SII-SWORD/CoKE huggingface dataset:
Vps52, coiled-coil domain (Vps52_CC)
Type: Domain

Vps52 complexes with Vps53 and Vps54 to form a multi-subunit complex, the Golgi-associated retrograde protein (GARP) complex that is involved in retrograde transport from early and late endosomes to the trans-Golgi network, regulating membrane trafficking events . It is also part of the EARP (Endosome-Associated Recycling Protein) complex, involved in endocytic recycling . GARP complex is part of the family of evolutionarily related complexes associated with tethering containing helical rods (CATCHR), which includes the conserved oligomeric Golgi (COG), Dsl1 and exocyst complexes. They share structural features consisting of an α-helical bundle at the C terminus and usually a coiled-coil (CC) region at the N terminus .

This entry represents the CC region found at the N terminus of Vps52.
Conserved oligomeric Golgi complex subunit 3, N-terminal (COG3_N)
Type: Domain

This entry represents the N-terminal domain of COG3.

This entry includes the Conserved oligomeric Golgi complex subunit 3 (COG3, also known as Sec34) which is a component of the peripheral membrane COG complex, involved in intra-Golgi protein trafficking . COG is a member of the complexes associated with tethering containing helical rods (CATCHR) family which also includes the exocyst, GARP and Dsl1 complexes, which are evolutionarily related and share structural features consisting of α-helical bundles towards the C-terminal and an N-terminal coiled-coil region .
Nuclear cap binding complex subunit CBP66, N-terminal domain (CBP66_1st)
Type: Domain

This entry represents the N-terminal domain of the CBP66 component of the trypanosoma nuclear cap binding complex. Trypanosomes have a different cap 4 structure for mRNAs . CBP66 is part of the complex that recognises this cap. This domain adopts an RRM-like structure.
Nuclear cap binding complex subunit CBP66, second domain (CBP66_2nd)
Type: Domain

This entry represents the second domain of the CBP66 component of the trypanosoma nuclear cap binding complex. Trypanosomes have a different cap 4 structure for mRNAs . CBP66 is part of the complex that recognises this cap.
Spo16 protein, C-terminal (Spo16_C)
Type: Domain

This entry represents the HHH motif found at the C-terminal of Spo16 protein.

This entry represents proteins related to budding yeast Spo16, which belongs to a conserved meiosis-specific group of proteins known as ZMM (Zip, Msh, Mer), which are critical for the control and crossover formation during gametogenesis. Spo16 forms a complex with Zip2 and Zip4. Zip2 and Spo16, form a meiosis-specific XPF-ERCC1-like complex. The recombinant Zip2 XPF domain together with Spo16 preferentially binds branched DNA structures, such as D loops and HJs. It is suggested that Zip2-Spo16 forms a 'nuclease-inactive' heterodimer that recognises DNA junctions during meiotic homologous recombination and then recruits other factors for DNA repair. Moreover, together with Zip2 and Zip4, Spo16 also plays a key role in synaptonemal complex assembly . The Spo16 protein contains a C-terminal HHH motif.
ZSWIM1/3, RNaseH-like domain (ZSWIM1-3_RNaseH-like)
Type: Domain

This is a domain found at the N-terminal of Zinc finger SWIM domain-containing protein 1 and in the central region of ZSWIM3, whose function is not yet clear. ZSWIM1 may play a role in the development or function of T helper cells . This domain may adopt an α/β conformation according to AlphaFold structure predictions, closely related to RNaseH-like domains.
ZSWIM3, N-terminal domain (ZSWIM3_N)
Type: Domain

This entry represents the N-terminal domain of ZSWIM3, a ZSWIM-type zinc finger domain containing protein whose function is not yet known. This domain appears to be related to the WRKY-like DNA-binding domains.
ZSWIM1/3, helical domain (ZSWIM1-3_helical)
Type: Domain

This entry represents a helical domain found in ZSWIM1 and ZSWIM3, ZSWIM-type zinc finger domain containing proteins. The function of ZSWIM3 is not yet clear. ZSWIM1 is thought to play in the development or function of T helper cells .
Dyp-type peroxidase, N-terminal domain (Dyp_perox_N)
Type: Domain

Dyp-type (dye-decolorizing) peroxidases are a family of heme proteins found in a wide range of bacteria and fungi . They have a wide substrate specificity and lack homology to most other peroxidases, with the ability to function well under much lower pH conditions compared with the other plant peroxidases . They consist of two domains that adopt a ferredoxin-like fold , connected by a loop. This entry represents the N-terminal domain .
Dyp-type peroxidase, C-terminal domain (Dyp_perox_C)
Type: Domain

Dyp-type (dye-decolorizing) peroxidases are a family of heme proteins found in a wide range of bacteria and fungi . They have a wide substrate specificity and lack homology to most other peroxidases, with the ability to function well under much lower pH conditions compared with the other plant peroxidases . They consist of two domains that adopt a ferredoxin-like fold , connected by a loop. This entry represents the C-terminal domain, which possess a large hydrophobic cavity for heme binding .
PcRGLX/YetA-like, N-terminal RIFT barrel domain (PcRGLX_1st)
Type: Domain

This entry includes Exo-rhamnogalacturonan lyase from Penicillium chrysogenum 31B (PcRGLX) and YetA from B. subtilis. YetA is functionally uncharacterised. This entry represents the N-terminal RIFT barrel like domain. Members of this entry share a 3 domain architecture .
PcRGLX/YetA-like, central beta-sandwich domain (PcRGLX/YetA_2nd)
Type: Domain

This entry includes Exo-rhamnogalacturonan lyase from Penicillium chrysogenum 31B (PcRGLX) and YetA from B. subtilis, which is functionally uncharacterised. Proteins in this family are typically between 863 and 928 amino acids in length. This entry represents the central β-sandwich domain. Members of this family share a 3 domain architecture .
PcRGLX/YetA-like, C-terminal alpha/alpha toroid domain (PcRGLX/YetA_3rd)
Type: Domain

This entry includes Exo-rhamnogalacturonan lyase from Penicillium chrysogenum 31B (PcRGLX) and YetA from B. subtilis, which is functionally uncharacterised. This entry represents the C-terminal α/α-toroid domain. Members of this entry share a 3 domain architecture .
D-galactarate/Altronate dehydratase, C-terminal domain (GD_AH_C)
Type: Domain

This entry represents the C-terminal domain of Galactarate dehydratase (GarD). GarD catalyses the dehydration of galactarate to 5-dehydro-4-deoxy-D-galactarate. In the crystal structure, GarD forms dimers and each monomer consists of three domains: the N-terminal SAF domain (

) connected to the second domain (

) through a long linker and the C-terminal domain which represents the core of the protein. This domain adopts a variant of a Rossmann fold with an unusual crossover, consisting of seven-stranded parallel β-sheets surrounded by nine α-helices . This domain may contain a catalytic metal binding site .
Helicase associated domain (HA2), winged-helix domain (HA2_WH)
Type: Domain

The helicase associated domain (HA2) has an all α-helical fold and consists of a N-terminal winged-helix (WH) domain and a C-terminal degenerate helical-bundle domain, referred to as the ratchet-like domain . These domains collaborate with RecA domains at the N-terminal in completing an RNA binding channel to allow the helicases to keep a stable grip on the RNA and assure its correct function. This entry represents the WH domain, which connects the N- (RecA domains) and C-terminal domains (ratchet-like and OB-fold) of helicases.
Pellino, FHA domain (Pellino_FHA)
Type: Domain

Pellino proteins are E3 ubiquitin ligases that play important roles in immunity, being involved in Toll-like signalling pathways, and associate with the kinase domain of the Pelle Ser/Thr kinase . Mammalian pellinos have been shown to mediate polyubiquitination of interleukin-1 receptor-associated kinase (IRAK) . They consist of a forkhead-associated (FHA) domain at the N-terminal and a RING domain at the C-terminal.

This entry represents the FHA domain, which is sufficient to interact with the ubiquitination substrates, such as IRAK1. This domain contains an unusual 'wing-like' appendage .
Pellino, RING domain (Pellino_RING)
Type: Domain

Pellino proteins are E3 ubiquitin ligases that play an important role in immunity, being involved in Toll-like signalling pathways, and associates with the kinase domain of the Pelle Ser/Thr kinase . Mammalian pellinos have been shown to mediate polyubiquitination of interleukin-1 receptor-associated kinase (IRAK) . These proteins consist of an N-terminal forkhead-associated (FHA) domain and a C-terminal RING domain .

This entry represents the RING domain, which is not required for interaction with phosphorylated IRAK1 .
Cysteine protease StiP-like (StiP-like)
Type: Family

This entry represents Cysteine protease StiP from Acinetobacter baylyi and similar bacterial proteins that contain the domains (

) and (

). StiP may play a role in regulating cell morphology in response to stressful conditions which likely cause oxidative damage. StiP has been shown to posses cysteine protease activity .
FAM50A/XAP5, C-terminal domain (FAM50A/XAP5_C)
Type: Domain

This entry represents a domain found at the C-terminal of FAM50A and XAP5 homologues from a wide range of eukaryotes. These are nuclear proteins previously suggested to be DNA binding but recent studies suggest that they play a role in the spliceosome complex . In plants, these proteins are essential for correct circadian clock functioning by acting as a light-quality regulator coordinating the activities of blue and red light signalling pathways during plant growth-inhibiting growth in red light but promoting growth in blue light . The AlphaFold prediction of this domain shows structural similarity to the RA domain (

).
Mediator complex, subunit Med16 (Mediator_Med16)
Type: Family

This entry represents a group of proteins from animal and fungi, including human Mediator of RNA polymerase II transcription subunit 16 (MED16).

Mediator is a large complex of up to 33 proteins that is conserved from plants through fungi to humans - the number and representation of individual subunits varying with species . It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function. Med16 is one of the subunits of the Tail portion of the Mediator complex and is required for lipopolysaccharide gene-expression . Several members including the human protein,

, have one or more WD40 domains on them.
Mediator complex subunit 16, C-terminal (Mediator_Med16_C)
Type: Domain

This entry represents the small α/β domain found at the C-terminal of Mediator complex subunit 16 .

Mediator is a large complex of up to 33 proteins that is conserved from plants through fungi to humans - the number and representation of individual subunits varying with species . It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function. Med16 is one of the subunits of the Tail portion of the Mediator complex and is required for lipopolysaccharide gene-expression . Several members including the human protein,

, have one or more WD40 domains on them.
DUF1285, N-terminal domain (DUF1285_N)
Type: Domain

This domain is found at the N-terminal of several hypothetical bacterial proteins, including SPO0140 from Ruegeria pomeroyi (

). It folds into a β-meander-α-helix- β-meander core bound to a twisted mixed six-stranded β-sheet. Its specific function is unknown .
DUF1285, C-terminal domain (DUF1285_C)
Type: Domain

This domain is found at the C-terminal end of several hypothetical bacterial proteins. The structure revealed a superficial similarity of this domain to pleckstrin homology-like fold .
Centromere/kinetochore protein zw10, C-terminal domain (ZW10_C)
Type: Domain

This entry represents a domain found towards the C terminus of Zw10, consisting of the conserved α-helical bundle.

Zw10 protein, in the context of the conserved Rod-Zwilch-Zw10 (RZZ) complex, is required for correct metaphase check-pointing during mitosis and it is also important in vesicle transport between Golgi and ER as part of a second complex together with the conserved conserved RINT1/Tip20p and NAG/Sec39p proteins . Zw10 is the metazoan homologue of yeast Dsl1, both included in the complexes associated with tethering containing helical rods (CATCHR) family, sharing structural features .
Centromere/kinetochore protein zw10, middle domain (Zw10_middle)
Type: Domain

This entry represents the middle domain of Zw10, which, from AlphaFold prediction, consists of four β-strands and four α-helices.

Zw10 protein, in the context of the conserved Rod-Zwilch-Zw10 (RZZ) complex, is required for correct metaphase check-pointing during mitosis and it is also important in vesicle transport between Golgi and ER as part of a second complex together with the conserved conserved RINT1/Tip20p and NAG/Sec39p proteins . Zw10 is the metazoan homologue of yeast Dsl1, both included in the complexes associated with tethering containing helical rods (CATCHR) family, sharing structural features .
Plasmid segregation protein ParM, C-terminal domain (ParM_C)
Type: Domain

This entry consists of several bacterial ParM/StbA plasmid stability proteins . ParM is involved in the control of plasmid partition and required for the accurate segregation of the plasmid, which forms filaments to drive partition. This protein is an actin homologue and consists of two domains (I and II) with the same conformation . This entry represents the C-terminal domain.
Sarcoglycan alpha/epsilon, N-terminal domain (Sarcoglycan_N)
Type: Domain

Sarcoglycans are a subcomplex of transmembrane proteins which are part of the dystrophin-glycoprotein complex. They are expressed in the skeletal, cardiac and smooth muscle. Although numerous studies have been conducted on the sarcoglycan subcomplex in skeletal and cardiac muscle, the manner of the distribution and localisation of these proteins along the non junctional sarcolemma is not clear . This entry represents the N-terminal domain of alpha and epsilon members.
Sarcoglycan alpha/epsilon second domain (Sarcoglycan_C)
Type: Domain

Sarcoglycans are a subcomplex of transmembrane proteins which are part of the dystrophin-glycoprotein complex. They are expressed in the skeletal, cardiac and smooth muscle. Although numerous studies have been conducted on the sarcoglycan subcomplex in skeletal and cardiac muscle, the manner of the distribution and localisation of these proteins along the non junctional sarcolemma is not clear . This entry represents the second domain of alpha and epsilon members, which has an Ig-like fold.
CCDC22, coiled-coil domain (CCDC22_CC)
Type: Domain

This entry represents the coiled-coil region of human coiled-coil domain-containing protein 22 (CCDC22).

CCDC22 is involved in regulation of NF-kappa-B signalling; the function may involve association with COMMD8 and a CUL1-dependent E3 ubiquitin ligase complex . It is part of the COMMD/CCDC22/CCDC93 (CCC) complex, which interacts with the multisubunit WASH complex required for endosomal deposition of F-actin and cargo trafficking in conjunction with the retromer . This entry also includes CCDC22 homologues from animals and plants.
CCDC22, N-terminal domain (CCDC22_N)
Type: Domain

This entry represents the N-terminal helical domain of the CCDC22 and its homologues from animals and plants.

CCDC22 is involved in regulation of NF-kappa-B signalling; the function may involve association with COMMD8 and a CUL1-dependent E3 ubiquitin ligase complex . It is part of the COMMD/CCDC22/CCDC93 (CCC) complex, which interacts with the multisubunit WASH complex required for endosomal deposition of F-actin and cargo trafficking in conjunction with the retromer . This entry also includes CCDC22 homologues from animals and plants.
S-Me-THD-like, C-terminal domain (S-Me-THD-like_C)
Type: Domain

This entry represents a domain found C-terminal in S-methyl thiohydantoin desulfurase from Variovorax sp. (S-Me-THD) and similar sequences mainly found in bacteria and fungi. S-Me-THD catalyses the hydrolysis of S-methyl-thiohydantoin-5-propanoate into hydantoin-5-propanoate and methanethiol, the third step in S-methyl ergothioneine degradation .

This domain is also found in the hypothetical protein from Chromobacterium violaceum

. It folds into a partly open β-barrel (

).
SOSEKI, DIX-like domain (SOK_DIX)
Type: Domain

This entry represents the DIX-like domain found in a group of plant proteins, including protein SOSEKI1-5 from Arabidopsis thaliana and Physcomitrium patens. SOK1-5 integrate apical-basal and radial organismal axes to localise to polar cell edges and contain a DIX oligomerization domain that resembles that in the animal Dishevelled polarity regulator .
TOD1/MUCI70, glycosyltransferase-like domain (TOD1_MUCI70_glycTrfase_dom)
Type: Domain

This entry represents a glycosyltransferase-like domain found in alkaline ceramidase TOD1 (

) and the probable hexosyltransferase MUCI70 from Arabidopsis (

).

MUCI70 is a predicted glycosyltransferase essential for the accumulation of seed mucilage, a gelatinous wall rich in unbranched rhamnogalacturonan I (RG I), and for shaping the surface morphology of seeds . TOD1 is an endoplasmic reticulum ceramidase that catalyses the hydrolysis of ceramides into sphingosine and free fatty acids at alkaline pH (e.g. pH 9.5) .
Malate synthase, C-terminal domain (MS_C)
Type: Domain

This entry represents the C-terminal domain of MS, which consists of a five-helix 'plug' connected to the barrel by an extended loop and caps the active site.

Malate synthase (MS) catalyses the aldol condensation of glyoxylate with acetyl-CoA to form malate as part of the second step of the glyoxylate bypass and an alternative to the tricarboxylic acid cycle in bacteria, fungi and plants. There have been identified two isoforms, A and G (MSA and MSG, respectively) that differ in size and is attributed to an inserted α/β domain in MSG that may have regulatory function . Proteins int his entry consist of an N-terminal α-helical clasp, a central TIM barrel and a C-terminal α-helical plug. In malate synthases, the TIM β/α-barrel fold and the C-terminal helical domain are well conserved and the cleft between them forms the active site .
Malate synthase, N-terminal domain (MS_N)
Type: Domain

This entry represents the N-terminal clasp that wraps around one side of the TIM barrel and buttressed it .

Malate synthase (MS) catalyses the aldol condensation of glyoxylate with acetyl-CoA to form malate as part of the second step of the glyoxylate bypass and an alternative to the tricarboxylic acid cycle in bacteria, fungi and plants. There have been identified two isoforms, A and G (MSA and MSG, respectively) that differ in size and is attributed to an inserted α/β domain in MSG that may have regulatory function . Proteins int his entry consist of an N-terminal α-helical clasp, a central TIM barrel and a C-terminal α-helical plug. In malate synthases, the TIM β/α-barrel fold and the C-terminal helical domain are well conserved and the cleft between them forms the active site .
Malate synthase G, alpha-beta insertion domain (MSG_insertion)
Type: Domain

Malate synthase (MS) catalyses the aldol condensation of glyoxylate with acetyl-CoA to form malate as part of the second step of the glyoxylate bypass and an alternative to the tricarboxylic acid cycle in bacteria, fungi and plants. There have been identified two isoforms, A and G (MSA and MSG, respectively) that differ in size and is attributed to an inserted α/β domain in MSG that may have regulatory function . Members of the isoform G family are only found in bacteria. This entry represents the α/β insertion domain from MSG, which buttressed one side of the TIM-barrel domain .
EZH1/2, MCSS domain (EZH1/2_MCSS)
Type: Domain

This entry represents the MCSS domain found in the middle region of the metazoan Histone-lysine N-methyltransferases EZH1/2 . It makes contacts with the adjacent SANT domain and the Vefs domain from EED. Additionally, this domain contains a zinc-binding motif and contributes two cysteine residues for a second one, formed with two cysteines from the SANT domain .

The Polycomb Repressive Complex 2 (PRC2) is a chromatin modifying complex that consists of three core components: EED, SUZ12 and one of the two histone H3K27 methyltransferases, EZH1 or EZH2 . The PRC2 complex catalyses di- and trimethylation of histone H3 lysine 27 (H3K37me2/3), which has a repressive role. Even though EZH1 and EZH2 form similar PRC2 complexes, they exhibit contrasting repressive roles. In terms of their expression in mice, EZH1 is more abundant in nonproliferative adult organs, while EZH2 expression is tightly associated with proliferation .
Exocyst complex component EXOC6/Sec15, N-terminal domain (EXOC6_Sec15_N)
Type: Domain

This entry represents a domain found at the N-terminal of Exocyst complex components EXOC6/Sec15, members of the complexes associated with tethering containing helical rods (CATCHR) fold family and homologous to subunits of other multisubunit tethering complexes (MTCs) such as Dsl1, Golgi-associated retrograde protein (GARP) and COG complexes , characterised by a coiled-coild region at the N-terminal and an α-helical bundle at the C-terminal .

This is a coiled-coil domain of Sec15 that forms an antiparallel zipper with Sec10 and interacts with the antiparallel zipper formed between Exo70-Exo84, which form a four-helical bundle part of the core of the exocyst .
EZH2, preSET CXC domain, fungi (Ezh2_CXC_fung)
Type: Domain

This domain is found in a group of fungal proteins, including the Histone-lysine N-methyltransferase EZH2 from Chaetomium thermophilum (

), which is the catalytic subunit of the of the Polycomb Repressive Complex 2 (PRC2), responsible for methylation of histone H3 lysine 27 (H3K27) and therefore involved in epigenetic gene silencing. This entry represents the domain found N-terminal to the SET domain (

). It contains a Zn3Cys8His and a Zn3Cys9 cluster .
Vps52, C-terminal (Vps52_C)
Type: Domain

Vps52 complexes with Vps53 and Vps54 to form the Golgi-associated retrograde protein (GARP) complex that is involved in retrograde transport from early and late endosomes to the trans-Golgi network, regulating membrane trafficking events . It is also part of EARP (Endosome-Associated Recycling Protein) complex, involved in endocytic recycling . This entry represents the C-terminal domain of Vps52, which consists of α-helical bundles, conserved among subunits of other multisubunit tethering complexes (MTC) such as conserved oligomeric Golgi (COG), Dsl1 and the exocyst, all belong to a family of evolutionarily conserved complexes associated with tethering containing helical rods (CATCHR). This domain may interact with the small GTPase Ypt6p/Rab6 .
Poly (ADP-ribose) glycohydrolase, helical domain (PARG_helical)
Type: Domain

Poly(ADP-ribose) glycohydrolase (PARG), is a ubiquitously expressed exo- and endoglycohydrolase which mediates oxidative and excitotoxic neuronal death . It catalyses hydrolysis of the O-glycosidic linkages of ADP-ribose polymers, which reverses the effects of poly(ADP-ribose) . This entry represents the helical domain of PARG from animals, plants and some fungal species that precedes the PARG catalytic domain .