YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|24376056, gi\|...
Organism:	Shewanella oneidensis MR-1
Length:	285 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|24376056, gi|....

Description	E-value	Query Range	Subject Range
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]	230.0	[0..3]	[281..83]
gi\|78044024, gi\|... - gi\|78044024\|ref\|YP_359316.1\| RNA polymerase sigma factor RpoD [Carboxydothermus hydrogenoformans Z-2...	230.0	[0..14]	[281..96]
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]	229.0	[0..3]	[281..83]
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\|...	228.0	[0..13]	[281..93]
gi\|90961886, gi\|... - gi\|90961886\|ref\|YP_535802.1\| RNA polymerase sigma factor RpoD [Lactobacillus salivarius UCC118], gi\|...	228.0	[0..9]	[281..93]
gi\|77406972, gi\|... - gi\|77406972\|ref\|ZP_00783989.1\| RNA polymerase sigma-70 factor [Streptococcus agalactiae H36B], gi\|77...	228.0	[0..13]	[281..93]
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...	228.0	[0..9]	[281..101]
gi\|1943995 - gi\|1943995\|dbj\|BAA19494.1\| sigA=sigma70 [Staphylococcus aureus]	228.0	[0..3]	[281..83]
gi\|92089653, gi\|... - gi\|92089653\|ref\|ZP_01274588.1\| RNA polymerase sigma factor RpoD-like [Lactobacillus reuteri 100-23],...	228.0	[0..9]	[281..101]
gi\|223932503, gi... - gi\|81096984\|ref\|ZP_00875303.1\| Sigma-70 region 1.1:Sigma-70 region 3:Sigma-70 region 2:Sigma-70 regi... gi\|146321288, gi... - gi\|146321288\|ref\|YP_001200999.1\| RNA polymerase sigma factor RpoD [Streptococcus suis 98HAH33], gi\|1... gi\|145689888, gi... - gi\|146319082\|ref\|YP_001198794.1\| RNA polymerase sigma factor RpoD [Streptococcus suis 05ZYH33], gi\|1... gi\|251820209, gi... - gi\|253753963\|ref\|YP_003027104.1\| RNA polymerase sigma factor RpoD [Streptococcus suis P1/7], gi\|2518... gi\|251816427, gi... - gi\|253752138\|ref\|YP_003025279.1\| RNA polymerase sigma factor RpoD [Streptococcus suis SC84], gi\|2518... gi\|253755898, gi... - gi\|253755898\|ref\|YP_003029038.1\| RNA polymerase sigma factor RpoD [Streptococcus suis BM407], gi\|251...	227.0	[0..11]	[281..94]

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Predicted Domain #1

Region A:
Residues: [1-285]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MTFQTQSMAL TVPQGSSSLE AYIHSVTSMN MLDAETEYEL AKRLQETGDL QAAKQLIMSH  60
   61 LRFVVHVAKG YAGYGLPQAD LIQEGNIGLM KAVKRFDPDV GVRLVSFAVH WIKAEIHEYV 120
  121 LKNWRIVKVA TTKAQRKLFF NIRKAKTRLG WFSDDEVTMV AENLGVSKAD VTEMESRMAA 180
  181 QDPAFDLSSD NDDEHDFAPV HYLEDHSSDL AENIENDNWE SNAQGRLLSA IKTLDERSQH 240
  241 ILRARWLDDD KTTLQELAET YQVSAERIRQ LEKNAMNKLK ACMEA

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	45.69897
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