SII-SWORD/CoKE huggingface dataset:
Pfam PF21266: RRP4, S1 domain (domain)
Exosome complex component RRP4 is a non-catalytic component of the RNA exosome complex which has 3'->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. It consists of a N-terminal beta-sandwich hybrid domain ([pfam:PF14382]), a central S1 domain and a C-terminal KH domain ([pfam:PF15985]). This entry represents the S1 RNA binding domain, which has an OB fold.
Pfam PF18179: SMODS- and Ubiquitin system-associated 2TM effector domain (domain)
Predicted pore-forming effector domain observed exclusively in conserved genome contexts with the SMODS nucleotide synthetases and the bacterial Ubiquitin conjugation systems.
Pfam PF19252: HIND motif (conserved_site)
The Hub1 interacting motif (HIND) is a short motif found in 1 to 3 copies in spliceosomal proteins such as Snu66. The motif is bound by the Hub1 protein.
Pfam PF03225: Viral heat shock protein Hsp90 homologue (family)
This family includes the Beet yellows virus heat shock protein 90 homologue and other hypothetical proteins.
Pfam PF11527: The ARF-like 2 binding protein BART (family)
BART binds specifically to ARL2.GTP with a high affinity however it does not bind to ARL2.GDP. It is thought that this specific interaction is due to BART being the first identified ARL2-specific effector. The function is not completely characterised. BART is predominantly cytosolic but can also be found to be associated with mitochondria. BART is also involved in binding to the adenine nucleotide transporter ANT1.
Pfam PF06611: Protein of unknown function (DUF1145) (family)
This family consists of several hypothetical bacterial 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 PF12446: Protein of unknown function (DUF3682) (disordered)
This domain family is found in eukaryotes, and is typically between 125 and 136 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 PF02691: Vacuolating cyotoxin (repeat)
This family consists of Vacuolating cyotoxin proteins form Proteobacteria. These proteins are an important virulence determinate in H. pylori and induce cytoplasmic vacuolation in a variety of mammalian cell lines.
Pfam PF06321: Major fimbrial subunit protein (FimA) (domain)
This family consists of several Porphyromonas gingivalis major fimbrial subunit protein (FimA) sequences. Fimbriae of Porphyromonas gingivalis, a periodontopathogen, play an important role in its adhesion to and invasion of host cells. The fimA genes encoding fimbrillin (FimA), a subunit protein of fimbriae, have been classified into five types, types I to V, based on nucleotide sequences. It has been found that type II FimA can bind to epithelial cells most efficiently through specific host receptors. Human dental plaque is a multispecies microbial biofilm that is associated with two common oral diseases, dental caries and periodontal disease. There is an inter-species contact-dependent communication system between P. gingivalis and S. cristatus that involces the Arc-A enzyme.
Pfam PF22609: Iron hydrogenase 1-like, iron-sulfur centre-binding domain (domain)
This entry represents a Fe-S centre binding domain found in iron hydrogenases.
Pfam PF13617: YnbE-like lipoprotein (family)
This family includes lipoproteins similar to E. coli YnbE [swissprot:P64448]. Protein in this family are typically 60 amino acids in length and contain an N-terminal lipid attachment site, which has been included in the alignment to increase sensitivity. The specific function of these proteins is unknown.
Pfam PF14147: Sporulation protein YhaL (family)
This family of proteins is involved in sporulation. In B. subtilis its expression is regulated by the early mother-cell-specific transcription factor sigma-E.
Pfam PF18597: Myosin X N-terminal SH3 domain (domain)
This is the N-terminal Sh3 domain found in myosin X. Myosin X is essential for neuritogenesis, wound healing, cancer metastasis and some pathogenic infections. Myosin X is required for filopodia formation and extension.
Pfam PF12992: Domain of unknown function, B. Theta Gene description (DUF3876) (family)
Based on Bacteroides thetaiotaomicron gene BT_0092, a conserved protein found in a conjugate transposon. As seen in gene expression experiments (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2231), it appears to be upregulated in the presence of host or other bacterial species vs when in culture.
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 PF16067: Domain of unknown function (DUF4809) (family)
This family of proteins is found in bacteria. Proteins in this family are typically between 120 and 137 amino acids in length. There is a conserved GGCNAC 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 PF11983: Cell division protein FtsA, C-terminal (family)
This family is the C-terminal region of essential streptococcal FtsA proteins and their homologues. It acts as an intra-molecular switch, triggered by ATP, to promote polymerisation of the whole protein and to attach it to the membrane. FtsA is essential for the formation of the septum that divides fully-grown cells into two daughter cells at cell-division. FtsA anchors the constricting FtsZ ring to the membrane.
Wikipedia: FtsA is a bacterial protein that is related to actin by overall structural similarity and in its ATP binding pocket.
Pfam PF16162: Kiwa protein KwaB-like (family)
This family includes Kiwa protein KwaB from E.coli, a component of antiviral defense system Kiwa composed of KwaA and KwaB. The expression of Kiwa in E.coli (strain MG1655) confers resistance to phages lambda and SECphi18. This family also includes a phylogenetically broad range of bacteria associated with the human gut microbiome. A member of this family from Lactobacillus casei CRL 705 is part of the gene cluster involved in synthesis of bacteriocin toxin.
Pfam PF05388: Carboxypeptidase Y pro-peptide (family)
This family is found at the N terminus of several carboxypeptidase Y proteins and contains a signal peptide and pro-peptide regions.
Pfam PF00530: Scavenger receptor cysteine-rich domain (domain)
These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions.
Wikipedia: In molecular biology, the protein domain SRCR is short for Scavenger receptor cysteine-rich domain. They are found solely in eukaryotes.
These domains are present on the cell membrane and have a role in binding to specific ligands and are often found to be involved with the immune system.
Pfam PF03382: Mycoplasma protein of unknown function, DUF285 (repeat)
This region appears distantly related to leucine rich repeats.
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 PF18196: Chromodomain helicase DNA-binding domain 1 (domain)
This domain can be found in chromodomain helicase DNA-binding protein 1 (Chd1) present in Saccharomyces cerevisiae. Cdh1 proteins have been associated with the efficient assembly and spacing of nucleosomes. The domain consists of four helices, alpha helix 1-4, and can be divided into regions SANT, HL1 and the beta-linker. The HL1 region comprises of some 40 residues specific to budding yeast that are unlikely to form such a prominent feature or perform a conserved function in other species. The domain itself forms part of the DNA-binding domain. Basic residues on the alpha-1 helix are thought to be important for DNA interaction.
Pfam PF16599: Unstructured linker region on PTN13 protein between PDZ (disordered)
This natively unstructured region lies between the first two PDZ domains on long eukaryotic tyrosine-protein phosphatase non-receptor type 13 proteins. The function is not known. However, since each of the PDZ domains binds with a different protein it is likely to be a linker region allowing flexibility between the PDZs.
Pfam PF00897: Orbivirus inner capsid protein VP7 (family)
In BTV, 260 trimers of VP7 are found in the core. The major proteins of the core are VP7 and VP3. VP7 forms an outer layer around VP3.
Pfam PF11750: Protein of unknown function (DUF3307) (family)
This family of 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 PF05913: 6-phospho-N-acetylmuramidase, C-terminal (domain)
This entry represents the C-terminal domain of 6-phospho-N-acetylmuramidase (MupG) found in bacteria. It characterises putative phospho sugar glycosidases found in Gram-negative and -positive species, but mainly in firmicutes. MupG from Staphylococcus aureus, specifically cleaves MurNAc 6P-GlcNAc, a product of cell wall turnover, into the sugars MurNAc 6P and GlcNAc, being involved in cell wall turnover and recycling. Since some species, for example Lactobacillus plantarum, possess several putative paralogs, the substrate specificity of these proteins may not be limited to cell wall sugars, but may include phosphorylated disaccharides in general. Most proteins containing this domain appear to consist of two structural subdomains, as it can be seen in the two available crystal structures of Enterococcus faecalis (PDB:2p0o) and Bacillus cereus (PDB:1X7F). The larger N-terminal domain constitutes a TIM-barrel like structure and the C-terminal domain (this entry) is similar to the cyclophilin family. It should be noted that some proteins lack this domain.
Pfam PF10011: Predicted membrane protein (DUF2254) (family)
Members of this family of bacterial proteins comprises various hypothetical and putative membrane proteins. Their exact function, has not, as yet, been defined.
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 PF13112: Protein of unknown function (DUF3965) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 380 amino acids in length.
Pfam PF16680: T-cell surface glycoprotein CD3 delta chain (domain)
This is an immunoglobulin-like domain. It is found on the T-cell surface glycoprotein CD3 delta chain. CD3delta and CD3epsilon complex together as part of the T-cell receptor complex.
Wikipedia: The immunoglobulin domain, also known as the immunoglobulin fold, is a type of protein domain that consists of a 2-layer sandwich of 7-9 antiparallel β-strands arranged in two β-sheets with a Greek key topology, consisting of about 125 amino acids.
Pfam PF23227: MROH2B-like, HEAT repeats (repeat)
This entry represents HEAT repeats from maestro heat-like repeat-containing proteins, including Maestro heat-like repeat -containing protein family member 2B from mouse (MROH2B, also known as SPIF), which may play a role in the process of sperm capacitation. This region is found at the C-terminal end of MROH2B.
Pfam PF04821: Timeless protein (family)
The timeless gene in Drosophila melanogaster and its homologues in a number of other insects and mammals (including human) are involved in circadian rhythm control. This family includes a related proteins from a number of fungal species.
Wikipedia: Timeless (tim) is a gene in multiple species but is most notable for its role in Drosophila for encoding TIM, an essential protein that regulates circadian rhythm. Timeless mRNA and protein oscillate rhythmically with time as part of a transcription-translation negative feedback loop involving the period (per) gene and its protein.
Pfam PF16253: Domain of unknown function (DUF4909) (family)
This family of proteins is found in bacteria. Proteins in this family are approximately 160 amino acids in length. Several members are associated with vancomycin virulence in Staph. aureus in some way. These proteins are all lipoproteins, carrying the characteristic prokaryotic membrane-attachment site at their N-termini.
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 PF05001: RNA polymerase Rpb1 C-terminal repeat (repeat)
The repetitive C-terminal domain (CTD) of Rpb1 (RNA polymerase Pol II) plays a critical role in the regulation of gene expression. The activity of the CTD is dependent on its state of phosphorylation.
Pfam PF12596: 87kDa Transposase (family)
This domain family is found in eukaryotes, and is typically between 78 and 110 amino acids in length. The family is found in association with [pfam:PF05485]. There are two completely conserved residues (D and G) that may be functionally important. This family is an 87kDa transposase protein which catalyses both the precise and imprecise excision of a nonautonomous P transposable element.
Pfam PF00620: RhoGAP domain (domain)
GTPase activator proteins towards Rho/Rac/Cdc42-like small GTPases.
Wikipedia: RhoGAP domain  is an evolutionary conserved protein domain of 
GTPase activating proteins towards Rho/Rac/Cdc42-like small GTPases.
Pfam PF15716: Domain of unknown function (DUF4672) (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 165 and 199 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 PF23655: LYR motif containing domain (domain)
This domain is found in uncharacterised plant proteins. It is predicted to fold into a three helical up-and-down bundle. It shares sequence similarity to LYR motif containing domains and has the motif conserved.
Pfam PF01493: GXGXG motif (family)
This domain is found in glutamate synthase, tungsten formylmethanofuran dehydrogenase subunit c (FwdC) and molybdenum formylmethanofuran dehydrogenase subunit c (FmdC). A repeated G-XX-G-XXX-G motif is seen in the alignment.
Pfam PF07102: Putative nuclease YbcO (family)
This family includes YbcO (pdbe:3G27), a putative  nuclease from E. coli. Proteins in the entry have been predicted to have the His-Me finger nuclease domain and may act as a Recombinase that participates in DNA repair and replication.
Pfam PF24084: Domain of unknown function (DUF7369) (domain)
This entry represents a small family of uncharacterised phage proteins. Structure prediction suggests that this protein forms a small domain that likely forms a stable dimeric complex. In this predicted complex there is a C-terminal alpha helix that binds to the opposite oligomer in a helix swapped arrangement.
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 PF15100: TMEM187 protein family (family)
The function of this family, TMEM187, is not known, however it is predicted to be a multi-pass membrane protein. Members of this family are as yet uncharacterised. This protein family is also alternatively named ITBA1. This family of proteins are found in eukaryotes. Proteins in this family are typically between 239 and 267 amino acids in length.
Pfam PF03924: CHASE domain (domain)
This domain is found in the extracellular portion of receptor-like proteins - such as serine/threonine kinases and adenylyl cyclases. This is a ligand-binding domain that binds cytokinin (Matilla et.al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).
Wikipedia: The CHASE domain is an extracellular protein domain, which is found in transmembrane receptor from bacteria, lower eukaryotes and plants. It has been named CHASE because of its presence in diverse receptor-like proteins with histidine kinase and nucleotide cyclase domains. The CHASE domain is 200-230 amino acids long and always occurs N-terminally in extracellular or periplasmic locations, followed by an intracellular tail housing diverse enzymatic signalling domains such as histidine kinase, adenyl cyclase, GGDEF-type nucleotide cyclase and EAL-type phosphodiesterase domains, as well as non-enzymatic domains such PAS, GAF, phosphohistidine and response regulatory domains. The CHASE domain is predicted to bind diverse low molecular weight ligands, such as the cytokinin-like adenine derivatives or peptides, and mediate signal transduction through the respective receptors.
Pfam PF15572: Immunity protein 45 (family)
A predicted immunity protein with an alpha+beta fold and a conserved C-terminal tryptophan residue. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, usually containing a domain of the Tox-ColE3 family.
Pfam PF24601: DOP1 TPR domain (repeat)
DOP1 is the founding member of the Dopey family and is required for correct cell morphology and spatiotemporal organisation of multicellular structures in the filamentous fungus Emericella nidulans (Aspergillus nidulans). Dop1 homologues are found in mammals, where they may play a role in regulating membrane trafficking of cargo proteins. Together with ATP9A and MON2, it regulates SNX3 retromer-mediated endosomal sorting of WLS away from lysosomal degradation. In S. cerevisiae, it is required for normal cellular morphogenesis. Loss of Dop1 activity affects endosome to Golgi transport and causes a severe perturbation of the organization of the endoplasmic reticulum; Mon2 a relative of large Arf exchange factors, recruits Dop1 to the Golgi apparatus. These are long proteins consisting of TPRs; this entry represents a domain found near the near the C-terminal of DOP1.
Pfam PF03645: Tctex-1 family (family)
Tctex-1 is a dynein light chain. It has been shown that Tctex-1 can bind to the cytoplasmic tail of rhodopsin. C-terminal rhodopsin mutations responsible for retinitis pigmentosa inhibit this interaction.
Pfam PF12790: Type VI secretion lipoprotein, VasD, EvfM, TssJ, VC_A0113 (family)
One of the virulence mechanisms of E coli is the production of toxins which it produces from dedicated machineries called secretion systems. Seven secretion systems have been described, which assemble from 3 to up to more than 20 subunits. These secretion systems derive from or have co-evolved with bacterial organelles such as ABC transporters (type I), type IV pili (type 2), flagella (type 3), or conjugative machines (type IV). The type VI secretion system (T6SS) is present in most pathogens that have contact with animals, plants, or humans. SciN is a lipoprotein tethered to the outer membrane and expressed in the periplasm of E coli and is essential for T6S-dependent secretion of the Hcp-like SciD protein and for biofilm formation.
Pfam PF19908: Family of unknown function (DUF6381) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001558) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the cosmomycin C biosynthetic gene cluster from Streptomyces sp. CNT302. This family appears to be predominantly found in actinobacteria.
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 PF21975: ASNSD1 upstream open reading frame protein (family)
This protein family includes human ASNSD1 upstream open reading frame protein (ASNSD1-SEP, for small/short open reading frame -encoded polypeptide) and similar sequences predominantly found in vertebrates. ASNSD1-SEP is a subunit of the prefoldin-like (PFDL) module of the PAQosome, an 11-subunit chaperone involved in the biogenesis of several human protein complexes. It shows great structural homology to beta-prefoldin.
Pfam PF16943: Cag pathogenicity island, type IV secretory system (family)
T4SS_CagC is a family of putative pathogenicity island, type IV, conjugal DNA-protein transfer, secretory system proteins from Gram-negative bacteria.
Pfam PF15648: Restriction endonuclease fold toxin 5 (family)
A predicted toxin of the restriction endonuclease fold present in bacterial polymorphic toxin systems. In bacterial polymorphic toxin systems, the toxin is exported by the type 2, type 5, type 6, or PrsW-peptidase dependent secretion system. Versions of this domain are also found in caudoviruses.
Pfam PF08142: AARP2CN (NUC121) domain (domain)
This domain is the central domain of AARP2.  It is weakly similar to  the GTP-binding domain of elongation factor TU.