YRC Public Data Repository - Protein Structure Prediction

Protein:	TFB4
Organism:	Saccharomyces cerevisiae
Length:	338 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 TFB4.

Description	E-value	Query Range	Subject Range
gi\|190407994 - gi\|190407994\|gb\|EDV11259.1\| RNA polymerase II transcription factor B subunit 4 [Saccharomyces cerevi... TFB4_YEAST - RNA polymerase II transcription factor B subunit 4 OS=Saccharomyces cerevisiae (strain ATCC 204508 /... TFB4 - Subunit of TFIIH complex, involved in transcription initiation, similar to 34 kDa subunit of human T...	0.0	[1..338]	[1..338]
GTF2H3 - general transcription factor IIH, polypeptide 3, 34kDa gi\|208966364 - gi\|208966364\|dbj\|BAG73196.1\| general transcription factor IIH, polypeptide 3, 34kDa [synthetic const...	0.0	[20..334]	[5..302]
gi\|7507776 - gi\|7507776\|pir\|\|T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans	0.0	[20..334]	[5..302]
TFB4_ARATH - RNA polymerase II transcription factor B subunit 4 OS=Arabidopsis thaliana GN=TFB4 PE=2 SV=1	1.0E-86	[12..314]	[3..282]
gi\|2257568 - gi\|2257568\|dbj\|BAA21460.1\| basic transcription factor 2.35KD subunit [Schizosaccharomyces pombe]	3.0E-86	[17..318]	[17..292]
tfb4 - transcription factor TFIIH complex subunit Tfb4 TFB4_SCHPO - RNA polymerase II transcription factor B subunit 4 OS=Schizosaccharomyces pombe (strain 972 / ATCC 2...	2.0E-85	[17..319]	[17..293]
Tfb4-PA - The gene Tfb4 is referred to in FlyBase by the symbol Dmel\Tfb4 (CG5041, FBgn0031309). It is a prote...	9.0E-83	[14..312]	[7..279]

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Predicted Domain #1

Region A:
Residues: [1-338]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MDAISDPTFK HARSRKQVTE ESPSLLTVII EIAPKLWTTF DEEGNEKGSI IKVLEALIVF  60
   61 LNAHLAFNSA NKVAVIAAYS QGIKYLYPES TSALKASESE NKTRSDLKII NSDMYRRFRN 120
  121 VDETLVEEIY KLFELEKKQI EQNSQRSTLA GAMSAGLTYV NRISKESVTT SLKSRLLVLT 180
  181 CGSGSSKDEI FQYIPIMNCI FSATKMKCPI DVVKIGGSKE STFLQQTTDA TNGVYLHVES 240
  241 TEGLIQYLAT AMFIDPSLRP IIVKPNHGSV DFRTSCYLTG RVVAVGFICS VCLCVLSIIP 300
  301 PGNKCPACDS QFDEHVIAKL KRKPVVPRLK AKKKVTKP

[Run NCBI BLAST on this sequence.]

Detection Method:	Pfam
Confidence:	188.552842
Match:	PF03850
Description:	Transcription factor Tfb4

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
binding	2.68315152218267	bayes_pls_golite062009
nucleic acid binding	2.10023916482665	bayes_pls_golite062009
DNA binding	1.9295508897092	bayes_pls_golite062009
protein complex binding	1.65763332955233	bayes_pls_golite062009
protein binding	1.42792331963866	bayes_pls_golite062009
hydrolase activity	0.589248272940562	bayes_pls_golite062009
structure-specific DNA binding	0.446181458443121	bayes_pls_golite062009
protein dimerization activity	0.244402438311177	bayes_pls_golite062009
protein heterodimerization activity	0.114607758890868	bayes_pls_golite062009
catalytic activity	0.0380261580236634	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [240-338]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 STEGLIQYLA TAMFIDPSLR PIIVKPNHGS VDFRTSCYLT GRVVAVGFIC SVCLCVLSII  60
   61 PPGNKCPACD SQFDEHVIAK LKRKPVVPRL KAKKKVTKP

[Run NCBI BLAST on this sequence.]

Detection Method:	FFAS03
Confidence:	0.954
Match:	2ozyA
Description:	No description for 2ozyA was found.

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: