Burkholderia Gene Search
Search by: Locus G Gene Symbol S b l Common Name All Annotation
Gene Page : NT01BPA0352
General Gene Page Organization 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
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 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 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 All of the p proteins in Pathema are routinely y blasted
against one another and the blast results are stored in the database. When a new genome is added to the database the all
vs. allll searches h are re-run. 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 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: Find the best potential Open Reading Frames (ORFs) in this sequence based b d on third hi d position ii GC Skew. This tool works only in GC rich organisms because position 1 & 2 are constrained t i d by b the th genetic ti code, so the 3rd position is the only one where the higher GC content can exist.
Frame 1
ATGATGAG TACTACTAC
Frame 5
Frame 2
ATGATGATG TACTACTAC
Frame 4
Frame 3
ATGATGATG TACTACTAC
Frame 6
Gene Page : 3rd Position GC Skew
Highlighted Gene Tools & Lists
Highlighted Gene Tools & Lists
Burkholderia Blast
Highlighted Gene Tools & Lists
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? We ea are e 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 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 ABC: the ATP-binding ATP binding cassette superfamily MFS: the major facilitator superfamily MOP: the multidrug/oligosaccharidyl-
lipid/polysaccharide flippase superfamily RND: the resistance/nodulation/cell division superfamily - SMR: the small multidrug resistance subfamily
Organis sms
Drug Efflux Transporters 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?
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