Database conventions
Text
Search
In order to start
a test search, you must first select one interested
field from the cascade menu above. There are four
options:
General information includes the characteristics
and disease caused by the pathogens, as well as the
general information of each genus.
Virulence factors include the name, full name,
characteristics, structure, function and mechanism
of each VFs.
Pathogenicity islands include the name, full
name, locus feature, phenotype and remark information
of each PAIs.
Gene refers the name and product description
of each VFs related gene (includes those genes located
in PAIs).
Comparative pathogenomics refers the names
of all VFs and related genes involved in the comparative pathogenomics
datasets.
Then, input the query
texts in the entry box and click the 'Search' button
below. You can input either a single keyword or multiple
alternative keywords separated by blanks.
Note that here alternative means any
keyword match will be reported to the users by default.
If you do need to
search the database by complex phrases that contain
blanks, please enclose them into double quotation
marks ("). For example, in order to use
'M protein' as one of the keywords to search the database,
you should input "M protein" instead
of just input M protein.
Please also pay attention
to the following search conventions:
By default, the search engine is case insensitive.
The search engine only report results with whole
words matches to the given keywords. For example,
the word 'pathogenicity' will NOT treat as good match
to the keyword 'pathogenic' by the search engine.
Hence, you might need to try more keywords sometimes.
In order to avoid numerous stochastic matches, those
input keywords with length less than 3
characters will be automatically ignored
by the search engine.
Any non-words special characters, such as semicolon,
are treated as invalid by the search engine and will
be removed automatically.
Figure
legends of circular and linear maps
In circular maps, each
ORF was represented as a small colored triangle around the
circle. Location in outer circle (red) and inner circle (blue) represent
genes located in leading and lagging strands, respectively.
In linear maps, the
meanings of all types of symbols are listed below:
Symbols
representations |
|
Symbols
|
Explain |
|
|
ORF with the arrow direction indicates
its coding strand, and the gene name is
displayed above the ruler. There is a cross
over the arrow if it's a pseudogene. |
|
|
tRNA gene and its type is displayed above. |
|
|
IS element and its type is displayed below. |
|
|
The ORFs in linear maps
were colored by its function category in COGs:
Color
representations |
|
Code |
|
Color
|
|
Function |
|
|
Information storage and processing |
|
J
|
|
|
|
Translation, ribosomal structure
and biogenesis |
|
|
|
A
|
|
|
|
RNA processing and modification |
|
|
|
K
|
|
|
|
Transcription |
|
|
|
L
|
|
|
|
Replication, recombination
and repair |
|
|
|
B
|
|
|
|
Chromatin structure and dynamics
|
|
|
|
|
Cellular processes and signaling |
|
D
|
|
|
|
Cell cycle control, cell division and chromosome partitioning |
|
|
|
V
|
|
|
|
Defense mechanisms
|
|
|
|
T
|
|
|
|
Signal transduction mechanisms
|
|
|
|
O
|
|
|
|
Posttranslational modification,
protein turnover, chaperones |
|
|
|
M
|
|
|
|
Cell wall/membrane/envelope biogenesis
|
|
|
|
N
|
|
|
|
Cell motility |
|
|
|
W
|
|
|
|
Extracellular structures
|
|
|
|
U
|
|
|
|
Intracellular trafficking, secretion, and vesicular transport |
|
|
|
|
Metabolism |
|
C
|
|
|
|
Energy production and conversion |
|
|
|
G
|
|
|
|
Carbohydrate transport and
metabolism |
|
|
|
E
|
|
|
|
Amino acid transport and metabolism |
|
|
|
F
|
|
|
|
Nucleotide transport and metabolism |
|
|
|
H
|
|
|
|
Coenzyme transport and metabolism |
|
|
|
I
|
|
|
|
Lipid transport and metabolism |
|
|
|
P
|
|
|
|
Inorganic ion transport and
metabolism |
|
|
|
Q
|
|
|
|
Secondary metabolites biosynthesis,
transport and catabolism |
|
|
|
|
Poorly characterized |
|
R
|
|
|
|
General function prediction
only |
|
|
|
S
|
|
|
|
Function unknown |
|
|
|
Table reproduced
from COG database
|
|