SII-SWORD/CoKE huggingface dataset:
Pfam PF13405: EF-hand domain (domain)
Many calcium-binding proteins belong to the same evolutionary family and share a type of calcium-binding domain known as the EF-hand. This type of domain consists of a twelve residue loop flanked on both sides by a twelve residue Î±-helical domain. In an EF-hand loop the calcium ion is coordinated in a pentagonal bipyramidal configuration. The six residues involved in the binding are in positions 1, 3, 5, 7, 9 and 12; these residues are denoted by X, Y, Z, -Y, -X and -Z. The invariant Glu or Asp at position 12 provides two oxygens for liganding Ca (bidentate ligand). Ca2 binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers .
Wikipedia: The EF hand is a helix–loop–helix structural domain or motif found in a large family of calcium-binding proteins.
Pfam PF12151: Mannan-binding protein (domain)
This domain family is found in bacteria, and is approximately 40 amino acids in length, There is a single completely conserved residue G that may be functionally important. The domain occurs in two types of proteins. In mannan binding proteins, it forms a homodimeric molecule which complexes into a homo-octamer. In thiamidases it occurs without repeats but in the presence of other domains. MVL is distinct amongst other oligomannoside binding proteins in that it exhibits specificity for certain tetrasaccharides. Each molecule of MVL has four distinct carbohydrate binding sites.
Pfam PF17745: Ydr279p protein triple barrel domain (domain)
RNases H are enzymes that specifically hydrolyse RNA when annealed to a complementary DNA and are present in all living organisms. In yeast RNase H2 is composed of a complex of three proteins (Rnh2Ap, Ydr279p and Ylr154p), this family represents the homologues of Ydr279p. It is not known whether non yeast proteins in this family fulfil the same function. This domain corresponds to the N-terminal triple barrel domain.
Pfam PF21465: Putative N-acetylmuramoyl-L-alanine amidase cwp6, N-terminal domain (domain)
This domain is found in the putative N-acetylmuramoyl-L-alanine amidase cwp6 from Clostridioides difficile and similar proteins from firmicutes. Cwp6, which is involved in cell wall remodelling, consists of five domains: an N-terminal (this entry), a trimer of CWB2 ([pfam:PF04122]) and a C-terminal ([pfam:PF01520]). This domain, which locates at the bottom of the molecule, folds into a seven-stranded beta-barrel with one alpha-helix and with two additional short beta-strands.
Pfam PF02750: Synapsin, ATP binding domain (domain)
Ca dependent ATP binding in this ATP grasp fold.  Function unknown.
Wikipedia: The synapsins are a family of proteins that have long been implicated in the regulation of neurotransmitter release at synapses. Specifically, they are thought to be involved in regulating the number of synaptic vesicles available for release via exocytosis at any one time. Synapsins are present in invertebrates and vertebrates and are strongly conserved across all species. They are expressed in highest concentration in the nervous system, although they also express in other body systems such as the reproductive organs, including both eggs and spermatozoa. Synapsin function also increases as the organism matures, reaching its peak at sexual maturity.
Pfam PF17016: Domain of unknown function (DUF5095) (family)
This is a family of microsporidial-specific sequences. The function is not known and there is no distant homology to any Pfam families so far.
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 PF06859: Bicoid-interacting protein 3 (Bin3) (family)
This family represents a conserved region of approximately 120 residues within eukaryotic Bicoid-interacting protein 3 (Bin3). Bin3, which shows similarity to a number of protein methyltransferases that modify RNA-binding proteins, interacts with Bicoid, which itself directs pattern formation in the early Drosophila embryo. The interaction might allow Bicoid to switch between its dual roles in transcription and translation. Note that family members contain a conserved HLN motif.
Pfam PF18261: Rpn9 C-terminal helix (family)
The 26S proteasome is the major ATP-dependent protease in eukaryotes which plays a key role in intracellular protein degradation. The lid of the 26S proteasome contains six PCI-domain-containing proteins (Rpn3/5/6/7/9/12), two MPN-domain-containing proteins (Rpn8/11), and one peptide, Sem1. The only catalytically active member of the lid is Rpn11, which serves as the essential deubiquitinase of the proteasome. The C terminus of each subunit in the lid is predicted to form one or more helices. These C-terminal helices are highly conserved and have been predicted to form a helical bundle structure. In yeast, Rpn9 was found to be necessary for the integrity and efficiency of the 26S proteasome. This entry represents a helix domain C-terminal to the PCI domain found in Rpn9, a subunit of the 26S proteasome. C-terminal truncations of Rpn5 or Rpn9 have been shown not to cause any major lid assembly defects but to prevent the association of Rpn12.
Pfam PF16381: Coatomer subunit gamma-1 C-terminal appendage platform (domain)
Coatomer_g_Cpla is the very C-terminal domain of the eukaryotic Coatomer subunit gamma-1 proteins. It acts as a platform domain to the C-terminal appendage. It carries one single protein/protein interaction site, which is the binding site for ARFGAP2 or ADP-ribosylation factor GTPase-activating protein. COPI-coated vesicles mediate retrograde transport from the Golgi back to the ER and intra-Golgi transport. The gamma-COPI is part of one of two subcomplexes that make up the heptameric coatomer complex along with the beta, delta and zeta subunits.
Pfam PF17106: Sigma domain on NACHT-NTPases (family)
NACHT_sigma is a short conserved region found on NACHT-NTPases. The function of this domain is not known.
Pfam PF05751: FixH (family)
This family consists of several Rhizobium FixH like proteins. It has been suggested that suggested that the four proteins FixG, FixH, FixI, and FixS may participate in a membrane-bound complex coupling the FixI cation pump with a redox process catalysed by FixG.
Pfam PF13263: PHP-associated (domain)
This is a subunit, probably the alpha, of bacterial and eukaryotic DNA polymerase III, associated with the PHP domain, [pfam:PF02811].
Pfam PF04148: Transmembrane adaptor Erv26 (family)
Erv26 is an integral membrane protein that is packed into COPII vesicles and cycles between the ER and Golgi compartments.  It directs pro-alkaline phosphatase into endoplasmic reticulum-derived COPII transport vesicles.
Pfam PF16979: SAPK-interacting protein 1 (Sin1), Pleckstrin-homology (domain)
SIN1_PH is a pleckstrin-homology domain found at the C-terminus of SIN1.  It is conserved from yeast to humans. PH-domains are involved in intracellular signalling or as constituents of the cytoskeleton. SIN1 (SAPK-interacting protein 1) plays an essential role in signal transduction, anf the PH domain is involved in lipid and membrane binding.
Pfam PF24882: ORC2 WHD (domain)
All DNA replication initiation is driven by a single conserved eukaryotic initiator complex termed he origin recognition complex (ORC). The ORC is a six protein complex. This entry represents the WHD of ORC2.
Pfam PF21873: Thioredoxin-like domain (domain)
This entry represents an N-terminal thioredoxin domain, which is a non-canonical thioredoxin fold-containing structural unit present in Sso1120, a protein disulfide oxidoreductase (PDO) from the hyperthermophilic archaeon Sulfolobus solfataricus. This domain is composed of four beta-strands and three alpha-helices, with a well-defined disulfide bond between Cys24 and Cys45. The domain does not contain any active site but is part of the larger structure that comprises the C-terminal unit with the CTKC active site motif. The N-terminal domain shows unexpected similarity with the N-terminal domain of the alkyl hydroperoxide reductase F component from Salmonella typhimurium, and a possible involvement of this atypical PDO in a new antioxidant system of S. solfataricus has been proposed.
Pfam PF02684: Lipid-A-disaccharide synthetase (family)
This is a family of lipid-A-disaccharide synthetases, [ec:2.4.2.128]. These enzymes catalyse the reaction: UDP-2,3-bis(3-hydroxytetradecanoyl) glucosamine + 2,3-bis(3-hydroxytetradecanoyl)-beta-D-glucosaminyl  1-phosphate  UDP + 2,3-bis(3-hydroxytetradecanoyl)-D-glucosaminyl-1,6 -beta-D-2,3-bis(3-hydroxytetradecanoyl)-beta-D-glucosaminyl 1-phosphate. These enzymes catalyse the fist disaccharide step in the synthesis of  lipid-A-disaccharide.
Pfam PF11686: Protein of unknown function (DUF3283) (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 PF08029: HisG, C-terminal domain (domain)
ATP phosphoribosyltransferase (2.4.2.17) is the enzyme that catalyzes the first step in the biosynthesis of histidine in bacteria, fungi and plants as shown below. It is a member of the larger phosphoribosyltransferase superfamily of enzymes which catalyse the condensation of 5-phospho-alpha-D-ribose 1-diphosphate with nitrogenous bases in the presence of divalent metal ions .

ATP + 5-phospho-alpha-D-ribose 1-diphosphate = 1-(5-phospho-D-ribosyl)-ATP + diphosphate

Histidine biosynthesis is an energetically expensive process and ATP phosphoribosyltransferase activity is subject to control at several levels. Transcriptional regulation is based primarily on nutrient conditions and determines the amount of enzyme present in the cell, while feedback inihibition rapidly modulates activity in response to cellular conditions. The enzyme has been shown to be inhibited by 1-(5-phospho-D-ribosyl)-ATP, histidine, ppGpp (a signal associated with adverse environmental conditions) and ADP and AMP (which reflect the overall energy status of the cell). As this pathway of histidine biosynthesis is present only in prokayrotes, plants and fungi, this enzyme is a promising target for the development of novel antimicrobial compounds and herbicides.

This entry represents the C-terminal portion of ATP phosphoribosyltransferase. The enzyme itself exists in equilibrium between an active dimeric form, an inactive hexameric form and higher aggregates . Interconversion between the various forms is largely reversible and is influenced by the binding of the natural substrates and inhibitors of the enzyme. This domain is not directly involved in catalysis but appears to be responsible for the formation of hexamers induced by the binding of inhibitors to the enzyme, thus regulating activity.
Wikipedia: In enzymology, an ATP phosphoribosyltransferase is an enzyme that catalyzes the chemical reaction1-(5-phospho-D-ribosyl)-ATP + diphosphate  ATP + 5-phospho-alpha-D-ribose 1-diphosphate
Pfam PF21707: Emaravirus ABC_AB protein (family)
This family corresponds to the ABC proteins of clades A and B of emaraviruses (plant-infecting bunyaviruses). They are involved in pathogenicity, and may act as silencing suppressors in some species. This family contains a hydrophobic region bordered by two highly conserved positions R/K and G. They may consist of three helices according to structure predictions.
Pfam PF22119: Glutathione S-transferase, C-terminal domain (domain)
This domain is found at the C-terminal end of Glutathione S-transferase from Agrobacterium fabrum (Atu5508, [swissprot:Q7D2W7]) and similar sequences mainly found in proteobacteria. This domain adopts an alpha-helical configuration.
Pfam PF12949: HeH/LEM domain (domain)
This is a HeH domain. HeH domains form helix-extended loop-helix (HeH) structures. It was demonstrated that the DNA-binding activity of the HEH/LEM domain assists the association of proteins with the centromeric region. This domain is closely related to [pfam:PF03020] and [pfam:PF02037].
Pfam PF23344: ZP-N domain (domain)
This entry represents the N-terminal structural domain of the zona pellucida domain as defined by sequence.
Wikipedia: The zona pellucida-like domain is a large protein region of about 260 amino acids. It has been recognised in a variety of receptor-like eukaryotic glycoproteins. All of these molecules are mosaic proteins with a large extracellular region composed of various domains, often followed by either a transmembrane domain and a short cytoplasmic region or by a GPI-anchor.
Pfam PF18396: TANK binding kinase 1 ubiquitin-like domain (domain)
This is the ubiquitin-like domain (ULD) found in TANK-binding kinase 1 (TBK1). TBK1 is a serine/threonine kinase and a noncanonical member of the IKK family implicated in diverse cellular functions, including innate immune response as well as tumorigenesis and development. It has been reported that the ULD of TBK1 regulates kinase activity, playing an important role in signaling and mediating interactions with other molecules in the IFN pathway. Deletion of ULD indicates that it is required for the kinase domain to form an enzymatically active conformation. TBK1 ULD has a ubiquitin-like structure and an Ile44 hydrophobic patch, which is conserved among ULDs and IKK and IKK-related proteins. This hydrophobic patch is involved in ULD-SDD interactions in TBK1 and other IKK and IKK-related proteins.
Pfam PF23830: Domain of unknown function (DUF7200) (domain)
This entry represents an uncharacterized protein found in various phages that infect bacteria including Escherichia, Salmonella, Shigella, Klebsiella, Enterobacter, Citrobacter and Cronobacter. The protein ranges in length from around 66 to 98 amino acids. The protein forms a single compact domain composed of a four stranded beta sheet and two alpha helices. The structure shows some weak structural similarity to the BRICHOS domain. No clear function is known for these 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 PF05225: helix-turn-helix, Psq domain (domain)
This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster. In pipsqueak this domain binds to GAGA sequence.
Wikipedia: Helix-turn-helix is a DNA-binding domain (DBD). The helix-turn-helix (HTH) is a major structural motif capable of binding DNA. Each monomer incorporates two α helices, joined by a short strand of amino acids, that bind to the major groove of DNA. The HTH motif occurs in many proteins that regulate gene expression. It should not be confused with the helix–loop–helix motif.
Pfam PF08574: Transcription factor Iwr1 (family)
Iwr1 is involved in transcription from polymerase II  promoters; it interacts with with most of the polymerase II  subunits. Deletion of this protein results in  hypersensitivity to the K1 killer toxin.
Pfam PF02601: Exonuclease VII, large subunit (family)
This family consist of exonuclease VII, large subunit [ec:3.1.11.6] This enzyme catalyses exonucleolytic cleavage in either 5'->3' or 3'->5'  direction to yield 5'-phosphomononucleotides.  This exonuclease VII enzyme is composed of one large subunit and 4 small ones.
Wikipedia: The enzyme exodeoxyribonuclease VII is a bacterial exonuclease enzyme. It is composed of two nonidentical subunits; one large subunit and 4 small ones. that catalyses exonucleolytic cleavage in either 5′- to 3′- or 3′- to 5′-direction to yield nucleoside 5′-phosphates. The large subunit also contains an N-terminal OB-fold domain that binds to nucleic acids.
Pfam PF15719: Domain of unknown function (DUF4674) (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 126 and 221 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 PF11727: Invariant surface glycoprotein (family)
This family is found in Trypanosome species, and appears to be one of two invariant surface glycoproteins, ISG65 and ISG75. that are found in the mammalian stage of the parasitic protozoan. the sequence suggests the two families are polypeptides with N-terminal signal sequences, hydrophilic extracellular domains, single trans-membrane alpha-helices and short cytoplasmic domains. they are both expressed in the bloodstream form but not in the midgut stage. Both polypeptides are distributed over the entire surface of the parasite.
Pfam PF03907: Spo7-like protein (family)
S. cerevisiae Spo7 [swissprot:P18410] has an unknown function, but has a role in formation of a spherical nucleus and meiotic division.
Pfam PF02158: Neuregulin intracellular region (disordered)
Neuregulins are a sub-family of EGF-like molecules that have been shown to play multiple essential roles in vertebrate embryogenesis including: cardiac development, Schwann cell and oligodendrocyte differentiation, some aspects of neuronal development, as well as the formation of neuromuscular synapses . Included in the family are heregulin; neu differentiation factor; acetylcholine receptor synthesis stimulator; glial growth factor; and sensory and motor-neuron derived factor . Multiple family members are generated by alternate splicing or by use of several cell type-specific transcription initiation sites. In general, they bind to and activate the erbB family of receptor tyrosine kinases (erbB2 (HER2), erbB3 (HER3), and erbB4 (HER4)), functioning both as heterodimers and homodimers.

The transmembrane forms of neuregulin 1 (NRG1) are present within synaptic vesicles, including those containing glutamate . After exocytosis, NRG1 is in the presynaptic membrane, where the ectodomain of NRG1 may be cleaved off. The ectodomain then migrates across the synaptic cleft and binds to and activates a member of the EGF-receptor family on the postsynaptic membrane. This has been shown to increase the expression of certain glutamate-receptor subunits. NRG1 appears to signal for glutamate-receptor subunit expression, localisation, and /or phosphorylation facilitating subsequent glutamate transmission.
Membrane-anchored Nrg-1 isoforms consist of a variable N-terminal extracellular domain and a conserved transmembrane and C-terminal cytoplasmic domains . This entry represents the C-terminal, intracellular domain.
Wikipedia: Neuregulins are a family of four structurally related proteins that are part of the EGF family of proteins. These proteins have been shown to have diverse functions in the development of the nervous system and play multiple essential roles in vertebrate embryogenesis including: cardiac development, Schwann cell and oligodendrocyte differentiation, some aspects of neuronal development, as well as the formation of neuromuscular synapses.
Pfam PF16313: Met-zincin (family)
This is a family of uncharacterised proteins that carry the highly characteristic met-zincin motif HExxHxxGxxH, the extended zinc-binding domain of metallopeptidases.
Pfam PF09712: Poly(R)-hydroxyalkanoic acid synthase subunit (PHA_synth_III_E) (family)
This entry represents the PhaE subunit of the heterodimeric class (class III) of polymerase for poly(R)-hydroxyalkanoic acids (PHAs), carbon and energy storage polymers of many bacteria. The most common PHA is polyhydroxybutyrate but about 150 different constituent hydroxyalkanoic acids (HAs) have been identified in various species.
Pfam PF03092: BT1 family (family)
Members of this family are transmembrane proteins. Several are Leishmania putative proteins that are thought to be pteridine transporters. One such protein [swissprot:Q25272], previously termed (and is still annotated as) ORFG, was shown to encode a biopterin transport protein using null mutants, thus being subsequently renamed BT1. The significant similarity of ORFG/BT1 to Trypanosoma brucei ESAG10 (a putative transmembrane protein and another member  of this family) was previously noted. This family also contains five putative Arabidopsis thaliana proteins of unknown function. In addition, it also contains two predicted  prokaryotic proteins (from the cyanobacteria Synechocystis and  Synechococcus).
Pfam PF20886: PWWP domain-containing DNA repair factor 3A/B, C-terminal (domain)
PWWP domain-containing DNA repair factor 3A (also known as EXPAND1 or MUM1) is a nucleosome-binding protein that contributes to the maintenance of chromatin state. Through its interaction with 53BP1, it serves as an accessory factor in the DNA damage response pathway to promote chromatin change in response to DNA damage. MUM1 promotes cell survival following DNA damage, suggesting that it may facilitate DNA repair by regulating the organisation of chromatin structure. This is the C-terminal alpha-helical domain from PWWP domain-containing DNA repair factor 3A/B.
Pfam PF13222: Protein of unknown function (DUF4030) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 164 and 197 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 PF02806: Alpha amylase, C-terminal all-beta domain (domain)
Alpha amylase is classified as family 13 of the glycosyl hydrolases. The structure is an 8 stranded alpha/beta barrel containing the  active site, interrupted by a ~70 a.a. calcium-binding domain  protruding between beta strand 3 and alpha helix 3, and a  carboxyl-terminal Greek key beta-barrel domain.
Wikipedia: α-Amylase is an enzyme that hydrolyses α bonds of large, α-linked polysaccharides, such as starch and glycogen, yielding shorter chains thereof, dextrins, and maltose, through the following biochemical process:Endohydrolysis of (1→4)-α-D-glucosidic linkages in polysaccharides containing three or more (1→4)-α-linked D-glucose units
Pfam PF19578: Family of unknown function (DUF6090) (family)
This family of proteins is functionally uncharacterised. Proteins in this family are primarily found in Bacteroidetes. Proteins in this family are typically between 241 and 255 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.