Providencia sneebia DSM 19967 plasmid pPSN3, whole genome shotgun sequence.
type: Entry
definition: Providencia sneebia DSM 19967 plasmid pPSN3, whole genome shotgun sequence.
sequence version: NZ_CM001855.1
sequence date: 2023-05-14
sequence: sequence
division: CON
label: NZ_CM001855.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN02428955
keyword: WGS
keyword: RefSeq
source: Providencia sneebia DSM 19967
organism: Providencia sneebia DSM 19967
taxonomy: Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Morganellaceae; Providencia.
reference: 1
references: 23145767
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCM001855.1.\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 Method :: SeqMan v. 8\nGenome Coverage :: 30.0x\nSequencing Technology :: 454\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 05/14/2023 09:46:31\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.5\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 3,240\nCDSs (total) :: 3,168\nGenes (coding) :: 2,964\nCDSs (with protein) :: 2,964\nGenes (RNA) :: 72\nrRNAs :: 5, 1, 1 (5S, 16S, 23S)\ncomplete rRNAs :: 5, 1, 1 (5S, 16S, 23S)\ntRNAs :: 58\nncRNAs :: 7\nPseudo Genes (total) :: 204\nCDSs (without protein) :: 204\nPseudo Genes (ambiguous residues) :: 0 of 204\nPseudo Genes (frameshifted) :: 86 of 204\nPseudo Genes (incomplete) :: 126 of 204\nPseudo Genes (internal stop) :: 14 of 204\nPseudo Genes (multiple problems) :: 19 of 204\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 4321
topology: circular
so has quality: SO_0000988
location: 1..4321
location: region:1-4321:1
RO_0002162: 1141660

NZ_CM001855
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN02428955
type: BioSample
SIO_000068: biosample

1
title: Comparative genomics of bacteria in the genus Providencia isolated from wild Drosophila melanogaster
author: Galac, M.R.
author: Lazzaro, B.P.
journal: BMC Genomics 13, 612 (2012)
pubmed: 23145767
comments: Publication Status: Online-Only

23145767
type: PubMed
SIO_000068: pubmed

2
title: Direct Submission
author: Galac, M.R.
author: Lazzaro, B.P.
journal: Submitted (08-JUN-2012) Field of Genetics & Development, Cornell University, 3125 Comstock Hall, Ithaca, NY 14850, USA

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

position:4321:1
position: 4321
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-4321:1:source
so part of: sequence
organism: Providencia sneebia DSM 19967
mol type: genomic DNA
strain: DSM 19967
isolation source: wild caught Drosophila melanogaster hemolymph
host: Drosophila melanogaster
culture collection: DSM:19967
type material: type strain of Providencia sneebia
plasmid: pPSN3
country: USA: State College, PA
collection date: 1999

1141660
type: Taxonomy
SIO_000068: taxonomy

OO7_RS16095
type: Gene
subclass of: SO_0000704
RO_0002162: 1141660
locus tag: OO7_RS16095
old locus tag: OO7_16375
so part of: sequence
location: complement(252..503)
location: region:252-503:-1
so has part: feature:252-503:-1:exon
subclass of: SO_0000010

position:252:-1
position: 252
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:503:-1
position: 503
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:252-503:-1:exon

OO7_RS16095
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1141660
locus tag: OO7_RS16095
old locus tag: OO7_16375
inference: COORDINATES: ab initio prediction:GeneMarkS-2+
note: Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
codon start: 1
transl table: 4
product: hypothetical protein
translation: MDKIISYWKEYNIAHYDEKKGFYVIYGKYNHLNNEEESRKCLGLHWEDYPKSRSVLAPMVVTAEIKNSILAGLLKDGLDKKIK
SIO_010081: OO7_RS16095
subclass of: SO_0000673
so part of: OO7_RS16095
location: complement(252..503)
location: region:252-503:-1
so has part: feature:252-503:-1:exon

WP_008917000.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:252-503:-1:exon

OO7_RS16100
type: Gene
subclass of: SO_0000704
RO_0002162: 1141660
locus tag: OO7_RS16100
old locus tag: OO7_16380
so part of: sequence
location: 530..1069
location: region:530-1069:1
so has part: feature:530-1069:1:exon
subclass of: SO_0000010

position:530:1
position: 530
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1069:1
position: 1069
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:530-1069:1:exon

OO7_RS16100
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1141660
locus tag: OO7_RS16100
old locus tag: OO7_16380
inference: COORDINATES: ab initio prediction:GeneMarkS-2+
note: Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
codon start: 1
transl table: 4
product: hypothetical protein
translation: MPKNHLIFSTITLITICYPIISLANDIPIECKSVEANALVNQAYKSQYDKAFVAKQRLDPNEQASLVYEKLTDYDYKNGDFKDIIIPLDISLTQNADTQLLAVREVAYDNKNKTRTCEAAVKISISGVLIENYQELIPNDIEFRDFTNQFKNKEIGTFNIKYILDKDYSGNNQIVVYGL
SIO_010081: OO7_RS16100
subclass of: SO_0000673
so part of: OO7_RS16100
location: 530..1069
location: region:530-1069:1
so has part: feature:530-1069:1:exon

WP_008917001.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:530-1069:1:exon

OO7_RS16105
type: Gene
subclass of: SO_0000704
RO_0002162: 1141660
locus tag: OO7_RS16105
old locus tag: OO7_16385
so part of: sequence
location: 1293..1706
location: region:1293-1706:1
so has part: feature:1293-1706:1:exon
subclass of: SO_0000010

position:1293:1
position: 1293
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1706:1
position: 1706
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1293-1706:1:exon

OO7_RS16105
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1141660
locus tag: OO7_RS16105
old locus tag: OO7_16385
inference: COORDINATES: ab initio prediction:GeneMarkS-2+
note: Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
codon start: 1
transl table: 4
product: relaxosome component
translation: MANLSNLKILIEDKKTYKDRYQRKNFISLCLSDEELTEVELLAEKLDLKRAAAIRALLLNKSAILKNKIKNNGNKEYLFLLNNISNNINQIAKKINANIDFFINSANGEQFAYLFEELTEDIEKIKEVYNDTQTDRR
SIO_010081: OO7_RS16105
subclass of: SO_0000673
so part of: OO7_RS16105
location: 1293..1706
location: region:1293-1706:1
so has part: feature:1293-1706:1:exon

WP_008917002.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1293-1706:1:exon

OO7_RS16110
type: Gene
subclass of: SO_0000704
RO_0002162: 1141660
locus tag: OO7_RS16110
old locus tag: OO7_16390
so part of: sequence
location: 1681..3120
location: region:1681-3120:1
so has part: feature:1681-3120:1:exon
subclass of: SO_0000010

position:1681:1
position: 1681
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:3120:1
position: 3120
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1681-3120:1:exon

OO7_RS16110
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1141660
locus tag: OO7_RS16110
old locus tag: OO7_16390
inference: COORDINATES: ab initio prediction:GeneMarkS-2+
note: Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
codon start: 1
transl table: 4
product: hypothetical protein
translation: MIHKQIGGKNKQRNVKNSLSYLLRKDKIEEQQYIKVLSTTTEQDILNFNEYIQSKNFSHPYTAGVLSFEEKDIDEDLKNKIMSEFEEMMFAEIAPENRPPVLWVQHQDKGRLELNYLTFNALADKRAYKTYYHYADKKLFNAFCEVVNYENNISSVIDVENHKERNKLINTLNNKIPKHKKDIVNKLQEEIIAKISIEEINNRKELIDFLTKEKNIIINRTGDNYISIKFSEEDKPVRLKGDIYEQSRDYKTYNEESRIDHRADREYVKNALREHTSVFDAELSKRTSRNKKRFKRTQNENKNSNEQNNKRTNDIQDVRSEISSNNNSLIRNEFIFLNFNNDFNKENLNNEQNNRSDKTEERTREQRIRSIGSEIENINQEQQSIYSKFEDRSREQQYINEKSKRIRRRIRLSNRYVDRFFRLFFDNIERFKRTQELKKSITQKVSKFFKKQEETQGQQNKIERRRRFKIWYSRHEKNA
SIO_010081: OO7_RS16110
subclass of: SO_0000673
so part of: OO7_RS16110
location: 1681..3120
location: region:1681-3120:1
so has part: feature:1681-3120:1:exon

WP_282553646.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1681-3120:1:exon

OO7_RS16115
type: Gene
subclass of: SO_0000704
RO_0002162: 1141660
locus tag: OO7_RS16115
old locus tag: OO7_16395
so part of: sequence
location: complement(3163..3423)
location: region:3163-3423:-1
so has part: feature:3163-3423:-1:exon
subclass of: SO_0000010

position:3163:-1
position: 3163
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3423:-1
position: 3423
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3163-3423:-1:exon

OO7_RS16115
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1141660
locus tag: OO7_RS16115
old locus tag: OO7_16395
inference: COORDINATES: similar to AA sequence:RefSeq:WP_001324694.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 4
product: plasmid replication protein
translation: MRVNRDGLTQKELAKKFNVSITTVIKYTAIDREDYEKEALNRRKTAYELREKGLSWKEVAEAMQCSYNAVTSLAKRYKQQDLKESV
SIO_010081: OO7_RS16115
subclass of: SO_0000673
so part of: OO7_RS16115
location: complement(3163..3423)
location: region:3163-3423:-1
so has part: feature:3163-3423:-1:exon

WP_008917004.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3163-3423:-1:exon

OO7_RS16120
type: Gene
subclass of: SO_0000704
RO_0002162: 1141660
locus tag: OO7_RS16120
old locus tag: OO7_16400
so part of: sequence
location: complement(3434..4279)
location: region:3434-4279:-1
so has part: feature:3434-4279:-1:exon
subclass of: SO_0000010

position:3434:-1
position: 3434
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4279:-1
position: 4279
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3434-4279:-1:exon

OO7_RS16120
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1141660
locus tag: OO7_RS16120
old locus tag: OO7_16400
inference: COORDINATES: protein motif:HMM:NF015076.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 4
product: replication initiation protein
translation: MFNNDNRQNFISQMPMKPYCSDDLSNGLRIRKKEKALEMLYIQANQPAIQTCLLFDLDEENCFYKFEEVNLPVPHFITKSPKSGRCHYGYILKNGVCKTQQAKLKPLRYASAVENSIANRLGSDPNYVGLITKNPLNSHWSPWWSGAELYDLDYLADFVDLNQPKSVKAENYGLGRNVNLFDDLRAWSYKRVLGFKSSSSFEQWMKEVERQAINLNAVCNQQNPLPFNEIKATARSIGKWTWKNFDVAKFSEIQSARGKKNLGKKKITIKNKAKYWICLIF
SIO_010081: OO7_RS16120
subclass of: SO_0000673
so part of: OO7_RS16120
location: complement(3434..4279)
location: region:3434-4279:-1
so has part: feature:3434-4279:-1:exon

WP_282553645.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3434-4279:-1:exon