YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|24372864, gi\|...
Organism:	Shewanella oneidensis MR-1
Length:	616 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|24372864, gi|....

Description	E-value	Query Range	Subject Range
gi\|45437587, gi\|... - gi\|45442721\|ref\|NP_994260.1\| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Microtus str. ...	517.0	[0..1]	[616..20]
gi\|238719206, gi... - gi\|77962309\|ref\|ZP_00826131.1\| COG0568: DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)...	516.0	[0..1]	[616..23]
gi\|71795952, gi\|... - gi\|71891846\|ref\|YP_277575.1\| RNA polymerase sigma-70 factor [Candidatus Blochmannia pennsylvanicus s...	516.0	[0..1]	[616..1]
gi\|77959510 - gi\|77959510\|ref\|ZP_00823529.1\| COG0568: DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)...	516.0	[0..1]	[616..23]
gi\|25288442, gi\|... - gi\|25288442\|pir\|\|AB0893 RNA polymerase sigma-70 factor [imported] - Salmonella enterica subsp. enter... gi\|29143472, gi\|... - gi\|29143472\|ref\|NP_806814.1\| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica s... gi\|16761985 - gi\|16761985\|ref\|NP_457602.1\| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica s...	516.0	[0..1]	[616..46]
gi\|62181728, gi\|... - gi\|62181728\|ref\|YP_218145.1\| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica s...	515.0	[0..1]	[616..46]
gi\|33519536, gi\|... - gi\|33519536\|ref\|NP_878368.1\| RNA polymerase sigma-70 factor [Candidatus Blochmannia floridanus], gi\|...	515.0	[0..1]	[616..1]
gi\|21960500, gi\|... - gi\|22127411\|ref\|NP_670834.1\| RNA polymerase sigma factor RpoD [Yersinia pestis KIM], gi\|21960500\|gb\|...	515.0	[0..1]	[616..21]
gi\|205333914, gi... - gi\|205358509\|ref\|ZP_02656872.2\| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enteric... gi\|205343355, gi... - gi\|205359720\|ref\|ZP_02831723.2\| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enteric... lcl\|NC_016856.1_... - [gene=rpoD] [protein=RNA polymerase sigma factor RpoD] [protein_id=YP_005239387.1] [location=3394519... gi\|16421768 - gi\|16421768\|gb\|AAL22085.1\| sigma D factor of RNA polymerase [Salmonella enterica subsp. enterica ser... gi\|197095558, gi... - gi\|197364081\|ref\|YP_002143718.1\| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enteri... gi\|56415151, gi\|... - gi\|56415151\|ref\|YP_152226.1\| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica s...	515.0	[0..1]	[616..46]
gi\|77974118 - gi\|77974118\|ref\|ZP_00829660.1\| COG0568: DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)...	514.0	[0..1]	[616..23]

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Predicted Domain #1

Region A:
Residues: [1-108]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MDHTPQSQLK LLLAKGKEQG YLTYAEVNDH LPADMVDSDQ IEDIIQMIND MGIRVFEEAP  60
   61 DADDMMMSED NTDEDAAEEA AAALATVESE LGRTTDPVRM YMREMGTV

[Run NCBI BLAST on this sequence.]

Detection Method:	FFAS03
Confidence:	2.89
Match:	1l9zH
Description:	DNA-directed RNA polymerase alpha(2), beta, beta-prime and omega subunits
Matching Structure (courtesy of the PDB):

Predicted Domain #2

Region A:
Residues: [109-278]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 ELLTREGEIV IAKRIEEGIN TVQSSVAEYP QAIAMILEQY DQYEADELRL SDIISGFVNP  60
   61 DEEDLGPTAT HIGSELSEED LEDEDDEEDD EDEDGDGDGD DDGNKGPDPE EARERFSQLR 120
  121 TAYESALKII DAKGREHPES IQALFEIGEI FKEFRLVPKQ FDRLVKSMRS

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	59.09691
Match:	1sigA
Description:	CRYSTAL STRUCTURE OF A SIGMA70 SUBUNIT FRAGMENT FROM ESCHERICHIA COLI RNA POLYMERASE
Matching Structure (courtesy of the PDB):

Predicted Domain #3

Region A:
Residues: [279-616]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MMDRVRVQER LLMKLCVEQA KMPKKNFVKF FTGNETNLDW FEAEKTSNKP YAEGLRMVEE  60
   61 DVQRCRSKLA AIEEETGLVI AAIKDINRRM SIGEAKARRA KKEMVEANLR LVISIAKKYT 120
  121 NRGLQFLDLI QEGNIGLMKA VDKFEYRRGY KFSTYATWWI RQAITRSIAD QARTIRIPVH 180
  181 MIETINKLNR ISRQMLQEMG REPSPEELAE RMMMPEDKIR KVLKIAKEPI SMETPIGDDE 240
  241 DSHLGDFIED TTLELPLDSA TSESLKSATH EVLAGLTARE AKVLRMRFGI DMNTDHTLEE 300
  301 VGKQFDVTRE RIRQIEAKAL RKLRHPSRSE ILKSFLDE

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	62.0
Match:	1iw7F
Description:	Sigma70
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