HMM Summary Page: TIGR03431

Functionphosphonate ABC transporter, periplasmic phosphonate binding protein
Gene SymbolphnD
Trusted Cutoff261.10
Domain Trusted Cutoff261.10
Noise Cutoff230.15
Domain Noise Cutoff230.15
Isology Typeequivalog
HMM Length288
AuthorSelengut J
Entry DateJun 14 2007 10:33AM
Last ModifiedFeb 14 2011 3:27PM
CommentThis model is a subset of the broader subfamily of phosphate/phosphonate binding protein ABC transporter components, TIGR01098. In this model all members of the seed have support from genomic context for association with pathways for the metabolims of phosphonates, particularly the C-P lyase system, GenProp0232. This model includes the characterized phnD gene from E. coli [1,2]. Note that this model does not identify all phnD-subfamily genes with evident phosphonate context, but all sequences above the trusted context may be inferred to bind phosphonate compounds even in the absence of such context. Furthermore, there is ample evidence to suggest that many other members of the TIGR01098 subfamily have a different primary function.
ReferencesRN [1] RM PMID:2155230 RT Molecular biology of carbon-phosphorus bond cleavage. Cloning and sequencing of the phn (psiD) genes involved in alkylphosphonate uptake and C-P lyase activity in Escherichia coli B. RA Chen CM, Ye QZ, Zhu ZM, Wanner BL, Walsh CT RL J Biol Chem. 1990 Mar 15;265(8):4461-71. RN [2] RM PMID:16751609 RT Identification of cognate ligands for the Escherichia coli phnD protein product and engineering of a reagentless fluorescent biosensor for phosphonates. RA Rizk SS , Cuneo MJ , Hellinga HW RL Protein Sci. 2006 Jul;15(7):1745-51. Epub 2006 Jun 2.
Genome PropertyGenProp0232: phosphonates C-P lyase system (HMM)
GenProp0236: phosphonates ABC transport (HMM)