Candidatus Campylobacter infans strain 19S00001 plasmid unnamed, complete sequence.
type: Entry
definition: Candidatus Campylobacter infans strain 19S00001 plasmid unnamed, complete sequence.
sequence version: NZ_CP049076.1
sequence date: 2023-03-17
sequence: sequence
division: CON
label: NZ_CP049076.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN14120449
keyword: RefSeq
source: Candidatus Campylobacter infans
organism: Candidatus Campylobacter infans
taxonomy: Bacteria; Campylobacterota; Epsilonproteobacteria; Campylobacterales; Campylobacteraceae; Campylobacter.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP049076.1.\nBacteria and source DNA available from Jaap Wagenaar, Birgitta\nDuim.\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 :: 30-JAN-2020\nAssembly Method :: SPAdes v. 3.10.1; Unicycler v. 0.4.7\nAssembly Name :: 19S00001-1\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 100.0x\nSequencing Technology :: Illumina NextSeq; Oxford Nanopore MiniION\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/17/2023 03:08:08\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) :: 1,790\nCDSs (total) :: 1,743\nGenes (coding) :: 1,720\nCDSs (with protein) :: 1,720\nGenes (RNA) :: 47\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 38\nncRNAs :: 3\nPseudo Genes (total) :: 23\nCDSs (without protein) :: 23\nPseudo Genes (ambiguous residues) :: 0 of 23\nPseudo Genes (frameshifted) :: 8 of 23\nPseudo Genes (incomplete) :: 19 of 23\nPseudo Genes (internal stop) :: 3 of 23\nPseudo Genes (multiple problems) :: 6 of 23\nCRISPR Arrays :: 1\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 5856
topology: circular
so has quality: SO_0000988
location: 1..5856
location: region:1-5856:1
RO_0002162: 2561898

NZ_CP049076
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN14120449
type: BioSample
SIO_000068: biosample

1
title: Complete genome sequence of the novel Campylobacter species Candidatus Campylobacter infans
author: Duim, B.
author: Zomer, A.
author: van der Graaf, L.
author: Wagenaar, J.
journal: Unpublished

2
title: Direct Submission
author: Duim, B.
author: Zomer, A.
author: van der Graaf, L.
author: Wagenaar, J.
journal: Submitted (20-FEB-2020) Infectious Diseases and Immunology, Utrecht University, Yalelaan 1, Utrecht 3845 CL, Netherlands

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

position:5856:1
position: 5856
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-5856:1:source
so part of: sequence
organism: Candidatus Campylobacter infans
mol type: genomic DNA
strain: 19S00001
isolation source: feces
host: Homo sapiens
plasmid: unnamed
country: Netherlands: Utrecht
lat lon: 52.090 N 5.121 E
collection date: 2019-01-20
collected by: Jaap Wagenaar, Birgitta Duim

2561898
type: Taxonomy
SIO_000068: taxonomy

CINF_RS08845
type: Gene
subclass of: SO_0000704
RO_0002162: 2561898
locus tag: CINF_RS08845
old locus tag: CINF_a0001
so part of: sequence
location: 366..1427
location: region:366-1427:1
so has part: feature:366-1427:1:exon
subclass of: SO_0000010

position:366:1
position: 366
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1427:1
position: 1427
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:366-1427:1:exon

CINF_RS08845
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2561898
locus tag: CINF_RS08845
old locus tag: CINF_a0001
inference: COORDINATES: protein motif:HMM:NF013235.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: replication initiation protein
translation: MNEIVKYHNDLHKLQINKFSELEQNLLFGILTHCRNKYDDFIFTLDDLNALSASRRYTANEMLQKVLKLQENIFKLDFTLVKSKNDEKHEHEIYNLFSKFAVCYEGKKNDWENARLTEIRLKVNEDFRYLIAYLTRDFIQYELEEFIFLNSRYTKTIYRYLKQFRTAGEWGISLADFRELLDIPANYRMCDIDTRILKPAIKQLSEPLNLFESARIPFKHLEVKKKKESGRGHRGRGGTITHLIFTFKPQPAGVLEARQAELNAQKIKQIQAQPQEPHYIKKIRELCANKTAFFWNKQEYFLDEIRRIENNTSISLNVCLMTNKELYNMSIKTYEEAQALIKACEHYKKTNRA
SIO_010081: CINF_RS08845
subclass of: SO_0000673
so part of: CINF_RS08845
location: 366..1427
location: region:366-1427:1
so has part: feature:366-1427:1:exon

WP_179975978.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:366-1427:1:exon

CINF_RS08850
type: Gene
subclass of: SO_0000704
RO_0002162: 2561898
locus tag: CINF_RS08850
old locus tag: CINF_a0002
so part of: sequence
location: 1589..1924
location: region:1589-1924:1
so has part: feature:1589-1924:1:exon
subclass of: SO_0000010

position:1589:1
position: 1589
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1924:1
position: 1924
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1589-1924:1:exon

CINF_RS08850
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2561898
locus tag: CINF_RS08850
old locus tag: CINF_a0002
inference: COORDINATES: similar to AA sequence:RefSeq:WP_018264009.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: type II toxin-antitoxin system RelE/ParE family toxin
translation: MKKIQAKFYQNTNGKEPVKEWLLELSKDDRIIIGKDIAVVEYGFPIGMPVCRSLGGSFYEVRSNISSNRIARVIFTIKGDFMILLHGFIKKTQKTPLNELNLAKLRAKEIQ
SIO_010081: CINF_RS08850
subclass of: SO_0000673
so part of: CINF_RS08850
location: 1589..1924
location: region:1589-1924:1
so has part: feature:1589-1924:1:exon

WP_179975979.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1589-1924:1:exon

CINF_RS08855
type: Gene
subclass of: SO_0000704
RO_0002162: 2561898
locus tag: CINF_RS08855
old locus tag: CINF_a0003
so part of: sequence
location: 1921..2199
location: region:1921-2199:1
so has part: feature:1921-2199:1:exon
subclass of: SO_0000010

position:1921:1
position: 1921
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2199:1
position: 2199
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1921-2199:1:exon

CINF_RS08855
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2561898
locus tag: CINF_RS08855
old locus tag: CINF_a0003
inference: COORDINATES: similar to AA sequence:RefSeq:WP_012855844.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: helix-turn-helix domain-containing protein
translation: MKANELNSFDDFLKRDGTFDEIQSYAIKKVITYQLQNEMKNQKITKTKLAQLMNTSRASINRLLDPSNKSLTLNTLECATRVLGKQLSINII
SIO_010081: CINF_RS08855
subclass of: SO_0000673
so part of: CINF_RS08855
location: 1921..2199
location: region:1921-2199:1
so has part: feature:1921-2199:1:exon

WP_179975980.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1921-2199:1:exon

CINF_RS08860
type: Gene
subclass of: SO_0000704
RO_0002162: 2561898
locus tag: CINF_RS08860
old locus tag: CINF_a0004
so part of: sequence
location: complement(2289..4175)
location: region:2289-4175:-1
so has part: feature:2289-4175:-1:exon
subclass of: SO_0000010

position:2289:-1
position: 2289
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4175:-1
position: 4175
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2289-4175:-1:exon

CINF_RS08860
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2561898
locus tag: CINF_RS08860
old locus tag: CINF_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: MLFKVIGSNFSKGANAVEYCLDLEKHKNAVPRVLKGNEKLTSMLIDLNDYKEKALFGVLSFSEKAADISDEKKLEIINRFEKAIFGDYILPHINTLWIEHSDKNGRLELNVIVPSINLTTQKSYKPYYHARDKARTALFCEIINIENNFTSPFDPERKQAVKIKNRQYVEAISEFKNLTQLDKLLRELVNKKELNSRDEIIEFLKENKVKFKIPKKPDGTILTDRIKIQLPNSKRFRDLQGDIYDERFINDQSVLELNREKHREIESYKKTRDTRHLHAMQERLLGAIQNINEYNAGRHASAIERVRKQTRAELEAARTNQARAEAELAASTQISQQIHASIDSISTSNSNSFHSDTTSNTSIQNHTSSAAMAARTSIDFHANNISSDSTRVYLDFELQEQDGLMSNDIEFLEFKQEQKRKDDEFINKEIERRERELEQREQELAKQDSEIDGIIKRERKQDSELANITTSAEQRNKELERNIDNSERFTKTINELDTRARNTISEFITRKISNYFTEFRERIKRVKDAASDYNTARKLIKDLKDKSKIAQNSRDYSDSEREQAIADINKILNNQQQQQLLFKFFKTQLKQIKDACDNALKQMKATREQAQQEQNNSYSYSVPRMRMR
SIO_010081: CINF_RS08860
subclass of: SO_0000673
so part of: CINF_RS08860
location: complement(2289..4175)
location: region:2289-4175:-1
so has part: feature:2289-4175:-1:exon

WP_179975981.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2289-4175:-1:exon

CINF_RS08865
type: Gene
subclass of: SO_0000704
RO_0002162: 2561898
locus tag: CINF_RS08865
old locus tag: CINF_a0005
so part of: sequence
location: complement(4165..4671)
location: region:4165-4671:-1
so has part: feature:4165-4671:-1:exon
subclass of: SO_0000010

position:4165:-1
position: 4165
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4671:-1
position: 4671
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4165-4671:-1:exon

CINF_RS08865
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2561898
locus tag: CINF_RS08865
old locus tag: CINF_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: MNKKNIIKSIRLTQKELESINQILENTDISFSELVKNNINLSRLDEIVKLKQEKNAQENAKIKSKFLKEIIFQLRAIGYNLFIATERARNSKESKIENLNYAAEQIYEVLNNLYNLLYIIHKNNDFSISNKIANDELVAQGESERLTRKALNIQSTIKQELAKNNNAF
SIO_010081: CINF_RS08865
subclass of: SO_0000673
so part of: CINF_RS08865
location: complement(4165..4671)
location: region:4165-4671:-1
so has part: feature:4165-4671:-1:exon

WP_179975976.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4165-4671:-1:exon

CINF_RS08870
type: Gene
subclass of: SO_0000704
RO_0002162: 2561898
locus tag: CINF_RS08870
so part of: sequence
location: complement(5451..5687)
location: region:5451-5687:-1
so has part: feature:5451-5687:-1:exon
subclass of: SO_0000010

position:5451:-1
position: 5451
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:5687:-1
position: 5687
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5451-5687:-1:exon

CINF_RS08870
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2561898
locus tag: CINF_RS08870
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: MNAFCATLKRVIIYRYTLLLARIRSLIACSSKLKGVKYCLLCFSSVALSSHTSSRYNAKKEKNIFEVALTLSASSCFL
SIO_010081: CINF_RS08870
subclass of: SO_0000673
so part of: CINF_RS08870
location: complement(5451..5687)
location: region:5451-5687:-1
so has part: feature:5451-5687:-1:exon

WP_179975977.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5451-5687:-1:exon