Mycolicibacterium madagascariense strain JCM 13574 plasmid pJCM13574.
Mycolicibacterium madagascariense (Mycobacterium madagascariense)
Bacteria; Actinomycetota; Actinomycetes; Mycobacteriales; Mycobacteriaceae; Mycolicibacterium.
Comprehensive subspecies identification of 175 nontuberculous mycobacteria species based on 7547 genomic profiles
Submitted (05-FEB-2020) Contact:Yuki Matsumoto Research Institute for Microbial Diseases, Osaka University, Department of infection metagenomics; Yamadaoka 3-1, Suita, Osaka 565-0871, Japan
REFSEQ INFORMATION: The reference sequence is identical to\nAP022611.1.\nAnnotated at DFAST https://dfast.nig.ac.jp/\n\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 :: Canu v. 1.7\nGenome Coverage :: 409x\nSequencing Technology :: Oxford Nanopore Technologies MinION;\n Illumina HiSeq2500\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 05/06/2023 01:46:14\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) :: 5,657\nCDSs (total) :: 5,601\nGenes (coding) :: 5,497\nCDSs (with protein) :: 5,497\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) :: 104\nCDSs (without protein) :: 104\nPseudo Genes (ambiguous residues) :: 0 of 104\nPseudo Genes (frameshifted) :: 51 of 104\nPseudo Genes (incomplete) :: 56 of 104\nPseudo Genes (internal stop) :: 7 of 104\nPseudo Genes (multiple problems) :: 7 of 104\n##Genome-Annotation-Data-END##
type strain of Mycolicibacterium madagascariense
COORDINATES: similar to AA sequence:RefSeq:WP_014805524.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_014805527.1
COORDINATES: similar to AA sequence:RefSeq:WP_007172127.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_014805531.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805371.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805372.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805373.1
COORDINATES: similar to AA sequence:RefSeq:WP_017206378.1
COORDINATES: similar to AA sequence:RefSeq:WP_005148616.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004521 - endoribonuclease activity [Evidence IEA]; GO:0003723 - RNA binding [Evidence IEA]
type II toxin-antitoxin system PemK/MazF family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_014805376.1
COORDINATES: similar to AA sequence:RefSeq:WP_006244013.1
COORDINATES: similar to AA sequence:RefSeq:WP_020663589.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_005068429.1
COORDINATES: similar to AA sequence:RefSeq:WP_003414864.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011724575.1
COORDINATES: similar to AA sequence:RefSeq:WP_009883506.1
COORDINATES: protein motif:HMM:NF024109.2
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005260637.1
GO:0016620 - oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor [Evidence IEA]
COORDINATES: protein motif:HMM:NF014564.2
GO:0008410 - CoA-transferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020459219.1
GO:0016740 - transferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013673522.1
GO:0003824 - catalytic activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF013098.2
COORDINATES: protein motif:HMM:NF025114.2
GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA]; GO:0050661 - NADP binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF016777.2
COORDINATES: similar to AA sequence:RefSeq:WP_014193371.1
COORDINATES: similar to AA sequence:RefSeq:WP_005560779.1
COORDINATES: protein motif:HMM:NF013920.2
COORDINATES: protein motif:HMM:NF024966.2
nuclear transport factor 2 family protein
COORDINATES: protein motif:HMM:NF016129.2
COORDINATES: similar to AA sequence:RefSeq:WP_009741138.1
GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010240726.1
GO:0016627 - oxidoreductase activity, acting on the CH-CH group of donors [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005256390.1
GO:0016812 - hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014214368.1
COORDINATES: similar to AA sequence:RefSeq:WP_020555536.1
COORDINATES: similar to AA sequence:RefSeq:WP_015632605.1
COORDINATES: protein motif:HMM:NF012946.2
COORDINATES: protein motif:HMM:NF012711.2
class I adenylate-forming enzyme family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011728068.1
COORDINATES: similar to AA sequence:RefSeq:WP_003933879.1
GO:0016829 - lyase activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014058461.1
MaoC/PaaZ C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_018532801.1
CaiB/BaiF CoA-transferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_020020487.1
COORDINATES: similar to AA sequence:RefSeq:WP_014375963.1
COORDINATES: similar to AA sequence:RefSeq:WP_009332259.1
GO:0051537 - 2 iron, 2 sulfur cluster binding [Evidence IEA]; GO:0010181 - FMN binding [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF019604.2
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_005182707.1
GO:0051539 - 4 iron, 4 sulfur cluster binding [Evidence IEA]; GO:0009055 - electron transfer activity [Evidence IEA]; GO:0005506 - iron ion binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF012935.2
GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA]; GO:0016614 - oxidoreductase activity, acting on CH-OH group of donors [Evidence IEA]
GMC family oxidoreductase N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_005484148.1
COORDINATES: similar to AA sequence:RefSeq:WP_016895512.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003897806.1
COORDINATES: similar to AA sequence:RefSeq:WP_003926709.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011768141.1
COORDINATES: similar to AA sequence:RefSeq:WP_011558931.1
COORDINATES: similar to AA sequence:RefSeq:WP_003930402.1
COORDINATES: similar to AA sequence:RefSeq:WP_011558933.1
COORDINATES: similar to AA sequence:RefSeq:WP_011558934.1
COORDINATES: similar to AA sequence:RefSeq:WP_011778199.1
COORDINATES: similar to AA sequence:RefSeq:WP_011558936.1
GO:0015914 - phospholipid transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011892996.1
COORDINATES: similar to AA sequence:RefSeq:WP_003881850.1
ATP-binding cassette domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_015355629.1
COORDINATES: similar to AA sequence:RefSeq:WP_007774770.1
COORDINATES: protein motif:HMM:NF014664.2
carboxymuconolactone decarboxylase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_003891925.1
COORDINATES: similar to AA sequence:RefSeq:WP_011892154.1
mycofactocin-coupled SDR family oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_011724106.1
COORDINATES: similar to AA sequence:RefSeq:WP_014001709.1
COORDINATES: similar to AA sequence:RefSeq:WP_018500749.1
COORDINATES: similar to AA sequence:RefSeq:WP_011727012.1
SDR family NAD(P)-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_005191105.1
COORDINATES: similar to AA sequence:RefSeq:WP_008262728.1
COORDINATES: similar to AA sequence:RefSeq:WP_011562310.1
COORDINATES: similar to AA sequence:RefSeq:WP_020785981.1
COORDINATES: similar to AA sequence:RefSeq:WP_007774750.1
GO:0050656 - 3'-phosphoadenosine 5'-phosphosulfate binding [Evidence IEA]; GO:0008146 - sulfotransferase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF024950.2
COORDINATES: similar to AA sequence:RefSeq:WP_007774746.1
COORDINATES: similar to AA sequence:RefSeq:WP_020104250.1
COORDINATES: similar to AA sequence:RefSeq:WP_011892167.1
GO:0010181 - FMN binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
GO:0008152 - metabolic process [Evidence IEA]
This protein belongs to a clade of FMN-dependent monooxygenases, within a broader family of flavin-dependent oxidoreductases, the luciferase-like monooxygenase (LMM) family, some of whose members use coenzyme F420 rather than FMN.; This protein belongs to a clade of FMN-dependent monooxygenases, within a broader family of flavin-dependent oxidoreductases, the luciferase-like monooxygenase (LMM) family, some of whose members use coenzyme F420 rather than FMN; Derived by automated computational analysis using gene prediction method: Protein Homology.
NtaA/DmoA family FMN-dependent monooxygenase
COORDINATES: similar to AA sequence:RefSeq:WP_014941476.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_020106600.1
COORDINATES: similar to AA sequence:RefSeq:WP_011559407.1
COORDINATES: similar to AA sequence:RefSeq:WP_007777326.1
COORDINATES: similar to AA sequence:RefSeq:WP_020105935.1
COORDINATES: similar to AA sequence:RefSeq:WP_007166367.1
lysophospholipid acyltransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011561138.1
GO:0008374 - O-acyltransferase activity [Evidence IEA]
wax ester/triacylglycerol synthase family O-acyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_014805380.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805381.1
COORDINATES: similar to AA sequence:RefSeq:WP_006246253.1
COORDINATES: protein motif:HMM:NF020387.2
COORDINATES: similar to AA sequence:RefSeq:WP_006246412.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805565.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805563.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805562.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805561.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_011212283.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805727.1
ParB N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_018179045.1
COORDINATES: similar to AA sequence:RefSeq:WP_015297987.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805729.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805730.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805852.1
COORDINATES: similar to AA sequence:RefSeq:WP_011856867.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805734.1
COORDINATES: similar to AA sequence:RefSeq:WP_015298181.1
COORDINATES: similar to AA sequence:RefSeq:WP_011857308.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014210461.1
COORDINATES: similar to AA sequence:RefSeq:WP_014211268.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0003910 - DNA ligase (ATP) activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]; GO:0006281 - DNA repair [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007769389.1
GO:0015035 - protein-disulfide reductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020100711.1
GO:0000166 - nucleotide binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019510147.1
COORDINATES: similar to AA sequence:RefSeq:WP_014850877.1
COORDINATES: similar to AA sequence:RefSeq:WP_016887611.1
metal-sensitive transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_014805470.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011562892.1
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_014805479.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014805480.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805481.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805482.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805483.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805484.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805485.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805487.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805488.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805489.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805490.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805491.1
GO:0009306 - protein secretion [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014805492.1
GO:0008236 - serine-type peptidase activity [Evidence IEA]
type VII secretion-associated serine protease mycosin
COORDINATES: similar to AA sequence:RefSeq:WP_014805493.1
GO:0003674 - molecular_function [Evidence IEA]
type VII secretion integral membrane protein EccD
COORDINATES: similar to AA sequence:RefSeq:WP_014805494.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805495.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805874.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805497.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805498.1
COORDINATES: protein motif:HMM:NF013127.2
COORDINATES: similar to AA sequence:RefSeq:WP_014805500.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805501.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805502.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805881.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805505.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805506.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805507.1
YbaB/EbfC family nucleoid-associated protein
COORDINATES: similar to AA sequence:RefSeq:WP_014805508.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805509.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805510.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805511.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805891.1
COORDINATES: protein motif:HMM:NF025107.2
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014805895.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805893.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805894.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805897.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805898.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805519.1
COORDINATES: similar to AA sequence:RefSeq:WP_005148441.1
GO:0016787 - hydrolase activity [Evidence IEA]; GO:0008233 - peptidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014805522.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805523.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805525.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805526.1
helicase C-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF022231.2
COORDINATES: similar to AA sequence:RefSeq:WP_019819475.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0016787 - hydrolase activity [Evidence IEA]