prokaryote name: Aeropyrum pernix

COG 0013 - alanyl-tRNA synthetase

    Prokaryotes and genes in the set:
  1. Aeropyrum pernix, APE2166
  2. Methanococcus jannaschii, MJ0564
  3. Archaeoglobus fulgidus, AF2255
  4. Methanothermobacter thermautotrophicus, MTH1683
  5. Thermoplasma acidophilum, TA0849
  6. Halobacterium sp. NRC-1
    Command line options for FootPrinter:
    FootPrinter.exe cog0013 cog0013.tree -size 4 -max_mutations 1 -loss_cost 1 -subregion_size 20 -compute_branch_lengths -losses universal6.config -sequence_type upstream -position_change_cost 1 -no_ps -no_txt
  • allow losses of the motif in the subtrees
  • motif size=4
  • persimony score=1
  • subregion size =20
Raw results: cog0013.html
    Motifs(same colorcoding as in the tree scheme):
  1. TGAC or TAAC
  2. AGGA or AGGT
  3. TATA
  4. GGTT
Note: the first and second motifs, the third and second, the third and fourth and the third and the first, conserve relative order of appearance in 4 out of 6 microbesThe first motif is present in all 6 species. Unfortunatly all motifs are too short. DIALIGN didn't find these motifs, but it fount one similar to the red motif (ATAT )at a different position.

COG0060 - isoleucyl-tRNA synthetase

    Prokaryotes and genes in the set:
  1. Aeropyrum pernix, APE0374
  2. Pyrococcus abyssi, PAB0616
  3. Pyrococcus horikoshii, PH1065
  4. Archaeoglobus fulgidus, AF0633
  5. Halobacterium, VNG2190G
  6. Thermoplasma volcanium, TVN0829
  7. Thermoplasma acidophilum, Ta0879
  8. Chlamydia trachomatis, CT019
  9. Treponema pallidum, TP0452
  10. Mycobacterium leprae, ML1195
  11. Mycobacterium tuberculosis, Rv1536
    Command line options for FootPrinter :
    FootPrinter.exe cog0060_1 cog0060.tree -size 4 -max_mutations 1 -loss_cost 1 -subregion_size 20 -compute_branch_lengths -losses universal6.config -sequence_type upstream -position_change_cost 1 -no_ps -no_txt
  • allow losses of the motif in the subtrees,
  • motif size 4
  • persimony score=1
  • subregion size =20

Raw results: cog0060_1.html
    Motifs(same colorcoding as in the tree scheme):
  1. TCGG or TCGA or TCGG
  2. CGAC or CGAA
  3. GCTC or GTGT
In 5 of these related species 2 motifs always overlap which might suggest that they share a longer motif : TCGAC or TCGAA this motif conserves position pretty well - about 50 bps from the 3-prime end. All 3 motifs appear in the same same subtree and in the same relative order - yellow, blue, red except the cases when yellow and blue overlap. DIALIGN or CLUSTALW didn't find these motifs.
A change in subregion size yealds additional motif which exists in all sequences, though at widely varying positions:
Raw results: cog0060.html
  1. GGCC or GGCA or GGCG

COG0495 - leucyl-tRNA synthetase

    Prokaryotes and genes in the set:
  1. Archaeoglobus fulgidus, AF2421
  2. Methanococcus jannaschii, MJ0633
  3. Pyrococcus abyssi, PAB1782
  4. Aeropyrum pernix, APE1015
  5. Pyrococcus horikoshii, PH0965
    Command line options for FootPrinter :
    FootPrinter.exe cog0495 cog0495.tree -size 5 -max_mutations 1 -loss_cost 1 -subregion_size 20 -compute_branch_lengths -losses universal6.config -sequence_type upstream -position_change_cost 1 -no_ps -no_txt
  • allow losses of the motif in the subtrees,
  • motif size 5
  • persimony score=1
  • subregion size =20

Raw results: cog0495.html 
PYROCOCCUS_HORIKOSHII  AACAT --------------|
                                           |-------|
PYROCOCCUS_ABYSSI AACAT  ------------------|       |
                                                   |-----------|
METHANOCOCCUS  AACAT   ----------------------------|           |
                                                               |---------------
ARCHAEOGLOBUS   -------------------|                           |
                                   |---------------------------|
AEROPYRUM       -------------------|
    Preserved across 1 subtree motif:(same color as in the tree scheme of the results file):
  1. AACAT
DIALIGN or CLUSTALW didn't find this motif.
Note about Footprinter version for Windows: -no_interactive_html option isn't recognized. Also the gif subdirectory is created in the directory which holdes the sequences file, but the actual gifs are created in the subdirectory of the footprinter directory. I.e. if input file is: "footprinter/in/cog0013" then gifs are in "footprinter/cog0013gif" directory but the html file refers to "footprinter/in/cog0013gif" directory.