SII-SWORD/CoKE huggingface dataset:
Pfam PF13056: Protein of unknown function (DUF3918) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 40 amino acids in length. There are two completely conserved residues (G and R) that may be functionally important.
Pfam PF23565: Transport and Golgi organization protein 6 homolog, ARM-like repeat (repeat)
This region is found in human Transport and Golgi organization protein 6 homolog (TANGO6) and similar proteins predominantly found in animals. This region, which is predicted to show ARM-like repeats, is often found N-terminal to [pfam:PF10363] and [pfam:PF10304].
Pfam PF10854: Protein of unknown function (DUF2649) (family)
Members in this family of proteins are annotated as Plectrovirus orf 10 transmembrane proteins however currently no function is known.
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 PF01642: Methylmalonyl-CoA mutase (family)
The enzyme methylmalonyl-CoA mutase is a member of a class of enzymes that uses coenzyme B12 (adenosylcobalamin) as a cofactor. The enzyme induces the formation of an adenosyl radical from the cofactor. This radical then initiates a free-radical rearrangement of its substrate, succinyl-CoA, to methylmalonyl-CoA.
Pfam PF21079: Glutamate dehydrogenase, helical motif 2 (conserved_site)
Glutamate dehydrogenases (GDHs) are a broadly distributed group of enzymes that catalyse the reversible oxidative deamination of glutamate to ketoglutarate and ammonia. The structure of GDH from Mycobacterium smegmatis revealed that it has a long N- and C-terminal segments flanking the catalytic core, comprising several domains. The flexible N-terminal domain comprises ACT-like and PAS-type domains which could act as metabolic sensors for allosteric regulation. It also has three helical motifs (HM1-3); this entry represents HM2.
Pfam PF19607: Family of unknown function (DUF6112) (family)
This family of putative integral membrane proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 88 and 112 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 PF17747: VID27 PH-like domain (domain)
This region has been predicted to contain a PH-like domain.
Pfam PF00972: Flavivirus RNA-directed RNA polymerase, fingers and palm domains (domain)
Flaviviruses produce a large polyprotein from the ssRNA genome, encoding structural proteins required for virus assembly and non-structural (NS1-5) proteins involved in replication of the viral genome. This polyprotein is cleaved by viral and cellular proteases to produce mature viral proteins. NS5 is the largest mature viral protein and contains a N-terminal methyltransferase (MTase) domain separated by a short linker from the C-terminal RNA-directed RNA polymerase domain (RdRp) that adopts a characteristic right-handed fingers-palm-thumb fold and possesses a number of short regions and motifs homologous to other RNA-directed RNA polymerases. This entry covers the fingers and palm domains of RNA-directed RNA polymerase (RdRp) from Flavivirus NS5. NS5 binds to a the stem loop A (SLA) at the 5' extremity of Flavivirus genome and regulates translation of the viral genome.
Wikipedia: RNA-dependent RNA polymerase (RdRp) or RNA replicase is an enzyme that catalyzes the replication of RNA from an RNA template. Specifically, it catalyzes synthesis of the RNA strand complementary to a given RNA template. This is in contrast to typical DNA-dependent RNA polymerases, which all organisms use to catalyze the transcription of RNA from a DNA template.
Pfam PF03903: Phage T4 tail fibre (family)
Irreversible binding of T-even bacteriophages to Escherichia coli is mediated by the short and long tail fibres, important for DNA injection. Long tail fibres consist of a phage-proximal (gp34) and a phage-distal rod, the latter containing two protein trimers (gp36 and gp37). Gp36 is present in the upper part of the distal rod, it forms a complex with gp35 and gp37, binding them through the N-terminal and C-terminal regions, respectively. The upper part of the distal rod has a beta-structure.
Pfam PF25144: IFT122, zinc ribbon domain (domain)
This zinc ribbon domain is found in the Intraflagellar transport protein 122 and related proteins. IFT122 is one of the core components (together with WDR19/IFT144 and IFT140) of the IFT-A complex which is required for retrograde ciliary transport and entry into cilia of G protein-coupled receptors (GPCRs), being involved in cilia function and/or assembly. IFT-A polymerises interacts with IFT-B, and uses an array of beta-propeller and TPR domains to create 'carriages' of the IFT train that engage TULP adaptor proteins. IFT122 contains to zinc ribbon domains toward the C-terminus. This one is the first of the pair.
Pfam PF01607: Chitin binding Peritrophin-A domain (domain)
This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Wikipedia: In molecular biology, a carbohydrate-binding module (CBM) is a protein domain found in carbohydrate-active enzymes. The majority of these domains have carbohydrate-binding activity. Some of these domains are found on cellulosomal scaffoldin proteins. CBMs were previously known as cellulose-binding domains. CBMs are classified into numerous families, based on amino acid sequence similarity. There are currently 64 families of CBM in the CAZy database.
Pfam PF07936: Potassium-channel blocking toxin (domain)
This family features the antihypertensive and antiviral proteins BDS-I ([swissprot:P11494]) and BDS-II ([swissprot:P59084]) expressed by Anemonia sulcata. BDS-I is organised into a triple-stranded antiparallel beta-sheet, with an additional small antiparallel beta-sheet at the N-terminus. Both peptides are known to specifically block the Kv3.4 potassium channel, and thus bring about a decrease in blood pressure. Moreover, they inhibit the cytopathic effects of mouse hepatitis virus strain MHV-A59 on mouse liver cells, by an unknown mechanism.
Wikipedia: Sea anemone neurotoxin is the name given to neurotoxins produced by sea anemones with related structure and function.
Sea anemone neurotoxins can be divided in two functional groups that either specifically target the sodium channel or the potassium channel.
Pfam PF00001: 7 transmembrane receptor (rhodopsin family) (domain)
This family contains, amongst other G-protein-coupled receptors (GCPRs), members of the opsin family, which have been considered to be typical members of the rhodopsin superfamily. They share several motifs, mainly the seven transmembrane helices, GCPRs of the rhodopsin superfamily. All opsins bind a chromophore, such as 11-cis-retinal. The function of most opsins other than the photoisomerases is split into two steps: light absorption and G-protein activation. Photoisomerases, on the other hand, are not coupled to G-proteins - they are thought to generate and supply the chromophore that is used by visual opsins.
Wikipedia: G protein-coupled receptors (GPCRs), also known as seven-(pass)-transmembrane domain receptors, 7TM receptors, heptahelical receptors, serpentine receptors, and G protein-linked receptors (GPLR), form a large group of evolutionarily related proteins that are cell surface receptors that detect molecules outside the cell and activate cellular responses. They are coupled with G proteins. They pass through the cell membrane seven times in the form of six loops of amino acid residues, which is why they are sometimes referred to as seven-transmembrane receptors. Ligands can bind either to the extracellular N-terminus and loops or to the binding site within transmembrane helices. They are all activated by agonists, although a spontaneous auto-activation of an empty receptor has also been observed.
Pfam PF15540: Bacterial toxin 47 (family)
A predicted RNase toxin found in bacterial polymorphic toxin systems that is proposed to adopt the BECR (Barnase-EndoU-ColicinE5/D-RelE) fold, and contains two conserved aspartates, a glutamate, a histidine and an arginine residue and an RT motif. In bacterial polymorphic toxin systems, the toxin is usually exported by the type 2, type 6 or type 7 secretion system.
Pfam PF11923: NFACT protein C-terminal domain (domain)
This is the C-terminal domain of the NFACT (NEMF, FbpA, Caliban, and Tae2) proteins involved in the ribosomal quality control pathway. This context is conserved in archaea and eukaryotes, but NFACT proteins in bacteria lack the NFACT-C domain.
Pfam PF15080: Domain of unknown function (DUF4547) (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 144 and 206 amino acids in length. The human member of this family is C3orf43.
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 PF15184: Mitochondrial import receptor subunit TOM6 homolog (family)
TOMM6 forms part of the pre-protein translocase complex of the outer mitochondrial membrane (TOM complex). This family of proteins is found in eukaryotes. Proteins in this family are typically between 43 and 74 amino acids in length.
Pfam PF22877: Thc1, RRM domain (domain)
The founder of this entry is a domain found in Thc1 protein from Schizosaccharomyces pombe. This protein is a subunit of sno(s)RNA-containing ribonucleoprotein complex and is involved in snRNA processing. This domain is predicted to adopt a typical RRM fold with a significant similarity to Poly (A)-specific ribonuclease PARN. Besides the global structural similarity, the residues involved in RNA-binding in PARN, are conserved within this  entry. These residues define a semi-conserved IWx(2)DTx(5)F sequence motif.
Pfam PF23483: Apicomplexa microprotein (family)
This protein family includes uncharacterised microproteins encoded by small open reading frames (smORFs) from apicomplexa, including [swissprot:A7ARQ5] from the parasite Babesia bovis.
Pfam PF04518: Effector from type III secretion system (family)
This is a family of effector proteins which are secreted by the type III secretion system. The precise function of this family is unknown.
Pfam PF05691: Raffinose synthase or seed imbibition protein Sip1 (family)
This family consists of several raffinose synthase proteins, also known as seed imbibition (Sip1) proteins. Raffinose (O-alpha- D-galactopyranosyl- (1-->6)- O-alpha- D-glucopyranosyl-(12)- O-beta- D-fructofuranoside) is a widespread oligosaccharide in plant seeds and other tissues. Raffinose synthase ([ec:2.4.1.82]) is the key enzyme that channels sucrose into the raffinose oligosaccharide pathway. Raffinose family oligosaccharides (RFOs) are ubiquitous in plant seeds and are thought to play critical roles in the acquisition of tolerance to desiccation and seed longevity. Raffinose synthases are alkaline alpha-galactosidases and are solely responsible for RFO breakdown in germinating maize seeds, whereas acidic galactosidases appear to have other functions.                  Glycoside hydrolase family 36 can be split into 11 families, GH36A to GH36K. This family includes enzymes from GH36C.
Wikipedia: In molecular biology, glycoside hydrolase family 36 is a family of glycoside hydrolases.
Pfam PF20020: Domain of unknown function (DUF6431) (domain)
This domain of unknown function is found in uncharacterised proteins from bacteria. This domain is about 90 amino acids in length. It contains the conserved sequences CxxC, RxxCxxxxC and a conserved LP motif.
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 PF19288: CofH/MqnC C-terminal region (family)
This entry represents the C-terminal half of the CofH and MqnC enzymes. This entry is found to the C-terminus of [pfam:PF04055].
Pfam PF21329: Peptidyl-prolyl cis-trans isomerase CYP38-like, PsbQ-like domain (domain)
Peptidyl-prolyl cis-trans isomerase CYP38 from Arabidopsis is required for the assembly and stabilization of PSII. It consists of an N-terminal helical bundle and a C-terminal cyclophilin beta-barrel ([pfam:PF00160]). This entry represents the N-terminal helical bundle found in Cyp37/38 from Arabidopsis and similar proteins from cyanobacteria. This domain establishes strong interactions with the C-terminal domain to avoid the access of the cyclophilin domain to other proteins.
Pfam PF02702: Osmosensitive K+ channel His kinase sensor domain (domain)
This entry represents an N-terminal domain found in KdpD sensor kinase proteins that regulate the kdpFABC operon responsible for potassium transport. The aligned region corresponds to a cytoplasmic part of the protein which functions as the sensor domain responsible for sensing turgor pressure. It recognises C-di-AMP and K+.
Wikipedia: In molecular biology, a two-component regulatory system serves as a basic stimulus-response coupling mechanism to allow organisms to sense and respond to changes in many different environmental conditions. Two-component systems typically consist of a membrane-bound histidine kinase that senses a specific environmental stimulus, and a corresponding response regulator that mediates the cellular response, mostly through differential expression of target genes. Although two-component signaling systems are found in all domains of life, they are most common by far in bacteria, particularly in Gram-negative and cyanobacteria; both histidine kinases and response regulators are among the largest gene families in bacteria. They are much less common in archaea and eukaryotes; although they do appear in yeasts, filamentous fungi, and slime molds, and are common in plants, two-component systems have been described as "conspicuously absent" from animals.
Pfam PF13397: RNA polymerase-binding protein (family)
RbpA is a family bacterial RNA polymerase-binding proteins. RbpA acts as a transcription factor by binding to the sigma subunit of RNA polymerase.
Pfam PF15413: Pleckstrin homology domain (domain)
This Pleckstrin homology domain is found in some fungal species.
Wikipedia: Pleckstrin homology domain or (PHIP) is a protein domain of approximately 120 amino acids that occurs in a wide range of proteins involved in intracellular signaling or as constituents of the cytoskeleton.
Pfam PF12891: Glycoside hydrolase family 44 (domain)
This is a family of bacterial glycoside hydrolases formerly known as cellulase family J, and now known as Cel44A. It is one of the major enzymatic components of the cellulosome of Clostridium thermocellum strain F1 and of many other Firmicutes.
Wikipedia: In molecular biology, glycoside hydrolase family 44 is a family of glycoside hydrolases.
Pfam PF14330: Domain of unknown function (DUF4387) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are approximately 110 amino acids in length. There is a conserved RSKN sequence motif.
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 PF06722: Erythromycin biosynthesis protein CIII-like, C-terminal domain (domain)
This domain is found at the C-terminal of Erythromycin biosynthesis protein CIII (EryCIII) from Saccharopolyspora erythraea and similar proteins found in bacteria and eukaryotes. This protein is organised into two domains, both of them with a Rossmann-like alpha/beta fold. The C-terminal domain contains the nucleotide disphospho-sugar (NDP-sugar) binding site.
Pfam PF15637: HNH/Endo VII superfamily nuclease toxin with a HHH motif (family)
A predicted toxin of the HNH/Endonuclease VII fold present in bacterial polymorphic toxin systems with characteristic conserved s[GD]xxR and HHH motifs. In bacterial polymorphic toxin systems, the toxin is exported by the type 2, type 5, type 6, type 7 or Photorhabdus virulence cassette (PVC)-type secretion system.
Pfam PF10808: Protein of unknown function (DUF2542) (family)
This family of proteins with unknown function appears to be restricted to Enterobacteriaceae. The family has a highly conserved sequence.
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 PF12345: Protein of unknown function (DUF3641) (family)
This domain family is found in bacteria and eukaryotes, and is approximately 140 amino acids in length. The family is found in association with [pfam:PF04055]. This family consists of proteins which are commonly annotated as Radical SAM domains but there is little annotation to back this up.
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 PF23065: PH domain associated with SMP domain (domain)
This entry represents a PH-like domain found at the N-terminus of SMP domain containing proteins.
Pfam PF19676: Family of unknown function (DUF6178) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001091) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide. It includes a member from the corallopyronin  biosynthetic gene cluster from Corallococcus coralloides.  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 PF13134: Protein of unknown function (DUF3948) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 40 amino acids in length.
Pfam PF21016: Ribosomal RNA large subunit methyltransferase N-terminal domain (domain)
This entry represents the N-terminal domain from the dual-specificity RNA methyltransferase RlmN.
Pfam PF22847: Arabinosidase BT_3657-like, N-terminal (repeat)
This domain is found at the N-terminal of BT_3657 from Bacteroides thetaiotaomicron and similar bacterial sequences. BT_3657 has been reported to be an arabinosidase.
Pfam PF06614: Neuromodulin (family)
This family consists of several neuromodulin (Axonal membrane protein GAP-43) sequences and is found in conjunction with [pfam:PF00612]. GAP-43 is a neuronal calmodulin-binding phosphoprotein that is concentrated in growth cones and pre-synaptic terminals.
Pfam PF03102: NeuB family (domain)
NeuB is the prokaryotic N-acetylneuraminic acid (Neu5Ac) synthase. It catalyses the direct formation of Neu5Ac (the most common sialic acid) by condensation of phosphoenolpyruvate (PEP) and N-acetylmannosamine (ManNAc). This reaction has only been observed in prokaryotes; eukaryotes synthesise the 9-phosphate form, Neu5Ac-9-P, and utilise ManNAc-6-P instead of ManNAc. Such eukaryotic enzymes are not present in this family. This family also contains SpsE spore coat polysaccharide biosynthesis proteins.
Pfam PF17014: Putative Mad3/BUB1 like region 1 protein (family)
This family of microsporidial sequences may be related to the Mad3_BUB1_I family [pfam:PF08311].
Pfam PF13814: Replication-relaxation (family)
This family includes proteins which are essential for plasmid replication and plasmid DNA relaxation.
Pfam PF09262: Peroxisome biogenesis factor 1, N-terminal (domain)
Members of this family adopt a double psi beta-barrel fold, similar in structure to the Cdc48 N-terminal domain. It has been suggested that this domain may be involved in interactions with ubiquitin, ubiquitin-like protein modifiers, or ubiquitin-like domains, such as Ubx. Furthermore, the domain may possess a putative adaptor or substrate binding site, allowing for peroxisomal biogenesis, membrane fusion and protein translocation.
Pfam PF21817: CapR homology domain (domain)
This entry represents a domain that is found in in the CapR proteins of PLE phage satellites. Proteins in this family are DNA-binding proteins.
Pfam PF10167: BLOC-1-related complex sub-unit 8 (family)
This is the N-terminal 80 residues of a family of proteins conserved from plants to humans. It contains a characteristic NEP sequence motif. Family members include BORCS8 (BLOC-1-related complex sub-unit 8) also known as MEF2BNB. It constitutes sub-unit 8 of the BORC complex (BLOC-one-related complex). BORC is a multisubunit complex that regulates the positioning of lysosomes at the cell periphery, and consequently affects cell migration. BORC associates with the lysosomal membrane, where it functions to recruit the small GTPase Arl8. This initiates a series of interactions that promote the microtubule-guided transport of lysosomes toward the cell periphery.
Pfam PF03783: Curli production assembly/transport component CsgG (family)
CsgG is an outer membrane-located lipoprotein that is highly resistant to protease digestion. During curli assembly, an adhesive surface fibre, CsgG is required to maintain the stability of CsgA and CsgB.