Methylomagnum ishizawai strain RS11D-Pr plasmid pRS11DPr3, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Methylococcales; Methylococcaceae; Methylomagnum.
Complete genome sequence of Methylomagnum ishizawai strain RS11D-Pr
Submitted (28-JUN-2019) Contact:Susumu Asakawa Nagoya University, Graduate School of Bioagricultural Sciences; Chikusa, Furocho 1, Nagoya, Aichi 464-8601, Japan URL :https://www.agr.nagoya-u.ac.jp/%7Esoil/ Soil_Biology_and_Chemistry/toppupeji.html
REFSEQ INFORMATION: The reference sequence is identical to\nAP019786.1.\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 :: Unicycler v. 0.4.7\nGenome Coverage :: 725x\nSequencing Technology :: Illumina NextSeq, GridION\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 05/07/2023 06:14:59\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) :: 4,693\nCDSs (total) :: 4,634\nGenes (coding) :: 4,584\nCDSs (with protein) :: 4,584\nGenes (RNA) :: 59\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 49\nncRNAs :: 4\nPseudo Genes (total) :: 50\nCDSs (without protein) :: 50\nPseudo Genes (ambiguous residues) :: 0 of 50\nPseudo Genes (frameshifted) :: 17 of 50\nPseudo Genes (incomplete) :: 34 of 50\nPseudo Genes (internal stop) :: 3 of 50\nPseudo Genes (multiple problems) :: 4 of 50\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
Japan:Aichi, Anjo, Anjo Agricultural and Extension Centre
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF022479.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF018714.2
COORDINATES: similar to AA sequence:RefSeq:WP_020563752.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF013235.2
GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006270 - DNA replication initiation [Evidence IEA]
COORDINATES: protein motif:HMM:NF018269.2
COORDINATES: protein motif:HMM:NF013434.2
GO:0071949 - FAD binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF024846.2
FAD/NAD(P)-binding domain-containing protein
COORDINATES: protein motif:HMM:NF024809.2
GO:0005515 - protein binding [Evidence IEA]
GO:0006749 - glutathione metabolic process [Evidence IEA]
glutathione S-transferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012233558.1
GO:0018784 - (S)-2-haloacid dehalogenase activity [Evidence IEA]
GO:0006805 - xenobiotic metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF013088.2
GO:0005215 - transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: protein motif:HMM:NF012798.2
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: nucleotide motif:Rfam:14.4:RF00177
Derived by automated computational analysis using gene prediction method: cmsearch.
Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
COORDINATES: nucleotide motif:Rfam:14.4:RF02541
COORDINATES: nucleotide motif:Rfam:14.4:RF00001
COORDINATES: similar to AA sequence:RefSeq:WP_019020826.1
RepB family plasmid replication initiator protein
COORDINATES: protein motif:HMM:NF019945.2
COORDINATES: protein motif:HMM:NF024776.2
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011479436.1
GO:0016491 - oxidoreductase activity [Evidence IEA]; GO:0016651 - oxidoreductase activity, acting on NAD(P)H [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010961496.1
COORDINATES: similar to AA sequence:RefSeq:WP_020564379.1
COORDINATES: protein motif:HMM:NF017021.2
COORDINATES: protein motif:HMM:NF023697.2
COORDINATES: protein motif:HMM:NF025049.2
COORDINATES: protein motif:HMM:NF018980.2
GO:0016020 - membrane [Evidence IEA]; GO:0005886 - plasma membrane [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011538908.1
COORDINATES: similar to AA sequence:RefSeq:WP_012702243.1
COORDINATES: similar to AA sequence:RefSeq:WP_020482736.1
COORDINATES: similar to AA sequence:RefSeq:WP_007413818.1
COORDINATES: similar to AA sequence:RefSeq:WP_020565455.1
COORDINATES: similar to AA sequence:RefSeq:WP_005369625.1
GO:0042314 - bacteriochlorophyll binding [Evidence IEA]
GO:0019684 - photosynthesis, light reaction [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013179235.1
COORDINATES: similar to AA sequence:RefSeq:WP_002714854.1
four-helix bundle copper-binding protein
COORDINATES: protein motif:HMM:NF023168.2
COORDINATES: similar to AA sequence:RefSeq:WP_010959414.1
COORDINATES: protein motif:HMM:NF016283.2
COORDINATES: protein motif:HMM:NF024803.2
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018234080.1
GO:0004176 - ATP-dependent peptidase activity [Evidence IEA]; GO:0004222 - metalloendopeptidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006787368.1
GO:0004803 - transposase activity [Evidence IEA]
RNA-guided endonuclease TnpB family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007417161.1
GO:0004751 - ribose-5-phosphate isomerase activity [Evidence IEA]
GO:0009052 - pentose-phosphate shunt, non-oxidative branch [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015445038.1
COORDINATES: similar to AA sequence:RefSeq:WP_018295283.1
GO:0030552 - cAMP binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
Crp/Fnr family transcriptional regulator
COORDINATES: protein motif:HMM:NF021098.2
COORDINATES: protein motif:HMM:NF016270.2
COORDINATES: similar to AA sequence:RefSeq:WP_019337684.1
COORDINATES: similar to AA sequence:RefSeq:WP_004248777.1
GO:0003690 - double-stranded DNA binding [Evidence IEA]
GO:0042262 - DNA protection [Evidence IEA]
host-nuclease inhibitor Gam family protein
COORDINATES: protein motif:HMM:NF033679.1