Материалы:NC 009784

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

   LOCUS       NC_009784            2204018 bp    DNA     circular BCT 07-SEP-2007
   DEFINITION  Vibrio harveyi ATCC BAA-1116 chromosome II, complete sequence.
   ACCESSION   NC_009784
   VERSION     NC_009784.1  GI:156975952
   KEYWORDS    .
   SOURCE      Vibrio harveyi ATCC BAA-1116
     ORGANISM  Vibrio harveyi ATCC BAA-1116
               Bacteria; Proteobacteria; Gammaproteobacteria; Vibrionales;
               Vibrionaceae; Vibrio.
   REFERENCE   1  (bases 1 to 2204018)
     CONSRTM   NCBI Genome Project
     TITLE     Direct Submission
     JOURNAL   Submitted (06-SEP-2007) National Center for Biotechnology
               Information, NIH, Bethesda, MD 20894, USA
   REFERENCE   2  (bases 1 to 2204018)
     AUTHORS   Bassler,B., Clifton,S.W., Fulton,L., Delehaunty,K., Fronick,C.,
               Harrison,M., Markivic,C., Fulton,R., Tin-Wollam,A.-M., Shah,N.,
               Pepin,K., Nash,W., Thiruvilangam,P., Bhonagiri,V., Waters,C.,
               Tu,K.C., Irgon,J. and Wilson,R.K.
     CONSRTM   The Vibrio harveyi Genome Sequencing Project
     TITLE     Direct Submission
     JOURNAL   Submitted (16-AUG-2007) Genetics, Genome Sequencing Center, 4444
               Forest Park Parkway, St. Louis, MO 63108, USA
   COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
               NCBI review. The reference sequence was derived from CP000790.
               Vibrio harveyi belongs to the group of bioluminescent bacteria that
               'glow in the dark,' just as the commonly known firefly. Based on
               their 16S  ribosomal RNA (rRNA) classification, they belong to the
               group of bacteria known as Proteobacteria, which is further
               sub-divided into five groups, including the gamma proteobacteria.
               This group includes many families, one of which is the Vibrionaceae
               (bioluminescent bacteria). One of the Vibrios is a human pathogen
               and causes cholera. Vibrio harveyi can be found globally in marine
               environments, either in a free-living state or in symbiosis with
               marine life.  The sequenced strain is BB120, ATCC BAA-1116
               http://www.atcc.org/common/catalog/numSearch/numResults.cfm
               Sequence/Assembly
               The genome of Vibrio harveyi was sequenced to 8X coverage using a
               combination of plasmid and fosmid end sequences. Additional 454
               sequence reads bring the present coverage to 10.8X. Assembly was
               performed using the PCAP software (Genome Res. 13(9):2164-70 2003).
                The genome has  undergone automated sequence improvement
               (pre-finishing) followed by  manual finishing, and automated
               annotation. The National Science  Foundation (NSF) is providing
               funding for the complete sequence of the  Vibrio harveyi genome.
               
               Annotation
               Coding sequences were predicted using GeneMark v3.3 and Glimmer2
               v2.13. Intergenic regions not spanned by GeneMark and Glimmer2 were
               blasted against NCBI's non-redundant (NR) database and predictions
               generated based on protein alignments. RNA genes were determined
               using tRNAscan-SE 1.23 or Rfam v8.0. Gene names are generated at
               the contig level and may not necessarily reflect any known order or
               orientation between contigs.For questions regarding this assembly
               or project, please visit the Vibrio harveyi genome page
               (http://genome.wustl.edu/genome.cgi?GENOME=Vibrio%20harveyi) and
               choose the designated contact person.
               COMPLETENESS: full length.

Расположение РНК

Начало	Конец	Направление	Длина	PID	Ген	COG	Комментарий
111193	111301	+	109	156975952	VIBHAR_04846	-	Qrr RNA
555291	555399	-	109	156975952	VIBHAR_05322	-	Qrr RNA
674548	674635	-	88	156975952	VIBHAR_05459	-	^{08 Ser tRNA}
882885	882955	+	71	156975952	VIBHAR_05672	-	^{19 Cys tRNA}
886895	886978	+	84	156975952	VIBHAR_05676	-	^{15 Leu tRNA}
887079	887151	+	73	156975952	VIBHAR_05677	-	^{01 Gly tRNA}
887160	887230	+	71	156975952	VIBHAR_05678	-	^{19 Cys tRNA}
890715	890798	+	84	156975952	VIBHAR_05682	-	^{15 Leu tRNA}
890855	890925	+	71	156975952	VIBHAR_05683	-	^{19 Cys tRNA}
891110	891180	+	71	156975952	VIBHAR_05684	-	^{19 Cys tRNA}
1080963	1081069	-	107	156975952	VIBHAR_05886	-	Qrr RNA
1336060	1336131	+	72	156975952	VIBHAR_06159	-	^{01 Gly tRNA}
1833376	1833484	-	109	156975952	VIBHAR_06697	-	Qrr RNA
1842706	1842786	+	81	156975952	VIBHAR_06707	-	^{15 Leu tRNA}
1864333	1864645	+	313	156975952	VIBHAR_06731	-	CsrB/RsmB RNA family
1921624	1921695	+	72	156975952	VIBHAR_06802	-	^{01 Gly tRNA}
1939217	1939304	-	88	156975952	VIBHAR_06826	-	^{08 Ser tRNA}
1939395	1939511	-	117	156975952	VIBHAR_06827	-	5S ribosomal RNA
1939607	1942491	+	2885	156975952	VIBHAR_07134	-	23S ribosomal RNA
1942813	1942885	-	73	156975952	VIBHAR_06828	-	^{13 Val tRNA}
1942924	1942996	-	73	156975952	VIBHAR_06829	-	^{02 Ala tRNA}
1943024	1943096	-	73	156975952	VIBHAR_06830	-	^{10 Lys tRNA}
1943102	1943174	-	73	156975952	VIBHAR_06831	-	^{04 Glu tRNA}
1944284	1944825	-	542	156975952	VIBHAR_06832	-	small subunit ribosomal RNA