LOCUS       NZ_CP084904             4363 bp    DNA     circular CON 17-NOV-2023
DEFINITION  Escherichia coli strain EC20 plasmid pEC22-NDM-5, complete sequence.
ACCESSION   NZ_CP084904
VERSION     NZ_CP084904.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN21906625
            Assembly: GCF_020535205.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4363)
  AUTHORS   Huang,J.
  TITLE     Whole genome sequence of EC22, an NDM-5-, CTX-M-15-, and
            blaOXA-1-co-producing Escherichia coli ST361 clinical isolate from
            China
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4363)
  AUTHORS   Huang,J.
  TITLE     Direct Submission
  JOURNAL   Submitted (30-SEP-2021) Department of Clinical Laboratory, Jinhua
            Central Hospital, Mingyue street 351, Jinhua, Zhejiang 321000, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: No
            Genome Coverage                   :: 200.0x
            Sequencing Technology             :: Oxford Nanopore PromethION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 11/17/2023 09:33:46
            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)                     :: 5,202
            CDSs (total)                      :: 5,084
            Genes (coding)                    :: 4,807
            CDSs (with protein)               :: 4,807
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 7
            Pseudo Genes (total)              :: 277
            CDSs (without protein)            :: 277
            Pseudo Genes (ambiguous residues) :: 0 of 277
            Pseudo Genes (frameshifted)       :: 86 of 277
            Pseudo Genes (incomplete)         :: 178 of 277
            Pseudo Genes (internal stop)      :: 56 of 277
            Pseudo Genes (multiple problems)  :: 40 of 277
            Pseudo Genes (short protein)      :: 4 of 277
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP084904.1.
            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..4363
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="EC20"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pEC22-NDM-5"
                     /geo_loc_name="China: Jinhua"
                     /collection_date="2019-10-18"
                     /genotype="ST11"
     gene            <3..131
                     /gene="cutA"
                     /locus_tag="LHL15_RS26080"
                     /pseudo=""
     CDS             <3..131
                     /gene="cutA"
                     /locus_tag="LHL15_RS26080"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004201171.1"
                     /GO_process="GO:0010038 - response to metal ion [Evidence
                     IEA]"
                     /note="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="divalent cation tolerance protein CutA"
                     /name="cutA"
     gene            136..>510
                     /locus_tag="LHL15_RS25785"
                     /pseudo=""
     CDS             136..>510
                     /locus_tag="LHL15_RS25785"
                     /inference="COORDINATES: protein motif:HMM:NF022853.3"
                     /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="protein-disulfide reductase DsbD family protein"
                     /name="protein-disulfide reductase DsbD family protein"
     gene            <610..1167
                     /locus_tag="LHL15_RS25790"
                     /pseudo=""
     CDS             <610..1167
                     /locus_tag="LHL15_RS25790"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_006399920.1"
                     /note="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="twin-arginine translocation (TAT) pathway signal
                     sequence domain protein"
                     /name="twin-arginine translocation (TAT) pathway signal
                     sequence domain protein"
     gene            complement(1178..1816)
                     /locus_tag="LHL15_RS25795"
     CDS             complement(1178..1816)
                     /locus_tag="LHL15_RS25795"
                     /EC_number="5.3.1.24"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004201168.1"
                     /GO_function="GO:0004640 - phosphoribosylanthranilate
                     isomerase activity [Evidence IEA]"
                     /GO_process="GO:0000162 - tryptophan biosynthetic process
                     [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="phosphoribosylanthranilate isomerase"
                     /protein_id="WP_004201168.1"
                     /translation="MPAKIKICGISTPEALDATIAARADYAGLVFYPASPRAVTSNVAG
                     ALTSRAAGQIAMVGLFVDADDAVIADALVAAKLNALQLHGSESPERVAQLRARFGKPVW
                     KALPVASASDVARAAAYAGAADLILFDAKTPKGALPGGMGLAFDWSLLAGYRGALPWGL
                     AGGLNPTNVAEAIARTGAPLVDTSSGVESAPGVKDTDKITNFAFAVRLA"
                     /name="phosphoribosylanthranilate isomerase"
     gene            complement(1821..2186)
                     /gene="ble"
                     /locus_tag="LHL15_RS25800"
     ARG             complement(1825..2186)
                     /name="ble"
                     /gene="ble"
                     /gene_name="bleomycin binding protein Ble-MBL"
                     /tool="amrfinderplus"
                     /drug_class="BLEOMYCIN"
                     /identity="100.0"
                     /coverage="100.0"
     gene            complement(2190..3002)
                     /locus_tag="LHL15_RS25805"
     CDS             complement(2190..3002)
                     /locus_tag="LHL15_RS25805"
                     /EC_number="3.5.2.6"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_032492661.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="subclass B1 metallo-beta-lactamase NDM-5"
                     /protein_id="WP_023408309.1"
                     /translation="MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQR
                     FGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLLVDTAWTDDQTAQILNW
                     IKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGLVAAQHSLTF
                     AANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLG
                     DADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR"
                     /name="subclass B1 metallo-beta-lactamase NDM-5"
     gene            3237..4217
                     /locus_tag="LHL15_RS25810"
     CDS             3237..4217
                     /locus_tag="LHL15_RS25810"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_416498.2"
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /GO_process="GO:0006313 - DNA transposition [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="IS5-like element IS5 family transposase"
                     /protein_id="WP_000019402.1"
                     /translation="MSHQLTFADSEFSSKRRQTRKEIFLSRMEQILPWQNMVEVIEPFY
                     PKAGNGRRPYPLETMLRIHCMQHWYNLSDGAMEDALYEIASMRLFARLSLDSALPDRTT
                     IMNFRHLLEQHQLARQLFKTINRWLAEAGVMMTQGTLVDATIIEAPSSTKNKEQQRDPE
                     MHQTKKGNQWHFGMKAHIGVDAKSGLTHSLVTTAANEHDLNQLGNLLHGEEQFVSADAG
                     YQGAPQREELAEVDVDWLIAERPGKVRTLKQHPRKNKTAINIEYMKASIRAKVEHPFRI
                     IKRQFGFVKARYKGLLKNDNQLAMLFTLANLFRADQMIRQWERSH"
                     /name="IS5-like element IS5 family transposase"
     ARG             complement(2194..3002)
                     /name="blaNDM-5"
                     /gene="blaNDM-5"
                     /gene_name="subclass B1 metallo-beta-lactamase NDM-5"
                     /tool="amrfinderplus"
                     /drug_class="BETA-LACTAM"
                     /identity="100.0"
                     /coverage="100.0"
     ARG             complement(1822..2186)
                     /name="BRP(MBL)"
                     /gene="BRP(MBL)"
                     /gene_name="Bleomycin resistant protein"
                     /tool="rgi"
                     /drug_class="glycopeptide antibiotic"
                     /identity="100.0"
                     /coverage="100.0"
ORIGIN
        1 cccccgccct gcaggaacgc ctgcgccaac tgcatcccta cgaactcccg gagctgctcg
       61 cggtcgaagc cgcgtccggc ctgcccgaat acctgcaatg gctggccgcc gagagccgac
      121 cggtaaactg agccaatgac cgcatccacg atccgcctgc gccgctggct ggccgggctc
      181 gccctgctgc ttgcgctgcc cgcgacctcg gccgtcgccc aggacttcga actgccgccg
      241 gtcgacgagg tcttcgtcct gtccgcgcag gccaccgcgc cggaccgcat cgaggtgcgc
      301 tggcggatcg ccgacggcta ttacctgtac cggcaccgca cctcggtcaa ggccgatgcc
      361 gccttcaccg gcgcgaccat ggcgctgccg aagggcaagg cctaccgcga cgaattcttc
      421 ggcgacgtcg aaacctaccg caaggaattg ctcggcaccc tcaccggcac gcccgcggcc
      481 ggcgcgagcg cgaccaccct gaccgtgaag taccagggct gcgccgatgc cggcgtgtgc
      541 tacccgccgc agacccgcac cctgaaggtc gcgttgccgg gcgaagcggg cgctggcggc
      601 ttcggctgta aggcgcgcgg gctgcatgat tatgtcgtca agaacggctc tgccgatcat
      661 cccaacgccg aggtgaaatt cgcactgggt gatgtggtca acaccatgat cggctgcact
      721 aatggtgaaa cgatcatgct gtgccacgac acctcgctgc cgcgccccta ttctctcggc
      781 tttcgggtgc aaggcaccga ggggctgtgg atggacgtca acaagtcgat ctatctggag
      841 ggcaagagcc cacagccgca ccgctgggag cctgccgagg gctggtttgc gaaatacgat
      901 cacccgctat ggaaacgcta cgccgatctg gcggcagggg ccgggcatgg cgggatggac
      961 tggttcgtga tccacgcttt tgtcgaggcg ctgaaggcca aggccccgat gccaatcgac
     1021 atttacgacg cgctggcctg gagcgcgatc acgcctctgt cggaacaatc gattgctgag
     1081 ggcaatcgca cgttagattt tcccgacttc acccgagggc agtggcgcac ccgcaagccg
     1141 atctttgcgc tgaacgacgc ctattgatcg acgcgattta ggccaagcgc accgcaaagg
     1201 cgaaattggt aatcttgtcg gtatccttga cgcccggcgc gctttcgacg ccgctggagg
     1261 tatcgaccag cggcgctccg gtgcgcgcaa tcgcctcggc aacattcgtc ggatttagcc
     1321 cgcctgccag cccccacggc aaggcaccgc gatatccggc cagcagcgac cagtcgaacg
     1381 ccaaccccat gccgccgggc agcgcgcctt tgggggtctt ggcgtcgaac aagatcaagt
     1441 ccgccgcccc ggcataggct gcggcgcgtg cgacatcgct ggcgctggcg acgggcagcg
     1501 ccttccacac cggcttgcca aaccgcgcgc gcaactgggc cacgcgttcg ggcgattccg
     1561 aaccgtgcag ctgcagcgcg ttcagcttgg ctgccaccag tgcgtcggcg atgacagcat
     1621 catccgcatc gacgaacaaa ccgaccatgg cgatctggcc agctgcgcgc gatgtcaaag
     1681 cgcccgcgac attcgacgta accgcacggg gcgacgctgg atagaacacc aacccggcat
     1741 agtccgcccg cgccgcgatg gtcgcatcga gcgcctcggg tgtgctgatc ccgcaaatct
     1801 tgattttcgc gggcatgcgg tcagtcgggg ttctggatca gccgcaccag cgtgcagtcg
     1861 ggatcgatca ggtagccgat cctcaggccg ctcgcctcca gttgcggagc tttgaagcgc
     1921 ggccagccgg tgcttttttc ctcggctccc gccgcgttca ccaatgccac catggcatcg
     1981 agatcatcca accgcaggca acagccgaac gagctcgtag ctgggtcgag gtcaggatag
     2041 gggaagaatt cgagctgcaa accgccgcgc tgcaggatca tccagccgcg atccttccaa
     2101 ctcgtcgcaa agcccagctt cgcataaaac gcctctgtca catcgaaatc gcgcgatggc
     2161 agattggggg tgacgtggtc agccatggct cagcgcagct tgtcggccat gcgggccgta
     2221 tgagtgattg cggcgcggct atcgggggcg gaatggctca tcacgatcat gctggccttg
     2281 gggaacgccg caccaaacgc gcgcgctgac gcggcgtagt gctcagtgtc ggcatcaccg
     2341 agattgccga gcgacttggc cttgctgtcc ttgatcaggc agccaccaaa agcgatgtcg
     2401 gtgccgtcga tcccaacggt gatattgtca ctggtgtggc cggggccggg gtaaaatacc
     2461 ttgagcgggc caaagttggg cgcggttgct ggttcgaccc agccattggc ggcgaaagtc
     2521 aggctgtgtt gcgccgcaac cagcccctct tgcggggcaa gctggttcga caacgcattg
     2581 gcataagtcg caatccccgc cgcatgcagc gcgtccatac cgcccatctt gtcctgatgc
     2641 gcgtgagtca ccaccgccag cgcgaccggc aggttgatct cctgcttgat ccagttgagg
     2701 atctgggcgg tctggtcatc ggtccaggcg gtatcgacca acagcacgcg gccgccatcc
     2761 ctgacgatca aaccgttgga agcgactgcc ccgaaacccg gcatgtcgag ataggaagtg
     2821 tgctgccaga cattcggtgc gagctggcgg aaaaccagat cgccaaaccg ttggtcgcca
     2881 gtttccattt gctggccaat cgtcgggcgg atttcaccgg gcatgcaccc gctcagcatc
     2941 aatgcagcgg ctaatgcggt gctcagcttc gcgaccgggt gcataatatt gggcaattcc
     3001 atcaagtttt ccttttattc agcattaaaa accccgcaaa tgcgaggcct agtaaataga
     3061 tgatcttaat ttggttcact gtagcaaaaa tatggggcga attcaaacat gaggtgcgac
     3121 agtttcaaaa gccatatgat aatcaacaag ctgagcaaat ttctctaagg aaggtgcgaa
     3181 caagtccctg atatgagatc atgtttgtca tctggagcca tggaacaggg ttcatcatga
     3241 gtcatcaact taccttcgcc gacagtgaat tcagcagtaa gcgccgtcag accagaaaag
     3301 agattttctt gtcccgcatg gagcagattc tgccatggca aaacatggtg gaagtcatcg
     3361 agccgtttta ccccaaggct ggtaatggcc ggcgacctta tccgctggaa accatgctac
     3421 gcattcactg catgcagcat tggtacaacc tgagcgatgg cgcgatggaa gatgctctgt
     3481 acgaaatcgc ctccatgcgt ctgtttgccc ggttatccct ggatagcgcc ttgcctgacc
     3541 gcaccaccat catgaatttc cgccacctgc tggagcagca tcaactggcc cgccaattgt
     3601 tcaagaccat caatcgctgg ctggccgaag caggcgtcat gatgactcaa ggcaccttgg
     3661 tcgatgccac catcattgag gcacccagct cgaccaagaa caaagagcag caacgcgatc
     3721 cggagatgca tcagaccaag aaaggcaatc aatggcactt tggcatgaag gcccacattg
     3781 gtgtcgatgc caagagtggc ctgacccaca gcctagtcac caccgcggcc aacgagcatg
     3841 acctcaatca gctgggtaat ctgctgcatg gagaggagca atttgtctca gccgatgccg
     3901 gctaccaagg ggcgccacag cgcgaggagc tggccgaggt ggatgtggac tggctgatcg
     3961 ccgagcgccc cggcaaggta agaaccttga aacagcatcc acgcaagaac aaaacggcca
     4021 tcaacatcga atacatgaaa gccagcatcc gggccaaggt ggagcaccca tttcgcatca
     4081 tcaagcgaca gttcggcttc gtgaaagcca gatacaaggg gttgctgaaa aacgataacc
     4141 aactggcgat gttattcacg ctggccaacc tgtttcgggc ggaccaaatg atacgtcagt
     4201 gggagagatc tcactaaaaa ctggggataa cgccttaaat ggcgaagaaa cggtctaaat
     4261 aggctgattc aaggcattta cgggagaaaa aatcggctca aacatgaaga aatgaaatga
     4321 ctgagtcagc cgagaagaat ttccccgctt attcgcacct tcc
//
