Protein Family Models

This family is closely related to the Pfam:PF09084 family. (from Pfam)

Date:

2024-08-14

This is a family of periplasmic proteins which are part of the transport system for alkylphosphonate uptake. (from Pfam)

Date:

2024-08-14

This family contains the NMT1 and THI5 proteins. These proteins are proposed to be required for the biosynthesis of the pyrimidine moiety of thiamine [1][2][3]. They are regulated by thiamine [2]. The protein adopts a fold related to the periplasmic binding protein (PBP) family. Both pyridoxal-5'-phosphate (PLP) and an iron atom are bound to the protein suggesting numerous residues of the active site necessary for HMP-P biosynthesis. The yeast protein is a dimer and, although exceptionally using PLP as a substrate, has notable similarities with enzymes dependent on this molecule as a cofactor [4]. [1]. 12271461. Functional analysis of yeast gene families involved in metabolism of vitamins B1 and B6. Rodriguez-Navarro S, Llorente B, Rodriguez-Manzaneque MT, Ramne A, Uber G, Marchesan D, Dujon B, Herrero E, Sunnerhagen P, Perez-Ortin JE;. Yeast. 2002;19:1261-1276. [2]. 2358444. nmt1 of fission yeast. A highly transcribed gene completely repressed by thiamine. Maundrell K;. J Biol Chem. 1990;265:10857-10864. [3]. 12777485. The THI5 gene family of Saccharomyces cerevisiae: distribution of homologues among the hemiascomycetes and functional redundancy in the aerobic biosynthesis of thiamin from pyridoxine. Wightman R, Meacock PA;. Microbiology. 2003;149:1447-1460. [4]. 23048037. The last piece in the vitamin B1 biosynthesis puzzle: structural and functional insight into yeast 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate (HMP-P) synthase. Coquille S, Roux C, Fitzpatrick TB, Thore S;. J Biol Chem. 2012;287:42333-42343. (from Pfam)

Date:

2024-10-16

Part of a high affinity multicomponent binding-protein-dependent transport system involved in bacterial osmoregulation. This domain is often fused to the permease component of the transporter complex. Family members are often integral membrane proteins or predicted to be attached to the membrane by a lipid anchor. Glycine betaine is involved in protection from high osmolarity environments for example in Bacillus subtilis [1]. The family member OpuBC is closely related, and involved in choline transport. Choline is necessary for the biosynthesis of glycine betaine [2]. L-carnitine is important for osmoregulation in Listeria monocytogenes. Family also contains proteins binding l-proline (ProX), histidine (HisX) and taurine (TauA). [1]. 7622480. OpuA, an osmotically regulated binding protein-dependent transport system for the osmoprotectant glycine betaine in Bacillus subtilis. Kempf B, Bremer E;. J Biol Chem 1995;270:16701-16713. [2]. 10216873. Two evolutionarily closely related ABC transporters mediate the uptake of choline for synthesis of the osmoprotectant glycine betaine in Bacillus subtilis. Kappes RM, Kempf B, Kneip S, Boch J, Gade J, Meier-Wagner J, Bremer E;. Mol Microbiol 1999;32:203-216. [3]. 11055912. Identification and characterization of an ATP binding cassette L-carnitine transporter in Listeria monocytogenes. Fraser KR, Harvie D, Coote PJ, O'Byrne CP;. Appl Environ Microbiol 2000;66:4696-4704. (from Pfam)

Date:

2024-10-16

Members of this family are substrate-binding periplasmic proteins of ABC transporters. This subfamily includes SsuA, a member of a transporter operon needed to obtain sulfur from aliphatic sulfonates. Related proteins outside the scope of this HMM include taurine (NH2-CH2-CH2-S03H) binding proteins, the probable sulfate ester binding protein AtsR, and the probable aromatic sulfonate binding protein AsfC. All these families make sulfur available when Cys and sulfate levels are low. Please note that phylogenetic analysis by neighbor-joining suggests that a number of sequences belonging to this family have been excluded because of scoring lower than taurine-binding proteins.

Date:

2024-06-14