LOCUS       NZ_CP145661             4081 bp    DNA     circular CON 05-APR-2024
DEFINITION  Escherichia coli strain S1-IND-01-A plasmid p4-S1-IND-01-A, complete
            sequence.
ACCESSION   NZ_CP145661
VERSION     NZ_CP145661.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN33052308
            Assembly: GCF_036884445.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4081)
  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  JOURNAL   Unpublished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 4081)
  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                   :: 360.8078X
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_036884445.1-RS_2024_04_05
            Annotation Date                   :: 04/05/2024 17:10:44
            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)                     :: 4,993
            CDSs (total)                      :: 4,870
            Genes (coding)                    :: 4,689
            CDSs (with protein)               :: 4,689
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 181
            CDSs (without protein)            :: 181
            Pseudo Genes (ambiguous residues) :: 0 of 181
            Pseudo Genes (frameshifted)       :: 67 of 181
            Pseudo Genes (incomplete)         :: 108 of 181
            Pseudo Genes (internal stop)      :: 46 of 181
            Pseudo Genes (multiple problems)  :: 37 of 181
            Pseudo Genes (short protein)      :: 2 of 181
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP145661.1.
            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..4081
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="S1-IND-01-A"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="p4-S1-IND-01-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(2579..4081,1..657))
                     /gene="mobQ"
                     /locus_tag="V6S40_RS24955"
                     /old_locus_tag="V6S40_24960"
     CDS             complement(join(2579..4081,1..657))
                     /gene="mobQ"
                     /locus_tag="V6S40_RS24955"
                     /old_locus_tag="V6S40_24960"
                     /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_023908709.1"
                     /translation="MAIYHLSMKIISRNSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPRELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNSGLTEPARRVADLLNIVLPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGASGLAALRVQL
                     LKREEELRRKEQEDRERSRAERRAEQLRKNDNAVMDSGVLSAVVTGYGEAPMPGNGEMT
                     CYLLLHNRNGEYTLWGNELEKYRTRIFERVDLMRDRSGYICDRSEIGQHPPLQRVYSSA
                     TFEQLLTQVCQTWPQYTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLLPTL
                     MPVMSSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKG
                     LRYAGYGVAVNHDADSHISPAPELMEFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRT
                     WDEWRREEDARTHATERRHDRGWSQ"
                     /name="mobQ"
     gene            836..1090
                     /gene="mobC"
                     /locus_tag="V6S40_RS24960"
                     /old_locus_tag="V6S40_24965"
     CDS             836..1090
                     /gene="mobC"
                     /locus_tag="V6S40_RS24960"
                     /old_locus_tag="V6S40_24965"
                     /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            1623..2324
                     /locus_tag="V6S40_RS24965"
                     /old_locus_tag="V6S40_24970"
     CDS             1623..2324
                     /locus_tag="V6S40_RS24965"
                     /old_locus_tag="V6S40_24970"
                     /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_023908708.1"
                     /translation="MSDLIAYKSNALVEASYKLTLQEQRFLLLCIGRLKSGADAESPKL
                     QKTMTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKDDEKREEFRWIQYRAQY
                     AKGEARAQITFSDAVMPYLTQLQGQFTRVVIKNISRLSRSYSIRIYELLQQFRSTGERI
                     ITLDDFRSMLDIEHKYQTYKSLNQQLLRPCIDELNKKSDLAVTVETIKKGRTVVALHFR
                     FKEDKQIKMTI"
                     /name="replication initiation protein"
     Typing          complement(300..658)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          659..835
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          1624..2324
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.858"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(2..744)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.597"
                     /coverage="100.0"
                     /evalue="7.369999999999999e-165"
ORIGIN
        1 gcgttctgtt tcgataccgc gtgtttccat cgcacaggca gactttccga ggtgaatacc
       61 aggcgttttc tcaagcccct gtcgctcgta tgaacgatgg tctatctctt cctgataacc
      121 ggcgttcgcc agtgccctgt tcgcatggtc agcccatgat gcacgccacg tctcggcatg
      181 tgtccggtcg ttccagtccc tgacctttcc accgaatcca gcaggtccga cagctctcgt
      241 ggtcagcatg atgtgcgcat ggggatttgt tttatccatg tgatggaacg ccacatcagc
      301 aatcatgccc tgactgacaa agttttctct gacaaaggcg agaacggttt cccgtgcggc
      361 atcctgcggt agttcgcggg ggatggcgag ttcaatttcc cgcgcaagtt gtgagttctt
      421 ccggcgttcg gccttctcaa cggcattcca gagttcggca cggttcgtac accaggcagg
      481 ggctgtcgcg ggagtcagaa tcacagcttc agccacaccg cttttgcggg tgtagtcgtg
      541 agtcagtccg gtacgctcat caagcatcag tgaaccggaa cgataggcag cagaagcaac
      601 ggcgctgtag ccgctgtttc tggagatgat tttcatgctg agatgataaa tcgccatttc
      661 tgccgtaatg cctttttgtg gttttctttc agccccgcag ggcgcacaca atcgaaacgg
      721 agtggagatt gtataagtgc gcacttcgtg attttccgtg cattatgcca gctcagtttt
      781 taaactacca gtgacgcgct aaaatgcgat ttttcatcgc gcacggagtt acatcatgag
      841 cagaacactc gaacagaaga ttgctgatgc tgaggccaga ttacagcgcc tgaaggcgaa
      901 gagcaggagt ctggacacag cgcagaaggt cattgtgggt gcagcattgc tggcaaaggt
      961 cagaaagccg gaggaggtgc agttgcgtgc ctggttactc cagttcctga aggcagaggt
     1021 gacacgacag gctgatgtga cgcgcatact gccgctgatt aacgagctgg aagcgctgcc
     1081 aggacagtga ttgtatcgtc cgctcgccgc agtcccagcg accgagcgtt agcgagcgag
     1141 tgggcgagga agcggaagtg aatccgtcgc ctgattgagc acatacgcac ggtttttcgg
     1201 gaggtgatat gcgctgaacc cgcatgaata ctggatttcc acagggttgg agggggtgta
     1261 ttcggaactt gcaattctgc ttttttgcaa cgcattgttt ttattggttt tttgttttca
     1321 gcactccaag ttatccacag gctcgtcgtt aagtttttag atcttgtttt taagatcttg
     1381 tttttaatac ttgttttagc gccaaaattc cttatagaaa acaaaatgtt acaacgctat
     1441 aggtaatatg atttaaggta aaggtaatat gatttaaggt gcttgggtaa tatgatttaa
     1501 ggtaaaggca atatgattta aggtaatatt cacagaaaaa gggatattaa aataaaaagg
     1561 cattgccttt cgttgagggt atgtttatct tttattcatt accttttggg gagggatgct
     1621 ctatgtcgga tctaattgcc tataaatcca atgcgctggt tgaagccagt tataaattga
     1681 ccctacagga acagcgattt ttgttacttt gcatcggtcg attgaagtct ggggctgatg
     1741 cagaatctcc aaaattgcaa aagacaatga ccattacagc tgcggaatat ttcgattcat
     1801 tccctgacat ggggcggaaa aatgccgagg ttcagttaca ggaagcaatt gatcgtttgt
     1861 gggacaggtc aatcattctc aaggatgacg agaaacgtga ggagttccgc tggatccagt
     1921 atcgggcaca gtacgctaaa ggcgaggcca gagcacaaat aacattttct gacgcagtaa
     1981 tgccttattt gacacaacta caagggcaat ttactagagt tgtaatcaag aatatatcta
     2041 gattatcaag aagttacagt ataaggatat acgaactcct ccagcagttc cgcagtactg
     2101 gcgaacgtat tatcactctc gatgattttc gctcaatgct tgatatagag cataaatatc
     2161 aaacatataa atcacttaac cagcaattat taagaccctg cattgacgaa ctgaacaaaa
     2221 aaagcgacct ggctgtaacg gttgagacga tcaaaaaggg gcgcacggtt gtagccctgc
     2281 attttcgctt caaggaagac aaacaaatca agatgacgat ctaaaatcga ttttaaggca
     2341 cctaaaacgc tccctgccgc gttttttttg tgttagtagt gcgaaggtac tattgaagtg
     2401 aaaaattgcg tcaaaagcgc tctaatgcag cgaaaaaaga acccccattt ttgggggcgg
     2461 aaaaacaaaa ctatgcttgc attatgtgtg tgcttcttgc attcatccct gtcgatgaac
     2521 atcgaagaac atcgacgaac ataacacgat gttaaacaaa acaaaatatt gttcacattc
     2581 actgtgacca accgcgatca tgtctcctct cggtggcgtg tgttcgtgca tcttcctcgc
     2641 gccgccattc gtcccaggta cgattaaaac ccagcgagcg gaacagatga tccggctgtt
     2701 tttctggtgt gttgacggca gcaaaaagcg gtgcctcacg ggttttcaga tgaaactcca
     2761 taagttccgg cgcaggtgat atgtggctgt ctgcatcgtg atttacggca acaccatacc
     2821 ctgcataccg taacccctta tcggtcagtg cactgatgac cagctggctg ttatcggctg
     2881 agggaacggc aaacgcggga tacagcgtac cattcagccg gacaacaccg cccagagagt
     2941 catccacgcc catgaccagc aaaagctgaa gctggcgggt ttcccggtcg acagaactca
     3001 ttaccggcat cagcgtcggt agcagacgtc cctgcgtaaa atccaccttc cttgctgcca
     3061 gtgatggcat ggctggctgg cggtcttctc caagacagaa agactccggc catgtcttcg
     3121 gctggcggag attgcgggta tattgcggcc atgtctggca aacctgcgtc agaagttgct
     3181 caaaggtcgc agaggaataa acacgttgca gtggtggatg ttgaccgatt tcgcttcggt
     3241 cacagatata accactcctg tcacgcatta aatcaacacg ctcaaagatt ctggtgcggt
     3301 atttctccag ctcgttcccc cagagcgtgt attctccgtt ccggttgtga agcagaaggt
     3361 aacaggtcat ttccccgtta ccaggcatgg gggcctcgcc ataccccgta acgactgcgc
     3421 tcagtacccc tgaatccata acggcattgt catttttcct gagctgttcc gctcgtcgct
     3481 ccgcgcgact acgttctcta tcctcctgct ccttccggcg caattcctct tcacgtttaa
     3541 gcaactggac tctgagagct gcaaggccgg atgcccccca ctgctgccac tgtttttcaa
     3601 atgccgtctg actcgcggga atgtcctgtt tctccacctt ccggtaatgt tgtcgcaatt
     3661 tttccatttg ctggctcagc gactggattt ttccctgttc gctacggtat tccggtgccg
     3721 cccattgcat caggggaata cgggaaaaac cggacgaaaa cggcgatgat tttttcaggc
     3781 tggcagcatg gctcatcgct tcctttcgtt cggtgttcag ctcttcccag cgtctgcgcg
     3841 tcgcctgcat atctgccatc atcgacatgg cattactggt gagtttccat gccgcattac
     3901 tgtccttcgg caacgcttcg atgatgtcac gtagtgtgta cgaagttgcg ttgtcaggaa
     3961 gcacgatatt cagaaggtca gccacacggc gggcaggctc tgtcagcccg ctgtttctga
     4021 gttcggtacg ggaaatctgt atttccaggt taagtctgtt aatcagacga ttctgttcgc
     4081 c
//
