Protein Family Models

Members of this family are long, repetitive, rich in apparent coiled-coil structure, variable in length, and extremely widespread in spirochetes. The name given is SpiroCoCo (Spirochete Coiled Coil). Members include BB0512 from Borrelia burgdorferi, TP0408 from Treponema pallidum, LIC_11498 from Leptospira interrogans, WP_167700059.1 from Entomospira, WP_335771792.1 from Brachyspira, etc. Long coiled-coil regions result in considerable sequence similarity (not necessarily homology) being detected with eukaryotic proteins such apolipoprotein A-IV. The model describes the rather well-conserved C-terminal region. The first 25 amino acid segment of the N-terminal region resembles transmembrane alpha-helices and therefore a signal peptide, but consistently lacks a basic residue at the start, suggesting the prevailing interpretation that most of the length of the protein is translocated through the plasma membrane and becomes extracytoplasmic may be in error. The apparent sequence similarity to bacterial chromosome segregation proteins may actually be informative about possible function.

Date:

2024-09-11

Members of this family are long, repetitive, rich in apparent coiled-coil structure, variable in length, and extremely widespread in spirochetes. The name given is SpiroCoCo (Spirochete Coiled Coil). Members include BB0512 from Borrelia burgdorferi, TP0408 from Treponema pallidum, LIC_11498 from Leptospira interrogans, WP_167700059.1 from Entomospira, WP_335771792.1 from Brachyspira, etc. Long coiled-coil regions result in considerable sequence similarity (not necessarily homology) being detected with eukaryotic proteins such apolipoprotein A-IV. The first 25 amino acid segment of the N-terminal region resembles transmembrane alpha-helices and therefore a signal peptide, but consistently lacks a basic residue at the start, suggesting the prevailing interpretation that most of the length of the protein is translocated through the plasma membrane and becomes extracytoplasmic may be in error. The apparent sequence similarity to bacterial chromosome segregation proteins may actually be informative about possible function.

Date:

2024-09-11

This roughly 80-amino acid domain belongs to the clan of ATP-binding domains with the Walker A motif (P-loop). It starts and ends with well-conserved alpha-helical regions, interrupted by a region of beta-strands that are prone to insertions of additional sequence. In a large fraction of members, the critical lysine (K) of the P-loop motif GxxGxGK[ST] is replaced by phenylalanine (F), making the function of the motif in those family members unclear. This domain tends to occur as a N-terminal domain of proteins that average over 1000 amino acids in length, such as the human protein sacsin.

Date:

2024-07-26

RcgA (Rhizobial Conjugative Gene A), from a Rhizobium favelukesii plasmid, plays an essential role in a quorum sensing-dependent conjugative transfer system. It is thought to be a transporter that allows uptake of a quorum-signaling lactone. Its partner protein, RgcR, with an alpha/beta hydrolase domain, inhibits the transfer, probably by inactivating the signaling molecule.

Date:

2024-07-15

RcgA (Rhizobial Conjugative Gene A), from a Rhizobium favelukesii plasmid, plays an essential role in a quorum sensing-dependent conjugative transfer system. It is thought to be a transporter that allows uptake of a quorum-signaling lactone. Its partner protein, RgcR, with an alpha/beta hydrolase domain, inhibits the transfer and may catabolize the signaling molecule.

Date:

2024-07-15

leucine-rich repeat (LRR) domain-containing protein may participate in protein-protein interactions

Date:

2024-04-01

alpha-2-macroglobulin is a multidomain membrane-anchored pan-peptidase inhibitor that provides protection to the cell by trapping external proteases through a covalent interaction with an activated thioester

Date:

2024-02-09

glycoside hydrolase family 97 protein such as Bacteroides thetaiotaomicron glucan 1,4-alpha-glucosidase SusB and retaining alpha-galactosidase, which hydrolyze terminal, non-reducing (1->4)-linked alpha-D-glucose and alpha-D-galactose, respectively

Date:

2024-02-09

ankyrin repeat and sterile alpha motif (SAM) domain-containing (Anks) protein similar to Homo sapiens ankyrin repeat and SAM domain-containing protein 1A/1B

Date:

2024-02-09

alpha-L-rhamnosidase cleaves the terminal nonreducing alpha-L-rhamnosyl residue from natural rhamnoglycosides

Date:

2024-02-09

voltage-dependent L-type (Long-lasting) calcium channel subunit alpha-1 is part of a multisubunit voltage-dependent calcium channel that mediates the entry of calcium ions into excitable cells and is also involved in a variety of calcium-dependent processes, including muscle contraction, hormone or neurotransmitter release, gene expression, cell motility, cell division, and cell death

Date:

2024-02-09

translation elongation factor EF1A (EF1-alpha) family protein similar to Homo sapiens eukaryotic peptide chain release factor GTP-binding subunit ERF3A that is involved in translation termination in response to the termination codons UAA, UAG and UGA

Date:

2024-02-09

glycoside hydrolase family 95 protein such as alpha-L-fucosidase, which hydrolyzes alpha-1,2-linked fucose and is involved in the degradation of fucosylated xyloglucans

Date:

2024-02-09

LITAF (lipopolysaccharide-induced tumor necrosis factor-alpha factor)-like zinc ribbon domain-containing protein similar to vertebrate cell death-inducing p53-target protein 1 that acts as an important p53/TP53-apoptotic effector

Date:

2024-02-09

DUF72 domain-containing protein adopting a TIM beta/alpha barrel fold; similar to Bacillus subtilis UPF0759 protein YunF

Date:

2024-02-09

GTPase-activating protein functions as a GTPase activator for small GTPases, similar to Ral GTPase-activating protein subunit alpha and Rap1 GTPase-activating protein 2

Date:

2024-02-09

bifunctional serine/threonine-protein kinase (STK)/formylglycine-generating enzyme family protein may catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates through the N-terminal STK domain and in the C-terminal domain, is similar to human sulfatase-modifying factor 1 (SUMF1), which oxidizes a cysteine residue in the substrate sulfatase, to an active site 3-oxoalanine residue, also called C(alpha)-formylglycine

Date:

2024-02-09

alpha/beta hydrolase family protein catalyzes the hydrolysis of substrates with different chemical composition or physicochemical properties using a nucleophile-His-acid catalytic triad

Date:

2024-02-09

glycogen synthase catalyzes the formation and elongation of the alpha-1,4-glucose backbone using ADP-glucose, a key step of glycogen/starch biosynthesis

Date:

2024-02-09

1,4-alpha-glucan-branching protein transfers a segment of a (1->4)-alpha-D-glucan chain to a primary hydroxy group in a similar glucan chain

Date:

2024-02-09