SII-SWORD/CoKE huggingface dataset:
Pfam PF23862: CdsD C-terminal (domain)
This domain is found at the C-terminal of CdsD from Chlamydia trachomatis ([swissprot:O84671]) and similar sequences. CdsD is a structural contact-dependent secretion (Cds) protein that form part of the basal body of the type III secretion system (T3SS) injectisome of the bacteria. The periplasmic part of this protein contains at least 3 domains: PD1, PD2 ([pfam:PF22598]) and PD3 ([pfam:PF04972]), all of them sharing the same alpha-beta-beta-alpha-beta topology, known as the BON fold.
Pfam PF03934: Type II secretion system (T2SS), protein K (domain)
Members of this family are involved in the Type II protein secretion system. The T2SK family includes proteins such as ExeK, PulK, OutX  and XcpX. They consist of two tandem SAM-like domains, this entry represents the second one.
Pfam PF03242: Late embryogenesis abundant protein (LEA_3a subfamily) (family)
Members of this family are similar to late embryogenesis abundant proteins. Members of the family have been isolated in a number of different screens.  However, the molecular function of these proteins remains obscure.
Pfam PF22715: Short NACHT-associated C-Terminal domain, family 9 (domain)
The SNaCT domains are a rapidly evolving, monophyletic assemblage of domains found C-terminal to the NACHT module in several bacterial NACHT conflict systems. They contain a well-conserved aspartate near the N-terminus of the domain. SNaCT domains are thought to occlude the NTP-binding region, potentially until they interact with phage-encoded bNACHT inhibitors.
Pfam PF16401: Domain of unknown function (DUF5009) (family)
This small family of proteins is functionally uncharacterised. This family is mainly found in various Bacteroides species. The members in this family are around 470 residues 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 PF02960: K1 glycoprotein (family)
Current genotyping systems for Human herpesvirus 8 (HHV-8) are based on the highly variable gene encoding the K1 glycoprotein . This entry represents the C-terminal region of the K1 glycoprotein.
Pfam PF10495: Pericentrin-AKAP-450 domain of centrosomal targeting protein (domain)
This domain is a coiled-coil region close to the C-terminus of centrosomal proteins that is directly responsible for recruiting AKAP-450 and pericentrin to the centrosome. Hence the suggested name for this region is a PACT domain (pericentrin-AKAP-450 centrosomal targeting). This domain is also present at the C-terminus of coiled-coil proteins from Drosophila and S. pombe, and that from the Drosophila protein is sufficient for targeting to the centrosome in mammalian cells. The function of these proteins is unknown but they seem good candidates for having a centrosomal or spindle pole body location. The final 22 residues of this domain in AKAP-450 appear specifically to be a calmodulin-binding domain indicating that this member at least is likely to contribute to centrosome assembly.
Pfam PF17778: Beta-lactamase associated winged helix domain (domain)
This winged helix domain is found at the C-terminus of some beta lactamase enzymes.
Pfam PF17690: Family of unknown function (DUF5537) (family)
This is a family of unknown function found in chordata.
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 PF23011: Histone-lysine N-methyltransferase NSD-like, PHD zinc finger 1 (domain)
This domain is found in the NSD (nuclear receptor SET domain- containing) family of histone-lysine N-methyltransferases such as NSD1, NSD2, NSD3 and other related proteins. The NSD family plays an important role in the chromatin integrity and disruption of the NSD protein folding or its expression in human cells has been linked to several diseases. The domain represented by this entry adopts a classical PHD finger fold and acts as a chromatin reader module.
Pfam PF05485: THAP domain (domain)
The THAP domain is a putative DNA-binding domain (DBD) and probably also binds a zinc ion. It features the conserved C2CH architecture (consensus sequence: Cys - 2-4 residues - Cys - 35-50 residues - Cys - 2 residues - His). Other universal features include the location of the domain at the N-termini of proteins, its size of about 90 residues, a C-terminal AVPTIF box and several other conserved residues. Orthologues of the human THAP domain have been identified in other vertebrates and probably worms and flies, but not in other eukaryotes or any prokaryotes.
Pfam PF13742: OB-fold nucleic acid binding domain (domain)
This family contains OB-fold domains that bind to nucleic acids.
Pfam PF24373: Family of unknown function (DUF7529) (family)
This family includes a group of proteins from archaea. Members are predicted to adopt an 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 PF22690: Fatty acid synthase central AT domain (domain)
This entry includes a domain found in the central region of the acyltransferase domain (AT) from fungal type I fatty acid synthase (FAS, such as FAS1 from yeast) and mycobacteria, which have secondary-structure elements and sequence homology. Mycobacterial fatty acid synthase (FAS) complex is an homohexameric multifunctional enzyme that catalyses the synthesis of fatty acid precursors of mycolic acids, the major components of the cell wall in Mycobacteria and play an important role in pathogenicity.
Pfam PF24781: FANCA helical domain (domain)
Fanconi anemia (FA) is a human disorder characterised by cancer susceptibility and cellular sensitivity to DNA crosslinks and other damages. The FA complex repairs the interstrand cross-linking (ICL) lesions and coordinates activities of the downstream DNA repair pathway including nucleotide excision repair, translesion synthesis, and homologous recombination. The FA core complex consists of FANCA, FANCB, FANCC, FANCE, FANCF, FANCG, FANCL, FANCM, FANCT (UBET2), FAAP100 and FAAP24. This entry represents the helical domain of FANCA, found in the central region of the protein, which is packed against the arcC half of the C-terminal domain.
Pfam PF19134: Domain of unknown function (DUF5817) (domain)
This domain is present in a family of proteins predominantly found in Halobacteria. These proteins are thought to be the replication protein H.
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 PF12587: Protein of unknown function (DUF3761) (family)
This family of proteins is found in bacteria. Proteins in this family are typically between 100 and 157 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 PF11478: Antimicrobial chitin binding protein tachystatin B (family)
Tachystatin B is an antimicrobial chitin binding peptide and consists of two isotopes B1 and B2.Both structures contain a short antiparallel beta sheet with an inhibitory cysteine knot motif. Tyr(14) and Arg(17) are thought to be the essential residues for chitin binding.
Pfam PF21156: Isoamylase 1-3, C-terminal (domain)
Isoamylases (ISOAs) are starch debranching enzymes, including ISOA1, ISOA2 and ISOA3. ISOA1-2 are known to form a large complex and being involved in the biosynthesis and crystallization of starch. ISOA3 is involved in starch catabolism and removes different branches than ISA1-ISA2, namely short chains that prevent amylopectin crystallization. This is the C-terminal beta-sandwich domain from ISOA1-3. In ISOA1, this domain is involved in dimerisation of homodimers and suggests a similar interaction to form ISOA1-ISOA2 heterodimers.
Pfam PF00474: Sodium:solute symporter family (family)
This family includes [swissprot:P33413] which is not in the Prosite entry.  Membership of this family is supported by a significant blast score.
Wikipedia: Members of the Solute:Sodium Symporter (SSS) Family (TC# 2.A.21) catalyze solute:Na+ symport. The SSS family is within the APC Superfamily. The solutes transported may be sugars, amino acids, organo cations such as choline, nucleosides, inositols, vitamins, urea or anions, depending on the system. Members of the SSS family have been identified in bacteria, archaea and eukaryotes. Almost all functionally well-characterized members normally catalyze solute uptake via Na+ symport.
Pfam PF05790: Immunoglobulin C2-set domain (domain)
The basic structure of immunoglobulin (Ig) molecules is a tetramer of two light chains and two heavy chains linked by disulphide bonds. There are two types of light chains: kappa and lambda, each composed of a constant domain (CL) and a variable domain (VL). There are five types of heavy chains: alpha, delta, epsilon, gamma and mu, all consisting of a variable domain (VH) and three (in alpha, delta and gamma) or four (in epsilon and mu) constant domains (CH1 to CH4). Ig molecules are highly modular proteins, in which the variable and constant domains have clear, conserved sequence patterns. The domains in Ig and Ig-like molecules are grouped into four types: V-set (variable; IPR013106), C1-set (constant-1; IPR003597), C2-set (constant-2; IPR008424) and I-set (intermediate; IPR013098) . Structural studies have shown that these domains share a common core Greek-key Î²-sandwich structure, with the types differing in the number of strands in the Î²-sheets as well as in their sequence patterns .

Immunoglobulin-like domains that are related in both sequence and structure can be found in several diverse protein families. Ig-like domains are involved in a variety of functions, including cell-cell recognition, cell-surface receptors, muscle structure and the immune system .
This entry represents C2-set domains, which are Ig-like domains resembling the antibody constant domain. C2-set domains are found primarily in the mammalian T-cell surface antigens CD2 (Cluster of Differentiation 2), CD4 and CD80, as well as in vascular (VCAM) and intercellular (ICAM) cell adhesion molecules.

CD2 mediates T-cell adhesion via its ectodomain, and signal transduction utilising its 117-amino acid cytoplasmic tail . CD2 displays structural and functional similarities with African swine fever virus (ASFV) LMW8-DR, a protein that is involved in cell-cell adhesion and immune response modulation, suggesting a possible role in the pathogenesis of ASFV infection . CD4 is the primary receptor for HIV-1. CD4 has four immunoglobulin-like domains in its extracellular region that share the same structure, but can differ in sequence. Certain extracellular domains may be involved in dimerisation .
Wikipedia: The basic structure of immunoglobulin (Ig) molecules is a tetramer of two light chains and two heavy chains linked by disulphide bonds. There are two types of light chains: kappa and lambda, each composed of a constant domain (CL) and a variable domain (VL). There are five types of heavy chains: alpha, delta, epsilon, gamma and mu, all consisting of a variable domain (VH) and three or four constant domains. Ig molecules are highly modular proteins, in which the variable and constant domains have clear, conserved sequence patterns. The domains in Ig and Ig-like molecules are grouped into four types: V-set, C1-set, C2-set and I-set. Structural studies have shown that these domains share a common core Greek-key beta-sandwich structure, with the types differing in the number of strands in the beta-sheets as well as in their sequence patterns.
Pfam PF01028: Eukaryotic DNA topoisomerase I, catalytic core (domain)
Topoisomerase I promotes the relaxation of DNA superhelical tension by introducing a transient single-stranded break in duplex DNA and are vital for the processes of replication, transcription, and recombination.
Pfam PF19339: Protein angel homolog 2 N-terminal (domain)
This family represents the N-terminal unstructured domain of the protein angel homolog 2 (ANGEL2). This protein is a member of the CCR4 nocturin family and 2',3'-cyclic phosphatase activity involved in RNA processing and modification.
Pfam PF20684: Fungal rhodopsin domain (domain)
This domain is found in a wide range of fungi. It can form a large multigene family in many species. As with other rhodopsin-like proteins this domain contains 7 transmembrane helices that form an integral membrane domain.
Pfam PF06115: Domain of unknown function (DUF956) (family)
Family of bacterial sequences with undetermined 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 PF15250: Raftlin (family)
This family of proteins plays a role in the formation and/or maintenance of lipid rafts.
Pfam PF07900: Protein of unknown function (DUF1670) (family)
The hypothetical eukaryotic proteins found in this family are of unknown 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 PF03296: Poxvirus poly(A) polymerase nucleotidyltransferase domain (domain)
Poly(A) polymerase (2.7.7.19) catalyses template-independent extension of the 3'-end of a DNA or RNA strand by one nucleotide at a time. The Poxvirus enzyme creates the 3'(poly)A tail of mRNAs, and is a heterodimer of a catalytic and a regulatory subunit. The Poxvirus enzyme creates the 3'(poly)A tail of mRNAs, and is a heterodimer composed of a catalytic (VP55, also known as PAP-L) and a regulatory subunit (VP39). VP55 comprises three domains: the N-terminal or N domain, the central or catalytic domain, and the C-terminal or C domain, all three domains having distinct topologies. The core comprises a mixed nine-stranded twisted Î² sheet, with the first seven strands being folded from one long (118 residue) polypeptide segment that follows the N domain and the last two strands originating from the extreme C-terminal-most 15 residues of the entire polypeptide chain. Of the four Î±-helices in the catalytic domain, the two longest (J and L) near the surface pack against one side of the Î²-sheet in a nearly parallel orientation to the Î²-strands .
Pfam PF23866: Domain of unknown function (DUF7224) (domain)
This entry represents a metalloprotease-like domain found in ABC transporter permease from bacteria, predominantly Streptomyces spp. 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 PF07621: Protein of unknown function (DUF1582) (family)
A family of hypothetical proteins in Rhodopirellula baltica.
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 PF10041: Uncharacterized conserved protein (DUF2277) (family)
Members of this family of hypothetical bacterial proteins have 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 PF14055: NVEALA protein (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 75 and 92 amino acids in length. There is a conserved NVEALA sequence motif.
Pfam PF14599: Zinc-ribbon (domain)
This is a typical zinc-ribbon finger, with each pair of zinc-ligands coming from more-or-less either side of two knuckles. It is found in eukaryotes.
Pfam PF23426: Family of unknown function (DUF7114) (family)
This family represents a group of proteins from halobacteria. It has several conserved motifs GVQLIYEGLR, EPW and GR/K/QxQT/S. Members are predicted to show an all-alpha 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 PF02941: Ferredoxin thioredoxin reductase variable alpha chain (domain)
Ferredoxin thioredoxin reductase is a  protein which plays an important role in the ferredoxin/thioredoxin regulatory chain. It converts an electron signal (photoreduced ferredoxin) to a thiol signal (reduced thioredoxin), regulating enzymes by reduction of specific disulphide groups. It catalyses the light-dependent activation of several photosynthesis enzymes. Ferredoxin thioredoxin reductase is a heterodimer of subunit a and subunit b. Subunit a is the variable subunit, and b is the catalytic chain .
Wikipedia: Ferredoxin-thioredoxin reductase EC 1.8.7.2, systematic name ferredoxin:thioredoxin disulfide oxidoreductase, is a [4Fe-4S] protein that plays an important role in the ferredoxin/thioredoxin regulatory chain. It catalyzes the following reaction:2 reduced ferredoxin + thioredoxin disulfide  2 oxidized ferredoxin + thioredoxin thiols + 2 H+
Pfam PF03217: Surface layer protein A domain (domain)
This short domain is found in a variety of bacterial cell surface proteins. The domain is about 60 residues in length (although previously defined as 2 copies of this domain). It usually occurs in tandem pairs. It may be distantly related to the SH3 domain.
Pfam PF21468: Tyrosine-protein kinase receptor torso, second FN3 domain (domain)
This domain is found in Tyrosine-protein kinase receptor torso from Bombyx mori (Tor), which is involved in the initiation of metamorphosis during postembryonic development. This protein is organised into three consecutive fibronectin type III (FN3) domains and a C-terminal Kinase domain. This entry represents the second FN3 domain.
Pfam PF04711: Apolipoprotein A-II (ApoA-II) (family)
Apolipoprotein A-II (ApoA-II) is the second major apolipoprotein of high density lipoprotein in human plasma.    Mature ApoA-II is present as a dimer of two 77-amino acid chains joined by a disulphide bridge. ApoA-II regulates many steps in HDL metabolism, and its role in coronary heart disease is unclear. In bovine serum, the ApoA-II homologue is present in almost free form.             Bovine ApoA-II shows antimicrobial activity against Escherichia coli and yeasts in phosphate buffered saline (PBS).
Wikipedia: Apolipoprotein A-II is a protein that in humans is encoded by the APOA2 gene. It is the second most abundant protein of the high density lipoprotein particles. The protein is found in plasma as a monomer, homodimer, or heterodimer with apolipoprotein D. ApoA-II regulates many steps in HDL metabolism, and its role in coronary heart disease is unclear. Remarkably, defects in this gene may result in apolipoprotein A-II deficiency or hypercholesterolemia.
Pfam PF09759: Spinocerebellar ataxia type 10 protein domain (repeat)
This is the conserved C-terminal 100 residues of Ataxin-10. Ataxin-10 belongs to the family of armadillo repeat proteins and in solution it tends to form homotrimeric complexes, which associate via a tip-to-tip association in a horseshoe-shaped contact with the concave sides of the molecules facing each other. This domain may represent the homo-association site since that is located near the C-terminus of Ataxin-10. The protein does not contain a signal sequence for secretion or any subcellular compartment confirming its cytoplasmic localisation, specifically to the olivocerebellar region.
Pfam PF23520: Apicomplexa microprotein (family)
This protein family includes uncharacterised microproteins encoded by small open reading frames (smORFs) from apicomplexa, including [swissprot:A7AWP6] from the parasite Babesia bovis.
Pfam PF17525: Family of unknown function (DUF5447) (family)
This is a family of unknown function found in Pseudomonas.
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 PF07429: 4-alpha-L-fucosyltransferase glycosyl transferase group 56 (family)
This family contains the bacterial enzyme 4-alpha-L-fucosyltransferase (Fuc4NAc transferase) (EC 2.4.1.-) (approximately 360 residues long). This catalyses the synthesis of Fuc4NAc-ManNAcA-GlcNAc-PP-Und (lipid III) as part of the biosynthetic pathway of enterobacterial common antigen (ECA), a polysaccharide comprised of the trisaccharide repeat unit Fuc4NAc-ManNAcA-GlcNAc.