Геном прокариот/Материалы:NC 008048

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Эта статья — часть материалов: лаборатории Биоинформатика, исследовательского проекта «Геном прокариот»

   LOCUS       NC_008048            3345170 bp    DNA     circular BCT 30-MAY-2006
   DEFINITION  Sphingopyxis alaskensis RB2256, complete genome.
   ACCESSION   NC_008048
   VERSION     NC_008048.1  GI:103485498
   KEYWORDS    .
   SOURCE      Sphingopyxis alaskensis RB2256
     ORGANISM  Sphingopyxis alaskensis RB2256
               Bacteria; Proteobacteria; Alphaproteobacteria; Sphingomonadales;
               Sphingomonadaceae; Sphingopyxis.
   REFERENCE   1  (bases 1 to 3345170)
     AUTHORS   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., Munk,A.C., Chertkov,O.,
               Gilna,P., Schmutz,J., Larimer,F., Land,M., Hauser,L., Kyrpides,N.,
               Kim,E., Cavicchioli,R., Robb,F., Ertan,H., Schut,F., Ting,L.M. and
               Richardson,P.
     CONSRTM   US DOE Joint Genome Institute
     TITLE     Complete sequence of chromosome of Sphingopyxis alaskensis RB2256
     JOURNAL   Unpublished
   REFERENCE   2  (bases 1 to 3345170)
     CONSRTM   NCBI Genome Project
     TITLE     Direct Submission
     JOURNAL   Submitted (30-MAY-2006) National Center for Biotechnology
               Information, NIH, Bethesda, MD 20894, USA
   REFERENCE   3  (bases 1 to 3345170)
     AUTHORS   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., Munk,A.C., Chertkov,O.,
               Gilna,P., Schmutz,J., Larimer,F., Land,M., Hauser,L., Kyrpides,N.,
               Kim,E., Cavicchioli,R., Robb,F., Ertan,H., Schut,F., Ting,L.M. and
               Richardson,P.
     CONSRTM   US DOE Joint Genome Institute
     TITLE     Direct Submission
     JOURNAL   Submitted (20-APR-2006) US DOE Joint Genome Institute, 2800
               Mitchell Drive B100, Walnut Creek, CA 94598-1698, USA
   COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
               NCBI review. The reference sequence was derived from CP000356.
               URL -- http://www.jgi.doe.gov
               JGI Project ID: 3634495
               Source DNA and bacteria available from Rick Cavicchioli
               (rcavicchioli@unsw.edu.au)
               Contacts: Rick Cavicchioli (rcavicchioli@unsw.edu.au)
                         Paul Richardson (microbes@cuba.jgi-psf.org)
               Quality assurance done by JGI-Stanford
               Annotation done by JGI-ORNL and JGI-PGF
               Finishing done by JGI-LLNL
               Finished microbial genomes have been curated to close all gaps with
               greater than 98% coverage of at least two independent clones. Each
               base pair has a minimum q (quality) value of 30 and the total error
               rate is less than one per 50000.
               The JGI and collaborators endorse the principles for the
               distribution and use of large scale sequencing data adopted by the
               larger genome sequencing community and urge users of this data to
               follow them. it is our intention to publish the work of this
               project in a timely fashion and we welcome collaborative
               interaction on the project and analysis.
               (http://www.genome.gov/page.cfm?pageID=10506376)
               Additional Notes:
               Sphingopyxis alaskensis RB2256 appears to have about a 28.5kb
               extrachromosomal piece of DNA with significantly lower coverage
               than the chromosome.  It appears to be of F plasmid origin because
               of the presence of traA gene, a conjugal transfer protein.  It can
               be integrated into the genome between 856688 and 859197, excising a
               piece of chromosomal DNA 2517 bp long. Perhaps a fraction of the
               population has this 28.5 kb fragment integrated.  Within 2 kb of
               the excision point is an IS21 element with ORF1 and ORF2 of
               transposase and perfect inverted repeats.  However, we have been
               unsuccessful in circularizing the 28.5 kb fragment with pcr,
               perhaps because of the low representation in the genome.
               COMPLETENESS: full length.

Расположение РНК

Начало	Конец	Направление	Длина	PID	Ген	COG	Комментарий
48696	48770	+	75	103485498	Sala_R0001	-	^{05 Gln tRNA}
316344	316430	-	87	103485498	Sala_R0002	-	^{15 Leu tRNA}
456132	456208	-	77	103485498	Sala_R0003	-	^{16 Met tRNA}
602240	602316	+	77	103485498	Sala_R0004	-	^{11 Arg tRNA}
765277	765350	+	74	103485498	Sala_R0005	-	^{01 Gly tRNA}
791522	791606	+	85	103485498	Sala_R0006	-	^{15 Leu tRNA}
806925	806999	+	75	103485498	Sala_R0007	-	^{13 Val tRNA}
850623	850707	+	85	103485498	Sala_R0008	-	^{15 Leu tRNA}
854471	854556	+	86	103485498	Sala_R0009	-	^{18 Tyr tRNA}
1089483	1089558	+	76	103485498	Sala_R0010	-	^{02 Ala tRNA}
1125685	1125774	-	90	103485498	Sala_R0011	-	^{08 Ser tRNA}
1306508	1306597	-	90	103485498	Sala_R0012	-	^{08 Ser tRNA}
1342805	1342881	+	77	103485498	Sala_R0013	-	^{03 Pro tRNA}
1343474	1343549	-	76	103485498	Sala_R0014	-	^{16 Met tRNA}
1381901	1381977	-	77	103485498	Sala_R0015	-	^{06 Asp tRNA}
1396698	1396774	+	77	103485498	Sala_R0016	-	^{03 Pro tRNA}
1398423	1398497	+	75	103485498	Sala_R0017	-	^{13 Val tRNA}
1401100	1401192	-	93	103485498	Sala_R0018	-	^{08 Ser tRNA}
1554964	1555039	-	76	103485498	Sala_R0019	-	^{02 Ala tRNA}
1561950	1562036	+	87	103485498	Sala_R0020	-	^{15 Leu tRNA}
1587403	1587479	-	77	103485498	Sala_R0021	-	^{09 His tRNA}
1619704	1619779	+	76	103485498	Sala_R0022	-	^{10 Lys tRNA}
1625357	1625481	-	125	103485498	Sala_R0023	-
1686630	1686704	-	75	103485498	Sala_R0024	-	^{12 Thr tRNA}
1688353	1688443	+	91	103485498	Sala_R0025	-	^{08 Ser tRNA}
1688559	1688635	-	77	103485498	Sala_R0026	-	^{11 Arg tRNA}
1713023	1713098	+	76	103485498	Sala_R0027	-	^{10 Lys tRNA}
1742368	1742442	+	75	103485498	Sala_R0028	-	^{07 Asn tRNA}
1806373	1806449	+	77	103485498	Sala_R0029	-	^{03 Pro tRNA}
1886679	1886755	-	77	103485498	Sala_R0030	-	^{11 Arg tRNA}
1957262	1957337	-	76	103485498	Sala_R0031	-	^{20 Trp tRNA}
1967796	1967897	-	102	103485498	Sala_R0032	-
1967903	1967999	-	97	103485498	Sala_R0033	-
2016678	2016753	-	76	103485498	Sala_R0034	-	^{17 Phe tRNA}
2180501	2180576	+	76	103485498	Sala_R0035	-	^{12 Thr tRNA}
2205868	2205943	-	76	103485498	Sala_R0036	-	^{13 Val tRNA}
2238706	2238781	+	76	103485498	Sala_R0037	-	^{12 Thr tRNA}
2239274	2239360	-	87	103485498	Sala_R0038	-	^{15 Leu tRNA}
2379346	2379419	-	74	103485498	Sala_R0039	-	^{19 Cys tRNA}
2437773	2437846	-	74	103485498	Sala_R0040	-	^{05 Gln tRNA}
2492584	2492695	+	112	103485498	Sala_R0041	-
2809614	2809688	-	75	103485498	Sala_R0042	-	^{01 Gly tRNA}
2847706	2847782	-	77	103485498	Sala_R0043	-	^{16 Met tRNA}
2847888	2848002	-	115	103485498	Sala_R0044	-	5S ribosomal RNA
2848120	2850903	-	2784	103485498	Sala_R0045	-	23S ribosomal RNA
2851208	2851283	-	76	103485498	Sala_R0046	-	^{02 Ala tRNA}
2851308	2851384	-	77	103485498	Sala_R0047	-	^{14 Ile tRNA}
2851569	2853052	-	1484	103485498	Sala_R0048	-	16S ribosomal RNA
2931415	2931488	+	74	103485498	Sala_R0049	-	^{01 Gly tRNA}
3045924	3046000	+	77	103485498	Sala_R0050	-	^{11 Arg tRNA}
3155557	3155631	-	75	103485498	Sala_R0051	-	^{04 Glu tRNA}
3155683	3155758	-	76	103485498	Sala_R0052	-	^{04 Glu tRNA}