LOCUS       NZ_CP083883             6188 bp    DNA     circular CON 05-NOV-2023
DEFINITION  Escherichia coli strain NDM3 plasmid unnamed3, complete sequence.
ACCESSION   NZ_CP083883
VERSION     NZ_CP083883.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN21398204
            Assembly: GCF_020149685.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 6188)
  AUTHORS   Simner,P., Mostafa,H., Bergman,Y., Ante,M., Tekle,T., Adebayo,A.,
            Beisken,S., Dzintars,K. and Tamma,P.D.
  TITLE     Progressive Development of Cefiderocol Resistance in Escherichia
            coli During Therapy Is Associated with Increased blaNDM-5 Copy
            Number and Gene Expression
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6188)
  AUTHORS   Simner,P., Mostafa,H., Bergman,Y., Ante,M., Tekle,T., Adebayo,A.,
            Beisken,S., Dzintars,K. and Tamma,P.D.
  TITLE     Direct Submission
  JOURNAL   Submitted (20-SEP-2021) BioIT, Ares-Genetics, Karl-Farkas-Gasse 18,
            Vienna 1180, Austria
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: JAN-2021
            Assembly Method                   :: Canu v. JAN-2021
            Assembly Name                     :: Isolate3
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 277x
            Sequencing Technology :: Oxford Nanopore MiniION + Illumina MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 11/05/2023 02:04:02
            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)                     :: 4,867
            CDSs (total)                      :: 4,744
            Genes (coding)                    :: 4,471
            CDSs (with protein)               :: 4,471
            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)              :: 273
            CDSs (without protein)            :: 273
            Pseudo Genes (ambiguous residues) :: 0 of 273
            Pseudo Genes (frameshifted)       :: 115 of 273
            Pseudo Genes (incomplete)         :: 164 of 273
            Pseudo Genes (internal stop)      :: 49 of 273
            Pseudo Genes (multiple problems)  :: 56 of 273
            Pseudo Genes (short protein)      :: 4 of 273
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP083883.1.
            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..6188
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="NDM3"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="unnamed3"
                     /geo_loc_name="USA: Baltimore"
                     /lat_lon="39.296 N 76.591 W"
                     /collection_date="2020"
                     /collected_by="Johns Hopkins University"
                     /genotype="ST167"
     gene            1..812
                     /gene="sul2"
                     /locus_tag="LCE26_RS24165"
                     /old_locus_tag="LCE26_24165"
                     /pseudo=""
     CDS             1..812
                     /gene="sul2"
                     /locus_tag="LCE26_RS24165"
                     /old_locus_tag="LCE26_24165"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001043260.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="sulfonamide-resistant dihydropteroate synthase
                     Sul2"
                     /name="sul2"
     gene            873..1676
                     /gene="aph(3'')-Ib"
                     /locus_tag="LCE26_RS24170"
                     /old_locus_tag="LCE26_24170"
     ARG             874..1673
                     /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            1676..2512
                     /locus_tag="LCE26_RS24175"
                     /old_locus_tag="LCE26_24175"
     CDS             1676..2512
                     /locus_tag="LCE26_RS24175"
                     /old_locus_tag="LCE26_24175"
                     /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(<2619..3023)
                     /locus_tag="LCE26_RS24180"
                     /old_locus_tag="LCE26_24180"
                     /pseudo=""
     CDS             complement(<2619..3023)
                     /locus_tag="LCE26_RS24180"
                     /old_locus_tag="LCE26_24180"
                     /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(3261..3458)
                     /locus_tag="LCE26_RS24185"
                     /old_locus_tag="LCE26_24185"
     CDS             complement(3261..3458)
                     /locus_tag="LCE26_RS24185"
                     /old_locus_tag="LCE26_24185"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_224435180.1"
                     /translation="MSTELNSGTVGGFGHMGPNDPPTMMVIAALEVREVVLTVVVMVAM
                     IIVVVHLILHPLVSSLADTR"
                     /name="hypothetical protein"
     gene            3676..4115
                     /locus_tag="LCE26_RS24190"
                     /old_locus_tag="LCE26_24190"
                     /pseudo=""
     CDS             3676..4115
                     /locus_tag="LCE26_RS24190"
                     /old_locus_tag="LCE26_24190"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005119689.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="entry exclusion protein 1"
                     /name="entry exclusion protein 1"
     gene            complement(4754..5005)
                     /locus_tag="LCE26_RS24195"
                     /old_locus_tag="LCE26_24195"
     CDS             complement(4754..5005)
                     /locus_tag="LCE26_RS24195"
                     /old_locus_tag="LCE26_24195"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_224435181.1"
                     /translation="MPSEYDEQLDSTDTQLPGEYDLFDLMAQVTEENLHAPVDFGSPVG
                     RKRYSFSLARVRGNTPVLPFISLFSCNYSGFLIPGYYS"
                     /name="hypothetical protein"
     gene            5568..5729
                     /locus_tag="LCE26_RS24415"
     CDS             5568..5729
                     /locus_tag="LCE26_RS24415"
                     /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="replication initiation protein"
                     /protein_id="WP_318010574.1"
                     /translation="MYARTPVQSDRCALSGNYQLESNPERHDKTPLAAAISNRSAREDR
                     LRGLEVEA"
                     /name="replication initiation protein"
     ARG             1677..2509
                     /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(5041..5213)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.857"
                     /coverage="100.0"
                     /evalue="1.99e-82"
     Typing          5137..5738
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="88.943"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 atgaataaat cgctcatcat tttcggcatc gtcaacataa cctcggacag tttctccgat
       61 ggaggccggt atctggcgcc agacgcagcc attgcgcagg cgcgtaagct gatggccgag
      121 ggggcagatg tgatcgacct cggtccggca tccagcaatc ccgacgccgc gcctgtttcg
      181 tccgacacag aaatcgcgcg tatcgcgccg gtgctggacg cgctcaaggc agatggcatt
      241 cccgtctcgc tcgacagtta tcaacccgcg acgcaagcct atgccttgtc gcgtggtgtg
      301 gcctatctca atgatattcg cggttttcca gacgctgcgt tctatccgca attggcgaaa
      361 tcatctgcca aactcgtcgt tatgcattcg gtgcaagacg ggcaggcaga tcggcgcgag
      421 gcacccgctg gcgacatcat ggatcacatt gcggcgttct ttgacgcgcg catcgcggcg
      481 ctgacgggtg ccggtatcaa acgcaaccgc cttgtccttg atcccggcat ggggtttttc
      541 tgggggctgc tcccgaaacc tcgctctcgg tgctggcgcg gttcgatgaa ttgcggctgc
      601 gcttcgattt gccggtgctt ctgtctgttt cgcgcaaatc ctttctgcgc gctcacaggc
      661 cgtggtccgg ggatgtcggg gccgcgacac tcgctgcaga gcttgccgcc gccgcaggtg
      721 gagctgactt catccgcaca cacgagccgc gccccttgcg cgacgggctg gcggtattgg
      781 cggcgctgaa agaaaccgca agaattcgtt aactgcacat tcgggatatt tctctatatt
      841 cgcgcttcat cagaaaactg aaggaacctc cattgaatcg aactaatatt ttttttggtg
      901 aatcgcattc tgactggttg cctgtcagag gcggagaatc tggtgatttt gtttttcgac
      961 gtggtgacgg gcatgccttc gcgaaaatcg cacctgcttc ccgccgcggt gagctcgctg
     1021 gagagcgtga ccgcctcatt tggctcaaag gtcgaggtgt ggcttgcccc gaggtcatca
     1081 actggcagga ggaacaggag ggtgcatgct tggtgataac ggcaattccg ggagtaccgg
     1141 cggctgatct gtctggagcg gatttgctca aagcgtggcc gtcaatgggg cagcaacttg
     1201 gcgctgttca cagcctatcg gttgatcaat gtccgtttga gcgcaggctg tcgcgaatgt
     1261 tcggacgcgc cgttgatgtg gtgtcccgca atgccgtcaa tcccgacttc ttaccggacg
     1321 aggacaagag tacgccgcag ctcgatcttt tggctcgtgt cgaacgagag ctaccggtgc
     1381 ggctcgacca agagcgcacc gatatggttg tttgccatgg tgatccctgc atgccgaact
     1441 tcatggtgga ccctaaaact cttcaatgca cgggtctgat cgaccttggg cggctcggaa
     1501 cagcagatcg ctatgccgat ttggcactca tgattgctaa cgccgaagag aactgggcag
     1561 cgccagatga agcagagcgc gccttcgctg tcctattcaa tgtattgggg atcgaagccc
     1621 ccgaccgcga acgccttgcc ttctatctgc gattggaccc tctgacttgg ggttgatgtt
     1681 catgccgcct gtttttcctg ctcattggca cgtttcgcaa cctgttctca ttgcggacac
     1741 cttttccagc ctcgtttgga aagtttcatt gccagacggg actcctgcaa tcgtcaaggg
     1801 attgaaacct atagaagaca ttgctgatga actgcgcggg gccgactatc tggtatggcg
     1861 caatgggagg ggagcagtcc ggttgctcgg tcgtgagaac aatctgatgt tgctcgaata
     1921 tgccggggag cgaatgctct ctcacatcgt tgccgagcac ggcgactacc aggcgaccga
     1981 aattgcagcg gaactaatgg cgaagctgta tgccgcatct gaggaacccc tgccttctgc
     2041 ccttctcccg atccgggatc gctttgcagc tttgtttcag cgggcgcgcg atgatcaaaa
     2101 cgcaggttgt caaactgact acgtccacgc ggcgattata gccgatcaaa tgatgagcaa
     2161 tgcctcggaa ctgcgtgggc tacatggcga tctgcatcat gaaaacatca tgttctccag
     2221 tcgcggctgg ctggtgatag atcccgtcgg tctggtcggt gaagtgggct ttggcgccgc
     2281 caatatgttc tacgatccgg ctgacagaga cgacctttgt ctcgatccta gacgcattgc
     2341 acagatggcg gacgcattct ctcgtgcgct ggacgtcgat ccgcgtcgcc tgctcgacca
     2401 ggcgtacgct tatgggtgcc tttccgcagc ttggaacgcg gatggagaag aggagcaacg
     2461 cgatctagct atcgcggccg cgatcaagca ggtgcgacag acgtcatact agatatcaag
     2521 cgacttctcc tatcccctgg gaacacatca atctcaccgg agaatatcgc tggccaaagc
     2581 cttagcgtag gattccgccc cttcccgcaa acgaccccaa acaggaaacg cagctgaaac
     2641 gggaagctca acacccactg acgcatgggt tgttcaggca gtacttcatc aaccagcaag
     2701 gcggcacttt cggccatccg ccgcgcccca cagctcgggc agaaaccgcg acgcttacag
     2761 ctgaaagcga ccaggtgctc ggcgtggcaa gactcgcagc gaacccgtag aaagccatgc
     2821 tccagccgcc cgcattggag aaattcttca aattcccgtt gcacatagcc cggcaattcc
     2881 tttccctgct ctgccataag cgcagcgaat gccgggtaat actcgtcaac gatctgatag
     2941 agaagggttt gctcgggtcg gtggctctgg taacgaccag tatcccgatc ccggctggcc
     3001 gtcctggccg ccacatgagg catgttccgc gtccttgcaa tactgtgttt acatacagtc
     3061 tatcgcttag cggaaagttc ttttaccctc agccgaaatg cctgccgttg ctagacattg
     3121 ccagccagtg cccgtcactc ccactcttac attgttcgca gtatctaggt acatgttatt
     3181 gcgtgcacct tcatgatgta taatgttatt aatgacagca gaaagatcga cagaattaat
     3241 attcttcgta cctgggacag ttatcgggtg tcggccagtg atgagaccaa aggatgcagt
     3301 ataagatgaa ccactactat tatcatggcc accattacca ccaccgttaa aactacctcc
     3361 cgaacttcca gagccgctat gaccatcatt gtaggggggt catttggtcc catgtgacca
     3421 aaaccaccga cagtaccgct atttaactct gtactcataa aattatcctc tttgactttt
     3481 aaaaacagca aaaactgtat ttataacaat gtgtttatat acagtattcg aaatactacg
     3541 cccgtcaaaa ccacaccgtc aacaggtttt ttgtgtattt ttcacgcctc acgggcagcc
     3601 tcagaccttt tgtgttaaaa cagtaatatg ttctgctgtt acaatacggt acacacagga
     3661 gacactgtca cttttatggc atggcacaca gttcaagaga cactgaaatt aacaggaaag
     3721 tcgcgctcgc aattatatcg tgacatggct aaaggccttg tcagctatcg cacaggaaaa
     3781 aatgatcgcc gggagttcga gaccagtgaa ctgattcggg cctatggcga gctgcgcact
     3841 tctgagacac caaaaggcac aaggagggac actccaaatc tgtcgttagc caggcggaaa
     3901 atgctcagct agacgtcatt cagcagaaac tggacgctct gcagcagact gttaccctaa
     3961 tgcttgaaga caagatggcg cgggaagcag aaaaccgcct gcgaaatgag gagagggaac
     4021 aactacaggc cgaaattagc cgtctggctg acgcgctggc acaggaaaaa aagcggggat
     4081 tctggtcgcg gctgtttcgc tccggttcag agtaacagtg caggtgactc tgatttacca
     4141 taacattcgt tgcgtgcacc atctcagacg ccctcagggc gtttctgacg ggaaaccggt
     4201 aaaacaggca acaaaccacc cgaaaacccg ccagaaacgc gcaggctctg tttttacggc
     4261 atgcatgagt atgcgcacaa gtgcatagcg cggaaattca caccattcag ccggggtaag
     4321 tcctgtttcc ggcgttcttc ccatccgaaa acggtgaacg gggacgcaat ttattgcgtg
     4381 gccgtgaagc gttgccggcg cagccggaaa acccgctgtc agcacgttca ggaaggggtg
     4441 atgtacaaat ggcacagagg atgaaagtga cgtatgagct gaaggaatga tgtaaaagtg
     4501 atgtataagt gatgtaaaac tgatgtatga actgaaggag cgatgtaatt ctgtagtcag
     4561 gaagaataac ccgttcatgc aggcatgaac gatacagtga ggaacgcttt tttgtcacga
     4621 tctcccctta acctgcgtaa atcacccgcc atggttgatt atttttcaac ctcaaaatgg
     4681 tcatacacct aacgcagccg cgattttcat cgcaactgca tgaattaaaa agaaaaaaag
     4741 gaatatttcg ttttcacgag taatacccgg gtattaaaaa tccactgtaa ttacatgaaa
     4801 ataaagaaat aaaaggtaat accggagtat taccacgtac gcgggcaagc gaaaagctat
     4861 aacgcttccg gccgacaggc gacccaaaat ccacaggggc atgcaggttc tcttcagtaa
     4921 cctgcgccat taaatcaaaa aggtcatatt cgccgggaag ctgcgtatca gtcgaatcca
     4981 gttgttcatc atattcagat ggcatggggt gatatccagt agctgagagg ttgttagcgg
     5041 gtttcgggcg cagccctgaa ccagtcatgt agcgctagcg gagtgtatac tggcttacta
     5101 tgttgccacg attgcgaaaa tcagtgaagt gcttcatgtg gcaggagaaa aaaggcagca
     5161 ccggcgcgtc agcagaatat gcgatacagg agatattccg cttcctcgct cactgactcg
     5221 ctacgctcgg tcgttcggct gcggcgagcg gtaccggctt acggacgggg acggaaattt
     5281 cctggaagat accaggaaga cacttagcaa agaagagata aggccacggc gaagcctttt
     5341 tccataggct ccgccccctg acaagcatcg caaaatctga cgctcaaatc agtggtggcg
     5401 aaacccgaca ggactataaa gatcccaggc gtttcccctg gtagctccct cgtgcgctct
     5461 cctgttcctg cctttcggtt taccggtgtc attccgctgt tatggccgcg gtttctcatt
     5521 ccacgcctga cactcagttc cgtgaaggca gttcgctcca agctggactg tatgcacgaa
     5581 cccccgttca gtccgaccgc tgcgccttgt ccggtaacta tcaacttgag tccaacccgg
     5641 aaagacacga caaaacgcca ctggcagcag ccattagtaa caggagtgca cgagaagata
     5701 gattaagagg tcttgaagta gaggcctgac tgcggctaca ctgaaagaac agttttggta
     5761 atggcggtct cgtgaaccct gttaccgggt taagcagttc cccaactgac ttaaccttcg
     5821 aacaaaccgc ctccccaggc ggttttttcg tttacagagc aagagattac gattcattga
     5881 aaaggatctc aagaagatcc tttgtagatt actatcaatt aatcttccga acatgacacc
     5941 agtcactgtt gattacggtt aaaccgctcc gtaacaggtt tccctcgtat tggtgacttg
     6001 cagcaccaaa gaagcaaaaa agataaatat atctacttat tgagagatga tatatttatt
     6061 tccaaaatgc tacagataca tcatcatgaa acggatcacc gcaaacaggt tactcgcctg
     6121 gggattccct ttcgacccga gcatccgtat gagactcatg ctcgattatt attattatag
     6181 aagccccc
//
