Mycolicibacterium crocinum strain JCM 16369 plasmid unnamed, complete sequence.
Mycolicibacterium crocinum (Mycobacterium crocinum)
Bacteria; Actinomycetota; Actinomycetes; Mycobacteriales; Mycobacteriaceae; Mycolicibacterium.
Complete Genome Sequences of 14 Nontuberculous Mycobacteria Type Strains
Microbiol Resour Announc 12 (2), e0121422 (2023)
Submitted (22-AUG-2022) Department of Mycobacterium Reference and Research, Research Institute of Tuberculosis, 3-1-24 Matsuyama, Kiyose, Tokyo 204-8533, Japan
Nucleotide sequence updated by submitter
Submitted (15-FEB-2022) Department of Mycobacterium Reference and Research, Research Institute of Tuberculosis, 3-1-24 Matsuyama, Kiyose, Tokyo 204-8533, Japan
REFSEQ INFORMATION: The reference sequence is identical to\nCP092363.2.\n\nOn Oct 6, 2022 this sequence version replaced NZ_CP092363.1.\nBacteria and source DNA available from Japan Collection of\nMicroorganisms (JCM).\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 :: Flye v. 2.9\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 90x\nSequencing Technology :: PacBio Sequel\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 06/25/2023 10:35:29\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) :: 6,068\nCDSs (total) :: 6,013\nGenes (coding) :: 5,901\nCDSs (with protein) :: 5,901\nGenes (RNA) :: 55\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 46\nncRNAs :: 3\nPseudo Genes (total) :: 112\nCDSs (without protein) :: 112\nPseudo Genes (ambiguous residues) :: 0 of 112\nPseudo Genes (frameshifted) :: 43 of 112\nPseudo Genes (incomplete) :: 74 of 112\nPseudo Genes (internal stop) :: 5 of 112\nPseudo Genes (multiple problems) :: 10 of 112\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_005148408.1
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_013470227.1
COORDINATES: similar to AA sequence:RefSeq:WP_007171762.1
COORDINATES: similar to AA sequence:RefSeq:WP_005148411.1
GO:0016887 - ATP hydrolysis activity [Evidence IEA]
GO:0009306 - protein secretion [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR03923.1
COORDINATES: similar to AA sequence:RefSeq:WP_005148415.1
GO:0008236 - serine-type peptidase activity [Evidence IEA]
type VII secretion-associated serine protease mycosin
COORDINATES: similar to AA sequence:RefSeq:WP_005148416.1
GO:0003674 - molecular_function [Evidence IEA]
type VII secretion integral membrane protein EccD
COORDINATES: protein motif:HMM:NF025001.2
COORDINATES: protein motif:HMM:NF025377.2
COORDINATES: similar to AA sequence:RefSeq:WP_005148419.1
COORDINATES: similar to AA sequence:RefSeq:WP_005148421.1
COORDINATES: protein motif:HMM:NF013021.2
COORDINATES: similar to AA sequence:RefSeq:WP_005148423.1
GO:0009986 - cell surface [Evidence IEA]; GO:0005576 - extracellular region [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005148424.1
COORDINATES: similar to AA sequence:RefSeq:WP_005148425.1
COORDINATES: similar to AA sequence:RefSeq:WP_006246558.1
GO:0016787 - hydrolase activity [Evidence IEA]; GO:0008233 - peptidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005148441.1
COORDINATES: similar to AA sequence:RefSeq:WP_005149435.1
COORDINATES: similar to AA sequence:RefSeq:WP_006246572.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_005148509.1
COORDINATES: similar to AA sequence:RefSeq:WP_005148510.1
COORDINATES: protein motif:HMM:NF014616.2
YbaB/EbfC family nucleoid-associated protein
COORDINATES: similar to AA sequence:RefSeq:WP_005148516.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805339.1
COORDINATES: similar to AA sequence:RefSeq:WP_011767793.1
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF014520.2
COORDINATES: similar to AA sequence:RefSeq:WP_011767787.1
ParB N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_005566945.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805512.1
COORDINATES: similar to AA sequence:RefSeq:WP_011896261.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805517.1
COORDINATES: similar to AA sequence:RefSeq:WP_015297724.1
COORDINATES: protein motif:HMM:NF014533.2
GO:0009294 - DNA-mediated transformation [Evidence IEA]
COORDINATES: protein motif:HMM:NF025398.2
COORDINATES: similar to AA sequence:RefSeq:WP_009979393.1
COORDINATES: similar to AA sequence:RefSeq:WP_015297937.1
GO:0005515 - protein binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007776198.1
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_003886042.1
COORDINATES: similar to AA sequence:RefSeq:WP_005148535.1
COORDINATES: similar to AA sequence:RefSeq:WP_005148536.1
COORDINATES: similar to AA sequence:RefSeq:WP_011728362.1
COORDINATES: similar to AA sequence:RefSeq:WP_003881064.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006242117.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
GO:0006826 - iron ion transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014213992.1
iron ABC transporter substrate-binding protein
COORDINATES: protein motif:HMM:NF024242.2
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0043565 - sequence-specific DNA binding [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005512857.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF014430.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - DNA transposition [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011896107.1
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_002856921.1
phenylacetate--CoA ligase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_006246590.1
COORDINATES: similar to AA sequence:RefSeq:WP_006246589.1
GO:0008168 - methyltransferase activity [Evidence IEA]
isoprenylcysteine carboxylmethyltransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011893742.1
GO:0008168 - methyltransferase activity [Evidence IEA]; GO:1904047 - S-adenosyl-L-methionine binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011893745.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
metalloregulator ArsR/SmtB family transcription factor
COORDINATES: similar to AA sequence:RefSeq:WP_014375725.1
COORDINATES: similar to AA sequence:RefSeq:WP_006335479.1
GO:0016787 - hydrolase activity [Evidence IEA]
serine hydrolase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019499059.1
GO:0005886 - plasma membrane [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003931103.1
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_018604265.1
GO:0005507 - copper ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014815918.1
COORDINATES: similar to AA sequence:RefSeq:WP_018604269.1
COORDINATES: similar to AA sequence:RefSeq:WP_011599022.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013006321.1
COORDINATES: similar to AA sequence:RefSeq:WP_011767892.1
COORDINATES: similar to AA sequence:RefSeq:WP_011780831.1
COORDINATES: similar to AA sequence:RefSeq:WP_011514822.1
COORDINATES: similar to AA sequence:RefSeq:WP_018604272.1
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_003887762.1
frameshifted; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_007321360.1
COORDINATES: similar to AA sequence:RefSeq:WP_020645876.1
COORDINATES: similar to AA sequence:RefSeq:WP_011781185.1
GO:0015035 - protein-disulfide reductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018803106.1
rhodanese-like domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_005089199.1
COORDINATES: similar to AA sequence:RefSeq:WP_015355689.1
COORDINATES: similar to AA sequence:RefSeq:NP_216282.2
metal-sensitive transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_016932384.1
frameshifted; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
sulfite exporter TauE/SafE family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011562684.1
COORDINATES: similar to AA sequence:RefSeq:NP_216508.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0005215 - transporter activity [Evidence IEA]
frameshifted; 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_011873643.1
COORDINATES: similar to AA sequence:RefSeq:WP_013828990.1
GO:0008657 - DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) inhibitor activity [Evidence IEA]; GO:0042803 - protein homodimerization activity [Evidence IEA]
GO:0030541 - plasmid partitioning [Evidence IEA]; GO:0051290 - protein heterotetramerization [Evidence IEA]
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_013423214.1
GO:0110001 - toxin-antitoxin complex [Evidence IEA]
GO:0003677 - DNA binding [Evidence IEA]; GO:0097351 - toxin sequestering activity [Evidence IEA]
GO:0045927 - positive regulation of growth [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
type II toxin-antitoxin system Phd/YefM family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_013838297.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805386.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805387.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805388.1
multiubiquitin domain-containing protein
COORDINATES: protein motif:HMM:NF017885.2
COORDINATES: protein motif:HMM:NF012311.2
COORDINATES: similar to AA sequence:RefSeq:WP_014391180.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF024109.2
COORDINATES: protein motif:HMM:NF024816.2
COORDINATES: similar to AA sequence:RefSeq:WP_018604278.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF014567.2
COORDINATES: similar to AA sequence:RefSeq:WP_011767870.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0019829 - ATPase-coupled monoatomic cation transmembrane transporter activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]; GO:0015662 - P-type ion transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011893698.1
GO:0004129 - cytochrome-c oxidase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF013700.2
GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011767864.1
GO:0045892 - negative regulation of DNA-templated transcription [Evidence IEA]
BlaI/MecI/CopY family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_011767863.1
COORDINATES: similar to AA sequence:RefSeq:WP_005628350.1
COORDINATES: similar to AA sequence:RefSeq:WP_011891808.1
COORDINATES: similar to AA sequence:RefSeq:WP_003881526.1
COORDINATES: similar to AA sequence:RefSeq:WP_011893708.1
COORDINATES: similar to AA sequence:RefSeq:WP_005142483.1
NlpC/P60 family peptidoglycan endopeptidase RipB
COORDINATES: similar to AA sequence:RefSeq:WP_011856831.1
COORDINATES: protein motif:HMM:NF016149.2
GO:0042597 - periplasmic space [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_033725343.1
COORDINATES: similar to AA sequence:RefSeq:WP_020556356.1
COORDINATES: similar to AA sequence:RefSeq:WP_019311198.1
GO:0008324 - monoatomic cation transmembrane transporter activity [Evidence IEA]
GO:0006812 - monoatomic cation transport [Evidence IEA]; GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005139600.1
COORDINATES: similar to AA sequence:RefSeq:WP_005110344.1
COORDINATES: similar to AA sequence:RefSeq:WP_005086309.1
COORDINATES: similar to AA sequence:RefSeq:WP_010949005.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]; GO:0009897 - external side of plasma membrane [Evidence IEA]; GO:0030288 - outer membrane-bounded periplasmic space [Evidence IEA]
GO:0015415 - ATPase-coupled phosphate ion transmembrane transporter activity [Evidence IEA]; GO:0042301 - phosphate ion binding [Evidence IEA]
phosphate ABC transporter substrate-binding protein PstS
COORDINATES: similar to AA sequence:RefSeq:WP_006339401.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0015446 - ATPase-coupled arsenite transmembrane transporter activity [Evidence IEA]
GO:0071722 - detoxification of arsenic-containing substance [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017679680.1
arsenite efflux transporter metallochaperone ArsD
COORDINATES: similar to AA sequence:RefSeq:WP_018604091.1
COORDINATES: similar to AA sequence:RefSeq:WP_003944644.1
GO:0030612 - arsenate reductase (thioredoxin) activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005141617.1
Rv2640c family ArsR-like transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_003887761.1
ArsI/CadI family heavy metal resistance metalloenzyme
COORDINATES: similar to AA sequence:RefSeq:WP_016881890.1
COORDINATES: similar to AA sequence:RefSeq:WP_005141614.1
GO:0015267 - channel activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008376397.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007172605.1
COORDINATES: similar to AA sequence:RefSeq:WP_014212710.1
COORDINATES: protein motif:HMM:NF026936.2
COORDINATES: similar to AA sequence:RefSeq:WP_019283825.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805373.1
COORDINATES: similar to AA sequence:RefSeq:WP_016889783.1
COORDINATES: similar to AA sequence:RefSeq:WP_005144173.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805438.1
COORDINATES: similar to AA sequence:RefSeq:WP_005144170.1
COORDINATES: similar to AA sequence:RefSeq:WP_005144169.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805435.1
COORDINATES: similar to AA sequence:RefSeq:WP_005144163.1
COORDINATES: similar to AA sequence:RefSeq:WP_006247664.1
COORDINATES: similar to AA sequence:RefSeq:WP_005144160.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805431.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805430.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805429.1
COORDINATES: similar to AA sequence:RefSeq:WP_005148395.1
COORDINATES: similar to AA sequence:RefSeq:WP_005148396.1
COORDINATES: similar to AA sequence:RefSeq:WP_005148400.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: protein motif:HMM:NF013540.2
COORDINATES: protein motif:HMM:NF024056.2
COORDINATES: similar to AA sequence:RefSeq:WP_005148407.1