LOCUS NC_002253 7786 bp DNA circular CON 24-DEC-2022
DEFINITION Buchnera aphidicola str. APS (Acyrthosiphon pisum) plasmid pLeu,
complete sequence.
ACCESSION NC_002253
VERSION NC_002253.1
DBLINK BioProject: PRJNA224116
BioSample: SAMD00061095
Assembly: GCF_000009605.1
KEYWORDS RefSeq.
SOURCE Buchnera aphidicola str. APS (Acyrthosiphon pisum)
ORGANISM Buchnera aphidicola str. APS (Acyrthosiphon pisum)
Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
Erwiniaceae; Buchnera.
REFERENCE 1
AUTHORS Shigenobu,S., Watanabe,H., Hattori,M., Sakaki,Y. and Ishikawa,H.
TITLE Genome sequence of the endocellular bacterial symbiont of aphids
Buchnera sp. APS
JOURNAL Nature 407 (6800), 81-86 (2000)
PUBMED 10993077
REFERENCE 2 (bases 1 to 7786)
AUTHORS Shigenobu,S., Hattori,M., Watanabe,H., Toyoda,A., Yada,T.,
Sakaki,Y. and Ishikawa,H.
TITLE Direct Submission
JOURNAL Submitted (17-JAN-2000) Contact:Shuji Shigenobu University of
Tokyo, Department of Biological Sciences; 7-3-1 Hongo, Bunkyo-ku,
Tokyo 113-0033, Japan URL :http://buchnera.gsc.riken.go.jp/
COMMENT REFSEQ INFORMATION: The reference sequence is identical to
AP001071.1.
Collaboration Information:
RIKEN, Genomic Sciences Center (GSC)
Kitasato Univ., 1-15-1 Kitasato, Sagamihara, Kanagawa 228-8555,
Japan
Tel:81-42-778-9923
FAX:81-42-778-9924
We determined the sequence by whole genome random shotgun
sequencing method. The trpEG plasmid is composed of the tandem
repeats of trpEG operon. These repeats are so highly similar to
each other that we could not determine the accurate number of the
repeat. Here we reported the sequence of the typical two units.
The annotation was added by the NCBI Prokaryotic Genome Annotation
Pipeline (PGAP). Information about PGAP can be found here:
https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
##Genome-Annotation-Data-START##
Annotation Provider :: NCBI RefSeq
Annotation Date :: 12/24/2022 00:47:56
Annotation Pipeline :: NCBI Prokaryotic Genome
Annotation Pipeline (PGAP)
Annotation Method :: Best-placed reference protein
set; GeneMarkS-2+
Annotation Software revision :: 6.4
Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA
Genes (total) :: 629
CDSs (total) :: 592
Genes (coding) :: 584
CDSs (with protein) :: 584
Genes (RNA) :: 37
rRNAs :: 1, 1, 1 (5S, 16S, 23S)
complete rRNAs :: 1, 1, 1 (5S, 16S, 23S)
tRNAs :: 31
ncRNAs :: 3
Pseudo Genes (total) :: 8
CDSs (without protein) :: 8
Pseudo Genes (ambiguous residues) :: 0 of 8
Pseudo Genes (frameshifted) :: 5 of 8
Pseudo Genes (incomplete) :: 2 of 8
Pseudo Genes (internal stop) :: 1 of 8
##Genome-Annotation-Data-END##
COMPLETENESS: full length.
FEATURES Location/Qualifiers
source 1..7786
/organism="Buchnera aphidicola str. APS (Acyrthosiphon
pisum)"
/mol_type="genomic DNA"
/strain="APS"
/isolate="Tokyo1998"
/host="Acyrthosiphon pisum"
/db_xref="taxon:107806"
/plasmid="pLeu"
/note="leucine plasmid;
primary endosymbiont of Acyrthosiphon pisum;
synonym:Buchnera sp. APS"
gene complement(346..1197)
/locus_tag="BU_RS00025"
/old_locus_tag="BUpL01"
CDS complement(346..1197)
/locus_tag="BU_RS00025"
/old_locus_tag="BUpL01"
/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="replication-associated protein repA1"
/protein_id="WP_010892291.1"
/translation="MIIRKCYINNPNPFFTPPKNNKRRPSFICYAMKRASEIDVARCE
LNYILQIKNIKIGFPVKRFRRLNEHRACAMRAMVLAMLYHFNISSDLVQASVEQLSDE
CGLSTLSKAGNKSITRASRLITNFMEPMGFVTCKKTWDKILGNYMPKMITLTPLFFML
FGVSEKKLMDAKKQQLGWINKNLISKGFKPITMIDAKRRSKDTQIKNIFQYRISKHAF
YKKKRNAQRLISLDEKEARQTILRALVAKYSITELTKLGPNGLKKQVNISYYYLRKIA
TNTYPDN"
gene 1514..2017
/locus_tag="BU_RS00030"
/old_locus_tag="BUpL02"
CDS 1514..2017
/locus_tag="BU_RS00030"
/old_locus_tag="BUpL02"
/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"
/protein_id="WP_010892292.1"
/translation="MEKIIEKSIYASRWLMFPVYVGLSFGFILLTLKFFQQIVFIMPD
IVAMSESGLVLVVLSLIDIALVGGLLVMVMFSGYENFISKMDIQDNQKRLGWMGTMDV
NSIKNKVASSIVAISSVHLLRLFMEAEKILDDKIMLCVIIHLTFVLSAFGMAYIDKMS
KKKHILH"
gene 2141..2893
/gene="repA"
/locus_tag="BU_RS00035"
/old_locus_tag="BUpL03"
CDS 2141..2893
/gene="repA"
/locus_tag="BU_RS00035"
/old_locus_tag="BUpL03"
/inference="COORDINATES: similar to AA
sequence:RefSeq:WP_014499733.1"
/note="Derived by automated computational analysis using
gene prediction method: Protein Homology."
/codon_start=1
/transl_table=11
/product="plasmid replication initiator RepA"
/protein_id="WP_164927321.1"
/translation="MPRKNYIYNLKPFFNPSKNERKKSTFICYAMKKVSEIDVARSHL
NRALLPIDPKTGNVLPRFRRLNKHRACAMRAIVPAMLYYFNINSKLVEASIEKLADEC
GLSTLSDSGNKSITRASRLISEFLEPMGFVKCKKINSKSMSNYIPKKIFLTPMFFMLC
GISPSEINHFLSKKIKPLKKLKKQEKSAFISFTDMKIISQLDERSARTKILNALINYY
TASELTKIGPKGLKKKIDIEYSNLCNLYKKKS"
gene 3032..4591
/gene="leuA"
/locus_tag="BU_RS00040"
/old_locus_tag="BUpL04"
CDS 3032..4591
/gene="leuA"
/locus_tag="BU_RS00040"
/old_locus_tag="BUpL04"
/EC_number="2.3.3.13"
/inference="COORDINATES: similar to AA
sequence:RefSeq:WP_010892294.1"
/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"
/protein_id="WP_010892294.1"
/translation="MKSKVVIFDTTLRDGEQALQASLSVKEKLQIALSLEKCGIDILE
IGFPVSSPGDFKSVQTISKNIKNSRICSLARCIEKDIDAAGEAMSSSDSFRIHIFLAT
STLHMESKLKKNFNEIIDMAVFSVKKALRYTDDIEFSCEDATRTTMDNLCRIVETLIK
SGVKTINIPDTVGYTVPNELSCIIKNLFERVPNIHKSIISVHCHDDLGMAVGNSISAI
QAGARQIEGTINGIGERAGNTALEEIIMAIKVREDILSVSTNINYKEIYRTSKIVSQI
CNMPIPSNKAIVGSNAFAHSSGIHQDGVLKNRKNYEIMEPSSIGLKEVKLNLTSRSGR
AAVKHYMDEMGYNNSDYNIDELYTAFLKLADKKGQVFDYDLEALAFINKQQDEWEYFS
LKFFSVQSISNSLSTASVKLLCGKKTYTESSTTSNGPVDAIYQALNRIACFPIILQKF
QLVAKGKGKDALGQVDILVEHKKRKFHGVGLATDIIEASAQAMINVLNNIWKAKQVNK
KLKILKDFKKK"
gene 4652..5743
/gene="leuB"
/locus_tag="BU_RS00045"
/old_locus_tag="BUpL05"
CDS 4652..5743
/gene="leuB"
/locus_tag="BU_RS00045"
/old_locus_tag="BUpL05"
/EC_number="1.1.1.85"
/inference="COORDINATES: similar to AA
sequence:RefSeq:WP_010892295.1"
/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"
/protein_id="WP_010892295.1"
/translation="MKKNYRIAVLSGDGIGPEVMQEACKILNVLKKYFFLSLEIQKFN
IGGIAIEREGVALPKTTLLGCENSDSILLGSVGGKKWDNLPVEQRPERAALLPLRKHF
NLFSNLRPAKLYPELKCLSPLRSDIVKNGFDILCVRELTGGIYFGEPKGFVNKNNTKY
AFDTEIYHEYEIIRIAHLAFKLARSRKKKVCSIDKSNVLQSSILWREVVESVSKKYPD
VHLSHLYIDNAAMQIIKDPNQFDVLLCSNLFGDIISDECATITGSIGMLPSASFNEKN
FGLYEPAGGSAPDIEGKNIANPIAQILSLSMLVRYGMNLNQIADKIDKAVNNVLKKGY
RTSDISHDNNFLKTDEMGDLIVDSLINGE"
gene 5745..7160
/gene="leuC"
/locus_tag="BU_RS00050"
/old_locus_tag="BUpL06"
CDS 5745..7160
/gene="leuC"
/locus_tag="BU_RS00050"
/old_locus_tag="BUpL06"
/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"
/protein_id="WP_164927322.1"
/translation="MKKTLYDKIYDSHIVYEEKNNTSLLYIDLHLLHEVTSPQAFDSL
RDKNRKVRQPKKTFATMDHNVSTTSQDINASGSMAKVQMQELIKNCSEFNISLYDIKN
PNQGIVHVISPEKGMTLPGMTIVCGDSHTSTHGAFGALSFGIGTSEVEHVLATQTLKQ
QRFKNMKIEITGEIQKFVTAKDLILFIIGKLGSSGGAGYIIEFCGNVIEKMSMEERMT
ICNMAIEIGAKSGLIAPDEVTFSYLKNKMYAPRGVFWKKALNFWKNLKSDKNAFFDKV
VNINISDLSPQITWGTNPDQVISIDQKIPDFSSFDNLIKKDLAKSACKYMGLKIGTYL
TNITVDKVFIGSCTNGRIEDLRAASKILKDKKIANNVKAIVVPGSGSVKREAENEGLD
KIFISAGFEWRLPGCSMCLGMNKDRLNDGERCASTSNRNFEGRQGRGGRTHLVSPIMA
AAAAVYGKFVDVRKLYNGENN"
gene 7163..7786
/gene="leuD"
/locus_tag="BU_RS00055"
/old_locus_tag="BUpL07"
CDS 7163..7786
/gene="leuD"
/locus_tag="BU_RS00055"
/old_locus_tag="BUpL07"
/EC_number="4.2.1.33"
/inference="COORDINATES: similar to AA
sequence:RefSeq:WP_032489588.1"
/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"
/protein_id="WP_010892297.1"
/translation="MFKFTGHAGIVVPLDISNIDTDIIIPKQFLKRVNKIGFGKYLFH
DWRFIDANQLVKNEDFILNKKIYKNASILLTRENFGCGSSREHAVWSLVDYGFKVIIA
PSFADIFYNNSFNNKLLLITLSSSEITFLFDIVKNNIGITFDVSLVEKTVTVNKEVFS
FELDDFHYFCLLNDLDNIDLTMKHLSEIKSYESRISDFLLERRDFKS"
CONTIG join(AP001071.1:1..7786)
//
