Buchnera aphidicola (Schizaphis graminum) isolate LNK plasmid p1.
type: Entry
definition: Buchnera aphidicola (Schizaphis graminum) isolate LNK plasmid p1.
sequence version: NZ_CP029203.1
sequence date: 2022-09-28
sequence: sequence
division: CON
label: NZ_CP029203.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN09004684
keyword: RefSeq
source: Buchnera aphidicola (Schizaphis graminum)
organism: Buchnera aphidicola (Schizaphis graminum)
taxonomy: Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Erwiniaceae; Buchnera.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP029203.1.\nBacteria and source DNA available from Gautam Sarath USDA-ARS 251\nFilley Hall Lincoln, NE 68583.\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 :: 22-APR-2018\nAssembly Method :: SPAdes v. 3.9.0\nExpected Final Version :: yes\nGenome Coverage :: 500.0x\nSequencing Technology :: Illumina HiSeq\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 09/28/2022 11:17:16\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.3\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA;\n repeat_region\nGenes (total) :: 640\nCDSs (total) :: 602\nGenes (coding) :: 579\nCDSs (with protein) :: 579\nGenes (RNA) :: 38\nrRNAs :: 1, 1, 1 (5S, 16S, 23S)\ncomplete rRNAs :: 1, 1, 1 (5S, 16S, 23S)\ntRNAs :: 32\nncRNAs :: 3\nPseudo Genes (total) :: 23\nCDSs (without protein) :: 23\nPseudo Genes (ambiguous residues) :: 0 of 23\nPseudo Genes (frameshifted) :: 17 of 23\nPseudo Genes (incomplete) :: 5 of 23\nPseudo Genes (internal stop) :: 7 of 23\nPseudo Genes (multiple problems) :: 6 of 23\n##Genome-Annotation-Data-END##

sequence
subclass of: SO_0000155
sequence length: 8035
topology: linear
so has quality: SO_0000987
location: 1..8035
location: region:1-8035:1
RO_0002162: 98794

NZ_CP029203
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN09004684
type: BioSample
SIO_000068: biosample

1
title: Genome sequence of Buchnera aphidicola from Schizaphis graminum biotpye I
author: Scully, E.D.
author: Geib, S.M.
author: Palmer, N.A.
author: Sattler, S.E.
author: Sarath, G.
journal: Unpublished

2
title: Direct Submission
author: Scully, E.D.
author: Geib, S.M.
author: Palmer, N.A.
author: Sattler, S.E.
author: Sarath, G.
journal: Submitted (01-MAY-2018) Stored Product Insect and Engineering Research Unit, USDA-ARS Center for Grain and Animal Health Research, 1515 College Avenue, Manhattan, KS 66502, USA

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

position:8035:1
position: 8035
reference: sequence
type: ForwardStrandPosition
type: ExactPosition
type: FuzzyPosition

feature:1-8035:1:source
so part of: sequence
organism: Buchnera aphidicola (Schizaphis graminum)
mol type: genomic DNA
isolate: LNK
isolation source: adult insect on Panicum virgatum
host: Schizaphis graminum biotype I
plasmid: p1
country: USA: Lincoln, NE
collection date: 2016-04

98794
type: Taxonomy
SIO_000068: taxonomy

DEO29_RS00005
type: Gene
subclass of: SO_0000704
RO_0002162: 98794
locus tag: DEO29_RS00005
old locus tag: DEO29_00005
pseudo: true
so part of: sequence
location: <1..424
location: region:1-424:1
so has part: feature:1-424:1:exon
subclass of: SO_0000010

75258543
type: Gene
SIO_000068: ncbigene

position:424:1
position: 424
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1-424:1:exon

DEO29_RS00005
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 98794
locus tag: DEO29_RS00005
old locus tag: DEO29_00005
inference: COORDINATES: similar to AA sequence:RefSeq:WP_010890613.1
note: incomplete; too short partial abutting assembly gap; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
pseudo: true
codon start: 2
transl table: 11
product: replication protein RepA
SIO_010081: DEO29_RS00005
subclass of: SO_0000673
so part of: DEO29_RS00005
location: <1..424
location: region:1-424:1
so has part: feature:1-424:1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:1-424:1:exon

DEO29_RS00010
type: Gene
subclass of: SO_0000704
RO_0002162: 98794
gene: leuA
locus tag: DEO29_RS00010
old locus tag: DEO29_00010
so part of: sequence
location: 561..2117
location: region:561-2117:1
so has part: feature:561-2117:1:exon
subclass of: SO_0000010

75258544
type: Gene
SIO_000068: ncbigene

position:561:1
position: 561
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2117:1
position: 2117
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:561-2117:1:exon

DEO29_RS00010
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 98794
gene: leuA
locus tag: DEO29_RS00010
old locus tag: DEO29_00010
EC number: 2.3.3.13
inference: COORDINATES: similar to AA sequence:RefSeq:WP_010890614.1
GO function: GO:0003852 - 2-isopropylmalate synthase activity [Evidence IEA]
GO process: GO:0019752 - carboxylic acid metabolic process [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: 2-isopropylmalate synthase
translation: MNSQVIIFDTTLRDGEQALQASLSVKQKLQIALSLENAGIDIIEVGFPISSPGDFKSVQTISKNIKKSKICSLARCLNKDIDTAAEAMSSSNTSRIHIFLATSTLHMESKLKKNFDQIIDMAISSVKRALRYTDDVEFSCEDASRTTMDNLCRIVEQLIKSGVKTINIPDTVGYTVPNELSTIIHNLFKRVPNIDQSIISVHCHNDLGMAVGNSISAIQAGARQIEGTINGIGERAGNTALEEVIMAIKVREDILGVSTNIKHKEIYRTSQIISQICNLPIPPNKAIVGSNAFAHSSGIHQDGVLKNRKNYEIMEPSSIGLKEVKLNLTSRSGRAAVKYYMTQMGYKECDYNIDELYTSFLKLADKKGQVFDYDLEALAFINMQQEESEYFSLSFFSVQSISNGLSTASVKLLCGKKVSIESATTSNGPIDAIYQALNRITNFSITLQKYQLVAKGKGRDALGQVDILVEYKKRKFHGVGLATDIIESSAQAMVNVLNNIWKANQVNEKLKTLKKVNN
SIO_010081: DEO29_RS00010
subclass of: SO_0000673
so part of: DEO29_RS00010
location: 561..2117
location: region:561-2117:1
so has part: feature:561-2117:1:exon

WP_108926778.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:561-2117:1:exon

DEO29_RS00015
type: Gene
subclass of: SO_0000704
RO_0002162: 98794
gene: leuB
locus tag: DEO29_RS00015
old locus tag: DEO29_00015
so part of: sequence
location: 2143..3234
location: region:2143-3234:1
so has part: feature:2143-3234:1:exon
subclass of: SO_0000010

75258545
type: Gene
SIO_000068: ncbigene

position:2143:1
position: 2143
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:3234:1
position: 3234
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2143-3234:1:exon

DEO29_RS00015
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 98794
gene: leuB
locus tag: DEO29_RS00015
old locus tag: DEO29_00015
EC number: 1.1.1.85
inference: COORDINATES: similar to AA sequence:RefSeq:WP_010890615.1
GO function: GO:0003862 - 3-isopropylmalate dehydrogenase activity [Evidence IEA]
GO process: GO:0009098 - leucine biosynthetic process [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: 3-isopropylmalate dehydrogenase
translation: MKKKFRIAVLPGDGIGPEVMREAYKILNILERKFFLKLELREFNIGGIAIDREGIALPEKTLRGCENSDAILFGSVGGKKWDYLPIESRPERASLLPLRKHFNLFSNLRPAKLHVDLKNLSPLRSDIVRDGFDILCIRELTGGIYFGKPKARFKNKNGEYAFDTEIYYDFEIERIANLAFELASSRRCKVCSIDKANVLESSVLWREIVKKVSKNYPDVHLSHLYIDNACMQIIKNPTQFDILLCSNIFGDIISDECAMITGSIGMLPSASLNNQKFGLYEPAGGSAPDIEGKNIANPIAQILSLSMLIRYSMNLNEIADKIDLSVHYALKEGYRTLDISDGKNYIKTNEMGDIIAEFLDNGK
SIO_010081: DEO29_RS00015
subclass of: SO_0000673
so part of: DEO29_RS00015
location: 2143..3234
location: region:2143-3234:1
so has part: feature:2143-3234:1:exon

WP_108926779.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2143-3234:1:exon

DEO29_RS00020
type: Gene
subclass of: SO_0000704
RO_0002162: 98794
gene: leuC
locus tag: DEO29_RS00020
old locus tag: DEO29_00020
so part of: sequence
location: 3236..4648
location: region:3236-4648:1
so has part: feature:3236-4648:1:exon
subclass of: SO_0000010

75258546
type: Gene
SIO_000068: ncbigene

position:3236:1
position: 3236
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:4648:1
position: 4648
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3236-4648:1:exon

DEO29_RS00020
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 98794
gene: leuC
locus tag: DEO29_RS00020
old locus tag: DEO29_00020
EC number: 4.2.1.33
inference: COORDINATES: similar to AA sequence:RefSeq:WP_010890616.1
GO component: GO:0009316 - 3-isopropylmalate dehydratase complex [Evidence IEA]
GO function: GO:0003861 - 3-isopropylmalate dehydratase activity [Evidence IEA]
GO process: GO:0009098 - leucine biosynthetic process [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: 3-isopropylmalate dehydratase large subunit
translation: MKKTLYEKIYDAHIVHKEKNNISILYIDLHLLHEVTSPQAFDSLRMRNRSVRQPKKTFATMDHNVSTESKDINASGSMAKIQMEQLIKNCEEFNIALYDLNNPKQGIVHVIGPEQGMTLPGTTIVCGDSHTSTHGAFGALSFGIGTSEVEHVLVTQTLKQQRFKNMRIKIVGKVKKFITAKDIILFIIGELGTSSGSGYVIEFCGDVIKKMNMEERMTICNMAIEMGAKSALIAPDETTYLYLKNKRYSPKNKYWDSAIRYWKTLVTDENALFDKEFTFDISDISPQVTWGTSPDQVLSINEKIPDFNSFKDSIKKDLARSACNYMDLKPGSYLKNIKIDKVFIGSCTNSRIEDLRSAATILKNKKISKNIKAIVVPGSGSVKNQAEKEGLDKIFIDAGFEWRLPGCSMCLGMNNDKLSDGERCASTSNRNFEGRQGRGGRTHLVSPIMAAAAAIYGHFVDVRNLNSETN
SIO_010081: DEO29_RS00020
subclass of: SO_0000673
so part of: DEO29_RS00020
location: 3236..4648
location: region:3236-4648:1
so has part: feature:3236-4648:1:exon

WP_108926780.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3236-4648:1:exon

DEO29_RS00025
type: Gene
subclass of: SO_0000704
RO_0002162: 98794
gene: leuD
locus tag: DEO29_RS00025
old locus tag: DEO29_00025
so part of: sequence
location: 4651..5274
location: region:4651-5274:1
so has part: feature:4651-5274:1:exon
subclass of: SO_0000010

75258547
type: Gene
SIO_000068: ncbigene

position:4651:1
position: 4651
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:5274:1
position: 5274
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4651-5274:1:exon

DEO29_RS00025
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 98794
gene: leuD
locus tag: DEO29_RS00025
old locus tag: DEO29_00025
EC number: 4.2.1.33
inference: COORDINATES: similar to AA sequence:RefSeq:WP_010890617.1
GO component: GO:0009316 - 3-isopropylmalate dehydratase complex [Evidence IEA]
GO function: GO:0003861 - 3-isopropylmalate dehydratase activity [Evidence IEA]
GO process: GO:0009098 - leucine biosynthetic process [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: 3-isopropylmalate dehydratase small subunit
translation: MFKFIEHTGVVVPLNISNIDTDAIIPKQFLKKVNKIGFGKYLFHDWRFLDKNQLKINPNFILNKSTYKNASILLTRENFGCGSSREHAVWSLLDYGFKVIIASSFSDIFYSNSFNNKLLLIVLENEDIDYLFDLVNTKIGMSFNVSLIHKKITVDNLDIPFQIDDFQRLCLLNNWDNIDLTMKIDHKIKLYEKNIFSFLLKREKFTS
SIO_010081: DEO29_RS00025
subclass of: SO_0000673
so part of: DEO29_RS00025
location: 4651..5274
location: region:4651-5274:1
so has part: feature:4651-5274:1:exon

WP_108926781.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4651-5274:1:exon

DEO29_RS00030
type: Gene
subclass of: SO_0000704
RO_0002162: 98794
gene: repA
locus tag: DEO29_RS00030
old locus tag: DEO29_00030
so part of: sequence
location: complement(5636..6487)
location: region:5636-6487:-1
so has part: feature:5636-6487:-1:exon
subclass of: SO_0000010

75258548
type: Gene
SIO_000068: ncbigene

position:5636:-1
position: 5636
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:6487:-1
position: 6487
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5636-6487:-1:exon

DEO29_RS00030
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 98794
gene: repA
locus tag: DEO29_RS00030
old locus tag: DEO29_00030
inference: COORDINATES: similar to AA sequence:RefSeq:WP_010892291.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: plasmid replication initiator RepA
translation: MSSRENYVYNRNPVFTAPKNNKRRPSFICYAMKKASEIDVARCELNYVIQPKNIKTGLPLKRFRRLNEHRACALRAMVSAMLYHFNISSELVQASVEQLSDECGLSTLSKVGNKSITRASRLITDFMEPMGFVTCKKIWDRVLGNYMPKMITLTPLFFMLLDISEKQLINAKKQQLGWINKNLITKGLKPITVIEAKRRAKDIQMRNLFKYRISKHNFYKKRKNAQRLIALDEKEARQKILRALVAKYSISELTTLGPSGLKKQVNISYYYLKKIATNRYPDN
SIO_010081: DEO29_RS00030
subclass of: SO_0000673
so part of: DEO29_RS00030
location: complement(5636..6487)
location: region:5636-6487:-1
so has part: feature:5636-6487:-1:exon

WP_108926782.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5636-6487:-1:exon

DEO29_RS00035
type: Gene
subclass of: SO_0000704
RO_0002162: 98794
locus tag: DEO29_RS00035
old locus tag: DEO29_00035
so part of: sequence
location: 6911..7414
location: region:6911-7414:1
so has part: feature:6911-7414:1:exon
subclass of: SO_0000010

75258549
type: Gene
SIO_000068: ncbigene

position:6911:1
position: 6911
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:7414:1
position: 7414
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:6911-7414:1:exon

DEO29_RS00035
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 98794
locus tag: DEO29_RS00035
old locus tag: DEO29_00035
inference: COORDINATES: similar to AA sequence:RefSeq:WP_010892292.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: TIGR00645 family protein
translation: MEKIIEKSIYASRWLMFPVYVGLSFGFILLTLKFFQQIIFIIPDILAMSESGLVLVVLSLIDIALVGGLLVMVMFSGYENFISKMDIQDNEKRLGWMGTMDVNSIKNKVASSIVAISSVHLLRLFMEAERILDNKIMLCVIIHLTFVLSAFGMAYIDKMSKKKDNLH
SIO_010081: DEO29_RS00035
subclass of: SO_0000673
so part of: DEO29_RS00035
location: 6911..7414
location: region:6911-7414:1
so has part: feature:6911-7414:1:exon

WP_108926783.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:6911-7414:1:exon

DEO29_RS00040
type: Gene
subclass of: SO_0000704
RO_0002162: 98794
gene: repA
locus tag: DEO29_RS00040
old locus tag: DEO29_00040
so part of: sequence
location: 7643..>8035
location: region:7643-8035:1
so has part: feature:7643-8035:1:exon
subclass of: SO_0000010

75258550
type: Gene
SIO_000068: ncbigene

position:7643:1
position: 7643
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:7643-8035:1:exon

DEO29_RS00040
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 98794
gene: repA
locus tag: DEO29_RS00040
old locus tag: DEO29_00040
inference: COORDINATES: similar to AA sequence:RefSeq:WP_010890613.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: plasmid replication initiator RepA
translation: MPRKNYICNLKPVFNPPKNEKKRSNFIDYAMKKASEIDVARSKLNYTLLAIDPKTGNILPRFRRLNEHRACAMRAIVLAMLYYWNTNSNLVEASIEKLSDECGLSTFSNSGNKSITRASRLITDFMEPMGF
SIO_010081: DEO29_RS00040
subclass of: SO_0000673
so part of: DEO29_RS00040
location: 7643..>8035
location: region:7643-8035:1
so has part: feature:7643-8035:1:exon

WP_261785709.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:7643-8035:1:exon