+Most proteins are composed of one or more conserved functional regions called +domains. This track shows the high-quality, manually-curated + +Pfam-A +domains found in transcripts located in the GENCODE Genes track by the software HMMER3. +
+ ++This track follows the display conventions for +gene +tracks. +
+ ++The sequences from the knownGenePep table (see +GENCODE Genes description page) +are submitted to the set of Pfam-A HMMs which annotate regions within the +predicted peptide that are recognizable as Pfam protein domains. These regions +are then mapped to the transcripts themselves using the + +pslMap utility. A complete shell script log for every version of UCSC genes can be found in +our GitHub repository under + +hg/makeDb/doc/ucscGenes, e.g. + +mm10.knownGenes17.csh is for the database mm10 and version 17 of UCSC known genes. +
+ ++Of the several options for filtering out false positives, the "Trusted cutoff (TC)" +threshold method is used in this track to determine significance. For more information regarding +thresholds and scores, see the HMMER +documentation and +results interpretation pages. +
+ ++Note: There is currently an undocumented but known HMMER problem which results in lessened +sensitivity and possible missed searches for some zinc finger domains. Until a fix is released for +HMMER /PFAM thresholds, please also consult the "UniProt Domains" subtrack of the UniProt +track for more comprehensive zinc finger annotations. +
+ ++pslMap was written by Mark Diekhans at UCSC. +
+ ++Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, +Forslund K et al. +The Pfam protein families database. +Nucleic Acids Res. 2010 Jan;38(Database issue):D211-22. +PMID: 19920124; PMC: PMC2808889 +