SII-SWORD/CoKE huggingface dataset:
Pfam PF15656: Toxin with a H, D/N and C signature (family)
A predicted alpha/beta fold peptidase domain with a strongly conserved triad of a histidine, aspartate/asparagine and cysteine residues that are predicted to comprise the active site of the predicted peptidase. Proteins bearing this predicted toxin domain are particularly common in both intracellular and extracellular pathogens.
Pfam PF06303: MatP N-terminal domain (domain)
This family, many of whose members are YcbG, organises the macrodomain Ter of the chromosome of bacteria such as E coli. In these bacteria, insulated macrodomains influence the segregation of sister chromatids and the mobility of chromosomal DNA. Organisation of the Terminus region (Ter) into a macrodomain relies on the presence of a 13 bp motif called matS repeated 23 times in the 800-kb-long domain. MatS sites are the main targets in the E. coli chromosome of YcbG or MatP (macrodomain Ter protein). MatP accumulates in the cell as a discrete focus that co-localises with the Ter macrodomain. The effects of MatP inactivation reveal its role as the main organiser of the Ter macrodomain: in the absence of MatP, DNA is less compacted, the mobility of markers is increased, and segregation of the Ter macrodomain occurs early in the cell cycle. A specific organisational system is required in the Terminus region for bacterial chromosome management during the cell cycle. This entry represents the N-terminal domain of MatP.
Pfam PF05208: ALG3 protein (family)
The formation of N-glycosidic linkages of glycoproteins involves the ordered assembly of the common Glc3Man9GlcNAc2 core-oligosaccharide on the lipid carrier dolichyl pyrophosphate. Whereas early mannosylation steps occur on the cytoplasmic side of the endoplasmic reticulum with GDP-Man as donor, the final reactions from Man5GlcNAc2-PP-Dol to Man9GlcNAc2-PP-Dol on the lumenal side use Dol-P-Man. ALG3 gene encodes the Dol-P-Man:Man5GlcNAc2-PP-Dol mannosyltransferase.
Pfam PF14984: CD24 protein (family)
Signal transducer CD24 (also known as cluster of differentiation 24) is a cell adhesion molecule that has been implicated in tumor invasion and metastasis of various solid tumours .
Wikipedia: Signal transducer CD24 also known as cluster of differentiation 24 or heat stable antigen CD24 (HSA) is a protein that in humans is encoded by the CD24 gene. CD24 is a cell adhesion molecule.
Pfam PF08580: Yeast cortical protein KAR9 (family)
The KAR9 protein in Saccharomyces cerevisiae is a cytoskeletal protein required for karyogamy, correct positioning of the mitotic spindle and for orientation of cytoplasmic microtubules. KAR9 localises at the shmoo tip in mating cells and at the tip of the growing bud in anaphase.
Pfam PF17279: Family of unknown function (DUF5344) (family)
This is a Bacterial family of unknown function. Family members are predicted to belong to Type VII secretion (T7S) system. There is a conserved YxxxD/E sequence. It is a general secretion signal that is present in all known mycobacterial T7S substrates or substrate complexes.
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 PF24040: Domain of unknown function (DUF7349) (domain)
This family of uncharacterized proteins is found in various phages that infect bacterial hosts such as Bacillus, Staphylococcus, Enterococcus, Listeria, Lactobacillus, and Brochothrix species. The proteins in the family are typically 75 to 100 amino acids in length. The protein contains a small N-terminal domain represented by this entry followed by a C-terminal disordered region.
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 PF15874: Putative Interleukin 2 receptor, gamma chain (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 137 and 197 amino acids in length.
Pfam PF07321: Type III secretion protein YscO (coiled_coil)
This family contains the bacterial type III secretion protein YscO, which is approximately 150 residues long. YscO has been shown to be required for high-level expression and secretion of the anti-host proteins V antigen and Yops in Yersinia pestis.
Pfam PF18566: Linalool dehydratase/isomerase (repeat)
This (alpha,alpha)6 barrel fold domain is found in linalool dehydratase/isomerase (Ldi) [ec:4.2.1.127] . An enzyme found in the betaproteobacterium Castellaniella defragrans 65Phen that mineralizes monoterpenes coupled to anaerobic denitrification. The periplasmic enzyme reversibly catalyzes the isomerisation from the primary alkenol geraniol into the tertiary alkenol (S)-linalool and its dehydration to beta-myrcene. Each monomer is built up of a classical (alpha,alpha)6 barrel fold composed of six inner helices. Structural data of Ldi revealed the terpene binding site between two monomers inside a hydrophobic channel, and three catalytic clusters involved in catalysis.
Pfam PF01230: HIT domain (domain)
The histidine triad motif (HIT) consists of the conserved sequence HXHXHXX (where X is a hydrophobic amino acid) at the enzymatic catalytic centre, in which the second histidine is strictly conserved and participates in catalysis with the third histidine . Proteins containing HIT domains form a superfamily of nucleotide hydrolases and transferases that act on the alpha-phosphate of ribonucleotides . They are highly conserved from archaea to humans and are involved in galactose metabolism, DNA repair, and tumor suppression . HIT-containing proteins can be divided in five families based on catalytic specificities, sequence compositions, and structural similarities of its members:


 * Hint family of protein kinase-interacting proteins, the most ancient class in this superfamily. These include adenosine 5'-monophosphoramide hydrolases (e.g. HIT-nucleotide-binding protein, or HINT) . They also have a conserved zinc-binding motif C-X-X-C (where C is a cysteine residue and X is a hydrophobic residue), and a zinc ion is coordinated by these cysteine residues, together with the first histidine residue .
 * Fragile HIT protein, or FINT, whose name is due to its high rate of mutation at its locus on chromosome 3 in many cancers has been characterised as a tumor suppressor and plays a role in the hydrolysis of dinucleotide polyphosphates . HINT and FINT HIT domains have a topology similar to that found in the N-terminal of protein kinases .
 * GalT family. These include specific nucleoside monophosphate transferases (e.g. galactose-1-phosphate uridylyltransferase, diadenosine tetraphosphate phosphorylase, and adenylyl sulphate:phosphate adenylytransferase). These HIT domains are a duplication consisting of 2 HIT-like motifs. This family binds zinc and iron .
 * Aprataxin, which hydrolyses both dinucleotide polyphosphates and phophoramidates, and is involved in DNA repair systems .
 * mRNA decapping enzyme family. These include enzymes such as DcpS and Dcp2. The HIT-domain is usually C-terminal in these proteins .
Pfam PF02889: Sec63 Brl domain (family)
This domain (also known as the Brl domain) is required for assembly of functional endoplasmic reticulum translocons.
Pfam PF22272: Late embryogenesis abundant protein (LEA_3b subfamily) (family)
This entry represents a family of late embryogenesis abundant proteins that are related to the LEA_3 family of proteins [pfam:PF03242] which we now term the LEA_3a subfamily.
Pfam PF00634: BRCA2 repeat (family)
The alignment covers only the most conserved region of the repeat.
Wikipedia: BRCA2 and BRCA2 are human genes and their protein products, respectively. The official symbol and the official name are maintained by the HUGO Gene Nomenclature Committee. One alternative symbol, FANCD1, recognizes its association with the FANC protein complex. Orthologs, styled Brca2 and Brca2, are common in other vertebrate species. BRCA2 is a human tumor suppressor gene, found in all humans; its protein, also called by the synonym breast cancer type 2 susceptibility protein, is responsible for repairing DNA.
Pfam PF22677: Bleomycin resistance protein-like N-terminal (domain)
This entry represents the N-terminal glyoxalase-like domain found in a group of bacterial proteins, such as bleomycin resistance protein (Ble) from Klebsiella pneumoniae, lactoglutathion lyase from Haemophilus influenzae, among others.
Pfam PF24210: RIIA.1-like protein (family)
This entry represents a family of small uncharacterised proteins found in phage, including T4 RIIA.1 protein. Structure prediction suggests the small proteins adopt a three helical bundle 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 PF15992: Domain of unknown function (DUF4769) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes. Proteins in this family are typically between 291 and 501 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 PF02042: RWP-RK domain (family)
This domain is named RWP-RK after a conserved motif at the C terminus of the presumed domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development.
Pfam PF07372: Protein of unknown function (DUF1491) (family)
This family consists of several bacterial proteins of around 115 residues in length. Members of this family seem to be found exclusively in the Class Alphaproteobacteria. The function of this family is unknown.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF11861: Ribosomal RNA methyltransferase Spb1, DUF3381 (domain)
This domain is functionally uncharacterised and it is found in the central region of fungal SPB1 and mammalian homologue FTSJ3. This domain is found associated with [pfam:PF07780], [pfam:PF01728]. SPB1 is an adoMet-dependent rRNA methyltransferase required for proper assembly of pre-ribosomal particles during the biogenesis of the 60S ribosomal subunit. FTSJ3, SPB1 homologue in humans, is associated with NIP7 (involved in the biogenesis of 40S subunit) and functions in pre-rRNA processing.
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 PF14165: YtzH-like protein (family)
The YtzH-like protein family includes the B. subtilis YtzH protein [swissprot:O32066], which is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length. There is a conserved DIL sequence motif.
Pfam PF24255: Family of unknown function (DUF7456) (family)
This entry represents a family of uncharacterised proteins found in Mycobacterial phage. The family includes gene 48 from phage Bxb1.
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 PF05569: BlaR1 peptidase M56 (domain)
Production of beta-Lactamase and penicillin-binding protein 2a (which mediate staphylococcal resistance to beta-lactam antibiotics) is regulated by a signal-transducing integral membrane protein       and a transcriptional repressor.  The signal transducer is a fusion protein with penicillin-binding and zinc metalloprotease domains.  The signal for protein expression is transmitted by site-specific proteolytic cleavage of both the transducer, which auto-activates, and the repressor, which is inactivated, unblocking gene transcription. Homologues to this peptidase domain, which corresponds to Merops family M56, are also found in a number of other bacterial genome sequences.
Pfam PF00738: Polyhedrin (family)
These proteins are found in occlusion bodies in various viruses. The polyhedrin protein protects the virus.
Wikipedia: For the three dimensional shape, see Polyhedron
Pfam PF19136: Family of unknown function (DUF5819) (family)
This is a family of uncharacterised 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 PF04052: TolB amino-terminal domain (domain)
TolB is an essential periplasmic component of the tol-dependent translocation system. This function of this amino terminal domain is uncertain.
Pfam PF09733: VEFS-Box of polycomb protein (family)
The VEFS-Box (VRN2-EMF2-FIS2-Su(z)12) box is the C-terminal region of these proteins, characterised by an acidic cluster and a tryptophan/methionine-rich sequence, the acidic-W/M domain. Some of these sequences are associated with a zinc-finger domain about 100 residues towards the N-terminus. This protein is one of the polycomb cluster of proteins which control HOX gene transcription as it functions in heterochromatin-mediated repression.
Pfam PF02570: Precorrin-8X methylmutase (family)
This is a family Precorrin-8X methylmutases also known as Precorrin  isomerase, CbiC/CobH,  [ec:5.4.1.2].  This enzyme catalyses the reaction: Precorrin-8X  hydrogenobyrinate. This enzyme is part of the Cobalamin (vitamin B12) biosynthetic pathway and catalyses a methyl rearrangement.
Pfam PF19203: Family of unknown function (DUF5875) (family)
This is a family of uncharacterised proteins of unknown function predominantly found in Iridoviridae.
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 PF12138: Spherulation-specific family 4 (family)
This protein is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 250 and 398 amino acids in length.  There is a conserved NPG sequence motif and there are two completely conserved G residues that may be functionally important. Starvation will often induce spherulation - the production of spores - and this process may involve DNA-methylation. Changes in the methylation of spherulin4 are associated with the formation of spherules, but these changes are probably transient. Methylation of the gene accompanies its transcriptional activation, and spherulin4 mRNA is only detectable in late spherulating cultures and mature spherules. It is a spherulation-specific protein.
Pfam PF03641: Possible lysine decarboxylase (family)
The members of this family share a highly conserved motif PGGXGTXXE that is probably functionally important. This family includes proteins annotated as lysine decarboxylases, although the evidence for this is not clear.
Pfam PF09454: Vps23 core domain (domain)
ESCRT complexes form the main machinery driving protein sorting from endosomes to lysosomes. The core domain of the Vps23 subunit of the heterotrimeric ESCRT-I complex is a helical hairpin sandwiched in a fan-like formation between two other helical hairpins from Vps28 ([pfam:PF03997]) and Vps37. Vps23 gives ESCRT-I complex its stability.
Wikipedia: Tumor susceptibility gene 101, also known as TSG101, is a human gene that encodes for a cellular protein of the same name.
Pfam PF05697: Bacterial trigger factor protein (TF) (family)
In the E. coli cytosol, a fraction of the newly synthesised proteins requires the activity of molecular chaperones for folding to the native state. The major chaperones implicated in this folding process are the ribosome-associated Trigger Factor (TF), and the DnaK and GroEL chaperones with their respective co-chaperones. Trigger Factor is an ATP-independent chaperone and displays chaperone and peptidyl-prolyl-cis-trans-isomerase (PPIase) activities in vitro. It is composed of at least three domains, an N-terminal domain which mediates association with the large ribosomal subunit, a central substrate binding and PPIase domain with homology to FKBP proteins, and a C-terminal domain of unknown function. The positioning of TF at the peptide exit channel, together with its ability to interact with nascent chains as short as 57 residues renders TF a prime candidate for being the first chaperone that binds to the nascent polypeptide chains. This family represents the N-terminal region of the protein.
Pfam PF03858: Crustacean neurohormone H (family)
These proteins are referred to as precursor-related peptides as they are typically co-transcribed and translated with the CHH neurohormone ([pfam:PF01147]).  However, in some species this neuropeptide is synthesised as a separate protein. Furthermore, neurohormone H can undergo proteolysis to give rise to 5 different neuropeptides.
Pfam PF04636: PA26 p53-induced protein (sestrin) (family)
PA26 is a p53-inducible protein. Its function is unknown. It has similarity to [pfam:PF04636] in its N-terminus.
Pfam PF05674: Baculovirus protein of unknown function (DUF816) (family)
This family includes proteins that are about 200 amino acids in length.  The proteins are all from baculoviruses. This family includes ORF107 from Orgyia pseudotsugata multicapsid polyhedrosis virus (OpMNPV) and a variety of other numbered ORF proteins, such as ORF52 [swissprot:Q91F03], ORF140 [swissprot:Q9YMI8]. The function of these proteins is unknown.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF13673: Acetyltransferase (GNAT) domain (domain)
This family contains proteins with N-acetyltransferase functions such as Elp3-related proteins.
Wikipedia: An acetyltransferase is any of a class of transferase enzymes that transfers an acetyl group in a reaction called acetylation. In biological organisms, post-translational modification of a protein via acetylation can profoundly transform its functionality by altering various properties like hydrophobicity, solubility, and surface attributes. These alterations have the potential to influence the protein's conformation and its interactions with substrates, cofactors, and other macromolecules.
Pfam PF11197: Protein of unknown function (DUF2835) (family)
This is a bacterial family of uncharacterised proteins. One member of this family ([swissprot:A4VM42]) is annotated as the A subunit of Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV).
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 PF07740: Ion channel inhibitory toxin (domain)
This is a family of potent toxins that function as ion-channel inhibitors for several different ions. Omega-Grammotoxin SIA is a VSCC antagonist that inhibits neuronal N- and P-type VSCC responses. Huwentoxin-IV, from the Chinese bird spider, is a highly potent neurotoxin that specifically inhibits the neuronal tetrodotoxin-sensitive voltage-gated sodium channel in rat dorsal root ganglion neurons. Hainantoxin-4, from the venom of spider Selenocosmia hainana, adopts an inhibitor cystine knot structural motif like huwentoin-IV, and is a potent antagonist that acts at site 1 on tetrodotoxin-sensitive (TTX-S) sodium channels. Study of the molecular nature of toxin-receptor interactions has helped elucidate the functioning of many ion-channels.
Wikipedia: Spider toxins are a family of proteins produced by spiders which function as neurotoxins. The mechanism of many spider toxins is through blockage of calcium channels.