LOCUS       NZ_AP024119             6079 bp    DNA     circular CON 20-SEP-2023
DEFINITION  Escherichia coli strain JML285 plasmid JML285_P5, complete sequence.
ACCESSION   NZ_AP024119
VERSION     NZ_AP024119.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00077348
            Sequence Read Archive: DRR102940, DRR252635
            Assembly: GCF_005389605.2
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1
  AUTHORS   Frederic,A., Alexandre,P., Arimizu,Y., Camille,V.C., Nadege,G.,
            Clemence,M., Hubert,B., Jean-Philippe,N., Hayashi,T., Priscilla,B.,
            Ogura,Y. and Eric,O.
  TITLE     Insights into the acquisition of the pks island and production of
            colibactin in the Escherichia coli population
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6079)
  AUTHORS   Hayashi,T., Ogura,Y. and Katsura,K.
  TITLE     Direct Submission
  JOURNAL   Submitted (23-OCT-2020) Contact:Yoshitoshi Ogura Kurume University
            School of Medicine, Department of Bacteriology; 67 asahi-machi,
            Kurume, Fukuoka 830-0011, Japan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: unicycler v. 0.4.8
            Genome Coverage                   :: 40x
            Sequencing Technology             :: Illumina Miseq, MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 09/20/2023 05:13:43
            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)                     :: 5,202
            CDSs (total)                      :: 5,084
            Genes (coding)                    :: 4,867
            CDSs (with protein)               :: 4,867
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 217
            CDSs (without protein)            :: 217
            Pseudo Genes (ambiguous residues) :: 0 of 217
            Pseudo Genes (frameshifted)       :: 91 of 217
            Pseudo Genes (incomplete)         :: 131 of 217
            Pseudo Genes (internal stop)      :: 49 of 217
            Pseudo Genes (multiple problems)  :: 48 of 217
            Pseudo Genes (short protein)      :: 3 of 217
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP024119.1.
            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..6079
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="JML285"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="JML285_P5"
                     /geo_loc_name="Japan"
                     /collection_date="2015"
     gene            join(5891..6079,1..1539)
                     /locus_tag="FFF71_RS25720"
     CDS             join(5891..6079,1..1539)
                     /locus_tag="FFF71_RS25720"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000012961.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin-like bacteriocin tRNase domain-containing
                     protein"
                     /protein_id="WP_040091419.1"
                     /translation="MSGGDGRDHNSGAHNTGGNINGGPTGLGGNGGASDGSGWSSENNP
                     WGGGSGSGVHWGGGSGHGNGGGNGNSGGGSNSSVAAVAFGFPALAAPGAGTLGIAVSGE
                     ALSAAIADIFAALKGPFKFSAWGIALYGILPSEIAKDDPKMMSKIVTSLPAETVTNVQV
                     STLPLDQATVSVTKRVTDVVKDTRQHIAVVAGVPMSVPVVNAKPTRTPGVFHASFPGVP
                     SLTVSTVKGLPVSTNLPRGITEYKGRTAVPAGFTFGGGSHEAVIRFPKESGQKPIYVSV
                     TDVLTPAQVKQRQDEENRLQQEWNDTHPVEVAERNYEQARAELDQANKDVARNQERQAK
                     AVQVYNSRKSELDAANKTLADAKAEIKQFERFAREPMAAGHRMWQMAGLKAQRAQTDVN
                     NKKAAFDAAAKDKSDADAALGAALERRKQKENKEKDSKDKLDKESKRNKPGKATGKGKP
                     VGDKWLDDAGKDSGAPIPDRIADKLRDKEFKSFDDFRKKFWEEVSKDPELSKQFKDSNK
                     TNIQKGKAPFARKKDQVGGRERFELHHDKPISQDGGVYDMDNIRVTTPKRHIDIHRGK"
                     /name="colicin-like bacteriocin tRNase domain-containing
                     protein"
     gene            1542..1802
                     /locus_tag="FFF71_RS25725"
                     /old_locus_tag="HmCmsJML285_5068"
     CDS             1542..1802
                     /locus_tag="FFF71_RS25725"
                     /old_locus_tag="HmCmsJML285_5068"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000412701.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="bacteriocin immunity protein"
                     /protein_id="WP_000420692.1"
                     /translation="MELKHSISDYTEAEFLEFVKKICRAEGATEEDDNKLVREFERLTE
                     HPDGSDLIYYPRDDREDSPEGIVKEIKEWRAANGKPGFKQG"
                     /name="bacteriocin immunity protein"
     gene            1864..2007
                     /locus_tag="FFF71_RS25730"
                     /old_locus_tag="HmCmsJML285_5069"
     CDS             1864..2007
                     /locus_tag="FFF71_RS25730"
                     /old_locus_tag="HmCmsJML285_5069"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000724569.1"
                     /GO_component="GO:0019867 - outer membrane [Evidence IEA]"
                     /GO_process="GO:0019835 - cytolysis [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin release lysis protein"
                     /protein_id="WP_001314446.1"
                     /translation="MKKITGIILLLLAVIILAACQANYIRDVQGGTVSPSSTAEVTGLA
                     TQ"
                     /name="colicin release lysis protein"
     gene            2504..3439
                     /locus_tag="FFF71_RS25735"
                     /old_locus_tag="HmCmsJML285_5070"
     CDS             2504..3439
                     /locus_tag="FFF71_RS25735"
                     /old_locus_tag="HmCmsJML285_5070"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011666805.1"
                     /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_059336724.1"
                     /translation="MSAALQYFEENLPLRPYHTDDLAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDREGAAIDWSDRNAPAPNITVKNPVNGHAHLLYALNIAVRTAPDASVKA
                     LKYAAAVERSLCEKICADVNYSGLICKNPFHLEWQVMEWREEAYTLDELADYLDLSASA
                     RRSIDKHYGMGRNCHLFEMTRKWAYRAIRQGWPAFSQWLDAVIQRVEMYNASLPVPLSP
                     AECRAIGRSIAKYTHRNFTPETFAQYVADTHTPEIQAKRGRKGGIAKGEAYDDKRFMAL
                     CMLENGYSQKAIAAMLEVSTRTIRNWKSGK"
                     /name="replication initiation protein"
     gene            complement(3633..4031)
                     /locus_tag="FFF71_RS25740"
                     /old_locus_tag="HmCmsJML285_5071"
     CDS             complement(3633..4031)
                     /locus_tag="FFF71_RS25740"
                     /old_locus_tag="HmCmsJML285_5071"
                     /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_001222916.1"
                     /translation="MRISNIEWLKKRIGFIRKLGEQTARQRQIIDLLDNEAGLTEQERK
                     LLHVLATAEKNDLQAQESERKQAVQKRIEGKKQRRERNHRLFLAAGLLIEAGLVDTKTG
                     ELCYKKDRILQALKEIKYDLETSPNPDA"
                     /name="hypothetical protein"
     gene            4208..5134
                     /locus_tag="FFF71_RS25745"
                     /old_locus_tag="HmCmsJML285_5072"
     CDS             4208..5134
                     /locus_tag="FFF71_RS25745"
                     /old_locus_tag="HmCmsJML285_5072"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221102.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobA/MobL family protein"
                     /protein_id="WP_001314449.1"
                     /translation="MATYHLSVKFGGKGQAANHADYIERKEKYRDRQDLEYSAHGNMPE
                     WARDNPSHFWQAADQFERANGSTYRELEIALPRELTAEQRLELVQDFVRQEAGERHAWS
                     FAIHNPKASIDGGEQPHAHIMMSQRVNDGIERTPEQYFRRYNARYPERGGAKKDSGSLT
                     LTQQKEQLRELRKRWEVKHNEHMRKHGFERGFIDCRTLKEQGIERRPEVHLGFEAAGRL
                     DDAQRHDIMQKRSEPDYSRHLEQARTVGHDIREWLDTPVKQHELVRRLQHDVAREHGFD
                     MRDRVSRQNRTEPERVKSPSRGFSMGF"
                     /name="MobA/MobL family protein"
     gene            5137..5670
                     /locus_tag="FFF71_RS25750"
                     /old_locus_tag="HmCmsJML285_5073"
     CDS             5137..5670
                     /locus_tag="FFF71_RS25750"
                     /old_locus_tag="HmCmsJML285_5073"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221103.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000168772.1"
                     /translation="MASTEEKLLTLLLSVEHLQHTAMEQQKAVADSLAVARETLRGYRD
                     ISDGVAKQVRDEVRNEVQKLDVAGLIGERISQDFQRLEESVANMKANADALNRDIATIH
                     SNIVQEYNTLKGYSWKWLGGVSVAFLVMFCVLGWGMKTMLDRNYNATAAVYQKVVTLED
                     KLAEKPVTGKSRKN"
                     /name="hypothetical protein"
     BGC             1..6079
                     /name="RiPP-like"
                     /gene="RiPP-like"
                     /tool="antismash"
     Typing          2505..3439
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.261"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          4209..5131
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.052"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 aatggcgggg ggaatggtaa ttccggtggt ggcagcaatt catccgtagc agcagtggca
       61 tttggttttc ctgctttggc agctcctggt gccggaacac tgggtatcgc cgtctctggt
      121 gaggctttat ctgcggcaat agcggatatc tttgcagccc tgaaaggtcc gtttaaattc
      181 agtgcatggg gtattgcgct ttacggcatt ctgccatctg aaatagcaaa agatgacccg
      241 aaaatgatgt caaagattgt gacgtcatta ccggcagaaa cagtaacaaa tgttcaggtc
      301 agtacacttc cgctggacca ggcaactgtt agcgtgacaa aacgtgtgac cgatgttgtg
      361 aaggacacac gacagcatat tgccgtagtt gcaggtgtac ctatgagtgt gcctgttgtg
      421 aatgctaaac caacacgtac cccaggtgta tttcacgcat catttcctgg tgtcccttct
      481 ctgacagtca gcacggtcaa aggtcttcct gtgtcaacaa accttccccg tggtattacg
      541 gagtataagg gccggactgc cgttcctgca ggatttacct ttggtggtgg ttcacatgaa
      601 gcggtgatcc gtttcccgaa agaaagtggg cagaagccga tttatgtatc agtgacagat
      661 gttcttaccc ctgcacaggt aaaacaacgt caggatgagg aaaatcgcct ccagcaggaa
      721 tggaatgaca cacatcctgt agaagtggct gaacgcaatt atgaacaggc ccgcgcagaa
      781 ctggatcagg ctaataaaga tgttgccaga aaccaggaac gacaggctaa agctgttcag
      841 gtttataatt ctcgtaaaag tgaacttgat gcagcgaata aaactcttgc tgatgcaaag
      901 gctgaaataa aacaattcga gcgatttgcc cgagaaccaa tggctgctgg tcaccgaatg
      961 tggcaaatgg cagggcttaa ggcccagcgg gcacagacgg atgtaaataa taagaaggct
     1021 gcatttgatg ctgctgcaaa agataagtct gatgctgatg ctgcgttagg tgctgcgctg
     1081 gaacgccgta agcagaagga aaataaagaa aaggactcta aggataaatt agataaggag
     1141 agtaaacgga ataagccagg gaaggcgacg ggtaaaggaa aaccagttgg tgataaatgg
     1201 cttgatgatg cgggtaaaga ttcaggagcg ccaattcctg atcgtattgc tgataagttg
     1261 cgtgataaag aatttaaaag ttttgacgat ttccggaaga aattctggga agaagtgtca
     1321 aaagatcccg agcttagtaa gcaatttaaa gacagtaata agacgaacat tcaaaaggga
     1381 aaagcacctt ttgcaaggaa gaaagaccaa gtaggtggta gggaacgctt tgaattacat
     1441 catgataaac caatcagtca ggatggtggt gtctatgata tggataatat cagagtgacc
     1501 acacctaagc gacatattga tattcataga ggtaagtaaa aatggaactg aaacatagta
     1561 ttagtgatta taccgaggct gaatttctgg agtttgtaaa aaaaatatgt agagctgaag
     1621 gtgctactga agaggatgac aataaattag tgagagagtt tgagcgatta actgagcacc
     1681 cagatggttc agatctgatt tattatcctc gcgatgacag ggaagatagt cctgaaggga
     1741 ttgttaaaga aattaaagaa tggcgagctg ctaatggtaa gccaggattt aaacagggct
     1801 aaaatatgaa tgccggttgt ttatggatga atggctggca ttctttcaca acaaggagtc
     1861 gttatgaaaa aaataacagg gattatttta ttgcttcttg cagtcattat tctggctgca
     1921 tgtcaggcaa actatatccg ggatgttcag ggcgggactg tatccccgtc atcaacagct
     1981 gaagtgaccg gattagcaac gcagtaaccc gaaatcctct ttgacaaaaa caaagcgtgt
     2041 caggctgatt ctgatgcgct tttttttgaa atgtcacaaa aattccatgc gggagatgag
     2101 agctaaaatc cccgtgcaga actttccacc cagggggaga aaacttgtca ttttgacctg
     2161 ttcgcccttc ggaacagtcg aaatcgatcg cgcatcgctt tcgtgcatag ttatgcaacg
     2221 ccctgaaaac gattctgacg cgtttttctg gtttggcctg gtgttttctt gtctttttgc
     2281 gttttttgcg ccagaaagcg actgagggcg ttttaagggg ggcgtacaac gggagttatg
     2341 gtaaatggat cggcttttcg ggaaggatcg acaggatttg ccgttgggtg tagtgtaagc
     2401 gactgaaaaa caaacgcccc tgaaatcatg tccagatccg gcaagattca acatgaaatg
     2461 cagagggcgt gtaggtcgca taacccggag agaatcgtaa cacatgagcg ccgcgcttca
     2521 atacttcgaa gaaaatttac ccctccgccc ctatcacacg gatgatctcg ctttcggcct
     2581 tcgtatctcc ggtaaagggc gtgcgcttct tgcacggtat atccagcaga accagcctca
     2641 tgcacagttc tggctggttt ttgacgttga ccgcgagggg gctgcgattg actggagcga
     2701 ccggaacgcc cccgcgccga acatcaccgt taaaaatcct gtgaacggac acgctcacct
     2761 gctctacgca ctcaacatcg ccgtgagaac cgcgcctgat gcctcggtta aggcgctgaa
     2821 atatgccgca gcggttgaac gttcgctgtg tgagaaaatt tgtgctgatg tgaactacag
     2881 cggcctgatt tgcaaaaatc cgttccacct ggaatggcag gtgatggagt ggcgagagga
     2941 agcctatacc ctcgatgaac tggctgatta tctcgatttg agcgcctcag cgcgtcgtag
     3001 catcgataaa cattacggga tggggcgaaa ctgccacctg ttcgaaatga cgcgcaaatg
     3061 ggcttacagg gcgattcgtc agggatggcc agcattctca cagtggcttg atgcggtgat
     3121 tcagcgtgtc gaaatgtaca acgcatcgct tcctgttccg ctttcaccag ctgaatgccg
     3181 ggctattggc aggagtattg cgaaatacac gcacaggaac ttcacgccgg aaactttcgc
     3241 acagtatgtg gctgatacgc acacgccaga aatacaggcc aagagaggca ggaaaggtgg
     3301 catcgctaaa ggcgaagcct acgatgacaa gcgtttcatg gcgctatgta tgctggagaa
     3361 tggatattct cagaaagcta ttgcggcgat gttggaggtt tctactcgaa ccattcgaaa
     3421 ctggaaaagc ggaaaatagc ctatatcaga taacagcgcc tttctggcgt ttttttgagc
     3481 cgtaggtctt ttgccgtttt tccccgttca gccctgcaat ggtgctgttt tccgcatgat
     3541 tgtgctggta gtgctcgccg cagtctcatg accgagcgta gcgagcgaat gagcgaggaa
     3601 gcaccaggga accggaacac ggatggaggc acttacgcgt ctgggtttgg ggatgtctcc
     3661 agatcgtact taatttcctt aagtgcctgt aatatcctgt cttttttata gcatagctcg
     3721 cctgtttttg tgtctaccag tcctgcttcg atcagtagcc cagccgcgag aaagagtcgg
     3781 tgattgcgtt ctcgtcgttg tttttttccc tcgattcgtt tttggaccgc ctgttttcgt
     3841 tcgctctcct gtgcctgtaa gtcgtttttt tccgctgttg ccagtacgtg gaggagtttg
     3901 cgttcctgtt ctgtgagtcc tgcttcgttg tcgagcaggt caataatctg tctctgtcgt
     3961 gcggtctgtt ctccgagctt cctgatgaat ccgatccgtt tcttcagcca ttcgatgttg
     4021 ctgatgcgca tgttcgtggt gctccctggt gtttttttgc ggtgtgttgt ggtcgtgcag
     4081 tatatcgctt gcggtcggcg ggtgcagggg gtatcttccg tgctaattcg taaaattaga
     4141 aggaagcgca cttatatgtt tctctccttc gtcgagaaac agtgcgctcc tgcggagggc
     4201 tgaaaccgtg gcaacctatc acctcagcgt taaatttggt ggcaaggggc aggctgcaaa
     4261 ccacgccgat tacatcgagc gcaaagagaa ataccgcgac cgtcaggatt tggaatattc
     4321 cgcacacgga aacatgccgg aatgggcgcg agataatccc tcacatttct ggcaggctgc
     4381 tgaccagttt gaacgtgcga acggttcgac ctatcgggaa cttgaaattg cattaccccg
     4441 tgaactgaca gcggaacagc gccttgaact ggtgcaggat tttgtacgtc aggaagctgg
     4501 cgaacggcac gcctggagtt ttgccattca caatccgaaa gcgagcattg acggcggcga
     4561 acagcctcat gcgcatatca tgatgagcca gcgtgtgaat gatggcattg aacgtacacc
     4621 ggaacagtat ttccggcgct ataacgccag gtatcccgag cggggaggtg cgaaaaagga
     4681 ttccggaagc ctgactctca ctcagcaaaa agagcagttg cgggaattgc gaaaacgctg
     4741 ggaggtgaag cacaacgaac atatgagaaa gcatggcttt gaaaggggct tcattgactg
     4801 ccggacgctg aaagaacagg gcattgaacg acgtcccgaa gtgcatctgg gttttgaagc
     4861 tgccggacgg cttgatgatg cccagcgtca tgacatcatg caaaaacggt ctgaaccgga
     4921 ctattcccgc catcttgaac aggcgcgaac ggtcgggcat gacatcaggg aatggctgga
     4981 cactccggtt aagcaacatg aactggtcag aaggctgcaa catgatgttg cgcgggagca
     5041 tggctttgac atgagagaca gagtgagcag acagaaccga actgaacctg aacgggttaa
     5101 atcaccgtca cgtggatttt ctatgggatt ctgaacatgg ccagcacaga agaaaaatta
     5161 ctcacgctcc tgttatcggt ggagcatctg caacataccg caatggagca acagaaagct
     5221 gttgctgatt ctctggctgt ggcaagggaa acacttcgcg gatatcggga tatttctgac
     5281 ggtgtggcaa aacaggtcag ggatgaagtc agaaacgagg tgcagaagct ggatgttgca
     5341 gggctgatag gtgagcgcat cagccaggat tttcagcggc tggaagagtc agtcgcaaac
     5401 atgaaggcaa acgcggatgc cctgaacagg gatattgcga caattcacag caatatcgtg
     5461 caggaataca acacccttaa agggtatagc tggaaatggc tgggtggggt gtcagtggct
     5521 tttctggtta tgttctgtgt gcttggatgg ggaatgaaaa caatgctcga caggaactac
     5581 aacgccacag cggcggtgta tcagaaagtt gtgacactgg aagataaact ggcggagaaa
     5641 cctgtcacgg gcaagagccg gaaaaactga cgcgcttcgc ttgtccaacg cctcacgacc
     5701 cgcgaaagga tttcgcgttc cgttcaccgt tttcatgagt gattcctccg aactgccaaa
     5761 aaatatcccc ccctgacttg acagaaaaaa taatggcgag tactttttga tctgtacata
     5821 aaaccagtgg ttttatgtac agtattaact atgtaattaa ttgttttaac gcttaaaaga
     5881 gggaattttt atgagcggtg gagatggacg cgaccacaac agtggcgcac ataacacagg
     5941 tggtaacatt aatggcggcc ctacggggct tggtggaaat ggtggggctt ctgacggctc
     6001 cggatggagt tcggaaaata acccatgggg tggcggttct ggtagtggtg ttcactgggg
     6061 aggtggctcc ggccatggc
//
