LOCUS       NZ_CP103539             5631 bp    DNA     circular CON 21-SEP-2023
DEFINITION  Escherichia coli strain 4238 plasmid pMB9108_6, complete sequence.
ACCESSION   NZ_CP103539
VERSION     NZ_CP103539.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN28174054
            Assembly: GCF_024917735.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5631)
  AUTHORS   Shropshire,W.C., Konovalova,A., McDaneld,P.M., Gohel,M., Strope,B.,
            Sahasrabhojane,P., Tran,C.N., Greenberg,D.E., Kim,J., Zhan,X.,
            Aitken,S.L., Bhatti,M., Tor,S., Treangen,T., Hanson,B.M., Arias,C.A.
            and Shelburne,S.A.
  TITLE     Systematic Analysis of Mobile Genetic Elements Mediating
            Beta-lactamase Gene Amplification in Non-Carbapenemase-Producing
            Carbapenem Resistant Enterobacterales Bloodstream Infections
  JOURNAL   mSystems (2022) In press
REFERENCE   2  (bases 1 to 5631)
  AUTHORS   Shropshire,W.C.
  TITLE     Direct Submission
  JOURNAL   Submitted (19-AUG-2022) Infectious Diseases and Infection Control,
            University of Texas MD Anderson Cancer Center, South Campus Research
            Building 4, Houston, TX 77054, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Flye v. 2.8.3-b1695
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 186x
            Sequencing Technology             :: Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 09/21/2023 03:16:44
            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)                     :: 5,040
            CDSs (total)                      :: 4,922
            Genes (coding)                    :: 4,655
            CDSs (with protein)               :: 4,655
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 267
            CDSs (without protein)            :: 267
            Pseudo Genes (ambiguous residues) :: 0 of 267
            Pseudo Genes (frameshifted)       :: 86 of 267
            Pseudo Genes (incomplete)         :: 179 of 267
            Pseudo Genes (internal stop)      :: 42 of 267
            Pseudo Genes (multiple problems)  :: 39 of 267
            Pseudo Genes (short protein)      :: 4 of 267
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP103539.1.
            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..5631
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="4238"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pMB9108_6"
                     /geo_loc_name="USA: Houston"
                     /lat_lon="29.7068 N 95.3971 W"
                     /collection_date="2019-09-28"
                     /collected_by="MDACC"
                     /genotype="ST410"
     gene            complement(join(4919..5631,1..340))
                     /locus_tag="M5T38_RS25050"
                     /old_locus_tag="M5T38_25050"
     CDS             complement(join(4919..5631,1..340))
                     /locus_tag="M5T38_RS25050"
                     /old_locus_tag="M5T38_25050"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001557502.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001053268.1"
                     /translation="MNLQQRINKLPQLSSSFSFGKDIDNIHSFIFNETSKDKIEDLLRK
                     WVSGNQPCVFGKLASKKIKGLDFHLSIVNSPQLYNDDGHLFDFLRNERVRFKERARRGE
                     VSAHLIYFIHPQLAFARPSEELVDIQKYICSLHMPECYPIKEDVIYTESVPFQDKDGLK
                     IYKAGVNVFYSSAHRTRNHDRRIPGGILISVNAPGHFMRLAIEKGFYKDQEQALADIRN
                     MTIQSVGKGGYSHPEGISTTWHSESNLDRFGCPVHTGNSSYYSGFYHTDVLIPGELTKD
                     ERLLHEIENSDPMIFNWNVLFYVSLEEFPIDDPYYGEFIGIPVDDASMFFNSFQPRKFE
                     NKPLYEKEDD"
                     /name="hypothetical protein"
     gene            complement(821..1054)
                     /locus_tag="M5T38_RS25055"
                     /old_locus_tag="M5T38_25055"
     CDS             complement(821..1054)
                     /locus_tag="M5T38_RS25055"
                     /old_locus_tag="M5T38_25055"
                     /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_000137437.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLNEWENAFVELQKMFSLTQRDNA
                     MLNGRVMQLSQQVQHLSERTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(1061..1591)
                     /locus_tag="M5T38_RS25060"
                     /old_locus_tag="M5T38_25060"
     CDS             complement(1061..1591)
                     /locus_tag="M5T38_RS25060"
                     /old_locus_tag="M5T38_25060"
                     /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_001673158.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNDEFRKLEESVNRELTSNE
                     SLIRNAINDHTTALKELLERYQKTTVDTMDAHWKTVLKMSVKRWLWLIIVSVLMFATTG
                     SLLWYQGMKINANMNILREQKESLEKLNAKTWGVRYHEDSNGRFLVLPKGMKAETNWTK
                     DNGKLNAVRLVQE"
                     /name="MbeB family mobilization protein"
     gene            complement(<1629..2327)
                     /locus_tag="M5T38_RS25250"
                     /pseudo=""
     CDS             complement(<1629..2327)
                     /locus_tag="M5T38_RS25250"
                     /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"
     gene            complement(2269..2592)
                     /locus_tag="M5T38_RS25070"
                     /old_locus_tag="M5T38_25070"
     CDS             complement(2269..2592)
                     /locus_tag="M5T38_RS25070"
                     /old_locus_tag="M5T38_25070"
                     /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="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_000955999.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            2657..2848
                     /locus_tag="M5T38_RS25075"
                     /old_locus_tag="M5T38_25075"
     CDS             2657..2848
                     /locus_tag="M5T38_RS25075"
                     /old_locus_tag="M5T38_25075"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165975.1"
                     /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_000165975.1"
                     /translation="MTKQEKTALNMARFIRGQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENR"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(4051..4917)
                     /locus_tag="M5T38_RS25080"
                     /old_locus_tag="M5T38_25080"
     CDS             complement(4051..4917)
                     /locus_tag="M5T38_RS25080"
                     /old_locus_tag="M5T38_25080"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001335763.1"
                     /GO_function="GO:0005215 - transporter activity [Evidence
                     IEA]"
                     /GO_process="GO:0055085 - transmembrane transport [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DMT family transporter"
                     /protein_id="WP_001335763.1"
                     /translation="MIKGMLFAFLAAFSWGAAIVMSKKGVEELDAGGVFFWQICSAVIL
                     SWIVLFIKRKKLPLNSKAILAYATGVFEPFLAYTFTLYGLYFISAGSASIIFSLESVFI
                     LVLSVLICSVKINSPQYFILFLIGAIVGSILVALPDISNGSNNIVGYCLVVAGVLSAAF
                     YVVISSRLIKSFEPITLLSGQLTFSLILSSLFIFISKSSIYLPLESVIIVFSSGILQYF
                     LAFCFYLNSLRWLPVHLAGIMLYFIPLVALFLSWLFLDEQFTFLQGVGFIVTVLSVYFL
                     NRKYSEE"
                     /name="DMT family transporter"
     Typing          complement(2943..3024)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.3400000000000002e-35"
     Typing          complement(3481..3668)
                     /name="rep_cluster_2401"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="4.63e-94"
     Typing          complement(718..2279)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gaataaaata aatgagatgc gcactgacct ctcctcttct tgcgcgttct ttaaaacgaa
       61 ctctttcatt acgcaaaaaa tcaaacaaat gaccatcatc attatatagt tgggggctat
      121 ttacaataga taaatggaaa tcaagccctt taattttctt gcttgccaat ttaccaaata
      181 cacagggctg attgcctgac acccattttc ttagtaaatc ttcaatttta tctttagaag
      241 tttcgttaaa gataaatgaa tgaatattat caatatcttt tccaaatgaa aaactggatg
      301 ataattgtgg tagtttattt atacgttgtt gaagattcat gaaagctccc acaagacacc
      361 tcatatattt ttttatatac tgaaactaca ttatatttat taccggcgta aaacgaaata
      421 atttattatc gttaccgata ttttaaaaaa atcattattt gcacagtgtt cgagttgtta
      481 gtatcactcc ttcctgaaaa tccgctccat ttaccataac gtcgcattgt acgcaccgcc
      541 aaaacgcgtt cggtgcgatc acggcagcag acaggtaaaa atggcaacaa accacccgaa
      601 aaactgccgc gatcgcacct gataaatttt aaccgcatga atacctatgc aaccagatgc
      661 tacaggccac attagcccgc cttaatccac tgaacacgtc atttttcatg gtttcaccat
      721 cccagcgaag ggccatccag tgtccgctcc tggatttccg gctgacgctc ccgctccaga
      781 gataactcat gttcgcgttc ctgcatcagc cgttcatccc ttatctcctg ttctcgctgt
      841 ataactggct caagcgttct gtccgctcgc tcaagtgctg cacctgctga ctcaactgca
      901 tgactcgccc gttcagcatc gcgttgtccc gttgcgtaag cgaaaacatt ttctgcaatt
      961 ccacgaaggc gttctcccat tcgttcagcc gctgcatata gtcctgttgc agttgctcta
     1021 atgcgttcag caaatgtctt tccagctccg tcatgctctg tcactcctgc accagtctca
     1081 ctgcgttcag tttgccgttg tccttcgtcc agttcgtttc ggctttcatc cccttcggca
     1141 acaccagaaa acgtccgttg ctgtcctcgt gataacgcac gccccatgtc ttcgcgttca
     1201 gcttctccag actctctttc tgctcgcgga gaatattcat attcgcgttt atcttcatgc
     1261 cctggtacca cagcagactc ccggtcgtgg caaacatcag tactgagacg ataatcagcc
     1321 acagccagcg tttcacgctc attttcagta cggttttcca gtgcgcgtcc atcgtatcga
     1381 cggtcgtttt ctgatacctc tccagcagtt ctttcagggc tgttgtatgg tcgttgatag
     1441 cgttcctgat taaagattcg tttgaggtca gttccctgtt tacagattct tcgagcttcc
     1501 tgaactcgtc gttcagcatt ttctctgtag attcggctct ctctttcagc tttttctcga
     1561 actccgcgcc cgtctgtaaa agattgctca taaaacgctc ctttcagtct gatattcctc
     1621 ccgccgttcg ggtctgcaat gctgatactg cttcgcgtca ccctgaccac ttcaagcccc
     1681 gcctctgtga gcgcctgaat cacatcctga cggcctttta tctctccggc atggtaaagc
     1741 gcgtctatcc cgcgtgtgac gccctcagca agcgcctgtt tcgtttccgg caggttatca
     1801 ggaagggtca gcgtccggcg gttctccggg gcgttggggt catgcagacc gtaatggtga
     1861 ttcaccagcg tctgccaggc atcaattctc ggcctgtctg cccggtcgta gtacggctgg
     1921 aggcgttttc cggtctgtag ctccatgttc ggaatgacaa aattcagctc aagccgtccc
     1981 ttgtcctggt gctccaccca caggatgctg tactgatttt tctcgagacc gggcatcagt
     2041 acacgctcaa agctcgccat cactttttca cgccctccag gcggcagctc cttctccgcg
     2101 aacgacagaa cacctgacgt gtatttcttc gcaaatggcg tggcatcgat gagttcccgg
     2161 acctcttccg gattcccctg aagcaccgtt gccccttccc ggttacgctc ccttcccagc
     2221 aggtaatcaa ccggaccact gccaccacct tttcccctgg catgaaactt aactatcatc
     2281 ccgcgccccc tgttccctga ccgccagacg cagccggcgc agctcatccc cgatggccat
     2341 cagtgcggcc accacctgaa cccggtcacc ggaagaccac tgcccgctgt tcaccttcct
     2401 cgctgtctgg ttaaggttat tcccgatggc ggccagctga cgcagtaacg gcggtgccag
     2461 tgtcggcagc ttcccggaac gggcaaccgg ctcacccagg cagacccgcc gcatccatac
     2521 cgccagttgt ttaccctcac agcgttccag taaccgggca tgttcatcat cagtaacccg
     2581 tatcgtgagc atcctctcgc gtttcatcgg tatcattacc cccatgaaca gaaccccccc
     2641 ttacacggag gcatcagtga ccaaacagga aaaaaccgcc cttaacatgg cccgcttcat
     2701 cagaggccag acattaacgc tgctggagaa gctcaacgaa ctggacgcgg atgaacaggc
     2761 agacatctgt gaatcgcttc acgaccacgc cgatgagctt taccgcagtt gcctcgcacg
     2821 cttcggggat gacggtgaaa accgctgaca catgcagctc ccggagacgg tcacagcttg
     2881 tctgtgagcg gatgccggga gcagacaagc ccgccagggc gcgtcaggcc gttgaccttt
     2941 ggggtgtcgg ggcgaagccc tgacccagtc acgtagcgat agcggagtgt atactggctt
     3001 aaccattcgg catcagtgcg gattgtatga aaagtgcgcc atgtccggtg tgaaatgccg
     3061 cacagatgcg taaggagaaa atgccagttc aggcgctctt ccgcttcctc gctcactgac
     3121 tcgctacgct cggtcgttcg gctgcggcga gcggactctc ctttctcaaa aacgctaacc
     3181 ctgttatcca cagaacccgg ggataaacca ggaaagaaca tgtgcgcaaa aaacgaaacc
     3241 ccgggaaagg ccgcgccgga ggcgcttttt ccataggctc cgcccccctg acggacttca
     3301 caaaacagac actttttcgg tgcatctgtg ggagccttgc ggctcaacca tgaaatccgc
     3361 cagcggtggc gaaacccgac gtggcttaaa gatcatcacc gtttccggtg aatcgctccc
     3421 tcctgcgccc ccacgttccc gccatatcga ttaccggata ccttttccgc ctttctccct
     3481 tacgggacac gtggcgcttt ctcatagctc acgtcttctg gtatctcggg gcgacttagg
     3541 cagttcgctc cgggctgggc tgtatgcagg aaccccccgt tcagcccgac tgctgcgcct
     3601 tctccggtaa ctgttctctt gggtccaacc cggaaaagac accacaaagc gccactggca
     3661 gcagccattg gtaaaagtca tgtgcgagat atttagagag tacttgaagt ggctgccgga
     3721 gtgcggctac actagaagaa caattttggt gactcgtctc gcataagaca gttacctggt
     3781 taagcagtct gcaagctgac ttaaccttcg atcaaaccgc cctgcaaggc ggttttttcg
     3841 tttacaggca gcagattacg cgcagaaaaa aaggatctca agaggatcct ttgatctttt
     3901 tgttacaaac gtctctattt gactcccctg agagcgtttt agcgcgcctc tgaccccctt
     3961 ggttacattc cgacaccaga aacgctcccg ttttttacgt gcatttggca cggtatcgat
     4021 ggaggccggg gggcaatcct gaacagaatg ttactcctct gagtattttc tgttaagaaa
     4081 atatacactt agcacagtta caataaatcc taccccctgt aagaatgtga attgttcatc
     4141 caaaaacaac catgacaaaa ataatgcaac tagcggaata aagtacaaca ttatccctgc
     4201 caaatgaact gggagccaac gcaaggagtt caagtaaaaa caaaaagcta aaaaatattg
     4261 taatattcca gatgaaaaaa caataatcac ggattccaac ggaagataaa ttgatgattt
     4321 agatataaaa ataaagagcg atgacagtat aagggagaat gtcaactgtc cgctcaataa
     4381 tgtgataggc tcaaacgatt taataaggcg agacgatata acaacataaa atgctgccga
     4441 taacacaccg gcaacaacaa gacaatatcc aacaatatta ttcgatccat tactgatgtc
     4501 tggcaaggct accaaaatac tgccaacaat tgcacctata aggaacaata taaaatattg
     4561 cggggaatta attttaactg agcaaataag aacagacaac accaatataa acactgattc
     4621 aagtgaaaaa ataattgatg cgcttcctgc tgaaataaaa taaagtccgt agagtgtaaa
     4681 agtatacgct aagaatggtt caaaaacgcc tgtcgcataa gcaagtatcg cttttgagtt
     4741 taatgggagt ttttttcttt ttataaaaag aactatccaa gatagtatta ctgcactaca
     4801 aatctgccag aaaaacaccc ctccggcatc tagttcttca actccttttt tgctcattac
     4861 gatagctgcc ccccatgaga acgctgctaa aaaagcaaaa agcattcctt taatcatatt
     4921 aatcatcctc tttctcataa aggggtttgt tttcaaattt ccttggttga aaggagttaa
     4981 aaaacataga tgcatcatct acaggaatac caataaactc tccataataa ggatcatcta
     5041 taggaaactc ttctaatgaa acataaaaca atacattcca gttgaagatc attggatcac
     5101 tattttctat ttcatggagc aatctttcat ccttagttaa ttctcctgga attaatacat
     5161 cagtatgata aaaaccgctg taataagaac tattaccggt gtgcactggg catccaaaac
     5221 gatccaaatt agattctgaa tgccatgttg tagaaatccc ttccggatgt gaatacccac
     5281 ccttaccaac agactgaata gtcatgttac gaatatccgc taacgcttgt tcttgatctt
     5341 tatagaaacc tttttctatc gccagcctca taaaatgccc cggggcattt acagaaataa
     5401 gtattccccc tggtattctt ctatcatgat ttcttgttct atgagcagaa gagtaaaaaa
     5461 cattaacacc agccttatat atttttagcc catctttatc ctgaaatggt acgctttcag
     5521 tataaataac atcctctttt attggatagc actctggcat atgcagcgaa caaatatatt
     5581 tttgtatgtc cactaactct tctgatggac gagcaaaggc aagttgtgga t
//
