SII-SWORD/CoKE huggingface dataset:
Pfam PF01699: Sodium/calcium exchanger protein (family)
This is a family of sodium/calcium exchanger integral membrane proteins. This family covers the integral membrane regions of the proteins. Sodium/calcium exchangers regulate intracellular Ca2+ concentrations in many cells; cardiac myocytes, epithelial cells, neurons retinal rod photoreceptors and smooth muscle cells. Ca2+ is moved into or out of the cytosol depending on Na+ concentration.  In humans and rats there are 3 isoforms; NCX1 NCX2 and NCX3 see [swissprot:Q01728], [swissprot:P48768] and [swissprot:P70549] respectively.
Pfam PF09823: Domain of unknown function (DUF2357) (domain)
This entry was previously the N terminal portion of DUF524 ([pfam:PF04411]) before it was split into two.  This domain has no known function.  It is predicted to adopt an all beta secondary structure pattern followed by mainly alpha-helical structures.
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 PF09038: Tumour suppressor p53-binding protein-1 Tudor (domain)
Members of this family consist of ten beta-strands and a carboxy-terminal alpha-helix. The amino-terminal five beta-strands and the C-terminal five beta-strands adopt folds that are identical to each other. This domain is essential for the recruitment of proteins to double stranded breaks in DNA, which is mediated by interaction with methylated Lys 79 of histone H3.
Pfam PF06374: NADH-ubiquinone oxidoreductase subunit b14.5b (NDUFC2) (family)
This family consists of several NADH-ubiquinone oxidoreductase subunit b14.5b proteins ([ec:1.6.5.3]).
Wikipedia: Respiratory complex I, EC 7.1.1.2 is the first large protein complex of the respiratory chains of many organisms from bacteria to humans. It catalyzes the transfer of electrons from NADH to coenzyme Q10 (CoQ10) and translocates protons across the inner mitochondrial membrane in eukaryotes or the plasma membrane of bacteria.
Pfam PF02502: Ribose/Galactose Isomerase (family)
This family of proteins contains the sugar isomerase enzymes ribose  5-phosphate isomerase B (rpiB), galactose isomerase subunit A (LacA) and galactose isomerase subunit B (LacB).
Pfam PF23143: P5A-ATPase, transmembrane helical hairpin (domain)
This domain is found in the homologues of endoplasmic reticulum P5A-ATPase (Spf1 in yeast; ATP13A1 in humans). The P5A-ATPase acts as a dislocase that mediates the ATP-dependent extraction of mislocalized mitochondrial transmembrane proteins from the endoplasmic reticulum membrane. It interacts directly with the TM of the mitochondrial tail-anchored proteins. The domain represented by this entry consists of two transmembrane helices that form a helical hairpin. This domain seems to be loosely associated with the core transmembrane domain.
Pfam PF14049: Dppa2/4 conserved region in higher vertebrates (family)
Developmental pluripotency associated genes (Dppa) in lower vertebrates have remained undetected until the discovery of a Dppa homologue in Xenopus laevis, reporting a new domain termed Dppa2/4 conserved region (DCR). In higher vertebrate Dppa proteins the DCR domain is located next to the here-reported domain. The domain is subject to structure determination by the Joint Center of Structural Genomics.
Pfam PF11507: Ebola virus-specific transcription factor VP30 (family)
VP30 is a nucleocapsid-associated Ebola virus-specific transcription factor. It acts by stabilising nascent mRNA in Ebola virus replication. The C terminal domain of VP30 folds into a dimeric helical assembly. VP30 assembles into hexamers in solution by an N-terminal oligomerisation domain which activates the transcription function of the protein. The oligomerisation is mediated by hydrophobic amino acids at 94-112.
Pfam PF14224: Domain of unknown function (DUF4331) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 223 and 526 amino acids in length. There is a conserved FPY 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 PF11785: Aft1 osmotic stress response (OSM) domain (disordered)
This domain is found in the transcription factor Aft1 which is required for a wide range of stress responses.  The OSM domain has been shown to be involved in the osmotic stress response.
Pfam PF04112: Mak10 subunit, NatC N(alpha)-terminal acetyltransferase (family)
NatC N(alpha)-terminal acetyltransferases contains Mak10p, Mak31p and Mak3p subunits.  All three subunits are associated with each other to form the active complex.
Pfam PF13303: Phosphotransferase system, EIIC (family)
The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. The sugar-specific permease of the PTS consists of three domains (IIA, IIB and IIC). The IIC domain catalyses the transfer of a phosphoryl group from IIB to the sugar substrate.
Pfam PF01436: NHL repeat (repeat)
The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies.  It is about 40 residues long and resembles the WD repeat [pfam:PF00400].  The repeats have a catalytic activity in [swissprot:P10731], proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localised to the repeats. [swissprot:Q13049] interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats.
Wikipedia: The NHL repeat, named after ncl-1, HT2A and lin-41, is an amino acid sequence found largely in a large number of eukaryotic and prokaryotic proteins. For example, the repeat is found in a variety of enzymes of the copper type II, ascorbate-dependent monooxygenase family which catalyse the C-terminus alpha-amidation of biological peptides. In many it occurs in tandem arrays, for example in the RING finger beta-box, coiled-coil (RBCC) eukaryotic growth regulators. The arthropod 'Brain Tumor' protein is one such growth regulator that contains a 6-bladed NHL-repeat beta-propeller.
Pfam PF09856: Short-chain fatty acyl coenzyme A regulator, C-terminal (domain)
This entry includes short-chain fatty acid regulators such as RAMB (regulator of acetate metabolism B), PCCR (Propionyl-CoA carboxylase regulator), PrpR (Propionate regulator). RamB is a negative transcriptional regulator of genes involved in acetate metabolism of C. glutamicum. It is responsible for expression control of the AK, PTA, ICL, and MS genes and, thus, for the proper adaptation to acetate as carbon and energy source. Nucleotide sequence analysis indicate the RamB protein consists of 469 aa with a putative HTH motif at the N terminus. PCCR prevents the accumulation of propionyl-CoA by controlling expression of the gene encoding propionyl-CoA carboxylase, which is responsible for propionyl-CoA consumption by Rhodobacter sphaeroides. Many other Proteobacteria and Actinomycetales contain one or several PccR homologs that group into distinct clades on the basis of the pathway of acyl-CoA metabolism that they control. PrpR is a transcriptional activator controlling prpDBC2 operon which encodes enzymes 2-methylcitrate dehydratase (PrpD2), 2-methylisocitrate lyase (PrpB2) and 2-methylcitrate synthase (PrpC2). They are essential for growth with propionate as carbon source. The regulatory protein belongs to the HTH_XRE regulator family. It has a length of 441 amino acids and an N-terminal lamda repressor-like DNA-binding domain. This is the C-terminal domain, which is likely an iron sensor domain that adopts a GAF-like fold.
Pfam PF06197: Protein of unknown function (DUF998) (family)
Family of conserved bacterial and archaeal 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 PF05566: Orthopoxvirus interleukin 18 binding protein (family)
Interleukin-18 (IL-18) is a proinflammatory cytokine that plays a key role in the activation of natural killer and T helper 1 cell responses principally by inducing interferon-gamma (IFN-gamma). Several poxvirus genes encode proteins with sequence similarity to IL-18BPs. It has been shown that vaccinia, ectromelia and cowpox viruses secrete from infected cells a soluble IL-18BP (vIL-18BP) that may modulate the host antiviral response. The expression of vIL-18BPs by distinct poxvirus genera that cause local or general viral dissemination, or persistent or acute infections in the host, emphasises the importance of IL-18 in response to viral infections.
Pfam PF20481: Domain of unknown function (DUF6721) (domain)
This presumed domain is functionally uncharacterised. This domain family is found in eukaryotes, and is typically a 100 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 PF18674: TarS beta-glycosyltransferase C-terminal domain 1 (domain)
Beta-glycosyltransferase TarS is an enzyme responsible for the glycosylation of wall teichoic acid polymers of the S. aureus cell wall, a process that has been shown to be specifically responsible for methicillin resistance in MRSA. It contains a trimerization domain composed of tandem carbohydrate binding motifs.The two C-terminally localized regions composed of a series of beta-sheets participate in an extensive trimerization interface and they assume an immunoglobulin-like fold. It is suggested that both carbohydrate binding domains may be involved in polyRboP binding, however unlike pullulanase, the CBMs of TarS are involved in the formation of an extensive trimerization interface.
Pfam PF19205: Family of unknown function (DUF5877) (family)
This is a family of uncharacterised proteins of unknown functions 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 PF07730: Histidine kinase (domain)
This is the dimerisation and phosphoacceptor domain of a sub-family of histidine kinases. It shares sequence similarity with [pfam:PF00512] and [pfam:PF07536].
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 PF19231: Family of unknown function (DUF5884) (family)
This is a family of uncharacterised proteins of unknown function predominantly found in Mimivirus.
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 PF10206: Mitochondrial F1F0-ATP synthase, subunit f (family)
This is a family of small proteins of approximately 110 amino acids, which are highly conserved from nematodes to humans. Some members of the family have been annotated in Swiss-Prot as being the f subunit of mitochondrial F1F0-ATP synthase but this could not be confirmed. The sequence has a well-conserved WRW motif. The exact function of the protein is not known.
Pfam PF04466: Phage terminase large subunit (domain)
Initiation of packaging of double-stranded viral DNA involves the specific interaction of the prohead with viral DNA in a process mediated by a phage-encoded terminase protein. The terminase enzymes are usually hetero-oligomers composed of a small and a large subunit.  This region is found on the large subunit and possess an endonuclease and ATPase activity that require Mg2+ and a neutral or slightly basic reaction.  This region is also found in bacterial sequences.
Pfam PF13980: Uncharacterised protein family (UPF0370) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 70 amino acids in length. There is a conserved DWP sequence motif.
Pfam PF09204: Bacterial self-protective colicin-like immunity (domain)
Colicin D, which is synthesised by various prokaryotes, adopts an antiparallel four helical bundle fold: the helices are tightly packed, forming a compact cylindrical molecule. The protein specifically cleaves the anticodon loop of all four tRNA-Arg isoacceptors, thereby inactivating prokaryotic protein synthesis and leading to cell death. This family also contains immunity proteins to klebicins and microcins. Many bacteria produce proteins that destroy their competitors. Colicin D is one such. The immunity proteins are expressed on the same operon as their cognate bacteriocins and protect the expressing bacterium from the effects of its own bacteriocin.
Pfam PF20811: Poly (ADP-ribose) glycohydrolase (PARG), helical domain (domain)
Poly(ADP-ribose) glycohydrolase (PARG), is a ubiquitously expressed exo- and endoglycohydrolase which mediates oxidative and excitotoxic neuronal death. It catalyses hydrolysis of the O-glycosidic linkages of ADP-ribose polymers, which reverses the effects of poly(ADP-ribose). This entry represents the helical domain of PARG catalytic domain from animals and plants, found at the N-terminal of PARG catalytic domain.
Pfam PF07394: Protein of unknown function (DUF1501) (family)
This family contains a number of hypothetical bacterial proteins of unknown function approximately 400 residues long.
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 PF20408: Alpha/beta hydrolase domain (domain)
This entry represents a protein that belongs to the alpha/beta hydrolase superfamily. Although proteins in this family are uncharacterised they are likely to have an enzymatic activity.
Pfam PF24125: Cds6 C-terminal NTF2-like domain (domain)
This entry represents the C-terminal domain of Cds6 from H. pylori, a cell shape-determining protein that plays key roles in alteration of cross-linking or by trimming of peptidoglycan muropeptides. It is also involved in deglycosylation of the flagellar protein FlaA. This domain adopts NTF2-like topology. This domain contains a putative binding pocket for pseudaminic acid suggesting this domain may function as pseudaminase.
Pfam PF14752: Retinol binding protein receptor (family)
Proteins in this family function as retinol binding protein receptors.
Pfam PF01873: Domain found in IF2B/IF5 (family)
This family includes the N terminus of eIF-5 [swissprot:P55010], and the C terminus of eIF-2 beta [swissprot:P20042]. This region corresponds to the whole of the archaebacterial eIF-2 beta homologue. The region contains a putative zinc binding C4 finger.
Pfam PF10405: Rad4 beta-hairpin domain 3 (domain)
This short domain is found in the Rad4 protein. This domain binds to DNA.
Pfam PF16607: Phosphorylation region of CYLD, unstructured (disordered)
CYLD_phos_site is a natively unstructured region on a subset of tumour-suppressor and de-ubiquitinating enzyme CYLD proteins in eukaryotes. It lies between the second pair of CAP_GLY domains, [pfam:PF01302], on these proteins. This region of CYLD, being unstructured, carries a number of serine residues which, in response to cellular stimuli, become phosphorylated. This transient phosphorylation-state induces ubiquitination of TRAF2, a ubiquitin ligase that catalyses both self-ubiquitination and the ubiquitination of specific target molecules involved in signal transduction.
Pfam PF10315: Altered inheritance of mitochondria protein 19 (family)
This is a family of conserved proteins found in fungi. The function is not known.
Pfam PF12633: Adenylate cyclase NT domain (domain)
Adenylate cyclase is the enzyme responsible for the synthesis of cAMP from ATP. On the basis of sequence similarity, it has been proposed that there are three different classes of adenylate cyclases . Class I cyclases are found in enterobacteria and related Gram-negative bacteria.
This entry represents the N-terminal domain of class-I adenylate cyclases.
Pfam PF08704: tRNA methyltransferase complex GCD14 subunit (family)
GCD14 is a subunit of the tRNA methyltransferase complex and is required for 1-methyladenosine modification and maturation of initiator methionyl-tRNA.
Pfam PF17706: Family of unknown function (DUF5552) (family)
This is a family of unknown function found in primates.
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 PF09773: Meckelin (Transmembrane protein 67) (family)
Members of this family are thought to be related to the ciliary basal body.  Defects result in Meckel syndrome type 3, [MIM:607361], an autosomal recessive disorder characterised by a combination of renal cysts and variably associated features including developmental anomalies of the central nervous system (typically encephalocele), hepatic ductal dysplasia and cysts, and polydactyly. Joubert syndrome type 6 [MIM:610688] is also a manifestation of certain mutations; it is an autosomal recessive congenital malformation of the cerebellar vermis and brainstem with abnormalities of axonal decussation (crossing in the brain) affecting the corticospinal tract and superior cerebellar peduncles. Individuals with Joubert syndrome have motor and behavioral abnormalities, including an inability to walk due to severe clumsiness and 'mirror' movements, and cognitive and behavioural disturbances.
Pfam PF12991: Domain of unknown function, B. Theta Gene description (DUF3875) (family)
Based on Bacteroides thetaiotaomicron gene BT_4769, a conserved protein found in a conjugate transposon. As seem in gene expression experiments (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2231). It appears to be upregulated in the presence of host or other bacterial species vs when in culture.
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 PF19298: 3-Ketosteroid 9alpha-hydroxylase C-terminal domain (domain)
KshAB is a complex of KshA and KshB that catalyses the 3-Ketosteroid 9alpha-hydroxylase reaction. This entry represents the C-terminal domain catalytic domain of KshA. This domain The catalytic domain shares the TBP-like fold found in other Rieske oxygenases.
Pfam PF11384: Protein of unknown function (DUF3188) (family)
This bacterial family of proteins has no known function.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF02868: Thermolysin metallopeptidase, alpha-helical domain (domain)
This entry represents a domain found in the C-terminal of the peptidase M4 family members.
This group of metallopeptidases that belong to the MEROPS peptidase family M4 (thermolysin family, clan MA(E)). The protein fold of the peptidase domain of thermolysin (MEROPS identifier M04.001), is the type example for members of the clan MA. The thermolysin family is composed only of secreted eubacterial endopeptidases. The zinc-binding residues of thermolysin are H-142, H-146 and E-166, with E-143 acting as the catalytic residue. Thermolysin also contains four calcium-binding sites, which contribute to its unusual thermostability. The family also includes enzymes from a number of pathogens, including Legionella and Listeria, and the protein pseudolysin (MEROPS identifier M04.005), all with a substrate specificity for an aromatic residue in the P1' position. Three-dimensional structure analysis has shown that the enzymes undergo a hinge-bend motion during catalysis. Pseudolysin has a broader specificity, acting on large molecules such as elastin and collagen, possibly due to its wider active site cleft .
Pfam PF03871: RNA polymerase Rpb5, N-terminal domain (domain)
Rpb5 has a bipartite structure which includes a eukaryote-specific  N-terminal domain and a C-terminal domain resembling the archaeal RNAP  subunit H.  The N-terminal domain is involved in DNA binding and is  part of the jaw module in the RNA pol II structure.  This module is important for positioning the downstream DNA.