SII-SWORD/CoKE huggingface dataset:
Pfam PF19227: Salyut domain (family)
This entry represents the Salyut domain found in the replicase of all viruses of the viral family Tymoviridae, composed of viruses that infect plants and insects.  it is located within a long, hypervariable, Proline-rich hinge region located between the Alphavirus-like methyltransferase ([pfam:PF01660]) and the [pfam:PF01443]. It is located 150-20aa downstream the Iceberg region that forms the C-terminus of Vmethyltransf. The function of this family is unknown.
Pfam PF06460: Coronavirus 2'-O-methyltransferase (domain)
This domain covers the NSP16 region of the coronavirus polyprotein. The SARS-CoV RNA cap SAM-dependent (nucleoside-2'-O-)-methyltransferase (2'-O-MTase) is a heterodimer comprising SARS-CoV nsp10 and nsp16. When bound to nsp10, nsp16 is active as a type-0 RNA cap-dependent 2'-O-MTase, ie., active only when the cap guanine is methylated at its N7 position. Nsp10 binds to nsp16 through an activation surface area in nsp10, and the resulting complex exhibits RNA cap (nucleoside-2'-O)-methyltransferase activity. Nsp10 is a double zinc finger protein together with nsp4, nsp5, nsp12, nsp14, and nsp16, nsp10 has been found to be essential in the assembly of a functional replication/transcription complex. NSP16 plays a key role in viral replication as it is involved in immune response evasion through the 2'-O-methylation of coronavirus RNA, which is essential for preventing recognition by the host. It mimics the human protein CMTr1 and, unlike CMTr1, it requires NSP10 as a binding partner to activate its enzymatic activity. Nsp16 adopts a typical fold of the S-adenosylmethionine-dependent methyltransferase (SAM) family as defined initially for the catechol O-MTase but it lacks several elements of the canonical MTase fold, such as helices B and C. The nsp16 topology matches those of dengue virus NS5 N-terminal domain and of vaccinia virus VP39 MTases. Structural analysis in NSP16 from SARS-CoV-2 identified a cryptic pocket (also present in other coronavirus such as SARS-CoV-1 and MERS) not present in human CMTr1, and the fact that NSP16 is one of the most conserved proteins of SARS-CoV-2 and related viruses, make it an interesting target for developing new antiviral treatment  for COVID-19 and other diseases caused by coronaviruses.
Pfam PF15136: Uncharacterised protein family UPF0449 (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes.  There is a conserved LPTRP sequence motif.
Pfam PF17159: Membrane-associated sensor domain (domain)
MASE3 (Membrane-Associated SEnsor) is an integral membrane sensor domain of unknown specificity found in histidine kinases, diguanylate cyclases and protein phosphatases in various bacteria and archaea.
Pfam PF10310: Family of unknown function (DUF5427) (family)
This is a domain of unknown function. Family members found in Saccharomyces cerevisiae, are synthetic lethal with genes involved in maintenance of telomere capping. However, experimental evidence is yet to verify the exact function of family members and the domain.
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 PF05628: Borrelia membrane protein P13 (family)
This family consists of P13 proteins from Borrelia species. P13 is a 13kDa integral membrane protein which is post-translationally processed at both ends and modified by an unknown mechanism.
Pfam PF06922: Citrus tristeza virus P13 protein (family)
This family consists of several Citrus tristeza virus (CTV) P13 13-kDa proteins. Citrus tristeza virus (CTV), a member of the closterovirus group, is one of the more complex single-stranded RNA viruses. The function of this family is unknown.
Pfam PF22805: Protein M, smaller domain (domain)
This domain is found in proteins from Mycoplasmaceae, including Uncharacterized protein MG281 from Mycoplasma genitalium, also known as protein M. This virulence protein consists of two domains. The larger one ([pfam:PF20757]) binds the IgG light chain to block the binding of antibody to antigen and includes a leucine-rich repeat (LRR)-like subdomain. This domain folds into two alpha-helices.
Pfam PF04898: Glutamate synthase central domain (domain)
The central domain of glutamate synthase connects the amino terminal amidotransferase domain with the FMN-binding domain and has an alpha / beta overall topology.  This domain appears to be a rudimentary form of the FMN-binding TIM barrel according to SCOP.
Pfam PF02807: ATP:guanido phosphotransferase, N-terminal domain (domain)
The N-terminal domain has an all-alpha fold.
Wikipedia: In molecular biology, the ATP:guanido phosphotransferase family is a family of structurally and functionally related enzymes, that reversibly catalyse the transfer of phosphate between ATP and various phosphagens. The enzymes belonging to this family include:Glycocyamine kinase, which catalyses the transfer of phosphate from ATP to guanidoacetate.
Arginine kinase, which catalyses the transfer of phosphate from ATP to arginine.
Taurocyamine kinase, an annelid-specific enzyme that catalyses the transfer of phosphate from ATP to taurocyamine.
Lombricine kinase, an annelid-specific enzyme that catalyses the transfer of phosphate from ATP to lombricine.
Smc74, a cercaria-specific enzyme from Schistosoma mansoni.
Creatine kinase (CK), which catalyses the reversible transfer of high energy phosphate from ATP to creatine, generating phosphocreatine and ADP.
Pfam PF17769: Phosphoribosylaminoimidazole carboxylase C-terminal domain (domain)
This entry represents the C-terminal domain of the PurK enzyme.
Pfam PF20697: Pol beta superfamily nucleotidyltransferase in conflict systems (domain)
This is a Pol beta superfamily nucleotidyltransferase domain found in bacterial conflict systems and predicted to function as an effector.
Pfam PF07265: Tapetum specific protein TAP35/TAP44 (family)
This family consists of several plant tapetum specific proteins. Members of this family are found in Arabidopsis thaliana, Brassica napus and Sinapis alba. Members of this family may be involved in sporopollenin formation and/or deposition.
Pfam PF06085: Lipoprotein Rz1 precursor (family)
This family consists of several bacteria and phage lipoprotein Rz1 precursors. Rz1 is a proline-rich lipoprotein from bacteriophage lambda which is known to have fusogenic properties. Rz1-induced liposome fusion is thought to be mediated primarily by the generation of local perturbation in the bilayer lipid membrane and to a lesser extent by electrostatic forces. This family Rz1 and the Rz protein Rz ([pfam:PF03245]) represent a unique example of two genes located in different reading frames in the same nucleotide sequence, which encode different proteins that are both required in the same physiological pathway.
Pfam PF20254: N,N-dimethylformamidase beta subunit-like, C-terminal (domain)
This entry represents a domain found at the C-terminal of bacterial proteins, including N,N-dimethylformamidase beta (DMFA2) subunit from Paracoccus, the large subunit of dimethylformamidase (DMFase), an enzyme containing a Fe+3 ion in the active site that catalyses the hydrolytic cleavage of the amide bond in N,N-dimethyl formamide. This domain is described as domain III, which adopts an alpha/beta/alpha fold, with five beta-strands that are parallel and sandwiched between alpha-helices. This domain is also found in some uncharacterised fungal sequences.
Pfam PF10140: WXG100 protein secretion system (Wss), protein YukC (family)
Members of this family of proteins include predicted membrane proteins homologous to YukC in B. subtilis. The YukC protein family would participate to the formation of a translocon required for the secretion of WXG100 proteins ([pfam:PF06013]) in monoderm bacteria, the WXG100 protein secretion system (Wss). This family includes EssB in Staphylococcus aureus.
Pfam PF17078: SWI5-dependent HO expression protein 3 (coiled_coil)
SWI5-dependent HO expression protein 3 (She3) is an RNA-binding protein that binds specific mRNAs, including the mRNA of Ash1, which is invalid in cell-fate determination. She3 acts as an adapter protein that docks the myosin motor Myo4p onto an Ash1-She2p ribonucleoprotein complex. She3 seems to bind to Myo4p and Shep2p via different domains.
Pfam PF16942: Putative cyclic bacteriocin (family)
This is a family of short proteins from Gram- putatively from the carnocylcin A family of bacteriocins.
Pfam PF17394: Uncharacterized KleE stable inheritance protein (family)
This is a family of unknown function found in Proteobacteria. Family Members are predicted to contain two trans-membrane regions.
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 PF22595: Cilia and flagella associated protein 107 (family)
This family represents the homologues of Cilia and flagella associated protein 107 (CFAP107, also known as C1orf158). CFAP107 is a microtubule inner protein (MIP) part of the doublet microtubules (DMTs) in cilia and sperm axoneme. CFAP107 belongs to the core MIPs and binds to protofilaments A10-A11 of the sperm DMTs.
Pfam PF24451: Family of unknown function (DUF7567) (family)
This entry represents a small family of uncharacterised proteins found in Halobacteria. They contain two pairs of conserved cysteines that are likely involved in metal coordination. These proteins are predicted to structurally resemble Zinc beta-ribbon domains.
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 PF01762: Galactosyltransferase (family)
This family includes the galactosyltransferases UDP-galactose:2-acetamido-2-deoxy-D-glucose3beta-galactosyltrans feras e [swissprot:O43825] and UDP-Gal:beta-GlcNAc beta 1,3-galactosyltranferase  [swissprot:O54904].  Specific galactosyltransferases transfer galactose to GlcNAc terminal chains in the synthesis of the lacto-series oligosaccharides types 1  and 2.
Wikipedia: Galactosyltransferase is a type of glycosyltransferase which catalyzes the transfer of galactose. An example is B-N-acetylglucosaminyl-glycopeptide b-1,4-galactosyltransferase.
Pfam PF07407: Seadornavirus VP6 protein (family)
This family consists of several VP6 proteins from the Banna virus as well as a related protein VP5 from the Kadipiro virus. Members of this family are typically of around 420 residues in length. The function of this family is unknown.
Pfam PF17314: Family of unknown function (DUF5360) (family)
This is a family of unknown function. It is present in Bacteria and most of the family members are predicted to have 4 trans-membrane regions.
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 PF02383: SacI homology domain (family)
This Pfam family represents a protein domain which shows homology to the yeast protein SacI [swissprot:P32368]. The SacI homology domain is most notably found at the amino terminal of the inositol  5'-phosphatase synaptojanin.
Wikipedia: SacI homology domain is most notably found at the amino terminal of the inositol 5'-phosphatase synaptojanin. Synaptic vesicles are recycled with remarkable speed and precision in nerve terminals. A major recycling pathway involves clathrin-mediated endocytosis at endocytic zones located around sites of release. Different 'accessory' proteins linked to this pathway have been shown to alter the shape and composition of lipid membranes, to modify membrane-coat protein interactions, and to influence actin polymerization. These include the GTPase dynamin, the lysophosphatidic acid acyl transferase endophilin, and the phosphoinositide phosphatase synaptojanin.
Pfam PF10809: Protein of unknown function (DUF2732) (family)
This 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 PF00955: HCO3- transporter integral membrane domain (domain)
This family contains Band 3 anion exchange proteins that exchange CL-/HCO3- such as [swissprot:P48751]. This family also includes cotransporters of Na+/HCO3- such as [swissprot:O15153].
Wikipedia: The anion exchanger family is a member of the large APC superfamily of secondary carriers. Members of the AE family are generally responsible for the transport of anions across cellular barriers, although their functions may vary. All of them exchange bicarbonate. Characterized protein members of the AE family are found in plants, animals, insects and yeast. Uncharacterized AE homologues may be present in bacteria. Animal AE proteins consist of homodimeric complexes of integral membrane proteins that vary in size from about 900 amino acyl residues to about 1250 residues. Their N-terminal hydrophilic domains may interact with cytoskeletal proteins and therefore play a cell structural role. Some of the currently characterized members of the AE family can be found in the Transporter Classification Database.
Pfam PF16270: Lipocalin-like domain (DUF4923) (domain)
This family consists of uncharacterized proteins around 200 residues in length and is mainly found in various Bacteroides and Parabacteroides species. The function of this family is unknown. This domain is distantly related to lipocalins.
Pfam PF21552: Transcription factor tau 138 kDa subunit, extended winged helix (domain)
This domain is found in Transcription factor tau 138 kDa subunit from Saccharomyces cerevisiae (TFC3), which may play a role in linking tauA, tauB, and TFIIIB to regulate the formation of the RNA polymerase III pre-initiation complex. This entry represents its extended winged helix (eWH) domain, which is centrally located.
Pfam PF07085: DRTGG domain (domain)
This presumed domain is about 120 amino acids in length. It is found associated with CBS domains [pfam:PF00571], as well as the CbiA domain [pfam:PF01656].  The function of this domain is unknown. It is named the DRTGG domain after some of the most conserved residues. This domain may be very distantly related to a pair of CBS domains. There are no significant sequence similarities, but its length and association with CBS domains supports this idea (Bateman A, pers. obs.).
Pfam PF16842: Occluded RNA-recognition motif (domain)
This family is an unusual, usually C-terminal, RNA-recognition motif found in fungi. In yeast it is the fourth RRM domain on the essential splicing factor Prp24. Structurally, it has a non-canonical RRM fold with the expected beta-aloha-beta-beta-alpha-beta RRM-fold is flanked by N- and C-terminal alpha-helices. These two additional flanking alpha-helices occlude the beta-sheet face. The electropositive surface thereby presented is an alternative RNA-binding surface that allows both binding and unwinding of the U6 small nuclear RNA's internal stem loop, at least in vitro.
Pfam PF24997: PSF1 C-terminal domain (domain)
This domain is found C-terminal in the human DNA replication complex GINS protein PSF1 and related proteins. PSF1 is required for correct functioning of the GINS complex, a complex that plays an essential role in the initiation of DNA replication, and progression of DNA replication forks.
Pfam PF12304: Beta-casein like protein (family)
This protein is found in eukaryotes. Proteins in this family are typically between 216 to 240 amino acids in length. This protein has two conserved sequence motifs: VLR and TRIY. BCLP is associated with cell morphology and a regulation of growth pattern of tumor. It is found in adenocarcinomas of uterine cervical tissues.
Pfam PF22546: 2-Component system ADP-ribosyltransferase domain (domain)
This entry represents the 2CompART domain, which coupled with its partner 2CompARG, forms a two-domain T-A-like association in the duplex-forming systems likely functioning as the principal effector of these systems. One is likely to function as the antitoxin, regulating the toxin activity of the other.
Pfam PF11842: Domain of unknown function (DUF3362) (family)
This domain is functionally uncharacterised. This domain is found in bacteria and archaea. This presumed domain is typically between 117 to 158 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 PF22767: Cyanobactin oxidase ThcOx, (domain)
Thus entry represents the second peptide-clamp domain described in cianobactin oxidase ThcOx from Cyanothece sp.. The first one is represented in [pfam:PF18679] and at the C-terminal it contains a nitroreductase domain ([pfam:PF00881]). In this domain, the binding site is buried by an interaction with the other clamp domain and thus it is unlikely to be active.
Pfam PF03319: Ethanolamine utilisation protein EutN/carboxysome (domain)
The crystal structure of EutN contains a central five-stranded beta-barrel, with an alpha-helix at the open end of this barrel (PDB:2HD3). The structure also contains three additional beta-strands, which help the formation of a tight hexamer, with a hole in the center. this suggests that EutN forms a pore, with an opening of 26 Angstrom in diameter on one face and 14 Angstrom on the other face. EutN is involved in the cobalamin-dependent degradation of ethanolamine.
Pfam PF05658: YadA head domain repeat (2 copies) (repeat)
This entry represents two copies of a fourteen residue repeat that makes up the head domain of bacterial haemagglutinins and invasins.
Wikipedia: In molecular biology, trimeric autotransporter adhesins (TAAs), are proteins found on the outer membrane of Gram-negative bacteria. Bacteria use TAAs in order to infect their host cells via a process called cell adhesion. TAAs also go by another name, oligomeric coiled-coil adhesins, which is shortened to OCAs. In essence, they are virulence factors, factors that make the bacteria harmful and infective to the host organism.
Pfam PF02780: Transketolase, C-terminal domain (domain)
The C-terminal domain of transketolase has been proposed as a regulatory molecule binding site.
Pfam PF09287: CEP-1, DNA binding (domain)
Members of this family of DNA-binding domains are found the transcription factor CEP-1. They adopt a beta sandwich structure, with nine strands in two beta-sheets, in a Greek-key topology.
Pfam PF05631: Sugar-tranasporters, 12 TM (family)
MFS_5 is a family of sugar-transporters from both prokaryotes and eukaryotes.
Pfam PF04216: FdhE, N-terminal (domain)
This domain is found at the N-terminal end of FdhE from Escherichia coli and similar proteins necessary for formate dehydrogenase activity. This domain shows a mainly alpha-helical configuration.
Pfam PF15148: Apolipoprotein F (family)
Human apolipoprotein F (APOF) is a minor apolipoprotein that associates with LDL. It inhibits cholesteryl ester transfer protein (CETP) activity and appears to be an important regulator of cholesterol transport. It also associates to a lesser degree with VLDL, Apo-AI and Apo-AII .
Wikipedia: Apolipoprotein F is a protein that in humans is encoded for by the APOF gene. The product of this gene is one of the minor apolipoproteins found in plasma. This protein forms complexes with lipoproteins and may be involved in transport and/or esterification of cholesterol.
Pfam PF16980: Putative citrate transport (family)
CitMHS is a family of putative citrate transporters, belonging to the Na+/H+ antiporter NhaD-like permease superfamily.
Pfam PF01203: Type II secretion system (T2SS), protein N (repeat)
Members of the T2SN family are involved in the Type II protein secretion system. The precise function of these proteins is unknown.
Pfam PF06019: Phage GP30.8 protein (family)
This family consists of several GP30.8 proteins from the T4-like phages. The function of this family is unknown.
Pfam PF18068: Npun R1517 (domain)
This domain belongs to NPun R1517 which is found in Nostoc punctiforme. Studies indicate that Npun R1517 is encoded by orphan gene 29. Npun R1517 adopts a sleigh-shaped structure with a two-stranded antiparallel beta-sheet forming the floor of the sleigh, a HTH forming the seat and a HTH forming the front of the sleigh.
Pfam PF04586: Caudovirus prohead serine protease (family)
Family of Caudovirus prohead serine proteases also found in a number of bacteria possibly as the result of horizontal transfer.
Pfam PF08536: Whirly transcription factor (domain)
This family contains the plant whirly transcription factors.
Wikipedia: In molecular biology, the protein domain Whirly is a transcription factor commonly found in plants. This means they aid the transcription of genes from DNA into a complementary copy of mRNA. In particular, in plants, they aid the transcription of plant defence genes.
Pfam PF09101: Exotoxin A binding (domain)
Members of this family are found in Pseudomonas aeruginosa exotoxin A, and are responsible for binding of the toxin to the alpha-2-macroglobulin receptor, with subsequent internalisation into endosomes. The domain adopts a thirteen-strand antiparallel beta jelly roll topology, which belongs to the Concanavalin A-like lectins/glucanases fold superfamily.