Corynebacterium phocae strain M408/89/1 plasmid pCpho, complete sequence.
type: Entry
definition: Corynebacterium phocae strain M408/89/1 plasmid pCpho, complete sequence.
sequence version: NZ_CP009250.1
sequence date: 2023-05-04
sequence: sequence
division: CON
label: NZ_CP009250.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN02996498
keyword: RefSeq
source: Corynebacterium phocae
organism: Corynebacterium phocae
taxonomy: Bacteria; Actinomycetota; Actinomycetes; Mycobacteriales; Corynebacteriaceae; Corynebacterium.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP009250.1.\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##Assembly-Data-START##\nAssembly Method :: Newbler v. 2.8\nCoverage :: 95.0x\nSequencing Technology :: Illumina\n##Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 05/04/2023 02:14:53\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) :: 2,504\nCDSs (total) :: 2,439\nGenes (coding) :: 2,418\nCDSs (with protein) :: 2,418\nGenes (RNA) :: 65\nrRNAs :: 4, 4, 4 (5S, 16S, 23S)\ncomplete rRNAs :: 4, 4, 4 (5S, 16S, 23S)\ntRNAs :: 50\nncRNAs :: 3\nPseudo Genes (total) :: 21\nCDSs (without protein) :: 21\nPseudo Genes (ambiguous residues) :: 0 of 21\nPseudo Genes (frameshifted) :: 5 of 21\nPseudo Genes (incomplete) :: 17 of 21\nPseudo Genes (internal stop) :: 0 of 21\nPseudo Genes (multiple problems) :: 1 of 21\nCRISPR Arrays :: 2\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 12274
topology: circular
so has quality: SO_0000988
location: 1..12274
location: region:1-12274:1
RO_0002162: 161895

NZ_CP009250
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN02996498
type: BioSample
SIO_000068: biosample

1
title: Complete genome sequence of Corynebacterium phocae M408/89/1(T)(=DSM 44612(T)), isolated from the common seal (Phoca vitulina)
author: Ruckert, C.
author: Albersmeier, A.
author: Winkler, A.
author: Kalinowski, J.
journal: Unpublished

2
title: Direct Submission
author: Ruckert, C.
author: Albersmeier, A.
author: Winkler, A.
author: Kalinowski, J.
journal: Submitted (18-AUG-2014) CeBiTec, Bielefeld University, Universitaetsstr. 27, Bielefeld, NRW 33615, Germany

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

position:12274:1
position: 12274
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-12274:1:source
so part of: sequence
organism: Corynebacterium phocae
mol type: genomic DNA
strain: M408/89/1
isolation source: nasal cavity of common seals (Phoca vitulina)
host: Phoca vitulina
culture collection: DSM:44612
type material: type strain of Corynebacterium phocae
plasmid: pCpho

161895
type: Taxonomy
SIO_000068: taxonomy

CPHO_RS13100
type: Gene
subclass of: SO_0000704
RO_0002162: 161895
locus tag: CPHO_RS13100
so part of: sequence
location: complement(join(11871..12274,1..94))
location: region:1-12274:-1
so has part: feature:1-94:-1:exon
so has part: feature:11871-12274:-1:exon
subclass of: SO_0000010

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

position:12274:-1
position: 12274
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1-94:-1:exon

position:94:-1
position: 94
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 2
SIO_000628: feature:11871-12274:-1:exon

position:11871:-1
position: 11871
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

CPHO_RS13100
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 161895
locus tag: CPHO_RS13100
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: MKILAPKTAIAALSIAVVTALSPHAYASEVNEGEFTVLEAVAPAPGQNSNGYAPRSADGGSWAPGGVGATNWLYVKGRGLNVKTAAVAYFPGKNVVNNNACVDKFEIAYYKNGRRVTETAGGNCAPGRVTHTFSLNKNLDAHKPFCGRVRVGSTWGNYACVNIKP
SIO_010081: CPHO_RS13100
subclass of: SO_0000673
so part of: CPHO_RS13100
location: complement(join(11871..12274,1..94))
location: region:1-12274:-1
so has part: feature:1-94:-1:exon
so has part: feature:11871-12274:-1:exon

WP_150385833.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1-94:-1:exon

urn:…
SIO_000300: 2
SIO_000628: feature:11871-12274:-1:exon

CPHO_RS13525
type: Gene
subclass of: SO_0000704
RO_0002162: 161895
locus tag: CPHO_RS13525
so part of: sequence
location: 606..737
location: region:606-737:1
so has part: feature:606-737:1:exon
subclass of: SO_0000010

position:606:1
position: 606
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:737:1
position: 737
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:606-737:1:exon

CPHO_RS13525
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 161895
locus tag: CPHO_RS13525
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: MARYFYDHATRPFKAFNLPGALVPLLSTLKSSSSALVAVKPRF
SIO_010081: CPHO_RS13525
subclass of: SO_0000673
so part of: CPHO_RS13525
location: 606..737
location: region:606-737:1
so has part: feature:606-737:1:exon

WP_281247324.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:606-737:1:exon

CPHO_RS12565
type: Gene
subclass of: SO_0000704
RO_0002162: 161895
locus tag: CPHO_RS12565
old locus tag: CPHO_12420
so part of: sequence
location: complement(2434..3936)
location: region:2434-3936:-1
so has part: feature:2434-3936:-1:exon
subclass of: SO_0000010

position:2434:-1
position: 2434
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3936:-1
position: 3936
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2434-3936:-1:exon

CPHO_RS12565
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 161895
locus tag: CPHO_RS12565
old locus tag: CPHO_12420
inference: COORDINATES: similar to AA sequence:RefSeq:WP_011069214.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: replication initiation protein
translation: MSLANVPQQRTFTVKRVGRRSLRADWGGLDDTPAGILERDDLAAHLGKKVIHASVDRDFKKSYTTTKNADGSGYTTKPRYYRLDSEALGKCEYAVLTSKQHAAVMVIDIDQPGTEGGHPSNLAPSVKKVLAQLVDAHIGPSWAGINPQSGKAQLIWLIDPVYADESGKSRHMDLLAATSRTLGQLLDHDPNFAHRFSRNPFYTGKSPTAYRWYFQHKNVVHLGIFLRQLRDMAGLDQHEKTPQRFDSGRDLINAAKARREQAEAFKALAQDVESELGDRLDKYDQELIDGVRVLWITPPTTNAHGEHVPGTAARDETAFRHALKTGHRLRQSGQRLKDAPIIDAYEHAYKIAQAHGAAGRAEDMPPAADRLTMARRVRGYVTTSTSPVYKAHSTSEKATSSERKALATLGRRGGKKTAERLKTDPNGDYAQAQRQKLAEANKRRKLAGNETRARVLAVYAAELAQTGKALTGAAIGRELGITRKTANAHLRALRVVGLID
SIO_010081: CPHO_RS12565
subclass of: SO_0000673
so part of: CPHO_RS12565
location: complement(2434..3936)
location: region:2434-3936:-1
so has part: feature:2434-3936:-1:exon

WP_084559846.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2434-3936:-1:exon

CPHO_RS12570
type: Gene
subclass of: SO_0000704
RO_0002162: 161895
locus tag: CPHO_RS12570
old locus tag: CPHO_12425
so part of: sequence
location: complement(4240..4770)
location: region:4240-4770:-1
so has part: feature:4240-4770:-1:exon
subclass of: SO_0000010

position:4240:-1
position: 4240
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4770:-1
position: 4770
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4240-4770:-1:exon

CPHO_RS12570
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 161895
locus tag: CPHO_RS12570
old locus tag: CPHO_12425
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: MKLREGFNFSTFSSAMMIWGVLAVIIGIPLIIVAWKNRNSATKSRVFLGVLLAVLAGFVSFTVWLSWNSRAGIADVILRYGMPYPAIWQVVACGLTVIILSGLVIYKLADSWAWVPMVSFFTAMGLAIAYTAGVSYGPPSQEGIGVMLSFIGVGMLTTLTNLVFVAIALKKRSSLK
SIO_010081: CPHO_RS12570
subclass of: SO_0000673
so part of: CPHO_RS12570
location: complement(4240..4770)
location: region:4240-4770:-1
so has part: feature:4240-4770:-1:exon

WP_157105786.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4240-4770:-1:exon

CPHO_RS12575
type: Gene
subclass of: SO_0000704
RO_0002162: 161895
locus tag: CPHO_RS12575
so part of: sequence
location: complement(4814..6406)
location: region:4814-6406:-1
so has part: feature:4814-6406:-1:exon
subclass of: SO_0000010

position:4814:-1
position: 4814
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:6406:-1
position: 6406
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4814-6406:-1:exon

CPHO_RS12575
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 161895
locus tag: CPHO_RS12575
inference: COORDINATES: similar to AA sequence:RefSeq:WP_006822509.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MMRFLSRKLLSFVASGLLIGIYPALAVAQTPDIYSPVQDILIQQDSENEPFSQWGLPTPPGAEGYEVNQVQEEEDLNPQGENEWYPTKHPKKRLVVGQMRSDREELPHGVDKGEADKAEIREAQLADPNARTVSARRGCGVYWPLNFQVCGAIKTKYDSIGGPTSFLGFPKSNELTNPDRVGKRSEFINGYIYWHPSTGAHTVSLPVSVVWARHGWEKGFLGYPITSDIPQGNAWYKQDFQGGHVYTHNELLPTQASIQGAIYDKWQSMGAQNSKLGYPISDELTTPDGIGRYNVFEGGMIYWTPQTGAHEVLGLPLQLWAFGGFEGSKWGYPTGSPVNSPDAPVAVRQSFAKADMDIRREFEEAGEVNVGGKPVNKLLMEMLQLNPNSSIFNRNEMQSNIRASKCALKDSTRSEFGGVTIPSNYDYWGCLPNWPIRDGIRRHDYCSHSPDKMVSVGRTAEFSGACARHDMCMDKADDNGNGYGGCNSDLYANMGGVCRSVYGIGALVNGCQKMREVYWTVVTAWNYDNL
SIO_010081: CPHO_RS12575
subclass of: SO_0000673
so part of: CPHO_RS12575
location: complement(4814..6406)
location: region:4814-6406:-1
so has part: feature:4814-6406:-1:exon

WP_075736776.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4814-6406:-1:exon

CPHO_RS12580
type: Gene
subclass of: SO_0000704
RO_0002162: 161895
locus tag: CPHO_RS12580
old locus tag: CPHO_12440
so part of: sequence
location: complement(6602..6856)
location: region:6602-6856:-1
so has part: feature:6602-6856:-1:exon
subclass of: SO_0000010

position:6602:-1
position: 6602
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:6856:-1
position: 6856
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:6602-6856:-1:exon

CPHO_RS12580
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 161895
locus tag: CPHO_RS12580
old locus tag: CPHO_12440
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: MPPKKKTNQIAATIRKPAKATDTPRTVRSTLTSPSDRELSRRTTIYLTPETWEGLKIAAAKHHTTLSMFMEQLSRDYLKTTKRT
SIO_010081: CPHO_RS12580
subclass of: SO_0000673
so part of: CPHO_RS12580
location: complement(6602..6856)
location: region:6602-6856:-1
so has part: feature:6602-6856:-1:exon

WP_075736778.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:6602-6856:-1:exon

CPHO_RS12585
type: Gene
subclass of: SO_0000704
RO_0002162: 161895
locus tag: CPHO_RS12585
old locus tag: CPHO_12445
so part of: sequence
location: complement(6856..7440)
location: region:6856-7440:-1
so has part: feature:6856-7440:-1:exon
subclass of: SO_0000010

position:7440:-1
position: 7440
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:6856-7440:-1:exon

CPHO_RS12585
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 161895
locus tag: CPHO_RS12585
old locus tag: CPHO_12445
inference: COORDINATES: similar to AA sequence:RefSeq:WP_006770511.1
GO function: GO:0005524 - ATP binding [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: ParA family protein
translation: MRIAFVHTKGGVGKTTGAVLLAAAAHARGLAVEVFDADPQGSATRWAEVASATGDPLPFPIRPVTARVLRSAPVVDGWQIVDTPPGTAAEIQAAIDTADLVIIPTHPTPIDIDRVWPTLETVEHRMTGVLLVGVQERRRLYRDTREVFESQGVATFYNFIPEREALKAAFGTNPTELFTFPDICQEILDIEEMD
SIO_010081: CPHO_RS12585
subclass of: SO_0000673
so part of: CPHO_RS12585
location: complement(6856..7440)
location: region:6856-7440:-1
so has part: feature:6856-7440:-1:exon

WP_075736780.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:6856-7440:-1:exon

CPHO_RS12590
type: Gene
subclass of: SO_0000704
RO_0002162: 161895
gene: mobF
locus tag: CPHO_RS12590
old locus tag: CPHO_12450
so part of: sequence
location: complement(7547..11206)
location: region:7547-11206:-1
so has part: feature:7547-11206:-1:exon
subclass of: SO_0000010

position:7547:-1
position: 7547
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:11206:-1
position: 11206
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:7547-11206:-1:exon

CPHO_RS12590
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 161895
gene: mobF
locus tag: CPHO_RS12590
old locus tag: CPHO_12450
inference: COORDINATES: similar to AA sequence:RefSeq:WP_006821243.1
GO function: GO:0003677 - DNA binding [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: MobF family relaxase
translation: MLTIAKMGAHSVAYYESTVEGEPGADSYYSEAGSSPGRAWVVASTRESFAEVSKRLGVVSGEFLRGGAVQDWFNKVVAPSGERLGRAPGEKSVPGFDLTFCAPKSVSVLWGLSDDEAVRAVIDSAHNKAVSAALGYLHEHAGYTRRQDPTVKEKRLIIEKVPALSGVRYEHRTSRAGDPHIHSHVLLANRQVCQDGKVRTLDSKGIFHEARAAGMIYQATLREILAENLGVEWGQRSNGCAEIAGLDDEELIKRFSTRAQEIDQWQQANGLEVRGGYQRVAQKITRQTKDVAIAIEELYERWLSNPFAKQVQRFARLLGGCKPQLRAGEDKHREQEWPSAEEILGAVVDERSTFTRADVVEKVAELLPVGVVASEKLAEVVEGLATEALAHADAWVVTPEKSRAVDNTEREGALRFTTKSVVSEVSGIVRMASSVTHRGVNASAIVPIEGVLSQEQADAMRTVVQSSYRASVVVAPAGAGKTSSLKAAREVWENAGKTVIGLAPTGKAADVMVGESVAHESMTIARALGRDEKVRPRARARALGWDSSTVVVVDEAGMVASPDMYAIMATVEAAGARVVFVGDPCQYSAVKARSGVLATLARELPDAVELTEVFRQRSEQEREASKWLRSGEQELTERAAQWYARNGRLHAGSVSAMLEDALAGWEKDTGQGKDSLLVAATGQQVHALNTAAQKIRAGRGELDMDAWAGLSDGVDCYVGDMILTRRNDYSLTTNAGDVVRNGQRWIVQDITDTGAVVAASDHNPEVTVTLPAEYLQEHTQLGYASTGHCAQGATVDIARVVAGVGNLDRASVYVPMTRGREGNCLYIAEVQPGDSDTGHGNTTPVKRRESVEYARDILASAASRDRADHTPQTVYGHARMEWELGRFINGSGRDVFAGTEMDKFMQCSEKNRARRFAEYGLKGLPGTRQDEFPRFTHYDLTESRKRSSGVHERYYYVRRDLESIERNIGYAQSEQERVEKKIRELDAKFEQLGKFSQWRKEKEYKRTREHLYGEWEKSTAALTELEKKYQRAKDNAEPLRVEVEGLDAETAVIEEYLNKQRNLPARPLGGETLGFDWDREYRQRNGSTPCPPEGISLAGLVKKHLNDQRIDLGENYRHPQERMSLRERLAQESRQRGNDSQDYDFGDRPVEEMTPQERFDLQMKREQGPDYDMDDRPVEDMTAQELLDLHWRKQSRYPSGESEQQAWVMGNNNDGGLEL
SIO_010081: CPHO_RS12590
subclass of: SO_0000673
so part of: CPHO_RS12590
location: complement(7547..11206)
location: region:7547-11206:-1
so has part: feature:7547-11206:-1:exon

WP_150385835.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:7547-11206:-1:exon