SII-SWORD/CoKE huggingface dataset:
Pfam PF13017: piRNA pathway germ-plasm component (family)
Maelstrom is a germ-plasm component protein, that is shown to be functionally involved in the piRNA pathway. It is conserved throughout Eukaryota, though it appears to have been lost from all examined teleost fish species.  The domain architecture shows that it is coupled with several DNA- and RNA- related domains such as HMG box, SR-25-like and HDAC_interact domains. Sequence analysis and fold recognition have found a distant similarity between Maelstrom domain and the DnaQ 3'-5' exonuclease family with the RNase H fold (Exonuc_X-T, [pfam:PF00929]); notably, that the Maelstrom domains from basal eukaryotes contain the conserved 3'-5' exonuclease active site residues (Asp-Glu-Asp-His-Asp, DEDHD). However, the animal and some amoeba maelstrom contain another set of conserved residues (Glu-His-His-Cys-His-Cys, EHHCHC). This evolutionary link together with structural examinations leads to the hypothesis that Maelstrom domains may have a potential nuclease-transposase activity or RNA-binding ability that may be implicated in piRNA biogenesis. A protein function evolution mode, namely "active site switch", has been proposed, in which the amoeba Maelstrom domains are the possible evolutionary intermediates due to their harbouring of the specific characteristics of both 3'-5' exonuclease and Maelstrom domains.
Pfam PF23045: Domain of unknown function (DUF7037) (domain)
This entry represents a small domain found in a family of uncharacterized proteins in nematodes. This domain is predicted to fold as a beta-sheet composed of four anti-parallel beta-strands.
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 PF24506: KNTC1, N-terminal (repeat)
This entry represents the beta-propeller domain found at the N-terminal of KNTC1 (also known as ROD) from vertebrates. KNTC1 is the major subunit of the RZZ (ROD-Zwilch-ZW10) complex, which plays a significant role in spindle assembly, kinetochore-microtubule attachment, and spindle pole separation. KNTC1 is required for the assembly of essential complexes onto kinetochores, including dynein-dynactin and MAD1-MAD2. This domain mediates extensive interactions with the other subunits of the complex, forming a RZZ module that binds Spindly, a DD adaptor that can activate dynein motility.
Pfam PF01745: Isopentenyl transferase (domain)
Isopentenyl transferase / dimethylallyl transferase synthesises isopentenyladensosine 5'-monophosphate, a cytokinin that induces shoot formation on host plants  infected with the Ti plasmid.
Pfam PF16843: Binding domain to Get4 on Get5, Golgi to ER traffic protein (domain)
Get5_bdg is the binding domain at the N-terminus of Get5, or Golgi to ER traffic protein 5, in yeast, that binds to Get4. Together with Get3, this tripartite complex is involved in the insertion of tail-anchored proteins in the ER membrane.
Pfam PF13153: Protein of unknown function (DUF3985) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 50 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 PF04039: Domain related to MnhB subunit of Na+/H+ antiporter (family)
Possible subunit of Na+/H+ antiporter,. Predicted integral membrane protein, usually four transmembrane regions in this domain.  Often found in bacterial NADH dehydrogenase subunit.
Pfam PF03790: KNOX1 domain (family)
The MEINOX region is comprised of two domains, KNOX1 and KNOX2. KNOX1 plays a role in suppressing target gene expression. KNOX2, essential for function, is thought to be necessary for homo-dimerisation.
Pfam PF11738: Protein of unknown function (DUF3298) (domain)
This family of bacterial protein C-terminal regions is highly conserved but the function is not known. Several members are annotated as being endo-1,4-beta-xylanase-like, but this could not be confirmed, and the structure can be defined as a heat-shock cognate 70kd protein 44kd ATPase.
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 PF05827: V-type proton ATPase subunit S1, luminal domain (domain)
This entry represents the luminal domain (LD) found in eukaryotic V-type proton ATPase subunit S1 involved in V-ATPase V0 assembly, including Ac45 subunit (ATP6AP1). This domain folds as a globular beta-prism structure which is structurally similar to LAMP1-3, thus, the LD domain of Ac45 is an evolutionarily conserved member of the LAMP family. Ac45 is an ER membrane protein that guides the  V-type ATPase into specialised subcellular compartments and is critical for Vo complex assembly as it connects to multiple Vo subunits and phospholipids in the c-ring. Missense mutations in the X-linked ATP6AP1 gene cause immunodeficiency in males that leads to recurrent bacterial infection, hepatopathy, cognitive impairment, and abnormal protein glycosylation.
Pfam PF13483: Beta-lactamase superfamily domain (domain)
This family is part of the beta-lactamase superfamily and is related to [pfam:PF00753].
Pfam PF05517: p25-alpha (domain)
This family encodes a 25 kDa protein that is phosphorylated by a Ser/Thr-Pro kinase.  It has been described as a brain specific protein, but it is found in Tetrahymena thermophila.
Pfam PF22665: DUF6293 C-terminal winged helix domain (domain)
This domain is found C-terminal in functionally uncharacterised archaeal proteins. This domain is predicted to adopt winged helix domain structure. It is usually located upstream [pfam:PF19810] and this domain organisation as well as the predicted structure are reminiscent of CRISPR-associated protein, Csa3.
Pfam PF07022: Bacteriophage CI repressor helix-turn-helix domain (domain)
This family consists of several phage CI repressor proteins and related bacterial sequences. The CI repressor is known to function as a transcriptional switch, determining whether transcription is lytic or lysogenic.
Pfam PF07926: TPR/MLP1/MLP2-like protein (coiled_coil)
The sequences featured in this family are similar to a region of human TPR protein ([swissprot:P12270]) and to yeast myosin-like proteins 1 (MLP1, [swissprot:Q02455]) and 2 (MLP2, [swissprot:P40457]). These proteins share a number of features; for example, they all have coiled-coil regions and all three are associated with nuclear pores. TPR is thought to be a component of nuclear pore complex- attached intra-nuclear filaments, and is implicated in nuclear protein import. Moreover, its N-terminal region is involved in the activation of oncogenic kinases, possibly by mediating the dimerisation of kinase domains or by targeting these kinases to the nuclear pore complex. MLP1 and MLP2 are involved in the process of telomere length regulation, where they are thought to interact with proteins such as Tel1p and modulate their activity.
Pfam PF08466: Inward rectifier potassium channel N-terminal (family)
This metazoan domain is found to the N-terminus of the [pfam:PF01007] domain in Inward rectifier potassium channels (KIR2 or IRK2).
Wikipedia: Inward-rectifier potassium channels (Kir, IRK) are a specific lipid-gated subset of potassium channels. To date, seven subfamilies have been identified in various mammalian cell types, plants, and bacteria. They are activated by phosphatidylinositol 4,5-bisphosphate (PIP2). The malfunction of the channels has been implicated in several diseases. IRK channels possess a pore domain, homologous to that of voltage-gated ion channels, and flanking transmembrane segments (TMSs). They may exist in the membrane as homo- or heterooligomers and each monomer possesses between 2 and 4 TMSs. In terms of function, these proteins transport potassium (K+), with a greater tendency for K+ uptake than K+ export. The process of inward-rectification was discovered by Denis Noble in cardiac muscle cells in 1960s and by Richard Adrian and Alan Hodgkin in 1970 in skeletal muscle cells.
Pfam PF01023: S-100/ICaBP type calcium binding domain (domain)
The S-100 domain is a subfamily of the EF-hand calcium binding proteins.
Wikipedia: The S100 proteins are a family of low molecular-weight proteins found in vertebrates characterized by two calcium-binding sites that have helix-loop-helix ("EF-hand-type") conformation. At least 21 different S100 proteins are known. They are encoded by a family of genes whose symbols use the S100 prefix, for example, S100A1, S100A2, S100A3.
They are also considered as damage-associated molecular pattern molecules (DAMPs), and knockdown of aryl hydrocarbon receptor downregulates the expression of S100 proteins in THP-1 cells.
Pfam PF10492: Nrf1 activator activation site binding domain (domain)
In Drosophila, the erect wing (ewg) protein is required for proper development of the central nervous system and the indirect flight muscles. The fly ewg gene encodes a novel DNA-binding domain that is also found in four genes previously identified in sea urchin, chicken, zebrafish, and human. Nuclear respiratory factor-1 is a transcriptional activator that has been implicated in the nuclear control of respiratory chain expression in vertebrates. The first 26 amino acids of nuclear respiratory factor-1 are required for the binding of dynein light chain. The interaction with dynein light chain is observed for both ewg and Nrf-1, transcription factors that are structurally and functionally similar between humans and Drosophila. The highest level of expression of both ewg and Nrf-1 was found in the central nervous system, somites, first branchial arch, optic vesicle, and otic vesicle. In the mouse Nrf-1 protein, [swissprot:Q8C4C0], there is an activation domain at 303-469, the most conserved part of which is this domain 446-469.  Ewg is a site-specific transcriptional activator, and evolutionarily conserved regions of ewg contribute both positively and negatively to transcriptional activity. The family Nrf1_DNA-bind is associated with this domain towards the N-terminal, as is the N terminal of the activation domain.
Pfam PF12913: SH3 domain (SH3b1 type) (domain)
This domain appears to be an SH3 domain of the SH3b1-type, and is just C-terminal to an N-terminal domain that is probably the stabilising domain for the structure from [swissprot:Q72DN3], PDB:3m1u, which is a four-domain protein. The next domain is an SH3b2 and the last, the C-terminal region, is the catalytic domain of the cysteine-peptidase type, ie family NLPC_P60, [pfam:PF00877] (details derived from TOPSAN).
Pfam PF03500: Cellulose synthase subunit D (family)
This entry represents Cellulose synthase operon protein D from Komagataeibacter xylinus and similar proteins from Proteobacteria. BcsD has been related with the level of crystalline structure of cellulose . The protein have a octamer pore-like structure with four inner passageways .
An operon encoding 4 proteins required for bacterial cellulose biosynthesis (bcs) in Acetobacter xylinus (Gluconacetobacter xylinus) has been isolated via genetic complementation with strains lacking cellulose synthase activity . Nucleotide sequence analysis showed the cellulose synthase operon to consist of 4 genes, designated bcsA, bcsB, bcsC and bcsD, all of which are required for maximal bacterial cellulose synthesis in A. xylinum.

The calculated molecular mass of the protein encoded by bcsD is 17.3kDa . The function of BcsD is unknown.
Cellulose, an aggregate of unbranched polymers of beta-1,4-linked glucose residues, is the major component of wood and thus paper, and is synthesized by plants, most algae, some bacteria and fungi, and even some animals. The genes that synthesize cellulose in higher plants differ greatly from the well-characterised genes found in Acetobacter and Agrobacterium spp. More correctly designated as "cellulose synthase catalytic subunits", plant cellulose synthase (CesA) proteins are integral membrane proteins, approximately 1,000 amino acids in length. There are a number of highly conserved residues, including several motifs shown to be necessary for processive glycosyltransferase activity .
Pfam PF16522: Flagellar FLiS export co-chaperone, HP1076 (domain)
FliS_cochap is a family of largely Campylobacterales proteins that are co-chaperones for FliS, one of the type III secretion system flagellar chaperones. The HP1076 (Flis_cochap) and FliS complex together prevents premature polymerisation of flagellins and is critical for flagellar assembly and bacterial colonisation. The HP1076 shows co-chaperone activity that promotes protein folding of FliS with mutations in the flagellin binding pocket and enhances the chaperone activity of FliS.
Pfam PF17477: Rotavirus VP4 membrane interaction domain (domain)
This entry represents the VP4 membrane interaction domain.
Pfam PF23253: PARP14, sixth type I KH domain (domain)
This domain is found in human Protein mono-ADP-ribosyltransferase PARP14 and related proteins. PARP14 is a large multidomain protein which in the N-terminal half contains a series of consecutive RRM and KH domains that are known to be nucleic acid-binding. PARP14 is involved in multiple signaling pathways linked to cancer, inflammation, and infection. PARP14 is an ADP-ribosyltransferase that mediates mono-ADP-ribosylation of glutamate residues on target proteins. In contrast to PARP1 and PARP2, it is not able to mediate poly-ADP-ribosylation. The domain represented by this entry is a KH domain found sixth in the human PARP14.
Pfam PF14218: Circadian oscillating protein COP23 (family)
This family includes the circadian oscillating protein COP23 from Cyanothece sp. (strain PCC 8801), [swissprot:Q54702]. The levels of this peripheral membrane protein display a circadian oscillation.
Pfam PF17318: Family of unknown function (DUF5361) (family)
This is a family of unknown function 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 PF18202: T-Q ester bond containing domain (domain)
This domain is found in gram positive bacterial surface proteins. It contains a very unusual ester bond between a conserved threonine residue on the N-terminal beta strand of the Ig-like fold and a glutamine residue in the final strand of the domain.
Pfam PF13655: N-terminal domain of reverse transcriptase (domain)
This domain is found at the N-terminus of bacterial reverse transcriptases.
Pfam PF19333: Failed axon connections homolog N-terminus (family)
This family represents the N-terminal domain of the failed axon connections homolog (FAXC). This protein is localised to the cellular membranes, thus it is likely that this region anchors it to the plasma membrane. It is thought to play a role in axonal development, being involved in cell-cell interactions.
Pfam PF03309: Type III pantothenate kinase (family)
Type III pantothenate kinase catalyses the phosphorylation of pantothenate (Pan), the first step in the universal pathway of CoA biosynthesis.
Pfam PF05287: PMG protein (family)
This family consists of several mouse anagen-specific protein mKAP13 (PMG1 and PMG2). PMG1 and 2 contain characteristic repeats reminiscent of the keratin-associated proteins (KAPs). Both genes are expressed in growing hair follicles in skin as well as in sebaceous and eccrine sweat glands. Interestingly, expression is also detected in the mammary epithelium where it is limited to the onset of the pubertal growth phase and is independent of ovarian hormones. Their broad, developmentally controlled expression pattern, together with their unique amino acid composition, demonstrate that pmg-1 and pmg-2 constitute a novel KAP gene family participating in the differentiation of all epithelial cells forming the epidermal appendages.
Pfam PF12588: Phophatidylserine decarboxylase (family)
This domain family is found in bacteria and eukaryotes, and is approximately 140 amino acids in length. The family is found in association with [pfam:PF02666]. Phosphatidylserine decarboxylase (PSD) is an important enzyme in the synthesis of phosphatidylethanolamine in both prokaryotes and eukaryotes.
Pfam PF19575: Helix-turn-helix domain (domain)
This family of proteins is functionally uncharacterised. However, it contains a helix-turn-helix domain which strongly suggests these proteins are transcriptional regulators. This family of proteins is primarily found in actinobacteria. Proteins in this family are typically between 69 and 86 amino acids in length.
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 PF18669: Trimeric autotransporter adhesin Trp ring domain (domain)
Autotransporters are synthesized as precursor proteins with three functional domains, namely, an N-terminal signal peptide, an internal passenger domain, and a C-terminal pore-forming translocator domain.  The C-terminal translocator domain is embedded in the outer membrane and facilitates delivery of the internal passenger domain to the bacterial surface. In conventional autotransporters, the C-terminal translocator domain contains approximately 300 amino acids and is monomeric. In contrast, in trimeric autotransporters, the translocator domain contains 60 to 70 amino acids and forms trimers in the outer membrane. This entry represents a Trp-ring domain which is found in the translocator region of H. influenzae Hia autotransporter, an adhesive protein that promotes adherence to respiratory epithelial cells. Trp-ring domains appear to be crucial repeated modular units in Hia, both in the general architecture of the passenger domain and in the structure of the binding domains.
Pfam PF24975: Fungal Rad5 UBA-like domain (domain)
This entry represents an N-terminal UBA-like domain found in fungal RAD5 proteins.  The RAD5 family comprises DNA repair proteins that function as probable helicases and are part of the UBC2/RAD6 epistasis group. These proteins collaborate with RAD18 in facilitating error-free postreplication DNA repair. They play a crucial role in maintaining the stability of simple repetitive sequences, such as poly(GT) repeats, and are involved in balancing mechanisms that favour error-prone non-homologous joining during DNA double-strand break repairs. The RAD5 family is characterized by its membership in the SNF2/RAD54 helicase family, indicating its involvement in DNA repair processes.
Wikipedia: Ubiquitin-associated (UBA) domains are protein domains that non-covalently interact with ubiquitin through protein-protein interactions. Ubiquitin is a small protein that is covalently linked to other proteins as part of intracellular signaling pathways, often as a signal for protein degradation. UBA domains are among the most common ubiquitin-binding domains.
Pfam PF06530: Phage antitermination protein Q (family)
This family consists of several phage antitermination protein Q and related bacterial sequences. Antiterminator proteins control gene expression by recognising control signals near the promoter and preventing transcriptional termination which would otherwise occur at sites that may be a long way downstream.
Pfam PF14162: YozD-like protein (family)
The YozD-like protein family includes the B. subtilis YozD protein [swissprot:O31863], which is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length.
Pfam PF19675: Origin recognition complex subunit 3 insertion domain (family)
This is the large domain insertion of ORC subunit 3 (ORC3) located between the N-terminal AAA+-like subunit and the C-terminal winged- helix (WH) DNA-binding domain. ORC3 is a component of the origin recognition complex (ORC) that binds origins of replication, required to assemble the pre-replication complex necessary to initiate DNA replication. This domain insertion forms a bi-lobed alpha-helical protuberance that engages a short alpha-helix formed at the ORC6 C-terminal, allowing its binding to ORC1-5 subunits, which constitute the ORC core.
Pfam PF03941: Inner centromere protein, ARK binding region (family)
This region of the inner centromere protein has been found to be necessary and sufficient for binding to aurora-related kinase. This interaction has been implicated in the coordination of chromosome segregation with cell division in yeast.
Wikipedia: Inner centromere protein is a protein that in humans is encoded by the INCENP gene. It is a regulatory protein in the chromosome passenger complex (CPC). It is involved in regulation of the catalytic proteins Aurora B and Aurora C. It acts in association with two other proteins - Survivin and Borealin. These proteins form a tight three-helical bundle. The N-terminal domain of INCENP is the domain involved in formation of this three-helical bundle while its C-terminal domain is responsible for the interaction with Aurora B.
Pfam PF09360: Iron-binding zinc finger CDGSH type (domain)
The CDGSH-type zinc finger domain binds iron rather than zinc as a redox-active pH-labile 2Fe-2S cluster. The conserved sequence C-X-C-X2-(S/T)-X3-P-X-C-D-G-(S/A/T)-H is a defining feature of this family. The domain is oriented towards the cytoplasm and is tethered to the mitochondrial membrane by a more N-terminal domain found in higher vertebrates, MitoNEET_N, [pfam:PF10660]. The domain forms a uniquely folded homo-dimer and spans the outer mitochondrial membrane, orienting the iron-binding residues towards the cytoplasm.
Pfam PF09939: Uncharacterized protein conserved in bacteria (DUF2171) (family)
This domain, found in various hypothetical prokaryotic proteins, has no known function.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.