LOCUS       NZ_AP027607             3904 bp    DNA     circular CON 04-APR-2024
DEFINITION  Escherichia coli strain LR-71-1 plasmid pLR-71-1_8, complete
            sequence.
ACCESSION   NZ_AP027607
VERSION     NZ_AP027607.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00562543
            Assembly: GCF_036498465.1
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  JOURNAL   Unpublished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 3904)
  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                   :: 84x
            Sequencing Technology :: MGI DNBSEQ-G400RS; ONT MinION Mk1c
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_036498465.1-RS_2024_04_04
            Annotation Date                   :: 04/04/2024 00:05:36
            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)                     :: 5,144
            CDSs (total)                      :: 5,026
            Genes (coding)                    :: 4,742
            CDSs (with protein)               :: 4,742
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 284
            CDSs (without protein)            :: 284
            Pseudo Genes (ambiguous residues) :: 0 of 284
            Pseudo Genes (frameshifted)       :: 78 of 284
            Pseudo Genes (incomplete)         :: 199 of 284
            Pseudo Genes (internal stop)      :: 46 of 284
            Pseudo Genes (multiple problems)  :: 38 of 284
            Pseudo Genes (short protein)      :: 3 of 284
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP027607.1.
            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..3904
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="LR-71-1"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pLR-71-1_8"
                     /geo_loc_name="Ecuador:Santo Domingo"
                     /collection_date="2019"
     gene            complement(171..617)
                     /locus_tag="AABJ98_RS25645"
                     /old_locus_tag="VEE28_49420"
     CDS             complement(171..617)
                     /locus_tag="AABJ98_RS25645"
                     /old_locus_tag="VEE28_49420"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000184721.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="conjugal transfer protein TraD"
                     /protein_id="WP_000184723.1"
                     /translation="MTNREEWLSAKIAYINGLKSPSEQQRLLVLLAEKKNRTTTDEKTL
                     SALIRAEKTAEKAAAAKARVTAIIAAERKAAARAERKARDHELYKAAGLMIVAGLVDSK
                     TGKPKFSAAELVGALAGIAELPRNHPKWQEWERRGKELLTKDSA"
                     /name="conjugal transfer protein TraD"
     gene            789..2339
                     /locus_tag="AABJ98_RS25650"
                     /old_locus_tag="VEE28_49430"
     CDS             789..2339
                     /locus_tag="AABJ98_RS25650"
                     /old_locus_tag="VEE28_49430"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001624483.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobA/MobL family protein"
                     /protein_id="WP_065336819.1"
                     /translation="MASYHCTVKAGAKGSALKHADYISRSGEYKSYKSREDLEFSSSGN
                     MPSWAKKNPAELWKAADEFERKNGTAYREIEIALPRELTREQRIELVEDFVQKELGDRH
                     AYQYAIHNPPGAIDGKEQPHAHIMFCERINDGIERDPQQFFKRANSKSPERGGAKKASI
                     PQTAGERKAALVALRSRWADVQNEHLARYGHESRVDHRSLKEQGINRTPEVHLGPVQAA
                     SLNGEQIVAIQERRNAERELKTARDAANAIQQEQEQKQKIKAVEPVRSARSPELLLQYR
                     KVMKTVIQGEARLARLGDANPNALKEHKLLQNAKAKKDSLSEWSRRIYEGARYLDKLGR
                     NVVSAQRELRELQEQRNALNGIRGLFRGADKREIDARILEQKSVLETAEHERNEFRNKL
                     QQAESEWDKENAAFKRTEGYKYVGDLDRYREREILAAASLENTRQKVAEEVSVARSQML
                     SLEPELSISGDEKAQMRHELLAEMAQERQQQEEKALRIQRSWAREASRSNARDQDMER"
                     /name="MobA/MobL family protein"
     gene            2795..3814
                     /locus_tag="AABJ98_RS25655"
                     /old_locus_tag="VEE28_49440"
     CDS             2795..3814
                     /locus_tag="AABJ98_RS25655"
                     /old_locus_tag="VEE28_49440"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001271373.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_031603333.1"
                     /translation="MSAALQYFEENLPHRPYHTNDLAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDREGAAIDWSDRNAPAPNITVKNPVNGHAHLLYALNIAVRTAPDSSVKA
                     LKYAAAIERSLCEKLCADVNYSGLICKNPFHLEWQVMEWREEAYTLDELADYLDLSASE
                     RRSIDKHYGMGRNCHLFEMTRKWAYRAIRQGWPAFSQWLDAVIQRVEMYNASLPVPLSP
                     PECRAIGKSIAKYTHRNFTPETFAQYVADTHTPEIQAARGRKGGKANSSENQSDKGKKS
                     AAVRWTANDDKRRRALDMYILGASTEDIAVAVGVSSRTIRRWMDNSGEWLTKKQIIKF"
                     /name="replication initiation protein"
     Typing          2796..3570
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="97.426"
                     /coverage="83.0"
                     /evalue="0.0"
     Typing          790..2336
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.436"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ttcggcgtct ttttgagcag cgggctttcc ggcggttttc tcctgtcagc ccagcaatgg
       61 tgcggcttac cgcatgattg aggtggttgt gctcgccgca gtctcatgac cgagcgtagc
      121 gagcgaatga gcgaggaagc accagggaac cggaacgtga acggaggctc ttacgcactg
      181 tctttggtta gtagctcctt cccgcgtctt tcccattcct gccattttgg atggttgcgc
      241 ggtagctctg cgattcctgc gagtgcgcct accagttcgg cagcactaaa ctttggtttt
      301 ccggttttgc tgtccaccag tcctgccaca atcatgaggc ctgcggcctt gtagagttca
      361 tgatcccgcg cctttcgttc cgcccttgcg gctgccttcc gttctgccgc tatgattgcc
      421 gttaccctgg cttttgctgc ggctgctttc tctgcggttt tttctgcccg tatcagtgcg
      481 gacaacgttt tttcatccgt cgttgttcgg ttttttttct ctgccagtaa cacaagtaat
      541 ctctgctgct ctgacggtga tttcagtccg ttgatgtagg caatttttgc acttaaccac
      601 tcttcacgat ttgtcattct tacctctgca cttttgccgt taatgtgagt tgttattgtg
      661 cataatatca ccttgtctgc ctgcgtgtga gaccgtaaaa tcatccctga ttaattcagg
      721 gatgcgcact tagtagtttc tctccttcgt cgagaaactg tgcgctcctg cggagggcta
      781 aaaggcagat ggcaagctac cattgcaccg tcaaagctgg agcaaaaggc agtgccttaa
      841 aacatgctga ttacatttcc agatccggcg aatataagag ctacaaatcg cgggaggatc
      901 tggaattttc gtcatccggt aacatgccat catgggcgaa gaaaaatccc gcagagctat
      961 ggaaagccgc agatgaattt gaacgaaaaa acgggactgc gtaccgtgaa attgagatcg
     1021 cgttaccgcg tgaactgaca cgcgaacaac ggatagaact tgttgaagat ttcgtgcaaa
     1081 aggaacttgg cgatcgccat gcctaccagt acgcgatcca caatccgcca ggtgcaatcg
     1141 acggaaagga acagccacac gcgcatatca tgttttgcga gcggattaat gatggtattg
     1201 aacgcgatcc gcagcaattt tttaaacgtg ccaacagcaa atcaccagaa cggggaggcg
     1261 caaaaaaagc gagtattccc cagacagccg gagagcgaaa agccgccctt gttgcgctgc
     1321 gttcccgctg ggcagatgtg cagaatgagc accttgcgcg atacggtcac gagtcgcgcg
     1381 tagatcatcg ttctctgaaa gaacagggta tcaatcgcac gccggaagtt catcttggcc
     1441 ccgttcaggc cgccagtctc aatggtgagc agattgttgc aatccaggaa cggaggaatg
     1501 ctgagcggga actcaagacc gccagagatg ccgcaaatgc cattcagcag gaacaggagc
     1561 aaaagcaaaa aatcaaggca gttgagcctg ttcgttcagc ccgttcaccg gagttattgc
     1621 ttcagtaccg caaggttatg aaaacggtca ttcagggaga agcaaggctt gctcgtttag
     1681 gggatgccaa tcccaatgcg ctcaaagaac ataagctgct tcagaatgcg aaagcaaaaa
     1741 aagactctct ttccgaatgg agcaggcgaa tatatgaagg agcacggtat ttagacaaac
     1801 tggggcgtaa tgtcgtttcc gcacaaaggg agctgcggga gctacaggaa caacgcaatg
     1861 ctttgaatgg gattcgtggc ctgtttcggg gggctgacaa aagggagatt gatgcgcgta
     1921 ttctggagca aaaaagtgtg ctggaaaccg ctgaacatga aaggaatgaa ttcaggaaca
     1981 agctacagca agctgaatcc gagtgggaca aagaaaacgc tgcttttaag cgtaccgagg
     2041 gatataagta cgttggggat ctggacaggt acagagaacg tgagattctg gccgcggcat
     2101 ctttagagaa taccaggcaa aaggttgctg aagaagtatc cgttgcccgt agccagatgt
     2161 tatctctgga gcctgaactc agtatatctg gagatgaaaa agctcaaatg cgacatgagt
     2221 tactggcaga aatggcgcag gaacggcagc aacaggagga aaaggcactg cgtatacagc
     2281 gatcctgggc cagggaggca tcacgtagta acgcacgtga tcaagatatg gagcgttgaa
     2341 aatgtagcaa tatcgggact gcgccccgaa ccccgccaac gtttcacgga acgcgaaaaa
     2401 attccgcgtc ccgttcaccg ttttctgatg agaaagtttg ctgttttgac ccgttcgccc
     2461 ttctgaacgc tcgaaaccga tcgcgcatcg ctttcgtgca tagttatgca gcaccctaaa
     2521 aacgattctg acgcattttt ctggttcagc ctggtgtttc cttgtctttt tgcgtttttt
     2581 gcgtcagaaa gcgattgagg gcgttttatg gggtacgtac aacgggagtt atggtaaatg
     2641 gatcggtttt gcgggaaggc tcgacaggtt ttgtcgttgg gggtagtgta agcgactgaa
     2701 aaacaaacgc ccctgaaatt cgtgtctctc cgccaagatt gtcacgaaaa tacaggggcg
     2761 atgtcggtcg ataacctgga aggaatcgta acacatgagc gccgcgcttc aatacttcga
     2821 agaaaattta ccccaccgtc cctatcacac gaatgatctc gcttttggtc ttcgcatctc
     2881 cggcaaaggg cgtgcgcttc ttgcgcggta catccagcag aaccagcctc atgcgcagtt
     2941 ctggctggtt tttgacgttg accgcgaggg ggccgcgatt gactggagcg accggaacgc
     3001 ccccgcgccg aacatcaccg taaaaaatcc tgtgaacggt catgctcacc tgctctacgc
     3061 actcaatatc gccgtgagaa ccgcgccgga cagctcggtt aaggcgctga aatatgccgc
     3121 cgcgattgaa cgttcgctgt gtgagaaact ttgtgctgat gtgaactaca gcggactgat
     3181 ttgcaaaaat ccgttccacc tggaatggca ggtgatggag tggcgcgagg aagcctatac
     3241 cctcgatgaa ctggcagatt atctcgattt gagcgcctca gagcgtcgta gcatcgataa
     3301 acattacggg atggggcgaa actgccacct gtttgaaatg acgcgcaaat gggcttacag
     3361 ggcgattcgt cagggctggc cagcattctc acagtggctt gatgccgtga ttcagcgtgt
     3421 cgaaatgtac aacgcatcgc ttcccgttcc gctttctccg cctgaatgtc gggctattgg
     3481 caagagcatt gcgaaataca cgcacaggaa cttcacgccg gaaactttcg cacagtatgt
     3541 ggctgatacg cacacgccag aaattcaggc agcacgcggt cgcaagggcg ggaaggccaa
     3601 ttcgtcagaa aatcagtcgg acaaaggaaa aaaaagcgcc gctgttcggt ggactgctaa
     3661 cgacgacaaa cgtcgtaggg cgcttgatat gtatatcttg ggagcgtcaa cggaagatat
     3721 tgcagtggcg gttggtgtta gcagccggac tattcgacgc tggatggata attctggaga
     3781 atggttaacc aagaaacaaa taattaaatt ttaattaaca gaaaaatgac aattaccccc
     3841 tgtttttgtt aatggatggt taaattcgcg gacatgaaca agcctatatc agataacagc
     3901 gcct
//
