SII-SWORD/CoKE huggingface dataset:
Pfam PF12486: Type VI secretion system, EvfB, or VasL (family)
EvfB or VasL is a domain found on many Gram-negative proteins with an ImpA_N domain at the N-terminus. These proteins are expressed from the pathogenicity locus that forms the bacterial type VI secretion system. The exact function of VasL is not known. One E.coli member is annotated as being EvfB, though the E.coli equivalent of ImpA would be expected to be EvfG. It is possible that in many bacteria what is a single protein in one species, eg E.coli, is a fusion of two genes in others, which would explain an ImpA at the N-terminus and a VasL at the C-terminus.
Pfam PF04538: Brain expressed X-linked like family (family)
This is a family of transcription elongation factors which includes those referred to as Bex proteins as well as those named TCEAL7. Bex1 was shown to be a novel link between neurotrophin signalling, the cell cycle, and neuronal differentiation, suggesting it might function by coordinating internal cellular states with the ability of cells to respond to external signals. TCEAL7 has been shown negatively to regulate the NF-kappaB pathway, hence being important in ovarian cancer as it one of the genes frequently downregulated in this cancer. A closely related protein, TFIIS/TCEA, found in [pfam:PF07500] is involved in transcription elongation and transcript fidelity. TFIIS/TCEA promotes 3' endoribonuclease activity of RNA polymerase II (pol II) and allows pol II to bypass transcript pause or 'arrest' during elongation process. It is thus possible that BEX is also acting in this way.
Pfam PF05443: ROS/MUCR transcriptional regulator protein (family)
This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti. This gene encodes a 15.5-kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid and is necessary for succinoglycan production. Sinorhizobium meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of alfalfa nodules. MucR from Sinorhizobium meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan.
Pfam PF17104: YBL010C/LAA2 (family)
This is a family of fungal sequences, including YBL010C (also known as LAA2) from S. cerevisiae and its orthologue from S. pombe, C8E11.05c. LAA2 is a clathrin adaptor (adaptin) accessory protein that physically interacts with and is involved in localization of clathrin adaptor protein complex-1 (AP-1).
Pfam PF23953: COPA/B TPR domain (repeat)
This entry represents the TPR domain found in Coatomer subunits alpha and beta (COPA1-3, COPB2 and COB21-3), from eukaryotes. The domain adopts an alpha-solenoid fold. Coatomer complexes function in the sorting and trafficking of proteins between subcellular organelles.Coat protein I (COPI)-coated vesicles mediate retrograde transport from the Golgi to the endoplasmic reticulum (ER), as well as transport within the Golgi. The Coatomer protein complex subunit beta 2 (COPB2) is involved in the formation of the COPI coatomer protein complex. COPB2 is a vital oncogene in many cancer types that regulates multiple biological behaviours of tumor cells, including proliferation, survival, tumourigenesis, invasion, and metastasis. COPA constitutes part of COPI, playing a role in the retrograde transport of cargo proteins between the Golgi and the ER and the movement of vesicles within the Golgi.
Pfam PF03079: ARD/ARD' family (domain)
The two acireductone dioxygenase enzymes (ARD and ARD', previously known as E-2 and E-2') from Klebsiella pneumoniae share the same amino acid sequence  [swissprot:Q9ZFE7], but bind different metal ions: ARD binds Ni2+, ARD' binds Fe2+. ARD and ARD' can be experimentally interconverted by removal of the bound metal ion and reconstitution with the appropriate metal ion.  The two enzymes share the same substrate, 1,2-dihydroxy-3-keto-5-(methylthio)pentene, but yield different products. ARD' yields the alpha-keto precursor of methionine (and formate), thus forming part of the ubiquitous methionine salvage  pathway that converts 5'-methylthioadenosine (MTA) to methionine. This pathway is responsible for the tight control of the concentration of MTA, which is a powerful inhibitor of polyamine biosynthesis and transmethylation reactions. ARD yields methylthiopropanoate, carbon monoxide and formate, and thus prevents the conversion of MTA to methionine. The role of the ARD catalysed reaction is unclear: methylthiopropanoate is cytotoxic, and carbon monoxide can activate guanylyl cyclase, leading to increased intracellular cGMP levels. This family also contains other members, whose functions are not well characterised.
Pfam PF21081: Virus-capping methyltransferase, C-terminal (domain)
This is the C-terminal domain of the Mononegavirales single-stranded RNA viral RNA polymerase enzymes. This region, together with the connector domain (CD), flanks the methyltransferase domain (MT) and is likely involved in the structural rearrangements that appear to coordinate the enzymatic activities during transcription and replication.
Pfam PF04783: Protein of unknown function (DUF630) (family)
This region is sometimes found at the N-terminus of putative plant bZIP proteins.  Its function is not known. Structural modelling suggests this domain may bind nucleic acids.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF16335: Glutaminase A six helical-hairpin domain (repeat)
This entry represents the six helical-hairpin domain found in homologues of Glutaminase A from Aspergillus oryzae. Glutaminase catalyzes the hydrolysis of glutamine to glutamic acid and plays a key role in nitrogen metabolism. It catalyzes the hydrolysis not only of L-glutamine but also of D-glutamine. This domain share similarity with six-hairpin glycosidases.
Pfam PF21244: PurT, C-terminal (domain)
Formate-dependent phosphoribosylglycinamide formyltransferase (PurT) is involved in de novo purine biosynthesis. PurT belongs to the ATP-grasp superfamily of enzymes and  catalyses the transfer of formate to 5-phospho-ribosyl-glycinamide (GAR), producing 5-phospho-ribosyl-N-formylglycinamide (FGAR). This entry represents the C-terminal domain which has a rudiment single hybrid motif consisting of a sandwich of half-barrel shaped beta-sheets.
Pfam PF19008: Family of unknown function (DUF5737) (family)
A highly conserved domain of unknown function found in various Platyhelminthes.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF23571: GH3 family central domain (domain)
The GH3 IAA-amido conjugating enzyme family consists of proteins that catalyze the synthesis of amino acid conjugates with indole-3-acetic acid (IAA) or jasmonate (JA), which are plant hormones. This entry represents the central domain of these enzymes. These enzymes play a crucial role in regulating plant hormone levels by conjugating excess IAA and JA to amino acids, thus providing a mechanism for plants to maintain hormonal homeostasis. The conjugation process is ATP-dependent and involves the adenylation of the hormone followed by the transfer to an amino acid. This family is involved in various plant physiological processes including disease resistance, stamen and carpel differentiation, floret fertility, and response to environmental stresses such as wounding and pathogen attack. Some members also exhibit activity towards synthetic auxins and may confer resistance to herbicides. The family's broad substrate specificity includes various amino acids and analogs of IAA, contributing to the complexity of hormone regulation in plants.
Pfam PF11568: Mediator complex subunit 29 (family)
Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species. It is arranged into four different sections, a core, a head, a tail and a kinase-active part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function. Med29, along with Med11 and Med28, in mammals, is part of the core head-region of the complex. Med29 is the apparent orthologue of the Drosophila melanogaster Intersex protein, which interacts directly with, and functions as a transcriptional coactivator for, the DNA-binding transcription factor Doublesex, so it is likely that mammalian Med29 serves as a target for one or more DNA-binding transcriptional activators.
Wikipedia: Mediator of RNA polymerase II transcription subunit 29 (Med29) is a transcription suppressor that in humans is encoded by the MED29 gene. It represents subunit MED29 of the Mediator complex.
Pfam PF22053: Domain of unknown function (DUF6938) (domain)
This domain is found C-terminal in a family of uncharacterised bacterial proteins. This domain has a significant sequence similarity to the C-terminal domains of a number of proteins members of UDP-Glycosyltransferase/glycogen phosphorylase superfamily. It is predicted to adopt the same alpha/beta structure.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF09882: Predicted membrane protein (DUF2109) (family)
This domain, found in various hypothetical archaeal proteins, has no known function.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF06791: Prophage tail length tape measure protein (family)
This family represents a conserved region located towards the N-terminal end of prophage tail length tape measure protein (TMP). TMP is important for assembly of phage tails and involved in tail length determination. Mutated forms TMP cause tail fibres to be shortened.
Pfam PF10292: Serpentine type 7TM GPCR receptor class ab chemoreceptor (family)
Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srab is part of the Sra superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. The expression pattern of the srab genes is biologically intriguing. Of the six promoters successfully expressed in transgenic organisms, one was exclusively expressed in the tail phasmid neurons, two were exclusively expressed in a head amphid neuron, and two were expressed both in the head and tail neurons as well as a limited number of other cells.
Pfam PF19579: Bacteriodetes cell division protein (FtsL-like) (domain)
This family of share similarity to [pfam:PF04977] and [pfam:PF04999] suggesting it is a cell division protein.  Proteins in this family are primarily found in Bacteroidetes.  Proteins in this family are typically between 105 and 129 amino acids in length.
Pfam PF19358: Family of unknown function (DUF5935) (family)
This presumed domain is functionally uncharacterised, but is is found in O-antigen polymerase proteins. This domain family is mainly found in proteobacteria, and is approximately 190 amino acids in length. The family is found in association with [pfam:PF04932].
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF08601: Transcription factor PAP1 (family)
The transcription factor Pap1 regulates antioxidant-gene transcription in response to H2O2.  This region is cysteine rich.  Alkylation of cysteine residues following treatment with a cysteine alkylating agent can mask the accessibility of the nuclear exporter Crm1, triggering nuclear accumulation and Pap1 dependent transcriptional expression.
Pfam PF16239: Domain of unknown function (DUF4898) (family)
A small family of uncharacterized proteins around 100 residues in length and found in various Sulfolobus species. The function of this family is unknown.
Pfam PF11717: RNA binding activity-knot of a chromodomain (family)
This is a novel knotted tudor domain which is required for binding to RNA. The know influences the loop conformation of the helical turn Ht2 - residues 61-6 3- that is located at the side opposite the knot in the tudor domain-chromodomain; stabilisation of Ht2 is essential for RNA binding.
Pfam PF23298: RECK, frizzled-like domain (domain)
This entry includes Reversion-inducing cysteine-rich protein with Kazal motifs (RECK), a GPI-anchored membrane protein that negatively regulates matrix metalloproteinase-9 (MMP-9) by suppressing MMP-9 secretion and by direct inhibition of its enzymatic activity. It also regulates two other MMPs, MMP-2 and MT1-MMP. It acts as a Wnt7-specific coactivator of canonical Wnt signaling by decoding Wnt ligands; it acts by interacting specifically with the disordered linker region of Wnt7, which confers ligand selectivity for Wnt7. This entry represents a frizzled-like domain which contains ten conserved cysteine residues.
Pfam PF20538: Family of unknown function (DUF6753) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in cyanobacteria. Proteins in this family are typically between 225 and 243 amino acids in length.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF15718: Protein moonraker (family)
Protein moonraker is a centriolar satellite component  involved in centriole duplication. It promotes centriole  duplication by localizing WDR62 to the centrosome.
Pfam PF11260: Major ampullate spidroin 1 and 2 (family)
Dragline silk is composed of two proteins, major ampullate spidroin 1 (MaSp1) and major ampullate spidroin 2 (MaSp2). MaSp1 contains five alpha-helices. Only the C-terminus of the proteins are shown.
Wikipedia: Spidroins are the main proteins in spider silk. Different types of spider silk contain different spidroins, all of which are members of a single protein family. The most-researched type of spidroins are the major ampullate silk proteins (MaSp) used in the construction of dragline silk, the strongest type of spider silk. Dragline silk fiber was originally thought to be made up of two types of spidroins, spidroin-1 (MaSp1) and spidroin-2 (MaSp2) however recent transcriptomic analysis of over 1000 spider species has revealed multiple spidroins are expressed making it much more complex.
Pfam PF09018: P3 major capsid protein (domain)
The P3 major capsid protein adopts a 'double-barrel' structure comprising two eight-stranded viral beta-barrels or jelly rolls, each of which contains a 12-residue alpha-helix. This protein then trimerises through a 'trimerisation loop' sequence, and is incorporated within the viral capsid.
Pfam PF17259: Family of unknown function (DUF5325) (family)
This is a family of unknown function mainly found in Bacilli. Family members of this family are predicted to have trans-membrane domains.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF07819: PGAP1-like alpha/beta domain (domain)
This domain is found in GPI inositol-deacylase PGAP1 and related proteins. PGAP1 is an endoplasmic reticulum membrane protein with a catalytic serine containing motif that is conserved in a number of lipases. PGAP1 functions as a GPI inositol-deacylase; this deacylation is important for the efficient transport of GPI-anchored proteins from the endoplasmic reticulum to the Golgi body. This entry also includes Tgl2, a mitochondria protein that serves as a triacylglycerol lipase in budding yeasts. The domain represented by this entry is found toward the N terminus and it is a lipase domain with a typical alpha/beta/alpha hydrolase architecture.
Pfam PF20848: ExoU toxin, middle helical domain (domain)
Many pathogenic Gram-negative bacteria use type III secretion systems (T3SS) to deliver effector proteins into the host cell cytosol and facilitate the infectious process. The effector protein ExoU from Pseudomonas aeruginosa, one of the most aggressive toxins injected by a T3SS, has four distinct domains. The chaperone-binding domain consists of two separate regions, a N-terminal region and a middle subdomain (this entry). The latter shows a mostly alpha-helical structure.
Pfam PF03187: Corona nucleocapsid I protein (family)
Members of this family are Coronavirus proteins that are located in the nucleocapsid .
Pfam PF17618: Uncharacterized Strongylid L4 protein (family)
Family members are predicted non-classically secreted proteins found in Ancylostoma ceylaniucum. Homologs are found in strongylids A. ceylanicum, N. americanus, H. contortus and Angiostrongylus cantonensis, where the corresponding genes in A. cantonensis are expressed in L4 larvae. Thus this family members found in A, ceylaniucum have been named strongylid L4 proteins (SL4Ps). Although SL4Ps do not resemble any domains of known function, they do have a conspicuous number of charged residues (both acidic and basic) in their N-terminal, most highly conserved regions.
Pfam PF19595: Family of unknown function (DUF6100) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in Firmicute bacteria. Proteins in this family are approximately 220 amino acids in length.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF00190: Cupin (domain)
This family represents the conserved barrel domain of the 'cupin' superfamily ('cupa' is the Latin term for a small barrel). This family contains 11S and 7S plant seed storage proteins, and germins.  Plant seed storage proteins provide the major nitrogen source for the developing plant.
Wikipedia: The cupin superfamily is a diverse superfamily of proteins named after its conserved barrel domain. The superfamily includes a wide variety of enzymes as well as non-enzymatic seed storage proteins.
Pfam PF05700: Breast carcinoma amplified sequence 2 (BCAS2) (family)
This family consists of several eukaryotic sequences of unknown function. The mammalian members of this family are annotated as breast carcinoma amplified sequence 2 (BCAS2) proteins. BCAS2 is a putative spliceosome associated protein.
Pfam PF01544: CorA-like Mg2+ transporter protein (family)
The CorA transport system is the primary Mg2+ influx system of Salmonella typhimurium and Escherichia coli. CorA is virtually ubiquitous in the Bacteria and Archaea. There are also eukaryotic relatives of this protein, like the plasma membrane magnesium transporter ALR2 from yeast ([swissprot:P43553]). This entry also includes related proteins such as the zinc transporter ZntB.
Wikipedia: The CorA transport system is the primary Mg2+ influx system of Salmonella typhimurium and Escherichia coli. CorA is ubiquitous in the Bacteria and Archaea. There are also eukaryotic members of the family localized to the mitochondrial membrane such as MRS2 and Lpe10 in yeast.
Pfam PF07788: PD-(D/E)XK nuclease superfamily (family)
This family is found to carry modified motifs characteristic of PD-(D/E)XK endonuclease superfamily. These are the conserved Glu of motif I, the Asp surreounded by hydrophobics of motif II, EIKS of motif III, and the lysine of mmotif IV has migrated to an alpha-helix following the third core beta-strand. The conserved patch of positively charged lysine and arginine residues in the motif IV apha-helix might be involved in substrate-binding or be contributing to active site formation. Members with an additional N-terminal coi9led-coil domain, are annotated as tropomyosin, coiled-coil or microtubule binding proteins.
Pfam PF07682: Sulphur oxygenase reductase (domain)
The sulphur oxygenase/reductase (SOR) of the thermo-acidophilic archaeon Acidianus ambivalens is an unusual enzyme consisting of 24 identical subunits arranged in a perfectly symmetrical hollow sphere and containing a mononuclear non-heme iron centre (personal communication: A. Kletzin). At 85 degrees C in vitro, elemental sulphur is oxidised to sulphite, thiosulphate and hydrogen sulphide with no external cofactors needed. The proposed equation is:  4S + O2 + 4 H2O ---> 2 HSO3- + 2 H2S + 2 H+.
Pfam PF03620: IBV 3C protein (family)
Product of ORF 3C from Avian infectious bronchitis virus (IBV). Currently, the function of this protein remains unknown.
Pfam PF23337: PTHB1 platform domain (domain)
This entry represents the platform domain of PTHB1 protein (also known as Bardet-Biedl syndrome 9 protein, BBS9). This protein forms a part of the BBSome complex, which is required for ciliogenesis. PTHB1 is the major binding subunit of IFT38 C-terminal domain, which assists the BBSome in some of its roles.
Pfam PF20719: Mediator complex subunit 16, C-terminal (domain)
Med16 is one of the subunits of the Tail portion of the Mediator complex and is required for lipopolysaccharide gene-expression. This is the small alpha-beta domain found at the C-terminal of Mediator complex subunit 16.
Pfam PF14525: AraC-binding-like domain (domain)
This domain is related to the AraC ligand binding domain [pfam:PF02311].