LOCUS       NZ_CP122907             3759 bp    DNA     circular CON 08-JUN-2024
DEFINITION  Escherichia coli strain ETEC1706 plasmid unnamed3, complete
            sequence.
ACCESSION   NZ_CP122907
VERSION     NZ_CP122907.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN32549588
            Assembly: GCF_030012725.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3759)
  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 3759)
  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_030012725.1-RS_2024_06_08
            Annotation Date                   :: 06/08/2024 06:03:10
            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)                     :: 6,261
            CDSs (total)                      :: 6,130
            Genes (coding)                    :: 5,570
            CDSs (with protein)               :: 5,570
            Genes (RNA)                       :: 131
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 97
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 560
            CDSs (without protein)            :: 560
            Pseudo Genes (ambiguous residues) :: 0 of 560
            Pseudo Genes (frameshifted)       :: 268 of 560
            Pseudo Genes (incomplete)         :: 343 of 560
            Pseudo Genes (internal stop)      :: 69 of 560
            Pseudo Genes (multiple problems)  :: 104 of 560
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP122907.1.
            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..3759
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="ETEC1706"
                     /isolation_source="feces"
                     /host="Sus scrofa"
                     /db_xref="taxon:562"
                     /plasmid="unnamed3"
                     /geo_loc_name="Belgium"
                     /collection_date="2020"
                     /collected_by="IMM_DI04"
     gene            1..927
                     /locus_tag="QDX08_RS24600"
                     /old_locus_tag="QDX08_24600"
     CDS             1..927
                     /locus_tag="QDX08_RS24600"
                     /old_locus_tag="QDX08_24600"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221102.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobA/MobL family protein"
                     /protein_id="WP_014342223.1"
                     /translation="MATYHLSVKFGGKGQAANHADYIERKEKYRDRQDLEYSAHGNMPE
                     WARDNPSHFWQAADQFERANGSTYRELEIALPRELTAEQRLELVQDFVRQEAGERHAWS
                     FAIHNPKASIDGGEQPHAHIMMSQRVNDGIERTPEQYFRRYNARYPERGGAKKDSGSLT
                     LTQQKEQLRELRKRWEVKHNEHMRKHGFERGFIDCRTLKEQGIERRPEVHLGFEAAGRL
                     DDAQRHDIMQKRSEPDYSRHLEQARTVGYDIREWLDTPVKQHELVRRLQHDVAREHGFD
                     MRDRVSRQNRTEPERVKSPSRGFSMGF"
                     /name="MobA/MobL family protein"
     gene            930..1463
                     /locus_tag="QDX08_RS24605"
                     /old_locus_tag="QDX08_24605"
     CDS             930..1463
                     /locus_tag="QDX08_RS24605"
                     /old_locus_tag="QDX08_24605"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221103.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000168772.1"
                     /translation="MASTEEKLLTLLLSVEHLQHTAMEQQKAVADSLAVARETLRGYRD
                     ISDGVAKQVRDEVRNEVQKLDVAGLIGERISQDFQRLEESVANMKANADALNRDIATIH
                     SNIVQEYNTLKGYSWKWLGGVSVAFLVMFCVLGWGMKTMLDRNYNATAAVYQKVVTLED
                     KLAEKPVTGKSRKN"
                     /name="hypothetical protein"
     gene            1898..2929
                     /locus_tag="QDX08_RS24610"
                     /old_locus_tag="QDX08_24610"
     CDS             1898..2929
                     /locus_tag="QDX08_RS24610"
                     /old_locus_tag="QDX08_24610"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001271373.1"
                     /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_050957666.1"
                     /translation="MSAALQYFEENLPHRPYHTDDLAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDREGAAIDWSDRNAPAPNITVKNPVNGHAHLLYALNIAVRTAPDASVKA
                     LKYAAAVERSLCEKLCADVNYSGLICKNPFHLEWQVMEWREDAYTLDELADYLDLSASE
                     RRSIDKHYGMGRNCHLFEMTRKWAYRAIRQGWPAFSQWLEAVIQRVEMYNASLPVPLSL
                     AECRAIGKSIAKYTHRNFTPETFAQYVADTHTPEIQAARGRKGGKANSSKNQADKGKVG
                     GKNSGVVRWTANDDKRRRALDMYILGASTEDIAVAVGVSSRTIRRWMDSSGEWLAKKQI
                     IKY"
                     /name="replication initiation protein"
     gene            complement(3310..3588)
                     /locus_tag="QDX08_RS24615"
                     /old_locus_tag="QDX08_24615"
     CDS             complement(3310..3588)
                     /locus_tag="QDX08_RS24615"
                     /old_locus_tag="QDX08_24615"
                     /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_179142683.1"
                     /translation="MRISNIEWLKKRIGFIRKLGEQTARQRQIIDLLDNEAGLTEQERK
                     LLHVLATAEKNDLQAQESERKQAVQKRIEGKNNDENAITDSFSRLGY"
                     /name="hypothetical protein"
     Typing          1899..2674
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="97.297"
                     /coverage="83.0"
                     /evalue="0.0"
     Typing          2..924
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.727"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gtggcaacct atcacctcag cgttaaattt ggtggcaagg ggcaggctgc aaaccacgcc
       61 gattacatcg agcgcaaaga gaaataccgc gaccgtcagg atttggaata ttccgcacac
      121 ggaaacatgc cggaatgggc gcgagataat ccctcacatt tctggcaggc tgctgaccag
      181 tttgaacgtg cgaacggttc gacctatcgg gaacttgaaa ttgcattacc ccgtgaactg
      241 acagcggaac agcgccttga actggtgcag gattttgtac gtcaggaagc tggcgaacgg
      301 cacgcctgga gttttgccat tcacaatccg aaagcgagca ttgacggcgg cgaacagcct
      361 catgcgcata tcatgatgag ccagcgtgtg aatgatggca ttgaacgtac accggaacag
      421 tatttccggc gctataacgc caggtatccc gagcggggag gtgcgaaaaa ggattccgga
      481 agcctgactc tcactcagca aaaagagcag ttgcgggaat tgcgaaaacg ctgggaggtg
      541 aagcacaacg aacatatgag aaagcatggc tttgaaaggg gcttcattga ctgccggacg
      601 ctgaaagaac agggcattga acgacgtccc gaagtgcatc tgggttttga agctgccgga
      661 cggcttgatg atgcccagcg tcatgacatc atgcaaaaac ggtctgaacc ggactattcc
      721 cgccatcttg aacaggcgcg aacggtcggg tatgacatca gggaatggct ggacactccg
      781 gttaagcaac atgaactggt cagaaggctg caacatgatg ttgcgcggga gcatggcttt
      841 gacatgagag acagagtgag cagacagaac cgaactgaac ctgaacgggt taaatcaccg
      901 tcacgtggat tttctatggg attctgaaca tggccagcac agaagaaaaa ttactcacgc
      961 tcctgttatc ggtggagcat ctgcaacata ccgcaatgga gcaacagaaa gctgttgctg
     1021 attctctggc tgtggcaagg gaaacacttc gcggatatcg ggatatttct gacggtgtgg
     1081 caaaacaggt cagggatgaa gtcagaaacg aggtgcagaa gctggatgtt gcagggctga
     1141 taggtgagcg catcagccag gattttcagc ggctggaaga gtcagtcgca aacatgaagg
     1201 caaacgcgga tgccctgaac agggatattg cgacaattca cagcaatatc gtgcaggaat
     1261 acaacaccct taaagggtat agctggaaat ggctgggtgg ggtgtcagtg gcttttctgg
     1321 ttatgttctg tgtgcttgga tggggaatga aaacaatgct cgacaggaac tacaacgcca
     1381 cagcggcggt gtatcagaaa gttgtgacac tggaagataa actggcggag aaacctgtca
     1441 cgggcaagag ccggaaaaac tgacgcgctt cgcttgtcca acgcctcacg acccgcgaaa
     1501 aaattccgcg tcccgttcac cgttttctga tgagaaagtt tgctgttttg acccgttcgc
     1561 ccttctgaac gctcgaaaca gatcgcgcat cgctttcgtg catagttatg cagcgcgcta
     1621 aaaacgattc tgacgcattt ttctggttta gcctggtgtt tccttgtctt tttgcgtttt
     1681 ttgcgccaga gagcgactga gggcgtttta aggggggcgt acaacggatg ttatggtaaa
     1741 tggatcgggt ttgcgggaag gctcgacagg ttttgtcgtt gggggtagtg taagcgactg
     1801 aaaaacaaac gcccctgaaa ttcgtgtctc tccgccaaga ttgtcacgaa aattcaaggg
     1861 gcgtgtgggt cgtaacacac ggaggaaatc ctaacacatg agcgccgcgc ttcaatactt
     1921 cgaagaaaat ttaccccacc gtccctatca cacggatgat ctcgcttttg gtcttcgcat
     1981 ctccggcaaa gggcgtgcgc ttcttgcgcg gtacatccag cagaaccagc ctcatgcgca
     2041 gttctggctg gtttttgacg ttgaccgcga gggggctgcg attgactgga gcgaccggaa
     2101 cgcccccgcg ccgaacatca ccgttaaaaa tcctgtgaac ggacacgctc acctgctcta
     2161 cgcactcaac atcgccgtga gaaccgcgcc tgatgcctcg gttaaggcgc tgaaatatgc
     2221 cgcagcggtt gaacgttcgc tgtgtgagaa actttgtgct gatgtgaact acagcggcct
     2281 gatttgcaaa aatccgttcc acctggaatg gcaggtgatg gagtggcgcg aggacgccta
     2341 taccctcgat gaactggcag attatctcga tttgagcgcc tcagagcgtc gtagcatcga
     2401 taaacattac gggatggggc gaaactgcca cctgttcgaa atgacgcgca aatgggctta
     2461 cagggcgatt cgtcagggct ggccagcgtt ctcacagtgg cttgaagcgg tgatccagcg
     2521 tgtcgaaatg tacaatgcat cgcttcccgt tccgctttca ctggctgaat gtcgggctat
     2581 tggcaagagc attgcgaaat acacgcacag gaacttcacg ccggaaactt tcgcacagta
     2641 tgtggctgat acgcacacgc cagaaattca ggccgcacga ggtcgcaagg gcggtaaggc
     2701 caattcgtca aaaaatcagg cggacaaagg gaaagttggc gggaaaaaca gcggtgttgt
     2761 ccggtggacg gctaacgatg ataaacgtcg tagggcgctt gatatgtaca tcttgggagc
     2821 gtcaacagaa gatattgcag tggcggttgg tgttagcagt cggactattc gacgctggat
     2881 ggatagctct ggagaatggc tagcaaagaa acaaataatt aaatattagt ttacaaaaaa
     2941 agcaacaaac cccctggttt ttgttaatgg gttgttaaat ttgcggacac gaagcaagcc
     3001 tatatcagat aacagcgcct ttcggcgtct ttttgagcag cgggctttcc ggcggttttc
     3061 tcctctcagc ccagcaatgg tgcggcttac cgcatgattg aggtggtcgt gctcgccgca
     3121 gtctcatgac cgagcgtagc gagcgaatga gcgaggaagc accagggaac cggaacacgg
     3181 atggaggcac ttacgcgtct gggtttgggg atgtctccag atcgtactta atttccttaa
     3241 gtgcctgtaa tatcctgtct tttttatagc atagctcgcc tgtttttgtg tctaccagtc
     3301 ctgcttcgat cagtagccca gccgcgagaa agagtcggtg attgcgttct cgtcgttgtt
     3361 ttttccctcg attcgttttt ggaccgcctg ttttcgttcg ctctcctgtg cctgtaagtc
     3421 gtttttttcc gctgttgcca gtacgtggag gagtttgcgt tcctgttctg tgagtcctgc
     3481 ttcgttgtcg agcaggtcaa taatctgtct ctgtcgtgcg gtctgttctc cgagcttcct
     3541 gatgaatccg atccgtttct tcagccattc gatgttgctg atgcgcatgt tcgtggtgct
     3601 ccctggtgtt tttttgcggt gtgttgtggt cgtgcagtat atcgcttgcg gtcggcgggt
     3661 gcagggggta tcttccgtgc taattcgtaa aattagaagg aagcgcactg tttctctcct
     3721 tcgtcgagaa acagtgcgct cctgcggagg gctgaaacc
//
