SII-SWORD/CoKE huggingface dataset:
Catalase, clade 3 (Catalase_3)
Type: Family

Catalases (

) are antioxidant enzymes that catalyse the conversion of hydrogen peroxide to water and molecular oxygen, serving to protect cells from its toxic effects . Hydrogen peroxide is produced as a consequence of oxidative cellular metabolism and can be converted to the highly reactive hydroxyl radical via transition metals, this radical being able to damage a wide variety of molecules within a cell, leading to oxidative stress and cell death. Catalases act to neutralise hydrogen peroxide toxicity, and are produced by all aerobic organisms ranging from bacteria to man. Most catalases are mono-functional, haem-containing enzymes, although there are also bifunctional haem-containing peroxidase/catalases (

) that are closely related to plant peroxidases, and non-haem, manganese-containing catalases (

) that are found in bacteria . Based on a phylogenetic analysis, catalases can be classified into clade 1, 2 and 3. Clade 1 contains small subunit catalases from plants and a subset of bacteria; clade 2 contains large subunit catalases from fungi and a second subset of bacteria; and clade 3 contains small subunit catalases from bacteria, fungi, protists, animals, and plants .

Clade 3 catalases are the most abundant subfamily and are found in all three kingdoms of life; they have a relatively small subunit size of 43 to 75kDa, and bind a protoheme IX (heme b) group buried deep inside the structure. Clade 3 catalases also bind NADPH as a second redox-active cofactor. They form tetramers, and in eukaryotic cells, catalases are located in peroxisomes .
Multivesicular body subunit 12A (MVB12A)
Type: Family

MVB12A (also known as CFBP) and MVB12B are subunits of the ESCRT-I complex, which mediates the sorting of ubiquitinated cargo protein from the plasma membrane to the endosomal vesicle . MVB12A plays a key role in the ligand-mediated internalization and down-regulation of the EGF receptor .
Uncharacterized GPI-anchored protein At1g61900-lke (At1g61900-like)
Type: Family

The representative of this family of uncharacterised proteins from plants is Arabidopsis thaliana GPI-anchored protein At1g61900.
Putative F-box protein At1g67623-like (At1g67623-like)
Type: Family

This family of uncharacterised proteins from plants includes At1g67623 and At2g35280 from Arabidopsis thaliana.
Uncharacterized membrane protein At1g16860-like (At1g16860-like)
Type: Family

At1g16860 is the representative member of this family of uncharacterised proteins from plants.
Chloroplast enhancing stress tolerance protein (CEST/Y3IP1)
Type: Family

Chloroplast protein CEST, also known as Ycf3-interacting protein 1 (Y3IP1), cooperates with Ycf3 in the assembly of stable photosystem I units in the thylakoid membrane . It also seems to induce tolerance to multiple environmental stresses and reduce photooxidative damage .
G patch domain-containing protein 3 (GPATCH3)
Type: Family

G patch domain-containing protein 3 (GPATCH3) is a transcriptional regulator during embryonic development, activating the CXCR4 promoter. The CXCR4 gene is involved in embryo neural crest cell migration. Because the GPATCH3 protein is detected in human tissues relevant to glaucoma, GPATCH3 may be involved in the pathogenesis of congenital glaucoma . GPATCH3 is also a negative regulator of retinoic acid-inducible gene I-like receptor-mediated antiviral signaling pathways, a means to control the response triggered by the presence of viral RNA by interacting with VISA (an adaptor of virus-triggered, RLR-mediated induction of innate antiviral responses), and disrupting the assembly of the virus-induced VISA signalosome .

Proteins in this family contain a G-patch domain.
Dynein axonemal assembly factor 9 DNAAF9 (DNAAF9)
Type: Family

This family describes DNAAF9 proteins.

Dynein axonemal assembly factor 9 DNAAF9 (Shulin) is a dynein axonemal assembly factor that regulates the transport and activation of outer dynein arms (ODAs) in cilia. It binds and inhibits ODAs in the cytoplasm, maintaining them in a closed conformation until they are delivered to cilia. It may interact with ARL-3. This GTP-dependent interaction might ensure spatiotemporal control of dynein function, critical for proper ciliary beating in multiciliated cells such as airway epithelia. Dysregulation of DNAAF9 is linked to primary ciliary dyskinesia (PCD), characterised by impaired mucociliary clearance and respiratory defects .
RNA 5'-triphosphatase Cet1/Ctl1 (Cet1/Ctl1)
Type: Family

This entry includes a group of RNA 5'-triphosphatases, including Cet1 and Ctl1 from fungi.
Uncharacterized protein At3g17950-like (At3g17950-like)
Type: Family

This family includes At3g17950 and other uncharacterised proteins from plants.
Mug56/Spo71 (Mug56/Spo71)
Type: Family

This entry includes a group of meiosis-specific fungal proteins, including Mug56 from fission yeasts and Spo71 from budding yeasts .

SPO71 is involved in the recruitment of the lipid transfer protein VPS13 to the prospore membrane during sporulation . It plays an important role in the prospore membrane development . MUG56 is required for meiosis .
GEX1/Brambleberry (GEX1/Brambleberry)
Type: Family

GEX1 and brambleberry belong to a family of karyogamy factors whose functional orthologue in yeast is KAR5 (

) . GEX1 from Arabidopsis is required for correct pollen maturation . Brambleberry is required for pronuclear fusion following fertilization .
YAP1-binding protein 1/2 (YBP1/2)
Type: Family

This entry represents YAP1-binding protein 1/2 (YBP1/2) from fungi. They are involved in cellular response to oxidative stress . In Candida albicans, Ybp1 and Gpx3 mediate Cap1-dependent oxidative stress responses .
Protein POLAR-like (POLAR-like)
Type: Family

Development of stomata in Arabidopsis thaliana begins with de novo asymmetric divisions producing meristemoids. POLAR is thought to be involved in this process. It is polarly localized and unequally segregated during asymmetric cell divisions of the stomatal lineage . This entry also includes Arabidopsis POLAR-like 1 (PL1), which acts as a stomatal lineage scaffold .
Monopolin complex subunit Csm1/Pcs1 (Csm1/Pcs1)
Type: Family

Saccharomyces cerevisiae Csm1 is part of the monopolin complex. Csm1 forms a complex with Mde4 and promotes monoorientation during meiosis . It plays a mitotic role in DNA replication and is required for condensin recruitment to the replication fork barrier site and rDNA repeat segregation . This entry also contains the Schizosaccharomyces pombe homologue to Csm1, Pcs1. Pcs1 forms a complex with Mde4 and acts in the central kinetochore domain to clamp microtubule binding sites together. The two complexes (Csm1/Lrs4 and Pcs1/Mde4) contribute to the prevention of merotelic attachment .
Transmembrane protein 272 (TMEM272)
Type: Family

The function of transmembrane protein 272 is not known.
Guanine nucleotide exchange factor RAB3IL/RAB3IP/Sec2 (RAB3IL/RAB3IP/Sec2)
Type: Family

Proteins in this entry are guanine nucleotide exchange factors (GEF), including RAB3IL1/RAB3IP from animals, Sec2 from budding yeasts and Spo13 from fission yeasts. The mammalian guanine nucleotide exchange factor for Rab-3A (RAB3IL1) may activate RAB3A, a GTPase that regulates synaptic vesicle exocytosis . The Rab-3A-interacting protein (RAB3IP) may activate RAB8A and RAB8B, which reorganizes actin and microtubules to form new cell surface domains .

In the yeast Saccharomyces cerevisiae, Rab guanine nucleotide exchange factor Sec2 activates Sec4 by catalyzing the dissociation of GDP from Sec4. Activation of Sec4 by Sec2 is needed for the directed transport of vesicles to sites of exocytosis . In the yeast Schizosaccharomyces pombe, sporulation-specific protein 13 (Spo13) is required for sporulation. During sporulation the spindle pole body (SPB) forms outer plaques, an essential precursor to the assembly of the forespore membrane (FSM). SPB associates with Spo13 and Spo2, and without these genes the SPB is not modified and the FSM does not form .
Transmembrane and ubiquitin-like domain-containing protein 1/2 (TMUB1/2)
Type: Family

The entry includes proteins with ubiquitin-like domains. Transmembrane and ubiquitin-like domain-containing protein 1 (TMUB1) is involved in the sterol-regulated ubiquitination and degradation of 3-hydroxy-3-methylglutaryl-coenzyme A reductase by the endoplasmic reticulum (ER)-associated degradation (ERAD) pathway. TMUB1 and SPFH2 associate with mammalian gp78, the membrane-bound ubiquitin ligase in the ERAD pathway .
FLC EXPRESSOR/FLX-like (FLX/FLX-like)
Type: Family

FLC EXPRESSOR (FLX) is a specific component of the FRI complex (FRI-C). Several FLX-like proteins exist in Arabidopsis. FLX-like 4 (FLX4) is known to be also a component of FRI-C and, like FLX, is required for the activation of FLC by FRI. FLC and FRI are determinants of the vernalization-requiring, winter-annual habit, blocking flowering prior to winter .
Tectonic-1-3 (TCTN1-3)
Type: Family

TCTN1, TCTN2, and TCTN3 are members of the tectonic protein family that play crucial roles in ciliogenesis and ciliary function. While they share some common functions, each protein also has specific roles in the process of cilia formation and maintenance. These proteins interact with several other ciliopathy proteins, forming a complex known as the Tectonic ciliopathy complex. This complex is required for hedgehog signalling transduction and regulation of ciliary membrane composition .
Protein FAM220A (FAM220A)
Type: Family

FAM220A, also known as SIPAR, inhibits STAT3 activity by accelerating its dephosphorylation . STAT3 is a member of the STAT family (signal transducers and activators of transcription) that plays an esential role in cell growth and differentiation.
SPEAR family (SPEAR)
Type: Family

SPEAR is a transcription repressor family specific in embryophyte, with many members in land plants. All of them contain a conserved SPL-motif in their N-terminal and an ethylene-responsive element binding factor-associated amphiphilic repression (EAR) motif in the C-terminal, and are therefore known as SPL-like, EAR-containing proteins (SPEARs). SPOROCYTELESS (SPL) belongs to this family. SPL and SPEARs may play a variety of developmental roles in plants .
Vma22/CCDC115 (Vma22/CCDC115)
Type: Family

This entry includes Vma22 from yeasts and CCDC115 from animals. Vma22 is an endoplasmic reticulum-associated protein required for V-ATPase activity . CCDC115 is an accessory component of the proton-transporting vacuolar (V)-ATPase protein pump involved in intracellular iron homeostasis . Mutations of CCDC115 have been found in patients affected by congenital disorders of glycosylation .
Uncharacterized protein At4g22758-like (At4g22758-like)
Type: Family

At4g22758 is the representative member of this family of uncharacterised plant proteins.
Protein glutamine dumper (GDU)
Type: Family

The Arabidopsis genome contains seven GLUTAMINE DUPMER (GDU)-encoding genes. GDUs stimulate amino acid export by activating nonselective amino acid facilitators . GDU1 has been shown to induce the secretion of glutamine from hydathodes and increased amino acid content in leaf apoplasm and xylem sap .
Tapetum determinant 1 (TPD1)
Type: Family

This family consist of protein TAPETUM DETERMINANT 1 (TPD1) and homologues from plants. TPD1 is required for the specialization of tapetal cells in the Arabidopsis anther . TPD1 serves as a ligand for the EMS1 receptor kinase to control anther cell differentiation during plant sexual reproduction .
RAB11-binding protein RELCH (RELCH)
Type: Family

RELCH is a RAB11 effector protein that regulates intracellular cholesterol distribution from recycling endosomes to the trans-Golgi network through its interactions with RAB11 and OSBP .
Homeobox-containing protein 1 (HMBOX1)
Type: Family

HMBOX1 binds to 5'-TTAGGG-3' repeats in telomeric DNA and may play a role in recruitment of the telomerase complex to telomeres . It also plays a role in the alternative lengthening of telomeres (ALT) pathway in telomerase-negative cells where it promotes formation and/or maintenance of ALT-associated promyelocytic leukemia bodies (APBs) .
Tetratricopeptide repeat protein 21A/21B (TTC21A/TTC21B)
Type: Family

This entry includes tetratricopeptide repeat proteins 21A (TTC21A) and 21B (TTC21B), and other homologues with numerous tetratricopeptide repeats. TTC21B is a component of the IFT complex A (IFT-A), which is required for retrograde ciliary transport. Intraflagellar transport (IFT) is required for cilium assembly and trafficking within cilia . Several diseases results from mutations in the TTC21B gene including nephronophthisis 12, short-rib thoracic dysplasia 4 with or without polydactyly, and Joubert syndrome 11 .
EF-hand domain-containing protein D1/2 (EFHD1/2)
Type: Family

This entry includes EF-hand domain-containing protein D1/2 (EFHD1/2). EFHD1 may function as a mitochondrial Ca(2+) sensor underlying Ca(2+)-dependent activation of mitoflashes . EFHD2 is a Ca2+ binding adapter protein involved in various cellular functions . In mice, EFHD2 (also known as Swiprosin-1) may regulate B-cell receptor (BCR)-induced immature and primary B-cell apoptosis .
Nuclear polyadenylated RNA-binding protein Nab2/ZC3H14 (Nab2/ZC3H14)
Type: Family

Budding yeast Nab2 is a nuclear polyadenylated RNA-binding protein that contains seven CCCH-type zinc fingers and an RGG box . It is required for nuclear mRNA export and poly(A) tail length control . The tertiary structure has been solved and the protein is all helical (

). Its animal homologue, known as ZC3H14, has been shown to control poly(A) tail length in neuronal cells .
LisH domain-containing protein ARMC9 (ARMC9)
Type: Family

Proteins in this family are mostly from animals. The only characterised protein is LisH domain-containing protein ARMC9, which is localised to the basal body of a cilium and is upregulated during ciliogenesis. Mutations in the ARMC9 gene cause Joubert Syndrome, a recessive neurodevelopmental disorder characterised by hypotonia, ataxia, abnormal eye movements, and variable cognitive impairment .
Coiled-coil domain-containing protein 74A/74B/92 (CCDC74A/CCDC74B/CCDC92)
Type: Family

This entry includes coiled-coil domain-containing proteins 74A (CCDC74A), 74B (CCDC74B) and 92 (CCDC92).

Coiled-coil domain-containing protein 92 (CCDC92) is an interferon-stimulated protein that plays a role in innate immunity. It strongly inhibits ebolavirus transcription and replication through the formation of a complex with viral RNA-bound nucleocapsid (NP) that prevents the transport of NP to the cell surface . It has also been shown to interact with centrosomal protein CEP164 , which is required for primary (nonmotile) cilium formation . CCDC92 is associated with obesity and type 2 diabetes in humans. Studies in wild-type (WT) and CCCDC92 whole-body knockout (KO) mice, it was found that CCDC92 KO reduced obesity and increased insulin sensitivity under high-fat diet (HFD) conditions, it inhibited macrophage infiltration and fibrosis in white adipose tissue (WAT), which might protect against adipose tissue dysfunction. This suggests a critical role of CCDC92 in metabolism, and may be a potential target for treating obesity and insulin resistance .

Coiled-coil domain-containing protein 74A/B are spindle-localized proteins that bind directly to microtubules through two separate domains and bundle microtubules, being important K-fiber crosslinkers required for bipolar spindle formation and chromosome alignment .
Regulator of MON1-CCZ1 complex (RMC1)
Type: Family

RMC1 is a componement of the the CCZ1-MON1 complex, which functions as a guanine exchange factor (GEF) for RAB7 during endocytic and autophagic flux to the lysosome. It positively regulates CCZ1-MON1 function that is necessary for endosomal/autophagic flux and efficient RAB7 localization on CD63-positive vesicle membranes .
YaeB-like (YaeB-like)
Type: Family

TrmO (also known as TsaA or YaeB) is a RNA methyltransferase responsible for N6-methylation of N6-threonylcarbamoyladenosine in tRNAs. It has a unique single-sheeted β-barrel structure and represent a new category of AdoMet-dependent methyltransferases .
Transcription factor castor (CASZ1)
Type: Family

CASZ1 is an evolutionarily conserved zinc-finger transcription factor. It acts as a transcriptional activator involved in vascular assembly and morphogenesis through regulating EGFL7 . CASZ1 interacts with the polycomb repressor complex in a splice variant-specific manner and controls rod genome organization . It also regulates the Th17/Th1/regulatory cell differentiation program .
Protein BIC (BIC)
Type: Family

BIC1 (blue-light inhibitor of cryptochromes 1) and homologue BIC2 suppress the functions of plant cryptochromes. They are thought to act redundantly to inhibit the function of CRYs. BIC1 has be shown to suppresss blue light-dependent CRY2 dimerization and inhibit CRY2-dependent photoresponses of plants .
Microprocessor complex subunit DGCR8 (DGCR8)
Type: Family

Primary microRNA transcripts (pri-miRs) are cleaved by Microprocessor, a complex containing RNase III DROSHA and its cofactor DGCR8 . DGCR8 functions as a molecular anchor necessary for the recognition of pri-miRNA at dsRNA-ssRNA junction and directs DROSHA to cleave 11 bp away form the junction to release hairpin-shaped pre-miRNAs that are subsequently cut by the cytoplasmic DICER to generate mature miRNAs . DGCR8 binds heme, and this binding activates DGCR8 to recognize pri-miRs by specifically binding the terminal loop near the 3' single-stranded segment .
At4g28100-like (At4g28100-like)
Type: Family

Arabidopsis thaliana At4g28100 is the representative of this family of uncharacterised plant proteins.
Thylakoid membrane protein Ssl2009-like (Ssl2009-like)
Type: Family

This family of uncharacterised proteins has members in plants and cyanobacteria.
Protein BREAKING OF ASYMMETRY IN THE STOMATAL LINEAGE (BASL)
Type: Family

Development of stomata in Arabidopsis thaliana begins with de novo asymmetric divisions in which a small cell, known as a meristemoid, and a larger daughter cell is formed. Stomatal protein BASL is a regulator of asymmetric cell division . It is required for the polar localization of POLAR .
WD repeat-containing protein 19/dyf-2 (WDR19/dyf-2)
Type: Family

Proteins in this entry contain WD40 repeats, and include WD repeat-containing proteins 19 (WDR19), from mammals, and dyf-2 from nematodes. Both WDR19 and dyf-2 are components of the IFT complex A (IFT-A), which is required for retrograde ciliary transport . Mutations in the WDR19 gene are associated with numerous diseases, including cranioectodermal dysplasia 4, short-rib thoracic dysplasia 5 with or without polydactyly, nephronophthisis 13 , and Senior-Loken syndrome 8 .
HAKAI-like, RING finger, HC subclass (HAKAI-like_RING-HC)
Type: Domain

Hakai is an E3 ubiquitin ligase that disrupts cell-cell contacts in epithelial cells and is upregulated in human colon and gastric adenocarcinomas. It was identified to mediate the posttranslational downregulation of E-cadherin (CDH1), a major component of adherens junctions in epithelial cells and a potent tumour suppressor . It also promotes ubiquitination of several other tyrosine-phosphorylated Src substrates, including cortactin (CTTN) and DOK1 .
Uncharacterized protein At4g14450-like (At4g14450-like)
Type: Family

This family consists of uncharacterised plant proteins of unknown function.
Nucleolar protein 10/Enp2 (NOL10/Enp2)
Type: Family

Proteins in this entry contain WD40 repeats. Nucleolar protein 10 (NOL10) is found in the nucleolus of vertebrates and contains seven WD40 repeats but is otherwise uncharacterised. Ribosome biogenesis protein Enp2 (Enp2) from Saccharomyces cerevisiae contains five WD40 repeats and is a component of 90S pre-ribosomes . Homologues are also known from plants.
E3 ubiquitin-protein ligase HAKAI/CBLL2 (HAKAI/CBLL2)
Type: Family

Hakai is an E3 ubiquitin ligase that disrupts cell-cell contacts in epithelial cells and is upregulated in human colon and gastric adenocarcinomas. It was identified to mediate the posttranslational downregulation of E-cadherin (CDH1), a major component of adherens junctions in epithelial cells and a potent tumour suppressor . It also promotes ubiquitination of several other tyrosine-phosphorylated Src substrates, including cortactin (CTTN) and DOK1 .
Orcokinin peptides type A/B (ORCKA/B)
Type: Family

This family of neuropeptides is found in invertebrates including Orcokinin peptides type A/B (ORCKA/B). Orcokinin precursor-related peptides have been identified in the brain of the crayfish Procambarus clarkii . Orcokinins are crustacean peptides eliciting potent myotropic effects in gut tissues, and are also found in other invertebrates .
Rab-like protein 6 (RABL6)
Type: Family

Rab-like protein 6 (RABL6 or RBEL1) is one of several proteins identified as binding partners of the ARF tumour suppressor, which protects against cancer through protein-protein interactions, interacting with CDKN2A . RABL6 binds GTP and is found either in the cytoplasm or the nucleus depending in the isoform; isoform 1 is O-glycosylated and cytoplasmic .
Transcriptional repressor p66 (P66)
Type: Family

P66alpha and P66beta interact with MBDs (methyl-binding domain-containing proteins) via a coiled-coil region on each . P66 and MBD2 form a complex with the nucleosome remodeling and deacetylation (NuRD) complex. This MBD2-NuRD complex recognizes methylated DNA and silences expression of associated genes through histone deacetylase and nucleosome remodeling functions .
RPM1-interacting protein 4/NOI4 (RIN4/NOI4)
Type: Family

RIN4 is an essential regulator of plant defense pathways. It functions with the plasma membrane H(+)-ATPase to regulate stomatal apertures, inhibiting the entry of bacterial pathogens during infection . It is required for RPM1-mediated Pseudomonas syringae resistance in Arabidopsis . Phosphorylated RIN4 activates the receptor RPM1 to mediate the plant defense . Arabidopsis RIN4 contains two nitrate-induced (NOI) domains and is a member of the larger NOI family . This entry also includes NOI4 (At5g55850), whose function is not known.
CXXC-type zinc finger protein CXXC4/CXXC5 (CXXC4/CXXC5)
Type: Family

This entry represents CXXC-type zinc finger proteins CXXC4 and CXXC5. CXXC4 is a potential tumour suppressor directly regulated by EZH2 . It has been shown to inactivate mitogen activated protein kinase signaling . CXXC5 is a retinoid-inducible nuclear factor (RINF) involved in normal myelopoiesis . It has been associated with various malignant tumours .
Cyclin-dependent protein kinase inhibitor SMR (SMR)
Type: Family

The SIAMESE-RELATED (SMR) family of cyclin-dependent kinase (CDK) inhibitors is a plant-specific family that consist of SIAMESE (SIM) and related proteins . SIM controls endoreplication during trichome development . SMR2 acts to restrict cell proliferation during leaf growth in Arabidopsis and SIM, SMR1/LGO, and SMR2 play overlapping roles in controlling the transition from cell division to endoreplication .
TIFY/JAZ family (TIFY/JAZ)
Type: Family

JASMONATE ZIM-domain (JAZ) proteins act as repressors of jasmonate (JA) signaling . The ZIM domain recruits the co-repressors NINJA and TOPLESS to JAZ-bound transcription factors, and contains a highly conserved TIF[F/Y]XG motif that defines the larger family of TIFY proteins to which JAZs belong. This family consists of TIFY/JAZ proteins, and also includes JAZ13 (At3g22275), a non-TIFY JAZ protein that is a repressor of JA signaling . Some of the members of the TIFY/JAZ family, such as TIFY8, are not involved in JA signaling. TIFY8 is found in protein complexes involved in regulation of dephosphorylation, deubiquitination and O-linked N-acetylglucosamine modification, suggesting an important role in nuclear signal transduction .
BEN domain-containing protein 5 (BEND5)
Type: Family

BEND5 binds to DNA and acts as a transcriptional repressor .