SII-SWORD/CoKE huggingface dataset:
Pfam PF00473: Corticotropin-releasing factor family (domain)
This entry represents a domain found in the corticotropin-releasing factor family members.

Corticotropin-releasing factor (CRF), urotensin-I, urocortin and sauvagine form a family of related neuropeptides in vertebrates. The family can be grouped into 2 separate paralogous lineages, with urotensin-I, urocortin and sauvagine in one group and CRF forming the other group. Urocortin and sauvagine appear to represent orthologues of fish urotensin-I in mammals and amphibians, respectively. The peptides have a variety of physiological effects on stress and anxiety, vasoregulation, thermoregulation, growth and metabolism, metamorphosis and reproduction in various species, and are all released as preprohormones .

CRF  is a hormone found mainly in the paraventricular nucleus of the mammalian hypothalamus that regulates the release of corticotropin (ACTH) from the pituitary gland. From here, CRF is transported to the anterior pituitary, stimulating adrenocorticotropic hormone (ACTH) release via CRF type 1 receptors, thereby activating the hypothalamo-pituitary-adrenocortical axis (HPA) and thus glucocorticoid release.

CRF is evolutionary related to a number of other active peptides. Urocortin acts in vitro to stimulate the secretion of adrenocorticotropic hormone. Urotensin is found in the teleost caudal neurosecretory system and may play a role in osmoregulation and as a corticotropin-releasing factor. Urotensin-I is released from the urophysis of fish, and produces ACTH and subsequent cortisol release in vivo. The nonhormonal portion of the prohormone is thought to be the urotensin binding protein (urophysin). Sauvagine (P01144), isolated from frog skin, has a potent hypotensive and diuretic effect.
Wikipedia: Corticotropin-releasing factor family, CRF family is a family of related neuropeptides in vertebrates. This family includes corticotropin-releasing hormone, urotensin-I, urocortin, and sauvagine. The family can be grouped into 2 separate paralogous lineages, with urotensin-I, urocortin and sauvagine in one group and CRH forming the other group. Urocortin and sauvagine appear to represent orthologues of fish urotensin-I in mammals and amphibians, respectively. The peptides have a variety of physiological effects on stress and anxiety, vasoregulation, thermoregulation, growth and metabolism, metamorphosis and reproduction in various species, and are all released as prohormones.
Pfam PF23707: P116-like protein (family)
The P116 protein (MPN213) from Mycoplasma pneumoniae is an essential cell surface protein that extracts lipids, including cholesterol, phosphatidylcholine and sphingomyelin, from the host environment for incorporation into the bacterial membrane. The structure of P116, solved by cryo-electron microscopy, reveals a novel protein fold consisting of a homodimeric core domain with a large hydrophobic cavity that binds and extracts lipids. Each monomer also contains an N-terminal domain. Conformational changes between the lipid-bound and lipid-free states suggest a mechanism for lipid uptake and delivery into the mycoplasma membrane. P116 orthologs are found in several other Mycoplasma species.
Pfam PF17644: Jelly-roll domain of 30K viral movement proteins (domain)
This entry represents the core domain found in viral movement proteins (MP) of the 30K type. The core domain is conserved among MPs of 30K sharing the same predicted secondary structure which consists of 1 alpha-helix and 7 predicted beta-strands. The only sequence feature common to all 30K MPs is a short region between beta-strands 1 and 2, which contains several conserved hydrophobic positions, and a nearly-invariant aspartate which constitutes the sequence signature of the superfamily. This signature aspartate has a conserved role in essential for viral cell-to-cell movement. It has been shown that this domain is structurally related to jelly roll capsid proteins from plant viruses.
Pfam PF16462: Phage tail assembly chaperone protein, TAC (family)
This is a family of Siphoviridae phage tail assembly chaperone proteins.
Pfam PF10258: Phosphorylated adapter RNA export protein, RNA-binding domain (domain)
The phosphorylated adaptor for RNA export (PHAX) protein transports U3 snoRNA from the nucleus after transcription. This entry represents the highly conserved U3 snoRNA-binding domain of PHAX, which is characterised by having two pairs of adjacent glycines with the sequence motif GGx12GG. This domain adopts a novel helical fold and binds non-specific single-stranded RNA and comprises five alpha-helices linked by short loops containing 1 to 4 residues, apart from helices alpha3 and 4 that are linked by 13 residues. The fold is unique to this kind of RNA binding domains which show no structural homology with other RNA-binding domains.
Pfam PF11102: Group 4 capsule polysaccharide lipoprotein gfcB, YjbF (family)
This family includes lipoprotein GfcB (YmcC), involved in group 4 capsule polysaccharide formation. YjbF is a family of Gram-negative bacterial outer-membrane lipoproteins, predicted to be a beta-barrel and possibly a porin that is one of four gene-products expressed from an operon, yjbEFGH, which is regulated by the Rcs phosphorelay in a RcsA-dependent manner, similar to that of other exopolysaccharide biosynthetic pathways. It is highly possible that the yjbEFGH operon encodes a system involved in EPS secretion since none of the products is predicted to have enzymic activity, the products are all secreted and YbjF and H are predicted to be beta-barrel lipoproteins similar to porins. It may be that the operon products play some role in biofilm formation and/or matrix production.
Pfam PF08990: Erythronolide synthase docking domain (domain)
Polyketide synthase (PKS) catalyzes the biosynthesis of polyketides, which are structurally and functionally diverse natural products in microorganisms and plants. Type I modular PKSs are the large, multifunctional enzymes responsible for the production of a diverse family of structurally rich and often biologically active natural products. The efficiency of acyl transfer at the interfaces of the individual PKS proteins is thought to be governed by helical regions, termed docking domains (dd).  Two such N-terminal domains dimerise to form amphipathic parallel alpha-helical coiled coils: dimerisation is essential for protein function.
Pfam PF12348: CLASP N terminal (repeat)
This region is found at the N terminal of CLIP-associated proteins (CLASPs).      CLASPs are widely conserved microtubule plus-end-tracking proteins that regulate the stability of dynamic microtubules.  In yeast, Drosophila, and Xenopus, a single CLASP orthologue is present.  In mammals, a second paralogue (CLASP2) exists which has some functional overlap with CLASP1.
Pfam PF15639: Metallopeptidase toxin 3 (family)
A zincin-like metallopeptidase domain found in bacterial polymorphic toxin systems.
Pfam PF03773: Predicted permease (family)
This family of integral membrane proteins are predicted to be permeases of unknown specificity.
Pfam PF07452: CHRD domain (domain)
CHRD (after SWISS-PROT abbreviation for chordin) is a novel domain identified in chordin, an inhibitor of bone morphogenetic proteins.  This family includes bacterial homologues. It is anticipated to have an immunoglobulin-like beta-barrel structure based on limited similarity to superoxide dismutases but, as yet, no clear functional prediction can be made. Its most conserved feature is a GE[I/L]RCG[V/I/L] motif towards its C-terminal end Most bacterial proteins in this family have only one CHRD domain, whereas it is found repeated in many eukaryotic proteins such as human chordin ([swissprot:Q9H2X0]) and Drosophila SOG ([swissprot:Q24025])..
Wikipedia: Chordin is a protein with a prominent role in dorsal–ventral patterning during early embryonic development. In humans it is encoded for by the CHRD gene.
Pfam PF06293: Lipopolysaccharide kinase (Kdo/WaaP) family (family)
These lipopolysaccharide kinases are related to protein kinases [pfam:PF00069]. This family includes waaP (rfaP) gene product is required for the addition of phosphate to O-4 of the first heptose residue of the lipopolysaccharide (LPS) inner core region. It has previously been shown that WaaP is  necessary for resistance to hydrophobic and polycationic antimicrobials in E. coli and that it is required for virulence in invasive strains of S. enterica.
Wikipedia: In molecular biology, the lipopolysaccharide kinase (Kdo/WaaP) family is a family of lipopolysaccharide kinases that includes lipopolysaccharide core heptose(I) kinase rfaP. Lipopolysaccharide core heptose(I) kinase rfaP is required for the addition of phosphate to O-4 of the first heptose residue of the lipopolysaccharide (LPS) inner core region. It has previously been shown that it is necessary for resistance to hydrophobic and polycationic antimicrobials in E. coli and that it is required for virulence in invasive strains of Salmonella enterica. The family also includes 3-deoxy-D-manno-octulosonic acid kinase from Haemophilus influenzae, which phosphorylates Kdo-lipid IV(A), a lipopolysaccharide precursor, and is involved in virulence.
Pfam PF21646: Actin maturation protease-like, C-terminal domain (domain)
This domain is found at the C-terminal end of a group of proteins that includes the human protein ACTMAP (actin maturation protease, also known as C19orf54) and similar sequences from animals. ACTMAP is responsible for the noncanonical excision of the acetylated methionine of actin molecules after translation. It seems to have a crucial effect in all cell types.
Pfam PF04313: Type I restriction enzyme R protein N terminus (HSDR_N) (family)
This family consists of a number of N terminal regions found in type I restriction enzyme R (HSDR) proteins. Restriction and modification (R/M) systems are found in a wide variety of prokaryotes and are thought to protect the host bacterium from the uptake of foreign DNA. Type I restriction and modification systems are encoded by three genes: hsdR, hsdM, and hsdS. The three polypeptides, HsdR, HsdM, and HsdS, often assemble to give an enzyme (R2M2S1) that modifies hemimethylated DNA and restricts unmethylated DNA.
Pfam PF23460: ZMYND8 protein coiled-coil (coiled_coil)
This entry represents a coiled-coil that is predicted to self associate to form a dimeric arrangement found in the ZMYND8 protein.  The coiled coil is adjacent to a MYND zinc finger and is similar to that found in the ZMYND11 protein.  The ZMYND8 family comprises chromatin readers that recognize specific histone modifications to regulate transcription. Members of this family play roles in neuronal development, transcriptional repression, DNA damage repair, and transcription elongation. They interact with histones through domains such as the bromo domain, MYND-type zinc finger domain, and PWWP domain. These interactions enable them to recognize dual histone signatures, recruit chromatin remodeling complexes, and influence gene expression relevant to cellular differentiation and cancer progression.
Pfam PF00537: Scorpion toxin-like domain (domain)
This family contains both neurotoxins and plant defensins.  The mustard trypsin inhibitor, MTI-2, is plant defensin. It is a potent inhibitor of trypsin with no activity towards chymotrypsin. MTI-2 is toxic for Lepidopteran insects, but has low activity against aphids.  Brazzein is plant defensin-like protein. It is pH-stable, heat-stable and intensely sweet protein. The scorpion toxin (a neurotoxin) binds to sodium channels and inhibits the activation mechanisms of the channels, thereby blocking neuronal transmission. Scorpion toxins bind to sodium channels and inhibit the activation mechanisms of the channels, thereby blocking neuronal transmission
Wikipedia: Scorpion toxins are proteins found in the venom of scorpions. Their toxic effect may be mammal- or insect-specific and acts by binding with varying degrees of specificity to members of the Voltage-gated ion channel superfamily; specifically, voltage-gated sodium channels, voltage-gated potassium channels, and Transient Receptor Potential (TRP) channels. The result of this action is to activate or inhibit the action of these channels in the nervous and cardiac organ systems. For instance, α-scorpion toxins MeuNaTxα-12 and MeuNaTxα-13 from Mesobuthus eupeus are neurotoxins that target voltage-gated Na+ channels (Navs), inhibiting fast inactivation. In vivo assays of MeuNaTxα-12 and MeuNaTxα-13 effects on mammalian and insect Navs show differential potency. These recombinants exhibit their preferential affinity for mammalian and insect Na+ channels at the α-like toxins' active site, site 3, in order to inactivate the cell membrane depolarization faster[6]. The varying sensitivity of different Navs to MeuNaTxα-12 and MeuNaTxα-13 may be dependent on the substitution of a conserved Valine residue for a Phenylalanine residue at position 1630 of the LD4:S3-S4 subunit or due to various changes in residues in the LD4:S5-S6 subunit of the Navs. Ultimately, these actions can serve the purpose of warding off predators by causing pain or to subdue predators.
Pfam PF01477: PLAT/LH2 domain (domain)
This domain is found in a variety of membrane or lipid associated proteins. It is called the PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology) domain.  The known structure of pancreatic lipase shows this domain binds to procolipase [pfam:PF01114], which mediates membrane association. So it appears possible that this domain mediates membrane attachment via other protein binding partners. The structure of this domain is known for many members of the family and is composed of a beta sandwich.
Wikipedia: In molecular biology the PLAT domain is a protein domain that is found in a variety of membrane or lipid associated proteins. It is called the PLAT domain or LH2 domain. The known structure
of pancreatic lipase shows this domain binds to procolipase Pfam PF01114, which mediates membrane association.
Pfam PF18776: Hexapeptide repeat including loop (repeat)
This entry contains a single hexapeptide repeat unit including a loop between two strands.
Pfam PF23978: Family of unknown function (DUF7303) (family)
This family consists of various uncharacterized phage proteins and a few bacterial proteins. The family members range in length from 82 to 229 amino acids, with most in the 180 to 200 amino acid range. They are found in phages that infect Pseudomonas, Xanthomonas, Acinetobacter, Escherichia, Rhodobacter, Sphingomonas, Achromobacter, and Burkholderia bacteria. Bacterial proteins in the family are from Candidatus Macondimonas diazotrophica, Verrucomicrobium sp. GAS474 and Pelodictyon phaeoclathratiforme. The function of these proteins is currently 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 PF17732: Family of unknown function (DUF5571) (family)
This is a family of unknown function found in chordata. Family members carry a zinc finger family on the N-terminal [pfam:PF15663].
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 PF09035: Excisionase from transposon Tn916 (domain)
The phage-encoded excisionase protein Tn916-Xis adopts a winged-helix structure that consists of a three-stranded anti-parallel beta-sheet that packs against a helix-turn-helix (HTH) motif and a third C-terminal alpha-helix. It is encoded for by Tn916, which also codes for the integrase Tn916-Int. The protein interacts with DNA by the insertion of helix alpha-2 into the major groove and the contact of the hairpin that connects strands beta-2 and beta-3 with the adjacent phosphodiester backbone and/or minor groove. Tn916-Xis stimulates phage excision and inhibits viral integration by stabilising distorted DNA structures.
Pfam PF06470: SMC proteins Flexible Hinge Domain (domain)
This family represents the hinge region of the SMC (Structural Maintenance of Chromosomes) family of proteins. The hinge region is responsible for formation of the DNA interacting dimer. It is also possible that the precise structure of it is an essential determinant of the specificity of the DNA-protein interaction ().
Pfam PF21341: TRAF2, second zinc finger (domain)
TRAF2 regulates activation of NF-kappa-B and JNK and plays a central role in the regulation of cell survival and apoptosis. It has E3-ubiquitin protein ligase activity and promotes K63-linked ubiquitination of target proteins. It consists of an N-terminal domain with RING ([pfam:PF00097]) and several zinc fingers, and a C-terminal TRAF domain that comprises a coiled-coil ([pfam:PF16673]) and a TRAF-C domain. This entry represents the second beta-beta-alpha zinc finger.
Pfam PF11391: Protein of unknown function (DUF2798) (family)
This family of 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 PF15589: Immunity protein 21 (family)
A predicted immunity protein with an alpha+beta fold and conserved WxG and YxxxC motif. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, usually containing a domain of the NGO1392-family of HNH/Endonuclease VII fold nucleases.
Pfam PF05309: TraE protein (family)
This family consists of several bacterial sex pilus assembly and synthesis proteins (TraE). Conjugal transfer of plasmids from donor to recipient  cells is a complex process in which a cell-to-cell contact plays a key role. Many genes encoded by self-transmissible plasmids are required for various processes of conjugation, including pilus formation, stabilisation of mating pairs, conjugative DNA metabolism, surface exclusion and regulation of transfer gene expression. The exact function of the TraE protein is unknown.
Pfam PF01520: N-acetylmuramoyl-L-alanine amidase (domain)
This enzyme domain cleaves the amide bond between N-acetylmuramoyl and L-amino acids in bacterial cell walls.
Wikipedia: In enzymology, a N-acetylmuramoyl-L-alanine amidase is an enzyme that catalyzes a chemical reaction that cleaves the link between N-acetylmuramoyl residues and L-amino acid residues in certain cell-wall glycopeptides.
Pfam PF19682: Family of unknown function (DUF6184) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000990) is described by MIBiG as an example of the following biosynthetic class, polyketide. It includes a member from  the epothilone biosynthetic gene cluster from Sorangium cellulosum. This family appears to be predominantly found in 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 PF14529: Endonuclease-reverse transcriptase (domain)
This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes.                These are enzymes largely from class [ec:2.7.7.49].
Wikipedia: Endonuclease/Exonuclease/phosphatase family is a structural domain found in the large family of proteins including magnesium dependent endonucleases and many phosphatases involved in intracellular signaling.
Pfam PF00745: Glutamyl-tRNAGlu reductase, dimerisation domain (domain)
Tetrapyrroles are large macrocyclic compounds derived from a common biosynthetic pathway . The end-product, uroporphyrinogen III, is used to synthesise a number of important molecules, including vitamin B12, haem, sirohaem, chlorophyll, coenzyme F430 and phytochromobilin .


 * The first stage in tetrapyrrole synthesis is the synthesis of 5-aminoaevulinic acid ALA via two possible routes: (1) condensation of succinyl CoA and glycine (C4 pathway) using ALA synthase (2.3.1.37), or (2) decarboxylation of glutamate (C5 pathway) via three different enzymes, glutamyl-tRNA synthetase (6.1.1.17) to charge a tRNA with glutamate, glutamyl-tRNA reductase (1.2.1.70) to reduce glutamyl-tRNA to glutamate-1-semialdehyde (GSA), and GSA aminotransferase (5.4.3.8) to catalyse a transamination reaction to produce ALA.


 * The second stage is to convert ALA to uroporphyrinogen III, the first macrocyclic tetrapyrrolic structure in the pathway. This is achieved by the action of three enzymes in one common pathway: porphobilinogen (PBG) synthase (or ALA dehydratase, 4.2.1.24) to condense two ALA molecules to generate porphobilinogen; hydroxymethylbilane synthase (or PBG deaminase, 2.5.1.61) to polymerise four PBG molecules into preuroporphyrinogen (tetrapyrrole structure); and uroporphyrinogen III synthase (4.2.1.75) to link two pyrrole units together (rings A and D) to yield uroporphyrinogen III.


 * Uroporphyrinogen III is the first branch point of the pathway. To synthesise cobalamin (vitamin B12), sirohaem, and coenzyme F430, uroporphyrinogen III needs to be converted into precorrin-2 by the action of uroporphyrinogen III methyltransferase (2.1.1.107). To synthesise haem and chlorophyll, uroporphyrinogen III needs to be decarboxylated into coproporphyrinogen III by the action of uroporphyrinogen III decarboxylase (4.1.1.37) .

This entry represents the helical dimerisation domain of glutamyl-tRNA reductase (1.2.1.70) . This enzyme 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.