LOCUS       NZ_AP027625             3180 bp    DNA     circular CON 04-APR-2024
DEFINITION  Escherichia coli strain PSJ-12 plasmid pPSJ-12_3, complete sequence.
ACCESSION   NZ_AP027625
VERSION     NZ_AP027625.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00562571
            Assembly: GCF_036499005.1
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  JOURNAL   Unpublished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 3180)
  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                   :: 360x
            Sequencing Technology :: MGI DNBSEQ-G400RS; ONT MinION Mk1c
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_036499005.1-RS_2024_04_03
            Annotation Date                   :: 04/03/2024 23:51:04
            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)                     :: 4,795
            CDSs (total)                      :: 4,674
            Genes (coding)                    :: 4,449
            CDSs (with protein)               :: 4,449
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 225
            CDSs (without protein)            :: 225
            Pseudo Genes (ambiguous residues) :: 0 of 225
            Pseudo Genes (frameshifted)       :: 57 of 225
            Pseudo Genes (incomplete)         :: 155 of 225
            Pseudo Genes (internal stop)      :: 39 of 225
            Pseudo Genes (multiple problems)  :: 29 of 225
            Pseudo Genes (short protein)      :: 4 of 225
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP027625.1.
            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..3180
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="PSJ-12"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pPSJ-12_3"
                     /geo_loc_name="Ecuador:Puyo"
                     /collection_date="2019"
     gene            join(2790..3180,1..212)
                     /locus_tag="AABJ53_RS23965"
     CDS             join(2790..3180,1..212)
                     /locus_tag="AABJ53_RS23965"
                     /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(570..1214)
                     /locus_tag="AABJ53_RS23970"
                     /old_locus_tag="VEE42_45770"
     CDS             complement(570..1214)
                     /locus_tag="AABJ53_RS23970"
                     /old_locus_tag="VEE42_45770"
                     /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(1308..>1463)
                     /locus_tag="AABJ53_RS23975"
                     /old_locus_tag="VEE42_45780"
                     /pseudo=""
     CDS             complement(1308..>1463)
                     /locus_tag="AABJ53_RS23975"
                     /old_locus_tag="VEE42_45780"
                     /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(574..1214)
                     /name="qnrB19"
                     /gene="qnrB19"
                     /gene_name="quinolone resistance pentapeptide repeat
                     protein QnrB19"
                     /tool="amrfinderplus"
                     /drug_class="QUINOLONE"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          2193..2366
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.5600000000000002e-86"
     Typing          complement(1723..2214)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.51"
                     /coverage="81.0"
                     /evalue="0.0"
ORIGIN
        1 cacttgcgcg catactcatg catgccgtaa aaacagagcc tgcgcgtttc tggcgggttt
       61 tcggggggtt tgttgcctgt tttaccggtt tcccgtcaga aacgccctca gagcctctca
      121 ggcggtgcac gcaagggatg ttatgtttaa tcggtctgac cgtcaggtac aaaaaaaagc
      181 ccttaggggg cttttttttt gctatgagtt agccatattt tcgtgcgaat ttttcatcgg
      241 aatcgcatag ataaataata aactcaataa acgcgatgat cgcggggtat ttgtattgag
      301 gatgtcagta aacgggatga catggctgaa gttgagatta taaataagac atggcttcat
      361 gattcgggag tggttattcg ttgttctcgc gaaaatgaat tggttagata ttcatcaaat
      421 tcctgtccag aatgcagcat tagatggcat gtcgttgatg cggtaggtca ggatattcgt
      481 ccactggaga aaacgtttca caatgcttgc caggagtcgt actggttaaa agtaaatcgt
      541 caaacgcatc tcccggtgta aacgctgaac taaccaatca cagcgatgcc aagccgctcc
      601 atgagcaacg atgcctggta gctgtctaac ttaacgcctt gtaaatcaac accccgaata
      661 tctaagtcac ctaactccga attggtcaga tcgcaatgtg tgaagtttgc tgctcgccag
      721 tcgaaagtcg aaaactcgcc gccggagaga tctgaaccac tgaacgtcgc acccagtacc
      781 tgagtcccca tccagcggtt ttcccacagc tcacactttt ccaacacgac tttcgaaaaa
      841 ttggcgtagc ttagattagt attagtgata tatgcgctgc aaaaccaggt gcgcgtggtg
      901 atcatattca taaagcttgc accgcggaaa tctgcgcctt gtgcgcggca gtggcgaatt
      961 tcaatgccca aggcactgac gttgcggaaa tctgccattg ataaatcaca gcttttgaaa
     1021 atggcatctt tcagcattgc gcgactaaaa ttgcaccctt tctgactttc gcgatcatag
     1081 aactggcagc cgataaattc agtgccgctc aggtcggcac ctgaaaaatc gcagttaaaa
     1141 aatgtactat tttcaacttt ctcaccggtg aagcgatttc tgtcaatttt ttcgccaact
     1201 aatgccagag tcatatctat gcctgtgttt ttatacagta atgacgccat ggtaaacctt
     1261 atgacgttat gcgtcaaacc cgccagtatg acacctgcaa atgcgtatta gatctggtgt
     1321 ttcttcagca aggcacgtag ctgatgataa gtcagaccca gtaattcagc ggcttttttc
     1381 tggttaaatt tagcctgctg taagctggtt tgtagaaagt ctttctcttg ctgctgctgg
     1441 aattcacgca gatccagcgt tataacgatg tgtatcctat gtgctcggat tggatagatt
     1501 tccattacgg tgaaggatct tcttgagatc ctttctgtgg cgtcgtaatc tcttgctctg
     1561 taaacgaaaa aaccgccctg caaggcggtt tttcgaaggt tctcagagca gcaactcttt
     1621 gaaccgtggt aactggctta cgaggagcgc agtaaccaaa tctgttcttt cagtttagcc
     1681 ttaacaggcg cataacttca agactaactc ctctaaatca gttaccagtg gctgctgcca
     1741 gtggcgataa gtcgtgtctt tccgggttgg actcaagatg atagttaccg gataaggcgc
     1801 agcagtcgga ctgaacgggg ggttcgtgca tacagtccat ccaggagcga actgccttcg
     1861 cggaactgag tgtcaggcgt ggaatgagat aaacgcggcc ataacagcgg aatgacaccg
     1921 gtaaaccgaa aggcaggaat gcgggggagc acgagggagc caccaggggg aaacgcctgg
     1981 tatctttaag ccgcatcggg tttcgccacc actgatttga gcgtcagatt tcatgatgtt
     2041 tgtcaggggg gcggagccta tggaaaaacg gcttcgccgc ggccttatct cttccctgtt
     2101 aagctccttc ctggtatctc ccaggaaatt tccgccccgc ctgtaagccg gcaccgctcg
     2161 ccgcagccga acgaccgagc gcagcgagtc agtgagcgag gaagcggaat atatcctgta
     2221 ctacatatcc tgctgacgcg ctggtgccgc cttttttctc ctgctacatg aagcacttca
     2281 ctgatttcca catccgtgcc aacatagtca gccagtatac actccgctag cgctacgtga
     2341 ctggttcagg gctgcgcccc gaaacccgct aacaacctct ctgctactgg atatcacccc
     2401 atgccatctg aatatgatga acaacggggt tcgactgata cgcagcttcc cggcgaatat
     2461 gacctttttg atttaatggc gaaggttact gaagagatcc tgcatgcccc tgtggattct
     2521 gggccgcctg tcggccggga agcgttatag ctttttcgct tgcccgcgta cgtggtaata
     2581 cgccggtatt accttttatt tctttatttt catgtaatta cagtgggttt ttaatacctg
     2641 ggtattactc gtgaaaacga aacattactt ttttttcttt taattcatgc agttgcgatg
     2701 aaaatcgcgg ctgcgttagg tgtatgacca ttttgaggtt gaaaaataat caaccatggc
     2761 gggtgattta cgcaggttaa ggggagatcg tgacaaaaaa aagcgttcct cactgtatcg
     2821 ttcatgcctg catgaacggg ttattcttcc tgactacaga attacatcgc tccttcagtt
     2881 catacatcac tttcacaaca cttttacaac actccttcgg cctgtacatc acttttacaa
     2941 cacttttaca tcatttatac atcactttta catcattcct tcagctcata cgtcactttc
     3001 atcctctgtg ccatttgtac atcaccccct tcctgaacgt gctgacagcg ggttttccgg
     3061 ctgcgccggc aacgcttcac ggccacgcaa taaattgcgt ccccgttcac cgttttcgga
     3121 tgggaagaac gccggaaaca ggacttcccc tggctgaatg gtgtgaattt ccgcgctatg
//
