LOCUS       NZ_CP122911             5899 bp    DNA     circular CON 08-JUN-2024
DEFINITION  Escherichia coli strain ETEC1706 plasmid unnamed7, complete
            sequence.
ACCESSION   NZ_CP122911
VERSION     NZ_CP122911.1
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 5899)
  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 5899)
  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
            CP122911.1.
            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..5899
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="ETEC1706"
                     /isolation_source="feces"
                     /host="Sus scrofa"
                     /db_xref="taxon:562"
                     /plasmid="unnamed7"
                     /geo_loc_name="Belgium"
                     /collection_date="2020"
                     /collected_by="IMM_DI04"
     gene            join(5310..5899,1..4)
                     /locus_tag="QDX08_RS25710"
                     /old_locus_tag="QDX08_25710"
     CDS             join(5310..5899,1..4)
                     /locus_tag="QDX08_RS25710"
                     /old_locus_tag="QDX08_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_012537770.1"
                     /translation="MSGRKFGRLPNWWARSSWLVNNVRSNEIGGGIASMKCLLALSVLI
                     DFHSRTASVSFTGMERLTGLSRPMIVKGVAKLEKDGLIKIDREMFVNSYELTVQPNDDR
                     WAKVPVDTIRKKLNTISNRGMAPFVALKLYLTIISLRYQSNNTVKVTHETLRSYTGVQP
                     NQIRFGLDVLYCSRLIHLQPKEDRESNIYEIIGL"
                     /name="hypothetical protein"
     gene            776..955
                     /locus_tag="QDX08_RS25720"
                     /old_locus_tag="QDX08_25720"
     CDS             776..955
                     /locus_tag="QDX08_RS25720"
                     /old_locus_tag="QDX08_25720"
                     /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_282857535.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHRVG
                     SLAAAACHGLELPL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1353..2540
                     /locus_tag="QDX08_RS25725"
                     /old_locus_tag="QDX08_25725"
     CDS             1353..2540
                     /locus_tag="QDX08_RS25725"
                     /old_locus_tag="QDX08_25725"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_013747467.1"
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /GO_process="GO:0006313 - DNA transposition [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="IS91-like element IS91 family transposase"
                     /protein_id="WP_000937612.1"
                     /translation="MLPRFADIFQQGNRWLNWLEKQPEGSVRPVVTESVTKIMACGTTL
                     MGYTQWCCSSPDCCHTKKVCFRCKSRSCPHCGVKAGAQWIQYLLSLVPDCPWQHIVFTL
                     PCQYWSLVFHNRWLLAEMSRIAADVILEICHQTDVEPGIFTVIHTWGRDQQWHPHIHLS
                     TTAGGVTSGHTWKNLHFYARKVMSMWRYRITRLLSRKYPELVIPDELAVEGNSKRDWNC
                     FLDTHYRRGWNVNISRVMDNATHVAVYFGSYLKKPPVPMSRLEHYAGQDEIGLRYNSHR
                     TKREEYLLMSGDEFMERFSWHVADKGFRMVRYYGFLSPVKRRLLEEVVYVITETVRKTA
                     MQIRWRGMYQRLLKVDPLKCILCGSQMRFTGLKRGYRLAELVLMHERLARQQVCG"
                     /name="IS91-like element IS91 family transposase"
     gene            3463..3576
                     /locus_tag="QDX08_RS25730"
                     /old_locus_tag="QDX08_25730"
     CDS             3463..3576
                     /locus_tag="QDX08_RS25730"
                     /old_locus_tag="QDX08_25730"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /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_071531573.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHALTPLAAATGN"
                     /name="replication initiation protein"
     gene            3802..4716
                     /locus_tag="QDX08_RS25735"
                     /old_locus_tag="QDX08_25735"
     CDS             3802..4716
                     /locus_tag="QDX08_RS25735"
                     /old_locus_tag="QDX08_25735"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001448734.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Abi family protein"
                     /protein_id="WP_195717845.1"
                     /translation="MPNTIHYPHVIPFISQGKINAIKSTFGNNLSDRECYGIYIWSQKA
                     SSAIYPLLQQLEVTLRNSIDKEATKLIGQKWWDNVYTDTSKSKHGDFIHNINKAIIRYE
                     NEFKKKNPSMANTKIIAPHDDIIAHTDFYTWQAVLSDAFHTQSRSEASRALWPRLTYRV
                     LKGLDRSKDEGTARIDFLNELNEIRNYRNRLSHNDCIWIKIHSKNLQSAVETIREKINK
                     IEGLIKTINPQVHLSLTKWGSFYHAKRICSQKEAELHLGKGIINSTTDEMNTILDQLYA
                     LTADGKLTGVVKRNTNNIAFHKF"
                     /name="Abi family protein"
     Typing          complement(263..517)
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="93.023"
                     /coverage="89.0"
                     /evalue="1.24e-101"
     Typing          complement(642..740)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.0"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          complement(2879..2965)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.43e-38"
     Typing          2976..3535
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.204"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atgaggaaat gcatttacca taacgtcgca ttacgcgcac cgctaaaacg cactgaacgc
       61 gattctgacg cagataccgc aaaaagagat gttttaccca gtgaaaaccg aaaaaatgcg
      121 tcaggatcgt tttcagccca ctgcatagct atgcatgaaa atgaatgacg aacggtttgg
      181 gcgcatacgg tgcccatgag acacattttc ggacattttc agttcgtgaa tccctgactc
      241 attgctacat atctgaacag acacccctgg cagcgccccc aggggcgtcc tgtaaaaaaa
      301 cacaccgcgc cgctagcagc acccctgata taaaatgatg ttttttataa aaatagtcag
      361 taccccccta caaagcggtg tcggcgcggt gttgtagctg cgccggcacc gcttttttaa
      421 atatcgcaaa gagagcaaga gaaactaatt tttcataact ctctatttat aaagaaaaat
      481 cagcaaaaac ttgtttttgc gtggggtgtg ggcatttcag gaatgagaac agactcgcgt
      541 ttttccggag tatcagcgga attattgatt aagaaacact cgacgcagag cgaaatttta
      601 tgcaacagcg gctgcactgc acagggatta tttatcagtt gatatgctgt gccatgatac
      661 gtcctaaaaa aacaggacag gatgtgcaat tgtaataccg tcgcccgcaa cgtcttacaa
      721 ttaccagctg ctcagggtcc ccccgacacc cggaactgac ggagaacaac ggaaggtgaa
      781 caaacaacaa caaactgcgc tgaatatggc gcgatttatc aaaagccaga gcctgacact
      841 gcttgaaaaa ctggatgctc tggatgccga cgaacaggca gccatgtgcg aacgactgca
      901 ccgagtaggc agcctggcgg ctgcggcttg tcatggtctg gaattaccgt tataaaaaaa
      961 gataatgtca ttgtctttca ggtagttata tggcccgttc agctaaaccc cgtaaacgca
     1021 aacccgcacc acaaagaagc aaacttcccc gctatgttgt gaaacttcat ccggatgatt
     1081 tttttgacga agaagacgct gaagttctgc gctttgataa ttttgacgat gccgttgagt
     1141 gctgcgctga cctgggtatt ccgttctttc tggatgcagg aaacaaaaag ctggtcttct
     1201 ggtttgttcg tgtcgatgac gaagggtatc cggaaatagc ccgctgtacg gagcgggagt
     1261 ttgcaaccat tcttgccggt atcagtgccg gtggtatgta ctgcccggaa tgcggcacag
     1321 ttcactggcc ggatggcgtt accccccgtc tgatgcttcc ccgttttgcc gatatttttc
     1381 agcagggtaa ccgctggctt aactggctgg agaaacagcc ggaaggttca gtgcgtccgg
     1441 tggtgactga gtcagtgaca aaaatcatgg catgcgggac cacgctgatg ggctacacgc
     1501 aatggtgctg ttcgtcaccg gactgttgcc acaccaaaaa ggtctgcttc cggtgtaaaa
     1561 gccgctcctg tccgcactgc ggggtgaagg ctggcgcaca gtggatacag tatctgctga
     1621 gcctggtccc cgactgcccg tggcagcata ttgtgttcac acttccctgc cagtactggt
     1681 ccctggtgtt ccacaaccgg tggttactgg cagagatgag ccgcattgca gcggatgtga
     1741 tactggaaat ctgccatcag acagatgtgg agccggggat attcacggtg atccacacat
     1801 gggggcgtga ccagcagtgg catccgcata tccatttatc gacaactgcc ggtggtgtga
     1861 cgtcgggcca cacctggaaa aatcttcatt tttacgcccg taaggtgatg agcatgtggc
     1921 gttaccggat aacgcggcta ctgtcccgga aatacccgga gctggtaata ccggatgaac
     1981 tggcagtgga aggaaacagc aaacgggact ggaattgctt cctggacacg cattaccgcc
     2041 gcggctggaa tgtcaacata tccagggtga tggataacgc cacacatgtg gcggtgtact
     2101 tcggctctta cctgaaaaag ccaccggtgc cgatgagtcg gctggagcat tatgccggtc
     2161 aggatgaaat cggtctgcgt tacaacagtc accgtacaaa acgggaagaa tacctgttga
     2221 tgagtggaga tgagttcatg gaaaggttct cctggcatgt agcagataag gggttccgta
     2281 tggtgaggta ctacggtttc ctgagtccgg tgaagcgccg cttactggaa gaagttgtgt
     2341 acgtcataac ggagacggtg agaaaaacgg cgatgcaaat caggtggaga gggatgtatc
     2401 agaggttact gaaggttgac ccgctgaagt gcattctgtg cggaagtcag atgcgtttta
     2461 cggggctgaa gcggggttac cgactggcag agctggtcct gatgcatgag cgactggcac
     2521 gacagcaggt gtgcggctga gagccgcaga ggggaagttg cgtccatttt accggaaacg
     2581 gagcaaaaaa ccgccattca taccctgtat caatcagtgt catcctgttt aatagtcgtt
     2641 tccgctcata tggtgcacaa ggggtgttga agaaacatcc gttttgtggt gcttttttag
     2701 tcttttgggg atttaaattc ctatcgatga actcgcggaa gaactccaga acagcatcca
     2761 ggttcgcttt gagaccgaaa gtgaaacagg aacataacga agctgacgga ggcgctcacg
     2821 gcttgtccgc gagcgttttc ggcagcagac aagcccgtca gggcgcgtca gggggtttta
     2881 gcgggtgtcg gggcgcagcc atgacccagt cacgtagcga tagcggagtg tatactggct
     2941 taaccatgcg gcatcagtgc ggattgtatg aaaagtgccc catgccgggt gtgaaatgcc
     3001 gcacagatgc gtaaggagaa aatgcacgtc caggcgcttt tccgcttcct cgctcactga
     3061 ctcgctacgc tcggtcgttc ggctgcggcg agcggtactg actcacacaa aaacggtaac
     3121 acagttatcc acagaatcag gggataagac cggaaagaac atgtgagcaa caaggcaaag
     3181 ccaggacaaa aggccgcgcc gctggcgttt ttccataggc tccgcccccc tgacgagcat
     3241 cacaaaaacc gacgctcaag tcagaggtgg cgaaacccga caggactata aagataccag
     3301 gcgtttcccc ctggaagctc cctcgtgcgc tctcctgttc cgaccctgcc gcttaccgga
     3361 tacctgtccg cctttctccc ttcgggaagc gtggcgcttt ctcatagctc acgctgttgg
     3421 tatctcagtt cggtgtaggt cgttcgctcc aagctgggct gtgtgcacga accccccgtt
     3481 cagcccgacc gctgcgcctt atccggtaac tatcgtcttg agtccaaccc ggtaaggcac
     3541 gccttaacgc cactggcagc agccactggt aactgattta gaggagtttg tcttgaagtt
     3601 atgcacctgt taaggctaaa ctgaaagaac agattttggt gactgcgctc ctccaagcca
     3661 gttaccttgg ttcacagagc gccaactctt tgaaccttcg aaaaaccgcc cgccaaggcg
     3721 gttttttcgt ttaacactct acaactatcc atacgtgtat ggcaacatcc aatcaccact
     3781 aagtgtatga tagagatgga tatgccaaat acaattcatt accctcatgt aataccattt
     3841 atatcccaag gaaaaataaa tgctataaaa agcacgtttg gtaataacct gtctgatagg
     3901 gagtgctacg ggatatatat atggagccag aaagcctcat ctgccatata tccattactg
     3961 caacaactcg aagttacttt gagaaactcg attgataaag aagcgacaaa actaataggc
     4021 caaaaatggt gggataatgt atacaccgac acatcaaaaa gcaaacacgg tgacttcata
     4081 cataatataa acaaagcaat aataagatat gagaatgaat tcaagaaaaa aaacccatca
     4141 atggcaaata ccaaaataat tgcacctcat gatgacatca ttgcacacac agatttttac
     4201 acatggcaag cggttttgag cgatgctttt catacacaat caagatctga agcatcaaga
     4261 gccttatggc ccaggctcac ctacagagta ctgaagggat tagatagaag caaagatgaa
     4321 ggcacagcca gaattgattt cttaaacgag ctgaatgaga tcagaaacta cagaaatagg
     4381 ttatcgcata atgattgcat atggataaaa atacactcta aaaatttgca atctgcagta
     4441 gaaacaataa gagaaaaaat aaacaaaata gaaggactga taaaaacgat aaacccacag
     4501 gtacacctat cattaacgaa gtggggttcc ttttatcacg ccaaaagaat atgttctcaa
     4561 aaagaggccg aattgcatct aggcaaagga ataatcaata gcacaacaga tgagatgaac
     4621 acaattctag atcaactata cgcactaact gctgacggaa agctaacggg tgttgtaaaa
     4681 cgaaatacca acaatatcgc atttcacaag ttttagatca caaaatagaa aaggcccgac
     4741 agtttcctgt cgagcctcat ccaaatctct tgccattatc acctttcggt ggagcgtggc
     4801 cttaatgtca ttgtgaatct ataaaaattt cacaatgcat taaagcgaaa gctcaaggct
     4861 tcactgccat acatgataca tcatcatcag gaaaaagagc aaactatttc ccatgatcac
     4921 gccaaagctt accatccacc atttaccaat agatcaaaaa acacacaaca aaaataacta
     4981 aaaacgccga ttaaaccagc attatcaaat ttacatttac cagttaaaaa acgataaaaa
     5041 caagataaca tcatgtttta tatgggaaaa caagcaacca ccaaatattg ctttatctag
     5101 atttattcta ataagcgtat ataaagttaa aacacaacaa cttagtatgc gactggagga
     5161 ccaattggaa accctcaaca atttgctggt aacgctaact tccgcaaagc cggaggtttt
     5221 ggtttctgtt gtatctttag gtgcaatggt tttcatgtat atgataataa agctatttat
     5281 atctctcctt gaccgaaaat ggggtaaaaa tgagcggtag aaaatttggc aggcttccaa
     5341 actggtgggc ccgaagctca tggcttgtaa acaatgttcg ttcaaatgag atagggggcg
     5401 gcattgcatc aatgaaatgc ttgttagctc tatccgtctt gattgatttc cattcaagaa
     5461 cagcctcagt atcatttacc ggaatggaaa gactgactgg actaagccgc cccatgatag
     5521 tgaaaggagt agccaaactt gagaaagatg gtcttataaa gatagataga gagatgtttg
     5581 ttaactccta tgaattaaca gtacagccaa atgatgatag gtgggcaaaa gtaccagtag
     5641 atactatcag gaaaaaacta aacaccatat cgaacagggg gatggcccca tttgtggcat
     5701 taaaactata tttaacaatt ataagccttc gttatcagtc aaataatact gttaaggtga
     5761 cacatgaaac actgagaagc tatacaggtg tccagccaaa ccagattagg ttcggcttag
     5821 atgtactgta ctgtagtcgc ctgatacatc tgcaaccaaa agaagataga gagtcaaaca
     5881 tctatgaaat aatcggcct
//
