Results: 5

1.
Figure 2

Figure 2. From: The COG database: an updated version includes eukaryotes.

Phyletic patterns of KOGs. All, include representatives from each of the 7 analyzed species; All-Ec, include representatives from each of 6 species other than Encephalitozoon cuniculi; All animals, include representatives from three animal genomes only; All fungi, include representatives from two fungal genomes only.

Roman L Tatusov, et al. BMC Bioinformatics. 2003;4:41-41.
2.
Figure 1

Figure 1. From: The COG database: an updated version includes eukaryotes.

Phyletic patterns of COGs. All, represented in all unicellular organisms included in the COG system; All archaea, All bacteria, All eukaryotes, represented in each species from the respective domain of life (and possibly in some species from other domains); All bacteria except the smallest, represented in all bacteria except, possibly, parasites with small genomes (mycoplasma, chlamydia, rickettsia, and spirochetes).

Roman L Tatusov, et al. BMC Bioinformatics. 2003;4:41-41.
3.
Figure 3

Figure 3. From: The COG database: an updated version includes eukaryotes.

An example of a complex eukaryotic KOG: globins and related hemoproteins. The systematic protein names of the KOG members are listed under each species. To the left of the KOG proper is the similarity dendrogram produced from the BLAST scores between the KOG members. This is a crude clustering, which should not be construed as a phylogenetic tree.

Roman L Tatusov, et al. BMC Bioinformatics. 2003;4:41-41.
4.
Figure 5

Figure 5. From: The COG database: an updated version includes eukaryotes.

Examples of phyletic pattern search. (A) COGs represented in Encephalitozoon cuniculi but missing in the two yeasts (B) COGs represented in Yersinia pestis but not in other Proteobacteria or eukaryotesThe sets of species included in COGs are color-coded as follows (from left to right): yellow, archaea; purple, eukaryotes; green, miscellaneous bacteria, including hyperthermophiles, cyanobacteria, Fusobacterium, and Deinococcus; dark yellow, actinobacteria; torqoise, low-GC Gram-positive bacteria (except for mycoplasmas); light blue, Gamma-proteobacteria; dark-blue, Beta- and Epsilon-proteobacteria; dark gray, Alpha-proteobacteria; green, chlamydia and spirochetes; dark green, mycoplasmas. The functional categories, designated as in Fig. 4, are also color-coded.

Roman L Tatusov, et al. BMC Bioinformatics. 2003;4:41-41.
5.
Figure 4

Figure 4. From: The COG database: an updated version includes eukaryotes.

Functional classification of prokaryotic (COGs) and eukaryotic (KOGs) clusters of orthologs. Designations of functional categories: A, RNA processing and modification (not used for prokaryotic COGs), B, chromatin structure and dynamics, C, energy production and conversion, D, cell cycle control and mitosis, E, amino acid metabolism and transport, F, nucleotide metabolism and transport, G, carbohydrate metabolism and transport, H, coenzyme metabolism, I, lipid metabolism, J, translation, K, transcription, L, replication and repair, M, cell wall/membrane/envelope biogenesis, N, Cell motility, O, post-translational modification, protein turnover, chaperone functions, P, Inorganic ion transport and metabolism, Q, secondary metabolites biosynthesis, transport and catabolism, T, signal transduction, U, intracellular trafficking and secretion, Y, nuclear structure (not applicable to prokaryotic COGs), Z, cytoskeleton (not applicable to prokaryotic COGs); R, general functional prediction only (typically, prediction of biochemical activity), S, function unknown. The numbers were obtained after subtracting the COGs that consisted entirely of proteins from unicellular eukaryotes from the COG collection.

Roman L Tatusov, et al. BMC Bioinformatics. 2003;4:41-41.

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