Paracoccus methylovorus strain H4-D09 plasmid p3, complete sequence.
type: Entry
definition: Paracoccus methylovorus strain H4-D09 plasmid p3, complete sequence.
sequence version: NZ_CP070370.1
sequence date: 2022-11-21
sequence: sequence
division: CON
label: NZ_CP070370.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN17922161
keyword: RefSeq
source: Paracoccus methylovorus
organism: Paracoccus methylovorus
taxonomy: Bacteria; Pseudomonadota; Alphaproteobacteria; Rhodobacterales; Paracoccaceae; Paracoccus.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP070370.1.\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/\n\n##Genome-Assembly-Data-START##\nAssembly Method :: HGAP v. 4\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 369.0x\nSequencing Technology :: PacBio Sequel\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 11/21/2022 10:33:19\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.3\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 4,346\nCDSs (total) :: 4,282\nGenes (coding) :: 4,169\nCDSs (with protein) :: 4,169\nGenes (RNA) :: 64\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 52\nncRNAs :: 3\nPseudo Genes (total) :: 113\nCDSs (without protein) :: 113\nPseudo Genes (ambiguous residues) :: 0 of 113\nPseudo Genes (frameshifted) :: 40 of 113\nPseudo Genes (incomplete) :: 93 of 113\nPseudo Genes (internal stop) :: 10 of 113\nPseudo Genes (multiple problems) :: 26 of 113\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 4983
topology: circular
so has quality: SO_0000988
location: 1..4983
location: region:1-4983:1
RO_0002162: 2812658

NZ_CP070370
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN17922161
type: BioSample
SIO_000068: biosample

1
title: Paracoccus methylovroum sp.nov., a new methanol and methylamine utilizing methylotrophic denitrifer
author: Timsy, T.
author: Behrendt, U.
author: Ulrich, A.
author: Spanner, T.
author: Foesel, B.U.
author: Horn, M.A.
author: Kolb, S.
journal: Unpublished

2
title: Direct Submission
author: Ulrich, A.
author: Foesel, B.
journal: Submitted (16-FEB-2021) Research Area Landscape Functioning, WG Microbial Biogeochemistry, Leibniz Centre for Agricultural Landscape Research (ZALF), Eberswalder Str. 84, Muencheberg D-15374, Germany

position:1:1
position: 1
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:4983:1
position: 4983
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-4983:1:source
so part of: sequence
organism: Paracoccus methylovorus
mol type: genomic DNA
strain: H4-D09
isolation source: grassland soil
culture collection: LMG:31941
type material: type strain of Paracoccus methylovorus
plasmid: p3
country: Germany: exploratory Hainich
collection date: 2017-05

2812658
type: Taxonomy
SIO_000068: taxonomy

JWJ88_RS21795
type: Gene
subclass of: SO_0000704
RO_0002162: 2812658
locus tag: JWJ88_RS21795
so part of: sequence
location: complement(join(4148..4983,1..406))
location: region:1-4983:-1
so has part: feature:1-406:-1:exon
so has part: feature:4148-4983:-1:exon
subclass of: SO_0000010

position:1:-1
position: 1
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4983:-1
position: 4983
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1-406:-1:exon

position:406:-1
position: 406
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 2
SIO_000628: feature:4148-4983:-1:exon

position:4148:-1
position: 4148
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

JWJ88_RS21795
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2812658
locus tag: JWJ88_RS21795
inference: COORDINATES: ab initio prediction:GeneMarkS-2+
note: Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
codon start: 1
transl table: 11
product: MobQ family relaxase
translation: MAIYHLRATMISRSAGRSATAAAAYRVGERIEDHRTGLTFDYRARGGVDHVETLAPANAPAWVQDRSALWNAVEAAETRKNSQVAREIRVALPAELDHGQRVELVREFCQREFVARGMVADIALHAPGREGDDRNHHAHILLTTREIGPEGFGAKNRDWNAVEVLEGWREAWARDSNRALERCGHDERIDHRTLEAQRIEAQERATAAHDRGDEAEALRQTVRAVELDRDPLPQLSAGAWQMKERGIEVAAVRVWREVKAQAVEVARVAEVLAGQVRDWIGRAVDRLGPPAQGLAYAGAADRDGREGRQDLAARLREAWEARQSRTASDTVAAPGQTPEPESARSLAERLREAAQGIDRGTLAEAAARLQESREAEERQRVQEAERLKEQERQQELLREREARDHDRDGGLTH
SIO_010081: JWJ88_RS21795
subclass of: SO_0000673
so part of: JWJ88_RS21795
location: complement(join(4148..4983,1..406))
location: region:1-4983:-1
so has part: feature:1-406:-1:exon
so has part: feature:4148-4983:-1:exon

WP_240200266.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1-406:-1:exon

urn:…
SIO_000300: 2
SIO_000628: feature:4148-4983:-1:exon

JWJ88_RS13075
type: Gene
subclass of: SO_0000704
RO_0002162: 2812658
locus tag: JWJ88_RS13075
old locus tag: JWJ88_13075
so part of: sequence
location: 560..826
location: region:560-826:1
so has part: feature:560-826:1:exon
subclass of: SO_0000010

position:560:1
position: 560
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:826:1
position: 826
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:560-826:1:exon

JWJ88_RS13075
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2812658
locus tag: JWJ88_RS13075
old locus tag: JWJ88_13075
inference: COORDINATES: similar to AA sequence:RefSeq:WP_009824546.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MARTIDQQIADAQAKLARLKTRQKASDTRRKIIVGAIVTTEALKDPKISKWLASTLRKNATRDVDQKEIAGLLADLDARAQSAGAGEA
SIO_010081: JWJ88_RS13075
subclass of: SO_0000673
so part of: JWJ88_RS13075
location: 560..826
location: region:560-826:1
so has part: feature:560-826:1:exon

WP_085787614.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:560-826:1:exon

JWJ88_RS13080
type: Gene
subclass of: SO_0000704
RO_0002162: 2812658
locus tag: JWJ88_RS13080
old locus tag: JWJ88_13080
so part of: sequence
location: 823..1389
location: region:823-1389:1
so has part: feature:823-1389:1:exon
subclass of: SO_0000010

position:823:1
position: 823
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1389:1
position: 1389
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:823-1389:1:exon

JWJ88_RS13080
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2812658
locus tag: JWJ88_RS13080
old locus tag: JWJ88_13080
inference: COORDINATES: ab initio prediction:GeneMarkS-2+
note: Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MSGNTDPFLVLVDDIGALRRQIENLQRTSLDRDEAEHLNATIAQSLDNMAQTGKRLEQRLEGQLQLATAKTNLAAIEAAQDAARAAIRESHAEILQTAKSLSQAAGEARREAWRWFGGFWVWLASIGAAGALIGALAVFWLQGRADAKAFGQYPSIYCRTAGGEFADQRDGSRYCIFMVSPPTQPAGE
SIO_010081: JWJ88_RS13080
subclass of: SO_0000673
so part of: JWJ88_RS13080
location: 823..1389
location: region:823-1389:1
so has part: feature:823-1389:1:exon

WP_205295612.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:823-1389:1:exon

JWJ88_RS13085
type: Gene
subclass of: SO_0000704
RO_0002162: 2812658
locus tag: JWJ88_RS13085
old locus tag: JWJ88_13085
so part of: sequence
location: complement(1394..1690)
location: region:1394-1690:-1
so has part: feature:1394-1690:-1:exon
subclass of: SO_0000010

position:1394:-1
position: 1394
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:1690:-1
position: 1690
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1394-1690:-1:exon

JWJ88_RS13085
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2812658
locus tag: JWJ88_RS13085
old locus tag: JWJ88_13085
inference: COORDINATES: similar to AA sequence:RefSeq:WP_014129874.1
GO function: GO:0003677 - DNA binding [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: putative addiction module antidote protein
translation: MPEEKFARYDSADYLKTEEDIAAYLEAVMEDGGDDPAYVARALGVVARARNMTALAREVGMSRVGLNKALSGDGNPTLSTVMKVAKALGLKVSIQPGA
SIO_010081: JWJ88_RS13085
subclass of: SO_0000673
so part of: JWJ88_RS13085
location: complement(1394..1690)
location: region:1394-1690:-1
so has part: feature:1394-1690:-1:exon

WP_085787616.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1394-1690:-1:exon

JWJ88_RS13090
type: Gene
subclass of: SO_0000704
RO_0002162: 2812658
locus tag: JWJ88_RS13090
old locus tag: JWJ88_13090
so part of: sequence
location: complement(1694..1990)
location: region:1694-1990:-1
so has part: feature:1694-1990:-1:exon
subclass of: SO_0000010

position:1694:-1
position: 1694
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:1990:-1
position: 1990
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1694-1990:-1:exon

JWJ88_RS13090
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2812658
locus tag: JWJ88_RS13090
old locus tag: JWJ88_13090
inference: COORDINATES: similar to AA sequence:RefSeq:WP_002813764.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: type II toxin-antitoxin system RelE/ParE family toxin
translation: MIELIRSGTFDTWLSGLRDRRAVARIAARLDRLAAGNPGDVEPVGEGVSELRINYGPGYRVYFIQRGPVLVILLCGGDKSTQSKDIKQAKVLAAEWKG
SIO_010081: JWJ88_RS13090
subclass of: SO_0000673
so part of: JWJ88_RS13090
location: complement(1694..1990)
location: region:1694-1990:-1
so has part: feature:1694-1990:-1:exon

WP_112313498.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1694-1990:-1:exon

JWJ88_RS13095
type: Gene
subclass of: SO_0000704
RO_0002162: 2812658
locus tag: JWJ88_RS13095
old locus tag: JWJ88_13095
so part of: sequence
location: 2539..3111
location: region:2539-3111:1
so has part: feature:2539-3111:1:exon
subclass of: SO_0000010

position:2539:1
position: 2539
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:3111:1
position: 3111
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2539-3111:1:exon

JWJ88_RS13095
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2812658
locus tag: JWJ88_RS13095
old locus tag: JWJ88_13095
inference: COORDINATES: similar to AA sequence:RefSeq:WP_004213409.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: helix-turn-helix domain-containing protein
translation: MAKPPPIPAKRPLGTWVQTDREAHEAWAILAKKPAASAVMHILCANLGEHNAVVISQDTIAKLCGLSTRSVRRAIVDLAEGRWIEVRQLGATSQTNAYVVNDRVAWQGSRDGLRYSLFSAAVVVSEEEQPDRAELDQQAPLRHLPRISEGQIPGGPGLPPPSQPFLKDMEPDLPTIDRAISPKFDQQEQG
SIO_010081: JWJ88_RS13095
subclass of: SO_0000673
so part of: JWJ88_RS13095
location: 2539..3111
location: region:2539-3111:1
so has part: feature:2539-3111:1:exon

WP_240200264.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2539-3111:1:exon

JWJ88_RS13100
type: Gene
subclass of: SO_0000704
RO_0002162: 2812658
locus tag: JWJ88_RS13100
old locus tag: JWJ88_13100
so part of: sequence
location: 3108..3506
location: region:3108-3506:1
so has part: feature:3108-3506:1:exon
subclass of: SO_0000010

position:3108:1
position: 3108
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:3506:1
position: 3506
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3108-3506:1:exon

JWJ88_RS13100
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2812658
locus tag: JWJ88_RS13100
old locus tag: JWJ88_13100
inference: COORDINATES: ab initio prediction:GeneMarkS-2+
GO function: GO:0003677 - DNA binding [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
codon start: 1
transl table: 11
product: helix-turn-helix domain-containing protein
translation: MKKVDKLSIREAVKHFDVSRPTLQKALKSGKISGVQDGQGTWTIDPSEMARIYQPRQVEVVKDDGKEHGNLSTKNTPLHGQVEALKERLADAEKRVAIAEALAEERGKHIEDLRRMLPAPEASQSRRRWWPF
SIO_010081: JWJ88_RS13100
subclass of: SO_0000673
so part of: JWJ88_RS13100
location: 3108..3506
location: region:3108-3506:1
so has part: feature:3108-3506:1:exon

WP_205295610.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3108-3506:1:exon

JWJ88_RS13105
type: Gene
subclass of: SO_0000704
RO_0002162: 2812658
locus tag: JWJ88_RS13105
old locus tag: JWJ88_13105
so part of: sequence
location: complement(3528..4028)
location: region:3528-4028:-1
so has part: feature:3528-4028:-1:exon
subclass of: SO_0000010

position:3528:-1
position: 3528
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4028:-1
position: 4028
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3528-4028:-1:exon

JWJ88_RS13105
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2812658
locus tag: JWJ88_RS13105
old locus tag: JWJ88_13105
inference: COORDINATES: similar to AA sequence:RefSeq:WP_015932721.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: GNAT family N-acetyltransferase
translation: MCVRVATTKDMQEIAALIGRSYSILMQSAYAQDVLARALPAMTRANPDLVASGTFYVAEDAGSLVGCGGWTFAPPGGGTIIDGLVHARHFAVEPERSGTGIGRAIFERVSNDACAAGAVRIQALSSLNAEPFYKRMGLDRLDLIPVAMGAGVEFPVVLMEGPLFLS
SIO_010081: JWJ88_RS13105
subclass of: SO_0000673
so part of: JWJ88_RS13105
location: complement(3528..4028)
location: region:3528-4028:-1
so has part: feature:3528-4028:-1:exon

WP_240200265.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3528-4028:-1:exon