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Protocols

Pfam specifications

Information


Unique identifier OMICS_01696
Name Pfam
Alternative name PFAM-A
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Version 32.0
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/Pfam

Maintainers


  • person_outline Robert Finn
  • person_outline Pfam Team

Additional information


http://pfam.xfam.org/help

Publications for Pfam

Pfam citations

 (5488)
library_books

AID/APOBEC like cytidine deaminases are ancient innate immune mediators in invertebrates

2018
Nat Commun
PMCID: 5956068
PMID: 29769532
DOI: 10.1038/s41467-018-04273-x

[…] rg) reveals that many of the coelomocyte transcripts do not correlate with known gene models. Notably, two of these novel transcripts are predicted to encode proteins that contain an APOBEC-N domain (pfam08210), and are hereafter referred to as S. purpuratus AID-like 1 and 4a (SpAIDL1 and SpAIDL4a; Genbank MH106904 and MH106905; Fig. ). This domain, which is present in all vertebrate AID/APOBEC CD […]

call_split

Endocytosis mediated siderophore uptake as a strategy for Fe acquisition in diatoms

2018
Sci Adv
PMCID: 5955625
PMID: 29774236
DOI: 10.1126/sciadv.aar4536
call_split See protocol

[…] kept only sequences fully covered by the multiple sequence alignment produced by the phylogenetic analysis, because ISIP1 does not belong to a particular protein family in any pHMM database, such as PFAM. We used the pHMM along with the software package HMMER () to retrieve all sequences from the Tara Oceans metagenome and metatranscriptome that matched our model of ISIP1. Only sequences taxonomi […]

call_split

Genomic and functional characterisation of IncX3 plasmids encoding blaSHV 12 in Escherichia coli from human and animal origin

2018
Sci Rep
PMCID: 5955891
PMID: 29769695
DOI: 10.1038/s41598-018-26073-5
call_split See protocol

[…] utative open reading frames (ORFs) were identified by RAST version 2.0 and manually curated when necessary. BLASTP analyses of the putative ORFs against the NCBI non-redundant proteins (NR) database, Pfam, and Interpro scan were used to assess their putative functions by identification of structural features and motifs,. ResFinder (version 2.1), PlasmidFinder (version 1.3) and ISfinder were used t […]

library_books

Comparative Genomics Reveals the Core Gene Toolbox for the Fungus Insect Symbiosis

2018
MBio
PMCID: 5954228
PMID: 29764946
DOI: 10.1128/mBio.00636-18

[…] e Funannotate v0.6.2 pipeline (https://github.com/nextgenusfs/funannotate), employing tools of Augustus (), GeneMark.hmm-ES (), and EVM (). Gene function was inferred from matches to the databases of Pfam (), Merops (), CAZy (), InterProScan (), and Swiss-Prot (). Product descriptions were assigned with homologues with 60% similarity across 60% of the protein length (). CEGMA v2.4.010312 was used […]

library_books

Discovering novel SNPs that are correlated with patient outcome in a Singaporean cancer patient cohort treated with gemcitabine based chemotherapy

2018
BMC Cancer
PMCID: 5948914
PMID: 29751792
DOI: 10.1186/s12885-018-4471-x

[…] with the SIFT score equal to or less than 0.05 (Additional file : Table S2). The fourth criterion is to check if the SNPs lie on any functional domain. To do this, we retrieved HMMER results against Pfam and SMART using “Prim-Seq-An w/Pfam” analysis on ANNOTATOR and found that 35 out of the 77 SNPs are located in a functional domain of their proteins. The final criterion was to investigate whethe […]

library_books

Genome wide analysis of differentially expressed profiles of mRNAs, lncRNAs and circRNAs during Cryptosporidium baileyi infection

2018
BMC Genomics
PMCID: 5946474
PMID: 29747577
DOI: 10.1186/s12864-018-4754-2

[…] Four analytic tools, namely coding-non-coding-index (CNCI) [], coding potential calculator (CPC) [], phylogenetic codon substitution frequency (PhyloCSF) [] and Pfam-scan [], were used to effectively distinguish protein-coding and non-coding sequences. Ultimately, the transcripts predicted with coding potential by any of the four tools were filtered out, and […]


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Pfam institution(s)
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, UK; HHMI, Harvard University, Cambridge, MA, USA; Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden; Department of Biomedical Sciences, University of Padua, Padova, Italy; Department of Engineering, Pontificia Universidad Catolica del Peru, Lima, Peru
Pfam funding source(s)
Supported by European Union’s Horizon 2020 research and innovation programme [654039]; the Wellcome Trust [108433/Z/15/Z]; the Biotechnology and Biosciences Research Council [BB/L024136/1]; the European Molecular Biology Laboratory core funds; the European Cooperation in Science and Technology COST Action [BM1405 NGP-net]; the National Human Genome Research Institute of the US National Institutes of Health [R01-HG009116].

Pfam review

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Amr Galal

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Dataset
with a huge database pfam is very good and important tool for protein family study