Protein Family Models

Members of this family average about 145 amino acids in length, with a signal peptide, a variable length low-complexity region rich in N, D, Q, E, K, and R, and the roughly 80 amino acid C-terminal region described by this HMM. A few members of the family have candidate lipoprotein signal peptides. The family is named for member protein MHO_1590 from Mycoplasma hominis.

Date:

2024-05-14

This HMM describes a well-conserved central region of putative proteins from the Mycoplasmatota. Member proteins have apparent N-terminal signal-anchor sequences but are not lipoproteins. The family is highly divergent, but the motif S[FY]ANDxxGxL[FY]L is extremely well conserved. The function is unknown.

Date:

2024-05-11

This HMM describes a protein region of a restriction system that occurs only in the Mycoplasmatota, as either the N-terminal region of a DNA (cytosine-5-)-methyltransferase or as a small protein, probably a small subunit, encoded next to a larger DNA (cytosine-5-)-methyltransferase subunit. Members of this family are found encoded near MAG4270 family putative restriction endonucleases (see NF045952). Member protein MAG4250 (CAL59123.1) is suggested to be a pseudogene, but the wide distribution of split forms of the DNA (cytosine-5-)-methyltransferase, in over twenty species, suggests the protein is functional. Because a region of GA dinucleotide repeats occurs near the end of the coding region for this domain (translating to Arg-Glu dipeptide repeats) in multiple short versions of this protein, we suggest that this N-terminal domain/subunit is always made, but that production of a full-length methyltransferase may be phase-variable in some species.

Gene:

dcm_N

Date:

2024-05-11

This HMM describes a variant form of lipoprotein signal peptide, as found at the N-termini of MAG6090 from Mycoplasma agalactiae.

Date:

2024-05-08

Gene:

erm(N)

Date:

2024-04-18

Gene:

pmtA

Date:

2024-04-12

Gene:

pmtA

Date:

2024-04-12

Members of this family, including Csac_0668 from Caldicellulosiruptor saccharolyticus, are homologous to the N-terminal half of the copper chaperone CopZ from Archaeoglobus fulgidus. While the C-terminal half of CopZ resembles other previously known copper-binding domain, and binds a copper atom, the N-terminus was found to bind an additional copper and a 2Fe-2S iron-sulfur cluster. Members of the family described here contain an additional 20 amino acids N-terminal to region that aligns to CopZ, containing multiple Cys residues (sometimes four in a row) or selenocysteine in a suggested metal-binding CU motif. The proposed function for members of this family is as a metallochaperone. Note that some homologs outside the scope of this family, such as WP_240162626.1, similarly are selenoproteins but have the selenocysteine at different site.

Date:

2024-04-11

This HMM describes the N-terminal domain of the Ureaplasma surface-exposed lipoprotein known as MBA (multiple banded antigen, UU375). It distinguishes MBA from at least 5 paralogs that share a homologous N-terminal region, described by model NF045871.

Gene:

mba

Date:

2024-04-08

MBA (Multiple Banded Antigen, UU375) is one of six lipoproteins in Ureaplasma parvum serovar 3 str. ATCC 700970 to share an N-terminal domain of about 132 amino acids. This HMM describes the domain that the paralogous family shares. MBA is a highly repetitive protein, explaining its wide variability in sizes on gels for alleles from different strains, but other members of the family (UU172, UU189, UU483, UU487, and UU526) have unique sequences instead of the region of hexapeptide repeats.

Date:

2024-04-08

This family of proteins, found exclusively in the Mycoplasmoidales, is related to PheT (phenylalanine--tRNA ligase subunit beta), found in the same species, but always encoded next to the tyrosine--tRNA ligase TyrS, and perhaps involved in tyrosine--tRNA ligase function. We name this probable tRNA-binding protein TapR (TyrS-Associated PheT-Related).

Gene:

tapR

Date:

2024-04-07

This family, involved in gliding motility in Mycoplasma mobile and a few other species, has a C-terminal domain that resembles both paralogs involved in the same system and F0F1 ATP synthase subunit beta. However, it has an N-terminal extension signature region that those other proteins lack.

Date:

2024-04-05

Members of this family are nucleases expressed on the cell surface of bacteria belonging to the Mycoplasmoidales. This HMM describes the well-conserved C-terminal domain. The N-terminal regions of member proteins have either a lipoprotein signal peptide or an uncleaved signal-anchor sequence, followed by a poorly conserved region highly variable in length. A number of related proteins, excluded by this model, have a circularly permuted form of the nuclease domain. The ability of membrane nuclease to degrade neutrophil extracellular traps likely contributes to virulence.

Date:

2024-04-03

This HMM describes the hydrophobic N-terminal half of MMCAP2_0566, found within an Integrative Conjugal Element (ICE) of Mycoplasma mycoides subsp. capri str. GM12. The domain shows distant sequence similarity to conjugal transfer protein TrbL (see PF19597).

Date:

2024-04-03

This family is known so far only in the genus Mesomycoplasma, and includes examples of tandem paralogs. The majority of family members are lipoproteins, while the rest appear to have N-terminal signal-anchor sequences.

Date:

2024-04-02

This HMM represents the N-terminal region, including a probable signal sequence or signal anchor which in most instances has four consecutive Lys residues before the hydrophobic stretch, of a family of large, virulence-associated proteins in Mycoplasma arthritidis and smaller proteins in Mycoplasma capricolum.

Date:

2024-04-02

Date:

2024-03-27

Date:

2024-03-27

Gene:

pgdA

Date:

2024-03-27

This HMM describes a 35-amino acid sequence region, with three invariant Cys residues, found as the N-terminal domain of a majority of halophilic archaeal forms of the gas vesicle protein GvpO, but not found elsewhere.

Gene:

gvpO

Date:

2024-03-21