Skip to main content

Table 3 RGP sites (genes flanking RGPs on the right or left) conserved in the P. luminescens TT01 (Pl), P. asymbiotica ATCC43949 (Pa), X. nematophila ATCC19061 (Xn) and X. bovienii strain SS-2004 (Xb) genomes.

From: Units of plasticity in bacterial genomes: new insight from the comparative genomics of two bacteria interacting with invertebrates, Photorhabdus and Xenorhabdus

  location sites * Xn Xb Pl Pa
  yjeS_tRNA-gly GI10 GI7 GI103 core genome
  ampH_tRNA-leu GI89 GI10 GI100 P95
  yjdC_tRNA-phe P75 GI23 GI94 GI23
  folD_tRNA-arg P75 P22bis GI95 GI25
  rpoD_tRNA-met P88 GI29 GI88 P86
  ylaC_tRNA-ans GI36 GI29 inside GI44 inside GI64
  ghrA_tRNA-ser GI45 GI33 GI49 GI60
tRNA gene integration site pgsA_tRNAleu_tRNAcys GI56 P46 GI47 GI61
  yjeM_tRNA-pro GI69 GI52 GI71 P39
  mltC_tRNAphe GI69 GI64 GI27 GI81
  gltX_tRNA-val_2tRNAlys_3tRNA-val GI71bis GI59 GI33 GI35
  vacJ_tRNA-arg GI71bis inside GI55 GI76 inside GI35
  rsmC_tRNA-leu GI76 GI67 GI95 GI13
  yccK_tRNA-ser P43 GI16 GI44 GI64
  aroH not present RGP43 RGP64 RGP48
  asmA/hisL RGP32 core genome RGP38 RGP68
  cheZ RGP35 RGP30 RGP45 RGP63
  cpxA/cysE GI2 RGP83 GI110 GI104
  cpxP RGP1 RGP82 GI109 P103
  cspE RGP28bis GI61 RGP31 RGP62
  deaD core genome RGP8 RGP101 RGP96
  dnaB/zur RGP84 P77 RGP96 RGP94
  dnaJ RGP17 RGP27 RGP17 inside RGP15
  dnaQ GI78 core genome GI26 GI22
  dxs GI22 GI25 core genome RGP82
  ecfL P88 GI76 GI88 P86
  eno GI20 RGP71 RGP25 inside GI21
Protein encoding gene integration site exbD RGP79 RGP26 RGP87 RGP84
  fbaA RGP65 RGP58 GI27 GI23
  fis GI20 RGP73 RGP92 RGP89
  flgL GP37 G I31 RGP46 GP62
  flgN G I38 GP30 GP45 GP63
  flhD G I36 G I29 G I44 GI64
  fliR GI37 RGP48 RGP46 RGP62
  TfrdA/yhhQ RGP15 core genome RGP93 RGP90
  gcvP RGP25 core genome GI81 GI27
  glnG RGP95 core genome RGP5 RGP5
  glnS RGP29 inside RGP22 GI32 RGP73
  glpD RGP96bis RGP2 GI3bis GI3
  gntX (yhgH) RGP97 RGP3 RGP4 RGP4
  gyrB/glmS RGP0 RGP0 P0 P0
  hrpA RGP49bis RGP38 RGP52 GI57
  kdpE RGP29 RGP22 GI33 RGP73
  leuB RGP22bis GI65 RGP85bis core genome
  lysS P26 GI64 P80 GI28
  malM GI91 core genome GI12 GI10
  mdtA core genome RGP48 GI68 RGP43
  mdtC/icd RGP60 GI49 GI69 GI42
  mltD RGP77 GI57 RGP25 GI21
  mobB GI91 RGP81 core genome RGP8
  nagC/ubiG core genome GI60 core genome GI75
  nhaA GI79 RGP27 RGP17 RGP15
  nth/yciH GI50 core genome GI56 RGP54
  pbgE RGP40 RGP43 RGP64 RGP48
  pckA RGP100 RGP1 RGP3 RGP3bis
  pgpA RGP19 GI25 core genome RGP82
  phoU RGP95 RGP4 RGP5 RGP5
  pntB RGP49 GI37 RGP53 inside GI57
  ppx core genome P32 GI68 RGP43
  prlC RGP96 RGP2 GI3bis GI3
  prmB RGP71 RGP55 RGP75 GI35
  pta GI63 RGP53 GI73 RGP37
  purC core genome P46 RGP67 RGP45
  purK core genome GI59 RGP86 RGP24
  putP GI36 P32 GI47 GI61
  rpmG RGP4 core genome RGP111 RGP105
  rpoC RGP94 core genome GI12 GI10
  rpoH RGP16 RGP14 RGP92 RGP89
  rpoS RGP81 core genome RGP22 RGP19
  rrmA/guaA RGP42 RGP44 RGP66 core genome
  sbcC RGP17 RGP26 RGP87 RGP84
  smpB RGP72 core genome P80 GI28
  sprT GI22 RGP71 GI85 GI25
  thiH RGP12 RGP79 RGP13 bis RGP11
  thrS GI39 core genome RGP65 RGP47
  tldD RGP19 core genome RGP90 RGP88
  tpiA GI5 RGP82 GI109 P103
  trmE RGP100 P85 RGP112 RGP106
  typA RGP99 RGP5 core genome RGP6
  tyrB core genome GI76 GI95 RGP93
  ung/srmB RGP73 core genome GI79 GI29
  uvrY GI57 RGP47 RGP48 inside GI61
  valS RGP90 RGP9 RGP101 RGP96bis
  xseA P43 RGP45 RGP67 RGP45
  yafK RGP66 GI63 RGP28 RGP79
  ybhL/folE GI31 RGP20 GI37 RGP69
  yccR RGP35 GI16bis core genome GI64
  ychM inside GI45 GI33 GI49 GI60
  yfaE RGP65 P15 RGP72 RGP38
  yfiF RGP28bis GI61 RGP31 core genome
  ygdE RGP86 GI10 core genome RGP16
  yheS RGP93 core genome RGP11 GI9
  yhgF RGP96 RGP3 RGP4 inside RGP4
  yicC GI5 P85 RGP112 RGP106
  yjeP core genome RGP81 RGP104 RGP98
  ynfK core genome GI37 RGP54 GI57
  1. *location sites are listed when they are conserved in at least three of the genomes panel.
  2. When the two RGP flanking genes are conserved, the gene pair is indicated as location site. If note, each flanking gene is considered as potential location site.