Results for:
> thrS (13815789 -
Threonyl-tRNA synthetase (thrS)) Sulfolobus solfataricus complete genome.
caatactctttgtaacagctaaagatttaagttaaatgacatagcgatatt
> NMB0720 (7225946 -
threonyl-tRNA synthetase) Neisseria meningitidis serogroup B strain MC58 complete
genome.
tgaatgtcagttgggcgacaggggtcgaaatatattttaaaagacggcattataaatgatttcccacggtttttcagacgacatccccaaatcttgccgcaatgttgcataaagaaacgcacatacctcttgcaaaaattaaaacgacccgataaaatgcaaaaattctttgaaggcacgtagctcagttggttagagcaccaccttgacatggtgggggtcgttggttcgaatccaatcgtgcctaccaaattcccataacggcatttatgccgttattttttaatctttcggagcgttt
> HI1367 (1574199 -
threonyl-tRNA synthetase (thrS)) Haemophilus influenzae Rd complete genome.
tttttattccttaactgggtatttaaaagtgcggttattctagcctttatttttaagagataaagcctttagtcagaaaaacattatttcctttttgtaaaatatgggcatttatttaacaatacttcaagaaagtgatagaattcgccacgcattttttgcctaatttcgctcgttcaatggtaggaatgaagccaagtagggcaaaagtgcggttaatttttatagaattttaaatgaacacgtcacctttcgtatgggtgaccactgtataaggaaaaaac
> TP0837 (3323150 -
threonyl-tRNA synthetase (thrS)) Treponema pallidum complete genome.
cgcgctcacatccaaaacagaaagcatcctctactataccctacataccacgtcccttcctacagactgcagtgacggcgcaggcgcactggctcagtgcttcctccaaaacggcgcccattgacaaaccacccataaggtctcacg
> XF0736 (9105624 -
threonyl-tRNA synthetase) Xylella fastidiosa, complete genome.
aggcgccctcctggcgctttttttgttgcttcgcgggaagctcaagattgcattgctgaatgtttgcattgatgcgtcggcattagcatcattgcctgatcctgcttagcagaattcaacaacaatgatccctaaatactcaatatatcaatcgctgacacgccttttatact
For:
> leuC (13815772 - 3-isopropylmalate dehydratase,
large subunit (isopropylmalate isomerase) (alpha IPM isomerase) (IPMI) (leuC))
Sulfolobus solfataricus complete genome.
gtttctttttcggatttagtacgatgtaaatgtaatttcttcgtaagaaatgcttatttattaataattttaactcctta
> VC2492 (9657072 - 3-isopropylmalate
dehydratase, large subunit) Vibrio cholerae chromosome I, complete chromosome.
agtttgagagtggggttaccccactcctctttagctctctgagctcaaggaagaagc
> NMB1036 (7226276 - 3-isopropylmalate
dehydratase, large subunit) Neisseria meningitidis serogroup B strain MC58
complete genome.
ctttcgtctacctctgtgtgttttttgacaagatgcagatgataatgcctttgaaagaatgacgacaagtattctttcgtatcgaatcatgctttagatataactgcttactgaaatggacaatatgtctaatttttttgttaaaattgtttacaaaataacaccgactcaaaaattagacaaaatctgttgcgcggtataaagaatacgtctaaaatccgcccaatccgcattaccatttatccaaaagaacaacatc
> CC0196 (13421319 - 3-isopropylmalate
dehydratase, large subunit) Caulobacter crescentus complete genome.
ggtcaagcttgggtgcaaccacacatagattgacaaaccagcgtttcgtgagaacgtgatgccacccccggcgcttgtcgctcgggcttccagaccgtcttctttctagtggacggccctcttcgggcggagcccatcggcccccgaaggctgaaaacgatgcgagggcgcgccgaaacatgggcgcgccctatgtcgttcggggctgttcgggagactggaaggccacagggcgcaagaaattgtcgcgagcctggggcgccactggattttggcgcacgatccgccctatatccccgcc
> HI0988 (1574017 - 3-isopropylmalate
dehydratase, alpha subunit (leuC)) Haemophilus influenzae Rd complete genome.
atacttgccttcctccgtttacgggggaaggtgcctgaagggcggaagggggcaatctccacccttagttatttagaaatatccccaataaacaggggggacaaagtatttaaagtgcggttgaaaaacacatcgaattttaaccgcacttcccttaacgaatagagaaaaatat
> XF2375 (9107553 - 3-isopropylmalate dehydratase
large subunit) Xylella fastidiosa, complete genome.
Tatcttgagctcattgagtctcatgatttctttgtggactggcctacttgttgggagtctccagatgaatcgcacatgggtttatgccgaggctaagtgccgagtgttcgacactctatatttttggcgtatgggatgacatggtgcgcacgtggagattccacacgaaatcatccaataattctcacatttgaaaatgctgaattcccatgattgatcttgataagctcgctctagtatggttgccaacgaagggtgatatcagtcgccgattgttgtaaccacattaggaattgctgct
For:
> alaS (13813483 - Alanyl-tRNA synthetase (alaS))
Sulfolobus solfataricus complete genome.
aattcttacaaaggataataaaagtaacactttttccgagaaatagtcacattttaaatttgtttttataatacagaatttaatttatggattagtcccttcctcatggaaatcttaaatgaaatcttaatggctatttgttttagaatctaaattacgagaggagtcagtttttaagctttagatacttttctttttattgt
> NMB1595 (7226845 - alanyl-tRNA synthetase)
Neisseria meningitidis serogroup B strain MC58 complete genome.
ttatcattccttgcatatcgggttggagaaagcggccattatagccgatattggcaacagggcttcagacggcattcaaaatcccgccacactcttccgaaaaccgccgcttccatagctagaaacagggatttgcggtaagataccgccgttcgttttccctgcttttaccatgacaagacatttgagagacattgaaaaaat
> CC2529 (13424088 - alanyl-tRNA synthetase)
Caulobacter crescentus complete genome.
ggggcttttggcttgcggcatgcagacgccgcgagcgagcatgcgctggatgcgccgatgtcggccttttccgcatccttgggcggccccaccttcgactcggtttccccttcgccgaaaaccgcgctatgcagcgcccgacttccggccgctcgccggaccggtattcaagactttgagacgctc
> HI0814 (1573826 - alanyl-tRNA synthetase
(alaS)) Haemophilus influenzae Rd complete genome.
ttaacaagaaattgttttttgaataatctgaaataacttaaattttaaccgcacttctcaaatagcgtcgtgaagtgcggttttattttggagttttggcaaaaagcctttttataaatttcaaaaatatgcaaaaatagggcgacttagtttttatttttattatgggtaacaaggattcttttta
> XF0124 (9104908 - alanyl-tRNA synthetase) Xylella
fastidiosa, complete genome.
atcgtgcatgagggaggatgaggattcggctattccgtgtcgtgtttgaaagcgctgctgcaaaccgttgtctatccgcgccacgctgtggcgcatgattgcatgcttgctctcttttctctcctggggttggtgctataaggagacgaattgcaacatgccgtgcatctgatgtggcccccgtttccgtcatgactgagtgatatctatagtgataagggcacactttcgtttgctttgttgctccggtctggtttctggatttcggcgatttgctgcgttgttgcctataacgcagagg
> VC0545 (9654973 - alanyl-tRNA synthetase)
Vibrio cholerae chromosome I, complete chromosome.
Atcgctttcaccctctacattccgcttattaatctcgctctggattttatgcatcttggttgagctgccgctcgccacacattcagtttgcggaagagaagaaactaggcgaactgttatccttgctttacaatagcgcaaaattctaacttgagtatttcaggaagagctg
ClustalW and DALIGN failed to produce any matching motifs, so there is nothing to compare the FootPrinter results to. In working with the parameters, I was unable to find any non-trivial motifs for my prokaryote. For the three cases listed above, all used settings of: size = 10, max mutations = 2, allow losses, significant spanned tree, and a motif loss of 1. I used the tree created by CLUSTALW.
I also performed extensive work with the local version of Footprinter using the tree-of-life and experienced similar results. Additionally, I ran over 1,000 sets of data through FootPrinter – I was not able to automate the phylogenetic tree generation from clustalw. Time constraints and limitations of the text output file prevented any meaningful systematic investigation of the 1,000 sets of results, though a spot check of a few produced promising results.