Caballeronia zhejiangensis strain A33_M4_a plasmid p4, complete sequence.
type: Entry
definition: Caballeronia zhejiangensis strain A33_M4_a plasmid p4, complete sequence.
sequence version: NZ_CP084289.1
sequence date: 2023-04-27
sequence: sequence
division: CON
label: NZ_CP084289.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN21547024
keyword: RefSeq
source: Caballeronia zhejiangensis
organism: Caballeronia zhejiangensis
taxonomy: Bacteria; Pseudomonadota; Betaproteobacteria; Burkholderiales; Burkholderiaceae; Caballeronia.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP084289.1.\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 Date :: 2020\nAssembly Method :: SPAdes v. 3.13.0; Unicycler v. 2.4.8-beta\nAssembly Name :: A33_M4_a\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 60x\nSequencing Technology :: Illumina HiSeq; Oxford Nanopore MinION\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 04/27/2023 07:38:59\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) :: 6,968\nCDSs (total) :: 6,881\nGenes (coding) :: 6,744\nCDSs (with protein) :: 6,744\nGenes (RNA) :: 87\nrRNAs :: 6, 6, 6 (5S, 16S, 23S)\ncomplete rRNAs :: 6, 6, 6 (5S, 16S, 23S)\ntRNAs :: 65\nncRNAs :: 4\nPseudo Genes (total) :: 137\nCDSs (without protein) :: 137\nPseudo Genes (ambiguous residues) :: 0 of 137\nPseudo Genes (frameshifted) :: 49 of 137\nPseudo Genes (incomplete) :: 101 of 137\nPseudo Genes (internal stop) :: 15 of 137\nPseudo Genes (multiple problems) :: 25 of 137\nCRISPR Arrays :: 2\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 8158
topology: circular
so has quality: SO_0000988
location: 1..8158
location: region:1-8158:1
RO_0002162: 871203

NZ_CP084289
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN21547024
type: BioSample
SIO_000068: biosample

1
title: Prevalence and functional effects of a genomic island for insect symbiosis within Burkholderiaceae
author: Stillson, P.T.
author: Baltrus, D.A.
author: Ravenscraft, A.
journal: Unpublished

2
title: Direct Submission
author: Stillson, P.T.
author: Baltrus, D.A.
author: Ravenscraft, A.
journal: Submitted (22-SEP-2021) Biology Department, University of Texas at Arlington, 501 S. Nedderman Dr., Arlington, TX 76019, USA

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

position:8158:1
position: 8158
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-8158:1:source
so part of: sequence
organism: Caballeronia zhejiangensis
mol type: genomic DNA
strain: A33_M4_a
host: Anasa tristis
plasmid: p4
country: USA: Georgia
collection date: 2014
collected by: J.R. Garcia

871203
type: Taxonomy
SIO_000068: taxonomy

LDZ23_RS34765
type: Gene
subclass of: SO_0000704
RO_0002162: 871203
locus tag: LDZ23_RS34765
so part of: sequence
location: 200..1054
location: region:200-1054:1
so has part: feature:200-1054:1:exon
subclass of: SO_0000010

position:200:1
position: 200
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1054:1
position: 1054
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:200-1054:1:exon

LDZ23_RS34765
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 871203
locus tag: LDZ23_RS34765
inference: COORDINATES: protein motif:HMM:NF024244.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: integrase domain-containing protein
translation: MEASLYKGAATLTRQKMLTTFRAFAAHAKLQRYGDVDPVTVTKKQLCNYVSTRIEAGITARTIQNEVSHLRRALHGAGRGAWADALTNLQLGVPAGTRIGGGHVVDEQVLAHALEHAAADTRAWIQLERCLGLRREEMIESHKSLKQWEAALARGQSFITVRYGTKGGRVRDTVIPAPYRTRALEAVQAALTVMATRSHLVDATTARAAQKHVHERFAALGLKGKDSGHALRRAFCRDNYEYYLREGHEVKEALALCSRDLGHGEGRGRWVWNNYLRASYEQQT
SIO_010081: LDZ23_RS34765
subclass of: SO_0000673
so part of: LDZ23_RS34765
location: 200..1054
location: region:200-1054:1
so has part: feature:200-1054:1:exon

WP_244808903.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:200-1054:1:exon

LDZ23_RS34770
type: Gene
subclass of: SO_0000704
RO_0002162: 871203
locus tag: LDZ23_RS34770
so part of: sequence
location: 1038..1298
location: region:1038-1298:1
so has part: feature:1038-1298:1:exon
subclass of: SO_0000010

position:1038:1
position: 1038
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1298:1
position: 1298
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1038-1298:1:exon

LDZ23_RS34770
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 871203
locus tag: LDZ23_RS34770
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: MSSKPEFVTAHRLPKGSVWKVKTELVGGTQLEALSDPADALPRVKISPEAFEALKGLRHRGETIREVVERLIFTAIGQPNSDPRQR
SIO_010081: LDZ23_RS34770
subclass of: SO_0000673
so part of: LDZ23_RS34770
location: 1038..1298
location: region:1038-1298:1
so has part: feature:1038-1298:1:exon

WP_244808904.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1038-1298:1:exon

LDZ23_RS34775
type: Gene
subclass of: SO_0000704
RO_0002162: 871203
locus tag: LDZ23_RS34775
so part of: sequence
location: 1794..2435
location: region:1794-2435:1
so has part: feature:1794-2435:1:exon
subclass of: SO_0000010

position:1794:1
position: 1794
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2435:1
position: 2435
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1794-2435:1:exon

LDZ23_RS34775
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 871203
locus tag: LDZ23_RS34775
inference: COORDINATES: similar to AA sequence:RefSeq:WP_004532770.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: AAA family ATPase
translation: MIITIGNTKGGVGKSTLAVQLALGLSLDGQRVWLVDGDRQGTSLGAITVRAESGRAPIAAAAYPDGATLRAQVTQQASAYDHVIIDAGGRDSTALRAALTVSDLMLVPFQPRSFDVWALSDVASLLREARSVRDVRALALLNAADPQGSDNEEASEALADIEGIELLPLRIGRRKAFASASGAGLYIDEYRPRDASASIELSALKNYIISILK
SIO_010081: LDZ23_RS34775
subclass of: SO_0000673
so part of: LDZ23_RS34775
location: 1794..2435
location: region:1794-2435:1
so has part: feature:1794-2435:1:exon

WP_244808907.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1794-2435:1:exon

LDZ23_RS34780
type: Gene
subclass of: SO_0000704
RO_0002162: 871203
locus tag: LDZ23_RS34780
so part of: sequence
location: 2450..2704
location: region:2450-2704:1
so has part: feature:2450-2704:1:exon
subclass of: SO_0000010

position:2450:1
position: 2450
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2704:1
position: 2704
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2450-2704:1:exon

LDZ23_RS34780
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 871203
locus tag: LDZ23_RS34780
inference: COORDINATES: similar to AA sequence:RefSeq:WP_013106014.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MSITKKPKSVASEPAASAFIARAPDATAAANTSPSARKNKVQIAITIAPDLLAAVDALAVRKGLSRAAAISLACAELVERDTKN
SIO_010081: LDZ23_RS34780
subclass of: SO_0000673
so part of: LDZ23_RS34780
location: 2450..2704
location: region:2450-2704:1
so has part: feature:2450-2704:1:exon

WP_244808905.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2450-2704:1:exon

LDZ23_RS34785
type: Gene
subclass of: SO_0000704
RO_0002162: 871203
locus tag: LDZ23_RS34785
so part of: sequence
location: complement(3019..3771)
location: region:3019-3771:-1
so has part: feature:3019-3771:-1:exon
subclass of: SO_0000010

position:3019:-1
position: 3019
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3771:-1
position: 3771
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3019-3771:-1:exon

LDZ23_RS34785
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 871203
locus tag: LDZ23_RS34785
inference: COORDINATES: similar to AA sequence:RefSeq:WP_009242021.1
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: MKTGLSAKPGSQTGIAERNVTMANAVTRAAHGLSLPEKRFIAAALAKTDSTDVRGLMDPKMQTVKLSAIEYAETFGITLDAAYQQLQAGAEALQQPKVIVETPTRRGVVREVRAWVITGKYAKGEGMVEVRWHPDLVPFLFGLRKEFTTYKLKHAAAFRSIYSWRLFECLRSWQGAGRWTPTIVEFQEATDATPTARANFKELRLRVIEPAVKELREKNGLIVKWEPIKAGRKVTALRFEFEPNPQGALF
SIO_010081: LDZ23_RS34785
subclass of: SO_0000673
so part of: LDZ23_RS34785
location: complement(3019..3771)
location: region:3019-3771:-1
so has part: feature:3019-3771:-1:exon

WP_244808906.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3019-3771:-1:exon

LDZ23_RS34790
type: Gene
subclass of: SO_0000704
RO_0002162: 871203
locus tag: LDZ23_RS34790
so part of: sequence
location: complement(4092..4388)
location: region:4092-4388:-1
so has part: feature:4092-4388:-1:exon
subclass of: SO_0000010

position:4092:-1
position: 4092
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4388:-1
position: 4388
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4092-4388:-1:exon

LDZ23_RS34790
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 871203
locus tag: LDZ23_RS34790
inference: COORDINATES: similar to AA sequence:RefSeq:WP_013699706.1
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: HigA family addiction module antitoxin
translation: MTQMFNPPHPGETLREDILPELGLTVTQAAEQLGVTRVALSRVLNEHAGISPEMALRIEGWLGVENGGRADVWLAQQTAYDLWQARSKGTPKVERAHA
SIO_010081: LDZ23_RS34790
subclass of: SO_0000673
so part of: LDZ23_RS34790
location: complement(4092..4388)
location: region:4092-4388:-1
so has part: feature:4092-4388:-1:exon

WP_008344540.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4092-4388:-1:exon

LDZ23_RS34795
type: Gene
subclass of: SO_0000704
RO_0002162: 871203
locus tag: LDZ23_RS34795
so part of: sequence
location: complement(4399..4677)
location: region:4399-4677:-1
so has part: feature:4399-4677:-1:exon
subclass of: SO_0000010

position:4399:-1
position: 4399
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4677:-1
position: 4677
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4399-4677:-1:exon

LDZ23_RS34795
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 871203
locus tag: LDZ23_RS34795
inference: COORDINATES: similar to AA sequence:RefSeq:WP_006477504.1
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: MIKSWKHKGLEEFFVSGSKAGIRPDHASKLKRQLARLSVAQSPHDMNLPGWKFHRLEGPLAGHYAISVNGNWRMTFTFEGTDAVLVDYQDYH
SIO_010081: LDZ23_RS34795
subclass of: SO_0000673
so part of: LDZ23_RS34795
location: complement(4399..4677)
location: region:4399-4677:-1
so has part: feature:4399-4677:-1:exon

WP_244808899.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4399-4677:-1:exon

LDZ23_RS34800
type: Gene
subclass of: SO_0000704
RO_0002162: 871203
locus tag: LDZ23_RS34800
so part of: sequence
location: complement(4827..5780)
location: region:4827-5780:-1
so has part: feature:4827-5780:-1:exon
subclass of: SO_0000010

position:4827:-1
position: 4827
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:5780:-1
position: 5780
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4827-5780:-1:exon

LDZ23_RS34800
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 871203
locus tag: LDZ23_RS34800
inference: COORDINATES: similar to AA sequence:RefSeq:WP_010516182.1
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: MGSILVLATSLPSLVTSAGEQASIRFLEFFASAIRNPHTRRAYARAAGDFLAWCASAGVTSITAVQPLHVAAWIELQTQTHAASTVKQRLAAIRHLFDWLVTGQIVPHNPAASVRGPSHTPKKGRTPVLDASEARQLLDSIDVSTPIGLRDRALIALMVFSFARIGAALAMRVEDVYVQQRRLWVRLREKGGKAHAMPCHHTLEAYLHDYLEQTGLRDEPKGPLFRTIARGTGQLSPSALPQANAYAMVRRRARVAGIDTLIGNHTFRATGITAYLKNGGTLENAAAMANHASTRTTQLYDRRHDEISLDEVERIRL
SIO_010081: LDZ23_RS34800
subclass of: SO_0000673
so part of: LDZ23_RS34800
location: complement(4827..5780)
location: region:4827-5780:-1
so has part: feature:4827-5780:-1:exon

WP_244808900.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4827-5780:-1:exon

LDZ23_RS34805
type: Gene
subclass of: SO_0000704
RO_0002162: 871203
locus tag: LDZ23_RS34805
so part of: sequence
location: complement(5789..6082)
location: region:5789-6082:-1
so has part: feature:5789-6082:-1:exon
subclass of: SO_0000010

position:5789:-1
position: 5789
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:6082:-1
position: 6082
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5789-6082:-1:exon

LDZ23_RS34805
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 871203
locus tag: LDZ23_RS34805
inference: COORDINATES: similar to AA sequence:RefSeq:WP_008343548.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MSDKLIADLRTEVAAALEALEGLVITVDFDSEDPDSVEAAIEKVEATIDATVAPYRGHPLIESAVADLKAECREGLYKQAERAAPITPGITTKPTLH
SIO_010081: LDZ23_RS34805
subclass of: SO_0000673
so part of: LDZ23_RS34805
location: complement(5789..6082)
location: region:5789-6082:-1
so has part: feature:5789-6082:-1:exon

WP_244808901.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5789-6082:-1:exon

LDZ23_RS34810
type: Gene
subclass of: SO_0000704
RO_0002162: 871203
locus tag: LDZ23_RS34810
so part of: sequence
location: complement(6110..6499)
location: region:6110-6499:-1
so has part: feature:6110-6499:-1:exon
subclass of: SO_0000010

position:6110:-1
position: 6110
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:6499:-1
position: 6499
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:6110-6499:-1:exon

LDZ23_RS34810
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 871203
locus tag: LDZ23_RS34810
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: MERAATLRLTLVRSAGDEAAFSPNYQRELKQFYHLVRADHTRISAIAFTMPGLSDDTGFTGEFVVPLSQEIGPVLARAALAWRNAQAGRVVRLTLGTLDFDVGTASALEALVTRAQALLVSQETTVPPK
SIO_010081: LDZ23_RS34810
subclass of: SO_0000673
so part of: LDZ23_RS34810
location: complement(6110..6499)
location: region:6110-6499:-1
so has part: feature:6110-6499:-1:exon

WP_244808902.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:6110-6499:-1:exon

LDZ23_RS34815
type: Gene
subclass of: SO_0000704
RO_0002162: 871203
locus tag: LDZ23_RS34815
so part of: sequence
location: 6664..6975
location: region:6664-6975:1
so has part: feature:6664-6975:1:exon
subclass of: SO_0000010

position:6664:1
position: 6664
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:6975:1
position: 6975
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:6664-6975:1:exon

LDZ23_RS34815
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 871203
locus tag: LDZ23_RS34815
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: MSDSDLHALALAVADCAQFSSLIRRALGKQQYEKTESTLCRDMSDLVGLVEWSLPLDMAQQSELNKARTYLALRRLDWALTCVDGVLQSVRTAIQDDCLPDSS
SIO_010081: LDZ23_RS34815
subclass of: SO_0000673
so part of: LDZ23_RS34815
location: 6664..6975
location: region:6664-6975:1
so has part: feature:6664-6975:1:exon

WP_008344535.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:6664-6975:1:exon

LDZ23_RS34820
type: Gene
subclass of: SO_0000704
RO_0002162: 871203
locus tag: LDZ23_RS34820
so part of: sequence
location: 7079..7501
location: region:7079-7501:1
so has part: feature:7079-7501:1:exon
subclass of: SO_0000010

position:7079:1
position: 7079
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:7501:1
position: 7501
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:7079-7501:1:exon

LDZ23_RS34820
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 871203
locus tag: LDZ23_RS34820
inference: COORDINATES: similar to AA sequence:RefSeq:WP_006051697.1
GO function: GO:0000156 - phosphorelay response regulator activity [Evidence IEA]
GO process: GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: response regulator
translation: MPLNQARLRVLVVDDNHDAALAMTVYLSLEDIESRAVFGGRDAIDLAPEWAPHIILMDIQMPACNGIEAARMLRRDPRTNHIAIIAYTALDETELRRQLVDDEFDGYLQKGRDLSQLIQLLKTFTQADGTGSGTRAGGVA
SIO_010081: LDZ23_RS34820
subclass of: SO_0000673
so part of: LDZ23_RS34820
location: 7079..7501
location: region:7079-7501:1
so has part: feature:7079-7501:1:exon

WP_235366130.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:7079-7501:1:exon