SII-SWORD/CoKE huggingface dataset:
WD-repeat protein SPA1/2/3/4 (SPA1/2/3/4)
Type: Family

In Arabidopsis, SPA1/2/3/4 play a central role in suppression of photomorphogenesis. SPA1 and SPA2 predominate in dark-grown seedlings, whereas SPA3 and SPA4 prevalently regulate the elongation growth in adult plants . SPAs contain a kinase-like domain, a coiled-coil domain and the WD-repeats. SPAs and COP1 (a ring finger E3 ubiquitin ligase) can form homo- and heterodimers via their respective coiled-coil domains, and the COP1/SPA complex forms a tetramer of two COP1 and two SPA proteins . The SPA proteins can self-associate or interact with each other, forming a heterogeneous group of SPA-COP1 complexes . Besides recognizing substrates, both COP1 and SPA bind DDB1 in the CUL4 complex through their C-terminal WD-repeat domains. They serve as DDB1-CUL4-associated factors (DCAFs) similar to other substrate adaptors in CUL4-based E3 ligases. SPA1 interacts with photoreceptor cry2 via its kinase-like domain, with cry1 via its WD-repeat domain and with phytochromes possibly via both . SPAs have also been shown to regulate the phyB-PIF4 module at high ambient temperature .
ETO1-like (ETO1-like)
Type: Family

Ethylene biosynthesis is directed by a family of 1-aminocyclopropane-1-carboxylic acid (ACC) synthases (ACS) that convert S-adenosyl-l-methionine to the immediate precursor ACC. This entry represents a group of plant BTB domain containing proteins involved in the the ethylene pathway, including ETO1, EOL1 and EOL2 from Arabidopsis. They contain six tetratricopeptide repeats (TPR), and a coiled-coil motif at their C-terminal. They act together to negatively regulate ethylene synthesis by directing the degradation of type-2 ACS proteins .
DnaJ homolog subfamily C member 25-like (DNAJC25-like)
Type: Family

This entry includes DNAJC25 from humans and its homologues from other animals, yeast and plants. Its homologues in plants such as At1g61770 from Arabidopsis and OsERdj7 from rice, and ERJ5 from yeast may play a role in protein folding in the endoplasmic reticulum .
Cleavage stimulation factor subunit 1-like (CstF1-like)
Type: Family

CstF1 (also known as CstF-50) is a cleavage stimulation factor required for polyadenylation and 3'-end cleavage of pre-mRNAs . This entry also includes CstF1 homologues from plants.
J-protein Zuotin/DnaJC2 (Zuotin/DnaJC2)
Type: Family

Ribosome-associated J protein-Hsp70 chaperones promote nascent-polypeptide folding and normal translational fidelity. This entry includes J protein DnaJC2 from humans, Zuo1 from budding yeasts, and their homologues from other animals, fungi and plants . DnaJC2 stimulates the ATPase activity of Hsp70 (Ssb1/2 in yeast) . Zuo1 forms a stable heterodimeric complex termed ribosome-associated complex (RAC) with Ssz1 (an atypical Hsp70 family member, known as HspA14 in humans), this complex is then anchored to the ribosome via its Zuo1 subunit . These three proteins (Ssb, Zuo1 and Ssz1) referred to as a chaperone triad lay a role together in folding of nascent polypeptides . Moreover, Zuo1 has been shown to interact with the 40S and 60S ribosomal subunits in budding yeasts .
Ubiquitin carboxyl-terminal hydrolase 14-like (UBP14-like)
Type: Family

This entry represents ubiquitin carboxyl-terminal hydrolase 14 (UBP14) and its homologues, such as Ubp2/6 from fungi and Ubp6/7 from Arabidopsis. They are ubiquitin-specific proteases responsible for disassembling ubiquitin chains at the proteasome, cleaving ubiquitin precursors, and editing ubiquitin side chains . It has been shown that an N-terminal ubiquitin-like (UBL) domain of USP14 associates with the base of the 26S proteasome and the interaction of USP14 with the proteasome activates the catalytic activity of USP14 . It has also be shown that Ubp6 has both deubiquitinating activity and proteasome-inhibitory activity .

This entry also includes deubiquitinating enzyme ubiquitin-specific protease 28 (USP28).
Transcription factor RADIALIS-like (RADIALIS-like)
Type: Family

This entry represents a group of plant MYB transcription factors, including RADIALIS and RADIALIS-like 1-6. RADIALIS is specifically expressed in the dorsal region of developing flowers and is involved in the dorsoventral asymmetry of flowers .
Aldehyde dehydrogenase family 7 member A1-like (ALDH7A1-like)
Type: Family

This entry includes ALDH7A1 and related proteins from all domains of life. Mammalian ALDH7A1 (an alpha-aminoadipic semialdehyde dehydrogenase) is homologous to the plant turgor-responsive ALDH protein, an enzyme that protects against various forms of stress, such as salinity, dehydration, and osmotic stress . Mutations in the ALDH7A1 gene cause pyridoxine-dependent epilepsy (PDE) .
Cystathionine gamma-synthase 1/2 (CGS1/2)
Type: Family

This entry represents a group of cystathionine gamma-synthases from bacteria and plants, including CGS1/2 from Arabidopsis. CGS1 catalyses the first committed step of methionine (Met) biosynthesis .
U2 small nuclear ribonucleoprotein A' (RU2A)
Type: Family

This entry represents the U2 small nuclear ribonucleoprotein A' (U2A') from animals, fungi and plants. Human U2 snRNP contains two specific proteins, U2A' and U2B", that interact with U2 snRNA stem-loop IV . The budding yeast homologue of U2A' is known as Lea1. The yeast U2A'/U2B complex is required for pre-spliceosome formation . It has been linked to nonobstructive azoospermia (NOA), a common cause of male infertility .
Sm-like protein Lsm7/SmG (Lsm7/SmG-like)
Type: Family

The Sm and the Lsm proteins, characterised by the Sm-domain, have RNA-related functions. The Sm heptamer ring associates with four (U1, U2, U4, U5) snRNPs, while Lsm2-8 heptamer is part of the U6 snRNP. Another Lsm heptameric complex, Lsm1-7, which differs from Lsm2-8 by one Lsm protein, functions in mRNA decapping, a crucial step in the mRNA degradation pathway .
U6 snRNA-associated Sm-like protein Lsm1/8 (PTHR15588)
Type: Family

This entry represents Sm-like protein Lsm1 and Lsm8. Lsm8 is found in the nuclear Lsm2-8 complex, which associates with multiple snRNP complexes containing the U6 snRNA (U4/U6 snRNP, U4/U6.U5 snRNP, and free U6 snRNP). The Lsm2-8 complex binds and stabilizes the 3'-terminal poly(U) tract of U6 snRNA and facilitates the assembly of U4-U6 di-snRNP and U4-U6-U5 tri-snRNP .

Lsm1 can be found in the cytoplasmic Lsm1-7 complex, which associates with deadenylated mRNA and promotes decapping in the 5'-3' mRNA decay pathway .

The Sm and the Lsm proteins, characterised by the Sm-domain, have RNA-related functions. The Sm heptamer ring associates with four (U1, U2, U4, U5) snRNPs, while Lsm2-8 heptamer is part of the U6 snRNP. Another Lsm heptameric complex, Lsm1-7, which differs from Lsm2-8 by one Lsm protein, functions in mRNA decapping, a crucial step in the mRNA degradation pathway .
N-(5'-phosphoribosyl)anthranilate isomerase family (TrpF_fam)
Type: Family

N-(5'-phosphoribosyl) anthranilate isomerase (PRAI) is an enzyme that catalyses the third step of tryptophan biosynthesis.

Phosphoribosylanthranilate isomerase is monomeric and labile in most mesophilic microorganisms, but dimeric and stable in the hyperthermophile Thermotoga maritima (tPRAI) . The comparison to the known 2.0 A structure of PRAI from Escherichia coli (ePRAI) shows that tPRAI has the complete TIM- or (β/α)8-barrel fold, whereas helix α5 in ePRAI is replaced by a loop. The subunits of tPRAI associate via the N-terminal faces of their central β-barrels. Two long, symmetry-related loops that protrude reciprocally into cavities of the other subunit provide for multiple hydrophobic interactions. Moreover, the side chains of the N-terminal methionines and the C-terminal leucines of both subunits are immobilized in a hydrophobic cluster, and the number of salt bridges is increased in tPRAI. These features appear to be mainly responsible for the high thermostability of tPRAI .
Multi antimicrobial extrusion protein DinF-like (DinF-like)
Type: Family

Escherichia coli DinF is a membrane protein that has been found to protect cells against oxidative stress and bile salts . The expression of DinF is regulated as part of the SOS system. It may act by detoxifying oxidizing molecules that have the potential to damage DNA . Some member of this family have been reported to enhance the virulence of plant pathogenic bacteria by enhancing their ability to grow in the presence of toxic compounds .

This entry also includes DETOXIFICATION 42-47 (DTX42-47) from Arabidopsis. DTX42 (also known as AtMATE) is a citrate transporter critical for aluminum tolerance . DTX43 is a citrate transporter responsible for loading citrate into xylem tissues, which helps facilitate iron transport to shoots .

In general, proteins from the MATE family are involved in exporting metabolites across the cell membrane and are often responsible for multidrug resistance (MDR) . These proteins mediate resistance to a wide range of cationic dyes, fluroquinolones, aminoglycosides and other structurally diverse antibodies and drugs. MATE proteins are found in bacteria, archaea and eukaryotes. These proteins are predicted to have 12 α-helical transmembrane regions, some of the animal proteins may have an additional C-terminal helix .
Pentatricopeptide repeat-containing protein DG1/EMB2279-like (DG1/EMB2279-like)
Type: Family

This entry represents a group of chloroplastic pentatricopeptide repeat-containing proteins, including DG1 (At5g67570) and EMB2279 (At1g30610) from Arabidopsis. DG1 is involved in the regulation of early chloroplast development and chloroplast gene expression . DG1 mutants have pale young leave and reduced accumulation of plastid encoded transcripts . DG1 has been shown to interact with SIG6, a chloroplast sigma factor responsible for the transcription of plastid-encoded RNA polymerase (PEP) dependent chloroplast genes in cotyledons . DG1 plays an important role in maintaining chloroplast mRNA editing . EMB2279 is required for intron splicing of plastid rpl2 and trnK. Mutations in the EMB2279 gene result in embryo lethality due to defects in chloroplast development .
Pentatricopeptide repeat-containing protein EMB1417-like (EMB1417-like)
Type: Family

This entry represents a group of plant pentatricopeptide repeat-containing proteins, including EMB1417 (At4g21190) and At4g18975 from Arabidopsis. The EMB1417 gene has been identified as the EMBRYO-DEFECTIVE (EMB) gene .
Reticulon-like protein B17/18/21 (RTNLB17/18/21)
Type: Family

Reticulons are a family of ER-localised proteins found in a wide range of eukaryotes and have been shown to localise to the ER in many species. This entry represents a group of plant reticulon-like proteins, including RTNLB17/18/21 from Arabidopsis. RTNLB17/18/21 are reticulon proteins with an additional N-terminal domain. However, there is no function predicted or identified for the N-terminal domain of RTNLB17/18/21 .
DNAJ protein JJJ1 homolog, plant (JJJ1_plant)
Type: Family

This entry includes a group of DNAJ domain-containing proteins from plants. Their function is not clear.
2-methyl-6-phytyl-1,4-hydroquinone methyltransferase (MPBQ/MSBQ_MT)
Type: Family

This entry represents a subgroup of the SAM-binding methyltransferase family, including VTE3 (At3g63410) from Arabidopsis. VTE3 catalyses the conversion of 2-methyl-6-phytyl-1,4-hydroquinone (MPBQ) to 2,3-dimethyl-6-phytyl-1,4-hydroquinone (DMPQ, a substrate for tocopherol cyclase), and 2-methyl-6-solanyl-1,4-benzoquinone (MSBQ) to plastoquinone . This entry also includes uncharacterised proteins from bacteria and archaea.

Methyl transfer from the ubiquitous S-adenosyl-L-methionine (SAM) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms ranging from bacteria to plants and mammals. The reaction is catalysed by methyltransferases (Mtases) and modifies DNA, RNA, proteins and small molecules, such as catechol for regulatory purposes. The various aspects of the role of DNA methylation in prokaryotic restriction-modification systems and in a number of cellular processes in eukaryotes including gene regulation and differentiation is well documented.
Tetratricopeptide repeat protein SRFR1-like (SRFR1-like)
Type: Family

This entry represents a group of tetratricopeptide repeat proteins from plants and bacteria, including suppressor of RPS4-RLD 1 (SRFR1) from Arabidopsis. SRFR1 is an effector-triggered immunity suppressor associated with the EDS1 resistance pathway . The srfr1 mutants have enhanced resistance to the bacterial effector AvrRps4 . The tetratricopeptide repeat proteins from bacteria in this entry are not characterised.
Trehalose 6-phosphate OTSB-like (OTSB-like)
Type: Family

This entry represents a group of trehalose-phosphate phosphatases, including OTSB from bacteria and PPA/C/I from Arabidopsis. In E. coli, OTSB removes the phosphate from trehalose 6-phosphate (Tre6P) to produce free trehalose and catalyses the dephosphorylation of glucose-6-phosphate (Glu6P) and 2-deoxyglucose-6-phosphate (2dGlu6P) .

Arabidopsis PPA has been shown to removes the phosphate from trehalose 6-phosphate to produce free trehalose .
C2H2-type zinc-finger protein AZF1/2/3-like (AZF1/2/3-like)
Type: Family

This entry represents a group of plant Cys2/His2 (C2H2)-type zinc-finger proteins, including AZF1/2/3 and ZAT6/10 from Arabidopsis. They belong to the C1-2i subclass of zinc-finger proteins in Arabidopsis . In general they function as transcription repressors under drought, cold, and high-salinity stress conditions . AZF1 and AZF2 have been shown to negatively regulate abscisic acid-repressive and auxin-inducible genes under abiotic stress conditions . ZAT6 has been shown to regulate root development and nutrient stress responses .
Fasciclin-like arabinogalactan protein 15/16/17/18 (FLA15/16/17/18)
Type: Family

This family includes group B of Fasciclin-like arabinogalactan proteins (FLAs) from Arabidopsis, which includes FLA 15, 16, 17, 18 . They are expressed throughout plant development. FLAs are extracellular glycoproteins containing the Fascilin 1 (FAS1) domains and glycomotif regions, thought to play structural and signalling functions through a wide range of interactions in the plant extracellular matrix .
BAG-associated GRAM protein 1-like (BAGP1-like)
Type: Family

This entry represents a group of plant PH-like domain-containing proteins, including BAGP1 from Arabidopsis. BAGP1 is involved in proteolytic processing of BAG6, which is required for basal resistance against this pathogen .
Heat shock protein HSP14.7/HSP23.5/HSP23.6-like (HSP14.7/HSP23.5/HSP23.6-like)
Type: Family

This entry represents a group of HSP20-like chaperones, including mitochondrial HSP14.7/HSP23.5/HSP23.6. It also includes At4g16560 from Arabidopsis and chloroplastic HSP23 from Oxybasis rubra.
Transcription factor bHLH92/bHLH041-like (bHLH92/bHLH041-like)
Type: Family

This entry represents a group of plant putative transcription factors, including bHLH92/bHLH041 from Arabidopsis and bHLH148 from Oryza sativa subsp. japonica. They contain the basic helix-loop-helix (bHLH) domain . bHLH148 may act on an initial response of jasmonate-regulated gene expression toward drought tolerance as part of a BHLH148-TIFY11D/JAZ12-COI1A complex .
Protein PELPK1/2 (PELPK1_2)
Type: Family

This entry includes protein PELPK1/2 from Arabidopsis thaliana and similar sequences predominantly found in plants. PELPK2 is a presumptive inparalog of PELPK1 (also known as Proline-rich protein 10, At5g09530), a positive regulator of germination and plant growth. They contain 36 repeats of a unique pentapeptide (Pro-Glu-Leu|Ile|Val-Pro-Lys), named the PELPK motif , which is also found in proteins from many other angiosperms. Members of this family localized to the cell wall, being part part of the hydroxyproline-rich glycoprotein (HRGP) super-family of cell wall proteins .

This entry also includes some uncharacterised proteins from bacteria, animals and fungi.
Transcription factor IBH1-like (IBH1-like)
Type: Family

This entry represents a group of transcription factors from plants, including IBH1 (ILI1-BINDING BHLH 1), IBHL1 and related proteins such as UPBEAT1, PAR1 and PAR2 from Arabidopsis. IBH1 (also known as AtbHLH158) and IBHL1 are atypical and probable non DNA-binding bHLH transcription factors that act as transcriptional repressors that negatively regulate cell and organ elongation in response to gibberellin (GA) and brassinosteroid (BR) signaling . IBH1 forms heterodimer with BHLH49, thus inhibiting DNA binding of BHLH49. Another atypical transcription factors included in this entry are PAR1 (also termed AtbHLH165) and PAR2 (also termed AtbHLH166) that act as negative regulators of a variety of shade avoidance syndrome (SAS) responses . UPBEAT1 (also known as AtbHLH151 or EN 146), modulates the balance between cellular proliferation and differentiation in root growth .
Mediator of RNA polymerase II transcription subunit 15a/b/c-like (MED15a/b/c-like)
Type: Family

MED15 is a component of the Mediator complex, a coactivator involved in transcriptional activation. MED15 is part of the tail module of this complex and is involved in diverse metabolism and developmental pathways. In Arabidopsis although five paralogs have been reported, only three of them (AtMed15a, b and c) have expression data . AtMed15a (At1g15780) is expressed in several tissues including root, leaf, flower and seeds. AtMed15a has a KIX domain at its N terminus, which interacts with different proteins such as transcription factors, single strand nucleic acid-binding proteins and splicing factors to mediate their transcriptional responses .
Stress-response A/B barrel domain-containing protein HS1/DABB1-like (HS1/DABB1-like)
Type: Family

This entry represents a group of stress-response A/B barrel domain-containing proteins, including HS1 (also known as Protein HEAT STABLE 1 or Pop3 family protein At3g17210) and DABB1 from Arabidopsis thaliana . Proteins in this family have two stress responsive dimeric A/B barrel domains (Dabb) whose function is not yet clear . In general, stress-response A/B barrel domain-containing proteins in plants are involved in defense against fungal pathogens. This entry also includes Cannabis sativa olivetolic acid cyclase (OAC), which is an A/B barrel domain-containing protein structurally similar to HS1 and contains amino acid residues that are conserved in plant stress-responsive DABB proteins . OAC functions in concert with OLS/TKS to form olivetolic acid, an alkylresorcinolic acid that forms the polyketide nucleus of the cannabinoids .

This entry also includes related proteins from bacteria and fungi.
MACPF domain-containing protein CAD1/NSL1-like (CAD1/NSL1-like)
Type: Family

This entry represents a group of plant MACPF domain-containing proteins, including CAD1 (also known as Protein CONSTITUTIVELY ACTIVATED CELL DEATH 1) and NSL1 (also known as Protein NECROTIC SPOTTED LESIONS 1) from Arabidopsis thaliana. They play a role in plant immunity acting as negative regulators of the salicylic acid (SA)-mediated pathway of programmed cell death .
Rhodanese-like domain-containing protein 11-like (STR11-like)
Type: Family

This entry represent s a group of plant rhodanese-like domain-containing proteins, including AtStr11 from Arabidopsis. AtStr11 (At4g24750) is a chloroplastic protein with unknown function.
Cyclophilin-type peptidyl-prolyl cis-trans isomerase, E. coli cyclophilin A-like (E_coli_cyclophilin_A-like)
Type: Family

Cyclophilins exhibit peptidyl-prolyl cis-trans isomerase (PPIase) activity (

), accelerating protein folding by catalysing the cis-trans isomerisation of proline imidic peptide bonds in oligopeptides . They also have protein chaperone-like functions and are the major high-affinity binding proteins for the immunosuppressive drug cyclosporin A (CSA) in vertebrates .

Cyclophilins are found in all prokaryotes and eukaryotes, and have been structurally conserved throughout evolution, implying their importance in cellular function . They share a common 109 amino acid cyclophilin-like domain (CLD) and additional domains unique to each member of the family. The CLD domain contains the PPIase activity, while the unique domains are important for selection of protein substrates and subcellular compartmentalisation .

This entry includes the cyclophilin-type peptidyl-prolyl cis-trans isomerase mostly found in bacteria, archea and plants, including the E. coli cyclophilin A and Streptomyces antibioticus SanCyp18. Compared to the archetypal cyclophilin human cyclophilin A, these have reduced affinity for cyclosporin A. E. coli cyclophilin A has a similar peptidyl-prolyl cis-trans isomerase activity to the human cyclophilin A. Most members of this subfamily contain a phenylalanine residue at the position equivalent to human cyclophilin W121, where a tryptophan has been shown to be important for cyclophilin binding .
Cyclophilin-type peptidyl-prolyl cis-trans isomerase, cyclophilin A-like (Cyclophilin_A-like)
Type: Family

Cyclophilins exhibit peptidyl-prolyl cis-trans isomerase (PPIase) activity (

), accelerating protein folding by catalysing the cis-trans isomerisation of proline imidic peptide bonds in oligopeptides . They also have protein chaperone-like functions and are the major high-affinity binding proteins for the immunosuppressive drug cyclosporin A (CSA) in vertebrates .

Cyclophilins are found in all prokaryotes and eukaryotes, and have been structurally conserved throughout evolution, implying their importance in cellular function . They share a common 109 amino acid cyclophilin-like domain (CLD) and additional domains unique to each member of the family. The CLD domain contains the PPIase activity, while the unique domains are important for selection of protein substrates and subcellular compartmentalisation .

This entry includes eukaryotic, bacterial and archeal proteins which exhibit a peptidylprolyl cis- trans isomerases activity (PPIase, Rotamase) and in addition bind the immunosuppressive drug cyclosporin (CsA). Immunosuppression in vertebrates is believed to be the result of the cyclophilin A-cyclosporin protein drug complex binding to and inhibiting the protein-phosphatase calcineurin . This entry also includes proteins that do not have the peptidyl-prolyl cis-trans isomerase activity, such as CWC27 from humans .
Peptidase C26, gamma-glutamyl-gamma-aminobutyrate hydrolase PuuD-like (PuuD-like)
Type: Family

This entry includes gamma-glutamyl-gamma-aminobutyrate hydrolases and related proteins mostly from bacteria, archaea and plants, including PuuD from E. coli and Cj1417c from Campylobacter jejuni. They belong to the peptidase C26 family. PuuD is involved in the breakdown of putrescine via hydrolysis of the gamma-glutamyl linkage of gamma-glutamyl-gamma-aminobutyrate . Cj1417c catalyses the hydrolysis of CDP-L-glutamine to L-glutamate and cytidine diphosphoramidate and is involved in the biosynthesis of the O-methyl phosphoramidate (MeOPN) group found on the capsular polysaccharide (CPS) of C.jejuni .
Voltage-dependent anion channel-forming protein YneE/VCCN1/2-like (YneE/VCCN1/2-like)
Type: Family

This entry represents a family of voltage-dependent anion channels from bacteria and eukaryotes, formerly known as UPF0187, including Voltage-dependent anion channel-forming protein YneE from E.coli and Voltage-dependent chloride channel 1/2 from Arabidopsis, which are related to the Bestrophin family. In bacteria, these anion transporters are poorly characterised. VCCN1/2 are chloride channels critical for proton motive force (PMF) partitioning across the thylakoid membrane by anion influx into the lumen during illumination, thus being required for photoprotection under fluctuating light conditions .