SII-SWORD/CoKE huggingface dataset:
Pfam PF03137: Organic Anion Transporter Polypeptide (OATP) family (family)
This family consists of several eukaryotic Organic-Anion-Transporting Polypeptides (OATPs). Several have been identified mostly in human and rat. Different OATPs vary in tissue distribution and substrate specificity. Since the numbering of different OATPs in particular species was based originally on the order of discovery, similarly numbered OATPs in humans and rats did not necessarily correspond in function, tissue distribution and substrate specificity (in spite of the name, some OATPs also transport organic cations and neutral molecules). Thus, Tamai et al. initiated the current scheme of using digits for rat OATPs and letters for human ones. Prostaglandin transporter (PGT) proteins (e.g. [swissprot:Q92959]) are also considered to be OATP family members. In addition, the methotrexate transporter OATK ([swissprot:P70502]) is closely related to OATPs. This family also includes several predicted proteins from Caenorhabditis elegans and Drosophila melanogaster. This similarity was not previously noted.  Note: Members of this family are described (in the Swiss-Prot database) as belonging to the SLC21 family of transporters.
Wikipedia: Members of the Organic Anion Transporter (OAT) Family are membrane transport proteins or 'transporters' that mediate the transport of mainly organic anions across the cell membrane. Therefore, OATPs are present in the lipid bilayer of the cell membrane, acting as the cell's gatekeepers. OATPs belong to the Solute Carrier Family (SLC) and the major facilitator superfamily.
Pfam PF07120: Protein of unknown function (DUF1376) (family)
This family consists of several hypothetical bacterial proteins of around 95 residues in length. 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 PF03087: Protein BPS1 (family)
This family includes protein BPS1 (Protein BYPASS 1) from Arabidopsis, which is required for normal root and shoot development. It prevents constitutive production of a root mobile carotenoid-derived signalling compound that is capable of arresting shoot and leaf development.
Pfam PF14503: YhfZ C-terminal domain (family)
This domain is often found in association with the helix-turn-helix domain HTH_41 ([pfam:PF14502]). It includes YhfZ proteins from Escherichia coli and Shigella flexneri.
Pfam PF02343: TRA-1 regulated protein R03H10.4 (family)
This family of proteins represents the protein product of the gene R03H10.4 which is located near a sequence that matches the TRA-1 binding consensus. TRA-1 is a transcription factor which controls sexual differentiation in C.elegans. R03H10.4 shows male-enriched reporter gene expression and acts as a direct target of TRA-1 regulation.
Pfam PF07332: Putative Actinobacterial Holin-X, holin superfamily III (domain)
Phage_holin_3_6 is a family of small hydrophobic proteins with two or three transmembrane domains of the Hol-X family. Holin proteins are produced by double-stranded DNA bacteriophages that use an endolysin-holin strategy to achieve lysis of their hosts. The endolysins are peptidoglycan-degrading enzymes that are usually accumulated in the cytosol until access to the cell wall substrate is provided by the holin membrane lesion.
Pfam PF17804: Tail specific protease N-terminal domain (domain)
The N-terminal domain of tail specific proteases has a novel fold composed of 10 alpha helices.
Pfam PF10882: Bacterial PH domain (domain)
This family of proteins with unknown function appear to be related to bacterial PH domains. This family was formerly known as DUF2679.
Wikipedia: Pleckstrin homology domain or (PHIP) is a protein domain of approximately 120 amino acids that occurs in a wide range of proteins involved in intracellular signaling or as constituents of the cytoskeleton.
Pfam PF03747: ADP-ribosylglycohydrolase (family)
This family includes enzymes that ADP-ribosylations, for example ADP-ribosylarginine hydrolase [ec:3.2.2.19] cleaves ADP-ribose-L-arginine. The family also includes dinitrogenase reductase activating glycohydrolase. Most surprisingly the family also includes jellyfish crystallins, these proteins appear to have lost the presumed active site residues.
Wikipedia: In molecular biology, the (ADP-ribosyl)hydrolase (ARH) family contains enzymes which catalyses the hydrolysis of ADP-ribosyl modifications from proteins, nucleic acids and small molecules.
Pfam PF17619: Secreted clade V proteins (family)
Family members are found in strongylid parasites (A. ceylanicum, N. americanus, H. contortus and Heterorhabditis bacteriophora) and in related non-parasitic clade V species (C. elegans, Caenorhabditis briggsae and P. pacificus), hence the name secreted clade V proteins (SCVPs). In A. ceylanicum, the encoded 150 residue proteins are predicted to be classically secreted.
Pfam PF15309: ALMS motif (family)
This domain is found at the C-terminus of centrosome-associated protein ALMS1, centrosomal protein of 295 kDa (CEP295, also known as KIAA1731) and (E2-independent) E3 ubiquitin-conjugating enzyme FATS (also known as C10orf90). These proteins play a role in centrosomal functions. ALMS1 is implicated in ciliary function, cell cycle control, and intracellular transport. It interacts with alpha-actinin and components of the endosomal recycling pathway. CEP295 is a centriole-enriched microtubule-binding protein involved in centriole biogenesis, essential for the generation of the distal portion of newborn centrioles and recruitment of centriolar proteins, such as POC1B, POC5 and CEP135.
Pfam PF23117: DpnD N-terminal domain (domain)
This entry represents a presumed helical domain found at the N-terminal of DpnD protein from Streptococcus pneumoniae and similar sequences from bacteria. These proteins are functionally uncharacterised.
Pfam PF15956: Domain of unknown function (DUF4760) (domain)
This entry represents an uncharacterised alpha helical domain found in bacteria, archaea and viruses.  Proteins in this family are typically between 147 and 190 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 PF01266: FAD dependent oxidoreductase (domain)
This family includes various FAD dependent oxidoreductases: Glycerol-3-phosphate dehydrogenase [ec:1.1.99.5], Sarcosine oxidase beta subunit [ec:1.5.3.1], D-alanine oxidase [ec:1.4.99.1], D-aspartate oxidase [ec:1.4.3.1].
Wikipedia: In molecular biology, the FAD dependent oxidoreductase family of proteins is a family of FAD dependent oxidoreductases. Members of this family include Glycerol-3-phosphate dehydrogenase EC 1.1.99.5, Sarcosine oxidase beta subunit EC 1.5.3.1, D-amino-acid dehydrogenase EC 1.4.99.1, D-aspartate oxidase EC 1.4.3.1.
Pfam PF18407: GCN5-related N-acetyltransferase like domain (domain)
This is a domain with a GCN5-related N-acetyltransferase (GNAT) fold which can be found in Rv1692 phophatases. Crystal structure of Rv1692 indicates that this C-temrinal extension, which is absent in other characterized HADSF members, resembles a small GCN5-related N-acetyltransferase (GNAT) fold. Furthermore, it is fused to the HADSF catalytic domain [pfam:PF13242] . Functional studies indicate that this GNAT region is not likely to be involved in acetyl group transfer using AcCoA and SucCoA, it could nonetheless be a regulatory domain. Furthermore, it is suggested that this GNAT domain is required for the solubility of the HADSF fold of Rv1692 and is potentially needed for the structural integrity of this enzyme.
Pfam PF22641: TiaS TCKD domain (domain)
This domain is found in tRNA(Ile2) 2-agmatinylcytidine synthetase TiaS and related proteins. TiaS is an ATP-dependent agmatine transferase that catalyses the formation of 2-agmatinylcytidine (agm2C) at the wobble position (C34) of tRNA(Ile2). This domain is found at the N-terminal of TiaS and it is responsible for ATP binding.
Pfam PF24832: Domain of unknown function (DUF7716) (domain)
This domain is found in uncharacterised bacterial proteins either standalone or in combination with other domains. It is predicted to adopt a globular structure consisting of an antiparallel three-stranded beta-sheet and alpha-helices packed on one side of it.
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 PF03029: Conserved hypothetical ATP binding protein (domain)
Members of this family are found in a range of archaea and eukaryotes and have hypothesised ATP binding activity.
Pfam PF05839: Apc13p protein (family)
The anaphase-promoting complex (APC) is a conserved multi-subunit ubiquitin ligase required for the degradation of key cell cycle regulators Members of this family are components of the anaphase-promoting complex homologous to Apc13p.
Pfam PF16745: RsgA N-terminal domain (domain)
This domain is found at the N-terminus of RsgA domains. It has an OB fold.
Pfam PF08952: Domain of unknown function (DUF1866) (domain)
This domain, found in Synaptojanin, 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 PF22138: Archaeal argonaute protein N-terminal domain (domain)
Argonaute (Ago) proteins are found in all three domains of life. They share a common molecular architecture, with the C-terminal lobe consisting of the middle (Mid) and PIWI (P element wimpy testis) domains and the N-terminal lobe containing the N-terminal and PIWI-Argonaute-Zwille (PAZ) domains. Archaeal argonaute proteins are guided by 5'-phosphorylated DNA strands and exclusively process cognate DNA targets. This entry represents the N-terminal domain of the archaeal argonaute protein found in M.jannaschii. This domain consists of a four stranded antiparallel beta-sheet and an alpha-helix.
Pfam PF12127: Flotillin-like protein FloA (family)
This entry represents flotillin-like protein FloA from bacteria. Bacterial flotillin-like proteins are found in membrane microdomains that may be equivalent to eukaryotic membrane rafts. Similarly to eukaryotic flotillin proteins, flotillins in bacteria play an essential role in organising and maintaining the correct architecture of the functional membrane microdomains. Bacillus subtilis has two flotillin paralogs, FloT and FloA. The absence of one of the flotillins has only minor effects, but the absence of both proteins has very severe effects: loss of proper cell shape, a defect in cell division.
Pfam PF23389: WDR19 first beta-propeller (repeat)
This entry represents the first beta-propeller of WRD19 (also known as IFT144) from animals and the orthologue from C.elegans DYF2. WDR19 is a core component of the IFT complex A (IFT-A, together with IFT140 and IFT122), a complex required for retrograde ciliary transport and entry into cilia of G protein-coupled receptors (GPCRs), being involved in cilia function and/or assembly. IFT-A polymerises interacts with IFT-B, and uses an array of beta-propeller and TPR domains to create 'carriages' of the IFT train that engage TULP adaptor proteins.
Pfam PF22851: CATSPERG Ig-like domain (domain)
The CATSPER (cation channel of sperm) complex is a tetrameric complex consisting of CATSPER1, CATSPER2, CATSPER3 and CATSPER4, it functions as an alkalinisation-activated calcium channel. This complex is involved in sperm cell hyperactivation, a process needed for sperm motility, which is essential late in the preparation of sperm for fertilisation. This complex requires four auxiliary subunits (beta, gamma, delta and epsilon), which play a role in channel assembly. These are multidomain proteins which share a similar domain organisation. This entry represents the Ig-like domain of CATSPERG (gamma subunit).
Pfam PF16685: zinc RING finger of MSL2 (domain)
zf-RING_10 is an N-terminal domain on E3 ubiquitin-protein ligase msl-2 proteins. The domain binds MSL1 and exhibits ubiquitin E3 ligase activity towards H2B K34, the histone proteins.
Pfam PF00673: ribosomal L5P family C-terminus (domain)
This region is found associated with [pfam:PF00281].
Pfam PF08651: DASH complex subunit Duo1 (family)
The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis. In Saccharomyces cerevisiae DASH forms both rings and spiral structures on microtubules in vitro.
Pfam PF07187: Protein of unknown function (DUF1405) (family)
This family consists of several bacterial and related archaeal protein of around 180 residues in length. 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 PF15611: EH_Signature domain (domain)
This domain with a strongly conserved glutamate at the N-terminus  and a histidine at the C-terminus, is found in a SWI2/SNF2 four gene operon. Its strict-neighbourhood association with         SWI2/SNF2 ATPase strongly suggests a function in conjunction with it. The other genes in the operon are a OmpA protein and a TM protein. This has a DNA related function along with the TerY-P triad.
Pfam PF02657: Fe-S metabolism associated domain (family)
This family consists of the SufE-related proteins. These have been implicated in Fe-S metabolism and export).
Pfam PF16883: Domain of unknown function (DUF5080) (family)
This protein is believed to be involved in the type VII secretion system.
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 PF13216: Protein of unknown function (DUF4024) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 40 amino acids in length. There is a conserved RDE 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 PF03060: Nitronate monooxygenase (domain)
Nitronate monooxygenase (NMO), formerly referred to as 2-nitropropane dioxygenase (NPD) ([ec:1.13.11.32]), is an FMN-dependent enzyme that uses molecular oxygen to oxidize (anionic) alkyl nitronates and, in the case of the enzyme from Neurospora crassa, (neutral) nitroalkanes to the corresponding carbonyl compounds and nitrite. Previously classified as 2-nitropropane dioxygenase, but it is now recognized that this was the result of the slow ionization of nitroalkanes to their nitronate (anionic) forms. The enzymes from the fungus Neurospora crassa and the yeast Williopsis saturnus var. mrakii (formerly classified as Hansenula mrakii) contain non-covalently bound FMN as the cofactor. Active towards linear alkyl nitronates of lengths between 2 and 6 carbon atoms and, with lower activity, towards propyl-2-nitronate. The enzyme from N. crassa can also utilize neutral nitroalkanes, but with lower activity. One atom of oxygen is incorporated into the carbonyl group of the aldehyde product. The reaction appears to involve the formation of an enzyme-bound nitronate radical and an a-peroxynitroethane species, which then decomposes, either in the active site of the enzyme or after release, to acetaldehyde and nitrite.
Pfam PF18008: Replication initiator protein A C-terminal domain (domain)
This is the C-terminal domain (CTD) that can be found in the conserved replication initiator, RepA,essential for staphylococcal propagation.  RepA CTD shared the strongest structural homology to the Enterococcus faecalis DnaD CTD, yet perform distinct functions. RepA CTD shows strong sequence homology between RepA_N plasmids in genus-specific clusters, suggesting that it may perform host-specific functions necessary for replication. The RepA CTD interacts with the host DnaG primase, which binds the replicative helicase. Structural data indicate that the RepA CTD exists as a monomeric entity, flexibly tethered to the DNA-bound NTD.
Pfam PF11802: Centromere-associated protein K (family)
CENP-K is one of seven new CENP-A-nucleosome distal (CAD) centromere components (the others being CENP-L, CENP-O, CENP-P, CENP-Q, CENP-R and CENP-S) that are identified as assembling on the CENP-A nucleosome associated complex, NAC. The CENP-A NAC is essential, as disruption of the complex causes errors of chromosome alignment and segregation that preclude cell survival despite continued centromere-derived mitotic checkpoint signalling. CENP-K is centromere-associated through its interaction with one or more components of the CENP-A NAC.
Pfam PF11289: Betacoronavirus viroporin (family)
This entry represents protein 3a encoded by Orf3/3a, also known as X1, which forms homotetrameric potassium, sodium or calcium sensitive ion channels (viroporin) that causes ER-stress in host cells and may modulate virus release. This is a pro-apoptosis-inducing protein that localises to the endoplasmic reticulum (ER)-Golgi compartment. SARS-CoV causes apoptosis of infected cells through NLRP3 inflammasome activation. Protein 3a also promotes the ubiquitination of apoptosis-associated speck-like protein containing a caspase recruitment domain (ASC) mediated by its interaction with TNF receptor-associated factor 3 (TRAF3). This protein induces NF-kappa B activation and upregulates fibrinogen secretion with high cytokine production. Through the activation of the PERK pathway of unfolded protein response (UPR), this protein causes phosphorylation of eIF2-alpha leading to reduced translation of cellular proteins and as the activation of pro-apoptotic downstream  effectors (i.e ATF4, CHOP).
Pfam PF13393: Histidyl-tRNA synthetase (domain)
This is a family of class II aminoacyl-tRNA synthetase-like and ATP phosphoribosyltransferase regulatory subunits.
Pfam PF14300: DMP19-like protein (domain)
This family of proteins contains Neisseria conserved protein DMP19 that has been demonstrated to act as a DNA mimic. This family was formerly known as DUF4375.
Pfam PF02190: ATP-dependent protease La (LON) substrate-binding domain (family)
This domain has been shown to be part of the PUA superfamily. This domain represents a general protein and polypeptide interaction domain for the ATP-dependent serine peptidase, LON, Peptidase_S16, [pfam:PF05362]. ATP-dependent Lon proteases are conserved in all living organisms and catalyse rapid turnover of short-lived regulatory proteins and many damaged or denatured proteins.
Wikipedia: In molecular biology, the Lon protease family is a family of enzymes that break peptide bonds in proteins resulting in smaller peptides or amino acids. They are found in archaea, bacteria and eukaryotes. Lon proteases are ATP-dependent serine peptidases belonging to the MEROPS peptidase family S16. In the eukaryotes the majority of the Lon proteases are located in the mitochondrial matrix. In yeast, the Lon protease PIM1 is located in the mitochondrial matrix. It is required for mitochondrial function, it is constitutively expressed but is increased after thermal stress, suggesting that PIM1 may play a role in the heat shock response. Lon proteases have two specific subfamilies: LonA and LonB, differentiated by the number of AAA+ domains found in the protein.
Pfam PF03021: Influenza C virus M2 protein (family)
Influenza C virus M1 protein is encoded by a spliced mRNA.  The unspliced mRNA is also found in small quantities and can encode the protein represented by this family.
Wikipedia: The Matrix-2 (M2) protein is a proton-selective viroporin, integral in the viral envelope of the influenza A virus. The channel itself is a homotetramer, where the units are helices stabilized by two disulfide bonds, and is activated by low pH. The M2 protein is encoded on the seventh RNA segment together with the M1 protein. Proton conductance by the M2 protein in influenza A is essential for viral replication.
Pfam PF08819: Domain of unknown function (DUF1802) (domain)
The function of this family is unknown.  This region is found associated with a [pfam:PF04471] suggesting they could be part of a restriction modification system..
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 PF24689: Immunity protein TriTu (family)
This entry represents the Immunity protein TriTu from Salmonella enterica and related proteins. TriTu is a part of the TreTu/TriTu toxin/antitoxin system. TriTu immunity protein neutralises TreTu activity by acting like a lid that closes the TreTu catalytic site and traps the NAD+. TriTu is composed of a flat five-stranded antiparallel beta-sheet flanked on one side by two alpha-helices.
Pfam PF11399: Protein of unknown function (DUF3192) (family)
Some members in this family of proteins are annotated as lipoproteins however this cannot be confirmed.
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 PF24909: Integrin beta-like protein A-E, vWA-like (domain)
This entry represents a presumed vWA-like domain (according to structure predictions) of Integrin beta-like proteins A-E (SIBA-E) from Dictyostelium discoideum and similar sequences. These proteins may be implicated in cellular adhesion to substrate or phagocytic particles.