SII-SWORD/CoKE huggingface dataset:
Pfam PF17847: Glucose ABC transporter C-terminal domain (domain)
This is the C-terminal domain found at the ATPase subunit of the glucose ABC transporter from Sulfolobus solfataricus. Overall, the C-terminal domain (residues 243-353) contains only beta-strands, which form an elongated barrel-shaped structure composed of two parts. This entry represents the upper part which includes a three-stranded anti-parallel beta-sheets and two small anti-parallel beta-strands. The overall structure of this domain is very similar to that of the C-terminal domain of MalK from T. litoralis however, the function of the C-terminal domain in GlcV is not clear.
Pfam PF02310: B12 binding domain (domain)
This domain binds to B12 (adenosylcobamide), it is found in several enzymes, such as glutamate mutase [swissprot:Q05488], methionine synthase [swissprot:Q99707] and methylmalonyl-CoA mutase [swissprot:P22033]. It contains a conserved DxHxxGx(41)SxVx(26)GG motif, which is important for B12 binding.
Wikipedia: In molecular biology, the vitamin B12-binding domain is a protein domain which binds to cobalamin. It can bind two different forms of the cobalamin cofactor, with cobalt bonded either to a methyl group (methylcobalamin) or to 5'-deoxyadenosine (adenosylcobalamin). Cobalamin-binding domains are mainly found in two families of enzymes present in animals and prokaryotes, which perform distinct kinds of reactions at the cobalt-carbon bond. Enzymes that require methylcobalamin carry out methyl transfer reactions. Enzymes that require adenosylcobalamin catalyse reactions in which the first step is the cleavage of adenosylcobalamin to form cob(II)alamin and the 5'-deoxyadenosyl radical, and thus act as radical generators. In both types of enzymes the B12-binding domain uses a histidine to bind the cobalt atom of cobalamin cofactors. This histidine is embedded in a DXHXXG sequence, the most conserved primary sequence motif of the domain. Proteins containing the cobalamin-binding domain include:Animal and prokaryotic methionine synthase, which catalyse the transfer of a methyl group from methyl-cobalamin to homocysteine, yielding enzyme-bound cob(I)alamin and methionine.
Animal and prokaryotic methylmalonyl-CoA mutase, which are involved in the degradation of several amino acids, odd-chain fatty acids and cholesterol via propionyl-CoA to the tricarboxylic acid cycle.
Prokaryotic lysine 5,6-aminomutase.
Prokaryotic glutamate mutase.
Prokaryotic methyleneglutarate mutase.
Prokaryotic isobutyryl-CoA mutase.
Pfam PF11918: N-terminal domain of Peptidase_S41 in eukaryotic IRBP (domain)
Peptidase_S41_N is a family found at the N-terminus of the functional unit of interphotoreceptor retinoid binding proteins 3, IRBP, in eukaryotes. From the structure of PDB:1j7x, the domain forms the N-terminal end of the module which is characterised as a serine-peptidase, [pfam:PF03572]. Peptidase_S41_N forms a three-helix bundle followed by a small beta strand and is termed domain A. Part of the peptidase domain folds back over domain A to create a largely hydrophobic cleft between the two domains. On binding of ligand domain A is structurally rearranged with respect to domain B.
Pfam PF13059: Protein of unknown function (DUF3992) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 87 and 98 amino acids in length.
Pfam PF16497: MHC-I family domain (domain)
Class I MHC glycoproteins are expressed on the surface of all somatic nucleated cells, with the exception of neurons. MHC class I receptors present peptide antigens that are synthesised in the cytoplasm, which includes self-peptides (presented for self-tolerance) as well as foreign peptides (such as viral proteins). These antigens are generated from degraded protein fragments that are transported to the endoplasmic reticulum by TAP proteins (transporter of antigenic peptides), where they can bind MHC I molecules, before being transported to the cell surface via the Golgi apparatus . MHC class I receptors display antigens for recognition by cytotoxic T cells, which have the ability to destroy viral-infected or malignant (surfeit of self-peptides) cells.

MHC class I molecules are comprised of two chains: a MHC alpha chain (heavy chain), and a beta2-microglobulin chain (light chain), where only the alpha chain spans the membrane. The alpha chain has three extracellular domains (alpha 1-3, with alpha1 being at the N terminus), a transmembrane region and a C-terminal cytoplasmic tail. The soluble extracellular beta-2 microglobulin chain associates primarily with the alpha-3 domain and is necessary for MHC stability. The alpha1 and alpha2 domains of the alpha chain are referred to as the recognition region, because the peptide antigen binds in a deep groove between these two domains.
This entry represents MHC antigen-recognition-like domains from:


 * MHC class I, alpha-1 and alpha-2 domains 
 * MHC class I homologue gammadelta T-cell ligand 
 * MHC class I related Ulbp3 
 * MHC class I related Fc (IgG) receptor, alpha-1 and alpha-2 domains 
 * MHC class I related CD1, alpha-1 and alpha-2 domains 
 * MHC class I related zinc-alpha-2-glycoprotein ZAG (fat depleting factor) 
 * Immunomodulatory protein m144, alpha-1 and alpha-2 domains 
 * Haemochromatosis protein Hfe, alpha-1 and alpha-2 domains 
 * Endothelial protein C receptor (phospholipid-binding protein) 
 * NK cell ligand RAE-1 . RAE-1 proteins (alpha, beta, delta, and gamma) are distant major histocompatibility complex (MHC) class I homologues, comprising isolated alpha-1 alpha-2 domains, and lack alpha3 domains .
Pfam PF08412: Ion transport protein N-terminal (family)
This metazoan domain is found to the N-terminus of [pfam:PF00520] in voltage- and cyclic nucleotide-gated K/Na ion channels.
Pfam PF12294: Protein of unknown function (DUF3626) (family)
This family of proteins is found in bacteria. Proteins in this family are typically between 294 and 374 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 PF08176: Small acid-soluble spore protein K family (family)
This family consists of the small acid-soluble spore proteins (SASP) belonging to the K type (sspK). The sspK are unique to the spores of Bacillus subtilis and are expressed only in the forespore compartment of sporulating cells of this organism. The sspK gene is monocistronic and transcription is primarily by the RNA polymerase with the forespore-specific sigma factor, sigma-G. Mutation deleting sspK results in loss of SspK from the spore but had no discernible effect on sporulation, spore properties or spore germination.
Pfam PF03698: Uncharacterised protein family (UPF0180) (family)
The members of this family are small uncharacterised proteins.
Pfam PF23219: LAMB1-like domain (domain)
This domain is found in human Laminin subunit beta-1 (LAMB1) and similar proteins from animals. LAMB1 is thought to mediate the attachment, migration and organisation of cells into tissues during embryonic development by interacting with other extracellular matrix components. This domain, which is located C-terminal to multiple Laminin EGF domains ([pfam:PF00053]), is predicted to adopt a mainly alpha-helical fold.
Pfam PF10355: Protein YTP1-like, C-terminal (family)
This is a family of proteins found in fungi. The region appears to contain regions similar to mitochondrial electron transport proteins.  The C-terminal domain is hydrophobic and negatively charged. There are consensus sites for both N-linked glycosylation and cAMP-dependent protein kinase phosphorylation.
Pfam PF20274: Cyclic-phosphate processing Receiver domain (domain)
This is a divergent version of the Receiver (Rec) domain linked to different NAD+/ADPr-processing enzymes. Unlike conventional Rec domains, cREC is never found in two-component Histidine Kinase signalling systems. Instead, it is found in association with NAD+-processing systems that generate or recognise cyclic nucleotides. Known Rec domains process phosphoester linkages by means of catalytic aspartate residues that are also conserved in cREC. Accordingly, it is predicted that these are cADPr or 2_-3_ cyclic nucleotide-processing enzymes.
Pfam PF23729: Dystrophin-1-like, spectrin repeat (domain)
This domain is found in Dystrophin-1 from Caenorhabditis elegans (Dys-1) and similar eukaryotic sequences. Dys-1 plays a role in cholinergic transmission and as a functional partner of dystrobrevin (Dyb-1), necessary for muscle maintenance. It is required for neuronal positioning.
Pfam PF14674: FANCI solenoid 1 cap (repeat)
This is the solenoid 1 cap (S1-cap) domain of the Fanconi anemia group I protein.
Pfam PF15147: Domain of unknown function (DUF4578) (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 44 and 137 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 PF00503: G-protein alpha subunit (domain)
G proteins couple receptors of extracellular signals to intracellular signaling pathways. The G protein alpha subunit binds guanyl nucleotide and is a weak GTPase. A set of residues that are unique to G-alpha as compared to its ancestor the Arf-like family form a ring  of residues centered on the nucleotide binding site. A Ggamma is  found fused to an inactive Galpha in the Dictyostelium protein gbqA.
Wikipedia: G alpha subunits are one of the three types of subunit of guanine nucleotide binding proteins, which are membrane-associated, heterotrimeric G proteins.
Pfam PF10152: Subunit CCDC53 of WASH complex (coiled_coil)
CCDC53 is a component of the WASH complex, which plays a key role in the fission of tubules that serve as transport intermediates during endosome sorting.
Pfam PF19241: Family of unknown function (DUF5891) (family)
This is a family of uncharacterised proteins predominantly found in viruses which is apparently a Putative RNA methyltransferase.
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 PF21247: Filamentation induced by cAMP protein Fic-like, C-terminal domain (domain)
This domain is found at the C-terminal end of Filamentation induced by cAMP protein Fic from Oleidesulfovibrio alaskensis and similar bacterial sequences. This domain shows a winged helix structure. It is often found associated with [pfam:PF02661].
Pfam PF09290: Prokaryotic acetaldehyde dehydrogenase, dimerisation (domain)
Members of this family are found in prokaryotic acetaldehyde dehydrogenase (acylating), and adopt a structure consisting of an alpha-beta-alpha-beta(3) core. They mediate dimerisation of the protein.
Wikipedia: Acetaldehyde dehydrogenases are dehydrogenase enzymes which catalyze the conversion of acetaldehyde into acetyl-CoA. This can be summarized as follows:
Pfam PF11045: Putative inner membrane protein of Enterobacteriaceae (family)
This family is conserved in the Enterobacteriaceae. It is a putative inner membrane protein, named YbjM, but the function is not known.
Pfam PF00931: NB-ARC domain (domain)
This is the NB-ARC domain, a novel signalling motif found in bacteria and eukaryotes, shared by plant resistance gene products and regulators of cell death in animals . This domain has been structurally characterised in the human protein apoptotic protease-activating factor 1 (Apaf-1) . It contains the three-layered Î±-Î² fold and subsequent short Î±-helical region characteristic of the AAA+ ATPase domain superfamily. While this domain is thought to bind and hyrolyse ATP, only ADP binding has been experimentally verified. It is proposed that binding and hydrolysis of ATP by this domain induces conformational changes the the overall protein, leading to formation of the apoptosome.
Pfam PF00811: Ependymin (domain)
Ependymins are secretory proteins found predominantly in the cerebrospinal fluid of teleost fish . A bound form of the glycoproteins is associated with the extracellular matrix, probably with collagen fibrils, that may be the functional form of ependymins . The proteins bind calcium via N-linked sialic acid residues. The molecular function of ependymins appear to be related to cell contact phenomena involving the extracellular matrix .
Pfam PF00702: haloacid dehalogenase-like hydrolase (domain)
This family is structurally different from the alpha/beta hydrolase family ([pfam:PF00561]). This family includes L-2-haloacid dehalogenase, epoxide hydrolases and phosphatases. The structure of the family consists of two domains. One is an inserted four helix bundle, which is the least well conserved region of the alignment, between residues 16 and 96 of [swissprot:P24069]. The rest of the fold is composed of the core alpha/beta domain. Those members with the characteristic DxD triad at the N-terminus are probably phosphatidylglycerolphosphate (PGP) phosphatases involved in cardiolipin biosynthesis in the mitochondria.
Pfam PF20497: SWI/SNF and RSC complexes subunit Ssr4 C-terminal (domain)
This entry represents the C-temrinal domain of Ssr4 (SWI/SNF and RSC complexes subunit ssr4), an essential component of the chromatin-remodelling SWI/SNF and RSC (remodelling the structure of chromatin) complexes only found in S. pombe. This domain contains a conserved RYxxxHEWMEEI/V motif. RSC is involved in transcription regulation and nucleosome positioning which controls, particularly, membrane and organelle development genes. The ATP-dependent chromatin remodelling complex SWI/SNF is required for the positive and negative regulation of gene expression of a large number of genes through the regulation of nucleosome remodelling.
Pfam PF10175: M-phase phosphoprotein 6 (family)
This family represents the M-phase phosphoprotein 6 (MPP6) which is involved in the generation of the 3' end of the 5.8S rRNA precursor. MPP6 is required for the integrity maintenance of the rRNA processing complex as it mediates the interaction between MTR4 (RNA helicase) and RRP6 (an 3'-5' exonuclease), and the recruitment of Nuclear VCP-like 2 (NVL2) to the nuclear exosome.
Pfam PF02025: Interleukin 5 (domain)
This entry represents interleukin-5 (IL5), also known as eosinophil differentiation factor (EDF), is a lineage-specific cytokine for eosinophilpoiesis . It regulates eosinophil growth and activation , and thus plays an important role in diseases associated with increased levels of eosinophils, including asthma . IL5 has a similar overall fold to other cytokines (e.g., IL2, IL4 and GCSF) , but while these exist as monomeric structures, IL5 is a homodimer. The fold contains an anti-parallel 4-Î±-helix bundle with a left handed twist, connected by a 2-stranded anti-parallel Î²-sheet . The monomers are held together by 2 interchain disulphide bonds .
Wikipedia: Interleukins (ILs) are a group of cytokines that are expressed and secreted by white blood cells (leukocytes) as well as some other body cells. The human genome encodes more than 50 interleukins and related proteins.
Pfam PF23771: Domain of unknown function (DUF7168) (domain)
This entry represents a protein domain found in phage proteins that usually contain an N-terminal [pfam:PF10979]. The function of these protein 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 PF11641: Glycosylphosphatidylinositol-anchored merozoite surface protein (family)
This family of proteins represents the core region of Bd37, a surface antigen of B.divergens which is GPI-anchored at the surface of the merozoite. The structure of the protein consists of mainly alpha folds and has three sub domains.
Pfam PF02873: UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain (domain)
Members of this family are UDP-N-acetylenolpyruvoylglucosamine reductase enzymes [ec:1.1.1.158]. This enzyme is involved in the biosynthesis of peptidoglycan.
Pfam PF15210: Surfactant-associated protein 2 (family)
This family of proteins are predicted to possess a signal peptide, indicating that they are secreted . They are found in eukaryotes.
Pfam PF20713: Domain of unknown function (DUF6826) (domain)
This presumed domain is functionally uncharacterised and is found in fungal sequences, N-terminal to a kinase domain. There are two conserved motifs: PD and QPxR.
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 PF11600: Chromatin assembly factor 1 complex p150 subunit, acidic region (disordered)
CAF-1_p150 is a polypeptide subunit of CAF-1, which functions in depositing newly synthesised and acetylated histones H3/H4 into chromatin during DNA replication and repair. CAF-1_p150 includes the HP1 interaction site, the PEST, KER and ED interacting sites. CAF-1_p150 interacts directly with newly synthesised and acetylated histones through the acidic KER and ED domains. The PEST domain is associated with proteins that undergo rapid proteolysis. This entry represents the acidic region, characterised by containing the conserved KER and acidic residues (EE/ED). This region constitutes part of the histone binding interface.
Pfam PF01577: Potyvirus P1 protease (family)
The potyviridae family positive stand RNA viruses with genome encoding a polyprotein. members include zucchini yellow mosaic virus, and turnip mosaic viruses which cause considerable losses of crops  worldwide. This family consists of a C terminus region from various plant potyvirus P1 proteins (found at the N terminus of the polyprotein). The C terminus of P1 is a serine-type protease responsible for  autocatalytic cleavage between P1 and the helper component protease  [pfam:PF00851]. The entire P1 protein may be involved in virus-host interactions.
Pfam PF10212: Protein phosphatase 1 regulatory subunit 21, six-helix bundle (domain)
Protein phosphatase 1 regulatory subunit 21 (PPP1R21) is a regulator of protein phosphatase 1 (PP1) activity and may play a role in the endosomal sorting process or in endosome maturation pathway. This entry represents a middle domain found between the N- and C-terminal coiled-coils. According to structure predictions, it appears to form a six-helix bundle.
Pfam PF01006: Hepatitis C virus non-structural protein NS4a (family)
NS4a forms an integral part of the NS3 serine protease, as  it is required in a number of cases as a cofactor of cleavage. It has also been reported that NS4a interacts with NS4b and NS3 to form a multi-subunit replicase complex.
Pfam PF12152: Eukaryotic translation initiation factor 4G1 (domain)
This domain is found in eukaryotes, and is about 80 amino acids in length. It is found in association with [pfam:PF02854]. This domain is part of the protein eIF_4G. It binds to eIF_4E by wrapping around its N terminal to form the eIF_4F complex. This complex binds various eIF_4E-BPs (binding proteins) to regulate initiation of translation.
Pfam PF23854: Domain of unknown function (DUF7217) (domain)
This entry represents an uncharacterized protein domain found in phage and bacterial 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 PF04958: Arginine N-succinyltransferase beta subunit (domain)
Arginine N-succinyltransferase [ec:2.3.1.109] catalyses the transfer of succinyl-CoA to arginine to produce succinyl-arginine. This is the first step in arginine catabolism by the arginine succinyltransferase pathway.
Pfam PF24150: SHIP1/2 first C2 domain (domain)
This entry represents the first C2 domain of Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatases 1/2. The C2 domains of these proteins modulate the activity of the phosphatase domain.
Pfam PF14026: Nickel responsive protein SCO4226-like (family)
This family of proteins is found in prokaryotes, including the nickel responsive protein SCO4226 from Streptomyces coelicolor ([swissprot:Q9FCE4]). SCO4226 adopts a dimeric configuration able to bind four nickel ions, with each monomer showing a typical ferredoxin-like fold with five beta-strands packing against two alpha-helices. It seems to play a role in cellular nickel homeostasis, detoxification, and/or nickel utilization in specialised cytoplasmic compartment.
Pfam PF13337: Lon-like protease BrxL-like, ATPase domain (domain)
This entry represents the ATPase domain found in BREX system Lon protease-like protein BrxL from Bacillus cereus and similar proteins. BrxL is part of a type 1 BREX system which contains a C-terminal Lon-like protease domain ([pfam:PF05362]. BREX systems (bacteriophage exclusion) provide immunity against bacteriophage, a system that allows phage adsorption but prevents phage DNA replication, without degradation of the phage DNA. Methylation of bacterial DNA by PglX probably guides self/non-self discrimination. This entry also includes a few uncharacterised viral sequences.
Pfam PF08398: Phospholipase A2-like domain (domain)
This entry represents a domain that is likely to be a phospholipase A2-like enzyme.  It is found in a variety of contexts across the tree of life. The family includes he N-terminal region of the Parvovirus VP1 coat protein.
Pfam PF19503: Family of unknown function (DUF6037) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000758) is described by MIBiG as an example of the following biosynthetic class, saccharide. This family includes a  protein from the capsular polysaccharide biosynthetic gene cluster  from Staphylococcus aureus.
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.