Mycolicibacterium gilvum Spyr1 plasmid pMSPYR102, complete sequence.
Bacteria; Actinomycetota; Actinomycetes; Mycobacteriales; Mycobacteriaceae; Mycolicibacterium.
Complete genome sequence of Mycobacterium sp. strain (Spyr1) and reclassification to Mycobacterium gilvum Spyr1
Complete sequence of plasmid2 of Mycobacterium sp. Spyr1
Submitted (14-DEC-2010) US DOE Joint Genome Institute, 2800 Mitchell Drive B310, Walnut Creek, CA 94598-1698, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP002387.1.\nURL -- http://www.jgi.doe.gov\nJGI Project ID: 4043073\nSource DNA and organism available from Nikos C. Kyrpides\n(nckyrpides@lbl.gov)\nContacts: Nikos C. Kyrpides (nckyrpides@lbl.gov)\n Tanja Woyke (microbe@cuba.jgi-psf.org)\nAnnotation done by JGI-ORNL and JGI-PGF\nFinishing done by JGI-LANL\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##MIGS-Data-START##\ninvestigation_type :: bacteria_archaea\nproject_name :: Mycobacterium gilvum Spyr1\ncollection_date :: Missing\nlat_lon :: 39.674495 20.840141\ndepth :: Missing\nalt_elev :: Missing\ncountry :: Greece\nenvironment :: Creosote-contaminated soil, Soil\nnum_replicons :: 3\nref_biomaterial :: Missing\nbiotic_relationship :: Free living\ntrophic_level :: Chemoorganotroph\nrel_to_oxygen :: Aerobe\nisol_growth_condt :: Missing\nsequencing_meth :: WGS\nassembly :: Arachne v. 3.0\nfinishing_strategy :: Finished\nGOLD Stamp ID :: Gi02013\nGreengenes ID :: 144250\nIsolation Site :: \"creosote contaminated site near Ioannina,\n Epirus, Greece\"\nCell Shape :: Rod-shaped\nMotility :: Nonmotile\nSporulation :: Nonsporulating\nTemperature Range :: Mesophile\nGram Staining :: Gram+\nDiseases :: None\n##MIGS-Data-END##\n\n##Genome-Assembly-Data-START##\nFinishing Goal :: Finished\nCurrent Finishing Status :: Finished\nAssembly Method :: Arachne v. 3.0\nGenome Coverage :: 30x\nSequencing Technology :: Sanger\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 04/27/2023 02:03:53\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.5\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 5,552\nCDSs (total) :: 5,496\nGenes (coding) :: 5,337\nCDSs (with protein) :: 5,337\nGenes (RNA) :: 56\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 47\nncRNAs :: 3\nPseudo Genes (total) :: 159\nCDSs (without protein) :: 159\nPseudo Genes (ambiguous residues) :: 0 of 159\nPseudo Genes (frameshifted) :: 66 of 159\nPseudo Genes (incomplete) :: 105 of 159\nPseudo Genes (internal stop) :: 12 of 159\nPseudo Genes (multiple problems) :: 21 of 159\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_011896304.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_007172374.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011896306.1
COORDINATES: similar to AA sequence:RefSeq:WP_011896339.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_013470249.1
COORDINATES: similar to AA sequence:RefSeq:WP_011896311.1
COORDINATES: similar to AA sequence:RefSeq:WP_011896312.1
GO:0005886 - plasma membrane [Evidence IEA]
GO:0005525 - GTP binding [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011896313.1
COORDINATES: similar to AA sequence:RefSeq:WP_020618004.1
COORDINATES: similar to AA sequence:RefSeq:WP_011896315.1
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_014711599.1
COORDINATES: similar to AA sequence:RefSeq:WP_012296238.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013470266.1
COORDINATES: similar to AA sequence:RefSeq:WP_011896322.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_011896323.1
COORDINATES: similar to AA sequence:RefSeq:WP_005147291.1
COORDINATES: similar to AA sequence:RefSeq:WP_011896326.1
COORDINATES: similar to AA sequence:RefSeq:WP_007170756.1
COORDINATES: similar to AA sequence:RefSeq:WP_011896327.1