LOCUS       NZ_CP145652             4072 bp    DNA     circular CON 05-APR-2024
DEFINITION  Escherichia coli strain S1-IND-02-A plasmid p6-S1-IND-02-A, complete
            sequence.
ACCESSION   NZ_CP145652
VERSION     NZ_CP145652.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN33052310
            Assembly: GCF_036884425.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4072)
  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  JOURNAL   Unpublished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 4072)
  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                   :: 276.8158X
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_036884425.1-RS_2024_04_05
            Annotation Date                   :: 04/05/2024 17:14:42
            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)                     :: 5,448
            CDSs (total)                      :: 5,327
            Genes (coding)                    :: 5,106
            CDSs (with protein)               :: 5,106
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 94
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 221
            CDSs (without protein)            :: 221
            Pseudo Genes (ambiguous residues) :: 0 of 221
            Pseudo Genes (frameshifted)       :: 81 of 221
            Pseudo Genes (incomplete)         :: 146 of 221
            Pseudo Genes (internal stop)      :: 40 of 221
            Pseudo Genes (multiple problems)  :: 44 of 221
            Pseudo Genes (short protein)      :: 5 of 221
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP145652.1.
            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="S1-IND-02-A"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="p6-S1-IND-02-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            278..979
                     /locus_tag="V6S42_RS27200"
                     /old_locus_tag="V6S42_27200"
     CDS             278..979
                     /locus_tag="V6S42_RS27200"
                     /old_locus_tag="V6S42_27200"
                     /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_001281395.1"
                     /translation="MSDLIAYKSNALIEASYKLTLQEQRFLLVCISRLKSGEDSPSPDE
                     QKTMTITAAEFHDAFPDMGRQHAEARLKEAIDRLWDRSVIIKNEEKREEFRWVQYRAQY
                     FKGEAKVDITFSDAIMPYLTQLKGQFTRVVVKNVSSLSSTYSIRIYELLQQFRSTGDRT
                     IAIDDFRTMLAVEDKYQQFKDLNKMIIKPAIAELNEKSDLVVTVETIKKGRTVVALHFR
                     FKEDKQIKMTI"
                     /name="replication initiation protein"
     gene            complement(1237..3384)
                     /gene="mobQ"
                     /locus_tag="V6S42_RS27205"
                     /old_locus_tag="V6S42_27205"
     CDS             complement(1237..3384)
                     /gene="mobQ"
                     /locus_tag="V6S42_RS27205"
                     /old_locus_tag="V6S42_27205"
                     /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_057077964.1"
                     /translation="MAIYHLSMKIISRSSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPHELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFSGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNGGLTEPARRVADLLNIGLPDNATSYTLRDIIEALPKDSN
                     SAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQMAFEKQWQQWGESGLAALRAQL
                     LKREEELRRKEQEDTERSRAEQLRKNDNAVMDSGVLRAVVTGYGEAPMPGNGEMTCYLL
                     LHNRNGEYTLWGNELEKYRTRIFESVDLMRDRSGYICDRSEIGQRPPLQRVYSSATFEQ
                     LLTQVCQTWPQHTRNLRQPKTWPESFCLGEDRQPAMPSPAARKVDFMQGRLPPTLMPVM
                     SSVDRENRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKGLRYA
                     GYGVAVNHDADSHISPAPELMEFHLKTREVPLFAAVNTPEKQPDHLFRSLGFNRTWDEW
                     RREEDARTHTTERRHDRGWSQ"
                     /name="mobQ"
     gene            3563..3817
                     /gene="mobC"
                     /locus_tag="V6S42_RS27210"
                     /old_locus_tag="V6S42_27210"
     CDS             3563..3817
                     /gene="mobC"
                     /locus_tag="V6S42_RS27210"
                     /old_locus_tag="V6S42_27210"
                     /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_000091746.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVVVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPEQ"
                     /name="mobC"
     Typing          complement(3027..3385)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          3386..3562
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.438"
                     /coverage="100.0"
                     /evalue="2.610000000000001e-86"
     Typing          279..979
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.715"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(1241..3471)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="96.658"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ccgttaagtt tttaagatct tatttttaga tctttttttt aaaacctttt taggtcttgt
       61 aacaccatga ttttaaagat gttctggcaa gataagtgga gcttttgggg gtgaaaggtg
      121 gagcttttgg gggtgaaagg tggagctttt gggggtgaaa ggtggagctt ttgggggtgt
      181 aatccacaga aaaagggggt tgcaaaaaaa aaacttccac ccatatgata agtggcgtac
      241 agtaaaaaaa cgccaccaat ggcaacgagc aagcgaaatg tcagatctga tagcttacaa
      301 atcaaacgcc cttatcgagg caagctacaa gctcactttg caggaacagc gcttcctgct
      361 ggtctgtatc agccgcctga aatccggaga agattcccct tcgcctgatg aacaaaaaac
      421 catgaccatc acggctgcag agtttcatga tgcctttcct gacatgggac ggcagcacgc
      481 tgaagctagg ctcaaggaag cgatagatcg cctctgggac aggtcagtaa tcatcaagaa
      541 cgaggaaaaa cgagaagagt tccgctgggt gcagtaccgg gcgcagtatt tcaaaggtga
      601 ggcgaaagta gatatcacct tctccgatgc catcatgccg tatctgacac agctcaaggg
      661 gcagtttacg cgggtagtcg tgaagaacgt ctccagcctt tccagcacct acagcatccg
      721 catttacgag ctgctccagc agttccgcag caccggtgac agaacgatag ctatcgatga
      781 tttccgaacc atgcttgccg ttgaagataa atatcaacaa ttcaaagact tgaataagat
      841 gataatcaag ccagccatcg ccgaactgaa cgaaaaaagc gatctggttg taactgttga
      901 gacgatcaaa aaggggcgca cggttgtagc cctgcatttt cgcttcaagg aagacaaaca
      961 gatcaagatg acgatctaaa atcgatttta aggcacctaa aacgctccct gctgcgtttt
     1021 ttttgtgtta gtagtgcgaa ggtactattg aagtgaaaaa ttgcgccaaa aacgctctga
     1081 tgcagcgaaa aaagaacccc caatttttgg gggcggaaaa acaaaactat gcttgcgtta
     1141 tgtgagtgtg cttcttgcat tcatccctgt cgatgaacat cgaagaacat caacgaacat
     1201 aacacgatgt taaacaaaac aaaatattgt tcacattcac tgtgaccaac cgcgatcatg
     1261 tctcctctcg gtggtgtgtg ttcttgcatc ttcctcgcgc cgccattcgt cccaggtacg
     1321 attgaaaccc agcgagcgga acagatgatc cggctgtttt tctggtgtgt tgacggcagc
     1381 aaaaagcggt acctcacggg ttttcagatg aaactccata agttccggcg caggtgatat
     1441 gtggctgtct gcatcgtgat ttacggcaac accataccct gcataccgta accccttatc
     1501 ggtcagtgca ctgatgacca gctggctgtt atcggctgag ggaacggcaa acgcgggata
     1561 cagcgtacca ttaagccgga caacaccgcc cagagagtca tccacgccca tgaccagcaa
     1621 aagctgaagc tggcggtttt cccggtcgac agaactcatg accggcatca gcgtcggtgg
     1681 cagacgtccc tgcataaaat ccaccttcct tgccgctggt gatggcatgg ctggctggcg
     1741 gtcttctcca agacagaaag actccggcca tgtcttcggc tggcggagat tgcgggtatg
     1801 ttgcggccat gtctggcaaa cctgcgtcag cagttgctca aaggttgcag aggaataaac
     1861 acgttgcagt ggcggacgtt ggccgatttc gcttcggtca cagatataac cactcctgtc
     1921 acgcattaaa tcaacactct caaagattct ggtgcggtat ttctccagct cgttccccca
     1981 gagcgtatat tctccgttcc ggttgtgaag cagaaggtaa caggtcattt ccccgttacc
     2041 aggcatggga gcctcgccat accccgtaac gactgctctc agcacccctg aatccataac
     2101 ggcattgtca tttttcctga gctgctccgc gcgactacgt tcagtatctt cctgttcctt
     2161 ccggcgcaat tcctcttcac gtttaagcaa ctgggctctg agagctgcaa ggccggattc
     2221 cccccactgc tgccactgtt tttcaaatgc catctgactc gcgggaatgt cctgtttctc
     2281 caccttccgg taatgctgtc gtaatttttc catttgctgg ctcagagact ggatttttcc
     2341 ctgctcacta cggtattccg gtgccgccca ttgcatcagg ggaatacggg aaaaaccgga
     2401 cgaaaacggc gatgattttt tcaggctggc agcatggctc atcgcttcct ttcgttcggt
     2461 gttcagctct tcccagcgtc tgcgcgtcgc ctgcatatct gccatcatcg acatggcatt
     2521 actggtgagt ttccatgccg agttactgtc cttcggcaac gcttcgataa tgtcacgtag
     2581 tgtgtacgaa gttgcgttgt caggaagccc gatattcaga aggtcagcca cacggcgggc
     2641 aggctctgtc agccctccgt tcctgagttc ggtgcgggaa atctgtattt ccaggttaag
     2701 cctgttaatc agacgattct gttcgccgcg ttctgtttcg ataccgcgtg tttccatcgc
     2761 acaggcagac tttccgaggt gaataccagg cgttttctca agcccctgtc gctcgtatga
     2821 acgatggtct atctcttcct gataaccggc gttcgccagt gccctgtttg catggtcagc
     2881 ccatgatgcc cgccacgtct cggcatgtgt ccggtcgttc cagtccctga cctttccgct
     2941 gaacccagca ggtccgacag ccctcgtggt cagcatgatg tgcgcatggg gatttgtttt
     3001 atccatgtga tggaacgcca catcagcaat catgccctga ctgacaaagt tttctctgac
     3061 aaaggcgaga acggtttccc gtgcggcatc ctgcggcagt tcgtggggga tggcgagttc
     3121 aatttcccgc gcaagttgtg agttcttccg gcgttcggcc ttctcaacgg cattccagag
     3181 ttcggcacgg ttcgtacacc aggcaggggc ggtggcgggg gtcagaatca cagcctcagc
     3241 cacaccgctt ttgcgggtgt agtcgtgagt cagtccggta cgctcatcaa gcatcagtga
     3301 accggaacga taggcagcgg aagctacggc gctgtagccg ctgcttctgg agataatttt
     3361 catgctgaga tgataaatcg ccatttctgc cgtaatgcct ttttgtagtt ttctttcagc
     3421 cccgcagggc gcacacaatc gaaacggagt ggagattgta taagtgcgca cttcgtgatt
     3481 tgccgtgcat tataccagct cagtttttaa actaccagtg acgcgctaaa atgcgatttt
     3541 tcatcgcgca cggagttaca tcatgagcag aacgctcgaa cagaagattg ctgatgctga
     3601 ggcgagatta cagcgcctga aggcgaagag ccggagcctg gacacagcgc agaaggttgt
     3661 tgtgggtgct gcattgctgg caaaggtcag aaagccggag gaggtgcagt tgcgtgcctg
     3721 gttactccag ttcctgaagg cagaggtgac acgacaggct gatgtgacgc gcatactgcc
     3781 gctgattaac gagctggagg cgctgccaga acagtgattg tatcgtccgc tcgccgcagc
     3841 cccagcgacc gagcgttagc gagcgagtgg gcgaggaagc ggaagtgaat cagtcgccag
     3901 gttgagcaca tacgcacggt ttttcggcag gtgatatgcg ctgaacccgc atgaatactg
     3961 ggtttccaca gggttggagg gggtgtattc gaaacttgca attctgcttt attgcaacgc
     4021 attgttttta ttggtttttt gtttttagca ccccaagtta tccacaggct cg
//
