The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.
This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.
Ssl1-like Provide feedback
Ssl1-like proteins are 40kDa subunits of the Transcription factor II H complex.
Wang Z, Buratowski S, Svejstrup JQ, Feaver WJ, Wu X, Kornberg RD, Donahue TF, Friedberg EC; , Mol Cell Biol 1995;15:2288-2293.: The yeast TFB1 and SSL1 genes, which encode subunits of transcription factor IIH, are required for nucleotide excision repair and RNA polymerase II transcription. PUBMED:7891722 EPMC:7891722
Internal database links
|SCOOP:||VWA_CoxE DUF1194 DUF2798 VWA_2 VWA_3 TrpP|
|Similarity to PfamA using HHSearch:||VWA VWA_2|
External database links
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
- the number of residues in the sequence
- the Pfam graphic itself.
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We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
- Pfam viewer
- an HTML-based viewer that uses DAS to retrieve alignment fragments on request
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
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Note: You can also download the data file for the tree.
Curation and family details
|Seed source:||Pfam-B_13499 (release 7.3);|
|Author:||Wood V, Finn RD|
|Number in seed:||6|
|Number in full:||716|
|Average length of the domain:||175.00 aa|
|Average identity of full alignment:||37 %|
|Average coverage of the sequence by the domain:||44.00 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||10|
|Download:||download the raw HMM for this family|
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Change the size of the sunburst
selected sequences to HMM
a FASTA-format file
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How the sunburst is generated
Colouring and labels
Anomalies in the taxonomy tree
Missing taxonomic levels
Unmapped species names
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The tree shows the occurrence of this domain across different species. More...
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