Геном прокариот/Материалы:NC 008309

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

   LOCUS       NC_008309            2007700 bp    DNA     circular BCT 16-AUG-2007
   DEFINITION  Haemophilus somnus 129PT, complete genome.
   ACCESSION   NC_008309
   VERSION     NC_008309.1  GI:113460149
   KEYWORDS    .
   SOURCE      Haemophilus somnus 129PT
     ORGANISM  Haemophilus somnus 129PT
               Bacteria; Proteobacteria; Gammaproteobacteria; Pasteurellales;
               Pasteurellaceae; Histophilus.
   REFERENCE   1  (bases 1 to 2007700)
     AUTHORS   Challacombe,J.F., Duncan,A.J., Brettin,T.S., Bruce,D., Chertkov,O.,
               Detter,J.C., Han,C.S., Misra,M., Richardson,P., Tapia,R.,
               Thayer,N., Xie,G. and Inzana,T.J.
     TITLE     Complete genome sequence of Haemophilus somnus (Histophilus somni)
               strain 129Pt and comparison to Haemophilus ducreyi 35000HP and
               Haemophilus influenzae Rd
     JOURNAL   J. Bacteriol. 189 (5), 1890-1898 (2007)
      PUBMED   17172329
   REFERENCE   2  (bases 1 to 2007700)
     CONSRTM   NCBI Genome Project
     TITLE     Direct Submission
     JOURNAL   Submitted (30-AUG-2006) National Center for Biotechnology
               Information, NIH, Bethesda, MD 20894, USA
   REFERENCE   3  (bases 1 to 2007700)
     AUTHORS   Copeland,A., Lucas,S., Lapidus,A., Barry,K., Glavina del Rio,T.,
               Hammon,N., Dalin,E., Tice,H., Pitluck,S., Brettin,T.S., Bruce,D.,
               Challacombe,J.F., Chertkov,O., Detter,J.C., Gilna,P., Han,S.,
               Misra,M., Tapia,R., Thayer,N.N., Xie,G., Inzana,T.J., Duncan,A.J.,
               Siddaramppa,S. and Richardson,P.
     TITLE     Direct Submission
     JOURNAL   Submitted (07-AUG-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 CP000436.
               URL -- http://www.jgi.doe.gov
                      JGI Project ID: 2662200
                      Source DNA and bacteria available from Tom Inzana
                      Contacts: Tom Inzana (tinzana@vt.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. Large
               (40 kb), median (8 kb) and small (3 kb) insert random sequencing
               libraries were sequenced for this genome project with average
               success rate of 96% and average high-quality read lengths of 685
               nucleotides. After shotgun stage, reads were assembled with
               parallel phrap (High Performance Software, LLC). Possible
               mis-assemblies were corrected with Dupfinisher (unpublished, S.
               Han) or transposon bomb of bridging clones. Gaps between contigs
               were closed by editing, custom primer walks or PCR amplification.
               The completed genome sequence of H. somnus 129PT contains 59147
               reads, achieving an average of 18-fold sequence coverage per base
               with error rate less than 1 in 100,000. 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, COGS 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 1880
               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[править]

Начало	Конец	Направление	Длина	PID	Ген	COG	Комментарий
1316	1393	+	78	113460149	HS_tPseudo01	-	Xaa tRNA
1397	1475	+	79	113460149	HS_tAsn03	-	^{07 Asn tRNA}
177054	177132	-	79	113460149	HS_tThr01	-	^{12 Thr tRNA}
177133	177210	-	78	113460149	HS_tGly01	-	^{01 Gly tRNA}
177250	177337	-	88	113460149	HS_tTyr01	-	^{18 Tyr tRNA}
177366	177444	-	79	113460149	HS_tThr02	-	^{12 Thr tRNA}
261158	261236	+	79	113460149	HS_tLys01	-	^{10 Lys tRNA}
261259	261337	+	79	113460149	HS_tLys03	-	^{10 Lys tRNA}
261360	261438	+	79	113460149	HS_tLys02	-	^{10 Lys tRNA}
327339	327431	+	93	113460149	HS_tSer03	-	^{08 Ser tRNA}
486229	486307	-	79	113460149	HS_tAla03	-	^{02 Ala tRNA}
488009	488087	+	79	113460149	HS_tVal04	-	^{13 Val tRNA}
488125	488203	+	79	113460149	HS_tVal01	-	^{13 Val tRNA}
488262	488340	+	79	113460149	HS_tVal02	-	^{13 Val tRNA}
561972	562061	+	90	113460149	HS_tLeu01	-	^{15 Leu tRNA}
646388	646467	-	80	113460149	HS_tAsp02	-	^{06 Asp tRNA}
646493	646572	-	80	113460149	HS_tAsp03	-	^{06 Asp tRNA}
766890	766969	-	80	113460149	HS_tMet02	-	^{16 Met tRNA}
772258	772354	+	97	113460149	HS_tSer02	-	^{08 Ser tRNA}
772362	772441	+	80	113460149	HS_tArg02	-	^{11 Arg tRNA}
772515	772594	+	80	113460149	HS_tArg03	-	^{11 Arg tRNA}
893293	893372	+	80	113460149	HS_tMet01	-	^{16 Met tRNA}
1124187	1124264	-	78	113460149	HS_tGln01	-	^{05 Gln tRNA}
1124308	1124385	-	78	113460149	HS_tGln02	-	^{05 Gln tRNA}
1124410	1124497	-	88	113460149	HS_tLeu03	-	^{15 Leu tRNA}
1124500	1124579	-	80	113460149	HS_tMet03	-	^{16 Met tRNA}
1195424	1195502	+	79	113460149	HS_tAsn02	-	^{07 Asn tRNA}
1234438	1234516	+	79	113460149	HS_tGly03	-	^{01 Gly tRNA}
1381469	1381548	-	80	113460149	HS_tArg04	-	^{11 Arg tRNA}
1381572	1381651	-	80	113460149	HS_tPro02	-	^{03 Pro tRNA}
1389530	1389609	-	80	113460149	HS_tVal03	-	^{13 Val tRNA}
1389669	1389782	-	114	113460149	HS_r5S02	-	5S ribosomal RNA
1389905	1392905	+	3001	113460149	HS_r23S02	-	23S ribosomal RNA
1393084	1393162	-	79	113460149	HS_tGlu01	-	^{04 Glu tRNA}
1393294	1394776	-	1483	113460149	HS_r16S02	-	16S ribosomal RNA
1394930	1395009	-	80	113460149	HS_tPro01	-	^{03 Pro tRNA}
1395013	1395091	-	79	113460149	HS_tHis01	-	^{09 His tRNA}
1395110	1395189	-	80	113460149	HS_tArg01	-	^{11 Arg tRNA}
1501839	1501927	+	89	113460149	HS_tLeu04	-	^{15 Leu tRNA}
1538413	1538491	+	79	113460149	HS_tGly02	-	^{01 Gly tRNA}
1538500	1538576	+	77	113460149	HS_tCys01	-	^{19 Cys tRNA}
1538598	1538687	+	90	113460149	HS_tLeu02	-	^{15 Leu tRNA}
1610992	1611084	-	93	113460149	HS_tSer01	-	^{08 Ser tRNA}
1640263	1640376	-	114	113460149	HS_r5S05	-	5S ribosomal RNA
1640499	1643499	+	3001	113460149	HS_r23S05	-	23S ribosomal RNA
1643712	1643790	-	79	113460149	HS_tAla01	-	^{02 Ala tRNA}
1643882	1643961	-	80	113460149	HS_tIle01	-	^{14 Ile tRNA}
1644077	1645561	-	1485	113460149	HS_r16S05	-	16S ribosomal RNA
1715918	1716031	-	114	113460149	HS_r5S01	-	5S ribosomal RNA
1716154	1719154	+	3001	113460149	HS_r23S01	-	23S ribosomal RNA
1719333	1719411	-	79	113460149	HS_tGlu02	-	^{04 Glu tRNA}
1719543	1721025	-	1483	113460149	HS_r16S01	-	16S ribosomal RNA
1774346	1774424	-	79	113460149	HS_tTrp01	-	^{20 Trp tRNA}
1774436	1774515	-	80	113460149	HS_tAsp01	-	^{06 Asp tRNA}
1774697	1774810	-	114	113460149	HS_r5S04	-	5S ribosomal RNA
1774933	1777933	+	3001	113460149	HS_r23S04	-	23S ribosomal RNA
1778112	1778190	-	79	113460149	HS_tGlu03	-	^{04 Glu tRNA}
1778322	1779804	-	1483	113460149	HS_r16S04	-	16S ribosomal RNA
1942556	1944038	+	1483	113460149	HS_r16S03	-	16S ribosomal RNA
1944156	1944235	+	80	113460149	HS_tIle02	-	^{14 Ile tRNA}
1944327	1944405	+	79	113460149	HS_tAla02	-	^{02 Ala tRNA}
1944618	1947618	-	3001	113460149	HS_r23S03	-	23S ribosomal RNA
1947741	1947852	+	112	113460149	HS_r5S03	-	5S ribosomal RNA
1952153	1952231	+	79	113460149	HS_tPhe01	-	^{17 Phe tRNA}
1952251	1952329	+	79	113460149	HS_tAsn01	-	^{07 Asn tRNA}