Additional file 1:

ATP synthase superfamily for 13 gamma proteobacteria. Superfamily of ATP synthases alpha and beta subunits, flagella and type III secretion system ATPases, and Rho-termination factors. The superfamily was assembled by all-to-all BLAST searches; BranchClust was applied with MANY/FEW = 8.

Format: JPEG Size: 27KB Download file

Additional file 2:

ATP synthase superfamily for 30 bacteria and archaea. Superfamily of ATP synthases alpha and beta subunits, flagella and type III secretion system ATPases, and Rho-termination factors. The superfamily was assembled by all-to-all BLAST searches; BranchClust was applied with MANY/FEW = 10.

Format: JPEG Size: 61KB Download file

Additional file 3:

ATP synthase superfamily for 317 bacteria and archaea. Superfamily of ATP synthases alpha and beta subunits, flagella and type III secretion system ATPases, and Rho-termination factors. The superfamily was assembled by on-to-all BLAST searches using genome of Escherichia coli K12 as a starting genome; BranchClust was applied with MANY/FEW = 150.

Format: JPEG Size: 52KB Download file

Additional file 4:

Superfamily of cell division proteins, ribonucleases E, ATP synthase chain B and hypothetical proteins for 13 gamma proteobacteria. The superfamily was assembled by all-to-all BLAST searches; BranchClust was applied with MANY/FEW = 8.

Format: PNG Size: 180KB Download file

Additional file 5:

Superfamily DNA topoisomerase IV subunit B and DNA gyrase subunit IV for 13 gamma proteobacteria. The superfamily was assembled by all-to-all BLAST searches; BranchClust was applied with MANY/FEW = 8.

Format: PNG Size: 37KB Download file

Additional file 6:

Superfamily of signal recognition particle proteins, chromosomal replication initiators, insertion sequence protein for 13 gamma proteobacteria. The superfamily was assembled by all-to-all BLAST searches; BranchClust was applied with MANY/FEW = 8.

Format: PNG Size: 190KB Download file

Additional file 7:

Superfamily of elongation factors, peptide chain release factors and GTP-binding proteins for 13 gamma proteobacteria. The superfamily was assembled by all-to-all BLAST searches; BranchClust was applied with MANY/FEW = 8.

Format: PNG Size: 323KB Download file

Additional file 8:

Superfamily of methyltransferases for 13 gamma proteobacteria. The superfamily was assembled by all-to-all BLAST searches; BranchClust was applied with MANY/FEW = 8.

Format: PNG Size: 131KB Download file

Additional file 9:

Superfamily of universal stress protein and amino-acid transporters for 14 archaea. The superfamily was assembled by all-to-all BLAST searches; BranchClust was applied with MANY/FEW = 8.

Format: PNG Size: 243KB Download file

Additional file 10:

Superfamily of kinases for 14 archaea. The superfamily was assembled by all-to-all BLAST searches; BranchClust was applied with MANY/FEW = 8.

Format: PNG Size: 52KB Download file

Additional file 11:

Superfamily of aminotransferases for 14 archaea. The superfamily was assembled by all-to-all BLAST searches; BranchClust was applied with MANY/FEW = 8.

Format: PNG Size: 227KB Download file

Additional file 12:

Superfamily of potential transcriptional regulators for 14 archaea. The superfamily was assembled by all-to-all BLAST searches; BranchClust was applied with MANY/FEW = 8.

Format: PNG Size: 80KB Download file

Additional file 13:

Superfamily of potential transcriptional regulators for 14 archaea. The superfamily was assembled by all-to-all BLAST searches; BranchClust was applied with MANY/FEW = 8.

Format: PNG Size: 287KB Download file

Additional file 14:

Superfamily of reductases, dehydrogenases, NADH oxidases for 16 bacteria and 14 archaea. The superfamily was assembled by all-to-all BLAST searches; BranchClust was applied with MANY/FEW = 24.

Format: PNG Size: 341KB Download file

Additional file 15:

Superfamily of translation elongation factors, peptide chain release factors and GTP-binding proteins for 16 bacteria and 14 archaea. The superfamily was assembled by all-to-all BLAST searches; BranchClust was applied with MANY/FEW = 24.

Format: PNG Size: 255KB Download file

Additional file 16:

Superfamily of replication factors C and DNA polymerases III for 16 bacteria and 14 archaea. The superfamily was assembled by all-to-all BLAST searches; BranchClust was applied with MANY/FEW = 24.

Format: PNG Size: 52KB Download file

Additional file 17:

Superfamily of ATP dependent RNA and DNA helicases for 16 bacteria and 14 archaea. The superfamily was assembled by all-to-all BLAST searches; BranchClust was applied with MANY/FEW = 24.

Format: PNG Size: 187KB Download file

Additional file 18:

Superfamily of ABC transporters for 16 bacteria and 14 archaea. The superfamily was assembled by all-to-all BLAST searches; BranchClust was applied with MANY/FEW = 24.

Format: PNG Size: 1.4MB Download file