LOCUS       NZ_CP086542             4440 bp    DNA     circular CON 28-MAY-2024
DEFINITION  Escherichia coli strain Ec-042-T5-MAC plasmid pEc-042-T5-MAC_4,
            complete sequence.
ACCESSION   NZ_CP086542
VERSION     NZ_CP086542.1
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 4440)
  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  JOURNAL   Unpublished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 4440)
  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
            CP086542.1.
            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..4440
                     /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_4"
                     /geo_loc_name="Switzerland"
                     /collection_date="2019"
                     /collected_by="Institute for Infectious Diseases Bern"
     gene            complement(1289..1711)
                     /locus_tag="LNN52_RS23460"
                     /old_locus_tag="LNN52_23455"
     CDS             complement(1289..1711)
                     /locus_tag="LNN52_RS23460"
                     /old_locus_tag="LNN52_23455"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005229777.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_004216558.1"
                     /translation="MARVSISEAARLVKVSRPTIYKMINSGKLSYTSVVKHGKGIKVID
                     TSELIRVFGSLDGVIDAVKYDVKSDAESTGINSVGLHDLQHRIALLEAENDGLKGAVKA
                     RDEHIDSLRQAMQLLEHKHEPSSPPHSPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(1711..1902)
                     /locus_tag="LNN52_RS23465"
                     /old_locus_tag="LNN52_23460"
     CDS             complement(1711..1902)
                     /locus_tag="LNN52_RS23465"
                     /old_locus_tag="LNN52_23460"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000166328.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_000166328.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLEKLNELDLDAEADLCEKLHDDA
                     EHLFRTLSSRLDALQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(2383..2532)
                     /locus_tag="LNN52_RS23470"
                     /old_locus_tag="LNN52_23465"
     CDS             complement(2383..2532)
                     /locus_tag="LNN52_RS23470"
                     /old_locus_tag="LNN52_23465"
                     /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_017880354.1"
                     /translation="MPSEYDEQLDSTDTQLPGEYDLFDLMAQVTEENLHAPVDSGPPVG
                     REAL"
                     /name="hypothetical protein"
     gene            3439..4353
                     /locus_tag="LNN52_RS23475"
                     /old_locus_tag="LNN52_23470"
     CDS             3439..4353
                     /locus_tag="LNN52_RS23475"
                     /old_locus_tag="LNN52_23470"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001448734.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Abi family protein"
                     /protein_id="WP_017880353.1"
                     /translation="MPNTVNYPQIIPFISKGKMDAIKNTFGNTLTDRECYGIYIWSQKA
                     SAAIYPLLQQLEVTLRNSIDKEATNVMGLNWWDGVYTDKTKPKWDDFIFNINKGRDRYK
                     KNYKKNNPSVLSSLIVVPHDDAIAHTDFYTWQAVLSDTFHTQNRKHVNKSLWPRLTYKV
                     LKGLDRKKTEKAARLDFINELNEIRNYRNRLSHNDCIWIKMNSNNLQSAVETVREKINK
                     IEDLIKTINPQIHSTLVKWGVFYHARRICSQREVEHHMGKNIVNCTNPTMSSILATIYS
                     WTDDGKLTSVVNDGKNDLAIHKF"
                     /name="Abi family protein"
     Typing          2688..3199
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.686"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 tccattataa ataatgcata aaagcgaaag ctctaggctt cattaaaaat gattctacat
       61 cacttactca aaaaagagca agaccttatg tcacaaggga tcacacgagc agccgtaaat
      121 gacttaactt gatgaaaaaa aacgttttta atctaactaa acttacctgc ctggctttaa
      181 taaagagctt aaaaatggta caatcaacca tccaagcaat tgttttataa agtcaattag
      241 cgttccatca gacaaaaaat aatggagaga aaggagaatg aaaacaatga aaacgttctt
      301 taaggttaaa aatcttttaa aatcaatgag atacttaaag cgtttcctgt cactgaatgc
      361 gacagtgaaa cgcgagtgcg cggtggtgtg taacaccttc gctgtcgcat tcagtgacag
      421 gcactagttt atcacaaaaa acgataaaag tcaatataac caacacttta aaaccaaaca
      481 ttttagctac tcgaaacggt aattttaacg aagccctccc ccccccctca atacaaaccc
      541 gaatattaag ctatttacca taacatccct tgcgtgcacc acctgagagg ccctcagggc
      601 gtttctgacg ggaaaccggc aaaacagaca acaaaccacc cgaaaacccg ccagaaacgc
      661 gcaggctctg tttttacggc atgcatgagt atgcgcgcaa gtgcatagcg cggaaattca
      721 cgccattcag ccggggtaag tcctgtttcc ggcgttcttc ccatccgaaa acggtgaacg
      781 gggacgcaat ttattgcgtg gccgtgaagc gttgccggcg cagccggaaa accggttttc
      841 agcacgttca ggaatcgggt tcgtcgacgg ccggcaatca cgttatggca agtcgccgga
      901 cgactcacca cacgattcac cggcgattcg actcgtgact tgactctaga gtcaccacgg
      961 tcaaaaaaac gccaaatcga cgattcgact ctagagtcaa gtcgtcataa gttactgata
     1021 gtgtggagtg agtcgtcgat gactctatga cgagtcgtcg gcaagtcgta cacgaatcac
     1081 cgacgacttg gattgacctt acagaaggta atactgcgta atttaataac aaccaactaa
     1141 ctgatattaa tgaattatct gcaaaaattt aattttgcgt ggggtgtgga tatttttagt
     1201 gtgaggagcg ttcagaggtc tgacgatttt tgggaaggtt cacgaacgcc ccggcatggc
     1261 cggagaggaa aactcaagca tggcgggatc aggatttttt ccagaatttc caccacgggg
     1321 aatggggtgg tgaagaaggt tcgtgcttgt gctccagaag ctgcatagcc tgacgaaggg
     1381 aatcaatatg ctcatctcga gccttaacag cccctttaag accatcgttt tcagcttcaa
     1441 gtaaagcgat tctatgttgt aaatcatgta aaccaacgct gttaatacct gtagattctg
     1501 cgtcactttt tacatcatat tttacagcat cgattacacc atcaagagaa ccaaacactc
     1561 taataagctc tgatgtatca ataactttaa tacccttccc gtgctttaca acagaggtgt
     1621 aacttaactt accactgtta atcatcttgt aaatagtagg gcgactaacc ttaacaagcc
     1681 gtgctgcttc actaatagac actctggcca tcagttacca tcctgtaatg catccagtct
     1741 cgaggacagt gtacggaaaa gatgctccgc atcatcgtgg agtttctcac aaaggtcggc
     1801 ctcagcatcg agatcaagct cgttaagctt ctccagcagg agcagagact gattctggat
     1861 gaatttagcc atgttcagcg cagttttctg ttgtttcgtc ataagggacc tcagagcatc
     1921 agtgctcagt gtaaaaccgg taagggggtc ggatgtacga atggttcaga gaacggatct
     1981 gaggtaatcc tgtagttatt ttgtagttta tctgtagtca tcgcactaaa aatcaggatt
     2041 aagtcatcag cttttgtagt ctttctgtag tttacctgta gtccggaaaa ataatccgtt
     2101 catgcgagca tgaacgaggt cgttaatgac gtttttttgt caccgacgcc ccttaacctc
     2161 cgcagatcac ccggccagaa tgataattgt ttggccctta aatggtcata cacctaacgc
     2221 agccgcgatt ttcatcgcaa ctgcatgaat taaaaggtaa aaattgaaac ctccgtttat
     2281 ttatgtaata cgcaacgtat tacaatcacc tgtaaccaca tgaaaataaa gaaataaaat
     2341 gtaataccgg cgtattacca cgtacgcggg caagcgaaaa agctataacg cttcccggcc
     2401 gacaggtggc ccggaatcca caggggcgtg caggttctct tcagtaacct gcgccattaa
     2461 atcaaaaagg tcatattcgc cgggaagctg cgtatcagtc gaatccagtt gttcatcata
     2521 ttcagatggc atggggtgat atccagtagc tgagaggttg ttagcgggtt tcggggcgca
     2581 gccctgaacc agtcaaatag cacgtgcgga gtgtatacgg gctcaatatg ctacggtgga
     2641 gtaacacgtt atgagagtgc gtcatgtgac agaggaaagt gcagcggcgg ggcgtacggg
     2701 agaaaatgga aacccgggga tatgacgcct cctcgctcac tcagtcgctg ccgctcctgc
     2761 cgttcggctg cggcgggcgt tacctgcaca cggataagag caaagacata cggcatgaca
     2821 agcggggcag caaaagaatg cgccgctgcc gtttttccat aggctccgcc cccctgacaa
     2881 gcatcacaga atcggacgct caaatcagtg gtggcgaaac ccgacaggac tataaagata
     2941 tcaggcgttt ccccctgatg gctccctcgt gcgctctcct gttcctgcct ttcggtttac
     3001 cggtgtcatt ccgctgttat ggccgcgttt gtctcattcc acgcctgaca ctcagttccg
     3061 ggtaggcagt tcgctccaag ctggactgta tgcacgaccc ccccgttcag tccgaccgct
     3121 gcgccttatc cggtaactat cgtcttgagt ccaacccgga tagacgtgca aatgcgccac
     3181 tggcaacggc cactggtaag caggatgtgc gagagatgta tcgagagttc ttgaagtgga
     3241 ggccttagtg aggctacact ggaaggacag atttggtgac atgtctcgca caagactgtt
     3301 accacggttc agaaacttgc cggttaatga accttcgaaa aaccaccttg ccgggtggtt
     3361 ttttcgtttc atactctaca actatgctga gccatatggc aacatcaatt catacctaca
     3421 tatgaagaag cgatgcccat gcctaacacc gttaattatc cgcaaataat cccgttcata
     3481 tcgaaaggga aaatggatgc tataaaaaac actttcggta ataccttaac agacagggaa
     3541 tgctacggga tatatatatg gtcgcaaaaa gcgtctgctg caatataccc tctcctacag
     3601 cagttagagg taacgcttag gaactcaata gataaagaag caacaaatgt tatgggtctg
     3661 aactggtggg atggagtcta tacagataaa accaaaccta aatgggatga ttttattttc
     3721 aacataaaca aaggccgaga tagatataag aagaattata aaaaaaacaa cccatctgta
     3781 ctcagctctt tgattgtcgt tccgcatgat gacgctatag ctcatactga cttttacaca
     3841 tggcaagcgg tcctaagtga cacatttcac acgcaaaata gaaaacacgt aaataaatct
     3901 ctctggccaa ggcttactta caaggtgcta aaaggtctag acagaaaaaa aacagagaaa
     3961 gcagcaaggc ttgattttat caacgaacta aatgagataa gaaattacag aaacagatta
     4021 tcgcacaatg actgtatatg gataaaaatg aactccaata acttacagtc cgcagtggaa
     4081 acagttagag aaaaaataaa taaaattgaa gacttaataa aaacaattaa ccctcaaata
     4141 cattcgaccc tggttaaatg gggagttttc taccatgcga gaagaatttg ctctcaaaga
     4201 gaggttgagc atcatatggg gaaaaacata gtaaactgca ccaacccaac tatgagctct
     4261 attttagcaa ccatttactc atggacggac gatggaaagc taaccagcgt cgtgaatgac
     4321 ggtaaaaacg accttgcgat acataagttc tagaaggaga aaaggcccga catgctaagc
     4381 atgtcgagcc ttttccaagt cttttgccaa tatcacctta cggcggagcg tggcctttat
//
