LOCUS       NZ_CP054944             3608 bp    DNA     circular CON 14-JUN-2023
DEFINITION  Escherichia coli strain MS6192 plasmid pMS6192D, complete sequence.
ACCESSION   NZ_CP054944
VERSION     NZ_CP054944.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13155204
            Assembly: GCF_013357345.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3608)
  AUTHORS   Ashcroft,M., Forde,B.M., Phan,M.-D., Peters,K.M., Henderson,A.M.,
            Hancock,S.J., Roberts,L.W., White,R.T., 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  JOURNAL   Unpublished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 3608)
  AUTHORS   Ashcroft,M., Forde,B.M., Phan,M.-D., Walsh,T.R., Schembri,M.A. and
            Beatson,S.A.
  TITLE     Direct Submission
  JOURNAL   Submitted (10-JUN-2020) 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
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 112.93x
            Sequencing Technology             :: PacBio RS; Illumina HiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/14/2023 02:25:29
            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)                     :: 5,132
            CDSs (total)                      :: 5,008
            Genes (coding)                    :: 4,803
            CDSs (with protein)               :: 4,803
            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)              :: 205
            CDSs (without protein)            :: 205
            Pseudo Genes (ambiguous residues) :: 0 of 205
            Pseudo Genes (frameshifted)       :: 78 of 205
            Pseudo Genes (incomplete)         :: 124 of 205
            Pseudo Genes (internal stop)      :: 37 of 205
            Pseudo Genes (multiple problems)  :: 36 of 205
            Pseudo Genes (short protein)      :: 3 of 205
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP054944.1.
            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..3608
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="MS6192"
                     /isolation_source="Clinical sample: urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pMS6192D"
                     /geo_loc_name="India:South"
                     /collection_date="2003/2009"
                     /collected_by="Timothy R Walsh"
                     /subtype="ST101"
     gene            complement(join(3333..3608,1..48))
                     /gene="mobA"
                     /locus_tag="MS6192_RS25380"
     CDS             complement(join(3333..3608,1..48))
                     /gene="mobA"
                     /locus_tag="MS6192_RS25380"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052604.1"
                     /GO_process="GO:0006355 - regulation of DNA-templated
                     transcription [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization protein MobA"
                     /protein_id="WP_000166966.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="mobA"
     gene            333..527
                     /locus_tag="MS6192_RS25385"
     CDS             333..527
                     /locus_tag="MS6192_RS25385"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041624.1"
                     /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_039023183.1"
                     /translation="MNKQQQTTLNMAKFIKSQSLTLLEKLDSLDADAQAAMCEKLHELA
                     EELQNSIQTRFESESGTGV"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1023..1181
                     /locus_tag="MS6192_RS25860"
     CDS             1023..1181
                     /locus_tag="MS6192_RS25860"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001354639.1"
                     /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_071532985.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPKRHDLSPLAAATGNWNSRAMIM
                     RSVLQSS"
                     /name="replication initiation protein"
     gene            complement(1386..2903)
                     /locus_tag="MS6192_RS25390"
                     /old_locus_tag="MS6192_D00002"
     CDS             complement(1386..2903)
                     /locus_tag="MS6192_RS25390"
                     /old_locus_tag="MS6192_D00002"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000739598.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="NERD domain-containing protein"
                     /protein_id="WP_020833675.1"
                     /translation="MKKNIVRQVLESYGPCISSELAERIKRQNPSMSSDAIRKMISRST
                     DIGKLPFLRFSHNRRFIYLKDDFGSFKFWRALKKCMREANSAYSHAILSVINNGGYLKV
                     KDFGIVSGSPIKQAKHLSYESVLKNLLSAKILRSVYIDGIGDCVLINNNIANDISIFNM
                     ANCESFFDKPIFELIKAWLRNLGIVAFNQIKTKYDGENNPVVGSFEWDITAPSYVSPLA
                     EYSSDGLIPGFVVCDFALGFNRNEITTDAADTFIRKVQMTKSSRTNQRIMFVLFARRFE
                     KNAFNKLRSEGVLAITIANAFGNKVDESLARLSKVIQGTLSIERHPDELLQMVKDLESI
                     SGENGNLRGYIFELFVSSQICNFYGYGNVRINKEYKINGKHAEADVVLETNDDIYIVEC
                     KNVKTLPSMEVSLWMKTRVPIINSYYKSNNPDNKNIHHRLWVTGNIYPKDINRLDEFKC
                     NNKKIDVDYLFGQSLDDFFYQKKQVFNLYRKVISPDYKKGQIPDFDL"
                     /name="NERD domain-containing protein"
     Typing          complement(58..295)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.167"
                     /coverage="99.0"
                     /evalue="2.15e-118"
     Typing          571..1091
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.905"
                     /coverage="95.0"
                     /evalue="0.0"
     Typing          complement(3337..3608)
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.901"
                     /coverage="85.0"
                     /evalue="1.77e-51"
ORIGIN
        1 gcgactgata gcccgcctgc gcgtattact tccacttcgt tttgtcataa aacatggctc
       61 cgtatctgac atggggtgtc ggggcgaagc cctgaccagg gtaattgtaa tagcgcgcat
      121 gtatgcgcgg tataacaatt acacatcctg tcctgtcagc aagttcgaat taccgacaaa
      181 ggcacggcag ttttttggca gtgacagtat tgtcaggcag aaatgcccgt caaagagtca
      241 gacggcagaa taccggcggc aaaactgtcg aaaagtggta cgcgatataa tcacacgacg
      301 cagatgacag acagaacgga gaaaacagaa agatgaacaa gcagcagcaa accacactta
      361 acatggcaaa attcataaaa agccagagcc tgacgctgct cgaaaaactg gactcactcg
      421 atgctgatgc acaggccgcc atgtgtgaga aactgcacga actcgcagaa gaactccaga
      481 acagcataca gacacgcttt gaatcggaaa gtggcaccgg ggtataacag tgtatcctgc
      541 tccagacagg atgcagaacg gtataccggt gcgtaaggag aaaatgccac ataaggcgct
      601 cttccgcttc ctcgctcact gactcgctac gctcggtcgt tcggctgcgg cgagcggtat
      661 cagctcactc aaagacggta atgcggttat ccacagaatc aggggataaa gccaaaagaa
      721 acatgtgagc aaaaaacaag aacccgaaaa aggccgcgcc ggtggcgttt ttccataggc
      781 tccgcccccc tgacgagcat cacaaaaatc gacgctcaag ccagaggtgg cgaaacccga
      841 caggactata aagataccag gcgtttcccc ctggaagctc cctcgtgcgc tctcctgttc
      901 cgaccctgcc gtttaccgga tacctgtccg cctttctccc ttcgggaagc gtggcgcttt
      961 ctcatagctc acgctgttgg tatctcggcc cggtgtaggt cgttcgctcc aagctgggct
     1021 gtgtgcacga accccccgtt cagcccgacc gctgcgcctt atccggtaac tatcgtcttg
     1081 agtccaaccc gaaaagacac gacttatcgc cactggcagc agccactggt aactggaata
     1141 gcagagcgat gataatgcgg tccgtactac agagttcttg aagtgatgcc ccaactacgg
     1201 ctacacttaa aggacaggat ttggtatctg cgctctgctg aagccagtta cctaggttag
     1261 gtaatctgcc aggattaact aaccttcgaa aaaccacctt gccgggtggt tttttcgttt
     1321 catggaggaa gatacgcttt tcaagccgtc atcgtcaaga aatgcagaga ctagaaaacg
     1381 tcattctata agtcaaaatc gggtatttgc ccttttttat aatctggcga aatgactttc
     1441 ctatataaat taaacacttg ttttttttgg tagaaaaaat catccaaaga ctgaccaaat
     1501 aaataatcaa catcaatctt cttattatta catttaaact cgtccaatcg gtttatatct
     1561 ttaggatata tattccccgt aacccacaaa cgatgatgta tatttttgtt atcagggtta
     1621 tttgatttgt agtaggaatt tataattggc actcttgttt tcatccaaag actaacctcc
     1681 atcgaaggta aagtcttaac atttttgcac tcaacgatat aaatatcatc gttagtttcc
     1741 aatacaacat cagcttcggc atgtttaccg tttattttat attctttatt aatacgaaca
     1801 tttccataac catagaaatt acaaatttga gaggaaacaa aaagctcaaa aatatacccc
     1861 cttaaatttc cattctctcc agagatagac tccagatctt ttaccatttg aagtaactca
     1921 tcaggatgtc tttcaataga taaagttccc tgaatcacct tcgatagtct ggccaagctc
     1981 tcatcgacct tattaccaaa cgcattagct atagttatag ccagaacccc ttcactcctt
     2041 agcttgttga aggcattctt ctcaaaacgt ctagcaaaaa gaacaaacat aatcctctgg
     2101 tttgtcctag aggacttggt catctgaact tttcttatga aggtatcagc agcatcggtg
     2161 gtaatttcat ttcgattaaa ccctagagca aaatcacaga caacaaaacc tgggatgagt
     2221 ccatcgctgg aatattcagc aagaggggac acataacttg gcgctgttat atcccactcg
     2281 aaagaaccaa ccacaggatt gttctctcca tcatattttg tttttatttg attaaaagcc
     2341 acaataccta aatttcgcaa ccatgcctta atcagttcaa atattggctt atcaaaaaaa
     2401 gactcgcaat ttgccatatt aaagatgctg atatcattag ctatattatt atttatcaaa
     2461 acacaatcac caataccatc aatatacaca gatctaagta ttttagctga aagcagattt
     2521 tttagaacag attcataact taaatgcttg gcctgcttta tcggagagcc agacacaatc
     2581 ccaaaatcct ttaccttcaa gtatccgcca ttattaatta cggaaagtat agcgtgagaa
     2641 tacgccgaat ttgcctcacg catacatttt ttgagcgccc gccaaaattt gaagctacca
     2701 aagtcatctt ttagataaat gaatctcctg ttatgactaa atcttaaaaa tggcaactta
     2761 ccaatatcag tgcttcgaga gatcatttta cgtattgcat cagatgacat agaaggattc
     2821 tgacgcttaa tcctctcagc aagttcagaa gatatgcacg gaccataact ctcaagcact
     2881 tgtctaacaa tgtttttttt cataaattca tcttattttt gtcacactac gctatttata
     2941 aaattacact acgtgtaata tctatagatc ccaaaaaaaa cacaaagaaa aaaatcataa
     3001 aaatcaaaca tttaacaaaa gcaacatatc acaaaaaaca cacctgcgag atttatcctt
     3061 aaaaatcaag atgttacgtt tgtgacattt catcatcata tatcaaccgc cctatttacc
     3121 ataatccctt aattacgcgc accgctaaaa cgcgctgaac gcgattctgc cgcaaacacc
     3181 gcaaaaagag atgttttacc cagtgaaaac cggaaaaatg cgtcaggacc gttttcagct
     3241 cactgcatag ctatgcatga aagtgaatgg cgatcggttt ggggccttac ggcgttcata
     3301 ccgtctgttt tcgacagttt ctctccggga agctaatctg ccataagcct ggataacagg
     3361 gcccggtgat actccgtaat agcgatcagc acctccgcat actctctgtc cccgacacgc
     3421 ttgccgtcga taaagagttt tttctgtaac gcccccagtc tcataacttc tttcagtacc
     3481 cgatcatcag tcagtgagtt aactttctta ccgagagctg ccgcccgtaa aaaaccggaa
     3541 acggtcttgc cgcattcagc agcccttttt ctgatttcct ggtcttcttc tgccgtcaga
     3601 cgaacagg
//
