LOCUS       NZ_CP109883             3255 bp    DNA     circular CON 22-NOV-2023
DEFINITION  Escherichia coli strain EC488 plasmid pEC488-9, complete sequence.
ACCESSION   NZ_CP109883
VERSION     NZ_CP109883.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN30088785
            Assembly: GCF_025946585.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3255)
  AUTHORS   He,X.
  TITLE     Carbapenemase - producing -Escherichia coli EC488
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3255)
  AUTHORS   He,X.
  TITLE     Direct Submission
  JOURNAL   Submitted (02-AUG-2022) Clinical Laboratory, Sir Run Run Shaw
            Hospital, Zhejiang University School of Medicine, Qingchun,
            Hangzhou, Zhejiang 310000, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: SPAdes v. v0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100.0x
            Sequencing Technology             :: Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 11/22/2023 18:08:23
            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)                     :: 5,510
            CDSs (total)                      :: 5,391
            Genes (coding)                    :: 5,160
            CDSs (with protein)               :: 5,160
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 92
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 231
            CDSs (without protein)            :: 231
            Pseudo Genes (ambiguous residues) :: 0 of 231
            Pseudo Genes (frameshifted)       :: 78 of 231
            Pseudo Genes (incomplete)         :: 160 of 231
            Pseudo Genes (internal stop)      :: 44 of 231
            Pseudo Genes (multiple problems)  :: 46 of 231
            Pseudo Genes (short protein)      :: 5 of 231
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP109883.1.
            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..3255
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="EC488"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pEC488-9"
                     /geo_loc_name="China"
                     /lat_lon="27 N 110 E"
                     /collection_date="2021-08-04"
                     /collected_by="Xianhong He"
     gene            complement(129..323)
                     /locus_tag="NQ150_RS27415"
                     /old_locus_tag="NQ150_27415"
     CDS             complement(129..323)
                     /locus_tag="NQ150_RS27415"
                     /old_locus_tag="NQ150_27415"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041627.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_001041633.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EELQNSIQVRFETESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(1467..1748)
                     /locus_tag="NQ150_RS27420"
                     /old_locus_tag="NQ150_27420"
     CDS             complement(1467..1748)
                     /locus_tag="NQ150_RS27420"
                     /old_locus_tag="NQ150_27420"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000586174.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RelE/ParE family
                     toxin"
                     /protein_id="WP_000586174.1"
                     /translation="MIINIKHKGLRKFAETGNNAGIPQQFTQRLKLILTALSTATNLQD
                     MMDLKALRCHPLKGDRQGEYSLEVNGNWRVVFKLEEPNVFDVDLEDYH"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     gene            2092..2388
                     /locus_tag="NQ150_RS27425"
                     /old_locus_tag="NQ150_27425"
     CDS             2092..2388
                     /locus_tag="NQ150_RS27425"
                     /old_locus_tag="NQ150_27425"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000609270.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="HigA family addiction module antitoxin"
                     /protein_id="WP_000609270.1"
                     /translation="MINLVDPVHPGVFIREMFMEPFEISAADLSEKLHVSPSTLSRVLN
                     GKADLSVEMALRLSRVLGRSAESWINMQTQYSLNASRKSPNVIKELDELVPIF"
                     /name="HigA family addiction module antitoxin"
     gene            complement(2619..2731)
                     /locus_tag="NQ150_RS27580"
                     /pseudo=""
     CDS             complement(2619..2731)
                     /locus_tag="NQ150_RS27580"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /name="replication initiation protein"
     Typing          360..458
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="6.22e-45"
     Typing          583..838
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.512"
                     /coverage="89.0"
                     /evalue="1.21e-116"
     Typing          complement(2660..3217)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.286"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 agtatacact ccgctatcgc tacgtgactg ggtcagggct tcgccccgac acccgctgac
       61 gcgccctggc gggcttgtcc gcgagcgttt tcggcagcag acaagcccgc cagggcgcgt
      121 cagcttcgtt atgttcctgt ttcactttcg gtctcaaagc gaacctggat gctgttctgg
      181 agttcttccg cgagttcgtg cagtcgttcg cacatggccg cctgttcgtc ggcatccaga
      241 gcatccagtt tttcaagcag tgtcaggctc tggcttttga taaatcgcgc catattcagc
      301 gcagtttgtt gctgtttgtt caccttccgt tgttctccgt cagtaccggg tgtcgggtgg
      361 accctgacca ggtggtaatt gtaagacgtt gcgggcgacg gtattacaat tgcacatcct
      421 gtcctgtttt tttaggacgt atcatggcac agcatatcaa ctgataaata atccctgtgc
      481 agtgcagccg ctgttgcata aaatttcgct ctgcgtcgag tgtttcttaa tcaataattc
      541 cgctgatact ccggaaaaac gcgagtctgt tctcatgcct gaaatgccca caccccacgc
      601 aaaaacaatt ttttgctgat ttttctttat aaatagagag ttatgacaaa ttagttcttc
      661 ttgctctctt tgtgatattt aaaaaagcgg tgtcggcgcg gtgttgtagc tgcgccaaca
      721 ccgcttttta ggggtggtac tgactatttt cataaaaaac atcattttat attaggggtg
      781 ctgctagcgg cgcggtgtgt ttttttacag gacgcccctg ggggcgctgc taggggtgtc
      841 tgttcagata tgtagcaatg agtcagggat tcacgaactg aaaatgtccg aaaatgtgtc
      901 tcatgggcac cgtatgcgcc caaaccgatc gccattcact ttcatgcata gctatgcagt
      961 gagctgaaag cgatcctgac gcatttttcc ggttttcgct tggtaaaaca tctctttttg
     1021 cggtgttcgc ggcagaatcg cgttcagcgc gttttagcgg tgcgcgtaat gcgacgttat
     1081 ggtaaatgct gtgatttacg ggatggtttt atctatgttg atatcaatac cacctcctat
     1141 ggaggtggct tacaccgatt tttccttgtt gtctgtttca gaacagatag aggctttttt
     1201 ggcaattatc caaccactat tgatagtgtt tattactact tagataactg agcctttact
     1261 gtatctgccc ctgcaagcag gaacccaaca gttaagaacc acccccagcc attgatacct
     1321 tttagcgcta gaattgctgc gctaatgatg gctgctatag ggactatctg gtacagaaaa
     1381 tacttcatat aacttacccc gaggttttgc ttttttatga gaccctaaag catcgatact
     1441 gtcactttga tgctttaagg accttcttag tgataatcct cgagatccac gtcaaagacg
     1501 ttaggttctt cgagcttaaa cactacgcgc cagtttccat tgacctctaa cgaatactct
     1561 ccttgacggt ctcccttcaa tggatggcag cgcaatgcct ttaaatccat catatcctgc
     1621 aagttcgtcg ctgtgcttaa ggctgttagg atcagcttca gacgttgagt aaactgttgc
     1681 ggaattcctg cgttgttacc tgtttcggca aacttacgca aacctttatg cttgatattt
     1741 atgatcatta atcaccatcc catatttgtt tagatagaaa catcgcagtt tatttttccg
     1801 gttcatccgt atttccattg caaacccctt gctctatttg aataaatgac gtaggtttta
     1861 cttaaccaag tcgcatttta atctgttgac attggtttga tgcgctgtac aatgccgggg
     1921 ccttgaattt cacatcaagt acccacatca taaggaatga ttagacgcac caatgtgcat
     1981 cataatgtca ttcttttttt agtcaacaat gagttgcgtt atgcgcaatg cgcaatctga
     2041 aaacgcaata ggcctatctt tttaaaacta atataggctt cagaggaagg tatgattaat
     2101 cttgtcgatc cagtacatcc aggggttttt atccgtgaga tgtttatgga accgtttgaa
     2161 atatcagccg cggacctgtc tgaaaaactg catgtatcac cttccactct aagtagagtg
     2221 ctgaatggaa aagctgattt aagtgttgag atggcattaa ggctttctcg agttcttggt
     2281 cgcagtgccg agtcgtggat aaacatgcag actcaataca gtcttaacgc gagcaggaag
     2341 tcacctaatg tcattaagga attagatgaa ttggttccta tattttgaga aaagaaaagg
     2401 ccgctatatg cggccttttt ctgtcttgac tctcaggcaa ctggatcgta tcgtttctcg
     2461 taaacgaaaa aaccacccgg caaggtggtt ttttcgaagg ttcagtaacc ggcaagtttc
     2521 tgaaccaggg taactggctt ggaggagcgc agtcaccaaa acttgttctt tcagtttagc
     2581 cttaactggc gcataacttc aagactaact cctctaaatc agttaccagt ggctgctgcc
     2641 aatggtgttt tgcatgtctt tccgggttgg actcaagatg atagttaccg gataaggcgc
     2701 agcggtcggg ctgaacgggg ggttcgtgca cacagcccag cttggagcga acgacctaca
     2761 ctgaaccgag atacctacag cgtgagctat gagaaagcgc cacgcttccc gaagggagaa
     2821 aggcggacag gtatccggta agcggcaggg tcggaacagg agagcgcacg agggagccac
     2881 cagggggaaa cgtctggtat ctttaagtcc tgtcgggttt cgccacctct gacttgagcg
     2941 tcgatttctg tgatgctcgt caggggggcg gagcctatgg aaaaacgcct gcggcgcggc
     3001 cttcttcctg ttcttggtct tttgctcaca tgttctttcc ggccttatcc cctgattctg
     3061 tagataaccg tgctgccgtt tttgtgtaag tcagtaccgc tcgccgcagc cgaacgaccg
     3121 agcgtagcga gtcagtgagc gaggaagcgg aaaagcgcct ggacgcgcat tttctcctta
     3181 cgcatctgtg cggaatttca cacccggcat ggggcacttt tcatacaatc tgcactgatg
     3241 ccgcatagtt aagcc
//
