Prevotella dentalis DSM 3688 plasmid pPREDE01, complete sequence.
type: Entry
definition: Prevotella dentalis DSM 3688 plasmid pPREDE01, complete sequence.
sequence version: NC_019961.1
sequence date: 2022-10-06
sequence: sequence
division: CON
label: NC_019961.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN02232045
keyword: GSC:MIGS:2.1
keyword: RefSeq
source: Prevotella dentalis DSM 3688
organism: Prevotella dentalis DSM 3688
taxonomy: Bacteria; Bacteroidota; Bacteroidia; Bacteroidales; Prevotellaceae; Prevotella.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP003370.1.\nURL -- http://www.jgi.doe.gov\nJGI Project ID: 4089468\nSource DNA and organism available from Hans-Peter Klenk at the\nGerman Collection of Microorganisms and Cell Cultures (DSMZ)\n(hans-peter.klenk@dsmz.de)\nContacts: Jonathan A. Eisen (jaeisen@ucdavis.edu)\n David Bruce (microbe@cuba.jgi-psf.org)\nWhole genome sequencing and draft assembly at JGI-PGF\nFinishing done by JGI-LANL\nAnnotation by JGI-ORNL and JGI-PGF\nThe JGI and collaborators endorse the principles for the\ndistribution and use of large scale sequencing data adopted by the\nlarger genome sequencing community and urge users of this data to\nfollow them. It is our intention to publish the work of this\nproject in a timely fashion and we welcome collaborative\ninteraction on the project and analysis.\n(http://www.genome.gov/page.cfm?pageID=10506376).\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##MIGS-Data-START##\ninvestigation_type :: bacteria_archaea\nproject_name :: Prevotella dentalis DSM 3688\ncollection_date :: Missing\nlat_lon :: Missing\ndepth :: Missing\nalt_elev :: Missing\ncountry :: Missing\nenvironment :: Host, Human oral microflora\nnum_replicons :: 4\nref_biomaterial :: ATCC 49559, CCUG 48288, DSM 3688, JCM 13448,\n NCTC 12043\nbiotic_relationship :: Free living\ntrophic_level :: Missing\nrel_to_oxygen :: Anaerobe\nisol_growth_condt :: Missing\nsequencing_meth :: WGS\nassembly :: Newbler v. 2.3 (pre-release)\nfinishing_strategy :: Finished\nGOLD Stamp ID :: Gi05356\nType Strain :: Yes\nFunding Program :: DOE-GEBA 2009\nGene Calling Method :: Prodigal 1.4, GenePRIMP\nIsolation Site :: Human dental root canal\nHost Name :: Homo sapiens\nBody Sample Site :: Oral\nCell Shape :: Rod-shaped\nMotility :: Nonmotile\nSporulation :: Nonsporulating\nTemperature Range :: Mesophile\nTempera…

sequence
subclass of: SO_0000155
sequence length: 4946
topology: circular
so has quality: SO_0000988
location: 1..4946
location: region:1-4946:1
RO_0002162: 908937

NC_019961
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN02232045
type: BioSample
SIO_000068: biosample

1
title: Complete sequence of plasmid 1 of Prevotella dentalis DSM 3688
author: Lucas, S.
author: Copeland, A.
author: Lapidus, A.
author: Glavina del Rio, T.
author: Dalin, E.
author: Tice, H.
author: Bruce, D.
author: Goodwin, L.
author: Pitluck, S.
author: Peters, L.
author: Mikhailova, N.
author: Chertkov, O.
author: Kyrpides, N.
author: Mavromatis, K.
author: Ivanova, N.
author: Brettin, T.
author: Detter, J.C.
author: Han, C.
author: Larimer, F.
author: Land, M.
author: Hauser, L.
author: Markowitz, V.
author: Cheng, J.-F.
author: Hugenholtz, P.
author: Woyke, T.
author: Wu, D.
author: Gronow, S.
author: Wellnitz, S.
author: Brambilla, E.
author: Klenk, H.-P.
author: Eisen, J.A.
journal: Unpublished

2
title: Direct Submission
author: Lucas, S.
author: Copeland, A.
author: Lapidus, A.
author: Glavina del Rio, T.
author: Dalin, E.
author: Tice, H.
author: Bruce, D.
author: Goodwin, L.
author: Pitluck, S.
author: Peters, L.
author: Mikhailova, N.
author: Chertkov, O.
author: Kyrpides, N.
author: Mavromatis, K.
author: Ivanova, N.
author: Brettin, T.
author: Detter, J.C.
author: Han, C.
author: Larimer, F.
author: Land, M.
author: Hauser, L.
author: Markowitz, V.
author: Cheng, J.-F.
author: Hugenholtz, P.
author: Woyke, T.
author: Wu, D.
author: Gronow, S.
author: Wellnitz, S.
author: Brambilla, E.
author: Klenk, H.-P.
author: Eisen, J.A.
journal: Submitted (29-FEB-2012) US DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598-1698, USA

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

position:4946:1
position: 4946
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-4946:1:source
so part of: sequence
organism: Prevotella dentalis DSM 3688
mol type: genomic DNA
strain: DSM 3688
isolation source: dental root canal
host: Homo sapiens
culture collection: DSM:3688
type material: type strain of Prevotella dentalis
plasmid: pPREDE01

908937
type: Taxonomy
SIO_000068: taxonomy

PREDE_RS13235
type: Gene
subclass of: SO_0000704
RO_0002162: 908937
locus tag: PREDE_RS13235
old locus tag: Prede_2717
so part of: sequence
location: complement(300..1235)
location: region:300-1235:-1
so has part: feature:300-1235:-1:exon
subclass of: SO_0000010

position:300:-1
position: 300
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:1235:-1
position: 1235
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:300-1235:-1:exon

PREDE_RS13235
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 908937
locus tag: PREDE_RS13235
old locus tag: Prede_2717
inference: COORDINATES: similar to AA sequence:RefSeq:WP_002489526.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: replication initiation factor domain-containing protein
translation: MTKENHSNYLQNKGSDKFSKTGYSNSRLNRHTMYTPEPKISFDAMTIVGNLNKNNAQKLSEFMSVEPQIRLWDILQTKFKAKALQEKVYIEYDKVKADTWDRRNMRVEFNPNKLTHEEMLWLKQNIIDYMEDYGFTRLDLAFDFEDDLNDYYAMTDKAVKKTIFYGRNGKPETKYFGVRDSDRFIRIYNKKQERKDNADVEISSEHLWRVEIELKRNMVDYWNDCFSDLHILQPDWKIIKRISDRAMVFMLLNEEEEWGKLERRTKNKYKQLIKEISPIDLTDLMKLTLRENEKQLQKQIDFWLSDFKIFK
SIO_010081: PREDE_RS13235
subclass of: SO_0000673
so part of: PREDE_RS13235
location: complement(300..1235)
location: region:300-1235:-1
so has part: feature:300-1235:-1:exon

WP_002467289.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:300-1235:-1:exon

PREDE_RS13995
type: Gene
subclass of: SO_0000704
RO_0002162: 908937
locus tag: PREDE_RS13995
so part of: sequence
location: complement(1468..1833)
location: region:1468-1833:-1
so has part: feature:1468-1833:-1:exon
subclass of: SO_0000010

position:1468:-1
position: 1468
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:1833:-1
position: 1833
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1468-1833:-1:exon

PREDE_RS13995
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 908937
locus tag: PREDE_RS13995
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: MKKLAVFFLSLIFVLSACNSNNSKERITKENIKIDPKDSHYVIKENSENKPQKIKVYKINKDGKEDITNNGVTKKENNHIEWRGTPDKYKDIKSLLGDTIQYKVYFKDKDSKQKELNIEYK
SIO_010081: PREDE_RS13995
subclass of: SO_0000673
so part of: PREDE_RS13995
location: complement(1468..1833)
location: region:1468-1833:-1
so has part: feature:1468-1833:-1:exon

WP_002467287.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1468-1833:-1:exon

PREDE_RS14000
type: Gene
subclass of: SO_0000704
RO_0002162: 908937
locus tag: PREDE_RS14000
so part of: sequence
location: complement(1905..2360)
location: region:1905-2360:-1
so has part: feature:1905-2360:-1:exon
subclass of: SO_0000010

position:1905:-1
position: 1905
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:2360:-1
position: 2360
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1905-2360:-1:exon

PREDE_RS14000
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 908937
locus tag: PREDE_RS14000
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: MKKSIQKTGKVLLATSIVLTTFSVGSIGFNHDNQAQAKGHENPTNPKPPKNSKIKTVKAHYSKKQVKKINDKLSTPSGGVATAFNYFLDTTTSIVAPELGASKTAVDIGSAQWKKTYAKHFKAAAKKGTGLTITYKVDVKNRTLEGVSFSS
SIO_010081: PREDE_RS14000
subclass of: SO_0000673
so part of: PREDE_RS14000
location: complement(1905..2360)
location: region:1905-2360:-1
so has part: feature:1905-2360:-1:exon

WP_002467291.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1905-2360:-1:exon

PREDE_RS14150
type: Gene
subclass of: SO_0000704
RO_0002162: 908937
locus tag: PREDE_RS14150
so part of: sequence
location: complement(2575..2727)
location: region:2575-2727:-1
so has part: feature:2575-2727:-1:exon
subclass of: SO_0000010

position:2575:-1
position: 2575
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:2727:-1
position: 2727
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2575-2727:-1:exon

PREDE_RS14150
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 908937
locus tag: PREDE_RS14150
inference: COORDINATES: similar to AA sequence:RefSeq:WP_012816704.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: Cop-6 protein
translation: MNSDKKTVTIRLSPKEIETLNRIKNKYGISNSLQVETLIKKYAKQEYGSY
SIO_010081: PREDE_RS14150
subclass of: SO_0000673
so part of: PREDE_RS14150
location: complement(2575..2727)
location: region:2575-2727:-1
so has part: feature:2575-2727:-1:exon

WP_100206256.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2575-2727:-1:exon

PREDE_RS13250
type: Gene
subclass of: SO_0000704
RO_0002162: 908937
locus tag: PREDE_RS13250
old locus tag: Prede_2721
so part of: sequence
location: complement(2980..3678)
location: region:2980-3678:-1
so has part: feature:2980-3678:-1:exon
subclass of: SO_0000010

position:2980:-1
position: 2980
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3678:-1
position: 3678
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2980-3678:-1:exon

PREDE_RS13250
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 908937
locus tag: PREDE_RS13250
old locus tag: Prede_2721
inference: COORDINATES: protein motif:HMM:NF015839.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: DUF334 domain-containing protein
translation: MSLKDEKEKKNENQNKTQSQRTQNNSTSTGTPSNITQSNLERQELDELKKQNKLIIKYLTEIQENQNARENEQKQLRSNLTEATKDFRDSAIKTHNDFIDILKKKLDKVETDELANIIGRDIYKVRDENKRMLQEVRASHEHYKKRQKQLFTGIGTMLLVFMLFALVMTIGSDFMDFIHVDILQKAIASKLKASEGFMTLVWYIAYGLPYILAISGFIYLYEWIRKKFEVFL
SIO_010081: PREDE_RS13250
subclass of: SO_0000673
so part of: PREDE_RS13250
location: complement(2980..3678)
location: region:2980-3678:-1
so has part: feature:2980-3678:-1:exon

WP_145477399.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2980-3678:-1:exon

PREDE_RS13785
type: Gene
subclass of: SO_0000704
RO_0002162: 908937
locus tag: PREDE_RS13785
old locus tag: Prede_2722
pseudo: true
so part of: sequence
location: complement(<3722..4375)
location: region:3722-4375:-1
so has part: feature:3722-4375:-1:exon
subclass of: SO_0000010

position:3722:-1
position: 3722
reference: sequence
type: ReverseStrandPosition
type: FuzzyPosition

position:4375:-1
position: 4375
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3722-4375:-1:exon

PREDE_RS13785
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 908937
locus tag: PREDE_RS13785
old locus tag: Prede_2722
inference: COORDINATES: protein motif:HMM:NF015397.2
note: incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
pseudo: true
codon start: 1
transl table: 11
product: relaxase/mobilization nuclease domain-containing protein
SIO_010081: PREDE_RS13785
subclass of: SO_0000673
so part of: PREDE_RS13785
location: complement(<3722..4375)
location: region:3722-4375:-1
so has part: feature:3722-4375:-1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:3722-4375:-1:exon

PREDE_RS13255
type: Gene
subclass of: SO_0000704
RO_0002162: 908937
locus tag: PREDE_RS13255
old locus tag: Prede_2723
so part of: sequence
location: complement(4553..4936)
location: region:4553-4936:-1
so has part: feature:4553-4936:-1:exon
subclass of: SO_0000010

position:4553:-1
position: 4553
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4936:-1
position: 4936
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4553-4936:-1:exon

PREDE_RS13255
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 908937
locus tag: PREDE_RS13255
old locus tag: Prede_2723
inference: COORDINATES: similar to AA sequence:RefSeq:WP_002449121.1
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: MSEQNNFVASDKTVGKNHKPNRKEPKQISFRVSESEYLKLKQSAETLNMSVPAFVKKKAQGSRLVAPKFDKETRQSIAKDLSMLGANVNQIAKYCNQHQHEAPNYDGLEYNIKAVRERLDEIWKSLN
SIO_010081: PREDE_RS13255
subclass of: SO_0000673
so part of: PREDE_RS13255
location: complement(4553..4936)
location: region:4553-4936:-1
so has part: feature:4553-4936:-1:exon

WP_015298620.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4553-4936:-1:exon