LOCUS       NZ_AP027872             3489 bp    DNA     circular CON 04-APR-2024
DEFINITION  Escherichia coli strain 2018-01-1CC plasmid p2018-01-1CC_3, complete
            sequence.
ACCESSION   NZ_AP027872
VERSION     NZ_AP027872.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00562620
            Assembly: GCF_036506995.1
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  JOURNAL   Unpublished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 3489)
  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                   :: 216x
            Sequencing Technology :: MGI DNBSEQ-G400RS; ONT MinION Mk1c
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_036506995.1-RS_2024_04_04
            Annotation Date                   :: 04/04/2024 00:07:56
            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)                     :: 4,685
            CDSs (total)                      :: 4,567
            Genes (coding)                    :: 4,356
            CDSs (with protein)               :: 4,356
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 211
            CDSs (without protein)            :: 211
            Pseudo Genes (ambiguous residues) :: 0 of 211
            Pseudo Genes (frameshifted)       :: 66 of 211
            Pseudo Genes (incomplete)         :: 147 of 211
            Pseudo Genes (internal stop)      :: 30 of 211
            Pseudo Genes (multiple problems)  :: 31 of 211
            Pseudo Genes (short protein)      :: 4 of 211
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP027872.1.
            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..3489
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="2018-01-1CC"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="p2018-01-1CC_3"
                     /geo_loc_name="Viet Nam:Thai Binh"
                     /collection_date="2018"
     gene            complement(533..733)
                     /locus_tag="AABK07_RS23415"
                     /old_locus_tag="VEE71_44880"
     CDS             complement(533..733)
                     /locus_tag="AABK07_RS23415"
                     /old_locus_tag="VEE71_44880"
                     /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_023139298.1"
                     /translation="MARSPDPRQRTEGFRKAEASLRLEGMDPAGTPLYENIKERVISGD
                     ITYEQGRAEILAHYQKRANGH"
                     /name="antitoxin VbhA family protein"
     gene            complement(1655..2506)
                     /locus_tag="AABK07_RS23420"
                     /old_locus_tag="VEE71_44890"
     CDS             complement(1655..2506)
                     /locus_tag="AABK07_RS23420"
                     /old_locus_tag="VEE71_44890"
                     /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_058799947.1"
                     /translation="MINIQELLAASKAKENNQLVKGVWFLIQWSPDDYSQERFNIGVAF
                     SSERGEKQVKFTKSFKELSNWYGCNLTKQGDMVIKIATHTFIGKSLDKFSSGFFESGIH
                     YVPMGMAQGESIEKIMNVLFKDVVPMAQEKQNIARASYTTTRNIITVVREAISKNSVLK
                     DIMPENPMVETLSGISVKVPIQFRSNAGTIVSADYATSDTVENELLRSFRDIDLILNGN
                     DFDNVNSFLLLPASAKGEAKKISNLIGDYTSSLKSKGVETISAHQPSSLVNKIDGWYKE
                     VA"
                     /name="hypothetical protein"
     gene            complement(2503..3342)
                     /locus_tag="AABK07_RS23425"
                     /old_locus_tag="VEE71_44900"
     CDS             complement(2503..3342)
                     /locus_tag="AABK07_RS23425"
                     /old_locus_tag="VEE71_44900"
                     /inference="COORDINATES: protein motif:HMM:NF042851.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="HipA family kinase"
                     /protein_id="WP_023139300.1"
                     /translation="MHIEFKPSSDFNNVKINRAPDGAMAETFSCNINWGENLDSRSYVK
                     CFSARKIMAISNEITGYILAKEAGLPVPEKCALIALPQEIKDEFKSRSGEECFEYGFAM
                     MMADGSTPNAIIKMHSPDEDFANSIFMDALNKWPQTARLIAFDEWVANEDRNLGNFIIT
                     PNNNIVVIDHSNLPCEMLWECDDLINEKAYTNKLVLIYELCKVKGRSYSIPDDAFINKE
                     ASHHALILTSSIAELEAWWDYLLDQPRKAKLKDFLNVRANKARTLPYNQQSGLRMTA"
                     /name="HipA family kinase"
     Typing          922..1468
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.201"
                     /coverage="90.0"
                     /evalue="1.2e-144"
ORIGIN
        1 ttccggcatc tttccctgtc catatcgtga aaaaacgcgc ctgatgattt ctgcgcggct
       61 gcatggctat gcacgcaggt gaatggcggt cgatttgggg tggatgctgg catgaaagcc
      121 tgctttccgg cgcataactc ccccgataac ggtgaacggg tgcacagttt actgtgcgac
      181 cgtgaggcgt tggccaggcc gtcaggcatg gcagaattta ctaccaagca ggaggtcgga
      241 tttaacgtgg ataatcagca cgcagtgatg aacgggattc ggaaggggaa cccttgcggc
      301 gcggcgatgt atacatcgct aacgtgcctt actcttttca cagcagaggg tagcaaacaa
      361 gtagcaaaca gatagcaaac agatagcaaa caagtagcaa acagacagca agcagatagc
      421 aaacaagtag caaacaagta gcaaacagat agcaaataca ggaaaagcct ggccggagag
      481 aggccacgcc tgtttttttg aggaagcgat ggtacctagt ttcctgtccg tgtcagtggc
      541 cgttcgcacg cttctggtaa tgagccagaa tttctgcccg tccctgttcg taagtgatat
      601 ccccggaaat aacccgctcc ttgatatttt cgtacagcgg cgttccggcg gggtccatgc
      661 cttcaagcct cagcgacgct tccgctttgc ggaaaccctc agtacgttgt cgtggatcgg
      721 gggacctggc catcgatgtt cctttgagct gtaagcgaat aaggcaggcg gtaaagtagg
      781 cctactttac atatcctgcc cgtactctgc cgttgtttat ccgtgcagac gaatgtgtaa
      841 accggaagga aagtattgca ggaaactgtg taatccggcg gtaaagagag ggtacggcgc
      901 gacacgagcc caatcaggca tcgcagatct tccgcttcct cgctcactga ctcgctacgc
      961 tcggccgttc ggctgcggcg agcggtaccg gcagtccacc tggagttacc cacagattcg
     1021 gaggtagcgg aaggagaaag aggggaacag aaaaggccgc ggcgaagccg tttttccata
     1081 ggcttcgccc ccctgacaag catcacagaa tctgacgctc aaatcagtgg tggcgaaacc
     1141 cgacaggact ataaagatcc caggcgtttc cccctggtag ctccctcgtg cgctctcctg
     1201 ttcctgcctt tcggtttacc ggtgtcattc cgctgttatg gccgcgtttg tctcattcca
     1261 cgcctgacac tcagttccgg gtaggcagtt cgctccaagc tggactgtat gcacgaaccc
     1321 cccgttcagt ccgactacca cgccttcaaa gcaactgtac tcttgattcc aatctctgaa
     1381 gacacaacga attgccactg gtggtagcca ctggtaacag gtttacggag cgaaggtgta
     1441 ttaacgcaga gttcttgaag tgaaagccca aatccggcta cactggaagg acagatttgg
     1501 ttactgcgct ccgttaaagc cagttaccac ggttcaaaag agcgccaact cttgcgaacc
     1561 ttcgaaaaaa ccgcccgcca aggcggtttt ttcgtttggc ctctaagata cgatcgccaa
     1621 tcctcagcgt caagaaatag gatgcgtata aagattatgc aacctcttta taccaaccat
     1681 caattttatt cactagggat gatggctgat gagcactaat agtttcaacg cccttagatt
     1741 ttaaagaaga tgtataatca ccaattagat tgctaatttt tttagcctcc cctttggcag
     1801 atgctggcaa caagagaaag ctatttacat tatcaaaatc attgccattt aagataagat
     1861 caatatctct aaaagaccta agcaactcat tttctactgt atcgctcgta gcgtaatcag
     1921 ccgacactat agttcctgca ttacttctaa attgaatagg aaccttaacc gaaattcctg
     1981 aaagcgtttc caccattgga ttctcaggca taatgtcttt aagtacgcta ttttttgata
     2041 tagcttctct aacaacagtt ataatatttc gtgttgttgt ataactagcc ctagcgatat
     2101 tttgcttttc ttgagccatg ggaactacat ctttaaatag cacattcatt attttttcta
     2161 ttgactcacc ttgagccata cccataggga cataatgaat cccactctcg aaaaacccac
     2221 tggaaaattt atcaaggctt ttcccaataa aagtatgggt agctattttt ataaccatat
     2281 caccttgctt tgttaagtta caaccatacc aattagataa ttccttgaag gatttggtga
     2341 acttaacttg tttctcgcct ctttctgatg aaaaagcaac accaatatta aaacgctctt
     2401 ggctatagtc atcaggtgac cattgaataa ggaaccaaac ccctttaaca agctgattgt
     2461 tttccttagc tttgcttgcg gcaagtaact cttgtatgtt tatcatgctg tcatccttag
     2521 cccagactgc tggttataag gcaatgttct tgctttgttg gcacgcacgt tcaaaaaatc
     2581 tttcaactta gcttttcttg gctgatctaa aagataatcc caccatgctt caagctctgc
     2641 aattgaagaa gttaatatta aagcatggtg gctagcttct ttattaataa aggcatcatc
     2701 aggaatggag tatgaacgcc cctttacctt acataattca taaatcaaca ccaatttatt
     2761 ggtgtatgcc ttttcattta ttaagtcatc acactcccat agcatttcgc atgggagatt
     2821 actatgatct atgaccacaa tattattatt gggcgtaata ataaagttac ctaaattcct
     2881 atcttcattg gcaacccatt catcaaacgc tataagccta gctgtttgag gccatttatt
     2941 taaagcatcc ataaagatgg aatttgcaaa atcctcatca gggctgtgca tttttataat
     3001 agcgttaggc gtgctcccgt cggccatcat catagcaaat ccgtattcaa agcactcttc
     3061 gccagacctg gatttaaatt catcttttat ttcttgtggc aatgctatta aagcacattt
     3121 ttcaggtaca ggcagccctg cctccttcgc caaaatataa ccagttattt cgttagaaat
     3181 tgccataatc ttgcgagcgc taaagcattt cacatagctt ctgctgtcaa gattctcgcc
     3241 ccagttaata ttgcagctaa aagtttctgc catagcgccg tcaggagctc tattaatttt
     3301 aacgttatta aagtcagatg acggcttaaa ttctatgtgc atagctctgg tccatcaaag
     3361 tttgtggttg ctgtattatt tttcttgaaa gcttttttat caaggtaaat gtttttcaca
     3421 tttaccataa catccgttgc gtgcaccatc tcagacgccc tcagggcatt tctgcgccct
     3481 cctgcctat
//
