Candidatus Doolittlea endobia isolate DEMHIR plasmid II, complete sequence.
type: Entry
definition: Candidatus Doolittlea endobia isolate DEMHIR plasmid II, complete sequence.
sequence version: NZ_LN999834.1
sequence date: 2022-12-24
sequence: sequence
division: CON
label: NZ_LN999834.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMEA3725905
keyword: RefSeq
source: Candidatus Doolittlea endobia
organism: Candidatus Doolittlea endobia
taxonomy: Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Candidatus Doolittlea.
reference: 1
comment: REFSEQ INFORMATION: The reference sequence is identical to\nLN999834.1.\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-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/24/2022 02:57:03\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) :: 632\nCDSs (total) :: 585\nGenes (coding) :: 504\nCDSs (with protein) :: 504\nGenes (RNA) :: 47\nrRNAs :: 1, 1, 1 (5S, 16S, 23S)\ncomplete rRNAs :: 1, 1, 1 (5S, 16S, 23S)\ntRNAs :: 41\nncRNAs :: 3\nPseudo Genes (total) :: 81\nCDSs (without protein) :: 81\nPseudo Genes (ambiguous residues) :: 0 of 81\nPseudo Genes (frameshifted) :: 67 of 81\nPseudo Genes (incomplete) :: 40 of 81\nPseudo Genes (internal stop) :: 46 of 81\nPseudo Genes (multiple problems) :: 50 of 81\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 11828
topology: circular
so has quality: SO_0000988
location: 1..11828
location: region:1-11828:1
RO_0002162: 1778262

NZ_LN999834
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMEA3725905
type: BioSample
SIO_000068: biosample

1
title: Direct Submission
author: Husnik, Filip.
journal: Submitted (18-JAN-2016) UNIVERSITY OF SOUTH BOHEMIA, Branisovska 31, Czech Republic

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

position:11828:1
position: 11828
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-11828:1:source
so part of: sequence
organism: Candidatus Doolittlea endobia
mol type: genomic DNA
isolate: DEMHIR
plasmid: II

1778262
type: Taxonomy
SIO_000068: taxonomy

A4A68_RS03040
type: Gene
subclass of: SO_0000704
RO_0002162: 1778262
gene: repA
locus tag: A4A68_RS03040
old locus tag: MHIR_DE00705
so part of: sequence
location: join(11694..11828,1..762)
location: region:1-11828:1
so has part: feature:11694-11828:1:exon
so has part: feature:1-762:1:exon
subclass of: SO_0000010

urn:…
SIO_000300: 1
SIO_000628: feature:11694-11828:1:exon

position:11694:1
position: 11694
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 2
SIO_000628: feature:1-762:1:exon

position:762:1
position: 762
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

A4A68_RS03040
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1778262
gene: repA
locus tag: A4A68_RS03040
old locus tag: MHIR_DE00705
inference: COORDINATES: similar to AA sequence:RefSeq:WP_011412274.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: plasmid replication initiator RepA
translation: MDKKNLSVFSQAIPKVFSSRCYVKNPHPCYRPPKGGVKPPHIIDAMRKAARENTPSHHPLWRIRPRYHAITHKLLSNERTMNLHRARAVDAIMECLAAHMNIVTGKVYMSLAQISDACGLTTYNAADKPCRSRASRAINEHLEAIGAVLCDRIWDDTTASYIPNIIWVTELFFVLIGYEYGKYLSAQQQQLSWENQKLRDVGKKSITLIEARCMAKADHIRRAFNYRTKKLARSKQRRQACKLKAIGEQQARKYILNDLVKLYGKKELEIMGYTELNRMIKQRYYTMCKLATAPPDIG
SIO_010081: A4A68_RS03040
subclass of: SO_0000673
so part of: A4A68_RS03040
location: join(11694..11828,1..762)
location: region:1-11828:1
so has part: feature:11694-11828:1:exon
so has part: feature:1-762:1:exon

WP_231938076.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:11694-11828:1:exon

urn:…
SIO_000300: 2
SIO_000628: feature:1-762:1:exon

A4A68_RS03045
type: Gene
subclass of: SO_0000704
RO_0002162: 1778262
locus tag: A4A68_RS03045
pseudo: true
so part of: sequence
location: 2235..4422
location: region:2235-4422:1
so has part: feature:2235-4422:1:exon
subclass of: SO_0000010

position:2235:1
position: 2235
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:4422:1
position: 4422
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2235-4422:1:exon

A4A68_RS03045
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1778262
locus tag: A4A68_RS03045
inference: COORDINATES: similar to AA sequence:RefSeq:WP_007039345.1
GO function: GO:0004386 - helicase activity [Evidence IEA]
note: frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
pseudo: true
codon start: 1
transl table: 11
product: ATP-dependent RecD-like DNA helicase
SIO_010081: A4A68_RS03045
subclass of: SO_0000673
so part of: A4A68_RS03045
location: 2235..4422
location: region:2235-4422:1
so has part: feature:2235-4422:1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:2235-4422:1:exon

A4A68_RS03365
type: Gene
subclass of: SO_0000704
RO_0002162: 1778262
gene: thiC
locus tag: A4A68_RS03365
old locus tag: MHIR_DE00708
pseudo: true
so part of: sequence
location: 4933..6746
location: region:4933-6746:1
so has part: feature:4933-6746:1:exon
subclass of: SO_0000010

position:4933:1
position: 4933
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:6746:1
position: 6746
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4933-6746:1:exon

A4A68_RS03365
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1778262
gene: thiC
locus tag: A4A68_RS03365
old locus tag: MHIR_DE00708
inference: COORDINATES: similar to AA sequence:RefSeq:WP_012882980.1
GO function: GO:0051536 - iron-sulfur cluster binding [Evidence IEA]
GO process: GO:0009228 - thiamine biosynthetic process [Evidence IEA]
note: frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
pseudo: true
codon start: 1
transl table: 11
product: phosphomethylpyrimidine synthase ThiC
SIO_010081: A4A68_RS03365
subclass of: SO_0000673
so part of: A4A68_RS03365
location: 4933..6746
location: region:4933-6746:1
so has part: feature:4933-6746:1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:4933-6746:1:exon

A4A68_RS03055
type: Gene
subclass of: SO_0000704
RO_0002162: 1778262
gene: thiD
locus tag: A4A68_RS03055
old locus tag: MHIR_DE00710
pseudo: true
so part of: sequence
location: 8430..9217
location: region:8430-9217:1
so has part: feature:8430-9217:1:exon
subclass of: SO_0000010

position:8430:1
position: 8430
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:9217:1
position: 9217
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:8430-9217:1:exon

A4A68_RS03055
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1778262
gene: thiD
locus tag: A4A68_RS03055
old locus tag: MHIR_DE00710
inference: COORDINATES: similar to AA sequence:RefSeq:WP_004170231.1
GO function: GO:0008902 - hydroxymethylpyrimidine kinase activity [Evidence IEA]; GO:0008972 - phosphomethylpyrimidine kinase activity [Evidence IEA]
GO process: GO:0009228 - thiamine biosynthetic process [Evidence IEA]
note: frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
pseudo: true
codon start: 1
transl table: 11
product: bifunctional hydroxymethylpyrimidine kinase/phosphomethylpyrimidine kinase
SIO_010081: A4A68_RS03055
subclass of: SO_0000673
so part of: A4A68_RS03055
location: 8430..9217
location: region:8430-9217:1
so has part: feature:8430-9217:1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:8430-9217:1:exon

A4A68_RS03060
type: Gene
subclass of: SO_0000704
RO_0002162: 1778262
locus tag: A4A68_RS03060
old locus tag: MHIR_DE00711
so part of: sequence
location: complement(9355..9427)
location: region:9355-9427:-1
so has part: feature:9355-9427:-1:exon
subclass of: SO_0000663

position:9355:-1
position: 9355
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:9427:-1
position: 9427
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:9355-9427:-1:exon

A4A68_RS03060
type: Transfer RNA
subclass of: SO_0000253
RO_0002162: 1778262
locus tag: A4A68_RS03060
old locus tag: MHIR_DE00711
product: tRNA-Lys
inference: COORDINATES: profile:tRNAscan-SE:2.0.12
note: Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
anticodon: (pos:complement(9392..9394),aa:Lys,seq:ctt)
SIO_010081: A4A68_RS03060
subclass of: SO_0000673
so part of: A4A68_RS03060
location: complement(9355..9427)
location: region:9355-9427:-1
so has part: feature:9355-9427:-1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:9355-9427:-1:exon

A4A68_RS03065
type: Gene
subclass of: SO_0000704
RO_0002162: 1778262
gene: mscS
locus tag: A4A68_RS03065
old locus tag: MHIR_DE00712
so part of: sequence
location: 10351..11217
location: region:10351-11217:1
so has part: feature:10351-11217:1:exon
subclass of: SO_0000010

position:10351:1
position: 10351
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:11217:1
position: 11217
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:10351-11217:1:exon

A4A68_RS03065
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1778262
gene: mscS
locus tag: A4A68_RS03065
old locus tag: MHIR_DE00712
inference: COORDINATES: similar to AA sequence:RefSeq:WP_017893892.1
GO component: GO:0016020 - membrane [Evidence IEA]
GO process: GO:0055085 - transmembrane transport [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: small-conductance mechanosensitive channel MscS
translation: MADLNVVNGISDAGSWLLKNQCLLIQYLVNTITAIIILAIGSVAARVISNALNRVIKLRGIDATIADFLSAIVRYVLLAFTFVAVLGRIGVQTSSVIAVLGAAGLAIALALQGSLSNFAAGVLLVIFRPLKVGEYVDLGGAVGTVNQVHIFTTTLHTTDNKIIVVPNGKIIAGNIINYSRAPDRRVDIEITVAYSANIDLVKKVLGDVIAADDRITHGKEVTVRLKEMTPSSLNFVTRSWTANAEYWNVYFDLMENFKRALDANDLSLPFQQTDTSLHRTEKRSAKVK
SIO_010081: A4A68_RS03065
subclass of: SO_0000673
so part of: A4A68_RS03065
location: 10351..11217
location: region:10351-11217:1
so has part: feature:10351-11217:1:exon

WP_067566593.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:10351-11217:1:exon