Mycolicibacterium alvei strain JCM 12272 plasmid pJCM12272, complete sequence.
Mycolicibacterium alvei (Mycobacterium alvei)
Bacteria; Actinobacteria; Corynebacteriales; 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\nAP022566.1.\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 :: 269x\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 :: 12/15/2022 00:43:53\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) :: 5,848\nCDSs (total) :: 5,763\nGenes (coding) :: 5,643\nCDSs (with protein) :: 5,643\nGenes (RNA) :: 85\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 76\nncRNAs :: 3\nPseudo Genes (total) :: 120\nCDSs (without protein) :: 120\nPseudo Genes (ambiguous residues) :: 0 of 120\nPseudo Genes (frameshifted) :: 63 of 120\nPseudo Genes (incomplete) :: 68 of 120\nPseudo Genes (internal stop) :: 6 of 120\nPseudo Genes (multiple problems) :: 15 of 120\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: similar to AA sequence:RefSeq:WP_015308205.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_003933635.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_005061889.1
COORDINATES: similar to AA sequence:RefSeq:WP_005572465.1
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_003883256.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612118.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015297576.1
COORDINATES: similar to AA sequence:RefSeq:WP_012832693.1
DDE-type integrase/transposase/recombinase
COORDINATES: similar to AA sequence:RefSeq:WP_005102168.1
Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
COORDINATES: similar to AA sequence:RefSeq:WP_005115630.1
COORDINATES: similar to AA sequence:RefSeq:WP_013830984.1
COORDINATES: similar to AA sequence:RefSeq:WP_007170454.1
COORDINATES: protein motif:HMM:NF022280.2
GO:0009306 - protein secretion [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015298172.1
COORDINATES: similar to AA sequence:RefSeq:WP_018601005.1
COORDINATES: protein motif:HMM:NF025398.2
COORDINATES: similar to AA sequence:RefSeq:WP_012688665.1
TerB family tellurite resistance protein
COORDINATES: protein motif:HMM:NF022655.2
COORDINATES: similar to AA sequence:RefSeq:WP_012623153.1
GO:0008168 - methyltransferase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF026936.2
COORDINATES: similar to AA sequence:RefSeq:WP_003881152.1
COORDINATES: similar to AA sequence:RefSeq:WP_003872282.1
COORDINATES: similar to AA sequence:RefSeq:WP_015298259.1
methyltransferase domain-containing protein
COORDINATES: protein motif:HMM:NF025502.2
COORDINATES: protein motif:HMM:NF017148.2
COORDINATES: similar to AA sequence:RefSeq:WP_006244163.1
COORDINATES: similar to AA sequence:RefSeq:WP_008720536.1
COORDINATES: similar to AA sequence:RefSeq:WP_015298252.1
COORDINATES: similar to AA sequence:RefSeq:WP_005147418.1
COORDINATES: protein motif:HMM:NF017885.2
COORDINATES: protein motif:HMM:NF024776.2
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_005110615.1
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF020419.2
nucleotidyl transferase AbiEii/AbiGii toxin family protein
COORDINATES: similar to AA sequence:RefSeq:WP_005147752.1
type IV toxin-antitoxin system AbiEi family antitoxin domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_015298128.1
COORDINATES: similar to AA sequence:RefSeq:WP_015993064.1
COORDINATES: protein motif:HMM:NF025447.2
cytochrome C oxidase subunit IV family protein
COORDINATES: similar to AA sequence:RefSeq:WP_006246409.1
COORDINATES: similar to AA sequence:RefSeq:WP_011562812.1
COORDINATES: similar to AA sequence:RefSeq:WP_017555358.1
COORDINATES: protein motif:HMM:NF024252.2
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_011562890.1
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_003899000.1
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_005113582.1
COORDINATES: similar to AA sequence:RefSeq:WP_002542529.1
COORDINATES: protein motif:HMM:NF024109.2
COORDINATES: protein motif:HMM:NF024767.2
COORDINATES: similar to AA sequence:RefSeq:WP_014526817.1
COORDINATES: similar to AA sequence:RefSeq:WP_018844924.1
COORDINATES: similar to AA sequence:RefSeq:WP_000230447.1
COORDINATES: similar to AA sequence:RefSeq:WP_005113490.1
COORDINATES: similar to AA sequence:RefSeq:WP_016889553.1
COORDINATES: protein motif:HMM:NF024949.2
COORDINATES: protein motif:HMM:NF018154.2
COORDINATES: similar to AA sequence:RefSeq:WP_005113534.1
COORDINATES: similar to AA sequence:RefSeq:WP_016032734.1
COORDINATES: protein motif:HMM:NF040044.1
COORDINATES: similar to AA sequence:RefSeq:WP_005114893.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_005204895.1
COORDINATES: protein motif:HMM:NF036921.2
COORDINATES: similar to AA sequence:RefSeq:WP_006379323.1
GO:0003938 - IMP dehydrogenase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015298176.1
GO:0016301 - kinase activity [Evidence IEA]
type II toxin-antitoxin system death-on-curing family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_014924776.1
COORDINATES: similar to AA sequence:RefSeq:WP_018604279.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016301 - kinase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018604280.1
winged helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011691690.1
COORDINATES: similar to AA sequence:RefSeq:WP_005059202.1
COORDINATES: similar to AA sequence:RefSeq:WP_005117047.1
COORDINATES: protein motif:HMM:NF025577.2
COORDINATES: protein motif:HMM:NF015944.2
COORDINATES: similar to AA sequence:RefSeq:WP_014877660.1
COORDINATES: similar to AA sequence:RefSeq:WP_014353637.1
COORDINATES: similar to AA sequence:RefSeq:WP_011595184.1
COORDINATES: similar to AA sequence:RefSeq:WP_009475141.1
COORDINATES: similar to AA sequence:RefSeq:WP_016882968.1
COORDINATES: similar to AA sequence:RefSeq:WP_006868574.1
COORDINATES: similar to AA sequence:RefSeq:WP_003976436.1
COORDINATES: similar to AA sequence:RefSeq:WP_005191909.1
HpcH/HpaI aldolase/citrate lyase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_005570617.1
phosphoribosyltransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_009475132.1
COORDINATES: similar to AA sequence:RefSeq:WP_006550715.1
COORDINATES: similar to AA sequence:RefSeq:WP_005141769.1
COORDINATES: protein motif:HMM:NF014404.2
COORDINATES: similar to AA sequence:RefSeq:WP_015298279.1
COORDINATES: similar to AA sequence:RefSeq:WP_015310006.1
COORDINATES: similar to AA sequence:RefSeq:WP_011896182.1
COORDINATES: protein motif:HMM:NF019146.2
COORDINATES: similar to AA sequence:RefSeq:WP_014214287.1
COORDINATES: similar to AA sequence:RefSeq:WP_014214286.1
beta-ketoacyl synthase N-terminal-like domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_005113541.1
COORDINATES: similar to AA sequence:RefSeq:WP_006244136.1
COORDINATES: similar to AA sequence:RefSeq:WP_006244135.1
COORDINATES: protein motif:HMM:NF033832.1
COORDINATES: similar to AA sequence:RefSeq:NP_214933.1
COORDINATES: similar to AA sequence:RefSeq:WP_007171766.1
COORDINATES: similar to AA sequence:RefSeq:WP_005115616.1
COORDINATES: similar to AA sequence:RefSeq:WP_014711748.1
ATP-binding cassette domain-containing protein
COORDINATES: protein motif:HMM:NF018822.2
COORDINATES: similar to AA sequence:RefSeq:WP_003898801.1
COORDINATES: protein motif:HMM:NF013793.2
COORDINATES: similar to AA sequence:RefSeq:WP_005147587.1
COORDINATES: protein motif:HMM:NF012708.2
GO:0005515 - protein binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_076611786.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF022388.2
COORDINATES: similar to AA sequence:RefSeq:WP_019512285.1
GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019512287.1
COORDINATES: protein motif:HMM:TIGR03930.1
GO:0005576 - extracellular region [Evidence IEA]
GO:0003674 - molecular_function [Evidence IEA]
GO:0008150 - biological_process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011557498.1
COORDINATES: protein motif:HMM:NF013021.2
COORDINATES: protein motif:HMM:NF013127.2
COORDINATES: similar to AA sequence:RefSeq:WP_011896251.1
ArdC-like ssDNA-binding domain-containing protein
COORDINATES: protein motif:HMM:TIGR03920.1
type VII secretion integral membrane protein EccD
COORDINATES: protein motif:HMM:TIGR03923.1
COORDINATES: similar to AA sequence:RefSeq:WP_019512272.1
GO:0008236 - serine-type peptidase activity [Evidence IEA]
type VII secretion-associated serine protease mycosin
COORDINATES: protein motif:HMM:NF025001.2
COORDINATES: similar to AA sequence:RefSeq:WP_007528492.1
COORDINATES: protein motif:HMM:TIGR03925.1
COORDINATES: protein motif:HMM:TIGR03924.1
COORDINATES: similar to AA sequence:RefSeq:WP_003399854.1
COORDINATES: protein motif:HMM:NF013073.2
COORDINATES: similar to AA sequence:RefSeq:WP_008262435.1
transglycosylase SLT domain-containing protein
COORDINATES: protein motif:HMM:NF013727.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0000166 - nucleotide binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF024254.2
COORDINATES: protein motif:HMM:NF014520.2
COORDINATES: protein motif:HMM:NF019416.2
COORDINATES: similar to AA sequence:RefSeq:WP_006242249.1
GO:0003678 - DNA helicase activity [Evidence IEA]
GO:0006260 - DNA replication [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006242248.1
TnsA-like heteromeric transposase endonuclease subunit
COORDINATES: similar to AA sequence:RefSeq:WP_005082790.1
Mu transposase C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013473272.1
COORDINATES: protein motif:HMM:NF012354.2
COORDINATES: similar to AA sequence:RefSeq:WP_016690848.1
COORDINATES: protein motif:HMM:NF037830.2
COORDINATES: protein motif:HMM:NF014045.2
COORDINATES: protein motif:HMM:NF014442.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0008170 - N-methyltransferase activity [Evidence IEA]
GO:0006306 - DNA methylation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017681372.1
class I SAM-dependent DNA methyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_003936279.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004519 - endonuclease activity [Evidence IEA]
GO:0006304 - DNA modification [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013126361.1
translation initiation factor IF-2 N-terminal domain-containing protein