HMM Summary Page: TIGR00358

FunctionVacB and RNase II family 3'-5' exoribonucleases
Trusted Cutoff368.60
Domain Trusted Cutoff368.60
Noise Cutoff139.00
Domain Noise Cutoff139.00
Isology Typesuperfamily
EC Number3.1.13.1
HMM Length657
Mainrole CategoryTranscription
Subrole CategoryDegradation of RNA
Gene Ontology TermGO:0006401: RNA catabolic process biological_process
GO:0016896: exoribonuclease activity, producing 5'-phosphomonoesters molecular_function
AuthorHaft DH
Entry DateApr 20 1999 2:03PM
Last ModifiedFeb 14 2011 3:27PM
CommentThis HMM is defined to identify a pair of paralogous 3-prime exoribonucleases in E. coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterized originally as required for the expression of virulence genes, but is now recognized as the exoribonuclease RNase R (Rnr). Its paralog in E. coli and H. influenzae is designated exoribonuclease II (Rnb). Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cutoff to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3-prime exoribonucleases.
ReferencesSE TIGR GA hmmls AL clustalw, belvu DR HAMAP; MF_01036; 50 of 51