SII-SWORD/CoKE huggingface dataset:
Inner capsid protein lambda-1/ VP3 superfamily (Lambda-1/VP3_sf)
Type: Homologous_superfamily

The reovirus inner capsid protein lambda-1 displays nucleoside triphosphate phosphohydrolase (NTPase), RNA-5'-triphosphatase (RTPase), and RNA helicase activity and may play a role in the transcription of the virus genome, the unwinding or reannealing of double-stranded RNA during RNA synthesis. The RTPase activity constitutes the first step in the capping of RNA, resulting in a 5'-diphosphorylated RNA plus-strand. Lambda1 is an Orthoreovirus core protein, VP3 is the homologous core protein in Aquareoviruses .
Protein TRACHEARY ELEMENT DIFFERENTIATION-RELATED 6/7 (TED6/7)
Type: Family

This entry represents a group of plant proteins, including Protein TRACHEARY ELEMENT DIFFERENTIATION-RELATED 6 and 7 (TED6/7) from Arabidopsis. They are involved in the secondary cell wall formation of vessel elements .
Kinetochore protein SPC24-like (SPC24-like)
Type: Family

This entry includes SPC24 homologue, MUN (MERISTEM UNSTRUCTURED), from Arabidopsis. SPC24 is part of the outer kinetochore complex NDC80. In Arabidopsis, MUN interacts with components of the NDC80 complex and is required for chromosome segregation to ensure proper cell division .
Protein SENSITIVE TO UV 2 (SUV2)
Type: Family

SUV2 (SENSITIVE TO UV 2) is a putative plant ATRIP homologue that is a component of the ATR-dependent cell checkpoint response . The suv2 mutant is defective in cell-cycle arrest in response to DNA damage .
BTB/POZ domain-containing protein At1g04390-like (At1g04390-like)
Type: Family

This entry represents a group of plant BTB/POZ domain-containing proteins, including At1g04390 from Arabidopsis . Its function is not clear.
Small ribosomal subunit protein uS3m, plant (Ribosomal_uS3m_plant)
Type: Family

This entry includes the small ribosomal subunit protein uS3m, which is found in plant mitochondria .
Cytochrome c biogenesis CcmF C-terminal-like mitochondrial protein (CCMFC)
Type: Family

This entry represents a group of plant proteins, including CCMFC from plants. CCMFC foms a complex with CCMFN1, CCMFN2 and CCMH that performs the assembly of heme with c-type apocytochromes in mitochondria .
Ankyrin repeat protein SKIP35 (SKIP35)
Type: Family

This entry represents a group of plant ankyrin repeat proteins, including SKIP35 from Arabidopsis. The function of SKIP35 is not clear.
Large ribosomal subunit protein bL32, bacterial type (Ribosomal_bL32_bact)
Type: Family

This entry represents 50S large ribosomal subunit protein bL32 from bacteria. It also includes 60S ribosomal protein bL32m from the protozoa Reclinomonas americana.

Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.

Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome .
Large ribosomal subunit protein bL32, plant/cyanobacteria type (Ribosomal_bL32_plant/cyanobact)
Type: Family

This entry includes 50S large ribosomal subunit protein bL32c from plants chloroplasts and bL32 from cyanobacteria.

Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.

Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome .
Classical arabinogalactan protein (AGP)
Type: Family

Arabinogalactan-proteins (AGPs) are cell wall proteoglycans widely distributed in the plant kingdom. They are thought to have important roles in various aspects of plant growth and development. AGPs are divided into two classes depending upon their core protein: 'classical' and 'nonclassical' AGPs. Classical AGPs contain hydroxyproline (Hyp), Ala, Ser, Thr and Gly as the major amino acid constituents . This entry represents a group of classical arabinogalactan proteins, including AGP1/2/3/4/5/7/10 from Arabidopsis .
Ribulose bisphosphate carboxylase/oxygenase activase-like (RCA-like)
Type: Family

This family represents ribulose bisphosphate carboxylase/oxygenase activase (Rubisco activase), which is a metabolic repair enzyme that acts as a molecular chaperone to remodel inhibited active sites of Rubisco, releasing tightly bound sugar phosphates . This family also includes Protein POST-ILLUMINATION CHLOROPHYLL FLUORESCENCE INCREASE (PIFI, At3g15840), which is involved in NAD(P)H dehydrogenase complex-mediated chlororespiratory electron transport that mediates electron flow from stromal reductants to the plastoquinone (PQ) pool during chlorophyll fluorescence increase after turning off actinic light. Its C-terminal redox-modulated domain is similar to that of the 46-kD isoform of Rubisco activase .
Tetratricopeptide repeat protein POLLENLESS 3/SULFUR DEFICIENCY-INDUCED 1 (MS5/SDI1)
Type: Family

This entry represents a group of plant tetratricopeptide repeat proteins, including POLLENLESS 3 (also known as MS5) and SULFUR DEFICIENCY-INDUCED 1 (SDI1). MS5 is involved in the regulation of cell division after male meiosis I and II to facilitate exit from meiosis and transition to G1. MS5 mutants are male sterile, pollen tetrads undergo an extra round of division after meiosis II without chromosome replication, resulting in chromosome abnormalities [

, . SDI1 is involved in the utilization of stored sulphate pools under sulphur-limiting conditions .
CLV3/ESR signal peptide family (CLV3/ESR)
Type: Family

This entry represents a group of CLAVATA3/ESR (CLE)-related proteins, including FON2 (FLORAL ORGAN NUMBER2) from rice, CLAVATA 3 from Arabidopsis and CLE-4D from Globodera rostochiensis. In plants, they have diverse roles in plant growth and development.

FON2 is a pobable extracellular signal that regulates meristem maintenance. May function as a putative ligand for a receptor complex including FON1. Regulates the size of the floral meristem and the number of floral organs .

CLAVATA3 may act as a ligand for the CLV1 receptor kinase in the regulation of stem cell specification at shoot and flower meristems. It is a secreted protein, with an N-terminal signal sequence and a conserved C-terminal domain of 15 amino acids, termed the CLE (CLV3/ESR-related) domain .

In potato cyst nematode, Globodera rostochiensis, CLE-4D mimics host plant CLE extracellular signal peptides and facilitates parasitism .
Succinate dehydrogenase subunit 4, mitochondrial (SDH4)
Type: Family

Complex II [succinate dehydrogenase (succinate-ubiquinone oxidoreductase); SDH] is the only enzyme shared by both the electron transport chain and the tricarboxylic acid (TCA) cycle in mitochondria. SDH is a heterotetrameric protein complex, anchored to the inner mitochondrial membrane by two integral membrane proteins, SDH3 and SDH4. The SDH3/SDH4 dimer binds to subunit SDH2, which contains three iron-sulfur (Fe-S) clusters and is assembled with the catalytic subunit SDH1 . These membrane proteins (SDH1-4) are structurally and evolutionarily related, and include three membrane-spanning helices each, forming a conserved six-helix bundle that binds a heme group .

This entry represents succinate dehydrogenase 4 (SDH4) from plants.
Inactive poly [ADP-ribose] polymerase RCD1/SRO1-5 (RCD1/SRO1-5)
Type: Family

This family represents plant-specific inactive ADP-ribosyltransferases that regulate oxidative stress, hormonal and developmental responses, including RCD1 (RADICAL-INDUCED CELL DEATH1) and the probable inactive poly [ADP-ribose] polymerases SRO (SIMILAR TO RCD) 1-5. RCD1 is required for embryogenesis, vegetative and reproductive development, and abiotic stress responses . These proteins have an N-terminal WWE domain (present in several but not all members) followed by a poly(ADP-ribose) polymerase domain, and a C-terminal RCD1, SRO and TAF4 (RST) domain . RST is a protein-protein interaction domain suggested to be critical for the interaction with several, mostly plant-specific transcription factors .
Glycoside hydrolase family 17, plant (Glyco_hydro_17_plant)
Type: Family

O-Glycosyl hydrolases (

) are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families . This classification is available on the CAZy (CArbohydrate-Active EnZymes) website.

This family represents plant members of the Glycoside hydrolase family 17

, which comprises enzymes with several known activities; endo-1,3-beta-glucosidase (

); lichenase (

); exo-1,3-glucanase (

).
Protein RESISTANCE TO PHYTOPHTHORA 1, chloroplastic (RPH1)
Type: Family

This entry represents a group of plant proteins, including RPH1 from Arabidopsis. RPH1 is a chloroplast protein that plays a role in immune reactions in response to pathogen Phytophthora brassicae .
Protein PLASTID TRANSCRIPTIONALLY ACTIVE 10 (PTAC10)
Type: Family

This entry represents a group of plant proteins, including PTAC10 from Arabidopsis. PTAC10 is a component of the PEP (plastid-encoded RNA polymerase) complex, which transcribes photosynthesis-related genes and plastid tRNAs during later developmental stages . PTAC10 contains a single S1 RNA-binding domain. PTAC10 knock-out lines have been shown to display an albino phenotype and impaired chloroplast development. PTAC10 is essential for plastid gene expression in Arabidopsis and can be phosphorylated by cpCK2. Phosphorylation of pTAC10 could enhance its RNA-binding activity .
Protein PUTATIVE RECOMBINATION INITIATION DEFECT 1 (PRD1)
Type: Family

This entry represent a group of plant proteins, including AtPRD1 from Arabidopsis. AtPRD1 is required for meiotic double strand break formation . AtPRD1 is homologous to MEI1 of humans and mice and contains a conserved N-terminal region that can interact with AtSPO11-1 and itself .

In flowering plants, gametophyte formation relies on meiosis. In meiosis I, the homologous chromosomes are separated into two daughter cells. In meiosis II, the sister chromosomes are then separated into newly formed daughter cells. During prophase I, several events occurs: sister chromatid cohesion, homologous chromosome synapsis, recombination, crossover formation and chromosome segregation. Homologous recombination is initiated from the formation of DNA double-strand breaks (DSBs). The formation of DSBs is catalyzed by Spo11 and its homologues. So far, six Arabidopsis proteins, AtSPO11-1, AtSPO11-2, AtPRD1, AtPRD2, AtPRD3 and AtDFO, have been shown to be involved in DSB formation .
Protein DOUBLE-STRAND BREAK FORMATION (DFO)
Type: Family

This entry represent a group of plant proteins, including AtDFO from Arabidopsis. AtDFO is a plant-specific protein involved in DNA double-strand break formation during meiosis .

In flowering plants, gametophyte formation relies on meiosis. In meiosis I, the homologous chromosomes are separated into two daughter cells. In meiosis II, the sister chromosomes are then separated into newly formed daughter cells. During prophase I, several events occurs: sister chromatid cohesion, homologous chromosome synapsis, recombination, crossover formation and chromosome segregation. Homologous recombination is initiated from the formation of DNA double-strand breaks (DSBs). The formation of DSBs is catalyzed by Spo11 and its homologues. So far, six Arabidopsis proteins, AtSPO11-1, AtSPO11-2, AtPRD1, AtPRD2, AtPRD3 and AtDFO, have been shown to be involved in DSB formation .
COFACTOR ASSEMBLY OF COMPLEX C SUBUNIT B CCB2, chloroplastic (CCB2)
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.
Stress enhanced protein 2, chloroplastic (SEP2)
Type: Family

This entry represents a family of plant proteins, including Stress enhanced protein 2 (Sep2), which is related to the chlorophyll a/b-binding gene family members. Its transcript was present under low light conditions, but their level increased 4- to 10-fold during illumination of plants with high-intensity light . It may be involved in non-photochemical quenching, a process that maintains the balance between dissipation and utilization of light energy to minimise generation of oxidising molecules, thereby protecting the plant against photo-oxidative damage.
TATA-binding protein-associated factor Mot1 (Mot1)
Type: Family

The TATA-binding protein (TBP) is a major target for transcriptional regulation. Mot1, a Swi2/Snf2-related ATPase, dissociates TBP from DNA in an ATP dependent process . The N-terminal domain of Mot1 has been shown to bind TBP, NC2 and DNA. Its ATPase domain is at the C terminus .
Senescence-associated protein AAF-like, chloroplastic (AAF-like)
Type: Family

This entry represents a group of plant senescence-associated proteins, including AAF from Arabidopsis, SPA15 from Ipomoea batatas (sweet potato) and OSA15 from rice. They are involved in regulating leaf senescence .
Disease resistance protein, plants (Disease_R_plants)
Type: Family

This entry represents a group of plant disease resistance proteins.

Plants are attacked by a range of phytopathogenic organisms, including viruses, mycoplasma, bacteria, fungi, nematodes, protozoa and parasites. Resistance to a pathogen is manifested in several ways and is often correlated with a hypersensitive response (HR), localised induced cell death in the host plant at the site of infection . The induction of the plant defence response that leads to HR is initiated by the plants recognition of specific signal molecules (elicitors) produced by the pathogen; R genes are thought to encode receptors for these elicitors. RPS2, N and L6 genes confer resistance to bacterial, viral and fungal pathogens.

Sequence analysis has shown that they contain C-terminal leucine-rich repeats, which are characteristic of plant and animal proteins involved in protein-protein interactions . In addition, the sequences contain a conserved nucleotide-binding site towards their N-terminal.
ATP synthase protein YMF19 (YMF19-like)
Type: Family

YMF19 is a subunit of the mitochondrial ATPase, F0 complex .
FIPS5/FIPS3-like (FIPS5/FIPS3-like)
Type: Family

This entry includes FIPS5 and FIPS3 from Arabidopsis, components of the cleavage and polyadenylation specificity factor (CPSF) complex that plays a key role in pre-mRNA 3'-end formation, recognising the AAUAAA signal sequence and interacting with poly(A) polymerase and other factors to bring about cleavage and poly(A) addition. FIPS5 is an homologue of yeast Fip1, which is a subunit providing a bridge of sorts between poly(A) polymerase, other subunits of the polyadenylation apparatus, and the substrate RNA. It is an RNA-binding protein that plays an role in plant development and stress responses .
Homeobox-DDT domain protein RLT1-3 (RLT1-3)
Type: Family

This entry represents a family of plant proteins, including the Homeobox-DDT domain proteins RLT1-3 from Arabidopsis thaliana.

The AtISWI chromatin remodelling complex physically interacts with RLTs, and this prevents plants from activating the vegetative-to-reproductive transition early by regulating several key genes that contribute to flower timing . RLT2 may also be involved in the transcriptional regulation of endogenous seed genes .
DnaJ homologue subfamily C, GRV2/DNAJC13 (GRV2/DNAJC13)
Type: Family

This entry represents a group of DnaJ homologue subfamily C proteins, including GRV2 from Arabidopsis and DNAJC13 (also known as RME-8) from humans. They are involved in endocytosis. GRV2 functions in vesicle trafficking from the multivesicular body/pre-vacuolar compartment to the lytic vacuole . In Arabidopsis grv2 mutants display enlarged aggregated endosomes, defective vacuole biogenesis and embryogenesis, and reduced gravitropic responses . DNAJC13 plays a role in the endosomal transport machinery, in which it coordinates the activity of the WASH complex with the function of the retromer SNX dimer to control endosomal tubulation .

DNAJC13 has been linked to Parkinson disease . In humans, DNAJC13 localizes to early endosomal compartments via an N-terminal PI(3)P targeting motif and binds the co-chaperone Heat shock cognate-70 (Hsc70) through the central J domain, whereas the remainder interacts with the BAR-domain containing sorting nexin 1 (SNX1) protein and the FAM21 subunit of the WASH complex
.
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, plant/fungi (NDUFB2_plant/fungi)
Type: Family

This entry represents NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2 from plants and fungi .

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2 is an accessory subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I), that is believed not to be involved in catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone .
Lysine-rich arabinogalactan protein AGP9/17/18 (AGP9/17/18)
Type: Family

This entry represents a subgroup of plant lysine-rich arabinogalactan proteins, including AGP9/17/18 from Arabidopsis. They are members of the lysine-rich arabinogalactan protein (AGP) subfamily within the hydroxyproline-rich glycoprotein (HRGP) superfamily. AGPs are hyperglycosylated proteins implicated in different aspects of plant growth and development. Protein backbones of AGPs are rich in Pro/Hyp (hydroxyproline), Ser, Ala and Thr and are modified by the addition of type II arabinogalactan polysaccharides and arabinose oligosaccharides to Hyp residues . They are predicted to contain the glycosylphosphatidylinositol (GPI) anchor and are localized to the plasma membrane. AtAGP18 is involved in a signal transduction pathway regulating plant growth and development .
O-FUCOSYLTRANSFERASE1-like (AtOFT1-like)
Type: Family

This entry represents a group of putative plant O-Fucosyltransferases (POFTs), including O-FUCOSYLTRANSFERASE1 (AtOFT1, At3g05320) from Arabidopsis. Interestingly, oft1 mutant pollen tubes are ineffective at penetrating the stigma-style interface leading to a drastic reduction in seed set and a nearly 2000-fold reduction in pollen transmission .
Photosynthetic NDH subunit of subcomplex B 1, chloroplastic (PNSB1)
Type: Family

PNSB1 is a subunit of the chloroplast NAD(P)H dehydrogenase complex that shuttles electrons from NAD(P)H:plastoquinone, via FMN and iron-sulfur (Fe-S) centers, to quinones in the photosynthetic chain and possibly in a chloroplast respiratory chain .
SEED MATURATION PROTEIN 1 (SMP1)
Type: Family

Secondary dormancy is an adaptive trait arising in previously non-dormant seeds due to unfavourable environmental conditions during germination. The SEED MATURATION PROTEIN1 (SMP1; AT3G12960) is involved in seed maturation and dormancy maintenance after high temperature fluctuation .
Large ribosomal RNA subunit accumulation protein YceD homologue 2, chloroplastic (YceD_plant)
Type: Family

This entry represents a group of plant YceD homologues, including At3g19800 from Arabidopsis. Its function is not clear.
Kinesin-like protein KIF15/KIN-12 (KIF15/KIN-12)
Type: Family

This entry represents a group of kinesin-like proteins, including KIF15 from animals and KIN-12A-G from plants. KIF15 homologue in Xenopus, Xklp2, is required for centrosome separation during mitosis . KIN-12E has been shown to regulate metaphase spindle flux and help control spindle size in Arabidopsis . KIN12 are plus-end directed kinesin-like motor enzymes that plays a critical role in the organization of phragmoplast microtubules during cytokinesis .
Uncharacterized mitochondrial protein AtMg00030-like (AtMg00030-like)
Type: Family

This entry represents a group of uncharacterised mitochondrial proteins from plants, including ATMG00030 from Arabidopsis.