SII-SWORD/CoKE huggingface dataset:
Methyltransferase MnmM-like (MnmM_MeTrfase)
Type: Family

This entry represents the family of tRNA (mnm(5)s(2)U34)-methyltransferase MnmM (also known as YtqB in Bacillus subtilis) and related proteins. This enzyme is involved in the biosynthesis of 5-methylaminomethyl-2-thiouridine (mnm5s2U) at the wobble position (U34) in tRNA by catalysing the transfer of a methyl group from S-adenosyl-L-methionine to nm5s2U34 to form mnm5s2U34 . It adopts a typical SAM-dependent class I methyltransferase fold .
Alpha-L-arabinofuranosidase, C-terminal (Alpha-L-AF_C)
Type: Domain

This entry represents the C terminus (approximately 200 residues) of bacterial and eukaryotic alpha-L-arabinofuranosidase (

). This catalyses the hydrolysis of non-reducing terminal alpha-L-arabinofuranosidic linkages in L-arabinose-containing polysaccharides .
Probable O-methyltransferase UstE-like (UstE-like)
Type: Family

This family contains a number of bacterial and eukaryotic proteins that are mostly uncharacterised. This entry includes UstE, a probable O-methyltransferase part of the gene cluster that mediates the biosynthesis of ustilaginoidins .
Biotin and thiamin synthesis-associated domain (BATS_dom)
Type: Domain

This domain is found in biotin synthase and 2-iminoacetate synthase. The latter enzyme is involved in thiamine diphosphate biosynthesis. The reactions catalysed by these enzymes involve the binding of co-factors and both enzymes function as dimers . This domain may therefore be involved in co-factor binding or dimerisation. The domain is also found in proteins that are currently uncharacterised, such as

.
HemN, C-terminal (HemN_C)
Type: Domain

This domain is found in the C-terminal region of oxygen-independent coproporphyrinogen-III oxidases (HemN) . This enzyme catalyses the oxygen-independent conversion of coproporphyrinogen-III to protoporphyrinogen-IX , one of the last steps in haem biosynthesis. The function of this domain is unclear, but comparison to other proteins containing a radical SAM domain suggest it may be a substrate binding domain.
Replication initiator A, N-terminal (RepA_N)
Type: Domain

This entry represents the N terminus (approximately 80 residues) of replication initiator protein A (RepA), a DNA replication initiator in plasmids . Most proteins in this entry are bacterial, but archaeal and eukaryotic members are also included.
Domain of unknown function DUF1299 (DUF1299)
Type: Domain

This entry represents a conserved region approximately 50 residues long within a number of proteins of unknown function that seem to be specific to Arabidopsis thaliana. Note that many proteins contain multiple copies of this region.
Protein of unknown function DUF1302 (DUF1302)
Type: Family

This family contains a number of hypothetical bacterial proteins of unknown function that are approximately 600 residues long. Most family members seem to be from Proteobacteria.
Large ribosomal subunit protein uL29m, mitochondrial (Ribosomal_uL29_mit)
Type: Family

This entry represents the eukaryotic mitochondrial ribosomal protein uL29 (also known as MRP-L47). Mitochondrial ribosomal proteins (MRPs) are the counterparts of the cytoplasmic ribosomal proteins, in that they fulfil similar functions in protein biosynthesis. However, they are distinct in number, features and primary structure .

Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.

Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome .
Heterokaryon incompatibility (HET)
Type: Domain

This entry represents a conserved region approximately 150 residues long within various heterokaryon incompatibility proteins that seem to be restricted to ascomycete fungi. Genetic differences in specific het genes prevent a viable heterokaryotic fungal cell from being formed by the fusion of filaments from two different wild-type strains . Many proteins of this entry also contain the WD domain, G-beta

repeat and the NACHT

domain.
Type VI secretion, TssG-like (T6SS_TssG-like)
Type: Family

The bacterial Type VI secretion system (T6SS) is capable of injecting toxins into eukaryotic cells, which contributes to a successful infection . This entry represents a group of Gram-negative bacterial proteins that form part of the type VI pathogenicity secretion system (T6SS), including TssG . TssG is homologues to phage tail proteins and is required for proper assembly of the Hcp tube (the T6SS inner tube) in bacteria. One other member in this family, SciB (

) from Salmonella enterica, is thought to be involved in virulence .
Domain of unknown function DUF1308 (DUF1308)
Type: Domain

This is a domain of unknown function found on the C-terminal of C7orf25 protein UPF0415. The C-terminal domain is homologous to the known PIN-like domains. The PIN-like domain is widespread among eukaryotes, including animals, plants, and fungi, but also present in some cyanobacteria, Deinococcus, and dsDNA viruses from the Mimiviridae family. The domain retains up to four potential catalytic residues, thus, depending on the protein is predicted to be an active or inactive nuclease and in a majority of the family members, the PIN-like domain is N-terminally fused with a potentially active PD-(D/E)XK-like domain

.
Copine, C-terminal (Copine_C)
Type: Domain

This represents a conserved region approximately 180 residues long within eukaryotic copines. Copines are Ca
2+
-dependent phospholipid-binding proteins that are thought to be involved in membrane-trafficking, and may also be involved in cell division and growth . They were originally identified in paramecium. They are found in human and orthologues have been found in C. elegans and Arabidopsis Thaliana. None have been found in D. Melanogaster or S. Cereviciae. Phylogenetic distribution suggests that copines have been lost in some eukaryotes . No functional properties have been assigned to the VWA domains present in copines. The members of this subgroup contain a functional MIDAS motif based on their preferential binding to magnesium and manganese. However, the MIDAS motif is not totally conserved, in most cases the MIDAS consists of the sequence DxTxS instead of the motif DxSxS that is found in most cases. The C2 domains present in copines mediate phospholipid binding .
Sperm-tail PG-rich repeat (SHIPPO-rpt)
Type: Repeat

This entry represents a short conserved region carrying a PGP motif that is repeated in the eukaryotic sperm tail protein, outer dense fibre protein 3 (also known as Ciliary microtubule associated protein 1A) . Orthologues from some species may include up to 40 Pro-Gly-Pro repeats.
Four-carbon acid sugar kinase, N-terminal domain (4-carb_acid_sugar_kinase_N)
Type: Domain

This conserved region is found in four-carbon acid sugar kinases from a range of Proteobacteria as well as the Gram-positive Oceanobacillus iheyensis. These four-carbon acid sugar kinases are composed of two domains: an N-terminal domain and a C-terminal domain connected by a variable linker sequence. The N-terminal domain exhibits an α/β-fold composed of an eight-stranded parallel β-sheet. The C-terminal domain also exhibits an α/β-fold composed of a seven-stranded mixed β-sheet. The acid sugar is bound by the N-terminal domain, while nucleotide by the C-terminal domain .

Proteins containing this domain include D-threonate kinase from Salmonella typhimurium (DtnK), 3-oxo-tetronate kinase from Methylobacterium radiotolerans, 3-oxo-isoapionate kinase from Paraburkholderia graminis and D-erythronate kinase from Heliobacterium modesticaldum. DtnK catalyzes the ATP-dependent phosphorylation of D-threonate to D-threonate 4-phosphate and is also able to phosphorylate 4-hydroxy-L-threonine, which may serve to deal with the toxicity of this compound .
Protein of unknown function DUF1310 (DUF1310)
Type: Family

This family consists of several hypothetical proteins of around 125 residues in length. Members of this family seem to be specific to Firmicutes and Actinobacteria. The function of this family is unknown.
Endomucin (Endomucin)
Type: Family

Endomucin, also known as sialomucin or mucin-like sialoglycoprotein, is a membrane-bound glycoprotein expressed luminally by endothelial cells that line postcapillary venules, a primary site of leukocyte recruitment during inflammation . It interferes with the assembly of focal adhesion complexes and inhibits interaction between cells and the extracellular matrix .
Protein of unknown function DUF1314 (DUF1314)
Type: Family

This family consists of several alphaherpesvirus proteins of around 200 residues in length. Their function is unknown .
Respirasome Complex Assembly Factor 1 (RCAF1)
Type: Family

This family represents the Respirasome Complex Assembly Factor 1 (RCAF1, also known as GEL complex subunit OPTI,) a Rab5-interacting protein involved in the assembly of mitochondrial respiratory complexes . It is a component of the multi-pass translocon (MPT) complex that mediates insertion of multi-pass membrane proteins into the lipid bilayer of membranes .
Methionine biosynthesis MetW (Methionine_synth_MetW)
Type: Family

This family consists of several bacterial and one archaeal methionine biosynthesis MetW proteins. Biosynthesis of methionine from homoserine in Pseudomonas putida takes place in three steps. The first step is the acylation of homoserine to yield an acyl-L-homoserine. This reaction is catalysed by the products of the metXW genes and is equivalent to the first step in enterobacteria, Gram-positive bacteria and fungi, except that in these microorganisms the reaction is catalysed by a single polypeptide (the product of the metA gene in Escherichia coli and the met5 gene product in Neurospora crassa). In P. putida, as in Gram-positive bacteria and certain fungi, the second and third steps are a direct sulphydrylation that converts the O-acyl-L-homoserine into homocysteine and further methylation to yield methionine. The latter reaction can be mediated by either of the two methionine synthetases present in the cells . MetW from P. aeruginosa activates the enzymatic activity of MetX and is essential for the feedback inhibition by S-adenosyl-L-homocysteine (SAH), which suggests that MetW is a regulatory protein of MetX .
Bacteriophage CI repressor, N-terminal (Phage_CI_N)
Type: Domain

The bacteriophage lambda cI repressor is a part of a phage molecular switch which transforms the phage from lysogenic to lytic growth. The CI repressor from Enterobacteria phage phi80 is known to function as a transcriptional switch, determining whether transcription is lytic or lysogenic . It contains two domains connected by a flexible "hinge" region with a cleavage site .

This entry represents the N-terminal domain of the CI repressor, which is involved in DNA binding .
Commelina yellow mottle virus, Orf1 (CYMV_Orf1)
Type: Family

This entry is represented by Commelina yellow mottle virus, Orf1. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

This family contains a number of viral proteins of unknown function approximately 200 residues long. Family members seem to be restricted to badnaviruses.
YfeC-like (YfeC-like)
Type: Family

This family consists of a group of proteins predominantly found in Enterobacteria, including Uncharacterized protein YfeC from Escherichia coli, a dual transcriptional regulator predicted to form homodimers .
SGF29 tudor-like domain (SGF29_tudor-like_dom)
Type: Domain

SAGA-associated factor 29 (SGF29) is involved in transcriptional regulation as a chromatin reader component of some histone acetyltransferase (HAT) SAGA-type complexes like the TFTC-HAT, ATAC or STAGA complexes . SGF29 specifically recognises and binds methylated 'Lys-4' of histone H3 (H3K4me), with a preference for the trimethylated form (H3K4me3). It also may be involved in MYC-mediated oncogenic transformation .

This entry represents the two tandem tudor-like domains found at the C-terminal of yeast and human SAGA-associated factor 29 proteins and the plant homologues. Each of them has a negatively-charged pocket capable of binding H3A1 and an aromatic cage for the recognition of H3K4me2/3 residues .
Plasmid replication initiator protein TrfA (TrfA)
Type: Family

This family consists of several bacterial TrfA proteins. The trfA operon of broad-host-range IncP plasmids is essential to activate the origin of vegetative replication in diverse species. The trfA operon encodes two ORFs. The first ORF is highly conserved and encodes a putative single-stranded DNA binding protein (Ssb). The second, trfA, contains two translational starts as in the IncP alpha plasmids, generating related polypeptides of 406 (TrfA1) and 282 (TrfA2) amino acids. TrfA2 is very similar to the IncP alpha product, whereas the N-terminal region of TrfA1 shows very little similarity to the equivalent region of IncP alpha TrfA1. This region has been implicated in the ability of IncP alpha plasmids to replicate efficiently in Pseudomonas aeruginosa .
Protein of unknown function DUF1329 (DUF1329)
Type: Family

This family consists of several hypothetical bacterial proteins of around 475 residues in length. The majority of family members are from Pseudomonas species but the family also contains sequences from Shewanella oneidensis and Thauera aromatica.
Domain of unknown function DUF1330 (DUF1330)
Type: Domain

This family consists of several hypothetical bacterial proteins of around 90 residues in length. The function of this family is unknown.
Optic atrophy 3-like (OPA3-like)
Type: Family

OPA3 deficiency causes type III 3-methylglutaconic aciduria (MGA) in humans. This disease manifests with early bilateral optic atrophy, spasticity, extrapyramidal dysfunction, ataxia, and cognitive deficits, but normal longevity .

This family consists of several optic atrophy 3 (OPA3) proteins and related proteins from other eukaryotic species, the function is unknown.
Telomere length and silencing protein 1-like (Tls1-like)
Type: Family

Tls1 in fission yeast is required for telomeric heterochromatin assembly as well as telomere length control . The human homologue, the splicing factor C9orf78 (also known as hepatocellular carcinoma-associated antigen 59), plays a role in pre-mRNA splicing by promoting usage of the upstream 3'-splice site at alternative NAGNAG splice sites . It may also modulate exon inclusion events and plays a role in spliceosomal remodeling by displacing WBP4 from SNRNP200 and may act to inhibit SNRNP200 helicase activity . C9orf78 is required for proper chromosome segregation .
Trans-2-enoyl-CoA reductase (Trans-2-enoyl-CoA_reductase)
Type: Family

This entry represents trans-2-enoyl-CoA reductase which catalyses reduction of enoyl-CoA to acyl-CoA, an important step of fatty acid biosynthesis which is performed under anaerobiosis . This entry also includes triclosan-resistant enoyl-acyl carrier protein reductase, such as FabV from Pseudomonas aeruginosa and Aeromonas salmonicida .
DNA repair protein, Swi5 (DNA-repair_Swi5)
Type: Family

This entry represents Swi5 and is involved in meiotic DNA repair synthesis and meiotic joint molecule formation . It is known to interact with Swi2, Rhp51 and Swi6 .
Clc protein-like (Clc_prot-like)
Type: Family

Clc proteins are a nine-member gene family of chloride channels that have diverse roles in the plasma membrane and in intracellular organelles, especially membrane excitability and the maintenance of osmotic balance . These proteins have been widely related with a variety of human diseases ranging from degeneration of the retina to lung cancer and epilepsy . This protein family includes Clc-like protein 2/5 from Caenorhabditis elegans and similar proteins from animals.
Capsid protein, T4-like bacteriophage-like (Gp23/Gp24_T4-like)
Type: Family

This family contains a number of capsid Gp23 and Gp24 proteins approximately 500 residues long, mainly from T4-like bacteriophages. Bacteriophage T4 Gp24 is a capsid protein that self-associates to form 11 pentons, building the T=13 laevo capsid in association with 160 hexamers of gp23* and one dodecamer of gp20 .
2-dehydro-3-deoxy-phosphogluconate aldolase (DgaF)
Type: Family

DgaF is part of the dga operon required for wild-type growth of Salmonella Typhimurium with D-glucosaminate. It catalyses the conversion of keto-3-deoxygluconate 6-phosphate (KDGP) to yield pyruvate and glyceraldehyde-3-phosphate. Orthologs of the dga genes are largely restricted to certain enteric bacteria and a few species in the phylum Firmicutes .
Protein of unknown function DUF1347 (DUF1347)
Type: Family

This family consists of several hypothetical bacterial proteins of around 610 residues in length. Members of this family are highly conserved and seem to be specific to Chlamydia species. The function of this family is unknown.
Protein of unknown function DUF1350 (DUF1350)
Type: Family

This family consists of several hypothetical proteins from both cyanobacteria and plants. Members of this family are typically around 250 residues in length. The function of this family is unknown but the species distribution indicates that the family may be involved in photosynthesis.
DRTGG (DRTGG)
Type: Domain

This presumed domain is about 120 amino acids in length. It is found associated with CBS domains

, as well as the CbiA domain

. The function of this domain is unknown. It is named the DRTGG domain after some of the most conserved residues. This domain may be very distantly related to a pair of CBS domains. There are no significant sequence similarities, but its length and association with CBS domains supports this idea.
Campylobacter phage CGC-2007, Cje0229 (Phage_CGC-2007_Cje0229)
Type: Family

This entry is represented by Campylobacter phage CGC-2007, Cje0229. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

This family consists of several hypothetical phage and bacterial proteins of around 100 residues in length. The function of this family is unknown.
Putative glutamine amidotransferase (GATase1-like)
Type: Domain

This domain can be found in several hypothetical bacterial proteins of around 250 residues in length. The function of this domain is unknown. The structure of this cytoplasmic domain was solved by the Midwest Center for Structural Genomics (MCSG). The structure has been classified as part of the Class-I Glutamine amidotransferase superfamily owing to similarity with other known structures. The monomer combines with itself to form a hexamer, and this hexamer exposes a potential catalytic surface rich in Glu, Asp, Tyr, Ser.Trp and His residues .
Ribosomal RNA aminoglycoside-resistance methyltransferase, Gram-negative bacteria (rRNA_MeTrfase_GmN_bac)
Type: Family

This family consists of several ribosomal RNA methyltransferases from Gram-negative bacteria involved in aminoglycoside-resistance .
Ecd family (Ecd)
Type: Family

This entry represents Ecd (ecdysoneless) family. Drosophila ecd mutants display reduced steroid titers during larval development . Mammalian Ecd (also known as SGT1 and hEcd in humans) has been shown to stimulate cell proliferation by interacting with the Retinoblastoma (Rb) proteins . Ecd proteins may be involved in pre-mRNA splicing .
Intracellular growth attenuator IgaA (IgaA)
Type: Family

This family consists of several bacterial intracellular growth attenuator (IgaA) proteins. IgaA is involved in negative control of bacterial proliferation within fibroblasts. IgaA is homologous to the Escherichia coli YrfF and Proteus mirabilis UmoB proteins. Whereas the biological function of YrfF is currently unknown, UmoB has been shown elsewhere to act as a positive regulator of FlhDC, the master regulator of flagella and swarming. FlhDC has been shown to repress cell division during P. mirabilis swarming, suggesting that UmoB could repress cell division via FlhDC. This biological function, if maintained in Salmonella enterica, could sustain a putative negative control of cell division and growth exerted by IgaA in intracellular bacteria .
Protein of unknown function DUF1359 (DUF1359)
Type: Family

This family consists of several hypothetical bacterial and phage proteins of around 100 residues in length. Members of this family seem to be found exclusively in Lactococcus lactis and the bacteriophages that infect this species. The function of this family is unknown.
Mycobacterium phage PG1, Gp7 (Mycophage_PG1_Gp7)
Type: Family

This entry is represented by Mycobacterium phage PG1, Gp7. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

This family consists of several bacterial proteins of around 115 residues in length. Members of this family are found in Bacillus species and Streptomyces coelicolor, the function of the family is unknown.
Putative nuclease YbcO (YbcO)
Type: Family

This entry includes YbcO (

), a putative nuclease from E. coli . Proteins in the entry have been predicted to have the His-Me finger nuclease domain and may act as a recombinase that participates in DNA repair and replication .
Protein of unknown function DUF1365 (DUF1365)
Type: Family

This family consists of several bacterial and plant proteins of around 250 residues in length. The function of this family is unknown.
Homologous-pairing protein 2, winged helix domain (Hop2_WH_dom)
Type: Domain

Homologous-pairing protein 2 (Hop2) is required for proper homologous pairing and efficient cross-over and intragenic recombination during meiosis .

The mammalian HOP2 homologue, TBPIP, was first identified as a factor interacting with TBP-1, which binds to the human immunodeficiency virus, type 1 Tat protein . Later, TBPIP was found to be an activator that specifically stimulates the homologous pairing catalyzed by DMC1 .

This entry represents the winged helix domain found in Hop2.
PipA (PipA)
Type: Family

This family consists of several Salmonella PipA (pathogenicity island-encoded protein A) and related phage sequences. PipA is thought to contribute to enteric but not to systemic salmonellosis . The family carries a highly conserved HEXXH sequence motif along with several highly conserved glutamic acid residues which might be indicative of the family being a metallopeptidase.
Protein of unknown function DUF1368 (DUF1368)
Type: Family

This family consists of several proteins with seem to be specific to red algae plasmids. Members of this family are typically around 415 residues in length. The function of this family is unknown.