LOCUS       NZ_CP103542             6200 bp    DNA     circular CON 21-SEP-2023
DEFINITION  Escherichia coli strain 5264 plasmid pMB9081_2, complete sequence.
ACCESSION   NZ_CP103542
VERSION     NZ_CP103542.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN28174088
            Assembly: GCF_024917815.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 6200)
  AUTHORS   Shropshire,W.C., Konovalova,A., McDaneld,P.M., Gohel,M., Strope,B.,
            Sahasrabhojane,P., Tran,C.N., Greenberg,D.E., Kim,J., Zhan,X.,
            Aitken,S.L., Bhatti,M., Tor,S., Treangen,T., Hanson,B.M., Arias,C.A.
            and Shelburne,S.A.
  TITLE     Systematic Analysis of Mobile Genetic Elements Mediating
            Beta-lactamase Gene Amplification in Non-Carbapenemase-Producing
            Carbapenem Resistant Enterobacterales Bloodstream Infections
  JOURNAL   mSystems (2022) In press
REFERENCE   2  (bases 1 to 6200)
  AUTHORS   Shropshire,W.C.
  TITLE     Direct Submission
  JOURNAL   Submitted (19-AUG-2022) Infectious Diseases and Infection Control,
            University of Texas MD Anderson Cancer Center, South Campus Research
            Building 4, Houston, TX 77054, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Flye v. 2.8.3-b1695
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 343x
            Sequencing Technology             :: Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 09/21/2023 03:12:29
            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)                     :: 4,780
            CDSs (total)                      :: 4,657
            Genes (coding)                    :: 4,416
            CDSs (with protein)               :: 4,416
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 241
            CDSs (without protein)            :: 241
            Pseudo Genes (ambiguous residues) :: 0 of 241
            Pseudo Genes (frameshifted)       :: 82 of 241
            Pseudo Genes (incomplete)         :: 159 of 241
            Pseudo Genes (internal stop)      :: 47 of 241
            Pseudo Genes (multiple problems)  :: 48 of 241
            Pseudo Genes (short protein)      :: 4 of 241
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP103542.1.
            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..6200
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="5264"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pMB9081_2"
                     /geo_loc_name="USA: Houston"
                     /lat_lon="29.7068 N 95.3971 W"
                     /collection_date="2019-09-25"
                     /collected_by="MDACC"
                     /genotype="ST167"
     gene            1..816
                     /gene="sul2"
                     /locus_tag="M5S66_RS23720"
                     /old_locus_tag="M5S66_23720"
     ARG             2..813
                     /name="sul2"
                     /gene="sul2"
                     /gene_name="sulfonamide-resistant dihydropteroate synthase
                     Sul2"
                     /tool="amrfinderplus"
                     /drug_class="SULFONAMIDE"
                     /identity="100.0"
                     /coverage="100.0"
     gene            877..1680
                     /gene="aph(3'')-Ib"
                     /locus_tag="M5S66_RS23725"
                     /old_locus_tag="M5S66_23725"
     ARG             878..1677
                     /name="aph(3'')-Ib"
                     /gene="aph(3'')-Ib"
                     /gene_name="aminoglycoside O-phosphotransferase
                     APH(3'')-Ib"
                     /tool="amrfinderplus"
                     /drug_class="AMINOGLYCOSIDE"
                     /identity="100.0"
                     /coverage="100.0"
     gene            1680..2516
                     /locus_tag="M5S66_RS23730"
                     /old_locus_tag="M5S66_23730"
     CDS             1680..2516
                     /locus_tag="M5S66_RS23730"
                     /old_locus_tag="M5S66_23730"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000480972.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="aminoglycoside O-phosphotransferase APH(6)-Id"
                     /protein_id="WP_000480968.1"
                     /translation="MFMPPVFPAHWHVSQPVLIADTFSSLVWKVSLPDGTPAIVKGLKP
                     IEDIADELRGADYLVWRNGRGAVRLLGRENNLMLLEYAGERMLSHIVAEHGDYQATEIA
                     AELMAKLYAASEEPLPSALLPIRDRFAALFQRARDDQNAGCQTDYVHAAIIADQMMSNA
                     SELRGLHGDLHHENIMFSSRGWLVIDPVGLVGEVGFGAANMFYDPADRDDLCLDPRRIA
                     QMADAFSRALDVDPRRLLDQAYAYGCLSAAWNADGEEEQRDLAIAAAIKQVRQTSY"
                     /name="aminoglycoside O-phosphotransferase APH(6)-Id"
     gene            complement(<2623..3027)
                     /locus_tag="M5S66_RS23735"
                     /old_locus_tag="M5S66_23735"
                     /pseudo=""
     CDS             complement(<2623..3027)
                     /locus_tag="M5S66_RS23735"
                     /old_locus_tag="M5S66_23735"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001120888.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="IS91 family transposase"
                     /name="IS91 family transposase"
     gene            complement(3071..3460)
                     /locus_tag="M5S66_RS23740"
                     /old_locus_tag="M5S66_23740"
     CDS             complement(3071..3460)
                     /locus_tag="M5S66_RS23740"
                     /old_locus_tag="M5S66_23740"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000102614.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000102614.1"
                     /translation="MSTELNSGTVGGFGHMGPNDPYNDGHSGSGSSGGSFNGGGNGGHD
                     NSSGSSYTASFGLITGRHPITVPGTKNINSVDLSAVINNIIHHEGARNNMYLDTANNVR
                     VGVTGTGWQCLATAGISAEGKRTFR"
                     /name="hypothetical protein"
     gene            3678..4118
                     /locus_tag="M5S66_RS23745"
                     /old_locus_tag="M5S66_23745"
     CDS             3678..4118
                     /locus_tag="M5S66_RS23745"
                     /old_locus_tag="M5S66_23745"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011161230.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_005119689.1"
                     /translation="MAWHTVQETLKLTGKSRSQLYRDMAKGLVSYRTGKNDRREFETSE
                     LIRAYGELRTSETPKRHKEGHSKSVVSQAENAQLDVIQQKLDALQQTVTLMLEDKMARE
                     AENRLRNEEREQLQAEISRLADALAQEKKRGFWSRLFRSGSE"
                     /name="hypothetical protein"
     gene            complement(4863..5012)
                     /locus_tag="M5S66_RS23750"
                     /old_locus_tag="M5S66_23750"
     CDS             complement(4863..5012)
                     /locus_tag="M5S66_RS23750"
                     /old_locus_tag="M5S66_23750"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017880354.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001138880.1"
                     /translation="MPSEYDEQLDSTDTQLPGEYDLFDLMAQVTEENLHAPVDFGSPVG
                     REAL"
                     /name="hypothetical protein"
     gene            5583..5741
                     /locus_tag="M5S66_RS23910"
     CDS             5583..5741
                     /locus_tag="M5S66_RS23910"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_032287700.1"
                     /translation="MHEPPVQSDRCALSGNYQLESNPERHDKTPLAAAISNRSAREDRL
                     RGLEVEA"
                     /name="hypothetical protein"
     ARG             1681..2513
                     /name="aph(6)-Id"
                     /gene="aph(6)-Id"
                     /gene_name="aminoglycoside O-phosphotransferase APH(6)-Id"
                     /tool="amrfinderplus"
                     /drug_class="AMINOGLYCOSIDE"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          complement(5048..5221)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.429"
                     /coverage="100.0"
                     /evalue="1.19e-84"
     Typing          5145..5750
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.593"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 atgaataaat cgctcatcat tttcggcatc gtcaacataa cctcggacag tttctccgat
       61 ggaggccggt atctggcgcc agacgcagcc attgcgcagg cgcgtaagct gatggccgag
      121 ggggcagatg tgatcgacct cggtccggca tccagcaatc ccgacgccgc gcctgtttcg
      181 tccgacacag aaatcgcgcg tatcgcgccg gtgctggacg cgctcaaggc agatggcatt
      241 cccgtctcgc tcgacagtta tcaacccgcg acgcaagcct atgccttgtc gcgtggtgtg
      301 gcctatctca atgatattcg cggttttcca gacgctgcgt tctatccgca attggcgaaa
      361 tcatctgcca aactcgtcgt tatgcattcg gtgcaagacg ggcaggcaga tcggcgcgag
      421 gcacccgctg gcgacatcat ggatcacatt gcggcgttct ttgacgcgcg catcgcggcg
      481 ctgacgggtg ccggtatcaa acgcaaccgc cttgtccttg atcccggcat ggggtttttt
      541 ctgggggctg ctcccgaaac ctcgctctcg gtgctggcgc ggttcgatga attgcggctg
      601 cgcttcgatt tgccggtgct tctgtctgtt tcgcgcaaat cctttctgcg cgcgctcaca
      661 ggccgtggtc cgggggatgt cggggccgcg acactcgctg cagagcttgc cgccgccgca
      721 ggtggagctg acttcatccg cacacacgag ccgcgcccct tgcgcgacgg gctggcggta
      781 ttggcggcgc tgaaagaaac cgcaagaatt cgttaactgc acattcggga tatttctcta
      841 tattcgcgct tcatcagaaa actgaaggaa cctccattga atcgaactaa tatttttttt
      901 ggtgaatcgc attctgactg gttgcctgtc agaggcggag aatctggtga ttttgttttt
      961 cgacgtggtg acgggcatgc cttcgcgaaa atcgcacctg cttcccgccg cggtgagctc
     1021 gctggagagc gtgaccgcct catttggctc aaaggtcgag gtgtggcttg ccccgaggtc
     1081 atcaactggc aggaggaaca ggagggtgca tgcttggtga taacggcaat tccgggagta
     1141 ccggcggctg atctgtctgg agcggatttg ctcaaagcgt ggccgtcaat ggggcagcaa
     1201 cttggcgctg ttcacagcct atcggttgat caatgtccgt ttgagcgcag gctgtcgcga
     1261 atgttcggac gcgccgttga tgtggtgtcc cgcaatgccg tcaatcccga cttcttaccg
     1321 gacgaggaca agagtacgcc gcagctcgat cttttggctc gtgtcgaacg agagctaccg
     1381 gtgcggctcg accaagagcg caccgatatg gttgtttgcc atggtgatcc ctgcatgccg
     1441 aacttcatgg tggaccctaa aactcttcaa tgcacgggtc tgatcgacct tgggcggctc
     1501 ggaacagcag atcgctatgc cgatttggca ctcatgattg ctaacgccga agagaactgg
     1561 gcagcgccag atgaagcaga gcgcgccttc gctgtcctat tcaatgtatt ggggatcgaa
     1621 gcccccgacc gcgaacgcct tgccttctat ctgcgattgg accctctgac ttggggttga
     1681 tgttcatgcc gcctgttttt cctgctcatt ggcacgtttc gcaacctgtt ctcattgcgg
     1741 acaccttttc cagcctcgtt tggaaagttt cattgccaga cgggactcct gcaatcgtca
     1801 agggattgaa acctatagaa gacattgctg atgaactgcg cggggccgac tatctggtat
     1861 ggcgcaatgg gaggggagca gtccggttgc tcggtcgtga gaacaatctg atgttgctcg
     1921 aatatgccgg ggagcgaatg ctctctcaca tcgttgccga gcacggcgac taccaggcga
     1981 ccgaaattgc agcggaacta atggcgaagc tgtatgccgc atctgaggaa cccctgcctt
     2041 ctgcccttct cccgatccgg gatcgctttg cagctttgtt tcagcgggcg cgcgatgatc
     2101 aaaacgcagg ttgtcaaact gactacgtcc acgcggcgat tatagccgat caaatgatga
     2161 gcaatgcctc ggaactgcgt gggctacatg gcgatctgca tcatgaaaac atcatgttct
     2221 ccagtcgcgg ctggctggtg atagatcccg tcggtctggt cggtgaagtg ggctttggcg
     2281 ccgccaatat gttctacgat ccggctgaca gagacgacct ttgtctcgat cctagacgca
     2341 ttgcacagat ggcggacgca ttctctcgtg cgctggacgt cgatccgcgt cgcctgctcg
     2401 accaggcgta cgcttatggg tgcctttccg cagcttggaa cgcggatgga gaagaggagc
     2461 aacgcgatct agctatcgcg gccgcgatca agcaggtgcg acagacgtca tactagatat
     2521 caagcgactt ctcctatccc ctgggaacac atcaatctca ccggagaata tcgctggcca
     2581 aagccttagc gtaggattcc gccccttccc gcaaacgacc ccaaacagga aacgcagctg
     2641 aaacgggaag ctcaacaccc actgacgcat gggttgttca ggcagtactt catcaaccag
     2701 caaggcggca ctttcggcca tccgccgcgc cccacagctc gggcagaaac cgcgacgctt
     2761 acagctgaaa gcgaccaggt gctcggcgtg gcaagactcg cagcgaaccc gtagaaagcc
     2821 atgctccagc cgcccgcatt ggagaaattc ttcaaattcc cgttgcacat agcccggcaa
     2881 ttcctttccc tgctctgcca taagcgcagc gaatgccggg taatactcgt caacgatctg
     2941 atagagaagg gtttgctcgg gtcggtggct ctggtaacga ccagtatccc gatcccggct
     3001 ggccgtcctg gccgccacat gaggcatgtt ccgcgtcctt gcaatactgt gtttacatac
     3061 agtctatcgc ttagcggaaa gttcttttac cctcagccga aatgcctgcc gttgctagac
     3121 attgccagcc agtgcccgtc actcccactc ttacattgtt cgcagtatct aggtacatgt
     3181 tattgcgtgc accttcatga tgtataatgt tattaatgac agcagaaaga tcgacagaat
     3241 taatattctt cgtacctggg acagttatcg ggtgtcggcc agtgatgaga ccaaaggatg
     3301 cagtataaga tgaaccacta ctattatcat ggccaccatt accaccaccg ttaaaactac
     3361 ctcccgaact tccagagccg ctatgaccat cattgtaggg gtcatttggt cccatgtgac
     3421 caaaaccacc gacagtaccg ctatttaact ctgtactcat aaaattatcc tctttgactt
     3481 ttaaaaacag caaaaactgt atttataaca atgtgtttat atacagtatt cgaaatacta
     3541 cgcccgtcaa aaccacaccg tcaacaggtt ttttgtgtat ttttcacgcc tcacgggcag
     3601 cctcagacct tttgtgttaa aacagtaata tgttctgctg ttacaatacg gtacacacag
     3661 gagacactgt cacttttatg gcatggcaca cagttcaaga gacactgaaa ttaacaggaa
     3721 agtcgcgctc gcaattatat cgtgacatgg ctaaaggcct tgtcagctat cgcacaggaa
     3781 aaaatgatcg ccgggagttc gagaccagtg aactgattcg ggcctatggc gagctgcgca
     3841 cttctgagac accaaaaagg cacaaggagg gacactccaa atctgtcgtt agccaggcgg
     3901 aaaatgctca gctagacgtc attcagcaga aactggacgc tctgcagcag actgttaccc
     3961 taatgcttga agacaagatg gcgcgggaag cagaaaaccg cctgcgaaat gaggagaggg
     4021 aacaactaca ggccgaaatt agccgtctgg ctgacgcgct ggcacaggaa aaaaagcggg
     4081 gattctggtc gcggctgttt cgctccggtt cagagtaaca gtgcaggtga ctctgattta
     4141 ccataacatt cgttgcgtgc accatctcag acgccctcag ggcgtttctg acgggaaacc
     4201 ggtaaaacag gcaacaaacc acccgaaaac ccgccagaaa cgcgcaggct ctgtttttac
     4261 ggcatgcatg agtatgcgca caagtgcata gcgcggaaat tcacaccatt cagccggggt
     4321 aagtcctgtt tccggcgttc ttcccatccg aaaacggtga acggggacgc aatttattgc
     4381 gtggccgtga agcgttgccg gcgcagccgg aaaacccgct gtcagcacgt tcaggaaggg
     4441 ggtgatgtac aaatggcaca gaggatgaaa gtgacgtatg agctgaagga atgatgtaaa
     4501 agtgatgtat aagtgatgta aaagtgatgt atgaactgaa ggagcgatgt aattctgtag
     4561 tcaggaagaa taacccgttc atgcaggcat gaacgataca gtgaggaacg ctttttttgt
     4621 cacgatctcc ccttaacctg cgtaaatcac ccgccatggt tgattatttt tcaacctcaa
     4681 aatggtcata cacctaacgc agccgcgatt ttcatcgcaa ctgcatgaat taaaagaaaa
     4741 aaaaggaata tttcgttttc acgagtaata cccgggtatt aaaaatccac tgtaattaca
     4801 tgaaaataaa gaaataaaag gtaataccgg agtattacca cgtacgcggg caagcgaaaa
     4861 agctataacg cttcccggcc gacaggcgac ccaaaatcca caggggcatg caggttctct
     4921 tcagtaacct gcgccattaa atcaaaaagg tcatattcgc cgggaagctg cgtatcagtc
     4981 gaatccagtt gttcatcata ttcagatggc atggggtgat atccagtagc tgagaggttg
     5041 ttagcgggtt tcggggcgca gccctgaacc agtcatgtag cgctagcgga gtgtatactg
     5101 gcttactatg ttgccacgat tgcgaaaatc agtgaagtgc ttcatgtggc aggagaaaaa
     5161 aggcagcacc ggcgcgtcag cagaatatgc gatacaggag atattccgct tcctcgctca
     5221 ctgactcgct acgctcggtc gttcggctgc ggcgagcggt accggcttac ggacggggac
     5281 ggaaatttcc tggaagatac caggaagaca cttagcaaag aagagataag gccacggcga
     5341 agccgttttt ccataggctc cgcccccctg acaagcatcg caaaatctga cgctcaaatc
     5401 agtggtggcg aaacccgaca ggactataaa gatcccaggc gtttccccct ggtagctccc
     5461 tcgtgcgctc tcctgttcct gcctttcggt ttaccggtgt cattccgctg ttatggccgc
     5521 ggtttctcat tccacgcctg acactcagtt ccgtgaaggc agttcgctcc aagctggact
     5581 gtatgcacga accccccgtt cagtccgacc gctgcgcctt gtccggtaac tatcaacttg
     5641 agtccaaccc ggaaagacac gacaaaacgc cactggcagc agccattagt aacaggagtg
     5701 cacgagaaga tagattaaga ggtcttgaag tagaggcctg actgcggcta cactgaaaga
     5761 acagttttgg taatggcggt ctcgtgaacc ctgttaccgg gttaagcagt tccccaactg
     5821 acttaacctt cgaacaaacc gcctccccag gcggtttttt cgtttacaga gcaagagatt
     5881 acgattcatt gaaaaggatc tcaagaagat cctttgtaga ttactatcaa ttaatcttcc
     5941 gaacatgaca ccagtcactg ttgattacgg ttaaaccgct ccgtaacagg tttccctcgt
     6001 attggtgact tgcagcacca aagaagcaaa aaagataaat atatctactt attgagagat
     6061 gatatattta tttccaaaat gctacagata catcatcatg aaacggatca ccgcaaacag
     6121 gttactcgcc tggggattcc ctttcgaccc gagcatccgt atgagactca tgctcgatta
     6181 ttattattat agaagccccc
//
