SII-SWORD/CoKE huggingface dataset:
Pfam PF11885: Protein of unknown function (DUF3405) (family)
This family of proteins are functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 636 to 810 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 PF20407: Domain of unknown function (DUF1583_N) (domain)
Most of these Rhodopirellula baltica hypothetical proteins also match [pfam:PF07619].
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 PF18320: Csc2 Crispr (family)
The Csc2 Crispr family of proteins forms a core RNA recognition motif-like domain, flanked by three peripheral insertion domains: a lid domain, a Zinc-binding domain and a helical domain. The CRISPR-Cas system is possibly a mechanism of defence against invading pathogens and plasmids that functions analogously to the RNA interference (RNAi) systems in eukaryotes.
Pfam PF10851: Protein of unknown function (DUF2652) (family)
This 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 PF03978: Borrelia burgdorferi REV protein (family)
This family consists of several REV proteins from Borrelia burgdorferi (Lyme disease spirochete). The function of REV is unknown although it known that gene is induced during the ingesting of host blood suggesting a role in the metabolic activation of borreliae to adapt to physiological stimuli.
Pfam PF17696: Another-regulin-like (family)
This is a family of short proteins from vertebrates, including mouse Another-regulin (ALN, previously known as the uncharacterised C4orf3 homolog). This protein is a SERCA regulator. The C-terminal has a strongly conserved WxxxW motif and is predicted to adopt an alpha-helical configuration.
Pfam PF20833: RNase E/G, Thioredoxin-like domain (domain)
Both RNase E and its homologue RNase G are endoribonucleases that play central roles in RNA processing. RNase E shows two globular domains. This entry represents the smaller domain, which shows a thioredoxin-like fold.
Pfam PF09086: Domain of unknown function (DUF1924) (domain)
This domain is found in a set of bacterial proteins, including Cytochrome c-type protein. It is functionally uncharacterised.
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 PF07430: Phloem filament protein PP1 cystatin-like domain (domain)
This domain represents a conserved region related to cystatins. Eight copies of which are found within the plant phloem filament protein PP1. This is one of the constituents of the proteinaceous filaments found in the sieve elements of Cucurbita phloem.
Pfam PF02906: Iron only hydrogenase large subunit, C-terminal domain (domain)
Proteins containing this domain may be involved in the mechanism of biological hydrogen activation and contain 4FE-4S clusters. They can use molecular hydrogen for the reduction of a variety of substances. This domain consists of two intertwined Î±/Î² subdomains with FE-S cluster located at the interface between these subdomains .
Pfam PF03823: Neurokinin B (family)
Tachykinins  are a group of biologically active peptides which excite neurons, evoke behavioral responses, are potent vasodilatators and contract (directly or indirectly) many smooth muscles. This family includes neurokinin B (also known as Tachykinin-3), as well as many other peptides. Like other tachykinins, neurokinins are synthesized as larger protein precursors that are enzymatically converted to their mature forms. Neurokinin B is a critical central regulator of human gonadal function .
Pfam PF16238: Domain of unknown function (DUF4897) (family)
This is a small family of uncharacterised proteins of around 200 residues  in length, found in various archaeal and bacterial species. The function of this family is unknown.
Pfam PF14302: Domain of unknown function (DUF4377) (family)
This domain family is found in bacteria and archaea, and is 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 PF02081: Tryptophan RNA-binding attenuator protein (domain)
The tryptophan RNA-binding attenuation protein (TRAP) regulates expression of the tryptophan biosynthetic genes in Bacillus sp. by binding to the leader region of the nascent trp operon mRNA . The crystal structure of the Trp RNA-binding attenuation protein of Bacillus subtilis (mtrB, P19466) has been solved . TRAP forms an oligomeric ring consisting of 11 single-domain subunits, where each subunit adopts a double-stranded Î²-helix structure with the appearance of a Î²-sandwich of distinct architecture and jelly-roll fold. The 11 subunits are stabilised by 11 inter-subunit strands, forming a Î²-wheel with a large central hole. TRAP is activated by binding to tryptophan in clefts between adjacent Î²-strands, which induces conformational changes in the protein. Activated TRAP binds an mRNA target sequence consisting of 11 (G/U)AG repeats, separated by 2-3 spacer nucleotides. The spacer nucleotides do not make direct contact with the TRAP protein, but they do influence the conformation of the RNA, which might influence the specificity of TRAP .
This entry represents the structural domain in the TRAP family of proteins.
Wikipedia: The Tryptophan operon leader is an RNA element found at the 5′ of some bacterial tryptophan operons. The leader sequence can form two different structures known as the terminator and the anti-terminator, based on the Tryptophan amounts in the cell. The leader also codes for very short peptide sequence that is rich in tryptophan. The terminator structure is recognised as a termination signal for RNA polymerase and the operon is not transcribed. This structure forms when the cell has an excess of tryptophan and ribosome movement over the leader transcript is not impeded. When there is a deficiency of the charged tryptophanyl tRNA the ribosome translating the leader peptide stalls and the antiterminator structure can form. This allows RNA polymerase to transcribe the operon.
Pfam PF11355: Protein of unknown function (DUF3157) (family)
This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
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 PF24677: Domain of unknown function (DUF7657) (domain)
This domain is found in uncharacterised bacterial proteins. It contains a semi-conserved sequence motif TxYPGxR. It is likely that this domain is a transmembrane domain composed of alpha-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 PF08508: Fungal domain of unknown function (DUF1746) (domain)
This is a fungal domain of unknown function. This domain can be found in DSC E3 ubiquitin ligase complex subunit 4 (Dsc4) from S. pombe, a component of the DSC E3 ubiquitin ligase complex required for the sre1 transcriptional activator proteolytic cleavage to release the soluble transcription factor from the membrane in low oxygen or sterol conditions. The complex plays also an important role in the multivesicular body (MVB) pathway and functions in a post-endoplasmic reticulum pathway for protein degradation. This domain is also found in GLD1 from S. cerevisiae, also a component of the DSC E3 ubiquitin ligase complex involved in the targeting of the DSC complex to the Golgi apparatus and endosome membranes via the AP3 pathway to ubiquitinate Golgi/endosome membrane 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 PF14552: Tautomerase enzyme (domain)
Members of the tautomerase superfamily (TSF) are characterised by a Î²-Î±-Î² building block and a catalytic amino terminal proline . There are five known TSF families, which are named for the first characterised member .

This entry represents the malonate semialdehyde decarboxylase (MSAD) family . MSAD is part of a bacterial pathway for the degradation of the soil fumigant known as 1,3-dichloropropene . There are five homologues identified, including YusQ/YodA/YrdN from Bacillus subtilis, IolK from Lactobacillus casei strain BL23, and Bp4401 from Burkholderia phymatum. IolK was found in a degradative pathway for myo-inositol, but its disruption does not affect growth or myo-inositol utilization . Bp4401 has a modest hydratase activity. YrdN, YodA, and IolK have comparable decarboxylase and hydratase activities, but this activity is missing in YusQ and Bp4401 .
Wikipedia: 4-Oxalocrotonate tautomerase or 4-OT is an enzyme that converts 2-hydroxymuconate to the αβ-unsaturated ketone, 2-oxo-3-hexenedioate. This enzyme forms part of a bacterial metabolic pathway that oxidatively catabolizes toluene, o-xylene, 3-ethyltoluene, and 1,2,4-trimethylbenzene into intermediates of the citric acid cycle. With a monomer size of just 62 amino acid residues, the 4-Oxalocrotonate tautomerase is one of the smallest enzyme subunits known. However, in solution, the enzyme forms a hexamer of six identical subunits, so the active site may be formed by amino acid residues from several subunits. This enzyme is also unusual in that it uses a proline residue at the amino terminus as an active site residue.
Pfam PF05437: Branched-chain amino acid transport protein (AzlD) (family)
This family consists of a number of bacterial and archaeal branched-chain amino acid transport proteins. AzlD is known to be involved in conferring resistance to 4-azaleucine although its exact role is uncertain.
Pfam PF20037: Family of unknown function (DUF6440) (family)
This family of proteins is functionally uncharacterised. This family of proteins is mainly found in Firmicutes but also in viruses. Proteins in this family are approximately 60 amino acids in length and they contain three conserved motifs: RF, TGxxY and TPLLD. Some members of this family are probably Xylan 1,4-beta-xylosidases.
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 PF06752: Enhancer of Polycomb C-terminus (family)
This family represents the C-terminus of eukaryotic enhancer of polycomb  proteins, which have roles in heterochromatin formation. This family contains several conserved motifs.
Pfam PF06424: PRP1 splicing factor, N-terminal (domain)
This domain is specific to the N-terminal part of the prp1 splicing factor, which is involved in mRNA splicing (and possibly also poly(A)+ RNA nuclear export and cell cycle progression). This domain is specific to the N terminus of the RNA splicing factor encoded by prp1. It is involved in mRNA splicing and possibly also poly(A)and RNA nuclear export and cell cycle progression.
Pfam PF22462: Ctf19, second RWD domain (domain)
This entry represents the second occurrence of the RWD domain within the Ctf19 subunit of the inner kinetochore in Kluyveromyces lactis. Ctf19 is a component of the constitutive centromere associated network (CCAN), which forms the structural basis of the kinetochore. The CCAN governs the timing of kinetochore assembly, establishes its position through interaction with a specialized nucleosome containing the histone H3 variant Cse4/CENP-A, and determines the arrangement of the microtubule attachment machinery. In this way, eukaryotic kinetochores establish a connection between spindle microtubules and chromosomal centromeres.
Pfam PF11561: Single strand annealing-weakened 1 (family)
This family of yeast proteins is involved in single-strand-annealing, or SSA. SSA entails multiple steps: end resection and ssDNA formation; annealing of complementary ssDNAs; removal of 3' single-stranded non-homologous tails; gap fill-in synthesis; and ligation. Saw1 in combination with Slx4 catalyses the 3' non-homologous tail removal during recombination. Saw1 interacts physically with Rad1/Rad10, Msh2/Msh3, and Rad52 proteins, and works by targeting Rad1/Rad10 to Rad52-coated recombination intermediates.
Pfam PF00208: Glutamate/Leucine/Phenylalanine/Valine dehydrogenase (domain)
Glutamate, leucine, phenylalanine, valine and tryptophan dehydrogenases are structurally and functionally related. They contain a Gly-rich region containing a conserved Lys residue, which has been implicated in the catalytic activity, in each case a reversible oxidative deamination reaction.

Glutamate dehydrogenases (1.4.1.2, 1.4.1.3, and 1.4.1.4) (GluDH) are enzymes that catalyse the NAD-and/or NADP-dependent reversible deamination of L-glutamate into alpha-ketoglutarate . GluDH isozymes are generally involved with either ammonia assimilation or glutamate catabolism. Two separate enzymes are present in yeasts: the NADP-dependent enzyme, which catalyses the amination of alpha-ketoglutarate to L-glutamate; and the NAD-dependent enzyme, which catalyses the reverse reaction  -this form links the L-amino acids with the Krebs cycle, which provides a major pathway for metabolic interconversion of alpha-amino acids and alpha-keto acids . In rice, glutamate dehydrogenase 3 is mitochondrial.

Leucine dehydrogenase (1.4.1.9) (LeuDH) is a NAD-dependent enzyme that catalyses the reversible deamination of leucine and several other aliphatic amino acids to their keto analogues . Each subunit of this octameric enzyme from Bacillus sphaericus contains 364 amino acids and folds into two domains, separated by a deep cleft. The nicotinamide ring of the NAD+ cofactor binds deep in this cleft, which is thought to close during the hydride transfer step of the catalytic cycle.

Phenylalanine dehydrogenase (1.4.1.20) (PheDH) is na NAD-dependent enzyme that catalyses the reversible deamidation of L-phenylalanine into phenyl-pyruvate .

Valine dehydrogenase (1.4.1.8) (ValDH) is an NADP-dependent enzyme that catalyses the reversible deamidation of L-valine into 3-methyl-2-oxobutanoate .

L-tryptophan dehydrogenase catalyses the reversible oxidative deamination of L-tryptophan to indole-3-pyruvate in the presence of NAD+ .
This entry represents the C-terminal domain of these proteins.
Wikipedia: In molecular biology, the ELFV dehydrogenase family of enzymes include glutamate, leucine, phenylalanine and valine dehydrogenases. These enzymes are structurally and functionally related. They contain a Gly-rich region containing a conserved Lys residue, which has been implicated in the catalytic activity, in each case a reversible oxidative deamination reaction.
Pfam PF17194: Transcriptional regulator, AbiEi antitoxin N-terminal domain (domain)
AbiEi_3 is the cognate antitoxin of the type IV toxin-antitoxin 'innate immunity' bacterial abortive infection (Abi) system that protects bacteria from the spread of a phage infection. The Abi system is activated upon infection with phage to abort the cell thus preventing the spread of phage through viral replication. There are some 20 or more Abis, and they are predominantly plasmid-encoded lactococcal systems. TA, toxin-antitoxin, systems on plasmids function by killing cells that lose the plasmid upon division. AbiE phage resistance systems function as novel Type IV TAs and are widespread in bacteria and archaea. The cognate antitoxin is [pfam:PF13338].
Pfam PF16350: FAD dependent oxidoreductase central domain (family)
This domain occurs in several FAD dependent oxidoreductases: Sarcosine dehydrogenase, Dimethylglycine dehydrogenase and Dimethylglycine dehydrogenase. It is situated between the DAO domain ([pfam:PF01266]) and the GCV_T domain ([pfam:PF01571]).
Pfam PF00723: Glycosyl hydrolases family 15 (repeat)
In higher organisms this family is represented by phosphorylase kinase subunits.
Wikipedia: In molecular biology, glycoside hydrolase family 15 is a family of glycoside hydrolases.
Pfam PF20342: Family of unknown function (DUF6637) (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 PF10326: Serpentine type 7TM GPCR chemoreceptor Str (family)
Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Str is a member of the Str superfamily of chemoreceptors. Almost a quarter (22.5%) of str and srj family genes and pseudogenes in C. elegans appear to have been newly formed by gene duplications since the species split.  Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Pfam PF00839: Cysteine rich repeat (family)
This cysteine rich repeat contains four cysteines.  It is found in multiple copies in a protein that binds to fibroblast growth factors. The repeat is also found in MG160 and E-selectin ligand (ESL-1).
Pfam PF22329: Negative regulator of ofd1, C-terminal (repeat)
This entry represents the C-terminal region of fission yeast Negative regulator of ofd1 (Nro1) whose alpha-helices are grouped in six helical hairpins.
Pfam PF04191: Phospholipid methyltransferase (family)
The S. cerevisiae phospholipid methyltransferase ([ec:2.1.1.16]) has a broad substrate specificity of unsaturated phospholipids.
Pfam PF06373: Cocaine and amphetamine regulated transcript protein (CART) (family)
This family consists of several cocaine and amphetamine regulated transcript type I protein (CART) sequences. Cocaine and amphetamine regulated transcript (CART) peptide has been shown to be an anorectic peptide that inhibits both normal and starvation-induced feeding and completely blocks the feeding response induced by neuropeptide Y and regulated by leptin in the hypothalamus. The C-terminal part containing the three disulfide bridges is the biologically active part of the molecule affecting food intake. The solution structure of the active part of CART has a fold equivalent to other functionally distinct small proteins. CART consists mainly of turns and loops spanned by a compact framework composed by a few small stretches of antiparallel beta-sheet common to cystine knots.
Wikipedia: Cocaine- and amphetamine-regulated transcript, also known as CART, is a neuropeptide protein that in humans is encoded by the CARTPT gene. CART appears to have roles in reward, feeding, and stress, and it has the functional properties of an endogenous psychostimulant.
Pfam PF07244: Surface antigen variable number repeat (domain)
This family is found primarily in bacterial surface antigens, normally as variable number repeats at the N-terminus. The C-terminus of these proteins is normally represented by [pfam:PF01103]. The alignment centres on a -GY- or -GF- motif. Some members of this family are found in the mitochondria. It is predicted to have a mixed alpha/beta secondary structure.
Pfam PF14019: Protein of unknown function (DUF4235) (family)
This family of integral membrane proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 88 and 119 amino acids in length.
Pfam PF25011: Vacuolar sorting receptor thioredoxin-like domain (domain)
This entry represents the thioredoxin-like domain found in vacuolar sorting receptors (VSRs) from plants. It is located in the central region of VSRs, between the N-terminal protease-associated (PA) domain and the C-terminal epidermal growth factor (EGF)-like domains. The domain has a thioredoxin-like fold but its exact function in VSRs is not fully understood. It may be involved in protein-protein interactions or potentially in disulfide bond isomerization of cargo proteins. This domain is found in VSR1 through VSR7 in Arabidopsis thaliana.  The domain contains multiple disulfide bonds, including a CxxxC motif that is structurally conserved with the CxxC active site motif found in canonical thioredoxins. However, whether this domain has catalytic activity remains to be determined. The domain is involved in intermolecular interactions that contribute to the formation of VSR trimers, which may be important for VSR function.  This domain may play a role in the pH and calcium-dependent binding and release of cargo proteins by VSRs during vacuolar protein sorting.
Pfam PF11513: Thermoplasma acidophilum protein TA0956 (family)
TA0956 is a protein from Thermoplasma acidophilum which currently has no known function however the structure has been determined. The protein has a two-layered alpha/beta-sandwich topology and is a putative Elongation factor 1-alpha binding motif.