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Pathway Analysis

At the next level, the pathway perspective, individual enzyme activities encoding protein reading frames are assembled and combined into specific pathways. A concise and integrated way of comparing pathway results from different genomes is comparative pathway alignment. Species-specific differences in terms of the presence or absence of individual enzymes are identified by insertions or gaps in this comparative table [5]. In general, potential target structures for medical intervention (e.g., for drug design of an inhibitor against a biosynthetic enzyme in the pathogen of interest) should not occur in the human patient (or at least in the human the target homology protein should have clear structural and affinity differences). The occurrence of the target in several pathogens will make the target

1.6 Network Analysis | 7

structure more interesting from an application point of view (e.g. cell wall synthesis enzymes in gram-positive bacteria - with a potential to lead to alternative drugs to penicillin-like substances).

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