SII-SWORD/CoKE huggingface dataset:
Uncharacterised conserved protein UCP030333, DNA/RNA-binding Alba-related (UCP030333_Alba)
Type: Family

This entry represents a group of proteins from plants and lower eukaryotes that are related to the archaeal DNA/RNA-binding protein Alba, also called histone-like protein (

), and its eukaryotic homologues RNase P/MRP subunits Pop7/Rpp20 (

) and Rpp25. Members of this family are the uncharacterised protein At2g34160 from Arabidopsis thaliana, which affects rRNA processing , and Endonuclease ALBA3 from Plasmodium falciparum, which can bind both DNA and RNA .

Structural comparisons have shown that Alba (Sso10b2 from the thermoacidophilic archaeon Sulfolobus solfataricus) is topologically similar to several RNA-binding proteins (or A-DNA-binding) and includes IF3-C, YhhP, and DNase I. All of them have a similar IF3-C fold and it has been suggested that the ancestral function of the IF3-C fold is related to RNA interaction, and that the Alba superfamily proteins originated as RNA-binding proteins that formed various ribonucleoprotein complexes, probably including RNase P, and were then recruited as a chromosomal protein within the crenarchaeal lineage . Based on this, it has been suggested that the archaeal Alba proteins (

) are involved in RNA binding as well as DNA binding , a prediction that has been confirmed experimentally .

For more information about Alba, please see

.
Uncharacterised conserved protein UCP030959, divergent TPR repeat-containing (UCP030959_TPR_rpt-cont)
Type: Family

The proteins in this family contain a divergent form of TPR repeats. Their function is unknown.
Uncharacterised conserved protein UCP031503, transmembrane (UCP031503_TM)
Type: Family

There is currently no experimental data for members of this group of predicted transmembrane proteins or their homologues, nor do they exhibit features indicative of any function.
Exopolysaccharide biosynthesis, EpsL, firmicutes (EpsL_firmicutes)
Type: Family

This group represents an exopolysaccharide biosynthesis protein and is restricted to Firmicutes.
Uncharacterised conserved protein UCP031900 (UCP031900)
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.
Ubiquinol-cytochrome c chaperone, CBP3-related (Ubq_cyt-c_CBP3-rel)
Type: Family

This entry represents a family of proteins from Alphaproteobacteria that display similarity to a chaperone identified in Saccharomyces cerevisiae (

), which plays a key role in the assembly of ubiquinol-cytochrome-c reductase. The crystal structure of this protein has been resolved in the homologue from the Brucella abortus, showing an all-helical fold .
Encapsidation protein CP3 (Encapsidation_CP3)
Type: Family

Staphylococcus aureus pathogenicity islands (SaPIs) are highly mobile phage-related pathogenicity islands that typically carry genes for one or more superantigens. They are the primary cause of superantigen-induced diseases, especially toxic shock syndrome. SaPIs are induced to excise and replicate by the presence of a temperate phage. The SaPI then induces the phage to produce special small capsids into which it is encapsidated, resulting in exteremly high transfer frequences .

This entry represents the SaPI CP3 protein, which is involved in the morphogenesis of the characteristic small SaPI capsids .
Uncharacterised conserved protein UCP032620 (UCP032620)
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 UCP032673 (UCP032673)
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 UCP032806 (UCP032806)
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 UCP032908 (UCP032908)
Type: Family

There is currently no experimental data for members of this group of proteins or their homologues, nor do they exhibit features indicative of any function. However, they are predicted to be membrane proteins.
Type III secretion system, secreted protein EspD (T3SS_EspD)
Type: Family

This entry represents the type III secretion protein EspD. The pathogenesis of enteropathogenic Escherichia coli (EPEC) involves the translocation of effector proteins by the type III secretion system into the host cell, including translocated intimin receptor (Tir) and several E. coli secreted proteins (Esp). Secretion of virulence proteins of EPEC is tightly regulated. CesD is the type III chaperone for the translocator proteins EspB and EspD . The translocation of virulence proteins into host cells results in attaching and effacing (A/E) lesions, actin rearrangements and pedestal formation . The translocator and effector proteins facilitate colonization of the mucosal surface of the intestine via formation of attaching and effacing (A/E) lesions.
Predicted phosphoesterase, YhaO type (Pesterase_YhaO)
Type: Family

These proteins contain one copy of the calcineurin-like phosphoesterase domain (

), followed by a carboxyl-terminal extension that is less well conserved. They possess motifs characteristic of a variety of enzymatically active phosphoesterases , including acid and alkaline phosphatases, phosphoprotein phosphatases, 5'-nucleotidase, bis(5'-nucleosyl)-tetraphosphatase (symmetrical), sphingomyelin phosphodiesterase, 2',3'-cylic-nucleotide 2'-phosphodiesterase, and 3',5'-nucleotide phosphodiesterase CpdA. They appear to be similar to exonuclease SbcD (

), but their catalytic activity has not been characterised.
Uncharacterised conserved protein UCP033093, metallophosphoesterase-type (UCP033093_metalloPase)
Type: Family

These conserved bacterial proteins contain one copy of the calcineurin-like phosphoesterase domain (

) and possess most of the motifs characteristic of a variety of enzymatically active phosphoesterases , including acid and alkaline phosphatases, phosphoprotein phosphatases, 5'-nucleotidase, bis(5'-nucleosyl)-tetraphosphatase (symmetrical), sphingomyelin phosphodiesterase, 2',3'-cylic-nucleotide 2'-phosphodiesterase, and 3',5'-nucleotide phosphodiesterase CpdA. Although this group appears to be similar to exonuclease SbcD (

), their catalytic activity, if any, is speculative.
Predicted phosphoesterase, CT488 type (Pesterase_CT488)
Type: Family

This group of conserved proteins found in some bacteria contain one copy of the calcineurin-like phosphoesterase domain (

) and possess motifs characteristic of a variety of enzymatically active phosphoesterases , including acid and alkaline phosphatases, phosphoprotein phosphatases, 5'-nucleotidase, bis(5'-nucleosyl)-tetraphosphatase (symmetrical), sphingomyelin phosphodiesterase, 2',3'-cylic-nucleotide 2'-phosphodiesterase, and 3',5'-nucleotide phosphodiesterase CpdA.
Predicted 5'-nucleotidase, SA0022 type (5NTD_SA0022)
Type: Family

This group represents a predicted 5'-nucleotidase, SA0022 type.
Uncharacterised conserved protein UCP033199 (UCP033199)
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 UCP033303 (UCP033303)
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 UCP033535, periplasmic lipoprotein (UCP033535_lipo)
Type: Family

There is currently no experimental data for members of this group of predicted periplasmic lipoproteins or their homologues, nor do they exhibit features indicative of any function.
Uncharacterised protein family, Sir2-like (Uncharacterised_Sir2-like)
Type: Family

This group represents a predicted uncharacterised conserved protein with Sir2 domain.
Uncharacterised conserved protein UCP033729 (UCP033729)
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 UCP033909 (UCP033909)
Type: Family

There is currently no experimental data for members of this group or their homologues.
Uncharacterised conserved protein UCP034077 (UCP034077)
Type: Family

This group represents an uncharacterised conserved protein.
ATPase, Atu1862 type, predicted (ATPase_Atu1862_pred)
Type: Family

This group represents a predicted ATPase, Atu1862 type (

).
Uncharacterised conserved protein MORN repeat-containing (UCP034300_MORN_rpt-cont)
Type: Family

This group represents a predicted uncharacterised protein with MORN repeat, SP2027 type.
Uncharacterised conserved protein UCP034455 (UCP034455)
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).
Predicted P-loop ATP-binding protein, VCA0200 (P-loop_UCP034888)
Type: Family

There are currently no experimental data for members of this group or their homologues. However, they contain a P-loop motif and are, therefore, predicted to be ATP-binding proteins.
Uncharacterised conserved protein UCP034961, SH3-2 (UCP034961_SH3_2)
Type: Family

SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues . They are found in a great variety of intracellular or membrane-associated proteins for example, in a variety of proteins with enzymatic activity, in adaptor proteins, such as fodrin and yeast actin binding protein ABP-1.

The SH3 domain has a characteristic fold which consists of five or six β-strands arranged as two tightly packed anti-parallel β-sheets. The linker regions may contain short helices. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes .

This group consists of prokaryotic proteins containing one to two SH3_2 domains, but there is currently no experimental data for these proteins.
Uncharacterised conserved protein UCP035836 (UCP035836)
Type: Family

This group represents a predicted uncharacterised conserved protein.
ABC transporter, periplasmic substrate-binding protein, predicted (ABC_tp_sb)
Type: Family

Bacterial high affinity transport systems are involved in active transport of solutes across the cytoplasmic membrane. Most of the bacterial ABC (ATP-binding cassette) importers are composed of one or two transmembrane permease proteins, one or two nucleotide-binding proteins and a highly specific periplasmic solute-binding protein. In Gram-negative bacteria the solute-binding proteins are dissolved in the periplasm, while in archaea and Gram-positive bacteria, their solute-binding proteins are membrane-anchored lipoproteins .

This group represents a predicted ABC transporter, periplasmic substrate-binding protein.
Uncharacterised conserved protein UCP035865 (UCP035865)
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 UCP035905, membrane protein (UCP035905_mem)
Type: Family

There is currently no experimental data for members of this group of predicted membrane proteins or their homologues, nor do they exhibit features indicative of any function.
Transcriptional regulator with MarR-type HTH domain (Trans_reg_MarR_HTH)
Type: Family

There are currently no experimental data for members of this group. However, they contain an HTH DNA-binding domain related to the MarR superfamily of HTH domains.
Uncharacterised conserved protein UCP036226 (UCP036226)
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.
Formate dehydrogenase iron-sulphur subunit (Formate_DH_Fe-S_su)
Type: Family

This entry represents the beta subunit (iron-sulphur subunit) of the formate dehydrogenase. This subunit contains four 4Fe-4S clusters and is involved in transmitting electrons from the alpha subunit (

) at the periplasmic space to the gamma subunit which spans the cytoplasmic membrane .
Signal transduction response regulator PhyR-like, alphaproteobacteria (Sig_resp-reg_PhyR)
Type: Family

This entry represents signal transduction response regulators with a C-terminal receiver domain, such as PhyR, which is found in the Alphaproteobacterium Methylobacterium extorquens (Protomonas extorquens). PhyR is a key regulator for adaptation to epiphytic life (leaf colonising) of the bacterium, and is essential for plant colonisation, possibly due to its suggested involvement in the regulation of a number of stress proteins . PhyR proteins have a structure consisting of two domains; a predicted amino-terminal extracytoplasmic function (ECF) sigma factor-like domain and a carboxy-terminal receiver domain .
D,D-heptose 7-phosphate kinase (Heptose_7-P_kinase)
Type: Family

This group of enzymes belongs to the GHMP kinase domain superfamily. GHMP kinases are a unique class of ATP-dependent enzymes (the abbreviation of which refers to the original members: galactokinase, homoserine kinase, mevalonate kinase, and phosphomevalonate kinase) . Enzymes belonging to this superfamily contain three well-conserved motifs, the second of which has the typical sequence Pro-X-X-X-Gly-Leu-X-Ser-Ser-Ala and is involved in ATP binding . The phosphate binding loop in GHMP kinases is distinct from the classical P-loops found in many ATP/GTP binding proteins. The bound ADP molecule adopts a rare syn conformation and is in the opposite orientation from those bound to the P-loop-containing proteins . GHMP kinases display a distinctly bilobal appearance with their N-terminal subdomains dominated by a mixed β-sheet flanked on one side by α-helices and their C-terminal subdomains containing a four stranded anti-parallel β-sheet .

Aneurinibacillus thermoaerophilus protein has been characterised as a D-glycero-D-manno-heptose 7-phosphate kinase that adds phosphate group to C-1 of D-glycero-D-manno-heptose 7-phosphate , and has been called GmhB or HddA. Note that HddA is the preferred name for this protein because the name GmhB has also been used for the D-glycero-D-manno-heptose 1,7-bisphosphate phosphatase,

. This enzyme catalyses a step in the biosynthesis of the nucleotide-activated form GDP-D-glycero-D-manno-heptose and is encoded by the heptose operon .

D-glycero-D-manno-heptose is a constituent of lipopolysaccharide (LPS) cores of Gram-negative bacteria, and also a component of the S-layer glycoprotein of the Gram-positive bacterium Aneurinibacillus thermoaerophilus. The principal architecture of S-layer glycoproteins resembles that of the LPS of Gram-negative bacteria and comparable pathways are used for the biosynthesis of these similar glycoconjugates .

WcbL of Burkholderia pseudomallei is also involved in the synthesis of an LPS (type I O-polysaccharide moieties) .

LmbP is thought to belong to the lincomycin-production gene cluster of Streptomyces lincolnensis .
Alkane 1-monooxygenase, rubredoxin-type (Alk_mOase_rubredoxin-type)
Type: Family

This entry represents a family of alkane 1-monooxygenases that contain a rubredoxin domain.
ATP-citrate synthase (ATP-citrate_synthase)
Type: Family

This entry represents eukaryotic ATP-citrate synthase (ACLY) (

), also known as ATP citrate lyase. In bacteria and archaea, ATP citrate synthase is composed of two distinct subunits . In eukaryotes, ATP citrate synthase is a homotetramer of a single large polypeptide, and is used to produce cytosolic acetyl-CoA from mitochondrial produced citrate . Acetyl-CoA is the building block for de novo lipid synthesis. As such, ACLY couples energy metabolism with fatty acids synthesis and plays a critical role in supporting cell growth .
Ribonucleases P/MRP protein subunit Rpp20/Pop7 (Pop7/Rpp20)
Type: Family

This entry includes fission yeast ribonucleases P/MRP protein subunit Pop7 and its homologue, Rpp20, from animals. Pop7/Rpp20 is a component of ribonuclease P, a protein complex that generates mature tRNA molecules by cleaving their 5'-ends. They are also a component of RNase MRP complex, which cleaves pre-rRNA sequences .
KsdD-like steroid dehydrogenase (KsdD_DH)
Type: Family

This entry represents family of KsdD-like steroid dehydrogenases and related proteins . 3-Ketosteroid delta(1)-dehydrogenase catalyzes the 1(2)-dehydrogenation of 3-ketosteroid substrates using flavin adenine dinucleotide as a cofactor. The enzyme plays a crucial role in microbial steroid degradation, both under aerobic and anaerobic conditions, by initiating the opening of the steroid nucleus.
Extracellular sulfatase (Extracellular_sulfatase)
Type: Family

This group represents an extracellular sulphatase. Please see the following relevant references: .
Predicted membrane protein, Bacillus YphA type (YphA_Bacsu)
Type: Family

This entry represents a family of proteins related to Bacillus subtilis YphA protein. These proteins are predicted as integral membrane proteins and are structurally related to

which contains α-helices.
Deoxycytidylate hydroxymethylase (Deoxycytidylate_hydroxyMease)
Type: Family

In bacteriophage T4, a specific DNA modification system has evolved in order to protect its own DNA from degradation by host nucleases . Firstly, the cytosine base in dCMP is hydroxymethylated by the T4 enzyme deoxycytidylate hydroxymethylase to produce hydroxymethyl-dCMP (Hm-dCMP). This product is subsequently converted to Hm-dCTP by the combined action of T4 deoxynucleoside monophosphate kinase and host nucleoside diphosphate kinase. Hm-dCTP is then incorporated into T4 DNA by the phage DNA polymerase enzyme. Glucosylation of the Hm-dCTP residues within the phage DNA by glucosyltransferases completes the modification. Degradation of host dCTP by a T4 dCTPase ensures that no unmodified cytosine residues are incorporated in the phage genome.

This entry represents the deoxycytidylate hydroxymethylase enzyme catalysing the first step in T4 the cytosine modification system. This enzyme is a dimer which, despite a low sequence identity, forms a similar fold to that of thymidylate synthases . Each monomer consists of several α helices surrounding a six-stranded β-sheet which forms the dimerisation interface. The active site is formed in a deep pocket, with the sugar and phosphate-binding residues in a similar configuration to that of thymidylate synthase, while the residues presumed to bind cytosine and the folate cofactor are more divergent. The enzyme has been shown to interact with proteins in the T4 deoxyribonucleoside triphosphate synthetase complex .
Thymidylate synthase, archaea (Thymidylate_synthase_arc)
Type: Family

Thymidylate synthase catalyses the reductive methylation of dUMP to dTMP using methylene tetrahydrofolate as a methyl donor, an essential step in DNA biosynthesis . This entry represents a number of proteins that are predicted thymidylate synthases though their function has not been proven. The Methanobacterium thermoautotrophicum protein was shown to catalyse the side reactions characteristic of thymidylate synthase, but conversion of dUTP to dTMP was not observed under the experimental conditions used . Partial sequence data showed no similarity to known thymidylate synthases simply because the region sequenced was from a distinctive N-terminal region not found in other thymidylate synthases. Members of this protein family appear, therefore, to a novel, tetrahydromethanopterin-dependent thymidylate synthase .
Uncharacterised conserved protein UCP036778, sugar epimerase-type (UCP036778_sugar_epimerase)
Type: Family

This entry represents a related group of proteins found in some proteobacteria. They have not been experimentally characterised but are predicted to contain a TIM barrel xylose isomerase-like domain and may function as sugar epimerases or isomerases. From their genomic contexts some may perform a similar function to IolI from Bacillus subtilis .
Uncharacterised conserved protein UCP036794, erythromycin esterase-type (UCP036794_erythomycin)
Type: Family

This group represents an uncharacterised conserved protein with an erythromycin esterase domain.
Transcription factor TFIIIC subunit Tfc7/tau55 (Tfc7/tau55)
Type: Family

This entry includes the yeast transcription factor TFIIIC subunit Tfc7 (tau55) and its paralogue, YNL108C, which is a protein phosphatase .
Predicted 26S proteasome regulatory complex, non-ATPase subcomplex, subunit s5a, Plasmodium (26S_protsm_s5a)
Type: Family

This group represents a predicted 26S proteasome regulatory complex, non-ATPase subcomplex, subunit s5a, Plasmodium type. Please see the following relevant reference: .
Filoviruses glycoprotein (GPC_FiloV)
Type: Family

Proteins in this family include the envelope glycoprotein and the pre-small/secreted glycoprotein from Filoviridae . The envelope glycoprotein can be cleaved into 3 chains: GP1, GP2 and GP2-delta.

GP1 is responsible for binding to the receptor(s), such as CD209 and CLEC4M, on target cells. These interactions not only facilitate virus cell entry, but also allow capture of viral particles by dendritic cells (DCs) and subsequent transmission to susceptible cells without DCs infection (trans infection) .

GP2 acts as a class I viral fusion protein. It is responsible for penetration of the virus into the cell cytoplasm by mediating the fusion of the membrane of the endocytosed virus particle with the endosomal membrane .