LOCUS       NZ_CP128937             6466 bp    DNA     circular CON 07-JUL-2023
DEFINITION  Escherichia coli strain TUM9757 plasmid pMTY9757_Col, complete
            sequence.
ACCESSION   NZ_CP128937
VERSION     NZ_CP128937.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN35769033
            Assembly: GCF_030389715.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 6466)
  AUTHORS   Ikegaya,K., Aoki,K., Komori,K., Ishii,Y. and Tateda,K.
  TITLE     Analysis of the stepwise acquisition of blaCTX-M-2 and subsequent
            acquisition of either blaIMP-1 or blaIMP-6 in highly conserved
            IncN-pST5 plasmids
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6466)
  AUTHORS   Ikegaya,K., Aoki,K., Komori,K., Ishii,Y. and Tateda,K.
  TITLE     Direct Submission
  JOURNAL   Submitted (20-JUN-2023) Department of Microbiology and Infectious
            Diseases, Toho University, 5-21-16, Omori-Nishi, Ota-Ku, Tokyo
            143-8540, Japan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 18-NOV-2021
            Assembly Method                   :: SPAdes v. v3.15.5
            Assembly Name                     :: Toho-u_TUM9757_Comp_v1.1
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Reference-guided Assembly         :: missing
            Genome Coverage                   :: 413x
            Sequencing Technology             :: Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/05/2023 08:03:42
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,507
            CDSs (total)                      :: 5,387
            Genes (coding)                    :: 5,109
            CDSs (with protein)               :: 5,109
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 91
            ncRNAs                            :: 7
            Pseudo Genes (total)              :: 278
            CDSs (without protein)            :: 278
            Pseudo Genes (ambiguous residues) :: 0 of 278
            Pseudo Genes (frameshifted)       :: 101 of 278
            Pseudo Genes (incomplete)         :: 168 of 278
            Pseudo Genes (internal stop)      :: 51 of 278
            Pseudo Genes (multiple problems)  :: 39 of 278
            Pseudo Genes (short protein)      :: 3 of 278
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP128937.1.
            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/
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..6466
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="TUM9757"
                     /db_xref="taxon:562"
                     /plasmid="pMTY9757_Col"
                     /geo_loc_name="Japan"
                     /collection_date="2010"
                     /collected_by="Toho University School of Medicine"
     gene            complement(join(6286..6466,1..530))
                     /locus_tag="QVM97_RS27480"
                     /old_locus_tag="QVM97_27480"
     CDS             complement(join(6286..6466,1..530))
                     /locus_tag="QVM97_RS27480"
                     /old_locus_tag="QVM97_27480"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000967646.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000967645.1"
                     /translation="MLYWKKMPSLWIGNRIAEFSDLDTAKAIAALKIYLTFCLFCKESD
                     SGHRTVELTFSNLCEIASLSRSLVNEGLKILYAKELIKNISPTARKKIYTVDVLENHND
                     GWCKLPFKGVVDEDKKISAFQSMHNRYPFELLALQTYMYLLYARDNNSDYTLARKKTIC
                     KKLKCKLPELNKAITYLIHIGLLDRVVKKSIENIPLEMFHDSYYFYIKTGSKSALTYRR
                     KSEPPVIPEADLPF"
                     /name="hypothetical protein"
     gene            complement(944..1459)
                     /locus_tag="QVM97_RS27485"
                     /old_locus_tag="QVM97_27485"
     CDS             complement(944..1459)
                     /locus_tag="QVM97_RS27485"
                     /old_locus_tag="QVM97_27485"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000675351.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type III toxin-antitoxin system ToxN/AbiQ family
                     toxin"
                     /protein_id="WP_000675351.1"
                     /translation="MKFYTISSRYIEYLKGFEDKVPNSEDPNYQNPKAFIGIVLEIQGH
                     KYLAPLTSPKPWHSTIKESSPSFFKLHENGVPENQLGLINLKFMIPIIEAEVSLLDLNG
                     MPNTAYKRMLYKQLQFIRVNSDKIAEKSELLRKLVLQGKMQGTCNFSLLEEKYRDFGKE
                     ANDTEEGE"
                     /name="type III toxin-antitoxin system ToxN/AbiQ family
                     toxin"
     gene            <2801..3385
                     /locus_tag="QVM97_RS27490"
                     /old_locus_tag="QVM97_27490"
                     /pseudo=""
     CDS             <2801..3385
                     /locus_tag="QVM97_RS27490"
                     /old_locus_tag="QVM97_27490"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001697689.1"
                     /note="internal stop; incomplete; partial in the middle of
                     a contig; missing N-terminus; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /name="replication initiation protein"
     gene            3382..5061
                     /locus_tag="QVM97_RS27495"
                     /old_locus_tag="QVM97_27495"
     CDS             3382..5061
                     /locus_tag="QVM97_RS27495"
                     /old_locus_tag="QVM97_27495"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000598747.1"
                     /GO_function="GO:0005524 - ATP binding [Evidence IEA];
                     GO:0016887 - ATP hydrolysis activity [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="AAA family ATPase"
                     /protein_id="WP_001774712.1"
                     /translation="MIKVQLPTREHRLHELNLNYGDVVFFIGQNGSGKSSLLNNLFQKI
                     GSQSSVYVLAHRKNTFSSDIIDFSNSEYKNAQGWIFNEIKGSQCRYRVNYDSQMVAIPI
                     VKLKNKVIARALSFVDSFKSNNNQPAELIKSEVDVLNMVFADAKLSIEFFLDDEANVMA
                     RNIKGENPDVYPISMLSDGEKSALIIASEIICADENTTIFLDEPERHMHRSIVSPLLSS
                     LMKYRRDCVFFVATHELSLPAFFDNVKVVNVKNCYFSEQREPIYWDFNVVEDYDELFNG
                     VDEQTKIDILGARDKVLFVEGVTSSLDRDLYSAIFPMVSVVSKQKCDLVELAVKGLRLN
                     DEIHRVSAFGIIDNDNKVQAKVDNLKKDFIFSLDVHSIESIYYHPRMIKFVIDFVKEAN
                     GIDNVDALFMEIHDFAIDAINEKRDHLCCRAVEKTIRADLMSAIPKQQDIKNRIKFNKE
                     IDIECYVNKEIAAFDAMIAERNLDALVSRYPIRETNLLAHVAKKCGFADRSRYELNVIR
                     TIKSNADARAFVLSLLGGLDEAILGCSDTENSPADTHTVFAM"
                     /name="AAA family ATPase"
     gene            complement(5298..5492)
                     /locus_tag="QVM97_RS27500"
                     /old_locus_tag="QVM97_27500"
     CDS             complement(5298..5492)
                     /locus_tag="QVM97_RS27500"
                     /old_locus_tag="QVM97_27500"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041627.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_001041636.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADVQAAMCERLHELA
                     EELQNSIQVHFEAENETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          5529..5628
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.02"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          5753..6008
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="94.186"
                     /coverage="89.0"
                     /evalue="1.23e-106"
     Typing          complement(2064..2636)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="86.828"
                     /coverage="90.0"
                     /evalue="5.34e-173"
ORIGIN
        1 attgctttgt ttagttcagg taatttgcat ttcaattttt tgcatatggt ctttttccta
       61 gccagtgtgt agtcgctgtt attatcacga gcgtaaagaa gatacatgta agtttgtaag
      121 gctagtaact caaagggata tctgttgtgc atggattgaa atgcacttat ttttttgtcc
      181 tcgtcgacaa ctcctttaaa tggaagcttg caccatccat cattatgatt ttctagcaca
      241 tccacggtat aaatcttttt tcgtgcagtc ggcgatatgt tttttatcag ctcttttgca
      301 taaagaattt taaggccttc gttcaccaag gaacggctta atgacgctat ctcgcaaagg
      361 ttgctaaagg ttaactcaac cgttctgtgg ccagagtctg actctttgca aaacaggcag
      421 aatgttaaat aaatttttaa tgccgctata gcttttgctg tatcaagatc gctgaattca
      481 gcgatcctat ttcctatcca tagtgaaggc atttttttcc agtacagcat gaatcacctc
      541 aaggccaagt tttgaaagat gaaatagacc aatcccaata tagaaagtga gagcacaagg
      601 ttagttatta ccgctgcgac tttcgcaagc ctctcaacca gacacacgcc tttctcaaac
      661 atttttcacc cctcgtaatc gcttcttgtt gtttttatta tctcagggtg tgaaggcgtt
      721 gtaacgcctt cacaaaaatc tatctagaaa gataaaagtg atgttaattt tttatcttgt
      781 tgtttttaaa ggttttttat ttgagttttg gtatttgtat taatcataat atggttcacc
      841 gtgaactatg tatgtgagtc gaaccgttga gttttgaata ttagacctga atagtgtcca
      901 agatcactcg gtttcggaca ctattcagga tggcaatgaa gcgttactcg ccttcttccg
      961 tgtcattagc ttctttgccg aaatctcggt atttttcttc taacagggaa aaattacatg
     1021 ttccttgcat ttttccttgc aggacgagct tccttaaaag ctctgatttc tcagctattt
     1081 tgtctgaatt tacacgaata aactggagct gcttatagag cattctcttg taggcggtat
     1141 tcggcatacc gttcaagtca agtaaggata cttcggcttc gatgattgga atcatgaact
     1201 tcagattaat caatccgagc tgattttcgg ggacaccatt ttcatggagc ttaaagaagc
     1261 taggcgatga ttctttaata gtgctatgcc atggctttgg ggatgttaaa ggggctagat
     1321 acttatgccc ttgaatctct aacacaatgc caatgaaagc tttcggattc tgatagttag
     1381 gatcttcgct attgggaact ttgtcttcga atccctttag gtattcaatg tatctgcttg
     1441 atatagtgta aaatttcatt tttttctcgt aaaaaaggcg actgtgtagt cgcctctttt
     1501 actgtattac tttaaggtag taaatgacct aaatttctag ctgcacttaa ggtagcaaat
     1561 cacctgaatt tctagctgca cttaaaggta gcaaatcacc tgaatttcta gctgcactta
     1621 aggtagcaaa tcacctgaat ttctagctgc acttaaaggt agcaaatcac ctgaatttct
     1681 agctgcactt aaaggtagca aatcaccttg attcgagtat acctgatctt cgcctaggct
     1741 tacaactagg taacttgcag ctgtgtagtt gtagcccttg ccgctgtatc ccctcaaaat
     1801 gtcatttgag gcttttttaa agtactgatt ccagagttga ctgttttttt catcagttca
     1861 gtgtgggggg gggtaagttg ggttatgaca tgaatcaaaa aggatctgct tgagatcctt
     1921 tttttctacg cgtaatctct tgctctgaaa acgaaaaaac cacctgggga ggtggttttt
     1981 cgatggttca gtaagttggg gaacttctga accgtggtaa cagggtgtac aagaccgctg
     2041 ccaccaaatt cgtccttcca gtttagccgt agtttggttc taacttcaag aactctgcat
     2101 cagtaatctc ttgtacaccc cttaccaatg gccgcagcca gtggcgataa gtcgtgtctt
     2161 tccgggttgg actcaagatg atagttaccg gacaaggcgc agcggtcgga ctgaacgggg
     2221 gggtcgtgca tacagtccag cttggagcga actgcctacc cggaaccgag tgtcaggcgt
     2281 ggaatgagat aaacgcggcc ataacagcgg aatgacaccg gtaaaccgaa aggcaggaac
     2341 aggagagcgc acgagggagc caccaggggg aaacgcctgg tatctttaag tcctgtcggg
     2401 tttcgccacc actgatttga gcgtcagatt ctgtgatgct tgtcaggggg gcggagccta
     2461 tggaaaaacg ccagcggcgc ggccttttgc cctggctttg cctttttgct cacatgttct
     2521 ttccggcctt atcccctgat tctgtggata accgtattac cgtctctgag tgagctgata
     2581 ccgctcgccg cagccgaacg accgagcgca gcgagttagt gagcgaggaa gcggaagagc
     2641 gtaggcattt gcattttctc cttacgcatc tgtgcggcat ttcacaccgt caatagcgca
     2701 cttttcatac aatccgcact gataccgcat agttaagtca gtactcacag cgtcccctct
     2761 gcgaggtgcc ttctgtgact ggttcagggg gctcgccgcc cccctcaaat atgcagccgt
     2821 cattgagaat gcgctgcgta aaaaattggg cgccgatgcg gggtattcag ggctaatttg
     2881 cgagaatccg aaccacctgc actggcagat caccgtttgg cagcctgagc tctacaccct
     2941 cgactgatta gccgactacc tcgaccttgg cgcagctaat gaccgcgaaa tcctaccgga
     3001 ctacggttta ggccgtaact gcaccctctt cgataaaacc cgcaagtggg attaccgcgc
     3061 tatccaccaa ggctggccgc agtatgacca atggctacaa gcttgctttg aacgcgctaa
     3121 agcctacaac ctgcagttct ccgcaccttt agacgagaac gaagtcatgg gtattgccaa
     3181 aagtgtagct aagtggacta ataaaaattt tacagagtca tcatttgatg attttataaa
     3241 aaagacccat tcggcagaca tccaatctct atgtgggaaa aaaagtaaag gaggaggtag
     3301 gccttcatta aactctccat ggattaattt aggaattagt cgttcaacgt attttagatt
     3361 aaaagctaaa gagaaaggaa aatgataaaa gttcagttac ctactagaga acatcgtctt
     3421 catgagctta atcttaatta tggcgatgtc gtttttttta ttggtcagaa tggtagtggt
     3481 aaatccagcc tattaaataa tctttttcaa aaaataggat ctcaatcatc agtatatgtt
     3541 ttagcgcata gaaaaaatac attcagcagc gacattattg atttcagtaa tagtgagtat
     3601 aaaaatgcgc agggatggat ttttaatgaa attaaaggca gtcaatgtag atacagagtt
     3661 aattatgact cacagatggt tgccatacct atagtaaaat taaaaaacaa agtgatagcc
     3721 agggctttaa gtttcgtaga ttcatttaaa tcaaataaca atcagccggc agagttaata
     3781 aagtcagagg ttgatgtgct aaacatggtt tttgctgatg ccaaattatc tattgagttc
     3841 tttctagatg atgaagccaa cgttatggca aggaatatta aaggtgaaaa tcctgatgtt
     3901 tatcctatat caatgctttc tgacggtgaa aaaagtgcac taattattgc cagtgagatt
     3961 atttgcgctg atgaaaacac aactattttc ttagatgagc ctgagcgaca tatgcacaga
     4021 agcattgtgt ctccgctgct ttcatcttta atgaaatatc gtagagattg tgtttttttt
     4081 gttgccaccc acgagttaag cttgcctgcg ttttttgata acgtgaaagt ggttaacgtt
     4141 aaaaactgct atttttccga acaaagagaa ccgatatact gggatttcaa tgttgttgag
     4201 gattatgacg aattattcaa tggtgttgat gagcaaacta aaatagatat acttggcgct
     4261 agggataagg ttctatttgt tgaaggtgtt acgtctagcc ttgaccgtga tttatattcg
     4321 gccatatttc ctatggtttc agttgtatct aaacaaaaat gtgatttggt tgaattggcg
     4381 gtaaaaggct tgagactaaa tgacgaaatt catcgagtat cggcgtttgg tatcattgat
     4441 aatgataaca aggtgcaggc gaaggtcgat aacttaaaga aagacttcat ttttagtctc
     4501 gacgttcatt ctattgagtc gatttattat catcctagaa tgattaagtt tgtcattgac
     4561 tttgtaaaag aggctaatgg gatagataat gttgatgcct tatttatgga aattcatgac
     4621 ttcgctattg atgccataaa tgaaaagcgc gatcacttat gctgccgtgc agttgaaaaa
     4681 acaataaggg cagacttaat gtcggccata ccaaaacagc aagatattaa gaaccgcatt
     4741 aagtttaata aagaaattga tattgaatgt tatgttaata aagaaattgc tgcatttgat
     4801 gcaatgatcg cggaacgaaa tttggatgcg ttagtctcac gctaccctat ccgagaaaca
     4861 aatttgttgg cacatgtagc taaaaaatgt ggttttgccg atcgctctag atatgagtta
     4921 aacgtgattc gtacgatcaa gagtaatgct gacgctagag catttgtttt atccctcctc
     4981 ggagggttag atgaagctat tttgggatgt tcagatacgg aaaatagccc agctgatacc
     5041 catacagttt ttgctatgtg agactaaaca acctatatca gataacagcc ctgcttttgc
     5101 ggggcttttt gtttgtgcgt gacttgaccg cgatgtacga tagttgctgt attaagtcag
     5161 tatacactcc gctatcgcta cgtgactggg tcagggctgc gccccgacac ccgttaaaac
     5221 ccgctgacgc gccctgacgg gcttgtctgc tgacgaaaat gctcacgggc aagccgtgac
     5281 cgccttcgtc agcttcgtta tgttcctgtt tcattttcgg cctcaaagtg aacctggatg
     5341 ctgttctgga gttcttctgc gagttcgtgc agtcgttcac acatggccgc ctgtacgtcg
     5401 gcatccagag catccagttt ttcaagcagt gtcaggctct ggcttttgat aaatcgcgcc
     5461 atattcagcg cagtttgttg ctgtttgttc accttccgtt gttctccgtc agtaccgggt
     5521 gtcgggtgga ccctgactag gtggtaattg taagacgttg cgggcgacgg tattacaatt
     5581 gcacatcctg tcctgttttt tttaggacgt atcatggcac agcatatcaa ctgataaata
     5641 atccctgtgc agtgcagccg ctgttgcata aaatttcgct ctgcgtcgag tgtttcttaa
     5701 tcaataattc cgctgatact ccggaaaaac gcgagtctgt tctcatgcct gaaatgccca
     5761 caccccacgc aaaaacaatt ttttgctgat ttttctttat aaatagagag ttatgacaaa
     5821 ttagtttctc ttgctctctt tgtgatattt aaaaaagcgg tgtcggcgcg gctacaacac
     5881 cgcgccgaca ccgctttgta ggggtggcac tgactatttt cataaaaaac atcattttat
     5941 attaggggtg ctgctagcgg cgcggtgtgt ttttttacag gatgcccctg ggggcgctgc
     6001 taggggtgtc tgttcagata tgtagcaatg agtcagggat tcacgaactg aaaatgtccg
     6061 aaaatgtgtc tcatggacac cgtatgcgcc caaaccgttc gccattcact ttcatgcata
     6121 gctatgcagc gagctgaaaa cgatcctgac gcattttttc ggtttacctt ggggaaaaca
     6181 tctctttttg cggtatttgc gtcagaatcg cgttcagcgc gtttctgagg tgcgggcaac
     6241 ggatgttatg ttcaatccgt gtgataattg gtgtggaata aacaatcaaa atggtaagtc
     6301 ggcttctgga ataactggcg gttctgattt ccttctgtag gttagagcgc tcttactgcc
     6361 tgtttttata tagaaatagt acgagtcatg aaacatctct agaggtatgt tttctatgga
     6421 ttttttcaca actctatcaa gcaaacctat atggataagg taggtg
//
