Campylobacter cuniculorum DSM 23162 = LMG 24588 plasmid pCUN1, complete sequence.
type: Entry
definition: Campylobacter cuniculorum DSM 23162 = LMG 24588 plasmid pCUN1, complete sequence.
sequence version: NZ_CP020868.1
sequence date: 2023-04-28
sequence: sequence
division: CON
label: NZ_CP020868.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN03737969
keyword: RefSeq
source: Campylobacter cuniculorum DSM 23162 = LMG 24588
organism: Campylobacter cuniculorum DSM 23162 = LMG 24588
taxonomy: Bacteria; Campylobacterota; Epsilonproteobacteria; Campylobacterales; Campylobacteraceae; Campylobacter.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP020868.1.\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 :: Newbler v. 2.6\nGenome Coverage :: 1363x\nSequencing Technology :: Sanger dideoxy sequencing; 454; Illumina;\n PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 04/28/2023 01:08:41\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) :: 1,923\nCDSs (total) :: 1,874\nGenes (coding) :: 1,847\nCDSs (with protein) :: 1,847\nGenes (RNA) :: 49\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 40\nncRNAs :: 3\nPseudo Genes (total) :: 27\nCDSs (without protein) :: 27\nPseudo Genes (ambiguous residues) :: 0 of 27\nPseudo Genes (frameshifted) :: 9 of 27\nPseudo Genes (incomplete) :: 20 of 27\nPseudo Genes (internal stop) :: 2 of 27\nPseudo Genes (multiple problems) :: 3 of 27\nCRISPR Arrays :: 1\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 4923
topology: circular
so has quality: SO_0000988
location: 1..4923
location: region:1-4923:1
RO_0002162: 1121267

NZ_CP020868
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN03737969
type: BioSample
SIO_000068: biosample

1
title: Complete genome sequence of the Campylobacter cuniculorum type strain LMG24588
author: Miller, W.G.
author: Yee, E.
author: Revez, J.
author: Bono, J.L.
author: Rossi, M.
journal: Unpublished

2
title: Direct Submission
author: Miller, W.G.
author: Yee, E.
author: Revez, J.
author: Bono, J.L.
author: Rossi, M.
journal: Submitted (18-APR-2017) Produce Safety and Microbiology, USDA, ARS, WRRC, 800 Buchanan St., Albany, CA 94710, USA

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

position:4923:1
position: 4923
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-4923:1:source
so part of: sequence
organism: Campylobacter cuniculorum DSM 23162 = LMG 24588
mol type: genomic DNA
strain: LMG 24588
isolation source: Rabbit, caecal
host: rabbit
culture collection: LMG:24588
type material: type strain of Campylobacter cuniculorum
plasmid: pCUN1
country: Italy: Bologna
collection date: 2005
note: type strain of Campylobacter cuniculorum; LMG24588 =CCUG56289 =150B; strains available from the LMG and CCUG culture collections

1121267
type: Taxonomy
SIO_000068: taxonomy

CCUN_RS09500
type: Gene
subclass of: SO_0000704
RO_0002162: 1121267
locus tag: CCUN_RS09500
old locus tag: CCUN_a0001
so part of: sequence
location: 1..1059
location: region:1-1059:1
so has part: feature:1-1059:1:exon
subclass of: SO_0000010

position:1059:1
position: 1059
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1-1059:1:exon

CCUN_RS09500
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1121267
locus tag: CCUN_RS09500
old locus tag: CCUN_a0001
inference: COORDINATES: similar to AA sequence:RefSeq:WP_002934484.1
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: replication initiation protein
translation: MNEIVKYHNDFNKIQLPNFNEIEQNLLCFLLTKIKEKQKNEMITLYPKDLTGFSEKNLSNREVTEILNSFENKFFKADFTIILKDEVRNLIGKMRVNLFNYFVIWKKWRDKYNMELGILDAWEEFTHIEIQVNEHFEYLVNQLTANFTAFELTEFIALSGKYTKTLYRLLKQYRATGKVYFKWEEFCKIMDIPENYRQSEVDKKILNPAIKELSKERNLFDQKRTPFKNLTYEKEKQKGTRGRGGKVSGIIFTFTPESILMQKLEKESEKIETPEQKYFKILNNMRQNQVRFIYKNQLWQFNDFNFDEFKIIAVELIRDEYENLNFRNHKRFTAKSQEQFFEMIDTFRNQIR
SIO_010081: CCUN_RS09500
subclass of: SO_0000673
so part of: CCUN_RS09500
location: 1..1059
location: region:1-1059:1
so has part: feature:1-1059:1:exon

WP_211093720.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1-1059:1:exon

CCUN_RS09505
type: Gene
subclass of: SO_0000704
RO_0002162: 1121267
locus tag: CCUN_RS09505
so part of: sequence
location: 1267..1497
location: region:1267-1497:1
so has part: feature:1267-1497:1:exon
subclass of: SO_0000010

position:1267:1
position: 1267
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1497:1
position: 1497
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1267-1497:1:exon

CCUN_RS09505
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1121267
locus tag: CCUN_RS09505
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: MSRADRIKAKLDLLKLLIIAILTALFGVVGFAVTHYKTLDFVLSLMVSLGIIVLLLALVYLSINFNKELDKLEKEK
SIO_010081: CCUN_RS09505
subclass of: SO_0000673
so part of: CCUN_RS09505
location: 1267..1497
location: region:1267-1497:1
so has part: feature:1267-1497:1:exon

WP_085296703.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1267-1497:1:exon

CCUN_RS09510
type: Gene
subclass of: SO_0000704
RO_0002162: 1121267
locus tag: CCUN_RS09510
old locus tag: CCUN_a0002
so part of: sequence
location: 1748..2137
location: region:1748-2137:1
so has part: feature:1748-2137:1:exon
subclass of: SO_0000010

position:1748:1
position: 1748
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2137:1
position: 2137
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1748-2137:1:exon

CCUN_RS09510
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1121267
locus tag: CCUN_RS09510
old locus tag: CCUN_a0002
inference: COORDINATES: similar to AA sequence:RefSeq:WP_002815874.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MIIYLKKYVIISQVQLYIFLKRSKAMLAQEKQDNLDYIYIEKLKTKSERQLKIMLDTLEKETIKIQAEKAKLESKLKDKIKKGHLIKDALMEKWRTPNAELLEAIEEIKNGGGTLCKSMEEFKAKMAED
SIO_010081: CCUN_RS09510
subclass of: SO_0000673
so part of: CCUN_RS09510
location: 1748..2137
location: region:1748-2137:1
so has part: feature:1748-2137:1:exon

WP_218917142.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1748-2137:1:exon

CCUN_RS09515
type: Gene
subclass of: SO_0000704
RO_0002162: 1121267
locus tag: CCUN_RS09515
old locus tag: CCUN_a0003
so part of: sequence
location: 2149..2418
location: region:2149-2418:1
so has part: feature:2149-2418:1:exon
subclass of: SO_0000010

position:2149:1
position: 2149
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2418:1
position: 2418
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2149-2418:1:exon

CCUN_RS09515
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1121267
locus tag: CCUN_RS09515
old locus tag: CCUN_a0003
inference: COORDINATES: similar to AA sequence:RefSeq:WP_002789000.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: type II toxin-antitoxin system YafQ family toxin
translation: MKYEIKYSTKFKKHYKKLNTKEQQEVITIINHLANDETLEPKYKDHALKGDFIGFRECHLKPDLLLIYQKQDDKLILYCLDIGSHSELF
SIO_010081: CCUN_RS09515
subclass of: SO_0000673
so part of: CCUN_RS09515
location: 2149..2418
location: region:2149-2418:1
so has part: feature:2149-2418:1:exon

WP_085296705.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2149-2418:1:exon

CCUN_RS09835
type: Gene
subclass of: SO_0000704
RO_0002162: 1121267
locus tag: CCUN_RS09835
old locus tag: CCUN_a0004
so part of: sequence
location: 2418..4040
location: region:2418-4040:1
so has part: feature:2418-4040:1:exon
subclass of: SO_0000010

position:4040:1
position: 4040
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2418-4040:1:exon

CCUN_RS09835
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1121267
locus tag: CCUN_RS09835
old locus tag: CCUN_a0004
inference: COORDINATES: similar to AA sequence:RefSeq:WP_014661885.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: LPD7 domain-containing protein
translation: MGAISSINFKKSNAIQARHNDRDLAPNYLIGGNYECNHTHKEALALKNQIIKNSIEKYTEITGQKFQAKSYEWSAVVNIKPDTTMQDLEKLAEHFHKKYGFQCYQIAIHRDEGHINEQGQKEINHHAHLEFITLNKENGRNMWRRELITPKVLRQMQSEVAEILEMQRGQDKRITKIKRIEPRKYAQMKEAEKKEKKELKQELLSTKEVKERLEAERKAWILEKNHTAKEYKALRELTNRIYTDKTELEKEIKALKERLSDLDNENALLKAENQKLRQEIGLNEANIISYSPPFLDFKTKLISEVYHNIKHDFSDYYFDKEKKEFSNHKLDFKVQDNGNSITLNSNNNQNMSEKVSLMLKMAMAKDWDLNNLNIKGSNKFKAECYKQITEIQKNKIKALESDLKAKEQKNNEIHQKENKNDLRGDSERLNAHNDNEYIIEALIRSLSNAYTNTHFIDENKNEIKIMPAKSEKQKQDKIKNIQESLRAIKKAISDYGFSEKFTEWEKQNPYYKEVLENYKAKAPIAKKQEQIKRQEQGRSL
SIO_010081: CCUN_RS09835
subclass of: SO_0000673
so part of: CCUN_RS09835
location: 2418..4040
location: region:2418-4040:1
so has part: feature:2418-4040:1:exon

WP_164502924.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2418-4040:1:exon