LOCUS       NZ_AP027585             3294 bp    DNA     circular CON 04-APR-2024
DEFINITION  Escherichia coli strain LR-62-2 plasmid pLR-62-2_9, complete
            sequence.
ACCESSION   NZ_AP027585
VERSION     NZ_AP027585.1
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  JOURNAL   Unpublished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 3294)
  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
            AP027585.1.
            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..3294
                     /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_9"
                     /geo_loc_name="Ecuador:Santo Domingo"
                     /collection_date="2019"
     gene            complement(121..636)
                     /locus_tag="AABK23_RS26710"
                     /old_locus_tag="VEE29_51080"
     CDS             complement(121..636)
                     /locus_tag="AABK23_RS26710"
                     /old_locus_tag="VEE29_51080"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_103743870.1"
                     /translation="MFGFVKKTVNAVSDTASSALSSASKAATSASASISDKASSTYSSI
                     SDSAEKITGAVSGAAQSAWLMAESVITDGLLDLTSDFLKDDEKIREVSLIFWQRIPREV
                     RFFLSEDKFHERTKSLRDNALLKLDESKQKRIRIPEATNAEDAIPVLISNEPASVTTLP
                     DGLQAKNS"
                     /name="hypothetical protein"
     gene            complement(775..1149)
                     /locus_tag="AABK23_RS26715"
                     /old_locus_tag="VEE29_51090"
     CDS             complement(775..1149)
                     /locus_tag="AABK23_RS26715"
                     /old_locus_tag="VEE29_51090"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_103743871.1"
                     /translation="MNDVSDVRLKKTTVDSLKEYVNDFGMTVDDVVLNLIEENNSLKSL
                     LGQDFSLPRGDKDTYLFKEYVIHKLPKGKILVTKNGLKVSNMKKVLIEAGSALGMDDKE
                     LNPGFTTYEIGRFLFKHLHG"
                     /name="hypothetical protein"
     gene            2114..2305
                     /locus_tag="AABK23_RS26720"
                     /old_locus_tag="VEE29_51100"
     CDS             2114..2305
                     /locus_tag="AABK23_RS26720"
                     /old_locus_tag="VEE29_51100"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165985.1"
                     /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_089718845.1"
                     /translation="MTKQEKTALNIARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2974..3087
                     /locus_tag="AABK23_RS26725"
     CDS             2974..3087
                     /locus_tag="AABK23_RS26725"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /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_071588254.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHDLSPLAAATGN"
                     /name="replication initiation protein"
     Typing          complement(2391..2472)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="93.0"
                     /evalue="1.48e-35"
     Typing          2502..3046
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.139"
                     /coverage="98.0"
                     /evalue="0.0"
ORIGIN
        1 taacgtacaa aaatttccgt tctccaaact acccaccatg agcacttacc aataataaaa
       61 atcatgatag gccactacgg tcgatgtctt ggagcaatgc tcggctatgg tagtttaccc
      121 ctaagaattt ttagcttgta aaccatcagg caaagttgtt actgatgccg gttcattaga
      181 gataagaacc ggtatcgcgt cttccgcgtt tgtggcttca ggaatccgaa ttcttttttg
      241 cttagattca tccagcttca acaaagcatt atctcttagt gatttcgttc gttcatgaaa
      301 tttatcttca gaaaggaaaa agcgaacttc tcttggtatc ctctgccaga aaatgagcga
      361 aacctccctg attttctcat cgtctttaag aaaatcagat gttaaatcaa gcaatccgtc
      421 tgtaatgact gactcagcca ttaaccacgc agactgagca gcaccagata ctgctcccgt
      481 aatcttctca gccgaatcag aaatagaaga atatgttgat gaggctttat ctgagataga
      541 tgccgaagcg cttgtggcag cctttgaagc tgaacttaac gcagatgaag ctgtatccga
      601 aactgcgttg actgtttttt ttacgaatcc aaacatctgt cacctttatt tttcgctagt
      661 aatgtttagc ccatggcaga cctgtgaatt ggtaatgcgc tgcaggtatt attttctata
      721 tcaccaacag agatttacca taaccccccc ccggtcacga actggtagac atcttcatcc
      781 atgaaggtgt ttgaagagaa aacggcctat ctcataggtt gtaaagccag ggtttagctc
      841 tttgtcatcc atccctaaag cgctgcctgc ctcgatcaat accttcttca tgttactaac
      901 cttgagtccg tttttggtta ccaagatctt tccttttggg agtttatgaa tcacgtattc
      961 cttaaataaa tacgtgtcct tatcacccct gggcagagaa aaatcctgac ctaataacga
     1021 ttttaatgaa ttattctctt caattaagtt cagaacaaca tcgtcaaccg tcataccaaa
     1081 gtcattcacg tattctttta ggctatcaac cgttgttttc ttaagcctta cgtcagaaac
     1141 atcgttcata tcagtgttac gccatctctt cacaatgaac taacaataca acaaaataca
     1201 aaatatacaa ataaattaag ttctgaacaa gaaagaaagg agggggaggc tgcaggaaaa
     1261 atgatgacca tgccagcctg atttaccata acatctgtat tgtacgcacc gccaaaacgc
     1321 gctgaacgcg attctgacgc gaacaccgca aaaagagatg ttttacccgg tacaaaccgg
     1381 aaaaatgcgt caggagcgtt ttcagctcgc tgcatagcta tgcatgaaag tgaatggcga
     1441 tcggtttggg tacatacggt gcccatgagg cacattttcg gatgttttca gccccgggaa
     1501 gaagaaatct gacagtagtt acagacgagt cgtaagcgat tcaccccgtg aatcgtcggc
     1561 aagtcatcca gtatttttcc tcgcgacttt ctggcaactc tccttctctg aacatcagag
     1621 cgacagagtg ttgattcatc gataaatcac cgacgactcg ttgccgagtc atccagtagt
     1681 cgctgacgac tcgcttttgt ataaatctga ataagaaaat atatttttca aaccataaga
     1741 agatgattta aaaagcaaat cagcaaaaag ttggttttgc gtggggtgtg ggcatttcag
     1801 gcatgagaac agactcgcgt ttttctggaa gaactgcggg gatttttgat taaacaatac
     1861 tcaccgcaga gcgaaacttt atgcaacagc ggctgtactg cacaaggatt atttatcagt
     1921 tgatatgctg tgccatgata ttgccgaaag ggacgtcgtt ttacggcgtt ttccctatcc
     1981 tgcatcgcac tggccccgtt cgaatgtttg cgcccctgac taaccgctca ctcagcttta
     2041 tcactctcgc ctgcgtcaca gttatcatgc tcccatgaaa acagaaatgc ccttacacgg
     2101 agacatcaga ccagtgacca aacaggaaaa aaccgccctg aacatagccc gcttcatcag
     2161 gagccagaca ttaaccctgc tggagaagct caacgaactg gacgcggatg aacaggcaga
     2221 tatctgtgaa tcgcttcacg accacgccga tgagctttac cgcagttgcc tcgcacgctt
     2281 cggggatgac ggtgaaaacc tctgacacag gcagctcccg gagacggtca cagcttgcct
     2341 gtgagaggat gccgggagca gacaagcccg tcagggcgcg tcagcgggtt ttagcgggtg
     2401 tcggggcgca gccatgaccc agtcacgtag cgatagcgga gtgtatactg gcttaatcat
     2461 gtggcatcag tgcggattgt atgaaaagtg ctccatggac ggtgtgaaat gccgcacaga
     2521 tgcgtaagga gaaaatgcaa atgcctacgc tcttccgctt cctcgctcac tgactcgcta
     2581 cgctcggtcg ttcggctgcg gcgagcggtg ccggctcact caaagacggt gatgcggtta
     2641 tccacggaat caggggataa cgccggaaag aacatgtgag caaaaagcca agaacaggaa
     2701 gaaggccgcg ccgctggcgt ttttccatag gctccgcccc cctgacgagc atcacaaaaa
     2761 tcgatgctca agtcagaggt ggcgaaaccc gacaggactt aaagatacca ggcgtttccc
     2821 cctggaagct ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctctcc
     2881 gcctttctcc cttcgggaag cgtggcgctt tctcatagct cacgctgttg gtatctcggc
     2941 tcggtgtagg tcgttcgctc cgagctgggc tgtgtgcacg aaccccccgt tcagcccgac
     3001 cgctgcgcct tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg
     3061 ccactggcag cagccactgg taactgattt agaggagttt gtcttgaagt tatgcgcctg
     3121 ttaaggctaa actgaaagaa cagactttgg tgactgcgct cctccaagcc agttacccgg
     3181 ttagataatc tgccaggatt agctaacctt cgaaaaacca cctgccaggg tggttttttc
     3241 gtttcttgga caagagatta cgacgacaaa tgatggatct caagaagatc cttt
//
