YRC Public Data Repository - Protein Structure Prediction

Protein:	RPOS_ECOLI
Organism:	Escherichia coli
Length:	330 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 RPOS_ECOLI.

Description	E-value	Query Range	Subject Range
gi\|69249285, gi\|... - gi\|69249285\|ref\|ZP_00604924.1\| Sigma-70 region 1.1:Sigma-70 region 3:Sigma-70 region 2:Sigma-70 regi... gi\|48823945 - ref\|ZP_00285397.1\| COG0568: DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Enterococc...	269.0	[0..3]	[326..39]
gi\|10197699 - gi\|10197699\|gb\|AAG14981.1\|AF242209_6 alternative sigma factor [Escherichia coli]	269.0	[0..1]	[330..1]
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]	268.0	[0..1]	[326..37]
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]	266.0	[0..1]	[326..37]
gi\|46880950, gi\|... - gi\|46907682\|ref\|YP_014071.1\| RNA polymerase sigma factor RpoD [Listeria monocytogenes str. 4b F2365]... SIGA_LISMO - RNA polymerase sigma factor SigA OS=Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e... gi\|47095405, gi\|... - gi\|47095405\|ref\|ZP_00233015.1\| RNA polymerase sigma factor RpoD [Listeria monocytogenes str. 1/2a F6... gi\|47092744, gi\|... - gi\|47092744\|ref\|ZP_00230530.1\| RNA polymerase sigma factor RpoD [Listeria monocytogenes str. 4b H785... gi\|153183809, gi... - gi\|254898380\|ref\|ZP_05258304.1\| RNA polymerase sigma factor RpoD [Listeria monocytogenes J0161], gi\|... gi\|153196232, gi... - gi\|254829787\|ref\|ZP_05234442.1\| RNA polymerase sigma factor RpoD [Listeria monocytogenes 10403S], gi... gi\|254912128, gi... - gi\|254912128\|ref\|ZP_05262140.1\| RNA polymerase sigma factor RpoD [Listeria monocytogenes J2818], gi\|... gi\|254827742, gi... - gi\|254827742\|ref\|ZP_05232429.1\| RNA polymerase sigma factor RpoD [Listeria monocytogenes FSL N3-165]... gi\|133735573, gi... - gi\|254932639\|ref\|ZP_05265998.1\| RNA polymerase sigma factor RpoD [Listeria monocytogenes HPB2262], g... gi\|224501605 - gi\|224501605\|ref\|ZP_03669912.1\| RNA polymerase sigma factor RpoD [Listeria monocytogenes FSL R2-561] gi\|225876517, gi... - gi\|226224055\|ref\|YP_002758162.1\| RNA polymerase sigma factor RpoD [Listeria monocytogenes Clip81459]... gi\|254824487 - gi\|254824487\|ref\|ZP_05229488.1\| RNA polymerase sigma factor RpoD [Listeria monocytogenes FSL J1-194] gi\|224499695 - gi\|224499695\|ref\|ZP_03668044.1\| RNA polymerase sigma factor RpoD [Listeria monocytogenes Finland 198... gi\|254852080 - gi\|254852080\|ref\|ZP_05241428.1\| RNA polymerase sigma factor RpoD [Listeria monocytogenes FSL R2-503] gi\|254936456 - gi\|254936456\|ref\|ZP_05268153.1\| RNA polymerase sigma factor RpoD [Listeria monocytogenes F6900] RPOD_LISMO - RNA polymerase sigma factor rpoD OS=Listeria monocytogenes GN=rpoD PE=3 SV=1 gi\|254994146 - gi\|254994146\|ref\|ZP_05276336.1\| RNA polymerase sigma factor RpoD [Listeria monocytogenes FSL J2-064] gi\|255029176 - gi\|255029176\|ref\|ZP_05301127.1\| RNA polymerase sigma factor RpoD [Listeria monocytogenes LO28] gi\|255522085 - gi\|255522085\|ref\|ZP_05389322.1\| RNA polymerase sigma factor RpoD [Listeria monocytogenes FSL J1-175]	266.0	[0..1]	[326..42]
gi\|56963455, gi\|... - gi\|56963455\|ref\|YP_175186.1\| RNA polymerase sigma factor RpoD [Bacillus clausii KSM-K16], gi\|5690969...	266.0	[0..1]	[326..42]
gi\|213960104, gi... - gi\|213960104\|ref\|ZP_03388387.1\| RNA polymerase sigma factor RpoD [Propionibacterium acnes SK137], gi... gi\|50840117, gi\|... - gi\|50842515\|ref\|YP_055742.1\| RNA polymerase sigma factor [Propionibacterium acnes KPA171202], gi\|508...	266.0	[0..2]	[326..153]
gi\|217964400, gi... - gi\|217964400\|ref\|YP_002350078.1\| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43) [Listeria mon... gi\|116872885, gi... - gi\|116872885\|ref\|YP_849666.1\| RNA polymerase sigma factor RpoD [Listeria welshimeri serovar 6b str. ... RPOD_LISIN - RNA polymerase sigma factor rpoD OS=Listeria innocua GN=rpoD PE=3 SV=1 gi\|254873717 - gi\|254873717\|ref\|ZP_05246427.1\| RNA polymerase sigma factor RpoD [Listeria monocytogenes FSL N1-017] SIGA_LISIN - RNA polymerase sigma factor SigA OS=Listeria innocua serovar 6a (strain CLIP 11262) GN=sigA PE=3 SV=...	265.0	[0..1]	[326..42]
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...	265.0	[0..1]	[326..91]

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Predicted Domain #1

Region A:
Residues: [1-330]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSQNTLKVHD LNEDAEFDEN GVEVFDEKAL VEQEPSDNDL AEEELLSQGA TQRVLDATQL  60
   61 YLGEIGYSPL LTAEEEVYFA RRALRGDVAS RRRMIESNLR LVVKIARRYG NRGLALLDLI 120
  121 EEGNLGLIRA VEKFDPERGF RFSTYATWWI RQTIERAIMN QTRTIRLPIH IVKELNVYLR 180
  181 TARELSHKLD HEPSAEEIAE QLDKPVDDVS RMLRLNERIT SVDTPLGGDS EKALLDILAD 240
  241 EKENGPEDTT QDDDMKQSIV KWLFELNAKQ REVLARRFGL LGYEAATLED VGREIGLTRE 300
  301 RVRQIQVEGL RRLREILQTQ GLNIEALFRE

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	54.045757
Match:	1iw7F
Description:	Sigma70
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
transcription initiation factor activity	5.78609205758337	bayes_pls_golite062009
sigma factor activity	5.64833683794078	bayes_pls_golite062009
transcription regulator activity	3.74356768143558	bayes_pls_golite062009
binding	1.07192234179226	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: