LOCUS       NZ_AP027707             3453 bp    DNA     circular CON 04-APR-2024
DEFINITION  Escherichia coli strain PSS-13 plasmid pPSS-13_3, complete sequence.
ACCESSION   NZ_AP027707
VERSION     NZ_AP027707.1
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  JOURNAL   Unpublished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 3453)
  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
            AP027707.1.
            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..3453
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="PSS-13"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pPSS-13_3"
                     /geo_loc_name="Ecuador:Puyo"
                     /collection_date="2019"
     gene            complement(join(3300..3453,1..>2))
                     /locus_tag="AABK00_RS23960"
                     /pseudo=""
     CDS             complement(join(3300..3453,1..>2))
                     /locus_tag="AABK00_RS23960"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_309907.2"
                     /GO_function="GO:0043565 - sequence-specific DNA binding
                     [Evidence IEA]"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /name="helix-turn-helix domain-containing protein"
     gene            1070..1318
                     /locus_tag="AABK00_RS23965"
     CDS             1070..1318
                     /locus_tag="AABK00_RS23965"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001676031.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_252494596.1"
                     /translation="MARLTNLTPAEKKFLDDAVAAAERASGKKLNQPNRHIVLNRARAQ
                     IELQRYADRQRALREDGVSLDIENYCTVSLFFEQTYL"
                     /name="hypothetical protein"
     gene            complement(2562..3206)
                     /locus_tag="AABK00_RS23970"
                     /old_locus_tag="VEE20_46340"
     CDS             complement(2562..3206)
                     /locus_tag="AABK00_RS23970"
                     /old_locus_tag="VEE20_46340"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017900990.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="quinolone resistance pentapeptide repeat protein
                     QnrB19"
                     /protein_id="WP_012954666.1"
                     /translation="MTLALVGEKIDRNRFTGEKVENSTFFNCDFSGADLSGTEFIGCQF
                     YDRESQKGCNFSRAMLKDAIFKSCDLSMADFRNVSALGIEIRHCRAQGADFRGASFMNM
                     ITTRTWFCSAYITNTNLSYANFSKVVLEKCELWENRWMGTQVLGATFSGSDLSGGEFST
                     FDWRAANFTHCDLTNSELGDLDIRGVDLQGVKLDSYQASLLMERLGIAVIG"
                     /name="quinolone resistance pentapeptide repeat protein
                     QnrB19"
     ARG             complement(2566..3206)
                     /name="qnrB19"
                     /gene="qnrB19"
                     /gene_name="quinolone resistance pentapeptide repeat
                     protein QnrB19"
                     /tool="amrfinderplus"
                     /drug_class="QUINOLONE"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          732..905
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.5600000000000002e-86"
     Typing          complement(262..753)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.51"
                     /coverage="81.0"
                     /evalue="0.0"
ORIGIN
        1 ataacgatgt gtatcctatg tgctcggatt ggatagattt ccattacggt gaaggatctt
       61 cttgagatcc tttctgtggc gtcgtaatct cttgctctgt aaacgaaaaa accgccctgc
      121 aaggcggttt ttcgaaggtt ctcagagcag caactctttg aaccgtggta actggcttac
      181 gaggagcgca gtaaccaaat ctgttctttc agtttagcct taacaggcgc ataacttcaa
      241 gactaactcc tctaaatcag ttaccagtgg ctgctgccag tggcgataag tcgtgtcttt
      301 ccgggttgga ctcaagatga tagttaccgg ataaggcgca gcagtcggac tgaacggggg
      361 gttcgtgcat acagtccatc caggagcgaa ctgccttcgc ggaactgagt gtcaggcgtg
      421 gaatgagata aacgcggcca taacagcgga atgacaccgg taaaccgaaa ggcaggaatg
      481 cgggggagca cgagggagcc accaggggga aacgcctggt atctttaagc cgcatcgggt
      541 ttcgccacca ctgatttgag cgtcagattt catgatgttt gtcagggggg cggagcctat
      601 ggaaaaacgg cttcgccgcg gccttatctc ttccctgtta agctccttcc tggtatctcc
      661 caggaaattt ccgccccgcc tgtaagccgg caccgctcgc cgcagccgaa cgaccgagcg
      721 cagcgagtca gtgagcgagg aagcggaata tatcctgtac tacatatcct gctgacgcgc
      781 tggtgccgcc ttttttctcc tgctacatga agcacttcac tgatttccac atccgtgcca
      841 acatagtcag ccagtataca ctccgctagc gctacgtgac tggttcaggg ctgcgccccg
      901 aaaccggcta aaagctaatg acgcgcctgc ggcttgtcca acgcctcacg gcaccggatt
      961 aaaatccgct cccgttcacc gtttctgact gcctttcacc gtcgctggcg cttcatcgtt
     1021 tctactgtgt ctggcagact gtgctgattt attctgactg gagaacgtta tggccagact
     1081 gacaaacttg acgcctgcag agaaaaaatt tcttgatgat gctgttgccg cagctgaaag
     1141 agcgtcaggt aaaaagctaa atcagcctaa ccggcacatc gtcctgaaca gagcgcgtgc
     1201 gcaaattgag ttgcagcgtt acgccgaccg ccagcgtgca ttacgtgagg atggggtcag
     1261 tttggatata gagaattatt gtacggtaag cctgtttttt gaacagactt acctatagca
     1321 atagggtgta ctcccgcgct atacggcatt ttcagaggtt tgaccttaat cggataacct
     1381 aaatgcgata ctgcaagagc gacaacttaa aagcgatagc cactgacgca aaatcaaccc
     1441 cttacgaacc aagattggtt aaataatgcg cttaacgtac aaaaatttcc gatctccaaa
     1501 ctgacccctt cttcgcctct tatgtttctc gaatgaatcg atggggacag gaaatgtttt
     1561 gtggccaccg ccgcttcgcc ggcaccacaa aactgtcgga caagatgtgt ttttggagta
     1621 ccgccggcac caaaaacatt tcatcaggcg cagcctgata ccctgaattt cgtacgtacg
     1681 aaattttgct tttgttcaga tcgagggcag gattcgcaaa gtgctggcgt ttgtactcac
     1741 atcctttaga cgttgcgatg caggataggg cagacgccgc aaaatgacgt catttgcggt
     1801 atctgccccg aaaacagaat gttttctcct gagcctgcag ctggctctca gaacccctac
     1861 cgcctcgcaa agctcgttgc tcaacgcctc acgaccgcac agtaaactgt gcacccgttc
     1921 accgttatcg atggggttca gcgagccttt tgagcagttc gcaggatttt agccgctaaa
     1981 attccggcca ggcatgttcg tgcatagcca tgcagatgcg cagaaatcat caggcgcgtt
     2041 ttttcacgat atggacaggg aaaggtgccg gaaacgcaga ggacgcggca gaaacgcgct
     2101 gagggcctct cagggggtgc gggcaaggga tgttatgttt aatcggtctg accgtcaggt
     2161 acaaaaaaaa gcccttaggg ggcttttttt ttgctatgag ttagccatat tttcgtgcga
     2221 atttttcatc ggaatcgcat agataaataa taaactcaat aaacgcgatg atcgcggggt
     2281 atttgtattg aggatgtcag taaacgggat gacatggctg aagttgagat tataaataag
     2341 acatggcttc atgattcggg agtggttatt cgttgttctc gcgaaaatga attggttaga
     2401 tattcatcaa attcctgtcc agaatgcagc attagatggc atgtcgttga tgcggtaggt
     2461 caggatattc gtccactgga gaaaacgttt cacaatgctt gccaggagtc gtactggtta
     2521 aaagtaaatc gtcaaacgca tctcccggtg taaacgctga actaaccaat cacagcgatg
     2581 ccaagccgct ccatgagcaa cgatgcctgg tagctgtcta acttaacgcc ttgtaaatca
     2641 acaccccgaa tatctaagtc acctaactcc gaattggtca gatcgcaatg tgtgaagttt
     2701 gctgctcgcc agtcgaaagt cgaaaactcg ccgccggaga gatctgaacc actgaacgtc
     2761 gcacccagta cctgagtccc catccagcgg ttttcccaca gctcacactt ttccaacacg
     2821 actttcgaaa aattggcgta gcttagatta gtattagtga tatatgcgct gcaaaaccag
     2881 gtgcgcgtgg tgatcatatt cataaagctt gcaccgcgga aatctgcgcc ttgtgcgcgg
     2941 cagtggcgaa tttcaatgcc caaggcactg acgttgcgga aatctgccat tgataaatca
     3001 cagcttttga aaatggcatc tttcagcatt gcgcgactaa aattgcaccc tttctgactt
     3061 tcgcgatcat agaactggca gccgataaat tcagtgccgc tcaggtcggc acctgaaaaa
     3121 tcgcagttaa aaaatgtact attttcaact ttctcaccgg tgaagcgatt tctgtcaatt
     3181 ttttcgccaa ctaatgccag agtcatatct atgcctgtgt ttttatacag taatgacgcc
     3241 atggtaaacc ttatgacgtt atgcgtcaaa cccgccagta tgacacctgc aaatgcgtat
     3301 tagatctggt gtttcttcag caaggcacgt agctgatgat aagtcagacc cagtaattca
     3361 gcggcttttt tctggttaaa tttagcctgc tgtaagctgg tttgtagaaa gtctttctct
     3421 tgctgctgct ggaattcacg cagatccagc gtt
//
