Methylocystis parvus strain BRCS2 plasmid unnamed2, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales; Methylocystaceae; Methylocystis.
Isolation and characterisation of Methylocystis spp. for poly-3-hydroxybutyrate production using waste methane feedstocks
Submitted (24-SEP-2019) Life Sciences, University of Nottingham, University Boulevard, Nottingham, Nottinghamshire NG7 2RD, United Kingdom
REFSEQ INFORMATION: The reference sequence is identical to\nCP044333.1.\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/\nThis genome has a base modification file available.\n\n##Genome-Assembly-Data-START##\nAssembly Method :: HGAP v. Sep-16\nGenome Representation :: Full\nExpected Final Version :: Yes\nReference-guided Assembly :: Methylocystis_sp._SC2_complete_genome\nGenome Coverage :: 245x\nSequencing Technology :: PacBio RSII\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/19/2023 15:51:34\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.4\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 4,398\nCDSs (total) :: 4,340\nGenes (coding) :: 4,253\nCDSs (with protein) :: 4,253\nGenes (RNA) :: 58\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 48\nncRNAs :: 4\nPseudo Genes (total) :: 87\nCDSs (without protein) :: 87\nPseudo Genes (ambiguous residues) :: 0 of 87\nPseudo Genes (frameshifted) :: 33 of 87\nPseudo Genes (incomplete) :: 62 of 87\nPseudo Genes (internal stop) :: 9 of 87\nPseudo Genes (multiple problems) :: 16 of 87\nCRISPR Arrays :: 2\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_016921910.1
GO:0000287 - magnesium ion binding [Evidence IEA]; GO:0030976 - thiamine pyrophosphate binding [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_016921911.1
glutathione S-transferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_016921912.1
COORDINATES: similar to AA sequence:RefSeq:WP_016921913.1
GO:0016787 - hydrolase activity [Evidence IEA]
GO:0008152 - metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016921914.1
GO:0016853 - isomerase activity [Evidence IEA]
GO:0006725 - cellular aromatic compound metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020372490.1
COORDINATES: similar to AA sequence:RefSeq:WP_008259794.1
COORDINATES: similar to AA sequence:RefSeq:WP_016921916.1
COORDINATES: similar to AA sequence:RefSeq:WP_016921917.1
COORDINATES: protein motif:HMM:NF017077.2
COORDINATES: similar to AA sequence:RefSeq:WP_016918562.1
COORDINATES: similar to AA sequence:RefSeq:WP_020094505.1
GO:0008703 - 5-amino-6-(5-phosphoribosylamino)uracil reductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019832346.1
COORDINATES: similar to AA sequence:RefSeq:WP_011983018.1
GO:0051304 - chromosome separation [Evidence IEA]
COORDINATES: protein motif:HMM:NF018841.2
COORDINATES: similar to AA sequence:RefSeq:WP_016919151.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF016167.2
COORDINATES: similar to AA sequence:RefSeq:WP_011655391.1
COORDINATES: similar to AA sequence:RefSeq:WP_018268287.1
COORDINATES: similar to AA sequence:RefSeq:WP_007637778.1
COORDINATES: similar to AA sequence:RefSeq:WP_018329036.1
COORDINATES: similar to AA sequence:RefSeq:WP_016919157.1
COORDINATES: similar to AA sequence:RefSeq:WP_003551406.1
frameshifted; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012778787.1
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_018308339.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012495756.1
COORDINATES: similar to AA sequence:RefSeq:WP_015719624.1
GO:0003824 - catalytic activity [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]
GO:0006304 - DNA modification [Evidence IEA]
Eco57I restriction-modification methylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017173568.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0009036 - type II site-specific deoxyribonuclease activity [Evidence IEA]
GO:0009307 - DNA restriction-modification system [Evidence IEA]
PaeR7I family type II restriction endonuclease
COORDINATES: similar to AA sequence:RefSeq:WP_015855874.1
COORDINATES: protein motif:HMM:NF037406.2
COORDINATES: similar to AA sequence:RefSeq:WP_009207852.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012214174.1
COORDINATES: similar to AA sequence:RefSeq:WP_017988802.1
COORDINATES: similar to AA sequence:RefSeq:WP_016922155.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0008270 - zinc ion binding [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: protein motif:HMM:NF013354.2
COORDINATES: similar to AA sequence:RefSeq:WP_076611806.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
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_009823918.1
COORDINATES: protein motif:HMM:NF015437.2
autoinducer binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_018409496.1
COORDINATES: similar to AA sequence:RefSeq:WP_015887125.1
COORDINATES: similar to AA sequence:RefSeq:WP_017504271.1
COORDINATES: similar to AA sequence:RefSeq:WP_018409499.1
VirB4 family type IV secretion/conjugal transfer ATPase
COORDINATES: similar to AA sequence:RefSeq:WP_011931076.1
GO:0043684 - type IV secretion system complex [Evidence IEA]
COORDINATES: protein motif:HMM:NF033894.1
COORDINATES: similar to AA sequence:RefSeq:WP_018409502.1
COORDINATES: similar to AA sequence:RefSeq:WP_018409503.1
COORDINATES: similar to AA sequence:RefSeq:WP_018409504.1
COORDINATES: similar to AA sequence:RefSeq:WP_018409505.1
P-type conjugative transfer protein VirB9
COORDINATES: similar to AA sequence:RefSeq:WP_018409506.1
COORDINATES: similar to AA sequence:RefSeq:WP_018409507.1
GO:0044097 - secretion by the type IV secretion system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018409508.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_018409509.1
COORDINATES: similar to AA sequence:RefSeq:WP_003163686.1
COORDINATES: similar to AA sequence:RefSeq:WP_018409518.1
relaxase/mobilization nuclease domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009859471.1
plasmid mobilization relaxosome protein MobC
COORDINATES: similar to AA sequence:RefSeq:WP_018409520.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: protein motif:HMM:NF013793.2
COORDINATES: similar to AA sequence:RefSeq:WP_018409523.1
GO:0003697 - single-stranded DNA binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_076611221.1
internal stop; 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_076612398.1
COORDINATES: similar to AA sequence:RefSeq:WP_016921902.1
COORDINATES: protein motif:HMM:NF013752.2
COORDINATES: protein motif:HMM:NF024895.2
COORDINATES: similar to AA sequence:RefSeq:WP_020160937.1
COORDINATES: similar to AA sequence:RefSeq:WP_003546103.1
COORDINATES: similar to AA sequence:RefSeq:WP_010967558.1
Crp/Fnr family transcriptional regulator
COORDINATES: protein motif:HMM:NF019310.2
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014198268.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611189.1
COORDINATES: similar to AA sequence:RefSeq:WP_011502641.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015340.1
COORDINATES: similar to AA sequence:RefSeq:WP_017183759.1
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; 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_016922180.1
COORDINATES: protein motif:HMM:NF024751.2
COORDINATES: protein motif:HMM:NF024776.2
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_003039902.1
GO:0000155 - phosphorelay sensor kinase activity [Evidence IEA]
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: protein motif:HMM:NF024206.2
ankyrin repeat domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_005369348.1
LytTR family DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_004348882.1
LuxR C-terminal-related transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_016921347.1
COORDINATES: similar to AA sequence:RefSeq:WP_016921346.1
COORDINATES: similar to AA sequence:RefSeq:WP_016920401.1
COORDINATES: protein motif:HMM:NF018305.2
COORDINATES: similar to AA sequence:RefSeq:WP_018409426.1
COORDINATES: protein motif:HMM:NF025658.2
COORDINATES: protein motif:HMM:NF025197.2
COORDINATES: similar to AA sequence:RefSeq:WP_008512667.1
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:NF018684.2
COORDINATES: similar to AA sequence:RefSeq:WP_009030140.1
3' terminal RNA ribose 2'-O-methyltransferase Hen1
COORDINATES: similar to AA sequence:RefSeq:WP_018431440.1
COORDINATES: similar to AA sequence:RefSeq:WP_018264830.1
FadR/GntR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_018406473.1
COORDINATES: similar to AA sequence:RefSeq:WP_016921679.1
COORDINATES: similar to AA sequence:RefSeq:WP_005026533.1
COORDINATES: similar to AA sequence:RefSeq:WP_007674248.1
COORDINATES: similar to AA sequence:RefSeq:WP_015934064.1
COORDINATES: protein motif:HMM:TIGR01783.1
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_003608598.1
COORDINATES: similar to AA sequence:RefSeq:WP_018268427.1
HAMP domain-containing sensor histidine kinase
COORDINATES: similar to AA sequence:RefSeq:WP_003610438.1
COORDINATES: protein motif:HMM:NF012870.2
COORDINATES: similar to AA sequence:RefSeq:WP_014857716.1
COORDINATES: protein motif:HMM:NF018259.2
COORDINATES: protein motif:HMM:NF015983.2
COORDINATES: protein motif:HMM:NF013677.2
COORDINATES: protein motif:HMM:NF017528.2
COORDINATES: protein motif:HMM:NF024408.2
IS66 family transposase zinc-finger binding domain-containing protein
COORDINATES: protein motif:HMM:NF015038.2
COORDINATES: similar to AA sequence:RefSeq:WP_076612204.1
COORDINATES: similar to AA sequence:RefSeq:WP_012976683.1
COORDINATES: protein motif:HMM:TIGR02937.1
sigma-70 family RNA polymerase sigma factor
COORDINATES: similar to AA sequence:RefSeq:WP_018265419.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611472.1
COORDINATES: similar to AA sequence:RefSeq:WP_018264825.1
COORDINATES: similar to AA sequence:RefSeq:WP_018265056.1
metallo-mystery pair system four-Cys motif protein
COORDINATES: similar to AA sequence:RefSeq:WP_019644800.1
COORDINATES: protein motif:HMM:TIGR04071.2
COORDINATES: similar to AA sequence:RefSeq:WP_018268275.1
methanobactin biosynthesis cassette protein MbnB
COORDINATES: similar to AA sequence:RefSeq:WP_018268274.1
methanobactin biosynthesis cassette protein MbnC
COORDINATES: similar to AA sequence:RefSeq:WP_003614730.1
COORDINATES: protein motif:HMM:NF013646.2
COORDINATES: similar to AA sequence:RefSeq:WP_018266134.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611915.1
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.
transposase zinc-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011511202.1
COORDINATES: similar to AA sequence:RefSeq:WP_003537135.1
COORDINATES: similar to AA sequence:RefSeq:WP_013845293.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_014252402.1
COORDINATES: similar to AA sequence:RefSeq:WP_003610959.1
COORDINATES: protein motif:HMM:NF012311.2
COORDINATES: similar to AA sequence:RefSeq:WP_009469622.1
Mu transposase C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019863962.1
COORDINATES: protein motif:HMM:NF022694.2
COORDINATES: similar to AA sequence:RefSeq:WP_018989579.1
COORDINATES: similar to AA sequence:RefSeq:WP_009726986.1
COORDINATES: similar to AA sequence:RefSeq:WP_008969326.1
GO:0000155 - phosphorelay sensor kinase activity [Evidence IEA]; GO:0046983 - protein dimerization activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003610181.1
COORDINATES: similar to AA sequence:RefSeq:WP_016918120.1
COORDINATES: similar to AA sequence:RefSeq:WP_019898324.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0043565 - sequence-specific DNA binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018420431.1
COORDINATES: similar to AA sequence:RefSeq:WP_016918858.1
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_012381852.1
COORDINATES: protein motif:HMM:NF024260.2
COORDINATES: similar to AA sequence:RefSeq:WP_012044064.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611419.1
COORDINATES: similar to AA sequence:RefSeq:WP_043766079.1
COORDINATES: similar to AA sequence:RefSeq:WP_011510441.1
COORDINATES: similar to AA sequence:RefSeq:WP_016922195.1
COORDINATES: protein motif:HMM:NF012861.2
COORDINATES: similar to AA sequence:RefSeq:WP_015137507.1
GO:0016530 - metallochaperone activity [Evidence IEA]; GO:0000166 - nucleotide binding [Evidence IEA]
GO:0036211 - protein modification process [Evidence IEA]
hydrogenase nickel incorporation protein HypB
COORDINATES: similar to AA sequence:RefSeq:WP_018409038.1
hydrogenase expression/formation protein HypE
COORDINATES: similar to AA sequence:RefSeq:WP_012040811.1
GO:0016530 - metallochaperone activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007594355.1
COORDINATES: similar to AA sequence:RefSeq:WP_012592703.1
GO:0003998 - acylphosphatase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003612933.1
COORDINATES: similar to AA sequence:RefSeq:WP_003612931.1
GO:0016151 - nickel cation binding [Evidence IEA]
nickel-dependent hydrogenase large subunit
COORDINATES: protein motif:HMM:NF040271.1
COORDINATES: similar to AA sequence:RefSeq:WP_003612925.1
COORDINATES: similar to AA sequence:RefSeq:WP_003612921.1
GO:0008233 - peptidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012592702.1
GO:0016530 - metallochaperone activity [Evidence IEA]; GO:0051082 - unfolded protein binding [Evidence IEA]
GO:0065003 - protein-containing complex assembly [Evidence IEA]
HypC/HybG/HupF family hydrogenase formation chaperone
COORDINATES: protein motif:HMM:NF013334.2
hydrogenase maturation nickel metallochaperone HypA
COORDINATES: protein motif:HMM:NF013397.2
formate/nitrite transporter family protein
COORDINATES: protein motif:HMM:NF037012.2
COORDINATES: similar to AA sequence:RefSeq:WP_009453051.1
COORDINATES: protein motif:HMM:NF012301.2
COORDINATES: similar to AA sequence:RefSeq:WP_016921550.1
COORDINATES: protein motif:HMM:NF017243.2
COORDINATES: similar to AA sequence:RefSeq:WP_018267509.1
COORDINATES: similar to AA sequence:RefSeq:WP_007439020.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611908.1
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:TIGR01730.1
GO:0005215 - transporter activity [Evidence IEA]
efflux RND transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_013501649.1
COORDINATES: protein motif:HMM:NF024997.2
DDE-type integrase/transposase/recombinase
COORDINATES: similar to AA sequence:RefSeq:WP_076611992.1
COORDINATES: similar to AA sequence:RefSeq:WP_009488682.1
COORDINATES: similar to AA sequence:RefSeq:WP_007181579.1
COORDINATES: similar to AA sequence:RefSeq:WP_018405944.1
COORDINATES: protein motif:HMM:NF012772.2
COORDINATES: similar to AA sequence:RefSeq:WP_012385523.1
COORDINATES: similar to AA sequence:RefSeq:WP_052642687.1
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_005148046.1