AAV63019.1\| DNA directed RNA polymerase sigma 42 protein [Streptococcus thermophilus CNRZ1066]	173.0	[0..1]	[234..120]
gi\|116494985, gi... - gi\|116494985\|ref\|YP_806719.1\| RNA polymerase sigma factor RpoD [Lactobacillus casei ATCC 334], gi\|11... gi\|191638497, gi... - gi\|191638497\|ref\|YP_001987663.1\| RNA polymerase sigma factor RpoD [Lactobacillus casei BL23], gi\|190... gi\|224453634 - gi\|224453634\|ref\|ZP_03662107.1\| RNA polymerase sigma factor RpoD [Lactobacillus paracasei subsp. par... gi\|227187324, gi... - gi\|227535009\|ref\|ZP_03965058.1\| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus paraca...	172.0	[0..1]	[234..174]
gi\|109644065, gi... - gi\|109646116\|ref\|ZP_01370036.1\| RNA polymerase, sigma 38 subunit, RpoS [Desulfitobacterium hafniense...	172.0	[0..1]	[234..144]
gi\|119717187, gi... - gi\|71369155\|ref\|ZP_00659620.1\| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4:Sigma-70 region...	171.0	[0..2]	[234..248]
gi\|78044024, gi\|... - gi\|78044024\|ref\|YP_359316.1\| RNA polymerase sigma factor RpoD [Carboxydothermus hydrogenoformans Z-2...	171.0	[0..1]	[234..122]
gi\|76563399, gi\|... - gi\|76788342\|ref\|YP_330069.1\| RNA polymerase sigma factor RpoD [Streptococcus agalactiae A909], gi\|76... gi\|77159097, gi\|... - gi\|77414847\|ref\|ZP_00790961.1\| RNA polymerase sigma-70 factor [Streptococcus agalactiae 515], gi\|771... gi\|22537572, gi\|... - gi\|22537572\|ref\|NP_688423.1\| RNA polymerase sigma factor RpoD [Streptococcus agalactiae 2603V/R], gi... gi\|77161430, gi\|... - gi\|77412516\|ref\|ZP_00788814.1\| RNA polymerase sigma-70 factor [Streptococcus agalactiae CJB111], gi\|... gi\|77409561, gi\|... - gi\|77409561\|ref\|ZP_00786243.1\| RNA polymerase sigma-70 factor [Streptococcus agalactiae COH1], gi\|77... gi\|25011538, gi\|... - gi\|25011538\|ref\|NP_735933.1\| RNA polymerase sigma factor RpoD [Streptococcus agalactiae NEM316], gi\|...	171.0	[0..1]	[234..120]
gi\|125973412, gi... - gi\|67916227\|ref\|ZP_00509945.1\| Sigma-70 region 1.1:Sigma-70 region 3:Sigma-70 region 2:Sigma-70 regi...	171.0	[0..1]	[234..110]
gi\|89084822, gi\|... - gi\|89100479\|ref\|ZP_01173341.1\| RNA polymerase sigma factor [Bacillus sp. NRRL B-14911], gi\|89084822\|...	171.0	[0..1]	[234..126]

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Predicted Domain #1

Region A:
Residues: [1-237]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MNKAAAYTCL DNKTSIVEQY APLVKRIAHH LLARLPASVQ LDDLLQAGMM GLLEASSKFD  60
   61 GGKGAKFETF AGIRIRGAML DEIRRGDWVP RSVHRNNRRI AQAIDELEQV LGRDARDTEI 120
  121 AEKLDMTLDE YHHILNDVSV GKIIGIEDLG VSEDILTTSD NVSDGTFEVL AETQFHSALV 180
  181 EAIKILPERD ALVLSLYYDE ALNLKEIGAI LEVSESRVSQ ILSQAMLRLK GKLKQWT

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	28.0
Match:	1rp3A
Description:	Cocrystal structure of the flagellar sigma/anti-sigma complex, Sigma-28/FlgM
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
transcription initiation factor activity	5.71806750193815	bayes_pls_golite062009
sigma factor activity	5.58029806879061	bayes_pls_golite062009
transcription regulator activity	3.67872017549582	bayes_pls_golite062009
binding	0.503184853376433	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: