LOCUS       NZ_CP086524             4440 bp    DNA     circular CON 28-MAY-2024
DEFINITION  Escherichia coli strain Ec-042-T20-ESBL plasmid pEc-042-T20-ESBL_4,
            complete sequence.
ACCESSION   NZ_CP086524
VERSION     NZ_CP086524.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN22108720
            Assembly: GCF_022759885.1
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  JOURNAL   Unpublished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                   :: 273x
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_022759885.1-RS_2024_05_28
            Annotation Date                   :: 05/28/2024 04:43:01
            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)                     :: 4,717
            CDSs (total)                      :: 4,596
            Genes (coding)                    :: 4,365
            CDSs (with protein)               :: 4,365
            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
            CP086524.1.
            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-T20-ESBL"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pEc-042-T20-ESBL_4"
                     /geo_loc_name="Switzerland"
                     /collection_date="2019"
                     /collected_by="Institute for Infectious Diseases Bern"
     gene            complement(1161..1583)
                     /locus_tag="LNN45_RS23430"
                     /old_locus_tag="LNN45_23425"
     CDS             complement(1161..1583)
                     /locus_tag="LNN45_RS23430"
                     /old_locus_tag="LNN45_23425"
                     /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(1583..1774)
                     /locus_tag="LNN45_RS23435"
                     /old_locus_tag="LNN45_23430"
     CDS             complement(1583..1774)
                     /locus_tag="LNN45_RS23435"
                     /old_locus_tag="LNN45_23430"
                     /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(2255..2404)
                     /locus_tag="LNN45_RS23440"
                     /old_locus_tag="LNN45_23435"
     CDS             complement(2255..2404)
                     /locus_tag="LNN45_RS23440"
                     /old_locus_tag="LNN45_23435"
                     /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            3311..4225
                     /locus_tag="LNN45_RS23445"
                     /old_locus_tag="LNN45_23440"
     CDS             3311..4225
                     /locus_tag="LNN45_RS23445"
                     /old_locus_tag="LNN45_23440"
                     /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          2560..3071
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.686"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 ttgatgaaaa aaaacgtttt taatctaact aaacttacct gcctggcttt aataaagagc
       61 ttaaaaatgg tacaatcaac catccaagca attgttttat aaagtcaatt agcgttccat
      121 cagacaaaaa ataatggaga gaaaggagaa tgaaaacaat gaaaacgttc tttaaggtta
      181 aaaatctttt aaaatcaatg agatacttaa agcgtttcct gtcactgaat gcgacagtga
      241 aacgcgagtg cgcggtggtg tgtaacacct tcgctgtcgc attcagtgac aggcactagt
      301 ttatcacaaa aaacgataaa agtcaatata accaacactt taaaaccaaa cattttagct
      361 actcgaaacg gtaattttaa cgaagccctc ccccccccct caatacaaac ccgaatatta
      421 agctatttac cataacatcc cttgcgtgca ccacctgaga ggccctcagg gcgtttctga
      481 cgggaaaccg gcaaaacaga caacaaacca cccgaaaacc cgccagaaac gcgcaggctc
      541 tgtttttacg gcatgcatga gtatgcgcgc aagtgcatag cgcggaaatt cacgccattc
      601 agccggggta agtcctgttt ccggcgttct tcccatccga aaacggtgaa cggggacgca
      661 atttattgcg tggccgtgaa gcgttgccgg cgcagccgga aaaccggttt tcagcacgtt
      721 caggaatcgg gttcgtcgac ggccggcaat cacgttatgg caagtcgccg gacgactcac
      781 cacacgattc accggcgatt cgactcgtga cttgactcta gagtcaccac ggtcaaaaaa
      841 acgccaaatc gacgattcga ctctagagtc aagtcgtcat aagttactga tagtgtggag
      901 tgagtcgtcg atgactctat gacgagtcgt cggcaagtcg tacacgaatc accgacgact
      961 tggattgacc ttacagaagg taatactgcg taatttaata acaaccaact aactgatatt
     1021 aatgaattat ctgcaaaaat ttaattttgc gtggggtgtg gatattttta gtgtgaggag
     1081 cgttcagagg tctgacgatt tttgggaagg ttcacgaacg ccccggcatg gccggagagg
     1141 aaaactcaag catggcggga tcaggatttt ttccagaatt tccaccacgg ggaatggggt
     1201 ggtgaagaag gttcgtgctt gtgctccaga agctgcatag cctgacgaag ggaatcaata
     1261 tgctcatctc gagccttaac agccccttta agaccatcgt tttcagcttc aagtaaagcg
     1321 attctatgtt gtaaatcatg taaaccaacg ctgttaatac ctgtagattc tgcgtcactt
     1381 tttacatcat attttacagc atcgattaca ccatcaagag aaccaaacac tctaataagc
     1441 tctgatgtat caataacttt aatacccttc ccgtgcttta caacagaggt gtaacttaac
     1501 ttaccactgt taatcatctt gtaaatagta gggcgactaa ccttaacaag ccgtgctgct
     1561 tcactaatag acactctggc catcagttac catcctgtaa tgcatccagt ctcgaggaca
     1621 gtgtacggaa aagatgctcc gcatcatcgt ggagtttctc acaaaggtcg gcctcagcat
     1681 cgagatcaag ctcgttaagc ttctccagca ggagcagaga ctgattctgg atgaatttag
     1741 ccatgttcag cgcagttttc tgttgtttcg tcataaggga cctcagagca tcagtgctca
     1801 gtgtaaaacc ggtaaggggg tcggatgtac gaatggttca gagaacggat ctgaggtaat
     1861 cctgtagtta ttttgtagtt tatctgtagt catcgcacta aaaatcagga ttaagtcatc
     1921 agcttttgta gtctttctgt agtttacctg tagtccggaa aaataatccg ttcatgcgag
     1981 catgaacgag gtcgttaatg acgttttttt gtcaccgacg ccccttaacc tccgcagatc
     2041 acccggccag aatgataatt gtttggccct taaatggtca tacacctaac gcagccgcga
     2101 ttttcatcgc aactgcatga attaaaaggt aaaaattgaa acctccgttt atttatgtaa
     2161 tacgcaacgt attacaatca cctgtaacca catgaaaata aagaaataaa atgtaatacc
     2221 ggcgtattac cacgtacgcg ggcaagcgaa aaagctataa cgcttcccgg ccgacaggtg
     2281 gcccggaatc cacaggggcg tgcaggttct cttcagtaac ctgcgccatt aaatcaaaaa
     2341 ggtcatattc gccgggaagc tgcgtatcag tcgaatccag ttgttcatca tattcagatg
     2401 gcatggggtg atatccagta gctgagaggt tgttagcggg tttcggggcg cagccctgaa
     2461 ccagtcaaat agcacgtgcg gagtgtatac gggctcaata tgctacggtg gagtaacacg
     2521 ttatgagagt gcgtcatgtg acagaggaaa gtgcagcggc ggggcgtacg ggagaaaatg
     2581 gaaacccggg gatatgacgc ctcctcgctc actcagtcgc tgccgctcct gccgttcggc
     2641 tgcggcgggc gttacctgca cacggataag agcaaagaca tacggcatga caagcggggc
     2701 agcaaaagaa tgcgccgctg ccgtttttcc ataggctccg cccccctgac aagcatcaca
     2761 gaatcggacg ctcaaatcag tggtggcgaa acccgacagg actataaaga tatcaggcgt
     2821 ttccccctga tggctccctc gtgcgctctc ctgttcctgc ctttcggttt accggtgtca
     2881 ttccgctgtt atggccgcgt ttgtctcatt ccacgcctga cactcagttc cgggtaggca
     2941 gttcgctcca agctggactg tatgcacgac ccccccgttc agtccgaccg ctgcgcctta
     3001 tccggtaact atcgtcttga gtccaacccg gatagacgtg caaatgcgcc actggcaacg
     3061 gccactggta agcaggatgt gcgagagatg tatcgagagt tcttgaagtg gaggccttag
     3121 tgaggctaca ctggaaggac agatttggtg acatgtctcg cacaagactg ttaccacggt
     3181 tcagaaactt gccggttaat gaaccttcga aaaaccacct tgccgggtgg ttttttcgtt
     3241 tcatactcta caactatgct gagccatatg gcaacatcaa ttcataccta catatgaaga
     3301 agcgatgccc atgcctaaca ccgttaatta tccgcaaata atcccgttca tatcgaaagg
     3361 gaaaatggat gctataaaaa acactttcgg taatacctta acagacaggg aatgctacgg
     3421 gatatatata tggtcgcaaa aagcgtctgc tgcaatatac cctctcctac agcagttaga
     3481 ggtaacgctt aggaactcaa tagataaaga agcaacaaat gttatgggtc tgaactggtg
     3541 ggatggagtc tatacagata aaaccaaacc taaatgggat gattttattt tcaacataaa
     3601 caaaggccga gatagatata agaagaatta taaaaaaaac aacccatctg tactcagctc
     3661 tttgattgtc gttccgcatg atgacgctat agctcatact gacttttaca catggcaagc
     3721 ggtcctaagt gacacatttc acacgcaaaa tagaaaacac gtaaataaat ctctctggcc
     3781 aaggcttact tacaaggtgc taaaaggtct agacagaaaa aaaacagaga aagcagcaag
     3841 gcttgatttt atcaacgaac taaatgagat aagaaattac agaaacagat tatcgcacaa
     3901 tgactgtata tggataaaaa tgaactccaa taacttacag tccgcagtgg aaacagttag
     3961 agaaaaaata aataaaattg aagacttaat aaaaacaatt aaccctcaaa tacattcgac
     4021 cctggttaaa tggggagttt tctaccatgc gagaagaatt tgctctcaaa gagaggttga
     4081 gcatcatatg gggaaaaaca tagtaaactg caccaaccca actatgagct ctattttagc
     4141 aaccatttac tcatggacgg acgatggaaa gctaaccagc gtcgtgaatg acggtaaaaa
     4201 cgaccttgcg atacataagt tctagaagga gaaaaggccc gacatgctaa gcatgtcgag
     4261 ccttttccaa gtcttttgcc aatatcacct tacggcggag cgtggccttt attccattat
     4321 aaataatgca taaaagcgaa agctctaggc ttcattaaaa atgattctac atcacttact
     4381 caaaaaagag caagacctta tgtcacaagg gatcacacga gcagccgtaa atgacttaac
//
