LOCUS       NZ_CP135506             4063 bp    DNA     circular CON 07-OCT-2023
DEFINITION  Escherichia coli strain isolateA plasmid pIsolateA_D, complete
            sequence.
ACCESSION   NZ_CP135506
VERSION     NZ_CP135506.1
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 4063)
  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  JOURNAL   Unpublished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 4063)
  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
            CP135506.1.
            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..4063
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="isolateA"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pIsolateA_D"
                     /geo_loc_name="Canada: Ottawa"
                     /collection_date="2015"
     gene            join(2779..4063,1..863)
                     /gene="mobQ"
                     /locus_tag="RRL06_RS24610"
                     /old_locus_tag="RRL06_24610"
     CDS             join(2779..4063,1..863)
                     /gene="mobQ"
                     /locus_tag="RRL06_RS24610"
                     /old_locus_tag="RRL06_24610"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016240513.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobQ family relaxase"
                     /protein_id="WP_001029354.1"
                     /translation="MAIYHLSMKIISRSSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPHELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAIGPAGFSGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNGGLTEPARRVADLLNIGLPDNATSYTLRDIIEALPKDSN
                     SAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQMAFEKQWQQWGESGLAALRAQL
                     LKREEELRRKEQEDTERSRAEQLRKNDNAVMDSGVLRAVVTGYGEAPMPGNGEMTCYLL
                     LHNRNGEYTLWGNELEKYRTRIFESVDLMRDRSGYICDRSEIGQRPPLQRVYSSATFEQ
                     LLTQVCQTWPQHTRNLRQPKTWPESFCLGEDRQPAMPSPAARKVDFMQGRLPPTLMPVM
                     SSVDRETRQLQLLLVMGVDDSLGGVIRLNGTLYPAFAVPSADNRHLVISALTDKGLRYA
                     GYGVAVNHDADSHISPAPELMQFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRTWEEW
                     QREEDARTHTTERRHDRGWSQ"
                     /name="mobQ"
     gene            complement(1111..1812)
                     /locus_tag="RRL06_RS24615"
                     /old_locus_tag="RRL06_24615"
     CDS             complement(1111..1812)
                     /locus_tag="RRL06_RS24615"
                     /old_locus_tag="RRL06_24615"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001281399.1"
                     /GO_function="GO:0003887 - DNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_001281395.1"
                     /translation="MSDLIAYKSNALIEASYKLTLQEQRFLLVCISRLKSGEDSPSPDE
                     QKTMTITAAEFHDAFPDMGRQHAEARLKEAIDRLWDRSVIIKNEEKREEFRWVQYRAQY
                     FKGEAKVDITFSDAIMPYLTQLKGQFTRVVVKNVSSLSSTYSIRIYELLQQFRSTGDRT
                     IAIDDFRTMLAVEDKYQQFKDLNKMIIKPAIAELNEKSDLVVTVETIKKGRTVVALHFR
                     FKEDKQIKMTI"
                     /name="replication initiation protein"
     gene            complement(2346..2600)
                     /gene="mobC"
                     /locus_tag="RRL06_RS24620"
                     /old_locus_tag="RRL06_24620"
     CDS             complement(2346..2600)
                     /gene="mobC"
                     /locus_tag="RRL06_RS24620"
                     /old_locus_tag="RRL06_24620"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000091747.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase accessory protein MobC"
                     /protein_id="WP_000091746.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVVVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPEQ"
                     /name="mobC"
     Typing          complement(2602..2778)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          2779..3137
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(1112..1812)
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          4..860
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.105"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          2693..4062
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="96.529"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 ttatggattc aggggtgctg agagcagtcg ttacggggta tggcgaggct cccatgcctg
       61 gtaacgggga aatgacctgt taccttctgc ttcacaaccg gaacggagaa tatacgctct
      121 gggggaacga gctggagaaa taccgcacca gaatctttga gagtgttgat ttaatgcgtg
      181 acaggagtgg ttatatctgt gaccgaagcg aaatcggcca acgtccgcca ctgcaacgtg
      241 tttattcctc tgcaaccttt gagcaactgc tgacgcaggt ttgccagaca tggccgcaac
      301 atacccgcaa tctccgccag ccgaagacat ggccggagtc tttctgtctt ggagaagacc
      361 gccagccagc catgccatca ccagcggcaa ggaaggtgga ttttatgcag ggacgtctgc
      421 caccgacgct gatgccggtc atgagttctg tcgaccggga aacccgccag cttcagcttt
      481 tgctggtcat gggcgtggat gactctctgg gcggtgttat ccggcttaat ggtacgctgt
      541 atcccgcgtt tgccgttccc tcagccgata acaggcatct ggtcatcagt gcgctgaccg
      601 ataaggggtt acggtatgca gggtatggtg ttgccgtaaa tcacgatgca gacagccaca
      661 tatcacctgc accagaactg atgcagtttc atctgaaaac ccgtgaggca ccgctttttg
      721 ctgccgtcaa cacaccagaa aaacagccgg atcatctgtt ccgctcgctg ggttttaatc
      781 gtacctggga ggaatggcag cgcgaggaag atgcacgaac acacaccacc gagaggagac
      841 atgatcgcgg ttggtcacag tgaatgtgaa caatattttg ttttgtttaa catcgtgtta
      901 tgttcgtcga tgttcatcga cagggatgaa tgcaagaagc acactcacat aacgcaagca
      961 tagttttgtt tttccgcccc caaaaattgg ggggtctttt ttcgctgcat cagagcgttt
     1021 ttgacgcaat ttttcacttc aatagtacct tcgcactact aacacaaaaa aaacgcagca
     1081 gggagcgttt taggtgcctt aaaatcgatt ttagatcgtc atcttgatct gtttgtcttc
     1141 cttgaagcga aaatgcaggg ctacaaccgt gcgccccttt ttgatcgtct caacagttac
     1201 aaccagatcg cttttttcgt tcagttcggc gatggctggc ttgattatca tcttattcaa
     1261 gtctttgaat tgttgatatt tatcttcaac ggcaagcatg gttcggaaat catcgatagc
     1321 tatcgttctg tcaccggtgc tgcggaactg ctggagcagc tcgtaaatgc ggatgctgta
     1381 ggtgctggaa aggctggaga cgttcttcac gactacccgc gtaaactgcc ccttgagctg
     1441 tgtcagatac ggcatgatgg catcggagaa ggtgatatct actttcgcct cacctttgaa
     1501 atactgcgcc cggtactgca cccagcggaa ctcttctcgt ttttcctcgt tcttgatgat
     1561 tactgacctg tcccagaggc gatctatcgc ttccttgagc ctagcttcag cgtgctgccg
     1621 tcccatgtca ggaaaggcat catgaaactc tgcagccgtg atggtcatgg ttttttgttc
     1681 atccggcgaa ggggaatctt ctccggattt taggcggctg atacagacca gcaggaagcg
     1741 ctgttcctgc aaagtgagct tgtagcttgc ctcgataagg gcgtttgatt tgtaagctat
     1801 cagatctgac atttcgcttg ctcgttgcta ttggtggcgt ttttttactg tacgccactt
     1861 atcatatggg tggaagtttt ttttttgcaa cccccttttt ctgtggatta cacccccaaa
     1921 agctccacct ttcaccccca aaagctccac ctttcacccc caaaagctcc acctttcacc
     1981 cccaaaagct ccacttatct tgccagaaca tctttaaaat catggtgtta caagacctaa
     2041 aaaggtttta aaaaaaaaga tctaaaaata agatcttaaa aacttaacgg cgagcctgtg
     2101 gataacttgg ggtgctgaaa acaaaaaacc aataaaaaca atgcgttgca ataaagcaga
     2161 attgcaagtt tcgaatacac cccctccaac cctgtggaaa cccagtattc atgcgggttc
     2221 agcgcatatc acctgccgaa aaaccgtgcg tatgtgctca acctggcgac tgattcactt
     2281 ccgcttcctc gcccactcgc tcgctaacgc tcggtcgctg gggctgcggc gagcggacga
     2341 tacaatcact gttctggcag cgcctccagc tcgttaatca gcggcagtat gcgcgtcaca
     2401 tcagcctgtc gtgtcacctc tgccttcagg aactggagta accaggcacg caactgcacc
     2461 tcctccggct ttctgacctt tgccagcaat gcagcaccca caacaacctt ctgcgctgtg
     2521 tccaggctcc ggctcttcgc cttcaggcgc tgtaatctcg cctcagcatc agcaatcttc
     2581 tgttcgagcg ttctgctcat gatgtaactc cgtgcgcgat gaaaaatcgc attttagcgc
     2641 gtcactggta gtttaaaaac tgagctggca taatgcacgg caaatcacga agtgcgcact
     2701 tatacaatct ccactccgtt tcgattgtgt gcgccctgcg gggctgaaag aaaactacaa
     2761 aaaggcatta cggcagaaat ggcgatttat catctcagca tgaaaattat ctccagaagc
     2821 agcggctaca gcgccgtagc ttccgctgcc tatcgttccg gttcactgat gcttgatgag
     2881 cgtaccggac tgactcacga ctacacccgc aaaagcggtg tggctgaggc tgtgattctg
     2941 acccccgcca ccgcccctgc ctggtgtacg aaccgtgccg aactctggaa tgccgttgag
     3001 aaggccgaac gccggaagaa ctcacaactt gcgcgggaaa ttgaactcgc catcccccac
     3061 gaactgccgc aggatgccgc acgggaaacc gttctcgcct ttgtcagaga aaactttgtc
     3121 agtcagggca tgattgctga tgtggcgttc catcacatgg ataaaacaaa tccccatgcg
     3181 cacatcatgc tgaccacgag ggctatcgga cctgctgggt tcagcggaaa ggtcagggac
     3241 tggaacgacc ggacacatgc cgagacgtgg cgggcatcat gggctgacca tgcaaacagg
     3301 gcactggcga acgccggtta tcaggaagag atagaccatc gttcatacga gcgacagggg
     3361 cttgagaaaa cgcctggtat tcacctcgga aagtctgcct gtgcgatgga aacacgcggt
     3421 atcgaaacag aacgcggcga acagaatcgt ctgattaaca ggcttaacct ggaaatacag
     3481 atttcccgca ccgaactcag gaacggaggg ctgacagagc ctgcccgccg tgtggctgac
     3541 cttctgaata tcgggcttcc tgacaacgca acttcgtaca cactacgtga cattatcgaa
     3601 gcgttgccga aggacagtaa ctcggcatgg aaactcacca gtaatgccat gtcgatgatg
     3661 gcagatatgc aggcgacgcg cagacgctgg gaagagctga acaccgaacg aaaggaagcg
     3721 atgagccatg ctgccagcct gaaaaaatca tcgccgtttt cgtccggttt ttcccgtatt
     3781 cccctgatgc aatgggcggc accggaatac cgtagtgagc agggaaaaat ccagtctctg
     3841 agccagcaaa tggaaaaatt acgacagcat taccggaagg tggagaaaca ggacattccc
     3901 gcgagtcaga tggcatttga aaaacagtgg cagcagtggg gggaatccgg ccttgcagct
     3961 ctcagagccc agttgcttaa acgtgaagag gaattgcgcc ggaaggaaca ggaagatact
     4021 gaacgtagtc gcgcggagca gctcaggaaa aatgacaatg ccg
//
