LOCUS       NZ_CP086536             4440 bp    DNA     circular CON 28-MAY-2024
DEFINITION  Escherichia coli strain Ec-042-T5-ESBL plasmid pEc-042-T5-ESBL_4,
            complete sequence.
ACCESSION   NZ_CP086536
VERSION     NZ_CP086536.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN22108718
            Assembly: GCF_022759845.1
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  JOURNAL   Unpublished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                   :: 325x
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_022759845.1-RS_2024_05_28
            Annotation Date                   :: 05/28/2024 04:37:50
            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)                     :: 4,718
            CDSs (total)                      :: 4,597
            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)              :: 232
            CDSs (without protein)            :: 232
            Pseudo Genes (ambiguous residues) :: 0 of 232
            Pseudo Genes (frameshifted)       :: 64 of 232
            Pseudo Genes (incomplete)         :: 155 of 232
            Pseudo Genes (internal stop)      :: 41 of 232
            Pseudo Genes (multiple problems)  :: 25 of 232
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP086536.1.
            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-ESBL"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pEc-042-T5-ESBL_4"
                     /geo_loc_name="Switzerland"
                     /collection_date="2019"
                     /collected_by="Institute for Infectious Diseases Bern"
     gene            172..1086
                     /locus_tag="LNN41_RS23435"
                     /old_locus_tag="LNN41_23430"
     CDS             172..1086
                     /locus_tag="LNN41_RS23435"
                     /old_locus_tag="LNN41_23430"
                     /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(2462..2884)
                     /locus_tag="LNN41_RS23440"
                     /old_locus_tag="LNN41_23435"
     CDS             complement(2462..2884)
                     /locus_tag="LNN41_RS23440"
                     /old_locus_tag="LNN41_23435"
                     /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(2884..3075)
                     /locus_tag="LNN41_RS23445"
                     /old_locus_tag="LNN41_23440"
     CDS             complement(2884..3075)
                     /locus_tag="LNN41_RS23445"
                     /old_locus_tag="LNN41_23440"
                     /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(3556..3705)
                     /locus_tag="LNN41_RS23450"
                     /old_locus_tag="LNN41_23445"
     CDS             complement(3556..3705)
                     /locus_tag="LNN41_RS23450"
                     /old_locus_tag="LNN41_23445"
                     /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          3861..4372
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.686"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 cagatttggt gacatgtctc gcacaagact gttaccacgg ttcagaaact tgccggttaa
       61 tgaaccttcg aaaaaccacc ttgccgggtg gttttttcgt ttcatactct acaactatgc
      121 tgagccatat ggcaacatca attcatacct acatatgaag aagcgatgcc catgcctaac
      181 accgttaatt atccgcaaat aatcccgttc atatcgaaag ggaaaatgga tgctataaaa
      241 aacactttcg gtaatacctt aacagacagg gaatgctacg ggatatatat atggtcgcaa
      301 aaagcgtctg ctgcaatata ccctctccta cagcagttag aggtaacgct taggaactca
      361 atagataaag aagcaacaaa tgttatgggt ctgaactggt gggatggagt ctatacagat
      421 aaaaccaaac ctaaatggga tgattttatt ttcaacataa acaaaggccg agatagatat
      481 aagaagaatt ataaaaaaaa caacccatct gtactcagct ctttgattgt cgttccgcat
      541 gatgacgcta tagctcatac tgacttttac acatggcaag cggtcctaag tgacacattt
      601 cacacgcaaa atagaaaaca cgtaaataaa tctctctggc caaggcttac ttacaaggtg
      661 ctaaaaggtc tagacagaaa aaaaacagag aaagcagcaa ggcttgattt tatcaacgaa
      721 ctaaatgaga taagaaatta cagaaacaga ttatcgcaca atgactgtat atggataaaa
      781 atgaactcca ataacttaca gtccgcagtg gaaacagtta gagaaaaaat aaataaaatt
      841 gaagacttaa taaaaacaat taaccctcaa atacattcga ccctggttaa atggggagtt
      901 ttctaccatg cgagaagaat ttgctctcaa agagaggttg agcatcatat ggggaaaaac
      961 atagtaaact gcaccaaccc aactatgagc tctattttag caaccattta ctcatggacg
     1021 gacgatggaa agctaaccag cgtcgtgaat gacggtaaaa acgaccttgc gatacataag
     1081 ttctagaagg agaaaaggcc cgacatgcta agcatgtcga gccttttcca agtcttttgc
     1141 caatatcacc ttacggcgga gcgtggcctt tattccatta taaataatgc ataaaagcga
     1201 aagctctagg cttcattaaa aatgattcta catcacttac tcaaaaaaga gcaagacctt
     1261 atgtcacaag ggatcacacg agcagccgta aatgacttaa cttgatgaaa aaaaacgttt
     1321 ttaatctaac taaacttacc tgcctggctt taataaagag cttaaaaatg gtacaatcaa
     1381 ccatccaagc aattgtttta taaagtcaat tagcgttcca tcagacaaaa aataatggag
     1441 agaaaggaga atgaaaacaa tgaaaacgtt ctttaaggtt aaaaatcttt taaaatcaat
     1501 gagatactta aagcgtttcc tgtcactgaa tgcgacagtg aaacgcgagt gcgcggtggt
     1561 gtgtaacacc ttcgctgtcg cattcagtga caggcactag tttatcacaa aaaacgataa
     1621 aagtcaatat aaccaacact ttaaaaccaa acattttagc tactcgaaac ggtaatttta
     1681 acgaagccct cccccccccc tcaatacaaa cccgaatatt aagctattta ccataacatc
     1741 ccttgcgtgc accacctgag aggccctcag ggcgtttctg acgggaaacc ggcaaaacag
     1801 acaacaaacc acccgaaaac ccgccagaaa cgcgcaggct ctgtttttac ggcatgcatg
     1861 agtatgcgcg caagtgcata gcgcggaaat tcacgccatt cagccggggt aagtcctgtt
     1921 tccggcgttc ttcccatccg aaaacggtga acggggacgc aatttattgc gtggccgtga
     1981 agcgttgccg gcgcagccgg aaaaccggtt ttcagcacgt tcaggaatcg ggttcgtcga
     2041 cggccggcaa tcacgttatg gcaagtcgcc ggacgactca ccacacgatt caccggcgat
     2101 tcgactcgtg acttgactct agagtcacca cggtcaaaaa aacgccaaat cgacgattcg
     2161 actctagagt caagtcgtca taagttactg atagtgtgga gtgagtcgtc gatgactcta
     2221 tgacgagtcg tcggcaagtc gtacacgaat caccgacgac ttggattgac cttacagaag
     2281 gtaatactgc gtaatttaat aacaaccaac taactgatat taatgaatta tctgcaaaaa
     2341 tttaattttg cgtggggtgt ggatattttt agtgtgagga gcgttcagag gtctgacgat
     2401 ttttgggaag gttcacgaac gccccggcat ggccggagag gaaaactcaa gcatggcggg
     2461 atcaggattt tttccagaat ttccaccacg gggaatgggg tggtgaagaa ggttcgtgct
     2521 tgtgctccag aagctgcata gcctgacgaa gggaatcaat atgctcatct cgagccttaa
     2581 cagccccttt aagaccatcg ttttcagctt caagtaaagc gattctatgt tgtaaatcat
     2641 gtaaaccaac gctgttaata cctgtagatt ctgcgtcact ttttacatca tattttacag
     2701 catcgattac accatcaaga gaaccaaaca ctctaataag ctctgatgta tcaataactt
     2761 taataccctt cccgtgcttt acaacagagg tgtaacttaa cttaccactg ttaatcatct
     2821 tgtaaatagt agggcgacta accttaacaa gccgtgctgc ttcactaata gacactctgg
     2881 ccatcagtta ccatcctgta atgcatccag tctcgaggac agtgtacgga aaagatgctc
     2941 cgcatcatcg tggagtttct cacaaaggtc ggcctcagca tcgagatcaa gctcgttaag
     3001 cttctccagc aggagcagag actgattctg gatgaattta gccatgttca gcgcagtttt
     3061 ctgttgtttc gtcataaggg acctcagagc atcagtgctc agtgtaaaac cggtaagggg
     3121 gtcggatgta cgaatggttc agagaacgga tctgaggtaa tcctgtagtt attttgtagt
     3181 ttatctgtag tcatcgcact aaaaatcagg attaagtcat cagcttttgt agtctttctg
     3241 tagtttacct gtagtccgga aaaataatcc gttcatgcga gcatgaacga ggtcgttaat
     3301 gacgtttttt tgtcaccgac gccccttaac ctccgcagat cacccggcca gaatgataat
     3361 tgtttggccc ttaaatggtc atacacctaa cgcagccgcg attttcatcg caactgcatg
     3421 aattaaaagg taaaaattga aacctccgtt tatttatgta atacgcaacg tattacaatc
     3481 acctgtaacc acatgaaaat aaagaaataa aatgtaatac cggcgtatta ccacgtacgc
     3541 gggcaagcga aaaagctata acgcttcccg gccgacaggt ggcccggaat ccacaggggc
     3601 gtgcaggttc tcttcagtaa cctgcgccat taaatcaaaa aggtcatatt cgccgggaag
     3661 ctgcgtatca gtcgaatcca gttgttcatc atattcagat ggcatggggt gatatccagt
     3721 agctgagagg ttgttagcgg gtttcggggc gcagccctga accagtcaaa tagcacgtgc
     3781 ggagtgtata cgggctcaat atgctacggt ggagtaacac gttatgagag tgcgtcatgt
     3841 gacagaggaa agtgcagcgg cggggcgtac gggagaaaat ggaaacccgg ggatatgacg
     3901 cctcctcgct cactcagtcg ctgccgctcc tgccgttcgg ctgcggcggg cgttacctgc
     3961 acacggataa gagcaaagac atacggcatg acaagcgggg cagcaaaaga atgcgccgct
     4021 gccgtttttc cataggctcc gcccccctga caagcatcac agaatcggac gctcaaatca
     4081 gtggtggcga aacccgacag gactataaag atatcaggcg tttccccctg atggctccct
     4141 cgtgcgctct cctgttcctg cctttcggtt taccggtgtc attccgctgt tatggccgcg
     4201 tttgtctcat tccacgcctg acactcagtt ccgggtaggc agttcgctcc aagctggact
     4261 gtatgcacga cccccccgtt cagtccgacc gctgcgcctt atccggtaac tatcgtcttg
     4321 agtccaaccc ggatagacgt gcaaatgcgc cactggcaac ggccactggt aagcaggatg
     4381 tgcgagagat gtatcgagag ttcttgaagt ggaggcctta gtgaggctac actggaagga
//
