Roseovarius indicus strain DSM 26383 plasmid pRIdsm_04, complete sequence.
type: Entry
definition: Roseovarius indicus strain DSM 26383 plasmid pRIdsm_04, complete sequence.
sequence version: NZ_CP031602.1
sequence date: 2023-03-25
sequence: sequence
division: CON
label: NZ_CP031602.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN09772271
keyword: RefSeq
source: Roseovarius indicus
organism: Roseovarius indicus
taxonomy: Bacteria; Pseudomonadota; Alphaproteobacteria; Rhodobacterales; Roseobacteraceae; Roseovarius.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP031602.1.\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 Date :: FEB-2018\nAssembly Method :: HGAP v. 3\nAssembly Name :: DSMZ_RIdsm\nExpected Final Version :: yes\nGenome Coverage :: 100.0x\nSequencing Technology :: PacBio RS; Illumina\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/25/2023 02:27:30\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) :: 6,061\nCDSs (total) :: 6,008\nGenes (coding) :: 5,922\nCDSs (with protein) :: 5,922\nGenes (RNA) :: 53\nrRNAs :: 1, 1, 1 (5S, 16S, 23S)\ncomplete rRNAs :: 1, 1, 1 (5S, 16S, 23S)\ntRNAs :: 47\nncRNAs :: 3\nPseudo Genes (total) :: 86\nCDSs (without protein) :: 86\nPseudo Genes (ambiguous residues) :: 0 of 86\nPseudo Genes (frameshifted) :: 25 of 86\nPseudo Genes (incomplete) :: 60 of 86\nPseudo Genes (internal stop) :: 16 of 86\nPseudo Genes (multiple problems) :: 15 of 86\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 7053
topology: circular
so has quality: SO_0000988
location: 1..7053
location: region:1-7053:1
RO_0002162: 540747

NZ_CP031602
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN09772271
type: BioSample
SIO_000068: biosample

1
title: Genetic Globetrotter - A new plasmid hitch-hiking vast phylogenetic and geographic distances
author: Vollmers, J.
author: Petersen, J.
journal: Unpublished

2
title: Direct Submission
author: Petersen, J.
journal: Submitted (12-AUG-2018) Single Cell Genomics, Leibniz Institute DSMZ, Inhoffenstr. 8, Brunswick 38126, Germany

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

position:7053:1
position: 7053
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-7053:1:source
so part of: sequence
organism: Roseovarius indicus
mol type: genomic DNA
strain: DSM 26383
culture collection: DSMZ:26383
type material: type strain of Roseovarius indicus
plasmid: pRIdsm_04
country: Indian Ocean:South-west Indian Ridge
collection date: 2005-12
collected by: Qiliang Lai, Third Inst. Oceanography, State Oceanic Administration, Xiamen, China

540747
type: Taxonomy
SIO_000068: taxonomy

RIdsm_RS29930
type: Gene
subclass of: SO_0000704
RO_0002162: 540747
locus tag: RIdsm_RS29930
old locus tag: RIdsm_06008
so part of: sequence
location: 28..570
location: region:28-570:1
so has part: feature:28-570:1:exon
subclass of: SO_0000010

position:28:1
position: 28
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:570:1
position: 570
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:28-570:1:exon

RIdsm_RS29930
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 540747
locus tag: RIdsm_RS29930
old locus tag: RIdsm_06008
inference: COORDINATES: similar to AA sequence:RefSeq:WP_006115964.1
GO process: GO:0006260 - DNA replication [Evidence IEA]; GO:0006276 - plasmid maintenance [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: replication/maintenance protein RepL
translation: MLPAKKQRGHFVQTDRAAHEAWGRLAVKSPAAGALLHVLVANVGEQNAIVASHKVLAKLMGSSPATVKRAIKILESGNWVEVVQIGASGTVNAYVLNSRVAWTEGRDKLRYSRLQAEVLVSEDEQPAGALDAAKEELHRLPRVGELQLPAGQGLPPVSQPSFPGLEPSLPAFGHPTEDSE
SIO_010081: RIdsm_RS29930
subclass of: SO_0000673
so part of: RIdsm_RS29930
location: 28..570
location: region:28-570:1
so has part: feature:28-570:1:exon

WP_111772960.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:28-570:1:exon

RIdsm_RS29935
type: Gene
subclass of: SO_0000704
RO_0002162: 540747
locus tag: RIdsm_RS29935
old locus tag: RIdsm_06009
so part of: sequence
location: 582..977
location: region:582-977:1
so has part: feature:582-977:1:exon
subclass of: SO_0000010

position:582:1
position: 582
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:977:1
position: 977
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:582-977:1:exon

RIdsm_RS29935
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 540747
locus tag: RIdsm_RS29935
old locus tag: RIdsm_06009
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: MANVSIREAVKIYQVSRPTLTKALKTGKVSGVQDGKGQWQIDPAELARVYQPRTESAKTGGQDEPDNFTNKNTHLPGEVNTLKAQLAEAEQRAAVAEALAEERGKHIEDLRRMLPAPQEAQRPGWRWPWKR
SIO_010081: RIdsm_RS29935
subclass of: SO_0000673
so part of: RIdsm_RS29935
location: 582..977
location: region:582-977:1
so has part: feature:582-977:1:exon

WP_050686563.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:582-977:1:exon

RIdsm_RS29940
type: Gene
subclass of: SO_0000704
RO_0002162: 540747
locus tag: RIdsm_RS29940
old locus tag: RIdsm_06010
so part of: sequence
location: 987..1370
location: region:987-1370:1
so has part: feature:987-1370:1:exon
subclass of: SO_0000010

position:987:1
position: 987
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1370:1
position: 1370
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:987-1370:1:exon

RIdsm_RS29940
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 540747
locus tag: RIdsm_RS29940
old locus tag: RIdsm_06010
inference: COORDINATES: similar to AA sequence:RefSeq:WP_013833376.1
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: type II toxin-antitoxin system PemK/MazF family toxin
translation: MAEETPPPRVAPTVKSAPRIRQVYWCKLPDDAQLPEFWKTRPVLIMSLKTTLHGKVTVLPFSTKSQPDNPHAYPMQSPLQAKQAWVICDHLMTVAVSRLSPPGRVIPRISEADFEHIKERALKNLPY
SIO_010081: RIdsm_RS29940
subclass of: SO_0000673
so part of: RIdsm_RS29940
location: 987..1370
location: region:987-1370:1
so has part: feature:987-1370:1:exon

WP_050686564.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:987-1370:1:exon

RIdsm_RS29945
type: Gene
subclass of: SO_0000704
RO_0002162: 540747
locus tag: RIdsm_RS29945
old locus tag: RIdsm_06011
so part of: sequence
location: 1823..2641
location: region:1823-2641:1
so has part: feature:1823-2641:1:exon
subclass of: SO_0000010

position:1823:1
position: 1823
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2641:1
position: 2641
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1823-2641:1:exon

RIdsm_RS29945
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 540747
locus tag: RIdsm_RS29945
old locus tag: RIdsm_06011
inference: COORDINATES: similar to AA sequence:RefSeq:WP_009175426.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: sulfurtransferase/chromate resistance protein
translation: MASYNEIPVSALARLIGTPYCPTLLDVRIDEDFDDDPRLIPGAYRHPFNSVVDLAETLKDRSVVVYCQKGLKISQGAAALLRASGVNAEVLEGGQFAWRDAKLPLVITDKLPPLDALGRTVWVTRHRPKIDRIACPWLIRRFIDPKAQILFVAASQVGNVAERFNATPFDIEDVFWSHRGETCTFDTMIEEFGIGHEALERLAVIVRGADTNRHDLAPEAAGLLAASLGLSRMFRDDLEQLDAGMLLYDAFYRWARDATSEGHDWPAASTKA
SIO_010081: RIdsm_RS29945
subclass of: SO_0000673
so part of: RIdsm_RS29945
location: 1823..2641
location: region:1823-2641:1
so has part: feature:1823-2641:1:exon

WP_043872397.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1823-2641:1:exon

RIdsm_RS29950
type: Gene
subclass of: SO_0000704
RO_0002162: 540747
gene: chrA
locus tag: RIdsm_RS29950
old locus tag: RIdsm_06012
so part of: sequence
location: 2645..3937
location: region:2645-3937:1
so has part: feature:2645-3937:1:exon
subclass of: SO_0000010

position:2645:1
position: 2645
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:3937:1
position: 3937
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2645-3937:1:exon

RIdsm_RS29950
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 540747
gene: chrA
locus tag: RIdsm_RS29950
old locus tag: RIdsm_06012
inference: COORDINATES: similar to AA sequence:RefSeq:WP_009175531.1
GO function: GO:0015109 - chromate transmembrane transporter activity [Evidence IEA]
GO process: GO:0015703 - chromate transport [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: chromate efflux transporter
translation: MSSMNDVQTDLAPSLSDATRVWWKIGILSFGGPAAQIALMHKEVVEDRSWLSEQQFLNALSLCMLLPGPEAMQLATYAGWRLHGTIGGLIAGLLFVVPGAAVIMALAAIYSIYGNVPLVEALFYGIKAAVLVIVVEALLRVAKKALSQKVHWVIAALAFVGIFFLSIPYPLIVLMAGLFGWFMGTADMDRQTVDMAHVSVGKTGLTIATWMAIWLLPLLALGWLGAPDLLVEVGRFFSTLAVVTFGGAYAVLAYMAQDVVVQFGWLTAGEMVDALGLAETTPGPLILVTQFVGFLAGFKEGGLLLGLSAAVVALWVTFAPCFLWIFAGAPYIEWISNQPRLKGALKAITAAVVGVILNLSLWFALHVLFTNVSRETLGPVTLWRPDLATIEWLAVALFLLSCFLAFRLHWGIIRILLVAALLGAALRLFL
SIO_010081: RIdsm_RS29950
subclass of: SO_0000673
so part of: RIdsm_RS29950
location: 2645..3937
location: region:2645-3937:1
so has part: feature:2645-3937:1:exon

WP_043872398.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2645-3937:1:exon

RIdsm_RS30445
type: Gene
subclass of: SO_0000704
RO_0002162: 540747
locus tag: RIdsm_RS30445
old locus tag: RIdsm_06013
so part of: sequence
location: 3987..4271
location: region:3987-4271:1
so has part: feature:3987-4271:1:exon
subclass of: SO_0000010

position:3987:1
position: 3987
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:4271:1
position: 4271
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3987-4271:1:exon

RIdsm_RS30445
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 540747
locus tag: RIdsm_RS30445
old locus tag: RIdsm_06013
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: MTDTPKPAHGPTQEHFVRGLPFKAHKIEGFTPELLEHYYEDTYGGSIRTLNEVETKIAASRRAGSPTADLGSLIAKQANPPMGPKAKRTCINSW
SIO_010081: RIdsm_RS30445
subclass of: SO_0000673
so part of: RIdsm_RS30445
location: 3987..4271
location: region:3987-4271:1
so has part: feature:3987-4271:1:exon

WP_043872399.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3987-4271:1:exon

RIdsm_RS29960
type: Gene
subclass of: SO_0000704
RO_0002162: 540747
gene: mobQ
locus tag: RIdsm_RS29960
old locus tag: RIdsm_06014
so part of: sequence
location: complement(4322..5554)
location: region:4322-5554:-1
so has part: feature:4322-5554:-1:exon
subclass of: SO_0000010

position:4322:-1
position: 4322
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:5554:-1
position: 5554
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4322-5554:-1:exon

RIdsm_RS29960
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 540747
gene: mobQ
locus tag: RIdsm_RS29960
old locus tag: RIdsm_06014
inference: COORDINATES: protein motif:HMM:NF041496.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: MobQ family relaxase
translation: MAIYHLRASMISRSQGRSATAAIAYRVAERIEDRRTGLTFDYAARGGVDHTEILAPDHAPDWGRDRSELWNRVEEAETRKNSQVAREVRVALPAELTHAQRVELVRDFAQEQFVDRGMIADIALHAPGRDGDDRNHHAHILLTTREIGPEGFTTKNRDWNKVEVLEGWREAWARDSNIALKRAGIEDRVDHRTLEAQRDEALELASAARERGDEGAELVQTVRAIELDRPPLPQLSPGAWQMKERGIEVGRVGAWHEAKARAAEVMEVARELAGHVRDWLDRAADRVLDRLGPEQSELALAGGREGREQEPDLATRLREAWEGRKEGREQHEADASEREVPDDLAARLRAAATGIDREAFGDRVSALREGREAEEQHTAQEQERQRTKELEQEQEREVHARRDRGHDYGL
SIO_010081: RIdsm_RS29960
subclass of: SO_0000673
so part of: RIdsm_RS29960
location: complement(4322..5554)
location: region:4322-5554:-1
so has part: feature:4322-5554:-1:exon

WP_082033416.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4322-5554:-1:exon

RIdsm_RS29965
type: Gene
subclass of: SO_0000704
RO_0002162: 540747
locus tag: RIdsm_RS29965
old locus tag: RIdsm_06015
so part of: sequence
location: 5708..5968
location: region:5708-5968:1
so has part: feature:5708-5968:1:exon
subclass of: SO_0000010

position:5708:1
position: 5708
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:5968:1
position: 5968
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5708-5968:1:exon

RIdsm_RS29965
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 540747
locus tag: RIdsm_RS29965
old locus tag: RIdsm_06015
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: MARSIDQQIAATQAKLARLKERQKASETRRKIIVGSVAISNALKDPEKARALAALLRRAVTREVDQKELVGLLEELDGVAAKAERP
SIO_010081: RIdsm_RS29965
subclass of: SO_0000673
so part of: RIdsm_RS29965
location: 5708..5968
location: region:5708-5968:1
so has part: feature:5708-5968:1:exon

WP_043872400.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5708-5968:1:exon

RIdsm_RS29970
type: Gene
subclass of: SO_0000704
RO_0002162: 540747
locus tag: RIdsm_RS29970
old locus tag: RIdsm_06016
so part of: sequence
location: 5965..6531
location: region:5965-6531:1
so has part: feature:5965-6531:1:exon
subclass of: SO_0000010

position:5965:1
position: 5965
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:6531:1
position: 6531
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5965-6531:1:exon

RIdsm_RS29970
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 540747
locus tag: RIdsm_RS29970
old locus tag: RIdsm_06016
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: MSVKDPFQQLVDEITLIRQDMERLKRTSLDKEDAEALHEMLAEGVDRMCKVGPEVQKAVEMRLLGVAAVLREETAKAAASAAEGAIAKTRTESLEAARSLSQAAGEARRQAWRYFGGFWVWLASMLATGAVLGLLLAYGMETAKSALSVDDLVRYNCGRSWFGGQVVDQDNGSSFCAFWIRQVPQGEN
SIO_010081: RIdsm_RS29970
subclass of: SO_0000673
so part of: RIdsm_RS29970
location: 5965..6531
location: region:5965-6531:1
so has part: feature:5965-6531:1:exon

WP_043872401.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5965-6531:1:exon