SII-SWORD/CoKE huggingface dataset:
Pfam PF04314: Copper chaperone PCu(A)C (family)
PCu(A)C is a periplasmic copper chaperone. Its role  may be to capture and transfer copper to two other copper chaperones, PrrC and Cox11, which in turn deliver Cu(I) to cytochrome c oxidase.
Pfam PF09932: Uncharacterized conserved protein (DUF2164) (family)
This domain, found in various hypothetical prokaryotic proteins, has no known function.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF15815: E3 ubiquitin-protein ligase makorin, C-terminal (domain)
MKRN1_C is the very C-terminus of E3 ubiquitin-protein ligase makorin-1, or MKRN1, a family of eukaryotic putative ribonucleoproteins with a distinctive array of zinc-finger motifs. MKRN1 plays an important role in modulating the homeostasis of telomere-length through a dynamic balance involving the stability of the protein hTERT. MKRN1 has been shown to be a a transcriptional co-regulator and an E3 ligase. It functions simultaneously as a differentially negative regulator of p53 and p21, preferentially leading cells to p53-dependent apoptosis by suppressing p21. The exact function of the C-terminal region has not been determined.
Pfam PF18200: Bacterial Ig-like domain (domain)
This presumed domain is found repeat in bacterial cell surface proteins.
Pfam PF16266: Domain of unknown function (DUF4919) (family)
This family consists of uncharacterized proteins around 230 residues in length and is mainly found in various Bacteroides and Prevotella species. The function of this family is unknown.
Pfam PF16380: Rhamnogalacturonan lyase BT_4170-like, C-terminal (domain)
This domain, previously known as DUF4990, is found at the C terminus of a group of proteins mainly from Bacteroides species, including the rhamnogalacturonan lyase BT_4170 from Bacteroides thetaiotaomicron.
Pfam PF12534: Pannexin-like TM region of LRRC8 (family)
Pannexin_like is a family of the four transmembrane domains of metazoan leucine-rich-repeat-containing 8 proteins.  These four TMs associate into hexamers resulting in homo- or heteromeric channels that connect the cytosol to the extracellular space. The family is found in association with [pfam:PF00560].
Wikipedia: Pannexins are a family of vertebrate proteins identified by their homology to the invertebrate innexins. While innexins are responsible for forming gap junctions in invertebrates, the pannexins have been shown to predominantly exist as large transmembrane channels connecting the intracellular and extracellular space, allowing the passage of ions and small molecules between these compartments.
Pfam PF06699: GPI biosynthesis protein family Pig-F (family)
PIG-F is involved in glycosylphosphatidylinositol (GPI) anchor biosynthesis.
Pfam PF05979: Bacterial protein of unknown function (DUF896) (domain)
In B. subtilis, one small SOS response operon under the control of LexA, the yneA operon, is comprised of three genes: yneA, yneB, and ynzC. This family consists of several short, hypothetical bacterial proteins of unknown function. These proteins are mainly found in gram-positive firmicutes. Structures show that the N-terminus is composed of two alpha helices forming a helix-loop-helix motif. The structure of ynzC from B. subtilis forms a trimeric complex. Structural modelling suggests this domain may bind nucleic acids. This family is also known as UPF0291.
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 PF06392: Acid shock protein (disordered)
The Asr protein is synthesised as a precursor and the cleavage is essential for moderate to high acid tolerance. The proteins generally consist of a conserved N-terminus followed by three disordered repeats.
Pfam PF03526: Colicin E1 (microcin) immunity protein (family)
The structural and functional relationships among independently cloned segments of the plasmid ColE1 region that regulates and codes for colicin E1 (cea), immunity (imm) and the mitomycin C-induced lethality function (lys) have been analysed . A model for the structure and expression of the colicin E1 operon has been proposed in which the cea and lys genes are expressed from a single inducible promoter that is controlled by the lexA repressor in response to the SOS system of Escherichia coli . The imm gene lies between the cea and lys genes and is expressed by transcription in the opposite direction from a promoter located within the lys gene . This arrangement indicates that the transcriptional units for all three genes overlap. It is proposed that the formation of anti-sense RNA may be an important element in the coordinate regulation of gene expression in this system .
Pfam PF00327: Ribosomal protein L30p/L7e (domain)
This family includes prokaryotic L30 and eukaryotic L7.
Pfam PF24427: Nuclear pore complex protein GP210, Ig-like domain (domain)
This domain is found in the Nuclear pore complex protein GP210 from Arabidopsis thaliana and related proteins. GP210 is predicted to contain 16 Ig-like domains. This entry represents the 16th of these domains.
Pfam PF22674: C2185-like, N-terminal (domain)
This domain is found at the N-terminal end of a group of uncharacterised proteins from Clostridia, including C2185 from Clostridium acetobutylicum ([swissprot:Q97H28]). This domain is found associated with [pfam:PF08942] and shows a NAD(P) binding Rossmann fold.
Pfam PF24905: TTC3, helical domain (domain)
This domain is found in human E3 ubiquitin-protein ligase TTC3, which catalyzes the formation of 'Lys-48'- polyubiquitin chains and regulates Akt signalling, TGFB1- induced epithelial -mesenchymal transition and myofibroblast differentiation, neuronal differentiation and cell proliferation. This domain is predicted to adopt a helical configuration.
Pfam PF02577: Bifunctional nuclease domain (domain)
This entry represents the bifunctional nuclease (BFN) domain which is specific to bacteria and plant organisms. It has both RNase and DNase activities. The dimer of the BFN domain forms a wedge, each monomer being a basic triangular shape. The BFN domain is composed of an eight-stranded, distorted beta-sheet consisting of a four-stranded antiparallel beta-sheet, and a four-stranded mixed beta-sheet. This domain can be found in M. tuberculosis Carbon monoxide resistance (Cor) proteins. Cor consists entirely of this domain with homologues in a variety of organisms, including most mycobacteria, Bacteroides sp., Chlamydia sp., Streptomyces sp., and Rhodococcussp. One of the homologs from Oryza minuta protein OmBBD was reported to exhibit DNase and RNAse activity in vitro. OmBBD carries a C-terminal UvrB domain that is absent in the mycobacterial sequences. UvrB is one component of the UvrABC endonuclease system. Hence, it was proposed that OmBBD's observed nuclease activity may come not from this domain but from an interaction of the C-terminal UvrB with the catalytic UvrC nuclease.
Pfam PF11251: Protein of unknown function (DUF3050) (family)
This bacterial family of proteins has no known function.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF04673: Polyketide synthesis cyclase (domain)
This family represents a number of cyclases involved in polyketide synthesis in a number of actinobacterial species.
Wikipedia: In molecular biology, the polyketide synthesis cyclase family of proteins includes a number of cyclases involved in polyketide synthesis in a number of actinobacterial species.
Pfam PF01948: Aspartate carbamoyltransferase regulatory chain, allosteric domain (domain)
The regulatory chain is involved in allosteric regulation of aspartate carbamoyltransferase. The N-terminal domain has ferredoxin-like fold, and provides the  regulatory chain dimerisation interface.
Pfam PF20575: Helix-turn-helix domain (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in archaea. Proteins in this family are typically between 161 and 201 amino acids in length. This family shares similarity with [pfam:PF01638] suggesting it is a transcriptional regulatory protein.
Pfam PF21007: Fas-binding factor 1 (coiled_coil)
Keratin-binding protein required for epithelial cell polarization. Involved in apical junction complex (AJC) assembly via its interaction with PARD3. Required for ciliogenesis.
Pfam PF16752: Tubulin-specific chaperone C N-terminal domain (domain)
This N-terminal domain of tubulin-specific chaperone C has a spectrin-like fold and binds to tubulin.
Pfam PF21665: Type III secretory system chaperone SycN (domain)
Chaperone protein SycN is part of the type III secretion system and functions as a specific chaperone for YopN which may facilitate the secretion and the subsequent translocation of YopN.
Pfam PF04724: Glycosyltransferase family 17 (family)
This family represents beta-1,4-mannosyl-glycoprotein beta-1,4-N-acetylglucosaminyltransferase ([ec:2.4.1.144]). This enzyme transfers the bisecting GlcNAc to the core mannose of complex N-glycans. The addition of this residue is regulated during development and has functional consequences for receptor signalling, cell adhesion, and tumour progression.
Pfam PF05180: DNL zinc finger (domain)
The domain is named after a short C-terminal motif of D(N/H)L. This domain is a novel zinc-finger protein essential for protein import into mitochondria.
Pfam PF01098: Cell cycle protein (family)
This entry includes the following members;    FtsW, RodA, SpoVE
Pfam PF00762: Ferrochelatase (domain)
Synonym(s): Protohaem ferro-lyase, Iron chelatase, etc.

Ferrochelatase is the terminal enzyme of the heme biosynthetic pathway. It catalyzes the insertion of ferrous iron into the protoporphyrin IX ring yielding protoheme. This enzyme is ubiquitous in nature and widely distributed in bacteria and eukaryotes. Recently, some archaeal members have been identified. The oligomeric state of these enzymes varies depending on the presence of a dimerization motif at the C terminus . In eukaryotic cells, it binds to the mitochondrial inner membrane with its active site on the matrix side of the membrane.

The X-ray structure ofBacillus subtilisand human ferrochelatase have been solved . The human enzyme exists as a homodimer. Each subunit contains one  cluster. The monomer is folded into two similar domains, each with a four-stranded parallel Î²-sheet flanked by an Î±-helix in a Î²-Î±-Î² motif that is reminiscent of the fold found in the periplasmic binding proteins. The topological similarity between the domains suggests that they have arisen from a gene duplication event. However, significant differences exist between the two domains, including an N-terminal section (residues 80-130) that forms part of the active site pocket, and a C-terminal extension (residues 390-423) that is involved in coordination of the  cluster and in stabilisation of the homodimer.
Wikipedia: Protoporphyrin ferrochelatase (EC 4.98.1.1, formerly EC 4.99.1.1, or ferrochelatase; systematic name protoheme ferro-lyase (protoporphyrin-forming)) is an enzyme encoded by the FECH gene in humans. Ferrochelatase catalyses the eighth and terminal step in the biosynthesis of heme, converting protoporphyrin IX into heme B. It catalyses the reaction:protoporphyrin + Fe2+ → protoheme + 2 H+
Pfam PF19448: Family of unknown function (DUF5986) (family)
This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 235 and 254 amino acids in length. There is a single completely conserved residue R that may be functionally important.
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 PF03367: ZPR1 zinc-finger domain (domain)
This entry represents the zinc-ribbon domain found in ZPR1 family. The zinc-finger protein ZPR1 is ubiquitous among eukaryotes. It is indeed known to be an essential protein in yeast. In quiescent cells, ZPR1 is localised to the cytoplasm. But in proliferating cells treated with EGF or with other mitogens, ZPR1 accumulates in the nucleolus. ZPR1 interacts with the cytoplasmic domain of the inactive EGF receptor (EGFR) and is thought to inhibit the basal protein tyrosine kinase activity of EGFR. This interaction is disrupted when cells are treated with EGF, though by themselves, inactive EGFRs are not sufficient to sequester ZPR1 to the cytoplasm. Upon stimulation by EGF, ZPR1 directly binds the eukaryotic translation elongation factor-1alpha (eEF-1alpha) to form ZPR1/eEF-1alpha complexes. These move into the nucleus, localising particularly at the nucleolus. Indeed, the interaction between ZPR1 and eEF-1alpha has been shown to be essential for normal cellular proliferation, and ZPR1 is thought to be involved in pre-ribosomal RNA expression. ZPR1 binds preferentially to GDP-bound eEF1A but does not directly influence the kinetics of nucleotide exchange or GTP hydrolysis. The alignment for the ZPR1 family shows a duplicated set composed of a zinc-ribbon domain (this entry) followed by a jelly-roll domain. This family also includes several hypothetical archaeal proteins (from both Crenarchaeota and Euryarchaeota). This similarity between ZPR1 and archaeal proteins was not previously noted.
Pfam PF12321: Protein of unknown function (DUF3634) (family)
This family of proteins is found in bacteria. Proteins in this family are typically between 103 and 114 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 PF00681: Plectin repeat (repeat)
This family includes repeats from plectin, desmoplakin, envoplakin and bullous pemphigoid antigen.
Pfam PF20171: Glucose-6-phosphate dehydrogenase subunit C-terminal domain (domain)
Members of this family are found in various prokaryotic OpcA and glucose-6-phosphate dehydrogenase proteins. This entry represents the C-terminal domain.
Pfam PF10532: Plant specific N-all beta domain (domain)
This domain was identified by Babu and colleagues. It is found associated with the WRKY domain [pfam:PF03106].
Pfam PF16254: Domain of unknown function (DUF4910) (domain)
This domain is related to aminopeptidase domains, but its function is not clear.
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 PF00724: NADH:flavin oxidoreductase / NADH oxidase family (domain)
The TIM-barrel fold is a closed barrel structure composed of an eight-fold repeat of Î²-Î± units, where the eight parallel Î² strands on the inside are covered by the eight Î± helices on the outside . It is a widely distributed fold which has been found in many enzyme families that catalyse completely unrelated reactions . The active site is always found at the C-terminal end of this domain.

Proteins in this entry are a variety of NADH:flavin oxidoreductase/NADH oxidase enzymes, found mostly in bacteria or fungi, that contain a TIM-barrel fold. They commonly use FMN/FAD as cofactor and include:


 * dimethylamine dehydrogenase
 * trimethylamine dehydrogenase
 * 12-oxophytodienoate reductase
 * NADPH dehydrogenase
 * NADH oxidase
Pfam PF04487: CITED (family)
CITED, CBP/p300-interacting transactivator with ED-rich tail, are characterised by a conserved 32-amino acid sequence at  the C-terminus. CITED proteins do not bind DNA directly  and are thought to function as transcriptional co-activators.
Pfam PF12508: Conjugative transposon, TraM (domain)
Proteins in this entry are designated TraM and are  found in a proposed transfer region of a class of  conjugative transposon found in the Bacteroides lineage.
Pfam PF03525: Meiotic recombination protein Rec7 N-terminal domain (domain)
This entry represents the N-terminal domain of the S. pombe Rec7 protein as predicted by AlphaFold. This domain adopts a PH-like domain fold.
Pfam PF14689: Sensor_kinase_SpoOB-type, alpha-helical domain (domain)
Sporulation initiation phospho-transferase B or SpoOB is part of a phospho-relay that initiates sporulation in Bacillus subtilis. Spo0B is a two-domain protein consisting of an N-terminal alpha-helical hairpin domain and a C-terminal alpha/beta domain. Two subunits of Spo0B dimerise by a parallel association of helical hairpins to form a novel four-helix bundle from which the active histidine - involved in the auto-phosphorylation - protrudes. In the phospho-relay, the signal-receptor histidine kinases are dephosphorylated by a common response regulator, Spo0F. Spo0B then takes phosphorylated Spo0F as substrate thereby mediating the transfer of a phosphoryl group to Spo0A, the ultimate transcription factor. The exact function of this alpha-helical domain is not known; it does not always occur just as the N-terminal domain of SPOB_ab, [pfam:PF14682]. SCOP describes this domain as a histidine kinase-like fold lacking the kinase ATP-binding site.
Pfam PF12261: Thermostable hemolysin (family)
This family of proteins is found in bacteria. Proteins in this family are typically between 200 and 228 amino acids in length. T_hemolysin is a pore-forming toxin of bacteria, able to lyse erythrocytes from a number of mammalian species.
Pfam PF16271: Domain of unknown function (DUF4924) (family)
This family consists of uncharacterized proteins around 180 residues in length and is mainly found in various Parabacteroides and  Bacteroides species. The function of this family is unknown.
Pfam PF20923: COMMD9, helical N-terminal domain (domain)
This domain is found at the N-terminal end of COMM domain-containing protein 9 from humans and similar proteins from vertebrates. COMMD9 contains a conserved and unique motif termed the COMM (copper metabolism gene MURR1, [pfam:PF07258]) domain at the C-terminal, which functions as an interface for protein-protein interactions. This entry represents the N-terminal domain, which shows a globular structure that consists of a six-helix bundle with a meander topology.
Pfam PF21428: Baseplate wedge protein gp7, helical domain (domain)
This domain is found in Baseplate wedge protein gp7 from Bacteriophage T4 and similar proteins predominantly found in tailed bacteriophages. Gp7 provides the primary control of the conformational changes of the viral baseplate during assembly and infection. This protein is organised into six domains connected by flexible linkers. This entry represents helix-turn-helix motif that is part of the long linker connecting the second and fourth domains.
Pfam PF05145: Transition state regulatory protein AbrB (family)
Bacillus subtilis respond to a multitude of environmental stimuli by using transcription factors called transition state regulators (TSRs). They play an essential role in cell survival by regulating spore formation, competence, and biofilm development. AbrB is one of the most known TSRs, acting as a pleotropic regulator for over 60 different genes where it directly binds to their promoter or regulatory regions. Many other genes are indirectly controlled by AbrB since it is a regulator of other regulatory proteins, including ScoC, Abh, SinR and SigH. Hence, AbrB is considered a global regulatory protein controlling processes such as Bacillus subtilis growth and cell division as well as production of extracellular degradative enzymes, nitrogen utilization and amino acid metabolism, motility, synthesis of antibiotics and their resistant determinants, development of competence, transport systems, oxidative stress response, phosphate metabolism, cell surface components and sporulation. AbrB is a tetramer consisting of identical 94 residue monomers. Its DNA-binding function resides solely in the N-terminal domain (AbrBN) of 53 residues. Although it does not recognize a well-defined DNA base-pairing sequence, instead, it appears to target a very weak pseudo consensus nucleotide sequence, TGGNA-5bp-TGGNA, which allows it to be rather promiscuous in binding. The N-terminal domains of very similar sequences are present in two more Bacillus subtilis proteins, Abh and SpoVT. Mutagenesis studies suggest that the role of the C-terminal domain is in forming multimers.
Pfam PF08691: DNA repair proteins Nse5 and Nse6 (family)
Nse5 and Nse6 are non essential nuclear proteins that are critical for chromosome segregation in fission yeast.  Nse5 forms a dimer with Nse6 and facilitates DNA repair as part of the Smc5-Smc6 holocomplex.
Pfam PF21842: Domain of unknown function (DUF6901) (domain)
This entry represents a family of uncharacterised proteins.  The possess a beta sheet packed against an alpha helical subdomain. This alignment contains three fully conserved cysteines that look like they form an Fe-S cluster or zinc binding site in the predicted structures.
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 PF17112: Mitochondrial import receptor subunit Tom6, fungal (family)
Tom6 is the Tom6 subunit of the protein translocase complex TOM in fungi. This complex of the outer membrane of mitochondria is the entry gate for the vast majority of precursor proteins that are encoded by nuclear DNA, synthesised in the cytosol and imported into the mitochondria. Tom6 and Tom7 together play a role in the assembly, stability and dynamics of the TOM complex.
Pfam PF21205: Initiator Rep protein, WH2 (domain)
This protein is an initiator of plasmid replication. RepB possesses nicking-closing (topoisomerase I) like activity. It is also able to perform a strand transfer reaction on ssDNA that contains its target. This family also includes RepA which is an E.coli protein involved in plasmid replication. The RepA protein binds to DNA repeats that flank the repA gene. These proteins consist of two domains containing a winged helix-turn-helix motif: the N-terminal one, WH1, is involved in the dimerization of RepE and an auxiliary binding to DNA; the C-terminal one, WH2, represented in this entry, is related to a sequence-specific binding to the common 8 bp of the iteron.