SII-SWORD/CoKE huggingface dataset:
Aldo-keto reductase family 5G (AKR5G)
Type: Family

This entry represents aldo-keto reductase family 5G (AKR5G), including glyoxal reductase (GR) and uncharacterised oxidoreductase YtbE from Bacillus subtilis . GR reduces glyoxal and methylglyoxal (2-oxopropanal). It is not involved in vitamin B6 biosynthesis .

In general, the aldo-keto reductase (AKR) protein superfamily members reduce carbonyl substrates such as: sugar aldehydes, keto-steroids, keto-prostaglandins, retinals, quinones, and lipid peroxidation by-products . However, there are some exceptions, such as the reduction of steroid double bonds catalysed by AKR1D enzymes (5beta-reductases); and the oxidation of proximate carcinogen trans-dihydrodiol polycyclic aromatic hydrocarbons; while the beta-subunits of potassium gated ion channels (AKR6 family) control Kv channel opening .

Structurally, they contain an (α/β)8-barrel motif, display large loops at the back of the barrel which govern substrate specificity, and have a conserved cofactor binding domain. The binding site is located in a large, deep, elliptical pocket in the C-terminal end of the β-sheet, the substrate being bound in an extended conformation. The hydrophobic nature of the pocket favours aromatic and apolar substrates over highly polar ones . They catalyse an ordered bi bi kinetic mechanism in which NAD(P)H cofactor binds first and leaves last . Binding of the NADPH coenzyme causes a massive conformational change, reorienting a loop, effectively locking the coenzyme in place. This binding is more similar to FAD- than to NAD(P)-binding oxidoreductases .
Dehydrogenase, bacteria (BaDH-like)
Type: Family

This entry represents a group of bacterial dehydrogenases (DHs).

In general, the aldo-keto reductase (AKR) protein superfamily members reduce carbonyl substrates such as: sugar aldehydes, keto-steroids, keto-prostaglandins, retinals, quinones, and lipid peroxidation by-products . However, there are some exceptions, such as the reduction of steroid double bonds catalysed by AKR1D enzymes (5beta-reductases); and the oxidation of proximate carcinogen trans-dihydrodiol polycyclic aromatic hydrocarbons; while the beta-subunits of potassium gated ion channels (AKR6 family) control Kv channel opening .

Structurally, they contain an (α/β)8-barrel motif, display large loops at the back of the barrel which govern substrate specificity, and have a conserved cofactor binding domain. The binding site is located in a large, deep, elliptical pocket in the C-terminal end of the β-sheet, the substrate being bound in an extended conformation. The hydrophobic nature of the pocket favours aromatic and apolar substrates over highly polar ones . They catalyse an ordered bi bi kinetic mechanism in which NAD(P)H cofactor binds first and leaves last . Binding of the NADPH coenzyme causes a massive conformational change, reorienting a loop, effectively locking the coenzyme in place. This binding is more similar to FAD- than to NAD(P)-binding oxidoreductases .
Homogentisate solanesyltransferase AtHST-like (AtHST-like)
Type: Family

This entry represents a group of plant members of the UbiA family of prenyltransferases, including AtHST from Arabidopsis. AtHST catalyses the prenylation and decarboxylation of homogentisate to form 2-methyl-6-solanesyl-1,4-benzoquinol, the first intermediate in plastoquinone-9 biosynthesis . This entry also includes naringenin 8-dimethylallyltransferase , glycinol 4-dimethylallyltransferase and 2-acylphloroglucinol 4-prenyltransferase , which share significant homology with homogentisate prenyltransferases.

Prenyltransferases (PTs) catalyse the regioselective transfer of prenyl moieties onto a wide variety of substrates and play an important role in many biosynthetic pathways. Plant aromatic PTs can be divided into two distinct sub-groups: one is 4-hydroxybenzoate PTs, which are involved in ubiquinone (benzoquinone) and naphthoquinone derivatives localised in mitochondria or the endoplasmic reticulum, and the second sub-group comprises members of the homogentisate PT (HGPT) family, which are involved in vitamin E and plastoquinone biosynthesis .
Aldo-keto reductase family 5C1 (AKR5C1)
Type: Family

This entry represents aldo-keto reductase family 5C1 (AKR5C1), including DkgA from Corynebacterium sp. DkgA catalyses the reduction of 2,5-diketo-D-gluconic acid (25DKG) to 2-keto-L-gulonic acid (2KLG). 5-keto-D-fructose and dihydroxyacetone can also serve as substrates .

In general, the aldo-keto reductase (AKR) protein superfamily members reduce carbonyl substrates such as: sugar aldehydes, keto-steroids, keto-prostaglandins, retinals, quinones, and lipid peroxidation by-products . However, there are some exceptions, such as the reduction of steroid double bonds catalysed by AKR1D enzymes (5beta-reductases); and the oxidation of proximate carcinogen trans-dihydrodiol polycyclic aromatic hydrocarbons; while the beta-subunits of potassium gated ion channels (AKR6 family) control Kv channel opening .

Structurally, they contain an (α/β)8-barrel motif, display large loops at the back of the barrel which govern substrate specificity, and have a conserved cofactor binding domain. The binding site is located in a large, deep, elliptical pocket in the C-terminal end of the β-sheet, the substrate being bound in an extended conformation. The hydrophobic nature of the pocket favours aromatic and apolar substrates over highly polar ones . They catalyse an ordered bi bi kinetic mechanism in which NAD(P)H cofactor binds first and leaves last . Binding of the NADPH coenzyme causes a massive conformational change, reorienting a loop, effectively locking the coenzyme in place. This binding is more similar to FAD- than to NAD(P)-binding oxidoreductases .
Aldo-keto reductase family 5C2 (AKR5C2)
Type: Family

This entry represents aldo-keto reductase family 5C2 (AKR5C2), including DkgA/YqhE from Escherichia coli. It catalyses the reduction of 2,5-diketo-D-gluconic acid (25DKG) to 2-keto-L-gulonic acid (2KLG). It is also capable of stereoselective -keto ester reductions on ethyl acetoacetate and other 2-substituted derivatives .

In general, the aldo-keto reductase (AKR) protein superfamily members reduce carbonyl substrates such as: sugar aldehydes, keto-steroids, keto-prostaglandins, retinals, quinones, and lipid peroxidation by-products . However, there are some exceptions, such as the reduction of steroid double bonds catalysed by AKR1D enzymes (5beta-reductases); and the oxidation of proximate carcinogen trans-dihydrodiol polycyclic aromatic hydrocarbons; while the beta-subunits of potassium gated ion channels (AKR6 family) control Kv channel opening .

Structurally, they contain an (α/β)8-barrel motif, display large loops at the back of the barrel which govern substrate specificity, and have a conserved cofactor binding domain. The binding site is located in a large, deep, elliptical pocket in the C-terminal end of the β-sheet, the substrate being bound in an extended conformation. The hydrophobic nature of the pocket favours aromatic and apolar substrates over highly polar ones . They catalyse an ordered bi bi kinetic mechanism in which NAD(P)H cofactor binds first and leaves last . Binding of the NADPH coenzyme causes a massive conformational change, reorienting a loop, effectively locking the coenzyme in place. This binding is more similar to FAD- than to NAD(P)-binding oxidoreductases .
Glycogen debranching enzyme GlgX/isoamylase, N-terminal Early set domain (GlgX_Isoamylase_N_E_set)
Type: Domain

This entry represents the N-terminal Early set domain found in bacterial glycogen debranching enzymes and isoamylases from bacteria and plants. Glycogen debranching enzymes have 4-alpha-glucanotransferase activity, that transfers a segment of the 1,4-alpha-D-glucan to a new 4-position in an acceptor, which may be glucose or another 1,4-alpha-D-glucan, and amylo-1,6-glucosidase activity, which catalyses the endohydrolysis of 1,6-alpha-D-glucoside linkages at points of branching in chains of 1,4-linked alpha-D-glucose residues . Isoamylase is one of the starch-debranching enzymes that catalyse the hydrolysis of alpha-1,6-glucosidic linkages specific in alpha-glucans such as amylopectin or glycogen .

This E or "early" set domains are associated with the catalytic domain of glycogen branching enzymes at the N-terminal end. The N-terminal domain of the 1,4 alpha glucan branching enzyme may be related to the immunoglobulin and/or fibronectin type III superfamilies. These domains are associated with different types of catalytic domains at either the N-terminal or C-terminal end and may be involved in homodimeric/tetrameric/dodecameric interactions .
Dual-specificity phosphatase CDC14, C-terminal (CDC14_C)
Type: Domain

This entry represents the C-terminal catalytic dual-specificity phosphatase domain of Cdc14. It has the PTP signature motif.

The cell division control protein 14 (CDC14) family is highly conserved in all eukaryotes, although the roles of its members seem to have diverged during evolution . Yeast Cdc14, the best characterised member of this family, is a dual-specificity phosphatase that plays key roles in cell cycle control. It preferentially dephosphorylates cyclin-dependent kinase (CDK) targets, which makes it the main antagonist of CDK in the cell. Cdc14 functions at the end of mitosis and it triggers the events that completely eliminates the activity of CDK and other mitotic kinases . It is also involved in coordinating the nuclear division cycle with cytokinesis through the cytokinesis checkpoint, and in chromosome segregation. Cdc14 phosphatases also function in DNA replication, DNA damage checkpoint, and DNA repair . Vertebrates may contain more than one Cdc14 homologues; humans have three (CDC14A, CDC14B, and CDC14C). CDC14 contains a highly conserved N-terminal pseudophosphatase domain that contributes to substrate specificity and a C-terminal catalytic dual-specificity phosphatase domain with the PTP signature motif .
D-alanine:D-alanyl carrier protein ligase-like (DltA-like)
Type: Family

This family represents D-alanyl carrier protein ligase DltA and similar proteins, including L-proline--[L-prolyl-carrier protein] ligase.

DltA is part of the operon for incorporation of D-Ala residues into lipoteichoic acids (LTAs), which requires the activity of four gene products (DltA to DltD). DltA is a cytoplasmic D-alanine-D-alanyl carrier protein ligase that catalyses the D-alanylation of the D-alanyl carrier protein DltC (or Dcp); DltB is a transmembrane protein thought to be involved in the efflux of activated D-alanine to the site of acylation; and DltD is thought to be a membrane-associated protein that may have multifunctional activities (hydrolysis of mischarged DltC, facilitation of D-alanine ligation to DltC and D-alanylation of LTAs) .

L-proline--[L-prolyl-carrier protein] ligase, also known as L-prolyl-AMP ligase, participates in the biosynthesis of undecylprodigiosin where it catalyses the conversion of L-proline to L-prolyl-AMP and the transfer of the L-prolyl group to acyl carrier protein RedO .
F-box protein At5g50450/At1g67340-like (At5g50450/At1g67340-like)
Type: Family

This entry represents a group of plant F-box proteins, including At5g50450 and At1g67340 from Arabidopsis. They contain the MYND-type zinc finger. At1g67340 may be the F-box subunit of the SCF E3 complex .
CRIB domain-containing protein RIC2/4 (RIC2/4)
Type: Family

This entry represents a group of plant CRIB domain-containing proteins including RIC2 and RIC4 from Arabidopsis. They belong to the RIC (ROP-interactive CRIB motif-containing protein) family. It has been shown that overexpression of RIC2 in tobacco germinating pollen reduces pollen tube elongation .

ROP1 and ROP6 have been shown to interact with RIC4, which promotes F-actin assembly. Together, they are involved in various processes of F-actin dynamics, cell growth, and plant/microbe interactions .

The RIC (ROP-interactive CRIB motif-containing protein) family members act as Rho GTPase (Rop) targets that function in distinct Rop signaling pathways . RICs interact with multiple ROP GTPases via their conserved CRIB motif, and link ROP proteins to diverse target molecules that bind to their variable domains . RICs share several consensus amino acid residues upstream of the CRIB motif and a consensus PSWMXDFK block downstream of the CRIB motif. Unlike other group members, members of group V, consisting of RIC4 and RIC2, lack the PSWMXDFK block and contain a relatively long N terminus in front of the CRIB motif and a short C terminus .
ProlycopenC2 and GRAM domain-containing protein At1g03370/At5g50170-like (At1g03370/At5g50170-like)
Type: Family

This entry represents the C2 and GRAM domain-containing proteins from plants, including At1g03370 and At5g50170 from Arabidopsis. At1g03370 and At5g50170 contain two VASt domains, two C2 domains and a GRAM domain. Their function is not clear.
BTB/POZ and TAZ domain-containing protein 1/2/3/4/5 (BT1/2/3/4/5)
Type: Family

This entry represents a group of plant BTB/POZ and TAZ domain-containing proteins, including BT1-5 from Arabidopsis. They are scaffold proteins that play roles in both male and female gametophyte development . BT2 can activate telomerase expression in mature Arabidopsis leaves . It mediates multiple responses to nutrients, stresses, and hormones in Arabidopsis .
Vernalization insensitive 3-like (VIN3-like)
Type: Family

The lineage specific VIN3 family of proteins includes VIN3, VIN3-like1-3 (VIL1-3) and similar proteins. They contain a plant homeodomain (PHD) finger, and collectively repress different sets of members of the Flowering LOCUS C (FLC) gene family during the course of vernalization . Both VIN3 and VIL1 are required for modifying the histone architecture of the MADS box floral repressor FLC in response to prolonged cold exposure in Arabidopsis . VIN3 is required for both Histone H3 Lys 9 (H3K9) and Histone H3 Lys 27 (H3K27) methylation at FLC chromatin, ultimately leading to its repression. It is regulated by the components of Polycomb Response Complex2 (PRC2), which trimethylates histone H3 Lys 27 (H3K27me3) . VIL1 appears to play a prominent role in regulating FLC by vernalization . VIL2 acts together with PRC2 to repress the floral repressor MAF5, an FLC clade member, in a photoperiod-dependent manner to accelerate flowering under non-inductive photoperiods .
Ankyrin repeat and BTB/POZ domain-containing protein 1-like (ABTB1)
Type: Family

This entry represents a group of ankyrin repeat-containing proteins, including ABTB1 from humans, Btb3 from fission yeasts, YIL001W from budding yeasts and At2g04740 from Arabidopsis. ABTB1 is an anti-proliferative factor that may act as a mediator of the phosphatase and tensin homologue (PTEN) growth-suppressive signaling pathway .
UDP-glucuronic acid decarboxylase-like (UXS-like)
Type: Family

This family represents UDP-glucuronic acid decarboxylases (UXS, also known as UDP-glucuronate decarboxylase or UDP-XYL synthase) which catalyse the NAD-dependent decarboxylation of UDP-glucuronic acid to form UDP-xylose, a sugar donor required for the synthesis of glycoproteins, polysaccharides, various metabolites, and oligosaccharides in plants, animals, fungi and bacteria . They are members of the short-chain dehydrogenase/reductase (SDR) superfamily that also include epimerases, dehydratases, and reductases that use nucleotide-activated monosaccharides as substrates and share a Rossmann-fold NAD(P)H/NAD(P)(+) binding domain .

This entry also includes UDP-N-acetyl-alpha-D-glucosaminuronate decarboxylase, a bacterial homologue that catalyses the NAD-dependent decarboxylation of UDP-N-acetylglucosaminuronic acid to UDP-N-acetylxylosamine and cannot utilise as substrates UDP-uronates, such as UDP-glucuronic acid and UDP-galacturonic acid .
Protein PHOX1-4 (PHOX1-4)
Type: Family

This entry represents a group of plant tetratricopeptide repeat proteins, including PHOX1-4 from Arabidopsis and HIP from Zea mays. They are putative co-chaperones of Hsp90/Hsp70 . PHOX2, also known as CLMP1, is required for plastid separation .
ADP-ribosylation factor GTPase-activating protein AGD11/12/13 (ARF_GAP_AGD11/12/13)
Type: Family

This entry represents a group of plant ADP-ribosylation factor GTPase-activating proteins (ArfGAPs), such as AGD11/12/13 from Arabidopsis. ArfGAPs are a family of proteins containing an ArfGAP catalytic domain that induces the hydrolysis of GTP bound to the small guanine nucleotide-binding protein Arf, a member of the Ras superfamily of GTPases. Of all known members belonging to the ARF-GAP protein family only AGD11, 12, and 13 possess a C2 domain enabling them to bind phospholipids, phosphoinositide and proteins in a calcium-dependent manner .
ADP-ribosylation factor GTPase-activating protein AGD6/7 (ARF_GAP_AGD6/7)
Type: Family

This entry represents a group of plant ADP-ribosylation factor GTPase-activating proteins (ArfGAPs), such as AGD6/7 from Arabidopsis. ArfGAPs are a family of proteins containing an ArfGAP catalytic domain that induces the hydrolysis of GTP bound to the small guanine nucleotide-binding protein Arf, a member of the Ras superfamily of GTPases. AGD7 interacts with Arf1 and stimulates Arf1 GTPase activity in a phosphatidic acid-dependent manner. It is localised to the Golgi complex and may play a critical role in protein trafficking by controlling Arf1 activity .
ADP-ribosylation factor GTPase-activating protein AGD5/15 (ARF_GAP_AGD5/15)
Type: Family

This entry represents a group of plant ADP-ribosylation factor GTPase-activating proteins (ArfGAPs), such as AGD5/15 from Arabidopsis. ArfGAPs are a family of proteins containing an ArfGAP catalytic domain that induces the hydrolysis of GTP bound to the small guanine nucleotide-binding protein Arf, a member of the Ras superfamily of GTPases. AGD5 (also known as EVERSHED) is localised to the trans-Golgi network (TGN), where it co-localises with ARF1, a crucial GTPase that is involved in membrane trafficking . It facilitates the intracellular movement of molecules required for organ abscission and fruit growth .
Basic leucine zipper 8/43 (AtbZIP8/43)
Type: Family

This entry represents a group of plant basic leucine zipper proteins (bZIPs), including AtbZIP8 and AtbZIP43. AtbZIP43 may act as positive regulator of BHLH109, which is associated with somatic embryogenesis (SE) induction .

The basic (region) leucine zippers (bZIPs) are evolutionarily conserved transcription factors in eukaryotic organisms. In plants bZIPs regulate processes including pathogen defence, light and stress signalling, seed maturation and flower development . The bZIP domain consists of a basic DNA-binding region and the adjacent ZIP domain. The ZIP domain consists of heptad repeats of leucine (L) or related hydrophobic amino acids. The DNA-binding region is a basic region of ~16 amino acid residues containing a nuclear localization signal followed by an invariant N-x7-R/K motif that contacts the DNA
The heptad repeat of leucines or other bulky hydrophobic amino acids positioned exactly nine amino acids towards the C terminus, creating an amphipathic helix. To bind DNA, two subunits adhere via interactions between the hydrophobic sides of their helices, which creates a superimposing coiled-coil structure. The ability to form homo- and heterodimers is influenced by the electrostatic attraction and repulsion of polar residues flanking the hydrophobic interaction surface of the helices . As bZIPs generally perform as dimers, heterodimerisation results in an enormous regulatory flexibility .
CRC domain-containing protein TSO1-like (TSO1-like)
Type: Family

This entry represents a group of CRC domain-containing proteins, including TSO1 and TCX2/3/4 from Arabidopsis. They are are homologues of the LIN54 DNA-binding components of the mammalian DREAM complex, a protein complex responsible for the regulation of cell cycle-dependent gene expression. TSO1 has been shown to regulate meristem organization and cell division . It may transcriptionally represses MYB3R1 (a conserved cell cycle regulator), and together they coordinate cell proliferation with differentiation in shoot and root . TCX3 (also known as SOL1) and TCX2 (also known as SOL2) have been shown to regulate fate transition and cell divisions in the Arabidopsis stomatal lineage .
Histidine biosynthesis, HisA-like (Isoase_HisA-like)
Type: Family

This protein family consists of HisA and its homologues from archaea, bacteria, fungi and plants. HisA is a phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (also known as 1-(5-phosphoribosyl)-5-(5-phosphoribosylamino methylideneamino) imidazole-4-carboxamide isomerase

) that catalyses the fourth step in histidine biosynthesis . It is closely related to the enzyme HisF for the sixth step. Examples of this enzyme in Actinobacteria have been found to be bifunctional, also possessing phosphoribosylanthranilate isomerase activity . This entry also includes chloroplastic HisA homologue from Arabidopsis and His6 from budding yeasts .
Digalactosyldiacylglycerol synthase 1/2 (DGDG1/2)
Type: Family

This entry represents a group of digalactosyldiacylglycerol synthases, including DGDG1 and DGDG2 from Arabidopsis. They are involved in the synthesis of the chloroplast lipid digalactosyldiacylglycerol (DGDG) . DGDG provides stability to the photosystem I (PSI) complex, especially to the PsaA, PsaB, PsaC, PsaL and PsaH subunits . The DGDG1 and DGDG2 homologues can also be found in soybean and Lotus. Besides in plastids, they are also expressed during later stages of nodule development in infected cells and in cortical tissue .
Protein SODIUM POTASSIUM ROOT DEFECTIVE 1-3 (NAKR1-3)
Type: Family

This entry represents a group of heavy metal-associated plant proteins, including Protein SODIUM POTASSIUM ROOT DEFECTIVE 1/2/3 (NAKR1/2/3) from Arabidopsis. NAKR1, also known as NPCC6, is necessary for phloem function and root meristem maintenance . It also promotes flowering through mediating FT (FLOWERING LOCUS T) translocation from leaves to shoot apices . It also plays an important role in the regulation of FT expression under long-day conditions . NaKR3 is involved in the salt stress response .