Summary: Putative helicase
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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.
Putative helicase Provide feedback
Some members of this family have been annotated as helicases.
Literature references
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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
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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
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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
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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
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Csitkovits VC, Zechner EL; , J Biol Chem 2003;278:48696-48703.: Extent of Single-stranded DNA Required for Efficient TraI Helicase Activity in Vitro. PUBMED:14506243 EPMC:14506243
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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
Internal database links
SCOOP: | HD HDOD |
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.
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
Alignments
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...
View options
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 (9) |
Full (405) |
Representative proteomes | UniProt (3866) |
NCBI (7833) |
Meta (36) |
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RP15 (33) |
RP35 (148) |
RP55 (378) |
RP75 (956) |
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Jalview | |||||||||
HTML | |||||||||
PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
Format an alignment
Download options
We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.
Seed (9) |
Full (405) |
Representative proteomes | UniProt (3866) |
NCBI (7833) |
Meta (36) |
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RP15 (33) |
RP35 (148) |
RP55 (378) |
RP75 (956) |
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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
HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...
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
This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.
Curation
Seed source: | Manual |
Previous IDs: | none |
Type: | Family |
Sequence Ontology: | SO:0100021 |
Author: |
Studholme DJ |
Number in seed: | 9 |
Number in full: | 405 |
Average length of the domain: | 272.90 aa |
Average identity of full alignment: | 29 % |
Average coverage of the sequence by the domain: | 48.30 % |
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: | 325 | ||||||||||||
Family (HMM) version: | 12 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Colour assignments
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Selections
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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...
Tree controls
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