YRC Public Data Repository - Protein Structure Prediction

Protein:	RPOC_YERPE
Organism:	Yersinia pestis
Length:	1406 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_YERPE.

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...	0.0	[1..1404]	[1..1404]
RPOC_SHIB3 - DNA-directed RNA polymerase subunit beta' OS=Shigella boydii serotype 18 (strain CDC 3083-94 / BS512...	0.0	[1..1404]	[1..1404]
gi\|168752049, gi... - gi\|188014026\|gb\|EDU52148.1\| DNA-directed RNA polymerase, beta' subunit [Escherichia coli O157:H7 str... gi\|168771458, gi... - gi\|189359756\|gb\|EDU78175.1\| DNA-directed RNA polymerase, beta' subunit [Escherichia coli O157:H7 str... gi\|168764566, gi... - gi\|189365452\|gb\|EDU83868.1\| DNA-directed RNA polymerase, beta' subunit [Escherichia coli O157:H7 str... gi\|168780371, gi... - gi\|189001663\|gb\|EDU70649.1\| DNA-directed RNA polymerase, beta' subunit [Escherichia coli O157:H7 str... gi\|187767353, gi... - gi\|187767353\|gb\|EDU31197.1\| DNA-directed RNA polymerase, beta' subunit [Escherichia coli O157:H7 str... gi\|168798380, gi... - gi\|189379118\|gb\|EDU97534.1\| DNA-directed RNA polymerase, beta' subunit [Escherichia coli O157:H7 str... EG10895 - RNA polymerase, beta prime subunit / RNA polymerase, beta' subunit; binds Zn(II) gi\|189370156, gi... - gi\|189370156\|gb\|EDU88572.1\| DNA-directed RNA polymerase, beta' subunit [Escherichia coli O157:H7 str... RPOC_SHIBS - DNA-directed RNA polymerase subunit beta' OS=Shigella boydii serotype 4 (strain Sb227) GN=rpoC PE=3 ... gi\|89110051, gi\|... - gi\|89110051\|ref\|AP_003831.1\| RNA polymerase, beta prime subunit [Escherichia coli str. K-12 substr. ... gi\|191168663, gi... - gi\|75228141\|ref\|ZP_00714810.1\| COG0086: DNA-directed RNA polymerase, beta' subunit/160 kD subunit [E... RPOC_ECOLC - DNA-directed RNA polymerase subunit beta' OS=Escherichia coli (strain ATCC 8739 / DSM 1576 / Crooks)... gi\|218434703, gi... - gi\|218707606\|ref\|YP_002415125.1\| DNA-directed RNA polymerase subunit beta' [Escherichia coli UMN026]... RPOC_SHIFL - DNA-directed RNA polymerase subunit beta' OS=Shigella flexneri GN=rpoC PE=3 SV=1 gi\|191174289, gi... - gi\|75236718\|ref\|ZP_00720791.1\| COG0086: DNA-directed RNA polymerase, beta' subunit/160 kD subunit [E... RPOC_ECODH - DNA-directed RNA polymerase subunit beta' OS=Escherichia coli (strain K12 / DH10B) GN=rpoC PE=3 SV=1 gi\|218697695, gi... - gi\|218697695\|ref\|YP_002405362.1\| DNA-directed RNA polymerase subunit beta' [Escherichia coli 55989],... gi\|24054566, gi\|... - gi\|24115273\|ref\|NP_709783.1\| DNA-directed RNA polymerase subunit beta' [Shigella flexneri 2a str. 30... RPOC_ECOHS - DNA-directed RNA polymerase subunit beta' OS=Escherichia coli O9:H4 (strain HS) GN=rpoC PE=3 SV=1 gi\|30064729, gi\|... - gi\|30064729\|ref\|NP_838900.1\| DNA-directed RNA polymerase subunit beta' [Shigella flexneri 2a str. 24... gi\|75208786, gi\|... - gi\|75208786\|ref\|ZP_00709072.1\| COG0086: DNA-directed RNA polymerase, beta' subunit/160 kD subunit [E... RPOC_ECO57 - DNA-directed RNA polymerase subunit beta' OS=Escherichia coli O157:H7 GN=rpoC PE=3 SV=1 gi\|188493980, gi... - gi\|75514755\|ref\|ZP_00736984.1\| COG0086: DNA-directed RNA polymerase, beta' subunit/160 kD subunit [E... EG10895 - RNA polymerase, beta prime subunit / RNA polymerase, beta' subunit; binds Zn(II) RPOC_SHISS - DNA-directed RNA polymerase subunit beta' OS=Shigella sonnei (strain Ss046) GN=rpoC PE=3 SV=1 gi\|15804578, gi\|... - gi\|15804578\|ref\|NP_290619.1\| DNA-directed RNA polymerase subunit beta' [Escherichia coli O157:H7 EDL... gi\|75238529, gi\|... - gi\|75238529\|ref\|ZP_00722518.1\| COG0086: DNA-directed RNA polymerase, beta' subunit/160 kD subunit [E... gi\|192925941, gi... - gi\|75255485\|ref\|ZP_00727284.1\| COG0086: DNA-directed RNA polymerase, beta' subunit/160 kD subunit [E... gi\|208805878, gi... - gi\|208805878\|ref\|ZP_03248215.1\| DNA-directed RNA polymerase, beta' subunit [Escherichia coli O157:H7... gi\|195939613 - gi\|195939613\|ref\|ZP_03084995.1\| DNA-directed RNA polymerase subunit beta' [Escherichia coli O157:H7 ... gi\|208820305, gi... - gi\|208820305\|ref\|ZP_03260625.1\| DNA-directed RNA polymerase, beta' subunit [Escherichia coli O157:H7... gi\|208733974, gi... - gi\|208812697\|ref\|ZP_03254026.1\| DNA-directed RNA polymerase, beta' subunit [Escherichia coli O157:H7... gi\|194439796, gi... - gi\|83584818\|ref\|ZP_00923478.1\| COG0086: DNA-directed RNA polymerase, beta' subunit/160 kD subunit [E... gi\|209921466, gi... - gi\|209921466\|ref\|YP_002295550.1\| DNA-directed RNA polymerase subunit beta' [Escherichia coli SE11], ... RPOC_ECO24 - DNA-directed RNA polymerase subunit beta' OS=Escherichia coli O139:H28 (strain E24377A / ETEC) GN=rp... gi\|209160568, gi... - gi\|209399168\|ref\|YP_002273504.1\| DNA-directed RNA polymerase, beta' subunit [Escherichia coli O157:H... gi\|218363311, gi... - gi\|218556542\|ref\|YP_002389456.1\| DNA-directed RNA polymerase subunit beta' [Escherichia coli IAI1], ... gi\|83569001, gi\|... - gi\|83569001\|ref\|ZP_00920464.1\| COG0086: DNA-directed RNA polymerase, beta' subunit/160 kD subunit [S... gi\|217325068, gi... - gi\|217325068\|ref\|ZP_03441152.1\| DNA-directed RNA polymerase, beta' subunit [Escherichia coli O157:H7... gi\|13364387, gi\|... - gi\|15834165\|ref\|NP_312938.1\| DNA-directed RNA polymerase subunit beta' [Escherichia coli O157:H7 str... RPOC_ECOLI - DNA-directed RNA polymerase beta' chain (EC 2.7.7.6) (RNAP beta' subunit) (Transcriptase beta' chain... gi\|124498588, gi... - gi\|124531374\|ref\|ZP_01701684.1\| DNA-directed RNA polymerase, beta' subunit [Escherichia coli B], gi\|... gi\|238903044, gi... - gi\|238903044\|ref\|YP_002928840.1\| RNA polymerase, beta prime subunit [Escherichia coli BW2952], gi\|23... gi\|253775383, gi... - gi\|254290679\|ref\|YP_003056427.1\| DNA-directed RNA polymerase subunit beta' [Escherichia coli BL21(DE... gi\|226838480, gi... - gi\|254039245\|ref\|ZP_04873294.1\| RNA polymerase beta' subunit [Escherichia sp. 1_1_43], gi\|226838480\|... gi\|254163929, gi... - gi\|254163929\|ref\|YP_003047037.1\| DNA-directed RNA polymerase subunit beta' [Escherichia coli B str. ... gi\|254595386, gi... - gi\|254795986\|ref\|YP_003080823.1\| RNA polymerase, beta prime subunit [Escherichia coli O157:H7 str. T...	0.0	[1..1404]	[1..1404]
RPOC_SHIF8 - DNA-directed RNA polymerase subunit beta' OS=Shigella flexneri serotype 5b (strain 8401) GN=rpoC PE=...	0.0	[1..1404]	[1..1404]
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	0.0	[1..1404]	[1..1404]
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	0.0	[1..1404]	[1..1404]
gi\|223476 - gi\|223476\|prf\|\|0808241A polymerase beta',RNA	0.0	[1..1404]	[1..1404]
RPOC_SHIDS - DNA-directed RNA polymerase subunit beta' OS=Shigella dysenteriae serotype 1 (strain Sd197) GN=rpoC ...	0.0	[1..1404]	[1..1404]
RPOC_ECOL5 - DNA-directed RNA polymerase subunit beta' OS=Escherichia coli O6:K15:H31 (strain 536 / UPEC) GN=rpoC...	0.0	[1..1404]	[1..1404]
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	0.0	[1..1404]	[1..1404]

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Predicted Domain #1

Region A:
Residues: [1-1172]

      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 MTNLERRQIL TEEQYLDALE EFGDEFDAKM 180
  181 GAEAIQALLK NMDLEAECEI 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 KEAERIYRAG 540
  541 LASLHARVKV RITEEIRNTE GESITRTSII DTTVGRAILW MIVPQGLPYS IVNQPLGKKA 600
  601 ISKMLNTCYR ILGLKPTVIF ADQIMYTGFA YAARSGASVG IDDMVIPEAK AGIIEEAETE 660
  661 VAEIQEQFQS GLVTAGERYN KVIDIWAAAN ERVAKAMMDN LSVEDVVNRD GVVEQQVSFN 720
  721 SIFMMADSGA RGSAAQIRQL AGMRGLMAKP DGSIIETPIT ANFREGLNVL QYFISTHGAR 780
  781 KGLADTALKT ANSGYLTRRL VDVAQDLVVT EDDCGTHNGI VMTPVIEGGD VKEPLRDRVL 840
  841 GRVTAEEVIK PGSADILVPR NTLLDEKWCD LLEENSVDSV KVRSVVSCET DFGVCANCYG 900
  901 RDLARGHIIN KGEAVGVIAA QSIGEPGTQL TMRTFHIGGA ASRAAAESSI QVKNKGSLKL 960
  961 SNVKFVTNAA GKLVITSRNT ELKLIDEFGR TKESYKVPYG AVMAKGDGAE VQGGETVANW1020
 1021 DPHIMPVVTE VSGFIRFADM VDGQTITRQT DELTGLSSLV VLDSAERTGS GKDLRPALKI1080
 1081 VDAKGNDVLI PGTDMPAQYF LPGKAIVQLE DGIQIGAGDT LARIPQESSG TKDITGGLPR1140
 1141 VADLFEARRP KEPAILAEIS GIISFGKETK GK

[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: [1173-1406]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 RRLVISPLDG SDAYEEMIPK WRQLNVFEGE VVERGDVVSD GPESPHDILR LRGVHAVTRY  60
   61 ITNEVQEVYR LQGVKINDKH IEVIVRQMLR KGTIVDAGST DFLEGEQAEM SRVKIANRKL 120
  121 AAEGKIEATF TRDLLGITKA SLATESFISA ASFQETTRVL TEAAVAGKRD ELRGLKENVI 180
  181 VGRLIPAGTG YAYHQDRMRR KAQGEAPVVP QVSADEATAN LAELLNAGFG NNKG

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	66.522879
Match:	1i3qA
Description:	RBP1
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

Predicted functions: