Campylobacter hyointestinalis subsp. lawsonii strain CHY5 plasmid pCHY5, complete sequence.
type: Entry
definition: Campylobacter hyointestinalis subsp. lawsonii strain CHY5 plasmid pCHY5, complete sequence.
sequence version: NZ_CP053829.1
sequence date: 2023-04-28
sequence: sequence
division: CON
label: NZ_CP053829.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN09274393
keyword: RefSeq
source: Campylobacter hyointestinalis subsp. lawsonii
organism: Campylobacter hyointestinalis subsp. lawsonii
taxonomy: Bacteria; Campylobacterota; Epsilonproteobacteria; Campylobacterales; Campylobacteraceae; Campylobacter.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP053829.1.\nBacteria and source DNA available from Bacteria available from the\nLMG culture collection.\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 :: 638x\nSequencing Technology :: PacBio; Illumina HiSeq\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 04/28/2023 03:57:48\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) :: 1,885\nCDSs (total) :: 1,828\nGenes (coding) :: 1,808\nCDSs (with protein) :: 1,808\nGenes (RNA) :: 57\nrRNAs :: 4, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 4, 3, 3 (5S, 16S, 23S)\ntRNAs :: 44\nncRNAs :: 3\nPseudo Genes (total) :: 20\nCDSs (without protein) :: 20\nPseudo Genes (ambiguous residues) :: 0 of 20\nPseudo Genes (frameshifted) :: 6 of 20\nPseudo Genes (incomplete) :: 15 of 20\nPseudo Genes (internal stop) :: 5 of 20\nPseudo Genes (multiple problems) :: 4 of 20\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 4413
topology: circular
so has quality: SO_0000988
location: 1..4413
location: region:1-4413:1
RO_0002162: 91353

NZ_CP053829
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN09274393
type: BioSample
SIO_000068: biosample

1
title: Complete genome sequencing of Campylobacter and Arcobacter type strains
author: Miller, W.G.
author: Yee, E.
journal: Unpublished

2
title: Direct Submission
author: Miller, W.G.
journal: Submitted (20-MAY-2020) 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:4413:1
position: 4413
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-4413:1:source
so part of: sequence
organism: Campylobacter hyointestinalis subsp. lawsonii
mol type: genomic DNA
strain: CHY5
isolation source: stomach
host: pig
sub species: lawsonii
type material: type strain of Campylobacter hyointestinalis subsp. lawsonii
plasmid: pCHY5

91353
type: Taxonomy
SIO_000068: taxonomy

CHLWT_RS09325
type: Gene
subclass of: SO_0000704
RO_0002162: 91353
locus tag: CHLWT_RS09325
old locus tag: CHLWT_a0001
so part of: sequence
location: 161..1219
location: region:161-1219:1
so has part: feature:161-1219:1:exon
subclass of: SO_0000010

56510937
type: Gene
SIO_000068: ncbigene

position:161:1
position: 161
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1219:1
position: 1219
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:161-1219:1:exon

CHLWT_RS09325
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 91353
locus tag: CHLWT_RS09325
old locus tag: CHLWT_a0001
inference: COORDINATES: protein motif:HMM:NF013235.2
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: MARQKPKQLVEYHNDLNLIAFKSFSKVENDVFFALMWKLKNQANKEIRLDFAELRELIDLRNMTNKEIEKSISDIGRKISSSLIEFETETERQFFTIFQVLAVPKDTDDFYIRAKINKPFLYILNNFEKGGFTMWELIEFSNLTSKYTQTLYRILKQFRSTGTVTIFENDWDKFVEIMDIPKGYAMSDIDKRILTPAIKELSEKTLFSTDRVIFENLKYEKKRGRSKGRPVVGIEFRFLPQTENQHKLEQVRTSLKNLEQIERQKQAMNQLKTTKINPITGQEVSILNGYISQYVSVIDLKTQLYNRLKIRNLKEDCGKIIAELYNADDDYLNEMKFESFEHFKNFFEKYRA
SIO_010081: CHLWT_RS09325
subclass of: SO_0000673
so part of: CHLWT_RS09325
location: 161..1219
location: region:161-1219:1
so has part: feature:161-1219:1:exon

WP_112000822.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:161-1219:1:exon

CHLWT_RS09330
type: Gene
subclass of: SO_0000704
RO_0002162: 91353
locus tag: CHLWT_RS09330
old locus tag: CHLWT_a0002
so part of: sequence
location: 1262..1540
location: region:1262-1540:1
so has part: feature:1262-1540:1:exon
subclass of: SO_0000010

56510938
type: Gene
SIO_000068: ncbigene

position:1262:1
position: 1262
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1540:1
position: 1540
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1262-1540:1:exon

CHLWT_RS09330
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 91353
locus tag: CHLWT_RS09330
old locus tag: CHLWT_a0002
inference: COORDINATES: similar to AA sequence:RefSeq:WP_013459398.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: BrnT family toxin
translation: MTYEWDEVKAQLNIAKHGVSFDEATTVFCDDYGIIVFDEEHSDDEERFYLLGMSEKNRILIVVHCYKDGDTIRIISARKATSREKTQYKEQL
SIO_010081: CHLWT_RS09330
subclass of: SO_0000673
so part of: CHLWT_RS09330
location: 1262..1540
location: region:1262-1540:1
so has part: feature:1262-1540:1:exon

WP_025370516.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1262-1540:1:exon

CHLWT_RS09335
type: Gene
subclass of: SO_0000704
RO_0002162: 91353
locus tag: CHLWT_RS09335
old locus tag: CHLWT_a0003
so part of: sequence
location: 1537..1743
location: region:1537-1743:1
so has part: feature:1537-1743:1:exon
subclass of: SO_0000010

56510939
type: Gene
SIO_000068: ncbigene

position:1537:1
position: 1537
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1743:1
position: 1743
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1537-1743:1:exon

CHLWT_RS09335
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 91353
locus tag: CHLWT_RS09335
old locus tag: CHLWT_a0003
inference: COORDINATES: similar to AA sequence:RefSeq:WP_002943187.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MKKEIDFSNAIRNPYVDKNLKRQITINLNGRAIDYFKDMASKKGVPYQTLINIFLNDCVDKKLDIAVI
SIO_010081: CHLWT_RS09335
subclass of: SO_0000673
so part of: CHLWT_RS09335
location: 1537..1743
location: region:1537-1743:1
so has part: feature:1537-1743:1:exon

WP_025370515.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1537-1743:1:exon

CHLWT_RS09340
type: Gene
subclass of: SO_0000704
RO_0002162: 91353
locus tag: CHLWT_RS09340
old locus tag: CHLWT_a0004
so part of: sequence
location: 1830..2039
location: region:1830-2039:1
so has part: feature:1830-2039:1:exon
subclass of: SO_0000010

56510940
type: Gene
SIO_000068: ncbigene

position:1830:1
position: 1830
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2039:1
position: 2039
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1830-2039:1:exon

CHLWT_RS09340
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 91353
locus tag: CHLWT_RS09340
old locus tag: CHLWT_a0004
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: MKKIIFSIAILGGLVSSSFAASWHYDTDGCTKIYAYGYDASECFDKARDIKKEAGRKFLCNAGYVRYCY
SIO_010081: CHLWT_RS09340
subclass of: SO_0000673
so part of: CHLWT_RS09340
location: 1830..2039
location: region:1830-2039:1
so has part: feature:1830-2039:1:exon

WP_059429782.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1830-2039:1:exon

CHLWT_RS09345
type: Gene
subclass of: SO_0000704
RO_0002162: 91353
locus tag: CHLWT_RS09345
old locus tag: CHLWT_a0005
so part of: sequence
location: 2039..2284
location: region:2039-2284:1
so has part: feature:2039-2284:1:exon
subclass of: SO_0000010

56510941
type: Gene
SIO_000068: ncbigene

position:2284:1
position: 2284
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2039-2284:1:exon

CHLWT_RS09345
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 91353
locus tag: CHLWT_RS09345
old locus tag: CHLWT_a0005
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: MDGLGLTCVPLSATEKQTIDLQKIIEEQQKAEQKALKKTNELKQKIEIQADFKEEITIKSDNKENKSDSNKDKNSLVDISA
SIO_010081: CHLWT_RS09345
subclass of: SO_0000673
so part of: CHLWT_RS09345
location: 2039..2284
location: region:2039-2284:1
so has part: feature:2039-2284:1:exon

WP_112000819.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2039-2284:1:exon

CHLWT_RS09350
type: Gene
subclass of: SO_0000704
RO_0002162: 91353
locus tag: CHLWT_RS09350
old locus tag: CHLWT_a0006
so part of: sequence
location: complement(2285..3643)
location: region:2285-3643:-1
so has part: feature:2285-3643:-1:exon
subclass of: SO_0000010

56510942
type: Gene
SIO_000068: ncbigene

position:2285:-1
position: 2285
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3643:-1
position: 3643
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2285-3643:-1:exon

CHLWT_RS09350
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 91353
locus tag: CHLWT_RS09350
old locus tag: CHLWT_a0006
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: MLVKFFSDKKGGGIGSINYLLNNRVEKGTARILQGDENITRDLINSMSQKHKTCVGCLSFEEKNIDEDTKKEIMRDFENMLLTPAMQGRYNILWVEHTDKKRLELNFVIPKIDLQSKTALNPYFHMADSKRKDLWTDYVNLKHNFTDPKNPAKQNTLKGSKKEYELIKDYQELDKLLHEQVKQGNINSRDEIIQLLKENSIEVTRQGKDYLSIKLPDSKKAKRFKGSIYDEQFTSTKELKSINTRQSERERAYNERDNETELRRLEKELAKFIQSKYEFYISRDKKRALQFSKRADKTKDIKPINELYYRDNDSNNFLNDCVVAVDNAKSNSKRIRDSRKFEQTRRLDDNSDRQDRNDTRQQEIQSDKNQIRAENDSIRERINKRNREIAERTRECFNSIREIIAKRARATERKQEFAERIREIRERIQRELKQISQKVERITRKISRGFSR
SIO_010081: CHLWT_RS09350
subclass of: SO_0000673
so part of: CHLWT_RS09350
location: complement(2285..3643)
location: region:2285-3643:-1
so has part: feature:2285-3643:-1:exon

WP_112000820.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2285-3643:-1:exon

CHLWT_RS09355
type: Gene
subclass of: SO_0000704
RO_0002162: 91353
gene: mobC
locus tag: CHLWT_RS09355
so part of: sequence
location: complement(3633..3941)
location: region:3633-3941:-1
so has part: feature:3633-3941:-1:exon
subclass of: SO_0000010

56510943
type: Gene
SIO_000068: ncbigene

position:3633:-1
position: 3633
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3941:-1
position: 3941
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3633-3941:-1:exon

CHLWT_RS09355
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 91353
gene: mobC
locus tag: CHLWT_RS09355
inference: COORDINATES: similar to AA sequence:RefSeq:WP_000413832.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: plasmid mobilization relaxosome protein MobC
translation: MKSTIKSIRFSQEQMIYIKEQMALNNQTFSDFIFESISKPKKKIAVVRANQDLIIELAKWGNNLNQVAKHLNTKKSGIDRVGLEMLSRIENHLEQIRAKYAC
SIO_010081: CHLWT_RS09355
subclass of: SO_0000673
so part of: CHLWT_RS09355
location: complement(3633..3941)
location: region:3633-3941:-1
so has part: feature:3633-3941:-1:exon

WP_111969495.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3633-3941:-1:exon