LOCUS       NZ_CP103648             6200 bp    DNA     circular CON 21-SEP-2023
DEFINITION  Escherichia coli strain 961 plasmid pMB5823_3, complete sequence.
ACCESSION   NZ_CP103648
VERSION     NZ_CP103648.1
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 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                   :: 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
            CP103648.1.
            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="961"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pMB5823_3"
                     /geo_loc_name="USA: Houston"
                     /lat_lon="29.7068 N 95.3971 W"
                     /collection_date="2018-06-18"
                     /collected_by="MDACC"
                     /genotype="ST617"
     ARG             5444..6198
                     /name="APH(3'')-Ib"
                     /gene="APH(3'')-Ib"
                     /gene_name="APH(3'')"
                     /tool="rgi"
                     /drug_class="aminoglycoside antibiotic"
                     /identity="99.21"
                     /coverage="94.38"
     ARG             5399..6198
                     /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            1..837
                     /locus_tag="M5R18_RS25490"
                     /old_locus_tag="M5R18_25490"
     CDS             1..837
                     /locus_tag="M5R18_RS25490"
                     /old_locus_tag="M5R18_25490"
                     /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(<944..1348)
                     /locus_tag="M5R18_RS25495"
                     /old_locus_tag="M5R18_25495"
                     /pseudo=""
     CDS             complement(<944..1348)
                     /locus_tag="M5R18_RS25495"
                     /old_locus_tag="M5R18_25495"
                     /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(1392..1781)
                     /locus_tag="M5R18_RS25500"
                     /old_locus_tag="M5R18_25500"
     CDS             complement(1392..1781)
                     /locus_tag="M5R18_RS25500"
                     /old_locus_tag="M5R18_25500"
                     /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            1999..2439
                     /locus_tag="M5R18_RS25505"
                     /old_locus_tag="M5R18_25505"
     CDS             1999..2439
                     /locus_tag="M5R18_RS25505"
                     /old_locus_tag="M5R18_25505"
                     /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(3184..3333)
                     /locus_tag="M5R18_RS25510"
                     /old_locus_tag="M5R18_25510"
     CDS             complement(3184..3333)
                     /locus_tag="M5R18_RS25510"
                     /old_locus_tag="M5R18_25510"
                     /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            3904..4062
                     /locus_tag="M5R18_RS25735"
     CDS             3904..4062
                     /locus_tag="M5R18_RS25735"
                     /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            4522..5337
                     /gene="sul2"
                     /locus_tag="M5R18_RS25515"
                     /old_locus_tag="M5R18_25515"
     ARG             4523..5334
                     /name="sul2"
                     /gene="sul2"
                     /gene_name="sulfonamide-resistant dihydropteroate synthase
                     Sul2"
                     /tool="amrfinderplus"
                     /drug_class="SULFONAMIDE"
                     /identity="100.0"
                     /coverage="100.0"
     ARG             2..834
                     /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(3369..3542)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.429"
                     /coverage="100.0"
                     /evalue="1.19e-84"
     Typing          3466..4071
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.431"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 atgttcatgc cgcctgtttt tcctgctcat tggcacgttt cgcaacctgt tctcattgcg
       61 gacacctttt ccagcctcgt ttggaaagtt tcattgccag acgggactcc tgcaatcgtc
      121 aagggattga aacctataga agacattgct gatgaactgc gcggggccga ctatctggta
      181 tggcgcaatg ggaggggagc agtccggttg ctcggtcgtg agaacaatct gatgttgctc
      241 gaatatgccg gggagcgaat gctctctcac atcgttgccg agcacggcga ctaccaggcg
      301 accgaaattg cagcggaact aatggcgaag ctgtatgccg catctgagga acccctgcct
      361 tctgcccttc tcccgatccg ggatcgcttt gcagctttgt ttcagcgggc gcgcgatgat
      421 caaaacgcag gttgtcaaac tgactacgtc cacgcggcga ttatagccga tcaaatgatg
      481 agcaatgcct cggaactgcg tgggctacat ggcgatctgc atcatgaaaa catcatgttc
      541 tccagtcgcg gctggctggt gatagatccc gtcggtctgg tcggtgaagt gggctttggc
      601 gccgccaata tgttctacga tccggctgac agagacgacc tttgtctcga tcctagacgc
      661 attgcacaga tggcggacgc attctctcgt gcgctggacg tcgatccgcg tcgcctgctc
      721 gaccaggcgt acgcttatgg gtgcctttcc gcagcttgga acgcggatgg agaagaggag
      781 caacgcgatc tagctatcgc ggccgcgatc aagcaggtgc gacagacgtc atactagata
      841 tcaagcgact tctcctatcc cctgggaaca catcaatctc accggagaat atcgctggcc
      901 aaagccttag cgtaggattc cgccccttcc cgcaaacgac cccaaacagg aaacgcagct
      961 gaaacgggaa gctcaacacc cactgacgca tgggttgttc aggcagtact tcatcaacca
     1021 gcaaggcggc actttcggcc atccgccgcg ccccacagct cgggcagaaa ccgcgacgct
     1081 tacagctgaa agcgaccagg tgctcggcgt ggcaagactc gcagcgaacc cgtagaaagc
     1141 catgctccag ccgcccgcat tggagaaatt cttcaaattc ccgttgcaca tagcccggca
     1201 attcctttcc ctgctctgcc ataagcgcag cgaatgccgg gtaatactcg tcaacgatct
     1261 gatagagaag ggtttgctcg ggtcggtggc tctggtaacg accagtatcc cgatcccggc
     1321 tggccgtcct ggccgccaca tgaggcatgt tccgcgtcct tgcaatactg tgtttacata
     1381 cagtctatcg cttagcggaa agttctttta ccctcagccg aaatgcctgc cgttgctaga
     1441 cattgccagc cagtgcccgt cactcccact cttacattgt tcgcagtatc taggtacatg
     1501 ttattgcgtg caccttcatg atgtataatg ttattaatga cagcagaaag atcgacagaa
     1561 ttaatattct tcgtacctgg gacagttatc gggtgtcggc cagtgatgag accaaaggat
     1621 gcagtataag atgaaccact actattatca tggccaccat taccaccacc gttaaaacta
     1681 cctcccgaac ttccagagcc gctatgacca tcattgtagg ggtcatttgg tcccatgtga
     1741 ccaaaaccac cgacagtacc gctatttaac tctgtactca taaaattatc ctctttgact
     1801 tttaaaaaca gcaaaaactg tatttataac aatgtgttta tatacagtat tcgaaatact
     1861 acgcccgtca aaaccacacc gtcaacaggt tttttgtgta tttttcacgc ctcacgggca
     1921 gcctcagacc ttttgtgtta aaacagtaat atgttctgct gttacaatac ggtacacaca
     1981 ggagacactg tcacttttat ggcatggcac acagttcaag agacactgaa attaacagga
     2041 aagtcgcgct cgcaattata tcgtgacatg gctaaaggcc ttgtcagcta tcgcacagga
     2101 aaaaatgatc gccgggagtt cgagaccagt gaactgattc gggcctatgg cgagctgcgc
     2161 acttctgaga caccaaaaag gcacaaggag ggacactcca aatctgtcgt tagccaggcg
     2221 gaaaatgctc agctagacgt cattcagcag aaactggacg ctctgcagca gactgttacc
     2281 ctaatgcttg aagacaagat ggcgcgggaa gcagaaaacc gcctgcgaaa tgaggagagg
     2341 gaacaactac aggccgaaat tagccgtctg gctgacgcgc tggcacagga aaaaaagcgg
     2401 ggattctggt cgcggctgtt tcgctccggt tcagagtaac agtgcaggtg actctgattt
     2461 accataacat ctgttatcag caccgcctga gaggccctca gggcgtttct gacgggaaac
     2521 cggtaaaaca ggcaacaaac cacccgaaaa cccgccagaa acgcgcaggc tctgttttta
     2581 cggcatgcat gagtatgcgc acaagtgcat agcgcggaaa ttcacaccat tcagccgggg
     2641 taagtcctgt ttccggcgtt cttcccatcc gaaaacggtg aacggggacg caatttattg
     2701 cgtggccgtg aagcgttgcc ggcgcagccg gaaaacccgc tgtcagcacg ttcaggaagg
     2761 gggtgatgta caaatggcac agaggatgaa agtgacgtat gagctgaagg aatgatgtaa
     2821 aagtgatgta taagtgatgt aaaagtgatg tatgaactga aggagcgatg taattctgta
     2881 gtcaggaaga ataacccgtt catgcaggca tgaacgatac agtgaggaac gctttttttg
     2941 tcacgatctc cccttaacct gcgtaaatca cccgccatgg ttgattattt ttcaacctca
     3001 aaatggtcat acacctaacg cagccgcgat tttcatcgca actgcatgaa ttaaaagaaa
     3061 aaaaaggaat atttcgtttt cacgagtaat acccgggtat taaaaatcca ctgtaattac
     3121 atgaaaataa agaaataaaa ggtaataccg gagtattacc acgtacgcgg gcaagcgaaa
     3181 aagctataac gcttcccggc cgacaggcga cccaaaatcc acaggggcat gcaggttctc
     3241 ttcagtaacc tgcgccatta aatcaaaaag gtcatattcg ccgggaagct gcgtatcagt
     3301 cgaatccagt tgttcatcat attcagatgg catggggtga tatccagtag ctgagaggtt
     3361 gttagcgggt ttcggggcgc agccctgaac cagtcatgta gcgctagcgg agtgtatact
     3421 ggcttactat gttgccacga ttgcgaaaat cagtgaagtg cttcatgtgg caggagaaaa
     3481 aaggcagcac cggcgcgtca gcagaatatg cgatacagga gatattccgc ttcctcgctc
     3541 actgactcgc tacgctcggt cgttcggctg cggcgagcgg taccggctta cggacgggga
     3601 cggaaatttc ctggaagata ccaggaagac acttagcaaa gaagagataa ggccacggag
     3661 aagccgtttt tccataggct ccgcccccct gacaagcatc gcaaaatctg acgctcaaat
     3721 cagtggtggc gaaacccgac aggactataa agatcccagg cgtttccccc tggtagctcc
     3781 ctcgtgcgct ctcctgttcc tgcctttcgg tttaccggtg tcattccgct gttatggccg
     3841 cggtttctca ttccacgcct gacactcagt tccgtgaagg cagttcgctc caagctggac
     3901 tgtatgcacg aaccccccgt tcagtccgac cgctgcgcct tgtccggtaa ctatcaactt
     3961 gagtccaacc cggaaagaca cgacaaaacg ccactggcag cagccattag taacaggagt
     4021 gcacgagaag atagattaag aggtcttgaa gtagaggcct gactgcggct acactgaaag
     4081 aacagttttg gtaatggcgg tctcgtgaac cctgttaccg ggttaagcag ttccccaact
     4141 gacttaacct tcgaacaaac cgcctcccca ggcggttttt tcgtttacag agcaagagat
     4201 tacgattcat tgaaaaggat ctcaagaaga tcctttgtag attactatca attaatcttc
     4261 cgaacatgac accagtcact gttgattacg gttaaaccgc tccgtaacag gtttccctcg
     4321 tattggtgac ttgcagcacc aaagaagcaa aaaagataaa tatatctact tattgagaga
     4381 tgatatattt atttccaaaa tgctacagat acatcatcat gaaacggatc accgcaaaca
     4441 ggttactcgc ctggggattc cctttcgacc cgagcatccg tatgagactc atgctcgatt
     4501 attattatta tagaagcccc catgaataaa tcgctcatca ttttcggcat cgtcaacata
     4561 acctcggaca gtttctccga tggaggccgg tatctggcgc cagacgcagc cattgcgcag
     4621 gcgcgtaagc tgatggccga gggggcagat gtgatcgacc tcggtccggc atccagcaat
     4681 cccgacgccg cgcctgtttc gtccgacaca gaaatcgcgc gtatcgcgcc ggtgctggac
     4741 gcgctcaagg cagatggcat tcccgtctcg ctcgacagtt atcaacccgc gacgcaagcc
     4801 tatgccttgt cgcgtggtgt ggcctatctc aatgatattc gcggttttcc agacgctgcg
     4861 ttctatccgc aattggcgaa atcatctgcc aaactcgtcg ttatgcattc ggtgcaagac
     4921 gggcaggcag atcggcgcga ggcacccgct ggcgacatca tggatcacat tgcggcgttc
     4981 tttgacgcgc gcatcgcggc gctgacgggt gccggtatca aacgcaaccg ccttgtcctt
     5041 gatcccggca tggggttttt tctgggggct gctcccgaaa cctcgctctc ggtgctggcg
     5101 cggttcgatg aattgcggct gcgcttcgat ttgccggtgc ttctgtctgt ttcgcgcaaa
     5161 tcctttctgc gcgcgctcac aggccgtggt ccgggggatg tcggggccgc gacactcgct
     5221 gcagagcttg ccgccgccgc aggtggagct gacttcatcc gcacacacga gccgcgcccc
     5281 ttgcgcgacg ggctggcggt attggcggcg ctgaaagaaa ccgcaagaat tcgttaactg
     5341 cacattcggg atatttctct atattcgcgc ttcatcagaa aactgaagga acctccatta
     5401 aatcgaacta atattttttt tggtgaatcg cattctgact ggttgcctgt cagaggcgga
     5461 gaatctggtg attttgtttt tcgacgtggt gacgggcatg ccttcgcgaa aatcgcacct
     5521 gcttcccgcc gcggtgagct cgctggagag cgtgaccgcc tcatttggct caaaggtcga
     5581 ggtgtggctt gccccgaggt catcaactgg caggaggaac aggagggtgc atgcttggtg
     5641 ataacggcaa ttccgggagt accggcggct gatctgtctg gagcggattt gctcaaagcg
     5701 tggccgtcaa tggggcagca acttggcgct gttcacagcc tatcggttga tcaatgtccg
     5761 tttgagcgca ggctgtcgcg aatgttcgga cgcgccgttg atgtggtgtc ccgcaatgcc
     5821 gtcaatcccg acttcttacc ggacgaggac aagagtacgc cgcagctcga tcttttggct
     5881 cgtgtcgaac gagagctacc ggtgcggctc gaccaagagc gcaccgatat ggttgtttgc
     5941 catggtgatc cctgcatgcc gaacttcatg gtggacccta aaactcttca atgcacgggt
     6001 ctgatcgacc ttgggcggct cggaacagca gatcgctatg ccgatttggc actcatgatt
     6061 gctaacgccg aagagaactg ggcagcgcca gatgaagcag agcgcgcctt cgctgtccta
     6121 ttcaatgtat tggggatcga agcccccgac cgcgaacgcc ttgccttcta tctgcgattg
     6181 gaccctctga cttggggttg
//
