LOCUS       NZ_AP027615             3372 bp    DNA     circular CON 04-APR-2024
DEFINITION  Escherichia coli strain LR-72 plasmid pLR-72_3, complete sequence.
ACCESSION   NZ_AP027615
VERSION     NZ_AP027615.1
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  JOURNAL   Unpublished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 3372)
  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
            AP027615.1.
            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..3372
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="LR-72"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pLR-72_3"
                     /geo_loc_name="Ecuador:Santo Domingo"
                     /collection_date="2019"
     gene            complement(140..331)
                     /locus_tag="AABJ55_RS23810"
                     /old_locus_tag="VEE35_45380"
     CDS             complement(140..331)
                     /locus_tag="AABJ55_RS23810"
                     /old_locus_tag="VEE35_45380"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165979.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_000165979.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNDLDADEQADICESLHDHA
                     DELYRSCLARFGDDGESN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            395..718
                     /locus_tag="AABJ55_RS23815"
                     /old_locus_tag="VEE35_45390"
     CDS             395..718
                     /locus_tag="AABJ55_RS23815"
                     /old_locus_tag="VEE35_45390"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_024132211.1"
                     /translation="MLTIRVTDEEHARLLERCEGKRLAEWMRRVCLGEPVARTGKLPTL
                     SPPLLRHLAAIGNNLNQTARKVNSGQWSSIDRVHVVAALMAIEGELRQLRQAVREQGVR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            927..>1364
                     /locus_tag="AABJ55_RS23820"
                     /pseudo=""
     CDS             927..>1364
                     /locus_tag="AABJ55_RS23820"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            1396..1956
                     /locus_tag="AABJ55_RS23825"
                     /old_locus_tag="VEE35_45400"
     CDS             1396..1956
                     /locus_tag="AABJ55_RS23825"
                     /old_locus_tag="VEE35_45400"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000067488.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_000067487.1"
                     /translation="MSNLLQMGTDFEKKLKERAASTENMLNSEFRKLEESVDKALSLNR
                     QKIRDAISEHTTSVKKQLDTLSTTVSMQFSTTEAELSRQQKKLLWRVIKGRILFPALTA
                     LSVTGGIFLGCWGLMEWQESKIAKNILTIREQENTLAKLEAKTWGVTFVNGENGKFLVL
                     PDGVKGENTWTVGDKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     gene            1963..2196
                     /locus_tag="AABJ55_RS23830"
                     /old_locus_tag="VEE35_45410"
     CDS             1963..2196
                     /locus_tag="AABJ55_RS23830"
                     /old_locus_tag="VEE35_45410"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137389.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_000137389.1"
                     /translation="MTELEGHLLNALEHLQQDYMRRLNEWESAFAELQKMHEVTQRNNA
                     ILNERVVILSQQVQRLAGQVDRLSRLFIANNS"
                     /name="MbeD family mobilization/exclusion protein"
     Typing          709..2279
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.628"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ccagtataca catcgctatc gctctgtgaa ctgggtcagg gctgcgcccc gacacccgca
       61 ctgacgcgcc ctggcgggct tgtctgctcc cggcatccgc tcacaggcaa gctgtgaacg
      121 tctccgggag ctgcatgttt cagttgcttt caccgtcatc gccgaagcgt gcgaggcaac
      181 tgcggtagag ttcgtcggcg tggtcgtgaa gtgattcgca gatgtctgcc tgttcgtccg
      241 cgtccagatc gttgagtttt tccagcaggg ttagcgtctg gcttctgata aagcgagcca
      301 tgttaagggc tgttttttcc tgtttggtca tggtcttaag gctccttgta tgggggattt
      361 gttaggggga atgataccga tgaaacgcga gaagatgctc acgatacggg ttaccgatga
      421 ggagcacgcc cggttactgg aacgctgcga gggtaaacga ctggcggaat ggatgcggcg
      481 ggtctgtctg ggggagccgg ttgcacgcac aggaaaactg ccgacactat cgccgccatt
      541 gctgcggcat ctggctgcca tcgggaacaa cctgaaccag acagcccgga aggtgaacag
      601 cggccagtgg tcttcgattg accgggttca tgtggtggcc gcactgatgg ccatcgaggg
      661 tgaattgcgt cagttgcggc aggctgtcag ggaacagggg gtacgggatg atagttaaat
      721 ttcatgccag ggggaaaggc ggtggaagtg gcccggtcga ttacctgctg gggcgggagc
      781 gtaaccgcga aggcgcaacg gtgctccggg gtaacccgga agaagtgcgg gaactcattg
      841 attccacgcc attctcgaag aaatacactt caggcgttct gtcgttcgcg gagaaggagt
      901 taccgccggg tgaacgcgaa agagtgatga cgagctttga gcgtgttctt atgcccggtc
      961 tcgaaaaaga ccagtacagc attctctggg tggaacacca ggataagggg cggctcgaac
     1021 tgaattttgt catcccgaac atggagctac agagcggtaa gcgcctccag ccgtactacg
     1081 accgcgcgga caggccgagg ataaatgcct ggcagacgct ggttaatcat cattacgggc
     1141 tgcgtgaccc gaacgcaccg gagaacagac ggacgcttgt cacgccaaat aatctgccaa
     1201 aagcgaaaca ggaggccgca gaagcgatta cacggggtct tgaggctctt taccatgccg
     1261 gagcaataaa aacgcgtcag gatgtcacag aggcgcttac agaggcaggt tttgaggtgg
     1321 tgaggacaac caaaagcagc atcagtattg ccgacccgga gggggggcgg aatctcaggc
     1381 taaagggggc gctgtatgag caatctttta caaatgggaa cagacttcga gaagaaactg
     1441 aaagagcgag ccgcttctac cgagaacatg ctgaacagcg agttcaggaa gctcgaagag
     1501 tctgtagaca aggcattgag cttaaacagg cagaaaatca gagacgctat cagcgaacat
     1561 acaacatccg tgaaaaagca actggatacg ctgagcacca ccgtgagcat gcagttcagc
     1621 accacagagg ccgaactgtc ccggcagcag aaaaaactgc tctggcgggt gatcaaaggg
     1681 cggatactgt ttccggcgct gaccgcgctc agcgtcacgg gcggcatttt cctggggtgc
     1741 tgggggctga tggagtggca ggaaagcaag attgcgaaaa atatcctgac tatcagagag
     1801 caggaaaaca cgctggcgaa actcgaggca aaaacctggg gggtgacgtt cgtcaatggc
     1861 gagaacggga aatttctggt gttgccggac ggggtgaaag gggaaaacac ctggacggtg
     1921 ggcgacaaga acgccgtgag gctggtcagg gagtaaacga gtatgacgga actggaaggg
     1981 catttgctga acgccttaga gcatttgcaa caggactata tgcggcggct gaacgagtgg
     2041 gagagcgcct tcgcggaatt gcagaagatg cacgaggtta cgcaacggaa caacgcgata
     2101 ctgaacgagc gcgtcgtgat attgagtcag caggtgcaga gattagccgg gcaagtggat
     2161 cgcttgagtc ggttatttat cgcgaacaac agctaaggga tgaacaggag cgtgcccggt
     2221 acagacatga ggtacaggaa cgcgcggcac gggttcggag tgggccatca atggagatgt
     2281 gaccggggaa gtgacgaaat cttgccattt tgaccagttc gacggctggg gcgagcgaaa
     2341 caaatcgtgt gccgtatttg tgcatagcta tgcaacatcc tgaaaacgca tttcacgagt
     2401 ttttggggat tcagccaggg gaaaacatgg tttttttact ttttgagcgt aaagacgtga
     2461 aaaatctcgt tattgcactt gcgatctttc gtcggcgggc gtagaacgaa aacagctcgc
     2521 caggaaggcg agctgtttcg ggttcattga ggtctctgac ctcctcaatg ttcctgtgga
     2581 aactgttgag atccacaaca gaaaccagtt cattcagttt gcatgagcct tctgtattct
     2641 tcaagaattt ttcaacagca cagtctccca ggaaccccga aaaaaacctg tttttgcaga
     2701 tacttgcgta tttgcgagaa tcgtttgcgg ttgggggagc tgtgacgacg gcgaccgcac
     2761 gcgtgagagt tccgctaccg gcgcagagag tttcatcgac agcggacacc tgatgagttg
     2821 ccacaaaaac cgtatgtagc gcggctagat tggttgagtt agaccttggc ggcagttccc
     2881 ggtatgtggt ggcgtgacgg gtgagatggt gcggcgaaga cgcatacgtc acgcaggcgc
     2941 gggttcttcc actgacgcgc cccgtgatcg atggccttgg ctccgtccgg catatcgaga
     3001 gcggcaaact acccgtccct tcactgggag gggtgagttg ttgccgttcc ctccaacctt
     3061 tcaccatccg gcatatcgca cgatcccatg tgcaccgcaa ctcctgataa ctccagtgca
     3121 aaaaaaaaaa cggatctgca tcacaacgag agtgatccca ccgctcgccg cagccccagc
     3181 gaccgaacgt agtgagcgag tgggcgagga agcggaagag tcacagatgc aagcattgtg
     3241 cacttacgcg cctgtgccag tgtccgcgtg tgtgctgttt atcgggtgcg ctgtttttac
     3301 atctgtgcgg ctttttactc ctgacatggt gcacttccca tccatgtctg caccgatgca
     3361 aaatgagata ag
//
