LOCUS       NZ_CP099757             5156 bp    DNA     circular CON 29-SEP-2023
DEFINITION  Escherichia coli strain 806883-9-2019 plasmid p806883-9-2019c,
            complete sequence.
ACCESSION   NZ_CP099757
VERSION     NZ_CP099757.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN29187367
            Assembly: GCF_025232475.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5156)
  AUTHORS   Fernandez,J.E., Seth-Smith,H.M.B., Nordmann,P., Egli,A.,
            Endimiani,A. and Perreten,V.
  TITLE     Intra and inter-species spread of a novel conjugative
            multidrug-resistant IncC plasmid co-harbouring blaOXA-181 and armA
            in a cystic fibrosis patient
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5156)
  AUTHORS   Fernandez,J.E. and Perreten,V.
  TITLE     Direct Submission
  JOURNAL   Submitted (21-JUN-2022) Institute of Veterinary Bacteriology,
            University of Bern, Laenggassstrasse 122, Bern 3012, Switzerland
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: MAR-2022
            Assembly Method                   :: Unicycler v. 0.4.9b
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 38x
            Sequencing Technology :: Illumina NextSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 09/29/2023 07:30:18
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,257
            CDSs (total)                      :: 5,141
            Genes (coding)                    :: 4,934
            CDSs (with protein)               :: 4,934
            Genes (RNA)                       :: 116
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 207
            CDSs (without protein)            :: 207
            Pseudo Genes (ambiguous residues) :: 0 of 207
            Pseudo Genes (frameshifted)       :: 81 of 207
            Pseudo Genes (incomplete)         :: 138 of 207
            Pseudo Genes (internal stop)      :: 38 of 207
            Pseudo Genes (multiple problems)  :: 45 of 207
            Pseudo Genes (short protein)      :: 5 of 207
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP099757.1.
            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..5156
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="806883-9-2019"
                     /isolation_source="Rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="p806883-9-2019c"
                     /geo_loc_name="Switzerland: Basel"
                     /lat_lon="47.5617 N 7.58339 E"
                     /collection_date="2019"
                     /collected_by="University Hospital Basel"
     gene            1..915
                     /locus_tag="NH020_RS26130"
                     /old_locus_tag="NH020_26130"
     CDS             1..915
                     /locus_tag="NH020_RS26130"
                     /old_locus_tag="NH020_26130"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001738986.1"
                     /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_001271348.1"
                     /translation="MSAALQYFDENLPHRPYHTDDLAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDREGAAIDWSDRNAPAPNITVKNPVNGHAHLLYALNIAVRTAPDASVKA
                     LKYAAAVERSLCEKLCADVNYSGLICKNPFHLEWLVMEWREEAYTLDELADYLDLSASE
                     RRSIDKHYGMGRNCHLFEMTRKWAYRAIRQGWPAFSQWLEAVIQRVEMYNASLPVPLSL
                     AECRAIGKSIAKYTHRNFTPETFAQYVADTHTPEIQAARGRKGGSKSKRSTVATSARTL
                     KPWEALGISRAWYYQLKKRGLVE"
                     /name="replication initiation protein"
     gene            complement(1109..1507)
                     /locus_tag="NH020_RS26135"
                     /old_locus_tag="NH020_26135"
     CDS             complement(1109..1507)
                     /locus_tag="NH020_RS26135"
                     /old_locus_tag="NH020_26135"
                     /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_001222914.1"
                     /translation="MRISNIEWLKKRIGFIRKLGEQTARQRQIIDLIDNEAGLTEQERK
                     LLHVLATAEKNDLQAQESERKQAVQKRIEGKKQRRERNHRLFLAAGLLIEAGLVDTKTG
                     ELCYKKDRILQALKELKYDLETSPNPDA"
                     /name="hypothetical protein"
     gene            1684..2610
                     /locus_tag="NH020_RS26140"
                     /old_locus_tag="NH020_26140"
     CDS             1684..2610
                     /locus_tag="NH020_RS26140"
                     /old_locus_tag="NH020_26140"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221102.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobA/MobL family protein"
                     /protein_id="WP_001331297.1"
                     /translation="MATYHLSVKFGGKGQAANHADYIERKEKYRDRQDLEYSAHGNMPE
                     WARDNPSHFWQAADQFERANGSTYRELEIALPRELTPEQRLELVQDFVRQEAGERHAWS
                     FAIHNPKASIDGGEQPHAHIMMSQRVNDGIERTPEQYFRRYNARYPERGGAKKDSGSLT
                     LTQQKEQLRELRKRWEVKHNEHMRKHGFERGFIDCRTLKEQGIERRPEVHLGFEAAGRL
                     DDAQRHDIMQKRSEPDYSRHLEQARTVGHDIREWLDTPVKQHELVRRLQHDVAREHGFD
                     MRDRVSRQNRTAPERVKSPSRGFSMGF"
                     /name="MobA/MobL family protein"
     gene            2613..3146
                     /locus_tag="NH020_RS26145"
                     /old_locus_tag="NH020_26145"
     CDS             2613..3146
                     /locus_tag="NH020_RS26145"
                     /old_locus_tag="NH020_26145"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221103.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000168770.1"
                     /translation="MASTEEKLLTLLLSVEHLQHTAMEQQKAVADSLAVARETLRGYRD
                     ISDGVAKQVRDEVRNEVQKLDVAGLIGERISQDFQRLEESVANMKANADALNRDIATIH
                     SNIVQEYNTLKGYSWKWLGGVSVAFLVMFCVLGWGMKTILDRNYNATAAVYQKVVTLED
                     KLVEKPVTGKSRKN"
                     /name="hypothetical protein"
     gene            complement(3212..3421)
                     /locus_tag="NH020_RS26150"
                     /old_locus_tag="NH020_26150"
     CDS             complement(3212..3421)
                     /locus_tag="NH020_RS26150"
                     /old_locus_tag="NH020_26150"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001618649.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001096196.1"
                     /translation="MAKLGENTPHIIDATVDFMASSQAFREYLKKLPPDNTIPPALTDE
                     HVPLYIRRLEYYRLLYRPKQTESY"
                     /name="hypothetical protein"
     gene            complement(4569..4877)
                     /locus_tag="NH020_RS26155"
                     /old_locus_tag="NH020_26155"
     CDS             complement(4569..4877)
                     /locus_tag="NH020_RS26155"
                     /old_locus_tag="NH020_26155"
                     /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_023909142.1"
                     /translation="MALHNYARKRCAIGFVRSEHRTAQNDKFSPLVRGALTGFPVSKLH
                     ISPGQKKTDLGSVARIRVYGKYFSYRMLNIHKRKKCLSDALKQPFQKESALYDARKR"
                     /name="hypothetical protein"
     Typing          2..776
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.778"
                     /coverage="83.0"
                     /evalue="0.0"
     Typing          1685..2607
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.052"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atgagcgccg cgcttcaata cttcgacgaa aatttacccc atcgtcccta tcacacggat
       61 gatctcgctt ttggtcttcg catctccggc aaagggcgtg cgcttcttgc gcggtacata
      121 cagcagaacc agcctcatgc gcagttctgg ctggtttttg acgttgaccg cgagggggct
      181 gcgattgact ggagcgaccg gaacgctccc gcgccgaaca tcaccgttaa aaatcctgtg
      241 aacggacacg ctcacctgct ctacgcactc aacatcgccg tgagaaccgc gcctgatgcc
      301 tcggttaagg cgctgaaata tgccgcagcg gttgaacgtt cgctgtgtga gaaactttgt
      361 gcggatgtga actacagcgg cctgatttgc aaaaatccgt tccacctgga atggctggtg
      421 atggagtggc gcgaggaagc ctataccctc gatgaactgg ctgattatct cgatttgagc
      481 gcctcagagc gtcgtagcat cgataaacat tacgggatgg ggcgaaactg ccacctgttc
      541 gaaatgacgc gcaaatgggc ttacagggcg attcgtcagg gctggccagc gttctcacag
      601 tggcttgaag cggtgatcca gcgtgtcgaa atgtacaatg catcgcttcc cgttccgctt
      661 tcactggctg aatgtcgggc tattggcaag agcattgcga aatacacgca caggaacttc
      721 acgccggaaa ctttcgcaca gtatgtggct gatacgcaca cgccagaaat tcaggctgca
      781 cgcggtcgca agggcggttc taagtctaag cgcagcacag tagctacatc tgcacgcacg
      841 ctgaaaccgt gggaggcatt agggatcagt cgcgcctggt attaccaact gaaaaaacga
      901 ggtctcgtag agtagaccaa ataagcctat atcagataac agcgcctttc tggcgtcttt
      961 ttgagcagca ggttttttgc cgttcagccc tgcaatggcg cggctttccg cgtgattgtg
     1021 gtggtagtgc tcgccgcagt ctcatgaccg agcgtagcga gcgaatgagc gaggaagcac
     1081 cagggaatcg gaacacggat ggaggcactt acgcgtctgg gtttggggat gtctccagat
     1141 cgtacttaag ttccttaagt gcttgtaata tcctgtcttt tttatagcat agctcgcctg
     1201 tttttgtgtc taccagtcct gcttcgatca gtagcccagc cgcgagaaag agccggtgat
     1261 tgcgttcccg tcgttgtttt tttccctcga ttcgtttttg gaccgcctgt tttcgttcgc
     1321 tctcctgtgc ctgtaagtcg tttttttccg ctgttgccag tacgtggaga agtttgcgtt
     1381 cctgttctgt gagtccggct tcgttgtcga tcaggtcaat aatctgtctc tgtcgtgcgg
     1441 tctgttctcc gagcttcctg atgaatccga tccgtttctt cagccattcg atgttgctga
     1501 tgcgcatgtt cgtgatgctc cctggtgttt ttttgcggtg tgttgtggtc gtgcagtata
     1561 tcgcttgcgg tcggcgggtg cagggggtat cttccgtgct aattcgtaaa attagaagga
     1621 agcgcactta tatgtttctc tccttcgtcg agaaacagtg cgctcctgca gagggctgaa
     1681 accgtggcaa cctatcacct cagcgttaaa tttggtggca aggggcaggc tgcaaaccac
     1741 gccgattaca tcgagcgcaa agagaaatac cgcgaccgtc aggatttgga atattccgca
     1801 cacggaaaca tgccggaatg ggccagggat aatccttccc atttctggca ggcggctgac
     1861 cagtttgaac gtgcgaacgg ttcgacctat agggaacttg aaattgcatt accccgtgaa
     1921 ctgacaccgg aacagcgcct tgaactggtg caggattttg tacgtcagga agctggcgaa
     1981 cggcacgcct ggagttttgc cattcacaat ccgaaagcga gcattgacgg cggcgaacag
     2041 cctcatgcgc atatcatgat gagtcagcgt gtgaatgatg gcattgaacg tacaccggaa
     2101 cagtatttcc ggcgctataa cgccaggtat cccgagcggg gaggtgcgaa aaaggattcc
     2161 ggaagcctga ctctcactca gcaaaaagag cagttgcggg aattgcgaaa acgctgggag
     2221 gtgaagcaca acgaacatat gagaaagcat ggctttgaaa ggggcttcat tgactgccgg
     2281 acgctgaaag aacagggcat tgaacgacgt cccgaagtgc atctgggttt tgaagctgcc
     2341 ggacggcttg atgatgccca gcgtcatgac atcatgcaaa aacggtctga accggactat
     2401 tcccgccatc ttgaacaggc gcgaacggtc gggcatgaca tcagggaatg gctggacact
     2461 ccggttaagc aacatgaact ggtcagaagg ctgcaacatg atgttgcgcg ggagcatggc
     2521 tttgacatga gagacagagt gagcagacag aaccgaactg cacctgaacg ggttaaatca
     2581 ccgtcacgtg gattttctat gggattctga acatggccag cacagaagaa aaattactca
     2641 cgctcctgtt atcggtggag catctgcaac ataccgcaat ggagcaacag aaagctgttg
     2701 ctgattctct ggctgtggca agggaaactc ttcgcggata tcgggatatt tctgacggtg
     2761 tggcaaaaca ggtcagggat gaagtcagaa atgaggtgca gaagctggac gtggcaggac
     2821 tgataggtga gcgcatcagc caggattttc agcggctgga agagtcagtc gcaaacatga
     2881 aggcaaacgc ggatgccctg aacagggata ttgcgacaat tcacagcaat atcgtgcagg
     2941 aatacaacac ccttaaaggg tatagctgga aatggctggg tggggtgtca gtggcttttc
     3001 tggttatgtt ctgtgtgctc ggatggggaa tgaaaacaat actcgacagg aactacaacg
     3061 ccacagcggc ggtgtatcag aaagttgtga cactggaaga taaactggtg gagaaacctg
     3121 tcacggggaa gagccggaaa aactgacgcg cttcgcttgt ccaacgcctc acgacccgcg
     3181 aaaggatttc gcgaaccgtt caccgttttt ttcaatatga ttctgtctgc tttggtcgat
     3241 aaagcagacg atagtattcc agccttcgta tatataacgg tacgtgctca tcagtaagag
     3301 ctggcggtat tgtgttatca gggggaagtt ttttcagata ctcacgaaat gcctggcttg
     3361 atgccataaa atctacagta gcatcgataa tatgtggggt gttttcacct aattttgcca
     3421 tgatgataat ccttatatta tcacggtttg tgaatgatag ggtgtcacta ttatttatgc
     3481 gttagtgaac cagaaaaaat cccccgttgg cataggggga tatgtaagga gaaataactt
     3541 cgcaggtgtt cttgtttgta taacgtgaaa agactgcacg caacttaata agtctgccgt
     3601 acttactttc agttttcaac ataaggttta taacaatgta tggaatggaa gtgagcttta
     3661 aggtttcagc tctaaaaaat aaaatattta ttagttggct ggttgttgtt cttgttctgt
     3721 atgtatataa acactatcga catattatga ccgggaacat tccttacccc ctctgcgctc
     3781 gcagaggttt tttttgtcat taattaataa tgaactgaaa tgcagttccg atacctccat
     3841 ttgcacatta tccctgacat atggtaccgg aaccgcatta attttatgtt ataagagttt
     3901 atttttaatg tccagatggt ttaatagtat ttatatgtaa ttagctgtat ggatagtact
     3961 ggttttattg tataacttgt cgtttttttt attgtttttg tgtggtgtgc taatctttaa
     4021 gttataaaaa aaccccttgg aatacagggg caaaagtaag gaaaacaaat ggatgctcag
     4081 tttgtgtgac actttaaact aatggaacta tagagtggag gttgttacag tcgcttttat
     4141 aaaacagcaa ccagtttttt tcaatagtct gatgatggtt gtgacagttt tgtgatattg
     4201 ttcaaaatgt ttcttgttga atgtttgttt tttggtctat tggtgtctgg ttttattttt
     4261 tctgctatta catatcaaga aatgtgattg gtgtagcaag agtggaatgc gatgtggata
     4321 aactaattgg ttgtcgaatc taatttactt agaaaactac acttgttttt gtgtatgaat
     4381 ttagtgaatt tgtctgtcta tgtgttttcg tgcatttata aatccttcgt caggatctta
     4441 aatttagtgt tgaatatgta gggcctgtac ggtaattatt atttagcgta gctacttcat
     4501 cgttgttcga acacaaccaa caacctgtaa ttgttgtttc tcttggttcc ccacttttgt
     4561 ggggtttttt atctcttccg tgcatcgtaa agcgcggact ccttctggaa aggttgtttt
     4621 agggcatcac tgaggcattt tttgcgtttg tgaatattga gcatccgata actaaaatat
     4681 ttcccataga ctctgattct tgccaccgac cccaggtcgg tttttttttg tcctggcgag
     4741 atgtgaagtt tggaaacagg aaaccccgtc agagcgccac gcaccagggg agaaaacttg
     4801 tcgttttgag ccgttcggtg ttcagaacgc acgaaaccga tcgcacatcg ctttcgtgca
     4861 tagttatgca acgccatgaa aacgattctg acgcgttttt ctggtttggc ctggtgtttt
     4921 cttgtctttt tgcgtttttt gcgccagaaa gcgactgagg gcgttttaag gggggcgtac
     4981 aacgggagtt atggtaaatg gatcgggttt tcgggaaggt tcgacaggat ttgccgttgg
     5041 gtgtagtgta agcgactgaa aaacaaacgc ccctgaaatc atgtccagat ccggcaagat
     5101 tcaacatgaa atacagaggg cgtgtaggtc gcataacccg gagagaatcg taacac
//
