LOCUS       NZ_CP103575             2699 bp    DNA     circular CON 20-SEP-2023
DEFINITION  Escherichia coli strain 3045 plasmid pMB8093_5, complete sequence.
ACCESSION   NZ_CP103575
VERSION     NZ_CP103575.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN28174015
            Assembly: GCF_024917235.1
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                   :: 289x
            Sequencing Technology             :: Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 09/20/2023 06:04:41
            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)                     :: 4,933
            CDSs (total)                      :: 4,814
            Genes (coding)                    :: 4,559
            CDSs (with protein)               :: 4,559
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 255
            CDSs (without protein)            :: 255
            Pseudo Genes (ambiguous residues) :: 0 of 255
            Pseudo Genes (frameshifted)       :: 80 of 255
            Pseudo Genes (incomplete)         :: 174 of 255
            Pseudo Genes (internal stop)      :: 52 of 255
            Pseudo Genes (multiple problems)  :: 48 of 255
            Pseudo Genes (short protein)      :: 3 of 255
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP103575.1.
            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="3045"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pMB8093_5"
                     /geo_loc_name="USA: Houston"
                     /lat_lon="29.7068 N 95.3971 W"
                     /collection_date="2019-04-25"
                     /collected_by="MDACC"
                     /genotype="ST44"
     gene            1..237
                     /locus_tag="M5S79_RS24520"
                     /old_locus_tag="M5S79_24520"
     CDS             1..237
                     /locus_tag="M5S79_RS24520"
                     /old_locus_tag="M5S79_24520"
                     /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            complement(739..1383)
                     /locus_tag="M5S79_RS24525"
                     /old_locus_tag="M5S79_24525"
     CDS             complement(739..1383)
                     /locus_tag="M5S79_RS24525"
                     /old_locus_tag="M5S79_24525"
                     /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(1477..>1632)
                     /locus_tag="M5S79_RS24530"
                     /old_locus_tag="M5S79_24530"
                     /pseudo=""
     CDS             complement(1477..>1632)
                     /locus_tag="M5S79_RS24530"
                     /old_locus_tag="M5S79_24530"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_309907.2"
                     /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             complement(743..1383)
                     /name="qnrB19"
                     /gene="qnrB19"
                     /gene_name="quinolone resistance pentapeptide repeat
                     protein QnrB19"
                     /tool="amrfinderplus"
                     /drug_class="QUINOLONE"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          2362..2535
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.5600000000000002e-86"
     Typing          complement(1892..2383)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.51"
                     /coverage="81.0"
                     /evalue="0.0"
ORIGIN
        1 atggccagac tgacaaactt gacgcctgca gagaaaaaat ttcttgatga tgctgttgcc
       61 gcagctgaaa gagcgtcagg taaaaagcta aatcagccta accggcacat cgtcctgaac
      121 agagcgcgtg cgcaaattga gttgcagcgt tacgccgacc gccagcgtgc attacgtgag
      181 gatgagcggc agcagtccga ttttgcctgg tcacgtccgc gcgcgccgcg ccgctgattt
      241 tggcttttgg cggtttagtg gtgctgacgc tgcgaaatca cctgccattc acctgcgtgc
      301 atagccatgc agtcgcgcag aaatcatcag gggcgttttt ccgggatact ggtgaggaaa
      361 ggtgctggaa acggccctga tgcagcagga ttgcgctgag ggcgcctgcg ggggtgcggg
      421 caagggatgt tatgtttaat cggtctgacc gtcaggtaca aaaaaaagcc cttagggggc
      481 tttttttttg ctatgagtta gccatatttt cgttaagaca tggcttcatg attcgggagt
      541 ggttattcgt tgttctcgcg aaaatgaatt ggttagatat tcatcaaatt cctgtccaga
      601 atgcagcatt agatggcatg tcgttgatgc ggtaggtcag gatattcgtc cactggagaa
      661 aacgtttcac aatgcttgcc aggagtcgta ctggttaaaa gtaaatcgtc aaacgcatct
      721 cccggtgtaa acgctgaact aaccaatcac agcgatgcca agccgctcca tgagcaacga
      781 tgcctggtag ctgtctaact taacgccttg taaatcaaca ccccgaatat ctaagtcacc
      841 taactccgaa ttggtcagat cgcaatgtgt gaagtttgct gctcgccagt cgaaagtcga
      901 aaactcgccg ccggagagat ctgaaccact gaacgtcgca cccagtacct gagtccccat
      961 ccagcggttt tcccacagct cacacttttc caacacgact ttcgaaaaat tggcgtagct
     1021 tagattagta ttagtgatat atgcgctgca aaaccaggtg cgcgtggtga tcatattcat
     1081 aaagcttgca ccgcggaaat ctgcgccttg tgcgcggcag tggcgaattt caatgcccaa
     1141 ggcactgacg ttgcggaaat ctgccattga taaatcacag cttttgaaaa tggcatcttt
     1201 cagcattgcg cgactaaaat tgcacccttt ctgactttcg cgatcataga actggcagcc
     1261 gataaattca gtgccgctca ggtcggcacc tgaaaaatcg cagttaaaaa atgtactatt
     1321 ttcaactttc tcaccggtga agcgatttct gtcaattttt tcgccaacta atgccagagt
     1381 catatctatg cctgtgtttt tatacagtaa tgacgccatg gtaaacctta tgacgttatg
     1441 cgtcaaaccc gccagtatga cacctgcaaa tgcgtattag atctggtgtt tcttcagcaa
     1501 ggcacgtagc tgatgataag tcagacccag taattcagcg gcttttttct ggttaaattt
     1561 agcctgctgt aagctggttt gtagaaagtc tttctcttgc tgctgctgga attcacgcag
     1621 atccagcgtt ataacgatgt gtatcctatg tgctcggatt ggatagattt ccattacggt
     1681 gaaggatctt cttgagatcc tttctgtggc gtcgtaatct cttgctctgt aaacgaaaaa
     1741 accgccctgc aaggcggttt ttcgaaggtt ctcagagcag caactctttg aaccgtggta
     1801 actggcttac gaggagcgca gtaaccaaat ctgttctttc agtttagcct taacaggcgc
     1861 ataacttcaa gactaactcc tctaaatcag ttaccagtgg ctgctgccag tggcgataag
     1921 tcgtgtcttt ccgggttgga ctcaagatga tagttaccgg ataaggcgca gcagtcggac
     1981 tgaacggggg gttcgtgcat acagtccatc caggagcgaa ctgccttcgc ggaactgagt
     2041 gtcaggcgtg gaatgagata aacgcggcca taacagcgga atgacaccgg taaaccgaaa
     2101 ggcaggaatg cgggggagca cgagggagcc accaggggga aacgcctggt atctttaagc
     2161 cgcatcgggt ttcgccacca ctgatttgag cgtcagattt catgatgttt gtcagggggg
     2221 cggagcctat ggaaaaacgg cttcgccgcg gccttatctc ttccctgtta agctccttcc
     2281 tggtatctcc caggaaattt ccgccccgcc tgtaagccgg caccgctcgc cgcagccgaa
     2341 cgaccgagcg cagcgagtca gtgagcgagg aagcggaata tatcctgtac tacatatcct
     2401 gctgacgcgc tggtgccgcc ttttttctcc tgctacatga agcacttcac tgatttccac
     2461 atccgtgcca acatagtcag ccagtataca ctccgctagc gctacgtgac tggttcaggg
     2521 ctgcgccccg aaaccggcta aaagctaatg acgcgcctgc ggcttgtcca acgcctcacg
     2581 gcaccggatt aaaatccgct cccgttcacc gtttctgact gcctttcacc gtcgctggcg
     2641 cttcatcgtt tctactgtgt ctggcagact gtgctgattt attctgactg gagaacgtt
//
