LOCUS       NZ_AP027708             3371 bp    DNA     circular CON 04-APR-2024
DEFINITION  Escherichia coli strain PSS-13 plasmid pPSS-13_4, complete sequence.
ACCESSION   NZ_AP027708
VERSION     NZ_AP027708.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00562527
            Assembly: GCF_036502125.1
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  JOURNAL   Unpublished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                   :: 172x
            Sequencing Technology :: MGI DNBSEQ-G400RS; ONT MinION Mk1c
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_036502125.1-RS_2024_04_04
            Annotation Date                   :: 04/04/2024 00:06:47
            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)                     :: 4,798
            CDSs (total)                      :: 4,680
            Genes (coding)                    :: 4,438
            CDSs (with protein)               :: 4,438
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 242
            CDSs (without protein)            :: 242
            Pseudo Genes (ambiguous residues) :: 0 of 242
            Pseudo Genes (frameshifted)       :: 71 of 242
            Pseudo Genes (incomplete)         :: 170 of 242
            Pseudo Genes (internal stop)      :: 43 of 242
            Pseudo Genes (multiple problems)  :: 40 of 242
            Pseudo Genes (short protein)      :: 4 of 242
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP027708.1.
            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="PSS-13"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pPSS-13_4"
                     /geo_loc_name="Ecuador:Puyo"
                     /collection_date="2019"
     gene            complement(278..601)
                     /locus_tag="AABK00_RS23975"
                     /old_locus_tag="VEE20_46350"
     CDS             complement(278..601)
                     /locus_tag="AABK00_RS23975"
                     /old_locus_tag="VEE20_46350"
                     /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            665..856
                     /locus_tag="AABK00_RS23980"
                     /old_locus_tag="VEE20_46360"
     CDS             665..856
                     /locus_tag="AABK00_RS23980"
                     /old_locus_tag="VEE20_46360"
                     /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            complement(2171..2404)
                     /locus_tag="AABK00_RS23985"
                     /old_locus_tag="VEE20_46370"
     CDS             complement(2171..2404)
                     /locus_tag="AABK00_RS23985"
                     /old_locus_tag="VEE20_46370"
                     /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(2411..2971)
                     /locus_tag="AABK00_RS23990"
                     /old_locus_tag="VEE20_46380"
     CDS             complement(2411..2971)
                     /locus_tag="AABK00_RS23990"
                     /old_locus_tag="VEE20_46380"
                     /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          complement(938..1018)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="87.805"
                     /coverage="93.0"
                     /evalue="8.68e-18"
     Typing          complement(282..634)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="84.746"
                     /coverage="100.0"
                     /evalue="9.41e-59"
     Typing          complement(2089..3371)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.686"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ttccacccag agaatgctgt actggtcttt ttcgagaccg ggcataagaa cacgctcaaa
       61 gctcgtcatc actctttcgc gttcacccgg cggtaactcc ttctccgcga acgacagaac
      121 gcctgaagtg tatttcttcg agaatggcgt ggaatcaatg agttcccgca cttcttccgg
      181 gttaccccgg agcaccgttg cgccttcgcg gttacgctcc cgccccagca ggtaatcgac
      241 cgggccactt ccaccgcctt tccccctggc atgaaattta actatcatcc cgtaccccct
      301 gttccctgac agcctgccgc aactggcgca attcaccctc gatggccatc agtgcggcca
      361 ccacatgaac ccggtcaatc gaagaccact ggccgctgtt caccttccgg gctgtctggt
      421 tcaggttgtt cccgatggca gccagatgcc gcagcaatgg cggcgatagt gtcggcagtt
      481 ttcctgtgcg tgcaaccggc tcccccagac agacccgccg catccattcc gccagtcgtt
      541 taccctcgca gcgttccagt aaccgggcgt gctcctcatc ggtaacccgt atcgtgagca
      601 tcttctcgcg tttcatcggt atcattcccc ctaacaaatc ccccatacaa ggagccttaa
      661 gaccatgacc aaacaggaaa aaacagccct taacatggct cgctttatca gaagccagac
      721 gctaaccctg ctggaaaaac tcaacgatct ggacgcggac gaacaggcag acatctgcga
      781 atcacttcac gaccacgccg acgaactcta ccgcagttgc ctcgcacgct tcggcgatga
      841 cggtgaaagc aactgaaaca tgcagctccc ggagacgttc acagcttgcc tgtgagcgga
      901 tgccgggagc agacaagccc gccagggcgc gtcagtgcgg gtgtcggggc gcagccctga
      961 cccagttcac agagcgatag cgatgtgtat actggcttat ctcattttgc atcggtgcag
     1021 aatggatggg aagtgcacca tgtcaggagt aaaaagccgc acagatgtaa aaacagcgca
     1081 cccgataaac agcacacacg cggacactgg cacaggcgcg taagtgcaca atgcttgcat
     1141 ctgtgactct tccgcttcct cgcccactcg ctcactacgt tcggtcgctg gggctgcggc
     1201 gagcggtggg atcactctcg ttgtgatgca gatccgtttt tttttttgca ctggagttat
     1261 caggagttgc ggtgcacatg ggatcgtgcg atatgccgga tggtgaaagg ttggagggaa
     1321 cggcaacaac tcacccctcc cagtgaaggg acgggtagtt tgccgctctc gatatgccgg
     1381 acggagccaa ggccatcgat cacggggcgc gtcagtggaa gaacccgcgc ctgcgtgacg
     1441 tatgcgtctt cgccgcacca tctcacccgt cacgccacca cataccggga actgccgcca
     1501 aggtctaact caaccaatct agccgcgcta catacggttt ttgtggcaac tcatcaggtg
     1561 tccgctgtcg atgaaactct ctgcgccggt agcggaactc tcacgcgtgc ggtcgccgtc
     1621 gtcacagctc ccccaaccgc aaacgattct cgcaaatacg caagtatctg caaaaacagg
     1681 tttttttcgg ggttcctggg agactgtgct gttgaaaaat tcttgaagaa tacagaaggc
     1741 tcatgcaaac tgaatgaact ggtttctgtt gtggatctca acagtttcca caggaacatt
     1801 gaggaggtca gagacctcaa tgaacccgaa acagctcgcc ttcctggcga gctgttttcg
     1861 ttctacgccc gccgacgaaa gatcgcaagt gcaataacga gatttttcac gtctttacgc
     1921 tcaaaaagta aaaaaaccat gttttcccct ggctgaatcc ccaaaaacgc gtgaaatgcg
     1981 ttttcaggat gttgcatagc tatgcacaaa tacggcacac gatttgtttc gctcgcccca
     2041 gccgtcgaac tggtcaaaat ggcaagattt cgtcacttcc ccggtcacat ctccattgat
     2101 ggcccactcc gaacccgtgc cgcgcgttcc tgtacctcat gtctgtaccg ggcacgctcc
     2161 tgttcatccc ttagctgttg ttcgcgataa ataaccgact caagcgatcc acttgcccgg
     2221 ctaatctctg cacctgctga ctcaatatca cgacgcgctc gttcagtatc gcgttgttcc
     2281 gttgcgtaac ctcgtgcatc ttctgcaatt ccgcgaaggc gctctcccac tcgttcagcc
     2341 gccgcatata gtcctgttgc aaatgctcta aggcgttcag caaatgccct tccagttccg
     2401 tcatactcgt ttactccctg accagcctca cggcgttctt gtcgcccacc gtccaggtgt
     2461 tttccccttt caccccgtcc ggcaacacca gaaatttccc gttctcgcca ttgacgaacg
     2521 tcacccccca ggtttttgcc tcgagtttcg ccagcgtgtt ttcctgctct ctgatagtca
     2581 ggatattttt cgcaatcttg ctttcctgcc actccatcag cccccagcac cccaggaaaa
     2641 tgccgcccgt gacgctgagc gcggtcagcg ccggaaacag tatccgccct ttgatcaccc
     2701 gccagagcag ttttttctgc tgccgggaca gttcggcctc tgtggtgctg aactgcatgc
     2761 tcacggtggt gctcagcgta tccagttgct ttttcacgga tgttgtatgt tcgctgatag
     2821 cgtctctgat tttctgcctg tttaagctca atgccttgtc tacagactct tcgagcttcc
     2881 tgaactcgct gttcagcatg ttctcggtag aagcggctcg ctctttcagt ttcttctcga
     2941 agtctgttcc catttgtaaa agattgctca tacagcgccc cctttagcct gagattccgc
     3001 cccccctccg ggtcggcaat actgatgctg cttttggttg tcctcaccac ctcaaaacct
     3061 gccgctgtaa gcgcctctgt gacatcctga cgcgttttta ttgctccggc atggtaaaga
     3121 gcctcaagac cccgtgtaat cgcttctgcg gcctcctgtt tcgcttttgg cagattattt
     3181 ggcgtgacaa gcgtccgtct gttctccggt gcgttcgggt cacgcagccc gtaatgatga
     3241 ttaaccagcg tctgccaggc atttatcctc ggcctgtccg cgcggtcgta gtacggctgg
     3301 aggcgcttac cgctctgtag ctccatgttc gggatgacaa aattcagttc gagccgcccc
     3361 ttatcctggt g
//
