LOCUS       NZ_CP122824             5128 bp    DNA     circular CON 08-JUN-2024
DEFINITION  Escherichia coli strain ETEC1732 plasmid unnamed1, complete
            sequence.
ACCESSION   NZ_CP122824
VERSION     NZ_CP122824.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN32549609
            Assembly: GCF_030013715.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5128)
  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 5128)
  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                   :: 125x
            Sequencing Technology             :: Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_030013715.1-RS_2024_06_08
            Annotation Date                   :: 06/08/2024 05:15:47
            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)                     :: 5,741
            CDSs (total)                      :: 5,607
            Genes (coding)                    :: 5,302
            CDSs (with protein)               :: 5,302
            Genes (RNA)                       :: 134
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 100
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 305
            CDSs (without protein)            :: 305
            Pseudo Genes (ambiguous residues) :: 0 of 305
            Pseudo Genes (frameshifted)       :: 138 of 305
            Pseudo Genes (incomplete)         :: 164 of 305
            Pseudo Genes (internal stop)      :: 52 of 305
            Pseudo Genes (multiple problems)  :: 42 of 305
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP122824.1.
            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..5128
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="ETEC1732"
                     /isolation_source="feces"
                     /host="Sus scrofa"
                     /db_xref="taxon:562"
                     /plasmid="unnamed1"
                     /geo_loc_name="Belgium"
                     /collection_date="2021"
                     /collected_by="IMM_DI04"
     gene            join(4816..5128,1..11)
                     /locus_tag="QDX01_RS26440"
                     /old_locus_tag="QDX01_26440"
     CDS             join(4816..5128,1..11)
                     /locus_tag="QDX01_RS26440"
                     /old_locus_tag="QDX01_26440"
                     /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="QDX01_RS26445"
                     /old_locus_tag="QDX01_26445"
                     /pseudo=""
     CDS             220..>651
                     /locus_tag="QDX01_RS26445"
                     /old_locus_tag="QDX01_26445"
                     /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="QDX01_RS26450"
                     /old_locus_tag="QDX01_26450"
     CDS             689..1207
                     /locus_tag="QDX01_RS26450"
                     /old_locus_tag="QDX01_26450"
                     /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="QDX01_RS26455"
                     /old_locus_tag="QDX01_26455"
     CDS             1214..1447
                     /locus_tag="QDX01_RS26455"
                     /old_locus_tag="QDX01_26455"
                     /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(2267..2668)
                     /locus_tag="QDX01_RS26460"
                     /old_locus_tag="QDX01_26460"
     CDS             complement(2267..2668)
                     /locus_tag="QDX01_RS26460"
                     /old_locus_tag="QDX01_26460"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001505260.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001505260.1"
                     /translation="MIDIQKLISWLGVEGAKAGLDKSEMTNAELIESFGNLLPKNPSKL
                     KRSDLVEEIILATRRMTHKSVEELMEMSKEDLYSYFHDQKYSRKELLDLLYTLEIRPGS
                     SAKKNLTEFTISEISDIGMYRRVAKGNHA"
                     /name="hypothetical protein"
     gene            complement(2665..3549)
                     /locus_tag="QDX01_RS26465"
                     /old_locus_tag="QDX01_26465"
     CDS             complement(2665..3549)
                     /locus_tag="QDX01_RS26465"
                     /old_locus_tag="QDX01_26465"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001505259.1"
                     /GO_function="GO:0005524 - ATP binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="ParA family protein"
                     /protein_id="WP_001505259.1"
                     /translation="MAVTVGFISEKGGVGKTTSCYHIAEGLSRFHEKRVLVIDADYQRG
                     GITGRFFPKLIENFGNQAPQGTTLFNKYQQLYSAAQQTTDIDIIKFNSGIDVIPADPRL
                     STVSTDKLPSTNNIRSNNAILLQHLKTISAVLSPIADNYDYILIDSHPEVSDVMRSIIY
                     ASDYCVSPVKLDRQSSIGVATVIGEINNVNEDIEMLRKALQVGDSYKDTVFAGAMGMMA
                     REYAEELKQTEQYEYNRLRQAGDIFKHYITEGDGLRVAAAERVSVYDVQISNAYKQASQ
                     FKNLTIEFMRTCR"
                     /name="ParA family protein"
     gene            complement(3798..3929)
                     /locus_tag="QDX01_RS26470"
                     /old_locus_tag="QDX01_26470"
     CDS             complement(3798..3929)
                     /locus_tag="QDX01_RS26470"
                     /old_locus_tag="QDX01_26470"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001505258.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001505258.1"
                     /translation="MHEPPVQSDCCACSGNYRLESNPERHDKAPLAAAMSKGVYKIY"
                     /name="hypothetical protein"
     gene            complement(4560..4751)
                     /locus_tag="QDX01_RS26475"
                     /old_locus_tag="QDX01_26475"
     CDS             complement(4560..4751)
                     /locus_tag="QDX01_RS26475"
                     /old_locus_tag="QDX01_26475"
                     /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          4292..4465
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="92.0"
                     /coverage="100.0"
                     /evalue="5.699999999999999e-63"
     Typing          complement(3782..4368)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.568"
                     /coverage="97.0"
                     /evalue="0.0"
     Typing          2..1551
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.603"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          4787..5127
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.105"
                     /coverage="97.0"
                     /evalue="2.02e-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 cgccagccgg aaatacagga atggacacag gatggccctt cgcttggatg 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 taggttcgtc cggtatgctc aatgaagata agccagtttt
     2041 taactgattc ttttttcgat cgtttgaaac aagaatagta tttggcaata gcggttgtct
     2101 ttatctagcc aagcacaatt agctagatct atgtaaccgt tattttgaga cgatccatat
     2161 ccgatgaccg tcatcgcttt tgattctgac tttaagtaaa ctatatcgcc tatattaaat
     2221 ggcatttttt tatcctataa aaagccacct cacaggtggc ttttatttat gcatgattcc
     2281 ctttcgctac gcgacgatac atgccaatat cacttatctc acttattgtg aactcggtta
     2341 gatttttctt tgctgagctc ccaggtctga tttcaagagt atataacaaa tcaagaagtt
     2401 cttttctgct atatttctga tcgtggaaat atgaatacag atcttctttt gacatttcca
     2461 tcagttcttc aactgattta tgtgtcattc tccttgttgc taaaataatc tcctcaacga
     2521 gatcggagcg ttttaatttg cttgggttct ttggaagtaa attaccaaag gattcaatta
     2581 gctcggcatt agtcatttca cttttatcca agccagcttt agctccctca acgccaagcc
     2641 aagatatcag tttttggata tctatcatcg acaagtcctc ataaactcaa tcgtcaagtt
     2701 cttaaactgt gacgcttgtt tgtaagcgtt acttatctgt acatcataca ctgaaacgcg
     2761 ctctgctgca gctactctta gcccatcacc ttccgttatg tagtgcttga agatgtcacc
     2821 tgcttgccga agcctgttgt attcatattg ctctgtttgc ttcagttctt ctgcatattc
     2881 tctggccatc attcccattg ctccggcgaa aactgtgtcc ttatatgaat cgccgacttg
     2941 cagtgccttt cttagcattt caatatcttc atttacatta tttatctcac ctatgaccgt
     3001 ggccacacca atagatgatt gcctgtctag ttttaccggt gatacacaat aatctgatgc
     3061 gtagattata gagcgcatga catcagaaac ttcggggtgt gaatcaatca atatgtagtc
     3121 ataattatct gcaataggtg ataatacagc gcttatggtt tttaaatgct gtaaaagaat
     3181 ggcattgttc gatcttatat tgtttgtact aggtagctta tcagttgaaa cggttgataa
     3241 gcgagggtcg gctggaatga catcgatacc actattaaat ttaattatgt ctatgtcagt
     3301 cgtttgttgt gccgcgctat ataattgctg atacttgtta aataacgttg ttccttgcgg
     3361 tgcttgattt ccaaagtttt cgatcagttt agggaaaaat cttccagtta tacccccgcg
     3421 ttgataatct gcatctataa ctaaaacacg tttttcatga aaacgactaa gtccttcggc
     3481 aatgtgataa caggacgttg ttttaccaac cccacctttc tcactaataa acccaactgt
     3541 cacagccatt tttattcctt acaaatctct tttttttggt agagggaaca gcgtcaacgc
     3601 tttccttgac gttcagtata acgtcagcgt actcttagcc atcaaacgaa aaaaaccgac
     3661 tggggagtcg gttttttcga gggttcagta agttggggaa cttctgaacc gtggtaacag
     3721 ggtgtacaag accgctgaaa ccaaattctg ttattccagt ttagcctctc taaggctgat
     3781 acttcaagaa ctctcactca gtaaatcttg tacacccctt tactcatggc tgctgccagt
     3841 ggcgctttgt cgtgtctttc cgggttggac tcaagtcgat agttaccgga acaggcgcag
     3901 cagtcggact gaacgggggg ttcgtgcata cagtccagct tggagcgaac tgcctacccg
     3961 gaactgagtg tcaggcgtgg aatgagataa acgcggccat aacagcggaa tgacaccggt
     4021 aaaccgaaag gcaggaacag gagagcgcac gagggagcca ccagggggaa acgcctggta
     4081 tctttatagt cctgtcgggt ttcgccacca ctgatttgag cgtcagattt cgtgatgctt
     4141 gtcagggggg cggagcctat ggaaaaacgg cttcgccgcg accctatcgc ttccctgtta
     4201 agtatcttcc tggcatcttc caggaaatct ccgccccgtt cgtaagccat ttccgctcgc
     4261 cgcagtcgaa cgaccgagcg tagcgagtca gtgagcgagg aagcggaata tatcctgtat
     4321 tacatattct gctgacgctc cggtgccgcc ttttttctcc tgccacatga agcactttcc
     4381 tgatacccgc actcatgcca acatagtaag ccagtataca ctccgctatc gctacgtgac
     4441 tgggtcatgg ctgcgccccg acacccgcaa ggtcaacggc ctgacgcgcc ctgacgggct
     4501 tgtctgctcc cggcatccgc tcacagacaa gctgtgaccg tctccgggag ctgtatgtgt
     4561 cagaggtttt caccgtcatc cccgaagcgt gcgaggcagc tgcggtaaag ctcatcggcg
     4621 tggtcgtgaa gcgattcaca gatgtctgcc tgttcatccg cgtccagttc gttgagcttt
     4681 tccagcagcg ttaatgtctg gcttctgata aagcgggcca tgttaagggc ggttttttcc
     4741 tgtttagtca ctgatgcctc cgtgtaaggg gggatttctg ttcatggggt aatgataccg
     4801 atgaaacgcg agaggatgct cacgatacgg gttactgatg atgaacatgc acggttactg
     4861 gaacgctgtg agggtaaaca gctggcggta tggatgcggc gggtctgtct gggtgagccg
     4921 gttgcccgtt ccgggaagct gccgacactg gcaccgccgt tactgcgcca gctggctgcc
     4981 atcgggaata atctgaatca gacggcgagg aaggtgaaca gcgggcagtg gtcttccggt
     5041 gaccgggttc aggtggtggc cgcactgatg gccatcgaga gagagttgcg cagcttacgg
     5101 caggtcgtca gggaacatgg agcgcggg
//
