LOCUS       NZ_AP027518             3071 bp    DNA     circular CON 04-APR-2024
DEFINITION  Escherichia coli strain LR-29-1 plasmid pLR-29-1_3, complete
            sequence.
ACCESSION   NZ_AP027518
VERSION     NZ_AP027518.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00562505
            Assembly: GCF_036495745.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1
  AUTHORS   Hoang,H.T.T., Yamamoto,M., Calvopina,M., Bastidas-Caldes,C.,
            Khong,D.T., Nguyen,T.N. and Yamamoto,Y.
  TITLE     Comparative genome analysis of colistin-resistant Escherichia coli
            strains possessing mcr isolated in Ecuador and Vietnam
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3071)
  AUTHORS   Yamamoto,Y. and Hoang,H.T.T.
  TITLE     Direct Submission
  JOURNAL   Submitted (22-MAR-2023) Contact:Yoshimasa Yamamoto The United
            Graduate School of Drug Discovery and Medical Information Sciences,
            Gifu University; Yanagido 1-1, Gifu 501-1194, Japan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8
            Genome Coverage                   :: 221x
            Sequencing Technology :: MGI DNBSEQ-G400RS; ONT MinION Mk1c
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_036495745.1-RS_2024_04_03
            Annotation Date                   :: 04/03/2024 23:58:59
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,759
            CDSs (total)                      :: 4,639
            Genes (coding)                    :: 4,440
            CDSs (with protein)               :: 4,440
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 199
            CDSs (without protein)            :: 199
            Pseudo Genes (ambiguous residues) :: 0 of 199
            Pseudo Genes (frameshifted)       :: 52 of 199
            Pseudo Genes (incomplete)         :: 143 of 199
            Pseudo Genes (internal stop)      :: 32 of 199
            Pseudo Genes (multiple problems)  :: 30 of 199
            Pseudo Genes (short protein)      :: 4 of 199
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP027518.1.
            Annotated by DFAST https://dfast.ddbj.nig.ac.jp/
            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..3071
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="LR-29-1"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pLR-29-1_3"
                     /geo_loc_name="Ecuador:Santo Domingo"
                     /collection_date="2019"
     gene            complement(2124..2768)
                     /locus_tag="AABJ68_RS23780"
                     /old_locus_tag="VEE08_45430"
     CDS             complement(2124..2768)
                     /locus_tag="AABJ68_RS23780"
                     /old_locus_tag="VEE08_45430"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017900990.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="quinolone resistance pentapeptide repeat protein
                     QnrB19"
                     /protein_id="WP_012954666.1"
                     /translation="MTLALVGEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQF
                     YDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGADFRGASFMNM
                     ITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFST
                     FDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDSYQASLLMERLGIAVIG"
                     /name="quinolone resistance pentapeptide repeat protein
                     QnrB19"
     gene            complement(2862..>3017)
                     /locus_tag="AABJ68_RS23785"
                     /pseudo=""
     CDS             complement(2862..>3017)
                     /locus_tag="AABJ68_RS23785"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_309907.2"
                     /GO_function="GO:0043565 - sequence-specific DNA binding
                     [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="helix-turn-helix domain-containing protein"
                     /name="helix-turn-helix domain-containing protein"
     ARG             complement(2128..2768)
                     /name="qnrB19"
                     /gene="qnrB19"
                     /gene_name="quinolone resistance pentapeptide repeat
                     protein QnrB19"
                     /tool="amrfinderplus"
                     /drug_class="QUINOLONE"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          676..849
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.5600000000000002e-86"
     Typing          complement(206..697)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.51"
                     /coverage="81.0"
                     /evalue="0.0"
ORIGIN
        1 tcttcttgag atcctttctg tggcgtcgta atctcttgct ctgtaaacga aaaaaccgcc
       61 ctgcaaggcg gtttttcgaa ggttctcaga gcagcaactc tttgaaccgt ggtaactggc
      121 ttacgaggag cgcagtaacc aaatctgttc tttcagttta gccttaacag gcgcataact
      181 tcaagactaa ctcctctaaa tcagttacca gtggctgctg ccagtggcga taagtcgtgt
      241 ctttccgggt tggactcaag atgatagtta ccggataagg cgcagcagtc ggactgaacg
      301 gggggttcgt gcatacagtc catccaggag cgaactgcct tcgcggaact gagtgtcagg
      361 cgtggaatga gataaacgcg gccataacag cggaatgaca ccggtaaacc gaaaggcagg
      421 aatgcggggg agcacgaggg agccaccagg gggaaacgcc tggtatcttt aagccgcatc
      481 gggtttcgcc accactgatt tgagcgtcag atttcatgat gtttgtcagg ggggcggagc
      541 ctatggaaaa acggcttcgc cgcggcctta tctcttccct gttaagctcc ttcctggtat
      601 ctcccaggaa atttccgccc cgcctgtaag ccggcaccgc tcgccgcagc cgaacgaccg
      661 agcgcagcga gtcagtgagc gaggaagcgg aatatatcct gtactacata tcctgctgac
      721 gcgctggtgc cgcctttttt ctcctgctac atgaagcact tcactgattt ccacatccgt
      781 gccaacatag tcagccagta tacactccgc tagcgctacg tgactggttc agggctgcgc
      841 cccgaaaccc gctaacaacc tctctgctac tggatatcac cccatgccat ctgaatatga
      901 tgaacaacgg ggttcgactg atacgcagct tcccggcgaa tatgaccttt ttgatttaat
      961 ggcgaaggtt actgaagaga tcctgcatgc ccctgtggat tctgggccgc ctgtcggccg
     1021 ggaagcgtta tagctttttc gcttgcccgc gtacgtggta atacgccggt attacctttt
     1081 atttctttat tttcatgtaa ttacagtggg tttttaatac ctgggtatta ctcgtgaaaa
     1141 cgaaacatta cttttttttc ttttaattca tgcagttgcg atgaaaatcg cggctgcgtt
     1201 aggtgtatga ccattttgag gttgaaaaat aatcaaccat ggcgggtgat ttacgcaggt
     1261 taaggggaga tcgtgacaaa aaaaagcgtt cctcactgta tcgttcatgc ctgcatgaac
     1321 gggttattct tcctgactac agaattacat cgctccttca gttcatacat cacttttaca
     1381 acacttttac aacactcctt cggcctgtac atcactttta caacactttt gcatcacttt
     1441 tacatcattt atacatcact tttacatcat tccttcagct catacgtcac tttcatcctc
     1501 tgtgccattt gtacatcacc cccttcctga acgtgctgac agcgggtttt ccggctgcgc
     1561 cggcaacgct tcacggccac gcaataaatt gcgtccccgt tcaccgtttt cggatgggaa
     1621 gaacgccgga aacaggactt cccctggctg aatggtgtga atttccgcgc tatgcacttg
     1681 cgcgcatact catgcatgcc gtaaaaacag agcctgcgcg tttctggcgg gttttcgggt
     1741 ggtttgttgc ctgttttacc ggtttcccgt cagaaacgcc ctcagagcct ctcaggcggt
     1801 gcacgcaagg gatgttatgt ttaatcggtc tgaccgtcag gtacaaaaaa aagcccttag
     1861 ggggcttttt ttttgctatg agttagccat attttcgtta agacatggct tcatgattcg
     1921 ggagtggtta ttcgttgttc tcgcgaaaat gaattggtta gatattcatc aaattcctgt
     1981 ccagaatgca gcattagatg gcatgtcgtt gatgcggtag gtcaggatat tcgtccactg
     2041 gagaaaacgt ttcacaatgc ttgccaggag tcgtactggt taaaagtaaa tcgtcaaacg
     2101 catctcccgg tgtaaacgct gaactaacca atcacagcga tgccaagccg ctccatgagc
     2161 aacgatgcct ggtagctgtc taacttaacg ccttgtaaat caacaccccg aatatctaag
     2221 tcacctaact ccgaattggt cagatcgcaa tgtgtgaagt ttgctgctcg ccagtcgaaa
     2281 gtcgaaaact cgccgccgga gagatctgaa ccactgaacg tcgcacccag tacctgagtc
     2341 cccatccagc ggttttccca cagctcacac ttttccaaca cgactttcga aaaattggcg
     2401 tagcttagat tagtattagt gatatatgcg ctgcaaaacc aggtgcgcgt ggtgatcata
     2461 ttcataaagc ttgcaccgcg gaaatctgcg ccttgtgcgc ggcagtggcg aatttcaatg
     2521 cccaaggcac tgacgttgcg gaaatctgcc attgataaat cacagctttt gaaaatggca
     2581 tctttcagca ttgcgcgact aaaattgcac cctttctgac tttcgcgatc atagaactgg
     2641 cagccgataa attcagtgcc gctcaggtcg gcacctgaaa aatcgcagtt aaaaaatgta
     2701 ctattttcaa ctttctcacc ggtgaagcga tttctgtcaa ttttttcgcc aactaatgcc
     2761 agagtcatat ctatgcctgt gtttttatac agtaatgacg ccatggtaaa ccttatgacg
     2821 ttatgcgtca aacccgccag tatgacacct gcaaatgcgt attagatctg gtgtttcttc
     2881 agcaaggcac gtagctgatg ataagtcaga cccagtaatt cagcggcttt tttctggtta
     2941 aatttagcct gctgtaagct ggtttgtaga aagtctttct cttgctgctg ctggaattca
     3001 cgcagatcca gcgttataac gatgtgtatc ctatgtgctc ggattggata gatttccatt
     3061 acggtgaagg a
//
