SII-SWORD/CoKE huggingface dataset:
Filamin family (Filamin)
Type: Family

Filamin family consists of Filamin-A (FLN-A), Filamin-B (FLN-B) and Filamin-C (FLN-C). They are a group of actin binding proteins that may be involved in actin microfilaments organisation .

This entry also includes gelation factor AbpC from Dictyostelium discoideum and protein GAMETE EXPRESSED 2 from Arabidopsis .
Calmodulin calcium-dependent NAD kinase NADKc-like (NADKc-like)
Type: Family

Most of the proteins in this entry contain the zeta toxin domain, including NADKc from Arabidopsis and uncharacterised proteins from bacteria. NADKc is a kinase that phosphorylates NAD to produces NADP in a calmodulin calcium-dependent manner .
Large ribosomal subunit protein eL20z-like (Ribosomal_eL20z-like)
Type: Family

This entry includes eL20z, which may be a non-functional duplication of the RPL18AA gene (encodes 60S ribosomal protein L18a-1). It has been suggested to be a pseudogene, RNA seq evidence shows that this protein is transcribed .
Protein WAVE-DAMPENED 2-like (WVD2/WDL1-4)
Type: Family

In animals, Targeting Protein for Xklp2 (TPX2) is critical for mitotic spindle assembly. It has a highly conserved TPX2 central domain, an Aurora-A binding domain and a TPX2_C domain that contains a conserved pentapeptide KLEEK motif. However, in plants besides the TPX2 homologue (with three domains), several proteins were found with only the TPX2_C domain. This group of TPX2_C domain only proteins in plants has been named as WDL (or WVD2-like) proteins, as the first identified member is known as WVD2. These WDL proteins bind to microtubules; however, they have lost the function of targeting Xklp2 and were found to play roles in plant development and responses to environment cues .

This entry includes WAVE-DAMPENED2 (WVD2) and WDL1-4. WVD2, and its closest paralogue WDL1, modulate both rotational polarity and anisotropic cell expansion during organ growth and also promote clockwise root and etiolated hypocotyls coiling, clockwise leaf curling, but left-handed petiole twisting . WDL3 stabilises microtubules, playing an important role in the regulation of hypocotyl cell elongation. WDL3 levels are regulated by an ubiquitin-26S proteasome-dependent pathway in response to light and functions as a negative regulator of hypocotyl cell elongation in the light .
E3 ubiquitin protein ligase DRIP1-like (DRIP1-like)
Type: Family

DREB2A-Interacting Proteins (DRIPs) are E3 ubiquitin-protein ligases that act as negative regulators of the response to water stress. This family includes DRIP1, DRIP2 and the DRIP homologue (DRIPH) At3g23060 from Arabidopsis, which mediate ubiquitination and subsequent proteasomal degradation of the drought-induced transcriptional activator Dehydration-Responsive Element-Binding Protein 2A (DREB2A) . DRIP1 and DRIP2 are functionally redundant. 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 . The RAWUL domain is responsible for the protein interaction with DREB2A.
Ethylene-responsive transcription factor (ERF_plant)
Type: Family

This entry represents a group of plant ethylene-responsive transcription factors, including ERF1 from Nicotiana tabacum (Common tobacco), RAP2-3 (also known as AtEBP) from Arabidopsis and ERF.C.3 from Solanum lycopersicum (Tomato). They are ethylene-inducible DNA binding proteins that bind to the GCC-box pathogenesis-related promoter element . ERFC3 acts downstream of MYC2 in the jasmonate-mediated response to Botrytis cinerea infection .
F-box protein AUF1-like (AUF1-like)
Type: Family

This entry represents a group of plant F-box proteins, including AUF1 (At1g78100) and AUF2 (At1g22220) from Arabidopsis . AUF1/2 may mediate the crosstalk between auxin and cytokinin, which modifies auxin distribution and ultimately root elongation .
WRKY transcription factor, plant (WRKY_plant)
Type: Family

This entry represents a group of plant WRKY transcription factors. In Arabidopsis, WRKY1 binds to a 5'-CGTTGACCGAG-3' consensus core sequence which contains a W box, a frequently occurring elicitor-responsive cis-acting element . WRKY33 regulates the antagonistic relationship between defense pathways mediating responses to the bacterial pathogen P. syringae and the necrotrophic pathogen B.cinerea . It functions as a convergent substrate of CPK5/CPK6 and MPK3/MPK6, which cooperatively regulate camalexin (an antimicrobial compound) biosynthesis via the differential phospho-regulation of WRKY33 activity . WRKY33 also functions with WRKY25 as positive regulator of salt stress response and abscisic acid (ABA) signalling and with WRKY25/WRKY26 as positive regulator of plant thermotolerance by partially participating in ethylene-response signal transduction pathway . WRKY5 from rice acts as positive regulator of leaf senescence being involved in onset and progression of this process . It acts as negative regulator of drought tolerance by inhibiting ABA-induced stomatal closure during drought stress .
DNA glycosylase, plant (DME/ROS1)
Type: Family

DNA glycosylases are required to regulate the DNA methylation pathway at discrete regions across the plant genome, and probably protect the genome from excess methylation . Arabidopsis encodes four active demethylases with 5-methylcytosine DNA glycosylase/lyase activities, namely DEMETER (DME), DME-Like 1 (DML1)/ROS1 (Repressor of Silencing 1), DML2 and DML3 . Both ROS1 and DME actively remove DNA methylation in all methylated cytosine contexts through a base excision repair (BER) mechanism . DML2/3 and ROS1 play important roles in the regulation of nucleotide-binding leucine-rich repeat (NLR) genes, a class of important plant disease resistance genes .

DEMETER functions mainly in the central cells of female gametophytes involved in gene imprinting, which allows the expression of the maternal copy of the imprinted MEA gene before fertilization, possibly by antagonizing or suppressing DNA methylation on target promoter and acts in a sequence nonspecific manner. The other three demethylases, ROS1, DML2, and DML3, were shown to be largely active in somatic cells . ROS1 is constitutively expressed and regulates gene expression by preventing the spread of DNA methylation and transcriptional silencing from transposons and is involved in UV-B induced- and oxidative DNA damage repair . It also regulates defence genes by demethylation of RMG1 (disease resistance gene) and RLP43 (an orphan immune receptor gene) promoters .
LysM domain receptor kinase CERK1/LYK3-like (CERK1/LYK3-like)
Type: Family

Plant receptor-like kinases and receptor-like proteins (RLKs or LYRK) (

) are involved in innate immunity and symbiotic interactions in plants. Members of this family function as cell surface receptors that recognise specific molecular patterns associated with microbial activity, such as chitin oligosaccharides and peptidoglycans. These receptors play crucial roles in plant defence by detecting pathogen-associated molecular patterns (PAMPs) and microbe-associated molecular patterns (MAMPs), leading to the activation of defence genes. They are also involved in symbiotic relationships, such as the nitrogen-fixing root nodule symbiosis with rhizobia, by recognising Nod factor signals such as LYK3/4 which contains two LysM domains in the extracellular region . The family includes kinases such as CERK1 (Chitin elicitor receptor kinase 1) (

) that phosphorylate downstream partners in response to elicitation, mediating signal transduction from the extracellular to intracellular spaces and contributing to resistance against pathogenic fungi and bacteria .
Acyl carrier protein, chloroplastic (ACP_chloroplastic)
Type: Family

Acyl carrier protein (ACP) is a highly conserved cofactor protein required by Type II fatty acid synthases (FASs). Plant fatty acid biosynthesis occurs in both plastids and mitochondria . In Arabidopsis, eight gene loci can be recognized by sequence homology to encode ACP isoforms, five of which are plastidic ACPs (ptACPs), and three of which appear to be mtACPs .

This entry represents the ptACPs, which includes AtACP1-5 from Arabidopsis . From phylogenetic studies, they can be classified in two groups, one comprising AtACP1, AtACP2, AtACP3 and AtACP5, the other comprises AtACP4 and ACP homologues from related species. These proteins respond to different abiotic stresses such as salt, drought and deficiencies in nitrogen, phosphorus, potassium and iron . AtACP1 (At3g05020), AtACP2 (At1g54580), and AtACP3 (At1g54630) are near constitutively expressed in leaves, roots, and seeds, whereas AtACP4 (At4g25050) is predominantly expressed in leaves and is induced upon illumination of plants and AtACP5 (At5g27200) is preferentially expressed in roots and down-regulated by salt stress .
Terpene cyclases, class 1, plant (Terpene_cyclase_plant_C1)
Type: Family

This entry includes a diverse group of monomeric plant terpene cyclases (Tspa-Tspf) that convert the acyclic isoprenoid diphosphates, geranyl diphosphate (GPP), farnesyl diphosphate (FPP), or geranylgeranyl diphosphate (GGPP) into cyclic monoterpenes, diterpenes, or sesquiterpenes, respectively; a few form acyclic species. Terpenoid cyclases are soluble enzymes localized to the cytosol (sesquiterpene synthases) or plastids (mono- and diterpene synthases). All monoterpene and diterpene synthases have restrict substrate specificity, however, some sesquiterpene synthases can accept both FPP and GPP .

The catalytic site consists of a large central cavity formed by mostly antiparallel α-helices with two aspartate-rich regions located on opposite walls. These residues mediate binding of prenyl diphosphates, via bridging Mg2+ ions (K+ preferred by gymnosperm cyclases), inducing conformational changes such that an N-terminal region forms a cap over the catalytic core. Loss of diphosphate from the enzyme-bound substrate (GPP, FPP, or GGPP) results in an allylic carbocation that electrophilically attacks a double bond further down the terpene chain to effect the first ring closure. Unlike monoterpene, sesquiterpene, and macrocyclic diterpenes synthases, which undergo substrate ionization by diphosphate ester scission, Tpsc-like diterpene synthases catalyse cyclization reactions by an initial protonation step producing a copalyl diphosphate intermediate. These enzymes lack the aspartate-rich sequences mentioned above . Most diterpene synthases have an N-terminal, internal element (approx 210 aa) whose function is unknown.
BURP domain-containing protein (BURP)
Type: Family

The BURP domain was named after the proteins in which it was first identified: BNM2, USP, RD22, and PG1beta. It is found in the C terminus of a number of plant cell wall proteins, which are defined not only by the BURP domain, but also by the overall similarity in their modular construction. The BURP domain-containing proteins consists of either three or four modules: (i) an N-terminal hydrophobic domain - a presumptive transit peptide, joined to (ii) a short conserved segment or other short segment, (iii) an optional segment consisting of repeated units which is unique to each member, and (iv) the C-terminal BURP domain. Although the BURP domain proteins share primary structural features, their expression patterns and the conditions under which they are expressed differ. The presence of the conserved BURP domain in diverse plant proteins suggests an important and fundamental functional role for this domain . It is possible that the BURP domain represents a general motif for localization of proteins within the cell wall matrix. The other structural domains associated with the BURP domain may specify other target sites for intermolecular interactions .

Some proteins known to contain a BURP domain are listed below :

Brassica protein BNM2, which is expressed during the induction of microspore embryogenesis.

Field bean USPs, abundant non-storage seed proteins with unknown function.

Soybean USP-like proteins ADR6 (or SALI5-4A), an auxin-repressible, aluminium-inducible protein and SALI3-2, a protein that is up-regulated by aluminium.

Soybean seed coat BURP-domain protein 1 (SCB1). It might play a role in the differentiation of the seed coat parenchyma cells.

Arabidopsis RD22 drought induced protein.

Maize ZRP2, a protein of unknown function in cortex parenchyma.

Tomato PG1beta, the beta-subunit of polygalacturonase isozyme 1 (PG1), which is expressed in ripening fruits.

Cereal RAFTIN. It is essential specifically for the maturation phase of pollen development.
Squamosa promoter-binding-like protein (SBP-like)
Type: Family

This entry represents a group of DNA binding proteins, known as SBP (SQUAMOSA-PROMOTER BINDING PROTEIN) family. They are putative transcription factors characterised by a highly conserved SBP-box of 76 amino acids involved in DNA binding and nuclear localisation . They are involved in the control of early flower development .
Transcription factor ILR3-like (ILR3-like)
Type: Family

This family represents a group of plant transcription factors, including ILR3 (also known as AtbHLH105) and its closest homologues bHLH34, bHLH104 and bHLH115 from Arabidopsis . These transcription factors can form homo- and heterodimers and are involved in the positive regulation of Fe homeostasis by directly activating bHLH38, bHLH39, bHLH100, and bHLH101 expression. ILR3 can also act as a transcriptional repressor when interacting with POPEYE (PYE)/bHLH47, which plays a negative role in the Fe deficiency responses . bHLH34 and bHLH104 are also involved in the glucose-mediated and ABA signalling pathways .
Triacylglycerol lipase OBL1-like (OBL-like)
Type: Family

This family includes triacylglycerol lipase OBL1 from Arabidopsis thaliana and Nicotiana tabacum, which are homologues of the acid lipase from castor bean (RcOBL1). OBL1 is an acid GXSXG-lipase localized to lipid droplets that can hydrolyse a range of triacylglycerols without a clear preference for acyl-chains . It can also cleave 1,2-diacylglycerol, 1,3-diacylglycerol and 1-monoacylglycerol, but not phosphatidylcholine, phosphatidylethanolamine, or sterol esters . It is required for pollen tube growth. Triacylglycerol hydrolysis by OBL1 may provide acyl groups for the synthesis of membrane lipids in growing pollen tubes .
ADP-ribosylation factor GTPase-activating protein AGD14-like (AGD14-like)
Type: Family

This entry represents a group of plant ADP-ribosylation factor GTPase-activating proteins, including AGD14 from Arabidopsis. Arabidopsis contains 15 proteins with ArfGAP domains (AGDs) which can be divided into four distinct classes based on phylogenetic analysis. AGD14 belongs to class 4 together with AGD15 in which the AGD comprises almost the entire open reading frames of these proteins. In AtAGD14, the AGD is followed by an apparent membrane-spanning α-helix, suggesting this ArfGAP could be an integral membrane protein .
Putative nucleotide-diphospho-sugar transferase At1g28695/At4g15970-like (At1g28695/At4g15970-like)
Type: Family

This entry represents a group of plant uncharacterised proteins, including At1g28695 and At4g15970 from Arabidopsis. They belong to the glycosyltransferase Family 77 (

) and contain a conserved domain found in other nucleotide-diphospho-sugar transferases.
Myb/SANT-like DNA-binding domain 4 (Myb_DNA-bind_4)
Type: Domain

This presumed domain appears to be related to other Myb/SANT-like DNA binding domains. In particular

seems most related. Proteins containing this domain are greatly expanded in plants and appears in several proteins annotated as transposon proteins.
Trihelix transcription factor ASIL1/2-like (ASIL1/2-like)
Type: Family

This entry represents a group of plant transcription factors, including ASIL1/2m FIP2 and ENAP1/2 from Arabidopsis. ASIL1 functions as a negative regulator of embryonic traits in seedlings and contributes to the maintenance of precise temporal control of seed filling . ASIL2 is a trihelix transcription factor that acts downstream of miRNAs to repress the maturation program early in embryogenesis . FIP2 is a FRI interacting protein. FRI up-regulates expression of the floral repressor FLOWERING LOCUS C (FLC) . ENAP1 associates with chromatin regions associated with ethylene-responses, preserving this regions in the absence of ethylene, while in its presence, ENAP1 interacts with EIN2. This promotes histone acetylation mainly on H3K14 and H3K23, which positively regulates ethylene-responsive genes .
Protein MAINTENANCE OF MERISTEMS-like (MAIN-like)
Type: Family

This entry represents a group of plant mobile domain containing proteins. They are required for the organisation of the root apical meristem (RAM) and the shoot apical meristem (SAM). Proteins in this entry include Protein MAINTENANCE OF MERISTEMS (MAIN) and its homologues, MAIN-like 1/2 (MAIL1/2) from Arabidopsis thaliana . They are required to maintain genome stability and cell division activity in meristematic cells . MAIL1 also plays a role in cell differentiation as it acts as an important factor for cell fate determination and maintenance throughout plant development .

In Arabidopsis, MAIN possess three closely related homologues, namely MAIL1/2/3. MAIN shows high protein sequence similarity to MAIL1 and MAIL2, while MAIL3 encodes a protein with an additional putative serine/threonine-specific protein phosphatase domain , not included in this entry.
Transcription activator GLK1/2-like (GLK1/2-like)
Type: Family

This entry represents a group of plant transcriptional activators, including GLK1/2 and APRR2 from Arabidopsis. GLK1 functions with GLK2 to promote chloroplast development. They may function in photosynthetic capacity optimization by integrating responses to variable environmental and endogenous cues . APRR2 interacts with calmodulin-like protein CML9 .
G-box-binding factor-like (GBF-like)
Type: Family

This family represents a group of plant regulatory factors that bind to G-box or G-box-like motifs (5'-CCACGTGG-3') in gene promoters. They are involved in responses to fungal pathogen infection and abiotic stresses. G-box and G-box-like motifs are cis-acting elements defined in promoters of certain plant genes which are regulated by such diverse stimuli as light-induction or hormone control. In Arabidopsis thaliana, the G-group includes G-box-binding factors 1-3 and bZIP transcription factors 16/68 which have a conserved protein structure containing a highly homological basic region and a proline-rich domain in the N-terminal region . Transcription factor HBP-1a and bZIP transcription factors 1-A/B/D from wheat are also included in this entry (Zhang Y. et al. Physiol. Mol. Plant Pathol. 73:88-94(2009)).
Stem-specific protein TSJT1-like (TSJT1-like)
Type: Family

This family represents a group of DUF3700 domain containing proteins from plants, including stem-specific protein TSJT1 from Nicotiana tabacum. Their function is not clear.
Class III homeodomain-leucine zipper family (HD-Zip_III)
Type: Family

This is the Class III homeodomain-leucine zipper (HD-Zip III) family of proteins, which includes the five members from Arabidopsis thaliana (REVOLUTA, ATHB-9/PHAVOLUTA, ATHB-14/PHABULOSA, ATHB-15/CORONA and ATHB8) and its homologues from Oryza sativa (OsHOX9-10, OSHOX29, OsHOX32-33) . These proteins contain an HD-Zip domain involved in DNA binding and protein dimerisation, a START domain and a conserved C-terminal domain of unknown function. This family regulates apical embryo patterning, embryonic shoot meristem formation, organ polarity, vascular development, and meristem function. They show overlapping, antagonistic and divergent functions: PHABULOSA and PHAVOLUTA perform overlapping functions with REVOLUTA, PHABULOSA, PHAVOLUTA, and CORONA/ATHB15 genes perform overlapping functions distinct from REVOLUTA, while ATHB8 and CORONA encode functions that are both antagonistic to those of REVOLUTA within certain tissues and overlapping with REVOLUTA in other tissues .
Heme-binding peroxidase Ccp1-like (Ccp1-like)
Type: Family

This entry represents a group of heme-binding peroxidases mostly from plants and fungi, including Ccp1 from budding yeasts and APX1-6 from Arabidopsis. APX1 is a L-ascorbate peroxidase that acts as a central component of the reactive oxygen gene network of Arabidopsis . Ccp1 is a mitochondrial cytochrome-c peroxidase that acts as hydrogen peroxide sensor and modulates antioxidant defense .
DCD domain-containing protein NRP-like (NRP-like)
Type: Family

This family represents a group of plant asparagine-rich proteins containing a Development and Cell Death (DCD) domain which is present in proteins with different architectures, some of them contain additional recognisable motifs, like the KELCH repeats or the ParB domain. They are involved in stress signalling pathway that mediate cell death in response to endoplasmic reticulum (ER) stress and osmotic stress . Including in this entry are soybean DCD domain-containing proteins NRP-A/B, NRP from Arabidopsis and B2 protein from carrot. NRP was first found in soybean as a component of the early pathogen response and was induced under ER stress . In Arabidopsis, NRP contributes to the initial phase of responses to abiotic and biotic stress signals. It binds the phytochrome-associated protein phosphatase FYPP3 and facilitates FYPP3 degradation to promote abscisic acid (ABA) response, a regulatory circuit which links intracellular trafficking with ABA signaling .
Protein WVD2-like 5/6 (WDL5/6)
Type: Family

In animals, Targeting Protein for Xklp2 (TPX2) is critical for mitotic spindle assembly. It has a highly conserved TPX2 central domain, an Aurora-A binding domain and a TPX2_C domain that contains a conserved pentapeptide KLEEK motif. However, in plants besides the TPX2 homologue (with three domains), several proteins were found with only the TPX2_C domain. This group of TPX2_C domain only proteins in plants has been named as WDL (or WVD2-like) proteins, as the first identified member is known as WVD2. These WDL proteins bind to microtubules; however, they have lost the function of targeting Xklp2 and were found to play roles in plant development and responses to environment cues .

This entry includes WDL5/6 from Arabidopsis.
Patellin (PATL)
Type: Family

This is a family of proteins widely distributed across the plant kingdom. Patellin (PATL) proteins are yeast Sec14 protein (Sec14p)-like phosphatidylinositol transfer proteins (PITPs) involved in several biological processes such as plant development and stress tolerance regulation, playing a role in membrane-trafficking events . In Arabidopsis, this family consists of six members, PATL1-6, and are characterised by the presence of two conserved domains observed in other membrane trafficking-related proteins: a Sec14p-like lipid-binding domain and a GOLD following the N-terminal variable domain. The GOLD domain is found in proteins related to Golgi function, membrane homeostasis and vesicle trafficking . PATL1 is the defining member of this family, associated to the cell-plate, and has a regulatory role during cytokinesis, which is thought to be involved in clathrin-dependent endocytosis that aids cell plate remodeling and completion . These proteins are able to interact with phosphoinositides, varying their affinity among them which results their involvement in different processes and signalling pathways. PATLs also respond to auxin and play a role in the regulation of PIN1, which suggests that they play a redundant and crucial role in polarity and patterning in Arabidopsis .

This entry also includes some CRAL-TRIO domain-containing proteins from fungi.