LOCUS       NZ_CP048369             3684 bp    DNA     circular CON 25-JUN-2024
DEFINITION  Escherichia coli strain 164 plasmid pC-F-164_B, complete sequence.
ACCESSION   NZ_CP048369
VERSION     NZ_CP048369.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13951916
            Assembly: GCF_010365525.1
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  JOURNAL   Unpublished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-164.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_010365525.1-RS_2024_06_25
            Annotation Date                   :: 06/25/2024 03:40:37
            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)                     :: 4,917
            CDSs (total)                      :: 4,797
            Genes (coding)                    :: 4,534
            CDSs (with protein)               :: 4,534
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 263
            CDSs (without protein)            :: 263
            Pseudo Genes (ambiguous residues) :: 0 of 263
            Pseudo Genes (frameshifted)       :: 96 of 263
            Pseudo Genes (incomplete)         :: 167 of 263
            Pseudo Genes (internal stop)      :: 55 of 263
            Pseudo Genes (multiple problems)  :: 49 of 263
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP048369.1.
            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="164"
                     /isolation_source="environment"
                     /db_xref="taxon:562"
                     /plasmid="pC-F-164_B"
                     /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            complement(join(3555..3684,1..164))
                     /locus_tag="GZS07_RS24220"
                     /old_locus_tag="GZS08_24210"
                     /old_locus_tag="GZS08_RS24210"
     CDS             complement(join(3555..3684,1..164))
                     /locus_tag="GZS07_RS24220"
                     /old_locus_tag="GZS08_24210"
                     /old_locus_tag="GZS08_RS24210"
                     /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            501..782
                     /locus_tag="GZS07_RS24225"
                     /old_locus_tag="GZS08_24215"
                     /old_locus_tag="GZS08_RS24215"
     CDS             501..782
                     /locus_tag="GZS07_RS24225"
                     /old_locus_tag="GZS08_24215"
                     /old_locus_tag="GZS08_RS24215"
                     /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"
     gene            complement(1240..1386)
                     /locus_tag="GZS07_RS24770"
                     /old_locus_tag="GZS08_24220"
     CDS             complement(1240..1386)
                     /locus_tag="GZS07_RS24770"
                     /old_locus_tag="GZS08_24220"
                     /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            1791..1982
                     /locus_tag="GZS07_RS24240"
                     /old_locus_tag="GZS08_24230"
                     /old_locus_tag="GZS08_RS24230"
     CDS             1791..1982
                     /locus_tag="GZS07_RS24240"
                     /old_locus_tag="GZS08_24230"
                     /old_locus_tag="GZS08_RS24230"
                     /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            1982..2404
                     /locus_tag="GZS07_RS24245"
                     /old_locus_tag="GZS08_24235"
                     /old_locus_tag="GZS08_RS24235"
     CDS             1982..2404
                     /locus_tag="GZS07_RS24245"
                     /old_locus_tag="GZS08_24235"
                     /old_locus_tag="GZS08_RS24235"
                     /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(3189..3491)
                     /locus_tag="GZS07_RS24250"
                     /old_locus_tag="GZS08_24240"
                     /old_locus_tag="GZS08_RS24240"
     CDS             complement(3189..3491)
                     /locus_tag="GZS07_RS24250"
                     /old_locus_tag="GZS08_24240"
                     /old_locus_tag="GZS08_RS24240"
                     /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"
     Typing          complement(1278..1650)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.467"
                     /coverage="91.0"
                     /evalue="1.28e-167"
ORIGIN
        1 gccatttcat agcttaagtc tgttttccca tttaacagtc tacttaaggt agactgggat
       61 acatcaagtt tatcggctaa ctctgcggca ggtatttcga acggttccat gaacatttct
      121 ctgataaact caccaggatg aacaggatcg taaagattta tcatgccttc ctctgtttgt
      181 tttgtatttg attatacaaa aaaattactg cctttcagta tgcgcattgc acaatgtgca
      241 agttcatgat attgacaaaa aaagcagtca gctttaggat actcgttgga gtcaaagcta
      301 ctgcgtatgt atgggctttt atggcctttt caaggcgcag tattttaccc ttaggattcg
      361 ttgaagtcaa atgaggtgat tgacctcaag aacaaactta cgtcaattgt tttaataaag
      421 caagggggca aaatggaact aattaaaatg attttaaaat atagatacag gtatagacga
      481 aaaaaatatg gggattgtag atgataaaaa acataaaaca taaaggactt aggagctttg
      541 ctgaagaagg tagcaccgcc ggtattcagc ccagtatggc gaaaagactt cgcatgattt
      601 tgactacgct aagcacagca acttgcattc aagacgttgt tgacgttagg gcgttagggt
      661 gccaccccct aaagggggag cgtaaaggcg agtattccgt tgaagttaat gggaactggc
      721 gggtagtttt caaggttgag gaaccaaacg tcttagacgt tgatcttgaa gattatcatt
      781 agttatcaat aagtaagttg ctaatccatc caagtgaaag tacggatgga ttagggactt
      841 tattaaaaaa gtaacctctg gagaaagtat gagatccttt atggttttat tgttcccgtt
      901 gattagcgta actattgctg gagtcctagc ttttcgtggt attgatggct ggggatggtt
      961 cttgttagct gctgtacttt gtgcaggggc tgatactgtc cagaagcatg tgtctaccaa
     1021 taaaaaggag cctgctggtg agtgagctgt cttggttctt ccttgactgc tttgaatgat
     1081 aaagcgtatc ttactcgccg agacgaaaaa accgcctggg gaggcggttt tttcgagggt
     1141 tcagtaagtt ggggaacttc tgaaccgtgg taacagggtg tacaagaccg ctgaaaccaa
     1201 attctgtcct ttcagtttag ccgtagttgg gctgagactt caagaactct gtatcagtaa
     1261 tctcttgtac accttcttac cagtggctgc tgccagtggc gcttgtgcgt gtcttaccgg
     1321 gttggactca agatgatagt taccggataa ggtgcagcag tcggactgaa cggggggttc
     1381 gtgcatacag tccagcttgg agcgaactgc ctacccggaa ctgagtgtct ggcgtggaat
     1441 gagataaacg cggccataac agcggaatga caccggtaaa ccgaaaggca ggaacaggag
     1501 agcgcacgag ggagccatca gggggaaacg cctggtatct ttatagtcct gtcggggttc
     1561 gccaccactg atttgagcgt cagatttcgt gatgcttgtc aggggggcgg agcctatgga
     1621 aaaacggccg gtgtgcggcc ttctccctct ccgtgctgtc tgtcctatgt cgttatgtgt
     1681 gtattgcgac cgctcgccgc agccgaacgg caggagcgta gcgactgagt gagcgaggaa
     1741 gcggaaaaga gaacatacct acactgagca ctgacgctct gaggcctctt atgtcgaaac
     1801 aacagaaaac agcgctgaac atggctaaat tcatccagaa tcagtctctg ctcctgctgg
     1861 agaagcttaa cgagcttgat cttgatgcag aggccgacct ttgtgagaaa ctccacgatg
     1921 atgcggagca tcttttccgt acactgtcct cgagactgga tgaattacag gatggtaact
     1981 gatggccaga gtgtctatta gtgaagcggc acggcttgtt aaggttagtc gccccacaat
     2041 ttacaagatg attaacagtg ggaagttaag ttacacctct gttttaaagc acgggaagac
     2101 cattaaagtt attgatactt cagagcttat tagagttttt ggttctcttg atggtgtcat
     2161 cgatactgta aaatatgatg taaaaagtga cgcaggatct acaggtgtta acagcgttgg
     2221 tttacatgat ttacaacata gaattgcttt actagaagct gaaaacgatg gtcttaaagg
     2281 ggctgttaag gctcgagatg agcatattga ttcccttcgt caggctatgc agcttctgga
     2341 gcacaagcac gaaccttctt caccacccga ttccccgtgg tggaaattct ggaaaaaatc
     2401 ctgactccgt catgcttccg ttttcctctc cggccatccc ggggagttcc tgaaccttcc
     2461 caaaaatcgc cagatctctg aacgctcctc acgactaaaa atacccacac actacgcaaa
     2521 attaaaattt tgcagatttg tatttaatat cagtagctta ctttcctgaa gtttcggttt
     2581 ttaaatttta tttacataga tccgactcta tgacgactcg tcatagagtc cccggcgagt
     2641 cgtcatagag tcggtaacga ctcagagcta taaaaacaat gagttaataa cgacccgact
     2701 ctagacccga ctccccgttt ggttgttttt tagactcggc gactctgggt acgactctag
     2761 tgaagagtcg ccggtgaatc gtgtggtgag tcgtccggcg acttgccatg acgtgattgc
     2821 cggccgtcga cgaacacgat tcctgaacgt gctgaaaacc ggttttccgg ctgcgccggc
     2881 aacgcttcac ggccacgcaa taaattgcgt ccccgttcac cgttttcgga tgggaagaac
     2941 gccggaaaca ggacttaccc tggctgaatg gcgtgaattt tcgcgctatg cacttgcgtg
     3001 catactcatg catgccgtaa aaacagagcc tgcgcgtttc tgacgggttt tcgggtggtt
     3061 tgttgcctgt tttaccggtt tcctgtcaga aacgccctga ggccgttctg gcggtgcgta
     3121 caattatgac tttatgttaa atcattaggg aggggattct gctggaactt agtggatgtt
     3181 attgcatatc agacaaattt cggcagattt cccaagttat cgagtttagt tttgtttgga
     3241 tctgtggtta tgtagccatc gtccatcgct tccactttgg ctcctaggtt ccacttacca
     3301 gtagagctgt tctttacaac tgtcataaag ctggcttttc ccatgctgat cagctcgctg
     3361 atgaatttgc gagagctgat tgagccggca gtgttccatg agccatctcg gtttatttta
     3421 tgaactttta cgaattcgat gtgctgacca gcactgtcca ttttgattgc tgagatatag
     3481 aaatctacca tggttgcctc ctgatggctg ctgggtgttt tacgtaacaa aagcccgcgt
     3541 tctgcgggct tttttcatgg aaacattgga tgcaagtgtt ccagctctgc cgctaaagat
     3601 ttgcgacttt ttgacaggct gaattgggtc tgcatgttta cccacgactc tgcagagcgg
     3661 cctacgacct tcgacaatct aagt
//
