LOCUS       NZ_CP145687             4091 bp    DNA     circular CON 05-APR-2024
DEFINITION  Escherichia coli strain S1-KEN-07-A plasmid p4-S1-KEN-07-A, complete
            sequence.
ACCESSION   NZ_CP145687
VERSION     NZ_CP145687.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN33052300
            Assembly: GCF_036884625.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4091)
  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  JOURNAL   Unpublished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 4091)
  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                   :: 188.6525X
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_036884625.1-RS_2024_04_05
            Annotation Date                   :: 04/05/2024 17:24:28
            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)                     :: 5,078
            CDSs (total)                      :: 4,960
            Genes (coding)                    :: 4,725
            CDSs (with protein)               :: 4,725
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 90
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 235
            CDSs (without protein)            :: 235
            Pseudo Genes (ambiguous residues) :: 0 of 235
            Pseudo Genes (frameshifted)       :: 89 of 235
            Pseudo Genes (incomplete)         :: 158 of 235
            Pseudo Genes (internal stop)      :: 43 of 235
            Pseudo Genes (multiple problems)  :: 52 of 235
            Pseudo Genes (short protein)      :: 4 of 235
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP145687.1.
            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..4091
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="S1-KEN-07-A"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="p4-S1-KEN-07-A"
                     /geo_loc_name="Switzerland"
                     /lat_lon="46.947928 N 7.422277 E"
                     /collection_date="2021"
                     /collected_by="Institute for Infectious Diseases (IFIK),
                     University of Bern"
     gene            complement(join(2620..4091,1..688))
                     /gene="mobQ"
                     /locus_tag="V6S32_RS25370"
                     /old_locus_tag="V6S32_25375"
     CDS             complement(join(2620..4091,1..688))
                     /gene="mobQ"
                     /locus_tag="V6S32_RS25370"
                     /old_locus_tag="V6S32_25375"
                     /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            876..1130
                     /gene="mobC"
                     /locus_tag="V6S32_RS25375"
                     /old_locus_tag="V6S32_25380"
     CDS             876..1130
                     /gene="mobC"
                     /locus_tag="V6S32_RS25375"
                     /old_locus_tag="V6S32_25380"
                     /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            1663..2364
                     /locus_tag="V6S32_RS25380"
                     /old_locus_tag="V6S32_25385"
     CDS             1663..2364
                     /locus_tag="V6S32_RS25380"
                     /old_locus_tag="V6S32_25385"
                     /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_001281397.1"
                     /translation="MSDLIAYKSNALVEASYKLTLQEQRFLLLCIGRLKSGADAESPKL
                     QKTMTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKDDEKREEFRWIQYRAQY
                     AKGEARAQITFSDAVMPYLTQLQGQFTRVVIKNISRLSRSYSIRIYELLQQFRSTGERI
                     IALDDFRSMLDIEHKYQTYKSLNQQLLRPCIDELNKKSDLAVTVETIKKGRTVVALHFR
                     FKEDKQIKMTI"
                     /name="replication initiation protein"
     Typing          complement(331..689)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          690..869
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.79"
                     /coverage="100.0"
                     /evalue="5.77e-83"
     Typing          1664..2364
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(3..775)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.612"
                     /coverage="99.0"
                     /evalue="1.21e-172"
     Typing          complement(2624..4089)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 taagtctgtt aatcagacga ttctgttcgc cgcgttctgt ttcgataccg cgtgtttcca
       61 tcgcacaggc agactttccg aggtgaatac caggcgtttt ctcaagcccc tgtcgctcgt
      121 atgaacgatg gtctatctct tcctgataac cggcgttcgc cagtgccctg ttcgcatggt
      181 cagcccatga tgcacgccac gtctcggcat gtgtccggtc gttccagtcc ctgacctttc
      241 caccgaatcc agcaggtccg acagctctcg tggtcagcat gatgtgcgca tggggatttg
      301 ttttatccat gtgatggaac gccacatcag caatcatgcc ctgactgaca aagttttctc
      361 tgacaaaggc gagaacggtt tcccgtgcgg catcctgcgg tagttcgcgg gggatggcga
      421 gttcaatttc ccgcgcaagt tgtgagttct tccggcgttc ggccttctca acggcattcc
      481 agagttcggc acggttcgta caccaggcag gggctgtcgc gggagtcaga atcacagctt
      541 cagccacacc gcttttgcgg gtgtagtcgt gagtcagtcc ggtacgctca tcaagcatca
      601 gtgaaccgga acgataggca gcagaagcaa cggcgctgta gccgctgttt ctggagatga
      661 ttttcatgct gagatgataa atcgccattt ctgccgtaat gcctttttgt ggttttcttt
      721 cagccccgca gggcgcacac aatcgaaacg gagtggagat tgtataagtg cgcacttcgt
      781 gcacttcgtg attttccgtg cattatgcca gctcagtttt taaactacca gtgacgcgct
      841 aaaatgcgat ttttcatcgc gcacggagtt acatcatgag cagaacactc gaacagaaga
      901 ttgctgatgc tgaggccaga ttacagcgcc tgaaggcgaa gagcaggagt ctggacacag
      961 cgcagaaggt cattgtgggt gcagcattgc tggcaaaggt cagaaagccg gaggaggtgc
     1021 agttgcgtgc ctggttactc cagttcctga aggcagaggt gacacgacag gctgatgtga
     1081 cgcgcatact gccgctgatt aacgagctgg aagcgctgcc aggacagtga ttgtatcgtc
     1141 cgctcgccgc agtcccagcg accgagcgtt agcgagcgag tgggcgagga agcggaagtg
     1201 aatccgtcgc ctgattgagc acatacgcac ggtttttcgg gaggtgatat gcgctgaacc
     1261 cgcatgaata ctggatttcc acagggttgg agggggtgta ttcggaactt gcaattctgc
     1321 ttttttgcaa cgcattgttt ttattggttt tttgttttca gcactccaag ttatccacag
     1381 gctcgtcgtt aagtttttag atcttgtttt taagatcttg tttttaatac ttgttttagc
     1441 gccaaaattc cttatagaaa acaaaatgtt acaatgctat aggtaatgtg atttaaggta
     1501 aaggtaatat gatttaaggt gtttaggtgg gggaatttaa ggtaaaggca atatgattta
     1561 aggtaatatt cacagaaaaa gggatattaa aataaaaagg cattgccttt cgttgagggt
     1621 atgtttatct tttattcatt accttttggg gagggatgct ctatgtcgga tctaattgcc
     1681 tataaatcca atgcgctggt tgaagccagt tataaattga ccctacagga acagcgattt
     1741 ttgttacttt gcatcggtcg attgaagtct ggggctgatg cagaatctcc aaaattgcaa
     1801 aagacaatga ccattacagc tgcggaatat ttcgattcat tccctgacat ggggcggaaa
     1861 aatgccgagg ttcagttaca ggaagcaatt gatcgtttgt gggacaggtc aatcattctc
     1921 aaggatgacg agaaacgtga ggagttccgc tggatccagt atcgggcaca gtacgctaaa
     1981 ggcgaggcca gagcacaaat aacattttct gacgcagtaa tgccttattt gacacaacta
     2041 caagggcaat ttactagagt tgtaatcaag aatatatcta gattatcaag aagttacagt
     2101 ataaggatat acgaactcct ccagcagttc cgcagtactg gcgaacgtat tatcgctctc
     2161 gatgattttc gctcaatgct tgatatagag cataaatatc aaacatataa atcacttaac
     2221 cagcaattat taagaccctg cattgacgaa ctgaacaaaa aaagcgacct ggctgtaacg
     2281 gttgagacga tcaaaaaggg gcgcacggtt gtagccctgc attttcgctt caaggaagac
     2341 aaacaaatca agatgacgat ctaaaatcga ttttaaggca cctaaaacgc tccctgctgc
     2401 gttttttttg tgttagtagt gcgaaggtac tattgaagtg aaaaattgcg tcaaaagcgc
     2461 tctaatgcag cgaaaaaaga acccccattt tttgggggcg gaaaaacaaa actatgcttg
     2521 cattatgtgt gtgcttcttg cattcatccc tgtcgatgaa catcgaagaa catcgacgaa
     2581 cataacacga tgttaaacaa aacaaaatat tgttcacatt cactgtgacc aaccgcgatc
     2641 atgtctcctc tcggtggcgt gtgttcgtgc atcttcctcg cgccgccatt cgtcccaggt
     2701 acgattaaaa cccagcgagc ggaacagatg atccggctgt ttttctggtg tgttgacggc
     2761 agcaaaaagc ggtgcctcac gggttttcag atgaaactcc ataagttccg gcgcaggtga
     2821 tatgtggctg tctgcatcgt gatttacggc aacaccatac cctgcatacc gtaacccctt
     2881 atcggtcagt gcactgatga ccagctggct gttatcggct gagggaacgg caaacgcggg
     2941 atacagcgta ccattaagcc ggacaacacc gcccagagag tcatccacgc ccatgaccag
     3001 caaaagctga agctggcggg tttcccggtc gacagaactc attaccggca tcagcgtcgg
     3061 tagcagacgt ccctgcgtaa aatccacctt ccttgctgcc agtgatggca tggctggctg
     3121 gcggtcttct ccaagacaga aagactccgg ccatgtcttc ggctggcgga gattgcgggt
     3181 atattgcggc catgtctggc aaacctgcgt cagaagttgc tcaaaggtcg cagaggaata
     3241 aacacgttgc agtggtggat gttgaccgat ttcgcttcgg tcacagatat aaccactcct
     3301 gtcacgcatt aaatcaacac gctcaaagat tctggtgcgg tatttctcca gctcgttccc
     3361 ccagagcgtg tattctccgt tccggttgtg aagcagaagg taacaggtca tttccccgtt
     3421 accaggcatg ggggcctcgc cataccccgt aacgactgcg ctcagtaccc ctgaatccat
     3481 aacggcattg tcatttttcc tgagctgttc cgctcgtcgc tccgcgcgac tacgttctgt
     3541 atcctcctgc tccttccggc gcaattcctc ttcacgttta agcaactgga ctctgagagc
     3601 tgcaaggccg gatgcccccc actgctgcca ctgtttttca aatgccgtct gactcgcggg
     3661 aatgtcctgt ttctccacct tccggtaatg ctgtcgcaat ttttccattt gctggctcag
     3721 cgactggatt tttccctgtt cgctacggta ttccggtgcc gcccattgca tcaggggaat
     3781 acgggaaaaa ccggacgaaa acggcgatga ttttttcagg ctggcagcat ggctcatcgc
     3841 ttcctttcgt tcggtgttca gctcttccca gcgtctgcgc gtcgcctgca tatctgccat
     3901 catcgacatg gcattactgg tgagtttcca tgccgcatta ctgtccttcg gcaacgcttc
     3961 gatgatgtca cgtagtgtgt acgaagttgc gttgtcagga agcacgatat tcagaaggtc
     4021 agccacacgg cgggcaggct ctgtcagccc gctgtttctg agttcggtac gggaaatctg
     4081 tatttccagg t
//
