SII-SWORD/CoKE huggingface dataset:
Ornithine/lysine/arginine decarboxylase (Orn/lys/arg_de-COase)
Type: Family

This family is composed of ornithine decarboxylases (ODC), arginine decarboxylases (ADC) and lysine decarboxylases (LDC), and belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase domain superfamily (fold I) . These enzymes catalyse the decarboxylation of ornithine, arginine, or lysine, respectively using PLP as a co-factor. ODC is active as a dimer and catalyses the decarboxylation of tryptophan . ADC catalyses the decarboxylation of arginine and LDC catalyses the decarboxylation of lysine. The PLP combines with the alpha-amino acid to form a Schiff base, which acts as the substrate in the decarboxylation (COOH group removal) reaction .

Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalysed. The availability of several structures allowed a comprehensive analysis of the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), D-amino acid superfamily (fold type IV) and glycogen phophorylase family (fold type V) .

For additional information please see .
Uncharacterised protein family UPF0306 (UPF0306)
Type: Family

There are currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. Members of this group are restricted to the Proteobacteria.
Uncharacterised conserved protein UCP010256 (UCP010256)
Type: Family

This group represents uncharacterised proteins with a vWA domain from bacterial and archaeal species.
Uncharacterised conserved protein UCP012318 (UCP012318)
Type: Family

This is a family of uncharacterised proteins from Proteobacteria and plants.
Bacillithiol biosynthesis BshC (Bacillithiol_biosynth_BshC)
Type: Family

Members of this protein family include BshC, which is an enzyme required for bacillithiol biosynthesis and described as a cysteine-adding enzyme . Bacillithiol is a low-molecular-weight thiol, an analog of glutathione and mycothiol, and is found largely in the Firmicutes.
Uncharacterised conserved protein UCP012608 (UCP012608)
Type: Family

This is a family of uncharacterised bacterial proteins.
Zinc-ribbon domain, bacteria (Zinc-ribbon_6_bact)
Type: Domain

This family appears to be a true zinc-ribbon, with two sets of putative zinc-binding domains in tandem.
Uncharacterised conserved protein UCP014677 (UCP014677)
Type: Family

This is a family of bacterial uncharacterised proteins.
Virulence protein RhuM-like (Virulence_RhuM-like)
Type: Family

There are currently no experimental data for members of this group or their homologues. However, these proteins are implicated in virulence/pathogenicity because RhuM is encoded in the SPI-3 pathogenicity island in Salmonella typhimurium .
Uncharacterised conserved protein UCP015417, vWA (UCP015417_vWA)
Type: Family

This is a family of uncharacterised proteins, the majority of which contain a C-terminal vWA domain.
Citrate lyase beta subunit-like (Citrate_lyase_beta/mcl1/mcl2)
Type: Family

This entry represents a group of proteins belonging to the HpcH/HpaI aldolase family. Proteins in this entry include citrate lyase subunit beta, malyl-CoA lyase and (3S)-malyl-CoA thioesterase. This entry also includes beta-methylmalyl-CoA lyase (rrnAC0690) from Haloarcula marismortui.

Citrate lyase catalyses the magnesium-dependent cleavage of citrate to acetate and oxaloacetate. In bacteria, this reaction is involved in citrate fermentation. The bacterial enzyme is composed of three subunits: alpha, beta and gamma. Catalytic activity resides on the alpha- and beta-subunits, whereas the gamma-subunit serves as an acyl carrier protein (ACP) . Mammalian citrate lyase beta proteins display similarity to the bacterial enzymes .

Malyl-CoA lyase catalyses the reversible condensation of glyoxylate and acetyl-CoA to L-malyl-CoA and the reversible condensation of glyoxylate and propionyl-CoA to beta-methylmalyl-CoA .

(3S)-malyl-CoA thioesterase catalyses the hydrolysis of (3S)-malyl-CoA to (3S)-malate and free CoA .
Orthopoxvirus protein F1 (Orthopox_F1)
Type: Family

The poxvirus F1 family members are related to Vaccinia virus protein F1L, also known as Apoptosis regulator OPG045, which plays a role in evading host innate immune response by inhibiting host inflammasome activation . F1interacts with and inhibits NLR-mediated interleukin-1 beta/IL1B production in infected cells. F1L suppresses mitochondrial-dependent apoptosis by binding to the BH3 domain of host BAK and prevents BAK from binding active BAX .
Poxvirus, Protein B14/B22/C16 (Poxvirus_B14/B22/C16)
Type: Family

This is a family of conserved poxvirus proteins related to Protein B14 and Protein B22/C16
from Vaccinia virus. B14 contributes to virulence by binding to the host IKBKB subunit of the IKK complex and preventing host NF-kappa-B activation in response to pro-inflammatory stimuli such as TNF-alpha or IL1B. Mechanistically, it sterically hinders the direct contact between the kinase domains of IKBKB in the IKK complex containing IKBKB, CHUK/IKKA and NEMO .
Nicotinic acid mononucleotide biosynthesis protein (NMN_biosyn)
Type: Family

This group contains uncharacterised proteins that are implicated in nicotinic acid mononucleotide (NMN) biosynthesis based on the genomic context of the corresponding genes (operon structure, gene neighbourhood) . The Rhizobium loti (Mesorhizobium loti) member (Msi362, ORF1) is encoded by the symbiosis island that contains operons required for the syntheses of nicotinic acid mononucleotide (NMN) and biotin, and belongs to the
nad
operon . The Neisseria meningitidis member is flanked by
nadA
and
nadC
genes whose products are part of the pathway for NMN synthesis in Escherichia coli. However, mutation in ORF1 failed to produce the vitamin auxotrophic phenotype , which suggests that members of this group may have a non-essential role in this process.
Uncharacterised conserved protein UCP020967 (UCP020967)
Type: Family

This is a family of uncharacterised bacterial proteins.
Cysteine protease StiP, N-terminal domain (StiP_N)
Type: Domain

This entry represents the N-terminal domain of Cysteine protease StiP from Acinetobacter baylyi, which may play a role in regulating cell morphology in response to stressful conditions which likely cause oxidative damage. StiP has been shown to posses cysteine protease activity . This domain is also found centrally located in several uncharacterised proteins including

from Streptomyces mobaraensis. Most members of this family have a C-terminal RNA binding PELOTA domain (

). These genes are found in the biosynthetic operon associated with the Ter stress response .
Virginiamycin B lyase Vgb (Vgb_bact)
Type: Family

Streptogramins consist of a mixture of two components: cyclic polyunsaturated macrolactones (group A) and cyclic hexadepsipeptides (group B). The latter are cyclized through an ester bond between the hydroxyl group of an N-terminal threonine and the C-terminal carboxyl . Inactivation of the B streptogramins (e.g., virginiamycin) can occur by linearization of the cyclic depsipeptide (lactone ring) by enzymes such as Vgb from Staphylococcus aureus .

The molecular mechanism of streptogramin B inactivation by S. aureus Vgb and orthologues from Bordetella pertussis and Streptomyces coelicolor has been demonstrated to involve elimination rather than hydrolysis . Vgb is a member of a large group of streptogramin B lyases that are present not only in resistant clinical isolates but also in the chromosomes of many bacteria .

Members of this group contain one or more copies of NHL repeats.
Insecticidal delta endotoxin (Insecticidal_delta_endotoxin)
Type: Family

This group represents an insecticidal delta endotoxin from bacteria. The spore-forming bacterium Bacillus thuringiensis produces several plasmid-encoded delta-endotoxins in large quantities during sporulation, which are packaged into intracellular inclusions as protoxins. The subsequent ingestion of the inclusions by insect larvae leads to the conversion of the different protoxins to toxins, each one specific for an order of insects . For example, the insecticidal delta-endotoxin cyr15Aa represented in this entry is specific for lepidopteran larvae (butterflies and moths). The toxins act by binding to the midgut epithelial cells forming cation-selective channels in their membranes, causing lethality.
Rubisco-cytochrome methylase MET (Rubisco-cyt_methylase_MET)
Type: Family

This group represents a predicted rubisco-cytochrome methylase, MET type.

Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is the key enzyme in photosynthetic carbon assimilation. The enzyme is composed of large (rbcL) and small (rbcS) subunits, and has been found in algae, cryptophytes and land plants. This entry represents the small subunit, N-methyltransferase I, of Rubisco from cryptophytes. Cryptophytes posses a DNA-containing nucleomorph in addition to a nucleus, mitochondria and plastids; these dwarf nucleomorphs are remnants of red-algae symbionts .
Uncharacterised conserved protein UCP028205 (UCP028205)
Type: Family

This is a family of uncharacterised bacterial proteins, restricted to the Proteobacteria.
Double-stranded DNA virus, group I, capsid (dsDNA_vir_gr_I_capsid)
Type: Homologous_superfamily

This entry represents viral capsid proteins from group I dsDNA viruses, including Papovaviridae-like Polyomaviruses and Papillomaviruses. Virus-encoded capsid proteins play a major role in the life cycles of all viruses. Structures have been determined for the major capsid protein VP1 (viral protein 1) from Murine polyomavirus (strain P16 small-plaque) (MPyV) and the major late protein L1 from Human papillomavirus (HPV) . These capsid proteins share a β-sandwich topology. Characteristic interactions between the domains of this fold allows the formation of 5-fold and pseudo 6-fold assemblies.

Polyomaviruses are dsDNA viruses with no RNA stage in their life cycle. The virus capsid is composed of 72 icosahedral units, each of which is composed of five copies of VP1. The virus attaches to the cell surface by recognition of oligosaccharides terminating in alpha(2,3)-linked sialic acid. The capsid protein VP1 forms a pentamer. The complete capsid is composed of 72 VP1 pentamers, with a minor capsid protein, VP2 or VP3, inserted into the centre of each pentamer like a hairpin. This structure restricts the exposure of internal proteins during viral entry. Polyomavirus coat assembly is rigorously controlled by chaperone-mediated assembly. During viral infection, the heat shock chaperone hsc70 binds VP1 and co-localises it in the nucleus, thereby regulating capsid assembly .

Papillomaviruses are members of the papovavirus superfamily. More than 70 different types of papillomavirus have been discovered in humans, some of which have been shown to cause genital carcinomas and cutaneous warts . The viruses contain a circular dsDNA genome surrounded by an icosahedral capsid (non-enveloped). Two proteins are involved in capsid formation: a major (L1) and a minor (L2) protein, in the approximate proportion 95:5%. L1 forms a pentameric assembly unit of the viral shell in a manner that closely resembles VP1 from polyomaviruses. Intermolecular disulphide bonding holds the L1 capsid proteins together . L1 capsid proteins can bind via its nuclear localisation signal (NLS) to karyopherins Kapbeta(2) and Kapbeta(3) and inhibit the Kapbeta(2) and Kapbeta(3) nuclear import pathways during the productive phase of the viral life cycle . Surface loops on L1 pentamers contain sites of sequence variation between HPV types.
Uncharacterised conserved protein UCP028770 (UCP028770)
Type: Family

This is a family of uncharacterised bacterial proteins, restricted to the Gammaproteobacteria.
Ribosomal RNA large subunit methyltransferase M (rRNA_MeTrfase_M)
Type: Family

This entry represents the ribosomal RNA large subunit methyltransferase M (RlmM), previously known as YdgE. RlmM specifically catalyses the 2'-O-methylation of nucleotide C2498 in the peptidyl transferase loop of 23S rRNA .
Type IV secretory pathway, VirJ component (IV_sec_VirJ)
Type: Family

Type IV secretion systems are virulence determinants in many bacteria and share homology with many conjugal transfer systems. The VirB system of Agrobacterium tumefaciens, which delivers both virulence proteins and oncogenic T-DNA to plant hosts, is the best studied Type IV secretion system.

This group contains the VirJ/AcvB component of Type IV secretion systems. A. tumefaciens VirJ and AcvB are Ti plasmid and chromosome-encoded, respectively , and are required for T-DNA transfer into plants . It has been suggested that VirJ evolved from AcvB, presumably for a more specialised role in tumorigenesis .

It is believed that AcvB binds to the T-strand in periplasm and mediates the transfer of the T-strand from A. tumefaciens to the host plant cell . Similarly, export substrates are believed to associate with the virulence protein VirJ in the periplasm, and VirJ is believed to be involved in the second step of type IV secretion, i.e. movement of substrates from the periplasm to the plant cell .
ATP-grasp family (ATP-grasp_fam)
Type: Family

This entry represents a family of bacterial proteins that contain an ATP-grasp domain. They are related to carbamoyl phosphate synthetases. Their genes are found in the biosynthetic operon associated with the Ter stress response operon and are predicted to be involved in the biosynthesis of a ribo-nucleoside involved in stress response .
Uncharacterised conserved protein UCP029730 (UCP029730)
Type: Family

This family is a group of uncharacterised proteins from the Proteobacteria.
Uncharacterised conserved protein UCP029766 (UCP029766)
Type: Family

This family is a group of uncharacterised conserved proteins from the Gammaproteobacteria.
Cell cycle protein GpsB (Cell_cycle_GpsB)
Type: Family

This entry contains GpsB (also known as YpsB), which is a cell cycle protein and a component of the divisome. It associates with the complex late in its assembly, after the Z-ring is formed, and is dependent on DivIC and PBP2B for its recruitment to the divisome. Together with EzrA, it is a key component of the system that regulates PBP1 localization during cell cycle progression. Its main role could be the removal of PBP1 from the cell pole after pole maturation is completed. GpsB also contributes to the recruitment of PBP1 to the division complex and is not essential for septum formation .
Probable inactive purple acid phosphatase 14/16/28/29 (PAP14/16/28/29)
Type: Family

This group of conserved proteins from plants and some bacteria contain one copy of the calcineurin-like phosphoesterase domain . Members from Arabidopsi lack the conserved His residue essential for phosphatase activity.
Bacteriophage VT1-Sakai, H0018 (Phage_VT1-Sakai_H0018)
Type: Family

This entry represents a large family of phage proteins. These proteins form a trimeric arrangement which stabilises the phage capsid. The proteins have what is known as a β-tulip fold.

This entry is represented by Bacteriophage VT1-Sakai, H0018. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probable tellurium resistance transcriptional regulator TerW (TerW)
Type: Family

This group represents Probable tellurium resistance transcriptional regulator TerW from the IncHI2 R478 plasmid in Serratia marcescens that specifies resistance to tellurite (Te(r)), to some bacteriophages (Phi) and to pore-forming colicins (PacB) . TerW binds specifically to the potential promoter region of the terZABCDE operon and probably regulates expression of the genes [Valkovicova et al., 2011, Biologia 66].
Fumarylacetoacetase-like, C-terminal (Fumarylacetoacetase-like_C)
Type: Domain

Fumarylacetoacetase (

; also known as fumarylacetoacetate hydrolase or FAH) catalyses the hydrolytic cleavage of a carbon-carbon bond in fumarylacetoacetate to yield fumarate and acetoacetate as the final step in phenylalanine and tyrosine degradation . This is an essential metabolic function in humans, the lack of FAH causing type I tyrosinaemia, which is associated with liver and kidney abnormalities and neurological disorders . The enzyme mechanism involves a catalytic metal ion, a Glu/His catalytic dyad, and a charged oxyanion hole . FAH folds into two domains: an N-terminal domain SH3-like β-barrel, and a C-terminal with an unusual fold consisting of three layers of β-sheet structures .

This entry represents the C-terminal domain of fumarylacetoacetase, as well as other domains that share a homologous α/β structure, including:

5-carboxymethyl-2-hydroxymuconate delta-isomerase (CHM isomerase;

), which catalyses the conversion of 5-carboxymethyl-2-hydroxymuconate to 5-carboxy-2-oxohept-3-enedioate .

5-oxopent-3-ene-1,2,5-tricarboxylate decarboxylase (OPET decarboxylase;

), which catalyses the conversion of 5-oxopent-3-ene-1,2,5-tricarboxylate to 2-oxohept-3-enedioate and carbon dioxide.

Bifunctional enzyme HpcE (OPET decarboxylase

/HHDD isomerase

), which is a duplication consisting of a tandem repeat of two FAH C-terminal-like domains. This enzyme is responsible for the degradation of 4-hydroxyphenylacetate, a product of tyrosine and phenylalanine metabolism also released by lignin catabolism .

2-keto-4-pentenoate hydratase MhpD (

; also known as 2-oxopent-4-enoate hydratase), which converts 4-hydroxy-2-oxopentanoate to 2-oxopent-4-enoate .

4-oxalocrotonate decarboxylase (4-OD;

), which catalyses the conversion of 4-oxalocrotonate to 2-oxopent-4-enoate and carbon dioxide .

2-oxo-hepta-3-ene-1,7-dioic acid hydratase, which hydrates the double bond of 2-oxo-hepta-3-ene-1,7-dioic acid to form 4-hydroxy-2-oxo-heptane-1,7-dioic acid in the catabolism of 4-hydroxyphenylacetic acid.

Oxaloacetate tautomerase FAHD1

that converts enol-oxaloacetate, a strong inhibitor of succinate dehydrogenase, to the physiological keto form of oxaloacetate
MepB-like (MepB-like)
Type: Family

In Staphylococcus aureus MepB is encoded by the MepRAB operon. This operon has been shown to play a role in drug resistance and, although the functions of MepR and MapA are known, there is still little information regarding MepB's function. Structural studies have shown that this protein is structural similar to the PD-(D/E)XK family of endonucleases, although PD-(D/E)XK's catalytic active site residues are not conserved in MepB. MepB binds DNA and RNA, with a higher affinity for RNA and single stranded DNA than for double stranded DNA. The association of MepB with this drug resistance operon suggests that this protein is involved in antimicrobial response, role which is believed to be carried out through its interactions with nucleic acids .
Bacterial microcompartment shell protein PduT (Micro_shell_prot_PduT)
Type: Family

Members of this group are bacterial microcompartment shell proteins: PduT of Salmonella enterica and its orthologs in the propriondiol and ethanolamine operons of bacteria .

Some non-autotrophic organisms form polyhedral organelles, enterosomes , that resemble the carboxysomes found in autotrophs, particularly the cyanobacteria. Carboxysomes are well-studied polyhedral organelles found in cyanobacteria and some chemoautotrophs . They are composed of a proteinaceous shell that houses most of the cell s ribulose bisphosphate carboxylase/oxygenase (RuBisCO). They are required for autotrophic growth at low CO
2
concentrations and are thought to function as part of a CO
2
-concentrating mechanism .

Polyhedral organelles, enterosomes, from non-autotrophic organisms are involved in coenzyme B12-dependent 1,2-propanediol utilization (e.g., in S. enterica, ) and ethanolamine utilization (e.g., in Salmonella typhimurium ). Genes needed for enterosome formation are located in the 1,2-propanediol utilization
pdu
or ethanolamine utilization
eut
operons, respectively. Although enterosomes of non-autotrophic organisms are apparently related to carboxysomes structurally, a functional relationship is uncertain. A role in CO
2
concentration, similar to that of the carboxysome, is unlikely since there is no known association between CO
2
and coenzyme B12-dependent 1,2-propanediol or ethanolamine utilization .

In S. enterica the propriondiol degrading enterosome consists of at least 15 proteins, of which, at least, seven are shell proteins: pduA , pduB, B', J, K, T and U. In addition the organelle contains four enzymes: B
12
-dependent diol dehydratase (pduCDE) and its reactivating factor (pduGH), CoA-dependent proprionaldehyde dehydrogenase (pduP, ) and adenosyl transferase (pduO) . It has been suggested that enterosomes sequester toxic aldehydes formed during both 1,2-propanediol and ethanolamine degradation and channel them to subsequent pathway enzymes. It has also been suggested that polyhedra might be used to protect diol dehydratase and ethanolamine ammonia-lyase from oxygen, to which both are sensitive . Mutational studies of PduA indicate that the organelles of S. enterica are not involved in concentrating 1,2-propanediol or CN-B12, but are consistent with a role in moderating aldehyde toxicity .
Phosphoesterase cyanobacterial, all2852 (Pesterase_cyn)
Type: Family

This group represents a predicted phosphoesterase, all members are Cyanobacteria.
Phosphoesterase-related protein YunD (Pesterase_YunD)
Type: Family

These conserved proteins from Gram-positive bacteria possess most of the motifs characteristic of a variety of enzymatically active phosphoesterases , including acid and alkaline phosphatases, phosphoprotein phosphatases, 5'-nucleotidase, bis(5'-nucleosyl)-tetraphosphatase (symmetrical), sphingomyelin phosphodiesterase, 2',3'-cylic-nucleotide 2'-phosphodiesterase, and 3',5'-nucleotide phosphodiesterase CpdA. Interestingly, the catalytically active histidine usually found has been replaced by asparagine in these proteins, so their catalytic activity is speculative.
Bifunctional acetylglutamate kinase/N-acetyl-gamma-glutamyl-phosphate reductase (NAGK/NAGSA)
Type: Family

This group represents a bifunctional acetylglutamate kinase (

)/N-acetyl-gamma-glutamyl-phosphate reductase (

), which is found in fungi. It contains an N-terminal acetylglutamate kinase (also known as N-acetyl-L-glutamate kinase, NAGK) domain and a C-terminal N-acetyl-gamma-glutamyl-phosphate reductase (NAGSA) domain .

The budding yeast member, Arg5,6, is expressed as a precursor that is then maturated in the mitochondria into acetylglutamate kinase and acetylglutamyl-phosphate reductase. It is involved in the arginine biosynthesis pathway, catalyzing the second and third steps in the pathway .