Rothia amarae strain KJZ-9 plasmid p3, complete sequence.
type: Entry
definition: Rothia amarae strain KJZ-9 plasmid p3, complete sequence.
sequence version: NZ_CP062959.1
sequence date: 2023-02-22
sequence: sequence
division: CON
label: NZ_CP062959.1
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\nCP062959.1.\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: 4444
topology: circular
so has quality: SO_0000988
location: 1..4444
location: region:1-4444:1
RO_0002162: 169480

NZ_CP062959
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journal: Unpublished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:4444:1
position: 4444
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-4444:1:source
so part of: sequence
organism: Rothia amarae
mol type: genomic DNA
strain: KJZ-9
isolation source: dirt
plasmid: p3
country: China: Minhang
collection date: 2019-12-20

169480
type: Taxonomy
SIO_000068: taxonomy

IDM48_RS11555
type: Gene
subclass of: SO_0000704
RO_0002162: 169480
locus tag: IDM48_RS11555
old locus tag: IDM48_11530
so part of: sequence
location: join(4219..4444,1..1067)
location: region:1-4444:1
so has part: feature:4219-4444:1:exon
so has part: feature:1-1067:1:exon
subclass of: SO_0000010

urn:…
SIO_000300: 1
SIO_000628: feature:4219-4444:1:exon

position:4219:1
position: 4219
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 2
SIO_000628: feature:1-1067:1:exon

position:1067:1
position: 1067
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

IDM48_RS11555
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 169480
locus tag: IDM48_RS11555
old locus tag: IDM48_11530
inference: COORDINATES: ab initio prediction:GeneMarkS-2+
GO function: GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0000166 - nucleotide binding [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
codon start: 1
transl table: 11
product: FtsK/SpoIIIE domain-containing protein
translation: MASTYLLTDLPKIKEFWESVGSDSTSKKPEITPGIAPHDALYYDRLKEVWADFCDTIGVNKSSTEERLSKSALILRREMVKKKYEVQDRSQVIETSSVNRGLQWLFTIPLGSQLSTYEKHLDYLSAALGGVDIEIESAGVGLGRMLARTVDPLEGSRDVAIYHSLTSETAVRMGRREDGQDLYIDMADAGHTIIQGQTRSGKSVFLYGLLSQLAYVDCVKIWGIDPNHVLLGPFRGLTPQIVLGTDPLAHLELLEEFVARMDSRIASLVTEGIEKISDFTPESPVEVLVLEEYASIIRGAEIYDCTQKPADRVGNKIKALVARIFAEGAKAGMRVILVIQRADASLVDGSTRANAVNRLTMGVDNGDAVRMLHPGASPELIEAITHFKNGRLFASIQREDTIAQADYIDYQDYRRAVQLSETAPAPIDYP
SIO_010081: IDM48_RS11555
subclass of: SO_0000673
so part of: IDM48_RS11555
location: join(4219..4444,1..1067)
location: region:1-4444:1
so has part: feature:4219-4444:1:exon
so has part: feature:1-1067:1:exon

WP_202939960.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4219-4444:1:exon

urn:…
SIO_000300: 2
SIO_000628: feature:1-1067:1:exon

IDM48_RS11560
type: Gene
subclass of: SO_0000704
RO_0002162: 169480
locus tag: IDM48_RS11560
old locus tag: IDM48_11535
so part of: sequence
location: 1510..2841
location: region:1510-2841:1
so has part: feature:1510-2841:1:exon
subclass of: SO_0000010

position:1510:1
position: 1510
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2841:1
position: 2841
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1510-2841:1:exon

IDM48_RS11560
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 169480
locus tag: IDM48_RS11560
old locus tag: IDM48_11535
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: MRERREVRYDLRERARQLAKSVPAQQAIRQRKKKADLFDAVIHESTQQGGHLFTLEKLPTWQSHRLTHCGKTVRDLQEPVIFRENADSAGIVNLQSCGSYACPVCAPKIANRRFEEVREVLTVAKEAGYDVAMVTMTLRHSKSDRLETLWDGLLAGWRKAVTHKDWVGESIELYEQSRQSWLERGEMHEMGLGRAPRGWKKQAGVFRLRRIGKREELGVFAPMRAIELTRGEAGWHPHIHALFVFKAEASDEVSKLAQAAQIGGFFHEKFESGIAEYGLESLANSGGLDVQVMKGTAESIASYATKMALEATRADLKKGRMGGETPLQLLERAVEGEEDAVYAWQDFATVSQGRRWLTISKVLRDFAKLSEEKSDQEIAEEETTGLEVAEVTAREWKKNRLWLKSSRLLRVLEEDGAESLFEEFKAWNVMYSDVREIKEPPQP
SIO_010081: IDM48_RS11560
subclass of: SO_0000673
so part of: IDM48_RS11560
location: 1510..2841
location: region:1510-2841:1
so has part: feature:1510-2841:1:exon

WP_202939961.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1510-2841:1:exon

IDM48_RS11565
type: Gene
subclass of: SO_0000704
RO_0002162: 169480
locus tag: IDM48_RS11565
old locus tag: IDM48_11540
so part of: sequence
location: complement(2856..3266)
location: region:2856-3266:-1
so has part: feature:2856-3266:-1:exon
subclass of: SO_0000010

position:2856:-1
position: 2856
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3266:-1
position: 3266
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2856-3266:-1:exon

IDM48_RS11565
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 169480
locus tag: IDM48_RS11565
old locus tag: IDM48_11540
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: MMFHDETQLLRFMTHDVTLCLMEDIDKIIARQEEKSRALYAELTAEGHIKMAEIERILKELEKIPEHIRSGPGTYDEGEDATLTAIEKYRRISDLAQEALRSSAEELLKRRYPQTEIAEAAGVTRQTIVRWKQAMK
SIO_010081: IDM48_RS11565
subclass of: SO_0000673
so part of: IDM48_RS11565
location: complement(2856..3266)
location: region:2856-3266:-1
so has part: feature:2856-3266:-1:exon

WP_202939957.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2856-3266:-1:exon

IDM48_RS11570
type: Gene
subclass of: SO_0000704
RO_0002162: 169480
locus tag: IDM48_RS11570
old locus tag: IDM48_11545
so part of: sequence
location: 3336..3701
location: region:3336-3701:1
so has part: feature:3336-3701:1:exon
subclass of: SO_0000010

position:3336:1
position: 3336
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:3701:1
position: 3701
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3336-3701:1:exon

IDM48_RS11570
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 169480
locus tag: IDM48_RS11570
old locus tag: IDM48_11545
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: MRATSLPVLTNSDLFPLVAMGMGGTPRQREKPAPTGEATYASGAILFVDRKGVPVADKSASIHVLSPDPVPLGQLLQAQGKIWVQPYESNGRSALSITVERLVPLSDGLDEINELMMEDED
SIO_010081: IDM48_RS11570
subclass of: SO_0000673
so part of: IDM48_RS11570
location: 3336..3701
location: region:3336-3701:1
so has part: feature:3336-3701:1:exon

WP_202939958.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3336-3701:1:exon

IDM48_RS11575
type: Gene
subclass of: SO_0000704
RO_0002162: 169480
locus tag: IDM48_RS11575
old locus tag: IDM48_11550
so part of: sequence
location: 3703..4026
location: region:3703-4026:1
so has part: feature:3703-4026:1:exon
subclass of: SO_0000010

position:3703:1
position: 3703
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:4026:1
position: 4026
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3703-4026:1:exon

IDM48_RS11575
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 169480
locus tag: IDM48_RS11575
old locus tag: IDM48_11550
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: MIRSYSASRAFDRFPGDFSDVTKSQLNQAKLNLHSIEAFIHAVQATPEDSPRLWEFWENSVSFYLTLGEAFYPDDFFDIYKESAILRQLYRGVDEGFALRSTRQPVA
SIO_010081: IDM48_RS11575
subclass of: SO_0000673
so part of: IDM48_RS11575
location: 3703..4026
location: region:3703-4026:1
so has part: feature:3703-4026:1:exon

WP_202939959.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3703-4026:1:exon