Геном прокариот/Материалы:NC 008255

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

   LOCUS       NC_008255            4433218 bp    DNA     circular BCT 25-JUL-2006
   DEFINITION  Cytophaga hutchinsonii ATCC 33406, complete genome.
   ACCESSION   NC_008255
   VERSION     NC_008255.1  GI:110636427
   KEYWORDS    .
   SOURCE      Cytophaga hutchinsonii ATCC 33406
     ORGANISM  Cytophaga hutchinsonii ATCC 33406
               Bacteria; Bacteroidetes; Sphingobacteria; Sphingobacteriales;
               Flexibacteraceae; Cytophaga.
   REFERENCE   1  (bases 1 to 4433218)
     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., Challacombe,J.F., Chertkov,O., Han,S.,
               Tapia,R., McBride,M.J., Misra,M., Myers,G.L., Thayer,N.N.,
               Thompson,L.S., Xie,G., Gilna,P., Schmutz,J., Larimer,F., Land,M.,
               Hauser,L., Kyrpides,N., Lykidis,A., Ivanova,N., Mavrommatis,K.,
               Rubin,E. and Richardson,P.
     CONSRTM   US DOE Joint Genome Institute
     TITLE     Complete sequence of Cytophaga hutchinsonii ATCC 33406
     JOURNAL   Unpublished
   REFERENCE   2  (bases 1 to 4433218)
     AUTHORS   .
     CONSRTM   NCBI Genome Project
     TITLE     Direct Submission
     JOURNAL   Submitted (24-JUL-2006) National Center for Biotechnology
               Information, NIH, Bethesda, MD 20894, USA
   REFERENCE   3  (bases 1 to 4433218)
     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., Challacombe,J.F., Chertkov,O., Han,S.,
               Tapia,R., McBride,M.J., Misra,M., Myers,G.L., Thayer,N.N.,
               Thompson,L.S., Xie,G., Gilna,P., Schmutz,J., Larimer,F., Land,M.,
               Hauser,L., Kyrpides,N., Lykidis,A., Ivanova,N., Mavrommatis,K.,
               Rubin,E. and Richardson,P.
     CONSRTM   US DOE Joint Genome Institute
     TITLE     Direct Submission
     JOURNAL   Submitted (02-JUN-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 CP000383.
               URL -- http://www.jgi.doe.gov
                      JGI Project ID: 2351473
                      Source DNA and bacteria available from Mark McBride
                      Contacts: Mark McBride (mcbride@uwm.edu)
                                Paul Richardson (microbes@cuba.jgi-psf.org)
               Plasmid and fosmid libraries were prepared at the Joint Genome
               Institute (JGI) Production Genomics Facility (JGI-PGF) in Walnut
               Creek, CA. Shotgun sequencing was performed at the JGI-PGF to a
               coverage of 15x. Large (40 kb), medium (8 kb) and small (3 kb)
               insert random libraries were partially sequenced with average
               success rate of 90% and average high-quality read lengths of 634
               nucleotides. Finishing was performed at JGI-LANL starting with 29
               contigs and 2 scaffolds. Repetitive regions were identified,
               assembled and finished by manually checking paired reads close to
               each repeat in the assembly with consed and then making a
               subassembly for each repetitive region. 27 gaps were closed with
               primer walks and 2 by PCR. Gene predictions were obtained using
               Glimmer and tRNAs were identified using tRNAScan-SE. Basic analysis
               of the gene predictions was performed by comparing coding sequences
               against the PFam, BLOCKS and Prodom databases. Gene definitions and
               functional classes were added manually by a team of annotators at
               JGI-LANL, using BLAST results in addition to information from the
               basic analysis. A total of 3793 features have been annotated on the
               sequence record.
                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).
               COMPLETENESS: full length.

Расположение РНК

Начало	Конец	Направление	Длина	PID	Ген	COG	Комментарий
63356	63435	-	80	110636427	CHU_tAsn01	-	^{07 Asn tRNA}
69568	69647	-	80	110636427	CHU_tAla01	-	^{02 Ala tRNA}
120118	121499	+	1382	110636427	CHU_r16S01	-	16S ribosomal RNA
121927	124436	+	2510	110636427	CHU_r23S01	-	23S ribosomal RNA
124780	124816	+	37	110636427	CHU_r5S01	-	5S ribosomal RNA
145782	145857	-	76	110636427	CHU_tPhe01	-	^{17 Phe tRNA}
178917	178992	+	76	110636427	CHU_tGly01	-	^{01 Gly tRNA}
179045	179136	+	92	110636427	CHU_tLeu01	-	^{15 Leu tRNA}
183235	184616	+	1382	110636427	CHU_r16S02	-	16S ribosomal RNA
184777	184853	+	77	110636427	CHU_tIle01	-	^{14 Ile tRNA}
184945	185021	+	77	110636427	CHU_tAla02	-	^{02 Ala tRNA}
185312	187821	+	2510	110636427	CHU_r23S02	-	23S ribosomal RNA
188165	188201	+	37	110636427	CHU_r5S02	-	5S ribosomal RNA
256242	256322	+	81	110636427	CHU_tVal01	-	^{13 Val tRNA}
724579	724658	+	80	110636427	CHU_tArg01	-	^{11 Arg tRNA}
1040456	1040532	-	77	110636427	CHU_tMet01	-	^{16 Met tRNA}
1157965	1158044	+	80	110636427	CHU_tHis01	-	^{09 His tRNA}
1210249	1210336	+	88	110636427	CHU_tSer01	-	^{08 Ser tRNA}
1751703	1751779	-	77	110636427	CHU_tAsp01	-	^{06 Asp tRNA}
1932378	1932457	-	80	110636427	CHU_tMet02	-	^{16 Met tRNA}
1973455	1973533	+	79	110636427	CHU_tThr01	-	^{12 Thr tRNA}
1973775	1973850	+	76	110636427	CHU_tThr02	-	^{12 Thr tRNA}
1993798	1993834	-	37	110636427	CHU_r5S03	-	5S ribosomal RNA
1994178	1996687	-	2510	110636427	CHU_r23S03	-	23S ribosomal RNA
1997115	1998496	-	1382	110636427	CHU_r16S03	-	16S ribosomal RNA
2005947	2006031	+	85	110636427	CHU_tLeu02	-	^{15 Leu tRNA}
2239147	2239224	-	78	110636427	CHU_tPro01	-	^{03 Pro tRNA}
2239296	2239372	-	77	110636427	CHU_tArg02	-	^{11 Arg tRNA}
2239455	2239532	-	78	110636427	CHU_tPro02	-	^{03 Pro tRNA}
2239626	2239717	-	92	110636427	CHU_tSer02	-	^{08 Ser tRNA}
2278047	2278120	-	74	110636427	CHU_tCys01	-	^{19 Cys tRNA}
2526598	2526690	-	93	110636427	CHU_tSer03	-	^{08 Ser tRNA}
2611557	2611631	+	75	110636427	CHU_tArg03	-	^{11 Arg tRNA}
3008953	3009031	-	79	110636427	CHU_tGln01	-	^{05 Gln tRNA}
3197420	3197506	-	87	110636427	CHU_tLeu03	-	^{15 Leu tRNA}
3198774	3198849	-	76	110636427	CHU_tLys01	-	^{10 Lys tRNA}
3199734	3199809	-	76	110636427	CHU_tLys02	-	^{10 Lys tRNA}
3325653	3325731	-	79	110636427	CHU_tPhe02	-	^{17 Phe tRNA}
3325763	3325851	-	89	110636427	CHU_tPseudo01	-	Xaa tRNA
3400034	3400118	-	85	110636427	CHU_tLeu04	-	^{15 Leu tRNA}
3422770	3422847	-	78	110636427	CHU_tGlu01	-	^{04 Glu tRNA}
3422949	3423026	-	78	110636427	CHU_tGlu02	-	^{04 Glu tRNA}
3614058	3614131	-	74	110636427	CHU_tTrp01	-	^{20 Trp tRNA}
3615488	3615566	-	79	110636427	CHU_tThr03	-	^{12 Thr tRNA}
3615577	3615655	-	79	110636427	CHU_tGly02	-	^{01 Gly tRNA}
3615732	3615820	-	89	110636427	CHU_tTyr01	-	^{18 Tyr tRNA}
3836007	3836085	-	79	110636427	CHU_tMet03	-	^{16 Met tRNA}
4426462	4426539	-	78	110636427	CHU_tArg04	-	^{11 Arg tRNA}