SII-SWORD/CoKE huggingface dataset:
Pfam PF08970: Sporulation inhibitor A (domain)
Members of this protein family contain two antiparallel alpha helices that are linked by a highly structured inter-helix loop to form a helical hairpin; the structure is stabilised by numerous hydrophobic and electrostatic interactions. These sporulation inhibitors are antikinases that bind to the histidine kinase KinA phosphotransfer domain and act as a molecular barricade that inhibit productive interaction between the ATP binding site and the phosphorylatable KinA His residue. This results in the inhibition of sporulation (by preventing phosphorylation of spo0A).
Wikipedia: In molecular biology, the protein domain Sda is short for suppressor of dnaA or otherwise known as sporulation inhibitor A. It is found only in bacteria. This protein domain is highly important to cell survival. When starved of nutrients, the cell is under extreme stress so undergoes a series of reactions to increase the chances of survival. One method is to form endospores which can withstand a large amount of environmental pressure. Sda protein domain is a checkpoint which prevents the formation of spores. The Sda domain affects cell signalling. It prevents the cell communicating the stress that it is under, which is crucial if the cell is to survive.
Pfam PF16185: Mitochondrial ABC-transporter N-terminal five TM region (family)
MTABC_N is the N-terminal five transmembrane helices of eukaryotic mitochondrial ABC-transporters.
Pfam PF16805: Phage late-transcription coactivator (domain)
This family of proteins is found in Caudovirales. It is a late-transcription coactivator which interacts with the host RNA polymerase forming a part of the initiation complex.
Pfam PF15782: GREB1 N-terminal domain (domain)
GREB1 (gene regulated by estrogen in breast cancer 1) was first identified as an estrogen-regulated gene expressed in breast cancer. Its exact function is not known but its expression is regulated by the coordinated binding of estrogen-receptors to distal sites interacting with Pol II to activate gene transcription from core promoters located at a considerable distance from the greb1 gene.  It acts as a regulator of hormone-dependent cancer growth in breast, ovarian and prostate cancers. This entry represents a N-terminal domain whose function is not yet known. Structure predictions suggest that it may have an alpha-beta fold.
Pfam PF16118: Domain of unknown function (DUF4834) (family)
This family consists of uncharacterized proteins around 90 residues in length and is mainly found in various Parabacteroides and Bacteroides species. Protein in this family are characterized by a strongly conserved KDEGEYVD motif on the C-terminal and a very divergent N-terminal. The function of this family is unknown.
Pfam PF22459: Pheromone cCF10 receptor, C-terminal TPR region (repeat)
This entry represents the C-terminal tetratrico peptide repeat region (TPR) of the pheromone cCF10 receptor from Enterococcus faecalis (PrgX), which serves as a molecular switch controlling expression of conjugation and virulence genes encoded by the conjugative plasmid pCF10. This region includes two domains: a large central dimerisation (and pheromone-binding) domain, and a C-terminal regulatory domain that is important for structural integrity.
Pfam PF04728: Lipoprotein leucine-zipper (coiled_coil)
This is leucine-zipper is found in the enterobacterial outer membrane lipoprotein LPP. It is likely that this domain oligomerises and is involved in protein-protein interactions. As such it is a bundle of alpha-helical coiled-coils, which are known to play key roles in mediating specific protein-protein interactions for in molecular recognition and the assembly of multi-protein complexes.
Wikipedia: Braun's lipoprotein, found in some gram-negative cell walls, is one of the most abundant membrane proteins; its molecular weight is about 7.2 kDa. It is bound at its C-terminal end by a covalent bond to the peptidoglycan layer and is embedded in the outer membrane by its hydrophobic head. BLP tightly links the two layers and provides structural integrity to the outer membrane.
Pfam PF08085: Entericidin EcnA/B family (family)
This family consists of the entericidin antidote/toxin peptides. The entericidin locus is activated in stationary phase under high osmolarity conditions by rho-S and simultaneously repressed by the osmoregulatory EnvZ/OmpR signal transduction pathway. The entericidin locus encodes tandem paralogous genes (ecnAB) and directs the synthesis of two small cell-envelope lipoproteins which can maintain plasmids in bacterial population by means of post-segregational killing.
Wikipedia: In molecular biology, entericidins are bacterial antidote/toxin peptides. The entericidin locus is activated in the stationary phase of growth under high osmolarity conditions by rho-S and simultaneously repressed by the osmoregulatory EnvZ/OmpR signal transduction pathway. The entericidin locus encodes tandem paralogous genes (ecnAB) and directs the synthesis of two small cell-envelope lipoproteins which can maintain plasmids in bacterial population by means of post-segregational killing.
Pfam PF03077: Putative vacuolating cytotoxin (family)
This family contains a number of Helicobacter outer membrane proteins with multiple copies of this small conserved region.
Pfam PF08997: Ubiquinol-cytochrome C reductase complex, 6.4kD protein (domain)
The ubiquinol-cytochrome C reductase complex (cytochrome bc1 complex) is an essential component of the mitochondrial cellular respiratory chain. This family represents the 6.4kD protein, which may be closely linked to the iron-sulphur protein in the complex and function as an iron-sulphur protein binding factor.
Wikipedia: The coenzyme Q : cytochrome c – oxidoreductase, sometimes called the cytochrome bc1 complex, and at other times complex III, is the third complex in the electron transport chain, playing a critical role in biochemical generation of ATP. Complex III is a multisubunit transmembrane protein encoded by both the mitochondrial and the nuclear genomes. Complex III is present in the mitochondria of all animals and all aerobic eukaryotes and the inner membranes of most bacteria. Mutations in Complex III cause exercise intolerance as well as multisystem disorders. The bc1 complex contains 11 subunits, 3 respiratory subunits, 2 core proteins and 6 low-molecular weight proteins.
Pfam PF21214: Selenocysteine-specific elongation factor, winged helix domain (domain)
This domain is found in Selenocysteine-specific elongation factor from Escherichia coli (SelB) and similar bacterial sequences. SelB is a translation factor necessary for the incorporation of selenocysteine into proteins. The C-terminal region of this protein in bacteria shows four winged-helix (WH) domains arranged in tandem, which form two globular structures. This entry represents the second pair of WH domains (WH3 and 4). Each WH domain is an alpha-beta structure consisting of three alpha-helices and a twisted three- stranded antiparallel beta-sheet.
Pfam PF09359: VTC domain (domain)
This presumed domain is found in the yeast vacuolar transport chaperone proteins VTC2, VTC3 and VTC4. This domain is also found in a variety of bacterial proteins.
Pfam PF08489: TiaS FLD domain (domain)
This is the FLD domain found in tRNA(Ile2) 2-agmatinylcytidine synthetase TiaS. TiaS is an archaeal ATP-dependent agmatine transferase that catalyses the formation of 2-agmatinylcytidine (agm2C) at the wobble position (C34) of tRNA(Ile2). This modified base specifically recognises AUA codons. TiaS consists of four domains, the TCKD domain ([pfam:PF22641]) at the N-terminal followed by the FLD domain, an OB fold domain and a zinc ribbon domain (ZRD) domain at the C-terminal. This domain is responsible for agmantine binding.
Pfam PF04690: YABBY protein, C-terminal (domain)
YABBY proteins are a group of plant-specific transcription involved in the specification of abaxial polarity in lateral organs. This entry represents the C-terminal domain of these proteins.
Pfam PF21539: ARC105/Med15 mediator subunit C-terminal domain (domain)
This domain is found at the C-terminus of the Med15 subunit of the ARC-Mediator co-activator. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development. This domain is structurally similar to the RWD domain.
Wikipedia: Mediator of RNA polymerase II transcription subunit 15, also known as Gal11, Spt13 in yeast and PCQAP, ARC105, or TIG-1 in humans is a protein encoded by the MED15 gene.
Pfam PF15821: Domain of unknown function (DUF4709) (family)
This domain family is found in eukaryotes, and is approximately 110 amino acids in length. There is a conserved QQL 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 PF09519: HindVP restriction endonuclease (family)
This family includes the HindVP (recognises GRCGYC bu the cleavage site is unknown) restriction endonucleases.
Pfam PF09546: Stage III sporulation protein AE (spore_III_AE) (family)
This represents the stage III sporulation protein AE, which is encoded in a spore formation operon spoIIIAABCDEFGH under the control of sigma G. A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species.
Pfam PF12283: Bacteriophage protein K (family)
This family of proteins is found in viruses. Proteins in this family are approximately 60 amino acids in length. This family is a protein expressed by bacteriophages which has an unknown function. There is evidence that it is non-essential for in vivo production of a mature phage.
Pfam PF15140: Domain of unknown function (DUF4573) (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically approximately 360 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 PF19317: Gag protein p24 C-terminal domain (domain)
p24 forms inner protein layer of the nucleocapsid. ELISA tests for p24 is the most commonly used method to demonstrate virus replication both in vivo and in vitro.
Pfam PF06277: Ethanolamine utilisation protein EutA (family)
This family consists of several bacterial EutA ethanolamine utilisation proteins. The EutA protein is thought to protect the lyase (EutBC) from inhibition by CNB12.
Pfam PF07327: Neuroparsin (family)
This family consists of several locust specific neuroparsin proteins. Neuroparsins are produced by the A1 type of protocerebral median neurosecretory cells of the PI-CC system and display pleiotropic activities: inhibition of the effect of juvenile hormone, stimulation of fluid reabsorption of isolated recta, induction of an increase in hemolymph lipid and trehalose levels, and neurotrophic effects.
Pfam PF23431: Broad-minded protein N-terminal domain (domain)
Broad-minded protein (BROMI) interacts with cell cycle-related kinase (CCRK), together these proteins regulate ciliary membrane and axonemal growth. This entry represents an N-terminal domain region of this protein.
Pfam PF15576: Domain of unknown function (DUF4661) (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 281 and 302 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 PF02359: Cell division protein 48 (CDC48), N-terminal domain (domain)
This domain has a double psi-beta barrel fold and includes VCP-like  ATPase and N-ethylmaleimide sensitive fusion protein N-terminal  domains.  Both the VAT and NSF N-terminal functional domains consist of two structural domains of which this is at the N-terminus. The VAT-N domain found in AAA ATPases [pfam:PF00004] is a substrate  185-residue recognition domain.
Wikipedia: In molecular biology, the CDC48 N-terminal domain is a protein domain found in AAA ATPases including cell division protein 48 (CDC48), VCP-like ATPase and N-ethylmaleimide sensitive fusion protein. It is a substrate recognition domain which binds polypeptides, prevents protein aggregation, and catalyses refolding of permissive substrates. It is composed of two equally sized subdomains. The amino-terminal subdomain (CDC48_N) forms a double-psi beta-barrel whose pseudo-twofold symmetry is mirrored by an internal sequence repeat of 42 residues. The carboxy-terminal subdomain (CDC48_2) forms a novel six-stranded beta-clam fold. Together these subdomains form a kidney-shaped structure, in close agreement with results from electron microscopy. CDC48_N is related to numerous proteins including prokaryotic transcription factors, metabolic enzymes, the protease cofactors UFD1 and PrlF, and aspartic proteinases.
Pfam PF21940: Pfc11 Rna14/15 interacting domain (domain)
This entry represents the RNA14/15 interacting domain (Rna14/15-ID) of Pfc11 from yeast. Pfc11 is a multidomain protein that links transcriptional elongation, 3'-end processing, and transcription termination.
Pfam PF13022: Helix-turn-helix of insertion element transposase (domain)
This is a family of largely phage proteins which are likely to be a helix-turn-helix insertion elements.
Pfam PF05481: Mycobacterium 19 kDa lipoprotein antigen (family)
Most of the antigens of Mycobacterium leprae and M. tuberculosis that have been identified are members of stress protein families, which are highly conserved throughout many diverse species. Of the M. leprae and M. tuberculosis antigens identified by monoclonal antibodies, all except the 18-kDa M. leprae antigen and the 19-kDa M. tuberculosis antigen are strongly cross-reactive between these two species and are coded within very similar genes.
Pfam PF22526: Family of unknown function (DUF7000) (family)
This is a family of uncharacterised bacterial proteins. They are predicted to adopt an alpha/beta structure consisting of a cradle-like beta-sheet with alpha-helices pocked on the convex side of it. These proteins contain a highly conserved GYMDFTYF sequence motif that may be of functional importance.
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 PF17840: Tethering Ubl4a to BAGS domain (domain)
This is the C-terminal domain of Ubiquitin-like protein 4A (Ubl4A), an orthologue of yeast Get5. In budding yeast, GET proteins directly mediate the insertion of newly synthesized TA proteins into endoplasmic reticulum membranes. Similarly, mammalian BAG6, Ubl4a, and SGTA make up a trimeric complex that binds TA proteins post-translationally and then loads them onto the cytosolic ATPase TRC40, which in turn targets them to the endoplasmic reticulum. Structural studies show that this C-terminal TUGS domain of Ubl4a is essential for BAG6 tethering. Given that BAG6 mediates oligomeric complex formation of Ubl4a, TRC35, and TRC40 (mammalian counterparts of Get5, Get4, and Get3, respectively), the C-terminal TUGS domain might be crucial for supporting BAG6-mediated Ubl4a-TRC35 complex formation in humans as an alternative to the direct Get5-Get4 interaction in yeast.
Pfam PF21771: CFAP58 central coiled coil (domain)
This domain is found in Cilia- and flagella-associated protein 58 (CFAP58) and related eukaryotic proteins. The human CFAP58 protein has an essential role in the assembly and organisation of the sperm flagellar axoneme. This domain forms a parallel coiled coil that in the C. reinhardtii axonemal structure lays on the doublet microtubule surface and interacts with the N terminus of the MIA coiled coil.
Pfam PF13481: AAA domain (domain)
This AAA domain is found in a wide variety of presumed DNA repair proteins.
Wikipedia: AAA proteins are a large group of protein family sharing a common conserved module of approximately 230 amino acid residues. This is a large, functionally diverse protein family belonging to the AAA+ protein superfamily of ring-shaped P-loop NTPases, which exert their activity through the energy-dependent remodeling or translocation of macromolecules.
Pfam PF01442: Apolipoprotein A1/A4/E domain (domain)
These proteins contain several 22 residue repeats which form a pair of alpha helices. This family includes: [swissprot:P02647] Apolipoprotein A-I. [swissprot:P06727] Apolipoprotein A-IV. [swissprot:P02649] Apolipoprotein E.
Wikipedia: Apolipoproteins are proteins that bind lipids to form lipoproteins. They transport lipids in blood, cerebrospinal fluid and lymph.
Pfam PF25101: Animal spectrin repeats (repeat)
This region of spectrin repeats is found in a group of uncharacterised proteins from animals.
Pfam PF02494: HYR domain (domain)
This domain is known as the HYR (Hyalin Repeat) domain, after the protein hyalin that is composed exclusively of this repeat. This domain probably corresponds to a new superfamily in the immunoglobulin fold. The function of this domain is uncertain it may be involved in cell adhesion.
Pfam PF03387: Herpesvirus UL46 protein (family)
The UL46 protein (VP11/12) is produced in the late phase of Herpes virus infection in a manner highly dependent on viral DNA synthesis, and is mainly distributed at the edge of the nucleus in the cytoplasm. It is a tegument phosphoprotein reported to modulate the activity of UL48 (anti-TNF) protein.
Pfam PF02578: Multi-copper polyphenol oxidoreductase laccase (family)
Laccases are multi-copper oxidoreductases able to oxidise a wide variety of phenolic and non-phenolic compounds and are widely distributed among both prokaryotes and eukaryotes. There are two main active catalytic sites with conserved histidines that are capable of binding four copper atoms.
Wikipedia: In molecular biology, multicopper oxidases are enzymes which oxidise their substrate by accepting electrons at a mononuclear copper centre and transferring them to a trinuclear copper centre; dioxygen binds to the trinuclear centre and, following the transfer of four electrons, is reduced to two molecules of water. There are three spectroscopically different copper centres found in multicopper oxidases: type 1, type 2 and type 3. Multicopper oxidases consist of 2, 3 or 6 of these homologous domains, which also share homology with the cupredoxins azurin and plastocyanin. Structurally, these domains consist of a cupredoxin-like fold, a beta-sandwich consisting of 7 strands in 2 beta-sheets, arranged in a Greek-key beta-barrel.
Pfam PF04608: Phosphatidylglycerophosphatase A (family)
This family represents a family of bacterial phosphatidylglycerophosphatases ([ec:3.1.3.27]), known as PgpA. It appears that bacteria possess several phosphatidylglycerophosphatases, and thus, PgpA is not essential in Escherichia coli.
Pfam PF05300: MICOS complex subunit MIC19/MIC25 (family)
MIC19 (also known as ChChd3) and MIC25 (also known as ChChd6) are components of the MICOS complex, a large protein complex of the mitochondrial inner membrane that plays crucial roles in the maintenance of crista junctions, inner membrane architecture, and formation of contact sites to the outer membrane. MIC19 plays an important role in the maintenance of the MICOS complex stability and the mitochondrial cristae morphology.
Pfam PF12392: Collagenase (family)
This domain family is found in bacteria, archaea and eukaryotes, and is approximately 120 amino acids in length. The family is found in association with [pfam:PF01136].
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 PF04390: Lipopolysaccharide-assembly (family)
LptE (formerly known as RplB) is involved in lipopolysaccharide-assembly on the outer membrane of Gram-negative organisms. The lipopolysaccharide component of the outer bacterial membrane is transported from its source of origin to the outer membrane by a set of proteins constituting a transport machinery that is made up of LptA, LptB, LptC, LptD, LptE. LptD appears to be anchored in the outer membrane, and LptE forms a complex with it. This part of the machinery complex is involved in the assembly of lipopolysaccharide in the outer leaflet of the outer membrane.
Wikipedia: The bacterial outer membrane is found in gram-negative bacteria. Gram-negative bacteria form two lipid bilayers in their cell envelopes - an inner membrane (IM) that encapsulates the cytoplasm, and an outer membrane (OM) that encapsulates the periplasm.
Pfam PF18673: interleukin receptor mimic protein A (domain)
The E. coli interleukin [IL] receptor mimic protein A (IrmA), is a small (13 kDa) Uropathogenic E. coli (UPEC) protein that was originally identified in a large reverse genetic screen as a broadly protective vaccine antigen. It has a fibronectin III (FNIII)-like fold that forms a domain-swapped dimer with structural mimicry to the binding domain of the IL-2 receptor (IL-2R), the IL-4 receptor (IL-4R) and, to a lesser extent, the IL-10 receptor (IL-10R). IrmA binds to all three cytokines, with the greatest affinity observed for IL-4. It is suggested that IrmA may contribute to manipulation of the innate immune response during UPEC infection.
Pfam PF19788: Family of unknown function (DUF6272) (family)
This family of proteins found in bacteria is functionally uncharacterised. Proteins in this family are approximately 180 amino acids in length. There are two conserved sequence motifs, ExxQN and GAGLG.
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 PF11459: Transcriptional regulator, AbiEi antitoxin, Type IV TA system (family)
AbiEi_3 is the cognate antitoxin of the type IV toxin-antitoxin 'innate immunity' bacterial abortive infection (Abi) system that protects bacteria from the spread of a phage infection. The Abi system is activated upon infection with phage to abort the cell thus preventing the spread of phage through viral replication. There are some 20 or more Abis, and they are predominantly plasmid-encoded lactococcal systems. TA, toxin-antitoxin, systems on plasmids function by killing cells that lose the plasmid upon division. AbiE phage resistance systems function as novel Type IV TAs and are widespread in bacteria and archaea. The cognate antitoxin is [pfam:PF13338].