Methylobacterium indicum strain VL1 plasmid pVL1_2, 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\nAP024147.1.\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+
GO:0044423 - virion component [Evidence IEA]
GO:0005198 - structural molecule activity [Evidence IEA]
GO:0016032 - viral process [Evidence IEA]
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF016736.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF016829.2
COORDINATES: similar to AA sequence:RefSeq:WP_006472980.1
COORDINATES: protein motif:HMM:NF020447.2
COORDINATES: protein motif:HMM:NF016927.2
COORDINATES: protein motif:HMM:NF018704.2
COORDINATES: protein motif:HMM:NF024661.2
COORDINATES: protein motif:HMM:NF015211.2
COORDINATES: similar to AA sequence:RefSeq:WP_012452336.1
Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
COORDINATES: similar to AA sequence:RefSeq:WP_018250437.1
COORDINATES: protein motif:HMM:NF013043.2
COORDINATES: similar to AA sequence:RefSeq:WP_003617408.1
COORDINATES: similar to AA sequence:RefSeq:WP_012338174.1
COORDINATES: similar to AA sequence:RefSeq:WP_015931601.1
COORDINATES: protein motif:HMM:NF028178.2
TAXI family TRAP transporter solute-binding subunit
COORDINATES: protein motif:HMM:NF012234.2
COORDINATES: protein motif:HMM:NF015983.2
GO:0051539 - 4 iron, 4 sulfur cluster binding [Evidence IEA]; GO:0003824 - catalytic activity [Evidence IEA]; GO:1904047 - S-adenosyl-L-methionine binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF016255.2
COORDINATES: protein motif:HMM:NF012951.2
GO:0004812 - aminoacyl-tRNA ligase activity [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]
GO:0043039 - tRNA aminoacylation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011831467.1
COORDINATES: protein motif:HMM:NF017663.2
GO:0000287 - magnesium ion binding [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]; GO:0006281 - DNA repair [Evidence IEA]
RusA family crossover junction endodeoxyribonuclease
COORDINATES: protein motif:HMM:NF018785.2
COORDINATES: protein motif:HMM:NF016724.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0004386 - helicase activity [Evidence IEA]; GO:0003676 - nucleic acid binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF024755.2
COORDINATES: protein motif:HMM:TIGR00621.2
GO:0003697 - single-stranded DNA binding [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]; GO:0006281 - DNA repair [Evidence IEA]; GO:0006260 - DNA replication [Evidence IEA]; GO:0006351 - DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018182209.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006260 - DNA replication [Evidence IEA]
COORDINATES: protein motif:HMM:NF021128.2
COORDINATES: similar to AA sequence:RefSeq:WP_003598308.1
trna delta -isopentenylpyrophosphate transferase
COORDINATES: similar to AA sequence:RefSeq:WP_006932031.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015821669.1
GO:0004748 - ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor [Evidence IEA]
adenosylcobalamin-dependent ribonucleoside-diphosphate reductase
COORDINATES: protein motif:HMM:NF015758.2
MazG nucleotide pyrophosphohydrolase domain-containing protein
TerB family tellurite resistance protein
COORDINATES: similar to AA sequence:RefSeq:WP_018390340.1
COORDINATES: protein motif:HMM:NF012413.2
GO:0004146 - dihydrofolate reductase activity [Evidence IEA]; GO:0005542 - folic acid binding [Evidence IEA]; GO:0050661 - NADP binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_002549231.1
GO:0004799 - thymidylate synthase activity [Evidence IEA]
GO:0009265 - 2'-deoxyribonucleotide biosynthetic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF013618.2
GO:0016798 - hydrolase activity, acting on glycosyl bonds [Evidence IEA]
lytic transglycosylase domain-containing protein
COORDINATES: protein motif:HMM:NF022151.2
COORDINATES: similar to AA sequence:RefSeq:WP_006470383.1
COORDINATES: similar to AA sequence:RefSeq:WP_007564968.1
COORDINATES: similar to AA sequence:RefSeq:WP_018263707.1
COORDINATES: protein motif:HMM:NF017316.2
COORDINATES: protein motif:HMM:NF018674.2
COORDINATES: protein motif:HMM:NF021648.2
COORDINATES: protein motif:HMM:NF021614.2
GO:0098003 - viral tail assembly [Evidence IEA]
COORDINATES: protein motif:HMM:NF016846.2
COORDINATES: protein motif:HMM:NF016845.2
phage tail sheath subtilisin-like domain-containing protein
COORDINATES: protein motif:HMM:NF025659.2