SII-SWORD/CoKE huggingface dataset:
Protein DEK (DEK)
Type: Family

Protein DEK is an abundant and ubiquitous chromatin protein in multicellular organisms (not in yeast) . It preferentially binds to superhelical and cruciform DNA, and induces positive supercoils into closed circular DNA . This protein has two DNA binding domains, the SAP/SAF box located at the centre of the protein, and the second one at the C-terminal, which contains several phosphorylation sites important for its activity. It is involved in cell proliferation, differentiation, senescence and apoptosis, being associated with cancers and autoimmune diseases and a possible therapeutic drug target . In humans DEK can be secreted by macrophages, and the secreted DEK regulates the proliferation of hematopoietic stem cells and hematopoietic progenitor cells through CXCR2 signaling .
NAD(P)H-quinone oxidoreductase subunit U, chloroplastic (NdhU_chloroplastic)
Type: Family

This entry represents a group of chaperone DnaJ-domain containing proteins, including NdhU (also known as CRRL, At5g21430) from Arabidopsis. NdhU is a subunit of chloroplast NDH, which 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 .
Uncharacterized protein At5g03900-like (At5g03900-like)
Type: Family

This entry represents a group of proteins from plants and bacteria, including At5g03900 from Arabidopsis. At5g03900 is an uncharacterised chloroplastic protein.
Divinyl reductase-like (DVR-like)
Type: Family

This entry represents a group of NAD(P)-binding proteins from plants and bacteria, including divinyl reductase (DVR) from higher plants. DVR converts 8-vinyl groups on various chlorophyll intermediates to ethyl groups, which is indispensable for chlorophyll biosynthesis. Interestingly, DVR proteins from different species have diverse and differing substrate preferences .
LETM1/MDM38-like (LETM1/MDM38-like)
Type: Family

This family represents a group of LETM1-like mitochondrial inner membrane proteins, including LETM1/LETM2 from mammals and YLH47/MDM38 from yeasts

LETM1 is a proton/calcium antiporter that mediates proton-dependent calcium efflux from mitochondrion . LETM2 is preferentially expressed in testis and sperm. In humans, deletion of LETM1 causes Wolf-Hirschhorn syndrome .
Group 2 truncated hemoglobin GlbO/Two-on-two hemoglobin-3-like (GlbO/GLB3-like)
Type: Family

This entry represents truncated haemoglobin group 2 proteins, including GlbO (also known as Hb) from Mycobacterium and Glb3 from Arabidopsis . Truncated hemoglobins (TrHbs) have a truncated 2-over-2 rather than the canonical 3-over-3 α-helical sandwich fold, found in eubacteria, cyanobacteria, protozoa and plants, but not in animals or yeast . The variability of the amino acid residues of the heme pocket suggested their partition into three groups that share less than 30% sequence similarity with each other .

Glb3 is a nuclear-encoded truncated haemoglobin from plants that appears more closely related to HbO than HbN. Glb3 from Arabidopsis thaliana exhibits an unusual concentration-independent binding of oxygen and carbon dioxide .
Protein IWS1 homolog 1/2 (IWS1/2)
Type: Family

This entry represents a group of IWS1 plant homologues, including AtIWS1/2 from Arabidopsis. AtIWS1, also known as HNI9, is an evolutionary conserved component of the RNA polymerase II complex. It plays a role in N signaling by regulating several hundred N-responsive genes in roots . It interacts with transcription factor BES1 and is involved in plant steroid hormone brassinosteroid regulated gene expression .
Calcium-binding protein KIC/PBP1/KRP1 (KIC/PBP1/KRP1)
Type: Family

This entry represents a group of plant calcium-binding proteins, including KRP1/PBP1/KIC from Arabidopsis. KIC interacts with kinesin-like calmodulin binding protein (KCBP) and modulates its activity in response to changes in cytosolic Ca2 and regulates trichome morphogenesis .
EG45-like domain containing protein, plant (EGC1/2)
Type: Family

This entry represents a group of EG45-like domain containing proteins, including EGC1/2 from Arabidopsis and CjBAp12 from Citrus jambhiri. EGC2, also known as AtPNP-A, is an immunoreactant plant natriuretic peptide (irPNP) analog . It shares some similarity with the cell wall loosening expansins but does not contain the carbohydrate-binding wall anchor. It signals via the second messenger cyclic guanosine 3',5'-monophosphate and modulates ion and water transport and homeostasis. It is secreted into the apoplastic space in response to stress and can enhance its own expression .
F-box protein At5g39250-like (At5g39250-like)
Type: Family

F-box proteins regulate a number of cellular processes, including cell cycle transition, transcriptional regulation and signal transduction, by playing roles in Skp1p-cullin-F-box protein (SCF) complexes or non-SCF complexes . F-box proteins have also a role of receptors recruiting substrates into a Skp1/Cdc53/Cdc34 complex for ubiquitination . The two largest classes of F-box proteins either contain WD-40 repeats like Cdc4 or leucine-rich repeats (LRR) .

The function of At5g39250 is not clear. It has been found to interact with ASK1, indicating that it might be a component of the SCF complex .
Peptidyl-prolyl cis-trans isomerase FKBP19-like (FKBP19-like)
Type: Family

This entry represents a group of predicted peptidyl-prolyl cis-trans isomerases, including AtFKBP19 from Arabidopsis. AtFKBP19 is a chloroplastic protein .
Protein MODIFIER OF SNC1 11 (MOS11)
Type: Family

MOS11 contributes to the transfer of mature mRNA from the nucleus to the cytosol . In Arabidospis, the THO/TREX component TEX1 interacts with MOS11 and modulates mRNA export and alternative splicing events .
Transcription factor Tfc3-like (Tfc3-like)
Type: Family

This entry includes a group of transcription factors, including Tfc3 from budding yeast, Sfc3 from fission yeasts and TF3C1 (also known as TFIIIC220) from mammals .

Tfc3 (also known as Tau138) is one of three subunits of the tauB subcomplex of yeast transcription factor IIIC (TFIIIC) that binds boxB DNA promoter sites of tRNA and similar genes. TFIIIC assembles the initiation complex TFIIIB-TFIIIC-tDNA, sufficient for RNA polymerase III recruitment and function. Tfc3 is essential for cell viability as it is required for RNA polymerase III-mediated transcription.
Pheophytinase, chloroplastic (PPH_chloroplastic)
Type: Family

This entry represents a group of pheophytinases from plants, including PPH, a chloroplast-located and senescence-induced hydrolase widely distributed in algae and land plants. In Arabidopsis, PPH (also known as CRN1) specifically dephytylates the Mg-free chlorophyll pigment, pheophytin (phein), yielding pheophorbide . It plays a crucial role in Chlorophyll degradation during leaf senescence .
Protein-tyrosine-phosphatase IBR5-like (IBR5-like)
Type: Family

This entry includes a group of plant protein-tyrosine-phosphatases, such as IBR5 from Arabidopsis. IBR5 is a dual-specificity MAPK phosphatase that modulates phytohormone signal transduction and support a link between auxin and abscisic acid signaling pathways .
Thylakoid lumenal 15kDa protein 1-like (At2g44920-like)
Type: Family

This entry represents a group of pentapeptide repeat containing proteins (PRPs) from plants and cyanobacteria, including At2g44920 (also known as p15) from Arabidopsis . PRP structures are dominated by four-sided right-handed β-helices typically consisting of mixtures of type II and type IV β-turns. At2g44920 is a thylakoid lumenal protein that consists of 25 pentapeptide repeats capped by N- and C-terminal α-helices. Unlike other PRPs, At2g44920 consists exclusively of type II β-turns .
EDS1-like (EDS1-like)
Type: Family

Proteins in this entry contain the highly conserved domain known as the EP domain, which consists of hydrophobic interactions, salt bridges, and an extensive hydrogen bonding network. In Arabidopsis EDS1 (ENHANCED DISEASE SUSCEPTIBILITY1, At3g48090) is a positive regulator of basal resistance and of effector-triggered immunity specifically mediated by Toll-interleukin-1 receptor-nucleotide binding-leucine-rich repeat (TIR-NB-LRR) resistance proteins . EDS1 associations with senescence-associated gene 101 (SAG101) or phytoalexin deficient 4 (PAD4) in separate complexes. Despite its homology to eukaryotic lipases, the catalytic activity of EDS1 is dispensable for immune function .

This entry includes EDS1, EDS1L and EDS1B from Arabidopsis.
Phosphatidylinositol N-acetylglucosaminyltransferase subunit H (PIG-H)
Type: Family

This entry also includes the PIG-H homologues from S. cerevisiae and S. pombe Gpi15 .

Phosphatidylinositol N-acetylglucosaminyltransferase subunit H (PIG-H, also known as Phosphatidylinositol-glycan biosynthesis class H protein) is part of the glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex that catalyses the transfer of N-acetylglucosamine from UDP-N-acetylglucosamine to phosphatidylinositol and participates in the first step of GPI biosynthesis .
Protein WVD2-like 7 (WDL7)
Type: Family

This entry includes WDL7 from Arabidopsis and related proteins. WDL7 is a TPX2 C-terminal domain containing protein. Similar to WVD2 and other WVD2-like proteins, it contains the KLEEK-motif, which is typical for microtubule-binding proteins . The function of WDL7 is not clear.
ATP-dependent Clp protease ATP-binding subunit CLPT1/2 (CLPT1/2)
Type: Family

This entry includes a group of plant proteins, including CLPT1/2 from Arabidopsis. CLPT1/2 are accessory proteins regulating the assembly of the plastidial Clp protease system . During assembly of the Clp proteolytic core, ClpT1 first binds to the P-ring (consisting of ClpP3-6 subunits) followed by ClpT2, and only then does the P-ring combine with the R-ring (ClpP1, ClpR1-4 subunits) . CLPT1/2 share structural similarities to the N-domains of bacterial ClpA/C chaperones .
Protein SWEETIE (SWEETIE)
Type: Family

This entry represents a group of plant proteins, including protein SWEETIE from Arabidopsis. SWEETIE may be involved in the general control of sugar flux and modulates many important processes such as morphogenesis, flowering, stress responses and senescence .
Alkaline ceramidase, plant (ACER_plant)
Type: Family

This entry represents a group of plant alkaline ceramidases, including AtACER from Arabidopsis. AtACER is an alkaline ceramidase that hydrolyses ceramide to long-chain base (LCB). It is involved in sphingolipid metabolism, disease resistance, nutrient limitation, and response to salt stress .
Protein DYAD/AMEIOTIC 1 (DYAD/AMEIOTIC1)
Type: Family

This entry represents a group of plant proteins, including DYAD from Arabidopsis and AMEIOTIC 1 from Zea mays (AM1) and Oryza sativa (OsAM1). DYAD, also known as SWITCH1, is required for the establishment of sister chromatid cohesion and for bivalent formation at meiosis . It may also be required for meiotic recombination initiation . AM1 plays an important role in multiple early meiotic processes and may be required for the initiation of meiosis . OsAM1 has a coiled-coil domain in its central region, it is required for the leptotene-zygotene transition step in meiocytes and plays an important role in the building the proper chromosome structure at the beginning of meiosis .
Aquaporin SIP1-1/2-like (SIP1-1/2-like)
Type: Family

Aquaporins are water channels, present in both higher and lower organisms, that belong to the major intrinsic protein family. Most aquaporins are highly selective for water, though some also facilitate the movement of small uncharged molecules such as glycerol . In higher eukaryotes these proteins play diverse roles in the maintenance of water homeostasis, indicating that membrane water permeability can be regulated independently of solute permeability. In microorganisms however, many of which do not contain aquaporins, they do not appear to play such a broad role. Instead, they assist specific microbial lifestyles within the environment, e.g. they confer protection against freeze-thaw stress and may help maintain water permeability at low temperatures . The regulation of aquaporins is complex, including transcriptional, post-translational, protein-trafficking and channel-gating mechanisms that are frequently distinct for each family member.

Structural studies show that aquaporins are present in the membrane as tetramers, though each monomer contains its own channel . The monomer has an overall "hourglass" structure made up of three structural elements: an external vestibule, an internal vestibule, and an extended pore which connects the two vestibules. Substrate selectivity is conferred by two mechanisms. Firstly, the diameter of the pore physically limits the size of molecules that can pass through the channel. Secondly, specific amino acids within the molecule regulate the preference for hydrophobic or hydrophilic substrates.

Aquaporins are classified into two subgroups: the aquaporins (also known as orthodox aquaporins), which transport only water, and the aquaglyceroporins, which transport glycerol, urea, and other small solutes in addition to water .

This entry represents a group of plant aquaporins, including SIP1-1 and SIP1-2 from Arabidopsis. They are water channels required to facilitate the transport of water across cell membrane .
Glycosyltransferase-like KOBITO 1 (KOBITO1-like)
Type: Family

This entry represents a group of glycosyltransferase-like proteins, including KOBITO1, At2g41451 and At3g57200 from Arabidopsis. KOBITO1 (also known as ELONGATION DEFECTIVE 1 or ABA INSENSITIVE 8) has been implicated in cellulose biosynthesis and hypocotyl elongation. It serves as a negative regulator of photomorphogenesis .
Ent-kaurene oxidase, chloroplastic (KO_chloroplastic)
Type: Family

This entry represents a group of ent-kaurene oxidases from plants, including AtKO1 (also known as CYP701A3) from Arabidopsis. KO (kaurene oxidase) is a multifunctional cytochrome P450 catalysing three sequential oxidations in gibberellin phytohormone biosynthesis. These serve to transform the C4alpha methyl of the ent-kaurene olefin intermediate into the carboxylic acid moiety of ent-kauren-19-oic acid .
Aquaporin SIP2-1-like (SIP2-1-like)
Type: Family

Aquaporins are water channels, present in both higher and lower organisms, that belong to the major intrinsic protein family. Most aquaporins are highly selective for water, though some also facilitate the movement of small uncharged molecules such as glycerol . In higher eukaryotes these proteins play diverse roles in the maintenance of water homeostasis, indicating that membrane water permeability can be regulated independently of solute permeability. In microorganisms however, many of which do not contain aquaporins, they do not appear to play such a broad role. Instead, they assist specific microbial lifestyles within the environment, e.g. they confer protection against freeze-thaw stress and may help maintain water permeability at low temperatures . The regulation of aquaporins is complex, including transcriptional, post-translational, protein-trafficking and channel-gating mechanisms that are frequently distinct for each family member.

Structural studies show that aquaporins are present in the membrane as tetramers, though each monomer contains its own channel . The monomer has an overall "hourglass" structure made up of three structural elements: an external vestibule, an internal vestibule, and an extended pore which connects the two vestibules. Substrate selectivity is conferred by two mechanisms. Firstly, the diameter of the pore physically limits the size of molecules that can pass through the channel. Secondly, specific amino acids within the molecule regulate the preference for hydrophobic or hydrophilic substrates.

Aquaporins are classified into two subgroups: the aquaporins (also known as orthodox aquaporins), which transport only water, and the aquaglyceroporins, which transport glycerol, urea, and other small solutes in addition to water .

This entry represents a group of plant aquaporins, including SIP2-1 from Arabidopsis. Unlike other aquaporins, SIP2-1 might act as an ER channel for other small molecules or ions .
Protein TONSOKU (TONSOKU)
Type: Family

TONSOKU (also known as MGOUN3 or BRUSHY1 (BRU1)) is a nuclear leucine-glycine-asparagine (LGN) domain protein that links responses to DNA damage and epigenetic gene silencing in Arabidopsis. Mutants with defects in TONSOKU display a fasciated stem and disorganized meristem structures . TONSOKU is specifically expressed during S phase and acts with GIP1 synergistically for the maintenance of centromeric cohesion .
Fatty-acid-binding protein 1 (FAP1)
Type: Family

This entry represents a group of plant fatty-acid-binding proteins, including AtFAP1 from Arabidopsis. The function of AtFAP1 is not clear. Despite its similarity with chalcone isomerase (CHI), AtFAP1 has substitutions at nearly all of the critical catalytic positions of AtCHI, and is devoid of catalytic activity . This entry also includes CHIL1 from Humulus lupulus (European hop). CHIL1 is involved in DMX (demethylxanthohumol) biosynthesis .
NO-associated protein 1 (NOA1)
Type: Family

This entry represents a group of plant cGTPases, including AtNOA1 from Arabidopsis and OsNOA1 (Os02g01440) from rice. They share homology with bacterial protein YqeH, a circularly permuted GTPase (cGTPase). AtNOA1 (also known as RIF1) has GTPase activity and targets chloroplasts . It is essential for proper chloroplast ribosome assembly and/or translation in plants .
General transcription factor 3C polypeptide 4 (GTF3C4)
Type: Family

General transcription factor 3C polypeptide 4 (GTF3C4, also known as Transcription factor IIIC 90kDa subunit (TFIIIC90) and Sfc9 in yeast) is a subunit of transcription factor IIIC (TFIIIC), a multisubunit complex that recognises promoter elements and recruits TFIIIB and RNA polymerase III. This subunit is essential for RNA polymerase III-mediated transcription . It has histone acetyltransferase activity with unique specificity for free and nucleosomal H3 .
E3 ubiquitin-protein ligase SP1-like (SP1/SPL1)
Type: Family

This entry represents a group of E3 ubiquitin-protein ligases, including SP1 and SPL1 from Arabidopsis. They are E3 ubiquitin-protein ligases involved in the regulation of protein import in the chloroplast . SP1 is associated with TOC (translocon at the outer envelope of chloroplasts) complexes and can mediate ubiquitination of TOC components, promoting their degradation .

This entry also includes some uncharacterised bacterial proteins.
Plant UBX domain-containing protein 1 (PUX1)
Type: Family

This entry represents a group of plant UBX domain-containing proteins, including AtPUX1 from Arabidopsis. AtPUX1 regulates the hexameric structure and ATPase activity of AtCDC48, an essential AAA-ATPase chaperone that functions in numerous diverse cellular activities .

The UBX domain is comprised of ~80 amino acids and shares common secondary structure organisation with ubiquitin. In contrast to ubiquitin, UBX domains lack the C-terminal glycine motif necessary for covalent coupling to target proteins .
Peptidyl-prolyl cis-trans isomerase CYP23-like (CYP23-like)
Type: Family

This entry represents a group of predicted plant peptidyl-prolyl cis-trans isomerases, including AtCYP23 from Arabidopsis and OsCYP23 from rice . OsCYP23 is ER-located and may be associated with specific substrates for metabolic regulation related to sodium or chloride ions .
Transmembrane protein 230 (TMEM230)
Type: Family

This family represents the transmembrane protein 230 (TMEM230) which is involved in trafficking and recycling of synaptic vesicles. Mutations in this protein lead to vesicle trafficking defects associated with Parkinson's disease pathogenesis .
E3 ubiquitin-protein ligase 1/2 (RNFT1/2)
Type: Family

This family represents E3 ubiquitin-protein ligase (also known as RING finger and transmembrane domain-containing protein) RNFT1 and RNTF2. RNFT1 is an E3 ubiquitin-protein ligase that acts in the endoplasmic reticulum (ER)-associated degradation (ERAD) pathway, a mechanism that protects cells from ER stress-induced apoptosis. Misfolded proteins that have been accumulated in the ER are targeted for ubiquitination and selectively transported to the cytosol for degradation by a ubiquitin-proteasome system . RNTF2 negatively regulates IL-3-dependent cellular responses through IL-3Ralpha ubiquitination and degradation in the proteasome. The RNFT2/IL-3Rα/IL-3 axis may have a role in regulating innate immune responses in the lung .
Glycerophosphodiester phosphodiesterase GDPD4 (GDPD4)
Type: Family

This entry represents a group plant glycerophosphodiester phosphodiesterases (GDPDs), including AtGDPD4 from Arabidopsis. AtGDPD4 contains a membrane-spanning region at the N-terminal before the GDPD domain and is predicted to target mitochondria. GDPD hydrolyses glycerophosphodiesters into sn-glycerol-3-phosphate (G-3-P) and the corresponding alcohols, plays an important role in various physiological processes in both prokaryotes and eukaryotes .
Histone-lysine N-methyltransferase ATXR2-like (ATXR2-like)
Type: Family

This entry includes ATXR2 from Arabidopsis. ATXR2 is a histone lysine methyltransferase that promotes the accumulation of histone H3 proteins that are trimethylated on lysine 36 (H3K36me3) during callus formation on callus-inducing medium. It promotes early stages of cellular dedifferentiation through activation of LATERAL ORGAN BOUNDARIES DOMAIN (LBD) genes and acts as a regulator of de novo root organogenesis .
Histone-lysine N-methyltransferase ASHR2-like (ASHR2-like)
Type: Family

This entry includes ASHR2 from Arabidopsis. ASHR2 (also known as SDG39) contains the a disrupted SET domain in which the N-terminal one-third of the SET domain is separated from the C-terminal two-thirds of the domain by 50 to 120 amino acids .
Peptidyl-prolyl cis-trans isomerase FKBP20-2-like (FKBP20-2-like)
Type: Family

This entry represents a group of plant predicted peptidyl-prolyl cis-trans isomerases, including AtFKBP20-2 from Arabidopsis. AtFKBP20-2 is a chloroplastic protein .
Rhodanese-like domain-containing protein STR4-like (STR4-like)
Type: Family

This entry represents a group of rhodanese-like domain-containing proteins from plants and bacteria, including AtStr4 from Arabidopsis. AtStr4 (also known as TROL, thylakoid rhodanese-like protein) is a nuclear-encoded component of thylakoid membranes that is required for tethering of FNR (ferredoxin-NADP(+) oxidoreductase) and sustaining efficient linear electron flow (LEF) in vascular plants .
Thiol:disulfide interchange protein TxlA/HCF164 (TxlA/HCF164)
Type: Family

This entry represents a group of thiol:disulfide interchange proteins, including TxlA from Cyanobacteria and HCF164 from Arabidopsis. HCF164 is a membrane-anchored thioredoxin-like protein that acts as a transducer of reducing equivalents in the thylakoid lumen. It contains a membrane-spanning sequence and a thioredoxin-like CXXC motif in the N- and C-terminal regions, respectively. The hcf164 mutant was found to be impaired in the stable assembly of the cytochrome b6 f complex within thylakoid membrane .
Protein LHCP TRANSLOCATION DEFECT-like (LTD-like)
Type: Family

Protein LHCP TRANSLOCATION DEFECT (LTD, also known as GDC1) is a chloroplast protein that interacts with both proteins from the signal recognition particle (SRP) pathway and the inner chloroplast envelope . It is required for chloroplast grana formation in Arabidopsis .
Protein FLUORESCENT IN BLUE LIGHT (FLU)
Type: Family

FLUORESCENT IN BLUE LIGHT (FLU) is a nuclear-encoded plastid protein that, after import and processing, becomes tightly associated with plastid membranes . It controls chlorophyll biosynthesis by interacting directly with Glu tRNA reductase (HEMA1) . It operates independently of heme and seems to selectively affect only the Mg(2+) branch of tetrapyrrole biosynthesis .
Tetratricopeptide repeat protein TTC27/Emw1 (TTC27/Emw1)
Type: Family

This entry includes TTC27 (Tetratricopeptide repeat protein 27) from animals, C19B12.01 from S. pombe and Emw1 (essential for maintenance of the cell wall protein 1) from Saccharomyces cerevisiae. Emw1 is required for the maintenance of the cell wall integrity .