SII-SWORD/CoKE huggingface dataset:
NURS complex subunit red1 (Red1)
Type: Family

This entry contains proteins with a putative zinc finger with three conserved cysteines and a histidine (Znf-C3H1) in the C-x8-C-x5-C-x3-H conformation.

NURS complex subunit red1 from the fission yeast
Schizosaccharomyces pombe
is required for the elimination of meiosis-specific mRNAs from mitotic cells by destabilising mRNAs containing a DSR degradation signal sequence . In addition to Red1, the nuclear RNA silencing (NURS) includes the Mtl1, Red5, Ars2, Rmn1, and Iss10 proteins and associates with several other complexes that are involved in either signalling or mediating RNA silencing .

This entry also includes human zinc finger C3H1 domain-containing protein (Znf-C3H1). This is also required for mRNA degradation, and is a subunit of the trimeric poly(A) tail exosome targeting (PAXT) complex, which directs a subset of long and polyadenylated poly(A) RNAs for exosomal degradation .
Polygalacturonase QRT3-like (QRT3-like)
Type: Family

This entry includes Arabidopsis QRT3 and related proteins from plants and fungi which share the β-helical structure like pectate lyase. AtQRT3 is a polygalacturonase required for degrading the pollen mother cell wall during microspore development . It contains PbH1 (parallel β-helix) repeats and is a member of glycosyl hydrolase 28 family. Fungal proteins such as BGN13.1 and ARB_02077 may be involved in mycoparasitism, in the hydrolysis of fungal cell wall.
VASCULAR-RELATED UNKNOWN PROTEIN (VUP)
Type: Family

This entry represents a group of plant proteins, including VASCULAR-RELATED UNKNOWN PROTEINS 1-4 (VUP1-4) from Arabidopsis. VUP1 may be involved in regulating xylem development by tissue or cell specific modulation of hormone signaling pathways .
Arabinogalactan protein 3/12/13/14/21 (AGP3/12/13/14/21)
Type: Family

Arabinogalactan proteins (AGPs) are a family of extracellular glycoproteins implicated in plant growth and development. This entry includes AGP1/3 from rice and AGP12, AGP13, AGP14 and AGP21 from Arabidopsis .
Protein response to low sulfur (LSU)
Type: Family

This entry includes proteins RESPONSE TO LOW SULFUR 1-4 (LSU1-4) from Arabidopsis. These proteins may be involved in plant responses to environmental challenges; they are up-regulated in several abiotic and biotic stress conditions . Three out of four of the Arabidopsis LSU genes (namely LSU1, LSU2, and LSU3) are induced by sulfur deficiency . LSU expression prevents chloroplastic reactive oxygen species (ROS) production and proper stomatal closure during sulphur stress. LSU1 has been shown to interact with and stimulates the activity of the chloroplastic superoxide dismutase FSD2 . Homologues are known only from plants.
Motile sperm domain-containing protein 1/3 (MOSPD1/3)
Type: Family

Motile sperm domain-containing protein 1/3 (MOSPD1/3) contain a motile sperm protein domain and two transmembrane domains. MOSPD1 is involved in mesenchymal versus epidermal cell differentiation . It is also involved in mesenchymal stem cell proliferation and differentiation .
Coiled-coil domain-containing protein 159/163 (CCDC159/163)
Type: Family

This entry represents a group of proteins including CCDC159 and CCDC163. The function of CCDC159/163 is not clear. Homologues are predominantly from chordates.
Dehydrin HIRD11-like (HIRD11-like)
Type: Family

Dehydrins (group 2 late embryogenesis abundant proteins) are plant proteins that are responsive to abiotic stresses such as drought, extreme temperature, and high salinity. This entry includes KS-type dehydrin HIRD11 from Arabidopsis . AtHIRD11 inhibits the reactive oxygen species (ROS) generation from copper .
Exosporium protein C (CsxC)
Type: Family

Cysteine-rich protein CsxC is a component of the exosporium of Clostridium. The exosporium is the sac-like outermost layer of spores of these species, and is likely to contribute to adhesion, dissemination, and virulence .
Mitochondrial intermembrane space import and assembly protein 40 (CHCHD4)
Type: Family

Mitochondrial intermembrane space import and assembly protein 40 (CHCHD4) is a chaperone and catalyses the formation of disulfide bonds in proteins within the mitochondrial intermembrane space (IMS) such as COX17 , COX19 , MICU1 and GFER . A precursor of one of these proteins in a reduced state is imported into the mitochondrion where it associates with CHCHD4 forming a transient intermolecular disulfide bridge. This leads to oxidation of the precursor, formation of an intramolecular disulfide bond and the folding in the IMS .

This entry also includes the Uncharacterized protein F42H10.2 from
Caenorhabditis elegans
.
Late embryogenesis abundant protein At5g17165-like (At5g17165-like)
Type: Family

This entry represents a group of plant proteins, including Late embryogenesis abundant protein At5g17165 from Arabidopsis. Members are related to the LEA_3a family of proteins (

) . Their function is not clear.
Protein SICKLE (SICKLE)
Type: Family

Plant protein SICKLE is required for development and abiotic stress tolerance, and is involved in microRNA biogenesis and mRNA splicing . SICKLE, also known as ROTUNDA 3, may contribute to plant development by phosphatase 2A-mediated regulation of auxin transporter recycling .
Transmembrane protein 81 (TMEM81)
Type: Family

TMEM81 is a type I transmembrane protein with a large, N-terminal lumenal domain with an immunoglobulin-like fold, and a short cytoplasmic tail. The function of TMEM81 is not clear. Homologues are found only in chordates.
Probable RNA-binding protein EIF1AD (EIF1AD)
Type: Family

EIF1AD (also known as haponin) is a probable RNA-binding protein that plays a role in the cellular response to oxidative stress and interacts with glyceraldehyde 3-phosphate dehydrogenase (GAPDH) . EIF1AD contains an S1-like domain, and nuclear localization signals.
Signaling mucin MSB2 (MSB2)
Type: Family

Yeast cells respond to hyperosmotic stress by activating the high-osmolarity glycerol (HOG) pathway, which consists of two branches, Hkr1/Msb2-Sho1 and Sln1 . The Sho1 branch involves two osmosensors, the transmembrane mucin-like glycoproteins Hkr1 and Msb2. Activation of Hog MAPK cascade by Msb2, but not by Hkr1, requires the scaffold protein Bem1 and the actin cytoskeleton, suggesting that Msb2 functions as an osmosensor to integrate the signals from external osmotic conditions with those from internal cytoskeletal conditions .
Cytochrome c oxidase subunit VII (COX7a)
Type: Family

Cytochrome c oxidase, a 13 sub-unit complex, is the terminal oxidase in the mitochondrial electron transport chain. This family contains both heart and liver isoforms of cytochrome c oxidase subunit VIIa .
Acyl-coenzyme A thioesterase 13 (ACOT13)
Type: Family

Acyl-coenzyme A thioesterases hydrolyse acyl-CoA to generate free fatty acid and coenzyme A. Acyl-coenzyme A thioesterase 13 (ACOT13) acts on medium (C12) and long-chain (C18) fatty acyl-CoA substrates. Naturally, it exists as a homotetramer and adopts a hotdog fold . Homologues are found in fungi, archaea and bacteria.
Protein SIEVE ELEMENT OCCLUSION (SEOA)
Type: Family

This entry includes protein SIEVE ELEMENT OCCLUSION (SEO) 1, 2 and 3 (or A, B and C) from Arabidopsis. They are phloem filament proteins required for filament formation .
Protein JASON (JASON)
Type: Family

This entry represents a group of plant proteins, including protein JASON from Arabidopsis. JASON positively regulates AtPS1 (Arabidopsis thaliana Parallel Spindles1) expression, allowing the proper organization and orientation of metaphase II spindle plates in MII .
Protein Sip5/DA2 (Sip5/DA2)
Type: Family

This entry includes a group of fungal and plant proteins, including Sip5 from budding yeasts and DA2 from Arabidopsis. The function of Sip5 is not clear. It interacts with both the Reg1/Glc7 protein phosphatase and the Snf1 protein kinase .

DA2 (At1g78420) is an E3 ubiquitin-protein ligase involved in the regulation of organ and seed size . This entry also includes DA2-like proteins such as At1g17145 and GW2 .
Microtubule associated protein 10 (MAP10)
Type: Family

Microtubule-associated protein 10 (MAP10, also known as MTR120/KIAA1383) localises to stabilised MTs during interphase and to the mitotic apparatus during mitosis. It may promote microtubule stability and ensures normal progress of cytokinesis .
Coiled-coil domain-containing protein 50 (CCDC50)
Type: Family

Human CCDC50 is overexpressed in mantle cell lymphoma and chronic lymphocytic leukemia. Its involvement in NFkappaB signalling pathways may have major effects on cell survival .
Dynein assembly factor 3, axonemal (DNAAF3)
Type: Family

Dynein assembly factor 3 (DNAAF3) is required for the assembly of axonemal inner and outer dynein arms. DNAAF3 is involved in preassembly of dyneins into complexes before their transport into cilia .
Protein PIN-LIKES 2/6 (PILS2/6)
Type: Family

This entry includes proteins PIN-LIKES 2 and 6 from Arabidopsis. They regulate intracellular auxin accumulation at the endoplasmic reticulum and thus auxin availability for nuclear auxin signalling .
Myosin-binding protein (MYOB)
Type: Family

This entry represents a group of plant myosin-binding protein (MYOB), including MYOB1-6. They are membrane-anchored myosin receptors that define a distinct, plant-specific transport vesicle compartment .
GPI-anchored protein LORELEI-like (LORELEI-like)
Type: Family

This entry represents a group of plant proteins, including LORELEI (LRE) and LORELEI-like proteins (LLG1, LLG2 and LLG3) from Arabidopsis. LORELEI is a female gametophyte-specific component of the signalling pathway required for fertilization . LLG1/LRE act as a chaperone and co-receptor for receptor kinase FERONIA, which is a multifunctional regulator for plant growth and reproduction .
Growth arrest-specific protein 8 (GAS8)
Type: Family

Growth arrest-specific protein 8 (Gas8; also known as dynein regulatory complex subunit 4, DRC4) is a microtubule-binding protein localised to regions of dynein regulation in mammalian cells. In mouse, Gas8 is predominantly a testicular protein, whose expression is developmentally regulated during puberty and spermatogenesis. In humans, it is absent in infertile males who lack the ability to generate gametes. The localisation of Gas8 in the motility apparatus of post-meiotic gametocytes and mature spermatozoa, together with the detection of Gas8 also in cilia at the apical surfaces of epithelial cells lining the pulmonary bronchi and Fallopian tubes suggests that the Gas8 protein may have a role in the functioning of motile cellular appendages . Homologues are also found in apicomplexans and invertebrates. In Chlamydomonas reinhardtii, Gas8 is a component of the nexin-dynein regulatory complex, which is a regulator of ciliary/flagellar motility .
Biopterin transporter family (BT1)
Type: Family

Members of this family are transmembrane proteins. Several are Leishmania putative proteins that are thought to be pteridine transporters. One such protein

, previously termed (and is still annotated as) ORFG, was shown to encode a biopterin transport protein using null mutants , thus being subsequently renamed BT1. The significant similarity of ORFG/BT1 to Trypanosoma brucei ESAG10 (a putative transmembrane protein and another member of this family) was previously noted . This family also contains folate-biopterin transporters (FBTs) from blue-green algae and plants, including Slr0642 protein from Synechocystis and its plastidial orthologue At2g32040 from Arabidopsis . Both Slr0642 protein and At2g32040 mediate folate monoglutamate transport involved in tetrahydrofolate biosynthesis. However, this entry also includes seven other Arabidopsis FBT proteins that lack conserved critical residues and may not have folate or pterin transport activity . In addition, it also contains two predicted prokaryotic proteins (from the cyanobacteria Synechocystis and Synechococcus).
UBA-like domain-containing protein 1/2 (UBALD1/2)
Type: Family

This entry includes UBA-like domain-containing protein 1 and 2 from animals. Their functions are not clear.
FAM187A/B (FAM187A/B)
Type: Family

This entry includes FAM187A and FAM187B from animals. Their functions are not clear.
Protein LITTLE ZIPPER (ZPR)
Type: Family

This entry represents a group of leucine zipper containing proteins from plants, including ZPR1-4 from Arabidopsis. ZPR3 is a competitive inhibitor of the HD-ZIP III transcription factors in shoot apical meristem development .
Protein HEAT INTOLERANT 4 (HIT4)
Type: Family

This entry represents a group of plant proteins, including protein HEAT INTOLERANT 4 (HIT4) from Arabidopsis. HIT4 is a chromocentre-localized protein involved in heat-triggered reorganization of chromatin and release of transcriptional gene silencing .
Calvin cycle protein CP12-like (CP12-like)
Type: Family

This entry includes CP12, a chloroplast protein that regulates the Calvin cycle responsible for CO2 assimilation . Oxidized CP12 forms a supramolecular complex with two key Calvin cycle enzymes, GAPDH (glyceraldehyde-3-phosphate dehydrogenase) and PRK (phosphoribulokinase), down-regulating their activity. It also interacts with other enzymes such as aldolase and malate dehydrogenase . This entry also includes proteins from Cyanobacteria (blue-green algae).
Chemotaxis protein CheW (CheW)
Type: Family

In bacterial chemotaxis, cellular movement is directed in response to chemical gradients. Transmembrane chemoreceptors that sense the stimuli are coupled via coupling protein CheW with a signal transduction histidine kinase (CheA) . CheA phosphorylates response regulators CheB and CheY. The two cytoplasmic proteins, CheW and CheA, both contain homologous SH3-like domains that interact with transmembrane chemoreceptors, or methyl accepting chemotaxis proteins (MCPs). CheV is a third type of protein with a CheW-like domain.

In Bacillus subtilis, CheW and CheV may be partially redundant in coupling the receptors to CheA; however, they are both necessary for efficient chemotaxis . CheV is phosphorylated in vitro on a conserved aspartate as a result of phosphoryl group transfer from phosphorylated CheA (CheA-P). This reaction is slower compared with the phospho-transfer reaction between CheA-P and one other response regulator of the system, CheB. It is part of a signal transduction pathway to facilitate adaptation to attractants . In Helicobacter pylori, CheV paralogues and CheW are not redundant and seem to have separate roles in chemotaxis . CheV is a two-domain protein with an N-terminal CheW-like (SH3-like) domain and a C-terminal CheY-like receiver domain. It is often regarded as a version of CheW, where the CheW-like domain is fused to the receiver domain .

This group contains chemotaxis response regulator proteins CheW.
CLAVATA3/ESR (CLE)-related protein 25/26 (CLE25/26)
Type: Family

This entry represents a group of plant proteins, including CLAVATA3/ESR (CLE)-related protein 25/26 (CLE25/26) from Arabidopsis. They are extracellular signal peptides involved in cell-to-cell communication in concert with different receptors in a range of processes during plant development .
Protein time for coffee (TIC)
Type: Family

Arabidopsis TIME FOR COFFEE (TIC) is a circadian regulator that coordinates developmental, metabolic, and environmental signals . It controls root meristem size by changes in auxin accumulation .
Protein O-mannose kinase (POMK)
Type: Family

Protein O-mannose kinase (POMK;

) is a type II membrane protein with a large lumenal domain. It phosphorylates the 6-position of O-mannose using ATP, a crucial step in the biosynthetic pathway of O-mannose glycan . Mutations in the POMK gene cause a severe congenital muscular dystrophy, Walker-Warburg syndrome .
Protein EARLY FLOWERING 3-like (ELF3-like)
Type: Family

This entry represents a group of plant proteins, including protein EARLY FLOWERING 3 (ELF3) from Arabidopsis and Hd17 from rice. It may function as a modulator of light signal transduction downstream of phytochromes . Hd17 (also known as OsELF3) is involved in rice photoperiodic flowering .
RING finger protein 207 (RNF207)
Type: Family

RING finger protein 207 (RNF207) is a regulator of cardiac excitation probably by effects on HERG trafficking and localization in a heat shock protein-dependent manner . RNF207 contains a RING-type ring finger and an atypical B box-type ring finger.
Increased DNA methylation 2/3-like (IDM2/3-like)
Type: Family

This entry represents a group of plant proteins, including IDM2/3 (increased DNA methylation 2/3) from Arabidopsis. IDM2 functions in active DNA demethylation . IDM3 acts as an anti-silencing factor that prevents DNA hypermethylation and gene repression .
MOM1 (MOM1)
Type: Family

This entry represents a group of plant proteins, including MOM1 from Arabidopsis. MOM1 is involved in transcriptional gene silencing (TGS) . It may transduce RNA-directed DNA methylation (RdDM) signals to repressive histone modification .
Ankyrin repeat domain-containing protein 45/46/60 (ANKRD_45/46/60)
Type: Family

This entry includes ankyrin repeat domain-containing proteins 45, 46 and 60 (ANKRD45, ANKRD46, ANKRD60). ANKRD45 was recently described to play a role during cell proliferation in both zebrafish embryos and mammalian cells and is required for cell division both in early and late mitotic stages .
Protein SHORT HYPOCOTYL IN WHITE LIGHT 1 (SHW1)
Type: Family

This entry represents a group of plant proteins, including protein SHORT HYPOCOTYL IN WHITE LIGHT 1 (SHW1) from Arabidopsis. SHW1 is a serine-arginine-aspartate rich protein that regulates the abscisic acid (ABA) and light signaling pathways . The shw1 mutants display shorter hypocotyl in the darkness. SHW1 acts as a negative regulator of photomorphogenesis . SHW1 is a transmembrane protein with a nuclear localization signal.
Nodulin homeobox (NDX)
Type: Family

This entry represents a group of plant proteins, including nodulin homeobox protein (NDX) from Arabidopsis. AtNDX associates with single-stranded DNA and inhibits COOLAIR transcription, which in turn modifies FLC (FLOWERING LOCUS C) expression . It is a key heterochromatin regulator that functions in pericentromeric regions to control siRNA production and non-CG methylation .
Protein Patronus (Patronus)
Type: Family

PATRONUS (PANS1) is an Arabidopsis protein required for protection of meiotic centromeric cohesion . It is also essential for growth adaptation to stress and required for mitotic onset control . PANS2, a paralogue of PANS1, is not required for centromeric cohesion, but may have a redundant role with PANS1 in gametophytic and somatic development, possibly at mitosis . At least one PANS homologue is present in all dicot species .
C2H2 finger domain transcription factor CON7-like (CON7-like)
Type: Family

This entry represents a group of proteins mostly from fungi, including CON7 from Magnaporthe grisea. CON7 is a transcription factor that regulates infection-related morphogenesis in the rice blast fungus Magnaporthe grisea .
WD repeat-containing protein 89 (WDR89)
Type: Family

This entry represents a group of WD repeat-containing proteins, including WDR89 from humans and GTS1 from Arabidopsis.
Sialate O-acetylesterase (SIAE)
Type: Family

Sialate O-acetylesterase (SIAE,

) is a lysosomal enzyme that removes the O-acetyl ester groups from position 9 of the parent sialic acid, N-acetylneuraminic acid. In humans, it is highly expressed in the testis, prostate, and colon . It negatively regulates B lymphocyte antigen receptor signalling and is required for the maintenance of immunological tolerance. Mutations in the gene result in autoimmune disease 6 . This entry also includes many uncharacterised bacterial proteins.
Chromosome alignment-maintaining phosphoprotein 1 (CAMP)
Type: Family

Chromosome alignment-maintaining phosphoprotein 1 (CAMP or CHAMP1) is a zinc-finger protein required for maintaining kinetochore-microtubule attachment during bi-orientation. It contains three characteristic repeat motifs termed the WK, SPE, and FPE motifs .
Purple acid phosphatase-like (PAPs-like)
Type: Family

Purple acid phosphatases (PAPs) (

) are a family of binuclear metallohydrolases that break down phosphate esters and anhydrides in acidic conditions; they have been identified in plants, animals, and fungi. The best-characterised enzyme is from kidney bean, and that enzyme binds Fe
3+
and Zn
2+
ions. The metals bound differ according to source species; for example, the enzyme from sweet potato binds iron and manganese . The structure of the kidney bean enzyme has been solved and shows a disulfide-linked homodimer, with each monomer having a two-domain structure . Human acid phosphatase type 7 is also known as purple acid phosphatase long form. It is associated with bone resorption and microbial killing through its phosphatase activity and hydroxyl radical production . While most of the PAPs are active on a wide range of substrates, some PAPs display higher activity on phytate or 2-phosphoenolpyruvate (PEP) .
Partner of Y14 and mago (PYM1)
Type: Family

Partner of Y14 and mago (PYM, also known as WIBG) is a key regulator of the exon junction complex (EJC), a multiprotein complex that associates immediately upstream of the exon-exon junction on mRNAs and serves as a positional landmarks for the intron exon structure of genes and directs post-transcriptional processes in the cytoplasm such as mRNA export, nonsense-mediated mRNA decay (NMD) or translation .
Sigma factor binding protein 1/2 (SIB1/2)
Type: Family

This entry represents a group of plant proteins, including Sigma factor binding protein 1/2 (SIB1/2) from Arabidopsis. They belong to the large plant-specific VQ motif-containing protein family. SIB1 is a component of the RNA polymerase machinery responsible for transcription of plastid genes . SIB1 and SIB2 function as activators of WRKY33 in plant defense against necrotrophic pathogens .

In general, Arabidopsis VQPs interacted specifically with the C-terminal WRKY domains of group I and the sole WRKY domains of group IIc WRKY transcription factors . Arabidopsis VQPs reported to control stress responses include the calmodulin (CaM)-binding protein CamBP25 and VQ9, which regulate osmotic and salinity tolerance, respectively, the sigma factor binding proteins SIB1 and SIB2, which act as activators of WRKY33 in plant defence, and the negative regulator of the jasmonate defence pathway .
Midnolin (Midnolin)
Type: Family

Polycomb proteins such as Pc function to ensure correct deployment of developmental programs by epigenetically repressing target gene expression. Pc itself is regulated by midnolin. Midnolin interacts with the proteasome and recruits Pc to the complex enabling ubiquitin-independent proteasomal degradation of Pc . In
Drosophila
, midnolin is known as stuxnet. In mouse embryos, midnolin is strongly expressed in the midbrain mesencephalon on day 12.5. Midnolin is located in the nucleus and nucleolus and contains a ubiquitin domain . In rat pancreatic beta cells, midnolin is also found in the cytoplasm where it interacts with and inhibits glucokinase, and the midnolin gene is upregulated when glucose levels are low .
Zinc finger TRAF-type-containing protein 1 (ZFTRAF1)
Type: Family

Zinc finger TRAF-type-containing protein 1 (also known as cysteine and histidine-rich protein 1 (CYHR1)) is an uncharacterised protein containing a degenerate RING-type zinc finger and a TRAF-type zinc finger. It binds to, and might assist in the intracellular trafficking of, the soluble beta-galactoside-binding protein, galectin-3 .