SII-SWORD/CoKE huggingface dataset:
Pfam PF12109: CXCR4 Chemokine receptor N terminal (domain)
CXCR4 and its ligand stromal cell-derived factor-1 (a.k.a. CXCL12) are essential for proper fetal development. CXCR4 is also the major coreceptor for T-tropic strains of human immunodeficiency virus 1 (HIV-1), and SDF-1 inhibits HIV-1 infection. Additionally, SDF-1 and CXCR4 mediate cancer cell migration and metastasis. The N terminal domain of most chemokine receptors is the ligand binding domain and so the N terminal domain of CXCR4 is the binding site for SDF-1.
Pfam PF00455: DeoR C terminal sensor domain (domain)
The sensor domains of the DeoR are catalytically inactive versions of the ISOCOT fold, but retain the substrate binding site. DeorC  senses diverse sugar derivatives such as deoxyribose nucleoside  (DeoR), tagatose phosphate (LacR), galactosamine (AgaR), myo-inositol (Bacillus IolR) and L-ascorbate (UlaR). It can also bind L-ascorbate 6-phosphate, agrocinopines, sn-glycerol 3-phosphate, and sulfoquinovose (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).
Pfam PF11503: YNR034W-A-like (family)
This family of proteins is predominantly found in Saccharomycetales, including YNR034W-A (also known as Ego4) and YCR075W-A (Ego2) from Saccharomyces cerevisiae. Ego2 is a component of the yeast EGO complex (EGOC), which is responsible for the amino acid-dependent activation of the target of rapamycin complex 1 (TORC1). Ego2 adopts a Roadblock domain fold that consists of a central core beta-sheet of five anti-parallel beta-strands flanked by a long alpha-helix on the bottom side. Ego4 shows a similar configuration. It interacts with the GTPase Gtr2, but its specific function remains unknown.
Pfam PF23973: Family of unknown function (DUF7299) (family)
This entry represents a small family of uncharacterised phage 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 PF10017: Histidine-specific methyltransferase, SAM-dependent (family)
The mycobacterial members of this family are expressed from part of the ergothioneine biosynthetic gene cluster. EGTD is the histidine methyltransferase that transfers three methyl groups to the alpha-amino moiety of histidine, in the first stage of the production of this histidine betaine derivative that carries a thiol group attached to the C2 atom of an imidazole ring.
Pfam PF07715: TonB-dependent Receptor Plug Domain (domain)
The Plug domain has been shown to be an independently folding subunit of the TonB-dependent receptors (). It acts as the channel gate, blocking the pore until the channel is bound by ligand. At this point it under goes conformational changes opens the channel.
Wikipedia: Outer membrane receptors, also known as TonB-dependent receptors, are a family of beta barrel proteins named for their localization in the outer membrane of gram-negative bacteria. TonB complexes sense signals from the outside of bacterial cells and transmit them into the cytoplasm, leading to transcriptional activation of target genes.
TonB-dependent receptors in gram-negative bacteria are associated with the uptake and transport of large substrates such as iron siderophore complexes and vitamin B12.
Pfam PF22885: Domain of unknown function (DUF7020) (domain)
This entry represents a family of phage proteins of unknown function. AlphaFold shows confident dimer interaction.
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 PF18096: THUMP domain-like (domain)
This is a domain of unknown function found in bacteria.
Pfam PF00109: Beta-ketoacyl synthase, N-terminal domain (domain)
The structure of beta-ketoacyl synthase is similar to that of the  thiolase family ([pfam:PF00108]) and also chalcone synthase. The active site of beta-ketoacyl synthase is located between the N and C-terminal domains.  The N-terminal domain contains most of  the structures involved in dimer formation and also the active site  cysteine.
Wikipedia: In molecular biology, Beta-ketoacyl-ACP synthase EC 2.3.1.41, is an enzyme involved in fatty acid synthesis. It typically uses malonyl-CoA as a carbon source to elongate ACP-bound acyl species, resulting in the formation of ACP-bound β-ketoacyl species such as acetoacetyl-ACP.
Pfam PF03937: Flavinator of succinate dehydrogenase (domain)
This family includes the highly conserved mitochondrial and bacterial proteins Sdh5/SDHAF2/SdhE. Both yeast and human Sdh5/SDHAF2 interact with the catalytic subunit of the succinate dehydrogenase (SDH) complex, a component of both the electron transport chain and the tricarboxylic acid cycle. Sdh5 is required for SDH-dependent respiration and for Sdh1 flavination (incorporation of the flavin adenine dinucleotide cofactor). Mutational inactivation of Sdh5 confers tumor susceptibility in humans. Bacterial homologues of Sdh5, termed SdhE, are functionally conserved being required for the flavinylation of SdhA and succinate dehydrogenase activity. Like Sdh5, SdhE interacts with SdhA. Furthermore, SdhE was characterised as a FAD co-factor chaperone that directly binds FAD to facilitate the flavinylation of SdhA. Phylogenetic analysis demonstrates that SdhE/Sdh5 proteins evolved only once in an ancestral alpha-proteobacteria prior to the evolution of the mitochondria and now remain in subsequent descendants including eukaryotic mitochondria and the alpha, beta and gamma proteobacteria. This family was previously annotated in Pfam as being a divergent TPR repeat but structural evidence has indicated this is not true. The E. coli protein, YgfY also acts as the antitoxin to the membrane-bound toxin family Cpta, [pfam:PF13166], whose E. coli member YgfX, expressed from the same operon as YgfY.
Wikipedia: Succinate dehydrogenase complex subunit C, also known as succinate dehydrogenase cytochrome b560 subunit, mitochondrial, is a protein that in humans is encoded by the SDHC gene. This gene encodes one of four nuclear-encoded subunits that comprise succinate dehydrogenase, also known as mitochondrial complex II, a key enzyme complex of the tricarboxylic acid cycle and aerobic respiratory chains of mitochondria. The encoded protein is one of two integral membrane proteins that anchor other subunits of the complex, which form the catalytic core, to the inner mitochondrial membrane. There are several related pseudogenes for this gene on different chromosomes. Mutations in this gene have been associated with pheochromocytomas and paragangliomas. Alternatively spliced transcript variants have been described.
Pfam PF01827: FTH domain (domain)
This presumed domain is likely to be a protein-protein interaction module. It is found in many proteins from C. elegans. The domain is found associated with the F-box [pfam:PF00646]. This domain is named FTH after FOG-2 homology domain.
Pfam PF12813: XPG domain containing (domain)
This family is largely of fungal proteins and is related to the XP-G protein family.
Pfam PF17130: beta-barrel domain of carboxypeptidase M99 (domain)
This is the central, beta-barrel, domain of the metallo-carboxypeptidase that maintains helical cell-shape in Helicobacter. It shows a novel fold. It has a highly positively charged surface which contributes to a high overall isoelectric point. A calcium-binding channel is formed from residues in the C-terminal Ig-like domain in conjunction with some of the long side-chains of residues from strands beta-14 and beta-18 of this domain.
Pfam PF03084: Reoviral Sigma1/Sigma2 family (family)
Reoviruses are double-stranded RNA viruses. They lack a membrane envelope and their capsid is organised in two concentric icosahedral layers: an inner core and an outer capsid layer. The sigma1 protein is found in the outer capsid, and the sigma2 protein is found in the core. There are four other kinds of protein (besides sigma2) in the core, termed lambda 1-3, mu2. Interactions between sigma2 and lambda 1 and lambda 3 are thought to initiate core formation, followed by mu2 and lambda2. Sigma1 is a trimeric protein, and is positioned at the 12 vertices of the icosahedral outer capsid layer. Its N-terminal fibrous tail, arranged as a triple coiled coil, anchors it in the virion, and a C-terminal globular head interacts with the cellular receptor.  These two parts form by separate trimerisation events. The N-terminal fibrous tail forms on the polysome, without the involvement of ATP or chaperones. The post- translational assembly of the C-terminal globular head involves the chaperone activity of Hsp90, which is associated with  phosphorylation of Hsp90 during the process. Sigma1 protein acts as a cell attachment protein, and determines viral virulence, pathways of spread, and tropism. Junctional adhesion molecule has been identified as a receptor for sigma1. In type 3  reoviruses, a small region, predicted to form a beta sheet, in the N-terminal tail was found to bind target cell surface sialic acid (i.e. sialic acid acts as a co-receptor) and promote apoptosis. The sigma1 protein also binds to the lambda2 core protein.
Pfam PF15676: Six6 opposite strand transcript 1 family (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 114 and 587 amino acids in length. The function is not known.
Pfam PF06055: Exopolysaccharide synthesis, ExoD (family)
Among the bacterial genes required for nodule invasion are the exo genes. These genes are involved in the production of an extracellular polysaccharide.  Mutations in the exoD result in altered exopolysaccharide production and defects in nodule invasion.
Pfam PF21012: Family of unknown function (DUF6850) (domain)
This bacterial protein forms a likely integral membrane beta barrel 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 PF04875: Protein of unknown function, DUF645 (family)
This family includes several uncharacterised proteins from Vibrio cholerae. There is some doubt regarding the existence of these proteins, they are encoded by open reading frames contained within a repeated region in the Vibrio superintegron.
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 PF18748: 5-hmdU DNA kinase (family)
5-hmdU DNA kinase (HMUDK) and 5-hmdU DNA kinase 1 (HDMU1) are P-loop nucleotide kinases that phosphorylates 5-hydroxymethyluracil (5hmdU) into 5-phosphomethyl-2'-deoxyuridine (5-PmdU) on DNA as a step in the pathway leading to thymidine hypermodifications in the viral genome. HMUDK also transfers glutamate to 5-pyrophosphoryloxymethyldeoxyuridine (5-PPmdU) to produce 5-Nalpha-glyutamylthymidine (Nalpha-GluT). These modifications probably prevent degradation of viral genome by the host restriction-modification antiviral defense system.
Pfam PF24324: ZMYND11/ZMYD8, MYND zinc finger (domain)
This entry represents the MYND zinc finger from ZMYND11 and ZMYND8 from human and relates sequences. These are chromatin readers that recognise methylated histones; ZMYND11 recognises H3.3 trimethylated at 'Lys-36' (H3.3K36me3) and regulates RNA polymerase II elongation. ZMYND8 recognises histone H3.1 dimethylated at 'Lys-36' and histone H4 acetylated at 'Lys-16' and histone H3 methylated at 'Lys-4' and histone H4 acetylated at 'Lys-14'.
Pfam PF05082: Rop-like (family)
This family contains several uncharacterised bacterial proteins. These proteins are found in nitrogen fixation operons so are likely to play some role in this process. They consist of two alpha helices which are joined by a four residue linker. The helices form an antiparallel bundle and cross towards their termini. They are likely to form a rod-like dimer. They have structural similarity to the regulatory protein Rop, [pfam:PF01815].
Pfam PF19474: Family of unknown function (DUF6011) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000413) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). This  family includes a protein encoded by the pyoverdin biosynthetic  gene cluster from Pseudomonas protegens Pf-5.
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 PF20103: Domain of unknown function (DUF6493) (repeat)
This presumed domain is functionally uncharacterised. This domain is found in bacteria, and is approximately 470 amino acids in length. This domain may consist of TPRs.
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 PF12677: Domain of unknown function (DUF3797) (family)
This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 50 amino acids in length. There is a conserved CGN 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 PF13080: Protein of unknown function (DUF3926) (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 46 and 63 amino acids in length. There is a single completely conserved residue P that may be functionally important.
Pfam PF09874: Predicted membrane protein (DUF2101) (family)
This domain, found in various archaeal and 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 PF06099: Phenol hydroxylase subunit (family)
This family consists of several bacterial phenol hydroxylase subunit proteins which are part of a multicomponent phenol hydroxylase. Some bacteria can utilise phenol or some of its methylated derivatives as their sole source of carbon and energy. The first step in this process is the conversion of phenol into catechol. Catechol is then further metabolised via the meta-cleavage pathway into TCA cycle intermediates.
Pfam PF14010: Phosphoenolpyruvate carboxylase (family)
This family of phosphoenolpyruvate carboxylases is based on seqeunces not picked up by the model for PEPcase, PF00311. Most of the family members are from Archaea.
Pfam PF09982: Outer membrane protein LpxR (family)
The outer membrane protein LpxR from Salmonella typhimurium is a lipid A deacylase that catalyses the removal of the 3'-acyloxyacyl moiety from lipid A. This protein folds into a 12-stranded antiparallel beta-barrel with the N- and C- terminal ends pointing towards the periplasm and three extracellular loops consisting of alpha-helical regions at the opposite side of the beta-barrel.
Pfam PF23519: Apicomplexa microprotein (family)
This protein family includes uncharacterised microproteins encoded by small open reading frames (smORFs) from apicomplexa, including [swissprot:A7ARR8] from the parasite Babesia bovis.
Pfam PF12916: Protein of unknown function (DUF3834) (family)
This family is likely to be related to solute-binding lipo-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 PF17610: Family of unknown function (DUF5505) (family)
This is a family of unknown function found in Alphabaculovirus.
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 PF05586: Anthrax receptor C-terminus region (family)
This region is found in the putatively cytoplasmic C-terminus of the anthrax receptor.
Pfam PF04199: Putative cyclase (family)
Proteins in this family are thought to be cyclase enzymes.  They are found in proteins involved in antibiotic synthesis.  However they are also found in organisms that do not make antibiotics pointing to a wider role for these proteins. The proteins contain a conserved motif HXGTHXDXPXH that is likely to form part of the active site.
Pfam PF24168: Straight fiber protein PB4 spike domain (domain)
This entry represents the Straight fiber protein PB4 spike found in T5-like bacteriophages. PB4 along with PB3, forms the central straight fiber, bearing the receptor binding protein PB5 at its C terminus. Upon PB5 binding to the host receptor FhuA, the central fiber reorganises and undergoes structural rearrangements that lead to its bending, bringing PB3 close to the host membrane for anchoring. In this process the PB4 spike undergoes structural rearrangement as well. The PB4 spike forms a hetero trimer containing several small distinct subdomains some of which defining a beta-helix, others beta-prism.
Pfam PF17813: RET Cadherin like domain 4 (domain)
RET is a single transmembrane-spanning receptor tyrosine kinase (RTK) that plays critical roles in the development of vertebrates. Structural analysis indicate that the ligand-binding RET ectodomain (RET-ECD) contains four consecutive cadherin-like domains (CLD1-CLD4) followed by a membrane-proximal cysteine-rich domain (CRD). This entry relates to CLD4 which is required for CRD folding.
Pfam PF04792: V antigen (LcrV) protein (family)
Yersinia pestis, the aetiologic agent of plague, secretes a set of environmentally regulated, plasmid pCD1-encoded virulence proteins termed Yops and V antigen (LcrV) by a type III secretion mechanism. LcrV is a multifunctional protein that has been shown to act at the level of secretion control by binding the Ysc inner-gate protein LcrG and to modulate the host immune response by altering cytokine production.  LcrV is also necessary for full induction of low-calcium response (LCR) stimulon virulence gene transcription.  Family members are not confined to Yersinia pestis.
Wikipedia: In molecular biology, LcrV is a protein found in Yersinia pestis and several other bacterial species. It forms part of the Yersinia pestis virulence protein factors that also includes all Yops, or Yersinia outer protein, but the name has been kept out of convention. LcrV's main function is not actually known, but it is essential for the production of other Yops.
Pfam PF14127: Domain of unknown function (DUF4294) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 192 and 226 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 PF12945: Flagellar protein YcgR (family)
This domain is found N terminal to [pfam:PF07238]. Proteins which contain YcgR domains are known to interact with the flagellar switch-complex proteins FliG and FliM.  This interaction results in a reduction of torque generation and induces CCW motor bias. This family contains members not captured by [pfam:PF07317]. This domain has a beta-barrel fold PilZ domains and lack the C-terminal alpha- helix.
Pfam PF18410: Basic tilted helix bundle domain (domain)
This domain is found on the N-terminal region of FKBPs such as FKBP25 and in the core region of E3 ubiquitin ligase HectD1. It adopts a compact 5-helix bundle, hence termed BTHB (Basic Tilted Helix Bundle) domain. In FKBP25, it has been suggested to have a role in regulating the association state of nucleosomes by interacting with nucleolin. Moreover, this basic domain in FKBP25 forms alternative complexes with other chromatin-related proteins, such as the HDAC1, HDAC2, and the transcriptional regulator YY1, the DNA binding activity of which is enhanced on binding FKBP25. Structural analysis of this fold suggests that the DNA binding properties of FKBP25 and HectD1 are presented by the conserved basic region.
Pfam PF13170: Protein of unknown function (DUF4003) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 327 and 345 amino acids in length.
Pfam PF21521: Myosin VI, lever arm (domain)
This entry represents the lever arm from the unconventional myosin 6 proteins, the only class of myosin that has been shown to move toward the minus-end of actin filaments. This domain comprises an insert (Insert2) that binds the structural calmodulin (CaM) followed by the IQ motif and a proximal tail domain described as the lever arm extension. The lever arm amplifies the conformational changes in the motor into a movement on the order of nanometers known as the powerstroke.