LOCUS       NZ_CP067317             3223 bp    DNA     circular CON 18-JUN-2023
DEFINITION  Escherichia coli strain 027_SK3 plasmid p027_SK3f, complete
            sequence.
ACCESSION   NZ_CP067317
VERSION     NZ_CP067317.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN17214836
            Assembly: GCF_017639165.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3223)
  AUTHORS   Biggel,M.
  TITLE     Characterization of fosA carrying plasmids from multidrug resistant
            Enterobacteriaceae food and environmental isolates
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3223)
  AUTHORS   Biggel,M.
  TITLE     Direct Submission
  JOURNAL   Submitted (05-JAN-2021) Institute for Food Safety and Hygiene,
            University of Zurich, Winterthurerstrasse 272, Zurich 8057,
            Switzerland
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100x
            Sequencing Technology :: Illumina MiniSeq, Oxford Nanopore MinIon
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/18/2023 03:51:22
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,098
            CDSs (total)                      :: 4,983
            Genes (coding)                    :: 4,789
            CDSs (with protein)               :: 4,789
            Genes (RNA)                       :: 115
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 194
            CDSs (without protein)            :: 194
            Pseudo Genes (ambiguous residues) :: 0 of 194
            Pseudo Genes (frameshifted)       :: 46 of 194
            Pseudo Genes (incomplete)         :: 137 of 194
            Pseudo Genes (internal stop)      :: 37 of 194
            Pseudo Genes (multiple problems)  :: 27 of 194
            Pseudo Genes (short protein)      :: 5 of 194
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP067317.1.
            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..3223
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="027_SK3"
                     /isolation_source="waste water"
                     /db_xref="taxon:562"
                     /plasmid="p027_SK3f"
                     /geo_loc_name="Switzerland: Basel"
                     /collection_date="2016"
                     /collected_by="ILS, University of Zurich"
     gene            complement(join(2926..3223,1..26))
                     /locus_tag="JJB21_RS25180"
                     /old_locus_tag="JJB21_25170"
     CDS             complement(join(2926..3223,1..26))
                     /locus_tag="JJB21_RS25180"
                     /old_locus_tag="JJB21_25170"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000957083.1"
                     /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_004193914.1"
                     /translation="MLTMWVTEDEHRRLLERCEGKQLAAWMRQTCLDEKPARAGKLPSI
                     SPALLRQLAGMGNNLNQIARQVNAGGGSGHDRVQIVAALMAIDAGLERLRHAVLEKGAD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            665..835
                     /locus_tag="JJB21_RS25185"
                     /old_locus_tag="JJB21_25175"
     CDS             665..835
                     /locus_tag="JJB21_RS25185"
                     /old_locus_tag="JJB21_25175"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_004193911.1"
                     /translation="MHEPPVQSDYHARSGNYQLESNPERHDKSPVAVAIGNWVHGAEIV
                     ENAYRVLEVKA"
                     /name="hypothetical protein"
     gene            complement(1044..1376)
                     /locus_tag="JJB21_RS25190"
                     /old_locus_tag="JJB21_25180"
     CDS             complement(1044..1376)
                     /locus_tag="JJB21_RS25190"
                     /old_locus_tag="JJB21_25180"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_008784643.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="EmrE family multidrug efflux SMR transporter"
                     /protein_id="WP_016807542.1"
                     /translation="MNTYIFLGGAIVAEVIGTIFMKYSEGFTRLWPSVGTAISYCAAFY
                     LLSQTLENIPTGIAYAIWSGAGIVLISLAGWLVSGQKLDWPAIAGMFLICVGVLVINIF
                     SKSSAH"
                     /name="EmrE family multidrug efflux SMR transporter"
     gene            complement(1544..1759)
                     /locus_tag="JJB21_RS25195"
                     /old_locus_tag="JJB21_25185"
     CDS             complement(1544..1759)
                     /locus_tag="JJB21_RS25195"
                     /old_locus_tag="JJB21_25185"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137421.1"
                     /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_024195375.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWENAFAEWRTMSGLIQRENA
                     ALNERVTVLSRQVQSLSEQLRRLSKG"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(1763..2248)
                     /locus_tag="JJB21_RS25200"
                     /old_locus_tag="JJB21_25190"
     CDS             complement(1763..2248)
                     /locus_tag="JJB21_RS25200"
                     /old_locus_tag="JJB21_25190"
                     /inference="COORDINATES: protein motif:HMM:NF016710.2"
                     /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_025367738.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQTTGEMLKAAFSEHEKSVRAELSESE
                     KRISAAILDHDRKLSSAMSQRTKGMLRMVSQTWLTIVLVSALLIASSAGILWWQGQQIL
                     ENYTTIREQKSTQAMLSERNSGVQLSTCGEQRRRCVRVNPEAGQFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            complement(<2283..2717)
                     /locus_tag="JJB21_RS25580"
                     /pseudo=""
     CDS             complement(<2283..2717)
                     /locus_tag="JJB21_RS25580"
                     /inference="COORDINATES: protein motif:HMM:NF015397.2"
                     /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"
     ARG             complement(1045..1376)
                     /name="qacG"
                     /gene="qacG"
                     /gene_name="small multidrug resistance (SMR) antibiotic
                     efflux pump"
                     /tool="rgi"
                     /drug_class="disinfecting agents and antiseptics"
                     /identity="41.35"
                     /coverage="102.8"
     Typing          complement(123..314)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="92.821"
                     /coverage="89.0"
                     /evalue="7.28e-73"
     Typing          294..777
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.756"
                     /coverage="93.0"
                     /evalue="1.73e-132"
     Typing          complement(1447..2936)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.784"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tcctcagtca cccacatggt gagcattttg ctgcgtttgt ctgccaatcc ggcctcctga
       61 taacgccggg acggacggga aatcttttcc cggtcggcac ggtgttggac aagccgcagg
      121 cgcggcagtg gttttagcgg gtttcggggc gcagccctga accagtcacg tagcgctagc
      181 ggagtgtata ctggctaaac atgttatgac ggagtggtaa tttatgaaag tgcttcatgt
      241 gacaggggaa aaatgcggct gccgggcgta agtgcaaaat gcaggtggtg atgaaatgac
      301 gcctcctcgc tcactcggtc gctacgctcc tgccgtgaga ctgcggcggg cgttaccagc
      361 tcacagatta cgggataagc aaatgccgct cgaagcagga aaggccaaga aaaggatgcg
      421 gagttgccgt ttttccatag gctccgcccc cctgacgagt atcacgaaaa tgacgctcaa
      481 atcagcggtg gcgaaacccg atgcggctta aagataccag gcgtttcccc ctggtggctc
      541 cctcgtgctc ccccgcattc ctgcctttcg gtttaccggt gtcattccgc tgttatggcc
      601 gcggtttctc attccacgcc tgaaactcgg ttccgggtag gcagttcgct ccaggatgga
      661 ctgtatgcac gaaccccccg ttcagtccga ctaccacgcc cgttccggta actatcaact
      721 tgagtccaac ccggaaagac acgacaaatc gccagtggcg gtagccattg gtaactgggt
      781 tcacggagca gagattgtag agaatgccta cagagttctt gaagtgaaag cctgagtgcg
      841 gctacactga aaggacagtt taggtatctg cgctccgtga aagccagtta ccatcggaac
      901 aaagagttgg tagctctgaa ttccggcaaa cgaaccaccg ttggtagcgg tggttttttt
      961 gtttacaggg aaaaagatta cgcgcagaaa gaaaggatct caaggaaatc cttttgcttt
     1021 ggccaatatg cttcggtaaa aagttaatgc gcagaagatt ttgaaaaaat attaataacc
     1081 aaaactccaa cgcaaataag gaacattcct gcaattgcgg gccaatcaag tttttgaccg
     1141 ctaaccaacc aaccagctag gcttattagt acaattcccg caccagacca aattgcgtaa
     1201 gcaataccgg taggtatatt ttccaatgtt tgggaaagca gataaaaggc agcgcaataa
     1261 cttattgcag ttcctacaga cggccacagg cgtgtaaatc cttctgaata tttcataaag
     1321 atggtgccta tgacttcagc cacaatagcc cctcccagga aaatatatgt attcataaaa
     1381 atacctcatg ttgaaaaatt taaatatctt tacataacaa ctaattaata gaacccggct
     1441 tatcatagcg aaggaccatg atgctgccac tgcgatcgtt ccagctccag cgctttctgg
     1501 tgctgcaccg cccgctcctg ctgccggtga gtttctatcg cgttcagcct ttcgacaacc
     1561 ggcgcagctg ctcgctcaaa ctctgcacct gcctgctcaa gaccgtgacg cgctcgttca
     1621 gcgccgcgtt ctcccgttga ataagaccag acatcgtccg ccattccgcg aaggcgttct
     1681 cccactcgtc cagccttttc gagtagtcct gctgtagctg ctctaatgcg ctcagcaact
     1741 gtttttccag ctccgtcatg tgctatttcc ccgccagtat catccagctc gagtcctctc
     1801 cgaactgtcc cgcttccggg ttcaccctca cgcagcggcg tctctgctcg ccgcaggtcg
     1861 agagctgtac gccgctgttc ctctctgaca gcatggcctg cgtgctcttc tgctcccgga
     1921 tggtcgtata gttctcgagt atctgctgcc cctgccacca cagaatgccc gcgctcgacg
     1981 ctatcagcag cgcggagacc agaacgatgg tcagccacgt ctggctgacc atgcgcagca
     2041 tccctttcgt gcgctggctc atggctgagg acagcttccg gtcgtggtcg aggatggcgg
     2101 cgctgattct cttctcgctt tcgctcagtt ccgctctgac agacttctcg tgctcgctga
     2161 atgcggcttt cagcatctcg ccggtagtct gctgctgcgc tttcgatttc tgctctaagt
     2221 ccttcgccag cgttaaaaga ctgttcatag atggctccct tcagtcggat gtttcgcccc
     2281 ccgtccgggt cggcaatgct gatgctgctt tttgtggtgc gcaccacctc aaaacctgcg
     2341 ctttccagcg cctcagtgac gtcctgacgc gttttcagct ccccggatga ggcaagggca
     2401 agcaggccgc tcgtaatcgc ctgggcggct tcctgcttcg cttccggcag cgcggaaggc
     2461 gagaccagca cccgccggtt ctccggcgcg ttcgggtcat gcagccccag cctgccgttc
     2521 actatggtct gccaggcatc gatgcgcgga cggtcggcgc ggtcgtaata cggctgtagc
     2581 cgcttgccgg tcagaagctc cgtgttcggg atcaggaagt tcagctccag ccgccccttg
     2641 tcccggtgct caacccacag cacgctgtac tggtctttat cgagtccggg catcagaacc
     2701 cgctcgaaac tcgccatcag cttttcgcgc tggccgggcg gtaaatcctg ttcggcaaaa
     2761 gacagaacgc cggaagtgta ctttttggcg tagggcgagg cgtcgataag ctcccggact
     2821 tcatccggct tcccctgcag aacgctggcg ccgtcgcgct ggcgatcttt acccagcaga
     2881 taatcgaccg gcccgccgcc gccgccgcgc ccccgaggat gaaacttaac gatcatcatc
     2941 agcacccttt tccagtacgg catgccgcaa ccgctcgagt ccggcatcga tggccatcag
     3001 cgcggcgaca atctgcacgc ggtcgtgtcc gcttccacca ccggcgttaa cctggcgggc
     3061 aatctggtta aggttgttcc ccatgccggc aagctgacga agcagcgccg gcgagatcga
     3121 cggaagtttg ccggcgcgtg cgggcttctc gtccaggcac gtctgccgca tccaggccgc
     3181 gagttgctta ccctcgcagc gctccagcag acgccggtgc tcg
//
