SII-SWORD/CoKE huggingface dataset:
Pfam PF16823: Atypical PilZ domain, cyclic di-GMP receptor (domain)
Tetrameric PilZ (tPliZ, previously known as PilZ_2) is a family of cyclic di-GMP receptors found in Proteobacteria plant pathogens. tPilZ forms a tetramer that adopts a novel 'house-like' construct, with a central pillar domain of the four vertical alpha3 helices, a roof-top domain made up of the eight inclined alpha2 and alpha4 helices, and four corner-stone domains making up the PilZ domain. Cyclic-di-GMP is a universal secondary messenger molecule extensively involved in regulating bacterial pathogenicity which binds to cytoplasmic receptors containing PilZ domains. This domain is referred to as an atypical PilZ domain, it has the same structure as canonical PilZ domains with the exception of a short N-terminal alpha-helix and an insert that forms two additional alpha-helices.
Pfam PF24103: Neurotrophin 1 N-terminal (domain)
This domain is found N-terminal in fruit fly Neurotrophin 1 (NT) and related proteins from arthropods. NT binds to Toll-7 and probably acts as its ligand in promoting motor axon targeting and neuronal survival in the central nervous system (CNS). In larvae, NT is involved in the negative regulation of the tracheal immune response to bacterial infection by acting as a ligand for the Toll-related receptor Tollo. This domain is predicted to fold into a globular structure consisting of alpha helices. It is frequently found N-terminal to [pfam:PF16077].
Pfam PF22733: NACHT N-terminal Helical domain 1 (domain)
This entry represents an helical domain found at the N-terminus of bacterial NACHT conflict systems. This position is frequently occupied by an effector domain.
Pfam PF06267: Family of unknown function (DUF1028) (family)
Family of bacterial and archaeal proteins with unknown function. Some members are associated with a C-terminal peptidoglycan binding domain. So perhaps this could be an enzyme involved in peptidoglycan metabolism.
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 PF23448: CFAP184 CAP-like domain (domain)
This entry represents a domain found in Cilia- and flagella-associated protein 184 (also known as CCDC96, SwissProt:I7M6D6) from Tetrahymena thermophila and similar sequences. CFAP184 forms a complex with CFAP263, and acts as a regulator of ciliary beating that connects radial spoke 3 (RS3) to the inner dynein arm (IDA) and the nexin-dynein regulatory complex (N-DRC). This domain may have a CAP-like (cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1 proteins) fold according to structure predictions and comparison.
Pfam PF10555: Phospho-N-acetylmuramoyl-pentapeptide-transferase signature 1 (conserved_site)
Phospho-N-acetylmuramoyl-pentapeptide-transferase (EC 2.7.8.13) (mraY) is a bacterial enzyme responsible for the formation of the first lipid intermediate of the cell wall peptidoglycan synthesis. It catalyses the formation of undecaprenyl-pyrophosphoryl-N-acetylmuramoyl-pentapeptide from UDP-MurNAc-pentapeptide and undecaprenyl-phosphate. It is an integral membrane protein with probably ten transmembrane domains. This domain is located at the end of the first cytoplasmic loop and the beginning of the second transmembrane domain.
Pfam PF25129: Pyr4-like transmembrane terpene cyclases (domain)
This entry represents Pyr4 and related transmembrane terpene cyclases. These are noncanonical terpene cyclases that are involved in the biosynthesis of pyripyropene A, diterpenoid pyrones, novofumigatonin, austinol and dehydroaustinol and others. Pyr4 was the first integral membrane terpene cyclase that was identified. It is involved in the biosynthesis of pyripyropene A, a polyketide-sesquiterpenoid hybrid that is a potent inhibitor of acyl-coenzyme A:cholesterol acyl-transferase. These enzymes are presdicted to contain seven transmembrane helices. There is a highly conserved glutamate residue, part of [W/Y]ExxY motif, which is probably functionally important.
Pfam PF22183: Atadenovirus fibre, head domain (domain)
This entry represents the carboxy-terminal virus-distal fibre head  domain present in Atadenovirus. This domain is putatively responsible for primary receptor recognition. Atadenovirus fibre head domains has a similar beta-sandwich propeller topology found in other adenovirus fibre proteins (PDB:4d0u).
Pfam PF07476: Methylaspartate ammonia-lyase C-terminus (domain)
Methylaspartate ammonia-lyase [ec:4.3.1.2] catalyses the second step of fermentation of glutamate. It is a homodimer. This family represents the C-terminal region of Methylaspartate ammonia-lyase and contains a TIM barrel fold similar to the [pfam:PF01188]. This family represents the catalytic domain and contains a metal binding site.
Pfam PF12722: High-temperature-induced dauer-formation protein (family)
Hid1 (high-temperature-induced dauer-formation protein 1) represents proteins of approximately 800 residues long and is conserved from fungi to humans. Functionally it might be involved in vesicle secretion or be an inter-cellular signalling protein or be a novel insulin receptor. It was previously thought to contain up to seven potential transmembrane domains separated by regions of low complexity. However, biochemical membrane fraction analysis demonstrate that HID-1 is a peripheral membrane protein tightly associated with the Golgi apparatus but not a transmembrane protein predicted by the bioinformatic programs. Furthermore, it contains a conserved N-terminal myristoylation site was required for HID-1 binding to the Golgi apparatus.
Pfam PF12129: Homeodomain containing protein PHTF1/2, N-terminal (domain)
This domain is found in a group of homeodomain containing proteins from animals, including PHTF1/2,eukaryotes, and is typically between 101 and 140 amino acids in length. PHTF proteins do not display any sequence similarity to known or predicted proteins, but their conservation among species suggests an essential function. The 84 kDa PHTF1 protein is an integral membrane protein, anchored to a cell membrane by six to eight trans-membrane domains, that is associated with a domain of the endoplasmic reticulum (ER) juxtaposed to the Golgi apparatus. It is present during meiosis and spermiogenesis, and, by the end of spermiogenesis, is released from the mature spermatozoon within the residual bodies. PHTF1 enhances the binding of FEM1B -feminisation homologue 1B - to cell membranes. Fem-1 was initially identified in the signaling pathway for sex determination, as well as being implicated in apoptosis, but its biochemical role is still unclear, and neither FEM1B nor PHTF1 is directly implicated in apoptosis in spermatogenesis. It is the ANK domain of FEM1B that is necessary for the interaction with the N-terminal region of PHTF1.
Pfam PF09356: Phage conserved hypothetical protein BR0599 (family)
This entry describes a family of proteins found almost exclusively in phage or in prophage regions of bacterial genomes, including the phage-like Rhodobacter capsulatus gene transfer agent, which packages DNA. An apparent exception is Wolbachia pipientis wMel, a bacterial endosymbiont of the fruit fly, which has several candidate phage-related genes physically separate from obvious prophage regions.
Pfam PF22036: MoaF-like (domain)
This family consists mainly of uncharacterized proteins that are related to MoaF and adopt very similar beta-barrel structure.
Pfam PF21908: Cel124 C-terminal catalytic domain (domain)
This entry represents the C-terminal catalytic domain of endo-acting cellulase Cel124 and related proteins. The active site architecture of this cellulase shares significant structural similarity to GH23 enzymes, a family that contains inverting lysozymes and lytic transglycosylases. These proteins adopt typical lysozyme (muramidase)-like fold.
Pfam PF02738: Molybdopterin cofactor-binding domain (domain)
The aldehyde oxido-reductase (Mop) from the sulphate reducing anaerobic Gram-negative bacterium Desulfovibrio gigas is a homodimer of 907 amino acid residues subunits and is a member of the xanthine oxidase family. The protein contains a molybdopterin cofactor (Mo-co) and two different  centres. It is folded into four domains of which the first two bind the iron sulphur centres and the last two are involved in Mo-co binding. Mo-co is a molybdenum molybdopterin cytosine dinucleotide. Molybdopterin forms a tricyclic system with the pterin bicycle annealed to a pyran ring. The molybdopterin dinucleotide is deeply buried in the protein. The cis-dithiolene group of the pyran ring binds the molybdenum, which is coordinated by three more (oxygen) ligands .

This domain represents the first molybdopterin cofactor (Mo-Co) binding domain.
Aldehyde oxidase (AOX 1.2.3.1) catalyses the conversion of an aldehyde in the presence of oxygen and water to an acid and hydrogen peroxide. The enzyme is a homodimer, and requires FAD, molybdenum and two 2FE-2S clusters as cofactors. Xanthine dehydrogenase (XDH 1.17.1.4) catalyses the hydrogenation of xanthine to urate, and also requires FAD, molybdenum and two 2FE-2S clusters as cofactors. This activity is often found in a bifunctional enzyme with xanthine oxidase (1.17.3.2) activity too. The enzyme can be converted from the dehydrogenase form to the oxidase form irreversibly by proteolysis or reversibly through oxidation of sulfhydryl groups .
Pfam PF25137: Fe-containing alcohol dehydrogenase family, C-terminal (domain)
This domain is found C-terminal in the family of iron- containing alcohol dehydrogenases. It is usually found associated with [pfam:PF00171] and [pfam:PF00465]. It folds into an array of alpha-helices.
Pfam PF17022: Polar tube protein 2 from Microsporidia (family)
PTP2 is a family of microsporidial polar-tube protein 2 sequences. Humans can be infected with the unicellular eukaryote Microsporidia which are obligate intracellular parasites that produce resistant spores. To initiate entry into a new host cell a unique motile process is formed by a sudden extrusion of the polar tube protein from the spore. There are a series of conserved cysteine residues.
Pfam PF03373: Octapeptide repeat (disordered)
This octapeptide repeat is found in several bacterial proteins. The function of this repeat is unknown.
Pfam PF01142: tRNA pseudouridine synthase D (TruD) (family)
TruD is responsible for synthesis of pseudouridine from uracil-13 in transfer RNAs.  The structure of TruD reveals an overall V-shaped molecule which contains an RNA-binding cleft.
Pfam PF06524: NOA36 protein (family)
This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.
Pfam PF10585: Ubiquitin-activating enzyme, SCCH domain (domain)
Ubiquitin-activating enzyme (E1 enzyme) activates ubiquitin by first adenylating with ATP its C-terminal glycine residue and thereafter linking this residue to the side chain of a cysteine residue in E1, yielding an ubiquitin-E1 thiolester and free AMP. Later the ubiquitin moiety is transferred to a cysteine residue on one of the many forms of ubiquitin-conjugating enzymes (E2). This domain carries the last of five conserved cysteines that is part of the active site of the enzyme, responsible for ubiquitin thiolester complex formation, the active site being represented by the sequence motif PICTLKNFP. The catalytic cysteine domain contains the E1 active site cysteine, and is divided in two half-domains, FCCH and SCCH, for 'first' and 'second' catalytic cysteine half-domain, respectively. This is the SCCH domain in which resides the catalytic cysteine.
Pfam PF04409: Protein of unknown function (DUF530) (family)
Family of hypothetical archaeal 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 PF14993: Neuropeptide S precursor protein (family)
Neuropeptide S (NPS) is a bioactive peptide that may be involved in several biological processes, including food intake, locomotion, wakefulness, arousal, and anxiety. NPS activates its cognate G protein-coupled receptor (NPSR1) at low nanomolar agonist concentrations and induces elevation of intracellular Ca2+ and cAMP .
Wikipedia: Neuropeptide S (NPS) is a neuropeptide found in human and mammalian brain, mainly produced by neurons in the amygdala and between Barrington's nucleus and the locus coeruleus, although NPS-responsive neurons extend projections into many other brain areas. NPS binds specifically to a G protein-coupled receptor, NPSR. Animal studies show that NPS suppresses anxiety and appetite, induces wakefulness and hyperactivity, including hyper-sexuality, and plays a significant role in the extinction of conditioned fear. It has also been shown to significantly enhance dopamine activity in the mesolimbic pathway, and inhibits motility and increases permeability in neurocrine fashion acting through NO in the myenteric plexus in rats and humans.
Pfam PF21420: Tautomerase-like (family)
This protein family includes [swissprot:A9W9V0] from Chloroflexus aurantiacus (Caur_1358), a 4-Oxalocrotonate tautomerase (4-OT). This protein adopts a beta-alpha-beta scaffold and forms part of a functional heterohexamer 4-OT (hh4-OT) that contains three heterodimer units, each composed of one alpha-subunit ([pfam:PF01361]) and one beta-subunit (this entry).
Pfam PF10878: Protein of unknown function (DUF2672) (family)
This family of proteins with unknown function appear to be restricted to Rickettsiae.
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 PF06276: Ferric iron reductase FhuF-like transporter (family)
This family consists of several bacterial ferric iron reductase protein (FhuF) sequences.            FhuF is involved in the reduction of ferric iron in cytoplasmic ferrioxamine B. This family also includes the IucA and IucC proteins.
Pfam PF18878: PPE-PPW subfamily C-terminal region (family)
This entry represents the C-terminal region of a subfamily of PPE proteins known as the PPW subfamily. The PPW refers to three conserved residues found in the sequence alignment.  The region also contains a second conserved motif GFGT.
Pfam PF13871: C-terminal domain on Strawberry notch homologue (domain)
Strawberry notch proteins carry DExD/H-box groups upstream of this domain. The function of this domain is not known. These proteins promote the expression of diverse targets, potentially through interactions with transcriptional activator or repressor complexes.
Pfam PF00711: Beta defensin (domain)
The beta defensins are antimicrobial peptides implicated in the resistance of epithelial surfaces to microbial colonisation.
Wikipedia: Beta defensins  are a family of vertebrate defensins. The beta defensins are antimicrobial peptides implicated in the resistance of epithelial surfaces to microbial colonization.
Pfam PF23744: LRRK2 ARM repeat (repeat)
This entry represents the armadillo repeat (ARM) found at the N-terminal of Leucine-rich repeat serine/threonine-protein kinase 2 (LRRK2) from eukaryotes. The domain adopts an ARM-like fold, consisting of a right-handed superhelix formed by two curved layers of repeated helical structural units. LRRK2 is a serine/threonine-protein kinase which phosphorylates a broad range of proteins involved in multiple processes such as neuronal plasticity, primary ciliogenesis, autophagy, and vesicle trafficking. Mutations in LRRK2 are the most common genetic cause of Parkinson's disease (PD). LRRK2 phosphorylates a group of Rab GTPase proteins, including Rab32. A patch of negatively charged residues within the ARM domain has been pointed to contribute to complex formation by binding a positive residue in Rab switch 1 region. ARM domain is also suggested to form connections between adjacent microtubules. Also included in this entry is the armadillo repeat domain of Protein aardvark from Dictyostelium discoideum, a component of the junctional complex, both involved in cell adhesion and signaling.
Pfam PF17913: FHA domain (domain)
This entry represents a divergent FHA domain which in PNK binds to phosphorylated segment of XRCC1.
Pfam PF07954: Protein of unknown function (DUF1689) (family)
Family of fungal proteins with unknown function. A member of this family has been found to localise in the  mitochondria.
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 PF22457: ATP-dependent 6-phosphofructokinase subunit gamma, C-terminal (domain)
This domain is found at the C-terminal end of the ATP-dependent 6-phosphofructokinase subunit gamma from the yeast Pichia pastoris (PpPFK_gamma, also known as PFK3). PpPFK, the most complex and eukaryotic Pfk, forms a dodecamer of four alpha-beta-gamma trimers. PpPFK_gamma is a unique subunit that participates in oligomerisation of the alpha-beta chains, modulates the allosteric behaviour of the enzyme and plays a role in the adaption of the organism to variation of the energy charge of the cell.
Pfam PF01842: ACT domain (domain)
This family of domains generally have a regulatory role. ACT domains are linked to a wide range of metabolic enzymes that are regulated by amino acid concentration. Pairs of ACT domains bind specifically to a particular amino acid leading to regulation of the linked enzyme.  The ACT domain is found in: D-3-phosphoglycerate dehydrogenase [ec:1.1.1.95] [swissprot:P08328], which is inhibited by serine. Aspartokinase [ec:2.7.2.4] [swissprot:P53553], which is regulated by lysine. Acetolactate synthase small regulatory subunit [swissprot:P00894], which is inhibited by valine. Phenylalanine-4-hydroxylase [ec:1.14.16.1] [swissprot:P00439], which is regulated by phenylalanine. Prephenate dehydrogenase [ec:4.2.1.51] [swissprot:P21203]. formyltetrahydrofolate deformylase [ec:3.5.1.10], [swissprot:P37051], which is activated by methionine and inhibited by glycine. GTP pyrophosphokinase [ec:2.7.6.5] [swissprot:P11585]
Wikipedia: In molecular biology, the ACT domain is a protein domain that is found in a variety of proteins involved in metabolism. ACT domains are linked to a wide range of metabolic enzymes that are regulated by amino acid concentration. The ACT domain is named after three of the proteins that contain it: aspartate kinase, chorismate mutase and TyrA. The archetypical ACT domain is the C-terminal regulatory domain of 3-phosphoglycerate dehydrogenase (3PGDH), which folds with a ferredoxin-like topology. A pair of ACT domains form an eight-stranded antiparallel sheet with two molecules of allosteric inhibitor serine bound in the interface. Biochemical exploration of a few other proteins containing ACT domains supports the suggestions that these domains contain the archetypical ACT structure.
Pfam PF06291: Bor protein (domain)
This family consists of several Bacteriophage lambda Bor and Escherichia coli Iss proteins. Expression of bor significantly increases the survival of the Escherichia coli host cell in animal serum. This property is a well known bacterial virulence determinant indeed, bor and its adjacent sequences are highly homologous to the iss serum resistance locus of the plasmid ColV2-K94, which confers virulence in animals. It has been suggested that lysogeny may generally have a role in bacterial survival in animal hosts, and perhaps in pathogenesis.
Pfam PF04188: Mannosyltransferase (PIG-V) (family)
This is a family of eukaryotic ER membrane proteins that are involved in the synthesis of glycosylphosphatidylinositol (GPI), a glycolipid that anchors many proteins to the eukaryotic cell surface.  Proteins in this family are involved in transferring the second mannose in the biosynthetic pathway of GPI.
Pfam PF05661: Protein of unknown function (DUF808) (family)
This family consists of several bacterial proteins of unknown 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 PF10473: Leucine-rich repeats of kinetochore protein Cenp-F/LEK1 (coiled_coil)
Cenp-F, a centromeric kinetochore, microtubule-binding protein consisting of two 1,600-amino acid-long coils, is essential for the full functioning of the mitotic checkpoint pathway. There are several leucine-rich repeats along the sequence of LEK1 that are considered to be zippers, though they do not appear to be binding DNA directly in this instance.
Pfam PF04190: Golgi to ER traffic protein 4 (repeat)
In budding yeast, Get4 is part of the GET complex that inserts the tail-anchored (TA) proteins into the endoplasmic reticulum membrane. In humans, Get4 is part the BAG6/BAT3 complex, maintains misfolded and hydrophobic patches-containing proteins in a soluble state and facilitates their proper delivery to the endoplasmic reticulum, or alternatively promotes their sorting to the proteasome where they undergo degradation. The BAG6/BAT3 complex is involved in the post-translational delivery of tail-anchored/type II transmembrane proteins to the endoplasmic reticulum membrane.
Pfam PF10522: RII binding domain (conserved_site)
This domain is found is a wide variety of AKAPs (A kinase anchoring proteins). The domain is also found on micro-tubule-associated proteins.
Pfam PF07432: Histone H1-like protein Hc1 (family)
This family consists of several bacterial histone H1-like Hc1 proteins. In Chlamydia, Hc1 is expressed in the late stages of the life cycle, concomitant with the reorganisation of chlamydial reticulate bodies into elementary bodies. This suggests that Hc1 protein plays a role in the condensation of chromatin during intracellular differentiation.
Pfam PF22981: Mediator of RNA polymerase II transcription subunit 14, RM2 (repeat)
This entry represents an alpha/beta motif that is found tandemly repeated in the homologues of human Mediator of RNA polymerase II transcription subunit 14 (Med14). Med14 is a component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Med14 along with Med17 are scaffold subunits in nucleating Mediator. The major portion of Med14 exists in the Head-Shoulder module of the Mediator and consists of nine tandem repeats (RM1 to RM9), which are arranged in an atypical right-handed helix. This entry represents repeat RM2.