This is last version (sequence version 7) of rhodobacter genome: chromosome ( rc.cont.7.gbf ) and plasmid ( rc.pRCB133.7.gbf ). The rest of page is annotation done on version 6. Diference between 6 and 7 is very minor.
- Gaps - diferences between IG version (published in Phot. res.) and final version (in GenBank) ( PDF )
- Gaps - genes in gaps (missed in IG version) - TABLE
- Gaps - genes in gaps (missed in IG version) - KEGG
- Genes duplicated in Rc genome - TABLE (sort by clicking on column head)
manualy currated, sources for annotation: SwissProt, UniProt, InterPro, CDD, Bacterial genomes
- Search in annotation - page
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Edit annotation - page
internal link - only for IMG -
View annotation - page
use random username and password -
CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) !!! NEW (2009-07-03) !!!
main page
private database
use email(username): rhodo@img.cas.cz and password: rhodo
local version
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CRISPR - blast search !!! NEW (2009-08-26) !!!
Search Description blast CAP vs. other Rhodo* Rhodobacter CAPs vs. proteins from Rhodobacter, Rhodobacterales bacterium, Roseobacter, Rhodopseudomonas (all finished genomes) blast CAP vs. Human proteins Rhodobacter CAPs vs. proteins from Homo sap. blast CRISPR vs. GTA sequence Rhodobacter CRISPR na sequences vs. GTA na sequence blast GTA proteins vs. other Rhodo* blast GTA proteins vs. proteins from Rhodobacter, Rhodobacterales bacterium, Roseobacter, Rhodopseudomonas (all finished genomes) blast CRISPR vs. Metagenomic DB Rhodobacter CRISPR na sequences vs. Metagenomic sequence blast CRISPR vs. all DNA sequences DB Rhodobacter CRISPR na sequences vs. all DNA sequences
- Files (special formates)
Replicon GenBank (gbk) Fasta (fna) Fasta (ffn) Fasta (faa) Fasta (frn) GFF (gff) GFF (gff) Table (ptt) Table (rnt) Chromosome (v6) all genome genes proteins RNA CDS RNA CDS RNA Plasmid (v6) all genome genes proteins RNA CDS RNA CDS RNA
- Files (result)
Table HTML PDF CSV Overview table link link link Genome table link link link CDS table - v1 link link link CDS table - v2 link link link RNA table link link link TIGR role table link link link COG table link link link EC table link link link Intergenic space link link link Gene overlaps link link link Exogenouse genes link link link
- Gene groups (for Vaclav Paces) !!! NEW (2009-07-10) !!!
Table HTML PDF CSV GTA
(Gene Transfer Agent - cryptic phage)link link link photosynthesis
(photosynthesis, chlorophyll / porphyrin metabolism, carbon fixation (role=164,191, gene=bch,puf,puh, cog=..., kegg=ko00195,ko00860,ko00710,ko00720))link link link nitrogen
(nitrogen metabolism, fixation, reduction, ... (role=160,179, gene=nif,ure,rnf,anf,nta,nos,ptsN, cog=nitr, kegg=ko00910))link link link RMS
(restriction-modification systems (role=183, product=restr, cog=restr))link link link PHA
(polyhydroxy alcanoate butanoate metabolism (ko00650) - (product=alkanoate,acetoacetyl))link link link electron
(electron transport / oxidative phosphorylation (role=111,112,709, kegg=ko00190))link link link CRISPR
(CRISPR associated proteins (product=CRISP))link link link
- CRISPR elements (for Robert Haselkorn) !!! NEW (2009-07-10) !!!
in rhodo was identified 8 CRISPRs - overview
results of analysis at crispr.u-psud.fr (Email: rhodo@img.cas.cz, Password: rhodo)
schema:
results:Table HTML PDF CSV CRISPR
(Clustered Regularly Interspaced Short Palindromic Repeats)
identified by CRISPRs web-servicelink link link CRISPR
(dump from source page)link link CRISPR
(dump from source page)link
Pathway tools: module PathoLogic, used currated annotation
KEGG: webservice KASS, based on BBH (best bidirectional hits) in KO (KEGG orthologs), bit score cutoff = 50
- Pathway Tools - local version @ img
- Pathway Tools - RHODO analysis @ img
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Pathway Tools - pathway list
exported from Pathway tools -
Pathway Tools - missing reactions
exported from Pathway tools - Pathway Tools (export)
Table File Table File Genes table file Enzymes table file Pathways table file Protcplxs table file Transporters table file BIOPAX table file
- KEGG (KAAS) - KO list (bit=50)
- KEGG (KAAS) - BRITE hierarchies (bit=50)
- KEGG (KAAS) - Pathway maps (bit=50)
- KEGG (KAAS results) - orthologs, maps, hierarchy (bit=50)
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KEGG (KAAS) - metabolic map (bit=50)
- Based on currated annotation
COG class: 
bar plot pie plot legend COG subclass: 
bar plot pie plot legend TIGR roles class: 
bar plot pie plot legend TIGR roles subclass: 
bar plot pie plot legend
- All in PDF - file
- Generated by Circos
Genome features (for Vaclav Paces):
!!! NEW (2009-07-10) !!!
chromosome legend 1 legend 2 Description: - histogram: number of homologs
- genes: groups (discussed metabolisms), description in legend 1
- genes: forward strain (color by COG), description in legend 1
- genes: reverse strain (color by COG), description in legend 1
- tRNA genes (green)
- rRNA genes (violete)
- regions: groups (phages, GTA, CRISPR elements), description in legend 1
- genes: groups (CRISPR associated proteins, RMS), description in legend 1
- plot: GC content (blue/red(extrems <62% >72%): window 5kb, black: window 50kb)
- plot: GC skew (blue: >0, red: <0, window 100kb)
Genome features: 
chromosome Description: - ideogram: tRNA (green), rRNA (violete), phage genes (red)
- histogram: number of homologs
- genes: forward strain (color by COG)
- genes: reverse strain (color by COG)
- tRNA genes (green)
- phage genes (red triangels)
- rRNA genes (violete)
- plot: GC content (blue/red(extrems <62% >72%): window 5kb, black: window 50kb)
- plot: GC skew (blue: >0, red: <0, window 100kb)
Self hits: 
35% identity 80% identity 50% identity, desc 80% identity, desc Description: - ideogram: tRNA (green), rRNA (violete), phage genes (red)
- curves: rRNA (black)
- curves: identity from 35 to 100% (from yellow to red)
- genes: forward strain (color by COG)
- genes: reverse strain (color by COG)
- tRNA genes (green)
Homologouse / Orthologous proteins: 
Description: - ideogram: tRNA (green), rRNA (violete), phage genes (red)
- genes: forward strain (color by COG)
- genes: reverse strain (color by COG)
- heatmap: bit score (white to black)
- orthologs: in color - BBH, grey - SBH
- plot: GC content (blue/red(extrems <62% >72%): window 5kb, black: window 50kb)
- plot: GC skew (blue: >0, red: <0, window 100kb)
- tRNA genes (green), rRNA genes (violete)
- pic A - 1-3: rhodobacter group, 4-10: rhodobacteraceae, 11-12: rhodobacterales
- pic B - alphaproteobacteria
- pic C - 80 most simillar bacteria by homology
tax level 5, 6 and 7 from rc tax level 4 from rc org. with most homologs 
Description: - same as priviouse - higher resolution
dtto (10x10kpx) dtto (10x10kpx) 
0-1 M 1-2 M 2-3 M 3-4 M Description: - same as priviouse (pic A) - chromosone regions (1Mb)
- in preparation: Michal Kolar
- in preparation: Michal Kolar
- in preparation: Jan Paces