LOCUS       NZ_CP122599             3708 bp    DNA     circular CON 08-JUN-2024
DEFINITION  Escherichia coli strain ETEC6335 plasmid unnamed11, complete
            sequence.
ACCESSION   NZ_CP122599
VERSION     NZ_CP122599.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN32549676
            Assembly: GCF_030013005.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3708)
  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 3708)
  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                   :: 260x
            Sequencing Technology             :: Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_030013005.1-RS_2024_06_08
            Annotation Date                   :: 06/08/2024 05:27:29
            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)                     :: 5,662
            CDSs (total)                      :: 5,534
            Genes (coding)                    :: 5,336
            CDSs (with protein)               :: 5,336
            Genes (RNA)                       :: 128
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 97
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 198
            CDSs (without protein)            :: 198
            Pseudo Genes (ambiguous residues) :: 0 of 198
            Pseudo Genes (frameshifted)       :: 83 of 198
            Pseudo Genes (incomplete)         :: 121 of 198
            Pseudo Genes (internal stop)      :: 29 of 198
            Pseudo Genes (multiple problems)  :: 27 of 198
            Pseudo Genes (short protein)      :: 1 of 198
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP122599.1.
            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..3708
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="ETEC6335"
                     /isolation_source="feces"
                     /host="Sus scrofa"
                     /db_xref="taxon:562"
                     /plasmid="unnamed11"
                     /geo_loc_name="Netherlands"
                     /collection_date="2021"
                     /collected_by="IMM_DI04"
     gene            join(3396..3708,1..11)
                     /locus_tag="QDY30_RS28250"
                     /old_locus_tag="QDY30_28260"
     CDS             join(3396..3708,1..11)
                     /locus_tag="QDY30_RS28250"
                     /old_locus_tag="QDY30_28260"
                     /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="plasmid mobilization relaxosome protein MobC"
                     /protein_id="WP_000955995.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIERELRSLRQVVREHGAR
                     DDS"
                     /name="plasmid mobilization relaxosome protein MobC"
     gene            220..>651
                     /locus_tag="QDY30_RS28255"
                     /old_locus_tag="QDY30_28265"
                     /pseudo=""
     CDS             220..>651
                     /locus_tag="QDY30_RS28255"
                     /old_locus_tag="QDY30_28265"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /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="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            689..1207
                     /locus_tag="QDY30_RS28260"
                     /old_locus_tag="QDY30_28270"
     CDS             689..1207
                     /locus_tag="QDY30_RS28260"
                     /old_locus_tag="QDY30_28270"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001447511.1"
                     /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="WP_000067503.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTETMLNDEFSKLEKSVSKAVTSNE
                     TKIKDAIALFTASTEESLKKHREGVKEAMMQHRKDVLKLAGNTGMMLLGMVLFLFTVSG
                     GTLWYLGGRIQANLEEIRIQEETLQKLNAKTWGVEFVQDGRRKFLVLPYGKSATVIPYQ
                     EKDWVQLTE"
                     /name="MbeB family mobilization protein"
     gene            1214..1447
                     /locus_tag="QDY30_RS28265"
                     /old_locus_tag="QDY30_28275"
     CDS             1214..1447
                     /locus_tag="QDY30_RS28265"
                     /old_locus_tag="QDY30_28275"
                     /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="WP_000137441.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLSEWESAFVELQKMFSLTQRDNA
                     MLNEQVMQLSQQVQHLSERTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(2023..2214)
                     /locus_tag="QDY30_RS28270"
                     /old_locus_tag="QDY30_28280"
     CDS             complement(2023..2214)
                     /locus_tag="QDY30_RS28270"
                     /old_locus_tag="QDY30_28280"
                     /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="WP_045892409.1"
                     /translation="MLKKDDIILIKSYGNEKTKIFLRGVNEVLMIDASFEEVKFAINND
                     LQDLQGMQAVSAPLKIAT"
                     /name="hypothetical protein"
     gene            complement(3140..3331)
                     /locus_tag="QDY30_RS28275"
                     /old_locus_tag="QDY30_28285"
     CDS             complement(3140..3331)
                     /locus_tag="QDY30_RS28275"
                     /old_locus_tag="QDY30_28285"
                     /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="WP_000165985.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          2872..3048
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="87.709"
                     /coverage="82.0"
                     /evalue="3.48e-51"
     Typing          2..1551
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.794"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          3367..3707
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.105"
                     /coverage="97.0"
                     /evalue="1.94e-61"
ORIGIN
        1 atgatagtta agtttcatgc caggggaaaa ggcggtggca gtggtccggt tgattacctg
       61 ctgggaaggg agcgtaaccg ggaaggggca acggtgcttc agggtaatcc ggaagaagtc
      121 cgggaactca tcgatgccac gccatttgcg aagaaataca cgtcaggtgt tctgtcgttc
      181 gcggagaagg agctgccgcc gggaggacgt gaaaaggtga tggcgagctt tgagcgtgta
      241 ctgatgcccg gtctcgaaaa aaatcagtac agcatcctgt gggtggagca ccaggacaag
      301 ggacggcttg agctgaattt tgtcattccg aacatggagc tacagagcgg aaaacgcctc
      361 cagccgtact acgaccgggc agacaggccg agaattgatg cctggcagac gctggttaat
      421 caccattacg ggctgcatga ccccaacgcc ccggagaacc gccggatact gactctccct
      481 gataacctgc cggaaacgaa acaggcgctt gcagagagcg tcacacgcgg gatagacgct
      541 ctttatcatg tcggggagat aaaaggccgt caggatgtga ttcaggcgct cacagaggca
      601 gggcttgaag tggtcagggt gacgcgaagc agtatcagca ttgcagaccc gaacggcggg
      661 aagaatatca gactgaaagg agcattctat gagcaatctt ttacagacgg gcgcggagtt
      721 cgagaaaaag ctgaaagaga gagccgaatc tacagagaca atgctgaacg acgagttcag
      781 caagctcgaa aaatctgtaa gcaaggctgt gacatcaaac gagacgaaaa tcaaagacgc
      841 tatagccctg ttcacagctt cgacagagga atcactgaaa aaacaccggg aaggggtgaa
      901 agaggcgatg atgcagcaca ggaaggacgt gttaaagctg gcagggaata cgggcatgat
      961 gttactgggg atggtccttt tcctgtttac cgtgagtggc gggacgctct ggtatcttgg
     1021 cgggcggata caggcgaacc tggaagaaat caggatacag gaagaaacat tgcagaaact
     1081 gaacgcgaag acatggggcg tggagtttgt gcaggacggg agaaggaaat ttctggtcct
     1141 tccgtacggg aaatcggcaa cggtgattcc ctatcaggag aaggactggg tacaactgac
     1201 ggagtgacac agagtgacgg agctggaaag acatttgctg aacgccttag agcaactgca
     1261 acaggactat atgcagcggc tgagcgaatg ggagagcgcc ttcgtggaat tgcagaaaat
     1321 gttttcgctt acgcaacggg acaacgcgat gctgaacgag caggtcatgc agttgagtca
     1381 gcaggtgcag cacttgagcg agcggacaga acgcttgagc cagttataca gcgagaacag
     1441 gagataaggg acgaacggct gatacaggag cgcgaacatg agttatccct ggagcgtgag
     1501 cgccagctgg aaatacagga acggacactg gatggccctt cgctgggatg gtaatcagag
     1561 acaggctaaa atgttgtcag cgcgtttccg gtgcattttt tgggataatg gttggttcgg
     1621 gggcaccggg aacgcgcttc agtcagacct tgctgaaaac acaggaacgc gttaaaacgc
     1681 atacgggcgc gattctggtg tgtcttttgt tgctgtgttt tgcctctatt gccagatcgc
     1741 gctcattccc ctgaacttct gttttcccgc tccggtcccc gtcttcttcg cttccgaaag
     1801 catgaaaaaa atccgtttca gctgtctctg gctggcaatt cctgcgtgat tcacatggct
     1861 gcatagctat gcatgtggtt aaaatttacc gggtgcgatc gcggcagttt ttcgggtggt
     1921 ttgttgccat ttttacctgt ctgctgccgt gatcgcaccg aacgcgtttc tgcggtgcgg
     1981 gcaacggatg ttatggtaaa tgttgagtgc tcttactaaa aatcaggttg ctatttttag
     2041 cggtgcgctt actgcctgca ttccctgaag atcctgaagg tcattattga tagcaaactt
     2101 tacctcttca aagctcgcgt caatcattag aacctcattc acaccccgta aaaatatttt
     2161 tgttttttcg ttaccatatg attttattag gataatatca tcttttttta gcatgatact
     2221 ttcgttactt attgttttga gatgaagcat cgtcatggtt ttttttgcat gtgcttgtta
     2281 aggggattga gattattcct aactccttga gtttgtacat acaaaaaaaa caaaaaaatc
     2341 ctaatgcccc cgtggtgggt atataaaaat cacggggagc gcagcgacct tcgtccagct
     2401 cgtttcttgt gtgtctcacc ctgcaaaagg tttgattgtg tgggcgctgt gctgacgtct
     2461 gagaatcaca ctttgccgct tactgctgtc ttattcgctc attttatcag gtgcttgtta
     2521 tcgtacagcg agacggggta gagcctaact ctttcgcggt taagttacgt tcccaccaat
     2581 ttgcctgttt atcctgccgg agtccggggc gtagacctga gcgtctaagg tgcagatatg
     2641 attttaatgt cgttgaatgg tattaagctg gtagtgacat cgctagccag ccctgctagg
     2701 atttagattc tcacgtctga tcctggcagg tatctgcgaa gaattagagt accgaagccc
     2761 tgtgattctg tcacggggct tttgtacatt tagcgcccga gaatcaaaaa catcccttca
     2821 gaacttatgt aacgcccgcc gcagtctcac ggcaggagcg cagcgaccga gtgagcgagg
     2881 aggcgacatt tcatccttac ctgcatgttg cacttacgcc ccgcagctac atttttcccc
     2941 tgccacatga agcacttccc tgaattccca cttcgcttta ccatattaag ccagtataca
     3001 ctccgctatc gctacgtgac tgggtcatgg ctgcgccccg acacccgcaa ggtcaacggc
     3061 ctgacgcgcc ctgacgggct tgtctgctcc cggcatccgc tcacagacaa gctgtgaccg
     3121 tctccgggag ctgtatgtgt cagaggtttt caccgtcatc cccgaagcgt gcgaggcagc
     3181 tgcggtaaag ctcatcggcg tggtcgtgaa gcgattcaca gatgtctgcc tgttcatccg
     3241 cgtccagttc gttgagcttt tccagcagcg ttaatgtctg gcttctgata aagcgggcca
     3301 tgttaagggc ggttttttcc tgtttagtca ctgatgcctc cgtgtaaggg gggatttctg
     3361 ttcatggggt aatgataccg atgaaacgcg agaggatgct cacgatacgg gttactgatg
     3421 atgaacatgc acggttactg gaacgctgtg agggtaaaca gctggcggta tggatgcggc
     3481 gggtctgtct gggtgagccg gttgcccgtt ccgggaagct gccgacactg gcaccgccgt
     3541 tactgcgcca gctggctgcc atcgggaata atctgaatca gacggcgagg aaggtgaaca
     3601 gcgggcagtg gtcttccggt gaccgggttc aggtggtggc cgcactgatg gccatcgaga
     3661 gagagttgcg cagcttacgg caggtcgtca gggaacatgg agcgcggg
//
