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Complete analysis of 13 gamma proteobacteria

Complete analysis of 14 archaea

Complete analysis of 30 taxa (16 bacteria and 14 archaea)

Complete analysis of 319 prokaryotic species

 

Here are several examples of clustering of different superfamilies for different number of taxa

 

 Superfamily of ATP synthases for 13 gamma proteobacteria

 

The superfamily consists of ATP synthases subunit A, subunit B, flagellum-specific ATP synthases, transcription termination factor Rho and type III secretion system ATPases.

With paramter MANY=8 BrunchClust produces 4 clusters: 3 clusters contain complete (13 members) families of ATP synthases subunit A, subunit B and transcription termination factor Rho, the last one has incomplete cluster with 10 flagellum-specific ATP synthases and type III secretion system ATPases.

 

List of 13 gamma proteobacteria:  Buchnera aphidicola, Escherichia coli, Haemophilus influenzae, Pasteurella multocida, Pseudomonas aeruginosa, Salmonella typhimurium, Vibrio cholerae, Wigglesworthia glossinidia, Xanthomonas campestris, Xanthomonas axonopodis, Xylella fastidiosa, Yersinia pestis KIM, Yersinia pestis CO92.

BranchClust output        Go to Examples

 

There is some confusion in annotation of ATP synthase’s subunits for bacteria and archaea: the beta chain in bacteria is the catalytic subunit and corresponds to subunit A in archaea and eukaryotic vacuolar type ATPases; the alpha chain, or non-catalytic subunit, in bacteria corresponds to subunit B in archaea. In addition the the archaeal A subunit is sometimes labeled as alpha subunit.  To simplify the diagramatic representation we designate all catalytic subunits, either from bacteria or from archaea as subunit A, or ATP-A, and all non-catalytic subunits as subunit B, or ATP-B.

 

 Superfamily of ATP synthases for 30 taxa (16 bacteria and 14 archaea)

 

     BrunchClust produces 7 clusters: two complete for ATP-A and ATP-B and one incomplete for ATP-F. ATP-A and ATP-B clusters contain paralogs that are also reported as a result of clustering. There are two paralogs on the ATP-A branch – one is of Rhodopirellula baltica and the second is of Methanosarcina acetivorans, and there are three paralogs on the ATP-B branch: two are from the same species as those on the ATP-A branch, i.e. Rhodopirellula baltica and Methanosarcina acetivoran, and the third is from Chlorobium tepidum.

 

List of  30 taxa: 16 Bacteria: Aquifex aeolicus, Bacillus subtilis, Chlorobium tepidum, Corynebacterium glutamicum, Deinococcus radiodurans, Geobacillus kaustophilus, Geobacter sulfurreducens, Gloeobacter violaceus, Nostoc sp., Pseudomonas aeruginosa, Rhodopirellula baltica, Rhodopseudomonas palustris, Streptococcus thermophilus, Streptomyces coelicolor, Thermotoga maritime, Thermus thermophilus, and 14 Archaea: Aeropyrum pernix,Archaeoglobus fulgidus,Haloarcula marismortui, Halobacterium sp.,Methanococcus maripaludis, Methanopyrus kandleri, Methanosarcina acetivorans, Methanothermobacter thermautotrophicus, Nanoarchaeum equitans, Pyrobaculum aerophilum, Pyrococcus abyssi, Sulfolobus solfataricus, Thermococcus kodakaraensis, Thermoplasma acidophilum.

BranchClust output        Go to Examples

 

 Superfamily of ATP synthases for 317 taxa (bacteria and archaea)

 

     BrunchClust produces 4 clusters: two complete for ATP-A and ATP-B, one incomplete for Rho-termination factor and one incomplete with both ATP-F and ATP III.. All four clusters contain paralogs that are also reported as a result of clustering.

 

For information about taxa, see gi_numbers.out file in the Examples.

 

BranchClust output        Go to Examples

 
 Superfamily of penicillin-binding proteins for 13 gamma proteobacteria

 

   BranchClust produces 2 clusters: one complete for penicillin-binding protein 3, and  one incomplete for penicillin-binding protein 2. There are two paralogs of Salmonella typhimurium,  in Cluster 1 and in Cluster 2 (red color), and there are two paralogs of Pseudomonas aeruginosa in Cluster 1 (violet color).

 

List of 13 gamma proteobacteria:  Buchnera aphidicola, Escherichia coli, Haemophilus influenzae, Pasteurella multocida, Pseudomonas aeruginosa, Salmonella typhimurium, Vibrio cholerae, Wigglesworthia glossinidia, Xanthomonas campestris, Xanthomonas axonopodis, Xylella fastidiosa, Yersinia pestis KIM, Yersinia pestis CO92.

BranchClust output        Go to Examples

 

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Gogarten Lab Home Page: http://gogarten.uconn.edu/

 

Email to: Maria.Poptsova@gmail.com

 

Page last updated: November 21, 2006