Methylobacterium indicum strain VL1 plasmid pVL1_1, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales; Methylobacteriaceae; Methylobacterium.
Complete genome sequence of a novel pathogenic Methylobacterium strain isolated from rice in Vietnam
Submitted (06-NOV-2020) Contact:Shin Okazaki Tokyo University of Agriculture and Technology, Graduate School of Agriculture; Saiwaicho 3-5-8, Fuchu, Tokyo 183-8509, Japan URL :http://web.tuat.ac.jp/~okazaki/enindex.html
REFSEQ INFORMATION: The reference sequence is identical to\nAP024146.1.\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 :: HGAP v. 3\nGenome Coverage :: 120x\nSequencing Technology :: PacBio RSII; HiSeq 2500\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 04/28/2023 10:57:43\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) :: 6,633\nCDSs (total) :: 6,493\nGenes (coding) :: 6,407\nCDSs (with protein) :: 6,407\nGenes (RNA) :: 140\nrRNAs :: 12, 12, 12 (5S, 16S, 23S)\ncomplete rRNAs :: 12, 12, 12 (5S, 16S, 23S)\ntRNAs :: 100\nncRNAs :: 4\nPseudo Genes (total) :: 86\nCDSs (without protein) :: 86\nPseudo Genes (ambiguous residues) :: 0 of 86\nPseudo Genes (frameshifted) :: 33 of 86\nPseudo Genes (incomplete) :: 68 of 86\nPseudo Genes (internal stop) :: 17 of 86\nPseudo Genes (multiple problems) :: 26 of 86\nCRISPR Arrays :: 2\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_018063987.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_007195960.1
COORDINATES: protein motif:HMM:NF024954.2
winged helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF033545.0
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_076612189.1
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_004126148.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011970376.1
TnpB, as the term is used for proteins encoded by IS66 family insertion elements, is considered an accessory protein, since TnpC, encoded by a neighboring gene, is a DDE family transposase; Derived by automated computational analysis using gene prediction method: Protein Homology.
IS66 family insertion sequence element accessory protein TnpB
COORDINATES: similar to AA sequence:RefSeq:WP_012778787.1
frameshifted; internal stop; 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:NF012488.2
GO:0030170 - pyridoxal phosphate binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF024580.2
COORDINATES: similar to AA sequence:RefSeq:WP_014415360.1
COORDINATES: similar to AA sequence:RefSeq:WP_015927377.1
phosphoadenosine phosphosulfate reductase family protein
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
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:TIGR04096.1
DNA phosphorothioation-associated putative methyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_015934223.1
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_012455796.1
COORDINATES: similar to AA sequence:RefSeq:WP_011505056.1
COORDINATES: protein motif:HMM:NF018841.2
COORDINATES: similar to AA sequence:RefSeq:WP_015918199.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015602268.1
COORDINATES: similar to AA sequence:RefSeq:WP_012757135.1
phospholipase D-like domain-containing protein
COORDINATES: protein motif:HMM:NF012376.2
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020720568.1
COORDINATES: similar to AA sequence:RefSeq:WP_020704126.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012755361.1
COORDINATES: similar to AA sequence:RefSeq:WP_012333165.1
COORDINATES: similar to AA sequence:RefSeq:WP_014258303.1
COORDINATES: protein motif:HMM:NF013970.2
COORDINATES: protein motif:HMM:NF016167.2
COORDINATES: similar to AA sequence:RefSeq:WP_007564051.1
COORDINATES: similar to AA sequence:RefSeq:WP_007564054.1
COORDINATES: similar to AA sequence:RefSeq:WP_020493691.1
COORDINATES: protein motif:HMM:NF015393.2
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012606240.1
COORDINATES: similar to AA sequence:RefSeq:WP_012778764.1
COORDINATES: similar to AA sequence:RefSeq:WP_012778763.1
COORDINATES: similar to AA sequence:RefSeq:WP_012778762.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606236.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606235.1
GO:0046872 - metal ion binding [Evidence IEA]; GO:0004222 - metalloendopeptidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012778862.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606232.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606231.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606230.1
COORDINATES: similar to AA sequence:RefSeq:WP_012778858.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012778857.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606227.1
COORDINATES: similar to AA sequence:RefSeq:WP_012778855.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606225.1
COORDINATES: similar to AA sequence:RefSeq:WP_012778853.1
DotI/IcmL family type IV secretion protein
COORDINATES: protein motif:HMM:NF023713.2
DotH/IcmK family type IV secretion protein
COORDINATES: similar to AA sequence:RefSeq:WP_012606222.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606221.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606220.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606219.1
COORDINATES: similar to AA sequence:RefSeq:WP_012778847.1
COORDINATES: similar to AA sequence:RefSeq:WP_017904630.1
GO:0043295 - glutathione binding [Evidence IEA]
GO:0006749 - glutathione metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF013353.2
GO:0036361 - racemase activity, acting on amino acids and derivatives [Evidence IEA]
GO:0006807 - nitrogen compound metabolic process [Evidence IEA]
aspartate/glutamate racemase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_014340198.1
COORDINATES: protein motif:HMM:NF013933.2
COORDINATES: protein motif:HMM:NF005072.0
COORDINATES: similar to AA sequence:RefSeq:WP_017904626.1
COORDINATES: similar to AA sequence:RefSeq:WP_008040395.1
GO:0004049 - anthranilate synthase activity [Evidence IEA]
GO:0000162 - tryptophan biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012778846.1
COORDINATES: similar to AA sequence:RefSeq:WP_012778845.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606210.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606207.1
Ti-type conjugative transfer relaxase TraA
COORDINATES: protein motif:HMM:NF019437.2
COORDINATES: similar to AA sequence:RefSeq:WP_012606205.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606204.1
COORDINATES: similar to AA sequence:RefSeq:WP_012778839.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606201.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606200.1
COORDINATES: similar to AA sequence:RefSeq:WP_012778833.1
COORDINATES: similar to AA sequence:RefSeq:WP_009338100.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606196.1
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_012606195.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606193.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606192.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606191.1
COORDINATES: similar to AA sequence:RefSeq:WP_012778827.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010916065.1
COORDINATES: protein motif:HMM:NF017277.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0008270 - zinc ion binding [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012318852.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: protein motif:HMM:NF019324.2
type II toxin-antitoxin system VapB family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_012606184.1
COORDINATES: similar to AA sequence:RefSeq:WP_020817743.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606183.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606182.1
GO:0110001 - toxin-antitoxin complex [Evidence IEA]
type II toxin-antitoxin system Phd/YefM family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_012606181.1
COORDINATES: similar to AA sequence:RefSeq:WP_006472572.1
COORDINATES: similar to AA sequence:RefSeq:WP_012340168.1
GO:0005215 - transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012455587.1
frameshifted; 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_076611646.1
COORDINATES: protein motif:HMM:NF012967.2
GO:0016740 - transferase activity [Evidence IEA]
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:NF015437.2
COORDINATES: similar to AA sequence:RefSeq:WP_013635235.1
COORDINATES: protein motif:HMM:NF019474.2
COORDINATES: similar to AA sequence:RefSeq:WP_020139887.1
COORDINATES: protein motif:HMM:NF012575.2
GO:0051537 - 2 iron, 2 sulfur cluster binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016125802.1
iron-containing redox enzyme family protein
COORDINATES: protein motif:HMM:NF018076.2
50S ribosomal protein L11 methyltransferase
COORDINATES: protein motif:HMM:NF012402.2
MOSC N-terminal beta barrel domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006310430.1
frameshifted; internal stop; 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_012694818.1
GO:0016765 - transferase activity, transferring alkyl or aryl (other than methyl) groups [Evidence IEA]
GO:0006535 - cysteine biosynthetic process from serine [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003601172.1
COORDINATES: similar to AA sequence:RefSeq:WP_020084914.1
COORDINATES: similar to AA sequence:RefSeq:WP_003601176.1
AlkA N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_020092544.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006281 - DNA repair [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
bifunctional DNA-binding transcriptional regulator/O6-methylguanine-DNA methyltransferase Ada
COORDINATES: similar to AA sequence:RefSeq:WP_002635770.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606163.1
COORDINATES: similar to AA sequence:RefSeq:WP_004152394.1
COORDINATES: similar to AA sequence:RefSeq:WP_006961684.1
COORDINATES: similar to AA sequence:RefSeq:WP_012751917.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_004446757.1
GO:0008641 - ubiquitin-like modifier activating enzyme activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012753790.1
COORDINATES: similar to AA sequence:RefSeq:WP_008600975.1
COORDINATES: similar to AA sequence:RefSeq:WP_004446753.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_012753789.1
COORDINATES: similar to AA sequence:RefSeq:WP_016921086.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612078.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: nucleotide motif:Rfam:14.4:RF01497
AL1L pseudoknot; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: protein motif:HMM:NF012383.2
GO:0009116 - nucleoside metabolic process [Evidence IEA]
phosphoribosyltransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_015934124.1
COORDINATES: similar to AA sequence:RefSeq:WP_010219940.1
AbrB/MazE/SpoVT family DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010164983.1
COORDINATES: similar to AA sequence:RefSeq:WP_019998550.1
COORDINATES: protein motif:HMM:NF013677.2
COORDINATES: similar to AA sequence:RefSeq:WP_011749831.1
COORDINATES: similar to AA sequence:RefSeq:WP_017980713.1