LOCUS       NZ_CP103650             3986 bp    DNA     circular CON 21-SEP-2023
DEFINITION  Escherichia coli strain 961 plasmid pMB5823_5, complete sequence.
ACCESSION   NZ_CP103650
VERSION     NZ_CP103650.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN28173990
            Assembly: GCF_024918295.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3986)
  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 3986)
  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                   :: 61x
            Sequencing Technology             :: Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 09/21/2023 03:24:23
            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)                     :: 5,145
            CDSs (total)                      :: 5,020
            Genes (coding)                    :: 4,743
            CDSs (with protein)               :: 4,743
            Genes (RNA)                       :: 125
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 14
            Pseudo Genes (total)              :: 277
            CDSs (without protein)            :: 277
            Pseudo Genes (ambiguous residues) :: 0 of 277
            Pseudo Genes (frameshifted)       :: 93 of 277
            Pseudo Genes (incomplete)         :: 197 of 277
            Pseudo Genes (internal stop)      :: 55 of 277
            Pseudo Genes (multiple problems)  :: 63 of 277
            Pseudo Genes (short protein)      :: 4 of 277
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP103650.1.
            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..3986
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="961"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pMB5823_5"
                     /geo_loc_name="USA: Houston"
                     /lat_lon="29.7068 N 95.3971 W"
                     /collection_date="2018-06-18"
                     /collected_by="MDACC"
                     /genotype="ST617"
     gene            1..834
                     /locus_tag="M5R18_RS25545"
                     /old_locus_tag="M5R18_25545"
     CDS             1..834
                     /locus_tag="M5R18_RS25545"
                     /old_locus_tag="M5R18_25545"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_008196747.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type-2 restriction enzyme EcoRI"
                     /protein_id="WP_001565219.1"
                     /translation="MSNKKQSNRLTEQHKLSQGVIGIFGDYAKAHDLAVGEVSKLVKKA
                     LSNEYPQLSFRYRDSIKKTEINEALKKIDPDLGGTLFVSNSSIKPDGGIVEVKDDYGEW
                     RVVLVAEAKHQGKDIINIRNGLLVGKRGDQDLMAAGNAIERSHKNISEIANFMLSESHF
                     PYVLFLEGSNFLTENISITRPDGRVVNLEYNSGILNRLDRLTAANYGMPINSNLCINKF
                     VNHKDKSIMLQAASIYTQGDGREWDSKIMFEIMFDISTTSLRVLGRDLFEQLTSK"
                     /name="type-2 restriction enzyme EcoRI"
     gene            864..1844
                     /locus_tag="M5R18_RS25550"
                     /old_locus_tag="M5R18_25550"
     CDS             864..1844
                     /locus_tag="M5R18_RS25550"
                     /old_locus_tag="M5R18_25550"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002670781.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="adenine-specific methyltransferase EcoRI family
                     protein"
                     /protein_id="WP_210172971.1"
                     /translation="MARNATNKLLHKAKKSKSDEFYTQYCDIENELQYYREHFSDKVVY
                     CNCDDPRVSNFFKYFAVNFDNLGLKKLIASCYVENKEGFSSSKAAKNGFYYEYHKENGK
                     KLVFDDISVSSFCGDGDFRSSESIDLLKKSDIVVTNPPFSLFREYLDQLIKYDKKFLII
                     ANVNSITYKEVFNLIKENKIWLGVHLGRGVSGFIVPEHYELYGTEARIDSNGNRIISPN
                     NCLWLTNLDVFIRHKDLPLTRKYFGNESSYPKYDNYDAINVNKTKDIPLDYNGVMGVPI
                     TFLHKFNPEQFELIKFRKGVDEKDLSINGKCPYFRILIKNKRLQK"
                     /name="adenine-specific methyltransferase EcoRI family
                     protein"
     gene            complement(2134..2292)
                     /locus_tag="M5R18_RS25745"
     CDS             complement(2134..2292)
                     /locus_tag="M5R18_RS25745"
                     /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_071593719.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHDLTPLAAATGNWTRWIEIL
                     RVLEVVA"
                     /name="replication initiation protein"
     Typing          2789..2875
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.43e-38"
     Typing          complement(2221..2778)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.118"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atgtctaata aaaaacagtc aaataggcta actgaacaac ataagttatc tcaaggtgta
       61 attgggattt ttggggatta tgcaaaagct catgatctcg ctgttggtga ggtttcaaaa
      121 ttagtaaaga aagctcttag caacgaatac cctcaattat catttcgata tagagatagt
      181 ataaagaaaa cagaaataaa tgaagcttta aaaaaaattg accctgatct tggcggtact
      241 ttatttgttt caaattccag catcaaacct gatggtggaa ttgtagaggt caaagatgat
      301 tatggtgaat ggagagttgt acttgttgct gaagccaaac accaaggtaa agatattata
      361 aatataagga atggtttgtt agttgggaaa agaggagatc aagatttaat ggctgctggt
      421 aatgctatcg aaagatctca taagaatata tcagagatag cgaattttat gctctctgag
      481 agccactttc cttacgtcct tttcttagag gggtctaact ttttaacaga aaatatctca
      541 ataacaagac cagatggaag ggttgttaat cttgagtata attctggtat attaaatagg
      601 ttagatcgac taactgcagc taattatgga atgcctataa atagtaatct atgtattaac
      661 aaatttgtaa atcataaaga caaaagcatt atgctacaag cagcatctat atatactcaa
      721 ggagatggga gggagtggga ttcgaaaatt atgtttgaaa taatgtttga tatatcaacg
      781 acttcgctca gagtgttggg gcgtgacttg tttgaacagc ttacatctaa gtgatatttt
      841 ttattttaat aaggttttaa ttaatggcta gaaatgcaac aaacaagtta ctgcacaaag
      901 ctaaaaaatc gaaaagcgac gaattttaca ctcagtattg tgatattgag aacgaactgc
      961 aatactacag agagcacttc tctgataagg ttgtttattg caattgtgat gatcctagag
     1021 taagcaattt ctttaaatat tttgcagtaa attttgataa tcttggcttg aaaaagttaa
     1081 tagcatcttg ctatgtagag aataaagaag gtttttctag tagcaaagcc gcgaagaacg
     1141 gattttacta tgaatatcat aaagaaaatg gaaagaaatt agtttttgat gatattagtg
     1201 tttcttcttt ctgtggcgat ggcgattttc gcagttcgga gagcattgat ctgctaaaaa
     1261 aatcagatat tgttgttaca aatcctccat tctcgttatt tagagagtat cttgatcaac
     1321 taattaagta tgataagaaa ttccttataa ttgctaatgt taattcaata acatataaag
     1381 aggtgtttaa tctaattaag gaaaataaga tttggcttgg ggttcatctc gggagaggtg
     1441 tttctggatt tattgttcca gagcattatg aattatatgg tactgaggcg agaattgatt
     1501 ctaatggtaa tagaattatc tcgccaaaca actgcttatg gctaactaac ctagatgtct
     1561 ttattaggca taaagacttg cctcttacaa gaaaatattt tgggaatgaa agttcatatc
     1621 caaaatatga taattatgat gctataaatg taaacaaaac aaaggatatt ccattagatt
     1681 acaatggggt tatgggggtt cctatcacat tcttgcataa gtttaaccct gagcaatttg
     1741 agttaataaa atttagaaag ggtgttgatg aaaaagattt gtctataaat ggtaaatgcc
     1801 cttatttcag aattttgata aaaaacaaac gattacaaaa gtaattgatg tttgttagtt
     1861 ttttcttgag atcattagct tcgtcgtaag cttcggtacc agaaacgaaa aaaccacctc
     1921 tcctggtggt ttttttgaag gttcagtaga aaagatcaaa ggatcttctt gagatccttt
     1981 ttttctgcgc gtaatctgct gcttgcaaac aaaaaaacca ccgctaccaa cggtggtttg
     2041 tttgccggat caagagctac caactctttt tccgaaggta actggcttgg tggagcgcag
     2101 ataccaaata ctgtccttct agtgtagccg cagttaggcc accacttcaa gaactcttaa
     2161 tatctcaatc caccttgtcc agttaccagt ggctgctgcc agtggcgtta agtcgtgtct
     2221 taccgggttg gactcaagac gatagttacc ggataaggcg cagcggtcgg gctgaacggg
     2281 gggttcgtgc acacagccca gcttggagcg aacgacctac accgaactga gataccaaca
     2341 gcgtgagcta tgagaaagcg ccacgcttcc cgaagggaga aaggcggaca ggtatccggt
     2401 aagcggcagg gtcggaacag gagagcgcac gagggagcca ccagggggaa acgcctggta
     2461 tctttatagt cctgtcgggt ttcgccacct ctgacttgag cgtcggtttt tgtgatgctc
     2521 gtcagggggg cggagcctat ggaaaaacgc cagcggcgtg gccttttccg ggttcttgtt
     2581 ttttgctcac atgtttcttt tggtgttatc ccctgattct gtggataacc gcattaccgt
     2641 ctttgagtga gctgataccg ctcgccgcag ccgaacgacc gagcgtagcg agtcagtgag
     2701 cgaggaagcg gaagagcgtc ggaagttgca ttttctcctt acacatctgc gcggcatttc
     2761 acacccggca tggcgcactt ttcatacaat ccgcactgat gccgcatggt taagccagta
     2821 tacactccgc tatcgctacg tgactgggtc atggctgcgc cccgacaccc gctaaaaccc
     2881 gctgacgcgc cctgacgggc ttgtcggctc ccggcatccg ctcacaggca agctgtgacc
     2941 gtctccggga gctgcctgta tcagcccgtt atgccatcat cgccgaagcg ttcccggcaa
     3001 cgttggtagc gttcatccgc cacttcgtga agttgttctg gtgaaaaaaa cacgtacagg
     3061 acggggcagg atgtgcattt gtcggaccgc gcacgcgcaa tcagacaaat gccacttggt
     3121 cagggcacag ccccgacacc ctggacaaca ccacagcaat aagataaaac gtgcccgggc
     3181 gcgtttctct gcctcttttt tcatcatctc tgggattcgc gctcacccgt cctctgctgt
     3241 cgggtttatg tatccccgtc gcccgtggag atgaataacg ggccggggga ttaaaaatcc
     3301 ccgtgcagca cagccggcgt tgcataaaat tccgctctgc gatgagtact gtttaatcaa
     3361 aaatccccgc agttcctcca gaaaaacgcg agtctgttct catgccccgg atgcccacac
     3421 cccacgcaaa actaactttt tgctgatttc ttttttaaat caggttgtta tgttttaaaa
     3481 aatgtatttt cttattcaga tttatacaaa agcgggtcgt cggcgactac tggatgactc
     3541 ggcaacgagt cgtcggtgat ttatcgatga ctcaacacac tgtcgctctg gtgttcagag
     3601 aaggcgagtc gccagagagt cgcgaggaaa aatactggat gactcgctga cgactcccgt
     3661 agtgaatcgc tcacgactcg tctgtaacta cagtctgatt tcttcttatc agggctgaaa
     3721 acgtcagaaa atacgcctta tgggcatcag acgcgcccaa actgctcgcc attcagtttt
     3781 atgcatagtc atgcaacgcg ctgaaagcgt tcctgacgca tttttccggt ttacccgggg
     3841 gaaaacatcc atttttacgg tttttgcgcc agaagcgcgc tgagcgcgtt ttaacggtgc
     3901 gtacaataag ggattatggt aaatcaaacg tatgttaatc tatcgacata tgtaacttta
     3961 taaaataaca gtggaaacat ggattc
//
