YRC Public Data Repository - Protein Structure Prediction

Protein:	FLIA_ECOLI
Organism:	Escherichia coli
Length:	239 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 FLIA_ECOLI.

Description	E-value	Query Range	Subject Range
gi\|104774139, gi... - gi\|104774139\|ref\|YP_619119.1\| RNA polymerase sigma factor RpoD [Lactobacillus delbrueckii subsp. bul...	191.0	[0..1]	[234..124]
gi\|116514229, gi... - gi\|116514229\|ref\|YP_813135.1\| RNA polymerase sigma factor RpoD [Lactobacillus delbrueckii subsp. bul...	191.0	[0..1]	[234..124]
gi\|42519241, gi\|... - gi\|42519241\|ref\|NP_965171.1\| RNA polymerase sigma factor RpoD [Lactobacillus johnsonii NCC 533], gi\|...	190.0	[0..1]	[234..124]
gi\|238853400, gi... - gi\|238853400\|ref\|ZP_04643779.1\| RNA polymerase sigma factor RpoD [Lactobacillus gasseri 202-4], gi\|2... gi\|23003602 - gi\|23003602\|ref\|ZP_00047259.1\| COG0568: DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)... gi\|116095333, gi... - gi\|23003602\|ref\|ZP_00047259.1\| hypothetical protein Lgas_03001424 [Lactobacillus gasseri ATCC 33323]... gi\|226819224 - gi\|226819224\|ref\|ZP_03808343.1\| RNA polymerase sigma factor RpoD [Lactobacillus gasseri MV-22] gi\|227521065, gi... - gi\|227521065\|ref\|ZP_03951114.1\| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus gasser...	190.0	[0..1]	[234..125]
gi\|1943995 - gi\|1943995\|dbj\|BAA19494.1\| sigA=sigma70 [Staphylococcus aureus]	190.0	[0..1]	[234..120]
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]	190.0	[0..1]	[234..120]
gi\|89159495, gi\|... - gi\|89210855\|ref\|ZP_01189238.1\| Sigma-70 region 1.2 [Halothermothrix orenii H 168], gi\|89159495\|gb\|EA...	189.0	[0..1]	[234..110]
gi\|58254795, gi\|... - gi\|58337478\|ref\|YP_194063.1\| RNA polymerase sigma factor RpoD [Lactobacillus acidophilus NCFM], gi\|5...	189.0	[0..1]	[234..108]
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...	189.0	[0..1]	[234..174]
gi\|88912059, gi\|... - gi\|88931788\|ref\|ZP_01137481.1\| Carbamoyl-phosphate synthase L chain, ATP-binding [Acidothermus cellu...	189.0	[0..2]	[234..230]

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Predicted Domain #1

Region A:
Residues: [1-239]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MNSLYTAEGV MDKHSLWQRY VPLVRHEALR LQVRLPASVE LDDLLQAGGI GLLNAVERYD  60
   61 ALQGTAFTTY AVQRIRGAML DELRSRDWVP RSVRRNAREV AQAIGQLEQE LGRNATETEV 120
  121 AERLGIDIAD YRQMLLDTNN SQLFSYDEWR EEHGDSIELV TDDHQRENPL QQLLDSNLRQ 180
  181 RVMEAIETLP EREKLVLTLY YQEELNLKEI GAVLEVGESR VSQLHSQAIK RLRTKLGKL

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	30.522879
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: