SII-SWORD/CoKE huggingface dataset:
Pfam PF02913: FAD linked oxidases, C-terminal domain (domain)
This domain has a ferredoxin-like fold.
Wikipedia: In molecular biology FAD-oxidases are a family of FAD-dependent oxidoreductases. They are flavoproteins that contain a covalently bound FAD group which is attached to a histidine via an 8-alpha-(N3-histidyl)-riboflavin linkage. The region around the histidine that binds the FAD group is conserved in these enzymes.
Pfam PF17740: Family of unknown function (DUF5577) (family)
This is a family of unknown function found in Metazoa.
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 PF23849: Phage tail tube protein (domain)
This entry represents a family of phage proteins that by structural similarity are highly likely to be phage tail tube proteins that oligomerise to make the phage tail. These proteins are composed of a distinctive beta barrel structure.
Pfam PF21944: Hemotin (family)
This protein family includes Hemotin from Drosophila melanogaster and similar sequences mainly found in arthropods. Hemotin is a 88-residues transmembrane small ORF (smORF) peptide that regulates endosomal maturation during phagocytosis. Its homologue in vertebrates is human Stannin ([swissprot:O75324]), a peptide involved in organometallic toxicity.
Pfam PF00558: Vpu protein (domain)
The Vpu protein contains an N-terminal transmembrane spanning region and a C-terminal cytoplasmic region. The HIV-1 Vpu protein stimulates virus production by enhancing  the release of viral particles from infected cells. The VPU protein binds specifically to CD4.
Pfam PF24502: TMEM131 homolog third Ig-like domain (domain)
This entry represents the third Ig-like domain of TMEM131 from Drosophila and related sequences from flies, which is the orthologue of human TMEM131. This is a collagen binding transmembrane protein involved in collagen secretion, probably by recruiting the ER-to-Golgi transport complex TRAPPIII.
Pfam PF21160: Serine/threonine protein kinase-like, C-terminal PASTA-like domain (domain)
This domain is found in Non-specific serine/threonine protein kinase from Staphylococcus aureus (PrkC) and similar bacterial proteins. PrkC is responsible for triggering spore germination in response to muropeptides, signaling bacteria to exit dormancy. The extracellular region of PrkC is a linear modular structure composed of three PASTA (penicillin binding-associated and serine/threonine kinase- associated, [pfam:PF03793]) domains and a PASTA-like C-terminal domain, which presents an immunoglobulin-like fold and the typical features of adhesive proteins.
Pfam PF00120: Glutamine synthetase, catalytic domain (domain)
This entry represents the C-terminal catalytic domain of GS enzymes.
Glutamine synthetase (6.3.1.2) (GS)  plays an essential role in the metabolism of nitrogen by catalysing the condensation of glutamate and ammonia to form glutamine.

There seem to be three different classes of GS :


 * Class I enzymes (GSI) are specific to prokaryotes, and are oligomers of 12 identical subunits. The activity of GSI-type enzyme is controlled by the adenylation of a tyrosine residue. The adenylated enzyme is inactive (see IPR001637).
 * Class II enzymes (GSII) are found in eukaryotes and in bacteria belonging to the Rhizobiaceae, Frankiaceae, and Streptomycetaceae families (these bacteria have also a class-I GS). GSII are octamer of identical subunits. Plants have two or more isozymes of GSII, one of the isozymes is translocated into the chloroplast.
 * Class III enzymes (GSIII) have been found in Bacteroides fragilis. in Butyrivibrio fibrisolvens. It is a hexamer of identical chains and in some protozoa. It is much larger (about 700 amino acids) than the GSI (450 to 470 amino acids) or GSII (350 to 420 amino acids) enzymes.


While the three classes of GS's are clearly structurally related, the sequence similarities are not so extensive.
Wikipedia: Glutamine synthetase (GS) is an enzyme that plays an essential role in the metabolism of nitrogen by catalyzing the condensation of glutamate and ammonia to form glutamine:
Pfam PF13016: Cys-rich Gliadin N-terminal (family)
This is a cysteine-rich N-terminal region of gliadin and avenin plant proteins. The exact function is not known.
Pfam PF06937: EURL protein (family)
This family consists of several animal EURL proteins. EURL is preferentially expressed in chick retinal precursor cells as well as in the anterior epithelial cells of the lens at early stages of development. EURL transcripts are found primarily in the peripheral dorsal retina, i.e., the most undifferentiated part of the dorsal retina. EURL transcripts are also detected in the lens at stage 18 and remain abundant in the proliferating epithelial cells of the lens until at least day 11. The distribution pattern of EURL in the developing retina and lens suggest a role before the events leading to cell determination and differentiation.
Pfam PF13550: Putative phage tail protein (domain)
This putative domain is found in the large gene transfer agent protein. These produce defective phage like particles. This domain is similar to other phage-tail protein families.
Pfam PF03737: Aldolase/RraA (family)
Members of this family include regulator of ribonuclease E activity A (RraA) and 4-hydroxy-4-methyl-2-oxoglutarate (HMG)/4-carboxy- 4-hydroxy-2-oxoadipate (CHA) aldolase, also known as RraA-like protein. RraA acts as a trans-acting modulator of RNA turnover, binding essential endonuclease RNase E and inhibiting RNA processing. RraA-like proteins seem to contain aldolase and/or decarboxylase activity either in place of or in addition to the RNase E inhibitor functions.
Pfam PF08445: FR47-like protein (family)
The members of this family are similar to the C-terminal region of the D. melanogaster hypothetical protein FR47 ([swissprot:Q9VR51]). This protein has been found to consist of two N-acyltransferase-like domains swapped with the C-terminal strands.
Pfam PF07827: KNTase C-terminal domain (domain)
Kanamycin nucleotidyltransferase (KNTase) is involved  in conferring resistance to aminoglycoside antibiotics  and catalyses the transfer of a nucleoside monophosphate  group from a nucleotide to kanamycin. This enzyme is dimeric with each subunit being composed of two domains.  The C-terminal domain contains five alpha helices, four of which are organised into an up-and-down alpha helical  bundle. Residues found in this domain may contribute to this enzyme's active site.
Wikipedia: In molecular biology, kanamycin nucleotidyltransferase EC 2.7.7.- (KNTase) is an enzyme which is involved in conferring resistance to aminoglycoside antibiotics. It catalyses the transfer of a nucleoside monophosphate group from a nucleotide to kanamycin. This enzyme is dimeric with each subunit being composed of two domains. The C-terminal domain contains five alpha helices, four of which are organised into an up-and-down alpha helical bundle. Residues found in this domain may contribute to this enzyme's active site.
Pfam PF12360: Paired box protein 7 (family)
This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with [pfam:PF00046], [pfam:PF00292].  Pax7 belongs to a family of genes that encode paired-box-containing transcription factors involved in the control of developmental processes. Pax7 has a distinct role in the specification of myogenic satellite cells.
Pfam PF21854: Treslin, N-terminal domain (domain)
This entry represents the N-terminal domain of treslin, the metazoan counterpart of Sld3 from yeast, which are the hub proteins mediating protein associations critical for the helicase formation. Treslin, as Sld3, interacts with TopBP1 in a Cdk2-dependent manner, which then collaborate in the Cdk2-mediated loading of Cdc45 onto replication origins. Treslin and Sld3 differ in their molecular sizes and amino acid sequences, however, they share a conserved Sld3/Treslin domain (STD). According to their similarities, it has been suggested that helicase activation in mammals has diverged in complexity during evolution from that in yeasts and may involve additional partners that interact with TopBP1. This N-terminal domain is also referred to as conserved in Treslins (CIT) which has a von Willebrand factor type A (vWA) fold and its function in replication is not clear.
Pfam PF18806: Importin 13 repeat (repeat)
Importin 13 serves as receptor for nuclear localization signals (NLS) in cargo substrates. It mediates docking of the importin/substrate complex to the nuclear pore complex (NPC). It contains several repeats structurally similar to the HEAT repeat. This Pfam entry represents a single repeat unit.
Pfam PF10592: AIPR protein (family)
This family of proteins was identified in as an abortive infection phage resistance protein often found in restriction modification system operons.
Pfam PF02203: Tar ligand binding domain homologue (domain)
This entry represents the ligand-binding domain found in a number of methyl-accepting chemotaxis receptors, such as E.coli Tar (taxis to aspartate and repellents), which is a receptor for the attractant L-aspartate and also recognises proteogenic amino acids, phthalic acid, Malic acid, 3,4-dihydroxymandelic acid, citrate, benzoate and derivatives, protocatechuate, vanillate, quinate, shikimate and dehydroshikimate (Matilla et al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).
Wikipedia: The methyl-accepting chemotaxis proteins are a family of transmembrane receptors that mediate chemotactic response in certain enteric bacteria, such as Salmonella enterica enterica and Escherichia coli. These methyl-accepting chemotaxis receptors are one of the first components in the sensory excitation and adaptation responses in bacteria, which act to alter swimming behaviour upon detection of specific chemicals. Use of the MCP allows bacteria to detect concentrations of molecules in the extracellular matrix so that the bacteria may smooth swim or tumble accordingly. If the bacterium detects rising levels of attractants (nutrients) or declining levels of repellents (toxins), the bacterium will continue swimming forward, or smooth swimming. If the bacterium detects declining levels of attractants or rising levels of repellents, the bacterium will tumble and re-orient itself in a new direction. In this manner, a bacterium may swim towards nutrients and away from toxins
Pfam PF07655: Secretin N-terminal domain (domain)
This is a short domain found in bacterial type II/III secretory system proteins. The architecture of these proteins suggest that this family may be functionally analogous to [pfam:PF03958].
Pfam PF08328: Adenylosuccinate lyase C-terminal (family)
This domain is found at the C-terminus of adenylosuccinate lyase(ASL; PurB in E. coli). It has been identified in bacteria, eukaryotes and archaea and is found together with the lyase domain [pfam:PF00206].  ASL catalyses the cleavage of succinylaminoimidazole carboxamide ribotide to aminoimidazole carboxamide ribotide and fumarate and the cleavage of adenylosuccinate to adenylate and fumarate.
Pfam PF15498: Nephrin and CD2AP-binding protein, Dendrin (family)
Dendrin is a family of eukaryotic proteins found in the podocytes of the kidneys. Dendrin, originally identified in telencephalic dendrites, is a constituent of the slit diaphragm, SD, complex of podocytes, where it directly binds to nephrin and CD2AP. Kidney podocytes and their slit diaphragms (SDs) form the final barrier to urinary protein loss. SD proteins also participate in intracellular signalling pathways. Dendrin appears to prevent programmed cell death (apoptosis) through its binding to nephrin. The SD protein nephrin serves as a component of a signalling complex that directly links podocyte junctional integrity to actin cytoskeletal dynamics. Thus, dendrin is identified as an SD family with proapoptotic signalling properties that accumulates in the podocyte nucleus in response to glomerular injury.
Pfam PF05676: NADH-ubiquinone oxidoreductase B18 subunit (NDUFB7) (family)
This family consists of several NADH-ubiquinone oxidoreductase B18 subunit proteins from different eukaryotic organisms. Oxidative phosphorylation is the well-characterised process in which ATP, the principal carrier of chemical energy of individual cells, is produced due to a mitochondrial proton gradient formed by the transfer of electrons from NADH and FADH2 to molecular oxygen. The oxidative phosphorylation (OXPHOS) system is located in the mitochondrial inner membrane and consists of five multi-subunit enzyme complexes and two small electron carriers: coenzyme Q10 and cytochrome C. At least 70 structural proteins involved in the formation of the whole OXPHOS system are encoded by nuclear genes, whereas 13 structural proteins are encoded by the mitochondrial genome. Deficiency of NADH ubiquinone oxidoreductase, the first enzyme complex of the mitochondrial respiratory chain, is one of the most frequent causes of human mitochondrial encephalomyopathies.
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 PF07711: Rab geranylgeranyl transferase alpha-subunit, insert domain (domain)
Rab geranylgeranyl transferase (RabGGT) catalyses the addition of two geranylgeranyl groups to the C-terminal cysteine residues of Rab proteins, which is crucial for membrane association and function of these proteins in intracellular vesicular trafficking.  This domain is inserted between [pfam:PF01239] repeats.  This domain adopts an Ig-like fold and is thought to be involved in protein-protein interactions and might be involved in the recognition and binding of REP.
Pfam PF05003: Protein of unknown function (DUF668) (family)
This entry represents the C-terminal domain of PSI proteins from Arabidopsis. This domain is found associated with [pfam:PF11961]. PSI1 was identified as a gene that is co-expressed with the phytosulfokine (PSK) receptor genes PSKR1 and PSKR2 in Arabidopsis thaliana. PSI proteins are plant-specific and promote growth.
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 PF20799: Protein-L-isoaspartyl O-methyltransferase, C-terminal domain (domain)
Protein-L-isoaspartyl O-methyltransferase (PIMT) from Thermotoga maritima is a conserved and nearly ubiquitous enzyme involved in the repair of proteins damaged by age-related isoaspartyl formation. PIMT consists of three domains. This entry represents its C-terminal domain, which shows a five-stranded beta meander flanked on both sides by alpha helices. Its function is unknown.
Pfam PF06593: Raspberry bushy dwarf virus coat protein (family)
This family consists of several Raspberry bushy dwarf virus coat proteins.
Pfam PF20735: Bacteriophage lambda ea8.5-related domain (domain)
This domain is found in Protein ea8.5 from Bacteriophage lambda and similar protein sequences mostly from tailed bacteriophages and bacterial prophages. It ranges from around 45 to 90 residues in length and is associated with nucleic acid binding function, playing an essential role in the inhibition of the initiation of DNA synthesis in the phage host. NMR analysis shows it adopts an homeodomain/zinc-finger fold, which suggests a regulatory role.
Pfam PF20635: Survival Motor Neuron, YG-box (domain)
Survival Motor Neuron (SMN) protein forms the oligomeric core of a multi-protein complex that functions in spliceosomal snRNP biogenesis. Mutations in the SMN gene cause spinal muscular atrophy (SMA). It has three highly conserved domains: a short N-terminal segment responsible for binding with high affinity to Gemin2, therefore, called Gemin2-binding domain (G2-BD), a central Tudor domain ([pfam:PF06003]) that recognises symmetric dimethylarginine (sDMA) modifications in proteins involved in RNA processing, and a C-terminal domain, represented in this entry, referred to as the 'YG-box'. This domain contains three overlapping motifs: GxxxGxxxG, YxxxYxxxY and SxxxSxxxSxxxT. The YG-box forms helical oligomers similar to the glycine zippers found in transmembrane channels. The YG-box oligomers are thought to be involved in oligomerization and are likely to be used directly in mediating interactions that are crucial for SMN's functions. It has been reported that nearly half of the known SMA patient missense mutations map to the SMN YG-box.
Pfam PF24941: Domain of unknown function (DUF7757) (domain)
This is a presumed domain found at the N-terminal of a set of sequences from  Strongyloides stercoralis and similar worms. It may  adopt a beta-sandwich fold, related to MATH domains.
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 PF09405: CASC3/Barentsz eIF4AIII binding (domain)
This domain is found on CASC3 (cancer susceptibility candidate gene 3 protein) which is also known as Barentsz (Btz).  CASC3 is a component of the EJC (exon junction complex) which is a complex that is involved in post-transcriptional regulation of mRNA in metazoa.  The complex is formed by the association of four proteins (eIF4AIII, Barentsz, Mago, and Y14), mRNA, and ATP. This domain wraps around eIF4AIII and stacks against the 5' nucleotide.
Wikipedia: In molecular biology, the Btz domain is a protein domain found on CASC3 which is also known as Barentsz (Btz). CASC3 is a component of the EJC which is a complex that is involved in post-transcriptional regulation of mRNA in metazoa. The complex is formed by the association of four proteins, mRNA, and ATP. This domain wraps around eIF4AIII and stacks against the 5' nucleotide.
Pfam PF01047: MarR family (domain)
The Mar proteins are involved in the multiple antibiotic resistance, a non-specific resistance system. The expression of the mar operon is controlled by a repressor, MarR.  A large number of compounds induce transcription of the mar operon. This is thought to be due to the compound binding to MarR, and the resulting complex stops MarR binding to the DNA. With the MarR repression lost, transcription of the operon proceeds. The structure of MarR is known and shows MarR as a dimer with each subunit containing a winged-helix DNA binding motif.
Pfam PF09811: Essential protein Yae1, N terminal (family)
Members of this family are found in the N terminal region of the essential protein Yae1. Their exact function has not, as yet, been determined. The family DUF1715, [pfam:PF08215] has now been merged into this family.
Pfam PF02316: Mu DNA-binding domain (family)
This family consists of MuA-transposase and repressor protein CI. These proteins contain homologous DNA-binding domains at their N-termini which compete for the same DNA site within the Mu bacteriophage genome.
Wikipedia: Helix-turn-helix is a DNA-binding domain (DBD). The helix-turn-helix (HTH) is a major structural motif capable of binding DNA. Each monomer incorporates two α helices, joined by a short strand of amino acids, that bind to the major groove of DNA. The HTH motif occurs in many proteins that regulate gene expression. It should not be confused with the helix–loop–helix motif.
Pfam PF00380: Ribosomal protein S9/S16 (family)
This family includes small ribosomal subunit S9 from prokaryotes and S16 from eukaryotes.
Pfam PF15541: Bacterial toxin 4 (family)
A predicted RNase toxin found in bacterial polymorphic toxin systems.  The toxin possesses an alpha+beta fold that is usually exported by the Photorhabdus virulence cassette (PVC)-type export system.
Pfam PF02466: Tim17/Tim22/Tim23/Pmp24 family (family)
The pre-protein translocase of the mitochondrial outer membrane (Tom) allows the import of pre-proteins from the cytoplasm. Tom forms a complex with a number of proteins, including Tim17. Tim17, Tim22, and Tim23, are the central components of the widely conserved multi-subunit protein translocases, TIM23 and TIM22, which mediate protein transport across and into the inner mitochondrial membrane, respectively. In addition, several Tim17 family proteins occupy the inner and outer membranes of plastids. This family also includes Pmp24 a peroxisomal protein. The involvement of this domain in the targeting of PMP24 remains to be proved. PMP24 was known as Pmp27. Family members are suggested to be exclusive to eukaryotes, where the distribution in the eukaryotic subgroups of the mitochondrial Tim17, Tim22 and Tim23 proteins, as well as the peroxisomal Tim17 family proteins, suggests that they all likely to be present in the last eukaryotic common ancestor (LECA).
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 PF22794: ZPR1 jelly-roll domain (domain)
This entry represents the jelly-roll domain found in ZPR1 family. The zinc-finger protein ZPR1 is ubiquitous among eukaryotes. It is indeed known to be an essential protein in yeast. In quiescent cells, ZPR1 is localised to the cytoplasm. But in proliferating cells treated with EGF or with other mitogens, ZPR1 accumulates in the nucleolus. ZPR1 interacts with the cytoplasmic domain of the inactive EGF receptor (EGFR) and is thought to inhibit the basal protein tyrosine kinase activity of EGFR. This interaction is disrupted when cells are treated with EGF, though by themselves, inactive EGFRs are not sufficient to sequester ZPR1 to the cytoplasm. Upon stimulation by EGF, ZPR1 directly binds the eukaryotic translation elongation factor-1alpha (eEF-1alpha) to form ZPR1/eEF-1alpha complexes. These move into the nucleus, localising particularly at the nucleolus. Indeed, the interaction between ZPR1 and eEF-1alpha has been shown to be essential for normal cellular proliferation, and ZPR1 is thought to be involved in pre-ribosomal RNA expression. ZPR1 binds preferentially to GDP-bound eEF1A but does not directly influence the kinetics of nucleotide exchange or GTP hydrolysis. The alignment for the ZPR1 family shows a duplicated set composed of a zinc-ribbon domain followed by a jelly- roll domain (this entry). This family also includes several hypothetical archaeal proteins (from both Crenarchaeota and Euryarchaeota). This similarity between ZPR1 and archaeal proteins was not previously noted.
Pfam PF16282: SANT/Myb-like domain of DAMP1 (domain)
This domain, approximately 90 residues, is mainly found in DNA methyltransferase 1-associated protein 1 (DAMP1) that plays an important role in development and maintenace of genome integrity in various mammalia species. It mainly consists of tandem repeats of three alpha-helices that are arranged in a helix-turn-helix motif and shows a structual similarity with SANT domain and Myb DNA-binding domain, indicating it contains a putative DNA binding site.