LOCUS       NZ_CP122933             5172 bp    DNA     circular CON 08-JUN-2024
DEFINITION  Escherichia coli strain ETEC1702 plasmid unnamed4, complete
            sequence.
ACCESSION   NZ_CP122933
VERSION     NZ_CP122933.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN32549585
            Assembly: GCF_030012765.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5172)
  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 5172)
  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                   :: 131x
            Sequencing Technology             :: Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_030012765.1-RS_2024_06_08
            Annotation Date                   :: 06/08/2024 05:03:28
            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)                     :: 5,103
            CDSs (total)                      :: 4,982
            Genes (coding)                    :: 4,631
            CDSs (with protein)               :: 4,631
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 351
            CDSs (without protein)            :: 351
            Pseudo Genes (ambiguous residues) :: 0 of 351
            Pseudo Genes (frameshifted)       :: 166 of 351
            Pseudo Genes (incomplete)         :: 195 of 351
            Pseudo Genes (internal stop)      :: 51 of 351
            Pseudo Genes (multiple problems)  :: 54 of 351
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP122933.1.
            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..5172
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="ETEC1702"
                     /isolation_source="feces"
                     /host="Sus scrofa"
                     /db_xref="taxon:562"
                     /plasmid="unnamed4"
                     /geo_loc_name="Belgium"
                     /collection_date="2012"
                     /collected_by="IMM_DI04"
     gene            join(4469..5172,1..2114)
                     /gene="traG"
                     /locus_tag="QDX05_RS25005"
                     /old_locus_tag="QDX05_25000"
                     /pseudo=""
     CDS             join(4469..5172,1..2114)
                     /gene="traG"
                     /locus_tag="QDX05_RS25005"
                     /old_locus_tag="QDX05_25000"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001007068.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="conjugal transfer mating-pair stabilization
                     protein TraG"
                     /name="traG"
     gene            2139..>2625
                     /locus_tag="QDX05_RS25010"
                     /old_locus_tag="QDX05_25005"
                     /pseudo=""
     CDS             2139..>2625
                     /locus_tag="QDX05_RS25010"
                     /old_locus_tag="QDX05_25005"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000792633.1"
                     /note="frameshifted; 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="entry exclusion protein"
                     /name="entry exclusion protein"
     gene            2721..3113
                     /gene="trbF"
                     /locus_tag="QDX05_RS25015"
                     /old_locus_tag="QDX05_25010"
                     /pseudo=""
     CDS             2721..3113
                     /gene="trbF"
                     /locus_tag="QDX05_RS25015"
                     /old_locus_tag="QDX05_25010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016230912.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="F-type conjugal transfer protein TrbF"
                     /name="trbF"
     gene            3100..4472
                     /gene="traH"
                     /locus_tag="QDX05_RS25020"
                     /old_locus_tag="QDX05_25015"
                     /pseudo=""
     CDS             3100..4472
                     /gene="traH"
                     /locus_tag="QDX05_RS25020"
                     /old_locus_tag="QDX05_25015"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001137361.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="conjugal transfer pilus assembly protein TraH"
                     /name="traH"
     Typing          2..1188
                     /name="MPF_F"
                     /typing="mate-pair-formation"
                     /tool="MOB-suite"
                     /identity="99.495"
                     /coverage="98.0"
                     /evalue="0.0"
     Typing          1249..2111
                     /name="MPF_F"
                     /typing="mate-pair-formation"
                     /tool="MOB-suite"
                     /identity="95.486"
                     /coverage="98.0"
                     /evalue="0.0"
     Typing          3101..3924
                     /name="MPF_F"
                     /typing="mate-pair-formation"
                     /tool="MOB-suite"
                     /identity="97.091"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          3922..4469
                     /name="MPF_F"
                     /typing="mate-pair-formation"
                     /tool="MOB-suite"
                     /identity="96.721"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 gtgcagcaga tatttggcgg cagaccggac ccggacctgt tattcagaca actggtcagt
       61 gacagttaca gttatttcta cggctccagt cagtctgcca gccagattat gcgccagaac
      121 gtcacaataa atgccctgaa agagggtatc accagtaatg ccgcccgtaa tggtgacacc
      181 gccagcctgg tgaatctggc caccacgtca tcgatggaga agcaacgtct ggcgcatgtc
      241 tctatcggtc atgtgacaat gcgaaacctg ccaatggtac agactatcct gacgggaatt
      301 gccattggta ttttcccgct tctggtactg gcagctgtct tcaacaaact gacactgtcc
      361 gtcctgaaag gctatgtgtt tgccctgatg tggctgcaga cctggccgtt gttgtatgcc
      421 attctgaaca gtgccatgac attctatgcg aagatgaatg gtgcgccggt cgtgctgtct
      481 gaactctctc agatacagct gaaatactct gacctggcct ctactgccgg gtatctttca
      541 gccatgatcc ccccgttgtc atggatgatg gtaaaaggcc ttggcgcagg tttttccagc
      601 gtgtacagcc acttcgcctc ttcctctatc agtccgacgg ccagtgcagc aggcagtgtg
      661 gttgacggta attactccta cggcaacatg cagacggaaa acgtgaacgg cttcagctgg
      721 agcaccaaca gcaccacgtc gtttggtcag atgatgtacc agaccggcag tggcgcaact
      781 gccacacaga cccgtgacgg taatatggtg atggatgcaa gcggagcgat gtcccggtta
      841 ccggttggta tcaatgcaac gcgtcagatt gcagcggcac aacaggaaat ggcccgggag
      901 gcgtcgaaca gagcagaaag tgccctgcat ggtttcagca gcagtattgc cagtgcctgg
      961 aactcgctca gtcagtttgg ttctaaccgg gggagcagtg attctgtcac cggtggtgct
     1021 gacagtacga tgagcgcaca ggactccatg atggccagcc gtatgcgcag tgcagtggaa
     1081 agctatgcga aggcgcataa tatcagtaat gagcaggcga ctcaggaact ggcatccaga
     1141 agtacgagag cttctgccgg gatgtatgga gatgctcatg ctgaatgggg gttaaaccta
     1201 aaattcttgg tgttggtgga ggattaggcg ttagaggcgg tggtcgggct ggcattgact
     1261 ggagtgatga tgatgcgcat caggccagca gtggttcacg ggccagcaat gatgctcgtc
     1321 atgatatcga tgccagagct acacaagact ttaaagaggc cagcgattac tttaccagtc
     1381 gcaaggtcag tgagtccggc agccatactg acaataatgc tgattcccgt gtggatcagt
     1441 tgtctgcagc cctgaattca gcgaagcaga gttacgacca gtacacgacg aatatgaccc
     1501 gcagccatga atatgctgaa atggcatccc gtactgaaag catgagtggg cagatgagtg
     1561 aagacttgtc gcaacagttt gcacagtatg taatgaaaca cgcgccacag gatgccgaag
     1621 ctattctgac aaacaccagt tcaccggaga ttgcagaacg tcgtcgggcg atggcctggt
     1681 cttttgtgca ggaacaggta cagcctggtg ttgataatgc ctggcgggaa tcccgtggcg
     1741 atattggtaa aggaatggag agcgtacctt cgggtggtgg cagtcaggat attattgctg
     1801 accatcagga acatcaggcc attattgagc aaagaacgca ggacagtaat atccgtaatg
     1861 atgtaaaaca tcaggttgat aatatggtca cagaatataa agggaatata ggtgatactc
     1921 agaacagcat acgtggcgag gaaaatattg taagaggaca gtattctgaa ctgcagaatc
     1981 accataaaac agaggcatta tctcagaata ataaatataa tgaagaaaag tcggttcagg
     2041 aaagaatgcc tggggctgac agtccacagg aactgatgaa aagggcaaag gagtatcagg
     2101 ataagtataa gtaataatgc tgtgtttggg agatgataat gagatgttta gctcatattg
     2161 ctctggtgac ggtgatacag ttcattgcct gttatctggc tgattggggg agtgccgaaa
     2221 cagtttttat cctgtgcttt attgtactat ggcagggatt gtttatatgg ttgttttctc
     2281 aaatacgaaa aaaacggcat gtgtcggatg agtttaaatt cagtaaaggc gtttggtata
     2341 taacgatgcc agtatcttcc ttactctctc cgttattaag cctgatggtt tttatcattg
     2401 gtacactata cgaattaagg cgagttagtg gttgcataag cataaaaaaa tggggtcaaa
     2461 atcaactcaa aaaccaatat gatgggagtg aaaagttaga cctcgggggc attgaacagc
     2521 cccccaacga cctaccataa cccctcaact ggatacccca tgcatggagg ctttgactca
     2581 gcgggaaata cttttgggac tcgttggcag gattattatg acaggcacaa agaaaaactt
     2641 cagtttgtaa aaaaggtaat ttatattaca ccgcataacc tgtctgaatg aatcatcaga
     2701 aatatcagag gaaacttata atgaaagaaa aaagaaatga tgcggaacta aaaaacagaa
     2761 aaactaaacg gaattatgat tatgaacgca gggtttctga tatatatttt gaatctgttt
     2821 tttgtgttcg ttgctgccgg aactttttta tgggtgatta tgcacagtat ttttgatgcc
     2881 tgtattgatt cgtggaaagc tgacccagca ttaaataatt ttcgttatat gtggaacatc
     2941 ctgatgtatg tcattccgta tacgttatgg gcgtttgcag gtggatttct tatcgtatac
     3001 gtcaggaacc ctttaaatga attaataaac gggggatcag gatattccgg ctgaaacgcc
     3061 gtatgcgccg ggagaacagt ttcagggagg ggaataacga tgcctcgcat taaacctctt
     3121 ctggttcttt gtgccgtttt actgacggtc acacccgcag cgtcagcgga tgtgaacagc
     3181 gacatgaatc agttctttaa taagctggga tttgcatcca atgtcaccca ggcgggcgtc
     3241 tggcaggggc aggccgccgg gtatgcctat ggtggctccc tgtatgcccg cacccaggtc
     3301 aaaaatatcc agctgatttc catgacgctg ccggatatca atgccggatg tggcggcatc
     3361 gacgcctatc tcggctcgtt cagttttatt aatggcgatc agttgcagcg ttttgttaag
     3421 cagattatga gcaatgctgc cggttacttt tttgaccttg ccctgcagac aacggtgccg
     3481 gaaataaaaa ccgcaaaaga cttcctgcag aaaatggcaa gtgacattaa cagtatgaac
     3541 ctcagttcct gtcaggtggc acaggggctt gtgggggggc tgttccctca gacgcaggaa
     3601 tctcagcaga aagtttgtca ggacattggc agtgaaagca atatcttcgc cgactgggcc
     3661 gcatctcgtc aggggtgcac ggtcggaggg cagtcctcat ctgttcgtga caaagccagc
     3721 gacaaggaca aggagcgggt gctgaaaaac cagaatatca tatgggaggc gctgaaaaaa
     3781 aacagaatgt ttgacggcaa caaagagttg aaagaattta tcatgacgct caccggtacg
     3841 ctgatttttg gggaagacag cgagattacc cccctgccgg cgcgtaccac tgaccgcgat
     3901 atcctccggg cgattatgga gggggaacgg caaaaattta ccactgcaac gattcggaca
     3961 agtgtctgaa ggtggtggcg gatgcaaatg tgaccatcgc ccgggataaa gccctgaagt
     4021 cacagattac aaaactgctg accagtattc agaataaagc agtgagtgac actccgcttg
     4081 acgcccggga acaggggttt atttccagca ccaccattcc cgtttttaaa tatctgattg
     4141 acccgcagat gctcggtgtg tccaacagcg tcgtttacca gctgacggac tatatcggct
     4201 acgacatcat gctccagtac attcaggaac tgcttcagca ggcccgggcc atgattgcca
     4261 ccgggaacta tccgcaggct gtgatggaca atgttctgga gaatctgaat caggcacagc
     4321 aacagattgc cattttccag agtcaggtac aggtccagca ggatgcgctg ctggttgtcg
     4381 aacgtcagat gagctacatg cgtcagcagc tttccgcccg tatgctcagc cgttaccaga
     4441 acaactatca cttcggaggg aattcactgt gaatgaagtt tatgtgattg ccggtggtga
     4501 gtggttgcgt aacaacctga atgccattgc agcatttatg aatacccgga cctgggattc
     4561 aattgaaaaa atcgcgctca ccctgtctgt tgttgctgtg gcttttatgt gggtacagcg
     4621 gcataacgtg atggatttgc tgggctgggt ggccgtgttt gtgcttatca gcctgctggt
     4681 taatgtccgt acatcggtgc agattattga taacagtgac ctggtcaaag tccatcgggt
     4741 ggataatgtg ccggtcggtc tggcgatgcc actttcactg acgacacgta tcgggcatgc
     4801 aatggtggtc agctacgaga tgatattcac ccaaccggac agcgtcacct acagcaagac
     4861 aggcatgctg ttcggggcga atctgattgt gaaaagcacc gatttcctgt cccggaatcc
     4921 ggaaatcatc aatctgttcc aggactacgt ccagaactgc gtgctgggtg atatttacct
     4981 gaatcataaa tacacgctgg aagatctgat ggcctccgct gacccctaca cgctgatttt
     5041 tcccgaccca gcccgctacg gggcgtttat gacaacaata ataatttcat aacctgtaag
     5101 gatgcgtcgg tcacgctgaa agacaggctg aatctcgata caaagacggg aggcaagacc
     5161 tggcattatt at
//
