SII-SWORD/CoKE huggingface dataset:
Pfam PF00643: B-box zinc finger (domain)
This entry represents B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitination. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins .

The microtubule-associated E3 ligase MID1 (6.3.2) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a Î²/Î²/Î± cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers .
Wikipedia: In molecular biology the B-box-type zinc finger domain is a short protein domain of around 40 amino acid residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains.
Pfam PF08793: 2-cysteine adaptor domain (domain)
The virus-specific 2-cysteine adaptor domain is found fused to OTU/A20-like peptidases and S/T protein kinases.  The domain associations of these proteins indicate that they might function as viral adaptors connecting the kinases and OTU/A20 peptidases to specific targets.
Pfam PF02059: Interleukin-3 (domain)
Interleukin-3 (IL3) is a cytokine that regulates blood-cell production by controlling the production, differentiation and function of granulocytes and macrophages . The protein, which exists in vivo as a monomer, is produced in activated T-cells and mast cells , and is activated by the cleavage of an N-terminal signal sequence .

IL3 is produced by T-lymphocytes and T-lymphomas only after stimulation with antigens, mitogens, or chemical activators such as phorbol esters. However, IL3 is constitutively expressed in the myelomonocytic leukaemia cell line WEHI-3B . It is thought that the genetic change of the cell line to constitutive production of IL3 is the key event in development of this leukaemia .
Wikipedia: Interleukins (ILs) are a group of cytokines that are expressed and secreted by white blood cells (leukocytes) as well as some other body cells. The human genome encodes more than 50 interleukins and related proteins.
Pfam PF01821: Anaphylotoxin-like domain (domain)
C3a, C4a and C5a anaphylatoxins are protein fragments generated enzymatically in serum during activation of complement molecules C3, C4, and C5. They induce smooth muscle contraction. These fragments are homologous to a three-fold repeat in fibulins.
Wikipedia: Anaphylatoxins, or complement peptides, are fragments that are produced as part of the activation of the complement system. Complement components C3, C4 and C5 are large glycoproteins that have important functions in the immune response and host defense. They have a wide variety of biological activities and are proteolytically activated by cleavage at a specific site, forming a- and b-fragments. A-fragments form distinct structural domains of approximately 76 amino acids, coded for by a single exon within the complement protein gene. The C3a, C4a and C5a components are referred to as anaphylatoxins: they cause smooth muscle contraction, vasodilation, histamine release from mast cells, and enhanced vascular permeability. They also mediate chemotaxis, inflammation, and generation of cytotoxic oxygen radicals. The proteins are highly hydrophilic, with a mainly alpha-helical structure held together by 3 disulfide bridges.
Pfam PF23416: Domain of unknown function (DUF7107) (domain)
This entry represents a family of uncharacterised domains that show similarities to members of the colipase 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 PF17432: Domain of unknown function (DUF3458_C) ARM repeats (repeat)
This presumed domain is functionally uncharacterised. This domain is found in bacteria, archaea and 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 PF12054: Domain of unknown function (DUF3535) (family)
This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 439 to 459 amino acids in length. This domain is found associated with [pfam:PF00271], [pfam:PF02985], [pfam:PF00176]. This domain has two completely conserved residues (P and K) 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 PF15738: Bacterial toxin of type II toxin-antitoxin system, YafQ (domain)
YafQ is a family of bacterial toxin ribonucleases of type II toxin-antitoxin systems. The E.coli gene is expressed from the dinB operon.  The cognate antitoxin for the E. coli protein is DinJ, in family RelB_antitoxin, [pfam:PF02604].
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 PF07408: Protein of unknown function (DUF1507) (family)
This family consists of several hypothetical bacterial proteins of around 90 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 PF08047: Histidine operon leader peptide (family)
This family consists of the leader peptide of  the histidine (his) operon. The his operon contains  all the genes necessary for histidine biosynthesis.  The region corresponding to the untranslated 5' end  of the transcript, named the his leader region, displays  the typical features of the T box transcriptional  attenuation mechanism which is involved in the regulation  of many amino acid biosynthetic operons.
Pfam PF09478: Carbohydrate binding domain CBM49 (domain)
This domain is found at the C terminal of cellulases and in vitro binding studies have shown it to binds to crystalline cellulose.
Wikipedia: In molecular biology, a carbohydrate-binding module (CBM) is a protein domain found in carbohydrate-active enzymes. The majority of these domains have carbohydrate-binding activity. Some of these domains are found on cellulosomal scaffoldin proteins. CBMs were previously known as cellulose-binding domains. CBMs are classified into numerous families, based on amino acid sequence similarity. There are currently 64 families of CBM in the CAZy database.
Pfam PF24742: CUL7/CUL9 ARM repeat domain (repeat)
This domain is found in human Cillin-7 (CUL7), Cullin-9 (CUL9) and related proteins. CUL7 is a core component of the 3M and Cul7-RING(FBXW8) complexes, which mediates the ubiquitination of target proteins. CUL9, a core component of the Cul9-RING ubiquitin-protein ligase complex, acts downstream of the 3M complex, which inhibits the CUL9 activity, leading to prevent ubiquitination of BIRC5. This domain is composed of ARM repeats.
Pfam PF19002: Family of unknown function (DUF5731) (family)
A highly conserved domain of unknown function found in Platyhelminthes.
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 PF19615: Family of unknown function (DUF6120) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 125 and 138 amino acids in length. There is a conserved MGK sequence motif.
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 PF05675: Protein of unknown function (DUF817) (family)
This family consists of several bacterial proteins of unknown 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 PF10056: Uncharacterized conserved protein (DUF2293) (family)
This domain, found in various hypothetical bacterial 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 PF13392: HNH endonuclease (domain)
This is a zinc-binding loop of Fold group 7 as found in endo-deoxy-ribonucleases and HNH nucleases.
Pfam PF03913: Ragweed group 5 pollen allergen (family)
This family contains several ragweed allergens including Amb a 5, Amb t 5 and Amb p 5.
Pfam PF19380: Family of unknown function (DUF5955) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001731) is described by MIBiG as an example of the following biosynthetic class, other (unspecified).
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 PF11958: Domain of unknown function (DUF3472) (family)
This presumed domain is functionally uncharacterised. This domain is found in bacteria, eukaryotes and viruses. This domain is typically between 174 to 190 amino acids in length. This domain has a single completely conserved residue G 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 PF03295: Poxvirus trans-activator protein A1 C-terminal (family)
Late transcription factor VLTF-2, acts with RNA polymerase to initiate transcription from late gene promoters .
Pfam PF10446: Protein of unknown function (DUF2457) (family)
This is a family of uncharacterised 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 PF05186: Dpy-30 motif (conserved_site)
This motif is found in a wide variety of domain contexts. It is found in the Dpy-30 proteins hence the motifs name. It is about 40 residues long and is probably formed of two alpha-helices. It may be a dimerisation motif analogous to [pfam:PF02197] (Bateman A pers obs).
Pfam PF01177: Asp/Glu/Hydantoin racemase (family)
This family contains aspartate racemase, maleate isomerases [ec:5.2.1.1], glutamate racemase, hydantoin racemase and arylmalonate decarboxylase [ec:4.1.1.76].
Pfam PF03657: UPF0113 PUA domain (domain)
This entry represents the PUA (PseudoUridine synthase and Archaeosine transglycosylase) domain found in 60S ribosome subunit biogenesis protein NIP7, some UPF0113 family members, such as KD93, and similar proteins found in eukaryotes and some archaeal species . PUA domains are predicted to bind RNA molecules with complex folded structures . NIP7 is required for efficient 60S ribosome subunit biogenesis and has been shown to interact with another essential nucleolar protein, Nop8p, and the exosome subunit Rrp43p. These proteins are required for 60S subunit synthesis and may be part of a dynamic complex involved in this process.

Nip7 orthologues share a two-domain architecture with the C-terminal PUA domain mediating interaction with RNA, suggesting that Nip7 is an adaptor protein with the C-terminal domain interacting with RNA targets and the N-terminal domain mediating interaction with protein targets. Structural analyses of the RNA-interacting surfaces of the orthologues from Saccharomyces cerevisiae and Pyrococcus abyssi Nip7 indicate that, in the archaeal PUA domain, C-terminal positively charged residues (arginines and lysines) are involved in RNA interaction while equivalent positions in eukaryotic orthologues are occupied by mostly hydrophobic residues. Both proteins can bind specifically to polyuridine, and RNA interaction requires specific residues of the PUA domain as determined by site-directed mutagenesis .
Pfam PF01033: Somatomedin B domain (family)
Somatomedin B (SMB), a serum factor of unknown function, is a small cysteine-rich peptide, derived proteolytically from the N terminus of the cell-substrate adhesion protein vitronectin . Cys-rich somatomedin B-like domains are found in a number of proteins , including ectonucleotide pyrophosphatase/phosphodiesterase family member proteins (previously known as plasma-cell membrane glycoprotein)  and placental protein 11 (also known as Poly(U)-specific endoribonuclease), which appears to possess amidolytic activity.

The SMB domain of vitronectin has been demonstrated to interact with both the urokinase receptor and the plasminogen activator inhibitor-1 (PAI-1) and the conserved cysteines of the NPP1 somatomedin B-like domain have been shown to mediate homodimerisation .

The SMB domain contains eight Cys residues, arranged into four disulphide bonds. It has been suggested that the active SMB domain may be permitted considerable disulphide bond heterogeneity or variability, provided that the Cys25-Cys31 disulphide bond is preserved. The three dimensional structure of the SMB domain is extremely compact and the disulphide bonds are packed in the centre of the domain forming a covalently bonded core . The structure of the SMB domain presents a new protein fold, with the only ordered secondary structure being a single-turn Î±-helix and a single-turn 3(10)-helix .
Wikipedia: Somatomedin B is a serum factor of unknown function, is a small cysteine-rich peptide, derived proteolytically from the N-terminus of the cell-substrate adhesion protein vitronectin. Cys-rich somatomedin B-like domains are found in a number of proteins, including plasma-cell membrane glycoprotein and placental protein 11.
Pfam PF23594: 26S proteasome regulatory subunit RPN11 C-terminal domain (domain)
This entry represents the C-terminal helical region of 26S proteosomal subunits. This region is involved in forming a helical bundle with other RPN subunits to help with assembly of the proteosome lid.
Pfam PF12503: Cucumber mosaic virus 1a protein C terminal (family)
This domain family is found in viruses, and is approximately 90 amino acids in length. The family is found in association with [pfam:PF01443], [pfam:PF01660]. There is a conserved GLG sequence motif. 1a protein is the major virulence factor of the cucumber mosaic virus (CMV). The Ns strain of CMV causes necrotic lesions to Nicotiana spp. while other strains cause systemic mosaic. The determinant of the pathogenesis of these different strains is the specific amino acid residue at the 461 residue of the 1a protein.
Pfam PF19331: Methylcrotonoyl-CoA carboxylase subunit alpha BT domain (domain)
This family represents the BT domain in the methylcrotonoyl-CoA carboxylase subunit alpha, located between the biotin carboxylase (BC) and biotin carboxyl carrier protein (BCCP) domains. This domain mediates crucial interactions between the BC domain in the the alpha subunit and the carboxyltransferase (CT) domain in the beta subunit of this enzyme which are based on ion-pair, hydrogen-bonding and hydrophobic interactions. This domain has a backbone fold with a long helix surrounded by an eight-stranded anti-parallel beta barrel. There is a hook comprising the C-terminal part of the helix and the loop connecting it to the first strand of the beta barrel, which appears to have a central role in alpha and beta subunits interactions.
Pfam PF01333: Apocytochrome F, C-terminal (domain)
This is a sub-family of cytochrome C.  See [pfam:PF00034].
Wikipedia: Cytochrome f is the largest subunit of cytochrome b6f complex. In its structure and functions, the cytochrome b6f complex bears extensive analogy to the cytochrome bc1 complex of mitochondria and photosynthetic purple bacteria. Cytochrome f plays a role analogous to that of cytochrome c1, in spite of their different structures.
Pfam PF00636: Ribonuclease III domain (family)
This domain is found in eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease . Prokaryotic RNAse III is important in post-transcriptional control of mRNA stability and translational efficiency. It is involved in the processing of ribosomal RNA precursors. Prokaryotic RNAse III also plays a role in the maturation of tRNA precursors and in the processing of phage and plasmid transcripts. Eukaryotic RNase III's participate (through direct cleavage) in rRNA processing, in processing of small nucleolar RNAs (snoRNAs) and snRNA's (components of the spliceosome). In eukaryotes RNase III or RNaseIII like enzymes such as Dicer are involved in RNAi (RNA interference) and miRNA (micro-RNA) gene silencing .
Wikipedia: Ribonuclease III (RNase III or RNase C)(BRENDA 3.1.26.3) is a type of ribonuclease that recognizes dsRNA and cleaves it at specific targeted locations to transform them into mature RNAs. These enzymes are a group of endoribonucleases that are characterized by their ribonuclease domain, which is labelled the RNase III domain. They are ubiquitous compounds in the cell and play a major role in pathways such as RNA precursor synthesis, RNA Silencing, and the pnp autoregulatory mechanism.
Pfam PF24853: Domain of unknown function (DUF7727) (domain)
This domain is found in uncharacterised fungal proteins. It has detectable similarity to proteins members of the Cytochrome b558 subunit alpha family and it is predicted to adopt similar structure composed of four helices.
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 PF00962: Adenosine deaminase (domain)
This entry represents the main structural domain of adenosine deaminase proteins.
Adenosine deaminases (3.5.4.4) are monomeric zinc dependent enzymes involved in purine metabolism. They are required for the breakdown of adenosine from food and for the turnover of nucleic acids in tissues. Adenosine deaminases convert adenosine to the related nucleoside inosine by the substitution of the amino group for a hydroxyl group. These enzymes are distantly related to AMP deaminases  as they share three regions of sequence similarities; these regions are centred on residues which are proposed to play an important role in the catalytic mechanism of these two enzymes.

This entry also includes a group of adenine deaminases more related to the bacterial and eukaryotic adenosine deaminases than to Bacillus subtilis adenine deaminase and its bacterial homologues . Adenine deaminase catalyses the hydrolytic deamination of adenine to hypoxanthine.
Wikipedia: Adenosine deaminase is an enzyme involved in purine metabolism. It is needed for the breakdown of adenosine from food and for the turnover of nucleic acids in tissues.