Genomic Distribution of ushA-like Genes in Bacteria: Comparison to cpdB-like Genes

Ribeiro, João Meireles; Cameselle, José Carlos

doi:10.3390/genes14081657

Open AccessArticle

Genomic Distribution of ushA-like Genes in Bacteria: Comparison to cpdB-like Genes

by

João Meireles Ribeiro

^*

and

José Carlos Cameselle

Grupo de Enzimología, Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Medicina y Ciencias de la Salud, Universidad de Extremadura, 06006 Badajoz, Spain

^*

Author to whom correspondence should be addressed.

Genes 2023, 14(8), 1657; https://doi.org/10.3390/genes14081657

Submission received: 17 July 2023 / Revised: 11 August 2023 / Accepted: 15 August 2023 / Published: 20 August 2023

(This article belongs to the Special Issue Feature Papers in Microbial Genetics in 2023)

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Abstract

:

UshA and CpdB are nucleotidases of the periplasm of several Gram-negative bacteria, while several Gram-positives contain cell wall-bound variants. UshA is a 5′-nucleotidase, a UDP-sugar hydrolase, and a CDP-alcohol hydrolase. CpdB acts as a 3′-nucleotidase and as a phosphodiesterase of 2′,3′-cyclic nucleotides and 3′,5′-linear and cyclic dinucleotides. Both proteins are pro-virulent for the pathogens producing them and facilitate escape from the innate immunity of the infected host. Recently, the genomic distribution of cpdB-like genes in Bacteria was found to be non-homogeneous among different taxa, and differences occur within single taxa, even at species level. Similitudes and differences between UshA-like and CpdB-like proteins prompted parallel analysis of their genomic distributions in Bacteria. The presence of ushA-like and cpdB-like genes was tested by TBlastN analysis using seven protein probes to query the NCBI Complete Genomes Database. It is concluded that the distribution of ushA-like genes, like that of cpdB-like genes, is non-homogeneous. There is a partial correlation between both gene kinds: in some taxa, both are present or absent, while in others, only one is present. The result is an extensive catalog of the genomic distribution of these genes at different levels, from phylum to species, constituting a starting point for research using other in silico or experimental approaches.

Keywords:

UshA; CpdB; nucleotidase; bacteria; genome; TBlastN

Graphical Abstract

1. Introduction

The proteins UshA and CpdB are prototypic nucleotidases of the periplasmic space of Escherichia coli [1,2] and other Gram-negative bacteria [3,4,5,6,7,8,9,10]. As far as enzyme activity is concerned, UshA is a highly efficient 5′-nucleotidase that is also active as a phosphoanhydride hydrolase of UDP-sugars, CDP-alcohols, and other nucleotidic derivatives [11,12,13]. CpdB is a highly efficient 3′-nucleotidase, also active as a phosphodiesterase of 2′,3′-cyclic mononucleotides, 3′,5′-cyclic or linear dinucleotides, and the artificial phosphodiester substrate bis-4-nitrophenylphosphate [14,15]. Both proteins are structurally related, as following the removable signal peptide for secretion (SP), they display the same two-domain architecture: an N-terminal metallophos domain (Pfam ID PF00149) that includes the catalytic site with a dimetal center, and a C-terminal 5_nucleotid_C domain (Pfam ID PF02872) that includes a substrate-binding site [16,17]. It is noteworthy that the designation of the 5_nucleotid_C domain does not imply the occurrence of 5′-nucleotidase activity. UshA is a 5′-nucleotidase devoid of 3′-nucleotidase activity, while CpdB is a 3′-nucleotidase devoid of 5′-nucleotidase activity. In both proteins, the N- and C-terminal domains are joined by a ≈20-amino acid linker [17,18]. Both enzymes are believed to share a remarkable catalytic cycle in which the typical 5′-AMP or 3′-AMP substrates bind to the specificity site in the 5_nucleotid_C domain, with the adenine ring forming a stacking sandwich between two aromatic residues. The substrate-charged domains then undergo large, 96° rotations that bring the substrate to the catalytic site in the metallophos domains, where dephosphorylation takes place [17,19,20].

Besides the periplasmic versions of UshA and CpdB, UshA-like and CpdB-like proteins occur in Gram-positive bacteria as cell wall-bound proteins that have received different names. Among them are ecto-5′-nucleotidases of Staphylococcus aureus (AdsA [21]), Streptococcus sanguinis (Nt5e [22]), S. agalactiae (NudP [23]), S. pyogenes (S5nA [24]), and S. suis (Ssads [25]), and ecto-3′-nucleotidases of S. agalactiae (CdnP [26]) and S. suis (SntA [27,28]). These proteins, in addition to the SP, metallophos, and 5_nucleotid_C domains typical of UshA and CpdB, bear 3′ extensions that constitute cell wall binding domains with a LPXTG or similar motif [29].

The periplasmic or cell wall locations of these enzymes make them able to act on non-cytoplasmic substrates, either secreted from the same cell or of exogenous origin, for instance, in the cytoplasm of eukaryotic cells invaded by bacterial pathogens such as Salmonella enterica or S. agalactiae. Both 5′-nucleotidases and 3′-nucleotidases have been identified and considered virulence factors for producing pathogens by mechanisms related to their nucleotide-degrading activities or to effects on complement that facilitate evasion from host innate immunity [21,22,23,24,25,26,27,30,31].

For these reasons, we consider it of utmost interest to gain knowledge of how widespread, among the genomes of different bacterial taxa, the occurrence of genes coding for nucleotidases is, which, either by being periplasmic or bound to the cell wall, have the potential to act extracytoplasmatically on nucleotidic substrates. In a recent study, we analyzed the genomic distribution of cpdB-like genes using the protein sequence of S. enterica CpdB as a probe (query) for TBlastN analyses of complete genomes, limited by bacterial taxa at different levels, from phyla to species [32]. The results revealed that cpdB-like genes are far from ubiquitous in the superkingdom Bacteria, being present in some phyla but not in others. At levels higher than species, the genomic distribution was not homogeneous since few taxa contained a cpdB-like gene in all the sequenced genomes. At the level of species, the distribution was more homogeneous, as out of 77 taxa considered, 38 showed a (near) widespread distribution of cpdB-like genes and 28 did not contain them. Interestingly, 11 species showed a partial distribution, with some sequenced genomes but not all containing a cpdB-like gene. This interesting panoramic view prompted us to extend the analysis to ushA-like genes and to perform it in a more detailed way by increasing the number of TBlastN probes from the single one used in the previous study [32] to a total of seven different probes in the current manuscript, five for usha-like genes and two for cpdB-like ones. The result is an extensive catalog of the genomic distribution of these genes at different levels, from phylum to species, constituting a starting point for research using other in silico or experimental approaches. Major observations were that the genomic distribution of ushA-like genes was not homogeneous and that the correlation with cpdB-like genes was partial, as in some taxa both were present or absent; however, in others only one was present. Other interesting outcomes worth further research by other approaches are pointed out.

2. Materials and Methods

TBlastN analyses [33,34] were run against NCBI complete microbial genomes (https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=TBlastN&PAGE_TYPE=BlastSearch&BLAST_SPEC=MicrobialGenomes&LINK_LOC=blasttab&LAST_PAGE=blastn, accessed on 15 July 2023). Default parameters were applied except that the maximum number of target sequences was adapted to the expected number of hits. The database was queried using the sequence identifiers of the seven-probe set selected (Figure 1). Routinely, the Entrez query “NOT plasmid [Title]” was applied. The searches within each taxonomical group (taxid) (Organism) were restricted in principle to genomes of type material [35]. This restriction was removed when less than five type-material genomes were available or, as a rule, for searches within genera and species. The typical conditions for launching a TBlastN search from the Microbial Translated Blast page are shown in Figure S1. When running searches limited by organism, a bug was observed in the organism menu as it occasionally chose the wrong taxid number. Therefore, all taxid numbers were checked in the NCBI Taxonomy browser (https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi, acceessed on 15 July 2023) [36]. Genomic hits were computed when the alignment score was >150 and query coverage was >70%.

3. Results

3.1. Selection of Probes for TBlastN Analysis

The probes for TBlastN analysis of UshA-like genes were selected among a set of 21 bacterial 5′-nucleotidases (Table 1). Eighteen of them were collected from a recent review by Zakataeva [37], to which two well-characterized CpdB-like 3′-nucleotidases were added [14,27] (no. 20 and 21 in Table 1). All of them are either periplasmic or cell wall-bound, experimentally studied nucleotidases. In addition, one uncharacterized, putative 5′-nucleotidase of B. subtilis, recovered from UniProtKB/Swiss-Prot (https://www.uniprot.org/help/uniprotkb, acceessed on 15 July 2023) [38], was included (no. 19 in Table 1).

Table 1. Periplasmic or cell wall-bound bacterial nucleotidases are used to select probes for TBlastN analysis of bacterial genomes. This protein set was taken from Zakataeva [37], except no. 19 (taken from UniProtKB/Swiss-Prot [38]) and no. 20 and 21 from [14,27].

No.	Accession	Description	Amino Acids
1 ¹	P07024	USHA_ECOLI [Escherichia coli]	550
2	Q9KQ30	5′-nucleotidase [Vibrio cholerae]	553
3	WP_005182369	UDP-sugar hydrolase/5′-nucleotidase UshA [Yersinia intermedia]	550
4	Q8EFH1	5′-nucleotidase [Shewanella oneidensis]	569
5	AAF12718	UDP-sugar hydrolase precursor [Klebsiella aerogenes]	550
6	P44569	NAD 5′-nucleotidase [Haemophilus influenzae]	603
7	WP_061821283	LPXTG-anchored adenosine synthase AdsA [Staphylococcus aureus]	772
8	WP_011837008	Cell surface ecto-5′-nucleotidase Nt5e [Streptococcus sanguinis]	719
9	WP_000726911	Bifunctional metallophosphatase/5′-nucleotidase [Streptococcus agalactiae]	690
10	AEJ25391	Surface-anchored 5′-nucleotidase [Streptococcus equi]	668
11	Q9A0A2	Putative secreted 5′-nucleotidase (5′-nucleotidase) [Streptococcus pyogenes]	670
12	CAR45827	Putative 5′-nucleotidase [Streptococcus suis P1/7]	721
13	WP_003099850	5′-Nucleotidase C-terminal domain-containing protein [Streptococcus iniae]	676
14	Q6HTQ7	2′,3′-Cyclic-nucleotide 2′-phosphodiesterase [Bacillus anthracis]	780
15	P22848	5′-Nucleotidase (Vibrio parahaemolyticus)	560
16	WP_102505627	UDP-sugar hydrolase/5′-nucleotidase UshA [Salinivibrio costicola)	557
17	WP_041419915	UDP-sugar hydrolase/5′-nucleotidase UshA [Shewanella violacea]	569
18	WP_011760134	UDP-sugar hydrolase/5′-nucleotidase UshA [Shewanella amazonensis]	571
19	O32133	Uncharacterized metallophosphoesterase YunD [Bacillus subtilis]	462
20	P08331	2′,3′-Cyclic-nucleotide 2′-phosphodiesterase/3′-nucleotidase [Escherichia coli]	647
21	AYV64543	Heme-binding protein SntA [Streptococcus suis]	813

¹ The probes selected for the study are shown in the background color as Figure 1 to facilitate cross-referencing.

The mutual relatedness among Table 1 proteins was evaluated by the scores of BlastP alignments (Figure 1). This allowed us to select seven proteins to be used as TBlastN probes; they are identified as proteins 1, 6, 8, 9, 19, 20, and 21 in Table 1 and Figure 1. According to the color code used in Figure 1, five of the selected probes (no. 1, 8, 9, 20, and 21) were highly related to a small group of nucleotidases, whereas the other two probes (no. 6 and 19) showed insignificant alignment scores with any other member of the set. Incidentally, one of the so-called 5′-nucleotidases (no. 14 in Table 1) was actually a CpdB-like protein, to judge from its strong relatedness to authentic CpdB-like enzymes (no. 20 and 21 in Table 1) and insignificant alignment scores to the other Table 1 proteins.

3.2. TBlastN Analysis of Bacterial Genomes

3.2.1. General Strategy for the Analysis and Presentation of Results

TBlastN searches were run between 30 June and 15 July 2023 as described under the Materials and Methods section. The number of hits obtained with each probe for each taxonomical group analyzed was recorded. A global TBlastN search was run on 30 June 2023, in the superkingdom Bacteria (taxid:2), with 4185 type-material genomes and a total of 40,608 genomes available on that date. Table 2 shows the results obtained with the seven probes, computing only hits found among type-material genomes.

Thereafter, searches were run in the Bacteria taxa of the NCBI Taxonomy browser [36] at different levels. Detailed results are shown in Tables S1–S6. Summaries of the results at different levels are shown in Table 3, Table 4, Table 5, Table 6, Table 7 and Table 8, where the presence or absence of ushA-like and cpdB-like genes is schematically indicated. In these summaries, “presence” does not mean that the genes are widespread in the taxon. In this concern, three levels are distinguished: ≤50%, >50% but <100%, and 100% of the analyzed genomes contain ushA-like and/or cpdB-like genes (hits). This is marked by the letters U (ushA-like) and C (cpdB-like) on different color backgrounds: green (≤50%), orange (>50% but <100%), and red (100%). It must be remarked that these percentages include hits obtained with any of the UshA-like or CpdB-like probes (see Table 2). For ushA-like genes, the results were strongly dependent on the probe (five different ones are used), whereas for cpdB-like genes, the two probes used gave similar results in most but not all the taxonomical groups. Finally, when “presence” of both types of genes is indicated for the same taxon, it does not necessarily mean they are in the same genome, unless 100% of the genomes gave positive results in both cases. Of course, 100% positivity for one gene type and <100% for the other means that some genomes contain both types of genes. On the other hand, logically, “absence” refers to 100% of the analyzed genomes with any probe.

In summary, when a taxonomical level is negative or 100% positive for both genes, or negative for one and 100% positive for the other gene type, the analysis of such a taxon is deemed complete and is not pursued further at lower taxonomical levels.

3.2.2. Genomic Distribution of ushA-like and cpdB-like Genes in Bacteria Phyla

Forty three phyla, including the Delta/epsilon subdivision, found in the NCBI Taxonomy browser within the superkingdom Bacteria (mostly coincident with [39]), were submitted to TBlastN analyses with UshA-like and CpdB-like probes (Table 2). The detailed results are shown in Table S1. A simpler summary of the presence/absence of ushA-like and cpdB-like genes is shown in Table 3.

Twelve phyla contained both types of genes; 14 showed neither; 11 showed ushA-like but not cpdB-like genes; and in six cases, the converse was true. With the criteria of Section 3.2.1, 19 phyla (those in black type in Table 3) were considered complete and not pursued at lower levels. The 24 phyla in red type are further analyzed in Table 4 and Table S2.

3.2.3. Genomic Distribution of ushA-like and cpdB-like Genes in Bacterial Classes of Selected Phyla

To continue the TBlastN exploration, 76 bacterial classes belonging to 24 different phyla were queried with the seven probes (Table 2). The detailed results are shown in Table S2. In six of those classes, there was no sequenced genome. A simpler summary of the presence/absence of ushA-like and cpdB-like genes in the 70 classes for which there were sequenced genome(s) is shown in Table 4. With the criteria defined in Section 3.2.1, the analyses of 31 classes (those in black type in Table 4) were considered complete and not pursued further at lower taxonomical levels. On the other hand, the 39 classes shown in red type in Table 4 were further analyzed (Table 5 and Table S3), with one exception marked with an asterisk.

3.2.4. Genomic Distribution of ushA-like and cpdB-like Genes in Bacterial Orders of Selected Classes

To continue the TBlastN exploration, 152 bacterial orders belonging to 38 different classes were queried with the seven probes (Table 2). The detailed results are shown in Table S3. In 20 of those classes, there was no sequenced genome. A simpler summary of the presence/absence of ushA-like and cpdB-like genes in the 132 classes for which there were sequenced genome(s) is shown in Table 5. With the criteria defined in Section 3.2.1, the analyses of 53 orders (those in black type in Table 5) were considered complete and not pursued further at lower taxonomical levels. On the other hand, the 79 orders shown in red type in Table 5 were further analyzed (Table 6 and Table S4).

3.2.5. Genomic Distribution of ushA-like and cpdB-like Genes in Bacterial Families of Selected Orders

To continue the TBlastN exploration, 403 bacterial families belonging to 79 different orders were queried with the seven probes (Table 2). The detailed results are shown in Table S4. In 99 of those families, there was no sequenced genome. A simpler summary of the presence/absence of ushA-like and cpdB-like genes in the 304 families for which there were sequenced genome(s) is shown in Table 6. With the criteria defined in Section 3.2.1, the analyses of 139 families (those in black type in Table 6) were considered complete and not pursued further at lower levels. On the other hand, the 165 families shown in red type in Table 6 were further analyzed (Table 7 and Table S5).

3.2.6. Genomic Distribution of ushA-like and cpdB-like Genes in Bacterial Genera of Selected Families

To continue the TBlastN exploration, 510 bacterial genera belonging to 165 different families were queried with the seven probes (Table 2). In contrast to previous steps (Section 3.2.3, Section 3.2.4 and Section 3.2.5), TBlastN analyses were not run for all the genera belonging to the families deemed not complete (those highlighted in red type in Table 6). Instead, while doing the TBlastN analyses of families, the genera giving the hits were annotated, thus avoiding running later lots of TBlastN searches that would not give any hits.

The detailed results obtained with the 510 selected genera are shown in Table S5. For all of them, the NCBI Complete Genomes Database contained at least one sequenced genome. A simpler summary of the presence/absence of ushA-like and cpdB-like genes in those genera is shown in Table 7.

With the criteria defined in Section 3.2.1, the analyses of 268 genera (those in black type in Table 7) were considered complete. Anyhow, for analyses at the level of species (Table 8 and Table S6), also at variance with previous steps, the selection was not based on the non-complete character of the genera. Instead, the selection was purely subjective and included species belonging to genera not mentioned in Table 7, as explained in Section 3.2.7.

3.2.7. Genomic Distribution of ushA-like and cpdB-like Genes in Selected Bacterial Species

To continue the TBlastN exploration, 107 bacterial species belonging to different families were queried with the seven probes (Table 2). In contrast to the strategy followed at the previous taxonomical levels, when systematic criteria were applied for taxa selection (Section 3.2.3, Section 3.2.4, Section 3.2.5 and Section 3.2.6), a subjective selection of species was made in this case. It included all the bacterial species analyzed in the earlier study of cpdB-like genes, which had been selected mainly for their pathogenicity [32]. In summary, 107 different species were queried with the seven probes. Of them, the 80 shown in black type were declared complete by the criteria described in Section 3.2.1. Non-complete species are highlighted in red. Detailed results are in Table S6, and a summary is in Table 8.

4. Discussion

4.1. Overview

This study is a follow-up of a previous analysis of the genomic distribution of cpdB-like genes in Bacteria, which was performed with S. enterica CpdB (GenBank accession P26265) as the probe [32]. That study was mainly centered on the phyla Pseudomonadota and Bacillota (named then more traditionally as Proteobacteria and Firmicutes, respectively) and their lower divisions. In the current manuscript, the former study has been extended in several aspects, mainly that besides cpdB-like genes, ushA-like genes have been analyzed, and the searches were run without a priori restriction to particular taxa. Moreover, several probes were used, two for cpdB-like genes and five for ushA-like genes (Table 2). The use of several UshA-like probes revealed different types of ushA-like genes, some of them specifically associated with different bacterial taxa. The result is an extensive catalog of the distribution of these genes in superkingdom Bacteria. Several resources are provided, including Supplementary Tables S1–S6 that contain the detailed results of the analyses at different levels: phylum (Table S1), class (Table S2), order (Table S3), family (Table S4), genus (Table S5), and species (Table S6). In the main manuscript, Table 3, Table 4, Table 5, Table 6, Table 7 and Table 8 contain summaries of the data at different levels, from phylum to species.

Table 9 summarizes the total numbers of taxa studied, including the counts of probed taxa of different levels, analyzed taxa (once discounted those for which, by the time of submission, upon TBlastN, no sequenced genomes were found in the NCBI Complete Genomes Database), and taxa declared complete according to the criteria explained in Section 3.2.1. For complete taxa, Table 9 also shows the breakdown by kind of results, depending on whether UshA-like and/or CpdB-like probes gave hits or not. To facilitate searching for particular taxa, alphabetical lists are provided of the 1291 taxa probed (Table S7) and of the 125 taxa without sequenced genomes in the NCBI Complete Genomes Database among those that were probed (Table S8).

4.2. About the Possible Correlation between ushA-like and cpdB-like Genes

UshA and CpdB have different specificities. UshA is a 5′-nucleotidase, UDP-sugar hydrolase, and CDP-alcohol hydrolase [11,12], and CpdB acts as a 3′-nucleotidase and as a phosphodiesterase of 2′,3′-cyclic nucleotides and 3′,5′-linear and cyclic dinucleotides [14]. They are periplasmic [1,2] or cell-wall [21,22,23,24,25,26,27] enzymes that act on extracellular substrates, either exogenous or endogenous. In addition, both are provirulent factors for the producing pathogens, facilitating escape from the innate immunity of the host [21,22,23,24,25,26,27]. The similitude between them was the main reason to study and compare their genomic distributions in Bacteria, with the aim of establishing the extent to which the occurrence of one correlates with the occurrence of the other. In this regard, it is worth recalling that, for instance, the action of CpdB-like proteins on linear and cyclic dinucleotides yields 5′-nucleotides as products but cannot continue their degradation to nucleosides [32]. To this end, the metabolic action of CpdB-like enzymes can be continued by UshA-like enzymes. Moreover, pointing to the correlation between both enzymes is the occurrence in some bacteria of natural fusions of UshA and CpdB as the result of two-gene fusion [40,41].

Table 10, Table 11, Table 12 and Table 13 summarize the non-homogeneous distribution of both gene kinds and the (lack of) correlation between them. A qualitative correlation was observed between both gene kinds for some taxa but not for others. In 416 out of 590 taxa (70.5%), they were both either present (31.4%; Table 10) or absent (39.1%; Table 11). However, 174 taxa (29.5%) failed to show such a correlation, as one of the gene types was present but not the other: 21.7% of the taxa bear ushA-like, not cpdB-like genes (Table 12), whereas for 7.8% the converse was true (Table 13).

4.3. Comments on Some Specific Stories

4.3.1. About Phylum Bacillota and Class Bacilli: Specificity of Probe O32133

A phylum worth special attention is Bacillota, as half of the sequenced type-material genomes (366/705) gave hits with probe O32133, which gave no hits in other phyla except four hits found when the limit to type material was removed for the TBlastN. In Bacillota, there were many hits with all the UshA-like and CpdB-like probes (Table S1). In Table 14, Bacillota is compared with the rest of the superkingdom Bacteria.

In Table 15, a similar comparison is made between the class Bacilli and the rest of the phylum Bacillota. In every case, the distribution of hits among the sequenced genomes was partial, i.e., there were genomes with ushA-like and cpdB-like genes and genomes without them. The degree of coincidence cannot be easily ascertained at this level. This must be attempted at lower taxonomical levels.

4.3.2. About the Occurrence of ushA-like and cpdB-like Genes in the Numerous Sequenced Genomes of Escherichia coli, Salmonella enterica, Pasteurella multocida, Klebsiella pneumoniae and Vibrio cholerae

The five species to be discussed in this section have in common that for them there are numerous genomes available in the NCBI Complete Genomes Database and that the TBlastN analyses did not give complete results for any of the two kinds of genes according to the criteria described in Section 3.2.1.

When complete results are obtained at least for one gene kind, e.g., ushA-like genes, the full picture can be inferred: there will be a number of genomes with both kinds present, and the remaining, up to the total number of genomes, will display only the ushA kind, or vice versa. This is the case for several of the species analyzed in Table 8 (with more details in Table S6). For instance, for Staphylococcus saprophyticus, there are 17 genomes available in the database; all of them gave a ushA-like hit, whereas only four gave a cpdB-like one (Table S6, line 92). It can be concluded that four genomes contain both gene kinds, and the remaining 13 contain only an ushA-like one.

In the cases to be discussed below, there were many hits with UshA-like and CpdB-like probes; however, since TBlastN did not give complete results in any case, for some genomes, it was unclear whether both kinds of genes were absent or one was present and the other absent.

The most important part of the structural and functional information of UshA and CpdB nucleotidases and their encoding genes has been obtained in E. coli [1,2,11,12,14,16,17,18,19]. For this species, a large number of genomes are available in the Complete Genomes Database (3565 when this manuscript was submitted). Most of them; however, not all contain both ushA-like and cpdB-like genes. According to data in line 35 of Table S6, there are 20 E. coli genomes that do not contain an ushA-like gene and 10 genomes that do not contain a cpdB-like gene. By downloading the TBlastN results obtained for E. coli with probes P07024 (UshA protein) and P08331 (CpdB protein), it was confirmed that the same 3559 E. coli genomes had been hit in both cases. Based on their alignment scores, it was possible to identify four genomes that contain an ushA-like gene but are devoid of a cpdB-like gene and 14 genomes for which the converse is true (Table 16). These exceptions were found in 10 different E. coli strains. In addition, there may be six non-identified genomes that contain neither ushA-like nor cpdB-like genes. These data confirm that, although E. coli is a major contributor to the occurrence of these genes in Bacteria, their distribution is near but not fully homogeneous, and there is a high but not full correlation between them.

A particular aspect of some E. coli genomes worthy of attention refers to those of the avian pathogenic E. coli (APEC) strains, for which the cpdB gene has been shown to be provirulent [30]. In the complete genome database, there are five APEC genomes, all of them containing ushA and cpdB genes with high scores (Table 17).

In contrast to what was found in E. coli, a similar analysis with S. enterica genomes led to different results. Table S6 (lines 79–80) shows data for two well-known variants of S. enterica subspecies enterica, serovars Typhi and Typhimurium. In the first case, the 125 genomes available for serovar Typhi gave all high-score hits with probes P07024 (UshA protein) and P08331 (CpdB protein). However, the 350 genomes available for serovar Typhimurium gave hits in only 219 cases with both probes. Downloading and inspection of TBlastN results indicated that all these genomes contained both ushA-like and cpdB-like genes, whereas the remaining 131 genomes of Salmonella Typhimurium deposited in the NCBI Complete Genomes Database contain none of them. In this case, no genome was identified containing one of the gene types but not the other. Therefore, the distribution of these genes in Salmonella Typhimurium is clearly not homogeneous; however, there is a good correlation between them.

In the case of P. multocida, 138 genomes were available in the database, of which 135 gave ushA-like hits and 137 gave cpdB-like ones (line 66 of Table S6). By downloading the TBlastN results obtained for this species with probes P07024 (UshA protein) and P08331 (CpdB protein), it was possible to identify one genome that, despite containing a high-score ushA-like gene, was devoid of a cpdB-like gene, and four genomes that, despite showing high-score cpdB-like genes, were devoid of ushA-like ones (or in one case, just a borderline hit) (Table 18). In this case, such as in E. coli, the distributions of both genes are near but not fully homogeneous, and there is a high but not full correlation between them.

K. pneumoniae is another species for which a large number of genomes are available in the Complete Genomes Database (1967, when this manuscript was submitted). Most of them; however, not all, contain both ushA-like and cpdB-like genes. According to data in line 44 of Table S6, five K. pneumoniae genomes do not contain an ushA-like gene, and five do not contain a cpdB-like gene. To find out whether they are the same or not, TBlastN results obtained with probes P07024 (UshA protein) and P08331 (CpdB protein) were downloaded and compared in Excel. This comparison indicated that the 1962 hits found with each probe were the same; therefore, it seems that there are five double-negative K. pneumoniae genomes, i.e., without both ushA-like and cpdB-like genes. So, the distribution of these genes in K. pneumoniae was near but not fully homogeneous, with a full correlation between them.

In the case of V. cholerae, 221 genomes were available in the database, of which 112 gave ushA-like and cpdB-like hits (line 106 of Table S6). By downloading the TBlastN results obtained for this species with probes P07024 (UshA protein) and P08331 (CpdB protein), it was confirmed that the 112 genomes found by the two probes were the same. Therefore, there are no genomes containing only one of the gene types. All the V. cholerae genomes are either double positive or double negative for these genes. Such as in the case of Salmonella Typhimurium (see above), the distribution of the genes is clearly not homogeneous; however, with full correlation between both kinds.

4.3.3. About the Variety of Distributions of ushA-like and cpdB-like Genes in Species of Streptococcus

The genus Streptococcus is interesting because different species showed different typologies concerning the distribution of ushA-like and cpdB-like genes (see Table 8 and details in lines 95–104 of Table S6). This includes: complete double positive (S. sanguinis and S. termophilus, although probes giving complete ushA positives were different); complete double negative (S. mitis and S. pneumoniae); complete positive for ushA and negative for cpdB (S. mutans and S. pyogenes, although the positives were obtained with different probes); complete positive for ushA and partial for cpdB (S. parasuis); partial positive for ushA and complete positive for cpdB (S. agalactiae); near complete but not fully positive for both genes (S. suis); near complete but not fully positive for ushA and partial for cpdB (S. dysgalactiae). Within Streptococcus species, there is both an irregular distribution and an irregular correlation between ushA-like and cpdB-like genes.

4.4. Repercussion of the Results

In the earlier study of the genomic distribution of cpdB-like genes [32], the possible repercussions of the different kinds of distribution found (widespread, partial, negative) were analyzed, taking into account the role of CpdB-like proteins in the virulence of pathogens, a feature that is shown both by CpdB-like and UshA-like proteins [21,22,23,24,25,26,27]. Therefore, the same analysis can be applied to the results of the current manuscript. This is summarized in three conclusions (adapted from [32]).

Species that do not contain ushA-like and/or cpdB-like genes cannot explode the UshA-like or CpdB-like protein-dependent strategies that facilitate innate immunity escape.

Species in which ushA-like and/or cpdB-like genes are widespread constitute a field to explore the possible role of genes in virulence by creating gene mutants and studying the enzyme activity and specificity of the proteins.

In species with a partial distribution of ushA-like and/or cpdB-like genes, their presence or absence could modulate the virulence of pathogen strains or isolates.

4.5. Strength and Limitations of this Study

The major strength of this study is that it constitutes an extensive catalog of the genomic distribution in Bacteria of two genes with related enzymatic function (but different specificities), structure, and role in virulence. Moreover, interesting is that the TBlastN results are analyzed in terms of alignment scores, which are a constant independent of database size.

On the other hand, the following limitations should be considered:

First, the classification of bacterial taxa is eventually subject to alterations, and, in fact, it has been so since the publication of our earlier study [32].

Second, the results obtained for each taxon are not necessarily stable over time. New bacterial genomes are being sequenced and added to the NCBI Complete Genomes Database or, eventually, retired. In some cases, this was observed to occur to a minor extent in the course of data collection. This can affect the results in a significant way for those taxa with few genomes deposited in the database.

Third, to interpret the results of TBlastN searches in terms of the presence of ushA-like and cpdB-like genes, a minimum alignment score of 151 and a minimum query coverage of 71% were established. This reduces the number of false positives but, in turn, can disregard true but distant homologs. This may have occurred, for instance, with the results of probe WP_011837008, as with some frequency it gave significant scores but with coverages somewhat below 71%.

Fourth, TBlastN hits, even with high scores, reveal the presence of the corresponding genes but do not warrant that they are expressed or that the proteins encoded are enzymatically active. In fact, for instance, silent alleles of ushA have been reported in S. enterica and E. coli [42,43,44,45].

Finally, in such a large collection of data, mistakes are expected. Therefore, in the case of special interest in any concrete result, the readers should be wise to check it by running themselves the relevant TBlastN searches.

5. General Summary of Conclusions and Outcomes Worth of Further Investigation

An extensive catalog of the distribution of ushA-like and cpdB-like genes in the genomes of bacterial taxa was constructed by TBlastN analyses of genomes, from phylum to species, run between 30 June and 15 July 2023, with seven different probes, five for ushA-like and two for cpdB-like genes. In total, the genomes of 43 phyla, 76 classes, 152 orders, 403 families, 510 genera, and 107 species were analyzed. This encompasses every bacterial taxon, since a taxon (class, order, family, or genus) was omitted from analysis only when the genomic analysis of the immediately higher taxonomical level was deemed complete (100% genomes positive and/or negative for both gene kinds).
The genomic distributions of both gene kinds are not homogeneous, as while significant homologs occur in many taxa, in many others they do not. For instance, considering only taxa declared complete, 359 contained one or both ushA-like and cpdB-like genes (Table 10, Table 12, and Table 13), and 231 contained none of them (Table 11).
The correlation between both gene kinds is partial, as among complete taxa there were 416 taxa in which both occurred or both were absent (Table 10 and Table 11), while 128 taxa contained only ushA-like genes (Table 12), and 46 taxa contained only cpdB-like genes (Table 13).
One of the probes used for ushA-like genes (accession number O32133) revealed the highly frequent occurrence in class Bacilli genomes (358/425) of homologs of an uncharacterized B. subtilis metallophosphoesterase named YUND_BACSU. This protein is widespread in B. subtilis genomes (331/346) and has good homologs in 100% of the genomes of B. anthracis and B. cereus. These uncharacterized proteins are therefore interesting candidates for cloning, expression, and enzyme characterization. Eventually, they could also be tested for effects on virulence.
The five complete genomes available for avian pathogenic E. coli (APEC; Table 17) contain high-score hits of ushA (probe accession number P070724) and cpdB genes (probe accession number P08331). The cpdB gene of APEC has been shown previously to be provirulent [30], while the effect of the ushA gene has not been investigated. Our data indicate that this is a possibility worth investigating by creating the ushA mutant and the double ushA and cpdB mutants of APEC.
The five complete genomes available for Salmonella Pullorum contain high-score hits for ushA (probe accession number P070724) and cpdB genes (probe accession number P08331) (Table S6, line 78). For this Salmonella serovar, the cpdB gene has been shown previously to be provirulent [31], while the effect of the ushA gene has not been investigated. Our data indicate that this is an interesting possibility to explore by creating the single ushA mutant and the double cpdB and ushA mutants of S. Pullorum.
The different species of the genus Streptococcus offer a variety of situations concerning the genomic distribution of ushA-like and cpdB-like genes (see Section 4.3.3). On the other hand, ushA-like genes of S. sanguinis, S. agalactiae, S. pyogenes, and S. suis, and cpdB-like genes of S. agalactiae and S. suis, individually considered, have been shown to be pro-virulent for the producing pathogens. However, the following cases remain to be studied: (i) the combined effect of ushA-like and cpdB-like genes on the virulence of S. agalactiae and S. suis; (ii) the possible effect of cpdB-like genes in the virulence of all the Streptococcus species that contain such genes but so far have not been studied in this concern; (iii) the possible effect of ushA-like genes in the virulence of all the Streptococcus species that contain such genes but so far have not been studied in this concern.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/genes14081657/s1; Figure S1: Example of a launch page for a TBlastN search; Table S1: TBlastN analysis of ushA-like and cpdB-like genes in Bacteria phyla; Table S2: TBlastN analysis of ushA-like and cpdB-like genes in Bacteria classes from selected phyla; Table S3: TBlastN analysis of ushA-like and cpdB-like genes in Bacteria orders from selected classes; Table S4: TBlastN analysis of ushA-like and cpdB-like genes in Bacteria families from selected orders; Table S5: TBlastN analysis of ushA-like and cpdB-like genes in Bacteria genera from selected families; Table S6: TBlastN analysis of ushA-like and cpdB-like genes in selected Bacteria species; Table S7: Alphabetical lists of Bacteria taxa analyzed; Table S8: Alphabetical lists of taxa probed that contain no sequenced genomes in the NCBI Complete Genomes Database.

Author Contributions

Conceptualization, J.M.R. and J.C.C.; Data curation, J.M.R. and J.C.C.; Formal analysis, J.M.R. and J.C.C.; Investigation, J.M.R. and J.C.C.; Validation, J.M.R.; Writing—original draft, J.C.C.; Writing—review and editing, J.M.R. All authors have read and agreed to the published version of the manuscript.

Funding

This research received no external funding. However, we would like to acknowledge recurrent funding to the Grupo de Enzimología from the Consejería de Economía, Ciencia y Agenda Digital, Junta de Extremadura, Spain (grant number GR21100) co-funded by FEDER (European Regional Development Fund). The APC was funded by a waiver benefit granted by MDPI.

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

Data are contained within the article or supplementary material.

Conflicts of Interest

The authors declare no conflict of interest.

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Figure 1. Mutual relatedness among the set of proteins used to select TBlastN probes for bacterial genome analysis. An internal BlastP comparison was run among the 21 proteins in Table 1. The grid intersections show the alignment scores obtained. On the top line, the seven proteins selected for use are colored as in Table 1 to facilitate cross-referencing. Within the grid, the colors identify the proteins with high scores, indicative of strong relatedness. The seven probes selected cover, with high scores, the whole set of proteins. Nss, not significant similitude.

Table 2. TBlastN analysis of superkingdom Bacteria (taxid:2) with hits recorded among 4185 type-material genomes.

Type of Probe	Probe ¹	Hits	Score Max.	Score Min.
UshA-like	P07024	630	1099	151
	P44569	456	1188	151
	WP_000726911	468	904	151
	WP_011837008	110	1297	151
	O32133	361	947	171
CpdB-like	P08331	1082	1301	151
CpdB-like	AYV64543	722	1579	153

¹ The probes are shown in the same background color as Figure 1 and Table 1 to facilitate cross-referencing.

Table 3. Presence (+) or absence (−) of ushA-like (U) and cpdB-like (C) genes in Bacteria phyla. The (+) background indicates: green, presence in ≤50% of the genomes analyzed; orange, presence in >50% but <100% of the genomes; red, presence in 100% of the genomes analyzed. Full data can be found in Table S1.

Phylum ¹	Taxid	U	C
Abditibacteriota	2109258	−	−
Acidobacteriota	57723	−	−
Actinomycetota	201174	+	+
Aquificota	200783	−	−
Armatimonadota	67819	+	+
Atribacterota	67818	+	−
Bacillota	1239	+	+
Bacteroidota	976	+	+
Balneolota	1936987	−	+
Bdellovibrionota	3018035	−	−
Caldisericota	67814	+	−
Calditrichota	1930617	−	+
Campylobacterota	29547	+	+
Chlamydiota	204428	−	−
Chlorobiota	1090	−	−
Chloroflexota	200795	+	−
Chrysiogenota	200938	−	−
Coprothermobacterota	2138240	−	+
Cyanobacteriota	1117	+	−
Deferribacterota	200930	+	−
Delta/epsilon subdivisions	68525	+	−
Deinococcota	1297	+	+
Dictyoglomota	68297	+	−
Elusimicrobiota	74152	−	−
Fibrobacterota	65842	+	−
Fusobacteriota	32066	+	+
Gemmatimonadota	142182	−	+
Ignavibacteriota	1134404	−	+
Kiritimatiellota	134625	−	−
Lentisphaerota	256845	−	−
Mycoplasmatota	544448	+	+
Myxococcota	2818505	+	+
Nitrospinota	1293497	−	−
Nitrospirota	40117	+	−
Planctomycetota	203682	−	−
Pseudomonadota	1224	+	+
Rhodothermota	1853220	−	−
Spirochaetota	203691	+	+
Synergistota	508458	+	−
Thermodesulfobacteriota	200940	+	−
Thermomicrobiota	3027942	−	−
Thermotogota	200918	+	+
Verrucomicrobiota	74201	−	+

¹ Phyla highlighted in red are not complete according to Section 3.2.1 and are divided into classes in Table 4 and Table S2.

Table 4. Presence (+) or absence (−) of ushA-like (U) and cpdB-like (C) genes in selected bacterial classes. The (+) background indicates: green, presence in ≤50% of the genomes analyzed; orange, presence in >50% but <100% of the genomes; red, presence in all the genomes. Full data are in Table S2.

Phylum	Class ¹	Taxid	U	C
Actinomycetota	Acidimicrobiia	84992	+	−
	Actinomycetes	1760	+	+
	Coriobacteriia	84998	−	−
	Nitriliruptoria	908620	+	+
	Rubrobacteria	84995	+	−
	Thermoleophilia	1497346	+	−
Armatimonadota	Armatimonadia	1042312	−	−
	Chthonomonadetes	1077257	+	−
	Fimbriimonadia	1663419	+	−
Bacillota	Bacilli	91061	+	+
	Clostridia	186801	+	+
	Erysipelotrichia	526524	+	+
	Limnochordia	1676648	+	+
	Negativicutes	909932	+	+
	Tissierellia	1737404	+	−
Bacteroidota	Bacteroidia	200643	+	+
	Chitinophagia	1853228	−	−
	Cytophagia	768503	−	−
	Flavobacteriia	117743	−	−
	Saprospiria	1937959	−	−
	Sphingobacteriia	117747	−	−
Campylobacterota	Desulfurellia	3031853	−	−
	Epsilonproteobacteria	3031852	+	+
Chloroflexota	Anaerolineae	292625	−	−
	Ardenticatenia *	1382928	+	−
	Caldilineae	475962	−	−
	Chloroflexia	32061	+	−
	Dehalococcoidia	301297	+	−
	Ktedonobacteria	388447	−	−
	Tepidiformia	2682225	−	−
	Thermoflexia	1495646	+	−
Cyanobacteriota	Cyanophyceae	3028117	+	−
Deferribacterota	Deferribacteres	68337	+	−
Delta/epsilon subdivisions	Deltaproteobacteria	28221	+	−
Deinococcota	Deinococci	188787	+	+
Dyctioglomota	Dictyoglomia	203486	+	−
Fibrobacterota	Fibrobacteria	204430	−	−
Fusobacteriota	Fusobacteriia	203490	+	+
Gemmatimonadota	Gemmatimonadetes	219685	−	+
	Longimicrobiia	1804991	−	−
Ignavibacteriota	Ignavibacteria	795747	−	+
Mycoplasmatota	Mollicutes	31969	+	−
	Mycoplasmoidales	2790996	−	−
Myxococcota	Myxococcia	32015	+	+
	Polyangia	3031711	+	+
Nitrospirota	Nitrospiria	203693	+	−
	Thermodesulfovibrionia	2811502	−	−
Pseudomonadota	Acidithiobacillia	1807140	−	−
	Alphaproteobacteria	28211	+	+
	Betaproteobacteria	28216	+	+
	Gammaproteobacteria	1236	+	+
	Hydrogenophilalia	2008785	−	−
	Zetaproteobacteria	580370	−	−
Spirochaetota	Spirochaetia	203692	+	+
Synergistota	Synergistia	649775	+	−
Thermodesulfobacteriota	Desulfarculia	3031646	−	−
	Desulfobaccia	3031647	−	−
	Desulfobacteria	3024418	+	−
	Desulfobulbia	3031451	+	−
	Desulfomonilia	3031650	+	−
	Desulfovibrionia	3031449	+	−
	Desulfuromonadia	3031651	+	−
	Syntrophia	3031648	+	−
	Syntrophobacteria	3024408	+	−
	Thermodesulfobacteria	67799	+	−
Thermotogota	Thermotogae	188708	+	+
Verrucomicrobiota	Methylacidiphilae	1955630	−	−
	Opitutae	414999	+	+
	Spartobacteria	134549	−	−
	Verrucomicrobiae	203494	−	−

¹ Classes highlighted in red are not complete according to Section 3.2.1 and are divided into orders in Table 5 and Table S3, except for one *. * The class Ardenticatenia does not appear in Table 5 because the single hit obtained in the TBlastN analysis corresponds to a “candidatus” order.

Table 5. Presence (+) or absence (−) of ushA-like (U) and cpdB-like (C) genes in selected bacterial orders. The (+) background indicates: green, presence in ≤50% of the genomes analyzed; orange, presence in >50% but <100% of the genomes; red, presence in all the genomes. Full data can be found in Table S3.

Class	Order ¹	Taxid	U	C
Acidimicrobiia	Acidimicrobiales	84993	+	−
Actinomycetes	Acidothermales	1643683	−	−
	Actinomycetales	2037	−	+
	Actinopolysporales	622450	−	−
	Bifidobacteriales	85004	−	−
	Catenulisporales	414714	−	−
	Frankiales	85013	−	−
	Geodermatophilales	1643682	+	−
	Glycomycetales	85014	+	−
	Jatrophihabitantales	2805415	+	+
	Kineosporiales	622452	−	+
	Kitasatosporales	85011	+	+
	Micrococcales	85006	+	+
	Micromonosporales	85008	+	+
	Mycobacteriales	85007	+	−
	Nakamurellales	1643684	−	−
	Propionibacteriales	85009	+	+
	Pseudonocardiales	85010	+	+
	Sporichthyales	2495578	−	+
	Streptosporangiales	85012	+	+
Nitriliruptoria	Egibacterales	1747768	−	−
	Egicoccales	1755823	+	+
	Euzebyales	908621	−	−
Rubrobacteria	Rubrobacterales	84996	+	−
Thermoleophilia	Miltoncostaeales	2843198	+	−
	Solirubrobacterales	588673	−	−
	Thermoleophilales	588674	−	−
Fimbriimonaadia	Fimbriimonadales	1663425	+	−
Bacilli	Bacillales	1385	+	+
	Lactobacillales	186826	+	+
Clostridia	Eubacteriales	186802	+	+
	Halanaerobiales	53433	+	+
	Koleobacterales	2786987	−	−
	Moorellales	3039167	−	−
	Natranaerobiales	485256	−	−
	Thermoanaerobacterales	68295	+	+
	Thermosediminibacterales	2770089	+	+
Erysipelotrichia	Erysipelotrichales	526525	+	+
Negativicutes	Acidaminococcales	1843488	−	−
	Selenomonadales	909929	+	+
	Veillonellales	1843489	+	−
Tissierella	Tissierellales	1737405	+	−
Bacteroidia	Bacteroidales	171549	+	+
	Marinilabiliales	1970189	−	−
Epsilonproteobacteria	Campylobacterales	213849	+	+
	Nautiliales	235899	+	−
Dehalococcoidia	Dehalococcoidales	1202465	−	−
	Dehalogenimonas	670486	−	−
Cyanophyceae	Chroococcidiopsidales	1890505	−	−
	Gloeobacterales	307595	−	−
	Gloeomargaritales	1955042	+	−
	Nostocales	1161	+	−
	Chroococcales	1118	−	−
	Oscillatoriales	1150	+	−
	Pleurocapsales	52604	−	−
	Pseudanabaenales	2881377	−	−
	Synechococcales	1890424	−	−
	Thermostichales	2881383	−	−
Deferribacteres	Deferribacterales	191393	+	−
Deltaproteobacteria	Bradymonadales	1779134	+	−
Deinococci	Deinococcales	118964	+	+
	Thermales	68933	+	−
	Trueperales	2762275	−	−
Fusobacteriia	Fusobacteriales	203491	+	+
Gemmatimonadetes	Gemmatimonadales	219686	−	+
Ignavibacteria	Ignavibacteriales	795748	−	+
Mollicutes	Acholeplasmatales	186329	−	−
	Entomoplasmatales	186328	−	−
	Mycoplasmatales	2085	+	−
Myxococcia	Myxococcales	29	+	+
Polyangia	Haliangiales	3031714	−	+
	Nannocystales	3031713	+	+
	Polyangiales	3031712	+	+
Nitrospiria	Nitrospirales	189778	+	−
Alphaproteobacteria	Caulobacterales	204458	−	−
	Emcibacterales	2066490	−	−
	Holosporales	1921002	−	−
	Hyphomicrobiales	356	+	+
	Hyphomonadales	2800060	+	−
	Kordiimonadales	362534	−	−
	Magnetococcales	1191478	−	−
	Maricaulales	2800059	−	−
	Minwuiales	2493627	−	−
	Parvularculales	255473	−	−
	Rhodobacterales	204455	+	+
	Rhodospirillales	204441	+	+
	Rickettsiales	766	−	−
	Sneathiellales	510684	−	−
	Sphingomonadales	204457	+	−
Betaproteobacteria	Burkholderiales	80840	+	+
	Ferrovales	1442155	−	−
	Neisseriales	206351	+	+
	Nitrosomonadales	32003	+	−
	Rhodocyclales	206389	+	+
Gammaproteobacteria	Acidiferrobacterales	1692040	−	−
	Aeromonadales	135624	+	+
	Alteromonadales	135622	+	+
	Cardiobacteriales	135615	−	+
	Cellvibrionales	1706369	+	+
	Chromatiales	135613	+	+
	Enterobacterales	91347	+	+
	Immundisolibacterales	1934945	+	−
	Kangiellales	2887327	−	−
	Legionellales	118969	+	−
	Methylococcales	135618	+	−
	Moraxellales	2887326	+	+
	Nevskiales	1775403	+	−
	Oceanospirillales	135619	+	+
	Orbales	1240482	+	+
	Pasteurellales	135625	+	+
	Pseudomonadales	72274	+	−
	Thiotrichales	72273	+	+
	Vibrionales	135623	+	+
	Xanthomonadales	135614	−	+
Spirochaetia	Brachyspirales	1643686	+	−
	Brevinematales	1643687	−	−
	Leptospirales	1643688	−	−
	Spirochaetales	136	+	+
Synergistia	Synergistales	649775	+	−
Desulfobacteria	Desulfobacterales	213118	+	−
Desulfobulbia	Desulfobulbales	3024411	+	−
Desulfovibrionia	Desulfovibrionales	213115	+	−
Desulfuromonadia	Desulfuromonadales	69541	+	−
	Geobacterales	3031668	+	−
Syntrophobacteria	Syntrophobacterales	213462	+	−
Thermodesulfobacteria	Thermodesulfobacteriales	188710	+	−
Thermotogae	Kosmotogales	1643946	+	+
	Mesoaciditogales	1769716	+	+
	Petrotogales	1643947	+	+
	Thermotogales	2419	+	+
Opitutae	Opitutales	415000	+	+
	Puniceicoccales	415001	−	−

¹ Orders highlighted in red are not complete according to Section 3.2.1 and are divided into families in Table 6 and Table S4.

Table 6. Presence (+) or absence (−) of ushA-like (U) and cpdB-like (C) genes in selected bacterial families. The (+) background indicates: green, presence in ≤50% of the genomes analyzed; orange, presence in >50% but <100% of the genomes; red, presence in all the genomes. Full data can be found in Table S4.

Order	Family ¹	Taxid	U	C
Acidimicrobiales	Acidimicrobiaceae	84994	−	−
	Iamiaceae	633392	−	−
	Ilumatobacteraceae	2448023	+	−
Actinomycetales	Actinomycetaceae	2049	−	+
Geodermathophilales	Geodermatophilaceae	85030	+	−
Jatrophihabitantales	Jatrophihabitantaceae	2805416	+	+
Kineosporiales	Kineosporiaceae	83778	−	+
Kitasatosporales	Streptomycetaceae	2062	+	+
Micrococcales	Beutenbergiaceae	125316	−	−
	Bogoriellaceae	145358	+	+
	Brevibacteriaceae	85019	+	+
	Cellulomonadaceae	85016	−	−
	Demequinaceae	1042322	−	−
	Dermabacteraceae	85020	−	+
	Dermacoccaceae	145357	+	+
	Dermatophilaceae	85018	+	−
	Intrasporangiaceae	85021	+	+
	Jonesiaceae	85022	−	−
	Kytococcaceae	2805426	+	−
	Microbacteriaceae	85023	+	+
	Micrococcaceae	1268	+	+
	Ornithinimicrobiaceae	2805590	+	−
	Promicromonosporaceae	85017	+	−
	Ruaniaceae	1331736	+	+
	Sanguibacteraceae	145360	+	−
	Tropherymataceae	2805591	−	−
Micromonosporales	Micromonosporaceae	28056	+	+
Mycobacteriales	Corynebacteriaceae	1653	+	−
	Dietziaceae	85029	−	−
	Gordoniaceae	85026	−	−
	Hoyosellaceae	3040680	−	−
	Lawsonellaceae	2805586	−	−
	Mycobacteriaceae	1762	−	−
	Nocardiaceae	85025	+	−
	Segniliparaceae	316606	−	−
	Tsukamurellaceae	85028	+	−
Propionibacteriales	Kribbellaceae	2726069	+	+
	Nocardioidaceae	85015	+	+
	Propionibacteriaceae	31957	−	+
Pseudonocardiales	Pseudonocardiaceae	2070	+	+
Streptosporangiales	Nocardiopsaceae	83676	−	−
	Streptosporangiaceae	2004	+	+
	Thermomonosporaceae	2012	+	+
Rubrobacterales	Baekduiaceae	2600303	+	−
	Rubrobacteraceae	84997	+	−
Miltoncostaeales	Miltoncostaeaceae	2843199	+	−
Fimbriimonadales	Fimbriimonadaceae	1663426	−	−
Bacillales	Alicyclobacillaceae	186823	+	+
	Bacillaceae	186817	+	+
	Listeriaceae	186820	+	−
	Paenibacillaceae	186822	+	+
	Planococcaceae	186818	+	+
	Sporolactobacillaceae	186821	+	+
	Staphylococcaceae	90964	+	+
	Thermoactinomycetaceae	186824	+	+
Lactobacillales	Aerococcaceae	186827	+	+
	Carnobacteriaceae	186828	+	+
	Enterococcaceae	81852	+	+
	Lactobacillaceae	33958	+	+
	Streptococcaceae	1300	+	+
Eubacteriales	Aristaeellaceae	3046368	−	−
	Cellulosilyticaceae	3018741	−	−
	Christensenellaceae	990719	−	−
	Clostridiaceae	31979	+	+
	Desulfallaceae	2867375	−	−
	Desulfitobacteriaceae	2937909	−	+
	Desulfotomaculaceae	2937910	−	−
	Eubacteriaceae	186806	+	−
	Heliobacteriaceae	31984	−	−
	Lachnospiraceae	186803	+	+
	Maliibacteriaceae	3047432	−	−
	Oscillospiraceae	216572	+	+
	Peptococcaceae	186807	−	−
	Peptostreptococcaceae	186804	+	−
	Proteinivoraceae	1491775	−	−
	Symbiobacteriaceae	543349	−	−
	Syntrophomonadaceae	68298	−	−
	Thermincolaceae	2937911	−	−
	Vallitaleaceae	2603322	+	+
Halanaerobiales	Halanaerobiaceae	972	+	+
	Halarsenatibacteraceae	3046411	−	−
	Halobacteroidaceae	53434	+	+
	Halothermotrichaceae	3046412	−	−
Thermoanaerobacterales	Thermoanaerobacteraceae	186814	+	+
	Thermodesulfobiaceae	227387	−	−
Thermosediminibacterales	Tepidanaerobacteraceae	2770092	−	−
	Thermosediminibacteraceae	2770093	+	+
Erysipelotrichales	Coprobacillaceae	2810280	−	−
	Erysipelotrichaceae	128827	+	+
	Turicibacteraceae	2810281	+	−
Selenomonadales	Selenomonadaceae	1843491	+	+
	Sporomusaceae	1843490	+	+
Veillonellales	Veillonellaceae	31977	+	−
Tissierellales	Acidilutibacteraceae	2992717	−	−
	Gottschalkiaceae	2042895	+	−
	Peptoniphilaceae	1570339	−	−
	Tepidimicrobiaceae	2992719	+	−
	Thermohalobacteraceae	2848916	+	−
	Tissierellaceae	1737406	+	+
Bacteroidales	Bacteroidaceae	815	−	+
	Barnesiellaceae	2005519	+	+
	Dysgonomonadaceae	2005520	−	−
	Muribaculaceae	2005473	−	+
	Odoribacteraceae	1853231	+	−
	Paludibacteraceae	2005523	−	−
	Porphyromonadaceae	171551	−	+
	Prevotellaceae	171552	−	+
	Rikenellaceae	171550	−	−
	Salinivirgaceae	1970190	−	−
	Tannerellaceae	2005525	−	+
	Tenuifilaceae	2760872	−	−
Campylobacterales	Arcobacteraceae	2808963	+	−
	Campylobacteraceae	72294	+	−
	Helicobacteraceae	72293	−	+
	Hydrogenimonadaceae	292630	−	−
	Sulfurimonadaceae	2771471	−	−
	Sulfurospirillaceae	2932623	−	−
	Sulfurovaceae	2771472	−	−
Nautiliales	Nautiliaceae	224467	+	−
	Nitratiruptoraceae	2795691	−	−
Nostocales	Aphanizomenonaceae	1892259	−	−
	Calotrichaceae	2661849	+	−
	Hapalosiphonaceae	1892263	−	−
	Nostocaceae	1162	−	−
	Rivulariaceae	1185	−	−
	Tolypothrichaceae	119859	−	−
Oscillatoriales	Coleofasciculaceae	1892251	−	−
	Gomontiellaceae	1892255	−	−
	Microcoleaceae	1892252	+	−
	Oscillatoriaceae	1892254	−	−
Deferribacterales	Calditerrivibrionaceae	2945021	−	−
	Deferribacteraceae	191394	−	−
	Flexistipitaceae	2945022	−	−
	Geovibrionaceae	2945019	+	−
	Mucispirillaceae	2945020	−	−
Deinococcales	Deinococcaceae	183710	+	+
Thermales	Thermaceae	188786	+	−
Fusobacteriales	Fusobacteriaceae	203492	+	−
	Leptotrichiaceae	1129771	+	+
Gemmatimonadales	Gemmatimonadaceae	219687	−	+
Ignavibacteriales	Ignavibacteriaceae	795749	−	+
	Melioribacteraceae	1334117	−	−
Mycoplasmatales	Mycoplasmataceae	2092	+	−
Myxococcales	Anaeromyxobacteraceae	1524215	−	−
	Archangiaceae	39	+	+
	Myxococcaceae	31	+	+
	Vulgatibacteraceae	1524213	−	+
Polyangiales	Labilitrichaceae	1524216	−	−
	Polyangiaceae	49	+	+
	Sandaracinaceae	1055686	−	−
Nitrospirales	Nitrospiraceae	189779	+	−
Hyphomicrobiales	Amorphaceae	2685818	−	−
	Aurantimonadaceae	255475	+	+
	Bartonellaceae	772	−	−
	Beijerinckiaceae	45404	−	−
	Blastochloridaceae	2831090	−	−
	Boseaceae	2831100	−	+
	Breoghaniaceae	2831104	+	+
	Brucellaceae	118882	+	−
	Chelatococcaceae	2036754	−	−
	Devosiaceae	2831106	+	+
	Hyphomicrobiaceae	45401	−	−
	Kaistiaceae	2831111	−	−
	Lichenihabitantaceae	2723775	−	−
	Methylobacteriaceae	119045	+	+
	Methylocystaceae	31993	−	−
	Nitrobacteraceae	41294	+	−
	Parvibaculaceae	2813035	−	−
	Phreatobacteraceae	2843305	−	−
	Phyllobacteriaceae	69277	+	+
	Pleomorphomonadaceae	2843308	+	−
	Rhizobiaceae	82115	+	+
	Stappiaceae	2821832	+	+
	Xanthobacteraceae	335928	−	−
Hyphomonadales	Hyphomonadaceae	69657	+	−
Rhodobacterales	Paracoccaceae	31989	+	+
	Roseobacteraceae	2854170	+	+
Rhodospirillales	Acetobacteraceae	433	+	+
	Azospirillaceae	2829815	+	+
	Elioraeaceae	2690195	+	−
	Geminicoccaceae	2066434	−	−
	Kiloniellaceae	597359	+	+
	Rhodospirillaceae	41295	−	−
	Stellaceae	2844601	−	−
	Terasakiellaceae	2813951	−	−
	Thalassobaculaceae	2844864	−	−
	Thalassospiraceae	2844866	+	+
Sphingomonadales	Erythrobacteraceae	335929	+	−
	Sphingomonadaceae	41297	+	−
	Sphingosinicellaceae	2820280	+	−
	Zymomonadaceae	2844881	−	−
Burkholderiales	Alcaligenaceae	506	+	+
	Burkholderiaceae	119060	+	+
	Comamonadaceae	80864	+	+
	Oxalobacteraceae	75682	+	+
	Sphaerotilaceae	2975441	+	+
	Sutterellaceae	995019	+	−
Neisseriales	Chromobacteriaceae	1499392	+	+
	Neisseriaceae	481	+	+
Nitrosomonadales	Gallionellaceae	90627	−	−
	Methylophilaceae	32011	−	−
	Nitrosomonadaceae	206379	−	−
	Sterolibacteriaceae	2008793	−	−
	Sulfuricellaceae	2772226	−	−
	Thiobacillaceae	2008790	+	−
	Usitatibacteraceae	2803844	+	−
Rhodocyclales	Azonexaceae	2008795	+	−
	Fluviibacteraceae	2808923	−	−
	Rhodocyclaceae	75787	+	+
	Zoogloeaceae	2008794	+	−
Aeromonadales	Aeromonadaceae	84642	+	+
	Succinivibrionaceae	83763	−	−
Alteromonadales	Alteromonadaceae	72275	+	+
	Colwelliaceae	267889	+	−
	Ferrimonadaceae	267892	+	+
	Idiomarinaceae	267893	+	+
	Moritellaceae	267891	+	+
	Pseudoalteromonadaceae	267888	+	+
	Psychromonadaceae	267894	+	+
	Shewanellaceae	267890	+	+
Cardiobacteriales	Cardiobacteriaceae	868	−	−
	Ignatzschineriaceae	3018589	−	+
Cellvibrionales	Cellvibrionaceae	1706371	+	+
	Halieaceae	1706372	−	−
	Microbulbiferaceae	1706373	+	+
	Porticoccaceae	1706374	−	−
	Spongiibacteraceae	1706375	+	−
Chromatiales	Chromatiaceae	1046	+	−
	Ectothiorhodospiraceae	72276	+	−
	Granulosicoccaceae	449719	+	+
	Halothiobacillaceae	255526	−	−
	Thioalkalibacteraceae	2035710	−	−
	Thioalkalispiraceae	1096778	−	−
	Wenzhouxiangellaceae	1676141	−	−
	Woeseiaceae	1738654	−	−
Enterobacterales	Bruguierivoracaceae	2812006	−	−
	Budviciaceae	1903416	−	+
	Enterobacteriaceae	543	+	+
	Erwiniaceae	1903409	+	+
	Hafniaceae	1903412	+	+
	Morganellaceae	1903414	+	+
	Pectobacteriaceae	1903410	+	+
	Yersiniaceae	1903411	+	+
Legionellales	Coxiellaceae	118968	−	−
	Legionellaceae	444	+	−
Methylococcales	Methylococcaceae	403	+	−
	Methylothermaceae	1486721	−	−
Moraxellales	Moraxellaceae	468	+	+
Nevskiales	Nevskiaceae	568386	+	–
	Steroidobacteraceae	2689614	–	–
Oceanospirillales	Alcanivoracaceae	224372	+	+
	Endozoicomonadaceae	2066474	+	+
	Hahellaceae	224379	+	−
	Halomonadaceae	28256	+	+
	Litorivicinaceae	449732	−	−
	Oceanospirillaceae	135620	+	+
	Oleiphilaceae	191033	+	+
	Saccharospirillaceae	255527	+	+
	Zooshikellaceae	2898533	+	−
Orbales	Orbaceae	1240483	+	+
Pasteurellales	Pasteurellaceae	712	+	+
Pseudomonadales	Marinobacteraceae	2887365	−	−
	Pseudomonadaceae	135621	+	−
Thiotrichales	Fastidiosibacteraceae	2056687	−	−
	Francisellaceae	34064	−	−
	Piscirickettsiaceae	135616	+	−
	Thiotrichaceae	135617	+	+
Vibrionales	Vibrionaceae	641	+	+
Xanthomonadales	Rhodanobacteraceae	1775411	−	+
	Xanthomonadaceae	32033	−	+
Brachyspirales	Brachyspiraceae	143786	+	−
Spirochaetales	Borreliaceae	1643685	−	−
	Breznakiellaceae	2951104	+	+
	Sphaerochaetaceae	2791015	+	+
	Spirochaetaceae	137	+	+
	Treponemataceae	2845253	+	+
Synergistales	Acetomicrobiaceae	3029086	−	−
	Aminithiophilaceae	3029085	+	−
	Aminobacteriaceae	3029087	−	−
	Dethiosulfovibrionaceae	3029088	−	−
	Synergistaceae	649777	+	−
	Thermovirgaceae	3029089	−	−
Desulfobacterales	Desulfatibacillaceae	3031627	+	−
	Desulfobacteraceae	213119	+	−
	Desulfococcaceae	2931039	−	−
	Desulfolunaceae	3031622	−	−
	Desulfosarcinaceae	3031624	+	−
	Desulfosudaceae	2904715	−	−
Desulfobulbales	Desulfobulbaceae	213121	+	−
	Desulfocapsaceae	2886822	+	−
Desulfovibrionales	Desulfohalobiaceae	213117	−	−
	Desulfomicrobiaceae	213116	+	−
	Desulfovibrionaceae	194924	+	−
Desulfuromonadales	Desulfuromonadaceae	213421	+	−
	Geoalkalibacteraceae	3031665	−	−
	Syntrophotaleaceae	2812024	−	−
Geobacterales	Geobacteraceae	213422	+	−
Syntrophobacteriales	Syntrophobacteraceae	213465	+	−
Thermodesulfobacteriales	Thermodesulfatatoraceae	3031464	+	−
	Thermodesulfobacteriaceae	188711	−	−
Petrotogales	Petrotogaceae	1643949	+	+
Thermotogales	Fervidobacteriaceae	1643950	+	+
	Thermotogaceae	188709	+	−
Opitutales	Opitutaceae	134623	+	+

¹ Families highlighted in red are not complete according to Section 3.2.1 and are divided into genera in Table 7 and Table S5.

Table 7. Presence (+) or absence (−) of ushA-like (U) and cpdB-like (C) genes in selected bacterial genera. The (+) background indicates: green, presence in ≤50% of the genomes analyzed; orange, presence in >50% but <100% of the genomes; red, presence in all the genomes. Full data can be found in Table S5.

Family	Genus ¹	Taxid	U	C
Actinomycetaceae	Flaviflexus	1522056	−	+
Geodermatophilaceae	Blastococcus	38501	+	−
	Geodermatophilus	1860	+	−
	Modestobacter	88138	+	−
Jatrophihabitantaceae	Jatrophihabitans	1434010	+	+
Kineosporiaceae	Kineococcus	33981	−	+
Streptomycetaceae	Kitasatospora	2063	+	+
	Peterkaempfera	2995704	+	+
	Streptantibioticus	2995706	−	+
	Streptomyces	1883	+	+
Bogoriellaceae	Georgenia	154116	+	+
Brevibacteriaceae	Brevibacterium	1696	+	+
Dermabacteraceae	Dermabacter	36739	−	+
Dermacoccaceae	Luteipulveratus	745364	+	+
Dermatophilaceae	Austwickia	1184606	+	−
	Dermatophilus	1862	+	−
Intrasporangiaceae	Arsenicicoccus	267408	+	−
	Intrasporangium	53357	+	+
	Janibacter	53457	+	−
	Phycicoccus	367298	+	+
	Tetrasphaera	99479	−	+
Microbacteriaceae	Clavibacter	1573	+	−
	Microbacterium	33882	+	+
	Protaetiibacter	2680004	+	−
	Rathayibacter	33886	−	+
Micrococcaceae	Arthrobacter	1663	+	+
Ornithinimicrobiaceae	Ornithinimicrobium	125287	+	−
	Serinicoccus	265976	+	−
Promicromonosporaceae	Isoptericola	254250	+	−
Ruaniaceae	Occultella	2828348	+	+
	Ruania	626119	+	−
Sanguibacteraceae	Sanguibacter	60919	+	−
Micromonosporaceae	Actinocatenispora	390988	−	+
	Actinoplanes	1865	+	+
	Dactylosporangium	35753	+	+
	Micromonospora	1873	+	+
	Phytohabitans	907364	+	−
	Salinispora	168694	+	−
Corynebacteriaceae	Corynebacterium	1716	+	+
Nocardiaceae	Nocardia	1817	+	−
	Rhodococcus	1827	+	−
Tsukamurellaceae	Tsukamurella	2060	+	−
Nocardioidaceae	Nocardioides	1839	+	+
Propionibacteriaceae	Cutibacterium	1912216	−	+
Pseudonocardiaceae	Actinosynnema	40566	+	−
	Amycolatopsis	1813	+	−
	Kibdelosporangium	2029	+	−
	Kutzneria	43356	+	+
	Lentzea	165301	+	+
	Pseudonocardia	1847	+	−
	Saccharopolyspora	1835	+	−
	Saccharothrix	2071	+	+
Streptosporangiaceae	Nonomuraea	83681	+	+
	Streptosporangium	2000	+	+
	Thermobispora	147067	+	−
Thermomonosporaceae	Actinomadura	1988	+	+
Baekduiaceae	Baekduia	2600304	+	−
Rubrobacteraceae	Rubrobacter	42255	+	−
Miltoncostaeaceae	Miltoncostaea	2843200	+	−
Alicyclobacillaceae	Alicyclobacillus	29330	+	+
	Effusibacillus	1502725	+	−
	Tumebacillus	432330	+	−
Bacillaceae	Alkalihalobacillus	2675234	+	+
	Allobacillus	1400133	+	+
	Amphibacillus	29331	+	−
	Anaerobacillus	704093	+	−
	Anoxybacillus	150247	+	+
	Bacillus	1386	+	+
	Cytobacillus	2675230	+	+
	Evansella	2837485	+	+
	Fervidibacillus	3033930	+	−
	Geobacillus	129337	+	+
	Gracilibacillus	74385	+	+
	Halalkalibacter	2893056	+	−
	Halobacillus	45667	+	+
	Heyndrickxia	2837504	+	+
	Lederbergia	2804231	+	−
	Lentibacillus	175304	+	+
	Lysinibacillus	400634	+	+
	Mangrovibacillus	2920444	+	+
	Metabacillus	2675233	+	+
	Oceanobacillus	182709	+	+
	Paenalkalicoccus	2944627	+	+
	Parageobacillus	1906945	+	−
	Paraliobacillus	200903	+	+
	Peribacillus	2675229	+	+
	Priestia	2800373	+	+
	Psychrobacillus	1221880	+	+
	Radiobacillus	2785518	+	+
	Salicibibacter	2685905	+	+
	Salimicrobium	351195	+	−
	Salisediminibacterium	1434042	+	+
	Sediminibacillus	482460	+	+
	Sutcliffiella	2837511	+	+
	Virgibacillus	84406	+	+
	Weizmannia	2817139	+	+
Paenibacillaceae	Aneurinibacillus	55079	+	−
	Brevibacillus	55080	+	+
	Cohnella	329857	+	+
	Paenibacillus	44249	+	+
	Saccharibacillus	456492	+	+
	Thermobacillus	76632	+	−
Planococcaceae	Jeotgalibacillus	157226	+	−
	Paenisporosarcina	651660	+	+
	Planococcus	1372	+	+
	Sporosarcina	1569	+	+
Sporolactobacillaceae	Pullulanibacillus	475230	+	−
	Sporolactobacillus	2077	+	+
Staphylococcaceae	Macrococcus	69965	+	+
	Mammaliicoccus	2803850	+	+
	Nosocomiicoccus	489909	+	−
	Staphylococcus	1279	+	+
Thermoactinomycetaceae	Kroppenstedtia	1274351	+	+
	Polycladomyces	1348505	+	+
	Novibacillus	1677050	+	−
	Staphylospora	2689589	+	−
Lactobacillaceae	Acetilactobacillus	2767874	+	+
	Amylolactobacillus	2767876	+	+
	Apilactobacillus	2767877	+	+
	Bombilactobacillus	2767878	+	+
	Companilactobacillus	2767879	+	−
	Fructilactobacillus	2767881	+	+
	Fructobacillus	559173	+	+
	Lacticaseibacillus	2759736	+	+
	Lactiplantibacillus	2767842	+	+
	Lactobacillus	1578	+	+
	Latilactobacillus	2767885	+	−
	Lentilactobacillus	2767893	+	+
	Leuconostoc	1243	+	+
	Levilactobacillus	2767886	+	+
	Limosilactobacillus	2742598	+	−
	Loigolactobacillus	2767889	+	+
	Nicoliella	2978367	+	+
	Oenococcus	46254	+	+
	Paucilactobacillus	2767890	+	−
	Pediococcus	1253	−	+
	Periweissella	2930384	+	+
	Weissella	46255	+	+
Streptococcaceae	Lactococcus	1357	+	+
	Streptococcus	1301	+	+
Enterococcaceae	Enterococcus	1350	+	+
	Tetragenococcus	51668	+	−
	Vagococcus	2737	+	+
Carnobacteriaceae	Carnobacterium	2747	+	+
	Granulicatella	117563	+	+
	Jeotgalibaca	1470540	+	−
Aerococcaceae	Aerococcus	1375	+	+
	Suicoccus	2689587	+	−
Clostridiaceae	Alkaliphilus	114627	+	+
	Clostridium	1485	+	+
	Crassaminicella	1848399	+	−
	Geosporobacter	390805	+	−
	Hathewaya	1769729	+	−
	Paraclostridium	1849822	+	+
Desulfitobacteriaceae	Desulfosporosinus	79206	−	+
Eubacteriaceae	Eubacterium	1730	+	−
Lachnospiraceae	Anaerocolumna	1843210	+	−
	Anaeromicropila	3024823	−	+
	Anaeropeptidivorans	2997360	+	−
	Herbinix	1663717	−	+
	Lachnoclostridium	1506553	−	+
	Tyzzerella	1506577	−	+
Oscillospiraceae	Anaerotruncus	244127	+	+
	Flavonifractor	946234	+	+
	Ruminiclostridium	1508657	+	−
	Vescimonas	2892396	−	+
Peptostreptococcaceae	Acetoanaerobium	186831	+	−
	Clostridioides	1870884	+	−
Vallitaleaceae	Petrocella	2603323	+	+
	Vallitalea	1348611	+	+
Halanaerobiaceae	Halanaerobium	2330	+	+
	Halocella	46466	+	+
	Iocasia	2899804	+	+
Halobacteroidaceae	Halobacteroides	42417	+	+
Thermoanaerobacteraceae	Aceticella	3051499	+	−
	Caldanaerobacter	249529	−	+
	Carboxydothermus	129957	+	+
	Thermoanaerobacter	1754	+	+
	Thermoanaerobacterium	28895	−	+
Erysipelotrichaceae	Erysipelothrix	1647	+	+
Turicibacteraceae	Turicibacter	191303	+	−
Selenomonadaceae	Selenomonas	970	+	+
Sporomusaceae	Methylomusa	2093783	+	+
	Pelosinus	365348	+	−
Veillonellaceae	Megasphaera	906	+	−
Tissierellaceae	Gudongella	2692382	+	−
	Tissierella	41273	+	+
Bacteroidaceae	Bacteroides	816	−	+
	Phocaeicola	909656	−	+
Barnesiellaceae	Barnesiella	397864	+	−
	Coprobacter	1348911	−	+
Muribaculaceae	Duncaniella	2518495	−	+
	Muribaculum	1918540	−	+
	Sodaliphilus	2815786	−	+
Odoribacteraceae	Odoribacter	283168	+	−
Porphyromonadaceae	Porphyromonas	836	−	+
Prevotellaceae	Prevotella	838	−	+
	Pseudoprevotella	2884814	−	+
Tannerellaceae	Parabacteroides	375288	−	+
Arcobacteraceae	Arcobacter	28196	+	−
	Malaciobacter	2321114	+	−
Campylobacteraceae	Campylobacter	194	+	−
Helicobacteraceae	Helicobacter	209	−	+
Nautiliaceae	Caminibacter	191301	+	−
Calotrichaceae	Calothrix	1186	+	−
Microcoleaceae	Planktothrix	54304	+	−
Deinococcaceae	Deinococcus	1298	+	+
Thermaceae	Allomeiothermus	2935559	+	−
	Meiothermus	2747271	+	−
	Oceanithermus	208447	+	−
	Thermus	270	+	−
Fusobacteriaceae	Fusobacterium	848	+	−
Leptotrichiaceae	Leptotrichia	32067	+	+
	Pseudoleptotrichia	2755140	+	−
	Sebaldella	32068	+	+
	Streptobacillus	34104	+	−
Gemmatimonadaceae	Gemmatimonas	173479	−	+
Mycoplasmataceae	Mycoplasmopsis	2767358	+	−
Archangiaceae	Archangium	47	+	+
	Cystobacter	42	+	+
	Melittangium	44	+	+
	Stigmatella	40	+	+
Myxococcaceae	Corallococcus	83461	+	+
	Myxococcus	32	+	+
Polyangiaceae	Chondromyces	50	+	−
	Polyangium	55	+	+
	Sorangium	39643	+	+
Nitrospiraceae	Nitrospira	1234	+	−
Aurantimonadaceae	Aurantimonas	182269	+	−
	Aureimonas	414371	+	+
	Jiella	1775688	+	−
	Martelella	293088	+	+
Boseaceae	Bosea	85413	−	+
Brucellaceae	Pseudochrobactrum	354349	+	−
Devosiaceae	Devosia	46913	+	+
	Paradevosia	1573407	+	+
	Pelagibacterium	1082930	+	+
	Youhaiella	1827478	+	+
Methylobacteriaceae	Microvirga	186650	+	+
Nitrobacteraceae	Bradyrhizobium	374	+	−
	Rhodopseudomonas	1073	+	−
Phyllobacteriaceae	Aquibium	2911176	+	+
	Mesorhizobium	68287	+	+
	Nitratireductor	245876	+	+
	Oricola	1594166	+	+
	Phyllobacterium	28100	+	+
	Roseitalea	1915401	+	−
	Salaquimonas	2712688	+	−
Rhizobiaceae	Agrobacterium	357	+	+
	Allorhizobium	78526	+	+
	Ciceribacter	1648508	+	+
	Ensifer	106591	+	+
	Georhizobium	2661800	+	+
	Neorhizobium	1525371	+	+
	Peteryoungia	2853332	+	+
	Pseudorhizobium	1903858	+	+
	Rhizobium	379	+	+
	Shinella	323620	+	+
	Sinorhizobium	28105	+	+
Stappiaceae	Labrenzia	478070	+	+
	Pannonibacter	227873	+	+
	Roseibium	150830	+	+
	Stappia	152161	+	−
Paracoccaceae	Algicella	3050722	+	+
	Cereibacter	1653176	+	+
	Frigidibacter	1775705	+	+
	Gemmobacter	204456	+	+
	Gymnodinialimonas	2937410	+	+
	Neotabrizicola	2946607	−	+
	Pacificitalea	2846749	+	+
	Paracoccus	265	+	+
	Parasedimentitalea	2738399	+	+
	Paroceanicella	2683599	+	+
	Pelagovum	2795377	+	+
	Polymorphum	991903	+	−
	Pontivivens	1844015	+	+
	Profundibacter	2778525	−	+
	Pseudooceanicola	1679449	+	+
	Pseudopuniceibacterium	2613960	+	+
	Pseudorhodobacter	238783	−	+
	Pukyongiella	2831925	+	+
	Qingshengfaniella	2816884	+	+
	Rhodobaca	119541	+	+
	Rhodovulum	34008	+	+
	Roseicitreum	1209946	+	+
	Silicimonas	1955420	+	+
	Tabrizicola	1443919	+	+
	Thioclava	285107	−	+
Roseobacteraceae	Celeribacter	875170	+	+
	Dinoroseobacter	309512	+	+
	Falsihalocynthiibacter	2854182	+	+
	Leisingera	191028	+	+
	Octadecabacter	53945	+	+
	Phaeobacter	302485	+	+
	Roseibacterium	159345	+	+
	Roseobacter	2433	+	+
	Roseovarius	74030	+	+
	Ruegeria	97050	+	+
	Salipiger	263377	+	+
	Sulfitobacter	60136	+	+
Acetobacteraceae	Acetobacter	434	−	+
	Lichenicola	2804525	−	+
	Roseomonas	125216	+	+
Azospirillaceae	Skermanella	204447	+	+
Thalassospiraceae	Thalassospira	168934	+	+
Erythrobacteraceae	Altererythrobacter	361177	+	−
	Aurantiacibacter	2800681	+	−
	Croceicoccus	1295327	+	−
	Pelagerythrobacter	2800685	+	−
	Qipengyuania	1855416	+	−
	Tsuneonella	2800686	+	−
Sphingomonadaceae	Novosphingobium	165696	+	−
	Sphingomonas	13687	+	−
Sphingosinicellaceae	Sphingosinicella	335405	+	−
Alcaligenaceae	Achromobacter	222	+	+
	Bordetella	517	+	+
Burkholderiaceae	Burkholderia	32008	−	+
	Chitinimonas	240411	+	−
	Cupriavidus	106589	+	+
	Ephemeroptericola	2680021	+	−
	Paraburkholderia	1822464	−	+
	Ralstonia	48736	+	+
Comamonadaceae	Acidovorax	12916	+	+
	Comamonas	283	+	+
	Delftia	80865	+	+
	Diaphorobacter	238749	+	+
	Ottowia	219181	+	+
	Paenacidovorax	3051138	+	+
	Paracidovorax	3051137	+	+
	Rhodoferax	28065	+	+
Oxalobacteraceae	Collimonas	202907	+	+
	Duganella	75654	+	+
	Janthinobacterium	29580	+	+
	Massilia	149698	+	+
	Pseudoduganella	1522432	+	+
	Telluria	34069	+	+
	Undibacterium	401469	+	+
Sphaerotilaceae	Caldimonas	196013	+	−
	Ideonella	36862	+	−
	Inhella	644355	+	+
Sutterellaceae	Sutterella	40544	+	−
Chromobacteriaceae	Chitinibacter	230666	+	−
	Chromobacterium	535	+	+
	Deefgea	400947	+	−
	Iodobacter	32014	+	+
	Paludibacterium	400060	+	+
Neisseriaceae	Alysiella	194195	+	+
	Chitinolyticbacter	1055692	+	−
	Conchiformibius	334107	+	−
	Kingella	32257	+	+
	Neisseria	482	+	−
	Simonsiella	71	−	+
	Wielerella	2944815	−	+
Thiobacillaceae	Thiobacillus	919	+	−
Azonexaceae	Dechloromonas	73029	+	−
	Ferribacterium	88875	+	−
Rhodocyclaceae	Niveibacterium	1769726	+	+
Zoogloeaceae	Azoarcus	12960	+	−
	Nitrogeniibacter	2891294	+	−
Aeromonadaceae	Aeromonas	642	+	+
Alteromonadaceae	Agarivorans	261825	+	+
	Hydrocarboniclastica	2650549	+	−
	Saliniradius	2661818	+	−
Colwelliaceae	Litorilituus	1407056	+	−
Ferrimonadaceae	Ferrimonas	44011	+	+
Idiomarinaceae	Idiomarina	135575	+	+
Pseudoalteromonadaceae	Pseudoalteromonas	53246	+	+
	Psychrosphaera	907197	−	+
Psychromonadaceae	Psychromonas	67572	+	+
Shewanellaceae	Parashewanella	2547964	+	+
	Shewanella	22	+	+
Cellvibrionaceae	Marinagarivorans	1792291	−	+
	Saccharophagus	316625	−	+
	Teredinibacter	2425	+	+
Microbulbiferaceae	Microbulbifer	48073	+	+
Spongiibacteraceae	Spongiibacter	630749	+	−
Chromatiaceae	Allochromatium	85072	+	−
	Caldichromatium	2828366	+	−
	Marichromatium	85076	+	−
	Thermochromatium	85073	+	−
	Thiocapsa	1056	+	−
	Thiocystis	13724	+	−
Ectothiorhodospiraceae	Thioalkalivibrio	106633	+	−
Granulosicoccaceae	Granulosicoccus	437504	+	+
Budviciaceae	Pragia	82984	−	+
Enterobacteriaceae	Atlantibacter	1903434	+	+
	Cedecea	158483	+	+
	Citrobacter	544	+	+
	Cronobacter	413496	+	+
	Enterobacter	547	+	+
	Escherichia	561	+	+
	Jejubacter	2815296	+	+
	Klebsiella	570	+	+
	Kluyvera	579	+	+
	Kosakonia	1330547	+	+
	Leclercia	83654	+	+
	Lelliottia	1330545	+	+
	Plesiomonas	702	+	+
	Pseudocitrobacter	1504576	+	+
	Raoultella	160674	+	+
	Salmonella	590	+	+
	Scandinavium	2726810	+	+
	Shigella	620	+	+
	Shimwellia	1335483	+	−
	Symbiopectobacterium	801	+	+
Erwiniaceae	Erwinia	551	+	+
	Mixta	2100764	+	+
	Pantoea	53335	+	+
Hafniaceae	Edwardsiella	635	+	−
	Hafnia	568	+	+
	Obesumbacterium	82982	+	+
Morganellaceae	Arsenophonus	637	+	−
	Morganella	581	+	+
	Photorhabdus	29487	+	+
	Proteus	583	+	+
	Providencia	586	+	+
	Xenorhabdus	626	+	+
Pectobacteriaceae	Brenneria	71655	+	+
	Dickeya	204037	+	+
Pectobacteriaceae	Pectobacterium	122277	+	+
Yersiniaceae	Chania	1745211	+	+
	Gibbsiella	929812	+	−
	Rouxiella	1565532	−	+
	Serratia	613	+	+
	Yersinia	629	+	+
Legionellaceae	Legionella	445	+	−
Methylococcaceae	Methylocaldum	73778	+	−
	Methylococcus	413	+	−
	Methylomagnum	1760987	+	−
	Methylomonas	416	+	−
Moraxellaceae	Acinetobacter	469	+	+
	Aquirhabdus	2824158	−	+
	Moraxella	475	−	+
Nevskiaceae	Solimonas	413435	+	–
Alcanivoracaceae	Alcanivorax	59753	+	+
	Alloalcanivorax	3020832	+	+
Endozoicomonadaceae	Endozoicomonas	305899	+	+
Halomonadaceae	Cobetia	204286	+	+
	Zymobacter	33073	+	−
Oceanospirillaceae	Aliamphritea	3018276	+	−
	Marinomonas	28253	+	+
	Neptunomonas	75687	+	−
	Thalassolituus	187492	+	+
Saccharospirillaceae	Gynuella	1445504	+	+
	Reinekea	230494	+	−
	Saccharospirillum	231683	+	+
Orbaceae	Frischella	1335631	−	+
	Gilliamella	1193503	+	+
	Zophobihabitans	2894762	+	−
Pasteurellaceae	Actinobacillus	713	+	+
	Aggregatibacter	416916	+	+
	Avibacterium	292486	+	+
	Basfia	697331	+	+
	Bisgaardia	109471	+	+
	Frederiksenia	1649317	+	+
	Haemophilus	724	+	+
	Mannheimia	75984	+	+
	Otariodibacter	1249016	+	+
	Pasteurella	745	+	+
	Rodentibacter	1960084	+	+
Pseudomonadaceae	Pseudomonas	286	+	−
	Stutzerimonas	2901164	+	−
Piscirickettsiaceae	Thiomicrorhabdus	2039723	+	−
Thiotrichaceae	Beggiatoa	1021	+	−
	Thiothrix	1030	+	+
Vibrionaceae	Aliivibrio	511678	+	+
	Paraphotobacterium	2042066	+	−
	Photobacterium	657	+	+
	Salinivibrio	51366	+	+
	Thaumasiovibrio	2014233	+	−
	Vibrio	662	+	+
Rhodanobacteraceae	Aerosticca	2707020	−	+
	Dokdonella	323413	−	+
	Dyella	231454	−	+
	Frateuria	70411	−	+
	Luteibacter	242605	−	+
	Rhodanobacter	75309	−	+
Xanthomonadaceae	Pseudolysobacter	2709666	−	+
Brachyspiraceae	Brachyspira	29521	+	−
Breznakiellaceae	Breznakiella	2845254	+	+
	Gracilinema	2951106	+	+
	Leadbettera	2951107	+	−
Sphaerochaetaceae	Sphaerochaeta	399320	+	+
Spirochaetaceae	Entomospira	2834378	+	+
	Sediminispirochaeta	1911556	+	−
	Thiospirochaeta	2792240	+	+
Treponemataceae	Brucepastera	2967962	+	−
	Treponema	157	+	+
Synergistaceae	Thermanaerovibrio	81461	+	−
Desulfobacteraceae	Desulforapulum	2904687	+	−
Desulfosarcinaceae	Desulfosarcina	2299	+	−
Desulfobulbaceae	Desulfobulbus	893	+	−
Desulfocapsaceae	Desulfosediminicola	2886823	+	−
Desulfomicrobiaceae	Desulfomicrobium	898	+	−
Desulfovibrionaceae	Desulfovibrio	872	+	−
	Pseudodesulfovibrio	2035811	+	−
	Salidesulfovibrio	2950010	+	−
	Solidesulfovibrio	2910984	+	−
Desulfuromonadaceae	Pelobacter	18	+	−
Geobacteraceae	Trichlorobacter	115782	+	−
Syntrophobacteraceae	Syntrophobacter	29526	+	−
Petrotogaceae	Defluviitoga	1511648	+	+
	Marinitoga	160798	+	+
	Oceanotoga	1255275	+	+
	Petrotoga	28236	+	+
	Tepiditoga	2778400	+	+
Fervidobacteriaceae	Fervidobacterium	2422	+	+
	Thermosipho	2420	+	+
Opitutaceae	Horticoccus	2986286	−	+
	Opitutus	178440	−	+

¹ Genera highlighted in red are not complete according to Section 3.2.1.

Table 8. Presence (+) or absence (−) of ushA-like (U) and cpdB-like (C) genes in selected bacterial species. The (+) background indicates: green, presence in ≤50% of the genomes analyzed; orange, presence in >50% but <100% of the genomes; red, presence in all the genomes. Full data can be found in Table S6.

Species ¹	Taxid	U	C
Acinetobacter calcoaceticus	471	+	−
Aerococcus urinae	1376	−	−
Aeromonas hydrophila	644	+	+
Bacillus anthracis	1392	+	+
Bacillus cereus	1396	+	+
Bacillus subtilis	1423	+	+
Borrelia burgdorferi	139	−	−
Brucella abortus	235	−	−
Brucella melitensis	29459	−	−
Brucella suis	29461	−	−
Campylobacter jejuni	197	−	−
Chlamydia abortus	83555	−	−
Chlamydia muridarum	83560	−	−
Chlamydia pecorum	85991	−	−
Chlamydia pneumoniae	83558	−	−
Chlamydia psittaci	83554	−	−
Chlamydia trachomatis	813	−	−
Citrobacter freundii	546	+	+
Citrobacter koseri	545	+	+
Citrobacter rodentium	67825	+	+
Clostridioides difficile	1496	+	−
Clostridium botulinum	1491	+	+
Clostridium perfringens	1502	+	+
Clostridium tetani	1513	−	+
Corynebacterium diphtheriae	1717	−	−
Coxiella burnetii	777	−	−
Enterobacter cloacae	550	+	+
Enterococcus avium	33945	+	+
Enterococcus faecalis	1351	+	+
Enterococcus faecium	1352	+	+
Escherichia albertii	208962	+	+
Escherichia coli	562	+	+
Escherichia fergusonii	564	+	+
Francisella tularensis	263	−	−
Haemophilus influenzae	727	+	+
Haemophilus parainfluenzae	729	+	+
Hafnia alvei	569	+	+
Helicobacter pylori	210	−	+
Klebsiella aerogenes	548	+	+
Klebsiella oxytoca	571	+	+
Klebsiella pneumoniae	573	+	+
Kluyvera ascorbate	51288	+	+
Legionella pneumophila	446	+	−
Leptospiraborgpetersenii	174	−	−
Leptospira interrogans	173	−	−
Leptospira kirschneri	29507	−	−
Leptospira noguchii	28182	−	−
Leptospira santarosai	28183	−	−
Leptospira weilii	28184	−	−
Listeria monocytogenes	1639	+	−
Moraxella catarrhalis	480	−	−
Morganella morganii	582	+	+
Mycobacterium avium	1764	−	−
Mycobacterium intracellulare	1767	−	−
Mycobacterium leprae	1769	−	−
Mycobacterium tuberculosis	1773	−	−
Mycobacterium ulcerans	1809	−	−
Mycoplasma leachii	2105	−	−
Mycoplasma mycoides	2102	−	−
Mycoplasma putrefaciens	2123	−	−
Neisseria gonorrhoeae	485	−	−
Neisseria meningitidis	487	−	−
Pasteurella multocida	747	+	+
Plesiomonas shigelloides	703	+	+
Proteus mirabilis	584	+	+
Proteus vulgaris	585	+	+
Providencia stuartii	588	+	+
Pseudomonas aeruginosa	287	−	−
Pseudomonas fluorescens	294	+	−
Rickettsia rickettsii	783	−	−
Salmonella bongori	54736	+	+
Salmonella enterica	28901	+	+
Salmonella enterica subsp. arizonae	59203	+	+
Salmonella enterica subsp. diarizonae	59204	+	+
S. enterica subsp. enterica ser. Pullorum	605	+	+
S. enterica subsp. enterica ser. Typhi	90370	+	+
S. enterica sub. enterica ser. Typhimurium	90371	−	+
Salmonella enterica subsp. houtenae	59205	+	+
Salmonella enterica subsp. salamae	59202	+	+
Salmonella enterica subsp. VII	59208	+	+
Serratia liquefaciens	614	+	+
Serratia marcescens	615	+	+
Shigella boydii	621	+	+
Shigella dysenteriae	622	+	+
Shigella flexneri	623	+	+
Shigella sonnei	624	+	+
Staphylococcus aureus	1280	+	−
Staphylococcus epidermidis	1282	+	−
Staphylococcus saprophyticus	29385	+	+
Staphylococcus warnerii	1292	+	+
Stenotrophomonas maltophilia	40324	−	−
Streptococcus agalactiae	1311	+	+
Streptococcus dysgalactiae	1334	+	+
Streptococcus mitis	28037	−	−
Streptococcus mutans	1309	+	−
Streptococcus parasuis	1501662	+	+
Streptococcus pneumoniae	1313	−	−
Streptococcus pyogenes	1314	+	−
Streptococcus sanguinis	1305	+	+
Streptococcus suis	1307	+	+
Streptococcus thermophilus	1308	+	+
Treponema pallidum	160	+	−
Vibrio cholerae	666	+	+
Yersinia enterocolitica	630	+	+
Yersinia intermedia	631	+	+
Yersinia pestis	632	+	+
Yersinia pseudotuberculosis	633	+	+

¹ Species highlighted in red are not complete according to Section 3.2.1.

Table 9. Numbers of taxa probed, analyzed, and deemed complete after TBlastN analyses with UshA-like (U) and CpdB-like (C) probes: breakdown by kind of results obtained, with presence (+) and/or absence (−) of hits with each probe type. The data are computed from the tables indicated.

Level	(Tables)	Number of Taxa Probed ¹	Number of Taxa without Genomes ²	Number of Taxa Analyzed ³	Number of Complete Taxa ⁴	Breakdown of Complete Taxa by Kind of Results
Level	(Tables)	Number of Taxa Probed ¹	Number of Taxa without Genomes ²	Number of Taxa Analyzed ³	Number of Complete Taxa ⁴	U+ C+	U+ C−	U− C+	U− C−
Phylum	Table 3 and Table S1	43	0	43	19	0	2	3	14
Class	Table 4 and Table S2	76	6	70	31	1	6	0	24
Order	Table 5 and Table S3	152	20	132	53	4	4	2	43
Family	Table 6 and Table S4	403	99	304	139	7	16	3	113
Genus	Table 7 and Table S5	510	0	510	268	136	95	37	0
Species	Table 8 and Table S6	107	0	107	80	37	5	1	37
Total	-	1291	125	1166	590	185	128	46	231

¹ Taxa that were submitted to TBlastN analysis with the seven probes. ² Taxa that, according to TBlastN analysis, do not contain sequenced genomes in the NCBI Complete Genomes Database. ³ Taxa with sequenced genomes in the NCBI Complete Genomes Database, and that were effectively analyzed. ⁴ Taxa declared complete according to Section 3.2.1: in Table 3, Table 4, Table 5, Table 6, Table 7 and Table 8, the names of non-complete taxa are written in red type.

Table 10. Complete taxa that contain both ushA-like and cpdB-like genes. No bacterial phylum showed these characteristics.

Class		Genus		Genus
Limnochordia	1676648	Kitasatospora	2063	Roseibium	150830
Order		Kluyvera	579	Roseicitreum	1209946
Egicoccales	1755823	Kosakonia	1330547	Roseobacter	2433
Kosmotogales	1643946	Kroppenstedtia	1274351	Saccharibacillus	456492
Mesoaciditogales	1769716	Labrenzia	478070	Saccharospirillum	231683
Nannocystales	3031713	Leclercia	83654	Scandinavium	2726810
Family		Leisingera	191028	Sebaldella	32068
Breoghaniaceae	2831104	Lentilactobacillus	2767893	Sediminibacillus	482460
Devosiaceae	2831106	Lentzea	165301	Silicimonas	1955420
Kiloniellaceae	597359	Luteipulveratus	745364	Sporolactobacillus	2077
Kribbellaceae	2726069	Mangrovibacillus	2920444	Stigmatella	40
Moritellaceae	267891	Marinomonas	28253	Streptosporangium	2000
Oleiphilaceae	191033	Martelella	293088	Sutcliffiella	2837511
Thermosediminibacteraceae	2770093	Melittangium	44	Symbiopectobacterium	801
Genus		Metabacillus	2675233	Tabrizicola	1443919
Acetilactobacillus	2767874	Methylomusa	2093783	Telluria	34069
Actinoplanes	1865	Mixta	2100764	Tepiditoga	2778400
Algicella	3050722	Morganella	581	Thalassospira	168934
Alloalcanivorax	3020832	Neorhizobium	1525371	Thermosipho	2420
Allobacillus	1400133	Nicoliella	2978367	Thiospirochaeta	2792240
Amylolactobacillus	2767876	Nitratireductor	245876	Tissierella	41273
Anaerotruncus	244127	Niveibacterium	1769726	Weizmannia	2817139
Apilactobacillus	2767877	Obesumbacterium	82982	Xenorhabdus	626
Aquibium	2911176	Occultella	2828348	Yersinia	629
Atlantibacter	1903434	Oceanotoga	1255275	Youhaiella	1827478
Basfia	697331	Oricola	1594166	Species
Bisgaardia	109471	Otariodibacter	1249016	Aeromonas hydrophila	644
Breznakiella	2845254	Pacificitalea	2846749	Bacillus anthracis	1392
Carboxydothermus	129957	Paenacidovorax	3051138	Bacillus cereus	1396
Cedecea	158483	Paenalkalicoccus	2944627	Citrobacter freundii	546
Celeribacter	875170	Pannonibacter	227873	Citrobacter koseri	545
Chania	1745211	Paracidovorax	3051137	Citrobacter rodentium	67825
Ciceribacter	1648508	Paradevosia	1573407	Enterobacter cloacae	550
Citrobacter	544	Paraliobacillus	200903	Escherichia albertii	208962
Cobetia	204286	Parasedimentitalea	2738399	Escherichia fergusonii	564
Cronobacter	413496	Parashewanella	2547964	Haemophilus influenzae	727
Cystobacter	42	Paroceanicella	2683599	H. parainfluenzae	729
Cytobacillus	2675230	Pelagibacterium	1082930	Hafnia alvei	569
Defluviitoga	1511648	Pelagovum	2795377	Klebsiella aerogenes	548
Dickeya	204037	Periweissella	2930384	Klebsiella oxytoca	571
Dinoroseobacter	309512	Peterkaempfera	2995704	Kluyvera ascorbata	51288
Duganella	75654	Peteryoungia	2853332	Morganella morganii	582
Entomospira	2834378	Petrocella	2603323	Proteus mirabilis	584
Falsihalocynthiibacter	2854182	Petrotoga	28236	Proteus vulgaris	585
Flavonifractor	946234	Phaeobacter	302485	Salmonella bongori	54736
Frederiksenia	1649317	Photorhabdus	29487	S. enterica subsp. arizonae	59203
Frigidibacter	1775705	Polyangium	55	S. enterica subsp. diarizonae	59204
Fructilactobacillus	2767881	Polycladomyces	1348505	S. enterica subsp. enterica ser. Pullorum	605
Fructobacillus	559173	Pontivivens	1844015	S. enterica subsp. enterica ser. Typhi	90370
Georhizobium	2661800	Priestia	2800373	S. enterica subsp. houtenae	59205
Gilliamella	1193503	Proteus	583	S. enterica subsp. salamae	59202
Gracilibacillus	74385	Pseudocitrobacter	1504576	S. enterica subsp. VII	59208
Gracilinema	2951106	Pseudoduganella	1522432	Serratia liquefaciens	614
Granulosicoccus	437504	Pseudooceanicola	1679449	Shigella boydii	621
Gymnodinialimonas	2937410	Pseudopuniceibacterium	2613960	Shigella dysenteriae	622
Gynuella	1445504	Pseudorhizobium	1903858	Shigella flexneri	623
Halobacteroides	42417	Psychrobacillus	1221880	Shigella sonnei	624
Hafnia	568	Pukyongiella	2831925	Streptococcus sanguinis	1305
Halocella	46466	Qingshengfaniella	2816884	Streptococcus thermophilus	1308
Inhella	644355	Radiobacillus	2785518	Yersinia enterocolitica	630
Intrasporangium	53357	Rhodobaca	119541	Yersinia intermedia	631
Iocasia	2899804	Rhodovulum	34008	Yersinia pestis	632
Jejubacter	2815296	Roseibacterium	159345	Yersinia pseudotuberculosis	633

Table 11. Complete taxa that do not contain ushA-like or cpdB-like genes. No complete genus showed these characteristics.

Phylum		Order		Family
Abditibacteriota	2109258	Synechococcales	1890424	Paludibacteraceae	2005523
Acidobacteriota	57723	Thermoleophilales	588674	Parvibaculaceae	2813035
Aquificota	200783	Thermostichales	2881383	Peptococcaceae	186807
Bdellovibrionota	3018035	Trueperales	2762275	Peptoniphilaceae	1570339
Chlamydiota	204428	Family		Phreatobacteraceae	2843305
Chlorobiota	1090	Acetomicrobiaceae	3029086	Porticoccaceae	1706374
Chrysiogenota	200938	Acidilutibacteraceae	2992717	Proteinivoraceae	1491775
Elusimicrobiota	74152	Acidimicrobiaceae	84994	Rhodospirillaceae	41295
Kiritimatiellota	134625	Aminobacteriaceae	3029087	Rikenellaceae	171550
Lentisphaerota	256845	Amorphaceae	2685818	Rivulariaceae	1185
Nitrospinota	1293497	Anaeromyxobacteraceae	1524215	Salinivirgaceae	1970190
Planctomycetota	203682	Aphanizomenonaceae	1892259	Sandaracinaceae	1055686
Rhodothermota	1853220	Aristaeellaceae	3046368	Segniliparaceae	316606
Thermomicrobiota	3027942	Bartonellaceae	772	Stellaceae	2844601
Class		Beijerinckiaceae	45404	Steroidobacteraceae	2689614
Acidithiobacillia	1807140	Beutenbergiaceae	125316	Sterolibacteriaceae	2008793
Anaerolineae	292625	Blastochloridaceae	2831090	Succinivibrionaceae	83763
Armatimonadia	1042312	Borreliaceae	1643685	Sulfuricellaceae	2772226
Caldilineae	475962	Bruguierivoracaceae	2812006	Sulfurimonadaceae	2771471
Chitinophagia	1853228	Calditerrivibrionaceae	2945021	Sulfurospirillaceae	2932623
Coriobacteriia	84998	Cardiobacteriaceae	868	Sulfurovaceae	2771472
Cytophagia	768503	Cellulomonadaceae	85016	Symbiobacteriaceae	543349
Desulfarculia	3031646	Cellulosilyticaceae	3018741	Syntrophomonadaceae	68298
Desulfobaccia	3031647	Chelatococcaceae	2036754	Syntrophotaleaceae	2812024
Desulfurellia	3031853	Christensenellaceae	990719	Tenuifilaceae	2760872
Fibrobacteria	204430	Coleofasciculaceae	1892251	Tepidanaerobacteraceae	2770092
Flavobacteriia	117743	Coprobacillaceae	2810280	Terasakiellaceae	2813951
Hydrogenophilalia	2008785	Coxiellaceae	118968	Thalassobaculaceae	2844864
Ktedonobacteria	388447	Deferribacteraceae	191394	Thermincolaceae	2937911
Longimicrobiia	1804991	Demequinaceae	1042322	Thermodesulfobacteriaceae	188711
Methylacidiphilae	1955630	Desulfallaceae	2867375	Thermodesulfobiaceae	227387
Mycoplasmoidales	2790996	Desulfococcaceae	2931039	Thermovirgaceae	3029089
Saprospiria	1937959	Desulfohalobiaceae	213117	Thioalkalibacteraceae	2035710
Spartobacteria	134549	Desulfolunaceae	3031622	Thioalkalispiraceae	1096778
Sphingobacteriia	117747	Desulfosudaceae	2904715	Tolypothrichaceae	119859
Tepidiformia	2682225	Desulfotomaculaceae	2937910	Tropherymataceae	2805591
Thermodesulfovibrionia	2811502	Dethiosulfovibrionaceae	3029088	Wenzhouxiangellaceae	1676141
Verrucomicrobiae	203494	Dietziaceae	85029	Woeseiaceae	1738654
Zetaproteobacteria	580370	Dysgonomonadaceae	2005520	Xanthobacteraceae	335928
Order		Fastidiosibacteraceae	2056687	Zymomonadaceae	2844881
Acholeplasmatales	186329	Fimbriimonadaceae	1663426	Species
Acidaminococcales	1843488	Flexistipitaceae	2945022	Aerococcus urinae	1376
Acidiferrobacterales	1692040	Fluviibacteraceae	2808923	Borrelia burgdorferi	139
Acidothermales	1643683	Francisellaceae	34064	Brucella abortus	235
Actinopolysporales	622450	Gallionellaceae	90627	Brucella melitensis	29459
Bifidobacteriales	85004	Geminicoccaceae	2066434	Brucella suis	29461
Brevinematales	1643687	Geoalkalibacteraceae	3031665	Campylobacter jejuni	197
Catenulisporales	414714	Gomontiellaceae	1892255	Chlamydia abortus	83555
Caulobacterales	204458	Gordoniaceae	85026	Chlamydia muridarum	83560
Chroococcidiopsidales	1890505	Halarsenatibacteraceae	3046411	Chlamydia pecorum	85991
Chroococcales	1118	Halieaceae	1706372	Chlamydia pneumoniae	83558
Dehalococcoidales	1202465	Halothermotrichaceae	3046412	Chlamydia psittaci	83554
Dehalogenimonas	670486	Halothiobacillaceae	255526	Chlamydia trachomatis	813
Egibacterales	1747768	Hapalosiphonaceae	1892263	Corynebacterium diphtheriae	1717
Emcibacterales	2066490	Heliobacteriaceae	31984	Coxiella burnetiid	777
Entomoplasmatales	186328	Hoyosellaceae	3040680	Francisella tularensis	263
Euzebyales	908621	Hydrogenimonadaceae	292630	Leptospira borgpetersenii	174
Ferrovales	1442155	Hyphomicrobiaceae	45401	Leptospira interrogans	173
Frankiales	85013	Iamiaceae	633392	Leptospira kirschneri	29507
Gloeobacterales	307595	Jonesiaceae	85022	Leptospira noguchii	28182
Holosporales	1921002	Kaistiaceae	2831111	Leptospira santarosai	28183
Kangiellales	2887327	Labilitrichaceae	1524216	Leptospira weilii	28184
Koleobacterales	2786987	Lawsonellaceae	2805586	Moraxella catarrhalis	480
Kordiimonadales	362534	Lichenihabitantaceae	2723775	Mycobacterium avium	1764
Leptospirales	1643688	Litorivicinaceae	449732	Mycobacterium intracellulare	1767
Magnetococcales	1191478	Maliibacteriaceae	3047432	Mycobacterium leprae	1769
Maricaulales	2800059	Marinobacteraceae	2887365	Mycobacterium tuberculosis	1773
Marinilabiliales	1970189	Melioribacteraceae	1334117	Mycobacterium ulcerans	1809
Minwuiales	2493627	Methylocystaceae	31993	Mycoplasma leachii	2105
Moorellales	3039167	Methylophilaceae	32011	Mycoplasma mycoides	2102
Nakamurellales	1643684	Methylothermaceae	1486721	Mycoplasma putrefaciens	2123
Natranaerobiales	485256	Mucispirillaceae	2945020	Neisseria gonorrhoeae	485
Parvularculales	255473	Mycobacteriaceae	1762	Neisseria meningitidis	487
Pleurocapsales	52604	Nitratiruptoraceae	2795691	Pseudomonas aeruginosa	287
Pseudanabaenales	2881377	Nitrosomonadaceae	206379	Rickettsia rickettsii	783
Puniceicoccales	415001	Nocardiopsaceae	83676	Stenotrophomonas maltophilia	40324
Rickettsiales	766	Nostocaceae	1162	Streptococcus mitis	28037
Sneathiellales	510684	Oscillatoriaceae	1892254	Streptococcus pneumoniae	1313
Solirubrobacterales	588673

Table 12. Complete taxa that contain ushA-like but not cpdB-like genes.

Phylum		Genus		Genus
Atribacterota	67818	Beggiatoa	1021	Pelagerythrobacter	2800685
Caldisericota	67814	Brucepastera	2967962	Pelobacter	18
Class		Caldichromatium	2828366	Phytohabitans	907364
Chloroflexia	32061	Chitinimonas	240411	Planktothrix	54304
Chthonomonadetes	1077257	Chitinolyticbacter	1055692	Polymorphum	991903
Desulfomonilia	3031650	Chondromyces	50	Pseudochrobactrum	354349
Dictyoglomia	203486	Clostridioides	1870884	Pseudoleptotrichia	2755140
Syntrophia	3031648	Companilactobacillus	2767879	Pullulanibacillus	475230
Thermoflexia	1495646	Conchiformibius	334107	Reinekea	230494
Order		Croceicoccus	1295327	Rhodopseudomonas	1073
Bradymonadales	1779134	Deefgea	400947	Roseitalea	1915401
Gloeomargaritales	1955042	Dermatophilus	1862	Salaquimonas	2712688
Glycomycetales	85014	Desulforapulum	2904687	Salidesulfovibrio	2950010
Immundisolibacterales	1934945	Edwardsiella	635	Salimicrobium	351195
Family		Effusibacillus	1502725	Saliniradius	2661818
Aminithiophilaceae	3029085	Ephemeroptericola	2680021	Salinispora	168694
Desulfatibacillaceae	3031627	Ferribacterium	88875	Sediminispirochaeta	1911556
Elioraeaceae	2690195	Fervidibacillus	3033930	Serinicoccus	265976
Geovibrionaceae	2945019	Geodermatophilus	1860	Shimwellia	1335483
Gottschalkiaceae	2042895	Geosporobacter	390805	Solidesulfovibrio	2910984
Hahellaceae	224379	Gibbsiella	929812	Solimonas	413435
Ilumatobacteraceae	2448023	Gudongella	2692382	Spongiibacter	630749
Kytococcaceae	2805426	Halalkalibacter	2893056	Staphylospora	2689589
Listeriaceae	186820	Hathewaya	1769729	Stappia	152161
Pleomorphomonadaceae	2843308	Hydrocarboniclastica	2650549	Suicoccus	2689587
Tepidimicrobiaceae	2992719	Ideonella	36862	Syntrophobacter	29526
Thermodesulfatatoraceae	3031464	Jeotgalibacillus	157226	Tetragenococcus	51668
Thermohalobacteraceae	2848916	Jiella	1775688	Thermanaerovibrio	81461
Thermotogaceae	188709	Kibdelosporangium	2029	Thermobacillus	76632
Usitatibacteraceae	2803844	Leadbettera	2951107	Thermobispora	147067
Zooshikellaceae	2898533	Lederbergia	2804231	Thermochromatium	85073
Genus		Litorilituus	1407056	Thermus	270
Aceticella	3051499	Marichromatium	85076	Thiocapsa	1056
Acetoanaerobium	186831	Meiothermus	2747271	Thiocystis	13724
Actinosynnema	40566	Methylocaldum	73778	Trichlorobacter	115782
Aliamphritea	3018276	Methylococcus	413	Tsuneonella	2800686
Allochromatium	85072	Methylomagnum	1760987	Tumebacillus	432330
Allomeiothermus	2935559	Modestobacter	88138	Zophobihabitans	2894762
Amphibacillus	29331	Nitrogeniibacter	2891294	Zymobacter	33073
Anaeropeptidivorans	2997360	Nosocomiicoccus	489909	Species
Arsenicicoccus	267408	Novibacillus	1677050	Clostridioides difficile	1496
Aurantimonas	182269	Oceanithermus	208447	Staphylococcus epidermidis	1282
Austwickia	1184606	Odoribacter	283168	Streptococcus mutans	1309
Barnesiella	397864	Parageobacillus	1906945	Streptococcus pyogenes	1314
				Treponema pallidum	160

Table 13. Complete taxa that contain cpdB-like but not ushA-like genes. There was no bacterial class showing these characteristics.

Phylum		Genus		Genus
Balneolota	1936987	Dokdonella	323413	Profundibacter	2778525
Calditrichota	1930617	Duncaniella	2518495	Pseudolysobacter	2709666
Coprothermobacterota	2138240	Dyella	231454	Pseudoprevotella	2884814
Order		Flaviflexus	1522056	Pseudorhodobacter	238783
Haliangiales	3031714	Frateuria	70411	Rhodanobacter	75309
Sporichthyales	2495578	Frischella	1335631	Rouxiella	1565532
Family		Gemmatimonas	173479	Saccharophagus	316625
Ignatzschineriaceae	3018589	Herbinix	1663717	Simonsiella	71
Ignavibacteriaceae	795749	Horticoccus	2986286	Sodaliphilus	2815786
Vulgatibacteraceae	1524213	Kineococcus	33981	Streptantibioticus	2995706
Genus		Lichenicola	2804525	Tetrasphaera	99479
Actinocatenispora	390988	Luteibacter	242605	Thioclava	285107
Aerosticca	2707020	Marinagarivorans	1792291	Tyzzerella	1506577
Anaeromicropila	3024823	Muribaculum	1918540	Wielerella	2944815
Aquirhabdus	2824158	Neotabrizicola	2946607	Species
Caldanaerobacter	249529	Opitutus	178440	Clostridium tetani	1513
Dermabacter	36739	Pragia	82984

Table 14. Specicity of probe O32133 for the phylum Bacillota. Comparison between results obtained by querying type-material genomes of the phylum Bacillota and of Superkingdom Bacteria excluding Bacillota.

		Phylum Bacillota (Taxid:1239) (705 Type-Material Genomes)			Superkingdom Bacteria (Taxid:2) Excluding Phylum Bacillota (Taxid:1239) (3526 Type-Material Genomes)
Type of Probe	Probe ¹	Hits	Score Max.	Score Min.	Hits	Score Max.	Score Min.
UshA-like	P07024	120	235	151	521	1099	151
	P44569	77	328	151	395	1188	151
	WP_000726911	147	904	151	324	247	151
	WP_011837008	94	1297	151	19	213	151
	O32133	366	947	171	0 (4) *	(416) *	(175) *
CpdB-like	P08331	288	686	151	813	1301	152
CpdB-like	AYV64543	161	1579	162	581	607	153

¹ The probes are shown in the same background color as Figure 1 and Table 1 to facilitate cross-referencing. * Numbers in parenthesis were obtained by removing the limit on type material in the TBlastN, which increased the number of genomes queried to 32,175. These four exceptional hits correspond to accession numbers CP080375.1, CP059263.1, CP051512.1, and CP074573.1.

Table 15. Specicity of probe O32133 for class Bacilli. Comparison between results obtained by querying type-material genomes of the class Bacilli and of the phylum Bacillota excluding Bacilli.

		Class Bacilli (Taxid:91061) (431 Type-Material Genomes)			Phylum Bacillota (Taxid:1239) Excluding Class Bacilli (Taxid:91061) (274 Type-Material Genomes)
Type of Probe	Probe ¹	Hits	Score Max.	Score Min.	Hits	Score Max.	Score Min.
UshA-like	P07024	90	235	151	30	230	151
	P44569	75	323	151	2	328	153
	WP_000726911	135	904	181	12	212	151
	WP_011837008	83	1297	151	62	439	154
	O32133	363	947	173	3	199	171
CpdB-like	P08331	231	686	151	57	521	152
CpdB-like	AYV64543	132	1579	162	54	509	156

¹ The probes are shown in the same background color as Figure 1 and Table 1 to facilitate cross-referencing.

Table 16. E. coli complete genomes lacking either an ushA-like or a cpdB-like gene. These genomes represent a minor fraction (0.5%) of the total number of E. coli genomes in the NCBI Complete Genomes Database.

Accession	Description	ushA-like Score Max.	cpdB-like Score Max.
NZ_AP023205.1	Escherichia coli strain TUM18781 chromosome, complete genome	1100	88
NZ_CP128950.1	Escherichia coli strain TUM2805 chromosome, complete genome	1100	86
CP054239.1	Escherichia coli strain STO_Bone7 chromosome, complete genome	769	73
CP061232.1	Escherichia coli strain STEC639 chromosome, complete genome	678	71
AP027461.1	Escherichia coli str. K-12 substr. MG1655 D41c DNA, complete genome	87	1308
AP027460.1	Escherichia coli str. K-12 substr. MG1655 D37c16 DNA, complete genome	87	1308
AP027459.1	Escherichia coli str. K-12 substr. MG1655 D37c146 DNA, complete genome	87	1308
AP027458.1	Escherichia coli str. K-12 substr. MG1655 D37c145 DNA, complete genome	87	1308
AP027457.1	Escherichia coli str. K-12 substr. MG1655 D37c143 DNA, complete genome	87	1308
AP027456.1	Escherichia coli str. K-12 substr. MG1655 D37c13 DNA, complete genome	87	1308
AP027455.1	Escherichia coli str. K-12 substr. MG1655 D37b DNA, complete genome	87	1308
AP027454.1	Escherichia coli str. K-12 substr. MG1655 D33b DNA, complete genome	87	1308
AP027453.1	Escherichia coli str. K-12 substr. MG1655 D33a DNA, complete genome	87	1308
NC_011750.1	Escherichia coli IAI39, complete sequence	118	1307
CP042982.1	Escherichia coli strain NCCP 14540 chromosome, complete genome	88	1306
CP061269.1	Escherichia coli strain STEC1012 chromosome, complete genome	87	1305
CP099173.1	Escherichia coli strain RHB23-SO-C02 chromosome, complete genome	87	1303
NZ_AP027411.1	Escherichia coli strain EC521 isolate EC521 chromosome, complete genome	87	1300

Table 17. Avian pathogenic E. coli complete genomes containing an ushA and a cpdB gene, respectively, were found with probes P07024 and P08331.

Accession	Description	ushA-like Score Max.	cpdB-like Score Max.
NC_020163.1	Escherichia coli APEC O78, complete sequence	1102	1306
NZ_CP006834.2	Escherichia coli APEC O2-211 chromosome, complete genome	1098	1308
NZ_CP006830.1	Escherichia coli APEC O18 chromosome, complete genome	1097	1308
NZ_008563.1	Escherichia coli APEC O1, complete sequence	1097	1308
NZ_CP005930.1	Escherichia coli APEC IMT5155 chromosome, complete genome	592	1308

Table 18. P. multocida complete genomes lacking either an ushA-like or a cpdB-like gene. These genomes represent a minor fraction (3.6%) of the total number of P. multocida genomes in the NCBI Complete Genomes Database.

Accession	Description	ushA-like Score Max.	cpdB-like Score Max.
CP090521.1	Pasteurella multocida strain AH09 chromosome, complete genome	628	98
NZ_CP038871.1	Pasteurella multocida strain FCf15 chromosome, complete genome	151 *	847
NZ_CP084165.1	Pasteurella multocida strain s4 chromosome, complete genome	67	851
NZ_CP020345.1	Pasteurella multocida subsp. multocida strain CIRMBP-0884 chromosome, complete genome	67	851
NZ_CP113522.1	Pasteurella multocida strain PF13 chromosome, complete genome	67	851

* This score is the minimum required to compute the hit as an ushA-like gene. It is mentioned here because it is much lower than the immediately higher ushA-like score for this species (625; data for line 66 of Table S6).

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Ribeiro, J.M.; Cameselle, J.C. Genomic Distribution of ushA-like Genes in Bacteria: Comparison to cpdB-like Genes. Genes 2023, 14, 1657. https://doi.org/10.3390/genes14081657

AMA Style

Ribeiro JM, Cameselle JC. Genomic Distribution of ushA-like Genes in Bacteria: Comparison to cpdB-like Genes. Genes. 2023; 14(8):1657. https://doi.org/10.3390/genes14081657

Chicago/Turabian Style

Ribeiro, João Meireles, and José Carlos Cameselle. 2023. "Genomic Distribution of ushA-like Genes in Bacteria: Comparison to cpdB-like Genes" Genes 14, no. 8: 1657. https://doi.org/10.3390/genes14081657

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Genomic Distribution of ushA-like Genes in Bacteria: Comparison to cpdB-like Genes

Abstract

1. Introduction

2. Materials and Methods

3. Results

3.1. Selection of Probes for TBlastN Analysis

3.2. TBlastN Analysis of Bacterial Genomes

3.2.1. General Strategy for the Analysis and Presentation of Results

3.2.2. Genomic Distribution of ushA-like and cpdB-like Genes in Bacteria Phyla

3.2.3. Genomic Distribution of ushA-like and cpdB-like Genes in Bacterial Classes of Selected Phyla

3.2.4. Genomic Distribution of ushA-like and cpdB-like Genes in Bacterial Orders of Selected Classes

3.2.5. Genomic Distribution of ushA-like and cpdB-like Genes in Bacterial Families of Selected Orders

3.2.6. Genomic Distribution of ushA-like and cpdB-like Genes in Bacterial Genera of Selected Families

3.2.7. Genomic Distribution of ushA-like and cpdB-like Genes in Selected Bacterial Species

4. Discussion

4.1. Overview

4.2. About the Possible Correlation between ushA-like and cpdB-like Genes

4.3. Comments on Some Specific Stories

4.3.1. About Phylum Bacillota and Class Bacilli: Specificity of Probe O32133

4.3.2. About the Occurrence of ushA-like and cpdB-like Genes in the Numerous Sequenced Genomes of Escherichia coli, Salmonella enterica, Pasteurella multocida, Klebsiella pneumoniae and Vibrio cholerae

4.3.3. About the Variety of Distributions of ushA-like and cpdB-like Genes in Species of Streptococcus

4.4. Repercussion of the Results

4.5. Strength and Limitations of this Study

5. General Summary of Conclusions and Outcomes Worth of Further Investigation

Supplementary Materials

Author Contributions

Funding

Institutional Review Board Statement

Informed Consent Statement

Data Availability Statement

Conflicts of Interest

References

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