LOCUS       NZ_CP103543             4072 bp    DNA     circular CON 21-SEP-2023
DEFINITION  Escherichia coli strain 5264 plasmid pMB9081_3, complete sequence.
ACCESSION   NZ_CP103543
VERSION     NZ_CP103543.1
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 4072)
  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 4072)
  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
            CP103543.1.
            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..4072
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="5264"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pMB9081_3"
                     /geo_loc_name="USA: Houston"
                     /lat_lon="29.7068 N 95.3971 W"
                     /collection_date="2019-09-25"
                     /collected_by="MDACC"
                     /genotype="ST167"
     gene            7..699
                     /locus_tag="M5S66_RS23755"
                     /old_locus_tag="M5S66_23755"
     CDS             7..699
                     /locus_tag="M5S66_RS23755"
                     /old_locus_tag="M5S66_23755"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001281399.1"
                     /GO_function="GO:0003887 - DNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_001281403.1"
                     /translation="MSDLIAYKSNALVEASYKLTLQEQRFLLLCISRLKSGADAELQKT
                     MTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKNDEKREEFRWIQYRAQYAKG
                     EAKARITFSDAVMPYLTQLKGQFTRVVIKNISGLSSSYSIRIYEFLQQFRSTGERIIAL
                     NDFRSMLGIENKYKQFRDLNKILIKPCVDELNKKSDLAVTVETIKKGRTVVALHFRFKE
                     DKQIKMTI"
                     /name="replication initiation protein"
     gene            complement(955..3114)
                     /gene="mobQ"
                     /locus_tag="M5S66_RS23760"
                     /old_locus_tag="M5S66_23760"
     CDS             complement(955..3114)
                     /gene="mobQ"
                     /locus_tag="M5S66_RS23760"
                     /old_locus_tag="M5S66_23760"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016240513.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobQ family relaxase"
                     /protein_id="WP_001029353.1"
                     /translation="MAIYHLSMKIISRSSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAECRKNSQLAREIELAIPRELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNSGLTEPARRVADLLNIVLPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGASGLAALRVQL
                     LKREEELRRKEQEDTERSRAERRAEQLRKNDNAVMDSGVLSAVVTGYGEAPMPGNGEMT
                     CYLLLHNRNGEYTLWGNELEKYRTRIFERVDLMRDRSGYICDRSEIGQHPPLQRVYSSA
                     TFEQLLTQVCQTWPQYTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLLPTL
                     MPVMSSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKG
                     LRYAGYGVAVNHDADSHISPAPELMEFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRT
                     WDEWRREEDARTHTTERRHDRGWSQ"
                     /name="mobQ"
     gene            3293..3547
                     /gene="mobC"
                     /locus_tag="M5S66_RS23765"
                     /old_locus_tag="M5S66_23765"
     CDS             3293..3547
                     /gene="mobC"
                     /locus_tag="M5S66_RS23765"
                     /old_locus_tag="M5S66_23765"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000091747.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase accessory protein MobC"
                     /protein_id="WP_000091747.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVVVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPGQ"
                     /name="mobC"
     Typing          complement(2757..3115)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.056"
                     /coverage="100.0"
                     /evalue="3.94e-177"
     Typing          3116..3292
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          8..699
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.965"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(959..3201)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.332"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ctttgtatgt cggacttgat tgcctacaag tcgaatgctt tggttgaggc cagctacaag
       61 ttgaccctac aggaacaacg ttttctgttg ctgtgtatca gtcgattgaa atctggtgct
      121 gatgctgaat tgcaaaagac aatgaccatt accgctgcgg aatattttga ttcattccct
      181 gacatggggc ggaaaaatgc cgaggttcag ttacaggaag cgatcgatcg tttatgggac
      241 aggtcgatca ttctcaagaa tgacgagaag cgtgaggagt tccgctggat ccagtatcgg
      301 gcacagtacg ctaaaggtga ggccaaggct cgaataacct tttctgacgc ggtaatgcct
      361 tatctgacgc aactgaaggg gcaattcacg cgcgttgtta taaaaaacat atcaggttta
      421 tcaagtagtt acagtataag aatatacgag ttcctccagc aattccgcag tacgggagag
      481 agaattattg ctcttaatga ctttcgttca atgttaggga ttgaaaataa atacaaacaa
      541 ttcagagact taaataaaat actaataaaa ccctgtgttg acgaactgaa caaaaaaagc
      601 gacctggctg taacggttga gacgatcaaa aaggggcgca cggttgtagc cctgcatttt
      661 cgcttcaagg aagacaaaca gatcaagatg acgatctaaa atcgatttta aggcacctaa
      721 aacgctccct gctgcgtttt ttttgtgtta gtagtgcgaa ggtactattg aagtgaaaaa
      781 ttgcgtcaaa agcgctctaa tgcagcgaaa aaagaacccc caatttttgg gggcggaaaa
      841 acaaaactat gcttgcatta tgtgtgtgct tcttgcattc atccctgtcg atgaacatag
      901 aagaacatcg acgaacataa cacgatgtta aacaaaacaa aatattgttc acattcactg
      961 tgaccaaccg cgatcatgtc tcctctcggt ggtgtgtgtt cttgcatctt cctcgcgccg
     1021 ccattcatcc caggtacgat tgaaacccag agagcggaac agatgatccg gctgtttttc
     1081 tggtgtgttg acggcagcaa aaagcggtgc ctcacgggtt ttcagatgaa actccataag
     1141 ttccggcgca ggtgatatgt ggctgtctgc atcgtgattt acggcaacac cataccctgc
     1201 ataccgtaac cccttatcgg tcagtgcact gatgaccagc tggctgttat cggctgaggg
     1261 aacggcaaac gcgggataca gcgtaccatt aagccggaca acaccgccca gagagtcatc
     1321 cacgcccatg accagcaaaa gctgaagctg gcgggtttcc cggtcgacag aactcattac
     1381 cggcatcagc gtcggtagca gacgtccctg cgtaaaatcc accttccttg ctgccagtga
     1441 tggcatggct ggctggcggt cttctccaag acagaaagac tccggccatg tcttcggctg
     1501 gcggagattg cgggtatatt gcggccatgt ctggcaaacc tgcgtcagaa gttgctcaaa
     1561 ggtcgcagag gaataaacac gttgcagtgg tggatgttga ccgatttcgc ttcggtcaca
     1621 gatataacca ctcctgtcac gcattaaatc aacacgctca aagattctgg tgcggtattt
     1681 ctccagctcg ttcccccaga gcgtgtattc tccgttccgg ttgtgaagca gaaggtaaca
     1741 ggtcatttcc ccgttaccag gcatgggggc ctcgccatac cccgtaacga ctgcgctcag
     1801 tacccctgaa tccataacgg cattgtcatt tttcctgagc tgttccgctc gtcgctccgc
     1861 gcgactacgt tctgtatcct cctgctcctt ccggcgcaat tcctcttcac gtttaagcaa
     1921 ctggactctg agagctgcaa ggccggatgc cccccactgc tgccactgtt tttcaaatgc
     1981 cgtctgactc gcgggaatgt cctgtttctc caccttccgg taatgctgtc gcaatttttc
     2041 catttgctgg ctcagcgact ggatttttcc ctgttcgcta cggtattccg gtgccgccca
     2101 ttgcatcagg ggaatacggg aaaaaccgga cgaaaacggc gatgattttt tcaggctggc
     2161 agcatggctc atcgcttcct ttcgttcggt gttcagctct tcccagcgtc tgcgcgtcgc
     2221 ctgcatatct gccatcatcg acatggcatt actggtgagt ttccatgccg cattactgtc
     2281 cttcggcaac gcttcgatga tgtcacgtag tgtgtacgaa gttgcgttgt caggaagcac
     2341 gatattcaga aggtcagcca cacggcgggc aggctctgtc agcccgctgt tcctgagttc
     2401 agtgcgggaa atctgtattt ccaggttaag cctgttaatc agacgattct gttcgccgcg
     2461 ttctgtttcg ataccgcgtg tttccatcgc acaggcagac tttccgaggt gaataccagg
     2521 cgttttctca agcccctgtc gctcgtatga acgatggtct atctcttcct gataaccggc
     2581 gttcgccagt gctctgtttg catggtcagc ccatgatgca cgccacgtct cggcatgtgt
     2641 ccggtcgttc cagtccctga cctttccgcc gaacccagca ggtccgacag ccctcgtggt
     2701 cagcatgatg tgcgcatggg gatttgtttt atccatgtga tggaacgcca catcagcaat
     2761 catgccctga ctgacaaagt tttctctgac aaaggcgaga acggtttccc gtgcggcatc
     2821 ctgcggcagt tcacggggga tagcgagttc aatttcccgc gcaagttgtg agttcttccg
     2881 gcattcggcc ttctcaacgg cattccagag ttcggcacgg ttcgtacacc aggcaggggc
     2941 tgtcgcgggg gtcagaatca cagcttcagc cacaccgctt ttgcgggtgt agtcgtgagt
     3001 cagtccggta cgctcatcaa gcatcagtga accggaacga taggcagcgg aagctacggc
     3061 gctgtagccg ctgcttctgg agataatttt catgctgaga tgataaatcg ccatttctgc
     3121 cgtaatgcct ttttgtagtt ttctttcagc cccgcagggc gcacacaatc gaaacggagt
     3181 ggagattgta taagtgcgca ctttgtgatt tgtcgcgcat tatgccagct cagtttttaa
     3241 actaccagtg acgcgctaaa atgcgatttt tcatcgcgca cggagttaca tcatgagcag
     3301 aacgctcgaa cagaagattg ctgatgctga ggcgagatta cagcgcctga aggcgaagag
     3361 ccggagcctg gacacagcgc agaaggttgt tgtgggtgca gcattgctgg caaaggtcag
     3421 aaagccggag gaggtgcagt tgcgtgcctg gttactccag ttcctgaagg cagaggtgac
     3481 acgacaggct gatgtgacgc gcatactgcc gctgattaac gagctggagg cgctgccagg
     3541 acagtgattg tatcgtccgc tcgccgcagc cccagcgacc gagcgttagc gagcgagtgg
     3601 gcgaggaagc ggaagtgaat ccgtcgccag gttgagcaca tacgcacggt ttttcggtag
     3661 gtgatatgcg ctgaacccgc atgaatactg gatttccaca gggttggaag gggagtattc
     3721 ggaacttgca attctgcttt cttgcaacac attgttttta ttggtttttt gttttcagcg
     3781 ccccaagtta tccacaggct cgccgttaag tttttagatc ttgtttttaa gatcttgttt
     3841 ttaatacttg ttttagggtc aaaattcatt aataaaatca atatgttata gaggtatatg
     3901 tggaggaatt taaggtaaag gtggaggaat ttaaggtgtt taggtggagg aatttaaggt
     3961 aaaggtggag gaatttaagg tgttattcac agaaatgtga ggatataaaa aaaaatattc
     4021 cacatttctt atttgtgggg cacattaaag catcaccaca tttgaacggg at
//
