SII-SWORD/CoKE huggingface dataset:
Pfam PF24848: Family of unknown function (DUF7723) (domain)
This small family of uncharacterised bacterial proteins are often found adjacent to proteins from [pfam:PF13711]. Structure prediction shows that these proteins are very likely to form a complex.
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 PF24440: Family of unknown function (DUF7559) (family)
This entry represents a small family of uncharacterised proteins found in archaea. They contain two pairs of conserved cysteines that are likely involved in metal coordination. It is predicted to structurally resemble Zinc-beta ribbon domains.
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 PF17684: PH domain of plant-specific actin-binding protein (domain)
This family is a PH domain found on plant-specific actin-binding proteins or SCABs. SCAB proteins bind, bundle and stabilise actin filaments and regulate stomatal movement. The Ig-PH fusion domain is at the C-terminus. This domain adopts the PH fold, of seven beta-strands, beta7-beta13 and two alpha-helices, alpha1 and alpha2 arranged into a beta-barrel. The canonical phosphoinositide-binding pocket of the classic PH domain is degenerate in this fused one, and the charge on the pocket suggest that the Ig-PH domain contains a non-canonical binding site for inositol phosphates.
Pfam PF17446: Late transcription unit A (family)
This is a family of unknown function found in Chlamydia.
Pfam PF10484: Mitochondrial ribosomal protein S23 (family)
MRP-S23 is one of the proteins that makes up the 55S ribosome in eukaryotes from nematodes to humans. It does not appear to carry any common motifs, either RNA binding or ribosomal protein motifs. All of the mammalian MRPs are encoded in nuclear genes that are evolving more rapidly than those encoding cytoplasmic ribosomal proteins. The MRPs are imported into mitochondria where they assemble coordinately with mitochondrially transcribed rRNAs into ribosomes that are responsible for translating the 13 mRNAs for essential proteins of the oxidative phosphorylation system. MRP-S23 is significantly up-regulated in uterine cancer cells.
Pfam PF04158: Sof1-like domain (family)
Sof1 is essential for cell growth and is a component of  the nucleolar rRNA processing machinery.
Pfam PF12977: Domain of Unknown Function with PDB structure (DUF3861) (family)
The 3cjl structure is likely a representative of a new fold with some resemblance to 3-helical bundle folds such as the serum albumin-like fold of SCOP. No significant hits reported by a Dali search. This protein is the first structural representative of a small (about 60 proteins) family of proteins that are found among proteo- and enterobacteria (REF http://www.topsan.org/Proteins/JCSG/3CJL).
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 PF02021: Uncharacterised protein family UPF0102 (family)
The function of this family is unknown.
Pfam PF06686: Stage III sporulation protein AC/AD protein family (family)
This family consists of several bacterial stage III sporulation protein AC (SpoIIIAC) and SpoIIIAD sequences. The exact function of this family is unknown.  SpoIIIAD is the an uncharacterised protein which is part of the spoIIIA operon that acts at sporulation stage III as part of a cascade of events leading to endospore formation. The operon is regulated by sigmaG.
Pfam PF22146: LicP N-terminal prodomain (domain)
LicP is a class II LanP protease that is involved in the biosynthesis of the lantibiotic lichenicidin. This enzyme is an extracellularly located serine protease expressed by some strains of Bacillus licheniformis and undergoes a self-cleavage maturation resulting in two fragments, the N-terminal prodomain and the C-terminal catalytic protease domain. The prodomain folds into a single compact domain consisting of four antiparallel beta-strands interconnected with two helices.
Pfam PF06212: GRIM-19 protein (family)
This family consists of several eukaryotic gene associated with retinoic-interferon-induced mortality 19 (GRIM-19) proteins. GRIM-19, was reported to encode a small protein primarily distributed in the nucleus and was able to promote cell death induced by IFN-beta and RA. A bovine homologue of GRIM-19 was co-purified with mitochondrial NADH:ubiquinone oxidoreductase (complex I) in bovine heart. Therefore, its exact cellular localisation and function are unclear. It has now been discovered that GRIM-19 is a specific interacting protein which negatively regulates Stat3 activity.
Wikipedia: Respiratory complex I, EC 7.1.1.2 is the first large protein complex of the respiratory chains of many organisms from bacteria to humans. It catalyzes the transfer of electrons from NADH to coenzyme Q10 (CoQ10) and translocates protons across the inner mitochondrial membrane in eukaryotes or the plasma membrane of bacteria.
Pfam PF18531: Polo box domain (domain)
In metazoans, Plk4 kinases control daughter centriole assembly. Plk4 homologs have an N-terminal kinase domain, a C-terminal polo box, and a central domain termed the 'cryptic polo box' (CPB) that has been shown to dimerize, to be sufficient for centriole localization and to be required for Plk4 to promote centriole assembly. Probable serine/threonine-protein kinase zyg-1 ([ec:2.7.11.1]) (ZYG-1) is a Plk4 homlog found in C. elegans. Crystal structure for the CPB of C. elegans ZYG-1, reveals that it forms a Z-shaped dimer containing an intermolecular beta-sheet with an extended basic surface patch. Electrostatic interactions between the basic patch on the ZYG-1 CPB dimer and the SPD-2 acidic region dock ZYG-1 onto centrioles to promote new centriole assembly.  ZYG-1 CPB contains two tandem polo boxes (PB1 and PB2), each containing a six-stranded beta-sheet with an alpha-helix packed against one side.
Pfam PF22620: OYE-like second alpha/beta domain (domain)
This domain is found in a group of diverse dehydrogenases from the old yellow enzyme (OYE)-like family, such as histamine dehydrogenase from Nocardioides simplex, trimethylamine dehydrogenase from Methylophilus methylotrophus (sp. W(3)A(1)) and 2-naphthoyl-CoA reductase (NCR), which has been described as a small, second alpha/beta domain.
Pfam PF22868: Protein YmiA-like (family)
This protein family includes Protein YmiA from Escherichia coli and similar sequences found in gammaproteobacteria. YmiA is the 46-residue product of a small open reading frame (smORF). Its specific function is unknown.
Pfam PF08598: Sds3-like (family)
Repression of gene transcription is mediated by histone deacetylases containing repressor-co-repressor complexes, which are recruited to promoters of target genes via interactions with sequence-specific transcription factors. The co-repressor complex contains a core of at least seven proteins. This family represents the conserved region found in Sds3, Dep1 and BRMS1-homologue p40 proteins.
Pfam PF22492: FimA4 pilin C-terminal domain (domain)
This entry represents the C-terminal domain of FimA4 pilin. It folds into a Ig-like beta-sandwich having the characteristic features of the FimA superfamily.
Pfam PF20510: Homogentisate 1,2-dioxygenase N-terminal (domain)
Homogentisate dioxygenase cleaves the aromatic ring during the metabolic degradation of Phe and Tyr. Homogentisate dioxygenase deficiency causes alkaptonuria.  The structure of homogentisate dioxygenase shows that the enzyme forms a hexamer arrangement comprised of a dimer of trimers. The active site iron ion is coordinated near the interface between the trimers. This entry represents the N-terminal domain which forms a jelly roll of beta-strands.
Pfam PF15858: Late cornified envelope protein 6A family (family)
LCE6A is a family of proteins is found in mammals. It was identified in a large-scale screening experiment as being involved in the barrier function of the epidermis.
Pfam PF14735: HAUS augmin-like complex subunit 4 (family)
This family includes HAUS augmin-like complex subunit 4. The HAUS augmin-like complex contributes to mitotic spindle assembly, maintenance of chromosome integrity and completion of cytokinesis.
Pfam PF18439: Ubiquitin-Binding Zinc Finger (domain)
This is ubiquitin-binding zinc finger (UBZ) domain found in DNA polymerase eta ([ec:2.7.7.7]). It is important in the recruitment of the polymerase to the stalled replication machinery in translesion synthesis. The UBZ domain adopts a classical C2H2 zinc-finger structure characterized by a beta-beta-alpha fold.
Pfam PF18460: Heterocyst differentiation regulator C-terminal Hood domain (domain)
This is the C-terminal hood domain found in Heterocyst differentiation control protein (HetR). HetR-C binds to PatS peptide. Two PatS6 peptides bind to the lateral clefts of HetR-Hood domain, and trigger significant conformational changes of the flap domain, resulting in dissociation of the auxiliary alpha-helix and eventually release of HetR from the DNA major grove and termination of transcription.
Pfam PF00531: Death domain (domain)
The death domain (DD) is a homotypic protein interaction module composed of a bundle of six Î±-helices. DD is related in sequence and structure to the death effector domain (DED, see IPR001875) and the caspase recruitment domain (CARD, see IPR001315), which work in similar pathways and show similar interaction properties . DD bind each other forming oligomers. Mammals have numerous and diverse DD-containing proteins . Within these proteins, the DD domains can be found in combination with other domains, including: CARDs, DEDs, ankyrin repeats (IPR002110), caspase-like folds, kinase domains, leucine zippers, leucine-rich repeats (LRR) (IPR001611), TIR domains (IPR000157), and ZU5 domains (IPR000906) .

Some DD-containing proteins are involved in the regulation of apoptosis and inflammation through their activation of caspases and NF-kappaB, which typically involves interactions with TNF (tumour necrosis factor) cytokine receptors . In humans, eight of the over 30 known TNF receptors contain DD in their cytoplasmic tails; several of these TNF receptors use caspase activation as a signalling mechanism. The DD mediates self-association of these receptors, thus giving the signal to downstream events that lead to apoptosis. Other DD-containing proteins, such as ankyrin, MyD88 and pelle, are probably not directly involved in cell death signalling. DD-containing proteins also have links to innate immunity, communicating with Toll family receptors through bipartite adapter proteins such as MyD88 .
Wikipedia: The death domain (DD) is a protein interaction module composed of a bundle of six alpha-helices. DD is a subclass of protein motif known as the death fold and is related in sequence and structure to the death effector domain (DED) and the caspase recruitment domain (CARD), which work in similar pathways and show similar interaction properties. DD bind each other forming oligomers. Mammals have numerous and diverse DD-containing proteins. Within these proteins, the DD domains can be found in combination with other domains, including: CARDs, DEDs, ankyrin repeats, caspase-like folds, kinase domains, leucine zippers, leucine-rich repeats (LRR), TIR domains, and ZU5 domains.
Pfam PF05577: Serine carboxypeptidase S28 (domain)
These serine proteases include several eukaryotic enzymes such as lysosomal Pro-X carboxypeptidase, dipeptidyl-peptidase II, and thymus-specific serine peptidase.
Pfam PF22619: DNA polymerase I, ribonuclease H-like domain (domain)
This domain is responsible for the 3'-5' exonuclease proofreading activity of E. coli DNA polymerase I (polI) and other related enzymes. It is one of the constituent domains of Klenow fragment.
Pfam PF10566: Glycoside hydrolase 97 (domain)
This domain is the catalytic region of the bacterial glycosyl-hydrolase family 97. This central part of the GH97 family protein sequences represents a typical and complete (beta/alpha)8-barrel or catalytic TIM-barrel type domain. The N- and C-terminal parts of the sequences, mainly consisting of beta-strands, form two additional non-catalytic domains.  In all known glycosidases with the (beta-alpha)8-barrel fold, the amino acid residues at the active site are located on the C-termini of the beta-strands.
Wikipedia: In molecular biology, glycoside hydrolase family 97 is a family of glycoside hydrolases.
Pfam PF22515: Domain of unknown function (DUF6996) (domain)
This domain is found N-terminal in a group of uncharacterised proteins. It is remotely related to AbiEi winged helix domain and it is predicted to adopt the same structure.
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 PF02459: Adenoviral DNA terminal protein (family)
This protein is covalently attached to the terminii of replicating DNA in vivo.
Pfam PF07228: Stage II sporulation protein E (SpoIIE) (family)
This family contains a number of bacterial stage II sporulation E proteins ([ec:3.1.3.16]). These are required for formation of a normal polar septum during sporulation. The N-terminal region is hydrophobic and is expected to contain up to 12 membrane-spanning segments.
Pfam PF08259: Periviscerokinin family (family)
Abdominal Perisympathetic organs of insects contain Periviscerokinins neuropeptides of about 11 amino acids.
Pfam PF00286: Viral coat protein (domain)
Family includes coat proteins from Potexviruses and carlaviruses.
Pfam PF16688: Replicase polyprotein N-term from Coronavirus nsp1 (domain)
CNV-Replicase_N is the N-terminal domain of a family of ssRNA positive-stranded porcine transmissible gastroenteritis coronaviruses.  the domain folds into a six-stranded beta-barrel fold with a long alpha helix on the rim of the barrel. This fold is shared with SARS-CoV nsp1.
Pfam PF15593: Immunity protein 42 (family)
A predicted immunity protein with an alpha+beta fold. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, usually containing a domain of the Ntox18 family.
Pfam PF20759: Domain of unknown function (DUF6835) (domain)
This domain of unknown function is found in proteins from bacteria, including the product of the gene SO_2669 from Shewanella oneidensis. Its structure has been solved and shows 16 alpha helices ([swissprot:Q8EDS4]).
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 PF14318: Mononegavirales mRNA-capping region V (domain)
This V domain of L RNA-polymerase carries a new motif, GxxTx(n)HR, that is essential for mRNA cap formation. Nonsegmented negative-sense (NNS) RNA viruses, Mononegavirales, cap their mRNA by an unconventional mechanism. Specifically, 5'-monophosphate mRNA is transferred to GDP derived from GTP through a reaction that involves a covalent intermediate between the large polymerase protein L and mRNA. The V region is essential for this process.
Pfam PF19265: Family of unknown function (DUF5908) (family)
This short protein of unknown function is found within the operon of a contractile injection system of Photorhabdus asymbiotica [swissprot:B6VNN9].
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 PF19260: Family of unknown function (DUF5903) (family)
This is a family of uncharacterised proteins of unknown function mostly found in Prasinoviruses.
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 PF10166: Uncharacterised conserved protein (DUF2368) (family)
This family is conserved from nematodes to humans. The function is not known.
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 PF24938: Domain of unknown function (DUF7755) (domain)
This is a domain of unknown function found in plants. This domain is structurally related to Lipase/lipooxygenase domain (PLAT/LH2 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 PF22335: Cas10/Cmr2, second palm domain (domain)
This entry represents the second palm domain of Cas10 subunit (named Csm1 in Type III-A and Cmr2 in III-B systems) from type III CRISPR-Cas systems. This domain contains a conserved GGDD motif that is important for DNA polymerase activity.
Pfam PF18282: RAP80 N-terminal ubiquitin interaction motif (domain)
This is the N-terminal domain found in RAP80 protein present in Homo sapiens. RAP80 is fundamental for protein recruitment in the DNA damage response. The N-terminal domain is a ubiquitin-interacting motif (UIM).  RAP80 is involved in multivalent recognition of polyUb chains through N-terminal domain.
Pfam PF18260: Nuclear polyadenylated RNA-binding 2 protein CCCH zinc finger 1 (domain)
This domain is found in nuclear polyadenylated RNA-binding 2 protein (Nab2p) present in Saccharomyces cerevisiae. Nab2p is a major family of Poly A-binding proteins whose interactions are thought to be crucial for the control of poly(A) tail length. This domain is the first of seven CCCH zinc fingers which are responsible for polyadenosine RNA binding. When combined with the next three zinc fingers (Zf1-4), these four zinc fingers together may bind RNA in the 3' to 5' direction.
Pfam PF09341: Transcription factor Pcc1 (family)
Pcc1 is a transcription factor that functions in regulating genes involved in cell cycle progression and polarised growth.
Pfam PF03860: Domain of Unknown Function (DUF326) (repeat)
This family is a small cysteine-rich repeat. The cysteines mostly follow a C-X(2)-C-X(3)-C-X(2)-C-X(3) pattern,  though they often appear at other positions in the repeat as well.
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 PF18147: Suv3 C-terminal domain 1 (domain)
This domain is found in Suv3 present in Homo sapiens. Suv3 is an NTP-dependent RNA/DNA helicase that is necessary for the degradation of mature mtRNAs. Suv3 has been found to interact in vitro with polynucleotide phosphorylase. This domain makes up part of the C-terminal domain.
Pfam PF13169: Poxvirus B22R protein N-terminal (family)
This is the highly conserved N-terminal region of poxvirus proteins from eg, Fowlpox virus, Myxoma virus, Lumpy skin disease, Variola virus and other members of the Poxviridae family of double-stranded, no-RNA stage poxviruses.
Pfam PF10148: Schwannomin-interacting protein 1, C-terminal (coiled_coil)
SCHIP-1 is a coiled-coil protein that specifically associates with schwannomin, a protein involved in NF2-associated and sporadic schwannomas and meningiomas. This entry represents the C-terminal domain, which contains a leucine zipper coiled-coil structure implicated in their dimerization. This domain is also found in its isoforms such as IQCJ-SCHIP-1.
Pfam PF25032: Serine/threonine-protein kinase ATR, N-HEAT region (repeat)
This region of HEAT repeats is found in human Serine/threonine -protein kinase ATR and similar proteins from vertebrates. ATR acts as a DNA damage sensor and is associated with severe disorders such as Seckel syndrome 1. This protein is organised into a large N-terminal alpha solenoid containing HEAT repeats, a FAT (FRAP, ATM, TRRAP) domain ([pfam:PF02259]), a kinase domain ([pfam:PF00454]), and a C-terminal short segment referred to as FATC ([pfam:PF02260]). N-terminal part has two continuous HEAT repeat regions, the N-HEAT and the M-HEAT. This entry represents the N-HEAT region.
Pfam PF00912: Transglycosylase (domain)
The penicillin-binding proteins are bifunctional proteins consisting of  transglycosylase and transpeptidase in the N- and C-terminus  respectively. The transglycosylase domain catalyses the  polymerisation of murein glycan chains ().
Pfam PF16241: Domain of unknown function (DUF4900) (family)
This family consists of uncharacterized proteins around 600 residues in length and is mainly found in various  Thermotoga and Fervidobaterium species. The function of  this family is unknown.