SII-SWORD/CoKE huggingface dataset:
Pfam PF01523: PmbA/TldA metallopeptidase domain 1 (domain)
This entry represents a group of metalloproteases. The tertiary structure of the Escherichia coli TdlD/TdlE complex has been solved, and shows that the TdlD subunit is the active peptidase, binding a single zinc ion at an HEXXXH motif in which the glutamic acid is a substrate-binding residue and the two histidines are zinc ligands. The third zinc ligand is a cysteine, C-terminal to the HEXXXH motif. The TldE (also known as PmbA) by itself has no catalytic activity, does not bind zinc, and does not carry the HEXXXH motif. TldD and TldE were originally identified as regulators of DNA gyrase. Later, they are shown to be metalloproteases involved in CcdA degradation.
Pfam PF17809: UPA domain (domain)
The UPA domain is conserved in UNC5, PIDD, and Ankyrins. It has a beta sandwich structure.
Pfam PF02576: RimP N-terminal domain (domain)
This entry represents the N-terminal domain of the ribosome maturation factor RimP (also known as yhbC). RimP facilitates the maturation of the 30S ribosomal subunit. The N-terminal domain contains two alpha-helices and a three-stranded beta-sheet. It is suggested that the N-terminal domain of SP14.3 (RimP orthologue) could function as a protein module that binds to other proteins, especially those that contain highly positively charged surfaces..
Pfam PF03406: Phage tail fibre repeat (repeat)
This repeat is found in the tail fibres of phage. For example protein K [swissprot:Q37842]. The repeats are about 40 residues long.
Pfam PF09134: Invasin, domain 3 (domain)
Members of this family adopt a structure consisting of an immunoglobulin-like beta-sandwich, with seven strands in two beta-sheets, arranged in a Greek-key topology. It forms part of the extracellular region of the protein, which can be expressed as a soluble protein (Inv497) that binds integrins and promotes subsequent uptake by cells when attached to bacteria.
Pfam PF01820: D-ala D-ala ligase N-terminus (family)
This family represents the N-terminal region of the D-alanine--D-alanine ligase enzyme [ec:6.3.2.4] which is thought to be involved in substrate binding. D-Alanine is one of the central molecules of the cross-linking step of peptidoglycan assembly. There are three enzymes involved in the D-alanine branch of peptidoglycan biosynthesis: the pyridoxal phosphate-dependent D-alanine racemase (Alr), the ATP-dependent D-alanine:D-alanine ligase (Ddl), and the ATP-dependent D-alanine:D-alanine-adding enzyme (MurF). This domain is structurally related to the PreATP-grasp domain.
Pfam PF03669: PAT complex subunit Asterix (family)
This family represents Asterix proteins which are a component of the PAT complex, an endoplasmic reticulum (ER)-resident membrane multiprotein complex that facilitates multi-pass membrane proteins insertion into membranes. The PAT complex acts as an intramembrane chaperone by directly interacting with nascent transmembrane domains (TMDs), releasing its substrates upon correct folding, and is needed for optimal biogenesis of multi-pass membrane proteins. Asterix is the substrate-interacting subunit of the PAT complex and associates with the first TMD of the nascent chain. The PAT complex favors the binding to TMDs with exposed hydrophilic amino acids within the lipid bilayer and provides a membrane-embedded partially hydrophilic environment in which TMD1 binds.
Pfam PF05452: Clavanin (family)
This family consists of clavanin proteins from the haemocytes of the invertebrate Styela clava, a solitary tunicate. The family is made up of four alpha-helical antimicrobial peptides, clavanins A, B, C and D. The tunicate peptides resemble magainins in size, primary sequence and antibacterial activity. Synthetic clavanin A displays comparable antimicrobial activity to magainins and cecropins. The presence of alpha-helical antimicrobial peptides in the haemocytes of a urochordate suggests that such peptides are primeval effectors of innate immunity in the vertebrate lineage.
Pfam PF19090: Family of unknown function (DUF5778) (family)
Family of unknown function predominantly found in Halobacteria.
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 PF09366: Protein of unknown function (DUF1997) (family)
This family of proteins are functionally uncharacterised.
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 PF05101: Type IV secretory pathway, VirB3-like protein (family)
This family includes the Type IV secretory pathway VirB3 protein, that is found associated with bacterial inner and outer membranes. The family also includes the conjugal transfer protein TrbD family that contains a nucleotide binding motif and may provide energy for the export of DNA or the export of other Trb proteins.
Pfam PF08844: Domain of unknown function (DUF1815) (domain)
This presumed domain is about 100 amino acids in length and is functionally uncharacterised.
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 PF13110: Protein of unknown function (DUF3966) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 86 amino acids in length.
Pfam PF18758: Kyakuja-Dileera-Zisupton transposase (family)
A transposase family with an RNaseH catalytic domain, often fused to DNA binding domains such as SAP or cysteine cluster domains. KDZ transposases are widely present in fungi, metazoa, chlorophytes and haotpohytes. Fungal versions are often associated with a TET/JBP family of dioxygenases.
Pfam PF11328: Protein of unknown function (DUF3130 (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 PF18305: 3' to 5' exonuclease C-terminal domain (domain)
This domain is found just after the C-terminal region of the HRDC domain ([pfam:PF00570]) in 3'-5' exonuclease proteins ([pfam:PF01612]). The domain is carried by species such as Streptomyces griseoaurantiacus and Streptomyces albulus.
Pfam PF09376: NurA domain (domain)
This family includes NurA a nuclease exhibiting both single-stranded endonuclease activity and 5'-3' exonuclease activity on single-stranded and double-stranded DNA from the hyperthermophilic archaeon Sulfolobus acidocaldarius.
Pfam PF04441: Poxvirus early transcription factor (VETF), large subunit (family)
The poxvirus early transcription factor (VETF), in addition to the viral RNA polymerase, is required for efficient transcription of early genes in vitro. VETF is a heterodimeric protein that binds  specifically to early gene promoters. The heterodimer is comprised of an 82 kDa (this family) subunit and a 70 kDa subunit.
Pfam PF21313: Transcriptional regulator EthR, C-terminal domain (domain)
HTH-type transcriptional regulator EthR is involved in the repression of the monooxygenase EthA which is responsible of the formation of the active metabolite of ethionamide (ETH). It is responsible for the low sensitivity of the human pathogen Mycobacterium tuberculosis to ethionamide. It consists of a DNA-binding HTH domain at the N-terminal and a C-terminal helical domain that binds its ligand.
Pfam PF03116: NQR2, RnfD, RnfE family (family)
This family of bacterial proteins includes a sodium-translocating  NADH-ubiquinone oxidoreductase (i.e. a respiration linked sodium  pump). In Vibrio cholerae, it negatively regulates the expression of virulence factors through inhibiting  (by an unknown mechanism) the transcription of the transcriptional activator ToxT. The family also includes proteins involved in nitrogen fixation, RnfD and RnfE. The similarity of these proteins to NADH-ubiquinone oxidoreductases was previously noted.
Wikipedia: NADH:ubiquinone reductase (Na+-transporting) (EC 1.6.5.8 is an enzyme with systematic name NADH:ubiquinone oxidoreductase (Na+-translocating). In bacteria, three different types of respiratory NADH:quinone oxidoreductases (NQr) have been described: the electrogenic complex I, also called NDH I in bacteria, the non-electrogenic NADH:quinone oxidoreductases (NDH II), and the Na+-translocating NADH:quinone oxidoreductases Na+-NQr. The common function of these transmembrane enzymes in respiration is to oxidize NADH using ubiquinone (Q) as electron acceptor. The net reaction thus yields ubiquinol (QH2), the reducing substrate of enzyme complexes further along the respiratory chain, and NAD+, which is used as oxidizing agent in numerous cellular processes.NADH + H+ + ubiquinone + n Na+in → NAD+ + ubiquinol + n Na+out
Pfam PF21129: Glycosyltransferase TibC, N-terminal domain (domain)
This domain is found at the N-terminal end of Glycosyltransferase TibC from Escherichia coli and similar bacterial. TibC is an autotransporter adhesin heptosyltransferase (AAH) homologue that catalyses the heptosylation of the autotransporters AIDA-I/TibA and confers AIDA-I-mediated bacterial adhesion to host cells. This domain adopts a beta-barrel fold with two four-stranded sheets that pack against each other.
Pfam PF23288: Transcription elongation factor SPT5, sixth KOW domain (domain)
This entry includes Transcription elongation factor SPT5, a component of the elongation factor DRB-sensitivity inducing factor (DSIF) that plays multiple roles during transcription. SPT5 is a multidomain protein consisting of an N-terminal NusG domain ([pfam:PF03439]), tandem of KOW domains and and a mobile C-terminal-repeat region. The KOW domains differ in number between yeast, which has five, and animals, which have seven. This entry represents the sixth KOW domain of SPT5 from animals. The KOW domains of these proteins play critical roles in recruitment of multiple other eukaryotic transcription elongation and RNA biogenesis factors, and they are also involved in the binding of the eukaryotic SPT5 proteins to RNA polymerases.
Pfam PF16964: Putative tight adherence pilin protein F (family)
TadF is a family of proteins from the tad locus that is part of the type IV bacterial secretory system.
Pfam PF03923: Uncharacterized lipoprotein (family)
The function of this presumed lipoprotein is unknown. The family includes E. coli YajG [swissprot:P36671].
Pfam PF02441: Flavoprotein (domain)
This domain is found in diverse flavoprotein enzymes, including covering the whole length of the sequence of epidermin biosynthesis protein from Staphylococcus epidermidis (EpiD, [swissprot:P30197]), which has been shown to bind FMN. This enzyme catalyses the removal of two reducing equivalents from the cysteine residue of the C-terminal meso-lanthionine of epidermin to form a --C==C-- double bond. This family also includes the B chain of dipicolinate synthase a small polar molecule that accumulates to high concentrations in bacterial endospores, and is thought to play a role in spore heat resistance, or the maintenance of heat resistance. dipicolinate synthase catalyses the formation of dipicolinic acid from dihydroxydipicolinic acid. This family also includes phenyl-acrylic acid decarboxylase [swissprot:P33751] ([ec:4.1.1.-]).
Wikipedia: Flavoproteins are proteins that contain a nucleic acid derivative of riboflavin. These proteins are involved in a wide array of biological processes, including removal of radicals contributing to oxidative stress, photosynthesis, and DNA repair. The flavoproteins are some of the most-studied families of enzymes.
Pfam PF03930: Recombinase Flp protein N-terminus (domain)
This entry describes the N-terminal domain of recombinase Flp protein from fungi. Flp proteins catalyse recombination between large inverted repetitions of the plasmid.
Pfam PF11104: Type IV pilus assembly protein PilM; (family)
The type IV pilus assembly protein PilM is required for competency and pilus biogenesis. It binds to PilN and ATP.
Pfam PF24000: Family of unknown function (DUF7316) (family)
This entry represents a small family of phage proteins. These proteins form a confident dimer according to structure prediction.  The dimer adopts a novel fold composed of a long four stranded beta sheet with two alpha helical elements packed at each end of the twisted sheet. There is quite a bit of structural variability across the family with a variety of alternative elaborations.
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 PF24866: Domain of unknown function (DUF7732) (domain)
This domain is found in uncharacterised proteins mainly from fungi. It contains a set of conserved cysteine residues which are predicted to form a disulfide bond.
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 PF06632: XRCC4 N-terminal domain (domain)
This family consists of several eukaryotic DNA double-strand break repair and V(D)J recombination protein XRCC4 sequences. In the non-homologous end joining pathway of DNA double-strand break repair, the ligation step is catalysed by a complex of XRCC4 and DNA ligase IV. It is thought that XRCC4 and ligase IV are essential for alignment-based gap filling, as well as for final ligation of the breaks. This entry represents the N-terminal beta sandwich domain.
Wikipedia: DNA repair protein XRCC4 (hXRCC4) also known as X-ray repair cross-complementing protein 4 is a protein that in humans is encoded by the XRCC4 gene. XRCC4 is also expressed in many other animals, fungi and plants. hXRCC4 is one of several core proteins involved in the non-homologous end joining (NHEJ) pathway to repair DNA double strand breaks (DSBs).
Pfam PF19233: Family of unknown function (DUF5886) (family)
This is a family of uncharacterised proteins of unknown function predominantly found in Mimiviridae.
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 PF04505: Interferon-induced transmembrane protein (family)
This family includes the human leukocyte antigen CD225, which is an interferon inducible transmembrane protein, and is associated with interferon induced cell growth suppression.
Wikipedia: In molecular biology, the protein family Dispanin is another name for Interferon-induced transmembrane protein (IFITM). This refers to a family of protein domains which have a specific formation, or in other words, topology containing two alpha helices in within the cell membrane which are called two transmembrane proteins. This includes proteins such as CD225. The function of this protein family is to inhibit cell invasion of many harmful, pathogenic viruses, such as HIV. Henceforth, they are being intensively studied in the hope of drug discovery. They mediate the immune response by interferons.
Pfam PF22640: MannoseP isomerase/GMP-like beta-helix domain (domain)
This entry represents a left-handed beta-helix domain found at the C-terminal of Guanosine-diphospho-d-mannose Pyrophosphorylase (GMP) from Thermotoga maritima and as a linker domain in mannose-1-phosphate guanylyltransferases, alginate biosynthesis protein AlgA and xanthan biosynthesis protein XanB, among others, located between the Nucleotidyl transferase domain at the N-terminal ([pfam:PF00483]) and the C-terminal isomerase cupin domain ([pfam:PF01050]). This domain is composed of an alpha-helix followed by a short left-handed beta-helix. GMP forms a dimer in which two molecules associate through a tail-to-tail arrangement of this domain..
Pfam PF05248: Adenovirus E3A (family)
Adenoviruses have evolved multiple mechanisms to evade the host immune response. Several of the immunomodulatory adenoviral proteins are encoded in early transcription unit 3 (E3). The E3A/19K protein interferes with antigen presentation and T cell recognition .
Pfam PF01456: Mucin-like glycoprotein (family)
This family of trypanosomal proteins resemble vertebrate mucins. The protein consists of three regions. The N and C terminii are conserved between all members of the family, whereas the central region is not well conserved and contains a large number of threonine residues which can be glycosylated. Indirect evidence suggested that these genes might encode the core protein of parasite mucins, glycoproteins that were proposed to be involved in the interaction with, and invasion of, mammalian host cells. This family contains an N-terminal signal peptide.
Pfam PF22210: Large MCP VP17 central beta-barrel (domain)
This entry represents the central beta-barrel of VP17, the large major capsid protein of of bacteriophage P23-77.
Pfam PF21928: XLF protein coiled-coil region (coiled_coil)
This entry represents the coiled-coil region of the XLF protein is involved in non-homologous end joining.
Pfam PF01694: Rhomboid family (family)
This family contains integral membrane proteins that are related to Drosophila rhomboid protein [swissprot:P20350]. Members of this family are found in bacteria and eukaryotes. Rhomboid promotes the cleavage of the membrane-anchored TGF-alpha-like growth factor Spitz, allowing it to activate the Drosophila EGF receptor.  Analysis has shown that Rhomboid-1 is an intramembrane serine protease ([ec:3.4.21.105]). Parasite-encoded rhomboid enzymes are also important for invasion of host cells by Toxoplasma and the malaria parasite.
Wikipedia: The rhomboid proteases are a family of enzymes that exist in almost all species. They are proteases: they cut the polypeptide chain of other proteins. This proteolytic cleavage is irreversible in cells, and an important type of cellular regulation. Although proteases are one of the earliest and best studied class of enzyme, rhomboids belong to a much more recently discovered type: the intramembrane proteases. What is unique about intramembrane proteases is that their active sites are buried in the lipid bilayer of cell membranes, and they cleave other transmembrane proteins within their transmembrane domains. About 30% of all proteins have transmembrane domains, and their regulated processing often has major biological consequences. Accordingly, rhomboids regulate many important cellular processes, and may be involved in a wide range of human diseases.
Pfam PF14972: Mitochondrial morphogenesis regulator (family)
This family of proteins regulate mitochondrial morphogenesis via a mechanism which is independent of mitofusins and dynamin-related protein 1.
Pfam PF21240: Nup98, Gle2-binding sequence (domain)
This is the Gle2-binding sequence (GLEBS) of Nup98, which forms a hairpin that binds with its C-terminal arm to an essentially invariant hydrophobic surface that extends over the top face of the Rae1 beta-propeller. This interaction is required for Rae1 binding. Rae1-Nup98(GLEBS) form a complex with single-stranded RNA-binding capability that directly binds to the mRNP in several steps of the mRNA export pathway.
Pfam PF04909: Amidohydrolase (domain)
These proteins are amidohydrolases that are related to [pfam:PF01979].
Pfam PF17573: GA-like domain (domain)
This domain is found in bacterial cell surface proteins. It is related to the GA domain that forms a three helix bundle.
Pfam PF16431: Domain of unknown function (DUF5028) (family)
This family consists of several uncharacterized proteins around 200 in length and is mainly found in Eubacterium and Clostridium. The function of this family is unknown.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF10583: Involucrin of squamous epithelia N-terminus (domain)
This is the N-terminal three beta strands of involucrin, a protein present in keratinocytes of epidermis and other stratified squamous epithelia. Involucrin first appears in the cell cytosol, but ultimately becomes cross-linked to membrane proteins by transglutaminase thus helping in the formation of an insoluble envelope beneath the plasma membrane. Apigenin is a plant-derived flavanoid that has significant promise as a skin cancer chemopreventive agent. It has been found that apigenin regulates normal human keratinocyte differentiation by suppressing it and this is associated with reduced cell proliferation without apoptosis. The downstream part of the protein is represented by the family Involucrin, [pfam:PF00904].
Wikipedia: Involucrin is a protein component of human skin and in humans is encoded by the IVL gene. In binding the protein loricrin, involucrin contributes to the formation of a cell envelope that protects corneocytes in the skin.
Pfam PF16616: Unstructured region on Polyhomeotic-like protein 1 and 2 (disordered)
PHC2_SAM_assoc is a natively unstructured region on Polyhomeotic-like proteins 1 and 2, that lies immediately upstream of the SAM domain, [pfam:PF00536].  The function is not known.
Pfam PF24629: Signal transducer and activator of transcription b N-terminal (domain)
This entry represents the N-terminal domain of Signal transducer and activator of transcription b (STATB) from C.elegans and simialr proteins from nematodes. STATB can have a dual function, signal transduction and activation of transcription. It is required, together with with transcription factor elt-3, for up-regulation of the vacuolar H+-ATPase and acceleration of lysosome maturation at molt. It plays a role in the innate immune response to molting and injury of the adult epidermis where it positively regulates the expression of epidermal antimicrobial peptides.