LOCUS       NZ_CP135677             5310 bp    DNA     circular CON 07-OCT-2023
DEFINITION  Escherichia coli strain TUM9803 plasmid pMTY9803_Col2, complete
            sequence.
ACCESSION   NZ_CP135677
VERSION     NZ_CP135677.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN35769040
            Assembly: GCF_032382315.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5310)
  AUTHORS   Komori,K., Aoki,K., Ishii,Y. and Tateda,K.
  TITLE     Analysis of the Plasmid-Driven Acquisition of blaCTX-M-14 in
            Escherichia coli ST131 Subclone H30
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5310)
  AUTHORS   Komori,K., Aoki,K., Ishii,Y. and Tateda,K.
  TITLE     Direct Submission
  JOURNAL   Submitted (21-SEP-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                     :: 13-SEP-2021
            Assembly Method                   :: SPAdes v. v3.15.5
            Assembly Name                     :: Toho-u_TUM9803_Comp_v1.1
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Reference-guided Assembly         :: missing
            Genome Coverage                   :: 179x
            Sequencing Technology             :: Complete Genomics
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 10/07/2023 15:02:47
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 6,120
            CDSs (total)                      :: 6,000
            Genes (coding)                    :: 5,606
            CDSs (with protein)               :: 5,606
            Genes (RNA)                       :: 120
            rRNAs                             :: 7, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 7, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 394
            CDSs (without protein)            :: 394
            Pseudo Genes (ambiguous residues) :: 0 of 394
            Pseudo Genes (frameshifted)       :: 148 of 394
            Pseudo Genes (incomplete)         :: 272 of 394
            Pseudo Genes (internal stop)      :: 84 of 394
            Pseudo Genes (multiple problems)  :: 93 of 394
            Pseudo Genes (short protein)      :: 4 of 394
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP135677.1.
            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..5310
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="TUM9803"
                     /db_xref="taxon:562"
                     /plasmid="pMTY9803_Col2"
                     /geo_loc_name="Japan"
                     /collection_date="2010"
                     /collected_by="Toho University School of Medicine"
     gene            <1..>114
                     /locus_tag="RS166_RS30550"
                     /old_locus_tag="RS166_30550"
                     /pseudo=""
     CDS             <1..>114
                     /locus_tag="RS166_RS30550"
                     /old_locus_tag="RS166_30550"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221104.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus and C-terminus; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /name="hypothetical protein"
     gene            complement(174..740)
                     /locus_tag="RS166_RS30555"
                     /old_locus_tag="RS166_30555"
     CDS             complement(174..740)
                     /locus_tag="RS166_RS30555"
                     /old_locus_tag="RS166_30555"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001681717.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="LysE family translocator"
                     /protein_id="WP_264873939.1"
                     /translation="MEYSTLFSFAIVTLSQTISIGPGVALVINNAFSQGLKSSIKTSVY
                     IRSGEAIVMVISLLTLSSTSSIEQHFYIIKILGGSYLIYIGVMGLINKKNKKSKVQKPL
                     LIPLLNPKAYLFFAALIPAFIDDNTNIALNFFILGVLFISFLTDIIYIAISLTIRDKLT
                     PSFSRYISICSSIFILGTGIYFILT"
                     /name="LysE family translocator"
     gene            1684..2385
                     /locus_tag="RS166_RS30560"
                     /old_locus_tag="RS166_30560"
     CDS             1684..2385
                     /locus_tag="RS166_RS30560"
                     /old_locus_tag="RS166_30560"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001281399.1"
                     /GO_function="GO:0003887 - DNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_011666799.1"
                     /translation="MSDLIAYKSNALVEASYKLTLQEQRFLLLCIGRLKSGSDAESTEL
                     QKTMTVTAEEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKDDEKREEFRWIQYRAQY
                     AKGEGKAQITFSDAVMPYLTQLKGQFTRVVIKNISNLSRSYSIRIYELLQQFRSTGERI
                     IALDDFRSMLDIEHKYQTYKSLNQQLLRPCVDELNQKSDLAVTLETIKKGRTVVALHFR
                     FKEDKQIKMTI"
                     /name="replication initiation protein"
     Typing          1685..2385
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.459"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gaatgtcggg ctattggcaa gagcattgcg aaatacacgc acaggaactt cacgccggaa
       61 actttcgcac agtatgtggc tgatacgcac acgccagaaa ttcaggctgc acgagatgaa
      121 gccgaaaagc aaatatgcca tgactaaggc tgtatgagta taaaaacggc gtttcacgtc
      181 aagataaaat aaatacctgt acctaatata aaaatggagc tacatatact tatgtacctt
      241 gagaatgacg gagttaattt atcccttatc gtcaagctaa tagctatgta aataatatct
      301 gtcaggaatg atataaacaa aacacccaat ataaagaaat ttaatgcgat atttgtatta
      361 tcatctataa atgctggtat taatgccgca aagaataaat acgcctttgg gtttaataat
      421 ggtataagta aaggtttttg tactttgctt tttttgtttt ttttattaat taaacccatt
      481 acccctatgt atattaaata gcttccacct aagatcttta taatgtaaaa gtgttgttct
      541 atgctggatg ttgaagataa cgttaaaaga gatattacca tgacgattgc ttcgccagat
      601 cttatgtata cacttgtttt tattgatgat ttaagtcctt gtgaaaaggc gttgtttata
      661 accaatgcaa caccaggtcc tattgatata gtttgagata aagttacgat agcaaatgaa
      721 aataatgttg aatattccat atttacttac catgatatat ttcgcgggag cttttcatat
      781 acatactcca tttattctcg gagcggatat acattcattt ataaagtcat tcatttttct
      841 atcccctggt ctgagttttt gcatttgttg ttatgactat ttaatgctaa ttatcagata
      901 acctttttta cacgccataa acacgattat gattgatgtt ttatattgtc gatatttcgt
      961 tgtccagact gtatatgtct ggaaatttgt ttgcatacgg gttcgttccg tttagctggc
     1021 tttttggatg agaaagtttg ctgttttgac ccgttcgcgc ttctgaacgg gggtttggtg
     1081 ttcttttgcg cggcgtctcc gatccgctcc cacacctcca aaccaaatac cgaaaccctg
     1141 caaaccaagc gagtggcggc tccgctcgcc gcagccccag cgaccgagcg ttagcgagca
     1201 agtgggcgag gaagcggaag tgaaccgtag ccaggttgag cacatacgca cggtttttcg
     1261 acaggtgata tgcgccgaac ccgcatgaat actggatttc cacagggttg agcggggttt
     1321 ttgctaaagt ccgcgaagtg gatttttgta acatcttgtt ttttcttgtt tttccttttg
     1381 cgcaccccaa gttttccaca ggctcgctgt taagttttta gatcttgttt ttaagatctt
     1441 gtttttaata cttgttttag ggtcgaattt tcttatggaa ttcaagagtt tagaagacta
     1501 taggtaatat aatttaaggt aaaggcaata tgatttaagg tggataggca atatgattta
     1561 aggtaaaggc aatatgattt aaggtaatat ccacaggaaa agggatatta aaattaaatc
     1621 atattgcctt tacctaaagg aatgtttata ttttactcat tgccttaggt tgagggattt
     1681 acaatgtcgg atctgattgc ctacaaatcc aatgcactgg ttgaggccag ctataaattg
     1741 actcttcagg aacagcgatt cttgttactt tgcattggtc gattgaagtc gggttctgat
     1801 gcagaatcca ctgaattgca aaagaccatg actgttaccg ccgaagagta tttcgactca
     1861 ttccctgata tggggcggaa aaatgccgag gttcagctac aggaagcaat tgatcgtttg
     1921 tgggacaggt cgatcatcct taaggacgat gagaagcgcg aggagttccg ctggatccag
     1981 tatcgggcac agtacgctaa aggtgagggc aaagcccaaa tcactttttc agatgcggtc
     2041 atgccttatc tgacacagtt gaaggggcaa tttactagag ttgtaattaa gaatatctcc
     2101 aatttatcaa gaagttacag cataagaata tacgaacttc tccagcaatt ccgcagcaca
     2161 ggggaacgta ttatcgccct cgatgatttt cgctcaatgc ttgatataga gcataaatat
     2221 caaacatata agtctctgaa ccagcaatta ttaagacctt gcgttgacga actgaatcaa
     2281 aaaagcgact tggctgtaac gcttgagacg atcaagaagg ggcgcacggt tgtagccctg
     2341 cattttcgct tcaaggaaga caaacagatc aagatgacga tctaaaatcg attttaaggc
     2401 atctaaaacg ccatctggtt cgtttttttg gtgtcaggta tgcgatggta ctaccaagca
     2461 aataaattgc gtcaaaatcg attttagaga gcggtatggc aaaccatgtc gaacattact
     2521 tgtgttactt gacgtgagag atgcgttaat gccgccagca gcagtccccc atcgaagtga
     2581 ctcatgtgtg actaaagagc aagcctgagc aacgtaggaa tctccaacct tcaggacggg
     2641 atggatatca agcaccaggg cacacttgaa aacaaaacct cgcctctggc aaagcgcgtc
     2701 ctttcacgat gacgtagagg tatttgaata tctgtaggag ttcatcacgc tattttaacg
     2761 cttaaaaagc gcgtttctga ttgtgtaact aaacacaggt agtaattagt aggtgtgggg
     2821 gggcagaaac gcgcaattaa tatttatcgt gaatttgatt ttatgtctag tatcgagaaa
     2881 cagaatataa aaagattatc tttggaaata tagaaaaaaa taaaataata aactaaaaac
     2941 aatcaaaaaa taataaatat tacactacaa tatggcaata atatattcat tcatatagtg
     3001 atatacgcta tggttttcaa aattttcctt gagctgaaga acggagtttt atggcaaacg
     3061 aggtaatctt gcacaggaaa aataggttgt atctatgtca tggttttgtt attttttttg
     3121 ctcagttatt gatggtcaat atgtaaaata aatcaggtac ttccttacac ttaccctcat
     3181 tcattgaggg ttttttttat ccatatctaa gttgacatcc tccatgccct gaaggacggg
     3241 gttttacagc acaccggata actatctcga catggatatt gatacacgtt aaaaatacgt
     3301 gacgcgtttc tggcagatat ctgaggtcta tttcgccgtg ttagccacac tgtcagaaac
     3361 gcgttcaatt tctcccgttg agctgatatg ctcatcaccg caatcacggt agtgtccgaa
     3421 gacgaaccgt taatgcatct tccccccgat actgggcttt cggggggaat atttactcgg
     3481 tgcgccgtaa aaccccgtcc ttcagggcat ggaggatgtc aacacgaatc ccctatcttc
     3541 ttttcagtaa gaaacggtca ttgaaaactt atataacact acttttggtg tgtattttgc
     3601 gataaaaata tcccctatcc taatgatagg ggatacaaac gatgaattaa cagttcttaa
     3661 ttctcacgtg aaaagataga ttttaacgaa gacacaatca gcagtcttat atcgaatggc
     3721 tatcgatcct gaatcctgat gagtggggat gtttctgtac tactaatgaa aagctatccg
     3781 gctagagact ttacgataca gaaacacccc tctttctttt atctcatcag atgccatagc
     3841 gcaaaacaat ttcgtttcac agatgtgact tacaatcaaa ctgtgcaaca taaatcacaa
     3901 aacaagaagg ttttgttatt attttgttga tgagttgttt ttcgttggtt gtttttttga
     3961 ggcgtacata cgcgcacaaa tgtaaaacta aattcgtgtt ttcgataatt ttaaggccac
     4021 aatcattatg gcatttttta tcctgatcgc cgtcaaaatc tgtccttcat ggcaggattt
     4081 acggcgatcc ggataacacc aaagatacct acatgctcat tcccctgtgg tttccaggat
     4141 atctttcctg ttttctgtgc tgttcatcgc gccgccatac cccgtaacga ctgcgctcag
     4201 tacccctgaa atttcgctcg ccggaaacac gcgggtgttg ttttaacgtg tcccggtagc
     4261 ggtgtccagg caggtatgct tccgccagcg gagttgttga tcttgtgttc tgtttttggc
     4321 tagtatttgt ccgaaaacct gtcgctccgg cgaccaacca atctcccggt ggtctgagag
     4381 ggaggcttac gcgaccacac tgtcatctca ggatgaccag ccaatgttcc ggcagtctga
     4441 gaggagcgcc ttcgggtgac tgcaatatcc catgagcctg gaagaggatg cctatatggc
     4501 ggcaacatcc gtttagcctc tggaaacgga tgtcaccagt agctggtgac tgaggtacgt
     4561 tatttttacc ttcggattac ccgtacggtt ttgtatgtca tgaaacttac gagttttcct
     4621 ctcgcagagt ggcgaaatgc cttatatatc tgcgtcttaa agattttctg tctggctgca
     4681 tgagcttctt gtgactgtgc gcacggcata aggccatttg aaatttggct gcttgcgtgt
     4741 gtacgtggag tctgaagctg tgcggcgtca cttgcgtgcg accggaggga acaccaagtg
     4801 acgccacaac aatctgccct gaaagcagca tcacgtaagg ccagccagaa aatcgtcgct
     4861 cgtgaccagc gttctgatga ccgtttcgtc tgtctgacag cgtctttcag taacgtgtcc
     4921 atgcctttcc ggcgcgtccg ttttcacgga cggccacgcc ggaatgtctt tttaaacttc
     4981 ataatacatg agaggtaagt gtattaaatt gttgaaaaaa ggaataaata tgaaaaatcg
     5041 ttctgatgtc ggaaggcgtc atcgtaagat gacggggagt aaaaaatcgc cctggtgcac
     5101 aggtagcgaa ctcctgtaaa aactcaacat gtgcaagctc tgctacatcg acatcaaacg
     5161 agccaggaag gcgagcaacc gcgttacaga gccgtccgtg atgacgaaaa actaacaata
     5221 tcaacgatct ggtctgttta tcggaagggc atctcatgca gttgaacttt cagaacggat
     5281 ggttttctgc atctttttta acagggggat
//
