LOCUS       NZ_CP103484             4051 bp    DNA     circular CON 21-SEP-2023
DEFINITION  Escherichia coli strain 4621 plasmid pMB9635_5, complete sequence.
ACCESSION   NZ_CP103484
VERSION     NZ_CP103484.1
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 4051)
  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 4051)
  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
            CP103484.1.
            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..4051
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="4621"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pMB9635_5"
                     /geo_loc_name="USA: Houston"
                     /lat_lon="29.7068 N 95.3971 W"
                     /collection_date="2019-12-22"
                     /collected_by="MDACC"
                     /genotype="ST68"
     gene            join(3798..4051,1..70)
                     /gene="mobA"
                     /locus_tag="M5T46_RS26490"
                     /old_locus_tag="M5T46_26490"
     CDS             join(3798..4051,1..70)
                     /gene="mobA"
                     /locus_tag="M5T46_RS26490"
                     /old_locus_tag="M5T46_26490"
                     /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            295..561
                     /locus_tag="M5T46_RS26495"
                     /old_locus_tag="M5T46_26495"
     CDS             295..561
                     /locus_tag="M5T46_RS26495"
                     /old_locus_tag="M5T46_26495"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001243419.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_224471576.1"
                     /translation="MVKLLLVRNEYFNKNNDLKTVARFDGKTLRDAFSRKIATFDGKVL
                     RDASLKKVATFDGQNLRDASSKIILSADAEVGIVVMAFVAELI"
                     /name="hypothetical protein"
     gene            1135..2274
                     /locus_tag="M5T46_RS26500"
                     /old_locus_tag="M5T46_26500"
     CDS             1135..2274
                     /locus_tag="M5T46_RS26500"
                     /old_locus_tag="M5T46_26500"
                     /EC_number="2.7.7.49"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761319.1"
                     /GO_function="GO:0003964 - RNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="reverse transcriptase family protein"
                     /protein_id="WP_259409789.1"
                     /translation="MNKPKFNGTPVASLDSLSAMLGIERKRLDWIVKSVSMSYKQFKVE
                     TGKNKKERQIFEPKRSLKGIQKKINKEIFEKIDYPHYLHGALSGRDYISNAAVHTRKRT
                     VICLDITNFYPSISKKDVCSIFKNLMRFSPDVSLCLTELVTLNNKVPQGGCCSSYIANL
                     LFFNSEYNLYNRLKSMGLSYSRLLDDITISSDKDLSSEEKTKVIKLVHGMVNQYRLSIN
                     ESKTTIEHSKDSSSKLSVTGLWVKHGVPKLTKENRRYIRYLVYICKKQGAYERHTKEYH
                     DLWNRCSGKVAQMSRLGHVQAVELRAILSEIMPVYDDYKISKLKLMAKHYLNKFTPPLT
                     DDQIRKIDRMLYDFDIVGRTNKNLAKLYRRKLVALLPDR"
                     /name="reverse transcriptase family protein"
     gene            2279..2482
                     /locus_tag="M5T46_RS26505"
                     /old_locus_tag="M5T46_26505"
     CDS             2279..2482
                     /locus_tag="M5T46_RS26505"
                     /old_locus_tag="M5T46_26505"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000427298.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="retron Se72 family effector protein"
                     /protein_id="WP_000427298.1"
                     /translation="MENGFVNFYDHVKGYGFIRRERGRDVFFRYDDFLFLGHDVDICKG
                     ILVRFKLEKTDKGFKAVAIQKV"
                     /name="retron Se72 family effector protein"
     gene            complement(3320..3514)
                     /locus_tag="M5T46_RS26510"
                     /old_locus_tag="M5T46_26510"
     CDS             complement(3320..3514)
                     /locus_tag="M5T46_RS26510"
                     /old_locus_tag="M5T46_26510"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041624.1"
                     /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_001041640.1"
                     /translation="MNKQQQTVLNMAGFIKSQSLTLLEKLDALDADEQAAMCEKLHELA
                     EELQNSIQTRFEAENRTGI"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          3550..3789
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.17"
                     /coverage="100.0"
                     /evalue="1.65e-119"
     Typing          complement(2764..3285)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.476"
                     /coverage="95.0"
                     /evalue="0.0"
ORIGIN
        1 gtatgcggag gtgctgatcg ctattacgga gtatcaccgt gccctgttat ccaggcttat
       61 ggcagattag cttccagggg agaaaactgt cgaaaacaga cggtatgaac accgtaagct
      121 cccaaagtga tcaccattcg ctttcatgca tagctatgca gcgagctgaa aacgatcctg
      181 acgcattttt ccggttttcg cttggtaaca catctctttt tgcggtgtct gcggcagaat
      241 cccgttcagc gcgtttctgc ggtgcgtaca attaagggat tatggtaaat acaattggtt
      301 aaattactat tggtgagaaa tgaatatttc aataaaaaca atgacttaaa aaccgttgct
      361 cggtttgacg gtaaaacctt aagagatgcc ttttcgagaa aaatagcgac ttttgatggc
      421 aaggttttaa gggatgcctc tttaaaaaaa gtagcaacct ttgacggtca gaatttaaga
      481 gatgctagtt caaaaattat cctgagtgcc gatgctgagg ttgggattgt tgttatggcc
      541 tttgtagctg agttgatttg aatctcatgc tgcatacctt ttagcctatc gctggcagga
      601 taaggcgctt tcttgttggt gacagaaaga taaaaaactt tataataatc agcgaagcgg
      661 gcgaaccacg cctggctctc gctctttaac aaatggttac gtgtatgttg cgcaaggaaa
      721 ccgatgcctt gtttttaagg cgatctcgca tgagatcatg accggcctgg ccgctaatta
      781 atggtgagaa cgcccctgag cgtgtatcag cactaaaaga atagcgacga ttgtctggca
      841 atgtgagtta aaagtcccaa agagccaata gagtttttcc ttgctttcct actggtctgg
      901 caaaatttca taaccaatag gagttgcatc atgtttatta tcaacatcaa cattaacgta
      961 accaagagct cttcatcttg ttctggagac ggtcagatga agaaaaaaag agaggttggc
     1021 tctctggagg cactgaaaaa aacacagttt ttgttttcta tgtgcttgat tatgtttaaa
     1081 gtaatagatt acgtatcgaa actttttaac taatcgactt ttaactcaaa catcatgaat
     1141 aaacccaagt ttaatggaac tcctgttgca tctttggatt ctttatctgc gatgttaggc
     1201 atagaaagaa aaagattgga ctggatagtc aagtctgtat cgatgtcgta caagcagttt
     1261 aaggttgaaa cagggaagaa taaaaaagaa aggcaaattt ttgaacccaa gagatctttg
     1321 aaaggaattc aaaaaaaaat aaataaagag atttttgaga aaattgatta ccctcattat
     1381 ttgcatgggg cgttaagtgg tcgcgattat atatctaatg ccgctgttca tactaggaaa
     1441 agaacagtta tatgtcttga tatcaccaat ttttatccca gcattagtaa aaaagatgtt
     1501 tgttctattt ttaaaaattt aatgcgtttt tctcctgatg tttctttatg cttaacggaa
     1561 cttgtgacgt tgaataataa ggtccctcag ggtgggtgct gttctagtta tattgcaaat
     1621 cttttatttt ttaatagtga gtataatctc tataatagat tgaagtctat ggggctttca
     1681 tattcaaggc ttttagatga tattactata tcctctgata aggatctttc atcagaggaa
     1741 aaaacaaaag taataaaact cgttcacgga atggtgaatc agtacagact ttcaataaat
     1801 gaaagtaaga caacgataga gcactcaaaa gattcgtctt ctaaacttag tgtcactggg
     1861 ttgtgggtaa agcatggtgt tcctaagtta acaaaagaaa atagacgtta tatcaggtac
     1921 ttagtttata tatgtaaaaa acaaggtgct tatgaacgtc atacgaaaga gtaccatgat
     1981 ttatggaata gatgctctgg caaggttgct caaatgtcga ggcttgggca tgtccaggcg
     2041 gttgaattga gggcgattct ttctgagata atgccagttt atgatgatta caagatatct
     2101 aaattaaagt tgatggctaa gcactatcta aataagttta cgccgccttt aactgatgat
     2161 cagattagga aaatagatag gatgctctat gattttgata tagtagggcg gactaataag
     2221 aatcttgcaa aactatatag acgtaagctc gtggcattac ttccagatag gtgattatat
     2281 ggaaaatgga tttgttaatt tttatgacca tgttaaaggg tatggcttta taaggcgtga
     2341 gcgtggacgt gatgttttct ttcggtatga tgatttttta tttttagggc atgatgtcga
     2401 tatatgtaaa ggtattttag ttaggtttaa attagaaaaa acagataaag ggtttaaagc
     2461 tgtagcgatt caaaaggtat aacatcgtgg atgtgtcagc ttgtttttat gatatgagaa
     2521 cttgagatcc tttctatctc gtcgtaatct cttgctgtgt aaacgaaaaa accgccttgc
     2581 agggcggttt ttcgaaggtt ctcagagcta ccaactcttt gagccgaggt aactggcttg
     2641 gaggagcgca gtcaccaaaa cttgttcttt cagtttagcc ttaacaggcg catgacttca
     2701 aggctaactc ctctaattcg gttaccagtg gctgctgcca gtggcgataa gtcgtgtctt
     2761 ctcggtttgg attcaagtcg atagttaccg gataaggcgc agcggtcgga ctgaacgggg
     2821 ggttcgtgca tacagtccag cttggagcga acgacctaca ccgggccgag ataccaacag
     2881 cgtgagctat gagaaagcgc cacgtttccc gaagggagaa aggcggacag gtatccggta
     2941 agcggcaggg tcggaacagg agagcgcacg agggagcttc cagggggaaa cgcctggtat
     3001 ctttatagtc ctgtcgggtt tcgccacctc tgacttgagc gtcggttttt gtgatgctcg
     3061 tcaggggggc ggagcctatg gaaaaacgcc atcggcgcgg cctttgtccc tggcttcggc
     3121 tttttgctca catgttcttt ccggcgttat cccctgattc tgtggataac cgtattaccg
     3181 cctttgagtg agctgacacc gctcgccgca gtcgaacgac cgagcgtagc gagtcagtga
     3241 gcgaggaagc ggaagagcgc cttatgtgac attttctcct tacgctcctc tatgccgttc
     3301 tgcatcctgt ccggatgcgt tatatcccgg tgcgattttc cgcttcaaag cgtgtctgta
     3361 tgctgttctg aagttcttcc gcgagttcgt gcagcttctc acacatggcg gcctgttcgt
     3421 cagcatcaag tgcgtccagt ttttcgagca gcgtcaggct ctggcttttt atgaatcctg
     3481 ccatgttgag tacggtttgc tgctgcttgt tcatctttct gttttctccg ttctttctgt
     3541 catctgcgtt gtgtgattat atcgcgtacc acttttcgac tgttttaccg tcggtattct
     3601 gctgtctgac tctttgacgg gcatttctgt cagacaacac tgtcactgcc aaaaaactgc
     3661 cgtgcctttg tcggtaattc gagcttgctg acaggacagg atgtgcaatt gttataccgc
     3721 gcatacatgc acgctattac aattaccctg gtcagggctt tgccccgaca cccatgtcag
     3781 atacggagcc atgttttatg acaaaacgaa gtggaagtaa tacgcgcagg cgggctatca
     3841 gtcgccctgt tcgtctgacg gcagaagaag accaggaaat cagaaaaagg gctgctgaat
     3901 gcggcaagac cgtttccggt tttttacggg cggcagctct cggtaagaaa gttaactcac
     3961 tgactgatga tcgggtactg aaagaagtta tgagactggg ggcgttacag aaaaaactct
     4021 ttatcgacgg caagcgtgtc ggggacaggg a
//
