LOCUS       NZ_CP086543             3727 bp    DNA     circular CON 28-MAY-2024
DEFINITION  Escherichia coli strain Ec-042-T5-MAC plasmid pEc-042-T5-MAC_5,
            complete sequence.
ACCESSION   NZ_CP086543
VERSION     NZ_CP086543.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN22108717
            Assembly: GCF_022759825.1
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  JOURNAL   Unpublished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                   :: 430x
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_022759825.1-RS_2024_05_28
            Annotation Date                   :: 05/28/2024 04:46:35
            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)                     :: 4,724
            CDSs (total)                      :: 4,603
            Genes (coding)                    :: 4,372
            CDSs (with protein)               :: 4,372
            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
            CP086543.1.
            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-MAC"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pEc-042-T5-MAC_5"
                     /geo_loc_name="Switzerland"
                     /collection_date="2019"
                     /collected_by="Institute for Infectious Diseases Bern"
     gene            join(3594..3727,1..70)
                     /locus_tag="LNN52_RS23480"
                     /old_locus_tag="LNN52_23475"
     CDS             join(3594..3727,1..70)
                     /locus_tag="LNN52_RS23480"
                     /old_locus_tag="LNN52_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(493..861)
                     /locus_tag="LNN52_RS23485"
                     /old_locus_tag="LNN52_23480"
     CDS             complement(493..861)
                     /locus_tag="LNN52_RS23485"
                     /old_locus_tag="LNN52_23480"
                     /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(1245..1394)
                     /locus_tag="LNN52_RS23490"
                     /old_locus_tag="LNN52_23485"
     CDS             complement(1245..1394)
                     /locus_tag="LNN52_RS23490"
                     /old_locus_tag="LNN52_23485"
                     /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            complement(2552..2833)
                     /locus_tag="LNN52_RS23495"
                     /old_locus_tag="LNN52_23490"
     CDS             complement(2552..2833)
                     /locus_tag="LNN52_RS23495"
                     /old_locus_tag="LNN52_23490"
                     /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            3227..3466
                     /locus_tag="LNN52_RS23500"
                     /old_locus_tag="LNN52_23495"
     CDS             3227..3466
                     /locus_tag="LNN52_RS23500"
                     /old_locus_tag="LNN52_23495"
                     /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"
     Typing          complement(1430..1603)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.143"
                     /coverage="100.0"
                     /evalue="5.58e-78"
     Typing          1527..2073
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.935"
                     /coverage="90.0"
                     /evalue="0.0"
ORIGIN
        1 cgcaccacca acaagcacac caggccgata ctggctacag atctatcgaa ccccagataa
       61 caccgagtaa ccaaaaatcc atccccagcg aaagcagcca cattacggtg actatcatta
      121 agagtgacta ggactgtcgc tcttatttac cataacatcc gttgcgtgca ccgcctgaga
      181 ggccctcagg gcgtttctga cgggaaaccg gtaaaacagg caacaaacca cccgaaaacc
      241 cgccagaaac gcgcaggctc tgtttttacg gcatgcatga gtatgcgcgc aagtgcatag
      301 cgcagaattt cacaccattc agccggggta agtcctgttt ccgatgttct tcttatccga
      361 aaacggtgaa cggggacgca atttattgcg tggccgtgag gcattgacca agccataagg
      421 cacggtaggt aattgcaggt atccgacaat ttcgagtaga ggatccacta tttcactact
      481 tagaattcaa aatcagaatc ctttcttcct gctaaggcta tctctgaatg attcaaccac
      541 tctttgagat tcttcttctg ctcgcatgaa gtcattcccg gacagaaaaa aatcattgtc
      601 aggcccactg gcttcagaga aattcgtttc tgcagcagac acagaatcca catcagcaag
      661 agacggttca tctgtacttt ttctcaatct gtaaagagcc ttatcaaacg caaccagtga
      721 gatattcagg ccgtaacgtt cattcagcac agtcacaatc tcttccctac ggataccatt
      781 tttcttccag gtttctatat cgttcttgga atccctgaca gctgcaatgg ctgttcttgg
      841 accagggtta aaattcgcca tataccgccc ataatgtctt acatttgtct cataatagtc
      901 caaaaataag agtaaaacgc aaaaaatgtc ttacaattgt cttattgttg tcctttccgg
      961 ttcatgtatc catgaaccgc ctgatgtgga acgcttttta tcgatctcat gcgctgccaa
     1021 agatagattc attctttaaa agtcaggtta cattatccct taaatggcca tacaccatac
     1081 gcaaccgcga ttttcatcgc aattgcatga attaaaaggt aaaaactgaa tttcccgttt
     1141 atttatgtaa tacacaacgt attacaacca tctgtaatca catgaaaata aagaaataag
     1201 atgtaatacc ggcgtattac acgtacgctg accagcgaaa aaagttataa cgcttccctg
     1261 ccgacaggcg gcccaaaatc caccggggcg tgcaggttct cttcagtaac ctgcgccatt
     1321 aaatcaaaaa ggtcatattc gccgggaagc tgcgtatcat tcgcatcccg ttgttcatca
     1381 tactcagatg gcatggggtg atatccagta gctaaggggt tgttagcggg tttcggggcg
     1441 cagccctgaa ccagtcacgt agcgctagca gagtgtatac tggcttacta tgttggcact
     1501 gatgagggtg tcagtgaagt gcttcatgtg gcaggagaaa aaaggctgca ccggtgcgtc
     1561 agcagaatat gtgatacagg atatattccg cttcctcgct cactgactcg ctgcgctcgg
     1621 tcgttcggct gcggcgagcg gtaccaactt acaggcgggg cggaaatttc ctgggagatg
     1681 ccaagaagaa gcttaacgga gaagcaataa ggccacggcg aagccgtttt tccataggct
     1741 ccgcccccct gacaagcatc acgaaatctg acgctcaaat cagtggtggc gaaacccgac
     1801 aggacttaaa gataccaggc gtttccccct ggtggctccc tcgtgcgctc tcctgttcct
     1861 gccttttggt ttaccggtgt cattccgctg ttatggccgc gtttatctca ttccacgcct
     1921 gacactcagt tccgggtagg cagttcgctc caagctggac tgtatgcacg aaccccccgt
     1981 tcagtccgac cgctgcgcct tgtccggtaa ctatcatctt gagtccaacc cggaaagaca
     2041 tgcaaaagcg ccactggcag cagccactgg taactgattt agaggagtta gtcttgaagt
     2101 tatgtgccgg ttaaggctaa actgaaagga cagatttggt tactgcgctc ctccaagcca
     2161 gttaccgcgg ttcaaagagt tggtagctct gagaaccttc gaaaaaccgc cttgcagggc
     2221 ggttttttcg tttcgaacat aagatacgct ttgtcgatta aatcagtcaa ggacgaaccc
     2281 taaaagcctc aatcgcttat ggaattattc ttgcaggaaa catgcttctg caccgtatca
     2341 gctccagtac acaaaacagc aacaaacaag aaccaccccc acccattcaa gtctcgaact
     2401 gcaagaaccc ctgcgatgac gacacacagc aaagggaaca acaaaatcat aaaggctctc
     2461 ataaaatcct ccagagggac ttttttttga ataaagtccc taatccatcc atattcaggt
     2521 caggatggat tagcaactta ctttttgatt actaatgata atcttcaagg tcgacgtcta
     2581 agacgttagg ttcttccacc ttgaaaacta ccctccagtt tccgttaacc tctacggaaa
     2641 actcaccttt acggtcacct ttgagggggt gacatcccaa cgccctaaca tccacaatat
     2701 cttgaaggca tgttgcggtg cttagcgtag ccaatatcat gcgaagtttt ttcgctaaat
     2761 ggggctgaat tccggcggtg ctaccgtctt cagcaaagct ccgaagtcct ttatgtttta
     2821 tgttttttat catctataat ctccataaaa atctcgtcga tatctgtctc tataaacaga
     2881 aaacaattta acagcgtcca tttgaacccc ttgcattatt aaaataattg acgtaagttt
     2941 gtctctgagg tcgattacct cgtttgactt ccatgagcga taaccataca atatggcgcc
     3001 ttgaaaaagt caatctatga caccatatta gcggtagctt tctgctccac agagcatcct
     3061 aaagcttact gctttttttg tcaataacag acacttgcac attgtgcaat gcgcaatacg
     3121 aaagaaaaca aaatgttttg tgtaatcaaa tacaaaacca actgaggaag gcatgataaa
     3181 tctttacgat cctgtacacc ccggtgagtt catcagggaa atgttcatgg aaccgttcga
     3241 aatacctgcc gcagagttag ctgataagct tgaagtatca caatctgcat taagcagatt
     3301 gctcaatgga aaaactgatc ttagttatga gatggctctt cgactatcta aagttatagg
     3361 ccgctctgca gagtcgtggg ttaatatgca ggctcagtac agcctctcta aaagccgtaa
     3421 ggctttatcc gagacgctag agcatctgca tccgatgttt ccataagtaa aagcccgcga
     3481 atgcgggctt ttcaccatcg aacgctccgc atatctaccg ttcatttgat gtagaagtga
     3541 ttgttgttaa acaccgataa gatgctcatt aactccctga aaaggaaaac aaaatggcaa
     3601 tttatgtagg accacacaac aaaataggtc gtgatggtgg ctcattccaa gaatgtgaca
     3661 tcaacaccat caatcatact gttatccgca aatacggacg atactgcacc attcgagata
     3721 atgagta
//
