LOCUS       NZ_CP122715             5262 bp    DNA     circular CON 08-JUN-2024
DEFINITION  Escherichia coli strain ETEC1749 plasmid unnamed3, complete
            sequence.
ACCESSION   NZ_CP122715
VERSION     NZ_CP122715.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN32549626
            Assembly: GCF_030013435.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5262)
  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 5262)
  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                   :: 408x
            Sequencing Technology             :: Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_030013435.1-RS_2024_06_08
            Annotation Date                   :: 06/08/2024 05:03:10
            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)                     :: 5,704
            CDSs (total)                      :: 5,579
            Genes (coding)                    :: 5,222
            CDSs (with protein)               :: 5,222
            Genes (RNA)                       :: 125
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 91
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 357
            CDSs (without protein)            :: 357
            Pseudo Genes (ambiguous residues) :: 0 of 357
            Pseudo Genes (frameshifted)       :: 160 of 357
            Pseudo Genes (incomplete)         :: 208 of 357
            Pseudo Genes (internal stop)      :: 73 of 357
            Pseudo Genes (multiple problems)  :: 74 of 357
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP122715.1.
            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..5262
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="ETEC1749"
                     /isolation_source="feces"
                     /host="Sus scrofa"
                     /db_xref="taxon:562"
                     /plasmid="unnamed3"
                     /geo_loc_name="Belgium"
                     /collection_date="2021"
                     /collected_by="IMM_DI04"
     gene            1..1569
                     /gene="cea"
                     /locus_tag="QDX02_RS27425"
                     /old_locus_tag="QDX02_27425"
     CDS             1..1569
                     /gene="cea"
                     /locus_tag="QDX02_RS27425"
                     /old_locus_tag="QDX02_27425"
                     /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            1955..2092
                     /locus_tag="QDX02_RS27430"
                     /old_locus_tag="QDX02_27430"
     CDS             1955..2092
                     /locus_tag="QDX02_RS27430"
                     /old_locus_tag="QDX02_27430"
                     /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            complement(2291..2449)
                     /locus_tag="QDX02_RS28595"
     CDS             complement(2291..2449)
                     /locus_tag="QDX02_RS28595"
                     /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(3103..3297)
                     /locus_tag="QDX02_RS27435"
                     /old_locus_tag="QDX02_27435"
     CDS             complement(3103..3297)
                     /locus_tag="QDX02_RS27435"
                     /old_locus_tag="QDX02_27435"
                     /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            complement(4066..4485)
                     /locus_tag="QDX02_RS27440"
                     /old_locus_tag="QDX02_27440"
     CDS             complement(4066..4485)
                     /locus_tag="QDX02_RS27440"
                     /old_locus_tag="QDX02_27440"
                     /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            complement(4566..5003)
                     /locus_tag="QDX02_RS27445"
                     /old_locus_tag="QDX02_27445"
     CDS             complement(4566..5003)
                     /locus_tag="QDX02_RS27445"
                     /old_locus_tag="QDX02_27445"
                     /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          2948..3030
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.79e-36"
     Typing          3334..3432
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="6.22e-45"
     Typing          3562..3806
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="92.683"
                     /coverage="88.0"
                     /evalue="1.55e-95"
     Typing          complement(2378..2923)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.536"
                     /coverage="98.0"
                     /evalue="0.0"
ORIGIN
        1 atggaaaccg cggtagcgta ctataaagat ggtgttcctt atgatgataa gggacaggta
       61 attattactc ttttgaatgg tactcctgac gggagtggct ctggcggcgg aggtggaaaa
      121 ggaggcagta aaagtgaaag ttctgcagct attcatgcaa ctgctaaatg gtctactgct
      181 caattaaaga aaacacaggc agagcaggct gcccgggcaa aagctgcagc ggaagcacag
      241 gcgaaagcaa aggcaaacag ggatgcgctg actcagcgcc tgaaggatat cgtgaatgag
      301 gctcttcgtc acaatgcctc acgtacgcct tcagcaacag agcttgctca tgctaataat
      361 gcagctatgc aggcggaagc agagcgtttg cgccttgcga aagcagaaga aaaagcccgt
      421 aaagaagcgg aagcagcaga aaaggctttt caggaagcag aacaacgacg taaagagatt
      481 gaacgggaga aggctgaaac agaacgccag ttgaaattgg ctgaagctga agagaaacga
      541 ctggctgcat tgagtgaaga agctaaagct gttgagatcg cccaaaaaaa actttctgct
      601 gcacaatctg aagtggtgaa aatggatgga gagattaaga ctctcaattc tcgtttaagc
      661 tccagtatcc atgcccgtga tgcagaaatg aaaacgctcg ctggaaaacg aaatgaactg
      721 gctcaggcat ccgctaaata taaagaactg gatgagctgg tcaaaaaact atcaccaaga
      781 gccaatgatc cgcttcagaa ccgtcctttt tttgaagcaa ccagacgacg ggttggggcc
      841 ggtaagatta gagaagaaaa acaaaaacag gtaacagcat cagaaacacg tattaaccgg
      901 ataaatgctg atataactca gatccagaag gctatttctc aggtcagtaa taatcgtaat
      961 gccggtatcg ctcgtgttca tgaagctgaa gaaaatttga aaaaagcaca gaataatctc
     1021 cttaattcac agattaagga tgctgttgat gcaacagtta gcttttatca aacgctgact
     1081 gaaaaatatg gtgaaaaata ttcgaaaatg gcacaggaac ttgctgataa gtctaaaggt
     1141 aagaaaatcg gcaatgtgaa tgaagctctc gctgcttttg aaaaatacaa ggatgtttta
     1201 aataagaaat tcagcaaagc cgatcgtgat gctattttta atgcgttggc atcggtgaag
     1261 tatgatgact gggctaaaca tttagatcag tttgccaagt acttgaagat tacggggcat
     1321 gtttcttttg gatatgatgt ggtatctgat atcctaaaaa ttaaggatac aggtgactgg
     1381 aagccactat ttcttacatt agagaagaaa gctgcagatg caggggtgag ttatgttgtt
     1441 gctttacttt ttagcttgct tgctggaact acattaggta tttggggtat tgctattgtt
     1501 acaggaattc tatgctccta tattgataag aataaactta atactataaa tgaggtgtta
     1561 gggatttaat tattctttat tgatataaaa agtcctagca atccaaatgg gattgctagg
     1621 accaaacaaa gtagattata tagcataaat aggtttaatt ttgctacggg ggcgttattt
     1681 aggttttttc ttctttcgaa aaaatctttc tttatgaagt taaaagctat gtgttcaata
     1741 gcatattttg aatatggaca tagaatagtg cttatcacta ttgcatatag catcttatct
     1801 gacacaagga aataataccc ttcgctgttt tttgttataa ggtatatata tataagtgtg
     1861 cagtacaggc caaataaaat attttttatg tagtatctta agctcataaa ttaaacctcg
     1921 ccatatattc ttttcatttt ataaggatcg agttatgagg aaaagatttt ttgtgggaat
     1981 attcgcgata aacctccttg ttggatgtca ggctaactat atacgtgatg ttcagggagg
     2041 gaccatcgca ccatcctcct cttctaaact gacggggatc gcggttcagt agaaaagatc
     2101 aaaggatctt cttgagatcc tttttttctg cgcgtaatct gctgcttgca aacaaaaaaa
     2161 ccaccgctac caacggtggt ttgtttgccg gatcaagagc taccaactct ttttccgaag
     2221 gtaactggct tcagcagagc gcagatacca aatactgtcc ttctagtgta gccgtagtcg
     2281 ggccactact tcaagaactc tgtagcaccg tttgtgccat catcgctctg ctaatccggt
     2341 taccagtggc tgctgccagt ggcgttaagg cgtgccttac cgggttggac tcaagacgat
     2401 agttaccgga taaggcgcag cggtcgggct gaacgggggg ttcgtgcaca cagcccagct
     2461 tggagcgaac gacctacacc gaactgagat accaacagcg tgagctatga gaaagcgcca
     2521 cgcttcccga agggagaaag gcggacaggt atccggtaag cggcagggtc ggaacaggag
     2581 agcgcacgag ggagcttcca gggggaaacg cctggtatct ttatagtcct gtcgggtttc
     2641 gccacctctg acttgagcgt ctatttttgt gatgctcgtc aggggggcgg agcctatgga
     2701 aaaacgcctg ctacgtggcc ttcttcctgt tcctggtctt ttgctcacat gttctttccg
     2761 gccttatccc ctgattctgt ggataactgt gttaccgttt ttgtgtgagt cagtaccgct
     2821 cgccgcagtc gaacgaccga gcgtagcgag tcagtgagcg aggaagcgga agtgcgcctg
     2881 atgcggcatt ttctccttac gcatctgtgc ggtatttcac accgcatatg gtgccctttc
     2941 ttataatctg cactgatgcc gcatagttaa gccagtatac actccgctat cgctacgtga
     3001 ctgggtcagg gcttcgcccc gacacccgct gacgcgccca ggcgggcttg tctgctgccg
     3061 aaaacgctcg cggacaagcc gtgagcgcct ccgtcagctt cgttatgttc ctgtttcact
     3121 ttcggtctca aagcgaacct ggatgctgtt ctggagttct tccgcgagtt cgtgcagtcg
     3181 ttcgcacatg gccgcctgtt cgtcggcatc cagagcatcc agtttttcaa gcagtgtcag
     3241 gctctggctt ttgataaatc gcgccatatt cagcgcagtt tgttgctgtt tgttcacctt
     3301 ccgttgttct ccgtcagtac cgggtgtcgg gtggaccctg accaggtggt aattgtaaga
     3361 cgttgcgggc gacggtatta caattgcaca tcctgtcctg tttttttagg acgtatcatg
     3421 gcacagcata tcaactgata aataatccct gtgcagtgca gccgctgttg cataaaattt
     3481 cgctctgcgt cgagtgtttc ttaatcaata attccgctga tactccggaa aaacgcgagt
     3541 ctgttctcat gcctgaaatg ccacacccca cgcaaaacta actttttgct gatttttctt
     3601 taatatcatt gagttatgtt tgtggattta tattgtttaa atctgattta tttaaaacag
     3661 cgtcgttaac gcagctacaa caccgcgccg acaccgcttt gtaggggtgg tactgactat
     3721 tttcataaaa aacatcgttt tatattaggg gtgctgctag cggcgcggtg tgttttttta
     3781 caggatgccc ctgggggcgc tgctaggggt gtctattcag atatatagca atgagtcagg
     3841 gattcacgaa ctgaaaatgt ccgaaaatgt gtctcatggg cactgtatgc gcccaaaccg
     3901 atcgtcattc actttcatgc atagctatgc agtgagctga aagcgatcct gacgcatttt
     3961 tccggtttac cccggggaaa acatctcttt ttgcggtgtt tgcggcagaa tcgcgttcag
     4021 cgcgttttag cggtgcgtac aattaaggga ttatggtaaa tccacttact gtctgccctc
     4081 gtagccatcg agataaaccg cagaaatcgt gtcagccagc agcctggatt ttttcggggt
     4141 aaggtctttg ctgcggtaat cagtacccgc aaattgagtt gtgccccgga gtgagtttaa
     4201 aaattcctgg ctgtgaaact gctgaatgcg ttgttgcaca tcactccgtg attttcctgt
     4261 cgctttatct ttagctccca tatcccagaa ctgccgaaaa aaaggcacca tcattcgtgt
     4321 tgtgtcggct ttttgggtgg aaaagttggg atcaaaaccg tcatcagaag catatacgta
     4381 atgccgggta tgttgttcca cgctgccctt tggggtacag gctgtgagag ctactgttgc
     4441 tgttatcatg gcgataagac aaagtttgtt tccggtacgt ctcatgagtg tctccctacc
     4501 ttaaagtatt tattctcggt gagttattat ccgaagacta ttttatcatc agtctctgac
     4561 agcgttcagc gaccgaacaa cctggaccag aatccccgtt tcttttccag ttccagtgcc
     4621 tgcctgagct gggctatctc attttgtagc tgttcccgtt ctgcttcctg gcgtctgcga
     4681 tccatatcct gtgcctgttt atcctcaagc atcagcgtca ggcattgttt cagctcattc
     4741 agctcccgga gaatgcgttc tgtctgctga tcatgtggat tttctgcatg tccctcactg
     4801 tgcctttctg gtgtctcatt ctgctttaat tcgccgtatg cccggatcag ttcactggtt
     4861 tcaaactccc gtcgtccgtc cctgccggta cggtaactga caaggcctgc gcgcatatca
     4921 cggtaaaact gtgaacgcga tctgcctgtc atttttagtg cgtcccggag tgtgtgccat
     4981 gccataaagt gacagtgtcc catagatgtc tcatctcata gtttcagtaa aacataatga
     5041 ggtctgagaa cggtaatgtt tgtgctggtt tttgtggcat cgggcgagaa tagcgcgtgg
     5101 tgtgaaagac tgtttttttg atcgttttca caaaaatgga agtccacagt cttgacaggg
     5161 aaaatgcagc ggcgtagctt ttatgctgta tataaaacca gtggttatat gtacagtatt
     5221 tatttttaac ttattgtttt aaaagtcaaa gaggatttta ta
//
