SII-SWORD/CoKE huggingface dataset:
Pfam PF15300: INTS6/SAGE1/DDX26B/CT45 C-terminus (family)
This domain is found at the C-terminus of integrator complex subunit 6 (INTS6), sarcoma antigen 1 (SAGE1), protein DDX26B (DDX26B) and members of the cancer/testis antigen family 45.
Pfam PF15228: Death-associated protein (family)
This family includes death-associated protein 1 (DAP1) and death-associated protein-like 1 (DAPL1). DAP1 is involved in mediating interferon-gamma-induced cell death . DAPL1 may play a role in the early stages of epithelial differentiation or in apoptosis .
Wikipedia: Death-associated protein 1 is a protein that in humans is encoded by the DAP gene.
Pfam PF12685: SpoIIIAH-like protein (family)
Stage III sporulation protein AH (SpoIIIAH) is a protein that is involved in forespore engulfment. It forms a channel with SpoIIIAH that is open on the forespore end and closed (or gated) on the mother cell end. This allows sigma-E-directed gene expression in the mother-cell compartment of the sporangium to trigger the activation of sigma-G forespore-specific gene expression by a pathway of intercellular signaling.  This family of proteins is found in bacteria, archaea and eukaryotes and so must have a wider function that in sporulation.  Proteins in this family are typically between 174 and 223 amino acids in length.
Pfam PF05464: Phi-29-like late genes activator (early protein GP4) (family)
This family consists of phi-29-like late genes activator (or early protein GP4). This protein is thought to be a positive regulator of late transcription and may function as a sigma like component of the host RNA polymerase.
Pfam PF09349: OHCU decarboxylase (domain)
The proteins in this family are OHCU decarboxylase - enzymes of the purine catabolism that catalyse the conversion of OHCU into S(+)-allantoin. This is the third step of the conversion of uric acid (a purine derivative) to allantoin. Step one is catalysed by urate oxidase ([pfam:PF01014]) and step two is catalysed by HIUases ([pfam:PF00576]).
Wikipedia: In molecular biology 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase EC 4.1.1.n1 is an enzyme involved in purine catabolism. It catalyses the decarboxylation of 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline (OHCU) into S(+)-allantoin. It is the third step of the conversion of uric acid to allantoin. Step one is catalysed by urate oxidase and step two is catalysed by hydroxyisourate hydrolase.
Pfam PF17377: Family of unknown function (DUF5399) (family)
This is a family of unknown function found in Chlamydiales.
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 PF09477: Bacterial type III secretion system chaperone protein (repeat)
YscG is a molecular chaperone for YscE, where both are part of the type III secretion system that in Yersinia is designated Ysc (Yersinia secretion). The secretion system delivers effector proteins, designated Yops (Yersinia outer proteins), in Yersinia. This entry consists of YscG from Yersinia and functionally equivalent type III secretion proteins in other species: e.g. AscG in Aeromonas and LscG in Photorhabdus luminescens.
Pfam PF06760: Protein of unknown function (DUF1221) (family)
This is a family of plant proteins, most of which are hypothetical and of unknown function. All members contain the [pfam:PF00069] domain, suggesting that they may possess kinase activity.
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 PF22406: DdMyo7 FERM domain (domain)
This entry represents the C-terminal FERM domain found in Myo7 from Dictyostelium discoideum, a protein that is essential for the extension of filopodia, plasma membrane protrusions filled with parallel bundles of F-actin similarly as metazoan Myo10, which suggests a high degree of functional conservation throughout evolution.
Pfam PF16063: Domain of unknown function (DUF4805) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes. Proteins in this family are typically between 244 and 363 amino acids in length. There is a conserved WEL sequence motif.
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 PF11168: Protein of unknown function (DUF2955) (family)
Some members in this family of proteins with unknown function annotate the proteins as membrane protein. However, this cannot be confirmed.
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 PF13884: Chaperone of endosialidase (domain)
This is the very C-terminal, chaperone, domain of the bacteriophage protein endosialidase. It releases itself, via the serine-lysine dyad at the N-terminus, from the remainder of the end-tail-spike. Cleavage occurs after the threonine which is the final residue of the End-tail-spike family, [pfam:PF12219]. The endosialidase protein forms homotrimeric molecules in bacteriophages. The catalytic dyad allows this portion of the molecule to be cleaved from the more N-terminal region such that the latter can fold and bind to polysialic acid in the bacterial outer envelope.
Pfam PF23025: C2 domain-containing protein 5, YbjQ-like domain (domain)
This domain is found in several copies in human C2 domain -containing protein 5 (C2CD5) and similar proteins predominantly found in animals. C2CD5 is required for insulin -stimulated glucose transport and glucose transporter SLC2A4 /GLUT4 translocation to the plasma membrane in adipocytes. This domain is predicted to show a beta-sheet and an alpha-helix.
Pfam PF15596: Immunity protein 57 (family)
A predicted immunity protein with a mostly alpha-helical fold and conserved aspartate and cysteine residues and an SE motif. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, usually containing a domain of the LD-peptidase or Tox-Caspase families.
Pfam PF24782: MABP1/WDR62 second WD40 domain (repeat)
This entry represents the second WD40 domain of MABP1 and WDR62. MABP1 (Mitogen-activated protein kinase-binding protein 1) is a negative regulator of NOD2 function, leading to the down-regulation of NOD2-induced processes such as activation of NF-kappa-B signalling, IL8 secretion and antibacterial response. WDR62 is a microcephaly-related, microtubule (MT)-associated protein (MAP) that localises to the spindle pole and regulates spindle organisation by recruiting katanin to the spindle pole by forming a complex with TPX2/Aurora A. The microtubule-binding (MT) affinity of WDR62 is autoinhibited through JNK phosphorylation-induced intramolecular interaction. Additionally, WRD62 is implicated in the development of the cerebral cortex influencing both the proliferation and migration of neurons. The WD40 domains of WDR62 mediate the interaction with Aurora A and (MT binding).
Pfam PF19019: Phlebovirus glycoprotein G2 C-terminal domain (domain)
This family consists of several Phlebovirus glycoprotein G2 C-terminal Ig-like domains.
Pfam PF15607: Bacterial toxin 44 (family)
A predicted RNase toxin found in bacterial polymorphic toxin systems.  The toxin possesses an all-alpha-helical fold with conserved DxK, GNxxxG, and DxxxD motifs. In bacterial polymorphic toxin systems, the toxin is exported by the type 2, type 6 or type 7 secretion systems.
Pfam PF04798: Baculovirus 19 kDa protein conserved region (family)
Family of Baculovirus proteins of approximate mass 19 kDa.
Pfam PF18766: SWI2/SNF2 ATPase (family)
A SWi2/SNF2 ATPase found in polyvalent proteins.
Pfam PF00452: Apoptosis regulator proteins, Bcl-2 family (family)
B cell CLL/lymphoma-2 (Bcl-2) and related proteins comprise the Bcl-2 family. Bcl-2 proteins are central regulators of caspase activation, and play a key role in cell death by regulating the integrity of the mitochondrial and endoplasmic reticulum (ER) membranes . Though originally characterised with respect to their roles in controlling outer mitochondrial membrane integrity and apoptosis, the members of the Bcl-2 family are involved in numerous cellular pathways .

Bcl-2 and its relatives are functionally classified as either antiapoptotic or proapoptotic. All members contain at least one of four conserved motifs, termed Bcl-2 Homology (BH) domains. Antiapoptotic BCL-2 proteins contain four Bcl-2 homology domains (BH1-4). The major antiapoptotic proteins are Bcl-2-related gene A1 (A1), Bcl-2, Bcl-2-related gene, long isoform (Bcl-xL), Bcl-w, and myeloid cell leukemia 1 (MCL-1). They preserve outer mitochondrial membrane (OMM) integrity by directly inhibiting the proapoptotic Bcl-2 proteins .

The proapoptotic Bcl-2 members are divided into the effector proteins and the BH3-only proteins. The effector proteins Bcl-2 antagonist killer 1 (BAK) and Bcl-2-associated x protein (BAX) were originally described to contain only BH1-3; however, structure-based alignments revealed a conserved BH4 motif . Upon activation BAK and BAX homo-oligomerise into proteolipid pores within the OMM to promote MOMP (mitochondrial outer membrane permeabilisation). The BH3-only proteins function in distinct cellular stress scenarios and are subdivided based on their ability to interact with the antiapoptotic or both the antiapoptotic and the effector proteins .
This entry covers the Bcl-2 homology regions 1, 2 and 3 (BH1-3).
Wikipedia: The Bcl-2 family consists of a number of evolutionarily-conserved proteins that share Bcl-2 homology (BH) domains. The Bcl-2 family is most notable for their regulation of apoptosis, a form of programmed cell death, at the mitochondrion. The Bcl-2 family proteins consists of members that either promote or inhibit apoptosis, and control apoptosis by governing mitochondrial outer membrane permeabilization (MOMP), which is a key step in the intrinsic pathway of apoptosis. A total of 25 genes in the Bcl-2 family were identified by 2008.
Pfam PF11838: ERAP1-like C-terminal domain (domain)
This large domain is composed of 16 alpha helices organized as 8 HEAT-like repeats. This domain forms a concave face that faces towards the active site of the peptidase.
Pfam PF22894: Domain of unknown function (DUF7023) (domain)
This domain is found in human Protein dispatched homolog 3 (DISP3) and related proteins mainly from vertebrates. DISP3 (PTCHD2), a sterol-sensing domain- containing protein, is highly expressed in neural tissue, promotes cell proliferation and alters expression of genes that are involved in tumourigenesis. The function of this domain is unknown.
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 PF23893: Uncharacterised protein Y4YQ C-terminal domain (domain)
This entry represents the C-terminal domain found in the uncharacterised protein Y4YQ from Sinorhizobium fredii. Y4YQ has been observed to be highly expressed in Rhizobium sp. upon treatment with daidzein, a known inductor of nod genes expression for symbiosis initiation. This domain closely resembles the C-terminal domain of type II secretion system protein B and C from bacteria. The function of this domain is unknown.
Pfam PF20571: Domain of unknown function (DUF6780) (domain)
This presumed domain is functionally uncharacterised. This domain family is found at the C-terminal of fungal sequences, and is typically between 48 and 62 amino acids in length. The domain is found in association with [pfam:PF00735]. There is a conserved sequence motif WxRHxAAxK that may be functionally important.
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 PF05937: EB-1 Binding Domain (family)
This region, found at the C-terminus of the APC proteins, binds the microtubule-associating protein EB-1. At the C-terminus of the alignment is also a [pfam:PF00595] binding domain. A short motif in the middle of the region appears to be found in the APC2  proteins (e.g [swissprot:O95996]).
Pfam PF20731: NgoFVII C-terminal B3-like DNA-binding domain (domain)
This family includes the NgoFVII (recognises GCSGC but cleavage site unknown) restriction endonuclease. This entry represents the RIFT related domain.
Pfam PF04116: Fatty acid hydroxylase (domain)
This entry includes fatty acid and carotene hydroxylases and sterol desaturases. Beta-carotene hydroxylase is involved in zeaxanthin synthesis by hydroxylating beta-carotene, but the enzyme may be involved in other pathways. This family includes C-5 sterol desaturase and C-4 sterol methyl oxidase. Members of this family are involved in cholesterol biosynthesis and biosynthesis a plant cuticular wax. These enzymes contain two copies of a HXHH motif which coordinate two irons at the catalytic centre. Members of this family are ER integral membrane proteins that share a novel mushroom-shaped fold consisting of four transmembrane (TM1-TM4) helices that anchor them to the membrane capped by a cytosolic domain containing the unique histidine- coordinating di metal centre.
Pfam PF06576: Protein of unknown function (DUF1133) (family)
This family consists of a number of hypothetical proteins from Escherichia coli O157:H7 and Salmonella typhi. The function of this family is unknown.
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 PF14495: Cytochrome c-550 domain (domain)
This domain is a heme binding cytochrome known as cytochrome c550, or cytochrome c549, or PsbV.
Pfam PF17657: Bacterial DNA polymerase III alpha subunit finger domain (domain)
The shape of DNA polymerases can be described as resembling a right hand with thumb, finger, and palm domains. This entry represents the finger domain of the alpha subunit of DNA pol III .
Wikipedia: DNA polymerase III holoenzyme is the primary enzyme complex involved in prokaryotic DNA replication. It was discovered by Thomas Kornberg and Malcolm Gefter in 1970. The complex has high processivity and, specifically referring to the replication of the E.coli genome, works in conjunction with four other DNA polymerases. Being the primary holoenzyme involved in replication activity, the DNA Pol III holoenzyme also has proofreading capabilities that corrects replication mistakes by means of exonuclease activity reading 3'→5' and synthesizing 5'→3'. DNA Pol III is a component of the replisome, which is located at the replication fork.
Pfam PF08227: DASH complex subunit Hsk3 like (family)
The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis. In Saccharomyces cerevisiae DASH forms both rings and spiral structures on microtubules in vitro.  This family also includes several higher eukaryotic proteins. However, other DASH subunits do not appear to be conserved in higher eukaryotes.
Pfam PF08417: Pheophorbide a oxygenase (family)
This domain is found in bacterial and plant proteins to the C-terminus of a Rieske 2Fe-2S domain ([pfam:PF00355]).  One of the proteins the domain is found in is Pheophorbide a oxygenase (PaO) which seems to be a key regulator of chlorophyll catabolism. Arabidopsis PaO (AtPaO) is a Rieske-type 2Fe-2S enzyme that is identical to Arabidopsis accelerated cell death 1 and homologous to lethal leaf spot 1 (LLS1) of maize, in which the domain described here is also found.
Pfam PF06666: Protein of unknown function (DUF1173) (family)
This family contains a group of hypothetical bacterial proteins that contain three conserved cysteine residues towards the N-terminal. The function of these proteins is unknown.
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 PF08073: CHDNT (NUC034) domain (domain)
The CHDNT domain is found in PHD/RING finger and chromo domain-associated helicases.
Pfam PF06411: HdeA/HdeB family (domain)
HdeA (hns-dependent expression protein A) is a single domain alpha-helical protein localised in the periplasmic space. HdeA is involved in acid resistance essential for infectivity of enteric bacterial pathogens. Functional studies demonstrate that HdeA is activated by a dimer-to-monomer transition at acidic pH, leading to suppression of aggregation by acid-denatured proteins. The gene encoding HdeA was initially identified as part of an operon regulated by the nucleoid protein H-NS. This family also contains HdeB.
Wikipedia: In molecular biology, the HdeA family of proteins is a stress response protein family found in highly acid resistant bacteria such as Shigella flexneri and Escherichia coli, but which is lacking in mildly acid tolerant bacteria such as Salmonella. HdeA is one of the most abundant proteins found in the periplasmic space of E. coli, where it is one of a network of proteins that confer an acid resistance phenotype essential for the pathogenesis of enteric bacteria. HdeA is thought to act as a chaperone, functioning to prevent the aggregation of periplasmic proteins denatured under acidic conditions. The HNS protein, a chromatin-associated protein that influences the gene expression of several environmentally-induced target genes, represses the expression of HdeA. HdeB, which is encoded within the same operon, may form heterodimers with HdeA. HdeA is a single domain protein with an overall fold that is similar to the fold of the N-terminal subdomain of the GluRS anticodon-binding domain.
Pfam PF07059: Protein ENHANCED DISEASE RESISTANCE 2, C-terminal (domain)
This family represents the C-terminus (approximately 250 residues) of protein ENHANCED DISEASE RESISTANCE 2 (EDR2) from plants. EDR2 is a negative regulator of the salicylic acid (SA)-mediated resistance to pathogens, including the biotrophic powdery mildew pathogens Golovinomyces cichoracearum and Blumeria graminis, and the downy mildew pathogen Hyaloperonospora parasitica, probably by limiting the initiation of cell death and the establishment of the hypersensitive response (HR).
Pfam PF00155: Aminotransferase class I and II (domain)
Aminotransferases share certain mechanistic features with other pyridoxal-phosphate dependent enzymes, such as the covalent binding of the pyridoxal-phosphate group to a lysine residue. On the basis of sequence similarity, these various enzymes can be grouped  into class I and class II. This entry includes proteins from both subfamilies, including class I LL-diaminopimelate aminotransferase, chloroplastic from Arabidopsis thaliana (Dap) and class II Histidinol-phosphate aminotransferase from Listeria welshimeri (HisC). Dap consists of two domains, a large domain and a small domain. This entry represents the large domain, which has a 3-layer Î±/Î²/Î± sandwich topology .
Wikipedia: Transaminases or aminotransferases are enzymes that catalyze a transamination reaction between an amino acid and an α-keto acid. They are important in the synthesis of amino acids, which form proteins.
Pfam PF03882: MukF winged-helix domain (domain)
The kicA and kicB genes are found upstream of mukB. It has been suggested that the kicB gene encodes a killing factor and the kicA gene codes for a protein that suppresses the killing function of the kicB gene product. It was also demonstrated that KicA and KicB can function as a post-segregational killing system, when the genes are transferred from the E. coli chromosome onto a plasmid.
Pfam PF17553: Family of unknown function (DUF5465) (family)
This is a family of unknown function found in Enterobacteria phage T7.
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 PF21350: CRISPR-associated protein Cas6, N-terminal (domain)
Cas6 is an endoribonuclease that generates crRNAs for invader defense in prokaryotes. Cas6 consists of two two ferredoxin-like folds that are also found in other RNA-binding proteins. This entry represents the N-terminal ferredoxin-like domain from  Cas6.
Pfam PF17163: Domain of unknown function (DUF5125) (family)
This entry represents a domain of unknown function found in a group of proteins from Bacteroidetes. It is often found N-terminal to IPR033430.
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.