LOCUS       NZ_CP091760             4089 bp    DNA     circular CON 26-JUL-2023
DEFINITION  Escherichia coli strain LC-1302-2020 plasmid p4-LC-1302-2020,
            complete sequence.
ACCESSION   NZ_CP091760
VERSION     NZ_CP091760.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN25301092
            Assembly: GCF_022559875.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4089)
  AUTHORS   Campos-Madueno,E.I., Mauri,C., Meroni,E., Paseiro,P.P., Consonni,A.,
            Luzzaro,F. and Endimiani,A.
  TITLE     Simultaneous gut colonization by Klebsiella grimontii and
            Escherichia coli co-possessing the blaKPC-3-carrying pQil plasmid
  JOURNAL   Eur J Clin Microbiol Infect Dis 41 (7), 1087-1091 (2022)
   PUBMED   35643963
REFERENCE   2  (bases 1 to 4089)
  AUTHORS   Campos-Madueno,E.I. and Endimiani,A.
  TITLE     Direct Submission
  JOURNAL   Submitted (27-JAN-2022) 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                   :: 339.6778x
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/26/2023 04:10:24
            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)                     :: 5,269
            CDSs (total)                      :: 5,144
            Genes (coding)                    :: 4,882
            CDSs (with protein)               :: 4,882
            Genes (RNA)                       :: 125
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 91
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 262
            CDSs (without protein)            :: 262
            Pseudo Genes (ambiguous residues) :: 0 of 262
            Pseudo Genes (frameshifted)       :: 80 of 262
            Pseudo Genes (incomplete)         :: 189 of 262
            Pseudo Genes (internal stop)      :: 40 of 262
            Pseudo Genes (multiple problems)  :: 46 of 262
            Pseudo Genes (short protein)      :: 4 of 262
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP091760.1.
            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..4089
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="LC-1302-2020"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="p4-LC-1302-2020"
                     /geo_loc_name="Italy"
                     /lat_lon="45.8523 N 9.4144 E"
                     /collection_date="2020-11-09"
                     /collected_by="Clinical Microbiology and Virology Unit, A.
                     Manzoni Hospital, Lecco, Italy"
     gene            complement(join(3140..4089,1..1210))
                     /gene="mobQ"
                     /locus_tag="L6507_RS26185"
                     /old_locus_tag="L6507_26185"
     CDS             complement(join(3140..4089,1..1210))
                     /gene="mobQ"
                     /locus_tag="L6507_RS26185"
                     /old_locus_tag="L6507_26185"
                     /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_001029343.1"
                     /translation="MAIYHLSMKIISRNSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPRELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNSGLTEPARRVADLLNIVLPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGASGLAALRVQL
                     LKREEELRRKEQEDTERSRAERRAEQLRKNDNAVMDSGVLSAVVTGYGEAPMPGNGEMT
                     CYLLLHNRNGEYTLWGNELEKYRTRIFERVDLMRDRSGYICDRSEIGQHPPLQRVYSSA
                     TFEQLLTQVCQTWPQYTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLLPTL
                     MPVMSSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKG
                     LRYAGYGVAVNHDADSHISPAPELMEFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRT
                     WDEWRREEDARTHATERRHDRGWSQ"
                     /name="mobQ"
     gene            1391..1645
                     /gene="mobC"
                     /locus_tag="L6507_RS26190"
                     /old_locus_tag="L6507_26190"
     CDS             1391..1645
                     /gene="mobC"
                     /locus_tag="L6507_RS26190"
                     /old_locus_tag="L6507_26190"
                     /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_000091745.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVIVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPGQ"
                     /name="mobC"
     gene            2177..2884
                     /locus_tag="L6507_RS26195"
                     /old_locus_tag="L6507_26195"
     CDS             2177..2884
                     /locus_tag="L6507_RS26195"
                     /old_locus_tag="L6507_26195"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001296720.1"
                     /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_001296720.1"
                     /translation="MTSNPLIAYKSNALVEASYKLTLQEQRFLLLCISRLNSGTDVASP
                     ELQKTMTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKDDEKREEFRWIQYRA
                     QYARGEGKAQITFSDAVMPYLTQLKGQFTRVVIKNISNLSRSYSIRIYEILQQFRSTGE
                     RIIALDDFKSSLMLDGKYKDFKTLNRDLIKPCVDELNKKSDLAVTVETIKKGRTVVALH
                     FRFKEDKQIKMTI"
                     /name="replication initiation protein"
     Typing          complement(853..1211)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          1212..1390
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.889"
                     /coverage="100.0"
                     /evalue="3.38e-85"
     Typing          2178..2884
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(30..1297)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.764"
                     /coverage="98.0"
                     /evalue="0.0"
     Typing          complement(3144..4063)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="98.0"
                     /evalue="0.0"
ORIGIN
        1 cttcacgttt aagcaactgg actctgagag ctgcaaggcc ggatgccccc cactgctgcc
       61 actgtttttc aaatgccgtc tgactcgcgg gaatgtcctg tttctccacc ttccggtaat
      121 gctgtcgcaa tttttccatt tgctggctca gcgactggat ttttccctgt tcgctacggt
      181 attccggtgc cgcccattgc atcaggggaa tacgggaaaa accggacgaa aacggcgatg
      241 attttttcag gctggcagca tggctcatcg cttcctttcg ttcggtgttc agctcttccc
      301 agcgtctgcg cgtcgcctgc atatctgcca tcatcgacat ggcattactg gtgagtttcc
      361 atgccgcatt actgtccttc ggcaacgctt cgatgatgtc acgtagtgtg tacgaagttg
      421 cgttgtcagg aagcacgata ttcagaaggt cagccacacg gcgggcaggc tctgtcagcc
      481 cgctgtttct gagttcggta cgggaaatct gtatttccag gttaagtctg ttaatcagac
      541 gattctgttc gccgcgttct gtttcgatac cgcgtgtttc catcgcacag gcagactttc
      601 cgaggtgaat accaggcgtt ttctcaagcc cctgtcgctc gtatgaacga tggtctatct
      661 cttcctgata accggcgttc gccagtgccc tgttcgcatg gtcagcccat gatgcacgcc
      721 acgtctcggc atgtgtccgg tcgttccagt ccctgacctt tccaccgaat ccagcaggtc
      781 cgacagctct cgtggtcagc atgatgtgcg catggggatt tgttttatcc atgtgatgga
      841 acgccacatc agcaatcatg ccctgactga caaagttttc tctgacaaag gcgagaacgg
      901 tttcccgtgc ggcatcctgc ggtagttcgc gggggatggc gagttcaatt tcccgcgcaa
      961 gttgtgagtt cttccggcgt tcggccttct caacggcatt ccagagttcg gcacggttcg
     1021 tacaccaggc aggggctgtc gcgggagtca gaatcacagc ttcagccaca ccgcttttgc
     1081 gggtgtagtc gtgagtcagt ccggtacgct catcaagcat cagtgaaccg gaacgatagg
     1141 cagcagaagc aacggcgctg tagccgctgt ttctggagat gattttcatg ctgagatgat
     1201 aaatcgccat ttctgccgta atgccttttt gtggttttct ttcagccccg cagggcgcac
     1261 acaatcgaaa cggagtggag attgtataag tgcgcacact tcgtgatttt ccgtgcatta
     1321 tgccagctca gtttttaaac taccagtgac gcgctaaaat gcgatttttc atcgcgcacg
     1381 gagttacatc atgagcagaa cactcgaaca gaagattgct gatgctgagg ccaggttaca
     1441 gcgcctgaag gcgaagagca ggagtctgga cacagcgcag aaggtcattg tgggtgcagc
     1501 attgctggca aaggtcagaa agccggagga ggtgcagttg cgtgcctggt tactccagtt
     1561 cctgaaggca gaggtgacac gacaggctga tgtgacgcgc atactgccgc tgattaacga
     1621 gctggaagcg ctgccaggac agtgattgta tcgtccgctc gccgcagtcc cagcgaccga
     1681 gcgttagcga gcgagtgggc gaggaagcgg aagtgaatcc gtcgcctgat tgagcacata
     1741 cgcacggttt ttcgggaggt gatatgcgct gaacccgcat gaatactgga tttccacagg
     1801 gttggagggg gtgtattcgg aacttgcaat tctgcttttt tgcaacgcat tgtttttatt
     1861 ggttttttgt tttcagcact ccaagttatc cacaggctcg tcgttaagtt tttagatctt
     1921 gtttttaaga tcttgttttt aatacttgtt ttagcgccaa aattccttat agaaaacaaa
     1981 atgttacaac gctataggtg atatgattta aggtaaaggt gatataattt aaggtgcttg
     2041 ggtgaggtaa tttaaggtaa aggtgaggag atttaaggta atattcacag gaaaatgggg
     2101 ggtgaaaata taattgctca ccaatgctaa aggtgatagg tttttatttc acctcatttt
     2161 tggcctggtg gttaaaatga catcaaaccc tctgatagcc tataagtcca atgcgctggt
     2221 tgaggccagt tacaagctaa ctttacaaga acagcgtttc ttattgctct gcataagccg
     2281 acttaactcc ggtactgacg tagcttcacc tgaattgcaa aagacaatga ccattacagc
     2341 tgcggaatat tttgattcat tccctgatat ggggcggaaa aatgccgagg ttcagctaca
     2401 ggaagcgatc gatcgtttgt gggacaggtc gatcattctc aaggacgacg agaagcgcga
     2461 ggagttccgc tggattcagt atcgggcaca gtacgcgagg ggagagggga aagcacaaat
     2521 cactttttct gacgcggtaa tgccttatct gacacagttg aaggggcaat tcaccagagt
     2581 cgtcattaaa aatatttcta atttatcaag aagttacagc ataagaatat acgaaattct
     2641 ccagcaattc cgcagtactg gggaacgtat tatcgccctc gatgatttta aatcatcact
     2701 gatgcttgat ggtaaatata aagatttcaa aacgttaaac agggatctaa taaaaccctg
     2761 tgttgacgaa ctgaacaaaa aaagcgacct ggctgtaacg gttgagacga tcaaaaaggg
     2821 gcgcacggtt gtagccctgc attttcgctt caaggaagac aaacagatca agatgacgat
     2881 ctagaatcga ttttaaggca cctaaaacgc tccctgctgc gttttttttg tgttagtagt
     2941 gcgaaggtac tattgaagtg aaaaattgcg tcaaaagcgc tctaatgcag cgaaaaaaga
     3001 acccccattt ttcgggggcg gaaaaacaaa actatgcttg cattatgtgt gtgcttcttg
     3061 cattcatccc tgtcgatgaa catcgaagaa catcgacgaa cataacacga tgttaaacaa
     3121 aacaaaatat tgttcacatt cactgtgacc aaccgcgatc atgtctcctc tcggtggcgt
     3181 gtgttcgtgc atcttcctcg cgccgccatt cgtcccaggt acgattaaaa cccagcgagc
     3241 ggaacagatg atccggctgt ttttctggtg tgttgacggc agcaaaaagc ggtgcctcac
     3301 gggttttcag atgaaactcc ataagttccg gcgcaggtga tatgtggctg tctgcatcgt
     3361 gatttacggc aacaccatac cctgcatacc gtaacccctt atcggtcagt gcactgatga
     3421 ccagctggct gttatcggct gagggaacgg caaacgcggg atacagcgta ccattaagcc
     3481 ggacaacacc gcccagagag tcatccacgc ccatgaccag caaaagctga agctggcggg
     3541 tttcccggtc gacagaactc attaccggca tcagcgtcgg tagcagacgt ccctgcgtaa
     3601 aatccacctt ccttgctgcc agtgatggca tggctggctg gcggtcttct ccaagacaga
     3661 aagactccgg ccatgtcttc ggctggcgga gattgcgggt atattgcggc catgtctggc
     3721 aaacctgcgt cagaagttgc tcaaaggtcg cagaggaata aacacgttgc agtggtggat
     3781 gttgaccgat ttcgcttcgg tcacagatat aaccactcct gtcacgcatt aaatcaacac
     3841 gctcaaagat tctggtgcgg tatttctcca gctcgttccc ccagagcgtg tattctccgt
     3901 tccggttgtg aagcagaagg taacaggtca tttccccgtt accaggcatg ggggcctcgc
     3961 cataccccgt aacgactgcg ctcagtaccc ctgaatccat aacggcattg tcatttttcc
     4021 tgagctgttc cgctcgtcgc tccgcgcgac tacgttctgt atcctcctgc tccttccggc
     4081 gcaattcct
//
