LOCUS       NZ_AP027662             3372 bp    DNA     circular CON 04-APR-2024
DEFINITION  Escherichia coli strain PSJ-42 plasmid pPSJ-42_10, complete
            sequence.
ACCESSION   NZ_AP027662
VERSION     NZ_AP027662.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00562565
            Assembly: GCF_036500485.1
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  JOURNAL   Unpublished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 3372)
  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                   :: 135x
            Sequencing Technology :: MGI DNBSEQ-G400RS; ONT MinION Mk1c
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_036500485.1-RS_2024_04_04
            Annotation Date                   :: 04/04/2024 00:14:17
            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)                     :: 5,040
            CDSs (total)                      :: 4,922
            Genes (coding)                    :: 4,743
            CDSs (with protein)               :: 4,743
            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)              :: 179
            CDSs (without protein)            :: 179
            Pseudo Genes (ambiguous residues) :: 0 of 179
            Pseudo Genes (frameshifted)       :: 78 of 179
            Pseudo Genes (incomplete)         :: 115 of 179
            Pseudo Genes (internal stop)      :: 32 of 179
            Pseudo Genes (multiple problems)  :: 41 of 179
            Pseudo Genes (short protein)      :: 2 of 179
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP027662.1.
            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..3372
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="PSJ-42"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pPSJ-42_10"
                     /geo_loc_name="Ecuador:Puyo"
                     /collection_date="2019"
     gene            join(3281..3372,1..142)
                     /locus_tag="AABK18_RS25155"
     CDS             join(3281..3372,1..142)
                     /locus_tag="AABK18_RS25155"
                     /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"
     gene            complement(1458..1649)
                     /locus_tag="AABK18_RS25160"
                     /old_locus_tag="VEE39_48120"
     CDS             complement(1458..1649)
                     /locus_tag="AABK18_RS25160"
                     /old_locus_tag="VEE39_48120"
                     /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            1713..2036
                     /locus_tag="AABK18_RS25165"
                     /old_locus_tag="VEE39_48130"
     CDS             1713..2036
                     /locus_tag="AABK18_RS25165"
                     /old_locus_tag="VEE39_48130"
                     /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            2245..>2682
                     /locus_tag="AABK18_RS25170"
                     /pseudo=""
     CDS             2245..>2682
                     /locus_tag="AABK18_RS25170"
                     /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            2714..3274
                     /locus_tag="AABK18_RS25175"
                     /old_locus_tag="VEE39_48140"
     CDS             2714..3274
                     /locus_tag="AABK18_RS25175"
                     /old_locus_tag="VEE39_48140"
                     /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"
     Typing          1294..1377
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="87.059"
                     /coverage="95.0"
                     /evalue="8.83e-18"
     Typing          2027..3372
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.105"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 ggaattgcag aagatgcacg aggttacgca acggaacaac gcgatactga acgagcgcgt
       61 cgtgatattg agtcagcagg tgcagagatt agccgggcaa gtggatcgct tgagtcggtt
      121 atttatcgcg aacaacagct aagggatgaa caggagcgtg cccggtacag acatgaggta
      181 caggaacgcg cggcacgggt tcggagtggg ccatcaatgg agatgtgacc ggggaagtga
      241 cgaaatcttg ccattttgac cagttcgacg gctggggcga gcgaaacaaa tcgtgtgccg
      301 tatttgtgca tagctatgca acatcctgaa aacgcatttc acgcgttttt ggggattcag
      361 ccaggggaaa acatggtttt tttacttttt gagcgtaaag acgtgaaaaa tctcgttatt
      421 gcacttgcga tctttcgtcg gcgggcgtag aacgaaaaca gctcgccagg aaggcgagct
      481 gtttcgggtt cattgaggtc tctgacctcc tcaatgttcc tgtggaaact gttgagatcc
      541 acaacagaaa ccagttcatt cagtttgcat gagccttctg tattcttcaa gaatttttca
      601 acagcacagt ctcccaggaa ccccgaaaaa aacctgtttt tgcagatact tgcgtatttg
      661 cgagaatcgt ttgcggttgg gggagctgtg acgacggcga ccgcacgcgt gagagttccg
      721 ctaccggcgc agagagtttc atcgacagcg gacacctgat gagttgccac aaaaaccgta
      781 tgtagcgcgg ctagattggt tgagttagac cttggcggca gttcccggta tgtggtggcg
      841 tgacgggtga gatggtgcgg cgaagacgca tacgtcacgc aggcgcgggt tcttccactg
      901 acgcgccccg tgatcgatgg ccttggctcc gtccggcata tcgagagcgg caaactaccc
      961 gtcccttcac tgggaggggt gagttgttgc cgttccctcc aacctttcac catccggcat
     1021 atcgcacgat cccatgtgca ccgcaactcc tgataactcc agtgcaaaaa aaaaaaagga
     1081 tctgcatcac aacgagagtg atcccaccgc tcgccgcagc cccagcgacc gaacgtagtg
     1141 agcgagtggg cgaggaagcg gaagagtcac agatgcaagc attgtgcact tacgcgcctg
     1201 tgccagtgtc cgcgtgtgtg ctgtttatcg ggtgcgctgt ttttacatct gtgcggcttt
     1261 ttactcctga catggtgcac ttcccatcca tgtctgcacc gatgcaaaat gagataagcc
     1321 agtatacaca tcgctatcgc tctgtgaact gggtcagggc tgcgccccga cacccgcact
     1381 gacgcgccct ggcgggcttg tctgctcccg gcatccgctc acaggcaagc tgtgaacgtc
     1441 tccgggagct gcatgtttca gttgctttca ccgtcatcgc cgaagcgtgc gaggcaactg
     1501 cggtagagtt cgtcggcgtg gtcgtgaagt gattcgcaga tgtctgcctg ttcgtccgcg
     1561 tccagatcgt tgagtttttc cagcagggtt agcgtctggc ttctgataaa gcgagccatg
     1621 ttaagggctg ttttttcctg tttggtcatg gtcttaaggc tccttgtatg ggggatttgt
     1681 tagggggaat gataccgatg aaacgcgaga agatgctcac gatacgggtt accgatgagg
     1741 agcacgcccg gttactggaa cgctgcgagg gtaaacgact ggcggaatgg atgcggcggg
     1801 tctgtctggg ggagccggtt gcacgcacag gaaaactgcc gacactatcg ccgccattgc
     1861 tgcggcatct ggctgccatc gggaacaacc tgaaccagac agcccggaag gtgaacagcg
     1921 gccagtggtc ttcgattgac cgggttcatg tggtggccgc actgatggcc atcgagggtg
     1981 aattgcgcca gttgcggcag gctgtcaggg aacagggggt acgggatgat agttaaattt
     2041 catgccaggg ggaaaggcgg tggaagtggc ccggtcgatt acctgctggg gcgggagcgt
     2101 aaccgcgaag gcgcaacggt gctccggggt aacccggaag aagtgcggga actcattgat
     2161 tccacgccat tctcgaagaa atacacttca ggcgttctgt cgttcgcgga gaaggagtta
     2221 ccgccgggtg aacgcgaaag agtgatgacg agctttgagc gtgttcttat gcccggtctc
     2281 gaaaaagacc agtacagcat tctctgggtg gaacaccagg ataaggggcg gctcgaactg
     2341 aattttgtca tcccgaacat ggagctacag agcggtaagc gcctccagcc gtactacgac
     2401 cgcgcggaca ggccgaggat aaatgcctgg cagacgctgg ttaatcatca ttacgggctg
     2461 cgtgacccga acgcaccgga gaacagacgg acgcttgtca cgccaaataa tctgccaaaa
     2521 gcgaaacagg aggccgcaga agcgattaca cggggtcttg aggctcttta ccatgccgga
     2581 gcaataaaaa cgcgtcagga tgtcacagag gcgcttacag cggcaggttt tgaggtggtg
     2641 aggacaacca aaagcagcat cagtattgcc gacccggagg gggggcggaa tctcaggcta
     2701 aagggggcgc tgtatgagca atcttttaca aatgggaaca gacttcgaga agaaactgaa
     2761 agagcgagcc gcttctaccg agaacatgct gaacagcgag ttcaggaagc tcgaagagtc
     2821 tgtagacaag gcactgagct taaacaggca gaaaatcaga gacgctatca gcgaacatac
     2881 aacatccgtg aaaaagcaac tggatacgct gagcaccacc gtgagcatgc agttcagcac
     2941 cacagaggcc gaactgtccc ggcagcagaa aaaactgctc tggcgggtga tcaaagggcg
     3001 gatactgttt ccggcgctga ccgcgctcag cgtcacgggc ggcattttcc tggggtgctg
     3061 ggggctgatg gagtggcagg aaagcaagat tgcgaaaaat atcctgacta tcagagagca
     3121 ggaaaacacg ctggcgaaac tcgaggcaaa aacctggggg gtgacgttcg tcaatggcga
     3181 gaacgggaaa tttctggtgt tgccggacgg ggtgaaaggg gaaaacacct ggacggtggg
     3241 cgacaagaac gccgtgaggc tggtcaggga gtaaacgagt atgacggaac tggaagggca
     3301 tttgctgaac gccttagagc atttgcaaca ggactatatg cggcggctga acgagtggga
     3361 gagcgccttc gc
//
