LOCUS       NZ_CP086525             3727 bp    DNA     circular CON 28-MAY-2024
DEFINITION  Escherichia coli strain Ec-042-T20-ESBL plasmid pEc-042-T20-ESBL_5,
            complete sequence.
ACCESSION   NZ_CP086525
VERSION     NZ_CP086525.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN22108720
            Assembly: GCF_022759885.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3727)
  AUTHORS   Moser,A.I., Endimiani,A., Campos-Madueno,E.I. and Vallone,A.
  TITLE     Genome plasticity in E. coli and K. pneumoniae: SNV accumulation
            over time
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3727)
  AUTHORS   Moser,A.I., Endimiani,A., Campos-Madueno,E.I. and Vallone,A.
  TITLE     Direct Submission
  JOURNAL   Submitted (04-NOV-2021) Institute for Infectious Diseases,
            University of Bern, Friedbuehlstrasse 51, Bern 3001, Switzerland
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 273x
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_022759885.1-RS_2024_05_28
            Annotation Date                   :: 05/28/2024 04:43:01
            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)                     :: 4,717
            CDSs (total)                      :: 4,596
            Genes (coding)                    :: 4,365
            CDSs (with protein)               :: 4,365
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 231
            CDSs (without protein)            :: 231
            Pseudo Genes (ambiguous residues) :: 0 of 231
            Pseudo Genes (frameshifted)       :: 63 of 231
            Pseudo Genes (incomplete)         :: 155 of 231
            Pseudo Genes (internal stop)      :: 41 of 231
            Pseudo Genes (multiple problems)  :: 25 of 231
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP086525.1.
            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..3727
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="Ec-042-T20-ESBL"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pEc-042-T20-ESBL_5"
                     /geo_loc_name="Switzerland"
                     /collection_date="2019"
                     /collected_by="Institute for Infectious Diseases Bern"
     gene            complement(join(3617..3727,1..93))
                     /locus_tag="LNN45_RS23450"
                     /old_locus_tag="LNN45_23445"
     CDS             complement(join(3617..3727,1..93))
                     /locus_tag="LNN45_RS23450"
                     /old_locus_tag="LNN45_23445"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017191052.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_071597489.1"
                     /translation="MAIYVGPHNKIGRDGGSFQECDINTINHTVIRKYGRYCTIRDNEY
                     APPTSTPGRYWLQIYRTPDNTE"
                     /name="hypothetical protein"
     gene            complement(221..460)
                     /locus_tag="LNN45_RS23455"
                     /old_locus_tag="LNN45_23450"
     CDS             complement(221..460)
                     /locus_tag="LNN45_RS23455"
                     /old_locus_tag="LNN45_23450"
                     /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_235241169.1"
                     /translation="MEPFEIPAAELADKLEVSQSALSRLLNGKTDLSYEMALRLSKVIG
                     RSAESWVNMQAQYSLSKSRKALSETLEHLHPMFP"
                     /name="HigA family addiction module antitoxin"
     gene            854..1135
                     /locus_tag="LNN45_RS23460"
                     /old_locus_tag="LNN45_23455"
     CDS             854..1135
                     /locus_tag="LNN45_RS23460"
                     /old_locus_tag="LNN45_23455"
                     /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_024167147.1"
                     /translation="MIKNIKHKGLRSFAEDGSTAGIQPHLAKKLRMILATLSTATCLQD
                     IVDVRALGCHPLKGDRKGEFSVEVNGNWRVVFKVEEPNVLDVDLEDYH"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     gene            2293..2442
                     /locus_tag="LNN45_RS23465"
                     /old_locus_tag="LNN45_23460"
     CDS             2293..2442
                     /locus_tag="LNN45_RS23465"
                     /old_locus_tag="LNN45_23460"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017880354.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001417847.1"
                     /translation="MPSEYDEQRDANDTQLPGEYDLFDLMAQVTEENLHAPVDFGPPVG
                     REAL"
                     /name="hypothetical protein"
     gene            2826..3194
                     /locus_tag="LNN45_RS23470"
                     /old_locus_tag="LNN45_23465"
     CDS             2826..3194
                     /locus_tag="LNN45_RS23470"
                     /old_locus_tag="LNN45_23465"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017880027.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001273380.1"
                     /translation="MANFNPGPRTAIAAVRDSKNDIETWKKNGIRREEIVTVLNERYGL
                     NISLVAFDKALYRLRKSTDEPSLADVDSVSAAETNFSEASGPDNDFFLSGNDFMRAEEE
                     SQRVVESFRDSLSRKKGF"
                     /name="hypothetical protein"
     Typing          2085..2258
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.143"
                     /coverage="100.0"
                     /evalue="5.58e-78"
     Typing          complement(1615..2161)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.935"
                     /coverage="90.0"
                     /evalue="0.0"
ORIGIN
        1 gataacagta tgattgatgg tgttgatgtc acattcttgg aatgagccac catcacgacc
       61 tattttgttg tgtggtccta cataaattgc cattttgttt tccttttcag ggagttaatg
      121 agcatcttat cggtgtttaa caacaatcac ttctacatca aatgaacggt agatatgcgg
      181 agcgttcgat ggtgaaaagc ccgcattcgc gggcttttac ttatggaaac atcggatgca
      241 gatgctctag cgtctcggat aaagccttac ggcttttaga gaggctgtac tgagcctgca
      301 tattaaccca cgactctgca gagcggccta taactttaga tagtcgaaga gccatctcat
      361 aactaagatc agtttttcca ttgagcaatc tgcttaatgc agattgtgat acttcaagct
      421 tatcagctaa ctctgcggca ggtatttcga acggttccat gaacatttcc ctgatgaact
      481 caccggggtg tacaggatcg taaagattta tcatgccttc ctcagttggt tttgtatttg
      541 attacacaaa acattttgtt ttctttcgta ttgcgcattg cacaatgtgc aagtgtctgt
      601 tattgacaaa aaaagcagta agctttagga tgctctgtgg agcagaaagc taccgctaat
      661 atggtgtcat agattgactt tttcaaggcg ccatattgta tggttatcgc tcatggaagt
      721 caaacgaggt aatcgacctc agagacaaac ttacgtcaat tattttaata atgcaagggg
      781 ttcaaatgga cgctgttaaa ttgttttctg tttatagaga cagatatcga cgagattttt
      841 atggagatta tagatgataa aaaacataaa acataaagga cttcggagct ttgctgaaga
      901 cggtagcacc gccggaattc agccccattt agcgaaaaaa cttcgcatga tattggctac
      961 gctaagcacc gcaacatgcc ttcaagatat tgtggatgtt agggcgttgg gatgtcaccc
     1021 cctcaaaggt gaccgtaaag gtgagttttc cgtagaggtt aacggaaact ggagggtagt
     1081 tttcaaggtg gaagaaccta acgtcttaga cgtcgacctt gaagattatc attagtaatc
     1141 aaaaagtaag ttgctaatcc atcctgacct gaatatggat ggattaggga ctttattcaa
     1201 aaaaaagtcc ctctggagga ttttatgaga gcctttatga ttttgttgtt ccctttgctg
     1261 tgtgtcgtca tcgcaggggt tcttgcagtt cgagacttga atgggtgggg gtggttcttg
     1321 tttgttgctg ttttgtgtac tggagctgat acggtgcaga agcatgtttc ctgcaagaat
     1381 aattccataa gcgattgagg cttttagggt tcgtccttga ctgatttaat cgacaaagcg
     1441 tatcttatgt tcgaaacgaa aaaaccgccc tgcaaggcgg tttttcgaag gttctcagag
     1501 ctaccaactc tttgaaccgc ggtaactggc ttggaggagc gcagtaacca aatctgtcct
     1561 ttcagtttag ccttaaccgg cacataactt caagactaac tcctctaaat cagttaccag
     1621 tggctgctgc cagtggcgct tttgcatgtc tttccgggtt ggactcaaga tgatagttac
     1681 cggacaaggc gcagcggtcg gactgaacgg ggggttcgtg catacagtcc agcttggagc
     1741 gaactgccta cccggaactg agtgtcaggc gtggaatgag ataaacgcgg ccataacagc
     1801 ggaatgacac cggtaaacca aaaggcagga acaggagagc gcacgaggga gccaccaggg
     1861 ggaaacgcct ggtatcttta agtcctgtcg ggtttcgcca ccactgattt gagcgtcaga
     1921 tttcgtgatg cttgtcaggg gggcggagcc tatggaaaaa cggcttcgcc gtggccttat
     1981 tgcttctccg ttaagcttct tcttggcatc tcccaggaaa tttccgcccc gcctgtaagt
     2041 tggtaccgct cgccgcagcc gaacgaccga gcgcagcgag tcagtgagcg aggaagcgga
     2101 atatatcctg tatcacatat tctgctgacg caccggtgca gccttttttc tcctgccaca
     2161 tgaagcactt cactgacacc ctcatcagtg ccaacatagt aagccagtat acactctgct
     2221 agcgctacgt gactggttca gggctgcgcc ccgaaacccg ctaacaaccc cttagctact
     2281 ggatatcacc ccatgccatc tgagtatgat gaacaacggg atgcgaatga tacgcagctt
     2341 cccggcgaat atgacctttt tgatttaatg gcgcaggtta ctgaagagaa cctgcacgcc
     2401 ccggtggatt ttgggccgcc tgtcggcagg gaagcgttat aacttttttc gctggtcagc
     2461 gtacgtgtaa tacgccggta ttacatctta tttctttatt ttcatgtgat tacagatggt
     2521 tgtaatacgt tgtgtattac ataaataaac gggaaattca gtttttacct tttaattcat
     2581 gcaattgcga tgaaaatcgc ggttgcgtat ggtgtatggc catttaaggg ataatgtaac
     2641 ctgactttta aagaatgaat ctatctttgg cagcgcatga gatcgataaa aagcgttcca
     2701 catcaggcgg ttcatggata catgaaccgg aaaggacaac aataagacaa ttgtaagaca
     2761 ttttttgcgt tttactctta tttttggact attatgagac aaatgtaaga cattatgggc
     2821 ggtatatggc gaattttaac cctggtccaa gaacagccat tgcagctgtc agggattcca
     2881 agaacgatat agaaacctgg aagaaaaatg gtatccgtag ggaagagatt gtgactgtgc
     2941 tgaatgaacg ttacggcctg aatatctcac tggttgcgtt tgataaggct ctttacagat
     3001 tgagaaaaag tacagatgaa ccgtctcttg ctgatgtgga ttctgtgtct gctgcagaaa
     3061 cgaatttctc tgaagccagt gggcctgaca atgatttttt tctgtccggg aatgacttca
     3121 tgcgagcaga agaagaatct caaagagtgg ttgaatcatt cagagatagc cttagcagga
     3181 agaaaggatt ctgattttga attctaagta gtgaaatagt ggatcctcta ctcgaaattg
     3241 tcggatacct gcaattacct accgtgcctt atggcttggt caatgcctca cggccacgca
     3301 ataaattgcg tccccgttca ccgttttcgg ataagaagaa catcggaaac aggacttacc
     3361 ccggctgaat ggtgtgaaat tctgcgctat gcacttgcgc gcatactcat gcatgccgta
     3421 aaaacagagc ctgcgcgttt ctggcgggtt ttcgggtggt ttgttgcctg ttttaccggt
     3481 ttcccgtcag aaacgccctg agggcctctc aggcggtgca cgcaacggat gttatggtaa
     3541 ataagagcga cagtcctagt cactcttaat gatagtcacc gtaatgtggc tgctttcgct
     3601 ggggatggat ttttggttac tcggtgttat ctggggttcg atagatctgt agccagtatc
     3661 ggcctggtgt gcttgttggt ggtgcgtact cattatctcg aatggtgcag tatcgtccgt
     3721 atttgcg
//
