LOCUS       NZ_AP028874             3066 bp    DNA     circular CON 03-APR-2024
DEFINITION  Escherichia coli strain JBEHAAB-19-0176 plasmid pJBEHAAB-19-0176_4,
            complete sequence.
ACCESSION   NZ_AP028874
VERSION     NZ_AP028874.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00502403
            Sequence Read Archive: DRR390907, DRR393831
            Assembly: GCF_036511735.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1
  AUTHORS   Zuo,H., Sugawara,Y., Kondo,K., Kayama,S., Kawakami,S., Uechi,K.,
            Nakano,A., Yahara,K. and Sugai,M.
  TITLE     Emergence of an IncX3 plasmid co-harboring the carbapenemase genes
            blaNDM-5 and blaOXA-181
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3066)
  AUTHORS   Sugawara,Y., Zuo,H. and Sugai,M.
  TITLE     Direct Submission
  JOURNAL   Submitted (24-AUG-2023) Contact:Yo Sugawara National Institute of
            Infectious Disease, Antimicrobial Resistance Research Center; 4-2-1,
            Aoba-cho, Higashimurayama, Tokyo 189-0002, Japan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8
            Genome Coverage                   :: 83.8x
            Sequencing Technology             :: GridION; Illumina HiSeq X
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_036511735.1-RS_2024_04_03
            Annotation Date                   :: 04/03/2024 15:48:34
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,583
            CDSs (total)                      :: 5,462
            Genes (coding)                    :: 5,197
            CDSs (with protein)               :: 5,197
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 94
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 265
            CDSs (without protein)            :: 265
            Pseudo Genes (ambiguous residues) :: 0 of 265
            Pseudo Genes (frameshifted)       :: 89 of 265
            Pseudo Genes (incomplete)         :: 193 of 265
            Pseudo Genes (internal stop)      :: 51 of 265
            Pseudo Genes (multiple problems)  :: 60 of 265
            Pseudo Genes (short protein)      :: 5 of 265
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP028874.1.
            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..3066
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="JBEHAAB-19-0176"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pJBEHAAB-19-0176_4"
                     /geo_loc_name="Japan:Okinawa"
                     /lat_lon="26.212523 N 127.680771 E"
                     /collection_date="2020-03-30"
                     /collected_by="AMRRC, NIID"
     gene            140..415
                     /locus_tag="AABE75_RS27900"
     CDS             140..415
                     /locus_tag="AABE75_RS27900"
                     /inference="COORDINATES: protein motif:HMM:NF016875.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RelE/ParE family
                     toxin"
                     /protein_id="WP_094544860.1"
                     /translation="MIKNFKSKKLKQFNSGDTSKVAQAHKKKIEIILNALDTATSINDL
                     DLPGLDLHSYAEYTPTRWSLKVSANYRIFFEWDGANVRNVDYDDPH"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     gene            1695..1922
                     /locus_tag="AABE75_RS27905"
     CDS             1695..1922
                     /locus_tag="AABE75_RS27905"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001046776.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_224019247.1"
                     /translation="MFGFSPGELMNLCPDERLLFVRMISAMLRRSGGDAGAVMFEAYRH
                     IVSDTNQARRSYMLDLLESVRHDYVHGGYT"
                     /name="hypothetical protein"
     gene            complement(1970..2158)
                     /locus_tag="AABE75_RS27910"
     CDS             complement(1970..2158)
                     /locus_tag="AABE75_RS27910"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165998.1"
                     /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_000165998.1"
                     /translation="MTKQESAALNMAKFIRAQSLLLLEKLDVLDLDDEAADCERMHEQA
                     EALYQKLSARFGIQDGE"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(2595..2936)
                     /locus_tag="AABE75_RS27915"
     CDS             complement(2595..2936)
                     /locus_tag="AABE75_RS27915"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011330340.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="HigA family addiction module antitoxin"
                     /protein_id="WP_049592808.1"
                     /translation="MFTLQKPMHPGEFIREVYLEPLELQIGTFAEKLGVDTSTVSRLVN
                     QKADLSYEMALRLSKALGRSADSWMKMQIAYGLYRAQDKVNLEEVEVVYRPRNLDAPEK
                     QVHEFYENI"
                     /name="HigA family addiction module antitoxin"
     Typing          complement(722..1226)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.788"
                     /coverage="98.0"
                     /evalue="0.0"
ORIGIN
        1 ttttgttctt gtagtgacta tctggcagtt ctaaagcttc gcaggcgtag aatactacct
       61 ataaatagaa cacagtcaag aaactttact aaacaagaag aacttctaaa acataaaaat
      121 tttcatatgg agaagttcaa tgattaaaaa ttttaaatcc aaaaaactaa aacaatttaa
      181 cagtggtgat acaagtaagg tagcacaagc gcataaaaag aaaatagaga ttatcttaaa
      241 cgctttagat accgctactt caataaatga tcttgacctt cctggtttgg atcttcattc
      301 gtatgctgaa tataccccaa cccgctggtc attaaaggtg tcggcgaact atcgtatttt
      361 ctttgagtgg gatggtgcca acgtccgtaa tgtggattac gacgatccac attaatgtca
      421 gttaaatcaa cgacttaggt catgggcttg aatcacttta gtgattcaag cccatgaggc
      481 tattatatgg ttttttttta ttaagtcaat ggcttggtaa agataatttc ttgagattga
      541 gtgggacgca gagtatcttt aatcctgaaa cgaaaaaacc acctggggag gtggtttttc
      601 gaaggttcag caagttgggg aacttctgaa ccgtggtaac agggtgtaca agaccgctgc
      661 caccaaatac gtccttccag tttagccgta gttaggctga tacttcaaga actctgcatt
      721 agtaatctct tgtacaccct cttaccagtg gccgctgcca gtggcgataa gtcgtgcctt
      781 tccgggttgg actcaagacg atagttaccg gaaaaggcgc agcggtcgga ctgaacgggg
      841 ggttcgtgca tacagtccag cttggagcga actgcctacc cggaactgag tgtcaggcgt
      901 ggaatgagat aaacgcggcc ataacagcgg agtgacaccg gtaaaccgaa aggcaggaac
      961 aggagagcgc acgagggagc taccaggggg aaacgcctgg gatctttata gtcctgtcgg
     1021 gtttcgccac cactgatttg agcgtcagat tctgtgatgc ttgtcagggg ggcggagcct
     1081 atggaaaacc ggcagcgccg cggcctttcc tccctcgctt tatctcgtct tcatcgccat
     1141 atgcctttgt gaatattctc cttccgctcg ccgcagccga acgaccgagc gtagcgagtc
     1201 agtgagcgag gaagcggaat atctccgggc ttatctttgg caccgtacgc gccatagctg
     1261 cattttttaa tacgatgcag gatagggcaa acgccgcaaa atgacgtcat ccgacatcat
     1321 tccgccgcgt tcgtccagtg acctacagtc ggctctgggg tgtcggggct gtgccctgac
     1381 caggcgtttt ggagtatcgc caccgtggtg gcggtgctac aaaacatatc ctgtcccttc
     1441 cttggcatct ctgaagttta gccagtatac actccgctag cgctacgtga ctggttcagg
     1501 gctgcgcccc gacacccgct aaaagcactg acgcgcctgc ggcttgccca accccgcgcc
     1561 gtccgggaaa gaatttcccg atcgacccga cgtttctgtt tacctgtgat gttaacgttt
     1621 ggatcttttt cccgggttta cctattttct tctaatgaag cgttcacagc tgacgttaat
     1681 agatgggtgc tttcatgttt ggtttttcac caggagaact tatgaacctt tgccccgatg
     1741 aacgtctgct ctttgtgcgg atgatttccg ctatgcttcg ccgttcgggc ggtgatgcgg
     1801 gtgctgttat gtttgaggcg tatcgccata ttgtgtccga taccaatcaa gctcgtcgtt
     1861 cctacatgct cgacctgctc gaaagcgtca ggcatgacta tgtacacggt ggatatacat
     1921 agttgccctg gatacgcttt tcgtctaagt gagcgttctt ttcgtctctt tattcgccgt
     1981 cctgtatacc gaagcgtgcg ctcagcttct gataaagcgc ttctgcctgt tcgtgcattc
     2041 gctcacagtc ggctgcctcg tcatcaagat cgagcacgtc gagtttttcg agcagcagca
     2101 gcgactgcgc ccggataaat tttgccatgt tcagtgcggc tgattcctgt tttgtcatac
     2161 ggctttttcc cggttttatg gtgatcgcag actgaaatct tacttcattc acttgagtgc
     2221 atagccatgc aggtacgcag aaatcatcag cgcgtttctg agcggttttc agggggtaag
     2281 atgtgttctt ttgcaggtga ggtcgtagaa acgccctgag agcctctcag gcggtgcacg
     2341 caacggatgt tatggtaaat tctctaggta agcatagaag ggggctggct atgaagtttg
     2401 gggttagtga agaggatata cagatcacta tcaatggttg atacaggctc aacacccgct
     2461 gtttaagcat cttcaggaat aacgatgctg ccgcctctgc gagtgcaagt taggtcttca
     2521 cataaataca caggtgtaga gacaaaaagc ccctatggtt aggagctttt ctttacctaa
     2581 atgaaatatc gtttttagat attttcataa aattcatgga cctgtttttc aggagcatcc
     2641 aagttccgtg ggcggtaaac cacctcaact tcttcaagat ttactttatc ttgagcacga
     2701 tataaaccat atgctatttg cattttcatc caagagtcag cagaacgccc taaggctttt
     2761 gataggcgta atgccatttc ataagaaagg tcagcttttt ggtttactaa ccggctaacg
     2821 gttgatgtat caaccccaag cttttctgca aacgttccta tttgaagctc taacggctct
     2881 aaatatactt cgcggataaa ctcgccgggg tgcataggtt tttgcaatgt aaacatgcaa
     2941 cctcctaaat actctgattt tgtgccttgc gcaacgcgca aacctattga cataagcaat
     3001 ccatttgtga taaaatggat tagttaaggg taattttttc ttaacgttaa cagtttggtt
     3061 cttctg
//
