YRC Public Data Repository - Protein Structure Prediction

Protein:	RPA135
Organism:	Saccharomyces cerevisiae
Length:	1203 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 RPA135.

Description	E-value	Query Range	Subject Range
gi\|468334 - gi\|468334\|gb\|AAA21416.1\| RNA polymerase beta-subunit [Mycobacterium tuberculosis]	0.0	[8..1174]	[21..1170]
gi\|228963202, gi... - gi\|228963202\|ref\|ZP_04124371.1\| DNA-directed RNA polymerase subunit beta [Bacillus thuringiensis ser... RPOB_BACCR - DNA-directed RNA polymerase subunit beta OS=Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 /... RPOB_BACC2 - DNA-directed RNA polymerase subunit beta OS=Bacillus cereus (strain G9842) GN=rpoB PE=3 SV=1 RPOB_BACC4 - DNA-directed RNA polymerase subunit beta OS=Bacillus cereus (strain B4264) GN=rpoB PE=3 SV=1 gi\|206972219, gi... - gi\|206972219\|ref\|ZP_03233166.1\| DNA-directed RNA polymerase, beta subunit [Bacillus cereus AH1134], ...	0.0	[19..1171]	[7..1174]
NRPB2_ARATH - DNA-directed RNA polymerase II subunit 2 OS=Arabidopsis thaliana GN=NRPB2 PE=1 SV=2	0.0	[10..1201]	[14..1179]
RPB2_SCHPO - DNA-directed RNA polymerase II subunit RPB2 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) G... rpb2 - DNA-directed RNA polymerase II complex subunit Rpb2	0.0	[18..1202]	[13..1208]
gi\|23129279 - gi\|23129279\|ref\|ZP_00111111.1\| COG0085: DNA-directed RNA polymerase, beta subunit/140 kD subunit [No...	0.0	[3..1161]	[9..1109]
gi\|15705366 - gi\|15705366\|gb\|AAL05611.1\| RpoB [bacterium DR-2001]	0.0	[26..1148]	[81..1189]
RPOB_CALS4 - DNA-directed RNA polymerase subunit beta OS=Caldanaerobacter subterraneus subsp. tengcongensis (stra... RPOB_THETN - DNA-directed RNA polymerase subunit beta OS=Thermoanaerobacter tengcongensis GN=rpoB PE=3 SV=1	0.0	[16..1154]	[2..1170]
gi\|34391545 - gi\|34391545\|gb\|AAN65350.1\| RpoB [Mycobacterium chelonae]	0.0	[9..1174]	[16..1164]
RPA2_MOUSE - DNA-directed RNA polymerase I subunit RPA2 OS=Mus musculus GN=Polr1b PE=2 SV=1	0.0	[7..1200]	[14..1134]
RPOB_STRCO - DNA-directed RNA polymerase subunit beta OS=Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M... RPOB_STRCO - DNA-directed RNA polymerase subunit beta OS=Streptomyces coelicolor GN=rpoB PE=3 SV=1	0.0	[5..1177]	[1..1159]

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Predicted Domain #1

Region A:
Residues: [1-895]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSKVIKPPGQ ARTADFRTLE RESRFINPPK DKSAFPLLQE AVQPHIGSFN ALTEGPDGGL  60
   61 LNLGVKDIGE KVIFDGKPLN SEDEISNSGY LGNKLSVSVE QVSIAKPMSN DGVSSAVERK 120
  121 VYPSESRQRL TSYRGKLLLK LKWSVNNGEE NLFEVRDCGG LPVMLQSNRC HLNKMSPYEL 180
  181 VQHKEESDEI GGYFIVNGIE KLIRMLIVQR RNHPMAIIRP SFANRGASYS HYGIQIRSVR 240
  241 PDQTSQTNVL HYLNDGQVTF RFSWRKNEYL VPVVMILKAL CHTSDREIFD GIIGNDVKDS 300
  301 FLTDRLELLL RGFKKRYPHL QNRTQVLQYL GDKFRVVFQA SPDQSDLEVG QEVLDRIVLV 360
  361 HLGKDGSQDK FRMLLFMIRK LYSLVAGECS PDNPDATQHQ EVLLGGFLYG MILKEKIDEY 420
  421 LQNIIAQVRM DINRGMAINF KDKRYMSRVL MRVNENIGSK MQYFLSTGNL VSQSGLDLQQ 480
  481 VSGYTVVAEK INFYRFISHF RMVHRGSFFA QLKTTTVRKL LPESWGFLCP VHTPDGSPCG 540
  541 LLNHFAHKCR ISTQQSDVSR IPSILYSLGV APASHTFAAG PSLCCVQIDG KIIGWVSHEQ 600
  601 GKIIADTLRY WKVEGKTPGL PIDLEIGYVP PSTRGQYPGL YLFGGHSRML RPVRYLPLDK 660
  661 EDIVGPFEQV YMNIAVTPQE IQNNVHTHVE FTPTNILSIL ANLTPFSDFN QSPRNMYQCQ 720
  721 MGKQTMGTPG VALCHRSDNK LYRLQTGQTP IVKANLYDDY GMDNFPNGFN AVVAVISYTG 780
  781 YDMDDAMIIN KSADERGFGY GTMYKTEKVD LALNRNRGDP ITQHFGFGND EWPKEWLEKL 840
  841 DEDGLPYIGT YVEEGDPICA YFDDTLNKTK IKTYHSSEPA YIEEVNLIGD ESNKF

[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 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
general RNA polymerase II transcription factor activity	6.31198922553685	bayes_pls_golite062009
transferase activity, transferring phosphorus-containing groups	5.44374972993429	bayes_pls_golite062009
transferase activity	4.83218811360621	bayes_pls_golite062009
transcription regulator activity	2.34884279395902	bayes_pls_golite062009
DNA binding	2.02586687916169	bayes_pls_golite062009
nucleic acid binding	1.91447180328254	bayes_pls_golite062009
binding	1.53568146966362	bayes_pls_golite062009
RNA polymerase II transcription mediator activity	1.53259746846673	bayes_pls_golite062009
catalytic activity	1.36406839864424	bayes_pls_golite062009
RNA binding	1.12618950637766	bayes_pls_golite062009
RNA polymerase II transcription factor activity	0.847783043631028	bayes_pls_golite062009
protein binding	0.35192339064931	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [896-977]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 QELQTVSIKY RIRRTPQIGD KFSSRHGQKG VCSRKWPTID MPFSETGIQP DIIINPHAFP  60
   61 SRMTIGMFVE SLAGKAGALH GI

[Run NCBI BLAST on this sequence.]

Detection Method:

deduced

Shown below is our most confident de novo (Rosetta) prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

Predicted Domain #3

Region A:
Residues: [978-1071]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 AQDSTPWIFN EDDTPADYFG EQLAKAGYNY HGNEPMYSGA TGEELRADIY VGVVYYQRLR  60
   61 HMVNDKFQVR STGPVNSLTM QPVKGRKRHG GIRV

[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 #4

Region A:
Residues: [1072-1203]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 GEMERDALIG HGTSFLLQDR LLNSSDYTQA SVCRECGSIL TTQQSVPRIG SISTVCCRRC  60
   61 SMRFEDAKKL LTKSEDGEKI FIDDSQIWED GQGNKFVGGN ETTTVAIPFV LKYLDSELSA 120
  121 MGIRLRYNVE PK

[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: