SII-SWORD/CoKE huggingface dataset:
Pfam PF13901: Rubicon Homology Domain (domain)
This is the Rubicon homology domain (RH) characterised at the C-terminal of Rubicon, PLEKHM1 and Pacer, proteins that modulate late steps in autophagy. Rubicon (RUBCN) negatively regulates autophagy and endolysosomal trafficking by inhibiting PI3K complex II (PI3KC3-C2), which impairs autophagosome maturation process. PLEKHM1 is an adapter protein that regulates Rab7-dependent and HOPS complex-dependent fusion events in the endolysosomal system and couples autophagic and the endocytic trafficking pathways. On the other hand, Pacer positively regulates autophagy, promoting autophagosome maturation by facilitating the biogenesis of phosphatidylinositol 3-phosphate (PtdIns3P) in late steps of autophagy; it antagonises RUBCN. This domain contains nine conserved cysteines and one conserved histidine, which have been predicted to bind divalent zinc cations being required for Rubicon and PLEKHM1 to interact with Rab7.
Wikipedia: The Rubicon homology domain is an evolutionarily conserved protein domain of approximately 250 amino acids that mediates protein–protein interaction. RH domains are present in several human proteins involved in regulation of autophagy and endosomal trafficking. While not all RH domains have been characterized, those of human Rubicon and PLEKHM1 mediate interaction with the small GTPase Rab7, which is found on late endosomes and autophagosomes.
Pfam PF18942: Family of unknown function (DUF5689) (domain)
This is a domain of unknown function. It is mostly found in bacteria and can be present in multiple copies.
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 PF10890: Cytochrome b-c1 complex subunit 8 (family)
This entry represents subunit 8 of the Cytochrome b-c1  complex.
Pfam PF24343: P-granule-associated protein DEPS-1, first OB-fold domain (domain)
This domain is found in the P-granule-associated protein DEPS-1 from C.elegans and related proteins. DEPS-1 is a component of the P-granules and is required for their formation and integrity in adult germ cells. This protein is also involved in RNA-mediated silencing (RNAi) of germline-expressed genes. DEPS-1 is predicted to contain six OB-fold-like beta-barrel domains. This entry represents the first of these domains.
Pfam PF18280: Nucleotidyltransferase, substrate binding domain (domain)
This domain is located on the central part of a nucleotidyltransferase from Pseudomonas aeruginosa (Ant(4')-IIb) and in other bacterial proteins. It shows a four-helical up-and-down bundle.
Pfam PF23599: Cartilage intermediate layer protein 1-like, C-terminal (domain)
This domain is found at the C-terminal end of human Cartilage intermediate layer protein 1 (CILP) and similar proteins mainly found in vertebrates. CILP is though to play a role in cartilage scaffolding. It is predicted to adopt a beta-sandwich fold.
Pfam PF22182: Domain of unknown function (DUF6945) (domain)
This entry represents a WH-like domain (PDB:4ro3) found at the N-terminal of an uncharacterised protein from Vibrio cholerae ([swissprot:M1RHE3]), whose function is unknown. This domain is also found in phage 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 PF12737: C-terminal domain of homeodomain 1 (domain)
Mating in fungi is controlled by the loci that determine the mating type of an individual, and only individuals with differing mating types can mate. Basidiomycete fungi have evolved a unique mating system, termed tetrapolar or bifactorial incompatibility, in which mating type is determined by two unlinked loci; compatibility at both loci is required for mating to occur. The multi-allelic tetrapolar mating system is considered to be a novel innovation that could have only evolved once, and is thus unique to the mushroom fungi. This domain is C-terminal to the homeodomain transcription factor region.
Pfam PF12942: Archaeal ammonia monooxygenase subunit A (AmoA) (family)
This is an archeael family that contains ammonia monooxygenase subunit A. Ammonia monooxygenase is an enzyme that oxidises ammonia to nitrite and nitrate, thus playing a significant role in the nitrogen cycle. Ammonia-oxidising archaea (AOA) are widespread in marine environments.
Pfam PF05232: Chlorhexidine efflux transporter (family)
This family represents a conserved pair of two transmembrane alpha-helices. All members carry the two pairs of TMs. BTP is a form of drug efflux pump, that actively tranports chlorhexidine out of the cell.  Chlorhexidine, a bisbiguanide antimicrobial agent, is commonly used as an antiseptic and disinfectant in hospitals, and there is an increasing problem with resistance to it in some pathogenic bacteria. BTP is localised in the cytoplasmic membrane.
Pfam PF00158: Sigma-54 interaction domain (domain)
Some bacterial regulatory proteins activate the expression of genes from promoters recognised by core RNA polymerase associated with the alternative sigma-54 factor. These have a conserved domain of about 230 residues involved in the ATP-dependent  interaction with sigma-54. About half of the proteins in which this domain is found (algB, dcdT, flbD, hoxA, hupR1, hydG, ntrC, pgtA and pilR) belong to signal transduction two-component systems  and possess a domain that can be phosphorylated by a sensor-kinase protein in their N-terminal section. Almost all of these proteins possess a helix-turn-helix DNA-binding domain in their C-terminal section.

The domain which interacts with the sigma-54 factor has an ATPase activity. This may be required to promote a conformational change necessary for the interaction . The domain contains an atypical ATP-binding motif A (P-loop) as well as a form of motif B. The two ATP-binding motifs are located in the N-terminal section of the domain.
Pfam PF24809: Domain of unknown function (DUF7708) (domain)
This domain is found N-terminal in uncharacterised fungal proteins. It shares detectable similarity to the N-terminal domain of NACHT proteins and it is predicted to adopt similar 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 PF19334: Domain of unknown function (DUF5920) (domain)
This domain is found in the Telomerase protein component 1 (TEP1) and it contains an homology region to the telomerase associated protein from Tetrahymena p80. TEP1 is a component of the telomerase ribonucleoprotein complex and is thought to be responsible for catalysing the addition of new telomeres to chromosomes. TEP1 is also a component of the vault particle, a cytoplasmic ribonucleoprotein complex, in which it is required for vault RNA stability and its association with the vault particle. This domain is localised between the TROVE ([pfam:PF05731]) and DUF4062 ([pfam:PF13271]) 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 PF19817: Family of unknown function (DUF6300) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0002024) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular, the nargenicin biosynthetic gene cluster from Nocardia argentinensis. This family appears to be predominantly found in bacteria and unclassified phages.
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 PF02728: Copper amine oxidase, N3 domain (domain)
This domain is the second or third structural domain in copper amine oxidases, it is known as the N3 domain. Its function is uncertain. The catalytic domain can be found in [pfam:PF01179]. Copper amine oxidases are a ubiquitous and novel group of quinoenzymes that catalyse the oxidative deamination of primary amines to the corresponding aldehydes, with concomitant reduction of molecular oxygen to hydrogen peroxide. The enzymes are dimers of identical 70-90 kDa subunits, each of which contains a single copper ion and a covalently bound cofactor formed by the post-translational modification of a tyrosine side chain to 2,4,5-trihydroxyphenylalanine quinone (TPQ).
Wikipedia: Amine oxidase (copper-containing) (AOC) (EC 1.4.3.21 and EC 1.4.3.22; formerly EC 1.4.3.6) is a family of amine oxidase enzymes which includes both primary-amine oxidase and diamine oxidase; these enzymes catalyze the oxidation of a wide range of biogenic amines including many neurotransmitters, histamine and xenobiotic amines. They act as a disulphide-linked homodimer. They catalyse the oxidation of primary amines to aldehydes, with the subsequent release of ammonia and hydrogen peroxide, which requires one copper ion per subunit and topaquinone as cofactor:RCH2NH2 + H2O + O2  RCHO + NH3 + H2O2
Pfam PF10899: Putative abortive phage resistance protein AbiGi, antitoxin (family)
This is a bacterial family of proteins with unknown function. AbiGi is a family of putative type IV toxin-antitoxin system antitoxins. The AbiG abortive phage resistance system affects lactococcal bacteriophages phiP335 and phiQ30 but not the other P335 phage species. AbiGii toxin appears to confer resistance to phages by a mechanism of abortive infection that acts by interfering with phage RNA synthesis. The cognate toxin is found in [pfam:PF16873].
Pfam PF16906: Ribosomal proteins L26 eukaryotic, L24P archaeal (family)
Ribosomal_L26 is a family of the 50S and the 60S ribosomal proteins from eukaryotes - L26 - and archaea - L25.
Pfam PF13527: Acetyltransferase (GNAT) domain (domain)
This domain catalyses N-acetyltransferase reactions.
Wikipedia: An acetyltransferase is any of a class of transferase enzymes that transfers an acetyl group in a reaction called acetylation. In biological organisms, post-translational modification of a protein via acetylation can profoundly transform its functionality by altering various properties like hydrophobicity, solubility, and surface attributes. These alterations have the potential to influence the protein's conformation and its interactions with substrates, cofactors, and other macromolecules.
Pfam PF04726: Microvirus J protein (family)
This small protein is involved in DNA packaging, interacting with DNA via its hydrophobic carboxyl terminus.  In bacteriophage phi-X174, J is present in 60 copies, and forms an S-shaped polypeptide chain without any secondary structure.  It is thought to interact with DNA through simple charge interactions.
Pfam PF02730: Aldehyde ferredoxin oxidoreductase, N-terminal domain (domain)
Aldehyde ferredoxin oxidoreductase (AOR) catalyses the reversible oxidation of aldehydes to their corresponding carboxylic acids with their accompanying reduction of the redox protein ferredoxin. This domain interacts with the tungsten cofactor.
Wikipedia: In enzymology, an aldehyde ferredoxin oxidoreductase (EC 1.2.7.5) is an enzyme that catalyzes the chemical reactionan aldehyde + H2O + 2 oxidized ferredoxin ⇌ an acid + 3 H+ + 2 reduced ferredoxin
Pfam PF03659: Glycosyl hydrolase family 71 (family)
Family of alpha-1,3-glucanases.
Wikipedia: In molecular biology, glycoside hydrolase family 71 is a family of glycoside hydrolases.
Pfam PF06273: Plant specific eukaryotic initiation factor 4B (family)
This family consists of several plant specific eukaryotic initiation factor 4B proteins.
Pfam PF08015: Fungal mating-type pheromone (family)
This family corresponds to mating-type pheromone proteins. The homobasidiomycetes, or mushroom fungi, have arguably the most complex mating system of all known organisms. Many species possess a mating system known as bifactorial incompatibility, where two unlinked loci control the mating -type of an individual incompatibility loci (the A and  B mating-type loci). Each A mating-type sublocus encodes a pair of divergently transcribed homeodomain transcription  factors while the genes responsible for B mating-type  activity encode lipopeptide pheromones and G-protein -coupled pheromone receptors.
Pfam PF05023: Phytochelatin synthase (domain)
Phytochelatin synthase is the enzyme responsible for the synthesis of heavy-metal-binding peptides (phytochelatins) from glutathione and related thiols. The crystal structure of a member of this family shows it to possess a papain fold. The enzyme catalyses the deglycination of a GSH donor molecule. The enzyme contains a catalytic triad of cysteine, histidine and aspartate residues.
Pfam PF05201: Glutamyl-tRNAGlu reductase, N-terminal domain (domain)
This entry represents the N-terminal domain of glutamyl-tRNA reductase (1.2.1.70), which reduces glutamyl-tRNA to glutamate-1-semialdehyde during the first stage of tetrapyrrole biosynthesis by the C5 pathway . The enzyme requires NADPH as a cofactor. This N-terminal domain is the catalytic domain .
Pfam PF17676: LD-carboxypeptidase C-terminal domain (domain)
Muramoyl-tetrapeptide carboxypeptidase hydrolyses a peptide bond between a di-basic amino acid and the C-terminal D-alanine in the tetrapeptide moiety in peptidoglycan. This cleaves the bond between an L- and a D-amino acid. The function of this activity is in murein recycling. This family also includes the microcin c7 self-immunity protein [swissprot:Q47511]. This family corresponds to Merops family S66.
Pfam PF23142: PLEKHM2 PH domain-like (domain)
This entry represents one or two PH domains found in the PLEKHM2 and related proteins. This domain does not appear to be found in the PLEKHM1 proteins.
Pfam PF16498: SWIRM-associated domain at the C-terminal (family)
Much of the higher eukaryote SWI/SNF complex subunit SMARCC2 proteins is of low-complexity and or disordered. However, there are several short regions that are quite highly conserved. This is one of these regions.  The function of the individual regions is not known.
Pfam PF12547: Ataxin-1 like family (disordered)
This entry represents the N-terminal and central region of the Ataxin-1 protein.
Pfam PF14853: Fis1 C-terminal tetratricopeptide repeat (repeat)
The mitochondrial fission protein Fis1 consists of two tetratricopeptide repeats. This domain is the C-terminal tetratricopeptide repeat
Pfam PF22489: BACOVA_00430, N-terminal domain (domain)
This entry represents a N-terminal domain of BACOVA_00430 protein from the human gut bacterium Bacteroides ovatus.
Pfam PF18692: Family of unknown function (DUF5640) (domain)
This domain is found in proteins of unknown function. It has composed of eight antiparallel beta strands and carries a G-X-W motif in the N-terminal region. The conserved glycine-X-tryptophan (G-X-W) motif is characteristic for the lipocalin family.
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 PF20808: Msx2-interacting protein, RAM7 domain (repeat)
This is the RBP-J binding domain (RAM7) found in the central region of  Msx2-interacting protein (MINT), a widely expressed transcription repressor that regulates key transcription effectors in several signalling pathways, including MSX2, RBP-J, and nuclear receptors. Structure predictions from AlphaFold suggest that this domain adopts a beta-solenoid structure which includes VNVLTGP/VNVLTTP repeats. RAM7 domain from MINT competes with the RAM domain of Notch for physical interaction with RBP-J. Through this domain, MINT sequesters and prevents RBP-J DNA binding thus, precluding trans-activation directed by the RBP-J coadapter, Notch1 intracellular domain.
Pfam PF18499: Ubc7p-binding region of Cue1 (domain)
Cue1p (coupling of ubiquitin conjugation to ER degradation protein 1) is an integral component of yeast endoplasmic reticulum (ER)-associated degradation (ERAD) ubiquitin ligase (E3) complexes. It tethers the ERAD ubiquitin-conjugating enzyme (E2), Ubc7p, to the ER and prevents its degradation, and also activates Ubc7p. This domain represents the Ubc7p-binding region (U7BR) of Cue1p with Ubc7p. The U7BR is as E2-binding domain that includes three alpha-helices that interact extensively with the 'backside' of Ubc7p. U7BR stimulates both RING-independent and RING-dependent ubiquitin transfer from Ubc7p. Moreover, the U7BR enhances ubiquitin-activating enzyme (E1)-mediated charging of Ubc7p with ubiquitin.
Pfam PF07405: Protein of unknown function (DUF1506) (family)
This family consists of several bacterial proteins of around 130 residues in length. Members of this family seem to be specific to Borrelia burgdorferi (Lyme disease spirochete). 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 PF16199: Radical_SAM C-terminal domain (family)
This domain is found as a C-terminal extension to a subset of Radical_SAM domains. It is found in archaeal, bacterial, fungal, plant and human proteins.
Pfam PF09695: Bacterial protein of unknown function (YtfJ_HI0045) (family)
These are sequences from gamma proteobacteria that are related to the E. coli protein, YtfJ.
Pfam PF08351: tRNA(Met) cytidine acetyltransferase TmcA, N-terminal (family)
This domain of unknown function is often found at the N-terminus of the bacterial tRNA(Met) cytidine acetyltransferase TmcA. TmcA catalyses the formation of N(4)-acetylcytidine (ac4C) at the wobble position of tRNA(Met) by using acetyl-CoA as an acetyl donor and either ATP or GTP. This modification is thought to ensure precise recognition of the AUG codon by strengthening C-G base-pair interaction and also prevent misrecognition of the near cognate AUA codon. This domain is also found in mammalian N-acetyltransferase 10 (NAT10) and fungal protein Kre33. Kre33 and NAT10 are RNA cytosine acetyltransferases with specificity toward both 18S rRNA and tRNAs and contain additional putative nuclear and nucleolar localization signals (NLS and NoLS respectively).
Pfam PF16113: Enoyl-CoA hydratase/isomerase (domain)
This family contains a diverse set of enzymes including: enoyl-CoA hydratase, napthoate synthase, carnitate racemase, 3-hydroxybutyryl-CoA dehydratase and dodecanoyl-CoA delta-isomerase. This family differs from [pfam:PF00378] in the structure of it's C-terminus.
Pfam PF17953: CRISPR Csm4 C-terminal domain (domain)
Clustered, regularly interspaced, short palindromic repeat (CRISPR) loci play a pivotal role in the prokaryotic host defense system against invading genetic materials. The CRISPR loci are transcribed to produce CRISPR RNAs (crRNAs), which form interference complexes with CRISPR-associated (Cas) proteins to target the invading nucleic acid for degradation. The interference complex of the type III-A CRISPR-Cas system is composed of five Cas proteins (Csm1-Csm5) and a crRNA, and targets invading DNA. This entry represents the C-terminal domain found in Csm4. Csm4 structurally resembles Cmr3, a component of the type III-B CRISPR-Cas interference complex. Studies indicate that Csm3-Csm4 complex binds single-stranded RNA in a non-sequence-specific manner. Structural analysis show , Csm3 and Csm4 have one and two ferredoxin-like folds (also known as an RRM-like fold), respectively. The long beta-hairpin inserted into the C-terminal ferredoxin-like fold of Csm4, is well-conserved in the Cmr3 structure. The corresponding beta-hairpin of Cmr3 binds the D1 domain of Cmr2, as observed in the Cmr2-Cmr3 complex structure. Furthermore, it is suggested that the hairpin of Csm4 is responsible for the interaction with Csm1 (ortholog of Cmr2).
Wikipedia: CRISPR is a family of DNA sequences found in the genomes of prokaryotic organisms such as bacteria and archaea. Each sequence within an individual prokaryotic cell is derived from a DNA fragment of a bacteriophage that had previously infected the prokaryote or one of its ancestors. These sequences are used to detect and destroy DNA from similar bacteriophages during subsequent infections. Hence these sequences play a key role in the antiviral defense system of prokaryotes and provide a form of heritable, acquired immunity. CRISPR is found in approximately 50% of sequenced bacterial genomes and nearly 90% of sequenced archaea.
Pfam PF03308: Methylmalonyl Co-A mutase-associated GTPase MeaB (domain)
Family members were previously thought to be ArgK proteins acting as ATPase enzymes and kinases. They are now believed to be methylmalonyl Co-A mutase-associated GTPase MeaB. Structural studies of MeaB and the human ortholog (methylmalonyl associated protein A) MMAA, reveal alpha-helical domains at the N- and C-termini as well as a Ras-like GTPase domain. Mutational analysis of MeaB, show prohibited growth in Methylobacterium due to the inability to convert methylmalonyl-CoA to succinyl-CoA caused by an inactive form of methylmalonyl-CoA mutatase (mcm). In humans, mutations in (MMAA) are associated with the fatal disease methylmalonyl aciduria.
Pfam PF15077: Membrane-anchored junction protein (family)
Membrane-anchored junction protein (MAJIN) is a meiosis-specific telomere-associated protein involved  in meiotic telomere attachment to the nucleus inner  membrane, a crucial step for homologous pairing  and synapsis. It is a component of the MAJIN-TERB1-TERB2  complex, which promotes telomere cap exchange by mediating  attachment of telomeric DNA to the inner nuclear membrane  and replacement of the protective cap of telomeric chromosomes.
Pfam PF17360: Family of unknown function (DUF5386) (family)
This is a family of unknown function found in Chromadorea.
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.