SII-SWORD/CoKE huggingface dataset:
Pfam PF07702: UTRA domain (domain)
The UbiC transcription regulator-associated (UTRA) domain is a conserved ligand-binding domain that has a similar fold to [pfam:PF04345]. It is believed to modulate activity of bacterial transcription factors in response to binding small molecules sugar phosphates and urocanate, Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).
Pfam PF00696: Amino acid kinase family (family)
This family includes kinases that phosphorylate a variety of amino acid substrates, as well as uridylate kinase and carbamate kinase. This family includes: Aspartokinase [ec:2.7.2.4], [swissprot:P00561]. Acetylglutamate kinase [ec:2.7.2.8], [swissprot:Q07905]. Glutamate 5-kinase [ec:2.7.2.11], [swissprot:P07005]. Uridylate kinase [ec:2.7.4.-], [swissprot:P29464]. Carbamate kinase [ec:2.7.2.2], [swissprot:O96432].
Wikipedia: In molecular biology, the amino acid kinase domain is a protein domain. It is found in protein kinases with various specificities, including the aspartate, glutamate and uridylate kinase families. In prokaryotes and plants the synthesis of the essential amino acids lysine and threonine is predominantly regulated by feed-back inhibition of aspartate kinase (AK) and dihydrodipicolinate synthase (DHPS). In Escherichia coli, thrA, metLM, and lysC encode aspartokinase isozymes that show feedback inhibition by threonine, methionine, and lysine, respectively. The lysine-sensitive isoenzyme of aspartate kinase from spinach leaves has a subunit composition of 4 large and 4 small subunits.
Pfam PF13495: Phage integrase, N-terminal SAM-like domain (domain)
Proteins containing this domain cleave DNA substrates by a series of staggered cuts, during which the protein becomes covalently linked to the DNA through a catalytic tyrosine residue at the carboxy end of the alignment .

The phage integrase N-terminal SAM-like domain is almost always found with the signature that defines the phage integrase family (see IPR002104).
Pfam PF24612: TgrO1-like, immunoglobulin-like domain (domain)
This immunoglobulin-like domain (Ig-like) is found in Tiger protein O1 from Dictyostelium discoideum (TgrO1) and similar sequences from lower eukaryotes. Its specific function is unknown.
Pfam PF14602: Hexapeptide repeat of succinyl-transferase (repeat)
A variety of bacterial transferases contain a repeat structure composed of tandem repeats of a [LIV]-G-X(4) hexapeptide, which, in the tertiary structure of LpxA (Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase) , has been shown to form a left-handed parallel Î²-helix. A number of different transferase protein families contain this repeat, such as the bifunctional protein GlmU, galactoside acetyltransferase-like proteins , the gamma-class of carbonic anhydrases , and tetrahydrodipicolinate-N-succinlytransferases (DapD), the latter containing an extra N-terminal 3-helical domain . It has been shown that most hexapeptide acyltransferases form catalytic trimers with three symmetrical active sites .
Pfam PF18483: Bacterial lectin (domain)
This entry primarily matches to legume-like lectin domains found in prokaryotes.
Wikipedia: In molecular biology, the leguminous lectin family is a family of lectin proteins.
Pfam PF20550: Family of unknown function (DUF6764) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically 165 and 195 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 PF04042: DNA polymerase alpha/epsilon subunit B (family)
This family contains a number of DNA polymerase subunits. The B subunit of the DNA polymerase alpha plays an essential role at the initial stage of DNA replication in S. cerevisiae and is phosphorylated in a cell cycle-dependent manner.  DNA polymerase epsilon is essential for cell viability and chromosomal DNA replication in budding yeast. In addition, DNA polymerase epsilon may be involved in DNA repair and cell-cycle checkpoint control. The enzyme consists of at least four subunits in mammalian cells as well as in yeast.  The largest subunit of DNA polymerase epsilon is responsible for polymerase epsilon is responsible for polymerase activity. In mouse, the DNA polymerase epsilon subunit B is the second largest subunit of the DNA polymerase. A part of the N-terminal was found to be responsible for the interaction with SAP18.  Experimental evidence suggests that this subunit may recruit histone deacetylase to the replication fork to modify the chromatin structure.
Pfam PF05732: Firmicute plasmid replication protein (RepL) (family)
This family consists of Firmicute RepL proteins which are involved in plasmid replication.
Pfam PF15340: Cooperator of PRMT5 family (family)
COPR5 is a family of histone H4-binding proteins expressed in the nucleus. It interacts with the N-terminus of histone H4 thereby mediating the association between histone H4 and PRMT5, PRMT5, the Janus kinase-binding protein 1 that catalyses the formation of symmetric dimethyl-arginine residues in proteins. COPR5 is specifically required for histone H4 'Arg-3' methylation mediated by PRMT5, but not histone H3 'Arg-8' methylation, suggesting that it modulates the substrate specificity of PRMT5. This family of proteins is found in eukaryotes.
Pfam PF12335: Myotubularin protein (family)
This domain family is found in eukaryotes, and is approximately 220 amino acids in length. The family is found in association with [pfam:PF02141], [pfam:PF03456], [pfam:PF03455]. This family is the middle region of SBF2, a member of the myotubularin family. Myotubularin-related proteins have been suggested to work in phosphoinositide-mediated signalling events that may also convey control of myelination. Mutations of SBF2 are implicated in Charcot-Marie-Tooth disease.
Pfam PF02543: Carbamoyltransferase N-terminus (domain)
This domain is found in NodU from Rhizobium, CmcH from Nocardia lactamdurans and the bifunctional carbamoyltransferase TobZ from Streptoalloteichus tenebrarius. NodU a Rhizobium nodulation protein involved in the synthesis of nodulation factors has 6-O-carbamoyltransferase-like activity.  CmcH is involved in cephamycin (antibiotic) biosynthesis and has 3-hydroxymethylcephem carbamoyltransferase activity, [ec:2.1.3.7] catalysing the reaction: Carbamoyl phosphate + 3-hydroxymethylceph-3-EM-4-carboxylate  phosphate + 3-carbamoyloxymethylcephem. TobZ functions as an ATP carbamoyltransferase and tobramycin carbamoyltransferase. These proteins contain two domains, this is the larger, N-terminal, domain.
Pfam PF07650: KH domain (domain)
The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins . It has been shown to bind RNA . Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary forin vitroRNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently .

According to structural analyses , the KH domain can be separated in two groups. The first group or type-1 contain a Î²-Î±-Î±-Î²-Î²-Î± structure, whereas in the type-2 the two last Î²-sheets are located in the N-terminal part of the domain (Î±-Î²-Î²-Î±-Î±-Î²). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-2 KH domain include eukaryotic and prokaryotic S3 family of ribosomal proteins, and the prokaryotic GTP-binding protein era.
Wikipedia: The K Homology (KH) domain is a protein domain that was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. An evolutionarily conserved sequence of around 70 amino acids, the KH domain is present in a wide variety of nucleic acid-binding proteins. The KH domain binds RNA, and can function in RNA recognition. It is found in multiple copies in several proteins, where they can function cooperatively or independently. For example, in the AU-rich element RNA-binding protein KSRP, which has 4 KH domains, KH domains 3 and 4 behave as independent binding modules to interact with different regions of the AU-rich RNA targets. The solution structure of the first KH domain of FMR1 and of the C-terminal KH domain of hnRNP K determined by nuclear magnetic resonance (NMR) revealed a beta-alpha-alpha-beta-beta-alpha structure. Autoantibodies to NOVA1, a KH domain protein, cause paraneoplastic opsoclonus ataxia. The KH domain is found at the N-terminus of the ribosomal protein S3. This domain is unusual in that it has a different fold compared to the normal KH domain.
Pfam PF17607: Family of unknown function (DUF5503) (family)
This is a family of unknown function found in Enterobacteriaceae.
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 PF18963: Family of unknown function (DUF5703) (family)
This family includes members mostly found in Actinobacteria. Some family members are thought to be dihydroorotate dehydrogenases, however there is no evidence to support the relationship to [pfam:PF01180].
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 PF20927: Huntingtin, C-terminal HEAT (repeat)
This entry represents the C-terminal domain of Huntingtin (Htt), which consists of HEAT repeats. Htt is expressed in many tissues with various expression levels and is involved in a number of cellular functions. However, its exact function is not yet clear. An an abnormal polyglutamine (polyQ) expansion in this protein causes Huntington's disease (HD) a progressive autosomal-dominant neurodegenerative disease characterised by an uncontrolled motor movement known as chorea, cognitive disorder and depression. HTT consists of multiple HEAT repeats organised in N-terminal ([pfam:PF20926] and [pfam:PF12372]), bridge ([pfam:PF20925]) and C-terminal domains, which function as a scaffold that mediated interactions with binding partners. It has been suggested that the polyQ expansion in Htt alters phosphorylation status along the protein which affects its structure and function. In particular, modifications of phosphorylation in this domain induce conformational changes that impair its movement and interaction with the N-HEAT domain.
Pfam PF11202: Tellurite-like stress resistance cysteine protease StiP (family)
This family is fused to a C-terminal RNA binding Pelota domain, [pfam:PF01248]. These genes are found in the biosynthetic operon associated with the Ter stress response operon and are predicted to be involved in the biosynthesis of a ribo-nucleoside involved in stress response.
Pfam PF22604: Tetracyclin repressor-like HI_0893, C-terminal domain (domain)
This entry represents the C-terminal domain of some HTH-type transcriptional repressors, such as HI_0893 from Haemophilus influenzae.
Pfam PF23172: Nuclear receptor coactivators bHLH domain (domain)
This bHLH domain is found in the family of nuclear receptor coactivators NCOA1, NCOA2, and NCOA3. The NCOAs bind to nuclear hormone receptors in a ligand-dependent manner and mediate the transcriptional activation of the downstream target genes in response to hormones, metabolites, xenobiotics, and drugs.
Pfam PF09867: TagF N-terminal domain, Type VI secretion system-associated (domain)
This is the N-terminal domain of the T6S-associated protein, TagF. A post-translational repressor of the hemolysin co-regulated secretion island I (HSI-I)-encoded type VI secretion system (H1-T6SS) found in Pseudomonas aeruginosa. The type VI secretion system (T6SS) is found broadly among the Proteobacteria and is implicated in diverse processes including host-cell interactions, biofilm formation and gene regulation. Furthermore, studies indicate that the T6SS plays a critical role in interbacterial interactions. TagF has been shown to regulate the activity of the H1-T6SS in a manner that does not require phosphorylated-Fha1, PpkA, or other Tag proteins. Additionally TagF is found to associate as a homodimer with nearly identical monomers composed of alpha and beta elements assembled as a three-layer sandwich (alpha-beta-alpha).
Pfam PF18237: Tk-SP N-propeptide domain (domain)
This is the N-propeptide domain found in Tk-SP, a subtilisin-like serine protease from Thermococcus kodakaraensis. The beta sheet of this domain packs tightly to the two nearly parallel alpha helices 2 and 3 located at the surface of the subtilisin domain. Gln105 and Asp107 of the N-propeptide domain also bind to the N-termini of these two alpha-helices to form helix caps.
Pfam PF16311: Transmembrane protein 100 (family)
This family of proteins is found in eukaryotes. Proteins in this family are approximately 130 amino acids in length. There is some apparent similarity with family the phosphoinositide-interacting protein family PIRT, [pfam:PF15099], because those proteins are also transmembrane proteins.
Pfam PF05719: Golgi phosphoprotein 3 (GPP34) (family)
This family consists of several eukaryotic GPP34 like proteins. GPP34 localises to the Golgi complex and is conserved from yeast to humans. The cytosolic-ally exposed location of GPP34 predict a role for a novel coat protein in Golgi trafficking.
Pfam PF13277: YmdB-like protein (domain)
This family of putative phosphoesterases contains the B. subtilis protein YmdB [swissprot:O31775].
Pfam PF17488: Herpesvirus glycoprotein H C-terminal domain (domain)
Herpesvirus glycoprotein H (gH) is a virion associated envelope glycoprotein. Complex formation between gH and gL has been demonstrated in both virions and infected cells. This entry represents the C-terminal domain.
Pfam PF16260: Domain of unknown function (DUF4914) (family)
This family consists of uncharacterized proteins around 630 residues in length and is mainly found in various Thermotoga, Thermoanaerobacter and Carboxydibrachium species. The function of this family is unknown.
Pfam PF06403: Lamprin (family)
This family consists of several lamprin proteins from the Sea lamprey Petromyzon marinus. Lamprin, an insoluble non-collagen, non-elastin protein, is the major connective tissue component of the fibrillar extracellular matrix of lamprey annular cartilage. Although not generally homologous to any other protein, soluble lamprins contain a tandemly repeated peptide sequence (GGLGY) which is present in both silkmoth chorion proteins and spider dragline silk. Strong homologies to this repeat sequence are also present in several mammalian and avian elastins. It is thought that these proteins share a structural motif which promotes self-aggregation and fibril formation in proteins through interdigitation of hydrophobic side chains in beta-sheet/beta-turn structures, a motif that has been preserved in recognisable form over several hundred million years of evolution.
Wikipedia: In molecular biology, the lamprin family of proteins consists of several lamprin proteins from the Sea lamprey Petromyzon marinus. Lamprin, an insoluble non-collagen, non-elastin protein, is the major connective tissue component of the fibrillar extracellular matrix of lamprey annular cartilage.
Pfam PF15041: Tektin bundle interacting protein 1 (family)
This family includes Tektin bundle interacting protein 1 (TKTI1) which has been recently characterised as a microtubule inner protein (MIP) part of the dynein-decorated doublet microtubules (DMTs) in cilia axoneme, which is required for motile cilia beating. It is located at the center of the tektin bundle where may function to recruit tektins or stabilize the bundle.
Pfam PF07928: Vps54-like protein (family)
This family contains various proteins that are homologs of the yeast Vps54 protein, such as the rat homolog  ([swissprot:Q9JMK8]), the human homolog ([swissprot:Q86YF7]), and  the mouse homolog ([swissprot:Q8R3X1]). In yeast, Vps54 associates with Vps52 and Vps53 proteins to form a trimolecular complex  that is involved in protein transport between Golgi, endosomal, and vacuolar compartments. All Vps54 homologs contain a coiled coil region (not found in the region featured in this family) and multiple dileucine motifs.
Pfam PF11624: MHC class I-like protein M157 (family)
This family of proteins represents M157,a divergent form of MHC class I-like proteins which is the protein product of the mouse cytomegalovirus. This protein is unique in its ability to engage both activating (Ly49H) and inhibitory (Ly49I) natural killer cell receptors. M157 is involved in intra- and intermolecular interacts within and between its domains to form a compact MHC-like molecule.
Pfam PF13475: Domain of unknown function (DUF4116) (repeat)
This entry represents a domain found in proteins from lower eukaryotes and bacteria. The function of this domain 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 PF06136: SOSEKI protein DIX-like domain (domain)
This entry represents a group of plant proteins, including protein SOSEKI1-5 from Arabidopsis thaliana and Physcomitrium patens. SOK1-5 integrate apical-basal and radial organismal axes to localise to polar cell edges and contain a DIX oligomerization domain that resembles that in the animal Dishevelled polarity regulator.
Pfam PF23256: Plant cation/H(+) antiporter domain (domain)
This domain is found in Cation/H(+) antiporter 17 from Arabidopsis thaliana (CHX17) and similar plant sequences. CHX17 functions as a K+/H+ antiporter that controls K+ acquisition and homeostasis. This protein has a highly hydrophobic N-terminal domain ([pfam:PF00999]) and a C-terminal region predicted to be non cytoplasmic. This entry represents the first domain of this region, which is thought to adopt an alpha-beta configuration.
Pfam PF03471: Transporter associated domain (domain)
This small domain is found in a family of proteins with the [pfam:PF01595] domain and two CBS domains with this domain found at the C-terminus of the proteins, the domain is also found at the C terminus of some Na+/H+ antiporters. This domain is also found in CorC that is involved in Magnesium and cobalt efflux. The function of this domain is uncertain but might be involved in modulating transport of ion substrates.
Pfam PF24517: Carbohydrate-binding module family 96 (domain)
This entry represents a CBM domain, a member of CBM96 family, found in functionally diverse multi-domain proteins including tRNA nuclease WapA, alginate lyase from Defluviitalea phaphyphila and chondroitinase from Dysgonomonas sp. The CBM96 domain from the latter proteins, has been structurally characterised. It fold into a beta-sandwich with significant structural similarity to nucleoplasmin (PDB:8WAB, PDB:7VBO).
Pfam PF01909: Nucleotidyltransferase domain (domain)
Members of this family belong to a large family of nucleotidyltransferases. This family includes kanamycin nucleotidyltransferase (KNTase) which is a plasmid-coded enzyme responsible for some types of bacterial resistance to aminoglycosides. KNTase in-activates antibiotics by catalysing the addition of a nucleotidyl group onto the drug.
Pfam PF11615: CCR4-associated factor 4 (family)
Caf4 is a WD40 repeats containing protein involved in mitochondrial  fission. It displays physical interactions with CCR4-NOT complex.  It has a paralogue, Mdv1. Both Caf4 and Mdv1 act as adapter proteins,  binding to Fis1 on the mitochondrial outer membrane and recruiting  the dynamin-like GTPase Dnm1 to form mitochondrial fission  complexes. However, Fis1 and Caf4, but not Mdv1, determine  the polar localization of Dnm1 clusters on the mitochondrial  surface.
Pfam PF07307: Heptaprenyl diphosphate synthase (HEPPP synthase) subunit 1 (domain)
This family contains subunit 1 of heptaprenyl diphosphate synthase (HEPPP synthase) ([ec:2.5.1.30]) (approximately 230 residues long) from Bacilli. The enzyme consists of two subunits, both of which are required for catalysis of heptaprenyl diphosphate synthesis. This family corresponds to the regulatory subunit.
Pfam PF03990: G5-linked-Ubiquitin-like domain (domain)
This domain normally occurs as tandem repeats; however it is found as a single copy in the S. cerevisiae DNA-binding nuclear protein YCR593 ([swissprot:P25357]). This protein is involved in sporulation part of the SET3C complex, which is required to repress early/middle sporulation genes during meiosis (). The bacterial proteins are likely to be involved in a cell wall function as they are found in conjunction with the [pfam:PF07501] domain, which is involved in various cell surface processes. This domain is also present in the resuscitation-promoting factors RpfB from Mycobacterium tuberculosis and Rpf2 from Corynebacterium glutamicum. These are factors that stimulate resuscitation of dormant cells. This domain has a beta grasp fold. Structural description of this domain revealed a structural conservation between these domains and ubiquitin, hence it is termed UBL-G5.
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 PF02323: Egg-laying hormone precursor (family)
This family consists of egg-laying hormone (ELH) precursor and atrial gland peptides form little and California sea hare. The family also includes ovulation prohormone precursor from great pond snail. This family thus represents a conserved gastropoda ovulation and  egg production prohormone.  Note that many of the proteins present  are further cleaved to give individual peptides. Neuropeptidergic bag cells of the marine mollusk Aplysia californica synthesise an egg-laying hormone (ELH) precursor protein which is  cleaved to generate several bioactive peptides including ELH,  bag cell peptides (BCP) and acidic peptide (AP).