LOCUS       NZ_CP062216             2255 bp    DNA     linear   CON 16-JUN-2023
DEFINITION  Escherichia coli strain L3Cip3 plasmid unnamed5.
ACCESSION   NZ_CP062216
VERSION     NZ_CP062216.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16242922
            Assembly: GCF_014854635.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 2255)
  AUTHORS   Silander,O.K., Freed,N.E., Ferguson,G., White,J. and Sajuthi,A.
  TITLE     CRISPR-based Enrichment and Long-Read Sequencing for Strain and
            Antimicrobial Resistance Profiling
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2255)
  AUTHORS   Silander,O.K., Ferguson,G. and Heinemann,J.
  TITLE     Direct Submission
  JOURNAL   Submitted (23-SEP-2020) School of Natural and Computational
            Sciences, Massey University, Gate 4, Building 11, Albany Highway,
            Auckland 0632, New Zealand
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 01-APR-2020
            Assembly Method                   :: unicycler v. 2020-04-01
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 150.0x
            Sequencing Technology             :: Oxford Nanopore; Illumina HiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/15/2023 02:17:42
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,293
            CDSs (total)                      :: 5,174
            Genes (coding)                    :: 4,935
            CDSs (with protein)               :: 4,935
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 239
            CDSs (without protein)            :: 239
            Pseudo Genes (ambiguous residues) :: 0 of 239
            Pseudo Genes (frameshifted)       :: 80 of 239
            Pseudo Genes (incomplete)         :: 169 of 239
            Pseudo Genes (internal stop)      :: 42 of 239
            Pseudo Genes (multiple problems)  :: 46 of 239
            Pseudo Genes (short protein)      :: 2 of 239
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP062216.1.
            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/
FEATURES             Location/Qualifiers
     source          1..2255
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="L3Cip3"
                     /isolation_source="river water"
                     /db_xref="taxon:562"
                     /plasmid="unnamed5"
                     /geo_loc_name="New Zealand: Christchurch"
                     /collection_date="2020-01-28"
     gene            712..1227
                     /locus_tag="IFO96_RS26195"
                     /old_locus_tag="IFO96_26195"
     CDS             712..1227
                     /locus_tag="IFO96_RS26195"
                     /old_locus_tag="IFO96_26195"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000097059.1"
                     /GO_process="GO:0006260 - DNA replication [Evidence IEA];
                     GO:0006276 - plasmid maintenance [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication/maintenance protein RepL"
                     /protein_id="WP_000097059.1"
                     /translation="MSSLSLQRYETNPFLELMTIPMKGKRIQVSRLGRDDNVLVNQNTG
                     EKFGTHVTTFKRVDSEQFVKLFTANIGLTFDLSSAGIKAFNVLLWAVQKQAFAKDQVLL
                     DSRALDDFLKSYDSLKLSYATLKRGINELEKAQIIAKTMRKGFYFINPNFVFNGDRIAF
                     TTLIERDC"
                     /name="replication/maintenance protein RepL"
     gene            1302..1586
                     /locus_tag="IFO96_RS26200"
                     /old_locus_tag="IFO96_26200"
     CDS             1302..1586
                     /locus_tag="IFO96_RS26200"
                     /old_locus_tag="IFO96_26200"
                     /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_000160398.1"
                     /translation="MTKHDAIRISQLHQIFYDDEGLIDSEKNVTILYSIGFTIDEIAYF
                     GNTTPGTVQGQLFNARAKLSCASASSLRPMILLRLLSLIIFEQDRLNRL"
                     /name="hypothetical protein"
     gene            1689..2192
                     /gene="ddp1"
                     /locus_tag="IFO96_RS26205"
                     /old_locus_tag="IFO96_26205"
     CDS             1689..2192
                     /gene="ddp1"
                     /locus_tag="IFO96_RS26205"
                     /old_locus_tag="IFO96_26205"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000809479.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DNA distortion polypeptide 1"
                     /protein_id="WP_192301395.1"
                     /translation="MKQIKFRLTDEEYNVAHINAISNGVNSVNAFAKRKVLDISATPSK
                     VIVSNEPSVPVKTCLYPHELELIKRNAALHGMSVSREIAIRLRKSVLKSEVCLYPEEVQ
                     VLRKLSTTINRIGRNIHFIISGDCFCTVNDPDFRNEIRELTALCETVDKTIEQLVFSVN
                     NRFG"
                     /name="ddp1"
     Typing          complement(183..443)
                     /name="Col(MG828)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.511"
                     /coverage="100.0"
                     /evalue="3.95e-106"
ORIGIN
        1 tcattttgcg gcgtttgccc tatcctgcat cggggttaaa ccacgaagat ttttattccc
       61 cgttcttcgg aacgaccgaa gccgccacgg ttccgattgc gccttgagcg caaccggaaa
      121 ccgactgggg agaaccccag acccccatcg cggcaacacc gacggtctac gaccacctac
      181 caaccgcgtg gctgcctgtt ccgtgcaaat gggctttgca gggggctgac gcggttcctg
      241 gcgacctgaa agcccctggt taggggtatc ggcgcgcctg acctcctgaa accctctgta
      301 agcgtttttc gcgccttcca tgccctgacg ggcatttaaa ccccgtctcg tgtgtctgag
      361 agcttctgag cgcgtttcag gggctatctg acgactcatc cccgaaagaa taacaacggg
      421 atcaccgaca acatgcgaga ggtgacaccg ctcgccgcag ccccagcgac cgaacgtagt
      481 gagcgagtgg gcgaggaagc ggaagagaac cagaagccat attgagcact tacgctcgta
      541 gttaagaact aagaagggaa tttcttgaaa cccgcatgaa tcctagaaag tggtgatcag
      601 gatctgtacc ttgtaagctc agatccggta ccttgcaggc tcaaaaaatc attgattttg
      661 agcttatgag gatttattgt gaatctccaa agcccaaaaa aggatgcaat aatgagctca
      721 ctaagcttgc agagatacga aacgaaccca tttttagagc ttatgacaat cccgatgaag
      781 gggaaacgga tacaagtatc tcgtcttgga cgtgatgaca acgttttggt taatcaaaac
      841 acgggagaaa agtttgggac gcatgtaacc acttttaagc gtgtggatag tgagcaattt
      901 gttaaattgt ttactgcgaa tattgggcta acatttgatt tatcatcggc aggaattaaa
      961 gcttttaatg tcctgttatg ggctgttcaa aaacaggctt ttgcaaaaga tcaggttctt
     1021 ttagattcca gagctcttga tgactttttg aaaagctatg atagcttaaa actaagttac
     1081 gctacgttaa agcgagggat caacgagtta gaaaaagctc agattatagc aaagacaatg
     1141 cgaaaaggat tttatttcat aaatcctaac tttgtattta atggcgatag aatagcgttt
     1201 acaactctga tcgagaggga ttgttaatat aatcgtcgca gtcgaacaaa actccacttt
     1261 tgttcgactg ctaatcacaa caacctatta gggaggttat tatgactaag catgatgcta
     1321 tacgcatttc tcaacttcat caaatctttt acgatgacga gggattaatt gattcagaaa
     1381 agaacgtgac cattttatac agcataggat ttactattga tgaaatagct tattttggga
     1441 atacaacacc gggaacagtt cagggacagt tatttaatgc aagagctaaa ttaagttgtg
     1501 cttcagcttc atctttaaga ccgatgattt tgttgagatt gctttcactc ataatctttg
     1561 agcaagaccg cttaaatagg ctgtaatcaa tgcaggatag acaatcatgg tcaaatgggt
     1621 accattttcc atgattgtcc aaaaacgggg tttttgcctg tgcctgccgc aggctcttag
     1681 gaggttctat gaagcaaatt aaattcagat tgaccgacga ggaatacaac gttgctcata
     1741 ttaatgctat ttcaaatggc gttaatagtg taaatgcttt tgcaaagagg aaggttttag
     1801 atattagcgc aacaccttca aaggttatcg tatcgaatga accatctgta ccagtaaaaa
     1861 catgtttata cccacatgaa ctggagttaa taaagcgtaa tgctgcatta cacgggatga
     1921 gcgttagccg agaaatagca atacgcttac gtaaatcagt gttgaaaagc gaagtttgtc
     1981 tttatcccga agaagtgcag gtgctcagaa agctttcaac aactattaat agaattggtc
     2041 gaaatattca ttttataatt agtggcgatt gtttttgcac agttaacgat cctgatttca
     2101 gaaatgagat aagggaactt acagcattat gcgaaacagt cgataaaaca atagagcaat
     2161 tagtttttag tgttaataat cgttttgggt aaaaacgtat tatcaagaac cgactgtagg
     2221 tcatgggcaa acgttgcaga attgcgtcag agacg
//
