LOCUS       NZ_CP147045             3180 bp    DNA     circular CON 22-APR-2024
DEFINITION  Escherichia coli strain 20A24 plasmid p20A24_1, complete sequence.
ACCESSION   NZ_CP147045
VERSION     NZ_CP147045.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN39992806
            Assembly: GCF_038396555.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3180)
  AUTHORS   Gomi,R.
  TITLE     Genomic analysis of environmental Escherichia coli carrying
            transferable quinolone resistance determinants
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3180)
  AUTHORS   Gomi,R.
  TITLE     Direct Submission
  JOURNAL   Submitted (05-MAR-2024) Department of environmental engineering,
            Kyoto University, KyotoDaigakuKatsura, Nishikyo-ku, Kyoto-city
            615-8540, Japan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Flye v. 2.9.1
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 150x
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_038396555.1-RS_2024_04_20
            Annotation Date                   :: 04/20/2024 17:58:50
            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)                     :: 4,778
            CDSs (total)                      :: 4,658
            Genes (coding)                    :: 4,479
            CDSs (with protein)               :: 4,479
            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)              :: 179
            CDSs (without protein)            :: 179
            Pseudo Genes (ambiguous residues) :: 0 of 179
            Pseudo Genes (frameshifted)       :: 52 of 179
            Pseudo Genes (incomplete)         :: 125 of 179
            Pseudo Genes (internal stop)      :: 35 of 179
            Pseudo Genes (multiple problems)  :: 32 of 179
            Pseudo Genes (short protein)      :: 4 of 179
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP147045.1.
            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..3180
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="20A24"
                     /isolation_source="municipal wastewater"
                     /db_xref="taxon:562"
                     /plasmid="p20A24_1"
                     /geo_loc_name="Japan"
                     /collection_date="2020"
                     /collected_by="Fumie Adachi"
     gene            join(2934..3180,1..356)
                     /locus_tag="WAZ56_RS23875"
                     /old_locus_tag="WAZ56_23875"
     CDS             join(2934..3180,1..356)
                     /locus_tag="WAZ56_RS23875"
                     /old_locus_tag="WAZ56_23875"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_172437497.1"
                     /translation="MTKKSVPHCIVHACMNGLFFLTTELHRSFSSYITFTTLLQHSFGL
                     YITFTTLLHHLYITFTSFLQLIRHFHPLCHLYITPFLNVLTAGFPAAPATLHGHAINCV
                     PVHRFRMGRTPETGLPLAEWCEFPRYALARILMHAVKTEPARFWRVFGGFVACFTGFPS
                     ETPSEPLRRCTQGMLCLIGLTVRYKKKPLGGFFFAMS"
                     /name="hypothetical protein"
     gene            complement(714..1358)
                     /locus_tag="WAZ56_RS23880"
                     /old_locus_tag="WAZ56_23880"
     CDS             complement(714..1358)
                     /locus_tag="WAZ56_RS23880"
                     /old_locus_tag="WAZ56_23880"
                     /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(1452..>1607)
                     /locus_tag="WAZ56_RS23885"
                     /old_locus_tag="WAZ56_23885"
                     /pseudo=""
     CDS             complement(1452..>1607)
                     /locus_tag="WAZ56_RS23885"
                     /old_locus_tag="WAZ56_23885"
                     /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            2545..2694
                     /locus_tag="WAZ56_RS23890"
                     /old_locus_tag="WAZ56_23890"
     CDS             2545..2694
                     /locus_tag="WAZ56_RS23890"
                     /old_locus_tag="WAZ56_23890"
                     /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"
     ARG             complement(718..1358)
                     /name="qnrB19"
                     /gene="qnrB19"
                     /gene_name="quinolone resistance pentapeptide repeat
                     protein QnrB19"
                     /tool="amrfinderplus"
                     /drug_class="QUINOLONE"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          2337..2510
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.5600000000000002e-86"
     Typing          complement(1867..2358)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.51"
                     /coverage="81.0"
                     /evalue="0.0"
ORIGIN
        1 acgtgctgac agcgggtttt ccggctgcgc cggcaacgct tcacggccac gcaataaatt
       61 gcgtccccgt tcaccgtttt cggatgggaa gaacgccgga aacaggactt cccctggctg
      121 aatggtgtga atttccgcgc tatgcacttg cgcgcatact catgcatgcc gtaaaaacag
      181 agcctgcgcg tttctggcgg gttttcgggg ggtttgttgc ctgttttacc ggtttcccgt
      241 cagaaacgcc ctcagagcct ctcaggcggt gcacgcaagg gatgttatgt ttaatcggtc
      301 tgaccgtcag gtacaaaaaa aagcccttag ggggcttttt ttttgctatg agttagccat
      361 attttcgtgc gaatttttca tcggaatcgc atagataaat aataaactca ataaacgcga
      421 tgatcgcggg gtatttgtat tgaggatgtc agtaaacggg atgacatggc tgaagttgag
      481 attataaata agacatggct tcatgattcg ggagtggtta ttcgttgttc tcgcgaaaat
      541 gaattggtta gatattcatc aaattcctgt ccagaatgca gcattagatg gcatgtcgtt
      601 gatgcggtag gtcaggatat tcgtccactg gagaaaacgt ttcacaatgc ttgccaggag
      661 tcgtactggt taaaagtaaa tcgtcaaacg catctcccgg tgtaaacgct gaactaacca
      721 atcacagcga tgccaagccg ctccatgagc aacgatgcct ggtagctgtc taacttaacg
      781 ccttgtaaat caacaccccg aatatctaag tcacctaact ccgaattggt cagatcgcaa
      841 tgtgtgaagt ttgctgctcg ccagtcgaaa gtcgaaaact cgccgccgga gagatctgaa
      901 ccactgaacg tcgcacccag tacctgagtc cccatccagc ggttttccca cagctcacac
      961 ttttccaaca cgactttcga aaaattggcg tagcttagat tagtattagt gatatatgcg
     1021 ctgcaaaacc aggtgcgcgt ggtgatcata ttcataaagc ttgcaccgcg gaaatctgcg
     1081 ccttgtgcgc ggcagtggcg aatttcaatg cccaaggcac tgacgttgcg gaaatctgcc
     1141 attgataaat cacagctttt gaaaatggca tctttcagca ttgcgcgact aaaattgcac
     1201 cctttctgac tttcgcgatc atagaactgg cagccgataa attcagtgcc gctcaggtcg
     1261 gcacctgaaa aatcgcagtt aaaaaatgta ctattttcaa ctttctcacc ggtgaagcga
     1321 tttctgtcaa ttttttcgcc aactaatgcc agagtcatat ctatgcctgt gtttttatac
     1381 agtaatgacg ccatggtaaa ccttatgacg ttatgcgtca aacccgccag tatgacacct
     1441 gcaaatgcgt attagatctg gtgtttcttc agcaaggcac gtagctgatg ataagtcaga
     1501 cccagtaatt cagcggcttt tttctggtta aatttagcct gctgtaagct ggtttgtaga
     1561 aagtctttct cttgctgctg ctggaattca cgcagatcca gcgttataac gatgtgtatc
     1621 ctatgtgctc ggattggata gatttccatt acggtgaagg atcttcttga gatcctttct
     1681 gtggcgtcgt aatctcttgc tctgtaaacg aaaaaaccgc cctgcaaggc ggtttttcga
     1741 aggttctcag agcagcaact ctttgaaccg tggtaactgg cttacgagga gcgcagtaac
     1801 caaatctgtt ctttcagttt agccttaaca ggcgcataac ttcaagacta actcctctaa
     1861 atcagttacc agtggctgct gccagtggcg ataagtcgtg tctttccggg ttggactcaa
     1921 gatgatagtt accggataag gcgcagcagt cggactgaac ggggggttcg tgcatacagt
     1981 ccatccagga gcgaactgcc ttcgcggaac tgagtgtcag gcgtggaatg agataaacgc
     2041 ggccataaca gcggaatgac accggtaaac cgaaaggcag gaatgcgggg gagcacgagg
     2101 gagccaccag ggggaaacgc ctggtatctt taagccgcat cgggtttcgc caccactgat
     2161 ttgagcgtca gatttcatga tgtttgtcag gggggcggag cctatggaaa aacggcttcg
     2221 ccgcggcctt atctcttccc tgttaagctc cttcctggta tctcccagga aatttccgcc
     2281 ccgcctgtaa gccggcaccg ctcgccgcag ccgaacgacc gagcgcagcg agtcagtgag
     2341 cgaggaagcg gaatatatcc tgtactacat atcctgctga cgcgctggtg ccgccttttt
     2401 tctcctgcta catgaagcac ttcactgatt tccacatccg tgccaacata gtcagccagt
     2461 atacactccg ctagcgctac gtgactggtt cagggctgcg ccccgaaacc cgctaacaac
     2521 ctctctgcta ctggatatca ccccatgcca tctgaatatg atgaacaacg gggttcgact
     2581 gatacgcagc ttcccggcga atatgacctt tttgatttaa tggcgaaggt tactgaagag
     2641 atcctgcatg cccctgtgga ttctgggccg cctgtcggcc gggaagcgtt atagcttttt
     2701 cgcttgcccg cgtacgtggt aatacgccgg tattaccttt tatttcttta ttttcatgta
     2761 attacagtgg gtttttaata cctgggtatt actcgtgaaa acgaaacatt actttttttt
     2821 cttttaattc atgcagttgc gatgaaaatc gcggctgcgt taggtgtatg accattttga
     2881 ggttgaaaaa taatcaacca tggcgggtga tttacgcagg ttaaggggag atcgtgacaa
     2941 aaaaaagcgt tcctcactgt atcgttcatg cctgcatgaa cgggttattc ttcctgacta
     3001 cagaattaca tcgctccttc agttcataca tcactttcac aacactttta caacactcct
     3061 tcggcctgta catcactttt acaacacttt tacatcattt atacatcact tttacatcat
     3121 tccttcagct catacgtcac tttcatcctc tgtgccattt gtacatcacc cccttcctga
//
