SII-SWORD/CoKE huggingface dataset:
Pfam PF03974: Ecotin (family)
Ecotin is a broad range serine protease inhibitor, which forms homodimers. The C-terminal region contains the dimerisation motif. Interestingly, the binding sites show a fluidity of protein contacts binding sites show a fluidity of protein contacts derived from ecotin's  innate flexibility in fitting itself to proteases while.
Wikipedia: In molecular biology, ecotin is a protease inhibitor which belongs to MEROPS inhibitor family I11, clan IN. Ecotins are dimeric periplasmic proteins from Escherichia coli and related Gram-negative bacteria that have been shown to be potent inhibitors of many trypsin-fold serine proteases of widely varying substrate specificity, which belong to MEROPS peptidase family S1. Phylogenetic analysis suggested that ecotin has an exogenous target, possibly neutrophil elastase. Ecotin from E. coli, Yersinia pestis, and Pseudomonas aeruginosa, all species that encounter the mammalian immune system, inhibit neutrophil elastase strongly while ecotin from the plant pathogen Pantoea citrea inhibits neutrophil elastase 1000-fold less potently. Ecotins all potently inhibit pancreatic digestive peptidases trypsin and chymotrypsin, while showing more variable inhibition of the blood peptidases Factor Xa, thrombin, and urokinase-type plasminogen activator.
Pfam PF07994: Myo-inositol-1-phosphate synthase (family)
This is a family of myo-inositol-1-phosphate synthases. Inositol-1-phosphate catalyses the conversion of glucose-6- phosphate to inositol-1-phosphate, which is then dephosphorylated  to inositol. Inositol phosphates play an important role in  signal transduction.
Pfam PF04408: Helicase associated domain (HA2), winged-helix (domain)
The helicase associated domain (HA2) has an all alpha-helical fold and consists of a N-terminal winged-helix (WH) domain  and a C-terminal degenerate helical-bundle domain, referred to as the ratchet-like domain. These domains collaborate with RecA domains at the N-terminal in completing an RNA binding channel to allow the helicases to keep a stable grip on the RNA and assure its correct function. This entry represents the WH domain, which connects the N- (RecA domains) and C-terminal domains (ratchet-like and OB-fold) of helicases.
Pfam PF24843: Family of unknown function (DUF7720) (domain)
This entry represents a small domain found in streptococcal phage proteins. Structurally the domain is composed of a three stranded beta sheet followed by an alpha helix.
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 PF08269: Cache domain (domain)
Double Cache domain 2 (dCache_2) may be a result of single Cache domain 2 (sCache_2) duplication.
Wikipedia: In molecular biology, the cache domain is an extracellular protein domain that is predicted to have a role in small-molecule recognition in a wide range of proteins, including the animal dihydropyridine-sensitive voltage-gated Ca2+ channel alpha-2delta subunit, and various bacterial chemotaxis receptors. The name Cache comes from CAlcium channels and CHEmotaxis receptors. This domain consists of an N-terminal part with three predicted strands and an alpha-helix, and a C-terminal part with a strand dyad followed by a relatively unstructured region. The N-terminal portion of the (unpermuted) Cache domain contains three predicted strands that could form a sheet analogous to that present in the core of the PAS domain structure. Cache domains are particularly widespread in bacteria such as Vibrio cholerae. The animal calcium channel alpha-2delta subunits might have acquired a part of their extracellular domains from a bacterial source. The Cache domain appears to have arisen from the GAF-PAS fold despite their divergent functions.
Pfam PF19511: Conjugal transfer protein TrbL (family)
This family includes conjugal transfer proteins predominantly found in Firmicutes. Proteins in this family are typically between 286 and 301 amino acids in length.
Pfam PF11204: Protein of unknown function (DUF2985) (family)
This eukaryotic family of proteins has no known function.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF23861: Ribophorin II second domain (domain)
This entry represents the second beta sandwich domain found in eukaryotic Ribophorin II (RPN2) proteins. The mammalian oligosaccharyltransferase (OST) is a protein complex that effects the cotranslational N-glycosylation of newly synthesised polypeptides, and is composed of the following proteins: ribophorins I and II (RI and RII), OST48, and Dadl, N33/IAP, OST4, STT3. The family also includes the SWP1 protein from yeast. In yeast the oligosaccharyltransferase complex is composed 7 or 8 subunits, SWP1, being one of them.
Pfam PF03688: Nepovirus coat protein, C-terminal domain (domain)
The members of this family are derived from nepoviruses. Together with comoviruses and picornaviruses, nepoviruses are classified in the picornavirus superfamily of plus strand single-stranded RNA viruses. This family aligns several nepovirus coat protein sequences. In several cases, this is found at the C-terminus of the RNA2-encoded viral polyprotein. The coat protein consists of three trapezoid-shaped beta-barrel domains, and forms a pseudo T = 3 icosahedral capsid structure.
Pfam PF22721: TATA-binding-like protein domain of the TOTE conflict systems (family)
This entry represents the principal predicted hybrid duplex-binding domain of the TOTE (TPR, OB, TBP, Effector) conflict systems described as TATA-binding-like protein (TBP) domain of the TOTE (TBP-TOTE) in.
Pfam PF08364: Bacterial translation initiation factor IF-2 associated region (family)
Most of the sequences in this alignment come from bacterial translation initiation factors (IF-2, also [pfam:PF04760]), but the domain is also found in the eukaryotic translation initiation factor 4 gamma in yeast and in a hypothetical Euglenozoa protein of unknown function.
Pfam PF22551: T3SS (YopN, CesT) and YbjN peptide-binding chaperone 1 (domain)
This domain is observed in host systems predicted to counter viral ribosylating toxins. They are predicted to function as peptide-binding chaperone domains that target proteins modified by ADPr and potentially misfolded as a consequence.
Pfam PF02878: Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I (domain)
This entry represents domain I found in alpha-D-phosphohexomutase enzymes. This domain has a 3-layer Î±/Î²/Î± topology.
The alpha-D-phosphohexomutase superfamily is composed of four related enzymes, each of which catalyses a phosphoryl transfer on their sugar substrates: phosphoglucomutase (PGM), phosphoglucomutase/phosphomannomutase (PGM/PMM), phosphoglucosamine mutase (PNGM), and phosphoacetylglucosamine mutase (PAGM) . PGM (5.4.2.2) converts D-glucose 1-phosphate into D-glucose 6-phosphate, and participates in both the breakdown and synthesis of glucose . PGM/PMM (5.4.2.2; 5.4.2.8) are primarily bacterial enzymes that use either glucose or mannose as substrate, participating in the biosynthesis of a variety of carbohydrates such as lipopolysaccharides and alginate . Both PNGM (5.4.2.3) and PAGM (5.4.2.10) are involved in the biosynthesis of UDP-N-acetylglucosamine .
Pfam PF22321: Zonadhesin, second cohesin-like domain (domain)
This entry represents the second cohesin-like domain present in zonadhesin protein from Pichia pastoris.
Pfam PF01070: FMN-dependent dehydrogenase (domain)
A number of oxidoreductases that act on alpha-hydroxy acids and which are FMN-containing flavoproteins have been shown  to be structurally related. These enzymes are:


 * Lactate dehydrogenase (1.1.2.3), which consists of a dehydrogenase domain and a haem-binding domain called cytochrome b2 and which catalyses the conversion of lactate into pyruvate.
 * Glycolate oxidase (1.1.3.15) ((S)-2-hydroxy-acid oxidase), a peroxisomal enzyme that catalyses the conversion of glycolate and oxygen to glyoxylate and hydrogen peroxide.
 * Long chain alpha-hydroxy acid oxidase from rat (1.1.3.15), a peroxisomal enzyme.
 * Lactate 2-monooxygenase (1.13.12.4) (lactate oxidase) from Mycobacterium smegmatis, which catalyses the conversion of lactate and oxygen to acetate, carbon dioxide and water.
 * (S)-mandelate dehydrogenase from Pseudomonas putida (gene mdlB), which catalyses the reduction of (S)-mandelate to benzoylformate.


The first step in the reaction mechanism of these enzymes is the abstraction of the proton from the Î±-carbon of the substrate producing a carbanion which can subsequently attach to the N5 atom of FMN. A conserved histidine has been shown  to be involved in the removal of the proton. The region around this active site residue is highly conserved and contains an arginine residue which is involved in substrate binding.
Pfam PF14209: Domain of unknown function (DUF4321) (family)
This family of proteins is functionally uncharacterised.  It is found in bacteria, and is approximately 50 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 PF14627: Domain of unknown function (DUF4453) (family)
This short domain is found only on a small subgroup of proteins from Gram-negative Proteobacteria that also carry a YARHG domain, [pfam:PF13308]. They carry three conserved tryptophan and three conserved cysteine residues.
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 PF01431: Peptidase family M13 (family)
Mammalian enzymes are typically type-II membrane anchored enzymes which are known, or believed to activate or inactivate oligopeptide (pro)-hormones such as opioid peptides. The family also contains a bacterial member believed to be involved with milk protein cleavage.
Pfam PF13744: Helix-turn-helix domain (domain)
Members of this family contains a DNA-binding helix-turn-helix domain.
Pfam PF15027: MGT5A-like, N-terminal (domain)
This domain is found at the N-terminal end of human Alpha-1,6 -mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A (MGT5A) and similar sequences mainly found in vertebrates. MGT5A is a glycosyltransferase family 18 enzyme that also has the catalytic region [pfam:PF15024]. This domain, which shows an all helical structure, plays a critical role in the recognition of glycoprotein substrates. It is also found in Coiled -coil domain-containing protein 126, a smaller sequence that only contains this domain.
Pfam PF24280: HVO_A0563, N-terminal (domain)
This domain is found at the N-terminal of the predicted transcription regulator HVO_A0563 from Haloferax volcanii and similar archaeal proteins. This domain is predicted to adopt an alpha-beta structure. It is often found associated with [pfam:PF04967].
Pfam PF12643: MazG-like family (domain)
This family of short proteins are distantly related to the MazG enzyme. This suggests that these proteins are enzymes that catalyse a related reaction.
Pfam PF13162: Protein of unknown function (DUF3997) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 140 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 PF12656: G-patch domain (domain)
Yeast Spp2, a G-patch protein and spliceosome component, interacts with the ATP-dependent DExH-box splicing factor Prp2. As this interaction involves the G-patch sequence in Spp2 and is required for the recruitment of Prp2 to the spliceosome before the first catalytic step of splicing, it is proposed that Spp2 might be an accessory factor that confers spliceosome specificity on Prp2.
Pfam PF18865: AbiJ N-terminal domain 5 (domain)
Mostly alpha helical. Found fused to AbiJ-lke HEPN, and to other domains presumably involved in defense.
Pfam PF07637: Protein of unknown function (DUF1595) (family)
A family of proteins in Rhodopirellula baltica, associated with [pfam:PF07635], [pfam:PF07626], [pfam:PF07631], [pfam:PF07627], and [pfam:PF07624].
Pfam PF09981: Uncharacterized protein conserved in bacteria (DUF2218) (family)
This domain, found in various hypothetical bacterial proteins, has no known function.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF02448: L71 family (family)
This family of insect proteins are each about 100 amino acids long and have 6 conserved cysteine residues. They all have a predicted signal peptide and are probably excreted. The function of the proteins is unknown.
Pfam PF19702: Family of unknown function (DUF6200) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001943) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). It  includes a member from the vioprolides A biosynthetic gene cluster from Cystobacter sp.. This family appears to be predominantly  found in bacteria.
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 PF01660: Viral methyltransferase (family)
This RNA methyltransferase domain is found in a wide range of ssRNA viruses, including Hordei-, Tobra-, Tobamo-, Bromo-, Clostero- and Caliciviruses.  This methyltransferase is involved in mRNA capping.  Capping of mRNA enhances its stability. This usually occurs in the nucleus.  Therefore, many viruses that replicate in the cytoplasm encode their own.  This is a specific guanine-7-methyltransferase domain involved in viral mRNA cap0 synthesis. Specificity for guanine 7 position is shown by NMR in and in vivo role in cap synthesis.  Based on secondary structure prediction, the basic fold is believed to be similar to the common AdoMet-dependent methyltransferase fold. A curious feature of this methyltransferase domain is that it together with flanking sequences seems to have guanylyltransferase activity coupled to the methyltransferase activity. The domain is found throughout the so-called Alphavirus superfamily, (including alphaviruses and several other groups). It forms the defining, unique feature of this superfamily.
Pfam PF11224: Protein of unknown function (DUF3023) (family)
This bacterial family of proteins with unknown function appear to be restricted to Alphaproteobacteria.
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 PF11881: C-terminal domain of SPAR protein (family)
This domain is found st the C-terminus of many spine-associated Rap GTPase-activating - SPAR - proteins in eukaryotes. This domain is found associated with [pfam:PF02145], [pfam:PF00595]. The exact function is not known.
Pfam PF05297: Herpesvirus latent membrane protein 1 (LMP1) (family)
This family consists of several latent membrane protein 1 or LMP1s mostly from Epstein-Barr virus. LMP1 of EBV is a 62-65 kDa plasma membrane protein possessing six membrane spanning regions, a short cytoplasmic N-terminus and a long cytoplasmic carboxy tail of 200 amino acids. EBV latent membrane protein 1 (LMP1) is essential for EBV-mediated transformation and has been associated with several cases of malignancies. EBV-like viruses in Cynomolgus monkeys (Macaca fascicularis) have been associated with high  lymphoma rates in immunosuppressed monkeys
Pfam PF05720: Cell-cell adhesion domain (family)
This family is based on a group of Dictyostelium discoideum proteins that are essential in early development (). [swissprot:P16642] and  [swissprot:P16643] are located on the cell surface and mediate cell-cell adhesion.
Pfam PF19434: Dynamin-like GTPase OPA1 C-terminal (domain)
This entry represents the C-terminal domain of Dynamin-like GTPase OPA1. This protein is involved in mitochondrial fusion and inner membrane remodelling, essential for normal mitochondrial morphology by regulating the equilibrium between mitochondrial fusion and mitochondrial fission. Mutations in human OPA1 cause optic atrophy. This domain includes the helix bundle (HB) domains HB1 (C-terminal) and HB2 (equivalent to extreme C-terminal bundle signaling element (BSE) and to the stalk domain of dynamin-1, respectively) and the lipid-interacting stalk (LIS, equivalent to the PH domain of dynamin-1).
Pfam PF18749: Secreted Novel AID/APOBEC-like Deaminase 3 (family)
A family of AID/APOBEC like deaminases found in vertebrates that were derived from secreted versions of the family.
Pfam PF09029: 5-aminolevulinate synthase presequence (domain)
The N terminal presequence domain found in 5-aminolevulinate synthase exists as an amphipathic helix, with a positively charged surface provided by lysine residues and no stable helix at the N-terminus. The domain is essential for the import process by which ALAS is transported into the mitochondria: translocase of the outer membrane (Tom) and translocase of the inner membrane protein complexes appear responsible for recognition and import through the mitochondrial membrane. The protein Tom20 is anchored to the mitochondrial outer membrane, and its interaction with presequences is thought to be the recognition step which allows subsequent import.
Pfam PF15205: Placenta-specific protein 9 (family)
This family of proteins was identified as being enriched in placenta.
Pfam PF19321: BTB/POZ domain-containing protein KCTD18 C-terminus (family)
This entry represents the C-terminal region of BTB/POZ domain-containing protein KCTD18. This domain is highly variable among the BTB domain-containing KCTD proteins and it has been proposed that it could be used to bind and recruit diverse cellular proteins destined for different processes such as ubiquitination and degradation or regulation of G-protein coupled receptors.
Pfam PF08504: Runx inhibition domain (family)
This domain lies to the C-terminus of Runx-related transcription factors and homologous proteins (AML, CBF-alpha, PEBP2).  Its function might be to interact with functional cofactors.
Pfam PF22040: Secreted glycosylated protein U9-ORF (family)
This family represents the secreted glycosylated protein U9-ORF from Mus musculus and similar sequences from vertebrates. U9-ORF is a 118-residues protein encoded by U90926, a long non-coding RNAs (lncRNAs) that has been associated with the proliferation of herpes simplex virus 1 (HSV-1) in retinal photoreceptor cells. U9-ORF is secreted by activated myeloid cells. Its expression has been associated with protection during endotoxic shock and with the proliferation of herpes simplex virus 1 (HSV-1) in murine retinal photoreceptor cells.
Pfam PF15684: Active regulator of SIRT1, or 40S ribosomal protein S19-binding 1 (family)
AROS is a family of chordate proteins active in the nucleolus. It has a stretch of polylysines at the N-terminus and in the middle regions and it localises to the nucleus and especially the nucleolus in high concentrations. It binds to the 40S ribosomal protein RPS19, which is implicated in erythropoiesis. AROS is an active regulator of Sirtuin (SIRT1), an NAD+-dependent deacetylase protein that plays a role in cell survival and hormonal signalling, and AROS regulates the activity of SIRT1 by enhancing SIRT1-mediated de-acetylation of p53 and thus regulates growth of the cell.
Pfam PF00161: Ribosome inactivating protein (domain)
A number of bacterial and plant toxins act by inhibiting protein synthesis in eukaryotic cells. The toxins of the shiga and ricin family inactivate 60S ribosomal subunits by an N-glycosidic cleavage which releases a specific adenine base from the sugar-phosphate backbone of 28S rRNA . Members of the family include shiga and shiga-like toxins, and type I (e.g. trichosanthin and luffin) and type II (e.g. ricin, agglutinin and abrin) ribosome inactivating proteins (RIPs). All these toxins are structurally related. RIPs have been of considerable interest because of their potential use, conjugated with monoclonal antibodies, as immunotoxins to treat cancers. Further, trichosanthin has been shown to have potent activity against HIV-1-infected T cells and macrophages . Elucidation of the structure-function relationships of RIPs has therefore become a major research effort. It is now known that RIPs are structurally related. A conserved glutamic residue has been implicated in the catalytic mechanism ; this lies near a conserved arginine, which also plays a role in catalysis .
Wikipedia: A ribosome-inactivating protein (RIP) is a protein synthesis inhibitor that acts at the eukaryotic ribosome. This protein family describes a large family of such proteins that work by acting as rRNA N-glycosylase. They inactivate 60S ribosomal subunits by an N-glycosidic cleavage, which releases a specific adenine base from the sugar-phosphate backbone of 28S rRNA. RIPs exist in bacteria and plants.
Pfam PF13473: Cupredoxin-like domain (domain)
The cupredoxin-like fold consists of a beta-sandwich with 7 strands in 2 beta-sheets, which is arranged in a Greek-key beta-barrel.
Pfam PF08297: U3 snoRNA associated (family)
This family of proteins is associated with U3 snoRNA. U3 snoRNA is required for nucleolar processing of pre-18S ribosomal RNA.
Pfam PF07141: Putative bacteriophage terminase small subunit (family)
This family consists of several putative Lactococcus bacteriophage terminase small subunit proteins. The exact function of this family is unknown.