LOCUS       NZ_CP083873             6291 bp    DNA     circular CON 05-NOV-2023
DEFINITION  Escherichia coli strain NDM5 plasmid unnamed1, complete sequence.
ACCESSION   NZ_CP083873
VERSION     NZ_CP083873.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN21398207
            Assembly: GCF_020149625.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 6291)
  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  JOURNAL   Unpublished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 6291)
  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                     :: Isolate5
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 285x
            Sequencing Technology :: Oxford Nanopore MiniION + Illumina MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 11/05/2023 01:52:57
            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)                     :: 4,938
            CDSs (total)                      :: 4,815
            Genes (coding)                    :: 4,483
            CDSs (with protein)               :: 4,483
            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)              :: 332
            CDSs (without protein)            :: 332
            Pseudo Genes (ambiguous residues) :: 0 of 332
            Pseudo Genes (frameshifted)       :: 148 of 332
            Pseudo Genes (incomplete)         :: 195 of 332
            Pseudo Genes (internal stop)      :: 49 of 332
            Pseudo Genes (multiple problems)  :: 61 of 332
            Pseudo Genes (short protein)      :: 4 of 332
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP083873.1.
            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..6291
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="NDM5"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="unnamed1"
                     /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..219
                     /locus_tag="LCE27_RS22965"
                     /old_locus_tag="LCE27_22965"
     CDS             1..219
                     /locus_tag="LCE27_RS22965"
                     /old_locus_tag="LCE27_22965"
                     /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_224450641.1"
                     /translation="MSTELNSGTVGGFGHMGPNDPYNDGHSGSGSSGGSFNGGGNGGHD
                     NSSGSSYTASFGLITGRHPITVRYEEY"
                     /name="hypothetical protein"
     gene            432..>836
                     /locus_tag="LCE27_RS22970"
                     /old_locus_tag="LCE27_22970"
                     /pseudo=""
     CDS             432..>836
                     /locus_tag="LCE27_RS22970"
                     /old_locus_tag="LCE27_22970"
                     /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(943..1779)
                     /locus_tag="LCE27_RS22975"
                     /old_locus_tag="LCE27_22975"
     CDS             complement(943..1779)
                     /locus_tag="LCE27_RS22975"
                     /old_locus_tag="LCE27_22975"
                     /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"
     ARG             complement(1780..2537)
                     /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             complement(1783..2567)
                     /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="98.13"
     gene            complement(2641..>3340)
                     /gene="folP"
                     /locus_tag="LCE27_RS22985"
                     /old_locus_tag="LCE27_22985"
                     /pseudo=""
     CDS             complement(2641..>3340)
                     /gene="folP"
                     /locus_tag="LCE27_RS22985"
                     /old_locus_tag="LCE27_22985"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001043260.1"
                     /GO_function="GO:0004156 - dihydropteroate synthase
                     activity [Evidence IEA]"
                     /GO_process="GO:0009396 - folic acid-containing compound
                     biosynthetic process [Evidence IEA]"
                     /note="frameshifted; incomplete; partial in the middle of a
                     contig; missing N-terminus; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="dihydropteroate synthase"
                     /name="folP"
     gene            complement(3322..3561)
                     /locus_tag="LCE27_RS22990"
                     /old_locus_tag="LCE27_22990"
     CDS             complement(3322..3561)
                     /locus_tag="LCE27_RS22990"
                     /old_locus_tag="LCE27_22990"
                     /EC_number="2.5.1.15"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_014407063.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="dihydropteroate synthase"
                     /protein_id="WP_224450640.1"
                     /translation="MNKSLIIFGIVNITSDSFSDGGRYLAPDAAIAQARKLMAEGADVI
                     DLGPASSNPDAAPVSSDTEIARIAPVLDALRGQM"
                     /name="dihydropteroate synthase"
     gene            complement(4019..4180)
                     /locus_tag="LCE27_RS24750"
     CDS             complement(4019..4180)
                     /locus_tag="LCE27_RS24750"
                     /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"
     gene            complement(5636..6075)
                     /locus_tag="LCE27_RS22995"
                     /old_locus_tag="LCE27_22995"
                     /pseudo=""
     CDS             complement(5636..6075)
                     /locus_tag="LCE27_RS22995"
                     /old_locus_tag="LCE27_22995"
                     /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"
     ARG             complement(947..1779)
                     /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"
     ARG             complement(3323..3561)
                     /name="sul2"
                     /gene="sul2"
                     /gene_name="sulfonamide resistant sul"
                     /tool="rgi"
                     /drug_class="sulfonamide antibiotic"
                     /identity="98.68"
                     /coverage="29.15"
     ARG             complement(2991..3325)
                     /name="sul2"
                     /gene="sul2"
                     /gene_name="sulfonamide resistant sul"
                     /tool="rgi"
                     /drug_class="sulfonamide antibiotic"
                     /identity="98.2"
                     /coverage="40.96"
     Typing          4537..4710
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.429"
                     /coverage="100.0"
                     /evalue="1.19e-84"
     Typing          complement(4011..4613)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.106"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 atgagtacag agttaaatag cggtactgtc ggtggttttg gtcacatggg accaaatgac
       61 ccctacaatg atggtcatag cggctctgga agttcgggag gtagttttaa cggtggtggt
      121 aatggtggcc atgataatag tagtggttca tcttatactg catcctttgg tctcatcact
      181 ggccgacacc cgataactgt ccggtacgaa gaatattaat tctgtcgatc tttctgctgt
      241 cattaataac attatacatc atgaaggtgc acgcaataac atgtacctag atactgcgaa
      301 caatgtaaga gtgggagtga cgggcactgg ctggcaatgt ctagcaacgg caggcatttc
      361 ggctgagggt aaaagaactt tccgctaagc gatagactgt atgtaaacac agtattgcaa
      421 ggacgcggaa catgcctcat gtggcggcca ggacggccag ccgggatcgg gatactggtc
      481 gttaccagag ccaccgaccc gagcaaaccc ttctctatca gatcgttgac gagtattacc
      541 cggcattcgc tgcgcttatg gcagagcagg gaaaggaatt gccgggctat gtgcaacggg
      601 aatttgaaga atttctccaa tgcgggcggc tggagcatgg ctttctacgg gttcgctgcg
      661 agtcttgcca cgccgagcac ctggtcgctt tcagctgtaa gcgtcgcggt ttctgcccga
      721 gctgtggggc gcggcggatg gccgaaagtg ccgccttgct ggttgatgaa gtactgcctg
      781 aacaacccat gcgtcagtgg gtgttgagct tcccgtttca gctgcgtttc ctgtttgggg
      841 tcgtttgcgg gaaggggcgg aatcctacgc taaggctttg gccagcgata ttctccggtg
      901 agattgatgt gttcccaggg gataggagaa gtcgcttgat atctagtatg acgtctgtcg
      961 cacctgcttg atcgcggccg cgatagctag atcgcgttgc tcctcttctc catccgcgtt
     1021 ccaagctgcg gaaaggcacc cataagcgta cgcctggtcg agcaggcgac gcggatcgac
     1081 gtccagcgca cgagagaatg cgtccgccat ctgtgcaatg cgtctaggat cgagacaaag
     1141 gtcgtctctg tcagccggat cgtagaacat attggcggcg ccaaagccca cttcaccgac
     1201 cagaccgacg ggatctatca ccagccagcc gcgactggag aacatgatgt tttcatgatg
     1261 cagatcgcca tgtagcccac gcagttccga ggcattgctc atcatttgat cggctataat
     1321 cgccgcgtgg acgtagtcag tttgacaacc tgcgttttga tcatcgcgcg cccgctgaaa
     1381 caaagctgca aagcgatccc ggatcgggag aagggcagaa ggcaggggtt cctcagatgc
     1441 ggcatacagc ttcgccatta gttccgctgc aatttcggtc gcctggtagt cgccgtgctc
     1501 ggcaacgatg tgagagagca ttcgctcccc ggcatattcg agcaacatca gattgttctc
     1561 acgaccgagc aaccggactg ctcccctccc attgcgccat accagatagt cggccccgcg
     1621 cagttcatca gcaatgtctt ctataggttt caatcccttg acgattgcag gagtcccgtc
     1681 tggcaatgaa actttccaaa cgaggctgga aaaggtgtcc gcaatgagaa caggttgcga
     1741 aacgtgccaa tgagcaggaa aaacaggcgg catgaacatc aaccccaagt cagagggtcc
     1801 aatcgcagat agaaggcaag gcgttcgcgg tcgggggctt cgatccccaa tacattgaat
     1861 aggacagcga aggcgcgctc tgcttcatct ggcgctgccc agttctcttc ggcgttagca
     1921 atcatgagtg ccaaatcggc atagcgatct gctgttccga gccgcccaag gtcgatcaga
     1981 cccgtgcatt gaagagtttt agggtccacc atgaagttcg gcatgcaggg atcaccatgg
     2041 caaacaacca tatcggtgcg ctcttggtcg agccgcaccg gtagctctcg ttcgacacga
     2101 gccaaaagat cgagctgcgg cgtactcttg tcctcgtccg gtaagaagtc gggattgacg
     2161 gcattgcggg acaccacatc aacggcgcgt ccgaacattc gcgacagcct gcgctcaaac
     2221 ggacattgat caaccgatag gctgtgaaca gcgccaagtt gctgccccat tgacggccac
     2281 gctttgagca aatccgctcc agacagatca gccgccggta ctcccggaat tgccgttatc
     2341 accaagcatg caccctcctg ttcctcctgc cagttgatga cctcggggca agccacacct
     2401 cgacctttga gccaaatgag gcggtcacgc tctccagcga gctcaccgcg gcgggaagca
     2461 ggtgcgattt tcgcgaaggc atgcccgtca ccacgtcgaa aaacaaaatc accagattct
     2521 ccgcctctga caggcaacca gtcagaatgc gattcaccaa aaaatattag ttcgattcaa
     2581 tggaggttcc ttcagttttc tgatgaagcg cgaatataga gaaatatccc gaatgtgcag
     2641 ttaacgaatt cttgcggttt ctttcagcgc cgccaatacc gccagcccgt cgcgcaaggg
     2701 gcgcggctcg tgtgtgcgga tgaagtcagc tccacctgcg gcggcggcaa gctctgcagc
     2761 gagtgtcgcg gcccccacat ccccggacca cggcctgtga gcgcgcgcag aaaggatttg
     2821 cgcgaaacag acagaagcac cggcaaatcg aagcgcagcc gcaattcatc gaaccgcgcc
     2881 agcaccgaga gcgaggtttc gggagcagcc ccagaaaaac cccatgccgg gatcaaggac
     2941 aaggcggttg cgtttgatac cggcacccgt cagcgccgcg atgcgcgcgt caaagaaacg
     3001 ccgcaatgtg atccatgatg tcgccagcgg gtgcctcgcg ccgatctgcc tgcccgtctt
     3061 gcaccgaatg cataacgacg agtttggcag atgatttcgc caattgcgga tagaacgcag
     3121 cgtctggaaa accgcgaata tcattgagat aggccacacc acgcgacaag gcataggctt
     3181 gcgtcgcggg ttgataactg tcgagcgaga cgggaatgcc atctgccttg agcgcgtcca
     3241 gcaccggcgc gatacgcgcg atttctgtgt cggacgaaac aggcgcggcg tcgggattgc
     3301 tggatgccgg accgaggtcg atcacatctg ccccctgagc gcgtccagca ccggcgcgat
     3361 acgcgcgatt tctgtgtcgg acgaaacagg cgcggcgtcg ggattgctgg atgccggacc
     3421 gaggtcgatc acatctgccc cctcggccat cagcttacgc gcctgcgcaa tggctgcgtc
     3481 tggcgccaga taccggcctc catcggagaa actgtccgag gttatgttga cgatgccgaa
     3541 aatgatgagc gatttattca tgggggcttc tataataata ataatcgagc atgagtctca
     3601 tacggatgct cgggtcgaaa gggaatcccc aggcgagtaa cctgtttgcg gtgatccgtt
     3661 tcatgatgat gtatctgtag cattttggaa ataaatatat catctctcaa taagtagata
     3721 tatttatctt ttttgcttct ttggtgctgc aagtcaccaa tacgagggaa acctgttacg
     3781 gagcggttta accgtaatca acagtgactg gtgtcatgtt cggaagatta attgatagta
     3841 atctacaaag gatcttcttg agatcctttt caatgaatcg taatctcttg ctctgtaaac
     3901 gaaaaaccgc ctgggaggcg gtttgttcga aggttaagtc agttggggaa ctgcttaacc
     3961 cggtaacagg gttcacgaga ccgccattac caaaactgtt ctttcagtgt agccgcagtc
     4021 aggcctctac ttcaagacct cttaatctat cttctcgtgc actcctgtta ctaatggctg
     4081 ctgccagtgg cgttttgtcg tgtctttccg ggttggactc aagttgatag ttaccggaca
     4141 aggcgcagcg gtcggactga acgggggttc gtgcatacag tccagcttgg agcgaactgc
     4201 cttcacggaa ctgagtgtca ggcgtggaat gagaaaccgc ggccataaca gcggaatgac
     4261 accggtaaac cgaaaggcag gaacaggaga gcgcacgagg gagctaccag gggaaacgcc
     4321 tgggatcttt atagtcctgt cgggtttcgc caccactgat ttgagcgtca gattttgcga
     4381 tgcttgtcag ggggcggagc ctatggaaaa acggcttcgc cgtggcctta tctcttcttt
     4441 gctaagtgtc ttcctggtat cttccaggaa atttccgtcc ccgtccgtaa gccggtaccg
     4501 ctcgccgcag ccgaacgacc gagcgtagcg agtcagtgag cgaggaagcg gaatatctcc
     4561 tgtatcgcat attctgctga cgcgccggtg ctgccttttt tctcctgcca catgaagcac
     4621 ttcactgatt ttcgcaatcg tggcaacata gtaagccagt atacactccg ctagcgctac
     4681 atgactggtt cagggctgcg ccccgaaacc cgctaacaac ctctcagcta ctggatatca
     4741 ccccatgcca tctgaatatg atgaacaact ggattcgact gatacgcagc ttcccggcga
     4801 atatgacctt ttgatttaat ggcgcaggtt actgaagaga acctgcatgc ccctgtggat
     4861 tttgggtcgc ctgtcggccg ggaagcgtta tagctttttc gcttgcccgc gtacgtggta
     4921 atactccggt attacctttt atttctttat tttcatgtaa ttacagtgga tttttaatac
     4981 ccgggtatta ctcgtgaaaa cgaaatattc ctttttttct tttaattcat gcagttgcga
     5041 tgaaaatcgc ggctgcgtta ggtgtatgac cattttgagg ttgaaaaata atcaaccatg
     5101 gcgggtgatt tacgcaggtt aaggggagat cgtgacaaaa aaagcgttcc tcactgtatc
     5161 gttcatgcct gcatgaacgg gttattcttc ctgactacag aattacatcg ctccttcagt
     5221 tcatacatca gttttacatc acttatacat cacttttaca tcattccttc agctcatacg
     5281 tcactttcat cctctgtgcc atttgtacat caccccttcc tgaacgtgct gacagcgggt
     5341 tttccggctg cgccggcaac gcttcacggc cacgcaataa attgcgtccc cgttcaccgt
     5401 tttcggatgg gaagaacgcc ggaaacagga cttaccccgg ctgaatggtg tgaatttccg
     5461 cgctatgcac ttgtgcgcat actcatgcat gccgtaaaaa cagagcctgc gcgtttctgg
     5521 cgggttttcg ggtggtttgt tgcctgtttt accggtttcc cgtcagaaac gccctgaggg
     5581 cgtctgagat ggtgcacgca acgaatgtta tggtaaatca gagtcacctg cactgttact
     5641 ctgaaccgga gcgaaacagc cgcgaccaga atccccgctt ttttcctgtg ccagcgcgtc
     5701 agccagacgg ctaatttcgg cctgtagttg ttccctctcc tcatttcgca ggcggttttc
     5761 tgcttcccgc gccatcttgt cttcaagcat tagggtaaca gtctgctgca gagcgtccag
     5821 tttctgctga atgacgtcta gctgagcatt ttccgcctgg ctaacgacag atttggagtg
     5881 tccctccttg tgcctttttg gtgtctcaga agtgcgcagc tcgccatagg cccgaatcag
     5941 ttcactggtc tcgaactccc ggcgatcatt ttttcctgtg cgatagctga caaggccttt
     6001 agccatgtca cgatataatt gcgagcgcga ctttcctgtt aatttcagtg tctcttgaac
     6061 tgtgtgccat gccataaaag tgacagtgtc tcctgtgtgt accgtattgt aacagcagaa
     6121 catattactg ttttaacaca aaaggtctga ggctgcccgt gaggcgtgaa aaatacacaa
     6181 aaaacctgtt gacggtgtgg ttttgacggg cgtagtattt cgaatactgt atataaacac
     6241 attgttataa atacagtttt gctgttttta aaagtcaaag aggataattt t
//
