SII-SWORD/CoKE huggingface dataset:
Pfam PF22990: Phosphatidylserine Lipase ABHD16 N-terminal domain (domain)
This entry represents the N-terminal domain from ABHD16 family proteins.  The ABHD16 family comprises enzymes with phosphatidylserine lipase activity, catalyzing the hydrolysis of phosphatidylserine to produce lysophosphatidylserine, a signaling lipid involved in immunological and neurological processes. These enzymes exhibit specificity, showing no activity towards diacylglycerol, triacylglycerol, or lysophosphatidylserine lipase. Additionally, they possess monoacylglycerol lipase activity, with a preference for certain monoacylglycerol substrates. The family's enzymatic functions highlight its role in lipid signaling pathways and potential implications in physiological regulation.
Pfam PF19968: vWA-MoxR associated protein middle region (VMAP-M) 7 (family)
Highly variable central region of the vWA-MoxR associated protein (VMAP) of the classical ternary system (vWA-MoxR-VMAP) in NTP-dependent conflict systems. VMAP-Ms may be involved in sensing of invasive entities.
Pfam PF06426: Serine acetyltransferase, N-terminal (domain)
The N-terminal domain of serine acetyltransferase has a sequence that is conserved in plants and bacteria.
Wikipedia: In enzymology, a serine O-acetyltransferase is an enzyme that catalyzes the chemical reactionacetyl-CoA + L-serine  CoA + O-acetyl-L-serine
Pfam PF21288: Complement component C6, KAZAL domain (domain)
Factor I-like modules (FIMs) are present in complement proteins C6, C7, and factor I, and participate in protein-protein interactions that critical to the progress of a complement-mediated immune response. Complement component C6 contains a FIM pair at the C-terminal, FIM1 and FIM2; each of them consists of a small N-terminal FOLN subdomain and a larger C-terminal KAZAL domain ([pfam:PF18434]). This entry represents the KAZAL domain of FIM1.
Pfam PF03025: Papillomavirus E5 (domain)
Human papillomaviruses (HPVs) are epitheliotropic viruses, and their life cycle is intimately linked to the stratification and differentiation state of the host epithelial tissues. The kinetics of E5a protein expression during the complete viral life cycle has been studied and the highest level was found to be coincidental with the onset of virion morphogenesis.  The E5 protein from papillomaviruses is about 80 amino acids long. The proteins contain three predicted transmembrane alpha helices. These proteins display transforming activity in cultured cells and animals, and they presumably also play a role in the productive virus life cycle. The E5 proteins are thought to act by modulating the activity of cellular proteins.
Pfam PF24943: Dep-1 second Fn3-like domain (domain)
This domain is found in the Receptor-type tyrosine-protein phosphatase Dep-1 from Caenorhabditis elegans and related proteins. Dep-1 is involved in the dephosphorylation of the receptor let-23 and the beta-integrin subunit pat-3. It is involved in the regulation of the  cell fate during the development of the vulva and the excretory system. It is also involved indirectly in the negative regulation of let-23 signaling and vulval induction. Dep-1 is a multidomain protein which is predicted to contain a number of Fn3-like domains arranged in tandem. This entry represents the second of them.
Pfam PF01645: Conserved region in glutamate synthase (domain)
This family represents a region of the glutamate synthase protein.  This region is expressed as a separate subunit in the glutamate synthase alpha subunit from archaebacteria, or part of a large multidomain enzyme in other organisms. The aligned region of these proteins contains a putative FMN binding site and Fe-S cluster.
Pfam PF14505: Domain of unknown function (DUF4438), N-terminal (domain)
This is the N-terminal domain of TM_1086 and related 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 PF21783: YNCE-like beta-propeller (repeat)
This entry includes bacterial YNCE proteins which consist of a beta-propeller structure (the so-called YVTN beta-propeller) which binds DNA.
Pfam PF22275: Domain of unknown function (DUF6957) (domain)
This domain is found in uncharacterised bacterial proteins. It is predicted to fold into a beta-barrel that has some similarity to the replication focus targeting sequence (RFTS) domain of Dnmt1 methyltransferase 1.
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 PF00804: Syntaxin (domain)
Syntaxins are the prototype family of SNARE proteins. They usually consist of three main regions - a C-terminal transmembrane region, a central SNARE domain which is characteristic of and conserved in all syntaxins ([pfam:PF05739]), and an N-terminal domain that is featured in this entry. This domain varies between syntaxin isoforms; in syntaxin 1A ([swissprot:O35526]) it is found as three alpha-helices with a left-handed twist. It may fold back on the SNARE domain to allow the molecule to adopt a 'closed' configuration that prevents formation of the core fusion complex - it thus has an auto-inhibitory role. The function of syntaxins is determined by their localisation. They are involved in neuronal exocytosis, ER-Golgi transport and Golgi-endosome transport, for example. They also interact with other proteins as well as those involved in SNARE complexes. These include vesicle coat proteins, Rab GTPases, and tethering factors.
Wikipedia: Syntaxins are a family of membrane integrated Q-SNARE proteins participating in exocytosis.
Pfam PF10630: Protein of unknown function (DUF2476) (family)
This is a family of proteins of unknown function. The family is rich in proline residues.
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 PF23211: Leucine-rich repeat and WD repeat-containing protein 1, LRR (repeat)
This entry represents the Leucine-rich repeat domain found at the N-terminal of Leucine-rich repeat and WD repeat-containing protein 1 (LRWD1) from animals and related sequences. LRWD1 (also known as CENP-33 and ORCA) is required for for G1/S transition. It recruits and stabilizes the origin recognition complex (ORC) onto chromatin during G1 to establish pre-replication complex (preRC) and to heterochromatic sites in pre-replicated cells. This proteins consist of a LRR domain at the N-terminal and a WD (beta-propeller) domain at the C-terminal.
Pfam PF23236: Large helicase-related protein, winged-helix domain (domain)
This is a winged-helix (WH) domain found in Large helicase -related protein from Escherichia coli (Lhr), DEAD/DEAH box helicase from Mycolicibacterium smegmatis ([swissprot:A0QT91]) and similar bacterial sequences. These proteins have a C-terminal domain composed of a series of five WH modules (named WH2 to WH6) and a beta-barrel module. This entry represents WH2. It shows three alpha-helices followed by two loops or 'wings' and two beta-strands forming an antiparallel beta-sheet.
Pfam PF06568: Domain of unknown function (DUF1127) (domain)
This family is found in several hypothetical bacterial proteins. In some cases it represents it represents the C-terminal region whereas in others it represents the whole sequence.
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 PF07925: Reovirus RNA-dependent RNA polymerase lambda 3 (family)
The sequences in this family are similar to the reoviral minor core protein lambda 3 ([swissprot:P17378]), which functions as a RNA-dependent RNA polymerase within the protein capsid. It is organised into 3 domains. N- and C-terminal domains create a 'cage' that encloses a conserved central catalytic domain within a hollow centre; this catalytic domain is arranged to form 'fingers', 'palm' and 'thumb' subdomains.  Unlike other RNA polymerases, like HIV reverse transcriptase and T7 RNA polymerase, lambda 3 protein binds template and substrate with only localised rearrangements, and catalytic activity can occur with little structural change. However, the structure of the catalytic complex is similar to that of other polymerase catalytic complexes with known structure.
Pfam PF10537: ATP-utilising chromatin assembly and remodelling N-terminal (domain)
ACF (for ATP-utilising chromatin assembly and remodelling factor) is a chromatin-remodelling complex that catalyses the ATP-dependent assembly of periodic nucleosome arrays. The WAC (WSTF/Acf1/cbp146) domain is an approximately 110-residue module present at the N-termini of Acf1-related proteins in a variety of organisms. The DNA-binding region of Acf1 includes the WAC domain, which is necessary for the efficient binding of ACF complex to DNA.
Wikipedia: In molecular biology, the WAC domain is a protein domain found on the N-terminus of WSTF protein. Its function is still unknown, but putatively thought to be involved in cell growth. The protein domain has been found to be present in both prokaryotes and eukaryotes
Pfam PF22520: Crb2, Tudor domain (domain)
This entry represents a Tudor domain in the DNA repair protein Crb2 from Schizosaccharomyces pombe. Crb2 possesses tandem Tudor domains which interact with histone H4 dimethylated at Lys20 (H4-K20me2).
Pfam PF00672: HAMP domain (domain)
The HAMP domain (present in Histidine kinases, Adenyl cyclases, Methyl-accepting proteins and Phosphatases) is an approximately 50-amino acid Î±-helical region common to chemoreceptors and histidine kinases that is present in several multidomain sensor proteins that participate in a variety of signal transduction processes. It is found in bacterial sensor and chemotaxis proteins and in eukaryotic histidine kinases. The bacterial proteins are usually integral membrane proteins and part of a two-component signal transduction pathway. One or several copies of the HAMP domain can be found in association with other domains, such as the histidine kinase domain, the bacterial chemotaxis sensory transducer domain, the PAS repeat, the EAL domain, the GGDEF domain, the protein phosphatase 2C-like domain, the guanylate cyclase domain, or the response regulatory domain. It has been suggested that the HAMP domain possesses a role of regulating the phosphorylation or methylation of homodimeric receptors by transmitting the conformational changes in periplasmic ligand-binding domains to cytoplasmic signalling kinase and methyl-acceptor domains .
Wikipedia: In molecular biology, the HAMP domain is an approximately 50-amino acid alpha-helical region that forms a dimeric, four-helical coiled coil. It is found in bacterial sensor and chemotaxis proteins and in eukaryotic histidine kinases. The bacterial proteins are usually integral membrane proteins and part of a two-component signal transduction pathway. One or several copies of the HAMP domain can be found in association with other domains, such as the histidine kinase domain, the bacterial chemotaxis sensory transducer domain, the PAS repeat, the EAL domain, the GGDEF domain, the protein phosphatase 2C-like domain, the guanylate cyclase domain, or the response regulatory domain. In its most common setting, the HAMP domain transmits conformational changes in periplasmic ligand-binding domains to cytoplasmic signalling kinase and methyl-acceptor domains and thus regulates the phosphorylation or methylation activity of homodimeric receptors.
Pfam PF07519: Tannase and feruloyl esterase (family)
This family includes fungal tannase and feruloyl esterase. It also includes several bacterial homologues of unknown function.
Pfam PF03919: mRNA capping enzyme, C-terminal domain (domain)
This domain is found at the C terminus of the mRNA capping enzyme. The mRNA capping enzyme in yeasts is composed of two separate chains: alpha a mRNA guanyltransferase and beta an RNA 5'-triphosphate. X-ray crystallography reveals a large conformational change during guanyl transfer by mRNA capping enzymes . Binding of the enzyme to nucleotides is specific to the GMP moiety of GTP. The viral mRNA capping enzyme is a monomer that transfers a GMP cap onto the end of mRNA that terminates with a 5'-diphosphate tail.
Pfam PF02452: PemK-like, MazF-like toxin of type II toxin-antitoxin system (domain)
PemK is a growth inhibitor in E. coli known to bind to the promoter region of the Pem operon, auto-regulating synthesis. This family represents the toxin molecule of a typical bacterial toxin-antitoxin system pairing. The family includes a number of different toxins, such as MazF, Kid, PemK, ChpA, ChpB and ChpAK.
Pfam PF00936: BMC domain (domain)
Bacterial microcompartments are primitive organelles composed entirely of protein subunits. The prototypical bacterial microcompartment is the carboxysome, a protein shell for sequestering carbon fixation reactions. These proteins for hexameric structure.
Wikipedia: In molecular biology the Bacterial Microcompartment (BMC) domain is a protein domain found in a variety of shell proteins, including CsoS1A, CsoS1B and CsoS1C of Thiobacillus neapolitanus and their orthologs from other bacteria. These shell proteins form the polyhedral structure of the carboxysome and related structures that plays a metabolic role in bacteria. The BMC domain consists of about 90 amino acid residues, characterized by β-α-β motif connected by a β-hairpin.
Pfam PF15484: Domain of unknown function (DUF4642) (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 115 and 196 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 PF13916: PP1-regulatory protein, Phostensin N-terminal (domain)
Phostensin has been identified as a PP1 regulatory protein binding protein. This domain is N-terminal to the PP1- and SH3-binding regions though may carry an additional SH3-binding motif. It is likely that Phostensin targets PP1 to the F-actin cytoskeleton.  Phostensin binds to actin and decreases the elongation and depolymerisation rates of actin filament pointed ends.
Pfam PF20082: Family of unknown function (DUF6476) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are 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 PF13943: WPP domain (domain)
The WPP domain is thought to be exclusively found in plants. The WPP stands for a tryptophan-proline-proline motif that is highly conserved in the domain . The WPP domain is known to direct RanGAP (Ran GTPase-activating protein) to the nuclear envelope . RanGAP is an accessory protein for the small signaling GTPase Ran, which is involved in nucleocytoplasmic transport. Non-RanGAP nuclear envelope proteins are also known to encode WPP domains, such as MFP1 attachment factor 1 (MAF1) , WPP1  and WPP2 .
Wikipedia: The WPP domain is a protein domain thought to be exclusively found in plants, first identified in 2000. The domain is about 90 amino acid residues long.
Pfam PF02023: SCAN domain (domain)
The SCAN domain (named after SRE-ZBP, CTfin51, AW-1 and Number 18 cDNA) is found in several [pfam:PF00096] proteins. The domain has been shown to be able to mediate homo- and hetero-oligomerisation.
Pfam PF22841: CATSPERE first N-terminal domain (domain)
This entry includes CATSPERE, the auxiliary subunit epsilon of the CatSper complex, a complex involved in sperm cell hyperactivation. This process is needed for sperm motility, which is essential late in the preparation of sperm for fertilisation. This is a multi-domain protein which has a similar domain organisation as the other auxiliary subunits, beta, gamma and delta. The epsilon subunit has an additional N-terminal domain (NTD2). This entry represents the first N-terminal domain.
Pfam PF19536: POU domain, class 2, transcription factor 1 C-terminal (domain)
This domain represents the C-terminal region of the POU domain, class 2 subfamily, transcription factor 1, which is localised adjacent to the homeobox domain. This transcription factor activates the promoters of the genes for some small nuclear RNAs (snRNA) and of genes such as those for histone H2B and immunoglobulins.
Pfam PF22192: GtgE peptidase (domain)
Salmonella Typhimurium GtgE is an effector protein contributing to the virulence of this pathogen. It was shown to possess highly selective proteolytic activity against a subset of Rab proteins that helps in evasion of Salmonella-containing vacuole (SCV) fusion with lysosomes. The protein displays papain-like fold with an assembled Cys-His-Asp catalytic triad.
Pfam PF19402: Lanthionine-containing peptide SapB precursor RamS (family)
This entry represents a member of a biosynthetic gene cluster (BGC). The BGC (BGC0000551) is described by MIBiG as an example of the  following biosynthetic class, RiPP (ribosomally synthesised and post- translationally modified peptide). This family includes RamS, the  precursor of lanthionine-containing peptide SapB (also known as  ProSapB). SapB, which does not appear to exhibit antibiotic activity,  is formed from RamS through proteolytic cleavage and subsequent  creation of lanthionine bridges.
Pfam PF01964: Radical SAM ThiC family (domain)
ThiC is found within the thiamine biosynthesis operon. ThiC is involved in pyrimidine biosynthesis.  ThiC participates in the formation of 4-Amino-5-hydroxymethyl-2-methylpyrimidine from AIR, an intermediate in the de novo pyrimidine biosynthesis. Thic is a member of the radical SAM superfamily.
Pfam PF09687: Plasmodium RESA N-terminal (domain)
The short, four-helical domain first identified in the Plasmodium export proteins PHISTa and PHISTc has been extended to become this six-helical PRESAN domain identified in the P. falciparum-specific RESA-type (Ring-infected erythrocyte surface antigen) proteins in association with the DnaJ domain. Overall, at least 67 proteins have been detected in P. falciparum with complete copies of the PRESAN domain. No versions of this domain were detected in other apicomplexan genera, suggesting that the domain was 'invented' after the divergence of the lineage leading to the genus Plasmodium undergoing a dramatic proliferation only in P. falciparum. A secondary structure-prediction derived from the multiple alignment of the PRESAN family reveals that it is composed of an all-helical fold with six conserved helical segments. There is some evidence it might localise to membranes.
Wikipedia: The Plasmodium helical interspersed subtelomeric proteins (PHIST) or ring-infected erythrocyte surface antigens (RESA) are a family of protein domains found in the malaria-causing Plasmodium species. It was initially identified as a short four-helical conserved region in the single-domain export proteins, but the identification of this part associated with a DnaJ domain in P. falciparum RESA has led to its reclassification as the RESA N-terminal domain. This domain has been classified into three subfamilies, PHISTa, PHISTb, and PHISTc.
Pfam PF06805: Bacteriophage lambda tail assembly protein I (domain)
This family consists of tail assembly proteins from lambdoid and T1 phages and related prophages, e.g. the tail assembly protein I  (TAPI). Members of this family contain a core ubiquitin fold domain. The exact function of TAPI is not clear but  it is not incorporated into the mature tail. Gene neighborhoods reveal that TAPI co-occurs with genes encoding the host-specificity  protein TapJ, and TapK, which contains a JAB metallopeptidase fused  to an NlpC/P60  peptidase. It is proposed that the TAPI protein is  processed by the  peptidase domains of TapK.
Pfam PF09441: ARS binding protein 2 (family)
This DNA-binding protein binds to the autonomously replicating sequence (ARS) binding element. It may play a role in regulating the cell cycle response to stress signals.
Pfam PF15792: Lung adenoma susceptibility protein 2 (family)
LAS2 is a family of eukaryotic proteins. Deletion of LAS2 is observed in approx. 40% of human lung adenocarcinomas, suggesting that loss of function of LAS2 may be a key step for promoting lung tumourigenesis.
Pfam PF19081: Ig-like domain CHU_C associated (domain)
Presumed Ig-like domain found as tandem repeats in proteins with the gliding motility-associated C-terminal domain CHU_C
Pfam PF09231: Rice dwarf virus p3 (family)
Members of this family are core structural proteins found in the double-stranded RNA virus Phytoreovirus. They are large proteins without apparent domain division, with a number of all-alpha regions and one all beta domain near the C-terminal end.
Pfam PF07284: 2-vinyl bacteriochlorophyllide hydratase (BCHF) (family)
This family contains the bacterial enzyme 2-vinyl bacteriochlorophyllide hydratase ([ec:4.2.1.-]) (approximately 150 residues long). This is involved in the light-independent bacteriochlorophyll biosynthesis pathway by adding water across the 2-vinyl group.
Pfam PF09482: Bacterial type III secretion apparatus protein (OrgA_MxiK) (family)
This protein is encoded by genes which are found in type III secretion operons, and has been shown to be essential for the invasion phenotype in Salmonella and a component of the secretion apparatus. The protein is known as OrgA in Salmonella due to its oxygen-dependent expression pattern in which low-oxygen levels up-regulate the gene. In Shigella the gene is called MxiK and has been shown to be essential for the proper assembly of the needle complex, which is the core component of type III secretion systems.
Pfam PF10276: Zinc-finger domain (domain)
This is a short zinc-finger domain conserved from fungi to humans. It is Cx8Hx14Cx2C.
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.