LOCUS       NZ_CP103519             3133 bp    DNA     circular CON 21-SEP-2023
DEFINITION  Escherichia coli strain 5444 plasmid pMB9292_4, complete sequence.
ACCESSION   NZ_CP103519
VERSION     NZ_CP103519.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN28174095
            Assembly: GCF_024917955.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3133)
  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 3133)
  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                   :: 209x
            Sequencing Technology             :: Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 09/21/2023 03:21:31
            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)                     :: 4,978
            CDSs (total)                      :: 4,858
            Genes (coding)                    :: 4,580
            CDSs (with protein)               :: 4,580
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 278
            CDSs (without protein)            :: 278
            Pseudo Genes (ambiguous residues) :: 0 of 278
            Pseudo Genes (frameshifted)       :: 87 of 278
            Pseudo Genes (incomplete)         :: 191 of 278
            Pseudo Genes (internal stop)      :: 58 of 278
            Pseudo Genes (multiple problems)  :: 53 of 278
            Pseudo Genes (short protein)      :: 3 of 278
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP103519.1.
            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..3133
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="5444"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pMB9292_4"
                     /geo_loc_name="USA: Houston"
                     /lat_lon="29.7068 N 95.3971 W"
                     /collection_date="2019-11-07"
                     /collected_by="MDACC"
                     /genotype="ST44"
     gene            1..324
                     /gene="mobA"
                     /locus_tag="M5S96_RS24725"
                     /old_locus_tag="M5S96_24725"
     CDS             1..324
                     /gene="mobA"
                     /locus_tag="M5S96_RS24725"
                     /old_locus_tag="M5S96_24725"
                     /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            783..1535
                     /locus_tag="M5S96_RS24730"
                     /old_locus_tag="M5S96_24730"
     CDS             783..1535
                     /locus_tag="M5S96_RS24730"
                     /old_locus_tag="M5S96_24730"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001127762.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_016249639.1"
                     /translation="MDTTSLISSISVPRLSFYETFLGCATDQEKVGAYVAYQDLSGDFF
                     CLVQMIEVALRNAINNTIKANHGPAWYDSIPQTKKSQDLVLNAKQKALDECGVRYTDDD
                     VICRLTFGFWVYMLDAPYRDTQRPCYIWTPENKAKTFPHAKNPLGGGDMKVKALFDEFH
                     KVLLFRNRLFHHEPIWKKHHCKSHSQAINNMLKEFNFLMNALSIVSNEKKELIEFIGHD
                     RRFYERCTIEYVMGIIGRIKCRELKVAG"
                     /name="hypothetical protein"
     gene            complement(1560..1703)
                     /locus_tag="M5S96_RS24735"
                     /old_locus_tag="M5S96_24735"
     CDS             complement(1560..1703)
                     /locus_tag="M5S96_RS24735"
                     /old_locus_tag="M5S96_24735"
                     /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_152918943.1"
                     /translation="MNTKVLFVKKALKSITCAILSLLPALSRAVTELRSLSAARLKAGK
                     SF"
                     /name="hypothetical protein"
     gene            complement(2065..2178)
                     /locus_tag="M5S96_RS24915"
     CDS             complement(2065..2178)
                     /locus_tag="M5S96_RS24915"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /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_071790583.1"
                     /translation="MHEPPVQSDYCALSGNYRLESNPERHDLSPLAAATGN"
                     /name="replication initiation protein"
     gene            complement(2655..2849)
                     /locus_tag="M5S96_RS24740"
                     /old_locus_tag="M5S96_24740"
     CDS             complement(2655..2849)
                     /locus_tag="M5S96_RS24740"
                     /old_locus_tag="M5S96_24740"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041623.1"
                     /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_025492124.1"
                     /translation="MNKQQQTALNMAKFIKSQSLTLLEKLDSLDADAQAAMCEKLHELA
                     EELQNSIQTRFESESGTGE"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          2888..3125
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.75"
                     /coverage="99.0"
                     /evalue="1e-116"
     Typing          complement(1908..2357)
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="88.494"
                     /coverage="90.0"
                     /evalue="1.02e-154"
     Typing          2..321
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="1.88e-62"
ORIGIN
        1 atgacaaaac gaagtggaag taatacgcgc aggcgggcta tcagtcgccc tgttcgtctg
       61 acggcagaag aagaccagga aatcagaaaa agggctgctg aatgcggcaa gaccgtttcc
      121 ggttttttac gggcggcagc tctcggtaag aaagttaact cactgactga tgatcgggta
      181 ctgaaagaag ttatgagact gggggcgtta cagaaaaaac tctttatcga cggcaagcgt
      241 gtcggggaca gagagtatgc ggaggtgctg atcgctatta cggagtatca ccgggccctg
      301 ttatccaggc ttatggcaga ttagcttccc ggagagaaac tgtcgaaaac agacggtatg
      361 aacgccgtaa ggccccaaac cgatcgccat tcactttcat gcatagctat gcagtgagct
      421 gaaaacggtc ctgacgcatt tttccggttt tcactgggta aaacatctct ttttgcggtg
      481 tttgcggcag aatcgcgttc agcgcgtttt agcggtgcgc gtaaggggag ttatggtaaa
      541 ttggcagcaa agtattttct gatgttgtgg attgtgaaga gtattcaatt cttattatga
      601 aacaataact ataactggtt gtttcatata gataaatata acaaaaaagc ccactctgta
      661 gtgggctttt ttgttatatt ttacgctcta gaggtacaca gaaaaacggt agttcgcctg
      721 ctcctcgaat gttgtaatgg tagtctgaaa aatattcata gtaaagagat aagtgagttt
      781 tcatggatac aacaagttta attagctcaa tttctgtacc aagattatct ttctatgaaa
      841 catttcttgg gtgcgctact gatcaagaaa aggttggggc atacgttgcc taccaagatc
      901 tgtctggcga ttttttttgt cttgtccaga tgattgaggt tgctctgcgt aatgcgataa
      961 acaatacaat caaagctaat catgggcctg cttggtacga ctctatacct caaacaaaga
     1021 aatctcagga tcttgtttta aatgcgaaac aaaaagcgct agatgagtgt ggcgtaaggt
     1081 atacggatga tgatgttatt tgccgtctaa cctttggctt ttgggtttat atgttagatg
     1141 ccccatatag ggatacgcaa aggccgtgct acatctggac tccagagaac aaggcaaaaa
     1201 catttcctca tgcgaagaat cctttgggtg ggggggatat gaaggttaaa gcgttgtttg
     1261 acgagtttca taaagttctt ttgtttagga atcgactttt tcaccatgag cctatttgga
     1321 aaaaacacca ctgcaagtcg catagtcaag ccataaataa tatgttgaaa gagttcaatt
     1381 ttttaatgaa tgccttgagt atcgtctcta acgagaaaaa ggaacttatt gagtttattg
     1441 ggcacgatag gcgcttttat gaacgctgca cgatagagta tgttatgggg attataggga
     1501 ggattaagtg cagggagctt aaggtagccg gttgactttt aaggaaaaat gtgatacaat
     1561 caaaagctct taccggcttt aagtcgcgca gccgaaaggc tacgtaactc tgttactgcg
     1621 cgacttaaag ccggtaagag cgaaagaatt gcgcaagtaa ttgatttcaa ggcttttttc
     1681 acaaaaagaa ctttagtatt cattttcata atcctctatt tcttatgccg ttctaatggc
     1741 agcgttgact ttttattcca tctatttgaa tggttaatta taccatatct gacatcaaat
     1801 cttaaggata aatagctgat tcacatcagt ttttccatta atccacaaac ttttataatt
     1861 taattgcgga tttccttgag ttcatatcgc gcccatcgta atcttaaaaa cgaaaaaacc
     1921 acccggcaag gtggtttttc gaaggttcag caaccggcaa gtttctgaac ctcggtaact
     1981 ggcttaagag gagcgcagtc accaaaactt gttcttccag tttagcctta actggcacgt
     2041 aacttcaaga ctaactcctc taaatcagtt accagtggct gctgccaatg gcgataagtc
     2101 gtgcctttcc gggttggact caagacgata gttaccggat aaggcgcagt agtcggactg
     2161 aacggggggt tcgtgcatac agtccagctt ggagcgaact gcctacccgg aactgagtgt
     2221 caggcgtgga atgagataac gcggccataa cagcggaatg acaccggtaa accgaaaggc
     2281 aggaacagga gagcgcacga gggagccatc agggggaaac gcctggtatc tttatagtcc
     2341 tgtcgggttt cgccacctct gacttgagcg tcgatttttg tgatgctcgt caggggggcg
     2401 gagcctatgg aaaaacgcca ccggcgcggc ctttttcggg ttcttgtttt ttgctcacat
     2461 gtttcttttg gcgttatccc ctgattctgt ggataacctc attaccgtct ttgagtgagc
     2521 tgataccgct cgccgcagcc gaacgaccga gcgtagcgag ttagtgagcg aggaagcgga
     2581 agagcgcctt atgtggtatt ttctccttac gcaccggtat atcgttctgc atcctgtctg
     2641 gtgtaggaac actgttattc cccggtgcca ctttccgatt caaagcgtgt ctgtatgctg
     2701 ttctggagtt cttctgcgag ttcgtgcagt ttctcacaca tggcggcctg tgcatcagca
     2761 tcgagtgagt ccagtttttc gagcagcgtc aggctctggc tttttatgaa ttttgccatg
     2821 ttaagtgcgg tttgctgctg cttgttcatc tttctgtttt ctccgttctg tctgtcatct
     2881 gcgtcgtgtg attatatcgc gtaccacttt tcgacagttt tgccgccggt attctgtcgt
     2941 ctgactcttt gacgggcatt tctgcctgac aatactgtca ctgccaaaaa actgccgtgc
     3001 ctttgtcggt aattcgaact tgctgacagg acaggatgtg taattgttat accgcgcata
     3061 catgcgcgct attacaatta ccctggtcag ggcttcgccc cgacacccca tgtcagatac
     3121 ggagccatgt ttt
//
