Methylomagnum ishizawai strain RS11D-Pr plasmid pRS11DPr1, 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\nAP019784.1.\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: similar to AA sequence:RefSeq:WP_010960709.1
GO:0016757 - glycosyltransferase activity [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012116318.1
COORDINATES: similar to AA sequence:RefSeq:WP_007734845.1
FIST C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012829311.1
GO:0004096 - catalase activity [Evidence IEA]; GO:0020037 - heme binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF024880.2
GO:0008168 - methyltransferase activity [Evidence IEA]; GO:1904047 - S-adenosyl-L-methionine binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010961468.1
COORDINATES: similar to AA sequence:RefSeq:WP_005369162.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005369163.1
COORDINATES: similar to AA sequence:RefSeq:WP_002809405.1
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010959728.1
GO:0004181 - metallocarboxypeptidase activity [Evidence IEA]; GO:0008270 - zinc ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013441856.1
COORDINATES: similar to AA sequence:RefSeq:WP_013229558.1
COORDINATES: similar to AA sequence:RefSeq:WP_008217108.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR03975.1
GO:0003824 - catalytic activity [Evidence IEA]
RiPP maturation radical SAM C-methyltransferase
COORDINATES: protein motif:HMM:TIGR04463.1
TIGR04463 family radical SAM/SPASM RiPP maturase
COORDINATES: protein motif:HMM:NF012859.2
COORDINATES: protein motif:HMM:NF023959.2
filamentous haemagglutinin family protein
COORDINATES: protein motif:HMM:NF015803.2
ShlB/FhaC/HecB family hemolysin secretion/activation protein
COORDINATES: protein motif:HMM:NF024257.2
substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019867935.1
COORDINATES: similar to AA sequence:RefSeq:WP_017365143.1
GO:0015368 - calcium:monoatomic cation antiporter activity [Evidence IEA]
GO:0006816 - calcium ion transport [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR02135.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0051049 - regulation of transport [Evidence IEA]
phosphate signaling complex protein PhoU
COORDINATES: similar to AA sequence:RefSeq:WP_010960383.1
COORDINATES: similar to AA sequence:RefSeq:WP_017774948.1
COORDINATES: similar to AA sequence:RefSeq:WP_020176912.1
COORDINATES: similar to AA sequence:RefSeq:WP_011766684.1
COORDINATES: protein motif:HMM:NF012311.2
GO:0008236 - serine-type peptidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010960472.1
COORDINATES: protein motif:HMM:NF014567.2
COORDINATES: similar to AA sequence:RefSeq:WP_019140404.1
COORDINATES: similar to AA sequence:RefSeq:WP_012627467.1
GO:0004553 - hydrolase activity, hydrolyzing O-glycosyl compounds [Evidence IEA]
GO:0005975 - carbohydrate metabolic process [Evidence IEA]
glycoside hydrolase family 2 TIM barrel-domain containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017878701.1
GO:0008108 - UDP-glucose:hexose-1-phosphate uridylyltransferase activity [Evidence IEA]
GO:0006012 - galactose metabolic process [Evidence IEA]
galactose-1-phosphate uridylyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_017718265.1
GO:0004335 - galactokinase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_002625658.1
COORDINATES: similar to AA sequence:RefSeq:WP_013294486.1
COORDINATES: similar to AA sequence:RefSeq:WP_012639134.1
COORDINATES: similar to AA sequence:RefSeq:WP_004261833.1
Lrp/AsnC family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_002923476.1
COORDINATES: similar to AA sequence:RefSeq:WP_015448340.1
COORDINATES: similar to AA sequence:RefSeq:WP_020819439.1
ATP-binding cassette domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_020819438.1
COORDINATES: similar to AA sequence:RefSeq:WP_014747816.1
COORDINATES: similar to AA sequence:RefSeq:WP_020157735.1
GO:0009279 - cell outer membrane [Evidence IEA]
GO:0015288 - porin activity [Evidence IEA]
efflux transporter outer membrane subunit
COORDINATES: similar to AA sequence:RefSeq:WP_011589373.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:1904680 - peptide transmembrane transporter activity [Evidence IEA]
GO:0015833 - peptide transport [Evidence IEA]
multidrug ABC transporter permease/ATP-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_005372448.1
GO:0019867 - outer membrane [Evidence IEA]
GO:0015343 - siderophore-iron transmembrane transporter activity [Evidence IEA]
GO:0015891 - siderophore transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014237990.1
PepSY-associated TM helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_015768398.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0016151 - nickel cation binding [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]; GO:0010045 - response to nickel cation [Evidence IEA]
nickel-responsive transcriptional regulator NikR
COORDINATES: similar to AA sequence:RefSeq:WP_019865431.1
TonB-dependent receptor plug domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010961409.1
GO:0046872 - metal ion binding [Evidence IEA]
zinc ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_017364213.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011456228.1
COORDINATES: similar to AA sequence:RefSeq:WP_017364211.1
COORDINATES: similar to AA sequence:RefSeq:WP_010961412.1
COORDINATES: similar to AA sequence:RefSeq:WP_010961405.1
COORDINATES: similar to AA sequence:RefSeq:WP_017364209.1
COORDINATES: similar to AA sequence:RefSeq:WP_006890223.1
L-dopachrome tautomerase-related protein
COORDINATES: similar to AA sequence:RefSeq:WP_003612569.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006890226.1
GO:0018597 - ammonia monooxygenase activity [Evidence IEA]
bacterial ammonia monooxygenase, subunit AmoA
COORDINATES: similar to AA sequence:RefSeq:WP_020483939.1
bacterial ammonia monooxygenase, subunit AmoB
COORDINATES: similar to AA sequence:RefSeq:WP_005370914.1
bacterial ammonia monooxygenase, subunit AmoC
COORDINATES: similar to AA sequence:RefSeq:WP_006890229.1
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: protein motif:HMM:NF012273.2
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_013818533.1
GO:0015116 - sulfate transmembrane transporter activity [Evidence IEA]
GO:0008272 - sulfate transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017366318.1
COORDINATES: similar to AA sequence:RefSeq:WP_007162128.1
GO:0007165 - signal transduction [Evidence IEA]
COORDINATES: protein motif:HMM:NF014577.2
DcaP family trimeric outer membrane transporter
COORDINATES: protein motif:HMM:NF013487.2
GO:0009055 - electron transfer activity [Evidence IEA]; GO:0020037 - heme binding [Evidence IEA]; GO:0005506 - iron ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020562238.1
COORDINATES: protein motif:HMM:NF024860.2
GO:0050656 - 3'-phosphoadenosine 5'-phosphosulfate binding [Evidence IEA]; GO:0008146 - sulfotransferase activity [Evidence IEA]
GO:0000155 - phosphorelay sensor kinase activity [Evidence IEA]
histidine kinase dimerization/phospho-acceptor domain-containing protein
COORDINATES: protein motif:HMM:TIGR00229.1
COORDINATES: protein motif:HMM:NF024946.2
COORDINATES: similar to AA sequence:RefSeq:WP_009553312.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013292737.1
COORDINATES: protein motif:HMM:NF028237.2
histidine kinase N-terminal 7TM domain-containing protein
COORDINATES: protein motif:HMM:NF012772.2
COORDINATES: protein motif:HMM:NF024240.2
COORDINATES: protein motif:HMM:NF020514.2
COORDINATES: protein motif:HMM:NF013382.2
methyltransferase domain-containing protein
COORDINATES: protein motif:HMM:NF016145.2
polysaccharide pyruvyl transferase family protein
COORDINATES: protein motif:HMM:NF024968.2
COORDINATES: protein motif:HMM:NF012744.2
COORDINATES: protein motif:HMM:NF012642.2
GO:0030089 - phycobilisome [Evidence IEA]
GO:0015979 - photosynthesis [Evidence IEA]
phycobilisome rod-core linker polypeptide
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_004882790.1
COORDINATES: similar to AA sequence:RefSeq:WP_018413376.1
CerR family C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019867491.1
COORDINATES: similar to AA sequence:RefSeq:WP_020483097.1
GO:0005215 - transporter activity [Evidence IEA]
efflux RND transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_013901016.1
COORDINATES: protein motif:HMM:NF013702.2
lysophospholipid acyltransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_010959431.1
COORDINATES: similar to AA sequence:RefSeq:WP_006892617.1
COORDINATES: similar to AA sequence:RefSeq:WP_012502099.1
COORDINATES: similar to AA sequence:RefSeq:WP_014560379.1
GO:0016051 - carbohydrate biosynthetic process [Evidence IEA]
N-acetylneuraminate synthase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_008512381.1
COORDINATES: similar to AA sequence:RefSeq:WP_014856157.1
GO:0030170 - pyridoxal phosphate binding [Evidence IEA]; GO:0008483 - transaminase activity [Evidence IEA]
aminotransferase class III-fold pyridoxal phosphate-dependent enzyme
COORDINATES: similar to AA sequence:RefSeq:WP_009280550.1
transketolase C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009280551.1
GO:0016624 - oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012825608.1
COORDINATES: similar to AA sequence:RefSeq:WP_012505599.1
COORDINATES: protein motif:HMM:NF024629.2
COORDINATES: similar to AA sequence:RefSeq:WP_016875196.1
COORDINATES: similar to AA sequence:RefSeq:WP_013334391.1
COORDINATES: protein motif:HMM:NF021616.2
COORDINATES: protein motif:HMM:NF024831.2
COORDINATES: similar to AA sequence:RefSeq:WP_015334856.1
COORDINATES: protein motif:HMM:NF012568.2
GO:0008299 - isoprenoid biosynthetic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF033640.1
twitch domain-containing radical SAM protein
COORDINATES: protein motif:HMM:TIGR01536.1
GO:0004066 - asparagine synthase (glutamine-hydrolyzing) activity [Evidence IEA]
GO:0006529 - asparagine biosynthetic process [Evidence IEA]
asparagine synthase (glutamine-hydrolyzing)
COORDINATES: protein motif:HMM:NF013226.2
GO:0016765 - transferase activity, transferring alkyl or aryl (other than methyl) groups [Evidence IEA]
COORDINATES: protein motif:HMM:NF013245.2
COORDINATES: protein motif:HMM:NF012235.2
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: protein motif:HMM:NF014414.2
COORDINATES: protein motif:HMM:NF017532.2
phytanoyl-CoA dioxygenase family protein
COORDINATES: protein motif:HMM:NF013752.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
COORDINATES: protein motif:HMM:NF036807.2
COORDINATES: protein motif:HMM:NF033516.0
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013817848.1
COORDINATES: protein motif:HMM:TIGR01596.1
GO:0004521 - endoribonuclease activity [Evidence IEA]
GO:0043571 - maintenance of CRISPR repeat elements [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR02165.1
GO:0003674 - molecular_function [Evidence IEA]
COORDINATES: protein motif:HMM:NF021156.2
type I-U CRISPR-associated RAMP protein Csb1/Cas7u
COORDINATES: protein motif:HMM:NF012798.2
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015958327.1
COORDINATES: protein motif:HMM:NF024751.2
COORDINATES: protein motif:HMM:NF024980.2
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF015038.2
COORDINATES: similar to AA sequence:RefSeq:WP_076611465.1
frameshifted; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012238196.1
GO:0010181 - FMN binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
LLM class flavin-dependent oxidoreductase
COORDINATES: protein motif:HMM:NF013927.2
GO:0016811 - hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020563499.1
COORDINATES: similar to AA sequence:RefSeq:WP_017256214.1
GO:0016746 - acyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019472803.1
COORDINATES: similar to AA sequence:RefSeq:WP_017479479.1
COORDINATES: similar to AA sequence:RefSeq:WP_011617409.1
COORDINATES: protein motif:HMM:NF004282.0
GO:0031177 - phosphopantetheine binding [Evidence IEA]
GO:0008610 - lipid biosynthetic process [Evidence IEA]
non-ribosomal peptide synthase/polyketide synthase
COORDINATES: protein motif:HMM:NF012873.2
COORDINATES: protein motif:HMM:NF003417.0
COORDINATES: similar to AA sequence:RefSeq:WP_019868432.1
COORDINATES: similar to AA sequence:RefSeq:WP_020157064.1
COORDINATES: similar to AA sequence:RefSeq:WP_011381157.1
COORDINATES: protein motif:HMM:NF013786.2
GO:0008897 - holo-[acyl-carrier-protein] synthase activity [Evidence IEA]; GO:0000287 - magnesium ion binding [Evidence IEA]
4'-phosphopantetheinyl transferase superfamily protein