LOCUS       NZ_CP048375             3684 bp    DNA     circular CON 25-JUN-2024
DEFINITION  Escherichia coli strain 163 plasmid pC-F-163_D, complete sequence.
ACCESSION   NZ_CP048375
VERSION     NZ_CP048375.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13951917
            Assembly: GCF_010365505.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3684)
  AUTHORS   Nuesch-Inderbinen,M., Stevens,M.J.A. and Stephan,R.
  TITLE     Environmental dissemination of Carbapenemase-producing
            Enterobacteriaceae in Switzerland
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3684)
  AUTHORS   Nuesch-Inderbinen,M., Stevens,M.J.A. and Stephan,R.
  TITLE     Direct Submission
  JOURNAL   Submitted (31-JAN-2020) Institute for Food Safety and Hygiene,
            University of Zurich, Winterthurerstrasse 272, Zurich, Zurich 8057,
            Switzerland
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 29-NOV-2019
            Assembly Method                   :: unicycler v. 0.4.8
            Assembly Name                     :: C-F-163.fa
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 80x
            Sequencing Technology :: Oxford Nanopore/illumina minniseq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_010365505.1-RS_2024_06_25
            Annotation Date                   :: 06/25/2024 03:31:44
            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)                     :: 4,875
            CDSs (total)                      :: 4,756
            Genes (coding)                    :: 4,502
            CDSs (with protein)               :: 4,502
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 254
            CDSs (without protein)            :: 254
            Pseudo Genes (ambiguous residues) :: 0 of 254
            Pseudo Genes (frameshifted)       :: 86 of 254
            Pseudo Genes (incomplete)         :: 165 of 254
            Pseudo Genes (internal stop)      :: 58 of 254
            Pseudo Genes (multiple problems)  :: 50 of 254
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP048375.1.
            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..3684
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="163"
                     /isolation_source="environment"
                     /db_xref="taxon:562"
                     /plasmid="pC-F-163_D"
                     /geo_loc_name="Switzerland"
                     /collection_date="2019"
                     /note="This genome was originally submitted with the wrong
                     strain name and BioSample. It was corrected on March 18,
                     2020."
     gene            join(3402..3684,1..11)
                     /locus_tag="GZS08_RS23940"
                     /old_locus_tag="GZS07_23940"
                     /old_locus_tag="GZS07_RS23940"
     CDS             join(3402..3684,1..11)
                     /locus_tag="GZS08_RS23940"
                     /old_locus_tag="GZS07_23940"
                     /old_locus_tag="GZS07_RS23940"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000609279.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="HigA family addiction module antitoxin"
                     /protein_id="WP_023317864.1"
                     /translation="MINLYDPVHPGEFIREMFMEPFEIPAAELADKLDVSQSTLSRLLN
                     GKTDLSYEMALRLSKVVGRSAESWVNMQTQFSLSKSRKSLAAELEHLHPMFP"
                     /name="HigA family addiction module antitoxin"
     gene            75..377
                     /locus_tag="GZS08_RS23945"
                     /old_locus_tag="GZS07_23945"
                     /old_locus_tag="GZS07_RS23945"
     CDS             75..377
                     /locus_tag="GZS08_RS23945"
                     /old_locus_tag="GZS07_23945"
                     /old_locus_tag="GZS07_RS23945"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_006326557.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF3892 domain-containing protein"
                     /protein_id="WP_039023182.1"
                     /translation="MVDFYISAIKMDSAGQHIEFVKVHKINRDGSWNTAGSISSRKFIS
                     ELISMGKASFMTVVKNSSTGKWNLGAKVEAMDDGYITTDPNKTKLDNLGNLPKFV"
                     /name="DUF3892 domain-containing protein"
     gene            complement(1162..1584)
                     /locus_tag="GZS08_RS23950"
                     /old_locus_tag="GZS07_23950"
                     /old_locus_tag="GZS07_RS23950"
     CDS             complement(1162..1584)
                     /locus_tag="GZS08_RS23950"
                     /old_locus_tag="GZS07_23950"
                     /old_locus_tag="GZS07_RS23950"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005229777.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_039023181.1"
                     /translation="MARVSISEAARLVKVSRPTIYKMINSGKLSYTSVLKHGKTIKVID
                     TSELIRVFGSLDGVIDTVKYDVKSDAGSTGVNSVGLHDLQHRIALLEAENDGLKGAVKA
                     RDEHIDSLRQAMQLLEHKHEPSSPPDSPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(1584..1775)
                     /locus_tag="GZS08_RS23955"
                     /old_locus_tag="GZS07_23955"
                     /old_locus_tag="GZS07_RS23955"
     CDS             complement(1584..1775)
                     /locus_tag="GZS08_RS23955"
                     /old_locus_tag="GZS07_23955"
                     /old_locus_tag="GZS07_RS23955"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000166328.1"
                     /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_039023180.1"
                     /translation="MSKQQKTALNMAKFIQNQSLLLLEKLNELDLDAEADLCEKLHDDA
                     EHLFRTLSSRLDELQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2180..2326
                     /locus_tag="GZS08_RS24495"
                     /old_locus_tag="GZS07_23965"
     CDS             2180..2326
                     /locus_tag="GZS08_RS24495"
                     /old_locus_tag="GZS07_23965"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001717510.1"
                     /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_073545459.1"
                     /translation="MHEPPVQSDCCTLSGNYHLESNPVRHAQAPLAAATGKKVYKRLLI
                     QSS"
                     /name="replication initiation protein"
     gene            complement(2784..3065)
                     /locus_tag="GZS08_RS23970"
                     /old_locus_tag="GZS07_23970"
                     /old_locus_tag="GZS07_RS23970"
     CDS             complement(2784..3065)
                     /locus_tag="GZS08_RS23970"
                     /old_locus_tag="GZS07_23970"
                     /old_locus_tag="GZS07_RS23970"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000594459.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RelE/ParE family
                     toxin"
                     /protein_id="WP_032440460.1"
                     /translation="MIKNIKHKGLRSFAEEGSTAGIQPSMAKRLRMILTTLSTATCIQD
                     VVDVRALGCHPLKGERKGEYSVEVNGNWRVVFKVEEPNVLDVDLEDYH"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     Typing          1917..2289
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.467"
                     /coverage="91.0"
                     /evalue="1.28e-167"
ORIGIN
        1 tgtttccatg aaaaaagccc gcagaacgcg ggcttttgtt acgtaaaaca cccagcagcc
       61 atcaggaggc aaccatggta gatttctata tctcagcaat caaaatggac agtgctggtc
      121 agcacatcga attcgtaaaa gttcataaaa taaaccgaga tggctcatgg aacactgccg
      181 gctcaatcag ctctcgcaaa ttcatcagcg agctgatcag catgggaaaa gccagcttta
      241 tgacagttgt aaagaacagc tctactggta agtggaacct aggagccaaa gtggaagcga
      301 tggacgatgg ctacataacc acagatccaa acaaaactaa actcgataac ttgggaaatc
      361 tgccgaaatt tgtctgatat gcaataacat ccactaagtt ccagcagaat cccctcccta
      421 atgatttaac ataaagtcat aattgtacgc accgccagaa cggcctcagg gcgtttctga
      481 caggaaaccg gtaaaacagg caacaaacca cccgaaaacc cgtcagaaac gcgcaggctc
      541 tgtttttacg gcatgcatga gtatgcacgc aagtgcatag cgcgaaaatt cacgccattc
      601 agccagggta agtcctgttt ccggcgttct tcccatccga aaacggtgaa cggggacgca
      661 atttattgcg tggccgtgaa gcgttgccgg cgcagccgga aaaccggttt tcagcacgtt
      721 caggaatcgt gttcgtcgac ggccggcaat cacgtcatgg caagtcgccg gacgactcac
      781 cacacgattc accggcgact cttcactaga gtcgtaccca gagtcgccga gtctaaaaaa
      841 caaccaaacg gggagtcggg tctagagtcg ggtcgttatt aactcattgt ttttatagct
      901 ctgagtcgtt accgactcta tgacgactcg ccggggactc tatgacgagt cgtcatagag
      961 tcggatctat gtaaataaaa tttaaaaacc gaaacttcag gaaagtaagc tactgatatt
     1021 aaatacaaat ctgcaaaatt ttaattttgc gtagtgtgtg ggtattttta gtcgtgagga
     1081 gcgttcagag atctggcgat ttttgggaag gttcaggaac tccccgggat ggccggagag
     1141 gaaaacggaa gcatgacgga gtcaggattt tttccagaat ttccaccacg gggaatcggg
     1201 tggtgaagaa ggttcgtgct tgtgctccag aagctgcata gcctgacgaa gggaatcaat
     1261 atgctcatct cgagccttaa cagccccttt aagaccatcg ttttcagctt ctagtaaagc
     1321 aattctatgt tgtaaatcat gtaaaccaac gctgttaaca cctgtagatc ctgcgtcact
     1381 ttttacatca tattttacag tatcgatgac accatcaaga gaaccaaaaa ctctaataag
     1441 ctctgaagta tcaataactt taatggtctt cccgtgcttt aaaacagagg tgtaacttaa
     1501 cttcccactg ttaatcatct tgtaaattgt ggggcgacta accttaacaa gccgtgccgc
     1561 ttcactaata gacactctgg ccatcagtta ccatcctgta attcatccag tctcgaggac
     1621 agtgtacgga aaagatgctc cgcatcatcg tggagtttct cacaaaggtc ggcctctgca
     1681 tcaagatcaa gctcgttaag cttctccagc aggagcagag actgattctg gatgaattta
     1741 gccatgttca gcgctgtttt ctgttgtttc gacataagag gcctcagagc gtcagtgctc
     1801 agtgtaggta tgttctcttt tccgcttcct cgctcactca gtcgctacgc tcctgccgtt
     1861 cggctgcggc gagcggtcgc aatacacaca taacgacata ggacagacag cacggagagg
     1921 gagaaggccg cacaccggcc gtttttccat aggctccgcc cccctgacaa gcatcacgaa
     1981 atctgacgct caaatcagtg gtggcgaacc ccgacaggac tataaagata ccaggcgttt
     2041 ccccctgatg gctccctcgt gcgctctcct gttcctgcct ttcggtttac cggtgtcatt
     2101 ccgctgttat ggccgcgttt atctcattcc acgccagaca ctcagttccg ggtaggcagt
     2161 tcgctccaag ctggactgta tgcacgaacc ccccgttcag tccgactgct gcaccttatc
     2221 cggtaactat catcttgagt ccaacccggt aagacacgca caagcgccac tggcagcagc
     2281 cactggtaag aaggtgtaca agagattact gatacagagt tcttgaagtc tcagcccaac
     2341 tacggctaaa ctgaaaggac agaatttggt ttcagcggtc ttgtacaccc tgttaccacg
     2401 gttcagaagt tccccaactt actgaaccct cgaaaaaacc gcctccccag gcggtttttt
     2461 cgtctcggcg agtaagatac gctttatcat tcaaagcagt caaggaagaa ccaagacagc
     2521 tcactcacca gcaggctcct ttttattggt agacacatgc ttctggacag tatcagcccc
     2581 tgcacaaagt acagcagcta acaagaacca tccccagcca tcaataccac gaaaagctag
     2641 gactccagca atagttacgc taatcaacgg gaacaataaa accataaagg atctcatact
     2701 ttctccagag gttacttttt taataaagtc cctaatccat ccgtactttc acttggatgg
     2761 attagcaact tacttattga taactaatga taatcttcaa gatcaacgtc taagacgttt
     2821 ggttcctcaa ccttgaaaac tacccgccag ttcccattaa cttcaacgga atactcgcct
     2881 ttacgctccc cctttagggg gtggcaccct aacgccctaa cgtcaacaac gtcttgaatg
     2941 caagttgctg tgcttagcgt agtcaaaatc atgcgaagtc ttttcgccat actgggctga
     3001 ataccggcgg tgctaccttc ttcagcaaag ctcctaagtc ctttatgttt tatgtttttt
     3061 atcatctaca atccccatat ttttttcgtc tatacctgta tctatatttt aaaatcattt
     3121 taattagttc cattttgccc ccttgcttta ttaaaacaat tgacgtaagt ttgttcttga
     3181 ggtcaatcac ctcatttgac ttcaacgaat cctaagggta aaatactgcg ccttgaaaag
     3241 gccataaaag cccatacata cgcagtagct ttgactccaa cgagtatcct aaagctgact
     3301 gctttttttg tcaatatcat gaacttgcac attgtgcaat gcgcatactg aaaggcagta
     3361 atttttttgt ataatcaaat acaaaacaaa cagaggaagg catgataaat ctttacgatc
     3421 ctgttcatcc tggtgagttt atcagagaaa tgttcatgga accgttcgaa atacctgccg
     3481 cagagttagc cgataaactt gatgtatccc agtctacctt aagtagactg ttaaatggga
     3541 aaacagactt aagctatgaa atggcactta gattgtcgaa ggtcgtaggc cgctctgcag
     3601 agtcgtgggt aaacatgcag acccaattca gcctgtcaaa aagtcgcaaa tctttagcgg
     3661 cagagctgga acacttgcat ccaa
//
