Burkholderia Gene Search

Search by:
Locus
G
Gene Symbol
S b l
Common Name
All Annotation
Gene Page : NT01BPA0352
General Gene Page Organization
ƒ Annotation Display
à Functional Curation Datatypes
- Putative identification, Gene symbol, EC #

- GO terms and Cellular role category

- Gene/protein length, coordinates, MW, pI

- Comments and additional supporting

pp g information
- Genome Properties

- Community
C i curation
i

ƒ Column Task Bar

Gene Page : NT01BPA0352
Gene Page : NT01BPA0352
Gene Page : Gene Ontology Display
The Gene Ontology: AmiGO

The Gene
Th G Ontology
O t l
http://www.geneontology.org/
Gene Page : NT01BPA0352
Community Curation Tool
Community Curation Example

Notation for:
Pending
Approved
General Gene Page Organization
ƒ Column Task Bar
à Annotation
- Annotation Display

- Nucleotide and protein sequence

- Pubmed search results

- Gene Ontology

à Evidence
à Analysis
Gene Page : Sequences
Gene Page : PubMed Search
General Gene Page Organization
ƒ Column Task Bar
à Annotation

à Evidence
- Gene Graphic
- TIGRFAM & PFAM matches
- Identification Alignment
- TmHMM Information
- COG Display
- Membrane Protein Information
- Protein vs All Alignment
- Region View / Compare Regions
à Analysis
a ys s
Gene Page : Gene Graphic
Gene Page : TIGRFAM & Pfam
Gene Page : Identification Alignment
Gene Page : TmHMM

The Center for Biological Sequence Analysis

Technical University of Denmark
http://www.cbs.dtu.dk/services/TMHMM/
Gene Page : COGs

Clusters of Orthologous Groups of proteins (COGs)

NCBI
http://www.ncbi.nlm.nih.gov/COG/
Gene Page : Membrane Protein

Currently not functional

 All vs. Protein Alignment
g
ƒ All of the p
proteins in Pathema are routinely
y blasted
against one another and the blast results are stored
in the database.

ƒ When a new genome is added to the database the all

vs. allll searches
h are re-run.

ƒ The information from the All vs.

s All blast searches is
displayed throughout Pathema for cross genome
analyses.
analyses
Gene Page : Protein vs All Alignment
 Pairwise Alignment Example

Summary statistics
off all
ll alignments
li t

Detailed statistics
of each alignment

Query nucleotide
sequence
Query protein translation
M t h protein
Match t i alignment
li t
Multiple Sequence Alignment
E
Example
l
Gene Page : Region View
Gateway Page
Gene Page : Compare Regions
General Gene Page Organization
ƒ Column Task Bar
à Annotation
A t ti
à Evidence

à Analysis
- Ge
Gene
e Codo
Codon Count
Cou t
- GC Content Display

- 3rd Postion GC Skew

- Primer Search
Gene Page : Gene Codon Count
Gene Page : GC Content Display
 Gene Page : 3rd Position GC Skew
Purpose:
Frame 1
Find the best potential Open ATGATGAG
Reading Frames (ORFs) in this TACTACTAC
Frame 5
sequence based
b d on third
hi d position
ii
GC Skew. Frame 2
ATGATGATG
This tool works only in GC rich TACTACTAC
organisms because position 1 & 2 Frame 4
are constrained
t i d by b the
th geneticti
code, so the 3rd position is the only Frame 3
ATGATGATG
one where the higher GC content TACTACTAC
can exist. Frame 6
Gene Page : 3rd Position GC Skew
Highlighted Gene Tools & Lists
Highlighted Gene Tools & Lists
Burkholderia Blast
Highlighted Gene Tools & Lists
ƒ Future capabilities
p of TCHAR:
à Integrate into the CMR
à Public availability: exportable/downloadable & BLASTable
Pathogenicity
LLNL Virulence Database
Pathogenicity
Burkholderia Virulence Factors
Comparative Analysis
Functional Genomics
htt // f
http://pfgrc.tigr.org/
ti /
Mobile Elements
Latest Publications
Favorite Tools
What is the future of Pathema?
ƒ Weea
aree relying
ey go on you
your feedback!
eedbac
à Genome sequence analysis
à Data exchange
à Custom data analysis
à Custom
C t ttooll development
d l t

ƒ Continued data curation

à Burkholderia Epitopes
à Burkholderia mallei virulence factors
à Other specialized gene lists …
Transporter Comparisons across Burkholderia Species
 Mutidrug
g Efflux Transporter
p Families

ƒ ABC: the ATP-binding

ATP binding cassette superfamily
ƒ MFS: the major facilitator superfamily
ƒ MOP: the multidrug/oligosaccharidyl-
lipid/polysaccharide flippase superfamily
ƒ RND: the resistance/nodulation/cell division
superfamily
- SMR: the small multidrug resistance subfamily
 Drug Efflux Transporters
sms
Organis Burkholderia sp. 383
Burkholderia pseudomallei 305
Burkholderia pseudomallei K96243
Burkholderia cenocepacia AU 1054
Burkholderia thailandensis E264
Burkholderia pseudomallei S13

Burkholderia pseudomallei Pasteur

Burkholderia pseudomallei 668
B kh ld i pseudomallei
Burkholderia d ll i 406e
406
Burkholderia pseudomallei 1710b
Burkholderia pseudomallei 1710a
Burkholderia pseudomallei 1655
Burkholderia pseudomallei 1106b
Burkholderia pseudomallei 1106a
Burkholderia mallei PRL-20
Burkholderia mallei 2002721280
Burkholderia mallei JHU

Burkholderia mallei FMH

Burkholderia mallei 10399
ABC
Burkholderia mallei NCTC10247 MFS
Burkholderia mallei 10229 RND

Burkholderia mallei SAVP1 MOP

DMT(SMR)
Burkholderia mallei ATCC 23344

0 50 100 150 200 250

T
Transporter
t Count
C t
 Questions?
Comments?
Sugges o s
Suggestions?

Burkholderia@tigr.org