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SUPFAM specifications

Information


Unique identifier OMICS_22828
Name SUPFAM
Restrictions to use None
Community driven No
Data access Browse
User data submission Not allowed
Maintained No

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Publications for SUPFAM

SUPFAM citations

 (50)
library_books

Comparative systems analysis of the secretome of the opportunistic pathogen Aspergillus fumigatus and other Aspergillus species

2018
Sci Rep
PMCID: 5919931
PMID: 29700415
DOI: 10.1038/s41598-018-25016-4

[…] ttp://www.jcvi.org/cgi-bin/tigrfams/index.cgi), SFLD (http://sfld.rbvi.ucsf.edu/django/), SMART (http://smart.embl-heidelberg.de/), CDD(https://www.ncbi.nlm.nih.gov/cdd), PROSITE, SUPERFAMILY (http://supfam.org/SUPERFAMILY/), PRINTS (http://130.88.97.239/PRINTS/index.php), PANTHER (http://www.pantherdb.org/), COILS (https://embnet.vital-it.ch/software/COILS_form.html) and MobiDB-lite (http://prote […]

library_books

The genomic tool kit of the truffle Tuber melanosporum programmed cell death

2018
PMCID: 5841409
PMID: 29531829
DOI: 10.1038/s41420-017-0019-0

[…] blast.html; Interpro: https://www.ebi.ac.uk/interpro/; Pfam: http://www.sanger.ac.uk/Software/Pfam/; Prosite: http://www.expasy.org/prosite/; Uniprot: http://www.pir.uniprot.org/; Superfamily: http://supfam.cs.bris.ac.uk/SUPERFAMILY/), as well as genome and EST databases (NCBI: http://www.ncbi.nlm.nih.gov/; Yeast database: http://ycelldeath.com/) were searched for PCD-related sequences in order to […]

library_books

Expression and specificity of a chitin deacetylase from the nematophagous fungus Pochonia chlamydosporia potentially involved in pathogenicity

2018
Sci Rep
PMCID: 5794925
PMID: 29391415
DOI: 10.1038/s41598-018-19902-0

[…] (http://web.expasy.org/translate). The multi-domain structure of PcCDA protein sequence was analysed using the online bioinformatic tools Prosite (http://prosite.expasy.org/) and Superfamily (http://supfam.org/SUPERFAMILY/). Signal peptide (http://www.cbs.dtu.dk/services/SignalP/), transmembrane helices (http://www.cbs.dtu. dk/services/TMHMM/), N-glycosylation (http://www.cbs.dtu.dk/services/NetN […]

library_books

Prokaryotic and Highly Repetitive WD40 Proteins: A Systematic Study

2017
Sci Rep
PMCID: 5587647
PMID: 28878378
DOI: 10.1038/s41598-017-11115-1

[…] tures in WD40 proteins. Concerning that these criteria may have been too strict, we also included all the other potential WD40 proteins supported by the annotations of SMART, Pfam, PROSITE, InterPro, SUPFAM, and Gene3D. The protein sequences that passed the pre-screening were submitted to the WDSP program, which predicted the locations of each repeat, the hydrogen bond network positions, and the c […]

library_books

Finding a partner in the ocean: molecular and evolutionary bases of the response to sexual cues in a planktonic diatom

2017
New Phytol
PMCID: 5485032
PMID: 28429538
DOI: 10.1111/nph.14557

[…] hidden Markov models (HMMs) of protein families classified in the SUPERFAMILY database (Wilson et al., ). The comparison was performed using Perl scripts provided by the SUPERFAMILY database (http://supfam.cs.bris.ac.uk/SUPERFAMILY/howto_use_models.html) and the hmmscan binary from HMMER3 (Eddy, ). For each SUPERFAMILY present in P. multistriata, a Z‐score was calculated using the following formu […]

library_books

Growth rate, transmission mode and virulence in human pathogens

2017
PMCID: 5352820
PMID: 28289261
DOI: 10.1098/rstb.2016.0094

[…] of data arising due to common ancestry between pathogen species, we generated a phylogeny of the species in our dataset using the Structural Classification of Proteins (SCOP) database v. 1.75 (http://supfam.org/SUPERFAMILY/cgi-bin/genome_names.cgi). SCOP constructs phylogenetic trees on the basis of structural protein similarities derived from whole genome sequencing. Where more than one genome fo […]

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SUPFAM institution(s)
Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India; National Centre for Biological Sciences, Tata Institute of Fundamental Research, UAS-GKVK campus, Bangalore, India
SUPFAM funding source(s)
Supported by CSIR, the Wellcome Trust, London, International Senior Fellowship in Biomedical Sciences and the Department of Biotechnology, New Delhi.

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