Protein Family Models

Members of this family, named YmfI after the founding member from Bacillus subtilis, are restricted to bacterial species in which the post-translational modification of elongation factor P (EF-P) is 5-aminopentanol at Lys-32. This protein, a homolog of the 3-keto-acyl ACP reductase FabG, reduces EF-P 5-aminopentanone to EF-P 5-aminopentanol. All 427 members of the seed alignment are from species in which YmfF and YmfH homologs are encoded by an adjacent gene pair.

Gene:

ymfI

Date:

2024-08-06

Members of this uncharacterized protein family, YfmF, and its paralog YfmH, share a conserved gene neighborhood with YfmI, which changes the side chain modification of elongation factor P Lys-32 from 5-aminopentanone to 5-aminopentanol, the functional form. Lineages with this particular form of EF-P modification included Bacillus, Staphylococcus, and Listeria. Both YfmF and YfmH belong to the M16 metalloprotease family. It is not clear yet if YfmF and YfmH represent missing components of the EF-P modification pathway that includes YfmI, or if the operon structure is widely conserved for some other reason. A solved crystal structure is available.

Gene:

yfmF

Date:

2024-08-06

Members of this uncharacterized protein family, YfmH, and its paralog YfmF, share a conserved gene neighborhood with YfmI, which changes the side chain modification of elongation factor P Lys-32 from 5-aminopentanone to 5-aminopentanol, the functional form. Lineages with this particular form of EF-P modification included Bacillus, Staphylococcus, and Listeria. Both YfmF and YfmH belong to the M16 metalloprotease family. It is not clear yet if YfmF and YfmH represent missing components of the EF-P modification pathway that includes YfmI, or if the operon structure is widely conserved for some other reason. A solved crystal structure is available.

Gene:

yfmH

Date:

2024-08-05

Members of this P-loop-containing domain, related to various AAA-type ATPases, have a well-conserved xKGGVGR[ST] that differs from the more typical GxxGxGK[ST] of P-loop motifs. This domain often is found in long, multidomain proteins that have an additional ATP-binding domain of a different type (see NF047389.1). Member protein Sll1563 was found to be downregulated during nitrogen starvation as part of the NtcA regulon, but its function was not determined.

Date:

2024-07-30

Members of this P-loop-containing ATPase (or possibly GTPase) protein family have been annotated as DNA repair protein, FunZ, but the function is unknown. Members often appear next to or fused to a second P-loop-containing ATPase domain more similar to that of ParA family proteins.

Date:

2024-07-30

Pfam model PF04296 identifies the DUF448 or YlxR family of RNA-binding proteins, a broad family with considerable variety in length. This model describes for now a limited set of the proteins from that family, similar to NP_389543.1 from Bacillus subtilis, with similar lengths and conservation of several motifs, pending confirmation that more distant homologs act in a similar manner.

Gene:

rnpM

Date:

2024-07-23

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

NB-LRR (nucleotide-binding-leucine rich repeat) family disease resistance protein guards the plant against pathogens via an indirect interaction with an avirulence protein contained in the plant, triggering a defense response that restricts the pathogen growth

Date:

2024-04-02

bifunctional NADH-quinone oxidoreductase subunit C/D (NuoC/NuoD) is part of the connecting domain of complex I of the respiratory chain that couples the transfer of electrons from NADH to quinone with the translocation of protons across the membrane

Date:

2024-04-11

phosphatidylinositol 4-kinase (PI4K) catalyzes the transfer of the gamma-phosphoryl group from ATP to the 4-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) to generate PtdIns(4)P, the major precursor in the synthesis of other phosphoinositides

Date:

2024-02-09

cation-translocating P-type ATPase is an integral membrane transporter that generates and maintains electrochemical gradients across cellular membranes by translocating cations or heavy metals, and is distinguished from other transport ATPases (F-, V-, and ABC- type) by the formation of a phosphorylated (P-) intermediate state in the catalytic cycle

Date:

2024-02-09

cation-translocating P-type ATPase is an integral membrane transporter that generates and maintains electrochemical gradients across cellular membranes by translocating cations or heavy metals, and is distinguished from other transport ATPases (F-, V-, and ABC- type) by the formation of a phosphorylated (P-) intermediate state in the catalytic cycle

Date:

2024-02-09

cation-translocating P-type ATPase is an integral membrane transporter that generates and maintains electrochemical gradients across cellular membranes by translocating cations or heavy metals, and is distinguished from other transport ATPases (F-, V-, and ABC- type) by the formation of a phosphorylated (P-) intermediate state in the catalytic cycle

Date:

2024-02-09

heavy metal translocating P-type ATPase is an integral membrane transporter that generates and maintains electrochemical gradients across cellular membranes by translocating heavy metals such as cadmium, zinc and cobalt, and is distinguished from other transport ATPases (F-, V-, and ABC- type) by the formation of a phosphorylated (P-) intermediate state in the catalytic cycle

Date:

2024-02-09

NAD(P)/FAD-dependent oxidoreductase catalyzes the transfer of electrons from one molecule, the electron donor or reductant, to another molecule, the electron acceptor or oxidant

Date:

2024-02-09

cation-translocating P-type ATPase is an integral membrane transporter that generates and maintains electrochemical gradients across cellular membranes by translocating cations or heavy metals, and is distinguished from other transport ATPases (F-, V-, and ABC- type) by the formation of a phosphorylated (P-) intermediate state in the catalytic cycle

Date:

2024-02-09

NAD(P)/FAD-dependent oxidoreductase catalyzes the transfer of electrons from one molecule, the electron donor or reductant, to another molecule, the electron acceptor or oxidant

Date:

2024-02-09

classical SDR (short-chain dehydrogenase/reductase) family NAD(P)-dependent oxidoreductase similar to very-long-chain 3-oxoacyl-CoA reductase that catalyzes the reduction of the 3-ketoacyl-CoA intermediate that is formed in each cycle of fatty acid elongation; classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue

Date:

2024-02-09

classical SDR (short-chain dehydrogenase/reductase) family NAD(P)-dependent oxidoreductase similar to human 17-beta-hydroxysteroid dehydrogenase type XI that preferentially converts 5 alpha-androstane-3 alpha,17 beta-diol (3-alpha-diol) to androsterone; classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue

Date:

2024-02-09

UDP-glucuronate decarboxylase catalyzes the NAD-dependent decarboxylation of UDP-glucuronic acid to UDP-xylose; it is an extended SDR (short-chain dehydrogenase/reductase) family NAD(P)-dependent oxidoreductase and is necessary for the biosynthesis of the core tetrasaccharide in glycosaminoglycan biosynthesis

Date:

2024-02-09