Nomenclature

Annotation

The complete Mycoplasma pneumoniae genome was assembled from 28 cosmid sequences. Each sequence is terminated by an EcoRI restriction site. Two adjacent cosmid sequences are only overlapping by their terminal EcoRI restriction site.

The cirular order of these cosmids is:

E07->C09->R02->D09->B01->D12->K05->E09->E30

->C12->D02->H03->G12->F04->P02->P01->H08->A05

->F11->A19->H91->F10->H10->A65->K04->G07->GT9

->VXpSPT7 (->E07)

Each cosmid is annotated with the prefix: pcosMP*** (eg. pcosMPE07) with the exception of VXpSPT7

Nomenclature of the ORFs

Instead of a numerical nomenclature of the ORFs like for M. genitalium or H. influenzae, we decided to take a cosmid orientated nomenclature.

All open reading frames are annotated as follows:

The name of an ORF is for example: E07_orf1627

This means that it is located on the cosmid pcosMPE07 and it has got the length of 1627 amino acids.
If two ORFs of one cosmid have the same length, then they are distinguishable by having an "a" or "b" at the end (eg. E09_orf283a; E09_orf283b)
ORF Names ending with "V" (eg. B01_orf299V) have GTG as proposed startcodon
ORF Names ending with "L" (eg. C12_orf948L) have TTG as proposed startcodon
ORF Names ending with "o" (eg. E07_orf540o) are overlapping("o") ORFs located at the ends of two adjacent cosmids. The start codon of E07_orf540o is located in pcosMPE07 and the stop codon is in the adjacent cosmid, depending on the orientation of this ORF.

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