LOCUS       NZ_CP063346             4664 bp    DNA     circular CON 17-JUN-2023
DEFINITION  Escherichia coli strain BS90R-A plasmid pBS90R-A_5, complete
            sequence.
ACCESSION   NZ_CP063346
VERSION     NZ_CP063346.1
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 4664)
  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  JOURNAL   Unpublished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 4664)
  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
            CP063346.1.
            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..4664
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="BS90R-A"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pBS90R-A_5"
                     /geo_loc_name="Switzerland"
                     /collection_date="2018"
                     /collected_by="Institute for Infectious Diseases Bern"
     gene            complement(join(4257..4664,1..1149))
                     /locus_tag="IN877_RS24440"
                     /old_locus_tag="IN877_24440"
     CDS             complement(join(4257..4664,1..1149))
                     /locus_tag="IN877_RS24440"
                     /old_locus_tag="IN877_24440"
                     /EC_number="2.7.7.65"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_013199864.1"
                     /GO_function="GO:0052621 - diguanylate cyclase activity
                     [Evidence IEA]; GO:0046872 - metal ion binding [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="sensor domain-containing diguanylate cyclase"
                     /protein_id="WP_224630669.1"
                     /translation="MRIKKPHLRPIVITLSVGGILLTSIFLIAVIMVFQRENIEKDLLY
                     ANSSYAMKMSDVMSGYIEMAQGELAYGAKKIKSTNDIDSLKDEADRLRLQSGMFNSVLV
                     VSNDAVVLATSPESLDLVGTRLNSSASKLAVEEKKPFISSPLKSVAGNLIILLSHPIYD
                     KGGNYIGYVGGSIYLKKHSLFGDVLSRHFFKNNTEISIVSDDGNVIFNNDKSAVDRPMV
                     MSDDLKSKLTASDRGEGAFFSSGHRYLLGYASMKNTAWNVLVYSRADSVTTILIAYAKS
                     VLVLLIIIIIVFSLISYFIASSISLPLEKLAISTNAKDIGASLVYIKAINAWYAEADRL
                     KKALFTYIKVMMERVDSLNEVALKDPLTGVNNRLGFLSKIQNHKRDSGCSVIVIDVDFF
                     KEINDSFGHGVGDEVLVSLAHIINSCCRSEDVVCRFGGEEFVVFLPNTSVVTAKCVAER
                     IRSVIESTVFPNNLRVTISAGVATQDDPLGRIDFLLKNADDALYQAKREGRNKVIVYSA
                     I"
                     /name="sensor domain-containing diguanylate cyclase"
     gene            complement(1495..1710)
                     /locus_tag="IN877_RS24445"
                     /old_locus_tag="IN877_24445"
     CDS             complement(1495..1710)
                     /locus_tag="IN877_RS24445"
                     /old_locus_tag="IN877_24445"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137422.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_015589619.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWESAFAEWRTMSGLMQRENA
                     ALSERVTGLSRQVQSLSEQLRRLSSD"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(1714..2199)
                     /locus_tag="IN877_RS24450"
                     /old_locus_tag="IN877_24450"
     CDS             complement(1714..2199)
                     /locus_tag="IN877_RS24450"
                     /old_locus_tag="IN877_24450"
                     /inference="COORDINATES: protein motif:HMM:NF016710.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_012565228.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQNTGEMLKAAFSEHEKSVKAELNESA
                     KRISAAILDHDRKLSSAMSQRTKGMVRMVSQTWLTIVLVSALLIASSAGILWWQGQQIL
                     DNYTTIREQKSTQAMLSERNSGVQLSTCGEQRRRCVKVNPEAGRFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            complement(<2234..2668)
                     /locus_tag="IN877_RS24810"
                     /pseudo=""
     CDS             complement(<2234..2668)
                     /locus_tag="IN877_RS24810"
                     /inference="COORDINATES: protein motif:HMM:NF015397.2"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            complement(2877..3200)
                     /locus_tag="IN877_RS24460"
                     /old_locus_tag="IN877_24460"
     CDS             complement(2877..3200)
                     /locus_tag="IN877_RS24460"
                     /old_locus_tag="IN877_24460"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000957083.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_015059937.1"
                     /translation="MLTMWVTEGEHRRLLERCDGRQLAAWMRQTCLDEKPARSGKLPSI
                     SPALLRQLAGMGNNLNQIARRVNAGGGTGHDRVQIVAALMAIDAGLERLRHAVLEKGTD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     ARG             complement(4258..4664)
                     /name="IND-6"
                     /gene="IND-6"
                     /gene_name="IND beta-lactamase"
                     /tool="rgi"
                     /drug_class="carbapenem"
                     /identity="100.0"
                     /coverage="56.49"
     Typing          complement(3314..3486)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.276"
                     /coverage="100.0"
                     /evalue="9.21e-81"
     Typing          3411..3962
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.639"
                     /coverage="91.0"
                     /evalue="0.0"
     Typing          complement(1392..2887)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.182"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(2884..3200)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.453"
                     /coverage="99.0"
                     /evalue="1.9499999999999998e-60"
ORIGIN
        1 atgattctgt attttactta aaaaccccaa tctattattc acgccggtaa ggggatcttt
       61 aagcgccacc tcatttagag aatcaactct ttccatcatt accttaatat acgtaaaaag
      121 cgccttttta agcctatcag cttcggcata ccaagcattg atagctttaa tataaactag
      181 cgaagctccg atatctttag cattggtaga tatagcaagc ttttctaaag gaagtgaaat
      241 actggaggca atgaaatatg aaataagtga aaacacaata attattataa ttagcagaac
      301 aagtacactt ttagcataag caataagaat agtagtcaca ctgtcagcac gactataaac
      361 caacacattc caagcggtat ttttcatact agcataacca agaagatatc tatgccccga
      421 agaaaaaaat gccccctcac ctctatcaga cgcagttaac tttgatttca aatcatcaga
      481 cataaccata ggccgatcaa cagcactttt atcgttatta aagatcacat tcccatcatc
      541 actaacaatg ctaatttcag tgttgttctt gaaaaaatgc ctgctcaaaa catcgccaaa
      601 taaactatgt ttttttagat atatagaccc accgacatac cctatgtaat tgccaccctt
      661 atcataaata ggatgtgaca acaaaataat caaattccca gcaactgatt ttaacggtga
      721 agatatgaat ggtttctttt cctcaaccgc caatttgctg gcacttgaat tcaagcgggt
      781 accaactaaa tcaagagatt ctggcgaagt cgccagaaca acagcatcat tactaacaac
      841 aagaactgaa ttaaacatac cagactgcaa tcttaaccta tccgcctcat ctttaagtga
      901 gtcaatatca ttagttgatt ttattttttt tgctccatat gctaattcac cttgagccat
      961 ttcaatataa ccactcatta catctgacat tttcatagcg tacgatgaat tagcataaag
     1021 caaatctttt tctatatttt cgcgctgaaa aaccataata acggcaatca gaaaaataga
     1081 agttaacaaa atcccaccaa cggacaaggt tatgactatc ggacgaaggt gaggcttttt
     1141 aattctcata aaaatacact ccatataata aaaaatgccg catttaccat aacatccctt
     1201 atcagcaccg ccccggacgg gttcggaaca aatgcggcgt cagcccggta aaaccggcag
     1261 caaactctcc gctaaaccgc gcattctgcg ccagataaat ttcacccggc tgcatggcta
     1321 tgcagtcggg tgaatggctc cggctttcag cgcagatgtc cgccgaaagc cccgttttat
     1381 caggttatca cagtgaaggg ctgttatacg tccgctgtcg ctgagatcgc tccagctcca
     1441 gcgctttctg atgctgcacc acgcgctcct gctcccggtg cagctcgacg gcattcagtc
     1501 gctcgacaac cggcgcagct gctcgctcaa actctgcacc tgcctgctca agcccgtgac
     1561 gcgctcgctc agcgctgcgt tctcccgttg cataagacca gacatcgtcc gccattccgc
     1621 gaaggcgctc tcccactcgt ccagcctttt cgagtagtcc tgctgtagct gctctaatgc
     1681 gctcagcaac tgtttttcca gctccgtcat gtgctatttc cccgccagta tcatccagct
     1741 cgaatcctct ccgaaccgtc ccgcttccgg gttcaccttc acgcagcggc gtctctgctc
     1801 gccgcaggtc gagagctgca cgccgctgtt cctctctgac agcatggcct gcgtgctctt
     1861 ctgctcccgg atggtcgtgt agttgtcgag tatctgctgc ccctgccacc acagaatgcc
     1921 cgcgctcgag gcgatcagca gcgcggagac caggacgatg gtcagccacg tctggctgac
     1981 catgcgcacc atgcctttcg tgcgctggct catggctgag gacagtttcc ggtcgtggtc
     2041 gaggatggcg gcgctgattc tcttcgcgct ttcgttcagt tccgctttta cagatttctc
     2101 gtgctcgctg aatgcggctt tcagcatctc gccggtattc tgctgctgcg ctttcgattt
     2161 ctgctctaag tccttcgcca gcgttaaaag actgttcata aatggctccc ttcagtcgga
     2221 tgtttcgccc cccgtccggg tcggcaatgc tgatactgct ttttgtggtg cggaccacct
     2281 caaaacctgc gctttccagc gcctcagtga catcctgacg ggttttcagc tccccggatg
     2341 aggcaagagc aagcagaccg cgtgtaatcg cttctgcagc ctcctgcttc gctttaggca
     2401 gtgcagacgg tgtgaccagt gcccgccggt tctccggtgc gttcgggtcg tgcagcccca
     2461 gtctgccgtt cacgatggtc tgccaggcat cgatgcgtgg acggtcggcg cgatcgtaat
     2521 acggctggag ccgtctgccg gtcagcagct ccgtgttcgg gatcagaaaa ttcagctcaa
     2581 gccgcccctt gtcacgatgc tccacccaca ggatgctgta ctggtcttta tcaagtccgg
     2641 gcatcagaac ccgctcaaag cttgccatca gcttttcccg ctggccggaa ggtaaatccg
     2701 cttccgcaaa cgacagtacc ccggaggtgt atttcttaac gtaaggcgac gcgtcaatca
     2761 gctcccggac ttcttccggc ttcccctgca ggacggtggc gccttcacgc tgccggtctt
     2821 tacccagcag atagtccacc ggcccggcgc caccgccgcg accgcgtgga tgaaatttaa
     2881 cgatcatcgt ccgttccttt ctcaagaacg gcgtgccgca gccgctcaag tccggcatcg
     2941 atggccatca gcgccgcaac aatctgcacc ctgtcatggc cggtaccgcc gccggcgtta
     3001 acacggcggg ctatctggtt caggttattg cccatgccgg caagctggcg cagcagcgcc
     3061 ggcgagattg agggaagctt tccggaacgt gccggctttt cgtccaggca ggtctgccgc
     3121 atccacgccg ccagctgcct gccgtcacag cgctcaagca gccgccggtg ctcgccctcc
     3181 gtcacccaca tggtgagcat cttgttccgt ttctctgaca aaccggcctc ctgataacgc
     3241 cgggacgggc gggaaaggct ttcccggtcg gcgcggggtt ggacaagccg caggcgcgtc
     3301 aggcttttgg cgggtttcgg ggcgcagccc tgaaccagtc acgtagcgct agcggagtgt
     3361 atactggctt actatgttgg cacggatgcg agtgtcagtg aagtgcttca tgtggcagga
     3421 gaaaaatgca gcagcggagc gtcagcagaa tatgtgatac aggatatatt ccgcttcctc
     3481 gctcactgac tcgctgcgct cggtcgttcg gctgcggcga gcggtaccga cttacaggcg
     3541 gggcggaaat ttcctgggag atgccaggaa gaagcttaac agggaagcga taaggccacg
     3601 gcgaagccgt ttttccatag gctccgcccc cctgacaagc atcacgaaat ctgacgctca
     3661 aatcagtggt ggcgaaaccc gacaggactt aaagatacca ggcgtttccc cctggtggct
     3721 ccctcgtgcg ctctcctgtt cctgcctttc ggtttaccga tgtcaatccg ctgttatggc
     3781 cgcgtttatc tcattccacg cctgacactc ggttccggga aggcagttcg ctccaagctg
     3841 gactgtatgc acgaaccccc cgttcagccc gactaccacg ttgtcccggt aactatcatc
     3901 ttgagtccaa cccggaacag acacgaaaaa tcgccagtgg cggtagccat tagtaagagg
     3961 attcacggag cggagtagta gagtgttcta cagagttctt gaagtggtgg cctgactgcg
     4021 gctacactgg aaggacagtt ttggtacctg cgctccgtga aagccagtta ccttcggaag
     4081 aaagagttgg tagctctgaa ttccggcaaa cgaaccaccg ttggtagcgg tggttttttt
     4141 gtttacaggg tatgagatta cgacgacatc gaagggataa caagaggatc cgcttcttgc
     4201 ccactcttcg ccacaaaaaa aacgacacac tagcgcgtaa agcatcatca aaaaactcaa
     4261 atagcgctat atacaatcac tttattacgc ccctcccttt tggcttgata aagagcatcg
     4321 tcagcatttt tcagcaaaaa atcgatccta ccaagaggat catcttgtgt tgccacacca
     4381 gcagatatgg tgacccgcaa gttattaggg aagacagtac tttcaataac actcctaata
     4441 cgctccgcaa cacacttagc tgttaccaca gatgtattcg gcaggaaaac aacaaactct
     4501 tcgccaccaa accgacaaac aacatcttca ctacggcaac aggaattaat aatatgagcc
     4561 aaagaaacaa gcacctcatc tccgacccca tgcccgaaac tgtcatttat ctctttaaaa
     4621 aaatcaacat caattacaat aactgaacac cctgaatccc gctt
//
