LOCUS       NZ_AP027519             2784 bp    DNA     circular CON 04-APR-2024
DEFINITION  Escherichia coli strain LR-29-1 plasmid pLR-29-1_4, complete
            sequence.
ACCESSION   NZ_AP027519
VERSION     NZ_AP027519.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00562505
            Assembly: GCF_036495745.1
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  JOURNAL   Unpublished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 2784)
  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                   :: 221x
            Sequencing Technology :: MGI DNBSEQ-G400RS; ONT MinION Mk1c
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_036495745.1-RS_2024_04_03
            Annotation Date                   :: 04/03/2024 23:58:59
            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)                     :: 4,759
            CDSs (total)                      :: 4,639
            Genes (coding)                    :: 4,440
            CDSs (with protein)               :: 4,440
            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)              :: 199
            CDSs (without protein)            :: 199
            Pseudo Genes (ambiguous residues) :: 0 of 199
            Pseudo Genes (frameshifted)       :: 52 of 199
            Pseudo Genes (incomplete)         :: 143 of 199
            Pseudo Genes (internal stop)      :: 32 of 199
            Pseudo Genes (multiple problems)  :: 30 of 199
            Pseudo Genes (short protein)      :: 4 of 199
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP027519.1.
            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..2784
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="LR-29-1"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pLR-29-1_4"
                     /geo_loc_name="Ecuador:Santo Domingo"
                     /collection_date="2019"
     gene            complement(join(2779..2784,1..1098))
                     /locus_tag="AABJ68_RS23790"
     CDS             complement(join(2779..2784,1..1098))
                     /locus_tag="AABJ68_RS23790"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004295514.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid recombination protein"
                     /protein_id="WP_005783389.1"
                     /translation="MGATSIHVQAVKPGSEIHNFREKELDYVRPELSHLNESWVGDSIS
                     HRLESAKQRYFDTVGQKMQTKAAPIREGVIVIKQETTMQELQQFAAVCKERFGIEAFQI
                     HIHKDEGYMNAKQWTPNLHAHVVFDWTQPNGKSVRLSRDDMAELQTIASEALGMERGVS
                     SDRKHLSAMQYKTECAKEQLQELSNDISSALDKHKDVQNQLLQLQKELRSIETKKNVQK
                     LISKASEKFYGLIGKTVNDREKDTLKAKIKALEGENEQLSDRLGKAILEKERNGTKVFK
                     AENDKEYYRQQMDNARTTSNRLRTENQELKTETKELKKELGKMKDLFNSEQLEALRHHF
                     PNISKAMEEGKDLLKQITRSRGFGMGM"
                     /name="plasmid recombination protein"
     gene            complement(1717..2307)
                     /locus_tag="AABJ68_RS23795"
                     /old_locus_tag="VEE08_45440"
     CDS             complement(1717..2307)
                     /locus_tag="AABJ68_RS23795"
                     /old_locus_tag="VEE08_45440"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_008670455.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_008670455.1"
                     /translation="MENKKVLKLTDFQKNEENPFMKQAIEGIENHVVKKYKSSTGSDKK
                     AVVAVADTDTGEVFKTSFIRQIEVDEEQFAKLYLANFAAFFNLSQSAIRVFGYILTCMK
                     PKNDMIIFDRRKCLEYTQYKSDKAIYKGLAELVQSEIIARGPNEYNWFINPLIVFNGDR
                     VSFTKTYVRKKTLAAQKKEEAEKRQLSLGFDEL"
                     /name="hypothetical protein"
     Typing          complement(1728..2307)
                     /name="rep_cluster_1868"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="80.479"
                     /coverage="95.0"
                     /evalue="2.71e-121"
     Typing          complement(2..1098)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.628"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 acccataccg aaacctctgc ttctggtgat ttgcttgagt aggtctttcc cctcttccat
       61 agcttttgat atgtttggga aatgatgcct taaagcctcc agttgttcgg aattgaacaa
      121 gtctttcatc ttaccaagtt cttttttcaa ttccttggtt tcggtcttta gttcttggtt
      181 ctccgttctt agtcggttac tggttgtcct tgcattgtcc atttgctgtc tataatactc
      241 cttgtcgttc tcggctttga atacctttgt gccgtttcgc tctttttcaa gtatagcctt
      301 tcccagtcta tcggatagct gttcattttc cccctctaaa gcctttattt tggcttttaa
      361 ggtatctttt tccctatcgt taaccgtttt ccctatcaag ccgtaaaact tctctgaagc
      421 cttagaaatg agtttttgga cgtttttctt tgtttcaatg gaacgtagtt ctttctgaag
      481 ctgaagaagc tggttttgca cgtccttgtg cttgtctaac gcactggata tatcgttgga
      541 tagttcctga agctgttctt tcgcacattc ggtcttgtac tgcatagccg ataagtgttt
      601 gcgatcagaa gaaacaccac gttccatgcc cagtgcttca gatgctatgg tttggagttc
      661 tgccatgtca tcacgcgata aacgcacact cttcccgttc ggctgcgtcc aatcgaaaac
      721 tacatgggcg tgaaggttag gtgtccattg ctttgcgttc atgtatcctt cgtccttgtg
      781 tatatggatt tgaaacgctt caataccgaa acgttccttg cagaccgcag cgaattgctg
      841 gagttcctgc atggtggttt cttgcttgat tactattacc ccctcccgta tgggtgctgc
      901 tttagtctgc atcttctgcc caaccgtatc gaaatatctc tgtttcgcac tctccagccg
      961 atgggagatg ctatctccaa cccagctttc attcaaatga ctaagttccg gacgaacata
     1021 gtccaactct ttttccctaa agttgtgaat ctcgctcccc ggcttcactg cttgtacatg
     1081 aatacttgtt gctcccataa gttaacattt ttgtgacaat cgataacagc cggtgacagc
     1141 cggctgacag ggggttaagg gggcttgtcc ccttacacac gtacccttta gggtgctagt
     1201 gtgctatcac catactgcat aggtgcgaag ttagtgaatg ttttgtaaat gcacaaataa
     1261 aggggaaaac atttggattt gcgacaataa agtactacct ttgttgctga ccaaacggta
     1321 gctgaccgat acgggagagt taccaaaata caagccgctg gagttaattg acggacatcc
     1381 gacatcccca gcggctttat ttttgcctat ctgcttcgtc taggcatacc agtacctcta
     1441 ctaaaaatgt acttcaaaga tacttatttt ctaccgactt gatagttttt accccatatt
     1501 cttggacatt tttcccccat gaggttatct ttgtagggtg aaagagaaac ccataaacgg
     1561 ggatagattg aatgctggga agcataaaca atcggggtaa ggttagcgaa ccttgccttt
     1621 catcccccat tataacttta catagaggaa ctttatctat cccccccccg cccccaaagg
     1681 gggagcgacc aaacggcagc ttcactcaat ggagtgttac agttcatcaa aaccaagtga
     1741 taactgtcgt ttctctgctt cttctttctt ttgggcagct aaagtctttt tccgaacgta
     1801 tgtttttgta aatgaaaccc tatccccatt aaagacaatc aacggattaa tgaaccaatt
     1861 atattcgttt ggacctcttg ctatgatttc actttgtacg agctctgcca atcctttgta
     1921 tatggctttg tctgatttgt attgggtgta ttctaagcat tttcgcctat cgaaaattat
     1981 catatcattc ttaggcttca tgcaagttag aatatacccg aaaacccgaa tagctgattg
     2041 tgatagattg aaaaaagcgg caaaattcgc aaggtatagt tttgcaaatt gctcttcatc
     2101 tacttctatt tgtcggataa acgaggtttt gaatacttct cctgtatctg tatcagcaac
     2161 agcaactaca gcttttttat cacttcccgt actacttttg tatttcttaa caacgtgatt
     2221 ttcaatccct tcaattgctt gtttcataaa ggggttttct tcgttttttt gaaaatcggt
     2281 taatttgagt actttcttat tttccataaa cattctattt aggcaaattt gactttctat
     2341 atatcggtga aaaagtataa tttgattttc cacaaaggaa tatttaaatt tccattaata
     2401 caataaaaaa gcaaaatata ttttcctttt taacatctaa taggaaagag tgactttcta
     2461 atatggaaaa tctgattttc caatatggaa aataccctat attgagtatc aactacttaa
     2521 cttattctat ttcttaagtt cttattatac cctaaaaacg gcatataatc aactacttaa
     2581 aaaatcatcg gtcggggagc gcccagcggc aaggggcggg accacccgtc ccgacgagcg
     2641 cccacaccat aaactttttt tcgaataagc acacaaccgt ttttcgaacc ctgcaaaatt
     2701 tcttccgaac ccgaacggcg taacactcca ttgagtgaag ctgccgtttg gtcgctcccc
     2761 ctttgggggc ggggggggtt acat
//
