LOCUS       NZ_CP103651             3202 bp    DNA     circular CON 21-SEP-2023
DEFINITION  Escherichia coli strain 961 plasmid pMB5823_6, complete sequence.
ACCESSION   NZ_CP103651
VERSION     NZ_CP103651.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN28173990
            Assembly: GCF_024918295.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3202)
  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 3202)
  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                   :: 61x
            Sequencing Technology             :: Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 09/21/2023 03:24:23
            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)                     :: 5,145
            CDSs (total)                      :: 5,020
            Genes (coding)                    :: 4,743
            CDSs (with protein)               :: 4,743
            Genes (RNA)                       :: 125
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 14
            Pseudo Genes (total)              :: 277
            CDSs (without protein)            :: 277
            Pseudo Genes (ambiguous residues) :: 0 of 277
            Pseudo Genes (frameshifted)       :: 93 of 277
            Pseudo Genes (incomplete)         :: 197 of 277
            Pseudo Genes (internal stop)      :: 55 of 277
            Pseudo Genes (multiple problems)  :: 63 of 277
            Pseudo Genes (short protein)      :: 4 of 277
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP103651.1.
            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..3202
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="961"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pMB5823_6"
                     /geo_loc_name="USA: Houston"
                     /lat_lon="29.7068 N 95.3971 W"
                     /collection_date="2018-06-18"
                     /collected_by="MDACC"
                     /genotype="ST617"
     gene            <43..198
                     /locus_tag="M5R18_RS25555"
                     /old_locus_tag="M5R18_25555"
                     /pseudo=""
     CDS             <43..198
                     /locus_tag="M5R18_RS25555"
                     /old_locus_tag="M5R18_25555"
                     /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"
     gene            292..936
                     /locus_tag="M5R18_RS25560"
                     /old_locus_tag="M5R18_25560"
     CDS             292..936
                     /locus_tag="M5R18_RS25560"
                     /old_locus_tag="M5R18_25560"
                     /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(2158..2307)
                     /locus_tag="M5R18_RS25565"
                     /old_locus_tag="M5R18_25565"
     CDS             complement(2158..2307)
                     /locus_tag="M5R18_RS25565"
                     /old_locus_tag="M5R18_25565"
                     /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_162846302.1"
                     /translation="MPSEYDEQRGSTDTQLPGEYDLFDLMAKVTEEILHAPVDSGPPVG
                     REAL"
                     /name="hypothetical protein"
     ARG             293..933
                     /name="qnrB19"
                     /gene="qnrB19"
                     /gene_name="quinolone resistance pentapeptide repeat
                     protein QnrB19"
                     /tool="amrfinderplus"
                     /drug_class="QUINOLONE"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          complement(2343..2516)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.5600000000000002e-86"
     Typing          2495..2986
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.51"
                     /coverage="81.0"
                     /evalue="0.0"
ORIGIN
        1 atggaaatct atccaatccg agcacatagg atacacatcg ttataacgct ggatctgcgt
       61 gaattccagc agcagcaaga gaaagacttt ctacaaacca gcttacagca ggctaaattt
      121 aaccagaaaa aagccgctga attactgggt ctgacttatc atcagctacg tgccttgctg
      181 aagaaacacc agatctaata cgcatttgca ggtgtcatac tggcgggttt gacgcataac
      241 gtcataaggt ttaccatggc gtcattactg tataaaaaca caggcataga tatgactctg
      301 gcattagttg gcgaaaaaat tgacagaaat cgcttcaccg gtgagaaagt tgaaaatagt
      361 acatttttta actgcgattt ttcaggtgcc gacctgagcg gcactgaatt tatcggctgc
      421 cagttctatg atcgcgaaag tcagaaaggg tgcaatttta gtcgcgcaat gctgaaagat
      481 gccattttca aaagctgtga tttatcaatg gcagatttcc gcaacgtcag tgccttgggc
      541 attgaaattc gccactgccg cgcacaaggc gcagatttcc gcggtgcaag ctttatgaat
      601 atgatcacca cgcgcacctg gttttgcagc gcatatatca ctaatactaa tctaagctac
      661 gccaattttt cgaaagtcgt gttggaaaag tgtgagctgt gggaaaaccg ctggatgggg
      721 actcaggtac tgggtgcgac gttcagtggt tcagatctct ccggcggcga gttttcgact
      781 ttcgactggc gagcagcaaa cttcacacat tgcgatctga ccaattcgga gttaggtgac
      841 ttagatattc ggggtgttga tttacaaggc gttaagttag acagctacca ggcatcgttg
      901 ctcatggagc ggcttggcat cgctgtgatt ggttagttca gcgtttacac cgggagatgc
      961 gtttgacgat ttacttttaa ccagtacgac tcctggcaag cattgtgaaa cgttttctcc
     1021 agtggacgaa tatcctgacc taccgcatca acgacatgcc atctaatgct gcattctgga
     1081 caggaatttg atgaatatct aaccaattca ttttcgcgag aacaacgaat aaccactccc
     1141 gaatcatgaa gccatgtctt atttataatc tcaacttcag ccatgtcatc ccgtttactg
     1201 acatcctcaa tacaaatacc ccgcgatcat cgcgtttatt gagtttatta tttatctatg
     1261 cgattccgat gaaaaattcg cacgaaaata tggctaactc atagcaaaaa aaaagccccc
     1321 taagggcttt tttttgtacc tgacggtcag accgattaaa cataacatcc cttgcgtgca
     1381 ccgcctgaga ggctctgagg gcgtttctga cgggaaaccg gtaaaacagg caacaaaccc
     1441 cccgaaaacc cgccagaaac gcgcaggctc tgtttttacg gcatgcatga gtatgcgcgc
     1501 aagtgcatag cgcggaaatt cacaccattc agccagggga agtcctgttt ccggcgttct
     1561 tcccatccga aaacggtgaa cggggacgca atttattgcg tggccgtgaa gcgttgccgg
     1621 cgcagccgga aaacccgctg tcagcacgtt caggaagggg gtgatgtaca aatggcacag
     1681 aggatgaaag tgacgtatga gctgaaggaa tgatgtaaaa gtgatgtata aatgatgtaa
     1741 aagtgatgca aaagtgttgt aaaagtgttg taaaagtgat gtacaggccg aaggagtgtt
     1801 gtaaaagtgt tgtgaaagtg atgtatgaac tgaaggagcg atgtaattct gtagtcagga
     1861 agaataaccc gttcatgcag gcatgaacga tacagtgagg aacgcttttt tttgtcacga
     1921 tctcccctta acctgcgtaa atcacccgcc atggttgatt atttttcaac ctcaaaatgg
     1981 tcatacacct aacgcagccg cgattttcat cgcaactgca tgaattaaaa gaaaaaaaag
     2041 taatgtttcg ttttcacgag taatacccag gtattaaaaa cccactgtaa ttacatgaaa
     2101 ataaagaaat aaaaggtaat accggcgtat taccacgtac gcgggcaagc gaaaaagcta
     2161 taacgcttcc cggccgacag gcggcccaga atccacaggg gcatgcagga tctcttcagt
     2221 aaccttcgcc attaaatcaa aaaggtcata ttcgccggga agctgcgtat cagtcgaacc
     2281 ccgttgttca tcatattcag atggcatggg gtgatatcca gtagcagaga ggttgttagc
     2341 gggtttcggg gcgcagccct gaaccagtca cgtagcgcta gcggagtgta tactggctga
     2401 ctatgttggc acggatgtgg aaatcagtga agtgcttcat gtagcaggag aaaaaaggcg
     2461 gcaccagcgc gtcagcagga tatgtagtac aggatatatt ccgcttcctc gctcactgac
     2521 tcgctgcgct cggtcgttcg gctgcggcga gcggtgccgg cttacaggcg gggcggaaat
     2581 ttcctgggag ataccaggaa ggagcttaac agggaagaga taaggccgcg gcgaagccgt
     2641 ttttccatag gctccgcccc cctgacaaac atcatgaaat ctgacgctca aatcagtggt
     2701 ggcgaaaccc gatgcggctt aaagatacca ggcgtttccc cctggtggct ccctcgtgct
     2761 cccccgcatt cctgcctttc ggtttaccgg tgtcattccg ctgttatggc cgcgtttatc
     2821 tcattccacg cctgacactc agttccgcga aggcagttcg ctcctggatg gactgtatgc
     2881 acgaaccccc cgttcagtcc gactgctgcg ccttatccgg taactatcat cttgagtcca
     2941 acccggaaag acacgactta tcgccactgg cagcagccac tggtaactga tttagaggag
     3001 ttagtcttga agttatgcgc ctgttaaggc taaactgaaa gaacagattt ggttactgcg
     3061 ctcctcgtaa gccagttacc acggttcaaa gagttgctgc tctgagaacc ttcgaaaaac
     3121 cgccttgcag ggcggttttt tcgtttacag agcaagagat tacgacgcca cagaaaggat
     3181 ctcaagaaga tccttcaccg ta
//
