LOCUS       NZ_CP086549             3727 bp    DNA     circular CON 28-MAY-2024
DEFINITION  Escherichia coli strain Ec-042-T0 plasmid pEc-042-T0_5, complete
            sequence.
ACCESSION   NZ_CP086549
VERSION     NZ_CP086549.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN22108716
            Assembly: GCF_022759905.1
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  JOURNAL   Unpublished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                   :: 294x
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_022759905.1-RS_2024_05_28
            Annotation Date                   :: 05/28/2024 04:42:41
            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)                     :: 4,720
            CDSs (total)                      :: 4,599
            Genes (coding)                    :: 4,368
            CDSs (with protein)               :: 4,368
            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
            CP086549.1.
            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-T0"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pEc-042-T0_5"
                     /geo_loc_name="Switzerland"
                     /collection_date="2019"
                     /collected_by="Institute for Infectious Diseases Bern"
     gene            complement(322..603)
                     /locus_tag="LNN55_RS23460"
                     /old_locus_tag="LNN55_23455"
     CDS             complement(322..603)
                     /locus_tag="LNN55_RS23460"
                     /old_locus_tag="LNN55_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            943..1236
                     /locus_tag="LNN55_RS23465"
                     /old_locus_tag="LNN55_23460"
     CDS             943..1236
                     /locus_tag="LNN55_RS23465"
                     /old_locus_tag="LNN55_23460"
                     /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            1364..1567
                     /locus_tag="LNN55_RS23470"
                     /old_locus_tag="LNN55_23465"
     CDS             1364..1567
                     /locus_tag="LNN55_RS23470"
                     /old_locus_tag="LNN55_23465"
                     /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(1990..2358)
                     /locus_tag="LNN55_RS23475"
                     /old_locus_tag="LNN55_23470"
     CDS             complement(1990..2358)
                     /locus_tag="LNN55_RS23475"
                     /old_locus_tag="LNN55_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(2742..2891)
                     /locus_tag="LNN55_RS23480"
                     /old_locus_tag="LNN55_23475"
     CDS             complement(2742..2891)
                     /locus_tag="LNN55_RS23480"
                     /old_locus_tag="LNN55_23475"
                     /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(2927..3100)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.143"
                     /coverage="100.0"
                     /evalue="5.58e-78"
     Typing          3024..3570
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.935"
                     /coverage="90.0"
                     /evalue="0.0"
ORIGIN
        1 tttcgaacat aagatacgct ttgtcgatta aatcagtcaa ggacgaaccc taaaagcctc
       61 aatcgcttat ggaattattc ttgcaggaaa catgcttctg caccgtatca gctccagtac
      121 acaaaacagc aacaaacaag aaccaccccc acccattcaa gtctcgaact gcaagaaccc
      181 ctgcgatgac gacacacagc aaagggaaca acaaaatcat aaaggctctc ataaaatcct
      241 ccagagggac ttttttttga ataaagtccc taatccatcc atattcaggt caggatggat
      301 tagcaactta ctttttgatt actaatgata atcttcaagg tcgacgtcta agacgttagg
      361 ttcttccacc ttgaaaacta ccctccagtt tccgttaacc tctacggaaa actcaccttt
      421 acggtcacct ttgagggggt gacatcccaa cgccctaaca tccacaatat cttgaaggca
      481 tgttgcggtg cttagcgtag ccaatatcat gcgaagtttt ttcgctaaat ggggctgaat
      541 tccggcggtg ctaccgtctt cagcaaagct ccgaagtcct ttatgtttta tgttttttat
      601 catctataat ctccataaaa atctcgtcga tatctgtctc tataaacaga aaacaattta
      661 acagcgtcca tttgaacccc ttgcattatt aaaataattg acgtaagttt gtctctgagg
      721 tcgattacct cgtttgactt ccatgagcga taaccataca atatggcgcc ttgaaaaagt
      781 caatctatga caccatatta gcggtagctt tctgctccac agagcatcct aaagcttact
      841 gctttttttg tcaataacag acacttgcac attgtgcaat gcgcaatacg aaagaaaaca
      901 aaatgttttg tgtaatcaaa tacaaaacca actgaggaag gcatgataaa tctttacgat
      961 cctgtacacc ccggtgagtt catcagggaa atgttcatgg aaccgttcga aatacctgcc
     1021 gcagagttag ctgataagct tgaagtatca caatctgcat taagcagatt gctcaatgga
     1081 aaaactgatc ttagttatga gatggctctt cgactatcta aagttatagg ccgctctgca
     1141 gagtcgtggg ttaatatgca ggctcagtac agcctctcta aaagccgtaa ggctttatcc
     1201 gagacgctag agcatctgca tccgatgttt ccataagtaa aagcccgcga atgcgggctt
     1261 ttcaccatcg aacgctccgc atatctaccg ttcatttgat gtagaagtga ttgttgttaa
     1321 acaccgataa gatgctcatt aactccctga aaaggaaaac aaaatggcaa tttatgtagg
     1381 accacacaac aaaataggtc gtgatggtgg ctcattccaa gaatgtgaca tcaacaccat
     1441 caatcatact gttatccgca aatacggacg atactgcacc attcgagata atgagtacgc
     1501 accaccaaca agcacaccag gccgatactg gctacagatc tatcgaaccc cagataacac
     1561 cgagtaacca aaaatccatc cccagcgaaa gcagccacat tacggtgact atcattaaga
     1621 gtgactagga ctgtcgctct tatttaccat aacatccgtt gcgtgcaccg cctgagaggc
     1681 cctcagggcg tttctgacgg gaaaccggta aaacaggcaa caaaccaccc gaaaacccgc
     1741 cagaaacgcg caggctctgt ttttacggca tgcatgagta tgcgcgcaag tgcatagcgc
     1801 agaatttcac accattcagc cggggtaagt cctgtttccg atgttcttct tatccgaaaa
     1861 cggtgaacgg ggacgcaatt tattgcgtgg ccgtgaggca ttgaccaagc cataaggcac
     1921 ggtaggtaat tgcaggtatc cgacaatttc gagtagagga tccactattt cactacttag
     1981 aattcaaaat cagaatcctt tcttcctgct aaggctatct ctgaatgatt caaccactct
     2041 ttgagattct tcttctgctc gcatgaagtc attcccggac agaaaaaaat cattgtcagg
     2101 cccactggct tcagagaaat tcgtttctgc agcagacaca gaatccacat cagcaagaga
     2161 cggttcatct gtactttttc tcaatctgta aagagcctta tcaaacgcaa ccagtgagat
     2221 attcaggccg taacgttcat tcagcacagt cacaatctct tccctacgga taccattttt
     2281 cttccaggtt tctatatcgt tcttggaatc cctgacagct gcaatggctg ttcttggacc
     2341 agggttaaaa ttcgccatat accgcccata atgtcttaca tttgtctcat aatagtccaa
     2401 aaataagagt aaaacgcaaa aaatgtctta caattgtctt attgttgtcc tttccggttc
     2461 atgtatccat gaaccgcctg atgtggaacg ctttttatcg atctcatgcg ctgccaaaga
     2521 tagattcatt ctttaaaagt caggttacat tatcccttaa atggccatac accatacgca
     2581 accgcgattt tcatcgcaat tgcatgaatt aaaaggtaaa aactgaattt cccgtttatt
     2641 tatgtaatac acaacgtatt acaaccatct gtaatcacat gaaaataaag aaataagatg
     2701 taataccggc gtattacacg tacgctgacc agcgaaaaaa gttataacgc ttccctgccg
     2761 acaggcggcc caaaatccac cggggcgtgc aggttctctt cagtaacctg cgccattaaa
     2821 tcaaaaaggt catattcgcc gggaagctgc gtatcattcg catcccgttg ttcatcatac
     2881 tcagatggca tggggtgata tccagtagct aaggggttgt tagcgggttt cggggcgcag
     2941 ccctgaacca gtcacgtagc gctagcagag tgtatactgg cttactatgt tggcactgat
     3001 gagggtgtca gtgaagtgct tcatgtggca ggagaaaaaa ggctgcaccg gtgcgtcagc
     3061 agaatatgtg atacaggata tattccgctt cctcgctcac tgactcgctg cgctcggtcg
     3121 ttcggctgcg gcgagcggta ccaacttaca ggcggggcgg aaatttcctg ggagatgcca
     3181 agaagaagct taacggagaa gcaataaggc cacggcgaag ccgtttttcc ataggctccg
     3241 cccccctgac aagcatcacg aaatctgacg ctcaaatcag tggtggcgaa acccgacagg
     3301 acttaaagat accaggcgtt tccccctggt ggctccctcg tgcgctctcc tgttcctgcc
     3361 ttttggttta ccggtgtcat tccgctgtta tggccgcgtt tatctcattc cacgcctgac
     3421 actcagttcc gggtaggcag ttcgctccaa gctggactgt atgcacgaac cccccgttca
     3481 gtccgaccgc tgcgccttgt ccggtaacta tcatcttgag tccaacccgg aaagacatgc
     3541 aaaagcgcca ctggcagcag ccactggtaa ctgatttaga ggagttagtc ttgaagttat
     3601 gtgccggtta aggctaaact gaaaggacag atttggttac tgcgctcctc caagccagtt
     3661 accgcggttc aaagagttgg tagctctgag aaccttcgaa aaaccgcctt gcagggcggt
     3721 tttttcg
//
