Mycolicibacterium poriferae strain JCM 12603 plasmid pJCM12603, complete sequence.
Mycolicibacterium poriferae (Mycobacterium poriferae)
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\nAP022571.1.\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 :: 150x\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 :: 05/22/2023 16:01:33\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) :: 5,653\nCDSs (total) :: 5,598\nGenes (coding) :: 5,462\nCDSs (with protein) :: 5,462\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) :: 136\nCDSs (without protein) :: 136\nPseudo Genes (ambiguous residues) :: 0 of 136\nPseudo Genes (frameshifted) :: 74 of 136\nPseudo Genes (incomplete) :: 77 of 136\nPseudo Genes (internal stop) :: 8 of 136\nPseudo Genes (multiple problems) :: 22 of 136\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
type strain of Mycolicibacterium poriferae
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF020729.2
GO:0005615 - extracellular space [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_013470225.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_011767731.1
COORDINATES: similar to AA sequence:RefSeq:WP_013470227.1
COORDINATES: protein motif:HMM:NF025200.2
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
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_013470229.1
COORDINATES: similar to AA sequence:RefSeq:WP_006247759.1
COORDINATES: similar to AA sequence:RefSeq:WP_006247664.1
COORDINATES: similar to AA sequence:RefSeq:WP_011767735.1
COORDINATES: similar to AA sequence:RefSeq:WP_011767736.1
COORDINATES: similar to AA sequence:RefSeq:WP_013470231.1
COORDINATES: similar to AA sequence:RefSeq:WP_006247669.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_006247670.1
COORDINATES: similar to AA sequence:RefSeq:WP_006247671.1
COORDINATES: similar to AA sequence:RefSeq:WP_011767739.1
COORDINATES: similar to AA sequence:RefSeq:WP_013470232.1
COORDINATES: similar to AA sequence:RefSeq:WP_013470233.1
COORDINATES: similar to AA sequence:RefSeq:WP_013470234.1
COORDINATES: similar to AA sequence:RefSeq:WP_006247564.1
COORDINATES: similar to AA sequence:RefSeq:WP_013470235.1
COORDINATES: similar to AA sequence:RefSeq:WP_011767743.1
COORDINATES: similar to AA sequence:RefSeq:WP_006247565.1
COORDINATES: similar to AA sequence:RefSeq:WP_013470237.1
COORDINATES: similar to AA sequence:RefSeq:WP_013470238.1
COORDINATES: similar to AA sequence:RefSeq:WP_011767746.1
COORDINATES: similar to AA sequence:RefSeq:WP_006247569.1
ParB N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006247570.1
COORDINATES: similar to AA sequence:RefSeq:WP_013470241.1
COORDINATES: similar to AA sequence:RefSeq:WP_011767749.1
COORDINATES: similar to AA sequence:RefSeq:WP_013470243.1
COORDINATES: similar to AA sequence:RefSeq:WP_013470244.1
COORDINATES: similar to AA sequence:RefSeq:WP_013470246.1
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_013470247.1
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_006247312.1
COORDINATES: similar to AA sequence:RefSeq:WP_013470249.1
COORDINATES: similar to AA sequence:RefSeq:WP_013470250.1
COORDINATES: similar to AA sequence:RefSeq:WP_011767771.1
COORDINATES: similar to AA sequence:RefSeq:WP_013470252.1
COORDINATES: similar to AA sequence:RefSeq:WP_011767773.1
COORDINATES: similar to AA sequence:RefSeq:WP_013470254.1
COORDINATES: similar to AA sequence:RefSeq:WP_011767776.1
COORDINATES: similar to AA sequence:RefSeq:WP_011767777.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006372941.1
COORDINATES: similar to AA sequence:RefSeq:WP_009774511.1
heavy metal-responsive transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_012296237.1
COORDINATES: similar to AA sequence:RefSeq:WP_011896320.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF025713.2
COORDINATES: similar to AA sequence:RefSeq:WP_014211414.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011767784.1
COORDINATES: similar to AA sequence:RefSeq:WP_011767785.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805518.1
COORDINATES: similar to AA sequence:RefSeq:WP_014805517.1
COORDINATES: similar to AA sequence:RefSeq:WP_011767787.1
COORDINATES: similar to AA sequence:RefSeq:WP_005566945.1
COORDINATES: similar to AA sequence:RefSeq:WP_011767789.1
COORDINATES: similar to AA sequence:RefSeq:WP_011767790.1
COORDINATES: similar to AA sequence:RefSeq:WP_011767791.1
COORDINATES: protein motif:HMM:NF014520.2
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_015297751.1
COORDINATES: similar to AA sequence:RefSeq:WP_011767795.1
COORDINATES: protein motif:HMM:NF012774.2
COORDINATES: similar to AA sequence:RefSeq:WP_006247493.1
COORDINATES: similar to AA sequence:RefSeq:WP_006247459.1
COORDINATES: similar to AA sequence:RefSeq:NP_216506.1
COORDINATES: similar to AA sequence:RefSeq:WP_011767806.1
COORDINATES: similar to AA sequence:RefSeq:WP_006247456.1
COORDINATES: similar to AA sequence:RefSeq:WP_011896121.1
COORDINATES: similar to AA sequence:RefSeq:WP_011767814.1
COORDINATES: similar to AA sequence:RefSeq:WP_011896117.1
COORDINATES: similar to AA sequence:RefSeq:WP_011896147.1
COORDINATES: similar to AA sequence:RefSeq:WP_011893689.1
COORDINATES: similar to AA sequence:RefSeq:WP_010908881.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011893693.1
COORDINATES: similar to AA sequence:RefSeq:WP_011767863.1
COORDINATES: similar to AA sequence:RefSeq:WP_011893696.1
GO:0045892 - negative regulation of DNA-templated transcription [Evidence IEA]
BlaI/MecI/CopY family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_011767865.1
GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003928730.1
GO:0004129 - cytochrome-c oxidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011767867.1
COORDINATES: similar to AA sequence:RefSeq:WP_011893700.1
GO:0020037 - heme binding [Evidence IEA]
GO:0017004 - cytochrome complex assembly [Evidence IEA]
c-type cytochrome biogenesis protein CcsB
COORDINATES: similar to AA sequence:RefSeq:WP_006246619.1
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_011767923.1
COORDINATES: similar to AA sequence:RefSeq:WP_014210456.1
COORDINATES: similar to AA sequence:RefSeq:WP_011896131.1
COORDINATES: similar to AA sequence:RefSeq:WP_011896111.1
cytochrome c biogenesis CcdA family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011893706.1
COORDINATES: similar to AA sequence:RefSeq:WP_011896127.1
COORDINATES: protein motif:HMM:NF012946.2
GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA]; GO:0050661 - NADP binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017562586.1
COORDINATES: protein motif:HMM:NF016107.2
phosphatidylethanolamine N-methyltransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011767883.1
GO:0009190 - cyclic nucleotide biosynthetic process [Evidence IEA]; GO:0035556 - intracellular signal transduction [Evidence IEA]
adenylate/guanylate cyclase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011780869.1
GO:0008168 - methyltransferase activity [Evidence IEA]
isoprenylcysteine carboxylmethyltransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011767885.1
COORDINATES: similar to AA sequence:RefSeq:WP_011767886.1
GO:0006629 - lipid metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011891809.1
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_005199813.1
COORDINATES: similar to AA sequence:RefSeq:WP_011767889.1
COORDINATES: similar to AA sequence:RefSeq:WP_011780863.1
COORDINATES: similar to AA sequence:RefSeq:WP_011780862.1
GO:0042625 - ATPase-coupled ion transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011896107.1
COORDINATES: similar to AA sequence:RefSeq:WP_011767893.1
COORDINATES: similar to AA sequence:RefSeq:WP_011767894.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0000156 - phosphorelay response regulator activity [Evidence IEA]; GO:0004673 - protein histidine kinase activity [Evidence IEA]
GO:0007165 - signal transduction [Evidence IEA]
HAMP domain-containing sensor histidine kinase
COORDINATES: similar to AA sequence:RefSeq:WP_011767895.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011767897.1
COORDINATES: similar to AA sequence:RefSeq:WP_011767898.1
COORDINATES: similar to AA sequence:RefSeq:WP_011896104.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0019829 - ATPase-coupled monoatomic cation transmembrane transporter activity [Evidence IEA]
GO:0006812 - monoatomic cation transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011780853.1
COORDINATES: similar to AA sequence:RefSeq:WP_011780852.1
metal-sensitive transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_011780843.1
NlpC/P60 family peptidoglycan endopeptidase RipA
COORDINATES: similar to AA sequence:RefSeq:WP_011780842.1
COORDINATES: similar to AA sequence:RefSeq:WP_011780841.1
COORDINATES: similar to AA sequence:RefSeq:WP_011891803.1
COORDINATES: similar to AA sequence:RefSeq:WP_011767914.1
NlpC/P60 family peptidoglycan endopeptidase RipB
COORDINATES: similar to AA sequence:RefSeq:WP_011767915.1
COORDINATES: similar to AA sequence:RefSeq:WP_014924910.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011558666.1
COORDINATES: similar to AA sequence:RefSeq:WP_011767916.1
COORDINATES: similar to AA sequence:RefSeq:WP_011767917.1
COORDINATES: similar to AA sequence:RefSeq:WP_086558018.1
COORDINATES: similar to AA sequence:RefSeq:WP_020725001.1
nitroreductase family deazaflavin-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_019971648.1
COORDINATES: similar to AA sequence:RefSeq:WP_015355423.1
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_006246363.1
COORDINATES: similar to AA sequence:RefSeq:WP_011767953.1
GO:0016787 - hydrolase activity [Evidence IEA]; GO:0008233 - peptidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011767954.1
COORDINATES: similar to AA sequence:RefSeq:WP_011767955.1
GO:0009306 - protein secretion [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006246368.1
COORDINATES: similar to AA sequence:RefSeq:WP_011767957.1
COORDINATES: similar to AA sequence:RefSeq:WP_011767958.1
COORDINATES: similar to AA sequence:RefSeq:WP_011767960.1
COORDINATES: similar to AA sequence:RefSeq:WP_006246373.1
COORDINATES: similar to AA sequence:RefSeq:WP_006246374.1
GO:0003674 - molecular_function [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011767963.1
COORDINATES: similar to AA sequence:RefSeq:WP_011767964.1
COORDINATES: similar to AA sequence:RefSeq:WP_006246377.1
COORDINATES: similar to AA sequence:RefSeq:WP_006246378.1
COORDINATES: similar to AA sequence:RefSeq:WP_006243193.1
COORDINATES: similar to AA sequence:RefSeq:WP_011767967.1
COORDINATES: similar to AA sequence:RefSeq:WP_011767968.1
COORDINATES: similar to AA sequence:RefSeq:WP_006243196.1
type VII secretion integral membrane protein EccD
COORDINATES: similar to AA sequence:RefSeq:WP_011767970.1
GO:0008236 - serine-type peptidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011767971.1
COORDINATES: similar to AA sequence:RefSeq:WP_011767972.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0000166 - nucleotide binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006246386.1
COORDINATES: similar to AA sequence:RefSeq:WP_011767974.1
TraM recognition domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011767975.1
COORDINATES: similar to AA sequence:RefSeq:WP_006243403.1
COORDINATES: similar to AA sequence:RefSeq:WP_011767715.1
COORDINATES: similar to AA sequence:RefSeq:WP_011767716.1
COORDINATES: similar to AA sequence:RefSeq:WP_011767717.1
COORDINATES: similar to AA sequence:RefSeq:WP_011767718.1
COORDINATES: similar to AA sequence:RefSeq:WP_006246394.1
COORDINATES: similar to AA sequence:RefSeq:WP_011767720.1
COORDINATES: similar to AA sequence:RefSeq:WP_011767721.1
COORDINATES: similar to AA sequence:RefSeq:WP_011767722.1
COORDINATES: similar to AA sequence:RefSeq:WP_006246398.1
GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015354550.1
COORDINATES: similar to AA sequence:RefSeq:WP_020785870.1
type ISP restriction/modification enzyme
COORDINATES: protein motif:HMM:NF014044.2
COORDINATES: protein motif:HMM:NF024685.2
COORDINATES: similar to AA sequence:RefSeq:WP_017883175.1
GO:0046872 - metal ion binding [Evidence IEA]; GO:0008237 - metallopeptidase activity [Evidence IEA]
SprT family zinc-dependent metalloprotease
COORDINATES: similar to AA sequence:RefSeq:WP_006437537.1
GO:0019812 - type I site-specific deoxyribonuclease complex [Evidence IEA]
GO:0009035 - type I site-specific deoxyribonuclease activity [Evidence IEA]
GO:0009307 - DNA restriction-modification system [Evidence IEA]
HsdR family type I site-specific deoxyribonuclease
COORDINATES: protein motif:HMM:NF013579.2
COORDINATES: similar to AA sequence:RefSeq:WP_019031692.1
GO:0015666 - restriction endodeoxyribonuclease activity [Evidence IEA]; GO:0009007 - site-specific DNA-methyltransferase (adenine-specific) activity [Evidence IEA]
GO:0006306 - DNA methylation [Evidence IEA]; GO:0009307 - DNA restriction-modification system [Evidence IEA]
type I restriction-modification system subunit M
COORDINATES: similar to AA sequence:RefSeq:WP_011855470.1
COORDINATES: similar to AA sequence:RefSeq:WP_011855471.1
COORDINATES: similar to AA sequence:RefSeq:WP_011855472.1
COORDINATES: similar to AA sequence:RefSeq:WP_005632887.1
COORDINATES: similar to AA sequence:RefSeq:WP_018354467.1
COORDINATES: similar to AA sequence:RefSeq:WP_009482149.1
COORDINATES: similar to AA sequence:RefSeq:WP_020663589.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006438767.1
COORDINATES: similar to AA sequence:RefSeq:WP_006246411.1
putative DNA binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006246412.1
COORDINATES: protein motif:HMM:NF024991.2
COORDINATES: protein motif:HMM:NF041492.1