YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|39995761, gi\|...
Organism:	Geobacter sulfurreducens PCA
Length:	284 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|39995761, gi|....

Description	E-value	Query Range	Subject Range
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...	240.0	[0..2]	[279..140]
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...	238.0	[0..2]	[279..87]
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]	238.0	[0..7]	[280..94]
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]	238.0	[0..7]	[280..94]
gi\|78044024, gi\|... - gi\|78044024\|ref\|YP_359316.1\| RNA polymerase sigma factor RpoD [Carboxydothermus hydrogenoformans Z-2...	238.0	[0..1]	[279..87]
gi\|89079310, gi\|... - gi\|89090874\|ref\|ZP_01163909.1\| Sigma-70 factor [Lactobacillus reuteri JCM 1112], gi\|89079310\|gb\|EAR5... gi\|227364887, gi... - gi\|227364887\|ref\|ZP_03848933.1\| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus reuter... gi\|227531077, gi... - gi\|227531077\|ref\|ZP_03961126.1\| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus reuter...	238.0	[0..7]	[279..106]
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\|...	237.0	[0..7]	[280..94]
gi\|90961886, gi\|... - gi\|90961886\|ref\|YP_535802.1\| RNA polymerase sigma factor RpoD [Lactobacillus salivarius UCC118], gi\|...	237.0	[0..7]	[279..98]
gi\|92089653, gi\|... - gi\|92089653\|ref\|ZP_01274588.1\| RNA polymerase sigma factor RpoD-like [Lactobacillus reuteri 100-23],...	237.0	[0..7]	[279..106]
gi\|77406972, gi\|... - gi\|77406972\|ref\|ZP_00783989.1\| RNA polymerase sigma-70 factor [Streptococcus agalactiae H36B], gi\|77...	237.0	[0..7]	[280..94]

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Predicted Domain #1

Region A:
Residues: [1-284]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSMSLPVVAD SLTVYLREIR KFPVLTPEEE YRFAVKFYED KDLEAAHSLI TSNLRFVVKI  60
   61 AAEYRSYGLK MLDLIQEGNV GLMMAVRKFN PYKGIRLISY AVWWIRAYIQ NHIISAWSLL 120
  121 KIGTTQAQKK LFFKLNQAKN AIKGLTGTDD IEATATSLHV KESEVLEMDQ RMRGDFYLDA 180
  181 EIKNGDGLTI LETLADERQN QEDTLAELQE SELLKQHIAG ALGKLNEKER FIVEQRVTAD 240
  241 TPLTLQEIAD RFSISRERVR QIEEAALRKI KSYLIPIIAE TRPV

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	45.0
Match:	1l9zH
Description:	DNA-directed RNA polymerase alpha(2), beta, beta-prime and omega subunits
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