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<h1>Help text for the field "Chose problem type" </h1> <br> <h2>Missing gene for a role</h2> The presence of a functional role in an organism is inferred, but the corresponding gene cannot be identified by reliable homology projection. Genome context analysis techniques, most notably clustering on the prokaryotic chromosome, may generate candidate genes for a sought functional role. <br> <br> <h2>Gene in subsystem without clear role</h2> This includes genes that have been implicated in a particular functional process but are still lacking specific functional annotation. For example, bioH has been known for years to be important for biotin biosynthesis, however it's exact biochemical role remained unknown. <br> <br> <h2>Role out of context</h2> This is appropriate when the presence of a gene assigned with specific functional role cannot be justified by functional context analysis. In some cases, this may reflect annotation/gene calling problem or merely an incomplete subsystem coverage. However, in other cases such orphan genes may lead to an inference of novel reactions and processes. <br> <br> <h2>Missing input/output</h2> Used to reflect the situation when the origin of a substrate or utilization of a product is unclear and cannot be reconciled with an existing biochemical knowledge captured in a subsystem. In some cases these observations may lead to the inference of a novel gene or pathway. <br> <br> <br> <h2>Functionally coupled hypothetical</h2> In many cases genes with unknown functions appear to be strongly functionally coupled with a subsystem via chromosomal clustering and other types of evidence provided by genome context analysis. A detailed subsystem analysis may help to suggest a specific function for this hypothetical. <br> <br> <h2>Orphan chromosomal cluster</h2> Genes that tend to co-localize on the chromosome in phylogenetically distant prokaryotes are often functionally related. Chromosomal clustering of hypothetical genes in combination with other types of evidence may lead to identification of a novel biological pathway. <br> <br> <h2>Unresolved paralogs</h2> Multiple genes associated with a single functional role (paralogs) may indicate incorrect annotations. In some cases these inconsistencies can be resolved based on genome context analysis
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