SII-SWORD/CoKE huggingface dataset:
Pfam PF12106: Colicin E5 ribonuclease domain (domain)
Colicin is a protein produced by bacteria with Col plasmids. Its function is to attack E. coli through actions on its inner membrane ion channels or through ribonuclease or deoxyribonuclease actions. The C terminal domain is the ribonuclease domain. It specifically cleaves tRNA anticodons which recognise codons in the form NAY (N:any nucleotide, A:adenosine, Y:pyrimidine) which corresponds to Tyrosine, Histidine, Asparagine and Aspartic Acid. E5-CRD can be referred to as an RNA restriction enzyme that specifically recognizes and cleaves single-stranded GU sequences.
Pfam PF22262: Domain of unknown function (DUF6950) (domain)
This domain if found in a group of uncharacterised bacterial proteins. It is related to NlpC/P60 domains and it is likely to adopt similar structure as well as to possess an endopeptidase activity. All members of this family contain a  conserved cysteine residue that is predicted to occupy equivalent spatial position as in the NlpC/P60 domains.
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 PF06495: Fruit fly transformer protein (family)
This family consists of transformer proteins from several Drosophila species and also from Ceratitis capitata (Mediterranean fruit fly). The transformer locus (tra) produces an RNA processing protein that alternatively splices the doublesex pre-mRNA in the sex determination hierarchy of Drosophila melanogaster.
Wikipedia: Female-specific protein transformer is a protein that in Drosophila melanogaster is encoded by the tra gene. Unlike the related tra2 protein, it is only produced in females.
Pfam PF20390: Family of unknown function (DUF6685) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 188 and 325 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 PF08656: DASH complex subunit Dad3 (family)
The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis. In Saccharomyces cerevisiae DASH forms both rings and spiral structures on microtubules in vitro.
Pfam PF19347: Domain of unknown function (DUF5925) (domain)
This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 180 amino acids in length. The family is found to the N-terminus of [pfam:PF00004]. There are three conserved sequence motifs: GWT, ELA and MGFW. Proteins in this family vary in length from 364 to 384 amino acids. The domains in this family vary in length from 177 to 180 amino acids.
Pfam PF15459: 60S ribosome biogenesis protein Rrp14 (family)
RRP14 is a family of nucleolar 60S ribosomal biogenesis proteins from eukaryotes. RRP14 functions in ribosome synthesis as it is required for the maturation of both small and large subunit rRNAs and it helps to prevent premature cleavage of the pre-rRNA at site C2. It also plays a role in cell polarity and/or spindle positioning 2],
Pfam PF03788: LrgA family (family)
This family is uncharacterised. It contains the protein LrgA that has been hypothesised to export murein hydrolases.
Pfam PF06280: Fn3-like domain (domain)
Fn3_5 is an fn3-like domain which is frequently found as the first of three on streptococcal C5a peptidase (SCP), a highly specific protease and adhesin/invasin. The family is found in conjunction with [pfam:PF00082], [pfam:PF02225] and [pfam:PF00746].
Wikipedia: The Fibronectin type III domain  is an evolutionarily conserved protein domain that is widely found in animal proteins. The fibronectin protein in which this domain was first identified contains 16 copies of this domain. The domain is about 100 amino acids long and possesses a beta sandwich structure. Of the three fibronectin-type domains, type III is the only one without disulfide bonding present. Fibronectin domains are found in a wide variety of extracellular proteins. They are widely distributed in animal species, but also found sporadically in yeast, plant and bacterial proteins.
Pfam PF22587: DNA polymerase II, insertion domain (domain)
This is the insertion domain found in DNA polymerase II from E. coli, a member of family B of DNA polymerases.
Pfam PF12849: PBP superfamily domain (family)
This domain belongs to the periplasmic binding protein superfamily.
Pfam PF23292: ULTRAPETALA1 SAND domain (domain)
This domain is found in the family of ULTRAPETALA proteins ULT1/2 from Arabidopsis thaliana and related plant proteins. ULT1/2 are putative transcription factors that act as regulators of cell accumulation in shoot and floral meristems. They also act as antirepressors that counteract EMBRYONIC FLOWER1 (EMF1) action through modulation of histone marks on target genes and thus regulating their transcriptional activities. This domain is predicted to adopt globular structure with significant similarity to SAND domains. It also contains several highly conserved cysteine residues that could be involved in metal coordination.
Pfam PF11508: Protein of unknown function (DUF3218) (family)
This family of proteins with unknown function appears to be restricted to Pseudomonas.
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 PF20801: Mastermind-like 1/3, transactivation domain 2 (domain)
Mastermind-like proteins are transcriptional coactivators that were first described as integral part of the Notch signalling pathway but also involved in Wnt/beta-catenin, Sonic Hh and Hippo pathways. MAML family consists of MAML1, 2 and 3, which have a conserved N-terminal basic domain ([pfam:PF09596]) but their amino acid sequence outside this region is more divergent which suggests that MAML2 and MAML3 may have different functions. This entry represents the transactivation domain 2 (TAD2) found at the C-terminal of Mastermind-like protein 1/3 (MAML1/3). TAD2 from MAML1 enhances the phosphorylation of CBP/p300 and ICN, required for Notch induced transcription. This is a glutamine rich domain that govern the MAML1 transcriptional activity. This domain directly recruits the cyclin C:CDK8 (cyclin-dependent kinase 8) complex that inhibits Notch signalling by promoting phosphorylation-dependent ubiquitination of nuclear ICN and its sequential proteasomal degradation.
Pfam PF07789: Protein of unknown function (DUF1627) (family)
This is a group of sequences found in hypothetical proteins predicted to be expressed in a number of  bacterial species. The region in question is  approximately 150 amino acid residues long.
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 PF19314: Family of unknown function (DUF5917) (family)
This short presumed domain is found close to the C-terminus of FHIP proteins, FAM160B proteins and UPF0518 family 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 PF08340: Endoribonuclease YicC-like, C-terminal (domain)
This domain is found at the C-terminal end of Endoribonuclease YicC from Escherichia coli and similar bacterial sequences. YicC, which is important for cells in the stationary phase, and essential for growth at high temperatures, contributes to degradation of the small RNA (sRNA) RhyB via collaboration with the exoribonuclease PNPase and seems to generate a 3'-OH and a 5'-phosphate group.
Pfam PF09394: Chagasin family peptidase inhibitor I42 (domain)
Chagasin is a cysteine peptidase inhibitor which forms a beta barrel structure.
Wikipedia: In biology and biochemistry, protease inhibitors, or antiproteases, are molecules that inhibit the function of proteases. Many naturally occurring protease inhibitors are proteins.
Pfam PF02337: Retroviral GAG p10 protein (family)
This family consists of various retroviral GAG (core) polyproteins and  encompasses the p10 region producing the p10 protein upon proteolytic  cleavage of GAG by retroviral protease. The p10 or matrix protein (MA) is associated with the virus envelope  glycoproteins in most mammalian retroviruses and may be involved in  virus particle assembly, transport and budding. Some of the GAG polyproteins have alternate cleavage sites leading to  the production of alternative and longer cleavage products (e.g. p19  [swissprot:P21411]) the alignment of this family only covers the approximately  N-terminal (GAG) 100 amino acid region of homology to p10.
Wikipedia: Retroviral matrix proteins are components of envelope-associated capsids of retroviruses. These proteins line the inner surface of viral envelopes and are associated with viral membranes.
Pfam PF20095: Domain of unknown function (DUF6485) (domain)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 80 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 PF00864: ATP P2X receptor (family)
Wikipedia: The P2X receptors, also ATP-gated P2X receptor cation channel family, is a protein family that consists of cation-permeable ligand-gated ion channels that open in response to the binding of extracellular adenosine 5'-triphosphate (ATP). They belong to a larger family of receptors known as the ENaC/P2X superfamily. ENaC and P2X receptors have similar 3-D structures and are homologous. P2X receptors are present in a diverse array of organisms including humans, mouse, rat, rabbit, chicken, zebrafish, bullfrog, fluke, and amoeba.
Pfam PF14765: Polyketide synthase dehydratase N-terminal domain (domain)
This entry represents the N-terminal HotDog domain of the dehydratase (DH) module of polyketide synthases.  Structural analysis shows these DH domains are double hotdogs in which the active site contains a histidine from the N-terminal hotdog and an aspartate from the C-terminal hotdog. Studies have uncovered that a substrate tunnel formed between the DH domains may be essential for loading substrates and unloading products.
Wikipedia: Polyketide synthases (PKSs) are a family of multi-domain enzymes or enzyme complexes that produce polyketides, a large class of secondary metabolites, in bacteria, fungi, plants, and a few animal lineages. The biosyntheses of polyketides share striking similarities with fatty acid biosynthesis.
Pfam PF18548: Metanogen output domain 2 (domain)
MetOD2 (Metanogen output domain 2) is found in euryarchaeal class Methanomicrobia, usually in combination with the Response_reg [pfam:PF00072] domain (Galperin et al., 2018, Phyletic distribution and lineage-specific domain architectures of archaeal two-component signal transduction systems).
Pfam PF15629: Permuted single zf-CXXC unit (family)
This is a permuted version of a single unit of the zf-CXXC domain  that is detected in the Demeter-like proteins of land plants.  Structural comparisons show that the mono-CXXC is homologous to  the structural-zinc binding domain of medium chain dehydrogenases. The classical zf-CXXC domain binds nonmethyl-CpG dinucleotides.
Pfam PF17048: Neutral/alkaline non-lysosomal ceramidase, C-terminal (domain)
This family represents C-terminal domain of a group of neutral/alkaline ceramidases found in both bacteria and eukaryotes. The EC classification is [ec:3.5.1.23].  The enzyme hydrolyses ceramide to generate sphingosine and fatty acid. The enzyme plays a regulatory role in a variety of physiological events in eukaryotes and also functions as an exotoxin in particular bacteria. This C-terminal tail of the enzyme is highly conserved across all species and may play a role in the interaction of the enzyme with the plasma membranes. The tail is also vital for the stabilisation of the enzyme as a whole.
Pfam PF20425: Neurobeachin alpha solenoid region (repeat)
This region is found in any neurobeachin homologues. It forms an extended alpha solenoid structure.
Pfam PF07863: Homologues of TraJ from Bacteroides conjugative transposon (family)
Members of this family have been implicated in as being involved in an unusual form of DNA transfer (conjugation) in Bacteroides (). The family has been named CtnDOT_TraJ to avoid confusion with other conjugative transfer systems.
Pfam PF23685: YtiC-like (family)
This protein family includes Protein YtiC from Escherichia coli, a 33-residue long sequence predicted to adopt an alpha -helical configuration.
Pfam PF06296: RelE toxin of RelE / RelB toxin-antitoxin system (domain)
RelE is a family of Gram-negative bacterial antitoxins of the RelE/RelB toxin-antitoxin system. Its cognate antitoxin is family RelB, [pfam:PF04221].
Wikipedia: A toxin-antitoxin system consists of a "toxin" and a corresponding "antitoxin", usually encoded by closely linked genes. The toxin is usually a protein while the antitoxin can be a protein or an RNA. Toxin-antitoxin systems are widely distributed in prokaryotes, and organisms often have them in multiple copies. When these systems are contained on plasmids – transferable genetic elements – they ensure that only the daughter cells that inherit the plasmid survive after cell division. If the plasmid is absent in a daughter cell, the unstable antitoxin is degraded and the stable toxic protein kills the new cell; this is known as 'post-segregational killing' (PSK).
Pfam PF17071: Outer capsid protein VP7 (family)
Outer capsid protein VP7 is a reoviral protein that interacts with VP4 to form the outer icosahedral capsid. Outer capsids are involved directly in viral host interactions.
Pfam PF04493: Endonuclease V (domain)
Endonuclease V is specific for single-stranded DNA or for duplex DNA that contains uracil or that is damaged by a variety of agents.
Wikipedia: Endonuclease V (endoV) is a highly conserved endonuclease enzyme family. The primary function of endoV differs significantly in prokaryotes and eukaryotes, as suggested by studies on the E. coli and human orthologs.
Pfam PF00823: PPE family (family)
This family named after a PPE motif near to the amino terminus of the domain.  The PPE family of proteins all contain an amino-terminal region of about 180 amino acids.  The carboxyl terminus of this family are variable, and on the basis of this region fall into at least three groups.  The MPTR subgroup has tandem copies of a motif NXGXGNXG. The second subgroup contains a conserved motif at about position 350. The third group are only related in the amino terminal region. The function of these proteins is uncertain but it has been suggested that they may be related to antigenic variation of Mycobacterium tuberculosis.
Pfam PF00022: Actin (family)
Actin  is a ubiquitous protein involved in the formation of filaments that are major components of the cytoskeleton. These filaments interact with myosin to produce a sliding effect, which is the basis of muscular contraction and many aspects of cell motility, including cytokinesis. Each actin protomer binds one molecule of ATP and has one high affinity site for either calcium or magnesium ions, as well as several low affinity sites. Actin exists as a monomer in low salt concentrations, but filaments form rapidly as salt concentration rises, with the consequent hydrolysis of ATP. Actin from many sources forms a tight complex with deoxyribonuclease (DNase I) although the significance of this is still unknown. The formation of this complex results in the inhibition of DNase I activity, and actin loses its ability to polymerise. It has been shown that an ATPase domain of actin shares similarity with ATPase domains of hexokinase and hsp70 proteins .

In vertebrates there are three groups of actin isoforms: alpha, beta and gamma. The alpha actins are found in muscle tissues and are a major constituent of the contractile apparatus. The beta and gamma actins co-exists in most cell types as components of the cytoskeleton and as mediators of internal cell motility. In plants there are many isoforms which are probably involved in a variety of functions such as cytoplasmic streaming, cell shape determination, tip growth, graviperception, cell wall deposition, etc.

Recently some divergent actin-like proteins have been identified in several species. These proteins include centractin (actin-RPV) from mammals, fungi yeast ACT5, Neurospora crassa ro-4 and Pneumocystis carinii, which seems to be a component of a multi-subunit centrosomal complex involved in microtubule based vesicle motility (this subfamily is known as ARP1); ARP2 subfamily, which includes chicken ACTL, Saccharomyces cerevisiae ACT2, Drosophila melanogaster 14D and Caenorhabditis elegans actC; ARP3 subfamily, which includes actin 2 from mammals, Drosophila 66B, yeast ACT4 and Schizosaccharomyces pombe act2; and ARP4 subfamily, which includes yeast ACT3 and Drosophila 13E.
Wikipedia: Actin is a family of globular multi-functional proteins that form microfilaments in the cytoskeleton, and the thin filaments in muscle fibrils. It is found in essentially all eukaryotic cells, where it may be present at a concentration of over 100 μM; its mass is roughly 42 kDa, with a diameter of 4 to 7 nm.
Pfam PF17811: Jumonji helical domain (domain)
This 4-helix bundle domain is associated with the Jumonji domain [pfam:PF02373].
Pfam PF08393: Dynein heavy chain, N-terminal region 2 (family)
Dyneins are described as motor proteins of eukaryotic cells, as they can convert energy derived from the hydrolysis of ATP to force and movement along cytoskeletal polymers, such as microtubules. This region is found C-terminal to the dynein heavy chain N-terminal region 1 ([pfam:PF08385]) in many members of this family. No functions seem to have been attributed specifically to this region.
Wikipedia: Dyneins are a family of cytoskeletal motor proteins that move along microtubules in cells. They convert the chemical energy stored in ATP to mechanical work. Dynein transports various cellular cargos, provides forces and displacements important in mitosis, and drives the beat of eukaryotic cilia and flagella. All of these functions rely on dynein's ability to move towards the minus-end of the microtubules, known as retrograde transport; thus, they are called "minus-end directed motors". In contrast, most kinesin motor proteins move toward the microtubules' plus-end, in what is called anterograde transport.
Pfam PF16251: Betacoronavirus nucleic acid-binding (NAB) (domain)
This is the nucleic acid-binding domain (NAB) from the multidomain nonstructural protein NSP3, and described as NSP3e domain. NSP3 is part of Orf1a polyproteins in SARS-CoV. It is an essential component of the replication/transcription complex. The global domain of the NAB represents a new fold, with a parallel four-strand beta-sheet holding two alpha-helices of three and four turns that are oriented antiparallel to the beta-strands and a group of residues form a positively charged patch on the protein surface as the binding site responsible for binding affinity for nucleic acids. When binding to ssRNA, the NAB prefers sequences with repeats of three consecutive Gs, such as (GGGA)5 and (GGGA)2. A positively charged surface patch (Lys75, Lys76, Lys99, and Arg106) is involved in RNA binding.
Pfam PF13519: von Willebrand factor type A domain (domain)
The von Willebrand factor is a large multimeric glycoprotein found in blood plasma. Mutant forms are involved in the aetiology of bleeding disorders . In von Willebrand factor, the type A domain (vWF) is the prototype for a protein superfamily. The vWF domain is found in various plasma proteins: complement factors B, C2, CR3 and CR4; the integrins (I-domains); collagen types VI, VII, XII and XIV; and other extracellular proteins . Although the majority of VWA-containing proteins are extracellular, the most ancient ones present in all eukaryotes are all intracellular proteins involved in functions such as transcription, DNA repair, ribosomal and membrane transport and the proteasome. A common feature appears to be involvement in multiprotein complexes. Proteins that incorporate vWF domains participate in numerous biological events (e.g. cell adhesion, migration, homing, pattern formation, and signal transduction), involving interaction with a large array of ligands . A number of human diseases arise from mutations in VWA domains.
Wikipedia: The von Willebrand factor type A (vWA) domain is a protein domain named after its occurrence in von Willebrand factor (vWF), a large multimeric glycoprotein found in blood plasma. Mutant forms of vWF are involved in the aetiology of bleeding disorders. This type A domain is the prototype for a protein superfamily.
Pfam PF01646: Herpes virus proteins UL24 and UL76 (family)
This family consists of various herpes virus proteins; the gene 20 product, U49 protein, UL24 and UL76 proteins and BXRF1. The UL24 gene (product of the 24th ORF) is not essential for virus replication, and mutants with lesions in UL24 show a reduced ability to replicate in tissue culture and have reduced thymidine kinase activity, as the UL24 gene overlaps with thymidine kinase. The family of proteins is involved in viral production, latency, and reactivation. Protein UL76 presents as globular aggresomes in the nuclei of transiently transfected cells. Bioinformatic analyses predict that UL76 has a propensity for aggregation and targets cellular proteins implicated in protein folding and ubiquitin-proteasome systems. UL76 interacts with the VWA domain of S5a, the 26S proteasome non-ATPase regulatory subunit 4 (or PSMD4, or Rpn10), forming a complex in the late phase of infection.
Pfam PF20966: MASE6 (domain)
This entry represents a predicted integral membrane sensory domain (MASE6), which has been observed in association with GGDEF domain ([pfam:PF00990]) and histidine sensor kinases.
Pfam PF16192: C-terminal four TMM region of protein-O-mannosyltransferase (family)
PMT_4TMC is the C-terminal four membrane-pass region of protein-O-mannosyltransferases and similar enzymes.