LOCUS       NZ_CP147042             2994 bp    DNA     circular CON 22-APR-2024
DEFINITION  Escherichia coli strain 21F61 plasmid p21F61_5, complete sequence.
ACCESSION   NZ_CP147042
VERSION     NZ_CP147042.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN39992807
            Assembly: GCF_038396565.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 2994)
  AUTHORS   Gomi,R.
  TITLE     Genomic analysis of environmental Escherichia coli carrying
            transferable quinolone resistance determinants
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2994)
  AUTHORS   Gomi,R.
  TITLE     Direct Submission
  JOURNAL   Submitted (05-MAR-2024) Department of environmental engineering,
            Kyoto University, KyotoDaigakuKatsura, Nishikyo-ku, Kyoto-city
            615-8540, Japan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Flye v. 2.9.1
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 150x
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_038396565.1-RS_2024_04_20
            Annotation Date                   :: 04/20/2024 18:26:42
            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)                     :: 4,859
            CDSs (total)                      :: 4,740
            Genes (coding)                    :: 4,562
            CDSs (with protein)               :: 4,562
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 178
            CDSs (without protein)            :: 178
            Pseudo Genes (ambiguous residues) :: 0 of 178
            Pseudo Genes (frameshifted)       :: 73 of 178
            Pseudo Genes (incomplete)         :: 128 of 178
            Pseudo Genes (internal stop)      :: 31 of 178
            Pseudo Genes (multiple problems)  :: 48 of 178
            Pseudo Genes (short protein)      :: 4 of 178
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP147042.1.
            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..2994
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="21F61"
                     /isolation_source="river water"
                     /db_xref="taxon:562"
                     /plasmid="p21F61_5"
                     /geo_loc_name="Japan"
                     /collection_date="2021"
                     /collected_by="Fumie Adachi"
     gene            complement(63..362)
                     /locus_tag="WAZ52_RS24275"
                     /old_locus_tag="WAZ52_24275"
     CDS             complement(63..362)
                     /locus_tag="WAZ52_RS24275"
                     /old_locus_tag="WAZ52_24275"
                     /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_023281092.1"
                     /translation="MATATNFDAWLDDVDGDYEEVMALYDSVQNVSDMGLYQCVEGGRG
                     DAWVVSSNHHPEALFLASAVARDTFLKLIRERLCGGEDVDSWYGFQRNISNDHS"
                     /name="hypothetical protein"
     gene            complement(1277..1468)
                     /locus_tag="WAZ52_RS24280"
                     /old_locus_tag="WAZ52_24280"
     CDS             complement(1277..1468)
                     /locus_tag="WAZ52_RS24280"
                     /old_locus_tag="WAZ52_24280"
                     /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_021314601.1"
                     /translation="MNKQQKTAVNMAKFIQDQSLLLLDRLNDLDLDHEADFCEKLHEDA
                     ERLYRSLSARLNEQQDGA"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1904..>1984
                     /locus_tag="WAZ52_RS24285"
                     /old_locus_tag="WAZ52_24285"
                     /pseudo=""
     CDS             1904..>1984
                     /locus_tag="WAZ52_RS24285"
                     /old_locus_tag="WAZ52_24285"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001333247.1"
                     /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="replication initiation protein"
                     /name="replication initiation protein"
     gene            complement(2258..2986)
                     /locus_tag="WAZ52_RS24290"
                     /old_locus_tag="WAZ52_24290"
     CDS             complement(2258..2986)
                     /locus_tag="WAZ52_RS24290"
                     /old_locus_tag="WAZ52_24290"
                     /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_157919132.1"
                     /translation="MALMVTRRYLLGGEYPSEEFVQASLEKYFFRQGFDIDTGSYIDLI
                     CRDKESRDVVWHIEVKGKTSQPGLDFRTCLGQLVQRMTKDNINYAIAVPRIKQYERLIE
                     ETSILAVSKLNLHWIFVGPDGSVTIKEPDSSTMKNGNGNGNGREVSLVNGGFKRFIPGD
                     FMPTCSYGKAPVVFKSSRREMWDWLDDFVISNGVIPSIADIKEEAESRGGKWTLSNVKI
                     EYQFWKIYHLYKGHFFYQSE"
                     /name="hypothetical protein"
     Typing          1636..2031
                     /name="rep_cluster_2370"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.462"
                     /coverage="92.0"
                     /evalue="2.95e-159"
ORIGIN
        1 cgcatcctat ttactataac gtcatatttt aagagttcct acaaagggaa ctctctgtac
       61 gattacgagt gatcattcga tatatttcgt tgaaatccat accatgaatc aacatcttcg
      121 ccgccacata gcctttctct aatcaatttg aggaaagtat ccctagccac agctgatgct
      181 agaaaaagag cttctggatg atgattagag ctcacgaccc aagcatcacc ccgaccaccc
      241 tcaacacact gatacaaccc catatcactt acattctgaa cggaatcata aagagccata
      301 acctcctcat aatcgccatc aacatcatct aaccacgcat caaaattagt agcagtcgcc
      361 atgccaatcc tccatttttt agttttcagg agttaattta catagtgata ggggctgtta
      421 agcaaataag tttttacctt ttttgcctca tgctctaaaa gtgagcaaga caggcattta
      481 ccataacgcc tcattacgcg caccgctcag acggcctgag cgcgtttctg acgggaaacc
      541 ggtaaaacag gcaacaaacc acccgaaaac ccgccagaaa cgcgcaggct ctgtttttac
      601 ggcatgcatg agtatgcgca caagtgcata gcgcggaaat tcacgccatt cagccggggt
      661 aagtcctgtt tccgatgttc ttcttacccg aaaacggtga acggggacgc aatttattgc
      721 gtggccgtga ggcgttgccg gcacagccgg aaaaaccatt ttcagcacgt gcaggaggcc
      781 caggaagagg gggcggatgt acgaatagct cagaggtcag atctgacgta aaaatgatgt
      841 aaaagtgatg tacttttgat gtaattctgt tgtacacccg cgatctgacg taaaagtgat
      901 gtaattttga tgtacttttg atgtaattct gttgtacacc cgcgttctgg ggtaaaagca
      961 gatgcaattt tgtagtttat gtgtagtcgc tgaacccata gggtcatacg agcatgaccc
     1021 tttcccggaa aaggacgctt tttagccaga atcatcctta acctgcggcg ccagcactcg
     1081 ggagtggtcg ttttatatac taaaaaatga catacaccta acgcagctgc gattttcatc
     1141 gcaacttcat gaaaaataaa taaaaaataa aaaatacagg gattctgggt attaccgggg
     1201 taataatgtt aagcgctaac acaatgaaaa ttaaggcgat gccggtatta ccccggtaat
     1261 acccagaacg gagccattac gcaccgtcct gctgctcatt caggcgcgct gacaggcttc
     1321 ggtaaaggcg ttccgcatcc tcatggagtt tctcgcagaa atcagcctca tgatccagat
     1381 ccaggtcatt aagcctgtcc agaagaagca gggactgatc ctggatgaat ttagccatgt
     1441 taacggcagt cttttgttgt ttgttcatga aagccccggc gcgaaagtgc ttactgtacg
     1501 ttctgatggt tttccgcttc ctcgctcatt cgctcactcc gttcggtcat gagtctgcgg
     1561 cgagcggagg gaggagaagc agataacgta acggtaagca taacgaaagc taaggacaag
     1621 ggcgaaaagg ccacgccccg ccggggcgtt tttccatagg ctccgccccc ctgacaagca
     1681 tcacagaatc tgacgctcaa atcagtggtg gcgaaacccg acaggactat aaagatacca
     1741 ggcgtttccc cctggtcgct ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccag
     1801 atacctgtcc gcctttctcc cttcgggaag cgtggcgctt tctcatagct cacgctgttg
     1861 gtatctcagt tcggtgtagg tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt
     1921 tcagcccgac cgctgcgcct tatccggtaa ctatcgtctt gagtccaacc cggtaagaca
     1981 cgactaatcg ccattgacaa cggccactgg tagacaggat gtgcgagaga tgtatcgaga
     2041 gttcttgaag tggtggcctg actgcggcta cactgaaagg acagatttgg tgacatgtct
     2101 cgcacaagac tgttaccacg gttcagaagt tccccaactt actgaacctt cgaaaaacca
     2161 cctccccagg tggttttttc gttttccgag aaagagatta cgctttgagc gaatgaatct
     2221 caagaagatc atggcatttg atgaacaaat gagtcagcta ctcagattga tagaaaaaat
     2281 gccccttata caagtgatat attttccaaa actgatactc tattttaaca ttagaaagcg
     2341 tccatttccc accccgcgat tcagcctctt ctttaatatc agcaatactt gggatcaccc
     2401 catttgaaat aacaaaatcg tccaaccaat cccacatttc tcgccgagat gatttaaata
     2461 caacaggagc tttcccatat gagcaagttg gcataaaatc ccccggaata aatcttttaa
     2521 accctccatt cacaagagaa acttctcttc cattaccatt accattacca tttttcatcg
     2581 tagagctatc aggttcctta attgtcacac tgccatcagg cccaacaaat atccagtgta
     2641 aattcaattt actaacagca agaatgctcg tttcttctat taatctttca tactgtttta
     2701 ttcttggaac agcaatagca taattaatat tatcttttgt cattctctgc actaattgtc
     2761 caagacaagt tcgaaaatcc aaccctggct gtgatgtttt cccttttact tcaatatgcc
     2821 acacaacatc cctagattct ttatcacgac aaataaggtc aatataagat cccgtatcta
     2881 tatcgaaccc ttgtcgaaaa aaatattttt ctaaagaagc ttgaacaaat tcctcggaag
     2941 gatattcacc acctagtaag taccttctcg tcaccataag agccacaacc ccta
//
