LOCUS       NZ_CP128985             3751 bp    DNA     circular CON 07-JUL-2023
DEFINITION  Escherichia coli strain TUM1881 plasmid pMTY1881_Col156, complete
            sequence.
ACCESSION   NZ_CP128985
VERSION     NZ_CP128985.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN35768950
            Assembly: GCF_030389945.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3751)
  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  JOURNAL   Unpublished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 3751)
  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_TUM1881_Comp_v1.1
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Reference-guided Assembly         :: missing
            Genome Coverage                   :: 270x
            Sequencing Technology             :: Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/05/2023 07:46:25
            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)                     :: 5,682
            CDSs (total)                      :: 5,558
            Genes (coding)                    :: 5,212
            CDSs (with protein)               :: 5,212
            Genes (RNA)                       :: 124
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 90
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 346
            CDSs (without protein)            :: 346
            Pseudo Genes (ambiguous residues) :: 0 of 346
            Pseudo Genes (frameshifted)       :: 105 of 346
            Pseudo Genes (incomplete)         :: 237 of 346
            Pseudo Genes (internal stop)      :: 53 of 346
            Pseudo Genes (multiple problems)  :: 49 of 346
            Pseudo Genes (short protein)      :: 4 of 346
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP128985.1.
            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..3751
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="TUM1881"
                     /db_xref="taxon:562"
                     /plasmid="pMTY1881_Col156"
                     /geo_loc_name="Japan"
                     /collection_date="2003"
                     /collected_by="Toho University School of Medicine"
     gene            complement(join(3389..3751,1..36))
                     /locus_tag="QVM90_RS28395"
                     /old_locus_tag="QVM90_28395"
     CDS             complement(join(3389..3751,1..36))
                     /locus_tag="QVM90_RS28395"
                     /old_locus_tag="QVM90_28395"
                     /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="hypothetical protein"
                     /protein_id="WP_001222916.1"
                     /translation="MRISNIEWLKKRIGFIRKLGEQTARQRQIIDLLDNEAGLTEQERK
                     LLHVLATAEKNDLQAQESERKQAVQKRIEGKKQRRERNHRLFLAAGLLIEAGLVDTKTG
                     ELCYKKDRILQALKEIKYDLETSPNPDA"
                     /name="hypothetical protein"
     gene            213..1139
                     /locus_tag="QVM90_RS28400"
                     /old_locus_tag="QVM90_28400"
     CDS             213..1139
                     /locus_tag="QVM90_RS28400"
                     /old_locus_tag="QVM90_28400"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221102.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobA/MobL family protein"
                     /protein_id="WP_014342223.1"
                     /translation="MATYHLSVKFGGKGQAANHADYIERKEKYRDRQDLEYSAHGNMPE
                     WARDNPSHFWQAADQFERANGSTYRELEIALPRELTAEQRLELVQDFVRQEAGERHAWS
                     FAIHNPKASIDGGEQPHAHIMMSQRVNDGIERTPEQYFRRYNARYPERGGAKKDSGSLT
                     LTQQKEQLRELRKRWEVKHNEHMRKHGFERGFIDCRTLKEQGIERRPEVHLGFEAAGRL
                     DDAQRHDIMQKRSEPDYSRHLEQARTVGYDIREWLDTPVKQHELVRRLQHDVAREHGFD
                     MRDRVSRQNRTEPERVKSPSRGFSMGF"
                     /name="MobA/MobL family protein"
     gene            1142..1675
                     /locus_tag="QVM90_RS28405"
                     /old_locus_tag="QVM90_28405"
     CDS             1142..1675
                     /locus_tag="QVM90_RS28405"
                     /old_locus_tag="QVM90_28405"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221103.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000168772.1"
                     /translation="MASTEEKLLTLLLSVEHLQHTAMEQQKAVADSLAVARETLRGYRD
                     ISDGVAKQVRDEVRNEVQKLDVAGLIGERISQDFQRLEESVANMKANADALNRDIATIH
                     SNIVQEYNTLKGYSWKWLGGVSVAFLVMFCVLGWGMKTMLDRNYNATAAVYQKVVTLED
                     KLAEKPVTGKSRKN"
                     /name="hypothetical protein"
     gene            2109..3128
                     /locus_tag="QVM90_RS28410"
                     /old_locus_tag="QVM90_28410"
     CDS             2109..3128
                     /locus_tag="QVM90_RS28410"
                     /old_locus_tag="QVM90_28410"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221104.1"
                     /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_001271364.1"
                     /translation="MSAALQYFEENLPHRPYHTDDLAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDREGAAIDWSDRNAPAPNITVKNPVNGHAHLLYALNIAVRTAPDASVKA
                     LKYAAAVERSLCEKLCADVNYSGLICKNPFHLEWQVMEWREDAYTLDELADYLDLSASE
                     RRSIDKHYGMGRNCHLFEMTRKWAYRAIRQGWPAFSQWLEAVIQRVEMYNASLPVPLSL
                     AECRAIGKSIAKYTHRNFTPETFAQYVADTHTPEIQAARGRKGGKANSSENQSDKGKKS
                     AAVRWTANDDKRRRALDMYILGASTEDIAVAVGVSSRTIRRWMDNSGEWLTKKQIIKC"
                     /name="replication initiation protein"
     Typing          2110..2884
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.907"
                     /coverage="83.0"
                     /evalue="0.0"
     Typing          214..1136
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.727"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ccgtttcttc agccattcga tgttgctgat gcgcatgttc gtggtgctcc ctggtgtttt
       61 tttgcggtgt gttgtggtcg tgcagtatat cgcttgcggt cggcgggtgc agggggtatc
      121 ttccgtgcta attcgtaaaa ttagaaggaa gcgcacttat atgtttctct ccttcgtcga
      181 gaaacagtgc gctcctgcgg agggctgaaa ccgtggcaac ctatcacctc agcgttaaat
      241 ttggtggcaa ggggcaggct gcaaaccacg ccgattacat cgagcgcaaa gagaaatacc
      301 gcgaccgtca ggatttggaa tattccgcac acggaaacat gccggaatgg gcgcgagata
      361 atccctcaca tttctggcag gctgctgacc agtttgaacg tgcgaacggt tcgacctatc
      421 gggaacttga aattgcatta ccccgtgaac tgacagcgga acagcgcctt gaactggtgc
      481 aggattttgt acgtcaggaa gctggcgaac ggcacgcctg gagttttgcc attcacaatc
      541 cgaaagcgag cattgacggc ggcgaacagc ctcatgcgca tatcatgatg agccagcgtg
      601 tgaatgatgg cattgaacgt acaccggaac agtatttccg gcgctataac gccaggtatc
      661 ccgagcgggg aggtgcgaaa aaggattccg gaagcctgac tctcactcag caaaaagagc
      721 agttgcggga attgcgaaaa cgctgggagg tgaagcacaa cgaacatatg agaaagcatg
      781 gctttgaaag gggcttcatt gactgccgga cgctgaaaga acagggcatt gaacgacgtc
      841 ccgaagtgca tctgggtttt gaagctgccg gacggcttga tgatgcccag cgtcatgaca
      901 tcatgcaaaa acggtctgaa ccggactatt cccgccatct tgaacaggcg cgaacggtcg
      961 ggtatgacat cagggaatgg ctggacactc cggttaagca acatgaactg gtcagaaggc
     1021 tgcaacatga tgttgcgcgg gagcatggct ttgacatgag agacagagtg agcagacaga
     1081 accgaactga acctgaacgg gttaaatcac cgtcacgtgg attttctatg ggattctgaa
     1141 catggccagc acagaagaaa aattactcac gctcctgtta tcggtggagc atctgcaaca
     1201 taccgcaatg gagcaacaga aagctgttgc tgattctctg gctgtggcaa gggaaacact
     1261 tcgcggatat cgggatattt ctgacggtgt ggcaaaacag gtcagggatg aagtcagaaa
     1321 cgaggtgcag aagctggatg ttgcagggct gataggtgag cgcatcagcc aggattttca
     1381 gcggctggaa gagtcagtcg caaacatgaa ggcaaacgcg gatgccctga acagggatat
     1441 tgcgacaatt cacagcaata tcgtgcagga atacaacacc cttaaagggt atagctggaa
     1501 atggctgggt ggggtgtcag tggcttttct ggttatgttc tgtgtgcttg gatggggaat
     1561 gaaaacaatg ctcgacagga actacaacgc cacagcggcg gtgtatcaga aagttgtgac
     1621 actggaagat aaactggcgg agaaacctgt cacgggcaag agccggaaaa actgacgcgc
     1681 ttcgcttgtc caacgcctca cgacccgcga aaaaattccg cgtcccgttc accgttttct
     1741 gatgagaaag tttgctgttt tgacccgttc gcccttctga acgctcgaaa cagatcgcgc
     1801 atcgctttcg tgcatagtta tgcaacgcgc taaaaacgat tctgacgcat ttttctggtt
     1861 tagcctggtg tttccttgtc tttttgcgtt ttttgcgcca gagagcgact gagggcgttt
     1921 taaggggggc gtacaacggg agttatggta aatggatcgg ttttgcggga aggctcgaca
     1981 ggttttgttg ttgggggtag tgtaagcgac tgaaaaacaa acgcccctga aattcgtgtc
     2041 tctccgccaa gattgtcacg agaatacagg ggcgaggtcg gtcgataacc tggaaggaat
     2101 cgtaacacat gagcgccgcg cttcaatact tcgaagaaaa tttaccccac cgcccctatc
     2161 acacggatga tctcgctttc ggccttcgca tctccggcaa agggcgtgcg cttcttgcgc
     2221 ggtacatcca gcagaaccag cctcatgcgc agttctggct ggtttttgac gttgaccgcg
     2281 agggggctgc gattgactgg agcgaccgga acgcccccgc gccgaacatc accgttaaaa
     2341 atcctgtgaa cggacacgct cacctgctct acgcactcaa catcgccgtg agaaccgcgc
     2401 ctgatgcctc ggttaaggcg ctgaaatatg ccgcagcggt tgaacgttcg ctgtgtgaga
     2461 aactttgtgc tgatgtgaac tacagcggcc tgatttgcaa aaatccgttc cacctggaat
     2521 ggcaggtgat ggagtggcgc gaggacgcct ataccctcga tgaactggca gattatctcg
     2581 atttgagcgc ctcagagcgt cgtagcatcg ataaacatta cgggatgggg cgaaactgcc
     2641 acctgttcga aatgacgcgc aaatgggctt acagggcgat tcgtcagggc tggccagcgt
     2701 tctcacagtg gcttgaagcg gtgatccagc gtgtcgaaat gtacaatgca tcgcttcccg
     2761 ttccgctttc actggctgaa tgtcgggcta ttggcaagag cattgcgaaa tacacgcaca
     2821 ggaacttcac gccggaaact ttcgcacagt atgtggctga tacgcacacg ccagaaattc
     2881 aggcagcacg cggtcgcaag ggcgggaagg ccaattcgtc agaaaatcag tcggacaaag
     2941 ggaaaaaaag cgccgctgtt cggtggactg ctaacgacga caaacgtcgt agggcgcttg
     3001 atatgtatat cttgggagcg tcaacggaag atattgcagt ggcggttggt gttagcagcc
     3061 ggactattcg acgctggatg gataattctg gagaatggct aaccaagaaa caaataatta
     3121 aatgttagtt aacaaagaag taacactacc ccccgttttt tgttaatggg gggttaaatt
     3181 cgcggacatg aacaagccta tatcagataa cagcgccttt cggcgtcttt ttgagcagcg
     3241 ggctttccgg cggttttctc ctctcagccc agcaatggtg cggcttaccg catgattgag
     3301 gtggtcgtgc tcgccgcagt ctcatgaccg agcgtagcga gcgaatgagc gaggaagcac
     3361 cagggaaccg gaacacggat ggaggcactt acgcgtctgg gtttggggat gtctccagat
     3421 cgtacttaat ttccttaagt gcctgtaata tcctgtcttt tttatagcat agctcgcctg
     3481 tttttgtgtc taccagtcct gcttcgatca gtagcccagc cgcgagaaag agtcggtgat
     3541 tgcgttctcg tcgttgtttt tttccctcga ttcgtttttg gaccgcctgt tttcgttcgc
     3601 tctcctgtgc ctgtaagtcg tttttttccg ctgttgccag tacgtggagg agtttgcgtt
     3661 cctgttctgt gagtcctgct tcgttgtcga gcaggtcaat aatctgtctc tgtcgtgcgg
     3721 tctgttctcc gagcttcctg atgaatccga t
//
