LOCUS       NZ_CP128969             2307 bp    DNA     circular CON 07-JUL-2023
DEFINITION  Escherichia coli strain TUM1887 plasmid pMTY1887_Col, complete
            sequence.
ACCESSION   NZ_CP128969
VERSION     NZ_CP128969.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN35768953
            Assembly: GCF_030389855.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 2307)
  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  JOURNAL   Unpublished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 2307)
  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_TUM1887_Comp_v1.1
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Reference-guided Assembly         :: missing
            Genome Coverage                   :: 171x
            Sequencing Technology             :: Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/05/2023 07:42:31
            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)                     :: 5,133
            CDSs (total)                      :: 5,015
            Genes (coding)                    :: 4,824
            CDSs (with protein)               :: 4,824
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 191
            CDSs (without protein)            :: 191
            Pseudo Genes (ambiguous residues) :: 0 of 191
            Pseudo Genes (frameshifted)       :: 71 of 191
            Pseudo Genes (incomplete)         :: 117 of 191
            Pseudo Genes (internal stop)      :: 44 of 191
            Pseudo Genes (multiple problems)  :: 39 of 191
            Pseudo Genes (short protein)      :: 3 of 191
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP128969.1.
            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..2307
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="TUM1887"
                     /db_xref="taxon:562"
                     /plasmid="pMTY1887_Col"
                     /geo_loc_name="Japan"
                     /collection_date="2003"
                     /collected_by="Toho University School of Medicine"
     gene            complement(420..923)
                     /gene="ddp1"
                     /locus_tag="QVM92_RS25655"
                     /old_locus_tag="QVM92_25655"
     CDS             complement(420..923)
                     /gene="ddp1"
                     /locus_tag="QVM92_RS25655"
                     /old_locus_tag="QVM92_25655"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000809479.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DNA distortion polypeptide 1"
                     /protein_id="WP_167821256.1"
                     /translation="MKQIKFRLTDEEYNVAHVNAISNGVNSVNAFAKRKVLDVSSTPSK
                     VIVSNEPSVPVKTCLYPHELELIKRNAALHGMSVSREIAIRLRKSVLKNEVCLYPEEVQ
                     VLRKLSTTINRVGRNIHFIISGDRFCTVNDPDFRNEIKELTALCETVDKTIEQLVFSVN
                     NRFG"
                     /name="ddp1"
     gene            complement(1026..1310)
                     /locus_tag="QVM92_RS25660"
                     /old_locus_tag="QVM92_25660"
     CDS             complement(1026..1310)
                     /locus_tag="QVM92_RS25660"
                     /old_locus_tag="QVM92_25660"
                     /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="LuxR family transcriptional regulator"
                     /protein_id="WP_109938089.1"
                     /translation="MTKHDAIRISQLHQIFYDDEGLIDSEKNVTILYGIGFTIDEIAYF
                     GNTTPGTVQGQLFNARAKLSCASASSLRPMILLRLLLLLIFEQDRLNGL"
                     /name="LuxR family transcriptional regulator"
     gene            complement(1386..1808)
                     /locus_tag="QVM92_RS25665"
                     /old_locus_tag="QVM92_25665"
     CDS             complement(1386..1808)
                     /locus_tag="QVM92_RS25665"
                     /old_locus_tag="QVM92_25665"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000097059.1"
                     /GO_process="GO:0006260 - DNA replication [Evidence IEA];
                     GO:0006276 - plasmid maintenance [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication/maintenance protein RepL"
                     /protein_id="WP_249940703.1"
                     /translation="MGKNEHVLVNQSTGEVTGTNVVTYKKVDSEEFVKLFSRNIALTFD
                     LTSSGIKSLNVLIWSVQNTAIQKDVVALDQLAFDDFMKENPNLKMTLRTFQRGLSELEA
                     SKIIAKTMRKGFYYINPNFVFNGDRIAFTTLIERDC"
                     /name="replication/maintenance protein RepL"
ORIGIN
        1 gatgcacgaa acgggtttta aatgcccgtc agggcatgga aggcgcgaaa aacgcttaca
       61 gaggctctca ggaggtcagg cgcgccgata cccctaagca ggggctttca ggtcgccagg
      121 aaccgcgtca gccccctgca aagcccattt gcacggtaca ggcagccacg cggttggtag
      181 gtggtcggag accgtcggtg ttacagcaat gggggtctgg gggtctcccc agacggtttc
      241 cggttgcgct caaggcgctg ccggaaccgt ggcggctcgg tcgttccgaa gaacggggaa
      301 taaaaatctt agtggtttaa ctccgatgca ggatagggca aacgccgcaa aatgacgtct
      361 ctgacgcaat tctgcaacgt ttgcccggtg acctactgtc ggttcttgat aatacgtttt
      421 tacccaaaac gattattaac actaaaaact aattgctcta ttgttttatc gactgtttcg
      481 cataatgctg taagttcctt tatctcattt ctgaaatcag gatcgttaac tgtgcaaaaa
      541 cgatcgccgc taattataaa atgaatattt cgaccaactc tattaatcgt agttgaaagc
      601 tttctaagca cctgcacttc ttcgggataa agacaaactt cgtttttcaa aactgattta
      661 cgtaagcgta tcgctatttc tcggctaaca ctcattccgt gtaatgcagc attacgcttt
      721 attaactcca gttcatgtgg gtataagcat gtttttactg gtacagatgg ttcattcgat
      781 actataacct ttgaaggtgt tgagctaaca tctaaaacct tcctctttgc aaaagcattt
      841 acactattaa cgccatttga aatggcatta acatgagcaa cgttgtattc ctcgtcggtc
      901 aatctgaatt taatttgctt catagtaccc cttaagagcc tgcggcaggc acaggcaaaa
      961 accacgtttt tggacaatca tgggaaatgg tacccatttg accatgattg tctatcctgc
     1021 attgatcaca gcccatttaa gcggtcttgc tcaaagatta ggagtaaaag caatctcaat
     1081 aagatcatcg gccttaaaga tgaagctgaa gcacaactca atttagctct tgcattaaat
     1141 agctgccctt gaactgttcc cggagttgta ttcccaaaat aagctatttc atcaatagta
     1201 aatcctatac catataaaat ggtcacgttc ttttccgaat caattaatcc ttcatcgtcg
     1261 taaaagattt gatgaagttg agaaatacgt atagcatcat gcttagtcat aataacctct
     1321 cttgcaggtt gttgtgatta gcaggcgaac aaaacaccac ttttgttcgc ctgcgacggt
     1381 atatattaac aatccctctc aataagagtt gtaaacgcta ttcgatcacc attaaaaaca
     1441 aagttagggt ttatataata aaatcccttt ctcattgttt ttgcaattat cttactagct
     1501 tcaagttcag ataatcctcg ttgaaacgtt ctcaatgtca tttttaaatt tggattttcc
     1561 ttcatgaaat catcaaaagc taattgatca agtgcaacga catctttttg aattgccgtg
     1621 ttttgcacac tccaaattaa aacatttaac gatttaatac ctgaggaagt aagatcaaaa
     1681 gttaatgcta tattacggct aaataactta acgaattctt cactatcaac ttttttataa
     1741 gtaacaacat tagtccccgt cacctcaccg gtcgattgat taacgagcac atgttcgttc
     1801 ttccccatag gggagatcat gactctttta gaggaaatag ttaacgctaa atcttttata
     1861 aaagggttct ctttgtacct taccaccgac ataaaaacct ctcatgattt cgccactaac
     1921 gacaaaataa gcgcgttttt tgtcgttgtc aatccgataa gcgagcctct aagcgacatt
     1981 ttttttttat ttttgtcgtt tatcgcgaaa ttaaattgtc gttatagacg tgccatcctg
     2041 tcgtttggaa cgcgtgatcg tgcaaatacg atctagcatt catgcgggtt acaagaaatt
     2101 cccttcttag ttcttattct acaccgagcg taggtgcttt tttgaccaga cgattctctt
     2161 ccgcttcctc gcccactcgc tcactaacgt tcggtcgctg gggctgcggc gagcggtgcc
     2221 acctctcgca tgttatcggt gattccgctg ttgttctttt ggggatgagt cgccagatag
     2281 ctcttcaaac gctctcagaa gctctca
//
