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Protocols

TMpred specifications

Information


Unique identifier OMICS_03883
Name TMpred
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Kay Hofmann

Publication for TMpred

TMpred citations

 (554)
library_books

A double helical motif in OCIAD2 is essential for its localization, interactions and STAT3 activation

2018
Sci Rep
PMCID: 5943604
PMID: 29743632
DOI: 10.1038/s41598-018-25667-3

[…] of these proteins corresponding to Uniprot IDs Q6NYD7, Q9CRD0, Q9NX40, Q5RHX2, Q9D8W7 and Q56VL3 were fed as the input. Hydrophobicity plots for mouse OCIAD1 and OCIAD2 sequences were predicted using TmPred (http://www.ch.embnet.org/software/TMPRED_form.html) web server with the default settings. Analysis of transcription factor binding sites in OCIAD1 and OCIAD2 was done using tools such as Genom […]

library_books

Clathrin mediated endocytosis is a candidate entry sorting mechanism for Bombyx mori cypovirus

2018
Sci Rep
PMCID: 5940776
PMID: 29740149
DOI: 10.1038/s41598-018-25677-1

[…] The membrane-spanning regions and orientations of the clathrin heavy chain (GenBank accession No. NP_001136443.1) and AP-1 (GenBank accession No. AFN25815.1) proteins were predicted using the TMpred program (https://embnet.vital-it.ch/software/TMPRED_form.html). The results showed that three and one putative transmembrane helices were found in silkworm clathrin heavy chain and AP-1, respec […]

library_books

One prophage WO gene rescues cytoplasmic incompatibility in Drosophila melanogaster

2018
Proc Natl Acad Sci U S A
PMCID: 5948995
PMID: 29686091
DOI: 10.1073/pnas.1800650115

[…] lasm, cytoplasmic membrane, periplasm, outer membrane, or extracellular space. A localization score is provided for each location, with scores of 7.5 or greater considered probable localizations. The TMpred web server () was used to predict transmembrane helices in wMel CifA. TMpred scores were generated for transmembrane helices spanning from inside-to-outside (i-o) and outside-to-inside (o-i), a […]

library_books

Clostridium sordellii outer spore proteins maintain spore structural integrity and promote bacterial clearance from the gastrointestinal tract

2018
PLoS Pathog
PMCID: 5927469
PMID: 29668758
DOI: 10.1371/journal.ppat.1007004

[…] nction Assignment server (FFAS, http://ffas.sanfordburnham.org [] failed to identify any known protein folds, nor were any conserved domains identified. No transmembrane domains were identified using TMpred (https://embnet.vital-it.ch/software/TMPRED_form.html) []. Blast and FFAS analysis of CsB showed that this protein did not share homology with any characterised protein. The BLAST analysis of t […]

call_split

The Zinc Finger Thylakoid Membrane Protein FIP Is Involved With Abiotic Stress Response in Arabidopsis thaliana

2018
Front Plant Sci
PMCID: 5915565
PMID: 29720990
DOI: 10.3389/fpls.2018.00504
call_split See protocol

[…] Arabidopsis FIP and FtsH sequences were obtained from TAIR. Transmembrane domains were predicted by TMPred.Data from the AtGenExpress Project () is part of the TAIR database (The Arabidopsis Information Resource, see foot note text 1) was analyzed with the package R/Bioconductor () and normalized by […]

call_split

A Gossypium hirsutum GDSL lipase/hydrolase gene (GhGLIP) appears to be involved in promoting seed growth in Arabidopsis

2018
PLoS One
PMCID: 5886685
PMID: 29621331
DOI: 10.1371/journal.pone.0195556
call_split See protocol

[…] oinformatics Institute, Cambridge, UK) with default settings. The online software of conserved domains (CD) on the NCBI website (https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi), and SignalP and TMpred on the ExPASy website (http://www.expasy.org/) were used for prediction analyses of conserved domains, signal peptides and transmembrane helixes, respectively. […]


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