LOCUS       NZ_AP027871             3692 bp    DNA     circular CON 04-APR-2024
DEFINITION  Escherichia coli strain 2018-01-1CC plasmid p2018-01-1CC_2, complete
            sequence.
ACCESSION   NZ_AP027871
VERSION     NZ_AP027871.1
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  JOURNAL   Unpublished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 3692)
  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
            AP027871.1.
            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..3692
                     /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_2"
                     /geo_loc_name="Viet Nam:Thai Binh"
                     /collection_date="2018"
     gene            join(3285..3692,1..27)
                     /locus_tag="AABK07_RS23385"
     CDS             join(3285..3692,1..27)
                     /locus_tag="AABK07_RS23385"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004193480.1"
                     /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_049595767.1"
                     /translation="MSKRITQIDTATGEEVGSFVAVIRPKQKSAFERHFTMNQDALKIL
                     AKTLTGEQFKVLMMLLADLDYENYIQIAQADIAEALGMQKTNVSRSVKALIDLSVILQG
                     PKVGRSYSYRLNPQFGWKGTVRNHKKALTNGLSVIQGGRS"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(255..488)
                     /locus_tag="AABK07_RS23390"
                     /old_locus_tag="VEE71_44830"
     CDS             complement(255..488)
                     /locus_tag="AABK07_RS23390"
                     /old_locus_tag="VEE71_44830"
                     /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="MbeD/MobD family mobilization/exclusion protein"
                     /protein_id="WP_049595772.1"
                     /translation="MTELETHLLNALKRMEQQFSEQLKASEKAQAALQSMFERTAEDNA
                     TLLKQVSFLDNRVTVLSEQLKQFGNLYRQNRR"
                     /name="MbeD/MobD family mobilization/exclusion protein"
     gene            complement(492..998)
                     /locus_tag="AABK07_RS23395"
                     /old_locus_tag="VEE71_44840"
     CDS             complement(492..998)
                     /locus_tag="AABK07_RS23395"
                     /old_locus_tag="VEE71_44840"
                     /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_049595771.1"
                     /translation="MSVSLTLQERLKQQHLAESETIQSLTKQQLSSLRSELNGIFQQEL
                     NTMLEDMRRQLHDTKEDMRQSRQSMLLTVVKNRVIFPALSAVTILAVIFLSGWGLSTFQ
                     ESQITANWQQINSQKATLAALESKTAGLNIVQDKNGTFVVLPKGAKVDDSGWTVGKQQA
                     LRIVR"
                     /name="hypothetical protein"
     gene            1234..1644
                     /locus_tag="AABK07_RS23400"
                     /old_locus_tag="VEE71_44850"
     CDS             1234..1644
                     /locus_tag="AABK07_RS23400"
                     /old_locus_tag="VEE71_44850"
                     /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_049595770.1"
                     /translation="MIRLSDLTCAPWVIRVSQAIPGVNFTAQVIESLFCGISGRADVQA
                     FPGAKLNAGRHKMQLVMSGMGMPDPEDVVLIGFKPGERDLFKAIHEILLHFWRDLLLRG
                     ERQHARSVFVPEIERVNEVAGSLRGSPQDFRR"
                     /name="hypothetical protein"
     gene            complement(1731..2030)
                     /locus_tag="AABK07_RS23405"
                     /old_locus_tag="VEE71_44860"
     CDS             complement(1731..2030)
                     /locus_tag="AABK07_RS23405"
                     /old_locus_tag="VEE71_44860"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016239790.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization relaxosome protein MobC"
                     /protein_id="WP_049595769.1"
                     /translation="MEKRDNMLRVRFSDAEFEALKQLAEDAGCTMSELVRDHLGRVSVR
                     NKDVDRERIAMLNRINANLNMIARWVNTHKSAASSVEVVAHLMDIERHIRELSQ"
                     /name="plasmid mobilization relaxosome protein MobC"
     gene            complement(2301..2951)
                     /locus_tag="AABK07_RS23410"
                     /old_locus_tag="VEE71_44870"
     CDS             complement(2301..2951)
                     /locus_tag="AABK07_RS23410"
                     /old_locus_tag="VEE71_44870"
                     /inference="COORDINATES: protein motif:HMM:NF020354.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="VRR-NUC domain-containing protein"
                     /protein_id="WP_049595768.1"
                     /translation="MKLLDRQCEQLGIALFDICFPYSGKPELALLSKYRNDGFLGASCE
                     GGAILTLIKSCMLDGLARYNSFGDRDDAVNRYLEAQMTILSDKKEELIDIISHVPENTI
                     FDNYDEIISSPFIQSIYPTLSRELGMAMFYAIGREKISEIAAAFSADPYQYRSGWPDLT
                     LVYENCIEFVEVKTTDNLHKTQLTTIPMILQILPGTVSVCRLKNRTAAEIVKQ"
                     /name="VRR-NUC domain-containing protein"
     Typing          complement(161..1734)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="96.571"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 agcgtgattc agggcggacg tagctgaata gttaccttga aacgtaacta tgggctcttt
       61 gaactaaaat attattatgt tgtccaatac gttacagaga tattcctctg taacgtattt
      121 tccccgccaa gcgcggtttt tttttacccg ccatctctac atgcttggcc cgtaatacct
      181 gtttggcttc ggcgccggag gctccggttc acgctgtttc tgctgcaacg cttcctgaaa
      241 ttccagctgc ttcctcaacg cctgttctgc ctgtagaggt tcccgaactg cttcagctgc
      301 tccgacaata cagtcacccg attgtctaag aagctgactt gcttcaacag cgtggcgttg
      361 tcttccgcag tacgctcgaa catgctctgc aaggcggcct gcgccttctc ggaagctttc
      421 agctgctcgc tgaattgctg ctccatacgc ttcaaggcgt tcaataagtg cgtttccagt
      481 tccgtcatgg tttacctcac gatccgcaga gcttgctgct tcccgactgt ccagccgctg
      541 tcgtccactt tcgccccttt gggcagcacg acgaacgtcc cgttcttgtc ctgaacgatg
      601 ttcaggcccg ctgttttgct ctccagcgcc gccagcgtgg ctttctggct gttgatctgc
      661 tgccagttgg ccgtgatctg gctttcctga aacgtactca ggccccagcc gctcagaaag
      721 ataacggcca agatcgtaac cgcgctcagg gccgggaata tcacccggtt tttcacgacg
      781 gtcagcaaca tgctctgccg gctctggcgc atatcctctt tcgtgtcgtg cagctgccgg
      841 cgcatatctt ccagcatggt attcagctct tgctgaaata tgccgttcaa ctcgcttcgc
      901 aaactgctca gctgctgctt cgtcaggctt tgaatagtct cgctctctgc gagatgctgc
      961 tgcttcaatc gctcctgcag cgtcaaactc acgctcataa agtccccctt tcatgcgcca
     1021 ccgctggccg ctctgcggat ctgacacggt gatgtaattt ttaccttcgc gcgttacctg
     1081 cattccaagg tctgaaacct gctcgataac gtcgctacga ctgcgtataa gcccctgtgc
     1141 ggccctctga gacaaaaccg cgtctatgag tagcctgacg tcttcctgcg gcttctcgcc
     1201 ccttctgagg gcttctgcgg cgattttcag ctcatgatca ggctgagcga tctcacgtgc
     1261 gcgccgtggg tcatccgggt cagccaggcc atacctggcg ttaatttcac tgcgcaggtc
     1321 atcgaaagcc tgttttgcgg catctccggg cgggcggatg ttcaggcttt tcccggtgct
     1381 aagctcaacg cggggcgtca caaaatgcag ctcgtgatgt ccggcatggg tatgcctgac
     1441 ccagaggatg ttgtactgat cggcttcaag cccggcgaac gcgacctgtt caaagcgatc
     1501 catgaaatac tgctccattt ctggcgtgac cttctcctcc ggggcgaaag acagcacgcc
     1561 agaagtgtat ttgtgccgga aatcgagcga gtcaatgagg ttgcgggtag cctccgggga
     1621 tcccctcagg acttccggcg gtgaatcttc ccgaccgggc cgcgttttat cggtgacata
     1681 gccgaccggc ccactgccac cgccagtgcc gtgcctgctg aaacccacaa tcattgcgac
     1741 agctcccgaa tatggcgctc gatatccatc aggtgagcaa cgacctcaac cgaggaagcc
     1801 gccgatttat gcgtattaac ccagcgggca atcatgttca ggttggcatt gatgcggtta
     1861 agcatggcaa tccgttcccg atcgacgtct ttgtttcgca cgctgaccct gccgagatga
     1921 tcgcgaacca gctcggacat ggtgcagcct gcatcttcgg ccagctgctt cagcgcctca
     1981 aattccgcgt cagaaaacct gacccgcagc atgttatcgc gcttttccat tccacctcca
     2041 tcgtcgcata ttgcacttta aacaaggcta cccgatgttg ctacatttcg ctacgctcaa
     2101 tgtcgcacac cgggccttgc aatgggagac ttcgcctccc cttgacccct cccttgcagc
     2161 ggtcgctttg ctccctcgcc cagggcaacg gcgtctatca ggtggatggc ctcacttcgt
     2221 gaaaccatcc acctctggta aggatatcta tgggggtgtc atcaaacagt aaatcggaac
     2281 cccaaagggg cccccacgat ttactgtttg acgatttcag cggcagtacg attttttaga
     2341 cggcaaacag aaaccgtacc tgggagaatt tgtagaatca ttgggatggt tgttaactgg
     2401 gttttatgaa gattatcagt agtctttact tctacaaact caatacaatt ttcatagact
     2461 aaagtgagat ctggccatcc actacgatat tggtaagggt ctgcagaaaa tgcagcagct
     2521 atttctgata ttttttcacg gccaatggca tagaacattg ccatgcctag ttctctggag
     2581 agagtgggat aaatgctttg tatgaaaggg ctagaaatta tttcatcgta attatcaaaa
     2641 atcgtatttt caggaacatg actaattatg tctataagct cttctttttt atcagataaa
     2701 attgtcatct gtgcttctaa atagcgattt actgcgtcat cccgatcacc aaaggagttg
     2761 tatctggcta agccgtctaa catgcatgat tttataagag ttaagattgc tccaccttcg
     2821 caagaggccc ctaaaaaacc atcatttcta tattttgaaa gcagagccaa ttctggcttt
     2881 ccagagtagg gaaaacatat atcaaacaaa gctattccaa gctgctcaca ctgcctatcc
     2941 agaagtttca tttggtctct ccagttaaaa aagccatcag atacatcaac gatttaatta
     3001 cagtaaccgc tcaccgcaag ttccggctga ggcgtaccgc agcgtagcga ggaacgaaca
     3061 gtcggaacga ggaagcggaa tatcacctga acgggcatag aaatgcttat gcactattcg
     3121 atgaaaacag ggggtctacc cgaccatcta agcctctcgc tataagatac agaaggaggg
     3181 cttctctcag cccttgtgtg gcgcggttct cgcttgacga tagttatcat tattgataac
     3241 gttgttatca ttattgataa ctattttttg ggagagcctc ttaaatgagt aaaagaatta
     3301 ctcagataga cactgctaca ggggaagagg taggtagttt tgtcgcagtt atccgaccca
     3361 aacagaagtc agcttttgag aggcatttca ctatgaacca agacgcgtta aagatccttg
     3421 ctaaaaccct tacaggggag caattcaaag tcttgatgat gctgttagct gatctcgatt
     3481 atgaaaatta cattcaaatt gcccaagctg atattgccga agctttaggc atgcagaaaa
     3541 ccaatgtgag ccgttcagtg aaagctctca tcgacctgtc tgtgatcctt cagggcccta
     3601 aagtagggcg cagttatagt taccgcctga atcctcagtt tggatggaaa ggcactgtaa
     3661 ggaaccacaa aaaggccctg acaaatggcc tg
//
