SII-SWORD/CoKE huggingface dataset:
Protein YebY (YebY)
Type: Family

This protein family, formerly known as DUF2511, includes Protein YebY from Escherichia coli and similar proteins predominantly found in Gammaproteobacteria. Together with YebA, encoded by the same operon, YebY is required for the activity of the copper-related NADH dehydrogenase II (NDH-2). The crystal structure of YebY shows great similarity to that of the lantibiotic self-resistance protein MlbQ, which has a hydrophobic surface patch .
Protein of unknown function DUF2512 (DUF2512)
Type: Family

Proteins in this entry are predicted to be integral membrane proteins, and many of them are annotated as being YndM protein. They are all found in Firmicutes. The true function is not known.
Protein of unknown function DUF2513 (DUF2513)
Type: Family

The function of this family is not known.
Glutamate dehydrogenase, NAD-specific (Glutamate_DH_NAD-spec)
Type: Family

The best-characterised protein in this entry is an NAD-specific glutamate dehydrogenase encoded in an antisense gene pair arrangement with a DnaK-J-like protein .
Protein of unknown function DUF2509 (DUF2509)
Type: Family

This entry represents a conserved protein found in Proteobacteria. The function is not known but many of the members are annotated as protein YgdB.
T4 endoribonuclease RegB (T4_endoribonuclease_RegB)
Type: Family

The RegB endoribonuclease encoded by Bacteriophage T4 is a unique sequence-specific nuclease that cleaves in the middle of GGAG or, in a few cases, GGAU tetranucleotides, preferentially those found in the Shine-Dalgarno regions of early phage mRNAs. T4 regB expression is regulated autogenously by attacking its own mRNA. The deduced primary structure of RegB proteins in many phages is almost identical to that of T4, while the sequences of RegB encoded by Enterobacteria phage RB69, Enterobacteria phage TuIa and Enterobacteria phage RB49 show substantial divergence from their T4 counterpart . In RB49 regB expression is regulated by both RegB and Escherichia coli endoribonuclease E.

It's worth noting that this family does not fall into the Lysozyme-like family, but rather is a new member of the RelE/YoeB structural and functional family of ribonucleases specialising in mRNA inactivation within the ribosome .
NAD(P)H-quinone oxidoreductase subunit L (NADH-quinone_OxRdatse_su_L)
Type: Family

NAD(P)H-quinone oxidoreductase subunit L (NdhL) is a component of the NDH-1L complex that is one of the proton-pumping NADH:ubiquinone oxidoreductases that catalyse the electron transfer from NADH to ubiquinone linked with proton translocation across the membrane. NDH-1L is essential for photoheterotrophic cell growth. NdhL appears to contain two transmembrane helices and it is necessary for the functioning of though not the correct assembly of the NDH-1 complex in Synechocystis 6803. The conservation between cyanobacteria and green plants suggests that chloroplast NDH-1 complexes contain related subunits .
Baculovirus occlusion-derived virus envelope, E18 (Baculo_ODV-E18)
Type: Family

Baculovirus occlusion-derived virus (ODV) derives its envelope from an intranuclear membrane source. Occlusion-derived viral envelope proteins that are detected in viral-induced intranuclear microvesicles, but not detected in the plasma membrane, cytoplasmic membranes, or the nuclear envelope. This entry represents ODV-E18 protein which is encoded by baculovirus late genes with transcription initiating from a TAAG motif. ODV-E18 exists as a dimer in the ODV envelope, which contains a hydrophobic domain that putatively acts as a target or retention signal for intranuclear microvesicles .
Uncharacterised protein family Ycf34 (Uncharacterised_Ycf34)
Type: Family

This entry represents Ycf34, a protein encoded in algal genomes and additionally found in cyanobacteria. The function is not known. As the family is exclusively found in phototrophic organisms it may play a role in photosynthesis.
Late competence development protein ComFB (ComFB)
Type: Family

Competence is the ability of a cell to take up exogenous DNA from its environment, resulting in transformation. It is widespread among bacteria and is probably an important mechanism for the horizontal transfer of genes. DNA usually becomes available by the death and lysis of other cells. Competent bacteria use components of extracellular filaments called type 4 pili to create pores in their membranes and pull DNA through the pores into the cytoplasm. This process, including the development of competence and the expression of the uptake machinery, is regulated in response to cell-cell signalling and/or nutritional conditions .

The development of genetic competence in Bacillus subtilis is a highly regulated adaptive response to stationary-phase stress. For competence to develop, the transcriptional regulator, ComK, must be activated. ComK is required for the expression of genes encoding proteins that function in DNA uptake. In log-phase cultures, ComK is inactive in a complex with MecA and ClpC. The comS gene is induced in response to high culture cell density and nutritional stress and its product functions to release active ComK from the complex. ComK then stimulates the transcription initiation of its own gene as well as that of the late competence operons .

The comF locus has three open reading frames and is driven by a single sigma A-like promoter in front of comFORF1. It is dependent on early regulatory competence genes and is only expressed in competence medium. ComFORF1 is similar to an extensive family of ATP-dependent RNA/DNA helicases with closer similarity to the DEAD protein subfamily and to the PriA protein in Escherichia coli. ComFORF1 late gene product plays an essential role during the binding and uptake events involved in B. subtilis transformation . ComFB is the second protein encoded within the late competence locus ComF . The function of ComFB within late competence development is not known.
Protein of unknown function DUF2515 (DUF2515)
Type: Family

This family is conserved in Firmicutes. Several members are annotated as YppC. The function of these proteins is not known.
Protein of unknown function DUF2514 (DUF2514)
Type: Family

This protein family is conserved in bacteria and some viruses. The function is not known. This entry includes the protein gp55 from Enterobacteria phage N15.
Putative sensory transduction regulator YbjN (Put_sensory_transdc_reg_YbjN)
Type: Family

YbjN is a putative sensory transduction regulator protein found in Proteobacteria. As it is a multi-copy suppressor of the coenzyme A-associated temperature sensitivity in temperature-sensitive mutant strains of Escherichia coli the suggestion is that it both helps CoA-A1 and possibly works as a general stabiliser for some other unstable proteins .
Replication regulatory protein RepA2 (RepA2)
Type: Family

This family of proteins regulates the replication of rolling circle replication (RCR) plasmids that have a double-strand replication origin (dso). Regulation of the replication of the RCR plasmids occurs mainly at the initiation of leading strand synthesis at the dso, such that concentration of Rep protein controls plasmid replication .
Protein of unknown function DUF2516 (DUF2516)
Type: Family

This entry represents a conserved protein in Actinobacteria. The function is not known.
Uncharacterised protein YbfA (YbfA)
Type: Family

This entry represents proteins conserved in Proteobacteria and includes the predicted protein YbfA. The function is not known.
Uncharacterised protein family Ycf51 (Uncharacterised_Ycf51)
Type: Family

This entry contains the Ycf51 protein family, which is conserved in Cyanobacteria. The function is not known.
Putative oxidoreductase/dehydrogenase, Rossmann-like domain (OxRdtase/DH_put_Rossmann_dom)
Type: Domain

This entry represents an NAD/NADP-binding domain with a core Rossmann-type fold, found in an uncharacterised protein family thought to be putative NADP oxidoreductase coenzyme F420-dependent proteins and/or NAD-dependent glycerol-3-phosphate dehydrogenase-like proteins. This Rossmann-fold domain consists of 3-layers α/β/α, where the six β strands are parallel in the order 321456.
Cell division activator CedA (Cell_div_activator_CedA)
Type: Family

CedA is involved in the regulation of cell division in Escherichia coli and related organisms. It is structurally similar to dsDNA-binding domains and has been found to interact with dsDNA. The protein comprises four antiparallel β-strands, an α-helix, and a large unstructured N terminus. As dsDNA binding domains, it may also bind dsDNA by inserting the β-sheet into the major groove of the DNA .
Uncharacterised protein family YbaK (Uncharacterised_YbaK)
Type: Family

This entry represents a protein of unknown function specific to Bacillus.
Uncharacterised protein family YtzC (Uncharacterised_YtzC)
Type: Family

This entry represents proteins with unknown function, and appear to be restricted to the Bacillaceae.
Uncharacterised bacterial stress protein YodD (Uncharacterised_YodD)
Type: Family

This entry represents the uncharacterised protein family YodD which appear to be restricted to Enterobacteriaceae, and are thought to be stress-related proteins .
Protein of unkown function DUF2523 (DUF2523)
Type: Family

This entry represents a family of phage-related proteins whose function is uncharacterised.
Protein of unknown function DUF2526 (DUF2526)
Type: Family

This entry represents proteins with unknown function and is a highly conserved sequence, it is restricted to Enterobacteriaceae.
Protein of unknown function DUF2627 (DUF2527)
Type: Family

This entry represents small proteins with unknown function and appear to be restricted to a family of Enterobacterial proteins. It has a highly conserved sequence. Some proteins are annotated as YobF and may be involved in stress responses in E. coli.
Spore germination protein GerPC (Spore_germination_GerPC)
Type: Family

GerPC is required for the formation of functionally normal spores. The gerP locus encodes a number of proteins which are thought to be involved in the establishment of normal spore coat structure and/or permeability, which allows the access of germinants to their receptor .
Lipoprotein LpqN/LpqT-like (Lipoprotein_LpqN/LpqT-like)
Type: Family

This protein is conserved in Mycobacteriaceae and is likely to be a lipoprotein . lpqN is involved in cell envelope lipid changes during biofilm maturation. It interacts with periplasmic loop domains of the MmpL3 and MmpL11 transporters that export mycolic acid-containing cell envelope lipids. It also interacts with secreted cell envelope biosynthetic enzymes such as Ag85A . It has been shown to interact with host CBL, a host ubiquitin ligase, and probably blocks the normal functions of CBL and disturbs CBL-mediated antibacterial activity .

This entry also includes LpqT and Mtc28. Their function is not clear.
Protein of unknown function DUF2550 (DUF2550)
Type: Family

The function of the proteins in this family is not known, though most members are annotated as either secreted or membrane proteins.
Domain of unknown function DUF2529 (DUF2529)
Type: Domain

This domain is conserved in the Bacillales. The function is not known, but given this domains relationship to the SIS domain it may carry out a sugar isomerase reaction. Several members are annotated as being YWJG, a protein expressed downstream of pyrG, a gene encoding for cytidine triphosphate synthetase.
Protein of unknown function DUF2555 (DUF2555)
Type: Family

This entry represents conserved proteins found in Cyanobacteria. The function is not known.
Regulatory phage protein Cox (Phage_P2_Cox)
Type: Family

Cox proteins are expressed by Enterobacteria phages. The Cox protein is a 79-residue basic protein with a predicted strong helix-turn-helix DNA-binding motif. It inhibits integrative recombination and it activates site-specific excision of the HP1 genome from the Haemophilus influenzae chromosome, Hp1. Cox appears to function as a tetramer. Cox binding sites consist of two direct repeats of the consensus motif 5'-GGTMAWWWWA, one Cox tetramer binding to each motif. Cox binding interferes with the interaction of HP1 integrase with one of its binding sites, IBS5. This competition is central to directional control. Both Cox binding sites are needed for full inhibition of integration and for activating excision, because it plays a positive role in assembling the nucleoprotein complexes that produce excisive recombination, by inducing the formation of a critical conformation in those complexes .
Mediator complex, subunit Med1 (Mediator_Med1)
Type: Domain

The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins.

The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11.

This entry represents subunit Med1 of the Mediator complex. The Med1 forms part of the Med9 submodule of the Srb/Med complex. It is one of three subunits essential for viability of the whole organism via its role in environmentally-directed cell-fate decisions .
Protein of unknown function DUF2530 (DUF2530)
Type: Family

This entry represents proteins with unknown function found in mycobacteria and in other Actinobacteria.
Bacteriophage T7, Gp17.5, holin (Phage_T7_Gp17.5_holin)
Type: Family

This entry represents a protein conserved in Caudovirales (known as tailed bacteriophages). Holins are a diverse family of proteins that cause bacterial membrane lysis during late-protein synthesis by forming micro-pores through which endolysins and virus particles can escape from the cell. Holins accumulate in the cytoplasm and induce lysis once a critical concentration is reached .
Sporulation inhibitor of replication protein SirA (SirA)
Type: Family

This entry represents the Sporulation inhibitor of replication (sirA) family of proteins from Bacillus sp. Induction of sporulation in rapidly growing cells inhibits replication; this is thought to be through the action of SirA protein and independent of phosphorylated Spo0A; however SirA protein synthesis is induced by Spo0A .
HofP protein (HofP)
Type: Family

The
Escherischia coli
protein HofP is a member of this family and is one of eight genes shown to be required for the utilization of extracellular DNA as a nutrient source in starving conditions, allowing DNA to be the sole source for carbon and energy . Proteins in this entry are found only in Enterobacteriaceae.
Protein of unknown function DUF2534 (DUF2534)
Type: Family

This entry represents proteins with unknown function, and appear to be restricted to Enterobacteriaceae.
Protein of unknown function DUF2536 (DUF2536)
Type: Family

This entry represents proteins with unknown function appears to be restricted to Bacillus spp.
Protein of unknown function DUF2535 (DUF2535)
Type: Family

This entry represents proteins with unknown function, and appear to be restricted to Bacillus spp.
Protein of unknown function DUF2533 (DUF2533)
Type: Family

This entry represents proteins with unknown function, and appear to be restricted to Bacillus spp.
Toxin GhoT/OrtT (Toxin_GhoT/OrtT)
Type: Family

GhoT is part of the GhoT-GhoS type V toxin-antitoxin (TA) system. GhoT is inhibited by antitoxin GhoS, which specifically cleaves its mRNA . OrtT is homologous to GhoT, but it is not part of a TA pair. In this case, it acts as an independent toxin to reduce growth during stress related to amino acid and DNA synthesis .
Protein of unknown function DUF2569 (DUF2569)
Type: Family

This entry represents a protein that is conserved in bacteria. The function is not known, but several members are annotated as being YdgK or a homologue thereof and associated to the inner membrane. This signature also matches proteins that are described as transglutaminase-like enzymes, although this could not be confirmed.
Protein of unknown function DUF2585 (DUF2585)
Type: Family

This family is conserved in Proteobacteria. The function is not known, but it is thought to be a transmembrane protein.
Low molecular weight protein antigen 6, PH domain (CFP-6_PH)
Type: Domain

This entry represents a domain found in prokaryotic proteins, mainly from Actinomycetales, including Low molecular weight protein antigen 6 from Mycobacterium tuberculosis (CFP-6, ). The domain, previously known as DUF2581, has a bacterial type PH domain structure.
Biofilm formation regulator YbaJ (Biofilm_formation_reg_YbaJ)
Type: Family

YbaJ regulates biofilm formation. It also has an important role in the regulation of motility in the biofilm. YbaJ functions in increasing conjugation, aggregation and decreasing the motility, resulting in an increase of biofilm .
Bacteriophage HP1, Orf23 (Phage_HP1_Orf23)
Type: Family

This entry is represented by Bacteriophage HP1, Orf23. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

This family of proteins is a component of a contractile injection system related to phage sheath proteins .
Bacterial proteasome activator (Proteasome_act)
Type: Family

This is a family of bacterial proteasome cofactors. The family member from Mycobacterium tuberculosis, protein Rv3780, was shown to form rings and cap proteasome core particles. It enhanced peptide and protein degradation by proteasomes in an adenosine triphosphate (ATP)-independent manner, promoting degradation of the heat shock protein repressor HspR .
Bacteriophage HP1, Orf28 (Phage_HP1_Orf28)
Type: Family

This entry is represented by Bacteriophage HP1, Orf28. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Protein of unknown function DUF2583 (DUF2583)
Type: Family

Some members in this entry are annotated as YchH however currently no function is known.
Protein of unknown function DUF2584 (DUF2584)
Type: Family

This entry represents a group of proteins mainly found in Bacilli, including Uncharacterized protein YtmB from Bacillus subtilis. Its function is unknown.
Anti-sigma-G factor Gin (Sigma-G_inhibitor_Gin)
Type: Family

Gin allows sigma-F to delay late forespore transcription by preventing sigma-G to take over before the cell has reached a critical stage of development. Gin is also known as CsfB .
NinX, bacteriophage P22 (Phage_P22_NinX)
Type: Family

This entry represents NinX protein from bacteriophage P22. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Multidrug efflux pump accessory protein AcrZ (AcrZ)
Type: Family

AcrA-AcrB-AcrZ-TolC is a drug efflux protein complex with a broad substrate specificity. AcrZ binds to AcrB and is required for efflux of some, but not all substrates, suggesting it may influence the specificity of drug export .
Inner membrane protein YbjO, dehydrogenase-like (YbjO_DH-like)
Type: Family

This entry includes the Inner membrane protein YbjO which appears to be restricted to Enterobacteriaceae. From AlphaFold structure predictions, it has been suggested that these proteins may function as dehydrogenases, accounting in its structural similarity with the C-terminal region of Acyl-CoA dehydrogenases.
Flagellar assembly regulator FliX, class II (Flagellar_assmbl_FliX_class2)
Type: Family

The FliX protein is possibly a transient component of the flagellum that is required for the assembly process. FliX may contribute to the targeting or assembly of the P- and L-ring protein monomers at the cell pole. The family carries a potential N-terminal signal sequence and at least one transmembrane domain indicating that it might function either in or in association with the cell membrane .
Protein of unknown function DUF2594 (DUF2594)
Type: Family

This entry represents proteins with unknown function and appear to be restricted to Enterobacteriaceae.
Winged helix-turn-helix domain (DUF2582) (DUF2582)
Type: Family

This domain is conserved in bacteria and archaea. The function is not known. The structure of two proteins in this family were solved using NMR and shown to adopt a winged helix-turn-helix fold . Structural analysis shows that these proteins form an unusual dimeric conformation. This dimer was shown to be similar to that found in the FadR and TubR wHTH domains. It was suggested that these proteins are not very likely to bind to DNA.
Bacteriophage HP1, Orf24 (Phage_HP1_Orf24)
Type: Family

This entry represents proteins with unknown function found in tailed bacteriophages and Proteobacteria, including Putative tail tube protein from Haemophilus phage HP1 (Orf24). The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Protein of unknown function DUF4226 (DUF4226)
Type: Family

This entry represents an uncharacterised family of proteins belonging to Mycobacteria. It was previously incorrectly annotated as biofilm regulator BssS (also known as YliH).
ATP synthase, F0 complex, subunit H (ATP_synth_F0_suH)
Type: Family

This entry represents subunit H found in the F0 complex of F-ATPases from fungal mitochondria. Subunit H is homologous to the mammalian factor F6 , and is essential for the correct assembly and/or functioning of F-ATPases, since yeast cells lacking it are not able to grow on non-fermentable carbon sources . Subunit H occupies a central place in the peripheral stalk between the F1 sector and the membrane .

Transmembrane ATPases are membrane-bound enzyme complexes/ion transporters that use ATP hydrolysis to drive the transport of protons across a membrane. Some transmembrane ATPases also work in reverse, harnessing the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP.

F-ATPases (also known as ATP synthases, F1F0-ATPase, or H(+)-transporting two-sector ATPase) (

) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), with additional subunits in mitochondria. Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the α(3)β(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis . These ATPases can also work in reverse in bacteria, hydrolysing ATP to create a proton gradient.
Tetraprenyl-beta-curcumene synthase YtpB-like (YtpB-like)
Type: Family

In Bacillus subtilis, YtpB catalyses the transformation of a linear C35 prenyl diphosphate chain to form tetraprenyl-beta-curcumene .

This entry also contains trifunctional sesterterpene/triterpene/sesquarterpene synthase which catalyses the conversion of geranylfarnesyl diphosphate (GFPP) into beta-geranylfarnesene and the conversion of hexaprenyl diphosphate (HexPP) into beta-hexaprene .
Inner membrane protein YlaC (Memb_YlaC)
Type: Family

Members of this family include proteins annotated as inner membrane protein YlaC in E. coli and Salmonella. The function of this family is unknown.