LOCUS       NZ_AP027583             4634 bp    DNA     circular CON 04-APR-2024
DEFINITION  Escherichia coli strain LR-62-2 plasmid pLR-62-2_7, complete
            sequence.
ACCESSION   NZ_AP027583
VERSION     NZ_AP027583.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00562545
            Assembly: GCF_036497865.1
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  JOURNAL   Unpublished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 4634)
  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                   :: 39x
            Sequencing Technology :: MGI DNBSEQ-G400RS; ONT MinION Mk1c
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_036497865.1-RS_2024_04_04
            Annotation Date                   :: 04/04/2024 00:18:12
            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)                     :: 5,347
            CDSs (total)                      :: 5,231
            Genes (coding)                    :: 5,030
            CDSs (with protein)               :: 5,030
            Genes (RNA)                       :: 116
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 201
            CDSs (without protein)            :: 201
            Pseudo Genes (ambiguous residues) :: 0 of 201
            Pseudo Genes (frameshifted)       :: 69 of 201
            Pseudo Genes (incomplete)         :: 137 of 201
            Pseudo Genes (internal stop)      :: 35 of 201
            Pseudo Genes (multiple problems)  :: 39 of 201
            Pseudo Genes (short protein)      :: 4 of 201
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP027583.1.
            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..4634
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="LR-62-2"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pLR-62-2_7"
                     /geo_loc_name="Ecuador:Santo Domingo"
                     /collection_date="2019"
     gene            complement(458..649)
                     /locus_tag="AABK23_RS26645"
                     /old_locus_tag="VEE29_51000"
     CDS             complement(458..649)
                     /locus_tag="AABK23_RS26645"
                     /old_locus_tag="VEE29_51000"
                     /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_000165986.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGESN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            712..1035
                     /locus_tag="AABK23_RS26650"
     CDS             712..1035
                     /locus_tag="AABK23_RS26650"
                     /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_001677263.1"
                     /translation="MLTIRVSDEEHARLLERCEGKRLAEWMRRVCLGEPVARTGKLPTL
                     SPPLLRHLAAIGNNLNQTARKVNSGHWSSIDRVHVVAALMAIEGELRQLRQAVREQGGR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            1244..>1681
                     /locus_tag="AABK23_RS26655"
                     /pseudo=""
     CDS             1244..>1681
                     /locus_tag="AABK23_RS26655"
                     /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            1713..2273
                     /locus_tag="AABK23_RS26660"
                     /old_locus_tag="VEE29_51020"
     CDS             1713..2273
                     /locus_tag="AABK23_RS26660"
                     /old_locus_tag="VEE29_51020"
                     /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_000067488.1"
                     /translation="MSNLLQMGTDFEKKLKERAASTENMLNSEFRKLEESVDKALSLNR
                     QKIRDAISEHTTSVKQQLDTLSTTVSTQLSTTEAELSRQQKNLLWQVIKGRVLFPALTA
                     LSVTGGIFLGCWGLIQWQESRIAKNILTIREQENTLAKLEAKTWGVTFVNGENGKFLVL
                     PDGVKGENTWTVGDKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     gene            2280..2513
                     /locus_tag="AABK23_RS26665"
                     /old_locus_tag="VEE29_51030"
     CDS             2280..2513
                     /locus_tag="AABK23_RS26665"
                     /old_locus_tag="VEE29_51030"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /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_000137388.1"
                     /translation="MTELEGHLLNALEHLQQDYMRRLNEWESAFAELQKMHAVTQQNNA
                     ILNERVVNLSQQVQLLAGQVDRLSRLFITNNR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(3242..4081)
                     /locus_tag="AABK23_RS26670"
     CDS             complement(3242..4081)
                     /locus_tag="AABK23_RS26670"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001354646.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001354646.1"
                     /translation="MLTLFIFFVLLIAACFFCFAPPRRGYDRNEIIPYKIKLSINKYRL
                     YIYSSGKVRQYLLFLVILSLYYSIAEPFKSELIKNISYSLMAAFIFDTGLNFSKENITK
                     GVISTRWHNDLYSSFERMKAINKIYYPSNKEINTEGLSKAITSSLFNDDANSFAKRDFR
                     LMWDLSSEKYLSYKEIIIRKGDKLDAVCLRFINDDYKFLVNFNRDEEVFKYFPSIMQPS
                     LKTYRALSRLVNSIKDPSRFKFTTESLEMELLEYLELRNELFNDIEEVMGSYAQRAP"
                     /name="hypothetical protein"
     gene            complement(4273..4422)
                     /locus_tag="AABK23_RS26675"
     CDS             complement(4273..4422)
                     /locus_tag="AABK23_RS26675"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001326446.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_032194431.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPERHVKTPLAAAIGNRLEELVLK
                     LCAG"
                     /name="hypothetical protein"
     Typing          286..370
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.03e-37"
     Typing          complement(4..275)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.971"
                     /coverage="99.0"
                     /evalue="5.41e-103"
     Typing          4081..4532
                     /name="ColRNAI_rep_cluster_1857"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="83.0"
                     /evalue="0.0"
     Typing          1026..2611
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.811"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tgtttttgtg atgctcgtca ggggggcgga gcctatggaa aaacgccagc ggcgcggcct
       61 tcttcctgtt cctggtcttt tgctcacatg tttcttttgg cgttatcccc tgattctgtg
      121 gataaccgca tcaccgtctt tgagtgagct gataccgctc gccgcagccg aacgaccgag
      181 cgtagcgagt cagtgagcga ggaagcggaa gagcgcctga tgcggcattt tctccttacg
      241 catatgtgcg gtatttcaca ccgcatatgg tgcacttttc ttataatccg cactgatgcc
      301 acatagttaa gccagtatac actccgctat cgctacgtga ctgggtcagg gctgcgcccc
      361 gacacccgct aaaacccgct gacgcgccct gacgggcttg tctgctcccg gcatccgctc
      421 acaggcaagc tgtgaacgtc tccgggagct gcatgtttca gttgctttca ccgtcatcgc
      481 cgaagcgtgc gaggcaacta cggtagagtt cgtcggcgtg gtcgtgaagt gattcgcaga
      541 tgtctgcctg ttcgtccgcg tccagctcgt tgagtttttc cagcagggtc agcgtctggc
      601 ttctgataaa gcgggccatg ttaagggctg ttttttcctg tttggtcatg gtcttaaggc
      661 tccttaatag gggatttttt agggggaatg ataccgatga aacgcgagaa gatgctcacg
      721 atacgggtta gcgatgagga gcacgcccgg ttactggaac gctgcgaggg taaacgactg
      781 gcagaatgga tgcggcgggt ctgtctgggg gagccggttg cgcgcacagg aaaactgccg
      841 acactatcgc cgccattgct gcggcatctg gctgccatcg ggaacaatct gaaccagaca
      901 gcccggaagg tgaacagcgg ccactggtct tcgattgacc gggttcatgt ggtggccgca
      961 ctgatggcca tcgagggtga attgcgccag ttgcggcagg ctgtcaggga acagggggga
     1021 cgggatgata gttaaatttc atgccagggg gaaaggcggt ggaagtggcc cggtcgatta
     1081 cctgctgggg cgggagcgta accgcgaagg cgcaacggtg ctccggggta acccggaaga
     1141 aatccgggaa ctcattgatg ccacgccatt ttcgaagaaa tacacgtcag gcgttctgtc
     1201 gttcgcggag aaggagttac cgccgggtga acgcgaaaga gtgatgacga gctttgagcg
     1261 tgttcttatg cccggtctcg aaaaagacca gtacagcatt ctctgggtgg aacaccagga
     1321 taaggggcgg ctcgaactga attttgtcat tccgaacatg gaactacaga gcggtaagcg
     1381 cctccagccg tactacgacc gtgcggacag gccgaggata aatgcctggc agacgctggt
     1441 taatcatcat tacgggctgc gtgacccgaa cgcaccggag aacagacgga cgcttgtcac
     1501 accgaataat ctgccaaaag cgaaacagga ggccgcagaa gcgattacac ggggtcttga
     1561 ggcgctttac cgtgccggag caataaaaac gcgtcaggat gtcactgagg cgctcacagc
     1621 ggcaggtttt gaggtggtga ggacaaccag aagcagtatc agtattgccg acccggaggg
     1681 ggggcggaat ctcaggctaa agggggcgct gtatgagcaa tcttttacaa atgggaacag
     1741 acttcgagaa gaaactgaaa gagcgagccg cttctaccga gaacatgctg aacagcgagt
     1801 tcaggaagct agaagagtct gtagacaagg cactgagctt aaacaggcag aaaatcagag
     1861 acgctatcag cgaacataca acatccgtga aacagcaact ggatacgctg agcaccaccg
     1921 tgagcacgca gctcagcacc acagaggccg aactgtcccg gcagcagaaa aacctgctct
     1981 ggcaggtgat caaagggcgg gtactgtttc cggcgctgac cgcgctcagc gtcacgggcg
     2041 gcattttcct ggggtgctgg gggctgattc agtggcagga aagcaggatt gcgaaaaata
     2101 tcttgaccat cagagagcag gaaaacacgc tggcgaaact cgaggcaaaa acctgggggg
     2161 tgacgttcgt caatggcgag aacgggaaat ttctggtgct gccggacggg gtgaaagggg
     2221 aaaacacctg gacggtgggc gacaagaacg ccgtgaggct ggtcagggag taaacgagta
     2281 tgacggaact ggaagggcat ttgctgaacg ccttagagca tttgcaacag gactatatgc
     2341 ggcggctgaa cgagtgggag agcgccttcg cagaattgca gaagatgcac gcggttacgc
     2401 aacagaacaa cgcgatactg aacgagcgtg tcgtgaactt gagtcagcag gtgcagctat
     2461 tagccggaca agtcgaccgc ttgagtcggt tatttatcac gaacaacaga taagggatga
     2521 acaggagcgt caggcgcagg agcttgcccg gcgctggcat gaagagcagg aacccgaagc
     2581 gcggatctgg cgtggcccgt caatggggat gtgaccgggg tgccccctga aatcgagcca
     2641 gtttgtggca cgccctaccc ggatggcgcc aatgttaatg tacgtacatt agcattaaca
     2701 atatccaaac ctccccattt tgccccgttc gacggctgga acgtgcgaaa ctgatcgtca
     2761 ttcagtttcg cgcataacta tgcatgaggt taaaatttac caggcgcgat cgcggcagtt
     2821 tttcgggtgg tttgttgctg tttttacctg tctgctgccg tgatcgcgct gaacgcgttt
     2881 aagcggtacg cgcaatgcga cgttatggta aatacggagt attttaattg cgggaattaa
     2941 aacaacaaag gcccgctgta ctctatacag cgggcctttg ttgtatatct ctgtcgtttg
     3001 tccccggggg ggaagcatta ctgctaacaa gtcccgtgag aaaactgcgc aatcgtattg
     3061 cgcaccatga acctattctc aaccgcaatc tggaggatga ttttgctacg ataaagagaa
     3121 ttatcgcgta tcggtgtcag cattcattgg agtggatgct gaaaaaccag gtgttactcc
     3181 ctctacttac acttaaacct ctctaaaaat ataagtaagt actatcgagg gctatcatga
     3241 actatggtgc cctctgagca tagctaccca ttacttcttc tatgtcattg aataattcat
     3301 ttcttaactc taagtattct agtaactcca tttctaatga ctctgtcgtg aacttaaatc
     3361 tagaaggatc tttgattgag tttactagtc ttgataacgc tctatatgtt ttgagtgaag
     3421 gttgcattat agatggaaag tatttgaaaa cctcttcatc tctgttgaaa ttaactaaaa
     3481 acttgtagtc atcatttata aatctcaagc atacagcgtc aagcttatcg ccttttctta
     3541 ttattatttc tttataggaa agatattttt cagaagataa gtcccacatc aagcgaaaat
     3601 ctctctttgc gaacgagttc gcgtcatcat tgaaaagaga tgatgtgatg gctttggata
     3661 gaccttctgt gtttatctct ttgttggatg ggtagtaaat tttattaatt gctttcattc
     3721 tctcaaatga tgaatatagg tcattatgcc accttgttga aatcacccct ttagttatat
     3781 tctccttgct aaaattaagc cctgtatcaa aaataaatgc agccatcagt gaatatgata
     3841 tgttttttat taactcagac ttaaatggtt ccgctatgga gtagtacagt gataaaataa
     3901 ctaaaaataa aaggtattgt cttacctttc ccgatgagta tatgtaaagg cgatatttat
     3961 ttattgatag ttttattttg tatggaatga tctcatttct gtcatatcct cttcgtggtg
     4021 gagcaaaaca aaagaaacat gcagctatta ataaaacaaa aaagatgaac agtgtaagca
     4081 agttcggctc ctgtgtatgc tcactatgca tgattgtctt gagatctaac gatcctgaag
     4141 gtagtcttgt ccgtaaacga aaaaaccgcc cagcaaggcg gcttttcgaa ggttctcaga
     4201 gcagcaactc tttgaaccaa ggtaactggc ttggaggagc acagccacca aatctgtcct
     4261 ttcagtttag ccttaaccgg cgcataactt caagactaac tcctctaaac ggttaccaat
     4321 ggctgctgcc agtggcgttt ttacgtgtct ttccgggttg gactcaagac gatagttacc
     4381 ggataaggcg cagcggtcgg gctgaacggg gggttcgtgc acacagccca gcttggagcg
     4441 aacgacctac accgggccga gataccaaca gcgtgagcta tgagaaagcg ccacgcttcc
     4501 cgaagggaga aaggcggaca ggtatccggt aagcggcagg gtcggaacag gagagcgcac
     4561 gagggagctt ccagggggaa acgcctggta tctttatagt cctgtcgggt ttcgccacct
     4621 ctgacttgag cgtc
//
