SII-SWORD/CoKE huggingface dataset:
Uncharacterised conserved protein UCP021591 (UCP021591)
Type: Family

There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. Members of this entry are mainly found in proteobacteria.
Uncharacterised conserved protein UCP21603, acetyltransferase-like (UCP21603_acetyltransf)
Type: Family

This group represents an uncharacterised protein with acetyltransferase domain.
Uncharacterised conserved protein UCP021697, membrane (UCP021697)
Type: Family

There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. However, they are predicted to be integral membrane proteins (with several transmembrane segments).
Uncharacterised conserved protein UCP021774 (UCP021774)
Type: Family

This group represents an uncharacterised conserved protein.

The proteins members of this protein family adopt α/β fold consisting of a five-stranded β-sheet and α-helices packed on one side of the sheet . They form stable dimers involving the other side of their β-sheet

. These proteins are structurally similar to TATA-binding proteins.
Uncharacterised conserved protein UCP021898 (UCP021898)
Type: Family

There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. Members of this entry are mainly found in proteobacteria.
Uncharacterised conserved protein UCP021980, OB-fold (UCP021980_OB-fold)
Type: Family

This group represents a protein family with a predicted nucleic acid binding function.
Uncharacterised conserved protein UCP022062 (UCP022062)
Type: Family

There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. Members of this entry are mainly found in proteobacteria.
Uncharacterised conserved protein UCP022080 (UCP022080)
Type: Family

This entry represents a family of archaeal proteins, including Ta0095 from Thermoplasma acidophilum (

). This protein shows an α/β two-layer sandwich architecture formed by three α-helices and five β-strands. It is thought to bind a negatively charged molecule such as DNA, but its specific function remains unknown .
Uncharacterised conserved protein UCP022207 (UCP022207)
Type: Family

This group represents an uncharacterised conserved protein.
Uncharacterised conserved protein UCP022260 (UCP022260)
Type: Family

There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. Members of this entry are mainly found in proteobacteria.
RGS1-HXK1-interacting protein 1 (RHIP1)
Type: Family

RHIP1 provides a physical connection between the glucose signaling sensors RGS1 and HXK1, and is required for some glucose-regulated gene expression in plants .
Uncharacterised protein family UPF0114, plant (UPF0114_pln)
Type: Family

There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. Members of this entry are mainly found in proteobacteria.
Intermembrane space protein MIX23, fungal (MIX23_fungal)
Type: Family

The intermembrane space protein MIX23, also known as Caffeine-induced death protein 2 (Cid2), regulates or stabilises the mitochondrial protein import machinery and is specifically up-regulated under stress conditions. It is critical for the efficient import of proteins into the mitochondrial matrix, particularly if the function of the translocase of the inner membrane 23 is compromised. This entry includes MIX23 from S. cerevisiae and related fungal proteins .
COP9 signalosome complex, subunit 9, fungi (Csn9_fungi)
Type: Family

Csn9 is a component of the COP9 signalosome (CSN) complex that acts as an regulator of the ubiquitin (Ubl) conjugation pathway by mediating the deneddylation of the cullin subunit of SCF-type E3 ubiquitin-protein ligase complexes . The CSN complex is involved in the regulation of the mating pheromone response .

The COP9 signalosome-like (CSN) complex in yeast is composed of at least 6 members:

Rri1/Csn5,

Csn9,

Rri2/Csn10,

Pci8/Csn11,

Csn12,

Csi1.

In the complex Csn9 probably interacts directly with Csn12 and Csi1 and also Rpn5.
Anaphase-promoting complex subunit Mnd2 (Mnd2)
Type: Family

Mnd2 is part of the yeast anaphase-promoting complex (APC), a multisubunit E3 ubiquitin ligase that regulates the metaphase-anaphase transition and exit from mitosis in eukaryotic cells . It is essential for maintaining sister chromatid cohesion in prophase I of meiosis by inhibiting premature ubiquitination and subsequent degradation of substrates by the APC(Ama1) ubiquitin ligase. It can be regulated by phosphorylation during the cell cycle .
Mitochondrial morphogenesis protein Sld7 (Sld7)
Type: Family

Sld7 interacts with Sld3 and is required for the proper function of Sld3 at the initiation of DNA replication . The origin association of Sld3, Sld7, and Cdc45 is the key to determining the temporal order of origin firing . Sld7 is also required for mitochondrial morphology .
DNA repair protein Rad59 (Rad59)
Type: Family

Rad59 is a paralogue of Rad52 and is involved in double-strand breaks (DSBs) DNA repair during vegetative growth via recombination and single-strand annealing . It is required for loading of Rad52 to DSBs .
Origin recognition complex, subunit 6, fungi (ORC6_fun)
Type: Family

This entry represents subunit 6, which directs DNA replication by binding to replication origins and is also involved in transcriptional silencing; interacts with Spp1 and with trimethylated histone H3; phosphorylated by Cdc28 .

The Origin Recognition Complex (ORC) is a six-subunit ATP-dependent DNA-binding complex encoded by ORC1-6 . ORC is a central component for eukaryotic DNA replication, and binds chromatin at replication origins throughout the cell cycle . ORC directs DNA replication throughout the genome and is required for its initiation . ORC bound at replication origins serves as the foundation for assembly of the pre-replicative complex (pre-RC), which includes Cdc6, Tah11 (aka Cdt1), and the Mcm2-7 complex . Pre-RC assembly during G1 is required for replication licensing of chromosomes prior to DNA synthesis during S phase . Cell cycle-regulated phosphorylation of ORC2, ORC6, Cdc6, and MCM by the cyclin-dependent protein kinase Cdc28 regulates initiation of DNA replication, including blocking reinitiation in G2/M phase .

In yeast, ORC also plays a role in the establishment of silencing at the mating-type loci Hidden MAT Left (HML) and Hidden MAT Right (HMR) . ORC participates in the assembly of transcriptionally silent chromatin at HML and HMR by recruiting the Sir1 silencing protein to the HML and HMR silencers .
Protein phosphatase methylesterase, eukaryotic (PPase_methylesterase_euk)
Type: Family

This group represents eukaryotic protein phosphatase methylesterase 1. It demethylates proteins that have been reversibly carboxymethylated . Carboxymethylation is a highly conserved means of regulation in eukaryotic cells.
NADH-ubiquinone oxidoreductase 21.3 kDa subunit (NADH_Ub_cplx-1_21kDa)
Type: Family

This family represents a NADH-ubiquinone oxidoreductase 21.3 kDa subunit from Neurospora crassa , NADH-ubiquinone oxidoreductase subunit NUO2 from Candida albicans and similar fungal proteins.
Profilin, apicomplexa (Profilin_apicomplexa)
Type: Family

Profilin is a small eukaryotic protein that binds to monomeric actin (G-actin) in a 1:1 ratio thus preventing the polymerisation of actin into filaments (F-actin). It can also in certain circumstance promote actin polymerisation. Profilin also binds to polyphosphoinositides such as PIP2. Overall sequence similarity among profilin from organisms which belong to different phyla (ranging from fungi to mammals) is low, but the N-terminal region is relatively well conserved. That region is thought to be involved in the binding to actin.

This group represents a profilin, apicomplexa type.
Rhoptry 4/5 (ROP4/5)
Type: Family

This entry represents rhoptry proteins ROP4 and ROP5 which are found in Toxoplasma gondii (phylum Apicomplexa), an obligate intracellular parasite for which the discharge of apical organelles named rhoptries is a key event in host cell invasion . These proteins contain a kinase-like domain (

).

ROP4 is localised to the rhoptries, secretory organelles at the apical end of the parasite, and is secreted from the parasite during host cell invasion . It has a typical bi-lobed protein kinase fold, but lack catalytic activity .

ROP5 is a pseudokinase that is essential for virulence in type I lineages of Toxoplasma gondii . It plays a critical role in promoting parasite survival within mouse monocytes and is required for the parasite's resistance to innate immune responses triggered by interferon-gamma (IFN-γ) in mice . ROP5 reduces the accumulation of immunity-related GTPases (IRGs), including IRGA6 (IIGP1) and IRGB6 (TGTP1/TGTP2), on the parasitophorous vacuole membrane, thereby limiting IRG-mediated killing of the parasite by mouse cells . It also regulates the activity of ROP18, an active kinase that directly targets IRGs to block their function and prevent parasite clearance. Additionally, ROP5 acts as an allosteric inhibitor of mouse IRGA6 (IIGP1) . Notably, ROP5 does not affect IFN-γ-mediated parasite killing in human cells, which lack the diverse IRG repertoire found in mice.
Surface antigen p22 (SAG2)
Type: Family

Toxoplasma gondii is an obligate intracellular apicomplexan protozoan parasite, with a complex lifestyle involving varied hosts. It has two phases of growth: an intestinal phase in feline hosts, and an extra-intestinal phase in other mammals. Oocysts from an infected cat develop into tachyzoites and, eventually, into bradyzoites and zoitocysts in the extraintestinal host. Transmission of the parasite occurs through contact with infected cats or raw/undercooked meat. In immunocompromised individuals, it can cause severe, often lethal, toxoplasmosis .

Toxoplasma gondii utilise a variety of secretory and antigenic proteins to invade a host and gain access to the intracellular environment. This group represents surface antigen p22 (SAG2) from Toxoplasma gondii .
Mannose-P-dolichol utilization defect 1 protein (MannP-dilichol_defect-1)
Type: Family

This entry represents a group of eukaryotic transmembrane proteins, including mannose-P-dolichol utilization defect 1 protein and solute carrier family 66 member 3 (SLC66A3).
Nitric oxide synthase-interacting protein (NOSIP)
Type: Family

This entry includes animal NOSIP (nitric oxide synthase-interacting protein) and plant CSU1. They are ubiquitin E3 ligases . Human NOSIP negatively regulates nitric oxide production by inducing NOS1 and NOS3 translocation to actin cytoskeleton and inhibiting their enzymatic activity .

Arabidopsis CSU1 plays a important role in maintaining COP1 homeostasis by targeting COP1 for ubiquitination and degradation in dark-grown seedlings .
Ribonuclease P/MRP protein subunit Pop5 (RNase_P/MRP_POP5)
Type: Family

Ribonuclease P (Rnp) is a ubiquitous ribozyme that catalyzes a Mg2 -dependent hydrolysis to remove the 5'-leader sequence of precursor tRNA (pre-tRNA) in all three domains of life . In bacteria, the catalytic RNA (typically ~120kDa) is aided by a small protein cofactor (~14kDa) . Archaeal and eukaryote RNase P consist of a single RNA and archaeal RNase P has four or five proteins, while eukaryotic RNase P consists of 9 or 10 proteins. Eukaryotic and archaeal RNase P RNAs cooperatively function with protein subunits in catalysis .

Eukaryotic nuclear RNase P shares most of its protein components with another essential RNP enzyme, nucleolar RNase MRP . RNase MRP (mitochondrial RNA processing) is an rRNA processing enzyme that cleaves various RNAs, including ribosomal, messenger, and mitochondrial RNAs. It can cleave a specific site within precursor rRNA to generate the mature 5'-end of 5.8S rRNA . Despite its name, the vast majority of RNase MRP is localized in the nucleolus . RNase MRP has been shown to cleave primers for mitochondrial DNA replication and CLB2 mRNA. In yeast, RNase MRP possesses one putatively catalytic RNA and at least 9 protein subunits (Pop1, Pop3-Pop8, Rpp1, Snm1 and Rmp1) . Human RNase MRP complex consists of 267 nucleotides and supports the interaction with and among at least seven protein components: hPop1, hPop5, Rpp20, Rpp25, Rpp30, Rpp38, and Rpp40) and three additional proteins, hPop4, Rpp21 and Rpp14, have been reported to be associated with at least a subset of RNase MRP complexes .

This entry represents the Pop5 from eukaryotes and related proteins from archaea.
G0/G1 switch protein 2 (G0S2)
Type: Family

This group represents the G0/G1 switch protein 2 (G0S2) . In humans, it promotes apoptosis by binding to BCL2, hence preventing the formation of protective BCL2-BAX heterodimers .
Sulfur oxidation c-type cytochrome SoxX, type II (Thiosulf_SoxX_II)
Type: Family

Members of this family are SoxX, a c-type cytochrome with a CxxCH motif, part of a heterodimer with SoxA. SoxAX cytochromes play a key role in bacterial thiosulfate oxidation .

There are three distinct types of SoxAX proteins. Type I and II SoxAX proteins are heterodimers, while the heterotrimeric SoxAXK proteins form the third group. Type I SoxAX proteins have SoxA subunits with two heme groups and SoxX subunits with a molecular mass of approximately 14kDa, while the Type II SoxA proteins only contain one heme group, and are associated with SoxX proteins that have a molecular mass of approximately 20kDa. The increased molecular mass in these SoxX proteins is largely due to the presence of an N-terminal extension .
Tfp pilus assembly protein FimT (Tfp-pilus_assembly_FimT)
Type: Family

This group represents a Tfp pilus assembly protein FimT.
Flagella-related protein F (Flagellin-rel_FlaF)
Type: Family

This group represents a predicted flagella-related protein F, found primarily, though not exclusively, in Pyrococcus spp.
Transcriptional adaptor 2 (Ada2/TADA2)
Type: Family

This entry represents a group of transcriptional adaptors, including transcriptional adapter 2 (TADA2) from animals and plants, and Ada2 from yeasts.

Ada2 is a component of the SAGA/ADA coactivator complex, which regulates numerous cellular processes by coordinating histone acetylation .

There are two Drosophila Ada2 homologues, dAda2a and dAda2b. dAda2b is a component of Spt-Ada-Gcn5-acetyltransferase (SAGA) complexes, while dAda2a associates with dGcn5 but is not incorporated into dSAGA-type complexes .
Alpha-L-arabinofuranosidase (Alpha-L-arabinofuranosidase)
Type: Family

Alpha-L-arabinofuranosidase hydrolyses the terminal non-reducing alpha-L-arabinofuranoside residues in alpha-L-arabinosides. The enzyme acts on alpha-L-arabinofuranosides, alpha-L-arabinans containing (1,3)-and/or (1,5)-linkages, arabinoxylans and arabinogalactans. Some beta-galactosidases (

) and beta-D-fucosidases (

) also hydrolyse alpha-L-arabinosides.

The enzyme is a hexamer and each monomer has two domains: a (β/α)8-barrel and a 12-stranded β sandwich with jelly-roll topology . It has no apparent requirement for cofactors, and its activity is strongly inhibited by 1 mM Hg2+ .
Spodoptera frugiperda nuclear polyhedrosis virus (SfNPV), sf27 (SfNPV_sf27)
Type: Family

This entry is represented by Spodoptera frugiperda nuclear polyhedrosis virus (SfNPV), sf27; it is a family of uncharacterised viral proteins.
Ubiquinone biosynthesis accessory factor UbiT (UbiT)
Type: Family

This family represents the UbiT (also known as YhbT) protein. It is involved in the ubiquinone biosynthesis pathway alongside UbiU (YhbU), and UbiV (YhbV). UbiT contains an SCP2 domain

which binds the hydrophobic UQ biosynthetic intermediates and structures a multiprotein Ubi complex .
PPi-dependent kinase (PPi-dep_kinase)
Type: Family

This family includes proteins predominantly found in Bacteroidetes, such as

from Thermotoga maritima. This enzyme, member of the ribokinase family, uses inorganic pyrophosphate (PPi) but neither ATP nor ADP to generate myo-inositol monophosphate. It contains two large hydrophobic residues partially obstructing the ATP-binding pocket and three basic residues involved in PPi recognition . Many members of this family show the domain

.
Uncharacterised conserved protein UCP025926, globin-related (UCP025926_globin-rel)
Type: Family

This group represents an uncharacterised conserved protein, related to globin.
Putative sodium bile acid cotransporter (Put_Na-Bile_cotransptr)
Type: Family

This family includes sodium/bile acid cotransporter 7 and other uncharacterised proteins with sodium bile acid cotransporter domain; they are found both in prokaryotes and eukaryotes.They are related to the human bile acid:sodium symporters, which are transmembrane proteins functioning in the liver in the uptake of bile acids from portal blood plasma, a process mediated by the co-transport of Na
+
.
Uncharacterised conserved protein UCP026306 (UCP026306)
Type: Family

This group represents an uncharacterised conserved protein.
Uncharacterised conserved protein UCP026317, WGR (UCP026317_WGR)
Type: Family

This group represents an uncharacterised protein with WGR domain.
Long-chain acyl-[acyl-carrier-protein] reductase (AAR)
Type: Family

This entry represents Long-chain acyl-[acyl-carrier-protein] reductase from Synechococcus elongatus (ARR) and similar proteins from Cyanobacteria. ARR reduces a long-chain (mainly C16 or C18) fatty acyl ACP ester to its corresponding fatty aldehyde, releasing the acyl carrier protein (ACP) . NADPH is the reductant for this reaction. Its structure shows the protein is composed of three domains, with the the mid-domain was designated as the dinucleotide recognition loop . This enzyme may be distantly related to the short-chain dehydrogenase or reductase (SDR) family (

).
Uncharacterised protein family Ycf55, cyanobacteria (Uncharacterised_Ycf55_cyanobac)
Type: Family

This entry represents proteins annotated as Ycf55. It is found encoded in the chloroplast genomes of algae, it is also found in plants and in the cyanobacteria. The function is unknown, though there are two completely conserved residues (L and D) that may be functionally important. As the family is exclusively found in the cyanobacteria and it may play a role in photosynthesis.
Uncharacterised conserved protein UCP026449 (UCP026449)
Type: Family

There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. Members of this entry are mainly found in proteobacteria.
Signal transduction diguanylate cyclase, CHASE2 sensor domain-containing, predicted (Sig_transdc_diG_cyclase_prd)
Type: Family

This entry represents predicted signal transduction diguanylate cyclases (diG cyclase) that have a CHASE2 sensor domain . DiG cyclase catalyses the synthesis of two molecules of cyclic dinucleotide bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) from two molecules of GTP. The cyclic nucleotide c-di-GMP acts as an important second messenger to regulate transitions between motile and sessile lifestyles by coordinating the many cellular functions necessary for existence as isolated planktonic cells or within multicellular communities of biofilms .
Glycoside hydrolase, family 43, endo-1, 5-alpha-L-arabinosidase (Glyco_hydro_43_endo_a_Ara-ase)
Type: Family

O-Glycosyl hydrolases (

) are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families . This classification is available on the CAZy (CArbohydrate-Active EnZymes) website.

Glycoside hydrolase family 43

includes enzymes with the following activities, beta-xylosidase (

), alpha-L-arabinofuranosidase (

); arabinanase (

), and xylanase (

).

This entry represents an endo-1,5-alpha-L-arabinosidase.
Transcription regulator DksA-related, predicted (Tscrpt_reg_DksA-rel_prd)
Type: Family

This group represents a predicted transcriptional regulator DksA-related protein.
Protein of unknown function UCP026546, HtH-CBS (UCP026546_HTH-CBS)
Type: Family

This group represents an uncharacterised protein with a N-termial HtH domain and a C-terminal CBS domain pair. Proteins in this entry include transcriptional repressor CcpN from Bacillus subtilis. CcpN is a transcription repressor that binds to the promoter of gapB and pckA genes, preventing their expression. It acts as a regulator for catabolite repression of gluconeogenic genes .
S-adenosyl-L-methionine dependent adenine methyltransferase, bacteria, predicted (S-AdoMet-dep_Ade-MeTrfase_prd)
Type: Family

This group represents a predicted S-adenosyl-L-methionine dependent adenine methyltransferase, bacterial type.
Uncharacterised conserved protein UCP026610 (UCP026610)
Type: Family

There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. Members of this entry are mainly found in proteobacteria.
Uncharacterised conserved protein UCP026633, TfuA-like, mycobacteria (UCP026633_TfuA-like)
Type: Family

This group represents an uncharacterised protein with TfuA-like domain, Mycobacterium type.
Predicted ion channel, cNMP-binding (cNMP-bd_ion_channel)
Type: Family

This entry represents a group of predicted ion channels with a cNMP-binding (cyclic nucleotide-binding) domain (

).
Mannose-6-phosphate isomerase, Firmicutes, long form, predicted (Man6P_Isoase_Firm_lng_prd)
Type: Family

This group represents a predicted mannose-6-phosphate isomerase, Firmicutes type, long form.

PMI_Firm_long_prd
Ribonuclease P/MRP subunit Rpp29 (RNase_P/MRP_Rpp29-subunit)
Type: Family

Ribonuclease P (Rnp) is a ubiquitous ribozyme that catalyzes a Mg2 -dependent hydrolysis to remove the 5'-leader sequence of precursor tRNA (pre-tRNA) in all three domains of life . In bacteria, the catalytic RNA (typically ~120kDa) is aided by a small protein cofactor (~14kDa) . Archaeal and eukaryote RNase P consist of a single RNA and archaeal RNase P has four or five proteins, while eukaryotic RNase P consists of 9 or 10 proteins. Eukaryotic and archaeal RNase P RNAs cooperatively function with protein subunits in catalysis .

Eukaryotic nuclear RNase P shares most of its protein components with another essential RNP enzyme, nucleolar RNase MRP . RNase MRP (mitochondrial RNA processing) is an rRNA processing enzyme that cleaves various RNAs, including ribosomal, messenger, and mitochondrial RNAs. It can cleave a specific site within precursor rRNA to generate the mature 5'-end of 5.8S rRNA . Despite its name, the vast majority of RNase MRP is localized in the nucleolus . RNase MRP has been shown to cleave primers for mitochondrial DNA replication and CLB2 mRNA. In yeast, RNase MRP possesses one putatively catalytic RNA and at least 9 protein subunits (Pop1, Pop3-Pop8, Rpp1, Snm1 and Rmp1) . Human RNase MRP complex consists of 267 nucleotides and supports the interaction with and among at least seven protein components: hPop1, hPop5, Rpp20, Rpp25, Rpp30, Rpp38, and Rpp40) and three additional proteins, hPop4, Rpp21 and Rpp14, have been reported to be associated with at least a subset of RNase MRP complexes .

This entry represents the p29 subunit (also known as Rpp29 or Pop4) of the related ribonucleoproteins ribonuclease (RNase) P and RNase MRP from eukaryotes . Rpp29 has a conserved C-terminal domain with an Sm-like fold . Rpp29 (

) catalyses the endonucleolytic cleavage of RNA, removing 5'-extranucleotides from tRNA precursor. It interacts with the Rpp25 and Pop5 subunits.