Kocuria flava strain HO-9041 plasmid 2, complete sequence.
type: Entry
definition: Kocuria flava strain HO-9041 plasmid 2, complete sequence.
sequence version: NZ_CP013256.1
sequence date: 2023-02-06
sequence: sequence
division: CON
label: NZ_CP013256.1
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\nCP013256.1.\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: 10611
topology: circular
so has quality: SO_0000988
location: 1..10611
location: region:1-10611:1
RO_0002162: 446860

NZ_CP013256
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journal: Unpublished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:10611:1
position: 10611
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-10611:1: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: 2
country: China: Xinjiang
collection date: 2008-03-09

446860
type: Taxonomy
SIO_000068: taxonomy

AS188_RS16190
type: Gene
subclass of: SO_0000704
RO_0002162: 446860
locus tag: AS188_RS16190
old locus tag: AS188_16190
so part of: sequence
location: 208..414
location: region:208-414:1
so has part: feature:208-414:1:exon
subclass of: SO_0000010

position:208:1
position: 208
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:414:1
position: 414
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:208-414:1:exon

AS188_RS16190
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 446860
locus tag: AS188_RS16190
old locus tag: AS188_16190
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: MILVGVMLAVLGMLLLFMLARVTVVEIDQFRRTAAVATLGVIMVAATLLSTGTALIGVSALLSFSAFR
SIO_010081: AS188_RS16190
subclass of: SO_0000673
so part of: AS188_RS16190
location: 208..414
location: region:208-414:1
so has part: feature:208-414:1:exon

WP_143709977.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:208-414:1:exon

AS188_RS16195
type: Gene
subclass of: SO_0000704
RO_0002162: 446860
locus tag: AS188_RS16195
old locus tag: AS188_16195
so part of: sequence
location: complement(610..2478)
location: region:610-2478:-1
so has part: feature:610-2478:-1:exon
subclass of: SO_0000010

position:610:-1
position: 610
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:2478:-1
position: 2478
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:610-2478:-1:exon

AS188_RS16195
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 446860
locus tag: AS188_RS16195
old locus tag: AS188_16195
inference: COORDINATES: similar to AA sequence:RefSeq:WP_012086883.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: S9 family peptidase
translation: MTNQVPVPVGEVIELAHHLVEAWGSWGPTMTPDARRVAFISDRCGVPEVWVQEVVLNGQPPEAIRLKFSDDPVVAVRWSPDSAWLACAVATHGGVRTQVWAVRPDGTDARLLAGSPQLHAELGPWTRSGHHVIITIPSVEPGEQTRSFLVNPADAAMVPVTEGELIHVLDVSVEERLIVVRDGQRGQEFCEVFDRLTDQHHPLLPDRSTGTTEVALLRPSPPTAPGPLTAYVVTDAGLPRRQLIAMALSVDGVQGQPRTLAAREDAELENLDADDAGRRLLLSWNVAGCSELELLDTTTGQRTPLRGLPGLVATDPVLSRDGNSIVMAVEGPERPRELWHVETSTHRWTRITSTPRLPRWHTIEPTLETYRARDGLTLTGWLYRAPGAREPGPAALYLHGGPEGQERPTFNPQHQAMATAGITVFAPNVRGSSGFGRAFVHADEVHHRYDAFEDVLASADHLIRLGVADPARIAVTGRSYGGYLTLASLAFFPAVFAAGVDICGMSDLHTFYRDTEPWIAAAAITKYGHPERDRELLHAISPLRQAHRITAPLLVIHGELDTNVPLGEARQIVTTLEKLGRPVQYLQLAGEGHEYRRAHSRKMLITTMLQFLSKHLELVPQP
SIO_010081: AS188_RS16195
subclass of: SO_0000673
so part of: AS188_RS16195
location: complement(610..2478)
location: region:610-2478:-1
so has part: feature:610-2478:-1:exon

WP_058860097.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:610-2478:-1:exon

AS188_RS16200
type: Gene
subclass of: SO_0000704
RO_0002162: 446860
locus tag: AS188_RS16200
old locus tag: AS188_16200
so part of: sequence
location: complement(2779..3207)
location: region:2779-3207:-1
so has part: feature:2779-3207:-1:exon
subclass of: SO_0000010

position:2779:-1
position: 2779
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3207:-1
position: 3207
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2779-3207:-1:exon

AS188_RS16200
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 446860
locus tag: AS188_RS16200
old locus tag: AS188_16200
inference: COORDINATES: similar to AA sequence:RefSeq:WP_011691966.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: Hsp20/alpha crystallin family protein
translation: MAGLMRRDAFDMLEPFRRLLEGDLQSDLNVSWPKVEEFQDGEAMVIRAELPDIDPDQDVELTVANDMLRLRAERREKSEHKDKATYRSEFRYGSFVRTLPLPAGTKEEDITATYKDGVLEVRAPVTEPDQVPGTKKIPVTRG
SIO_010081: AS188_RS16200
subclass of: SO_0000673
so part of: AS188_RS16200
location: complement(2779..3207)
location: region:2779-3207:-1
so has part: feature:2779-3207:-1:exon

WP_058860098.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2779-3207:-1:exon

AS188_RS16205
type: Gene
subclass of: SO_0000704
RO_0002162: 446860
locus tag: AS188_RS16205
old locus tag: AS188_16205
so part of: sequence
location: complement(3522..3595)
location: region:3522-3595:-1
so has part: feature:3522-3595:-1:exon
subclass of: SO_0000663

position:3522:-1
position: 3522
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3595:-1
position: 3595
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3522-3595:-1:exon

AS188_RS16205
type: Transfer RNA
subclass of: SO_0000253
RO_0002162: 446860
locus tag: AS188_RS16205
old locus tag: AS188_16205
product: tRNA-Gln
inference: COORDINATES: profile:tRNAscan-SE:2.0.12
note: Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
anticodon: (pos:complement(3559..3561),aa:Gln,seq:ctg)
SIO_010081: AS188_RS16205
subclass of: SO_0000673
so part of: AS188_RS16205
location: complement(3522..3595)
location: region:3522-3595:-1
so has part: feature:3522-3595:-1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:3522-3595:-1:exon

AS188_RS16210
type: Gene
subclass of: SO_0000704
RO_0002162: 446860
gene: glgX
locus tag: AS188_RS16210
old locus tag: AS188_16210
so part of: sequence
location: complement(3833..6022)
location: region:3833-6022:-1
so has part: feature:3833-6022:-1:exon
subclass of: SO_0000010

position:3833:-1
position: 3833
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:6022:-1
position: 6022
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3833-6022:-1:exon

AS188_RS16210
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 446860
gene: glgX
locus tag: AS188_RS16210
old locus tag: AS188_16210
inference: COORDINATES: similar to AA sequence:RefSeq:WP_003805335.1
GO function: GO:0004133 - glycogen debranching enzyme activity [Evidence IEA]
GO process: GO:0005980 - glycogen catabolic process [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: glycogen debranching protein GlgX
translation: MDVWTGSPYPLGATYDGNGTNFAVFSEAATAVHLCLFDAEGTEHRIALEAVDAFVWHCYLPHVIPGQKYGYRVEGPYDPSRGVRCNPAKLLLDPYAKAISGQVRWGPAVFSHHPGDPGSFNAEDSAPSTMRSVVISPFFDWQGDRPPRIPYHDSVIYEAHVKGLTILHPEVPAAERGTYAGVAHPAVIEHLQKLGVTAIELMPVHQFVHDGLLLDKGLCNYWGYNSIGFFAPHNAYSSTAEPGQQVQEFKAMVRSLHRAGIEVILDVVYNHTAEGNHLGPTLAFKGLDNSAYYRLVEGEKQYYMDYTGTGNTLNVRHPHALQLIMDSLRYWVTEMHVDGFRFDLAATLAREFYDVDRLASFFDLVQQDPVVSQVKLIAEPWDIGPGGYQVGNFPPQWTEWNGRYRDAVRDFWRGAPATLGEFASRLAGSADLYESSGRRPFASINFVTAHDGFTLRDLVSYNEKHNQANGEDNNDGESHNRSWNCGVEGPTDDPEVLALRARQQRNFLATLLLSQGVPMLVHGDELGRSQNGNNNAYCQDNELTWINWESMDAPLSEFVAAVARLRRQHPTFRRNRFFSGRPVDREQGQPLPDIVWLNPDASPMVPADWGQPLARALGVFYNGAAIGKDWRGRTITDVNFLLCFNSHDGPVTFTLPPAEYAPQWEVVLDTAGKSAGTRLVAADAPLEVAGKSVLILRAYTAPPAEPDHSVAASLAILTAGTDATAPSTS
SIO_010081: AS188_RS16210
subclass of: SO_0000673
so part of: AS188_RS16210
location: complement(3833..6022)
location: region:3833-6022:-1
so has part: feature:3833-6022:-1:exon

WP_058860099.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3833-6022:-1:exon

AS188_RS16215
type: Gene
subclass of: SO_0000704
RO_0002162: 446860
gene: ftsH
locus tag: AS188_RS16215
old locus tag: AS188_16215
so part of: sequence
location: complement(7463..9514)
location: region:7463-9514:-1
so has part: feature:7463-9514:-1:exon
subclass of: SO_0000010

position:7463:-1
position: 7463
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:9514:-1
position: 9514
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:7463-9514:-1:exon

AS188_RS16215
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 446860
gene: ftsH
locus tag: AS188_RS16215
old locus tag: AS188_16215
inference: COORDINATES: similar to AA sequence:RefSeq:WP_009482803.1
GO function: GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0004222 - metalloendopeptidase activity [Evidence IEA]
GO process: GO:0051301 - cell division [Evidence IEA]; GO:0006508 - proteolysis [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: ATP-dependent zinc metalloprotease FtsH
translation: MADRTKSDGNTGTREQRPARFARWSRWRRDAPAPRPWRTEGLPEDGQGPQKPGWWRLLAWFLMWWFLLFTLTTLQDVGSAQVASVPYTEFTDQVRDGNVEEVFARGNTIQGVLREPVERPEGEGAYTEFTTERPVFAQDDLLAALETRGAEVSATPVTTERGFLANLFISLLPVALLVWFWLWLLRRQTGGAGGLLGRGRKPRRVDPAEIRVTFADVAGIDEVKGQVAEIVDFLKNPDKYRKLGARMPKGVLLEGPPGTGKTLLARATAGEAGVPFFSASAAEFIEMIVGVGASRVRELFGEARKVAPAIVFIDEIDTIGRARSAVGSVGGRDEHEQTLNQILTEMDGFTGTEGVVVLAATNRADILDPALTRAGRFDRKITVGVPDQHGREQILAVHTRKVPLAPEVDLAHIARTTPGMTGADLANLVNEAALLAARRGHEQVSTRDFTDALEKVQLGAERSVVLPREERLRTAYHEAGHALLGMLQPGADPVRKISIVPRGRALGVTLSTPETDRYGYDRDYLKGRIIGALGGMAAEEEVFGVITTGAESDLQTATGIARQMIGRWGMSPRVGPVQVYPLEGDPRQAGASEALLEAVDEEVRTLIADCYAEARRLLADNRDRLEAIVAALMERESLDEAEVYAVVGIERRPASSQLVGAASDSPVRENPAGDTVATHRRDG
SIO_010081: AS188_RS16215
subclass of: SO_0000673
so part of: AS188_RS16215
location: complement(7463..9514)
location: region:7463-9514:-1
so has part: feature:7463-9514:-1:exon

WP_083529640.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:7463-9514:-1:exon

AS188_RS16220
type: Gene
subclass of: SO_0000704
RO_0002162: 446860
locus tag: AS188_RS16220
old locus tag: AS188_16220
so part of: sequence
location: complement(9930..10595)
location: region:9930-10595:-1
so has part: feature:9930-10595:-1:exon
subclass of: SO_0000010

position:9930:-1
position: 9930
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:10595:-1
position: 10595
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:9930-10595:-1:exon

AS188_RS16220
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 446860
locus tag: AS188_RS16220
old locus tag: AS188_16220
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: MSASNLIVRQSLAVDDKAERDSHTTGQEVAAQGPRPDTSRSGIMRAMEWLSVAVALLALVAAVWAVVELRRMKRTAQHRDAVSQQEGRRRQANEVMAWLSAELGKPSDRGSVIEVHNRSGAPIYDLVVMSSDLVYRDHRRVRVDNPRLAVRIFPPGHLIYGLDPEHAWDLGHRPDEYERLRPVTMSPDRRVTAFEFTDASGTRWRRYEDGVLEEVAPEPDE
SIO_010081: AS188_RS16220
subclass of: SO_0000673
so part of: AS188_RS16220
location: complement(9930..10595)
location: region:9930-10595:-1
so has part: feature:9930-10595:-1:exon

WP_058860100.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:9930-10595:-1:exon