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Outer membrane protein prediction and classification
Michael Remmert - Dep. of Protein Evolution at the Max-Planck Institute for Developmental Biology
HHomp is a tool available for the prediction and classification of outer membrane proteins.
Outer membrane proteins (OMPs) are the transmembrane proteins found in the outer membranes of Gram-negative bacteria, mitochondria and plastids. HHomp identifies proteins as OMPs by detecting their homologous relationships to known OMPs using sequence similarity. Given an input sequence, HHomp builds a profile hidden Markov model (HMM) and compares it with an OMP database by pairwise HMM comparison, integrating OMP predictions by PROFtmb. A crucial ingredient is the OMP database, which contains profile HMMs for over 20 000 putative OMP sequences.
The HHomp webserver consists of an OMP prediction and searching interface and a browsing interface for the underlying OMP database. With the prediction interface, the user can search the database with a query protein sequence. Various parameters for alignment building and searching can be modified (explained in the online help). After a few minutes, the server returns a graphical overview of the matched regions, a detailed and annotated list of matched OMP database HMMs and the corresponding alignments. An alternative view of the alignments can be selected, in which the columns of the aligned profile HMMs are represented as coloured histograms. The detected OMP HMMs are linked to the browsing interface with detailed description pages for the OMP clusters, containing alignments and 3D models for the TM domain if available.
Download HHomp & OMP database: ftp://ftp.tuebingen.mpg.de/pub/protevo/HHomp
See Help:References for how to manage references in EcoliWiki.
- Remmert, M et al. (2009) HHomp--prediction and classification of outer membrane proteins. Nucleic Acids Res. 37 W446-51 PubMed