SII-SWORD/CoKE huggingface dataset:
Pfam PF00845: Geminivirus BL1 movement protein (family)
Geminiviruses encode two movement proteins that are essential for systemic infection of their host but dispensable for replication and encapsidation.
Pfam PF08949: Bacteriophage PRD1, spike protein P5, C-terminal (domain)
This domain is found at the C-terminal of bacteriophage PRD1 spike protein P5.. The spike structure of bacteriophage PRD1 is comprised of proteins P2, P5, and P31. P5 is an elongated multidomain trimer. This C-terminal domain appears to contain the residues responsible for the trimerization of the protein.
Pfam PF13964: Kelch motif (repeat)
Wikipedia: The Kelch motif is a region of protein sequence found widely in proteins from bacteria and eukaryotes. This sequence motif is composed of about 50 amino acid residues which form a structure of a four stranded beta-sheet "blade". This sequence motif is found in between five and eight tandem copies per protein which fold together to form a larger circular solenoid structure called a beta-propeller domain.
Pfam PF14673: Domain of unknown function (DUF4459) (domain)
This family appears only on sequences from Salmonella spp. These sequences also all carry a YARHG domain, [pfam:PF13308].
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 PF17865: Midasin AAA lid domain (domain)
This entry represents the alpha helical AAA+ lid domain that is found to the C-terminus of AAA domains. This lid domain is found in midasin proteins.
Pfam PF04001: Transcription factor Vhr1 (family)
Vhr1 is a transcription factor which regulates the biotin-dependent expression of transporters VHT1 and BIO5.
Pfam PF21109: Stonustoxin helical domain (domain)
This entry represents the stonustoxin helical domain. Stonustoxin is a large pore forming toxin found in stonefish. This entry contains stonustoxin as well as a variety of other toxin proteins such as veruccotoxin.
Pfam PF22298: Tsr1, G-like domain (domain)
This entry represents the G-like (guanine nucleotide-binding domain) domain, found in Tsr1, a protein required for normal export of the pre-40S particles from the nucleus to the cytoplasm during 40S ribosomal subunit synthesis. This domain adopts a GTPase-like fold, but lacks a P-loop and is not predicted to bind GTP.
Pfam PF23605: 1,3-beta-glucan synthase component FKS1, second domain (domain)
This domain is found in 1,3-beta-glucan synthase component FKS1 from Saccharomyces cerevisiae and similar fungal proteins. FKS1 is involved in cell wall synthesis, maintenance and remodelling. This domain is predicted to adopt an all-alpha structure. It is often found C-terminal to [pfam:PF14288]. Proteins with this domain also have [pfam:PF02364].
Pfam PF21022: Rap/Ran-GAP protein dimerization domain (domain)
This entry represents an alpha+beta domain found in some Rap-GAP proteins. It mediates dimerization in Rap1GAP protein.
Pfam PF06231: Protein of unknown function (DUF1010) (family)
Family of plasmid encoded proteins with 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 PF14124: Domain of unknown function (DUF4291) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 190 and 214 amino acids in length. There are two conserved sequence motifs: VYQAY and RMTW.
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 PF12662: Complement Clr-like EGF-like (domain)
cEGF, or complement Clr-like EGF, domains have six conserved cysteine residues disulfide-bonded into the characteristic pattern 'ababcc'. They are found in blood coagulation proteins such as fibrillin, Clr and Cls, thrombomodulin, and the LDL receptor. The core fold of the EGF domain consists of two small beta-hairpins packed against each other. Two major structural variants have been identified based on the structural context of the C-terminal cysteine residue of disulfide 'c' in the C-terminal hairpin: hEGFs and cEGFs. In cEGFs the C-terminal thiol resides on the C-terminal beta-sheet, resulting in long loop-lengths between the cysteine residues of disulfide 'c', typically C[10+]XC. These longer loop-lengths may have arisen by selective cysteine loss from a four-disulfide EGF template such as laminin or integrin.  Tandem cEGF domains have five linking residues between terminal cysteines of adjacent domains. cEGF domains may or may not bind calcium in the linker region. cEGF domains with the consensus motif CXN4X[F,Y]XCXC are hydroxylated exclusively on the asparagine residue.
Wikipedia: The EGF-like domain is an evolutionary conserved protein domain, which derives its name from the epidermal growth factor where it was first described. It comprises about 30 to 40 amino-acid residues and has been found in a large number of mostly animal proteins. Most occurrences of the EGF-like domain are found in the extracellular domain of membrane-bound proteins or in proteins known to be secreted. An exception to this is the prostaglandin-endoperoxide synthase. The EGF-like domain includes 6 cysteine residues which in the epidermal growth factor have been shown to form 3 disulfide bonds. The structures of 4-disulfide EGF-domains have been solved from the laminin and integrin proteins. The main structure of EGF-like domains is a two-stranded β-sheet followed by a loop to a short C-terminal, two-stranded β-sheet. These two β-sheets are usually denoted as the major (N-terminal) and minor (C-terminal) sheets. EGF-like domains frequently occur in numerous tandem copies in proteins: these repeats typically fold together to form a single, linear solenoid domain block as a functional unit.
Pfam PF24846: DNA polymerase II large subunit DP2, catalytic domain (domain)
This entry represents the catalytic domain of DNA polymerase II large subunit from Pyrococcus abyssi (PolC) and similar sequences mainly found in archaea. This domain is found C-terminal to [pfam:PF24844] and shows a six-stranded double-psi beta-barrel (DPBB).
Pfam PF22494: Choice-of-anchor I domain (repeat)
This entry represents the choice-of-anchor I domain.
Pfam PF18957: Long Rib domain (domain)
This entry represents the Long Rib domain that is closely related to the [pfam:PF08428] Rib domain but has a conserved insertion. These domains are found in bacterial cell surface proteins.
Pfam PF16532: Sf6-type phage tail needle knob or tip of some Caudovirales (domain)
Phage_tail_NK is the globular tip protein of some tailed bacteriophages. Tailed bacteriophage virions deliver DNA to susceptible cells after adsorbing to specific receptors on the surface of the bacteria. In the Gram-negative bacteria these receptors are surface proteins or polysaccharides. In the phage Sf6-type needle, this distal tip folds into a knob with a TNF-like fold, similar to the fibre knobs of bacteriophage PRD1 and Adenovirus. It contains three bound L-glutamate molecules that are bind tightly in the crevices between the trimers of this trimeric tip.
Pfam PF13759: Putative 2OG-Fe(II) oxygenase (domain)
This family has structural similarity to the 2OG-Fe(II) oxygenase superfamily.
Pfam PF09748: Transcription factor subunit Med10 of Mediator complex (family)
Med10 is one of the protein subunits of the Mediator complex, tethered to Rgr1 protein. The Mediator complex is required for the transcription of most RNA polymerase II (Pol II)-transcribed genes. Med10 specifically mediates basal-level HIS4 transcription via Gcn4, and, additionally, there is a putative requirement for Med10 in Bas2-mediated transcription. Med10 is part of the middle region of Mediator.
Wikipedia: Mediator is a multiprotein complex that functions as a transcriptional coactivator in all eukaryotes. It was discovered in 1990 in the lab of Roger D. Kornberg, recipient of the 2006 Nobel Prize in Chemistry. Mediator complexes interact with transcription factors and RNA polymerase II. The main function of mediator complexes is to transmit signals from the transcription factors to the polymerase.
Pfam PF12769: 4TM region of pyridine nucleotide transhydrogenase, mitoch (family)
PNTB_4TM is the region upstream of family PNTB, [pfam:PF02233], that carries four of this transporters transmembrane regions. PNTB is the beta-subunit of pyridine nucleotide transhydrogenase. This family forms part of the Proton-translocating Transhydrogenase (PTH) Family.
Pfam PF03270: Protein of unknown function, DUF269 (family)
Members of this family may be involved in nitrogen fixation, since they are found within nitrogen fixation operons.
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 PF11963: Betacoronavirus, lineage A, NSP1 (family)
This family the N-terminal region of the Betacoronavirus polyprotein which contains non-structural protein 1 (Nsp1) from Betacoronavirus lineage A. This protein is important for viral replication and pathogenesis. It suppresses the host innate immune functions by inhibiting type I interferon expression and host antiviral signalling pathways.
Pfam PF24661: Domain of unknown function (DUF7649) (domain)
This domain is found in uncharacterised bacterial proteins. It is predicted to adopt a non-compact structure consisting of four highly hydrophobic alpha-helices that could potentially dimerise.
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 PF02563: Polysaccharide biosynthesis/export protein (family)
This is a family of periplasmic proteins involved in polysaccharide biosynthesis and/or export.
Wikipedia: The extracellular polysaccharide colanic acid is produced by species of the family Enterobacteriaceae. In Escherichia coli strain K12 the colanic acid cluster comprises 19 genes. The wzx gene encodes a protein with multiple transmembrane segments that may function in export of the colanic acid repeat unit from the cytoplasm into the periplasm in a process analogous to O-unit export. The colanic acid gene clusters may be involved in the export of polysaccharide from the cell.
Pfam PF12557: Cob(I)alamin adenosyltransferase N terminal (family)
This domain family is found in bacteria and eukaryotes, and is approximately 20 amino acids in length. The family is found in association with [pfam:PF02572]. Cob(I)alamin adenosyltransferase adenosylates Co(I) in an ATP-dependent manner in the conversion of aquacobalamin to its coenzyme form. This is the third step in this process, after two steps involved in the reduction of Co(III) to Co(I).
Pfam PF24215: Phage head to tail associated domain (domain)
This entry represents a protein domain that is found associated with phage head to tail connector domains [pfam:PF24214], which suggests this domain is part of the phage structure. This region forms a large mainly alpha helical domain.
Pfam PF12842: CCR4-Not complex, Not1 subunit, domain of unknown function DUF3819 (domain)
This is an uncharacterised domain that is found on the CCR4-Not complex component Not1. Not1 is a global regulator of transcription that affects genes positively and negatively and is thought to regulate transcription factor TFIID.
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 PF04317: YcjX-like family, DUF463 (family)
This family represents a group of uncharacterised proteins including a bacterial stress protein YcjX. The crystal structure of YcjX from  Shewanella oneidensis has now been solved, and shows it to be a  Ras-like GTP-binding protein. However, YcjX utilizes a non-canonical  switch 2' motif not found in any other G protein.
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 PF06883: RNA polymerase I, Rpa2 specific domain (domain)
This domain is found between domain 3 ([pfam:PF04565]) and domain 5  ([pfam:PF04565]), but shows no homology to domain 4 of Rpb2. The external  domains in multisubunit RNA polymerase (those most distant from the  active site) are known to demonstrate more sequence variability.
Pfam PF18430: Putative DNA-binding domain (domain)
This is a putative DNA-binding protein dimerization domain found bacterial proteins such as CD3330, (a transposon-related DNA-binding protein from Clostridium difficile). Crystal structure analysis suggests that CD3330 N-terminus is involved in dimer formation and also in crystal packing but the C-terminus is open to solvent.
Pfam PF21751: Probable sensor domain DACNV (domain)
This entry represents a potential sensor domain found at the N-terminal of bacterial diadenylate cyclases, which is typically followed by the DAC ([pfam:PF02457]) domain. DACND consists of a compact core formed by seven beta-strands and two or three alpha-helices, according to structure predictions. It is found in various phyla, including acidobacteria, actinobacteria, bacteroidetes, cyanobacteria and planctomycetes.
Pfam PF16997: Wap1 domain (repeat)
The Wap1 domain is found at the C-terminus of fungal Wpl1 proteins (also known as Rad61). These proteins are members of the cohesin complex. The Wap1 domain binds to the ATPase domain of Smc3.
Pfam PF20628: Dyp-type peroxidase, C-terminal (domain)
Dyp-type (dye-decolorizing) peroxidases are a family of heme proteins found in a wide range of bacteria and fungi. They have a wide substrate specificity and lack homology to most other peroxidases, with the ability to function well under much lower pH conditions compared with the other plant peroxidases. They consist of two domains that adopt a ferredoxin-like fold, connected by a loop. This entry represents the C-terminal domain, which possess a large hydrophobic cavity for heme binding.
Wikipedia: In molecular biology, the DyP-type peroxidase family is a family of haem peroxidase enzymes.
Haem peroxidases were originally divided into two superfamilies, namely, the animal peroxidases and the plant peroxidases, which include fungal and bacterial peroxidases. The DyP family constitutes a novel class of haem peroxidase. Because these enzymes were derived from fungal sources, the DyP family was thought to be structurally related to the class II secretory fungal peroxidases. However, the DyP family exhibits only low sequence similarity to classical fungal peroxidases, such as LiP and MnP, and does not contain the conserved proximal and distal histidines and an essential arginine found in other plant peroxidase superfamily members.
Pfam PF22742: PspA associated protein B (domain)
PspA associated protein B is a component of the Psp system. It occurs in an operon with a membrane-associated metallopeptidase. In addition, these two genes occur in operon with the PspA-PspAA dyad.
Pfam PF07761: Protein of unknown function (DUF1617) (family)
This is a family of sequences from hypothetical bacterial and bacteriophage proteins. The region in question is approximately 150 residues long and is highly conserved throughout the family.
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 PF18646: Family of unknown function (DUF5632) (domain)
This an alpha-beta-alpha domain found at the N-terminal region of Rv3899c, a hypothetical protein from Mycobacterium tuberculosis which is conserved across mycobacteria.
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 PF23087: ELAPOR1-like, mannose 6-phosphate receptor homology domain (domain)
This domain is found in Endosome/lysosome-associated apoptosis and autophagy regulator family member 2 from humans (ELAPOR1), which may protect cells from cell death by inducing cytosolic vacuolisation and up-regulating the autophagy pathway and may play a role in apoptosis and cell proliferation. This domain is predicted to form two orthogonally oriented beta-sheets that compose a beta-barrel. It is known as the mannose 6-phosphate receptor homology (MRH) domain.
Pfam PF16226: Domain of unknown function (DUF4885) (family)
This family consists of several uncharacterized proteins around 390 residues in length and is mainly found in various Bacillus subtillis species. This family is predicted to be functional in biosynthesis of rhizocticins and antifungal phosphonate oligopeptides, but the specific function of this family is still unknown.
Pfam PF14995: Transmembrane protein (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 138 and 164 amino acids in length. There are two completely conserved residues (H and E) that may be functionally important and four transmembrane helices. The domains in this family vary in length from 124 to 126 amino acids. The precise function of the protein family is still unknown.
Pfam PF02535: ZIP Zinc transporter (family)
The ZIP family consists of zinc transport proteins and many putative metal transporters.  The main contribution to this family is from  the Arabidopsis thaliana ZIP protein family these proteins are responsible for zinc uptake in the plant. Also found within this family are  C. elegans proteins of unknown function which are annotated as being similar to human growth arrest inducible gene product, although this protein in not found within this family.
Wikipedia: Zinc transporter proteins (Zrt), or simply zinc transporters, are membrane transport proteins of the solute carrier family which control the membrane transport of zinc and regulate its intracellular and cytoplasmic concentrations. They include two major groups: (1) the zinc transporter (ZnT) or solute carrier 30 (SLC30) family, which controls the efflux of zinc from the cytoplasm out of the cell and from the cytoplasm into vesicles; and (2) the zinc importer, Zrt- and Irt-like protein (ZIP), or solute carrier 39A (SLC39A) family, which controls the influx of zinc into the cytoplasm from outside the cell and from vesicles.
Pfam PF22054: BVU_2266-like (family)
This family represents BVU_2266 from Phocaeicola vulgatus ([swissprot:A6L2L1]) and similar sequences from bacteroidetes. Members of this family show 16-stranded beta barrels resembling outer membrane porins. The interior of the barrels is mostly occupied by an insert with a partially helical structure.
Pfam PF03409: Transmembrane glycoprotein (family)
This family of proteins has some GO annotations for positive regulation of growth rate and nematode larval development. This is probably a family of membrane glycoproteins.
Pfam PF19262: Family of unknown function (DUF5905) (family)
This is a family of uncharacterised proteins of unknown function predominantly found in Marseilleviridae.
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 PF12593: Microcystin synthetase C terminal (family)
This domain family is found in bacteria, and is approximately 40 amino acids in length. The family is found in association with [pfam:PF08242], [pfam:PF00501]. There is a conserved YAN sequence motif. Microcystins form a large family of small cyclic heptapeptides harbouring extensive modifications in amino acid residue composition and functional group chemistry. These peptide hepatotoxins contain a range of non-proteinogenic amino acids and unusual peptide bonds, and are typically N-methylated. They are synthesized on large enzyme complexes consisting of non-ribosomal peptide synthetases and polyketide synthases. This family is made up of the C terminal of microcystin synthetase, one of the proteins involved in this synthesis pathway.
Pfam PF04968: CHORD (family)
CHORD represents a Zn binding domain. Silencing of the  C. elegans CHORD-containing gene results in semisterility and embryo lethality, suggesting an essential function of  the wild-type gene in nematode development.
Pfam PF01552: Picornavirus 2B protein (family)
Poliovirus infection leads to drastic alterations in membrane permeability late during infection. Proteins 2B and 2BC enhance membrane permeability.
Pfam PF04569: Protein of unknown function (family)
This family represents a conserved region in a number of uncharacterised plant 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 PF01385: Probable transposase (family)
This family includes IS891, IS1136 and IS1341. DUF1225, [pfam:PF06774], has now been merged into this family.