LOCUS       NZ_CP135492             2213 bp    DNA     circular CON 07-OCT-2023
DEFINITION  Escherichia coli strain isolateD plasmid pIsolateD_D, complete
            sequence.
ACCESSION   NZ_CP135492
VERSION     NZ_CP135492.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN37529175
            Assembly: GCF_032351055.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 2213)
  AUTHORS   Lerminiaux,N., Fakharuddin,K., Mulvey,M.R. and Mataseje,L.
  TITLE     Do we still need Illumina sequencing data?: Evaluating Oxford
            Nanopore Technologies R10.4.1 flow cells and v14 library prep kits
            for Gram negative bacteria whole genome assemblies
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2213)
  AUTHORS   Lerminiaux,N., Fakharuddin,K., Mulvey,M.R. and Mataseje,L.
  TITLE     Direct Submission
  JOURNAL   Submitted (25-SEP-2023) National Microbiology Lab, Public Health
            Agency of Canada, 1015 Arlington Street, Winnipeg R3E3R2, Canada
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 21-JUN-2023
            Assembly Method :: Trycycler v. v0.5.0; Flye v. v2.9.2; Raven v.
            v1.8.1; Miniasm/minipolish v. v0.3_r179
            Assembly Name                     :: isolateD
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 245X
            Sequencing Technology :: Oxford Nanopore MinION; Illumina MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 10/07/2023 13:56:47
            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)                     :: 4,954
            CDSs (total)                      :: 4,833
            Genes (coding)                    :: 4,558
            CDSs (with protein)               :: 4,558
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 275
            CDSs (without protein)            :: 275
            Pseudo Genes (ambiguous residues) :: 0 of 275
            Pseudo Genes (frameshifted)       :: 84 of 275
            Pseudo Genes (incomplete)         :: 187 of 275
            Pseudo Genes (internal stop)      :: 46 of 275
            Pseudo Genes (multiple problems)  :: 40 of 275
            Pseudo Genes (short protein)      :: 4 of 275
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP135492.1.
            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..2213
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="isolateD"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pIsolateD_D"
                     /geo_loc_name="Canada: Ottawa"
                     /collection_date="2020"
     gene            1..132
                     /locus_tag="RRL15_RS24755"
                     /old_locus_tag="RRL15_24755"
     CDS             1..132
                     /locus_tag="RRL15_RS24755"
                     /old_locus_tag="RRL15_24755"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001354639.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_032159035.1"
                     /translation="MHEPPVQSDCCAFSGNYQLESNPERHDKAPLAAAIGNWISRAG"
                     /name="hypothetical protein"
     gene            587..1012
                     /locus_tag="RRL15_RS24760"
                     /old_locus_tag="RRL15_24760"
     CDS             587..1012
                     /locus_tag="RRL15_RS24760"
                     /old_locus_tag="RRL15_24760"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001676030.1"
                     /GO_function="GO:0005515 - protein binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="PH domain-containing protein"
                     /protein_id="WP_001676030.1"
                     /translation="MGSYVDQSLTRNESVISRAQTSWIPTIIPVIIGILLLPFYGLGLL
                     IIVPVLLRVWSTELALTNQRVIAKVGLIRRNTVELRIDKVESLGIHQGILGRIFNYGSI
                     VIKGTGGTNTPIPNIKAPMQFRSIVNNHIEEMDSKQQ"
                     /name="PH domain-containing protein"
     gene            complement(1279..1515)
                     /locus_tag="RRL15_RS24765"
                     /old_locus_tag="RRL15_24765"
     CDS             complement(1279..1515)
                     /locus_tag="RRL15_RS24765"
                     /old_locus_tag="RRL15_24765"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001676031.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001676031.1"
                     /translation="MNRLTNLTPAEKKFLDDAIAAAERASGKKLNQPNRHIVLNRARAQ
                     IESQRYADRQRALREDERQQSEFAWSRPRAPRR"
                     /name="hypothetical protein"
     Typing          complement(1680..1853)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.143"
                     /coverage="100.0"
                     /evalue="5.58e-78"
     Typing          2..162
                     /name="rep_cluster_2405"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="87.195"
                     /coverage="95.0"
                     /evalue="4.41e-44"
     Typing          1777..2213
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.545"
                     /coverage="90.0"
                     /evalue="0.0"
ORIGIN
        1 atgcacgaac cccccgttca gtccgactgc tgcgcctttt ccggtaacta tcaacttgag
       61 tccaacccgg aaagacacga caaagcgcca ctggcagcag ccattggtaa ctggattagc
      121 agagcgggat aatgtaggca gtgctacaga gttcttgaag tggtggcctg agtgcggcta
      181 cactggaagg acagtttagg tatctgcgct ctgctgaagc cagttaccac ggttagaaaa
      241 tctgccagga tttactaacc ttcgaaaaac cacctgccag ggtggttttt tcgtttccaa
      301 ggcaagagat tacccgcaga gaaagacgat ctcaagaaga tcatctgtga tattcgacag
      361 atatgggata aaggtttcta acgccaggag tatatggggc gtagcagcag cgttcaccac
      421 cgttgaatca agctactttc atggcaagaa ataaaagaac cgagcagtcc gagagtcgct
      481 acgctcccct taatttttgt atatctacca cgcggatata aggtttctat tgccgattca
      541 tcttaaaaag ggaaaaatcc tattttttct aaatggatgt aaccttatgg gaagctacgt
      601 agaccaatca ttgacgagaa atgaatctgt aatatctcgc gctcaaacct cctggattcc
      661 aacaatcatc ccagtaatta tcggaatcct gttgctacct ttttacggct taggattact
      721 tataatagtc cctgtgcttc ttagagtttg gtcaacggag cttgcattga ctaaccaaag
      781 agtcatcgca aaagtagggt tgatccgacg taatacggtg gaactccgta ttgataaagt
      841 tgaaagcctt ggcatacatc aagggatact aggacgaatc tttaattatg ggtcgatcgt
      901 aattaaaggt accggcggaa ccaacacgcc aattccaaac atcaaggcac caatgcaatt
      961 cagatctatt gtgaacaatc acattgagga aatggattct aagcagcagt agtttcctca
     1021 taagcattac aaaaaaagcc ccgcagggct ttttttgtac ctgccagtga gtcagattta
     1081 ccataacatc cgttgtctgc actgcctgag aggccctcag cgcgtttctg cggcctgaca
     1141 gccgtttccg gcacctttca ccgcaccacc ccctgaaaaa cgcccctgat gatttctgcg
     1201 cgtctgcatg gctattcaca ggagtgaatg gcgggcaatt tcggagtgtc agcaccacta
     1261 aaccgccaaa aggcgcaatc agcggcgcgg cgcgcgcgga cgtgaccagg caaactcgga
     1321 ctgctgccgc tcatcctcac gtaatgcacg ctggcggtcg gcgtaacgct gcgactcaat
     1381 ctgcgcacgc gctctgttca ggacgatatg ccggttcggc tgatttagct ttttgcctga
     1441 cgctctctca gctgcggcaa tagcatcatc aagaaatttt ttctctgcag gtgtcaggtt
     1501 tgtcagtctg ttcatagcat tctcccatca gaataacgcc gcacagtctg ccagacacag
     1561 cagaaccgat gaagcgctgg cggtgctgaa agacagccag aaacggtgaa cgggagcgga
     1621 ttttaatccg gtgacgtgag acgttgggca agccgcaggc gcgtcagtgg ttttagcggg
     1681 tttcggggcg cagccctgaa ccagtcacgc agcgctagcg gagtgtatac tggcttacta
     1741 tgttggcacg gatgcgaata tcagtgaagt gcttcatgtg gcaggagaaa aaaggcggca
     1801 ccggcgcgtc agcagaatat gcgatacagg atatattccg cttcctcgct cactgactcg
     1861 ctgcgctcgg tcgttcggct gcggcgagcg gtgcgggctt actggcgggg cggaaatttc
     1921 ctggaagatg ccaggaagaa acttaacagg gaagcgagaa ggccacggcg aagccgtttt
     1981 tccataggct ccgcccccct gacaagcatc acgaaatctg acgctcaaat cagtggtggc
     2041 gaaacccgac aggacttaaa gataccaggc gtttccccct ggtggctccc tcgtgcgctc
     2101 tcctgttcct gcctttcggt ttaccggtgt cattccgctg ttatggccgc gtttatctca
     2161 ttccacgcct gacactcggt tccgggaagg cagttcgctc caagctggac tgt
//
