LOCUS       NZ_AP027608             3370 bp    DNA     circular CON 04-APR-2024
DEFINITION  Escherichia coli strain LR-71-1 plasmid pLR-71-1_9, complete
            sequence.
ACCESSION   NZ_AP027608
VERSION     NZ_AP027608.1
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  JOURNAL   Unpublished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 3370)
  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
            AP027608.1.
            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..3370
                     /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_9"
                     /geo_loc_name="Ecuador:Santo Domingo"
                     /collection_date="2019"
     gene            complement(895..1128)
                     /locus_tag="AABJ98_RS25660"
                     /old_locus_tag="VEE28_49450"
     CDS             complement(895..1128)
                     /locus_tag="AABJ98_RS25660"
                     /old_locus_tag="VEE28_49450"
                     /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"
     gene            complement(1135..1695)
                     /locus_tag="AABJ98_RS25665"
                     /old_locus_tag="VEE28_49460"
     CDS             complement(1135..1695)
                     /locus_tag="AABJ98_RS25665"
                     /old_locus_tag="VEE28_49460"
                     /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            complement(<1727..2383)
                     /locus_tag="AABJ98_RS25670"
                     /pseudo=""
     CDS             complement(<1727..2383)
                     /locus_tag="AABJ98_RS25670"
                     /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            complement(2373..2696)
                     /locus_tag="AABJ98_RS25675"
                     /old_locus_tag="VEE28_49470"
     CDS             complement(2373..2696)
                     /locus_tag="AABJ98_RS25675"
                     /old_locus_tag="VEE28_49470"
                     /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            2760..2951
                     /locus_tag="AABJ98_RS25680"
                     /old_locus_tag="VEE28_49480"
     CDS             2760..2951
                     /locus_tag="AABJ98_RS25680"
                     /old_locus_tag="VEE28_49480"
                     /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"
     Typing          complement(3033..3113)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="87.805"
                     /coverage="93.0"
                     /evalue="8.68e-18"
     Typing          complement(813..2383)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.817"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 catgggatcg tgcgatatgc cggatggtga aaggttggag ggaacggcaa caactcaccc
       61 ctcccagtga agggacgggt agtttgccgc tctcgatatg ccggacggag ccaaggccat
      121 cgatcacggg gcgcgtcagt ggaagaaccc gcgcctgcgt gacgtatgcg tcttcgccgc
      181 accatctcac ccgtcacgcc accacatacc gggaactgcc gccaaggtct aactcaacca
      241 atctagccgc gctacatacg gtttttgtgg caactcatca ggtgtccgct gtcgatgaaa
      301 ctctctgcgc cggtagcgga actctcacgc gtgcggtcgc cgtcgtcaca gctcccccaa
      361 ccgcaaacga ttctcgcaaa tacgcaagta tctgcaaaaa caggtttttt tcggggttcc
      421 tgggagactg tgctgttgaa aaattcttga agaatacaga aggctcatgc aaactgaatg
      481 aactggtttc tgttgtggat ctcaacagtt tccacaggaa cattgaggag gtcagagacc
      541 tcaatgaacc cgaaacagct cgccttcctg gcgagctgtt ttcgttctac gcccgccgac
      601 gaaagatcgc aagtgcaata acgagatttt tcacgtcttt acgctcaaaa agtaaaaaaa
      661 ccatgttttc ccctggctga atccccaaaa acgcgtgaaa tgcgttttca ggatgttgca
      721 tagctatgca caaatacggc acacgatttg tttcgctcgc cccagccgtc gaactggtca
      781 aaatggcaag atttcgtcac ttccccggtc acatctccat tgatggccca ctccgaaccc
      841 gtgccgcgcg ttcctgtacc tcatgtctgt accgggcacg ctcctgttca tcccttagct
      901 gttgttcgcg ataaataacc gactcaagcg atccacttgc ccggctaatc tctgcacctg
      961 ctgactcaat atcacgacgc gctcgttcag tatcgcgttg ttccgttgcg taacctcgtg
     1021 catcttctgc aattccgcga aggcgctctc ccactcgttc agccgccgca tatagtcctg
     1081 ttgcaaatgc tctaaggcgt tcagcaaatg cccttccagt tccgtcatac tcgtttactc
     1141 cctgaccagc ctcacggcgt tcttgtcgcc caccgtccag gtgttttccc ctttcacccc
     1201 gtccggcaac accagaaatt tcccgttctc gccattgacg aacgtcaccc cccaggtttt
     1261 tgcctcgagt ttcgccagcg tgttttcctg ctctctgata gtcaggatat ttttcgcaat
     1321 cttgctttcc tgccactcca tcagccccca gcaccccagg aaaatgccgc ccgtgacgct
     1381 gagcgcggtc agcgccggaa acagtatccg ccctttgatc acccgccaga gcagtttttt
     1441 ctgctgccgg gacagttcgg cctctgtggt gctgaactgc atgctcacgg tggtgctcag
     1501 cgtatccagt tgctttttca cggatgttgt atgttcgctg atagcgtctc tgattttctg
     1561 cctgtttaag ctcaatgcct tgtctacaga ctcttcgagc ttcctgaact cgctgttcag
     1621 catgttctcg gtagaagcgg ctcgctcttt cagtttcttc tcgaagtctg ttcccatttg
     1681 taaaagattg ctcatacagc gcccccttta gcctgagatt ccgccccccc tccgggtcgg
     1741 caatactgat gctgcttttg gttgtcctca ccacctcaaa acctgccgct gtaagcgcct
     1801 ctgtgacatc ctgacgcgtt tttattgctc cggcatggta aagagcctca agaccccgtg
     1861 taatcgcttc tgcggcctcc tgtttcgctt ttggcagatt atttggcgtg acaagcgtcc
     1921 gtctgttctc cggtgcgttc gggtcacgca gcccgtaatg atgattaacc agcgtctgcc
     1981 aggcatttat cctcggcctg tccgcgcggt cgtagtacgg ctggaggcgc ttaccgctct
     2041 gtagctccat gttcgggatg acaaaattca gttcgagccg ccccttatcc tggtgttcca
     2101 cccagagaat gctgtactgg tctttttcga gaccgggcat aagaacacgc tcaaagctcg
     2161 tcatcactct ttcgcgttca cccggcggta actccttctc cgcgaacgac agaacgcctg
     2221 aagtgtattt cttcgagaat ggcgtggaat caatgagttc ccgcacttct tccgggttac
     2281 cccggagcac cgttgcgcct tcgcggttac gctcccgccc cagcaggtaa tcgaccgggc
     2341 cacttccacc gcctttcccc ctggcatgaa atttaactat catcccgtac cccctgttcc
     2401 ctgacagcct gccgcaactg gcgcaattca ccctcgatgg ccatcagtgc ggccaccaca
     2461 tgaacccggt caatcgaaga ccactggccg ctgttcacct tccgggctgt ctggttcagg
     2521 ttgttcccga tggcagccag atgccgcagc aatggcggcg atagtgtcgg cagttttcct
     2581 gtgcgtgcaa ccggctcccc cagacagacc cgccgcatcc attccgccag tcgtttaccc
     2641 tcgcagcgtt ccagtaaccg ggcgtgctcc tcatcggtaa cccgtatcgt gagcatcttc
     2701 tcgcgtttca tcggtatcat tccccctaac aaatccccca tacaaggagc cttaagacca
     2761 tgaccaaaca ggaaaaaaca gcccttaaca tggctcgctt tatcagaagc cagacgctaa
     2821 ccctgctgga aaaactcaac gatctggacg cggacgaaca ggcagacatc tgcgaatcac
     2881 ttcacgacca cgccgacgaa ctctaccgca gttgcctcgc acgcttcggc gatgacggtg
     2941 aaagcaactg aaacatgcag ctcccggaga cgttcacagc ttgcctgtga gcggatgccg
     3001 ggagcagaca agcccgccag ggcgcgtcag tgcgggtgtc ggggcgcagc cctgacccag
     3061 ttcacagagc gatagcgatg tgtatactgg cttatctcat tttgcatcgg tgcagaatgg
     3121 atgggaagtg caccatgtca ggagtaaaaa gccgcacaga tgtaaaaaca gcgcacccga
     3181 taaacagcac acacgcggac actggcacag gcgcgtaagt gcacaatgct tgcatctgtg
     3241 actcttccgc ttcctcgccc actcgctcac tacgttcggt cgctggggct gcggcgagcg
     3301 gtgggatcac tctcgttgtg atgcagatcc gttttttttt tgcactggag ttatcaggag
     3361 ttgcggtgca
//
