(Below N is a link to NCBI taxonomic web page and E link to ESTHER at designed phylum.) > cellular organisms: NE > Bacteria: NE > Proteobacteria: NE > Gammaproteobacteria: NE > Alteromonadales: NE > Alteromonadaceae: NE > Alteromonas: NE > Alteromonas macleodii: NE
Warning: This entry is a compilation of different species or line or strain with more than 90% amino acid identity. You can retrieve all strain data
(Below N is a link to NCBI taxonomic web page and E link to ESTHER at designed phylum.) Alteromonas macleodii str. 'Ionian Sea UM4b': N, E.
Alteromonas macleodii str. 'Ionian Sea UM7': N, E.
Alteromonas macleodii str. 'Aegean Sea MED64': N, E.
Alteromonas macleodii AltDE1: N, E.
Alteromonas macleodii str. 'Ionian Sea U8': N, E.
Alteromonas mediterranea: N, E.
Alteromonas macleodii str. 'Deep ecotype': N, E.
Alteromonas macleodii str. 'Ionian Sea U7': N, E.
Alteromonas macleodii str. 'English Channel 615': N, E.
Alteromonas macleodii str. 'Ionian Sea U4': N, E.
Alteromonas mediterranea DE: N, E.
LegendThis sequence has been compared to family alignement (MSA) red => minority aminoacid blue => majority aminoacid color intensity => conservation rate title => sequence position(MSA position)aminoacid rate Catalytic site Catalytic site in the MSA MKYIHMLMYVLTFSFAPITLATTDPMHDNKPPLPQAASEALINSISAFSH FTKEEVKASTPGTNEAWRNYVHARNSEQKKKIKKMKKALNVDIELMNLND VVVRKLTPKAITPEFKDKVYLDIHGGAFVLFGGLPSIEEGLLVAERLGIV VYSVDYRMPPTFPFPAALNDVVAVYNALLDQAGEGNIFVGGTSAGGGLVL SLVQSLIKSETPLPNAVYAGTPWADLTKTSDSLYTNEGIDNVLVTYDGQL EAAAKLYAGKKALTDPAISPLYGSFGHFPPTFLVTGTRDLFLSDTVRVNR AIRDSKGVTQLEVFEGLSHAEYLIFYKTPESETTYHLMKSFFLSYL
Esterases receive special attention because their wide distribution in biological systems and environments and their importance for physiology and chemical synthesis. The prediction of esterases substrate promiscuity level from sequence data and the molecular reasons why certain such enzymes are more promiscuous than others, remain to be elucidated. This limits the surveillance of the sequence space for esterases potentially leading to new versatile biocatalysts and new insights into their role in cellular function. Here we performed an extensive analysis of the substrate spectra of 145 phylogenetically and environmentally diverse microbial esterases, when tested with 96 diverse esters. We determined the primary factors shaping their substrate range by analyzing substrate range patterns in combination with structural analysis and protein-ligand simulations. We found a structural parameter that helps ranking (classifying) promiscuity level of esterases from sequence data at 94% accuracy. This parameter, the active site effective volume, exemplifies the topology of the catalytic environment by measuring the active site cavity volume corrected by the relative solvent accessible surface area (SASA) of the catalytic triad. Sequences encoding esterases with active site effective volumes (cavity volume/SASA) above a threshold show greater substrate spectra, which can be further extended in combination with phylogenetic data. This measure provides also a valuable tool for interrogating substrates capable of being converted. This measure, found to be transferred to phosphatases of the haloalkanoic acid dehalogenase superfamily and possibly other enzymatic systems, represents a powerful tool for low-cost bioprospecting for esterases with broad substrate ranges, in large scale sequence datasets.
Title: Genomic diversity of deep ecotype Alteromonas macleodii isolates: evidence for Pan-Mediterranean clonal frames Lopez-Perez M, Gonzaga A, Rodriguez-Valera F Ref: Genome Biol Evol, 5:1220, 2013 : PubMed
We have compared genomes of Alteromonas macleodii "deep ecotype" isolates from two deep Mediterranean sites and two surface samples from the Aegean and the English Channel. A total of nine different genomes were analyzed. They belong to five clonal frames (CFs) that differ among them by approximately 30,000 single-nucleotide polymorphisms (SNPs) over their core genomes. Two of the CFs contain three strains each with nearly identical genomes (~100 SNPs over the core genome). One of the CFs had representatives that were isolated from samples taken more than 1,000 km away, 2,500 m deeper, and 5 years apart. These data mark the longest proven persistence of a CF in nature (outside of clinical settings). We have found evidence for frequent recombination events between or within CFs and even with the distantly related A. macleodii surface ecotype. The different CFs had different flexible genomic islands. They can be classified into two groups; one type is additive, that is, containing different numbers of gene cassettes, and is very variable in short time periods (they often varied even within a single CF). The other type was more stable and produced the complete replacement of a genomic fragment by another with different genes. Although this type was more conserved within each CF, we found examples of recombination among distantly related CFs including English Channel and Mediterranean isolates.
Alteromonas macleodii is a common marine heterotrophic gamma-proteobacterium. Isolates from this microbe cluster by molecular analysis into two major genotypic groups or ecotypes, one found in temperate latitudes in the upper water column and another that is for the most part found in the deep water column of the Mediterranean. Here, we describe the genome of one strain of the 'deep ecotype' (AltDE) isolated from 1000 m in the Eastern Mediterranean and compare this genome with that of the type strain ATCC 27126, a representative of the global 'surface' ecotype. The genomes are substantially different with DNA sequence similarity values that are borderline for microbes belonging to the same species, and a large differential gene content, mainly found in islands larger than 20 kbp, that also recruit poorly to the Global Ocean Sampling project (GOS). These genomic differences indicate that AltDE is probably better suited to microaerophilic conditions and for the degradation of recalcitrant compounds such as urea. These, together with other features, and the distribution of this genotypic group, indicate that this microbe colonizes relatively large particles that sink rapidly to meso and bathypelagic depths. The genome of ATCC 27126 on the other hand has more potential for regulation (two component systems) and degrades more sugars and amino acids, which is consistent with a more transient particle attachment, as would be expected for lineages specialized in colonizing smaller particulate organic matter with much slower sinking rates. The genomic data are also consistent with a picture of incipient speciation driven by niche specialization.
