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TMBase specifications

Information


Unique identifier OMICS_30168
Name TMBase
Restrictions to use None
Community driven No
Data access File download
User data submission Not allowed
Maintained Yes

Maintainer


  • person_outline Kay Hofmann

TMBase citations

 (20)
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

[…] lease and deubiquitilase domains (, ). Only the deubiquitilase annotation has been functionally tested and confirmed (). Based on subcellular localization (PSORTb) and transmembrane helix predictors (TMbase), CifA is a cytoplasmic protein without transmembrane helices (Fig. S3). Codon-based and Fisher’s exact tests of neutrality demonstrate that closely related (76.2–99.8% pairwise nucleotide iden […]

library_books

Structure Based Virtual Screening Studies to Identify Novel Potential Compounds for GPR142 and Their Relative Dynamic Analysis for Study of Type 2 Diabetes

2018
PMCID: 5817085
PMID: 29492402
DOI: 10.3389/fchem.2018.00023

[…] the mechanism of ligand movement and probable binding sites, tunnels were located in the modeled structure of GPR142 using CAVER2.1 (Beneš, ; Beneš et al., ). Domain predictions were performed using TMbase (Hofmann and Stoffel, ) and GPCRHMM server (Wistrand et al., ). TMbase and GPRCRHMM algorithm were based on statistical and HMM analysis, respectively. […]

library_books

Lipoteichoic acid deficiency permits normal growth but impairs virulence of Streptococcus pneumoniae

2017
Nat Commun
PMCID: 5727136
PMID: 29233962
DOI: 10.1038/s41467-017-01720-z

[…] d-PP-linked precursor. This reaction is catalyzed by the O-antigen ligase WaaL (RfaL).TacL of S. pneumoniae may be located in the cytoplasmic membrane with nine transmembrane helices (as predicted by TMbase25; http://embnet.vital-it.ch/software/TMPRED_form.html) and a Wzy_C Pfam domain (STRING database v. 10.0). Wzy_C superfamily domains are characteristic of enzymes involved in the synthesis of O […]

call_split

Genetic evidence for a novel competence inhibitor in the industrially important Bacillus licheniformis

2017
PMCID: 5503854
PMID: 28697584
DOI: 10.1186/s13568-017-0447-5
call_split See protocol

[…] Analysis of the primary protein structure of ComI was performed with TMBASE (Hofmann and Stoffel ). Sequence analysis was performed with BioEdit 7.0.7.0. Evolutionary history was inferred using the Neighbor-Joining algorithm (Saitou and Nei ). The evolutionary distance […]

call_split

A loss of Pdxk model of Parkinson disease in Drosophila can be suppressed by Buffy

2017
BMC Res Notes
PMCID: 5468966
PMID: 28606139
DOI: 10.1186/s13104-017-2526-8
call_split See protocol

[…] lar localisation was performed by MultiLoc2 [] (https://abi.inf.uni-tuebingen.de/Services/MultiLoc2). Transmembrane domains were identified using TMpred [], a program based on statistical analysis of TMbase (http://www.ch.embnet.org/software/TMPRED_form.html). […]

library_books

Overexpression of a Plasma Membrane Localized SbSRP Like Protein Enhances Salinity and Osmotic Stress Tolerance in Transgenic Tobacco

2017
Front Plant Sci
PMCID: 5397517
PMID: 28473839
DOI: 10.3389/fpls.2017.00582

[…] rmatics). The TMpred program predicts membrane-spanning regions and their respective orientation (Figure ). The prediction was made using an amalgamation of several weight matrices for the scoring of TMbase, a database of naturally occurring transmembrane proteins. The prediction of the topology of the membrane spanning domains revealed the presence of one transmembrane domain score from 25 to 44 […]

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