SII-SWORD/CoKE huggingface dataset:
Pfam PF12156: Putative metal-binding domain of cation transport ATPase (family)
This domain is found in bacteria, and is approximately 90 amino acids in length. It is found associated with [pfam:PF00403], [pfam:PF00122], [pfam:PF00702]. The cysteine-rich nature and composition suggest this might be a cation-binding domain; most members are annotated as being cation transport ATPases.
Pfam PF19419: Family of unknown function (DUF5983) (family)
This family of proteins are likely to be phage derived.
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 PF00291: Pyridoxal-phosphate dependent enzyme (family)
Members of this family are all pyridoxal-phosphate dependent enzymes. This family includes: serine dehydratase [ec:4.2.1.13] P20132, threonine dehydratase [ec:4.2.1.16] [swissprot:P04968], tryptophan synthase beta chain [ec:4.2.1.20] [swissprot:P00932], threonine synthase [ec:4.2.99.2] [swissprot:P04990], cysteine synthase [ec:4.2.99.8] P11096, cystathionine beta-synthase [ec:4.2.1.22] [swissprot:P35520], 1-aminocyclopropane-1-carboxylate deaminase [ec:4.1.99.4] [swissprot:P76316].
Pfam PF00810: ER lumen protein retaining receptor (repeat)
Proteins resident in the lumen of the endoplasmic reticulum (ER) contain a C-terminal tetrapeptide, commonly known as Lys-Asp-Glu-Leu (KDEL) in mammals and His-Asp-Glu-Leu (HDEL) in yeast (Saccharomyces cerevisiae) that acts as a signal for their retrieval from subsequent compartments of the secretory pathway. The receptor for this signal is a ~26kDa Golgi membrane protein, initially identified as the ERD2 gene product in S. cerevisiae. The receptor molecule, known variously as the ER lumen protein retaining receptor or the 'KDEL receptor', is believed to cycle between the cis side of the Golgi apparatus and the ER. It has also been characterised in a number of other species, including plants, Plasmodium, Drosophila and mammals. In mammals, 2 highly related forms of the receptor are known.
Pfam PF20734: PA2201 N-terminal domain-like (domain)
This entry represents the N-terminal helical bundle domain from the Pseudomonas aeruginosa PA2201 protein. This protein also contains a C-terminal [pfam:PF08929] domain.
Pfam PF12113: SVM protein signal sequence (conserved_site)
This region is presumed to be a signal peptide sequence found in Sequence-variable mosaic (SVM) proteins. This domain is found in phytoplasmas. This presumed signal sequence is about 30 amino acids in length.
Pfam PF24745: Domain of unknown function (DUF7693) (domain)
This entry represents a group of uncharacterised bacterial proteins. They are predicted to adopt a globular structure consisting of a five-stranded antiparallel beta-sheet and helices packed on one side of it.
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 PF18164: GNAT-like C-terminal domain (domain)
This is the C-terminal domain found in N-acyltransferase (NAT) proteins present in Actinoplanes teichomyceticus. In this organism, NAT proteins are responsible for N-acylation in the synthesis of the antibiotic teicoplanin. The C-terminal domain undergoes a substantial conformational change upon binding to Acyl-CoA. The C-terminal domain is considered Gcn5-related N-acetyltransferase like (GNAT-like) but differs from the canonical GNAT fold in that it lacks the first beta strand and has an additional four alpha helices.
Pfam PF19991: Heavy metal associated domain 2 (domain)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 180 and 190 amino acids in length. These proteins are distantly related to the HMA domain [pfam:PF00403] particularly in the N-terminal half of the family. This family lacks the conserved pair of cysteines found in the HMA domain but does have an N-terminal conserved histidine that may fulfil a similar role.
Wikipedia: In molecular biology, the HMA domain is a conserved protein domain found in a number of heavy metal transport or detoxification proteins.
Pfam PF13554: Phage tail terminator protein (domain)
The three-dimensional structure of NP_888769.1, PDB:2L25, reveals a tail terminator protein gpU fold, which suggests that the protein could have a bacteriophage origin.
Pfam PF15237: PTRF/SDPR family (family)
This family of proteins includes muscle-related coiled-coil protein (MURC), protein kinase C delta-binding protein (PRKCDBP), polymerase I and transcript release factor (PTRF) and serum deprivation-response protein (SDPR). MURC activates the Rho/ROCK pathway. PRKCDBP appears to act as an immune potentiator. PTRF is involved in caveolae formation and function. SDPR is involved in the targetting of protein kinase Calpha to caveolae.
Pfam PF22652: Family of unknown function (DUF7006) (family)
Proteins in this family are found in Firmicutes. They  are approximately 120 amino acids in length and are predicted to adopt an alpha helical structure. Members of this family contain two highly conserved acid residues aspartate and glutamate.
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 PF15525: Domain of unknown function (DUF4652) (repeat)
This family of uncharacterised proteins from Clostridia and Bacilli classes has an unusual structure of three beta propeller repeats that do not form a barrel, as in well known 6-, 7- etc beta propeller barrels, but instead are stacked in a three-layer beta-sheet sandwich. The function of all the proteins from this family is unknown.
Pfam PF08196: UL2 protein (family)
Orf UL2 of Human cytomegalovirus (HCMV) which is a short protein of unknown function
Pfam PF18251: Fungal defensin Copsin (domain)
This domain is Copsin present in Coprinopsis cinerea. Copsin is a defensin that interferes with peptidoglycan synthesis and has a CS-alpha-beta fold. Copsin is stabilized by a unique connectivity of six cysteine bonds in contrast to most other CS-alpha-beta defensins which are linked by three or four disulfide bonds.
Pfam PF04736: Eclosion hormone (family)
Eclosion hormone is an insect neuropeptide that triggers the performance of ecdysis behaviour, which causes shedding of the old cuticle at the end of a molt,.
Pfam PF16157: Domain of unknown function (DUF4865) (family)
This family consists of uncharacterized proteins around 180 residues in length and is mainly found in various Bacillus species.  Distant homology and fold prediction suggests proteins from this family would have a ferrodoxin dimeric fold and specifically be related to the putative mono-oxygenase ydhR family PF08803, however this prediction has not been verified by experiment
Pfam PF05928: Zea mays MURB-like protein (MuDR) (family)
This family consists of several Zea mays specific MURB-like proteins. The transposition of Mu elements underlying Mutator activity in maize requires a transcriptionally active MuDR element. Despite variation in MuDR copy number and RNA levels in Mutator lines, transposition events are consistently late in plant development, and Mu excision frequencies are similar.
Pfam PF08723: Gag protein p15 (domain)
Gag p15 is a viral membrane-binding matrix protein which is alpha helical in structure.
Pfam PF08093: Magi 5 toxic peptide family (family)
This family consists of toxic peptides (Magi 5) found in the venom of the Hexathelidae spider. Magi 5 is the first spider toxin with binding affinity to site 4 of a mammalian sodium channel and the toxin has an insecticidal effect on larvae, causing paralysis when injected into the larvae.
Pfam PF14500: Dos2-interacting transcription regulator of RNA-Pol-II (domain)
This domain, along with the C-terminal part, [pfam:PF12460], is an essential component of a silencing complex in fission yeast that contains Dos2, Rik1, Mms19 and Cdc20 (the catalytic subunit of DNA polymerase-epsilon). This complex regulates RNA polymerase II (RNA Pol II) activity in heterochromatin and is required for DNA replication and heterochromatin assembly.
Pfam PF23446: NFP/LYK LysM1 domain (domain)
This entry represents the first LysM domain found in proteins from plants, including the NFP from Medicago truncatula and LYK from Arabidopsis thaliana. The LysM domain adopt a beta-alpha-alpha-beta fold, according to structure predictions and. NFP/NFR5 class of receptors are crucial for initial lipochitooligosaccharide (LCO) perception and essential for LCO-mediated root nodule symbiosis. LYK4 is a chitin-binding protein and contributes to chitin-triggered immunity. LYK5 has been identified as a receptor with a very high affinity to chitooligosaccharides. Receptors recognising Nod factors and chitin have a very similar structure but contain two diverging motifs in the LysM1 domain that are necessary for discriminating between immunity and symbiotic functions.
Pfam PF08442: ATP-grasp domain (domain)
The ATP-grasp superfamily currently includes 17 groups of enzymes, catalysing ATP-dependent ligation of a carboxylate containing molecule to an amino or thiol group-containing molecule . They contribute predominantly to macromolecular synthesis. ATP-hydrolysis is used to activate a substrate. For example, DD-ligase transfers phosphate from ATP to D-alanine on the first step of catalysis. On the second step the resulting acylphosphate is attacked by a second D-alanine to produce a DD dipeptide following phosphate elimination .

The ATP-grasp domain contains three conserved motifs, corresponding to the phosphate binding loop and the Mg(2+) binding site . The fold is characterised by two Î±-Î² subdomains that grasp the ATP molecule between them. Each subdomain provides a variable loop that forms a part of the active site, completed by region of other domains not conserved between the various ATP-grasp enzymes .

The ATP-grasp domain represented by this entry is found primarily in succinyl-CoA synthetases (6.2.1.5).
Pfam PF03115: Astrovirus capsid protein nucleoplasmin-like domain (domain)
This product is encoded by astrovirus ORF2, one of the three astrovirus ORFs (1a, 1b, 2). The 87kD precursor protein undergoes an intracellular cleavage to form a 79kD protein. Subsequently, extracellular trypsin cleavage yields the three proteins forming the infectious virion.
Pfam PF03339: Poxvirus L3/FP4 protein (family)
This is a family of proteins expressed by members of the Poxviridae. Protein L3, also known as Protein OPG097, is required for transcription of early genes .
Pfam PF10229: Methylmalonic aciduria and homocystinuria type D protein (family)
This entry represents methylmalonic aciduria and  homocystinuria type D protein and homologues. These  proteins are involved in cobalamin (vitamin B12)  metabolism.
Pfam PF17290: Arenavirus nucleocapsid C-terminal domain (domain)
This domain represents the the C-terminal domain that contains 3'-5' exoribonuclease activity involved in suppressing interferon induction. This domain has an RNaseH-like fold.
Pfam PF07362: Post-segregation antitoxin CcdA (domain)
This family consists of several Enterobacterial post-segregation antitoxin CcdA proteins. The F plasmid-carried bacterial toxin, the CcdB protein, is known to act on DNA gyrase in two different ways. CcdB poisons the gyrase-DNA complex, blocking the passage of polymerases and leading to double-strand breakage of the DNA. Alternatively, in cells that overexpress CcdB, the A subunit of DNA gyrase (GyrA) has been found as an inactive complex with CcdB. Both poisoning and inactivation can be prevented and reversed in the presence of the F plasmid-encoded antidote, the CcdA protein.
Wikipedia: The CcdA/CcdB Type II Toxin-antitoxin system is one example of the bacterial toxin-antitoxin (TA) systems that encode two proteins, one a potent inhibitor of cell proliferation (toxin) and the other its specific antidote (antitoxin). These systems preferentially guarantee growth of plasmid-carrying daughter cells in a bacterial population by killing newborn bacteria that have not inherited a plasmid copy at cell division.
Pfam PF24607: Arabinofuranosyltransferase D, third carbohydrate binding module (domain)
This is the third carbohydrate binding module (CBM) found in Arabinofuranosyltransferase D from Mycolicibacterium smegmatis (AftD) and similar proteins from actinomycetes. AftD is made up of five distinct domains: a domain of mixed alpha/beta folds ([pfam:PF11847]) three CBMs and one structural beta-sandwich domain.
Pfam PF07242: Protein of unknown function (DUF1430) (family)
This family represents the C-terminus (approximately 120 residues) of a number of hypothetical bacterial proteins of unknown function. These are possibly membrane proteins involved in immunity.
Pfam PF09796: Ubiquinol-cytochrome-c reductase complex subunit (QCR10) (family)
The QCR10 family of proteins are a component of the ubiquinol-cytochrome c reductase complex (also known as complex III or cytochrome b-c1 complex).  This complex is located on the inner mitochondrial membrane and it couples electron transfer from ubiquinol to cytochrome.  This subunit (QCR10) is required for stable association of the iron-sulfur protein with the complex.
Pfam PF24623: Putative DNA-binding phage zinc finger domain (domain)
This entry represents a large family of zinc binding domains that are found in both phage and bacterial proteins. The phage examples tend to be single domain proteins. The bacterial examples are often found in multidomain proteins. Structure predictions suggest this domain may bind to dsDNA. In about quarter if the proteins this domain is found associated with a resolvase domains [pfam:PF00239] found in site specific recombinases..
Pfam PF24698: Domain of unknown function (DUF7662) (domain)
This domain is found in uncharacterised bacterial proteins. It is frequently found in combination with [pfam:PF21818] and [pfam:PF20815] which suggests that it may be involved in DNA binding and recognition. It is predicted to adopt a globular structure consisting of a three-stranded antiparallel beta-sheet and alpha-helices packed on one side of it.
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 PF09325: Vps5 C terminal like (domain)
Vps5 is a sorting nexin that functions in membrane trafficking. This is the C terminal dimerisation domain.
Wikipedia: Sorting nexins are a large group of proteins that are localized in the cytoplasm and have the potential for membrane association either through their lipid-binding PX domain or through protein–protein interactions with membrane-associated protein complexes Some members of this family have been shown to facilitate protein sorting.
Pfam PF02805: Metal binding domain of Ada (family)
The Escherichia coli Ada protein repairs O6-methylguanine residues and methyl phosphotriesters in DNA by direct transfer of the methyl group to a cysteine residue. This domain contains four conserved cysteines that form a zinc binding site. One of these cysteines is a methyl group acceptor. The methylated domain can then specifically bind to the ada box on a DNA duplex.
Pfam PF07014: Hs1pro-1 protein C-terminus (family)
This family represents the C-terminus (approximately 270 residues) of a number of plant Hs1pro-1 proteins, which are believed to confer nematode resistance.
Pfam PF18487: Thrombospondin type 1 repeat (repeat)
This is a thrombospondin type I repeat (TSR) found in properdin. Properdin, also known as factor P (fP), is a glycoprotein constructed from a common pool of structure units or modules, which are homologous to the thrombospondin type 1 repeat, TSR. It is positive regulator of the complement system that stabilises the alternative pathway C3-convertase C3bBb. Properdin also inhibits the factor H-mediated cleavage of C3b by factor I. In addition, properdin acts as a pattern recognition molecule capable of identifying and interacting with microbial surfaces, apoptotic cells, and necrotic cells. However this role of pattern recognition is controversial. Studies indicate that this domain is a TSR variants. It is present at the N-terminal of properdin and has been denoted as TSR-0. It is suggested that the TSR-0 domain of properdin which possesses only the six Cys residues and no CWR-layered motif (which is usually found in other TSR domains) may constitute a truncated TSR domain.
Pfam PF20148: Domain of unknown function (DUF6531) (domain)
This putative domain is found in a range of RHS 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 PF04826: Armadillo-like (repeat)
This domain contains armadillo-like repeats. Proteins containing this domain interact with numerous other proteins, through these interactions they are involved in a wide variety of processes including carcinogenesis, control of cellular ageing and survival, regulation of circadian rhythm and lysosomal sorting of G protein-coupled receptors.
Wikipedia: An armadillo repeat is a characteristic, repetitive amino acid sequence of about 42 residues in length that is found in many proteins. Proteins that contain armadillo repeats typically contain several tandemly repeated copies. Each armadillo repeat is composed of a pair of alpha helices that form a hairpin structure. Multiple copies of the repeat form what is known as an alpha solenoid structure.
Pfam PF21525: Neuropeptide-like peptide 36 (family)
Caenorhabditis elegans possesses three groups of neuropeptides designated as MRFamide-like peptide (FLP), insulin-like (INS), as well as neuropeptide-like proteins (NLP). The NLP family keeps expanding, but the function of most of the members is still unknown. This family represents NLP-36 from C. elegans and related proteins.
Pfam PF01458: SUF system FeS cluster assembly, SufBD core domain (domain)
Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S]. FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA. SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. SufA is homologous to IscA, acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. This entry represents the core domain of SufB and SufD proteins, which are homologous, and form part of the SufBCD complex in the SUF system. SufB accepts sulfur transferred from SufE, whereas SufD may play a role in iron acquisition.
Pfam PF13442: Cytochrome C oxidase, cbb3-type, subunit III (domain)
After cytochrome c is synthesized in the cytoplasm as apocytochrome c, it is transported through the outer mitochondrial membrane to the intermembrane space, where haem is covalently attached by thioester bonds to two cysteine residues located in the cytochrome c centre. Cytochrome c is required during oxidative phosphorylation as an electron shuttle between Complex III (cytochrome c reductase) and IV (cytochrome c oxidase). In addition, cytochrome c is involved in apoptosis in more complex organisms such as Xenopus, rats and humans. Cellular stress can induce cytochrome c release from the mitochondrial membrane. In mammals, cytochrome c triggers the assembly of the apoptosome, consisting of cytochrome c, Apaf-1 and dATP, which activates caspase-9, leading to cell death . There are several different members of the cytochrome c family with different functional roles, for instance cytochrome c549 is associated with photosystem II .
Pfam PF15187: Oesophageal cancer-related gene 4 (family)
Augurin is alternatively named oesophageal cancer-related gene 4 protein. The function of this family of transmembrane proteins, is to induce the senescence of oligodendrocyte and neural precursor cells, characterised by G1 arrest, RB1 dephosphorylation and accelerated CCND1 and CCND3 proteasomal degradation. Augurin has been found to stimulate the release of ACTH via the release of hypothalamic CRF. This family of proteins is found in eukaryotes. Proteins in this family are typically 145 amino acids in length.
Pfam PF16443: Domain of unknown function (DUF5040) (family)
This family consists of several uncharacterized proteins around 260 residues in length and is mainly found in various Bacteroides species. The function of this family 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 PF23968: Phage cement protein (family)
This entry represents a small family of phage proteins. These proteins form a trimeric arrangement which stabilises the phage capsid. The proteins have what is known as a beta-tulip fold.
Pfam PF24419: Polynucleotide 5'-hydroxyl-kinase NOL9, N-terminal domain (domain)
This domain is found towards the N-terminal end of human Polynucleotide 5'-hydroxyl-kinase NOL9 and similar animal sequences. NOL9 can phosphorylate single-stranded and double-stranded RNA and DNA substrates. This domain is predicted to adopt a cupin fold.