Q. Structural analyses on small sets of proteins have shown that the domains from a pair of families bind to each other with the same geometry in multi-domain proteins and in transient interactions.

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Q. In the phylogenetic profile method for predicting protein interaction, presence or absence of orthologous genes is scored across a variety of genomes.

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Q. In the assessment of methods to predict protein-protein interactions, one third of such pairs were found to physically interact, and an additional third to belong to the same metabolic pathway or functional process.

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Q. The phylogenetic profile method relies on detection of orthologs (or homologs, in a variation of the method) in a set of genomes.

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Q. Due to the requirement for co-regulation as well as colocalization, the method is mostly limited to certain classes of protein-protein interactions.

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Q. Domains that are part of a multidomain protein are ______

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Q. An approach for predicting ______ to look for cases across a set of genomes where _____ are part of the same gene in one genome resulted in gene fusion method.

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Q. Conservation of gene order due to operon structure is _______ so interactions of proteins specific to eukaryotes cannot be detected by method of Conservation of gene order.

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Q. In a quantitative assessment of this method (Conservation of gene order) using the genome of the parasitic organism Mycoplasma genitalium as a benchmark.

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Q. Members of a stable complex are often co-regulated and thus will be detected by the method of Conservation of gene order.

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Q. When comparing pairs of genes or sets of genes in different genomes for this purpose, it is not mandatory for the genes to be orthologs.

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Q. Genes that are consistently part of the same operon across different, distantly related genomes are likely to be part of the same protein complex or functional process across all species.

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Q. Interactions between proteins can be predicted computationally by looking for sets of genes that occur as a _______

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Q. Experimentation is most desirable over computational methods by every means.

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Q. Across the different types of catalytic families, the position of the two domains with respect to one another varied, but only within a range of about ______

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Q. The linkers between the catalytic domain and the Rossmann domain were conserved in each family.

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Q. The investigation (Aloy and Russel) of domain combinations in multidomain proteins by Bashton and Chothia focuses on two-domain proteins belonging to the Rossmann domain family.

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Q. In order to understand the geometry of domain combinations, different structures of homologous pairs of domains must be studied.

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Q. Almost ______ engage in interactions with domains from their own family when one includes oligomeric proteins.

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Q. Most domain families only interact with one or two other families, while a few families are extremely versatile in their interactions and are connected to many families.

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