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Table 2 Representative proteins used to compute Figure 2. Class is the COG functional code [18]. Rank is rank in a list of most conserved proteins (families of orthologs), from 0 to 199, for the set of genomes under study; thus FtsH (rank 2) is more conserved than DNA polymerase I (rank 59). Coeff, S. Dev, and Max are respectively the correlation coefficient, the standard deviation, and the maximum elementwise difference between the scaled distance matrix given by this protein and the consensus distance matrix. Distances for this set of organisms were approximately 0–150. Each sequence was limited to the most conserved 300-long amino acid sequence for the protein.

From: Automatic selection of representative proteins for bacterial phylogeny

Gene Class   Name COG Rank Coeff S.Dev Max
GidA D   glucose-inhibited division protein 0445 23 .92 4.27 11.90
- R   GTP-binding protein 0012 43 .94 3.84 12.43
RuvB L   Holliday junction DNA helicase 2255 19 .89 4.32 12.51
Pnp J   polynucleotide phosphorylase 1185 25 .86 4.94 13.11
PyrG F   CTP synthetase 0504 26 .91 4.19 13.95
LepA N   GTP-binding elongation factor 0481 15 .92 4.88 14.00
DnaX L   DNA polymerase III subunits gamma and tau 2812 86 .90 4.37 14.59
Mfd LK   transcription-repair coupling factor 1197 31 .88 4.82 14.94
UvrB L   DNA excision nuclease subunit B 0556 12 .93 4.44 16.29
InfB J   translation initiation factor IF-2 0532 32 .90 4.59 17.46
Exo L   DNA polymerase I 0258 59 .89 4.85 17.60
PolC L   DNA polymerase III, alpha chain 0587 61 .77 6.43 17.81
RecA L   RecA protein 0468 4 .85 6.22 19.18
GyrA L   DNA gyrase subunit A 0188 10 .88 5.60 19.74
HflB 0   cell division protein FtsH 0465 2 .86 5.29 19.89
ClpX O   ATP-dependent Clp protease, ClpX 1219 13 .89 5.12 20.10
ThrS J   threonyl-tRNA synthetase 0441 33 .77 6.94 20.19
Rho K   transcription termination factor rho 1158 3 .87 5.83 20.20
GroL O   GroEL, chaperone Hsp60 0459 8 .92 5.90 20.35
ClpB 0   ClpB protein 0542 7 .75 6.23 21.01
- R   putative GTP-binding protein 1160 165 .94 7.93 21.07
DnaK 0   dnaK, chaperone Hsp70 0443 5 .81 6.48 21.27
RpSA J   30S ribosomal subunit protein S1 0539 38 .88 8.14 22.48
RpoA K   DNA-directed RNA polymerase alpha chain 0202 102 .91 10.93 32.41
TrxB 0   thioredoxin reductase 0492 66 .87 8.67 32.54
UvrC L   excinuclease ABC subunit C 0322 133 .93 6.67 32.68
NusA K   transcription pausing 0195 106 .83 11.11 39.39
QRI7 O   o-sialoglycoprotein endopeptidase 0533 123 .89 7.53 43.68
YidC N   60 kD inner membrane protein 0706 179 .85 13.69 53.24
SecY N   subunit of translocase 0201 82 .86 8.00 58.78