SII-SWORD/CoKE huggingface dataset:
SOB-five-like (SOFL)
Type: Family

This entry represents the SUPPRESSOR OF PHYTOCHROME B (SOB) five-Like (SOFL) family of novel plant-specific proteins which have high sequence similarity and similar protein structures . These proteins are involved in cytokinin-mediated development and contain two highly conserved domains SOFL-A and SOFL-B, which are necessary for their function . These proteins are positive modulators of the endogenous content of specific cytokinin levels derived from the biosynthetic intermediates trans-zeatin riboside monophosphate (tZRMP) and N6-(Delta2-isopentenyl)adenosine monophosphate (iPRMP) such as N-glucosides trans-zeatin 7-glucoside (tZ7G), cis-zeatin 7-glucoside (cZ7G) and N6-(Delta2-isopentenyl)adenine 7-glucoside (iP7G) .
Metallothionein-like protein 3 (MT3)
Type: Family

Metallothioneins (MTs) are small proteins with a high content of cysteine residues that bind various heavy metals. Plant MTs are classified into four types based on the arrangement of cysteine residues, and all are involved in copper and other metals homeostasis . This entry represents MT3 that in Arabidopsis is predominantly expressed in leaf mesophyll cells. It functions as copper (Cu) and zinc (Zn) chelator and plays a role in Cu homeostasis, specifically in the remobilization of Cu from senescing leaves. The mobilization of Cu is important for seed development .
Molybdopterin synthase sulfur carrier subunit (MOCS2A)
Type: Family

MOCS2A is a the small subunit of the molybdopterin synthase complex that catalyses the conversion of precursor Z into molybdopterin by mediating the incorporation of 2 sulfur atoms into precursor Z to generate a dithiolene group. In the complex, MOCS2A serves as sulfur donor by being thiocarboxylated at its C terminus by UBA4 . After interaction with MOCS2B, the sulfur is then transferred to precursor Z to form molybdopterin .

This entry includes the Molybdopterin synthase sulfur carrier subunit MOCS2A from eukaryotes and MoaD from bacteria and archaea . This entry also includes Small archaeal modifier protein 1, which functions as a protein modifier covalently attached to lysine residues of substrate proteins, as well as a sulfur carrier in molybdenum cofactor (MoCo) biosynthesis.
Protein DCL-like (DCL-like)
Type: Family

Defective chloroplasts and leaves protein (DCL), first identified in tomato, is a small protein that plays a role in the early stage of chloroplast development and palisade cell morphogenesis

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]. It is required for correct plastid ribosome assembly and for processing and maturation of 4.5S rRNA . This entry includes DCL from Solanum lycopersicum (Tomato) and its orthologue from Arabidopsis . Also included in this entry is the Protein EMBRYO DEFECTIVE 514 (also known as DOMINO1) from Arabidopsis thaliana, which is involved in ribosome biogenesis and in a process essential for nuclear and nucleolar functions. It shares high sequence similarities with DCL proteins .
ER degradation-enhancing alpha-mannosidase-like protein 1/2/3 (EDEM1/2/3)
Type: Family

This entry represents a group of alpha-1,2-specific exomannosidases that are involved in endoplasmic reticulum-associated degradation (ERAD), including EDEM1/2/3 from humans, Mnl1 from yeasts and MNS4/5 from Arabidopsis. Mnl1 forms a complex with Pdi1 to process unfolded protein-bound Man8GlcNAc2 oligosaccharides to Man7GlcNAc2, promoting degradation in unfolded protein response . In humans, mannose trimming from Man8GlcNAc2 to Man7GlcNAc2 is performed mainly by EDEM3 and to a lesser extent by EDEM1, while EDEM2 catalyses the first mannose trimming step from Man9GlcNAc2 . EDEM1 has been shown to recognise and deliver misfolded proteins to the SEL1L-containing ERAD complex . MNS4/5 function in the formation of unique N-glycan structures that are specifically recognized by components of the endoplasmic reticulum-associated degradation (ERAD) machinery, which leads to the degradation of misfolded glycoproteins .
MYB-like transcription factor EOBI/EOBII-like, plant (EOBI/EOBII-like_plant)
Type: Family

This entry represents a group of plant MYB-like transcription factors, including EOBI and EOBII from Petunia hybrida. EOBII controls the production of volatile organic compounds (VOCs), including floral volatile benzenoids and phenylpropanoids (FVBP), in flowers of fragrant cultivars (e.g. cv. Mitchell and cv. V26) by regulating the expression of ODO1 and EOBI, key regulators of the shikimate pathway, and of several biosynthetic floral scent-related genes including IGS, PAL2 and CFAT . EOBII binds to and activates the ODO1 and EOBI promoters via MYB binding sites (MBS) 5'-AAACCTAAT-3' and 5'-CTAACT-3' .

Other MYB-like transcription factors included in this entry include MYB21/MYB24/MYB108 from Arabidopsis and MYB2/JAMYB from rice . They are involved in different processes, such as abiotic stress responses, defense responses, plant development and photomorphogenesis.
Mitochondrial phosphate carrier protein SLC25A3/Pic2/Mir1-like (SLC25A3/Pic2/Mir1-like)
Type: Family

This entry represents a group of mitochondrial phosphate carrier proteins, including Mir1 and Pic2 from budding yeasts and SLC25A3 from animals . They are copper and phosphate carriers that imports copper and inorganic phosphate into mitochondria .
Cold-regulated protein 27/28 (COR27/28)
Type: Family

Cold-regulated proteins 27 and 28 are regulated by low temperature and light. They are involved in central circadian clock regulation and in flowering promotion, by binding to the chromatin of clock-associated evening genes TOC1, PRR5, ELF4 and cold-responsive genes in order to repress their transcription . They are also involved in freezing tolerance regulation.
PWWP domain containing protein PWWP2-like (PWWP2-like)
Type: Family

This entry includes a group of plant proteins, such as the PWWP domain containing protein PWWP2 (At1g51745, also known SL1) from Arabidopsis thaliana . Its exact function is not known. It is part of PEAT complexes (for PWWPs-EPCRs-ARIDs-TRBs) which mediate histone deacetylation and heterochromatin condensation to facilitate heterochromatin silencing. These complexes repress the production of small interfering RNAs (siRNAs) and DNA methylation .
Protein EXECUTER 1/2 (EX1/2)
Type: Family

Proteins EXECUTER 1/2 (EX1/2) are located in chloroplasts and essential for singlet oxygen signalling, which is a stress signal that triggers the programmed cell death (PCD) . This singlet oxygen-induced stress-related signalling that triggers a PCD pathway is unique to photosynthetic eukaryotes and operates under mild stress conditions, invokes photoinhibition of photosystem II (PSII) without causing photooxidative damage of the plant .
Calmodulin binding protein PICBP-like (PICBP-like)
Type: Family

This entry represents a group of plant calmodulin binding proteins, including PICBP from Arabidopsis which binds calmodulin in a calcium-dependent manner and may play a role in general plant defense .
Violaxanthin de-epoxidase (VDE)
Type: Family

Violaxanthin de-epoxidase (VDE) is localised in the thylakoid lumen and catalyses the two-step mono de-epoxidation of violaxanthin to form antheraxanthin and zeaxanthin, to control the concentration of zeaxanthin in chloroplasts. It is part of a conserved system that dissipates excess energy as heat in the light-harvesting complexes of photosystem II (PSII) and protects them from photodamage . The thylakoid lumen pH decreases under excessive light that allows VDE to attach to the thylakoid membrane where violaxanthin is located. This acidic condition causes the opening of the lipocalin barrel .
LAZY family (LAZY)
Type: Family

This entry represents the LAZY proteins (also known as NEGATIVE GRAVITROPIC RESPONSE OF ROOTS (NGR) or DEEPER ROOTING (DRO)), a family of plant proteins involved in the proper distribution of auxin and in the regulation of both roots and shoots response to gravitropism (Jiao et al, Front. Plant Sci, 2021, doi:10.3389/fpls.2020.606241) . Statocytes are gravity-sensing cells that perceive directional signals of gravity, which leads to asymmetric distribution of auxin in the responding organs. These proteins are involved in the development of the root system architecture by influencing lateral root angles and primary root length .
Rhodanese-like domain-containing protein STR17/STR18/HARC1-like (STR17/STR18/HARC1-like)
Type: Family

This entry represents a group of rhodanese-like domain-containing proteins from bacteria, archaea and plants, including STR17/STR18/HARC1 from Arabidopsis. HARC1 is an arsenate reductase that reduces arsenate to arsenite in the root, facilitating efflux of arsenic back into the soil to limit both its accumulation in the root and transport to the shoot . STR17/STR18 are sulfurtransferases . STR18 catalyses the transfer of a sulfur ion from a donor to cyanide or to other thiol compounds .
Plastid division protein CDP1-like (CPD1-like)
Type: Family

This family represents plant plastid division protein CDP1-like , Protein ACCUMULATION AND REPLICATION OF CHLOROPLASTS 6 (ARC6) and its paralogue PARC6, components of the plastid division machinery which are essential for the chloroplast replication process . ARC6 is evolutionarily related to the cyanobacterial cell division protein Ftn2/ZipN , being unique to the division machineries of cyanobacteria and chloroplasts. Their sequences share about 19% identity and are quite conserved along their length. Chloroplast division implies the assembly and constriction of the tubulin-like FtsZ ring on the stromal surface of the inner envelope membrane (IEM) and the dynamin-like ARC5 ring on the cytosolic surface of the outer envelope membrane (OEM). The assembly of these structures is coordinated by a pair of paralogous proteins, ARC6 and PARC6 from the IEM, and PDV2 and PDV1 from the OEM. They contain single transmembrane (TM) domains towards their C terminus with short C-terminal regions extending into the intermembrane space (IMS) .
Transcription repressor OFP17 (OFP17)
Type: Family

OFP17 is a plant transcriptional repressor belonging to the Ovate Family Proteins (OFPs), which are characterised by a conserved OVATE domain. OFP17 is highly expressed in roots and may regulate multiple aspects of plant growth and development through the regulation of BEL1-LIKE (BLH) and KNOX TALE (KNAT) homeodomain transcription factors .
Protein LOW PSII ACCUMULATION 3 (LPA3)
Type: Family

Protein LOW PSII ACCUMULATION 3 (LPA3) is probably located in chloroplast stroma or associated with thylakoid membranes. LPA3 works cooperatively with LPA2 as auxiliary proteins in the incorporation of psbC (also known as CP43) into PSII via interaction with cpSRP translocase ALB3. They are thought to be also involved in synthesis and assembly of psbC .
Style cell-cycle inhibitor 1-like (SCI-1-like)
Type: Family

This family includes the style cell-cycle inhibitor 1 (SCI-1) from Arabidopsis thaliana and related proteins from other plants and fungi. SCI-1 is a component of the auxin signalling transduction pathway that regulates cell proliferation and differentiation during flowers stigmas and styles development . It is involved in the regulation of auxin-related genes .
Pectin methyltransferase CGR2/3 (CGR2/3)
Type: Family

This family includes two functionally redundant pectin methyltransferases, Cotton Golgi-related 2 and 3 (CGR2/3), which are required for homogalacturonan pectins (HG) methylesterification in the Golgi apparatus prior to integration into cell walls, essential for general growth and development . Changes in pectin composition impacts carbon (C) partitioning, photosynthesis and respiration efficiency by influencing leaf mesophyll cell walls morphology and physiology. Pectin methylesterification modulates both expansion and positioning of cells in leaves, probably by changing cell walls plasticity .
Calcium sensing receptor, plant (CAS_plant)
Type: Family

The calcium sensing receptor (CAS) from Arabidopsis is a thylakoid-localised phosphoprotein that possesses a single transmembrane domain that splits the protein into two halves: the N-terminal domain which binds Ca2 with low affinity and high capacity, and the C-terminal domain that contains a non-catalytic rhodanese homology domain and phosphorylation sites . It modulates cytoplasmic Ca2 levels and it is required for proper stomatal regulation in response to elevated levels of external Ca2 and it is also involved in de-etiolation . This protein also plays a role in the STN7/STN8/TAP38 network of phosphorylation-mediated photoacclimation processes in Arabidopsis .
Thioredoxin DCC1 (DCC1_Trx)
Type: Family

This entry includes DCC1 (thioredoxin DXXCXXC motif-containing protein 1, AT5G50100) from Arabidopsis thaliana , which belongs to the thiol-disulfide oxidoreductase family. Members of this family contain a conserved DxxCxxC motif in their N-terminal. Two Cys residues present in this motif determined the function of these proteins as Thioredoxins (Trxs), key enzymes for modulating ROS scavenging through the reduction of specific S-S groups. DCC1 is localised in mitochondria and directly interacts with CARBONIC ANHYDRASE2 (CA2), an essential subunit of the respiratory chain NADH dehydrogenase complex (Complex I). DCC1 catalyses a redox modification on CA2, resulting in the regulation of Complex I activity and ROS homeostasis which is important for de novo shoot initiation and improvement the capacity of plant regeneration .

This entry also includes uncharacterised proteins from bacteria.
WPP domain-containing protein 1/2/3 (WPP1/2/3)
Type: Family

This family includes WPP domain-containing proteins 1/2/3 (also known as MFP1 attachment factors 1/2/3), homologues of the MFP1 attachment factor 1 (MAF1), a plant-specific nuclear envelope (NE)-associated protein first identified in tomato. These proteins are NE-associated proteins containing a WPP domain predicted to consist of a β-strand and three α-helices, sufficient for NE targeting . These proteins regulate the mitotic activity in roots and play a role with HSP70-1 in facilitating WIT1 (WPP domain-interacting tail-anchored protein 1) nuclear envelope targeting .
Shugoshin, plant (SGO_plant)
Type: Family

The Shugoshin (SGO) protein family plays a major role in the protection of centromeric cohesion in Drosophila and yeast. This entry represents plant shugoshins, including SGO1 and SGO2 from Arabidopsis . SGO1 is required for the maintenance of centromeric cohesion of sister chromatids in meiosis I, but not through the control of AtSYN1/AtREC8 localisation. Together with SGO2, it is required for protection of centromeric cohesion during anaphase I . However, SGO2 is dispensable for meiosis. In rice, OsSGO1 is also involved in the assembly and maintenance of the synaptonemal complex (SC) during early prophase I . In maize, ZmSGO1 is required for maintenance of centromeric cohesion before prophase II and correct segregation of chromatids during meiosis II .
Nuclear pore complex protein NUP214 (NUP214)
Type: Family

Nuclear pore complex protein NUP214 (also known as Protein LONO1 and Protein EMBRYO DEFECTIVE 1011) is a component of the nuclear pore complex in Arabidopsis, required for mature mRNA export from the nucleus to the cytoplasm, essential for normal embryogenesis and seed viability . It is important during early embryogenesis, being involved in the first asymmetrical cell division of the zygote and regulates the number and planes of cell divisions required for generating the normal embryo proper and suspensor, apical-basal axis, cotyledons and meristem .
Small ribosomal subunit protein bTHXc/bTHXc, plant (Ribosomal_bTHXc/bTHXc_plant)
Type: Family

This entry includes small ribosomal subunit protein bTHXc/bTHXm from plant chloroplast and mitochondria, closely related to bacterial ribosomal small subunit protein bTHX (previously THX). Proteins in this entry have additional N-terminal transit peptides .
WPP domain-interacting protein 1/2/3 (WIP1/2/3)
Type: Family

This entry represents the WPP domain-interacting protein (WIP) family which includes WIP1, 2 and 3 from Arabidopsis. These proteins are specific to plants and required for the localisation and anchorage of Ran GTPase-activating proteins (RanGAP) to the nuclear envelope (NE) mediated by WIT1 and WIT2 in undifferentiated cells of root tips . They are part of the SUN-WIP-WIT2-KAKU1 complex, in which they mediate the transfer of cytoplasmic forces to the nuclear envelope (NE), leading to nuclear shape changes .
(S)-ureidoglycine aminohydrolase, C-terminal cupin domain (UGlyAH_cupin_C)
Type: Domain

(S)-ureidoglycine aminohydrolase (UGHY or UGlyAH) is involved in the ureide pathway, a metabolic route of purine catabolism in plants, some bacteria and probably in some fungi where, uric acid is degraded into glyoxylate and ammonia . This enzyme is involved in the anaerobic nitrogen utilization via the assimilation of allantoin. It catalyses the second step in the allantoin degradation pathway, the deamination of the allantoin producing S-ureidoglycolate and ammonia from S-ureidoglycine .

The structure of UGlyAH from Arabidopsis thaliana (AtUGlyAH) has been studied. It contains two structurally similar β-barrel domains, called N and C (cupin) domains. AtUGlyAH binds a Mn ion through its C-terminal domain which acts as a molecular anchor to bind (S)-ureidoglycine. Its structure showed a bi-cupin fold with a conserved jelly roll-like β-barrel fold and an octameric functional unit. Several structural homologues of UGlyAH, including the Escherichia coli ortholog YlbA (also known as GlxB6), also exhibit similar features .

This entry represents the C-terminal cupin domain found in (S)-ureidoglycine aminohydrolases, including UGlyAH from E.coli and its homologues from plants and fungi .
Vitamin K epoxide reductase-like VKOR/LOT1 (VKOR/LTO1)
Type: Domain

Proteins containing this domain (also known as VKOR domain) are from bacteria, plants and archaea. They are homologous to mammalian Vitamin K epoxide reductases (VKORC1). In some plant and bacterial homologues, the VKOR domain is fused with domains of the thioredoxin family of oxidoreductases which may function as redox partners in initiating the reduction cascade . Proteins containing this domain include Thiol-disulfide oxidoreductase LTO1 (also known as Vitamin K reductase, AtVKOR) from Arabidopsis and Vitamin K epoxide reductase homologue (VKOR) from Synechococcus sp. . In general, they disulfide bond-forming enzymes which control disulfide bond formation . All homologues of VKOR contain an active site CXXC motif, which is switched between reduced and disulfide-bonded states during the reaction cycle .

In Arabidopsis LTO1 catalyses disulfide bond formation of chloroplast proteins and is involved in thylakoid redox regulation and photosynthetic electron transport . It is required for the assembly of photosystem II (PSII) through the formation of disulfide bond in PSBO, a subunit of the PSII oxygen-evolving complex in the thylakoid lumen . Bacterial VKOR homologues catalyse disulphide bridge formation in secreted proteins by cooperating with a periplasmic, Trx-like redox partner .
Membrane-associated kinase regulator 6 (MAKR6)
Type: Family

This entry represents the membrane-associated kinase regulator 6 (MAKR6) which acts as a kinase regulator that may be involved in abscisic acid signalling .
PIP2/PIPL1 (PIP2/PIPL1)
Type: Family

This entry includes PAMP-induced secreted peptide 2 (PIP2) and PAMP-INDUCED PEPTIDE-LIKE 1 (PIPL1, also known as CEP16 or PREPIPL1) from Arabidopsis, which are part of the PIP/PIPL family . These secreted proteins contain two conserved core SGPS motifs at the C terminus and the GxGH motif at the extreme C terminus . The double peptide motif might be processed into two different peptides or, alternatively, may act as a functional unit, being able to interact with distinct binding sites resulting in the activation of different pathways. PIP2 is involved in innate immune and stress responses. It also acts as a negative regulator of root growth . PIPL1 is involved in seed development and was also induced by stress .
Thioredoxin-like fold domain-containing protein MRL7/MRL7L (MRL7/MRL7L)
Type: Family

This family represents a group of plant thioredoxin-like fold domain-containing proteins, including MRL7 (Protein MESOPHYLL-CELL RNAI LIBRARY LINE 7, also known as Protein EARLY CHLOROPLAST BIOGENESIS 1 (ECB1) or Protein SUPPRESSOR OF VARIEGATION 4 SVR4) and its paralog MRL7L from Arabidopsis. These proteins are required for early chloroplast development and involved in the regulation of plastid gene expression . They also mediate the degradation of two repressors of chloroplast biogenesis, PIF1 and PIF3 in nucleus . MRL7L is a necessary component of phytochrome signalling for photosynthesis-associated plastid-encoded genes (PhAPGs) activation .
Arabinogalactan protein 23/40 (AGP23/40)
Type: Family

Arabinogalactan proteins (AGPs) are proteoglycans of the plant extracellular matrix that have been implicated in diverse developmental roles such as differentiation, cell-cell recognition, embryogenesis and programmed cell death. This entry includes AGP23 (At3g57690) and AGP40 (At3g20865) from Arabidopsis thaliana. AGP40 is only expressed in pollen, while AGP23 is only expressed in flowers .
(S)-ureidoglycine aminohydrolase, N-terminal cupin domain (UGlyAH_cupin_N)
Type: Domain

(S)-ureidoglycine aminohydrolase (UGHY or UGlyAH) is involved in the ureide pathway, a metabolic route of purine catabolism in plants, some bacteria and probably in some fungi where, uric acid is degraded into glyoxylate and ammonia . This enzyme is involved in the anaerobic nitrogen utilization via the assimilation of allantoin. It catalyses the second step in the allantoin degradation pathway, the deamination of the allantoin producing S-ureidoglycolate and ammonia from S-ureidoglycine .

The structure of UGlyAH from Arabidopsis thaliana (AtUGlyAH) has been studied. It contains two structurally similar β-barrel domains, called N and C (cupin) domains. AtUGlyAH binds a Mn ion through its C-terminal domain which acts as a molecular anchor to bind (S)-ureidoglycine. Its structure showed a bi-cupin fold with a conserved jelly roll-like β-barrel fold and an octameric functional unit. Several structural homologues of UGlyAH, including the Escherichia coli ortholog YlbA (also known as GlxB6), also exhibit similar features .

This entry represents the N-terminal cupin domain found in (S)-ureidoglycine aminohydrolases, including UGlyAH from E.coli and its homologues from plants and fungi .
COFACTOR ASSEMBLY OF COMPLEX C SUBUNIT B CCB4 (CCB4)
Type: Family

Cofactor maturation pathways such as the CCB system (system IV) for cytochrome c-heme attachment are conserved in all organisms performing oxygenic photosynthesis . The CCB system consists of four proteins: CCB1-4. CCB2 and CCB4 are paralogues derived from a unique cyanobacterial ancestor . Orthologues are conserved in higher plants .

This entry includes the plant CCB4 and its homologues from cyanobacteria.
AUGMIN subunit 5, plant (AUG5_plant)
Type: Family

The augmin complex regulates gamma-tubulin localization in mitotic spindles, but not at the centrosome. Plant and animal augmin complexes have similar functions in microtubule nucleation and organisation in mitotic microtubule arrays. The Arabidopsis augmin complex contains both conserved and unique subunits compared with its animal counterparts .
Constitutive expression of pathogenesis-related genes 5 (CPR5)
Type: Family

This entry represents a nuclear membrane plant protein known as constitutive expression of pathogenesis-related genes 5 (CPR5, also Protein hypersenescence-1), which is part of the nuclear pore complex (NPC) and play a role in gating . It is involved in plant growth and immunity . It plays a role in the control of programmed cell death (PCD), acting as a negative regulator of the senescence and chlorotic lesions induced by biotic (e.g. pathogens) and abiotic (e.g. sugars, darkness) agents . CPR5 also promotes cell division and endoduplication through CPR5-CKI (CYCLIN-DEPENDENT KINASE INHIBITOR) signalling pathway .