Q-motif - background
First 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
W
W
W
W
W
W
W
D
N
K
N
N
D
N
R
T
T
T
V
L
V
V
V
S
E
A
S
K
S
S
D
N
N
N
N
N
K
N
N
I
V
V
V
I
V
V
V
V
T
K
K
Q
V
K
T
S
D
T
N
E
N
T
D
M
M
M
M
L
M
M
M
S
N
R
K
D
D
R
D
S
Y
S
N
H
S
S
R
M
M
M
M
M
M
M
M
F
F
F
F
F
F
F
F
Q
D
S
Y
F
N
S
Q
Q
G
D
R
G
G
D
N
A
A
T
A
A
A
T
A
R
T
K
E
S
H
K
L
N
K
Q
K
E
D
Q
S
F
F
F
F
F
F
F
F
N
N
N
N
N
N
N
N
Q
S
Q
K
S
Q
Q
K
V
D
D
S
D
N
D
D
L
L
I
L
I
I
I
I
S
S
S
S
F
T
K
S
N
S
S
D
K
N
N
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”
Mycoplasma
subgroups
16S rRNA phylogeny vs whole genome
phylogeny
M. pnemoniae clade
M. hominis clade
Spirolasma-M.mycoides clade
Phytoplasma asteris OY strain
Mycoplasma
subgroups
16S rRNA phylogeny vs whole genome
phylogeny
M. pnemoniae clade
M. hominis clade
Spirolasma-M.mycoides 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
Mycoplasma Lipoprotein Q
Salinibacter transmembrane protein
Ostreococcus transmembrane protein
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