Kocuria flava strain HO-9041 plasmid 3, complete sequence.
type: Entry
definition: Kocuria flava strain HO-9041 plasmid 3, complete sequence.
sequence version: NZ_CP013257.1
sequence date: 2023-02-06
sequence: sequence
division: CON
label: NZ_CP013257.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN04270876
keyword: RefSeq
source: Kocuria flava
organism: Kocuria flava
taxonomy: Bacteria; Actinomycetota; Actinomycetes; Micrococcales; Micrococcaceae; Kocuria.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP013257.1.\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 :: SOAP denovo v. 2.04\nGenome Coverage :: 505\nSequencing Technology :: Illumina\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 02/05/2023 20:16:33\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) :: 3,304\nCDSs (total) :: 3,242\nGenes (coding) :: 3,189\nCDSs (with protein) :: 3,189\nGenes (RNA) :: 62\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 50\nncRNAs :: 3\nPseudo Genes (total) :: 53\nCDSs (without protein) :: 53\nPseudo Genes (ambiguous residues) :: 0 of 53\nPseudo Genes (frameshifted) :: 18 of 53\nPseudo Genes (incomplete) :: 34 of 53\nPseudo Genes (internal stop) :: 5 of 53\nPseudo Genes (multiple problems) :: 4 of 53\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 5666
topology: circular
so has quality: SO_0000988
location: 1..5666
location: region:1-5666:1
RO_0002162: 446860

NZ_CP013257
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN04270876
type: BioSample
SIO_000068: biosample

1
title: Complete Genome Sequence of Kocuria flava strain HO-9041
author: Zhou, M.
author: Dai, J.
journal: Unpublished

2
title: Direct Submission
author: Zhou, M.
author: Dai, J.
journal: Submitted (24-NOV-2015) Food and Pharmaceutical Engineering, Hubei University of Technology, 28 Nanli Street, Wuhan, Hubei 430068, China

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

position:5666:1
position: 5666
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-5666:1:source
so part of: sequence
organism: Kocuria flava
mol type: genomic DNA
strain: HO-9041
isolation source: air
culture collection: CCTCC:AB 206106
type material: type strain of Kocuria flava
plasmid: 3
country: China: Xinjiang
collection date: 2008-03-09

446860
type: Taxonomy
SIO_000068: taxonomy

AS188_RS16225
type: Gene
subclass of: SO_0000704
RO_0002162: 446860
locus tag: AS188_RS16225
old locus tag: AS188_16225
so part of: sequence
location: join(5385..5666,1..117)
location: region:1-5666:1
so has part: feature:5385-5666:1:exon
so has part: feature:1-117:1:exon
subclass of: SO_0000010

urn:…
SIO_000300: 1
SIO_000628: feature:5385-5666:1:exon

position:5385:1
position: 5385
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 2
SIO_000628: feature:1-117:1:exon

position:117:1
position: 117
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

AS188_RS16225
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 446860
locus tag: AS188_RS16225
old locus tag: AS188_16225
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: MPNPPHPGPDVHPAYWPALAYAGADEAKTHARAVRWALHAGDPDQAIEAAEAATAAAEKSRYGAEQTARYAPAKEAEARAHAEEAEATARAARRKSAFRDDWGKLFSVYVNEADGTVFATNKAPGGSGCSEY
SIO_010081: AS188_RS16225
subclass of: SO_0000673
so part of: AS188_RS16225
location: join(5385..5666,1..117)
location: region:1-5666:1
so has part: feature:5385-5666:1:exon
so has part: feature:1-117:1:exon

WP_058860105.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5385-5666:1:exon

urn:…
SIO_000300: 2
SIO_000628: feature:1-117:1:exon

AS188_RS16230
type: Gene
subclass of: SO_0000704
RO_0002162: 446860
locus tag: AS188_RS16230
old locus tag: AS188_16230
so part of: sequence
location: complement(316..972)
location: region:316-972:-1
so has part: feature:316-972:-1:exon
subclass of: SO_0000010

position:316:-1
position: 316
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:972:-1
position: 972
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:316-972:-1:exon

AS188_RS16230
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 446860
locus tag: AS188_RS16230
old locus tag: AS188_16230
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: MPTTAEDFALHAWGDESYREDPGADPLYLLGAVVADPTMCEDLRDQLRTVQREAVEDLQERYAKAKTPANSRTLQKARRKLHWHDIKDDRKGSAVELIASFDMLHVIVVAAPVAPKKQERARRLCLEQLSWRLDGIGVSCLFLESRSEGQNQRDRNLVESLRGRQAFPPGLRLEHVHPSDEPMVWVPDQVLGAVGAEERGDRQYVERIGLIDRVPIDL
SIO_010081: AS188_RS16230
subclass of: SO_0000673
so part of: AS188_RS16230
location: complement(316..972)
location: region:316-972:-1
so has part: feature:316-972:-1:exon

WP_147050694.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:316-972:-1:exon

AS188_RS16235
type: Gene
subclass of: SO_0000704
RO_0002162: 446860
locus tag: AS188_RS16235
old locus tag: AS188_16235
so part of: sequence
location: 1395..2426
location: region:1395-2426:1
so has part: feature:1395-2426:1:exon
subclass of: SO_0000010

position:1395:1
position: 1395
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2426:1
position: 2426
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1395-2426:1:exon

AS188_RS16235
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 446860
locus tag: AS188_RS16235
old locus tag: AS188_16235
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: MTGTSDATGHALTEWPPLTATTVDRDGLFPADLTPAYPRKSPGLPPVIACDYWPMTDTTGQPETVDPATMTGRSDGRQSGRHVAEQPAADARQGAKEAPVTATVDALQTFNLKEAAEVTGLSVSTMRRRRAELAKLGATVTEDGVWSIPITALEAAGLLDTTRPEESAPAEAPEAPGDAPVSPSLAPEAPEQPEIDSDPLEQLRALEAELAATRERLAEEERQRVEERHRAELAEVRQAAAEQRARAAEVLAEERRQTLEVERRMLTAGPAVYAPSWPTPEAGYQQPRQQSAPQPEEPAEEQPASRPTEPAASEAPTEQPASEQPAASPQAPTRRRWRDWLGL
SIO_010081: AS188_RS16235
subclass of: SO_0000673
so part of: AS188_RS16235
location: 1395..2426
location: region:1395-2426:1
so has part: feature:1395-2426:1:exon

WP_058860102.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1395-2426:1:exon

AS188_RS16240
type: Gene
subclass of: SO_0000704
RO_0002162: 446860
locus tag: AS188_RS16240
old locus tag: AS188_16240
so part of: sequence
location: 2851..4353
location: region:2851-4353:1
so has part: feature:2851-4353:1:exon
subclass of: SO_0000010

position:2851:1
position: 2851
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:4353:1
position: 4353
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2851-4353:1:exon

AS188_RS16240
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 446860
locus tag: AS188_RS16240
old locus tag: AS188_16240
inference: COORDINATES: protein motif:HMM:NF025107.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: helix-turn-helix domain-containing protein
translation: MPHKSTERTAPVSTTAPVAPCELPAGVIDLDQARRVRLHGYDKFDLEDVAETDPNLTHAEFRTFMALWKHADSETLEARPTQGTIAKRLNLNDAKTAGRRIDALAAKGYLIVKRTGYFDKATGRNIASLYRLTMPAGAMTEAERKAAAQAEIRADSVPGGGVGVTTNPTVGVTTNPTGGFTTTPLTNQETNQETDQKNPAAATAPPPADSRDVDNSINYGRGGYDADGTPWESTVKAAWIAWAQAVGNTTAEAGALDALLSLIAARNGEDAADWARDYWGWHDARALDICLAPSLDAARYEAGAQYSNMLNAAAADPYRAVTVNNPPRVHRQQPVTVVDRDNAAAVAAEAEQLHATGQLNPDVAAWLDAQPKAAPATTAPAAENHDTDPADAEQLHTAQVEKELAARIAEQEAEDRRRRARARLDARYLAEAERTAAALEETDTASPQDWAEAAVLFADYPAAHDVCTAPEPTPDFEYLADPTPEDHAEFVRLFLTSSAA
SIO_010081: AS188_RS16240
subclass of: SO_0000673
so part of: AS188_RS16240
location: 2851..4353
location: region:2851-4353:1
so has part: feature:2851-4353:1:exon

WP_058860103.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2851-4353:1:exon

AS188_RS16245
type: Gene
subclass of: SO_0000704
RO_0002162: 446860
locus tag: AS188_RS16245
old locus tag: AS188_16245
so part of: sequence
location: 4356..5207
location: region:4356-5207:1
so has part: feature:4356-5207:1:exon
subclass of: SO_0000010

position:4356:1
position: 4356
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:5207:1
position: 5207
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4356-5207:1:exon

AS188_RS16245
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 446860
locus tag: AS188_RS16245
old locus tag: AS188_16245
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: MENPTVGKPLSPAKEDRARQALTAALNARKHPEAPAPVVPGPRLRQAFRDGTEAALDEYTATAPPNGEGPPITWGRMIRMFAATRGTLRARGFSRKIADDYAAAVTVHVADLLRKLPAGTDLRRTVLESIPREPLDPNTVWPRVFPLFNEHESWEEFLAAVRGVFAEANAETAKGITETAAAPGPLDPEALEAAALKAARWTWEKFTTSAAILDALRARLSLDESRPVDLAEIAAEAGADEQTTAAAVDNMERKGYLIRDVEDGQPATYRLAPEPPTEDGATA
SIO_010081: AS188_RS16245
subclass of: SO_0000673
so part of: AS188_RS16245
location: 4356..5207
location: region:4356-5207:1
so has part: feature:4356-5207:1:exon

WP_147050692.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4356-5207:1:exon