LOCUS       NZ_CP145677             4074 bp    DNA     circular CON 05-APR-2024
DEFINITION  Escherichia coli strain S1-ZIM-01-A plasmid p6-S1-ZIM-01-A, complete
            sequence.
ACCESSION   NZ_CP145677
VERSION     NZ_CP145677.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN33052302
            Assembly: GCF_036884545.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4074)
  AUTHORS   Campos-Madueno,E.I., Aldeia,C. and Endimiani,A.
  TITLE     Strains isolated from intestinal colonization screening for
            multidrug-resistant Enterobacterales in stool samples from healthy
            people living abroad
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4074)
  AUTHORS   Campos-Madueno,E.I., Aldeia,C. and Endimiani,A.
  TITLE     Direct Submission
  JOURNAL   Submitted (09-FEB-2024) Institute for Infectious Diseases,
            University of Bern, Friedbuehlstrasse 25, Bern 3001, Switzerland
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 363.5853X
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_036884545.1-RS_2024_04_05
            Annotation Date                   :: 04/05/2024 17:24:20
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,478
            CDSs (total)                      :: 5,356
            Genes (coding)                    :: 5,141
            CDSs (with protein)               :: 5,141
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 91
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 215
            CDSs (without protein)            :: 215
            Pseudo Genes (ambiguous residues) :: 0 of 215
            Pseudo Genes (frameshifted)       :: 71 of 215
            Pseudo Genes (incomplete)         :: 162 of 215
            Pseudo Genes (internal stop)      :: 29 of 215
            Pseudo Genes (multiple problems)  :: 48 of 215
            Pseudo Genes (short protein)      :: 4 of 215
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP145677.1.
            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..4074
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="S1-ZIM-01-A"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="p6-S1-ZIM-01-A"
                     /geo_loc_name="Switzerland"
                     /lat_lon="46.947928 N 7.422277 E"
                     /collection_date="2022"
                     /collected_by="Institute for Infectious Diseases (IFIK),
                     University of Bern"
     gene            join(3636..4074,1..254)
                     /locus_tag="V6S34_RS27375"
                     /old_locus_tag="V6S34_27375"
     CDS             join(3636..4074,1..254)
                     /locus_tag="V6S34_RS27375"
                     /old_locus_tag="V6S34_27375"
                     /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"
     gene            complement(512..2671)
                     /gene="mobQ"
                     /locus_tag="V6S34_RS27380"
                     /old_locus_tag="V6S34_27380"
     CDS             complement(512..2671)
                     /gene="mobQ"
                     /locus_tag="V6S34_RS27380"
                     /old_locus_tag="V6S34_27380"
                     /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_016245161.1"
                     /translation="MAIYHLSMKIISRSSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPRELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNSGLTEPARRVADLLNIVLPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGASGLAALRVQL
                     LKREEELRRKEQEDTERSRAERRAEQLRKNDNAVMDSGVLSAVVTGYGEAPMPGNGEMT
                     CYLLLHNRNGEYTLWGNELEKYRTRIFERVDLMRDRSGYICDRSEIGQHPPLQRVYSSA
                     TFEQLLTQVCQTWPQYTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLPPTL
                     MPVMSSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKG
                     LRYAGYGVAVNHDADSHISPAPELMEFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRT
                     WDEWRREEDARTHTTERRHDRGWSQ"
                     /name="mobQ"
     gene            2850..3104
                     /gene="mobC"
                     /locus_tag="V6S34_RS27385"
                     /old_locus_tag="V6S34_27385"
     CDS             2850..3104
                     /gene="mobC"
                     /locus_tag="V6S34_RS27385"
                     /old_locus_tag="V6S34_27385"
                     /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"
     Typing          complement(2314..2672)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.333"
                     /coverage="100.0"
                     /evalue="8.460000000000002e-179"
     Typing          2673..2849
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          2..254
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.606"
                     /coverage="100.0"
                     /evalue="3.12e-128"
     Typing          3637..4074
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="97.494"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(516..2758)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.332"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 acgagttcct ccagcaattc cgcagtacgg gagagagaat tattgctctt aatgactttc
       61 gttcaatgtt agggattgaa aataaataca aacaattcag agatttaaat aaaatactaa
      121 taaaaccctg tgttgacgaa ctgaacaaaa aaagcgacct ggctgtaacg gttgagacga
      181 tcaaaaaggg gcgcacggtt gtagccctgc attttcgctt caaggaagac aaacagatca
      241 agatgacgat ctaaaatcga ttttaaggca cctaaaacgc tccctgctgc gttttttttg
      301 tgttagtagt gcgaaggtac tattgaagtg aaagattgcg tcaaaaacgc tataatgcag
      361 cgaaaaaaga acccccaatt tttgggggcg gaaaaacaaa actatgcttg cgttatgtga
      421 gtgtgcttct tgcattcatc cctgtcgatg aacatcgaag aacatcgacg aacataacac
      481 gatgttaaac aaaacaaaat attgttcaca ttcactgtga ccaaccgcga tcatgtctcc
      541 tctcggtggt gtgtgttctt gcatcttcct cgcgccgcca ttcgtcccag gtacgattga
      601 aacccagcga gcggaacaga tgatccggct gtttttctgg tgtgttgacg gcagcaaaaa
      661 gcggtgcctc acgggttttc agatgaaact ccataagttc cggcgcaggt gatatgtggc
      721 tgtctgcatc gtgatttacg gcaacaccat accctgcata ccgtaacccc ttatcggtca
      781 gtgcactgat gaccagctgg ctgttatcgg ctgagggaac ggcaaacgcg ggatacagcg
      841 taccattaag ccggacaaca ccgcccagag agtcatccac gcccatgacc agcaaaagct
      901 gaagctggcg ggtttcccgg tcgacagaac tcattaccgg catcagcgtc ggtggcagac
      961 gtccctgcgt aaaatccacc ttccttgctg ccagtgatgg catggctggc tggcggtctt
     1021 ctccaagaca gaaagactcc ggccatgtct tcggctggcg gagattgcgg gtatattgcg
     1081 gccatgtctg gcaaacctgc gtcagaagtt gctcaaaggt cgcagaggaa taaacacgtt
     1141 gcagtggtgg atgttgaccg atttcgcttc ggtcacagat ataaccactc ctgtcacgca
     1201 ttaaatcaac acgctcaaag attctggtgc ggtatttctc cagctcgttc ccccagagcg
     1261 tgtattctcc gttccggttg tgaagcagaa ggtaacaggt catttccccg ttaccaggca
     1321 tgggggcctc gccatacccc gtaacgactg cgctcagtac ccctgaatcc ataacggcat
     1381 tgtcattttt cctgagctgt tccgctcgtc gctccgcgcg actacgttct gtatcctcct
     1441 gctccttccg gcgcaattcc tcttcacgtt taagcaactg gactctgaga gctgcaaggc
     1501 cggatgcccc ccactgctgc cactgttttt caaatgccgt ctgactcgcg ggaatgtcct
     1561 gtttctccac cttccggtaa tgctgtcgca atttttccat ttgctggctc agcgactgga
     1621 tttttccctg ttcgctacgg tattccggtg ccgcccattg catcagggga atacgggaaa
     1681 aaccggacga aaacggcgat gattttttca ggctggcagc atggctcatc gcttcctttc
     1741 gttcggtgtt cagctcttcc cagcgtctgc gcgtcgcctg catatctgcc atcatcgaca
     1801 tggcattact ggtgagtttc catgccgcat tactgtcctt cggcaacgct tcgatgatgt
     1861 cacgtagtgt gtacgaagtt gcgttgtcag gaagcacgat attcagaagg tcagccacac
     1921 ggcgggcagg ctctgtcagc ccgctgttcc tgagttcagt gcgggaaatc tgtatttcca
     1981 ggttaagcct gttaatcaga cgattctgtt cgccgcgttc tgtttcgata ccgcgtgttt
     2041 ccatcgcaca ggcagacttt ccgaggtgaa taccaggcgt tttctcaagc ccctgtcgct
     2101 catatgaacg atggtctatc tcttcctgat aaccggcgtt cgccagtgct ctgtttgcat
     2161 ggtcagccca tgatgcacgc cacgtctcgg catgtgtccg gtcgttccag tccctgacct
     2221 ttccgccgaa cccagcaggt ccgacagccc tcgtggtcag catgatgtgc gcatggggat
     2281 ttgttttatc catgtgatgg aacgccacat cagcaatcat gccctgactg acaaagtttt
     2341 ctctgacaaa ggcgagaacg gtttcccgtg cggcatcctg cggcagttca cgggggatag
     2401 cgagttcaat ttcccgcgca agttgtgagt tcttccggcg ttcggccttc tcaacggcat
     2461 tccagagttc ggcacggttc gtacaccagg caggggctgt cgcgggggtc agaatcacag
     2521 cttcagccac accgcttttg cgggtgtagt cgtgagtcag tccggtacgc tcatcaagca
     2581 tcagtgaacc ggaacgatag gcagcggaag ctacggcgct gtagccgctg cttctggaga
     2641 taattttcat gctgagatga taaatcgcca tttctgccgt aatgcctttt tgtagttttc
     2701 tttcagcccc gcagggcgca cacaatcgaa acggagtgga gattgtataa gtgcgcactt
     2761 cgtgatttgc cgtgcattat gccagctcag tttttaaact accagtgacg cgctaaaatg
     2821 cgatttttca tcgcgcacgg agttacatca tgagcagaac gctcgaacag aagattgctg
     2881 atgctgaggc gagattacag cgcctgaagg cgaagagccg gagcctggac acagcgcaga
     2941 aggttgttgt gggtgcagca ttgctggcaa aggtcagaaa gccggaggag gtgcagttgc
     3001 gtgcctggtt actccagttc ctgaaggcag aggtgacacg acaggctgat gtgacgcgca
     3061 tactgccgct gattaacgag ctggaggcgc tgccaggaca gtgattgtat cgtccgctcg
     3121 ccgcagcccc agcgaccgag cgttagcgag cgagtgggcg aggaagcgga agtgaatccg
     3181 tcgccaggtt gagcacatac gcacggtttt tcggcaggtg atatgcgctg aacccgcatg
     3241 aatactggat ttccacaggg ttggaagggg agtattcgga acttgcaatt ctgctttctt
     3301 gcaacacatt gtttttattg gttttttgtt ttcagcgccc caagttatcc acaggctcgc
     3361 cgttaagttt ttagatcttg tttttaagat cttgttttta atacttgttt tagggtcaaa
     3421 attcattaat aaaatcaata tgttatagtg gtatatgtgg aggaatttaa ggtaaaggtg
     3481 gaggaattta aggtgtttag gtggaggaat ttaaggtaaa ggtggaggaa tttaaggtgt
     3541 tattcacaga aatgtgagga tataaaaaaa aatattccac atttcttatt tgtggggcac
     3601 attaaagcat caccacattt gaacgggatc tttgtatgtc ggacttgatt gcttacaagt
     3661 cgaatgcttt ggttgaggcc agctacaagt tgaccctaca ggaacaacgt tttctgttgc
     3721 tgtgtatcag tcgattgaaa tctggtgctg atgctgaatt gcaaaagaca atgaccatta
     3781 ccgctgcgga atattttgat tcattccctg acatggggcg gaaaaatgcc gaggttcagt
     3841 tacaggaagc gatcgatcgt ttatgggaca ggtcgatcat tctcaagaat gacgagaagc
     3901 gtgaggagtt ccgctggatc cagtatcggg cacagtacgc taaaggtgag gccaaggctc
     3961 gaataacctt ttctgacgcg gtaatgcctt atctgacgca actgaagggg caattcacgc
     4021 gcgttgttat aaaaaacata tcaggtttat caagtagtta cagtataaga atat
//
