Macrococcus equipercicus strain Epi0143-OL plasmid pEpi0143-OL-2, complete sequence.
type: Entry
definition: Macrococcus equipercicus strain Epi0143-OL plasmid pEpi0143-OL-2, complete sequence.
sequence version: NZ_CP073811.1
sequence date: 2023-07-21
sequence: sequence
division: CON
label: NZ_CP073811.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN18897987
keyword: RefSeq
source: Macrococcus equipercicus
organism: Macrococcus equipercicus
taxonomy: Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae; Macrococcus.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP073811.1.\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 :: 300x\nSequencing Technology :: Oxford Nanopore MinION; Illumina NovaSeq\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 07/21/2023 04:16:28\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.5\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 2,340\nCDSs (total) :: 2,256\nGenes (coding) :: 2,237\nCDSs (with protein) :: 2,237\nGenes (RNA) :: 84\nrRNAs :: 6, 5, 5 (5S, 16S, 23S)\ncomplete rRNAs :: 6, 5, 5 (5S, 16S, 23S)\ntRNAs :: 64\nncRNAs :: 4\nPseudo Genes (total) :: 19\nCDSs (without protein) :: 19\nPseudo Genes (ambiguous residues) :: 0 of 19\nPseudo Genes (frameshifted) :: 2 of 19\nPseudo Genes (incomplete) :: 18 of 19\nPseudo Genes (internal stop) :: 4 of 19\nPseudo Genes (multiple problems) :: 4 of 19\nCRISPR Arrays :: 1\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 8752
topology: circular
so has quality: SO_0000988
location: 1..8752
location: region:1-8752:1
RO_0002162: 69967

NZ_CP073811
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN18897987
type: BioSample
SIO_000068: biosample

1
title: Complete Genome Sequences of Macrococcus spp. from dog and cattle
author: Schwendener, S.
author: Perreten, V.
journal: Unpublished

2
title: Direct Submission
author: Schwendener, S.
author: Perreten, V.
journal: Submitted (28-APR-2021) Institute of Veterinary Bacteriology, University of Bern, Langgassstrasse 122, Bern 3012, Switzerland

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

position:8752:1
position: 8752
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-8752:1:source
so part of: sequence
organism: Macrococcus equipercicus
mol type: genomic DNA
strain: Epi0143-OL
isolation source: Ear swab
host: dog
plasmid: pEpi0143-OL-2
country: Switzerland
collection date: 2017

69967
type: Taxonomy
SIO_000068: taxonomy

KFV11_RS11510
type: Gene
subclass of: SO_0000704
RO_0002162: 69967
locus tag: KFV11_RS11510
old locus tag: KFV11_11505
so part of: sequence
location: 38..865
location: region:38-865:1
so has part: feature:38-865:1:exon
subclass of: SO_0000010

position:38:1
position: 38
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:865:1
position: 865
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:38-865:1:exon

KFV11_RS11510
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 69967
locus tag: KFV11_RS11510
old locus tag: KFV11_11505
inference: COORDINATES: protein motif:HMM:NF019884.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: HTH domain-containing protein
translation: MNDFDNNFETIIAMDRTVERYNRYLKKTEYLILNVLKQHSLKIIGYSHLKLQTIADLLHISKKTVYRTLKNLDEKGYITKIHTVSGKRKNNGALVFRINTYTQYEVIREKNVHAKMSTLNQVIKTGKELSQQALQHVHAKQETIFFLNLLNIFLSNRKRLNKTHSKVLYHNIKNSDIRVKPMEVPDAIYNVAKPFFSDEEILSLYKTMLKETISNNIYDTENHIEIMIYAIKSLVKAKKKEFNGLASKIKNDRAYYIGILREYIGQHYFVYNAVI
SIO_010081: KFV11_RS11510
subclass of: SO_0000673
so part of: KFV11_RS11510
location: 38..865
location: region:38-865:1
so has part: feature:38-865:1:exon

WP_254250638.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:38-865:1:exon

KFV11_RS11515
type: Gene
subclass of: SO_0000704
RO_0002162: 69967
locus tag: KFV11_RS11515
old locus tag: KFV11_11510
so part of: sequence
location: complement(869..1372)
location: region:869-1372:-1
so has part: feature:869-1372:-1:exon
subclass of: SO_0000010

position:869:-1
position: 869
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:1372:-1
position: 1372
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:869-1372:-1:exon

KFV11_RS11515
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 69967
locus tag: KFV11_RS11515
old locus tag: KFV11_11510
inference: COORDINATES: similar to AA sequence:RefSeq:WP_012655843.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MPLSLIVFIIGITMSTWTPLSPLPFYQQHLHVQKVNEQYKVAESYLDNLMNKGFLDFNTTVKKHVTHRHFSVAQQKINRIDDRDKRKALMNKHSEYLAIYEQHIGDHLIQKIQLEYLSVSEYSHLTAQDYDNVRYQIRQQIQNSQTEKDFLERIQKLQKEHDTLYSQ
SIO_010081: KFV11_RS11515
subclass of: SO_0000673
so part of: KFV11_RS11515
location: complement(869..1372)
location: region:869-1372:-1
so has part: feature:869-1372:-1:exon

WP_246143169.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:869-1372:-1:exon

KFV11_RS11520
type: Gene
subclass of: SO_0000704
RO_0002162: 69967
locus tag: KFV11_RS11520
old locus tag: KFV11_11515
so part of: sequence
location: complement(1672..2772)
location: region:1672-2772:-1
so has part: feature:1672-2772:-1:exon
subclass of: SO_0000010

position:1672:-1
position: 1672
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:2772:-1
position: 2772
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1672-2772:-1:exon

KFV11_RS11520
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 69967
locus tag: KFV11_RS11520
old locus tag: KFV11_11515
inference: COORDINATES: protein motif:HMM:NF015397.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: relaxase/mobilization nuclease domain-containing protein
translation: MAQTKVASSKSATASIKYGRDGKDKDTQEKKCIAMSGINCDPSNAEYEFGVVRKAFNKAKNEGKDIQAHLVEQSFKGRDIDPFEVNQMGYELAERLNEELGGGFQAVVYTHGNTNNYHNHIVFNAVNLEDGHKYHCYQEKKIVERINDAIVREHGYPVIEKNKERGTSVTIKEQKLKDKGEYVWKDDLRDTIDKAFEKTKDSLHFDLERFKAHLTDLGVNIRERFNQKQKITRFSYDFIDQDGKQRVTREKNLGVDYGAEGIKYGLEQERKSYEQFKQQQSGFTPSPASRTSDIEIPEGRDSIQQYAGQVLDARIRDTGNERTQREPRTRDEHSHQRKQSTQDRTPKDHSVKSKQNRQHDRGGLER
SIO_010081: KFV11_RS11520
subclass of: SO_0000673
so part of: KFV11_RS11520
location: complement(1672..2772)
location: region:1672-2772:-1
so has part: feature:1672-2772:-1:exon

WP_254250639.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1672-2772:-1:exon

KFV11_RS11525
type: Gene
subclass of: SO_0000704
RO_0002162: 69967
locus tag: KFV11_RS11525
old locus tag: KFV11_11520
so part of: sequence
location: complement(2754..3149)
location: region:2754-3149:-1
so has part: feature:2754-3149:-1:exon
subclass of: SO_0000010

position:2754:-1
position: 2754
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3149:-1
position: 3149
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2754-3149:-1:exon

KFV11_RS11525
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 69967
locus tag: KFV11_RS11525
old locus tag: KFV11_11520
inference: COORDINATES: similar to AA sequence:RefSeq:WP_012655831.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MSETKKKSKIISFRVNADEYDVIAGTASSANLNITSYLKARALGGKIHRPLMKSEDIQSILPPLSKLSGEISRVGNNMNQSTRALKVLSRESFLEQQEMNEVKKLTEEFNALKQEFEMLQSEVHQIWHKLK
SIO_010081: KFV11_RS11525
subclass of: SO_0000673
so part of: KFV11_RS11525
location: complement(2754..3149)
location: region:2754-3149:-1
so has part: feature:2754-3149:-1:exon

WP_254250640.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2754-3149:-1:exon

KFV11_RS11530
type: Gene
subclass of: SO_0000704
RO_0002162: 69967
locus tag: KFV11_RS11530
old locus tag: KFV11_11525
so part of: sequence
location: complement(3716..4087)
location: region:3716-4087:-1
so has part: feature:3716-4087:-1:exon
subclass of: SO_0000010

position:3716:-1
position: 3716
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4087:-1
position: 4087
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3716-4087:-1:exon

KFV11_RS11530
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 69967
locus tag: KFV11_RS11530
old locus tag: KFV11_11525
inference: COORDINATES: similar to AA sequence:RefSeq:WP_012655832.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MTNIDYEKELQALEEKRKQLLKEKREKDRKELQMLKEVFGKDFPRKENGKFISLDEFKKNYMISHKDQSAIDPNELNAVQEELNQLKKALNGIANAMDDSKGYWHVSDLKGLTNWLSQFRTKN
SIO_010081: KFV11_RS11530
subclass of: SO_0000673
so part of: KFV11_RS11530
location: complement(3716..4087)
location: region:3716-4087:-1
so has part: feature:3716-4087:-1:exon

WP_254250641.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3716-4087:-1:exon

KFV11_RS11535
type: Gene
subclass of: SO_0000704
RO_0002162: 69967
locus tag: KFV11_RS11535
old locus tag: KFV11_11530
so part of: sequence
location: 4250..4342
location: region:4250-4342:1
so has part: feature:4250-4342:1:exon
subclass of: SO_0000010

position:4250:1
position: 4250
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:4342:1
position: 4342
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4250-4342:1:exon

KFV11_RS11535
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 69967
locus tag: KFV11_RS11535
old locus tag: KFV11_11530
inference: COORDINATES: similar to AA sequence:RefSeq:WP_020006632.1
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: MDFLLVNVIAPIIVGVILMLFSHWLDQRKS
SIO_010081: KFV11_RS11535
subclass of: SO_0000673
so part of: KFV11_RS11535
location: 4250..4342
location: region:4250-4342:1
so has part: feature:4250-4342:1:exon

WP_133418524.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4250-4342:1:exon

KFV11_RS11540
type: Gene
subclass of: SO_0000704
RO_0002162: 69967
locus tag: KFV11_RS11540
old locus tag: KFV11_11535
so part of: sequence
location: 5062..5646
location: region:5062-5646:1
so has part: feature:5062-5646:1:exon
subclass of: SO_0000010

position:5062:1
position: 5062
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:5646:1
position: 5646
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5062-5646:1:exon

KFV11_RS11540
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 69967
locus tag: KFV11_RS11540
old locus tag: KFV11_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: MKSCIDLANELNVSKQTVFNNAKKLEIELTKQDNTLYVSSADDVEAIKNRILNNKAKSLNVDVSELINNDSSSKQDNDTQDVSNNNNKIELLRQMIDDKNKQIQSLQDDKQDLTSLLKQQQQLLHNQQSLQLQSNDKIKALELELQEVKEDTSKADNVQDTNKIDNFYRDLREDKQESNSTTNKKGGLLSRFFK
SIO_010081: KFV11_RS11540
subclass of: SO_0000673
so part of: KFV11_RS11540
location: 5062..5646
location: region:5062-5646:1
so has part: feature:5062-5646:1:exon

WP_254250628.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5062-5646:1:exon

KFV11_RS11545
type: Gene
subclass of: SO_0000704
RO_0002162: 69967
locus tag: KFV11_RS11545
old locus tag: KFV11_11540
so part of: sequence
location: 5751..6368
location: region:5751-6368:1
so has part: feature:5751-6368:1:exon
subclass of: SO_0000010

position:5751:1
position: 5751
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:6368:1
position: 6368
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5751-6368:1:exon

KFV11_RS11545
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 69967
locus tag: KFV11_RS11545
old locus tag: KFV11_11540
inference: COORDINATES: similar to AA sequence:RefSeq:WP_002449206.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: CadD family cadmium resistance transporter
translation: MFQTIITATVLYTATAVDLLVILLIFFARASTKKEYRNIYIGQYLGSIILILVSLFLAFVLNYVPEKWMLGLLGIIPIYFGVKVALYDDCAGEKRAKKELDKKGLSKLIGTVALVTIASCGADNIGLFVPYFVSLNMSNLIVTLITFLVLIFVLVFTAQKIANIPGIGGTIEKYSRWIMAVIYIGLGMFIIIENKTIQTILEFLF
SIO_010081: KFV11_RS11545
subclass of: SO_0000673
so part of: KFV11_RS11545
location: 5751..6368
location: region:5751-6368:1
so has part: feature:5751-6368:1:exon

WP_149459927.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5751-6368:1:exon

KFV11_RS11550
type: Gene
subclass of: SO_0000704
RO_0002162: 69967
locus tag: KFV11_RS11550
old locus tag: KFV11_11545
so part of: sequence
location: 6388..6723
location: region:6388-6723:1
so has part: feature:6388-6723:1:exon
subclass of: SO_0000010

position:6388:1
position: 6388
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:6723:1
position: 6723
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:6388-6723:1:exon

KFV11_RS11550
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 69967
locus tag: KFV11_RS11550
old locus tag: KFV11_11545
inference: COORDINATES: similar to AA sequence:RefSeq:WP_012657303.1
GO function: GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO process: GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: metalloregulator ArsR/SmtB family transcription factor
translation: MNKSITCDIVCVHEDKVDKALDFLKIEKSQRLLNIFQKICDEKKLKIVLSLLSEKELCVCDIAIILDMSVASTSHHLRLLYKNDVLDFYKNGKMVYYFIKDEEIKLFFSNN
SIO_010081: KFV11_RS11550
subclass of: SO_0000673
so part of: KFV11_RS11550
location: 6388..6723
location: region:6388-6723:1
so has part: feature:6388-6723:1:exon

WP_133418528.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:6388-6723:1:exon

KFV11_RS11555
type: Gene
subclass of: SO_0000704
RO_0002162: 69967
locus tag: KFV11_RS11555
old locus tag: KFV11_11550
so part of: sequence
location: 6893..7459
location: region:6893-7459:1
so has part: feature:6893-7459:1:exon
subclass of: SO_0000010

position:6893:1
position: 6893
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:7459:1
position: 7459
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:6893-7459:1:exon

KFV11_RS11555
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 69967
locus tag: KFV11_RS11555
old locus tag: KFV11_11550
inference: COORDINATES: similar to AA sequence:RefSeq:WP_012657302.1
GO function: GO:0003677 - DNA binding [Evidence IEA]
GO process: GO:0015074 - DNA integration [Evidence IEA]; 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: tyrosine-type recombinase/integrase
translation: MNSVEPIRDVKKIQEMKEALAYYGSERDVFLFNLGINCGLRVSDMLGLKKKDIKDYTIKLREQKTRKQKQIPLYHLKEDIDRYIQFLEDEDYLFKSNKLDSDGNDKPISRVQAYRILNHSAKSIGLSEIGTHSMRKTFGYHYYKKTKDVALLMDLFNHSSQSVTLRYIGINQDIMNESISNVMINIYV
SIO_010081: KFV11_RS11555
subclass of: SO_0000673
so part of: KFV11_RS11555
location: 6893..7459
location: region:6893-7459:1
so has part: feature:6893-7459:1:exon

WP_149459939.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:6893-7459:1:exon

KFV11_RS11560
type: Gene
subclass of: SO_0000704
RO_0002162: 69967
locus tag: KFV11_RS11560
old locus tag: KFV11_11555
so part of: sequence
location: complement(7477..8181)
location: region:7477-8181:-1
so has part: feature:7477-8181:-1:exon
subclass of: SO_0000010

position:7477:-1
position: 7477
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:8181:-1
position: 8181
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:7477-8181:-1:exon

KFV11_RS11560
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 69967
locus tag: KFV11_RS11560
old locus tag: KFV11_11555
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: MDLYLYFSLTRREIERNEKNYRIYYATTLLLGGFTSTTLASEIKVSNNTNDVVNDAVKNEMTIVSEELINKANPFISVDDTNDKFILDKESARNTLTENEVELVQKQLNKTNHLLHEENVNYVQHGESLIPENNAKVEKSITTYSTSEGINKVEFYWWGAKIWISKTAVRKVLETGAEGGGAALGAYLGGVPGALLGTIAGSLVSKFGGPAAARAVYIKYNYALGIQDFQIFNK
SIO_010081: KFV11_RS11560
subclass of: SO_0000673
so part of: KFV11_RS11560
location: complement(7477..8181)
location: region:7477-8181:-1
so has part: feature:7477-8181:-1:exon

WP_149459938.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:7477-8181:-1:exon