COG3157

Organism	Protein ID	Description
Escherichia coli EDL933	16445223	Z0266 gene product
Vibrio cholerae	15640032	hcp protein
Pseudomonas aeruginosa	15595198:5933394-5933687	secreted protein Hcp
Pseudomonas aeruginosa	15595198:1644725-1645211	secreted protein Hcp
Pseudomonas aeruginosa	15595198:297561-297861	secreted protein Hcp

Parameters:

-details -triplet_filtering -post_filtering -size 7 -max_mutations 2 -max_mutations_per_branch 1 -sequence_type upstream -subregion_size 100 -position_change_cost 1

URL:

http://abstract.cs.washington.edu/~blanchem/FootPrinterWeb/__webquery__.fasta0.1309668974837060.359234229181297.main.html

Motifs found:

Motif #1
Parsimony score: 2.00
AERUGINOSA2       -271  tgtgcaa
AERUGINOSA3       -271  tgtgcaa
AERUGINOSA1       -280  tgtgcaa
AERUGINOSA1       -176  tgtgcaa
ECOLI             -116  tgtaaaa
VIBRIO            -102  tgtgaaa

Motif #2
Parsimony score: 2.00
AERUGINOSA2        -16  acaagga
AERUGINOSA3        -16  acaagga
AERUGINOSA1        -16  acaagga
ECOLI             -101  aaaatga
VIBRIO             -28  aaaatga

Motif #3
Parsimony score: 2.00
AERUGINOSA2        -15  caaggaa
AERUGINOSA3        -15  caaggaa
AERUGINOSA1        -15  caaggaa
ECOLI              -15  caaggag
VIBRIO            -182  caagcaa
VIBRIO             -14  aaaggaa

Motif #4
Parsimony score: 2.00
AERUGINOSA2       -246  tgtggat
AERUGINOSA3       -246  tgtggat
AERUGINOSA1       -245  tgtggat
ECOLI             -122  tttgtat
VIBRIO             -76  tttgtat

Motif #2 was also found in HW 4 (using DiAlign). I could not get Footprinter to find any other motifs that I found in HW 4 (which were all found with DiAlign).

COG1049

Organism	Protein ID	Description
Neisseria meningitidis Z2491	15793034	aconitate hydratase
Vibrio cholerae	15640032	aconitate hydratase 2
Pseudomonas aeruginosa	15595198:1937644-1937944	aconitate hydratase 2
Pasteurella multocida	15601865	AcnB
Xylella fastidiosa	15836605	aconitate hydratase 2
Neisseria meningitidis MC58	15675948	aconitate hydratase 2
Helicobacter pylori 26695	15644634	aconitase B (acnB)
Helicobacter pylori J99	15611071	aconitate hydratase
Campylobacter jejuni	15791399	aconitate hydratase

Parameters:

-details -triplet_filtering -post_filtering -size 9 -max_mutations 3 -max_mutations_per_branch 2 -losses /homes/gws/blanchem/FootPrinterWeb/universal9loose.config -compute_branch_lengths -loss_cost 2 -sequence_type upstream -subregion_size 100 -position_change_cost 0.5

URL:

http://abstract.cs.washington.edu/~blanchem/FootPrinterWeb/__webquery__.fasta0.402899996273010.183616094276644.main.html

For this set of genes, Footprinter found only a few short motifs unless I enabled “Allow regulatory element losses”. After doing so, almost all motifs were found only in the Xylella and Aeruginosa organisms. None of the motifs found in HW4 were found by Footprinter, and vice-versa. The best motifs that I found are given below.

Motifs found:

Motif #1
Parsimony score: 3.00
NEISSERIA         -100  ttaaaa
NEISSERIA          -99  taaaac
NEISSERIA          -77  tacaaa
NEISSERIA          -26  gaaaaa
NEISSERIA2        -100  ttaaaa
NEISSERIA2         -99  taaaac
NEISSERIA2         -77  tacaaa
NEISSERIA2         -26  gaaaaa
CAMPYLOBACTER      -25  taaaaa
CAMPYLOBACTER      -24  aaaaaa
HELICOBACTER       -72  gtaaaa
HELICOBACTER       -71  taaaaa
HELICOBACTER       -13  taaaaa
HELICOBACTER2      -75  gtaaaa
HELICOBACTER2      -74  taaaaa
HELICOBACTER2       -9  gagaaa
PASTEURELLA       -185  gaaaaa
VIBRIO             -10  gaaaaa
AERUGINOSA          -9  gaaata
XYLELLA           -115  gaaata

Motif #2
Parsimony score: 3.00
NEISSERIA          -58  atttaa
NEISSERIA2         -58  atttaa
CAMPYLOBACTER      -17  atttaa
HELICOBACTER       -16  atttaa
HELICOBACTER2      -19  atttaa
PASTEURELLA        -91  ttttaa
VIBRIO            -170  ttttaa
AERUGINOSA        -136  tttgaa
XYLELLA           -192  ttagaa
XYLELLA            -34  ttttaa
XYLELLA            -33  tttaaa
XYLELLA            -25  tatgaa

Motif #3
Parsimony score: 0.00
Significance score: 0.08
Span: 9.39
NEISSERIA          -61  aatatttaa
NEISSERIA2         -61  aatatttaa
CAMPYLOBACTER      -20  aatatttaa