LOCUS       NZ_OY839924             3746 bp    DNA     circular CON 08-DEC-2023
DEFINITION  Escherichia coli isolate F1059 plasmid pF1059-3, complete sequence.
ACCESSION   NZ_OY839924
VERSION     NZ_OY839924.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMEA113543013
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1
  AUTHORS   Leclercq,S.
  TITLE     Direct Submission
  JOURNAL   Submitted (30-OCT-2023) INRAE, ISP, Centre INRAE Val de Loire, Site
            de Tours, Bat 213, 37380 Nouzilly, France
COMMENT     ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 12/08/2023 12:30:51
            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)                     :: 180
            CDSs (total)                      :: 180
            Genes (coding)                    :: 146
            CDSs (with protein)               :: 146
            Genes (RNA)                       :: 0
            tRNAs                             :: 0
            ncRNAs                            :: 0
            Pseudo Genes (total)              :: 34
            CDSs (without protein)            :: 34
            Pseudo Genes (ambiguous residues) :: 0 of 34
            Pseudo Genes (frameshifted)       :: 11 of 34
            Pseudo Genes (incomplete)         :: 28 of 34
            Pseudo Genes (internal stop)      :: 5 of 34
            Pseudo Genes (multiple problems)  :: 9 of 34
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            OY839924.1.
            Complete plasmid sequences of E. coli strain F1059.
            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..3746
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /isolate="F1059"
                     /db_xref="taxon:562"
                     /plasmid="pF1059-3"
     gene            join(3735..3746,1..906)
                     /locus_tag="U0072_RS00880"
                     /old_locus_tag="FGAF1059_47060"
     CDS             join(3735..3746,1..906)
                     /locus_tag="U0072_RS00880"
                     /old_locus_tag="FGAF1059_47060"
                     /EC_number="2.1.1.-"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0008170 - N-methyltransferase activity [Evidence IEA]"
                     /GO_process="GO:0009307 - DNA restriction-modification
                     system [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="site-specific DNA-methyltransferase"
                     /protein_id="WP_016243916.1"
                     /translation="MLKEIPLLDEIEHNSITNGDSIELIKKVQTQSAHLILSDIPYGIG
                     ADDWDVLHKNSNNAYLGSSPAQKSAGAIFKKRGKPINGWSDADRKIPLEYQQWCEEWAS
                     EWYRTLKPGASAIIFAGRRFSHRCICAMENAGFNLRDIIAWMRTKAPHRAQRLSCVYER
                     RGDKYNTEKWEGWRVGNLQPTFEPILWFSKPYKIGGTIADNVLLHGVGAYNQDAFVARN
                     GKPENVIHAGFASKESGLHPTQKPISLMKTLIELTTQEGQLVIDPFSGSGSTLVAAKEL
                     GRSYIGFELNPAYVEISKKRLKDK"
                     /name="site-specific DNA-methyltransferase"
     gene            complement(907..1833)
                     /locus_tag="U0072_RS00885"
                     /old_locus_tag="FGAF1059_47070"
     CDS             complement(907..1833)
                     /locus_tag="U0072_RS00885"
                     /old_locus_tag="FGAF1059_47070"
                     /EC_number="3.1.21.-"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000362418.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="HindIII family type II restriction endonuclease"
                     /protein_id="WP_053531176.1"
                     /translation="MELGDFKFINKDAVIRRRYWIDEIVKLSGHFVNDSSRVENEIIDE
                     VKKSGNQALLDHLRLCTAIPESYGHDSSEEKLYSKYTDALISECFKYLGLNSIVLTERA
                     DAADVEVVCDNYSFVADAKVFRLSRTAKNQKDFKVQAMDGWRNTKDFAMVVCPIYQLPT
                     KSSQIYQQAILRNVCIFTYTHLAVLIRYSSIATTEDSKKILSDIFKSVSLLNPSKDSVQ
                     YWVNINRTMLNYDDRIAALWADEKLATTEGIAVSKKMAIEFLSSERTRMLMMTKDEAVN
                     ALIKMHKIDSRIDQINKVTDNNILSLK"
                     /name="HindIII family type II restriction endonuclease"
     gene            complement(2746..2937)
                     /locus_tag="U0072_RS00890"
                     /old_locus_tag="FGAF1059_47080"
     CDS             complement(2746..2937)
                     /locus_tag="U0072_RS00890"
                     /old_locus_tag="FGAF1059_47080"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041614.1"
                     /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_001041614.1"
                     /translation="MNKQQKTAVNMAKFIQDQSLLLLDRLNELDLDHEADFCEKLHEDA
                     ERLYRSLSARLNEQQDGA"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            3355..3513
                     /locus_tag="U0072_RS00895"
     CDS             3355..3513
                     /locus_tag="U0072_RS00895"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001403044.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_053893437.1"
                     /translation="MHEPPVQPDCCACSGNYRLESNPERHDKTPLAAAIGIWFTEQRGA
                     YKHTQSS"
                     /name="hypothetical protein"
     Typing          3175..3652
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.776"
                     /coverage="91.0"
                     /evalue="0.0"
ORIGIN
        1 attccattgc ttgatgagat agaacacaac tccataacaa atggtgactc aatcgagcta
       61 ataaaaaaag tacaaactca atccgcacac ttgatactga gtgacatccc ttacggaata
      121 ggtgctgatg attgggatgt actacataaa aactcaaaca atgcctacct aggttcaagc
      181 cctgcacaaa aatcggctgg agccattttc aaaaaaagag gaaagcctat aaatggctgg
      241 tcagatgcag atagaaaaat acctttagag tatcagcaat ggtgtgaaga gtgggcgagt
      301 gagtggtatc gaactttaaa accaggagct agtgccatta tttttgctgg tagaagattt
      361 tcacatagat gtatttgtgc aatggaaaat gctggattta acctcagaga tataatcgcc
      421 tggatgagaa caaaagcacc tcatcgcgca caaaggctaa gctgcgtata tgaaaggcgt
      481 ggcgacaaat ataacacaga aaaatgggaa ggctggagag tgggtaactt acaaccaaca
      541 tttgagccta tactatggtt ttcaaaacct tataaaatag gaggtaccat tgctgataac
      601 gttctattgc atggcgtggg tgcatataac caagacgcgt tcgtagcgag aaatggaaaa
      661 ccggaaaatg taatacatgc aggttttgcg agcaaggaaa gcggattaca cccaacgcag
      721 aaacctattt ctctgatgaa aaccctaata gaactaacca ctcaagaagg tcagctagta
      781 atagatccat ttagtggtag cggttcaact cttgttgccg caaaagagct gggtagaagc
      841 tatataggct ttgaacttaa cccagcatat gtagaaataa gcaaaaaaag attaaaagac
      901 aaataattat ttaagtgaca gtatgttatt atctgtcact ttatttattt ggtctatcct
      961 gctatctatt ttatgcattt ttatcagcgc gttgacagcc tcatctttgg tcatcattaa
     1021 cattcttgta cgttcagaag ataagaattc gatagccatt ttttttgaaa cggcaatgcc
     1081 ctcagttgtg gctagctttt catcagccca aagggcagct atcctgtcat catagtttag
     1141 cattgttcta tttatattaa cccaatattg aacactatct ttgctggggt taagtaaaga
     1201 tacagattta aatatatcac taagaatttt tttgctatct tcagttgttg caatacttga
     1261 atatcttatc agtacagcca gatgtgtata tgtaaaaata caaacattgc gcaatatggc
     1321 ttgctgatat atttgacttg atttagttgg tagctgatat attgggcaga ccaccattgc
     1381 aaagtctttg gtatttctcc aaccatccat agcttgaact ttaaaatcct tttgattttt
     1441 ggctgttcta cttaaacgaa atacctttgc atcggctaca aatgaatagt tatcgcaaac
     1501 aacctcaaca tcagctgcat ctgccctttc ggttaaaaca atgctattta accctaagta
     1561 tttaaagcac tctgatatta gtgcatctgt atactttgag tacagcttct cttcacttga
     1621 atcatgacca tatgactcag gtattgctgt gcataatctc aggtgatcta gcaacgcttg
     1681 atttccggac ttcttaacct catcgattat ttcattttca accctacttg aatcgttaac
     1741 aaaatgaccg cttagtttta ctatttcatc aatccagtag cgccttctta ttactgcatc
     1801 tttattaatg aatttgaaat cacctaattc catttttaat tcccaatatt attgttcaat
     1861 aactcaatat aatttctcga tcataacaac ttttttacct ggataataat acctccatca
     1921 gttatgtggc tagacattca cttgatttac cataacatcc gttgcgtgca ccgcctgaga
     1981 ggctctcagg gcgtttctga cgggaaaccg gtaaaacagg caacaaacca cccgaaaacc
     2041 cgccagaaac gcgcaggctc tgtttttacg gcatgcatga gtatgcgcac aagtgcatag
     2101 cgcggaaatt cacgccattc agccggggta agtcctgttt ccgatgttct tcttacccga
     2161 aaacggtgaa cggggacgca atttattgcg tggccgtgag gcgttgccgg cacagccgga
     2221 aaaaccattt tcagcacgtg caggaggccc aggaagaggg ggcggatgta cgaatagctc
     2281 agaggtcaga tctgacgtaa aaatgatgta aaagtgatgt acttttgatg taattctgtt
     2341 gtacacccgc gatctgacgt aaaagtgatg taattttgat gtacttttga tgtaattctg
     2401 ttgtacaccc gcgttctggg gtaaaagcag atgcaatttt gtagtttatg tgtagtcgct
     2461 gaacccatag ggtcatacga gcatgaccct ttcccggaaa aggacgcttt ttagccagaa
     2521 tcatccttaa cctgcggcgc cagcactcgg gagtggtcgt tttatatact aaaaaatgac
     2581 atacacctaa cgcagctgcg attttcatcg caacttcatg aaaagtaaat aaaaaataaa
     2641 aaacacaggg attctgggta ttaccggggt aataatgtta agcgctaaca caatgaaaat
     2701 taaggcgatg ccggtattac tccggtaata cccagaacgg agccattacg caccgtcctg
     2761 ctgctcattc aggcgcgctg acaggcttcg gtaaaggcgt tccgcatcct catggagttt
     2821 ctcgcagaaa tcagcctcat gatccagatc cagctcatta agcctgtcca gaagaagcag
     2881 ggactgatcc tggatgaatt tagccatgtt aacggcagtc ttttgttgtt tgttcatgaa
     2941 agccccggcg cgaaagtgct tattgtacgt tctgatggtt ttccgcttcc tcgctcattc
     3001 gctcactccg ttcggtcatg agtctgcggc gagcggaggg aggataagca gataacgtaa
     3061 cggtaagcat aacgaaagct aaggacaagg gcgaaaaggc cacgccccgc cggggcgttt
     3121 ttccataggc tccgcccccc tgacaagcat cacagaatct gacgctcaaa tcagtggtgg
     3181 cgaaacccga caggacttaa agataccagg cgtttccccc tggtggctcc ctcgtgcgct
     3241 ctcctgttcc tgcctttcgg tttaccggtg tcattccgct gttatggccg cgtttatctc
     3301 attccacgcc tgacactcga ttccgggaag gcagttcgct ccaagctgga ctgtatgcac
     3361 gaaccccccg ttcagcccga ctgctgcgcc tgttccggta actatcgact tgagtccaac
     3421 ccggaaagac acgacaaaac gccactggca gcagccattg gtatctggtt tacggagcag
     3481 agaggcgcgt acaagcatac acagagttct tgaagtgttg acctgactac ggctacactg
     3541 gaaggacaga tttggtcact gcgctccgtt taagccagtt accacggttc agaagttccc
     3601 caactaactg aaccctgaaa aaaccgcctc cccaggcggt tttttctttt caaaaggcta
     3661 cgacgaaagg ttatcctgcg tcaagatact ttaacagtta taatgaagtg aaataatcgc
     3721 gggtaaggtg ttgaatgtta aaagaa
//
