HMM Summary Page: TIGR03304

Functionouter membrane insertion C-terminal signal
Trusted Cutoff10.00
Domain Trusted Cutoff10.00
Noise Cutoff7.50
Domain Noise Cutoff7.50
Isology Typedomain
HMM Length10
Gene Ontology TermGO:0019867: outer membrane cellular_component
AuthorHaft DH
Entry DateFeb 6 2007 12:41PM
Last ModifiedFeb 14 2011 3:27PM
CommentThis hidden Markov model detects a 10-residue targeting sequence common to beta-barrel outer membrane proteins (OMP) that rely on Omp85-like proteins for insertion into the outer membrane. Hits should be trusted if they include the last amino acid of a protein sequence that occurs in Gram-negative bacteria. It has been noted that Omp85 target sequences differ somewhat by species, while this model works generally for most Proteobacteria. For a given species, an iterated approach, in which trusted matches to this model become the basis of a new model that finds additional OMP signals, is recommended. Note that this model does not work well under HMMER3, but works better under HMMER2 when the model is built with the -g option from the seed alignment.
ReferencesRN [1] RM PMID: 17090219 RT Assembly factor Omp85 recognizes its outer membrane protein substrates by a species-specific C-terminal motif. RA Robert V, Volokhina EB, Senf F, Bos MP, Van Gelder P, Tommassen J RL PLoS Biol. 2006 Nov;4(11):e377.
Genome PropertyGenProp0725: outer membrane protein assembly complex (HMM)