SII-SWORD/CoKE huggingface dataset:
Pfam PF21728: PADR1, N-terminal helical domain (domain)
This entry represents de N-terminal helical region of PADR1 zinc-binding domain found in poly(ADP-ribose) polymerase-1 (PARP-1) from human and its homologues. The PADR1, known as the third zinc-binding domain (Zn3) localises between the N-terminal PARP-type zinc fingers (Zn1 and Zn2) and the central BRCT domain; it is involved in protein-protein interactions that orchestrate PARP-1 activation and are critical to the DNA-dependent stimulation of PARP-1.
Pfam PF02052: Gallidermin (family)
Lantibiotics are heavily-modified bacteriocin-like peptides from Gram-positive bacteria. They contain alpha,beta-unsaturated amino acids (dehydroalanine and dehydrobutyrine) and lanthionine or 3-methyllanthionine rings (collectively known as thioether rings). There are 2 types of lantibiotic:


 * Type A (which include nisin, subtilin, epidermin, gallidermin and Pep5) are strongly cationic and bactericidal - nisin, subtilin and Pep5 inhibit the growth of Gram-positive bacteria, probably by voltage-dependent pore formation in the cytoplasmic membrane, resulting in cellular efflux of electrolytes, amino acids and ATP;
 * Type B lantibiotics possess at most one positive charge and are not bactericidal.


This entry represents type A Lantibiotics that are mostly from Bacillales.
Wikipedia: Lantibiotics are a class of polycyclic peptide antibiotics that contain the characteristic thioether amino acids lanthionine or methyllanthionine, as well as the unsaturated amino acids dehydroalanine, and 2-aminoisobutyric acid. They belong to ribosomally synthesized and post-translationally modified peptides.
Pfam PF22747: DUF2089 zinc ribbon (domain)
This entry represents the zinc ribbon found at the N-terminal of DUF2089, which usually occurs as a fusion of ZnR+HTH+SHOCT-like.
Pfam PF14809: C1 domain of tRNA-guanine transglycosylase dimerisation (domain)
This short region of the tRNA-guanine transglycosylase enzyme acts as the dimerisation domain of the whole protein.
Pfam PF10421: 2'-5'-oligoadenylate synthetase 1, domain 2, C-terminus (domain)
This is the largely alpha-helical, C-terminal half of 2'-5'-oligoadenylate synthetase 1, being described as domain 2 of the enzyme and homologous to a tandem ubiquitin repeat. It carries the region of enzymic activity between 320 and 344 at the extreme C-terminal end. Oligoadenylate synthetases are antiviral enzymes that counteract vial attack by degrading viral RNA. The enzyme uses ATP in 2'-specific nucleotidyl transfer reactions to synthesise 2'.5'-oligoadenylates, which activate latent ribonuclease, resulting in degradation of viral RNA and inhibition of virus replication. This domain is often associated with NTP_transf_2 [pfam:PF01909].
Wikipedia: In molecular biology, 2'-5'-oligoadenylate synthetase is an enzyme that reacts to interferon signal. It is an antiviral enzyme that counteracts viral attack by degrading RNAs, both viral and host. The enzyme uses ATP in 2'-specific nucleotidyl transfer reactions to synthesize 2'-5'-oligoadenylates, which activate latent ribonuclease (RNase-L), resulting in degradation of viral RNA and inhibition of virus replication.
Pfam PF19044: TraG P-loop domain (family)
This entry represents the P-loop domain found in the TraG conjugation protein.
Pfam PF14273: Domain of unknown function (DUF4360) (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 200 and 228 amino acids in length. There is a conserved GCP sequence motif near the N-terminus.
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 PF16117: Domain of unknown function (DUF4833) (family)
This family consists of uncharacterized proteins  around 170 residues in length and is mainly found  in various Parabacteroides and Bacteroides species.  The function of this family is unknown.
Pfam PF22979: Winged helix-turn-helix domain (domain)
This entry represents a winged helix-turn-helix domain that may bind to DNA.
Pfam PF17407: Nrap protein domain 6 (domain)
Members of this family are nucleolar RNA-associated proteins (Nrap) which are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localised in the nucleolus. Nrap is a large nucleolar protein (of more than 1000 amino acids). Nrap appears to be associated with ribosome biogenesis by interacting with pre-rRNA primary transcript.
Pfam PF06368: Methylaspartate mutase E chain (MutE) (family)
This family consists of several methylaspartate mutase E chain proteins ([ec:5.4.99.1]). Glutamate mutase catalyses the first step in the fermentation of glutamate by Clostridium tetanomorphum. This is an unusual isomerisation in which L-glutamate is converted to threo-beta-methyl L-aspartate.
Pfam PF17521: Honey bee peptides (family)
Family members are bee venom peptides such as Secapin. Mature secapin is composed of 25 amino acid residues that contain a disulfide link. Secapin has been demonstrated to act as a potent neurotoxin. In Apis mellifera secapin exhibits anti-bacterial activity and induces inflammation and pain with anti-fibrinolytic, anti-elastolytic, and anti-microbial activities. Secapin shares a common folding pattern with apamin, mast cell degranulating peptide and tertiapin; it is centred on a beta-turn covalently linked to an alpha-helical segment by one disulphide link (two disulphide links in the other peptides).
Pfam PF01388: ARID/BRIGHT DNA binding domain (domain)
This domain is know as ARID for AT-Rich Interaction Domain, and also known as the BRIGHT domain.
Wikipedia: In molecular biology, the ARID domain ) is a protein domain that binds to DNA. ARID domain-containing proteins are found in fungi, plants and invertebrate and vertebrate metazoans. ARID-encoding genes are involved in a variety of biological processes including embryonic development, cell lineage gene regulation and cell cycle control. Although the specific roles of this domain and of ARID-containing proteins in transcriptional regulation are yet to be elucidated, they include both positive and negative transcriptional regulation and a likely involvement in the modification of chromatin structure. The basic structure of the ARID domain appears to be a series of six alpha-helices separated by beta-strands, loops, or turns, but the structured region may extend to an additional helix at either or both ends of the basic six. Based on primary sequence homology, they can be partitioned into three structural classes: Minimal ARID proteins that consist of a core domain formed by six alpha helices; ARID proteins that supplement the core domain with an N-terminal alpha-helix; and Extended-ARID proteins, which contain the core domain and additional alpha-helices at their N- and C-termini.
Pfam PF06229: FRG1-like domain (domain)
The human FRG1 gene maps to human chromosome 4q35 and has been identified   as a candidate for facioscapulohumeral muscular dystrophy.  Currently, the function of FRG1 is unknown.
Pfam PF05841: Apc15p protein (family)
The anaphase-promoting complex (APC) is a conserved multi-subunit ubiquitin ligase required for the degradation of key cell cycle regulators Members of this family are components of the anaphase-promoting complex homologous to Apc15p [swissprot:O94688].
Pfam PF12892: Spy0128-like isopeptide containing domain (domain)
The FCT and equivalent region genes of Streptococcus pyogenes and other related bacteria encode surface proteins that include fibronectin- and collagen-binding proteins and the serological markers known as T antigens. Some of these proteins give rise to pilus-like appendages. The FctA family is found in many Firmicutes and related bacteria. In S. pyogenes, the pili have a role in bacterial adherence and colonisation of human tissues. Members of this family have a conserved N-terminal lysine and C-terminal asparagine that can form a covalent isopeptide bond.
Pfam PF19884: Family of unknown function (DUF6357) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000368) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide), in  particular the streptobactin biosynthetic gene cluster from  Streptomyces sp. ATCC 700974.
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 PF07495: Y_Y_Y domain (domain)
This domain is mostly found at the end of the beta propellers ([pfam:PF07494]) in a family of two component regulators. However they are also found tandemly repeated in [swissprot:Q891H4] without other signal conduction domains being present. It's named after the conserved tyrosines found in the alignment. The exact function is not known.
Wikipedia: In molecular biology, the YYY domain is a protein domain that is considered to be important in bacterial signal transduction, however the exact function of this protein domain is not known. It is named after the three conserved tyrosines found in the alignment. The domain forms part of the periplasmic sensor domain which binds to unsaturated disaccharides.
Pfam PF07987: Domain of unkown function (DUF1775) (domain)
Domain found in bacteria with undetermined function. Its structure has been determined and is an immunoglobulin-like fold.
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 PF19505: Family of unknown function (DUF6039) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001101) is described by MIBiG as an example of the following biosynthetic classes, NRP and Polyketide (Macrolide). This family includes a protein from the leinamycin biosynthetic gene  cluster from Streptomyces atroolivaceus 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.
Pfam PF11256: SAV0927-like (family)
This family of proteins includes SAV0927 from Staphylococcus aureus and similar proteins predominantly found in Firmicutes. This protein forms a structure that contains five dimers. Each protomer shows an anti-parallel five-stranded beta-sheet, with one strand from the other subunit in the dimer, and three alpha- helices at the C-terminal end. Its function is unknown.
Pfam PF19680: Family of unknown function (DUF6182) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001774) is described by MIBiG as an example of the following biosynthetic class, other (unspecified). It includes a  member from the spicamycin biosynthetic gene cluster from  Streptomyces fimbriatus. 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 PF06992: Replication protein P (family)
This family consists of several Bacteriophage lambda replication protein P like proteins. The bacteriophage lambda P protein promoters replication of the phage chromosome by recruiting a key component of the cellular replication machinery to the viral origin. Specifically, P protein delivers one or more molecules of Escherichia coli DnaB helicase to a nucleoprotein structure formed by the lambda O initiator at the lambda replication origin.
Pfam PF00623: RNA polymerase Rpb1, domain 2 (domain)
RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases).  This domain, domain 2, contains the active site. The invariant motif -NADFDGD- binds the active site magnesium ion.
Pfam PF18932: Family of unknown function (DUF5681) (family)
This domain family is found in bacteria, archaea and viruses, and is typically between 75 and 86 amino acids in length. There is a conserved SGNP sequence motif. There are two completely conserved G residues that may be functionally important.
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 PF12564: Type III restriction/modification enzyme methylation subunit (family)
This domain family is found in bacteria, and is approximately 60 amino acids in length. The family is found in association with [pfam:PF01555].  There are two completely conserved residues (F and S) that may be functionally important. This family is a bacterial phage resistance protein. It functions in a type III restriction/modification enzyme complex. It is part of the methylation subunit of the complex. It binds DNA and methylates it.
Pfam PF13237: 4Fe-4S dicluster domain (domain)
This family includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. The structure of the domain is an alpha-antiparallel beta sandwich.
Pfam PF16534: Ubiquitin-like oligomerisation domain of SATB (domain)
ULD is an N-terminal oligomerisation domain of SATB or special AT-rich sequence-binding proteins.  SATBs are global chromatin organisers and regulators of gene expression that are essential for T-cell development, breast cancer tumour growth and metastasis. SATBs assemble into a tetramer via the ULD domain, and the tetramerisation of SATBs are essential for recognising specific DNA sequences (such as multiple AT-rich DNA fragments). Thus, SATBs may regulate gene expression directly by binding to various promoters and upstream regions and thereby influencing promoter activity.
Pfam PF24423: Major antigen, helical domain (domain)
This domain is found twice towards the C-terminal end of Major antigen from Onchocerca volvulus (OVT1) and similar animal proteins. It is predicted to adopt an all-alpha helical structure.
Pfam PF13521: AAA domain (domain)
This entry represents the AAA domain found in a group of proteins, including NadR from Escherichia coli and Ttd14 from Drosophila melanogaster. NadR has three activities: DNA binding, nicotinamide mononucleotide (NMN) adenylyltransferase and ribosylnicotinamide (RN) kinase . Ttd14 is a GTP-binding protein that regulates trafficking of the TRPL ion channel in Drosophila photoreceptor cells .
AAA ATPases belong to the AAA+ superfamily of ringshaped P-loop NTPases, which exert their activity through the energy-dependent unfolding of macromolecules .
Wikipedia: AAA proteins are a large group of protein family sharing a common conserved module of approximately 230 amino acid residues. This is a large, functionally diverse protein family belonging to the AAA+ protein superfamily of ring-shaped P-loop NTPases, which exert their activity through the energy-dependent remodeling or translocation of macromolecules.
Pfam PF06330: Trichodiene synthase (TRI5) (domain)
This family consists of several fungal trichodiene synthase proteins ([ec:4.2.3.6]). TRI5 encodes the enzyme trichodiene synthase, which has been shown to catalyse the first step in the trichothecene pathways of Fusarium and Trichothecium species.
Pfam PF04650: YSIRK type signal peptide (conserved_site)
Many surface proteins found in Streptococcus, Staphylococcus, and related lineages share apparently homologous signal sequences. A motif resembling [YF]SIRKxxxGxxS[VIA] appears at the start of the transmembrane domain. The GxxS motif appears perfectly conserved, suggesting a specific function and not just homology.  There is a strong correlation between proteins carrying this region at the N-terminus and those carrying the Gram-positive anchor domain with the LPXTG sortase processing site at the C-terminus.
Pfam PF11336: Protein of unknown function (DUF3138) (family)
This family of proteins with unknown function appear to be restricted to Proteobacteria.
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 PF11171: Protein of unknown function (DUF2958) (family)
Some members are annotated as lipoproteins however this cannot be confirmed. This family of 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 PF18081: Fanconi anemia-associated nuclease SAP domain (domain)
This domain is found in Fanconi-anemia-associated nuclease 1 (FAN1) present in Pseudomonas aeruginosa. FAN1 is a nuclease associated with Fanconi anemia (FA), an autosomal recessive genetic disorder caused by defects in FA genes responsible for processing DNA inter-strand cross-links (ICLs). The domain, known as the SAP domain, helps to augment the overall protein DNA interaction by interacting with the 3' and 5' ends of the template strand. Support of the pre-nick segment binding is crucial as multiple mutations in this domain resulted in hypersensitivity to a cross-linking agent in the SAP domain of Caenorhabditis elegans' FAN1. The helix-hairpin-helix of the SAP recognize three consecutive phosphate groups (C19, A20 and A21) at the 3' end of the template via the basic residues K116, K135 and K117.
Pfam PF09005: Far upstream element-binding protein, C-terminal (domain)
This entry represents the transactivation domain of Far upstream element-binding protein 1/2 (FUBP1/2) which is found at the C-terminal. FUBP1 regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. FUBP2, also known as KSRP (K homology-type splicing regulatory protein), is a single-strand-RNA binding protein that integrate different levels of gene expression and is required for proper immune response, lipid metabolism, cell fate decisions, and tissue regeneration. This domain contains the tyrosine residues required for transactivation and adopts an alpha-helical configuration.
Pfam PF16161: Domain of unknown function (DUF4867) (family)
This family consists of uncharacterised proteins around 220 residues in length and is mainly found in various human gut Firmicutes and a few eubacteria species. It is also amply represented in human gut metagenomic datasets. Distant homology analysis and marginal HMM overlaps suggest this family is a distant homologue of Ureidoglycolate hydrolase [pfam:PF04115], but this prediction is not verified by experiment, therefore the function of this family is still unknown.
Pfam PF16116: Domain of unknown function (DUF4832) (family)
This family consists of uncharacterised proteins around 200 residues in length and is mainly found in various Bacteroides and Capnocytophaga species. The function of this family is unknown. Distant homology analysis suggests a possible similarity of proteins from this family to TIM barrel glycoside hydrolases and, subsequently its involvement in carbohydrate metabolism.The domain lies downstream of glycosyl hydrolases 42 suggesting that as a domain it might represent the carbohydrate-binding region of the enzyme.
Pfam PF08577: PI31 proteasome regulator (family)
PI31 is a cellular regulator of proteasome formation and of proteasome-mediated antigen processing.
Pfam PF23570: Histone acetyltransferase p300-like, PHD domain (domain)
This domain is found in human Histone acetyltransferase p300 (EP300) and similar animal proteins. EP300 functions as a histone acetyltransferase and regulates transcription via chromatin remodelling. This entry represents the PHD (plant homeodomain) domain, which forms a module with the bromodomain ([pfam:PF00439]) and the RING domain ([pfam:PF06001]) that associates intimately with the HAT domain ([pfam:PF08214]) through numerous conserved contacts.
Pfam PF11024: Dispersed gene family protein 1 of Trypanosoma cruzi region 4 (domain)
This protein is likely to be highly expressed, and is expressed from the sub-telomeric region. However, the function is not known. Other domains on this protein include DGF-1_N, DGF-1_2, and DGF-1_5. This domain is just downstream from the C-terminus, but not the C-terminus of proteins, also annotated as being DGF-1, that constitute family DGF-1_C.
Pfam PF17787: PH domain (domain)
This entry corresponds to the PH domain found at the N-terminus of phospholipase C enzymes.
Wikipedia: Pleckstrin homology domain or (PHIP) is a protein domain of approximately 120 amino acids that occurs in a wide range of proteins involved in intracellular signaling or as constituents of the cytoskeleton.
Pfam PF09700: CRISPR-associated protein (Cas_Cmr3) (family)
CRISPR is a term 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 highly divergent family, found in at least ten different archaeal and bacterial species, is represented by TM1793 from Thermotoga maritima.