Summary: Transcription factor TFIIB repeat
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Transcription factor TFIIB repeat Provide feedback
No Pfam abstract.
Internal database links
SCOOP: | Cyclin_C Cyclin_N RB_B Sigma70_r4 |
External database links
HOMSTRAD: | transcript_fac2 |
PRINTS: | PR00685 |
PROSITE: | PDOC00624 |
SCOP: | 1vol |
This tab holds annotation information from the InterPro database.
InterPro entry IPR013150
In eukaryotes, transcription initiation of all protein encoding genes involves the polymerase II system. This sytem is modulated by both general and specific transcription factors. The general factors (which include TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIG and TFIIH) operate through common promoter elements, such as the TATA box. Transcription factor IIB (TFIIB) is of central importance in transcription of class II genes. It associates with TFIID-TFIIA bound to DNA (the DA complex) to form a ternary TFIID-IIA-IBB (DAB) complex, which is recognised by RNA polymerase II [PUBMED:1876184, PUBMED:1949150]. TFIIB comprises ~315-340 residues and contains an imperfect C-terminal repeat of a 75-residue domain that may contribute to the symmetry of the folded protein. The basal archaeal transcription machinery resembles that of the eukaryotic polymerase II system and includes a homologue of TFIIB [PUBMED:7597027].
This entry represents a cyclin-like domain which is found repeated in the C-terminal region of a variety of eukaryotic TFIIB's and their archaeal counterparts. These domains individually form the typical cyclin fold, and in the transcription complex they straddle the C-terminal region of the TATA-binding protein - an interaction essential for the formation of the transcription initiation complex [PUBMED:9177165, PUBMED:10619841].
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Molecular function | TBP-class protein binding (GO:0017025) |
Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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Pfam Clan
This family is a member of clan Cyclin (CL0065), which has the following description:
This Clan contains cyclins, Transcription factor IIB (TFIIB), and the Retinoblastoma tumour suppressor proteins. These were predicted to be related by sequence [1].
The clan contains the following 12 members:
CDK5_activator Cyclin Cyclin_C Cyclin_C_2 Cyclin_N DUF3452 Herp-Cyclin K-cyclin_vir_C RB_A RB_B TFIIB TFIIB_C_1Alignments
We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...
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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.
Seed (11) |
Full (8720) |
Representative proteomes | UniProt (20316) |
NCBI (22524) |
Meta (672) |
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RP15 (1343) |
RP35 (3875) |
RP55 (6864) |
RP75 (10388) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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Seed (11) |
Full (8720) |
Representative proteomes | UniProt (20316) |
NCBI (22524) |
Meta (672) |
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---|---|---|---|---|---|---|---|---|---|
RP15 (1343) |
RP35 (3875) |
RP55 (6864) |
RP75 (10388) |
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Raw Stockholm | |||||||||
Gzipped |
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
HMM logo
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Trees
This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.
Note: You can also download the data file for the tree.
Curation and family details
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Curation
Seed source: | Prosite |
Previous IDs: | transcript_fac2; |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Finn RD |
Number in seed: | 11 |
Number in full: | 8720 |
Average length of the domain: | 70.60 aa |
Average identity of full alignment: | 26 % |
Average coverage of the sequence by the domain: | 29.95 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 71 | ||||||||||||
Family (HMM) version: | 20 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Interactions
There are 7 interactions for this family. More...
RNA_pol_Rpb2_1 TFIIB RNA_pol_Rpb2_6 HSV_VP16_C TBP RNA_pol_Rpb1_1 TBPStructures
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the TFIIB domain has been found. There are 88 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.
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