LOCUS       NZ_CP103518             6222 bp    DNA     circular CON 21-SEP-2023
DEFINITION  Escherichia coli strain 5444 plasmid pMB9292_3, complete sequence.
ACCESSION   NZ_CP103518
VERSION     NZ_CP103518.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN28174095
            Assembly: GCF_024917955.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 6222)
  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 6222)
  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                   :: 209x
            Sequencing Technology             :: Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 09/21/2023 03:21:31
            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)                     :: 4,978
            CDSs (total)                      :: 4,858
            Genes (coding)                    :: 4,580
            CDSs (with protein)               :: 4,580
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 278
            CDSs (without protein)            :: 278
            Pseudo Genes (ambiguous residues) :: 0 of 278
            Pseudo Genes (frameshifted)       :: 87 of 278
            Pseudo Genes (incomplete)         :: 191 of 278
            Pseudo Genes (internal stop)      :: 58 of 278
            Pseudo Genes (multiple problems)  :: 53 of 278
            Pseudo Genes (short protein)      :: 3 of 278
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP103518.1.
            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..6222
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="5444"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pMB9292_3"
                     /geo_loc_name="USA: Houston"
                     /lat_lon="29.7068 N 95.3971 W"
                     /collection_date="2019-11-07"
                     /collected_by="MDACC"
                     /genotype="ST44"
     ARG             2..378
                     /name="sul2"
                     /gene="sul2"
                     /gene_name="sulfonamide resistant sul"
                     /tool="rgi"
                     /drug_class="sulfonamide antibiotic"
                     /identity="100.0"
                     /coverage="46.13"
     ARG             5786..6222
                     /name="sul2"
                     /gene="sul2"
                     /gene_name="sulfonamide resistant sul"
                     /tool="rgi"
                     /drug_class="sulfonamide antibiotic"
                     /identity="100.0"
                     /coverage="53.87"
     gene            439..1242
                     /gene="aph(3'')-Ib"
                     /locus_tag="M5S96_RS24695"
                     /old_locus_tag="M5S96_24695"
     ARG             440..1239
                     /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            1242..2078
                     /locus_tag="M5S96_RS24700"
                     /old_locus_tag="M5S96_24700"
     CDS             1242..2078
                     /locus_tag="M5S96_RS24700"
                     /old_locus_tag="M5S96_24700"
                     /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(<2185..2589)
                     /locus_tag="M5S96_RS24705"
                     /old_locus_tag="M5S96_24705"
                     /pseudo=""
     CDS             complement(<2185..2589)
                     /locus_tag="M5S96_RS24705"
                     /old_locus_tag="M5S96_24705"
                     /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(2633..3022)
                     /locus_tag="M5S96_RS24710"
                     /old_locus_tag="M5S96_24710"
     CDS             complement(2633..3022)
                     /locus_tag="M5S96_RS24710"
                     /old_locus_tag="M5S96_24710"
                     /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"
     gene            3240..3680
                     /locus_tag="M5S96_RS24715"
                     /old_locus_tag="M5S96_24715"
     CDS             3240..3680
                     /locus_tag="M5S96_RS24715"
                     /old_locus_tag="M5S96_24715"
                     /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(4447..4596)
                     /locus_tag="M5S96_RS24720"
                     /old_locus_tag="M5S96_24720"
     CDS             complement(4447..4596)
                     /locus_tag="M5S96_RS24720"
                     /old_locus_tag="M5S96_24720"
                     /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            5167..5325
                     /locus_tag="M5S96_RS24910"
     CDS             5167..5325
                     /locus_tag="M5S96_RS24910"
                     /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"
     ARG             1243..2075
                     /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(4632..4805)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.429"
                     /coverage="100.0"
                     /evalue="1.19e-84"
     Typing          4729..5334
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.593"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 atggatcaca ttgcggcgtt ctttgacgcg cgcatcgcgg cgctgacggg tgccggtatc
       61 aaacgcaacc gccttgtcct tgatcccggc atggggtttt ttctgggggc tgctcccgaa
      121 acctcgctct cggtgctggc gcggttcgat gaattgcggc tgcgcttcga tttgccggtg
      181 cttctgtctg tttcgcgcaa atcctttctg cgcgcgctca caggccgtgg tccgggggat
      241 gtcggggccg cgacactcgc tgcagagctt gccgccgccg caggtggagc tgacttcatc
      301 cgcacacacg agccgcgccc cttgcgcgac gggctggcgg tattggcggc gctgaaagaa
      361 accgcaagaa ttcgttaact gcacattcgg gatatttctc tatattcgcg cttcatcaga
      421 aaactgaagg aacctccatt gaatcgaact aatatttttt ttggtgaatc gcattctgac
      481 tggttgcctg tcagaggcgg agaatctggt gattttgttt ttcgacgtgg tgacgggcat
      541 gccttcgcga aaatcgcacc tgcttcccgc cgcggtgagc tcgctggaga gcgtgaccgc
      601 ctcatttggc tcaaaggtcg aggtgtggct tgccccgagg tcatcaactg gcaggaggaa
      661 caggagggtg catgcttggt gataacggca attccgggag taccggcggc tgatctgtct
      721 ggagcggatt tgctcaaagc gtggccgtca atggggcagc aacttggcgc tgttcacagc
      781 ctatcggttg atcaatgtcc gtttgagcgc aggctgtcgc gaatgttcgg acgcgccgtt
      841 gatgtggtgt cccgcaatgc cgtcaatccc gacttcttac cggacgagga caagagtacg
      901 ccgcagctcg atcttttggc tcgtgtcgaa cgagagctac cggtgcggct cgaccaagag
      961 cgcaccgata tggttgtttg ccatggtgat ccctgcatgc cgaacttcat ggtggaccct
     1021 aaaactcttc aatgcacggg tctgatcgac cttgggcggc tcggaacagc agatcgctat
     1081 gccgatttgg cactcatgat tgctaacgcc gaagagaact gggcagcgcc agatgaagca
     1141 gagcgcgcct tcgctgtcct attcaatgta ttggggatcg aagcccccga ccgcgaacgc
     1201 cttgccttct atctgcgatt ggaccctctg acttggggtt gatgttcatg ccgcctgttt
     1261 ttcctgctca ttggcacgtt tcgcaacctg ttctcattgc ggacaccttt tccagcctcg
     1321 tttggaaagt ttcattgcca gacgggactc ctgcaatcgt caagggattg aaacctatag
     1381 aagacattgc tgatgaactg cgcggggccg actatctggt atggcgcaat gggaggggag
     1441 cagtccggtt gctcggtcgt gagaacaatc tgatgttgct cgaatatgcc ggggagcgaa
     1501 tgctctctca catcgttgcc gagcacggcg actaccaggc gaccgaaatt gcagcggaac
     1561 taatggcgaa gctgtatgcc gcatctgagg aacccctgcc ttctgccctt ctcccgatcc
     1621 gggatcgctt tgcagctttg tttcagcggg cgcgcgatga tcaaaacgca ggttgtcaaa
     1681 ctgactacgt ccacgcggcg attatagccg atcaaatgat gagcaatgcc tcggaactgc
     1741 gtgggctaca tggcgatctg catcatgaaa acatcatgtt ctccagtcgc ggctggctgg
     1801 tgatagatcc cgtcggtctg gtcggtgaag tgggctttgg cgccgccaat atgttctacg
     1861 atccggctga cagagacgac ctttgtctcg atcctagacg cattgcacag atggcggacg
     1921 cattctctcg tgcgctggac gtcgatccgc gtcgcctgct cgaccaggcg tacgcttatg
     1981 ggtgcctttc cgcagcttgg aacgcggatg gagaagagga gcaacgcgat ctagctatcg
     2041 cggccgcgat caagcaggtg cgacagacgt catactagat atcaagcgac ttctcctatc
     2101 ccctgggaac acatcaatct caccggagaa tatcgctggc caaagcctta gcgtaggatt
     2161 ccgccccttc ccgcaaacga ccccaaacag gaaacgcagc tgaaacggga agctcaacac
     2221 ccactgacgc atgggttgtt caggcagtac ttcatcaacc agcaaggcgg cactttcggc
     2281 catccgccgc gccccacagc tcgggcagaa accgcgacgc ttacagctga aagcgaccag
     2341 gtgctcggcg tggcaagact cgcagcgaac ccgtagaaag ccatgctcca gccgcccgca
     2401 ttggagaaat tcttcaaatt cccgttgcac atagcccggc aattcctttc cctgctctgc
     2461 cataagcgca gcgaatgccg ggtaatactc gtcaacgatc tgatagagaa gggtttgctc
     2521 gggtcggtgg ctctggtaac gaccagtatc ccgatcccgg ctggccgtcc tggccgccac
     2581 atgaggcatg ttccgcgtcc ttgcaatact gtgtttacat acagtctatc gcttagcgga
     2641 aagttctttt accctcagcc gaaatgcctg ccgttgctag acattgccag ccagtgcccg
     2701 tcactcccac tcttacattg ttcgcagtat ctaggtacat gttattgcgt gcaccttcat
     2761 gatgtataat gttattaatg acagcagaaa gatcgacaga attaatattc ttcgtacctg
     2821 ggacagttat cgggtgtcgg ccagtgatga gaccaaagga tgcagtataa gatgaaccac
     2881 tactattatc atggccacca ttaccaccac cgttaaaact acctcccgaa cttccagagc
     2941 cgctatgacc atcattgtag gggtcatttg gtcccatgtg accaaaacca ccgacagtac
     3001 cgctatttaa ctctgtactc ataaaattat cctctttgac ttttaaaaac agcaaaaact
     3061 gtatttataa caatgtgttt atatacagta ttcgaaatac tacgcccgtc aaaaccacac
     3121 cgtcaacagg ttttttgtgt atttttcacg cctcacgggc agcctcagac cttttgtgtt
     3181 aaaacagtaa tatgttctgc tgttacaata cggtacacac aggagacact gtcactttta
     3241 tggcatggca cacagttcaa gagacactga aattaacagg aaagtcgcgc tcgcaattat
     3301 atcgtgacat ggctaaaggc cttgtcagct atcgcacagg aaaaaatgat cgccgggagt
     3361 tcgagaccag tgaactgatt cgggcctatg gcgagctgcg cacttctgag acaccaaaaa
     3421 ggcacaagga gggacactcc aaatctgtcg ttagccaggc ggaaaatgct cagctagacg
     3481 tcattcagca gaaactggac gctctgcagc agactgttac cctaatgctt gaagacaaga
     3541 tggcgcggga agcagaaaac cgcctgcgaa atgaggagag ggaacaacta caggccgaaa
     3601 ttagccgtct ggctgacgcg ctggcacagg aaaaaaagcg gggattctgg tcgcggctgt
     3661 ttcgctccgg ttcagagtaa cagtgcaggt gactctgatt taccataaca tctgttatca
     3721 gcaccgcctg agaggccctc agggcgtttc tgacgggaaa ccggtaaaac aggcaacaaa
     3781 ccacccgaaa acccgccaga aacgcgcagg ctctgttttt acggcatgca tgagtatgcg
     3841 cacaagtgca tagcgcggaa attcacacca ttcagccggg gtaagtcctg tttccggcgt
     3901 tcttcccatc cgaaaacggt gaacggggac gcaatttatt gcgtggccgt gaagcgttgc
     3961 cggcgcagcc ggaaaacccg ctgtcagcac gttcaggaag ggggtgatgt acaaatggca
     4021 cagaggatga aagtgacgta tgagctgaag gaatgatgta aaagtgatgt ataagtgatg
     4081 taaaagtgat gtataagtga tgtaaaagtg atgtatgaac tgaaggagcg atgtaattct
     4141 gtagtcagga agaataaccc gttcatgcag gcatgaacga tacagtgagg aacgcttttt
     4201 ttgtcacgat ctccccttaa cctgcgtaaa tcacccgcca tggttgatta tttttcaacc
     4261 tcaaaatggt catacaccta acgcagccgc gattttcatc gcaactgcat gaattaaaag
     4321 aaaaaaaagg aatatttcgt tttcacgagt aatacccggg tattaaaaat ccactgtaat
     4381 tacatgaaaa taaagaaata aaaggtaata ccggagtatt accacgtacg cgggcaagcg
     4441 aaaaagctat aacgcttccc ggccgacagg cgacccaaaa tccacagggg catgcaggtt
     4501 ctcttcagta acctgcgcca ttaaatcaaa aaggtcatat tcgccgggaa gctgcgtatc
     4561 agtcgaatcc agttgttcat catattcaga tggcatgggg tgatatccag tagctgagag
     4621 gttgttagcg ggtttcgggg cgcagccctg aaccagtcat gtagcgctag cggagtgtat
     4681 actggcttac tatgttgcca cgattgcgaa aatcagtgaa gtgcttcatg tggcaggaga
     4741 aaaaaggcag caccggcgcg tcagcagaat atgcgataca ggagatattc cgcttcctcg
     4801 ctcactgact cgctacgctc ggtcgttcgg ctgcggcgag cggtaccggc ttacggacgg
     4861 ggacggaaat ttcctggaag ataccaggaa gacacttagc aaagaagaga taaggccacg
     4921 gcgaagccgt ttttccatag gctccgcccc cctgacaagc atcgcaaaat ctgacgctca
     4981 aatcagtggt ggcgaaaccc gacaggacta taaagatccc aggcgtttcc ccctggtagc
     5041 tccctcgtgc gctctcctgt tcctgccttt cggtttaccg gtgtcattcc gctgttatgg
     5101 ccgcggtttc tcattccacg cctgacactc agttccgtga aggcagttcg ctccaagctg
     5161 gactgtatgc acgaaccccc cgttcagtcc gaccgctgcg ccttgtccgg taactatcaa
     5221 cttgagtcca acccggaaag acacgacaaa acgccactgg cagcagccat tagtaacagg
     5281 agtgcacgag aagatagatt aagaggtctt gaagtagagg cctgactgcg gctacactga
     5341 aagaacagtt ttggtaatgg cggtctcgtg aaccctgtta ccgggttaag cagttcccca
     5401 actgacttaa ccttcgaaca aaccgcctcc ccaggcggtt ttttcgttta cagagcaaga
     5461 gattacgatt cattgaaaag gatctcaaga agatcctttg tagattacta tcaattaatc
     5521 ttccgaacat gacaccagtc actgttgatt acggttaaac cgctccgtaa caggtttccc
     5581 tcgtattggt tacttgcagc accaaagaag caaaaaagat aaatatatct acttattgag
     5641 agatgatata tttatttcca aaatgctaca gatacatcat catgaaacgg atcaccgcaa
     5701 acaggttact cgcctgggga ttccctttcg acccgagcat ccgtatgaga ctcatgctcg
     5761 attattatta ttatagaagc ccccatgaat aaatcgctca tcattttcgg catcgtcaac
     5821 ataacctcgg acagtttctc cgatggaggc cggtatctgg cgccagacgc agccattgcg
     5881 caggcgcgta agctgatggc cgagggggca gatgtgatcg acctcggtcc ggcatccagc
     5941 aatcccgacg ccgcgcctgt ttcgtccgac acagaaatcg cgcgtatcgc gccggtgctg
     6001 gacgcgctca aggcagatgg cattcccgtc tcgctcgaca gttatcaacc cgcgacgcaa
     6061 gcctatgcct tgtcgcgtgg tgtggcctat ctcaatgata ttcgcggttt tccagacgct
     6121 gcgttctatc cgcaattggc gaaatcatct gccaaactcg tcgttatgca ttcggtgcaa
     6181 gacgggcagg cagatcggcg cgaggcaccc gctggcgaca tc
//
