LOCUS       NZ_CP103749             6200 bp    DNA     circular CON 21-SEP-2023
DEFINITION  Escherichia coli strain 3090 plasmid pMB2791_4, complete sequence.
ACCESSION   NZ_CP103749
VERSION     NZ_CP103749.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN28174017
            Assembly: GCF_024917995.1
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                   :: 85x
            Sequencing Technology             :: Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 09/21/2023 03:09:24
            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)                     :: 5,088
            CDSs (total)                      :: 4,967
            Genes (coding)                    :: 4,683
            CDSs (with protein)               :: 4,683
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 284
            CDSs (without protein)            :: 284
            Pseudo Genes (ambiguous residues) :: 0 of 284
            Pseudo Genes (frameshifted)       :: 96 of 284
            Pseudo Genes (incomplete)         :: 192 of 284
            Pseudo Genes (internal stop)      :: 60 of 284
            Pseudo Genes (multiple problems)  :: 62 of 284
            Pseudo Genes (short protein)      :: 4 of 284
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP103749.1.
            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="3090"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pMB2791_4"
                     /geo_loc_name="USA: Houston"
                     /lat_lon="29.7068 N 95.3971 W"
                     /collection_date="2016-10-27"
                     /collected_by="MDACC"
                     /genotype="ST167"
     gene            1..441
                     /locus_tag="M5T02_RS25210"
                     /old_locus_tag="M5T02_25210"
     CDS             1..441
                     /locus_tag="M5T02_RS25210"
                     /old_locus_tag="M5T02_25210"
                     /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(1186..1335)
                     /locus_tag="M5T02_RS25215"
                     /old_locus_tag="M5T02_25215"
     CDS             complement(1186..1335)
                     /locus_tag="M5T02_RS25215"
                     /old_locus_tag="M5T02_25215"
                     /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            1906..2064
                     /locus_tag="M5T02_RS25460"
     CDS             1906..2064
                     /locus_tag="M5T02_RS25460"
                     /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"
     gene            2524..3339
                     /gene="sul2"
                     /locus_tag="M5T02_RS25220"
                     /old_locus_tag="M5T02_25220"
     ARG             2525..3336
                     /name="sul2"
                     /gene="sul2"
                     /gene_name="sulfonamide-resistant dihydropteroate synthase
                     Sul2"
                     /tool="amrfinderplus"
                     /drug_class="SULFONAMIDE"
                     /identity="100.0"
                     /coverage="100.0"
     gene            3400..4203
                     /gene="aph(3'')-Ib"
                     /locus_tag="M5T02_RS25225"
                     /old_locus_tag="M5T02_25225"
     ARG             3401..4200
                     /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            4203..5039
                     /locus_tag="M5T02_RS25230"
                     /old_locus_tag="M5T02_25230"
     CDS             4203..5039
                     /locus_tag="M5T02_RS25230"
                     /old_locus_tag="M5T02_25230"
                     /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(<5146..5550)
                     /locus_tag="M5T02_RS25235"
                     /old_locus_tag="M5T02_25235"
                     /pseudo=""
     CDS             complement(<5146..5550)
                     /locus_tag="M5T02_RS25235"
                     /old_locus_tag="M5T02_25235"
                     /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(5594..5983)
                     /locus_tag="M5T02_RS25240"
                     /old_locus_tag="M5T02_25240"
     CDS             complement(5594..5983)
                     /locus_tag="M5T02_RS25240"
                     /old_locus_tag="M5T02_25240"
                     /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"
     ARG             4204..5036
                     /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(1371..1544)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.429"
                     /coverage="100.0"
                     /evalue="1.19e-84"
     Typing          1468..2073
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.593"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 atggcatggc acacagttca agagacactg aaattaacag gaaagtcgcg ctcgcaatta
       61 tatcgtgaca tggctaaagg ccttgtcagc tatcgcacag gaaaaaatga tcgccgggag
      121 ttcgagacca gtgaactgat tcgggcctat ggcgagctgc gcacttctga gacaccaaaa
      181 aggcacaagg agggacactc caaatctgtc gttagccagg cggaaaatgc tcagctagac
      241 gtcattcagc agaaactgga cgctctgcag cagactgtta ccctaatgct tgaagacaag
      301 atggcgcggg aagcagaaaa ccgcctgcga aatgaggaga gggaacaact acaggccgaa
      361 attagccgtc tggctgacgc gctggcacag gaaaaaaagc ggggattctg gtcgcggctg
      421 tttcgctccg gttcagagta acagtgcagg tgactctgat ttaccataac atctgttatc
      481 agcaccgcct gagaggccct cagggcgttt ctgacgggaa accggtaaaa caggcaacaa
      541 accacccgaa aacccgccag aaacgcgcag gctctgtttt tacggcatgc atgagtatgc
      601 gcacaagtgc atagcgcgga aattcacacc attcagccgg ggtaagtcct gtttccggcg
      661 ttcttcccat ccgaaaacgg tgaacgggga cgcaatttat tgcgtggccg tgaagcgttg
      721 ccggcgcagc cggaaaaccc gctgtcagca cgttcaggaa gggggtgatg tacaaatggc
      781 acagaggatg aaagtgacgt atgagctgaa ggaatgatgt aaaagtgatg tataagtgat
      841 gtaaaagtga tgtatgaact gaaggagcga tgtaattctg tagtcaggaa gaataacccg
      901 ttcatgcagg catgaacgat acagtgagga acgctttttt tgtcacgatc tccccttaac
      961 ctgcgtaaat cacccgccat ggttgattat ttttcaacct caaaatggtc atacacctaa
     1021 cgcagccgcg attttcatcg caactgcatg aattaaaaga aaaaaaagga atatttcgtt
     1081 ttcacgagta atacccgggt attaaaaatc cactgtaatt acatgaaaat aaagaaataa
     1141 aaggtaatac cggagtatta ccacgtacgc gggcaagcga aaaagctata acgcttcccg
     1201 gccgacaggc gacccaaaat ccacaggggc atgcaggttc tcttcagtaa cctgcgccat
     1261 taaatcaaaa aggtcatatt cgccgggaag ctgcgtatca gtcgaatcca gttgttcatc
     1321 atattcagat ggcatggggt gatatccagt agctgagagg ttgttagcgg gtttcggggc
     1381 gcagccctga accagtcatg tagcgctagc ggagtgtata ctggcttact atgttgccac
     1441 gattgcgaaa atcagtgaag tgcttcatgt ggcaggagaa aaaaggcagc accggcgcgt
     1501 cagcagaata tgcgatacag gagatattcc gcttcctcgc tcactgactc gctacgctcg
     1561 gtcgttcggc tgcggcgagc ggtaccggct tacggacggg gacggaaatt tcctggaaga
     1621 taccaggaag acacttagca aagaagagat aaggccacgg cgaagccgtt tttccatagg
     1681 ctccgccccc ctgacaagca tcgcaaaatc tgacgctcaa atcagtggtg gcgaaacccg
     1741 acaggactat aaagatccca ggcgtttccc cctggtagct ccctcgtgcg ctctcctgtt
     1801 cctgcctttc ggtttaccgg tgtcattccg ctgttatggc cgcggtttct cattccacgc
     1861 ctgacactca gttccgtgaa ggcagttcgc tccaagctgg actgtatgca cgaacccccc
     1921 gttcagtccg accgctgcgc cttgtccggt aactatcaac ttgagtccaa cccggaaaga
     1981 cacgacaaaa cgccactggc agcagccatt agtaacagga gtgcacgaga agatagatta
     2041 agaggtcttg aagtagaggc ctgactgcgg ctacactgaa agaacagttt tggtaatggc
     2101 ggtctcgtga accctgttac cgggttaagc agttccccaa ctgacttaac cttcgaacaa
     2161 accgcctccc caggcggttt tttcgtttac agagcaagag attacgattc attgaaaagg
     2221 atctcaagaa gatcctttgt agattactat caattaatct tccgaacatg acaccagtca
     2281 ctgttgatta cggttaaacc gctccgtaac aggtttccct cgtattggtg acttgcagca
     2341 ccaaagaagc aaaaaagata aatatatcta cttattgaga gatgatatat ttatttccaa
     2401 aatgctacag atacatcatc atgaaacgga tcaccgcaaa caggttactc gcctggggat
     2461 tccctttcga cccgagcatc cgtatgagac tcatgctcga ttattattat tatagaagcc
     2521 cccatgaata aatcgctcat cattttcggc atcgtcaaca taacctcgga cagtttctcc
     2581 gatggaggcc ggtatctggc gccagacgca gccattgcgc aggcgcgtaa gctgatggcc
     2641 gagggggcag atgtgatcga cctcggtccg gcatccagca atcccgacgc cgcgcctgtt
     2701 tcgtccgaca cagaaatcgc gcgtatcgcg ccggtgctgg acgcgctcaa ggcagatggc
     2761 attcccgtct cgctcgacag ttatcaaccc gcgacgcaag cctatgcctt gtcgcgtggt
     2821 gtggcctatc tcaatgatat tcgcggtttt ccagacgctg cgttctatcc gcaattggcg
     2881 aaatcatctg ccaaactcgt cgttatgcat tcggtgcaag acgggcaggc agatcggcgc
     2941 gaggcacccg ctggcgacat catggatcac attgcggcgt tctttgacgc gcgcatcgcg
     3001 gcgctgacgg gtgccggtat caaacgcaac cgccttgtcc ttgatcccgg catggggttt
     3061 tttctggggg ctgctcccga aacctcgctc tcggtgctgg cgcggttcga tgaattgcgg
     3121 ctgcgcttcg atttgccggt gcttctgtct gtttcgcgca aatcctttct gcgcgcgctc
     3181 acaggccgtg gtccggggga tgtcggggcc gcgacactcg ctgcagagct tgccgccgcc
     3241 gcaggtggag ctgacttcat ccgcacacac gagccgcgcc ccttgcgcga cgggctggcg
     3301 gtattggcgg cgctgaaaga aaccgcaaga attcgttaac tgcacattcg ggatatttct
     3361 ctatattcgc gcttcatcag aaaactgaag gaacctccat tgaatcgaac taatattttt
     3421 tttggtgaat cgcattctga ctggttgcct gtcagaggcg gagaatctgg tgattttgtt
     3481 tttcgacgtg gtgacgggca tgccttcgcg aaaatcgcac ctgcttcccg ccgcggtgag
     3541 ctcgctggag agcgtgaccg cctcatttgg ctcaaaggtc gaggtgtggc ttgccccgag
     3601 gtcatcaact ggcaggagga acaggagggt gcatgcttgg tgataacggc aattccggga
     3661 gtaccggcgg ctgatctgtc tggagcggat ttgctcaaag cgtggccgtc aatggggcag
     3721 caacttggcg ctgttcacag cctatcggtt gatcaatgtc cgtttgagcg caggctgtcg
     3781 cgaatgttcg gacgcgccgt tgatgtggtg tcccgcaatg ccgtcaatcc cgacttctta
     3841 ccggacgagg acaagagtac gccgcagctc gatcttttgg ctcgtgtcga acgagagcta
     3901 ccggtgcggc tcgaccaaga gcgcaccgat atggttgttt gccatggtga tccctgcatg
     3961 ccgaacttca tggtggaccc taaaactctt caatgcacgg gtctgatcga ccttgggcgg
     4021 ctcggaacag cagatcgcta tgccgatttg gcactcatga ttgctaacgc cgaagagaac
     4081 tgggcagcgc cagatgaagc agagcgcgcc ttcgctgtcc tattcaatgt attggggatc
     4141 gaagcccccg accgcgaacg ccttgccttc tatctgcgat tggaccctct gacttggggt
     4201 tgatgttcat gccgcctgtt tttcctgctc attggcacgt ttcgcaacct gttctcattg
     4261 cggacacctt ttccagcctc gtttggaaag tttcattgcc agacgggact cctgcaatcg
     4321 tcaagggatt gaaacctata gaagacattg ctgatgaact gcgcggggcc gactatctgg
     4381 tatggcgcaa tgggagggga gcagtccggt tgctcggtcg tgagaacaat ctgatgttgc
     4441 tcgaatatgc cggggagcga atgctctctc acatcgttgc cgagcacggc gactaccagg
     4501 cgaccgaaat tgcagcggaa ctaatggcga agctgtatgc cgcatctgag gaacccctgc
     4561 cttctgccct tctcccgatc cgggatcgct ttgcagcttt gtttcagcgg gcgcgcgatg
     4621 atcaaaacgc aggttgtcaa actgactacg tccacgcggc gattatagcc gatcaaatga
     4681 tgagcaatgc ctcggaactg cgtgggctac atggcgatct gcatcatgaa aacatcatgt
     4741 tctccagtcg cggctggctg gtgatagatc ccgtcggtct ggtcggtgaa gtgggctttg
     4801 gcgccgccaa tatgttctac gatccggctg acagagacga cctttgtctc gatcctagac
     4861 gcattgcaca gatggcggac gcattctctc gtgcgctgga cgtcgatccg cgtcgcctgc
     4921 tcgaccaggc gtacgcttat gggtgccttt ccgcagcttg gaacgcggat ggagaagagg
     4981 agcaacgcga tctagctatc gcggccgcga tcaagcaggt gcgacagacg tcatactaga
     5041 tatcaagcga cttctcctat cccctgggaa cacatcaatc tcaccggaga atatcgctgg
     5101 ccaaagcctt agcgtaggat tccgcccctt cccgcaaacg accccaaaca ggaaacgcag
     5161 ctgaaacggg aagctcaaca cccactgacg catgggttgt tcaggcagta cttcatcaac
     5221 cagcaaggcg gcactttcgg ccatccgccg cgccccacag ctcgggcaga aaccgcgacg
     5281 cttacagctg aaagcgacca ggtgctcggc gtggcaagac tcgcagcgaa cccgtagaaa
     5341 gccatgctcc agccgcccgc attggagaaa ttcttcaaat tcccgttgca catagcccgg
     5401 caattccttt ccctgctctg ccataagcgc agcgaatgcc gggtaatact cgtcaacgat
     5461 ctgatagaga agggtttgct cgggtcggtg gctctggtaa cgaccagtat cccgatcccg
     5521 gctggccgtc ctggccgcca catgaggcat gttccgcgtc cttgcaatac tgtgtttaca
     5581 tacagtctat cgcttagcgg aaagttcttt taccctcagc cgaaatgcct gccgttgcta
     5641 gacattgcca gccagtgccc gtcactccca ctcttacatt gttcgcagta tctaggtaca
     5701 tgttattgcg tgcaccttca tgatgtataa tgttattaat gacagcagaa agatcgacag
     5761 aattaatatt cttcgtacct gggacagtta tcgggtgtcg gccagtgatg agaccaaagg
     5821 atgcagtata agatgaacca ctactattat catggccacc attaccacca ccgttaaaac
     5881 tacctcccga acttccagag ccgctatgac catcattgta ggggtcattt ggtcccatgt
     5941 gaccaaaacc accgacagta ccgctattta actctgtact cataaaatta tcctctttga
     6001 cttttaaaaa cagcaaaaac tgtatttata acaatgtgtt tatatacagt attcgaaata
     6061 ctacgcccgt caaaaccaca ccgtcaacag gttttttgtg tatttttcac gcctcacggg
     6121 cagcctcaga ccttttgtgt taaaacagta atatgttctg ctgttacaat acggtacaca
     6181 caggagacac tgtcactttt
//
