Материалы:NC 008048

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CONSRTM US DOE Joint Genome Institute TITLE Complete sequence of chromosome of Sphingopyxis alaskensis RB2256 JOURNAL Unpublished REFERENCE 2 (bases 1 to 3345170) CONSRTM NCBI Genome Project TITLE Direct Submission JOURNAL Submitted (30-MAY-2006) National Center for Biotechnology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
|