LOCUS       NZ_CP122689             5272 bp    DNA     circular CON 08-JUN-2024
DEFINITION  Escherichia coli strain ETEC4067 plasmid unnamed4, complete
            sequence.
ACCESSION   NZ_CP122689
VERSION     NZ_CP122689.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN32549644
            Assembly: GCF_030013385.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5272)
  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 5272)
  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                   :: 257x
            Sequencing Technology             :: Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_030013385.1-RS_2024_06_08
            Annotation Date                   :: 06/08/2024 05:02:54
            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)                     :: 5,276
            CDSs (total)                      :: 5,153
            Genes (coding)                    :: 4,886
            CDSs (with protein)               :: 4,886
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 267
            CDSs (without protein)            :: 267
            Pseudo Genes (ambiguous residues) :: 0 of 267
            Pseudo Genes (frameshifted)       :: 88 of 267
            Pseudo Genes (incomplete)         :: 167 of 267
            Pseudo Genes (internal stop)      :: 48 of 267
            Pseudo Genes (multiple problems)  :: 32 of 267
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP122689.1.
            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..5272
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="ETEC4067"
                     /isolation_source="feces"
                     /host="Sus scrofa"
                     /db_xref="taxon:562"
                     /plasmid="unnamed4"
                     /geo_loc_name="Belgium"
                     /collection_date="2021"
                     /collected_by="IMM_DI04"
     gene            join(4960..5272,1..11)
                     /locus_tag="QDX30_RS26305"
                     /old_locus_tag="QDX30_26305"
     CDS             join(4960..5272,1..11)
                     /locus_tag="QDX30_RS26305"
                     /old_locus_tag="QDX30_26305"
                     /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="WP_053904986.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARFGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIERELRSLRQVVRGQGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            220..>651
                     /locus_tag="QDX30_RS26310"
                     /old_locus_tag="QDX30_26310"
                     /pseudo=""
     CDS             220..>651
                     /locus_tag="QDX30_RS26310"
                     /old_locus_tag="QDX30_26310"
                     /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="QDX30_RS26315"
                     /old_locus_tag="QDX30_26315"
     CDS             689..1207
                     /locus_tag="QDX30_RS26315"
                     /old_locus_tag="QDX30_26315"
                     /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_282843153.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNDEFSRLGESVNEAVTSNE
                     TKIKGAIAQFTASTEESLKKHREGVKEAMMQHRKDMLKLAGSSGMRLLGIVFLLFTASG
                     GTLWYLGGRIQTNLEEIRVQEETLRKLNAKTWGVEFVQDGRRKFLVLPYGKSAEVTHYQ
                     GKDWIQLTE"
                     /name="MbeB family mobilization protein"
     gene            1214..1447
                     /locus_tag="QDX30_RS26320"
                     /old_locus_tag="QDX30_26320"
     CDS             1214..1447
                     /locus_tag="QDX30_RS26320"
                     /old_locus_tag="QDX30_26320"
                     /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_236305822.1"
                     /translation="MTELETHLLNALEQLQQDYMQRLNEWESAFVELQRMFSLTQRDNA
                     MLNERVMQLSQQVQHLSERTERLSQLYSENWR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(2019..2603)
                     /locus_tag="QDX30_RS26325"
                     /old_locus_tag="QDX30_26325"
     CDS             complement(2019..2603)
                     /locus_tag="QDX30_RS26325"
                     /old_locus_tag="QDX30_26325"
                     /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_000213998.1"
                     /translation="MTTTIYREFEFAACDSKWSVDGHLRRDVIEKKAIHIDFKGKEAIS
                     LMCGDHPMIVLMQAMQLKVITPEQYASLMSLYMDVEDFTFGMVVLDKHSGAILVGMYTP
                     PMIAIKSKQIVYDLGSTGGEFAAHCLYYAEKRLRKKSVIVDTLHRQWDVRSPALSNMHT
                     DEIATPVVKYTKSFGKITASCTTTYRYLTTR"
                     /name="hypothetical protein"
     gene            complement(2659..3195)
                     /locus_tag="QDX30_RS26330"
                     /old_locus_tag="QDX30_26330"
     CDS             complement(2659..3195)
                     /locus_tag="QDX30_RS26330"
                     /old_locus_tag="QDX30_26330"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001555327.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_236305820.1"
                     /translation="MKDDKAVVVFTGKDLNIMRAEGGSGYWLAKAERLNDAKYLIAVRN
                     RRETWAVKDLEHGTGFLIAKITGCFKNPDYDDRNVITFEEYAEISVEKAWKMLTGGQRY
                     PVAYLTAEEAFSRIGITLEQLEWKKLQTSTLSQPIPSAEAPKKLSLNEAVERAKQDISN
                     ATDIDVSSITITINI"
                     /name="hypothetical protein"
     gene            complement(4703..4894)
                     /locus_tag="QDX30_RS26335"
                     /old_locus_tag="QDX30_26335"
     CDS             complement(4703..4894)
                     /locus_tag="QDX30_RS26335"
                     /old_locus_tag="QDX30_26335"
                     /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          4541..4625
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.03e-37"
     Typing          complement(3991..4530)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="86.477"
                     /coverage="100.0"
                     /evalue="6.380000000000001e-167"
     Typing          2..1545
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="96.893"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          4928..5271
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.304"
                     /coverage="97.0"
                     /evalue="7.349999999999999e-61"
ORIGIN
        1 atgatagtta agtttcatgc cagggggaaa ggtggtggca gtggtccggt tgattacctt
       61 ctgggaaggg agcgtaaccg ggaaggtgca acggtactgc agggtaaccc ggaagaagtc
      121 cgggaactca tcgatgccac gccatttgcg aagaaatata cgtccggtgt tctgtcgttc
      181 gcggagaagg aactgccgcc gggaggacgt gaaaaagtta tggcgagctt tgagcgtgta
      241 ctgatgcccg gtcttgaaaa aaatcagtac agcattctgt gggtggagca ccaggacaag
      301 gggcggcttg agctgaattt tgtcattccg aacatggagc tacagaccgg aaaacgcctc
      361 cagccgtact acgaccgcgc agacaggccg agaattgatg cctggcagac gctggtgaat
      421 caccattacg ggctgcatga ccccaacgcc ccggagaacc gccggacgct gacccttcct
      481 gataacctgc cggaaacgaa acaggcgctt gctgagagcg ttacacgagg cctggaggtg
      541 ctttaccatg ccggggagat aaaaggccgt caggatgtga ttcaggcgct cacagaggcg
      601 gggcttgacg tggtcagggt gacgcgaagc agtatcagta ttgcagaccc gaacggcggg
      661 aggaatatca gactgaaagg agcattttat gagcaatctt ttacagacgg gcgcggagtt
      721 cgagaaaaag ctgaaagaga gagccgaatc tacagagaaa atgctgaacg acgaattcag
      781 caggctcggc gaatctgtca acgaggctgt gacctcaaac gagacgaaaa tcaaaggcgc
      841 tatagcccag tttacggcct cgacggagga atcgctgaaa aaacaccggg aaggggtgaa
      901 agaggcgatg atgcagcacc ggaaggacat gttaaagctg gcagggagtt cgggcatgag
      961 gttgctgggg atagtctttc tcctgtttac cgcgagtggc gggacgctct ggtatctcgg
     1021 cgggaggata cagacgaacc tggaagaaat cagggtacag gaagagacat tgcggaaact
     1081 gaacgcgaag acatggggcg tggagtttgt tcaggacggg agaaggaaat ttctggtcct
     1141 tccgtacggg aaatcagcag aggtgacgca ctatcagggg aaggactgga tacaactgac
     1201 ggagtgatac ggaatgacag agctggaaac acatttgctg aacgccttag agcagctgca
     1261 acaggactat atgcagcggc tgaacgaatg ggagagcgcc ttcgtggaat tgcagaggat
     1321 gttttcgctt acgcaacggg acaacgcgat gctgaacgag cgggtcatgc agttgagtca
     1381 gcaggtgcag cacttgagcg agcggacaga acgcttgagc cagttataca gcgagaactg
     1441 gagataagag aggaacggtt gataaaggag cgcgaacatg cgttatccct ggaacgggaa
     1501 cgccagctgg aaatacagga acgcacactg gatggtcctt cgttgtcgct gtgatggcga
     1561 aactatgaaa aatggcaggt tcggtggatt ttgacgggct aatgtggtct gcaccatctg
     1621 gttgcatagg tattcatacg gttaaaattt atcaggcgcg atcgcggcag tttttcgggt
     1681 ggtttgttgc catttttacc tgtctgctgc cgtgatcgcg atgaacgcgt tttagcggtg
     1741 cgtacaataa gggattatgg taaatctagc tgtacagtat cagtcagaaa aaaggcgagc
     1801 atagttaatg gctcgagaca tagtcatctg atggctttta tcagcactcg cactaggtgc
     1861 ttggttatgt ggctgacttt gtgttttcgg ctgacccgtc tgagagagcg aggctgccgc
     1921 tgtatttaac tgggcattct gtctcatgtt tattttctct tcgtacctgc tatgaatgat
     1981 ctttaatgtt tcttttaaaa tccgccggta atggtttttt accgagttgt tagataacgg
     2041 tatgttgttg tacatgatgc cgttattttt ccaaatgatt ttgtatactt taccaccgga
     2101 gtagcgatct cgtctgtatg catatttgac agcgctggtg atcttacatc ccactgacga
     2161 tgtagagtat ccacgatgac gctttttttt ctaagccttt tttccgcata gtagagacaa
     2221 tgtgctgcaa attcgccgcc agttgaacct aaatcgtaaa ctatttgttt gctttttatc
     2281 gcaatcatcg ggggggtata catacctact aatatagcac ctgagtgttt atcgaggacc
     2341 accatgccga aggtgaagtc ttctacatcc atgtagagac tcattaagct agcgtactgc
     2401 tctggagtta tgactttcag ctgcatagct tgcataagga cgatcatcgg atgatcacca
     2461 cacataaggg atattgcttc ttttcctttg aaatctatat gtattgcttt tttttcaata
     2521 acatctcttc gaagatgtcc atcaactgac catttgctat cacaagcagc aaattcaaac
     2581 tctctgtata ttgttgttgt catatcaatg gcttaattct ttttcgacta tcgttaagat
     2641 accagatata cgaaaaaatc agatattgat agttatcgta atagaagata catcgatatc
     2701 agttgcattg cttatatctt gcttagctct ttcaactgcc tcgttgaggc ttagtttttt
     2761 cggcgcttct gcagagggga ttggctgaga tagtgttgaa gtctggagtt ttttccactc
     2821 cagctgctct agcgttatcc ctatacggga aaaagcttcc tctgctgtca gataagcaac
     2881 cggataacgc tgaccgccag ttagcatttt ccatgccttt tccactgaaa tttcagcata
     2941 ttcctcaaat gtaattacgt ttctgtcgtc gtaatcaggg tttttaaagc atccggtgat
     3001 ctttgcaatc agaaagccag ttccgtgttc gaggtctttc accgcccatg tttctctccg
     3061 gtttcttact gcgatgagat atttggcgtc attaagccgt tctgcttttg ctagccaata
     3121 acctgaacct ccctcagctc tcattatgtt tagatctttg cctgtaaata cgacaactgc
     3181 tttatcatct ttcatataga aatcccatgc tttagttttt tatcgttatg atttcaatta
     3241 tacacgatta aatgagggga tggaatttta tttatgcgat aaaagtaagt ttacaaattc
     3301 tgtgcttatc tctttcttat ttttgcttat tttgtgctta agttgttttt atttgatttt
     3361 atgttttttt atgtgtatct tattttgatg ttattctttt tgggggttat atgtcgatat
     3421 ctatgcagca aatagattca tgtattgaaa cgaccatcaa tcgtctttct agcgaagctg
     3481 gtacgatggt tagtaatttc tatcttgacc tgcgctctcc cggtagacag cgcattactg
     3541 aaaagctggt agagcaatca atagatcttt gcaggtctcg tggtatctat gctgagcggg
     3601 aaggtaatgg gttgcttgtg agagtagatc tgagaacgtg ctatctgaat ccaggtcaag
     3661 ctgaaatgtt taatatagct attggatata cgcgttcagt tcacgggaat catctataag
     3721 ctgtctacaa aaaggatctt cttgagatcc tttttttcta cgcgtaatct ctagctctga
     3781 aaacgaaaaa accaccctgg caggtggttt ttcgaaggtt agttaatcct ggcagattct
     3841 ctaaccgtgg taacagtctt gtgcgagaca tgccaccaaa tctgtccttc cagtgtagcc
     3901 gcactaaggg caccacttca agaactctcg atacatctct cgcacatcct gtttaccaat
     3961 ggccgctgcc agtggcgttt tgtcgtgtct ttccgggttg gactcaagtc gatagttacc
     4021 ggataagacg cagcggtcgg actgaacggg gggttcgtgc atacagtcca gcttggagcg
     4081 aactgccttc ccggaaccga gtgtcaggcg tggaatgaga caaacgcggc cataacagcg
     4141 gagtgacacc agtaaaccga aaggtaggaa caggagagcg cacgagggag cttccagggg
     4201 gaaacgcctg gtatctttat agtcctgtcg ggtttcgcca cctctgactt gagcgtcgat
     4261 tttgtgatgc tcgtcagggg ggcggagcct atggaaaaac gccagcggcg tggccttttc
     4321 cgggttctcg ttttttgctc acatgtttct tttggcgtta tcccctgatt ctgtggataa
     4381 ccgcatctcc gcttttgagt gagcagacac cgctcgccgc agccgaacga ccgagcgtag
     4441 cgagtcagtg agcgaggaag cggaatagcg ccggaagctg cattttctcc ttacgcatct
     4501 gtgcggtatt tcacaccgta tatggtgcac tctcagtaca atctgcactg atgccgcata
     4561 gttaagccag tatacactcc gctatcgcta cgtgactggt tcagggcttc gccccgaaac
     4621 cccctgacgc gccctgacgg gcttgtctgc tcccggtatc cgctcacagg caagctgtga
     4681 ccgtctccgg gagctgtatg tgtcagaggt tttcaccgtc atccccgaag cgcgcgaggc
     4741 agctgcggta aagctcatcg gcgtggtcgt gaagcgattc acagatatct gcctgttcgt
     4801 ccgcgtccag ttcgttgagc ttctccagca gcgttaatgt ctggcttctg ataaagcggg
     4861 ccatgttaag ggcggttttt tcctgtttag tcactgatgc ctccgtgtaa gggggtattt
     4921 ctgttcatgg gggtaatgat accgatgaaa cgcgagagga tgctcaccat acgggttact
     4981 gatgatgaac atgcccggtt actggaacgc tgtgagggta aacaactggc ggtatggatg
     5041 cggcgggtct gcctgggtga gccggttgcc cgtttcggga agctgccgac actggcaccg
     5101 ccgttactgc gtcagctggc cgccatcggg aataacctga atcagacagc gaggaaggtg
     5161 aacagcgggc agtggtcttc cggcgaccgg gttcaggtgg tggccgcact gatggccatc
     5221 gagagagagt tgcgcagctt acggcaggtc gtcaggggac agggagcgcg gg
//
