LOCUS       NZ_AP027610             2579 bp    DNA     circular CON 04-APR-2024
DEFINITION  Escherichia coli strain LR-71-1 plasmid pLR-71-1_11, complete
            sequence.
ACCESSION   NZ_AP027610
VERSION     NZ_AP027610.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00562543
            Assembly: GCF_036498465.1
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  JOURNAL   Unpublished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 2579)
  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                   :: 84x
            Sequencing Technology :: MGI DNBSEQ-G400RS; ONT MinION Mk1c
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_036498465.1-RS_2024_04_04
            Annotation Date                   :: 04/04/2024 00:05:36
            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)                     :: 5,144
            CDSs (total)                      :: 5,026
            Genes (coding)                    :: 4,742
            CDSs (with protein)               :: 4,742
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 284
            CDSs (without protein)            :: 284
            Pseudo Genes (ambiguous residues) :: 0 of 284
            Pseudo Genes (frameshifted)       :: 78 of 284
            Pseudo Genes (incomplete)         :: 199 of 284
            Pseudo Genes (internal stop)      :: 46 of 284
            Pseudo Genes (multiple problems)  :: 38 of 284
            Pseudo Genes (short protein)      :: 3 of 284
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP027610.1.
            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..2579
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="LR-71-1"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pLR-71-1_11"
                     /geo_loc_name="Ecuador:Santo Domingo"
                     /collection_date="2019"
     gene            complement(join(2528..2579,1..185))
                     /locus_tag="AABJ98_RS25705"
     CDS             complement(join(2528..2579,1..185))
                     /locus_tag="AABJ98_RS25705"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001676031.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_012772745.1"
                     /translation="MARLTNLTPAEKKFLDDAVAAAERASGKKLNQPNRHIVLNRARAQ
                     IELQRYADRQRALREDERQQSDFAWSRPRAPRR"
                     /name="hypothetical protein"
     gene            <1253..1408
                     /locus_tag="AABJ98_RS25710"
                     /old_locus_tag="VEE28_49540"
                     /pseudo=""
     CDS             <1253..1408
                     /locus_tag="AABJ98_RS25710"
                     /old_locus_tag="VEE28_49540"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_707212.3"
                     /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"
     gene            1502..2146
                     /locus_tag="AABJ98_RS25715"
                     /old_locus_tag="VEE28_49550"
     CDS             1502..2146
                     /locus_tag="AABJ98_RS25715"
                     /old_locus_tag="VEE28_49550"
                     /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"
     ARG             1503..2143
                     /name="qnrB19"
                     /gene="qnrB19"
                     /gene_name="quinolone resistance pentapeptide repeat
                     protein QnrB19"
                     /tool="amrfinderplus"
                     /drug_class="QUINOLONE"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          complement(351..524)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.5600000000000002e-86"
     Typing          503..994
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.51"
                     /coverage="81.0"
                     /evalue="0.0"
ORIGIN
        1 tcatcctcac gtaatgcacg ctggcggtcg gcgtaacgct gcaactcaat ttgcgcacgc
       61 gctctgttca ggacgatgtg ccggttaggc tgatttagct ttttacctga cgctctttca
      121 gctgcggcaa cagcatcatc aagaaatttt ttctctgcag gcgtcaagtt tgtcagtctg
      181 gccataacgt tctccagtca gaataaatca gcacagtctg ccagacacag tagaaacgat
      241 gaagcgccag cgacggtgaa aggcagtcag aaacggtgaa cgggagcgga ttttaatccg
      301 gtgccgtgag gcgttggaca agccgcaggc gcgtcattag cttttagccg gtttcggggc
      361 gcagccctga accagtcacg tagcgctagc ggagtgtata ctggctgact atgttggcac
      421 ggatgtggaa atcagtgaag tgcttcatgt agcaggagaa aaaaggcggc accagcgcgt
      481 cagcaggata tgtagtacag gatatattcc gcttcctcgc tcactgactc gctgcgctcg
      541 gtcgttcggc tgcggcgagc ggtgccggct tacaggcggg gcggaaattt cctgggagat
      601 accaggaagg agcttaacag ggaagagata aggccgcggc gaagccgttt ttccataggc
      661 tccgcccccc tgacaaacat catgaaatct gacgctcaaa tcagtggtgg cgaaacccga
      721 tgcggcttaa agataccagg cgtttccccc tggtggctcc ctcgtgctcc cccgcattcc
      781 tgcctttcgg tttaccggtg tcattccgct gttatggccg cgtttatctc attccacgcc
      841 tgacactcag ttccgcgaag gcagttcgct cctggatgga ctgtatgcac gaaccccccg
      901 ttcagtccga ctgctgcgcc ttatccggta actatcatct tgagtccaac ccggaaagac
      961 acgacttatc gccactggca gcagccactg gtaactgatt tagaggagtt agtcttgaag
     1021 ttatgcgcct gttaaggcta aactgaaaga acagatttgg ttactgcgct cctcgtaagc
     1081 cagttaccac ggttcaaaga gttgctgctc tgagaacctt cgaaaaaccg ccttgcaggg
     1141 cggttttttc gtttacagag caagagatta cgacgccaca gaaaggatct caagaagatc
     1201 cttcaccgta atggaaatct atccaatccg agcacatagg atacacatcg ttataacgct
     1261 ggatctgcgt gaattccagc agcagcaaga gaaagacttt ctacaaacca gcttacagca
     1321 ggctaaattt aaccagaaaa aagccgctga attactgggt ctgacttatc atcagctacg
     1381 tgccttgctg aagaaacacc agatctaata cgcatttgca ggtgtcatac tggcgggttt
     1441 gacgcataac gtcataaggt ttaccatggc gtcattactg tataaaaaca caggcataga
     1501 tatgactctg gcattagttg gcgaaaaaat tgacagaaat cgcttcaccg gtgagaaagt
     1561 tgaaaatagt acatttttta actgcgattt ttcaggtgcc gacctgagcg gcactgaatt
     1621 tatcggctgc cagttctatg atcgcgaaag tcagaaaggg tgcaatttta gtcgcgcaat
     1681 gctgaaagat gccattttca aaagctgtga tttatcaatg gcagatttcc gcaacgtcag
     1741 tgccttgggc attgaaattc gccactgccg cgcacaaggc gcagatttcc gcggtgcaag
     1801 ctttatgaat atgatcacca cgcgcacctg gttttgcagc gcatatatca ctaatactaa
     1861 tctaagctac gccaattttt cgaaagtcgt gttggaaaag tgtgagctgt gggaaaaccg
     1921 ctggatgggg actcaggtac tgggtgcgac gttcagtggt tcagatctct ccggcggcga
     1981 gttttcgact ttcgactggc gagcagcaaa cttcacacat tgcgatctga ccaattcgga
     2041 gttaggtgac ttagatattc ggggtgttga tttacaaggc gttaagttag acagctacca
     2101 ggcatcgttg ctcatggagc ggcttggcat cgctgtgatt ggttagttca gcgtttacac
     2161 cgggagatgc gtttgacgat ttacttttac ccgcgatcat cgcgtttatt gagtttatta
     2221 tttatctatg cgattccgat gaaaaattcg cacgaaaata tggctaactc atagcaaaaa
     2281 aaaagccccc taagggcttt tttttgtacc tgacggtcag accgattaaa cataacatcc
     2341 cttgcccgca cccccgcagg cgccctcagc gcaatcctgc tgcatcaggg ccgtttccag
     2401 cacctttcct caccagtatc ccggaaaaac gcccctgatg atttctgcgc gactgcatgg
     2461 ctatgcacgc aggtgaatgg caggtgattt cgcagcgtca gcaccactaa accgccaaaa
     2521 gccaaaatca gcggcgcggc gcgcgcggac gtgaccaggc aaaatcggac tgctgccgc
//
