LOCUS       NZ_CP059335             4090 bp    DNA     circular CON 03-SEP-2023
DEFINITION  Escherichia coli strain MS10860 plasmid pMS10860C, complete
            sequence.
ACCESSION   NZ_CP059335
VERSION     NZ_CP059335.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN10141462
            Assembly: GCF_030991405.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4090)
  AUTHORS   White,R.T.
  TITLE     Escherichia coli ST410 strain MS10860 plasmid pMS10860C
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4090)
  AUTHORS   White,R.T.
  TITLE     Direct Submission
  JOURNAL   Submitted (17-JUL-2020) School of Chemistry and Molecular
            Biosciences, The University of Queensland, Building 76, Cooper Road,
            St Lucia, QLD 4072, Australia
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 2019
            Assembly Method                   :: Flye v. 2.5
            Assembly Name                     :: MS10860_QU059_ST1193
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 177.0x
            Sequencing Technology :: Oxford Nanopore MiniION; Illumina NextSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 08/31/2023 16:40:09
            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)                     :: 5,074
            CDSs (total)                      :: 4,956
            Genes (coding)                    :: 4,697
            CDSs (with protein)               :: 4,697
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 90
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 259
            CDSs (without protein)            :: 259
            Pseudo Genes (ambiguous residues) :: 0 of 259
            Pseudo Genes (frameshifted)       :: 110 of 259
            Pseudo Genes (incomplete)         :: 161 of 259
            Pseudo Genes (internal stop)      :: 43 of 259
            Pseudo Genes (multiple problems)  :: 50 of 259
            Pseudo Genes (short protein)      :: 4 of 259
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP059335.1.
            Bacteria and source DNA available from Escherichia coli.
            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..4090
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="MS10860"
                     /serotype="O75:H5"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pMS10860C"
                     /geo_loc_name="Australia: New South Wales"
                     /collection_date="2007"
     gene            join(2707..4090,1..775)
                     /gene="mobQ"
                     /locus_tag="MS10860_RS25295"
                     /pseudo=""
     CDS             join(2707..4090,1..775)
                     /gene="mobQ"
                     /locus_tag="MS10860_RS25295"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016240513.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="MobQ family relaxase"
                     /name="mobQ"
     gene            complement(1037..1738)
                     /locus_tag="MS10860_RS25300"
                     /old_locus_tag="MS10860_C0002"
     CDS             complement(1037..1738)
                     /locus_tag="MS10860_RS25300"
                     /old_locus_tag="MS10860_C0002"
                     /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(2274..2528)
                     /gene="mobC"
                     /locus_tag="MS10860_RS25305"
                     /old_locus_tag="MS10860_C0003"
     CDS             complement(2274..2528)
                     /gene="mobC"
                     /locus_tag="MS10860_RS25305"
                     /old_locus_tag="MS10860_C0003"
                     /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(2530..2706)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.438"
                     /coverage="100.0"
                     /evalue="2.610000000000001e-86"
     Typing          2707..3065
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.444"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(1038..1738)
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          4..581
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.409"
                     /coverage="99.0"
                     /evalue="1.87e-136"
     Typing          2621..4089
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="89.228"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 ttcacaaccg gaacggagaa tacacgctct gggggaacga gctggagaaa taccgcacca
       61 gaatctttga gcgtgttgat ttaatgcgtg acaggagtgg ttatatctgt gaccgaagcg
      121 aaatcggtca acatccacca ctgcaacgtg tttattcctc tgcgaccttt gagcaactgc
      181 tgacgcaggt ttgccagaca tggccgcaac atacccgcaa tctccgccag ccgaagacat
      241 ggccggagtc tttctgtctt ggagaagacc gccagccagc catgccatca ctggcagcaa
      301 ggaaggtgga ttttacgcag ggacgtctgc caccgacgct gatgccggtc atgagttctg
      361 tcgaccggga aacccgccag cttcagcttt tgctggtcat gggcgtggat gactctctgg
      421 gcggtgttat ccggcttaat ggtacgctgt atcccgcgtt tgccgttccc tcagccgata
      481 acaggcatct ggtcatcagt gcgctgaccg ataaggggtt acggtatgca gggtatggtg
      541 ttgccgtaaa tcacgatgca gacagccaca tatcacctgc gaccagaact gatggagttt
      601 catctgaaaa cccgtgaggc accgcttttt gctgccgtca acacaccaga aaaacagccg
      661 gatcatctgt tccgctcgct gggttttcaa tcgtacctgg gaggaatggc agcgcgagga
      721 agatgcacga acacacacca ccgagaggag acatgatcgc ggttggtcac agtgaatgtg
      781 aacaatattt tgttttgttt aacatcgtgt tatgttcgtc gatgttcttc gatgttcatc
      841 gacagggatg aatgcaagaa gcacactcac ataacgcaag catagttttg tttttccgcc
      901 cccaaaaatt ggggggggtt cttttttcgc tgcatcagag cgctttttga cgcaattttt
      961 cacttcaata gtaccttcgc actactaaca caaaaaaaac gcagcaggga gcgttttagg
     1021 tgccttaaaa tcgattttag atcgtcatct tgatctgttt gtcttccttg aagcgaaaat
     1081 gcagggctac aaccgtgcgc ccctttttga tcgtctcaac agttacaacc agatcgcttt
     1141 tttcgttcag ttcggcgatg gctggcttga ttatcatctt attcaagtct ttgaattgtt
     1201 gatatttatc ttcaacggca agcatggttc ggaaatcatc gatagctatc gttctgtcac
     1261 cggtgctgcg gaactgctgg agcagctcgt aaatgcggat gctgtaggtg ctggaaaggc
     1321 tggagacgtt cttcacgact acccgcgtaa actgcccctt gagctgtgtc agatacggca
     1381 tgatggcatc ggagaaggtg atatctactt tcgcctcacc tttgaaatac tgcgcccggt
     1441 actgcaccca gcggaactct tctcgttttt cctcgttctt gatgattact gacctgtccc
     1501 agaggcgatc tatcgcttcc ttgagcctag cttcagcgtg ctgccgtccc atgtcaggaa
     1561 aggcatcatg aaactctgca gccgtgatgg tcatggtttt ttgttcatcc ggcgaagggg
     1621 aatcttctcc ggattttagg cggctgatac agaccagcag gaagcgctgt tcctgcaaag
     1681 tgagcttgta gcttgcctcg ataagggcgt ttgatttgta agctatcaga tctgacattt
     1741 cgcttgctcg ttgctattgg tggcgttttt ttactgtacg ccacttatca tatgggtgga
     1801 agtttttttt ttgcaacccc ctttttctgt ggattacacc cccaaaagct ccacctttca
     1861 cccccaaaag ctccaccttt cacccccaaa agctccacct ttcaccccca aaagctccac
     1921 ttatcttgcc agaacatctt taaaatcatg gtgttacaag acctaaaaag gttttaaaaa
     1981 aaaagatcta aaaataagat cttaaaaact taacggcgag cctgtggata acttggggtg
     2041 ctgaaaacaa aaaaccaata aaaacaatgc gttgcaataa agcagaattg caagttccga
     2101 atacaccccc cttccaaccc tgtggaaacc cagtattcat gcgggttcag cgcatatcac
     2161 ctgccgaaaa accgtgcgta tgtgctcaac ctggcgactg attcacttcc gcttcctcgc
     2221 ccactcgctc gctaacgctc ggtcgctggg gctgcggcga gcggacgata caatcactgt
     2281 tctggcagcg cctccagctc gttaatcagc ggcagtatgc gcgtcacatc agcctgtcgt
     2341 gtcacctctg ccttcaggaa ctggagtaac caggcacgca actgcacctc ctccggcttt
     2401 ctgacctttg ccagcaatgc agcacccaca acaaccttct gcgctgtgtc caggctccgg
     2461 ctcttcgcct tcaggcgctg taatctcgcc tcagcatcag caatcttctg ttcgagcgtt
     2521 ctgctcatga tgtaactccg tgcgcgatga aaaatcgcat tttagcgcgt cactggtagt
     2581 ttaaaaactg agctggcata atgcgcgaca aatcacgaag tgcgcactta tacaatctcc
     2641 actccgtttc gattgtgtgc gccctgcggg gctgaaagaa aactacaaaa aggcattacg
     2701 gcagaaatgg cgatttatca tctcagcatg aaaattatct ccagaagcag cggctacagc
     2761 gccgtagctt ccgctgccta tcgttccggt tcactgatgc ttgatgagcg taccggactg
     2821 actcacgact acacccgcaa aagcggtgtg gctgaagctg tgattctgac ccccgccacc
     2881 gcccctgcct ggtgtacgaa ccgtgccgaa ctctggaatg ccgttgagaa ggccgaacgc
     2941 cggaagaact cacaacttgc gcgggaaatt gaactcgcca tcccccatga actgccgcag
     3001 gatgccgcac gggaaaccgt tctcgccttt gtcagagaaa actttgtcag tcagggcatg
     3061 attgctgatg tggcgttcca tcacatggat aaaacaaatc cccatgcgca catcatgctg
     3121 accacgaggg ctgtcggacc tgctgggttc ggcggaaagg tcagggactg gaacgaccgg
     3181 acacatgccg agacgtggcg ggcatcatgg gctgaccatg caaacagagc actggcgaac
     3241 gccggttatc aggaagagat agaccatcgt tcatacgagc gacaggggct tgagaaaacg
     3301 cctggtattc acctcggaaa gtctgcctgt gcgatggaaa cacgcggtat cgaaacagaa
     3361 cgcggcgaac agaatcgtct gattaacagg cttaacctgg aaatacagat ttcccgcacc
     3421 gaactcagga acggagggct gacagagcct gcccgccgtg tggctgacct tctgaatatc
     3481 gggcttcctg acaacgcaac ttcgtacaca ctacgtgaca tcatcgaagc gttgccgaag
     3541 gacagtaatg cggcatggaa actcaccagt aatgccatgt cgatgatggc agatatgcag
     3601 gcgacgcgca gacgctggga agagctgaac accgaacgaa aggaagcgat gagccatgct
     3661 gccagcctga aaaaatcatc gccgttttcg tccggttttt cccgtattcc cctgatgcaa
     3721 tgggcggcac cggaataccg tagtgagcag ggaaaaatcc agtctctgag ccagcaaatg
     3781 gaaaaattac gacagcatta ccggaaggtg gagaaacagg acattcccgc gagtcagatg
     3841 gcatttgaaa aacagtggca gcagtggggg gcatccggcc ttgcagctct cagagtccca
     3901 gttgcttaaa cgtgaagagg aattgcgccg gaaggaacag gaggatactg aacgtagtcg
     3961 cgcgacgagc ggaacagctc aggaaaaatg acaatgccgt tatggattca ggggtgctga
     4021 gcgcagtcgt tacggggtat ggcgaggctc cccatgcctg gtaacgggga aatgacctgt
     4081 taccttctgc
//
