SII-SWORD/CoKE huggingface dataset:
SNF2 domain-containing protein CLSY/DRD1 (CLSY/DRD1)
Type: Family

This entry represents a group of SNF2 domain-containing proteins from plants, including CLSY1-3 and DRD1 from Arabidopsis. CLSY and DRD1 contain a SNF2-like domain and a helicase domain near the C terminus. They are required for siRNA-directed DNA methylation in Arabidopsis . Polymerases IVa/Pol IV and Pol IVb/Pol V are plant-specific RNA polymerases involved in in multiple small RNA-mediated gene silencing pathways. CLSY1 is required for proper localization of both NRPD1 (the largest subunit of Pol IV) and RDR2 . DRD1 has been shown to mediate RNA polymerases IV and V (Pol IV and Pol V) recruitment to chromatin . Interestingly, DRD1 and Pol V appear to be required not only for RNA-directed de novo methylation, but also for full erasure of methylation when the RNA trigger is withdrawn .
Histone-lysine N-methyltransferase Set1-like (Set1-like)
Type: Family

The COMPASS complex (complex proteins associated with Set1) is conserved in yeasts and in other eukaryotes up to humans. This entry represents Set1 and its homologues. Set1 is a methyltransferase and the catalytic component of the COMPASS that produces trimethylated histone H3 at Lys(4).

The yeast COMPASS (Set1C) complex specifically mono-, di- and trimethylates histone H3 to form H3K4me1/2/3, which subsequently plays a role in telomere length maintenance and transcription elongation regulation . In yeasts, the Set1C complex consists of Set1(2), Bre2(2), Spp1(2), Sdc1(1), Shg1(1), Swd1(1), Swd2(1), and Swd3(1) .

In animals, SETD1A/B are histone methyltransferases that produce mono-, di-, and trimethylated histone H3 at 'Lys-4. However, if 'Lys-9' residue is already methylated, 'Lys-4' will not be. The 'Lys-4' methylation is a tag for epigenetic transcriptional activation . The animal COMPASS complex is composed of at least the catalytic subunit (SETD1A or SETD1B), WDR5, WDR82, RBBP5, ASH2L/ASH2, CXXC1/CFP1, HCFC1 and DPY30 .

ATXR7, the Arabidopsis homologue to Set1, is required for the expression of the flowering repressors FLC and MADS-box genes of the MAF family . ATXR7 is also involved in the control of seed dormancy and germination .
Phosphatidylinositol 4-kinase gamma 1-8 (P4KG1-8)
Type: Family

This entry includes phosphatidylinositol 4-kinase gamma 1-8 (PI4KG1-8) from Arabidopsis and related proteins. They are protein kinases that contain the PI3K/PI4K domain. AtPI4Kgamma4 (also known as PI4KG4) has been shown to interact with and phosphorylate UFD1 (ubiquitin fusion degradation 1) and RPN10 (regulatory particle non-ATPase 10) . In rice PI4KG4 (also known as OsUbDKgamma4) is involved in the control of flowering under long day conditions by promoting degradation of FTIP1 .

This entry also includes uncharacterised bacterial proteins.
ARIP4, DEXH-box helicase domain (ARIP4_DEXHc)
Type: Domain

Androgen receptor-interacting protein 4 (ARIP4) modulates androgen receptor (AR)-dependent transactivation in a promoter-dependent manner . This entry represents the DEXH-box helicase domain, which contains the ATP-binding region.
ATPase ARIP4-like (ARIP4-like)
Type: Family

This entry includes animal ARIP4 and its homologues from fungi and plants. ARIP4 contains a SNF2 ATPase domain and is an active DNA-dependent ATPase that activate AR (androgen receptor) function . The Drosophila homologue, XNP, interacts with DLP (DAXX-like protein) and is involved in heterochromatin assembly and maintenance .
Beta-arabinofuranosyltransferase RAY1-like (RAY1-like)
Type: Family

This entry includes RAY1 from Arabidopsis and some uncharacterised proteins from bacteria. RAY1 catalyses the addition of a beta-arabinofuranose residue onto a beta-galactosyl residue of an Yariv-precipitable wall polymer in vivo .
Receptor-like serine/threonine-protein kinase At4g25390-like (At4g25390-like)
Type: Family

This entry represents a group of putative receptor-like serine/threonine-protein kinases, including At4g25390, At2g45590 and At1g80870 from Arabidopsis.
Heavy metal-associated isoprenylated plant protein 4/7/8/17/18/19 (HIPP4/7/8/17/18/19)
Type: Family

This entry represents a group of heavy metal-associated isoprenylated plant proteins, including HIPP4/7/8/17/18/19 from Arabidopsis .
Pentatricopeptide repeat-containing protein BIR6-like (BIR6-like)
Type: Family

This entry represents a group of pentatricopeptide repeat-containing proteins from plants, including BIR6 (also known as At3g48250) from Arabidopsis. BIR6 is a mitochondrial protein implicated in splicing of intron 1 of mitochondrial nad7 transcripts . Small ribosomal subunit protein mS81 (rPPR8, previously known as At5g15980), is also included in this entry .
Transcription factor bHLH11/121 (bHLH11/121)
Type: Family

This entry represents a group of plant transcription factors, including bHLH11 and bHLH121 from Arabidopsis. They belong to the members of clade IVb of bHLH transcription factors. bHLH121 can bind to the promoters of the FIT (a crucial regulator of Fe-deficiency response) and bHLH Ib genes. It interacts with bHLH105 (ILR3) transcription factors and its closest homologues to positively regulate the expression of FIT . bHLH11 functions as a negative regulator of FIT-dependent Fe uptake and modulates Fe levels in Arabidopsis plants .
5'-Methylthioadenosine/S-adenosylhomocysteine nucleosidase (MTAN)
Type: Family

This entry represents 5'-Methylthioadenosine/S-adenosylhomocysteine (MTA/SAH) nucleosidase (MTAN), which plays a key role in the methionine-recycling pathway of bacteria and plants. Bacterial and plant MTANs show significant conservation in the overall structure, and the adenine- and ribose-binding sites . Two similar nucleosidases for hydrolysing MTA in Arabidopsis thaliana (AtMTAN1 and AtMTAN2) exist, but only AtMTAN2 shows markedly broad substrate specificity for hydrolysis of SAH .
Two pore calcium channel protein 1, plant (TPC1_plant)
Type: Family

In Arabidopsis, AtTPC1 mediates Ca(2+) flux and regulates germination and stomatal movement . In tobacco cells, NtTPC1 has roles in defense responses and acts as the major ROS-responsive Ca2+ channel .
E3 ubiquitin-protein ligase KEG (KEG)
Type: Family

This entry represents a group of plant proteins, including KEG from Arabidopsis. KEG is a RING-type E3 ligase and a negative regulator of abscisic acid (ABA) signaling . ABA also promotes KEG degradation via the ubiquitin dependent 26S proteasome pathway . KEG can recruit the ENHANCED DISEASE RESISTANCE1 protein to trans-Golgi network/early endosome vesicles . KEG can also ubiquitinate and mediate the degradation of MKK4 and MKK5 to regulate plant immunity .
FCS-Like Zinc finger 10/11 (FLZ10/11)
Type: Family

This entry includes FCS-like zinc finger (FLZ) 10 and 11 from Arabidopsis. They are adaptor proteins which facilitate the interaction of kinase SnRK1 with other proteins . FLZ10 has been shown to work as repressors of SnRK1 signalling .
Heat shock protein 21-like (HSP21-like)
Type: Family

This entry represents a group of heat shock proteins, including HSP21 from Arabidopsis. HSP21 interacts with plastid nucleoid protein pTAC5 and is essential for chloroplast development under heat stress by maintaining PEP (plastid-encoded RNA polymerase) function . This family also includes small heat shock proteins from bacteria.
PX domain-containing protein EREX-like (EREX-like)
Type: Family

This entry represents a group of plant PX domain-containing proteins, including EREX and EREL1/2 from Arabidopsis. EREX interacts with ARA7 and RHA1 (RAB5 members), whereas EREL1/2 was not shown to interact with these RAB5 members. EREX serves as an effector of canonical RAB5 GTPases and regulates membrane trafficking to protein storage vacuole. EREX and EREL1 act in the same trafficking and developmental events, while EREL2 has a partially redundant function with EREX and EREL1 .
GATA transcription factor 26/27 (GATA26/27)
Type: Family

This entry represents a group of GATA transcription factors, including GATA26/27 from Arabidopsis .
Probable calcium-binding protein CML48/49/50 (CML48/49/50)
Type: Family

This entry represents a group of putative plant calcium-binding proteins, including CML48/49/50 from Arabidopsis and CBP from rice. CBP functions in calcium-mediated signalling processes .
Microtubule-associated kinase-like protein RUNKEL (RUK)
Type: Family

RUNKEL is a microtubule-associated kinase-like protein, also known as Serine/threonine-protein kinase RUNKEL, involved in both phragmoplast-based cytokinesis in somatic cells and syncytial cytokinesis in reproductive cells . RUNKEL may not have kinase activity .
Putative E3 ubiquitin-protein ligase RING1a/b (RING1A/B)
Type: Family

This entry represents a group of plant putative E3 ubiquitin-protein ligases, including RING1A and RING1B from Arabidopsis. Together with LHP1, they form a PRC1-like complex, which binds trimethyl-H3K27 marked by the CLF-containing PRC2, resulting in transcriptional suppression of KNOX .
FCS-Like Zinc finger 8/MARD1 (FLZ8/MARD1)
Type: Family

The SNF1-related protein kinase 1 (SnRK1) is a heterotrimeric eukaryotic kinase that interacts with diverse proteins and regulates their activity in response to starvation and stress signals. This entry represents a group of plant FCS-Like Zinc finger proteins, including FLZ8 and MARD1 from Arabidopsis. They may act as an adapter to facilitate the interaction of SnRK1 complex with effector proteins, conferring tissue- and stimulus-type specific differences in the SnRK1 regulation pathway .
Heavy metal-associated isoprenylated plant protein 1/3/5/6 (HIPP01/3/5/6)
Type: Family

This entry represents a group of heavy metal-associated isoprenylated plant proteins, including HIPP01/3/5/6 from Arabidopsis . HIPP03 acts as an upstream regulator of the salicylate-dependent plant immunity pathway and of flowering time . HIPP06, also known as CdI19, plays an important role in the maintenance of heavy metal homeostasis and/or in detoxification by endowing plasma membranes with the capacity to serve as an initial barrier against inflow of free heavy metal ions into cells .
F-box/kelch-repeat protein KMD1-4 (KMD1-4)
Type: Family

This entry represents a group of plant F-box/kelch-repeat proteins, including KMD1-4 from Arabidopsis. They belong to the kiss me deadly (KMD) family, whose members target type-B ARR proteins for degradation. They form an S-phase kinase-associated PROTEIN1 (SKP1)/Cullin/F-box protein (SCF) E3 ubiquitin ligase complex and directly interact with type-B ARR proteins, which then regulates the transcriptional response to cytokinin . KMD1 (At1g80440, also known as KFB20), KMD2 (AT1G15670, also known KFB01) and KDM4 (also known as SKIP20) interact with four PAL isozymes and mediate their proteolytic turnover via the ubiquitination-26S proteasome pathway .
Phosphatidylglycerophosphatase and protein-tyrosine phosphatase 1-like (PTPMT1-like)
Type: Family

This entry includes phosphatidylglycerophosphatase and protein-tyrosine phosphatase 1 (PTPMT1) and its homologues from animals and plants.

Phosphatidylglycerophosphatase and protein-tyrosine phosphatase 1 (PTPMT1) regulates phospholipid biosynthesis . In mammals, it is a mitochondrial phosphatidylglycerophosphate (PGP) phosphatase that regulates cardiolipin biosynthesis .

In Arabidopsis there are two homologues, PTPMT1 and PTPMT2. They are involved in root growth and columella cells organization .
Single myb histone 1-6 (SMH1-6)
Type: Family

This entry includes single myb histone 1-6 (SMH1-6) from maize and telomere repeat-binding factor 1-5 (TRB1-5) from Arabidopsis. They are a group of proteins that bind telomere DNA repeats . This entry also includes uncharacterised proteins from fungi.
Zinc finger CCHC-type and RNA-binding motif-containing protein 1 (ZCRB1)
Type: Family

ZCRB1 is a novel multi-functional nuclear factor that may be involved in morphine dependence, cold/heat stress, and hepatocarcinoma. It is located in the nucleoplasm, but outside the nucleolus . ZCRB1 is one of the components of U11/U12 snRNPs that bind to U12-type pre-mRNAs and form a di-snRNP complex, simultaneously recognizing the 5' splice site and branchpoint sequence . ZCRB1 is characterised by an RNA recognition motif (RRM), and a CCHC-type zinc finger motif. In addition, it contains core nucleocapsid motifs, and Lys- and Glu-rich domains.
CRS2-associated factor, plant (CAF1P_plant)
Type: Family

This entry represents a group of plant CRS2-associated factors, including At4g31010/At5g54890 found in Arabidopsis mitochondrions and At2g20020/At1g23400 found in chloroplasts. They are required for the splicing of group IIB introns .
RING-H2 finger protein ATL1/ATL16-like (ATL1/ATL16-like)
Type: Family

This entry represents a group of plant RING-H2 finger proteins, including ATL1 and ATL16 from Arabidopsis. They are ubiquitin ligases that contain a RING-H2 domain . ATL1 plays a central role in regulating plant defense responses and programmed cell death . ATL16 is involved in carbon (C) and nitrogen nutrients (N) regulation and the defense response . This entry also includes ATL55 that localises to the plasma membrane lipid rafts to trigger the FB1-induced plant programmed cell death pathway .
3xHMG-box protein HMGB6/HMGB13 (HMGB6/HMGB13)
Type: Family

This entry represents a group of 3xHMG-box proteins (containing three copies of the HMG-box domain and a unique basic N-terminal domain), including 3xHMG-box1 (AT4G11080, also known as HMGB13) and 3xHMG-box2 (AT4G23800, also known as HMGB6) from Arabidopsis. Their three HMG-box domains and the basic N-terminal domain contribute to DNA binding . Their expression is induced in late G2 phase of the cell cycle, and upon nuclear envelope breakdown in prophase they rapidly associate with the chromosomes. Shortly after mitosis they are degraded and an N-terminal destruction-box mediates the proteolysis. They may play a role in the organisation of plant mitotic chromosomes .
RING-H2 finger protein ATL10/ATL72-79-like (ATL10/ATL72-79-like)
Type: Family

This entry represents a group of plant RING-H2 finger proteins, including ATL10 and ATL72-79 from Arabidopsis. They are ubiquitin ligases that contain a RING-H2 domain .
Senescence-associated carboxylesterase 101-like (SAG101-like)
Type: Family

This entry includes Senescence-associated carboxylesterase 101 (SAG101) from Arabidopsis. SAG101 forms a complex with EDS1 and PAD4 and is required for plant defense .
FCS-Like Zinc finger 12/13/14 (FLZ12/13/14)
Type: Family

This entry represents a group of plant FCS-Like Zinc finger proteins, including FLZ12/13/14 from Arabidopsis . They are adaptor proteins which facilitate the interaction of kinase SnRK1 with other proteins . The FLZ domain of FLZ12 alone has been found to be sufficient to mediate interaction with SnRK1alpha subunit .
Pentatricopeptide repeat-containing protein At1g26460-like (At1g26460-like)
Type: Family

This entry represents a group of plant pentatricopeptide repeat-containing proteins, including At1g26460 from Arabidopsis. At1g26460 is a mitochondrial protein that binds RNA .
5'-adenylylsulfate reductase-like 4/6 (APRL4/6)
Type: Family

This entry represents a group of plant 5'-adenylylsulfate reductase-like proteins, including APRL4/6 from Arabidopsis and APRL2/3/4 from rice. They contain a thioredoxin (TRX) domain .
Transcription factor RKD-like (RKD-like)
Type: Family

This entry represents a group of transcription factors, including RWP-RK domain-containing RKD1-5 from Arabidopsis. RKD1-5 are involved in the control of cell differentiation and are required for normal gametophytic development in Arabidopsis .
Ethanolamine-phosphate cytidylyltransferase (Ect1/PCYT2)
Type: Family

This entry represents a group of ethanolamine-phosphate cytidylyltransferases and related proteins, including Ect1 from budding yeasts, PCYT2 from animals and PECT1 from plants. They catalyse the second step in the synthesis of phosphatidylethanolamine (PE) from ethanolamine via the CDP-ethanolamine pathway and are involved in the maintenance of plasma membrane . In humans, mutations in the PCYT2 gene disrupt etherlipid biosynthesis and cause a complex hereditary spastic paraplegia . In plants, defects in PECT1 affect embryonic and postembryonic development in Arabidopsis .
Peptidyl-prolyl cis-trans isomerase FKBP2/11 (FKBP2/11)
Type: Family

This entry includes FKBP2/11 and related proteins from bacteria, animals, fungi and plants. They are PPIases (peptidyl-prolyl cis-trans isomerases) that catalyse the cis-trans isomerization of proline imidic peptide bonds in oligopeptides and accelerate the folding of proteins .
Beta-glucuronosyltransferase GlcAT14A/B/C (GLCAT14A/B/C)
Type: Family

This entry includes beta-glucuronosyltransferase GlcAT14A/B/C from Arabidopsis. They belong to the glycosyltransferase family 14 (GT14) . GlcAT14A is involved in the biosynthesis of type II arabinogalactan (AG) and has a role in cell elongation during seedling growth .

This entry also includes uncharacterised bacterial proteins.
Ubiquitin-protein ligase E3A/B/C-like (E3A/B/C-like)
Type: Family

This entry represents a group of E3 ubiquitin-protein ligases, including UBE3A/B/C from animals, Hul5 from budding yeasts, Etc-1 from C. elegans and UPL6/7 from Arabidopsis. They are HECT (Homologous to E6AP C terminus) domain E3 that synthesizes K29- and K48-linked chains .
ADP-ribosylation factor-like protein 2/3 (ARL2/3)
Type: Family

This entry represents a group of Arf-like small GTP-binding proteins, including ARL2/3 from animals, Cin4 from budding yeasts, Alp41 from fission yeasts and ARL2 from Arabidopsis. They are involved in microtubule-dependent processes . Despite the structural similarity of ARL2 and ARL3, they have different biochemical properties and biological functions . ARL2 plays roles in both the regulation of tubulin folding and microtubule destruction. It is also essential to a number of mitochondrial functions, including mitochondrial morphology, motility, and maintenance of ATP levels . ARL3 is required for normal cytokinesis and cilia signaling . Alp41 is essential for the cofactor-dependent biogenesis of microtubules .
NEDD8-specific protease 1/2-like (Nep1/2-like)
Type: Family

This entry represents a group of proteases from bacteria, animals, fungi and plants, including Nep1/2 from Schizosaccharomyces pombe which are orthologues of human SENP8. In Nep1/2 are deneddylating enzymes that process full-length nedd8 to its mature form and deconjugate nedd8 from targeted proteins .
Rhodanese-like domain-containing protein 10 (STR10)
Type: Family

This entry includes STR10 and related proteins from plants. The function of STR10 is not clear.
Rhodanese-like domain-containing protein 9, chloroplastic (STR9)
Type: Family

This entry includes STR9 and related proteins from plants. The function of STR9 is not clear.
WD repeat-containing protein RUP1/2 (RUP1/2)
Type: Family

This entry represents a group of plant WD repeat-containing proteins, including RUP1/2 (or EFO1/2) from Arabidopsis. EFO2 acts as a floral repressor, while EFO1 may not be directly involved in flowering, however, they have overlapping roles in regulating other developmental processes. Moreover, both EFO1/2 genes are regulated by the circadian clock .
Tetrachlorohydroquinone dehalogenase (TCHQD)
Type: Family

This entry includes bacterial tetrachlorohydroquinone dehalogenase (TCHQD) pcpC and its homologues from plants. Sphingobium chlorophenolicum pcpC is a zeta-class glutathione S-transferase that catalyses the isomerization of maleylacetoacetate to fumarylacetoacetate, which is an essential step in the catabolism of tyrosine and phenylalanine. It also catalyses the dechlorination of dichloroacetate to glyoxylate and isomerizes maleylacetone (an analog of maleylacetoacetate) and consumes dichloroacetate .
NAD(P)H-quinone oxidoreductase subunit T-like (NdhT-like)
Type: Family

This entry represents a group of DnaJ domain-containing proteins from cyanobacteria and plants, including chloroplast NAD(P)H-quinone oxidoreductase subunit T (NdhT) from Arabidopsis. Interestingly, chloroplast NDH is more similar to cyanobacterial NDH-1, which is believed to be an origin of chloroplast NDH .
Protein NEDD1 (NEDD1)
Type: Family

This entry includes NEDD1 and related proteins from plants. Arabidopsis thaliana NEDD1 is a WD40 repeat protein that interacts with the gamma-tubulin complex. It plays a role in microtubule (MT) organization during mitosis and controls gamma-TuRC positioning and function in the interphase MT arrays .
WD repeat-containing protein PCN (PCN)
Type: Family

This entry represents a group of plant WD repeat-containing proteins, including POPCORN (PCN) from Arabidopsis. PCN is required for embryo development and meristem organization. It functions in the auxin pathway, integrating auxin signaling in the organization and maintenance of the shoot and root apical meristems .
ERAD-associated E3 ubiquitin-protein ligase component HRD3 (HRD3)
Type: Family

This entry includes HRD3 and related proteins from plants. In Arabidopsis there are two homologues, HRD3A and HRD3B. HRD3 is part of the HRD1/HRD3 complex involved in the ERAD (endoplasmic reticulum and subsequently degraded by ER-associated degradation) pathway . HRD3A is involved in salt acclimation memory .
Tetratricopeptide-like repeat protein Mbb1-like (Mbb1-like)
Type: Family

This entry represents a group of tetratricopeptide-like repeat chloroplast proteins, including MBB1/NAC2 from Chlamydomonas reinhardtii and HCF107 from Arabidopsis. MBB1 is required for expression of the chloroplast psbB/psbT/psbH gene cluster . NAC2 is involved in psbD mRNA stability . HCF107 is a sequence-specific RNA binding protein involved in RNA stabilizing, RNA processing, and translational activation in chloroplast . It is required for processing, stabilization and translation of plastid-encoded psbH mRNA .
NADPH-dependent oxidoreductase AOR-like (AOR-like)
Type: Family

This entry represents a group of plant NADPH-dependent oxidoreductases, including FaQR from Fragaria ananassa and AOR from Arabidopsis thaliana. FaQR is an enone oxidoreductase involved in the biosynthesis of 4-hydroxy-2,5-dimethyl-3(2H)-furanone (HDMF or furaneol), the key flavour compound in strawberries . AOR is a NADPH-dependent reductase involved in the detoxification of reactive carbonyls .
Dehydroascorbate reductases DHAR1/2/3/4 (DHAR1/2/3/4)
Type: Family

This entry represents a group of dehydroascorbate reductases (DHARs), including DHAR1/2/3/4 from Arabidopsis. They act as thiol transferases but have no glutathione conjugating activity . They catalyse the glutathione (GSH)-dependent reduction of oxidized ascorbate (dehydroascorbate, DHA). As a result, DHARs regenerate a pool of reduced ascorbate and detoxify reactive oxygen species (ROS) . Unlike most other glutathione transferases, DHARs are monomeric . DHAR2 and DHAR4 are predicted to be cytosolic, while DHAR3 is predicted to be chloroplastic, and DHAR1 is predicted to be mitochondrial. The cytosolic DHAR is important for ozone tolerance .
Elongation factor 1-gamma, plant (EF-1-gamma_plant)
Type: Family

This entry represents the plant elongation factor EF-1 gamma subunit. It has been shown to possess glutathione S-transferase (GST) activity .
Glutathione S-transferase L1/2/3 (GSTL1/2/3)
Type: Family

This entry represents a group of plant Glutathione S-transferases, including GSTL1/2/3 from Arabidopsis. They have glutathione-dependent thiol transferase activity . GSTL1/3 are cytosolic, while GSTL2 is chloroplastic .