Predicting transmembrane protein topology with a hidden markov model: application to complete genomes11Edited by F. Cohen

Krogh, Anders; Larsson, Birgit; Heijne, Gunnar von; Sonnhammer, Erik L. L.

doi:10.1006/jmbi.2000.4315

Cited by 11,405 publications

(9,394 citation statements)

References 35 publications

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“…The transmembrane domain that immediately follows the short cytoplasmic sequence is variable in sequence among subtypes, but in all subtypes is predicted to form a transmembrane helix encompassing amino acids 7–29 when analyzed by the highly reliable program TMHMM 13,14 . The transmembrane sequence has a combined signal peptide-anchor function of directing the NA across the endoplasmic reticulum and also retaining it in the membrane.…”

Section: Neuraminidase Structural Domainsmentioning

confidence: 99%

Influenza neuraminidase

Air

2011

Influenza Resp Viruses

208

216

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Influenza neuraminidase is the target of two licensed antivirals that have been very successful, with several more in development. However, neuraminidase has been largely ignored as a vaccine target despite evidence that inclusion of neuraminidase in the subunit vaccine gives increased protection. This article describes current knowledge on the structure, enzyme activity and antigenic significance of neuraminidase.

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Section: Neuraminidase Structural Domainsmentioning

confidence: 99%

Influenza neuraminidase

Air

2011

Influenza Resp Viruses

208

216

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“…2A). The predicted protein has 10 transmembrane domains (data not shown) according to TMHMM Server v. 2.0 [30]. Sequence comparison shows the highest similarity in the two regions containing NBDs of PRP1 with others PGPs from the MRP-like family of Leishmania spp.…”

Section: Molecular Characterization and Analysis Of The Prp1 Genementioning

confidence: 99%

Functional genetic identification of PRP1, an ABC transporter superfamily member conferring pentamidine resistance in Leishmania major

Coelho¹,

Beverley

Cotrim³

2003

Molecular and Biochemical Parasitology

123

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“…Membrane proteins were initially predicted based on positive predictions as lipoproteins, using LipoP 1.0 [52], and PRED-LIPO [53]. Non-lipoproteins were then analyzed for transmembrane domain prediction using TMHMM v.2.0 [54], Phobius [55], HMMTOP [56], CW-PRED [57], and HMM-TM [58]. Non-transmembrane proteins were further analyzed for subcellular localization using PSORTb v. 3.0.2 [59], iLoc-Gpos [60], and CELLO v.2.5 [61].…”

Section: Methodsmentioning

confidence: 99%

Comparative proteomics of twoMycoplasma hyopneumoniaestrains andMycoplasma flocculareidentified potential porcine enzootic pneumonia determinants

et al. 2018

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Mycoplasma hyopneumoniae and Mycoplasma flocculare are genetically similar bacteria, which coinhabit the porcine respiratory tract. These mycoplasmas share most of the known virulence factors, but, while M. hyopneumoniae causes porcine enzootic pneumonia (PEP), M. flocculare is a commensal species. To identify potential PEP determinants and provide novel insights on mycoplasma-host interactions, the whole cell proteomes of two M. hyopneumoniae strains, one pathogenic (7448) and other non-pathogenic (J), and M. flocculare were compared. A cell fractioning approach combined with mass spectrometry (LC-MS/MS) proteomics was used to analyze cytoplasmic and surface-enriched protein fractions. Average detection of ~ 50% of the predicted proteomes of M. hyopneumoniae 7448 and J, and M. flocculare was achieved. Many of the identified proteins were differentially represented in M. hyopneumoniae 7448 in comparison to M. hyopneumoniae J and M. flocculare, including potential PEP determinants, such as adhesins, proteases, and redox-balancing proteins, among others. The LC-MS/MS data also provided experimental validation for several genes previously regarded as hypothetical for all analyzed mycoplasmas, including some coding for proteins bearing virulence-related functional domains. The comprehensive proteome profiling of two M. hyopneumoniae strains and M. flocculare provided tens of novel candidates to PEP determinants or virulence factors, beyond those classically described.

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Predicting transmembrane protein topology with a hidden markov model: application to complete genomes11Edited by F. Cohen

Cited by 11,405 publications

References 35 publications

Influenza neuraminidase

Influenza neuraminidase

Functional genetic identification of PRP1, an ABC transporter superfamily member conferring pentamidine resistance in Leishmania major

Comparative proteomics of twoMycoplasma hyopneumoniaestrains andMycoplasma flocculareidentified potential porcine enzootic pneumonia determinants

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