SII-SWORD/CoKE huggingface dataset:
NPSN/SNAP25-like, N-terminal SNARE domain (NPSN/SNAP25-like_N_SNARE)
Type: Domain

Soluble N-ethylmaleimide attachment protein receptor (SNARE) proteins are a family of membrane-associated proteins characterised by an α-helical coiled-coil domain called the SNARE motif . These proteins are classified as v-SNAREs and t-SNAREs based on their localisation on vesicle or target membrane; another classification scheme defines R-SNAREs and Q-SNAREs, as based on the conserved arginine or glutamine residue in the centre of the SNARE motif . SNAREs are localised to distinct membrane compartments of the secretory and endocytic trafficking pathways, and contribute to the specificity of intracellular membrane fusion processes.

The t-SNARE domain consists of a 4-helical bundle with a coiled-coil twist. The SNARE motif contributes to the fusion of two membranes. SNARE motifs fall into four classes: homologues of syntaxin 1a (t-SNARE), VAMP-2 (v-SNARE), and the N- and C-terminal SNARE motifs of SNAP-25.

This entry represents the N-terminal SNARE motif found in plant SNAP25 homologues, SNAP29, SNAP30, SNAP32 and SNAP33 , and in the novel plant SNAREs (NPSNs) 11, 12 and 13 from Arabidopsis thaliana . SNAP33 and NPS11 play a key role in cytokinesis . SNAP33, the most studied SNAP25 homologue in Arabidopsis, is also involved in triggering innate immune responses. SNAP29 and SNAP30 have not been well-characterised yet .
Phytochrome A/B/C/D/E-like, histidine-kinase-related domain (Phy_HATPase-like)
Type: Domain

Canonical phytochromes have a conserved N-terminal photosensory core and a C-terminal regulatory region which typically includes a histidine-kinase-related domain (HKRD, also known as the HATPase domain) . This entry represents the histidine-kinase-related domain found in Arabidopsis thaliana phytochrome phyA-phyE . Following red light absorption, biologically inactive forms of phytochromes convert to active forms, which rapidly convert back to inactive forms upon far-red light irradiation. Phytochromes control the expression of a number of nuclear genes including those encoding the small subunit of ribulose-bisphosphate carboxylase, chlorophyll A/B binding protein, protochlorophyllide reductase or rRNA, and they also regulate temperature responses by associating with the promoters of key target genes in a temperature-dependent manner and subsequently repressing their expression probably in a PIF4-dependent manner . Phytochromes can be considered as having an N-terminal photosensory region to which a bilin chromophore is bound, and a C-terminal output region, which includes the HATPase domain, and is involved in dimerisation and presumably contributes to relaying the light signal to downstream signalling events.
DRIP1/2, RAWUL domain (DRIP-like_RAWUL)
Type: Domain

DREB2A-Interacting Proteins (DRIPs) are E3 ubiquitin-protein ligases that act as negative regulators of the response to water stress, that mediate ubiquitination and subsequent proteasomal degradation of the drought-induced transcriptional activator Dehydration-Responsive Element-Binding Protein 2A (DREB2A). DREB2A regulates the expression of stress-inducible genes via the dehydration-responsive elements and requires posttranslational modification for its activation. DRIPs contain a RING finger, and a RING finger- and WD40-associated ubiquitin-like (RAWUL) domain .

This entry represents the RAWUL domain found in E3 ubiquitin protein ligases DRIP1, DRIP2 and the DRIP homologue (DRIPH, At3g23060) from Arabidopsis.
1-phosphatidylinositol-3-phosphate 5-kinase, PIPK catalytic domain (PIKfyve_PIPKc)
Type: Domain

This entry represents the C-terminal catalytic lipid kinase domain related to PtdInsP kinases (PIPKc domain) found in PIKfyve and related proteins.

1-phosphatidylinositol-3-phosphate 5-kinase (

), also called FYVE finger-containing phosphoinositide kinase (PIKfyve), forms a complex with its regulators, the scaffolding protein Vac14 and the lipid phosphatase Fig4. The complex synthesises phosphatidylinositol 3,5-bisphosphate [PtdIns(3,5)P2] through the phosphorylation of phosphatidylinositol 3-phosphate (PtdIns3P or PI3P) on the fifth hydroxyl of the myo-inositol ring. Then phosphatidylinositol-5-phosphate (PtdIns5P) is generated directly from PtdIns(3,5)P2. PtdIns(3,5)P2 and PtdIns5P regulate endosomal trafficking and responses to extracellular stimuli . It is vital in early embryonic development and plays a role in different pathways, such as receptor tyrosine kinase (RTK) or EGFR degradation, regulation of the glutamate transporters EAAT2, EAAT3 and EAAT4 and the cystic fibrosis transmembrane conductance regulator (CFTR). It is also essential for systemic glucose homeostasis and insulin-regulated glucose uptake/GLUT4 translocation in skeletal muscle .

The yeast orthologue of human PIKfyve, Fab1, is required for endocytic-vacuolar pathway and nuclear migration . The plant orthologues such as FAB1A-D from Arabidopsis are important for the maintenance of endomembrane homeostasis and for development of viable pollen .

PIKfyve and its orthologues share a similar architecture consisting of a N-terminal FYVE domain, a middle region related to the CCT/TCP-1/Cpn60 chaperonins that are involved in productive folding of actin and tubulin, a second middle domain that contains a number of conserved cysteine residues (CCR) unique to these proteins, and a C-terminal catalytic lipid kinase domain related to PtdInsP kinases (or the PIPKc domain).
Protein spinster-like (MFS_spinster-like)
Type: Family

The entry includes Drosophila protein spinster , its vertebrate homologues, and the MFS-type efflux pumps from bacteria. Humans contain three homologues called protein spinster homologues 1 (SPNS1), 2 (SPNS2), and 3 (SPNS3). Protein spinster and its homologues may be sphingolipid transporters that play central roles in endosomes and/or lysosomes storage. SPNS2 is also called sphingosine 1-phosphate (S1P) transporter and is required for migration of myocardial precursors. S1P is a secreted lipid mediator that plays critical roles in cardiovascular, immunological, and neural development and function . These proteins belong to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Also included in this family are the probable sphingolipid transporter spinster homologues 1-3 from Arabidopsis thaliana.
UNC93-like protein 3, plant (UN933_plant)
Type: Family

This family represents the plant homologues of C. elegans uncoordinated protein 93 (also called putative potassium channel regulatory protein unc-93), including UNC93-like protein 3 from Arabidopsis thaliana. It maintains K+ homeostasis through abscisic acid (ABA) signalling pathway, which positively regulates abiotic stress tolerance and plant growth .
Nitrate transporter (NO3_transporter)
Type: Family

This entry represents a group of nitrate transporters that belong to the Major Facilitator Superfamily (MFS) of membrane transport proteins. Proteins in this entry include high-affinity nitrate transporters NRT2 from plants, and nitrate/nitrite transporters NarK2/NarT/NasA/NarU from bacteria .

NRT2 family proteins are involved in the uptake of nitrate by plant roots from the soil through the high-affinity transport system (HATS). There are seven Arabidopsis thaliana NRT2 proteins, called AtNRT2:1 to AtNRT2:7 . This entry also includes fungal nitrate transporters such as CRNA from Emericella nidulans .
DDX18/Has1, DEAD-box helicase domain (DDX18/Has1_DEADc)
Type: Domain

This entry represents the DEAD-box helicase domain found in DDX18 from animals and Has1 from fungi. This domain contains the ATP-binding region. Has1 is a ATP-dependent RNA helicase involved in 40S and 60S ribosomal subunit biogenesis . DDX18 is a putative RNA-dependent helicase which is activated by Myc protein .
Suv3, DEXQ-box helicase domain (Suv3_DEXQc)
Type: Domain

This entry represents the DEXQ-box helicase domain found in Suv3 and related proteins. Suv3 is an NTP-dependent RNA/DNA helicase that is necessary for the degradation of mature mtRNAs. It localizes predominantly in the mitochondria, where it forms an RNA-degrading complex called mitochondrial degradosome (mtEXO) with exonuclease PNP (polynucleotide phosphorylase), that degrades 3' overhang double-stranded RNA with a 3'-to-5' directionality in an ATP-dependent manner. Suv3 plays a role in the RNA surveillance system in mitochondria; it regulates the stability of mature mRNAs, the removal of aberrantly formed mRNAs and the rapid degradation of non coding processing intermediates . It also confers salinity and drought stress tolerance by maintaining both photosynthesis and antioxidant machinery, probably via an increase in plant hormone levels such as gibberellic acid (GA3), the cytokinin zeatin (Z), and indole-3-acetic acid (IAA) .

Proteins containing this domain also include some bacterial RNA helicases.
Sugar transporter ERD6/Tret1-like (MFS_ERD6/Tret1-like)
Type: Family

This family belong to the Glucose transporter-like (GLUT-like) family of the Major Facilitator Superfamily (MFS) of membrane transport proteins and consists of sugar transporters including plant early dehydration-induced gene ERD6-like proteins , and similar insect proteins such as facilitated trehalose transporter Tret1-1. ERD6-like transporters can be induced under abiotic stress conditions. EDR6 might transport sucrose, while ESL1 transports monosaccharides across the vacuolar membrane and functions together with the vacuolar invertase to regulate osmotic pressure by affecting the accumulation of sugar in the cells under abiotic stress conditions . Insect Tret1-1 is a low-capacity facilitative transporter for trehalose that mediates the transport of trehalose synthesised in the fat body and the incorporation of trehalose into other tissues that require a carbon source . Proteins in this family show similarities with mammalian glucose transporters GLUT6/ GLUT8 and myo-inositol transporters (HMIT) .
Polyol transporter 1-6 (PLT1-6)
Type: Family

The plant Polyol transporter (PLT) subfamily includes PLT1-6 from Arabidopsis thaliana and similar transporters . The best characterised member of the group is Polyol transporter 5, also called Sugar-proton symporter PLT5, which mediates the H-symport of numerous substrates including linear polyols (such as sorbitol, xylitol, erythritol or glycerol), cyclic polyol myo-inositol, and different hexoses, pentoses (including ribose), tetroses, and sugar alcohols. It functions to transport a wide range of substrates into specific sink tissues in the plant . The PLT subfamily belongs to the Glucose transporter-like (GLUT-like) family of the Major Facilitator Superfamily (MFS) of membrane transport proteins. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement .
Solute carrier family 17 member 9-like (SLC17A9-like)
Type: Family

This subfamily includes solute carrier family 17 member 9 (SLC17A9) and similar proteins including plant inorganic phosphate transporters (PHT4) that are also probably anion transporters. SLC17A9, also called voltage-gated purine nucleotide uniporter SLC17A9 and vesicular nucleotide transporter (VNUT), is involved in vesicular storage and exocytosis of ATP. It facilitates the accumulation of ATP and other nucleotides in secretory vesicles such as adrenal chromaffin granules and synaptic vesicles . It also functions as a lysosomal ATP transporter and regulates cell viability . By controlling ATP storage in lysosomes, it regulates ATP-dependent proteins of these organelles . Plant PHT4 family transporters mediate the transport of inorganic phosphate and may also transport organic anions. The Arabidopsis protein AtPHT4;4 is a chloroplast-localized ascorbate transporter . PHT4 proteins show differential expression that suggests specialized functions .

The SLC17A9-like subfamily belongs to the Solute carrier 17 (SLC17) family of the Major Facilitator Superfamily (MFS) of membrane transport proteins. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement .
Sugar transport protein STP/MST-like, plant (MFS_STP/MST-like_plant)
Type: Family

The family represents plant sugar transport proteins (STPs), also known as hexose transporters, including STP1-STP14 from Arabidopsis and Sugar transport proteins MST1-8 from Oryza sativa subsp. japonica . They mediate the active uptake of hexoses such as glucose, 3-O-methylglucose, fructose, xylose, mannose, galactose, fucose, 2-deoxyglucose and arabinose, by sugar/hydrogen symport. Several STP family transporters are expressed in a tissue-specific manner, or at specific developmental stages. STP1 is the member with the highest expression level of all members and high expression is detected in photosynthetic tissues, such as leaves and stems, while roots, siliques, and flowers show lower expression levels. It plays a major role in the uptake and response of Arabidopsis seeds and seedlings to sugars .
Heh2/Src1-like (Heh2/Src1)
Type: Family

This family includes inner membrane proteins from plants and fungi, including Heh2/Src1 from budding yeasts and Lem2/Mug61 from fission yeasts . These proteins contain the N-terminal HEH/LEM domain that anchors the chromatin to the nuclear periphery, and a MSC (MAN1/Src1C-terminal) domain in their C-terminal region. They are involved in meiosis, required for the correct meiotic chromosome segregation.
Pentatricopeptide repeat-containing protein At5g10690-like (At5g10690-like)
Type: Family

This is a family of plant pentatricopeptide repeat-containing proteins, including At5g10690 from Arabidopsis thaliana. Its exact function is not clear.
Sialyltransferase-like protein 1/5 (SIA1/STLP5)
Type: Family

This entry represents plant sialyltransferase-like proteins, including SIA1 (also known as Protein MALE GAMETOPHYTE DEFECTIVE 2 MGP2) from Arabidopsis and STLP5 from Oryza sativa subsp. japonica. SIA1 is localised to the Golgi apparatus and is required for normal pollen grain germination and pollen tube growth .
Phytolongin (PHYL)
Type: Family

Phytolongin is a longin-related family of proteins specific to plants. Similar to longin, they contain the N-terminal longin domain and the C-terminal transmembrane domain. However, the central SNARE motif is replaced in Phytolongins by another domain termed the 'Phyl domain'. Phylogenetic analysis revealed that the Phytolongins are derivatives of the plant specific VAMP72 longin sub-family and allows elucidation of Phytolongin evolution. These proteins are involved in membrane-trafficking machinery .

Four phytolongins in Arabidopsis have been shown to be distributed along the secretory pathway: Phyl2.1 and Phyl2.2 are strictly located at the endoplasmic reticulum network, Phyl1.2 associates with the Golgi bodies, and Phyl1.1 locates mainly at the plasma membrane and partially in the Golgi bodies and post-Golgi compartments .
BTB/POZ domain containing protein At1g01640-like (At1g01640-like)
Type: Family

This is a group of plant BTB/POZ domain-containing proteins including At1g01640, At5g48510 and At3g56230 from Arabidopsis. They may act as a substrate-specific adapter of an E3 ubiquitin-protein ligase complex (CUL3-RBX1-BTB), which mediates the ubiquitination and subsequent proteasomal degradation of target proteins .
Rho GTPase-activating protein 1-5 (RopGAP1-5)
Type: Family

This entry represents a group of plant Rho GTPase-activating proteins, including RopGAP1-5 from Arabidopsis. RopGAP4 is a Rop deactivator, elevates ADH expression in response to oxygen deprivation but decreases tolerance to stress . RopGAP3 and RopGAP4 mediate local activation of ARAC10/ROP11 to initiate the distinct pattern of secondary cell walls in xylem cells .
Multifunctional Ser/Thr-tRNA deacylase ProXp-y (PROXY)
Type: Family

Multifunctional Ser/Thr-tRNA deacylase ProXp-y (formerly known as YeaK) is an aminoacyl-tRNA editing enzyme that deacylates Ser-tRNA and/or Thr-tRNA mischarged by lysyl-tRNA synthetase (LysRS), threonyl-tRNA synthetase (ThrRS), seryl_tRNA synthetase (SerRS), alanyl-tRNA synthetase (AlaRS), valyl-tRNA synthetase (ValRS) and isoleucyl-tRNA synthetase (IleRS) in vitro. However, it may be required in vivo to prevent mistranslation and to maintain growth when the error prone stress-inducible lysyl-tRNA synthetase (LysU) is expressed under environmental pressure .
Myb family transcription factor HRS1-like (HRS1-like)
Type: Family

This entry represents a group of plant Myb family transcription factors, including HHO1-6, HRS1 and EFM from Arabidopsis. HRS1 represses primary root development in response to phosphate deficiency conditions, only when nitrate is present . It is also required for suppressing abscisic acid (ABA) signalling in germinating embryo axis, which promotes the timely germination of seeds . EFM functions as a flowering repressor, directly repressing FT expression in a dosage-dependent manner in the leaf vasculature .
Carbohydrate-binding X8 domain-containing protein, plant (X8_dom_prot)
Type: Family

This entry represents a group of plant proteins, including Ole e 10 from Olea europaea (Common olive), and PLASMODESMATA CALLOSE-BINDING PROTEIN 1-8 (PDCB1-8)/CBX8D from Arabidopsis. They contain the carbohydrate-binding module, which is the most common non-catalytic module associated with enzymes active in plant cell-wall hydrolysis. Ole e 10 has been shown to bind preferentially 1,3-beta-glucans. It is a major pollen allergen that may be involved in pollen tube wall re-formation during germination . In Arabidopsis, PDCBs may be involved in cell-to-cell trafficking regulation .
Putative alpha 1,4-glycosyltransferase, plant (Put_A1-4-GlycosylTfrase_plant)
Type: Family

This family includes uncharacterised plant proteins such as At4g19900 and At1g61050 from Arabidopsis. Proteins in this family have been predicted to be Alpha 1,4-glycosyltransferases.
Mediator of RNA polymerase II transcription subunit 26c-like (MD26C-like)
Type: Family

MEDIATOR is a conserved multi-subunit complex that links transcription factors and RNA polymerase II and that thereby facilitates transcriptional initiation. This entry includes a MEDIATOR subunit known as MED26C from Arabidopsis, also known as MED26_3. This subunit may play a role in transcription elongation .
Beta-glucanase/XTH (Beta-glucanase/XTH)
Type: Family

This entry represents a subgroup of the glycoside hydrolase family 16. This entry includes beta-glucanases (

) from bacteria and xyloglucan endotransglucosylase/hydrolases (XTHs,

) from plants.

This entry includes a group of xyloglucan endotransglucosylase/hydrolases (XTHs) from plants . Xyloglucan is a soluble hemicellulose with a backbone of beta-1,4-linked glucose units, partially substituted with alpha-1,6-linked xylopyranose branches. It binds noncovalently to cellulose, cross-linking the adjacent cellulose microfibrils, giving it a key structural role as a matrix polymer. XTHs catalyses xyloglucan endohydrolysis (XEH) and/or endotransglycosylation (XET) and are involved in the modification of cell wall structure by cleaving and, often, also re-joining xyloglucan molecules in primary plant cell walls .

The glycosyl hydrolases family 16 (GH16) contains functionally heterogeneous members, including lichenase (

); xyloglucan xyloglucosyltransferase (

); agarase (

); kappa-carrageenase (

); endo-beta-1,3-glucanase (

); endo-beta-1,3-1,4-glucanase (

); endo-beta-galactosidase (

). These enzymes share a common ancestor and have diverged significantly in their primary sequence.

The GH16 catalytic domain has a classical sandwich-like β-jelly roll fold, formed by two main, closely packed and curved antiparallel β-sheets, creating a deep channel harboring the catalytic machinery. Even though the GH16 domains have now diverged significantly in their primary sequences, they all feature a common catalytic motif, E-[ILV]-D-[IVAF]-[VILMF](0,1)-E. The two glutamic acid residues in the conserved motif are the nucleophile and the general base involved in catalysis, whereas the aspartic acid residue is important in maintaining the relative position of these catalytic amino acids .

Two closely clustered conserved glutamates have been shown to be involved in the catalytic activity of Bacillus licheniformis lichenase. This domain contains these residues.
Protein TAR1 (TAR1)
Type: Family

This entry includes transcript antisense to ribosomal RNA protein 1 (TAR1) from Saccharomyces cerevisiae and Kluyveromyces lactis . TAR1 might be involved in regulation of respiratory metabolism expression as it is induced under respiratory conditions to maintain oxidative phosphorylation capacity. Its levels in mitochondria are tightly controlled and usually low. It is down-regulated to manage oxidative stress when respiration is defective . This entry also includes uncharacterised plant proteins.
E3 ubiquitin-protein ligase SIS3 (SIS3)
Type: Family

This family represents a group of plant E3 ubiquitin protein ligases, including SIS3 (Protein SUGAR INSENSITIVE 3) from Arabidopsis. SIS3 is a RING finger protein involved in a ubiquitination pathway that acts as positive regulator of sugar signalling during early seedling development .
5'-adenylylsulfate reductase-like 5/7 (APRL5/7)
Type: Family

This entry represents a group of plant 5'-adenylylsulfate reductase-like proteins, including APRL5/7 from Arabidopsis and APRL5/6 from rice. They contain a thioredoxin (TRX) domain .
Pentatricopeptide repeat-containing protein THA8L-like (THA8L-like)
Type: Family

This entry represents a group of plant pentatricopeptide repeat-containing proteins, including Protein THYLAKOID ASSEMBLY 8-like (THA8L) and the uncharacterised Arabidopsis protein At1g62350. THA8L resembles THA8 and binds weakly to specific single strand RNA .
Protein MLN51 homolog, plant (MLN51_plant)
Type: Family

The exon-junction complex (EJC) is involved in post-transcriptional regulation of mRNA. The core of EJC consists of Y14, Magoh, MLN51 and eIF4AIII, a DEAD-box RNA helicase. EJC marks the position of the exon-exon junction in the mature mRNA for the gene expression machinery, and its core components remain bound to spliced mRNAs throughout all stages of mRNA metabolism. Human MLN51 has been shown to stimulate the ATPase activity of eIF4AIII . This entry represents the plant MLN51 homologues. Similar to animal MLN51, Arabidopsis MLN51 is also a core component of the plant EJC .
Uncharacterized protein At4g06598-like (At4g06598-like)
Type: Family

This family represents a group of uncharacterised BZIP domain-containing plant proteins, including At4g06598 from Arabidopsis thaliana.
Chromatin modification-related protein EAF1A/B (EAF1A/B)
Type: Family

This family includes the chromatin modification-related protein EAF1A/B from Arabidopsis. They are components of the NuA4 histone acetyltransferase complex involved in transcriptional activation of selected genes principally by acetylation of nucleosomal histone H4 and H2A .
NAC domain-containing protein SOG1-like (SOG1-like)
Type: Family

This entry represents a group of plant NAC domain-containing proteins, including SOG1 (At1g25580) and NAC10/73/75 from Arabidopsis. They are a group of transcription activators that function in genomic stress response and plant development. SOG1 regulates the transcriptional activation response to gamma irradiation . NAC10 and NAC73 plays a regulatory role in the development of secondary cell wall fibres , while NAC75 is involved in xylem formation .
B3 domain-containing transcription factor LEC2-like (LEC2-like)
Type: Family

This entry represents a group of plant B3 domain-containing transcription factors, including LEC2, NGA1/2/3/4, RAV1/2 and related proteins from Arabidopsis. LEC2 plays a central role in embryo development . RAV1 binds specifically to bipartite recognition sequences composed of two unrelated motifs, 5'-CAACA-3' and 5'-CACCTG-3' . RAV2 has been shown to affect FT expression . NGA1/2/3/4 regulate lateral organ growth .