Pseudodesulfovibrio profundus strain 500-1 plasmid pbDPRO, complete sequence.
type: Entry
definition: Pseudodesulfovibrio profundus strain 500-1 plasmid pbDPRO, complete sequence.
sequence version: NZ_LT907977.1
sequence date: 2022-12-25
sequence: sequence
division: CON
label: NZ_LT907977.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMEA104288281
keyword: RefSeq
source: Pseudodesulfovibrio profundus
organism: Pseudodesulfovibrio profundus
taxonomy: Bacteria; Thermodesulfobacteriota; Desulfovibrionia; Desulfovibrionales; Desulfovibrionaceae.
reference: 1
comment: REFSEQ INFORMATION: The reference sequence is identical to\nLT907977.1.\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-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/25/2022 02:39:51\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) :: 3,998\nCDSs (total) :: 3,927\nGenes (coding) :: 3,902\nCDSs (with protein) :: 3,902\nGenes (RNA) :: 71\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 58\nncRNAs :: 4\nPseudo Genes (total) :: 25\nCDSs (without protein) :: 25\nPseudo Genes (ambiguous residues) :: 0 of 25\nPseudo Genes (frameshifted) :: 4 of 25\nPseudo Genes (incomplete) :: 20 of 25\nPseudo Genes (internal stop) :: 5 of 25\nPseudo Genes (multiple problems) :: 4 of 25\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 6167
topology: circular
so has quality: SO_0000988
location: 1..6167
location: region:1-6167:1
RO_0002162: 57320

NZ_LT907977
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMEA104288281
type: BioSample
SIO_000068: biosample

1
title: Direct Submission
author: Regsiter, A.
author: William, W.
journal: Submitted (08-SEP-2017) Genoscope CEA, 2 rue Gaston Cremieux CP5706 91057 Evry cedex, France

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

position:6167:1
position: 6167
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-6167:1:source
so part of: sequence
organism: Pseudodesulfovibrio profundus
mol type: genomic DNA
strain: 500-1
type material: type strain of Pseudodesulfovibrio profundus
plasmid: pbDPRO

57320
type: Taxonomy
SIO_000068: taxonomy

DPRO_RS19845
type: Gene
subclass of: SO_0000704
RO_0002162: 57320
locus tag: DPRO_RS19845
old locus tag: DPRO_PB0002
so part of: sequence
location: complement(323..562)
location: region:323-562:-1
so has part: feature:323-562:-1:exon
subclass of: SO_0000010

position:323:-1
position: 323
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:562:-1
position: 562
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:323-562:-1:exon

DPRO_RS19845
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 57320
locus tag: DPRO_RS19845
old locus tag: DPRO_PB0002
inference: COORDINATES: protein motif:HMM:NF012974.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: DnaB-like helicase N-terminal domain-containing protein
translation: MISSIFSDGQFDKFSFLNPEDFTDKNCMVIFTAMKNLAGKKSPIDLVTVKEELESMTMLAPIGGPVELFEIADILPDSD
SIO_010081: DPRO_RS19845
subclass of: SO_0000673
so part of: DPRO_RS19845
location: complement(323..562)
location: region:323-562:-1
so has part: feature:323-562:-1:exon

WP_269459723.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:323-562:-1:exon

DPRO_RS19850
type: Gene
subclass of: SO_0000704
RO_0002162: 57320
locus tag: DPRO_RS19850
old locus tag: DPRO_PB0003
so part of: sequence
location: complement(584..1579)
location: region:584-1579:-1
so has part: feature:584-1579:-1:exon
subclass of: SO_0000010

position:584:-1
position: 584
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:1579:-1
position: 1579
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:584-1579:-1:exon

DPRO_RS19850
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 57320
locus tag: DPRO_RS19850
old locus tag: DPRO_PB0003
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: MSENRKSIVVKSNALIESMSDMNLQEMRFLAFAAAHLPHELVPEKGKPYDMEINVQSFASTFEITEKNAYREIKKLATKLMQKIVEFDDEEGYEVGVGLLSKRKYHHGEGRLWFRFDEDLLPHLMGLTERFTQYRLKDVYQFTKTSTWRLYELLRQYKKVGKREIDLEDLRWKLGIEGKYPRIDNLKLKVLDPAKEEINATSDIKIEYDQRKRGRRVVGFTFHIIENQGTKTPREKIREKVEKATGDTSLWPEMQLVLQNDYRINQKQAQQLANGFSKRRDELEKKLPTLKKRWEKLPEKNPKTGRKKTQLGGYIFAALKDEIMSGQGSLI
SIO_010081: DPRO_RS19850
subclass of: SO_0000673
so part of: DPRO_RS19850
location: complement(584..1579)
location: region:584-1579:-1
so has part: feature:584-1579:-1:exon

WP_157917583.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:584-1579:-1:exon

DPRO_RS19855
type: Gene
subclass of: SO_0000704
RO_0002162: 57320
locus tag: DPRO_RS19855
so part of: sequence
location: 2142..3014
location: region:2142-3014:1
so has part: feature:2142-3014:1:exon
subclass of: SO_0000010

position:2142:1
position: 2142
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:3014:1
position: 3014
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2142-3014:1:exon

DPRO_RS19855
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 57320
locus tag: DPRO_RS19855
inference: COORDINATES: protein motif:HMM:NF019377.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: class I SAM-dependent methyltransferase
translation: MKRAAEVSNTAKYGYAGGGSSIVFTKSLILILLHRLQLFDKRFFFNVKSVVKMKSDIKKYFTNKEHLKKRTYDRFNNYLHYLKRPQRIWWRVVSKDYGKVVARTHEIVKLSEQVKDFEGYGKYRNFKRYFNINFRRIFELGLHKEKSIKILDIGCGGGFFLYISRMFGHTPHGIDIDSHKIFNHMVKYFDIPRLEHRIEPNQPIPSLDQKFDLITSFAICFHKCGKKPWNHQEWKFFLNDIENNFIKNNGRLHLFFNNDPHGDFQYALEQISKCGYEMTVNHKTIDIFFK
SIO_010081: DPRO_RS19855
subclass of: SO_0000673
so part of: DPRO_RS19855
location: 2142..3014
location: region:2142-3014:1
so has part: feature:2142-3014:1:exon

WP_097013858.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2142-3014:1:exon

DPRO_RS19860
type: Gene
subclass of: SO_0000704
RO_0002162: 57320
locus tag: DPRO_RS19860
old locus tag: DPRO_PB0005
so part of: sequence
location: complement(3112..3831)
location: region:3112-3831:-1
so has part: feature:3112-3831:-1:exon
subclass of: SO_0000010

position:3112:-1
position: 3112
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3831:-1
position: 3831
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3112-3831:-1:exon

DPRO_RS19860
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 57320
locus tag: DPRO_RS19860
old locus tag: DPRO_PB0005
inference: COORDINATES: protein motif:HMM:NF014414.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: class I SAM-dependent methyltransferase
translation: MDKISTAIPEHFSKEKKKRYLDACKRYNDCTCRKINNKHRGIYKAIRKHPSKNLLDVGCGDGYFACFLAKLGYNVTGIDLSKESLSVAKSLAKTVGVDKVNFSYINAHELWRGSYDAAYCFDVVEHILWEEQGSFLESIYNRLKPKGAFFVRAPHAFNIRQYIPGHIGLPTYEQFMGLATEVGFTPKVIIGHSGIASIINYAIPYEKAVDMLFSSSSYWRYTFMKYLSLANVVVKLEKK
SIO_010081: DPRO_RS19860
subclass of: SO_0000673
so part of: DPRO_RS19860
location: complement(3112..3831)
location: region:3112-3831:-1
so has part: feature:3112-3831:-1:exon

WP_097013859.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3112-3831:-1:exon

DPRO_RS19865
type: Gene
subclass of: SO_0000704
RO_0002162: 57320
gene: traD
locus tag: DPRO_RS19865
old locus tag: DPRO_PB0006
so part of: sequence
location: complement(3864..4253)
location: region:3864-4253:-1
so has part: feature:3864-4253:-1:exon
subclass of: SO_0000010

position:3864:-1
position: 3864
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4253:-1
position: 4253
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3864-4253:-1:exon

DPRO_RS19865
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 57320
gene: traD
locus tag: DPRO_RS19865
old locus tag: DPRO_PB0006
inference: COORDINATES: protein motif:HMM:NF018152.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: conjugal transfer protein TraD
translation: MASLTSQFKEKYPHMTDKEINQLVKLHNREAKAKEQQRKLRAKASKRKRKERTKLLCDLGGLVLKSGLENMDRATLLGALLAIKKSEGDSARLEAWKFAGTEAMGEKESKEVKKETSTQSEVIQKPFGQ
SIO_010081: DPRO_RS19865
subclass of: SO_0000673
so part of: DPRO_RS19865
location: complement(3864..4253)
location: region:3864-4253:-1
so has part: feature:3864-4253:-1:exon

WP_232005812.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3864-4253:-1:exon

DPRO_RS19870
type: Gene
subclass of: SO_0000704
RO_0002162: 57320
locus tag: DPRO_RS19870
old locus tag: DPRO_PB0007
so part of: sequence
location: 4458..6158
location: region:4458-6158:1
so has part: feature:4458-6158:1:exon
subclass of: SO_0000010

position:4458:1
position: 4458
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:6158:1
position: 6158
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4458-6158:1:exon

DPRO_RS19870
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 57320
locus tag: DPRO_RS19870
old locus tag: DPRO_PB0007
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: MobQ family relaxase
translation: MIQKDNEEYQIGKASRSQNGNFLYGPIYHFSAKVVSRGKGQSAVASAAYRAGAELVDERTGEVKDFTRKERVDFSEIAAPENAPEWVRDRQRLWNEVESGEKRKDAQLCREVNAALPKALTLDEQKNIVREFVAENYTKRGMVTDWNIHDSQGKNPHVHMMITMREIGPEGFAKKKNRDWNRKEFLEQQREGWAKTTNKELNRVGFDYRIDHRSLEAQGIDRIPQKHLGPRPNIYQKAEHSQIIQANKELAQLTKDLKEIQARQKEIHGKAAELQEQQQERTQEPQRVQAKERAAEPVREPQNPKQPERKAPTKKKALQIKQPELDPRREALRQKVEARQRANDNEQKRLSNKGREVWPEHEREQWRMEERPKIKEKELHKMIEERKAQSKYNKPIQEHEAKAKAHEDEAKRQSRTAEAEKQSRMSRLLGKDKRAERAAEEARRKAEIEKGQANKLTEIRDKHVTEAVKAKLAADPIAKKAFESTVEKQLKKTEQIKEKKIGMNVDRSEKLERQRKAREEKAAEKKREKKMLEAMTLPEHQAWFKEKRKKERGQDKERIRSRSRGR
SIO_010081: DPRO_RS19870
subclass of: SO_0000673
so part of: DPRO_RS19870
location: 4458..6158
location: region:4458-6158:1
so has part: feature:4458-6158:1:exon

WP_157917584.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4458-6158:1:exon