YRC Public Data Repository - Protein Structure Prediction

Protein:	RPB2
Organism:	Saccharomyces cerevisiae
Length:	1224 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 RPB2.

Description	E-value	Query Range	Subject Range
gi\|15920466, gi\|... - gi\|15920466\|ref\|NP_376135.1\| DNA-directed RNA polymerase subunit beta [Sulfolobus tokodaii str. 7], ...	0.0	[23..1221]	[1..1117]
gi\|14520830, gi\|... - gi\|5458046\|emb\|CAB49536.1\| rpoB DNA-directed RNA polymerase, subunit B (EC 2.7.7.6) [Pyrococcus abys... gi\|7434758, gi\|5... - pir\|\|A75182 DNA-directed RNA polymerase (EC 2.7.7.6) chain B PAB0423 - Pyrococcus abyssi (strain Ors...	0.0	[24..1221]	[8..1116]
gi\|6606109 - gi\|6606109\|gb\|AAF19067.1\|AF107795_1 DNA-dependent RNA polymerase II RPB140 [Trichophyton rubrum]	0.0	[60..1130]	[1..1109]
NRPB2_ARATH - DNA-directed RNA polymerase II subunit 2 OS=Arabidopsis thaliana GN=NRPB2 PE=1 SV=2	0.0	[8..1219]	[4..1179]
gi\|6606137 - gi\|6606137\|gb\|AAF19081.1\|AF107809_1 DNA-dependent RNA polymerase II RPB140 [Peziza quelepidotia]	0.0	[208..1130]	[1..927]
gi\|168277428 - gi\|168277428\|dbj\|BAG10692.1\| DNA-directed RNA polymerase II subunit RPB2 [synthetic construct] gi\|62660340, gi\|... - gi\|62660340\|ref\|XP_214021.3\| PREDICTED: similar to DNA-directed RNA polymerase II 140 kDa polypeptid... gi\|114594586 - gi\|114594586\|ref\|XP_517275.2\| PREDICTED: DNA directed RNA polymerase II polypeptide B isoform 2 [Pan... ENSCJAT00000008049 - null ENSMMUT000000196... - null, null POLR2B - polymerase (RNA) II (DNA directed) polypeptide B, 140kDa	0.0	[5..1217]	[4..1172]
gi\|7507776 - gi\|7507776\|pir\|\|T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans	0.0	[7..1218]	[4..1175]
gi\|172211 - gi\|172211\|gb\|AAA68096.1\| RNA polymerase II 48 kd subunit [Saccharomyces cerevisiae]	0.0	[1..1224]	[1..1224]
gi\|5514652 - gi\|5514652\|emb\|CAA29180.2\| RNA polymerase [Drosophila melanogaster]	0.0	[59..1218]	[3..1122]

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Predicted Domain #1

Region A:
Residues: [1-220]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSDLANSEKY YDEDPYGFED ESAPITAEDS WAVISAFFRE KGLVSQQLDS FNQFVDYTLQ  60
   61 DIICEDSTLI LEQLAQHTTE SDNISRKYEI SFGKIYVTKP MVNESDGVTH ALYPQEARLR 120
  121 NLTYSSGLFV DVKKRTYEAI DVPGRELKYE LIAEESEDDS ESGKVFIGRL PIMLRSKNCY 180
  181 LSEATESDLY KLKECPFDMG GYFIINGSEK VLIAQERSAG

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [398-551]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 RDHFGKKRLD LAGPLLAQLF KTLFKKLTKD IFRYMQRTVE EAHDFNMKLA INAKTITSGL  60
   61 KYALATGNWG EQKKAMSSRA GVSQVLNRYT YSSTLSHLRR TNTPIGRDGK LAKPRQLHNT 120
  121 HWGLVCPAET PEGQACGLVK NLSLMSCISV GTDP

[Run NCBI BLAST on this sequence.]

Region C:
Residues: [598-750]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 ETLRTLRRKG DINPEVSMIR DIREKELKIF TDAGRVYRPL FIVEDDESLG HKELKVRKGH  60
   61 IAKLMATEYQ DIEGGFEDVE EYTWSSLLNE GLVEYIDAEE EESILIAMQP EDLEPAEANE 120
  121 ENDLDVDPAK RIRVSHHATT FTHCEIHPSM ILG

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	11000.0
Match:	1k83B_
Description:	RBP2
Matching Structure (courtesy of the PDB):

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
nucleic acid binding	2.33174616086951	bayes_pls_golite062009
DNA binding	2.27079409864244	bayes_pls_golite062009
binding	1.73416306650822	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	0.45174975126993	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [221-397]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NIVQVFKKAA PSPISHVAEI RSALEKGSRF ISTLQVKLYG REGSSARTIK ATLPYIKQDI  60
   61 PIVIIFRALG IIPDGEILEH ICYDVNDWQM LEMLKPCVED GFVIQDRETA LDFIGRRGTA 120
  121 LGIKKEKRIQ YAKDILQKEF LPHITQLEGF ESRKAFFLGY MINRLLLCAL DRKDQDD

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [552-597]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MPIITFLSEW GMEPLEDYVP HQSPDATRVF VNGVWHGVHR NPARLM

[Run NCBI BLAST on this sequence.]

Region C:
Residues: [751-1128]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 VAASIIPFPD HNQSPRNTYQ SAMGKQAMGV FLTNYNVRMD TMANILYYPQ KPLGTTRAME  60
   61 YLKFRELPAG QNAIVAIACY SGYNQEDSMI MNQSSIDRGL FRSLFFRSYM DQEKKYGMSI 120
  121 TETFEKPQRT NTLRMKHGTY DKLDDDGLIA PGVRVSGEDV IIGKTTPISP DEEELGQRTA 180
  181 YHSKRDASTP LRSTENGIVD QVLVTTNQDG LKFVKVRVRT TKIPQIGDKF ASRHGQKGTI 240
  241 GITYRREDMP FTAEGIVPDL IINPHAIPSR MTVAHLIECL LSKVAALSGN EGDASPFTDI 300
  301 TVEGISKLLR EHGYQSRGFE VMYNGHTGKK LMAQIFFGPT YYQRLRHMVD DKIHARARGP 360
  361 MQVLTRQPVE GRSRDGGL

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	11000.0
Match:	1k83B_
Description:	RBP2
Matching Structure (courtesy of the PDB):

Predicted Domain #3

Region A:
Residues: [1129-1224]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 RFGEMERDCM IAHGAASFLK ERLMEASDAF RVHICGICGL MTVIAKLNHN QFECKGCDNK  60
   61 IDIYQIHIPY AAKLLFQELM AMNITPRLYT DRSRDF

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	11000.0
Match:	1k83B_
Description:	RBP2
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: