SII-SWORD/CoKE huggingface dataset:
Pfam PF00480: ROK family (family)
This family, known as ROK (Repressor, ORF, Kinase) includes the xylose operon repressor, xylR, from Bacillus subtilis, Lactobacillus pentosus and Staphylococcus xylosus; N-acetylglucosamine repressor, nagC, from Escherichia coli; glucokinase from Streptomyces coelicolor; fructokinase from from Pediococcus pentosaceus, Streptococcus mutans and Zymomonas mobilis; allokinase and mlc from E. coli; and E. coli hypothetical proteins yajF and yhcI and the corresponding Haemophilus influenzae proteins. The repressor proteins (xylR and nagC) from this family possess an N-terminal region not present in the sugar kinases and which contains an helix-turn-helix DNA-binding motif.
Pfam PF19854: Family of unknown function (DUF6329) (family)
This domain is predominantly found in uncharacterised bacterial proteins and its function is unknown. This domain is approximately 60 amino acids in length and it contains three conserved residues, a cysteine, a leucine and a tryptophan.
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 PF04936: Protein of unknown function (DUF658) (family)
Protein of unknown function found in Lactococcus lactis bacteriophages.
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 PF03113: Respiratory synctial virus non-structural protein NS2 (family)
The molecular structure and function of the NS2 protein is not known. However, mutants lacking the NS2 grow at slower rates when compared to the wild-type. Nevertheless, NS2 is not essential for viral replication.
Pfam PF12034: Uncharacterized protein YfbK, C-terminal (domain)
This domain is functionally uncharacterised. This domain represents the C-terminal of the uncharacterized protein YfbK. This domain is about 180 amino acids in length. This domain is found at the C-terminal of [pfam:PF00092].
Pfam PF06691: Protein of unknown function (DUF1189) (family)
This family consists of several hypothetical bacterial proteins of around 260 residues in length. 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 PF14202: Transposon-encoded protein TnpW (family)
This family of proteins is found in bacteria. Proteins in this family are typically between 54 and 75 amino acids in length. There is a single completely conserved residue G that may be functionally important.
Pfam PF03064: HSV U79 / HCMV P34 (family)
This family represents herpes virus protein U79 and cytomegalovirus early phosphoprotein P34 (UL112).
Pfam PF10070: Probable inorganic carbon transporter subunit DabA (family)
This entry represents the probable inorganic carbon transporter subunit DabA, which is part of an energy-coupled inorganic carbon pump together with DabB subunit in DAB operons (DAB1 and DAB2), found in a wide range of bacteria and archaea. Members of this family were previously known as UPF0753. DAB operon is required for CO2 concentrating mechanisms. The substrate of this subunit may be CO2 rather than carbonate ions based on kinetic calculations and in experimental assays in which E.coli was deleted of its carbonic anhydrase genes and expression of DAB2 operon restores its growth. Structural homology modelling suggests that DabA contains a domain that is distantly homologous to a type II beta-carbonic anhydrase (CA).
Pfam PF03801: HEC/Ndc80p family (family)
Members of this family are components of the mitotic spindle. It has been shown that Ndc80/HEC from yeast is part of a complex called the Ndc80p complex. This complex is thought to bind to the microtubules of the spindle.
Pfam PF13642: protein structure with unknown function (family)
A family based on the three-dimensional structure of YP_926445.1 (PDB:2L6O)
Pfam PF10476: Protein of unknown function C-terminus (DUF2448) (family)
The family DUF2349 is the N-terminal part of this family. This protein is found in eukaryotes but its function is not known.
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 PF00334: Nucleoside diphosphate kinase (domain)
Nucleoside diphosphate kinases (2.7.4.6) (NDK) are enzymes required for the synthesis of nucleoside triphosphates (NTP) other than ATP. They provide NTPs for nucleic acid synthesis, CTP for lipid synthesis, UTP for polysaccharide synthesis and GTP for protein elongation, signal transduction and microtubule polymerisation.

NDK are proteins of 17 Kd that act via a ping-pong mechanism in which a histidine residue is phosphorylated, by transfer of the terminal phosphate group from ATP. In the presence of magnesium, the phosphoenzyme can transfer its phosphate group to any NDP, to produce an NTP.

NDK isozymes have been sequenced from prokaryotic and eukaryotic sources. It has also been shown  that the Drosophila awd (abnormal wing discs) protein, is a microtubule-associated NDK. Mammalian NDK is also known as metastasis inhibition factor nm23. The sequence of NDK has been highly conserved through evolution. There is a single histidine residue conserved in all known NDK isozymes, which is involved in the catalytic mechanism .
The enzyme is a hexamer composed by identical subunits with a novel mononucleotide binding fold. Each subunit contains an Î±/Î² domain with a four stranded, anti-parallel Î²-sheet .
This Î±/Î² domain is also found at the C terminus of retinitis pigmentosa 2 protein (XRP2/RP2) . XRP2, a GTPase-activating protein, is required for maintenance of rod and cone photoreceptor cells in the retina .
Pfam PF19907: Family of unknown function (DUF6380) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000663) is described by MIBiG as an example of the following biosynthetic class, terpene, in particular the hopene biosynthetic gene cluster from Streptomyces coelicolor A3(2).
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 PF07684: NOTCH protein (family)
NOTCH  signalling plays a fundamental role during a great number of developmental processes in multicellular animals. NOD and NODP represent a region present in many NOTCH proteins and NOTCH homologs in multiple species such as NOTCH2 and NOTCH3, LIN12, SC1 and TAN1. The role of the NOD and NODP domains remains to be  elucidated.
Pfam PF16957: Malonate decarboxylase, alpha subunit, transporter (family)
Mal_decarbox_Al is a family of Na+-transporting carboxylic acid decarboxylases.
Pfam PF22727: NACHT C-terminal Helical domain 2 (domain)
This is an helical domain found at the C-terminus of bacterial NACHT conflict systems.
Pfam PF15404: Pleckstrin homology domain (domain)
This Pleckstrin homology domain is found in some fungal species.
Wikipedia: Pleckstrin homology domain or (PHIP) is a protein domain of approximately 120 amino acids that occurs in a wide range of proteins involved in intracellular signaling or as constituents of the cytoskeleton.
Pfam PF13451: Probable treble clef domain (domain)
This is a probable zinc-binding domain with two CxxC sequence motifs, found in various families of bacteria.
Pfam PF05866: Endodeoxyribonuclease RusA (family)
This family consists of several bacterial and phage Holliday junction resolvase (RusA) like proteins. The RusA protein of Escherichia coli is an endonuclease that can resolve Holliday intermediates and correct the defects in genetic recombination and DNA repair associated with inactivation of RuvAB or RuvC.
Pfam PF21073: Glutamate dehydrogenase, helical motif 1 (conserved_site)
Glutamate dehydrogenases (GDHs) are a broadly distributed group of enzymes that catalyse the reversible oxidative deamination of glutamate to ketoglutarate and ammonia. The structure of GDH from Mycobacterium smegmatis revealed that it has a long N- and C-terminal segments flanking the catalytic core, comprising several domains. The flexible N-terminal domain comprises ACT-like and PAS-type domains which could act as metabolic sensors for allosteric regulation. It also has three helical motifs (HM1-3), this entry represents the first one (HM1).
Pfam PF21110: GlxA beta barrel domain (domain)
This entry represents the second domain of the GlxA protein. GlxA contains a beta propeller domain and this beta sandwich domain is inserted within it.
Pfam PF18243: Metal-independent restriction enzyme BfiI DNA binding domain (domain)
This domain is found in the metal-independent restriction enzyme BfiI present in Bacillus firmus. This domain is found in the C-terminal of the protein and is responsible for DNA binding. The domain exhibits a beta-barrel-like structure similar to the effector DNA-binding domain of the Mg2+ dependent restriction enzyme EcoRII and to the B3-like DNA-binding domain of plant transcription factors.
Pfam PF17700: Family of unknown function (DUF5546) (family)
This is a family of unknown function found in primates.
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 PF25034: Nesprin-1, spectrin repeats (repeat)
This entry represents a region of spectrin repeats found in human Nesprin-1 (SYNE1), a multi-isomeric modular protein which forms a linking network between organelles and the actin cytoskeleton to maintain the subcellular spatial organisation. This protein has been associated with several severe disorders.
Pfam PF24899: ATP-dependent RNA helicase DHX29, UBA domain (domain)
This predicted UBA domain is found towards the N terminus of human ATP-dependent RNA helicase DHX29, which is involved in translation initiation. This domain is predicted to show a mainly alpha-helical configuration. Proteins in this family are found in Eukaryota.
Pfam PF04124: Dor1-like family (repeat)
Dor1 is involved in vesicle targeting to the yeast Golgi apparatus and complexes with a number of other trafficking proteins, which include Sec34 and Sec35.
Pfam PF14590: Domain of unknown function (DUF4447) (family)
This family of proteins is found in bacteria. Proteins in this family are approximately 170 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 PF09803: Pet100 (family)
Pet100 is a chaperone required for the assembly of cytochrome c oxidase. The human Pet100 homologue (also known as C19orf79) has been shown to be located in the mitochondrial inner membrane and forms a ~300 kDa subcomplex with mitochondrial complex IV subunits.
Pfam PF16588: C2H2 zinc-finger (domain)
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 PF01570: Flavivirus polyprotein propeptide (family)
The flaviviruses are small enveloped animal viruses containing a single positive strand genomic RNA.  The genome encodes one large ORF a polyprotein which undergos proteolytic processing into mature viral  peptide chains. This family consists of a propeptide region of approximately 90 amino acid length.
Pfam PF16387: Domain of unknown function (domain)
This domain of around 100 residues locates at the C-terminal of some glycerophosphoryl diester phosphodiesterases and uncharacterized proteins in various Bacteroides and Prevotella species. The function  of this domain is not yet clear, however, it is described as a putative glycerophosphoryl diester phosphodiesterase (PDBe:3i10).
Pfam PF19046: GM130 C-terminal binding motif (conserved_site)
This entry represents the C-terminal motif from the GM130 protein that is bound by the GRASP65 PDZ domain [pfam:PF04495].
Pfam PF22411: Mre11 nuclease, second domain (domain)
This entry represents the second calcineurin-like nuclease domain of DNA double-strand break repair protein Mre11 from Pyrococcus furiosus and similar archaeal proteins. Mre11, also known as Mre11 nuclease, is part of the Rad50/Mre11 complex, which is involved in the early steps of DNA double-strand break (DSB) repair. This domain shows a beta-sheet and two alpha-helices.
Pfam PF24958: Domain of unknown function (DUF7765) (domain)
This domain is found in uncharacterised proteins mainly from Enterobacterales. It is predicted to fold into a beta-barrel.
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 PF06214: Signaling lymphocytic activation molecule (SLAM) protein (family)
This family consists of several mammalian signaling lymphocytic activation molecule (SLAM) proteins. Optimal T cell activation and expansion require engagement of the TCR plus co-stimulatory signals delivered through accessory molecules. SLAM, a 70-kDa co-stimulatory molecule belonging to the Ig superfamily, is defined as a human cell surface molecule that mediates CD28-independent proliferation of human T cells and IFN-gamma production by human Th1 and Th2 clones. SLAM has also been recognised as a receptor for measles virus.
Wikipedia: Signaling lymphocytic activation molecule (SLAM) is a family of genes. Homophilic binding between SLAMs is involved in cell-to-cell adhesion during antigen presentation.
Pfam PF15675: CLLAC-motif containing domain (family)
This short domain is found in chordates. It carries a highly conserved CLLAC sequence motif. The function is not known.
Pfam PF10613: Ligated ion channel L-glutamate- and glycine-binding site (domain)
This region, sometimes called the S1 domain, is the luminal domain just upstream of the first, M1, transmembrane region of transmembrane ion-channel proteins, and it binds L-glutamate and glycine. It is found in association with Lig_chan, [pfam:PF00060].
Pfam PF24017: SCAP Beta-propeller (repeat)
This entry represents the beta-propeller domain found at the C-terminal of SCAP proteins, key regulators of lipid homeostasis in cells. It acts as a cholesterol sensor and escort for SREBP, therefore, when cholesterol levels are low, SCAP binds to SREBP and facilitates its transport from the ER to the Golgi, where it undergoes proteolytic cleavage and activates it, leading to its activation and translocation to the nucleus to activate the transcription of genes involved in cholesterol synthesis. This domain is involved in the interaction with SREBP [1.2].
Pfam PF11947: Photosynthesis affected mutant 68 (family)
This entry includes chloroplastic protein PAM68 and the Sll0933 homolog from Cyanobacteria (blue-green algae). PAM68 is involved in early steps in photosystem II (PSII) biogenesis and in maturation and stability of newly synthesized psbA protein.
Pfam PF18440: Putative GlcNAc-1 phosphotransferase regulatory domain (domain)
The Golgi enzyme UDP-GlcNAc-lysosomal enzyme N-acetylglucosamine-1-phosphotransferase (GlcNAc-1-phosphotransferase), an alpha2beta2gamma2 hexamer, mediates the initial step in the addition of the mannose 6-phosphate targeting signal on newly synthesized lysosomal enzymes. GNPTAB encodes the alpha and beta subunits of GlcNAc-1-phosphotransferase, and mutations in this gene cause the lysosomal storage disorders mucolipidosis II and III alpha-beta The alpha-beta subunits contain three identifiable domains separated by so-called spacer regions. This domain is part of the first spacer region, Spacer-1. Studies indicate that GlcNAc-1 lacking spacer-1 exhibits enhanced phosphorylation of several non-lysosomal glycoproteins, while the phosphorylation of lysosomal acid hydrolases is not altered. In view of these effects on the maturation and function of GlcNAc-1, it is suggested to rename 'spacer-1' the 'regulatory-1' domain.
Wikipedia: N-acetylglucosamine-1-phosphate transferase (GlcNAc-1-phosphotransferase) is a transferase enzyme.
Pfam PF06899: WzyE protein, O-antigen assembly polymerase (family)
This family consists of several WzyE proteins which appear to be specific to Enterobacteria. Members of this family are described as putative ECA polymerases this has been found to be incorrect. The function of this family is unknown. The family is a transmembrane family with up to 11 TM regions, and is necessary for the assembly of O-antigen lipopolysaccharide.
Pfam PF15069: FAM163 family (family)
This protein family is alternatively named Neuroblastoma-derived secretory proteins. Highly expressed in neuroblastoma compared to other tissues, suggesting that it may be used as a marker for metastasis in bone marrow.
Pfam PF08198: Thymopoietin protein (domain)
Short protein of 49 amino acid isolated from bovine spleen cells. Thymopoietins (TMPOs) are a group of ubiquitously expressed nuclear proteins. They are suggested to play an important role in nuclear envelope organisation and cell cycle control.
Pfam PF00115: Cytochrome C and Quinol oxidase polypeptide I (family)
Cytochrome c oxidase (E.C:7.1.1.9) is a key enzyme in aerobic metabolism. Proton pumping haem-copper oxidases represent the terminal, energy-transfer enzymes of respiratory chains in prokaryotes and eukaryotes. The CuB-haem a3 (or haem o) binuclear centre, associated with the largest subunit I of cytochrome c and ubiquinol oxidases (E.C:1.10.3.11), is directly involved in the coupling between dioxygen reduction and proton pumping. Some terminal oxidases generate a transmembrane proton gradient across the plasma membrane (prokaryotes) or the mitochondrial inner membrane (eukaryotes). The enzyme complex consists of 3-4 subunits (prokaryotes) up to 13 polypeptides (mammals) of which only the catalytic subunit (equivalent to mammalian subunit I (COXI) is found in all haem-copper respiratory oxidases. The presence of a bimetallic centre (formed by a high-spin haem and copper B) as well as a low-spin haem, both ligated to six conserved histidine residues near the outer side of four transmembrane spans within CO I is common to all family members.
Wikipedia: Cytochrome c oxidase I (COX1) also known as mitochondrially encoded cytochrome c oxidase I (MT-CO1) is a protein that is encoded by the MT-CO1 gene in eukaryotes. The gene is also called COX1, CO1, or COI. Cytochrome c oxidase I is the main subunit of the cytochrome c oxidase complex. In humans, mutations in MT-CO1 have been associated with Leber's hereditary optic neuropathy (LHON), acquired idiopathic sideroblastic anemia, Complex IV deficiency, colorectal cancer, sensorineural deafness, and recurrent myoglobinuria.
Pfam PF11119: Protein of unknown function (DUF2633) (family)
This family is conserved largely in Gammaproteobacteria. Several members are named as YfgG. The function is not known.
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 PF09815: XK-related protein (family)
Members of this family comprise various XK-related proteins, that are involved in sodium-dependent transport of neutral amino acids or oligopeptides. These proteins are responsible for the Kx blood group system - defects results in McLeod syndrome [MIM:314850], an X-linked multi-system disorder characterised by late onset abnormalities in the neuromuscular and hematopoietic systems.
Pfam PF20906: S-Me-THD-like, C-terminal domain (domain)
This beta barrel domain is found at the C-terminal of S-methyl thiohydantoin desulfurase from Variovorax sp. (S-Me-THD) and similar sequences mainly found in bacteria and fungi. S-Me-THD catalyses the hydrolysis of S-methyl -thiohydantoin-5-propanoate into hydantoin-5-propanoate and methanethiol, the third step in S-methyl ergothioneine degradation.
Pfam PF09676: Type IV conjugative transfer system lipoprotein (TraV) (family)
This entry includes TraV, which is a component of conjugative type IV secretion system. TraV is an outer membrane lipoprotein that is believed to interact with the secretin TraK. The alignment contains three conserved cysteines in the N-terminal half.
Pfam PF21165: Fibroblast growth factor receptor 3 transmembrane domain (domain)
Fibroblast growth factor receptor 3 (FGFR3) is a receptor tyrosine kinase that transduces biochemical signals by lateral dimerization in the plasma membrane, followed by receptor autophosphorylation and stimulation of downstream signaling cascades. This entry represents the transmembrane helix of FGFR3 which is involved in dimerization, forming a symmetric left-handed dimer. Mutations in this segment are associated with pathogenesis of cancers and growth disorders.