LOCUS       CP122658                2810 bp    DNA     circular BCT 15-MAY-2023
DEFINITION  Escherichia coli strain ETEC4074 plasmid plunc_1, complete sequence.
ACCESSION   CP122658
VERSION     CP122658.1
DBLINK      BioProject: PRJNA917806
            BioSample: SAMN32549651
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 2810)
  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 2810)
  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                   :: 223x
            Sequencing Technology             :: Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 04/14/2023 12:11:32
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,071
            CDSs (total)                      :: 4,950
            Genes (coding)                    :: 4,588
            CDSs (with protein)               :: 4,588
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 362
            CDSs (without protein)            :: 362
            Pseudo Genes (ambiguous residues) :: 0 of 362
            Pseudo Genes (frameshifted)       :: 206 of 362
            Pseudo Genes (incomplete)         :: 150 of 362
            Pseudo Genes (internal stop)      :: 40 of 362
            Pseudo Genes (multiple problems)  :: 33 of 362
            Pseudo Genes (short protein)      :: 3 of 362
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            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/
FEATURES             Location/Qualifiers
     source          1..2810
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="ETEC4074"
                     /isolation_source="feces"
                     /host="Sus scrofa"
                     /db_xref="taxon:562"
                     /plasmid="plunc_1"
                     /geo_loc_name="Belgium"
                     /collection_date="2021"
                     /collected_by="IMM_DI04"
     gene            58..456
                     /locus_tag="QDW60_25335"
     CDS             58..456
                     /locus_tag="QDW60_25335"
                     /inference="COORDINATES: protein motif:HMM:NF025361.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="YebF family protein"
                     /protein_id="WHH84815.1"
                     /translation="MIKTSITIIIVAIIAFLFSEYRDNAEAKNCNDISNTQARQDVKSH
                     FMNFLSRAISLQQELGTTDIMFTWGDINREKDNKSELLGINFSAKGHRGEKHFIALYTC
                     SNGKIEYSVVPEDDVSPSGSNVNVDQNP"
                     /name="YebF family protein"
     gene            complement(434..1267)
                     /locus_tag="QDW60_25340"
     CDS             complement(434..1267)
                     /locus_tag="QDW60_25340"
                     /inference="COORDINATES: protein motif:HMM:NF026209.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology. GO_process:
                     GO:0042742 - defense response to bacterium [Evidence IEA]"
                     /codon_start=1
                     /transl_table=11
                     /product="lipid II-degrading bacteriocin"
                     /protein_id="WHH84816.1"
                     /translation="MADTLIVLASPTGYEPPGYGGGYFPPSLSGRHPAASGTGPRAIQG
                     AISFFNSSAMCANTLSWLADYVKKHGASDPLTIQVVTNNIRYFLNADRNLCLNPHISVF
                     DAYMSTKSPAARYNYRSMSMKQMSGKNVTVLAAFGHYLWGNGEARYVNLQDVGLNITPQ
                     QIPELMKIISSGVTGNIPIDIRFNHNTFDSGGVIPAAYLGNVSLQTKGTLSIKQGGAWS
                     YNGVVRAYNDYYDFNLGGFRGPIAESLTYLGSQFKGTPYEISMPGEISIKGSGQR"
                     /name="lipid II-degrading bacteriocin"
     gene            2330..2800
                     /locus_tag="QDW60_25345"
     CDS             2330..2800
                     /locus_tag="QDW60_25345"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016240432.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WHH84817.1"
                     /translation="MHSEKRQKQLSDEAKKANEELEEAKKNSRFTQVSPKGWERVRELL
                     KDSQGVSALKLYTFLAEHIDPACGAVVADQQFLAEKLGVSRSTIIRWLNYLESKNAVVR
                     IPVAGKVCAYALDPHEVWKGYNTTKDYAAFVTKTLVNKDGDIQRRIMAMFSK"
                     /name="helix-turn-helix domain-containing protein"
     Typing          complement(2126..2226)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="85.294"
                     /coverage="93.0"
                     /evalue="5.670000000000001e-21"
     Typing          complement(1485..1741)
                     /name="Col(MG828)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.86"
                     /coverage="98.0"
                     /evalue="3.1e-97"
ORIGIN
        1 atgaatggtt tatttaagtt gaattatttt atggtgataa atatgaaacg gaactcaatg
       61 ataaaaacat caataacaat tattattgtt gctattattg cctttttgtt tagtgaatat
      121 agagacaatg cagaagcaaa gaactgcaat gacatttcta atacacaagc aagacaagat
      181 gtaaagtctc attttatgaa ttttctttct cgcgctattt ctctccaaca ggaactagga
      241 actacagata taatgtttac atggggggat attaatcgag aaaaggataa taaaagtgaa
      301 ttattgggaa tcaacttctc tgccaaagga catagaggag aaaaacattt cattgcatta
      361 tacacttgca gtaatggaaa aatagaatat tcagtagtac cagaggatga cgtttcaccc
      421 tctggatcta atgttaacgt tgaccagaac ccttgatact tatttctcca ggcatagata
      481 tttcataagg tgtaccctta aattgtgaac cgaggtaagt taatgactca gcaataggcc
      541 ccctaaatcc ccctaaattg aaatcataat aatcattata cgctcgaaca accccattat
      601 aggaccatgc accaccttgt ttaatgctca aagttccttt tgtttgtaga gaaacattac
      661 caagatatgc agcaggaatt acgccaccgc tatcaaaagt attatgatta aatctaatat
      721 caataggaat attccccgtt acgccagaac taattatctt catcagttcc ggtatttgtt
      781 gcggtgtgat gttcaaaccg acatcttgca gatttacata tcttgcttca ccattacccc
      841 ataaataatg tccaaatgca gcaagtacag taacattttt tccactcatc tgcttcatgc
      901 tcatggaacg ataattatat ctagctgctg gagacttagt gctcatataa gcatcaaata
      961 cagaaatatg aggatttaaa caaaggtttc tatcagcgtt taaaaaatat ctaatattat
     1021 tagtcaccac ctgaatagta agtggatcgc tagcaccatg ttttttcaca taatcagcaa
     1081 gccaagacaa agtatttgca cacattgcgg aagagttaaa aaaactaata gctccctgta
     1141 tcgctcttgg acctgttcct gaagcagctg gatgtcttcc agataaactt ggagggaaat
     1201 aacctccacc atatcccggt ggttcatatc cggtagggga agcaagtaca atcaatgtat
     1261 cagccataaa taacctcatt cacacattaa agcactgtat aagcatacag tgtttgagcg
     1321 tgttattttt tgaccttaat ctcaaaaata tacgaaccat taattcaaaa cgatcgcatc
     1381 accacggttt ccggttgcgc tcaaggcgct gccggaaacc gtctggggag aaccccagac
     1441 ccccattgct gtaacatcga cggtctacga ccaccaacta gctgaatagc tgcctgtacc
     1501 gtgcaaatga gctttgcagg gggctgacgc ggttcttggc gacctgaaag cccctagtta
     1561 ggggtatcgg cgcgcctgac ctcctgaaac tctctgtaag cgtttttcgc gccttccatg
     1621 ccctgacggg catctaaaac ccgtctcgtg catctgagag cttctgagcg cgttttaggg
     1681 gctatctggc gactcattcc cgaaagaaca acaacggaat cactgacaac atgtgagagg
     1741 tggctccgct cgccgcagcc ccagcgaccg aacgtagtga gcgagtgggc gaggaagcgg
     1801 aagataaccg gaagttacat tgagcactta cgcatagatg cgggggtcgg ggcgaagtcc
     1861 tgattgagat agcgtcgcgt gtgacggtat ctcaattgca catcctgtcc cgatttctgc
     1921 ggagtttaac ggtgaacgga cggcaaaaaa cgtgcaggcg ctgttgaacg tgaaaaccac
     1981 gaaatctggc aaaaatcacg gctggcgagg cttgcagagg agtaagccag tatacactcc
     2041 gctatcgcta cgtgactggt tcagggcttc gccccgaaac cccaaaatag tgttgcttaa
     2101 cgcgcaacac tattacacag aatagatata ttacgtagat ttgtaagttg ttgtttttta
     2161 aggttatgta ttaattatct gtcgcatcca ggatgcgaca acgttgtcgc atcctggatg
     2221 cgacaataga caacaagatg ttgcataagt gagttatcat gttttacatt tgcatcattg
     2281 ttggttcatg ggattttcgg agacaaagat cgtgtttatc agtccagaaa tgcattcaga
     2341 aaaacggcag aaacaactct cagatgaagc taaaaaagcc aatgaagaac ttgaagaagc
     2401 taagaagaat tcaagattta ctcaggtatc cccaaaaggc tgggaacgcg tcagagagct
     2461 tttgaaggat agtcagggag tatctgctct aaagttatat acgtttttag ctgaacatat
     2521 agatcctgca tgtggtgcgg ttgttgcaga tcagcaattt cttgctgaga aacttggcgt
     2581 tagcaggagc acaataatca ggtggctcaa ctacttagaa tcaaaaaatg ctgtagttag
     2641 aattcccgta gctggtaaag tctgtgcgta tgcactcgat cctcatgagg tctggaaggg
     2701 atataacaca acaaaagact atgctgcatt tgttactaaa acattggtca acaaagacgg
     2761 agatattcag cgtcgaatta tggccatgtt ttcaaaataa tgttattaaa
//
