LOCUS       NZ_CP122731             5261 bp    DNA     circular CON 08-JUN-2024
DEFINITION  Escherichia coli strain ETEC1746 plasmid unnamed4, complete
            sequence.
ACCESSION   NZ_CP122731
VERSION     NZ_CP122731.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN32549623
            Assembly: GCF_030013495.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5261)
  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 5261)
  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                   :: 389x
            Sequencing Technology             :: Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_030013495.1-RS_2024_06_08
            Annotation Date                   :: 06/08/2024 05:11:47
            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)                     :: 4,961
            CDSs (total)                      :: 4,845
            Genes (coding)                    :: 4,596
            CDSs (with protein)               :: 4,596
            Genes (RNA)                       :: 116
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 249
            CDSs (without protein)            :: 249
            Pseudo Genes (ambiguous residues) :: 0 of 249
            Pseudo Genes (frameshifted)       :: 103 of 249
            Pseudo Genes (incomplete)         :: 144 of 249
            Pseudo Genes (internal stop)      :: 38 of 249
            Pseudo Genes (multiple problems)  :: 32 of 249
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP122731.1.
            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..5261
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="ETEC1746"
                     /isolation_source="feces"
                     /host="Sus scrofa"
                     /db_xref="taxon:562"
                     /plasmid="unnamed4"
                     /geo_loc_name="Belgium"
                     /collection_date="2021"
                     /collected_by="IMM_DI04"
     gene            1..420
                     /locus_tag="QDW99_RS24145"
                     /old_locus_tag="QDW99_24145"
     CDS             1..420
                     /locus_tag="QDW99_RS24145"
                     /old_locus_tag="QDW99_24145"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016247941.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Exc2 family lipoprotein"
                     /protein_id="WP_001254967.1"
                     /translation="MRRTGNKLCLIAMITATVALTACTPKGSVEQHTRHYVYASDDGFD
                     PNFSTQKADTTRMMVPFFRQFWDMGAKDKATGKSRSDVQQRIQQFHSQEFLNSLRGTTQ
                     FAGTDYRSKDLTPKKSRLLADTISAVYLDGYEGRQ"
                     /name="Exc2 family lipoprotein"
     gene            1189..1383
                     /locus_tag="QDW99_RS24150"
                     /old_locus_tag="QDW99_24150"
     CDS             1189..1383
                     /locus_tag="QDW99_RS24150"
                     /old_locus_tag="QDW99_24150"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041627.1"
                     /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_001041633.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EELQNSIQVRFETESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2037..2195
                     /locus_tag="QDW99_RS24845"
     CDS             2037..2195
                     /locus_tag="QDW99_RS24845"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001354639.1"
                     /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_071531517.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHALTPLAAATGNRISRAMMA
                     QTVLQSS"
                     /name="replication initiation protein"
     gene            complement(2393..2530)
                     /locus_tag="QDW99_RS24155"
                     /old_locus_tag="QDW99_24155"
     CDS             complement(2393..2530)
                     /locus_tag="QDW99_RS24155"
                     /old_locus_tag="QDW99_24155"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001405930.1"
                     /GO_component="GO:0019867 - outer membrane [Evidence IEA]"
                     /GO_process="GO:0019835 - cytolysis [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin release lysis protein"
                     /protein_id="WP_001405930.1"
                     /translation="MRKRFFVGIFAINLLVGCQANYIRDVQGGTIAPSSSSKLTGIAVQ
                     "
                     /name="colicin release lysis protein"
     gene            2692..2919
                     /locus_tag="QDW99_RS24160"
                     /old_locus_tag="QDW99_24160"
     CDS             2692..2919
                     /locus_tag="QDW99_RS24160"
                     /old_locus_tag="QDW99_24160"
                     /inference="COORDINATES: protein motif:HMM:NF015489.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin E1 immunity protein"
                     /protein_id="WP_230498631.1"
                     /translation="MLYAIVISTILCPYSKYAIEHIAFNFIKKDFFERRKNLNNAPVAK
                     LNLFMLYNLLCLVLAIPFGLLGLFISIKNN"
                     /name="colicin E1 immunity protein"
     gene            complement(2916..4484)
                     /gene="cea"
                     /locus_tag="QDW99_RS24165"
                     /old_locus_tag="QDW99_24165"
     CDS             complement(2916..4484)
                     /gene="cea"
                     /locus_tag="QDW99_RS24165"
                     /old_locus_tag="QDW99_24165"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000447006.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="pore-forming bacteriocin colicin E1"
                     /protein_id="WP_000447006.1"
                     /translation="METAVAYYKDGVPYDDKGQVIITLLNGTPDGSGSGGGGGKGGSKS
                     ESSAAIHATAKWSTAQLKKTQAEQAARAKAAAEAQAKAKANRDALTQRLKDIVNEALRH
                     NASRTPSATELAHANNAAMQAEAERLRLAKAEEKARKEAEAAEKAFQEAEQRRKEIERE
                     KAETERQLKLAEAEEKRLAALSEEAKAVEIAQKKLSAAQSEVVKMDGEIKTLNSRLSSS
                     IHARDAEMKTLAGKRNELAQASAKYKELDELVKKLSPRANDPLQNRPFFEATRRRVGAG
                     KIREEKQKQVTASETRINRINADITQIQKAISQVSNNRNAGIARVHEAEENLKKAQNNL
                     LNSQIKDAVDATVSFYQTLTEKYGEKYSKMAQELADKSKGKKIGNVNEALAAFEKYKDV
                     LNKKFSKADRDAIFNALASVKYDDWAKHLDQFAKYLKITGHVSFGYDVVSDILKIKDTG
                     DWKPLFLTLEKKAADAGVSYVVALLFSLLAGTTLGIWGIAIVTGILCSYIDKNKLNTIN
                     EVLGI"
                     /name="cea"
     gene            4744..5181
                     /locus_tag="QDW99_RS24170"
                     /old_locus_tag="QDW99_24170"
     CDS             4744..5181
                     /locus_tag="QDW99_RS24170"
                     /old_locus_tag="QDW99_24170"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001405929.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001405929.1"
                     /translation="MGHCHFMAWHTLRDALKMTGRSRSQFYRDMRAGLVSYRTGRDGRR
                     EFETSELIRAYGELKQNETPERHSEGHAENPHDQQTERILRELNELKQCLTLMLEDKQA
                     QDMDRRRQEAEREQLQNEIAQLRQALELEKKRGFWSRLFGR"
                     /name="hypothetical protein"
     Typing          complement(681..925)
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="92.683"
                     /coverage="88.0"
                     /evalue="1.55e-95"
     Typing          complement(1055..1153)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="6.22e-45"
     Typing          complement(1457..1539)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.81"
                     /coverage="100.0"
                     /evalue="1.76e-34"
     Typing          1564..2109
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.353"
                     /coverage="98.0"
                     /evalue="0.0"
ORIGIN
        1 atgagacgta ccggaaacaa actttgtctt atcgccatga taacagcaac agtagctctc
       61 acagcctgta ccccaaaggg cagcgtggaa caacataccc ggcattacgt atatgcttct
      121 gatgacggtt ttgatcccaa cttttccacc caaaaagccg acacaacacg aatgatggtg
      181 cctttttttc ggcagttctg ggatatggga gctaaagata aagcgacagg aaaatcacgg
      241 agtgatgtgc aacaacgcat tcagcagttt cacagccagg aatttttaaa ctcactccgg
      301 ggcacaactc aatttgcggg tactgattac cgcagcaaag accttacccc gaaaaaatcc
      361 aggctgctgg ctgacacgat ttctgcggtt tatctcgatg gctacgaggg cagacagtaa
      421 gtggatttac cataatccct taattgtacg caccgctaaa acgcgctgaa cgcgattctg
      481 ccgcaaacac cgcaaaaaga gatgttttcc ccggggtaaa ccggaaaaat gcgtcaggat
      541 cgctttcagc tcactgcata gctatgcatg aaagtgaatg acgatcggtt tgggcgcata
      601 cagtgcccat gagacacatt ttcggacatt ttcagttcgt gaatccctga ctcattgcta
      661 tatatctgaa tagacacccc tagcagcgcc cccaggggca tcctgtaaaa aaacacaccg
      721 cgccgctagc agcaccccta atataaaacg atgtttttta tgaaaatagt cagtaccacc
      781 cctacaaagc ggtgtcggcg cggtgttgta gctgcgttaa cgacgctgtt ttaaataaat
      841 cagatttaaa caatataaat ccacaaacat aactcaatga tattaaagaa aaatcagcaa
      901 aaagttagtt ttgcgtgggg tgtggcattt caggcatgag aacagactcg cgtttttccg
      961 gagtatcagc ggaattattg attaagaaac actcgacgca gagcgaaatt ttatgcaaca
     1021 gcggctgcac tgcacaggga ttatttatca gttgatatgc tgtgccatga tacgtcctaa
     1081 aaaaacagga caggatgtgc aattgtaata ccgtcgcccg caacgtctta caattaccac
     1141 ctggtcaggg tccacccgac acccggtact gacggagaac aacggaaggt gaacaaacag
     1201 caacaaactg cgctgaatat ggcgcgattt atcaaaagcc agagcctgac actgcttgaa
     1261 aaactggatg ctctggatgc cgacgaacag gcggccatgt gcgaacgact gcacgaactc
     1321 gcggaagaac tccagaacag catccaggtt cgctttgaga ccgaaagtga aacaggaaca
     1381 taacgaagct gacggaggcg ctcacggctt gtccgcgagc gttttcggca gcagacaagc
     1441 ccgcctgggc gcgtcagcgg gtgtcggggc gaagccctga cccagtcacg tagcgatagc
     1501 ggagtgtata ctgacttaac tatgcggcat cagtgcagat tataagaaag ggcaccatat
     1561 gcggtgtgaa ataccgcaca gatgcgtaag gagaaaatgc cgcatcaggc gcacttccgc
     1621 ttcctcgctc actgactcgc tacgctcggt cgttcgactg cggcgagcgg tactgactca
     1681 cacaaaaacg gtaacacagt tatccacaga atcaggggat aaggccggaa agagcatgtg
     1741 agcaaaagac caggaacagg aagaaggcca cgtagcaggc gtttttccat aggctccgcc
     1801 cccctgacga gcatcacaaa aatagacgct caagtcagag gtggcgaaac ccgacaggac
     1861 tataaagata ccaggcgttt ccccctggaa gctccctcgt gcgctctcct gttccgaccc
     1921 tgccgcttac cggatacctg tccgcctttc tcccttcggg aagcgtggcg ctttctcata
     1981 gctcacgctg ttggtatctc agttcggtgt aggtcgttcg ctccaagctg ggctgtgtgc
     2041 acgaaccccc cgttcagccc gaccgctgcg ccttatccgg taactatcgt cttgagtcca
     2101 acccggtaag gcacgcctta acgccactgg cagcagccac tggtaaccgg attagcagag
     2161 cgatgatggc acaaacggtg ctacagagtt cttgaagtag tggcccgact acggctacac
     2221 tagaaggaca gtatttggta tctgcgctct gctgaagcca gttaccttcg gaaaaagagt
     2281 tggtagctct tgatccggca aacaaaccac cgttggtagc ggtggttttt ttgtttgcaa
     2341 gcagcagatt acgcgcagaa aaaaggatct caagaagatc ctttgatctt ttctactgaa
     2401 ccgcgatccc cgtcagttta gaagaggagg atggtgcgat ggtccctccc tgaacatcac
     2461 gtatatagtt agcctgacat ccaacaagga ggtttatcgc gaatattccc acaaaaaatc
     2521 ttttcctcat aactcgatcc ttataaaatg aaaagaatat atggcgaggt ttaatttatg
     2581 agcttaagat actacataaa aaatatttta tttggcctgt actgcacact tatatatata
     2641 taccttataa caaaaaacag cgaagggtat tatttccttg tgtcagataa gatgctatat
     2701 gcaatagtga taagcactat tctatgtcca tattcaaaat atgctattga acacatagct
     2761 tttaacttca taaagaaaga ttttttcgaa agaagaaaaa acctaaataa cgcccccgta
     2821 gcaaaattaa acctatttat gctatataat ctactttgtt tggtcctagc aatcccattt
     2881 ggattgctag gactttttat atcaataaag aataattaaa tccctaacac ctcatttata
     2941 gtattaagtt tattcttatc aatataggag catagaattc ctgtaacaat agcaataccc
     3001 caaataccta atgtagttcc agcaagcaag ctaaaaagta aagcaacaac ataactcacc
     3061 cctgcatctg cagctttctt ctctaatgta agaaatagtg gcttccagtc acctgtatcc
     3121 ttaattttta ggatatcaga taccacatca tatccaaaag aaacatgccc cgtaatcttc
     3181 aagtacttgg caaactgatc taaatgttta gcccagtcat catacttcac cgatgccaac
     3241 gcattaaaaa tagcatcacg atcggctttg ctgaatttct tatttaaaac atccttgtat
     3301 ttttcaaaag cagcgagagc ttcattcaca ttgccgattt tcttaccttt agacttatca
     3361 gcaagttcct gtgccatttt cgaatatttt tcaccatatt tttcagtcag cgtttgataa
     3421 aagctaactg ttgcatcaac agcatcctta atctgtgaat taaggagatt attctgtgct
     3481 tttttcaaat tttcttcagc ttcatgaaca cgagcgatac cggcattacg attattactg
     3541 acctgagaaa tagccttctg gatctgagtt atatcagcat ttatccggtt aatacgtgtt
     3601 tctgatgctg ttacctgttt ttgtttttct tctctaatct taccggcccc aacccgtcgt
     3661 ctggttgctt caaaaaaagg acggttctga agcggatcat tggctcttgg tgatagtttt
     3721 ttgaccagct catccagttc tttatattta gcggatgcct gagccagttc atttcgtttt
     3781 ccagcgagcg ttttcatttc tgcatcacgg gcatggatac tggagcttaa acgagaattg
     3841 agagtcttaa tctctccatc cattttcacc acttcagatt gtgcagcaga aagttttttt
     3901 tgggcgatct caacagcttt agcttcttca ctcaatgcag ccagtcgttt ctcttcagct
     3961 tcagccaatt tcaactggcg ttctgtttca gccttctccc gttcaatctc tttacgtcgt
     4021 tgttctgctt cctgaaaagc cttttctgct gcttccgctt ctttacgggc tttttcttct
     4081 gctttcgcaa ggcgcaaacg ctctgcttcc gcctgcatag ctgcattatt agcatgagca
     4141 agctctgttg ctgaaggcgt acgtgaggca ttgtgacgaa gagcctcatt cacgatatcc
     4201 ttcaggcgct gagtcagcgc atccctgttt gcctttgctt tcgcctgtgc ttccgctgca
     4261 gcttttgccc gggcagcctg ctctgcctgt gttttcttta attgagcagt agaccattta
     4321 gcagttgcat gaatagctgc agaactttca cttttactgc ctccttttcc acctccgccg
     4381 ccagagccac tcccgtcagg agtaccattc aaaagagtaa taattacctg tcccttatca
     4441 tcataaggaa caccatcttt atagtacgct accgcggttt ccattataaa atcctctttg
     4501 acttttaaaa caataagtta aaaataaata ctgtacatat aaccactggt tttatataca
     4561 gcataaaagc tacgccgctg cattttccct gtcaagactg tggacttcca tttttgtgaa
     4621 aacgatcaaa aaaacagtct ttcacaccac gcgctattct cgcccgatgc cacaaaaacc
     4681 agcacaaaca ttaccgttct cagacctcat tatgttttac tgaaactatg agatgagaca
     4741 tctatgggac actgtcactt tatggcatgg cacacactcc gggacgcact aaaaatgaca
     4801 ggcagatcgc gttcacagtt ttaccgtgat atgcgcgcag gccttgtcag ttaccgtacc
     4861 ggcagggacg gacgacggga gtttgaaacc agtgaactga tccgggcata cggcgaatta
     4921 aagcagaatg agacaccaga aaggcacagt gagggacatg cagaaaatcc acatgatcag
     4981 cagacagaac gcattctccg ggagctgaat gagctgaaac aatgcctgac gctgatgctt
     5041 gaggataaac aggcacagga tatggatcgc agacgccagg aagcagaacg ggaacagcta
     5101 caaaatgaga tagcccagct caggcaggca ctggaactgg aaaagaaacg gggattctgg
     5161 tccaggttgt tcggtcgctg aacgctgtca gagactgatg ataaaatagt cttcggataa
     5221 taactcaccg agaataaata ctttaaggta gggagacact c
//
