Gordonia bronchialis DSM 43247 plasmid pGBRO01, complete sequence.
Bacteria; Actinobacteria; Corynebacteriales; Gordoniaceae; Gordonia.
Complete genome sequence of Gordonia bronchialis type strain (3410)
The complete plasmid of Gordonia bronchialis DSM 43247
Submitted (21-OCT-2009) US DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598-1698, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP001803.1.\nURL -- http://www.jgi.doe.gov\nJGI Project ID: 4083028\nSource DNA and organism available from Hans-Peter Klenk at the\nGerman Collection of Microorganisms and Cell Cultures (DSMZ)\n(hans-peter.klenk@dsmz.de)\nContacts: Jonathan A. Eisen (jaeisen@ucdavis.edu)\n David Bruce (microbe@cuba.jgi-psf.org)\nWhole genome sequencing and draft assembly at JGI-PGF\nFinishing done by JGI-LANL\nAnnotation by JGI-ORNL and JGI-PGF\nThe JGI and collaborators endorse the principles for the\ndistribution and use of large scale sequencing data adopted by the\nlarger genome sequencing community and urge users of this data to\nfollow them. It is our intention to publish the work of this\nproject in a timely fashion and we welcome collaborative\ninteraction on the project and analysis.\n(http://www.genome.gov/page.cfm?pageID=10506376).\nThe annotation was added by the NCBI Prokaryotic Genome Annotation\nPipeline (PGAP). Information about PGAP can be found here:\nhttps://www.ncbi.nlm.nih.gov/genome/annotation_prok/\n\n##Metadata-START##\nOrganism Display Name :: Gordonia bronchialis DSM 43247\nCulture Collection ID :: DSM 43247, ATCC 25592, JCM 3198, NCTC\n 10667, LMG 5355\nGOLD Stamp ID :: Gi02258\nFunding Program :: DOE-GEBA 2007\nGene Calling Method :: Prodigal\nIsolation Site :: Sputum of woman with cavitary disease of\n both upper lungs\nHost Name :: Homo sapiens\nHost Gender :: Female\nHost Health :: Patient with cavitary disease\nBody Sample Site :: Airways\nOxygen Requirement :: Aerobe\nCell Shape :: Rod-shaped\nMotility :: Nonmotile\nTemperature Range :: Mesophile\nTemperature Optimum :: 28C\nGram Staining :: gram+\nBiotic Relationship :: Free living\nDiseases :: Bacteremia, Endocarditis\nHabitat :: Host\nPhenotypes :: Pathogen\n##Metadata-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/07/2022 17:01:36\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.3\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 4,985\nCDSs (total) :: 4,927\nGenes (coding) :: 4,694\nCDSs (with protein) :: 4,694\nGenes (RNA) :: 58\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 49\nncRNAs :: 3\nPseudo Genes (total) :: 233\nCDSs (without protein) :: 233\nPseudo Genes (ambiguous residues) :: 0 of 233\nPseudo Genes (frameshifted) :: 121 of 233\nPseudo Genes (incomplete) :: 113 of 233\nPseudo Genes (internal stop) :: 23 of 233\nPseudo Genes (multiple problems) :: 22 of 233\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF025001.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF013265.2
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF024835.2
helix-turn-helix transcriptional regulator
COORDINATES: protein motif:HMM:NF016777.2
COORDINATES: protein motif:HMM:NF012296.2
GO:0020037 - heme binding [Evidence IEA]; GO:0005506 - iron ion binding [Evidence IEA]; GO:0016705 - oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011331202.1
COORDINATES: similar to AA sequence:RefSeq:WP_016881281.1
COORDINATES: protein motif:HMM:NF022388.2
COORDINATES: similar to AA sequence:RefSeq:WP_005203791.1
CPBP family intramembrane metalloprotease
COORDINATES: similar to AA sequence:RefSeq:WP_005179525.1
COORDINATES: protein motif:HMM:NF020387.2
HEPN-associated N-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF013775.2
COORDINATES: protein motif:HMM:NF021255.2
COORDINATES: similar to AA sequence:RefSeq:WP_076612120.1
GO:0004803 - transposase activity [Evidence IEA]
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_014928933.1
COORDINATES: similar to AA sequence:RefSeq:WP_012836489.1
class I SAM-dependent DNA methyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_014928931.1
COORDINATES: similar to AA sequence:RefSeq:WP_014928930.1
COORDINATES: similar to AA sequence:RefSeq:WP_012836492.1
COORDINATES: protein motif:HMM:NF024758.2
trypsin-like peptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014928908.1
type IV toxin-antitoxin system AbiEi family antitoxin domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014928907.1
nucleotidyl transferase AbiEii/AbiGii toxin family protein
COORDINATES: similar to AA sequence:RefSeq:WP_014928911.1
COORDINATES: similar to AA sequence:RefSeq:WP_015298271.1
COORDINATES: similar to AA sequence:RefSeq:WP_012880200.1
GO:0008168 - methyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007322720.1
GO:0097573 - glutathione oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014928897.1
COORDINATES: similar to AA sequence:RefSeq:WP_014928896.1
COORDINATES: similar to AA sequence:RefSeq:WP_014928894.1
COORDINATES: similar to AA sequence:RefSeq:WP_014928892.1
conjugative relaxase TrwC/TraI family protein
COORDINATES: protein motif:HMM:NF016724.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF027584.2
COORDINATES: similar to AA sequence:RefSeq:WP_014928879.1
COORDINATES: protein motif:HMM:NF013618.2
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_003900223.1
incomplete; partial in the middle of a contig; missing N-terminus and C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF013700.2
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.