SII-SWORD/CoKE huggingface dataset:
Mechanosensitive ion channel MscS, archaea/bacteria type (MscS_archaea/bacteria_type)
Type: Family

This entry represent a group of mechanosensitive (MS) ion channel proteins mainly from archaea and bacteria.

Mechanosensitive channels provide protection against hypo-osmotic shock, responding both to stretching of the cell membrane and to membrane depolarisation. They are present in the membranes of organisms from the three domains of life: bacteria, archaea, and eukarya . There are two families of MS channels: large-conductance MS channels (MscL) and small-conductance MS channels (MscS or YGGB). The pressure threshold for MscS opening is 50% that of MscL . The MscS family is much larger and more variable in size and sequence than the MscL family. Much of the diversity in MscS proteins occurs in the size of the transmembrane regions, which ranges from three to eleven transmembrane helices, although the three C-terminal helices are conserved.
Mechanosensitive ion channel YbiO (YbiO_bact)
Type: Family

This entry represents mechanosensitive (MS) ion channel proteins such as YbiO, mainly from bacteria .

Mechanosensitive channels provide protection against hypo-osmotic shock, responding both to stretching of the cell membrane and to membrane depolarisation. They are present in the membranes of organisms from the three domains of life: bacteria, archaea, and eukarya . There are two families of MS channels: large-conductance MS channels (MscL) and small-conductance MS channels (MscS or YGGB). The pressure threshold for MscS opening is 50% that of MscL . The MscS family is much larger and more variable in size and sequence than the MscL family. Much of the diversity in MscS proteins occurs in the size of the transmembrane regions, which ranges from three to eleven transmembrane helices, although the three C-terminal helices are conserved.
Dehydration-responsive element-binding protein 1A-I (DRE1A-I)
Type: Family

This entry represents a group of plant DREB1/CBF-type transcription factors, including DREB1A-I from rice. They interact with the DRE/CRT cis-acting element and control the expression of many stress-inducible genes .
Intron splicing facilitator CRS1/CFM2/CFM3 (CRS1/CFM2/CFM3)
Type: Family

This entry represents a group of plant intron splicing facilitator, including CRS1/CFM2/CFM3 from Arabidopsis. They contain the CRM domain, which is a RNA binding domain . CRS1 is a chloroplastic protein required for the splicing of group IIA introns by regulating the intron folding . CFM3 is involved in group IIB intron splicing , while CFM2 functions dually in group I and group II intron splicing .
Two-component response regulator ARR-like (ARR-like)
Type: Family

Plant response regulators (RRs, called ARRs in Arabidopsis thaliana) are a class of MYB-type transcription factors that act as major players in the transcriptional activation of cytokinin-responsive genes. They directly regulate the expression of type-A ARR genes and other downstream target genes. Cytokinin is a plant hormone implicated in many growth and development processes including shoot organogenesis, leaf senescence, sink/source relationships, vascular development, lateral bud release, and photomorphogenic development. Cytokinin signaling involves a phosphorelay cascade by histidine kinase receptors (AHKs), histidine phosphotransfer proteins (AHPs) and downstream ARRs .

ARRs are divided into two groups, type-A and -B, according to their sequence and domain structure. Type-A ARRs contain a central receiver domain along with short N- and C-terminal extensions and are transcriptionally induced by cytokinin. Type-B ARRs contain a receiver domain followed by a DNA binding domain and function as transcription factors .
GATA transcription factor TIFY-like (TIFY-like)
Type: Family

This entry represents a group of plant GATA transcription factors, including GATA24/25/28 from Arabidopsis. They contain the GATA-type zinc-finger domain with a longer spacer between its two sets of conserved cysteine residues (C-X2-C-X20-C-X2-C) . This family is known as the ZIM or the TIFY family. Proteins in this family are plant-specific transcription factors that play crucial roles in cross talk between Jasmonic Acid and other phytohormones like gibberellins, salicylic acid, abscisic acid, auxin, and ethylene signaling pathways .
Zinc finger protein CONSTANS-like (CONSTANS-like)
Type: Family

This entry represents a group of plant zinc finger proteins, including CONSTANS and related proteins. CONSTANS is a transcription factor that acts in the long day flowering pathway and may mediate between the circadian clock and the control of flowering . This entry also includes rice Ghd7 and CO3, which also control rice flowering .
At4g08330-like (At4g08330-like)
Type: Family

This entry includes a group of uncharacterised plant proteins, including At4g08330 from Arabidopsis.

These proteins are predicted to adopt a typical β-tent fold with zinc coordinating residues conserved. It is closely related to SelR domain [

].
Cytokinin-induced F-Box protein AT3G44326-like (AT3G44326-like)
Type: Family

This entry represents a group of plant cytokinin-induced F-box proteins, including At2g27310, At3g44326 and At2g36090 from Arabidopsis. AT3G44326, also known as CFB, is expressed in all plant tissues, predominantly in root tissue .
At2g27730-like (At2g27730-like)
Type: Family

This entry represents a group of uncharacterised plant mitochondrial proteins, including A22g27730 from Arabidopsis .
GPI-anchored protein At5g19230-like (At5g19230-like)
Type: Family

This entry represents a group of plant GPI-anchored proteins, including AT5G19230 from Arabidopsis . Their function is not clear.
F-box protein FBS1-like (FBS1-like)
Type: Family

This entry represents a group of plant F-box proteins, including AT1G61340 (FBS1) , AT4G21510 (FBS2/F-box protein SKIP27), AT4G05010 (FBS3) and AT4G35930 (FBS4) from Arabidopsis. AtFBS1 has been shown to interact with ASK1, the component of the SCF complex that binds the F-box. AtFBS1 and AtFBS3 are induced in response to osmotic stress, hormone treatment or A. brassicicola infection .
Protein IN CHLOROPLAST ATPASE BIOGENESIS (PAB)
Type: Family

This entry represents a group of plant proteins, including PAB (Protein IN CHLOROPLAST ATPASE BIOGENESIS) from Arabidopsis. PAB is a chloroplastic chaperone that functions downstream of chaperonin 60 (Cpn60)-mediated CF1gamma subunit folding to promote its assembly into the catalytic core of the chloroplast ATP synthase .
Membrane protein At1g75140-like (At1g75140-like)
Type: Family

This entry represent a group of plant proteins, including At1g75140 from Arabidopsis. At1g75140 is a membrane protein with unknown function .
KIN14B-interacting protein At4g14310-like (At4g14310-like)
Type: Family

This entry represents a group of plant proteins, including At4g14310 from Arabidopsis. At4g14310 may be involved in division plane determination .
Holliday junction resolvase MOC1-like (MOC1-like)
Type: Family

This entry represents a group of proteins mostly from proteobacteria and plants, including MOC1 from Arabidopsis. MOC1 is a chloroplastic protein and a structure-specific endonuclease that resolves Holliday junction (HJ) intermediates during genetic recombination. It is structurally similar to a bacterial Holliday junction resolvase, resistance to ultraviolet (Ruv) C . Its structure has been resolved .
LYRM9, LYR domain (Complex1_LYR_LYRM9)
Type: Domain

LYRM9 is an uncharacterised LYR motif-containing protein that belongs to the Complex1_LYR-like superfamily which consists of proteins of diverse functions that are exclusively found in eukaryotes and contain the conserved tripeptide 'LYR' close to the N terminus.
NDUFB9, LYR domain (Complex1_LYR_NDUFB9_LYRM3)
Type: Domain

NDUFB9, also called LYR motif-containing protein 3 (LYRM3), is an accessory subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (complex I), and is believed to be not involved in catalysis. In general, accessory subunits are integral for assembly and function of Complex I, which functions in the transfer of electrons from NADH to the respiratory chain . NDUFB9 belongs to the Complex1_LYR-like superfamily that consists of proteins of diverse functions that are exclusively found in eukaryotes and contain the conserved tripeptide 'LYR' close to the N terminus.
LYRM2, LYR domain (Complex1_LYR_LYRM2)
Type: Domain

LYRM2 is an uncharacterised LYR motif-containing protein that belongs to the Complex1_LYR-like superfamily which consists of proteins of diverse functions that are exclusively found in eukaryotes; these proteins contain the conserved tripeptide 'LYR' close to the N terminus .
LYRM1, LYR domain (Complex1_LYR_LYRM1)
Type: Domain

LYR motif-containing protein 1 (LYRM1) may promote cell proliferation and inhibition of apoptosis of preadipocytes . Overexpression of the human LYRM1 causes mitochondrial dysfunction and induces insulin resistance in 3T3-L1 adipocytes . LYRM1 belongs to the Complex1_LYR-like superfamily that consists of proteins of diverse functions that are exclusively found in eukaryotes and contain the conserved tripeptide 'LYR' close to the N terminus.
SDHAF1, LYR domain (Complex1_LYR_SDHAF1_LYRM8)
Type: Domain

SDHAF1, also called LYRM8, is a LYR complex-II specific assembly factor that plays an essential role in the assembly of succinate dehydrogenase (SDH), an enzyme complex (also referred to as respiratory complex II) that is a component of both the tricarboxylic acid (TCA) cycle and the mitochondrial electron transport chain, and which couples the oxidation of succinate to fumarate with the reduction of ubiquinone (coenzyme Q) to ubiquinol. It promotes maturation of the iron-sulfur protein subunit SDHB of the SDH catalytic dimer, protecting it from the deleterious effects of oxidants . SDHAF1 may act together with SDHAF3 . It is mutated in SDH-defective infantile leukoencephalopathy . SDHAF1 belongs to the Complex1_LYR-like superfamily that consists of proteins of diverse functions that are exclusively found in eukaryotes and contain the conserved tripeptide 'LYR' close to the N terminus.
ETFRF1, LYR domain (Complex1_LYR_ETFRF1_LYRM5)
Type: Domain

ETFRF1, also called LYR motif-containing protein 5 (LYRM5), or Ghiso (growth-factor inducible soluble) factor, acts as a regulator of the electron transfer flavoprotein by promoting the removal of flavin from the ETF holoenzyme (composed of ETFA and ETFB) . It belongs to the Complex1_LYR-like superfamily that consists of proteins of diverse functions that are exclusively found in eukaryotes and contain the conserved tripeptide 'LYR' close to the N terminus.
LYRM4, LYR domain (Complex1_LYR_LYRM4)
Type: Domain

LYRM4, also called ISD11, is a eukaryote-specific component of the mitochondrial biogenesis of Fe-S clusters which are essential cofactors in multiple processes, including oxidative phosphorylation . It is required for nuclear and mitochondrial iron-sulfur protein biosynthesis by forming a complex with, and stabilizing, the sulfur donor NFS1 . LYRM4 belongs to the Complex1_LYR-like superfamily that consists of proteins of diverse functions that are exclusively found in eukaryotes and contain the conserved tripeptide 'LYR' close to the N terminus.
LYRM7, LYR domain (Complex1_LYR_LYRM7)
Type: Domain

LYRM7 is an assembly factor required for Rieske iron sulfur (Fe-S) protein UQCRFS1 incorporation into the cytochrome b-c1 (CIII) complex. It functions as a chaperone, binding to this subunit within the mitochondrial matrix and stabilizing it prior to its translocation and insertion into the late CIII dimeric intermediate within the mitochondrial inner membrane . LYRM7 mutations cause a multifocal cavitating leukoencephalopathy with a distinct and recognizable magnetic resonance imaging (MRI) pattern . LYRM7 belongs to the Complex1_LYR-like superfamily that consists of proteins of diverse functions that are exclusively found in eukaryotes and contain the conserved tripeptide 'LYR' close to the N terminus.
NDUFA6, LYR domain (Complex1_LYR_NDUFA6_LYRM6)
Type: Domain

NDUFA6, also called LYR motif-containing protein 6 (LYRM6), is an accessory subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I), and is believed to be not involved in catalysis . In general, accessory subunits are integral for assembly and function of Complex I, which functions in the transfer of electrons from NADH to the respiratory chain . NDUFA6 belongs to the Complex1_LYR-like superfamily that consists of proteins of diverse functions that are exclusively found in eukaryotes and contain the conserved tripeptide 'LYR' close to the N terminus.
MIEF1-MP, LYR domain (Complex1_LYR_MIEF1-MP)
Type: Domain

MIEF1-MP, also called alternative mitochondrial elongation factor 1 (MIEF1) protein (AltMIEF1), or MIEF1 upstream open reading frame protein, is involved in the regulation of mitochondrial fission mediated by dynamin-1-like protein (DNM1L). It positively regulates mitochondrial translation . MIEF1-MP belongs to the Complex1_LYR-like superfamily that consists of proteins of diverse functions that are exclusively found in eukaryotes and contain the conserved tripeptide 'LYR' close to the N terminus.
Protein GAMETE EXPRESSED 3-like (GEX3-like)
Type: Family

This entry represents a group of plant proteins, including GEX3 from Arabidopsis. GEX3 is essential for micropylar pollen tube guidance and plays a role during early embryogenesis .
NHL2, NHL repeat domain (NHL2_NHL_rpt_dom)
Type: Domain

This entry represents the NHL repeat domain found in NHL2 and related proteins. The NHL repeat domain is found C-terminally of a thioredoxin domain. The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other β-propeller structures .

This domain can also be found in Protein SUPPRESSOR OF QUENCHING 1 (SOQ1) from Arabidopsis. SOQ1 is a chloroplastic protein required to maintain light harvesting efficiency, especially during nonphotochemical quenching (NPQ) recovery, via the regulation of chlorophyll excited-state lifetime probably by preventing the formation of a slowly reversible form of antenna quenching .
HMGB9-like, ARID/BRIGHT DNA binding domain (ARID_HMGB9-like)
Type: Domain

Proteins containing this domain includes a group of conserved plant DNA-binding proteins, such as HMGB9 (or ARID-HMG1), HMGB10 (or ARID-HMG2), HMGB11, and HMGB15. They have been termed ARID-HMG proteins, due to containing two DNA-binding domains, an N-terminal AT-rich DNA-interacting domain (ARID, also known as BRIGHT), and a C-terminal high mobility group (HMG)-box domain. They are widely expressed in Arabidopsis and localize primarily to the nucleus. HMGB9/ARID-HMG1 binds specifically to A/T-rich DNA . HMGB15 is a transcription factor predominantly expressed in mature pollen grains and pollen tubes. It may work in the form of a homodimer, or interact with HMGB9, HMGB10 and HMGB11 to form heteromultimers in plant cells. HMGB15 is required for pollen tube growth in Arabidopsis and is involved in transcriptional regulation through the interaction with AGL66 and AGL104 .
Serine acetyltransferase, LbH domain (LbH_SAT)
Type: Domain

Serine acetyltransferase (SAT) catalyses the CoA-dependent acetylation of the side chain hydroxyl group of L-serine to form O-acetylserine, as the first step of a two-step biosynthetic pathway in bacteria and plants leading to the formation of L-cysteine. This reaction represents a key metabolic point of regulation for the cysteine biosynthetic pathway due to its feedback inhibition by cysteine . The enzyme is a 175 kDa homohexamer, composed of a dimer of homotrimers. Each subunit contains an N-terminal α helical region and a C-terminal left-handed β-helix (LbH) subdomain with 5 turns, each containing a hexapeptide repeat motif characteristic of the acyltransferase superfamily of enzymes. The trimer interface mainly involves the C-terminal LbH subdomain while the dimer (of trimers) interface is mediated by the N-terminal α helical subdomain .
Sorbitol dehydrogenase-like (SDH-like)
Type: Family

Sorbitol dehydrogenase is an NAD(+) binding protein of the polyol pathway, which interconverts glucose and fructose. Sorbitol dehydrogenase is tetrameric and has a single catalytic zinc per subunit . Proteins in this entry also includes D-xylulose reductases and L-arabinitol 4-dehydrogenases from fungi, such as XdhA from Aspergillus oryzae and Lad1 from Hypocrea jecorina. XdhA catalyses the conversion of xylitol to D-xylulose. Xylose is a major component of hemicelluloses such as xylan . Lad1 catalyses the NAD-dependent oxidation of L-arabinitol to L-xylulose in the fungal L-arabinose catabolic pathway .
ADCK1-like domain (ADCK1_dom)
Type: Domain

This entry represents a domain found in AarF domain containing kinase 1 (ADCK1) and related proteins. Drosophila ADCK1 plays an important role in maintaining mitochondrial morphologies and functions in the muscle . Proteins containing this domain also include Mcp2, which is a component of MIOREX complexes, large expressome-like assemblies of ribosomes with factors involved in all the steps of post-transcriptional gene expression . It is also involved in mitochondrial lipid homeostasis .
UbiB domain, bacteria (UbiB_bact)
Type: Domain

UbiB kinases are present in archaea, bacteria and eukaryotes. The founding member of the UbiB family, UbiB from Escherichia coli, is required for the aerobic biosynthesis of coenzyme Q (CoQ). In eukaryotes, UbiB homologues are found exclusively in mitochondria and plastids. This entry represents the UbiB domain found in bacteria .
Xanthoxin dehydrogenase ABA2-like (ABA2-like)
Type: Family

This entry represents a group of plant oxidoreductases, including ABA2 from Arabidopsis and momilactone A synthase from rice. Momilactone A synthase catalyses the conversion of 3beta-hydroxy-9betaH-pimara-7,15-dien-19,6beta-olide into momilactone A , while Arabidopsis ABA2 catalyses the conversion of xanthoxin to abscisic aldehyde during abscisic acid (ABA) biosynthesis .
Oxalate--CoA ligase Pcs60-like (Pcs60-like)
Type: Family

Proteins in this entry includes Fum10 from Gibberella moniliformis and Pcs60 from Saccharomyces cerevisiae. Fum10 is an acyl-CoA synthetase and part of the gene cluster that mediates the biosynthesis of fumonisins B1 (FB1), B2 (FB2), B3 (FB3), and B4 (FB4), which are carcinogenic mycotoxins . Pcs60 catalyses the first step in a degradation pathway of oxalate to CO2 to protect the cell against the harmful effects of oxalate derived from endogenous processes or an environmental sources .
Long-chain fatty acid CoA synthetase, eukaryotic (LC-FACS_euk)
Type: Family

The members of this family are eukaryotic fatty acid CoA synthetases that activate fatty acids with chain lengths of 12 to 20. LC-FACS catalyses the formation of fatty acyl-CoA in a two-step reaction: the formation of a fatty acyl-AMP molecule as an intermediate, and the formation of a fatty acyl-CoA. This is a required step before free fatty acids can participate in most catabolic and anabolic reactions . Organisms tend to have multiple isoforms of LC-FACS genes with multiple splice variants. For example, nine genes are found in Arabidopsis and six genes are expressed in mammalian cells .
Phenylcoumaran benzylic ether reductase-like (PCBER-like)
Type: Domain

Phenylcoumaran benzylic ether reductases and pinoresinol-lariciresinol reductases are NADPH-dependent aromatic alcohol reductases, and are atypical members of the SDR (short-chain dehydrogenase/reductase) family. Other proteins containing this domain are identified as eugenol synthase . These proteins contain an N-terminal characteristic of NAD(P)-binding proteins and a small C-terminal domain presumed to be involved in substrate binding, but they do not have the conserved active site Tyr residue typically found in SDRs .
Carbonyl reductase [NADPH] 1-like (CBR1-like)
Type: Family

This entry represents a group of NADPH-dependent short chain dehydrogenase/reductases, including human carbonyl reductase 1 (CBR1) and CBR3. CBR1 is an NADPH-dependent SDR with broad substrate specificity and may be responsible for the in vivo reduction of quinones, prostaglandins, and other carbonyl-containing compounds . This entry also includes poppy NADPH-dependent salutaridine reductase which catalyses the stereospecific reduction of salutaridine to 7(S)-salutaridinol in the biosynthesis of morphine , and Arabidopsis SDR1, a menthone reductase, which catalyses the reduction of menthone to neomenthol, a compound with antimicrobial activity; SDR1 can also carry out neomenthol oxidation .
G-box binding factor 1-like, bZIP domain, plant (bZIP_plant_GBF1)
Type: Domain

This domain can be found in plant bZIP transcription factors, including Arabidopsis thaliana G-box binding factor 1 (GBF1) , Zea mays Opaque-2 and Ocs element-binding factor 1 (OCSBF-1) , Triticum aestivum Histone-specific transcription factor HBP1 (or HBP-1a) , Petroselinum crispum Light-inducible protein CPRF3 and CPRF6, and Nicotiana tabacum BZI-3 , among many others . Opaque-2 plays a role in affecting lysine content and carbohydrate metabolism, acting indirectly on starch/amino acid ratio . bZIP G-box binding factors (GBFs) contain an N-terminal proline-rich domain in addition to the bZIP domain. GBFs are involved in developmental and physiological processes in response to stimuli such as light or hormones .

bZIP factors act in networks of homo and heterodimers in the regulation of a diverse set of cellular processes. The bZIP structural motif contains a basic region and a leucine zipper, composed of α helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization of leucine zippers creates a pair of the adjacent basic regions that bind DNA and undergo conformational change. Dimerization occurs in a specific and predictable manner resulting in hundreds of dimers having unique effects on transcription .
Mitochondrial carrier protein Mtm1-like (Mtm1-like)
Type: Family

This entry represents a group of mitochondrial carrier proteins, including Mtm1 from budding yeasts and SLC25A39/40 from humans. Mtm1 is a pyridoxal 5'-phosphate (PLP) transporter and is involved in mitochondrial iron homeostasis . SLC25A39 and its paralogue SLC25A40 are mitochondrial transporters essential for glutathione import into mitochondria, which is required for the activity and stability of proteins containing iron-sulfur clusters, as well as erythropoiesis . Knockdown of SLC25A39 in a zebrafish model has been shown to disrupt heme biosynthesis and results in profound anemia .
Zinc transporter Msc2-like (Msc2-like)
Type: Family

This entry represents a group of metal transporters, including Msc2 from budding yeasts, Cis4 from fission yeasts, SLC30A5/7 (also known as ZNT7/5) from humans and MTPC2/MTP12 from Arabidopsis. They are zinc transporters involved in zinc ion homeostasis . ZNT5/7 in the early secretory pathway, regulate the activation and folding of enzymes like alkaline phosphatases and enzymes involved in phosphatidylinositol glycan anchor biosynthesis .
E3 ubiquitin-protein ligase RGLG1/2, RING finger (RING-HC_RGLG1/2)
Type: Domain

This entry represents the RING finger found in a group of plant E3 ubiquitin-protein ligases, including RGLG1/2 from Arabidopsis.

RGLG1 is a ubiquitously expressed E3 ubiquitin-protein ligase that interacts with UBC13 and, together with UBC13, catalyses the formation of K63-linked polyubiquitin chains, which is involved in DNA damage repair . It also regulates apical dominance by acting on the auxin transport proteins abundance . RGLG1 has overlapping functions with its closest sequelog, RGLG2. They both function as RING E3 ligases that interact with ethylene response factor 53 (ERF53) in the nucleus and negatively regulate the plant drought stress response . All members in this family contain a Von Willebrand factor type A (vWA) domain and a C3HC4-type RING-HC finger.