Staphylococcus capitis subsp. capitis strain H17 plasmid unnamed1, complete sequence.
type: Entry
definition: Staphylococcus capitis subsp. capitis strain H17 plasmid unnamed1, complete sequence.
sequence version: NZ_CP102090.1
sequence date: 2023-03-26
sequence: sequence
division: CON
label: NZ_CP102090.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN29057146
keyword: RefSeq
source: Staphylococcus capitis subsp. capitis
organism: Staphylococcus capitis subsp. capitis
taxonomy: Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae; Staphylococcus.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP102090.1.\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 :: 08-OCT-2021\nAssembly Method :: Unicycler v. 0.4.9\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 65.0x\nSequencing Technology :: Illumina MiSeq; Oxford Nanopore MinION\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/26/2023 11:38:45\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) :: 2,410\nCDSs (total) :: 2,324\nGenes (coding) :: 2,289\nCDSs (with protein) :: 2,289\nGenes (RNA) :: 86\nrRNAs :: 7, 6, 6 (5S, 16S, 23S)\ncomplete rRNAs :: 7, 6, 6 (5S, 16S, 23S)\ntRNAs :: 63\nncRNAs :: 4\nPseudo Genes (total) :: 35\nCDSs (without protein) :: 35\nPseudo Genes (ambiguous residues) :: 0 of 35\nPseudo Genes (frameshifted) :: 13 of 35\nPseudo Genes (incomplete) :: 19 of 35\nPseudo Genes (internal stop) :: 9 of 35\nPseudo Genes (multiple problems) :: 5 of 35\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 9274
topology: circular
so has quality: SO_0000988
location: 1..9274
location: region:1-9274:1
RO_0002162: 72758

NZ_CP102090
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN29057146
type: BioSample
SIO_000068: biosample

1
title: Phenotypic and genomic assessment of the potential threat of human spaceflight-relevant Staphylococcus capitis isolates under stress conditions
author: Siems, K.
journal: Unpublished

2
title: Direct Submission
author: Siems, K.
journal: Submitted (29-JUL-2022) Radiation Biology, German Aerospace Center (DLR), Linder Hoehe, Cologne, NRW 51147, Germany

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

position:9274:1
position: 9274
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-9274:1:source
so part of: sequence
organism: Staphylococcus capitis subsp. capitis
mol type: genomic DNA
strain: H17
isolation source: human skin, forehead (bedrest study)
sub species: capitis
culture collection: DSM:113836
plasmid: unnamed1
country: Germany
collection date: 2019

72758
type: Taxonomy
SIO_000068: taxonomy

NF392_RS12010
type: Gene
subclass of: SO_0000704
RO_0002162: 72758
locus tag: NF392_RS12010
so part of: sequence
location: 9..101
location: region:9-101:1
so has part: feature:9-101:1:exon
subclass of: SO_0000010

77314780
type: Gene
SIO_000068: ncbigene

position:9:1
position: 9
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:101:1
position: 101
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:9-101:1:exon

NF392_RS12010
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 72758
locus tag: NF392_RS12010
inference: COORDINATES: protein motif:HMM:NF033608.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: type I toxin-antitoxin system Fst family toxin
translation: MSLIFVCIIAPIIVECCVAIFTFWLNNRNK
SIO_010081: NF392_RS12010
subclass of: SO_0000673
so part of: NF392_RS12010
location: 9..101
location: region:9-101:1
so has part: feature:9-101:1:exon

WP_115172131.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:9-101:1:exon

NF392_RS12015
type: Gene
subclass of: SO_0000704
RO_0002162: 72758
locus tag: NF392_RS12015
so part of: sequence
location: complement(370..1230)
location: region:370-1230:-1
so has part: feature:370-1230:-1:exon
subclass of: SO_0000010

77314781
type: Gene
SIO_000068: ncbigene

position:370:-1
position: 370
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:1230:-1
position: 1230
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:370-1230:-1:exon

NF392_RS12015
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 72758
locus tag: NF392_RS12015
inference: COORDINATES: similar to AA sequence:RefSeq:WP_001829553.1
GO function: GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO process: GO:0006270 - DNA replication initiation [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: RepB family plasmid replication initiator protein
translation: MSGETVVYRNEMNLVPLRRFTSTEVDLFFTLCNKLKEQDTRKVIIPFEELKYLSNYYTRSQERFINDLEHVYDKMLNLTYVERNDRSFEKFVLFTSYKLDLDEECLSISVNPDLKHILNSITADFTKFELKEMTHLKSTYAKNMFRLLKQYKHTGYIKINIADFKNRLDIPKTYQMNDITKRVLKPIINELSSIFNNLNINKIKAKKGRKIEWLEFTFDAEKRIHNKRQPQITNIGKSHQYTNREKTPKWLETGLYKGQHAHTDYDPQLKKDREAFQRQLEEKWEE
SIO_010081: NF392_RS12015
subclass of: SO_0000673
so part of: NF392_RS12015
location: complement(370..1230)
location: region:370-1230:-1
so has part: feature:370-1230:-1:exon

WP_002452565.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:370-1230:-1:exon

NF392_RS12020
type: Gene
subclass of: SO_0000704
RO_0002162: 72758
gene: mobV
locus tag: NF392_RS12020
so part of: sequence
location: complement(1861..3069)
location: region:1861-3069:-1
so has part: feature:1861-3069:-1:exon
subclass of: SO_0000010

77314782
type: Gene
SIO_000068: ncbigene

position:1861:-1
position: 1861
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3069:-1
position: 3069
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1861-3069:-1:exon

NF392_RS12020
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 72758
gene: mobV
locus tag: NF392_RS12020
inference: COORDINATES: similar to AA sequence:RefSeq:WP_002958641.1
GO function: GO:0003677 - DNA binding [Evidence IEA]
GO process: GO:0006310 - DNA recombination [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: MobV family relaxase
translation: MKLAWNTQKNKMSDVKGKEMEQERKGRIKNDEIDLKRTNLNFDLVEDERHLYHRVKDRVDYYKEQGSRVQKNSVVMYSNIITLSKEEADRMGETRTKHYFKTCKDYFSERFGEANVVSAKVHMDESAPHMHLHFIPVNHQGRLSARTAMNRQAIHHIHDELTTHLCQQGFDVERGSTDDNKTYIQDIHEYKRKAKVLSELDQQIETKKQLLRDINDLHDEKENLTRDIQNLKRKNHFLQEDSQQAQEDIDLYKQLRTISRDDFKKEEEKYQQEIEAYEASLSGLRMNYRDLDKRNQHLTTQNNQLEHHLDMLNARHQTMNDMVRNDTRILFAGLRCALKDRNIDLSAEIKYQRMPEVGIDPDTVDQGALTHAYQGNVSGIDHHIRKASAPIKKETENDLELE
SIO_010081: NF392_RS12020
subclass of: SO_0000673
so part of: NF392_RS12020
location: complement(1861..3069)
location: region:1861-3069:-1
so has part: feature:1861-3069:-1:exon

WP_260832889.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1861-3069:-1:exon

NF392_RS12025
type: Gene
subclass of: SO_0000704
RO_0002162: 72758
locus tag: NF392_RS12025
so part of: sequence
location: 3524..3934
location: region:3524-3934:1
so has part: feature:3524-3934:1:exon
subclass of: SO_0000010

77314783
type: Gene
SIO_000068: ncbigene

position:3524:1
position: 3524
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:3934:1
position: 3934
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3524-3934:1:exon

NF392_RS12025
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 72758
locus tag: NF392_RS12025
inference: COORDINATES: similar to AA sequence:RefSeq:WP_002958643.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MPKKQNSKEKILTIRVSQSQYEKICALADIREMNVTEYIRHTAIGNRIKPTVIEQIKESSEVSELFKKDNEALKSSNQALQRHIHQLEDEIDQLRQENDVFHHLLQHFDSTAFMNFNTYRDDRPLKNAIKRLKEQQ
SIO_010081: NF392_RS12025
subclass of: SO_0000673
so part of: NF392_RS12025
location: 3524..3934
location: region:3524-3934:1
so has part: feature:3524-3934:1:exon

WP_143978091.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3524-3934:1:exon

NF392_RS12030
type: Gene
subclass of: SO_0000704
RO_0002162: 72758
gene: hemA
locus tag: NF392_RS12030
pseudo: true
so part of: sequence
location: complement(4099..5285)
location: region:4099-5285:-1
so has part: feature:4099-5285:-1:exon
subclass of: SO_0000010

77314784
type: Gene
SIO_000068: ncbigene

position:4099:-1
position: 4099
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:5285:-1
position: 5285
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4099-5285:-1:exon

NF392_RS12030
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 72758
gene: hemA
locus tag: NF392_RS12030
inference: COORDINATES: similar to AA sequence:RefSeq:WP_019468027.1
GO function: GO:0003870 - 5-aminolevulinate synthase activity [Evidence IEA]
GO process: GO:0006783 - heme biosynthetic process [Evidence IEA]
note: frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
pseudo: true
codon start: 1
transl table: 11
product: 5-aminolevulinate synthase
SIO_010081: NF392_RS12030
subclass of: SO_0000673
so part of: NF392_RS12030
location: complement(4099..5285)
location: region:4099-5285:-1
so has part: feature:4099-5285:-1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:4099-5285:-1:exon

NF392_RS12035
type: Gene
subclass of: SO_0000704
RO_0002162: 72758
locus tag: NF392_RS12035
so part of: sequence
location: complement(5286..6431)
location: region:5286-6431:-1
so has part: feature:5286-6431:-1:exon
subclass of: SO_0000010

77314785
type: Gene
SIO_000068: ncbigene

position:5286:-1
position: 5286
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:6431:-1
position: 6431
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5286-6431:-1:exon

NF392_RS12035
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 72758
locus tag: NF392_RS12035
inference: COORDINATES: similar to AA sequence:RefSeq:WP_019468028.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: MFS transporter
translation: MKKIWILTIGMFALGMDAYIVAGLIPSISQSFNKNSSAIGQGVTVFTLFFSISAPIFSTILAKSPVKKILVIAISVFTLANIITAISMNYTVYIISRAIAGLGAGVFSPIAISASNHLVSEKHKGKAIAFTVGGMSVGTVIGVPLGLEISKLSNWRFAMLVIIVISFIALISISILMPKFKIQAPPNLKDRFQLFLNRHVLRVISVTLCAAVASLGLYTYLADIIKANTDIKSLTYYLTAWGIGGLIGSFGIGFVIDKFKNTRLVMLIILILLALSFVLIPVSIKLPLLGLLPFILWGAMGWATQAPQQHILLKNHPKHGGSAVALNSSINYLGSAIGSAIGGIILFNVNNTNVLIYSALGITIIGILLQLLNISIDREKL
SIO_010081: NF392_RS12035
subclass of: SO_0000673
so part of: NF392_RS12035
location: complement(5286..6431)
location: region:5286-6431:-1
so has part: feature:5286-6431:-1:exon

WP_103175433.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5286-6431:-1:exon

NF392_RS12040
type: Gene
subclass of: SO_0000704
RO_0002162: 72758
locus tag: NF392_RS12040
so part of: sequence
location: complement(6434..7492)
location: region:6434-7492:-1
so has part: feature:6434-7492:-1:exon
subclass of: SO_0000010

77314786
type: Gene
SIO_000068: ncbigene

position:6434:-1
position: 6434
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:7492:-1
position: 7492
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:6434-7492:-1:exon

NF392_RS12040
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 72758
locus tag: NF392_RS12040
inference: COORDINATES: protein motif:HMM:NF013567.2
GO function: GO:0016491 - oxidoreductase activity [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: Gfo/Idh/MocA family oxidoreductase
translation: MNVLIIGMGFAGNMYQQVLSHLKKYDNYSLNIAYHSKSRNNFSIKYYSTLRTALKEHKPSLIIVTVNDVYHLEILNELKDFKGTILCEKPLVANQEQLDIIKNSLSNEINLILSTVIRFSRASQKLKNFLKNRKTSIKKINFVWKKNRINDYRPTVGVISEVIHPLDTIQWLLDKNINIQNTLTTSSNYSVDRNKKTLDSVFILGETDDKEVISGYSSFISLQVERSIEIVLKDLELDTHFFITLTFDKDEWFSDKLIIFQEDQEGYKEIINFNSMDIKTHYSKKIERTLLMVKNILNSEMKSTDLCLKEDTFSIQSLLNDISKNEPKSEIDYDFSSKNILKKNSTTFDRIG
SIO_010081: NF392_RS12040
subclass of: SO_0000673
so part of: NF392_RS12040
location: complement(6434..7492)
location: region:6434-7492:-1
so has part: feature:6434-7492:-1:exon

WP_103175434.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:6434-7492:-1:exon

NF392_RS12045
type: Gene
subclass of: SO_0000704
RO_0002162: 72758
locus tag: NF392_RS12045
so part of: sequence
location: complement(7507..7986)
location: region:7507-7986:-1
so has part: feature:7507-7986:-1:exon
subclass of: SO_0000010

77314787
type: Gene
SIO_000068: ncbigene

position:7507:-1
position: 7507
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:7986:-1
position: 7986
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:7507-7986:-1:exon

NF392_RS12045
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 72758
locus tag: NF392_RS12045
inference: COORDINATES: protein motif:HMM:NF025054.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: GNAT family N-acetyltransferase
translation: MIYFSTAEVDDIDSVASFRMILLNNGKSHYGSANNDELLKIKNHFKSWMKKNLKKDDVHIVISKNDDEEIISMGIGIIDNRAPVQGSLNGKSGWISSLIVHPNYRKQGLGKETLNTLIKWFDMNYVSKIILHSTKEGEFLYNKLGFLKDNENIFIKTIY
SIO_010081: NF392_RS12045
subclass of: SO_0000673
so part of: NF392_RS12045
location: complement(7507..7986)
location: region:7507-7986:-1
so has part: feature:7507-7986:-1:exon

WP_103175435.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:7507-7986:-1:exon

NF392_RS12050
type: Gene
subclass of: SO_0000704
RO_0002162: 72758
locus tag: NF392_RS12050
so part of: sequence
location: 8094..8954
location: region:8094-8954:1
so has part: feature:8094-8954:1:exon
subclass of: SO_0000010

77314788
type: Gene
SIO_000068: ncbigene

position:8094:1
position: 8094
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:8954:1
position: 8954
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:8094-8954:1:exon

NF392_RS12050
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 72758
locus tag: NF392_RS12050
inference: COORDINATES: similar to AA sequence:RefSeq:WP_002489187.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: LysR family transcriptional regulator
translation: MDFNYMKDFIKVVEYNSLNKASKELNISTPALSKRIKSIENYFDCDLFYRTSKGIFLTKSGNIVFHSFLKMNEQIKDLKNKISNSKNRKIRLGVIPSFSLYKLHERNYLTKNVVLVIENSTSVLIEELYKDNIDVIIGDITNLRNDSLYIEKIYTEDFIVAYADKNKFTNTKQVNVKSLKKENIYIQTPPCDTYNFLKSYSLKDKLHINYVDYYETILANVKANKGITLTPQSLTTRLESMNLYQKKLQNYKRVVGVVSHDKSKMNKIIDIIQSMNRLYNSTTYNS
SIO_010081: NF392_RS12050
subclass of: SO_0000673
so part of: NF392_RS12050
location: 8094..8954
location: region:8094-8954:1
so has part: feature:8094-8954:1:exon

WP_103175436.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:8094-8954:1:exon