Methylobacterium indicum strain VL1 plasmid pVL1_4, 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\nAP024149.1.\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: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_009870292.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_011583106.1
phospholipase D-like domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011583107.1
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_008872303.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606213.1
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_012333594.1
GO:0030253 - protein secretion by the type I secretion system [Evidence IEA]
HlyD family type I secretion periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_015928636.1
COORDINATES: protein motif:HMM:NF018319.2
COORDINATES: similar to AA sequence:RefSeq:WP_000904945.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020485770.1
COORDINATES: similar to AA sequence:RefSeq:WP_020665240.1
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_012652878.1
COORDINATES: similar to AA sequence:RefSeq:WP_020809782.1
GO:0004176 - ATP-dependent peptidase activity [Evidence IEA]; GO:0004252 - serine-type endopeptidase activity [Evidence IEA]
ATP-dependent Clp protease proteolytic subunit
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015822169.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_015930107.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012332933.1
COORDINATES: similar to AA sequence:RefSeq:WP_012634249.1
COORDINATES: similar to AA sequence:RefSeq:WP_018264048.1
COORDINATES: similar to AA sequence:RefSeq:WP_011199109.1
COORDINATES: similar to AA sequence:RefSeq:WP_013044870.1
COORDINATES: protein motif:HMM:TIGR02768.1
Ti-type conjugative transfer relaxase TraA
COORDINATES: similar to AA sequence:RefSeq:WP_019170003.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009602860.1
frameshifted; internal stop; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.