Download - Q-motif - background
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Q-motif - backgroundFirst description of a 25 amino acid peptide motif:
LppQ Lipoprotein from M. mycoides subsp. mycoides SC E-M. Abdo, J. Nicolet, and J. Frey, Clin. and Diagn. Lab. Imm. (2000)
LP-Signal
W D T S N I V S M S S M F Q Q A R N F N Q V L S N W N T E N V T D M N Y M F D G A T K F N S D L S SW K T A N V K T M R S M F S D T K Q F N Q D I S SW N V S N V K N M K N M F Y R A E K F N K S L S DW N L K N I Q E L D H M F F G A S E F N S D I F KW D V S K V V N M D S M F N G A H D F N Q N I T NW N V S N V K T M R S M F S D T K Q F N Q D I K NW R V D N V T D M D R M F Q N A L S F N K D I S S
W x x x x V x x M x x M F x x x x x F N x x I x x I L L
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Publicly accessible motifs that describe the repeating sequence
DUF 285: “mycoplasmal protein…”
TIGR 02167: “26 AA repeat/mycoplasma”
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16S rRNA phylogeny vs whole genome phylogeny
Myc
op
lasm
a s
ub
gro
up
s M. pnemoniae clade
Spirolasma-M.mycoides clade
M. hominis clade
Phytoplasma asteris OY strain
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16S rRNA phylogeny vs whole genome phylogeny
Myc
op
lasm
a s
ub
gro
up
s M. pnemoniae clade
Spirolasma-M.mycoides clade
M. hominis clade
Phytoplasma asteris OY strain
DUF285 occurs in some taxa on these branches
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Questions arising from initial observations
Evidence for HGT?
How widely dispersed among species?
Degree of similarity among disparate seq?
Seq diversity of reps within/between ORFs?
Clues to function by protein features?
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Distribution of DUF285
(NCBI search for the DUF)
-Includes Eukayote Minimal Green Alga Ostreococcus CAL57751
Also includes an Archeae Salinibacter (plasmid) YP446962
-GOALS:
-Compare prototype ORFs from each of 3 phylogenetic domains
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Location of DUF 285 motifs
Ostreococcus transmembrane protein
Salinibacter transmembrane protein
Mycoplasma Lipoprotein Q
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Alignment of tandemly arranged “regions” of representative Ostreococcus ORF designated “DUF285”
(Workbench ClustalW)
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Sample Blast Analysis
• TIGR2167_motif vs. Ostreococcus• Length = 26 • Score = 26.6 bits (57), Expect = 5e-04 Identities = 12/26
(46%), Positives = 20/26 (76%), Gaps = 1/26 (3%)
• 1024 MFSNSTAFNQ--DISNWNTASVTNMAS 1048 • MFS ++ D+SN++ T++ VTNM+S • 1 MFSGCSSLTSLDVSNFDTSNVTNMSS 26
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Tree of BLAST best hits (query=Salinibacter YP446962) (0.75)
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Tree of BLAST best hits (query=Salinibacter YP446962) (0.65)
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Salinibacter DUF285 ORF topology features
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Ostreococcus DUF285 ORF topology features