LOCUS       NZ_AP027690             3372 bp    DNA     circular CON 04-APR-2024
DEFINITION  Escherichia coli strain PSS-10 plasmid pPSS-10_5, complete sequence.
ACCESSION   NZ_AP027690
VERSION     NZ_AP027690.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00562535
            Assembly: GCF_036501505.1
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  JOURNAL   Unpublished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                   :: 159x
            Sequencing Technology :: MGI DNBSEQ-G400RS; ONT MinION Mk1c
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_036501505.1-RS_2024_04_04
            Annotation Date                   :: 04/04/2024 00:10:24
            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)                     :: 5,072
            CDSs (total)                      :: 4,948
            Genes (coding)                    :: 4,638
            CDSs (with protein)               :: 4,638
            Genes (RNA)                       :: 124
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 90
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 310
            CDSs (without protein)            :: 310
            Pseudo Genes (ambiguous residues) :: 0 of 310
            Pseudo Genes (frameshifted)       :: 83 of 310
            Pseudo Genes (incomplete)         :: 226 of 310
            Pseudo Genes (internal stop)      :: 46 of 310
            Pseudo Genes (multiple problems)  :: 42 of 310
            Pseudo Genes (short protein)      :: 3 of 310
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP027690.1.
            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="PSS-10"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pPSS-10_5"
                     /geo_loc_name="Ecuador:Puyo"
                     /collection_date="2019"
     gene            join(2911..3372,1..99)
                     /locus_tag="AABK11_RS25325"
     CDS             join(2911..3372,1..99)
                     /locus_tag="AABK11_RS25325"
                     /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="MbeB family mobilization protein"
                     /protein_id="WP_000067487.1"
                     /translation="MSNLLQMGTDFEKKLKERAASTENMLNSEFRKLEESVDKALSLNR
                     QKIRDAISEHTTSVKKQLDTLSTTVSMQFSTTEAELSRQQKKLLWRVIKGRILFPALTA
                     LSVTGGIFLGCWGLMEWQESKIAKNILTIREQENTLAKLEAKTWGVTFVNGENGKFLVL
                     PDGVKGENTWTVGDKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     gene            106..339
                     /locus_tag="AABK11_RS25330"
                     /old_locus_tag="VEE24_48620"
     CDS             106..339
                     /locus_tag="AABK11_RS25330"
                     /old_locus_tag="VEE24_48620"
                     /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(1655..1846)
                     /locus_tag="AABK11_RS25335"
                     /old_locus_tag="VEE24_48630"
     CDS             complement(1655..1846)
                     /locus_tag="AABK11_RS25335"
                     /old_locus_tag="VEE24_48630"
                     /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            1895..2233
                     /locus_tag="AABK11_RS25340"
                     /old_locus_tag="VEE24_48640"
     CDS             1895..2233
                     /locus_tag="AABK11_RS25340"
                     /old_locus_tag="VEE24_48640"
                     /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="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_251302571.1"
                     /translation="MKREKMLTIRVTDEEHARLLERCEGKRLAEWMRRVCLGEPVARTG
                     KLPTLSPPLLRHLAAIGNNLNQTARKVNSGQWSSIDRVHVVAALMAIEGELRQLRQAVR
                     EQGVRDDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     Typing          1491..1574
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="87.059"
                     /coverage="95.0"
                     /evalue="8.83e-18"
     Typing          4..422
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="82.759"
                     /coverage="99.0"
                     /evalue="1.55e-49"
     Typing          2224..3371
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="96.867"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 ggcgagaacg ggaaatttct ggtgttgccg gacggggtga aaggggaaaa cacctggacg
       61 gtgggcgaca agaacgccgt gaggctggtc agggagtaaa cgagtatgac ggaactggaa
      121 gggcatttgc tgaacgcctt agagcatttg caacaggact atatgcggcg gctgaacgag
      181 tgggagagcg ccttcgcgga attgcagaag atgcacgagg ttacgcaacg gaacaacgcg
      241 atactgaacg agcgcgtcgt gatattgagt cagcaggtgc agagattagc cgggcaagtg
      301 gatcgcttga gtcggttatt tatcgcgaac aacagctaag ggatgaacag gagcgtgccc
      361 ggtacagaca tgaggtacag gaacgcgcgg cacgggttcg gagtgggcca tcaatggaga
      421 tgtgaccggg gaagtgacga aatcttgcca ttttgaccag ttcgacggct ggggcgagcg
      481 aaacaaatcg tgtgccgtat ttgtgcatag ctatgcaaca tcctgaaaac gcatttcacg
      541 cgtttttggg gattcagcca ggggaaaaca tggttttttt actttttgag cgtaaagacg
      601 tgaaaaatct cgttattgca cttgcgatct ttcgtcggcg ggcgtagaac gaaaacagct
      661 cgccaggaag gcgagctgtt tcgggttcat tgaggtctct gacctcctca atgttcctgt
      721 ggaaactgtt gagatccaca acagaaacca gttcattcag tttgcatgag ccttctgtat
      781 tcttcaagaa tttttcaaca gcacagtctc ccaggaaccc cgaaaaaaac ctgtttttgc
      841 agatacttgc gtatttgcga gaatcgtttg cggttggggg agctgtgacg acggcgaccg
      901 cacgcgtgag agttccgcta ccggcgcaga gagtttcatc gacagcggac acctgatgag
      961 ttgccacaaa aaccgtatgt agcgcggcta gattggttga gttagacctt ggcggcagtt
     1021 cccggtatgt ggtggcgtga cgggtgagat ggtgcggcga agacgcatac gtcacgcagg
     1081 cgcgggttct tccactgacg cgccccgtga tcgatggcct tggctccgtc cggcatatcg
     1141 agagcggcaa actacccgtc ccttcactgg gaggggtgag ttgttgccgt tccctccaac
     1201 ctttcaccat ccggcatatc gcacgatccc atgtgcaccg caactcctga taactccagt
     1261 gcaaaaaaaa aaacggatct gcatcacaac gagagtgatc ccaccgctcg ccgcagcccc
     1321 agcgaccgaa cgtagtgagc gagtgggcga ggaagcggaa gagtcacaga tgcaagcatt
     1381 gtgcacttac gcgcctgtgc cagtgtccgc gtgtgtgctg tttatcgggt gcgctgtttt
     1441 tacatctgtg cggcttttta ctcctgacat ggtgcacttc ccatccatgt ctgcaccgat
     1501 gcaaaatgag ataagccagt atacacatcg ctatcgctct gtgaactggg tcagggctgc
     1561 gccccgacac ccgcactgac gcgccctggc gggcttgtct gctcccggca tccgctcaca
     1621 ggcaagctgt gaacgtctcc gggagctgca tgtttcagtt gctttcaccg tcatcgccga
     1681 agcgtgcgag gcaactgcgg tagagttcgt cggcgtggtc gtgaagtgat tcgcagatgt
     1741 ctgcctgttc gtccgcgtcc agatcgttga gtttttccag cagggttagc gtctggcttc
     1801 tgataaagcg agccatgtta agggctgttt tttcctgttt ggtcatggtc ttaaggctcc
     1861 ttgtatgggg gatttgttag ggggaatgat accgatgaaa cgcgagaaga tgctcacgat
     1921 acgggttacc gatgaggagc acgcccggtt actggaacgc tgcgagggta aacgactggc
     1981 ggaatggatg cggcgggtct gtctggggga gccggttgca cgcacaggaa aactgccgac
     2041 actatcgccg ccattgctgc ggcatctggc tgccatcggg aacaacctga accagacagc
     2101 ccggaaggtg aacagcggcc agtggtcttc gattgaccgg gttcatgtgg tggccgcact
     2161 gatggccatc gagggtgaat tgcgccagtt gcggcaggct gtcagggaac agggggtacg
     2221 ggatgatagt taaatttcat gccaggggga aaggcggtgg aagtggcccg gtcgattacc
     2281 tgctggggcg ggagcgtaac cgcgaaggcg caacggtgct ccggggtaac ccggaagaag
     2341 tgcgggaact cattgattcc acgccattct cgaagaaata cacttcaggc gttctgtcgt
     2401 tcgcggagaa ggagttaccg ccgggtgaac gcgaaagagt gatgacgagc tttgagcgtg
     2461 ttcttatgcc cggtctcgaa aaagaccagt acagcattct ctgggtggaa caccaggata
     2521 aggggcggct cgaactgaat tttgtcatcc cgaacatgga gctacagagc ggtaagcgcc
     2581 tccagccgta ctacgaccgc gcggacaggc cgaggataaa tgcctggcag acgctggtta
     2641 atcatcatta cgggctgcgt gacccgaacg caccggagaa cagacggacg cttgtcacgc
     2701 caaataatct gccaaaagcg aaacaggagg ccgcagaagc gattacacgg ggtcttgagg
     2761 ctctttacca tgccggagca ataaaaacgc gtcaggatgt cacagaggcg cttacagcgg
     2821 caggttttga ggtggtgagg acaaccaaaa gcagcatcag tattgccgac ccggaggggg
     2881 ggcggaatct caggctaaag ggggcgctgt atgagcaatc ttttacaaat gggaacagac
     2941 ttcgagaaga aactgaaaga gcgagccgct tctaccgaga acatgctgaa cagcgagttc
     3001 aggaagctcg aagagtctgt agacaaggca ctgagcttaa acaggcagaa aatcagagac
     3061 gctatcagcg aacatacaac atccgtgaaa aagcaactgg atacgctgag caccaccgtg
     3121 agcatgcagt tcagcaccac agaggccgaa ctgtcccggc agcagaaaaa actgctctgg
     3181 cgggtgatca aagggcggat actgtttccg gcgctgaccg cgctcagcgt cacgggcggc
     3241 attttcctgg ggtgctgggg gctgatggag tggcaggaaa gcaagattgc gaaaaatatc
     3301 ctgactatca gagagcagga aaacacgctg gcgaaactcg aggcaaaaac ctggggggtg
     3361 acgttcgtca at
//
