Methylomonas koyamae strain Fw12E-Y plasmid pFW12EY, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Methylococcales; Methylococcaceae; Methylomonas.
Complete genome sequence of Methylomonas koyamae strain Fw12E-Y
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\nAP019778.1.\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 :: 148x\nSequencing Technology :: Illumina MiSeq, GridION\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 04/29/2023 04:33:30\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) :: 4,589\nCDSs (total) :: 4,529\nGenes (coding) :: 4,476\nCDSs (with protein) :: 4,476\nGenes (RNA) :: 60\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 47\nncRNAs :: 4\nPseudo Genes (total) :: 53\nCDSs (without protein) :: 53\nPseudo Genes (ambiguous residues) :: 0 of 53\nPseudo Genes (frameshifted) :: 23 of 53\nPseudo Genes (incomplete) :: 40 of 53\nPseudo Genes (internal stop) :: 11 of 53\nPseudo Genes (multiple problems) :: 18 of 53\nCRISPR Arrays :: 3\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
Japan: Aichi, Anjo, Aichi Agricultural Research Center
COORDINATES: similar to AA sequence:RefSeq:WP_012475076.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_010939304.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0008170 - N-methyltransferase activity [Evidence IEA]
GO:0006306 - DNA methylation [Evidence IEA]
BREX-1 system adenine-specific DNA-methyltransferase PglX
COORDINATES: similar to AA sequence:RefSeq:WP_011499287.1
PDDEXK nuclease domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013292862.1
COORDINATES: similar to AA sequence:RefSeq:WP_019485326.1
GO:0003824 - catalytic activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008734415.1
GO:0004176 - ATP-dependent peptidase activity [Evidence IEA]
GO:0030163 - protein catabolic process [Evidence IEA]
BREX system Lon protease-like protein BrxL
COORDINATES: similar to AA sequence:RefSeq:WP_016346204.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]; GO:0042578 - phosphoric ester hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017841051.1
COORDINATES: similar to AA sequence:RefSeq:WP_016809404.1
COORDINATES: similar to AA sequence:RefSeq:WP_007644175.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0004386 - helicase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006892627.1
GO:0003676 - nucleic acid binding [Evidence IEA]
frameshifted; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_006892169.1
AbrB/MazE/SpoVT family DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006892170.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF015049.2
GO:0016746 - acyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018078807.1
COORDINATES: similar to AA sequence:RefSeq:WP_020481733.1
COORDINATES: similar to AA sequence:RefSeq:WP_020481732.1
GO:0003674 - molecular_function [Evidence IEA]
GO:0015074 - DNA integration [Evidence IEA]
Members of this protein family are the putative conjugative coupling factor, TraD, as the term is used for the SXT and TOL plasmid systems; Derived by automated computational analysis using gene prediction method: Protein Homology.
conjugative transfer system coupling protein TraD
COORDINATES: protein motif:HMM:NF041494.1
COORDINATES: similar to AA sequence:RefSeq:WP_020481741.1
COORDINATES: similar to AA sequence:RefSeq:WP_017839079.1
COORDINATES: similar to AA sequence:RefSeq:WP_020485765.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020485766.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: protein motif:HMM:NF017183.2
COORDINATES: protein motif:HMM:NF013961.2
transglutaminase domain-containing protein
COORDINATES: protein motif:HMM:NF012790.2
rhodanese-like domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_005342517.1
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF016906.2
COORDINATES: protein motif:HMM:NF013156.2
COORDINATES: protein motif:HMM:NF037144.2
COORDINATES: protein motif:HMM:NF039622.1
COORDINATES: similar to AA sequence:RefSeq:WP_017086038.1
GO:0000166 - nucleotide binding [Evidence IEA]
GO:0030541 - plasmid partitioning [Evidence IEA]
COORDINATES: protein motif:HMM:NF013618.2
transglycosylase SLT domain-containing protein
COORDINATES: protein motif:HMM:NF017094.2
GO:0044780 - bacterial-type flagellum assembly [Evidence IEA]; GO:0045893 - positive regulation of DNA-templated transcription [Evidence IEA]
flagellar transcriptional regulator FlhD
COORDINATES: similar to AA sequence:RefSeq:WP_019959482.1
GO:0004520 - endodeoxyribonuclease activity [Evidence IEA]
GO:0043571 - maintenance of CRISPR repeat elements [Evidence IEA]
type I-F CRISPR-associated endonuclease Cas1f
COORDINATES: similar to AA sequence:RefSeq:WP_013818079.1
GO:0004386 - helicase activity [Evidence IEA]
type I-F CRISPR-associated helicase Cas3f
COORDINATES: similar to AA sequence:RefSeq:WP_003579568.1
GO:0008080 - N-acetyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005371069.1
COORDINATES: protein motif:HMM:TIGR02564.1
COORDINATES: similar to AA sequence:RefSeq:WP_005371074.1
COORDINATES: similar to AA sequence:RefSeq:WP_005217651.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:TIGR02563.1
GO:0004521 - endoribonuclease activity [Evidence IEA]
type I-F CRISPR-associated endoribonuclease Cas6/Csy4
COORDINATES: protein motif:HMM:NF019530.2
conjugal transfer protein TraG N-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF017892.2
COORDINATES: protein motif:HMM:TIGR02740.1
COORDINATES: protein motif:HMM:NF013506.2
GO:0008236 - serine-type peptidase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF011458.0
conjugal transfer mating pair stabilization protein TraN
COORDINATES: similar to AA sequence:RefSeq:WP_007191263.1
COORDINATES: protein motif:HMM:NF021209.2
TrbC family F-type conjugative pilus assembly protein
COORDINATES: similar to AA sequence:RefSeq:WP_005369509.1
COORDINATES: similar to AA sequence:RefSeq:WP_020481792.1
COORDINATES: similar to AA sequence:RefSeq:WP_020482839.1
TraA family conjugative transfer protein
COORDINATES: similar to AA sequence:RefSeq:WP_020563520.1
COORDINATES: protein motif:HMM:NF024498.2
COORDINATES: protein motif:HMM:NF015688.2
COORDINATES: protein motif:HMM:NF018311.2
type-F conjugative transfer system secretin TraK
COORDINATES: similar to AA sequence:RefSeq:WP_005369496.1
TraE/TraK family type IV conjugative transfer system protein
COORDINATES: similar to AA sequence:RefSeq:WP_005369494.1
type IV conjugative transfer system protein TraL
COORDINATES: similar to AA sequence:RefSeq:WP_006746759.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003300053.1
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_004303513.1
GO:0008452 - RNA ligase activity [Evidence IEA]
GO:0006396 - RNA processing [Evidence IEA]
COORDINATES: protein motif:HMM:NF025639.2
COORDINATES: similar to AA sequence:RefSeq:WP_000021280.1
helix-turn-helix transcriptional regulator
COORDINATES: protein motif:HMM:NF024676.2
COORDINATES: similar to AA sequence:RefSeq:WP_013819951.1
COORDINATES: similar to AA sequence:RefSeq:WP_003145717.1
COORDINATES: similar to AA sequence:RefSeq:WP_020160094.1
COORDINATES: similar to AA sequence:RefSeq:WP_013818646.1
translesion error-prone DNA polymerase V autoproteolytic subunit
COORDINATES: similar to AA sequence:RefSeq:WP_013818648.1
GO:0008233 - peptidase activity [Evidence IEA]; GO:0003697 - single-stranded DNA binding [Evidence IEA]
GO:0018142 - protein-DNA covalent cross-linking [Evidence IEA]; GO:0009432 - SOS response [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013817538.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF013793.2
COORDINATES: protein motif:HMM:NF014273.2
ParB N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_076612082.1
COORDINATES: similar to AA sequence:RefSeq:WP_020484481.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:NP_490533.1
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_011366069.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_004514518.1
putative addiction module antidote protein
COORDINATES: similar to AA sequence:RefSeq:WP_013032669.1
GO:0015562 - efflux transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020563057.1
GO:0005215 - transporter activity [Evidence IEA]
efflux RND transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_013517142.1
GO:0051139 - metal cation:proton antiporter activity [Evidence IEA]
CusA/CzcA family heavy metal efflux RND transporter
COORDINATES: similar to AA sequence:RefSeq:WP_020485838.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0019829 - ATPase-coupled monoatomic cation transmembrane transporter activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]; GO:0015662 - P-type ion transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011733771.1
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_007183004.1
COORDINATES: similar to AA sequence:RefSeq:WP_001262004.1
COORDINATES: similar to AA sequence:RefSeq:WP_011282515.1
COORDINATES: similar to AA sequence:RefSeq:WP_019331447.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611358.1
COORDINATES: similar to AA sequence:RefSeq:WP_020561388.1
COORDINATES: similar to AA sequence:RefSeq:WP_020562081.1
COORDINATES: similar to AA sequence:RefSeq:WP_020562080.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020562079.1
GO:0000155 - phosphorelay sensor kinase activity [Evidence IEA]
GO:0007165 - signal transduction [Evidence IEA]
histidine kinase dimerization/phospho-acceptor domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_005368751.1
NirD/YgiW/YdeI family stress tolerance protein
COORDINATES: similar to AA sequence:RefSeq:WP_020562078.1
COORDINATES: protein motif:HMM:NF013970.2
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_002808809.1
GO:0008168 - methyltransferase activity [Evidence IEA]; GO:1904047 - S-adenosyl-L-methionine binding [Evidence IEA]
class I SAM-dependent DNA methyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_005375206.1
COORDINATES: similar to AA sequence:RefSeq:WP_020484204.1
GO:0004190 - aspartic-type endopeptidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005374376.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004519 - endonuclease activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012636692.1
COORDINATES: similar to AA sequence:RefSeq:WP_011485869.1
COORDINATES: similar to AA sequence:RefSeq:WP_020481819.1
COORDINATES: similar to AA sequence:RefSeq:WP_005369561.1
nitric oxide reductase activation protein
COORDINATES: similar to AA sequence:RefSeq:WP_020481815.1
COORDINATES: similar to AA sequence:RefSeq:WP_020482869.1
COORDINATES: similar to AA sequence:RefSeq:WP_020482866.1
COORDINATES: similar to AA sequence:RefSeq:WP_020481809.1
GO:0006259 - DNA metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006891123.1
COORDINATES: similar to AA sequence:RefSeq:WP_013816755.1
COORDINATES: similar to AA sequence:RefSeq:WP_020485757.1
COORDINATES: similar to AA sequence:RefSeq:WP_007349122.1
COORDINATES: protein motif:HMM:TIGR03696.1
RHS repeat-associated core domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006891677.1
COORDINATES: similar to AA sequence:RefSeq:WP_019658752.1
COORDINATES: protein motif:HMM:NF012798.2
COORDINATES: protein motif:HMM:NF023168.2
COORDINATES: protein motif:HMM:NF018381.2
COORDINATES: protein motif:HMM:TIGR03734.1
COORDINATES: protein motif:HMM:NF025810.2
COORDINATES: protein motif:HMM:TIGR03737.1
COORDINATES: protein motif:HMM:TIGR03735.1
COORDINATES: protein motif:HMM:TIGR03736.1
COORDINATES: protein motif:HMM:NF017243.2
COORDINATES: similar to AA sequence:RefSeq:WP_006890178.1
COORDINATES: similar to AA sequence:RefSeq:WP_001278583.1
frameshifted; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF014898.2
COORDINATES: similar to AA sequence:RefSeq:WP_059669267.1
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: protein motif:HMM:NF018319.2
COORDINATES: similar to AA sequence:RefSeq:WP_014630869.1
COORDINATES: similar to AA sequence:RefSeq:WP_013209362.1
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_012366848.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611179.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
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_020485770.1
COORDINATES: similar to AA sequence:RefSeq:WP_015190421.1
COORDINATES: similar to AA sequence:RefSeq:WP_015282027.1
COORDINATES: similar to AA sequence:RefSeq:WP_020484027.1
COORDINATES: similar to AA sequence:RefSeq:WP_020482878.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020482879.1
COORDINATES: similar to AA sequence:RefSeq:WP_020482880.1
COORDINATES: similar to AA sequence:RefSeq:WP_020482881.1
COORDINATES: similar to AA sequence:RefSeq:WP_020482882.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
frameshifted; internal stop; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_020712789.1
COORDINATES: similar to AA sequence:RefSeq:WP_018055511.1
GO:0110001 - toxin-antitoxin complex [Evidence IEA]
type II toxin-antitoxin system Phd/YefM family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_018055512.1
GO:0004521 - endoribonuclease activity [Evidence IEA]; GO:0005515 - protein binding [Evidence IEA]
putative toxin-antitoxin system toxin component, PIN family
COORDINATES: protein motif:HMM:NF013752.2
COORDINATES: similar to AA sequence:RefSeq:WP_015448732.1
GO:0004519 - endonuclease activity [Evidence IEA]; GO:0003676 - nucleic acid binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF022182.2
COORDINATES: similar to AA sequence:RefSeq:WP_020484203.1
GO:0002953 - 5'-deoxynucleotidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015434978.1
ADP-ribosylglycohydrolase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_003294211.1
COORDINATES: similar to AA sequence:RefSeq:WP_012475077.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611570.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: nucleotide motif:Rfam:14.4:RF01497
AL1L pseudoknot; Derived by automated computational analysis using gene prediction method: cmsearch.