Protein Family Models

This HMM describes a 56 amino acid region found near or at the C-terminus of many bacterial tetratricopeptide repeat (TPR) proteins, containing a variant form of the TPR repeat (about 34 amino acids) followed by a stretch of sequence unique to this sequence region.

Date:

2024-09-20

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

LenC (Leptospira endostatin-like outer membrane C), a surface protein and apparent lipoprotein, is most closely related to the LenF family, which is about 60 percent identical. The approximately 450 amino acid length of this protein contains two tandem copies of a 200 region containing the DUF1554 domain (see PF07588).

Gene:

lenC

Date:

2024-08-21

This HMM, with a length of 30, describes two tandem 15-amino acid repeats. Numbers of repeats in proteins vary. Notable surface-exposed proteins with this repeat domain include lipoproteins LA_2272 and LA_2273 from Leptospira interrogans and VC2662 from Vibrio cholerae.

Date:

2024-08-10

Tandem lipoproteins from LA_2272 and LA_2273 Leptospira interrogans serovar Lai str. 56601 share both an N-terminal unique domain, modeled by this HMM. Those lipoproteins also have a novel family 15 amino-acid repeats that is now modeled by NF047436. These 15 amino-acid repeats are found much more broadly, including in VC2662 from Vibrio cholerae.

Date:

2024-08-10

This HMM described a 65-amino acid conserved N-terminal region largely restricted to the genus Leptospira, and shared by seven otherwise mostly unrelated proteins in the model strain Leptospira interrogans serovar Lai str. 56601 (LA_0442, LA_0875, LA_1192, LA_1904, LA_2672, LA_3334, and LA_3681). A signal-anchor-like region is followed by the most strongly conserved motif in the domain, [LVI][LVI][LF]KXG.

Date:

2024-08-08

AuxB, an apparent membrane protein found in methicillin-resistant Staphylococcus aureus (MRSA), contributes to lipoteichoic acid (LTA) stability and therefore to a beta-lactam resistance phenotype that depends primarily on the cell wall biosynthesis enzyme PBP2a encoded by mecA.

Gene:

auxB

Date:

2024-08-03

AuxA, an apparent membrane protein and probable transporter found in methicillin-resistant Staphylococcus aureus (MRSA), contributes to lipoteichoic acid (LTA) stability and therefore to beta-lactam resistance phenotype that depends primarily on the cell wall biosynthesis enzyme PBP2a encoded by mecA.

Gene:

auxA

Date:

2024-08-03

LtaA, a member of the major facilitator superfamily (MFS) transporters, is a proton-coupled antiporter flippase for the lipid-linked disaccharide that anchors lipoteichoic acid (LTA) to the staphylococcal cell surface.

Gene:

ltaA

Date:

2024-07-30

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

peptidase S9 family protein, a serine petidase which may cleave the prolyl bond of short peptides, similar to acylaminoacyl peptidase, a prolyl oligopeptidase, which removes acylated amino acid residues from the N terminus of oligopeptides

Date:

2024-02-09

N-acetylmuramoyl-L-alanine amidase family protein such as N-acetylmuramoyl-L-alanine amidase CwlA that hydrolyzes the link between N-acetylmuramoyl residues and L-amino acid residues in certain cell-wall glycopeptides

Date:

2024-02-09

3-deoxy-7-phosphoheptulonate synthase catalyzes the condensation of phosphoenolpyruvate (PEP) and D-erythrose-4-phosphate (E4P) to produce 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP), the first step of the shikimate pathway for aromatic amino acid biosynthesis

Date:

2024-02-09

N-acetylmuramoyl-L-alanine amidase hydrolyzes the link between N-acetylmuramoyl residues and L-amino acid residues in certain cell-wall glycopeptides

Date:

2024-02-09

cob(I)yrinic acid a,c-diamide adenosyltransferase catalyzes the formation of the cobalt-carbon bond in the biosynthetic pathway for adenosylcobalamin

Date:

2024-02-09

peptidase S9 family protein, a serine petidase which may cleave the prolyl bond of short peptides, similar to acylaminoacyl peptidase, a prolyl oligopeptidase, which removes acylated amino acid residues from the N terminus of oligopeptides

Date:

2024-02-09

acyl carrier protein may function as a carrier of the growing fatty acid chain in fatty acid biosynthesis or as the carrier of activated (amino) acid groups in polyketide synthases and non-ribosomal peptide synthases

Date:

2024-02-09

DDHD family phospholipase similar to Homo sapiens phospholipase DDHD1 that hydrolyzes phosphatidic acid, including 1,2-dioleoyl-sn-phosphatidic acid

Date:

2024-02-09

amiloride-sensitive sodium channel family protein such as mammalian acid-sensing ion channel 5, Drosophila melanogaster sodium channel protein Nach, and Caenorhabditis elegans degenerin-like protein del-10

Date:

2024-02-09