Pseudomonas fragi strain NL20W plasmid unnamed1, complete sequence.
type: Entry
definition: Pseudomonas fragi strain NL20W plasmid unnamed1, complete sequence.
sequence version: NZ_CP064355.1
sequence date: 2022-12-03
sequence: sequence
division: CON
label: NZ_CP064355.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN16674530
keyword: RefSeq
source: Pseudomonas fragi
organism: Pseudomonas fragi
taxonomy: Bacteria; Pseudomonadota; Gammaproteobacteria; Pseudomonadales; Pseudomonadaceae; Pseudomonas.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP064355.1.\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 :: 2020\nAssembly Method :: unicycler v. 0.4.8\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 200.0x\nSequencing Technology :: Illumina; Nanopore\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/03/2022 03:46:02\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\nGenes (total) :: 4,649\nCDSs (total) :: 4,547\nGenes (coding) :: 4,488\nCDSs (with protein) :: 4,488\nGenes (RNA) :: 102\nrRNAs :: 9, 8, 8 (5S, 16S, 23S)\ncomplete rRNAs :: 9, 8, 8 (5S, 16S, 23S)\ntRNAs :: 73\nncRNAs :: 4\nPseudo Genes (total) :: 60\nCDSs (without protein) :: 59\nPseudo Genes (ambiguous residues) :: 0 of 60\nPseudo Genes (frameshifted) :: 10 of 60\nPseudo Genes (incomplete) :: 42 of 60\nPseudo Genes (internal stop) :: 11 of 60\nPseudo Genes (multiple problems) :: 4 of 60\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 4480
topology: circular
so has quality: SO_0000988
location: 1..4480
location: region:1-4480:1
RO_0002162: 296

NZ_CP064355
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN16674530
type: BioSample
SIO_000068: biosample

1
title: The complete genome sequence of Pseudomonas fragi NL20W, a wonderful lactose oxidation biocatalyst
author: Zheng, Z.
author: Wu, J.
author: Ou, Y.
journal: Unpublished

2
title: Direct Submission
author: Zheng, Z.
journal: Submitted (06-NOV-2020) College of Chemical Engineering, Nanjing Forestry University, Longpan Road 159, Xuanwu District, Nanjing, Jiangsu 210037, China

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

position:4480:1
position: 4480
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-4480:1:source
so part of: sequence
organism: Pseudomonas fragi
mol type: genomic DNA
strain: NL20W
isolation source: soil
plasmid: unnamed1
country: China:Nanjing
collection date: 2019-09-27

296
type: Taxonomy
SIO_000068: taxonomy

IS178_RS23130
type: Gene
subclass of: SO_0000704
RO_0002162: 296
locus tag: IS178_RS23130
old locus tag: IS178_23130
so part of: sequence
location: 368..796
location: region:368-796:1
so has part: feature:368-796:1:exon
subclass of: SO_0000010

72390705
type: Gene
SIO_000068: ncbigene

position:368:1
position: 368
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:796:1
position: 796
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:368-796:1:exon

IS178_RS23130
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 296
locus tag: IS178_RS23130
old locus tag: IS178_23130
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: MQRLVKPSDYVLQDVLGQSMYQIPWEPRLCPGSPAEDPEAGALLYNAFVQDQAKGVVPRTPAEQMSDILDWVFETAGEPARSLAADLAAAYLGNHAFLIDDLDDWDAETKSHRAHMVFHGEDIRGLSARTVMKLRARAAAGF
SIO_010081: IS178_RS23130
subclass of: SO_0000673
so part of: IS178_RS23130
location: 368..796
location: region:368-796:1
so has part: feature:368-796:1:exon

WP_084357100.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:368-796:1:exon

IS178_RS23135
type: Gene
subclass of: SO_0000704
RO_0002162: 296
locus tag: IS178_RS23135
old locus tag: IS178_23135
so part of: sequence
location: 895..1143
location: region:895-1143:1
so has part: feature:895-1143:1:exon
subclass of: SO_0000010

72390706
type: Gene
SIO_000068: ncbigene

position:895:1
position: 895
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1143:1
position: 1143
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:895-1143:1:exon

IS178_RS23135
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 296
locus tag: IS178_RS23135
old locus tag: IS178_23135
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: MRMTFGSACRNAGLMAVVYFLYVGFQKGHFDVFGWYGVGWSWGDWLVLAVLTGVFGVILFEEWWGQRKRAKAKAREQGEDFQ
SIO_010081: IS178_RS23135
subclass of: SO_0000673
so part of: IS178_RS23135
location: 895..1143
location: region:895-1143:1
so has part: feature:895-1143:1:exon

WP_010657470.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:895-1143:1:exon

IS178_RS23140
type: Gene
subclass of: SO_0000704
RO_0002162: 296
locus tag: IS178_RS23140
old locus tag: IS178_23140
so part of: sequence
location: complement(1207..1497)
location: region:1207-1497:-1
so has part: feature:1207-1497:-1:exon
subclass of: SO_0000010

72390707
type: Gene
SIO_000068: ncbigene

position:1207:-1
position: 1207
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:1497:-1
position: 1497
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1207-1497:-1:exon

IS178_RS23140
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 296
locus tag: IS178_RS23140
old locus tag: IS178_23140
inference: COORDINATES: protein motif:HMM:TIGR02385.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: type II toxin-antitoxin system RelE/ParE family toxin
translation: MPKIALTSKADSDLEGIYEHYEPRLGAEKAEEVISQVLEAITRLETFPQLGKASDIPDCRELIISKYPYRSIYTRKGDTILIYRILHQHAERPEDW
SIO_010081: IS178_RS23140
subclass of: SO_0000673
so part of: IS178_RS23140
location: complement(1207..1497)
location: region:1207-1497:-1
so has part: feature:1207-1497:-1:exon

WP_084357101.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1207-1497:-1:exon

IS178_RS23145
type: Gene
subclass of: SO_0000704
RO_0002162: 296
locus tag: IS178_RS23145
old locus tag: IS178_23145
so part of: sequence
location: complement(1460..1723)
location: region:1460-1723:-1
so has part: feature:1460-1723:-1:exon
subclass of: SO_0000010

72390708
type: Gene
SIO_000068: ncbigene

position:1460:-1
position: 1460
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:1723:-1
position: 1723
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1460-1723:-1:exon

IS178_RS23145
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 296
locus tag: IS178_RS23145
old locus tag: IS178_23145
inference: COORDINATES: similar to AA sequence:RefSeq:WP_003198119.1
GO process: GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: ribbon-helix-helix protein, CopG family
translation: MASPVLSFRVESELINQLDQLAEATDRDRQYHLKRALARYVESESWHFRAVAEGIADAEAGNLIDLDAVKAKWVARAENRINQQSGQ
SIO_010081: IS178_RS23145
subclass of: SO_0000673
so part of: IS178_RS23145
location: complement(1460..1723)
location: region:1460-1723:-1
so has part: feature:1460-1723:-1:exon

WP_010657468.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1460-1723:-1:exon

IS178_RS23150
type: Gene
subclass of: SO_0000704
RO_0002162: 296
locus tag: IS178_RS23150
old locus tag: IS178_23150
so part of: sequence
location: 2016..2333
location: region:2016-2333:1
so has part: feature:2016-2333:1:exon
subclass of: SO_0000010

72390709
type: Gene
SIO_000068: ncbigene

position:2016:1
position: 2016
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2333:1
position: 2333
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2016-2333:1:exon

IS178_RS23150
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 296
locus tag: IS178_RS23150
old locus tag: IS178_23150
inference: COORDINATES: similar to AA sequence:RefSeq:WP_010657467.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MPLPVTPYYERRLRDLRTLSPAAAALAERIALDLQPQMLATSTEMLEAQLLDHLQEVAEQQTRCVTRFWDWLNAVVDAGALPPPQAAVFACEAATLGGPSGVVPE
SIO_010081: IS178_RS23150
subclass of: SO_0000673
so part of: IS178_RS23150
location: 2016..2333
location: region:2016-2333:1
so has part: feature:2016-2333:1:exon

WP_084357102.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2016-2333:1:exon

IS178_RS23155
type: Gene
subclass of: SO_0000704
RO_0002162: 296
locus tag: IS178_RS23155
old locus tag: IS178_23155
so part of: sequence
location: 2330..2590
location: region:2330-2590:1
so has part: feature:2330-2590:1:exon
subclass of: SO_0000010

72390710
type: Gene
SIO_000068: ncbigene

position:2330:1
position: 2330
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2590:1
position: 2590
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2330-2590:1:exon

IS178_RS23155
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 296
locus tag: IS178_RS23155
old locus tag: IS178_23155
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: MSGRYGNGSDPLAAISTSPAVLATLRRRMTAIELAADTLQVHLASERAQGFVEMLEELKVLKPADIESLYLTIDDAAQARVTALLL
SIO_010081: IS178_RS23155
subclass of: SO_0000673
so part of: IS178_RS23155
location: 2330..2590
location: region:2330-2590:1
so has part: feature:2330-2590:1:exon

WP_084357103.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2330-2590:1:exon

IS178_RS23160
type: Gene
subclass of: SO_0000704
RO_0002162: 296
locus tag: IS178_RS23160
old locus tag: IS178_23160
so part of: sequence
location: 2587..2835
location: region:2587-2835:1
so has part: feature:2587-2835:1:exon
subclass of: SO_0000010

72390711
type: Gene
SIO_000068: ncbigene

position:2587:1
position: 2587
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2835:1
position: 2835
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2587-2835:1:exon

IS178_RS23160
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 296
locus tag: IS178_RS23160
old locus tag: IS178_23160
inference: COORDINATES: similar to AA sequence:RefSeq:WP_010657465.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MIGDGIHEDALQHLVQQNAVREFVAGRDTTRTKWTFSVRLGGPHSRLILVRSRREAIRTWASLTAVGRFAEGLGVRGFAVEL
SIO_010081: IS178_RS23160
subclass of: SO_0000673
so part of: IS178_RS23160
location: 2587..2835
location: region:2587-2835:1
so has part: feature:2587-2835:1:exon

WP_073510320.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2587-2835:1:exon

IS178_RS23165
type: Gene
subclass of: SO_0000704
RO_0002162: 296
locus tag: IS178_RS23165
old locus tag: IS178_23165
so part of: sequence
location: complement(2867..3286)
location: region:2867-3286:-1
so has part: feature:2867-3286:-1:exon
subclass of: SO_0000010

72390712
type: Gene
SIO_000068: ncbigene

position:2867:-1
position: 2867
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3286:-1
position: 3286
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2867-3286:-1:exon

IS178_RS23165
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 296
locus tag: IS178_RS23165
old locus tag: IS178_23165
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: MAKLTIGRMAKLYGLHRSTLHEAVSKGRVTAGLDGKGQKVIDLSEMIRVYGEPQGITLHRPTLDPTPSPYTSPTPEIDALHPALHSLVEEVRLLRAEIQELQQSLRLIEHKPEPKPALPHNTKPGEAPTWANLLDALDN
SIO_010081: IS178_RS23165
subclass of: SO_0000673
so part of: IS178_RS23165
location: complement(2867..3286)
location: region:2867-3286:-1
so has part: feature:2867-3286:-1:exon

WP_073515003.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2867-3286:-1:exon