LOCUS       NZ_CP071524             5627 bp    DNA     circular CON 18-DEC-2023
DEFINITION  Escherichia coli strain UPEC129 plasmid p2_UPEC129, complete
            sequence.
ACCESSION   NZ_CP071524
VERSION     NZ_CP071524.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16443699
            Sequence Read Archive: SRR12831697, SRR12831696
            Assembly: GCF_017356665.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5627)
  AUTHORS   Auvray,F., Perrat,A., Arimizu,Y., Chagneau,C.V., Bossuet-Greif,N.,
            Massip,C., Brugere,H., Nougayrede,J.P., Hayashi,T., Branchu,P.,
            Ogura,Y. and Oswald,E.
  TITLE     Insights into the acquisition of the pks island and production of
            colibactin in the Escherichia coli population
  JOURNAL   Microb Genom 7 (5) (2021)
   PUBMED   33961542
REFERENCE   2  (bases 1 to 5627)
  AUTHORS   Auvray,F., Perrat,A., Arimizu,Y., Chagneau,C.V., Boussuet-Greif,N.,
            Massip,C., Brugere,H., Nougayrede,J.-P., Hayashi,T., Branchu,P.,
            Ogura,Y. and Oswald,E.
  TITLE     Direct Submission
  JOURNAL   Submitted (08-MAR-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 Date                     :: MAY-2019
            Assembly Method                   :: Unicycler v. MAY-2019
            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                   :: 12/17/2023 10:34:42
            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)                     :: 5,081
            CDSs (total)                      :: 4,958
            Genes (coding)                    :: 4,764
            CDSs (with protein)               :: 4,764
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 95
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 194
            CDSs (without protein)            :: 194
            Pseudo Genes (ambiguous residues) :: 0 of 194
            Pseudo Genes (frameshifted)       :: 75 of 194
            Pseudo Genes (incomplete)         :: 125 of 194
            Pseudo Genes (internal stop)      :: 41 of 194
            Pseudo Genes (multiple problems)  :: 44 of 194
            Pseudo Genes (short protein)      :: 4 of 194
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP071524.1.
            Bacteria and source DNA available from Microbiology, Graduate
            School of Medical Sciences, Kyushu University.
            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..5627
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="UPEC129"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="p2_UPEC129"
                     /geo_loc_name="Japan"
                     /collection_date="2011"
                     /collected_by="Microbiology, Graduate School of Medical
                     Sciences, Kyushu University"
     gene            complement(556..747)
                     /locus_tag="J3P56_RS25030"
                     /old_locus_tag="J3P56_25030"
     CDS             complement(556..747)
                     /locus_tag="J3P56_RS25030"
                     /old_locus_tag="J3P56_25030"
                     /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            811..1134
                     /locus_tag="J3P56_RS25035"
                     /old_locus_tag="J3P56_25035"
     CDS             811..1134
                     /locus_tag="J3P56_RS25035"
                     /old_locus_tag="J3P56_25035"
                     /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_000955999.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            1343..>1774
                     /locus_tag="J3P56_RS25460"
                     /pseudo=""
     CDS             1343..>1774
                     /locus_tag="J3P56_RS25460"
                     /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            1812..2342
                     /locus_tag="J3P56_RS25045"
                     /old_locus_tag="J3P56_25045"
     CDS             1812..2342
                     /locus_tag="J3P56_RS25045"
                     /old_locus_tag="J3P56_25045"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001673158.1"
                     /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_001673158.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNDEFRKLEESVNRELTSNE
                     SLIRNAINDHTTALKELLERYQKTTVDTMDAHWKTVLKMSVKRWLWLIIVSVLMFATTG
                     SLLWYQGMKINANMNILREQKESLEKLNAKTWGVRYHEDSNGRFLVLPKGMKAETNWTK
                     DNGKLNAVRLVQE"
                     /name="MbeB family mobilization protein"
     gene            2349..2582
                     /locus_tag="J3P56_RS25050"
                     /old_locus_tag="J3P56_25050"
     CDS             2349..2582
                     /locus_tag="J3P56_RS25050"
                     /old_locus_tag="J3P56_25050"
                     /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_000137437.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLNEWENAFVELQKMFSLTQRDNA
                     MLNGRVMQLSQQVQHLSERTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            3063..4115
                     /locus_tag="J3P56_RS25055"
                     /old_locus_tag="J3P56_25055"
     CDS             3063..4115
                     /locus_tag="J3P56_RS25055"
                     /old_locus_tag="J3P56_25055"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001557502.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_113233994.1"
                     /translation="MNLQQRINKLPQLSSSFSFGKDIDNIHSFIFNETSKDKIEDLLRK
                     WVSGNQPCVFGKLASKKIKGLDFHLSIVNSPQLYNDDGHLFDFLRNERVRFKERARRGE
                     VSAHLIYFIHPQLAFARPSEELVDIQKYICSLHMPECYPIKEDVIYTESVPFQDKDGLK
                     IYKAGVNVFYSSAHRTRNHDRRIPGGILISVNAPGHFMRLAIEKGFYKDQEQALADIRN
                     MTIQSVGKGGYSHPEGISTTWHSESNLDRFGCPVHTGNSSYYSGFYHTDVLIPGELTKD
                     ERLLHEIESSDPMIFNWNVLFYVSLEEFPIDDPYYGEFIGIPVDDASMFFNSFQPRKFE
                     NKPLYEKEDD"
                     /name="hypothetical protein"
     gene            4117..4983
                     /locus_tag="J3P56_RS25060"
                     /old_locus_tag="J3P56_25060"
     CDS             4117..4983
                     /locus_tag="J3P56_RS25060"
                     /old_locus_tag="J3P56_25060"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001335763.1"
                     /GO_function="GO:0005215 - transporter activity [Evidence
                     IEA]"
                     /GO_process="GO:0055085 - transmembrane transport [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DMT family transporter"
                     /protein_id="WP_001335763.1"
                     /translation="MIKGMLFAFLAAFSWGAAIVMSKKGVEELDAGGVFFWQICSAVIL
                     SWIVLFIKRKKLPLNSKAILAYATGVFEPFLAYTFTLYGLYFISAGSASIIFSLESVFI
                     LVLSVLICSVKINSPQYFILFLIGAIVGSILVALPDISNGSNNIVGYCLVVAGVLSAAF
                     YVVISSRLIKSFEPITLLSGQLTFSLILSSLFIFISKSSIYLPLESVIIVFSSGILQYF
                     LAFCFYLNSLRWLPVHLAGIMLYFIPLVALFLSWLFLDEQFTFLQGVGFIVTVLSVYFL
                     NRKYSEE"
                     /name="DMT family transporter"
     Typing          384..471
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.876"
                     /coverage="100.0"
                     /evalue="3.19e-37"
     Typing          5367..5554
                     /name="rep_cluster_2401"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="4.63e-94"
     Typing          1125..2686
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ggaaacggtg atgatcttta agccacgtcg ggtttcgcca ccgctggcgg atttcatggt
       61 tgagccgcaa ggctcccaca gatgcaccga aaaagtgtct gttttgtgaa gtccgtcagg
      121 ggggcggagc ctatggaaaa agcgcctccg gcgcggcctt tcccggggtt tcgttttttg
      181 cgcacatgtt ctttcctggt ttatccccgg gttctgtgga taacagggtt agcgtttttg
      241 agaaaggaga gtccgctcgc cgcagccgaa cgaccgagcg tagcgagtca gtgagcgagg
      301 aagcggaaga gcgcctgaac tggcattttc tccttacgca tctgtgcggc atttcacacc
      361 ggacatggcg cacttttcat acaatccgca ctgatgccga atggttaagc cagtatacac
      421 tccgctatcg ctacgtgact gggtcagggc tgcgccccga cacccgctaa aacctgctga
      481 cgcgccctga cgggcttgtc agctcccggc atccgctcac agacaagctg tgaccgtctc
      541 cgggagctgc atgtatcaga gattttcacc gtcatccccg aaacgtgcga ggcagctgcg
      601 gtaaagctca tcggcgtggt cgtgaagcga ttcacaaata tcggcctgtt catctgcgtc
      661 cagttcgttg agcttctcca gcagcgttaa tgtctggctt ctgataaagc gggccatgtt
      721 aagggcggtt ttttcctgtt tagtcactga tgcctccgtg taagggggat ttctgttcat
      781 ggggtaatga taccgatgaa acgcgagagg atgctcacaa tacgggttac tgatgatgaa
      841 catgcccggt tacttgaacg ctgtgagggt aaacaactgg cggtatggat gcggcgggtc
      901 tgcctggggg agccggttgc ccgttccgga aaactgccga cactggcacc gccgttactg
      961 cgtcagctgg ccgccatcgg aaataacctg aatcagacag cccgtaaggt gaacagcggg
     1021 cagtggtctt ccggtgaccg ggttcaggtg gtggccgcac tgatggccat cggggatgag
     1081 ctgcgccggc tgcgtctggc cgtcagggaa cagggggcgc gggatgatag ttaaatttca
     1141 tgccagggga aaaggtggtg gcagtggtcc ggttgattac ctgctgggga gggagcgtaa
     1201 ccgcgaaggc gcaacggtgc ttcagggtaa tccggaagaa gtccgggaac tcatcgatgc
     1261 cacgccattt gcgaagaaat acacgtccgg tgttctgtcg ttcgcggaga aggagctgcc
     1321 gccgggagga cgtgaaaaag tgatggcgag ctttgagcgt gtactgatgc ccggtctcga
     1381 aaaaaatcag tacagcatcc tgtgggtgga gcaccaggac aagggacggc ttgagctgaa
     1441 ttttgtcatt ccgaacatgg agctacagac cggaaaacgc ctccagccgt actacgaccg
     1501 cgcagacagg cctagaattg atgcctggca gacgctggtg aatcaccatt acgggctgca
     1561 tgacccgaac gccccggaga accgccggac gctgaccctt cctgataacc tgccggaaac
     1621 gaaacaggcg cttgctgagg gcgtcacacg cgggatagac gcgctttacc atgccggaga
     1681 gataaaaggc cgtcaggatg tgattcaggc gctcacagag gcggggcttg aagtggtcag
     1741 ggtgacgcga agcagtatca gcattgcaga cccgaacggc gggaggaata tcagactgaa
     1801 aggagcgttt tatgagcaat cttttacaga cgggcgcgga gttcgagaaa aagctgaaag
     1861 agagagccga atctacagag aaaatgctga acgacgagtt caggaagctc gaagaatctg
     1921 taaacaggga actgacctca aacgaatctt taatcaggaa cgctatcaac gaccatacaa
     1981 cagccctgaa agaactgctg gagaggtatc agaaaacgac cgtcgatacg atggacgcgc
     2041 actggaaaac cgtactgaaa atgagcgtga aacgctggct gtggctgatt atcgtctcag
     2101 tactgatgtt tgccacgacc gggagtctgc tgtggtacca gggcatgaag ataaacgcga
     2161 atatgaatat tctccgcgag cagaaagaga gtctggagaa gctgaacgcg aagacatggg
     2221 gcgtgcgtta tcacgaggac agcaacggac gttttctggt gttgccgaag gggatgaaag
     2281 ccgaaacgaa ctggacgaag gacaacggca aactgaacgc agtgagactg gtgcaggagt
     2341 gacagagcat gacggagctg gaaagacatt tgctgaacgc attagagcaa ctgcaacagg
     2401 actatatgca gcggctgaac gaatgggaga acgccttcgt ggaattgcag aaaatgtttt
     2461 cgcttacgca acgggacaac gcgatgctga acgggcgagt catgcagttg agtcagcagg
     2521 tgcagcactt gagcgagcgg acagaacgct tgagccagtt atacagcgag aacaggagat
     2581 aagggatgaa cggctgatgc aggaacgcga acatgagtta tctctggagc gggagcgtca
     2641 gccggaaatc caggagcgga cactggatgg cccttcgctg ggatggtgaa accatgaaaa
     2701 atgacgtgtt cagtggatta aggcgggcta atgtggcctg tagcatctgg ttgcataggt
     2761 attcatgcgg ttaaaattta tcaggtgcga tcgcggcagt ttttcgggtg gtttgttgcc
     2821 atttttacct gtctgctgcc gtgatcgcac cgaacgcgtt ttggcggtgc gtacaatgcg
     2881 acgttatggt aaatggagcg gattttcagg aaggagtgat actaacaact cgaacactgt
     2941 gcaaataatg atttttttaa aatatcggta acgataataa attatttcgt tttacgccgg
     3001 taataaatat aatgtagttt cagtatataa aaaaatatat gaggtgtctt gtgggagctt
     3061 tcatgaatct tcaacaacgt ataaataaac taccacaatt atcatccagt ttttcatttg
     3121 gaaaagatat tgataatatt cattcattta tctttaacga aacttctaaa gataaaattg
     3181 aagatttact aagaaaatgg gtgtcaggca atcagccctg tgtatttggt aaattggcaa
     3241 gcaagaaaat taaagggctt gatttccatt tatctattgt aaatagcccc caactatata
     3301 atgatgatgg tcatttgttt gattttttgc gtaatgaaag agttcgtttt aaagaacgcg
     3361 caagaagagg agaggtcagt gcgcatctca tttattttat tcatccacaa cttgcctttg
     3421 ctcgtccatc agaagagtta gtggacatac aaaaatatat ttgttcgctg catatgccag
     3481 agtgctatcc aataaaagag gatgttattt atactgaaag cgtaccattt caggataaag
     3541 atgggctaaa aatatataag gctggtgtta atgtttttta ctcttctgct catagaacaa
     3601 gaaatcatga tagaagaata ccagggggaa tacttatttc tgtaaatgcc ccggggcatt
     3661 ttatgaggct ggcgatagaa aaaggtttct ataaagatca agaacaagcg ttagcggata
     3721 ttcgtaacat gactattcag tctgttggta agggtgggta ttcacatccg gaagggattt
     3781 ctacaacatg gcattcagaa tctaatttgg atcgttttgg atgcccagtg cacaccggta
     3841 atagttctta ttacagcggt ttttatcata ctgatgtatt aattccagga gaattaacta
     3901 aggatgaaag attgctccat gaaatagaaa gtagtgatcc aatgatcttc aactggaatg
     3961 tattgtttta tgtttcatta gaagagtttc ctatagatga tccttattat ggagagttta
     4021 ttggtattcc tgtagatgat gcatctatgt tttttaactc ctttcaacca aggaaatttg
     4081 aaaacaaacc cctttatgag aaagaggatg attaatatga ttaaaggaat gctttttgct
     4141 tttttagcag cgttctcatg gggggcagct atcgtaatga gcaaaaaagg agttgaagaa
     4201 ctagatgccg gaggggtgtt tttctggcag atttgtagtg cagtaatact atcttggata
     4261 gttcttttta taaaaagaaa aaaactccca ttaaactcaa aagcgatact tgcttatgcg
     4321 acaggcgttt ttgaaccatt cttagcgtat acttttacac tctacggact ttattttatt
     4381 tcagcaggaa gcgcatcaat tattttttca cttgaatcag tgtttatatt ggtgttgtct
     4441 gttcttattt gctcagttaa aattaattcc ccgcaatatt ttatattgtt ccttataggt
     4501 gcaattgttg gcagtatttt ggtagccttg ccagacatca gtaatggatc gaataatatt
     4561 gttggatatt gtcttgttgt tgccggtgtg ttatcggcag cattttatgt tgttatatcg
     4621 tctcgcctta ttaaatcgtt tgagcctatc acattattga gcggacagtt gacattctcc
     4681 cttatactgt catcgctctt tatttttata tctaaatcat caatttatct tccgttggaa
     4741 tccgtgatta ttgttttttc atctggaata ttacaatatt ttttagcttt ttgtttttac
     4801 ttgaactcct tgcgttggct cccagttcat ttggcaggga taatgttgta ctttattccg
     4861 ctagttgcat tatttttgtc atggttgttt ttggatgaac aattcacatt cttacagggg
     4921 gtaggattta ttgtaactgt gctaagtgta tattttctta acagaaaata ctcagaggag
     4981 taacattctg ttcaggattg ccccccggcc tccatcgata ccgtgccaaa tgcacgtaaa
     5041 aaacgggagc gtttctggtg tcggaatgta accaaggggg tcagaggcgc gctaaaacgc
     5101 tctcagggga gtcaaataga gacgtttgta acaaaaagat caaaggatcc tcttgagatc
     5161 ctttttttct gcgcgtaatc tgctgcctgt aaacgaaaaa accgccttgc agggcggttt
     5221 gatcgaaggt taagtcagct tgcagactgc ttaaccaggt aactgtctta tgcgagacga
     5281 gtcaccaaaa ttgttcttct agtgtagccg cactccggca gccacttcaa gtactctcta
     5341 aatatctcgc acatgacttt taccaatggc tgctgccagt ggcgctttgt ggtgtctttt
     5401 ccgggttgga cccaagagaa cagttaccgg agaaggcgca gcagtcgggc tgaacggggg
     5461 gttcctgcat acagcccagc ccggagcgaa ctgcctaagt cgccccgaga taccagaaga
     5521 cgtgagctat gagaaagcgc cacgtgtccc gtaagggaga aaggcggaaa aggtatccgg
     5581 taatcgatat ggcgggaacg tgggggcgca ggagggagcg attcacc
//
