LOCUS       NZ_AP022330             4060 bp    DNA     circular CON 21-MAY-2024
DEFINITION  Escherichia coli O25:H4 strain 18044 plasmid p18044_4, complete
            sequence.
ACCESSION   NZ_AP022330
VERSION     NZ_AP022330.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00199041
            Sequence Read Archive: DRR203158, DRR203159
            Assembly: GCF_016756455.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli O25:H4
  ORGANISM  Escherichia coli O25:H4
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1
  AUTHORS   Nagaoka,H., Hirai,S., Morinushi,H., Mizumoto,S., Suzuki,K.,
            Shigemura,H., Takahashi,N., Suzuki,F., Mochizuki,M., Asanuma,M.,
            Maehata,T., Ogawa,A., Ohkoshi,K., Sekizuka,T., Ishioka,T.,
            Suzuki,S., Kimura,H., Kuroda,M., Suzuki,M., Murakami,K. and Kanda,T.
  TITLE     Coinfection with Human Norovirus and Escherichia coli O25:H4
            Harboring Two Chromosomal blaCTX-M-14 Genes in a Foodborne Norovirus
            Outbreak in Shizuoka Prefecture, Japan
  JOURNAL   J Food Prot 83 (9), 1584-1591 (2020)
   PUBMED   32866241
  REMARK    DOI:10.4315/JFP-20-042
REFERENCE   2  (bases 1 to 4060)
  AUTHORS   Hirai,S., Shigemura,H. and Murakami,K.
  TITLE     Direct Submission
  JOURNAL   Submitted (20-JAN-2020) Contact:Hiroaki Shigemura Fukuoka Institute
            of Health and Environmental Sciences; Mukaizano 39, Dazaifu
            818-0135, Japan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.4
            Genome Coverage                   :: 56x
            Sequencing Technology             :: Sequel; GridION X5; MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_016756455.1-RS_2024_05_21
            Annotation Date                   :: 05/21/2024 02:44:44
            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)                     :: 5,234
            CDSs (total)                      :: 5,121
            Genes (coding)                    :: 4,896
            CDSs (with protein)               :: 4,896
            Genes (RNA)                       :: 113
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 225
            CDSs (without protein)            :: 225
            Pseudo Genes (ambiguous residues) :: 0 of 225
            Pseudo Genes (frameshifted)       :: 80 of 225
            Pseudo Genes (incomplete)         :: 166 of 225
            Pseudo Genes (internal stop)      :: 41 of 225
            Pseudo Genes (multiple problems)  :: 52 of 225
            Pseudo Genes (short protein)      :: 1 of 225
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP022330.1.
            Annotated at DFAST https://dfast.nig.ac.jp/
            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..4060
                     /organism="Escherichia coli O25:H4"
                     /mol_type="genomic DNA"
                     /strain="18044"
                     /serovar="O25:H4"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:2067421"
                     /plasmid="p18044_4"
                     /geo_loc_name="Japan"
                     /collection_date="2018"
     gene            101..802
                     /locus_tag="ECO25NV_RS25795"
                     /old_locus_tag="ECO25NV_49830"
     CDS             101..802
                     /locus_tag="ECO25NV_RS25795"
                     /old_locus_tag="ECO25NV_49830"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001281399.1"
                     /GO_function="GO:0003887 - DNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /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_001281395.1"
                     /translation="MSDLIAYKSNALIEASYKLTLQEQRFLLVCISRLKSGEDSPSPDE
                     QKTMTITAAEFHDAFPDMGRQHAEARLKEAIDRLWDRSVIIKNEEKREEFRWVQYRAQY
                     FKGEAKVDITFSDAIMPYLTQLKGQFTRVVVKNVSSLSSTYSIRIYELLQQFRSTGDRT
                     IAIDDFRTMLAVEDKYQQFKDLNKMIIKPAIAELNEKSDLVVTVETIKKGRTVVALHFR
                     FKEDKQIKMTI"
                     /name="replication initiation protein"
     gene            complement(1048..3195)
                     /gene="mobQ"
                     /locus_tag="ECO25NV_RS25800"
                     /old_locus_tag="ECO25NV_49840"
     CDS             complement(1048..3195)
                     /gene="mobQ"
                     /locus_tag="ECO25NV_RS25800"
                     /old_locus_tag="ECO25NV_49840"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016240513.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobQ family relaxase"
                     /protein_id="WP_171874286.1"
                     /translation="MAIYHLSMKIISRSSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPHELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAIGPAGFSGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNGGLTEPARRVADLLNIGLPDNATSYTLRDIIEALPKDSN
                     SAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQMAFEKQWQQWGKSGLAALRAQL
                     LKREEELRRKEQEDTERSRAEQLRKNDNAVMDSGVLRAVVTGYGEAPMPGNGEMTCYLL
                     LHNRNGEYTLWGNELEKYRTRIFESVDLMRDRSGYICDRSEIGQRPPLQRVYSSATFEQ
                     LLTQVCQTWPQHTRNLRQPKTWPESFCLGEDRQPAMPSPAARKVDFMQGRLPPTLMPVM
                     SSVDRETRQLQLLLVMGVDDSLGGVIRLNGTLYPAFAVPSADNRHLVISALTDKGLRYA
                     GYGVAVNHDADSHISPAPELMQFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRTWDEW
                     RREEDARTHATERRHDRGWSQ"
                     /name="mobQ"
     gene            3374..3628
                     /gene="mobC"
                     /locus_tag="ECO25NV_RS25805"
                     /old_locus_tag="ECO25NV_49850"
     CDS             3374..3628
                     /gene="mobC"
                     /locus_tag="ECO25NV_RS25805"
                     /old_locus_tag="ECO25NV_49850"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000091747.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase accessory protein MobC"
                     /protein_id="WP_000091746.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVVVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPEQ"
                     /name="mobC"
     Typing          complement(2838..3196)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          3197..3373
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          102..802
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(1052..3282)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="96.39"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tgtaatccac agaaaaaggg ggttgcaaaa aaaaaacttc cacccatatg ataagtggcg
       61 tacagtaaaa aaacgccacc aatagcaacg agcaagcgaa atgtcagatc tgatagctta
      121 caaatcaaac gcccttatcg aggcaagcta caagctcact ttgcaggaac agcgcttcct
      181 gctggtctgt atcagccgcc taaaatccgg agaagattcc ccttcgccgg atgaacaaaa
      241 aaccatgacc atcacggctg cagagtttca tgatgccttt cctgacatgg gacggcagca
      301 cgctgaagct aggctcaagg aagcgataga tcgcctctgg gacaggtcag taatcatcaa
      361 gaacgaggaa aaacgagaag agttccgctg ggtgcagtac cgggcgcagt atttcaaagg
      421 tgaggcgaaa gtagatatca ccttctccga tgccatcatg ccgtatctga cacagctcaa
      481 ggggcagttt acgcgggtag tcgtgaagaa cgtctccagc ctttccagca cctacagcat
      541 ccgcatttac gagctgctcc agcagttccg cagcaccggt gacagaacga tagctatcga
      601 tgatttccga accatgcttg ccgttgaaga taaatatcaa caattcaaag acttgaataa
      661 gatgataatc aagccagcca tcgccgaact gaacgaaaaa agcgatctgg ttgtaactgt
      721 tgagacgatc aaaaaggggc gcacggttgt agccctgcat tttcgcttca aggaagacaa
      781 acagatcaag atgacgatct aaaatcgatt ttaaggcacc taaaacgctc cctgctgcgt
      841 tttttttgtg ttagtagtgc gaaggtacta ttgaagtgaa aaattgcgtc aaaagcgctc
      901 taatgcagcg aaaaaagaac ccccattttt tgggggcgga aaaacaaaac tatgcttgca
      961 ttatgtgtgt gcttcttgca ttcatccctg tcgatgaaca tcgaagaaca taacacgatg
     1021 ttaaacaaaa caaaatattg ttcacattca ctgtgaccaa ccgcgatcat gtctcctctc
     1081 ggtggcgtgt gttcgtgcat cttcctcgcg ccgccattcg tcccaggtac gattaaaacc
     1141 cagcgagcgg aacagatgat ccggctgttt ttctggtgtg ttgacggcag caaaaagcgg
     1201 tgcctcacgg gttttcagat gaaactgcat cagttctggt gcaggtgata tgtggctgtc
     1261 tgcatcgtga tttacggcaa caccataccc tgcataccgt aaccccttat cggtcagcgc
     1321 actgatgacc agatgcctgt tatcggctga gggaacggca aacgcgggat acagcgtacc
     1381 attaagccgg ataacaccgc ccagagagtc atccacgccc atgaccagca aaagctgaag
     1441 ctggcgggtt tcccggtcga cagaactcat gaccggcatc agcgtcggtg gcagacgtcc
     1501 ctgcataaaa tccaccttcc ttgccgctgg tgatggcatg gctggctggc ggtcttctcc
     1561 aagacagaaa gactccggcc atgtcttcgg ctggcggaga ttgcgggtat gttgcggcca
     1621 tgtctggcaa acctgcgtca gcagttgctc aaaggttgca gaggaataaa cacgttgcag
     1681 tggcggacgt tggccgattt cgcttcggtc acagatataa ccactcctgt cacgcattaa
     1741 atcaacactc tcaaagattc tggtgcggta tttctccagc tcgttccccc agagcgtata
     1801 ttctccgttc cggttgtgaa gcagaaggta acaggtcatt tccccgttac caggcatggg
     1861 agcctcgcca taccccgtaa cgactgctct cagcacccct gaatccataa cggcattgtc
     1921 atttttcctg agctgctccg cgcgactacg ttcagtatct tcctgttcct tccggcgcaa
     1981 ttcctcttca cgtttaagca actgggctct gagagctgca aggccggatt tcccccactg
     2041 ctgccactgt ttttcaaatg ccatctgact cgcgggaatg tcctgtttct ccaccttccg
     2101 gtaatgctgt cgtaattttt ccatttgctg gctcagagac tggatttttc cctgctcact
     2161 acggtattcc ggtgccgccc attgcatcag gggaatacgg gaaaaaccgg acgaaaacgg
     2221 cgatgatttt ttcaggctgg cagcatggct catcgcttcc tttcgttcgg tgttcagctc
     2281 ttcccagcgt ctgcgcgtcg cctgcatatc tgccatcatc gacatggcat tactggtgag
     2341 tttccatgcc gagttactgt ccttcggcaa cgcttcgata atgtcacgta gtgtgtacga
     2401 agttgcgttg tcaggaagcc cgatattcag aaggtcagcc acacggcggg caggctctgt
     2461 cagccctccg ttcctgagtt cggtgcggga aatctgtatt tccaggttaa gcctgttaat
     2521 cagacgattc tgttcgccgc gttctgtttc gataccgcgt gtttccatcg cacaggcaga
     2581 ctttccgagg tgaataccag gcgttttctc aagcccctgt cgctcgtatg aacgatggtc
     2641 tatctcttcc tgataaccgg cgttcgccag tgccctgttt gcatggtcag cccatgatgc
     2701 ccgccacgtc tcggcatgtg tccggtcgtt ccagtccctg acctttccgc tgaacccagc
     2761 aggtccgata gccctcgtgg tcagcatgat gtgcgcatgg ggatttgttt tatccatgtg
     2821 atggaacgcc acatcagcaa tcatgccctg actgacaaag ttttctctga caaaggcgag
     2881 aacggtttcc cgtgcggcat cctgcggcag ttcgtggggg atggcgagtt caatttcccg
     2941 cgcaagttgt gagttcttcc ggcgttcggc cttctcaacg gcattccaga gttcggcacg
     3001 gttcgtacac caggcagggg cggtggcggg ggtcagaatc acagcctcag ccacaccgct
     3061 tttgcgggtg tagtcgtgag tcagtccggt acgctcatca agcatcagtg aaccggaacg
     3121 ataggcagcg gaagctacgg cgctgtagcc gctgcttctg gagataattt tcatgctgag
     3181 atgataaatc gccatttctg ccgtaatgcc tttttgtagt tttctttcag ccccgcaggg
     3241 cgcacacaat cgaaacggag tggagattgt ataagtgcgc acttcgtgat ttgccgtgca
     3301 ttatgccagc tcagttttta aactaccagt gacgcgctaa aatgcgattt ttcatcgcgc
     3361 acggagttac atcatgagca gaacgctcga acagaagatt gctgatgctg aggcgagatt
     3421 acagcgcctg aaggcgaaga gccggagcct ggacacagcg cagaaggttg ttgtgggtgc
     3481 tgcattgctg gcaaaggtca gaaagccgga ggaggtgcag ttgcgtgcct ggttactcca
     3541 gttcctgaag gcagaggtga cacgacaggc tgatgtgacg cgcatactgc cgctgattaa
     3601 cgagctggag gcgctgccag aacagtgatt gtatcgtccg ctcgccgcag ccccagcgac
     3661 cgagcgttag cgagcgagtg ggcgaggaag cggaagtgaa tcagtcgcca ggttgagcac
     3721 atacgcacgg tttttcggca ggtgatatgc gctgaacccg catgaatact gggtttccac
     3781 agggttggag ggggtgtatt cgaaacttgc aattctgctt tattgcaacg cattgttttt
     3841 attggttttt tgttttcagc accccaagtt atccacaggc tcgccgttaa gtttttaaga
     3901 tcttattttt agatcttttt tttaaaacct ttttaggtct tgtaacacca tgattttaaa
     3961 gatgttctgg caagataagt ggagcttttg ggggtgaaag gtggagcttt tgggggtgaa
     4021 aggtggagct tttgggggtg aaaggtggag cttttggggg
//
