Protein Family Models

This family includes the glycan-binding N-terminal domain (called the translocation domain) of the nicotine adenine dinucleotide glycohydrolase toxin (NADase) of Steptococcus pyogenes. Related domains are often referred to as the discoidin domain.

Date:

2024-10-02

This HMM describes an N-terminal domain restricted to the genus Leptospira, and shared by two homolgous proteins in Leptospira biflexa, LBF_1751 and LBF_2017. The domain is followed in Leptospira by two tandem copies of a domain about 90 amino acids long that can be repeated 10 or more times in homologs from other lineages, such as WP_165822350.1 from Paenibacillus.

Date:

2024-10-01

Members of this family include the transposase accessory protein TnpA of IS66-like insertion sequences. It shows N-terminal domain of IS3 family transposases.

Gene:

tnpA

Date:

2024-10-01

This family is named for founding protein LA_3659, even though that protein appears not to be complete at the N-terminus. For members in the genus Leptospira, a large number of fragmentary sequences occur in non-redundant protein sequence databases, suggesting negative selection in certain growth conditions. Members of this family are also found broadly outside of Leptospira. The function is unknown.

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 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

Bat (Bacteriodes aerotolerance)-related operons are found broadly in bacteria, but differ in their makeup in different lineages. This HMM describes the family of the von Willebrand factor A (VWA) domain-containing protein BatB, as found in the genus Leptospira, or the N-terminal domain of a BatBC fusion protein. The function may not actually be related to tolerance of oxidative stress. Recombinant Leptospira BatB is reported to function as a serine protease active on thrombin, fibrin, fibrinogen, gelatin and casein.

Gene:

batB

Date:

2024-09-10

Members of this family, found primarily but not exclusively in the genus Leptospira, share this homology domain at the N-terminus, typically share a shorter C-terminal domain as well, and are variable in length and sequence between the two well-conserved regions. The function is unknown.

Date:

2024-08-20

LvrA and LvrB (Leptospira virulence regulator system A and B) are hybrid histidine kinase/response regulators encoded by tandem genes. Neither protein has either a transmembrane domain or a DNA-binding domain. From N-terminus toward C-terminus, LvrA has a PAS-like sensor domain, a histidine kinase (HK) region, a response regulator domain, and then another HK region, and it is described as the hybrid histidine kinase component of a two-component system. LvrB has a domain architecture similar to the C-terminal region of LvrA, from the response regulator domain to the C-terminus.

Gene:

lvrB

Date:

2024-08-20

LvrA and LvrB (Leptospira virulence regulator system A and B) are hybrid histidine kinase/response regulators encoded by tandem genes. Neither protein has either a transmembrane domain or a DNA-binding domain. From N-terminus toward C-terminus, LvrA has a PAS-like sensor domain, a histidine kinase (HK) region, a response regulator domain, and then another HK region, and it is described as the hybrid histidine kinase component of a two-component system. LvrB has a domain architecture similar to the C-terminal region of LvrA, from the response regulator domain to the C-terminus.

Gene:

lvrA

Date:

2024-08-20

This extremely hydrophobic domain is found in Clostridia and related Gram-positive species, either as the C-terminal portion of a protein with an N-terminal helix-turn-helix predicted DNA-binding domain, or as nearly the full length of a protein. This domain includes a highly unusual motif within a strongly hydrophobic stretch, WxxxWxxWxxY, in which all four aromatic residues are invariant.

Date:

2024-08-15

The PEP-CTERM domain is a protein-sorting domain, about 25 amino acids in length, typically found as the most C-terminal domain feature in any bacterial protein. However, a subset of choice-of-anchor J family proteins with PEP-CTERM domains have an additional, extremely unusual novel domain located C-terminally to the PEP-CTERM domain. This domain is found also in proteins that have very little sequence N-terminal to this domain. This HMM represents the first observation of this that has resulting in the naming of a novel domain, and so the domain is named the post-PEP-CTERM-1 domain (PPC1 domain).

Date:

2024-08-14

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

SSU0496 from porcine pathogen Streptococcus suis, an IdeS/Mac family cysteine endopeptidase, was shown to cleave porcine IgM efficiently, but not IgG nor IgA, and not IgM from other species. The gene symbol assigned was Ide-Ssuis. The N-terminal region contains a YSIRK-type sorting signal (see TIGR01168 and PMID:18800056), which allows for targeted localization of surface proteins in Gram-positive bacteria.

Gene:

ide-Ssuis

Date:

2024-08-09

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

This uncharacterized bacterial protein, with an N-terminal probable signal-anchor domain and a His-rich C-terminal region, is here named BRANT because of its observation in the genera Bradyrhizobium, Rhodopseudomonas, Afipia, Nitrobacter, and Tardiphaga.

Date:

2024-08-02

Date:

2024-08-02

In spirochetes, flagella are located within the periplasm. FlcA is one of several structural proteins involved in formation of the flagellar collar. Conserved N-terminal domain of about 40 amino acids and C-terminal region domain of about 650 amino acids are separated by a long and variable length stretch of low-complexity sequence.

Gene:

flcA

Date:

2024-07-26

In spirochetes, flagella are located within the periplasm. FlcA is one of several structural proteins involved in formation of the flagellar collar. Conserved N-terminal domain of about 40 amino acids and C-terminal region domain of about 650 amino acids are separated by a long and variable length stretch of low-complexity sequence.

Gene:

flcA

Date:

2024-07-26

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