LOCUS       NZ_AP027476             4663 bp    DNA     circular CON 04-APR-2024
DEFINITION  Escherichia coli strain LR-03 plasmid pLR-03_2, complete sequence.
ACCESSION   NZ_AP027476
VERSION     NZ_AP027476.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00562502
            Assembly: GCF_036493855.1
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  JOURNAL   Unpublished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 4663)
  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                   :: 186x
            Sequencing Technology :: MGI DNBSEQ-G400RS; ONT MinION Mk1c
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_036493855.1-RS_2024_04_03
            Annotation Date                   :: 04/03/2024 23:47:34
            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)                     :: 4,506
            CDSs (total)                      :: 4,389
            Genes (coding)                    :: 4,209
            CDSs (with protein)               :: 4,209
            Genes (RNA)                       :: 117
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 180
            CDSs (without protein)            :: 180
            Pseudo Genes (ambiguous residues) :: 0 of 180
            Pseudo Genes (frameshifted)       :: 48 of 180
            Pseudo Genes (incomplete)         :: 130 of 180
            Pseudo Genes (internal stop)      :: 26 of 180
            Pseudo Genes (multiple problems)  :: 25 of 180
            Pseudo Genes (short protein)      :: 4 of 180
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP027476.1.
            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..4663
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="LR-03"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pLR-03_2"
                     /geo_loc_name="Ecuador:Santo Domingo"
                     /collection_date="2019"
     gene            complement(194..307)
                     /locus_tag="AABJ47_RS22505"
     CDS             complement(194..307)
                     /locus_tag="AABJ47_RS22505"
                     /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(1492..1614)
                     /locus_tag="AABJ47_RS22510"
     CDS             complement(1492..1614)
                     /locus_tag="AABJ47_RS22510"
                     /inference="COORDINATES: protein motif:HMM:NF017007.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_115209648.1"
                     /translation="MGQGFLYLIFCWTFIPAIIAFIEFIIYLCDSDEKFARKYG"
                     /name="hypothetical protein"
     gene            1575..1913
                     /locus_tag="AABJ47_RS22515"
                     /old_locus_tag="VEE06_43120"
     CDS             1575..1913
                     /locus_tag="AABJ47_RS22515"
                     /old_locus_tag="VEE06_43120"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_014833142.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="cupin domain-containing protein"
                     /protein_id="WP_305955934.1"
                     /translation="MSSKKLDTGIPVLFYLSKIYVRQIHQGRMLRKMMAVEVNFEQGAI
                     GPMHNHPHEQLTYVLSGEFEFTIGEEKQIVTAGDTLYKAPHVMHGCICLKPGTLLDTFT
                     PVRDDFLK"
                     /name="cupin domain-containing protein"
     gene            complement(1951..3093)
                     /gene="wzz(fepE)"
                     /locus_tag="AABJ47_RS22520"
                     /old_locus_tag="VEE06_43130"
     CDS             complement(1951..3093)
                     /gene="wzz(fepE)"
                     /locus_tag="AABJ47_RS22520"
                     /old_locus_tag="VEE06_43130"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010435173.1"
                     /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: Protein Homology."
                     /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            3288..4269
                     /locus_tag="AABJ47_RS22525"
                     /old_locus_tag="VEE06_43140"
     CDS             join(3288..4079,4081..4269)
                     /locus_tag="AABJ47_RS22525"
                     /old_locus_tag="VEE06_43140"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_048909999.1"
                     /ribosomal_slippage=""
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /GO_process="GO:0006313 - DNA transposition [Evidence IEA]"
                     /note="programmed frameshift; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="IS5-like element IS5 family transposase"
                     /protein_id="WP_225899375.1"
                     /translation="MSHQLTFADSEFSSKRRQTRKEIFLSRMEQILPWQNMVEVIEPFY
                     PKAGNGRRPYPLETMLRIHCMQHWYNLSDGAIEDALYEIASMRLFARLSLDSALPDRTT
                     IMNFRHLLEQHQLARQLFKTINRWLAEAGVMMTQGTLVDATIIEAPSSTKNKEQQRDPE
                     MHQTKKGNQWHFGMKAHIGVDAKSGLTHSLVTTAANEHDLNQLGNLLHGEEQFVSADAG
                     YQGAPQREELAEVDVDWLIAERPGKVRTLKQHPRKNKTAHQHEYMKASIRAKVEHPFRI
                     IKRQFGFVKARYKGLLKNDNQLAMLFTLANLFRADQMIRQWERSH"
                     /name="IS5-like element IS5 family transposase"
     gene            complement(<4418..4549)
                     /locus_tag="AABJ47_RS22530"
                     /pseudo=""
     CDS             complement(<4418..4549)
                     /locus_tag="AABJ47_RS22530"
                     /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"
     Typing          complement(191..576)
                     /name="rep_cluster_2373"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.373"
                     /coverage="90.0"
                     /evalue="1.04e-173"
ORIGIN
        1 gagatccttt ctgtagcgtc gtaatctctt gctcagtaaa cgaaaaaacc gcccagcaag
       61 gcggtttttc gaaggttctc agagctgcaa ctctttgaac cgtggtaact ggcttatgag
      121 gagcgcagta accaaatctg ttctttcagt ttagccttaa caggcgcata acttcaagac
      181 taactcctct aaatcagtta ccagtggctg ctgccagtgg cgctttgtcg tgtctttccg
      241 gcttggactc aagtcgatag ttaccggaga agacgcagcg gtcggactga acggggggtt
      301 cgtgcataca gtccagcttg gagcgaactg cctacccgga actgagtgtc aggcgtggaa
      361 tgagataaac gcggccataa cagcggaatg acaccggtaa accgaaaggc aggaacagga
      421 gagcgcacga gggagccacc agggggaaac gcctggtatc tttaagtcct gtcgggtttc
      481 gccaccactg atttgagcgt cagattctgt gatgcttgtc aggggggcgg agcctatgga
      541 aaaccggcaa cgccgcggcc ttttcttttg cctctcgatc ctctctcatt gcctgtgcct
      601 taatgtctcc gttccctccg ctcgccgcag ccgaacgacc gagcgtagcg agtcagtgag
      661 cgaggaagcg gaatatcccc ggacttatct tcggcaccgt acgcgccagt gctgcatttt
      721 ttaatacgat gcaggatagg gctaacgccg caaagtgacg tcacctgacg ttcctggatt
      781 acaaaggtta aagcagcgga caggaaatgt tttgtgccca cagctatgct ggcttattca
      841 caaaacagcg ggacaagatg tgtttttgga gtaccgccgg cccgctaaag actcctggtt
      901 agctcccgca tgtttgctat ctttttgcta ccattttgct acttttttgc tatctccaga
      961 gtcttctggt ctttcggttg ctatcctttt gctacttttt tgctatcaaa atgctacctc
     1021 tcccttcttg caataaatga ccaaggcacg ttagcgatgt atacatcgcc gcgccgcaag
     1081 ggtgcccctt ccgaatcccg ttcatcactg cgtgctgatt catccacgtt aaatccgacc
     1141 cccttagcaa taaatccagc catgcctgac ggcctggcca acgcctcacg gccgcacagt
     1201 aaactgcaca cccgtgaggc gttattcgtg aggttcagtg gtgcttttgg gcgtccagcc
     1261 ggattttagc cgctaaaatc ccggccatgc atgtgtgtgc atagccatgc agacgcgcca
     1321 gaatcatcag gcgcgttttt tcacgatata ggtacaggga agtgtcggaa acaggcagga
     1381 agacccagaa acgccctgag agcctctcag gcggtgcacg caacggatgt tatggtaaat
     1441 ctgcctcaca gactggtaca aaaaaagccc gaagggcttt tttgctatga gttagccata
     1501 ttttcttgcg aatttttcat cggaatcgca tagataaata ataaactcaa taaacgcgat
     1561 gatcgcgggt atgaatgtcc agcaaaaaat tagatacagg aatccctgtc ctattttacc
     1621 taagtaaaat ttatgtacgc caaatccacc aaggaagaat gctaagaaag atgatggcgg
     1681 tggaggtcaa ttttgagcag ggtgcgattg gcccgatgca caatcacccg catgaacagc
     1741 ttacctatgt gctctccggg gagttcgagt ttacgatagg tgaagaaaag cagatcgtga
     1801 cggcgggcga tacgctctat aaagcgccgc acgtgatgca cggctgcatt tgcctgaagc
     1861 ccggcaccct tctggatacc tttacgccgg tgcgcgacga tttcctgaaa taaaaaaagg
     1921 cgctgaatca gcgccttttt aatatcgtcg ttactctgtt gctggcgtta cggccgttat
     1981 cggctctggc aacggattac gcgagagcat tgcctcacgc agcagcacgc tgccgcaggc
     2041 aaacaggccg cccagaatcc ctgccagcag cacaatcagg gctttgcccg gaccgtcttt
     2101 tttcaccggc agtgacggtg aaagctgata cctgaagggt tcaagcttca cgtcttccac
     2161 ggacagtttt tgcaactgag tcagatagta ttcacggttc tggaaatccg cattcagctc
     2221 ggccacgtcc ttcagattct tttcaatctg cagcttttgc gcaataccgt cagcacccag
     2281 cgccacggag tagtcaggat cgtcttttac cgcctgtccg ttgctgtaaa ccggcttctt
     2341 aatgcctgcc gcgttcgcca cttccagcga atagttgagg cgctgcaggt tggtgttgtg
     2401 gatattggtc agacgcacgc gatccagctc cagctgctgc tgaacgactt tcgttttcag
     2461 cgtgatctgg ttacggatat tttccatcgt ctcctgctca acaatgcggg agatatagtt
     2521 gatgtaacct tccagaaccg tctgcgcgtc tcccgccgtc ggggcggtaa agctcagcgt
     2581 ccatgaggta tacggcgctt tgtctgcgtc tttaacctgc gtgttatctg tcgctttcat
     2641 tttctcagca atattcacca ccgcgcgatg cagctccagc gggtctacct cggtgccttc
     2701 cagctgagac atcacgtacg gggaggtttt catgtactct tcgagcagcg actgcgactg
     2761 aaactttttg atgaacaggt taaacacgtc tccacggctc accttcgcgt cgacgtccag
     2821 cacctgcagc gtcaccatca tctggcgcag cgtgttccac tgcgtctgct cggccggcgt
     2881 gatcacggct ttactggtcc atttttgcgg gattaaaaac gcaatggcca accctactac
     2941 ggcgaacgcc aggacgatcg tcacaatacg ttttttggct gccagaagta cgtctaacaa
     3001 ccccaggaga tctatctctt tggtgcttac cgccggagtg gcataacggg gaaaatcgag
     3061 gtccgtgttt ttcttgaaat ccatcgctga cataaccgtt cttctttttg gagcgcagta
     3121 aatttctgcc tgattggttg cagtggtcgg atgatacaag aaagtaagaa taatctgaac
     3181 gccagattga tctatctgta gaccgactat cagatttagg gaaggtgcga acaagtccct
     3241 gatatgagat catgtttgtc atctggagcc atggaacagg gttcatcatg agtcatcaac
     3301 ttaccttcgc cgacagtgaa ttcagcagta agcgccgtca gaccagaaaa gagattttct
     3361 tgtcccgcat ggagcagatt ctgccatggc aaaacatggt ggaagtcatc gagccgtttt
     3421 accccaaggc tggtaatggc cggcgacctt atccgctgga aaccatgcta cgcattcact
     3481 gcatgcagca ttggtacaac ctgagcgatg gcgcgatcga agatgctctg tacgaaatcg
     3541 cctccatgcg tctgtttgcc cggttatccc tggatagcgc cttgccggac cgcaccacca
     3601 tcatgaattt ccgccacctg ctggagcagc atcaactggc ccgccaattg ttcaagacca
     3661 tcaatcgctg gctggccgaa gcaggcgtca tgatgactca aggcaccttg gtcgatgcca
     3721 ccatcattga ggcacccagc tcgaccaaga acaaagagca gcaacgcgat ccggagatgc
     3781 atcagactaa gaaaggcaat cagtggcact ttggcatgaa ggcccacatt ggtgtcgatg
     3841 ccaagagtgg cctgacccac agcctagtca ccaccgcggc caacgagcat gacctcaatc
     3901 agctgggtaa tctgctgcat ggagaggagc aatttgtctc agccgatgcc ggctaccaag
     3961 gggcgccaca gcgcgaggag ctggccgagg tggatgtgga ctggctgatc gccgagcgcc
     4021 ccggcaaggt aagaaccttg aaacagcatc cacgcaagaa caaaacggcc catcaacatc
     4081 gaatacatga aagccagcat ccgggccaag gtggagcacc catttcgcat catcaagcga
     4141 cagttcggct tcgtgaaagc cagatacaag gggttgctga aaaacgataa ccaactggcg
     4201 atgttattca cgctggccaa cctgtttcgg gcggaccaaa tgatacgtca gtgggagaga
     4261 tctcactaaa aactgggaat aacgccttaa atggcgaaga aacggtctaa ataggctgat
     4321 tcaaggcatt tacgggagaa aaaaatcggc tcaaacatga agaaatgaaa tgactgagtc
     4381 aaccgagaag aatttccccg cttattcgca ccttccctaa tagcgcggct gcgattctac
     4441 ttttttcacc tgaacctgaa gaggcgtttg tggctccgca gtgtgggcat gactttgctg
     4501 tttcgtgtat ttccttgccg catcctcggc agtaaaccat tgaactcatt ttttatcctc
     4561 gagcttattt ttagttggga tgcataatat ccgatgtttt ataacgatat gcatcctata
     4621 tgctcgggtg ggatagattt ccattatggt gaaggatctt ctt
//
