LOCUS       NZ_CP067316             4664 bp    DNA     circular CON 18-JUN-2023
DEFINITION  Escherichia coli strain 027_SK3 plasmid p027_SK3e, complete
            sequence.
ACCESSION   NZ_CP067316
VERSION     NZ_CP067316.1
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 4664)
  AUTHORS   Biggel,M.
  TITLE     Characterization of fosA carrying plasmids from multidrug resistant
            Enterobacteriaceae food and environmental isolates
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4664)
  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
            CP067316.1.
            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..4664
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="027_SK3"
                     /isolation_source="waste water"
                     /db_xref="taxon:562"
                     /plasmid="p027_SK3e"
                     /geo_loc_name="Switzerland: Basel"
                     /collection_date="2016"
                     /collected_by="ILS, University of Zurich"
     gene            join(3916..4664,1..233)
                     /locus_tag="JJB21_RS25155"
                     /old_locus_tag="JJB21_25145"
     CDS             join(3916..4664,1..43,45..233)
                     /locus_tag="JJB21_RS25155"
                     /old_locus_tag="JJB21_25145"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_048909999.1"
                     /ribosomal_slippage=""
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /note="programmed frameshift; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="IS5-like element IS5 family transposase"
                     /protein_id="WP_225899375.1"
                     /translation="MSHQLTFADSEFSSKRRQTRKEIFLSRMEQILPWQNMVEVIEPFY
                     PKAGNGRRPYPLETMLRIHCMQHWYNLSDGAIEDALYEIASMRLFARLSLDSALPDRTT
                     IMNFRHLLEQHQLARQLFKTINRWLAEAGVMMTQGTLVDATIIEAPSSTKNKEQQRDPE
                     MHQTKKGNQWHFGMKAHIGVDAKSGLTHSLVTTAANEHDLNQLGNLLHGEEQFVSADAG
                     YQGAPQREELAEVDVDWLIAERPGKVRTLKQHPRKNKTAHQHEYMKASIRAKVEHPFRI
                     IKRQFGFVKARYKGLLKNDNQLAMLFTLANLFRADQMIRQWERSH"
                     /name="IS5-like element IS5 family transposase"
     gene            complement(<382..513)
                     /locus_tag="JJB21_RS25575"
                     /pseudo=""
     CDS             complement(<382..513)
                     /locus_tag="JJB21_RS25575"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_013578013.1"
                     /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="zinc-ribbon domain-containing protein"
                     /name="zinc-ribbon domain-containing protein"
     gene            complement(821..934)
                     /locus_tag="JJB21_RS25160"
                     /old_locus_tag="JJB21_25150"
     CDS             complement(821..934)
                     /locus_tag="JJB21_RS25160"
                     /old_locus_tag="JJB21_25150"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_071778980.1"
                     /translation="MHEPPVQSDRCVFSGNYRLESKPERHDKAPLAAATGN"
                     /name="replication initiation protein"
     gene            complement(2120..>2302)
                     /locus_tag="JJB21_RS25165"
                     /old_locus_tag="JJB21_25155"
                     /pseudo=""
     CDS             complement(2120..>2302)
                     /locus_tag="JJB21_RS25165"
                     /old_locus_tag="JJB21_25155"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007798797.1"
                     /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="NINE protein"
                     /name="NINE protein"
     gene            <2299..2541
                     /locus_tag="JJB21_RS25170"
                     /old_locus_tag="JJB21_25160"
                     /pseudo=""
     CDS             <2299..2541
                     /locus_tag="JJB21_RS25170"
                     /old_locus_tag="JJB21_25160"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_003862821.1"
                     /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="cupin domain-containing protein"
                     /name="cupin domain-containing protein"
     gene            complement(2579..3721)
                     /gene="wzz(fepE)"
                     /locus_tag="JJB21_RS25175"
                     /old_locus_tag="JJB21_25165"
     CDS             complement(2579..3721)
                     /gene="wzz(fepE)"
                     /locus_tag="JJB21_RS25175"
                     /old_locus_tag="JJB21_25165"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010435173.1"
                     /GO_component="GO:0016020 - membrane [Evidence IEA]"
                     /GO_process="GO:0009103 - lipopolysaccharide biosynthetic
                     process [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="LPS O-antigen length regulator Wzz(fepE)"
                     /protein_id="WP_021544858.1"
                     /translation="MSAMDFKKNTDLDFPRYATPAVSTKEIDLLGLLDVLLAAKKRIVT
                     IVLAFAVVGLAIAFLIPQKWTSKAVITPAEQTQWNTLRQMMVTLQVLDVDAKVSRGDVF
                     NLFIKKFQSQSLLEEYMKTSPYVMSQLEGTEVDPLELHRAVVNIAEKMKATDNTQVKDA
                     DKAPYTSWTLSFTAPTAGDAQTVLEGYINYISRIVEQETMENIRNQITLKTKVVQQQLE
                     LDRVRLTNIHNTNLQRLNYSLEVANAAGIKKPVYSNGQAVKDDPDYSVALGADGIAQKL
                     QIEKNLKDVAELNADFQNREYYLTQLQKLSVEDVKLEPFRYQLSPSLPVKKDGPGKALI
                     VLLAGILGGLFACGSVLLREAMLSRNPLPEPITAVTPATE"
                     /name="wzz(fepE)"
     Typing          complement(818..1203)
                     /name="rep_cluster_2373"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.373"
                     /coverage="90.0"
                     /evalue="1.04e-173"
ORIGIN
        1 cttgaaacag catccacgca agaacaaaac ggcccatcaa catcgaatac atgaaagcca
       61 gcatccgggc caaggtggag cacccatttc gcatcatcaa gcgacagttc ggcttcgtga
      121 aagccagata caaggggttg ctgaaaaacg ataaccaact ggcgatgtta ttcacgctgg
      181 ccaacctgtt tcgggcggac caaatgatac gtcagtggga gagatctcac taaaaactgg
      241 gaataacgcc ttaaatggcg aagaaacggt ctaaataggc tgattcaagg catttacggg
      301 agaaaaaaat cggctcaaac atgaagaaat gaaatgactg agtcaaccga gaagaatttc
      361 cccgcttatt cgcaccttcc ctaatagcgc ggctgcgatt ctactttttt cacctgaacc
      421 tgaagaggcg tttgtggctc cgcagtgtgg gcatgacttt gctgtttcgt gtatttcctt
      481 gccgcatcct cggcagtaaa ccattgaact cattttttat cctcgagctt atttttagtt
      541 gggatgcata atatccgatg ttttataacg atatgcatcc tatatgctcg ggtgggatag
      601 atttccatta tggtgaagga tcttcttgag atcctttctg tagcgtcgta atctcttgct
      661 cagtaaacga aaaaaccgcc cagcaaggcg gtttttcgaa ggttctcaga gctgcaactc
      721 tttgaaccgt ggtaactggc ttatgaggag cgcagtaacc aaatctgttc tttcagttta
      781 gccttaacag gcgcataact tcaagactaa ctcctctaaa tcagttacca gtggctgctg
      841 ccagtggcgc tttgtcgtgt ctttccggct tggactcaag tcgatagtta ccggagaaga
      901 cgcagcggtc ggactgaacg gggggttcgt gcatacagtc cagcttggag cgaactgcct
      961 acccggaact gagtgtcagg cgtggaatga gataaacgcg gccataacag cggaatgaca
     1021 ccggtaaacc gaaaggcagg aacaggagag cgcacgaggg agccaccagg gggaaacgcc
     1081 tggtatcttt aagtcctgtc gggtttcgcc accactgatt tgagcgtcag attctgtgat
     1141 gcttgtcagg ggggcggagc ctatggaaaa ccggcaacgc cgcggccttt tcttttgcct
     1201 ctcgatcctc tctcattgcc tgtgccttaa tgtctccgtt ccctccgctc gccgcagccg
     1261 aacgaccgag cgtagcgagt cagtgagcga ggaagcggaa tatccccgga cttatcttcg
     1321 gcaccgtacg cgccagtgct gcatttttta atacgatgca ggatagggct aacgccgcaa
     1381 agtgacgtca cctgacgttc ctggattaca aaggttaaag cagcggacag gaaatgtttt
     1441 gtgcccacag ctatgctggc ttattcacaa aacagcggga caagatgtgt ttttggagta
     1501 ccgccggccc gctaaagact cctggttagc tcccgcatgt ttgctatctt tttgctacca
     1561 ttttgctact tttttgctat ctccagagtc ttctggtctt tcggttgcta tccttttgct
     1621 acttttttgc tatcaaaatg ctacctctcc cttcttgcaa taaatgacca aggcacgtta
     1681 gcgatgtata catcgccgcg ccgcaagggt gccccttccg aatcccgttc atcactgcgt
     1741 gctgattcat ccacgttaaa tccgaccccc ttagcaataa atccagccat gcctgacggc
     1801 ctggccaacg cctcacggcc gcacagtaaa ctgcacaccc gtgaggcgtt attcgtgagg
     1861 ttcagtggtg cttttgggcg tccagccgga ttttagccgc taaaatcccg gccatgcatg
     1921 tgtgtgcata gccatgcaga cgcgccagaa tcatcaggcg cgttttttca cgatataggc
     1981 acagggaagt gtcggaaaca ggcaggaaga accagaaacg ccctgagagc ctctcaggcg
     2041 gtgcacgcaa cggatgttat ggtaaatctg cctcacagac tggtacaaaa aaagccccgc
     2101 agggcttttt tgctatgagt tagccatatt ttcttgcgaa tttttcatcg gaatcgcata
     2161 gataaataat aaactcaata aacgcgatga tcgcgggtat gaatgtccag caaaaaatta
     2221 gatacaggaa tccctgtcct attttaccta agtaaaattt atgtacgcca aatccaccaa
     2281 ggaagaatgc taagaaagat gatggcggtg gaggtcaatt ttgagcaggg tgcgattggc
     2341 ccgatgcaca atcacccgca tgaacagctt acctatgtgc tctccgggga gttcgagttt
     2401 acgataggtg aagaaaagca gatcgtgacg gcgggcgata cgctctataa agcgccgcac
     2461 gtgatgcacg gctgcatttg cctgaagccc ggcacccttc tggatacctt tacgccggtg
     2521 cgcgacgatt tcctgaaata aaaaaaggcg ctgaatcagc gcctttttaa tatcgtcgtt
     2581 actctgttgc tggcgttacg gccgttatcg gctctggcaa cggattacgc gagagcattg
     2641 cctcacgcag cagcacgctg ccgcaggcaa acaggccgcc cagaatccct gccagcagca
     2701 caatcagggc tttgcccgga ccgtcttttt tcaccggcag tgacggtgaa agctgatacc
     2761 tgaagggttc aagcttcacg tcttccacgg acagtttttg caactgagtc agatagtatt
     2821 cacggttctg gaaatccgca ttcagctcgg ccacgtcctt cagattcttt tcaatctgca
     2881 gcttttgcgc aataccgtca gcacccagcg ccacggagta gtcaggatcg tcttttaccg
     2941 cctgtccgtt gctgtaaacc ggcttcttaa tgcctgccgc gttcgccact tccagcgaat
     3001 agttgaggcg ctgcaggttg gtgttgtgga tattggtcag acgcacgcga tccagctcca
     3061 gctgctgctg aacgactttc gttttcagcg tgatctggtt acggatattt tccatcgtct
     3121 cctgctcaac aatgcgggag atatagttga tgtaaccttc cagaaccgtc tgcgcgtctc
     3181 ccgccgtcgg ggcggtaaag ctcagcgtcc atgaggtata cggcgctttg tctgcgtctt
     3241 taacctgcgt gttatctgtc gctttcattt tctcagcaat attcaccacc gcgcgatgca
     3301 gctccagcgg gtctacctcg gtgccttcca gctgagacat cacgtacggg gaggttttca
     3361 tgtactcttc gagcagcgac tgcgactgaa actttttgat gaacaggtta aacacgtctc
     3421 cacggctcac cttcgcgtcg acgtccagca cctgcagcgt caccatcatc tggcgcagcg
     3481 tgttccactg cgtctgctcg gccggcgtga tcacggcttt actggtccat ttttgcggga
     3541 ttaaaaacgc aatggccaac cctactacgg cgaacgccag gacgatcgtc acaatacgtt
     3601 ttttggctgc cagaagtacg tctaacaacc ccaggagatc tatctctttg gtgcttaccg
     3661 ccggagtggc ataacgggga aaatcgaggt ccgtgttttt cttgaaatcc atcgctgaca
     3721 taaccgttct tctttttgga gcgcagtaaa tttctgcctg attggttgca gtggtcggat
     3781 gatacaagaa agtaagaata atctgaacgc cagattgatc tatctgtaga ccgactatca
     3841 gatttaggga aggtgcgaac aagtccctga tatgagatca tgtttgtcat ctggagccat
     3901 ggaacagggt tcatcatgag tcatcaactt accttcgccg acagtgaatt cagcagtaag
     3961 cgccgtcaga ccagaaaaga gattttcttg tcccgcatgg agcagattct gccatggcaa
     4021 aacatggtgg aagtcatcga gccgttttac cccaaggctg gtaatggccg gcgaccttat
     4081 ccgctggaaa ccatgctacg cattcactgc atgcagcatt ggtacaacct gagcgatggc
     4141 gcgatcgaag atgctctgta cgaaatcgcc tccatgcgtc tgtttgcccg gttatccctg
     4201 gatagcgcct tgccggaccg caccaccatc atgaatttcc gccacctgct ggagcagcat
     4261 caactggccc gccaattgtt caagaccatc aatcgctggc tggccgaagc aggcgtcatg
     4321 atgactcaag gcaccttggt cgatgccacc atcattgagg cacccagctc gaccaagaac
     4381 aaagagcagc aacgcgatcc ggagatgcat cagactaaga aaggcaatca gtggcacttt
     4441 ggcatgaagg cccacattgg tgtcgatgcc aagagtggcc tgacccacag cctagtcacc
     4501 accgcggcca acgagcatga cctcaatcag ctgggtaatc tgctgcatgg agaggagcaa
     4561 tttgtctcag ccgatgccgg ctaccaaggg gcgccacagc gcgaggagct ggccgaggtg
     4621 gatgtggact ggctgatcgc cgagcgcccc ggcaaggtaa gaac
//
