LOCUS       CP122887                4599 bp    DNA     circular BCT 15-MAY-2023
DEFINITION  Escherichia coli strain ETEC1715 plasmid unnamed1, complete
            sequence.
ACCESSION   CP122887
VERSION     CP122887.1
DBLINK      BioProject: PRJNA917806
            BioSample: SAMN32549594
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4599)
  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 4599)
  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                   :: 237x
            Sequencing Technology             :: Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 04/14/2023 12:15:12
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,046
            CDSs (total)                      :: 4,930
            Genes (coding)                    :: 3,820
            CDSs (with protein)               :: 3,820
            Genes (RNA)                       :: 116
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 1,110
            CDSs (without protein)            :: 1,110
            Pseudo Genes (ambiguous residues) :: 0 of 1,110
            Pseudo Genes (frameshifted)       :: 892 of 1,110
            Pseudo Genes (incomplete)         :: 243 of 1,110
            Pseudo Genes (internal stop)      :: 57 of 1,110
            Pseudo Genes (multiple problems)  :: 78 of 1,110
            Pseudo Genes (short protein)      :: 3 of 1,110
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            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/
FEATURES             Location/Qualifiers
     source          1..4599
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="ETEC1715"
                     /isolation_source="feces"
                     /host="Sus scrofa"
                     /db_xref="taxon:562"
                     /plasmid="unnamed1"
                     /geo_loc_name="Belgium"
                     /collection_date="2020"
                     /collected_by="IMM_DI04"
     gene            16..663
                     /locus_tag="QDX13_22745"
     CDS             16..663
                     /locus_tag="QDX13_22745"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001423320.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="NYN domain-containing protein"
                     /protein_id="WHF94965.1"
                     /translation="MKTIVYVDGFNFYYRKLKDSNKKWLNIKAMVEKLLPDDEIIGINY
                     YTARISGRIDSDAPRRQQIYFNALKSIDNLSIHYGTFSVNESRMFLVQPLDFKHHLKNP
                     NQKIKFANVLKTEEKGSDVNLGCHLVRDGFQGKYEKAVIITNDTDLAEPMRVVKSELSL
                     YIELLSPVNKPARTLSAICDKVTLISDQSIADSQFEDVIVVGEKTVTKPAQW"
                     /name="NYN domain-containing protein"
     gene            complement(784..1020)
                     /locus_tag="QDX13_22750"
     CDS             complement(784..1020)
                     /locus_tag="QDX13_22750"
                     /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="WHF94966.1"
                     /translation="MSIIIDREKYTALMTLIQTSQGYVGSKVQPNGYTLKCSFDTGFAC
                     CISRNTRNSNLSVHFENESTDPATHFAILSAIS"
                     /name="hypothetical protein"
     gene            complement(1384..1617)
                     /locus_tag="QDX13_22755"
     CDS             complement(1384..1617)
                     /locus_tag="QDX13_22755"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WHF94967.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLNEWESAFVELQKMFSLTQRDNA
                     MLNEQVMQLSQQVQHLSERTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(1624..2142)
                     /locus_tag="QDX13_22760"
     CDS             complement(1624..2142)
                     /locus_tag="QDX13_22760"
                     /inference="COORDINATES: protein motif:HMM:NF016710.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WHF94968.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTETMLNDEFSKLEKSVSKAVTSNE
                     TKIKDAIALFSTSTEESLEKHREGVKEAMMQHRKDVLKLAGNTGMRLLGIVFLLFTASG
                     GTLWYLGGRIQANLEEIRIQEETLQKLNAKTWGVEFVQDGRRKFLVLPYGKSATVIPYQ
                     GKDWVQLTE"
                     /name="MbeB family mobilization protein"
     gene            complement(2180..2611)
                     /locus_tag="QDX13_22765"
                     /pseudo=""
     CDS             complement(2180..2611)
                     /locus_tag="QDX13_22765"
                     /inference="COORDINATES: protein motif:HMM:NF015397.2"
                     /note="incomplete; partial on complete genome; missing
                     C-terminus; Derived by automated computational analysis
                     using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            complement(2820..3143)
                     /locus_tag="QDX13_22770"
     CDS             complement(2820..3143)
                     /locus_tag="QDX13_22770"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WHF94969.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIERELRSLRQVVREQGVR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            3207..3398
                     /locus_tag="QDX13_22775"
     CDS             3207..3398
                     /locus_tag="QDX13_22775"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165985.1"
                     /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="WHF94964.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(3477..3561)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.674"
                     /coverage="100.0"
                     /evalue="6.569999999999999e-34"
     Typing          3581..4110
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="85.507"
                     /coverage="99.0"
                     /evalue="2.98e-155"
     Typing          complement(1281..2830)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.412"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atggagctaa ccccattgaa aacaatagtt tatgttgatg gctttaactt ttattatcgt
       61 aagctgaaag attccaacaa aaagtggctg aacataaaag caatggtcga aaaattgcta
      121 ccggatgatg aaataatagg aattaactat tacacggcta ggatctcagg aaggattgat
      181 tctgacgcac ctcgtaggca acaaatatat ttcaatgcac tgaaaagcat agataaccta
      241 agtatccatt atggtacttt ttcggtgaat gaaagcagaa tgtttttagt gcagcctctt
      301 gatttcaaac atcacttaaa aaacccgaat caaaaaataa agtttgcaaa cgtcttaaag
      361 acagaagaaa agggttctga cgttaattta ggttgccact tggttagaga tggtttccaa
      421 gggaaatacg agaaggctgt aataataact aatgatacag atttggctga accaatgaga
      481 gtagtcaaat cagagctcag cctttatatt gaactacttt ctcctgtaaa caaaccagca
      541 agaaccctga gcgcaatatg cgataaggtc actcttataa gcgaccaatc aatagctgat
      601 agccagtttg aagacgttat tgtagttggt gagaaaaccg tgacaaaacc agcacagtgg
      661 tagtggctac atactcgttc tgttgaaaaa aagcccgtcc cccgggcttt ttatgttttg
      721 cattatacct tcaggcaaat ataaagagta tgaaatctat agctatgtgc agaaaataaa
      781 aaattagcta atagcactta aaatagcaaa gtgagttgca ggatctgtac tttcattttc
      841 aaaatgaaca gataagttac tatttctagt atttctagag atacaacatg caaaaccagt
      901 gtcgaaagaa cacttcaatg tatatccatt tggttgtact tttgagccaa catatccttg
      961 agatgtctgg atcaacgtca tcaaagcagt atatttttca cgatcaataa taatactcat
     1021 cacatcccca ttagtattac tctgcaggca ttaaacctca gcaataaatc tatttaccat
     1081 aactcccgtt gcccgcaccg cctcagacgc tctcagcgcg tttctgacgg gaaaccggaa
     1141 aaacaggcaa caaacctccc gaaaaactgc cgcgatcgcg cctgataaat tttaaccgca
     1201 tgaataccta tgcaacaaga tggtgcagac tacattagtc cgtcaaaatc cactgaacct
     1261 gccatttttc atagtttcac catcccagcg aaggaccatc cagtgtgcgt tcctgtattt
     1321 ccggctggtg ctcacgctcc agggataact catgttcgcg ttcctgtatc agccgttcgt
     1381 cccttatctc ctgttctcgc tgtataactg gctcaagcgt tctgtccgct cgctcaagtg
     1441 ctgcacctgc tgactcaact gcatgacctg ctcgttcagc atcgcgttgt cccgttgcgt
     1501 aagcgaaaac attttctgca attccacgaa ggcgctctcc cattcgttca gccgctgcat
     1561 atagtcctgt tgcagttgct ctaatgcgtt cagcaaatgt ctttccagct ccgtcactct
     1621 gtatcactcc gtcagttgta cccagtcctt cccctgatag ggaatcaccg ttgccgattt
     1681 cccgtacgga aggaccagaa atttccttct cccgtcctgc acaaactcca cgccccatgt
     1741 cttcgcgttc agtttctgca atgtttcttc ctgtatcctg atttcttcca ggttcgcctg
     1801 tatccgcccg ccaagatacc agagcgtccc gccactcgcg gtaaacagga gaaagactat
     1861 ccccagcaac ctcatgcccg tattccctgc cagctttaac acgtccttcc tgtgctgcat
     1921 catcgcctct ttcacccctt cccggtgttt ttccagcgat tcctctgtcg acgttgagaa
     1981 cagggctata gcgtctttga ttttcgtctc gtttgaggtc acagccttgc ttacagattt
     2041 ttcgagcttg ctgaactcgt cgttcagcat tgtctctgta gattcggctc tctctttcag
     2101 ctttttctcg aactccgcgc ccgtctgtaa aagattgctc ataaaatgct cctttcagcc
     2161 tgatattctt cccaccgttc gggtctgcaa tgctgatact gcttcgcgtc accctgacca
     2221 cttcaagccc tgcctctgtg agcgcctgaa tcacatcctg acggcctttt atctccccga
     2281 catgataaag agcgtctatc ccgcgtgtga cgctctctgc aagcgcctgt ttcgtttccg
     2341 gcaggttatc aggaagggtc agcgtccggc ggttctccgg ggcgttgggg tcatgcagcc
     2401 cgtaatggtg attaaccagc gtctgccagg catcaattct cggcctgtct gcccggtcgt
     2461 agtacggctg gaggcgtttt ccggtctgta gctccatgtt cggaatgaca aaattcagct
     2521 caagccgtcc cttgtcctgg tgctccaccc acaggatgct gtactgattc ttttcgagac
     2581 cgggcatcag tacacgctca aagctcgcca tcaccttttc acgtcctccc ggcggcagct
     2641 ccttctccgc gaacgacaga acacctgacg tgtatttctt cgcaaatggc gtggcatcga
     2701 tgagttcccg gacttcttcc ggattaccct gaagcaccgt tgccccttcc cggttacgct
     2761 cccttcccag caggtaatca accggaccac tgccaccacc ttttcccctg gcatgaaact
     2821 taactatcat cccgcactcc ctgttccctg accacctgcc gtaagctgcg caactctctc
     2881 tcgatggcca tcagtgcggc caccacctga acccggtcac cggaagacca ctgcccgctg
     2941 ttcaccttcc tcgctgtctg attcaggtta ttcccgatgg cagccagctg acgcagtaac
     3001 ggcggcgcca gtgtcggcag tttcccggaa cgggcaaccg gctcccccag gcagacccgc
     3061 cgcatccata ccgccagttg tttaccctca cagcgttcaa gtaaccgggc atgttcatca
     3121 tcagtaaccc gtattgtgag catcctctcg cgtttcatcg gtatcattac cccatgaaca
     3181 gaaacccccc ttacacggag gcatcagtga ctaaacagga aaaaaccgcc cttaacatgg
     3241 cgcgctttat cagaagccag acattaacgc tgctggagaa gctcaacgaa ctggacgcgg
     3301 atgaacaggc agacatctgt gaatcgcttc acgaccacgc cgatgagctt taccgcagct
     3361 gcctcgcacg cttcggggat gacggtgaaa acctctgaca catacagctc ccggagacgg
     3421 tcacagcttg tctgtgagcg gatgccggga gcagacaagc ccgtcagggc gcgtcagggg
     3481 gtttcggggc gaagccctga accagtcacg tagcgatagc ggagtgtata ctggcttaac
     3541 tatgtggcat cagtgcggat tataagaaaa gagcagcata tgcggtgtga aataccgcac
     3601 agatgcgtaa ggagaaaata ccgcatcagg cgctcttccg cttcctcgct cactgactcg
     3661 ctacgctcgg tcgttcggct gcggcgagcg gtatcagctc acgcaaagac ggtaatgcgg
     3721 ttatccacag aatcagggga taaggccgga aagaacatgt gaacaaaaag gcaaaaccaa
     3781 ggaaaaaggc cgcgccgcag gcgtttttcc ataggctccg cccccctgac gagcatcaca
     3841 aaaattgacg ctcaagtcag aggtggcgaa acccgacagg actataaaga taccaggcgt
     3901 ttccccctgg aagctccctc gtgcgctctc ctgttcctgc ctttcggtgt accggtgtca
     3961 ttccgctgtt atggccgcgg tttctcattc cacgcctgac actcggctcc gggaaggcag
     4021 ttcgctccaa gctggactgt atgcacgaac cccccgttca gtccgaccgc tgcgtcttat
     4081 ccggtaacta tcaacttgag tccaacccgg aaagacacga ctaatcgcca ttggcaacgg
     4141 ccactggtaa acaggatgtg cgagagatgt atcgagagtt cttgaagtgg cggcctgact
     4201 acggctacac tgaaaggaca gatttggtga catgtctcgc acaagaccgt taccgcggtt
     4261 agagaatctg ccaggattaa ctaaccttcg aaaaaccacc tgccagggtg gttttttcgt
     4321 tttcaaagca ggagattacg cgcagaaaaa aaggatctca agaagatctt ttctccttta
     4381 ggtagggctt acttcgtcac catataaaac atttgcacta gacaaaaaaa atgcaataat
     4441 gttggtacag acctgtggcg tgccgcaggc gaagaaacaa cccccctgtg gcgtgccgca
     4501 ggcgaagaaa caaccctcct gtggcgagcc gcaggcaaac acccctccta cggcgtgccg
     4561 taggaaaaaa ccgcagatgc ggtttttttt atatctaaa
//
