SII-SWORD/CoKE huggingface dataset:
Pfam PF10063: Uncharacterized integral membrane protein (DUF2301) (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 PF12254: DNA polymerase alpha subunit p180 N terminal (family)
This domain family is found in eukaryotes, and is approximately 70 amino acids in length. The family is found in association with [pfam:PF00136], [pfam:PF08996], [pfam:PF03104]. This family is the N terminal of DNA polymerase alpha subunit p180 protein. The N terminal contains the catalytic region of the alpha subunit.
Pfam PF23797: ELP1 N-terminal second beta-propeller (repeat)
This entry represents second out of two N-terminal beta-propeller domains, found in Elongator complex protein 1 (ELP1) from eukaryotes.  Elongator is a conserved protein complex implicated in multiple processes including regulation of transcription, alpha-tubulin acetylation, and tRNA modification. Mutations in the ELP1 gene have been shown to cause the neurodegenerative disease familial dysautonomia. ELP1 binds members of the Elongator complex ELP2 and ELP3; and the beta-propellers are suggested to act as scaffold for this protein-protein interaction. Also known as IKAP, ELP1 acts as a regulator of IkB kinase complex involved in proinflammatory cytokine signaling. Residues within this second beta propeller have been shown to be required for interaction with upstream regulatory kinase NIK, acting as a scaffold that assembles IKKs with NIK.
Pfam PF10067: Predicted membrane protein (DUF2306) (family)
Members of this family of hypothetical bacterial proteins have 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 PF20364: Family of unknown function (DUF6659) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 121 and 132 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 PF07237: Protein of unknown function (DUF1428) (domain)
This family consists of several hypothetical bacterial and one archaeal sequence of around 120 residues in length. The function of this family is unknown. The structure of this family shows it to be part of the Dimeric-alpha-beta-barrel superfamily. Many members are annotated as being RNA signal recognition particle 4.5S RNA, but this could not be verified.
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 PF10723: Replication regulatory protein RepB (domain)
This is a family of proteins which regulate replication of rolling circle replication (RCR) plasmids that have a double-strand replication origin (dso). Regulation of replication of RCR plasmids occurs mainly at initiation of leading strand synthesis at the dso, such that Rep protein concentration controls plasmid replication.
Pfam PF14284: PcfJ-like protein (family)
The PcfJ-like protein family includes the E. faecalis PcfJ protein [swissprot:Q5G3N2], which is functionally uncharacterised.  It is found in bacteria and viruses, and is typically between 159 and 170 amino acids in length. There is a conserved HCV sequence motif.
Pfam PF10015: ThermoDBP-related, archaea (family)
This protein family is related to archaeal non-canonical single- stranded DNA-binding proteins (ThermoDBPs) named ThermoDBP-related proteins. These proteins have been related to genome maintenance in particularly challenging environments, but their specific function is still unknown.
Pfam PF02204: Vacuolar sorting protein 9 (VPS9) domain (family)
This domain acts as a GDP-GTP exchange factor (GEF). It activates Rab GTPases by stimulating the release of GDP and allowing GTP to bind.
Pfam PF01256: NAD(P)H-hydrate dehydratase (domain)
Hydration of NAD(P)H to NAD(P)HX, which inhibits several dehydrogenases, is corrected by an ATP-dependent dehydratase and an  epimerase. The ATP-dependent dehydratase has been identified as the  product of the vertebrate Carkd (carbohydrate kinase domain) gene. Variants of this enzyme leads to deficient NADHX repair  mitochondrial dysfunction in humans, associated with a lethal  neurometabolic disorder in early childhood. In E. coli, it is  found as the C-terminal domain of a bifunctional enzyme (YjeF) that  also includes the epimerase and uses ADP instead of ATP. These  enzymes are widespread in eukaryotes, prokaryotes, and archaea.
Wikipedia: Carbohydrate kinase domain containing protein, encoded by CARKD gene, is a human protein of unknown function. The CARKD gene encodes proteins with a predicted mitochondrial propeptide (mCARKD), a signal peptide (spCARKD) or neither of them (cCARKD). Confocal microscopy analysis of transfected CHO cells indicated that cCARKD remains in the cytosol, whereas mCARKD and spCARKD are targeted to the mitochondria and the endoplasmic reticulum respectively. The protein is conserved throughout many species, and has predicted orthologs through eukaryotes, bacteria, and archea.
Pfam PF14647: FAM91 N-terminus (family)
This domain is found at the N terminus of proteins from the FAM91 family.
Pfam PF22085: Nitric oxide reductase subunit B, cytochrome c-like domain (domain)
This domain is found in Nitric oxide reductase subunit B from Pseudomonas aeruginosa (NorB) and similar bacterial sequences. NorB is the large component of the anaerobic respiratory chain that transforms nitrate to dinitrogen (denitrification). This entry represents the cytochrome C-like domain of NorB, which has 12 alpha-helices in the transmembrane region with two heme irons and and one non-heme iron.
Pfam PF22471: Mcm2-like, OB fold, archaea (domain)
This entry represents the OB fold domain of a monomeric MCM homologue (known as Mcm2) from Methanopyrus kandleri. This is a noncanonical domain and contains a long beta-hairpin extending from the core OB fold that is thought to mediate hexamerization.
Pfam PF21245: PI4KB/PIK1, accessory (PIK) domain (repeat)
Phosphatidylinositol 4-kinase beta (PI4KB) is one of four mammalian PI4K enzymes that phosphorylate phosphatidylinositol to generate phosphatidylinositol 4-phosphate (PI4P). It localizes at the Golgi and is essential for Golgi formation and function. PI4KB consists of two domains, a right-handed helical solenoid at the N-terminal, also referred to as accessory (PIK) domain, and a C-terminal kinase domain. This entry represents the N-terminal PIK domain from mammalian PI4KB and the yeast orthologue Pik1, which may be involved in substrate presentation.
Pfam PF01611: Filovirus glycoprotein (family)
This family includes an extracellular region from the envelope glycoprotein of Ebola and Marburg viruses. This region is also produced as a separate transcript that gives rise to a non-structural, secreted glycoprotein, which is produced in large amounts and has an unknown function. Processing of this protein may be involved in viral pathogenicity.
Pfam PF11971: CAMSAP CH domain (domain)
This domain is the N-terminal CH domain from the CAMSAP proteins.
Pfam PF01286: XPA protein N-terminal (domain)
Xeroderma pigmentosum (XP)  is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30kDa nuclear protein called XPA (or XPAC) . The sequence of the XPA protein is conserved from higher eukaryotes  to yeast (gene RAD14) . XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section.
This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to (IPR022656)
Pfam PF15588: Immunity protein 10 (family)
A predicted immunity protein with a mostly all-beta fold and a conserved arginine residue. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, usually containing a Pput_2613 deaminase domain. The protein is also found in heterogeneous poly-immunity loci.
Pfam PF04969: CS domain (domain)
The CS and CHORD ([pfam:PF04968]) are fused into a single polypeptide chain in metazoans but are found in separate proteins in plants; this is thought to be indicative of an interaction between CS and CHORD. It has been suggested that the CS domain is a binding module for HSP90, implying that CS domain-containing proteins are involved in recruiting heat shock proteins to multiprotein assemblies. Two CS domains are found at the N-terminus of Ubiquitin carboxyl-terminal hydrolase 19 (USP19) ([swissprot:O94966]), these domains may play a role in the interaction of USP19 with cellular inhibitor of apoptosis 2.
Pfam PF23062: M02D8_5-like, third CUB domain (domain)
This entry represents the third occurrence of the CUB domain in a family of uncharacterised proteins present in nematodes. Consecutive repetitions of this domain are common in this protein family. The CUB domain (for complement C1r/C1s, Uegf, Bmp1) is a structural motif of approximately 110 residues found predominantly in extracellular and plasma membrane-associated proteins, many of which undergo developmental regulation. CUB domains appear to be involved in oligomerisation and/or recognition of substrates and binding  partners.
Pfam PF18414: C2H2 type zinc-finger (domain)
This is a zinc finger domain C2H2 which can be found in optineurin (optic neuropathy inducing protein) and NF-kappa-B essential modulator (NEMO) furthermore, it can be found in kinase TBK1, a member of the IKK (inhibitor of nuclear factor kappa-B kinase) family. The C-terminal region, which carries the zinc finger domain, constitutes the regulatory domain of NEMO, as it receives the activation signal from upstream molecules, and subsequently transmits this activation to the kinases bound to the N-terminal domain. The isolated NEMO zinc finger is thought to be involved in protein-protein rather than protein-DNA interaction.
Pfam PF18019: Cas3, HD domain (domain)
This HD domain is found at the N-terminus of Cas3 enzymes fused to a helicase domain. This domain is sometimes found as a separate protein. It acts as a nuclease that cleaves ssDNA.
Wikipedia: In molecular biology, the HD domain is a conserved protein domain, named after the conserved histidine (H) and/or aspartate (D) amino acid residues. It is found in a superfamily of enzymes with a predicted or known phosphohydrolase activity. These enzymes appear to be involved in nucleic acid metabolism, signal transduction and possibly other functions in bacteria, archaea and eukaryotes. The fact that all the highly conserved residues in the HD superfamily are histidines or aspartates suggests that coordination of divalent cations is essential for the activity of these proteins.
Pfam PF06858: Nucleolar GTP-binding protein 1 (NOG1) (family)
This family represents a conserved region of approximately 60 residues in length within nucleolar GTP-binding protein 1 (NOG1). In S. cerevisiae, the NOG1 gene has been shown to be essential for cell viability, suggesting that NOG1 may play an important role in nucleolar functions. Family members include eukaryotic, bacterial and archaeal proteins.
Pfam PF04172: LrgB-like family (family)
The two products of the lrgAB operon are potential membrane proteins, and LrgA and LrgB are both thought to control of murein hydrolase activity and penicillin tolerance.
Pfam PF02852: Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain (domain)
This family includes both class I and class II oxidoreductases and also NADH oxidases and peroxidases.
Pfam PF23924: Family of unknown function (DUF7263) (family)
This entry represents uncharacterised proteins found mainly in Halobacteria.
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 PF14418: OST-HTH Associated domain (domain)
OHA occurs with OST-HTH.
Pfam PF17200: Single Cache domain 2 (family)
This entry represents the single Cache domain 2 (sCache_2), which contains the long N-terminal helix domain. This domain recognises pyruvate, acetate, propionate, glycolate, L-lactate, acetoacetate, urea and hydroxyurea, acetamide, formamide, L-malate and citromalate, malonate, methyl and bromosuccinate and citraconic acid (Matilla et al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).
Wikipedia: In molecular biology, the cache domain is an extracellular protein domain that is predicted to have a role in small-molecule recognition in a wide range of proteins, including the animal dihydropyridine-sensitive voltage-gated Ca2+ channel alpha-2delta subunit, and various bacterial chemotaxis receptors. The name Cache comes from CAlcium channels and CHEmotaxis receptors. This domain consists of an N-terminal part with three predicted strands and an alpha-helix, and a C-terminal part with a strand dyad followed by a relatively unstructured region. The N-terminal portion of the (unpermuted) Cache domain contains three predicted strands that could form a sheet analogous to that present in the core of the PAS domain structure. Cache domains are particularly widespread in bacteria such as Vibrio cholerae. The animal calcium channel alpha-2delta subunits might have acquired a part of their extracellular domains from a bacterial source. The Cache domain appears to have arisen from the GAF-PAS fold despite their divergent functions.
Pfam PF17570: Bacteriophage T7-like, protein 6.7 (family)
Protein 6.7 is ejected from the infecting virion. It is found in tail-less particles and has been defined as a head protein.
Pfam PF06366: Flagellar protein FlhE (family)
This family consists of several Enterobacterial FlhE flagellar proteins. The exact function of this family is unknown.
Pfam PF09109: Switch protein XOL-1, GHMP-like (domain)
Members of this family, which are required for the formation of the active site of the sex-determining protein Xol-1, adopt a secondary structure consisting of five alpha helices and seven antiparallel beta sheets, in a beta-alpha-beta-alpha-alpha-alpha-beta-beta-alpha-beta-beta-beta arrangement. The fold of this family is structurally similar to that found in the C-terminal domain of GHMP Kinase.
Pfam PF04785: Rhabdovirus matrix protein M2 (family)
M protein is involved in condensing and targeting the ribonucleoprotein (RNP) coil to the plasma membrane.  M interacts specifically with the transmembrane spike protein (G) is important for the incorporation of G  protein into budding virions.
Pfam PF09030: Creb binding (domain)
The Creb binding domain assumes a structure comprising of three alpha-helices which pack in a bundle, exposing a hydrophobic groove between alpha-1 and alpha-3 within which complimentary domains found in the protein 'activator for thyroid hormone and retinoid receptors' (ACTR) can dock. Docking of these domains is required for the recruitment of RNA polymerase II and the basal transcription machinery.
Wikipedia: In biochemistry, the KIX domain (kinase-inducible domain (KID) interacting domain) or CREB binding domain is a protein domain of the eukaryotic transcriptional coactivators CBP and P300. It serves as a docking site for the formation of heterodimers between the coactivator and specific transcription factors. Structurally, the KIX domain is a globular domain consisting of three α-helices and two short 310-helices.
Pfam PF20931: Dicer, platform domain (domain)
This domain is found in Endoribonuclease Dicer from chordates. This dsRNA endoribonuclease is involved in the cleavage of long RNA precursors into short dsRNAs and plays a role in gene silencing. Dicer shows two N-terminal helicase domains ([pfam:PF04851] and [pfam:PF00271]), a dimerisation domain ([pfam:PF03368]), a Platform domain, a PAZ domain ([pfam:PF02170]), an RNase IIIa/b domain ([pfam:PF00636]) and a dsRNA-binding domain in its C-terminal region. This entry represents the platform domain, which sits on the top of the L-shaped Dicer structure and shows a phosphate pocket.
Pfam PF24708: Lipase-like, C-terminal domain (domain)
This domain is found in lipases from Staphylococcus hyicus (Lip) and related proteins. Lip has a broad substrate specificity hydrolysing a variety of triglycerides and phosphatidylcholines. This domain adopts a fold typical for alpha/beta hydrolases.
Pfam PF16109: Domain of unknown function (DUF4827) (family)
This family consists of uncharacterized proteins around 200 residues in length and is mainly found in various Bacteroides species. Distant homology prediction algorithms consistently suggest a homology between this family and FKBP-type peptidyl-prolyl              cis-trans isomerases (PF00254), but this relation is as yet not confirmed. The function of this family is unknown.
Pfam PF08567: TFIIH p62 subunit, N-terminal domain (domain)
The N-terminal domain of the TFIIH basal transcription factor complex p62 subunit (BTF2-p62) forms an interaction with the 3' endonuclease XPG, which is essential for activity.  The 3' endonuclease XPG is a major component of the nucleotide excision repair machinery. The structure of the N-terminal domain reveals that it adopts a pleckstrin homology (PH) fold. This PH-type domain has been shown to bind to a mono-phosphorylated inositide.
Pfam PF18871: HEPN/Toprim N-terminal domain 1 (domain)
Alpha + beta domain. Fused to two distinct HEPN families: MAE_28990 and ERFG_01251 families, TOPRIM and a Mrr-like REase domain.
Pfam PF16453: PH domain (domain)
This PH domain is found in IQ motif and SEC7 domain-containing proteins.
Pfam PF24261: Family of unknown function (DUF7462) (family)
This entry represents a family of uncharacterised mycobacterial phage proteins. The family includes Phage Bxb1 gene 76. These proteins are short around 40 residues 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 PF03445: Putative nucleotidyltransferase DUF294 (domain)
This domain is found associated with [pfam:PF00571].  This region is uncharacterised, however it seems to be similar to [pfam:PF01909], conserving the DXD motif.                 This strongly suggests that members of this family are also nucleotidyltransferases (Bateman A pers. obs.).
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 PF19889: Domain of unknown function (DUF6362) (domain)
This domain of unknown function is found in uncharacterised bacterial proteins. It has a conserved WP motif and  it may contain a helix-turn-helix motif as it overlaps with members in clan CL0123.
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 PF13776: Domain of unknown function (DUF4172) (family)
The family is often found in association with [pfam:PF02661].
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 PF04231: Endonuclease I (family)
Bacterial periplasmic or secreted endonuclease I ([ec:3.1.21.1]) E. coli endonuclease I (EndoI) is a sequence independent endonuclease located in the periplasm. It is inhibited by different RNA species.  It is thought to normally generate double strand breaks in DNA, except in the presence of high salt concentrations and RNA, when it generates single strand breaks in DNA. Its biological role is unknown.  Other family members are known to be extracellular.  This family also includes a non-specific, Mg2+ activated ribonuclease precursor ([swissprot:Q03091]).
Pfam PF15741: Ligand-dependent nuclear receptor-interacting factor 1 (family)
This family of proteins interacts with the retinoic acid receptor RARalpha and inhibit it's ligand-dependent transcriptional activation.
Pfam PF14037: YoqO-like protein (family)
The YoqO-like protein family includes the B. subtilis YoqO protein [swissprot:O31923], which is functionally uncharacterised. This family of proteins is found in bacteria and viruses. Proteins in this family are approximately 120 amino acids in length. There are two completely conserved residues (I and Y) that may be functionally important.