LOCUS       NZ_CP086531             3727 bp    DNA     circular CON 28-MAY-2024
DEFINITION  Escherichia coli strain Ec-042-T20-MAC plasmid pEc-042-T20-MAC_5,
            complete sequence.
ACCESSION   NZ_CP086531
VERSION     NZ_CP086531.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN22108719
            Assembly: GCF_022759865.1
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  JOURNAL   Unpublished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                   :: 290x
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_022759865.1-RS_2024_05_28
            Annotation Date                   :: 05/28/2024 04:47:49
            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)                     :: 4,723
            CDSs (total)                      :: 4,602
            Genes (coding)                    :: 4,369
            CDSs (with protein)               :: 4,369
            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)              :: 233
            CDSs (without protein)            :: 233
            Pseudo Genes (ambiguous residues) :: 0 of 233
            Pseudo Genes (frameshifted)       :: 64 of 233
            Pseudo Genes (incomplete)         :: 156 of 233
            Pseudo Genes (internal stop)      :: 41 of 233
            Pseudo Genes (multiple problems)  :: 25 of 233
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP086531.1.
            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-MAC"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pEc-042-T20-MAC_5"
                     /geo_loc_name="Switzerland"
                     /collection_date="2019"
                     /collected_by="Institute for Infectious Diseases Bern"
     gene            23..391
                     /locus_tag="LNN58_RS23475"
                     /old_locus_tag="LNN58_23470"
     CDS             23..391
                     /locus_tag="LNN58_RS23475"
                     /old_locus_tag="LNN58_23470"
                     /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(814..1017)
                     /locus_tag="LNN58_RS23480"
                     /old_locus_tag="LNN58_23475"
     CDS             complement(814..1017)
                     /locus_tag="LNN58_RS23480"
                     /old_locus_tag="LNN58_23475"
                     /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(1145..1438)
                     /locus_tag="LNN58_RS23485"
                     /old_locus_tag="LNN58_23480"
     CDS             complement(1145..1438)
                     /locus_tag="LNN58_RS23485"
                     /old_locus_tag="LNN58_23480"
                     /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            1778..2059
                     /locus_tag="LNN58_RS23490"
                     /old_locus_tag="LNN58_23485"
     CDS             1778..2059
                     /locus_tag="LNN58_RS23490"
                     /old_locus_tag="LNN58_23485"
                     /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            3217..3366
                     /locus_tag="LNN58_RS23495"
                     /old_locus_tag="LNN58_23490"
     CDS             3217..3366
                     /locus_tag="LNN58_RS23495"
                     /old_locus_tag="LNN58_23490"
                     /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          3009..3182
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.143"
                     /coverage="100.0"
                     /evalue="5.58e-78"
     Typing          complement(2539..3085)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.935"
                     /coverage="90.0"
                     /evalue="0.0"
ORIGIN
        1 tgtaagacat tatgggcggt atatggcgaa ttttaaccct ggtccaagaa cagccattgc
       61 agctgtcagg gattccaaga acgatataga aacctggaag aaaaatggta tccgtaggga
      121 agagattgtg actgtgctga atgaacgtta cggcctgaat atctcactgg ttgcgtttga
      181 taaggctctt tacagattga gaaaaagtac agatgaaccg tctcttgctg atgtggattc
      241 tgtgtctgct gcagaaacga atttctctga agccagtggg cctgacaatg atttttttct
      301 gtccgggaat gacttcatgc gagcagaaga agaatctcaa agagtggttg aatcattcag
      361 agatagcctt agcaggaaga aaggattctg attttgaatt ctaagtagtg aaatagtgga
      421 tcctctactc gaaattgtcg gatacctgca attacctacc gtgccttatg gcttggtcaa
      481 tgcctcacgg ccacgcaata aattgcgtcc ccgttcaccg ttttcggata agaagaacat
      541 cggaaacagg acttaccccg gctgaatggt gtgaaattct gcgctatgca cttgcgcgca
      601 tactcatgca tgccgtaaaa acagagcctg cgcgtttctg gcgggttttc gggtggtttg
      661 ttgcctgttt taccggtttc ccgtcagaaa cgccctgagg gcctctcagg cggtgcacgc
      721 aacggatgtt atggtaaata agagcgacag tcctagtcac tcttaatgat agtcaccgta
      781 atgtggctgc tttcgctggg gatggatttt tggttactcg gtgttatctg gggttcgata
      841 gatctgtagc cagtatcggc ctggtgtgct tgttggtggt gcgtactcat tatctcgaat
      901 ggtgcagtat cgtccgtatt tgcggataac agtatgattg atggtgttga tgtcacattc
      961 ttggaatgag ccaccatcac gacctatttt gttgtgtggt cctacataaa ttgccatttt
     1021 gttttccttt tcagggagtt aatgagcatc ttatcggtgt ttaacaacaa tcacttctac
     1081 atcaaatgaa cggtagatat gcggagcgtt cgatggtgaa aagcccgcat tcgcgggctt
     1141 ttacttatgg aaacatcgga tgcagatgct ctagcgtctc ggataaagcc ttacggcttt
     1201 tagagaggct gtactgagcc tgcatattaa cccacgactc tgcagagcgg cctataactt
     1261 tagatagtcg aagagccatc tcataactaa gatcagtttt tccattgagc aatctgctta
     1321 atgcagattg tgatacttca agcttatcag ctaactctgc ggcaggtatt tcgaacggtt
     1381 ccatgaacat ttccctgatg aactcaccgg ggtgtacagg atcgtaaaga tttatcatgc
     1441 cttcctcagt tggttttgta tttgattaca caaaacattt tgttttcttt cgtattgcgc
     1501 attgcacaat gtgcaagtgt ctgttattga caaaaaaagc agtaagcttt aggatgctct
     1561 gtggagcaga aagctaccgc taatatggtg tcatagattg actttttcaa ggcgccatat
     1621 tgtatggtta tcgctcatgg aagtcaaacg aggtaatcga cctcagagac aaacttacgt
     1681 caattatttt aataatgcaa ggggttcaaa tggacgctgt taaattgttt tctgtttata
     1741 gagacagata tcgacgagat ttttatggag attatagatg ataaaaaaca taaaacataa
     1801 aggacttcgg agctttgctg aagacggtag caccgccgga attcagcccc atttagcgaa
     1861 aaaacttcgc atgatattgg ctacgctaag caccgcaaca tgccttcaag atattgtgga
     1921 tgttagggcg ttgggatgtc accccctcaa aggtgaccgt aaaggtgagt tttccgtaga
     1981 ggttaacgga aactggaggg tagttttcaa ggtggaagaa cctaacgtct tagacgtcga
     2041 ccttgaagat tatcattagt aatcaaaaag taagttgcta atccatcctg acctgaatat
     2101 ggatggatta gggactttat tcaaaaaaaa gtccctctgg aggattttat gagagccttt
     2161 atgattttgt tgttcccttt gctgtgtgtc gtcatcgcag gggttcttgc agttcgagac
     2221 ttgaatgggt gggggtggtt cttgtttgtt gctgttttgt gtactggagc tgatacggtg
     2281 cagaagcatg tttcctgcaa gaataattcc ataagcgatt gaggctttta gggttcgtcc
     2341 ttgactgatt taatcgacaa agcgtatctt atgttcgaaa cgaaaaaacc gccctgcaag
     2401 gcggtttttc gaaggttctc agagctacca actctttgaa ccgcggtaac tggcttggag
     2461 gagcgcagta accaaatctg tcctttcagt ttagccttaa ccggcacata acttcaagac
     2521 taactcctct aaatcagtta ccagtggctg ctgccagtgg cgcttttgca tgtctttccg
     2581 ggttggactc aagatgatag ttaccggaca aggcgcagcg gtcggactga acggggggtt
     2641 cgtgcataca gtccagcttg gagcgaactg cctacccgga actgagtgtc aggcgtggaa
     2701 tgagataaac gcggccataa cagcggaatg acaccggtaa accaaaaggc aggaacagga
     2761 gagcgcacga gggagccacc agggggaaac gcctggtatc tttaagtcct gtcgggtttc
     2821 gccaccactg atttgagcgt cagatttcgt gatgcttgtc aggggggcgg agcctatgga
     2881 aaaacggctt cgccgtggcc ttattgcttc tccgttaagc ttcttcttgg catctcccag
     2941 gaaatttccg ccccgcctgt aagttggtac cgctcgccgc agccgaacga ccgagcgcag
     3001 cgagtcagtg agcgaggaag cggaatatat cctgtatcac atattctgct gacgcaccgg
     3061 tgcagccttt tttctcctgc cacatgaagc acttcactga caccctcatc agtgccaaca
     3121 tagtaagcca gtatacactc tgctagcgct acgtgactgg ttcagggctg cgccccgaaa
     3181 cccgctaaca accccttagc tactggatat caccccatgc catctgagta tgatgaacaa
     3241 cgggatgcga atgatacgca gcttcccggc gaatatgacc tttttgattt aatggcgcag
     3301 gttactgaag agaacctgca cgccccggtg gattttgggc cgcctgtcgg cagggaagcg
     3361 ttataacttt tttcgctggt cagcgtacgt gtaatacgcc ggtattacat cttatttctt
     3421 tattttcatg tgattacaga tggttgtaat acgttgtgta ttacataaat aaacgggaaa
     3481 ttcagttttt accttttaat tcatgcaatt gcgatgaaaa tcgcggttgc gtatggtgta
     3541 tggccattta agggataatg taacctgact tttaaagaat gaatctatct ttggcagcgc
     3601 atgagatcga taaaaagcgt tccacatcag gcggttcatg gatacatgaa ccggaaagga
     3661 caacaataag acaattgtaa gacatttttt gcgttttact cttatttttg gactattatg
     3721 agacaaa
//
