SII-SWORD/CoKE huggingface dataset:
Fis-like DNA-binding domain-containing signal transduction response regulator, predicted (Sig_transdc_resp-reg_prd)
Type: Family

Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions . Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk . These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more . Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) . The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK.

A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response .

This entry represents predicted response regulators with Fis-like DNA-binding domain.
Uncharacterised conserved protein UCP016792 (UCP016792)
Type: Family

This entry represents a small family of archaeal uncharacterised proteins.
Predicted phosphoesterase, C1039.02 type (Pesterase_C1039)
Type: Family

These proteins, mainly from ascomycetes but with distant relatives in Giardia intestinalis, contain one copy of the calcineurin-like phosphoesterase domain (

), followed by a C-terminal extension. 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.
Protein of unknown function DUF3151 (DUF3151)
Type: Family

This group represents an uncharacterised conserved protein.
Uncharacterised conserved protein UCP017371 (UCP017371)
Type: Family

This group represents an uncharacterised conserved protein.
DNA-binding protein from starved cells-like (Dps-like)
Type: Family

The initial member of this family to be characterised was described as a DNA-binding protein from starved cells-like (Dps-like) protein, from the hyperthermophilic acidophile Sulfolobus solfataricus . The protein was shown to share high sequence similarity with hypothetical proteins in other archaeal and bacterial genomes, several of which form a monophyletic cluster within the broad superfamily of ferritin-like diiron-carboxylate proteins, which are non-haem iron storage proteins .

The S. solfataricus Dps-like protein has been shown to self-assemble into a hollow dodecameric protein cage having tetrahedral symmetry, which uses H2O2 to oxidize Fe(II) to Fe(III), storing the oxide as a mineral core on the interior surface of the protein cage. It may be involved in the mitigation of oxidative damage .
Curli production protein CsgC (Curli_production_prot_CsgC)
Type: Family

Thin aggressive fibres known as curli fibres or fimbriae (curli; Tafi) are cell-surface protein polymers found in Salmonella typhimurium and Escherichia coli that mediate interactions important for host and environmental persistence, development of biofilms, motility, colonisation and invasion of cells, and conjugation . Four general assembly pathways for different fimbriae have been proposed, one of which is extracellular nucleation-precipitation (ENP), which differs from the others in that fibre-growth occurs extracellularly. Thin aggregative fimbriae are the only fimbriae dependent on the ENP pathway. Tafi were first identified in Salmonella spp and the controlling operon termed agf; however subsequent isolation of the homologous operon in E coli led to its being called csg. Tafi are known as curli because, in the absence of extracellular polysaccharides, their morphology appears curled; however, when expressed with such polysaccharides their morphology appears as a tangled amorphous matrix. The gene agfC is found to be transcribed at low levels, localised to the periplasm in a mature form, and in combination with AgfE is important for AgfA extracellular assembly, which facilitates the synthesis of Tafi. The genes involved in Tafi production are organised into two adjacent divergently transcribed operons, agfBAC and agfDEFG, both of which are required for biosynthesis and assembly .
Poly(A) polymerase (PolyA_polymerase)
Type: Family

Members of this group are poly(A) polymerases (polynucleotide adenylyltransferases, PAP,

). In eukaryotes, polyadenylation of pre-mRNA plays an essential role in the initiation step of protein synthesis, as well as in the export and stability of mRNAs. Poly(A) polymerase, the central enzyme of the polyadenylation machinery, is a template-independent RNA polymerase that specifically incorporates ATP at the 3' end of mRNA .

The catalytic domain of poly(A) polymerase shares substantial structural homology with other nucleotidyl transferases such as DNA polymerase beta and kanamycin transferase . The three invariant aspartates of the catalytic triad ligate two of the three active site metals. One of these metals also contacts the adenine ring. Other conserved, catalytically important residues contact the nucleotide. These contacts, taken together with metal coordination of the adenine base, provide a structural basis for ATP selection by poly(A) polymerase .

The central domain of poly(A) polymerase shares structural similarity with the allosteric activity domain of ribonucleotide reductase R1, which comprises a four-helix bundle and a three-stranded mixed β-sheet. Even though the two enzymes bind ATP, the ATP-recognition motifs are different . The C-terminal domain is predicted to be an RNA-binding domain because it folds into a compact domain reminiscent of the RNA-recognition motif fold .

The C-terminal region beyond the predicted RNA-binding domain is only conserved in vertebrates and is dispensable for catalytic activity
in vitro
. The extended C-terminal domain of vertebrate PAPs is rich in serines and threonines, and enzyme activity can be down regulated by phosphorylation at multiple sites . The extreme C terminus of PAP is also the target for another type of regulation. The U1A protein, a component of the U1 snRNP which functions in 5 splice site recognition, is known to inhibit polyadenylation of its own mRNA by binding to PAP . The C terminus of PAP is also involved in protein-protein interactions with the splicing factor U2AF65 and the snRNP protein U1-70K .
Predicted Fe-S oxidoreductase, NifB/MoaA-like family, euryarchaeota type (Fe-S_OxRdtase_NifB-like_arc)
Type: Family

This group represents a predicted Fe-S oxidoreductase, related to NifB/MoaA family, euryarchaeota type.
Uncharacterised conserved protein UCP018671 (UCP018671)
Type: Family

This entry represents a group of integral membrane proteins with unknown function.
Uncharacterised conserved protein UCP018863 (UCP018863)
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.
Methylmalonyl-CoA decarboxylase, delta subunit (MeMalonyl-CoA_deCOase_dsu)
Type: Family

This group represents the delta subunit of predicted methylmalonyl-CoA decarboxylases found in the archaea; they function as a sodium ion transporters .
Diadenylate cyclase, DacZ-type (DAC_DacZ)
Type: Family

Diadenylate cyclase (DAC, also known as diadenylyl cyclase and cyclic-di-AMP synthase) catalyses the condensation of 2 ATP molecules into cyclic di-AMP (c-di-AMP), a putative second messenger in bacteria and archaea . DAC proteins contain a DisA_N domain, first identified as a DAC domain in the T. maritima protein DisA .

This entry refers to the DacZ subfamily of DACs.
Uncharacterised conserved protein UCP019307, cupin-type (UCP019307_cupin)
Type: Family

This group contains proteins with the conserved barrel domain of the cupin superfamily (cupin fold) . There are currently no experimental data for members of this group.
Uncharacterised conserved protein UCP019317 (UCP019317)
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.
Clavaminate synthase-like (Clavaminate_syn-like)
Type: Family

This entry includes clavaminate synthases and related proteins from bacteria. Proteins in this entry include VioC from Streptomyces vinaceus, MppO from Streptomyces hygroscopicus and AsnO from Streptomyces coelicolor. They are non-heme iron, alpha-ketoglutarate-dependent oxygenases.

VioC catalyses Fe(II)-dependent and alpha-ketoglutarate-dependent Cbeta-hydroxylation of L-arginine during the biosynthesis of the tuberactinomycin antibiotic viomycin .
UMP-CMP kinase 2, mitochondrial (UMP-CMP_kinase_2)
Type: Family

This group represents a UMP-CMP kinase, mitochondrial-type. It is able to phosphorylate dUMP, dCMP, CMP, UMP and monophosphates of the pyrimidine nucleoside analogues ddC, dFdC, araC, BVDU and FdUrd with ATP as phosphate donor .
Uncharacterised conserved protein UCP020479, signal transduction CheW-like (UCP020479_CheW)
Type: Family

Members of this group of proteins from Proteobacteria contain a CheW-like chemotaxis signal transduction domain and an uncharacterised N-terminal domain. They are predicted to be signal transduction proteins, possibly involved in chemotaxis. The N-terminal domain is distantly related to periplasmic/solute binding domains.

There are no experimental data for members of this group.
Baseplate assembly protein J, predicted (Baseplate_assembly_J_pred)
Type: Family

The temperate bacteriophage P2 has four defined tail genes: V, J, W and I. Their order is the late gene promoter, VWJI, followed by the tail fibre genes H and G and then a transcription terminator. BAP V protein is the small spike at the tip of the tail and basal plate assembly protein J lies at the edge of the baseplate . This group represents the predicted baseplate assembly protein J.
Uncharacterised conserved protein withTPR-like repeats (UCP020555_TPR-like)
Type: Family

This family of proteins is found in bacteria. There is a conserved PES sequence motif. They are putative lipoproteins.
Uncharacterised conserved protein UCP020606 (UCP020606)
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.
Tellurite resistance predicted, YeaR (Tellurite-R_YeaR)
Type: Family

Proteins in this group are stand-alone YeaR proteins, the predication is based on domain association, and is known to be involved in tellurite resistance.

Tellurite resistance protein TehB is encoded by the tellurite-reducing operon
tehAB
. TehB exists in a two-domain form (

) with a C-terminal SAM-dependent methyltransferase domain and an N-terminal domain of unknown function; and in the form of two stand-alone proteins: YeaR protein (this group) and single-domain TehB methyltransferase (

).

When upregulated or present in high copy number, TehB of Streptococcus pneumoniae is responsible for potassium tellurite resistance, this is achieved by increasing the reduction rate of tellurite to metallic tellurium within the bacterium. TehB is a cytoplasmic protein that possesses three conserved motifs (I, II, and III) found in S-adenosyl-L-methionine (SAM)-dependent non-nucleic acid methyltransferases . Conformational changes in TehB are observed upon binding of both tellurite and SAM, suggesting that TehB utilises a methyltransferase activity in the detoxification of tellurite .

The role of YeaR protein and of the corresponding domain in two-domain TehB in tellurite resistance is not known.
Protein of unknown function DUF2068, transmembrane, subgroup (DUF2068_TM_subgr)
Type: Family

This entry, found in various prokaryotic proteins, has no known function, but contains at least two predicted transmembrane regions.
Predicted O-glycosyl hydrolase (O_gly_hydro)
Type: Family

This group represents a predicted O-glycosyl hydrolase.
Uncharacterised conserved protein UCP021525 (UCP021525)
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 UCP021940 (UCP021940)
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 UCP921964 (UCP921964)
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.
ArsR transcriptional regulator (ArsR_tscrpt_regulator)
Type: Family

Members of this family of archaeal proteins are conserved transcriptional regulators belonging to the ArsR family.
Uncharacterised conserved protein UCP022079 (UCP022079)
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 archaea.
Uncharacterised conserved protein UCP024492 (UCP024492)
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.
Archaeosortase A (ArtA)
Type: Family

This family is an archaeal variant of the (normally bacterial) putative protein-sorting integral membrane protein exosortase, hence archaeosortase. The PGF-CTERM/archaeosortase A system is related to S-layer (surface layer) production . Moreover, it has been shown that archaeosortase A (ArtA) is involved in carboxy-terminal post-translational processing of the S-layer glycoprotein . Archaeosortase, similarly to sortase, mediate proteolysis-coupled, covalent cell surface attachment .
Outer membrane protein assembly factor BamC (BamC)
Type: Family

Outer membrane protein (OMP) assembly factor BamC is part of the outer membrane protein assembly Bam complex (composed of the outer membrane protein BamA, and four lipoproteins BamB, BamC, BamD and BamE), which is involved in assembly and insertion of β-barrel proteins into the outer membrane . E. coli BamC is a nonessential member of the Bam complex that stabilises the interaction between the essential proteins BamA and BamD .
Ethylene receptor (ETR)
Type: Family

This entry represents hybrid ethylene sensor histidine kinases from plants, also known as ethylene receptors. It includes ETR1, ETR2, and EIN4 from Arabidopsis thaliana, all of which contain a receiver domain at the C terminus. ETR1 has His kinase activity, whereas ETR2 and EIN4 have Ser/Thr kinase activity . They are related to bacterial two-component regulators and act as a redundant negative regulator of ethylene signalling .
Excinuclease GIY-YIG catalytic domain-containing uncharacterised conserved protein (UCP026568_excinuclease)
Type: Family

This group represents a predicted uncharacterised protein with excinuclease GIY-YIG catalytic domain.
Cyclic-di-AMP phosphodiesterase GdpP/PdeA (GdpP/PdeA)
Type: Family

This entry includes a group of cyclic-di-AMP phosphodiesterases, including GdpP (also known as yybT) from Bacillus subtilis and PdeA from Listeria monocytogenes serotype 1/2a. They contribute to the degradation of cyclic di-AMP (c-di-AMP), which controls cell wall and potassium homeostasis and secures the integrity of their DNA .
Uncharacterised conserved protein UCP026631 (UCP026631)
Type: Family

This group represents a predicted membrane protein.
Predicted heptaprenyl diphosphate synthase, component I (Hpre_diP_synt_I)
Type: Family

Proteins in this group all contain a domain that is predicted to be component I of bacterial heptaprenyl diphosphate (HepPP) synthase (

). In Bacillus subtilis the enzyme is composed of two dissociable subunits, component I and component II; both are essential for enzyme catalysis .
Sorting nexin 9 family (Snx9_fam)
Type: Family

Proteins in the sorting nexin 9 subfamily includes SNX9, SNX18 and SNX33 . They are characterised by the presence of an N-terminal SH3 domain (

), a PX domain that is a phosphoinositide-binding module (

), and a Bin/Amphiphysin/Rvs (BAR) domain at the C terminus, which allows membrane binding and bending. They are required for progression and completion of mitosis .
Uncharacterised conserved protein UCP027893 (UCP027893)
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, topoisomerase zinc finger (UCP028063_topo_Znf)
Type: Family

Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates . Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few . Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target.

This group represents a predicted uncharacterised protein with a topoisomerase zinc finger domain.
Uncharacterised conserved protein UCP028175 (UCP028175)
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.
Predicted amidinotransferase, FN0238 type (Amdntrnsf_FN0238)
Type: Family

This group represents a predicted amidinotransferase, FN0238 type. Please see the following relevant reference: .
Uncharacterised conserved protein UCP028291 (UCP028291)
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 UCP028408 (UCP028408)
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 UCP028415 (UCP028415)
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, lipid A biosynthesis (UCP028440_lipidA_biosyn)
Type: Family

Members if this group contain a lipid A biosynthesis domain (

). However, There is currently no experimental data for members of this group indicative of any function.
Uncharacterised conserved protein UCP028477 (UCP028477)
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.
Predicted acyltransferase (Ac_Trasf)
Type: Family

This group represents a predicted acyltransferase.
Flagellar protein FlgO (FlgO)
Type: Family

This family includes FlgO from Vibrio cholerae, which is part of an operon with two genes, flgO and flgP, positively regulated by FlrC, the activator of class III flagellar genes . FlgO and FlgP function in motility to mediate flagellar stability and influence attachment and colonization .
Uncharacterised conserved protein UCP028704, OpgC (UCP028704_OpgC)
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.
Beta-glucosidase GBA2-type (B_Glucosidase_GBA2-typ)
Type: Family

Non-lysosomal glucosylceramidase, also known as beta-glucosidase 2 (GBA2) is an enzyme involved in an alternative catabolic pathway of glucosylceramide . GBA2, has been characterised as a bile acid beta-glucosidase . It is unrelated to other known glucosidases, but it has homologues among bacteria and archaea .
Predicted aminopeptidase (Aminopept)
Type: Family

This family of bacterial proteins has a conserved HEXXH motif, suggesting that members are putative peptidases of zincin fold .
RecF-like (RecF-like)
Type: Family

This group represents a predicted RecF protein.
Uncharacterised conserved protein UCP029407 (UCP029407)
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 UCP029548, STAS-type (UCP029548_STAS-type)
Type: Family

This group represents a predicted uncharacterised protein with STAS domain, PA2797 type.
Uncharacterised conserved lipoprotein (UCP029720)
Type: Family

There is currently no experimental data for members of this group of lipoproteins or their homologues, nor do they exhibit features indicative of any function.