LOCUS       NZ_CP122591             5720 bp    DNA     circular CON 08-JUN-2024
DEFINITION  Escherichia coli strain ETEC6335 plasmid unnamed3, complete
            sequence.
ACCESSION   NZ_CP122591
VERSION     NZ_CP122591.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN32549676
            Assembly: GCF_030013005.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5720)
  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 5720)
  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                   :: 260x
            Sequencing Technology             :: Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_030013005.1-RS_2024_06_08
            Annotation Date                   :: 06/08/2024 05:27:29
            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)                     :: 5,662
            CDSs (total)                      :: 5,534
            Genes (coding)                    :: 5,336
            CDSs (with protein)               :: 5,336
            Genes (RNA)                       :: 128
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 97
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 198
            CDSs (without protein)            :: 198
            Pseudo Genes (ambiguous residues) :: 0 of 198
            Pseudo Genes (frameshifted)       :: 83 of 198
            Pseudo Genes (incomplete)         :: 121 of 198
            Pseudo Genes (internal stop)      :: 29 of 198
            Pseudo Genes (multiple problems)  :: 27 of 198
            Pseudo Genes (short protein)      :: 1 of 198
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP122591.1.
            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..5720
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="ETEC6335"
                     /isolation_source="feces"
                     /host="Sus scrofa"
                     /db_xref="taxon:562"
                     /plasmid="unnamed3"
                     /geo_loc_name="Netherlands"
                     /collection_date="2021"
                     /collected_by="IMM_DI04"
     gene            1..999
                     /locus_tag="QDY30_RS25675"
                     /old_locus_tag="QDY30_25675"
     CDS             1..999
                     /locus_tag="QDY30_RS25675"
                     /old_locus_tag="QDY30_25675"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000012467.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type IV secretion system protein"
                     /protein_id="WP_033550755.1"
                     /translation="MSGFFEKFNSEVVSKIEEMTKPLQSQLGQDMLSLLSAGISVYILW
                     VGYQILAGKRQTPLQDLVWDLSKFAIILTFVSNADGYLTAAMDAIKSMKDGFLGKPVWA
                     TLDTMWSTTQLLADKVYAMDQSKYVSVEGGIGSMLVWGGSILIMSVAAVIYMLADVTMQ
                     LAILVAPIFIGCHMFGFTRVMFNNWLGILFSSVFTVIFAGVLVKIGTEFQTDMLSQISR
                     DANSTNILTMGAMAFVIGVLIAVFVWKSSSFAQQLAGAGVEGTLQGMALLGIGAAGMAV
                     EKTRNQMKRGTQTAAEWAGEKVEQKRASTGALGMEARRRASLEKARARSSA"
                     /name="type IV secretion system protein"
     gene            996..1709
                     /locus_tag="QDY30_RS25680"
                     /old_locus_tag="QDY30_25680"
     CDS             996..1709
                     /locus_tag="QDY30_RS25680"
                     /old_locus_tag="QDY30_25680"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001590713.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type IV secretion system protein"
                     /protein_id="WP_033550757.1"
                     /translation="MNKKLIFSVLLCLFSFGSVAGIPVAIDASPEWAIEATRWTERLKQ
                     WSETARHYQSQIQAYKDQLATATGIRNIAAFTNELSNLQSELANIYKQGNSYISDFTSN
                     PEGALSSQAKNLFSKYGAFDMCNTGIESSDNLCKARIVSTAASIEQGNEINKQLSSAMS
                     QIQSLSSRIESSKDMKESQDLANALQAQSLKIQAIKMQYDVWDSKNRADAEMLKEQKYA
                     EYRLRQKNAKIPSFE"
                     /name="type IV secretion system protein"
     gene            complement(2046..2549)
                     /gene="ddp1"
                     /locus_tag="QDY30_RS25685"
                     /old_locus_tag="QDY30_25685"
     CDS             complement(2046..2549)
                     /gene="ddp1"
                     /locus_tag="QDY30_RS25685"
                     /old_locus_tag="QDY30_25685"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000781816.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DNA distortion polypeptide 1"
                     /protein_id="WP_169023835.1"
                     /translation="MKNVCFRLNDDEYELARVNAASYGVDSVNVFAKMKVLDVPTKPVS
                     IPVKNEAAKPVFTYLYPHEIELVKRNAVLHGMSMSREIAIRVRQSLLKNEVCLYPDEVK
                     ELKKLSTAVDRVGRNIHFIIKGERFCTVNDPDFRKDVIEVIELCKQIDSKLETLTKSVV
                     NRFG"
                     /name="ddp1"
     gene            2790..3039
                     /locus_tag="QDY30_RS25690"
                     /old_locus_tag="QDY30_25690"
                     /pseudo=""
     CDS             2790..3039
                     /locus_tag="QDY30_RS25690"
                     /old_locus_tag="QDY30_25690"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005653200.1"
                     /GO_function="GO:0003729 - mRNA binding [Evidence IEA]"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system HicA family toxin"
                     /name="type II toxin-antitoxin system HicA family toxin"
     gene            3036..3380
                     /locus_tag="QDY30_RS25695"
                     /old_locus_tag="QDY30_25695"
     CDS             3036..3380
                     /locus_tag="QDY30_RS25695"
                     /old_locus_tag="QDY30_25695"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001016018.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system HicB family
                     antitoxin"
                     /protein_id="WP_000681612.1"
                     /translation="MKHLKYKGYLGTVEPDFENNVLYGKLAFIRDLVTYEASTLAELEQ
                     EFKTSVDLYLQSCVEDGKEPDIPFKGVFNVRLDPELHRRVAEMAMEEDLSLNAFVNKAL
                     EKEVTNHSIR"
                     /name="type II toxin-antitoxin system HicB family
                     antitoxin"
     gene            complement(3484..3591)
                     /locus_tag="QDY30_RS25700"
                     /old_locus_tag="QDY30_25700"
     CDS             complement(3484..3591)
                     /locus_tag="QDY30_RS25700"
                     /old_locus_tag="QDY30_25700"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001529707.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_033550228.1"
                     /translation="MPTDARQGMEGAKNAYRGFQEAKRADTPNQGLSGR"
                     /name="hypothetical protein"
     gene            4241..4990
                     /locus_tag="QDY30_RS25705"
                     /old_locus_tag="QDY30_25705"
     CDS             4241..4990
                     /locus_tag="QDY30_RS25705"
                     /old_locus_tag="QDY30_25705"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001677229.1"
                     /GO_function="GO:0003887 - DNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /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_000676688.1"
                     /translation="MKGKKTESITMTLNLRGKNIVMSNAITRAAQSLSLAEKRIIFAAI
                     AKMGGQYTPIKITAEEYANTFGMPLKQAYSQLKIAADNFFNRYISFRINEVSETDVDVW
                     KIRWLGAYKYNEGEAHVVLSFTPQVTPYLCELEENFTKYQLSQACGLRSVHSWRLLELF
                     EQMNTHKDNNGWLSISLDDFHHAMESPESYKKTFGLLRERVIEPAVKELTEKDNWIIQW
                     KPLKRGKKVVRLEFWFQKDEQSKIIKN"
                     /name="replication initiation protein"
     gene            5067..5351
                     /locus_tag="QDY30_RS25710"
                     /old_locus_tag="QDY30_25710"
     CDS             5067..5351
                     /locus_tag="QDY30_RS25710"
                     /old_locus_tag="QDY30_25710"
                     /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_000160397.1"
                     /translation="MTKHDAIRISQLHQIFYDDEGLIDAEKSVTILYSIGFTIDEIAYF
                     RNTTPGTVQGQLFNARAKLSCASASSLRPMILLRLLLNIKEIRFGFEAD"
                     /name="hypothetical protein"
     gene            5453..5716
                     /locus_tag="QDY30_RS25715"
                     /old_locus_tag="QDY30_25715"
     CDS             5453..5716
                     /locus_tag="QDY30_RS25715"
                     /old_locus_tag="QDY30_25715"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001677227.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="EexN family lipoprotein"
                     /protein_id="WP_000717654.1"
                     /translation="MKKICTLLISIFILSACGEDTKSSDWWLNHPKEATEKYKECKKSG
                     EDSVNCQNVKKVAGIIGRTYGPMLEILKAESAEYDKQHGLNR"
                     /name="EexN family lipoprotein"
     Typing          2..804
                     /name="MPF_T"
                     /typing="mate-pair-formation"
                     /tool="MOB-suite"
                     /identity="89.179"
                     /coverage="91.0"
                     /evalue="5.3900000000000007e-157"
ORIGIN
        1 atgtctggtt tctttgaaaa gtttaatagc gaagttgtta gtaaaatcga agagatgacc
       61 aaaccacttc aaagtcaatt aggccaagat atgttatctc ttctaagtgc aggtattagc
      121 gtttatatcc tctgggttgg ctatcaaata ttggcaggga aacgccaaac cccattacaa
      181 gatctcgttt gggacctatc aaaatttgcc attattttaa cattcgtaag caatgctgat
      241 ggctatctga cggcagcaat ggatgctatt aaatctatga aggatgggtt ccttggtaaa
      301 cctgtatggg caacgctaga taccatgtgg agtacaactc agcttttggc agacaaagtt
      361 tatgctatgg atcaatccaa atatgtgtca gttgagggtg ggatcggttc aatgttggtt
      421 tggggaggaa gcatcctgat tatgtctgta gcggctgtta tttacatgct tgccgatgta
      481 acaatgcagt tagctattct tgtagctccg atatttatcg gttgtcatat gtttggattc
      541 accagagtaa tgtttaataa ctggcttggt atattatttt ctagtgtatt tactgttatt
      601 tttgcaggag ttctcgtcaa aattggtact gagtttcaaa ctgatatgct tagtcagata
      661 tcgagagatg ctaactcaac aaatatttta acaatgggcg caatggcatt tgtaattgga
      721 gttctgattg ctgtctttgt ctggaaatca tcgagtttcg cgcagcagct tgctggtgca
      781 ggtgtcgaag gtactcttca gggaatggct cttttaggga ttggggctgc tgggatggcc
      841 gtagagaaaa cgagaaacca aatgaaacgg ggaacgcaaa cagccgccga atgggcaggt
      901 gaaaaagtgg agcagaaacg ggcttcaaca ggcgcattgg gaatggaagc aagaagacga
      961 gcatccctgg aaaaagcacg tgcgaggagt tcagcatgaa caaaaaacta attttttcag
     1021 tacttttgtg cttattttca tttggttctg tcgcaggtat tccggttgct attgatgcca
     1081 gtccggaatg ggccattgaa gccacaagat ggacagaacg actcaaacaa tggtctgaaa
     1141 cagcgcggca ttatcaaagt cagattcagg catataaaga ccagttagcc acggcaacag
     1201 gtataaggaa tattgcggca ttcacaaatg aactaagtaa cctgcaatca gagttggcaa
     1261 acatttataa gcaggggaac agttatattt ctgattttac cagtaatccc gaaggtgcat
     1321 taagcagcca ggctaaaaat ctgttcagta agtatggagc gtttgatatg tgtaatacag
     1381 gcattgaaag ttctgataac ctttgtaagg ccagaatagt ttcaacggcc gccagcattg
     1441 aacagggaaa tgagataaat aagcagctat caagtgcaat gtctcagatt cagagtttaa
     1501 gtagccgaat tgagtcttca aaggatatga aggaatccca ggatttagct aacgcattac
     1561 aggctcagtc gttaaaaata caggcaatta aaatgcagta tgatgtatgg gatagtaaaa
     1621 acagggctga tgcggaaatg ttgaaagaac aaaagtatgc agagtatcgt ttacgtcaga
     1681 aaaatgccaa aataccgagt ttcgaatgat atgataaagc taaataagct aaaagaatgg
     1741 gtagataatc attggtctag attgaatagt accggttcta caccgccgcc actgttaata
     1801 tctctaccaa taatagttat tgttttaagt atggagctta cgttaaagct ggttaatgct
     1861 tttatgtatt atggcacatt gcaatttatc actgatagaa ttgaaaagag gtttgttccc
     1921 agcggtggta taaaagaaag actccttttt acgttgaagc tgttttgtat tttacttctg
     1981 ttattaatcg taatgcgatt tacgatgaga taacagctag ggccatctat ttgatggcct
     2041 tgattttaac caaatctgtt aacaacactc ttggttaacg tttcaagttt tgaatcaatt
     2101 tgcttacaca gttcaatcac ttcaataacg tcttttctga aatctggatc gttaaccgtg
     2161 cagaatcttt caccttttat gataaaatga atgttgcgac caacacgatc tacagcagtt
     2221 gatagttttt taagttcctt aacttcatca gggtaaagac agacttcatt ctttaacaaa
     2281 gactgacgca cacgaatagc aatttctctg ctcatgctca tgccgtgaag gacagcatta
     2341 cgtttaacaa gttctatttc atgagggtag agataagtga aaactggttt tgcagcctca
     2401 ttcttaacag gaatagatac tggctttgtt ggtacatcaa gaactttcat ttttgcgaat
     2461 acatttacac tatcaactcc atatgaagct gcatttactc tcgcaagttc atattcatca
     2521 tcatttaatc taaaacatac atttttcatt ctttcaccat agagcctgcg gcaggcacag
     2581 gcaaaaaccc tgtttttgga caatccgata tcgaatggta ccatttgaca tcggattgtc
     2641 tatcctgcat tggttctttg cagcctttaa gtaattcctc tctaattttg ggggtctcca
     2701 agctttagtt tctgctcaaa tgttccattg agggcacgtt tgacaaaaac aacactgtaa
     2761 ctataattag ttacaaacaa ggggagcgta tgggaaaaac agataaacta ctggcgaagt
     2821 ttttaaacag caaaaaaaac gtttgaatgg gatgaactgg tcgttttgtt ttcctctttg
     2881 ggatatgtca aaaaagaaat gcaggggtca agagtgcggt ttttcaatgc tgatatcaac
     2941 cacaccatat taatgcatcg cccacatccg gaaagttata ttaaaggtgg tacgctgaaa
     3001 gcgattaaac agaatctgaa agaggccgga ttattatgaa acatttaaaa tataaaggat
     3061 atttaggtac agttgaaccc gattttgaaa ataatgtcct gtatggaaaa ctggcgttta
     3121 ttcgggacct ggtaacttat gaggcttcta cattagctga actggaacag gagtttaaaa
     3181 catcggttga tctgtattta cagtcttgtg tggaggatgg aaaggaacct gatatcccgt
     3241 ttaaaggcgt gtttaacgtc aggcttgatc cagaactgca tcgtcgggta gcagaaatgg
     3301 cgatggaaga agatttatcg ttgaatgctt ttgttaataa ggctctggaa aaagaagtca
     3361 ccaaccatag cattagatga ttaatacaat catcgctgca acatcgacgg tctacgacca
     3421 cctgccaacc gagtggctgc ctgtttcgtg caatttttgc tttgcagggg gctgacgcgg
     3481 ttcttagcga cctgaaagcc cctggttagg ggtatcggcg cgcttggcct cctgaaaccc
     3541 tctgtaagcg tttttcgcac cttccatgcc ctgacgggca tctgttggca ttttagcgcc
     3601 tcagagagtt tctgagcgcg ttttaagggc taagacgtgg gataccatta ccgggaccag
     3661 aaaatcgagt tctggtgttc tggatggctc acagaacgaa tttccgaaca gtacagcaac
     3721 ggaataaccg acaacatgcg ggaggtggca ccgctcgccg cagccccagc gaccgaacgt
     3781 tagtgagcga gtgggcgagg aagcggaaga gagcaggtat tgatttgagc acttacgcgt
     3841 agcggttaaa aaatgagcgc gtcgtttatt aggtttgttg tcttaacgta acgtgatctg
     3901 tcctcttggt ttaagcagag ttatccacag attttggggg taaattcctt tttaaatcct
     3961 ttttatcttt tttttaaaac ctttttagtc gctagaaatt cttttgaatc atcaagttac
     4021 agcgttaaaa gtaacttttt tcgggttaaa agtaactttt ttcgggttaa aagtaacttt
     4081 tttcgggtta aaagtaactt ttttcgggca atatccacag gcaaaagtaa cagcaacaag
     4141 caatgttact ttacttgtgc gataacatcg tttatcttcg ttacagttgc ccgatacctg
     4201 ttacttttcc aagtgccagt tgacctattt aggcggagag atgaaaggga aaaaaactga
     4261 atccattacc atgaccttga acctgcgcgg gaaaaatatc gtgatgagca atgccattac
     4321 gagagcagcg caaagcctgt cactggctga aaaacgcatc atttttgctg caatagccaa
     4381 aatgggcgga cagtacaccc cgattaaaat cacggctgaa gaatacgcca atacatttgg
     4441 aatgccttta aaacaagcgt attcacaatt aaaaatcgct gctgacaatt tttttaaccg
     4501 ctacattagc ttcagaataa acgaagtaag cgaaacagat gttgatgtct ggaaaatcag
     4561 atggttaggt gcttataaat acaatgaagg tgaagcgcac gttgttttga gcttcacacc
     4621 acaggtcacc ccctatctat gcgaactgga agaaaatttc actaaatacc agctatctca
     4681 ggcttgcgga ctgcgctctg ttcactcatg gcggttgctt gaattattcg agcaaatgaa
     4741 tacccacaaa gacaataacg gatggttatc tatatcgctg gatgattttc atcacgcaat
     4801 ggaatctcct gaaagttata aaaaaacctt tggattactc agagaaaggg tgatagaacc
     4861 tgccgtaaaa gagttgaccg aaaaagataa ttggataatc cagtggaagc cattaaaaag
     4921 aggcaaaaaa gtcgttcgtc ttgaattctg gtttcaaaaa gatgagcaat caaagattat
     4981 aaaaaattga tatttaatcg gcgcgatttg ccagaggttg caactctgac aaaccgctaa
     5041 tcacaacaac ctggctagag gttattatga ctaagcatga tgctatacgc atttctcaac
     5101 ttcatcaaat cttttacgac gatgaaggat taatcgatgc ggaaaagagc gtgaccattt
     5161 tatacagcat aggatttact attgatgaaa tagcttattt tagaaataca acaccgggaa
     5221 cagttcaggg gcagttattt aatgcaagag ctaaattaag ttgtgcttca gcttcatcgt
     5281 taagaccgat gatcttattg agattgcttt tgaacataaa agagattcgt tttggatttg
     5341 aagcggatta attgcaaaaa atagcataat gcaataggtg ttttttttag ttgacaaaaa
     5401 ttacaattgc tgattgcatc agcaattgta atgtccatac gaggaatcaa agatgaaaaa
     5461 aatttgtaca ctcttgatat ctatttttat tctttccgca tgtggtgaag atacaaaatc
     5521 atcagattgg tggctaaatc atcccaaaga agcaacggag aaatataagg agtgtaaaaa
     5581 gtcaggggaa gactctgtta attgtcaaaa tgttaaaaaa gttgccggaa ttattggtag
     5641 aacctatggg cctatgcttg aaatacttaa ggctgagtca gctgaatatg ataagcaaca
     5701 tggattgaac aggtgataac
//
