LOCUS       NZ_CP086548             4440 bp    DNA     circular CON 28-MAY-2024
DEFINITION  Escherichia coli strain Ec-042-T0 plasmid pEc-042-T0_4, complete
            sequence.
ACCESSION   NZ_CP086548
VERSION     NZ_CP086548.1
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 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  JOURNAL   Unpublished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                   :: 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
            CP086548.1.
            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-T0"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pEc-042-T0_4"
                     /geo_loc_name="Switzerland"
                     /collection_date="2019"
                     /collected_by="Institute for Infectious Diseases Bern"
     gene            667..1581
                     /locus_tag="LNN55_RS23440"
                     /old_locus_tag="LNN55_23435"
     CDS             667..1581
                     /locus_tag="LNN55_RS23440"
                     /old_locus_tag="LNN55_23435"
                     /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"
     gene            complement(2957..3379)
                     /locus_tag="LNN55_RS23445"
                     /old_locus_tag="LNN55_23440"
     CDS             complement(2957..3379)
                     /locus_tag="LNN55_RS23445"
                     /old_locus_tag="LNN55_23440"
                     /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(3379..3570)
                     /locus_tag="LNN55_RS23450"
                     /old_locus_tag="LNN55_23445"
     CDS             complement(3379..3570)
                     /locus_tag="LNN55_RS23450"
                     /old_locus_tag="LNN55_23445"
                     /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(4051..4200)
                     /locus_tag="LNN55_RS23455"
                     /old_locus_tag="LNN55_23450"
     CDS             complement(4051..4200)
                     /locus_tag="LNN55_RS23455"
                     /old_locus_tag="LNN55_23450"
                     /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"
     Typing          2..427
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.253"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 gcgggcgtta cctgcacacg gataagagca aagacatacg gcatgacaag cggggcagca
       61 aaagaatgcg ccgctgccgt ttttccatag gctccgcccc cctgacaagc atcacagaat
      121 cggacgctca aatcagtggt ggcgaaaccc gacaggacta taaagatatc aggcgtttcc
      181 ccctgatggc tccctcgtgc gctctcctgt tcctgccttt cggtttaccg gtgtcattcc
      241 gctgttatgg ccgcgtttgt ctcattccac gcctgacact cagttccggg taggcagttc
      301 gctccaagct ggactgtatg cacgaccccc ccgttcagtc cgaccgctgc gccttatccg
      361 gtaactatcg tcttgagtcc aacccggata gacgtgcaaa tgcgccactg gcaacggcca
      421 ctggtaagca ggatgtgcga gagatgtatc gagagttctt gaagtggagg ccttagtgag
      481 gctacactgg aaggacagat ttggtgacat gtctcgcaca agactgttac cacggttcag
      541 aaacttgccg gttaatgaac cttcgaaaaa ccaccttgcc gggtggtttt ttcgtttcat
      601 actctacaac tatgctgagc catatggcaa catcaattca tacctacata tgaagaagcg
      661 atgcccatgc ctaacaccgt taattatccg caaataatcc cgttcatatc gaaagggaaa
      721 atggatgcta taaaaaacac tttcggtaat accttaacag acagggaatg ctacgggata
      781 tatatatggt cgcaaaaagc gtctgctgca atataccctc tcctacagca gttagaggta
      841 acgcttagga actcaataga taaagaagca acaaatgtta tgggtctgaa ctggtgggat
      901 ggagtctata cagataaaac caaacctaaa tgggatgatt ttattttcaa cataaacaaa
      961 ggccgagata gatataagaa gaattataaa aaaaacaacc catctgtact cagctctttg
     1021 attgtcgttc cgcatgatga cgctatagct catactgact tttacacatg gcaagcggtc
     1081 ctaagtgaca catttcacac gcaaaataga aaacacgtaa ataaatctct ctggccaagg
     1141 cttacttaca aggtgctaaa aggtctagac agaaaaaaaa cagagaaagc agcaaggctt
     1201 gattttatca acgaactaaa tgagataaga aattacagaa acagattatc gcacaatgac
     1261 tgtatatgga taaaaatgaa ctccaataac ttacagtccg cagtggaaac agttagagaa
     1321 aaaataaata aaattgaaga cttaataaaa acaattaacc ctcaaataca ttcgaccctg
     1381 gttaaatggg gagttttcta ccatgcgaga agaatttgct ctcaaagaga ggttgagcat
     1441 catatgggga aaaacatagt aaactgcacc aacccaacta tgagctctat tttagcaacc
     1501 atttactcat ggacggacga tggaaagcta accagcgtcg tgaatgacgg taaaaacgac
     1561 cttgcgatac ataagttcta gaaggagaaa aggcccgaca tgctaagcat gtcgagcctt
     1621 ttccaagtct tttgccaata tcaccttacg gcggagcgtg gcctttattc cattataaat
     1681 aatgcataaa agcgaaagct ctaggcttca ttaaaaatga ttctacatca cttactcaaa
     1741 aaagagcaag accttatgtc acaagggatc acacgagcag ccgtaaatga cttaacttga
     1801 tgaaaaaaaa cgtttttaat ctaactaaac ttacctgcct ggctttaata aagagcttaa
     1861 aaatggtaca atcaaccatc caagcaattg ttttataaag tcaattagcg ttccatcaga
     1921 caaaaaataa tggagagaaa ggagaatgaa aacaatgaaa acgttcttta aggttaaaaa
     1981 tcttttaaaa tcaatgagat acttaaagcg tttcctgtca ctgaatgcga cagtgaaacg
     2041 cgagtgcgcg gtggtgtgta acaccttcgc tgtcgcattc agtgacaggc actagtttat
     2101 cacaaaaaac gataaaagtc aatataacca acactttaaa accaaacatt ttagctactc
     2161 gaaacggtaa ttttaacgaa gccctccccc ccccctcaat acaaacccga atattaagct
     2221 atttaccata acatcccttg cgtgcaccac ctgagaggcc ctcagggcgt ttctgacggg
     2281 aaaccggcaa aacagacaac aaaccacccg aaaacccgcc agaaacgcgc aggctctgtt
     2341 tttacggcat gcatgagtat gcgcgcaagt gcatagcgcg gaaattcacg ccattcagcc
     2401 ggggtaagtc ctgtttccgg cgttcttccc atccgaaaac ggtgaacggg gacgcaattt
     2461 attgcgtggc cgtgaagcgt tgccggcgca gccggaaaac cggttttcag cacgttcagg
     2521 aatcgggttc gtcgacggcc ggcaatcacg ttatggcaag tcgccggacg actcaccaca
     2581 cgattcaccg gcgattcgac tcgtgacttg actctagagt caccacggtc aaaaaaacgc
     2641 caaatcgacg attcgactct agagtcaagt cgtcataagt tactgatagt gtggagtgag
     2701 tcgtcgatga ctctatgacg agtcgtcggc aagtcgtaca cgaatcaccg acgacttgga
     2761 ttgaccttac agaaggtaat actgcgtaat ttaataacaa ccaactaact gatattaatg
     2821 aattatctgc aaaaatttaa ttttgcgtgg ggtgtggata tttttagtgt gaggagcgtt
     2881 cagaggtctg acgatttttg ggaaggttca cgaacgcccc ggcatggccg gagaggaaaa
     2941 ctcaagcatg gcgggatcag gattttttcc agaatttcca ccacggggaa tggggtggtg
     3001 aagaaggttc gtgcttgtgc tccagaagct gcatagcctg acgaagggaa tcaatatgct
     3061 catctcgagc cttaacagcc cctttaagac catcgttttc agcttcaagt aaagcgattc
     3121 tatgttgtaa atcatgtaaa ccaacgctgt taatacctgt agattctgcg tcacttttta
     3181 catcatattt tacagcatcg attacaccat caagagaacc aaacactcta ataagctctg
     3241 atgtatcaat aactttaata cccttcccgt gctttacaac agaggtgtaa cttaacttac
     3301 cactgttaat catcttgtaa atagtagggc gactaacctt aacaagccgt gctgcttcac
     3361 taatagacac tctggccatc agttaccatc ctgtaatgca tccagtctcg aggacagtgt
     3421 acggaaaaga tgctccgcat catcgtggag tttctcacaa aggtcggcct cagcatcgag
     3481 atcaagctcg ttaagcttct ccagcaggag cagagactga ttctggatga atttagccat
     3541 gttcagcgca gttttctgtt gtttcgtcat aagggacctc agagcatcag tgctcagtgt
     3601 aaaaccggta agggggtcgg atgtacgaat ggttcagaga acggatctga ggtaatcctg
     3661 tagttatttt gtagtttatc tgtagtcatc gcactaaaaa tcaggattaa gtcatcagct
     3721 tttgtagtct ttctgtagtt tacctgtagt ccggaaaaat aatccgttca tgcgagcatg
     3781 aacgaggtcg ttaatgacgt ttttttgtca ccgacgcccc ttaacctccg cagatcaccc
     3841 ggccagaatg ataattgttt ggcccttaaa tggtcataca cctaacgcag ccgcgatttt
     3901 catcgcaact gcatgaatta aaaggtaaaa attgaaacct ccgtttattt atgtaatacg
     3961 caacgtatta caatcacctg taaccacatg aaaataaaga aataaaatgt aataccggcg
     4021 tattaccacg tacgcgggca agcgaaaaag ctataacgct tcccggccga caggtggccc
     4081 ggaatccaca ggggcgtgca ggttctcttc agtaacctgc gccattaaat caaaaaggtc
     4141 atattcgccg ggaagctgcg tatcagtcga atccagttgt tcatcatatt cagatggcat
     4201 ggggtgatat ccagtagctg agaggttgtt agcgggtttc ggggcgcagc cctgaaccag
     4261 tcaaatagca cgtgcggagt gtatacgggc tcaatatgct acggtggagt aacacgttat
     4321 gagagtgcgt catgtgacag aggaaagtgc agcggcgggg cgtacgggag aaaatggaaa
     4381 cccggggata tgacgcctcc tcgctcactc agtcgctgcc gctcctgccg ttcggctgcg
//
