Mycobacterium kubicae strain NJH_MKUB1 plasmid pNJH01.
Bacteria; Actinomycetota; Actinomycetes; Mycobacteriales; Mycobacteriaceae; Mycobacterium; Mycobacterium simiae complex.
Complete genomes of two Mycobacterium kubicae isolates
Submitted (03-OCT-2019) Center for Genes, Environment, and Health, National Jewish Health, 1400 Jackson Street, Denver, CO 80206, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP045082.1.\nAssembly not circularized.\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##Genome-Assembly-Data-START##\nAssembly Method :: Unicycler v. 0.4.4\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 313x\nSequencing Technology :: Oxford Nanopore MiniION; Illumina HiSeq\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 04/28/2023 11:04:01\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) :: 5,156\nCDSs (total) :: 5,101\nGenes (coding) :: 4,992\nCDSs (with protein) :: 4,992\nGenes (RNA) :: 55\nrRNAs :: 1, 1, 1 (5S, 16S, 23S)\ncomplete rRNAs :: 1, 1, 1 (5S, 16S, 23S)\ntRNAs :: 49\nncRNAs :: 3\nPseudo Genes (total) :: 109\nCDSs (without protein) :: 109\nPseudo Genes (ambiguous residues) :: 0 of 109\nPseudo Genes (frameshifted) :: 48 of 109\nPseudo Genes (incomplete) :: 64 of 109\nPseudo Genes (internal stop) :: 12 of 109\nPseudo Genes (multiple problems) :: 14 of 109\n##Genome-Annotation-Data-END##
COORDINATES: similar to AA sequence:RefSeq:WP_005632887.1
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: similar to AA sequence:RefSeq:WP_011723608.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_011723607.1
COORDINATES: similar to AA sequence:RefSeq:WP_016888813.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016888812.1
COORDINATES: similar to AA sequence:RefSeq:WP_016888811.1
COORDINATES: similar to AA sequence:RefSeq:WP_012157504.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0004674 - protein serine/threonine kinase activity [Evidence IEA]
GO:0006468 - protein phosphorylation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014096231.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0016787 - hydrolase activity [Evidence IEA]
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_016889553.1
COORDINATES: similar to AA sequence:RefSeq:WP_018513759.1
GO:0009007 - site-specific DNA-methyltransferase (adenine-specific) activity [Evidence IEA]
GO:0032775 - DNA methylation on adenine [Evidence IEA]
COORDINATES: protein motif:HMM:NF016724.2
COORDINATES: similar to AA sequence:RefSeq:WP_015297902.1
COORDINATES: protein motif:HMM:NF024109.2
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019738165.1
COORDINATES: protein motif:HMM:NF014520.2
COORDINATES: protein motif:HMM:NF024949.2
helix-turn-helix transcriptional regulator
COORDINATES: protein motif:HMM:NF013073.2
GO:0016787 - hydrolase activity [Evidence IEA]; GO:0008233 - peptidase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF013793.2
COORDINATES: similar to AA sequence:RefSeq:WP_014384952.1
RNA-guided endonuclease TnpB family protein
COORDINATES: similar to AA sequence:RefSeq:WP_020458292.1
GO:0004803 - transposase activity [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012393308.1
COORDINATES: similar to AA sequence:RefSeq:WP_019811983.1
type II toxin-antitoxin system PemK/MazF family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_015993801.1
ribbon-helix-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011291581.1
COORDINATES: similar to AA sequence:RefSeq:WP_017583129.1
COORDINATES: protein motif:HMM:NF037368.2
COORDINATES: similar to AA sequence:RefSeq:WP_011777820.1
COORDINATES: similar to AA sequence:RefSeq:WP_005113034.1
COORDINATES: similar to AA sequence:RefSeq:WP_011855063.1
COORDINATES: similar to AA sequence:RefSeq:WP_005113038.1
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
COORDINATES: similar to AA sequence:RefSeq:WP_013882312.1
GO:0008168 - methyltransferase activity [Evidence IEA]
isoprenylcysteine carboxylmethyltransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_005629236.1
GO:0008168 - methyltransferase activity [Evidence IEA]; GO:1904047 - S-adenosyl-L-methionine binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016895222.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
metalloregulator ArsR/SmtB family transcription factor
COORDINATES: similar to AA sequence:RefSeq:WP_016892222.1
COORDINATES: similar to AA sequence:RefSeq:WP_005106763.1
COORDINATES: similar to AA sequence:RefSeq:WP_005100828.1
COORDINATES: similar to AA sequence:RefSeq:WP_005101385.1
COORDINATES: similar to AA sequence:RefSeq:WP_005102337.1
COORDINATES: similar to AA sequence:RefSeq:WP_005109162.1
COORDINATES: similar to AA sequence:RefSeq:WP_005103111.1
COORDINATES: similar to AA sequence:RefSeq:WP_005113485.1
COORDINATES: protein motif:HMM:NF013127.2
COORDINATES: protein motif:HMM:NF013677.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
COORDINATES: protein motif:HMM:NF033516.0
COORDINATES: similar to AA sequence:RefSeq:WP_005113488.1
nucleotidyl transferase AbiEii/AbiGii toxin family protein
COORDINATES: similar to AA sequence:RefSeq:WP_005115616.1
COORDINATES: protein motif:HMM:NF013561.2
COORDINATES: similar to AA sequence:RefSeq:WP_005113456.1
COORDINATES: similar to AA sequence:RefSeq:WP_011562805.1
RAMP superfamily CRISPR-associated protein
COORDINATES: similar to AA sequence:RefSeq:WP_011896166.1
COORDINATES: similar to AA sequence:RefSeq:WP_011896165.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF012403.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0004386 - helicase activity [Evidence IEA]; GO:0003676 - nucleic acid binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005113452.1
COORDINATES: similar to AA sequence:RefSeq:WP_015298111.1
phosphoadenosine phosphosulfate reductase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_013470245.1
COORDINATES: similar to AA sequence:RefSeq:WP_016334836.1
COORDINATES: protein motif:HMM:NF014898.2
GO:0015074 - DNA integration [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005113447.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011599951.1
COORDINATES: similar to AA sequence:RefSeq:WP_006244162.1
COORDINATES: similar to AA sequence:RefSeq:WP_005114948.1
COORDINATES: protein motif:HMM:NF025200.2
COORDINATES: similar to AA sequence:RefSeq:WP_076611777.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.