Rothia amarae strain KJZ-9 plasmid p2, complete sequence.
type: Entry
definition: Rothia amarae strain KJZ-9 plasmid p2, complete sequence.
sequence version: NZ_CP062958.1
sequence date: 2023-02-22
sequence: sequence
division: CON
label: NZ_CP062958.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN16132388
keyword: RefSeq
source: Rothia amarae
organism: Rothia amarae
taxonomy: Bacteria; Actinomycetota; Actinomycetes; Micrococcales; Micrococcaceae; Rothia.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP062958.1.\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 :: Unicycler v. 0.4.8\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 409.0x\nSequencing Technology :: Oxford Nanopore; Illumina\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 02/22/2023 16:07:22\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) :: 2,309\nCDSs (total) :: 2,246\nGenes (coding) :: 2,218\nCDSs (with protein) :: 2,218\nGenes (RNA) :: 63\nrRNAs :: 4, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 4, 3, 3 (5S, 16S, 23S)\ntRNAs :: 50\nncRNAs :: 3\nPseudo Genes (total) :: 28\nCDSs (without protein) :: 28\nPseudo Genes (ambiguous residues) :: 0 of 28\nPseudo Genes (frameshifted) :: 13 of 28\nPseudo Genes (incomplete) :: 13 of 28\nPseudo Genes (internal stop) :: 11 of 28\nPseudo Genes (multiple problems) :: 9 of 28\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 4524
topology: circular
so has quality: SO_0000988
location: 1..4524
location: region:1-4524:1
RO_0002162: 169480

NZ_CP062958
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN16132388
type: BioSample
SIO_000068: biosample

1
title: Investigation of environmental microbe
author: Ou, Y.
author: Kang, Q.
journal: Unpublished

2
title: Direct Submission
author: Ou, Y.
author: Kang, Q.
journal: Submitted (29-SEP-2020) School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan RD., Shanghai 200240, China

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

position:4524:1
position: 4524
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-4524:1:source
so part of: sequence
organism: Rothia amarae
mol type: genomic DNA
strain: KJZ-9
isolation source: dirt
plasmid: p2
country: China: Minhang
collection date: 2019-12-20

169480
type: Taxonomy
SIO_000068: taxonomy

IDM48_RS11525
type: Gene
subclass of: SO_0000704
RO_0002162: 169480
locus tag: IDM48_RS11525
old locus tag: IDM48_11500
so part of: sequence
location: complement(192..464)
location: region:192-464:-1
so has part: feature:192-464:-1:exon
subclass of: SO_0000010

position:192:-1
position: 192
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:464:-1
position: 464
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:192-464:-1:exon

IDM48_RS11525
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 169480
locus tag: IDM48_RS11525
old locus tag: IDM48_11500
inference: COORDINATES: similar to AA sequence:RefSeq:WP_006947269.1
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: MSALKPVRRQFTAREAAERLGVTTRTVQRLMAEPREQYLARANSKREQVAELRANGLSVRAIAEKLEISKSAAGRYVQEYETRINQPSAS
SIO_010081: IDM48_RS11525
subclass of: SO_0000673
so part of: IDM48_RS11525
location: complement(192..464)
location: region:192-464:-1
so has part: feature:192-464:-1:exon

WP_238398090.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:192-464:-1:exon

IDM48_RS11530
type: Gene
subclass of: SO_0000704
RO_0002162: 169480
locus tag: IDM48_RS11530
old locus tag: IDM48_11505
so part of: sequence
location: complement(451..1323)
location: region:451-1323:-1
so has part: feature:451-1323:-1:exon
subclass of: SO_0000010

position:451:-1
position: 451
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:1323:-1
position: 1323
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:451-1323:-1:exon

IDM48_RS11530
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 169480
locus tag: IDM48_RS11530
old locus tag: IDM48_11505
inference: COORDINATES: protein motif:HMM:NF015076.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: replication initiation protein
translation: MSFENVFTEHWLPQKPLCSHRKDGSYKRQTRARALEHAYIETNPLAMQSLIVTDHDGADADYIADLAGLPQPSWVAMNPQTRSGHIVYALNSPVCLTDAAHRAPVNLLARVEQGLTDVLGGDIGYGGRITKNPTHNAHMPLWGEAEALYGLRELARALGDVGALPAPHRQAQTVLDSTVGRNVALFNITRQWAYRARLRYTDSTEWAETVYAFASMKNASVIADEFSRGPMSESEVAQIAKSIAGWVWGNITPEQTKANRARWAKNLEQGRVQKMKERLEALEAMNSERT
SIO_010081: IDM48_RS11530
subclass of: SO_0000673
so part of: IDM48_RS11530
location: complement(451..1323)
location: region:451-1323:-1
so has part: feature:451-1323:-1:exon

WP_202939954.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:451-1323:-1:exon

IDM48_RS11535
type: Gene
subclass of: SO_0000704
RO_0002162: 169480
locus tag: IDM48_RS11535
old locus tag: IDM48_11510
so part of: sequence
location: complement(1564..2479)
location: region:1564-2479:-1
so has part: feature:1564-2479:-1:exon
subclass of: SO_0000010

position:1564:-1
position: 1564
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:2479:-1
position: 2479
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1564-2479:-1:exon

IDM48_RS11535
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 169480
locus tag: IDM48_RS11535
old locus tag: IDM48_11510
inference: COORDINATES: similar to AA sequence:RefSeq:WP_012803697.1
ribosomal slippage: true
GO function: GO:0004803 - transposase activity [Evidence IEA]
note: programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: IS5 family transposase
translation: MAKVRSRFRVFSDEEWARIEPLLPSNEGRRGHPFGHNRKVVEGIAYRYRTGIPWRDLPREEYGPWQTVWKRHRRYAEDGTWDRVLTQILAEADAEGKIEWSVSVDATIARAHQHASNTTRPEQDTGACSNYKNSPLDEVEPAGHGVGRSRGGLTTKIHHAVDGKGRPLAIVVTGGQRNDGAMLLEVLADISVPRLGRGRARTRPDAVIADRAYATGVIRTELRRRRITAVIPAKSDQIAARKRRGSKGGRPHGFDAEAYKGRNVVERSFNKSKQWRGLATRYDKLAITYRAAATILAIITWLRT
SIO_010081: IDM48_RS11535
subclass of: SO_0000673
so part of: IDM48_RS11535
location: complement(join(1564..2103,2105..2479))
location: region:1564-2479:-1
so has part: feature:2105-2479:-1:exon
so has part: feature:1564-2103:-1:exon

WP_238398091.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2105-2479:-1:exon

position:2105:-1
position: 2105
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 2
SIO_000628: feature:1564-2103:-1:exon

position:2103:-1
position: 2103
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

IDM48_RS11540
type: Gene
subclass of: SO_0000704
RO_0002162: 169480
locus tag: IDM48_RS11540
old locus tag: IDM48_11515
so part of: sequence
location: 2612..3217
location: region:2612-3217:1
so has part: feature:2612-3217:1:exon
subclass of: SO_0000010

position:2612:1
position: 2612
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:3217:1
position: 3217
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2612-3217:1:exon

IDM48_RS11540
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 169480
locus tag: IDM48_RS11540
old locus tag: IDM48_11515
inference: COORDINATES: similar to AA sequence:RefSeq:WP_010119327.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: DUF1269 domain-containing protein
translation: MMTQYAAAVTFPDNATAYQTISELRDSSLIQSITAAALVERDQNGQLRVPEGDDSVIGLGAAGGSLVGMLIGVIGGPLGMLLGVSSGALVGGLFDLNRADKAETALAEFGQAVQPGHNALVLQTDEPDTTALDGFVKGKGGTIIRRPLDEVVDELEAQQAAAEAAADAADAKLREQRREERKEKWDERVENLRKKFSRGEK
SIO_010081: IDM48_RS11540
subclass of: SO_0000673
so part of: IDM48_RS11540
location: 2612..3217
location: region:2612-3217:1
so has part: feature:2612-3217:1:exon

WP_238398089.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2612-3217:1:exon

IDM48_RS11545
type: Gene
subclass of: SO_0000704
RO_0002162: 169480
locus tag: IDM48_RS11545
old locus tag: IDM48_11520
so part of: sequence
location: 3163..3477
location: region:3163-3477:1
so has part: feature:3163-3477:1:exon
subclass of: SO_0000010

position:3163:1
position: 3163
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:3477:1
position: 3477
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3163-3477:1:exon

IDM48_RS11545
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 169480
locus tag: IDM48_RS11545
old locus tag: IDM48_11520
inference: COORDINATES: similar to AA sequence:RefSeq:WP_003847959.1
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: MGRACGEPAQEVLARREVGPSPAALARELELTRSNVSNHLTCLRDCGIVVADPEGRKTRYEIVDAHLAQALNLLLDTTLAADENAPCIDSACDVPGCATGEGNR
SIO_010081: IDM48_RS11545
subclass of: SO_0000673
so part of: IDM48_RS11545
location: 3163..3477
location: region:3163-3477:1
so has part: feature:3163-3477:1:exon

WP_202939953.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3163-3477:1:exon

IDM48_RS11550
type: Gene
subclass of: SO_0000704
RO_0002162: 169480
locus tag: IDM48_RS11550
old locus tag: IDM48_11525
so part of: sequence
location: 3478..4071
location: region:3478-4071:1
so has part: feature:3478-4071:1:exon
subclass of: SO_0000010

position:3478:1
position: 3478
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:4071:1
position: 4071
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3478-4071:1:exon

IDM48_RS11550
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 169480
locus tag: IDM48_RS11550
old locus tag: IDM48_11525
inference: COORDINATES: similar to AA sequence:RefSeq:WP_003859025.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: cadmium resistance transporter
translation: MVTSLLGAVGLFIATNIDDIIVLSLFFARGAGQAGTTLRILTGQYLGFAGILAATILVTLGADAFLPTEAIPYFGLIPLALGLWAAWQAWRGDDDDDDAKVSGKNVSVLTVAGVTFANGGDNIGVYVPVFLHVNTATVIIYCVVFLILVAGLVLLAKFVATRPPIAEVLERWEHVLFPIVLIGLGIFILVSGGAFGL
SIO_010081: IDM48_RS11550
subclass of: SO_0000673
so part of: IDM48_RS11550
location: 3478..4071
location: region:3478-4071:1
so has part: feature:3478-4071:1:exon

WP_190616929.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3478-4071:1:exon