LOCUS       NZ_CP103708             3133 bp    DNA     circular CON 21-SEP-2023
DEFINITION  Escherichia coli strain ST361 plasmid pMB3362_4, complete sequence.
ACCESSION   NZ_CP103708
VERSION     NZ_CP103708.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN28174001
            Assembly: GCF_024918335.1
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                   :: 48x
            Sequencing Technology             :: Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 09/21/2023 03:32:18
            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)                     :: 5,004
            CDSs (total)                      :: 4,884
            Genes (coding)                    :: 4,624
            CDSs (with protein)               :: 4,624
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 91
            ncRNAs                            :: 7
            Pseudo Genes (total)              :: 260
            CDSs (without protein)            :: 260
            Pseudo Genes (ambiguous residues) :: 0 of 260
            Pseudo Genes (frameshifted)       :: 84 of 260
            Pseudo Genes (incomplete)         :: 163 of 260
            Pseudo Genes (internal stop)      :: 49 of 260
            Pseudo Genes (multiple problems)  :: 34 of 260
            Pseudo Genes (short protein)      :: 4 of 260
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP103708.1.
            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="ST361"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pMB3362_4"
                     /geo_loc_name="USA: Houston"
                     /lat_lon="29.7068 N 95.3971 W"
                     /collection_date="2017-02-23"
                     /collected_by="MDACC"
                     /genotype="ST361"
     gene            1..144
                     /locus_tag="M5T41_RS24855"
                     /old_locus_tag="M5T41_24855"
     CDS             1..144
                     /locus_tag="M5T41_RS24855"
                     /old_locus_tag="M5T41_24855"
                     /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(169..921)
                     /locus_tag="M5T41_RS24860"
                     /old_locus_tag="M5T41_24860"
     CDS             complement(169..921)
                     /locus_tag="M5T41_RS24860"
                     /old_locus_tag="M5T41_24860"
                     /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(1380..1703)
                     /gene="mobA"
                     /locus_tag="M5T41_RS24865"
                     /old_locus_tag="M5T41_24865"
     CDS             complement(1380..1703)
                     /gene="mobA"
                     /locus_tag="M5T41_RS24865"
                     /old_locus_tag="M5T41_24865"
                     /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            1988..2182
                     /locus_tag="M5T41_RS24870"
                     /old_locus_tag="M5T41_24870"
     CDS             1988..2182
                     /locus_tag="M5T41_RS24870"
                     /old_locus_tag="M5T41_24870"
                     /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"
     gene            2659..2772
                     /locus_tag="M5T41_RS25055"
     CDS             2659..2772
                     /locus_tag="M5T41_RS25055"
                     /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"
     Typing          complement(1713..1950)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.75"
                     /coverage="99.0"
                     /evalue="1e-116"
     Typing          2481..2930
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="88.494"
                     /coverage="90.0"
                     /evalue="1.02e-154"
     Typing          complement(1384..1703)
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="2.32e-62"
ORIGIN
        1 atgaatacta aagttctttt tgtgaaaaaa gccttgaaat caattacttg cgcaattctt
       61 tcgctcttac cggctttaag tcgcgcagta acagagttac gtagcctttc ggctgcgcga
      121 cttaaagccg gtaagagctt ttgattgtat cacatttttc cttaaaagtc aaccggctac
      181 cttaagctcc ctgcacttaa tcctccctat aatccccata acatactcta tcgtgcagcg
      241 ttcataaaag cgcctatcgt gcccaataaa ctcaataagt tcctttttct cgttagagac
      301 gatactcaag gcattcatta aaaaattgaa ctctttcaac atattattta tggcttgact
      361 atgcgacttg cagtggtgtt ttttccaaat aggctcatgg tgaaaaagtc gattcctaaa
      421 caaaagaact ttatgaaact cgtcaaacaa cgctttaacc ttcatatccc ccccacccaa
      481 aggattcttc gcatgaggaa atgtttttgc cttgttctct ggagtccaga tgtagcacgg
      541 cctttgcgta tccctatatg gggcatctaa catataaacc caaaagccaa aggttagacg
      601 gcaaataaca tcatcatccg tataccttac gccacactca tctagcgctt tttgtttcgc
      661 atttaaaaca agatcctgag atttctttgt ttgaggtata gagtcgtacc aagcaggccc
      721 atgattagct ttgattgtat tgtttatcgc attacgcaga gcaacctcaa tcatctggac
      781 aagacaaaaa aaatcgccag acagatcttg gtaggcaacg tatgccccaa ccttttcttg
      841 atcagtagcg cacccaagaa atgtttcata gaaagataat cttggtacag aaattgagct
      901 aattaaactt gttgtatcca tgaaaactca cttatctctt tactatgaat atttttcaga
      961 ctaccattac aacattcgag gagcaggcga actaccgttt ttctgtgtac ctctagagcg
     1021 taaaatataa caaaaaagcc cactacagag tgggcttttt tgttatattt atctatatga
     1081 aacaaccagt tatagttatt gtttcataat aagaattgaa tactcttcac aatccacaac
     1141 atcagaaaat actttgctgc caatttacca taactcccct tacgcgcacc gctaaaacgc
     1201 gctgaacgcg attctgccgc aaacaccgca aaaagagatg ttttacccag tgaaaaccgg
     1261 aaaaatgcgt caggaccgtt ttcagctcac tgcatagcta tgcatgaaag tgaatggcga
     1321 tcggtttggg gccttacggc gttcataccg tctgttttcg acagtttctc tccgggaagc
     1381 taatctgcca taagcctgga taacagggcc cggtgatact ccgtaatagc gatcagcacc
     1441 tccgcatact ctctgtcccc gacacgcttg ccgtcgataa agagtttttt ctgtaacgcc
     1501 cccagtctca taacttcttt cagtacccga tcatcagtca gtgagttaac tttcttaccg
     1561 agagctgccg cccgtaaaaa accggaaacg gtcttgccgc attcagcagc cctttttctg
     1621 atttcctggt cttcttctgc cgtcagacga acagggcgac tgatagcccg cctgcgcgta
     1681 ttacttccac ttcgttttgt cataaaacat ggctccgtat ctgacatggg gtgtcggggc
     1741 gaagccctga ccagggtaat tgtaatagcg cgcatgtatg cgcggtataa caattacaca
     1801 tcctgtcctg tcagcaagtt cgaattaccg acaaaggcac ggcagttttt tggcagtgac
     1861 agtattgtca ggcagaaatg cccgtcaaag agtcagacga cagaataccg gcggcaaaac
     1921 tgtcgaaaag tggtacgcga tataatcaca cgacgcagat gacagacaga acggagaaaa
     1981 cagaaagatg aacaagcagc agcaaaccgc acttaacatg gcaaaattca taaaaagcca
     2041 gagcctgacg ctgctcgaaa aactggactc actcgatgct gatgcacagg ccgccatgtg
     2101 tgagaaactg cacgaactcg cagaagaact ccagaacagc atacagacac gctttgaatc
     2161 ggaaagtggc accggggaat aacagtgttc ctacaccaga caggatgcag aacgatatac
     2221 cggtgcgtaa ggagaaaata ccacataagg cgctcttccg cttcctcgct cactaactcg
     2281 ctacgctcgg tcgttcggct gcggcgagcg gtatcagctc actcaaagac ggtaatgagg
     2341 ttatccacag aatcagggga taacgccaaa agaaacatgt gagcaaaaaa caagaacccg
     2401 aaaaaggccg cgccggtggc gtttttccat aggctccgcc cccctgacga gcatcacaaa
     2461 aatcgacgct caagtcagag gtggcgaaac ccgacaggac tataaagata ccaggcgttt
     2521 ccccctgatg gctccctcgt gcgctctcct gttcctgcct ttcggtttac cggtgtcatt
     2581 ccgctgttat ggccgcgtta tctcattcca cgcctgacac tcagttccgg gtaggcagtt
     2641 cgctccaagc tggactgtat gcacgaaccc cccgttcagt ccgactactg cgccttatcc
     2701 ggtaactatc gtcttgagtc caacccggaa aggcacgact tatcgccatt ggcagcagcc
     2761 actggtaact gatttagagg agttagtctt gaagttacgt gccagttaag gctaaactgg
     2821 aagaacaagt tttggtgact gcgctcctct taagccagtt accgaggttc agaaacttgc
     2881 cggttgctga accttcgaaa aaccaccttg ccgggtggtt ttttcgtttt taagattacg
     2941 atgggcgcga tatgaactca aggaaatccg caattaaatt ataaaagttt gtggattaat
     3001 ggaaaaactg atgtgaatca gctatttatc cttaagattt gatgtcagat atggtataat
     3061 taaccattca aatagatgga ataaaaagtc aacgctgcca ttagaacggc ataagaaata
     3121 gaggattatg aaa
//
