LOCUS       NZ_CP063347             3461 bp    DNA     circular CON 17-JUN-2023
DEFINITION  Escherichia coli strain BS90R-A plasmid pBS90R-A_6, complete
            sequence.
ACCESSION   NZ_CP063347
VERSION     NZ_CP063347.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16387358
            Assembly: GCF_016942505.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3461)
  AUTHORS   Moser,A.I., Campos-Madueno,E.I. and Endimiani,A.
  TITLE     Complete genome and plasmid sequences of MDR Escherichia coli
            acquired by Swiss travelers in Laos
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3461)
  AUTHORS   Moser,A.I., Campos-Madueno,E.I. and Endimiani,A.
  TITLE     Direct Submission
  JOURNAL   Submitted (20-OCT-2020) 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                   :: 344x
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/17/2023 06:07:55
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,949
            CDSs (total)                      :: 4,830
            Genes (coding)                    :: 4,674
            CDSs (with protein)               :: 4,674
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 156
            CDSs (without protein)            :: 156
            Pseudo Genes (ambiguous residues) :: 0 of 156
            Pseudo Genes (frameshifted)       :: 54 of 156
            Pseudo Genes (incomplete)         :: 103 of 156
            Pseudo Genes (internal stop)      :: 26 of 156
            Pseudo Genes (multiple problems)  :: 25 of 156
            Pseudo Genes (short protein)      :: 3 of 156
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP063347.1.
            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..3461
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="BS90R-A"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pBS90R-A_6"
                     /geo_loc_name="Switzerland"
                     /collection_date="2018"
                     /collected_by="Institute for Infectious Diseases Bern"
     gene            complement(join(3105..3461,1..249))
                     /locus_tag="IN877_RS24465"
                     /old_locus_tag="IN877_24465"
     CDS             complement(join(3105..3461,1..249))
                     /locus_tag="IN877_RS24465"
                     /old_locus_tag="IN877_24465"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012537770.1"
                     /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_224706372.1"
                     /translation="MSGRRFGRLPNWWSRSANGDDFLLMSLKSNDTGTGIAAMKCLLAL
                     SVLIDFHSRIAEVSLSGMEELTGLSRPMVIRGLARLEELGVVVSDKDYRTNRYELTIKS
                     NDSYWAKVPVDTVRKRLKTISNRGIAPFTALKLYITILNLRYKDKTTVQVMHDTLRNYT
                     GIQTNQVRHGLDVLYSSALLHLMPREDRATNEYQILGL"
                     /name="helix-turn-helix domain-containing protein"
     gene            918..1571
                     /locus_tag="IN877_RS24470"
                     /old_locus_tag="IN877_24470"
     CDS             918..1571
                     /locus_tag="IN877_RS24470"
                     /old_locus_tag="IN877_24470"
                     /inference="COORDINATES: protein motif:HMM:NF014045.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="NYN domain-containing protein"
                     /protein_id="WP_074581898.1"
                     /translation="MKKQRTIVYVDGFNLYYGALKDKAGCRWLNIEEMVKSILPSKPTP
                     INDIVAVKYFTAKISSRANHPNQVNHQNIYLKALKTIPNLEVVLGRYDTHIVRSKLAAP
                     IVGVGSYVDVYKTEEKGSDVNLATHLLHDAHTSAFDVAIVITNDSDLALPIEFVVSKLN
                     KKVGVISPYPKASMHLCKVSSFTRVIRRSNITSSQFADQITDSDGTVLVKPTGW"
                     /name="NYN domain-containing protein"
     gene            2471..2671
                     /locus_tag="IN877_RS24475"
                     /old_locus_tag="IN877_24475"
     CDS             2471..2671
                     /locus_tag="IN877_RS24475"
                     /old_locus_tag="IN877_24475"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001558245.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="antitoxin VbhA family protein"
                     /protein_id="WP_085011975.1"
                     /translation="MIDDRTRQLRVDGFRKAEASLRLEGMDPSGTPLYESVKARILSGE
                     ITYGEGRDEILAHYQKRGDRN"
                     /name="antitoxin VbhA family protein"
     Typing          complement(1762..2428)
                     /name="rep_cluster_2324"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="90.76"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ttcttcaagc ctagctaacc cgcggataac cattggtcta ctaagcccgg ttagctcttc
       61 cataccgctt aaagagactt ctgctattcg agaatgaaaa tcaatgagca cagacaaggc
      121 tagcagacac ttcattgccg caattcctgt tcctgtgtca ttagatttta ggctcattaa
      181 tagaaaatca tctccattcg cggagcgcga ccaccaattt ggaagcctgc caaaacgtct
      241 gccactcatt ttaattccat ttcttttcta aaaacgagaa aaataccttt attatcatga
      301 atataaaaaa catggcacct agtgatacta ttgcaaccaa agcttcaggt ggtgccgaag
      361 ctaaagtaga aattatgttg tttagagttt ccataaacct cagcctccta aggtgatcgt
      421 cgagactgaa agttttaaca ccacactaca atactaatct agattaagcg atattttatt
      481 tttgtgaact tattcataaa attcaaatac ttaatcattg ttttccatgt tttttactag
      541 taaatgggag agctataaat gcaaaataat gcgggttgag atggtgtttt ttagcttaat
      601 aattaatcac atggtaaatg acaagcaagg ccgatagagg tcctagatcc catggctaca
      661 agtaagttgt tgattttttc tatcaccatg ctacaattag acttggcgag cttgctaaag
      721 caagctcgcc aagtctaatt gtagcatggt gaattttttt ggttgcaagt tttatacttc
      781 cgtatagaat ttgcatcact acccagcgtt ctgcgctggc gcgagggcaa cctcagcaaa
      841 aaatatacaa cctcgcacta cggtgcgacc gcgaaacctc cctagtggag gtttcagcat
      901 atatggacat aacaaaaatg aaaaaacaaa gaacgattgt ttatgtcgac ggattcaact
      961 tatattatgg tgctctaaaa gataaagctg ggtgccgctg gttgaatatc gaagagatgg
     1021 ttaaatcaat acttccatca aagcctacac ctattaatga tatagttgca gttaaatact
     1081 tcactgcgaa aatatcatca agagcaaacc atcctaatca ggttaatcat caaaatatat
     1141 accttaaagc tttaaaaaca attcctaatc ttgaagtcgt attgggccgc tatgacaccc
     1201 acatagtgcg ttctaagctt gctgcgccga tagtaggcgt agggtcatat gttgatgttt
     1261 ataaaacaga agaaaaaggt tcagatgtaa accttgcaac gcatttatta catgatgctc
     1321 atacttctgc ttttgatgtc gccatagtta ttaccaacga ctctgattta gcattgccta
     1381 ttgaatttgt tgttagcaaa ttaaacaaga aggttggggt gatttcccca tacccgaaag
     1441 ctagcatgca tttatgcaaa gtatcttctt ttactagggt tataagacgt tcgaatataa
     1501 ctagctcgca gtttgctgat caaattacgg atagtgatgg taccgtttta gtgaaaccta
     1561 ctggatggtg acgtcgcttg acgtttagag gatgaaacgc gtatctttct atggaaacga
     1621 aaaaaccacc ctggcaggtg gttttttcga aggttaaaaa tcctggcaga ttcttaacca
     1681 aggtaactgg ctttaacgga gcgcagtcac caaaactgtc ctttcagtgt agctgtagtt
     1741 aggctgacac ttcaagaact ctatgtgtac ttgcatgtac tttcccgctc cgtgaaccag
     1801 ctaccaatgg ctaccgccag tggcgctttg tcgtgtcttt cagggttgga ttcaagagta
     1861 cagttacctg aataggcgcg gtagtcgggt tgaacgggga gttcgtgcat acagcccagc
     1921 ttggagcgaa ccacctacaa ggaactcagt tgcacgggta ggaatgagaa aacgccacct
     1981 tacggcggtc tgcaacgggt aaacctcagg gtgggaacag gagagcgcac gagggagcga
     2041 cccatcggaa acggtgggga tctttaagtc ctgtcgggtt tcgccacttc tgatttgagc
     2101 tccggaaatt gcctgatttc tgtgagtctc gtcaggaggg cgaagcctat ggaaaaccgg
     2161 caacgtccca gttctctttt actctccgcc atggccttct gcctgagcaa gtacaagtaa
     2221 cgctcgccgc agcgtcatga ccgaacgaag tgagcgaatg accgaggaag cgtaatgtct
     2281 gtaatgctga acagggctcg tatcgctcgg tactcctgtt tcctctccaa ttacatatcc
     2341 ggttgcaacg gtttcctgtc gttttccact tttgtctgca cagctataca acggcaagat
     2401 tcgggcagga tatgtaaagt gggcccactt tacgcctgcc ttattcgcat gactgctcaa
     2461 cggaaaaccc atgattgatg atcgtacacg acaacttcgt gtagacggat tccgtaaggc
     2521 cgaggcttct ctccggcttg aaggcatgga cccctccgga actccgctct atgaatcggt
     2581 taaggcgcgt attctttccg gtgagatcac ctatggagaa ggccgtgatg aaatactggc
     2641 tcattaccag aagcgcggtg accgcaactg acgcggacaa gatgtgtctt tggagtaccg
     2701 ccggcacgcc aaagcctctt ggtcaggctc cgcccgacac cctgaaaaat ttcgacgcgt
     2761 cgaaatttct gcgtgctgat cacccacgtt aaatctgctc tcctcatgtt gctcagccat
     2821 gcctgacggc ctggccaacg cctcacggtc gcacagtaaa ctgcgcaccc gttcaccgtt
     2881 atcggggaag ttaatcaccg aaaatccgcc tttagtgcca gcatccgccc gaaatcggct
     2941 gctattcact cgtatgcata gccatgcagg cgcgcagaaa tcatcagggg cactttttag
     3001 ggatctggag agggaaagat gccggaaacg gcccggacgc gtcaggatcg cgctgagggc
     3061 ctctcagggg gtgcgggcaa gggatgttat ggtaaatatg gatgctatag gcctaatatt
     3121 tgatactcat ttgtcgcacg gtcttcacgc ggcatgaggt gaagcagagc actgctgtat
     3181 agcacatcaa gaccatgtct tacctggttt gtctgaattc cggtgtagtt tctgagtgta
     3241 tcgtgcatga cttgaacagt tgttttatct ttgtacctta gattcaatat tgttatgtac
     3301 aattttaaag cagtgaatgg tgcaatccct ctattggata tggttttaag tctttttcgg
     3361 actgtatcga caggaacttt tgcccagtaa ctgtcattac tttttatcgt aagttcatac
     3421 cggtttgttc tgtaatcctt gtcagagaca acaactccta g
//
