SII-SWORD/CoKE huggingface dataset:
Pfam PF10128: Glucose-6-phosphate dehydrogenase subunit N-terminal domain (domain)
Members of this family are found in various prokaryotic OpcA and glucose-6-phosphate dehydrogenase proteins. This entry represents the N-terminal Rossmann like domain.
Pfam PF18777: Chromosome region maintenance or exportin repeat (repeat)
Chromosome region maintenance 1 or exportin 1 mediates the nuclear  transport of proteins bearing a leucin-rich nuclear export signal  (NES). It contains helical repeats that are structurally similar to HEAT repeats, but share little sequence similarity with them. N-terminal, C-terminal and central repeats show slightly different  structural arrangements, with N- and C- termini repeats interacting with each other. This entry represents the central repeats of CRM1.
Pfam PF22557: Dual OB-containing domain (domain)
This entry contains two domain copies of the OB fold. There is nearly absolutely conserved cysteine, serine/threonine, arginine, and aspartate residues which are predicted to line a deep cleft formed at the interface of the two OB domains. The predicted spatial arrangement of the tandem OB domains closely parallels OB-dyads from single-stranded nucleic acid-end binding proteins, such as the telomere-binding domain alpha-subunit, with the nucleic acid being lodged in a cleft formed by the two OB domains. Drawing an analogy to the SRAP domain, it has been suggested that the DuOB domain could potentially form crosslinks to DNA at the abasic sites via its conserved cysteine. It is found on the genome adjacent to DUF488 and DUF4326 proteins, which could potentially also catalyse thiotransfer reactions required for forming or resolving the cysteine-DNA crosslinks, paralleling recent findings where HD phosphatases mediate the transfer of a phosphorylated substrate to a hydroxyl-group-containing residue.
Pfam PF15456: Up-regulated During Septation (family)
Uds1 is a domain family is found mostly in fungi, and is typically between 120 and 138 amino acids in length. The GO annotation for the S.pombe protein describes the protein as barrier septum assembly involved in cell cycle cytokinesis, GO:0071937. Many of the uncharacterised members are listed as being involucrin repeat proteins, but this can not be substantiated.
Pfam PF08546: Ketopantoate reductase PanE/ApbA C terminal (domain)
This is a family of 2-dehydropantoate 2-reductases also known as ketopantoate reductases, [ec:1.1.1.169].  The reaction catalysed by this enzyme is: (R)-pantoate + NADP(+)  2-dehydropantoate + NADPH.  AbpA catalyses the NADPH reduction of ketopantoic acid to pantoic acid in the alternative pyrimidine biosynthetic (APB) pathway.  ApbA and PanE are allelic.  ApbA, the ketopantoate reductase enzyme is required for the synthesis of thiamine via the APB biosynthetic pathway.
Pfam PF17111: Pigment biosynthesis cluster protein PigL N-terminal (domain)
This entry represents the N-terminal domain of Azaphilone pigments biosynthesis cluster protein L (PigL) and similar fungal sequences which were formerly known as Helo_like, predicted fungal STAND NTPases. PigL which is part of the gene cluster that mediates the biosynthesis of azaphilone pigments (MonAzPs), a complex mixture of compounds with a common azaphilone skeleton very widely used as food colourants.
Pfam PF23290: Transcription elongation factor SPT5, fifth KOW domain (domain)
This entry includes Transcription elongation factor SPT5, a component of the elongation factor DRB-sensitivity inducing factor (DSIF) that plays multiple roles during transcription. SPT5 is a multidomain protein consisting of an N-terminal NusG domain ([pfam:PF03439]), tandem of KOW domains and and a mobile C-terminal-repeat region. The KOW domains differ in number between yeast, which has five, and animals, which have seven. This entry represents the fifth KOW domain of SPT5. The KOW domains of these proteins play critical roles in recruitment of multiple other eukaryotic transcription elongation and RNA biogenesis factors, and they are also involved in the binding of the eukaryotic SPT5 proteins to RNA polymerases.
Pfam PF21765: A2MG, CUB domain (domain)
This domain is found in a group of proteins predominantly found in proteobacteria, including Alpha-2-macroglobulin (A2MG) from Salmonella typhimurium, a protein that protects the bacterial cell from host peptidases. A2MG is composed of 13 domains, 12 of them folding as beta sandwiches. This entry represents the CUB (complement C1r/C1s, Uegf, Bmp1) domain, which is connected to the TED domain ([pfam:PF07678]).
Pfam PF11515: Mouse development and cellular proliferation protein Cullin-7 (family)
The Cullin Ring Ligase family member, Cul7, is required for normal mouse development and cellular proliferation. Cul7 has a CPH domain which is a p53 interaction domain. The CPH domain interaction surface of P53 is present in the tetramerisation domain.
Pfam PF05633: Protein ROH1-like (family)
This family consists of several plant proteins and includes RHO1, an interactor of the exocyst subunit Exo70A1 and has been shown to be required for seed coat mucilage deposition.
Pfam PF07304: Steroid receptor RNA activator (SRA1) (family)
This family consists of several hypothetical mammalian steroid receptor RNA activator proteins. SRA-RNAs likely to encode stable proteins are widely expressed in breast cancer cell lines. SRA-RNA is a steroid receptor co-activator which acts as a functional RNA and is classified as belonging to the growing family of functional non-coding RNAs.
Pfam PF05134: Type II secretion system (T2SS), protein L (family)
This family consists of Type II secretion system protein L sequences from several Gram-negative (diderm) bacteria. The Type II secretion system, also called Secretion-dependent pathway (SDP), is responsible for extracellular secretion of a number of different proteins, including proteases and toxins. This pathway supports secretion of proteins across the cell envelope in two distinct steps, in which the second step, involving translocation through the outer membrane, is assisted by at least 13 different gene products. T2SL is predicted to contain a large cytoplasmic domain represented by this family and has been shown to interact with the autophosphorylating cytoplasmic membrane protein T2SE. It is thought that the tri-molecular complex of T2SL, T2SE ([pfam:PF00437]) and T2SM ([pfam:PF04612]) might be involved in regulating the opening and closing of the secretion pore and/or transducing energy to the site of outer membrane translocation.
Pfam PF07742: BTG family (family)
This entry represents a conserved domain found in the N-terminal of the BTG family members (also known as anti-proliferative proteins). In mammals, BTG family comprises six proteins: BTG1, BTG2/PC3/Tis21, BTG3/ANA, BTG4/PC3B, Tob1/Tob and Tob2. They regulate cell cycle progression in a variety of cell types .

These proteins have from 158 to 363 amino acid residues, that are highly similar and include 3 conserved cysteine residues. BTG2 seems to have a signal sequence; while the other proteins may lack such a domain.
Pfam PF25096: Domain of unknown function (DUF7808) (domain)
This domain is found in Uncharacterized protein T05H10.3 from C.elegans and related nematode proteins. It is predicted to adopt a beta-sandwich with similarity to domains members of H-lectin-like superfamily. This domain contains several highly conserved cysteine residues that are predicted to form disulfide bonds.
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 PF15152: Kisspeptin (domain)
Kisspeptin (KiSS-1) is a metastasis suppressor protein found in malignant melanomas and in some breast cancers . KiSS-1 may regulate events downstream of cell-matrix adhesion, which could involve cytoskeletal reorganisation. KiSS-1 generates a C-terminally amidated peptide, metastin, which functions as the endogenous ligand of the G-protein coupled receptor GPR54. Activation of the receptor inhibits cell proliferation and cell migration, key characteristics of tumour metastasis. Kp-10 is a decapeptide derived from the primary translation product, isolated in conditioned medium of first trimester trophoblast . Kp-10, but not other kisspeptins, increased intracellular Ca2+ levels in isolated first trimester trophoblasts. Kp-10 is a paracrine/endocrine regulator in fine-tuning trophoblast invasion generated by the trophoblast itself. The receptor is also essential for normal gonadotropin-released hormone physiology and for puberty. The hypothalamic KiSS1/GPR54 system is a pivotal factor in central regulation of the gonadotropic axis at puberty and in adulthood .
Wikipedia: Kisspeptins are proteins encoded by the KISS1 gene in humans. Kisspeptins are ligands of the G-protein coupled receptor, GPR54. Kiss1 was originally identified as a human metastasis suppressor gene that has the ability to suppress melanoma and breast cancer metastasis. Kisspeptin-GPR54 signaling has an important role in initiating secretion of gonadotropin-releasing hormone (GnRH) at puberty, the extent of which is an area of ongoing research. Gonadotropin-releasing hormone is released from the hypothalamus to act on the anterior pituitary triggering the release of luteinizing hormone (LH), and follicle stimulating hormone (FSH). These gonadotropic hormones lead to sexual maturation and gametogenesis. Disrupting GPR54 signaling can cause hypogonadotrophic hypogonadism in rodents and humans. The Kiss1 gene is located on chromosome 1. It is transcribed in the brain, adrenal gland, and pancreas.
Pfam PF14671: Dual specificity protein phosphatase, N-terminal half (domain)
The active core of the dual specificity protein phosphatase is made up of two globular domains both with the DSP-like fold. This family represents the N-terminal half of the core. These domains are arranged in tandem, and are associated via an extensive interface to form a single globular whole. The conserved PTP signature motif (Cys-[X]5-Arg) that defines the catalytic centre of all PTP-family members is located within the C-terminal domain, family DSPc, [pfam:PF00782]. Although the centre of the catalytic site is formed from DSPc, two loops from the N-terminal domain, DSPn, also contribute to the catalytic site, facilitating peptide substrate specificity.
Pfam PF19257: BURAN domain (domain)
This presumed domain is found exclusively in the CCAR1 protein.
Pfam PF05157: MshEN domain (domain)
This domain is found at the N-terminus of the Type II secretion secretion system protein E (GspE) and type IV pilus extensin ATPase PilB and near the C-terminus of the glycosyltransferase NfrB. A variant of this domain, called MshEN, binds cyclic di-GMP, which modulates the activity of the respective protein. The structure of this domain is now known.
Pfam PF03661: Transmembrane protein 33/Nucleoporin POM33 (family)
This is an integral membrane protein family. Family members include TMEM33/Pom33 proteins. Budding yeast Pom33 is a transmembrane nucleoporin that contributes to proper distribution and/or efficient assembly of nuclear pores. Proteins in this entry also include Tts1 from fission yeasts, Kr-h2 (krueppel homologue 2) from flies and TMEM33 from vertebrates. Tts1 is required for the correct positioning of the cellular division plane by delimiting the actomyosin ring assembly at the cell equator. Kr-h2 is a member of the dosage-dependent hierarchy effective upon white gene expression. TMEM33 regulates the tubular structure of endoplasmic reticulum by suppressing the membrane-shaping activity of reticulons.
Pfam PF13425: O-antigen ligase like membrane protein (family)
This entry represents a functionally uncharacterised group of proteins predominantly found in firmicutes (Bacillota bacteria). AlphaFold predicts that this family adopts a fold structurally similar to O-antigen ligase WaaL and peptidoglycan glycosyltransferase RodA .
Pfam PF01208: Uroporphyrinogen decarboxylase (URO-D) (domain)
Uroporphyrinogen decarboxylase (URO-D), the fifth enzyme of the haem biosynthetic pathway, catalyses the sequential decarboxylation of the four acetyl side chains of uroporphyrinogen to yield coproporphyrinogen . URO-D deficiency is responsible for the human genetic diseases familial porphyria cutanea tarda (fPCT) and hepatoerythropoietic porphyria (HEP). The sequence of URO-D has been well conserved throughout evolution. The best conserved region is located in the N-terminal section; it contains a perfectly conserved hexapeptide. There are two arginine residues in this hexapeptide which could be involved in the binding, via salt bridges, to the carboxyl groups of the propionate side chains of the substrate.

The crystal structure of human uroporphyrinogen decarboxylase shows it as comprised of a single domain containing a (Î²/Î±)8-barrel with a deep active site cleft formed by loops at the C-terminal ends of the barrel strands. URO-D is a dimer in solution. Dimerisation juxtaposes the active site clefts of the monomers, suggesting a functionally important interaction between the catalytic centres .
Pfam PF23916: Endo-beta-N-acetylglucosaminidase EndoS TIM-barrel domain (domain)
This entry represents the TIM barrel domain found in Endo-beta-N-acetylglucosaminidase EndoS from Streptococcus spp. EndoS is a secreted protein that catalyses the hydrolysis of the N-linked oligosaccharides on opsonizing immunoglobulin G, thus contributing to immune response evasion and increased survival of the bacteria in patients. This domain binds to complex-type N-glycans and has enzymatic activity.
Pfam PF11546: Staphylococcal complement inhibitor SCIN (family)
SCIN is released by Staphylococcus aureus to counteract the host immune defense. The protein binds to and inhibits C3 convertases on the bacterial surface, reducing phagocytosis and blocking downstream effector functions by C3b deposition on its surface. An 18 residue stretch 31-48 is crucial for SCIN activity.
Pfam PF02789: Cytosol aminopeptidase family, N-terminal domain (domain)
This group of metallopeptidases belong to the MEROPS peptidase family M17 (leucyl aminopeptidase family, clan MF), the type example being leucyl aminopeptidase from Bos taurus (Bovine).
Over 70 metallopeptidase families have been identified to date. In these enzymes a divalent cation which is usually zinc, but may be cobalt, manganese or copper, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. In some families of co-catalytic metallopeptidases, two metal ions are observed in crystal structures ligated by five amino acids, with one amino acid ligating both metal ions. The known metal ligands are His, Glu, Asp or Lys. At least one other residue is required for catalysis, which may play an electrophillic role. Many metalloproteases contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site . The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases .
Pfam PF18129: Xrn1 SH3-like domain (domain)
This is the C-terminal SH3-like domain which can be found in the exoribonuclease Xrn1. Xrn1 is a 175 kDa processive exoribonuclease that is conserved from yeast to mammals which targets cytoplasmic RNA substrates marked by a 5' monophosphate for processive 5'-to-3' degradation.  The Sh3-like domain in Xrn1 lacks the canonical SH3 residues normally involved in binding proline-rich peptide motifs and instead engages in non-canonical interactions with the catalytic domain. Additionally it is essential in maintaining the structural integrity of Xrn1, since partial truncation of this domain in yeast Xrn1 yields an inactive protein. There is a long loop projecting from the SH3-like domain that contacts the PAZ/Tudor domain, occluding the functional surface that binds RNA or peptide motifs containing methylated arginines, respectively, in canonical PAZ and Tudor domain.
Pfam PF22610: Histidine kinase, HAMP domain (domain)
This domain is found at the N-terminal end of the histidine kinase SMU_1516 from Streptococcus mutans (CovS) and similar proteins mainly found in bacilli. CovS plays a role in the regulation of acid production and tolerance conducive to dental caries, including proton expulsion. This protein has one transmembrane domain before a HAMP signal transducer domain (this entry), a PAS sensor domain ([pfam:PF00989]), a DHp domain ([pfam:PF00512]) and a CA domain ([pfam:PF02518]). This domain shows two alpha- helices that form a parallel four-helical coiled-coil when the protein dimerises.
Pfam PF16516: Leucine zipper of domain CC2 of NEMO, NF-kappa-B essential modulator (coiled_coil)
CC2-LZ is a leucine-zipper domain associated with the CC2 coiled-coil region of NF-kappa-B essential modulator, NEMO. It plays a regulatory role, along with the very C-terminal zinc-finger; it contains a ubiquitin-binding domain (UBD) and represents one region that contributes to NEMO oligomerisation. NEMO itself is an integral part of the IkappaB kinase complex and serves as a molecular switch via which the NF-kappaB signalling pathway is regulated.
Pfam PF07032: Protein of unknown function (DUF1322) (family)
This family consists of several hypothetical 9.4 kDa Borrelia burgdorferi (Lyme disease spirochete) proteins of around 78 residues in length. The function of this family is unknown.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF24007: Domain of unknown function (DUF7321) (domain)
This domain is found in uncharacterised archaeal proteins. It is predicted to fold into a four-helical bundle and it is likely associated with the membrane.
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 PF11660: Protein of unknown function (DUF3262) (family)
This family of proteins with unknown function appears to be restricted to Proteobacteria.
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 PF09749: Uncharacterised conserved protein (family)
This entry is of proteins of approximately 300 residues conserved from plants to humans.  It contains two conserved motifs, HxSL and FHVSL. The function is unknown.
Pfam PF19706: Family of unknown function (DUF6203) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001944) is described by MIBiG as an example of the following biosynthetic class, polyketide. It includes a member from the funisamine biosynthetic gene cluster from Streptosporangium sp..
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 PF18294: Peptidase S41 N-terminal domain (domain)
This domain is found in the N-terminal region of proteins carrying the peptidase S41 domain (Pfam: PF03572) in Bacteroidetes.
Pfam PF01650: Peptidase C13 family (family)
Members of this family are asparaginyl peptidases. The blood fluke parasite Schistosoma mansoni has at least five Clan CA cysteine peptidases in its digestive tract including cathepsins B (2 isoforms), C, F and L. All have been recombinantly expressed as active enzymes, albeit in various stages of activation. In addition, a Clan CD peptidase, termed asparaginyl endopeptidase or 'legumain' has been identified. This has formerly been characterised as a 'haemoglobinase', but this term is probably incorrect.  Two cDNAs have been described for Schistosoma mansoni legumain; one encodes an active enzyme whereas the active site cysteine residue encoded by the second cDNA is substituted by an asparagine residue. Both forms have been recombinantly expressed.
Pfam PF22231: DEAD box helicase Hera, RNA-binding domain (domain)
This domain is found at the C-terminal end DEAD box helicase Hera from Thermus thermophilus. This entry represents the RNA binding domain, which is located C-terminal to the dimerisation domain [pfam:PF21591]. This domain is responsible for binding of Hera to 23S rRNA. It consists of a central four-stranded beta-sheet, flanked by an alpha-helix, and a long loop connecting beta-strands 3 and 4 that replaces helix alpha2 present in canonical RNA recognition motif (RRM).
Pfam PF10562: Calmodulin-binding domain C0 of NMDA receptor NR1 subunit (domain)
This is a very short highly conserved domain that is C-terminal to the cytosolic transmembrane region IV of the NMDA-receptor 1. It has been shown to bind Calmodulin-Calcium with high affinity. The ionotropic N-methyl-D-aspartate receptor (NMDAR) is a major source of calcium flux into neurons in the brain and plays a critical role in learning, memory, neural development, and synaptic plasticity. Calmodulin (CaM) regulates NMDARs by binding tightly to the C0 and C1 regions of their NR1 subunit. The conserved tryptophan is considered to be the anchor residue.
Pfam PF08600: NuBaID, C-terminal domain (domain)
This entry represents the C-terminal zinc finger domain of Zinc finger C3HC-type protein 1 (ZC3HC1, also known as Nuclear- interacting partner of ALK (NIPA)) and mRNA export factor Rsm1 which is a homologue from S. pombe. These proteins contain a C3HC-type zinc finger at the N terminus followed by the domain represented in this entry. These N- and C-terminal zinc finger domains are homologous and both are related to BIR domains. The zinc ion coordination occurs exclusively via four invariant amino acids (C2HC), in a mode similar to the BIR domains. This domain can harbour a large insert after the first two conserved cysteine residues, which is probably intrinsically disordered. Both N- and C-terminal (this entry) zinc finger domains were found to be essential for binding TPR/Mlp1 and therefore denoted as the nuclear basket-interaction domain (NuBaID), representing an evolutionary conserved integral functional unit.
Pfam PF04525: LURP-one-related (domain)
The structure of this family has been solved. It comprises a 12-stranded beta barrel with a central C-terminal alpha helix. This helix is thought to be a transmembrane helix. It is structurally similar to the C-terminal domain of the Tubby protein. In plants it plays a role in defense against pathogens.