Formicincola oecophyllae strain F3b2 plasmid unnamed1, complete sequence.
type: Entry
definition: Formicincola oecophyllae strain F3b2 plasmid unnamed1, complete sequence.
sequence version: NZ_CP038232.1
sequence date: 2023-06-24
sequence: sequence
division: CON
label: NZ_CP038232.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN11175497
keyword: RefSeq
source: Formicincola oecophyllae
organism: Formicincola oecophyllae
taxonomy: Bacteria; Pseudomonadota; Alphaproteobacteria; Rhodospirillales; Acetobacteraceae; Formicincola.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP038232.1.\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 :: 19-MAR-2019\nAssembly Method :: HGAP v. 4\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 400.0x\nSequencing Technology :: PacBio Sequel\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 06/24/2023 05:09:06\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) :: 1,740\nCDSs (total) :: 1,686\nGenes (coding) :: 1,671\nCDSs (with protein) :: 1,671\nGenes (RNA) :: 54\nrRNAs :: 1, 1, 1 (5S, 16S, 23S)\ncomplete rRNAs :: 1, 1, 1 (5S, 16S, 23S)\ntRNAs :: 47\nncRNAs :: 4\nPseudo Genes (total) :: 15\nCDSs (without protein) :: 15\nPseudo Genes (ambiguous residues) :: 0 of 15\nPseudo Genes (frameshifted) :: 1 of 15\nPseudo Genes (incomplete) :: 14 of 15\nPseudo Genes (internal stop) :: 1 of 15\nPseudo Genes (multiple problems) :: 1 of 15\nCRISPR Arrays :: 4\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 6500
topology: circular
so has quality: SO_0000988
location: 1..6500
location: region:1-6500:1
RO_0002162: 2558361

NZ_CP038232
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN11175497
type: BioSample
SIO_000068: biosample

1
title: The complete genome sequence of Swingsia_sp. F3b2 LMG30590(T)
author: Chua, K.-O.
author: Chan, K.-G.
author: See-Too, W.-S.
journal: Unpublished

2
title: Direct Submission
author: Chua, K.-O.
author: Chan, K.-G.
author: See-Too, W.-S.
journal: Submitted (25-MAR-2019) Institute of Biological Sciences, University of Malaya, University of Malaya, Kuala Lumpur, Kuala Lumpur 50603, Malaysia

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

position:6500:1
position: 6500
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-6500:1:source
so part of: sequence
organism: Formicincola oecophyllae
mol type: genomic DNA
strain: F3b2
host: Oecophylla smaragdina
culture collection: NBRC:113640
type material: type strain of Formicincola oecophyllae
plasmid: unnamed1
country: Malaysia: Kuala Lumpur
collection date: 2017-07-15
collected by: Kah-Ooi Chua

2558361
type: Taxonomy
SIO_000068: taxonomy

E3E12_RS08680
type: Gene
subclass of: SO_0000704
RO_0002162: 2558361
locus tag: E3E12_RS08680
old locus tag: E3E12_08585
so part of: sequence
location: 1..702
location: region:1-702:1
so has part: feature:1-702:1:exon
subclass of: SO_0000010

position:702:1
position: 702
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1-702:1:exon

E3E12_RS08680
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2558361
locus tag: E3E12_RS08680
old locus tag: E3E12_08585
inference: COORDINATES: similar to AA sequence:RefSeq:WP_008344542.1
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: MKSSPLTLIAMSNALVKAGQGLSLPEKRIVMLAISKLDSRQPITNLVPITRITAREYADLTQCDMPTAYQALQSAGEQLFKRKITFHKITKKGVITTEMRWVGRCTYQAGEGWAELAWWPELLPCLLDLKKQFTTYHLQQATALRSVYSWRLMELLMRFKNSGWAEYNLKDFCNSMEATEKQRLNFANIRRRIIEPAVNELIKKDHWNIKWFSIKEGRRVVRLKFIFSHHIRS
SIO_010081: E3E12_RS08680
subclass of: SO_0000673
so part of: E3E12_RS08680
location: 1..702
location: region:1-702:1
so has part: feature:1-702:1:exon

WP_206338688.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1-702:1:exon

E3E12_RS08685
type: Gene
subclass of: SO_0000704
RO_0002162: 2558361
locus tag: E3E12_RS08685
old locus tag: E3E12_08590
so part of: sequence
location: complement(762..838)
location: region:762-838:-1
so has part: feature:762-838:-1:exon
subclass of: SO_0000663

position:762:-1
position: 762
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:838:-1
position: 838
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:762-838:-1:exon

E3E12_RS08685
type: Transfer RNA
subclass of: SO_0000253
RO_0002162: 2558361
locus tag: E3E12_RS08685
old locus tag: E3E12_08590
product: tRNA-Met
inference: COORDINATES: profile:tRNAscan-SE:2.0.12
note: Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
anticodon: (pos:complement(802..804),aa:Met,seq:cat)
SIO_010081: E3E12_RS08685
subclass of: SO_0000673
so part of: E3E12_RS08685
location: complement(762..838)
location: region:762-838:-1
so has part: feature:762-838:-1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:762-838:-1:exon

E3E12_RS08690
type: Gene
subclass of: SO_0000704
RO_0002162: 2558361
gene: rrf
locus tag: E3E12_RS08690
old locus tag: E3E12_08595
so part of: sequence
location: complement(864..978)
location: region:864-978:-1
so has part: feature:864-978:-1:exon
subclass of: SO_0000573

position:864:-1
position: 864
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:978:-1
position: 978
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:864-978:-1:exon

E3E12_RS08690
type: Ribosomal RNA
subclass of: SO_0000252
RO_0002162: 2558361
gene: rrf
locus tag: E3E12_RS08690
old locus tag: E3E12_08595
product: 5S ribosomal RNA
inference: COORDINATES: nucleotide motif:Rfam:14.4:RF00001
inference: COORDINATES: profile:INFERNAL:1.1.4
note: Derived by automated computational analysis using gene prediction method: cmsearch.
SIO_010081: E3E12_RS08690
subclass of: SO_0000673
so part of: E3E12_RS08690
location: complement(864..978)
location: region:864-978:-1
so has part: feature:864-978:-1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:864-978:-1:exon

E3E12_RS08695
type: Gene
subclass of: SO_0000704
RO_0002162: 2558361
locus tag: E3E12_RS08695
old locus tag: E3E12_08600
so part of: sequence
location: complement(1040..3775)
location: region:1040-3775:-1
so has part: feature:1040-3775:-1:exon
subclass of: SO_0000573

position:1040:-1
position: 1040
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3775:-1
position: 3775
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1040-3775:-1:exon

E3E12_RS08695
type: Ribosomal RNA
subclass of: SO_0000252
RO_0002162: 2558361
locus tag: E3E12_RS08695
old locus tag: E3E12_08600
product: 23S ribosomal RNA
inference: COORDINATES: nucleotide motif:Rfam:14.4:RF02541
inference: COORDINATES: profile:INFERNAL:1.1.4
note: Derived by automated computational analysis using gene prediction method: cmsearch.
SIO_010081: E3E12_RS08695
subclass of: SO_0000673
so part of: E3E12_RS08695
location: complement(1040..3775)
location: region:1040-3775:-1
so has part: feature:1040-3775:-1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:1040-3775:-1:exon

E3E12_RS08700
type: Gene
subclass of: SO_0000704
RO_0002162: 2558361
locus tag: E3E12_RS08700
old locus tag: E3E12_08605
so part of: sequence
location: complement(4017..4092)
location: region:4017-4092:-1
so has part: feature:4017-4092:-1:exon
subclass of: SO_0000663

position:4017:-1
position: 4017
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

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

urn:…
SIO_000300: 1
SIO_000628: feature:4017-4092:-1:exon

E3E12_RS08700
type: Transfer RNA
subclass of: SO_0000253
RO_0002162: 2558361
locus tag: E3E12_RS08700
old locus tag: E3E12_08605
product: tRNA-Ala
inference: COORDINATES: profile:tRNAscan-SE:2.0.12
note: Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
anticodon: (pos:complement(4057..4059),aa:Ala,seq:tgc)
SIO_010081: E3E12_RS08700
subclass of: SO_0000673
so part of: E3E12_RS08700
location: complement(4017..4092)
location: region:4017-4092:-1
so has part: feature:4017-4092:-1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:4017-4092:-1:exon

E3E12_RS08705
type: Gene
subclass of: SO_0000704
RO_0002162: 2558361
locus tag: E3E12_RS08705
old locus tag: E3E12_08610
so part of: sequence
location: complement(4101..4177)
location: region:4101-4177:-1
so has part: feature:4101-4177:-1:exon
subclass of: SO_0000663

position:4101:-1
position: 4101
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4177:-1
position: 4177
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4101-4177:-1:exon

E3E12_RS08705
type: Transfer RNA
subclass of: SO_0000253
RO_0002162: 2558361
locus tag: E3E12_RS08705
old locus tag: E3E12_08610
product: tRNA-Ile
inference: COORDINATES: profile:tRNAscan-SE:2.0.12
note: Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
anticodon: (pos:complement(4141..4143),aa:Ile,seq:gat)
SIO_010081: E3E12_RS08705
subclass of: SO_0000673
so part of: E3E12_RS08705
location: complement(4101..4177)
location: region:4101-4177:-1
so has part: feature:4101-4177:-1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:4101-4177:-1:exon

E3E12_RS08710
type: Gene
subclass of: SO_0000704
RO_0002162: 2558361
locus tag: E3E12_RS08710
old locus tag: E3E12_08615
so part of: sequence
location: complement(4281..5763)
location: region:4281-5763:-1
so has part: feature:4281-5763:-1:exon
subclass of: SO_0000573

position:4281:-1
position: 4281
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:5763:-1
position: 5763
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4281-5763:-1:exon

E3E12_RS08710
type: Ribosomal RNA
subclass of: SO_0000252
RO_0002162: 2558361
locus tag: E3E12_RS08710
old locus tag: E3E12_08615
product: 16S ribosomal RNA
inference: COORDINATES: nucleotide motif:Rfam:14.4:RF00177
inference: COORDINATES: profile:INFERNAL:1.1.4
note: Derived by automated computational analysis using gene prediction method: cmsearch.
SIO_010081: E3E12_RS08710
subclass of: SO_0000673
so part of: E3E12_RS08710
location: complement(4281..5763)
location: region:4281-5763:-1
so has part: feature:4281-5763:-1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:4281-5763:-1:exon