LOCUS       NZ_CP122767             4763 bp    DNA     circular CON 08-JUN-2024
DEFINITION  Escherichia coli strain ETEC1739 plasmid unnamed9, complete
            sequence.
ACCESSION   NZ_CP122767
VERSION     NZ_CP122767.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN32549616
            Assembly: GCF_030013575.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4763)
  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 4763)
  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                   :: 225x
            Sequencing Technology             :: Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_030013575.1-RS_2024_06_08
            Annotation Date                   :: 06/08/2024 05:11:44
            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)                     :: 5,204
            CDSs (total)                      :: 5,086
            Genes (coding)                    :: 4,727
            CDSs (with protein)               :: 4,727
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 359
            CDSs (without protein)            :: 359
            Pseudo Genes (ambiguous residues) :: 0 of 359
            Pseudo Genes (frameshifted)       :: 124 of 359
            Pseudo Genes (incomplete)         :: 249 of 359
            Pseudo Genes (internal stop)      :: 50 of 359
            Pseudo Genes (multiple problems)  :: 58 of 359
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP122767.1.
            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..4763
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="ETEC1739"
                     /isolation_source="feces"
                     /host="Sus scrofa"
                     /db_xref="taxon:562"
                     /plasmid="unnamed9"
                     /geo_loc_name="Belgium"
                     /collection_date="2021"
                     /collected_by="IMM_DI04"
     gene            join(4297..4763,1)
                     /locus_tag="QDW95_RS25935"
                     /old_locus_tag="QDW95_25935"
                     /pseudo=""
     CDS             join(4297..4763,1)
                     /locus_tag="QDW95_RS25935"
                     /old_locus_tag="QDW95_25935"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_014640312.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="DUF1380 family protein"
                     /name="DUF1380 family protein"
     gene            52..831
                     /locus_tag="QDW95_RS25940"
                     /old_locus_tag="QDW95_25940"
     CDS             52..831
                     /locus_tag="QDW95_RS25940"
                     /old_locus_tag="QDW95_25940"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052647.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_047662418.1"
                     /translation="MNENCTLNALICRHARNLLLAQGWPEETDVDQRDPQNYPGWISIY
                     VRLDAPRLATLLVNRHDCVLPPVLASAMQKLTGTGAELVLSGSQWQSLPVLPADGTQVS
                     FPYAGEWLIEDEIRAVLAAVRDAVRSVSCRVAEDARRIRAALTTTGQTLLTRQTRRFRL
                     VVKESDYPCWLDEDDENLPVVLDAILNRGARFSSVEMYLVCECVEHILASGLVCDVLRI
                     PDEPSRRWFDRDILREVVLEARDEIRSMADALAKIRK"
                     /name="hypothetical protein"
     gene            1249..1674
                     /locus_tag="QDW95_RS25945"
                     /old_locus_tag="QDW95_25945"
     CDS             1249..1674
                     /locus_tag="QDW95_RS25945"
                     /old_locus_tag="QDW95_25945"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001198918.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="antirestriction protein"
                     /protein_id="WP_040073598.1"
                     /translation="MQYAKPVTLNVEECDRLSFLPYLFGNDFLYAEAYVYALAQKMMPE
                     YQGGFWHFIRLPDGGGYMMPDGDRFHLVNGANWFDRTVSADAAGIILTSLVINRQLWLY
                     HDSGDAGLTQLYRMRDAQLWRHIEFHPECNAIYAALD"
                     /name="antirestriction protein"
     gene            1720..2142
                     /locus_tag="QDW95_RS25950"
                     /old_locus_tag="QDW95_25950"
     CDS             1720..2142
                     /locus_tag="QDW95_RS25950"
                     /old_locus_tag="QDW95_25950"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052650.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF1380 family protein"
                     /protein_id="WP_063078191.1"
                     /translation="MYCTVKEIIRDVLDTDVPHSECVFAVVLTRGDVRHIAQDWSLTDD
                     ELETVMQRLDDAFEHGADVSIVHDVVRELMEEKRASRQVTVPAVMLEKVMALAGSEMKR
                     LYAVGSENGGDGDAFVREEREAMDVVLQALDGETMS"
                     /name="DUF1380 family protein"
     gene            2139..2330
                     /locus_tag="QDW95_RS25955"
                     /old_locus_tag="QDW95_25955"
     CDS             2139..2330
                     /locus_tag="QDW95_RS25955"
                     /old_locus_tag="QDW95_25955"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016238862.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_063078190.1"
                     /translation="MNISTESREILRNYRAVINARRREMGQKPLTTAQIVDEICDFVAN
                     QQAVFLGGHYILQGSRHW"
                     /name="hypothetical protein"
     gene            <2524..3024
                     /locus_tag="QDW95_RS25960"
                     /old_locus_tag="QDW95_25960"
                     /pseudo=""
     CDS             <2524..3024
                     /locus_tag="QDW95_RS25960"
                     /old_locus_tag="QDW95_25960"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052643.1"
                     /note="frameshifted; 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="hypothetical protein"
                     /name="hypothetical protein"
     gene            3028..3334
                     /locus_tag="QDW95_RS25965"
                     /old_locus_tag="QDW95_25965"
                     /pseudo=""
     CDS             3028..3334
                     /locus_tag="QDW95_RS25965"
                     /old_locus_tag="QDW95_25965"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052644.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /name="hypothetical protein"
     gene            3410..4093
                     /locus_tag="QDW95_RS25970"
                     /old_locus_tag="QDW95_25970"
     CDS             3410..4093
                     /locus_tag="QDW95_RS25970"
                     /old_locus_tag="QDW95_25970"
                     /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="DNA methylase"
                     /protein_id="WP_282869432.1"
                     /translation="MSRFVLGNCIDVMARIPDNAIDFILTDPPYLVGFRDRSGRTIAGD
                     KTDEWLQPACNEMYRVLKKDALMVSFYGWNRVDRFMAAWKNAGFSVVGHLVFTKTYTSK
                     RRICGLSPRMRLHPGKRGPALPQKPLPDVLGWKYSGNRHHPTEKPVTSLQPLIESFTHP
                     NAIVLDPFAGSGSTCVAALQSRRRYIGIELLEQYHRAGQQRLAARQRAMQQGAANNNWF
                     EPEAA"
                     /name="DNA methylase"
     gene            4094..4316
                     /locus_tag="QDW95_RS25975"
                     /old_locus_tag="QDW95_25975"
                     /pseudo=""
     CDS             4094..4316
                     /locus_tag="QDW95_RS25975"
                     /old_locus_tag="QDW95_25975"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_958723.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /name="hypothetical protein"
ORIGIN
        1 atgttatcgc cgcctgccct gcgggcggcg atacagggag aacgcttaat catgaacgaa
       61 aactgcacgc tgaacgcact gatttgtcgt cacgctcgca acctgctgct ggcgcagggc
      121 tggccggagg agacggatgt tgatcagcga gatccacaga actatccggg ctggatcagc
      181 atttacgtgc ggctggatgc gccccggctg gcgacgttac tcgtcaaccg ccacgattgc
      241 gtactgccgc cggtcctggc ttccgccatg caaaaactga ccggaaccgg ggcggagctg
      301 gtactgtccg gcagtcagtg gcagtcgctg ccggtacttc cggcagacgg aacgcaggtg
      361 tctttcccgt atgccggcga atggctgatc gaagacgaaa tcagggctgt acttgcggcg
      421 gtgcgcgatg cggtacgcag tgtcagttgc cgggtggcag aagatgcacg gcgtatccgg
      481 gcggcgctga ccaccaccgg tcagacgttg ctgacccgcc agacgcgccg ctttcgtctg
      541 gttgtgaagg aaagcgatta cccctgctgg cttgatgaag atgacgaaaa tctgcccgtg
      601 gtgctcgatg ccattctgaa ccgtggcgca cgtttttcct ctgtggaaat gtacttggtc
      661 tgtgagtgtg tggagcatat cctggccagt ggtctggtct gtgatgtgct gcgtataccg
      721 gatgaaccgt cccgtcgctg gtttgaccgg gatattctgc gggaggttgt tctggaggca
      781 cgggatgaaa tccgcagcat ggcggatgca ctggcgaaaa tccggaaatg atgacgctgg
      841 cggggaaaaa tctccgcctt ttccagccgg tccccggaca gagcacaaag gaagtcgctg
      901 ccggctccag ctttacccgg ccatgcaggg catggccttg tggtttttca gttatgtggc
      961 ctcagcgtcg tgtgagaggc tgtgccgtgc ctccatctta gccgggctgg cgttgatgca
     1021 agggtacgct tcgccgctgc ggtcacccgg tccctccttc ccgtctgccg tgattttccg
     1081 gtcgttcacc cgctcagatt tcgcggtctc accctccaac tcccgtcagc cgtgtgcgtc
     1141 aggctgcggc ttcccttgcg cccttgcatc cccgccttat cgcccggctt ttctggaggc
     1201 acggcaccgc ccggtgtcgc ggaatatgtg aacaacggag gaaatcccat gcagtatgcg
     1261 aaacctgtca ctctgaatgt tgaagagtgc gaccgtctct cctttctgcc ttacctgttt
     1321 ggcaacgatt ttctgtatgc cgaggcgtat gtgtacgcgc tggcgcaaaa aatgatgccg
     1381 gaatatcagg gaggcttctg gcacttcatc cgcctgccgg acggtggcgg ttacatgatg
     1441 ccggatggcg accgttttca tctggtcaac ggtgcaaact ggtttgaccg tacggtcagc
     1501 gccgatgccg caggcatcat tctgacttcc cttgtgatta accgccagtt gtggctgtac
     1561 cacgacagcg gggatgcagg actgacccag ctttaccgga tgcgcgatgc gcagttgtgg
     1621 cgtcacatcg aatttcaccc tgaatgcaac gcgatttacg cagcactgga ctgattaacg
     1681 gacgggcggc aatgccgccc ctgtaaagga gacgagaaca tgtactgtac tgttaaagaa
     1741 atcatccgcg atgtactgga tacagacgtg ccgcacagtg aatgcgtttt tgccgtggtg
     1801 ctgacccgtg gggatgtgcg ccacatagcc caggactgga gtctgacaga cgatgagctg
     1861 gaaaccgtca tgcagcgact ggacgatgcc tttgagcatg gtgcggatgt cagcattgtt
     1921 cacgacgttg ttcgtgagct gatggaagaa aagcgcgcca gccgtcaggt gacagttccg
     1981 gcggtgatgc tggaaaaagt gatggcgctg gcaggcagtg aaatgaagcg cctgtatgcc
     2041 gtcgggagcg agaacggggg cgacggtgac gcattcgtca gggaagaacg cgaagcaatg
     2101 gacgttgtgt tacaggcgct ggacggggag acgatgtcat gaatatcagc acggaatccc
     2161 gcgaaattct gcgtaattac agggccgtga ttaatgcgcg gcgtcgtgaa atggggcaga
     2221 aaccgctcac caccgcgcag attgttgatg aaatctgcga ttttgtggcg aatcagcagg
     2281 ctgttttcct gggcggacac tacatcttac agggtagcag acactggtga tacagggcag
     2341 gcggtggagg ccgcctgtca gtccgcgcga aaaccctggc aggctggcgc ctgccggaag
     2401 ggaagcgggc cacgctggcg cgtcgcccgt tacccttccc gtctgtgatg tgtctgactc
     2461 aggagtgttt ctttcttatg ttatggaact gttcctgatg ttgttgttcc tttatctggc
     2521 ttctggagta acgaggatgt atcggcgtgg tggaaccgtc tgtgtgacaa catcctgccg
     2581 gaaaaaacca tgctgtttga cctgctgatt gttctgccca cccgcctgga tgttgaaatg
     2641 aacagcttta acggtggtgt tctgaacggt gattccttct gcatatcact ggtatacgga
     2701 acagtatggc gtgaagtggc ctgtggggta tgaggtgaat atcagtagtc agggagacaa
     2761 cttcattcag gttgatttcg acacgccgtg gtgtcagccg gaaagcgacg ttattgcaga
     2821 attaagccgc cgtttcagct gcacgctgga gcacggtatg ccgaacaggg ctggatttct
     2881 gtggctggca gctgtatgag cgcggagagc cgttgagtgc tgtgggggga actggaatgg
     2941 tcttccccga cagatgacga tgagctgccg gaagtcaccg gacctgcgtg gatagtcgac
     3001 aatgtggcgc attatggcgg atgaagtatg acggagacgg gcgggcaacc cgcccgattt
     3061 cttttccggt aaaggatgtc gccgtgctcc tctttttact gcgccggctg acgcggcgcg
     3121 gcataaacgc tgcctgtggt cagtgtcccg cgtccggtgg gtacgggacg ggcgctttta
     3181 ccgctcccgg ctggcgtcgg tgacagtgta cgccagcctg tcgccctttt ctgatgagcg
     3241 cccttcaagc cgctttcgcg gcacagcctt gccgtcaaaa agacgactgc tgcggtattc
     3301 cacggtcggc ctgacccgtt accggacgcg gtgaacagcc cacaggcagc ggggaacggg
     3361 caccacaggg gtgccctccc ggtgccttct gtaggagaag gagtttcgta tgtcccgttt
     3421 tgtcctcggt aactgcatcg atgttatggc ccgtattcct gataatgcca ttgatttcat
     3481 actgactgac ccgccatatc tcgtcggttt ccgtgaccgt tccgggcgca ccatcgccgg
     3541 tgataaaacc gacgaatggc tgcaaccggc ctgtaatgaa atgtaccgcg tgctgaaaaa
     3601 agatgcgctg atggtgagct tctatggctg gaaccgcgtc gatcgcttta tggccgcctg
     3661 gaaaaatgcg ggattcagcg tggttggcca cctggtattt accaaaacct acacatcgaa
     3721 gcgccgcata tgtgggctat cgccacgaat gcgcttacat cctggcaaaa ggggtccggc
     3781 gctgcctcag aagccattgc ccgacgtgct gggctggaaa tattcaggca accgccatca
     3841 cccgacggaa aagcctgtta ccagcctgca accactgatt gagagcttca cacacccgaa
     3901 cgcgattgtg ctggacccgt ttgcaggcag cggctcaacc tgcgtggctg cccttcagtc
     3961 cagacgccgg tatatcggta tcgagctgct tgaacagtat caccgtgccg gacagcaacg
     4021 actggccgcc aggcaacggg ccatgcagca gggggccgcg aataataact ggtttgaacc
     4081 ggaggctgcg taaatgaact atgccggaca cgaaaacctt cgtgctgaag tggcggaggt
     4141 ggccaatgcc atgtgcgacc tgcgggccag gctgaatgat atggagcatt gccgtacagc
     4201 tttgattccg acgcgcgccg gaacgcctgg cacgccagac gctgtatcgc gccaatcgcc
     4261 tgttcatgga ggcatatacc gaaattcgtg aactggatgc gtgcttcaaa gattaagggg
     4321 gagacgaaat gtacggaaca tgcaaaacgc tctgccggga gctggcagca aagtatccgg
     4381 gagacacgcc gctgatgctg cttatctggt ccccggaaga gattcaggcc ctcgctgacg
     4441 gaatggatat ttccctgtcc gatcatgaaa tcaggactgt cctggcgcgc ctggaggaca
     4501 tcccggaaga ccagcggact gaagtccggt atttcttccg ccgctgcgat ggagattatc
     4561 agcaacgtga gcgaaaaccg ccaggtgacc gtctctgctg aactgctggc gtccctgatt
     4621 cagactgctg aacaggcact gtggaaacgt gaatgggccg cccgggatca tggcctcgcc
     4681 gtcccggaat gcgtcacccg ccgtcaggcg gtgattaatc aggcccgcac cctgctgaaa
     4741 aacaacacac acgaaaacga ctg
//
