LOCUS       NZ_AP025213             2442 bp    DNA     circular CON 18-DEC-2023
DEFINITION  Escherichia coli strain 2017.06.04CC plasmid p20170604CC-4, complete
            sequence.
ACCESSION   NZ_AP025213
VERSION     NZ_AP025213.1
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  JOURNAL   Unpublished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 2442)
  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
            AP025213.1.
            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..2442
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="2017.06.04CC"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="p20170604CC-4"
                     /geo_loc_name="Viet Nam:Thai Binh"
                     /collection_date="2017-11"
     gene            join(2118..2442,1..116)
                     /locus_tag="LPH28_RS23875"
     CDS             join(2118..2442,1..116)
                     /locus_tag="LPH28_RS23875"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001565850.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000344119.1"
                     /translation="MDENGEVKQDSKIETFSIPAEPPYVKLYIADIAMIHGLSKSQNDV
                     LLQLAMLIGWDGFVSVSKTRFEKTIQPRVHIEYQTFKNIIAALVDKQIFFRAGRGELEA
                     NPFLFARGDWPSIYERRKKIELKISYDTNGRTVQTKVMDDEC"
                     /name="hypothetical protein"
     gene            103..333
                     /locus_tag="LPH28_RS23880"
                     /old_locus_tag="VEGS18_46270"
     CDS             103..333
                     /locus_tag="LPH28_RS23880"
                     /old_locus_tag="VEGS18_46270"
                     /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_198872674.1"
                     /translation="MMNAEDKLFKNVDRLMLHDSLKKNEVLTVWERTFLSSVYSIYRRT
                     SGNKYSTKGLSPKQKNTAFSILKKHNYHLND"
                     /name="hypothetical protein"
     gene            complement(403..1371)
                     /gene="mobV"
                     /locus_tag="LPH28_RS23885"
                     /old_locus_tag="VEGS18_46280"
     CDS             complement(403..1371)
                     /gene="mobV"
                     /locus_tag="LPH28_RS23885"
                     /old_locus_tag="VEGS18_46280"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000024818.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /GO_process="GO:0006310 - DNA recombination [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobV family relaxase"
                     /protein_id="WP_000024818.1"
                     /translation="MANYAIMRCKKLTGMGSVASALQHCYRERETPNANAERTPENYCS
                     VSKSTDQAMGRVRELLPEKRRKDAVLAVEYVMTASPEWWKEATPRQQAEFFARSEQWLE
                     KKYGKDRVVAAVVHRDEATPHLSAFVVPLTQDGRLSAKEFIGGRSKMREDQSTYAESVK
                     KLGLERGIEGSRATHQTVQHYYESINRGTRSQVSISPEALEPRVLRKGIFTKDVEDQAA
                     IAKRLSHAVNDGFAGTIAMASQSAQNAKRARELQKTMDAQQKRLQSVTEPFKGLSREQM
                     TEILMMAQRFKQQNQEKEKQQRIEREKQRQTRSRGMGGMER"
                     /name="mobV"
     Typing          complement(407..1380)
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.077"
                     /coverage="96.0"
                     /evalue="0.0"
ORIGIN
        1 ttgcacgggg agactggcca tcaatttacg aaagaagaaa gaaaattgag ttaaagatca
       61 gttatgacac caatggaaga acggtgcaga cgaaggtaat ggatgatgaa tgctgaagat
      121 aaacttttta aaaatgtaga caggctaatg ctgcatgatt cactaaaaaa gaatgaggtt
      181 ctgactgttt gggagcgtac ttttttaagc agtgtttaca gcatatatcg tagaactagc
      241 ggtaataaat actcaactaa gggtttgtca ccaaagcaga aaaacacagc tttttctatt
      301 ttaaaaaaac ataattacca tctgaatgat taattttttc gtggtgaatg ccgcaaatga
      361 cgtcactttg cggcgttagc cctatcctgc atcgcatcaa aactaacgct ccataccacc
      421 catgccacgc gatcgcgtct gtcgctgttt ttcacgttca atacgctgct gtttttcctt
      481 ttcctggttt tgctgcttaa accgctgagc catcatcagg atttcggtca tctgctctct
      541 ggaaagcccc ttaaaaggct ctgtgacgct ctgtaggcgt ttctgctgcg catccatagt
      601 cttctgtagc tcacgcgctc tttttgcgtt ctgggcgctc tgagaggcca tagcgatggt
      661 tcctgcaaag ccatcgttca ctgcgtggct tagacgtttg gctatggctg cctgatcttc
      721 cacgtctttg gtgaaaatgc ccttccgcaa tacacgcggc tccagcgcct ccggcgagat
      781 cgatacctgg ctacgggtgc cacggtttat cgattcgtag tagtgctgaa ctgtctgatg
      841 cgtggcgcgg cttccctcga tgccgcgctc aagacccagt ttttttactg attcagcgta
      901 ggtgctctga tcttcacgca tctttgaccg cccgccaata aactctttcg cggacagccg
      961 tccatcctgc gtcaatggca ccacgaacgc agacaggtgc ggggtggcct cgtcccggtg
     1021 aaccaccgcc gccacaacac gatccttccc gtatttcttc tccagccatt gctcagagcg
     1081 ggcgaaaaac tccgcctgct gccgtggtgt ggcctctttc caccactcag ggcttgctgt
     1141 cataacgtat tcaacggcca gtaccgcatc tttacggcgt ttttccggca gcagctcccg
     1201 cacacgcccc attgcctgat ccgttgattt ggacacagag cagtagtttt ctggtgtccg
     1261 ttcagcgtta gcgttcggcg tctcacgctc tcggtagcag tgctgcaacg cgctggccac
     1321 gcttcccatt cccgtcagct ttttgcagcg cattatcgcg tagttcgcca tgttcccccc
     1381 tgattccggc attcattcag ccaggcgggg gagcgcattg cgatacctcc ggcgggccac
     1441 tatcaagatg atagtgtact cactagactt tgctacgcaa aatcgttcgg gcagcaagct
     1501 gccagaaggt caaaatcaac ggcggtctgg caggtggaag gcgtcgcttc gcgccacccc
     1561 ccaccactgc caagcctgtt ttatccggag tgtcgtcaag ggtaaatggc actcgctacg
     1621 ctcgcccttg acgaaatcag gcaatgaaat cgtctttgaa agagcaggaa ccgctcgccg
     1681 cagctttggc tgaggcgtac cgcaggagca acgcgacgag gaacgaacag ccaaagcgag
     1741 gaagcggaat ttccactccc cgtacataga aatgcgtaca ctccttgcta aaaaaaggca
     1801 gtttttcagt gtctaaaaat gccgtttttc agcccttatt ttccccctta atatatagat
     1861 atagatatgg gaacccgctt gtaccaaggg ctagagcgaa gaatcgtact cacctcaagt
     1921 accaatcgta ctcacctcaa gtactaatcg tactcacctc aaggactaat cgtactcacc
     1981 tcaagtacta atcgtacttg atacaaagga cttgactgta tgtctcttta gtacttaaat
     2041 gcgagtacta aatcatggcg aaacgtgggg ctggagtgaa tacgaaaaag atttctaggc
     2101 ttgaacggca tacatacatg gatgaaaacg gtgaggtaaa acaagactct aagatcgaga
     2161 ccttttccat cccagccgaa cctccctacg tcaagctata cattgcagac attgcgatga
     2221 ttcatggttt atcaaaatct caaaatgatg tgcttttaca attggcaatg ctgattggat
     2281 gggatgggtt tgtgtctgta tcaaaaacta gatttgaaaa aaccatacag cccagggttc
     2341 atattgaata tcagaccttt aaaaacataa ttgcggctct tgtagataaa caaatattct
     2401 tccgggcagg gcgtggggaa cttgaagcta acccctttct tt
//
