LOCUS       NZ_CP103485             3373 bp    DNA     circular CON 21-SEP-2023
DEFINITION  Escherichia coli strain 4621 plasmid pMB9635_6, complete sequence.
ACCESSION   NZ_CP103485
VERSION     NZ_CP103485.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN28174065
            Assembly: GCF_024917715.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3373)
  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 3373)
  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                   :: 345x
            Sequencing Technology             :: Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 09/21/2023 03:32:47
            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)                     :: 5,329
            CDSs (total)                      :: 5,210
            Genes (coding)                    :: 4,989
            CDSs (with protein)               :: 4,989
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 221
            CDSs (without protein)            :: 221
            Pseudo Genes (ambiguous residues) :: 0 of 221
            Pseudo Genes (frameshifted)       :: 89 of 221
            Pseudo Genes (incomplete)         :: 150 of 221
            Pseudo Genes (internal stop)      :: 43 of 221
            Pseudo Genes (multiple problems)  :: 54 of 221
            Pseudo Genes (short protein)      :: 4 of 221
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP103485.1.
            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..3373
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="4621"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pMB9635_6"
                     /geo_loc_name="USA: Houston"
                     /lat_lon="29.7068 N 95.3971 W"
                     /collection_date="2019-12-22"
                     /collected_by="MDACC"
                     /genotype="ST68"
     gene            1..192
                     /locus_tag="M5T46_RS26515"
                     /old_locus_tag="M5T46_26515"
     CDS             1..192
                     /locus_tag="M5T46_RS26515"
                     /old_locus_tag="M5T46_26515"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165979.1"
                     /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_000165979.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNDLDADEQADICESLHDHA
                     DELYRSCLARFGDDGESN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(1509..1742)
                     /locus_tag="M5T46_RS26520"
                     /old_locus_tag="M5T46_26520"
     CDS             complement(1509..1742)
                     /locus_tag="M5T46_RS26520"
                     /old_locus_tag="M5T46_26520"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137389.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_000137389.1"
                     /translation="MTELEGHLLNALEHLQQDYMRRLNEWESAFAELQKMHEVTQRNNA
                     ILNERVVILSQQVQRLAGQVDRLSRLFIANNS"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(1749..2309)
                     /locus_tag="M5T46_RS26525"
                     /old_locus_tag="M5T46_26525"
     CDS             complement(1749..2309)
                     /locus_tag="M5T46_RS26525"
                     /old_locus_tag="M5T46_26525"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000067488.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_000067486.1"
                     /translation="MSNLLQMGTDFEKKLKERAASTENMLNSEFRKLEESVDKALSLNR
                     QKIRDAISEHTTSVKKQLDTLSTTVSMQFSTTEAELSRQQKKLLWRVIKGRILFPALTA
                     LSVTGGIFLGCWGLMEWQESKIAKNILTIREQENTLAKLEAKTWGVTFVNGENGKFLVL
                     PDGMKGENTWTVGDKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     gene            complement(<2338..2997)
                     /locus_tag="M5T46_RS26530"
                     /old_locus_tag="M5T46_26530"
                     /pseudo=""
     CDS             complement(<2338..2997)
                     /locus_tag="M5T46_RS26530"
                     /old_locus_tag="M5T46_26530"
                     /inference="COORDINATES: protein motif:HMM:NF015397.3"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            complement(2987..3310)
                     /locus_tag="M5T46_RS26535"
                     /old_locus_tag="M5T46_26535"
     CDS             complement(2987..3310)
                     /locus_tag="M5T46_RS26535"
                     /old_locus_tag="M5T46_26535"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_001696562.1"
                     /translation="MLTIRVTDEEHARLLERCEGKRLAEWMRRVCLGEPVARTGKLPTL
                     APPLLRHLAAIGNNLNQTARKVNSGQWSSIDRVHVVAALMAIEGELRQLRQAVREQGVR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     Typing          complement(274..354)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="87.805"
                     /coverage="93.0"
                     /evalue="8.68e-18"
     Typing          complement(1427..2997)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.439"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atgaccaaac aggaaaaaac agcccttaac atggctcgct ttatcagaag ccagacgcta
       61 accctgctgg aaaaactcaa cgatctggac gcggacgaac aggcagacat ctgcgaatca
      121 cttcacgacc acgccgacga actctaccgc agttgcctcg cacgcttcgg cgatgacggt
      181 gaaagcaact gaaacatgca gctcccggag acgttcacag cttgcctgtg agcggatgcc
      241 gggagcagac aagcccgcca gggcgcgtca gtgcgggtgt cggggcgcag ccctgaccca
      301 gttcacagag cgatagcgat gtgtatactg gcttacctca ttttgcatcg gtgcagagtg
      361 gatgggaagt gcaccatgtc aggagtaaaa agccgcacag atgcgtaaaa acagcgcgcc
      421 cgataaacaa cacacacgcg gacactggca caggcgcgta agtgcacaat gcttgcctct
      481 gtgactcttc cgcttcctcg cccactcgct cactacgttc ggtcgctggg gctgcggcga
      541 gcggtgggat cactctcgtt gtgatgcaga tccgtttttt tttttgcact ggagttatca
      601 ggagtagcgg tgcacatggg atcgtgcgat atgctggatg gtggaaggtc ggagggaacg
      661 gcaacaactc acccctccca gtgaagggac gggtagtttg ccgctctcga tatgccggac
      721 ggagccaagg ccatcgatca cggggcgcgt cagtggaaga acccgcgcct gcgtgacgta
      781 tgcgtcttcg ccgcaccatc tcacccgtca cgccaccaca taccgggaac tgccgccaag
      841 gtctaactca accaatctag ccgcgctaca tacggttttt gtggcaactc atcaggtgtc
      901 cgctgtcgat gaaactctct gcgccggtag cggaactctc acgcgtgcgg tcgccgtcgt
      961 cacagctccc ccaaccgcaa acgattctca caaatacgca agtatctgca aaaacaggtt
     1021 tttttcgggg ttcctgggag actgtgctgt tgaaaaattc ttgaagaata cagaaggctc
     1081 atgcaaactg aatgaactgg tttctgttgt ggatctcaac agtttccaca ggaacattga
     1141 ggaggtcaga gacctcaatg aacccgaaac agctcgcctt cctggcgagc tgttttcgtt
     1201 ctacgcccgc cgacgaaaga tcgcaagtgc aataacgaga tttttcacgt ctttacgctc
     1261 aaaaagtaaa aaaaccatgt tttcccctgg ctgaatcccc aaaaacgcgt gaaatgcgtt
     1321 ttcaggatgt tgcatagcta tgcacaaata cggcacacga tttgtttcgc tcgccccagc
     1381 cgtcgaacgg gtcaaaatgg caagatttcg tcacttcccc ggtcacatct ccattgatgg
     1441 cccactccga acccgtgccg cgcgttcctg tacctcatgt ctgtaccggg cacgctcctg
     1501 ttcatccctt agctgttgtt cgcgataaat aaccgactca agcgatccac ttgcccggct
     1561 aatctctgca cctgctgact caatatcacg acgcgctcgt tcagtatcgc gttgttccgt
     1621 tgcgtaacct cgtgcatctt ctgcaattcc gcgaaggcgc tctcccactc gttcagccgc
     1681 cgcatatagt cctgttgcaa atgctctaag gcgttcagca aatgcccttc cagttccgtc
     1741 atactcgttt actccctgac cagcctcacg gcgttcttgt cgcccaccgt ccaggtgttt
     1801 tcccctttca tcccgtccgg caacaccaga aatttcccgt tctcgccatt gacgaacgtc
     1861 accccccagg tttttgcctc gagtttcgcc agcgtgtttt cctgctctct gatagtcagg
     1921 atatttttcg caatcttgct ttcctgccac tccatcagcc cccagcaccc caggaaaatc
     1981 ccgcccgtga cgctgagcgc ggtcagcgcc ggaaacagta tccgcccttt gatcacccgc
     2041 cagagcagtt ttttctgctg ccgggacagt tcggcctctg tggtgctgaa ctgcatgctc
     2101 acggtggtgc tcagcgtatc cagttgcttt ttcacggatg ttgtatgttc gctgatagcg
     2161 tctctgattt tctgcctgtt taagctcaat gccttgtcta cagactcttc gagcttcctg
     2221 aactcgctgt tcagcatgtt ctcggtagaa gcggctcgct ctttcagttt cttctcgaag
     2281 tctgttccca tttgtaaaag attgctcata cagcgccccc tttagcctga gattccgccc
     2341 cccctccggg tcggcaatac tgatgctgct tttggttgtc ctcaccacct caaaacctgc
     2401 cgctgtaagc gcctctgtga catcctgacg cgtttttatt gctccggcat ggtaaagagc
     2461 ctcaagaccc cgtgtaatcg cttctgcggc ctcctgtttc gcttttggca gattatttgg
     2521 cgtgacaagc gtccgtctgt tctccggtgc gttcgggtca cgcagcccgt aatgatgatt
     2581 aaccagcgtc tgccaggcat ttatcctcgg cctgtccgca cggtcgtagt acggctggag
     2641 gcgcttaccg ctctgtagct ccatgttcgg gatgacaaaa ttcagttcga gccgcccctt
     2701 atcctggtgt tccacccaga gaatgctgta ctggtctttt tcgagaccgg gcataagaac
     2761 acgctcaaag ctcgtcatca ctctttcgcg ttcacccggt ggtagctcct tctccgcgaa
     2821 cgacagaacg cctgacgtgt atttcttcga aaatggcgtg gaatcaatga gttcccgcac
     2881 ttcttccggg ttaccccgga gcaccgttgc gccttcgcgg ttacgctccc gccccagcag
     2941 gtaatcgacc gggccacttc caccgccttt ccccctggca tgaaatttaa ctatcatccc
     3001 gtaccccctg ttccctgaca gcctgccgca actggcgcaa ttcaccctcg atggccatca
     3061 gtgcggccac cacatgaacc cggtcaatcg aagaccactg gccgctgttc accttccggg
     3121 ctgtctggtt caggttgttc ccgatggcag ccagatgccg cagcaatggc ggtgccagtg
     3181 tcggcagttt tcctgtgcgt gcaaccggct cccccagaca gacccgccgc atccattccg
     3241 ccagtcgttt accctcgcag cgttccagta accgggcgtg ctcctcatcg gtaacccgta
     3301 tcgtgagcat cttctcgcgt ttcatcggta tcattccccc taacaaatcc cccatacaag
     3361 gagccttaag acc
//
