LOCUS       NZ_AP025212             4371 bp    DNA     circular CON 18-DEC-2023
DEFINITION  Escherichia coli strain 2017.06.04CC plasmid p20170604CC-3, complete
            sequence.
ACCESSION   NZ_AP025212
VERSION     NZ_AP025212.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00407181
            Assembly: GCF_020886435.2
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1
  AUTHORS   Yamamoto,Y., Higashi,A., Ikawa,K., Yamaguchi,T., Kawahara,R.,
            Nguyen,T.N., Khong,D.T. and Tran,H.T.
  TITLE     Horizontal transfer of mcr-1 marked with a single nucleotide
            mutation between clinical isolates from community residents
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4371)
  AUTHORS   Yamaguchi,T. and Kawahara,R.
  TITLE     Direct Submission
  JOURNAL   Submitted (25-OCT-2021) Contact:Takahiro Yamaguchi Osaka Institute
            of Public Health, Division of Microbiology; Higasinariku nakamichi
            1-3-69, Osaka, Osaka 537-0025, Japan URL :https://www.iph.osaka.jp/
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8
            Genome Coverage                   :: 202x
            Sequencing Technology :: MGI DNBSEQ-G400RS; ONT MinION Mk1c
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 12/18/2023 04:06:10
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,830
            CDSs (total)                      :: 4,711
            Genes (coding)                    :: 4,439
            CDSs (with protein)               :: 4,439
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 272
            CDSs (without protein)            :: 272
            Pseudo Genes (ambiguous residues) :: 0 of 272
            Pseudo Genes (frameshifted)       :: 81 of 272
            Pseudo Genes (incomplete)         :: 187 of 272
            Pseudo Genes (internal stop)      :: 43 of 272
            Pseudo Genes (multiple problems)  :: 40 of 272
            Pseudo Genes (short protein)      :: 4 of 272
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP025212.1.
            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..4371
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="2017.06.04CC"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="p20170604CC-3"
                     /geo_loc_name="Viet Nam:Thai Binh"
                     /collection_date="2017-11"
     gene            571..1002
                     /locus_tag="LPH28_RS23850"
                     /old_locus_tag="VEGS18_46230"
     CDS             571..1002
                     /locus_tag="LPH28_RS23850"
                     /old_locus_tag="VEGS18_46230"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_003511628.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF6530 family protein"
                     /protein_id="WP_001025244.1"
                     /translation="MNIPTHLKHKPIIAVENYDRIDGPYADDTDAMGLSVGIAQWNTPG
                     YTELSAKVWRNTGEKWSRQSEELPLHRVIDLATLICIAMDYSKHGRLSSSDDFPVSRSG
                     GNPELSRHIDLMKNELKENHEHLDESLKRLAAELKRLGY"
                     /name="DUF6530 family protein"
     gene            1086..1415
                     /locus_tag="LPH28_RS23855"
                     /old_locus_tag="VEGS18_46240"
     CDS             1086..1415
                     /locus_tag="LPH28_RS23855"
                     /old_locus_tag="VEGS18_46240"
                     /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_052909321.1"
                     /translation="MKILPAEPGLYFFASFESGAHVYKVVAWSENENGGLDPQCVLTAL
                     YDKSSSSQQWELHSTSASAYQHSNDGRPFMYFITYFTSNGGIPELYNAINTLAERWGYP
                     LIDLP"
                     /name="hypothetical protein"
     gene            complement(1560..2093)
                     /locus_tag="LPH28_RS23860"
                     /old_locus_tag="VEGS18_46250"
     CDS             complement(1560..2093)
                     /locus_tag="LPH28_RS23860"
                     /old_locus_tag="VEGS18_46250"
                     /inference="COORDINATES: protein motif:HMM:NF025323.3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system YafO family toxin"
                     /protein_id="WP_112909245.1"
                     /translation="MPPHLPRIIVHIHDDLSRQPGVESVAREFETYKSYAFQIATDSEC
                     DVSNFLPTLDEEDQKAFRPDHPFFGRDRLFYGQRIRAANDPVFHVHLHHQETIKSWYAF
                     DKADVFVSQWDCVSDAALVYAYLKTESDDYHFLLLEIVAPGAHDLYQTEGKIAEWRHKT
                     RNFRYSSQNPSLRT"
                     /name="type II toxin-antitoxin system YafO family toxin"
     gene            2523..3113
                     /locus_tag="LPH28_RS23865"
     CDS             2523..3113
                     /locus_tag="LPH28_RS23865"
                     /inference="COORDINATES: protein motif:HMM:NF025107.3"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_072775496.1"
                     /translation="MSTTKEKEKTDFPEALLSIWGRTILGSGWTTVPNELLKNQSHLGI
                     SNSELVLLIHLISFMHSASAKIFPSIDSLAERMNQDRRTIQRTIQRLEDKELIRKRVRS
                     TGKTDVGMSNVYDISPLMLKLINIQLPTMSPPPNTHTCPKCKKFAKSESDIERLFGYRR
                     ISAEKMVIQSWCKECRGAPKKPQSPKEGSPDLP"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(3722..3922)
                     /locus_tag="LPH28_RS23870"
                     /old_locus_tag="VEGS18_46260"
     CDS             complement(3722..3922)
                     /locus_tag="LPH28_RS23870"
                     /old_locus_tag="VEGS18_46260"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000166333.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="antitoxin VbhA family protein"
                     /protein_id="WP_052909318.1"
                     /translation="MARSPDPRQRTEGFRKAEASLRLEGMDPAGTQLYENIKERVISGD
                     ITYEQGRADILAHYQKRANGH"
                     /name="antitoxin VbhA family protein"
     Typing          2..454
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="86.526"
                     /coverage="98.0"
                     /evalue="4.8599999999999996e-138"
     Typing          4117..4366
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.556"
                     /coverage="95.0"
                     /evalue="2.52e-61"
ORIGIN
        1 ccctcgtgcg ctctcctgtt cctgccattc ggtttaccgg tgtcattccg ctgttatggc
       61 cgcgtttatc tcattccacg cctgacactc agttccgggt aggcagttcg ctccaagctg
      121 gactgtatgc acgaaccccc cgttcagtcc gaccgctgcg ccttttccgg taactatcaa
      181 cttgagtcca acccggaaag acacgacaaa gcgccactgg cagcagccac tggtaaacag
      241 gatgtgcgag agatgtatcg agagttcttg aagtggtggc ctgactgcgg ctacactgaa
      301 aggacagatt tggtgacatg tctcgcacaa gactgttacc acggttagag aatctgccag
      361 gattaactaa ccttcgaaaa accacctgcc agggtggttt tttcgttttc tgagcaagag
      421 attacgctct gccataaatg atctcaagaa gatccacgcc aacaacttca aatccatcaa
      481 ttcacaaaat gttacactta ctaattagta aaataagctg ttttgttatt ttgttaatta
      541 acaacctaaa ttcacataaa agagaatgat atgaacatcc ctactcatct gaaacacaaa
      601 ccgattatcg ctgtagaaaa ctatgatcga attgatggac cttatgctga tgacactgat
      661 gctatggggc tttccgttgg aattgctcaa tggaacaccc ccgggtatac cgagctatca
      721 gcaaaagtgt ggcgcaacac cggagaaaag tggtcacggc aatcagaaga attacctctt
      781 catcgtgtta tcgacttggc aacgcttatc tgcatagcaa tggattacag taaacatggc
      841 cgcttatctt ccagcgacga ctttccggtc agtcgttcag gaggcaatcc tgagttatct
      901 cgtcacattg atttaatgaa aaacgagcta aaagagaatc acgagcattt agatgagagt
      961 cttaagcgtt tagcagcaga actaaaacgt ttaggttatt aacctcccag tgatttttta
     1021 tacccaccac ggggaattag gtagttattg cctctcagac agaataaaca aaaggaagct
     1081 agctaatgaa gatcctacca gctgaaccgg gattatattt tttcgcatct tttgagtccg
     1141 gtgctcacgt ttacaaagta gtggcctggt cagaaaatga gaatggtggt ttagatccac
     1201 agtgtgtgtt aacggcctta tatgacaaga gcagttccag ccagcaatgg gaacttcact
     1261 caacttcagc atctgcatat cagcacagca atgacggcag accatttatg tattttatca
     1321 cctacttcac cagcaatggc gggatacctg aactttataa cgcaataaac acactagccg
     1381 aacgatgggg atacccatta attgatttac cataacattc gttatcggaa ggtagctccc
     1441 cccgagcgaa ttcttgttcc gaccctgccg cttaccaaat acctgtcccg ccgttttccc
     1501 ttcgggaagc gtgaaagcac aaaggcccgt aaatacgggc ctttgtgctt tcattggatt
     1561 caagttctca gagaaggatt ctggctgcta tagcggaaat ttctagtttt atgtctccac
     1621 tctgcaattt taccttctgt ttgataaagg tcatgagccc ctggagccac gatctctaac
     1681 aacaaaaagt ggtaatcatc actttctgtt ttcaaatatg catagaccaa tgcagcgtca
     1741 cttacacaat cccactgact aacaaaaaca tctgctttat caaaagcata ccaagattta
     1801 atagtttctt ggtgatgcaa gtgaacgtga aagacaggat cgtttgctgc ccttatcctt
     1861 tggccataga aaagacgatc tcgaccaaaa aacgggtggt cgggacgaaa tgccttttga
     1921 tcttcttcat ccaatgtagg aaggaagttc gaaacatcac attcactatc tgtcgctatc
     1981 tgaaacgcat aggatttata tgtttcaaat tccctagcca cggactcaac tccaggttgc
     2041 ctagataagt catcatgaat atgaacaatg attcgaggaa ggtgcggcgg catccacgta
     2101 ctcccgagca aaataggagt acgaatgata tcacagacaa gtatcagttc tgattggtaa
     2161 tccgatgatt tttaacagca gacttagcct catcgctctt ctgagctgcc agccccgcat
     2221 tgataaaatc ttggaacaga gcgtaactca tggcgggttt tatcggagaa cgatgttccg
     2281 atgcttttct catcccagac atgtgaatac ctcgcttaat gacgtagtag gaatagcaaa
     2341 ctattcctct tcgaatcatg ttaagagcaa gcgtcgtgac atgtcacgaa aaggcgtgcc
     2401 tttaaggtaa aattagggtg gcgttaacgc caccctaata ataactactc ttacatacac
     2461 tatgatatag tgtatgtaag agtagttatg tcatgataaa tgattcaaaa aaagtaaccg
     2521 ctatgagtac aactaaagag aaagaaaaga ctgatttccc tgaagcctta ctatccatat
     2581 gggggaggac aatccttggt tcaggatgga caacagtccc caacgaactg ctaaaaaatc
     2641 aatctcactt gggtatcagt aactcagagt tagttctcct tatccatttg atatcattta
     2701 tgcatagtgc ttctgcaaaa atattcccat caatagattc tctagcagaa agaatgaacc
     2761 aagaccggcg taccattcag agaaccatac aaaggctcga agataaggag ctgataagaa
     2821 aaagagtacg ttcaactggg aaaaccgatg tagggatgag taatgtgtat gatatttctc
     2881 cattaatgct caagcttatc aacatacagc taccaacaat gagccctcct ccaaacacac
     2941 atacatgtcc aaaatgtaaa aaatttgcaa aatccgaatc tgacatcgaa cgattatttg
     3001 gttaccgaag gatttcggca gaaaagatgg tcatacaaag ctggtgtaaa gaatgcagag
     3061 gtgctccaaa aaaaccgcaa agtcccaaag aaggctcgcc tgatttacca taacatctgt
     3121 tgcgtgcacc atctcagacg ccctcagggc atttctgcgc cctccagcct atttccggca
     3181 tctttccctg tccatatcgt gaaaaaacgc gcctgatgat ttctgcgcgg ctgcatggct
     3241 atgcacgcag gtgaatggcg gtcgatttgg ggtggatgct ggcatgaaag cctgctttcc
     3301 ggcgcataac tcccccgata acggtgaacg ggtgcacagt ttactgtgcg accgtgaggc
     3361 gttggccaag ccgtcaggca tggcagaatt tactaccaag caggaggtcg gatttaacgt
     3421 ggataatcag cacgcagtga tgaacgggat tcggaagggg aacccttgcg gcgcggcgat
     3481 gtatacatcg ctaacgtgcc ttactctttt cacagcagag ggtagcggta gcaaacaagt
     3541 agcaaacaga tagcaaacag atagcaaaca gatagcaaaa aagtagcaaa cagatagcaa
     3601 acaagtagca aacagatagc aaacaagtag caaacagata gcaaatacag gaaaagcctg
     3661 gccggagaga ggccacgcct gtttttttga ggaagcgatg gtacctagtt tcctgtccgt
     3721 gtcagtggcc gttcgcacgc ttctggtaat gagccagaat gtctgcccgt ccctgttcgt
     3781 aagtgatatc cccggaaata acccgctcct tgatattttc gtacagctgc gttccggcgg
     3841 ggtccatgcc ttcaagcctc agcgacgctt ccgctttgcg gaaaccctca gtacgttgtc
     3901 gtggatcggg ggacctggcc atcgatgttc ctttgagctg taagcgaata aggcaggcgg
     3961 taaagtaggc ctactttaca tatcctgccc gtactctgcc gttgtttatc cgtgcagacg
     4021 aatgtgtaaa ccggaaggaa agtattgcag gaaactgtgt aatccggcgg taaagagagg
     4081 gtacggcgcg acacgagccc aatcaggcat cgcagatctt ccgcttcctc gctcactgac
     4141 tcgctacgct cggccgttcg gctgcggcga gcggtaccgg cagtccacct ggagttaccc
     4201 acagattcgg gggtagcgga aggagaaaga ggggaacaga aaaggccgcg gcgaagccgt
     4261 ttttccatag gcttcgcccc cctgacaagc atcacagaat ctgacgctca aatcagtggt
     4321 ggcgaaaccc gacaggacta taaagatccc aggcgtttcc ccctggtagc t
//
