SII-SWORD/CoKE huggingface dataset:
Pfam PF07090: Putative glutamine amidotransferase (domain)
This family consists of several hypothetical bacterial proteins of around 250 residues in length. The function of this family is unknown. The structure of this cytoplasmic domain was solved by the Midwest Center for Structural Genomics (MCSG). The structure has been classified as part of the Class-I Glutamine amidotransferase superfamily owing to similarity with other known structures. The monomer combines with itself to form a hexamer, and this hexamer exposes a potential catalytic surface rich in Glu, Asp, Tyr, Ser.Trp and His residues.
Pfam PF00172: Fungal Zn(2)-Cys(6) binuclear cluster domain (domain)
The N-terminal region of a number of fungal transcriptional regulatory proteins contains a Cys-rich motif that is involved in zinc-dependent binding of DNA. The region forms a binuclear Zn cluster, in which two Zn atoms are bound by six Cys residues . A wide range of proteins are known to contain this domain. These include the proteins involved in arginine, proline, pyrimidine, quinate, maltose and galactose metabolism, amide and GABA catabolism, leucine biosynthesis, amongst others. The structure of Zn2Cys6 DNA-binding domain from different proteins has been determined in free and DNA bound state (1PYI) revealing details of the molecular basis of DNA recognition .
Wikipedia: A zinc finger is a small protein structural motif that is characterized by the coordination of one or more zinc ions (Zn2+) which stabilizes the fold. It was originally coined to describe the finger-like appearance of a hypothesized structure from the African clawed frog (Xenopus laevis) transcription factor IIIA. However, it has been found to encompass a wide variety of differing protein structures in eukaryotic cells. Xenopus laevis TFIIIA was originally demonstrated to contain zinc and require the metal for function in 1983, the first such reported zinc requirement for a gene regulatory protein followed soon thereafter by the Krüppel factor in Drosophila. It often appears as a metal-binding domain in multi-domain proteins.
Pfam PF23474: Anti-CBASS protein Acb1 (family)
This family represents Anti-CBASS protein Acb1 and related homologs. These proteins are components of the cyclic oligonucleotide-based antiphage signalling system (CBASS) which is one of the antiphage defence systems in diverse bacteria that use cyclic nucleotide signals to induce cell death and prevent viral propagation. Acb1 are phosphodiesterases that enable metal-independent hydrolysis of the cyclic di- and trinucleotide CBASS signals. Acb1 enzymes adopt a fold typical for phosphodiesterases consisting of a duplicated beta-alpha-beta-alpha-beta structural motif that coils into a beta-barrel.
Pfam PF18862: ApeA N-terminal domain 1 (domain)
Mostly beta strands. Fused to HEPN (Apea). Several conserved aromatic residues, abundant but poorly conserved.
Pfam PF09396: Thrombin light chain (domain)
Thrombin is an enzyme that cleaves bonds after Arg and Lys, converts fibrinogen to fibrin and activates factors V, VII, VIII. Prothrombin is activated on the surface of a phospholipid membrane where factor Xa removes the activation peptide and cleaves the remaining part into light and heavy chains. This domain corresponds to the light chain of thrombin.
Pfam PF06230: LpxI C-terminal domain (domain)
This entry represents the catalytic C-terminal domain of the LpxI enzyme that is involved in biosynthesis of lipid A. Specifically it carried out the hydrolysis of UDP-2,3-diacyl- glucosamine. This step is either carried out by LpxI or LpxH. This domain comprises a five-stranded mixed beta-sheet bracketed by one alpha-helix on one side and three on the other. This domain is structurally related to a superfamily that includes cytosine deaminase.
Pfam PF10306: Hypothetical protein FLILHELTA (family)
This is a family of conserved proteins found in fungi. It contains a characteristic FL(I)LHE(L)TA sequence motif, where the bracketed residues are I, L or V. The function is not known.
Pfam PF09208: Restriction endonuclease MspI (domain)
Members of this family of prokaryotic restriction endonucleases recognise the palindromic tetranucleotide sequence 5'-CCGG and cleave between the first and second nucleotides, leaving 2 base 5' overhangs. They fold into an alpha/beta architecture, with a five-stranded mixed beta-sheet sandwiched on both sides by alpha-helices.
Pfam PF12727: PBP superfamily domain (family)
This family belongs to the periplasmic binding domain superfamily. It is often associated with a helix-turn-helix domain.
Pfam PF24831: Domain of unknown function (DUF7715) (domain)
This entry represents a family of uncharacterised actinobacterial proteins that are related to [pfam:PF20115].
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 PF12814: Meiotic cell cortex C-terminal pleckstrin homology (domain)
The PH domain of these largely fungal proteins is necessary for the cortical localisation of the protein during meiosis, since the overall function of the protein is to anchor dynein at the cell cortex during the horsetail phase. During prophase I of fission yeast, horsetail nuclear movement occurs, and this starts when all the telomeres become bundled at the spindle pole body - SPB. Subsequent to this, the nucleus undergoes a dynamic oscillation, resulting in elongated nuclear morphology. Horsetail nuclear movement is thought to be predominantly due to the pulling of astral microtubules that link the SPB to cortical microtubule-attachment sites at the opposite end of the cell; the pulling force is believed to be provided by cytoplasmic dynein and dynactin.
Pfam PF23261: UNK-like, CCCH zinc finger (domain)
This entry represents a CCCH zinc finger found in human RING finger protein unkempt homolog (UNK) and similar sequences mainly from animals. UNK is a sequence-specific RNA-binding protein that plays an important role in the establishment and maintenance of the early morphology of cortical neurons during embryonic development.
Pfam PF05642: Sporozoite P67 surface antigen (family)
This family consists of several Theileria P67 surface antigens. A stage specific surface antigen of Theileria parva, p67, is the basis for the development of an anti-sporozoite vaccine for the control of East Coast fever (ECF) in cattle. The antigen has been shown to contain five distinct linear peptide sequences recognised by sporozoite-neutralising murine monoclonal antibodies.
Pfam PF11426: Tn7 transposition regulator TnsC (family)
TnsC is a molecular switch that regulates transposition and interacts with TnsA which is a component of the transposase. The two proteins interact via the residues 504-555 on TnsC. The TnsA/TnsC interaction is very important in Tn7 transposition.
Pfam PF22153: Elongation factor SelB, first winged-helix domain (domain)
This domain is found in Elongation factor SelB from Aquifex aeolicus and similar bacterial proteins. SelB is a selenocysteine(Sec)-specific elongation factor that brings the selenocysteinyl-tRNA(Sec) to the ribosome. It consists of three EF-Tu-like domains (D1-3, where [pfam:PF00009] is the first one), followed by four winged-helix domains (WHD1-4). This entry represents the first winged-helix domain (WHD1).
Pfam PF03360: Glycosyltransferase family 43 (family)
The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates (2.4.1.-) and related proteins into distinct sequence based families has been described . This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'.
Glycosyltransferase family 43 GT43 comprises enzymes with only one known activity: beta-glucuronyltransferase(GlcAT-I; 2.4.1.135) .

GlcAT-I is a key enzyme involved in the initial steps of proteoglycan synthesis . GlcAT-I catalyzes the transfer of a glucuronic acid moiety from the uridine diphosphate-glucuronic acid (UDP-GlcUA) to the common linkage region of trisaccharide Gal-beta-(1-3)-Gal-beta-(1-4)-Xyl of proteoglycans. The enzyme has two subdomains that bind the donor and acceptor substrate separately . The active site is located at the cleft between both subdomains in which the trisaccharide molecule is oriented perpendicular to the UDP .
Pfam PF07769: psiF repeat (repeat)
This region is approximately 35 residues long. It is found repeated in a number of putative phosphate starvation- inducible proteins expressed by various bacterial species. psiF ([swissprot:Q7AH28]) is known to be an example of such phosphate starvation-inducible proteins.
Pfam PF04387: Protein tyrosine phosphatase-like protein, PTPLA (family)
This family includes the mammalian protein tyrosine phosphatase-like protein, PTPLA. A significant variation of PTPLA from other protein tyrosine phosphatases is the presence of proline instead of catalytic arginine at the active site. It is thought that PTPLA proteins have a role in the development, differentiation, and maintenance of a number of tissue types.
Wikipedia: Protein tyrosine phosphatases (EC	3.1.3.48, systematic name protein-tyrosine-phosphate phosphohydrolase) are a group of enzymes that remove phosphate groups from phosphorylated tyrosine residues on proteins:[a protein]-tyrosine phosphate + H2O = [a protein]-tyrosine + phosphate
Pfam PF00458: WHEP-TRS domain (domain)
A conserved domain of 46 amino acids, called WHEP-TRS has been shown  to exist in a number of higher eukaryote aminoacyl-transfer RNA synthetases. This domain is present one to six times in the several enzymes. There are three copies in mammalian multifunctional aminoacyl-tRNA synthetase in a region that separates the N-terminal glutamyl-tRNA synthetase domain from the C-terminal prolyl-tRNA synthetase domain, and six copies in the intercatalytic region of the Drosophila enzyme. The domain is found at the N-terminal extremity of the mammalian tryptophanyl-tRNA synthetase and histidyl-tRNA synthetase, and the mammalian, insect, nematode and plant glycyl-tRNA synthetases . The structure of a human WHEP-TRS domain has been solved and consists of two helices arranged in a helix-turn-helix . The WHEP-TRS domain may play a role in the association of tRNA-synthetases into multienzyme complexes .
Wikipedia: In molecular biology, the protein domain WHEP-TRS refers to helix-turn-helix domains. They are found in variable numbers in glutamyl-prolyl tRNA synthetase (EPRS). This protein domain has an important function in protein–protein interactions between synthetases. WHEP domains exhibit high-affinity interactions with tRNA, indicating a putative evolutionary relationship to facilitate tRNA binding to fused synthetases, thereby enhancing catalytic efficiency.
Pfam PF24070: T4 MRH-like protein family (domain)
This family includes the mrh gene [swissprot:P16007] and the uncharacterised gene y01F from bacteriophage T4. Mrh plays a role in transcriptional regulation of late T4 genes. It modulates the phosphorylation status of host heat shock sigma factor rpoH which is an initiation factor that promotes the attachment of host RNA polymerase to specific initiation sites. Structure prediction suggests that this protein may oligomerise with the C-terminus contacting the next subunit in a cyclic homo-oligomer. Structure prediction weakly suggests Mrh forms a hexamer.
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 PF17453: Sigma-M inhibitor (family)
This family includes members such as Sigma M inhibitor proteins YhdK. In Bacillus subtilis, sigM (yhdM) gene, is required for growth and survival after salt stress. Expression of sigM is positively autoregulated and is controlled by growth phase and medium composition. SigM-dependent transcription is regulated by the products of both the yhdL and the yhdK genes, which are co-transcribed with the sigM gene. The small hydrophobic protein YhdK, appears to interact with the trans-membrane domain of YhdL, suggesting some specific role for YhdK in the anti-sigma function of YhdL.
Pfam PF06840: Programmed cell death protein 10, C-terminal (domain)
Programmed cell death 10 protein (PDCD10/CCM3) is part of the CCM complex and is required for neuronal migration. Outside of this complex, it is crucial in vascularization and in angiogenesis as it functions in vessel permeability and stability. PDCD10/CCM3 contains an N-terminal dimerisation domain and a C-terminal focal adhesion targeting-homology (FAT-H) domain (represented in this entry).
Pfam PF19193: Tectonin domain (repeat)
This entry represents proteins homologous to tectonin. This protein adopts a 6 bladed beta propeller structure.
Pfam PF09170: CST, complex subunit STN1, C terminal (domain)
STN1 is a component of the CST complex, a complex that binds to single-stranded DNA and is required for protecting telomeres from DNA degradation. The CST complex binds single-stranded DNA with high affinity in a sequence-independent manner, while isolated subunits bind DNA with low affinity on their own. In addition to telomere protection, the CST complex probably has a more general role in DNA metabolism at non-telomeric sites. This entry represents the C-terminal region of Stn1 which has two winged helix-turn-helix (wHTH) motifs, wHTH1 and wHTH2. wHTH1 is structurally similar to that in RPA32 with a large insertion between helices alpha2 and alpha3, unique to Stn1, that may allow interaction with a different set of proteins that function at telomeres such as Ctc1. wHTH2 is most similar to the DNA-binding wHTH motifs of the pur operon repressor and RepE replication initiator, but it does not bind double-stranded DNA.
Pfam PF07968: Leukocidin/Hemolysin toxin family (domain)
This entry represents a structural domain consisting of a Î²-sandwich fold with an immunoglobulin-like Greek-key topology, and a Î²-ribbon arm that forms an oligomeric transmembrane barrel. Haemolysins attack blood cell membranes and cause cell rupture by forming water-filled homoheptameric transmembrane pores. Leukocidin consists of two polypeptides, F and S, and form pores in polymorphonuclear leukocytes .
Wikipedia: Hemolysins or haemolysins are lipids and proteins that cause lysis of red blood cells by disrupting the cell membrane. Although the lytic activity of some microbe-derived hemolysins on red blood cells may be of great importance for nutrient acquisition, many hemolysins produced by pathogens do not cause significant destruction of red blood cells during infection. However, hemolysins are often capable of lysing red blood cells in vitro.
Pfam PF05356: Inovirus Coat protein B (family)
The major coat protein in the capsid of filamentous bacteriophage forms a helical assembly of about 7000 identical protomers, with each protomer comprised of 46 amino acid, after the cleavage of the signal peptide.  Each protomer forms a slightly curved helix that combine to form a tubular structure that encapsulates the viral DNA.
Pfam PF15180: Neuropeptides B and W (family)
The function of this family, NPBW, which includes Neuropeptides B and W, is thought to be involved in activating G-protein coupled receptors, GPR7 and GPR8. It is thought to play a regulatory role in the organisation of neuroendocrine signals accessing the anterior pituitary gland. It is predicted that this effect will stimulate the increase in water-drinking and food-intake. This suggests it plays a role in the hypothalamic response to stress. This family of proteins is found in eukaryotes.
Pfam PF10508: Proteasome non-ATPase 26S subunit (repeat)
The 26S proteasome, a eukaryotic ATP-dependent, dumb-bell shaped, protease complex with a molecular mass of approx 20kDa consists of a central 20S proteasome,functioning as a catalytic machine, and two large V-shaped terminal modules, having possible regulatory roles,composed of multiple subunits of 25- 110 kDa attached to the central portion in opposite orientations. It is responsible for degradation of abnormal intracellular proteins, including oxidatively damaged proteins, and may play a role as a component of a cellular anti-oxidative system. Expression of catalytic core subunits including PSMB5 and peptidase activities of the proteasome were elevated following incubation with 3-methylcholanthrene. The 20S proteasome comprises a cylindrical stack of four rings, two outer rings formed by seven alpha-subunits (alpha1-alpha7) and two inner rings of seven beta-subunits (beta1-beta7). Two outer rings of alpha subunits maintain structure, while the central beta rings contain the proteolytic active core subunits beta1 (PSMB6), beta2 (PSMB7), and beta5 (PSMB5). Expression of PSMB5 can be altered by chemical reactants, such as 3-methylcholanthrene.
Pfam PF25132: TYW2 N-terminal domain (domain)
This entry represents the N-terminal domain of tRNA wybutosine-synthesizing protein 2 homolog (TWY2), a SAM-dependent transferase that acts as a component of the wybutosine biosynthesis pathway. It may consist of three beta-sheets and two alpha-helices.
Pfam PF08609: Nucleotide exchange factor Fes1 (repeat)
Fes1 is a cytosolic homologue of Sls1, an ER protein which has nucleotide exchange factor activity.  Fes1 in yeast has been shown to bind to the molecular chaperone Hsp70 and has adenyl-nucleotide exchange factor activity.
Pfam PF02834: LigT like Phosphoesterase (family)
Members of this family are bacterial and archaeal RNA ligases that are able to ligate tRNA half molecules containing 2',3'-cyclic phosphate and 5' hydroxyl termini to products containing the 2',5' phosphodiester linkage. Each member of this family contains an internal duplication, each of which contains an HXTX motif that defines the family. The structure of a related protein is known. They belong to the 2H phosphoesterase superfamily. They share a common active site, characterised by two conserved histidines, with vertebrate myelin-associated 2',3' phosphodiesterases, plant Arabidopsis thaliana CPDases and several several bacteria and virus proteins.
Pfam PF04894: Archaeal Nre, N-terminal (family)
This conserved region is found in the N-terminal region of archaeal Nre proteins. While most archaeal organisms  encode only a single Nre protein, some encode two, NreA  and NreB.
Pfam PF16661: Metallo-beta-lactamase superfamily domain (domain)
This family is part of the metallo-beta-lactamase superfamily.
Wikipedia: The metallo-β-lactamase (MBL) superfamily constitutes a group of proteins found in all domains of life that share a characteristic αββα fold with the ability to bind transition metal ions. Such metal binding sites may have divalent transition metal ions like Zn(II), Fe(II)/Fe(III) and Mn(II), and are located at the bottom of a wide cleft able to accommodate diverse substrates. The name was adopted after the first members of the superfamily to be studied experimentally: a group of zinc-dependent hydrolytic enzymes conferring bacterial resistance to β-lactam antibiotics. These zinc-β-lactamases (ZBLs) inactivate β-lactam antibiotics through hydrolysis of the β-lactam ring. Early studies on MBLs were conducted on the enzyme βLII isolated from strain 569/H/9 of Bacillus cereus. It was named βLII because it was the second β-lactamase shown to be produced by the bacterium; the first one, βLI, was a non-metallic β-lactamase, i.e., insensitive to inhibition with EDTA.
Pfam PF08261: Carcinustatin peptide (family)
A total of 20 peptides of the superfamily allostatin were isolated from the shore crab Carcinus maenas. They are named carcinustatin 1 to 20 and their length ranges from 5 to 27 amino acids. This family includes carcinustatin 8,9,15 and 16.
Pfam PF24919: Meiotically up-regulated gene 62 protein-like domain (domain)
This domain is found in Meiotically up-regulated gene 62 protein from Schizosaccharomyces pombe (Mug62) and similar proteins predominantly found in fungi. Mug62 plays a role in meiosis. This domain is often found associated to [pfam:PF00501] and [pfam:PF23024].
Pfam PF24273: HVO_1752, C-terminal TRASH domain (domain)
This TRASH domain is found at the C-terminal end of the predicted Lrp/AsnC family transcription regulator from Haloferax volcanii and similar archaeal proteins.
Pfam PF03893: Lipase 3 N-terminal region (domain)
N terminal region to [pfam:PF01764], found on a subset of Lipase 3 containing proteins.
Pfam PF11704: Vesicle coat protein involved in Golgi to plasma membrane transport (family)
In yeast cells this family functions in the regulated delivery of Gap1p (a general amino acid permease) to the cell surface, perhaps as a component of a post-Golgi secretory-vesicle coat complex. Birt-Hogg-Dube (BHD)4 syndrome is an autosomal dominant disorder characterised by hamartomas of skin follicles, lung cysts, spontaneous pneumothorax, and renal cell carcinoma. Folliculin is the protein from the BHD4 gene and is found to have no significant homology to any other human proteins. It is expressed in most tissues. These same symptoms also occur in TSC or tuberous sclerosis complex, suggesting that the same pathway is involved, and it is likely that the target is the down-stream Tor2 - an essential gene. Folliculin appears to bind Tor2, and down-regulation of Tor2 activity leads to up-regulation of nitrogen responsive genes including membrane transporters and amino acid permeases.
Pfam PF17212: Tail tubular protein (family)
This family includes the tail tubular gp11 protein from bacteriophage T7.
Pfam PF08915: Archaea-specific editing domain of threonyl-tRNA synthetase (domain)
Archaea-specific editing domain of threonyl-tRNA synthetase, with marked structural similarity to D-amino acids deacylases found in eubacteria and eukaryotes. This domain can bind D-amino acids, and ensures high fidelity during translation. It is especially responsible for removing incorrectly attached serine from tRNA-Thr. The domain forms a fold that can be be defined as two layers of beta-sheets (a three-stranded sheet and a five-stranded sheet), with two alpha-helices located adjacent to the five-stranded sheet.
Pfam PF12528: Type II secretion prepilin peptidase dependent protein C (domain)
This entry represents a domain found al proteins mainly found in Enterobacterales, including Prepilin peptidase-dependent protein C from Escherichia coli (PpdC). PpdC is predicted to be a bitopic inner membrane protein. This domain is found in association with IPR012902. There are two completely conserved C residues that may be functionally important.
Pfam PF19785: Family of unknown function (UPF0738) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in Firmicute bacteria. Proteins in this family are approximately 120 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.