LOCUS       NZ_CP071079             4072 bp    DNA     circular CON 19-JUN-2023
DEFINITION  Escherichia coli strain 3347558 plasmid p3347558_6, complete
            sequence.
ACCESSION   NZ_CP071079
VERSION     NZ_CP071079.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN17736024
            Assembly: GCF_018128405.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4072)
  AUTHORS   Moser,A.I., Campos-Madueno,E.I. and Endimiani,A.
  TITLE     Polycolonization with MDR bacteria in a patient transferred from
            intensive care unit
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4072)
  AUTHORS   Moser,A.I., Campos-Madueno,E.I. and Endimiani,A.
  TITLE     Direct Submission
  JOURNAL   Submitted (02-FEB-2021) 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                   :: 144x
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/19/2023 02:55:44
            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)                     :: 5,587
            CDSs (total)                      :: 5,464
            Genes (coding)                    :: 5,238
            CDSs (with protein)               :: 5,238
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 92
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 226
            CDSs (without protein)            :: 226
            Pseudo Genes (ambiguous residues) :: 0 of 226
            Pseudo Genes (frameshifted)       :: 68 of 226
            Pseudo Genes (incomplete)         :: 166 of 226
            Pseudo Genes (internal stop)      :: 37 of 226
            Pseudo Genes (multiple problems)  :: 45 of 226
            Pseudo Genes (short protein)      :: 4 of 226
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP071079.1.
            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..4072
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="3347558"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="p3347558_6"
                     /geo_loc_name="Switzerland"
                     /collection_date="2020"
                     /collected_by="Institute for Infectious Diseases Bern"
     gene            complement(join(3387..4072,1..1474))
                     /gene="mobQ"
                     /locus_tag="JY392_RS27655"
                     /old_locus_tag="JY392_27650"
     CDS             complement(join(3387..4072,1..1474))
                     /gene="mobQ"
                     /locus_tag="JY392_RS27655"
                     /old_locus_tag="JY392_27650"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016240513.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobQ family relaxase"
                     /protein_id="WP_001029353.1"
                     /translation="MAIYHLSMKIISRSSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAECRKNSQLAREIELAIPRELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNSGLTEPARRVADLLNIVLPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGASGLAALRVQL
                     LKREEELRRKEQEDTERSRAERRAEQLRKNDNAVMDSGVLSAVVTGYGEAPMPGNGEMT
                     CYLLLHNRNGEYTLWGNELEKYRTRIFERVDLMRDRSGYICDRSEIGQHPPLQRVYSSA
                     TFEQLLTQVCQTWPQYTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLLPTL
                     MPVMSSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKG
                     LRYAGYGVAVNHDADSHISPAPELMEFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRT
                     WDEWRREEDARTHTTERRHDRGWSQ"
                     /name="mobQ"
     gene            1653..1907
                     /gene="mobC"
                     /locus_tag="JY392_RS27660"
                     /old_locus_tag="JY392_27655"
     CDS             1653..1907
                     /gene="mobC"
                     /locus_tag="JY392_RS27660"
                     /old_locus_tag="JY392_27655"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000091747.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase accessory protein MobC"
                     /protein_id="WP_000091747.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVVVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPGQ"
                     /name="mobC"
     gene            2439..3131
                     /locus_tag="JY392_RS27665"
                     /old_locus_tag="JY392_27660"
     CDS             2439..3131
                     /locus_tag="JY392_RS27665"
                     /old_locus_tag="JY392_27660"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001281399.1"
                     /GO_function="GO:0003887 - DNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /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_001281403.1"
                     /translation="MSDLIAYKSNALVEASYKLTLQEQRFLLLCISRLKSGADAELQKT
                     MTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKNDEKREEFRWIQYRAQYAKG
                     EAKARITFSDAVMPYLTQLKGQFTRVVIKNISGLSSSYSIRIYEFLQQFRSTGERIIAL
                     NDFRSMLGIENKYKQFRDLNKILIKPCVDELNKKSDLAVTVETIKKGRTVVALHFRFKE
                     DKQIKMTI"
                     /name="replication initiation protein"
     Typing          complement(1117..1475)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.056"
                     /coverage="100.0"
                     /evalue="3.94e-177"
     Typing          1476..1652
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          2440..3131
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.965"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(3..1561)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.231"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(3391..4070)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.559"
                     /coverage="99.0"
                     /evalue="1.17e-150"
ORIGIN
        1 gcattaaatc aacacgctca aagattctgg tgcggtattt ctccagctcg ttcccccaga
       61 gcgtgtattc tccgttccgg ttgtgaagca gaaggtaaca ggtcatttcc ccgttaccag
      121 gcatgggggc ctcgccatac cccgtaacga ctgcgctcag tacccctgaa tccataacgg
      181 cattgtcatt tttcctgagc tgttccgctc gtcgctccgc gcgactacgt tctgtatcct
      241 cctgctcctt ccggcgcaat tcctcttcac gtttaagcaa ctggactctg agagctgcaa
      301 ggccggatgc cccccactgc tgccactgtt tttcaaatgc cgtctgactc gcgggaatgt
      361 cctgtttctc caccttccgg taatgctgtc gcaatttttc catttgctgg ctcagcgact
      421 ggatttttcc ctgttcgcta cggtattccg gtgccgccca ttgcatcagg ggaatacggg
      481 aaaaaccgga cgaaaacggc gatgattttt tcaggctggc agcatggctc atcgcttcct
      541 ttcgttcggt gttcagctct tcccagcgtc tgcgcgtcgc ctgcatatct gccatcatcg
      601 acatggcatt actggtgagt ttccatgccg cattactgtc cttcggcaac gcttcgatga
      661 tgtcacgtag tgtgtacgaa gttgcgttgt caggaagcac gatattcaga aggtcagcca
      721 cacggcgggc aggctctgtc agcccgctgt tcctgagttc agtgcgggaa atctgtattt
      781 ccaggttaag cctgttaatc agacgattct gttcgccgcg ttctgtttcg ataccgcgtg
      841 tttccatcgc acaggcagac tttccgaggt gaataccagg cgttttctca agcccctgtc
      901 gctcgtatga acgatggtct atctcttcct gataaccggc gttcgccagt gctctgtttg
      961 catggtcagc ccatgatgca cgccacgtct cggcatgtgt ccggtcgttc cagtccctga
     1021 cctttccgcc gaacccagca ggtccgacag ccctcgtggt cagcatgatg tgcgcatggg
     1081 gatttgtttt atccatgtga tggaacgcca catcagcaat catgccctga ctgacaaagt
     1141 tttctctgac aaaggcgaga acggtttccc gtgcggcatc ctgcggcagt tcacggggga
     1201 tagcgagttc aatttcccgc gcaagttgtg agttcttccg gcattcggcc ttctcaacgg
     1261 cattccagag ttcggcacgg ttcgtacacc aggcaggggc tgtcgcgggg gtcagaatca
     1321 cagcttcagc cacaccgctt ttgcgggtgt agtcgtgagt cagtccggta cgctcatcaa
     1381 gcatcagtga accggaacga taggcagcgg aagctacggc gctgtagccg ctgcttctgg
     1441 agataatttt catgctgaga tgataaatcg ccatttctgc cgtaatgcct ttttgtagtt
     1501 ttctttcagc cccgcagggc gcacacaatc gaaacggagt ggagattgta taagtgcgca
     1561 ctttgtgatt tgtcgcgcat tatgccagct cagtttttaa actaccagtg acgcgctaaa
     1621 atgcgatttt tcatcgcgca cggagttaca tcatgagcag aacgctcgaa cagaagattg
     1681 ctgatgctga ggcgagatta cagcgcctga aggcgaagag ccggagcctg gacacagcgc
     1741 agaaggttgt tgtgggtgca gcattgctgg caaaggtcag aaagccggag gaggtgcagt
     1801 tgcgtgcctg gttactccag ttcctgaagg cagaggtgac acgacaggct gatgtgacgc
     1861 gcatactgcc gctgattaac gagctggagg cgctgccagg acagtgattg tatcgtccgc
     1921 tcgccgcagc cccagcgacc gagcgttagc gagcgagtgg gcgaggaagc ggaagtgaat
     1981 ccgtcgccag gttgagcaca tacgcacggt ttttcggtag gtgatatgcg ctgaacccgc
     2041 atgaatactg gatttccaca gggttggaag gggagtattc ggaacttgca attctgcttt
     2101 cttgcaacac attgttttta ttggtttttt gttttcagcg ccccaagtta tccacaggct
     2161 cgccgttaag tttttagatc ttgtttttaa gatcttgttt ttaatacttg ttttagggtc
     2221 aaaattcatt aataaaatca atatgttata gaggtatatg tggaggaatt taaggtaaag
     2281 gtggaggaat ttaaggtgtt taggtggagg aatttaaggt aaaggtggag gaatttaagg
     2341 tgttattcac agaaatgtga ggatataaaa aaaaatattc cacatttctt atttgtgggg
     2401 cacattaaag catcaccaca tttgaacggg atctttgtat gtcggacttg attgcctaca
     2461 agtcgaatgc tttggttgag gccagctaca agttgaccct acaggaacaa cgttttctgt
     2521 tgctgtgtat cagtcgattg aaatctggtg ctgatgctga attgcaaaag acaatgacca
     2581 ttaccgctgc ggaatatttt gattcattcc ctgacatggg gcggaaaaat gccgaggttc
     2641 agttacagga agcgatcgat cgtttatggg acaggtcgat cattctcaag aatgacgaga
     2701 agcgtgagga gttccgctgg atccagtatc gggcacagta cgctaaaggt gaggccaagg
     2761 ctcgaataac cttttctgac gcggtaatgc cttatctgac gcaactgaag gggcaattca
     2821 cgcgcgttgt tataaaaaac atatcaggtt tatcaagtag ttacagtata agaatatacg
     2881 agttcctcca gcaattccgc agtacgggag agagaattat tgctcttaat gactttcgtt
     2941 caatgttagg gattgaaaat aaatacaaac aattcagaga cttaaataaa atactaataa
     3001 aaccctgtgt tgacgaactg aacaaaaaaa gcgacctggc tgtaacggtt gagacgatca
     3061 aaaaggggcg cacggttgta gccctgcatt ttcgcttcaa ggaagacaaa cagatcaaga
     3121 tgacgatcta aaatcgattt taaggcacct aaaacgctcc ctgctgcgtt ttttttgtgt
     3181 tagtagtgcg aaggtactat tgaagtgaaa aattgcgtca aaagcgctct aatgcagcga
     3241 aaaaagaacc cccaattttt gggggcggaa aaacaaaact atgcttgcat tatgtgtgtg
     3301 cttcttgcat tcatccctgt cgatgaacat agaagaacat cgacgaacat aacacgatgt
     3361 taaacaaaac aaaatattgt tcacattcac tgtgaccaac cgcgatcatg tctcctctcg
     3421 gtggtgtgtg ttcttgcatc ttcctcgcgc cgccattcat cccaggtacg attgaaaccc
     3481 agagagcgga acagatgatc cggctgtttt tctggtgtgt tgacggcagc aaaaagcggt
     3541 gcctcacggg ttttcagatg aaactccata agttccggcg caggtgatat gtggctgtct
     3601 gcatcgtgat ttacggcaac accataccct gcataccgta accccttatc ggtcagtgca
     3661 ctgatgacca gctggctgtt atcggctgag ggaacggcaa acgcgggata cagcgtacca
     3721 ttaagccgga caacaccgcc cagagagtca tccacgccca tgaccagcaa aagctgaagc
     3781 tggcgggttt cccggtcgac agaactcatt accggcatca gcgtcggtag cagacgtccc
     3841 tgcgtaaaat ccaccttcct tgctgccagt gatggcatgg ctggctggcg gtcttctcca
     3901 agacagaaag actccggcca tgtcttcggc tggcggagat tgcgggtata ttgcggccat
     3961 gtctggcaaa cctgcgtcag aagttgctca aaggtcgcag aggaataaac acgttgcagt
     4021 ggtggatgtt gaccgatttc gcttcggtca cagatataac cactcctgtc ac
//
