LOCUS       NZ_CP122940             4670 bp    DNA     circular CON 08-JUN-2024
DEFINITION  Escherichia coli strain ETEC1701 plasmid unnamed2, complete
            sequence.
ACCESSION   NZ_CP122940
VERSION     NZ_CP122940.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN32549584
            Assembly: GCF_030012785.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4670)
  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 4670)
  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                   :: 128x
            Sequencing Technology             :: Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_030012785.1-RS_2024_06_08
            Annotation Date                   :: 06/08/2024 05:10:59
            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)                     :: 5,261
            CDSs (total)                      :: 5,136
            Genes (coding)                    :: 4,825
            CDSs (with protein)               :: 4,825
            Genes (RNA)                       :: 125
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 92
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 311
            CDSs (without protein)            :: 311
            Pseudo Genes (ambiguous residues) :: 0 of 311
            Pseudo Genes (frameshifted)       :: 139 of 311
            Pseudo Genes (incomplete)         :: 167 of 311
            Pseudo Genes (internal stop)      :: 45 of 311
            Pseudo Genes (multiple problems)  :: 35 of 311
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP122940.1.
            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..4670
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="ETEC1701"
                     /isolation_source="feces"
                     /host="Sus scrofa"
                     /db_xref="taxon:562"
                     /plasmid="unnamed2"
                     /geo_loc_name="Belgium"
                     /collected_by="IMM_DI04"
     gene            1..264
                     /locus_tag="QDX07_RS25330"
                     /old_locus_tag="QDX07_25330"
     CDS             1..264
                     /locus_tag="QDX07_RS25330"
                     /old_locus_tag="QDX07_25330"
                     /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_282832541.1"
                     /translation="MLPLSAARNLGDLLPLSAARNLGDLLPLSAARNSGDLLPLSAARN
                     LGDLLPLSAARNSGDLLPLSAARNLGDLLPLSAARNLGHLLP"
                     /name="hypothetical protein"
     gene            319..834
                     /locus_tag="QDX07_RS25335"
                     /old_locus_tag="QDX07_25335"
     CDS             319..834
                     /locus_tag="QDX07_RS25335"
                     /old_locus_tag="QDX07_25335"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000675352.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type III toxin-antitoxin system ToxN/AbiQ family
                     toxin"
                     /protein_id="WP_282832542.1"
                     /translation="MKFYTISSSYTKYLKDFDDKVPNSEDPTYNNPKAFIGIVLEIEGH
                     KYLAPLTSPKAWHANVKESSPAFFKLHENGVPDNQLGLINLKFMIPIIEAEVSLLDLDS
                     MPDTPYKRMLYKQLQFIRVNEDKISEKSKLLRNLALQGRMQGTCDFAVLEEKYQHFGKK
                     PEDMEIDD"
                     /name="type III toxin-antitoxin system ToxN/AbiQ family
                     toxin"
     gene            complement(945..1655)
                     /locus_tag="QDX07_RS25340"
                     /old_locus_tag="QDX07_25340"
     CDS             complement(945..1655)
                     /locus_tag="QDX07_RS25340"
                     /old_locus_tag="QDX07_25340"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000967646.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_024165718.1"
                     /translation="MLYWKRMPSLWIGIKISEFNDLDTAKAIAALKIYLTFCLFCKESD
                     SGQRTVELTFSNLCEIASLSRSLVNEGLKILYAKELIKNLSTTVRKKIYTVDVLEKHDD
                     GWCKLPFKGIVGEDGKISAFQSMHNRYPFELLALQTYMYLLYARDNRNEYTLARKKTIC
                     KKLKCKLPELNKAITYLIHIGLLDRIVKKSIENKPLEMFHDSCYFYFRAGSNSALTYKR
                     KSEVLNLSEEDLPF"
                     /name="hypothetical protein"
     gene            2200..2457
                     /locus_tag="QDX07_RS25345"
                     /old_locus_tag="QDX07_25345"
     CDS             2200..2457
                     /locus_tag="QDX07_RS25345"
                     /old_locus_tag="QDX07_25345"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001508827.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001125013.1"
                     /translation="MPKKTSKPNDLSNTINNIKKEINSGFTELLNRVEALEASDAQHSM
                     AIRDLQIQARAARGDKRMDIARDFDLSEGRISQIVNAGRN"
                     /name="hypothetical protein"
     gene            2467..2748
                     /locus_tag="QDX07_RS25350"
                     /old_locus_tag="QDX07_25350"
     CDS             2467..2748
                     /locus_tag="QDX07_RS25350"
                     /old_locus_tag="QDX07_25350"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000786945.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000786946.1"
                     /translation="MKNEDDYKTGWTTQTTNPATGKKCSGGAARNLRIYQAGGANSVRV
                     KAAIEGVQSIQPIIDVQQSQIEQQQVQIAMLTQSLSQAINELTKSRNK"
                     /name="hypothetical protein"
     gene            complement(2982..3305)
                     /gene="mobA"
                     /locus_tag="QDX07_RS25355"
                     /old_locus_tag="QDX07_25355"
     CDS             complement(2982..3305)
                     /gene="mobA"
                     /locus_tag="QDX07_RS25355"
                     /old_locus_tag="QDX07_25355"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052604.1"
                     /GO_process="GO:0006355 - regulation of DNA-templated
                     transcription [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization protein MobA"
                     /protein_id="WP_000166966.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="mobA"
     gene            3589..3783
                     /locus_tag="QDX07_RS25360"
                     /old_locus_tag="QDX07_25360"
     CDS             3589..3783
                     /locus_tag="QDX07_RS25360"
                     /old_locus_tag="QDX07_25360"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041624.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_001041618.1"
                     /translation="MNKQQQAVLNMAGFIKSQSLTLLEKLDALDADEQAAICEKLHELA
                     EELQNSIQTRFEAENRTGI"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(3315..3551)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.49e-121"
     Typing          4075..4576
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="81.015"
                     /coverage="99.0"
                     /evalue="1.1e-104"
     Typing          complement(2986..3305)
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="3.1e-62"
ORIGIN
        1 ttgctacctt taagtgcagc tagaaattta ggtgatttgc tacctttaag tgcagctaga
       61 aatttaggtg atttgctacc tttaagtgca gctagaaatt caggtgattt gctaccttta
      121 agtgcagcta gaaatttagg tgatttgcta cctttaagtg cagctagaaa ttcaggtgat
      181 ttgctacctt taagtgcagc tagaaattta ggtgatttgc tacctttaag tgcagctaga
      241 aatttaggtc atttactacc ttaaagtaat aaagtaaaaa aggcgactat acacagtcgc
      301 cttttttacg agaaaaaaat gaaattttac acaatatcaa gcagttacac aaaatacctg
      361 aaggactttg atgacaaagt tcccaatagc gaagatccta catacaacaa tcctaaggct
      421 ttcattggca tagtactaga gattgaagga cataaatatt tagcaccttt aacgtcgcca
      481 aaagcatggc atgctaatgt aaaagagtca tcacccgcct tcttcaaact tcatgaaaac
      541 ggtgtccctg acaatcagct tggattgatt aatctgaaat ttatgattcc aataatcgaa
      601 gctgaagtgt ctttacttga tctggatagc atgcctgata cgccttacaa aagaatgcta
      661 tataaacagt tacaatttat tcgtgtaaat gaagataaaa tatctgaaaa atcaaaacta
      721 ttaagaaacc ttgccttgca aggcagaatg caaggaacat gcgactttgc cgtattagaa
      781 gaaaaatatc aacatttcgg taaaaaacct gaagacatgg aaatagacga ttaaccattc
      841 ttttttatgg aattgaaggt ccaaaatcaa gcggttttgg acctattttt ttgctctcat
      901 ccaatataag aataaaatat tctaattttg atttcgagaa gcaatcaaaa aggcaagtcc
      961 tcctctgaaa gattaagcac ctctgatttc cttttgtaag tgagagcgct gttacttccc
     1021 gctctaaagt agaagtaaca tgaatcatga aacatttcca acggcttgtt ttctattgat
     1081 tttttaacaa tcctatcaag taaaccaata tgaataagat aggtaatggc tttatttagt
     1141 tcaggtagtt tgcatttcag ttttttacat attgtttttt tcctagcaag agtatactca
     1201 tttctattat cacgagcata aagaaggtac atgtaggttt gtaaagctag caactcaaat
     1261 ggatatctgt tgtgcatgga ttgaaatgca cttatttttc catcttcacc tacaattcct
     1321 ttaaagggaa gcttacacca accatcatca tgcttctcta atacatctac ggtataaatt
     1381 tttttacgta ctgtcgttga taaatttttt atcaactctt ttgcataaag aattttaagc
     1441 ccttcgttaa ctaacgatcg gcttaatgat gctatctcac ataggttact aaaagttagc
     1501 tcaacagttc tctgtcctga atctgactct ttgcagaaaa ggcaaaatgt taaataaatc
     1561 tttaacgcgg cgatggcttt tgctgtatca agatcgttga attcagatat tttgatacct
     1621 atccatagtg aaggcattct tttccagtac agcataaatc acctcattcc cagaatttga
     1681 aaaatgaaat agaccaaccc caatacagac agagatagca ccagattagt tagcaccact
     1741 gcgaccttcg caagcctttc agccaaaaac acacctttct caaacatttt ttatccctcc
     1801 tgatagcttt gtttttttga ttatctcagg ctgtgaaggc gttgtaacgc cttcacaaaa
     1861 atctatctag aaagaaaaaa taaggcaaaa gaaaggtatc tatatgttat ataagagatt
     1921 ttattttgct tttggtattc ttagaaatca tattatggtt catggtgaac tgtaaatgca
     1981 gtgctgatgc atttttagtt acgttaaatg ttttcacatt aggactttag atcagaacaa
     2041 acaaagcgtt gtgccttgca agccaccctg cataaagcac taaatttctt tatctcatta
     2101 aatttacctt gccaaaagga gcaataatcc ctaccttaca actttaacaa aactaaaaat
     2161 ctttagcgga cttagccgcc gagtatagag aaatatgcca tgcctaaaaa aacatcaaaa
     2221 ccaaacgatt taagcaacac tatcaacaac ataaagaaag aaattaactc cggttttact
     2281 gagttactta atcgcgtaga agccttagag gctagtgacg cacaacacag catggcgata
     2341 cgtgatttac aaattcaggc tagagccgct cgcggagaca aacgtatgga tatagcaaga
     2401 gactttgacc tcagcgaggg acgaattagc cagatcgtta atgcgggtcg taactaaggc
     2461 agacttatga aaaatgaaga cgactacaaa acaggatgga cgactcagac aacaaacccg
     2521 gcaacaggga aaaaatgttc tggaggcgca gcccgaaact taagaatata ccaagctggc
     2581 ggagcaaact ccgtgcgggt taaagctgca atcgagggtg tgcagtcaat acagccaatc
     2641 attgatgtac aacagtcaca aattgagcaa cagcaagttc aaatagcaat gctgactcaa
     2701 tctttgtctc aggcaatcaa tgagctaaca aaaagcagga ataaataggc tataacggat
     2761 gttatttacc ataacatccg ttacccgcac cgcagaaacg cgctgaacgc gattctgacg
     2821 cagacaccgc aaaaagagat gttttacccc gggaaaacag gaaggatgcg tcaggatcgt
     2881 tttcagctcg ctgcatagct atgcatgaaa gcgaatggtg atcactttgg gagcttacgg
     2941 tgttcatacc gtctgttttc gacagttttc tctccgggaa gctaatctgc cataagcctg
     3001 gataacaggg cacggtgata ctccgtaata gcgatcagca cctccgcata ctccctgtcc
     3061 ccgacacgct tgccgtcgat aaagagtttt ttctgtaacg cccccagtct cataacttct
     3121 ttcagtaccc gatcatcagt cagtgagtta actttcttac cgagagctgc cgcccgtaaa
     3181 aaaccggaaa cggtcttgcc gcattcagca gccctttttc tgatttcctg gtcttcttct
     3241 gccgtcagac gaacagggcg actgatagcc cgcctgcgcg tattacttcc acttcttttt
     3301 gtcataaaac atggctccgt atctgacatg ggtgtcgggg caaagccctg accagggtaa
     3361 ttgtaatagc gtgcatgcat gcgcggtata acaattacac atcctgtcct gtcagcaagt
     3421 tcgaattacc gacaaagaca cggcagtttt ttggcagtga cagtattgtc aggcagaaat
     3481 acccgtcaaa gcgtcagacg gcagaatacc ggcggtaaaa cagtcgaaaa gtggtacgcg
     3541 atataatcac acaacgcaga tgacagacag aacggagaaa acgaaaagat gaacaagcag
     3601 cagcaagccg tactcaacat ggcaggattc ataaaaagcc agagcctgac gctgctcgaa
     3661 aaactggacg cactcgatgc tgacgaacag gccgccatat gtgagaagct gcacgaactc
     3721 gcggaagaac ttcagaacag catacagaca cgctttgaag cggaaaatcg caccgggata
     3781 taacgcatcc ggacaggatg cagaacggca tagaggagcg taaggagaaa atgtcacata
     3841 aggcgctctt ccgcttcctc gctcactgac tcgctacgct cggtcgttcg actgcggcga
     3901 gcggtgtcag ctcactcaaa agcggtaata cggttatcca cagaatcagg ggataaagcc
     3961 ggaaagaaca tgtgagcaaa aagcaaagca ccggaagaag ccagcgccgc aggcgttttt
     4021 ccataggctc cgcccccctg acgagcatca caaaaatcga cgctcaagtc agaggtggcg
     4081 aaacccgaca ggacttaaag ataccaggcg tttccccctg gcggctccct cttgcgctct
     4141 cctgttcccg tcctgcggca tccgtgttgt ggtggaagct ttacctaaat caccacgtcc
     4201 cgttccgttt agacagttcg ctccaagctg ggctgtgtgc aagaaccccc cgttcagccc
     4261 gactaccacg ttgtcccggt aactatcatc ttgagtccaa cccggaacag acacgaaaaa
     4321 tcgccagtgg cggtagccat tggtaacttg gttcgcagat gatttgttag ctaaacacga
     4381 ggttgctctt gaagtgtgcg cctcagtacg gctacactgg aaggacagat ttggttgctg
     4441 tgctctgcga aagccagtta ccacggttca gaaacttgcc ggtttactga accttcgaaa
     4501 aaaccacctt gccgggtggt ttttccgttt tcagaccaag agattacgcg cagaaaaaga
     4561 tgatctcaag aagatccttt tgattagtgc cgtcatttga ctgaacatcc catgctaagc
     4621 acctagttgt aagcccaagc gaagatcatg tatacttagt tcaaggtgat
//
