SII-SWORD/CoKE huggingface dataset:
Pfam PF18145: SMODS-associated and fused to various effectors sensor domain (domain)
Predicted to function as a sensor domain, sensing nucleotides or nucleotide derivatives generated by SMODS and other nucleotide synthetase domains. This domain has been characterised in CD-NTase-associated protein 4 (Cap4), the founding member of a major family of downstream receptors that specifically respond to nucleotide second messenger signals in CBASS immunity, a bacterial system that provides immunity against bacteriophage. SAVED exhibits divergence in its nucleotide binding pocket which enables the recognition of a wide range of CD-NTase products such as bacterial second messengers with alternative ring size, nucleobase, and 3'-5' or 2'-5' phosphodiester linkages. The sensing of ligands by SAVED activates effectors that are essential for CBASS-mediated protection of bacteria from phage infection.
Pfam PF19170: Family of unknown function (DUF5852) (family)
This is a family of uncharacterised proteins of unknown function predominantly found in Iridoviridae.
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 PF22684: LFE_1968-like (family)
This protein family includes a group of uncharacterised prokaryotic proteins that show an alpha-beta configuration with similarity to haem iron utilisation proteins, such as LFE_1968 from Leptospirillum ferrooxidans.
Pfam PF04486: SchA/CurD like domain (domain)
Members of this family have only been identified in species of the Streptomyces genus.  Two family members are known to be part of gene clusters involved in the synthesis of polyketide-based spore pigments, homologous to clusters involved in the synthesis of polyketide antibiotics.  The function of this protein is unknown, but it has been speculated to contain a NAD(P) binding site. Many of these proteins contain two copies of this presumed domain.
Pfam PF24544: TPPC8 third Ig-like domain (domain)
This entry represents the third Ig-like domain found in the middle region of TPPC8 from human and related sequences from vertebrates, a protein that plays a role in endoplasmic reticulum to Golgi apparatus trafficking at a very early stage. Together with TBC1D14, it maintains the cycling pool of ATG9 required for initiation of autophagy. It is one of the TRAPPIII complex specific subunits.
Pfam PF14877: Mitochondrial translation initiation factor (family)
This is a family of mitochondrial initiation factors IF3.
Pfam PF03199: Eukaryotic glutathione synthase (domain)
This entry represents the substrate-binding domain of glutathione synthetase (6.3.2.3) (GSS), a homodimeric enzyme that catalyses the conversion of gamma-L-glutamyl-L-cysteine and glycine to phosphate and glutathione in the presence of ATP. This is the second step in glutathione biosynthesis, the first step being catalysed by gamma-glutamylcysteine synthetase . In humans, defects in GSS are inherited in an autosomal recessive way and are the cause of severe metabolic acidosis, 5-oxoprolinuria, and increased rate of haemolysis and defective function of the central nervous system. The substrate-binding domain has a 3-layer Î±/Î²/Î± structure .
Wikipedia: Glutathione synthetase (GSS) is the second enzyme in the glutathione (GSH) biosynthesis pathway. It catalyses the condensation of gamma-glutamylcysteine and glycine, to form glutathione. Glutathione synthetase is also a potent antioxidant. It is found in many species including bacteria, yeast, mammals, and plants.
Pfam PF09144: Yersinia pseudo-tuberculosis mitogen (domain)
Members of this family of Yersinia pseudo-tuberculosis mitogens adopt a sandwich structure consisting of nine strands in two beta sheets, in a jelly-roll topology. As with other super-antigens, they are able to excessively activate T cells by binding to the T cell receptor.
Pfam PF12435: Protein of unknown function (DUF3678) (family)
This domain family is found in eukaryotes, and is approximately 40 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 PF04845: PurA ssDNA and RNA-binding protein (family)
This family represents most of the length of the protein.
Pfam PF18707: Interleukin-2 receptor subunit beta N-terminal domain 1 (domain)
IL-2Rbeta is a member of the class I cytokine receptor superfamily. It carries a cytokine-binding homology region, which is divided in two fibronectin type-III (FN-III) domains termed D1 and D2. Each domain contains seven beta-strands that form a sandwich of two antiparallel beta-sheets. The N-terminal D1 domain of IL-2Rbeta includes two highly conserved disulfide bridges. This entry describes D1 of the N-terminal region of IL2Rbeta.
Pfam PF07194: P2 response regulator binding domain (domain)
The response regulators for CheA bind to the P2 domain, which is found between [pfam:PF01627] and [pfam:PF02895] as either one or two copies.  Highly flexible linkers connect P2 to the  rest of CheA and impart remarkable mobility to the P2 domain. This feature is thought to enhance the inter CheA dimer phosphotransfer reactions within the signalling complex, thereby amplifying the phosphorylation signal.
Pfam PF18201: PIH1 CS-like domain (domain)
This domain is found in yeast PIH1 and its homologues. This domain consists of a seven-stranded beta sandwich with the topology of a CS domain, a structural motif also found in Hsp90 co-chaperones such as p23/Sba1 and Sgt1.
Pfam PF00755: Choline/Carnitine o-acyltransferase (family)
The choline/carnitine acyltransferase domain is found in a number of eukaryotic acetyltransferases. These enzymes include:


 * Choline o-acetyltransferase 2.3.1.6, an enzyme that catalyses the biosynthesis of the neurotransmitter acetylcholine .
 * Carnitine o-acetyltransferase 2.3.1.7 .
 * Peroxisomal carnitine octanoyltransferase 2.3.1.137, a fatty acid beta-oxidation pathway enzyme which is involved in the transport of medium-chain acyl-coenzyme A's from peroxisome to mitochondria .
 * Mitochondrial carnitine palmitoyltransferases I and II 2.3.1.21 (CPT), enzymes involved in fatty acid metabolism and transport .
 * Mycoplasma pneumoniae putative acetyltransferase C09_orf600.

This domain is also found at the C terminus of highly reducing polyketide synthase SdnO. SdnO is part of the gene cluster that mediates the biosynthesis of glycoside antibiotics sordarin and hypoxysordarin .
Wikipedia: Carnitine O-palmitoyltransferase is a mitochondrial transferase enzyme involved in the metabolism of palmitoylcarnitine into palmitoyl-CoA. A related transferase is carnitine acyltransferase.
Pfam PF18699: Mitoribosomal protein mL52 (family)
Members of this family include the mamalian mitoribosomal proteins mL52 which is found in the 39S subunit. The mL52 has no homologues in yeast.
Pfam PF12825: Domain of unknown function in PX-proteins (DUF3818) (domain)
This domain is found on proteins carrying a PX domain. Its function 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 PF01980: tRNA-methyltransferase O N-terminal domain (domain)
This family includes members such as TrmO (tRNA-methyltransferase O) also known as YaeB, which contains a single-sheeted beta-barrel structure. TrmO is an AdoMet-dependent methyltransferase responsible for m6t6A formation. Its human homolog, is responsible for formation of m6t6A37 in cytoplasmic tRNASer. Lack of TrmO decreases attenuation activity of the thr operon, indicating that N6 methylation of m6t6A37 ensures efficient decoding of ACY codons. In bacteria and eukaryotes, TrmO has a C-terminal domain containing the conserved DPRxxY motif. Where the Asp194 and Arg196 in this motif of E. coli TrmO are necessary for N6-methylation. However, no archaeal YaeB has a C-terminal domain containing the DPRxxY motif that is conserved in bacterial and mammalian TrmO homologs. This entry represents the N-terminal domain of TrmO.
Pfam PF17005: WD40-like domain (repeat)
This is a family of proteins which have weak homology to the WD40 repeat family. Members are largely from microsporidia and related species.
Wikipedia: The WD40 repeat is a short structural motif of approximately 40 amino acids, often terminating in a tryptophan-aspartic acid (W-D) dipeptide. Tandem copies of these repeats typically fold together to form a type of circular solenoid protein domain called the WD40 domain.
Pfam PF10548: P22AR C-terminal domain (domain)
This domain was identified by Iyer and colleagues. It is found associated with [pfam:PF10547].
Pfam PF11824: Protein of unknown function (DUF3344) (family)
This family of proteins are functionally uncharacterised. This protein is found in bacteria and archaea. Proteins in this family are typically between 367 to 1857 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 PF11612: Type II secretion system (T2SS), protein J (family)
The T2SJ proteins are pseudopilins, which are targeted to the membrane in E. Coli. T2SJ forms a complex with T2SI ([pfam:PF02501]) and T2SK ([pfam:PF03934]) which is part of the Type II secretion apparatus involved in the translocation of proteins across the outer membrane in E.coli. The T2SK-I-J complex has quasihelical characteristics.
Pfam PF22516: PreP C-terminal domain (domain)
PreP is a protease that degrades targeting peptides as well as other unstructured peptides in both mitochondria and chloroplasts. This entry represents the C-terminal domain of PreP and related proteins.
Pfam PF08087: Conotoxin O-superfamily (domain)
This family consists of members of the conotoxin  O-superfamily. The O-superfamily of conotoxins  consists of 3 groups of Conus peptides that belong  to the same structural group. These 3 groups differ  in their pharmacological properties: the w-conotoxins  which inhibit calcium channels, the delta-conotoxins  which slow down the inactivation rate of voltage -sensitive sodium channels and the muO-conotoxins block the voltage sensitive sodium currents.
Pfam PF24374: Family of unknown function (DUF7530) (family)
This family includes a group of proteins from archaea. Members are predicted to adopt an all-alpha structure.
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 PF08475: Viral capsid protein 91 N-terminal (family)
This domain is found in Baculoviridae including the nucleopolyhedrovirus at the N-terminus of the viral capsid protein 91 (VP91).
Pfam PF17736: C17orf99 Ig domain (domain)
This Ig domain is found in tandem in the uncharacterized human protein C17orf99, which is found across mammalian species.
Pfam PF03779: SPW repeat domain (domain)
This entry represents a small integral membrane domain that contains two copies of the SPW repeat.  his is a short repeat found in a small family of membrane-bound proteins.  This repeat contains a conserved SPW motif in the first of two transmembrane helices. Two copies of the SPW repeat form a 4 helical bundle domain.
Pfam PF15063: Thyroid cancer protein 1 (family)
Thyroid cancer protein 1 (TC1) is thought to decrease in apoptosis and increase cell proliferation. It is found to be expressed in thyroid papillary carcinoma. This suggests its importance in thyroid cancer. The molecular mechanism of TC1, involves up-regulating cell signalling through ERK-1/2 signalling pathway and it positively regulates transition between the G1 and S phase in the cell cycle. It is thought to positively regulate Wnt/beta-catenin signalling pathway by interacting with its repressor. In humans, it is located in the chromosomal position, C8orf4. This family of proteins is found in eukaryotes and contains a conserved NIF sequence motif.
Wikipedia: TCIM is a protein that in humans is encoded by the TCIM gene.
Pfam PF03716: WCCH motif (conserved_site)
The WCCH motif is found in a retrotransposons and Gemini viruses. A specific function has not been associated to this motif.
Pfam PF24709: Domain of unknown function (DUF7670) (domain)
This entry represents a family of uncharacterised bacterial membrane proteins that contain four transmembrane alpha helices.
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 PF09758: Uncharacterised conserved protein (family)
This entry represents an N-terminal region of approximately 150 residues of a family of proteins of unknown function. It contains a highly conserved FPL motif.
Pfam PF20430: E+ motif (conserved_site)
This is the E+ motif found in some plant pentatricopeptide repeat (PPR) proteins which contain a C-terminal DYW deaminase domain. The DYW domain is required for RNA editing, a process that deaminates specific cytidines to uridines. This motif, together with the E motif, precedes the DYW domain and, although their role is not clear, they are essential in th RNA editing reaction. The E/E+ motifs may contain two degenerate PPR motifs that could be involved in RNA or protein binding.
Pfam PF06506: Propionate catabolism activator (domain)
This domain is found at the N terminus of several sigma54- dependent transcriptional activators including PrpR, which activates catabolism of propionate.
Pfam PF19053: EccD-like transmembrane domain (family)
This entry represents an integral membrane component of the ESX type VII secretion systems, EccD. This region includes 11 predicted transmembrane alpha helices.
Pfam PF22629: AHAS small subunit-like ACT domain (domain)
This entry represents the ACT domain found at the N-terminal of acetolactate synthase small subunit from Escherichia coli and similar sequences. This domain is also found at the C-terminal of D-3-phosphoglycerate dehydrogenase, which are closely related. Acetolactate synthase small subunit (ILVH) is the regulatory subunit of acetohydroxyacid synthase (AHAS), an enzyme hat catalyses the first step in the biosynthesis of the three branched-chain amino acids.
Pfam PF14214: Helitron helicase-like domain at N-terminus (domain)
This domain is found in Helitrons, widespread eukaryotic DNA transposons that have significantly contributed to genome variability and evolution, as they perform a distinctive, replicative rolling-circle mechanism, which often mobilizes adjacent genes. Helitron transposases contain a single-stranded DNA (ssDNA)-specific HUH endonuclease domain, with structural similarity to viral replication initiator (Rep) proteins. In many instances a protein-coding gene is disrupted by their insertion.
Pfam PF12658: Telomere capping, CST complex subunit (domain)
Stn1 and Ten1 are DNA-binding proteins with specificity for telomeric DNA substrates and both protect chromosome termini from unregulated resection and regulate telomere length. Stn1 complexes with Ten1 and Cdc13 to function as a telomere-specific replication protein A (RPA)-like complex. These three interacting proteins associate with the telomeric overhang in budding yeast, whereas a single protein known as Pot1 (protection of telomeres-1) performs this function in fission yeast, and a two-subunit complex consisting of POT1 and TPP1 associates with telomeric ssDNA in humans. S.pombe has Stn1- and Ten1-like proteins that are essential for chromosome end protection. Stn1 orthologues exist in all species that have Pot1, whereas Ten1-like proteins can be found in all fungi. Fission yeast Stn1 and Ten1 localise at telomeres in a manner that correlates with the length of the ssDNA overhang, suggesting that they specifically associate with the telomeric ssDNA. Two separate protein complexes are required for chromosome end protection in fission yeast.  Protection of telomeres by multiple proteins with OB-fold domains is conserved in eukaryotic evolution. Ten1 is one of the three components of the CST complex, which, in conjunction with the Shelterin complex helps protect telomeres from attack by DNA-repair mechanisms.
Pfam PF07508: Recombinase (domain)
This domain is usually found associated with [pfam:PF00239] in putative integrases/recombinases of mobile genetic elements of diverse bacteria and phages.
Pfam PF00205: Thiamine pyrophosphate enzyme, central domain (domain)
The central domain of TPP enzymes contains a 2-fold Rossman fold.
Pfam PF00149: Calcineurin-like phosphoesterase (domain)
This family includes a diverse range of phosphoesterases, including protein phosphoserine phosphatases, nucleotidases, sphingomyelin phosphodiesterases and 2'-3' cAMP phosphodiesterases as well as nucleases such as bacterial SbcD [swissprot:P13457] or yeast MRE11 [swissprot:P32829]. The most conserved regions in this superfamily centre around the metal chelating residues.
Wikipedia: The calcineurin-like phosphoesterases are a family of enzymes related to calcineurin. It includes a diverse range of phosphoesterases, including protein phosphoserine phosphatases, nucleotidases, sphingomyelin phosphodiesterases and 2'-3' cAMP phosphodiesterases as well as some bacterial nucleases. The most conserved region is a centre on the metal chelating residues.
Pfam PF10718: Hypothetical chloroplast protein Ycf34 (family)
This family is of proteins annotated as hypothetical chloroplast protein YCF34.  The function is not known.
Pfam PF17494: Family of unknown function (DUF5429) (family)
This is a family of unknown 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 PF03814: Potassium-transporting ATPase A subunit (family)
Kdp is a high affinity ATP-driven K+ transport system in Escherichia coli. It is a membrane complex (KdpFABC) composed of four subunits, KdpA, KdpB, KdpC and KdpF, although KdpF is not present in some species . It maintains intracellular homeostasis, cell shape and turgor under potassium-limiting conditions. KdpA is the K+-transporting subunit of this complex, while KdpB is a P-type ATPase that provides the energy for K+ transport. Both subunits are joined by KdpC, a probable catalytic chaperone and KdpF, that may stabilize the complex. KdpC and KdpF have single transmembrane helices and no known homologues outside of Kdp .
This family represents the KdpA subunit of KdpFABC complex.
Pfam PF23699: PAR-amplifying and CtIP-maintaining micropeptide (family)
This protein family includes PAR-amplifying and CtIP-maintaining micropeptide (also known as Poly-ADP-ribosylation-amplifying and CtIP-maintaining micropeptide, PACMP), which is recruited to DNA damage sites and acts as a regulator via association with poly -ADP-ribose chains, and enhances the poly-ADP-ribosyltransferase activity of PARP1. This protein sequence is 44-residues long.
Pfam PF19477: Family of unknown function (DUF6014) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000332) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). This  family includes a protein from the cyanopeptolin biosynthetic gene cluster from Microcystis sp. NIVA-CYA 172/5 and appears to be  predominantly found in Cyanobacteria.
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 PF10933: Protein of unknown function (DUF2827) (family)
This is a family of uncharacterised proteins found in Burkholderia.
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 PF12801: 4Fe-4S binding domain (domain)
Superfamily includes proteins containing  domains which bind to iron-sulfur clusters. Members  include bacterial ferredoxins, various dehydrogenases, and various reductases.  Structure of the domain is an alpha-antiparallel beta sandwich.
Pfam PF24251: Family of unknown function (DUF7453) (family)
This entry represents a group of uncharacterised sequences from bacteria. According to structure predictions, these proteins may comprise novel repeats consisting of an arrangement of four beta-strands in which the second one is longer and curved. This arrangement is repeated eight times in SwissProt:A0A5B9QB27, which form a closed repeat.
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 PF01777: Ribosomal L27e protein family (family)
The N-terminal region of the eukaryotic ribosomal L27 has the KOW motif.  C-terminal region is represented by this family.