SII-SWORD/CoKE huggingface dataset:
11-S seed storage protein, conserved site (11S_seedstore_CS)
Type: Conserved_site

Plant seed storage proteins, whose principal function appears to be the major nitrogen source for the developing plant, can be classified, on the basis of their structure, into different families. 11-S are non-glycosylated proteins which form hexameric structures . Each of the subunits in the hexamer is itself composed of an acidic and a basic chain derived from a single precursor and linked by a disulphide bond. This structure is shown in the following representation.

+-------------------------+
| |
xxxxxxxxxxxCxxxxxxxxxxxxxxxxxxxxxxNGxCxxxxxxxxxxxxxxxxxxxxxxx
|------Acidic-subunit-------------||-----Basic-subunit------|
|-----------------About-480-to-500-residues-----------------|

'C': conserved cysteine involved in a disulphide bond.

Members of the 11-S family include pea and broad bean legumins, oil seed rape cruciferin, rice glutelins, cotton beta-globulins, soybean glycinins, pumpkin 11-S globulin, oat globulin, sunflower helianthinin G3, etc. This family represents the precursor protein which is cleaved into the two chains. These proteins contain two β-barrel domains. This family is a member of the 'cupin' superfamily on the basis of their conserved barrel domain ('cupa' is the Latin term for a small barrel).

The signature pattern for this family includes the conserved cleavage site between the acidic and basic subunits (Asn-Gly) and a proximal cysteine residue which is involved in the inter-chain disulphide bond.
Glutamyl-Q tRNA(Asp) synthetase (Glu-Q_tRNA(Asp)_Synthase)
Type: Family

This protein resembles a shortened glutamyl-tRNA ligase, but its purpose is to modify tRNA(Asp) at a queuosine position in the anticodon rather than to charge a tRNA with its cognate amino acid . It catalyses the tRNA-independent activation of glutamate in presence of ATP and the subsequent transfer of glutamate onto the tRNA(Asp). In Escherichia coli, the glutamylated tRNA(Asp) might be involved in ribosomal protein biosynthesis, as it interacts with the elongation factor EF-Tu . Comparison of the three-dimensional structure of Glu-Q-RS with that of GluRS, both with a unique zinc-binding site, shows that a restricted number of residues determine the distinct catalytic properties of amino acid recognition and activation in both enzymes . Members of this protein family are found in bacteria.
Uncharacterised protein family MG067 (Uncharacterised_MG067)
Type: Family

Mycoplasma genitalium has the smallest known genome of any free-living organism. Its complete genome sequence has been determined by whole genome random sequencing and assembly. Only 470 putative coding regions were identified, including genes for DNA replication, transcription and translation, DNA repair, cellular transport and energy metabolism. One family of hypothetical proteins, which includes products of the MG067/MG068/MG395 genes, has been shown to have homologues of similarly unknown function in Mycoplasma pneumoniae.
Mycoplasma peptidase DUF31 (Mycoplasma_peptidase_DUF31)
Type: Domain

This domain is found in various uncharacterised proteins and putative lipoproteins from mycoplasmas. Although its function is not clear, it has been suggested that this is a serine protease domain; sequence analysis revealed that the amino acid sequence is similar to that of serine proteases. It is related to pathogenicity as this domain is present in proteins encoded by animal and human pathogenic Mycoplasmas . It has been proposed that the Ig binding protein M may function together with this domain playing a role in evading host Ig-mediated defense against the MIB-MIP (mycoplasma Ig binding protein (MIB) and mycoplasma Ig protease (MIP)) system, which is a novel mechanism that protects mycoplasma against host immune response .
Lactate/malate dehydrogenase, C-terminal (Lactate/malate_DH_C)
Type: Domain

L-lactate dehydrogenases are metabolic enzymes which catalyse the conversion of
L-lactate to pyruvate, the last step in anaerobic glycolysis . L-lactate dehydrogenase is also found as a lens crystallin in bird and crocodile eyes. L-2-hydroxyisocaproate dehydrogenases are also members of the family. Malate dehydrogenases catalyse the interconversion of malate to oxaloacetate . The enzyme participates in the citric acid cycle.

This entry represents the C-terminal, and is thought to be an is an unusual α+β fold.
Formiminotransferase catalytic domain superfamily (FormiminoTrfase_cat_dom_sf)
Type: Homologous_superfamily

This entry represents the formiminotransferase (FT) domain of formiminotransferase-cyclodeaminase (FTCD), which forms a homodimer, with each protomer being comprised of two subdomains. Each subdomain has the structure consisting of an α/β sandwich with antiparallel β-sheet in the form (β-α-β)x2. Tetrahydrofolate (THF)-dependent glutamate formiminotransferase is involved in the histidine utilization pathway. This enzyme interconverts L-glutamate and N-formimino-L-glutamate. The enzyme is bifunctional as it also catalyzes the cyclodeaminase reaction on N-formimino-THF, converting it to 5,10-methenyl-THF and releasing ammonia; part of the process of regenerating THF. This model covers enzymes from metazoa as well as Gram-positive bacteria and archaea. In humans, deficiency of this enzyme results in a disease phenotype . The crystal structure of the enzyme has been studied in the context of the catalytic mechanism .

This superfamily represents both individual subdomains of the formiminotransferase catalytic domain.
Rhs repeat-associated core (Rhs_assc_core)
Type: Domain

This entry represents a conserved unique core sequence shared by large numbers of proteins. It is occasionally found in the Archaea, including Methanosarcina barkeri) but commonly found in the bacteria and eukaryotes. Most fall into two large classes. One class consists of long proteins in which two classes of repeats are abundant: an FG-GAP repeat (

) class, and an RHS repeat (

) or YD repeat (

). This class includes secreted bacterial insecticidal toxins and intercellular signalling proteins such as the teneurins in animals. The other class consists of uncharacterised proteins shorter than 400 amino acids, where this core domain of about 75 amino acids tends to occur in the N-terminal half. Over twenty such proteins are found in Pseudomonas putida alone; little sequence similarity or repeat structure is found among these proteins outside of this domain.
Carbohydrate ABC transporter, N-acetylglucosamine/diacetylchitobiose-binding protein (Chitin_NgcE)
Type: Family

Bacterial high affinity transport systems are involved in active transport of solutes across the cytoplasmic membrane. Most of the bacterial ABC (ATP-binding cassette) importers are composed of one or two transmembrane permease proteins, one or two nucleotide-binding proteins and a highly specific periplasmic solute-binding protein. In Gram-negative bacteria the solute-binding proteins are dissolved in the periplasm, while in archaea and Gram-positive bacteria, their solute-binding proteins are membrane-anchored lipoproteins .

Members of this protein family include the substrate-binding protein diacetylchitobiose binding protein NgcE. NgcE binds both N-acetylglucosamine and the chitin dimer, N,N'-diacetylchitobiose .
Carbohydrate ABC transporter substrate-binding, CPR0540 (Bind_CPR0540)
Type: Family

Members of this protein are the substrate-binding protein of a predicted carbohydrate transporter operon, together with permease subunits of ABC transporter homology families. This substrate-binding protein frequently co-occurs in genomes with a family of disaccharide phosphorylases,

, suggesting that the molecule transported will include beta-D-galactopyranosyl-(1->3)-N-acetyl-D-glucosamine and related carbohydrates. Members of this family are sporadically strain by strain, often in species with a human host association, including Propionibacterium acnes and Clostridium perfringens (protein CPR_0540, which gives its name to the group), and Bacillus cereus.

Bacterial high affinity transport systems are involved in active transport of solutes across the cytoplasmic membrane. Most of the bacterial ABC (ATP-binding cassette) importers are composed of one or two transmembrane permease proteins, one or two nucleotide-binding proteins and a highly specific periplasmic solute-binding protein. In Gram-negative bacteria the solute-binding proteins are dissolved in the periplasm, while in archaea and Gram-positive bacteria, their solute-binding proteins are membrane-anchored lipoproteins .
Conserved hypothetical protein CHP03808 (CHP03808)
Type: Family

Members of this protein family have a Sec-independent twin-arginine tranlocation (TAT) signal sequence, which enables tranfer of proteins folded around prosthetic groups to cross the plasma membrane. These proteins have four copies of a repeat of about 23 amino acids that resembles the β-helix repeat. β-helix refers to a structural motif in which successive β strands wind around to stack parallel in a right-handed helix, as in AlgG and related enzymes of carbohydrate metabolism. The twin-arginine motif suggests that members of this protein family bind some unknown cofactor.
ParB-related, ThiF-related cassette, protein D (PRTRC_protein-D)
Type: Family

A novel genetic system, often found on plasmids, encodes six major proteins, included a ParB homologue and a ThiF homologue, and is designated PRTRC (ParB-Related, ThiF-Related Cassette). This entry represents PRTRC system protein D.
4-hydroxybenzoate decarboxylase subunit C (HBDC)
Type: Family

This entry represents a group of bacterial archaeal decarboxylases, including the 4-hydroxybenzoate decarboxylase subunit C (also known as HBDC) from Chlamydophila pneumoniae AR39. HBDC catalyses the reversible decarboxylation of 4-hydroxybenzoate .
Integrating conjugative element relaxase, PFGI-1 class (ICE_relaxase_PFGI-1)
Type: Domain

Proteins in this entry are the TraI putative relaxases required for transfer by a subclass of integrating conjugative elements (ICE) as found in Pseudomonas fluorescens Pf-5, and understood from study of two related ICE, SXT and R391. There is no homology detected to the similarly named TraI relaxase of the F plasmid. This entry represents the N-terminal domain of these proteins.
Anchored repeat-type ABC transporter, permease subunit (Anch_rpt-typ_ABC_trnsprt_perm)
Type: Family

This entry represents the permease subunit of a binding protein-dependent ABC transporter complex. The gene encoding this subunit is strictly associated with an adjacent gene encoding a sunbstrate binding protein containing the

domain. Homologous permease subunits outside the scope of this family include manganese transporter MntB in Synechocystis sp PCC 6803 and chelated iron transporter subunits. The function of this transporter complex is unknown.
Conjugative transposon, TraJ (Conjugative_transposon_TraJ)
Type: Family

Proteins in this entry are designated TraJ and are found in a proposed transfer region of a class of conjugative transposon found primarily in the Bacteroides lineage. They are related to conjugation system proteins in the Proteobacteria, including TrbL of Agrobacterium Ti plasmids and VirB6.
Methylamine utilisation protein, MauG (Methylamine_utilis_MauG)
Type: Family

This entry represents methylamine utilisation protein, MauG, as found in Methylobacterium extorquens and related species. This protein is involved in methylamine metabolism and is required to complete the maturation of the tryptophan tryptophylquinone (TTQ) cofactor in the methylamine dehydrogenase light (beta) chain .
Conserved hypothetical protein CHP03773, ABC transporter-like (CHP03773_ABC_transptr-like)
Type: Family

Members of this protein family occur in genomes that contain a three-gene ABC transporter operon associated with the presence of domain

. That domain occurs as a single-copy insert in the substrate-binding protein, and occurs in two or more copies in members of this protein family. Members of this family typically are encoded adjacent to the said transporter operon and may serve as a substrate receptor.
ParB-related, ThiF-related cassette, ParB (PRTRC_ParB)
Type: Family

A novel genetic system characterised by six major proteins, included a ParB homologue and a ThiF homologue, is designated PRTRC, or ParB-Related,ThiF-Related Cassette. It is often found on plasmids. In this entry the members are related to ParB.
Tyrosine decarboxylase, bacteria (Tyrosine_deCO2ase_bac)
Type: Family

Pyridoxal phosphate is the active form of vitamin B6 (pyridoxine or pyridoxal). Pyridoxal 5'-phosphate (PLP) is a versatile catalyst, acting as a coenzyme in a multitude of reactions, including decarboxylation, deamination and transamination . PLP-dependent enzymes are primarily involved in the biosynthesis of amino acids and amino acid-derived metabolites, but they are also found in the biosynthetic pathways of amino sugars and in the synthesis or catabolism of neurotransmitters; pyridoxal phosphate can also inhibit DNA polymerases and several steroid receptors . Inadequate levels of pyridoxal phosphate in the brain can cause neurological dysfunction, particularly epilepsy .

PLP enzymes exist in their resting state as a Schiff base, the aldehyde group of PLP forming a linkage with the ε-amino group of an active site lysine residue on the enzyme. The α-amino group of the substrate displaces the lysine ε-amino group, in the process forming a new aldimine with the substrate. This aldimine is the common central intermediate for all PLP-catalysed reactions, enzymatic and non-enzymatic .

A number of pyridoxal-dependent decarboxylases share regions of sequence similarity, particularly in the vicinity of a conserved lysine residue, which provides the attachment site for the pyridoxal-phosphate (PLP) group . Among these enzymes are aromatic-L-amino-acid decarboxylase (L-dopa decarboxylase or tryptophan decarboxylase), which catalyses the decarboxylation of tryptophan to tryptamine ; tyrosine decarboxylase, which converts tyrosine into tyramine; histidine decarboxylase, which catalyses the decarboxylation of histidine to histamine ; L-aspartate decarboxylase, which converts aspartate to beta-alanine ; and phenylacetaldehyde synthase that catalyses the decarboxylation of L-phenylalanine to 2-phenylethylamine . These enzymes belong to the group II decarboxylases .

This entry represents a family of tyrosine decarboxylases found in Enterococcus faecalis and related species. These enzymes often are encoded next to tyrosine/tyramine antiporter, together comprising a system in which tyrosine decarboxylation can protect against exposure to acid conditions . This clade differs from the archaeal tyrosine decarboxylases associated with methanofuran biosynthesis.
Peptidase S8, subtilisin, His-active site (Peptidase_S8_His-AS)
Type: Active_site

This entry represents the conserved sequence around the His active site of Subtilisin-like proteases.

Subtilases are an extensive family of serine proteases belonging to the MEROPS peptidase family S8 (subtilisin, clan SB). Members of this family have a catalytic triad in the order Asp, His and Ser in the sequence, which is a different order to that of families S1, S9 and S10. The catalytic activity is provided by a charge relay system similar to that of the trypsin family of serine proteases but which evolved by independent convergent evolution. The sequence around the residues involved in the catalytic triad (Asp, Ser and His) are completely different from that of the analogous residues in the trypsin serine proteases and can be used as signatures specific to that category of proteases. If a protein includes at least two of the three active site signatures, the probability of it being a serine protease from the subtilase family is 100%.
TadA-like conjugal transfer-associated ATPase (TadA-like_ATPase)
Type: Family

This protein family represent a group of putative conjugal transfer-associated TadA-like ATPases associated with an integral membrane complex likely to act in pilus formation, secretion, or conjugal transfer .
Adhesin P1 (Adhesin_P1)
Type: Family

Members of this protein family are the major adhesin of the Mycoplasma terminal organelle. The protein is called adhesin P1 and is found in Mycoplasma genitalium, Mycoplasma pneumoniae and Mycoplasma gallisepticum. A conserved C-terminal region is shared by additional paralogs in M. pneumoniae and M. gallisepticum.
Cysteate synthase (Cysteate_synthase)
Type: Family

This entry represents cysteate synthase, an enzyme of alternate pathway to sulphopyruvate, a precursor of coenzyme M .
F420-dependent oxidoreductase-predicted, MSMEG3544 (F420_OxRdatse_MSMEG3544_pred)
Type: Family

Coenzyme F420 has a limited phylogenetic distribution, including methanogenic archaea, Mycobacterium tuberculosis and related species, Colwellia psychrerythraea 34H and Rhodopseudomonas palustris HaA2. Partial phylogenetic profiling identifies protein subfamilies, within the larger family called luciferase-like monooxygenanases (

), that appear only in F420-positive genomes and are likely to be F420-dependent. This entry describes a small family, closely related to other such families in the putative F420-binding region, exemplified by MSMEG_3544 in Mycobacterium smegmatis.
Alcohol ABC transporter, permease protein (Alc_ABC_transptr_permease)
Type: Family

Members of this protein family, part of a larger class of efflux-type ABC transport permease proteins, are found exclusively in genomic contexts with pyrroloquinoline-quinone (PQQ) biosynthesis enzymes and/or PQQ-dependent alcohol dehydrogenases, such as the phenylethanol dehydrogenase PedE of Pseudomonas putida U. Members include PedC, an apparent phenylethanol transport protein whose suggested role is efflux to limit intracellular concentrations of toxic metabolites during phenylethanol catalysis.
Diphtheria toxin, receptor-binding domain (Diphtheria_toxin_rcpt-bd_dom)
Type: Domain

This entry represents the C-terminal receptor-binding domain, also known as the R domain. This domain has a β-sandwich fold consisting of nine strands in two sheet with greek-key topology; it is a subclass of immunoglobin-like fold . The R domain binds to cell surface receptor, permitting the toxin to enter the cell by receptor mediated endocytosis .

Diphtheria toxin (

) is a 58kDa protein secreted by lysogenic strains of Corynebacterium diphtheriae. The toxin causes the disease diphtheria in humans by gaining entry into the cell cytoplasm and inhibiting protein synthesis . The mechanism of inhibition involves transfer of the ADP-ribose group of NAD to elongation factor-2 (EF-2), rendering EF-2 inactive. The catalysed reaction is as follows:

NAD
+
+ peptide diphthamide = nicotinamide + peptide N-(ADP-D-ribosyl)diphthamide

The crystal structure of the diphtheria toxin homodimer has been determined to 2.5A resolution . The structure reveals a Y-shaped molecule of 3 domains, a catalytic domain (fragment A), whose fold is of the α+β type; a transmembrane (TM) domain, which consists of 9 α-helices, 2 pairs of which may participate in pH-triggered membrane insertion and translocation; and a receptor-binding domain, which forms a flattened β-barrel with a jelly-roll-like topology . The TM- and receptor binding-domains together constitute fragment B.
Diphtheria toxin, catalytic domain (Diphtheria_toxin_catalytic_dom)
Type: Domain

This entry represents the N-terminal catalytic domain (also known as the C domain). This domain has an unusual β+α fold . The C domain blocks protein synthesis by transfer of ADP-ribose from NAD to a diphthamide residue of EF-2 .

Diphtheria toxin (

) is a 58kDa protein secreted by lysogenic strains of Corynebacterium diphtheriae. The toxin causes the disease diphtheria in humans by gaining entry into the cell cytoplasm and inhibiting protein synthesis . The mechanism of inhibition involves transfer of the ADP-ribose group of NAD to elongation factor-2 (EF-2), rendering EF-2 inactive. The catalysed reaction is as follows:

NAD
+
+ peptide diphthamide = nicotinamide + peptide N-(ADP-D-ribosyl)diphthamide

The crystal structure of the diphtheria toxin homodimer has been determined to 2.5A resolution . The structure reveals a Y-shaped molecule of 3 domains, a catalytic domain (fragment A), whose fold is of the α+β type; a transmembrane (TM) domain, which consists of 9 α-helices, 2 pairs of which may participate in pH-triggered membrane insertion and translocation; and a receptor-binding domain, which forms a flattened β-barrel with a jelly-roll-like topology . The TM- and receptor binding-domains together constitute fragment B.
Oxidoreductase, molybdopterin binding site (OxRdtase_Mopterin_BS)
Type: Binding_site

This entry represents a motif surrounding a cysteine residue that could be involved in binding the molybdopterin cofactor.

A number of different eukaryotic oxidoreductases that require and bind a molybdopterin cofactor have been shown to share a few regions of sequence similarity. These enzymes include xanthine dehydrogenase (

), aldehyde oxidase (

), nitrate reductase (

), and sulphite oxidase (

). The multidomain redox enzyme NAD(P)H:nitrate reductase (NR) catalyses the reduction of nitrate to nitrite in a single polypeptide electron transport chain with electron flow from NAD(P)H-FAD-cytochrome b5-molybdopterin-NO(3). Three forms of NR are known, an NADH-specific enzyme found in higher plants and algae (

); an NAD(P)H-bispecific enzyme found in higher plants, algae and fungi (

); and an NADPH-specific enzyme found only in fungi (

) . The mitochondrial enzyme sulphite oxidase (sulphite:ferricytochrome c oxidoreductase;

) catalyses oxidation of sulphite to sulphate, using cytochrome c as the physiological electron acceptor. Sulphite oxidase consists of two structure/function domains, an N-terminal haem domain, similar to cytochrome b5; and a C-terminal molybdopterin domain .
Acyl-CoA-binding protein, ACBP, conserved site (Acyl-CoA-binding_prot_CS)
Type: Conserved_site

This entry represents a motif that corresponds to residue 19 to 37 in mammalian ACBP, adn which contains a conserved site.

Acyl-CoA-binding protein (ACBP) is a small (10 Kd) protein that binds medium-and long-chain acyl-CoA esters with very high affinity and may function as an intracellular carrier of acyl-CoA esters . ACBP is also known as diazepam binding inhibitor (DBI) or endozepine (EP) because of its ability to displace diazepam from the benzodiazepine (BZD) recognition site located on the GABA type A receptor. It is therefore possible that this protein also acts as a neuropeptide to modulate the action of the GABA receptor .

ACBP is a highly conserved protein of about 90 residues that is found in all four eukaryotic kingdoms, Animalia, Plantae, Fungi and Protista, and in some eubacterial species .

Although ACBP occurs as a completely independent protein, intact ACB domains have been identified in a number of large, multifunctional proteins in a variety of eukaryotic species. These include large membrane-associated proteins with N-terminal ACB domains, multifunctional enzymes with both ACB and peroxisomal enoyl-CoA Delta(3), Delta(2)-enoyl-CoA isomerase domains, and proteins with both an ACB domain and ankyrin repeats (

) .

The ACB domain consists of four α-helices arranged in a bowl shape with a highly exposed acyl-CoA-binding site. The ligand is bound through specific interactions with residues on the protein, most notably several conserved positive charges that interact with the phosphate group on the adenosine-3'phosphate moiety, and the acyl chain is sandwiched between the hydrophobic surfaces of CoA and the protein .

Other proteins containing an ACB domain include:

Endozepine-like peptide (ELP) (gene DBIL5) from mouse . ELP is a testis-specific ACBP homologue that may be involved in the energy metabolism of the mature sperm.

MA-DBI, a transmembrane protein of unknown function which has been found in mammals. MA-DBI contains a N-terminal ACB domain.

DRS-1 , a human protein of unknown function that contains a N-terminal ACB domain and a C-terminal enoyl-CoA isomerase/hydratase domain.