SII-SWORD/CoKE huggingface dataset:
Pfam PF02119: Flagellar P-ring protein (family)
The flgH, flgI and fliF genes of Salmonella typhimurium encode the major proteins for the L, P and M rings of the flagellar basal body . In fact, the basal body consists of four rings (L,P,S and M) surrounding the flagellar rod, which is believed to transmit motor rotation to the filament . The M ring is integral to the inner membrane of the cell, and may be connected to the rod via the S (supramembrane) ring, which lies just distal to it. The L and P rings reside in the outer membrane and periplasmic space, respectively.

The sequences of the FlgH, FlgI and FliF gene products have been determined . FlgH and FlgI, which are exported across the cell membrane to their destinations in the outer membrane and periplasmic space, have typical N-terminal cleaved signal-peptide sequences . FlgH is predicted to have an extensive Î²-sheet structure, in keeping with other outer membrane proteins, and FlgI is thought to have even more Î²-structure content . Several aspects of the DNA sequence of these genes and their surrounds suggest complex regulation of the flagellar gene system.
Pfam PF22525: S13-like H2TH domain (domain)
This entry represents helix-two turn-helix (H2TH) domains that is found in ribosomal S13 proteins and related proteins.
Pfam PF15139: Protein CFAP95 (family)
This family includes Protein CFAP95, whose function is unknown, found in eukaryotes. Proteins in this family are typically between 160 and 220 amino acids in length.
Pfam PF11345: Protein of unknown function (DUF3147) (family)
Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently no function is known.
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 PF20115: Family of unknown function (DUF6505) (family)
This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 100 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 PF23039: TMEM132 cohesin-like domain (domain)
This is the third domain of TMEM132 family members which includes TMEM132A-E. These are transmembrane proteins that that regulate neuronal structure and function. In mammalian cells, they may regulate NAP1 in the WAVE regulatory complex (WRC) to finely modulate actin nucleation, cellular cytoskeletal and morphological changes. TMEM132D member has been associated with panic disorders, anxiety and major depressive disorders. This is a beta-sandwich domain closely related to cohesin, which may be involved in cellular adhesion.
Pfam PF23199: Domain of unknown function (DUF7060) (domain)
This entry represents a domain found at the C-terminal of a group of proteins from nematodes, members of the BPI/LBP/Plunc family of proteins which share homology with cholesterol ester transfer protein (CETP) and phospholipid transfer protein (PLTP). The exact function of these proteins is unknown, however, according to their structure predictions and homology to CEPT/PLTP, they may play a role in lipid binding.
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 PF19363: Family of unknown function (DUF5939) (family)
This presumed domain is functionally uncharacterised. This domain family is found in a wide variety of bacteria such as proteobacteria, spirochaetes, firmicutes and actinobacteria, and is approximately 280 amino acids in length. The family is found in to the N-terminus of [pfam:PF00211].
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 PF15106: TMEM156 protein family (family)
The function of this family of transmembrane proteins, TMEM 156, has not, as yet, been determined. Members of this family are as yet uncharacterised. This family of proteins are found in eukaryotes. Proteins in this family are approximately 310 amino acids in length. In humans, the gene encoding this protein is located in the chromosomal position, 4p14.
Pfam PF15252: Domain of unknown function (DUF4589) (family)
This protein family is a domain of unknown function. The precise function of the protein domain remains to be elucidated. This family of proteins is found in eukaryotes and are typically between 215 and 293 amino acids in length. The protein contains two conserved sequence motifs: SSS and KST.
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 PF09484: CRISPR-associated protein TM1802 (cas_TM1802) (family)
Clusters of short DNA repeats with non-homologous spacers, which are found at regular intervals in the genomes of phylogenetically distinct prokaryotic species, comprise a family with recognisable features. This family is known as CRISPR (short for Clustered, Regularly Interspaced Short Palindromic Repeats). A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This minor cas protein is found in at least five prokaryotic genomes: Methanosarcina mazei, Sulfurihydrogenibium azorense, Thermotoga maritima, Carboxydothermus hydrogenoformans, and Dictyoglomus thermophilum, the first of which is archaeal while the rest are bacterial.
Pfam PF06910: Male enhanced antigen 1 (MEA1) (family)
This family consists of several mammalian male enhanced antigen 1 (MEA1) proteins. The Mea-1 gene is found to be localised in primary and secondary spermatocytes and spermatids, but the protein products are detected only in spermatids. Intensive transcription of Mea-1 gene and specific localisation of the gene product suggest that Mea-1 may play a important role in the late stage of spermatogenesis.
Pfam PF10184: Uncharacterized conserved protein (DUF2358) (domain)
DUF2358 is a family of conserved proteins found from plants to humans. The function 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 PF15429: Domain of unknown function (DUF4628) (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 152 and 673 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 PF12011: RNA helicase NPH-II (family)
RNA helicase NPH-II or I8 is found in Poxviridae. It is essential for viral replication and plays an important role during  transcription of early mRNAs, presumably by preventing R-loop formation behind the elongating RNA polymerase.  It acts as NTP-dependent helicase that catalyzes unidirectional unwinding of 3'tailed duplex RNAs. It might also play a role  in the export of newly synthesized mRNA chains out of the  core into the cytoplasm and is required for propagation of viral particles.
Pfam PF06633: Protein of unknown function (DUF1155) (family)
This family consists of several Cucumber mosaic virus ORF IIB proteins. The function of this family is unknown.
Pfam PF17519: Family of unknown function (DUF5444) (family)
This is a family of unknown function found in Enterobacterales.
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 PF01746: tRNA (Guanine-1)-methyltransferase (family)
This is a family of tRNA (Guanine-1)-methyltransferases [ec:2.1.1.31]. In E.coli K12 this enzyme catalyses the conversion of a guanosine residue to N1-methylguanine in position 37, next to the anticodon, in tRNA.
Pfam PF13538: UvrD-like helicase C-terminal domain (domain)
This domain is found at the C-terminus of a wide variety of helicase enzymes. This domain has a AAA-like structural fold.
Pfam PF18050: Cyclophilin-like family (domain)
This entry represents a family of cyclophilin-like proteins found in a range of bacterial species.
Pfam PF20981: AAR2 N-terminal domain (domain)
This family consists of several eukaryotic AAR2-like proteins. The yeast protein AAR2 is involved in splicing pre-mRNA of the a1 cistron and other genes that are important for cell growth. This entry represents the N-terminal Ig-like domain.
Pfam PF14856: Pathogen effector; putative necrosis-inducing factor (family)
The domain corresponds to the mature part of the Ecp2 effector protein from the tomato pathogen Cladopsorium fulvum. Effectors are low molecular weight proteins that are secreted by bacteria, oomycetes and fungi to manipulate their hosts and adapt to their environment. Ecp2 is a 165 amino acid secreted protein that was originally identified as a virulence factor in C. fulvum, since disruption reduces virulence of the fungus on tomato plants. We have recently determined that Ecp2 is a member of a novel, widely distributed and highly diversified within the fungal kingdom multigene superfamily, which we have designated Hce2, for Homologs of C. fulvum Ecp2 effector. Although Ecp2 is present in most organisms as a small secreted protein, the mature part of this protein can be found fused to other protein domains, including the fungal Glycoside Hydrolase family 18, Glyco_hydro_18 [pfam:PF00704] and other, unknown, protein domains. The intrinsic function of Ecp2 remains unknown but it is postulated by that it is a necrosis-inducing factor in plants that serves pathogenicity on the host.
Pfam PF00245: Alkaline phosphatase (domain)
This entry represents alkaline phosphatases (3.1.3.1) (ALP), which act as non-specific phosphomonoesterases to hydrolyse phosphate esters, optimally at high pH. The reaction mechanism involves the attack of a serine alkoxide on a phosphorus of the substrate to form a transient covalent enzyme-phosphate complex, followed by the hydrolysis of the serine phosphate. Alkaline phosphatases are found in all kingdoms of life, with the exception of some plants. Alkaline phosphatases are metalloenzymes that exist as a dimer, each monomer binding metal ions. The metal ions they carry can differ, although zinc and magnesium are the most common. For example, Escherichia coli alkaline phosphatase (encoded by phoA) requires the presence of two zinc ions bound at the M1 and M2 metal sites, and one magnesium ion bound at the M3 site . However, alkaline phosphatases from Thermotoga maritima and Bacillus subtilis require cobalt for maximal activity .
Wikipedia: The enzyme alkaline phosphatase is a phosphatase with the physiological role of dephosphorylating compounds. The enzyme is found across a multitude of organisms, prokaryotes and eukaryotes alike, with the same general function, but in different structural forms suitable to the environment they function in. Alkaline phosphatase is found in the periplasmic space of E. coli bacteria. This enzyme is heat stable and has its maximum activity at high pH. In humans, it is found in many forms depending on its origin within the body – it plays an integral role in metabolism within the liver and development within the skeleton. Due to its widespread prevalence in these areas, its concentration in the bloodstream is used by diagnosticians as a biomarker in helping determine diagnoses such as hepatitis or osteomalacia.
Pfam PF05120: Gas vesicle protein G (domain)
Gas vesicles are intracellular, protein-coated, and hollow organelles found in cyanobacteria and halophilic archaea. They are permeable to ambient gases by diffusion and provide buoyancy, enabling cells to move upwards in water to access oxygen and/or light. Proteins containing this family are found in gas vesicles and play a role in the formation of gas vesicles.
Pfam PF10942: Protein of unknown function (DUF2619) (family)
This bacterial family of proteins has no known function. This family includes the B. subtilis YqhV protein which is found just upstream of the SpoIIIA operon, suggesting it may play a role in sporulation or its regulation. The protein is composed of three hydrophobic alpha helices that may form transmembrane helices.
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 PF02353: Mycolic acid cyclopropane synthetase (family)
This family consist of Cyclopropane-fatty-acyl-phospholipid synthase or CFA synthase [ec:2.1.1.79] this enzyme catalyse the reaction: S-adenosyl-L-methionine + phospholipid olefinic fatty acid  S-adenosyl-L-homocysteine + phospholipid cyclopropane fatty acid.
Pfam PF15088: NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial (family)
Subunit C1 is a accessory subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I), that is believed not to be involved in catalysis. NADH dehydrogenase complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone .
Wikipedia: Respiratory complex I, EC 7.1.1.2 is the first large protein complex of the respiratory chains of many organisms from bacteria to humans. It catalyzes the transfer of electrons from NADH to coenzyme Q10 (CoQ10) and translocates protons across the inner mitochondrial membrane in eukaryotes or the plasma membrane of bacteria.
Pfam PF08064: UME (NUC010) domain (domain)
This domain is characteristic of UVSB PI-3 kinase, MEI-41 and ESR1.
Pfam PF23158: Domain of unknown function (DUF7056) (domain)
This is a presumed domain found in a group of uncharacterised sequences from bacteria. According to structure predictions, this domain is found towards the C-terminal, after a glycosyltransferase domain ([pfam:PF13231]), and it may adopt an alpha/beta structure. In some instances, this domain is followed by and all-beta domain at the very C-terminal of the sequences ([pfam:PF23157]). The function of this domain 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 PF10607: CTLH/CRA C-terminal to LisH motif domain (domain)
RanBPM is a scaffolding protein and is important in regulating cellular function in both the immune system and the nervous system.  This domain is at the C-terminus of the proteins and is the binding domain for the CRA motif (for CT11-RanBPM), which is comprised of approximately 100 amino acids at the C terminal of RanBPM. It was found to be important for the interaction of RanBPM with fragile X messenger ribonucleoprotein 1 (FMRP), but its functional significance has yet to be determined. This region contains CTLH and CRA domains annotated by SMART; however, these may be a single domain, and it is refereed to as a C-terminal to LisH motif.
Pfam PF22477: Replication initiation protein, N-terminal (domain)
This domain is found at the N-terminal end of Replication initiation protein from Staphylococcus aureus (RepD) and similar bacterial sequences. RepD shows similarity with the extended beta-sheet in TATA binding protein (TBP).
Pfam PF21520: Integrin alpha-X-like, Ig-like domain 3 (domain)
This domain is found in Integrin alpha-X from humans (ITGAX) and similar proteins predominantly found in vertebrates. ITGAX is a receptor for fibrinogen. This region composed of an immunoglobulin-like domain.
Pfam PF04250: Protein of unknown function (DUF429) (family)
This is a family of uncharacterised 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 PF06991: Microfibril-associated/Pre-mRNA processing (family)
MFAP1 was first named for proteins associated with microfibrils which are an important component of the extracellular matrix (ECM) of many tissues. For example, MFAP1 has been shown to be associated with elastin-like fibres at the base of Schlemm's canal endothelium cells, in the juxtacanalicular tissue, and in the uveal region. Based on its role in the ECM and the proximity of the MFAP1 gene to FBN1 it was hypothesised that mutations in MFAP1 contributed to heritable diseases affecting microfibrils, Marfan syndrome but this has now been shown not to be the case.  MFAP1 has also been shown to interact directly with certain pre-mRNA processing factor proteins, Prps, which are also spliceosome components and is thus required for pre-mRNA processing. MAFP1 bound to Pr38 of yeast is necessary for cells in vivo to progress from G2 to M phase.
Pfam PF23077: Zinc finger protein 462, first C2H2 zinc finger (domain)
This domain is found in the human Zinc finger protein 462 and related proteins. This protein is involved in transcription by regulating chromatin structure and organisation. ZNF462 is a multidomain protein that contains a number of classical C2H2 zinc fingers. This entry represents one of them.
Pfam PF08091: Spider insecticidal peptide (domain)
This family consists of insecticidal peptides isolated  from venom of spiders of Aptostichus schlingeri and  Calisoga sp. Nine insecticidal peptides were isolated  from the venom of the Aptostichus schlingeri spider and  seven of these toxins cause flaccid paralysis to insect  larvae within 10 min of injection. However, all nine  peptides were lethal within 24 hours. The structure of Aps III was solved and shown to be an atypical knottin peptide with four disulphide bridges.
Pfam PF10568: Outer mitochondrial membrane transport complex protein (family)
The TOM37 protein is one of the outer membrane proteins that make up the TOM complex for guiding cytosolic mitochondrial beta-barrel proteins from the cytosol across the outer mitochondrial membrane into the intra-membrane space. In conjunction with TOM70 it guides peptides without an MTS into TOM40, the protein that forms the passage through the outer membrane. It has homology with Metaxin-1, also part of the outer mitochondrial membrane beta-barrel protein transport complex.
Pfam PF02560: Cyanate lyase C-terminal domain (domain)
Cyanate lyase (also known as cyanase) [ec:4.2.1.104] is responsible for the hydrolysis of cyanate, allowing organisms that possess the enzyme to overcome the toxicity of environmental cyanate. This enzyme is composed of two domains, an N-terminal helix-turn-helix and this structurally unique C-terminal domain.
Wikipedia: The enzyme cyanase, catalyses the bicarbonate dependent metabolism of cyanate to produce ammonia and carbon dioxide. The systematic name of this enzyme is carbamate hydrolyase. In E. coli, cyanase is an inducible enzyme and is encoded for by the cynS gene. Cyanate is a toxic anion, and cyanase catalyzes the metabolism into the benign products of carbon dioxide and ammonia.
Pfam PF11876: Type VI immunity for VRR-NUC (family)
This entry represents bacterial immunity proteins that in  are encoded by the PAAR2 cluster and have been named Type  VI immunity for VRR-NUC (TsiV). These proteins form an effector-immunity pair with TseV (type VI effector VRR-NUC), the TseV-TsiV pair. These are alpha+beta class of proteins whose surface is mainly electronegative with a a hydrophobic core formed by the N-terminal region.
Pfam PF18538: Domain of unknown function (DUF5624) (domain)
This is a domain of unknown function found mainly in bacteria.
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 PF19586: Family of unknown function (DUF6093) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000703) is described by MIBiG as an example of the following biosynthetic class, saccharide. This family includes  a member from the kanamycin biosynthetic gene cluster from Streptomyces kanamyceticus and 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.