LOCUS       NZ_AP027598             4145 bp    DNA     circular CON 04-APR-2024
DEFINITION  Escherichia coli strain LR-64-2 plasmid pLR-64-2_3, complete
            sequence.
ACCESSION   NZ_AP027598
VERSION     NZ_AP027598.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00562553
            Assembly: GCF_036498285.1
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  JOURNAL   Unpublished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 4145)
  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                   :: 318x
            Sequencing Technology :: MGI DNBSEQ-G400RS; ONT MinION Mk1c
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_036498285.1-RS_2024_04_04
            Annotation Date                   :: 04/04/2024 00:00:58
            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)                     :: 4,720
            CDSs (total)                      :: 4,600
            Genes (coding)                    :: 4,390
            CDSs (with protein)               :: 4,390
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 210
            CDSs (without protein)            :: 210
            Pseudo Genes (ambiguous residues) :: 0 of 210
            Pseudo Genes (frameshifted)       :: 60 of 210
            Pseudo Genes (incomplete)         :: 142 of 210
            Pseudo Genes (internal stop)      :: 37 of 210
            Pseudo Genes (multiple problems)  :: 31 of 210
            Pseudo Genes (short protein)      :: 4 of 210
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP027598.1.
            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..4145
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="LR-64-2"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pLR-64-2_3"
                     /geo_loc_name="Ecuador:Santo Domingo"
                     /collection_date="2019"
     gene            complement(join(3529..4145,1..526))
                     /gene="wzz(fepE)"
                     /locus_tag="AABJ48_RS23575"
     CDS             complement(join(3529..4145,1..526))
                     /gene="wzz(fepE)"
                     /locus_tag="AABJ48_RS23575"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /GO_component="GO:0016020 - membrane [Evidence IEA]"
                     /GO_process="GO:0009103 - lipopolysaccharide biosynthetic
                     process [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="LPS O-antigen length regulator Wzz(fepE)"
                     /protein_id="WP_021544858.1"
                     /translation="MSAMDFKKNTDLDFPRYATPAVSTKEIDLLGLLDVLLAAKKRIVT
                     IVLAFAVVGLAIAFLIPQKWTSKAVITPAEQTQWNTLRQMMVTLQVLDVDAKVSRGDVF
                     NLFIKKFQSQSLLEEYMKTSPYVMSQLEGTEVDPLELHRAVVNIAEKMKATDNTQVKDA
                     DKAPYTSWTLSFTAPTAGDAQTVLEGYINYISRIVEQETMENIRNQITLKTKVVQQQLE
                     LDRVRLTNIHNTNLQRLNYSLEVANAAGIKKPVYSNGQAVKDDPDYSVALGADGIAQKL
                     QIEKNLKDVAELNADFQNREYYLTQLQKLSVEDVKLEPFRYQLSPSLPVKKDGPGKALI
                     VLLAGILGGLFACGSVLLREAMLSRNPLPEPITAVTPATE"
                     /name="wzz(fepE)"
     gene            721..1183
                     /locus_tag="AABJ48_RS23580"
                     /old_locus_tag="VEE33_44630"
                     /pseudo=""
     CDS             721..1183
                     /locus_tag="AABJ48_RS23580"
                     /old_locus_tag="VEE33_44630"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_416498.2"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="transposase"
                     /name="transposase"
     gene            complement(<1332..1463)
                     /locus_tag="AABJ48_RS23585"
                     /pseudo=""
     CDS             complement(<1332..1463)
                     /locus_tag="AABJ48_RS23585"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_013578013.1"
                     /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="zinc-ribbon domain-containing protein"
                     /name="zinc-ribbon domain-containing protein"
     gene            complement(1771..1884)
                     /locus_tag="AABJ48_RS23590"
     CDS             complement(1771..1884)
                     /locus_tag="AABJ48_RS23590"
                     /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="replication initiation protein"
                     /protein_id="WP_071778980.1"
                     /translation="MHEPPVQSDRCVFSGNYRLESKPERHDKAPLAAATGN"
                     /name="replication initiation protein"
     gene            complement(3070..>3252)
                     /locus_tag="AABJ48_RS23595"
                     /pseudo=""
     CDS             complement(3070..>3252)
                     /locus_tag="AABJ48_RS23595"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007798797.1"
                     /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="NINE protein"
                     /name="NINE protein"
     gene            <3249..3491
                     /locus_tag="AABJ48_RS23600"
                     /old_locus_tag="VEE33_44640"
                     /pseudo=""
     CDS             <3249..3491
                     /locus_tag="AABJ48_RS23600"
                     /old_locus_tag="VEE33_44640"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_003862821.1"
                     /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="cupin domain-containing protein"
                     /name="cupin domain-containing protein"
     Typing          complement(1768..2153)
                     /name="rep_cluster_2373"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.373"
                     /coverage="90.0"
                     /evalue="1.04e-173"
ORIGIN
        1 taaagctcag cgtccatgag gtatacggcg ctttgtctgc gtctttaacc tgcgtgttat
       61 ctgtcgcttt cattttctca gcaatattca ccaccgcgcg atgcagctcc agcgggtcta
      121 cctcggtgcc ttccagctga gacatcacgt acggggaggt tttcatgtac tcttcgagca
      181 gcgactgcga ctgaaacttt ttgatgaaca ggttaaacac gtctccacgg ctcaccttcg
      241 cgtcgacgtc cagcacctgc agcgtcacca tcatctggcg cagcgtgttc cactgcgtct
      301 gctcggccgg cgtgatcacg gctttactgg tccatttttg cgggattaaa aacgcaatgg
      361 ccaaccctac tacggcgaac gccaggacga tcgtcacaat acgttttttg gctgccagaa
      421 gtacgtctaa caaccccagg agatctatct ctttggtgct taccgccgga gtggcataac
      481 ggggaaaatc gaggtccgtg tttttcttga aatccatcgc tgacataacc gttcttcttt
      541 ttggagcgca gtaaatttct gcctgattgg ttgcagtggt cggatgatac aagaaagtaa
      601 gaataatctg aacgccagat tgatctatct gtagaccgac tatcagattt agggaaggtg
      661 cgaacaagtc cctgatatga gatcatgttt gtcatctgga gccatggaac agggttcatc
      721 atgagtcatc aacttacctt cgccgacagt gaattcagca gtaagcgccg tcagaccaga
      781 aaagagattt tcttgtcccg catggagcag attctgccat ggcaaaacat ggtggaagtc
      841 atcgagccgt tttaccccaa ggctggtaat ggccggcgac cttatccgct ggaaaccatg
      901 ctacgcattc actgcatgca gcattggtac aacctgagcg atggcgcgat cgaagatgct
      961 ctgtacgaaa tcgcctccat gcgtctgttt gcccggttac atgaaagcca gcatccgggc
     1021 caaggtggag cacccatttc gcatcatcaa gcgacagttc ggcttcgtga aagccagata
     1081 caaggggttg ctgaaaaacg ataaccaact ggcgatgtta ttcacgctgg ccaacctgtt
     1141 tcgggcggac caaatgatac gtcagtggga gagatctcac taaaaactgg gaataacgcc
     1201 ttaaatggcg aagaaacggt ctaaataggc tgattcaagg catttacggg agaaaaaaat
     1261 cggctcaaac atgaagaaat gaaatgactg agtcaaccga gaagaatttc cccgcttatt
     1321 cgcaccttcc ctaatagcgc ggctgcgatt ctactttttt cacctgaacc tgaagaggcg
     1381 tttgtggctc cgcagtgtgg gcatgacttt gctgtttcgt gtatttcctt gccgcatcct
     1441 cggcagtaaa ccattgaact cattttttat cctcgagctt atttttagtt gggatgcata
     1501 atatccgatg ttttataacg atatgcatcc tatatgctcg ggtgggatag atttccatta
     1561 tggtgaagga tcttcttgag atcctttctg tagcgtcgta atctcttgct cagtaaacga
     1621 aaaaaccgcc cagcaaggcg gtttttcgaa ggttctcaga gctgcaactc tttgaaccgt
     1681 ggtaactggc ttatgaggag cgcagtaacc aaatctgttc tttcagttta gccttaacag
     1741 gcgcataact tcaagactaa ctcctctaaa tcagttacca gtggctgctg ccagtggcgc
     1801 tttgtcgtgt ctttccggct tggactcaag tcgatagtta ccggagaaga cgcagcggtc
     1861 ggactgaacg gggggttcgt gcatacagtc cagcttggag cgaactgcct acccggaact
     1921 gagtgtcagg cgtggaatga gataaacgcg gccataacag cggaatgaca ccggtaaacc
     1981 gaaaggcagg aacaggagag cgcacgaggg agccaccagg gggaaacgcc tggtatcttt
     2041 aagtcctgtc gggtttcgcc accactgatt tgagcgtcag attctgtgat gcttgtcagg
     2101 ggggcggagc ctatggaaaa ccggcaacgc cgcggccttt tcttttgcct ctcgatcctc
     2161 tctcattgcc tgtgccttaa tgtctccgtt ccctccgctc gccgcagccg aacgaccgag
     2221 cgtagcgagt cagtgagcga ggaagcggaa tatccccgga cttattttcg gcaccgtacg
     2281 cgccagtgct gcatttttta atacgatgca ggatagggct aacgccgcaa agtgacgtca
     2341 cctgacgttc ctggattaca aaggttaaag cagcggacag gaaatgtttt gtgcccacag
     2401 ctatgctggc ttattcacaa aacagcggga caagatgtgt ttttggagta ccgccggccc
     2461 gctaaagact cctggttagc tcccgcatgt ttgctatctt tttgctacca ttttgctact
     2521 tttttgctat ctccagagtc ttctggtctt tcggttgcta tccttttgct acttttttgc
     2581 tatcaaaatg ctacctctcc cttcttgcaa taaatgacca aggcacgtta gcgatgtata
     2641 catcgccgcg ccgcaagggt gccccttccg aatcccgttc atcactgcgt gctgattcat
     2701 ccacgttaaa tccgaccccc ttagcaataa atccagccat gcctgacggc ctggccaacg
     2761 cctcacggcc gcacagtaaa ctgcacaccc gtgaggcgtt attcgtgagg ttcagtggtg
     2821 cttttgggcg tccagccgga ttttagccgc taaaatcccg gccatgcatg tgtgtgcata
     2881 gccatgcaga cgcgccagaa tcatcaggcg cgttttttca cgatataggc acagggaagt
     2941 gtcggaaaca ggcaggaaga cccagaaacg ccctgagagc ctctcaggcg gtgcacgcaa
     3001 cggatgttat ggtaaatctg cctcacagac tggtacaaaa aaagccccgc agggcttttt
     3061 tgctatgagt tagccatatt ttcttgcgaa tttttcatcg gaatcgcata gataaataat
     3121 aaactcaata aacgcgatga tcgcgggtat gaatgtccag caaaaaatta gatacaggaa
     3181 tccctgtcct attttaccta agtaaaattt atgtacgcca aatccaccaa ggaagaatgc
     3241 taagaaagat gatggcggtg gaggtcaatt ttgagcaggg tgcgattggc ccgatgcaca
     3301 atcacccgca tgaacagctt acctatgtgc tctccgggga gttcgagttt acgataggtg
     3361 aagaaaagca gatcgtgacg gcgggcgata cgctctataa agcgccgcac gtgatgcacg
     3421 gctgcatttg cctgaagccc ggcacccttc tggatacctt tacgccggtg cgcgacgatt
     3481 tcctgaaata aaaaaaggcg ctgaatcagc gcctttttaa tatcgtcgtt actctgttgc
     3541 tggcgttacg gccgttatcg gctctggcaa cggattacgc gagagcattg cctcacgcag
     3601 cagcacgctg ccgcaggcaa acaggccgcc cagaatccct gccagcagca caatcagggc
     3661 tttgcccgga ccgtcttttt tcaccggcag tgacggtgaa agctgatacc tgaagggttc
     3721 aagcttcacg tcttccacgg acagtttttg caactgagtc agatagtatt cacggttctg
     3781 gaaatccgca ttcagctcgg ccacgtcctt cagattcttt tcaatctgca gcttttgcgc
     3841 aataccgtca gcacccagcg ccacggagta gtcaggatcg tcttttaccg cctgtccgtt
     3901 gctgtaaacc ggcttcttaa tgcctgccgc gttcgccact tccagcgaat agttgaggcg
     3961 ctgcaggttg gtgttgtgga tattggtcag acgcacgcga tccagctcca gctgctgctg
     4021 aacgactttc gttttcagcg tgatctggtt acggatattt tccatcgtct cctgctcaac
     4081 aatgcgggag atatagttga tgtaaccttc cagaaccgtc tgcgcgtctc ccgccgtcgg
     4141 ggcgg
//
