Pelagovum pacificum strain SM1903 plasmid p_SM1903_2, complete sequence.
type: Entry
definition: Pelagovum pacificum strain SM1903 plasmid p_SM1903_2, complete sequence.
sequence version: NZ_CP065917.1
sequence date: 2023-01-01
sequence: sequence
division: CON
label: NZ_CP065917.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN17036614
keyword: RefSeq
source: Pelagovum pacificum
organism: Pelagovum pacificum
taxonomy: Bacteria; Pseudomonadota; Alphaproteobacteria; Rhodobacterales; Paracoccaceae; Pelagovum.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP065917.1.\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 :: ABySS v. 2.2.0; GapCloser v. 1.12\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 910.0x\nSequencing Technology :: Illumina NovaSeq; Oxford Nanopore\n PromethION\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 01/01/2023 03:18:36\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) :: 4,031\nCDSs (total) :: 3,975\nGenes (coding) :: 3,958\nCDSs (with protein) :: 3,958\nGenes (RNA) :: 56\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 46\nncRNAs :: 4\nPseudo Genes (total) :: 17\nCDSs (without protein) :: 17\nPseudo Genes (ambiguous residues) :: 0 of 17\nPseudo Genes (frameshifted) :: 2 of 17\nPseudo Genes (incomplete) :: 16 of 17\nPseudo Genes (internal stop) :: 2 of 17\nPseudo Genes (multiple problems) :: 2 of 17\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 9705
topology: circular
so has quality: SO_0000988
location: 1..9705
location: region:1-9705:1
RO_0002162: 2588711

NZ_CP065917
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN17036614
type: BioSample
SIO_000068: biosample

1
title: The complete genome sequence of Pelagovum pacificum SM1903
author: Ren, X.
journal: Unpublished

2
title: Direct Submission
author: Ren, X.
journal: Submitted (09-DEC-2020) State Key Laboratory of Microbial Technology, Shandong University, Binhai Road No.72, Qingdao 266237, China

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

position:9705:1
position: 9705
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-9705:1:source
so part of: sequence
organism: Pelagovum pacificum
mol type: genomic DNA
strain: SM1903
isolation source: seawater
type material: type strain of Pelagovum pacificum
plasmid: p_SM1903_2
country: Pacific Ocean: Mariana Trench
lat lon: 11.2 N 142.2 E
collection date: 2017-02

2588711
type: Taxonomy
SIO_000068: taxonomy

I8N54_RS20040
type: Gene
subclass of: SO_0000704
RO_0002162: 2588711
gene: mobC
locus tag: I8N54_RS20040
old locus tag: I8N54_20045
so part of: sequence
location: 1..360
location: region:1-360:1
so has part: feature:1-360:1:exon
subclass of: SO_0000010

position:360:1
position: 360
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1-360:1:exon

I8N54_RS20040
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2588711
gene: mobC
locus tag: I8N54_RS20040
old locus tag: I8N54_20045
inference: COORDINATES: protein motif:HMM:NF020265.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: plasmid mobilization relaxosome protein MobC
translation: MARPKKDPTERRTEQVNIRLSPAELSLLQQKADAGGLSLTAFVRAAAERKPVRVAATSDDFELRQELRRIGVNLNQIAKALNTRKEALPASLVRSCEQLEVIFDQMLGHDRQSHSRREL
SIO_010081: I8N54_RS20040
subclass of: SO_0000673
so part of: I8N54_RS20040
location: 1..360
location: region:1-360:1
so has part: feature:1-360:1:exon

WP_140197667.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1-360:1:exon

I8N54_RS20045
type: Gene
subclass of: SO_0000704
RO_0002162: 2588711
locus tag: I8N54_RS20045
old locus tag: I8N54_20050
so part of: sequence
location: 326..1585
location: region:326-1585:1
so has part: feature:326-1585:1:exon
subclass of: SO_0000010

position:326:1
position: 326
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1585:1
position: 1585
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:326-1585:1:exon

I8N54_RS20045
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2588711
locus tag: I8N54_RS20045
old locus tag: I8N54_20050
inference: COORDINATES: protein motif:HMM:NF015397.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: relaxase/mobilization nuclease domain-containing protein
translation: MIVKATQGASFKGVGAYLLHDKGAATSERVAFVETANLPTDDAARAIAHMIDTATHADALKRAAGVKVGKAIDKPVYHYSLAWHPSEAPSMADQVQAARDTLKALGMADRQALIVAHNDTDHPHVHVVVNRVCAETGRAASTGNDRLKLSNWALAYRRQQGMEHLCPARASNDFRRRVGEFVKDASPTRQTYLEWKKAQTAELWEQHRAETAAMKPDRKTQFEALWQQKEARFAARRAEVKELWRPIWRDVFRRQRDELEAYDRRLSVRLRHARRLSGSSIIKTFRAVVNDQVQRADFIKTQEAERKALASRQGQTVRDAGREITKAWRHDRDQLRAAHRAQDTARYEATRGKVDDVWKRQQKDEQAKGEEHVARNPSSVLKDFDRKKDPERVKAIRERTRSKARKRTRKRGDEGRTLD
SIO_010081: I8N54_RS20045
subclass of: SO_0000673
so part of: I8N54_RS20045
location: 326..1585
location: region:326-1585:1
so has part: feature:326-1585:1:exon

WP_140197666.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:326-1585:1:exon

I8N54_RS20055
type: Gene
subclass of: SO_0000704
RO_0002162: 2588711
locus tag: I8N54_RS20055
old locus tag: I8N54_20060
so part of: sequence
location: 1922..2323
location: region:1922-2323:1
so has part: feature:1922-2323:1:exon
subclass of: SO_0000010

position:1922:1
position: 1922
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2323:1
position: 2323
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1922-2323:1:exon

I8N54_RS20055
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2588711
locus tag: I8N54_RS20055
old locus tag: I8N54_20060
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: MSSNDDEMKLHTDTYHAEIKRLRNENAIIEKQIQRWKADKGLKPSDSKFLGAAKTEAEIHKAAKEKADKVIVEQRKLDKAGLTKEQQDKLLRDFDGEKDPARMKAIRERARKKDLERQRTLRSRGGGGRKMDM
SIO_010081: I8N54_RS20055
subclass of: SO_0000673
so part of: I8N54_RS20055
location: 1922..2323
location: region:1922-2323:1
so has part: feature:1922-2323:1:exon

WP_197097715.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1922-2323:1:exon

I8N54_RS20060
type: Gene
subclass of: SO_0000704
RO_0002162: 2588711
locus tag: I8N54_RS20060
old locus tag: I8N54_20065
so part of: sequence
location: 2410..2982
location: region:2410-2982:1
so has part: feature:2410-2982:1:exon
subclass of: SO_0000010

position:2410:1
position: 2410
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2982:1
position: 2982
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2410-2982:1:exon

I8N54_RS20060
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2588711
locus tag: I8N54_RS20060
old locus tag: I8N54_20065
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: super-infection exclusion protein B
translation: MEWFSQAFQFVKSPRLAFVVFVCSAALIFIPFDRLGVDKPIFAENYESQIVIAAIASAAVLSLELVSTIWRIIQWPYQRFRAKQARKKSSEKAFYSLNLNELCVCWAMTQQGVETVLAYYNSPVIVSMRHKGALRAVPGMGSLTELPHAMPEELYNLVKERGLSRFPDDFRNSPRFEDEVRRMYHDAIDW
SIO_010081: I8N54_RS20060
subclass of: SO_0000673
so part of: I8N54_RS20060
location: 2410..2982
location: region:2410-2982:1
so has part: feature:2410-2982:1:exon

WP_140197663.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2410-2982:1:exon

I8N54_RS20065
type: Gene
subclass of: SO_0000704
RO_0002162: 2588711
locus tag: I8N54_RS20065
old locus tag: I8N54_20070
so part of: sequence
location: complement(2991..3788)
location: region:2991-3788:-1
so has part: feature:2991-3788:-1:exon
subclass of: SO_0000010

position:2991:-1
position: 2991
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3788:-1
position: 3788
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2991-3788:-1:exon

I8N54_RS20065
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2588711
locus tag: I8N54_RS20065
old locus tag: I8N54_20070
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: short-chain dehydrogenase
translation: MLEVTTPEEFFFSTPLYTQCDISHIMDSLINLGLDQGNIDGHCVWCGRTVPFKINRIMAPVVSNQYIHERIKGVQVIRLDCQRQTNHKYYYYFIKDGTTGKKIGQLPSLADISLDEIKPYRKDMERIDSQELHKAIGLAAHGSGVGSFVYLRRVFERLIYSHFESNKGEEGWKDDDFYKLRMEEKILQLKSYLPDFLVENRNVYSILSVGIHELDEDTCLGWFDVMRESIFIILEEDRKNREEKKRQKAFSEIIKTFKAPPSTEP
SIO_010081: I8N54_RS20065
subclass of: SO_0000673
so part of: I8N54_RS20065
location: complement(2991..3788)
location: region:2991-3788:-1
so has part: feature:2991-3788:-1:exon

WP_140197662.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2991-3788:-1:exon

I8N54_RS20070
type: Gene
subclass of: SO_0000704
RO_0002162: 2588711
locus tag: I8N54_RS20070
old locus tag: I8N54_20075
so part of: sequence
location: complement(3799..4599)
location: region:3799-4599:-1
so has part: feature:3799-4599:-1:exon
subclass of: SO_0000010

position:3799:-1
position: 3799
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4599:-1
position: 4599
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3799-4599:-1:exon

I8N54_RS20070
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2588711
locus tag: I8N54_RS20070
old locus tag: I8N54_20075
inference: COORDINATES: protein motif:HMM:NF013235.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: replication initiation protein
translation: MLTVLWGVAHEIDRLRLPPNYPDAKWLEIPTRLLRNPEGRSDNVWLKSCLRRLMGVELEGGNKDTEWGAVVLAQWEMTEGGSKVRLLIPPAAIAAIRAPKTFAKIEITAAYRLKGHARRLYAALADKKRMGQTWWEYTLPELQTLFDLRGKYSKWYDFSRYVLTPAIAEINDFGTVEVTAMPVKFGRSIGSVRFDWRWKDIRAAEVTDEQNERHGSARHKDQGDGSAPPLTEEAKATERQSAFLEWSKENKGQPYSDFIYWYDSKH
SIO_010081: I8N54_RS20070
subclass of: SO_0000673
so part of: I8N54_RS20070
location: complement(3799..4599)
location: region:3799-4599:-1
so has part: feature:3799-4599:-1:exon

WP_198571767.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3799-4599:-1:exon

I8N54_RS20075
type: Gene
subclass of: SO_0000704
RO_0002162: 2588711
locus tag: I8N54_RS20075
old locus tag: I8N54_20080
so part of: sequence
location: 5353..5646
location: region:5353-5646:1
so has part: feature:5353-5646:1:exon
subclass of: SO_0000010

position:5353:1
position: 5353
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:5646:1
position: 5646
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5353-5646:1:exon

I8N54_RS20075
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2588711
locus tag: I8N54_RS20075
old locus tag: I8N54_20080
inference: COORDINATES: similar to AA sequence:RefSeq:WP_011663209.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: BrnT family toxin
translation: MVFEGFDWDDGNWPKCGKHGMTRAEIEEVFLNTPAIKPHPNHSQVEERMKAIGKTDEGRAAYVSFTLRPSRAGGALIRPVSARYMHRKEVKKYEQDN
SIO_010081: I8N54_RS20075
subclass of: SO_0000673
so part of: I8N54_RS20075
location: 5353..5646
location: region:5353-5646:1
so has part: feature:5353-5646:1:exon

WP_140197668.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5353-5646:1:exon

I8N54_RS20080
type: Gene
subclass of: SO_0000704
RO_0002162: 2588711
locus tag: I8N54_RS20080
old locus tag: I8N54_20085
so part of: sequence
location: 5630..5914
location: region:5630-5914:1
so has part: feature:5630-5914:1:exon
subclass of: SO_0000010

position:5630:1
position: 5630
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:5914:1
position: 5914
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5630-5914:1:exon

I8N54_RS20080
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2588711
locus tag: I8N54_RS20080
old locus tag: I8N54_20085
inference: COORDINATES: similar to AA sequence:RefSeq:WP_006746533.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: CopG family antitoxin
translation: MSKTTKTDKPLPVHTTDEAAQAFTDEADLSEYDLSGFQPVTFTLGKKDARLEMRISQTELETLKAEAKRRGIPHSRLARAFIEQGLRALPLSPR
SIO_010081: I8N54_RS20080
subclass of: SO_0000673
so part of: I8N54_RS20080
location: 5630..5914
location: region:5630-5914:1
so has part: feature:5630-5914:1:exon

WP_140197660.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5630-5914:1:exon

I8N54_RS20090
type: Gene
subclass of: SO_0000704
RO_0002162: 2588711
locus tag: I8N54_RS20090
old locus tag: I8N54_20095
so part of: sequence
location: complement(7181..8005)
location: region:7181-8005:-1
so has part: feature:7181-8005:-1:exon
subclass of: SO_0000010

position:7181:-1
position: 7181
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:8005:-1
position: 8005
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:7181-8005:-1:exon

I8N54_RS20090
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2588711
locus tag: I8N54_RS20090
old locus tag: I8N54_20095
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: MLVEYPRDKLTLDLESDNPKVTYEVTSYLLTLETTPYHSSVDTTQIFVENEIVRDFTLSLREGKLGEHSVYDLGTFEIVNAHQWDGRQPNALVGKGPSRTRILEEPPLFHIAAVNVATGERVVAVRTHCEKDQVFTVMNRLNAMLDYTRRVCAPWQDLIQNDELIPVDEIRDALQDMPPRFKFSPLPERELSEKAATLVRKYVRSHVITTEINKAAAAQEAKTAAMATTRNEKERAKEEARQQSVERIAESGPRWRPAIIVVVLFGVFLILLNL
SIO_010081: I8N54_RS20090
subclass of: SO_0000673
so part of: I8N54_RS20090
location: complement(7181..8005)
location: region:7181-8005:-1
so has part: feature:7181-8005:-1:exon

WP_140197658.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:7181-8005:-1:exon

I8N54_RS20095
type: Gene
subclass of: SO_0000704
RO_0002162: 2588711
locus tag: I8N54_RS20095
old locus tag: I8N54_20100
so part of: sequence
location: complement(8009..9475)
location: region:8009-9475:-1
so has part: feature:8009-9475:-1:exon
subclass of: SO_0000010

position:8009:-1
position: 8009
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:9475:-1
position: 9475
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:8009-9475:-1:exon

I8N54_RS20095
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2588711
locus tag: I8N54_RS20095
old locus tag: I8N54_20100
inference: COORDINATES: protein motif:HMM:NF014581.2
GO component: GO:0016020 - membrane [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: type IV secretory system conjugative DNA transfer family protein
translation: MSPEKPLELPRGHRRARQEKPPAAEWMTDANIAQLLPYEEGAILLGKHAGQLVGVTDDRHLLTVAGSRAGKSSTCLKPNLKRWPSSVLCIDPKGELAMETADARAAMGQAVYILDPFEEVKGPAAQYRVGFNPLAEIREGDPRDIVDNASIVADALILPSKGDNSDHWSLSAKNLLRGLILYMLAKNADAASLTLLRKLVNSPLRAPDDADADAPMSLSERFTEMVEDYPDDFGGVVAGVGGTMDGKPPNELGSIVSTAVEQTAFLDGDPMTEHLGSIGLPSMPSLRQLKRTPTTIYLVLPASRMATHFRWLRVVLTLALAALEREPMALPAPRKDTAPSVLFVLEEFPQLGYMRQIEAAAGLMAGYGVKLWTVLQDLSQLRTLYRDSWETFIGNAGVVQAFGNTDATTLEYISRTLGTRQITETQDNRPTPSAMTSGARVSSETRNTVPLLAPFEIALYGGRDTGRQFVMMAGKPPAYIERLLHTEV
SIO_010081: I8N54_RS20095
subclass of: SO_0000673
so part of: I8N54_RS20095
location: complement(8009..9475)
location: region:8009-9475:-1
so has part: feature:8009-9475:-1:exon

WP_140197657.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:8009-9475:-1:exon