LOCUS       NZ_CP135507             3372 bp    DNA     circular CON 07-OCT-2023
DEFINITION  Escherichia coli strain isolateA plasmid pIsolateA_E, complete
            sequence.
ACCESSION   NZ_CP135507
VERSION     NZ_CP135507.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN37529172
            Assembly: GCF_032354275.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3372)
  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  JOURNAL   Unpublished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 3372)
  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                     :: isolateA
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 155X
            Sequencing Technology :: Oxford Nanopore MinION; Illumina MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 10/07/2023 14:01:40
            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)                     :: 4,929
            CDSs (total)                      :: 4,805
            Genes (coding)                    :: 4,539
            CDSs (with protein)               :: 4,539
            Genes (RNA)                       :: 124
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 266
            CDSs (without protein)            :: 266
            Pseudo Genes (ambiguous residues) :: 0 of 266
            Pseudo Genes (frameshifted)       :: 85 of 266
            Pseudo Genes (incomplete)         :: 188 of 266
            Pseudo Genes (internal stop)      :: 57 of 266
            Pseudo Genes (multiple problems)  :: 58 of 266
            Pseudo Genes (short protein)      :: 4 of 266
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP135507.1.
            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..3372
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="isolateA"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pIsolateA_E"
                     /geo_loc_name="Canada: Ottawa"
                     /collection_date="2015"
     gene            complement(join(2858..3372,1..46))
                     /locus_tag="RRL06_RS24625"
                     /old_locus_tag="RRL06_24625"
     CDS             complement(join(2858..3372,1..46))
                     /locus_tag="RRL06_RS24625"
                     /old_locus_tag="RRL06_24625"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000067488.1"
                     /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_032329292.1"
                     /translation="MSNLLQMGTDFEKKLKERAASTENMLNSEFRKLEESVDKALSLNR
                     QKIRDAISGHTTSVKQQLDTLSATVSTQFSTTEAELSRQQKKLLWQVIKGRILFPALTA
                     LSVTGGIFLGCWGLMEWQESKIAKNILTIREQENTLAKLEAKTWGVTFVNGENGKFLVL
                     PDGVKGENTWTVGDKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     gene            complement(<84..734)
                     /locus_tag="RRL06_RS24630"
                     /old_locus_tag="RRL06_24630"
                     /pseudo=""
     CDS             complement(<84..734)
                     /locus_tag="RRL06_RS24630"
                     /old_locus_tag="RRL06_24630"
                     /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            complement(724..1047)
                     /locus_tag="RRL06_RS24635"
                     /old_locus_tag="RRL06_24635"
     CDS             complement(724..1047)
                     /locus_tag="RRL06_RS24635"
                     /old_locus_tag="RRL06_24635"
                     /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_024132211.1"
                     /translation="MLTIRVTDEEHARLLERCEGKRLAEWMRRVCLGEPVARTGKLPTL
                     SPPLLRHLAAIGNNLNQTARKVNSGQWSSIDRVHVVAALMAIEGELRQLRQAVREQGVR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            1111..1302
                     /locus_tag="RRL06_RS24640"
                     /old_locus_tag="RRL06_24640"
     CDS             1111..1302
                     /locus_tag="RRL06_RS24640"
                     /old_locus_tag="RRL06_24640"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165979.1"
                     /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_000165979.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNDLDADEQADICESLHDHA
                     DELYRSCLARFGDDGESN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(2618..2851)
                     /locus_tag="RRL06_RS24645"
                     /old_locus_tag="RRL06_24645"
     CDS             complement(2618..2851)
                     /locus_tag="RRL06_RS24645"
                     /old_locus_tag="RRL06_24645"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137389.1"
                     /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_000137389.1"
                     /translation="MTELEGHLLNALEHLQQDYMRRLNEWESAFAELQKMHEVTQRNNA
                     ILNERVVILSQQVQRLAGQVDRLSRLFIANNS"
                     /name="MbeD family mobilization/exclusion protein"
     Typing          complement(1384..1464)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="87.805"
                     /coverage="93.0"
                     /evalue="8.68e-18"
     Typing          complement(4..734)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.361"
                     /coverage="99.0"
                     /evalue="4.08e-162"
     Typing          complement(2536..3371)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="88.028"
                     /coverage="99.0"
                     /evalue="5.72e-135"
ORIGIN
        1 tcagtttctt ctcgaagtct gttcccattt gtaaaagatt gctcatacag cgcccccttt
       61 agcctgagat tccgcccacc ctccgggtcg gcaatactga tactgcttct ggttgtcctc
      121 accacctcaa aacctgccgc tgtgagcgcc tcagtgacat cctgacgcgt ttttattgct
      181 ccggcatggt aaagcgcctc aagaccccgt gtaatcgctt ctgcggcctc ctgtttcgct
      241 tttggcagat tatttggcgt gacaagcgtc cgtctgttct ccggtgcgtt cgggtcacgc
      301 agcccgtaat gatgattaac cagcgtctgc caggcattta tcctcggcct gtccgcacgg
      361 tcgtagtacg gctggaggcg cttaccgctc tgtagctcca tgttcgggat gacaaaattc
      421 agttcgagcc gccccttatc ctggtgttcc acccagagaa tgctgtactg gtctttttcg
      481 agaccgggca taagaacacg ctcaaagctc gtcatcactc tttcgcgttc acccggcggt
      541 aactccttct ccgcgaacga cagaacgcct gacgtgtatt tcttcgaaaa tggcgtggaa
      601 tcaatgagtt cccgcacttc ttccgggtta ccccggagca ccgttgcgcc ttcgcggtta
      661 cgctcccgcc ccagcaggta atcgaccggg ccacttccac cgcctttccc cctggcatga
      721 aatttaacta tcatcccgta ccccctgttc cctgacagcc tgccgcaact ggcgcaattc
      781 accctcgatg gccatcagtg cggccaccac atgaacccgg tcaatcgaag accactggcc
      841 gctgttcacc ttccgggctg tctggttcag gttgttcccg atggcagcca gatgccgcag
      901 caatggcggc gatagtgtcg gcagttttcc tgtgcgtgca accggctccc ccagacagac
      961 ccgccgcatc cattccgcca gtcgtttacc ctcgcagcgt tccagtaacc gggcgtgctc
     1021 ctcatcggta acccgtatcg tgagcatctt ctcgcgtttc atcggtatca ttccccctaa
     1081 caaatccccc atacaaggag ccttaagacc atgaccaaac aggaaaaaac agcccttaac
     1141 atggctcgct ttatcagaag ccagacgcta accctgctgg aaaaactcaa cgatctggac
     1201 gcggacgaac aggcagacat ctgcgaatca cttcacgacc acgccgacga actctaccgc
     1261 agttgcctcg cacgcttcgg cgatgacggt gaaagcaact gaaacatgca gctcccggag
     1321 acgttcacag cttgcctgtg agcggatgcc gggagcagac aagcccgcca gggcgcgtca
     1381 gtgcgggtgt cggggcgcag ccctgaccca gttcacagag cgatagcgat gtgtatactg
     1441 gcttatctca ttttgcatcg gtgcagacat ggatgggaag tgcaccatgt caggagtaaa
     1501 aagccgcaca gatgtaaaaa cagcgcaccc gataaacagc acacacgcgg acactggcac
     1561 aggcgcgtaa gtgcacaatg cttgcatctg tgactcttcc gcttcctcgc ccactcgctc
     1621 actacgttcg gtcgctgggg ctgcggcgag cggtgggatc actctcgttg tgatgcagat
     1681 ccgttttttt ttttgcactg gagttatcag gagttgcggt gcacatggga tcgtgcgata
     1741 tgccggatgg tgaaaggttg gagggaacgg caacaactca cccctcccag tgaagggacg
     1801 ggtagtttgc cgctctcgat atgccggacg gagccaaggc catcgatcac ggggcgcgtc
     1861 agtggaagaa cccgcgcctg cgtgacgtat gcgtcttcgc cgcaccatct cacccgtcac
     1921 gccaccacat accgggaact gccgccaagg tctaactcaa ccaatctagc cgcgctacat
     1981 acggtttttg tggcaactca tcaggtgtcc gctgtcgatg aaactctctg cgccggtagc
     2041 ggaactctca cgcgtgcggt cgccgtcgtc acagctcccc caaccgcaaa cgattctcgc
     2101 aaatacgcaa gtatctgcaa aaacaggttt ttttcggggt tcctgggaga ctgtgctgtt
     2161 gaaaaattct tgaagaatac agaaggctca tgcaaactga atgaactggt ttctgttgtg
     2221 gatctcaaca gtttccacag gaacattgag gaggtcagag acctcaatga acccgaaaca
     2281 gctcgccttc ctggcgagct gttttcgttc tacgcccgcc gacgaaagat cgcaagtgca
     2341 ataacgagat ttttcacgtc tttacgctca aaaagtaaaa aaaccatgtt ttcccctggc
     2401 tgaatcccca aaaacgcgtg aaatgcgttt tcaggatgtt gcatagctat gcacaaatac
     2461 ggcacacgat ttgtttcgct cgccccagcc gtcgaactgg tcaaaatggc aagatttcgt
     2521 cacttccccg gtcacatctc cattgatggc ccactccgaa cccgtgccgc gcgttcctgt
     2581 acctcatgtc tgtaccgggc acgctcctgt tcatccctta gctgttgttc gcgataaata
     2641 accgactcaa gcgatccact tgcccggcta atctctgcac ctgctgactc aatatcacga
     2701 cgcgctcgtt cagtatcgcg ttgttccgtt gcgtaacctc gtgcatcttc tgcaattccg
     2761 cgaaggcgct ctcccactcg ttcagccgcc gcatatagtc ctgttgcaaa tgctctaagg
     2821 cgttcagcaa atgcccttcc agttccgtca tactcgttta ctccctgacc agcctcacgg
     2881 cgttcttgtc gcccaccgtc caggtgtttt cccctttcac cccgtccggc aacaccagaa
     2941 atttcccgtt ctcgccattg acgaacgtca ccccccaggt ttttgcctcg agtttcgcca
     3001 gcgtgttttc ctgctctctg atagtcagga tatttttcgc aatcttgctt tcttgccact
     3061 ccatcagccc ccagcacccc aggaaaatgc cgcccgtgac gctgagcgcg gtcagcgccg
     3121 gaaacagtat ccgccctttg atcacctgcc agagcagttt tttctgctgc cgggacagtt
     3181 cggcctctgt ggtgctgaac tgcgtgctca cggtggcgct cagtgtatcc agttgctgtt
     3241 tcacggatgt tgtatgtccg ctgatagcgt ctctgatttt ctgcctgttt aagctcagtg
     3301 ccttgtctac agactcttcg agcttcctga actcgctgtt cagcatgttc tcggtagaag
     3361 cggctcgctc tt
//
