Solidesulfovibrio carbinolicus strain DSM 3852 plasmid pDCAR3, complete sequence.
type: Entry
definition: Solidesulfovibrio carbinolicus strain DSM 3852 plasmid pDCAR3, complete sequence.
sequence version: NZ_CP026541.1
sequence date: 2022-12-16
sequence: sequence
division: CON
label: NZ_CP026541.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN08449371
keyword: RefSeq
source: Solidesulfovibrio carbinolicus
organism: Solidesulfovibrio carbinolicus
taxonomy: Bacteria; Proteobacteria; Deltaproteobacteria; Desulfovibrionales; Desulfovibrionaceae; Solidesulfovibrio.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP026541.1.\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 :: MAR-2015\nAssembly Method :: HGAP v. v3\nAssembly Name :: DvCab\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 200.0x\nSequencing Technology :: PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/14/2022 17:50:02\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) :: 4,215\nCDSs (total) :: 4,143\nGenes (coding) :: 4,108\nCDSs (with protein) :: 4,108\nGenes (RNA) :: 72\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 54\nncRNAs :: 9\nPseudo Genes (total) :: 35\nCDSs (without protein) :: 35\nPseudo Genes (ambiguous residues) :: 0 of 35\nPseudo Genes (frameshifted) :: 6 of 35\nPseudo Genes (incomplete) :: 31 of 35\nPseudo Genes (internal stop) :: 2 of 35\nPseudo Genes (multiple problems) :: 4 of 35\nCRISPR Arrays :: 2\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 8394
topology: circular
so has quality: SO_0000988
location: 1..8394
location: region:1-8394:1
RO_0002162: 296842

NZ_CP026541
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN08449371
type: BioSample
SIO_000068: biosample

1
title: Genome sequence of Desulfovibrio carbinolicus DSM 3852
author: Wilbanks, E.
author: Skennerton, C.T.
author: Orphan, V.J.
journal: Unpublished

2
title: Direct Submission
author: Wilbanks, E.
author: Skennerton, C.T.
author: Orphan, V.J.
journal: Submitted (01-FEB-2018) Division of Geological and Planetary Sciences, California Institute of Technology, 1200 East California Blvd, Pasadena, CA 91125, USA

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

position:8394:1
position: 8394
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-8394:1:source
so part of: sequence
organism: Solidesulfovibrio carbinolicus
mol type: genomic DNA
strain: DSM 3852
isolation source: water
culture collection: DSM:3852
type material: type strain of Desulfovibrio carbinolicus
plasmid: pDCAR3
country: Netherlands:De Krim
lat lon: 52.1167 N 5.9 E
collection date: 1995

296842
type: Taxonomy
SIO_000068: taxonomy

C3Y92_RS20885
type: Gene
subclass of: SO_0000704
RO_0002162: 296842
locus tag: C3Y92_RS20885
so part of: sequence
location: join(8232..8394,1..116)
location: region:1-8394:1
so has part: feature:8232-8394:1:exon
so has part: feature:1-116:1:exon
subclass of: SO_0000010

urn:…
SIO_000300: 1
SIO_000628: feature:8232-8394:1:exon

position:8232:1
position: 8232
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 2
SIO_000628: feature:1-116:1:exon

position:116:1
position: 116
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

C3Y92_RS20885
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 296842
locus tag: C3Y92_RS20885
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: MSDEQYTQEQLAALGEKLLARRERQAQSQARRRKKLKDAGWITTTMQAPKNRIAEIRKVVALLSRAKSGSYYIATVDENNKAKVVSERFTMK
SIO_010081: C3Y92_RS20885
subclass of: SO_0000673
so part of: C3Y92_RS20885
location: join(8232..8394,1..116)
location: region:1-8394:1
so has part: feature:8232-8394:1:exon
so has part: feature:1-116:1:exon

WP_129356200.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:8232-8394:1:exon

urn:…
SIO_000300: 2
SIO_000628: feature:1-116:1:exon

C3Y92_RS20890
type: Gene
subclass of: SO_0000704
RO_0002162: 296842
locus tag: C3Y92_RS20890
old locus tag: C3Y92_20590
so part of: sequence
location: 119..970
location: region:119-970:1
so has part: feature:119-970:1:exon
subclass of: SO_0000010

position:119:1
position: 119
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:970:1
position: 970
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:119-970:1:exon

C3Y92_RS20890
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 296842
locus tag: C3Y92_RS20890
old locus tag: C3Y92_20590
inference: COORDINATES: protein motif:HMM:NF015354.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: MobA/MobL family protein
translation: MAIYRLEVKMVQRSHGHSAVAAAAYRGCSRLIDEQTGEIQDYTRKEGHAYNEIIQPVGCEPITSNELWNKVENDETKINASLARDFLLTLPRELPSSVRKQLSIDFTEWLVERYNVQAELNIHEPTVEQRAKNASARCVPVDDIPEQPHAHILVSTRDVFGKKIRVLADKKSGREEIKEIRKKWEILLNEQLVPRGFPPLSCETKETQDTLAAEEAKRILAVAAKEIPKIKAEIKSLSKFIQRQERFAKVGSLAAKSQISQVGYAATQQTTQKDVYDAPRQRM
SIO_010081: C3Y92_RS20890
subclass of: SO_0000673
so part of: C3Y92_RS20890
location: 119..970
location: region:119-970:1
so has part: feature:119-970:1:exon

WP_129356186.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:119-970:1:exon

C3Y92_RS20895
type: Gene
subclass of: SO_0000704
RO_0002162: 296842
locus tag: C3Y92_RS20895
so part of: sequence
location: 948..1205
location: region:948-1205:1
so has part: feature:948-1205:1:exon
subclass of: SO_0000010

position:948:1
position: 948
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1205:1
position: 1205
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:948-1205:1:exon

C3Y92_RS20895
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 296842
locus tag: C3Y92_RS20895
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: MLQDNECDCEKCQHGTLHKHILKKWVKVEDKNYLVRARQLVVTCDAHLRQFVIYQEYFDDCEDLFDPVFQFEACEAYAPREAAND
SIO_010081: C3Y92_RS20895
subclass of: SO_0000673
so part of: C3Y92_RS20895
location: 948..1205
location: region:948-1205:1
so has part: feature:948-1205:1:exon

WP_165352195.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:948-1205:1:exon

C3Y92_RS20900
type: Gene
subclass of: SO_0000704
RO_0002162: 296842
locus tag: C3Y92_RS20900
old locus tag: C3Y92_20595
so part of: sequence
location: 1198..1506
location: region:1198-1506:1
so has part: feature:1198-1506:1:exon
subclass of: SO_0000010

position:1198:1
position: 1198
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1506:1
position: 1506
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1198-1506:1:exon

C3Y92_RS20900
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 296842
locus tag: C3Y92_RS20900
old locus tag: C3Y92_20595
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: MIKEKTKRLQMLEERLENKVKAAKKAADELEVIEQRAQNRAKQREKRQSDKDRYTLGLVLKFVYLKRFSMPAVKKEWILEAFPKEKPERYIECLEKHGIKVE
SIO_010081: C3Y92_RS20900
subclass of: SO_0000673
so part of: C3Y92_RS20900
location: 1198..1506
location: region:1198-1506:1
so has part: feature:1198-1506:1:exon

WP_129356190.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1198-1506:1:exon

C3Y92_RS20905
type: Gene
subclass of: SO_0000704
RO_0002162: 296842
locus tag: C3Y92_RS20905
so part of: sequence
location: complement(1524..2822)
location: region:1524-2822:-1
so has part: feature:1524-2822:-1:exon
subclass of: SO_0000010

position:1524:-1
position: 1524
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:2822:-1
position: 2822
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1524-2822:-1:exon

C3Y92_RS20905
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 296842
locus tag: C3Y92_RS20905
inference: COORDINATES: ab initio prediction:GeneMarkS-2+
GO function: GO:0003677 - DNA binding [Evidence IEA]
GO process: GO:0006260 - DNA replication [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
codon start: 1
transl table: 11
product: protein rep
translation: MPSKSTWCCGHGVIPAERHGKPTGAPGQAQIHAYEDMDGDDDAMARYHAVIGVVRCASPHVCPVCGAKIQAKRRKDVSFVTKRMLELGYTYVFATFTAGHKFGDKLIENVEKFQESSRKMKQGKAYKALTTKWDIKHYIRTAETTLDHPESTQKTGWHWHGHHILYLNRPHLTREEAEQLEAELSALWAKACAKYDLKVSLEHGLRIERPHFKSKKDGVIYLDDANAKRLGDYAAKTVSFEAAPAPNVKKGRKGQRISSWELIGLVVFGKRKDLLGLLSEFLIAMKGRRSMYMSRGLAALTGLDELDDEEVMKGKGNEGIYAFDDESWSKFSRHGKVRSAMHKLDDGMPVREVVKATIDGCISMQQLERIDMQLEEAALEVFDEDTGEVLISREDVQGHFAGDYVPKLEVIDRSPDKKNQAPARPAGCRSAA
SIO_010081: C3Y92_RS20905
subclass of: SO_0000673
so part of: C3Y92_RS20905
location: complement(1524..2822)
location: region:1524-2822:-1
so has part: feature:1524-2822:-1:exon

WP_129356192.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1524-2822:-1:exon

C3Y92_RS20910
type: Gene
subclass of: SO_0000704
RO_0002162: 296842
locus tag: C3Y92_RS20910
so part of: sequence
location: 4041..4313
location: region:4041-4313:1
so has part: feature:4041-4313:1:exon
subclass of: SO_0000010

position:4041:1
position: 4041
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:4313:1
position: 4313
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4041-4313:1:exon

C3Y92_RS20910
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 296842
locus tag: C3Y92_RS20910
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: MSNTHKNNLRPLVKKLLARRERQAQSQARRRKKLKDAGWITTTMQAPKNRIAEIRKVVALLSRAKSGSYYIATVDENNKAKVVSERFTMK
SIO_010081: C3Y92_RS20910
subclass of: SO_0000673
so part of: C3Y92_RS20910
location: 4041..4313
location: region:4041-4313:1
so has part: feature:4041-4313:1:exon

WP_129356194.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4041-4313:1:exon

C3Y92_RS20915
type: Gene
subclass of: SO_0000704
RO_0002162: 296842
locus tag: C3Y92_RS20915
old locus tag: C3Y92_20600
so part of: sequence
location: 4316..5008
location: region:4316-5008:1
so has part: feature:4316-5008:1:exon
subclass of: SO_0000010

position:4316:1
position: 4316
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:5008:1
position: 5008
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4316-5008:1:exon

C3Y92_RS20915
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 296842
locus tag: C3Y92_RS20915
old locus tag: C3Y92_20600
inference: COORDINATES: protein motif:HMM:NF015354.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: MobA/MobL family protein
translation: MAIYRLEVKMVQRSHGHSAVAAAAYRGCSRLIDEQTGEIQDYTRKEGHAYNEIIQPVGCEPITSNELWNKVENDETKINASLARDFLLTLPRELPSSVRKQLSIDFTEWLVERYNVQAELNIHEPTVEQRAKNASARCVPVDDIPEQPHAHILVSTRDVFGKKIRVLADKKSGREEIKEIRKKWEILLNEQLVPRGFPPLSCETKETQDTLAAEEAKRILAVAAKEISKD
SIO_010081: C3Y92_RS20915
subclass of: SO_0000673
so part of: C3Y92_RS20915
location: 4316..5008
location: region:4316-5008:1
so has part: feature:4316-5008:1:exon

WP_129356196.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4316-5008:1:exon

C3Y92_RS20920
type: Gene
subclass of: SO_0000704
RO_0002162: 296842
locus tag: C3Y92_RS20920
so part of: sequence
location: 5143..5403
location: region:5143-5403:1
so has part: feature:5143-5403:1:exon
subclass of: SO_0000010

position:5143:1
position: 5143
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:5403:1
position: 5403
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5143-5403:1:exon

C3Y92_RS20920
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 296842
locus tag: C3Y92_RS20920
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: MMLQDNECDCEKCQHGTLHKHILKKWVKVEDKNYLVRARQLVVTCDAHLRQFVIYQEYFDDCEDLFDPVFQFEACEAYAPREAAND
SIO_010081: C3Y92_RS20920
subclass of: SO_0000673
so part of: C3Y92_RS20920
location: 5143..5403
location: region:5143-5403:1
so has part: feature:5143-5403:1:exon

WP_129356188.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5143-5403:1:exon

C3Y92_RS20925
type: Gene
subclass of: SO_0000704
RO_0002162: 296842
locus tag: C3Y92_RS20925
so part of: sequence
location: 5396..5677
location: region:5396-5677:1
so has part: feature:5396-5677:1:exon
subclass of: SO_0000010

position:5396:1
position: 5396
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:5677:1
position: 5677
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5396-5677:1:exon

C3Y92_RS20925
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 296842
locus tag: C3Y92_RS20925
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: MIKEKTKRLQMLEERLENKVKAAKKAADELEVIEQRAQNRAKQREKRQSDKDRYTLGLVLKFLFKAVFNAGSKERMDSGGFSERKTRKIHRMS
SIO_010081: C3Y92_RS20925
subclass of: SO_0000673
so part of: C3Y92_RS20925
location: 5396..5677
location: region:5396-5677:1
so has part: feature:5396-5677:1:exon

WP_129356198.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5396-5677:1:exon

C3Y92_RS20930
type: Gene
subclass of: SO_0000704
RO_0002162: 296842
locus tag: C3Y92_RS20930
so part of: sequence
location: complement(5721..7019)
location: region:5721-7019:-1
so has part: feature:5721-7019:-1:exon
subclass of: SO_0000010

position:5721:-1
position: 5721
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:7019:-1
position: 7019
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5721-7019:-1:exon

C3Y92_RS20930
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 296842
locus tag: C3Y92_RS20930
inference: COORDINATES: ab initio prediction:GeneMarkS-2+
GO function: GO:0003677 - DNA binding [Evidence IEA]
GO process: GO:0006260 - DNA replication [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
codon start: 1
transl table: 11
product: protein rep
translation: MPSKSTWCCGHGVIPAERHGKPTGAPGQAQIHAYEDMDGDDDAMARYHAVIGVVRCASPHVCPVCGAKIQAKRRKDVSFVTKRMLELGYTYVFATFTAGHKFGDKLIENVEKFQESSRKMKQGKAYKALTTKWDIKHYIRTAETTLDHPESTQKTGWHWHGHHILYLNRPHLTREEAEQLEAELSALWAKACAKYDLKVSLEHGLRIERPHFKSKKDGVIYLDDANAKRLGDYAAKTVSFEAAPAPNVKKGRKGQRISSWELIGLVVFGKRKDLLGLLSEFLIAMKGRRSMYMSRGLAALTGLDELDDEEVMKGKGNEGIYAFDDESWSKFSRHGKVRSAMHKLDDGMPVREVVKATIDGCISMQQLERIDMQLEEAALEVFDEDTGEVLISREDVQGHFAGDYVPKLEVIDRSPDKKNQAPARPAGCRSAA
SIO_010081: C3Y92_RS20930
subclass of: SO_0000673
so part of: C3Y92_RS20930
location: complement(5721..7019)
location: region:5721-7019:-1
so has part: feature:5721-7019:-1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:5721-7019:-1:exon