LOCUS       NZ_AP027584             4171 bp    DNA     circular CON 04-APR-2024
DEFINITION  Escherichia coli strain LR-62-2 plasmid pLR-62-2_8, complete
            sequence.
ACCESSION   NZ_AP027584
VERSION     NZ_AP027584.1
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  JOURNAL   Unpublished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 4171)
  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
            AP027584.1.
            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..4171
                     /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_8"
                     /geo_loc_name="Ecuador:Santo Domingo"
                     /collection_date="2019"
     gene            join(4124..4171,1..168)
                     /locus_tag="AABK23_RS26680"
     CDS             join(4124..4171,1..168)
                     /locus_tag="AABK23_RS26680"
                     /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_152920530.1"
                     /translation="MNKTKGCLIANFATVPAQVHSAEIHTIQPGEVLFPAFFPSENGER
                     GRNLLRGREALPAQPENPLSARSGRG"
                     /name="hypothetical protein"
     gene            1371..1484
                     /locus_tag="AABK23_RS26685"
     CDS             1371..1484
                     /locus_tag="AABK23_RS26685"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_059570819.1"
                     /translation="MHEPPVQSDRCALSGNYRLESNPERHAKAPLAAATGN"
                     /name="hypothetical protein"
     gene            complement(1741..2286)
                     /locus_tag="AABK23_RS26690"
     CDS             complement(1741..2286)
                     /locus_tag="AABK23_RS26690"
                     /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="SHOCT domain-containing protein"
                     /protein_id="WP_039004747.1"
                     /translation="MRERYLNKISNFDTARIVLFIAIQIISCIFMFWGAIPALIVFFSY
                     LAMRKECNLKPIEKSKDYISVYMLLTAALVLFLFVYKAGMFRRGGDYFLLVFVFILLYV
                     YHLAFHKLWLRTIDENSSIIIENGIFNFNRKNASVGFSRKDVNNIDTLLKLNEARKEGI
                     ISEDEFNKLKKRLNILND"
                     /name="SHOCT domain-containing protein"
     gene            complement(2588..>2761)
                     /locus_tag="AABK23_RS26695"
                     /pseudo=""
     CDS             complement(2588..>2761)
                     /locus_tag="AABK23_RS26695"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001389365.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="IS6 family transposase"
                     /name="IS6 family transposase"
     gene            complement(2763..3224)
                     /locus_tag="AABK23_RS26700"
                     /old_locus_tag="VEE29_51060"
     CDS             complement(2763..3224)
                     /locus_tag="AABK23_RS26700"
                     /old_locus_tag="VEE29_51060"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_014198269.1"
                     /GO_component="GO:0005886 - plasma membrane [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DMT family transporter"
                     /protein_id="WP_196451626.1"
                     /translation="MQNILMNLAFYLLVVAAGASFSLQQAANNHLRAELLSPWWAGFIS
                     YVGGSLAMLVMALVCRGPGLSWDMLSRTSPFSWTGGILGAIYIATAIFMIPKLGATTVL
                     ALMVVGQMLLSLMLDHYGLLGIPVYPVTGIRLLGVVLLVLGVVLIRWQA"
                     /name="DMT family transporter"
     gene            3414..4118
                     /locus_tag="AABK23_RS26705"
                     /old_locus_tag="VEE29_51070"
                     /pseudo=""
     CDS             3414..4118
                     /locus_tag="AABK23_RS26705"
                     /old_locus_tag="VEE29_51070"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_042893601.1"
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /GO_process="GO:0006313 - DNA transposition [Evidence IEA]"
                     /note="internal stop; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="IS6-like element IS26 family transposase"
                     /name="IS6-like element IS26 family transposase"
     Typing          complement(836..1009)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.286"
                     /coverage="100.0"
                     /evalue="2.58e-81"
     Typing          976..1480
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.097"
                     /coverage="96.0"
                     /evalue="0.0"
ORIGIN
        1 gcgcaagtgc atagcgcgga aattcacacc attcagccag gggaagtcct gtttccggcg
       61 ttcttcccat ccgaaaacgg tgaacgggga cgcaatttat tgcgtggccg tgaagcgttg
      121 ccggcgcagc cggaaaaccc gctgtcagca cgttcaggaa gggggtgatg tacaaatggc
      181 acagaggatg aaagtgacgt atgagctgaa ggaatgatgt aaaagtgatg tataaatgat
      241 gtaaaagtga tgcaaaagtg ttgtaaaagt gatgtacagg ccgaaggagt gttgtaaaag
      301 tgttgtaaaa gtgatgtatg aactgaagga gcgatgtaat tctgtagtca ggaagaataa
      361 cccgttcatg caggcatgaa cgatacagtg aggaacgctt ttttttgtca cgatctcccc
      421 ttaacctgcg taaatcaccc gccatggttg attatttttc aacctcaaaa tggtcataca
      481 cctaacgcag ccgcgatttt catcgcaact gcatgaatta aaagaaaaaa aaggaatgtt
      541 tcgttttcac gagtaatacc caggtattaa aaacccactg taattacatg aaaataaaga
      601 aataaaaggt aataccggcg tattaccacg tacgcgggca agcgaaaaag ctataacgct
      661 tcccggccga caggcggccc agaatccaca ggggcatgca ggatctcttc agtaaccttc
      721 gccattaaat caaaaaggtc atattcgccg ggaagctgcg tatcagtcga accccgttgt
      781 tcatcatact cagatggcat ggggtgatat ccagtagcag agaggttgtt agcgggtttc
      841 ggggcgcagc cctgaaccag tcacgtagcg ctagcggagt gtatactggc ttactatgtt
      901 ggcactgatg aggatgtcag tgaagtgctt catgtggcag gagaaaaaag gctgcaccgg
      961 tgcgtcagca gaatatgtga tacaggatat attccgcttc ctcgctcact gactcgctac
     1021 gctcggtcgt tcgactgcgg cgagcggaaa tggcttacga acggggcagg gatttcctgg
     1081 aagatgccag gaagagactt aacagggaag agatagggcc gcggcaaagc cgtttttcca
     1141 taggctccgc ccccctgaca agcatcacga aatctgacgc tcaaatcagt ggtggcgaaa
     1201 cccgacagga ctataaagat accaggcgtt tccccctggc ggctccctcg tgcgctctcc
     1261 tgttcctgcc tttcggttta ccggtgtcat tccgctgtta tggccgcgtt tgtctcattc
     1321 cacgcctgac actcagttcc gggtagacag ttcgctccaa gctggactgt atgcacgaac
     1381 cccccgttca gtccgaccgc tgcgccttat ccggtaacta tcgtcttgag tccaacccgg
     1441 aaagacatgc aaaagcacca ctggcagcag ccactggtaa ttgatttaga ggagttagtc
     1501 ttgaagtcat gcgccggtta aggctaaact gaaaggacaa gttttggtga ctgtgctcct
     1561 ccaagccagt taccgcggtt caaaagagcg tcaactcttg cgaaccttcg aaaaaccacc
     1621 ttgccgggtg gttttttcgt ttgcagggaa gaagattacg acgataaaaa atcaatgaca
     1681 agaagatatt caatcttatc aaagattcat aagcttgctt tacctttagt tagcaaaaaa
     1741 tcagtcgtta agaatattta gtcttttttt taatttatta aactcatctt cacttataat
     1801 accttctttt ctagcctcgt ttaatttaag aagagtatca atgttattta catctttccg
     1861 actaaatcct acagatgcat ttttacgatt aaaattaaaa atcccgtttt caattattat
     1921 tgatgagttt tcatctatcg ttcgcaacca taatttatga aaagcgagat ggtaaacata
     1981 aagcaaaata aaaacaaaaa cgagaaggaa ataatcaccg ccccttctaa acatgccagc
     2041 tttatacacg aaaagaaaca gtaccaaagc ggctgtaaga agcatgtaaa cggatatgta
     2101 atccttagac ttctctatcg gctttaaatt acattccttc ctcatggcca aatatgagaa
     2161 aaaaacaatc aaggcaggaa tagcccccca gaacataaaa atacaagaga taatttgaat
     2221 ggctataaac aacactattc ttgccgtatc aaaattagat attttattta aataccgttc
     2281 gcgcataaat caccaccatt caatcatagt taattaattt aaaatcaatc gcctgatatt
     2341 aatattattt caaaaaatag aaaagcagta actgaatatg gggcatttac cataacaccc
     2401 cttgcgtgca ccgcctgaga ggctctgagg gcgtttctga cgggaaaccg gtaaaacagg
     2461 caacaaacca cccgaaaacc cgccagaaac gcgcaggctc tgtttttacg gcatgcatga
     2521 gtatgcgcgc aagggctctg ttgcaaagat tggcggcagt cagaggtagg ctgtcgctct
     2581 gcgccgatca ggcggctgct gcgaaatggt ggttgagcat gcccatggcc tccgtcagcg
     2641 ccgagggccc aatgccaaaa gctctctcca caaggcgcac ctcgcccctg atgccgggct
     2701 gcaggcacca ggggcgagcc tgtcctttgc gcagggctcg catgacttcg aatcccttga
     2761 tcttatgcct gccatctgat cagcactacc ccaagaacaa gcaggacaac gcccagcagg
     2821 cggataccgg tgacaggata aaccgggata ccaagaaggc catagtgatc gagcatcagg
     2881 gaaagcagca tttgcccgac caccatcaat gccagaaccg ttgttgctcc cagtttcggg
     2941 atcatgaaaa tggccgtggc aatgtaaatc gcccctaaaa taccgcctgt ccatgaaaac
     3001 gggctggtac gcgaaagcat atcccatgac aggccagggc cgcgacaaac cagcgccatg
     3061 accagcatgg ccagggaacc gccgacataa ctgatgaaac ctgcccacca tggtgaaagc
     3121 agttctgcgc gaagatggtt gttggccgcc tgttgcaggg aaaagctggc gccggcagca
     3181 acaaccagga gataaaacgc cagattcatc agaatgtttt gcatggtttt tctcgtcgaa
     3241 gaagtgaacc gccccgggtt tggcggaggg tattttgttt aagttaaggc gtgttgacgg
     3301 atagttcgtc aagttgccga tagtagtcct gttcaagata ttcgccgact ggcactgttg
     3361 caaatagtcg gtggtgataa acttatcatc cccttttgct gatggagctg cacatgaacc
     3421 cattcaaagg ccggcatttt cagcgtgaca tcattctgtg ggccgtacgc tggtactgaa
     3481 aatacggcat cagttaccgt gagctgcagg agatgctggc tgaacgcgga gtgaatgtcg
     3541 atcactccac gatttaccgc tgggttcagc gttatgcgcc tgaaatggaa aaacggctgc
     3601 gctggtactg gcgtaaccct tccgatcttt gcccgtggca catggatgaa acctacgtga
     3661 aggtcaatgg ccgctgggcg tatctgtacc gggccgtcga cagccggggc cgcactgtcg
     3721 atttttatct ctcctcccgt cgtaacagca aagctgcata ccggtttctg ggtaaaatcc
     3781 tcaacaacgt gaagaagtgg cagatcccgc gattcatcaa cacggataaa gcgcccgcct
     3841 atggtcgcgc gcttgctctg ctcaaacgcg aaggccggtg cccgtctgac gttgaacacc
     3901 gacagattaa gtaccggaac aacgtgattg aatgcgatca tggcaaactg aaacggataa
     3961 tcggcgccac gctgggattt aaatccatga agacggctta cgccaccatc aaaggtattg
     4021 aggtgatgcg tgcactacgc aaaggccagg cctcagcatt ttattatggt gatcccctgg
     4081 gcgaaatgcg cctggtaagc agagtttttg aaatgtaagg cctttgaata agacaaaagg
     4141 ctgcctcatc gctaactttg caacagtgcc c
//
