Methylomagnum ishizawai strain RS11D-Pr plasmid pRS11DPr2, 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\nAP019785.1.\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+
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: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_020157762.1
GO:0004803 - transposase activity [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF016906.2
COORDINATES: protein motif:HMM:NF025180.2
COORDINATES: similar to AA sequence:RefSeq:WP_013817848.1
COORDINATES: protein motif:HMM:NF033516.0
COORDINATES: protein motif:HMM:NF015038.2
COORDINATES: protein motif:HMM:NF013752.2
COORDINATES: protein motif:HMM:NF017197.2
COORDINATES: similar to AA sequence:RefSeq:WP_011683398.1
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: protein motif:HMM:NF021524.2
COORDINATES: similar to AA sequence:RefSeq:WP_015280997.1
COORDINATES: similar to AA sequence:RefSeq:WP_018054505.1
GO:0006812 - monoatomic cation transport [Evidence IEA]; GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017366178.1
GO:0005886 - plasma membrane [Evidence IEA]
GO:0005247 - voltage-gated chloride channel activity [Evidence IEA]
GO:0006821 - chloride transport [Evidence IEA]; GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010960522.1
GO:0051139 - metal cation:proton antiporter activity [Evidence IEA]
CusA/CzcA family heavy metal efflux RND transporter
COORDINATES: similar to AA sequence:RefSeq:WP_020482819.1
COORDINATES: similar to AA sequence:RefSeq:WP_020482820.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: protein motif:HMM:NF021633.2
COORDINATES: similar to AA sequence:RefSeq:WP_013030243.1
GO:0006812 - monoatomic cation transport [Evidence IEA]; GO:1902600 - proton transmembrane transport [Evidence IEA]; GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015314236.1
GO:0016798 - hydrolase activity, acting on glycosyl bonds [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008437675.1
COORDINATES: similar to AA sequence:RefSeq:WP_016951978.1
COORDINATES: similar to AA sequence:RefSeq:WP_016862542.1
COORDINATES: similar to AA sequence:RefSeq:WP_020602821.1
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_015747846.1
COORDINATES: similar to AA sequence:RefSeq:WP_005368935.1
GO:0015562 - efflux transmembrane transporter activity [Evidence IEA]
GO:1905887 - autoinducer AI-2 transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020565081.1
nuclear transport factor 2 family protein
COORDINATES: similar to AA sequence:RefSeq:WP_014750970.1
COORDINATES: similar to AA sequence:RefSeq:WP_007766126.1
pyridoxamine 5'-phosphate oxidase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_009551433.1
carboxymuconolactone decarboxylase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_013820142.1
COORDINATES: similar to AA sequence:RefSeq:WP_011421305.1
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_013816906.1
COORDINATES: similar to AA sequence:RefSeq:WP_013959219.1
COORDINATES: protein motif:HMM:NF021364.2
COORDINATES: similar to AA sequence:RefSeq:WP_020564277.1
COORDINATES: similar to AA sequence:RefSeq:WP_011350688.1
protein-methionine-sulfoxide reductase heme-binding subunit MsrQ
COORDINATES: similar to AA sequence:RefSeq:WP_020563554.1
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.; 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_020563555.1
COORDINATES: similar to AA sequence:RefSeq:WP_014956965.1
COORDINATES: similar to AA sequence:RefSeq:WP_011751253.1
COORDINATES: protein motif:HMM:TIGR00180.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_008370838.1
GO:0016787 - hydrolase activity [Evidence IEA]
isochorismate family cysteine hydrolase YcaC
COORDINATES: protein motif:HMM:NF019581.2
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:NF012976.2
COORDINATES: similar to AA sequence:RefSeq:WP_015247134.1
lipocalin-like domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_005964840.1
COORDINATES: similar to AA sequence:RefSeq:WP_011395428.1
COORDINATES: protein motif:HMM:NF025000.2
COORDINATES: protein motif:HMM:NF024752.2
COORDINATES: protein motif:HMM:NF033592.1
COORDINATES: similar to AA sequence:RefSeq:WP_015865884.1
COORDINATES: protein motif:HMM:NF041518.1
choice-of-anchor Q domain-containing protein
COORDINATES: protein motif:HMM:TIGR02276.1
COORDINATES: protein motif:HMM:NF024592.2
COORDINATES: similar to AA sequence:RefSeq:WP_017265718.1
GO:0003964 - RNA-directed DNA polymerase activity [Evidence IEA]
GO:0000373 - Group II intron splicing [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
group II intron reverse transcriptase/maturase
COORDINATES: similar to AA sequence:RefSeq:WP_076612036.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611114.1
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_008954052.1
COORDINATES: similar to AA sequence:RefSeq:WP_006889996.1
COORDINATES: similar to AA sequence:RefSeq:WP_002714351.1
COORDINATES: similar to AA sequence:RefSeq:WP_014777014.1
COORDINATES: similar to AA sequence:RefSeq:WP_009118641.1
nucleotidyl transferase AbiEii/AbiGii toxin family protein
COORDINATES: similar to AA sequence:RefSeq:WP_018866576.1
AbiEi antitoxin N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_020507645.1
COORDINATES: similar to AA sequence:RefSeq:WP_020717633.1
type 1 glutamine amidotransferase domain-containing protein
COORDINATES: protein motif:HMM:NF019228.2
COORDINATES: protein motif:HMM:NF012759.2
GO:0000036 - acyl carrier activity [Evidence IEA]
GO:0006633 - fatty acid biosynthetic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF014698.2
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF012873.2
COORDINATES: similar to AA sequence:RefSeq:WP_012161924.1
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_076611896.1
frameshifted; 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:NF012869.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF012745.2
COORDINATES: protein motif:HMM:NF025025.2
COORDINATES: similar to AA sequence:RefSeq:WP_007461464.1
COORDINATES: protein motif:HMM:NF013882.2
COORDINATES: similar to AA sequence:RefSeq:WP_002786448.1
COORDINATES: similar to AA sequence:RefSeq:WP_015956151.1
COORDINATES: similar to AA sequence:RefSeq:WP_018396894.1
COORDINATES: protein motif:HMM:NF024980.2
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF024751.2
COORDINATES: similar to AA sequence:RefSeq:WP_011883961.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006352 - DNA-templated transcription initiation [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018281872.1
COORDINATES: protein motif:HMM:NF019265.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0016987 - sigma factor activity [Evidence IEA]
sigma factor-like helix-turn-helix DNA-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_012098849.1
COORDINATES: similar to AA sequence:RefSeq:WP_020476395.1
COORDINATES: protein motif:HMM:NF024736.2
COORDINATES: similar to AA sequence:RefSeq:WP_012701884.1
COORDINATES: similar to AA sequence:RefSeq:WP_007438512.1
COORDINATES: protein motif:HMM:NF012235.2
ATP-binding cassette domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013148423.1
MlaE family lipid ABC transporter permease subunit