LOCUS       NZ_AP027482             3071 bp    DNA     circular CON 04-APR-2024
DEFINITION  Escherichia coli strain LR-17-1 plasmid pLR-17-1_3, complete
            sequence.
ACCESSION   NZ_AP027482
VERSION     NZ_AP027482.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00562517
            Assembly: GCF_036494325.1
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  JOURNAL   Unpublished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                   :: 101x
            Sequencing Technology :: MGI DNBSEQ-G400RS; ONT MinION Mk1c
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_036494325.1-RS_2024_04_03
            Annotation Date                   :: 04/03/2024 23:40:27
            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)                     :: 4,622
            CDSs (total)                      :: 4,506
            Genes (coding)                    :: 4,306
            CDSs (with protein)               :: 4,306
            Genes (RNA)                       :: 116
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 200
            CDSs (without protein)            :: 200
            Pseudo Genes (ambiguous residues) :: 0 of 200
            Pseudo Genes (frameshifted)       :: 65 of 200
            Pseudo Genes (incomplete)         :: 129 of 200
            Pseudo Genes (internal stop)      :: 40 of 200
            Pseudo Genes (multiple problems)  :: 32 of 200
            Pseudo Genes (short protein)      :: 4 of 200
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP027482.1.
            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-17-1"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pLR-17-1_3"
                     /geo_loc_name="Ecuador:Santo Domingo"
                     /collection_date="2019"
     gene            complement(188..337)
                     /locus_tag="AABJ42_RS23100"
     CDS             complement(188..337)
                     /locus_tag="AABJ42_RS23100"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017880354.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_162846302.1"
                     /translation="MPSEYDEQRGSTDTQLPGEYDLFDLMAKVTEEILHAPVDSGPPVG
                     REAL"
                     /name="hypothetical protein"
     gene            <1275..1430
                     /locus_tag="AABJ42_RS23105"
                     /old_locus_tag="VEE14_44260"
                     /pseudo=""
     CDS             <1275..1430
                     /locus_tag="AABJ42_RS23105"
                     /old_locus_tag="VEE14_44260"
                     /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            1524..2168
                     /locus_tag="AABJ42_RS23110"
                     /old_locus_tag="VEE14_44270"
     CDS             1524..2168
                     /locus_tag="AABJ42_RS23110"
                     /old_locus_tag="VEE14_44270"
                     /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             1525..2165
                     /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(373..546)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.5600000000000002e-86"
     Typing          525..1016
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.51"
                     /coverage="81.0"
                     /evalue="0.0"
ORIGIN
        1 ctcaaaatgg tcatacacct aacgcagccg cgattttcat cgcaactgca tgaattaaaa
       61 gaaaaaaaag taatgtttcg ttttcacgag taatacccag gtattaaaaa cccactgtaa
      121 ttacatgaaa ataaagaaat aaaaggtaat accggcgtat taccacgtac gcgggcaagc
      181 gaaaaagcta taacgcttcc cggccgacag gcggcccaga atccacaggg gcatgcagga
      241 tctcttcagt aaccttcgcc attaaatcaa aaaggtcata ttcgccggga agctgcgtat
      301 cagtcgaacc ccgttgttca tcatattcag atggcatggg gtgatatcca gtagcagaga
      361 ggttgttagc gggtttcggg gcgcagccct gaaccagtca cgtagcgcta gcggagtgta
      421 tactggctga ctatgttggc acggatgtgg aaatcagtga agtgcttcat gtagcaggag
      481 aaaaaaggcg gcaccagcgc gtcagcagga tatgtagtac aggatatatt ccgcttcctc
      541 gctcactgac tcgctgcgct cggtcgttcg gctgcggcga gcggtgccgg cttacaggcg
      601 gggcggaaat ttcctgggag ataccaggaa ggagcttaac agggaagaga taaggccgcg
      661 gcgaagccgt ttttccatag gctccgcccc cctgacaaac atcatgaaat ctgacgctca
      721 aatcagtggt ggcgaaaccc gatgcggctt aaagatacca ggcgtttccc cctggtggct
      781 ccctcgtgct cccccgcatt cctgcctttc ggtttaccgg tgtcattccg ctgttatggc
      841 cgcgtttatc tcattccacg cctgacactc agttccgcga aggcagttcg ctcctggatg
      901 gactgtatgc acgaaccccc cgttcagtcc gactgctgcg ccttatccgg taactatcat
      961 cttgagtcca acccggaaag acacgactta tcgccactgg cagcagccac tggtaactga
     1021 tttagaggag ttagtcttga agttatgcgc ctgttaaggc taaactgaaa gaacagattt
     1081 ggttactgcg ctcctcgtaa gccagttacc acggttcaaa gagttgctgc tctgagaacc
     1141 ttcgaaaaac cgccttgcag ggcggttttt tcgtttacag agcaagagat tacgacgcca
     1201 cagaaaggat ctcaagaaga tccttcaccg taatggaaat ctatccaatc cgagcacata
     1261 ggatacacat cgttataacg ctggatctgc gtgaattcca gcagcagcaa gagaaagact
     1321 ttctacaaac cagcttacag caggctaaat ttaaccagaa aaaagccgct gaattactgg
     1381 gtctgactta tcatcagcta cgtgccttgc tgaagaaaca ccagatctaa tacgcatttg
     1441 caggtgtcat actggcgggt ttgacgcata acgtcataag gtttaccatg gcgtcattac
     1501 tgtataaaaa cacaggcata gatatgactc tggcattagt tggcgaaaaa attgacagaa
     1561 atcgcttcac cggtgagaaa gttgaaaata gtacattttt taactgcgat ttttcaggtg
     1621 ccgacctgag cggcactgaa tttatcggct gccagttcta tgatcgcgaa agtcagaaag
     1681 ggtgcaattt tagtcgcgca atgctgaaag atgccatttt caaaagctgt gatttatcaa
     1741 tggcagattt ccgcaacgtc agtgccttgg gcattgaaat tcgccactgc cgcgcacaag
     1801 gcgcagattt ccgcggtgca agctttatga atatgatcac cacgcgcacc tggttttgca
     1861 gcgcatatat cactaatact aatctaagct acgccaattt ttcgaaagtc gtgttggaaa
     1921 agtgtgagct gtgggaaaac cgctggatgg ggactcaggt actgggtgcg acgttcagtg
     1981 gttcagatct ctccggcggc gagttttcga ctttcgactg gcgagcagca aacttcacac
     2041 attgcgatct gaccaattcg gagttaggtg acttagatat tcggggtgtt gatttacaag
     2101 gcgttaagtt agacagctac caggcatcgt tgctcatgga gcggcttggc atcgctgtga
     2161 ttggttagtt cagcgtttac accgggagat gcgtttgacg atttactttt aaccagtacg
     2221 actcctggca agcattgtga aacgttttct ccagtggacg aatatcctga cctaccgcat
     2281 caacgacatg ccatctaatg ctgcattctg gacaggaatt tgatgaatat ctaaccaatt
     2341 cattttcgcg agaacaacga ataaccactc ccgaatcatg aagccatgtc ttaacgaaaa
     2401 tatggctaac tcatagcaaa aaaaaagccc cctaagggct tttttttgta cctgacggtc
     2461 agaccgatta aacataacat cccttgcgtg caccgcctga gaggctctga gggcgtttct
     2521 gacgggaaac cggtaaaaca ggcaacaaac cacccgaaaa cccgccagaa acgcgcaggc
     2581 tctgttttta cggcatgcat gagtatgcgc gcaagtgcat agcgcggaaa ttcacaccat
     2641 tcagccaggg gaagtcctgt ttccggcgtt cttcccatcc gaaaacggtg aacggggacg
     2701 caatttattg cgtggccgtg aagcgttgcc ggcgcagccg gaaaacccgc tgtcagcacg
     2761 ttcaggaagg gggtgatgta caaatggcac agaggatgaa agtgacgtat gagctgaagg
     2821 aatgatgtaa aagtgatgta taaatgatgt aaaagtgatg caaaagtgtt gtaaaagtga
     2881 tgtacaggcc gaaggagtgt tgtaaaagtg ttgtaaaagt gatgtatgaa ctgaaggagc
     2941 gatgtaattc tgtagtcagg aagaataacc cgttcatgca ggcatgaacg atacagtgag
     3001 gaacgctttt ttttgtcacg atctcccctt aacctgcgta aatcacccgc catggttgat
     3061 tatttttcaa c
//
