LOCUS       NZ_AP027672             2699 bp    DNA     circular CON 04-APR-2024
DEFINITION  Escherichia coli strain PSS-04 plasmid pPSS-04_6, complete sequence.
ACCESSION   NZ_AP027672
VERSION     NZ_AP027672.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00562521
            Assembly: GCF_036500705.1
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  JOURNAL   Unpublished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 2699)
  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                   :: 150x
            Sequencing Technology :: MGI DNBSEQ-G400RS; ONT MinION Mk1c
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_036500705.1-RS_2024_04_03
            Annotation Date                   :: 04/03/2024 23:58:23
            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)                     :: 4,746
            CDSs (total)                      :: 4,625
            Genes (coding)                    :: 4,365
            CDSs (with protein)               :: 4,365
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 260
            CDSs (without protein)            :: 260
            Pseudo Genes (ambiguous residues) :: 0 of 260
            Pseudo Genes (frameshifted)       :: 56 of 260
            Pseudo Genes (incomplete)         :: 189 of 260
            Pseudo Genes (internal stop)      :: 54 of 260
            Pseudo Genes (multiple problems)  :: 38 of 260
            Pseudo Genes (short protein)      :: 3 of 260
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP027672.1.
            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..2699
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="PSS-04"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pPSS-04_6"
                     /geo_loc_name="Ecuador:Puyo"
                     /collection_date="2019"
     gene            complement(join(2084..2699,1..29))
                     /locus_tag="AABJ69_RS23720"
     CDS             complement(join(2084..2699,1..29))
                     /locus_tag="AABJ69_RS23720"
                     /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(123..>278)
                     /locus_tag="AABJ69_RS23725"
                     /old_locus_tag="VEE17_45580"
                     /pseudo=""
     CDS             complement(123..>278)
                     /locus_tag="AABJ69_RS23725"
                     /old_locus_tag="VEE17_45580"
                     /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"
     gene            1346..1582
                     /locus_tag="AABJ69_RS23730"
                     /old_locus_tag="VEE17_45590"
     CDS             1346..1582
                     /locus_tag="AABJ69_RS23730"
                     /old_locus_tag="VEE17_45590"
                     /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"
     ARG             complement(2088..2698)
                     /name="qnrB"
                     /gene="qnrB"
                     /gene_name="QnrB family quinolone resistance pentapeptide
                     repeat protein"
                     /tool="amrfinderplus"
                     /drug_class="QUINOLONE"
                     /identity="100.0"
                     /coverage="95.33"
     ARG             complement(4..65)
                     /name="QnrB59"
                     /gene="QnrB59"
                     /gene_name="quinolone resistance protein (qnr)"
                     /tool="rgi"
                     /drug_class="fluoroquinolone antibiotic"
                     /identity="95.24"
                     /coverage="9.29"
     ARG             complement(2085..2698)
                     /name="QnrB5"
                     /gene="QnrB5"
                     /gene_name="quinolone resistance protein (qnr)"
                     /tool="rgi"
                     /drug_class="fluoroquinolone antibiotic"
                     /identity="99.51"
                     /coverage="90.27"
     Typing          1008..1181
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.5600000000000002e-86"
     Typing          complement(538..1029)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.51"
                     /coverage="81.0"
                     /evalue="0.0"
ORIGIN
        1 attttttcgc caactaatgc cagagtcata tctatgcctg tgtttttata cagtaatgac
       61 gccatggtaa accttatgac gttatgcgtc aaacccgcca gtatgacacc tgcaaatgcg
      121 tattagatct ggtgtttctt cagcaaggca cgtagctgat gataagtcag acccagtaat
      181 tcagcggctt ttttctggtt aaatttagcc tgctgtaagc tggtttgtag aaagtctttc
      241 tcttgctgct gctggaattc acgcagatcc agcgttataa cgatgtgtat cctatgtgct
      301 cggattggat agatttccat tacggtgaag gatcttcttg agatcctttc tgtggcgtcg
      361 taatctcttg ctctgtaaac gaaaaaaccg ccctgcaagg cggtttttcg aaggttctca
      421 gagcagcaac tctttgaacc gtggtaactg gcttacgagg agcgcagtaa ccaaatctgt
      481 tctttcagtt tagccttaac aggcgcataa cttcaagact aactcctcta aatcagttac
      541 cagtggctgc tgccagtggc gataagtcgt gtctttccgg gttggactca agatgatagt
      601 taccggataa ggcgcagcag tcggactgaa cggggggttc gtgcatacag tccatccagg
      661 agcgaactgc cttcgcggaa ctgagtgtca ggcgtggaat gagataaacg cggccataac
      721 agcggaatga caccggtaaa ccgaaaggca ggaatgcggg ggagcacgag ggagccacca
      781 gggggaaacg cctggtatct ttaagccgca tcgggtttcg ccaccactga tttgagcgtc
      841 agatttcatg atgtttgtca ggggggcgga gcctatggaa aaacggcttc gccgcggcct
      901 tatctcttcc ctgttaagct ccttcctggt atctcccagg aaatttccgc cccgcctgta
      961 agccggcacc gctcgccgca gccgaacgac cgagcgcagc gagtcagtga gcgaggaagc
     1021 ggaatatatc ctgtactaca tatcctgctg acgcgctggt gccgcctttt ttctcctgct
     1081 acatgaagca cttcactgat ttccacatcc gtgccaacat agtcagccag tatacactcc
     1141 gctagcgcta cgtgactggt tcagggctgc gccccgaaac cggctaaaag ctaatgacgc
     1201 gcctgcggct tgtccaacgc ctcacggcac cggattaaaa tccgctcccg ttcaccgttt
     1261 ctgactgcct ttcaccgtcg ctggcgcttc atcgtttcta ctgtgtctgg cagactgtgc
     1321 tgatttattc tgactggaga acgttatggc cagactgaca aacttgacgc ctgcagagaa
     1381 aaaatttctt gatgatgctg ttgccgcagc tgaaagagcg tcaggtaaaa agctaaatca
     1441 gcctaaccgg cacatcgtcc tgaacagagc gcgtgcgcaa attgagttgc agcgttacgc
     1501 cgaccgccag cgtgcattac gtgaggatga gcggcagcag tccgattttg cctggtcacg
     1561 tccgcgcgcg ccgcgccgct gattttggct tttggcggtt tagtggtgct gacgctgcga
     1621 aatcacctgc cattcacctg cgtgcatagc catgcagtcg cgcagaaatc atcaggggcg
     1681 tttttccggg atactggtga ggaaaggtgc tggaaacggc cctgatgcag caggattgcg
     1741 ctgagggcgc ctgcgggggt gcgggcaagg gatgttatgt ttaatcggtc tgaccgtcag
     1801 gtacaaaaaa aagcccttag ggggcttttt ttttgctatg agttagccat attttcgtta
     1861 agacatggct tcatgattcg ggagtggtta ttcgttgttc tcgcgaaaat gaattggtta
     1921 gatattcatc aaattcctgt ccagaatgca gcattagatg gcatgtcgtt gatgcggtag
     1981 gtcaggatat tcgtccactg gagaaaacgt ttcacaatgc ttgccaggag tcgtactggt
     2041 taaaagtaaa tcgtcaaacg catctcccgg tgtaaacgct gaactaacca atcacagcga
     2101 tgccaagccg ctccatgagc aacgatgcct ggtagctgtc taacttaacg ccttgtaaat
     2161 caacaccccg aatatctaag tcacctaact ccgaattggt cagatcgcaa tgtgtgaagt
     2221 ttgctgctcg ccagtcgaaa gtcgaaaact cgccgccgga gagatctgaa ccactgaacg
     2281 tcgcacccag tacctgagtc cccatccagc ggttttccca cagctcacac ttttccaaca
     2341 cgactttcga aaaattggcg tagcttagat tagtattagt gatatatgcg ctgcaaaacc
     2401 aggtgcgcgt ggtgatcata ttcataaagc ttgcaccgcg gaaatctgcg ccttgtgcgc
     2461 ggcagtggcg aatttcaatg cccaaggcac tgacgttgcg gaaatctgcc attgataaat
     2521 cacagctttt gaaaatggca tctttcagca ttgcgcgact aaaattgcac cctttctgac
     2581 tttcgcgatc atagaactgg cagccgataa attcagtgcc gctcaggtcg gcacctgaaa
     2641 aatcgcagtt aaaaaatgta ctattttcaa ctttctcacc ggtgaagcga tttctgtca
//
