LOCUS       NZ_CP103625             2088 bp    DNA     circular CON 21-SEP-2023
DEFINITION  Escherichia coli strain 3985 plasmid pMB6420_2, complete sequence.
ACCESSION   NZ_CP103625
VERSION     NZ_CP103625.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN28174042
            Assembly: GCF_024918195.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 2088)
  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 2088)
  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                   :: 221x
            Sequencing Technology             :: Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 09/21/2023 03:20:19
            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)                     :: 4,779
            CDSs (total)                      :: 4,661
            Genes (coding)                    :: 4,494
            CDSs (with protein)               :: 4,494
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 167
            CDSs (without protein)            :: 167
            Pseudo Genes (ambiguous residues) :: 0 of 167
            Pseudo Genes (frameshifted)       :: 63 of 167
            Pseudo Genes (incomplete)         :: 108 of 167
            Pseudo Genes (internal stop)      :: 28 of 167
            Pseudo Genes (multiple problems)  :: 30 of 167
            Pseudo Genes (short protein)      :: 2 of 167
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP103625.1.
            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..2088
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="3985"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pMB6420_2"
                     /geo_loc_name="USA: Houston"
                     /lat_lon="29.7068 N 95.3971 W"
                     /collection_date="2018-09-07"
                     /collected_by="MDACC"
                     /genotype="ST156"
     gene            join(1825..2088,1..702)
                     /locus_tag="M5T36_RS23760"
                     /old_locus_tag="M5T36_23760"
     CDS             join(1825..2088,1..702)
                     /locus_tag="M5T36_RS23760"
                     /old_locus_tag="M5T36_23760"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012421200.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_001287824.1"
                     /translation="MSEDKFLSDYSPRDAVWDTQRTLTDSVGGIYQTAAEFERYALRMA
                     SCSGLLRFGWSTIMETGETRLRLRSAQFCRVRHCPVCQWRRTLMWQARFYQALPKIVVD
                     YPSSRWLFLTLTVRNCEIGELGTVLTAMNAAFKRMEKRKELSPVQGWIRATEVTRGKDG
                     SAHPHFHCLLMVQPSWFKGKNYVKHERWVELWRDCLRVNYEPNIDIRAVKTKTGEVVAN
                     VAEQLQSAVAETLKYSVKPEDMANDPEWFLELTRQLHKRRFISTGGALKNVLQLDRETN
                     EDLVIADDVGDGTDDGKRTAFVWDSGKRRYKRAPEKDKSD"
                     /name="protein rep"
     gene            706..972
                     /locus_tag="M5T36_RS23765"
                     /old_locus_tag="M5T36_23765"
     CDS             706..972
                     /locus_tag="M5T36_RS23765"
                     /old_locus_tag="M5T36_23765"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001024536.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001024536.1"
                     /translation="MNINIEYLNGNKTIGLFFLRSEAVIPDRFKNLILLIDGLSFGTFG
                     FHPHEGFEDELILYIQKTNERVKTLFVKIDLNGIKFGFLRTHS"
                     /name="hypothetical protein"
     Typing          131..362
                     /name="Col(BS512)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.05e-118"
ORIGIN
        1 atgtggcaag cccgttttta tcaggctcta ccgaaaatcg ttgtggatta cccgtcttcc
       61 cgatggttgt ttctgacgtt aactgtcagg aactgcgaga taggtgaact tggaacagtc
      121 cttacagcaa tgaatgcggc gtttaagcga atggaaaagc gaaaggagct atcacctgtt
      181 caggggtgga tcagggctac ggaggtgacg cgaggtaagg atggcagcgc acatccgcat
      241 tttcactgtc tgctgatggt gcaaccttct tggtttaaag ggaagaacta cgttaagcac
      301 gaacgttggg tagaactctg gcgcgattgc ttgcgggtga actatgagcc gaatatcgat
      361 attcgggcag taaaaactaa gacaggtgag gttgtggcca acgttgccga gcaactgcaa
      421 agcgcggttg ctgaaacgct gaaatactcc gttaaaccgg aagatatggc aaacgatcct
      481 gagtggtttc ttgagctgac gcggcagctt cacaagcgcc gttttatctc gaccggtggg
      541 gcgctaaaaa acgtcctcca gttggatcga gaaaccaatg aggatcttgt cattgccgac
      601 gatgtagggg atggcactga tgacgggaag cggacggcgt ttgtctggga ttcaggtaaa
      661 cggcgttaca aacgcgcccc tgagaaggat aaatcggatt aacgtatgaa tattaatatt
      721 gaatacctga atggaaataa gactattggt ttattttttt taagaagtga agcggtgatt
      781 cctgacaggt ttaaaaacct tattttgctt attgatggat taagttttgg cacatttggt
      841 tttcatccgc acgaaggttt tgaggatgaa ttaattttat atattcagaa aacaaacgag
      901 agggtaaaaa ctctttttgt gaaaatagat ttaaacggta tcaagtttgg atttttaaga
      961 acgcattctt agttctggaa aagagccagc ggcaggctga ggtgataggt acgagattgc
     1021 atgcaatctc tagtgctctg tctatcctgc attatcctca gcattatcct cagccttgcc
     1081 aactcgacac caatgcagga tagacaatcc gatgtcaaat gttaacactc tgcgagtggt
     1141 acattttccc cggattatcg tcctgagcct gccgctggct ctctttctac cgcctcgctt
     1201 tgctcgttgc tcaacgcctc acagacacgg attaaaatcc gcatccgttc accgtttttt
     1261 aaagtccgtt aaaagcatga tgccatctcc gagagttaat ctcgtcaaat gctaaatcgt
     1321 gggggtcccc tttggggttc cgatttagtg attgacgaca ccaccgatta aaaaacttat
     1381 gcggggtgga tggtttcacg aagtgaggcc atccacctgt aagacagggt tttgttttta
     1441 ttccctgttt tggtgatcgg gtgtgtggaa aaggttgggg taagccgttc gggggtgctt
     1501 gttttggggg ttaaaattgt ggttattttt tgcgcaattc tcgcgcgtga tccttgtatt
     1561 tatacttaag ggataaatgg cggatatgaa atagtggttt agcccagtaa tgacgaggct
     1621 ttgagtgggt tttgacaggt caaagaaaat ggagcagaat tgaggcgttt ttaatcggcg
     1681 ttggggagtg cgtcaacact ccccaacatt tcgaatgtgt cacctcagcg gcaaactctg
     1741 gtgacatgta ctggctcgca atgcacaggt acgtgatgaa tataccacat caaatcacag
     1801 cctgcccaga tcggagcagg cttaatgtca gaagataaat tcctttcgga ctacagcccc
     1861 cgtgatgcag tttgggatac ccagcgcacg cttaccgatt ctgtcggggg tatctaccag
     1921 actgctgctg aattcgagcg ctatgcactc cgtatggcct cctgtagcgg tttgttacgt
     1981 tttggttggt ctaccatcat ggaaaccgga gaaacgcgcc tacggcttcg tagtgcgcaa
     2041 ttttgccgtg tccgtcattg ccctgtctgc cagtggagaa gaaccctc
//
