LOCUS       NZ_CP086537             3727 bp    DNA     circular CON 28-MAY-2024
DEFINITION  Escherichia coli strain Ec-042-T5-ESBL plasmid pEc-042-T5-ESBL_5,
            complete sequence.
ACCESSION   NZ_CP086537
VERSION     NZ_CP086537.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN22108718
            Assembly: GCF_022759845.1
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  JOURNAL   Unpublished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                   :: 325x
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_022759845.1-RS_2024_05_28
            Annotation Date                   :: 05/28/2024 04:37:50
            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)                     :: 4,718
            CDSs (total)                      :: 4,597
            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)              :: 232
            CDSs (without protein)            :: 232
            Pseudo Genes (ambiguous residues) :: 0 of 232
            Pseudo Genes (frameshifted)       :: 64 of 232
            Pseudo Genes (incomplete)         :: 155 of 232
            Pseudo Genes (internal stop)      :: 41 of 232
            Pseudo Genes (multiple problems)  :: 25 of 232
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP086537.1.
            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-T5-ESBL"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pEc-042-T5-ESBL_5"
                     /geo_loc_name="Switzerland"
                     /collection_date="2019"
                     /collected_by="Institute for Infectious Diseases Bern"
     gene            complement(213..494)
                     /locus_tag="LNN41_RS23455"
                     /old_locus_tag="LNN41_23450"
     CDS             complement(213..494)
                     /locus_tag="LNN41_RS23455"
                     /old_locus_tag="LNN41_23450"
                     /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            834..1127
                     /locus_tag="LNN41_RS23460"
                     /old_locus_tag="LNN41_23455"
     CDS             834..1127
                     /locus_tag="LNN41_RS23460"
                     /old_locus_tag="LNN41_23455"
                     /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_077636472.1"
                     /translation="MINLYDPVHPGEFIREMFMEPFEIPAAELADKLEVSQSALSRLLN
                     GKTDLSYEMALRLSKVIGRSAESWVNMQAQYSLSKSRKALSETLEHLHPMFP"
                     /name="HigA family addiction module antitoxin"
     gene            1255..1458
                     /locus_tag="LNN41_RS23465"
                     /old_locus_tag="LNN41_23460"
     CDS             1255..1458
                     /locus_tag="LNN41_RS23465"
                     /old_locus_tag="LNN41_23460"
                     /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(1881..2249)
                     /locus_tag="LNN41_RS23470"
                     /old_locus_tag="LNN41_23465"
     CDS             complement(1881..2249)
                     /locus_tag="LNN41_RS23470"
                     /old_locus_tag="LNN41_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"
     gene            complement(2633..2782)
                     /locus_tag="LNN41_RS23475"
                     /old_locus_tag="LNN41_23470"
     CDS             complement(2633..2782)
                     /locus_tag="LNN41_RS23475"
                     /old_locus_tag="LNN41_23470"
                     /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"
     Typing          complement(2818..2991)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.143"
                     /coverage="100.0"
                     /evalue="5.58e-78"
     Typing          2915..3461
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.935"
                     /coverage="90.0"
                     /evalue="0.0"
ORIGIN
        1 agctccagta cacaaaacag caacaaacaa gaaccacccc cacccattca agtctcgaac
       61 tgcaagaacc cctgcgatga cgacacacag caaagggaac aacaaaatca taaaggctct
      121 cataaaatcc tccagaggga cttttttttg aataaagtcc ctaatccatc catattcagg
      181 tcaggatgga ttagcaactt actttttgat tactaatgat aatcttcaag gtcgacgtct
      241 aagacgttag gttcttccac cttgaaaact accctccagt ttccgttaac ctctacggaa
      301 aactcacctt tacggtcacc tttgaggggg tgacatccca acgccctaac atccacaata
      361 tcttgaaggc atgttgcggt gcttagcgta gccaatatca tgcgaagttt tttcgctaaa
      421 tggggctgaa ttccggcggt gctaccgtct tcagcaaagc tccgaagtcc tttatgtttt
      481 atgtttttta tcatctataa tctccataaa aatctcgtcg atatctgtct ctataaacag
      541 aaaacaattt aacagcgtcc atttgaaccc cttgcattat taaaataatt gacgtaagtt
      601 tgtctctgag gtcgattacc tcgtttgact tccatgagcg ataaccatac aatatggcgc
      661 cttgaaaaag tcaatctatg acaccatatt agcggtagct ttctgctcca cagagcatcc
      721 taaagcttac tgcttttttt gtcaataaca gacacttgca cattgtgcaa tgcgcaatac
      781 gaaagaaaac aaaatgtttt gtgtaatcaa atacaaaacc aactgaggaa ggcatgataa
      841 atctttacga tcctgtacac cccggtgagt tcatcaggga aatgttcatg gaaccgttcg
      901 aaatacctgc cgcagagtta gctgataagc ttgaagtatc acaatctgca ttaagcagat
      961 tgctcaatgg aaaaactgat cttagttatg agatggctct tcgactatct aaagttatag
     1021 gccgctctgc agagtcgtgg gttaatatgc aggctcagta cagcctctct aaaagccgta
     1081 aggctttatc cgagacgcta gagcatctgc atccgatgtt tccataagta aaagcccgcg
     1141 aatgcgggct tttcaccatc gaacgctccg catatctacc gttcatttga tgtagaagtg
     1201 attgttgtta aacaccgata agatgctcat taactccctg aaaaggaaaa caaaatggca
     1261 atttatgtag gaccacacaa caaaataggt cgtgatggtg gctcattcca agaatgtgac
     1321 atcaacacca tcaatcatac tgttatccgc aaatacggac gatactgcac cattcgagat
     1381 aatgagtacg caccaccaac aagcacacca ggccgatact ggctacagat ctatcgaacc
     1441 ccagataaca ccgagtaacc aaaaatccat ccccagcgaa agcagccaca ttacggtgac
     1501 tatcattaag agtgactagg actgtcgctc ttatttacca taacatccgt tgcgtgcacc
     1561 gcctgagagg ccctcagggc gtttctgacg ggaaaccggt aaaacaggca acaaaccacc
     1621 cgaaaacccg ccagaaacgc gcaggctctg tttttacggc atgcatgagt atgcgcgcaa
     1681 gtgcatagcg cagaatttca caccattcag ccggggtaag tcctgtttcc gatgttcttc
     1741 ttatccgaaa acggtgaacg gggacgcaat ttattgcgtg gccgtgaggc attgaccaag
     1801 ccataaggca cggtaggtaa ttgcaggtat ccgacaattt cgagtagagg atccactatt
     1861 tcactactta gaattcaaaa tcagaatcct ttcttcctgc taaggctatc tctgaatgat
     1921 tcaaccactc tttgagattc ttcttctgct cgcatgaagt cattcccgga cagaaaaaaa
     1981 tcattgtcag gcccactggc ttcagagaaa ttcgtttctg cagcagacac agaatccaca
     2041 tcagcaagag acggttcatc tgtacttttt ctcaatctgt aaagagcctt atcaaacgca
     2101 accagtgaga tattcaggcc gtaacgttca ttcagcacag tcacaatctc ttccctacgg
     2161 ataccatttt tcttccaggt ttctatatcg ttcttggaat ccctgacagc tgcaatggct
     2221 gttcttggac cagggttaaa attcgccata taccgcccat aatgtcttac atttgtctca
     2281 taatagtcca aaaataagag taaaacgcaa aaaatgtctt acaattgtct tattgttgtc
     2341 ctttccggtt catgtatcca tgaaccgcct gatgtggaac gctttttatc gatctcatgc
     2401 gctgccaaag atagattcat tctttaaaag tcaggttaca ttatccctta aatggccata
     2461 caccatacgc aaccgcgatt ttcatcgcaa ttgcatgaat taaaaggtaa aaactgaatt
     2521 tcccgtttat ttatgtaata cacaacgtat tacaaccatc tgtaatcaca tgaaaataaa
     2581 gaaataagat gtaataccgg cgtattacac gtacgctgac cagcgaaaaa agttataacg
     2641 cttccctgcc gacaggcggc ccaaaatcca ccggggcgtg caggttctct tcagtaacct
     2701 gcgccattaa atcaaaaagg tcatattcgc cgggaagctg cgtatcattc gcatcccgtt
     2761 gttcatcata ctcagatggc atggggtgat atccagtagc taaggggttg ttagcgggtt
     2821 tcggggcgca gccctgaacc agtcacgtag cgctagcaga gtgtatactg gcttactatg
     2881 ttggcactga tgagggtgtc agtgaagtgc ttcatgtggc aggagaaaaa aggctgcacc
     2941 ggtgcgtcag cagaatatgt gatacaggat atattccgct tcctcgctca ctgactcgct
     3001 gcgctcggtc gttcggctgc ggcgagcggt accaacttac aggcggggcg gaaatttcct
     3061 gggagatgcc aagaagaagc ttaacggaga agcaataagg ccacggcgaa gccgtttttc
     3121 cataggctcc gcccccctga caagcatcac gaaatctgac gctcaaatca gtggtggcga
     3181 aacccgacag gacttaaaga taccaggcgt ttccccctgg tggctccctc gtgcgctctc
     3241 ctgttcctgc cttttggttt accggtgtca ttccgctgtt atggccgcgt ttatctcatt
     3301 ccacgcctga cactcagttc cgggtaggca gttcgctcca agctggactg tatgcacgaa
     3361 ccccccgttc agtccgaccg ctgcgccttg tccggtaact atcatcttga gtccaacccg
     3421 gaaagacatg caaaagcgcc actggcagca gccactggta actgatttag aggagttagt
     3481 cttgaagtta tgtgccggtt aaggctaaac tgaaaggaca gatttggtta ctgcgctcct
     3541 ccaagccagt taccgcggtt caaagagttg gtagctctga gaaccttcga aaaaccgcct
     3601 tgcagggcgg ttttttcgtt tcgaacataa gatacgcttt gtcgattaaa tcagtcaagg
     3661 acgaacccta aaagcctcaa tcgcttatgg aattattctt gcaggaaaca tgcttctgca
     3721 ccgtatc
//
