Methylocystis parvus strain BRCS2 plasmid unnamed1, 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\nCP044332.1.\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: protein motif:HMM:NF012651.2
GO:0003697 - single-stranded DNA binding [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_003612723.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_003612725.1
AbrB/MazE/SpoVT family DNA-binding domain-containing protein
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_009682508.1
COORDINATES: protein motif:HMM:NF017524.2
plasmid mobilization relaxosome protein MobC
COORDINATES: protein motif:HMM:NF037421.2
COORDINATES: similar to AA sequence:RefSeq:WP_007587148.1
isoprenylcysteine carboxylmethyltransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_003608702.1
phospholipase D-like domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_018266398.1
COORDINATES: similar to AA sequence:RefSeq:WP_012049926.1
GO:0015035 - protein-disulfide reductase activity [Evidence IEA]
GO:0006662 - glycerol ether metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009489524.1
GO:0004386 - helicase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF024486.2
COORDINATES: similar to AA sequence:RefSeq:WP_011474335.1
COORDINATES: similar to AA sequence:RefSeq:WP_009762564.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_010915833.1
GO:0043684 - type IV secretion system complex [Evidence IEA]
GO:0044097 - secretion by the type IV secretion system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004129402.1
COORDINATES: similar to AA sequence:RefSeq:WP_009762567.1
TrbG/VirB9 family P-type conjugative transfer protein
COORDINATES: similar to AA sequence:RefSeq:WP_009762568.1
COORDINATES: protein motif:HMM:NF016491.2
COORDINATES: similar to AA sequence:RefSeq:WP_009762579.1
COORDINATES: similar to AA sequence:RefSeq:WP_009762572.1
VirB4 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_012653134.1
VirB3 family type IV secretion system protein
COORDINATES: protein motif:HMM:NF016820.2
COORDINATES: protein motif:HMM:NF013618.2
lytic transglycosylase domain-containing protein
COORDINATES: protein motif:HMM:NF024755.2
COORDINATES: protein motif:HMM:NF013980.2
SprT family zinc-dependent metalloprotease
COORDINATES: similar to AA sequence:RefSeq:WP_008125165.1
GO:0019812 - type I site-specific deoxyribonuclease complex [Evidence IEA]
GO:0009035 - type I site-specific deoxyribonuclease activity [Evidence IEA]
GO:0009307 - DNA restriction-modification system [Evidence IEA]
HsdR family type I site-specific deoxyribonuclease
COORDINATES: protein motif:HMM:NF019334.2
COORDINATES: protein motif:HMM:NF013579.2
GO:0006304 - DNA modification [Evidence IEA]
COORDINATES: protein motif:HMM:NF025625.2
COORDINATES: similar to AA sequence:RefSeq:WP_018079455.1
GO:0015666 - restriction endodeoxyribonuclease activity [Evidence IEA]; GO:0009007 - site-specific DNA-methyltransferase (adenine-specific) activity [Evidence IEA]
GO:0006306 - DNA methylation [Evidence IEA]; GO:0009307 - DNA restriction-modification system [Evidence IEA]
type I restriction-modification system subunit M
COORDINATES: similar to AA sequence:RefSeq:WP_008387851.1
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_006199590.1
COORDINATES: similar to AA sequence:RefSeq:WP_011444039.1
COORDINATES: similar to AA sequence:RefSeq:WP_018409475.1
COORDINATES: similar to AA sequence:RefSeq:WP_011654946.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_003548608.1
COORDINATES: similar to AA sequence:RefSeq:WP_016920731.1
COORDINATES: similar to AA sequence:RefSeq:WP_011971032.1
COORDINATES: similar to AA sequence:RefSeq:WP_003498000.1
COORDINATES: similar to AA sequence:RefSeq:WP_018409469.1
COORDINATES: similar to AA sequence:RefSeq:WP_009574187.1
COORDINATES: protein motif:HMM:NF012442.2
COORDINATES: similar to AA sequence:RefSeq:WP_018329048.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF018841.2
COORDINATES: similar to AA sequence:RefSeq:WP_011505056.1
COORDINATES: protein motif:HMM:NF028506.2
LysM peptidoglycan-binding domain-containing protein
COORDINATES: protein motif:HMM:NF016005.2
GO:0051304 - chromosome separation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014891365.1
COORDINATES: protein motif:HMM:NF025885.2
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_003615111.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF012801.2
COORDINATES: protein motif:HMM:NF013648.2
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_020174980.1
COORDINATES: similar to AA sequence:RefSeq:WP_018268395.1
COORDINATES: similar to AA sequence:RefSeq:WP_003615116.1
GO:0015291 - secondary active transmembrane transporter activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF015431.2
COORDINATES: similar to AA sequence:RefSeq:WP_013912755.1
COORDINATES: similar to AA sequence:RefSeq:WP_014891350.1
COORDINATES: similar to AA sequence:RefSeq:WP_012563562.1
GO:0009291 - unidirectional conjugation [Evidence IEA]
P-type conjugative transfer protein TrbG
COORDINATES: similar to AA sequence:RefSeq:WP_012287851.1
COORDINATES: similar to AA sequence:RefSeq:WP_016919731.1
P-type conjugative transfer protein TrbL
COORDINATES: similar to AA sequence:RefSeq:WP_014891346.1
GO:0009292 - horizontal gene transfer [Evidence IEA]
putative entry exclusion protein TrbK-alt
COORDINATES: similar to AA sequence:RefSeq:WP_011665406.1
P-type conjugative transfer protein TrbJ
COORDINATES: similar to AA sequence:RefSeq:WP_008391275.1
COORDINATES: similar to AA sequence:RefSeq:WP_014891343.1
COORDINATES: similar to AA sequence:RefSeq:WP_018272745.1
COORDINATES: similar to AA sequence:RefSeq:WP_014891341.1
COORDINATES: protein motif:HMM:NF025495.2
GO:0004518 - nuclease activity [Evidence IEA]
dsDNA nuclease domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014779765.1
COORDINATES: protein motif:HMM:NF024867.2
COORDINATES: similar to AA sequence:RefSeq:WP_020038284.1
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF016724.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015916661.1
COORDINATES: protein motif:HMM:NF024700.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009734048.1
COORDINATES: similar to AA sequence:RefSeq:WP_011474311.1
COORDINATES: similar to AA sequence:RefSeq:WP_019086915.1
COORDINATES: similar to AA sequence:RefSeq:WP_014891330.1
COORDINATES: similar to AA sequence:RefSeq:WP_014891329.1
COORDINATES: similar to AA sequence:RefSeq:WP_016919718.1
COORDINATES: similar to AA sequence:RefSeq:WP_014891326.1
COORDINATES: similar to AA sequence:RefSeq:WP_014889617.1
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF021581.2
COORDINATES: similar to AA sequence:RefSeq:WP_014891322.1
COORDINATES: similar to AA sequence:RefSeq:WP_008065140.1
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_011473987.1
COORDINATES: similar to AA sequence:RefSeq:WP_012813161.1
GO:0110001 - toxin-antitoxin complex [Evidence IEA]
GO:0004540 - ribonuclease activity [Evidence IEA]
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
type II toxin-antitoxin system YhaV family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_014891314.1
COORDINATES: similar to AA sequence:RefSeq:WP_012047445.1
COORDINATES: similar to AA sequence:RefSeq:WP_014891312.1
COORDINATES: similar to AA sequence:RefSeq:WP_012563595.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611638.1
COORDINATES: similar to AA sequence:RefSeq:WP_017486992.1
COORDINATES: similar to AA sequence:RefSeq:WP_015670171.1
COORDINATES: similar to AA sequence:RefSeq:WP_018308339.1
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_011502641.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015340.1
GO:0004803 - transposase activity [Evidence IEA]
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
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_076612246.1
COORDINATES: similar to AA sequence:RefSeq:WP_032490240.1
frameshifted; 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_015277522.1
COORDINATES: protein motif:HMM:NF013961.2
COORDINATES: similar to AA sequence:RefSeq:WP_011578756.1
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_076611992.1
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_018412437.1
trypsin-like peptidase domain-containing protein
COORDINATES: protein motif:HMM:NF025063.2
GO:0015074 - DNA integration [Evidence IEA]
integrase core domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017927508.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_014891045.1
COORDINATES: similar to AA sequence:RefSeq:WP_018405947.1
COORDINATES: similar to AA sequence:RefSeq:WP_018409220.1
COORDINATES: similar to AA sequence:RefSeq:WP_003615995.1
UDP-N-acetylglucosamine-peptide N-acetylglucosaminyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_017269716.1
GO:0015385 - sodium:proton antiporter activity [Evidence IEA]
GO:1902600 - proton transmembrane transport [Evidence IEA]; GO:0006814 - sodium ion transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014893112.1
COORDINATES: similar to AA sequence:RefSeq:WP_016921308.1
COORDINATES: similar to AA sequence:RefSeq:WP_019488817.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_015179995.1
COORDINATES: similar to AA sequence:RefSeq:WP_006205581.1
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.
COORDINATES: similar to AA sequence:RefSeq:WP_014893040.1
COORDINATES: similar to AA sequence:RefSeq:WP_018409244.1
COORDINATES: similar to AA sequence:RefSeq:WP_014893113.1
COORDINATES: similar to AA sequence:RefSeq:WP_018408069.1
COORDINATES: similar to AA sequence:RefSeq:WP_016921306.1
COORDINATES: similar to AA sequence:RefSeq:WP_020086932.1
COORDINATES: similar to AA sequence:RefSeq:WP_018269030.1
GO:0022627 - cytosolic small ribosomal subunit [Evidence IEA]; GO:0000314 - organellar small ribosomal subunit [Evidence IEA]
GO:0003735 - structural constituent of ribosome [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007283918.1
type II toxin-antitoxin system HigB family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_018272471.1
COORDINATES: protein motif:HMM:NF013540.2
COORDINATES: similar to AA sequence:RefSeq:WP_006611675.1
COORDINATES: protein motif:HMM:NF016362.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0004519 - endonuclease activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010121309.1
COORDINATES: similar to AA sequence:RefSeq:WP_010121307.1
COORDINATES: protein motif:HMM:NF014069.2
COORDINATES: similar to AA sequence:RefSeq:WP_018420431.1
COORDINATES: protein motif:HMM:TIGR03696.1
COORDINATES: similar to AA sequence:RefSeq:WP_018406890.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0008270 - zinc ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009469622.1
Mu transposase C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014857716.1
COORDINATES: similar to AA sequence:RefSeq:WP_019863962.1
COORDINATES: similar to AA sequence:RefSeq:WP_013896421.1
COORDINATES: similar to AA sequence:RefSeq:WP_013896420.1
type II toxin-antitoxin system Phd/YefM family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_012457137.1
COORDINATES: protein motif:HMM:NF024776.2
COORDINATES: similar to AA sequence:RefSeq:WP_015282028.1
COORDINATES: similar to AA sequence:RefSeq:WP_010969960.1
COORDINATES: similar to AA sequence:RefSeq:WP_009489589.1
COORDINATES: protein motif:HMM:NF014567.2
HAMP domain-containing sensor histidine kinase
COORDINATES: similar to AA sequence:RefSeq:WP_011350801.1
COORDINATES: similar to AA sequence:RefSeq:WP_015484714.1
COORDINATES: similar to AA sequence:RefSeq:WP_012592057.1
COORDINATES: similar to AA sequence:RefSeq:WP_016921902.1
COORDINATES: similar to AA sequence:RefSeq:WP_010512303.1
COORDINATES: similar to AA sequence:RefSeq:WP_016920710.1
GO:0000287 - magnesium ion binding [Evidence IEA]; GO:0030976 - thiamine pyrophosphate binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016920711.1
glutathione S-transferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_016920712.1
COORDINATES: similar to AA sequence:RefSeq:WP_016920713.1
GO:0016787 - hydrolase activity [Evidence IEA]
GO:0008152 - metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016920714.1
COORDINATES: similar to AA sequence:RefSeq:WP_016920715.1
COORDINATES: similar to AA sequence:RefSeq:WP_008259794.1
COORDINATES: similar to AA sequence:RefSeq:WP_016920717.1
COORDINATES: similar to AA sequence:RefSeq:WP_016920718.1
COORDINATES: protein motif:HMM:NF033564.0
COORDINATES: similar to AA sequence:RefSeq:WP_076611540.1
COORDINATES: protein motif:HMM:NF019984.2
group II intron maturase-specific domain-containing protein
COORDINATES: protein motif:HMM:NF024811.2
COORDINATES: similar to AA sequence:RefSeq:WP_013845224.1
type II toxin-antitoxin system prevent-host-death family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_003615618.1
COORDINATES: similar to AA sequence:RefSeq:WP_003615620.1
COORDINATES: protein motif:HMM:NF039739.1
COORDINATES: protein motif:HMM:NF024117.2
COORDINATES: protein motif:HMM:NF012789.2
COORDINATES: protein motif:HMM:NF024793.2
COORDINATES: protein motif:HMM:NF038336.1
COORDINATES: similar to AA sequence:RefSeq:WP_012708748.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0003676 - nucleic acid binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012592673.1
COORDINATES: similar to AA sequence:RefSeq:WP_012564811.1