LOCUS       NZ_CP059337             5219 bp    DNA     circular CON 03-SEP-2023
DEFINITION  Escherichia coli strain MS10860 plasmid pMS10860E, complete
            sequence.
ACCESSION   NZ_CP059337
VERSION     NZ_CP059337.1
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 5219)
  AUTHORS   White,R.T.
  TITLE     Escherichia coli ST410 strain MS10860 plasmid pMS10860E
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5219)
  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
            CP059337.1.
            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..5219
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="MS10860"
                     /serotype="O75:H5"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pMS10860E"
                     /geo_loc_name="Australia: New South Wales"
                     /collection_date="2007"
     gene            complement(join(5110..5219,1..214))
                     /locus_tag="MS10860_RS25315"
     CDS             complement(join(5110..5219,1..214))
                     /locus_tag="MS10860_RS25315"
                     /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="plasmid mobilization relaxosome protein MobC"
                     /protein_id="WP_000955995.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIERELRSLRQVVREHGAR
                     DDS"
                     /name="plasmid mobilization relaxosome protein MobC"
     gene            279..470
                     /locus_tag="MS10860_RS25320"
     CDS             279..470
                     /locus_tag="MS10860_RS25320"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165985.1"
                     /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_000165985.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1138..1251
                     /locus_tag="MS10860_RS25325"
     CDS             1138..1251
                     /locus_tag="MS10860_RS25325"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001422066.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001427889.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHDLTPLAAAIGN"
                     /name="hypothetical protein"
     gene            1657..2046
                     /locus_tag="MS10860_RS25330"
                     /old_locus_tag="MS10860_E0003"
     CDS             1657..2046
                     /locus_tag="MS10860_RS25330"
                     /old_locus_tag="MS10860_E0003"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001679965.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000477210.1"
                     /translation="MFKSSVKSITSSTILTLLIGCSSTETNKNIVYKVGGDSIILNKYC
                     ILKMYPSQSEKNKGVIIEVNTDSLCKKKLNEITSKNIGKPLISYFDGKVISQPAIIHSA
                     LNPTHYYQPVNDETTVMEIIKAYSK"
                     /name="hypothetical protein"
     gene            complement(2110..2394)
                     /locus_tag="MS10860_RS25335"
                     /old_locus_tag="MS10860_E0004"
     CDS             complement(2110..2394)
                     /locus_tag="MS10860_RS25335"
                     /old_locus_tag="MS10860_E0004"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000625497.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin Z C-terminal domain-related protein"
                     /protein_id="WP_000625497.1"
                     /translation="MISQNVWAPPFFFGPWVELENHTGDIAYTVYFDTLSNVPGPFIAF
                     IWYAPNGPRTVNVIGPASYQISCKGAGVDKIKFKSVSGTGQIIHVYTTL"
                     /name="colicin Z C-terminal domain-related protein"
     gene            complement(2412..2609)
                     /locus_tag="MS10860_RS25340"
                     /old_locus_tag="MS10860_E0005"
     CDS             complement(2412..2609)
                     /locus_tag="MS10860_RS25340"
                     /old_locus_tag="MS10860_E0005"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001335786.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001335786.1"
                     /translation="MKEEKVLLHRFLFVVRNKNGCELSCSADLMGTRDDVYKYFSDSVS
                     GLDVELIDVSCESEWEEHSH"
                     /name="hypothetical protein"
     gene            2821..3117
                     /locus_tag="MS10860_RS25345"
                     /old_locus_tag="MS10860_E0006"
     CDS             2821..3117
                     /locus_tag="MS10860_RS25345"
                     /old_locus_tag="MS10860_E0006"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001679964.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000047647.1"
                     /translation="MSKTKSGRHRLSKTDKRLLAALIAAGYEERTARDLIQKHVYTLTQ
                     ADLRHLVSEISNGVGQSQAYDAIYQARRIRLARKFLNGKKPEEGLNAWKGDLP"
                     /name="hypothetical protein"
     gene            complement(3662..3895)
                     /locus_tag="MS10860_RS25350"
     CDS             complement(3662..3895)
                     /locus_tag="MS10860_RS25350"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /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_000137439.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLNEWESAFVELQKMFSLTQRDNA
                     MLNERVMQLSQQVQHLSEQTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(3902..4432)
                     /locus_tag="MS10860_RS25355"
     CDS             complement(3902..4432)
                     /locus_tag="MS10860_RS25355"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001673158.1"
                     /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_015386306.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTETILNDEFRKLEKSVSKAVTSNE
                     TKIKDAIALFTASTEESLKKHREGVKEAMMQHRKDVLKLAGNTGMMLLGMVIFLFTVSG
                     GTLWYLGGMIQANLEEIRKQNENLEKLNAKTWGVRYHEGSNGRFLVLPEGMKAETNWTM
                     ENGKQNAVRLVQE"
                     /name="MbeB family mobilization protein"
     gene            complement(<4470..5132)
                     /locus_tag="MS10860_RS25360"
                     /pseudo=""
     CDS             complement(<4470..5132)
                     /locus_tag="MS10860_RS25360"
                     /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"
     Typing          complement(556..642)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="99.0"
                     /evalue="2.47e-38"
     Typing          654..1210
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.642"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(3..247)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="96.341"
                     /coverage="99.0"
                     /evalue="5.89e-46"
     Typing          complement(3559..5120)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 actgcccgct gttcaccttc ctcgccgtct gattcaggtt attcccgatg gcagccagct
       61 ggcgcagtaa cggcggtgcc agtgtcggca gcttcccgga acgggcaacc ggctcaccca
      121 gacagacccg ccgcatccat accgccagct gtttaccctc acagcgttca agtaaccggg
      181 catgttcatc atcagtaacc cgtattgtga gcatcctctc gcgtttcatc ggtatcatta
      241 tccccatgaa cagaaatccc ccttacacgg aggcatcagt gaccaaacag gaaaaaaccg
      301 cccttaacat ggcccgcttt ataagaagcc agacattaac gctgctggag aagctcaacg
      361 aactggacgc ggatgaacag gcagatatct gtgaatcgct tcacgaccac gccgatgagc
      421 tttaccgcag ttgcctcgct cgcttcgggg atgacggtga aaacctctga cacatgcagc
      481 tcccggagac ggtcacagct tgtctgtgag cggatgccgg gagctgacaa gcccgtcagg
      541 gcacgtcagc gggttttagc gggtgtcggg gcgcagccct gacccagtca cgtagcgata
      601 gcggagtgta tactggctta accatgcggc atcagtgcgg atggtatgaa aagtgcgcca
      661 taccgggtgt gaaatgccgc acagatgcgt aaggagaaaa tgcacgtcca gccgcttttc
      721 cgcttcctcg ctcactgact cgctacgctc ggtcgttcga ctgcggcgag cggtatctac
      781 tcactcaaaa acgaaatgct gttatccaca gaatcagggg ataacaccgg aaaaaacatg
      841 tgagcaaaag accaggaaca ggaagaaggc cgcgccgctg gcgtttttcc ataggctccg
      901 cccccctgac gagcatcaca aaaatcgacg ctcaagtcag aggtggcgaa acccgacagg
      961 acttaaagat accaggcgtt tccccccgga agctccctcg tgcgctctcc tgttccgacc
     1021 ttaccgttta ccggatacct gtccgccttt ctcccttcgg gaagcgtggc gctttctcat
     1081 agctcacgct gtaggtatct cagttcggtg taggtcgttc gctccaagct gggctgtgtg
     1141 cacgaacccc ccgttcagcc cgaccgctgc gccttatccg gtaactatcg tcttgagtcc
     1201 aacccggtaa gacacgactt aacgccactg gcagcagcca ttggtaacta aaaagtggat
     1261 ttagatacgc agaactcttg aagttgaagc cttatagcgg ctacactgaa aggacatctt
     1321 ttggtatctg tgctccactt aagccagcta cccggttagg taatctgcca ggattagcta
     1381 accttcgaaa aaccacctgc cagggtggtt ttttcgttta caggcagcag attacgcgca
     1441 gaaaaaaagg atctcaagaa gatcctttga tcttttttct ctaaactgca atcccatcag
     1501 ttcaggagag aaagatagta taattgccct ctcttatatg gaaccaccat tcaatcacat
     1561 catgggaata atataagtga aaacgttcgc attgtttatt tttacgtgta tatgtattta
     1621 tagattggaa ttttaacaaa ataaaatgga gttaatatgt tcaaatcatc agtaaagtca
     1681 ataacatcga gtactatact gaccttactt ataggatgtt caagtactga aacaaacaaa
     1741 aacattgttt acaaagttgg tggtgacagc atcattctga ataaatattg catacttaaa
     1801 atgtaccctt cccaatcaga aaaaaacaaa ggcgtcataa tagaagtaaa cacagatagt
     1861 ttatgtaaga aaaaactaaa cgaaataact agtaaaaata tagggaaacc cctgatttca
     1921 tattttgatg gaaaagtaat atcccaacct gcaatcattc attctgcact aaatccaacc
     1981 cattattatc aacctgtgaa cgatgaaaca acagtgatgg aaatcataaa agcatattca
     2041 aaataatatt aatagatata atcctgctta aggtatagct taggcaggat tatatctatt
     2101 cagctcttat tataaggtag tgtatacatg aataatctgc cctgtcccac tgacactttt
     2161 aaatttaatt ttatcaacac cagcgccctt gcaagagatc tgataagatg ctggaccaat
     2221 aacgttaact gttcttggcc cattaggggc ataccagata aaagcaataa atggaccggg
     2281 tacattagac aatgtatcaa aatagacagt gtacgcgata tcaccagtat gattttcaag
     2341 ttcaacccaa ggaccaaaaa agaaaggagg agcccaaaca ttttgagaaa tcatataatc
     2401 tcctgattag ttcaatgcga atgttcttcc cattcactct cgcaagaaac atctataagc
     2461 tcaacatcta gcccactaac agaatcagag aaatacttat aaacatcatc ccttgttccc
     2521 ataaggtctg ccgaacatga tagttcacaa ccattcttat tcctaactac aaataagaaa
     2581 cggtgaagca atactttttc ttctttcatt ttatccctcc ctttatttac acagaatata
     2641 ctgtatatat aaatactagt tttatataca gtataaatta cgccgcatta tttttcctgt
     2701 caatgatatg aattttcatt tttgtgatct gaatcaccct tataaaaatc aggaagggaa
     2761 gattcgcagc agaaaaacag caccggataa catcaagaga aaaaacagag aggagataac
     2821 gtgagcaaaa caaaatctgg tcgccaccga ctgagcaaaa cagacaaacg cctgctggct
     2881 gcacttatcg ctgccggata cgaagagcgg acagcccgtg acctcatcca gaaacacgtt
     2941 tacacactga cacaggccga cctgcgccat ctggtcagtg aaatcagtaa cggtgtggga
     3001 cagtcacagg cctacgatgc gatttaccag gcaagacgca ttcgtctcgc ccgtaaattc
     3061 ctgaacggaa aaaaaccgga agaagggctg aacgcctgga agggtgattt accataatca
     3121 cttattgtac gcaccgctga aacgcgttcg gcgcgatcac ggcagcagac aggtaaaaat
     3181 ggcaacaaac cacccgaaaa actgccgcga tcgtacccgg taaattttaa ccacatgcat
     3241 agctatgcag ctatgtgaat catgcaggaa ttgccagcca gagacagctg aaacggattt
     3301 ttttcatgct ttcggaagcg aagaagacgg ggaccggagc gggaaaacag aagttcaggg
     3361 gaatgagcgc gatctggcaa tagaggcaaa acacagcaac aaaagacaca ccagaatcgc
     3421 gcccgtatgc gttttaacgc gttcctgtgt tttcagcaag gtctgactga agcgcgttcc
     3481 cggtgccccc gaaccaacca ttatcccaaa aaatgcaccg gaaacgcgct gacaacattt
     3541 tagcctgtct ctgattacca tcccagcgaa gggccatcca gtgtccgttc ctgtatttcc
     3601 agctggcgct cacgctccag ggataacgca tgttcgcgtt cctgtatcag ccgttcgtcc
     3661 cttatctcct gttctcgctg tataactggc tcaagcgttc tgtctgctcg ctcaagtgct
     3721 gcacctgctg actcaactgc atgacccgct cgttcagcat cgcgttgtcc cgttgcgtaa
     3781 gcgaaaacat tttctgcaat tccacgaagg cgctctccca ttcgttcagc cgctgcatat
     3841 agtcctgttg cagttgctct aatgcgttca gcaaatgtct ttccagctcc gtcatgctct
     3901 gttactcctg taccagcctt acggcattct gtttcccgtt ttccatcgtc cagttcgttt
     3961 cggctttcat cccctcgggc aacaccagaa aacgtccgtt gctcccctcg tgataacgca
     4021 cgccccatgt cttcgcgttc agcttctcca gattctcgtt ctgcttcctg atttcttcca
     4081 ggttcgcctg tatcatcccg ccaagatacc agagcgtccc gccactcacg gtaaacagga
     4141 aaatgaccat ccccagtaac atcatgcccg tattccctgc cagctttaac acgtccttcc
     4201 tgtgctgcat catcgcctct ttcacccctt cccggtgttt tttcagtgat tcctctgtcg
     4261 aagctgtgaa cagggctata gcgtctttga ttttcgtctc gtttgatgtc acagccttgc
     4321 ttacagattt ttcgagcttc ctgaactcgt cgttcagtat tgtctctgta gattcggctc
     4381 tctctttcag ctttttctcg aactccgcgc ccgtctgtaa aagattgctc ataaaatgct
     4441 cctttcagcc tgatattctt cccaccgttc gggtctgcaa tgctgatact gcttcgcgtc
     4501 accctgacca cttcaagccc tgcctctgtg agcgcctgaa tcacatcctg acggcctttt
     4561 atctccccga catgataaag agcgtctatc ccgcgtgtga cgctctctgc aagcgcctgt
     4621 ttcgtttccg gcaggttatc agggagagtc agtatccggc ggttctccgg ggcgttgggg
     4681 tcatgcagcc cgtaatggtg attaaccagc gtctgccagg catcaattct cggcctgtct
     4741 gcccggtcgt agtacggctg gaggcgtttt ccgctctgta gctccatgtt cggaatgaca
     4801 aaattcagct caagccgtcc cttgtcctgg tgctccaccc acaggatgct gtactgattt
     4861 ttttcgagac cgggcatcag tacacgctca aagctcgcca tcaccttttc acgtcctccc
     4921 ggcggcagct ccttctccgc gaacgacaga acacctgacg tgtatttctt cgcaaatggc
     4981 gtggcatcga tgagttcccg gacttcttcc ggattaccct gaagcaccgt tgccccttcc
     5041 cggttacgct cccttcccag caggtaatca accggaccac tgccaccgcc ttttcccctg
     5101 gcatgaaact taactatcat cccgcgctcc atgttccctg acgacctgcc gtaagctgcg
     5161 caactctctc tcgatggcca tcagtgcggc caccacctga acccggtcac cggaagacc
//
