LOCUS       CP122656                3638 bp    DNA     circular BCT 15-MAY-2023
DEFINITION  Escherichia coli strain ETEC4074 plasmid unnamed1, complete
            sequence.
ACCESSION   CP122656
VERSION     CP122656.1
DBLINK      BioProject: PRJNA917806
            BioSample: SAMN32549651
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3638)
  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 3638)
  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                   :: 223x
            Sequencing Technology             :: Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 04/14/2023 12:11:32
            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)                     :: 5,071
            CDSs (total)                      :: 4,950
            Genes (coding)                    :: 4,588
            CDSs (with protein)               :: 4,588
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 362
            CDSs (without protein)            :: 362
            Pseudo Genes (ambiguous residues) :: 0 of 362
            Pseudo Genes (frameshifted)       :: 206 of 362
            Pseudo Genes (incomplete)         :: 150 of 362
            Pseudo Genes (internal stop)      :: 40 of 362
            Pseudo Genes (multiple problems)  :: 33 of 362
            Pseudo Genes (short protein)      :: 3 of 362
            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..3638
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="ETEC4074"
                     /isolation_source="feces"
                     /host="Sus scrofa"
                     /db_xref="taxon:562"
                     /plasmid="unnamed1"
                     /geo_loc_name="Belgium"
                     /collection_date="2021"
                     /collected_by="IMM_DI04"
     gene            596..1114
                     /locus_tag="QDW60_24740"
     CDS             596..1114
                     /locus_tag="QDW60_24740"
                     /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="MbeB family mobilization protein"
                     /protein_id="WHH84719.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTETMLNDEFSKLEKSVSKAVTSNE
                     TKIKDAIALFTASTEESLKKHREGVKEAMMQHRKDVLKLAGNTGMMLLGMVIFLFTVSG
                     GTLWYLGGRIQANLEEIRIQEETLQKLNAKTWGVEFVQDGRRKFLVIPQGKSATVIPYQ
                     GKDWVQLTE"
                     /name="MbeB family mobilization protein"
     gene            1121..1354
                     /locus_tag="QDW60_24745"
     CDS             1121..1354
                     /locus_tag="QDW60_24745"
                     /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="WHH84720.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLNEWESAFVELQKMFSLTQRDNA
                     MLNEQVMQLSQQVQHLSERTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(2162..2317)
                     /locus_tag="QDW60_24750"
     CDS             complement(2162..2317)
                     /locus_tag="QDW60_24750"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001333247.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WHH84716.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHDLTPLAAAFDKSRCAREKF
                     REYLKW"
                     /name="replication initiation protein"
     gene            complement(2977..3168)
                     /locus_tag="QDW60_24755"
     CDS             complement(2977..3168)
                     /locus_tag="QDW60_24755"
                     /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="WHH84717.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGGDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            3218..3556
                     /locus_tag="QDW60_24760"
     CDS             3218..3556
                     /locus_tag="QDW60_24760"
                     /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="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WHH84718.1"
                     /translation="MKRERMLTIRVTDDEHARLLERCEGKQLAVWMRRICLGEPVARSG
                     KLPTLAPPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIERELRSLRQVVR
                     EHGVRDDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     Typing          2815..2896
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.3400000000000002e-35"
     Typing          complement(2246..2791)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.891"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          2..1458
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="90.204"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          3204..3553
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.453"
                     /coverage="99.0"
                     /evalue="1.23e-63"
ORIGIN
        1 gtgcttcagg gtaatccgga agaagtccgg gagctcatcg atgccacgcc atttgcgaag
       61 aaatacacgt caggtgttct gtcgttcgcg gagaaggagc tgccgccggg aggacgtgaa
      121 aaggtgatgg cgagctttga gcgtgtactg atgcccggtc tcgaaaagaa tcagtacagc
      181 atcctgtggg tggagcacca ggacaaggga cggcttgagc tgaattttgt cattccgaac
      241 atggagctac agaccggaaa acgcctccag ccgtactacg accgggcaga caggccgaga
      301 attgatgcct ggcagacgct ggtgaatcac cattacgggc tgcatgaccc caacgccccg
      361 gagaaccgcc ggatactgac tctccctgat aacctgccgg aaacgaaaca ggcgcttgca
      421 gagagcgtca cacgcgggat agacgctctt tatcatgtcg gggagataaa aggccgtcag
      481 gatgtgattc aggcgctcac agaggcaggg cttgaagtgg tcagggtgac gcgaagcagt
      541 atcagcattg cagacccgaa cggtgggaag aatatcaggc tgaaaggagc attctatgag
      601 caatctttta cagacgggcg cggagttcga gaaaaagctg aaagagagag ccgaatctac
      661 agagacaatg ctgaacgacg agttcagcaa gctcgaaaaa tctgtaagca aggctgtgac
      721 atcaaacgag acgaaaatca aagacgctat agccctgttc acagcttcga cagaggaatc
      781 actgaaaaaa caccgggaag gggtgaaaga ggcgatgatg cagcacagga aggacgtgtt
      841 aaagctggca gggaatacgg gcatgatgtt actggggatg gtcattttcc tgtttaccgt
      901 gagtggcggg acgctctggt atcttggcgg gcggatacag gcgaacctgg aagaaatcag
      961 gatacaggaa gaaacattgc agaaactgaa cgcgaagaca tggggcgtgg agtttgtgca
     1021 ggacgggaga aggaaatttc tggtcatccc gcaggggaaa tcggcaacgg tgattcccta
     1081 tcaggggaag gactgggtac aactgacgga gtgacacaga gtgacggagc tggaaagaca
     1141 tttgctgaac gccttagagc aactgcaaca ggactatatg cagcggctga acgaatggga
     1201 gagcgccttc gtggaattgc agaaaatgtt ttcgcttacg caacgggaca acgcgatgct
     1261 gaacgagcag gtcatgcagt tgagtcagca ggtgcagcac ttgagcgagc ggacagaacg
     1321 cttgagccag ttatacagcg agaacaggag ataagggacg aacggctgat acaggagcgc
     1381 gaacatgcgt tatccctgga gcgtgagcgc cagccggaaa tacaggaatg gacacaggat
     1441 ggcccttcgc ttggatggta atcagagaca ggctaaaatg ttgtcagcgc gtttccggtg
     1501 cattttttgg gataatggtt ggttcggggg caccgggaac gcgcttcagt cagaccttgc
     1561 tgaaaacaca ggaacgcgtt aaaacgcata cgggcgcgat tctggtgtat cttttgttgc
     1621 tgtgttttgc ctctattgcc agatcgcgct cattcccctg aacttctgtt ttcccgctcc
     1681 ggttcccgtc ttcttcgctt ccgaaagcat gaaaaaaatc cgtttcagca gtctctggct
     1741 ggaaattcct gcgtgattca catggctgca tagctatgca tgtggttaaa atttaccggg
     1801 tgcgatcgcg gcagtttttc gggtggtttg ttgccatttt tacctgtctg ctgccgtgat
     1861 cgcaccgaac gcgtttcagt ggtgcgtaca ataacgcaca tagtactatt atgtatattc
     1921 aatccgggtg gctgattttg tatgttacgt gatgtgatgg tgggctgttt tctagggatc
     1981 caagtaagat cctcttgaga tcgatggctg ctgcgcgtaa tctcttgcct tgtaaacgaa
     2041 aaaaccgcct tgcagggcgg tttgatcgaa ggttaagcca gcttgcagac tgtttaacca
     2101 ggtaactgtc ttgtgcgaga cgagtcacca aaactgtcct ttcagtgtag ccggactccg
     2161 gtcaccactt caagtactct ctaaatttct ctctcgcaca ccgactttta tcaaaggctg
     2221 ctgccagtgg cgttaagtcg tgtcttaccg ggttggactc aagacgatag ttaccggata
     2281 aggcgcagcg gtcgggctga acggggggtt cgtgcacaca gcccagcttg gagcgaacga
     2341 cctacaccga actgagatac caacagcgtg agctatgaga aagcgccacg cttcccgaag
     2401 ggagaaaggc ggacaggtat ccggtaagcg gcagggtcgg aacaggagag cgcacgaggg
     2461 agcttccagg gggaaacgcc tggtatcttt atagtcctgt cgggtttcgc cacctctgac
     2521 tagagcgtcg atttttgtga tgctcgtcag gggggcggag cctatggaaa aacgccatcg
     2581 gcgtagcctt tctcccggcc tttgcctttt gcgcacatgt tctttccggc gttatcccct
     2641 gattctgtgg ataaccgtat taccgccttt gagtgagctg ataccgctcg ccgcagccga
     2701 acgaccgagc gtagcgagtc agtgagcgag gaagcggaag agcgtcggaa gctgcatttt
     2761 ctccttacgc atctgtgcgg catttcacac ccggcatggc gcacttttca tacaatctgc
     2821 actgatgccg catggttaag ccagtataca ctccgctatc gctacgtgac tggttcaggg
     2881 cttcgccccg aaaccccctg acgcgccctg acgggcttgt ctgctcccgg catccgctca
     2941 cagacaagct gtgaccgtct ccgggagctg tatgtgtcag aggttttcac cgtcaccccc
     3001 gaagcgtgcg aggcagctgc ggtaaagctc gtcggcgtgg tcgtgaagtg attcacaaat
     3061 atcggcctgt tcatctgcat ccagttcgtt gagcttctcc agcagcgtta atgtctggct
     3121 tcttataaag cgggccatgt taagggcggt tttttcctgt ttagtcactg atgcctccgt
     3181 gtaagggggg atttctgttc atggggtaat gataccgatg aaacgcgaga ggatgctcac
     3241 gatacgggtt actgatgatg aacatgcacg gttactggaa cgctgtgagg gtaaacagct
     3301 ggcggtatgg atgcggcgga tctgcctggg tgagccggtt gcccgttccg ggaagctgcc
     3361 gacactggca ccgccgttac tgcgccagct ggctgccatc gggaataacc tgaatcagac
     3421 ggcgaggaag gtgaacagcg ggcagtggtc ttccggtgac cgggttcagg tggtggccgc
     3481 actgatggcc atcgagagag agttgcgcag cttacggcag gtcgtcaggg aacatggagt
     3541 gcgggatgat agttaagttt catgccaggg gaaaaggcgg tggcagtggt ccggttgatt
     3601 acctgctggg aagggagcga aaccgggaag gggcaacg
//
