LOCUS       NZ_AP027574             3904 bp    DNA     circular CON 04-APR-2024
DEFINITION  Escherichia coli strain LR-60 plasmid pLR-60_4, complete sequence.
ACCESSION   NZ_AP027574
VERSION     NZ_AP027574.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00562497
            Assembly: GCF_036497705.1
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  JOURNAL   Unpublished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                   :: 107x
            Sequencing Technology :: MGI DNBSEQ-G400RS; ONT MinION Mk1c
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_036497705.1-RS_2024_04_04
            Annotation Date                   :: 04/04/2024 00:03:11
            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)                     :: 5,132
            CDSs (total)                      :: 5,013
            Genes (coding)                    :: 4,860
            CDSs (with protein)               :: 4,860
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 92
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 153
            CDSs (without protein)            :: 153
            Pseudo Genes (ambiguous residues) :: 0 of 153
            Pseudo Genes (frameshifted)       :: 59 of 153
            Pseudo Genes (incomplete)         :: 102 of 153
            Pseudo Genes (internal stop)      :: 30 of 153
            Pseudo Genes (multiple problems)  :: 34 of 153
            Pseudo Genes (short protein)      :: 4 of 153
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP027574.1.
            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-60"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pLR-60_4"
                     /geo_loc_name="Ecuador:Santo Domingo"
                     /collection_date="2019"
     gene            join(3000..3904,1..115)
                     /locus_tag="AABJ89_RS25625"
     CDS             join(3000..3904,1..115)
                     /locus_tag="AABJ89_RS25625"
                     /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"
     gene            complement(376..822)
                     /locus_tag="AABJ89_RS25630"
                     /old_locus_tag="VEE03_49130"
     CDS             complement(376..822)
                     /locus_tag="AABJ89_RS25630"
                     /old_locus_tag="VEE03_49130"
                     /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            994..2544
                     /locus_tag="AABJ89_RS25635"
                     /old_locus_tag="VEE03_49140"
     CDS             994..2544
                     /locus_tag="AABJ89_RS25635"
                     /old_locus_tag="VEE03_49140"
                     /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"
     Typing          3001..3775
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="97.426"
                     /coverage="83.0"
                     /evalue="0.0"
     Typing          995..2541
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.436"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gggagcgtca acggaagata ttgcagtggc ggttggtgtt agcagccgga ctattcgacg
       61 ctggatggat aattctggag aatggttaac caagaaacaa ataattaaat tttaattaac
      121 agaaaaatga caattacccc ctgtttttgt taatggatgg ttaaattcgc ggacatgaac
      181 aagcctatat cagataacag cgcctttcgg cgtctttttg agcagcgggc tttccggcgg
      241 ttttctcctg tcagcccagc aatggtgcgg cttaccgcat gattgaggtg gttgtgctcg
      301 ccgcagtctc atgaccgagc gtagcgagcg aatgagcgag gaagcaccag ggaaccggaa
      361 cgtgaacgga ggctcttacg cactgtcttt ggttagtagc tccttcccgc gtctttccca
      421 ttcctgccat tttggatggt tgcgcggtag ctctgcgatt cctgcgagtg cgcctaccag
      481 ttcggcagca ctaaactttg gttttccggt tttgctgtcc accagtcctg ccacaatcat
      541 gaggcctgcg gccttgtaga gttcatgatc ccgcgccttt cgttccgccc ttgcggctgc
      601 cttccgttct gccgctatga ttgccgttac cctggctttt gctgcggctg ctttctctgc
      661 ggttttttct gcccgtatca gtgcggacaa cgttttttca tccgtcgttg ttcggttttt
      721 tttctctgcc agtaacacaa gtaatctctg ctgctctgac ggtgatttca gtccgttgat
      781 gtaggcaatt tttgcactta accactcttc acgatttgtc attcttacct ctgcactttt
      841 gccgttaatg tgagttgtta ttgtgcataa tatcaccttg tctgcctgcg tgtgagaccg
      901 taaaatcatc cctgattaat tcagggatgc gcacttagta gtttctctcc ttcgtcgaga
      961 aactgtgcgc tcctgcggag ggctaaaagg cagatggcaa gctaccattg caccgtcaaa
     1021 gctggagcaa aaggcagtgc cttaaaacat gctgattaca tttccagatc cggcgaatat
     1081 aagagctaca aatcgcggga ggatctggaa ttttcgtcat ccggtaacat gccatcatgg
     1141 gcgaagaaaa atcccgcaga gctatggaaa gccgcagatg aatttgaacg aaaaaacggg
     1201 actgcgtacc gtgaaattga gatcgcgtta ccgcgtgaac tgacacgcga acaacggata
     1261 gaacttgttg aagatttcgt gcaaaaggaa cttggcgatc gccatgccta ccagtacgcg
     1321 atccacaatc cgccaggtgc aatcgacgga aaggaacagc cacacgcgca tatcatgttt
     1381 tgcgagcgga ttaatgatgg tattgaacgc gatccgcagc aattttttaa acgtgccaac
     1441 agcaaatcac cagaacgggg aggcgcaaaa aaagcgagta ttccccagac agccggagag
     1501 cgaaaagccg cccttgttgc gctgcgttcc cgctgggcag atgtgcagaa tgagcacctt
     1561 gcgcgatacg gtcacgagtc gcgcgtagat catcgttctc tgaaagaaca gggtatcaat
     1621 cgcacgccgg aagttcatct tggccccgtt caggccgcca gtctcaatgg tgagcagatt
     1681 gttgcaatcc aggaacggag gaatgctgag cgggaactca agaccgccag agatgccgca
     1741 aatgccattc agcaggaaca ggagcaaaag caaaaaatca aggcagttga gcctgttcgt
     1801 tcagcccgtt caccggagtt attgcttcag taccgcaagg ttatgaaaac ggtcattcag
     1861 ggagaagcaa ggcttgctcg tttaggggat gccaatccca atgcgctcaa agaacataag
     1921 ctgcttcaga atgcgaaagc aaaaaaagac tctctttccg aatggagcag gcgaatatat
     1981 gaaggagcac ggtatttaga caaactgggg cgtaatgtcg tttccgcaca aagggagctg
     2041 cgggagctac aggaacaacg caatgctttg aatgggattc gtggcctgtt tcggggggct
     2101 gacaaaaggg agattgatgc gcgtattctg gagcaaaaaa gtgtgctgga aaccgctgaa
     2161 catgaaagga atgaattcag gaacaagcta cagcaagctg aatccgagtg ggacaaagaa
     2221 aacgctgctt ttaagcgtac cgagggatat aagtacgttg gggatctgga caggtacaga
     2281 gaacgtgaga ttctggccgc ggcatcttta gagaatacca ggcaaaaggt tgctgaagaa
     2341 gtatccgttg cccgtagcca gatgttatct ctggagcctg aactcagtat atctggagat
     2401 gaaaaagctc aaatgcgaca tgagttactg gcagaaatgg cgcaggaacg gcagcaacag
     2461 gaggaaaagg cactgcgtat acagcgatcc tgggccaggg aggcatcacg tagtaacgca
     2521 cgtgatcaag atatggagcg ttgaaaatgt agcaatatcg ggactgcgcc ccgaaccccg
     2581 ccaacgtttc acggaacgcg aaaaaattcc gcgtcccgtt caccgttttc tgatgagaaa
     2641 gtttgctgtt ttgacccgtt cgcccttctg aacgctcgaa accgatcgcg catcgctttc
     2701 gtgcatagtt atgcagcacc ctaaaaacga ttctgacgca tttttctggt tcagcctggt
     2761 gtttccttgt ctttttgcgt tttttgcgtc agaaagcgat tgagggcgtt ttatggggta
     2821 cgtacaacgg gagttatggt aaatggatcg gttttgcggg aaggctcgac aggttttgtc
     2881 gttgggggta gtgtaagcga ctgaaaaaca aacgcccctg aaattcgtgt ctctccgcca
     2941 agattgtcac gaaaatacag gggcgatgtc ggtcgataac ctggaaggaa tcgtaacaca
     3001 tgagcgccgc gcttcaatac ttcgaagaaa atttacccca ccgtccctat cacacgaatg
     3061 atctcgcttt tggtcttcgc atctccggca aagggcgtgc gcttcttgcg cggtacatcc
     3121 agcagaacca gcctcatgcg cagttctggc tggtttttga cgttgaccgc gagggggccg
     3181 cgattgactg gagcgaccgg aacgcccccg cgccgaacat caccgtaaaa aatcctgtga
     3241 acggtcatgc tcacctgctc tacgcactca atatcgccgt gagaaccgcg ccggacagct
     3301 cggttaaggc gctgaaatat gccgccgcga ttgaacgttc gctgtgtgag aaactttgtg
     3361 ctgatgtgaa ctacagcgga ctgatttgca aaaatccgtt ccacctggaa tggcaggtga
     3421 tggagtggcg cgaggaagcc tataccctcg atgaactggc agattatctc gatttgagcg
     3481 cctcagagcg tcgtagcatc gataaacatt acgggatggg gcgaaactgc cacctgtttg
     3541 aaatgacgcg caaatgggct tacagggcga ttcgtcaggg ctggccagca ttctcacagt
     3601 ggcttgatgc cgtgattcag cgtgtcgaaa tgtacaacgc atcgcttccc gttccgcttt
     3661 ctccgcctga atgtcgggct attggcaaga gcattgcgaa atacacgcac aggaacttca
     3721 cgccggaaac tttcgcacag tatgtggctg atacgcacac gccagaaatt caggcagcac
     3781 gcggtcgcaa gggcgggaag gccaattcgt cagaaaatca gtcggacaaa ggaaaaaaaa
     3841 gcgccgctgt tcggtggact gctaacgacg acaaacgtcg tagggcgctt gatatgtata
     3901 tctt
//
