SII-SWORD/CoKE huggingface dataset:
Catalase, mono-functional, haem-containing, clade 2 (Catalase_clade2)
Type: Family

Catalases (

) are antioxidant enzymes that catalyse the conversion of hydrogen peroxide to water and molecular oxygen, serving to protect cells from its toxic effects . Hydrogen peroxide is produced as a consequence of oxidative cellular metabolism and can be converted to the highly reactive hydroxyl radical via transition metals, this radical being able to damage a wide variety of molecules within a cell, leading to oxidative stress and cell death. Catalases act to neutralise hydrogen peroxide toxicity, and are produced by all aerobic organisms ranging from bacteria to man. Most catalases are mono-functional, haem-containing enzymes, although there are also bifunctional haem-containing peroxidase/catalases (

) that are closely related to plant peroxidases, and non-haem, manganese-containing catalases (

) that are found in bacteria . Based on a phylogenetic analysis, catalases can be classified into clade 1, 2 and 3. Clade 1 contains small subunit catalases from plants and a subset of bacteria; clade 2 contains large subunit catalases from fungi and a second subset of bacteria; and clade 3 contains small subunit catalases from bacteria, fungi, protists, animals, and plants .

This entry represents clade 2 of the mono-functional, haem-containing catalases.
Fructosamine deglycase FrlB (Fructosamine_deglycase_FrlB)
Type: Family

This group represents fructosamine deglycase FrlB, which catalyses the conversion of a range of fructosamine 6-phosphates to glucose 6-phosphate and a free amino acid .
Coagulation factor 5/8-like (Factor_5/8-like)
Type: Family

This entry represents coagulation factors V and VIII, as well as other members of the multicopper oxidase family including the functionally similar venom prothrombin activator subunits, and the possible ferroxidase, hephaestin.

Mammalian coagulation factors V and VIII play analogous roles as non-enzymatic cofactors in the activation of prothrombin and factor X, respectively. They are proteolytically activated by thrombin and inactivated by activated protein C (APC).

The structures of factor V and VIII have been determined . The domain architecture of their precursor molecules can be represented as A1-A2-B-A3-C1-C2. The A domains are diverged versions of the multicopper oxidase domain (

). The B domain is highly variable and is removed during activation to yield non-covalently-associated heavy and light chains; this domain in mammalian factor V contains multiple copies of a 9-residue repeat (see

). The C domains (

) promote membrane binding.
Denitrification system component NapC/NirT/NrfH (NapC/NirT/NrfH)
Type: Family

This family includes NapC, a predicted membrane-anchored four-heme c-type cytochrome that forms one component of the periplasmic nitrate reductase along with NapA, NapB, NapD, NapE, and NapF subunits. The family also includes the nitrite reductase component NirT, and NrfH - a subunit of the nitrite reductase complex that mediates electron transfer from quinol to the catalytic subunit .
HpaB/PvcC/4-BUDH C-terminal (HpaB/PvcC/4-BUDH_C)
Type: Domain

This C-terminal domain is found in HpaB, which encodes part of the 4-hydroxyphenylacetate 3-hydroxylase from Escherichia coli . The enzyme is NADH-dependent and uses FAD as the redox chromophore. This domain is also found in pyoverdin chromophore biosynthetic protein PvcC, which may play a role in one of the proposed hydroxylation steps of pyoverdine chromophore biosynthesis and in 4-hydroxybutyryl-CoA dehydratase (4-BUDH), a key enzyme in the metabolism of gamma-aminobutyrate .
Snurportin-1, N-terminal (Snurportin-1_N)
Type: Domain

Snurportin-1 is a nuclear import receptor that contains an N-terminal importin beta binding domain which is essential for its function as an snRNP-specific nuclear import receptor . Snurportin-1 interacts with m3G-cap where it enhances the m3G-cap dependent nuclear import of U snRNPs in Xenopus laevis oocytes and digitonin-permeabilized HeLa cells .

This entry represents the snurportin-1 N-terminal importin beta binding domain (IBB). The essential role of the IBB domain for snurportin-1 function suggests that snurportin-1 cooperates with importin beta in mediating nuclear import of snRNPs.
Termicin (Termicin)
Type: Family

Termicin is a cysteine-rich antifungal peptide, which also exhibits weak antibacterial activity.
The global fold of termicin consists of an α-helical segment and a two-stranded antiparallel β-sheet forming a cysteine stabilised alphabeta motif that is also found in antibacterial and antifungal defensins from insects and from plants. The antifungal properties of termicin may be related to its marked hydrophobicity and its amphipatic structure compared to the antibacterial defensins .
Molybdenum cofactor biosynthesis protein F, N-terminal (MoaF_N)
Type: Domain

This entry represents the N-terminal domain of MoaF.

Molybdenum cofactor biosynthesis protein F (MoaF) is essential for the production of the monoamine-inducible 30kDa protein in Klebsiella . It is necessary for reconstituting organoautotrophic growth in Ralstonia eutropha . MoaF is conserved in proteobacteria and some lower eukaryotes. The operon regulating the Moa genes is responsible for molybdenum cofactor biosynthesis.
E3 ubiquitin-protein ligase UBR5, ubiquitin-associated domain (UBR5_UBA)
Type: Domain

This entry represents the N-terminal ubiquitin-associated (UBA) domain (also known as CUE domain) of UBR5 and similar animal proteins. Ubiquitin is recognised by helices alpha-1 and -3 in in the UBA domain. UBR5 binds to mono-ubiquitinated proteins .

E3 ubiquitin-protein ligase UBR5 (also known as E3 ligase identified by differential display, EDD), the ER ubiquitin ligase from the HECT ligases, acts as a key regulator of the ubiquitin proteasome system in both cancer and developmental biology. It is frequently overexpressed in breast and ovarian cancer. It is required for Wnt signal responses in Drosophila and human cell lines downstream of activated Armadillo/beta-catenin . It also plays a key role in ciliogenesis by regulating centriolar satellite stability and primary cilia . UBR5 contains an N-terminal ubiquitin-associated (UBA) domain which binds ubiquitin, a zinc-finger-like domain termed the ubiquitin-recognin (UBR) box, a MLLE (mademoiselle) domain, and a C-terminal catalytic HECT domain .
Ferric siderophore reductase, C-terminal (FhuF_C)
Type: Domain

Ferric siderophore reductase (FhuF) is a siderophore-iron reductase involved in iron removal from the hydroxamate-type siderophores coprogen, ferrichrome and ferrioxamine B after their transport into the cell . It binds both the iron-loaded and the apo forms of ferrichrome . This entry represents the C-terminal domain that contains 4 conserved cysteine residues found to be part of a 2Fe-2S cluster .
NAD-glutamate dehydrogenase, N-terminal ACT1 domain (NAD_Glu_DH_N_ACT1)
Type: Domain

This entry represents the first ACT-like domain (ACT1) found at the N-terminal of a bacterial family of NAD-specific glutamate dehydrogenases. The ACT domains of these proteins differ from the archetypal ACT fold in that strand strand β1 is located in the position usually occupied by strand β4 creating an ACT-like topology with a β1-4 antiparallel sheet .

Glutamate dehydrogenases (GDHs) are a broadly distributed group of enzymes that catalyse the reversible oxidative deamination of glutamate to ketoglutarate and ammonia . The structure of GDH from Mycobacterium smegmatis revealed that it has a long N- and C-terminal segments flanking the catalytic core, comprising several domains. The flexible N-terminal domain comprises ACT-like and PAS-type domains which could act as metabolic sensors for allosteric regulation .
DNA polymerase type-Y, HhH motif (PolY_HhH_motif)
Type: Conserved_site

This helix-hairpin-helix motif is found in proteins belonging to the type-Y family of DNA polymerases . This type of polymerases are thought to be involved in UV protection and mutation .
Ubiquitin carboxyl-terminal hydrolase 7, ICP0-binding domain (USP7_ICP0-binding_dom)
Type: Domain

This domain is found in proteins of the peptidase C19 family, which contains ubiquitinyl hydrolases like ubiquitin carboxyl-terminal hydrolase 7 (USP7) . This domain is one of two C-terminal domains on the much longer ubiquitin-specific proteases. It is found to interact with the herpesvirus 1 trans-acting transcriptional protein ICP0/VMW110.
Merozoite surface protein, EGF domain 1 (MSP1_EGF_1)
Type: Domain

This EGF-like domain is found at the C terminus of the malaria parasite MSP1 protein. MSP1 is the merozoite surface protein 1. This domain is part of the C-terminal fragment that is proteolytically processed from the the rest of the protein and is left attached to the surface of the invading parasite .
NELL2-like, EGF domain (NELL2-like_EGF)
Type: Domain

This entry represents an EGF domain found in several proteins, including NELL2, Cubilin, Uromodulin, Fibrillin and related proteins that contain EGF repeats. Some of these proteins have calcium-binding properties.

NELL2 is almost exclusively expressed in the nervous system. In the mammalian brain, NELL2 expression is mostly neuronal. NELL2 was previously found to be a secreted protein that functions during embryonic development as a neuronal differentiation and survival factor . NELL2 is a component of glutamatergic neurons and provide evidence for its physiological involvement in a major, glutamate-dependent, process of neuroendocrine regulation.
Alpha-N-acetylglucosaminidase, C-terminal (NAGLU_C)
Type: Domain

Alpha-N-acetylglucosaminidase is a lysosomal enzyme required for the stepwise degradation of heparan sulphate . Mutations on the alpha-N-acetylglucosaminidase (NAGLU) gene can lead to Mucopolysaccharidosis type IIIB (MPS IIIB, or Sanfilippo syndrome type B) characterised by neurological dysfunction but relatively mild somatic manifestations . The structure shows that the enzyme is composed of three domains. This C-terminal domain has an all α helical fold .
Alpha-N-acetylglucosaminidase, tim-barrel domain (NAGLU_tim-barrel)
Type: Domain

Alpha-N-acetylglucosaminidase is a lysosomal enzyme that is required for the stepwise degradation of heparan sulphate . Mutations on the alpha-N-acetylglucosaminidase gene can lead to mucopolysaccharidosis type IIIB (MPS IIIB; or Sanfilippo syndrome type B), characterised by neurological dysfunction but relatively mild somatic manifestations .

Alpha-N-acetylglucosaminidase is composed of three domains. This entry represents the central domain, which has a tim barrel fold .
Conjugative transposon protein TcpC (TcpC)
Type: Family

TcpC is required for efficient conjugative transfer, localizing to the cell membrane independently of other conjugation proteins, where membrane localization is important for its function, oligomerization and interaction with the conjugation proteins TcpA, TcpH, and TcpG . Its C-terminal domain is critical for interactions with these other conjugation proteins . TcpC has low level sequence identity to proteins encoded by the conjugative transposon Tn916, which is responsible for a large proportion of the tetracycline resistance in different pathogens .
Oestrogen-type nuclear receptor final C-terminal domain (Oestrogen-typ_rcpt_final_C_dom)
Type: Domain

This is the very C-terminal region of a subfamily of nuclear receptors that includes oestrogen receptors and other subfamily 3 group A members. The actual function of this region is not known, but the domain is absent from all the other types of nuclear receptors. Oestrogen receptors modulate AP-1-dependent transcription through two distinct mechanisms: via protein-protein interactions on DNA; and via non-genomic actions. The mechanism used depends on the cellular localisation of the receptor. In addition to the more extensively studied cross-talk on DNA, additional non-genomic actions might be very important in target tissues in which membrane-associated ERs are found. These non-genomic actions probably contribute to the overall physiological responses mediated by ligand-bound ERs and might possibly be mediated via this C-terminal domain.
Get5, N-terminal domain (Get5_N)
Type: Domain

This entry represents the N-terminal domain of Get5 from Aspergillus fumigatus and similar proteins found primarily in Ascomycetes. Get5 is a component of the get4/get5/sgt2 sorting complex involved in the GET (guided entry of TA proteins) pathway that leads to the insertion of tail-anchored proteins into the endoplasmic reticulum .

Tail-anchored trans-membrane proteins are targeted to membranes post-translationally. The proteins Get4 and Get5 form an obligate complex that catalyses the transfer of tail-anchored proteins destined to the endoplasmic reticulum from Sgt2 to the cytosolic targeting factor Get3 .
Transcriptional coactivator Hfi1/Transcriptional adapter 1 (Hfi1/Tada1)
Type: Family

The yeast Spt-Ada-Gcn5-Acetyl (SAGA) transferase complex is a multifunctional coactivator involved in multiple cellular processes , including regulation of transcription by RNA polymerase II . It is formed of five major modular subunits and shows a high degree of structural conservation to human TFTC and STAGA . This entry represents Hfi1 (known as Transcriptional adapter 1, Tada1 in higher eukaryotes), one of the subunits that constitute the SAGA core. It also functions as a component of the SALSA and SLIK complexes.
Protein tyrosine phosphatase, receptor type, N-terminal (PTP_recept_N)
Type: Domain

Protein tyrosine (pTyr) phosphorylation is a common post-translational modification which can create novel recognition motifs for protein interactions and cellular localisation, affect protein stability, and regulate enzyme activity. Consequently, maintaining an appropriate level of protein tyrosine phosphorylation is essential for many cellular functions. Tyrosine-specific protein phosphatases (PTPase;

) catalyse the removal of a phosphate group attached to a tyrosine residue, using a cysteinyl-phosphate enzyme intermediate. These enzymes are key regulatory components in signal transduction pathways (such as the MAP kinase pathway) and cell cycle control, and are important in the control of cell growth, proliferation, differentiation and transformation . The PTP superfamily can be divided into four subfamilies :

(1) pTyr-specific phosphatases

(2) dual specificity phosphatases (dTyr and dSer/dThr)

(3) Cdc25 phosphatases (dTyr and/or dThr)

(4) LMW (low molecular weight) phosphatases

Based on their cellular localisation, PTPases are also classified as:

Receptor-like, which are transmembrane receptors that contain PTPase domains

Non-receptor (intracellular) PTPases

All PTPases carry the highly conserved active site motif C(X)5R (PTP signature motif), employ a common catalytic mechanism, and share a similar core structure made of a central parallel β-sheet with flanking α-helices containing a β-loop-α-loop that encompasses the PTP signature motif . Functional diversity between PTPases is endowed by regulatory domains and subunits.

This entry represents a domain found in various protein tyrosine phosphatase haematopoietic receptors, e.g. CD45, which dephosphorylate growth stimulating proteins. The domain is found in eukaryotes, and is approximately 30 amino acids in length. There is a single completely conserved residue L that may be functionally important.
Hen1, N-terminal (Hen1_N)
Type: Domain

This entry represents the N-terminal domain of the bacterial Hen1 protein, which is a 3' terminal RNA ribose 2'-O-methyltransferase that is involved in bacterial RNA repair . Hen1 forms a heterotetramer with Pnkp. The heterotetramer has been shown to repair transfer RNAs cleaved by ribotoxins in vitro . The N-terminal domain of Hen1 contributes to the ligase activity of the heterotetramer.
Condensin-2 complex subunit G2 (Condensin2_G2)
Type: Family

Subunit G2 is a non-SMC subunit of condensin II, which is involved in maintenance of the structural integrity of chromosomes. Condensin II is made up of SMC (structural maintenance of chromosomes) and non-SMC subunits. The non-SMC subunits bind to the catalytic ends of the SMC subunit dimer. The condensin holocomplex is able to introduce superhelical tension into DNA in an ATP hydrolysis- dependent manner, resulting in the formation of positive supercoils in the presence of topoisomerase I and of positive knots in the presence of topoisomerase II .
Glycogen debranching enzyme, bacterial and archaeal type, N-terminal (Glycogen_debranch_N)
Type: Domain

This domain is found in bacteria and archaea glycogen debranching enzyme, and is typically between 218 and 229 amino acids in length. Glycogen debranching enzyme catalyses the debranching of amylopectin in glycogen. This is done by transferring three glucose subunits of glycogen from one parallel chain to another. This has the effect of enabling the glucose residues to become more accessible for glycolysis .
Dynein heavy chain, coiled coil stalk (Dynein_HC_stalk)
Type: Domain

The 380kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380kDa motor unit contains a concatenated chain of six AAA modules (D1-6), of which four correspond to the ATP binding sites with P-loop signatures, and two are modules in which the P loop has been lost in evolution. This domain occurs between D4 and D5 and includes the two predicted α-helical coiled coil segments that form the stalk supporting the ATP-sensitive microtubule binding component .
Putative cyclic diguanylate phosphodiesterase, CSS motif-containing domain (CSS-motif_dom)
Type: Domain

This domain, with its characteristic highly conserved CSS sequence motif, is found N-terminal to the EAL domain (

), found in many putative cyclic diguanylate phosphodiesterases, such as PdeB/C/D/G/N from E. coli K-12 . It has two highly conserved cysteine residues with potential disulfide bonds formation which might control the enzymatic activity of the cytoplasmic C-terminal EAL domain.
Glycoside hydrolase, family 44, catalytic domain (GH44_cat)
Type: Domain

This is the catalytic domain of a family of bacterial glycoside hydrolases formerly known as cellulase family J, and now known as Cel44A. It is one of the major enzymatic components of the cellulosome of Clostridium thermocellum strain F1 and of many other Firmicutes.
Glycosyl hydrolase family 100 (Glyco_hydro_100)
Type: Family

O-Glycosyl hydrolases (

) are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families . This classification is available on the CAZy (CArbohydrate-Active EnZymes) website.

Glycosyl hydrolase family 100 includes enzymes with invertase activity .
Pyridoxamine 5'-phosphate oxidase-related (Pyridox_Oxase-rel)
Type: Family

Pyridoxamine 5'-phosphate oxidase is a FMN flavoprotein that catalyses the oxidation of pyridoxamine-5-P (PMP) and pyridoxine-5-P (PNP) to pyridoxal-5-P (PLP). This entry contains several uncharacterised proteins, some annotated as pyridoxamine 5'-phosphate oxidase-related.
Putative collagen-binding domain (Collagen-bd_put)
Type: Domain

This domain is likely to be the collagen-binding domain of a family of bacterial collagenase enzymes.
The structure of one family member,

, has been characterised. The domain occurs in the C-terminal region of the protein.
Calcium-transporting P-type ATPase, N-terminal autoinhibitory domain (Ca_ATPase_N_dom)
Type: Domain

This entry represents the N-terminal autoinhibitory calmodulin-binding domain characteristic of certain calcium-transporting ATPases . This domain binds calmodulin in a calcium-dependent fashion and has a conserved RRFR sequence motif. There are two completely conserved residues (F and W) that may be functionally important.
Variant erythrocyte surface antigen-1 (VESA1)
Type: Family

This entry represents variant erythrocyte surface antigen 1, versions a and b, of Babesia. Babesia bovis is a tick-borne, intra-erythrocytic, protozoal parasite of cattle that shares many lifestyle parallels with the most virulent of the human malarial parasites, Plasmodium falciparum. Babesia uses antigenic variation to establish consistent infections of long duration. The two variants of VESA1, a and b, are expressed from different but closely related genes, and variation is achieved through the involvement of a segmental gene conversion mechanism and low-frequency epigenetic in situ switching of transcriptional activity from the VESA1 gene-pair to a possible other gene pair .
Myb/SANT-like domain (Myb/SANT-like_dom)
Type: Domain

This domain, found in L10-interacting MYB domain-containing protein (LIMYB) and At2g29880 from Arabidopsis, is related to Myb/SANT-like DNA binding domains. LIMYB is a transcription factor that associates with ribosomal protein promoters. It is involved in global translation suppression as an antiviral immunity strategy in plants .
Regulatory protein AriR (AriR)
Type: Family

AriR, also known as YmgB, is part of the three gene cluster ymgABC which has a role in biofilm development and stability. YmgB represses biofilm formation in rich medium containing glucose, decreases cellular motility and also protects the cell from acid, which indicates that YmgB has an important function in acid-resistance . YmgB binds as a dimer to genes which are important for biofilm formation via a ligand. Due to its important function in acid resistance it is also known as AriR (regulator of acid resistance influenced by indole) . AriR may be a non-specific DNA-binding protein that binds genes and/or intergenic regions via a geometric recognition.
DNA polymerase III PolC-like, N-terminal domain II (DNA_PolC-like_N_II)
Type: Domain

This entry represents the second N-terminal domain, NII domain, of the DNA polymerase III PolC subunit A. DNA polymerase PolC-type III enzyme functions as the 'replicase' in low G + C Gram-positive bacteria . It has been predicted that the N terminus of PolC folds into two globular domains, NI and NII. A predicted hydrophobic surface patch suggests this domain may be involved in protein binding . This domain is associated with bacterial DNA polymerase III, alpha subunit

and DNA polymerase III PolC-like, N-terminal domain I (

).
Circularly permutated YpsA SLOG (cpYpsA)
Type: Family

The structure of proteins in this family contain central β strands with flanking α helices. The structure is similar to that of a molybdenum cofactor carrier protein.This family belongs in the SLOG superfamily, circularly-permuted version of YspA famiy showing fusions to NAD utilization and ADP-ribosylation domains including NUDIX, NADAR and MACRO. Members of this family are predicted to function as sensors of nucleotide, nucleotide-derived ligands, or nucleic acids, which are potentially processed/modified by associating effectors .
Protocatechuate 3,4-dioxygenase beta subunit, N-terminal (PCDO_beta_N)
Type: Domain

This entry represents the N-terminal domain of the beta subunit of protocatechuate 3,4-dioxidase. Protocatechuate 3,4-dioxidase utilises a mononuclear, non-heme Fe3+ centre to catalyse metabolic cellular reactions . This domain is found in bacteria, and is approximately 40 amino acids in length. It is found in association with

. There are two completely conserved residues (Y and R) that may be functionally important.
Cell division protein FtsZ, C-terminal (FtsZ_C)
Type: Domain

The FtsZ family of proteins are involved in polymer formation. FtsZ is the polymer-forming protein of bacterial cell division. It is part of a ring in the middle of the dividing cell that is required for constriction of cell membrane and cell envelope to yield two daughter cells. FtsZ is a GTPase, like tubulin . FtsZ can polymerise into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria and archaea .

This entry represents a domain of FtsZ. In most FtsZ proteins is found in the C terminus, except in some alphaproteobacteria proteins where there is an extension C-terminal domain

.