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HAMAP: Silicibacter sp. (strain TM1040) complete proteome
General information

Species:  Silicibacter sp. (strain TM1040)
Species code: SILST
Taxonomy: Bacteria; Proteobacteria; Alphaproteobacteria; Rhodobacterales; Rhodobacteraceae; Ruegeria (TaxID: 292414) [NEWT/ NCBI]
Description: Silicibacter sp. (strain TM1040) belongs to the Roseobacter clade of the alpha-proteobacteria, which is among the most abundant and ecologically relevant marine bacterial groups. It was originally isolated as part of an investigation to understand the role of the bacteria in the physiology and toxigenesis of the dinoflagellate Pfiesteria piscicida. Silicibacter sp. (strain TM1040) is found within the phycosphere or physically attached to the surface of the dinoflagellate cell. Axenic cultures of P.piscicida grow poorly (and ultimately die) compared to cultures with associated bacterial assemblages. Although P.piscicida is a heterotrophic dinoflagellate, the Pfiesteria /TM1040 association is the only known "obligate" association between a dinoflagellate and a culturable bacterium. In addition, Silicibacter sp. (strain TM1040) metabolizes the dinoflagellate secondary metabolite dimethylsulfoniopropionate (DMSP) via demethylation to methylmercaptopropionic acid (MMPA). DMSP is the major source of organic sulfur in the world's oceans and plays a significant role in the global sulfur cycle. The genome of Silicibacter sp. (strain TM1040) is made up of one chromosome, one megaplasmid and one plasmid.
Properties: Presence of flagella: Yes
Human pathogen: No
Interaction: Dinoflagellate symbiont (obligate symbiont)
Number of membranes: 2
Number of inteins:0
Statistics: Number of SILST entries in the UniProt Knowledgebase: 3849 (320 in UniProtKB/Swiss-Prot + 3529 in UniProtKB/TrEMBL)


Genome(s) sequenced

Strain:    TM1040
Genome structure:
• Chromosome EMBL accession number CP000377 (circular; 3,200,938 bp) (download entry)
• Plasmid megaplasmid TM1040 EMBL accession number CP000376 (circular; 821,788 bp) (download entry)
• Plasmid pTM1040 EMBL accession number CP000375 (circular; 130,973 bp) (download entry)
Reference(s):
[1] Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H., Pitluck S., Brettin T., Bruce D., Han C., Tapia R., Goodwin L., Thompson L.S., Gilna P., Schmutz J., Larimer F., Land M., Hauser L., Kyrpides N., Kim E., Belas R., Moran M.A., Buchan A., Gonzalez J.M., Schell M.A., Sun F., Richardson P. ;
"Complete sequence of chromosome of Silicibacter sp. TM1040.";
Submitted (MAY-2006) to the EMBL/GenBank/DDBJ databases.
[2] Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H., Pitluck S., Brettin T., Bruce D., Han C., Tapia R., Goodwin L., Thompson L.S., Gilna P., Schmutz J., Larimer F., Land M., Hauser L., Kyrpides N., Kim E., Belas R., Moran M.A., Buchan A., Gonzalez J.M., Schell M.A., Sun F., Richardson P. ;
"Complete sequence of megaplasmid of Silicibacter sp. TM1040.";
Submitted (MAY-2006) to the EMBL/GenBank/DDBJ databases.
[3] Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H., Pitluck S., Brettin T., Bruce D., Han C., Tapia R., Goodwin L., Thompson L.S., Gilna P., Schmutz J., Larimer F., Land M., Hauser L., Kyrpides N., Kim E., Belas R., Moran M.A., Buchan A., Gonzalez J.M., Schell M.A., Sun F., Richardson P. ;
"Complete sequence of plasmid of Silicibacter sp. TM1040.";
Submitted (MAY-2006) to the EMBL/GenBank/DDBJ databases.
Web links:
Entrez Genome Project: http://www.ncbi.nlm.nih.gov/sites/entrez?Db=genomeprj&Cmd=DetailsSearch&Term=txid292414%5Borgn%5D
GIB (DDBJ): http://gib.genes.nig.ac.jp/single/index.php?spid=Sili_TM1040
PEDANT: http://pedant.gsf.de/pedant3htmlview/pedant3view?Method=analysis&Db=p3_p13040_Sil_TM104
 EBI Proteome Analysis page



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