SII-SWORD/CoKE huggingface dataset:
Pfam PF16844: Dinitrogenase iron-molybdenum cofactor, N-terminal (domain)
DIMCO_N is the N-terminal domain of the gamma (Y) subunit of nitrogenase. An alternative name is NafY_N, for nitrogenase accessory factor Y N-terminal. This region is negatively charged and appears to be necessary for recognising and interacting with the apo state of dinitrogenase. The full-length NafY protein facilitates the transfer of iron-molybdenum cofactor, or FeMo-co, into apodinitrogenase by binding to both. The C-terminal region, family Nitro_FeMo-Co, [pfam:PF02579], is the part that binds to the cofactor, and the N-terminus binds to apodinitrogenase. Nitrogenase is the bacterial enzyme responsible for nitrogen fixation by catalysing the reduction of nitrogen gas (N2) to ammonium in an ATP-dependent manner. It has two components, dinitrogenase and dinitrogenase reductase.
Pfam PF22250: Vacuolar membrane protease, C-terminal domain (domain)
This entry includes fungal vacuolar membrane proteases, such as PFF1 from yeast, which may be involved in vacuolar sorting and osmoregulation. It is an homologue of human ERMP1. According to AlphaFold structure prediction, these proteins consist of a M28 peptidase domain ([pfam:PF04389]) at the N-terminal, a central transmembrane domain and a C-terminal domain with an elongated beta-sandwich-like fold, similar to the Mu homology domain (MHD) ([pfam:PF00928]). This entry represents the C-terminal MHD-like domain of PFF1 and its fungal homologues.
Pfam PF23764: GLAA-B beta-barrel domain II (domain)
This entry represents the second beta-barrel domain found in Alpha-1,3-galactosidase A-B (GLAA-B)from bacteria. This proteins share a domain architecture consisting of a core beta-helix surrounded by two small beta-barrel domains (domains I and II), which are involved in protein dimerization. The alpha-helix of domain II folds over and along the wall of the active site of the adjacent monomer, with several residues protruding into the cleft that contains the active site pocket. Proteins GLAA-B are alpha-galactosidases grouped in the GH110 subfamily by its narrow subtract specificity. This remove branched alpha-1,3-linked galactose residues present in blood group B antigens.
Pfam PF02192: PI3-kinase family, p85-binding domain (family)
Phosphatidylinositol 3-kinases (PI3Ks) are lipid kinases that phosphorylate 4,5-bisphonate (PI(4,5) P2 or PIP2) at the 3-position of the inositol ring, and thus generate phosphatidylinositol 3,4,5-trisphosphate (PIP3), which, in turns, initiates a vast array of signaling events. PI3Ks can be grouped into three classes based on their domain organisation. Class I PI3Ks are heterodimers consisting of a p110 catalytic subunit and a regulatory subunit of either the p85 type (associated with the class IA p110 isoforms p110alpha, p110beta or p110delta) or the p101 type (associated with the class IB p110 isoform p110gamma). Common to all catalytic subunits are an N-terminal adaptor-binding domain (ABD) that binds to p85/p101, a Ras-binding domain (RBD), a putative membrane-binding domain (C2), a helical domain of unknown function, and a kinase catalytic domain .

PI3K_ABD is a small globular domain of about 100 residues in length with an Î±/Î²-sandwich topology .
Pfam PF17027: Histone-fold protein (domain)
This is a family of microsporidia-specific sequences that have distant homology to the Bromo_TP family, [pfam:PF07524].
Pfam PF08853: Domain of unknown function (DUF1823) (domain)
This presumed domain is functionally uncharacterised.
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 PF11877: Protein of unknown function (DUF3397) (family)
This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 114 to 128 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 PF00890: FAD binding domain (family)
This family includes members that bind FAD.  This family includes the flavoprotein subunits from succinate and fumarate dehydrogenase, aspartate oxidase and the alpha subunit of adenylylsulphate reductase.
Wikipedia: Succinate dehydrogenase (SDH) or succinate-coenzyme Q reductase (SQR) or respiratory complex II is an enzyme complex, found in many bacterial cells and in the inner mitochondrial membrane of eukaryotes. It is the only enzyme that participates in both the citric acid cycle and oxidative phosphorylation. Histochemical analysis showing high succinate dehydrogenase in muscle demonstrates high mitochondrial content and high oxidative potential.
Pfam PF25095: KIN17 C2H2-type zinc finger domain (domain)
KIN17 is an essential nuclear protein that functions in DNA replication, DNA repair and cell cycle control. This entry represents the C2H2-type zinc finger domain found at the N-terminal which is involved in RNA binding.
Pfam PF15052: TMEM169 protein family (family)
This domain is thought to be structured transmembrane helices and includes the intermediary cytoplasmic domain. It is found in eukaryotes, and is approximately 130 amino acids in length.
Pfam PF18651: Surface adhesin CshA non-repetitive domain 2 (domain)
The multifunctional fibrillar adhesin CshA, which mediates binding to both host molecules and other microorganisms, is an important determinant of colonization by Streptococcus gordonii, an oral commensal and opportunistic pathogen of animals and humans. CshA binds the high-molecular-weight glycoprotein fibronectin (Fn) via an N-terminal non-repetitive region, and this protein-protein interaction has been proposed to promote S. gordonii colonization at multiple sites within the host. This 259-kDa polypeptide is organized in the form of a leader peptide (residues 1-41), a non-repetitive region (residues 42-778), 17 repeat domains (R1-R17, each about 101-aa residues), and a C-terminal cell wall anchor. The non-repetitive Fn-binding region of CshA in turn is composed of three distinct domains, designated as non-repetitive domain 1 (NR1, CshA(42-222)), non-repetitive domain 2 (NR2, CshA(223-540)), and non-repetitive domain 3 (NR3, CshA(582-814)). The NR2 domain of CshA is shown to adopt a globular structure with a lectin-like fold and a ligand-binding site on its surface with structural homologues identified as those involved in binding carbohydrates or glycoproteins.
Pfam PF23757: Insect HPS5 TPR domain (repeat)
This entry represents the TPR domain found at the C-terminal of HPS5 protein from insects, a component of the biogenesis of lysosome-related organelles complex-2 (BLOC-2). Its mutation or absence has been linked to eye-colour mutations. The function of this domain is unknown.
Pfam PF24292: Domain of unknown function (DUF7479) (domain)
This domain is found in uncharacterised bacterial proteins. It contains four invariant cysteines and it is predicted to adopt a Zn-ribbon 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 PF22599: SecDF, P1 head subdomain (domain)
This entry represents the head subdomain from P1 domain from SecDF proteins, which constitutes a critical element for proton transport. P1 domain P1 binds an unfolded protein, and undergoes functionally important conformational changes. SecDF functions as a membrane-integrated chaperone that mediates ATP-independent protein translocation.
Pfam PF19903: Family of unknown function (DUF6376) (family)
This family of bacterial proteins is functionally uncharacterised. Proteins in this family are approximately 150 amino acids in length. Probably, this family correspond to lipoproteins.
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 PF06387: D1 dopamine receptor-interacting protein (calcyon) (family)
This family consists of several  D1 dopamine receptor-interacting (calcyon) proteins.  D1/D5 dopamine receptors in the basal ganglia, hippocampus, and cerebral cortex modulate motor, reward, and cognitive behaviour. D1-like dopamine receptors likely modulate neocortical and hippocampal neuronal excitability and synaptic function via Ca(2+) as well as cAMP-dependent signaling. Defective calcyon proteins have been implicated in both attention-deficit/hyperactivity disorder (ADHD) and schizophrenia.
Pfam PF22230: CRISPR system endoribonuclease Csx1, CARF domain (domain)
CRISPR system endoribonuclease Csx1 is a metal-independent, endoribonuclease that acts selectively on ssRNA and cleaves specifically after adenosines, as part of the type III-B CRISP-Cas system and it is homologous to Csm6, sharing the same domain domain architecture consisting of a CARF domain at the N-terminal that is relatively well conserved, and a HEPN nuclease domain at the C-terminal. This entry represents the CARF (CRISPR-associated Rossmann fold) domain, which binds and cleaves the cyclic oligoadenylate molecule (cA) that then activates the HEPN domain.
Pfam PF01922: SRP19 protein (family)
The signal recognition particle (SRP) binds to the signal peptide of proteins as they are being translated. The binding of the SRP halts translation and the complex is then transported to the endoplasmic reticulum's cytoplasmic surface. The SRP then aids translocation of the protein through the ER membrane. The SRP is a ribonucleoprotein that is composed of a small RNA and several proteins. One of these proteins is the SRP19 protein (Sec65 in yeast).
Pfam PF18959: Family of unknown function (DUF5701) (family)
This is a family of unknown function mostly found in bacteria.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF07106: TBPIP/Hop2 winged helix domain (domain)
This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation. TBPIP was found to be an activator that specifically stimulates the homologous pairing catalyzed by DMC1. Family members also include yeast homologous-pairing protein 2 (Hop2) and its homologues from animals and plants. They are required for proper homologous pairing and efficient cross-over and intragenic recombination during meiosis.
Pfam PF12046: Cofactor assembly of complex C subunit B (family)
Cofactor maturation pathways such as the CCB system (system IV) for cytochrome c-heme attachment are conserved in all organisms performing oxygenic photosynthesis. The CCB system consists of four protein, CCB1-4. The four CCBs are well conserved between green algae and plants.
Pfam PF09637: Med18 protein (domain)
Med18 is one subunit of Mediator, a head-module multiprotein complex, that stimulates basal RNA polymerase II (Pol II) transcription. Med18 consists of an eight-stranded beta-barrel with a central pore and three flanking helices. It complexes with Med8 and Med20 proteins by forming a heterodimer of two-fold symmetry with Med20 and binding the C-terminal alpha-helix region of Med8 across the top of its barrel. This complex creates a multipartite TBP-binding site that can be modulated by transcriptional activators.
Wikipedia: Mediator is a multiprotein complex that functions as a transcriptional coactivator in all eukaryotes. It was discovered in 1990 in the lab of Roger D. Kornberg, recipient of the 2006 Nobel Prize in Chemistry. Mediator complexes interact with transcription factors and RNA polymerase II. The main function of mediator complexes is to transmit signals from the transcription factors to the polymerase.
Pfam PF03931: Skp1 family, tetramerisation domain (domain)
SKP1 (together with SKP2) was identified as an essential component of the cyclin A-CDK2 S phase kinase complex . It was found to bind several F-box containing proteins (e.g., Cdc4, Skp2, cyclin F) and to be involved in the ubiquitin protein degradation pathway. A yeast homologue of SKP1 (P52286) was identified in the centromere bound kinetochore complex  and is also involved in the ubiquitin pathway . In Dictyostelium discoideum (Slime mold) FP21 was shown to be glycosylated in the cytosol and has homology to SKP1 .

This entry represents a POZ domain with a core structure consisting of Î²(2)/Î±(2)/Î²(2)/Î±(2) in two layers, Î±/Î². This domain is found at the N-terminal of SKP1 proteins  as well as in subunit D of the centromere DNA-binding protein complex Cbf3 .
Pfam PF11942: Spt5 transcription elongation factor, acidic N-terminal (disordered)
This is the very acidic N-terminal region of the early transcription elongation factor Spt5. The Spt5-Spt4 complex regulates early transcription elongation by RNA polymerase II and has an imputed role in pre-mRNA processing via its physical association with mRNA capping enzymes. The actual function of this N-terminal domain is not known although it is dispensable for binding to Spt4.
Pfam PF18997: Domain of unknown function (DUF5727) (domain)
A conserved domain of unknown function found in Platyhelminthes, closely related to glycosylphosphatidylinositol (GPI)-anchored protein GP50, known as Diagnostic antigen GP50. GP50 is a family of highly expressed antigens exclusive to tapeworms. This domain, according to structure predictions, seems to consist of two beta-sandwiches.
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 PF20432: Antitoxin Xre-like helix-turn-helix domain (domain)
This entry represents the N-terminal domain of the antitoxin component Xre of a type II toxin-antitoxin (TA) system, which is the helix-turn-helix (HTH) DNA binding domain, structurally similar to the Cro repressor, therefore, also referred to as HTH/Cro-like DNA-binding domain. This domain is also found in other antitoxin components, associated with a C-terminal toxin-binding domain [pfam:PF09722].
Pfam PF00637: Region in Clathrin and VPS (repeat)
Each region is about 140 amino acids long. The regions are composed of multiple alpha helical repeats. They occur in the arm region of the Clathrin heavy chain.
Pfam PF02480: Alphaherpesvirus glycoprotein E (domain)
Glycoprotein E (gE) of Alphaherpesvirus forms a complex with glycoprotein I (gI) ([pfam:PF01688]), functioning as an immunoglobulin G (IgG) Fc binding protein. gE is involved in virus spread but is not essential for propagation. This entry represents the Ig-like domain of gE, identified as the Fc-binding domain.
Pfam PF15449: Retinal protein (family)
This family of proteins is found in the photoreceptor cells of the retina. Mutations of the gene encoding this protein have been associated with retinal disorders such as retinitis pigmentosa and late-onset progressive retinal atrophy. The function of this family of proteins is unknown, but it is likely to be important in the development and function of the retina.
Pfam PF14832: Putative oxalocrotonate tautomerase enzyme (domain)
4-oxalocrotonate tautomerase enzyme is involved in the anthranilate synthase pathway.1
Wikipedia: 4-Oxalocrotonate tautomerase or 4-OT is an enzyme that converts 2-hydroxymuconate to the αβ-unsaturated ketone, 2-oxo-3-hexenedioate. This enzyme forms part of a bacterial metabolic pathway that oxidatively catabolizes toluene, o-xylene, 3-ethyltoluene, and 1,2,4-trimethylbenzene into intermediates of the citric acid cycle. With a monomer size of just 62 amino acid residues, the 4-Oxalocrotonate tautomerase is one of the smallest enzyme subunits known. However, in solution, the enzyme forms a hexamer of six identical subunits, so the active site may be formed by amino acid residues from several subunits. This enzyme is also unusual in that it uses a proline residue at the amino terminus as an active site residue.
Pfam PF20513: Prokaryotic ubiquitin-like protein UBact (family)
UBact is a ubiquitin-like protein found in Gram-negative bacteria. It differs from ubiquitin and most ubiquitin-like proteins (including the mycobacterial Pup) in that it lacks the characteristic C-terminal di-glycine motif. UBact conjugation-degradation system appears to be homologous to the pupylation system for proteasomal degradation in bacteria.
Pfam PF01564: Spermine/spermidine synthase domain (domain)
Spermine and spermidine are polyamines. This family includes spermidine synthase that catalyses the fifth (last) step in the biosynthesis of spermidine from arginine, and spermine synthase.
Pfam PF21748: UPF0150-like (domain)
This is a family of uncharacterized proteins that fold into an alpha-beta-beta-beta-alpha fold and are structurally similar to HicB-like antitoxin. They are probably involved in RNA metabolism, RNA cleavage and binding.
Pfam PF03388: Legume-like lectin family (domain)
Lectins are structurally diverse proteins that bind to specific carbohydrates. This family includes the VIP36 [swissprot:P49256] and ERGIC-53 [swissprot:P49257] lectins. These two proteins were the first recognised members of a family of animal lectins similar (19-24%) to the leguminous plant lectins. The alignment for this family aligns residues lying towards the N-terminus, where the similarity of VIP36 and ERGIC-53 is greatest. However, while Fiedler and Simons identified these proteins as a new family of animal lectins, our alignment also includes yeast sequences. ERGIC-53 is a 53kD protein, localised to the intermediate region between the endoplasmic reticulum and the Golgi apparatus (ER-Golgi-Intermediate Compartment, ERGIC). It was identified as a calcium-dependent, mannose-specific lectin. Its dysfunction has been associated with combined factors V and VIII deficiency OMIM:227300 OMIM:601567, suggesting an important and substrate-specific role for ERGIC-53 in the glycoprotein- secreting pathway.
Wikipedia: In molecular biology the L-like lectin domain is a protein domain found in lectins which are similar to the leguminous plant lectins.
Pfam PF06068: TIP49 P-loop domain (domain)
This family consists of the C-terminal region of several eukaryotic and archaeal RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin or TIP49b) proteins. The N-terminal domain contains the [pfam:PF00004] domain. In zebrafish, the liebeskummer (lik) mutation, causes development of hyperplastic embryonic hearts. lik encodes Reptin, a component of a DNA-stimulated ATPase complex. Beta-catenin and Pontin, a DNA-stimulated ATPase that is often part of complexes with Reptin, are in the same genetic pathways. The Reptin/Pontin ratio serves to regulate heart growth during development, at least in part via the beta-catenin pathway. TBP-interacting protein 49 (TIP49) was originally identified as a TBP-binding protein, and two related proteins are encoded by individual genes, tip49a and b. Although the function of this gene family has not been elucidated, they are supposed to play a critical role in nuclear events because they interact with various kinds of nuclear factors and have DNA helicase activities.TIP49a has been suggested to act as an autoantigen in some patients with autoimmune diseases.
Pfam PF12257: Vacuolar membrane-associated protein Iml1, N-terminal domain (domain)
Proteins in this family contain a DEP domain, which is a globular domain of about 80 residues. This entry includes vacuolar membrane-associated protein Iml1 and DEP domain-containing protein 5/DDB_G0279099. In Saccharomyces cerevisiae, Iml1 is a subunit of both the  SEA (Seh1-associated) and Iml1 complexes (Iml1-Npr2-Npr3). SEA complex is associates dynamically with the vacuole and is involved in autophagy. Iml1 complex is required  for non-nitrogen-starvation (NNS)-induced autophagy.
Pfam PF18062: Restriction endonuclease AspBHI N-terminal (domain)
This is the N-terminal domain found in modification-dependent restriction endonuclease proteins such as AspBHI, which can be found in Azoarcus sp. AspBHI is a homo-tetrameric protein that recognizes 5-methylcytosine in the double-strand DNA sequence context of (C/T) (C/G) (5mC) nucleotide (C/G) and cleaves the two strands at a fixed distance (N12/N16) 3 to the modified cytosine. The N-terminal domain is responsible for DNA-recognition and resembles an SRA-like 5-methylcytosine binding domain in structure and function.
Pfam PF11559: Afadin- and alpha -actinin-Binding (coiled_coil)
This family is found in mammals where it is localised at cell-cell adherens junctions, and in Sch. pombe and other fungi where it anchors spindle-pole bodies to spindle microtubules. It is a coiled-coil structure, and in pombe, it is required for anchoring the minus end of spindle microtubules to the centrosome equivalent, the spindle-pole body. The name ADIP derives from the family being composed of Afadin- and alpha -Actinin-Binding Proteins Localised at Cell-Cell Adherens Junctions.
Pfam PF00079: Serpin (serine protease inhibitor) (domain)
Structure is a multi-domain fold containing a bundle of helices and a beta sandwich.
Wikipedia: Serpins are a superfamily of proteins with similar structures that were first identified for their protease inhibition activity and are found in all kingdoms of life. The acronym serpin was originally coined because the first serpins to be identified act on chymotrypsin-like serine proteases. They are notable for their unusual mechanism of action, in which they irreversibly inhibit their target protease by undergoing a large conformational change to disrupt the target's active site. This contrasts with the more common competitive mechanism for protease inhibitors that bind to and block access to the protease active site.