LOCUS       NZ_CP063336             4655 bp    DNA     circular CON 17-JUN-2023
DEFINITION  Escherichia coli strain BS74R-D plasmid pBS74R-D_4, complete
            sequence.
ACCESSION   NZ_CP063336
VERSION     NZ_CP063336.1
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 4655)
  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  JOURNAL   Unpublished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 4655)
  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
            CP063336.1.
            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..4655
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="BS74R-D"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pBS74R-D_4"
                     /geo_loc_name="Switzerland"
                     /collection_date="2018"
                     /collected_by="Institute for Infectious Diseases Bern"
     gene            complement(759..1238)
                     /locus_tag="IN878_RS24810"
                     /old_locus_tag="IN878_24830"
     CDS             complement(759..1238)
                     /locus_tag="IN878_RS24810"
                     /old_locus_tag="IN878_24830"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001050742.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001050742.1"
                     /translation="MNLLLPRDIVEAVLNDKKTKNARVAKCDGSEFFLELPSMNADFPA
                     GKIILKLGDSGFYNKRTKSLEGAYGLRHIWDKHRVEIGATSAEDIVIFLESILLAGAEV
                     LIDPKKGQNKAIVVESGTGMMILELKKPNGEDPYYSIITAYDRKSHPGTKLHTLI"
                     /name="hypothetical protein"
     gene            1498..2073
                     /locus_tag="IN878_RS26025"
     CDS             1498..2073
                     /locus_tag="IN878_RS26025"
                     /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_251301859.1"
                     /translation="MQPRELLMLSMYILVQAPVLTGLSKNQTESLTTNNKRGRRTAFYR
                     IKKHLQHDFYRIDSIKNEIHSPIKGFYMKDMKAVVVFTGKDLNIMRTEGGSGYWHARTD
                     RLNDADYLIAVRNRRETWAVKDLEHGTAFLIAKITGCFKSPDYDDRNVITFDEYAEIHT
                     PKAWKMLTDGQRYPVAYLSAQEAFYVLG"
                     /name="hypothetical protein"
     gene            complement(2463..2678)
                     /locus_tag="IN878_RS24820"
                     /old_locus_tag="IN878_24840"
     CDS             complement(2463..2678)
                     /locus_tag="IN878_RS24820"
                     /old_locus_tag="IN878_24840"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137421.1"
                     /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_000137421.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWENAFAEWRTMSGLMQRENA
                     ALSERVTGLSRQVQSLSEQLRRLSQG"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(2682..3167)
                     /locus_tag="IN878_RS24825"
                     /old_locus_tag="IN878_24845"
     CDS             complement(2682..3167)
                     /locus_tag="IN878_RS24825"
                     /old_locus_tag="IN878_24845"
                     /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_001086854.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQSTGEMLKAAFSEHEKSVRAELSESE
                     KRISAAILDHDRKLSAAMSQRTKGMLRMVSQTWLTIVLVSTLLTASGASILWWQGQQIL
                     DNYTTIREQKRTQAMLSERNSGVQLSTCGEQRRRCVRVNPEAGRFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            complement(<3202..3636)
                     /locus_tag="IN878_RS26030"
                     /pseudo=""
     CDS             complement(<3202..3636)
                     /locus_tag="IN878_RS26030"
                     /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(3845..4168)
                     /locus_tag="IN878_RS24835"
                     /old_locus_tag="IN878_24855"
     CDS             complement(3845..4168)
                     /locus_tag="IN878_RS24835"
                     /old_locus_tag="IN878_24855"
                     /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_001347450.1"
                     /translation="MLTMWVTEDEHRRLLERCDGKQLAAWMRQTCLDEKPARAGKLPSL
                     SPALLRQLAGMGNNLNQIARQVNAGGGSGHDRVQVVAALMAIDAGLERLRHAVLEKGAD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     Typing          complement(4270..4456)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="85.263"
                     /coverage="87.0"
                     /evalue="2.7100000000000003e-47"
     Typing          2..449
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="88.223"
                     /coverage="94.0"
                     /evalue="2.86e-150"
     Typing          4436..4655
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.071"
                     /coverage="92.0"
                     /evalue="2.5e-51"
     Typing          complement(2360..3855)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.583"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 accaggcgtt tcccctggtg gctccctcgt gcgctctcct gttcctgcct ttcggtttac
       61 cggtgtcatt ccgctgttat ggccgcgttt atctcattcc acgcctgaca ctcagttccg
      121 ggtaggcagt tcgctccaag ctggactgta tgcacgaacc ccccgttcag tccgaccgct
      181 gcgccttatc cggtaactat cgtcttgagt ccaacccgaa aagacacgac ttaacgccac
      241 tggcagcggc cactggtaag caggatgtgc gagagatgta tcgagagttc ttgaagtgga
      301 ggccttagtg aggctacact ggaaggacag tatttggtga catgtctcgc acaagactgt
      361 taccacggtt cagaaacttg ccggtttact gaaccttcga aaaaccacct tgccgggtgg
      421 ttttttcgtt tacagggaga gagattacga cgagagtaaa acgatcacaa ggagatctga
      481 ccgtttacca gtgatttggc ttcgttttgg tttccactga acaccaaaat agcacttttt
      541 gcaaaaagat gagcagtgat agagttgtat tctgtatgtg tagaagggct tggtatgtaa
      601 cctgaactct ggattggtta catatttgta ggctacttgt cggaaaccag atttcgacaa
      661 tgcgttgtta aggtcaaaga cctgtcccga accgaaatgc taagggaatg ccacgaacaa
      721 cactattacg aagaagtcgg ctatttagcc ggcttttttc atattagggt atgaagtttt
      781 gtacctggat ggctcttcct atcataagca gtaatgatgc tgtagtacgg gtcttcgccg
      841 tttggttttt tcaattctag tatcatcatc cccgttcctg actctacaac aatcgctttg
      901 ttttggcctt ttttaggatc tatgagcact tctgccccag ctaataatat gctctccaaa
      961 aagatgacaa tatcctcagc ggaagtagct cctatctcga cacgatgctt gtcccatata
     1021 tgcctaaggc cataggctcc ctcgagactt tttgtccttt tgttgtaaaa accggaatct
     1081 cctagcttga ggatgatttt ccctgcggga aagtctgcat tcatgcttgg cagttctaga
     1141 aaaaattcac ttccatcaca cttagccact cgtgcatttt ttgttttctt atcattaaga
     1201 acagcttcaa ctatatcgcg tggaagtaac aagttcacaa actacacctc tatagccttc
     1261 actattatgt ttaggcgtta aatccctttt tgaagggctg attctaacac tgacgtaatg
     1321 agcaatttcc agtaaatctt gatagaaaaa accagttgta tttaccataa cattccttgc
     1381 ccgcaccgct ccggacgggt tcagcgtgaa agcggcgtta gcccggtaaa atcggcagta
     1441 aactccccgc taaaccgcgc attctgcgcc tgataaattt cacgtggctg catagccatg
     1501 cagccacgtg aattgctcat gctttcaatg tatatcctcg tccaagcccc tgttttaacc
     1561 ggtttatcaa aaaaccaaac agaaagcctt accactaaca ataaaagagg taggaggact
     1621 gcattttatc gcataaaaaa acatttacaa cacgattttt atcgtataga ttccataaaa
     1681 aatgaaattc actcacctat taagggtttc tatatgaaag atatgaaagc tgttgtggtt
     1741 tttaccggga aggatttgaa cataatgaga actgaggggg ggtcaggcta ctggcatgcc
     1801 agaacagaca ggctcaacga tgccgattac ctcatagcag taagaaacag aagggaaacg
     1861 tgggcagtaa aagacctgga acacggcaca gcattcctga tcgccaaaat taccgggtgt
     1921 tttaaaagcc ctgattacga cgacaggaac gtcataacct ttgatgaata cgcagaaatt
     1981 cacacgccaa aagcatggaa aatgctaacc gatggtcagc gctatccggt tgcttacctg
     2041 agcgcacagg aagcttttta cgtattgggg taacaccgga acaactggaa tggaagaaat
     2101 tccatccttc atccccatcg gttcctaata cagtgattcc tggtctggct gaagagaaaa
     2161 cagaaaaact ctcccttaac gaggcaattg aaagagccaa aaaggatatt agcaacgcaa
     2221 cagggattga tagctcagcc ataacaataa gcatcaagat ctgatgaagc gtgaacaaca
     2281 agatagcagc ctcatgttct agaactgaac ctgtacgcca gaaacagcaa gcccatgctt
     2341 ttccggcgca cagattcaaa gtgacggacc gttgtacgtt cgctgtcgct gagatcgttc
     2401 cagctccagc gctttctgat gctgcgccgc ccgttcctgc tcacgatgtg cctctatcac
     2461 gttcagcctt gtgacaaccg gcgcagctgc tcgctcaaac tctgcacctg cctgctcaag
     2521 cccgtgacgc gctcgctcag cgccgcgttc tcccgttgca taagaccaga catcgtccgc
     2581 cattccgcga aggcgttctc ccactcgtcc agccttttcg agtagtcctg ctgtagctgc
     2641 tctaatgcgc tcagcaactg tttttccagc tccgtcatgt gctatttccc cgccagtatc
     2701 atccagctcg aatcctctcc gaaccgtccc gcttccgggt tcaccctcac gcagcggcgt
     2761 ctctgctctc cgcaggtcga gagctgcaca ccgctgttcc tctcggacag catggcctgc
     2821 gtgcgcttct gctcccggat ggtcgtgtaa ttgtcgagta tctgctgccc ctgccaccac
     2881 agaatacttg cgcccgatgc tgtcagcagt gtagacacca agacgatggt cagccacgtc
     2941 tggctgacca tccgcagcat acctttcgtg cgctggctca tggcagcgga cagcttcctg
     3001 tcgtggtcga ggatggcggc gctgattctc ttctcgcttt cgctcagttc cgctctgaca
     3061 gacttctcgt gctcgctgaa tgcggctttc agcatctcgc cggtactctg ctgctgcgct
     3121 ttcgatttct gctctaagtc cttcgccagc gttaaaagac tgttcataga tggctccctt
     3181 cagtcggatg tttcgccccc cgtccgggtc ggcaatgctg atgctgcttt ttgtggtgcg
     3241 taccacctca aaacctgcgc tttccagcgc ctcagtgacg tcctggcggg ttttcagctc
     3301 cccggacgag gctaaggcca gtaaaccccg tgtaattgcc tgagcggctt cctgcttcgt
     3361 ttccggcagc gcggacggcg tgaccagcac ccgccggttt tcaggcgcgt tcgggtcatg
     3421 cagccccagc ctgccgttca cgatggtctg ccaggcatca atgcgcggac ggtcggcgcg
     3481 gtcgtaatac ggctggagac gcttgccggt cagcagctcc gtgttcggga tcaggaagtt
     3541 cagctccagc cgccccttat cctggtgctc aacccacagc acgctgtact ggtctttatc
     3601 gagtccgggc atcagaaccc gttcaaagct cgccatcagc ttttcgcgct gcccgggcgg
     3661 taaatccttt tcggcaaagg acaagacgcc ggatgtgtac ttttttgcgt agggcgaggc
     3721 gtcgataagc tccctgactt cttccggctt cccctgcaga acggtggcgc cgtcgcgctg
     3781 tcggtctttc cccagcagat aatccaccgg accggcgcca ccgccgcgcc ctcgcgggtg
     3841 aaacttaacg atcatcgtct gcaccctttt ccagcacggc atgccgcagc cgctcgagtc
     3901 cggcatctat ggccatcagc gcggcgacga cctgcacgcg gtcgtgcccg ctgccaccac
     3961 cggcgttaac ctgccgggca atctggttga ggttgttccc catgccggca agctgacgaa
     4021 gcagcgccgg cgagagcgag ggaagcttgc cggcgcgggc gggtttctcg tccaggcacg
     4081 tctggcgcat ccaggctgca agctgtttac cgtcgcagcg ctccagcaga cggcggtgct
     4141 catcttcggt cacccacatc gtgagcattt tgctgcgttt gtctgccaat ccggcctcct
     4201 gataacgccg agacgggcgg gaaatctttt cccggtcggc gcggtgttgg acaagccgca
     4261 ggcgcgtcag tggttttagc gggtttcggg gcgcagccct gaaccagtca cgtagcgcta
     4321 gcggagtgta tactggctta gtatggtaaa tcgaagtgga aattcaggga agtgcttcat
     4381 gtggcaggta aaaaattcag ctgtggggcg taagtgcgaa atgctggaga cgatgaaatg
     4441 acgcctcctc gctcactcgg tcgctacgct cctgccgtga gactgcggcg ggcgttacct
     4501 gctcaagaat gacgagataa atagcgctca aatcaagaag gaaggggaaa aggatccggc
     4561 gttgccgttt ttccataggc tccgcccccc tgacaagcat cacgaaatct gacgctcaaa
     4621 tcagtggtgg cgaaacccga caggactata aagat
//
