2006
DOI: 10.1093/nar/gkj149
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Pfam: clans, web tools and services

Abstract: Pfam is a database of protein families that currently contains 7973 entries (release 18.0). A recent development in Pfam has enabled the grouping of related families into clans. Pfam clans are described in detail, together with the new associated web pages. Improvements to the range of Pfam web tools and the first set of Pfam web services that allow programmatic access to the database and associated tools are also presented. Pfam is available on the web in the UK (), the USA (), France () and Sweden ().

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Cited by 2,098 publications
(1,697 citation statements)
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“…For example, the tool SuperFamily only uses seeds with solved structure, while Pfam starts with any recognizable domain 34, 35. Tools also differ in the curation of the profiles obtained, with Pfam using human intervention to group structurally related families into clans 36. Tools also vary in the way profiles calculate the MSA.…”
Section: Profile‐sequence Tools Currently Used To Define Domainsmentioning
confidence: 99%
“…For example, the tool SuperFamily only uses seeds with solved structure, while Pfam starts with any recognizable domain 34, 35. Tools also differ in the curation of the profiles obtained, with Pfam using human intervention to group structurally related families into clans 36. Tools also vary in the way profiles calculate the MSA.…”
Section: Profile‐sequence Tools Currently Used To Define Domainsmentioning
confidence: 99%
“…This effect of BAX and hMtch2. ANT1 is a 298 amino acids long sequence composed of three tandem Mito Carr domains according to Pfam [84] here coloured in green (from amino acids 6 to 101), yellow (from 126 to 206), and red (from 206 to 297), respectively. hMtch2, with a similar length of 303 amino acids, apparently has a single middle Mito Carr domain from positions 123 to 206 (coloured in yellow).…”
Section: Ant Bax and Tbidmentioning
confidence: 99%
“…1a). Each of these domains is found in other DNA ligases, as indicated by their Pfam nomenclature (Finn et al 2006): Pfam04675 relates to a conserved N-terminal region present in many, but not all, ATP-dependent DNA ligases; Pfam01068 relates to the conserved catalytic (adenylation) domain of DNA ligases; Pfam04679 relates to a conserved C-terminal region present in many, but not all, ATP-dependent DNA ligases. Interestingly, BLAST analysis of FaLig at the NCBI database identified that eukaryotic sequences have relatively high similarity to FaLig.…”
Section: Identification Of An Atp-dependent Dna Ligase Within the Genmentioning
confidence: 99%