SII-SWORD/CoKE huggingface dataset:
Uracil DNA glycosylase family 5 (UdgB-like)
Type: Domain

Uracil-DNA glycosylases are DNA repair enzymes that excise uracil residues from DNA by cleaving the N-glycosylic bond, initiating the base excision repair pathway. Uracil in DNA can arise either through the deamination of cytosine to form mutagenic U:G mispairs, or through the incorporation of dUMP by DNA polymerase to form U:A pairs . These aberrant uracil residues are genotoxic . The sequence of uracil-DNA glycosylase is extremely well conserved in bacteria and eukaryotes as well as in herpes viruses. More distantly related uracil-DNA glycosylases are also found in poxviruses .

Uracil DNA glycosylase family 5 includes Thermus thermophilus HB8 TTUDGB (also called UDGb) which is not only a Uracil-DNA glycosylase (UDG) acting on double-stranded uracil-containing DNA, but also a hypoxanthine DNA glycosylase acting on double-stranded hypoxanthine-containing DNA (except for the C/I base pair), as well as a xanthine DNA glycosylase acting on both, double-stranded and single-stranded xanthine-containing DNA. TTUDGB also excises thymine from G:T mismatched DNA, and removes analogs of uracil from DNA, including 5-hydroxymethyluracil (hmU) and 5-fluorouracil (fU) . This entry also contains Bradyrhizobium diazoefficiens family 5 homologue Blr5068 (UdgB) which has been found to efficiently excise uracil from ssDNA and dsDNA . Similar to family 4 UDGs, members of family 5 possess four conserved cysteine residues required to coordinate the [4Fe-4S] iron-sulfur cluster .
Succinate-semialdehyde dehydrogenase GabD1-like (ALDH_GabD1-like)
Type: Domain

This entry represents a domain found in a group of succinate-semialdehyde dehydrogenases, including SSADH1 from Mycobacterium tuberculosis and Sad from Escherichia coli. Succinate-semialdehyde dehydrogenase 1 (SSADH1 or GabD1) catalyzes the NADP(+)-dependent oxidation of succinate semialdehyde (SSA) to succinate. SSADH activity in Mycobacterium tuberculosis (Mtb) is encoded by both gabD1 (Rv0234c) and gabD2 (Rv1731). The Mtb GabD1 SSADH1 reportedly is an enzyme of the gamma-aminobutyrate shunt, which forms a functional link between two TCA half-cycles by converting alpha-ketoglutarate to succinate . Sad catalyses the NAD+-dependent oxidation of succinate semialdehyde to succinate. It acts preferentially with NAD as cosubstrate but can also use NADP .

Proteins containing this domain also includes Aldh from Paenarthrobacter nicotinovorans. Aldh does not display succinate semialdehyde dehydrogenase activity. Instead, it acts as an aldehyde dehydrogenase involved in the oxidative D-xylose degradation pathway. It Is able to use both NAD+ and NADP+; however, it shows a preference for NADP+ .
Nitrilase/Cyanide hydratase (Nitrilases_CHs)
Type: Family

This entry includes nitrilases, cyanide hydratases (CHs) and related proteins. This subgroup belongs to a larger nitrilase superfamily comprised of nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes, which depend on a Glu-Lys-Cys catalytic triad. This superfamily has been classified in the literature based on global and structure based sequence analysis into thirteen different enzyme classes (referred to as 1-13), this subgroup corresponds to class 1 .

Nitrilases (

) are enzymes that convert nitriles into their corresponding acids and ammonia. They are widespread in microbes as well as in plants where they convert indole-3-acetonitrile to the hormone indole-3-acetic acid. A conserved cysteine has been shown to be essential for enzyme activity; it seems to be involved in a nucleophilic attack on the
nitrile carbon atom. Cyanide hydratase (

) converts HCN to formamide. In phytopathogenic fungi, it is used to avoid the toxic effect of cyanide released by wounded plants .
Histone deacetylase 11 (HDAC_classIV)
Type: Domain

This entry represents a domain found in class IV histone deacetylases (

), also known as histone deacetylase 11 (HDAC11) . This class includes animal HDAC11, plant HDA2 and related bacterial deacetylases. Enzymes in this subfamily participate in regulation of a number of different processes through protein modification (deacetylation) . HDAC11 and HDAC6 interact with each other in the cytoplasm and nuclei of APCs (antigen presenting cells) and are recruited to the IL-10 gene promoter to regulate its transcriptional activity .

In mammals, HDAC11 proteins are known to be involved in progression of various tumours. HDAC11 plays an essential role in regulating OX40 ligand (OX40L) expression in Hodgkin lymphoma (HL); selective inhibition of HDAC11 expression significantly up-regulates OX40L and induces apoptosis in HL cell lines. Thus, inhibition of HDAC11 could be a therapeutic drug option for antitumor immune response in HL patients .
Alpha-ketoglutaric semialdehyde dehydrogenase (ALDH_KGSADH)
Type: Family

Alpha-Ketoglutaric Semialdehyde (KGSA) Dehydrogenase (KGSADH,

) catalyses the NAD(P)-dependent conversion of KGSA to alpha-ketoglutarate. This entry includes KGSADH-II (D-glucarate/D-galactarate-inducible) and KGSADH-III (hydroxy-L-proline-inducible) from Azospirillum brasilense. Both show similar high substrate specificity for KGSA and different coenzyme specificity; KGSADH-II is NAD-dependent and KGSADH-III is NADP-dependent . This entry also includes the NADP(+)-dependent aldehyde dehydrogenase from Vibrio harveyi which catalyses the oxidation of long-chain aliphatic aldehydes to acids .
NADPH dehydrogenase YqjM-like (YqjM-like)
Type: Family

This entry represents a group of NADPH dehydrogenases, including NamA (also known as YqjM) from Bacillus subtilis. YqjM is a member of the Old Yellow Enzyme (OYE) family of flavin oxidoreductases. Similar to other OYE members, YqjM binds the FMN cofactor non-covalently and reduces the flavin in the reductive half-reaction at the expense of NADPH. It transfers electrons from the reduced flavin to the double bond of a variety of alpha, beta-unsaturated carbonyl compounds and accepts also electrophilic xenobiotics such as nitroglycerin, N-ethylmaleimide, and trinitrotoluene as substrates for the oxidative half-reaction .

This entry also includes AfvA from Aspergillus flavus. AfvA is part of the gene cluster that mediates the biosynthesis of aflavarin, a bicoumarin that exhibits anti-insectan activity against the fungivorous beetle C.hemipterus .
Pae0151-like, PIN domain (PIN_Pae0151-like)
Type: Domain

This PIN domain can be found in the Pyrobaculum aerophilum proteins, Pae0151 (also known as VapC3) and Pae2754 (also known as VapC9), and their homologues . They are similar to the PIN domains of the Mycobacterium tuberculosis VapC and Neisseria gonorrhoeae FitB toxins of the prokaryotic toxin/antitoxin operons, VapBC and FitAB, respectively, which are believed to be involved in growth inhibition by regulating translation. These toxins are nearly always co-expressed with an antitoxin, a cognate protein inhibitor, forming an inert protein complex. Disassociation of the protein complex activates the ribonuclease activity of the toxin by an, as yet undefined mechanism .

PIN domains are small protein domains identified by the presence of three strictly conserved acidic residues. Apart from these three residues, there is poor sequence conservation . PIN domains are found in eukaryotes, eubacteria and archaea. In eukaryotes they are ribonucleases involved in nonsense mediated mRNA decay and in processing of 18S ribosomal RNA . In prokaryotes, they are the toxic components of toxin-antitoxin (TA) systems, their toxicity arising by virtue of their ribonuclease activity. The PIN domain TA systems are now called VapBC TAs(virulence associated proteins), where VapB is the inhibitor and VapC, the PIN-domain ribonuclease toxin .
ADP-ribosylation factor-like protein 8A/8B (Arl8a/8b)
Type: Family

This entry includes ADP-ribosylation factor-like protein 8A/8B (Arl8a/Arl8b) and related proteins. In animals, Arl8a and Arl8b are small GTPases that regulate axonal transport of synaptic vesicle proteins and lysosome motility . Human Arl8a/Arl8b (also known as GIE2/GIE1) are required for chromosome segregation .
Galectin-like (Galectin-like)
Type: Family

This entry represents members of a family of galactoside-binding lectins (galectins) with related amino acid sequences, sometimes referred to as S-type or S-Lac lectins. Members of this family are found in tissues of many animals, ranging from lower invertebrates such as sponges and nematodes to mammals, including humans . This family also includes Galectin-related protein and Grifin, galectin relatives which lack of beta-galactosides binding activity.

Animal lectins are proteins that bind to sugars and are involved in most non-structural roles of sugars, including trafficking of glycoconjugates and cell-cell recognition. Although they may be structurally very complex, they typically bind through the activity of a specific compact protein domain known as a carbohydrate-binding domain or CRD . Animal lectins display a wide variety of architectures, and are classified according to the carbohydrate-recognition domain (CRD) of which there are two main types, S-type and C-type.

Galectins (previously S-lectins) bind exclusively beta-galactosides like lactose. They do not require metal ions for activity. Galectins are found predominantly, but not exclusively in mammals . Their function is unclear. They are developmentally regulated and may be involved in differentiation, cellular regulation and tissue construction. Mammalian galectins typically bind beta-galactosides. Their CRD shows a structural similarity to L-type lectin CRDs, but no strong sequence similarity, suggesting convergent evolution . They are classified into three subgroups: proto type, which contain one CRD (Gal-1, -2, -5, -7, -10, -11, -13, -14 and -15); tandem repeat type, which contain two CRDs in tandem (Gal-4, -6, -8, -9 and -12); and chimera type, which contain one CRD and an additional non-lectin domain (Gal-3) .
IQ domain-containing protein IQM (IQM)
Type: Family

This entry includes IQM1-6 from Arabidopsis. They contain the IQ motif, IQxxxRGxxxR, which is one of a few recognition motifs for CaM-binding protein. Besides one copy of IQ motif, they share domains related to pea heavy-metal induced protein 6A and ribosome-inactivating protein, trichosanthin, which is able to bind to and remove adenine residues from rRNA . This entry also includes some uncharacterised bacterial and fungal proteins.
Protein TRIGALACTOSYLDIACYLGLYCEROL 4-like (TGD4-like)
Type: Family

TGDs are trigalactosyldiacylglycerol proteins required for chloroplast membrane lipid synthesis. The TGD1, -2, and -3 proteins form a putative ABC (ATP-binding cassette) transporter transporting ER-derived lipids through the inner envelope membrane of the chloroplast, while TGD4 binds phosphatidic acid and resides in the outer chloroplast envelope .

This entry represents TGD4, which is involved in endoplasmic reticulum-to-chloroplast lipid trafficking .
Sucrose-phosphate synthase (SPS)
Type: Family

In plants, sucrose synthesis involves just two enzymes: sucrose-phosphate synthase (SPS) catalyses the synthesis of sucrose-6F-phosphate (Suc6P), which is then hydrolysed to sucrose by sucrose-phosphatase (SPP) . This entry represents the sucrose-phosphate synthase (SPS) family. In Arabidopsis there are 4 SPS proteins, including AtSPSA1 (At5g20280), AtSPSA2 (At5g11110), AtSPSB (At1g04920) and AtSPSC (At4g10120). It has been shown that the four SPS proteins are functionally redundant in processes that are important for plant growth, vegetative and reproductive development, and nonstructural carbohydrate metabolism . This entry also includes bacterial sequences.
Universal stress protein PHOS32/34 (PHOS32/34)
Type: Family

This entry includes a group of plant proteins, including AtPHOS32 and AtPHOS34 from Arabidopsis. They show similarity to bacterial universal stress protein A. AtPHOS32 is a substrate of MAP kinases 3 and 6 .
Sanguinarine reductase SARED1-like (SARED1-like)
Type: Family

This entry includes SARED1 from Eschscholzia californica, and At5g02240, At2g37660 from Arabidopsis. This group of proteins evolved from a plant-specific branch of the ubiquitous Rossmann fold NAD(P)H/NAD(P)(+) binding reductases, with NADP-dependent epimerases or hydroxysteroid reductases as the most likely ancestors .

Sanguinarine (SA) belongs to a family of plant secondary metabolites called quaternary benzo[c]phenanthridine alkaloids (QBAs). SARED1 is a sanguinarine reductase that catalyses the reduction of benzophenanthridines, preferentially sanguinarine, to the corresponding dihydroalkaloids .
Chalcone--flavonone isomerase (CFI)
Type: Family

This entry represents a group of plant chalcone--flavonone isomerases (CHIs), including CHI1/2 from Arabidopsis and CHIA/B from Petunia hybrida . CHI catalyses the conversion of chalcones to chiral (S)-flavanones, which is a committed step in the production of plant flavonoids, compounds that contribute to attraction, defence and development .
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 4, plant (OST4_plant)
Type: Family

This entry represents OST4 from plants, including OST4A/4B/4C from Arabidopsis. They share the protein sequence similarity with animals OST4, which is part of the oligosaccharyl transferase (OST) complex that catalyses the initial transfer of a defined glycan (Glc3Man9GlcNAc2 in eukaryotes) from the lipid carrier dolichol-pyrophosphate to an asparagine residue within an Asn-X-Ser/Thr consensus motif in nascent polypeptide chains, the first step in protein N-glycosylation .
Ferredoxin-thioredoxin reductase, variable chain (FTRV)
Type: Family

The ferredoxin-thioredoxin reductase (FTR) is the essential enzyme of the light dependent regulatory system controlling enzyme activities in oxygenic, photosynthetic cells. The ferredoxin-thioredoxin reductase (FTR) is composed of a catalytic containing a [4Fe-4S] cluster, and a variable subunit. This entry represents the variable subunit of the ferredoxin-thioredoxin reductase (FTR) from plants and cyanobacteria .
Bowman-Birk type wound-induced proteinase inhibitor WIP1 (WIP1)
Type: Family

WIP1 is a wound-induced serine protease inhibitor. It shows high similarity to members of the Bowman-Birk family of serine protease inhibitors .
bZIP transcription factor RISBZ3/4/5 (RISBZ3/4/5)
Type: Family

This entry includes a group of plant bZIP transcription factors, including RISBZ3/4/5 from rice. RISBZ1 has been shown to interact with the GCN4 motif and affect the expression of storage protein genes .
Protein PYRICULARIA ORYZAE RESISTANCE 21 (PI21)
Type: Family

This entry includes a group of plant proteins, including protein PYRICULARIA ORYZAE RESISTANCE 21 (PI21) from rice. PI21 is a proline rich protein that includes a putative heavy metal-binding domain and putative protein-protein interaction motifs. PI21 appears to slow the plant's defense responses, which may support optimization of defense mechanisms .
Protein RICE SALT SENSITIVE 3-like (RSS3-like)
Type: Family

This entry includes a group of plant proteins, including Protein RICE SALT SENSITIVE 3 (RSS3) from rice. RSS3 interacts with non-R/B-like bHLH transcription factors and forms an RSS3-JAZ-bHLH ternary complex in the nucleus. It also interacts with JASMONATE ZIM-DOMAIN proteins, which are the key regulators of jasmonate (JA) signaling .
Protein LAX PANICLE 2-like (LAX2-like)
Type: Family

This entry represents a group of plant proteins, including protein LAX PANICLE 2 (LAX2) from rice. LAX2 is a nuclear protein that acts together with LAX1 in rice to regulate the process of axillary meristem formation .
Transcription factor ILI2-like (ILI2-like)
Type: Family

This entry comprises a group of plant proteins, including ILI2 from rice. ILI2 is a putative transcription factor.
Casparian strip membrane protein/CASP-like protein (CASPL)
Type: Family

Casparian Strip Membrane Domain Proteins (CASPs) are four-membrane-span proteins that recruit the lignin polymerisation machinery necessary for the deposition of Casparian strips in the endodermis. CASP-like proteins (CASPLs) are found in all major divisions of land plants as well as in green algae. In Arabidopsis, CASPLs show specific expression in a variety of cell types .

This entry represents a group of CASP domain-containing proteins, including casparian strip membrane protein 1-7, CASP-like protein 1E1, 1D1 and CASP-like proteins 1U1/2/3 from rice.
Glycosyltransferase BC10-like (BC10-like)
Type: Family

This entry represents a group of glycosyltransferases mostly from plants, including BC10 from rice. BC10 is a Golgi-located type II membrane protein required for the regulation of cellulose biosynthesis in the cell wall . It possesses low glycosyltransferase activity .
Pentatricopeptide repeat-containing protein At5g66631-like (At5g66631-like)
Type: Family

This entry represents a group of pentatricopeptide repeat-containing proteins, including At5g66631 from Arabidopsis. Their function is not clear.
Thioredoxin-like 4, chloroplastic (TRL4_chloroplastic)
Type: Family

This entry represents thioredoxin-like 4 from plants. It is a predicted thiol-disulfide oxidoreductase that may participate in various redox reactions .
Reticulon-like protein B22/B23 (RTNLB22/23)
Type: Family

This entry represents a group of Reticulon-like proteins from plants, including RTNLB22/23 from Arabidopsis. Their function is not clear.
Peptidyl-prolyl cis-trans isomerase CYP28-like (CYP28-like)
Type: Family

This entry represents a group of predicted peptidyl-prolyl cis-trans isomerases from plants, including CYP28 from Arabidopsis .
Pentatricopeptide repeat-containing protein PPR5-like (PPR5-like)
Type: Family

This entry represents a group of plant pentatricopeptide repeat-containing proteins, including PPR5 from maize and rice and At2g30780/At4g39620/At2g48000/At3g06430 from Arabidopsis. PPR5 is a chloroplastic protein that binds to single-stranded RNA and influences both RNA stability and splicing . It has been shown to stabilise the chloroplast trnG pre-RNA by directly binding to a group II intron, where it protects an endonuclease-sensitive site and stimulates splicing . At4g39620 is involved in embryo morphogenesis . At3g06430, also known as PPR2 and EMBRYO DEFECTIVE 2750 (EMB2750), binds to plastid 23S rRNA and plays an important role in the first mitotic division during gametogenesis and in cell proliferation during embryogenesis .
Peptidyl-prolyl cis-trans isomerase FKBP18-like (FKBP18-like)
Type: Family

This entry represents a group of predicted plant peptidyl-prolyl cis-trans isomerases, including FKBP18 (At1g20810,

) from Arabidopsis.
FCS-Like Zinc finger 17/18 (FLZ17/18)
Type: Family

This entry represents a group plant FCS-Like Zinc finger proteins, including FLZ17 and FLZ18 from Arabidopsis. They have been shown to interact with SNF1-related kinase (SnRK1) and may act as mediators conferring tissue- and stimulu-type specific differences in SnRK1 regulation .
Thioredoxin-like protein CITRX, chloroplastic (CITRX)
Type: Family

This entry represents thioredoxin-like protein CITRX and related proteins from plants. In Arabidopsis, TRX z (At3g06730) is a thiol-disulfide oxidoreductase that plays a role in chloroplast development . It interacts with fructokinase-like protein 1 (FLN1) represent subunits of the plastid-encoded RNA polymerase (PEP), suggesting a role of chloroplast gene expression .
Photosynthetic NDH subunit of lumenal location 4/FKBP13-like (PNSL4/FKBP13-like)
Type: Family

This family represents a group of plant FKBP-type peptidylprolyl isomerases, including photosynthetic NDH subunit of lumenal location 4 (PNSL4, also known as FKBP16-2, At4g39710), FKBP13 and related proteins. In Arabidopsis, FKBP16-2 is localized to the lumen side of the thylakoid and may be an NAD(P)H dehydrogenase (NDH) complex subunit specific to chloroplasts . FKBP13 shows significant sequence similarity to PNSL4 . It interacts with the Rieske Fe-S subunit of the cytochrome b6f complex .
F-box protein SNE/GID2 (SNE/GID2)
Type: Family

This entry represents F-box proteins SNE and GID2. In Arabidopsis, SNE (SNEEZY or SLY2, At5g48170) and its closest homologue GID2 (also known as SLEEPY1, SLY1) are the F-box subunits of a Skp-Cullin-F-box (SCF) E3 ubiquitin ligase complex that positively regulates the gibberellin (GA) signaling pathway. SCF interacts with its substrates, the DELLA proteins, to promote their ubiquitination and degradation, and mediate GA responses . SNE over-expression can partially compensate sly1-10 mutant phenotype of dwarfism . It may function as a redundant positive regulator of GA signaling .
Peptidyl-prolyl cis-trans isomerase CYP26-2-like (CYP26-2-like)
Type: Family

This entry represents a group predicted peptidyl-prolyl cis-trans isomerases from plants, including CYP26-2 from Arabidopsis.
WUSCHEL-related homeobox 4 (WOX4)
Type: Family

This entry represents WOX4, a WUSCHEL-related homeobox protein from plants. Proteins in this family contain a sequence of eight residues (TLPLFPMH) downstream of the homeodomain called the WUS box. WOX4 is a transcription factor and part of the TDIF-TDR-WOX4 signaling pathway that plays a crucial role in the maintenance of the vascular meristem organisation during secondary growth .
Universal stress protein A-like protein, plant (At3g01520-like_plant)
Type: Family

This entry represents a group of plant universal stress protein (USP)-like proteins, including AT3G01520 from Arabidopsis. AT3G01520 binds to AMP and contains the ATP-binding loop, which suggests that it belongs to the ATP-binding USP subfamily .
Exportin 4/7-like (XPO4/7-like)
Type: Family

This entry includes Ran-binding protein 17 from humans and similar proteins.

Exportins bind cargo molecules in the nuclei and transport them through nuclear pores to the cytoplasm, a process that requires RanGTP. XPO7 mediates the nuclear export of proteins with broad substrate specificity. They bind cooperatively to its cargo and to the GTPase Ran in its active GTP-bound form .
Protein THYLAKOID ASSEMBLY 8-like (THA8-like)
Type: Family

THYLAKOID ASSEMBLY 8 (THA8) is a pentatricopeptide repeat (PPR)-containing protein that mediates group II organellar RNA introns splicing. It is required for embryo development in Arabidopsis . In maize, mutation of the THA8 gene causes defects in the biogenesis of chloroplast thylakoid membranes .
Chalcone--flavonone isomerase 3-like (CHI3-like)
Type: Family

This entry includes a group of predicted chalcone--flavonone isomerases from plants, such as CHI3 (also known as CHIL, At5g05270) from Arabidopsis. It may function with TT5 to promote flavonoid production . This entry also includes CHIL2 from Humulus lupulus (European hop). CHIL2 is involved in DMX (demethylxanthohumol) biosynthesis .
Thioredoxin-like 3-3 (TRL33)
Type: Family

Thioredoxins (Trxs) are ubiquitous enzymes with a CXXC active site that catalyses the reduction of disulfide bonds. This entry represents a group of plant thioredoxin-like proteins, including At3g53220 from Arabidopsis. The active site of At3g53220 contains a CGVC motif which differs from the conserved CGPC motif.
Protein BLISTER (BLISTER)
Type: Family

This entry represents a group of plant proteins, including protein BLISTER (BLI) from Arabidopsis thaliana. BLI interacts with the Pc-G histone methyltransferase CURLY LEAF (CLF) and may also act independently in Arabidopsis development . It negatively controls the activity of IRE1A/IRE1B under normal growth condition .
Uncharacterized protein At5g19025-like (At5g19025-like)
Type: Family

The function of At5g19025 is not clear.
Peptidyl-prolyl cis-trans isomerase FKBP17-1-like (FKBP17-1-like)
Type: Family

This entry represents a group of predicted plant peptidyl-prolyl cis-trans isomerases, including FKBP17-1 (At4g19830) from Arabidopsis.