Summary: Putative helicase
Putative helicase Provide feedback
Some members of this family have been annotated as helicases.
Tian QB, Ohnishi M, Tabuchi A, Terawaki Y; , Biochem Biophys Res Commun 1996;220:280-284.: A new plasmid-encoded proteic killer gene system: cloning, sequencing, and analyzing hig locus of plasmid Rts1. PUBMED:8645296 EPMC:8645296
Janosi L, Yonemitsu H, Hong H, Kaji A; , J Mol Biol 1994;242:45-61.: Molecular cloning and expression of a novel hydroxymethylcytosine-specific restriction enzyme (PvuRts1I) modulated by glucosylation of DNA. PUBMED:8078071 EPMC:8078071
Larbig KD, Christmann A, Johann A, Klockgether J, Hartsch T, Merkl R, Wiehlmann L, Fritz HJ, Tummler B; , J Bacteriol 2002;184:6665-6680.: Gene islands integrated into tRNA(Gly) genes confer genome diversity on a Pseudomonas aeruginosa clone. PUBMED:12426355 EPMC:12426355
Beaber JW, Hochhut B, Waldor MK; , J Bacteriol 2002;184:4259-4269.: Genomic and functional analyses of SXT, an integrating antibiotic resistance gene transfer element derived from Vibrio cholerae. PUBMED:12107144 EPMC:12107144
Street LM, Harley MJ, Stern JC, Larkin C, Williams SL, Miller DL, Dohm JA, Rodgers ME, Schildbach JF; , Biochim Biophys Acta 2003;1646:86-99.: Subdomain organization and catalytic residues of the F factor TraI relaxase domain. PUBMED:12637015 EPMC:12637015
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR011119
The members of this family are restricted to the proteobacteria. Some members have been annotated as helicase, conjugative relaxase or nickase. The majority contain an HD domain, which is found in a superfamily of enzymes with a predicted or known phosphohydrolase activity. These enzymes appear to be involved in the nucleic acid metabolism, signal transduction and possibly other functions in bacteria.
- 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
|Number in seed:||21|
|Number in full:||472|
|Average length of the domain:||271.90 aa|
|Average identity of full alignment:||31 %|
|Average coverage of the sequence by the domain:||46.79 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||6|
|Download:||download the raw HMM for this family|
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a FASTA-format file
- 0 sequences
- 0 species
How the sunburst is generated
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The tree shows the occurrence of this domain across different species. More...
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