Protein Family Models

sodium:solute symporter co-transports Na(+) with a variety of solutes such as sugars, amino acids, inorganic ions or vitamins; similar to Aliivibrio fischeri N-acetylneuraminate transporter and Proteus mirabilis Na(+)-coupled sialic acid symporter

Date:

2024-02-09

sodium:solute symporter co-transports Na(+) with a variety of solutes such as sugars, amino acids, inorganic ions or vitamins; similar to Aliivibrio fischeri N-acetylneuraminate transporter and Proteus mirabilis Na(+)-coupled sialic acid symporter

Date:

2024-02-09

Members of this family resemble TadF, a pseudopilin encoded as part of the tight adherence (tad) loci in species such as Actinobacillus actinomycetemcomitans and Vibrio fischeri.

Gene:

tadF

Date:

2024-08-14

VF530 contains a unique four-helix motif that shows some similarity to the C-terminal double-stranded DNA (dsDNA) binding domain of RecA, as well as other nucleic acid binding domains [1]. [1]. 21905121. Solution NMR structure of VF0530 from Vibrio fischeri reveals a. nucleic acid-binding function.. Aramini JM, Rossi P, Fischer M, Xiao R, Acton TB, Montelione GT;. Proteins. 2011;79:2988-2991. (from Pfam)

Date:

2024-08-14

This is a family of bifunctional uridylyl-removing enzymes/uridylyltransferases (UR/UTases, GlnD) that are responsible for the modification (EC:2.7.7.59) of the regulatory protein P-II, or GlnB (e.g. Swiss:P05826, Pfam:PF00543). In response to nitrogen limitation, these transferases (e.g. Swiss:P27249) catalyse the uridylylation of the PII protein, which in turn stimulates deadenylylation of glutamine synthetase (GlnA). Deadenylylated glutamine synthetase is the more active form of the enzyme [1]. Moreover, uridylylated PII can act together with NtrB and NtrC to increase transcription of genes in the sigma54 regulon, which include glnA and other nitrogen-level controlled genes [2]. It has also been suggested that the product of the glnD gene is involved in other physiological functions such as control of iron metabolism in certain species [2]. The region described in this family is found in many of its members to be C-terminal to a nucleotidyltransferase domain (Pfam:PF01909), and N-terminal to an HD domain (Pfam:PF01966) and two ACT domains (Pfam:PF01842) [3]. [1]. 8412694. The genes of the glutamine synthetase adenylylation cascade are. not regulated by nitrogen in Escherichia coli.. van Heeswijk WC, Rabenberg M, Westerhoff HV, Kahn D;. Mol Microbiol 1993;9:443-457.. [2]. 10931314. Novel effects of a transposon insertion in the Vibrio fischeri. glnD gene: defects in iron uptake and symbiotic persistence in. addition to nitrogen utilization.. Graf J, Ruby EG;. Mol Microbiol 2000;37:168-179.. [3]. 12384297. Isolation and characterization of the glnD gene of. Gluconacetobacter diazotrophicus, encoding a putative. uridylyltr. TRUNCATED at 1650 bytes (from Pfam)

Date:

2024-08-14

Members of this family, including VF_A0006 of Vibrio fischeri, PSPA7_2531 of Pseudomonas aeruginosa, and BPSL3341 from Burkholderia pseudomallei, have an N-terminal signal peptide and four invariant Cys residues suggesting the formation of two disulfide bonds. The function is unknown.

Date:

2023-03-18

nucleoside-diphosphate sugar epimerase/dehydratase similar to UDP-glucose 4-epimerase that epimerizes UDP-galactose to UDP-glucose

Date:

2023-03-07

pterin-binding domain-containing protein, similar to dihydropteroate synthase (DHPS) and cobalamin-dependent methyltransferases such as methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) and methionine synthase (MetH)

Date:

2023-01-10

HIT (Histidine triad) family protein, named for a motif related to the sequence HxHxH/Qxx (x, a hydrophobic amino acid), is part of a superfamily of nucleotide hydrolases and transferases, which act on the alpha-phosphate of ribonucleotides

Date:

2024-05-01

Members of this family are the original transcriptional regulator of bioluminescence, LuxR as the name is used in Aliivibrio [Vibrio] fischeri, an autoinducer-binding protein with a C-terminal helix-turn-helix DNA-binding domain. Note that the same term was suggested later for an unrelated protein from Vibrio harveyi.

Gene:

luxR

Date:

2021-05-25

sodium:solute symporter co-transports Na(+) with a variety of solutes such as sugars, amino acids, inorganic ions or vitamins; similar to Aliivibrio fischeri N-acetylneuraminate transporter and Proteus mirabilis Na(+)-coupled sialic acid symporter

Date:

2019-03-21

VF530 family protein, also known as DUF2132 domain-containing protein, similar to Vibrio fischeri VF0530 protein that has a potential dsDNA-binding function

Date:

2021-01-19

pyridoxal-dependent decarboxylase similar to Aliivibrio fischeri aspartate 1-decarboxylase PanP which catalyzes the pyridoxal-dependent decarboxylation of aspartate to produce beta-alanine; may have a decarboxylase activity with glutamate

Date:

2020-08-08

sodium:solute symporter co-transports Na(+) with a variety of solutes such as sugars, amino acids, inorganic ions or vitamins; similar to Aliivibrio fischeri N-acetylneuraminate transporter and Proteus mirabilis Na(+)-coupled sialic acid symporter

Date:

2019-10-22

GGDEF domain and EAL domain-containing protein similar to the regulatory proteins Escherichia coli RNase E specificity factor CsrD and Vibrio cholerae biofilm architecture maintenance protein MbaA; GGDEF domain-containing protein similar to E.coli diguanylate cyclases DgcZ (YdeH) and DgcT (YcdT), and to E. coli CdgI (YeaI), a c-di-GMP-binding effector with a degenerate GGDEF domain which binds c-di-GMP; GGDEF domain-containing protein similar to the Vibrio cholerae diguanylate cyclase VdcA, which catalyzes the synthesis of cyclic diguanylate (c-di-GMP) via the condensation of 2 GTP molecules; GGDEF domain-containing protein with PAS sensor domain(s), may have diguanylate cyclase activity; similar to Azospirillum brasilense diguanylate cyclase A, CdgA; GGDEF domain-containing protein with a Cache sensor domain, may have diguanylate cyclase activity; GGDEF domain-containing protein with a HAMP domain, similar to Pseudomonas aeruginosa diguanylate cyclase YfiN/TpbB; diguanylate cyclase (GGDEF) with a HAMP domain; sensor domain-containing diguanylate cyclase (GGDEF) containing a CACHE sensor domain and a HAMP signaling domain; sensor domain-containing diguanylate cyclase (GGDEF) with a Cache sensor domain; GGDEF domain-containing protein, with a PAS sensor domain, may function as a diguanylate cyclase; sensor domain-containing diguanylate cyclase with PAS sensor domains; similar to E. coli DgcM/YdaM; diguanylate cyclase (GGDEF) with a HAMP domain similar to Pseudomonas aeruginosa diguanylate cyclase YfiN/TpbB; sensor domain-containing diguanylate cyclase (GGDEF) with one or more PAS sensor domains and a HAMP domain; sensor domain-containing diguanylate cyclase with PAS sensor domains; similar to E. coli DgcM/YdaM; sensor domain-containing diguanylate cyclase with PAS sensor domain(s); sensor domain-containing diguanylate cyclase with PAS sensor domains; similar to E. coli DgcM/YdaM; GGDEF domain-containing protein having an EAL domain and one or more PAS sensor or lig; GGDEF domain and EAL domain-containing protein similar to the regulatory proteins Escherichia coli RNase E specificity factor CsrD and Vibrio cholerae biofilm architecture maintenance protein MbaA; GGDEF domain-containing protein similar to E.coli diguanylate cyclases DgcZ (YdeH) and DgcT (YcdT), and to E. coli CdgI (YeaI), a c-di-GMP-binding effector with a degenerate GGDEF domain which binds c-di-GMP; GGDEF domain-containing protein similar to the Vibrio cholerae diguanylate cyclase VdcA, which catalyzes the synthesis of cyclic diguanylate (c-di-GMP) via the condensation of 2 GTP molecules; GGDEF domain-containing protein with PAS sensor domain(s), may have diguanylate cyclase activity; similar to Azospirillum brasilense diguanylate cyclase A, CdgA; GGDEF domain-containing protein with a Cache sensor domain, may have diguanylate cyclase activity; GGDEF domain-containing protein with a HAMP domain, similar to Pseudomonas aeruginosa diguanylate cyclase YfiN/TpbB; diguanylate cyclase (GGDEF) with a HAMP domain; sensor domain-containing diguanylate cyclase (GGDEF) containing a CACHE sensor domain and a HAMP signaling domain; sensor domain-containing diguanylate cyclase (GGDEF) with a Cache sensor domain; GGDEF domain-containing protein, with a PAS sensor domain, may function as a diguanylate cyclase; sensor domain-containing diguanylate cyclase with PAS sensor domains; similar to E. coli DgcM/YdaM; diguanylate cyclase (GGDEF) with a HAMP domain similar to Pseudomonas aeruginosa diguanylate cyclase YfiN/TpbB; sensor domain-containing diguanylate cyclase (GGDEF) with one or more PAS sensor domains and a HAMP domain; sensor domain-containing diguanylate cyclase with PAS sensor domains; similar to E. coli DgcM/YdaM; sensor domain-containing diguanylate cyclase with PAS sensor domain(s); sensor domain-containing diguanylate cyclase with PAS sensor domains; similar to E. coli DgcM/YdaM; sensor domain-containing diguanylate cyclase with PAS sensor domain(s); GGDEF domain-containing protein similar to E.coli diguanylate cyclases DgcZ (YdeH) and DgcT (YcdT), and to E. coli CdgI (YeaI), a c-di-GMP-binding effector with a degenerate GGDEF domain which binds c-di-GMP; sensor domain-containing diguanylate cyclase (GGDEF) with a Cache sensor domain; sensor domain-containing diguanylate cyclase with PAS sensor domains; similar to E. coli DgcM/YdaM; GGDEF domain-containing protein may have diguanylate cyclase activity, similar to Escherichia coli DgcT (YcdT) and to E. coli CdgI (YeaI), a c-di-GMP-binding effector with a degenerate GGDEF domain which binds c-di-GMP; GGDEF domain-containing protein similar to E.coli diguanylate cyclases DgcZ (YdeH) and DgcT (YcdT), and to E. coli CdgI (YeaI), a c-di-GMP-binding effector with a degenerate GGDEF domain which binds c-di-GMP; GGDEF domain-containing protein with one or more PAS sensor domains; sensor domain-containing diguanylate cyclase with PAS sensor domain(s); sensor domain-containing diguanylate cyclase with PAS sensor domains; similar to E. coli DgcM/YdaM; sensor domain-containing diguanylate cyclase with PAS sensor domains; similar to E. coli DgcM/YdaM; GGDEF domain-containing protein may have diguanylate cyclase activity, similar to Escherichia coli DgcT (YcdT) and to E. coli CdgI (YeaI), a c-di-GMP-binding effector with a degenerate GGDEF domain which binds c-di-GMP; GGDEF domain-containing protein similar to E.coli diguanylate cyclases DgcZ (YdeH) and DgcT (YcdT), and to E. coli CdgI (YeaI), a c-di-GMP-binding effector with a degenerate GGDEF domain which binds c-di-GMP; GGDEF domain-containing protein with one or more PAS sensor domains; sensor domain-containing diguanylate cyclase with PAS sensor domain(s); sensor domain-containing diguanylate cyclase with PAS sensor domains; similar to E. coli DgcM/YdaM; sensor domain-containing diguanylate cyclase with PAS sensor domains; similar to E. coli DgcM/YdaM; GGDEF domain-containing protein similar to E.coli diguanylate cyclases DgcZ (YdeH) and DgcT (YcdT), and to E. coli CdgI (YeaI), a c-di-GMP-binding effector with a degenerate GGDEF domain which binds c-di-GMP; GGDEF domain-containing protein with one or more PAS sensor domains; sensor domain-containing diguanylate cyclase with PAS sensor domain(s); sensor domain-containing diguanylate cyclase with PAS sensor domains; similar to E. coli DgcM/YdaM; GGDEF domain-containing protein similar to the Vibrio cholerae diguanylate cyclase VdcA, which catalyzes the synthesis of cyclic diguanylate (c-di-GMP) via the condensation of 2 GTP molecules; GGDEF domain-containing protein with PAS sensor domain(s), may have diguanylate cyclase activity; similar to Azospirillum brasilense diguanylate cyclase A, CdgA; GGDEF domain-containing protein with a Cache sensor domain, may have diguanylate cyclase activity; sensor domain-containing diguanylate cyclase with PAS sensor domain(s); sensor domain-containing diguanylate cyclase with PAS sensor domains; similar to E. coli DgcM/YdaM; GGDEF domain-containing protein similar to the Vibrio cholerae diguanylate cyclase VdcA, which catalyzes the synthesis of cyclic diguanylate (c-di-GMP) via the condensation of 2 GTP molecules; GGDEF domain-containing protein with PAS sensor domain(s), may have diguanylate cyclase activity; similar to Azospirillum brasilense diguanylate cyclase A, CdgA; diguanylate cyclase (GGDEF) with a HAMP domain; sensor domain-containing diguanylate cyclase (GGDEF) with one or more PAS sensor domains and a HAMP domain; sensor domain-containing diguanylate cyclase with PAS sensor domain(s); sensor domain-containing diguanylate cyclase with PAS sensor domains; similar to E. coli DgcM/YdaM; sensor domain-containing diguanylate cyclase (GGDEF) with one or more PAS sensor domains and a HAMP domain; GGDEF domain-containing protein with a Cache sensor domain, may have diguanylate cyclase activity; similar to Vibrio fischeri MifB ; GGDEF domain-containing protein similar to E.coli diguanylate cyclases DgcZ (YdeH) a

Date:

2019-03-21

Members of this protein family show distant local sequence similarity to a number of S-adenosyl-methionine-dependent methyltransferases. The family is identified by Partial Phylogenetic Profiling as closely tied to the DNA phosphorothioation system (dnd), and members are found adjacent to dnd genes in at least 13 species (Streptomyces lividans TK24, Shewanella frigidimarina NCIMB 400, Mycobacterium abscessus ATCC 19977, Nostoc punctiforme PCC 73102, Vibrio fischeri MJ11, etc.). The DNA phosphorothioation enables a novel form of restriction enzyme activity. Most members of this family appear in species with the DNA phosphorothioation system.

Date:

2019-09-10

GGDEF domain-containing protein with a Cache sensor domain, may have diguanylate cyclase activity; similar to Vibrio fischeri MifB which is an inhibitor of flagellar motility and involved in the formation of mature biofilms

Date:

2018-12-13

GGDEF domain-containing protein with a Cache sensor domain, may have diguanylate cyclase activity; similar to Vibrio fischeri MifB which is an inhibitor of flagellar motility and involved in the formation of mature biofilms

Date:

2018-12-13

TfoX/Sxy family DNA transformation protein such as Vibrio fischeri DNA transformation proteins TfoX1 and TfoX2, which are jointly required for efficient DNA transformation

Date:

2018-08-15

Na+/H+ antiporter family protein such as Aliivibrio fischeri glutamine transporter 1 which may be involved in glutamine transport

Date:

2018-11-26