LOCUS       NZ_AP027540             3372 bp    DNA     circular CON 04-APR-2024
DEFINITION  Escherichia coli strain LR-46 plasmid pLR-46_3, complete sequence.
ACCESSION   NZ_AP027540
VERSION     NZ_AP027540.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00562547
            Assembly: GCF_036496705.1
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  JOURNAL   Unpublished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                   :: 150x
            Sequencing Technology :: MGI DNBSEQ-G400RS; ONT MinION Mk1c
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_036496705.1-RS_2024_04_03
            Annotation Date                   :: 04/03/2024 23:59:16
            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)                     :: 5,093
            CDSs (total)                      :: 4,976
            Genes (coding)                    :: 4,721
            CDSs (with protein)               :: 4,721
            Genes (RNA)                       :: 117
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 8
            Pseudo Genes (total)              :: 255
            CDSs (without protein)            :: 255
            Pseudo Genes (ambiguous residues) :: 0 of 255
            Pseudo Genes (frameshifted)       :: 80 of 255
            Pseudo Genes (incomplete)         :: 154 of 255
            Pseudo Genes (internal stop)      :: 56 of 255
            Pseudo Genes (multiple problems)  :: 36 of 255
            Pseudo Genes (short protein)      :: 3 of 255
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP027540.1.
            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-46"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pLR-46_3"
                     /geo_loc_name="Ecuador:Santo Domingo"
                     /collection_date="2019"
     gene            complement(join(3298..3372,1..486))
                     /locus_tag="AABJ70_RS25425"
     CDS             complement(join(3298..3372,1..486))
                     /locus_tag="AABJ70_RS25425"
                     /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(<518..1174)
                     /locus_tag="AABJ70_RS25430"
                     /pseudo=""
     CDS             complement(<518..1174)
                     /locus_tag="AABJ70_RS25430"
                     /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(1164..1487)
                     /locus_tag="AABJ70_RS25435"
                     /old_locus_tag="VEE30_48550"
     CDS             complement(1164..1487)
                     /locus_tag="AABJ70_RS25435"
                     /old_locus_tag="VEE30_48550"
                     /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            1551..1742
                     /locus_tag="AABJ70_RS25440"
                     /old_locus_tag="VEE30_48560"
     CDS             1551..1742
                     /locus_tag="AABJ70_RS25440"
                     /old_locus_tag="VEE30_48560"
                     /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            complement(3058..3291)
                     /locus_tag="AABJ70_RS25445"
                     /old_locus_tag="VEE30_48570"
     CDS             complement(3058..3291)
                     /locus_tag="AABJ70_RS25445"
                     /old_locus_tag="VEE30_48570"
                     /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          complement(1824..1904)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="87.805"
                     /coverage="93.0"
                     /evalue="8.68e-18"
     Typing          complement(3..1174)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="96.675"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(2976..3370)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="82.482"
                     /coverage="99.0"
                     /evalue="1.91e-45"
ORIGIN
        1 caccagaaat ttcccgttct cgccattgac gaacgtcacc ccccaggttt ttgcctcgag
       61 tttcgccagc gtgttttcct gctctctgat agtcaggata tttttcgcaa tcttgctttc
      121 ctgccactcc atcagccccc agcaccccag gaaaatgccg cccgtgacgc tgagcgcggt
      181 cagcgccgga aacagtatcc gccctttgat cacccgccag agcagttttt tctgctgccg
      241 ggacagttcg gcctctgtgg tgctgaactg catgctcacg gtggtgctca gcgtatccag
      301 ttgctttttc acggatgttg tatgttcgct gatagcgtct ctgattttct gcctgtttaa
      361 gctcaatgcc ttgtctacag actcttcgag cttcctgaac tcgctgttca gcatgttctc
      421 ggtagaagcg gctcgctctt tcagtttctt ctcgaagtct gttcccattt gtaaaagatt
      481 gctcatacag cgcccccttt agcctgagat tccgcccccc ctccgggtcg gcaatactga
      541 tgctgctttt ggttgtcctc accacctcaa aacctgccgc tgtaagcgcc tctgtgacat
      601 cctgacgcgt ttttattgct ccggcatggt aaagagcctc aagaccccgt gtaatcgctt
      661 ctgcggcctc ctgtttcgct tttggcagat tatttggcgt gacaagcgtc cgtctgttct
      721 ccggtgcgtt cgggtcacgc agcccgtaat gatgattaac cagcgtctgc caggcattta
      781 tcctcggcct gtccgcgcgg tcgtagtacg gctggaggcg cttaccgctc tgtagctcca
      841 tgttcgggat gacaaaattc agttcgagcc gccccttatc ctggtgttcc acccagagaa
      901 tgctgtactg gtctttttcg agaccgggca taagaacacg ctcaaagctc gtcatcactc
      961 tttcgcgttc acccggcggt aactccttct ccgcgaacga cagaacgcct gaagtgtatt
     1021 tcttcgagaa tggcgtggaa tcaatgagtt cccgcacttc ttccgggtta ccccggagca
     1081 ccgttgcgcc ttcgcggtta cgctcccgcc ccagcaggta atcgaccggg ccacttccac
     1141 cgcctttccc cctggcatga aatttaacta tcatcccgta ccccctgttc cctgacagcc
     1201 tgccgcaact ggcgcaattc accctcgatg gccatcagtg cggccaccac atgaacccgg
     1261 tcaatcgaag accactggcc gctgttcacc ttccgggctg tctggttcag gttgttcccg
     1321 atggcagcca gatgccgcag caatggcggc gatagtgtcg gcagttttcc tgtgcgtgca
     1381 accggctccc ccagacagac ccgccgcatc cattccgcca gtcgtttacc ctcgcagcgt
     1441 tccagtaacc gggcgtgctc ctcatcggta acccgtatcg tgagcatctt ctcgcgtttc
     1501 atcggtatca ttccccctaa caaatccccc atacaaggag ccttaagacc atgaccaaac
     1561 aggaaaaaac agcccttaac atggctcgct ttatcagaag ccagacgcta accctgctgg
     1621 aaaaactcaa cgatctggac gcggacgaac aggcagacat ctgcgaatca cttcacgacc
     1681 acgccgacga actctaccgc agttgcctcg cacgcttcgg cgatgacggt gaaagcaact
     1741 gaaacatgca gctcccggag acgttcacag cttgcctgtg agcggatgcc gggagcagac
     1801 aagcccgcca gggcgcgtca gtgcgggtgt cggggcgcag ccctgaccca gttcacagag
     1861 cgatagcgat gtgtatactg gcttatctca ttttgcatcg gtgcagacat ggatgggaag
     1921 tgcaccatgt caggagtaaa aagccgcaca gatgtaaaaa cagcgcaccc gataaacagc
     1981 acacacgcgg acactggcac aggcgcgtaa gtgcacaatg cttgcatctg tgactcttcc
     2041 gcttcctcgc ccactcgctc actacgttcg gtcgctgggg ctgcggcgag cggtgggatc
     2101 actctcgttg tgatgcagat ccgttttttt ttttgcactg gagttatcag gagttgcggt
     2161 gcacatggga tcgtgcgata tgccggatgg tgaaaggttg gagggaacgg caacaactca
     2221 cccctcccag tgaagggacg ggtagtttgc cgctctcgat atgccggacg gagccaaggc
     2281 catcgatcac ggggcgcgtc agtggaagaa cccgcgcctg cgtgacgtat gcgtcttcgc
     2341 cgcaccatct cacccgtcac gccaccacat accgggaact gccgccaagg tctaactcaa
     2401 ccaatctagc cgcgctacat acggtttttg tggcaactca tcaggtgtcc gctgtcgatg
     2461 aaactctctg cgccggtagc ggaactctca cgcgtgcggt cgccgtcgtc acagctcccc
     2521 caaccgcaaa cgattctcgc aaatacgcaa gtatctgcaa aaacaggttt ttttcggggt
     2581 tcctgggaga ctgtgctgtt gaaaaattct tgaagaatac agaaggctca tgcaaactga
     2641 atgaactggt ttctgttgtg gatctcaaca gtttccacag gaacattgag gaggtcagag
     2701 acctcaatga acccgaaaca gctcgccttc ctggcgagct gttttcgttc tacgcccgcc
     2761 gacgaaagat cgcaagtgca ataacgagat ttttcacgtc tttacgctca aaaagtaaaa
     2821 aaaccatgtt ttcccctggc tgaatcccca aaaacgcgtg aaatgcgttt tcaggatgtt
     2881 gcatagctat gcacaaatac ggcacacgat ttgtttcgct cgccccagcc gtcgaactgg
     2941 tcaaaatggc aagatttcgt cacttccccg gtcacatctc cattgatggc ccactccgaa
     3001 cccgtgccgc gcgttcctgt acctcatgtc tgtaccgggc acgctcctgt tcatccctta
     3061 gctgttgttc gcgataaata accgactcaa gcgatccact tgcccggcta atctctgcac
     3121 ctgctgactc aatatcacga cgcgctcgtt cagtatcgcg ttgttccgtt gcgtaacctc
     3181 gtgcatcttc tgcaattccg cgaaggcgct ctcccactcg ttcagccgcc gcatatagtc
     3241 ctgttgcaaa tgctctaagg cgttcagcaa atgcccttcc agttccgtca tactcgttta
     3301 ctccctgacc agcctcacgg cgttcttgtc gcccaccgtc caggtgtttt cccctttcac
     3361 cccgtccggc aa
//
