LOCUS       NZ_AP027618             1551 bp    DNA     circular CON 04-APR-2024
DEFINITION  Escherichia coli strain LR-72 plasmid pLR-72_6, complete sequence.
ACCESSION   NZ_AP027618
VERSION     NZ_AP027618.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00562557
            Assembly: GCF_036498665.1
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  JOURNAL   Unpublished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 1551)
  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                   :: 162x
            Sequencing Technology :: MGI DNBSEQ-G400RS; ONT MinION Mk1c
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_036498665.1-RS_2024_04_04
            Annotation Date                   :: 04/04/2024 00:14:07
            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)                     :: 4,769
            CDSs (total)                      :: 4,647
            Genes (coding)                    :: 4,428
            CDSs (with protein)               :: 4,428
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 8 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 219
            CDSs (without protein)            :: 219
            Pseudo Genes (ambiguous residues) :: 0 of 219
            Pseudo Genes (frameshifted)       :: 73 of 219
            Pseudo Genes (incomplete)         :: 144 of 219
            Pseudo Genes (internal stop)      :: 42 of 219
            Pseudo Genes (multiple problems)  :: 39 of 219
            Pseudo Genes (short protein)      :: 4 of 219
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP027618.1.
            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..1551
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="LR-72"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pLR-72_6"
                     /geo_loc_name="Ecuador:Santo Domingo"
                     /collection_date="2019"
     gene            1..477
                     /locus_tag="AABJ55_RS23840"
                     /old_locus_tag="VEE35_45420"
     CDS             1..477
                     /locus_tag="AABJ55_RS23840"
                     /old_locus_tag="VEE35_45420"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000469298.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_000469298.1"
                     /translation="MFIDSEKRLKQLSDEAKKNTEDLEEAKKNSRFTQVSPKGWERVRE
                     LLKDSQGISALKLYSFLAEHIDPTCGAVVADQQFLAEKLGVSRSTIIRWLNYLESKNAL
                     VRIPVAGKVCAYALDPHEVWKGYNTTKNHAAFVTKTLVNKDGDIQRRIMAMFSN"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(922..1143)
                     /locus_tag="AABJ55_RS23845"
     CDS             complement(922..1143)
                     /locus_tag="AABJ55_RS23845"
                     /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_152921959.1"
                     /translation="MCKCNTVTRDDIPFAIWSGLRPDTPHQCVRAQCGFRFSSASSPTR
                     SLRSVAGAAASGITSRMLSVIPVLFFWG"
                     /name="hypothetical protein"
     Typing          1071..1162
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="91.398"
                     /coverage="100.0"
                     /evalue="3.4000000000000004e-27"
     Typing          complement(1365..1473)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.182"
                     /coverage="100.0"
                     /evalue="4.23e-47"
     Typing          complement(709..969)
                     /name="Col(MG828)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.985"
                     /coverage="100.0"
                     /evalue="1.85e-99"
ORIGIN
        1 atgtttattg attcagaaaa acgactgaaa caactttcag atgaggcaaa gaaaaacacc
       61 gaggatctcg aagaagcaaa gaaaaattca aggtttacac aggtatcccc aaaaggttgg
      121 gaacgtgttc gagagctgct gaaggatagc caaggcatat cagcactgaa gctgtactca
      181 tttttagcgg agcatatcga tcctacgtgt ggcgctgtcg ttgcggatca gcaattccta
      241 gctgaaaaac ttggagttag cagaagcaca attattcggt ggctcaatta cttagaatca
      301 aaaaatgcat tagttagaat ccccgttgct ggtaaggttt gtgcgtatgc cctcgatcca
      361 catgaagtct ggaagggata caacactacg aaaaaccatg cagcgtttgt cactaaaaca
      421 ctggtcaaca aagacggtga tattcagcgc cgaatcatgg ccatgttttc aaattgagct
      481 agcggcaggc ggacaatcag gggctacgtg ttaacgttct gaccatgatt gtctatcctg
      541 cattgctctt ttgccgcctc aaaatccttt gcgtgttttt gctccccgtt ctccagaaaa
      601 aaccgagccg ccacggttcc ggcagcgcct tgagcgctac cggaaaccgt ctggggagaa
      661 ccccagaccc ccatcgctgc aacaccgacg gtctacgacc acctaccaac cgcatggctg
      721 cctgttccgt gcaaatgggc tttgcagggg gctggcgcgg ttcctggcga cctgaaagcc
      781 cctggttagg ggtatcggcg cgcttgacct cctgagagcc tctgtaagcg tttttcgcgc
      841 cttccatgcc ctggcgggca tctaaaaccc gtttcgtgcg tctgagagct tttgagcgcg
      901 tttgaggggc tatctggcga ctcatcccca aaagaacaac accgggatca ccgacaacat
      961 gcgagaggtg atcccgctcg ccgcagcccc agcgaccgaa cgtagtgagc gagtgggcga
     1021 ggaagcggaa gagaaccgga aaccacattg agcacgtacg cactgatgcg gggtgtcggg
     1081 gcgaagccct gaccagatgg caaacggaat atcgtcgcgg gtgacggtat tacatttgca
     1141 catcctgtcc cgatttttgg ggcgttttag cggtgaacgg aaggcaaaaa catgatcgag
     1201 ctgttgaacg tggagagcgc gaaatcgtgc aaaatcacgg ctgacgaggc ttgcagagga
     1261 gtaagccagt atacactccg ctatcgctac gtgactgggt cagggcttcg ccccgacacc
     1321 cccaaagggc gttgcgttgc acgcaacacc cttgcctaga atagatcttt tacgccgatt
     1381 tgtaagtgct tgttttttta gtgtgttttt tatttacctg tcgcatccag gatgacacaa
     1441 cgttgtcgca tcctggatgc gacaacacgc aacaaggtgt tgcacatatg tgtcatgatg
     1501 gcttagattt gaaccaacgt tagtgcatgg gattttcaga gggaaaaaat c
//
