Protein Family Models

Date:

2024-08-14

This domain family is found in bacteria, archaea and eukaryotes, and is approximately 90 amino acids in length. The family is found in association with Pfam:PF07715 and Pfam:PF00593. [1]. 10986238. Characterization of four outer membrane proteins involved in binding starch to the cell surface of Bacteroides thetaiotaomicron. Shipman JA, Berleman JE, Salyers AA;. J Bacteriol. 2000;182:5365-5372. [2]. 11717282. Biochemical analysis of interactions between outer membrane proteins that contribute to starch utilization by Bacteroides thetaiotaomicron. Cho KH, Salyers AA;. J Bacteriol 2001;183:7224-7230. (from Pfam)

Date:

2024-10-16

This is a short domain found at the N-terminus of the Secretins of the bacterial type II/III secretory system as well as the TonB-dependent receptor proteins. These proteins are involved in TonB-dependent active uptake of selective substrates. (from Pfam)

Date:

2024-08-14

The Plug domain has been shown to be an independently folding subunit of the TonB-dependent receptors ([1]). It acts as the channel gate, blocking the pore until the channel is bound by ligand. At this point it under goes conformational changes opens the channel. [1]. 15111112. The plug domain of a neisserial TonB-dependent transporter retains structural integrity in the absence of its transmembrane beta-barrel. Oke M, Sarra R, Ghirlando R, Farnaud S, Gorringe AR, Evans RW, Buchanan SK;. FEBS Lett 2004;564:294-300. (from Pfam)

Date:

2024-10-16

SusC/RagA family TonB-linked outer membrane protein

Date:

2018-12-13

This model describes a 31-residue signature region of the SusC/RagA family of outer membrane proteins from the Bacteriodetes. While many TonB-dependent outer membrane receptors are associated with siderophore import, this family seems to include generalized nutrient receptors that may convey fairly large oligomers of protein or carbohydrate. This family occurs in high copy numbers in the most abundant species of the human gut microbiome.

Date:

2019-09-10

This model describes a distinctive clade among the TonB-linked outer membrane proteins (OMP). Members of this family are restricted to the Bacteriodetes lineage (except for Gemmatimonas aurantiaca T-27 from the novel phylum Gemmatimonadetes) and occur in high copy numbers, with over 100 members from Bacteroides thetaiotaomicron VPI-5482 alone. Published descriptions of members of this family are available for RagA from Porphyromonas gingivalis, SusC from Bacteroides thetaiotaomicron, and OmpW from Bacteroides caccae. Members form pairs with members of the SusD/RagB family (PF07980). Transporter complexes including these outer membrane proteins are likely to import large degradation products of proteins (e.g. RagA) or carbohydrates (e.g. SusC) as nutrients, rather than siderophores.

Date:

2024-07-01