YRC Public Data Repository - Protein Structure Prediction

Protein:	RPOC_ECOLC
Organism:	Escherichia coli ATCC 8739
Length:	1407 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 RPOC_ECOLC.

Description	E-value	Query Range	Subject Range
gi\|22774033 - gi\|22774033\|gb\|AAN07183.1\| RNA polymerase beta prime subunit/intein-CBD fusion protein [Cloning vect...	1696.0	[0..1]	[1407..1]
RPOC_ECOUT - DNA-directed RNA polymerase subunit beta' OS=Escherichia coli (strain UTI89 / UPEC) GN=rpoC PE=3 SV=... gi\|226903069, gi... - gi\|237702756\|ref\|ZP_04533237.1\| RNA polymerase [Escherichia sp. 3_2_53FAA], gi\|226903069\|gb\|EEH89328... gi\|218561054, gi... - gi\|218561054\|ref\|YP_002393967.1\| DNA-directed RNA polymerase subunit beta' [Escherichia coli S88], g... gi\|218429833, gi... - gi\|218692269\|ref\|YP_002400481.1\| DNA-directed RNA polymerase subunit beta' [Escherichia coli ED1a], ... RPOC_ECOK1 - DNA-directed RNA polymerase subunit beta' OS=Escherichia coli O1:K1 / APEC GN=rpoC PE=3 SV=1	1688.0	[0..1]	[1407..1]
RPOC_SHIF8 - DNA-directed RNA polymerase subunit beta' OS=Shigella flexneri serotype 5b (strain 8401) GN=rpoC PE=...	1688.0	[0..1]	[1407..1]
RPOC_SHIB3 - DNA-directed RNA polymerase subunit beta' OS=Shigella boydii serotype 18 (strain CDC 3083-94 / BS512...	1688.0	[0..1]	[1407..1]
RPOC_ECOL6 - DNA-directed RNA polymerase subunit beta' OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / U... RPOC_ECOL6 - DNA-directed RNA polymerase subunit beta' OS=Escherichia coli O6 GN=rpoC PE=3 SV=1	1688.0	[0..1]	[1407..1]
gi\|223476 - gi\|223476\|prf\|\|0808241A polymerase beta',RNA	1687.0	[0..1]	[1407..1]
RPOC_SHIDS - DNA-directed RNA polymerase subunit beta' OS=Shigella dysenteriae serotype 1 (strain Sd197) GN=rpoC ...	1687.0	[0..1]	[1407..1]
RPOC_ECOL5 - DNA-directed RNA polymerase subunit beta' OS=Escherichia coli O6:K15:H31 (strain 536 / UPEC) GN=rpoC...	1684.0	[0..1]	[1407..1]
gi\|238913733 - gi\|238913733\|ref\|ZP_04657570.1\| DNA-directed RNA polymerase subunit beta' [Salmonella enterica subsp... gi\|194404810, gi... - gi\|194446147\|ref\|YP_002043406.1\| DNA-directed RNA polymerase, beta' subunit [Salmonella enterica sub... gi\|195629010, gi... - gi\|195629010\|gb\|EDX48402.1\| DNA-directed RNA polymerase, beta' subunit [Salmonella enterica subsp. e... gi\|168264591, gi... - gi\|205346976\|gb\|EDZ33607.1\| DNA-directed RNA polymerase, beta' subunit [Salmonella enterica subsp. e... RPOC_SALCH - DNA-directed RNA polymerase subunit beta' OS=Salmonella choleraesuis GN=rpoC PE=3 SV=1 RPOC_SALTY - DNA-directed RNA polymerase subunit beta' OS=Salmonella typhimurium GN=rpoC PE=3 SV=1 lcl\|NC_016856.1_... - [gene=rpoC] [protein=DNA-directed RNA polymerase subunit beta'] [protein_id=YP_005240433.1] [locatio... gi\|224585696, gi... - gi\|224585696\|ref\|YP_002639495.1\| DNA-directed RNA polymerase beta' subunit [Salmonella enterica subs... gi\|213650889 - gi\|213650889\|ref\|ZP_03380942.1\| DNA-directed RNA polymerase subunit beta' [Salmonella enterica subsp... gi\|213582657 - gi\|213582657\|ref\|ZP_03364483.1\| DNA-directed RNA polymerase subunit beta' [Salmonella enterica subsp... RPOC_SALCH - DNA-directed RNA polymerase subunit beta' OS=Salmonella choleraesuis (strain SC-B67) GN=rpoC PE=3 SV... gi\|197264212, gi... - gi\|197264212\|ref\|ZP_03164286.1\| DNA-directed RNA polymerase, beta' subunit [Salmonella enterica subs... gi\|197215260, gi... - gi\|197251557\|ref\|YP_002149065.1\| DNA-directed RNA polymerase, beta' subunit [Salmonella enterica sub... RPOC_SALTY - DNA-directed RNA polymerase subunit beta' OS=Salmonella typhimurium GN=rpoC PE=3 SV=1 gi\|194469670, gi... - gi\|194469670\|ref\|ZP_03075654.1\| DNA-directed RNA polymerase, beta' subunit [Salmonella enterica subs... gi\|194450168, gi... - gi\|194450168\|ref\|YP_002048141.1\| DNA-directed RNA polymerase subunit beta' [Salmonella enterica subs... gi\|213425738 - gi\|213425738\|ref\|ZP_03358488.1\| DNA-directed RNA polymerase subunit beta' [Salmonella enterica subsp... gi\|207859332, gi... - gi\|207859332\|ref\|YP_002245983.1\| DNA-directed RNA polymerase subunit beta' [Salmonella enterica subs... gi\|204319887, gi... - gi\|204931272\|ref\|ZP_03222032.1\| DNA-directed RNA polymerase, beta' subunit [Salmonella enterica subs... gi\|199603876, gi... - gi\|200386778\|ref\|ZP_03213390.1\| DNA-directed RNA polymerase, beta' subunit [Salmonella enterica subs... RPOC_SALTY - DNA-directed RNA polymerase subunit beta' OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 70... gi\|29139422, gi\|... - gi\|29143787\|ref\|NP_807129.1\| DNA-directed RNA polymerase subunit beta' [Salmonella enterica subsp. e... RPOC_SALTI - DNA-directed RNA polymerase subunit beta' OS=Salmonella typhi GN=rpoC PE=3 SV=1 RPOC_SALTI - DNA-directed RNA polymerase subunit beta' OS=Salmonella typhi GN=rpoC PE=3 SV=1 gi\|16762299 - gi\|16762299\|ref\|NP_457916.1\| DNA-directed RNA polymerase subunit beta' [Salmonella enterica subsp. e... RPOC_SALCH - DNA-directed RNA polymerase subunit beta' OS=Salmonella choleraesuis GN=rpoC PE=3 SV=1	1680.0	[0..1]	[1407..1]

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Predicted Domain #1

Region A:
Residues: [1-1215]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MKDLLKFLKA QTKTEEFDAI KIALASPDMI RSWSFGEVKK PETINYRTFK PERDGLFCAR  60
   61 IFGPVKDYEC LCGKYKRLKH RGVICEKCGV EVTQTKVRRE RMGHIELASP TAHIWFLKSL 120
  121 PSRIGLLLDM PLRDIERVLY FESYVVIEGG MTNLERQQIL TEEQYLDALE EFGDEFDAKM 180
  181 GAEAIQALLK SMDLEQECEQ LREELNETNS ETKRKKLTKR IKLLEAFVQS GNKPEWMILT 240
  241 VLPVLPPDLR PLVPLDGGRF ATSDLNDLYR RVINRNNRLK RLLDLAAPDI IVRNEKRMLQ 300
  301 EAVDALLDNG RRGRAITGSN KRPLKSLADM IKGKQGRFRQ NLLGKRVDYS GRSVITVGPY 360
  361 LRLHQCGLPK KMALELFKPF IYGKLELRGL ATTIKAAKKM VEREEAVVWD ILDEVIREHP 420
  421 VLLNRAPTLH RLGIQAFEPV LIEGKAIQLH PLVCAAYNAD FDGDQMAVHV PLTLEAQLEA 480
  481 RALMMSTNNI LSPANGEPII VPSQDVVLGL YYMTRDCVNA KGEGMVLTGP KEAERLYRSG 540
  541 LASLHARVKV RITEYEKDAN GELVAKTSLK DTTVGRAILW MIVPKGLPYS IVNQALGKKA 600
  601 ISKMLNTCYR ILGLKPTVIF ADQIMYTGFA YAARSGASVG IDDMVIPEKK HEIISEAEAE 660
  661 VAEIQEQFQS GLVTAGERYN KVIDIWAAAN DRVSKAMMDN LQTETVINRD GQEEKQVSFN 720
  721 SIYMMADSGA RGSAAQIRQL AGMRGLMAKP DGSIIETPIT ANFREGLNVL QYFISTHGAR 780
  781 KGLADTALKT ANSGYLTRRL VDVAQDLVVT EDDCGTHEGI MMTPVIEGGD VKEPLRDRVL 840
  841 GRVTAEDVLK PGTADILVPR NTLLHEQWCD LLEENSVDAV KVRSVVSCDT DFGVCAHCYG 900
  901 RDLARGHIIN KGEAIGVIAA QSIGEPGTQL TMRTFHIGGA ASRAAAESSI QVKNKGSIKL 960
  961 SNVKSVVNSS GKLVITSRNT ELKLIDEFGR TKESYKVPYG AVLAKGDGEQ VAGGETVANW1020
 1021 DPHTMPVITE VSGFVRFTDM IDGQTITRQT DELTGLSSLV VLDSAERTAG GKDLRPALKI1080
 1081 VDAQGNDVLI PGTDMPAQYF LPGKAIVQLE DGVQISSGDT LARIPQESGG TKDITGGLPR1140
 1141 VADLFEARRP KEPAILAEIS GIVSFGKETK GKRRLVITPV DGSDPYEEMI PKWRQLNVFE1200
 1201 GERVERGDVI SDGPE

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	1000.0
Match:	2ghoD
Description:	No description for 2ghoD was found.

Predicted functions:

Term	Confidence	Notes
DNA-directed RNA polymerase activity	10.2021663255698	bayes_pls_golite062009
RNA polymerase activity	10.2021663255698	bayes_pls_golite062009
nucleotidyltransferase activity	7.6240729546188	bayes_pls_golite062009
transferase activity, transferring phosphorus-containing groups	5.44374972993429	bayes_pls_golite062009
transferase activity	4.83218811360621	bayes_pls_golite062009
binding	1.61743849829314	bayes_pls_golite062009
catalytic activity	1.36406839864424	bayes_pls_golite062009
transcription regulator activity	1.30860843987842	bayes_pls_golite062009
DNA binding	1.06504127306982	bayes_pls_golite062009
nucleic acid binding	1.04375863237637	bayes_pls_golite062009
protein binding	0.251709363216351	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [1216-1407]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 APHDILRLRG VHAVTRYIVN EVQDVYRLQG VKINDKHIEV IVRQMLRKAT IVNAGSSDFL  60
   61 EGEQVEYSRV KIANRELEAN GKVGATYSRD LLGITKASLA TESFISAASF QETTRVLTEA 120
  121 AVAGKRDELR GLKENVIVGR LIPAGTGYAY HQDRMRRRAA GEAPAAPQVT AEDASASLAE 180
  181 LLNAGLGGSD NE

[Run NCBI BLAST on this sequence.]

Detection Method:

MSA

Shown below is our most confident prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

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: