SII-SWORD/CoKE huggingface dataset:
Pfam PF24893: Domain of unknown function (DUF7743) (domain)
This is a presumed domain of unknown function found in uncharacterised proteins from Dictyosteliales. It may adopt a Ig-like 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 PF02373: JmjC domain, hydroxylase (domain)
The JmjC domain belongs to the Cupin superfamily. JmjC-domain proteins may be protein hydroxylases that catalyse a novel histone modification. This is confirmed to be a hydroxylase: the human JmjC protein named Tyw5p unexpectedly acts in the biosynthesis of a hypermodified nucleoside, hydroxy-wybutosine, in tRNA-Phe by catalysing hydroxylation.
Pfam PF04444: Catechol dioxygenase N terminus (family)
This family consists of the N termini of catechol, chlorocatechol or  hydroxyquinol 1,2-dioxygenase proteins.  This region is always found  adjacent to the dioxygenase domain ([pfam:PF00775]).
Wikipedia: Dioxygenases are oxidoreductase enzymes. Aerobic life, from simple single-celled bacteria species to complex eukaryotic organisms, has evolved to depend on the oxidizing power of dioxygen in various metabolic pathways. From energetic adenosine triphosphate (ATP) generation to xenobiotic degradation, the use of dioxygen as a biological oxidant is widespread and varied in the exact mechanism of its use. Enzymes employ many different schemes to use dioxygen, and this largely depends on the substrate and reaction at hand.
Pfam PF11852: Alpha-1,6-glucosidases, pullulanase-type, C-terminal (family)
This entry represents the uncharacterised C-terminal domain of secreted (or membrane-anchored) pullulanases of Gram-negative bacteria and pullulanase-type starch debranching enzymes of plants. Both enzymes hydrolyse alpha-1,6 glycosidic linkages. Pullulan is an unusual, industrially important polysaccharide in which short alpha-1,4 chains (maltotriose) are connected in alpha-1,6 linkages. Enzymes that cleave alpha-1,6 linkages in pullulan and release maltotriose are called pullulanases although pullulan itself may not be the natural substrate.
Pfam PF06949: Protein of unknown function (DUF1292) (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 PF24805: EIF3I (repeat)
This entry includes EIF3I, a component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is required for several steps in the initiation of protein synthesis. The eIF-3 complex specifically targets and initiates translation of a subset of mRNAs involved in cell proliferation including cell cycling, differentiation and apoptosis, and uses different modes of RNA stem-loop binding to exert either translational activation or repression.
Pfam PF20831: Reovirus VP3 protein, Methyltransferase domain 1 (domain)
Cytoplasmic polyhedrosis virus (CPV) has a turreted single-layer capsid consisting of 12 pentameric turrets on the five-fold vertices. Each turret has one Turret protein (TP), also known as VP3, which shows a polyhedrin-binding domain (PBD), a guanylyltransferase (GTase) domain ([pfam:PF20790]), two methyltransferase domains and a bridge domain. This entry represents the first methyltransferase domain (MTase-1), which has the small brace domain inserted on it.
Pfam PF20849: Protelomerase, muzzle domain (domain)
This domain is found in Protelomerase from Klebsiella phage phiKO2 (TelK) and similar proteins from tailed bacteriophages and bacterial prophages mainly from Gammaproteobacteria. TelK is a hairpin telomere resolvase with DNA cleavage-rejoining activity that resolves the catenated circular dimer produced from the bidirectional replication of a chromosome. The core of the TelK monomer consists of an N-terminal domain and a catalytic domain connected by a long alpha- helical linker. However, there are two extensions of the protein: a C-terminal DNA binding domain named the stirrup ([pfam:PF20818]) and an N-terminal domain. The latter has an insertion termed the muzzle (this entry), which folds into two long alpha-helices. This protruding element is packed against the DNA-binding catalytic and N-terminal domains of the opposite subunit in each dimer.
Pfam PF12489: Nuclear coactivator (family)
This domain family is found in eukaryotes, and is typically between 127 and 138 amino acids in length. This family is ARA70, a nuclear coactivator which interacts with peroxisome proliferator-activated receptor gamma (PPARgamma) to regulate transcription and the addition of the PPARgamma ligand (prostaglandin J2) enhances this interaction.
Pfam PF03458: Glycine transporter (domain)
This domain contains three transmembrane helices. Proteins containing this domain are important for glycine utilisation, being identified as glycine transporters. Some members of the family are also important for alanine utilisation. In these proteins this domain is found in pairs. An archaeal member of this family which contains this domain is a TRIC-type potassium channel.
Pfam PF02372: Interleukin 15 (domain)
Interleukin-15 (IL-15) is a cytokine that possesses a variety of biological functions, including stimulation and maintenance of cellular immune responses. Structurally these proteins are short-chain 4-helical cytokines.
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 PF13557: Putative MetA-pathway of phenol degradation (family)
This family includes the functional amyloid transporter FapF from Pseudomonas aeruginosa and similar bacterial proteins. FapF transports fibril components across the outer membrane . Many sequences in this family are classified by TCDB as belonging to the putative Î²-barrel porin/alpha amylase or MetA-pathway of phenol degradation superfamily, including A5W3Z9 from Pseudomonas putida (4rl8).
Pfam PF23174: ILI bHLH domain (domain)
This bHLH domain is found in the family of Increased Leaf Inclination (ILI) family of atypical bHLH transcription factors in rice. The members of this family ILI1/2/3/4/5/6/7 lack the basic region for DNA binding and have been implicated in brassinosteroids signaling. This domain is also found in Arabidopsis thaliana Paclobutrazol Resistance proteins PRE1/2/3/4/5/6 that have a regulatory role in various aspects of gibberellin-dependent growth and development.
Pfam PF01363: FYVE zinc finger (domain)
The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn++ ions. The FYVE finger has eight potential zinc coordinating cysteine positions.  Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue.  We have included members which do not conserve these histidine residues but are clearly related.
Wikipedia: In molecular biology the FYVE zinc finger domain is named after the four cysteine-rich proteins: Fab 1, YOTB, Vac 1, and EEA1, in which it has been found. FYVE domains bind phosphatidylinositol 3-phosphate, in a way dependent on its metal ion coordination and basic amino acids. The FYVE domain inserts into cell membranes in a pH-dependent manner. The FYVE domain has been connected to vacuolar protein sorting and endosome function.
Pfam PF22529: Family of unknown function (DUF7001) (family)
This is a family of uncharacterised proteins found in Archaea. They have sequence similarity to Zincin-like metalloproteases and are predicted to adopt the same structure. Only one of the two zinc binding sites are conserved suggesting that these proteins may possess different 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 PF08291: Peptidase M15 (domain)
This entry represents the C-terminal domain of zinc D-Ala-D-Ala carboxypeptidases from Streptomyces species and non-peptidase homologues that belong to MEROPS peptidase family M15 (subfamily M15A, clan MD) .
Pfam PF17193: MukF C-terminal domain (domain)
This presumed domain is found at the C-terminus of the MukF protein.
Pfam PF14753: Protein FAM221A/B (family)
This family of proteins is found in eukaryotes. Proteins  in this family are typically between 99 and 305 amino  acids in length.
Pfam PF08204: CD47 immunoglobulin-like domain (domain)
This family represents the CD47 leukocyte antigen V-set like Ig domain.
Pfam PF11676: Protein of unknown function (DUF3272) (family)
This family of proteins with unknown function appears to be restricted to Streptococcus.
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 PF03950: tRNA synthetases class I (E and Q), anti-codon binding domain (domain)
This entry represents the first of the two ribosomal L25-like domains of the anticodon binding domain. Other tRNA synthetase sub-families are too dissimilar to be included. This family includes only glutamyl and glutaminyl tRNA synthetases. In some organisms, a single glutamyl-tRNA synthetase aminoacylates both tRNA(Glu) and tRNA(Gln).
Pfam PF12799: Leucine Rich repeats (2 copies) (repeat)
Leucine rich repeats are short sequence motifs present in a number of proteins with diverse functions and cellular locations. These repeats are usually involved in protein-protein interactions.  Each Leucine Rich Repeat is composed of a beta-alpha unit. These units form elongated non-globular structures. Leucine Rich Repeats are often flanked by cysteine rich domains.
Wikipedia: A leucine-rich repeat (LRR) is a protein structural motif that forms an α/β horseshoe fold. It is composed of repeating 20–30 amino acid stretches that are unusually rich in the hydrophobic amino acid leucine. These tandem repeats commonly fold together to form a solenoid protein domain, termed leucine-rich repeat domain. Typically, each repeat unit has beta strand-turn-alpha helix structure, and the assembled domain, composed of many such repeats, has a horseshoe shape with an interior parallel beta sheet and an exterior array of helices. One face of the beta sheet and one side of the helix array are exposed to solvent and are therefore dominated by hydrophilic residues. The region between the helices and sheets is the protein's hydrophobic core and is tightly sterically packed with leucine residues.
Pfam PF08857: Putative ParB-like nuclease (domain)
This domain is probably distantly related to [pfam:PF02195]. Suggesting these uncharacterised proteins have a nuclease function.
Pfam PF01837: Homocysteine biosynthesis enzyme, sulfur-incorporation (domain)
This presumed domain is about is about 360 residues long. The function of this domain is unknown. It is found in some proteins that have two C-terminal CBS [pfam:PF00571] domains. There are also proteins that contain two inserted Fe4S domains near the C-terminal end of the domain.  The protein [swissprot:O26943] has been misannotated as an inosine monophosphate dehydrogenase based on the similarity to the CBS domains. Based on genetic analyses in the methanogen Methanosarcina acetivorans, this family is a key component of the metabolic network for sulfide assimilation and trafficking in methanogens. It is essential to a novel, O-acetylhomoserine sulfhydrylase-independent pathway for homocysteine biosynthesis, and may catalyse sulfur incorporation into the side chain of an as yet unidentified amino acid precursor. The DUF39-CBS and DUF39-ferredoxin architectures repeatedly occur together in the genomes of methanogenic Archaea, suggesting they may be of diverged function. This is consistent with a phylogenetic reconstruction of the DUF39 family, which clearly distinguishes the CBS-associated and ferredoxin-associated DUF39s.
Pfam PF17677: Glycosyl hydrolases family 38 C-terminal beta sandwich domain (domain)
This domain is found at the C-terminal end of various glycosyl hydrolases belonging to family 38. The domain has a beta sandwich fold.
Wikipedia: In molecular biology, glycoside hydrolase family 38 is a family of glycoside hydrolases.
Pfam PF17770: Ribonuclease J C-terminal domain (domain)
This domain is found at the C-terminus of Ribonuclease J proteins. Its function is unknown, but deletion of this domain causes dissociation to monomers.
Pfam PF12599: Protein of unknown function (DUF3768) (family)
This family of proteins is found in bacteria. Proteins in this family are typically between 108 and 129 amino acids in length. There are two conserved sequence motifs: NDP and RVLT.
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 PF18048: TNF receptor-associated factor 6 zinc finger 2 (domain)
This domain is the second of three zinc fingers of Homo sapiens TNF receptor associated factor 6 (TRAF6). TRAF6 mediates Lys63 (K63)-linked polyubiquitination for Necrosis Factor-kappaB activation. The first three residues and the last Cys of finger 1 form a classical type I beta-turn.
Pfam PF08381: Transcription factor regulating root and shoot growth via Pin3 (domain)
The BREVIS RADIX (BRX) domain was characterised as being a transcription factor in plants regulating the extent of cell proliferation and elongation in the growth zone of the root. BRX is rate limiting for auxin-responsive gene-expression by mediating cross-talk with the brassino-steroid pathway.  BRX has a ubiquitous, although quantitatively variable role in modulating the growth rate in both the root and the shoot. The family features a short region of alpha-helix, approximately 60 residues in length, which is found repeated up to three times. BRX is expressed in the vasculature and is rate-limiting for transcriptional auxin action.
Pfam PF05185: PRMT5 arginine-N-methyltransferase (domain)
The human homologue of yeast Skb1 (Shk1 kinase-binding protein 1) is PRMT5, an arginine-N-methyltransferase.  These proteins appear to be key mitotic regulators. They play a role in Jak signalling in higher eukaryotes.
Pfam PF18663: Pallilysin beta barrel domain (domain)
The Treponema pallidum protein, Tp0751 (also known as pallilysin), possesses adhesive properties and has been previously reported to mediate attachment to the host extracellular matrix components laminin, fibronectin, and fibrinogen. Tp0751 adopts an eight-stranded beta-barrel with a profile of short conserved regions consistent with a non-canonical lipocalin fold. Lipocalins, along with fatty acid-binding proteins and avidins, are members of the calycin superfamily, which is defined by the distinct features of a central beta-barrel and a key structural signature consisting of three short conserved regions (SCR1, SCR2, and SCR3). However, Tp0751 does not contain all three conserved regions, hence it is considered an outlier to canonical lipocalins. In SCR1, there is a GxW motif.
Pfam PF20825: Saposin-like domain (family)
This entry represents a saposin-like domain found at the N-terminus of some SGNH hydrolase enzymes such as Acyloxyacyl hydrolase. In this enzyme the substrate's lipid moiety is accommodated in a large hydrophobic pocket formed by the saposin and catalytic domains with a secondary acyl chain inserted into a narrow lateral hydrophobic tunnel at the active site.
Wikipedia: The saposin domains refers to two evolutionally-conserved protein domains found in saposin and related proteins (SAPLIP). Saposins are small lysosomal proteins that serve as activators of various lysosomal lipid-degrading enzymes. They probably act by isolating the lipid substrate from the membrane surroundings, thus making it more accessible to the soluble degradative enzymes. All mammalian saposins are synthesized as a single precursor molecule (prosaposin) which contains four Saposin-B domains, yielding the active saposins after proteolytic cleavage, and two Saposin-A domains that are removed in the activation reaction.
Pfam PF19830: Family of unknown function (DUF6311) (family)
This presumed integral membrane domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 300 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 PF16965: Ceramide synthase regulator (family)
CSG2 is an integral membrane protein with up to 10 transmembrane segments that, when over-expressed, localises to the endoplasmic reticulum.  CSG2 is a family of fungal transmembrane proteins that regulate mannosyl phosphorylinositol ceramide synthase and are thereby implicated in calcium homoeostasis in the cell.
Pfam PF14979: Transmembrane 52 (family)
This family of transmembrane proteins is found in eukaryotes. Proteins in this family are typically between 160 and 236 amino acids in length. There is a conserved LLCG sequence motif. The function of this family is unknown.
Pfam PF15199: D-amino acid oxidase activator (family)
Members of this family were first described as activators of D-amino acid oxidase (DAO), however, it was later found that it acts as a repressor of DAO and SOD1 activity and promote their degradation . It may stimulate the degradation of DDO (D-aspartate oxidase) . DAO catalyzes the oxidative deamination of D-3,4-dihydroxyphenylalanine (D-DOPA) and D-serine, a precursor of dopamine and a participant in glutamatergic transmission, respectively . Variation in the DAO activator gene have been associated with bipolar disorder and major depression , although other studies have cast doubt on such a link .
Wikipedia: D-amino acid oxidase activator is a protein enriched in various parts of brain, spinal cord, and testis. DAOA is thought to interact with D-amino acid oxidase, a peroxisomal enzyme, and its gene was associated with schizophrenia in a number of studies. In separate studies it has been shown to confer susceptibility to bipolar disorder. Therefore, it has been important in researching whether the Kraepelinian dichotomy is genuine. The gene itself was discovered during an investigation of chromosomal 13q22-q34 region, which was previously linked to schizophrenia. G72 is transcribed into several proteins due to alternative splicing; the longest protein is called LG72 and consists of 153 amino acids. Although the protein was initially found to interact with DAO in yeast 2-hybrid experiment, one recent in vivo experiment showed LG72 presence only in mitochondria and failed to confirm the interaction.
Pfam PF05010: Transforming acidic coiled-coil-containing protein (TACC), C-terminal (coiled_coil)
This entry represents a C-terminal domain found in the the proteins TACC 1, 2 and 3 (TACC1-3). TACC1 is found concentrated in the centrosomes of eukaryotes which may play a conserved role in organising centrosomal microtubules. The human TACC proteins have been linked to cancer and TACC2 has been identified as a possible tumour suppressor (AZU-1). TACC 3 from Xenopus laevis, also known as maskin, associates XMAP215 and promotes efficient microtubule elongation during mitosis. Maskin is also found to bind CPEB and elF-4E. Interestingly, the functional homologue (Alp7) in Schizosaccharomyces pombe (not included in this entry) has been shown to be required for organisation of bipolar spindles.
Pfam PF23576: Helicase SEN1 beta-barrel domain (domain)
This domain is found in the yeast Helicase SEN1 and related proteins. SEN1 is an ATP-dependent 5'->3' DNA/RNA helicase required for the expression and maturation of diverse classes of non-protein -coding RNAs like precursor tRNAs, rRNAs and small nuclear (snRNA) and nucleolar (snoRNA) RNAs. It directs RNA polymerase II transcription termination on snoRNAs as well as on several short protein-coding genes. This domain folds into a beta-barrel that has a structural similarity to alanine racemase C-terminal domain.
Pfam PF02061: Lambda Phage CIII (family)
The CIII protein from bacteriophage lambda is an inhibitor of the FtsH peptidase.
Pfam PF15999: Domain of unknown function (DUF4774) (family)
This presumed domain is functionally uncharacterised. This domain family is found in bacteria, eukaryotes and viruses, and is approximately 50 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 PF01423: LSM domain (domain)
The LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) in common, which assemble around the Sm site present in four of the major spliceosomal small nuclear RNAs. The U6 snRNP binds to the LSM (Like Sm) proteins. Sm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Sm proteins. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. This family also includes the bacterial Hfq (host factor Q) proteins. Hfq are also RNA-binding proteins, that form hexameric rings.
Wikipedia: In molecular biology, LSm proteins are a family of RNA-binding proteins found in virtually every cellular organism. LSm is a contraction of 'like Sm', because the first identified members of the LSm protein family were the Sm proteins. LSm proteins are defined by a characteristic three-dimensional structure and their assembly into rings of six or seven individual LSm protein molecules, and play a large number of various roles in mRNA processing and regulation.