SII-SWORD/CoKE huggingface dataset:
Pfam PF00216: Bacterial DNA-binding protein (domain)
Bacteria synthesise a set of small, usually basic proteins of about 90 residues that bind DNA and are known as histone-like proteins . Examples include the HU protein in Escherichia coli which is a dimer of closely related alpha and beta chains and in other bacteria can be a dimer of identical chains. HU-type proteins have been found in a variety of eubacteria, cyanobacteria and archaebacteria, and are also encoded in the chloroplast genome of some algae . The integration host factor (IHF), a dimer of closely related chains which seem to function in genetic recombination as well as in translational and transcriptional control  is found in enterobacteria and viral proteins include the African Swine fever virus protein Pret-047 (also known as A104R or LMW5-AR) .

The exact function of these proteins is not yet clear but they are capable of wrapping DNA and stabilising it from denaturation under extreme environmental conditions. The structure is known for one of these proteins . The protein exists as a dimer and two "Î²-arms" function as the non-specific binding site for bacterial DNA.
Wikipedia: In molecular biology, bacterial DNA binding proteins are a family of small, usually basic proteins of about 90 residues that bind DNA and are known as histone-like proteins. Since bacterial binding proteins have a diversity of functions, it has been difficult to develop a common function for all of them. They are commonly referred to as histone-like and have many similar traits with the eukaryotic histone proteins. Eukaryotic histones package DNA to help it to fit in the nucleus, and they are known to be the most conserved proteins in nature. Examples include the HU protein in Escherichia coli, a dimer of closely related alpha and beta chains and in other bacteria can be a dimer of identical chains. HU-type proteins have been found in a variety of bacteria and archaea, and are also encoded in the chloroplast genome of some algae. The integration host factor (IHF), a dimer of closely related chains which is suggested to function in genetic recombination as well as in translational and transcriptional control is found in Enterobacteria and viral proteins including the African swine fever virus protein A104R.
Pfam PF11781: Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7 (domain)
This is the zinc-finger at the start of transcription-binding factor that associates strongly with both Rrn6 and Rrn7 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter.
Pfam PF02085: Class III cytochrome C family (domain)
Cytochromes c (cytC) can be defined as electron-transfer proteins having one or several haem c groups, bound to the protein by one or, more generally, two thioether bonds involving sulphydryl groups of cysteine residues. The fifth haem iron ligand is always provided by a histidine residue. CytC possess a wide range of properties and function in a large number of different redox processes .

Ambler  recognised four classes of cytC.

Class III comprises the low redox potential multiple haem cytochromes: C3 (tetrahaem), and high-molecular-weight cytC, HMC (hexadecahaem), with only 30-40 residues per haem group. The haem c groups, all bis-histidinyl coordinated, are structurally and functionally nonequivalent and present different redox potentials in the range 0 to -400 mV . The 3D structures of a number of cyt C3 proteins have been determined. The proteins consist of 4-5 Î±-helices and 2 Î²-strands wrapped around a compact core of four non-parallel haems, which present a relatively high degree of exposure to the solvent. The overall protein architecture, haem plane orientations and iron-iron distances are highly conserved .
Wikipedia: Cytochromes c  cytochromes, or heme-containing proteins, that have heme C covalently attached to the peptide backbone via one or two thioether bonds. These bonds are in most cases part of a specific Cys-X-X-Cys-His (CXXCH) binding motif, where X denotes a miscellaneous amino acid. Two thioether bonds of cysteine residues bind to the vinyl sidechains of heme, and the histidine residue coordinates one axial binding site of the heme iron. Less common binding motifs can include a single thioether linkage, a lysine or a methionine instead of the axial histidine or a CXnCH binding motif with n&gt;2. The second axial site of the iron can be coordinated by amino acids of the protein, substrate molecules or water. Cytochromes c possess a wide range of properties and function as electron transfer proteins or catalyse chemical reactions involving redox processes. A prominent member of this family is mitochondrial cytochrome c.
Pfam PF17880: Yos9 dimerzation domain (domain)
This is the dimerization domain (DD) found in Yos9 proteins in yeast. Structural analysis revealed that this domain contributes to self association of Yos9. The overall fold of the domain can be classified as an alpha-beta-roll architecture, comprising two alpha-helices and seven beta-strands.
Pfam PF21798: Family of unknown function (DUF6878) (domain)
This entry represents an uncharacterised protein that adopts a beta-grasp fold.
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 PF13065: Protein of unknown function (DUF3928) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 100 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 PF16733: Rhomboid N-terminal domain (domain)
This is the N-terminal domain of rhomboid protease.
Pfam PF11126: Transcriptional regulator DsbA (family)
DsbA is a double stranded binding protein found in bacteriophage T4 which is involved in transcriptional regulation. DsbA, along with other viral proteins, interacts with the host RNA polymerase core enzyme enabling initiation of transcription. DsbA acts as an enhancer protein of late genes in vitro. The protein consists of mainly alpha helices.
Pfam PF15144: Domain of unknown function (DUF4576) (family)
This family of uncharacterised proteins is found in eukaryotes.
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 PF05141: Pyoverdine/dityrosine biosynthesis protein (family)
DIT1 is involved in synthesising dityrosine. Dityrosine is a sporulation-specific component of the yeast ascospore wall that is essential for the resistance of the spores to adverse environmental conditions. Pyoverdine biosynthesis protein PvcA is involved in the biosynthesis of pyoverdine, a cyclized isocyano derivative of tyrosine. It has a modified Rossmann fold.
Pfam PF21134: Bacteriophage T4, Recombination and repair protein, C-terminal domain (domain)
This domain is mainly found in proteins from tailed bacteriophages, including Recombination and repair protein from Bacteriophage T4 (UVSX). This protein is organised into a larger N-terminal 'core' domain and a smaller C-terminal domain (this entry) with mainly alpha-helical structure.
Pfam PF10637: Oxoglutarate and iron-dependent oxygenase degradation C-term (domain)
Ofd1 is a prolyl 4-hydroxylase-like 2-oxoglutarate-Fe(II) dioxygenase that accelerates the degradation of Sre1N in the presence of oxygen.  The domain is conserved from yeasts to humans. Yeast Sre1 is the orthologue of mammalian sterol regulatory element binding protein (SREBP), and it responds to changes in oxygen-dependent sterol synthesis as an indirect measure of oxygen availability. However, unlike the prolyl 4-hydroxylases that regulate mammalian hypoxia-inducible factor, Ofd1 uses multiple domains to regulate Sre1N degradation by oxygen; the Ofd1 N-terminal dioxygenase domain is required for oxygen sensing and this Ofd1 C-terminal domain accelerates Sre1N degradation in yeasts.
Pfam PF11710: G protein-coupled glucose receptor regulating Gpa2 (domain)
Git3 is one of six proteins required for glucose-triggered adenylate cyclase activation, and is a G protein-coupled receptor responsible for the activation of adenylate cyclase through Gpa2 - heterotrimeric G protein alpha subunit, part of the glucose-detection pathway. Git3 contains seven predicted transmembrane domains, a third cytoplasmic loop and a cytoplasmic tail. This is the conserved N-terminus of these proteins, and the C-terminal conserved region is now in family Git3_C.
Pfam PF22708: S1/CSD-like domain 1 of the TOTE conflict systems (domain)
This entry represents a presumed ribonucleoprotein complex-forming domain of the TOTE systems, potentially binding ssRNAs derived from hybrid duplexes bound by the systems. It is typically found in a two-domain tandem repeat arrangement, this is the first domain of the two.
Pfam PF22025: ThiI ferredoxin-like domain (domain)
This entry represents the ferredoxin-like domain found at the N-terminal of ThiI proteins (NFLD). ThiI is responsible for the formation of the modified base S(4)U (4-thiouridine) found at position 8 in some prokaryotic tRNA. This domain connects the C-terminal catalytic PP-loop pyrophosphatase domain with the THUMP ([pfam:PF02926]). NFLD and the THUMP domains jointly form the tRNA-binding surface shaped like a channe which may be of particular importance in ThiI for the correct orientation and distance between residues involved in RNA binding and the active site of the enzyme.
Pfam PF02439: Adenovirus E3 region protein CR2 (family)
Early region 3 (E3) of human adenoviruses (Ads) codes for proteins that appear to control viral interactions with the host. This region called CR2 (conserved region 1) is found in Adenovirus type 19 (a subgroup D virus) 49 Kd protein in the E3 region. CR2 is also found in the 20.1 Kd protein of subgroup B adenoviruses. The function of this 50 amino acid region is unknown.
Pfam PF21090: SecA P-loop domain (domain)
SecA is the preprotein translocase ATPase subunit and a superfamily 2 (SF2) RNA helicase. This entry corresponds to the second P-loop domain.
Pfam PF23203: KIF21A-like domain (domain)
This domain is found in human Kinesin-like protein KIF21A and similar eukaryotic sequences. KIF21A is a microtubule-binding motor protein probably involved in neuronal axonal transport. Mutations in this protein are associated with ocular abnormalities. This domain, which is found associated to [pfam:PF00225] and several [pfam:PF00400] repeats, folds into two long alpha-helices.
Pfam PF14791: DNA polymerase beta thumb (family)
The catalytic region of DNA polymerase beta is split into three domains. An N-terminal fingers domain, a central palm domain and a C-terminal thumb domain. This entry represents the thumb domain.
Pfam PF12888: Lipid-binding putative hydrolase (family)
This is a small family of lipid-binding proteins found in Bacteroidetes.
Pfam PF05640: Na,K-Atpase Interacting protein (family)
NKAIN (Na,K-Atpase INteracting) proteins are a family of evolutionary conserved transmembrane proteins that localise to neurons, that are critical for neuronal function, and that interact with the beta subunits, beta1 in vertebrates and beta in Drosophila, of Na,K-ATPase. NKAINs have highly conserved trans-membrane domains but otherwise no other characterised domains. NKAINs may function as subunits of pore or channel structures in neurons or they may affect the function of other membrane proteins. They are likely to function within the membrane bilayer.
Pfam PF24989: Domain of unknown function (DUF7776) (domain)
This domain is found in HFX_2341 from Haloferax mediterranei and similar archaeal proteins. HFX_2341 is a global regulator involved in cas gene regulation. This domain is often found associated with [pfam:PF19810].
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 PF20813: Factor H binding protein B (domain)
Treponema denticola, a human pathogen that contributes to periodontitis, survives by binding factor H (FH) to its surface through its Factor H binding protein B (FhbB). The structure of this protein is highly ordered consisting of an alpha-beta fold. This highly thermostable protein forms a weak dimer with an interface occurring along one alpha helix from each subunit in an anti-parallel alignment with no direct hydrogen bonding between the subunits.
Pfam PF02501: Type II secretion system (T2SS), protein I (domain)
The Type II secretion system, also called Secretion-dependent pathway (SDP), is responsible for the transport of proteins across the outer membrane first exported to the periplasm by the Sec or Tat translocon in Gram-negative (diderm) bacteria. As members of the T2SJ family, members of the T2SI family are pseudopilins containing prepilin signal sequences.
Pfam PF11402: Antifungal protein (family)
Antifungal protein consists of five antiparallel beta strands which are highly twisted creating a beta barrel stabilised by four internal disulphide bridges. A cationic site adjacent to a hydrophobic stretch on the protein surface may constitute a phospholipid binding site.
Wikipedia: The antifungal protein family is a protein family, with members sharing a structure consisting of five antiparallel beta strands which are highly twisted creating a beta barrel stabilised by four internal disulphide bridges. A cationic site adjacent to a hydrophobic stretch on the protein surface may constitute a phospholipid binding site.
Pfam PF21310: Inositol polyphosphate 5-phosphatase OCRL-like, ASH domain (domain)
This domain is found in Inositol polyphosphate 5-phosphatase OCRL from humans and similar eukaryotic proteins. OCRL is an enzyme that dephosphorylate the 5' position of the inositol ring. It is thought to help coordinate intracellular membrane traffic through changes in the phosphoinositide composition of associated membranes. Mutations in this protein are responsible for Lowe syndrome. This entry represents a domain found C-terminal to [pfam:PF03372] and N-terminal to [pfam:PF00620]. It is comprised by two layers of beta- sheets and is closely related to the members of the family of immunoglobulin-like beta-sandwiches.
Pfam PF02089: Palmitoyl protein thioesterase (domain)
Wikipedia: Palmitoyl protein hydrolase/thioesterases is an enzyme (EC 3.1.2.22) that removes thioester-linked fatty acyl groups such as palmitate from modified cysteine residues in proteins or peptides during lysosomal degradation. It catalyzes the reactionpalmitoyl[protein] + H2O  palmitate + protein
Pfam PF18120: Domain of unknown function (DUF5597) (domain)
This is the C-terminal domain of xyloglucan utilization locus (XyGUL) present in Cellvibrio japonicas. XyGUL is required for xyloglucan utilization. It is also the C-terminal domain of PF02449 and PF01301.
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 PF04426: Bul1 C terminus (family)
This family contains the C terminus of Saccharomyces cerevisiae Bul1. Bul1 binds the ubiquitin ligase Rsp5, via an N terminal PPSY motif (157-160 in [swissprot:P48524]).  The complex containing Bul1 and Rsp5 is involved in  intracellular trafficking of the general amino acid permease Gap1, degradation of Rog1 in cooperation with Bul2 and GSK-3, and mitochondrial inheritance. Bul1 may contain HEAT repeats.
Pfam PF15396: Protein Family FAM60A (family)
This protein family, FAM60A is a family of proteins is found in eukaryotes. It is known to be a cell cycle protein that binds to the promoter of a gene transcription repressor complex, named SIN4-HDAC complex. This means that FAM60A has an important role to play in 'switching on' gene expression. Proteins in this family are typically between 179 and 324 amino acids in length.
Pfam PF00883: Cytosol aminopeptidase family, catalytic domain (domain)
The two associated zinc ions and the active site are entirely enclosed within the C-terminal catalytic domain in leucine aminopeptidase.
Pfam PF17908: APAF-1 helical domain (domain)
This domain represents the C-terminal alpha helical domain of the apoptotic Apaf-1 protein.
Pfam PF06270: Protein of unknown function (DUF1030) (family)
This family consists of several short Circovirus proteins of unknown function.
Pfam PF21696: TECR, ubiquitin-like domain (domain)
This entry represents the ubiquitin-like domain found at the N-terminal of Very-long-chain enoyl-CoA reductase (also known as TECR or or synaptic glycoprotein SC2) from animals. TECR is a synaptic glycoprotein that catalyzes the fourth reaction in the synthesis of very long-chain fatty acids (VLCFA).
Pfam PF00405: Transferrin (domain)
Transferrins are eukaryotic iron-binding glycoproteins that control the level of free iron in biological fluids . Evidence suggests that members of the TF family arose from the duplication and fusion of two homologous domains, with each duplicated domain binding one iron atom. Members of the family include blood serotransferrin (siderophilin); milk lactotransferrin (lactoferrin); egg white ovotransferrin (conalbumin); and membrane-associated melanotransferrin. Family members that do not bind iron have also been discovered, including inhibitor of carbonic anhydrase (ICA), which strongly binds to and inhibits certain isoforms of carbonic anhydrase .

This entry represents the transferrin-like domain, which can be further divided into two subdomains that form a cleft inside of which the iron atom is bound in iron-transporting transferrin . The iron-coordinating residues consist of an aspartic acid, two tyrosines and a histidine, as well as an arginine that coordinates a requisite anion. In addition to iron and anion liganding residues, the transferrin-like domain contains conserved cysteine residues involved in disulphide bond formation.
Wikipedia: Transferrins are glycoproteins found in vertebrates which bind and consequently mediate the transport of iron (Fe) through blood plasma. They are produced in the liver and contain binding sites for two Fe3+ ions. Human transferrin is encoded by the TF gene and produced as a 76 kDa glycoprotein.
Pfam PF23621: BP74 N-terminal domain (domain)
This domain is found N-terminal in the Cyclic AMP-inducible protein BP74 from Dictyostelium discoideum and related proteins. The BP74 gene is a cyclic AMP-regulated and expressed during the Dictyostelium development. This domain is predicted to fold into an open beta-barrel capped with two alpha-helices.
Pfam PF06500: Esterase FrsA-like (family)
The FrsA-like family includes FrsA, an esterase found to have the alpha/beta-hydrolase fold. t also includes the hydrolytic polyketide shortening protein Ayg1 from fungi, 2,6-dihydropseudooxynicotine hydrolase from Paenarthrobacter nicotinovorans and Fus2 from Gibberella species. The enzyme 2,6-dihydroxy-pseudo-oxynicotine hydrolase is involved in the nicotine-degradation pathway of Arthrobacter nicotinovorans. Fus2 is part of the gene cluster that mediates the biosynthesis of the mycotoxin fusarin C. Fus2 catalyses closure of the 2-pyrrolidone ring of the intermediate 20-hydroxy-prefusarin to form another intermediate, 20-hydroxy-fusarin, which is then oxidized by Fus8.
Pfam PF24118: Domain of unknown function (DUF7392) (domain)
This domain is found in uncharacterised proteins from plants. It has sequence and structural similarity to domains members of Dimeric alpha/beta barrel superfamily.
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 PF22934: Spartan-like zinc binding domain (family)
This zinc binding domain is found in the homologues of DNA-dependent metalloprotease Spartan (SPRTN). SPRTN cleaves DNA-protein crosslinks (DPCs) and protects cells from DPC-induced genome instability. The zinc binding domain is located in close proximity to the catalytic domain and contributes to the ssDNA specificity of SPRTN.
Pfam PF07731: Multicopper oxidase (domain)
This entry contains many divergent copper oxidase-like domains that are not recognised by the [pfam:PF00394] model.
Wikipedia: In molecular biology, multicopper oxidases are enzymes which oxidise their substrate by accepting electrons at a mononuclear copper centre and transferring them to a trinuclear copper centre; dioxygen binds to the trinuclear centre and, following the transfer of four electrons, is reduced to two molecules of water. There are three spectroscopically different copper centres found in multicopper oxidases: type 1, type 2 and type 3. Multicopper oxidases consist of 2, 3 or 6 of these homologous domains, which also share homology with the cupredoxins azurin and plastocyanin. Structurally, these domains consist of a cupredoxin-like fold, a beta-sandwich consisting of 7 strands in 2 beta-sheets, arranged in a Greek-key beta-barrel.
Pfam PF08044: DUF1707 SHOCT-like domain (domain)
This domain is found in a variety of Actinomycetales proteins. All of the proteins containing this domain are uncharacterised and probably membrane bound or associated. It is unclear to the function  of this domain.
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 PF17638: HCMV UL42 (family)
Family members include UL42 proteins found in Human cytomegalovirus (HCMV). UL42 has two Pro-Pro-X-Tyr (PPxY) sequences, a hydrophobic region at the C terminus and no N-terminal signal peptide. These features are shared with herpes simplex virus (HSV) UL56. UL42 has a putative C-terminal trans-membrane region. HCMV UL42 interacts with Itch, a member of the Nedd4 family of ubiquitin E3 ligases, through its PY motifs as observed in HSV UL56, suggestive of a regulatory function.