SII-SWORD/CoKE huggingface dataset:
2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine 1-reductase, archaeal (Rib_reduct_arc)
Type: Family

These sequences represent a specific reductase of riboflavin biosynthesis in the archaea, diaminohydroxyphosphoribosylaminopyrimidine reductase. It should not be confused with bacterial 5-amino-6-(5-phosphoribosylamino)uracil reductase. The intermediate 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine in riboflavin biosynthesis is reduced first and then deaminated in both archaea and fungi, opposite to the order in bacteria. The subsequent deaminase is not presently known and is not closely homologous to the deaminase domain fused to the reductase domain, which is similar to this protein but found in most bacteria.
Nicotinate phosphoribosyltransferase pncB-type (Nic_PRibTrfase_pncB)
Type: Family

A deep split separates two related families of proteins, one of which includes experimentally characterised examples of nicotinate phosphoribosyltransferase (

), the first enzyme of NAD salvage biosynthesis. This entry represents the other family. Members have a different (longer) spacing of several key motifs and have an additional C-terminal domain of up to 100 residues. One argument suggesting that this family represents the same enzyme is that no species has a member of both families. Another is that the gene encoding this protein is located near other NAD salvage biosynthesis genes in Nostoc and in at least four different Gram-positive bacteria. NAD and NADP are ubiquitous in life. Most members of this family are from Gram-positive bacteria. An additional set of mutually closely related archaeal sequences score between the trusted and noise cut-offs.
Nicotinate phosphoribosyltransferase (Nic_PRibTrfase)
Type: Family

This family represents nicotinate phosphoribosyltransferase, the first enzyme in the salvage pathway of NAD biosynthesis from nicontinate (niacin). Members are primarily proteobacterial but also include yeasts and Methanosarcina acetivorans. A related family, apparently non-overlapping in species distribution, is

. Members of that family differ in substantially in sequence and have a long C-terminal extension missing from this family, but are proposed also to act as nicotinate phosphoribosyltransferase.
1,4-alpha-glucan-branching enzyme, GlgB (GlgB)
Type: Family

This entry represents the glycogen branching enzyme, GlgB, which is responsible for the transfer of chains of approximately seven alpha(1,4)-linked glucosyl residues to other similar chains (in new alpha-(1,6) linkages) in the biosynthesis of glycogen . The branching enzyme is responsible for the degree of alpha(1,6) branch linkages found in polysaccharides .
P-type ATPase, subfamily IIB (P-type_ATPase_IIB)
Type: Family

This family describes the P-type ATPase responsible for translocating calcium ions across the plasma membrane of eukaryotes , out of the cell. In some organisms, this type of pump may also be found in vacuolar membranes . In humans and mice, at least, there are multiple isoforms of the PMCA pump with overlapping but not redundant functions. Accordingly, there are no human diseases linked to PMCA defects, although alterations of PMCA function do elicit physiological effects . The calcium P-type ATPases have been characterised as Type IIB based on a phylogenetic analysis which distinguishes this group from the Type IIA SERCA calcium pump .

P-ATPases (also known as E1-E2 ATPases) (

) are found in bacteria and in a number of eukaryotic plasma membranes and organelles . P-ATPases function to transport a variety of different compounds, including ions and phospholipids, across a membrane using ATP hydrolysis for energy. There are many different classes of P-ATPases, which transport specific types of ion: H
+
, Na
+
, K
+
, Mg
2+
, Ca
2+
, Ag
+
and Ag
2+
, Zn
2+
, Co
2+
, Pb
2+
, Ni
2+
, Cd
2+
, Cu
+
and Cu
2+
. P-ATPases can be composed of one or two polypeptides, and can usually assume two main conformations called E1 and E2.

Transmembrane ATPases are membrane-bound enzyme complexes/ion transporters that use ATP hydrolysis to drive the transport of protons across a membrane. Some transmembrane ATPases also work in reverse, harnessing the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP.
Glycerol-3-phosphate cytidylyltransferase (G3P_cytidylTrfase)
Type: Family

This entry represents glycerol-3-phosphate cytidyltransferase, also called CDP-glycerol pyrophosphorylase. A closely related protein assigned a different function experimentally is a human ethanolamine-phosphate cytidylyltransferase (

). Glycerol-3-phosphate cytidyltransferase acts in pathways of teichoic acid biosynthesis. Teichoic acids are substituted polymers, linked by phosphodiester bonds, of glycerol, ribitol, etc. An example is poly(glycerol phosphate), the major teichoic acid of the Bacillus subtilis cell wall. Most but not all species encoding proteins in this family are Gram-positive bacteria.
Conserved hypothetical protein CHP01519, Plasmodium falciparum (isolate 3D7) (CHP01519_PLAF7)
Type: Family

These sequences represent an uncharacterised family consisting of a small number of hypothetical proteins of the malaria parasite Plasmodium falciparum (isolate 3D7).
Fructose-bisphosphate aldolase, class II, yeast/E. coli subtype (Fruct_bisP_bact)
Type: Family

Members of this family are class II examples of the glycolytic enzyme fructose-bisphosphate aldolase (FBA). They represent one of two deeply split, architecturally distinct clades of the family that includes class II fructose-bisphosphate aldolases, tagatose-bisphosphate aldolases, and related uncharacterised proteins. The type A and type B Class II FBPA's differ in the presence and absence of distinct indels in the sequence that result in differing loop lengths in the structures . This family is well-conserved and includes characterised FBA from Saccharomyces cerevisiae (Baker's yeast), Escherichia coli, and Corynebacterium glutamicum.
Fructose-bisphosphate aldolase, class II, Calvin cycle subtype (Fruct_bisP_Calv)
Type: Family

Members of this family are class II examples of the enzyme fructose-bisphosphate aldolase, an enzyme both of glycolysis and (in the opposite direction) of the Calvin cycle of CO2 fixation. A deep split separates the tightly conserved yeast/Escherichia coli/Mycobacterium subtype (all species lacking the Calvin cycle) represented by

from a broader group of aldolases that includes both tagatose- and fructose-bisphosphate aldolases. This family represents a distinct, elongated, very well conserved subtype within the latter group. Most species with this aldolase subtype have the Calvin cycle.
P-type ATPase, subfamily IIA, PMR1-type (P-type_ATPase_IIA_PMR1)
Type: Family

Transmembrane ATPases are membrane-bound enzyme complexes/ion transporters that use ATP hydrolysis to drive the transport of protons across a membrane. Some transmembrane ATPases also work in reverse, harnessing the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP.

P-ATPases (also known as E1-E2 ATPases) (

) are found in bacteria and in a number of eukaryotic plasma membranes and organelles . P-ATPases function to transport a variety of different compounds, including ions and phospholipids, across a membrane using ATP hydrolysis for energy. There are many different classes of P-ATPases, which transport specific types of ion: H
+
, Na
+
, K
+
, Mg
2+
, Ca
2+
, Ag
+
and Ag
2+
, Zn
2+
, Co
2+
, Pb
2+
, Ni
2+
, Cd
2+
, Cu
+
and Cu
2+
. P-ATPases can be composed of one or two polypeptides, and can usually assume two main conformations called E1 and E2.

This family represents the P-type ATPase responsible for translocating calcium ions across the golgi membrane of fungi and animals and is of particular importance in the sarcoplasmic reticulum of skeletal and cardiac muscle in vertebrates . The calcium P-type ATPases have been characterised as Type IIA based on a phylogenetic analysis which distinguishes this group from the Type IIB PMCA calcium pump described in

. A separate analysis divides Type IIA into sub-types, SERCA and PMR1 the former of which is described in

.
P-type ATPase, subfamily IID (P-type_ATPase_IID)
Type: Family

This entry represents a group of ATPases has been classified by phylogentic analysis as type IID. They were initially described as a calcium efflux ATPases , but more recent work has shown that the Schizosaccharomyces pombe (Fission yeast) CTA3 gene is in fact a potassium ion efflux pump . These sequences form the clade which represents the fungal P-type ATPases which are responsible for potassium and sodium efflux. The degree to which these pumps show preference for sodium or potassium varies.

Transmembrane ATPases are membrane-bound enzyme complexes/ion transporters that use ATP hydrolysis to drive the transport of protons across a membrane. Some transmembrane ATPases also work in reverse, harnessing the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP.

P-ATPases (also known as E1-E2 ATPases) (

) are found in bacteria and in a number of eukaryotic plasma membranes and organelles . P-ATPases function to transport a variety of different compounds, including ions and phospholipids, across a membrane using ATP hydrolysis for energy. There are many different classes of P-ATPases, which transport specific types of ion: H
+
, Na
+
, K
+
, Mg
2+
, Ca
2+
, Ag
+
and Ag
2+
, Zn
2+
, Co
2+
, Pb
2+
, Ni
2+
, Cd
2+
, Cu
+
and Cu
2+
. P-ATPases can be composed of one or two polypeptides, and can usually assume two main conformations called E1 and E2.
P-type ATPase, subfamily IIIB (P-type_ATPase_IIIB)
Type: Family

Transmembrane ATPases are membrane-bound enzyme complexes/ion transporters that use ATP hydrolysis to drive the transport of protons across a membrane. Some transmembrane ATPases also work in reverse, harnessing the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP.

P-ATPases (also known as E1-E2 ATPases) (

) are found in bacteria and in a number of eukaryotic plasma membranes and organelles . P-ATPases function to transport a variety of different compounds, including ions and phospholipids, across a membrane using ATP hydrolysis for energy. There are many different classes of P-ATPases, which transport specific types of ion: H
+
, Na
+
, K
+
, Mg
2+
, Ca
2+
, Ag
+
and Ag
2+
, Zn
2+
, Co
2+
, Pb
2+
, Ni
2+
, Cd
2+
, Cu
+
and Cu
2+
. P-ATPases can be composed of one or two polypeptides, and can usually assume two main conformations called E1 and E2.

This group describes the magnesium translocating P-type ATPase found in a limited number of bacterial species and best described in Salmonella typhimurium, which contains two isoforms . These transporters are active in low external Mg2+ concentrations and pump the ion into the cytoplasm. The magnesium ATPases have been classified as type IIIB by a phylogenetic analysis .
Nicotinamide-nucleotide adenylyltransferase (NadR_NMN_Atrans)
Type: Domain

The NadR protein of Escherichia coli and closely related bacteria is both enzyme and regulatory protein. The first 60 or so amino acids, N-terminal region is a DNA-binding helix-turn-helix domain (

) responsible for repressing the nadAB genes of NAD de novo biosynthesis. The NadR homologues in Mycobacterium tuberculosis, Haemophilus influenzae, amongst others, appear to lack the repressor domain. NadR has recently been shown to act as an enzyme of the salvage pathway of NAD biosynthesis, nicotinamide-nucleotide adenylyltransferase; members of this family are presumed to share this activity. E. coli NadR has also been found to regulate the import of its substrate, nicotinamide ribonucleotide, but it is not known if the other members of this family share that activity.
Nicotinamide-nucleotide adenylyltransferase, archaeal type (NMN_Atrans_arc)
Type: Family

This family of archaeal proteins exhibits NAD salvage biosynthesis enzyme nicotinamide-nucleotide adenylyltransferase (

) activity. In some cases, the enzyme was tested and found also to have the activity of nicotinate-nucleotide adenylyltransferase (

), an enzyme of NAD de novo biosynthesis, although with a higher Km. In some archaeal species, a number of proteins which are uncharacterised with respect to activity, are also present.
Nicotinamide mononucleotide transporter PnuC (NMN_transpt_PnuC)
Type: Family

PnuC is a membrane protein responsible for nicotinamide mononucleotide transport , subject to regulation by interaction with the NadR (also called NadI) protein (see

). The extreme N- and C-terminal regions are poorly conserved.
NAD pyrophosphatase/5-nucleotidase NadN (NadN)
Type: Family

This family describes NadN of Haemophilus influenzae and a small number of close homologues in pathogenic, Gram-negative bacteria. NadN is a periplasmic enzyme that cleaves NAD (nicotinamide adenine dinucleotide) to NMN (nicotinamide mononucleotide) and AMP. The NMN must be converted by a 5-nucleotidase to nicotinamide riboside for import. NadN belongs a large family of 5-nucleotidases and has NMN 5-nucleotidase activity for NMN, AMP, etc.
Glycogen debranching enzyme, metazoa (Glycogen_debranch_met)
Type: Family

Glycogen debranching enzyme possesses two different catalytic activities; oligo-1,4-->1,4-glucantransferase (

) and amylo-1,6-glucosidase (

). Site-directed mutagenesis studies in Saccharomyces cerevisiae (Baker's yeast) indicate that the transferase and glucosidase activities are independent and located in different regions of the polypeptide chain. Proteins in this family belong to the larger alpha-amylase family. The family contains eukaryotic proteins.
D-erythrose-4-phosphate dehydrogenase (E4P_DH_bac)
Type: Family

This entry contains a small clade of dehydrogenases in gammaproteobacteria which utilise NAD+ to oxidize erythrose-4-phosphate (E4P) to 4-phospho-erythronate, a precursor for the de novo synthesis of pyridoxine via 4-hydroxythreonine and D-1-deoxyxylulose . This enzyme activity appears to have evolved from glyceraldehyde-3-phosphate dehydrogenase, whose substrate differs only in the lack of one carbon relative to E4P. It is possible that some of the GAPDH enzymes may prove to be bifunctional in certain species.
5-nucleotidase lipoprotein e(P4) (Lipo_e_P4)
Type: Family

This entry represents a set of bacterial lipoproteins belonging to a larger acid phosphatase family (

), which in turn belongs to the haloacid dehalogenase (HAD) superfamily of aspartate-dependent hydrolases. Members are found on the outer membrane of Gram-negative bacteria and the cytoplasmic membrane of Gram-positive bacteria. Most members have classic lipoprotein signal sequences. A critical role of this 5'-nucleotidase in Haemophilus influenzae is the degradation of external riboside in order to allow transport into the cell. An earlier suggested role in hemin transport is no longer current. This enzyme may also have other physiologically significant roles .
Glyceraldehyde-3-phosphate dehydrogenase, type I (Glyceraldehyde-3-P_DH_1)
Type: Family

This group of sequences represent glyceraldehyde-3-phosphate dehydrogenase (GAPDH), the enzyme responsible for the interconversion of 1,3-diphosphoglycerate and glyceraldehyde-3-phosphate, a central step in glycolysis and gluconeogenesis. Forms exist which utilise NAD (

), NADP (

) or either (

). In some species, NAD- and NADP- utilising forms exist, generally being responsible for reactions in the anabolic and catabolic directions respectively . An additional form of gap gene is found in gammaproteobacteria and is responsible for the conversion of erythrose-4-phosphate (E4P) to 4-phospho-erythronate in the biosynthesis of pyridoxine . This pathway of pyridoxine biosynthesis appears to be limited, however, to a relatively small number of bacterial species although it is prevalent among the gammaproteobacteria . This enzyme is described by

. These two groups of sequences exhibit a close evolutionary relationship. There exists the possibility that some forms of GAPDH may be bifunctional and act on E4P in species which make pyridoxine and via hydroxythreonine and lack a separate E4PDH enzyme (for instance, the GAPDH from Bacillus stearothermophilus has been shown to possess a limited E4PD activity as well as a robust GAPDH activity ).
Glucoamylase, bacterial (Glucoamylase_bac)
Type: Family

Glucoamylase (GA), also known as glucan 1,4-alpha-glucosidase, which belongs to family 15 (

) in the classification of glycosyl hydrolases.

GA catalyses the release of D-glucose from the non-reducing ends of starch and other oligo- or poly-saccharides. Studies of fungal GA have indicated 3 closely-clustered acidic residues that play a role in the catalytic mechanism . This region is also conserved in a recently sequenced bacterial GA .

This entry represents a bacterial glucoamylase subfamily that contains a glucodextranase N domain (

).
Asparagine synthase, glutamine-hydrolyzing (Asn_synth_AEB)
Type: Family

These sequences represent glutamine-hydrolysing asparagine synthase. The group have a poorly conserved C-terminal extension while bacterial members of the family tend to have a long, poorly conserved insert lacking from archaeal and eukaryotic sequences. Multiple isozymes have been demonstrated, such as in Bacillus subtilis .
Phage portal protein, HK97 (Portal_HK97)
Type: Family

This entry represents one of several distantly related families of phage portal proteins. This protein forms a hole, or portal, that enables DNA passage during packaging and ejection. It also forms the junction between the phage head (capsid) and the tail proteins. It functions as a dodecamer of a single polypeptide of average mol. wt. of 40-90kDa .
Portal protein, SPP1-type (Portal_SPP1-type)
Type: Family

The portal protein is a bacteriophage component that forms a hole, or portal, enabling DNA passage during packaging and ejection. It also forms the junction between the phage head (capsid) and the tail proteins .

This entry represents one particular subfamily of portal proteins consisting of the Bacillus phage SPP1 protein and similar sequences.
Phage portal protein, lambda family (Phage_lambda_portal)
Type: Family

This entry represents one of several distantly related families of phage portal protein. This protein forms a hole, or portal, that enables DNA passage during packaging and ejection. It also forms the junction between the phage head (capsid) and the tail proteins. It functions as a dodecamer of a single polypeptide of average mol. wt. of 40-90kDa.
Phage portal protein PBSX family (Phage_portal_PBSX)
Type: Family

This entry represents one of several distantly related families of phage portal protein. This protein forms a hole, or portal, that enables DNA passage during packaging and ejection. It also forms the junction between the phage head (capsid) and the tail proteins. It functions as a dodecamer of a single polypeptide of average molecular weight of 40-90kDa. This family shows clear homology to sequences represented by

.
Bacteriophage tail tape measure, C-terminal (Phage_tape_meas_C)
Type: Domain

This entry represents a domain found near the C terminus of bacteriophage tape measure proteins. Long-tailed bacteriophages possess a large gene encoding a tape measure protein (TMP) . TMP is important for assembly of phage tails and involved in tail length determination . Mutated forms of TMP cause tail fibres to be shortened .

This protein is also found in bacteria, particularly Enterobacteriaceae, suggesting prophage matches occur in addition to the phage matches.

This entry includes a domain found near the C terminus of Bacteriophage lambda tail measure protein, GpH.
Phage portal protein, A118-type (Phage_portal_A118-type)
Type: Family

These entry represents a family of phage minor structural proteins. They are proposed to be portal proteins on the basis of their gene positions within the phage gene order, presence in mature phage, size, and conservation across a number of complete genomes of tailed phage that lack other candidate portal proteins .

The portal protein is a bacteriophage component that forms a hole, or portal, enabling DNA passage during packaging and ejection. It also forms the junction between the phage head (capsid) and the tail proteins .
Prohead protease (Prohead_protease)
Type: Family

This entry represents the prohead protease from bacteriophage HK97 and related phages . It is generally encoded next to the gene for the capsid protein that it processes, and in some cases may be fused to it. It is also found in a number of bacteria, possibly as the result of horizontal transfer.
Pyrimidine 5'-nucleotidase, eukaryotic (Pyrimidine_nucleotidase_eu)
Type: Family

This family is a small group of metazoan sequences with sequences from Arabidopsis thaliana (Mouse-ear cress) and rice. The sequences represent pyrimidine 5-nucleotidases, apparently in reference to HSPC233, the Homo sapiens (Human) homologue . The structure of mouse sequence has been reported . This group of sequences was originally found during searches for members of the haloacid dehalogenase (HAD) superfamily. All of the conserved catalytic motifs are found. The placement of the variable domain between motifs 1 and 2 indicates membership in subfamily I of the superfamily, but these sequences are sufficiently different from any of the branches of that subfamily (IA-ID) as to constitute a separate branch to now be called IE. Considering that the closest identifiable hit outside of the noise range is to a phosphoserine phosphatase, this group may be considered to be most closely allied to subfamily IB.
HAD-superfamily hydrolase, subfamily IF, YfhB (HAD-SF_hydro_IF_YfhB)
Type: Family

This entry represents of sequences limited to the gamma proteobacteria, including Phosphatidylglycerophosphatase C (PgpC, previously known as YfhB) from Escherichia coli . This group is a member of the haloacid dehalogenase (HAD) superfamily of aspartate-dependent hydrolases and all of the conserved catalytic motifs are present . Although structurally similar to subfamily IA in that the variable domain is predicted to consist of five consecutive α-helices (by PSI-PRED), it is sufficiently divergent to warrant being regarded as a separate sub-family (IF).
Glyceraldehyde-3-phosphate dehydrogenase, type II (Glyceraldehyde-3-P_DH_2_arc)
Type: Family

This family describes the type II glyceraldehyde-3-phosphate dehydrogenases. These enzymes catalyze the interconversion of 1,3-diphosphoglycerate and glyceraldehyde-3-phosphate, a central step in glycolysis and gluconeogenesis. In archaea, either NAD or NADP may be utilised as the cofactor.
Bacteriophage terminase, large subunit (Phage_terminase_lsu)
Type: Family

This group of sequences represent a highly divergent family of the large subunit of phage terminase. All members are encoded by phage genomes or within prophage regions of bacterial genomes. This is a distinct family from the phage terminase family represented by

.

Initiation of packaging of double-stranded viral DNA involves the specific interaction of the prohead with viral DNA in a process mediated by a phage-encoded terminase protein. The terminase are usually hetero-oligomers composed of a small and a large subunit . This entry includes the large subunit, including GP2 from Bacillus phage SPP1 .