YRC Public Data Repository - Protein Structure Prediction

Protein:	RPA190
Organism:	Saccharomyces cerevisiae
Length:	1664 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 RPA190.

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	[124..1659]	[4..1472]
RPOC_BACSU - DNA-directed RNA polymerase subunit beta' OS=Bacillus subtilis GN=rpoC PE=3 SV=3	0.0	[130..1462]	[14..1182]
gi\|13310932 - gi\|13310932\|gb\|AAF36438.2\|AF126254_1 RNA polymerase II largest subunit [Leishmania donovani]	0.0	[171..1662]	[46..1450]
gi\|16505 - gi\|16505\|emb\|CAA37130.1\| RNA polymerase II [Arabidopsis thaliana]	0.0	[126..1662]	[5..1465]
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	[109..1659]	[4..1368]
RPOC_XYLFT - DNA-directed RNA polymerase subunit beta' OS=Xylella fastidiosa (strain Temecula1 / ATCC 700964) GN=... RPOC_XYLF2 - DNA-directed RNA polymerase subunit beta' OS=Xylella fastidiosa (strain M23) GN=rpoC PE=3 SV=1	0.0	[109..1652]	[4..1362]
RPOC_STAES - DNA-directed RNA polymerase subunit beta' OS=Staphylococcus epidermidis (strain ATCC 12228) GN=rpoC ... RPOC_STAEQ - DNA-directed RNA polymerase subunit beta' OS=Staphylococcus epidermidis (strain ATCC 35984 / RP62A) ... RPOC_STAEP - (Q8CQ83) DNA-directed RNA polymerase beta' chain (EC 2.7.7.6) (RNAP beta' subunit) (Transcriptase be...	0.0	[117..1478]	[2..1202]
gi\|18307453 - gi\|18307453\|emb\|CAD21513.1\| probable DNA-directed RNA polymerase I [Neurospora crassa] gi\|157072001, gi... - gi\|164428077\|ref\|XP_956006.2\| hypothetical protein NCU01638 [Neurospora crassa OR74A], gi\|157072001\|...	0.0	[1..1661]	[1..1693]
POLR1A - polymerase (RNA) I polypeptide A, 194kDa	0.0	[1..1661]	[1..1717]
gi\|56405368 - gi\|56405368\|sp\|P91875.2\|RPA1_DROME RecName: Full=DNA-directed RNA polymerase I subunit RPA1; Short=R...	0.0	[14..1660]	[16..1643]

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Predicted Domain #1

Region A:
Residues: [1-103]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MDISKPVGSE ITSVDFGILT AKEIRNLSAK QITNPTVLDN LGHPVSGGLY DLALGAFLRN  60
   61 LCSTCGLDEK FCPGHQGHIE LPVPCYNPLF FNQLYIYLRA SCL

[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.

Predicted Domain #2

Region A:
Residues: [104-1664]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 FCHHFRLKSV EVHRYACKLR LLQYGLIDES YKLDEITLGS LNSSMYTDDE AIEDNEDEMD  60
   61 GEGSKQSKDI SSTLLNELKS KRSEYVDMAI AKALSDGRTT ERGSFTATVN DERKKLVHEF 120
  121 HKKLLSRGKC DNCGMFSPKF RKDGFTKIFE TALNEKQITN NRVKGFIRQD MIKKQKQAKK 180
  181 LDGSNEASAN DEESFDVGRN PTTRPKTGST YILSTEVKNI LDTVFRKEQC VLQYVFHSRP 240
  241 NLSRKLVKAD SFFMDVLVVP PTRFRLPSKL GEEVHENSQN QLLSKVLTTS LLIRDLNDDL 300
  301 SKLQKDKVSL EDRRVIFSRL MNAFVTIQND VNAFIDSTKA QGRTSGKVPI PGVKQALEKK 360
  361 EGLFRKHMMG KRVNYAARSV ISPDPNIETN EIGVPPVFAV KLTYPEPVTA YNIAELRQAV 420
  421 INGPDKWPGA TQIQNEDGSL VSLIGMSVEQ RKALANQLLT PSSNVSTHTL NKKVYRHIKN 480
  481 RDVVLMNRQP TLHKASMMGH KVRVLPNEKT LRLHYANTGA YNADFDGDEM NMHFPQNENA 540
  541 RAEALNLANT DSQYLTPTSG SPVRGLIQDH ISAGVWLTSK DSFFTREQYQ QYIYGCIRPE 600
  601 DGHTTRSKIV TLPPTIFKPY PLWTGKQIIT TVLLNVTPPD MPGINLISKN KIKNEYWGKG 660
  661 SLENEVLFKD GALLCGILDK SQYGASKYGI VHSLHEVYGP EVAAKVLSVL GRLFTNYITA 720
  721 TAFTCGMDDL RLTAEGNKWR TDILKTSVDT GREAAAEVTN LDKDTPADDP ELLKRLQEIL 780
  781 RDNNKSGILD AVTSSKVNAI TSQVVSKCVP DGTMKKFPCN SMQAMALSGA KGSNVNVSQI 840
  841 MCLLGQQALE GRRVPVMVSG KTLPSFKPYE TDAMAGGYVK GRFYSGIKPQ EYYFHCMAGR 900
  901 EGLIDTAVKT SRSGYLQRCL TKQLEGVHVS YDNSIRDADG TLVQFMYGGD AIDITKESHM 960
  961 TQFEFCLDNY YALLKKYNPS ALIEHLDVES ALKYSKKTLK YRKKHSKEPH YKQSVKYDPV1020
 1021 LAKYNPAKYL GSVSENFQDK LESFLDKNSK LFKSSDGVNE KKFRALMQLK YMRSLINPGE1080
 1081 AVGIIASQSV GEPSTQMTLN TFHFAGHGAA NVTLGIPRLR EIVMTASAAI KTPQMTLPIW1140
 1141 NDVSDEQADT FCKSISKVLL SEVIDKVIVT ETTGTSNTAG GNAARSYVIH MRFFDNNEYS1200
 1201 EEYDVSKEEL QNVISNQFIH LLEAAIVKEI KKQKRTTGPD IGVAVPRLQT DVANSSSNSK1260
 1261 RLEEDNDEEQ SHKKTKQAVS YDEPDEDEIE TMREAEKSSD EEGIDSDKES DSDSEDEDVD1320
 1321 MNEQINKSIV EANNNMNKVQ RDRQSAIISH HRFITKYNFD DESGKWCEFK LELAADTEKL1380
 1381 LMVNIVEEIC RKSIIRQIPH IDRCVHPEPE NGKRVLVTEG VNFQAMWDQE AFIDVDGITS1440
 1441 NDVAAVLKTY GVEAARNTIV NEINNVFSRY AISVSFRHLD LIADMMTRQG TYLAFNRQGM1500
 1501 ETSTSSFMKM SYETTCQFLT KAVLDNEREQ LDSPSARIVV GKLNNVGTGS FDVLAKVPNA1560
 1561 A

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	1986.9897
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