LOCUS       NZ_CP080231             5128 bp    DNA     circular CON 07-SEP-2023
DEFINITION  Escherichia coli O141:H4 strain P13-6 plasmid pP136-8, complete
            sequence.
ACCESSION   NZ_CP080231
VERSION     NZ_CP080231.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN20003587
            Assembly: GCF_019431295.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli O141:H4
  ORGANISM  Escherichia coli O141:H4
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5128)
  AUTHORS   Perrat,A., Branchu,P., Decors,A., Turci,S., Bayon-Auboyer,M.-H.,
            Petit,G., Grosbois,V., Brugere,H., Auvray,F. and Oswald,E.
  TITLE     Wild boars as the reservoir of a highly virulent clone of hybrid
            Shiga toxigenic and enterotoxigenic Escherichia coli responsible of
            edema disease
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5128)
  AUTHORS   Auvray,F., Oswald,E. and Perrat,A.
  TITLE     Direct Submission
  JOURNAL   Submitted (03-JUL-2021) Pathogenesis and commensalism of
            enterobacteria, INSERM IRSD U1220, CHU Purpan, Place du Dr Baylac,
            CS60039, Toulouse 31024, France
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 50.0x
            Sequencing Technology             :: PacBio RSII; Illumina HiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 09/04/2023 15:06:45
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,817
            CDSs (total)                      :: 5,678
            Genes (coding)                    :: 5,354
            CDSs (with protein)               :: 5,354
            Genes (RNA)                       :: 139
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 105
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 324
            CDSs (without protein)            :: 324
            Pseudo Genes (ambiguous residues) :: 0 of 324
            Pseudo Genes (frameshifted)       :: 104 of 324
            Pseudo Genes (incomplete)         :: 233 of 324
            Pseudo Genes (internal stop)      :: 46 of 324
            Pseudo Genes (multiple problems)  :: 55 of 324
            Pseudo Genes (short protein)      :: 4 of 324
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP080231.1.
            Bacteria and source DNA available from IRSD.
            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 O141:H4"
                     /mol_type="genomic DNA"
                     /strain="P13-6"
                     /serotype="O141:H4"
                     /isolation_source="clinical sample"
                     /host="Sus scrofa domesticus"
                     /db_xref="taxon:2861806"
                     /plasmid="pP136-8"
                     /geo_loc_name="France"
                     /lat_lon="46.00 N 2.00 E"
                     /collection_date="2013"
                     /collected_by="Labocea; IRSD"
     gene            join(4817..5128,1..90)
                     /locus_tag="KZW89_RS28635"
                     /old_locus_tag="KZW89_28640"
     CDS             join(4817..5128,1..90)
                     /locus_tag="KZW89_RS28635"
                     /old_locus_tag="KZW89_28640"
                     /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(910..1143)
                     /locus_tag="KZW89_RS28645"
                     /old_locus_tag="KZW89_28650"
     CDS             complement(910..1143)
                     /locus_tag="KZW89_RS28645"
                     /old_locus_tag="KZW89_28650"
                     /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(1150..1668)
                     /locus_tag="KZW89_RS28650"
                     /old_locus_tag="KZW89_28655"
     CDS             complement(1150..1668)
                     /locus_tag="KZW89_RS28650"
                     /old_locus_tag="KZW89_28655"
                     /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            complement(<1706..2368)
                     /locus_tag="KZW89_RS29100"
                     /old_locus_tag="KZW89_28660"
                     /pseudo=""
     CDS             complement(<1706..2368)
                     /locus_tag="KZW89_RS29100"
                     /old_locus_tag="KZW89_28660"
                     /inference="COORDINATES: protein motif:HMM:NF015397.3"
                     /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            complement(2346..2669)
                     /locus_tag="KZW89_RS28660"
                     /old_locus_tag="KZW89_28665"
     CDS             complement(2346..2669)
                     /locus_tag="KZW89_RS28660"
                     /old_locus_tag="KZW89_28665"
                     /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            2734..2925
                     /locus_tag="KZW89_RS28665"
                     /old_locus_tag="KZW89_28670"
     CDS             2734..2925
                     /locus_tag="KZW89_RS28665"
                     /old_locus_tag="KZW89_28670"
                     /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"
     gene            3556..3687
                     /locus_tag="KZW89_RS28670"
                     /old_locus_tag="KZW89_28675"
     CDS             3556..3687
                     /locus_tag="KZW89_RS28670"
                     /old_locus_tag="KZW89_28675"
                     /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="replication initiation protein"
                     /protein_id="WP_096169391.1"
                     /translation="MHEPPVQSDCCACSGNYRLESNPERHDKAPLAAAMGKGVYKIY"
                     /name="replication initiation protein"
     gene            3936..4820
                     /locus_tag="KZW89_RS28675"
                     /old_locus_tag="KZW89_28680"
     CDS             3936..4820
                     /locus_tag="KZW89_RS28675"
                     /old_locus_tag="KZW89_28680"
                     /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"
     Typing          complement(3021..3194)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="92.571"
                     /coverage="100.0"
                     /evalue="1.23e-64"
     Typing          3118..3704
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.709"
                     /coverage="97.0"
                     /evalue="0.0"
     Typing          complement(807..2356)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.603"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tcagcaaaga aaaatctaac cgagttcaca ataagtgaga taagtgatat tggcatgtat
       61 cgtcgcgtag cgaaagggaa tcatgcataa ataaaagcca cctgtgaggt ggctttttat
      121 aggataaaaa aatgccattt aatataggcg atatagttta cttaaagtca gaatcaaaag
      181 cgatgacggt catcggatat ggatcgtctc aaaataacgg ttacatagat ctagctaatt
      241 gtgcttggct agataaagac aaccgctatt gccaaatact attcttgttt caaacgatcg
      301 aaaaaagaat cagttaaaaa ctggcttatc ttcattgagc ataccggacg aacctattta
      361 ccataacatc cgttgcccgc accgcagaaa cgcgttcggt gcgatcacgg cagcagacag
      421 gtaaaaatgg caacaaacca cccgaaaaac tgccgcgatc gcacccggta aattttaacc
      481 acatgcatag ctatgcagcc atgtgaatca cgcaggaatt gccagccaga gacagctgaa
      541 acggattttt ttcatgcttt cggaagcgaa gaagacgggg accggagcgg gaaaacagaa
      601 gttcagggga atgagcgcga tctggcaata gaggcaaaac acagcaacaa aagacacacc
      661 agaatcgcgc ccgtatgcgt tttaacgcgt tcctgtgttt tcagcaaggt ctgactgaag
      721 cgcgttcccg gtgcccccga accaaccatt atcccaaaaa atgcaccgga aacgcgctga
      781 caacatttta gcctgtctct gattaccatc caagcgaagg gccatcctgt gtccattcct
      841 gtatttccgg ctggcgctca cgctccaggg ataactcatg ttcgcgctcc tgtatcagcc
      901 gttcgtccct tatctcctgt tctcgctgta taactggctc aagcgttctg tccgctcgct
      961 caagtgctgc acctgctgac tcaactgcat gacctgctcg ttcagcatcg cgttgtcccg
     1021 ttgcgtaagc gaaaacattt tctgcaattc cacgaaggcg ctctcccatt cgctcagccg
     1081 ctgcatatag tcctgttgca gttgctctaa ggcgttcagc aaatgtcttt ccagctccgt
     1141 cactctgtgt cactccgtca gttgtaccca gtccttctcc tgatagggaa tcaccgttgc
     1201 cgatttcccg tacggaagga ccagaaattt ccttctcccg tcctgcacaa actccacgcc
     1261 ccatgtcttc gcgttcagtt tctgcaatgt ttcttcctgt atcctgattt cttccaggtt
     1321 cgcctgtatc cgcccgccaa gataccagag cgtcccgcca ctcacggtaa acaggaaaag
     1381 gaccatcccc agtaacatca tgcccgtatt ccctgccagc tttaacacgt ccttcctgtg
     1441 ctgcatcatc gcctctttca ccccttcccg gtgttttttc agtgattcct ctgtcgaagc
     1501 tgtgaacagg gctatagcgt ctttgatttt cgtctcgttt gatgtcacag ccttgcttac
     1561 agatttttcg agcttgctga actcgtcgtt cagcattgtc tctgtagatt cggctctctc
     1621 tttcagcttt ttctcgaact ccgcgcccgt ctgtaaaaga ttgctcatag aatgctcctt
     1681 tcagtctgat attcttcccg ccgttcgggt ctgcaatgct gatactgctt cgcgtcaccc
     1741 tgaccacttc aagccctgcc tctgtgagcg cctgaatcac atcctgacgg ccttttatct
     1801 ccccgacatg ataaagagcg tctatcccgc gtgtgacgct ctctgcaagc gcctgtttcg
     1861 tttccggcag gttatcaggg agagtcagta tccggcggtt ctccggggcg ttggggtcat
     1921 gcagcccgta atggtgatta accagcgtct gccaggcatc aattctcggc ctgtctgccc
     1981 ggtcgtagta cggctggagg cgttttccgc tctgtagctc catgttcgga atgacaaaat
     2041 tcagctcaag ccgtcccttg tcctggtgct ccacccacag gatgctgtac tgattttttt
     2101 cgagaccggg catcagtaca cgctcaaagc tcgccatcac cttttcacgt cctcccggcg
     2161 gcagctcctt ctccgcgaac gacagaacac ctgacgtgta tttcttcgca aatggcgtgg
     2221 catcgatgag ttcccggact tcttccggat taccctgaag caccgttgcc ccttcccggt
     2281 tacgctccct tcccagcagg taatcaaccg gaccactgcc accgcctttt cccctggcat
     2341 gaaacttaac tatcatcccg cgctccatgt tccctgacga cctgccgtaa gctgcgcaac
     2401 tctctctcga tggccatcag tgcggccacc acctgaaccc ggtcaccgga agaccactgc
     2461 ccgctgttca ccttcctcgc cgtctgattc agattattcc cgatggcagc cagctggcgc
     2521 agtaacggcg gtgccagtgt cggcagcttc ccggaacggg caaccggctc acccagacag
     2581 acccgccgca tccataccgc cagctgttta ccctcacagc gttccagtaa ccgtgcatgt
     2641 tcatcatcag taacccgtat cgtgagcatc ctctcgcgtt tcatcggtat cattacccca
     2701 tgaacagaaa tcccccctta cacggaggca tcagtgacta aacaggaaaa aaccgccctt
     2761 aacatggccc gctttatcag aagccagaca ttaacgctgc tggaaaagct caacgaactg
     2821 gacgcggatg aacaggcaga catctgtgaa tcgcttcacg accacgccga tgagctttac
     2881 cgcagctgcc tcgcacgctt cggggatgac ggtgaaaacc tctgacacat acagctcccg
     2941 gagacggtca cagcttgtct gtgagcggat gccgggagca gacaagcccg tcagggcgcg
     3001 tcaggccgtt gaccttgcgg gtgtcggggc gcagccatga cccagtcacg tagcgatagc
     3061 ggagtgtata ctggcttact atgttggcat gagtgcgggt atcaggaaag tgcttcatgt
     3121 ggcaggagaa aaaaggcggc accggagcgt cagcagaata tgtgatacag gatatattcc
     3181 gcttcctcgc tcactgactc gctacgctcg gtcgttcgac tgcggcgagc ggaaatggct
     3241 tacgaacggg gcggagattt cctggaagat gccaggaaga tacttaacag ggaagcgata
     3301 gggtcgcggc gaagccgttt ttccataggc tccgcccccc tgacaagcat cacgaaatct
     3361 gacgctcaaa tcagtggtgg cgaaacccga caggactata aagataccag gcgtttcccc
     3421 ctggtggctc cctcgtgcgc tctcctgttc ctgcctttcg gtttaccggt gtcattccgc
     3481 tgttatggcc gcgtttatct cattccacgc ctgacactca gttccgggta ggcagttcgc
     3541 tccaagctgg actgtatgca cgaacccccc gttcagtccg actgctgcgc ctgttccggt
     3601 aactatcgac ttgagtccaa cccggaaaga cacgacaaag cgccactggc agcagccatg
     3661 ggtaaagggg tgtacaagat ttactgagtg agagttcttg aagtatcagc cttagagagg
     3721 ctaaactgga ataacagaat ttggtttcag cggtcttgta caccctgtta ccacggttca
     3781 gaagttcccc aacttactga accctcgaaa aaaccgactc cccagtcggt ttttttcgtt
     3841 tgatggctaa gagtacgctg acgttatact gaacgtcaag gaaagcgttg acgctgttcc
     3901 ctctaccaaa aaaaagagat ttgtaaggaa taaaaatggc tgtgacagtt gggtttatta
     3961 gtgagaaagg tggggttggt aaaacaacgt cctgttatca cattgccgaa ggacttagtc
     4021 gttttcatga aaaacgtgtt ttagttatag atgcagatta tcaacgcggg ggtataactg
     4081 gaagattttt ccctaaactg atcgaaaact ttggaaatca agcaccgcaa ggaacaacgt
     4141 tatttaacaa gtatcagcaa ttatatagcg cggcacaaca aacgactgac atagacataa
     4201 ttaaatttaa tagtggtatc gatgtcattc cagccgaccc tcgcttatca accgtttcaa
     4261 ctgataagct acctagtaca aacaatataa gatcgaacaa tgccattctt ttacagcatt
     4321 taaaaaccat aagcgctgta ttatcaccta ttgcagataa ttatgactac atattgattg
     4381 attcacaccc cgaagtttct gatgtcatgc gctctataat ctacgcatca gattattgtg
     4441 tatcaccggt aaaactagac aggcaatcat ctattggtgt ggccacggtc ataggtgaga
     4501 taaataatgt aaatgaagat attgaaatgc taagaaaggc actgcaagtc ggcgattcat
     4561 ataaggacac agttttcgcc ggagcaatgg gaatgatggc cagagaatat gcagaagaac
     4621 tgaagcaaac agagcaatat gaatacaaca ggcttcggca agcaggtgac atcttcaagc
     4681 actacataac ggaaggtgat gggctaagag tagctgcagc agagcgcgtt tcagtgtatg
     4741 atgtacagat aagtaacgct tacaaacaag cgtcacagtt taagaacttg acgattgagt
     4801 ttatgaggac ttgtcgatga tagatatcca aaaactgata tcttggcttg gcgttgaggg
     4861 agctaaagct ggcttggata aaagtgaaat gactaatgcc gagctaattg aatcctttgg
     4921 taatttactt ccaaagaacc caagcaaatt aaaacgctcc gatctcgttg aggagattat
     4981 tttagcaaca aggagaatga cacataaatc agttgaagaa ctgatggaaa tgtcaaaaga
     5041 agatctgtat tcatatttcc acgatcagaa atatagcaga aaagaacttc ttgatttgtt
     5101 atatactctt gaaatcagac ctgggagc
//
