Formicincola oecophyllae strain F3b2 plasmid unnamed2, complete sequence.
type: Entry
definition: Formicincola oecophyllae strain F3b2 plasmid unnamed2, complete sequence.
sequence version: NZ_CP042424.1
sequence date: 2023-06-24
sequence: sequence
division: CON
label: NZ_CP042424.1
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\nCP042424.1.\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 :: 27-JUL-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: 9362
topology: circular
so has quality: SO_0000988
location: 1..9362
location: region:1-9362:1
RO_0002162: 2558361

NZ_CP042424
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journal: Unpublished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 (31-JUL-2019) High Impact Research, University of Malaya, Jalan University, Kuala Lumpur 50603, Malaysia

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

position:9362:1
position: 9362
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-9362:1: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: unnamed2
country: Malaysia: Kuala Lumpur
collection date: 2017-07-15
collected by: Kah-Ooi Chua

2558361
type: Taxonomy
SIO_000068: taxonomy

E3E12_RS08720
type: Gene
subclass of: SO_0000704
RO_0002162: 2558361
locus tag: E3E12_RS08720
old locus tag: E3E12_08745
so part of: sequence
location: complement(join(9346..9362,1..169))
location: region:1-9362:-1
so has part: feature:1-169:-1:exon
so has part: feature:9346-9362:-1:exon
subclass of: SO_0000010

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

position:9362:-1
position: 9362
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1-169:-1:exon

position:169:-1
position: 169
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 2
SIO_000628: feature:9346-9362:-1:exon

position:9346:-1
position: 9346
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

E3E12_RS08720
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2558361
locus tag: E3E12_RS08720
old locus tag: E3E12_08745
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: MKIILDLQGAQTESRLRGIGRQNVALADAIIKRSRNRHDIHILFNHRLTSERENLFQNMLH
SIO_010081: E3E12_RS08720
subclass of: SO_0000673
so part of: E3E12_RS08720
location: complement(join(9346..9362,1..169))
location: region:1-9362:-1
so has part: feature:1-169:-1:exon
so has part: feature:9346-9362:-1:exon

WP_149498306.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1-169:-1:exon

urn:…
SIO_000300: 2
SIO_000628: feature:9346-9362:-1:exon

E3E12_RS08725
type: Gene
subclass of: SO_0000704
RO_0002162: 2558361
locus tag: E3E12_RS08725
old locus tag: E3E12_08750
so part of: sequence
location: complement(187..732)
location: region:187-732:-1
so has part: feature:187-732:-1:exon
subclass of: SO_0000010

position:187:-1
position: 187
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:732:-1
position: 732
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:187-732:-1:exon

E3E12_RS08725
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2558361
locus tag: E3E12_RS08725
old locus tag: E3E12_08750
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: MCQNVIFKKKRREYILRADNERDNGNSDQAAALYQIIIDRWGATPGLLMQYGNALKDSASFKQAENIYKQVWMSPHRNADVALQLGHLMKIQGNSVKALEWYNRSIDLDKSITNPAHIECKNLDRSSKEAEENRIKIEKINDEKQQNIPEVRHIPPPTDSLNLRDRIVLCQLYEQLKFRRI
SIO_010081: E3E12_RS08725
subclass of: SO_0000673
so part of: E3E12_RS08725
location: complement(187..732)
location: region:187-732:-1
so has part: feature:187-732:-1:exon

WP_149498298.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:187-732:-1:exon

E3E12_RS08730
type: Gene
subclass of: SO_0000704
RO_0002162: 2558361
locus tag: E3E12_RS08730
old locus tag: E3E12_08755
so part of: sequence
location: complement(1156..1752)
location: region:1156-1752:-1
so has part: feature:1156-1752:-1:exon
subclass of: SO_0000010

position:1156:-1
position: 1156
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:1752:-1
position: 1752
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1156-1752:-1:exon

E3E12_RS08730
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2558361
locus tag: E3E12_RS08730
old locus tag: E3E12_08755
inference: COORDINATES: similar to AA sequence:RefSeq:WP_012290097.1
GO function: GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO process: 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: recombinase family protein
translation: MSDLFVMGQVLGYARTSTLYQNLEPQLEALEAAGARFIFREQATGTKADQKTRPQLTALLDGVREGDTVLVTRIDRLARSLPDLLQITKCLADKGVTLRAVEQPFDCDSLTGRLTLGILGVIAEFETGLRAERQAEGIERAKRSGKYRGRPADQAQHKRILALVAEGLNPTEISRHPTISMTRQGISKLLKKHRDAQK
SIO_010081: E3E12_RS08730
subclass of: SO_0000673
so part of: E3E12_RS08730
location: complement(1156..1752)
location: region:1156-1752:-1
so has part: feature:1156-1752:-1:exon

WP_240810646.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1156-1752:-1:exon

E3E12_RS08735
type: Gene
subclass of: SO_0000704
RO_0002162: 2558361
locus tag: E3E12_RS08735
old locus tag: E3E12_08760
so part of: sequence
location: 2380..3003
location: region:2380-3003:1
so has part: feature:2380-3003:1:exon
subclass of: SO_0000010

position:2380:1
position: 2380
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:3003:1
position: 3003
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2380-3003:1:exon

E3E12_RS08735
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2558361
locus tag: E3E12_RS08735
old locus tag: E3E12_08760
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: MSKQTSKVQFFQRTPWMTLLGDLRRHGRITYATLCIGEYLCSRFIHALKQGKPCILAHDEIGAQVGACRRTVVEALKTLESLGLVVSRTRRVAFWANGRKRMVNSAKAYTLHAAAELLAKWRQKATIKTREIMRAARARARETRRFFQSANTPPNVNNLFSLGRKLSTAKTQKVLPLKQQGPKEGLGRLEATLKRLEATIRKRKNQQ
SIO_010081: E3E12_RS08735
subclass of: SO_0000673
so part of: E3E12_RS08735
location: 2380..3003
location: region:2380-3003:1
so has part: feature:2380-3003:1:exon

WP_149498300.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2380-3003:1:exon

E3E12_RS08740
type: Gene
subclass of: SO_0000704
RO_0002162: 2558361
locus tag: E3E12_RS08740
old locus tag: E3E12_08765
so part of: sequence
location: complement(4214..5719)
location: region:4214-5719:-1
so has part: feature:4214-5719:-1:exon
subclass of: SO_0000010

position:4214:-1
position: 4214
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:5719:-1
position: 5719
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4214-5719:-1:exon

E3E12_RS08740
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2558361
locus tag: E3E12_RS08740
old locus tag: E3E12_08765
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: MFLLIQGRLLSPSRANGVFLSSLSSQKTEKYNKSYTVYNCDGMHDDTEALNNLLQYSHDIHISNRSGICHIKHTIHIINNDTSIKGDDSSSTKIEISSPSEPIIEVKEGLKNFSIKGISISRSTFVKDSQVCGLRIGNNQIFADLDDIISSGSGNGFCLGSIAFGRLNNAISTGNYGNGFFITNKDSTQPAQWSITNSLSQTNDNYGFYVESGNNPLILLPWINIETFANGHGGVRMTGNPYGGYIVSATIEAGVFSSDGGDEISLDTYAGYVKIGSGTFIEEAGQHPTGRNFHFLPSHKGHGIVATTNVADIQIVDTLISHNSEEGIMNGSYHTLLSASTLYGNGVTNENLCGYYGENIELGNSTIISATRSGNLNANLLSGHQGGGLCFATGEGVSISGSDVTFNRKNNIYFDHNPNQAKIMNVIGYNNISEGELKISPGEQSIIIYHHLTTKPRFINLTPLTEINGGWYIDKVTTLSFRVNLDKVDNKIIHMLWQASL
SIO_010081: E3E12_RS08740
subclass of: SO_0000673
so part of: E3E12_RS08740
location: complement(4214..5719)
location: region:4214-5719:-1
so has part: feature:4214-5719:-1:exon

WP_149498302.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4214-5719:-1:exon

E3E12_RS08745
type: Gene
subclass of: SO_0000704
RO_0002162: 2558361
locus tag: E3E12_RS08745
old locus tag: E3E12_08770
so part of: sequence
location: complement(5783..9319)
location: region:5783-9319:-1
so has part: feature:5783-9319:-1:exon
subclass of: SO_0000010

position:5783:-1
position: 5783
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:9319:-1
position: 9319
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5783-9319:-1:exon

E3E12_RS08745
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2558361
locus tag: E3E12_RS08745
old locus tag: E3E12_08770
EC number: 2.4.-.-
inference: COORDINATES: protein motif:HMM:NF012744.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: glycosyltransferase
translation: MPPGSPAERHEENGWRTRAAELIREQFIAELSPDIVHLGSLFEGYVDDAVTSIGLFDTNFLTAVTLHDLIPIVDPKRYLSELRPRRHWLRRAQFLKRADLLLSVSEYSKREAIQWLGISPEKIAVMMAGATENFVPASSHTIEHEILRRKFNLRKKFILHVGAVDPRKNVDFIFKALSTLSSDEQNVYQVVFVGRLFDEEVSRLRLAAARLGIDTTRLVFCQFVSEDDLVTLYQMCTAVVFPSTHEGFGLPALEGMAAGAPTFVANATSLPEVVGSAEQTFDPYDPKDLGKKLSRLLRDPEYYRSLKTNGLARASELTWERSADVALDSFEKLSEERSLPLRAVHKITGPMLSIRQKPKLAFVSPLPGINSGIATYSGKLLRELACHYEIECVPLPGQIITDEWILANFVIRDTGFFKRNSDDYEEIIYSVGNNEHCFYVIDLLKKIRGAVILHDYFLSDLYNFVSSTGVLPEEDFFRVLYKTNGISALLEERSLGRNHAVTKFPCNAEIFENASGIIVHSKWAYNQAISLYGKALQEKISIIPHLKNIQESSARVSARQALKLNDDDYLVCVFGYIQARKRPEEIINAWKDSNLSKHQNAKLVFVGELEKSSFGNHIQDMCCEYGISITGYVSDAIYQNYVNAADLAIQLRKESRGETSGTILDCMASGVPVIVQGDGAFLELSLKEELTFGPNVHHKTLQSVLDAVAQAPESYKTLGEEGRKSISKFHRGEDVARQIQSFLAALPASPDGGRQVLLKALTEFTAPKSPDKDDWERTAHAINFQQPALRQRQILYDVTVLAESDAKTGIQRVVRGVLASLFASPPKGYRIEPVRMDGNRLVYARQFSTNVFGAPTWVYPDSPVEFDKDDIYLSIDWVPDRLKNIEEVLLDLRRAGGKVVICVHDLLPLELPQYFPNSMENTTEQWFQCVLRVATQIVCVSQTTAEKVNFFAHALSIKPSQPIALDYFPLAADLANSKPSKGIPSYGSQLLSKLKTSTSFLMVGTIEPRKGYRDILEAMRELWSKGGKEILIFVGKKGWMMDDLCTEIEADPEFNKKLYWLSGISDEFLDSLYQNTSALIAASEGEGFGLPLVEAAHHKCHLIARDISVFREVAGEGAFYFKGPTPSKISEELQQWVRLYKKGQAPHPRNTVTTTWKNSTEILLERIFGDDHYGFLNS
SIO_010081: E3E12_RS08745
subclass of: SO_0000673
so part of: E3E12_RS08745
location: complement(5783..9319)
location: region:5783-9319:-1
so has part: feature:5783-9319:-1:exon

WP_149498304.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5783-9319:-1:exon