SII-SWORD/CoKE huggingface dataset:
Pfam PF12312: Nepovirus subgroup A polyprotein (family)
This family of proteins is found in viruses. Proteins in this family are typically between 259 and 1110 amino acids in length. The family is found in association with [pfam:PF03688], [pfam:PF03689], [pfam:PF03391]. This family is one of the polyproteins expressed by Nepoviruses in subgroup A.
Pfam PF05959: Nucleopolyhedrovirus protein of unknown function (DUF884) (family)
This family consists of several hypothetical Nucleopolyhedrovirus proteins of unknown function.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF05049: Interferon-inducible GTPase (IIGP) (family)
Interferon-inducible GTPase (IIGP) is thought to play a role in in intracellular defence. IIGP is predominantly associated with the Golgi apparatus and also localises to the endoplasmic reticulum and exerts a distinct role in IFN-induced intracellular membrane trafficking or processing.
Wikipedia: In molecular biology, the interferon-inducible GTPase (IIGP) family of proteins is thought to play a role in intracellular defence. IIGP is predominantly associated with the Golgi apparatus and also localises to the endoplasmic reticulum and exerts a distinct role in IFN-induced intracellular membrane trafficking or processing.
Pfam PF09753: Membrane fusion protein Use1 (family)
This entry is of a family of proteins all approximately 300 residues in length. The proteins have a single C-terminal trans-membrane domain and a SNARE [soluble NSF (N-ethylmaleimide-sensitive fusion protein) attachment protein receptor] domain of approximately 60 residues. The SNARE domains are essential for membrane fusion and are conserved from yeasts to humans. Use1 is one of the three protein subunits that make up the SNARE complex and it is specifically required for Golgi-endoplasmic reticulum retrograde transport.
Pfam PF05152: Protein of unknown function (DUF705) (family)
This family contains several uncharacterised Baculovirus proteins.
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 PF24951: PAC1 LisH domain (domain)
This entry represents a presumed LisH dimerisation domain found at the N-terminus of the PAC1 protein. PAC1 is the yeast homologue of the Lis1 protein.
Wikipedia: In molecular biology, the LisH domain is a protein domain found in a large number of eukaryotic proteins, from metazoa, fungi and plants that have a wide range of functions. The recently solved structure of the LisH domain in the N-terminal region of LIS1 depicted it as a novel dimerisation motif, and that other structural elements are likely to play an important role in dimerisation.
Pfam PF17308: Pro-corazonin (family)
This domain family is found in Corazonin proteins in Drosophila and other Anthropods. Corazonin (Crz)is a neuropeptide with a wide spectrum of biological functions in diverse insect groups. It was first discovered due to its myostimulatory activities on the heart muscle of Periplaneta Americana and the hyper-neural muscle of Carausius morosus. In Drosophila melanogaster, Crz plays diverse roles ranging from a regulator of insulin producing cells in the brain to roles specific to tissues, life stages, and gender.
Wikipedia: Corazonin is a highly conserved neuropeptide found in many insects, in particular locusts and cockroaches.
Pfam PF06549: Protein of unknown function (DUF1118) (family)
This family consists of several hypothetical plant proteins of unknown function.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF06717: Protein of unknown function (DUF1202) (family)
This family consists of several hypothetical bacterial proteins of around 335 residues in length. Members of this family are found exclusively in Escherichia coli and Salmonella species and are often referred to as YggM proteins. 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 PF16100: RecQ-mediated genome instability protein 2 (family)
RMI2 is a eukaryotic family of an OB3, oligo-nucleotide-binding proteins. It is an essential component of the RMI complex that plays a vital role in the processing of homologous recombination intermediates in order to limit DNA-crossover-formation in cells.
Pfam PF10060: Uncharacterized membrane protein (DUF2298) (family)
This domain, found in various hypothetical bacterial 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 PF10950: Organ specific protein (family)
This eukaryotic family includes a number of plant organ-specific proteins. The predicted amino acid sequence suggests that these proteins could be exported and glycosylated. Family members consist of an N-terminal region with no repeats and a C-terminal region which carries multiple tandem repeats. The N-terminal region ends before the repeats region and is defined as the area that extends from the end of the signal peptide to the start of the tandem repeat region. Its length varies considerably, ranging from 30 to 80 amino acids. Generally, these proteins vary in size where it is suggested that thirty-six percent of the sequences had fewer than 150 amino acids; 41% ranged from 150 to 250, and 23% had more than 250 amino acids. Accordingly, these proteins belong to category II of proteins having repeats in tandem; that is, those with the repeats ranging in length from 20 to 40 residues. The second region (C-terminal) in the mature protein is the tandem repeat oligopeptide area. The repeats start with a common hexapeptide (E/D)FEPRP and end with X4Y i .e. (D/E)FEPRPX4Y. Full-length sequences revealed considerable variability in the number of repeats, ranging from 2 to 17. The length of the repeats also varied, ranging from 12 amino acids to 34 amino acids.
Pfam PF03536: Salmonella virulence-associated 28kDa protein (family)
This entry includes the virulence protein SpvC and the phosphothreonine lyase OspF.
The spv region of the Salmonella virulence plasmids consists of five genes located on an 8-kb fragment, shown to be essential for virulence in mice . SpvC (also known as mkfA and VirA ) is part of this gene cluster and is utilised by the microbe upon entry into macrophages, although the exact mechanism is unclear.
Pfam PF08919: F-actin binding (domain)
The F-actin binding domain forms a compact bundle of four antiparallel alpha-helices, which are arranged in a left-handed topology. Binding of F-actin to the F-actin binding domain may result in cytoplasmic retention and subcellular distribution of the protein, as well as possible inhibition of protein function.
Pfam PF04070: Domain of unknown function (DUF378) (family)
Predicted transmembrane domain of unknown function.  The majority of the family have two predicted transmembrane 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 PF05852: Gammaherpesvirus protein of unknown function (DUF848) (family)
This family consists of several uncharacterised proteins from the Gammaherpesvirinae.
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 PF08352: Oligopeptide/dipeptide transporter, C-terminal region (family)
This family features a region found towards the C-terminus of oligopeptide ABC transporter ATP binding proteins, immediately following the ATP-binding domain ([pfam:PF00005]). All characterised members appear able to be involved in the transport of oligopeptides or dipeptides. Some are important for sporulation or antibiotic resistance. Some dipeptide transporters also act on the heme precursor delta-aminolevulinic acid.
Pfam PF03381: LEM3 (ligand-effect modulator 3) family / CDC50 family (family)
Members of this family have been predicted to contain transmembrane helices. The family member LEM3 ([swissprot:P42838]) is a ligand-effect modulator, mutation of which increases glucocorticoid receptor activity in response to dexamethasone and also confers increased activity on other intracellular receptors including the progesterone, oestrogen and mineralocorticoid receptors. LEM3 is thought to affect a downstream step in the glucocorticoid receptor pathway. Factors that modulate ligand responsiveness are likely to contribute to the context-specific actions of the glucocorticoid receptor in mammalian cells. The products of genes YNR048w ([swissprot:P53740]), YNL323w ([swissprot:P42838]) and YCR094w ([swissprot:P25656]) (CDC50) show redundancy of function and are involved in regulation of transcription via CDC39. CDC39 (also known as NOT1) is normally a negative regulator of transcription either by affecting the general RNA polymerase II machinery or by altering chromatin structure. One function of CDC39 is to block activation of the mating response pathway in the absence of pheromone, and mutation causes arrest in G1 by activation of the pathway. It may be that the cold-sensitive arrest in G1 noticed in CDC50 mutants may be due to inactivation of CDC39.  The effects of LEM3 on glucocorticoid receptor activity may also be due to effects on transcription via CDC39.
Pfam PF21179: DNA-binding protein BldD-like, C-terminal domain (domain)
This domain is found at the C-terminal end of DNA-binding protein BldD from Streptomyces venezuelae ([swissprot:F2RCL8]) and similar proteins found in Actinobacteria. This domain shows two beta-alpha- alpha repeats and a short C-terminal helix. It is responsible for the binding of the protein to the second messenger 3',5'-cyclic diguanylic acid (c-di-GMP).
Pfam PF05477: Surfeit locus protein 2 (SURF2) (family)
Surfeit locus protein 2 is part of a group of at least six sequence unrelated genes (Surf-1 to Surf-6). The six Surfeit genes have been classified as housekeeping genes, being expressed in all tissue types tested and not containing a TATA box in their promoter region. The exact function of SURF2 is unknown.
Pfam PF02768: DNA polymerase III beta subunit, C-terminal domain (domain)
A dimer of the beta subunit of DNA polymerase beta forms a ring which encircles duplex DNA.  Each monomer contains three domains of identical topology and DNA clamp fold.
Wikipedia: A DNA clamp, also known as a sliding clamp, is a protein complex that serves as a processivity-promoting factor in DNA replication. As a critical component of the DNA polymerase III holoenzyme, the clamp protein binds DNA polymerase and prevents this enzyme from dissociating from the template DNA strand. The clamp-polymerase protein–protein interactions are stronger and more specific than the direct interactions between the polymerase and the template DNA strand; because one of the rate-limiting steps in the DNA synthesis reaction is the association of the polymerase with the DNA template, the presence of the sliding clamp dramatically increases the number of nucleotides that the polymerase can add to the growing strand per association event. The presence of the DNA clamp can increase the rate of DNA synthesis up to 1,000-fold compared with a nonprocessive polymerase.
Pfam PF23533: Apicomplexa microprotein (family)
This protein family includes uncharacterised microproteins encoded by small open reading frames (smORFs) from apicomplexa, including [swissprot:A7AVA0] from the parasite Babesia bovis.
Pfam PF04376: Arginine-tRNA-protein transferase, N terminus (family)
This family represents the N terminal region of the enzyme arginine-tRNA-protein transferase (EC 2.3.2.8), which catalyses the post-translational conjugation of arginine to the N terminus of a protein. In eukaryotes, this functions as part of the N-end rule pathway  of protein degradation by conjugating a de-stabilising amino acid to the amino terminal aspartate or glutamate of a protein, targeting the protein for ubiquitin-dependent proteolysis.  N terminal cysteine is sometimes  modified. In S cerevisiae, Cys20, 23, 94 and/or 95 are thought to be important  for activity.  Of these, only Cys 94 appears to be completely conserved in this family.
Pfam PF02944: BESS motif (conserved_site)
The BESS motif is named after the proteins in which it is found (BEAF, Suvar(3)7 and Stonewall). The motif is 40 amino acid residues long and is composed of two predicted alpha helices. Based on the protein in which it is found and the presence of conserved positively charged residues it is predicted to be a DNA binding domain. This domain appears to be specific to drosophila.
Wikipedia: In molecular biology, the BESS domain is a protein domain which has been named after the three proteins that originally defined the domain: BEAF, Suvar(3)7 and Stonewall ). The BESS domain is 40 amino acid residues long and is predicted to be composed of three alpha helices, as such it might be related to the myb/SANT HTH domain. The BESS domain directs a variety of protein-protein interactions, including interactions with itself, with Dorsal, and with a TBP-associated factor. It is found in a single copy in Drosophila proteins and is often associated with the MADF domain.
Pfam PF15035: Ciliary rootlet component, centrosome cohesion (family)
This is a coiled-coil domain found in rootletin (also known as Ciliary rootlet coiled-coil protein, CROCC), CROCC2, the centrosome-associated protein CEP250 and related sequences, involved in centrosome cohesion .

Rootletin is the major structural component of the ciliary rootlet, a cytoskeletal-like structure in ciliated cells which originates from the basal body at the proximal end of a cilium and extends proximally toward the cell nucleus. It is required for the correct positioning of the cilium basal body relative to the cell nucleus, to allow for ciliogenesis  and contributes to centrosome cohesion before mitosis .

CEP250 (also known as C-Nap1) is a Nek2-interacting protein localised at centrosomes during interphase and has been implicated in the cell-cycle regulated cohesion of microtubule-organizing centers . It recruits CCDC102B to the proximal ends of centrioles .
Wikipedia: Rootletin, also known as ciliary rootlet coiled-coil protein (CROCC) is a protein in humans that is encoded by the CROCC gene.
Rootletin is a component of the ciliary rootlet and, together with CEP68 and CEP250, is required for centrosome cohesion.
Pfam PF11088: Glycoprotein encoding membrane proteins RL5A and RL6 (family)
RL5A and RL6 are part of the RL11 family which are predicted to encode membrane glycoproteins. Two adjacent open reading frames potentially encode a domain that is the hallmark of proteins encoded by the RL11 family.
Pfam PF07252: Protein of unknown function (DUF1433) (family)
This family contains a number of hypothetical bacterial proteins of unknown function approximately 100 residues 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 PF24873: DUF2110 C-terminal domain (domain)
This domain, found in various hypothetical archaeal proteins, has no known function. It is found at the C-terminus of DUF2110 family proteins.
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 PF10341: Shelterin complex subunit, TPP1/ACD (domain)
TPP1 is a component of the telomerase holoenzyme, involved in telomere replication.  It has been demonstrated that TPP1 dimerises and binds to DNA and RNA. Furthermore, TPP1 stimulates the dissociation of RNA/DNA hetero-duplexes. Yeast telomerase protein TPP1 (Est3 in yeast) is a novel type of GTPase. The key residues in [swissprot:Q03096] are an Asp at residue 86 and the Arg at residue 110.  The Asp is totally conserved in the family, whereas the Arg is not so well conserved. The N-terminal of TPP1 is likely to be the binding surface for TINF2, whereas the C-terminus probably binds to POT1, thereby tethering POT1 to the shelterin complex.  The complex bound to telomeric DNA increases the activity and processivity of the human telomerase core enzyme, thus helping to maintain the length of the telomeres. This domain is conserved from fungi to mammals, hence family Telomere_Pot1 has been merged into the family. The human shelterin complex includes six proteins: telomere repeat binding factor 1 (TRF1), TRF2, repressor/activator protein 1 (RAP1), TRF1-interacting nuclear protein 2 (TIN2), TIN2-interacting protein 1 (TPP1) and protection of telomeres 1 (POT1).
Pfam PF04771: Chicken anaemia virus VP-3 protein (family)
This protein is found in the nucleus of infected cells and may act as a transcriptional regulator.  It induces apoptosis, and is also known as apoptin [SwissProt annotation for [swissprot:P54094]].
Pfam PF07415: Gammaherpesvirus latent membrane protein (LMP2) protein (family)
This family consists of several Gammaherpesvirus latent membrane protein (LMP2) proteins. Epstein-Barr virus is a human Gammaherpesvirus that infects and establishes latency in B lymphocytes in vivo. The latent membrane protein 2 (LMP2) gene is expressed in latently infected B cells and encodes two protein isoforms, LMP2A and LMP2B, that are identical except for an additional N-terminal 119 aa cytoplasmic domain which is present in the LMP2A isoform. LMP2A is thought to play a key role in either the establishment or the maintenance of latency and/or the reactivation of productive infection from the latent state. The significance of LMP2B and its role in pathogenesis remain unclear.
Pfam PF12795: Mechanosensitive ion channel porin domain (coiled_coil)
The small mechanosensitive channel, MscS, is a part of the turgor-driven solute efflux system that protects bacteria from lysis in the event of osmotic shock. The MscS protein alone is sufficient to form a functional mechanosensitive channel gated directly by tension in the lipid bilayer. The MscS proteins are heptamers of three transmembrane subunits with seven converging M3 domains, and this MscS_porin is towards the N-terminal of the molecules. The high concentration of negative charges at the extracellular entrance of the pore helps select the cations for efflux.
Pfam PF16399: Intron-binding protein aquarius N-terminal (repeat)
This entry represents the ARM repeats domain found at the N-terminal of intron-binding protein aquarius, a splicing factor which links excision of introns from pre-mRNA with snoRP assembly.
Pfam PF15113: TMEM117 protein family (family)
The function of this family of transmembrane proteins has not, as yet, been determined. Members of this family are as yet uncharacterised. This family of proteins is found in eukaryotes. Proteins in this family are typically between 181 and 504 amino acids in length.
Pfam PF08065: KI67R (NUC007) repeat (repeat)
This family represents the KI67/Chmadrin repeat. The function of this repeat is unknown.
Pfam PF08497: Radical SAM N-terminal (family)
This domain tends to occur to the N-terminus of the [pfam:PF04055] domain in hypothetical bacterial proteins.
Pfam PF11941: Domain of unknown function (DUF3459) (domain)
This presumed domain is functionally uncharacterised. This domain is found in bacteria. This domain is about 110 amino acids in length. This domain is found associated with [pfam:PF00128], [pfam:PF02922].
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 PF07727: Reverse transcriptase (RNA-dependent DNA polymerase) (domain)
A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. This Pfam entry includes reverse transcriptases not recognised by the [pfam:PF00078] model.
Pfam PF05491: RuvB C-terminal winged helix domain (domain)
The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein. This family consists of the C-terminal region of the RuvB protein which is thought to be helicase DNA-binding domain.
Pfam PF07114: Transmembrane protein 126 (family)
This entry includes the transmembrane protein 126 A/B (TMEM126A/B) from animals. Human TMEM126B  participates in constructing the membrane arm of  mitochondrial respiratory complex I.