LOCUS       NZ_CP103474             2699 bp    DNA     circular CON 21-SEP-2023
DEFINITION  Escherichia coli strain 4973 plasmid pMB9698_6, complete sequence.
ACCESSION   NZ_CP103474
VERSION     NZ_CP103474.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN28174076
            Assembly: GCF_024918135.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 2699)
  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 2699)
  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                   :: 250x
            Sequencing Technology             :: Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 09/21/2023 03:21:07
            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)                     :: 5,330
            CDSs (total)                      :: 5,209
            Genes (coding)                    :: 5,011
            CDSs (with protein)               :: 5,011
            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)              :: 198
            CDSs (without protein)            :: 198
            Pseudo Genes (ambiguous residues) :: 0 of 198
            Pseudo Genes (frameshifted)       :: 68 of 198
            Pseudo Genes (incomplete)         :: 129 of 198
            Pseudo Genes (internal stop)      :: 42 of 198
            Pseudo Genes (multiple problems)  :: 38 of 198
            Pseudo Genes (short protein)      :: 5 of 198
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP103474.1.
            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..2699
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="4973"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pMB9698_6"
                     /geo_loc_name="USA: Houston"
                     /lat_lon="29.7068 N 95.3971 W"
                     /collection_date="2020-01-09"
                     /collected_by="MDACC"
                     /genotype="ST648"
     gene            join(2651..2699,1..596)
                     /locus_tag="M5S50_RS26495"
                     /old_locus_tag="M5S50_26500"
     CDS             join(2651..2699,1..596)
                     /locus_tag="M5S50_RS26495"
                     /old_locus_tag="M5S50_26500"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017900990.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="quinolone resistance pentapeptide repeat protein
                     QnrB19"
                     /protein_id="WP_012954666.1"
                     /translation="MTLALVGEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQF
                     YDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGADFRGASFMNM
                     ITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFST
                     FDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDSYQASLLMERLGIAVIG"
                     /name="quinolone resistance pentapeptide repeat protein
                     QnrB19"
     gene            complement(1098..1334)
                     /locus_tag="M5S50_RS26500"
                     /old_locus_tag="M5S50_26505"
     CDS             complement(1098..1334)
                     /locus_tag="M5S50_RS26500"
                     /old_locus_tag="M5S50_26505"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001676031.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_012772745.1"
                     /translation="MARLTNLTPAEKKFLDDAVAAAERASGKKLNQPNRHIVLNRARAQ
                     IELQRYADRQRALREDERQQSDFAWSRPRAPRR"
                     /name="hypothetical protein"
     gene            2034..2147
                     /locus_tag="M5S50_RS26505"
                     /old_locus_tag="M5S50_26510"
     CDS             2034..2147
                     /locus_tag="M5S50_RS26505"
                     /old_locus_tag="M5S50_26510"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_006122515.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_032667588.1"
                     /translation="MHEPPVQSDCCALSGNYHLESNPERHDLSPLAAATGN"
                     /name="hypothetical protein"
     gene            <2402..2557
                     /locus_tag="M5S50_RS26510"
                     /old_locus_tag="M5S50_26515"
                     /pseudo=""
     CDS             <2402..2557
                     /locus_tag="M5S50_RS26510"
                     /old_locus_tag="M5S50_26515"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_707212.3"
                     /GO_function="GO:0043565 - sequence-specific DNA binding
                     [Evidence IEA]"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /name="helix-turn-helix domain-containing protein"
     ARG             4..593
                     /name="qnrB"
                     /gene="qnrB"
                     /gene_name="QnrB family quinolone resistance pentapeptide
                     repeat protein"
                     /tool="amrfinderplus"
                     /drug_class="QUINOLONE"
                     /identity="100.0"
                     /coverage="92.06"
     ARG             2616..2698
                     /name="QnrB59"
                     /gene="QnrB59"
                     /gene_name="quinolone resistance protein (qnr)"
                     /tool="rgi"
                     /drug_class="fluoroquinolone antibiotic"
                     /identity="96.43"
                     /coverage="12.39"
     ARG             4..596
                     /name="QnrB5"
                     /gene="QnrB5"
                     /gene_name="quinolone resistance protein (qnr)"
                     /tool="rgi"
                     /drug_class="fluoroquinolone antibiotic"
                     /identity="99.49"
                     /coverage="87.17"
     Typing          complement(1500..1673)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.5600000000000002e-86"
     Typing          1652..2143
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.308"
                     /coverage="81.0"
                     /evalue="0.0"
ORIGIN
        1 gtgagaaagt tgaaaatagt acatttttta actgcgattt ttcaggtgcc gacctgagcg
       61 gcactgaatt tatcggctgc cagttctatg atcgcgaaag tcagaaaggg tgcaatttta
      121 gtcgcgcaat gctgaaagat gccattttca aaagctgtga tttatcaatg gcagatttcc
      181 gcaacgtcag tgccttgggc attgaaattc gccactgccg cgcacaaggc gcagatttcc
      241 gcggtgcaag ctttatgaat atgatcacca cgcgcacctg gttttgcagc gcatatatca
      301 ctaatactaa tctaagctac gccaattttt cgaaagtcgt gttggaaaag tgtgagctgt
      361 gggaaaaccg ctggatgggg actcaggtac tgggtgcgac gttcagtggt tcagatctct
      421 ccggcggcga gttttcgact ttcgactggc gagcagcaaa cttcacacat tgcgatctga
      481 ccaattcgga gttaggtgac ttagatattc ggggtgttga tttacaaggc gttaagttag
      541 acagctacca ggcatcgttg ctcatggagc ggcttggcat cgctgtgatt ggttagttca
      601 gcgtttacac cgggagatgc gtttgacgat ttacttttaa ccagtacgac tcctggcaag
      661 cattgtgaaa cgttttctcc agtggacgaa tatcctgacc taccgcatca acgacatgcc
      721 atctaatgct gcattctgga caggaatttg atgaatatct aaccaattca ttttcgcgag
      781 aacaacgaat aaccactccc gaatcatgaa gccatgtctt aacgaaaata tggctaactc
      841 atagcaaaaa aaaagccccc taagggcttt tttttgtacc tgacggtcag accgattaaa
      901 cataacatcc cttgcccgca cccccgcagg cgccctcagc gcaatcctgc tgcatcaggg
      961 ccgtttccag cacctttcct caccagtatc ccggaaaaac gcccctgatg atttctgcgc
     1021 gactgcatgg ctatgcacgc aggtgaatgg caggtgattt cgcagcgtca gcaccactaa
     1081 accgccaaaa gccaaaatca gcggcgcggc gcgcgcggac gtgaccaggc aaaatcggac
     1141 tgctgccgct catcctcacg taatgcacgc tggcggtcgg cgtaacgctg caactcaatt
     1201 tgcgcacgcg ctctgttcag gacgatgtgc cggttaggct gatttagctt tttacctgac
     1261 gctctttcag ctgcggcaac agcatcatca agaaattttt tctctgcagg cgtcaagttt
     1321 gtcagtctgg ccataacgtt ctccagtcag aataaatcag cacagtctgc cagacacagt
     1381 agaaacgatg aagcgccagc gacggtgaaa ggcagtcaga aacggtgaac gggagcggat
     1441 tttaatccgg tgccgtgagg cgttggacaa gccgcaggcg cgtcattagc ttttagccgg
     1501 tttcggggcg cagccctgaa ccagtcacgt agcgctagcg gagtgtatac tggctgacta
     1561 tgttggcacg gatgtggaaa tcagtgaagt gcttcatgta gcaggagaaa aaaggcggca
     1621 ccagcgcgtc agcaggatat gtagtacagg atatattccg cttcctcgct cactgactcg
     1681 ctgcgctcgg tcgttcggct gcggcgagcg gtgccggctt acaggcgggg cggaaatttc
     1741 ctgggagata ccaggaagga gcttaacagg gaagagataa ggccgcggcg aagccgtttt
     1801 tccataggct ccgcccccct gacaaacatc atgaaatctg acgctcaaat cagtggtggc
     1861 gaaacccgat gcggcttaaa gataccaggc gtttccccct ggtggctccc tcgtgctccc
     1921 ccgcattcct gcctttcggt ttaccggcgt cattccgctg ttatggccgc gtttatctca
     1981 ttccacgcct gacactcagt tccgcgaagg cagttcgctc ctggatggac tgtatgcacg
     2041 aaccccccgt tcagtccgac tgctgcgcct tatccggtaa ctatcatctt gagtccaacc
     2101 cggaaagaca cgacttatcg ccactggcag cagccactgg taactgattt agaggagtta
     2161 gtcttgaagt tatgcgcctg ttaaggctaa actgaaagaa cagatttggt tactgcgctc
     2221 ctcgtaagcc agttaccacg gttcaaagag ttgctgctct gagaaccttc gaaaaaccgc
     2281 cttgcagggc ggttttttcg tttacagagc aagagattac gacgccacag aaaggatctc
     2341 aagaagatcc ttcaccgtaa tggaaatcta tccaatccga gcacatagga tacacatcgt
     2401 tataacgctg gatctgcgtg aattccagca gcagcaagag aaagactttc tacaaaccag
     2461 cttacagcag gctaaattta accagaaaaa agccgctgaa ttactgggtc tgacttatca
     2521 tcagctacgt gccttgctga agaaacacca gatctaatac gcatttgcag gtgtcatact
     2581 ggcgggtttg acgcataacg tcataaggtt taccatggcg tcattactgt ataaaaacac
     2641 aggcatagat atgactctgg cattagttgg cgaaaaaatt gacagaaatc gcttcaccg
//
