LOCUS       NZ_CP122826             4448 bp    DNA     circular CON 08-JUN-2024
DEFINITION  Escherichia coli strain ETEC1732 plasmid unnamed3, complete
            sequence.
ACCESSION   NZ_CP122826
VERSION     NZ_CP122826.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN32549609
            Assembly: GCF_030013715.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4448)
  AUTHORS   Vereecke,N., Van Hoorde,S., Sperling,D., Theuns,S., Devriendt,B. and
            Cox,E.
  TITLE     Virotyping and genetic antimicrobial susceptibility testing of
            porcine ETEC/STEC strains and associated plasmid types
  JOURNAL   Front Microbiol 14, 1139312 (2023)
   PUBMED   37143544
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 4448)
  AUTHORS   Vereecke,N., Van hoorde,S., Sperling,D., Theuns,S., Devriendt,B. and
            Cox,E.
  TITLE     Direct Submission
  JOURNAL   Submitted (08-APR-2023) Department of Pathobiology, Pharmacology and
            Zoological Medicine, Universiteit Gent, Salisburylaan 133, Merelbeke
            9820, Belgium
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method :: Trycycler; minimap2; medaka v. v0.5.3; v2.20;
            v1.5.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 125x
            Sequencing Technology             :: Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_030013715.1-RS_2024_06_08
            Annotation Date                   :: 06/08/2024 05:15:47
            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)                     :: 5,741
            CDSs (total)                      :: 5,607
            Genes (coding)                    :: 5,302
            CDSs (with protein)               :: 5,302
            Genes (RNA)                       :: 134
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 100
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 305
            CDSs (without protein)            :: 305
            Pseudo Genes (ambiguous residues) :: 0 of 305
            Pseudo Genes (frameshifted)       :: 138 of 305
            Pseudo Genes (incomplete)         :: 164 of 305
            Pseudo Genes (internal stop)      :: 52 of 305
            Pseudo Genes (multiple problems)  :: 42 of 305
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP122826.1.
            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..4448
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="ETEC1732"
                     /isolation_source="feces"
                     /host="Sus scrofa"
                     /db_xref="taxon:562"
                     /plasmid="unnamed3"
                     /geo_loc_name="Belgium"
                     /collection_date="2021"
                     /collected_by="IMM_DI04"
     gene            1..273
                     /locus_tag="QDX01_RS26510"
                     /old_locus_tag="QDX01_26510"
     CDS             1..273
                     /locus_tag="QDX01_RS26510"
                     /old_locus_tag="QDX01_26510"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_145811.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000019163.1"
                     /translation="MSHNLEHQKVHTRMVKEVLKAVARANNHPYQSVFTDFIAGHPSCT
                     VCFWETFHKMYPDSPYEYVTFCHTCRRFDLYETEAEMKADDPKWW"
                     /name="hypothetical protein"
     gene            254..1462
                     /locus_tag="QDX01_RS26515"
                     /old_locus_tag="QDX01_26515"
     CDS             254..1462
                     /locus_tag="QDX01_RS26515"
                     /old_locus_tag="QDX01_26515"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000198547.1"
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="IS91 family transposase"
                     /protein_id="WP_000198533.1"
                     /translation="MTRSGGDFQPRPLKRLFTANQCWTSFLDAGGLRDIEVEAVTKMLA
                     CGTRILGVKEYNCDKPECPHVRYVTNSCGSRACPSCGKKATDLWIATQLNRLPDCDWVH
                     LVFTLPDTLWPVFESNRWLLNDVCRLAVENLLYAARKRGLEPGIFCAIHTYGRRLNWHP
                     HVHVSVTCGGLNKHGHWKKLSFLKDAMRSRWMWNMRQLLLKAWSEGLAMPESLSHITTE
                     SQWRSLVLKAGGKYWHVYMSKKTAGGRNTARYLGRYLKKPPIAASRLAHYNGGASLSFR
                     YLDHKTGETATETLTQRELVARLKQHIPEKFFKMVRYFGFLANRVCGEKLPQVYRALGM
                     DKPEPVAKVCYAQMVKQFLSRDPFECVLCGGRMVYRRAIAGLNVSGLKKNARDISLLRY
                     MPA"
                     /name="IS91 family transposase"
     gene            2246..2404
                     /locus_tag="QDX01_RS28745"
     CDS             2246..2404
                     /locus_tag="QDX01_RS28745"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001354639.1"
                     /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_071531517.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHALTPLAAATGNRISRAMMA
                     QTVLQSS"
                     /name="replication initiation protein"
     gene            complement(2603..2740)
                     /locus_tag="QDX01_RS26520"
                     /old_locus_tag="QDX01_26520"
     CDS             complement(2603..2740)
                     /locus_tag="QDX01_RS26520"
                     /old_locus_tag="QDX01_26520"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001405930.1"
                     /GO_component="GO:0019867 - outer membrane [Evidence IEA]"
                     /GO_process="GO:0019835 - cytolysis [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin release lysis protein"
                     /protein_id="WP_001405930.1"
                     /translation="MRKRFFVGIFAINLLVGCQANYIRDVQGGTIAPSSSSKLTGIAVQ
                     "
                     /name="colicin release lysis protein"
     gene            2902..3129
                     /locus_tag="QDX01_RS26525"
                     /old_locus_tag="QDX01_26525"
     CDS             2902..3129
                     /locus_tag="QDX01_RS26525"
                     /old_locus_tag="QDX01_26525"
                     /inference="COORDINATES: protein motif:HMM:NF015489.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin E1 immunity protein"
                     /protein_id="WP_229471606.1"
                     /translation="MLYAIVISTILCPYSKYAIEYIAFNFIKKDFFERRKNLNNAPVAK
                     LNLFMLYNLLCLVLAIPFGLLGLFISIKNN"
                     /name="colicin E1 immunity protein"
     gene            complement(3126..>4370)
                     /gene="cea"
                     /locus_tag="QDX01_RS26530"
                     /old_locus_tag="QDX01_26530"
                     /pseudo=""
     CDS             complement(3126..>4370)
                     /gene="cea"
                     /locus_tag="QDX01_RS26530"
                     /old_locus_tag="QDX01_26530"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000447006.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="pore-forming bacteriocin colicin E1"
                     /name="cea"
     Typing          complement(1662..1749)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="6.86e-39"
     Typing          1760..2318
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.365"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atgtcacaca acctggagca ccagaaagtc cacaccagaa tggtgaaaga ggttctgaaa
       61 gccgtcgcca gggccaataa tcacccttat cagtctgtat ttacagactt tatcgccggt
      121 catccctcct gtacggtctg tttctgggaa accttccaca aaatgtaccc ggattcaccg
      181 tacgaatacg tcacgttctg ccatacctgc cgtcgttttg atttatacga aactgaagcg
      241 gagatgaagg cggatgaccc gaagtggtgg tgattttcag ccccgaccgc tgaaacgcct
      301 gttcacagcc aaccagtgct ggacatcctt cctggatgcg ggcggcctgc gcgatatcga
      361 ggttgaggct gtcacaaaaa tgctggcctg cggcacgcgg atactgggtg tgaaggaata
      421 caactgcgat aaacctgagt gcccccacgt cagatacgtc actaactcat gtggcagccg
      481 tgcctgcccg tcctgcggaa aaaaggccac agacctgtgg atagcgacac agctgaatcg
      541 tcttcctgac tgcgactggg tgcacctggt cttcaccctg ccggacacgc tgtggccggt
      601 gttcgaaagc aaccgctggc tgctgaatga cgtgtgccgt ctggcggtgg agaatctgct
      661 gtatgcagcc cggaaacggg gtctggaacc cggtatcttc tgcgccatcc atacgtatgg
      721 ccgtcgtctc aactggcatc cgcatgtgca tgtgtcagtg acctgcggag gtctgaataa
      781 acacggacac tggaaaaagc tgagcttcct gaaagacgcg atgcgttcgc ggtggatgtg
      841 gaatatgcgg cagctgcttc tgaaagcgtg gtcagaaggt ctggcgatgc cggaatcgtt
      901 gtcacatatc acgacggaat cacagtggag aagcctggtg ctgaaagccg gcggaaaata
      961 ctggcatgtg tacatgtcga agaagacagc cggagggcgg aatacggcac gctacctggg
     1021 tcgttatctg aagaagccac caatagcggc ttcccggctg gcgcattaca acggaggagc
     1081 gagtctgagc ttccgttacc tggaccacaa aacgggagaa acggcgacgg aaacgctgac
     1141 acagcgggag ctggtcgcga ggctgaaaca gcacatcccg gagaagtttt ttaagatggt
     1201 gagatacttc gggttccttg ccaaccgggt gtgtggagag aagctgccgc aggtgtaccg
     1261 tgctctgggg atggataagc cggaaccagt ggcgaaagtg tgctatgcac aaatggtgaa
     1321 acagttcctg agtcgtgacc cgttcgaatg cgtgctgtgt ggcggccgga tggtataccg
     1381 ccgggccatt gcggggctga atgtatcagg gctgaagaaa aacgcgcggg atatcagtct
     1441 gctgaggtat atgccggcct gacacaggct aagtgtgccc gggaatcggt gcaggtataa
     1501 aaaacagcct gttacggtat aaaaatcgac catgcagaga gagaaaccac cggagtggag
     1561 ggaaaagcag aaaggctcac gtggcataag gcgtggacag cggtatcgtc tggtttttca
     1621 atttcctata cgtcaagccc gtcagggcgc gtcagcaggt tttagcgggt gtcggggcgc
     1681 agccctgacc cagtcacgta gcgatagcgg agtgtatact ggcttaacca tgcggcatca
     1741 gtgcggattg tatgaaaagt acgccatgcc gggtgtgaaa tgccgcacag atgcgtaagg
     1801 agaaaatgca cgtccaggcg cttttccgct tcctcgctca ctgactcgct acgctcggtc
     1861 gttcgactgc ggcgagcggt actgactcac acaaaaacgg taacacagtt atctacagaa
     1921 tcaggggata aggccggaaa gaacatgtga gcaaaagacc aggaacagga agaaggccac
     1981 gtagcaggcg tttttccata ggctccgccc ccctgacgag catcacaaaa atagacgctc
     2041 aagtcagagg tggcgaaacc cgacaggact ataaagatac caggcgtttc cccctggaag
     2101 ctccctcgtg cgctctcctg ttccgaccct gccgcttacc ggatacctgt ccgcctttct
     2161 cccttcggga agcgtggcgc tttctcatag ctcacgctgt tggtatctca gttcggtgta
     2221 ggtcgttcgc tccaagctgg gctgtgtgca cgaacccccc gttcagcccg accgctgcgc
     2281 cttatccggt aactatcgtc ttgagtccaa cccggtaagg cacgccttaa cgccactggc
     2341 agcagccact ggtaaccgga ttagcagagc gatgatggca caaacggtgc tacagagttc
     2401 ttgaagtagt ggcccgacta cggctacact agaaggacag tatttggtat ctgcgctctg
     2461 ctgaagccag ttaccttcgg aaaaagagtt ggtagctctt gatccggcaa acaaaccacc
     2521 gttggtagcg gtggtttttt tgtttgcaag cagcagatta cgcgcagaaa aaaaggatct
     2581 caagaagatc ctttgatctt ttctactgaa ccgcgatccc cgtcagttta gaagaggagg
     2641 atggtgcgat ggtccctccc tgaacatcac gtatatagtt agcctgacat ccaacaagga
     2701 ggtttatcgc gaatattccc acaaaaaatc ttttcctcat aactcgatcc ttataaaatg
     2761 aaaagaatat atggcgaggt ttaatttatg agcttaagat actacataaa aaatatttta
     2821 tttggcctgt actgcacact tatatatata taccttataa caaaaaacag cgaagggtat
     2881 tatttccttg tgtcagataa gatgctatat gcaatagtga taagcactat tctatgtcca
     2941 tattcaaaat atgctattga atacatagct tttaacttca taaagaaaga ttttttcgaa
     3001 agaagaaaaa acctaaataa cgcccccgta gcaaaattaa acctatttat gctatataat
     3061 ctactttgtt tggtcctagc aatcccattt ggattgctag gactttttat atcaataaag
     3121 aataattaaa tccctaacac ctcatttata gtattaagtt tattcttatc aatataggag
     3181 catagaattc ctgtaacaat agcaataccc caaataccta atgtagttcc agcaagcaag
     3241 ctaaaaagta aagcaacaac ataactcacc cctgcatctg cagctttctt ctctaatgta
     3301 agaaatagtg gcttccagtc acctgtatcc ttaattttta ggatatcaga taccacatca
     3361 tatccaaaag aaacatgccc cgtaatcttc aagtacttgg caaactgatc taaatgttta
     3421 gcccagtcat catacttcac cgatgccaac gcattaaaaa tagcatcacg atcggctttg
     3481 ctgaatttct tatttaaaac atccttgtat ttttcaaaag cagcgagagc ttcattcaca
     3541 ttgccgattt tcttaccttt agacttatca gcaagttcct gtgccatttt cgaatatttt
     3601 tcaccatatt tttcagtcag cgtttgataa aagctaactg ttgcatcaac agcatcctta
     3661 atctgtgaat taaggagatt attctgtgct tttttcaaat tttcttcagc ttcatgaaca
     3721 cgagcgatac cggcattacg attattactg acctgagaaa tagccttctg gatctgagtt
     3781 atatcagcat ttatccggtt aatacgtgtt tctgatgctg ttacctgttt ttgtttttct
     3841 tctctaatct taccggcccc aacccgtcgt ctggttgctt caaaaaaagg acggttctga
     3901 agcggatcat tggctcttgg tgatagtttt ttgaccagct catccagttc tttatattta
     3961 gcggatgcct gagccagttc atttcgtttt ccagcgagcg ttttcatttc tgcatcacgg
     4021 gcatggatac tggagcttaa acgagaattg agagtcttaa tctctccatc cattttcacc
     4081 acttcagatt gtgcagcaga aagttttttt tgggcgatct caacagcttt agcttcttca
     4141 ctcaatgcag ccagtcgttt ctcttcagct tcagccagtt tcaactggcg ttctgtttca
     4201 gccttctccc gttcaatctc tttacgtcgt tgttctgctt cctgaaaagc cttttctgct
     4261 gcttccgctt ctttacgggc tttttcttct gctttcgcaa ggcgcaaacg ctctgcttcc
     4321 gcctgcatag ctgcattatt agcatgagca agctctgttg ctgaaggcga accacggcag
     4381 cctggcggct gcaaatcgtg gtgtggcaga atatgagctt tcagagtaac catccagaat
     4441 gagttccc
//
