PMC

Using the ICEberg database and search tools (HMMER3 and WU-BLAST2) (http://db-mml.sjtu.edu.cn/ICEberg/), we identified 128 HelP homologues in 72 ICEs. The homologues were analyzed using CLUSTAL X and grouped into clades if they were within a distance of <0.22. The diagram is of an unrooted tree with the number of homologues in each clade shown in parentheses. Branch lengths indicate relative phylogenic distances. The width and length of branch tips indicate the number of homologues and the relative phylogenic distance between homologues in the clade, respectively. Of the seven clades, six are named for a representative ICE and its HelP homologue and one is named “Orf23-like” to reflect its close relationship to the Tn916 Orf23 clade. Twelve homologues in the ICE6013 Orf14 clade have the identical 106 amino acid sequence. The two homologues in the ICEBs1 HelP clade only differ by 5 of 126 amino acids. The two homologues in the Orf23-like clade only differ by 7 of 108 amino acids. Sixteen ICEs encode a single homologue of HelP. These sixteen homologues are from three clades - ICEBs1 HelP (2), ICE6013 Orf14 (12) and Tn916 Orf23 (2). The remaining 56 ICEs encode pairs of HelP homologues. The members of each pair of homologues fall into separate clades as exemplified by Tn916 Orf22 (128 aa) and Tn916 Orf23 (104 aa), and ICESa2 SAPIG1865 (141 aa) and ICESa2 SAPIG1866 (107 aa).

Phylogenetic tree of XdhC homologues. Protein phylogeny of XdhC homologues based on a full length sequence alignment. The tree was constructed by the neighbor-joining method from a matrix of estimated numbers of amino acid substitutions per site calculated with the Dayhoff option of Phylip. Numbers near branches indicate the bootstrap proportion for 100 replicas using the same method. The scale bar indicates 0.1 substitutions per site. Bacterial XdhC homologues from (partially) characterized operons are marked in red, XdhC homologues from Archaea are marked in blue, and in case several XdhC homologues present in one genome, they are marked by H1, H2, H3; class: b: Bacilli; c: Clostridia; α: Alphaproteobacteria; β: Betaproteobacteria; γ: Gammaproteobacteria; δ: Deltaproteobacteria; Act: Actinobacteria; fla: Flavobacteria; Halo: Halobacteria; Ther: Thermoprotei. Underlined XdhC homologues are part of an operon encoding Moco biosynthesis proteins, XdhC homologues in bold are part of an operon encoding a molybdoenzyme, putative molybdoenzyme partners were annotated based on a full length sequence alignment of the Moco binding subunit and by comparison of active site amino acids: PaoC homologues (filled square), XOR homologues (open square), CoxL/CutL homologues (filled star), isoquinoline 1-oxidoreductase homologues (filled circle) and quinaldine 4-oxidase (filled diamond).

Footnote: The developmental stage of ticks from which sequences were obtained is in bold type. ▴ indicates Salp15 homologues from I. sinensis collected in southern China; • indicates the Salp15 homologues from I. persulcatus collected in northern China. *indicates the Salp15 homologues from I. persulcatus collected in Russia; ⧫ indicates Salp15 homologues from I. persulcatus collected in Japan; ▪ indicates Salp15 homologues from I. ricinus collected in Europe; ★ indicates the Salp15 from I. scapularis collected in easternNorth America. ▾ indicates the Salp15 from I.pacificus collected in western North America.

Venn diagrams indicating the relationship (numbers in the circles) between PFK (encoded by pfkA), the glucose-specific PTS transporter EIIB^Glc (encoded by ptsG) and glucokinase (GK; encoded by glk) in γ-Proteobacteria, β-Proteobacteria, Firmicutes and Actinobacteria. For example, in 76 of the listed γ-Proteobacteria, pfkA, ptsG and glk homologues are present in 44, 39 and 51 species, respectively. In 34 species, pfkA and ptsG homologues are both present, whereas in 27 species, pfkA and ptsG homologues are both absent (number outside the circles). Hence, in 61 (27+34) of the 76 cases (80 %), PFK and EIIB^Glc are correlated. In 25 species, pfkA and glk homologues are both present, whereas in six species, pfkA and glk homologues are both absent. Therefore, in 31 cases (41 %), PFK and GK are correlated. In 27 species, glk and ptsG homologues are both present, whereas in 13 organisms, glk and ptsG homologues are both absent (correlation in 53 % of the cases). In 24 of the 76 γ-Proteobacteria (number in the centre), all three homologues are present, whereas homologues are absent in four cases (4/76), which means that in 37 % of the cases, PFK, EIIB^Glc and GK are correlated.