LOCUS       NZ_CP122930             3456 bp    DNA     circular CON 08-JUN-2024
DEFINITION  Escherichia coli strain ETEC1702 plasmid unnamed1, complete
            sequence.
ACCESSION   NZ_CP122930
VERSION     NZ_CP122930.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN32549585
            Assembly: GCF_030012765.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3456)
  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 3456)
  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                   :: 131x
            Sequencing Technology             :: Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_030012765.1-RS_2024_06_08
            Annotation Date                   :: 06/08/2024 05:03:28
            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)                     :: 5,103
            CDSs (total)                      :: 4,982
            Genes (coding)                    :: 4,631
            CDSs (with protein)               :: 4,631
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 351
            CDSs (without protein)            :: 351
            Pseudo Genes (ambiguous residues) :: 0 of 351
            Pseudo Genes (frameshifted)       :: 166 of 351
            Pseudo Genes (incomplete)         :: 195 of 351
            Pseudo Genes (internal stop)      :: 51 of 351
            Pseudo Genes (multiple problems)  :: 54 of 351
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP122930.1.
            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..3456
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="ETEC1702"
                     /isolation_source="feces"
                     /host="Sus scrofa"
                     /db_xref="taxon:562"
                     /plasmid="unnamed1"
                     /geo_loc_name="Belgium"
                     /collection_date="2012"
                     /collected_by="IMM_DI04"
     gene            join(3134..3456,1..8)
                     /locus_tag="QDX05_RS23340"
                     /old_locus_tag="QDX05_23335"
                     /pseudo=""
     CDS             join(3134..3456,1..8)
                     /locus_tag="QDX05_RS23340"
                     /old_locus_tag="QDX05_23335"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001377845.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="conjugal transfer protein TrbD"
                     /name="conjugal transfer protein TrbD"
     gene            1..251
                     /gene="trbG"
                     /locus_tag="QDX05_RS23345"
                     /old_locus_tag="QDX05_23340"
                     /pseudo=""
     CDS             1..251
                     /gene="trbG"
                     /locus_tag="QDX05_RS23345"
                     /old_locus_tag="QDX05_23340"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001038337.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="conjugal transfer protein TrbG"
                     /name="trbG"
     gene            258..767
                     /gene="traV"
                     /locus_tag="QDX05_RS23350"
                     /old_locus_tag="QDX05_23345"
                     /pseudo=""
     CDS             258..767
                     /gene="traV"
                     /locus_tag="QDX05_RS23350"
                     /old_locus_tag="QDX05_23345"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000802746.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="type IV conjugative transfer system lipoprotein
                     TraV"
                     /name="traV"
     gene            793..999
                     /locus_tag="QDX05_RS23355"
                     /old_locus_tag="QDX05_23350"
     CDS             793..999
                     /locus_tag="QDX05_RS23355"
                     /old_locus_tag="QDX05_23350"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_282864503.1"
                     /translation="MSRWQWRQKFGIQNLPKKMSAPEGGKGMGGSVSGTCREENSVSDE
                     VDEVYSVTEQLTMTGIKPDTPGK"
                     /name="hypothetical protein"
     gene            1320..>1816
                     /locus_tag="QDX05_RS23360"
                     /old_locus_tag="QDX05_23355"
                     /pseudo=""
     CDS             1320..>1816
                     /locus_tag="QDX05_RS23360"
                     /old_locus_tag="QDX05_23355"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001064255.1"
                     /note="frameshifted; incomplete; partial in the middle of a
                     contig; missing C-terminus; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="TraC family protein"
                     /name="TraC family protein"
     gene            <1867..2562
                     /locus_tag="QDX05_RS23365"
                     /old_locus_tag="QDX05_23360"
                     /pseudo=""
     CDS             <1867..2562
                     /locus_tag="QDX05_RS23365"
                     /old_locus_tag="QDX05_23360"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001553749.1"
                     /note="frameshifted; internal stop; 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="TrbI/VirB10 family protein"
                     /name="TrbI/VirB10 family protein"
     gene            2559..3147
                     /gene="traP"
                     /locus_tag="QDX05_RS23370"
                     /old_locus_tag="QDX05_23365"
                     /pseudo=""
     CDS             2559..3147
                     /gene="traP"
                     /locus_tag="QDX05_RS23370"
                     /old_locus_tag="QDX05_23365"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001345836.1"
                     /note="frameshifted; internal stop; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="conjugal transfer pilus-stabilizing protein TraP"
                     /name="traP"
ORIGIN
        1 atgaataagc tggtttctta cggcagcgtc aaaaaagtaa attatccggt gctgtatgaa
       61 tccggaataa cacctccgtt atgtgtagtc actgcaccag aacctgatgt gtggccaaat
      121 gcattgtggc atatgtttat aaatcatcac ggaatacggt tttcgaaaat cctgacattg
      181 taaaaacctg tacggtcagg gatttgaaga atgattttgt gaactgcgat gagaaaggag
      241 agggacaatg aaacaggatt tcttgctggc ttcctctgct ggggacctta ttactttccc
      301 gctgtgccgg aaccagtacg gaatttgagt gtaaacgcca ccacatccga tacctgtatg
      361 acgatggagc aggccaatga gaaggccaaa aagctggaaa agcagtcctc agaagcaagc
      421 cggttgcgtg gcatcactgc cgcgcctggc tgaagggaac ttccggacac tgttggtgcg
      481 gtgaccatca ccgcgaccga tcagtccggc agcagacctg cggtgacggc acttccggag
      541 cagaaactgc tggcaccacg tccgttgttt acggctgccc gggaagtgaa aacgattgtt
      601 ccggtcagtt cagttgcgcc ggtaacaagt tcccgcccgc taagaacggg tgagcagacg
      661 gctgcattat ggatagcgcc cgagcaccga taatcaggat gtttatcatc agccatccag
      721 gcgtgttttt tgttattaaa ccgtctgcgt gggggaaaac cacgtaataa ttaactggcc
      781 ccctgaagtt atatgtcacg ctggcaatgg cggcaaaaat tcggtattca aaatctgcct
      841 aaaaaaatga gcgctcccga aggtggaaaa gggatgggcg gtagcgtgtc aggaacatgt
      901 cgggaagaaa attccgtgag tgatgaagtc gatgaagtat attcagtaac agaacaattg
      961 accatgacag gaattaaacc ggatacgcca ggaaaataaa tgctcaagcg gtattcctgt
     1021 ttgacatctc tgtgattcat gcggtaatcc tattccgaaa gcctggcgga aaatatttct
     1081 gggtgtgatg tttatgcaaa aggtgaatgt caaatatatc aggaaagcgc agagaaaaca
     1141 ttacgtataa gtcagtcgca gaacatattg atttatttcc agaagcacta gagttgatat
     1201 tcagaaaacc gtagtctagg gacatgcgct tctttctcag aaatggcgcg ttactcatag
     1261 ggacctctct tcatggctac cgcatttcag tttttatttt tcaactaagg aatttagctg
     1321 tgaataaccc actagagggc cgtcactcag gcggttaact ccctcgtcac agcactgaaa
     1381 ctgcctgacg aatccgcaaa ggccaatgaa gttctgggcg aaatggtttt cccccagttc
     1441 agccgtctgc tgccgtaccg gggccccggg gggtggggtt ttatgaatga caccacgatg
     1501 ggctttatcc cccaagccat tcccatcaat ggggcgaatg agtccattgt ggaggccctc
     1561 gataaatgcc cccaaaaatg ccggggtatt ccttgtgttc catctgatgt ccagtcagct
     1621 ggttggtgac aggattgaat acgggctgcg tgagttctcc tggtcaggtg aacaggctga
     1681 acgggttttt aaaaaccctt acccgggcct attatatgaa agcggcagcg acacagtttt
     1741 ccccccgccg gaggggatgg ggaaaaagcc cctgaccctg cgcccttacc gggtgtttat
     1801 ctctctgttc tccctttgaa gaaaaaaaaa agggggccca actggaaaaa aaaacccttt
     1861 aaaatcctgc gtatcaccgg tctggtggaa atgccgaaca gcaaaacgta tgacgcaacg
     1921 ggatgttttg tggggctgga agcctggggg gatgtgtcca gtgaacgtgc cattgtacgc
     1981 acccgtaata tcagctgcct gaagaatggc aaaaccattg atatgccgat taaggggcat
     2041 gtcagcttcc gtactaaaaa tggtgtcatg ggcgaagtgg tgatgcgtgt cggcaaaatc
     2101 ctcggctggg catggggcgc gggatttgtt gacggtatcg gtcagggaat ggattgcgct
     2161 tcctagccgg tcgtcgggct gtcttccaca gccgcttacg gggctggtga tgtcctgaaa
     2221 atgggtatcg gtggcggcgc atcgaaagcc gcacagacgc tcagtgacta ctacatcaaa
     2281 cgtgccgaac agtatcaccc cggtgatacc gattggtgcg ggcaacgaag tgaccgtggt
     2341 gttctatgac ggcttccagc tgaaaaccgt ggaagagatg gcgctggaac gcacgcagag
     2401 cagagcggaa gaagagaatc aggaaagtcc ggtcccttta acgccatcgg ctgaaagtca
     2461 tcttaacggc tttaatactg accagatgct gaagcagcta cccaacctga atccgcagca
     2521 gtttatgtcc ggcagccagg agggggcaac gatggcaaat aataagggta tcgtcccgtc
     2581 aggcgtgcca tgccgcccgg tatgttgtcg cccgggttct gcgaggactg ttctgcaggt
     2641 ctcagcagca caccgtcatt ctgccatcag ctgcaatggc cctgatggct ctgtttgttt
     2701 tatggaagga caacaccacg ccagggcagt taccggttca ggaaattgac ttcgtaagac
     2761 aaacagcccc tgccgggcag tttcctgcaa gagagtgctt ggccttcccc gcatgatctt
     2821 ccaggagcag aagagaaaat ctgccgttac cgtgctgctg atgctgcaga ttatgtcagg
     2881 gagactgacc ggtcactgat gcaactggtt accgcattat gggcaacact ggcattgatg
     2941 tatgtctcac tggcagttat ctccgggaaa tatccggtgc tgcccggaaa atgaaatgta
     3001 tccgggggaa aacctggcag atgaacgtct gacggaaagc ctatacggaa gacgcttccc
     3061 ttgccggaaa aaatcaggaa atgccctgtt tattttcctg atgacagaac aaacagaaac
     3121 aacggagata aaaatgaaca tgcgtaatat taatgttatt actgcccgct ctgtaccgga
     3181 taaaagcgta tcagatgatt ttatgcatgc tgttctcctc agtaactgca ccacaagaat
     3241 cgcatttccg tgcacccgaa ggaattcagt tctgaatcat tgccgcacaa ttttaatatg
     3301 gctgctgtcg gtgtgatgaa agaagggaat gtcgatgagc ttattttctc ttccggggca
     3361 ttattgtggt tgccgggaca atccgagcgg cggaaaatct gttccggtga aagaactaat
     3421 cgacagaatt attccagaaa tataaggaac ccttcg
//
