Protein Family Models

FetB (Fe Transport B) is one subunit of the iron efflux ABC transporter FetAB. FetA is the ATP-binding subunit and FetB is the permease subunit. Note that model originally was defined more broadly, with membership including a number of proteins distinct in function from FetB, but has now been narrowed. All members of the seed alignment occur in the Enterobacterales and are encoded next to FetA.

Gene:

fetB

Date:

2024-09-15

This HMM describes coenzyme PQQ biosynthesis protein B, a gene required for the biosynthesis of pyrrolo-quinoline-quinone (coenzyme PQQ). PQQ is required for some glucose dehydrogenases and alcohol dehydrogenases. Note that this gene appears to be required for PQQ in biosynthesis in Methylobacterium extorquens (under the name pqqG) and in Klebiella pneumoniae but that the equivalent pqqV in Acinetobacter calcoaceticus is not necessary for heterologous expression of PQQ biosynthesis in E. coli. Based on this latter finding, it is suggested (Goosen, et al. 1989) that PqqB might be a transporter or a PQQ-dependent enzyme rather than a PQQ biosynthesis enzyme.

Gene:

pqqB

Date:

2024-08-23

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 model finds the cassette chromosome recombinase B (CcrB), known from methicillin resistance determinant-carrying staphylococcal cassette chromosome elements (SCCmet). CcrB works together with CcrA, encoded by an adjacent gene.

Gene:

ccrB

Date:

2024-07-19

sterol desaturase family protein similar to C-5 sterol desaturase, which catalyzes a dehydrogenation reaction to introduce a C5-6 double bond into substrates such as lathosterol and the B ring of ergosterol

Date:

2024-02-09

NADH-quinone oxidoreductase subunit B (NuoB) family protein such as Escherichia coli formate hydrogenlyase subunit 7

Date:

2024-02-09

peptidase S9 family protein, an oligopeptidase which may cleave the prolyl bond of short peptides, similar to oligopeptidase B, which cleaves on the C-terminal side of lysyl and argininyl residues

Date:

2024-02-09

STAS (Sulphate Transporter and AntiSigma factor antagonist) domain-containing protein similar to anti-sigma-B factor antagonist, a positive regulator of sigma-B activity

Date:

2024-02-09

cytochrome c1 is a component of the ubiquinol-cytochrome c reductase complex (complex III or cytochrome b-c1 complex), which is a respiratory chain that generates an electrochemical potential coupled to ATP synthesis

Date:

2024-02-09

cytochrome c1 is a component of the ubiquinol-cytochrome c reductase complex (complex III or cytochrome b-c1 complex), which is a respiratory chain that generates an electrochemical potential coupled to ATP synthesis

Date:

2024-02-09

microfibrillar-associated 1 family protein similar to human microfibrillar-associated protein 1, also called spliceosome B complex protein MFAP1, which is involved in pre-mRNA splicing as a component of the spliceosome

Date:

2024-02-09

bacterial immunoglobulin (Ig)-like domain-containing protein such as Marinobacter hydrocarbonoclasticus alkane uptake protein B (AupB), which is involved in growth/biofilm formation on alkane substrates, together with AupA

Date:

2024-02-09

carbohydrate porin belonging to the porin LamB (TC 1.B.3) family, whose members are thought to bind various sugars; carbohydrate porin forms aqueous channels for the diffusion of carbohydrate molecules across the membrane

Date:

2024-02-09

M23 family metallopeptidase is an endopeptidase that lyses bacterial cell wall peptidoglycans; similar to Achromobacter lyticus beta-lytic metalloendopeptidase that catalyzes cleavage of N-acetylmuramoyl-Ala, and of the insulin B chain at Gly23-Phe > Val18-Cya

Date:

2024-02-09

class B sortase is a membrane-bound cysteine transpeptidase which cleaves its surface protein substrate at a conserved cell wall sorting signal and covalently links it to peptidoglycan, and also functions as a pilin polymerase responsible for the assembly of pili

Date:

2024-02-09

ephrin type-B receptor 2 is a receptor tyrosine kinase which binds promiscuously transmembrane ephrin-B family ligands residing on adjacent cells, leading to contact-dependent bidirectional signaling into neighboring cells

Date:

2024-02-09

sterol desaturase family protein similar to C-5 sterol desaturase, which catalyzes a dehydrogenation reaction to introduce a C5-6 double bond into substrates such as lathosterol and the B ring of ergosterol

Date:

2024-02-09

sterol desaturase family protein similar to C-5 sterol desaturase, which catalyzes a dehydrogenation reaction to introduce a C5-6 double bond into substrates such as lathosterol and the B ring of ergosterol

Date:

2024-02-09

SAP (SAF-A/B, Acinus and PIAS) domain-containing protein may bind DNA or RNA and act as a transcriptional regulator.

Date:

2024-02-09