Methylobacterium indicum strain VL1 plasmid pVL1_3, 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\nAP024148.1.\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_006921239.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF012920.2
translesion error-prone DNA polymerase V autoproteolytic subunit
COORDINATES: similar to AA sequence:RefSeq:WP_019402838.1
COORDINATES: protein motif:HMM:TIGR03454.1
COORDINATES: protein motif:HMM:NF012774.2
COORDINATES: similar to AA sequence:RefSeq:WP_012634249.1
COORDINATES: protein motif:HMM:NF022337.2
COORDINATES: similar to AA sequence:RefSeq:WP_010686022.1
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: protein motif:HMM:NF013540.2
helix-turn-helix transcriptional regulator
COORDINATES: protein motif:HMM:NF015437.2
autoinducer binding domain-containing protein
COORDINATES: protein motif:HMM:NF012967.2
GO:0016740 - transferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012335780.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_012338196.1
COORDINATES: similar to AA sequence:RefSeq:WP_011580614.1
COORDINATES: similar to AA sequence:RefSeq:WP_012330183.1
GO:0004803 - transposase activity [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF020037.2
COORDINATES: protein motif:HMM:NF012385.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0008134 - transcription factor binding [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
sigma 54-interacting transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_018860138.1
COORDINATES: similar to AA sequence:RefSeq:WP_018860139.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018860140.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]; GO:0005886 - plasma membrane [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018860141.1
COORDINATES: similar to AA sequence:RefSeq:WP_018860142.1
COORDINATES: similar to AA sequence:RefSeq:WP_008067120.1
COORDINATES: similar to AA sequence:RefSeq:WP_014763233.1
GO:0003867 - 4-aminobutyrate transaminase activity [Evidence IEA]
GO:0009450 - gamma-aminobutyric acid catabolic process [Evidence IEA]
4-aminobutyrate--2-oxoglutarate transaminase
COORDINATES: similar to AA sequence:RefSeq:WP_002965457.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611965.1
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_018001317.1
CaiB/BaiF CoA-transferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_019997600.1
COORDINATES: similar to AA sequence:RefSeq:WP_009806317.1
LysR substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012606184.1
COORDINATES: similar to AA sequence:RefSeq:WP_012453293.1
type II toxin-antitoxin system VapB family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_012606186.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_010918726.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606258.1
AbrB/MazE/SpoVT family DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_015934124.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF012354.2
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012606163.1
COORDINATES: similar to AA sequence:RefSeq:WP_012778817.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606181.1
COORDINATES: similar to AA sequence:RefSeq:WP_012382872.1
COORDINATES: similar to AA sequence:RefSeq:WP_012318852.1
COORDINATES: protein motif:HMM:NF017277.2
COORDINATES: similar to AA sequence:RefSeq:WP_013831281.1
COORDINATES: similar to AA sequence:RefSeq:WP_012778826.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606190.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019998519.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606195.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606196.1
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_018045297.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0008270 - zinc ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012606199.1
COORDINATES: similar to AA sequence:RefSeq:WP_012778834.1
COORDINATES: similar to AA sequence:RefSeq:WP_015821260.1
COORDINATES: similar to AA sequence:RefSeq:WP_003599780.1
GO:0030552 - cAMP binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
Crp/Fnr family transcriptional regulator
COORDINATES: protein motif:HMM:NF024954.2
winged helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF033545.0
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_019906531.1
COORDINATES: similar to AA sequence:RefSeq:WP_019841194.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF024880.2
GO:0008168 - methyltransferase activity [Evidence IEA]
methyltransferase domain-containing protein
COORDINATES: protein motif:HMM:NF025054.2
GO:0008080 - N-acetyltransferase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF018264.2
COORDINATES: similar to AA sequence:RefSeq:WP_007698924.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0016987 - sigma factor activity [Evidence IEA]
GO:0006352 - DNA-templated transcription initiation [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
sigma-70 family RNA polymerase sigma factor
COORDINATES: similar to AA sequence:RefSeq:WP_012752414.1
COORDINATES: similar to AA sequence:RefSeq:WP_012322285.1
GO:0017004 - cytochrome complex assembly [Evidence IEA]
COORDINATES: protein motif:HMM:NF019057.2
COORDINATES: protein motif:HMM:NF025005.2
COORDINATES: protein motif:HMM:NF024755.2
COORDINATES: similar to AA sequence:RefSeq:WP_012606201.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606203.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606204.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012606205.1
COORDINATES: protein motif:HMM:NF019437.2
COORDINATES: similar to AA sequence:RefSeq:WP_012606207.1
Ti-type conjugative transfer relaxase TraA
COORDINATES: similar to AA sequence:RefSeq:WP_012606210.1
COORDINATES: similar to AA sequence:RefSeq:WP_012778845.1
COORDINATES: similar to AA sequence:RefSeq:WP_012778846.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606218.1
COORDINATES: similar to AA sequence:RefSeq:WP_012778848.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606220.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606221.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606222.1
COORDINATES: similar to AA sequence:RefSeq:WP_012778852.1
DotH/IcmK family type IV secretion protein
COORDINATES: similar to AA sequence:RefSeq:WP_012778853.1
DotI/IcmL family type IV secretion protein
COORDINATES: similar to AA sequence:RefSeq:WP_012778854.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606227.1
COORDINATES: similar to AA sequence:RefSeq:WP_012778858.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606230.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606231.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606232.1
COORDINATES: similar to AA sequence:RefSeq:WP_012778862.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606235.1
GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012606236.1
COORDINATES: similar to AA sequence:RefSeq:WP_012778762.1
COORDINATES: similar to AA sequence:RefSeq:WP_012778763.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606239.1
COORDINATES: similar to AA sequence:RefSeq:WP_012606240.1
COORDINATES: similar to AA sequence:RefSeq:WP_007564051.1
COORDINATES: similar to AA sequence:RefSeq:WP_012745879.1
COORDINATES: similar to AA sequence:RefSeq:WP_004213291.1