LOCUS       NZ_CP103750             3172 bp    DNA     circular CON 21-SEP-2023
DEFINITION  Escherichia coli strain 3090 plasmid pMB2791_5, complete sequence.
ACCESSION   NZ_CP103750
VERSION     NZ_CP103750.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN28174017
            Assembly: GCF_024917995.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3172)
  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 3172)
  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                   :: 85x
            Sequencing Technology             :: Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 09/21/2023 03:09:24
            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)                     :: 5,088
            CDSs (total)                      :: 4,967
            Genes (coding)                    :: 4,683
            CDSs (with protein)               :: 4,683
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 284
            CDSs (without protein)            :: 284
            Pseudo Genes (ambiguous residues) :: 0 of 284
            Pseudo Genes (frameshifted)       :: 96 of 284
            Pseudo Genes (incomplete)         :: 192 of 284
            Pseudo Genes (internal stop)      :: 60 of 284
            Pseudo Genes (multiple problems)  :: 62 of 284
            Pseudo Genes (short protein)      :: 4 of 284
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP103750.1.
            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..3172
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="3090"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pMB2791_5"
                     /geo_loc_name="USA: Houston"
                     /lat_lon="29.7068 N 95.3971 W"
                     /collection_date="2016-10-27"
                     /collected_by="MDACC"
                     /genotype="ST167"
     gene            1..132
                     /locus_tag="M5T02_RS25245"
                     /old_locus_tag="M5T02_25245"
     CDS             1..132
                     /locus_tag="M5T02_RS25245"
                     /old_locus_tag="M5T02_25245"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005019281.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_023151671.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHDLTPLATATGKQDVREM"
                     /name="hypothetical protein"
     gene            complement(348..776)
                     /locus_tag="M5T02_RS25250"
                     /old_locus_tag="M5T02_25250"
     CDS             complement(348..776)
                     /locus_tag="M5T02_RS25250"
                     /old_locus_tag="M5T02_25250"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000534558.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000534558.1"
                     /translation="MGSGAGAQNPQLNIVSFSETFNLYYTSRYSAKTLDKIDDFIEHFE
                     KYNLFGDPLKGYPAWTGKVSPSWKVPDHYENKEAIEKYARANKLWHAHLGDPVFKDTFH
                     GKYKVSDWVIHFQRLTPNHIKLLELGYHDPMKLPQNFE"
                     /name="hypothetical protein"
     gene            complement(740..910)
                     /locus_tag="M5T02_RS25255"
                     /old_locus_tag="M5T02_25255"
     CDS             complement(740..910)
                     /locus_tag="M5T02_RS25255"
                     /old_locus_tag="M5T02_25255"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001531327.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001531327.1"
                     /translation="MKTEQRHDLVKDIEVFGVSLSLLISRANEKSVTMPSGLSREQRRA
                     WAAEQARKIHN"
                     /name="hypothetical protein"
     gene            1068..1496
                     /locus_tag="M5T02_RS25260"
                     /old_locus_tag="M5T02_25260"
     CDS             1068..1496
                     /locus_tag="M5T02_RS25260"
                     /old_locus_tag="M5T02_25260"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000222531.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_000222531.1"
                     /translation="MTYSVKNKWKAGGLSLGWTAVPTVLFFIQNEKKLTSVAFNTLLNL
                     IVHWWSLQEWPHPSMESLAIRMGVSVRTVQRAINDLEKANLLDKKPTSKSDRRYGGRNI
                     YDLTKLVDYLDTMGPSVAEQVKKPRHKKPVYTVRKTTA"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(1885..2208)
                     /gene="mobA"
                     /locus_tag="M5T02_RS25265"
                     /old_locus_tag="M5T02_25265"
     CDS             complement(1885..2208)
                     /gene="mobA"
                     /locus_tag="M5T02_RS25265"
                     /old_locus_tag="M5T02_25265"
                     /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            2492..2686
                     /locus_tag="M5T02_RS25270"
                     /old_locus_tag="M5T02_25270"
     CDS             2492..2686
                     /locus_tag="M5T02_RS25270"
                     /old_locus_tag="M5T02_25270"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041639.1"
                     /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_001041621.1"
                     /translation="MNKQQQAVLNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELA
                     EELQNSIQTRFEVENSTER"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(2218..2457)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.585"
                     /coverage="100.0"
                     /evalue="3.54e-121"
     Typing          complement(2..90)
                     /name="ColRNAI_rep_cluster_1857"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.889"
                     /coverage="99.0"
                     /evalue="2.5000000000000003e-37"
     Typing          2716..3172
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.305"
                     /coverage="97.0"
                     /evalue="0.0"
     Typing          complement(1889..2208)
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="2.23e-62"
ORIGIN
        1 gtgcacgaac cccccgttca gcccgaccgc tgcgccttat ccggtaacta tcgtcttgaa
       61 tccaacccgg taagacacga cttaacgcca ctggcaacgg ccactggtaa gcaggatgtg
      121 cgagagatgt aacaagagtt cttgaagtgg cggcctaact gaggctacac tgaaaggaca
      181 gtatttggtg acatgtctcg cacaagactg ttaccacggt tagagaatct gccaggatta
      241 actaaccttc gaaaaaccac ctgccagggt ggttttttcg tttttacaat agtgagatta
      301 cgacgagact gaatgaatct caagatttca tttagcctgc cgctcgatca ttcaaagttt
      361 tgaggtagct tcattgggtc atggtatcca agctctaaaa gctttatatg gttcggtgtc
      421 agccgctgga aatgaataac ccagtcagaa accttgtatt tcccatgaaa cgtatcttta
      481 aaaaccggat cgcctaaatg agcatgccat aatttgttag ctctagcata cttctcaata
      541 gcttctttgt tttcgtaatg atcaggcact ttccacgatg gcgatacttt gccagtccaa
      601 gctggatatc cttttaaagg atcgccaaag agattgtatt tttcaaaatg ctcaatgaaa
      661 tcatcgattt tatcgagtgt ttttgcagaa tatctggatg tgtaataaag gttgaaggtc
      721 tcagagaatg agacaatatt caattgtgga ttttgcgcgc ctgctccgct gcccatgctc
      781 ttctctgctc ccgacttaga ccagatggca ttgtaacaga cttctcattc gctctggaaa
      841 tcaacagaga caaggatacg ccaaaaacct caatatcttt aacaagatca tgacgttgtt
      901 cggttttcat atcgctaact ccgtatctaa ttcaggcagg aaaaaatctt ttcctcgttt
      961 tcagagtagt cttttttggt tgcacaataa tggcgccagt gtcaccctat tcatatgaat
     1021 ataccatata atatatactt taaatatttt ggagcttagg aaaatcaatg acttactccg
     1081 ttaagaataa atggaaagct ggcggtttgt ctcttggctg gacggcagtg cctaccgtat
     1141 tgttttttat acaaaacgag aaaaagctaa cttcagtggc ctttaacaca ctacttaacc
     1201 tgatcgttca ctggtggagt ttgcaagagt ggccgcatcc gtcaatggaa agtctagcca
     1261 tacgtatggg ggtttctgta cggactgttc agagagctat caatgatctt gaaaaagcta
     1321 atctcttgga caagaaacca acatcgaaga gtgatcgccg atatggtggt cgcaatattt
     1381 atgatctaac aaagctagtt gactacctag atacaatggg tccatcagta gctgaacaag
     1441 ttaagaaacc acgccataaa aaaccggtat ataccgtaag aaaaacgaca gcttaaaaaa
     1501 gcacaatgga actgagcgcg agcgatgcac gatagcaaaa cgatatatta cttattgcat
     1561 tggtcttggt agccctgctt ctggctaaac cactgtcagg agtaattggc tttgcctgta
     1621 atgggttcat cgcttcacag ttaaagttat cgcatagctc atatatttac cataatccct
     1681 taattgtacg caccactgaa acgcgctgaa cgcgattctg acgcagacac cgcaaaaaga
     1741 gatgttttac cccggaaaaa caggaaggat gcgtcaggat cgttttcagc tcgctgcata
     1801 gctatgcatg aaagcgaatg gtgatcactt tgggagctta cggtgttcat accgtcagtt
     1861 ttcgacagtt ttctctccgg gaagctaatc tgccataagc ctggataaca gggcacggtg
     1921 atactccgta atagcgatca gcacctccgc atactccctg tccccgacac gcttgccgtc
     1981 gataaagagt tttttctgta acgcccccag tctcataact tctttcagta cccgatcatc
     2041 agtcagtgag ttaactttct taccgagagc tgccgcccgt aaaaaaccgg aaacggtctt
     2101 gccgcattca gcagcccttt ttctgatttc ctggtcttct tctgccgtca gacgaacagg
     2161 gcgactgata gcccgcctgc gcgtattact tccacttcgt tttgtcataa aacatggctc
     2221 cgtatctgac atgggtgtcg gggcaaagcc ctgaccaggg taattgtaat agcgtgcatg
     2281 tatgcgcggt ataacaatta cacatcctgt cctgtcagca agttcgaatt actgacaaag
     2341 gcacggcagt tttttggcag tgacagtatt gtcaggcaga aatacccgtc aaagcgtcag
     2401 acggcagaat accggcggta aaacagtcga aaagtggtac gcgatataat cacacaacgc
     2461 agatgacaga cagaacggag aaaacgaaaa gatgaacaag cagcagcaag ccgtactcaa
     2521 catggcagga ttcataaaaa gccaaagcct gacgctgctc gaaaagctgg acgcactcga
     2581 tgctgacgaa caggctacca tgtgtgagaa gctgcacgaa ctcgcagaag aactccagaa
     2641 cagcatccag acacgctttg aagtagaaaa tagcacagag agataacgct caggacagga
     2701 tgccgaacgg cacaacagag cgtaaggaga aaatgtcaca taaggcgctc ttccgcttcc
     2761 tcgctcactg actcgctacg ctcggacgtt cgactgcggc gagcggtgtc agctcactca
     2821 aaagcagtaa tacggttatc cacagaatca ggggataaag ccggaaagaa catgtgagca
     2881 aaaagcaaag caccggaaga agccagcgcc gcaggcgttt ttccataggc tccgcccccc
     2941 tgacgagcat cacaaaaatc gacgctcaag ccagaggtgg cgaaacccga caggactata
     3001 aagataccag gcgtttcccc ctggaagctc cctcgtgcgc tctcctgttc cgaccctgcc
     3061 gcttaccgga tacctgtccg cctttctccc ttcgggaagc gtggcgcttt ctcatagctc
     3121 acgctgttgg tatctcggcc cggtgtaggt cgttcgctcc aagctgggct gt
//
