LOCUS       NZ_CP047408             4367 bp    DNA     circular CON 13-JUN-2023
DEFINITION  Escherichia coli strain MS6193 plasmid pMS6193C, complete sequence.
ACCESSION   NZ_CP047408
VERSION     NZ_CP047408.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13155539
            Assembly: GCF_013317085.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4367)
  AUTHORS   Ashcroft,M., Forde,B.M., Phan,M.-D., Peters,K.M., Henderson,A.M.,
            Hancock,S.J., Roberts,L.W., Chan,K.-G., Chong,T.M., Yin,W.-F.,
            Paterson,D.L., Walsh,T.R., Schembri,M.A. and Beatson,S.A.
  TITLE     Genomic characterisation and context of the blaNDM-1 carbapenemase
            in Escherichia coli ST101
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4367)
  AUTHORS   Ashcroft,M., Forde,B.M., Phan,M.-D., Walsh,T.R., Schembri,M.A. and
            Beatson,S.A.
  TITLE     Direct Submission
  JOURNAL   Submitted (31-DEC-2019) Microbiology and Immunology, The University
            of Melbourne, 792 Elizabeth Street, Melbourne, Vic 3000, Australia
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 08-JAN-2019
            Assembly Method                   :: HGAP v. 2.3.0
            Assembly Name                     :: Ecoli_MS6193
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 86.7x
            Sequencing Technology             :: PacBio RSII; Illumina HiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/13/2023 04:02:37
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,078
            CDSs (total)                      :: 4,954
            Genes (coding)                    :: 4,746
            CDSs (with protein)               :: 4,746
            Genes (RNA)                       :: 124
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 93
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 208
            CDSs (without protein)            :: 208
            Pseudo Genes (ambiguous residues) :: 0 of 208
            Pseudo Genes (frameshifted)       :: 76 of 208
            Pseudo Genes (incomplete)         :: 129 of 208
            Pseudo Genes (internal stop)      :: 36 of 208
            Pseudo Genes (multiple problems)  :: 35 of 208
            Pseudo Genes (short protein)      :: 3 of 208
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP047408.1.
            Bacteria and source DNA available from Professor Mark Schembri, The
            University of Queensland, St Lucia, QLD, 4067 Australia.
            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..4367
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="MS6193"
                     /isolation_source="Clinical sample: urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pMS6193C"
                     /geo_loc_name="India: South"
                     /collection_date="2003/2009"
                     /collected_by="Timothy R Walsh"
                     /subtype="ST101"
     gene            268..735
                     /locus_tag="MS6193_RS25100"
                     /old_locus_tag="MS6193_C00001"
     CDS             268..735
                     /locus_tag="MS6193_RS25100"
                     /old_locus_tag="MS6193_C00001"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011899450.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_158661896.1"
                     /translation="MPAPNNYGVVGSPNSAIAHPDGLDCYGRVPEINSKGDVIPAGDIF
                     LRVGRHTGPNRGFGVRHIWAEHEQELVKLGYATVNDVARFVRDIIRRGVPIYCEFNSTS
                     GKHRPAVLKSSVGIVILEPREAPETESGWIYVVVTAYTRRTAHGTLVGHIE"
                     /name="hypothetical protein"
     gene            2050..2373
                     /locus_tag="MS6193_RS25105"
                     /old_locus_tag="MS6193_C00004"
     CDS             2050..2373
                     /locus_tag="MS6193_RS25105"
                     /old_locus_tag="MS6193_C00004"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000957083.1"
                     /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_000957080.1"
                     /translation="MLTMWVTEDEHRRLLERCDGKQLAAWMRQTCLAEKPARAGKLPSI
                     SPALLRQLAGMGNNLNQIARQVNAGGGSGHDRVQVVAALMAIDAGLERLRHAVLEKGAD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            2582..>3016
                     /locus_tag="MS6193_RS25605"
                     /pseudo=""
     CDS             2582..>3016
                     /locus_tag="MS6193_RS25605"
                     /inference="COORDINATES: protein motif:HMM:NF015397.2"
                     /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            3051..3536
                     /locus_tag="MS6193_RS25115"
     CDS             3051..3536
                     /locus_tag="MS6193_RS25115"
                     /inference="COORDINATES: protein motif:HMM:NF016710.2"
                     /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_089624851.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQSTGEMLKVAFSEHEKSVRAELSESE
                     KRISAAILDHDRKLSSAMSQRTKGMVRMVSQTWLTIVLVSTLLTASGASILWWQGQQIL
                     DNYTIIREQKSTQAMLSERNSGVQLSTCGEQRRRCVRVNPEAGRFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            3540..3755
                     /locus_tag="MS6193_RS25120"
     CDS             3540..3755
                     /locus_tag="MS6193_RS25120"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137421.1"
                     /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_000137420.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWENAFAEWRTMFGLMQRENA
                     ALSERVTGLSRQVQSLSEQLRRLSQG"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(3954..4217)
                     /locus_tag="MS6193_RS25610"
                     /old_locus_tag="MS6193_C00006"
     CDS             complement(3954..4217)
                     /locus_tag="MS6193_RS25610"
                     /old_locus_tag="MS6193_C00006"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_249939065.1"
                     /translation="MLTDGQRYPVAYLSAQEAFLRIGVTPEQLEWKKFHPSSPSVPNTV
                     IPGLAEEKTEKLSLNEAIERAKKDISNATGIDSSAITISIKI"
                     /name="hypothetical protein"
     Typing          1762..1946
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="86.17"
                     /coverage="86.0"
                     /evalue="5.83e-49"
     Typing          complement(1304..1816)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.829"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          2364..3859
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.385"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 agtttactgc cggttttacc gggctaacgc cgctttcacg ctgaacccgt ccggagcggt
       61 gcgggcaagg gatgttatgg taaatctagc tgctagggcg attcgcacgt cacattttca
      121 ggtgtgatat ccttatgcgc caaggatgaa aggacaaaaa aataatccat aaggattctt
      181 tttatcgtct ctgctttttt cttgggctcc ttccgcttgt ttcctctctg gtaccatatg
      241 cggactctac tcaataagga tcgttttgtg cctgctccaa acaattacgg tgtagttggt
      301 tcacctaaca gcgctatagc tcaccctgat gggcttgatt gctatggccg tgtccctgaa
      361 attaattcta aaggtgatgt tattcctgct ggcgacatct tcttgcgtgt tggtaggcat
      421 actggcccta accggggctt tggtgttcgc catatctggg ctgagcacga gcaggaactg
      481 gttaagctgg gatatgcgac cgttaatgat gtggctcgtt ttgtccggga tattattcgt
      541 cgtggcgtac caatatattg cgagttcaac agtacaagcg gtaaacatcg gcctgcagtg
      601 ctaaagtcgt cggtaggcat cgtaattctt gagcccagag aagcgcctga aactgagtca
      661 ggttggatct atgtcgttgt gactgcgtac acacgaagga cggcgcacgg tactttggtt
      721 ggtcatattg aataaaaaaa tagggcgcta aaaagcgccc tttatgaatt cgttggtagt
      781 cgcagcattt ccttagcaca tagggttcag aaaccgacgc ttgtcgtaac tacccggcag
      841 atgaccagcc atctgactgc ccggcacaga aggcctatta ctggttgatg ccccctgcga
      901 atgctcttgc agtacaataa tcataaacat cgtgatgtag atttgcaacc aacattttgg
      961 ttgcaaccta tatactaatt tttttcgata accctggaat ccattgctgt gtctggattt
     1021 cttgaagctc ctggctatag ataccctata tcctaacagt tattctgctg tgaatatcag
     1081 aaatgaacac ttgagatcat cagtggctcg tcgtagtctc ttgctcagaa acgaaaaaac
     1141 caccctggca ggtggttttt tcgaaggtta gttaatcctg gcagattctc taaccgtggt
     1201 aacagtcttg tgcgagacat gtcaccaaat actgtccttt cagtgtagcc tcagttaggc
     1261 cgccacttca agaactctcg ttacatctct cgcacatcct gcttaccagt ggccgttgcc
     1321 aatggcgatt agtcgtgtct atccgggttg gactcaagac gatagttacc ggacaaggcg
     1381 cagcggtcgg actgaacggg gggttcgtgc atacagtcca gcttggagcg aactgcctac
     1441 ccggaactga gtgtcaggcg tggaatgaga taaacgcggc cataacagcg gaatgacacc
     1501 ggtaaaccga aaggcaggaa caggagagcg cacgagggag ccaccagggg gaaacgcctg
     1561 gtatctttaa gtcctgtcgg gtttcgccac cactgatttg agcgtcagat ttcgtgatgc
     1621 ttgtcagggg ggcggagcct atggaaaaac ggcagcgccg catccttttc ctgtcctgct
     1681 tgccatgccg tatgcctttg ctcttatccg tttgcaggta acgcccgccg cagccgaacg
     1741 tcaggagcgg aagcgaccga gtgagcgagg aggcgtcata tcaccgtaac ctccattttc
     1801 tcctgtacgc cctgcagctg catttttccc ctgccacatg aagcactttc attacgtgtt
     1861 actccgccgt aacatattga gccagtatac actccgctag cgctacgtga ctggttcagg
     1921 gctgcgcccc gaaacctgct aaaaccactg acgcgcctgc ggcttgtcca acaccgcgcc
     1981 gaccgggaaa agatttcccg cccgtcccgg cgttatcagg agatcggttt gtcagagaaa
     2041 cggaacaaga tgctcaccat gtgggtgacc gaagatgagc accgccgtct gctggaacgc
     2101 tgcgacggta aacagcttgc agcctggatg cgccagacgt gcctggccga gaaacccgcc
     2161 cgcgccggca agcttccctc gatctcgccg gcgctgctcc gtcagcttgc cggcatgggg
     2221 aataacctca accagattgc ccggcaggtt aacgccggtg gcggcagcgg gcacgaccgc
     2281 gtgcaggtcg tcgccgcgct gatggccata gatgccggac tcgagcggct gcggcatgcc
     2341 gtgctggaaa agggtgcaga cgatgatcgt taagtttcac ccgcgagggc gcggcggtgg
     2401 cgccggtccg gtggattatc tgctggggaa agaccgacag cgcgacggcg ccaccgttct
     2461 gcaggggaag ccggaagaag tcagggagct tatcgacgcc tcgccctacg caaaaaagta
     2521 cacatccggc gtcctgtcct ttgccgaaaa ggatttaccg cccgggcagc gcgaaaagct
     2581 gatggcgagc tttgaacggg ttctgatgcc cggactcgat aaagaccagt acagcgtgct
     2641 gtgggttgag caccaggata aggggcggct ggagctgaac ttcctgatcc cgaacatgga
     2701 gctgctgaca ggcaggcgtc tccagccgta ttacgaccgc gccgaccgtc cgcgcattga
     2761 tgcctggcag accatcgtga acggcaggct ggggctgcat gacccgaacg cacctgaaaa
     2821 ccggcgggcg ctggtcacgc cgtccgcgct gccgaaaacg aagcaggaag ccgctcaggc
     2881 aattacacgg ggtttactgg ccttagcctc gtccggggag ctgaaaaccc gccaggacgt
     2941 cactgaggcg ctagaaagcg caggttttga ggtggtgcgc accacaaaaa gcagcatcag
     3001 cattgccgac ccggacgggg ggcgaaacat ccgactgaag ggagccatct atgaacagtc
     3061 ttttaacgct ggcgaaggac ttagagcaga aatcgaaagc gcagcagcag agtaccggcg
     3121 agatgctgaa agtcgcattc agcgagcacg agaagtctgt cagagcggaa ctgagcgaaa
     3181 gcgagaagag aatcagcgcc gccatcctcg accacgaccg gaagctgtcc tcagccatga
     3241 gccagcgcac gaaaggcatg gtgcgtatgg tcagccagac gtggctgacc atcgtcctgg
     3301 tgtctacact gctgacagca tcgggcgcca gcattctatg gtggcagggg cagcagatac
     3361 tcgacaatta tacgatcatc cgggagcaga agagcacgca ggccatgctg tccgagagga
     3421 acagcggcgt gcagctctcg acctgcggag agcagagacg ccgctgcgtg agggtgaacc
     3481 cggaagcggg acggttcgga gaggattcga gctggatgat actggcgggg aaatagcaca
     3541 tgacggagct ggaaaaacag ttgctgagcg cattagagca gctacagcag gactactcga
     3601 aaaggctgga cgagtgggag aacgccttcg cggaatggcg gacgatgttt ggtcttatgc
     3661 aacgggagaa cgcggcgctg agcgagcgcg tcacgggctt gagcaggcag gtgcagagtt
     3721 tgagcgagca gctgcgccgg ttgtcacaag gctgaacgtg atagaggcac atcgtgagca
     3781 ggaacgggcg gcgcagcatc agaaagcgct ggagctggaa cgatctcagc gacagcgaac
     3841 gtacaacggt ccgtcacttt gaatctgtgc gccggaaaag catgggcttg ctgtttctgg
     3901 cgcataggtt cagttctaga acatgaggct gctatcttgt tgttcacgct tcatcagatc
     3961 ttgatgctta ttgttatggc tgagctatca atccctgttg cgttgctaat atcctttttg
     4021 gctctttcaa ttgcctcgtt aagggagagt ttttctgttt tctcttcagc cagaccagga
     4081 atcactgtat taggaaccga tggggatgaa ggatggaatt tcttccattc cagttgttcc
     4141 ggtgttaccc caatacgtaa aaaagcttcc tgtgcgctca ggtaagcaac cggatagcgc
     4201 tgaccatcgg ttagcatttt ccatgctttt ggagtgtgaa tttctgcgta ttcatcaaag
     4261 gttatgacgt tcctgtcgtc gtaatcaggg cttttaaaac acccggtaat tttggcgatc
     4321 aggaatgctg tgccgtgttc caggtctttt actgcccacg tttccct
//
