SII-SWORD/CoKE huggingface dataset:
FAM86, N-terminal (FAM86_N)
Type: Domain

This conserved domain can be found at the N terminus of EEF2KMT (also known as FAM86A), FAM86B and related proteins. EEF2KMT (also known as Efm3 in budding yeasts) catalyzes the trimethylation of eukaryotic elongation factor 2 (EEF2) on 'Lys-525' .
Altered inheritance of mitochondria protein 23, mitochondrial (AIM23)
Type: Family

This entry represents the mitochondrial altered inheritance of mitochondria protein 23 (AIM23). Its function is not clear.
Mapk-regulated corepressor-interacting protein (MCRIP)
Type: Family

This family consist of Mapk-regulated corepressor-interacting protein 1 (MCRIP1) and 2 (MCRIP2). MCRIP1 binds to and inhibits the transcriptional co-repressor CtBP. MCRIP1 is an ERK substrate; when phosphorylated by ERK, MCRIP1 releases CtBP to induce chromatin modifications .
Ciliary BBSome complex subunit 2, middle region (BBS2_Mid)
Type: Domain

This entry represents the middle region of the Bardet-Biedl syndrome 2 protein.
Ciliary BBSome complex subunit 2, N-terminal (BBS2_N)
Type: Domain

This entry represents the N-terminal domain of the Bardet-Biedl syndrome 2 protein.
Tumour protein p53-inducible nuclear protein (TP53INP)
Type: Family

This entry represents tumour protein p53-inducible nuclear protein 1 and 2 (Tp53inp1 and Tp53inp2). There is only DOR/Tp53inp2 in invertebrates, while both Tp53inp1 and Tp53inp2 can be found in vertebrates. The vertebrates Tp53inp1 gene may have arisen by gene duplication .
Gp28/Gp37-like domain (Gp28/Gp37-like_dom)
Type: Domain

This entry includes proteins from tailed bacteriophages and bacterial prophages, including Minor tail protein Gp28 from Mycobacterium phages and Gp37 from Rhodococcus phage ReqiPepy6 .
DUF4438, N-terminal (DUF4438_N)
Type: Domain

This entry represents the N-terminal domain of TM_1086 from Thermotoga maritima (

) and related bacterial proteins with unknown function.
Putative transcriptional regulator (Put_trans_reg)
Type: Family

Members of this family are putative transcriptional regulators that appear to be related to

.
Protein TOPAZ1 domain (TOPAZ1_dom)
Type: Domain

This domain is found in protein TOPAZ1, which may play an important role in germ cell development . Homology suggests that it is a putative aspartate racemase.

Protein TOPAZ1 was previously called testis and ovary-specific PAZ domain-containing protein 1 , but the name was changed to Protein TOPAZ1 as it does not contain a PAZ domain.
Eukaryotic glycogen debranching enzyme, N-terminal domain (AGL_euk_N)
Type: Domain

This domain is found at the N terminus of the eukaryotic variant of the glycogen debranching enzyme (GDE), where it is immediately followed by the aldolase-like domain. The eukaryotic GDE performs two functions: 4-alpha-glucanotransferase (

) and amylo-alpha-1,6-glucosidase (

), performed by the N- and C-terminal halves of the enzyme respectively .
BLOC-2 complex member HPS3, N-terminal domain (HPS3_N)
Type: Domain

This entry represents the N-terminal domain of BLOC-2 complex member HPS3. In human HPS3, this region carries the clathrin-binding motif LLDFE at residues 172-176. Hermansky-Pudlak syndrome caused by mutations in HPS3 gene is a genetically heterogeneous autosomal recessive disorder characterised by oculocutaneous albinism, bleeding due to platelet storage pool deficiency, and lysosomal storage defects .
BLOC-2 complex member HPS3, C-terminal domain (HPS3_C)
Type: Domain

This entry represents the C-terminal domain of BLOC-2 complex member HPS3. In human HPS3, this region carries a number of tyrosine sorting motifs and the second of two di-leucine sorting boxes at residues 711-717, as well as the ER membrane-retention signal KKPL at residues 1000-1003. Hermansky-Pudlak syndrome caused by mutations in HPS3 gene is a genetically heterogeneous autosomal recessive disorder characterised by oculocutaneous albinism, bleeding due to platelet storage pool deficiency, and lysosomal storage defects .
Wzt, C-terminal (Wzt_C)
Type: Domain

This domain is found at the C terminus of O-antigen export proteins, such as Wzt. The N-terminal domain of Wzt is a conventional ABC protein, whereas the C-terminal domain of Wzt (C-Wzt) is a unique structural element that determines the specificity of the transporter for either the O8 or O9a O-antigenic polysaccharides (O-PS) . The crystal structure of C-Wzt(O9a) reveals a β sandwich with an immunoglobulin-like topology that contains the O-PS binding pocket .
Dynein regulatory complex protein 1, C-terminal (DRC1_C)
Type: Domain

This entry represents the C-terminal domain of dynein regulatory complex protein 1 (DRC1, also known as CCDC164). DRC1 is a key component of the nexin-dynein regulatory complex (N-DRC), essential for N-DRC integrity. It is required for the assembly and regulation of specific classes of inner dynein arm motors. It may also function to restrict dynein-driven microtubule sliding, thus aiding in the generation of ciliary bending .
Integron-associated effector binding protein (Cass2)
Type: Domain

Cass2 from Vibrio cholerae is an integron-associated protein that has been shown to bind cationic drug compounds with submicromolar affinity . Cass2 has been proposed to be representative of a larger family of independent effector-binding proteins associated with lateral gene transfer within Vibrio and other closely-related species. The structure of Cass2 defines a monomeric β-barrel protein with a fold related to the effector-binding portion of AraC/XylS transcription activators (

).

This domain is also found in BrlR from Pseudomonas aeruginosa which is a receptor for both cyclic di-GMP and pyocyanin . It contains the pyocyanin-binding site (

).
GyrI-like small molecule binding domain (GyrI-like)
Type: Domain

This entry represents a small molecule binding domain in a number of different bacterial transcription activators and DNA gyrase inhibitors (GyrI). In members of the GyrI superfamily this domain originated from a dimeric version of an SHS2 module that has been adapted for small-molecule binding . Members of the GyrI superfamily with this domain include a family of secreted forms that is found only in animals and the bacterial pathogen Leptospira .
Integrator complex subunit 5, C-terminal (INTS5_C)
Type: Domain

This entry represents the C-terminal of the integrator complex subunit 5 (INTS5). The integrator complex is involved in the small nuclear RNAs (snRNA) U1 and U2 transcription and in their 3'-box-dependent processing .
Integrator complex subunit 5, N-terminal (INTS5_N)
Type: Domain

This entry represents the N-terminal of the integrator complex subunit 5 (INTS5). The integrator complex is involved in the small nuclear RNAs (snRNA) U1 and U2 transcription and in their 3'-box-dependent processing .
Coatomer beta subunit, appendage platform domain (COPB1_appendage_platform_dom)
Type: Domain

This entry represents a domain found in the C-terminal of the coatamer beta subunit proteins (Beta-coat proteins). It is a platform domain on the appendage that carries a highly conserved tryptophan .

Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer . While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins . For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi . Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes . COPI coated vesicle assembly is initiated by recruitment of the small GTPase Arf1 which recruits the coatomer protein complex from the cytoplasm and anchors it at the membrane. Then, Arf1 is activated by a guanine exchange factor and hydrolyses GTP to mediate uncoating of the vesicle which subsequently fuses with its target membrane . As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits, and can be subdivided into an outer-coat and an adaptor subcomplex .
Domain of unknown function DUF4439 (DUF4439)
Type: Domain

This domain has a ferritin-like fold.
Fanconi anaemia protein FANCD2 (FANCD2)
Type: Family

The Fanconi Anemia (FA) pathway is responsible for interstrand crosslink DNA repair . The name originates the recessive syndrome known as Fanconi anemia, which causes developmental problems and cancer predisposition . In this pathway, the FANCI-FANCD2 (ID) complex is ubiquitinated by the FA core complex and then travels to sites of damage to coordinate repair . FA pathway activation seems to trigger dissociation of FANCD2 from FANCI, coinciding with FANCD2 monoubiquitination which precedes monoubiquitination of FANCI . This suggests a functional separation for FANCD2 from FANCI .

Monoubiquitinated FANCD2 functions to recruit DNA repair factors FAN1 (Fanconi-associated nuclease 1) and SLX4 , suggesting that chromatin-bound FANCD2Ub is a docking platform for certain DNA repair nucleases. FANCD2 has also a role in replication fork recovery .
Apoptosis regulator M11 (Apo_reg_M11)
Type: Family

Some herpesviruses encode homologues of the antiapoptotic, cellular Bcl-2 to promote viral replication and pathogenesis. Members of this small group of viral proteins are homologues of Bcl-2 and seem to inhibit autophagy through binding to autophagy effector Beclin1 .
Rapamycin-insensitive companion of mTOR, middle domain (RICTOR_M)
Type: Domain

This domain is found in the more conserved central section of Rictor (rapamycin-insensitive companion of mTOR) that may include several individual domains.

The mammalian target of rapamycin (mTOR) is a conserved Ser/Thr kinase that forms two functionally distinct complexes, mTROC1 and mTORC2, important for nutrient and growth-factor signalling. Rictor is a component of mTORC2 . There is a regulatory link between the two mTOR complexes, whereby Rictor phosphorylation by mTORC1 regulates mTORC2 signalling . Over-expression of Rictor increases mTORC2 activity and promotes cell growth and motility .
Rapamycin-insensitive companion of mTOR, domain 5 (RICTOR_V)
Type: Domain

This entry represent the conserved domain 5 of the Rictor (Rapamycin-insensitive companion of mTOR) protein.

The mammalian target of rapamycin (mTOR) is a conserved Ser/Thr kinase that forms two functionally distinct complexes, mTROC1 and mTORC2, important for nutrient and growth-factor signalling. Rictor (rapamycin-insensitive companion of mTOR) is a component of mTORC2 . There is a regulatory link between the two mTOR complexes, whereby Rictor phosphorylation by mTORC1 regulates mTORC2 signalling . Over-expression of Rictor increases mTORC2 activity and promotes cell growth and motility .
Rapamycin-insensitive companion of mTOR, domain 4 (Rictor_IV)
Type: Domain

This entry represents the domain 4 of the Rictor (rapamycin-insensitive companion of mTOR) protein. It is found in the more conserved central section that may include several individual domains

The mammalian target of rapamycin (mTOR) is a conserved Ser/Thr kinase that forms two functionally distinct complexes, mTROC1 and mTORC2, important for nutrient and growth-factor signalling. Rictor (rapamycin-insensitive companion of mTOR) is a component of mTORC2 . There is a regulatory link between the two mTOR complexes, whereby Rictor phosphorylation by mTORC1 regulates mTORC2 signalling . Over-expression of Rictor increases mTORC2 activity and promotes cell growth and motility .
ODR-4-like (ODR-4-like)
Type: Family

This entry represents the odorant response abnormal protein 4 (ODR-4)-like proteins from animals and plants.
Hypothetical glycosyl hydrolase family 15 (GHL15)
Type: Family

GHL15 is a family of hypothetical glycoside hydrolases.
Sialidase, N-terminal (Sialidase_N)
Type: Domain

This domain is found in the N-terminal of sialidases.

Sialidases catalyse hydrolysis of alpha-(2->3)-, alpha-(2->6)-, alpha-(2->8)- glycosidic linkages of terminal sialic acid residues in oligosaccharides, glycoproteins, glycolipids, colominic acid and synthetic substrates. In some bacteria, sialidases have been suggested to be pathogenic factors in microbial infections .
Hypothetical glycoside hydrolase 5 (GHL5)
Type: Family

GHL5 is a family of hypothetical glycoside hydrolases.
Ras-binding domain of Byr2 (Ras-bd_By2)
Type: Domain

This entry represents the Ras binding/interacting domain of the Byr2 protein from Schizosaccharomyces pombe. The Ras binding domain (RBD) of Byr2 is necessary and sufficient for the protein to be translocated by Ras to the plasma membrane . This domain can also be found in Ste11 protein from Saccharomyces cerevisiae.

Byr2 is mitogen-activated protein/ERK kinase kinase (MEKK) that responds to pheromone signalling and controls mating through a mitogen-activated protein kinase (MAPK) pathway . The small GTP binding protein Ras binds and activates Byr2 .
Elongation factor Tu-type domain (EFTU-type)
Type: Domain

Translation initiation factor IF-2 consists of several structural domains: an N-terminal G domain followed by an EF-Tu-type β barrel domain, followed by a novel α/β/α-sandwich connected via an α helix to a second EF-Tu-type β barrel domain . This entry represents the fourth domain.
DNA polymerase, helix-hairpin-helix motif (DNAPol_HHH)
Type: Domain

The HHH (helix-hairpin-helix) domain is a short DNA-binding domain .
Metallophosphoesterase, TT1561-like (TT1561-like)
Type: Domain

This entry represents a putative metallophosphoesterase domain found in archaea bacteria, such as that of uncharacterised protein TT1561 from Thermus thermophilus (

).
Regulator of nucleoside diphosphate kinase, N-terminal domain (Rnk_N)
Type: Domain

This domain occurs at the N terminus of Rnk (regulator of nucleoside diphosphate kinase), an RNA polymerase-interacting protein of the GreA/GreB family . It has a coiled coil structure .
Lysine-specific metallo-endopeptidase (Lys_MEP)
Type: Domain

This is the catalytic domain of aspzincins, a group of lysine-specific metallo-endopeptidases in the MEROPS M35 family. They exhibit the following active-site architecture: the active site is composed of two helices and a loop region and includes the HExxH and GTxDxxYG motifs. In protein

, His117, His121 and Asp130 coordinate to the catalytic zinc ligands. An electrostatically negative region composed of Asp154 and Glu157 attracts a positively charged Lys side chain of a substrate in a specific manner .
Type I restriction enzyme R protein, N-terminal domain (HSDR_N)
Type: Domain

This entry represents the N-terminal domain found in type I restriction enzyme R (HSDR) proteins. Restriction and modification (R/M) systems are found in a wide variety of prokaryotes and are thought to protect the host bacterium from the uptake of foreign DNA . Type I restriction and modification systems are encoded by three genes: hsdR, hsdM, and hsdS. The three polypeptides, HsdR, HsdM, and HsdS, often assemble to give an enzyme (R2M2S1) that modifies hemimethylated DNA and restricts unmethylated DNA .
TupA-like ATPgrasp protein (ATPgrasp_TupA)
Type: Family

Proteins in this family contain the ATP-grasp fold predicted to be involved in the biosynthesis of cell surface polysaccharides such as the O-antigen in proteobacteria, the capsule in firmicutes, and the polyglutamate chain of teichuronopeptide .
No apical meristem-associated, C-terminal domain (NAM-associated_C)
Type: Domain

This domain is found in a number of fungal and plant proteins including NAM (no apical meristem)-like proteins.
Cytochrome c7-like (Cyt_c7-like)
Type: Domain

This family includes cytochromes c7 and c7-type. In cytochromes c7 all three haems are bis-His coordinated, while in c7-type the last haem is His-Met coordinated . Desulfuromonas acetoxidans and Geobacter metallireducens cytochrome c7 participate in the anaerobic iron respiration, but Geobacter metallireducens cytochrome c7 hasn't a Fe(III) reductase activity .

This entry also includes cytochrome c nitrite reductase subunit NrfH from Desulfovibrio vulgaris which forms a complex with cytochrome c nitrite reductase NrfA .
O-antigen polysaccharide polymerase Wzy (O-ag_pol_Wzy)
Type: Family

This family includes O-antigen polysaccharide polymerases . These enzymes link O-units via a glycosidic linkage to form a long O-antigen . These enzymes vary in specificity and sequence .
PD-(D/E)XK nuclease superfamily 4 (PDDEXK_4)
Type: Family

Members of this family belong to the PD-(D/E)XK nuclease superfamily. Their function is not clear.
HNH endonuclease 5 (HNH_5)
Type: Domain

This domain is related to other HNH domain families such as

, suggesting that these proteins have a nucleic acid cleaving function.
Retrotransposon Copia-like, N-terminal (Copia-like_N)
Type: Domain

This entry represents a domain found at the N terminus of polyprotein-like retroelements or retrotransposons of the copia-type mainly from plants.
Cell morphogenesis central region (MOR2-PAG1_mid)
Type: Domain

This entry represents the central region of proteins that are involved in cell morphogenesis. Among these are furry proteins from flies , proteins PAG1 from budding yeasts and Mor2 from fission yeasts .
Haem-oxygenase-associated, N-terminal helices (HOASN)
Type: Domain

This domain represents a pair of α helices, which are found at the N terminus of some Haem-oxygenase globular domains.
Protein of unknown function DUF6807 (DUF6807)
Type: Family

This family includes bacterial proteins of unknown function.
Diacylglycerol kinase type I, N-terminal (DAG_kinase_typeI_N)
Type: Domain

This domain is found at the N terminus of the EF-hand domain of the type I diacylglycerol kinases (DGKs). DGKs phosphorylate diacylglycerol (DAG) to produce phosphatidic acid (PA) and play an important role in signal transduction by modulating the balance between these signalling lipids. DGKs can be classified into five types. Proteins containing this domain are EF-hand domain containing type I DGKs, including DGK-alpha, beta and gamma .
Putative nitroreductase TM1586 (TM1586_NiRdase)
Type: Domain

Compared with the more traditional NADH oxidase/flavin reductases, this domain is a duplication, consisting of two similar domains arranged as the subunits of the dimeric NADH oxidase/flavin reductase with one conserved active site. It gets its name from uncharacterised protein TM1586 from Thermotoga maritima (

).
Nitroreductase (Nitroreductase)
Type: Domain

The entry represents a domain found in a group of FMN- or FAD-dependent and NAD(P)H-dependent nitroreductases that are able to metabolise nitrosubstituted compounds .
Transposase-associated domain (Transpos_assoc)
Type: Domain

This entry represents a domain found in some putative transposases from plants.
Pleiotropic ABC efflux transporter, N-terminal domain (ABC_trans_N)
Type: Domain

This domain is found at the N terminus of ABC-transporter proteins from fungi and plants such as the pleiotropic ABC efflux transporters MDR1 from Trichophyton interdigitale and PDR5 from yeast . They may be involved in the modulation susceptibility to a wide range of unrelated cytotoxic compounds. It is predicted to be an intracellular domain .
Putative peptidase domain, HRXXH (HRXXH)
Type: Domain

Proteins containing this domain are putative peptidases closely related to the M35 family (

). In this family the metal binding HEXXH motif is replaced with HRXXH. The exact function of these fungal proteins is unknown. Proteins containing this domain include members of the Zps1 (Zinc- and pH-regulated Surface protein) family . Some of them are fungal allergens; including Asp f2, a major allergen from Aspergillus fumigatus, which reacts with serum from patients with ABPA (allergic bronchopulmonary aspergillosis) , and pH-regulated antigen 1 (PRA1) from Candida albicans, which has a role in fungal morphogenesis and perhaps in the host-parasite interaction during candidal infection .
Glycosyl-hydrolase 97, C-terminal oligomerisation domain (GH97_C)
Type: Domain

Proteins containing this domain include the aglycoside hydrolase family 97 enzyme, SusB protein, from Bacteroides thetaiotaomicron. SusB has three domains: the N-terminal, catalytic, and C-terminal domains. This entry represents the C-terminal domain that is found to be necessary for oligomerisation of the whole molecule in order to create the active-site pocket and the Ca++-binding site .
Cationic amino acid transporter, C-terminal (CAT_C)
Type: Domain

This entry represents the C-terminal of the cationic amino acid transporters (CATs) from bacteria, plants and animals. CATs are permeases involved in the transport of the cationic amino acids.
Glycosyl-hydrolase 97, N-terminal domain (GH97_N)
Type: Domain

Proteins containing this domain include the aglycoside hydrolase family 97 enzyme, SusB protein, from Bacteroides thetaiotaomicron. SusB has three domains: the N-terminal, catalytic, and C-terminal domains. This entry represents the N-terminal domain that contributes to part of the active site pocket and is important for contact with the catalytic and the C-terminal domains .
Novel E3 ligase domain (NEL_dom)
Type: Domain

This NEL or novel E3 ligase domain is found at the C terminus of bacterial virulence factors. Its sequence is different from those of the eukaryotic HECT and RING-finger E3 ligases, and it subverts the host ubiquitination process . At the N terminus of the family-members there is a series of LRR repeats, and the NEL domain interacts with the most N-terminal repeat. The key residue for the ligation step is a cysteine, and the LRR domain sequesters the catalytic cysteine residue contained in the NEL domain until invasion has occurred .
Hemingway/CFA97 (Hmw/CFAP97)
Type: Family

Drosophila Hemingway (Hmw) is required for motile cilia function and sperm flagella assembly . The human orthologue, known as cilia- and flagella-associated protein 97 (CFAP97) or KIAA1430, localises to the primary cilium . Another member of this family is the uncharacterised protein CFAP97D1/2 (CFAP97 domain-containing protein 1/2).
O-GlcNAc transferase, C-terminal (OGT/SEC/SPY_C)
Type: Domain

This entry represents the C-terminal domain of the O-linked beta-N-acetylglucosamine transferase (OGT, also known as UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase), which catalyses the transfer of a single GlcNAc to the Ser or Thr of nucleocytoplasmic proteins . OGTs have two known domains: the N-terminal tetratricopeptide repeat domain and the C-terminal glycosyltransferase domain . Deletions of the C-terminal domain result in a complete loss of the enzyme activity .
Cytochrome c-550 domain (Cytochrom_C550)
Type: Domain

This domain is found in the heme binding cytochrome known as cytochrome c550, or cytochrome c549, or PsbV . PsbV is an extrinsic subunit found in the lumen of photosystem II (PSII), which functions as a light-driven water plastoquinone oxidoreductase. PSII utilised light energy to extract electrons from H2O, creating a proton gradient that is later utilised for ATP synthesis. The extrinsic proteins serve to reinforce the structural integrity of the oxygen-evolving complex (OEC) within photosystem II .