Prevotella denticola strain F0115 plasmid unnamed, complete sequence.
type: Entry
definition: Prevotella denticola strain F0115 plasmid unnamed, complete sequence.
sequence version: NZ_CP072376.1
sequence date: 2023-03-26
sequence: sequence
division: CON
label: NZ_CP072376.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN18352182
keyword: RefSeq
source: Prevotella denticola
organism: Prevotella denticola
taxonomy: Bacteria; Bacteroidota; Bacteroidia; Bacteroidales; Prevotellaceae; Prevotella.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP072376.1.\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 :: 22-DEC-2020\nAssembly Method :: Pacbio MA v. 9.0.0.92188\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 266x\nSequencing Technology :: PacBio Sequel\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/26/2023 05:54:28\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) :: 2,483\nCDSs (total) :: 2,418\nGenes (coding) :: 2,374\nCDSs (with protein) :: 2,374\nGenes (RNA) :: 65\nrRNAs :: 4, 4, 4 (5S, 16S, 23S)\ncomplete rRNAs :: 4, 4, 4 (5S, 16S, 23S)\ntRNAs :: 50\nncRNAs :: 3\nPseudo Genes (total) :: 44\nCDSs (without protein) :: 44\nPseudo Genes (ambiguous residues) :: 0 of 44\nPseudo Genes (frameshifted) :: 12 of 44\nPseudo Genes (incomplete) :: 32 of 44\nPseudo Genes (internal stop) :: 8 of 44\nPseudo Genes (multiple problems) :: 8 of 44\nCRISPR Arrays :: 4\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 4574
topology: circular
so has quality: SO_0000988
location: 1..4574
location: region:1-4574:1
RO_0002162: 28129

NZ_CP072376
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN18352182
type: BioSample
SIO_000068: biosample

1
title: Human Oral Microbial Genomes
author: Johnston, C.D.
author: Chen, T.
author: Dewhirst, F.E.
journal: Unpublished

2
title: Direct Submission
author: Johnston, C.D.
author: Chen, T.
author: Dewhirst, F.E.
journal: Submitted (21-MAR-2021) Microbiology, The Forsyth Institute, 245 First Street, Cambridge, MA 02142, USA

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

position:4574:1
position: 4574
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-4574:1:source
so part of: sequence
organism: Prevotella denticola
mol type: genomic DNA
strain: F0115
isolation source: human oral cavity
host: Homo sapiens
plasmid: unnamed
country: USA: Blacksberg, Virginia
lat lon: 37.23 N 80.42 W
altitude: 634 m
collection date: 1993-02
collected by: Moores, Virginia Polytechnic Institute

28129
type: Taxonomy
SIO_000068: taxonomy

J4866_RS12325
type: Gene
subclass of: SO_0000704
RO_0002162: 28129
locus tag: J4866_RS12325
old locus tag: J4866_12325
so part of: sequence
location: join(4410..4574,1..1275)
location: region:1-4574:1
so has part: feature:4410-4574:1:exon
so has part: feature:1-1275:1:exon
subclass of: SO_0000010

66712481
type: Gene
SIO_000068: ncbigene

urn:…
SIO_000300: 1
SIO_000628: feature:4410-4574:1:exon

position:4410:1
position: 4410
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 2
SIO_000628: feature:1-1275:1:exon

position:1275:1
position: 1275
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

J4866_RS12325
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 28129
locus tag: J4866_RS12325
old locus tag: J4866_12325
inference: COORDINATES: similar to AA sequence:RefSeq:WP_007369093.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: plasmid recombination protein
translation: MLPPTPPSNIFACSFLVVENVFVPLLAGKHCVQVIAHYNPCMVVGSPRAGGCTPLTPAATHRTPPTEKLKIMKQQTSIHVQPVKGGSEQHNKREKELDYIRPELSHLNEYWEKDTQTDRLENIKSRYLKSTGQKMQAKATPIREAVVVIKSETTMEDLKRLSDAYLQRFGIDTFQIAIHKDEGYPQVEEWKPNLHAHLVFDWTDQETGKSLKLNRQDMVEMQTITAEVLQMDRGVSSDKQHLTAQQYKSFAEEAKLRRLEEERARKEKQMKEELERFKVAKAHKEAAIETAKTLSEGVKGLFGQSSKDKTIKALREQINTKQKEIFDIKAGMVGLKAQQEEQKEQQKAALNETRREAVSKYNELVVKHNKVVERNEELQEVIKDFQEIPIIERCLAIIRSFVFHICGRFDADDRRLLSFVMQGNEDAAKSLRNAAFNLGGVICQYQYGSRWDQAERELRNIANGVREEEQQQRNRGLRR
SIO_010081: J4866_RS12325
subclass of: SO_0000673
so part of: J4866_RS12325
location: join(4410..4574,1..1275)
location: region:1-4574:1
so has part: feature:4410-4574:1:exon
so has part: feature:1-1275:1:exon

WP_244972445.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4410-4574:1:exon

urn:…
SIO_000300: 2
SIO_000628: feature:1-1275:1:exon

J4866_RS12330
type: Gene
subclass of: SO_0000704
RO_0002162: 28129
locus tag: J4866_RS12330
old locus tag: J4866_12330
so part of: sequence
location: complement(1280..1618)
location: region:1280-1618:-1
so has part: feature:1280-1618:-1:exon
subclass of: SO_0000010

66712482
type: Gene
SIO_000068: ncbigene

position:1280:-1
position: 1280
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:1618:-1
position: 1618
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1280-1618:-1:exon

J4866_RS12330
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 28129
locus tag: J4866_RS12330
old locus tag: J4866_12330
inference: COORDINATES: similar to AA sequence:RefSeq:WP_000009988.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MNFRIIPTPTFAKSLKALAKRHKSMRADMEEFTKSLEENPLQGAELIPGVRKIRMAIKSKGGGKSGGARIITYNVLATEQEGAVYLLEIYDKSEYSTVKENVLKDIIKNLDL
SIO_010081: J4866_RS12330
subclass of: SO_0000673
so part of: J4866_RS12330
location: complement(1280..1618)
location: region:1280-1618:-1
so has part: feature:1280-1618:-1:exon

WP_007369092.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1280-1618:-1:exon

J4866_RS12335
type: Gene
subclass of: SO_0000704
RO_0002162: 28129
locus tag: J4866_RS12335
old locus tag: J4866_12335
so part of: sequence
location: complement(1608..1865)
location: region:1608-1865:-1
so has part: feature:1608-1865:-1:exon
subclass of: SO_0000010

66712483
type: Gene
SIO_000068: ncbigene

position:1608:-1
position: 1608
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:1865:-1
position: 1865
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1608-1865:-1:exon

J4866_RS12335
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 28129
locus tag: J4866_RS12335
old locus tag: J4866_12335
inference: COORDINATES: similar to AA sequence:RefSeq:WP_004379751.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MAVLNFTSREFRSQQAHVFDLADQGEKIVIRRSKKQAYTLVPVEDEDITFTKSLEERIGMALQEVKQMREGKIKELSMKELLDEL
SIO_010081: J4866_RS12335
subclass of: SO_0000673
so part of: J4866_RS12335
location: complement(1608..1865)
location: region:1608-1865:-1
so has part: feature:1608-1865:-1:exon

WP_025068497.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1608-1865:-1:exon

J4866_RS12340
type: Gene
subclass of: SO_0000704
RO_0002162: 28129
locus tag: J4866_RS12340
old locus tag: J4866_12340
so part of: sequence
location: 2284..3264
location: region:2284-3264:1
so has part: feature:2284-3264:1:exon
subclass of: SO_0000010

66712484
type: Gene
SIO_000068: ncbigene

position:2284:1
position: 2284
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:3264:1
position: 3264
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2284-3264:1:exon

J4866_RS12340
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 28129
locus tag: J4866_RS12340
old locus tag: J4866_12340
inference: COORDINATES: similar to AA sequence:RefSeq:WP_008782578.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: replication initiation protein
translation: MARTIKGSQAAIQSYIFTTAKYDFSAYEKRIMYRLIEFAQDELKGIMIRDNMHKIEPTLFGREITMPVADILKDEDDKNHDKAKKAFRTLSQKHIEYEDDEIWQFTPIITNPKIKKREGLSKFYVFDEIWRCLLDFTKGYRKYELVTAMGFKSVYSMRMYELMSGQKRPLDFTFEDLKLRFGVKDKYKLVGHFKTRVLDIAKKELDESSPYSFNYIEIKERRKVVGFKFFPTFHPDKQDPELLQVEMRSKLSASIQISQEAYSYLRYSFEFKAEEISKNKKTIIEGEKKIPDFIGFLSSLVGPSRTAKNRIGYVINAIKKKTAEVK
SIO_010081: J4866_RS12340
subclass of: SO_0000673
so part of: J4866_RS12340
location: 2284..3264
location: region:2284-3264:1
so has part: feature:2284-3264:1:exon

WP_021583533.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2284-3264:1:exon

J4866_RS12345
type: Gene
subclass of: SO_0000704
RO_0002162: 28129
locus tag: J4866_RS12345
old locus tag: J4866_12345
so part of: sequence
location: 3391..4134
location: region:3391-4134:1
so has part: feature:3391-4134:1:exon
subclass of: SO_0000010

66712485
type: Gene
SIO_000068: ncbigene

position:3391:1
position: 3391
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:4134:1
position: 4134
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3391-4134:1:exon

J4866_RS12345
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 28129
locus tag: J4866_RS12345
old locus tag: J4866_12345
inference: COORDINATES: similar to AA sequence:RefSeq:WP_007411236.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MKKFIYFYLCLLVFILGGCQFSDDDYQKASTIHTLEMDLESAKKYMHIDSAAHQYTIAITDEQQEAEGISKENLAKIFKIVTDLNQRIDNDFNAGKIVTMYLTTKENFISYTIDPLHQLHDINFKDVRTKQPYIATRAGKWLYSGYFMDGNWERGTRDPDFKTSASHVTSELDICYARGAWNFGMTCLTGKSAYGTSFSTNGIGHTYGGIQRYWWWTGGGSAPFNWKFTLGGPLGGEANGGISIYES
SIO_010081: J4866_RS12345
subclass of: SO_0000673
so part of: J4866_RS12345
location: 3391..4134
location: region:3391-4134:1
so has part: feature:3391-4134:1:exon

WP_007369094.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3391-4134:1:exon