SII-SWORD/CoKE huggingface dataset:
Pfam PF21139: Methylcrotonyl-CoA carboxylase, alpha-subunit, BT domain (domain)
This domain is found in the biotin-containing alpha subunit of the Methylcrotonyl-CoA carboxylase complex (MCC) from Pseudomonas aeruginosa ([swissprot:Q9I299]) and similar proteins. MCC is essential for the metabolism of leucine. The alpha subunit is organised into the N-terminal biotin carboxylase (BC), the C-terminal biotin carboxyl carrier protein (BCCP) domains, and a domain that mediates BC-CT interactions (BT domain, this entry). This domain shows a central alpha-helix surrounded by a seven-stranded, highly-twisted anti-parallel beta-sheet, with an overall structure that has great similarity with the beta-barrel of the BT domain of the human MCC.
Pfam PF09413: Putative prokaryotic signal transducing protein (domain)
This is a family of putative prokaryotic signal transducing proteins of Pii-type.
Pfam PF24606: CEMIP beta-helix (repeat)
This entry represents the beta-helix domain of CEMIP, CEMIP2 and related sequences. Proteins in this entry proteins are involved in the metabolism of hyaluronic acid (HA) and mediate the depolymerization of high-molecular-weight HA into intermediate-sized fragments, a process crucial for various physiological functions, including the regulation of angiogenesis, heart development, and cell migration. This domain has the common structural motif of enzymes involved in polysaccharide degradation, encompassing both hydrolases and lyases, however, biochemical experiments failed to detect any hyaluronidase activity in CEMIP2 and the putative active site remains to be elucidated. This entry also includes Fibrocystin (PKHD), a protein that promotes ciliogenesis within renal epithelial cells, contributing to the formation of kidney tubules and maintaining the lumen architecture. It may participate in the regulation of the cholangiocytes proliferation and the CCN2 production in an CXCL8-dependent manner.
Pfam PF21815: PdeA-like PAS domain (domain)
This family is based on PAS domain from phosphodiesterase PdeA and similar proteins. PAS domains are found in all kingdoms of life and  are involved in diverse functions but have an especially strong  presence in signaling networks. They often serve as protein-protein  interaction modules. In PdeA, the PAS domain serves as an adaptor recognition site needed for regulated proteolysis by the ClpXP protease.
Pfam PF21515: Baseplate wedge protein gp6, domain II (domain)
This domain is found in Baseplate wedge protein gp6 from Enterobacteria phage T4 and similar sequences predominantly from tailed bacteriophages. Gp6 is a protein involved in tail assembly. This entry represents the first part of Domain II.
Pfam PF13716: Divergent CRAL/TRIO domain (domain)
This family includes divergent members of the CRAL-TRIO domain family. This family includes ECM25 that contains a divergent CRAL-TRIO domain identified by Gallego and colleagues.
Wikipedia: CRAL-TRIO domain is a protein structural domain that binds small lipophilic molecules. This domain is named after cellular retinaldehyde-binding protein (CRALBP) and TRIO guanine exchange factor.
Pfam PF15944: Domain of unknown function (DUF4752) (family)
This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 90 and 105 amino acids in length.  There is a conserved GLA 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 PF16304: Domain of unknown function (DUF4946) (family)
This small family consists of uncharacterized proteins around 180 residues in length and is mainly found in various Pseudomonas species, especially in Pseudomonas aeruginosa. The function of this family is unknown.
Pfam PF06721: Protein of unknown function (DUF1204) (family)
This family represents the C-terminus of a number of Arabidopsis thaliana hypothetical proteins of unknown function. Family members contain a conserved DFD 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 PF13546: DDE superfamily endonuclease (domain)
This family of proteins are related to [pfam:PF00665] and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction.
Pfam PF11603: Sir1, ORC-binding domain (domain)
This entry represents the ORC-binding domain of Sir1. Sir1 interacts with the BAH domain of the Orc1 subunit of the origin recognition complex (ORC) resulting in the establishment of silent chromatin at HMR and HML in S.cerevisiae. The amino acids from the ORC interaction region of Sir1 are presented on a conserved, convex surface that forms a complementary interface with the Orc1 BAH domain, critical for transcriptional silencing.  Proteins containing this domain also include Y' element ATP-dependent helicase protein 1, which catalyses DNA unwinding and is involved in telomerase-independent telomere maintenance.
Pfam PF11319: Type VI secretion system VasI, EvfG, VC_A0118 (family)
VasI is a family of Gram-negative proteins that form part of the pathogenicity apparatus for bacteria-to-bacteria attack.  The exact function of this com[onent is not known.
Pfam PF18660: Tsi6 (domain)
Tsi6 inhibits the NADase activity of Tse6, an integral membrane toxin from Pseudomonas aeruginosa. The Tsi6 immunity protein adopts an all-alpha-helical fold that binds to a surface of Tse6.
Pfam PF10625: Universal stress protein B (UspB) (family)
UspB in Escherichia coli is a 14kDa protein which is predicted to be an integral membrane protein.  Overexpression of UspB results in cell death in stationary phase, and mutants of uspB are sensitive to ethanol exposure during stationary phase.
Pfam PF11417: Loader and inhibitor of phage G40P (family)
G39P inhibits the initiation of DNA replication by blocking G40P replicative helicase. G39P has a bipartite stricture consisting of a folded N-terminal domain and an unfolded C-terminal domain. The C terminal is essential for helicase interaction.
Pfam PF18874: QPE domain (domain)
This sort presumed domain is found in a small set of gram positive organisms in cell surface proteins with an N-terminal collagen binding domain. We have named this domain QPE after the most conserved sequence motif.
Pfam PF03244: Photosystem I reaction centre subunit VI (family)
Photosystem I (PSI) is an integral membrane protein complex that uses light energy to mediate electron transfer from plastocyanin to ferredoxin.
Pfam PF23425: Family of unknown function (DUF7113) (family)
This family represents a group of proteins from halobacteria. It has several conserved motifs YVWVCD, RGF and RTQFxR. Members are predicted to show an alpha-beta configuration.
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 PF13885: Keratin, high sulfur B2 protein (family)
Keratin-associated proteins (KAPs) are cysteine-rich proteins synthesized during the differentiation of hair matrix cells, and form hair fibres in association with hair keratin intermediate filaments . This entry also includes the high-sulfur and high-tyrosine keratins from sheep and goats.

In the hair cortex, hair keratin intermediate filaments are embedded in an interfilamentous matrix, consisting of hair keratin-associated proteins, which are essential for the formation of a rigid and resistant hair shaft through their extensive disulfide bond cross-linking with abundant cysteine residues of hair keratins . The matrix proteins include the high-sulfur and high-glycine-tyrosine keratins.
Pfam PF06692: Melon necrotic spot virus P7B protein (family)
This family consists of several Melon necrotic spot virus (MNSV) P7B proteins. The function of this family is unknown.
Pfam PF22542: Utp8, C-terminal (domain)
This domain is found at the C-terminal end of U3 small nucleolar RNA-associated protein 8 from Saccharomyces cerevisiae (Utp8) and similar proteins from fungi. Utp8 is an essential component of the nuclear tRNA export machinery in S.cerevisiae. It is a tRNA binding protein that act at a step between tRNA maturation /aminoacylation, and translocation of the tRNA across the nuclear pore complex. This domain shows an all-alpha structure.
Pfam PF19724: Family of unknown function (DUF6217) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001142) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). It  includes a member of the tryptoquialanine biosynthetic gene cluster from Penicillium aethiopicum. This family appears to be  predominantly found in fungi.
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 PF21321: Putative DNA-binding HTH domain (domain)
This domain is found at the N-terminus of the VapB45 protein that is thought to be part the antitoxin component of a Toxin-Antitoxin system. This domain adopts a helix-turn-helix structure that is likely to be a DNA-binding domain.
Pfam PF17410: Subtelomeric Variable Open Reading frame (family)
The parasite protein STEVOR (Subtelomeric Variable Open Reading frame) is an erythrocyte-binding protein recognizing Glycophorin C on the red blood cell (RBC) surface. The cytoplasmic domain of STEVOR is shown to interact with ankyrin complex at the erythrocyte skeleton. It is phosphorylated by protein kinase A (PKA) at a specific serine residue (S324). The N-terminal semi-conserved region of Stevor that is present in this domain is shown to specifically bind to to a chymotrypsin-resistant RBC receptor. The expression of STEVOR in multiple parasite stages including merozoites suggests that STEVOR mediates multiple distinct functions in parasitic infectious cycle.
Pfam PF20998: Nucleolar protein 11 C-terminal domain (repeat)
This alpha-solenoid repeat in found at the C-terminus of nucleolar protein 11.
Pfam PF03581: Herpesvirus UL33-like protein (family)
This is a family of Herpesvirus proteins including UL33 [swissprot:P10217] ,UL51 [swissprot:P16792]. The proteins in this  family are involved in packaging viral DNA.
Pfam PF23134: TRIP4, third domain (domain)
This entry represents a presumed domain found in TRIP4 (also known as ASC-1) from human and related sequences. TRIP4 is the orthologue of yeast RQT4 and is part of the RQC trigger (RQT) complex that activates the ribosome quality control (RQC) pathway, a pathway that degrades nascent peptide chains during problematic translation. TRIP4 has also been described as a transcription coactivator which associates with nuclear receptors and transcriptional coactivators including EP300, CREBBP and NCOA1, and basal transcription factors like TBP and TFIIA to facilitate nuclear receptors-mediated transcription. The function of this domain is known.
Pfam PF07855: Autophagy-related protein 101 (family)
Atg101 is a critical autophagy factor that functions together with ULK, Atg13 and FIP200. Atg101 has been shown to be a HORMA (Hop1, Rev7 and MAD2) domain protein with an open conformation.
Wikipedia: Autophagy-related protein 101 also known as ATG101 is a protein that in humans is encoded by the C12orf44 gene.
Pfam PF09180: Prolyl-tRNA synthetase, C-terminal (domain)
Members of this family are predominantly found in prokaryotic prolyl-tRNA synthetase. They contain a zinc binding site, and adopt a structure consisting of alpha helices and antiparallel beta sheets arranged in 2 layers, in a beta-alpha-beta-alpha-beta motif.
Pfam PF11621: C3 binding domain 4 of IgG-bind protein SBI (domain)
This family of proteins represents Sbi domain IV which binds the central complement protein C3. Sbi-IV interacts with Sbi-III to induce a consumption of complement via alternative pathway activation. When not interacting with Sbi-III, Sbi-IV inhibits the alternative pathway without complement consumption. The structure of Sbi-IV consists of a three-helix bundle fold.
Pfam PF06839: GRF zinc finger (domain)
This presumed zinc binding domain is found in a variety of DNA-binding proteins.  It seems likely that this domain is involved in nucleic acid binding.  It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to [pfam:PF01396].
Pfam PF22412: Phage G20C small terminase C-terminal domain (domain)
This domain is found at the C-terminal end of terminase small subunit (TerS) from Thermus phage G20c, which oligomerises into a nonamer that binds DNA, stimulates terminase large subunit ATPase activity, and inhibits TerL nuclease activity. TerS is organised into an N-terminal helix-turn-helix (HTH) motif ([pfam:PF21434]) followed by an oligomerisation domain consisting of two antiparallel helices (this entry) that pack against the oligomerisation domain helices of the neighbouring subunit, forming a helical barrel.
Pfam PF07434: CblD like pilus biogenesis initiator (family)
This family consists of several minor pilin proteins including CblD from Burkholderia cepacia which is known to CblD be the initiator of pilus biogenesis. The family also contains a variety of Enterobacterial minor pilin proteins.
Pfam PF06729: Kinetochore component, CENP-R (family)
This family consists of mammalian kinetochore sub-complex proteins CENP-R, also referred to as nuclear receptor co-activator NRIF3 proteins. NRIF3 exhibits a distinct receptor specificity in interacting with and potentiating the activity of only TRs and RXRs but not other examined nuclear receptors. NRIF3 as a co-regulator that possesses both transactivation and transrepression domains and/or functions. Collectively, the NRIF3 family of co-regulators may play dual roles in mediating both positive and negative regulatory effects on gene expression. CENP-R is one of the 15 components that make up the constitutive centromere associated complex (CCAN) part of the kinetochore. A sub-complex of CCAN, consisting of CENP-P/O/R/Q/U self-assembles on kinetochores with varying stoichiometry and undergoes a pre-mitotic maturation step. Kinetochore assembly is a cell cycle regulated multi-step process. The initial step occurs during interphase and involves loading of the 15-subunit constitutive centromere associated complex (CCAN). Kinetochores are multi-protein megadalton assemblies that are required for attachment of microtubules to centromeres and, in turn, the segregation of chromosomes in mitosis.
Pfam PF14679: FANCI helical domain 1 (repeat)
This is the helical domain 1 (HD1) of the Fanconi anemia group I protein.
Pfam PF17266: Family of unknown function (DUF5332) (family)
This family of uncharacterized proteins is mostly found in Chromadorea. Family members include dct-5 proteins. Dct-5 is a target of DAF-16, a forkhead transcription factor, which is a key regulator of longevity, metabolism and dauer diapause in Caenorhabditis elegans.
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 PF20469: Overcoming lysogenization defect protein-like, TOPRIM domain (domain)
This entry represents the topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain found in bacterial and archaeal nucleases of the OLD (overcome lysogenization defect) family. The bacteriophage P2 OLD protein, which has DNase as well as RNase activity consists of an N-terminal ABC-type ATPase domain and a C-terminal Toprim domain. The nuclease activity of OLD is stimulated by ATP, though the ATPase activity is not DNA-dependent. The TOPRIM domain has two conserved motifs, one of which centres at a conserved glutamate and the other one at two conserved aspartates (DxD). The conserved glutamate may act as a general acid in strand cleavage by nucleases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Pfam PF14842: FliG N-terminal domain (family)
This is the N-terminal domain of the flagellar rotor protein FliG.
Pfam PF03777: ChpA-C (domain)
Small domain found in a family of secreted streptomyces proteins. It occurs singly or as a pair. Many of the domains have two cysteines that may form a disulphide bridge. This domain is found in chaplins ChpA-C (coelicolor hydrophobic aerial) proteins. ChpA-C contain a canonical C-terminal sortase signal, which is recognized by sortase enzymes that covalently couple their substrates to the peptidoglycan present in the cell wall. Indeed, direct evidence for sortase-mediated coupling of ChpC has been demonstrated, and it is expected that ChpA and ChpB are also anchored to the cell wall.
Pfam PF15168: Triple QxxK/R motif-containing protein family (family)
TRIQK member-proteins share a characteristic triple repeat of the sequence QXXK/R, as well as a hydrophobic C-terminal region. Xenopus and mouse triqk genes are broadly expressed throughout embryogenesis, and mtriqk is also generally expressed in mouse adult tissues. TRIQK proteins are localized to the endoplasmic reticulum membrane.  This family is found in eukaryotes and members are typically between and 86 amino acids in length.
Pfam PF08898: Domain of unknown function (DUF1843) (domain)
This domain is found at the C-terminus of a family of proteins that are functionally uncharacterised. The presumed domain is about 60 amino acid residues in length and is found independently in some proteins.
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 PF02064: MAS20 protein import receptor (family)
Virtually all mitochondrial precursors are imported via the same mechanism : precursors first bind to receptors on the mitochondrial surface, then insert into the translocation channel in the outer membrane. Many outer-membrane proteins participate in the early stages of import, four of which (MAS20, MAS22, MAS37 and MAS70) are components of the receptor. MAS20, which forms a subcomplex with MAS22, seems to interact with most or all mitochondrial precursors, suggesting that the protein binds directly to mitochondrial targeting sequences. The MAS37 and MAS70 components also form a subcomplex, the two subcomplexes possibly binding via their trans- membrane (TM) regions - the TM region of MAS70 promotes oligomerisation of attached protein domains and shares sequence similarity with the TM region of MAS20 .

MAS20 is also known as TOM20.
Pfam PF19583: ODP family beta lactamase (domain)
The ODP (Oxygen-binding Di-iron Protein) domain is a distinct member of the metallo-beta-lactamase superfamily recruited to various bacterial and archaeal signal transduction pathways, including chemotaxis, to function as oxygen and iron sensors (1). ODP was shown to act as a sensor for chemotactic responses to both iron and oxygen in the human pathogen Treponema denticola (Td). The ODP di-iron site binds oxygen at high affinity to reversibly form an unusually stable peroxo adduct.
Wikipedia: The metallo-β-lactamase (MBL) superfamily constitutes a group of proteins found in all domains of life that share a characteristic αββα fold with the ability to bind transition metal ions. Such metal binding sites may have divalent transition metal ions like Zn(II), Fe(II)/Fe(III) and Mn(II), and are located at the bottom of a wide cleft able to accommodate diverse substrates. The name was adopted after the first members of the superfamily to be studied experimentally: a group of zinc-dependent hydrolytic enzymes conferring bacterial resistance to β-lactam antibiotics. These zinc-β-lactamases (ZBLs) inactivate β-lactam antibiotics through hydrolysis of the β-lactam ring. Early studies on MBLs were conducted on the enzyme βLII isolated from strain 569/H/9 of Bacillus cereus. It was named βLII because it was the second β-lactamase shown to be produced by the bacterium; the first one, βLI, was a non-metallic β-lactamase, i.e., insensitive to inhibition with EDTA.
Pfam PF11287: Protein of unknown function (DUF3088) (family)
This family of proteins with unknown function appears to be restricted to Proteobacteria.
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 PF14509: Glycosyl-hydrolase 97 C-terminal, oligomerisation (domain)
Glycosyl-hydrolase-97 is made up of three tightly linked and highly conserved globular domains.  The C-terminal domain is found to be necessary for oligomerisation of the whole molecule in order to create the active-site pocket and the Ca++-binding site.
Wikipedia: In molecular biology, glycoside hydrolase family 97 is a family of glycoside hydrolases.
Pfam PF09862: Domain of unknown function (DUF2089)-HTH (domain)
This domain, found in various hypothetical prokaryotic proteins, has no known function. It occurs as a fusion of ZnR+HTH+SHOCT-like.
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.