LOCUS       NZ_CP063340             2149 bp    DNA     circular CON 17-JUN-2023
DEFINITION  Escherichia coli strain BS74R-D plasmid pBS74R-D_8, complete
            sequence.
ACCESSION   NZ_CP063340
VERSION     NZ_CP063340.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16387362
            Assembly: GCF_016942475.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 2149)
  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  JOURNAL   Unpublished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 2149)
  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                   :: Flye v. 2.7.1
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 445x
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/17/2023 06:02:34
            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)                     :: 5,200
            CDSs (total)                      :: 5,077
            Genes (coding)                    :: 4,781
            CDSs (with protein)               :: 4,781
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 90
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 296
            CDSs (without protein)            :: 296
            Pseudo Genes (ambiguous residues) :: 0 of 296
            Pseudo Genes (frameshifted)       :: 82 of 296
            Pseudo Genes (incomplete)         :: 207 of 296
            Pseudo Genes (internal stop)      :: 46 of 296
            Pseudo Genes (multiple problems)  :: 38 of 296
            Pseudo Genes (short protein)      :: 4 of 296
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP063340.1.
            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..2149
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="BS74R-D"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pBS74R-D_8"
                     /geo_loc_name="Switzerland"
                     /collection_date="2018"
                     /collected_by="Institute for Infectious Diseases Bern"
     gene            join(1843..2149,1..17)
                     /locus_tag="IN878_RS25575"
                     /old_locus_tag="IN878_25590"
     CDS             join(1843..2149,1..17)
                     /locus_tag="IN878_RS25575"
                     /old_locus_tag="IN878_25590"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_205561505.1"
                     /translation="MSLNMTFSITEVREGRIGSLVITKELYDKLEKYSRSNGLITSTYD
                     HGHGVVRYYTVKYCLQMNYHGQNHPQKYLIKRGGRYPSKYAMVKKTVEELEYSTPTFEY
                     AGT"
                     /name="hypothetical protein"
     gene            complement(886..1077)
                     /locus_tag="IN878_RS25580"
                     /old_locus_tag="IN878_25595"
     CDS             complement(886..1077)
                     /locus_tag="IN878_RS25580"
                     /old_locus_tag="IN878_25595"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041614.1"
                     /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_001041614.1"
                     /translation="MNKQQKTAVNMAKFIQDQSLLLLDRLNELDLDHEADFCEKLHEDA
                     ERLYRSLSARLNEQQDGA"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1496..1609
                     /locus_tag="IN878_RS25585"
                     /old_locus_tag="IN878_25600"
     CDS             1496..1609
                     /locus_tag="IN878_RS25585"
                     /old_locus_tag="IN878_25600"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_071789001.1"
                     /translation="MHEPPVQSDCCALSGNYRLESNPVRHAKAPLAAATGN"
                     /name="replication initiation protein"
     Typing          1254..1609
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="97.207"
                     /coverage="87.0"
                     /evalue="2.13e-170"
ORIGIN
        1 aatatgcagg aacatagcaa taaaataccc acacatggtc aagtttgcta attacatatc
       61 agaaacccca ttaaaaggct tcgccgcaac ctttaataac tccgttggta atgattaagt
      121 gttatttacc ataacatccc ttgcccgcac cgcctcaggc gccctcagag cgtttctgac
      181 gggaaaccgg caaaacaggc aacaaaccac ccgaaaaccc gccagaaacg cgcaggctct
      241 gtttttacgg catgaatgag tatgcgcaca agtgcatagc gcggaaattc acgccattca
      301 gccggggtaa gtcctgtttc cgatgttctt cttacccgaa aacggtgaac ggggacgcaa
      361 tttattgcgt ggccgtgagg cgttgccggc gcagccggaa aacccgtttt cagcacgttc
      421 aggaaggggg gcgatgtacg aatggttcag ggaacggatc tgaggtaatc cggtagttac
      481 tttgtagttt atctgtagtt ttcttgtagt ctattagtag tctgccacgt tttttgtagt
      541 tttcttgtag tctgccatca ctaatgcaaa acgttttttg tagtttatct gtagtttttg
      601 gttgctcaga tggtcatgca agcatgacca tcaaagaata ggacgcttta tagccaaata
      661 acccttaacc tacggagagc gccctaccaa aaatgatgat tttttaaccc ttaaatggtc
      721 atacacctaa cgcagccgcg attttcatcg caacttcatg aaaaataaat aaaaaagaaa
      781 aaatacaggg attctgggta ttaccggggt aataatgtta agcgccaaga caatgaaaat
      841 taaggcgatg ccggtattac tccggtaata cccagaacgg agccattacg caccgtcctg
      901 ctgctcattc aggcgcgctg acaggcttcg gtaaaggcgt tccgcatcct catggagttt
      961 ctcgcagaaa tcagcctcat gatccagatc cagctcatta agcctgtcca gaagaagcag
     1021 ggactgatcc tggatgaatt tagccatgtt aacggcagtc ttttgttgtt tgttcatgaa
     1081 ggccccggcg cgaaagtgct tactgtacgt tctgatggtt ttccgcttcc tcgctcattc
     1141 gctcactccg ttcggtcatg agtctgcggc gagcggaggg aagataagca gataacataa
     1201 cggtaagcat aacgaaagct aaggacaagg gcgaaaaggc cacgccccgc cggggcgttt
     1261 ttccataggc tccgcccccc tgacaagcat cacgaaatct gacgctcaaa tcagtggtgg
     1321 cgaaacccga caggactata aagataccag gcgtttcccc ctggtggctc cctcgtgcgc
     1381 tctcctgttc ctgcctttcg gtttaccggt gtcattccgc tgttatggcc gcgtttgtct
     1441 cattccacgc ctgacactca gttccgggaa ggcagttcgc tccaagctgg actgtatgca
     1501 cgaacccccc gttcagtccg actgctgcgc cttatccggt aactatcgtc ttgagtccaa
     1561 cccggtaaga catgcaaaag cgccactggc agcagccact ggtaactgat ttagaggaga
     1621 tggacttgaa gtcatgtgcc ggttaaggct aaactgaaag gacaagtttt ggtgactgcg
     1681 ctcctccaag ccagttacct cggttcaaag agttggtagc tctgagaacc ttcgaaaaac
     1741 cgccctgcaa ggcggttttt tcgtttctgg ataagagact acgacgacag acggataatc
     1801 tcaagaaaat cctctctaac aggttatatt cagagtaaaa aagtgagctt aaatatgact
     1861 ttttcaataa cagaagtgcg tgaggggcgt atcggctctt tagttattac aaaagagctt
     1921 tacgataaat tagaaaaata ctctcgctca aatggattaa taacatccac atacgaccat
     1981 ggtcatggcg ttgttagata ctacaccgtg aaatattgcc tccagatgaa ctatcacgga
     2041 caaaatcatc ctcaaaaata tcttattaaa agagggggga gatatcccag caagtatgca
     2101 atggtcaaaa aaaccgttga agagttagag tattcaacac cgacatttg
//
