Sign in to NCBI
skip to main content

Sequence Set Browser

 

NZ_AAUJ00000000.2 Comamonas testosteroni KF-1

Master
# of Scaffolds/Chrs: 1
BioProject: PRJNA224116
BioSample: SAMN02441780
Assembly: GCF_000168855.1
Keywords: WGS
Annotation: Scaffolds
Organism: Comamonas testosteroni KF-1show lineagehide lineage
Biosource:
/mol_type = genomic
/strain = KF-1
WGS: AAUJ02000001
Scaffolds: NZ_AAUJ02000001:NZ_AAUJ02000001
1 scaffold, 5,303 proteins, total length is 6,026,527 bases
Reference:
Mineralization of individual congeners of linear alkylbenzenesulfonate by defined pairs of heterotrophic bacteria : Appl. Environ. Microbiol. 70 (7), 4053-4063 (2004) – Schleheck,D., Knepper,T.P., Fischer,K., Cook,A.M.
Submission:
Submitted (13-NOV-2006) US DOE Joint Genome Institute, 2800 Mitchell Drive B100, Walnut Creek, CA 94598-1698, USA – show 11 authorshide authors
Copeland,A., Lucas,S., Lapidus,A., Barry,K., Glavina del Rio,T., Dalin,E., Tice,H., Bruce,D., Pitluck,S., Richardson,P., US DOE Joint Genome Institute (JGI-PGF)
Submission:
Submitted (02-JAN-2009) US DOE Joint Genome Institute, 2800 Mitchell Drive B100, Walnut Creek, CA 94598-1698, USA – show 22 authorshide authors
Lucas,S., Copeland,A., Lapidus,A., Glavina del Rio,T., Dalin,E., Tice,H., Bruce,D., Goodwin,L., Pitluck,S., LaButti,K.M., Lowry,S., Sun,H., Larimer,F., Land,M.L., Hauser,L., Kjelleberg,S., Cook,A., Knepper,T.P., Fischer,K., Schleheck,D., Richardson,P., US DOE Joint Genome Institute (JGI-PGF)

On Jan 21, 2009 this sequence version replaced gi:118054397.

The Comamonas testosteroni KF-1 whole genome shotgun (WGS) project has the project accession NZ_AAUJ00000000. This version of the project (02) has the accession number NZ_AAUJ02000000, and consists of sequence AAUJ02000001.

URL -- http://www.jgi.doe.gov JGI Project ID: 4002763 Source DNA available from David Schleheck (david.schleheck@uni-konstanz.de) Bacteria available from DSMZ: DSM 14576 (http://www.dsmz.de) Contacts: David Schleheck (david.schleheck@uni-konstanz.de) Staffan Kjelleberg (s.kjelleberg@unsw.edu.au) Alasdair Cook (alasdair.cook@uni-konstanz.de) David Bruce (microbe@cuba.jgi-psf.org) Comamonas testosteroni KF-1 was isolated from a sewage treatment plant and is part of a defined three-member bacterial community which completely mineralises representative congeners of linear alkylbenzenesulfonate (LAS) surfactants (reference 1). The community genome was kindly established by DOE-JGI as part of the 2006 Microbes Program (see also JGI PROJECT ID 4003071 [Parvibaculum lavamentivorans DS-1] and 4002762 [Delftia acidovorans SPH-1]). The first-tier organism Parvibaculum lavamentivorans DS-1 converts LAS surfactants into many sulfophenylcarboxylates (SPCs), and Comamonas testosteroni KF-1 represents a second-tier organism, by completely degrading some of these SPCs; Delftia acidovorans SPH-1 degrades a different set of SPCs. Whole genome sequencing and draft assembly at JGI-PGF Annotation by JGI-ORNL 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) We are labeling this project as Permanent Draft. The assembly is NOT closed. We could not close the genome due to clone viability issues. The fosmid data for this project was suspect and likely contaminated. Several clones do circularize the contig, and a PCR product was obtained that spans the ends but all attempts at primer walking and transforming the amplicon were unsucessful. At this time no additional work is planned for this project.

##Genome-Annotation-Data-START##
Annotation Provider : NCBI
Annotation Date : 05/15/2017 21:28:50
Annotation Pipeline : NCBI Prokaryotic Genome Annotation Pipeline
Annotation Method : Best-placed reference protein set; GeneMarkS+
Annotation Software revision : 4.2
Features Annotated : Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
Genes (total) : 5,555
CDS (total) : 5,435
Genes (coding) : 5,328
CDS (coding) : 5,328
Genes (RNA) : 120
rRNAs : 6, 6, 6 ( 5S, 16S, 23S )
complete rRNAs : 6, 6, 6 ( 5S, 16S, 23S )
partial rRNAs :
tRNAs : 99
ncRNAs : 3
Pseudo Genes (total) : 107
Pseudo Genes (ambiguous residues) : 0 of 107
Pseudo Genes (frameshifted) : 54 of 107
Pseudo Genes (incomplete) : 61 of 107
Pseudo Genes (internal stop) : 35 of 107
Pseudo Genes (multiple problems) : 35 of 107
##Genome-Annotation-Data-END##