SII-SWORD/CoKE huggingface dataset:
ATP synthase, F0 complex, subunit MI25, plants (MI25_plants)
Type: Family

Transmembrane ATPases are membrane-bound enzyme complexes/ion transporters that use ATP hydrolysis to drive the transport of protons across a membrane. Some transmembrane ATPases also work in reverse, harnessing the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP.

F-ATPases (also known as ATP synthases, F1F0-ATPase, or H(+)-transporting two-sector ATPase) (

) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), with additional subunits in mitochondria. Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the α(3)β(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis . These ATPases can also work in reverse in bacteria, hydrolysing ATP to create a proton gradient.

This entry represents subunit B from the F0 complex in F-ATPases found in mitochondria of eukaryotes (known as MI25/ORF25 in plants ). The B subunits are part of the peripheral stalk that links the F1 and F0 complexes together, and which acts as a stator to prevent certain subunits from rotating with the central rotary element. The peripheral stalk differs in subunit composition between mitochondrial, chloroplast and bacterial F-ATPases. In mitochondria, the peripheral stalk is composed of one copy each of subunits OSCP (oligomycin sensitivity conferral protein), F6, B and D .
Protein TILLER ANGLE CONTROL 1 (TAC1)
Type: Family

TAC1 (tiller angle control 1) is involved in the regulation of inflorescence branch growth angle . TAC1 belongs to a family known as IGT due to its universally conserved motif (GL(A/T)IGT) present in domain II of all sequences identified .
Tetraspani, plant (TET_plant)
Type: Family

This entry represents tetraspanin (TET) from plants, including TET1-17 from Arabidopsis. TET1, also known as TORNADO 2, is involved in the basipetal transport of auxin (IAA) that modulates growth and organs organization, as well as cell differentiation . It plays an role in cellular decisions in the peripheral zone of the shoot apical meristem . Together with WIH1 and WIH2, TET1 promotes megasporogenesis .

Tetraspanins are a distinct family of proteins, containing four transmembrane domains: a small outer loop (EC1), a larger outer loop (EC2), a small inner loop (IL) and short cytoplasmic tails. They contain characteristic structural features, including 4-6 conserved extracellular cysteine residues, and polar residues within transmembrane domains. A fundamental role of tetraspanins appears to be organizing other proteins into a network of multimolecular membrane microdomains, sometimes called the 'tetraspanin web'.
Glutamine amidotransferase domain containing protein ChyE-like (ChyE-like)
Type: Family

This entry represents a subgroup of class 1 glutamine amidotransferase (GATase1). GATase activity catalyses the transfer of ammonia from the amide side chain of glutamine to an acceptor substrate. Glutamine amidotransferases (GATase) includes the triad family of amidotransferases which have a conserved Cys-His-Glu catalytic triad in the glutaminase active site. In this subgroup this triad is conserved.

Proteins in this subgroup are mostly from archaea, bacteria, plants and fungi. This entry includes ChyE from Penicillium rubens, YLR126C from budding yeast, GGP1-5 from plants. ChyE converts 2-(2-aminopropanamido)benzoic acid and 2-(2-aminopropanamido)benzamidine into 2-(2-(2-carboxyacetamido)propanamido)benzoic acid and 3-((1-((2-carbamoylphenyl)amino)-1-oxopropan-2-yl)amino)-3-oxopropanoic acid, respectively . In Arabidopsis, GGP1 hydrolyzes the gamma-glutamyl peptide bond of several glutathione (GSH) conjugates to produce Cys-Gly conjugates related to glucosinolates. The gamma-Glu-Cys-Gly-GSH conjugates are the sulfur-donating molecule in glucosinolate biosynthesis . The function of YLR126C is still not clear.
Beta-D-xylosidase (BXL)
Type: Family

This entry represents a group of beta-D-xylosidases mainly from bacteria, fungi, animals and plants. They belong to a subgroup of the glycoside hydrolase family 3.

Xylan, a prominent component of cellulosic biomass, has a high potential for degradation into reducing sugars, and subsequent conversion into bioethanol. This process requires a range of xylanolytic enzymes, including beta-xylosidases. This entry includes fungal exo-1,4-beta-xylosidase xlnD and bxlB .

In bacteria, Prevotella ruminicola Xyl3A has been shown to have beta-xylosidase activity via its capacity to hydrolyze glycosidic linkages of beta-1,4-xylo-oligosaccharides of various lengths (X2 to X6), releasing xylose monomers .

In Arabidopsis, there are seven members AtBXL1-7 in this entry. AtBXL1 is a bifunctional beta-d-xylosidase/alpha-l-arabinofuranosidase required for pectic arabinan modification and is involved in secondary cell wall metabolism and plant development .
Coenzyme Q-binding protein COQ10-like (COQ10-like)
Type: Family

COQ10 is a hydrophobic protein located in the inner membrane of mitochondria that binds coenzyme Q (CoQ), also called ubiquinone, which is an essential electron carrier of the respiratory chain. Deletion of the gene encoding COQ10p (COQ10 or YOL008W) in Saccharomyces cerevisiae results in respiratory defect because of the inability to oxidize NADH and succinate. COQ10 may function in the delivery of CoQ (Q6 in budding yeast) to its proper location for electron transport . The human homologue, called Q-binding protein COQ10 homologue A (COQ10A), is able to fully complement for the absence of COQ10 in fission yeast. Human COQ10A also has a splice variant COQ10B
.
F-box protein, plant (F-box_plant)
Type: Family

This is a group of F-box proteins from plants, whose function is not known.
Timeless (Timeless)
Type: Family

The timeless gene in Drosophila melanogasteris involved in circadian rhythm control . Drosophila contains two paralogs, dTIM and dTIM2, acting in clock/photoreception and chromosome integrity/photoreception respectively. The mammalian TIMELESS (TIM) protein, originally identified based on its similarity to Drosophila dTIM, interacts with the clock proteins dCRY and dPER and is essential for circadian rhythm generation and photo-entrainment in the fly . However, phylogenetic sequence analysis has demonstrated that dTIM2 is likely to be the orthologue of mammalian TIM and other widely conserved TIM-like proteins in eukaryotes . These proteins include Saccharomyces cerevisiae Tof1, Schizosaccharomyces pombe Swi1, and Caenorhabditis elegans TIM. These proteins are not involved in the core clock mechanism, but instead play important roles in chromosome integrity, efficient cell growth and/or development , with the exception of dTIM-2, that has an additional function in retinal photoreception .

Saccharomyces cerevisiae Tof1 is a subunit of a replication-pausing checkpoint complex (Tof1-Mrc1-Csm3) that acts at the stalled replication fork to promote sister chromatid cohesion after DNA damage, facilitating gap repair of damaged DNA . Schizosaccharomyces pombe Swi1 and Swi3 form the fork protection complex that coordinates leading- and lagging-strand synthesis and stabilizes stalled replication forks .
Protein CbbY-like (CbbY-like)
Type: Family

This entry represents CbbY-like proteins mostly from bacteria, fungi and plants. In Rhodobacter sphaeroides and Arabidopsis thaliana, CbbY is a xylulose-1,5-bisphosphate phosphatase, which convert xylulose-1,5-bisphosphate (a potent inhibitor of Ribulose-1,5-bisphosphate carboxylase/oxygenase, Rubisco), to the non-inhibitory compound xylulose-5-phosphate .
Tropinone reductase (TR)
Type: Family

This entry represents a group of tropinone reductase-like short-chain dehydrogenases (SDRs) from bacteria and plants. This entry includes tropinone reductase 1/2 (TR1/2) from Datura stramonium (Common thornapple). TR1 catalyses the stereospecific reduction of tropinone to tropine . The Arabidopsis thaliana homologues show high sequence similarity, but do not reduce tropinone . One of the Arabidopsis thaliana homologue, SAG13 (At2g29350), has been shown to reduce small lipophilic ketones and several monoterpene ketones . This entry also includes noroxomaritidine/norcraugsodine reductase (NR) rom Narcissus aff. pseudonarcissus MK-2014 (Daffodil). NR catalyses the conversion of noroxomaritidine to oxomaritidine, a precursor of haemanthamine- and crinamine-type alkaloids, promising anticancer agents .
Developmentally regulated GTP-binding protein (DRG)
Type: Family

Developmentally regulated G-proteins (DRGs) are a highly conserved family of GTP-binding proteins found in archaea, plants, fungi and animals, indicating important roles in fundamental pathways. DRG is a member of the Obg family, an evolutionary branch of GTPase superfamily proteins. GTPases act as molecular switches regulating diverse cellular processes. DRG2 and DRG1 comprise the DRG subfamily in eukaryotes. It has been proposed that the DRG subfamily proteins play their physiological roles through RNA binding .
Delta(3,5)-Delta(2,4)-dienoyl-CoA isomerase Ech1-like (Ech1-like)
Type: Family

This entry represents a group of delta 3,5,delta 2,4-dienoyl-CoA isomerase, including ECH1 from animals and AtDCI1 from Arabidopsis. ECH1 is an auxiliary enzyme of unsaturated fatty acid beta-oxidation .

This entry also includes uncharacterised bacterial proteins.
Fasciclin-like arabinogalactan protein, group A (FLA_A)
Type: Family

Fasciclin-like arabinogalactan proteins (FLAs) proteins from Arabidopsis, a subclass of arabinogalactan proteins (AGPs), can be classified in four groups (A-D) based on pair-wise sequence similarity, domain structure, and phylogenetic analysis . Group A FLAs are characterised by a single fasciclin domain that is flanked by AGP regions and a C-terminal GPI-anchor signal; group B contain two fasciclin domains flanking an AGP region and lack a C-terminal GPI anchor signal sequence; group C have a variable domain structure with one or two fasciclin domains, one or two AGP regions, and a C-terminal GPI anchor signal; FLAs 4 and 19 to 21 formed group D as they have low similarity to each other or to any of the other FLAs .

This family represents Group A Fasciclin-like arabinogalactan proteins (FLAs) from plants, which includes FLAs 6, 7, 9,11,12 and 13 from Arabidopsis . They are probably cell surface adhesion proteins.
Enoyl-CoA hydratase/isomerase domain (ECH_dom)
Type: Domain

This entry represents a domain found in enoyl-CoA hydratase/isomerase HIBYL-CoA-H and related proteins.

The enoyl-CoA hydratase/isomerase family contains a diverse set of enzymes including: enoyl-CoA hydratase, napthoate synthase, carnitate racemase, 3-hydroxybutyryl-CoA dehydratase and dodecanoyl-CoA delta-isomerase. This entry represents a subset of the enoyl-CoA hydratase/isomerase family. Proteins in this entry includes 3-hydroxyisobutyryl-CoA hydrolases (HIBYL-CoA-H) from eukaryotes and their homologues from bacteria.

The EHD3 protein, found in Saccharomyces cerevisiae, has been recognised as a constituent of the mitochondrial ribosome. Hence, it is alternatively referred as small ribosomal subunit mS47 .
BTB/POZ and MATH domain-containing protein 1-6 (BPM1-6)
Type: Family

This entry represents a group of BTB/POZ and MATH domain-containing proteins mostly from plants, including BPM1-6 from Arabidopsis. They are part of the Cullin E3 ubiquitin ligase complexes and are known to bind at least three families of transcription factors: ERF/AP2 class I, homeobox-leucine zipper and R2R3 MYB. BPMs play an important role in plant flowering, seed development and abiotic stress response .
Magnesium-chelatase subunit ChlI-like (CHLI-like)
Type: Family

Magnesium-chelatase is a three-component enzyme, consisting of CHLI, CHLD and CHLH subunits, that catalyses the insertion of Mg2 into protoporphyrin IX, the first unique step in the synthesis of (bacterio)chlorophyll. As a result, Mg-chelatase has an important role in channeling intermediates into the (bacterio)chlorophyll branch in response to conditions suitable for photosynthetic growth . The reaction takes place in two steps including an ATP-dependent activation followed by an ATP-dependent chelation step.

This family represents CHLI subunit (38-42kDa), which possesses high affinity for ATP and play a major role in chlorophyll biosynthesis, as ATP hydrolysis by this subunit is crucial for this reaction and its activity is a determinant of the rate of Mg insertion into the tetrapyrrole ring . In Arabidopsis there are two CHLI isoforms, CHLI1 and CHLI2, which share similar expression profiles but CHLI2 has a lower ATPase activity than CHLI1 and a limited role in chlorophyll biosynthesis. However, CHLI2 contributes to the assembly of the Mg-chelatase complex . It does not bind abscisic acid (ABA), but is a positive regulator of ABA signaling .
LAS seventeen-binding protein 5 (LSB5)
Type: Family

Lsb5 plays important roles in membrane-trafficking events through association with the actin regulators, the yeast Wiskott-Aldrich syndrome protein (WASP) homologue Las17 and the cortical protein Sla1, the yeast Arf3 (orthologous with mammalian Arf6), and ubiquitin. Lsb5 contains an N-terminal VHS (Vps27p/Hrs/STAM)-domain and a GAT (GGA and TOM1) domain. In contrast to GGA proteins, Lsb5 harbours a C-terminal NPF (Asn-Pro-Phe) motif, but does not have either a GAE (gamma-adaptin ear homology) domain or a clathrin-binding motif .
Acyl-coenzyme A oxidase 4-like (ACX4-like)
Type: Family

This entry represents a group of acyl-CoA dehydrogenases from bacteria and plants, including acyl-coenzyme A oxidase 4 (ACX4) from Arabidopsis. ACX4 catalyses the desaturation of short-chain acyl-CoAs to 2-trans-enoyl-CoAs in plant peroxisomes . It is essential for embryo development and is required for nuclear histone acetylation and DNA demethylation at some endogenous genomic loci .
CASP-like protein 5 (CASPL-5)
Type: Family

Casparian strip membrane proteins (CASPs) are four-membrane-span proteins that mediate the deposition of Casparian strips in the endodermis by recruiting the lignin polymerization machinery. CASP-like proteins (CASPLs) contain a CASP domain and are also able to form transmembrane scaffolds. The transmembrane domains, particularly the first (TM1) and the third (TM3) are highly conserved among these proteins. CASPLs can be classified in five groups (1-5); this family represents group 5 (CASPL5). In Arabidopsis, CASPLs showed specific expression in a variety of cell types, such as trichomes, abscission zone cells, peripheral root cap cells, and xylem pole pericycle cells .
Medium-chain dehydrogenase/reductase (MDR_fam)
Type: Family

This entry represents the MDR (medium-chain dehydrogenase/reductase) family.

The MDR/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH . MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR) . The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a β-α form and an N-terminal catalytic domain with distant homology to GroES .
Arogenate dehydrogenase 1/2 (TYRAAT1/2)
Type: Family

This entry includes arogenate dehydrogenase 1/2 from plants and some uncharacterised proteins from bacteria.

Proteins in this entry belong to the prephenate dehydrogenase (PDH) domain superfamily (

). Members of this group catalyse a step in tyrosine biosynthesis in the shikimate pathway, which is present only in bacteria, archaea, fungi, and plants . Many of the PDH enzymes are able to use the alternative intermediates of tyrosine biosynthesis, prephenate or L-arogenate, as substrates, having both prephenate dehydrogenase and arogenate dehydrogenase activities, and are sometimes collectively called cyclohexadienyl dehydrogenases . Arogenate dehydrogenase 2 has a weak prephenate dehydrogenase activity .

Arabidopsis thaliana has two arogenate dehydrogenase isoforms, tyrAAT1 and tyrAAT2. TyrAAT1 is unusual in that it contains a duplication of the PDH domain. Both copies of the PDH domain have arogenate dehydrogenase activity with similar biochemical characteristics . The experimentally studied plant enzymes are NADP-dependent arogenate dehydrogenases that are very sensitive toward feedback inhibition by the product of the reaction (tyrosine); in fact, they exhibit a higher affinity for tyrosine than for their arogenate substrate . Interestingly, these proteins do not seem to have any additional domain that can be suggested to be responsible for this regulation.
Protein NLP (NLP)
Type: Family

This family represents NIN-like proteins (NLPs), key transcription factors involved in a process of establishment of symbiosis between legumes and nitrogen fixing bacteria (Rhizobium) and nitrate signalling in other plants . NLPs bind the nitrate-responsive cis-element and activate nitrate-responsive cis-element-dependent and nitrate-responsive transcription, thus being master regulators of the nitrate response .
Transmembrane protein 41A/B (TM41A/B)
Type: Family

This entry includes human transmembrane protein 41A/B (TMEM41A/B) and related proteins. TMEM41B is involved in early stages of autophagosome biogenesis at the ER membrane probably via mobilization of neutral lipids from lipid droplets . TMEM41B and its homologues from fish are involved in motor neuron development . It is also a critical host factor required for infection by human coronaviruses SARS-CoV-2, HCoV-OC43, HCoV-NL63, and HCoV-229E, as well as all flaviviruses tested such as Zika virus and Yellow fever virus . The function of TMEM41A is not clear.
C-terminal binding protein AN-like (AN-like)
Type: Family

This entry represents a group of plant proteins, including ANGUSTIFOLIA (AN) from Arabidopsis. AN is related to C-terminal binding protein/brefeldin A ADP-ribosylated substrate (CtBP/BARS) with an important role in animal development. It plays a major role in microtubule-dependent cell morphogenesis. The phenotype of the AN mutants include narrow cotyledons, narrow rosette leaves, twisted seed pods (siliques) and less-branched trichome. Moreover, it has been shown to be involved in a wide range of biological processes, including facilitating both abiotic and biotic stress tolerance through ROS-mediated redox activity .
Na(+)/H(+) antiporter NhaD-like (NhaD-like)
Type: Family

This entry includes Na(+)/H(+) antiporter NhaD from bacteria and its homologue, NHD1/2 from Arabidopsis. In Vibrio cholerae, NhaD is a Na(+)/H(+) antiporter with a sharp maximum of activity at pH approximately 8.0 . NhaD homologues have been found in plants. Physcomitrella patens PpNHAD1 has been shown to serve as a chloroplast transporter . Expression of Mesembryanthemum crystalllinum NHAD has been shown to complement the Escherichia coli NhaA NhaB mutant, which lacks endogenous Na(+)/H(+) antiporters . Arabidopsis NHD1 functions as a chloroplast sodium exporter and protects chloroplasts from deleterious Na+ concentrations after salt exposure .
Peroxisomal 2,4-dienoyl-CoA reductase [(3E)-enoyl-CoA-producing] (DECR2-like)
Type: Family

This entry includes peroxisomal 2,4-dienoyl CoA reductases (pDCR) from eukaryotes and its homologues from bacteria and archaea. DCR is an auxiliary enzyme of fatty acid beta-oxidation. Proteins in this family belong to the short chain dehydrogenase/reductase (SDR) superfamily. They share a highly conserved Rossmann fold used for binding cofactors like NADH or NADPH. Unlike other members belonging to the SDR family, catalysis by pDCR does not involve a tyrosine-serine pair. Instead, a catalytically critical aspartate, together with an invariant lysine, polarizes a water molecule to donate a proton for the formation of the product .
Azaguanine-like transporters (Azg-like)
Type: Family

Azaguanine transporters (AzgA) are found in bacteria, fungi and plants. In plants, NCS2 has broad and mixed solute transport and binding profiles including combinations of xanthine, uric acid, uracil, adenine, guanine, cytosine and hypoxanthine. Bacterial NCS2 has more restricted solute transport and binding profiles. Fungal nucleobase transporters have been well studied in Aspergillus nidulans including two NCS2, UapA and UapC, that transport uric acid and xanthine and the purine transporter AzgA that moves adenine, hypoxanthine and guanine .

In plants, AZG2 is a purine transporter found in Arabidopsis. It transports natural purines (adenine and guanine) as well as purine analogues .

This entry also includes AdeP/AdeQ from E. coli, PbuG/PbuO from Bacillus subtilis and PlAzg1 from Paenibacillus larvae subsp. larvae. AdeP/AdeQ are adenine permeases , PbuG/PbuO are guanine/hypoxanthine permeases , while PlAzg1 is a nucleobase transporter that transports adenine, hypoxanthine, xanthine and uracil .
Beta-carotene hydroxylase-like (BETA-OHASE-like)
Type: Family

This family includes beta-carotene hydroxylases (

) and related proteins from bacteria and plants. Beta-carotene hydroxylases are nonheme diiron monooxygenases involved in the biosynthesis of xanthophylls that specifically hydroxylates the β-ring of beta-carotene, using ferredoxin as an electron donor. Plant members have also a low activity toward the β- and ε-rings of alpha-carotene and no activity towards acyclic carotenoids such as lycopene and neurosporene .
1-Cys peroxiredoxin (PRX_1cys)
Type: Family

This subfamily of peroxiredoxin (known as 1-cys PRX) composed of PRXs containing only one conserved cysteine, which serves as the peroxidatic cysteine. They are homodimeric thiol-specific antioxidant (TSA) proteins that confer a protective role in cells by reducing and detoxifying hydrogen peroxide, peroxynitrite, and organic hydroperoxides . As with all other PRXs, a cysteine sulfenic acid intermediate is formed upon reaction of 1-cys PRX with its substrates. Having no resolving cysteine, the oxidized enzyme is resolved by an external small-molecule or protein reductant such as thioredoxin or glutaredoxin. Similar to typical 2-cys PRX, 1-cys PRX forms a functional dimeric unit with a B-type interface, as well as a decameric structure which is stabilized in the reduced form of the enzyme. Other oligomeric forms, tetramers and hexamers, have also been reported . Mammalian 1-cys PRX is localized cellularly in the cytosol and is expressed at high levels in brain, eye, testes and lung . The seed-specific plant 1-cys PRXs protect tissues from reactive oxygen species during desiccation and are also called rehydrins .
Protein PSK SIMULATOR (PSI1/2/3)
Type: Family

This family represents the plant-specific proteins PSI 1-3 (Protein PSK SIMULATOR 1-3) from Arabidopsis. These proteins promote plant growth, especially at the vegetative stage, probably via the regulation of phytosulfokine (PSK) signalling; PSKs are peptide phytohormones acting as growth factors . They are required during vegetative growth and reproduction, PSI1 acts predominantly at the seedling stage whereas PSI2 and 3 are required for vegetative growth where they act synergistically. PSI1 and 3 may also have a function in carbohydrate metabolism .