LOCUS       NZ_AP027481             3371 bp    DNA     circular CON 04-APR-2024
DEFINITION  Escherichia coli strain LR-17-1 plasmid pLR-17-1_2, complete
            sequence.
ACCESSION   NZ_AP027481
VERSION     NZ_AP027481.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00562517
            Assembly: GCF_036494325.1
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  JOURNAL   Unpublished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 3371)
  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                   :: 101x
            Sequencing Technology :: MGI DNBSEQ-G400RS; ONT MinION Mk1c
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_036494325.1-RS_2024_04_03
            Annotation Date                   :: 04/03/2024 23:40:27
            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)                     :: 4,622
            CDSs (total)                      :: 4,506
            Genes (coding)                    :: 4,306
            CDSs (with protein)               :: 4,306
            Genes (RNA)                       :: 116
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 200
            CDSs (without protein)            :: 200
            Pseudo Genes (ambiguous residues) :: 0 of 200
            Pseudo Genes (frameshifted)       :: 65 of 200
            Pseudo Genes (incomplete)         :: 129 of 200
            Pseudo Genes (internal stop)      :: 40 of 200
            Pseudo Genes (multiple problems)  :: 32 of 200
            Pseudo Genes (short protein)      :: 4 of 200
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP027481.1.
            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..3371
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="LR-17-1"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pLR-17-1_2"
                     /geo_loc_name="Ecuador:Santo Domingo"
                     /collection_date="2019"
     gene            complement(292..483)
                     /locus_tag="AABJ42_RS23075"
                     /old_locus_tag="VEE14_44220"
     CDS             complement(292..483)
                     /locus_tag="AABJ42_RS23075"
                     /old_locus_tag="VEE14_44220"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165979.1"
                     /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_000165979.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNDLDADEQADICESLHDHA
                     DELYRSCLARFGDDGESN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            547..870
                     /locus_tag="AABJ42_RS23080"
                     /old_locus_tag="VEE14_44230"
     CDS             547..870
                     /locus_tag="AABJ42_RS23080"
                     /old_locus_tag="VEE14_44230"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_024132211.1"
                     /translation="MLTIRVTDEEHARLLERCEGKRLAEWMRRVCLGEPVARTGKLPTL
                     SPPLLRHLAAIGNNLNQTARKVNSGQWSSIDRVHVVAALMAIEGELRQLRQAVREQGVR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            1079..>1516
                     /locus_tag="AABJ42_RS23085"
                     /pseudo=""
     CDS             1079..>1516
                     /locus_tag="AABJ42_RS23085"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            1548..2108
                     /locus_tag="AABJ42_RS23090"
                     /old_locus_tag="VEE14_44240"
     CDS             1548..2108
                     /locus_tag="AABJ42_RS23090"
                     /old_locus_tag="VEE14_44240"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000067488.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_000067487.1"
                     /translation="MSNLLQMGTDFEKKLKERAASTENMLNSEFRKLEESVDKALSLNR
                     QKIRDAISEHTTSVKKQLDTLSTTVSMQFSTTEAELSRQQKKLLWRVIKGRILFPALTA
                     LSVTGGIFLGCWGLMEWQESKIAKNILTIREQENTLAKLEAKTWGVTFVNGENGKFLVL
                     PDGVKGENTWTVGDKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     gene            2115..2348
                     /locus_tag="AABJ42_RS23095"
                     /old_locus_tag="VEE14_44250"
     CDS             2115..2348
                     /locus_tag="AABJ42_RS23095"
                     /old_locus_tag="VEE14_44250"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137389.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_000137389.1"
                     /translation="MTELEGHLLNALEHLQQDYMRRLNEWESAFAELQKMHEVTQRNNA
                     ILNERVVILSQQVQRLAGQVDRLSRLFIANNS"
                     /name="MbeD family mobilization/exclusion protein"
     Typing          128..211
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="87.059"
                     /coverage="95.0"
                     /evalue="8.83e-18"
     Typing          861..2431
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.817"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gtcacagatg caagcattgt gcacttacgc gcctgtgcca gtgtccgcgt gtgtgctgtt
       61 tatcgggtgc gctgttttta catctgtgcg gctttttact cctgacatgg tgcacttccc
      121 atccattctg caccgatgca aaatgagata agccagtata cacatcgcta tcgctctgtg
      181 aactgggtca gggctgcgcc ccgacacccg cactgacgcg ccctggcggg cttgtctgct
      241 cccggcatcc gctcacaggc aagctgtgaa cgtctccggg agctgcatgt ttcagttgct
      301 ttcaccgtca tcgccgaagc gtgcgaggca actgcggtag agttcgtcgg cgtggtcgtg
      361 aagtgattcg cagatgtctg cctgttcgtc cgcgtccaga tcgttgagtt tttccagcag
      421 ggttagcgtc tggcttctga taaagcgagc catgttaagg gctgtttttt cctgtttggt
      481 catggtctta aggctccttg tatgggggat ttgttagggg gaatgatacc gatgaaacgc
      541 gagaagatgc tcacgatacg ggttaccgat gaggagcacg cccggttact ggaacgctgc
      601 gagggtaaac gactggcgga atggatgcgg cgggtctgtc tgggggagcc ggttgcacgc
      661 acaggaaaac tgccgacact atcgccgcca ttgctgcggc atctggctgc catcgggaac
      721 aacctgaacc agacagcccg gaaggtgaac agcggccagt ggtcttcgat tgaccgggtt
      781 catgtggtgg ccgcactgat ggccatcgag ggtgaattgc gccagttgcg gcaggctgtc
      841 agggaacagg gggtacggga tgatagttaa atttcatgcc agggggaaag gcggtggaag
      901 tggcccggtc gattacctgc tggggcggga gcgtaaccgc gaaggcgcaa cggtgctccg
      961 gggtaacccg gaagaagtgc gggaactcat tgattccacg ccattctcga agaaatacac
     1021 ttcaggcgtt ctgtcgttcg cggagaagga gttaccgccg ggtgaacgcg aaagagtgat
     1081 gacgagcttt gagcgtgttc ttatgcccgg tctcgaaaaa gaccagtaca gcattctctg
     1141 ggtggaacac caggataagg ggcggctcga actgaatttt gtcatcccga acatggagct
     1201 acagagcggt aagcgcctcc agccgtacta cgaccgcgcg gacaggccga ggataaatgc
     1261 ctggcagacg ctggttaatc atcattacgg gctgcgtgac ccgaacgcac cggagaacag
     1321 acggacgctt gtcacgccaa ataatctgcc aaaagcgaaa caggaggccg cagaagcgat
     1381 tacacggggt cttgaggctc tttaccatgc cggagcaata aaaacgcgtc aggatgtcac
     1441 agaggcgctt acagcggcag gttttgaggt ggtgaggaca accaaaagca gcatcagtat
     1501 tgccgacccg gagggggggc ggaatctcag gctaaagggg gcgctgtatg agcaatcttt
     1561 tacaaatggg aacagacttc gagaagaaac tgaaagagcg agccgcttct accgagaaca
     1621 tgctgaacag cgagttcagg aagctcgaag agtctgtaga caaggcattg agcttaaaca
     1681 ggcagaaaat cagagacgct atcagcgaac atacaacatc cgtgaaaaag caactggata
     1741 cgctgagcac caccgtgagc atgcagttca gcaccacaga ggccgaactg tcccggcagc
     1801 agaaaaaact gctctggcgg gtgatcaaag ggcggatact gtttccggcg ctgaccgcgc
     1861 tcagcgtcac gggcggcatt ttcctggggt gctgggggct gatggagtgg caggaaagca
     1921 agattgcgaa aaatatcctg actatcagag agcaggaaaa cacgctggcg aaactcgagg
     1981 caaaaacctg gggggtgacg ttcgtcaatg gcgagaacgg gaaatttctg gtgttgccgg
     2041 acggggtgaa aggggaaaac acctggacgg tgggcgacaa gaacgccgtg aggctggtca
     2101 gggagtaaac gagtatgacg gaactggaag ggcatttgct gaacgcctta gagcatttgc
     2161 aacaggacta tatgcggcgg ctgaacgagt gggagagcgc cttcgcggaa ttgcagaaga
     2221 tgcacgaggt tacgcaacgg aacaacgcga tactgaacga gcgcgtcgtg atattgagtc
     2281 agcaggtgca gagattagcc gggcaagtgg atcgcttgag tcggttattt atcgcgaaca
     2341 acagctaagg gatgaacagg agcgtgcccg gtacagacat gaggtacagg aacgcgcggc
     2401 acgggttcgg agtgggccat caatggagat gtgaccgggg aagtgacgaa atcttgccaa
     2461 tttgaccagt tcgacggctg gggcgagcga aacaaatcgt gtgccgtatt tgtgcatagc
     2521 tatgcaacat cctgaaaacg catttcacgc gtttttgggg attcagccag gggaaaacat
     2581 ggttttttta ctttttgagc gtaaagacgt gaaaaatctc gttattgcac ttgcgatctt
     2641 tcgtcggcgg gcgtagaacg aaaacagctc gccaggaagg cgagctgttt cgggttcatt
     2701 gaggtctctg acctcctcaa tgttcctgtg gaaactgttg agatccacaa cagaaaccag
     2761 ttcattcagt ttgcatgagc cttctgtatt cttcaaggat ttttcaacag cacagtctcc
     2821 caggaacccc gaaaaaaacc tgtttttgca gatacttgcg tatttgcgag aatcgtttgc
     2881 ggttggggga gctgtgacga cggcgaccgc acgcgtgaga gttccgctac cggcgcagag
     2941 agtttcatcg acagcggaca cctgatgagt tgccacaaaa accgtatgta gcgcggctag
     3001 attggttgag ttagaccttg gcggcagttc ccggtatgtg gtggcgtgac gggtgagatg
     3061 gtgcggcgaa gacgcatacg tcacgcaggc gcgggttctt ccactgacgc gccccgtgat
     3121 cgatggcctt ggctccgtcc ggcatatcga gagcggcaaa ctacccgtcc cttcactggg
     3181 aggggtgagt tgttgccgtt ccctccaacc tttcaccatc cggcatatcg cacgatccca
     3241 tgtgcaccgc aactcctgat aactccagtg caaaaaaaaa aacggatctg catcacaacg
     3301 agagtgatcc caccgctcgc cgcagcccca gcgaccgaac gtagtgagcg agtgggcgag
     3361 gaagcggaag a
//
