YRC Public Data Repository - Protein Structure Prediction

Protein:	RPOD_ECOLI
Organism:	Escherichia coli
Length:	613 amino acids
Reference:	Drew K, et al. (2011) The proteome folding project: Proteome-scale prediction of structure and function. Genome Res. 2011 Sep 16

[What does the above image mean?]

[Show Ginzu Version Information]

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 RPOD_ECOLI.

Description	E-value	Query Range	Subject Range
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...	550.0	[0..1]	[613..46]
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...	549.0	[0..1]	[613..46]
gi\|238719206, gi... - gi\|77962309\|ref\|ZP_00826131.1\| COG0568: DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)...	548.0	[0..1]	[613..23]
gi\|77959510 - gi\|77959510\|ref\|ZP_00823529.1\| COG0568: DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)...	548.0	[0..1]	[613..23]
gi\|62181728, gi\|... - gi\|62181728\|ref\|YP_218145.1\| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica s...	547.0	[0..1]	[613..46]
gi\|45437587, gi\|... - gi\|45442721\|ref\|NP_994260.1\| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Microtus str. ...	545.0	[0..1]	[613..20]
gi\|77974118 - gi\|77974118\|ref\|ZP_00829660.1\| COG0568: DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)...	545.0	[0..1]	[613..23]
gi\|21960500, gi\|... - gi\|22127411\|ref\|NP_670834.1\| RNA polymerase sigma factor RpoD [Yersinia pestis KIM], gi\|21960500\|gb\|...	544.0	[0..1]	[613..21]
gi\|77977904 - gi\|77977904\|ref\|ZP_00833342.1\| COG0568: DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)...	544.0	[0..1]	[613..23]
RPOD_SALTY - RNA polymerase sigma factor rpoD OS=Salmonella typhimurium GN=rpoD PE=3 SV=1 RPOD_SALTI - RNA polymerase sigma factor rpoD OS=Salmonella typhi GN=rpoD PE=3 SV=1 RPOD_SALTY - RNA polymerase sigma factor RpoD OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) GN=... gi\|168262827, gi... - gi\|205348629\|gb\|EDZ35260.1\| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica se... gi\|168243042, gi... - gi\|205337819\|gb\|EDZ24583.1\| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica se... gi\|197289083, gi... - gi\|197289083\|gb\|EDY28452.1\| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica se... gi\|205331247, gi... - gi\|205331247\|gb\|EDZ18011.1\| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica se... gi\|238910014 - gi\|238910014\|ref\|ZP_04653851.1\| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enteric... gi\|194472915, gi... - gi\|194472915\|ref\|ZP_03078899.1\| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enteric... gi\|194451693, gi... - gi\|194451693\|ref\|YP_002047209.1\| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enteri... gi\|194445988, gi... - gi\|194445988\|ref\|YP_002042478.1\| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enteri... gi\|168463576, gi... - gi\|195633147\|gb\|EDX51561.1\| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica se... gi\|167551873, gi... - gi\|205323318\|gb\|EDZ11157.1\| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica se... gi\|161616204, gi... - gi\|161616204\|ref\|YP_001590169.1\| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enteri... gi\|213865054 - gi\|213865054\|ref\|ZP_03387173.1\| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enteric... gi\|213646106 - gi\|213646106\|ref\|ZP_03376159.1\| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enteric... gi\|213586893 - gi\|213586893\|ref\|ZP_03368719.1\| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enteric... RPOD_SALTI - RNA polymerase sigma factor RpoD OS=Salmonella typhi GN=rpoD PE=3 SV=1 gi\|198242489, gi... - gi\|198242489\|ref\|YP_002217192.1\| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enteri... RPOD_SALTY - RNA polymerase sigma factor rpoD OS=Salmonella typhimurium GN=rpoD PE=3 SV=1 gi\|197264102, gi... - gi\|197264102\|ref\|ZP_03164176.1\| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enteric... gi\|197215575, gi... - gi\|197251872\|ref\|YP_002148141.1\| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enteri... gi\|194736124, gi... - gi\|194736124\|ref\|YP_002116168.1\| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enteri... gi\|213425630 - gi\|213425630\|ref\|ZP_03358380.1\| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enteric... gi\|207858469, gi... - gi\|207858469\|ref\|YP_002245120.1\| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enteri... gi\|204322416, gi... - gi\|204928094\|ref\|ZP_03219294.1\| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enteric... gi\|200389116, gi... - gi\|200389116\|ref\|ZP_03215728.1\| RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enteric...	543.0	[0..1]	[613..1]

Back

Predicted Domain #1

Region A:
Residues: [1-109]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MEQNPQSQLK LLVTRGKEQG YLTYAEVNDH LPEDIVDSDQ IEDIIQMIND MGIQVMEEAP  60
   61 DADDLMLAEN TADEDAAEAA AQVLSSVESE IGRTTDPVRM YMREMGTVE

[Run NCBI BLAST on this sequence.]

Detection Method:	FFAS03
Confidence:	2.9
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: [110-240]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 LLTREGEIDI AKRIEDGINQ VQCSVAEYPE AITYLLEQYD RVEAEEARLS DLITGFVDPN  60
   61 AEEDLAPTAT HVGSELSQED LDDDEDEDEE DGDDDSADDD NSIDPELARE KFAELRAQYV 120
  121 VTRDTIKAKG R

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	67.69897
Match:	1sigA
Description:	CRYSTAL STRUCTURE OF A SIGMA70 SUBUNIT FRAGMENT FROM ESCHERICHIA COLI RNA POLYMERASE
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	1.02634976114785	bayes_pls_golite062009

Predicted Domain #3

Region A:
Residues: [241-613]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SHATAQEEIL KLSEVFKQFR LVPKQFDYLV NSMRVMMDRV RTQERLIMKL CVEQCKMPKK  60
   61 NFITLFTGNE TSDTWFNAAI AMNKPWSEKL HDVSEEVHRA LQKLQQIEEE TGLTIEQVKD 120
  121 INRRMSIGEA KARRAKKEMV EANLRLVISI AKKYTNRGLQ FLDLIQEGNI GLMKAVDKFE 180
  181 YRRGYKFSTY ATWWIRQAIT RSIADQARTI RIPVHMIETI NKLNRISRQM LQEMGREPTP 240
  241 EELAERMLMP EDKIRKVLKI AKEPISMETP IGDDEDSHLG DFIEDTTLEL PLDSATTESL 300
  301 RAATHDVLAG LTAREAKVLR MRFGIDMNTD YTLEEVGKQF DVTRERIRQI EAKALRKLRH 360
  361 PSRSEVLRSF LDD

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	67.09691
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:

Predicted functions: