SII-SWORD/CoKE huggingface dataset:
Large ribosomal subunit protein mL46, N-terminal (Ribosomal_mL46_N)
Type: Domain

This entry represents the N-terminal domain found in the mitochondrial large ribosomal subunit protein mL46, also known as MRLP46 in mammals and MRLP17 in yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe .
Baculoviridae late expression factor 5, C-terminal (Baculo_LEF5_C)
Type: Domain

This C-terminal domain is likely to be a zinc-binding domain.
WxL Interacting Protein, host binding domain (WxLIP_HBD)
Type: Domain

This entry represents a domain found in WxL interacting proteins (WxLIP) which play a role in virulence and are widely distributed in firmicutes. The WxL proteins usually occur within a gene cluster that contains two WxL proteins and a WxL interacting protein composed of three domains: peptidoglycan binding domain (PGBD), host binding domain (HBD), and transmembrane helix (TMH). The domain represented by this entry, previously known as DUF3324, is likely to interact with proteins on the surface of eukaryotic host endothelial cells. This HBD domain is frequently found in combination with PGBD domain (

) and both were shown to function synergistically as a single unit that binds to the peptidoglycan and interacts with the eukaryotic host . The HBD domain is predicted to adopt a β-sandwich with an Ig-like topology.
Plasmid replication protein C, C-terminal (RepC_C)
Type: Domain

Proteins in this group have homology with the RepC protein of Agrobacterium Ri and Ti plasmids . repABC plasmids are widely distributed among alphaproteobacteria; all repABC operons contain at least three protein-encoding genes: repA, repB and repC. The first two genes encode proteins involved in plasmid segregation, whereas repC encodes a protein crucial for replication. The origin of replication maps within the repC gene . RepC is rate limiting for pT181 replication and it is likely that pT181 replication is regulated at the level of RepC synthesis . This entry represents the C-terminal domain of plasmid replication protein RepC.
UDP-glucuronate decarboxylase N-terminal (UXS1_N)
Type: Domain

The N terminus of the UDP-glucuronate decarboxylases may be involved in localisation to the perinuclear Golgi membrane .
Protein of unknown function DUF3325 (DUF3325)
Type: Family

This family of short proteins are functionally uncharacterised. This family is restricted to Alpha-, Beta- and Gamma-proteobacteria.
Protein of unknown function DUF3326 (DUF3326)
Type: Family

This family of functionally uncharacterised proteins is found in plants and bacteria.
Enterochelin esterase, N-terminal (Enterochelin_esterase_N)
Type: Domain

This entry represents the N-terminal domain of enterochelin esterase. The activity of the enzyme has been characterised . Fes catalyses the hydrolysis of the 2,3-dihydroxy-N-benzoyl-L-serine trimer, enterochelin, forming 2,3-dihydroxybenzoylserine. It also catalyses hydrolysis of free enterobactin and ferric enterobactin. Upon hydrolysis of ferric enterobactin by Fes, released iron is probably reduced by a second enzyme.
Mycotoxin biosynthesis protein UstYa-like (UstYa-like)
Type: Family

Oxidase ustYa is involved in the the production of ustiloxins, toxic cyclic peptides, in fungi. Ustiloxins were found to be the first example of cyclic peptidyl secondary metabolites that are ribosomally synthesized in filamentous fungi. The homologous genes ustYa and ustYb (which are found in the gene cluster for ustiloxins) have been shown to be involved in cyclization of the peptide .

Other proteins in this entry include cyclochlorotine biosynthesis proteins O, P and R from
Talaromyces islandicus
which are encoded within a cluster of genes required for biosynthesis of the mycotoxin cyclochlorotine. CccP is probably the phenylalanine aminomutase that provides the unusual beta-Phe amino acid, but the roles of the other proteins are unknown .
Phosphate regulon sensor protein PhoR (PhoR)
Type: Family

PhoR is a member of the two-component regulatory system PhoR/PhoB involved in the phosphate regulon genes expression. PhoR is the bifunctional histidine autokinase/phospho-PhoB phosphatase that donates a phosphoryl group to PhoB when environmental Pi is limiting and removes the phosphoryl group from phosphorylated PhoB (PhoB~P) when environmental Pi is abundant .
Transposon Tn21 modulator protein (TnpM)
Type: Family

TnpM enhances the Tn21 transposition by activating expression of the transposase gene and decreases the resolution of the cointegrated DNA by suppressing expression of the resolvase gene .
Protein of unknown function DUF3332 (DUF3332)
Type: Family

This family of proteins is functionally uncharacterised.
Protein of unknown function DUF3331 (DUF3331)
Type: Family

This family of proteins are functionally uncharacterised. This family is only found in bacteria. Proteins in this family vary in length from 96 to 160 amino acids.
Protein of unknown function DUF3335 (DUF3335)
Type: Family

This family of proteins are functionally uncharacterised. This family is only found in bacteria. This presumed domain is typically between 226 to 230 amino acids in length.
Triacylglycerol lipase, N-terminal (Triacylglycerol_lipase_N)
Type: Domain

This is an N-terminal domain that is found adjacent to the patatin/phospholipase A2-related domain (see

) in a group of proteins. Proteins containing this domain include Tgl3/4/5 from Saccharomyces cerevisiae. Tgl3 is a bifunctional triacylglycerol lipase and lysophospholipid acyltransferase . Tgl4/5 are multifunctional lipase/hydrolase/phospholipases . They are generally involved in triacylglycerol mobilisation and localized to lipid particles .

This entry also includes plant sugar-dependent 1 (SDP1) protein, which is a triacylglycerol lipase that initiates storage oil breakdown in germinating Arabidopsis seeds .
WDR48/Bun107 (WDR48/Bun107)
Type: Family

This entry includes WDR48 from animals, Bun107 from fission yeasts and Duf1 from budding yeasts. WDR48 (also known as UAF1) is a regulator of deubiquitinating complexes . Bun107 is required for the Ubp9 recruitment to septa and cell tips but also for its enzymatic activity at these specific locations .
Trafficking protein particle complex subunit 11 (TPC11)
Type: Domain

This entry represents a domain found in trafficking protein particle complex subunit 11 (Trappc11), which is involved in endoplasmic reticulum to Golgi apparatus trafficking at a very early stage . The C terminus of this region contains TPR repeats.

In zebrafish, Trappc11 is also known as protein foie gras. It has been shown to affect development; the mutants develop large, lipid-filled hepatocytes in the liver, resembling those in individuals with fatty liver disease .
Cytohesin Ubiquitin Protein Inducing Domain (CUPID)
Type: Domain

This entry represents a domain named CUPID (Cytohesin Ubiquitin Protein Inducing Domain) that is found in animal proteins. It is found towards the N-terminal end of Innate immunity activator protein (INAVA, Innate Immune Activator), a risk factor for the chronic inflammatory bowel diseases (IBD). Mice lacking the protein show defects in intestinal barrier integrity at steady state and greater susceptibility to mucosal infection.

CUPID is also found towards the N-terminal end of Coiled-coil domain-containing protein 120 (CC120) and C-terminal to the FERM domain in FERM domain-containing protein 4A/B (FRM4A/B), which are implicated in neurite outgrowth, and in human cancer, Alzheimer's, celiac, and heart disease.

All appear to bind the ARF-GEF (guanine nucleotide-exchange factors) cytohesin family members, such as proteins (ARF 1-4), which regulate cell membrane and F-actin dynamics. INAVA-CUPID binds cytohesin 2 (also known as ARNO), targets the molecule to lateral membranes of epithelial monolayers, and enables ARNO to affect F-actin assembly that underlies cell-cell junctions and barrier function. In the case of inflammatory signalling, ARNO can coordinate CUPID function by binding and inhibiting CUPID activity of acting as an enhancer of TRAF6 dependent polyubiquitination. In other words, ARNO acts as a negative-regulator of inflammatory responses. In summary, INAVA-CUPID exhibits dual functions, coordinated directly by ARNO, that bridge epithelial barrier function with extracellular signals and inflammation .
Protein of unknown function DUF3339 (DUF3339)
Type: Family

This family of proteins are functionally uncharacterised. This family is found in eukaryotes. Proteins in this family are about 70 amino acids in length.
Alternative complex III, ActD subunit (ActD)
Type: Family

Alternative complex III (ACIII) is a multisubunit quinol:electron acceptor oxidoreductase that couples quinol oxidation with transmembrane proton translocation similar to bc1 complex (or complex III). It is a key component of the respiratory and photosynthetic electron transport chains in many bacteria. It has six subunits (ActA-F), ActD subunit represented in this entry. The transmembrane regions of this subunit is part of the TM arm of the complex . Although the function of this subunit is not clear, it may play a role in stabilizing the TM region of ACIII which contributes to a stable menaquinol binding pocket and proton translocation passage .
SANT and BTB domain regulator of CSR, BTB domain (SANBR_BTB)
Type: Domain

Class switch recombination (CSR) is the process by which B cells switch production from IgM/IgD to other immunoglobulin isotypes in the immune response process. This entry represents the BTB domain found at the N-terminal half of the protein SANT and BTB domain regulator of class switch recombination (SANBR, previously known as KIAA1841). This domain is responsible for the negative regulation of CSR . This entry includes proteins predominantly found in animals.
Putative Se/S carrier protein-like (Se/S_carrier-like)
Type: Domain

This domain is found in bacteria and archaea. It has been suggested that proteins in this family may be chaperones involved in Se or S trafficking in the cell .
Domain of unknown function DUF3344 (DUF3344)
Type: Domain

This presumed domain is found proteins that are functionally uncharacterised, found in bacteria and archaea. Proteins in this family are typically between 367 to 1857 amino acids in length.
Nuclear/hormone receptor activator site AF-1 (Nuc_recep-AF1)
Type: Domain

Nuclear receptors (NRs) are a family of ligand-inducible transcription factors, and, like other transcription factors, they contain a distinct DNA binding domain that allows for target gene recognition and several activation domains that possess the ability to activate transcription . One of these activation domains is at the N-terminal, although there are two distinct motifs within this domain, between residues 20-36 and between 74 and the end of this domain, which are the binding regions. One of the co-activators is TIF1beta, which appears to bind at the first motif .
Replication initiator protein RctB, central region (RctB_central_dom)
Type: Domain

This region is found in the replication initiator protein RctB from Vibrio cholerae

and similar sequences predominantly found in Vibrionales. RctB mediates oriCII-based replication and other regulatory processes. This protein is organised into four
domains and adopts a dimeric configuration, which occurs with the interface in one of the two central domains: a seven-stranded β-sheet form a swapped configuration with the same domain of the other monomer. It seems to be involved in DNA binding .
Domain of unknown function DUF3347 (DUF3347)
Type: Domain

This entry represents a functionally uncharacterised domain found in bacterial proteins.
Protein of unknown function DUF3348 (DUF3348)
Type: Family

This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 244 to 323 amino acids in length.
Protein of unknown function DUF3349 (DUF3349)
Type: Family

This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 99 to 124 amino acids in length. According to literature, the DUF3349 proteins are predicted to be good drug targets because they are predominantly in the Mycobacterium and Rhodococcus bacterial species .
Domain of unknown function DUF3350 (DUF3350)
Type: Domain

This domain is functionally uncharacterised, and it is found in eukaryotic proteins such as TBC1 domain family member 1 and 4 (TBC1D1 and TBCD4). This presumed domain is typically between 50 to 64 amino acids in length. TBC1 and 4 may act as GTPase-activating proteins for Rab family proteins .
Pre-mRNA splicing factor component Cdc5p/Cef1, C-terminal (Cdc5p/Cef1_C)
Type: Domain

This domain is found in Myb-Related Cdc5p/Cef1 proteins, which are part of the pre-mRNA splicing factor complex .
Protein of unknown function DUF3352 (DUF3352)
Type: Family

This family of proteins are functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 538 to 575 amino acids in length.
Protein CHAPERONE-LIKE PROTEIN OF POR1-like (CPP1-like)
Type: Family

This entry includes proteins from plants and bacteria. The plant members CHAPERONE-LIKE PROTEIN OF POR1 (CPP1) and Protein CHLOROPLAST J-LIKE DOMAIN 1 (CJD1) have a J-like domain and three transmembrane domains. CPP1 is an essential protein for chloroplast development, plays a role in the regulation of POR (light-dependent protochlorophyllide oxidoreductase) stability and function . CJD1 may be involved in the regulation of the fatty acid metabolic process in chloroplasts, especially chloroplastic galactolipids monogalactosyldiacylglycerol (MGDG) and digalactosyldiacylglycerol (DGDG) .
KHA domain (KHA_dom)
Type: Domain

Potassium channels take part in important processes of higher plants, including opening and closing of stomatal pores and leaf movement. Inward rectifying potassium (K(+)in) channels play an important role in turgor regulation and ion uptake in higher plants. All of them comprise, from their N-terminal to their C-terminal ends: a short hydrophilic region, a hydrophobic region structurally analogous and partially homologous to the transmembrane domain of voltage-gated animal channels from the Shaker superfamily, a putative cyclic nucleotide-binding domain, and a conserved C-terminal KHA domain. Between these last two regions, some of them (AKT1, AKT2 and SKT1) contain an ankyrin-repeat domain with six repeats homologous to those of human erythrocyte ankyrin.
PTBP1-like, RNA recognition motif 2 (PTBP1-like_RRM2)
Type: Domain

This entry represents the RNA recognition motif 2 (RRM2) of polypyrimidine tract-binding protein 1 (PTBP1) and related proteins. Proteins containing this domain include PTBP1/2/3 (or PTB1/2/3) and heterogeneous nuclear ribonucleoprotein L-like (HNRNPLL) proteins.

PTB can shuttle between nucleus and cytoplasm. It is a splicing repressor factor implicated in the control of alternative exon selection during mRNA processing of many different transcribed genes, including its own pre-mRNA. It is also involved in internal ribosome entry site (IRES)-mediated translation initiation. It may also be involved in the 3'-end processing, localization, and stability of several mRNAs. Two PTB homologues, PTBP2 and PTBP3, are generally expressed in mammalian tissues. PTBP2 is expressed at high levels in adult brain, muscle and testis, while PTBP3 is expressed preferentially in haematopoietic cells . PTB and PTBP2 bind to the same RNA sequences and have similar effects on alternative splicing events. However, differential expression of PTB and PTBP2 can lead to the generation of alternatively spliced mRNAs . During neuronal differentiation, MicroRNA miR-124 downregulates PTBP1 expression, which in turn leads to upregulation of PTBP2. Later in development, the expression of PTBP2 decreases and this leads to a second wave of alternative splicing changes characteristic of adult brain and essential for brain development . PTBP3 may be involved in nonsense-mediated mRNA decay .
Phage tail tube protein, GTA-gp10 (Phage_TAC_11)
Type: Family

This entry consists of bacterial and phage proteins whose function is not currently known. Many of the bacterial sequences are found within known or suspected prophages or gene transfer agents (GTA). Gene transfer agents are related to bacteriophages, but are distinguished by cellular regulatory mechanisms that strongly suggest they are more than just defective prophages . This entry includes a group of phage tail tube proteins .
Beta-fructofuranosidase, N-terminal domain (Beta-fructofuranosidase_N)
Type: Domain

This entry represents the N-terminal domain of beta-fructofuranosidase (also known as vacuolar invertase) (

), which is involved in the hydrolysis of terminal non-reducing beta-D-fructofuranoside residues in beta-D-fructofuranosides .
Major outer membrane lipoprotein Oprl (Oprl)
Type: Family

Oprl is a major outer membrane lipoprotein that contains an alanine-zipper . Zipper motifs are a seven-repeat motif where the first and fourth positions are occupied by an aliphatic residue, usually a leucine. These residues are positioned on the outside of the coil such as to bind firmly to one or more monomers of the protein to create a triple or five-helical coiled-coil that probably forms a seam in a membrane.
Protein of unknown function DUF3360 (DUF3360)
Type: Family

This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 489 to 517 amino acids in length.
Protein of unknown function DUF3363 (DUF3363)
Type: Family

This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 323 to 658 amino acids in length.
Tll0287-like domain (Tll0287-like_dom)
Type: Domain

This domain covers the full length of Tll0287 from Thermosynechococcus vestitus (

) and similar bacterial proteins. Tll0287 is a c-type haem protein that shows a β-sheet with four antiparallel β-strands surrounded by five α-helices. This structure is similar to some kinases and sensor proteins, but its specific function is unknown .

This domain is also found associated with

in many uncharacterised bacterial sequences.
Virulence factor membrane-bound polymerase, C-terminal (Wzy_C_2)
Type: Domain

Wzy is a membrane-bound polymerase of 12 TMs, found in Gram-positive bacteria such as Streptococcus pnuemoniae. It forms part of the EPS or exopolysaccharide system. This entry represents the 6xTMs at the C-terminal end of the molecule. Wzy functions in polymerising the oligosaccharide repeat subunits to form high-molecular-weight capsular polysaccharides. A contiguous emebrane-bound flippase, Wzx (

), transports the repeat units to the external surface of the membrane. These polysaccharides form the capsule and their differing compositions contribute to the multidudinous pneumococcal capsular serotypes, all being structurally and antigenically different .
Alpha-(1->3)-arabinofuranosyltransferase, N-terminal GT-C domain (AftD_N)
Type: Domain

This domain is found at the N-terminal of alpha-(1->3)- arabinofuranosyltransferase from Mycolicibacterium smegmatis (AftD, EC:2.4.2.47), which is involved in the biosynthesis of the arabinogalactan (AG) region of the mycolylarabinogalactan -peptidoglycan (mAGP) complex, an essential component of the mycobacterial cell wall. It catalyses the addition of an arabinofuranosyl (Araf) residue from the sugar donor decaprenyl-phospho-arabinose (DPA) on the C-3 of an alpha-(1->5)-linked Araf from the arabinan backbone of AG . This domain shows mixed α/β folds homologous to other solved GT-C glycosyltransferase structures .
Protein of unknown function DUF3368 (DUF3368)
Type: Family

This domain is functionally uncharacterised. This domain is found in bacteria and archaea. This presumed domain is about 50 amino acids in length.
Domain of unknown function DUF3369 (DUF3369)
Type: Domain

This domain is functionally uncharacterised. It is found in bacterial sequences, is around 170 amino acids in length, and may be related to the GAF domain.
Protein of unknown function DUF3370 (DUF3370)
Type: Family

This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 452 to 532 amino acids in length.
MiT/TFE transcription factors, C-terminal (MiT/TFE_C)
Type: Domain

This entry represents a domain found at the C terminus of the MiT/TFE family members, which include MITF (microphthalmia-associated transcription factor) and its related family members TFE3, TFEB and TFEC . They are basic helix-loop-helix leucine zipper transcription factors found in chordata. These transcription factors heterodimerize with each other and bind to the E-box core sequence (3'-CANNTG-5') .
Protein of unknown function DUF3373 (DUF3373)
Type: Family

This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 472 to 574 amino acids in length.
Protein of unknown function DUF3375 (DUF3375)
Type: Family

This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 479 to 499 amino acids in length.
Peptidase M10A, matrix metallopeptidase, C-terminal (Pept_M10A_metallopeptidase_C)
Type: Domain

This domain is functionally uncharacterised and found at the C terminus of peptidases belonging to MEROPS peptidase family M10A, membrane-type matrix metallopeptidases (clan MA).
Protein of unknown function DUF3379 (DUF3379)
Type: Family

This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 234 to 251 amino acids in length.
High-affinity branched-chain amino acid transport system permease, LivHM, N-terminal (LivHM_N)
Type: Domain

This entry represents the N-terminal domain of the LivHM type high-affinity branched-chain amino acid transport system permease proteins. The domain is about 100 amino acids in length, and is found associated with

.
Protein of unknown function DUF3383 (DUF3383)
Type: Family

This family of proteins are functionally uncharacterised. This protein is found in bacteria and viruses. Proteins in this family are typically between 356 to 501 amino acids in length.
Protein of unknown function DUF3386 (DUF3386)
Type: Family

This family of proteins are functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are about 220 amino acids in length.
Type I restriction enzyme HindI endonuclease subunit-like, C-terminal (T1RH-like_C)
Type: Domain

This domain is found at the C-terminal of Type I restriction enzyme HindI endonuclease subunit (also known as R protein) from Haemophilus influenzae and related sequences from bacteria and archaea . This domain is typically between 255 to 340 amino acids in length and its function is unknown. This domain is found associated with

,

.
Protein of unknown function DUF3389 (DUF3389)
Type: Family

This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 80 amino acids in length.
Domain of unknown function DUF3391 (DUF3391)
Type: Domain

This functionally uncharacterised, N-terminal domain is found in a number of bacterial proteins, including Cyclic di-GMP phosphodiesterase PA4108. It is often found associated with the HD domain

.
Protein of unknown function DUF3392 (DUF3392)
Type: Family

This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 110 amino acids in length.
Protein of unknown function DUF3394 (DUF3394)
Type: Family

This domain is functionally uncharacterised. This domain is found in bacteria. This presumed domain is about 190 amino acids in length. This domain is found associated with

.