As genes in Arabidopsis and other model systems are annotated, the identification of some of these novel genes will be accomplished.
By comparing our EST database with known immune proteins encoded by other insects, especially D. melanogaster, putative regulatory pathways of L. striatellus immune system were annotated.
For example, Quilt's authoring system is annotated with email messages.
A novel restriction modification system was annotated on the genome of DPC6026.
Concordantly, the CAP (crp, APJL2012 -cAMP (cyAPJL2012 -cAMPsystem was annotated, whicyaAenerAPJL1072ulatesystemtranscriptional rate of sugar utilization operons in multiple sugar utilization bacteria [20].
The antitoxin component of this system is annotated as such in the latter strain (CLL_A3363), but as a conserved hypothetical protein in the former (CB17B3277).
Finally, a single Type I RM system is annotated in the draft genome sequence of C. pasteurianum ATCC 6013 [ 33] and encodes the three host specificity domains, corresponding to restriction (hsdR; locus tag CP6013_1662), modification (hsdM; locus tag CP6013_1663), and specificity (hsdS; locus tag CP6013_1664), that are typical characteristics of Type I RM systems [ 40].
Of 95 sequenced sulfate-reducers genomes available from IMG database, phoBR system was annotated in most of them, including D. balticum, D. autotrophicum HRM2, D. vulgaris vulgaris Hildenborough, whereas the phoPR system was coded in only 6 genomes including one Gram-positive representative - Desulfosporosinus sp. Strain OT.
When various studies described a species with different sexual systems, all of them were annotated with the respective reference; however, the principal or most frequent sexual system was used for calculating the frequency at the genus or subgenus level (see Jürgens et al. 2002 for similar criteria).
Moreover, the model compartments, entities and reactions were annotated using Systems Biology Ontology (SBO) (http://www.ebi.ac.uk/sbo/) terms.
