YRC Public Data Repository - Protein Structure Prediction

Protein:	TFB3
Organism:	Saccharomyces cerevisiae
Length:	321 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 TFB3.

Description	E-value	Query Range	Subject Range
gi\|151942424 - gi\|151942424\|gb\|EDN60780.1\| transcription initiation factor TFIIH subunit [Saccharomyces cerevisiae ... TFB3 - Subunit of TFIIH and nucleotide excision repair factor 3 complexes, involved in transcription initia... gi\|190404617 - gi\|190404617\|gb\|EDV07884.1\| RNA polymerase II transcription factor B subunit 3 [Saccharomyces cerevi... gi\|207346252 - gi\|207346252\|gb\|EDZ72804.1\| YDR460Wp-like protein [Saccharomyces cerevisiae AWRI1631] TFB3_YEAST - RNA polymerase II transcription factor B subunit 3 OS=Saccharomyces cerevisiae (strain ATCC 204508 /...	2.0E-83	[1..321]	[1..321]
gi\|208966756 - gi\|208966756\|dbj\|BAG73392.1\| menage a trois homolog 1 [synthetic construct] gi\|109083843 - gi\|109083843\|ref\|XP_001097131.1\| PREDICTED: menage a trois 1 (CAK assembly factor) isoform 3 [Macaca... gi\|114653355 - gi\|114653355\|ref\|XP_001167724.1\| PREDICTED: menage a trois 1 (CAK assembly factor) isoform 3 [Pan tr... MNAT1 - menage a trois homolog 1, cyclin H assembly factor (Xenopus laevis)	7.0E-65	[9..313]	[2..304]
MAT1_MOUSE - CDK-activating kinase assembly factor MAT1 OS=Mus musculus GN=Mnat1 PE=1 SV=2	2.0E-61	[9..313]	[2..304]
MAT1_XENLA - CDK-activating kinase assembly factor MAT1 OS=Xenopus laevis GN=mnat1 PE=2 SV=1 gi\|2134192 - gi\|2134192\|pir\|\|S60120 RING finger protein chain MAT1 - clawed frog	1.0E-60	[9..313]	[2..304]
MAT1_MARGL - CDK-activating kinase assembly factor MAT1 OS=Marthasterias glacialis PE=1 SV=1	4.0E-57	[9..313]	[3..305]
gi\|7507776 - gi\|7507776\|pir\|\|T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans	1.0E-56	[9..313]	[2..262]
TFB3_SCHPO - RNA polymerase II transcription factor B subunit 3 OS=Schizosaccharomyces pombe (strain 972 / ATCC 2... pmh1 - transcription factor TFIIH complex subunit Pmh1	2.0E-51	[10..313]	[10..304]

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Predicted Domain #1

Region A:
Residues: [1-67]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MLMDEYEENK DMCPICKTDR YLSPDVKFLV NPECYHRICE SCVDRIFSLG PAQCPYKGCD  60
   61 KILRKNK

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	127.035458
Match:	1g25A_
Description:	TFIIH Mat1 subunit
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
general RNA polymerase II transcription factor activity	6.51043144330453	bayes_pls_golite062009
ubiquitin-protein ligase activity	5.97121728620188	bayes_pls_golite062009
small conjugating protein ligase activity	5.78935175140238	bayes_pls_golite062009
acid-amino acid ligase activity	4.75377804653841	bayes_pls_golite062009
ligase activity, forming carbon-nitrogen bonds	3.82459130917693	bayes_pls_golite062009
binding	2.78710909602478	bayes_pls_golite062009
transcription regulator activity	2.72498741013971	bayes_pls_golite062009
nucleic acid binding	2.32387297115017	bayes_pls_golite062009
DNA binding	2.00904221080834	bayes_pls_golite062009
transcription repressor activity	1.98209395225978	bayes_pls_golite062009
protein binding	1.5975811408548	bayes_pls_golite062009
transcription factor activity	1.22579085356684	bayes_pls_golite062009
small conjugating protein-specific protease activity	1.2126425713931	bayes_pls_golite062009
transcription factor binding	1.11842175076436	bayes_pls_golite062009
ubiquitin-specific protease activity	1.03469202541773	bayes_pls_golite062009
RNA polymerase II transcription factor activity	0.90321253993065	bayes_pls_golite062009
ligase activity	0.63517530468004	bayes_pls_golite062009
cysteine-type peptidase activity	0.50197530717959	bayes_pls_golite062009
transcription corepressor activity	0.384990496120483	bayes_pls_golite062009
ubiquitin thiolesterase activity	0.265769062717221	bayes_pls_golite062009
transcription coactivator activity	0.255669498391574	bayes_pls_golite062009
transcription cofactor activity	0.233838999434784	bayes_pls_golite062009
catalytic activity	0.14112008370434	bayes_pls_golite062009
transcription activator activity	0.126093965701234	bayes_pls_golite062009
enzyme binding	0.104373352314595	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [68-264]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 FKTQIFDDVE VEKEVDIRKR VFNVFNKTID DFNGDLVEYN KYLEEVEDII YKLDHGIDVA  60
   61 KTEEKLRTYE ELNKQLIMNN LERSRTEIES FEQRQKFEKE MKLKKRLLER QIEEEERMNK 120
  121 EWTKKEIVNR LSTTTQDINE TIEGVKNTVK LKKSSARRKL EELNRVLKNN PYFNSNVNVQ 180
  181 NSRLKDAVPF TPFNGDR

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	5.0
Match:	1i84S_
Description:	Heavy meromyosin subfragment
Matching Structure (courtesy of the PDB):

Predicted Domain #3

Region A:
Residues: [265-321]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 EAHPRFTLKG SVYNDPFIKD LEHRKEFIAS GFNTNYAYER VLTEAFMGLG CVISEEL

[Run NCBI BLAST on this sequence.]

Detection Method:

deduced

Shown below are all of our de novo (Rosetta) predictions for this domain.
Click here to view only most confident match.

		MCM Score	GO Score	GO Term	SCOP Match	SCOP Description
View	Download	0.546	0.821	nucleotide-excision repair	a.2.9	C-terminal UvrC-binding domain of UvrB
View	Download	0.542	0.821	nucleotide-excision repair	d.58.17	Metal-binding domain
View	Download	0.717	0.821	nucleotide-excision repair	a.8.1	Bacterial immunoglobulin/albumin-binding domains
View	Download	0.508	0.821	nucleotide-excision repair	a.30.1	ROP protein
View	Download	0.440	0.821	nucleotide-excision repair	a.16.1	S15/NS1 RNA-binding domain
View	Download	0.437	0.821	nucleotide-excision repair	d.58.17	Metal-binding domain
View	Download	0.436	0.821	nucleotide-excision repair	d.58.25	Killer toxin KP6 alpha-subunit
View	Download	0.423	0.821	nucleotide-excision repair	a.32.1	Transcription factor IIA (TFIIA), alpha-helical domain
View	Download	0.372	0.821	nucleotide-excision repair	d.58.18	Regulatory domain in the aminoacid metabolism
View	Download	0.365	0.821	nucleotide-excision repair	f.13.1	Family A G protein-coupled receptor-like
View	Download	0.361	0.821	nucleotide-excision repair	a.159.2	FF domain
View	Download	0.359	0.821	nucleotide-excision repair	d.58.4	Dimeric alpha+beta barrel
View	Download	0.338	0.821	nucleotide-excision repair	a.2.7	tRNA-binding arm
View	Download	0.335	0.821	nucleotide-excision repair	a.2.8	Eukaryotic DNA topoisomerase I, dispensable insert domain
View	Download	0.332	0.821	nucleotide-excision repair	a.16.1	S15/NS1 RNA-binding domain
View	Download	0.327	0.821	nucleotide-excision repair	a.157.1	Skp1 dimerisation domain-like
View	Download	0.314	0.821	nucleotide-excision repair	d.58.23	Probable ACP-binding domain of malonyl-CoA ACP transacylase
View	Download	0.310	0.821	nucleotide-excision repair	d.58.48	MTH1187-like
View	Download	0.305	0.821	nucleotide-excision repair	a.144.1	PABC (PABP) domain
View	Download	0.288	0.821	nucleotide-excision repair	d.58.1	4Fe-4S ferredoxins
View	Download	0.285	0.821	nucleotide-excision repair	a.6.1	Putative DNA-binding domain
View	Download	0.285	0.821	nucleotide-excision repair	a.108.1	Ribosomal protein L7/12, oligomerisation (N-terminal) domain
View	Download	0.283	0.821	nucleotide-excision repair	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.277	0.821	nucleotide-excision repair	d.58.17	Metal-binding domain
View	Download	0.276	0.821	nucleotide-excision repair	d.58.23	Probable ACP-binding domain of malonyl-CoA ACP transacylase
View	Download	0.268	0.821	nucleotide-excision repair	a.30.2	Homodimeric domain of signal transducing histidine kinase
View	Download	0.267	0.821	nucleotide-excision repair	d.96.1	Tetrahydrobiopterin biosynthesis enzymes-like
View	Download	0.267	0.821	nucleotide-excision repair	a.35.1	lambda repressor-like DNA-binding domains
View	Download	0.259	0.821	nucleotide-excision repair	d.58.11	EF-G/eEF-2 domains III and V
View	Download	0.257	0.821	nucleotide-excision repair	d.59.1	Ribosomal protein L30p/L7e
View	Download	0.257	0.821	nucleotide-excision repair	a.144.2	Ribosomal protein L20
View	Download	0.256	0.821	nucleotide-excision repair	a.27.1	Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
View	Download	0.253	0.821	nucleotide-excision repair	a.74.1	Cyclin-like
View	Download	0.252	0.821	nucleotide-excision repair	d.58.24	CheY-binding domain of CheA
View	Download	0.251	0.821	nucleotide-excision repair	a.32.1	Transcription factor IIA (TFIIA), alpha-helical domain
View	Download	0.247	0.821	nucleotide-excision repair	a.4.7	Ribosomal protein L11, C-terminal domain
View	Download	0.246	0.821	nucleotide-excision repair	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.237	0.821	nucleotide-excision repair	a.5.1	DNA helicase RuvA subunit, C-terminal domain
View	Download	0.236	0.821	nucleotide-excision repair	a.17.1	p8-MTCP1
View	Download	0.231	0.821	nucleotide-excision repair	a.2.10	Epsilon subunit of F1F0-ATP synthase C-terminal domain
View	Download	0.226	0.821	nucleotide-excision repair	d.58.5	GlnB-like
View	Download	0.223	0.821	nucleotide-excision repair	d.58.17	Metal-binding domain
View	Download	0.215	0.821	nucleotide-excision repair	d.58.36	Sulfite reductase, domains 1 and 3
View	Download	0.213	0.821	nucleotide-excision repair	d.43.1	Elongation factor Ts (EF-Ts), dimerisation domain
View	Download	0.211	0.821	nucleotide-excision repair	a.56.1	CO dehydrogenase ISP C-domain like
View	Download	0.210	0.821	nucleotide-excision repair	d.58.3	Protease propeptides/inhibitors
View	Download	0.204	0.821	nucleotide-excision repair	d.58.5	GlnB-like
View	Download	0.202	0.821	nucleotide-excision repair	a.46.2	Nucleoside phosphorylase/phosphoribosyltransferase N-terminal 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: