q-motif - background

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

Publicly accessible motifs that describe the repeating sequence

DUF 285: “mycoplasmal protein…”

TIGR 02167: “26 AA repeat/mycoplasma”

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

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

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?

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

Location of DUF 285 motifs

Ostreococcus transmembrane protein

Salinibacter transmembrane protein

Mycoplasma Lipoprotein Q

Alignment of tandemly arranged “regions” of representative Ostreococcus ORF designated “DUF285”

(Workbench ClustalW)

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

Tree of BLAST best hits (query=Salinibacter YP446962) (0.75)

Tree of BLAST best hits (query=Salinibacter YP446962) (0.65)

Salinibacter DUF285 ORF topology features

Ostreococcus DUF285 ORF topology features