SII-SWORD/CoKE huggingface dataset:
Pfam PF05298: Bombinin (family)
This family consists of Bombinin and Maximin proteins from Bombina maxima (Chinese red belly toad). Two groups of antimicrobial peptides have been isolated from skin secretions of Bombina maxima. Peptides in the first group, named maximins 1, 2, 3, 4 and 5, are structurally related to bombinin-like peptides (BLPs). Unlike BLPs, sequence variations in maximins occurred all through the molecules. In addition to the potent antimicrobial activity, cytotoxicity against tumour cells and spermicidal action of maximins, maximin 3 possessed a significant anti-HIV activity. Maximins 1 and 3 have been found to be toxic to mice. Peptides in the second group, termed maximins H1, H2, H3 and H4, are homologous with bombinin H peptides.
Wikipedia: The bombinin family of antimicrobial peptides includes the bombinin and maximin proteins from Bombina maxima. Two groups of antimicrobial peptides have been isolated from skin secretions of B. maxima. Peptides in the first group, named maximins 1, 2, 3, 4 and 5, are structurally related to bombinin-like peptides (BLPs). Unlike BLPs, sequence variations in maximins occurred all through the molecules. In addition to the potent antimicrobial activity, cytotoxicity against tumour cells and spermicidal action of maximins, maximin 3 possessed a significant anti-Simian-Human immunodeficiency virus (HIV) activity. Maximins 1 and 3 have been found to be toxic to mice. Peptides in the second group, termed maximins H1, H2, H3 and H4, are homologous with bombinin H peptides.
Pfam PF14156: Antirepressor AbbA (family)
This family inactivates the repressor AbrB, which represses genes switched on during the transition from the exponential to the stationary phase of growth.  It binds to AbrB and prevents it from binding to DNA.
Pfam PF17799: Rrp7 RRM-like N-terminal domain (domain)
This domain corresponds to the N-terminal RNA-binding domain found in the Rrp7 protein.  It has an RRM-like fold with a circular permutation.
Pfam PF13516: Leucine Rich repeat (repeat)
Leucine-rich repeats (LRR) consist of 2-45 motifs of 20-30 amino acids in length that generally folds into an arc or horseshoe shape . LRRs occur in proteins ranging from viruses to eukaryotes, and appear to provide a structural framework for the formation of protein-protein interactions .Proteins containing LRRs include tyrosine kinase receptors, cell-adhesion molecules, virulence factors, and extracellular matrix-binding glycoproteins, and are involved in a variety of biological processes, including signal transduction, cell adhesion, DNA repair, recombination, transcription, RNA processing, disease resistance, apoptosis, and the immune response .

Sequence analyses of LRR proteins suggested the existence of several different subfamilies of LRRs. The significance of this classification is that repeats from different subfamilies never occur simultaneously and have most probably evolved independently. It is, however, now clear that all major classes of LRR have curved horseshoe structures with a parallel Î² sheet on the concave side and mostly helical elements on the convex side. At least six families of LRR proteins, characterised by different lengths and consensus sequences of the repeats, have been identified. Eleven-residue segments of the LRRs (LxxLxLxxN/CxL), corresponding to the Î²-strand and adjacent loop regions, are conserved in LRR proteins, whereas the remaining parts of the repeats (herein termed variable) may be very different. Despite the differences, each of the variable parts contains two half-turns at both ends and a "linear" segment (as the chain follows a linear path overall), usually formed by a helix, in the middle. The concave face and the adjacent loops are the most common protein interaction surfaces on LRR proteins. 3D structure of some LRR proteins-ligand complexes show that the concave surface of LRR domain is ideal for interaction with Î±-helix, thus supporting earlier conclusions that the elongated and curved LRR structure provides an outstanding framework for achieving diverse protein-protein interactions . Molecular modeling suggests that the conserved pattern LxxLxL, which is shorter than the previously proposed LxxLxLxxN/CxL is sufficient to impart the characteristic horseshoe curvature to proteins with 20-to 30-residue repeats .
Wikipedia: A leucine-rich repeat (LRR) is a protein structural motif that forms an α/β horseshoe fold. It is composed of repeating 20–30 amino acid stretches that are unusually rich in the hydrophobic amino acid leucine. These tandem repeats commonly fold together to form a solenoid protein domain, termed leucine-rich repeat domain. Typically, each repeat unit has beta strand-turn-alpha helix structure, and the assembled domain, composed of many such repeats, has a horseshoe shape with an interior parallel beta sheet and an exterior array of helices. One face of the beta sheet and one side of the helix array are exposed to solvent and are therefore dominated by hydrophilic residues. The region between the helices and sheets is the protein's hydrophobic core and is tightly sterically packed with leucine residues.
Pfam PF00456: Transketolase, thiamine diphosphate binding domain (domain)
This family includes transketolase enzymes [ec:2.2.1.1]. and also partially matches to 2-oxoisovalerate dehydrogenase beta subunit [swissprot:P37941] [ec:1.2.4.4].  Both these enzymes utilise thiamine pyrophosphate as a cofactor, suggesting there may be common aspects in their mechanism of catalysis.
Pfam PF14796: Clathrin-adaptor complex-3 beta-1 subunit C-terminal (family)
This domain lies at the C-terminus of the clathrin-adaptor protein complex-3 beta-1 subunit. The AP-3 complex is associated with the Golgi region of the cell as well as with more peripheral structures. The AP-3 complex may be directly involved in trafficking to lysosomes or alternatively it may be involved in another pathway, but that mis-sorting in that pathway may indirectly lead to defects in pigment granules.
Pfam PF12556: Cobaltochelatase CobS subunit N terminal (family)
This domain family is found in bacteria, and is approximately 40 amino acids in length. The family is found in association with [pfam:PF07728].  There are two completely conserved residues (P and F) that may be functionally important. This family is the N terminal of the CobS subunit of cobaltochelatase. Cobaltochelatase belongs to the AAA+ superfamily of proteins. CobS and CobT form a chaperone like complex.
Pfam PF04289: Protein of unknown function (DUF447) N-terminal domain (domain)
Archaeal protein of unknown function. A fungal member UniProtKB:M2LN89 is clearly a Flavine-reductase enzyme by homology, and UniProtKB:O28442 has been shown to bind riboflavin 5'-phosphate (unpublished structural Xray analysis).
Pfam PF02624: YcaO cyclodehydratase, ATP-ad Mg2+-binding (family)
YcaO is an ATP- an Mg2+-binding protein involved in the peptidic biosynthesis of azoline. There three motifs involved in the binding are, in UniProtKB:P75838, 71-79: Sx3ExxER, 184-203: Sx6Ex3Qx3ExxER, and 286-290: RxxxE. Three slightly different functional families are represented in this family, proteins involved in TOMM (thiazole/oxazole-modified microcin) biogenesis, non-TOMM proteins such as UniProtKB:P75838, and TfuA-associated non-TOMM proteins involved in trifolitoxin biosynthesis. UniProtKB:P75838 hydrolyses ATP to AMP and pyrophosphate.
Wikipedia: YcaO is a protein found in bacteria which is involved in the synthesis of thiazole/oxazole modified microcin antibiotics, such as bottromycin. YcaO performs ATP dependent cyclodehydration to form the oxazole and thiazole moieties of the microcin.
Pfam PF15495: Major fimbrial subunit protein type IV, Fimbrillin, C-terminal (domain)
Fimbrillin_C is a C-terminal family of major fimbrial subunit protein type IV proteins largely from Bacillus species. The family is associated with family P_gingi_FimA, [pfam:PF06321].
Pfam PF19761: Family of unknown function (DUF6248) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000703) is described by MIBiG as an example of the following biosynthetic class, saccharide. It includes a member from the kanamycin biosynthetic gene cluster from Streptomyces  kanamyceticus.
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 PF02246: Protein L b1 domain (domain)
Protein L is a bacterial protein with immunoglobulin (Ig) light chain-binding properties. It contains a number of homologous b1 repeats towards the N-terminus. These repeats have been found to be responsible for the interaction of protein L with Ig light chains.
Pfam PF14769: Flagellar C1a complex subunit C1a-32 (family)
This family represents one small subunit, C1a-32, of the C1a projection (the seventh projection of flagellar). Numerous studies have indicated that each of the seven projections associated with the central pair of microtubules in flagellar plays a distinct role in regulating eukaryotic ciliary/flagellar motility. The C1a projection is a complex of proteins including PF6, C1a-86, C1a-34, C1a-32, C1a-18, and calmodulin. C1a projection is involved in modulating flagellar beat frequency and this is mediated via the C1a-34, C1a-32, and C1a-18 sub-complex by modulating the activity of both the inner and outer dynein arms.
Pfam PF05822: Pyrimidine 5'-nucleotidase (UMPH-1) (family)
This family consists of several eukaryotic pyrimidine 5'-nucleotidase proteins. P5'N-1, also known as uridine monophosphate hydrolase-1 (UMPH-1), is a member of a large functional group of enzymes, characterised by the ability to dephosphorylate nucleic acids. P5'N-1 catalyses the dephosphorylation of pyrimidine nucleoside monophosphates to the corresponding nucleosides. Deficiencies in this proteins function can lead to several different disorders in humans.
Pfam PF11790: Glycosyl hydrolase catalytic core (family)
This family is probably a glycosyl hydrolase, and is conserved in fungi and some Proteobacteria. The pombe member is annotated as being from IPR013781.
Pfam PF02845: CUE domain (domain)
CUE domains have been shown to bind ubiquitin. It has been suggested that CUE domains are related to [pfam:PF00627] and this has been confirmed by the structure of the domain. CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2.
Pfam PF15127: Small membrane A-kinase anchor protein (family)
SmAKAP is a small membrane-bound PKA-RI-specific protein kinase A-anchoring protein, referred to as small membrane-AKAP. It is probably tethered to the plasma membrane most through a dual acylation of its N-terminal Met-Gly-Cys- motif (myristoylation and palmitoylation, respectively). It specifically targets PKA-RI isoforms to the plasma membrane. It localizes to plasma membranes, is enriched at cell-cell junctions and associates with filopodia.
Pfam PF15462: Bartter syndrome, infantile, with sensorineural deafness (Barttin) (family)
Barttin is a family of mammalian proteins that are chloride ion channel beta-subunits crucial for renal Cl-re-absorption and inner ear K+ secretion. Bartter syndrome is a term covering a heterogeneous group of autosomal recessive salt-losing nephropathies that are caused by disturbed transepithelial sodium chloride re-absorption in the distal nephron. Mutations in the BCD proteins lead to sensorial deafness.
Pfam PF14950: Domain of unknown function (DUF4502) (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 181 and 876 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 PF16252: Domain of unknown function (DUF4908) (family)
A small family of uncharacterized proteins around 260 residues in length and found in various Caulobacter and Brevundimonas species. The function of this family is unknown.
Pfam PF20509: Family of unknown function (DUF6735) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in archaea. Proteins in this family are typically between 178 and 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 PF16621: Neutrophil cytosol factor 1, PBR/AIR (domain)
This entry represents the polybasic or autoinhibitory region (PBR/AIR, an arginine/lysine rich region) found after the second SH3 domain in neutrophil cytosol factor 1 (NCF1 or p47phox). NCF1 is one of the cytosolic regulatory components of NADPH oxidase and consists of a PX domain at the N-terminal ([pfam:PF00787]), two tandem SH3 domains ([pfam:PF00018]), a PBR/AIR and a proline-rich region at the C-terminal ([pfam:PF08944]). In the resting state, the SH3 domains of NCF1 are masked by an intramolecular interaction with the PBR/AIR, which maintains the enzyme in an inactive form.
Pfam PF23018: Cypovirus WIV domain (domain)
This entry corresponds to the WIV domain found in p44 (also known as nsp2, NS2 or NS) protein from Bombyx mori cypovirus 1 and similar proteins from cypoviruses, which infect butterflies such as Bombyx mori. The WIV domain probably facilitates viral infection of arthropods. WIV stands for 'Widespread, Intriguing, Versatile'.
Pfam PF21362: E3 ubiquitin-protein ligase sina/sinah, RING finger (domain)
This is the RING finger domain of Sina and its homologues from animals, Sinah1/2 and plants, such as SINAT3 from Arabidopsis. Sina (seven in absentia) was first identified in Drosophila and is essential for the determination of the R7 pathway in photoreceptor cell development. It consists of a RING zinc finger at the N-terminal, followed by two zinc  finger (C2H2 type) domains ([pfam:PF21361]) and a C-terminal TRAF-like domain ([pfam:PF03145]). This domain gives the E3 ubiquitin ligase activity to these proteins.
Pfam PF03018: Dirigent-like protein (family)
This family contains a number of proteins which are induced during disease response in plants. Members of this family are involved in lignification.
Pfam PF16882: Domain of unknown function (DUF5079) (family)
This protein is believed to be involved in the type VII secretion system.
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 PF00324: Amino acid permease (domain)
Amino acid permeases are integral membrane proteins involved in the transport of amino acids into the cell. A number of such proteins have been found to be evolutionary related . These proteins seem to contain up to 12 transmembrane segments. The best conserved region in this family is located in the second transmembrane segment.

This domain is found in amino acid permeases, as well as in solute carrier family 12A (SLC12A) sequences.
Wikipedia: The Amino Acid-Polyamine-Organocation (APC) Family of transport proteins includes members that function as solute:cation symporters and solute:solute antiporters. They occur in bacteria, archaea, fungi, unicellular eukaryotic protists, slime molds, plants and animals. They vary in length, being as small as 350 residues and as large as 850 residues. The smaller proteins are generally of prokaryotic origin while the larger ones are of eukaryotic origin. Most of them possess twelve transmembrane α-helical spanners but have a re-entrant loop involving TMSs 2 and 3. The APC Superfamily was established to encompass a wider range of homologues.
Pfam PF23679: UPA-FIIND domain (domain)
The so-called function-to-find (FIIND) was initially discovered in two proteins, NLRP1 (aka NALP1, CARD7, NAC, DEFCAP) and CARD8 (aka TUCAN, Cardinal). NLRP1 is a member of the Nod-like receptor (NLR) protein  superfamily and is involved in apoptosis and inflammation. To date,  it is the only NLR protein known to have a FIIND domain. The FIIND domain is also present in the CARD8 protein where, like in NLRP1,  it is followed by a C-terminal CARD domain. Both proteins are described to form an "inflammasome", a macro-molecular complex able to process caspase 1 and activate pro-IL1beta. The FIIND domain is composed of two subdomains ZU5 (found in the tight-junction protein ZO-1 and the netrin receptor UNC5) and UPA (conserved in UNC5, the death-domain-containing protein PIDD and proteins of the ankyrin family). This entry represents the UPA domain.
Pfam PF10660: Iron-containing outer mitochondrial membrane protein N-terminus (domain)
MitoNEET_N is the N-terminal region of the MitoNEET and Miner-type proteins that carry a zf-CDGSH, [pfam:PF09360], redox-active 2Fe-2S cluster.  The whole protein regulates oxidative capacity. The domain is an anchor sequence that tethers the protein to the outer membrane.
Wikipedia: The CDGSH iron sulfur domain are a group of iron-sulfur (2Fe-2S) clusters and a unique 39 amino acid CDGSH domain [C-X-C-X2-(S/T)-X3-P-X-C-D-G-(S/A/T)-H].
Pfam PF14557: Putative AphA-like transcriptional regulator (domain)
Members of this family are putative transcriptional regulators that appear to be related to the [pfam:PF03551] family. This family includes AphA-like members.
Pfam PF10204: Dual oxidase maturation factor (family)
DuoxA (Dual oxidase maturation factor) is the essential protein necessary for the final release of DUOX2 (an NADPH:O2 oxidoreductase flavoprotein) from the endoplasmic reticulum. Dual oxidases (DUOX1 and DUOX2) constitute the catalytic core of the hydrogen peroxide generator, which generates H2O2 at the apical membrane of thyroid follicular cells, essential for iodination of thyroglobulin by thyroid peroxidases.  DuoxA carries five membrane-integral regions including a reverse signal-anchor with external N-terminus (type III) and two N-glycosylation sites. It is conserved from nematodes to humans.
Pfam PF10672: S-adenosylmethionine-dependent methyltransferase (family)
Members of this family are S-adenosylmethionine-dependent methyltransferases from gamma-proteobacterial species. The diversity in the roles of methylation is matched by the almost bewildering number of methyltransferase enzymes that catalyse the methylation reaction. Although several classes of methyltransferase enzymes are known, the great majority of methylation reactions are catalysed by the S-adenosylmethionine-dependent methyltransferases.
Pfam PF22142: Hydroxylamine oxidoreductase, C-terminal domain (domain)
This domain is found at the C-terminal end of Hydroxylamine oxidoreductase from Kuenenia stuttgartiensis (Hao, [swissprot:Q1PX48]) and similar bacterial sequences. This enzyme is responsible for the formation of NO from hydroxylamine in aerobic ammonium -oxidising bacteria. This domain shows a predominantly alpha -helical structure.
Pfam PF05288: Poxvirus A3L Protein (family)
This family consists of several poxvirus A3L or A2_5L proteins.
Pfam PF12428: Protein of unknown function (DUF3675) (family)
This domain family is found in eukaryotes, and is approximately 120 amino acids in length. The family is found in association with [pfam:PF00097]. There are two completely conserved residues (R and L) 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 PF16201: Nucleolar pre-ribosomal-associated protein 1 (family)
This family is found on the long vertebral and plant nucleolar proteins that also carry Npa1, [pfam:PF11707].
Pfam PF18135: Type ISP C-terminal specificity domain (domain)
This is the C-terminal domain of Type ISP restriction-modification enzyme LLaBIII present in Lactococcus lactis subsp. cremoris. Type ISP restriction-modification (RM) enzymes provide a potent defence against infection by foreign and bacteriophage DNA. This domain interacts extensively with DNA and is known as the target recognition domain (TRD). TRD works by recognising 6/7 base pairs of asymmetric sequence.
Pfam PF02489: Herpesvirus glycoprotein H main domain (domain)
Herpesvirus glycoprotein H (gH) is a virion associated envelope glycoprotein. Complex formation between gH and gL has been demonstrated in both virions and infected cells.
Pfam PF20106: Family of unknown function (DUF6496) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 64 and 166 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 PF20745: Tailspike protein-like, Ig-like domain (domain)
This domain is found in Tail spike protein (TSP) from Shigella phage Sf6 and similar sequences from tailed bacteriophages and bacterial prophages. It forms a beta-sandwich consisting of two antiparallel, three stranded beta-sheets. A short alpha helix is included in the connecting loop between the third and fourth strand. This domain is structurally homologous to viral coat proteins.
Pfam PF10886: Protein of unknown function (DUF2685) (family)
Members in this family of proteins are annotated as uvdY.-2 which is an open reading frame within uvsY. However currently there is 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.