LOCUS       NZ_AP027609             3264 bp    DNA     circular CON 04-APR-2024
DEFINITION  Escherichia coli strain LR-71-1 plasmid pLR-71-1_10, complete
            sequence.
ACCESSION   NZ_AP027609
VERSION     NZ_AP027609.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00562543
            Assembly: GCF_036498465.1
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  JOURNAL   Unpublished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 3264)
  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                   :: 84x
            Sequencing Technology :: MGI DNBSEQ-G400RS; ONT MinION Mk1c
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_036498465.1-RS_2024_04_04
            Annotation Date                   :: 04/04/2024 00:05:36
            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)                     :: 5,144
            CDSs (total)                      :: 5,026
            Genes (coding)                    :: 4,742
            CDSs (with protein)               :: 4,742
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 284
            CDSs (without protein)            :: 284
            Pseudo Genes (ambiguous residues) :: 0 of 284
            Pseudo Genes (frameshifted)       :: 78 of 284
            Pseudo Genes (incomplete)         :: 199 of 284
            Pseudo Genes (internal stop)      :: 46 of 284
            Pseudo Genes (multiple problems)  :: 38 of 284
            Pseudo Genes (short protein)      :: 3 of 284
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP027609.1.
            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..3264
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="LR-71-1"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pLR-71-1_10"
                     /geo_loc_name="Ecuador:Santo Domingo"
                     /collection_date="2019"
     gene            complement(561..1016)
                     /locus_tag="AABJ98_RS25685"
                     /old_locus_tag="VEE28_49490"
     CDS             complement(561..1016)
                     /locus_tag="AABJ98_RS25685"
                     /old_locus_tag="VEE28_49490"
                     /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_039023474.1"
                     /translation="MTTKFNKFELHSAFRDGKLNEKYFVDLPYLKEEQRRALASFLGAI
                     TREEPLPGKNKPSWLDDNSIKISGTDAYEDGNYWHYHCGPYPEGVKLRSMTFNLGMNVA
                     GLTSAEVIHYQKLNDGTVFVVGFSPTHEPFPKSDAPHYNPLFTESDD"
                     /name="hypothetical protein"
     gene            1413..1991
                     /locus_tag="AABJ98_RS25690"
     CDS             1413..1991
                     /locus_tag="AABJ98_RS25690"
                     /inference="COORDINATES: protein motif:HMM:NF025107.4"
                     /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_052266651.1"
                     /translation="MKSEIELKKTEHSSVEIPERILAIWGRSILNSGWTSVPNELLKNQ
                     SKLGIGNTELVLLINLISFMHHPDARVYPSISLLCERMNQDRRTIQRNLNKLVEMDILR
                     IKIRSTGKNSKGMTNLYDITPLMLKLINLKIPSLNTPDEKHTCPKCGKIAISREEITKE
                     FGFRTDTNGKMRTQSWCKDCRGRKIADLP"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(2199..2522)
                     /gene="mobA"
                     /locus_tag="AABJ98_RS25695"
                     /old_locus_tag="VEE28_49520"
     CDS             complement(2199..2522)
                     /gene="mobA"
                     /locus_tag="AABJ98_RS25695"
                     /old_locus_tag="VEE28_49520"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052604.1"
                     /GO_process="GO:0006355 - regulation of DNA-templated
                     transcription [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization protein MobA"
                     /protein_id="WP_000166966.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="mobA"
     gene            2795..2989
                     /locus_tag="AABJ98_RS25700"
                     /old_locus_tag="VEE28_49530"
     CDS             2795..2989
                     /locus_tag="AABJ98_RS25700"
                     /old_locus_tag="VEE28_49530"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041624.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_001041643.1"
                     /translation="MNKQQQTVLNMAGFIKSQSLTLLEKLDALDADEQAAMCEKLHELA
                     EELQNSIQTRFEVENSTEI"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(2532..2758)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="88.797"
                     /coverage="99.0"
                     /evalue="6.34e-74"
     Typing          2..340
                     /name="rep_cluster_2370"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.294"
                     /coverage="98.0"
                     /evalue="2.31e-150"
     Typing          3019..3264
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.4"
                     /coverage="96.0"
                     /evalue="4.19e-94"
     Typing          complement(2203..2522)
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="9.74e-63"
ORIGIN
        1 gacgctcaag tcagaggtgg cgaaacccga caggactata aagataccag gcgtttcccc
       61 ctggaagctc cctcgtgcgc tctcctgttc cgaccctgcc gcttaccgga tacctgtccg
      121 cctttctccc ttcgggaagc gtggcgcttt ctcatagctc acgctgttgg tatctcagtt
      181 cggtgtaggt cgttcgctcc aagctgggct gtgtgcacga accccccgtt cagcccgacc
      241 gctgcgcctt atccggtaac tatcgtcttg agtccaaccc ggaaagacac gacttatcgc
      301 cattggctgc ggccattggt agacaggatg tgcgagagat gtatcgagag ttcttgaagt
      361 gatggcctga ctgcggctac actgaaagga cagatttggt gacatgtctc gcacaagact
      421 gttaccacgg ttcagaagtt ccccaactta ctgaaccttc gaaaaaccac ctccccaggt
      481 ggttttttcg tttcaggaaa agagactaca gctgagagaa aaaaatctca acatatcctt
      541 accagccact attcagatat ttaatcatct gattcagtga agagtgggtt gtaatgcggc
      601 gcatcagact tagggaaggg ctcatgtgta ggggagaagc ctacgacaaa caccgtgcca
      661 tcgttgagtt tttgatagtg gatcacttca gcggaggtta gccccgcaac gttcataccc
      721 aagttaaaag tcatcgatct aagtttgacc ccttctggat atggaccgca atgataatgc
      781 cagtagttcc cgtcttcgta cgcatcagta ccggaaattt taatggaatt atcatcaagc
      841 catgaaggct tgtttttccc tggaagaggc tcttcacgag ttatcgcacc caagaaagag
      901 gctaatgccc ggcgttgctc ttctttgagg tagggtaaat ctacgaaata cttttcattc
      961 agcttcccgt ctcggaaagc cgaatgaagc tcaaacttat tgaatttggt tgtcatcaaa
     1021 cactttccac ttaccttact gagtaagtag atagcatatc aaagatcgat tcatcagact
     1081 gcggagaatc gcattttaac gcttcatgtg cctgattctt gtatgaacgc gagagcagca
     1141 cttcgtcagc acgagatttg tactgctgac gacgttctgt atcgcagctg tgattatcaa
     1201 atcgtacgtt tgccaacatg tcagtcctat gtttgaagaa gtctgggaag ataaaatctt
     1261 actcaattag atggtaagag aggtcctttc ccagtgctag acattaggcc tttttggtca
     1321 aattaaaggg cggcattgat gccgcccaaa taataaatca taataacaat acctatgtat
     1381 ataggtattg ttattatgat tggtgacaga aattgaaatc agaaatcgaa ctcaaaaaaa
     1441 cagaacactc atcagtagag atcccagaaa ggatcttagc catatggggg cgcagcattt
     1501 taaactctgg ctggacatcc gtccccaatg aactattaaa aaaccaatct aagctaggaa
     1561 taggaaacac agagcttgta cttttgatta atctgatatc tttcatgcat catcctgacg
     1621 caagagtgta cccatcaatt tcacttctat gcgaaagaat gaatcaggac agacgaacaa
     1681 ttcagagaaa tttaaacaag ttagtagaaa tggacattct gaggataaaa atacgctcca
     1741 ccggcaaaaa ctctaaagga atgactaact tgtatgacat aaccccttta atgctgaagt
     1801 taatcaacct aaaaatacca tctttaaata cgcccgatga aaaacatacg tgtccaaaat
     1861 gcggaaaaat agccatatca agagaagaaa taacaaagga gtttggattc agaactgaca
     1921 ctaatggaaa gatgagaacg caaagttggt gcaaggattg tcgaggtagg aaaattgcgg
     1981 atttaccata acgtcgcatt acgcgcaccg cagaaacgcg ctgaacgcga ttctgccgca
     2041 aacaccgcaa aaagagatgt tttccccggg gtaaaccgga aaaatgcgtc aggattgttt
     2101 tcagcgcgtt gcatgactat gcatgaaact gaatggcgat cggtttgggg gcttacggcg
     2161 ttcatatcgt ctgttttcga cagtttctct ccgggaagct aatcagccat aagcctggat
     2221 aacagggcac ggtgatactc cgtaatagcg atcagcacct ccgcatactc cctgtccccg
     2281 acacgcttgc cgtcgataaa gagttttttc tgtaacgccc ccagtctcat aacttctttc
     2341 agtacccggt catcagtcag tgagttaact ttcttaccga gagctgccgc ccgtaaaaaa
     2401 ccagaaacgg tcttgccgca ttcagcagcc ctttttctga tttcctggtc ttcttctgcc
     2461 gtcagacgaa cagggcgact gatagcccgc ctgcgcgtat tacttccact tcgttttgtc
     2521 ataaaacatg gctccgtatc tgacatgggg tgtcggggcg aagccctgac cagggtaatt
     2581 gtaatagcgt gcatgtatgc gcggtataac aattgcacat cctgtcctgt ctgcaagttc
     2641 gaattaccaa caaagcactg ctgttttttt ggcagtgaca gtgttgtctg actgaaatgt
     2701 ccgtcggcag aataccggcg gtaagacggt ccaaaagtgg tgcgcgatat aatcacacga
     2761 cgcagatgac agacagaacg gagaaaacag aaagatgaac aagcagcagc aaactgtact
     2821 caacatggcg ggattcataa aaagccagag cctgacgctg ctcgaaaaac tggacgcact
     2881 cgatgctgac gagcaggccg ccatgtgtga gaagctgcac gaactcgcag aagaactcca
     2941 gaacagcata cagacacgct ttgaagtaga aaatagcaca gagatataac gctcagggca
     3001 ggatgccgaa cggcacaaca gagcgtaagg agaaaatgtc acataaggcg ctcttccgct
     3061 tcctcgctca ctgactcgct acgctcggtc gttcgactgc ggcgagcggt gtcagctcac
     3121 tcaaaggcgg taatacggtt atccacagaa tcaggggata acgccggaaa gaacatgtga
     3181 gcaaaaagcc gaagccaggg acaaaggccg cgccgatggc gtttttccat aggctccgcc
     3241 cccctgacga gcatcacaaa aacc
//
