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[[Image:Comparison of the Shewanella oneidensis open reading frames with those of completely sequenced organisms.gif | center | 300px | thumb | link=http://www.nature.com/nbt/journal/v20/n11/fig_tab/nbt749_F2.html | Comparison of the Shewanella oneidensis open reading frames with those of completely sequenced organisms.]]

[[Image:Comparison of the Shewanella oneidensis open reading frames with those of completely sequenced organisms.gif | center | 300px | thumb | link=http://www.nature.com/nbt/journal/v20/n11/fig_tab/nbt749_F2.html | Comparison of the Shewanella oneidensis open reading frames with those of completely sequenced organisms.]]

Most of the shewanella oneidensis MR-1 predicted protein-encoding open reading frames are similar to vibrio cholerae genes. Shwanella oneidensis MR-1 matched with 1,265 predicted protein-encoding open reading frames in vibrio cholerae, 32.33% of the vibrio cholerae genome. Furthermore, 683 of the shewanella oneidensis predicted protein-encoding open reading frames are similar to other shewanella oneidensis genes, which suggests lineage-specific duplications.

Most of the shewanella oneidensis MR-1 predicted protein-encoding open reading frames are similar to vibrio cholerae genes. Shwanella oneidensis MR-1 matched with 1,265 predicted protein-encoding open reading frames in vibrio cholerae, 32.33% of the vibrio cholerae genome. Furthermore, 683 of the shewanella oneidensis predicted protein-encoding open reading frames are similar to other shewanella oneidensis genes, which suggests lineage-specific duplications.

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[[Image:Whole-genome proteome alignments between Shewanella oneidensis and Vibrio cholerae.gif | center | 300px | thumb | link=http://www.nature.com/nbt/journal/v20/n11/fig_tab/nbt749_F3.html | Whole-genome proteome alignments between Shewanella oneidensis and vibrio cholerae.]]

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The study revealed that vibrio cholerae was the only organism with extensive regions of similar gene order. These syntenic regions are only on the vibrio cholerae chromosome I. This suggests that the second chromosome of vibrio cholerae was captured after the divergence of vibrio cholerae and shewanella oneidensis, that the second chromosome was lost in the shewanella oneidensis lineage, or that the second chromosome was rearranged in the shewanella lineage.

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[[Image:Comparison of the MuSo1 (A) and MuSo2 (B) phage with Mu, MuHi, PNM1, PNM2, and MuMenB phage.gif | center | 300px | thumb | link=http://www.nature.com/nbt/journal/v20/n11/fig_tab/nbt749_F4.html | Comparison of the MuSo1 (A) and MuSo2 (B) phage with Mu, MuHi, PNM1, PNM2, and MuMenB phage.]]

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Genome analysis revealed a 51,857 base-pair lambda-like phage genome, both integrated in the shewanella oneidensis genome and present in non-integrated form, suggesting that it is a functional phage. The discovery of the shewanella lambda-like phage may provide an avenue for genetic manipulation of this group of microbes and allow the design of strains for specific bioremediation purposes.

====Comparison to previous studies====

====Comparison to previous studies====

* Through genome analysis, 39 c-type cytochromes were revealed, including 32 ''previously unidentified'' in shewanella oneidensis, and a novel periplasmic hydrogenase, integral members of the electron transport system.

* Through genome analysis, 39 c-type cytochromes were revealed, including 32 ''previously unidentified'' in shewanella oneidensis, and a novel periplasmic hydrogenase, integral members of the electron transport system.

* Shewanella oneidensis was found to possess a classic hydrogenase operon and a heterodimeric hydrogenase, which is an important element for its anaerobic respiratory capability as well as its metal-reducing capability. There have been ''no previous reports'' of the presence of this hydrogenase enzyme family in a facultative aerobe.

* Shewanella oneidensis was found to possess a classic hydrogenase operon and a heterodimeric hydrogenase, which is an important element for its anaerobic respiratory capability as well as its metal-reducing capability. There have been ''no previous reports'' of the presence of this hydrogenase enzyme family in a facultative aerobe.

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* Genome analysis revealed a 51,857 base-pair lambda-like phage genome, both integrated in the shewanella oneidensis genome and present in non-integrated form, suggesting that it is a functional phage. The discovery of the shewanella lambda-like phage may provide an avenue for genetic manipulation of this group of microbes and allow the design of strains for specific bioremediation purposes.

===Model Organism Database===

===Model Organism Database===

# What types of data can be found in the database (sequence, structures, annotations, etc.); is it a primary or “meta” database; is it curated electronically, manually [in-house], or manually [community])?

# What types of data can be found in the database (sequence, structures, annotations, etc.); is it a primary or “meta” database; is it curated electronically, manually [in-house], or manually [community])?

Jkuroda Week 11 - Revision history

Jkuroda: more figures