SII-SWORD/CoKE huggingface dataset:
Pfam PF04173: TQO small subunit DoxD (family)
[swissprot:P97207] is a subunit of the terminal quinol oxidase present in the plasma  membrane of Acidianus ambivalens, with calculated molecular mass of 20.4 kDa. Thiosulphate:quinone oxidoreductase (TQO) is one of the early steps in elemental sulphur oxidation.  A novel TQO enzyme was purified from the thermo-acidophilic archaeon Acidianus ambivalens and shown to consist of a large subunit (DoxD) and a smaller subunit (DoxA). The DoxD- and DoxA-like two subunits are fused together in a single polypeptide in [swissprot:Q8AAF0].
Pfam PF13490: Putative zinc-finger (domain)
This is a putative zinc-finger found in some anti-sigma factor proteins.
Pfam PF19927: Family of unknown function (DUF6390) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001065) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the herboxidiene biosynthetic gene cluster from Streptomyces chromofuscus. This family appears to be predominantly found in  actinobacteria.
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 PF14105: Domain of unknown function (DUF4278) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 58 and 136 amino acids in length. There is a single completely conserved residue R that may be functionally important.
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 PF08913: Vinculin Binding Site (domain)
Vinculin binding sites are predominantly found in talin and talin-like molecules, enabling binding of vinculin to talin, stabilising integrin-mediated cell-matrix junctions. Talin, in turn, links integrins to the actin cytoskeleton. The consensus sequence for Vinculin binding sites is LxxAAxxVAxxVxxLIxxA, with a secondary structure prediction of four amphipathic helices. The hydrophobic residues that define the VBS are themselves 'masked' and are buried in the core of a series of helical bundles that make up the talin rod.
Wikipedia: Talin is a high-molecular-weight cytoskeletal protein concentrated at regions of cell–substratum contact and, in lymphocytes, at cell–cell contacts. Discovered in 1983 by Keith Burridge and colleagues, talin is a ubiquitous cytosolic protein that is found in high concentrations in focal adhesions. It is capable of linking integrins to the actin cytoskeleton either directly or indirectly by interacting with vinculin and α-actinin.
Pfam PF13651: Adenine-specific methyltransferase EcoRI (family)
This methylase recognizes the double-stranded sequence GAATTC, causes specific methylation on A-3 on both strands, and protects the DNA from cleavage by the EcoRI endonuclease.
Pfam PF09065: Haemadin (domain)
Members of this family adopt a secondary structure consisting of five short beta-strands (beta1-beta5), which are arranged in two antiparallel distorted sheets formed by strands beta1-beta4-beta5 and beta2-beta3 facing each other. This beta-sandwich is stabilised by six enclosed cysteines arranged in a disulphide pairing resulting in a disulphide-rich hydrophobic core that is largely inaccessible to bulk solvent. The close proximity of disulfide bonds [] and [] organises haemadin into four distinct loops. The N-terminal segment of this domain binds to the active site of thrombin, inhibiting it.
Pfam PF05805: L6 membrane protein (family)
This family consists of several eukaryotic L6 membrane proteins. L6, IL-TMP, and TM4SF5 are cell surface proteins predicted to have four transmembrane domains. Previous sequence analysis led to their assignment as members of the tetraspanin superfamily it has now been found that that they are not significantly related to genuine tetraspanins, but instead constitute their own L6 family. Several members of this family have been implicated in human cancer.
Pfam PF16294: RNSP1-SAP18 binding (RSB) motif (conserved_site)
The RSB motif on the Acinus protein is the core around which the ASAP complex is built. The apoptosis and splicing-associated protein complex, ASAP, is made up of three proteins, SAP18 (Sin3-associated protein of 18 kDa), RNA-binding protein S1 (RNPS1) and apoptotic chromatin inducer in the nucleus (Acinus). The ASAP complex appears to be an assembly of proteins at the interface between transcription, splicing and NMD, acting as a hub in the network of protein-interactions that regulate gene-expression.
Pfam PF06887: Protein of unknown function (DUF1265) (family)
This family represents a conserved region approximately 50 residues long within a number of proteins of unknown function that seem to be restricted to C. elegans. The GO annotation for this protein indicate that its a protein involved in nematode larval development and has a positive regulation on growth rate.
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 PF15941: FidL-like putative membrane protein (family)
FidL-like is a family of bacterial proteins that are purported to be membrane proteins.
Pfam PF00478: IMP dehydrogenase / GMP reductase domain (domain)
This family is involved in biosynthesis of guanosine nucleotide. Members of this family contain a TIM barrel  structure. In the inosine monophosphate dehydrogenases 2 CBS domains [pfam:PF00571] are inserted in the TIM barrel. This family is a member of the common phosphate binding site TIM barrel family.
Wikipedia: In molecular biology, the IMPDH/GMPR family of enzymes includes IMP dehydrogenase and GMP reductase. These enzymes are involved in purine metabolism. These enzymes adopt a TIM barrel structure.
Pfam PF18783: Isopullulanase beta-solenoid repeat (repeat)
IPU and dextranase repeat unit includes three (or one long and one  short) parallel beta-strands. The repeat region as a whole folds into a beta-helix, known as beta-solenoid.
Pfam PF13820: Nuclear receptor coactivator 6, TRADD-N domain (domain)
This entry represents the TRADD-N domain found in the nuclear receptor coactivator 6 (NCOA6), which belong to the TRADD-N domain superfamily. NCOA6 is a component of SET domain histone methyltransferase complexes such as the ASCOM coactivator, involved in nuclear hormone receptor transactivation.
Pfam PF23805: Family of unknown function (DUF7180) (family)
This entry represents an uncharacterized protein that is found in a variety of phage, predominantly infecting bacteria from the Enterobacteriaceae family such as Escherichia and Salmonella. The protein is typically between 75-120 amino acids in length. These proteins have a highly conserved N-terminus.
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 PF18231: L-serine kinase SerK, C-terminal domain (domain)
This domain is found in the C-terminal region of free serine kinase (SerK) in the hyperthermophilic archaeon Thermococcus kodakarensis. SerK converts ADP and l-serine (Ser) into AMP and O-phospho-l-serine (Sep), which is a precursor of l-cysteine. The domain is not conserved in the ParB/Srx family. The differences between SerK and the other members of the ParB/Srx family is concentrated in the C-terminal region, which may include residues involved in the Sep binding. Members of this group are mainly found in archaea.
Pfam PF22460: Neopullulanase-like, C-terminal domain (domain)
This entry represents the C-terminal all-beta domain found in (Neo)pullulanase ([swissprot:Q5SI17]) from Thermus thermophilus (PDBe:2Z1K) and similar sequences.
Pfam PF16353: Beta-galactosidase, domain 4 (domain)
This entry represents domain 4 found in beta-galactosidase and it is organised in a jelly-roll type barrel (Rutkiewicz-Krotewicz M. et al. Crystals 2018, 8(1), 13, https://doi.org/10.3390/cryst8010013).
Pfam PF04026: SpoVG (family)
Stage V sporulation protein G. Essential for sporulation and specific to stage V sporulation in Bacillus megaterium and subtilis. In B. subtilis, expression decreases after 30-60 minutes of cold shock.
Pfam PF20716: ATPTG10-like (domain)
This entry, previously known as DUF6828, represents a domain found in the T. gondii ATP synthase subunit 10 (ATPTG10) and related proteins from Apicomplexan species. This domain adopts an alpha-helical structure consisting of five helices. It contains two highly conserved sequence motifs: FSWxD and MxLWI/LKxRI/L. The formation of the T.gondii ATP synthase hexamer involves two contact sites in the lumenal region. ATPTG10 contributes to the the second site via interaction with ATP synthase subunit 11 (ATPTG11).
Pfam PF03432: MobA/VirD2-like, nuclease domain (domain)
Relaxases/mobilisation proteins are required for the horizontal transfer of genetic information contained on plasmids that occurs during bacterial conjugation. The relaxase, in conjunction with several auxiliary proteins, forms the relaxation complex or relaxosome. Relaxases nick duplex DNA in a specific manner by catalysing trans-esterification. This entry represents the nuclease domain of VirD2 and similar sequences.
Pfam PF12295: Symplekin tight junction protein C terminal (family)
This domain family is found in eukaryotes, and is approximately 180 amino acids in length. There is a single completely conserved residue P that may be functionally important. Symplekn has been localized, by light and electron microscopy, to the plaque associated with the cytoplasmic face of the tight junction-containing zone (zonula occludens) of polar epithelial cells and of Sertoli cells of testis. However, both the mRNA and the protein can also be detected in a wide range of cell types that do not form tight junctions. Careful analyses have revealed that the protein occurs in all these diverse cells in the nucleoplasm, and only in those cells forming tight junctions is it recruited, partly but specifically, to the plaque structure of the zonula occludens.
Pfam PF06758: Olduvai domain (domain)
This domain formerly known as DUF1220 or NBPF domain has been renamed as the Olduvai domain. It is found highly duplicated in the human lineage.
Wikipedia: The Olduvai domain, known until 2018 as DUF1220 and the NBPF repeat, is a protein domain that shows a striking human lineage-specific (HLS) increase in copy number and appears to be involved in human brain evolution. The protein domain has also been linked to several neurogenetic disorders such as schizophrenia and increased severity of autism. In 2018, it was named by its discoverers after Olduvai Gorge in Tanzania, one of the most important archaeological sites for early humans, to reflect data indicating its role in human brain size and evolution.
Pfam PF21961: AppA, four helix bundle (domain)
This domain is found in AppA protein from Rhodobacter sphaeroides and similar sequences from alphaproteobacteria. AppA is a light -sensing antirepressor involved in oxygen and light control of photosynthesis-gene expression. This protein senses blue-light via its N-terminal sensor of blue-light using FAD (BLUF) domain ([pfam:PF04940]) and oxygen via its SCHIC (sensor containing heme instead of cobalamin) domain. This entry represents the domain that locates in between them, which folds as a four helix bundle (4HB) and acts as a binding platform for the adjacent domains.
Pfam PF12341: Minichromosome loss protein, Mcl1, middle region (repeat)
Mcl1_mid, or the middle domain of minichromosome loss protein 1, is the domain that lies between a 7-bladed beta-propeller at the N-terminus, family WD40 [pfam:PF00400] etc, and a Homeobox (HMG) domain, [pfam:PF00505], at the C-terminus. The full length proteins with all three domains are referred to as DNA polymerase alpha accessory factor Mcl1, but the exact function of this domain is not known.
Pfam PF23017: Tospovirus NSs-like, WIV_2 domain (domain)
This entry corresponds to the WIV domain of viruses related to the WIV domain of Tospovirus NSs. Tospoviruses infect plants and arthropods (such as thrips), which serve as vectors for plant transmission. The WIV domain probably facilitates viral infection of arthropods. WIV stands for 'Widespread, Intriguing, Versatile'.
Pfam PF23169: Halogenase D (domain)
This domain is found in ornithine halogenase HalD and related proteins including L-lysine 4-chlorinase BesD and L-lysine 5-chlorinase HalB. In addition to ornithine, HalD chlorinates lysine but with slower rate. This preference of HalD for ornithine is due to a narrower active site pocket. These enzymes are structurally very similar and adopt a typical cupin-like fold.
Pfam PF19894: Family of unknown function (DUF6367) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001053) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide, in particular the tubulysin A biosynthetic gene cluster from Archangium disciforme.
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 PF03743: Bacterial conjugation TrbI-like protein (family)
Although not essential for conjugation, the TrbI protein greatly increase the conjugational efficiency.
Pfam PF16179: Rel homology dimerisation domain (domain)
The Rel homology domain (RHD) is composed of two structural domains, an N-terminal DNA_binding domain ([pfam:PF00554]) and a C-terminal dimerisation domain. This is the dimerisation domain.
Wikipedia: The Rel homology domain (RHD) is a protein domain found in a family of eukaryotic transcription factors, including both NF-κB and NFAT, among others. Some of these transcription factors appear to form multi-protein DNA-bound complexes. Phosphorylation of the RHD appears to play a role in the regulation of some of these transcription factors, acting to modulate the expression of their target genes.
Pfam PF01747: ATP-sulfurylase (domain)
This domain is the catalytic domain of ATP-sulfurylase or sulfate adenylyltransferase [ec:2.7.7.4] some of which are part of a bifunctional polypeptide chain associated with adenosyl phosphosulphate (APS) kinase [pfam:PF01583]. Both enzymes are required for PAPS (phosphoadenosine-phosphosulfate) synthesis from inorganic sulphate. ATP sulfurylase catalyses the synthesis of adenosine-phosphosulfate APS from ATP and inorganic sulphate.
Wikipedia: In enzymology, a sulfate adenylyltransferase is an enzyme that catalyzes the chemical reactionATP + sulfate ⇌ pyrophosphate + adenylyl sulfate
Pfam PF04823: Herpesvirus UL49 tegument protein (family)
This is a family of herpesvirus UL49 tegument proteins. It was shown that interactions between herpesvirus envelope and tegument proteins may play a role in secondary envelopment during herpesvirus virion maturation.
Pfam PF23350: BBS2 platform domain (domain)
This entry represents the platform domain of BBS2. BBS2 is one of the BBS proteins that form the BBSome complex found in vertebrates and nematodes, including humans, mice, and Caenorhabditis elegans. BBSome complex is required for ciliogenesis and the assembly and movement of intraflagellar transport proteins along the ciliary membrane.
Pfam PF21146: ICAM-1/3/5, D2 domain (domain)
ICAMs promote intercellular adhesion and are important in inflammation, immune responses and in intracellular signalling events. They belong to the Ig-like superfamily and differ in their cell expression patterns and numbers of Ig-like domains (ICAM-2 and ICAM-4 have two, ICAM-1 and ICAM-3 have five and ICAM-5 has nine). Domain 2 (D2), represented in this entry, is most similar between ICAM-1, 3 and 5.
Pfam PF05196: PTN/MK heparin-binding protein family, N-terminal domain (domain)
Several extracellular heparin-binding proteins involved in regulation of growth and differentiation belong to a new family of growth factors. These growth factors are highly related proteins of about 140 amino acids that contain 10 conserved cysteines probably involved in disulphide bonds, and include pleiotrophin  (also known as heparin-binding growth-associated molecule HB-GAM, heparin-binding growth factor 8 HBGF-8, heparin-binding neutrophic factor HBNF and osteoblast specific protein OSF-1); midkine (MK) ; retinoic acid-induced heparin-binding protein (RIHB) ; and pleiotrophic factors alpha-1 and -2 and beta-1 and -2 from Xenopus laevis, the homologues of midkine and pleiotrophin respectively. Pleiotrophin is a heparin-binding protein that has neurotrophic activity and has mitogenic activity towards fibroblasts. It is highly expressed in brain and uterus tissues, but is also found in gut, muscle and skin. It is thought to possess an important brain-specific function. Midkine is a regulator of differentiation whose expression is regulated by retinoic acid, and, like pleiotrophin, is a heparin-binding growth/differentiation factor that acts on fibroblasts and nerve cells.
This entry represents the N-terminal domain of pleiotrophin and midkine .
Pfam PF05604: Protein of unknown function (DUF776) (family)
This family consists of several highly related mouse and human proteins 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 PF21993: Transcriptional regulator LmrA/YxaF-like, C-terminal domain (domain)
This entry represents the C-terminal domain found in a group of TetR transcription regulators, including YxaF (also known as T1414) and LmrA from Bacillus subtilis, which are paralogous to each other. LmrA and YxaF are repressors that bind specifically to almost the same cis sequences, LmrA/YxaF boxes, located in the promoter regions of the lmrAB operon, the yxaF gene, and the yxaGH operon.
Pfam PF17204: Sid-5 family (family)
SID-5 is a C. elegans endosome-associated protein that is required for efficient systemic RNA.
Pfam PF03917: Eukaryotic glutathione synthase, ATP binding domain (domain)
This entry represents glutathione synthetase (6.3.2.3) (GSH-S), 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 .
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 PF12080: GldM C-terminal domain (domain)
This domain is found in bacteria at the C-terminus of the GldM protein. This domain is typically between 169 to 182 amino acids in length. This domain has two completely conserved residues (Y and N) that may be functionally important. GldM, is named for the member from Cytophaga johnsonae (Flavobacterium johnsoniae), which is required for a type of rapid gliding motility found in certain members of the Bacteriodetes.
Pfam PF02028: BCCT, betaine/carnitine/choline family transporter (family)
These prokaryotic transport proteins belong to a family known as BCCT (for Betaine/Carnitine/Choline Transporters)  and are specific for compounds containing a quaternary nitrogen atom. The BCCT proteins contain 12 transmembrane regions and are energised by proton symport. They contain a conserved region with four tryptophans in their central region .
Wikipedia: The Betaine/Carnitine/Choline Transporter (BCCT) family proteins are found in Gram-negative and Gram-positive bacteria and archaea. The BCCT family members a large group of secondary transporters, the APC superfamily. Their common functional feature is that they all transport molecules with a quaternary ammonium group [R-N (CH3)3]. The BCCT family proteins vary in length between 481 and 706 amino acyl residues and possess 12 putative transmembrane α-helical spanners (TMSs). The x-ray structures reveal two 5 TMS repeats, with the total TMSs being 10. These porters catalyze bidirectional uniport or are energized by pmf-driven or smf-driven proton or sodium ion symport, respectively, or substrate: substrate antiport. Some of these permeases exhibit osmosensory and osmoregulatory properties inherent to their polypeptide chains.
Pfam PF05047: Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain (domain)
The proteins in this family are located in the mitochondrion. The family includes ribosomal protein L51, and S25. This family also includes mitochondrial NADH-ubiquinone oxidoreductase B8 subunit (CI-B8) [ec:1.6.5.3]. It is not known whether all members of this family form part of the NADH-ubiquinone oxidoreductase and whether they are also all ribosomal proteins. Structurally related to thioredoxin-fold.
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 PF22517: Mcm-like, N-terminal domain, archaea (domain)
This entry represents the N-terminal domain of a monomeric MCM homologue (known as Mcm2) from Methanopyrus kandleri. The MCM (minichromosome maintenance) proteins, which belong to the AAA superfamily, serve as the replicative helicase in eukaryotic and archaeal organisms.
Pfam PF03233: Aphid transmission protein (family)
This protein is found in various caulimoviruses. It codes for an 18 kDa protein (PII), which is dispensable for infection but which is required for aphid transmission of the virus. This protein interacts with the PIII protein.