Геном прокариот/Материалы:NC 009719
(перенаправлено с «Материалы:NC 009719»)
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LOCUS NC_009719 3914745 bp DNA circular BCT 05-SEP-2007
DEFINITION Parvibaculum lavamentivorans DS-1, complete genome.
ACCESSION NC_009719
VERSION NC_009719.1 GI:154250456
KEYWORDS .
SOURCE Parvibaculum lavamentivorans DS-1
ORGANISM Parvibaculum lavamentivorans DS-1
Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales;
Phyllobacteriaceae; Parvibaculum.
REFERENCE 1 (bases 1 to 3914745)
AUTHORS Schleheck,D., Knepper,T.P., Eichhorn,P. and Cook,A.M.
TITLE Parvibaculum lavamentivorans DS-1T degrades centrally-substituted
congeners of commercial linear alkylbenzenesulfonate (LAS) to
sulfophenyl carboxylates and sulfophenyl dicarboxylates
JOURNAL (er) Appl. Environ. Microbiol. (2007) In press
PUBMED 17557839
REFERENCE 2 (bases 1 to 3914745)
AUTHORS Schleheck,D. and Cook,A.M.
TITLE Omega-oxygenation of the alkyl sidechain of linear
alkylbenzenesulfonate (LAS) surfactant in Parvibaculum
lavamentivorans(T)
JOURNAL Arch. Microbiol. 183 (6), 369-377 (2005)
PUBMED 16075201
REFERENCE 3 (bases 1 to 3914745)
AUTHORS Schleheck,D., Tindall,B.J., Rossello-Mora,R. and Cook,A.M.
TITLE Parvibaculum lavamentivorans gen. nov., sp. nov., a novel
heterotroph that initiates catabolism of linear
alkylbenzenesulfonate
JOURNAL Int. J. Syst. Evol. Microbiol. 54 (PT 5), 1489-1497 (2004)
PUBMED 15388700
REFERENCE 4 (bases 1 to 3914745)
AUTHORS Schleheck,D., Knepper,T.P., Fischer,K. and Cook,A.M.
TITLE Mineralization of individual congeners of linear
alkylbenzenesulfonate by defined pairs of heterotrophic bacteria
JOURNAL Appl. Environ. Microbiol. 70 (7), 4053-4063 (2004)
PUBMED 15240283
REFERENCE 5 (bases 1 to 3914745)
AUTHORS Dong,W., Eichhorn,P., Radajewski,S., Schleheck,D., Denger,K.,
Knepper,T.P., Murrell,J.C. and Cook,A.M.
TITLE Parvibaculum lavamentivorans converts linear alkylbenzenesulphonate
surfactant to sulphophenylcarboxylates, alpha,beta-unsaturated
sulphophenylcarboxylates and sulphophenyldicarboxylates, which are
degraded in communities
JOURNAL J. Appl. Microbiol. 96 (3), 630-640 (2004)
PUBMED 14962144
REFERENCE 6 (bases 1 to 3914745)
AUTHORS Schleheck,D., Lechner,M., Schonenberger,R., Suter,M.J. and
Cook,A.M.
TITLE Desulfonation and degradation of the
disulfodiphenylethercarboxylates from linear
alkyldiphenyletherdisulfonate surfactants
JOURNAL Appl. Environ. Microbiol. 69 (2), 938-944 (2003)
PUBMED 12571015
REFERENCE 7 (bases 1 to 3914745)
AUTHORS Schleheck,D., Dong,W., Denger,K., Heinzle,E. and Cook,A.M.
TITLE An alpha-proteobacterium converts linear alkylbenzenesulfonate
surfactants into sulfophenylcarboxylates and linear
alkyldiphenyletherdisulfonate surfactants into
sulfodiphenylethercarboxylates
JOURNAL Appl. Environ. Microbiol. 66 (5), 1911-1916 (2000)
PUBMED 10788359
REFERENCE 8 (bases 1 to 3914745)
AUTHORS Copeland,A., Lucas,S., Lapidus,A., Barry,K., Glavina del Rio,T.,
Dalin,E., Tice,H., Pitluck,S., Saunders,E., Brettin,T., Bruce,D.,
Detter,J.C., Han,C., Schmutz,J., Larimer,F., Land,M., Hauser,L.,
Kyrpides,N., Mikhailova,N. and Richardson,P.
CONSRTM US DOE Joint Genome Institute
TITLE Complete genome sequence and annotation of Parvibaculum
lavamentivorans DS-1
JOURNAL Unpublished
REFERENCE 9 (bases 1 to 3914745)
CONSRTM NCBI Genome Project
TITLE Direct Submission
JOURNAL Submitted (31-JUL-2007) National Center for Biotechnology
Information, NIH, Bethesda, MD 20894, USA
REFERENCE 10 (bases 1 to 3914745)
AUTHORS Copeland,A., Lucas,S., Lapidus,A., Barry,K., Glavina del Rio,T.,
Dalin,E., Tice,H., Pitluck,S., Saunders,E., Brettin,T., Bruce,D.,
Detter,J.C., Han,C., Schmutz,J., Larimer,F., Land,M., Hauser,L.,
Kyrpides,N., Mikhailova,N. and Richardson,P.
CONSRTM US DOE Joint Genome Institute
TITLE Direct Submission
JOURNAL Submitted (18-JUL-2007) 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 CP000774.
URL -- http://www.jgi.doe.gov
JGI Project ID: 4003071
Source DNA available from David Schleheck
(david.schleheck@unsw.edu.au)
Bacteria available from DSMZ or NCIMB: DSM 13023 = NCIMB 13966.
Parvibaculum lavamentivorans DS-1 was enriched from a sewage
treatment plant in Germany, was difficult to isolate (reference 1),
and is the first representative of a novel genus in the
alpha-subclass of Proteobacteria (reference 5). Parvibaculum
lavamentivorans DS-1 is part of a defined three-member bacterial
community which completely mineralises representative congeners of
linear alkylbenzenesulfonate surfactants (reference 4). The
community genome was established by DOE-JGI as part of the 2006
Microbes Program (see also JGI Project Id 4002763 [Comamonas
testosteroni] and 4002762 [Delftia acidovorans]). In addition,
strain DS-1 catalyses the degradation of 16 other anionic and
non-ionic commercial surfactants (reference 5), and generates
degradation intermediates thereof. The organism thus represents the
first tier of many environmentally important surfactant-degrading
communities.
Contacts: David Schleheck (david.schleheck@unsw.edu.au)
Staffan Kjelleberg (kjelleberg@unsw.edu.au)
Alasdair Cook (alasdair.cook@uni-konstanz.de)
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-LANL
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).
COMPLETENESS: full length.
Расположение РНК
[править]| Начало | Конец | Направление | Длина | PID | Ген | COG | Комментарий |
|---|---|---|---|---|---|---|---|
| 112793 | 112869 | - | 77 | 154250456 | Plav_R0001 | - | 11 Arg tRNA |
| 168564 | 168639 | + | 76 | 154250456 | Plav_R0002 | - | 02 Ala tRNA |
| 221491 | 221577 | - | 87 | 154250456 | Plav_R0003 | - | 15 Leu tRNA |
| 244777 | 244866 | + | 90 | 154250456 | Plav_R0004 | - | 08 Ser tRNA |
| 276642 | 276743 | + | 102 | 154250456 | Plav_R0005 | - | SRP RNA; RNA component of signal recognition particle |
| 337190 | 337266 | + | 77 | 154250456 | Plav_R0006 | - | 11 Arg tRNA |
| 448263 | 448336 | + | 74 | 154250456 | Plav_R0007 | - | 01 Gly tRNA |
| 558464 | 558538 | - | 75 | 154250456 | Plav_R0008 | - | 12 Thr tRNA |
| 568078 | 568153 | + | 76 | 154250456 | Plav_R0009 | - | 17 Phe tRNA |
| 609872 | 609948 | + | 77 | 154250456 | Plav_R0010 | - | 09 His tRNA |
| 879651 | 879727 | - | 77 | 154250456 | Plav_R0011 | - | 03 Pro tRNA |
| 879908 | 879982 | + | 75 | 154250456 | Plav_R0012 | - | 05 Gln tRNA |
| 1193339 | 1193414 | - | 76 | 154250456 | Plav_R0013 | - | 13 Val tRNA |
| 1295070 | 1295143 | - | 74 | 154250456 | Plav_R0014 | - | 05 Gln tRNA |
| 1450297 | 1450371 | + | 75 | 154250456 | Plav_R0015 | - | 01 Gly tRNA |
| 1485877 | 1485952 | + | 76 | 154250456 | Plav_R0016 | - | 12 Thr tRNA |
| 1503665 | 1503740 | - | 76 | 154250456 | Plav_R0017 | - | 02 Ala tRNA |
| 1617112 | 1617201 | + | 90 | 154250456 | Plav_R0018 | - | 08 Ser tRNA |
| 1770727 | 1770812 | + | 86 | 154250456 | Plav_R0019 | - | 15 Leu tRNA |
| 1825642 | 1825718 | - | 77 | 154250456 | Plav_R0020 | - | 11 Arg tRNA |
| 1901257 | 1902735 | + | 1479 | 154250456 | Plav_R0021 | - | 16S ribosomal RNA |
| 1902944 | 1903020 | + | 77 | 154250456 | Plav_R0022 | - | 14 Ile tRNA |
| 1903071 | 1903146 | + | 76 | 154250456 | Plav_R0023 | - | 02 Ala tRNA |
| 1903534 | 1906273 | + | 2740 | 154250456 | Plav_R0024 | - | 23S ribosomal RNA |
| 1906370 | 1906487 | + | 118 | 154250456 | Plav_R0050 | - | 5S ribosomal RNA |
| 1906619 | 1906695 | + | 77 | 154250456 | Plav_R0025 | - | 16 Met tRNA |
| 2183140 | 2183214 | + | 75 | 154250456 | Plav_R0026 | - | 13 Val tRNA |
| 2346100 | 2346174 | + | 75 | 154250456 | Plav_R0027 | - | 04 Glu tRNA |
| 2370646 | 2370722 | + | 77 | 154250456 | Plav_R0028 | - | 16 Met tRNA |
| 2494195 | 2494271 | + | 77 | 154250456 | Plav_R0029 | - | 16 Met tRNA |
| 2603077 | 2603398 | + | 322 | 154250456 | Plav_R0030 | - | RNA component of RNaseP |
| 2686129 | 2686204 | + | 76 | 154250456 | Plav_R0031 | - | 10 Lys tRNA |
| 2805410 | 2805496 | + | 87 | 154250456 | Plav_R0032 | - | 15 Leu tRNA |
| 2925484 | 2925559 | - | 76 | 154250456 | Plav_R0033 | - | 12 Thr tRNA |
| 2927938 | 2928022 | + | 85 | 154250456 | Plav_R0034 | - | 18 Tyr tRNA |
| 2928078 | 2928151 | + | 74 | 154250456 | Plav_R0035 | - | 01 Gly tRNA |
| 2929516 | 2929591 | + | 76 | 154250456 | Plav_R0036 | - | 20 Trp tRNA |
| 2977755 | 2977841 | + | 87 | 154250456 | Plav_R0037 | - | 15 Leu tRNA |
| 3054491 | 3054583 | + | 93 | 154250456 | Plav_R0038 | - | 08 Ser tRNA |
| 3126096 | 3126172 | + | 77 | 154250456 | Plav_R0039 | - | 03 Pro tRNA |
| 3148021 | 3148095 | + | 75 | 154250456 | Plav_R0040 | - | 04 Glu tRNA |
| 3171924 | 3172000 | + | 77 | 154250456 | Plav_R0041 | - | 03 Pro tRNA |
| 3172821 | 3172897 | + | 77 | 154250456 | Plav_R0042 | - | 11 Arg tRNA |
| 3191545 | 3191619 | - | 75 | 154250456 | Plav_R0043 | - | 07 Asn tRNA |
| 3203759 | 3203832 | - | 74 | 154250456 | Plav_R0044 | - | 19 Cys tRNA |
| 3262777 | 3262851 | + | 75 | 154250456 | Plav_R0045 | - | 10 Lys tRNA |
| 3315731 | 3315820 | + | 90 | 154250456 | Plav_R0046 | - | 08 Ser tRNA |
| 3444118 | 3444194 | - | 77 | 154250456 | Plav_R0047 | - | 06 Asp tRNA |
| 3444309 | 3444384 | - | 76 | 154250456 | Plav_R0048 | - | 13 Val tRNA |
| 3455338 | 3455422 | - | 85 | 154250456 | Plav_R0049 | - | 15 Leu tRNA |