Геном прокариот/Материалы:NC 008048

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   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     JOURNAL   Unpublished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[править]

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