LOCUS       NZ_AP027826             3824 bp    DNA     circular CON 04-APR-2024
DEFINITION  Escherichia coli strain 2017.17.01CC plasmid p2017.17.01CC_4,
            complete sequence.
ACCESSION   NZ_AP027826
VERSION     NZ_AP027826.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00562603
            Assembly: GCF_036505675.1
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  JOURNAL   Unpublished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 3824)
  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                   :: 67x
            Sequencing Technology :: MGI DNBSEQ-G400RS; ONT MinION Mk1c
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_036505675.1-RS_2024_04_04
            Annotation Date                   :: 04/04/2024 00:10:44
            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)                     :: 4,673
            CDSs (total)                      :: 4,556
            Genes (coding)                    :: 4,337
            CDSs (with protein)               :: 4,337
            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)              :: 219
            CDSs (without protein)            :: 219
            Pseudo Genes (ambiguous residues) :: 0 of 219
            Pseudo Genes (frameshifted)       :: 59 of 219
            Pseudo Genes (incomplete)         :: 140 of 219
            Pseudo Genes (internal stop)      :: 49 of 219
            Pseudo Genes (multiple problems)  :: 30 of 219
            Pseudo Genes (short protein)      :: 4 of 219
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP027826.1.
            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..3824
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="2017.17.01CC"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="p2017.17.01CC_4"
                     /geo_loc_name="Viet Nam:Thai Binh"
                     /collection_date="2017"
     gene            join(3797..3824,1..86)
                     /locus_tag="AABJ82_RS23340"
     CDS             join(3797..3824,1..86)
                     /locus_tag="AABJ82_RS23340"
                     /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_071587628.1"
                     /translation="MHEPPVQSDCCALSGNYRLESNPERHDKTPLAAAIGN"
                     /name="replication initiation protein"
     gene            347..1264
                     /locus_tag="AABJ82_RS23345"
                     /old_locus_tag="VEE60_45200"
     CDS             347..1264
                     /locus_tag="AABJ82_RS23345"
                     /old_locus_tag="VEE60_45200"
                     /EC_number="2.1.1.-"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016243916.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0008170 - N-methyltransferase activity [Evidence IEA]"
                     /GO_process="GO:0009307 - DNA restriction-modification
                     system [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="site-specific DNA-methyltransferase"
                     /protein_id="WP_044069000.1"
                     /translation="MLKKIPLFDEIENNSVTNGDSIELIKKVQTQSAHLILSDIPYGIG
                     ADDWDVLHKNSNNAYLGSSPAQKSAGAIFKKRGKPINGWSDADRKIPLEYQQWCEEWAS
                     EWYRTLKPGASAIIFAGRRFSHRCICAMENAGFNLRDIIAWMRTKAPHRAQRLSCVYER
                     RGDQYNKEKWDGWRVGNLQPTFEPILWFSKPYKIGGTIADNVLLHGVGAYNQDAFTARN
                     GKPENVIHAGFERNEGGLHPTQKPVSLMKALIELTTQEGQLVIDPFSGSGSTLVAAKEL
                     GRNYIGFEFNPAYVEISKKRLEDK"
                     /name="site-specific DNA-methyltransferase"
     gene            complement(1265..2191)
                     /locus_tag="AABJ82_RS23350"
                     /old_locus_tag="VEE60_45210"
     CDS             complement(1265..2191)
                     /locus_tag="AABJ82_RS23350"
                     /old_locus_tag="VEE60_45210"
                     /EC_number="3.1.21.-"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_006621132.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="HindIII family type II restriction endonuclease"
                     /protein_id="WP_000362418.1"
                     /translation="MDLCNFKFITEDAIIRRRYWIDEIVKLSGHFVNDSSRVENEIIDE
                     VKKSGSQALLDHLRLCTAIPESYDHDSSEEKLYSKYTDALISECFKYLGLNSIVLTERA
                     DAADVEVVCDSYSFVADAKVFRLSRTAKNQKDFKVQAMDGWRNTKDFAMVVCPIYQLPT
                     KSSQIYQQAILRNVCVFTYTHLAVLIRYSAIATTEDSKNLLGEIFKSVSLLNPSKDSVQ
                     YWVNINRTMLSYDSRIAELWSDEKSATTEGIAVSKKMAIEFLSSERTRMLMMTKDEAVS
                     ALIKMHKIDSRIDQINKVTDNNILSLK"
                     /name="HindIII family type II restriction endonuclease"
     gene            complement(3078..3227)
                     /locus_tag="AABJ82_RS23355"
                     /old_locus_tag="VEE60_45220"
     CDS             complement(3078..3227)
                     /locus_tag="AABJ82_RS23355"
                     /old_locus_tag="VEE60_45220"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017880354.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_003978816.1"
                     /translation="MPSEYDEQRDATDTQLPGEYDLFDLMAQVTEENLHAPVDFGPPVG
                     REAL"
                     /name="hypothetical protein"
     Typing          complement(3263..3435)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="92.529"
                     /coverage="100.0"
                     /evalue="4.3800000000000006e-64"
     Typing          2..263
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.249"
                     /coverage="91.0"
                     /evalue="3.23e-65"
     Typing          3402..3824
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.575"
                     /coverage="80.0"
                     /evalue="0.0"
ORIGIN
        1 gctgcgcctt gtccggtaac tatcgtcttg agtccaaccc ggaaagacac gataaaacgc
       61 cactggcagc agccattggt aactgattta cggagcgaag cgttaagtgt aatagagttc
      121 ttgaagtgag cggcttacta cagctacact ggaaggacaa attaggtcac tgcgctccgt
      181 gaaagccagt taccacggtt cagaagttcc ccaactaact gaaccctgaa aaagccgcct
      241 ccccaggcgg ttttttcttt tcaaaaggct acgacgaaag gttatcctgc gtcaagataa
      301 ctttggtagt tataatgaag tgaataaacc attggtaagg tgttgaatgt taaaaaaaat
      361 cccattattt gacgagatag aaaacaactc cgtgacaaat ggtgactcta tcgagctaat
      421 aaaaaaagta caaactcaat ccgctcactt aatactgagt gatattcctt acggaatagg
      481 agctgatgat tgggatgtac ttcataaaaa ctcgaacaat gcctacctag gttcaagccc
      541 cgcacaaaaa tcagctgggg ccattttcaa aaaaagagga aagcctataa atggctggtc
      601 tgatgcagat agaaaaatac ctttagagta tcaacaatgg tgtgaagagt gggcgagcga
      661 atggtatcgg accttaaaac caggagctag tgcaatcatt ttcgctggta ggagattttc
      721 acacagatgt atttgcgcaa tggaaaatgc tggatttaac ctcagagata taatcgcctg
      781 gatgcgaaca aaagctcctc atcgtgcaca aaggctaagc tgcgtatatg aaaggcgtgg
      841 agaccaatat aacaaagaaa aatgggacgg ctggagggtt ggaaacttac agccaacatt
      901 tgagcccata ctatggtttt caaaacccta caaaatagga gggactattg ctgataacgt
      961 tctattgcat ggtgttggag catataacca agatgcgttc acagcaagaa atggaaaacc
     1021 tgaaaatgta atacatgctg gctttgagag aaatgaaggt ggattacatc caacgcagaa
     1081 gcctgtttcg ctgatgaaag cgctaataga actaactact caagaaggac agctagtaat
     1141 agatccattt agtggtagcg gttcaactct tgtggcagca aaagagctgg gcagaaacta
     1201 tataggcttc gagtttaacc cagcatatgt agaaataagc aaaaaaagat tagaagataa
     1261 ataactactt aagtgacagt atattattat ctgtcacttt atttatttgg tctatcctac
     1321 tgtctatttt atgcattttt atcaacgcac tgacagcctc atccttggtc atcattagca
     1381 tccttgtacg ttcagaagat agaaattcta tagccatttt ttttgaaacg gcaataccct
     1441 cagttgtggc tgatttttca tcactccaaa gctcagctat cctactatca tagcttaaca
     1501 ttgttctatt tatattcacc caatattgca cactatcttt gctagggttg agtaaagata
     1561 cagatttaaa tatttcacca agaaggtttt tactatcttc agttgttgct atagctgaat
     1621 atcttatgag aacggccagg tgtgtatatg taaaaacaca aacatttcgc aatatagctt
     1681 gctgatatat ttgacttgat tttgttggca actgatatat tggacataca accattgcaa
     1741 agtctttggt atttctccaa ccatccatag cctgaacttt aaagtctttt tgattttttg
     1801 cagttctact caagcgaaat actttggcat ctgccacaaa tgaatagcta tcgcaaacaa
     1861 cctcaacatc agccgcatct gccctttcag tcaaaacaat actatttaac cctaaatatt
     1921 taaaacattc tgatatcagt gcatctgtat actttgagta cagtttttct tcgcttgaat
     1981 catgatcata tgactcaggt attgctgtgc ataacctaag gtggtctagt aatgcttgac
     2041 ttccagattt cttaacctca tctattattt cattttcaac tctgcttgag tcgttaacaa
     2101 agtgaccact tagttttact atttcatcaa tccagtaacg ccttcttatt attgcatctt
     2161 cagtaatgaa tttaaaatta cataagtcca tttttaatac ccgatataat taatcaataa
     2221 ctcagtataa tctcgcgatc ataacagatt ttttcatctg ccgaataata gaactatcag
     2281 tttatatggc tagagattcg cttgtattta ccataacatc cgttgcgtgc accgcctgag
     2341 aggctctcag ggcgtttctg acgggaaacc ggtaaaacag gcaacaaacc acccgaaaac
     2401 ccgccagaaa cgcgcaggct ctgtttttac ggcatgcatg agtatgcgcg caagtgcata
     2461 gcgcggaaat tcacgccatt cagccggggt aagtcctgtt tccgtcgttc ttcccacccg
     2521 aaaacggtga acggggacgc aatttattgc gtggccgtga ggcgttgccg gcacagccgg
     2581 aaaacccgtt ttcagcacgt tcaggaaggg ggccgatgta cgaatggttc agggaacgga
     2641 tctgaggtaa tccggtagtt actttgtagt ttatctgtag ttttcttgta gtctattagt
     2701 agtccgccac ggtttttgta gtttttttgt agtctgccat cactaatgca aaacgttttt
     2761 tgtagtttat ctgtagtttt tggttgctca gatggtcatg cttgcatgac catcaaagaa
     2821 taggacgctt tttagccaaa taccccttaa cctacggaga gcgccctacc aaaaaagatg
     2881 attttttatc ccttaaatgg tcatacacca tacgcaaccg cgattttcat cgcaattgca
     2941 tgaattaaaa ggtaaaaact gaatttcccg tttatttatg taatacgcaa cgtattacaa
     3001 ccacctgtaa tcacatgaaa ataaagaaat aagatgtaat accggcgtat tacacgtacg
     3061 ctgaccagcg aaaaaagtta taacgcttcc ctgccgacag gcgggccaaa atccaccggg
     3121 gcgtgcaggt tctcttcagt aacctgcgcc attaaatcaa aaaggtcata ttcgccggga
     3181 agctgcgtat cagtcgcatc ccgttgttca tcatattcag atggcatggg gtgatatcca
     3241 gtagctgaaa ggttgttagc gggtttcggg gcgcagccct gaaccagtca cgtagcgcta
     3301 gcggagtgta tccgagctta ttatgttggc atgagtgcga tgatcaggaa agtgcttcat
     3361 gtggcaggag aaaaatgcag cagcggagcg taagcagaat atgcgataca ggagatattc
     3421 cgcttcctcg ctcactgact cgctgcgctc ggtcgttcgg ctgcggcgag cggtacaggc
     3481 ttacgggcgg ggcggaagtg tccgggaaga tgccagggag agacggaaaa gggaagcgag
     3541 aaggtcgcgg cgaagccgtt tttccatagg ctccgccccc ctgacaagca tcgcgaaatc
     3601 tgacgctcaa atcagtggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc
     3661 cctggtggct ccctcgtgcg ctctcctgtt cctgcctttc ggtttaccgg tgtcattccg
     3721 ctgttatggc cgcgtttgtc tcattccacg cctgacactc agttccgggt aggcagttcg
     3781 ctccaagctg gactgtatgc acgaaccccc cgttcagtcc gact
//
