YRC Public Data Repository - Protein Structure Prediction

Protein:	RPO31
Organism:	Saccharomyces cerevisiae
Length:	1460 amino acids
Reference:	Malmström L, et al. (2007) Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PLoS Biol 5(4): e76. doi:10.1371/journal.pbio.0050076

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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 RPO31.

Description	E-value	Query Range	Subject Range
gi\|83767526, gi\|... - gi\|9955855\|dbj\|BAB12227.1\| RNA polymerase II largest subunit [Aspergillus oryzae], gi\|83767526\|dbj\|B... gi\|169770395 - gi\|169770395\|ref\|XP_001819667.1\| hypothetical protein [Aspergillus oryzae RIB40]	0.0	[7..1441]	[9..1480]
gi\|13310932 - gi\|13310932\|gb\|AAF36438.2\|AF126254_1 RNA polymerase II largest subunit [Leishmania donovani]	0.0	[7..1453]	[10..1467]
gi\|16505 - gi\|16505\|emb\|CAA37130.1\| RNA polymerase II [Arabidopsis thaliana]	0.0	[2..1444]	[4..1473]
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..1457]	[5..1396]
gi\|9587193, gi\|9... - gi\|9587199\|gb\|AAF89203.1\|AF272653_1 RNA polymerase II largest subunit [Drosophila subobscura], gi\|95...	0.0	[1..1458]	[1..1493]
RpII215-PA - The gene RNA polymerase II 215kD subunit is referred to in FlyBase by the symbol Dmel\RpII215 (CG155...	0.0	[1..1458]	[1..1493]
gi\|7507776 - gi\|7507776\|pir\|\|T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans	0.0	[12..1447]	[16..1486]
gi\|3172136 - gi\|3172136\|gb\|AAC18417.1\| RNA polymerase II largest subunit [Acanthamoeba castellanii]	0.0	[76..1443]	[1..1389]
gi\|229839428, gi... - gi\|229839428\|ref\|ZP_04459587.1\| RNA polymerase, beta prime subunit [Yersinia pestis biovar Orientali... gi\|229704180, gi... - gi\|229837492\|ref\|ZP_04457654.1\| RNA polymerase, beta prime subunit [Yersinia pestis Pestoides A], gi... RPOC_YERPY - DNA-directed RNA polymerase subunit beta' OS=Yersinia pseudotuberculosis serotype O:3 (strain YPIII)... RPOC_YERPP - DNA-directed RNA polymerase subunit beta' OS=Yersinia pestis (strain Pestoides F) GN=rpoC PE=3 SV=2 RPOC_YERPN - DNA-directed RNA polymerase subunit beta' OS=Yersinia pestis bv. Antiqua (strain Nepal516) GN=rpoC P... RPOC_YERPB - DNA-directed RNA polymerase subunit beta' OS=Yersinia pseudotuberculosis serotype IB (strain PB1/+) ... RPOC_YERPG - DNA-directed RNA polymerase subunit beta' OS=Yersinia pestis bv. Antiqua (strain Angola) GN=rpoC PE=... RPOC_YERPA - DNA-directed RNA polymerase subunit beta' OS=Yersinia pestis bv. Antiqua (strain Antiqua) GN=rpoC PE... RPOC_YERP3 - DNA-directed RNA polymerase subunit beta' OS=Yersinia pseudotuberculosis serotype O:1b (strain IP 31... gi\|165938177, gi... - gi\|89103186\|ref\|ZP_01175775.1\| COG0086: DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Y... RPOC_YERPS - DNA-directed RNA polymerase subunit beta' OS=Yersinia pseudotuberculosis serotype I (strain IP32953)... gi\|45437729, gi\|... - gi\|45442863\|ref\|NP_994402.1\| DNA-directed RNA polymerase subunit beta' [Yersinia pestis biovar Micro... RPOC_YERPE - DNA-directed RNA polymerase subunit beta' OS=Yersinia pestis GN=rpoC PE=3 SV=2 gi\|15981662, gi\|... - gi\|218930751\|ref\|YP_002348626.1\| DNA-directed RNA polymerase subunit beta' [Yersinia pestis CO92], g... RPOC_YERPS - DNA-directed RNA polymerase subunit beta' OS=Yersinia pseudotuberculosis GN=rpoC PE=3 SV=1 gi\|165928333, gi... - gi\|165928333\|ref\|ZP_02224165.1\| DNA-directed RNA polymerase, beta' subunit [Yersinia pestis biovar O... gi\|166012056, gi... - gi\|166012056\|ref\|ZP_02232954.1\| DNA-directed RNA polymerase, beta' subunit [Yersinia pestis biovar A... gi\|166204397, gi... - gi\|166214393\|ref\|ZP_02240428.1\| DNA-directed RNA polymerase, beta' subunit [Yersinia pestis biovar A... gi\|167048199, gi... - gi\|167402419\|ref\|ZP_02307879.1\| DNA-directed RNA polymerase, beta' subunit [Yersinia pestis biovar A... gi\|149289328, gi... - gi\|153997220\|ref\|ZP_02022327.1\| DNA-directed RNA polymerase beta' chain [Yersinia pestis CA88-4125],... gi\|166957153, gi... - gi\|167422942\|ref\|ZP_02314695.1\| DNA-directed RNA polymerase, beta' subunit [Yersinia pestis biovar O... gi\|167426817, gi... - gi\|167426817\|ref\|ZP_02318570.1\| DNA-directed RNA polymerase, beta' subunit [Yersinia pestis biovar M... gi\|229899990, gi... - gi\|229899990\|ref\|ZP_04515130.1\| RNA polymerase, beta prime subunit [Yersinia pestis biovar Orientali...	0.0	[1..1457]	[5..1396]
gi\|447739 - gi\|447739\|prf\|\|1915304A nylB upstream ORF	0.0	[1..1457]	[5..1396]

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Predicted Domain #1

Region A:
Residues: [1-1460]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MKEVVVSETP KRIKGLEFSA LSAADIVAQS EVEVSTRDLF DLEKDRAPKA NGALDPKMGV  60
   61 SSSSLECATC HGNLASCHGH FGHLKLALPV FHIGYFKATI QILQGICKNC SAILLSETDK 120
  121 RQFLHELRRP GVDNLRRMGI LKKILDQCKK QRRCLHCGAL NGVVKKAAAG AGSAALKIIH 180
  181 DTFRWVGKKS APEKDIWVGE WKEVLAHNPE LERYVKRCMD DLNPLKTLNL FKQIKSADCE 240
  241 LLGIDATVPS GRPETYIWRY LPAPPVCIRP SVMMQDSPAS NEDDLTVKLT EIVWTSSLIK 300
  301 AGLDKGISIN NMMEHWDYLQ LTVAMYINSD SVNPAMLPGS SNGGGKVKPI RGFCQRLKGK 360
  361 QGRFRGNLSG KRVDFSGRTV ISPDPNLSID EVAVPDRVAK VLTYPEKVTR YNRHKLQELI 420
  421 VNGPNVHPGA NYLLKRNEDA RRNLRYGDRM KLAKNLQIGD VVERHLEDGD VVLFNRQPSL 480
  481 HRLSILSHYA KIRPWRTFRL NECVCTPYNA DFDGDEMNLH VPQTEEARAE AINLMGVKNN 540
  541 LLTPKSGEPI IAATQDFITG SYLISHKDSF YDRATLTQLL SMMSDGIEHF DIPPPAIMKP 600
  601 YYLWTGKQVF SLLIKPNHNS PVVINLDAKN KVFVPPKSKS LPNEMSQNDG FVIIRGSQIL 660
  661 SGVMDKSVLG DGKKHSVFYT ILRDYGPQEA ANAMNRMAKL CARFLGNRGF SIGINDVTPA 720
  721 DDLKQKKEEL VEIAYHKCDE LITLFNKGEL ETQPGCNEEQ TLEAKIGGLL SKVREEVGDV 780
  781 CINELDNWNA PLIMATCGSK GSTLNVSQMV AVVGQQIISG NRVPDGFQDR SLPHFPKNSK 840
  841 TPQSKGFVRN SFFSGLSPPE FLFHAISGRE GLVDTAVKTA ETGYMSRRLM KSLEDLSCQY 900
  901 DNTVRTSANG IVQFTYGGDG LDPLEMEGNA QPVNFNRSWD HAYNITFNNQ DKGLLPYAIM 960
  961 ETANEILGPL EERLVRYDNS GCLVKREDLN KAEYVDQYDA ERDFYHSLRE YINGKATALA1020
 1021 NLRKSRGMLG LLEPPAKELQ GIDPDETVPD NVKTSVSQLY RISEKSVRKF LEIALFKYRK1080
 1081 ARLEPGTAIG AIGAQSIGEP GTQMTLKTFH FAGVASMNVT LGVPRIKEII NASKVISTPI1140
 1141 INAVLVNDND ERAARVVKGR VEKTLLSDVA FYVQDVYKDN LSFIQVRIDL GTIDKLQLEL1200
 1201 TIEDIAVAIT RASKLKIQAS DVNIIGKDRI AINVFPEGYK AKSISTSAKE PSENDVFYRM1260
 1261 QQLRRALPDV VVKGLPDISR AVINIRDDGK RELLVEGYGL RDVMCTDGVI GSRTTTNHVL1320
 1321 EVFSVLGIEA ARYSIIREIN YTMSNHGMSV DPRHIQLLGD VMTYKGEVLG ITRFGLSKMR1380
 1381 DSVLQLASFE KTTDHLFDAA FYMKKDAVEG VSECIILGQT MSIGTGSFKV VKGTNISEKD1440
 1441 LVPKRCLFES LSNEAALKAN

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	11000.0
Match:	1k83A_
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