Prevotella dentalis DSM 3688 plasmid pPREDE02, complete sequence.
type: Entry
definition: Prevotella dentalis DSM 3688 plasmid pPREDE02, complete sequence.
sequence version: NC_019969.1
sequence date: 2022-10-06
sequence: sequence
division: CON
label: NC_019969.1
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\nCP003371.1.\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: 4175
topology: circular
so has quality: SO_0000988
location: 1..4175
location: region:1-4175:1
RO_0002162: 908937

NC_019969
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN02232045
type: BioSample
SIO_000068: biosample

1
title: Complete sequence of plasmid 2 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:4175:1
position: 4175
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-4175:1: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: pPREDE02

908937
type: Taxonomy
SIO_000068: taxonomy

PREDE_RS13790
type: Gene
subclass of: SO_0000704
RO_0002162: 908937
locus tag: PREDE_RS13790
so part of: sequence
location: complement(314..616)
location: region:314-616:-1
so has part: feature:314-616:-1:exon
subclass of: SO_0000010

position:314:-1
position: 314
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:616:-1
position: 616
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:314-616:-1:exon

PREDE_RS13790
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 908937
locus tag: PREDE_RS13790
inference: COORDINATES: similar to AA sequence:RefSeq:WP_019236263.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MFKKFFTISVVLFAIDMLSVVFKDLFLLGEKTTTMNGFVLFLTILFTISMIVTTFFYFISKKNHNTEEYKGLYFTVLISLPFVWLIVGHIITSPLPYILK
SIO_010081: PREDE_RS13790
subclass of: SO_0000673
so part of: PREDE_RS13790
location: complement(314..616)
location: region:314-616:-1
so has part: feature:314-616:-1:exon

WP_100051356.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:314-616:-1:exon

PREDE_RS13260
type: Gene
subclass of: SO_0000704
RO_0002162: 908937
locus tag: PREDE_RS13260
old locus tag: Prede_2726
so part of: sequence
location: complement(872..1567)
location: region:872-1567:-1
so has part: feature:872-1567:-1:exon
subclass of: SO_0000010

position:872:-1
position: 872
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:1567:-1
position: 1567
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:872-1567:-1:exon

PREDE_RS13260
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 908937
locus tag: PREDE_RS13260
old locus tag: Prede_2726
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: MSLKDEREKKKNQSETQSQSTQTNSKSIGTQSNTTQSNLERQEIEELKKQNKLIIKYLTEIQENQNAREKDQKEITSKLTGATKDFRDNGVKTHNAFINILKEKLDKVDTDELANIIGRDIYKVRDENERMLQEVRSSHEEYQKRIKLMYRGFGAMLLVFMLFALVMTIGSDFMDFIHIDILQKAIASKIKASEGFMTFIWYIAYGLPYIVAIGGFIYLYEWIRKKFEVFF
SIO_010081: PREDE_RS13260
subclass of: SO_0000673
so part of: PREDE_RS13260
location: complement(872..1567)
location: region:872-1567:-1
so has part: feature:872-1567:-1:exon

WP_077126318.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:872-1567:-1:exon

PREDE_RS13795
type: Gene
subclass of: SO_0000704
RO_0002162: 908937
locus tag: PREDE_RS13795
old locus tag: Prede_2727
pseudo: true
so part of: sequence
location: complement(<1611..2264)
location: region:1611-2264:-1
so has part: feature:1611-2264:-1:exon
subclass of: SO_0000010

position:1611:-1
position: 1611
reference: sequence
type: ReverseStrandPosition
type: FuzzyPosition

position:2264:-1
position: 2264
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1611-2264:-1:exon

PREDE_RS13795
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 908937
locus tag: PREDE_RS13795
old locus tag: Prede_2727
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_RS13795
subclass of: SO_0000673
so part of: PREDE_RS13795
location: complement(<1611..2264)
location: region:1611-2264:-1
so has part: feature:1611-2264:-1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:1611-2264:-1:exon

PREDE_RS13265
type: Gene
subclass of: SO_0000704
RO_0002162: 908937
locus tag: PREDE_RS13265
old locus tag: Prede_2728
so part of: sequence
location: complement(2246..2629)
location: region:2246-2629:-1
so has part: feature:2246-2629:-1:exon
subclass of: SO_0000010

position:2246:-1
position: 2246
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:2629:-1
position: 2629
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2246-2629:-1:exon

PREDE_RS13265
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 908937
locus tag: PREDE_RS13265
old locus tag: Prede_2728
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: MobC family plasmid mobilization relaxosome protein
translation: MSEQNNFVASDKTVGRNQKPNRKEPKQISFRVSESEYLKLRQSADTLNMSVPNFVKKKAQGSRLVAPKFDKETRQSIAKDLSKLGANANQIAKYCNQHQYDAPNYPALERNISELRERLDEIWQQLN
SIO_010081: PREDE_RS13265
subclass of: SO_0000673
so part of: PREDE_RS13265
location: complement(2246..2629)
location: region:2246-2629:-1
so has part: feature:2246-2629:-1:exon

WP_015310586.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2246-2629:-1:exon

PREDE_RS13275
type: Gene
subclass of: SO_0000704
RO_0002162: 908937
locus tag: PREDE_RS13275
old locus tag: Prede_2730
so part of: sequence
location: complement(3236..4165)
location: region:3236-4165:-1
so has part: feature:3236-4165:-1:exon
subclass of: SO_0000010

position:3236:-1
position: 3236
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4165:-1
position: 4165
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3236-4165:-1:exon

PREDE_RS13275
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 908937
locus tag: PREDE_RS13275
old locus tag: Prede_2730
inference: COORDINATES: similar to AA sequence:RefSeq:WP_015365429.1
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: MTEKNHSNYLQNKDLDNFSKTGYSNSRLSGNFFTTPQPNLSFDAMTIVGNLNKDNAEQLSKFMSVEPRFRLWDILQTKFKAKALQEKVYIEYDKVRADSWDRRNMRVEFNPNKLTYDEMLWLKRNVISYMEDDGFTRLDLAFDFEEDLSDYYTMTDKAVKKTIFYGRNGKPETKYFGVRDSDRFIRIYNKKQERKDNADIEINSEHLWRVEIELKRNMVDMWNSCFDDLHILKPNWTVLEKIKEQAMVYMLIHEEDTWGKLERHAKYKYKNLIKEISPVDLTELMKSTLRENEKQLQKQITFWQNDFRI
SIO_010081: PREDE_RS13275
subclass of: SO_0000673
so part of: PREDE_RS13275
location: complement(3236..4165)
location: region:3236-4165:-1
so has part: feature:3236-4165:-1:exon

WP_015310588.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3236-4165:-1:exon