LOCUS       NZ_CP122760             6197 bp    DNA     circular CON 08-JUN-2024
DEFINITION  Escherichia coli strain ETEC1739 plasmid unnamed2, complete
            sequence.
ACCESSION   NZ_CP122760
VERSION     NZ_CP122760.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN32549616
            Assembly: GCF_030013575.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 6197)
  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 6197)
  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                   :: 225x
            Sequencing Technology             :: Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_030013575.1-RS_2024_06_08
            Annotation Date                   :: 06/08/2024 05:11:44
            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)                     :: 5,204
            CDSs (total)                      :: 5,086
            Genes (coding)                    :: 4,727
            CDSs (with protein)               :: 4,727
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 359
            CDSs (without protein)            :: 359
            Pseudo Genes (ambiguous residues) :: 0 of 359
            Pseudo Genes (frameshifted)       :: 124 of 359
            Pseudo Genes (incomplete)         :: 249 of 359
            Pseudo Genes (internal stop)      :: 50 of 359
            Pseudo Genes (multiple problems)  :: 58 of 359
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP122760.1.
            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..6197
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="ETEC1739"
                     /isolation_source="feces"
                     /host="Sus scrofa"
                     /db_xref="taxon:562"
                     /plasmid="unnamed2"
                     /geo_loc_name="Belgium"
                     /collection_date="2021"
                     /collected_by="IMM_DI04"
     gene            join(4553..6197,1..23)
                     /gene="ltrA"
                     /locus_tag="QDW95_RS23455"
                     /old_locus_tag="QDW95_23455"
     CDS             join(4553..6197,1..23)
                     /gene="ltrA"
                     /locus_tag="QDW95_RS23455"
                     /old_locus_tag="QDW95_23455"
                     /EC_number="2.7.7.49"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001748652.1"
                     /GO_function="GO:0003964 - RNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /GO_process="GO:0000373 - Group II intron splicing
                     [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="group II intron reverse transcriptase/maturase"
                     /protein_id="WP_282869375.1"
                     /translation="MNTHISVSTIPHPTGWHTINWKACHARVRKLQLRIAKATRQQQWR
                     QVRELQRILTRSFSGKAVAVRRVTENTGKRTPGIDGKIWHTPKEKWEGICSLNLCGYRP
                     QPLRRIHIPKSNGKTRPLGIPTMRDRAMQALWLLALEPVSETTADHNSYGFRPMRSTHD
                     AIESIFLRMSQKVSPKWILEGDIKGCFDNISHDWLLSHIPMDRRLLKKWLKAGYMERGV
                     FNHTNSGTPQGGIISPVLANMALDGLEKELMQTFRKSGYHSAKHQVNYVRYADDFICSG
                     SSRELLENEVRPLIAAFMRERGLELSEEKTAITHIDKGFDFLGQNVRKYNGKMLIKPSK
                     KNLKNFLCKVREIIKRNPTLPAWKLIGQLNPVIRGWVTYHRHVVAKETFNYVDTQIWRA
                     IWRWCVRRHPRKGLRWIAGRYFSFEGRRWIFKAITPEGKILTLFRAMETPIKRHIKIKG
                     EATPYTPGMEIYFERRLDLIWKGKSKKMKTVVQLWKRQGKHCPQCGQLITNQTGWNIHH
                     RIRKVMGGSDELTNLELLHPNCHRQLHSREAGAHRKHL"
                     /name="ltrA"
     gene            complement(425..547)
                     /locus_tag="QDW95_RS23460"
                     /old_locus_tag="QDW95_23460"
     CDS             complement(425..547)
                     /locus_tag="QDW95_RS23460"
                     /old_locus_tag="QDW95_23460"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004118124.1"
                     /GO_component="GO:0016020 - membrane [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Hok/Gef family protein"
                     /protein_id="WP_223200913.1"
                     /translation="MVCCTLLIFTLLTRNRLCEVRLKDGYREVTATMAYESGGK"
                     /name="Hok/Gef family protein"
     gene            complement(<492..644)
                     /locus_tag="QDW95_RS23465"
                     /old_locus_tag="QDW95_23465"
                     /pseudo=""
     CDS             complement(<492..644)
                     /locus_tag="QDW95_RS23465"
                     /old_locus_tag="QDW95_23465"
                     /inference="COORDINATES: protein motif:HMM:NF010277.0"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="DUF5431 family protein"
                     /name="DUF5431 family protein"
     gene            complement(818..1580)
                     /locus_tag="QDW95_RS23470"
                     /old_locus_tag="QDW95_23470"
                     /pseudo=""
     CDS             complement(818..1580)
                     /locus_tag="QDW95_RS23470"
                     /old_locus_tag="QDW95_23470"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052659.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid SOS inhibition protein A"
                     /name="plasmid SOS inhibition protein A"
     gene            complement(1577..2011)
                     /gene="psiB"
                     /locus_tag="QDW95_RS23475"
                     /old_locus_tag="QDW95_23475"
     CDS             complement(1577..2011)
                     /gene="psiB"
                     /locus_tag="QDW95_RS23475"
                     /old_locus_tag="QDW95_23475"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052658.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="conjugation system SOS inhibitor PsiB"
                     /protein_id="WP_000845928.1"
                     /translation="MKTELTLNVLQTMNAQEYEDIRAAGSDERRELTHAVMRELDAPDN
                     WTMNGEYGSEFGGFFPVQVRFTPAHERFHLALCSPGDVSQVWVLVLVNAGGEPFAVVQV
                     QRRFASEAVSHSLALAASLDTQGYSVNDIIHILMAEGGQV"
                     /name="psiB"
     gene            complement(2066..>2431)
                     /locus_tag="QDW95_RS23480"
                     /old_locus_tag="QDW95_23480"
                     /pseudo=""
     CDS             complement(2066..>2431)
                     /locus_tag="QDW95_RS23480"
                     /old_locus_tag="QDW95_23480"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052657.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /name="hypothetical protein"
     gene            complement(<2433..2834)
                     /locus_tag="QDW95_RS23485"
                     /old_locus_tag="QDW95_23485"
                     /pseudo=""
     CDS             complement(<2433..2834)
                     /locus_tag="QDW95_RS23485"
                     /old_locus_tag="QDW95_23485"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052643.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="DUF1281 domain-containing protein"
                     /name="DUF1281 domain-containing protein"
     gene            3252..3455
                     /locus_tag="QDW95_RS23490"
                     /old_locus_tag="QDW95_23490"
     CDS             3252..3455
                     /locus_tag="QDW95_RS23490"
                     /old_locus_tag="QDW95_23490"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001697964.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_282869373.1"
                     /translation="MIRIEILFDRQSTKNLKSGTLQALQNEIEQRLKPHYPEIWLLSFG
                     SRGFDVLRGPAFCSLRYSPSPV"
                     /name="hypothetical protein"
     gene            complement(<3376..3549)
                     /locus_tag="QDW95_RS26015"
                     /pseudo=""
     CDS             complement(<3376..3549)
                     /locus_tag="QDW95_RS26015"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001369404.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="single-stranded DNA-binding protein"
                     /name="single-stranded DNA-binding protein"
     gene            <3658..>3812
                     /locus_tag="QDW95_RS23495"
                     /old_locus_tag="QDW95_23495"
                     /pseudo=""
     CDS             <3658..>3812
                     /locus_tag="QDW95_RS23495"
                     /old_locus_tag="QDW95_23495"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052655.1"
                     /note="frameshifted; incomplete; partial in the middle of a
                     contig; missing N-terminus and C-terminus; Derived by
                     automated computational analysis using gene prediction
                     method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /name="hypothetical protein"
ORIGIN
        1 gtgctcaccg aaagcactta taaaggcttg agcggagtgc gggaaaactc gcacgctccg
       61 ttcttagggg gcggcggcgc agcaatgtgc cgctgctacc cgacccggca gacaggacaa
      121 cactgcagta gtcagaatca gagcaggaag aaaaagagaa taatcacggg aaaggtaatg
      181 tcatttctga caactggcca taaacagaga aaacggagga aaagaacggg cgccgcaggc
      241 gcacgttcat ccccgttccc agagggaaac ggccttcctg gcagcctggt tgttcatgcc
      301 cgcacaatgc cagcaaggag aaaggggcca ccggcgaacc agcagcccct ttataaaggc
      361 gcttcagtgc agtcagacca gcatcagccc ctgaaaaggc gggcctgcgc ccgcctccag
      421 gttgctactt accgccggat tcgtaagcca ttgttgccgt aacttccctg tatccgtcct
      481 tcagccggac ttcgcacagg cgattccggg tcaggagtgt gaatatcaac aacgtgcagc
      541 acacgattaa tacgcaccag ataagggcgt ttcccggtag tttcatggtt tactcctcct
      601 tgcaatttgc acggtaagag gccatactgg tgttggttag acatacagtg ggcctcgtgg
      661 gttaatgaaa attaactacg gggctttctg ctttctgcca cacaacacgg taacaaacca
      721 ccttcacgtc atgaggcaga aagcctcaag cgccaggcac atcatagccc atatacctgc
      781 acgctgacca cactcacttt tcctgaaaat aacccgctca ttcaggctgt ttacgggtaa
      841 tctgtgtgat tgttgccgca tcacgccgcc tcccggagtt tgttcggcac catccatctc
      901 tccatctcac ggacggcatg accggcctcc cttgccgcca taccagcctc tgcgatgacc
      961 tgccagaatg gcatatcctg ccactgccag cgttccatcc cggtcagtga cggaaaacgc
     1021 tcgccccact gccagaacag ggtttccagg tcatgctctg ccacccggtc actccagcgt
     1081 gcatgccagc ttccgactgt ttccggcgaa tggaatgcca gttcgatttc agcctgagcg
     1141 accagcgcct ggtacgcacg ggctttctgc tctgcctccc tcgcctgctg gcggctgtac
     1201 ttctgcatga ccagcgcgga tttatggcga ctgcgttccc tgacacgaaa ccgcaccgac
     1261 gggaacaagt gttctgctgc atcgcccgga aggggaagga ggcagacctc gccctgtgtt
     1321 tcaatcagca catcgatggc atacagccac tgaagacggt tgccgtgcag ttcttctgcg
     1381 gtcagggacg gcatgaaaaa tcgcaggtca gacagcgata tcctgcggct tccgttcaga
     1441 cagcggaaaa acgcccccgc atacggatat tccgccagcg tgttatcctg atggcggcgt
     1501 ttttctgtct ccgccaccgc ccgccatgcg gcctgttgct ctgtgctgag gggaaccagt
     1561 gcctgtgaac gtacgctcat acctgacctc cttccgccat caggatatgg atgatgtcgt
     1621 taacgctgta cccctgcgta tccagtgacg ccgccagtgc cagtgaatgg ctgacggctt
     1681 ccgatgcaaa ccgccgctgt acctgaacca ccgcaaacgg ctcaccaccg gcattcacca
     1741 gaaccagcac ccagacctga gagacatcgc ccggtgaaca taacgccagg tgaaaacgtt
     1801 cgtgggcagg cgtgaaacgg acctggacgg ggaaaaagcc gccaaactcg ctgccgtact
     1861 cgccgttcat cgtccagtta tccggcgcat ccagctcccg catcacggcg tgagtcagct
     1921 cacggcgttc atcacttccg gcagcccgga tatcttcata ttcctgtgcg ttcatggtct
     1981 gtaatacatt cagggtcagt tcagttttca tcacggtatc tcccttgctg ccgccccgtc
     2041 tccggcgggg cggtgtggtt gttcatcagg cggcatcagc caggttatca gtacgttcag
     2101 tggcatccgt ctgtgggcgt ggtgcacaca tccagccagg cacccagcgg ttgtctttca
     2161 tgtggaactc tgcatgttca gccgcatcgc ctttcttcat cttctccgcg tcccgtgcag
     2221 caccggacag tccggcctca ttcagggctg cgataatctg cggctttttc aggtgtccga
     2281 agaagtttgc ttttgtcggc tgccaccagt cgcgcatgtg gaatccgata gcggtttcca
     2341 gcgggtcaag cggactgcgt gacgtgtgac cacactcgcg ggtctgaacg ccgtggatgc
     2401 tgcacgcagt gcagaaactg agcagggata ccccagatgt cacaccagtc acctcttttt
     2461 gcggtgaaat gcacagtgat ggtttccctg acatcatccg gtaatccttt ccagcgacgc
     2521 cggccaatac cgctctgcag ccagagttca tgcagcatca ggcagttttt ctcatccagc
     2581 agtacaccat tctgcaggtg tgtcagccag cgggtgaacg cgatattttc cgtcgataca
     2641 gcaccacgtc cggcagccgt cactccgggg cactgctcag agcggatatt ttcagtgatc
     2701 tgcagaagtc cggcacttcc ggccagaaac agctgaatac cttcatttgt ggcgcggcga
     2761 taaagcggtg tgactgcacc gctggccagt cgtttaatct cagcaatctg tgccggttca
     2821 ccagaaaaat gcatacgatt tgagcaccag tttggcatgg gaattctcct ctcacatgcg
     2881 gcctccatca ggccgtgccg cacctgtaac cgggcgaccg catacgaatg caggtgcggc
     2941 cccgaagccg cagcgcgtgg aggaggaacg acgaaacgtg accgggtgag gaggccggcg
     3001 acagcgacac acttgcatcg gatgcagccc ggttaacgtg ccggcacggc ctgggtaacc
     3061 aggtatttta ttcacagaac cgtgcgcaaa atgctgtgga taagctggac acagcagtcc
     3121 acagcaggca tacagccaca ccctcagaga attgagcgtt ttttagtcac aataatgaca
     3181 tttgactgtg tgtggattca gttattagaa tactgtatat acatacagca atagaagagg
     3241 gagatgagaa catgatccgc attgaaattc ttttcgaccg ccagagcaca aaaaacctca
     3301 aatcaggcac acttcaggcg ctacagaatg aaatcgaaca acgtctgaaa ccacactacc
     3361 cggaaatctg gctgctgagt ttcgggagcc gcggttttga cgttttgcgg ggacctgcct
     3421 tttgttccct ccggtattca ccatcacctg tttgagaacc ttcttcgccg cccgaggtat
     3481 ccctgcgacg gccggaaacg gacctgaccc ggcggcagac cgcaaagttt tttgcctgca
     3541 ctctggcaaa aagttttttt ttttgccggg atgtgcattt cacccctgga ctggccgaga
     3601 gacggttatg gctgtcttta cccccggcga caggggttta aagaaggtga atggcacccg
     3661 gacacaacaa cgggcaggga cccgccgcaa cgacgtgaag cgcggtttgc gaaacggcgt
     3721 tgccccttac atcccggcgg tcttttgccg gatgcgggga gcgcaggtca cggcgcgaca
     3781 gaggcggcgc gaccggaacg gtcgctgcaa gctctgtggt tttcacgcat cggaccgtag
     3841 cggcagcccg aaaccgcgcc agcgggttcg gcggagactg gcaggtgcgc cagcagctgc
     3901 ctgtcggagt cgggcctgac gaccggatgc cgccaggcag ccgggagccg aaggtgcgcg
     3961 tgcgacagga agtcgcttaa cgtattgttt tacattgata aaaccagcta tcccattagc
     4021 tgtagcctac cgggacaggc gttgccggca acggcggggt ctgaagctcc cgggacaacg
     4081 agagccgggc gtcagcccgg gtaaagcccg tgaggggctt taccttgctg caagcatcat
     4141 gcggcaggag agcaaggctg gtcagaaggg ttaacacatg tgaactgttg ataaacaccg
     4201 ttatcggcaa caggccaaag atgctgacag gcctgaacca aaaggtacgg ggtccggttg
     4261 ctacctcgcg cacagggagc acatgggcgc agagaccccc ggtgaagaga cagaacccgc
     4321 cctgaccctc tgtatgttaa gcggaacctg gtaaacccgt atcgctgcct cacaggcagg
     4381 tgaaccgcaa ggaacactgt tagcggtgcg ggcataggag gacggaaaaa gcgaatgccc
     4441 ggccgtaata accgggatac ggggcaggtt ccccgacgcg aaagcgggca gacttccgtc
     4501 tggtctttaa ttgcatgaaa agctgtaaag cagtcaaaag gatatcagcg agatgaatac
     4561 acacatcagt gtgtccacga taccccaccc gacaggctgg cacaccataa actggaaagc
     4621 atgccatgcc cgggtgcgaa agctacagtt acggattgca aaggcaaccc gacagcaaca
     4681 atggcggcag gtcagagaac tacagcgcat cctcacccgc tcattctccg gcaaagccgt
     4741 ggctgtcagg cgtgtaactg aaaataccgg taaaaggaca cccggtattg acggaaaaat
     4801 atggcacaca ccgaaggaga aatgggaagg aatatgcagc ctgaatctgt gtggttacag
     4861 gccacagcca ctacggcgaa tacatatccc aaaatcaaac ggcaaaacgc gaccgctggg
     4921 catacccaca atgagggacc gggccatgca ggcactgtgg ctgctggctc tggaacccgt
     4981 atccgagacc actgctgacc ataacagcta tggtttcaga ccaatgcgca gcacgcatga
     5041 cgccattgag tccatttttc tgcggatgag ccagaaagta tcgcccaaat ggatactgga
     5101 gggcgatatt aaagggtgtt tcgataacat cagccatgac tggctgcttt cccatattcc
     5161 gatggacagg agactgctta aaaaatggtt gaaagcaggt tacatggaaa gaggcgtgtt
     5221 taaccatacg aacagcggga caccgcaggg aggcatcata tcccctgttc tcgccaacat
     5281 ggctctggac ggactggaga aggaactgat gcaaacgttc aggaaaagtg gttatcacag
     5341 tgcaaagcac caggtgaatt atgtgagata tgctgatgat ttcatctgtt caggcagctc
     5401 ccgtgaattg ctggaaaatg aggtcagacc actgattgca gctttcatgc gcgaacgagg
     5461 gctggaactg tcggaagaaa aaacagcgat cacacatata gataaaggct tcgacttttt
     5521 agggcagaac gtcaggaagt acaacggtaa aatgctgatt aaaccgtcga agaaaaacct
     5581 gaagaacttc ctctgtaaag tcagagaaat aattaaacgc aatccgacgc tcccggcatg
     5641 gaaactgata ggccagctaa acccggtgat ccggggatgg gttacctatc accgacacgt
     5701 cgtggcgaaa gaaacattta attatgtcga cacccaaatc tggcgagcta tatggcgatg
     5761 gtgtgtaaga cggcatcccc ggaaaggatt gcggtggatc gccggacgat acttctcctt
     5821 tgaaggcagg cgctggatct ttaaagccat aaccccggaa gggaaaattc tgacactctt
     5881 ccgggcaatg gaaacaccga taaagcgcca tataaaaatc aaaggcgaag caacaccata
     5941 cacccccgga atggaaatct actttgaacg tcgtctggat ctaatctgga aaggcaaatc
     6001 aaagaagatg aagacagtag ttcaactctg gaagaggcag gggaaacact gtccgcagtg
     6061 cggacaactc ataaccaacc agaccggatg gaatatacat caccggatca ggaaagttat
     6121 gggcggcagt gacgaactga ccaatctcga gttgttacat ccgaactgcc accgacagtt
     6181 acacagcagg gaagccg
//
