Prevotella nigrescens strain F0109 plasmid unnamed, complete sequence.
type: Entry
definition: Prevotella nigrescens strain F0109 plasmid unnamed, complete sequence.
sequence version: NZ_CP072337.1
sequence date: 2022-10-07
sequence: sequence
division: CON
label: NZ_CP072337.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN18352181
keyword: RefSeq
source: Prevotella nigrescens
organism: Prevotella nigrescens
taxonomy: Bacteria; Bacteroidota; Bacteroidia; Bacteroidales; Prevotellaceae; Prevotella.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP072337.1.\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 :: 546x\nSequencing Technology :: PacBio Sequel\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 10/06/2022 20:46:01\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;\n repeat_region\nGenes (total) :: 2,448\nCDSs (total) :: 2,385\nGenes (coding) :: 2,329\nCDSs (with protein) :: 2,329\nGenes (RNA) :: 63\nrRNAs :: 4, 4, 4 (5S, 16S, 23S)\ncomplete rRNAs :: 4, 4, 4 (5S, 16S, 23S)\ntRNAs :: 48\nncRNAs :: 3\nPseudo Genes (total) :: 56\nCDSs (without protein) :: 56\nPseudo Genes (ambiguous residues) :: 0 of 56\nPseudo Genes (frameshifted) :: 25 of 56\nPseudo Genes (incomplete) :: 42 of 56\nPseudo Genes (internal stop) :: 2 of 56\nPseudo Genes (multiple problems) :: 13 of 56\nCRISPR Arrays :: 3\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 5179
topology: circular
so has quality: SO_0000988
location: 1..5179
location: region:1-5179:1
RO_0002162: 28133

NZ_CP072337
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN18352181
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journal: Unpublished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:5179:1
position: 5179
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-5179:1:source
so part of: sequence
organism: Prevotella nigrescens
mol type: genomic DNA
strain: F0109
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: 1990-11
collected by: Moores, Virginia Polytechnic Institute

28133
type: Taxonomy
SIO_000068: taxonomy

J5A59_RS00005
type: Gene
subclass of: SO_0000704
RO_0002162: 28133
locus tag: J5A59_RS00005
old locus tag: J5A59_00005
so part of: sequence
location: join(5141..5179,1..564)
location: region:1-5179:1
so has part: feature:5141-5179:1:exon
so has part: feature:1-564:1:exon
subclass of: SO_0000010

67364887
type: Gene
SIO_000068: ncbigene

urn:…
SIO_000300: 1
SIO_000628: feature:5141-5179:1:exon

position:5141:1
position: 5141
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 2
SIO_000628: feature:1-564:1:exon

position:564:1
position: 564
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

J5A59_RS00005
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 28133
locus tag: J5A59_RS00005
old locus tag: J5A59_00005
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: outer membrane beta-barrel protein
translation: MNLKYRIVFFLFATTYSVSSLGQIKLGGKIGYSHTNTAKVIGGRGYDGLIYGLTSSFPIYKSLRVNSDVLLEGRGYVIDKGIYDTANLTYKDCKVTFKYIDIPVLLETDVNNFLSIEFGPYIGMQVGRNLFYDNEKQDKDLLGKKQFFDMGFLAGMKGEYKGVFLEILYQYGLSQAFKDVNDFKTKGVCINFGYMFNLKK
SIO_010081: J5A59_RS00005
subclass of: SO_0000673
so part of: J5A59_RS00005
location: join(5141..5179,1..564)
location: region:1-5179:1
so has part: feature:5141-5179:1:exon
so has part: feature:1-564:1:exon

WP_211795062.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5141-5179:1:exon

urn:…
SIO_000300: 2
SIO_000628: feature:1-564:1:exon

J5A59_RS00010
type: Gene
subclass of: SO_0000704
RO_0002162: 28133
locus tag: J5A59_RS00010
old locus tag: J5A59_00010
so part of: sequence
location: 567..1217
location: region:567-1217:1
so has part: feature:567-1217:1:exon
subclass of: SO_0000010

67364888
type: Gene
SIO_000068: ncbigene

position:567:1
position: 567
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1217:1
position: 1217
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:567-1217:1:exon

J5A59_RS00010
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 28133
locus tag: J5A59_RS00010
old locus tag: J5A59_00010
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: MKHWFIFLSTMAIFMFSSCSNDESDLQSATSIKDVPMKLSGTLTPENPVQTVKVGNRYVTLLLENSEQLAEGTRAIVPIEDPRPKPGEIGPFYAQGTPKKMVGKEFKNRKVFIPNTFGVPTGVYFGDVWETAGIIRLPDNAYIARVAFPRPSGFKNYKTLVPGVSWKLDTEEGDKISVEWSFYTFVLNFNAAGMRINEVVPIDGKKVRIPYFYKVD
SIO_010081: J5A59_RS00010
subclass of: SO_0000673
so part of: J5A59_RS00010
location: 567..1217
location: region:567-1217:1
so has part: feature:567-1217:1:exon

WP_211795063.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:567-1217:1:exon

J5A59_RS00015
type: Gene
subclass of: SO_0000704
RO_0002162: 28133
locus tag: J5A59_RS00015
old locus tag: J5A59_00015
so part of: sequence
location: complement(1327..2697)
location: region:1327-2697:-1
so has part: feature:1327-2697:-1:exon
subclass of: SO_0000010

67364889
type: Gene
SIO_000068: ncbigene

position:1327:-1
position: 1327
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:2697:-1
position: 2697
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1327-2697:-1:exon

J5A59_RS00015
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 28133
locus tag: J5A59_RS00015
old locus tag: J5A59_00015
inference: COORDINATES: similar to AA sequence:RefSeq:WP_001161483.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MKGSKKGACSSNTQTAKANCLAHNRRDNSTEKVPSYVNQNRSHLNRIIFEDDIIKGRKSIVPLIHAAEKLYTEKTGQKCQKSFAPFREACLHLKEGITDAQLLDFKTKVEQETKWKVIGIYLHEDEGHAKSKYIEGEEGFEINHHAHVLFSCQDLNTGKAIRADRKKLSKMQDILAEATGMERGNKASETGRRHRSAMEQRIYSQEQRVKELEAKVSMRWQAVYEANTMLKQIQQQNQEEEEERKRIKERQEEDLKVYNTKKAAKEAIINVYEGVKGLFEQSSKDKQIKALKTQINAQKKELFNLKSEHIGQLGNATQKIEKAYQEGFSKAYGEVYNLQAQLKKAKEQAADAQKYRADIEKFQSIPVIERCINAIRSYVRHINGHFDAEDRRLLSFVMQGDADAAEKLKDAAYYGCGIIGQYQYSSKWNQAERELRNIANGVICEERQRQSRGLKR
SIO_010081: J5A59_RS00015
subclass of: SO_0000673
so part of: J5A59_RS00015
location: complement(1327..2697)
location: region:1327-2697:-1
so has part: feature:1327-2697:-1:exon

WP_211795064.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1327-2697:-1:exon

J5A59_RS00020
type: Gene
subclass of: SO_0000704
RO_0002162: 28133
locus tag: J5A59_RS00020
old locus tag: J5A59_00020
so part of: sequence
location: complement(2749..3066)
location: region:2749-3066:-1
so has part: feature:2749-3066:-1:exon
subclass of: SO_0000010

67364890
type: Gene
SIO_000068: ncbigene

position:2749:-1
position: 2749
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3066:-1
position: 3066
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2749-3066:-1:exon

J5A59_RS00020
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 28133
locus tag: J5A59_RS00020
old locus tag: J5A59_00020
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: MGSFRFRFALSTRAQGVPFLHTTGRTSNHSVSWCYRYGGYAAPYTPFYSPALISKTHPKKTPIRLAVSVFRCIFAPSKYAEKNAHEHLYMILYAKSSKSAVCKEG
SIO_010081: J5A59_RS00020
subclass of: SO_0000673
so part of: J5A59_RS00020
location: complement(2749..3066)
location: region:2749-3066:-1
so has part: feature:2749-3066:-1:exon

WP_211795059.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2749-3066:-1:exon

J5A59_RS00025
type: Gene
subclass of: SO_0000704
RO_0002162: 28133
locus tag: J5A59_RS00025
old locus tag: J5A59_00025
so part of: sequence
location: complement(3411..4394)
location: region:3411-4394:-1
so has part: feature:3411-4394:-1:exon
subclass of: SO_0000010

67364891
type: Gene
SIO_000068: ncbigene

position:3411:-1
position: 3411
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4394:-1
position: 4394
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3411-4394:-1:exon

J5A59_RS00025
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 28133
locus tag: J5A59_RS00025
old locus tag: J5A59_00025
inference: COORDINATES: similar to AA sequence:RefSeq:WP_008782591.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: replication initiation protein
translation: MQEKDPNINDLLLLQPKSVTFGQYDISERQENILTLITESLQKHMTKEKPLNTDLFGEPYVIIKCDEAGGTNNKNKVIQAAKELIPKLFSFRWKGKGDKWVTSTGTIITTIHNVEDSNNLTITFNKWAIPFLLYYGEGSGGGLFRKNVALTLRGNMTKRIYKMISAYKDKTRYEYPIEAFRKDFNISSSYSNYLIGKKILEPAMKRIKESNSDVWFDYELITKYKQDNGRKPKADTIVFKIKTTAATQGTDQFRRNETIRRWVDIAFDHPTDNKTITTTDKIISSDKCEMFFNKCIYYDDQITAGNMTTQHVKNTLRKILRDEFNIR
SIO_010081: J5A59_RS00025
subclass of: SO_0000673
so part of: J5A59_RS00025
location: complement(3411..4394)
location: region:3411-4394:-1
so has part: feature:3411-4394:-1:exon

WP_211795060.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3411-4394:-1:exon

J5A59_RS00030
type: Gene
subclass of: SO_0000704
RO_0002162: 28133
locus tag: J5A59_RS00030
old locus tag: J5A59_00030
so part of: sequence
location: complement(4397..4591)
location: region:4397-4591:-1
so has part: feature:4397-4591:-1:exon
subclass of: SO_0000010

67364892
type: Gene
SIO_000068: ncbigene

position:4397:-1
position: 4397
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4591:-1
position: 4591
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4397-4591:-1:exon

J5A59_RS00030
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 28133
locus tag: J5A59_RS00030
old locus tag: J5A59_00030
inference: COORDINATES: similar to AA sequence:RefSeq:WP_017645822.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MDKRLFEAQLKAAEVQTLLAHISKNVNYKQDLEELATRNIDEINATLSEVCQKLEKLNQEVTNQ
SIO_010081: J5A59_RS00030
subclass of: SO_0000673
so part of: J5A59_RS00030
location: complement(4397..4591)
location: region:4397-4591:-1
so has part: feature:4397-4591:-1:exon

WP_211795061.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4397-4591:-1:exon