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Molecular Pathogens 2012, Vol.3, No.1, 1
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of proteins, for example, the uninvestigated GGDEF
domain proteins.
1 Results and Analysis
1.1 The protein sequence characteristics of
Xcc
8004 containing GGDEF domain
According to the sequence alignment, the homology
in the overall amino acid sequences containing the
GGDEF domain in
Xcc
8004 is very low. And the
sequence conservation is not high as the the other
species based on the phylogenetic tree (Figure 1),
which may associate with the functional diversity of
the GGDEF domain proteins.
Figure 1 Phylogenetic tree of GGDEF domain proteins of
Xcc
8004
Note: The tree was constructed based on sequences of
Xcc
8004
GGDEG domain proteins using Maximum likelihood method
of Phylogeny Inference Package (PHYLIP, version 3.69)
1.2 The domain architecture characteristics of
Xcc
8004 containing GGDEF domain
In order to gain more relatively bioinformatics
information on these proteins, we analyze the domain
architecture of them. The domain architecture is
defined as the sequential order of the domains in a
protein, and the common domain architecture is defined
as the architecture shared by more than two proteins.
Both these architectures provide important information
sources for studying proteins and their functions (Geer
et al., 2002; Nikolskaya et al., 2007; Paliakasis et al.,
2008; Byungwook and Doheon, 2009). We used the
Pfam (Finn et al., 2010) and SMART (Letunic et al.,
2009) websites to search the protein sequence of
Xcc
8004. The results showed that there were 32 proteins
containing GGDEF domains in
Xcc
8004. Function of
these proteins were diverse according the previous
reports (Ryan et al., 2007; Ryan et al., 2010; Ryan and
Dow, 2010; Mao et al., 2011), which allowed us to
analyze the domain architecture of the proteins using
bioinformatics web services.
1.2.1 Domain architecture of GGDEF domain
proteins involved in virulence in
Xcc
8004
Ryan et al (2007) found 9 mutants with GGDEF
domain proteins were involved in pathogenesis in
Xcc
8004 by assay the virulence capability of all mutants
with single-gene disruption. We compared the domain
architecture of the proteins encoded by
XC
_
0249
,
XC
_
0420
,
XC
_
0637
,
XC
_
0831
,
XC
_
1036
,
XC
_
1476
,
XC
_
1582
,
XC
_
1841
and
XC
_
2324
(Figure 2). The
results showed that these 9 proteins share little common
domain architecture except
XC
_
1476
and
XC
_
2324
,
which shared the PAS_4
-
GGDEF-EAL architecture.
These 8 specific domain architectures with GGDEF
Figure 2 The domain architectures of GGDEF domain proteins
involved in virulence of
Xcc
8004