LOCUS       CP134897                3371 bp    DNA     circular BCT 27-SEP-2023
DEFINITION  Escherichia coli strain 4080 plasmid pMB4926_6, complete sequence.
ACCESSION   CP134897
VERSION     CP134897.1
DBLINK      BioProject: PRJNA924946
            BioSample: SAMN32977769
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3371)
  AUTHORS   Shropshire,W.C., Strope,B., Selvaraj Anand,S., Bremer,J.,
            McDaneld,P., Bhatti,M., Flores,A.R., Kalia,A. and Shelburne,S.A.
  TITLE     Temporal Dynamics of Genetically Heterogeneous Extended-Spectrum
            Cephalosporin Resistant Escherichia coli Bloodstream Infections
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3371)
  AUTHORS   Shropshire,W.C., Strope,B., Selvaraj Anand,S., Bremer,J.,
            McDaneld,P., Bhatti,M., Flores,A.R., Kalia,A. and Shelburne,S.A.
  TITLE     Direct Submission
  JOURNAL   Submitted (14-JUN-2023) Infectious Diseases and Infection Control,
            University of Texas MD Anderson Cancer Center, South Campus Research
            Building 4, Houston, TEXAS 77054, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Flye v. 2.9.2
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 197x
            Sequencing Technology             :: Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 09/21/2023 12:23:24
            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)                     :: 4,847
            CDSs (total)                      :: 4,726
            Genes (coding)                    :: 4,605
            CDSs (with protein)               :: 4,605
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 121
            CDSs (without protein)            :: 121
            Pseudo Genes (ambiguous residues) :: 0 of 121
            Pseudo Genes (frameshifted)       :: 47 of 121
            Pseudo Genes (incomplete)         :: 65 of 121
            Pseudo Genes (internal stop)      :: 29 of 121
            Pseudo Genes (multiple problems)  :: 21 of 121
            Pseudo Genes (short protein)      :: 2 of 121
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            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/
FEATURES             Location/Qualifiers
     source          1..3371
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="4080"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pMB4926_6"
                     /geo_loc_name="USA: Houston"
                     /lat_lon="29.7068 N 95.3971 W"
                     /collection_date="2018-01-03"
                     /collected_by="MDACC"
                     /note="genotype: ST196"
     gene            complement(559..750)
                     /locus_tag="RNQ29_24215"
     CDS             complement(559..750)
                     /locus_tag="RNQ29_24215"
                     /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="WNL70659.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNDLDADEQADICESLHDHA
                     DELYRSCLARFGDDGESN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            814..1137
                     /locus_tag="RNQ29_24220"
     CDS             814..1137
                     /locus_tag="RNQ29_24220"
                     /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="WNL70660.1"
                     /translation="MLTIRVTDEEHARLLERCEGKRLAEWMRRVCLGEPVARTGKLPTL
                     SPPLLRHLAAIGNNLNQTARKVNSGQWSSIDRVHVVAALMAIEGELRQLRQAVREQGVR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            1346..1786
                     /locus_tag="RNQ29_24225"
                     /pseudo=""
     CDS             1346..1786
                     /locus_tag="RNQ29_24225"
                     /inference="COORDINATES: protein motif:HMM:NF015397.3"
                     /note="incomplete; partial on complete genome; 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            1815..2375
                     /locus_tag="RNQ29_24230"
     CDS             1815..2375
                     /locus_tag="RNQ29_24230"
                     /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="WNL70657.1"
                     /translation="MSNLLQMGTDFEKKLKERAASTENMLNSEFRKLEESVDKALSLNR
                     QKIRDAISEHTTSVKKQLDTLSTTVSMQFSTTEAELSRQQKKLLWRVIKGRILFPALTA
                     LSVTGGIFLGCWGLMEWQESKIAKNILTIREQENTLAKLEAKTWGVTFVNGENGKFLVL
                     PDGVKGENTWTVGDKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     gene            2382..2615
                     /locus_tag="RNQ29_24235"
     CDS             2382..2615
                     /locus_tag="RNQ29_24235"
                     /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="WNL70658.1"
                     /translation="MTELEGHLLNALEHLQQDYMRRLNEWESAFAELQKMHEVTQRNNA
                     ILNERVVILSQQVQRLAGQVDRLSRLFIANNS"
                     /name="MbeD family mobilization/exclusion protein"
     Typing          395..478
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="87.059"
                     /coverage="95.0"
                     /evalue="8.83e-18"
     Typing          1128..2698
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.817"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tgacgcgccc cgtgatcgat ggccttggct ccgtccggca tatcgagagc ggcaaactac
       61 ccgtcccttc actgggaggg gtgagttgtt gccgttccct ccaacctttc accatccggc
      121 atatcgcacg atcccatgtg caccgcaact cctgataact ccagtgcaaa aaaaaaaacg
      181 gatctgcatc acaacgagag tgatcccacc gctcgccgca gccccagcga ccgaacgtag
      241 tgagcgagtg ggcgaggaag cggaagagtc acagatgcaa gcattgtgca cttacgcgcc
      301 tgtgccagtg tccgcgtgtg tgctgtttat cgggtgcgct gtttttacat ctgtgcggct
      361 ttttactcct gacatggtgc acttcccatc cattctgcac cgatgcaaaa tgagataagc
      421 cagtatacac atcgctatcg ctctgtgaac tgggtcaggg ctgcgccccg acacccgcac
      481 tgacgcgccc tggcgggctt gtctgctccc ggcatccgct cacaggcaag ctgtgaacgt
      541 ctccgggagc tgcatgtttc agttgctttc accgtcatcg ccgaagcgtg cgaggcaact
      601 gcggtagagt tcgtcggcgt ggtcgtgaag tgattcgcag atgtctgcct gttcgtccgc
      661 gtccagatcg ttgagttttt ccagcagggt tagcgtctgg cttctgataa agcgagccat
      721 gttaagggct gttttttcct gtttggtcat ggtcttaagg ctccttgtat gggggatttg
      781 ttagggggaa tgataccgat gaaacgcgag aagatgctca cgatacgggt taccgatgag
      841 gagcacgccc ggttactgga acgctgcgag ggtaaacgac tggcggaatg gatgcggcgg
      901 gtctgtctgg gggagccggt tgcacgcaca ggaaaactgc cgacactatc gccgccattg
      961 ctgcggcatc tggctgccat cgggaacaac ctgaaccaga cagcccggaa ggtgaacagc
     1021 ggccagtggt cttcgattga ccgggttcat gtggtggccg cactgatggc catcgagggt
     1081 gaattgcgcc agttgcggca ggctgtcagg gaacaggggg tacgggatga tagttaaatt
     1141 tcatgccagg gggaaaggcg gtggaagtgg cccggtcgat tacctgctgg ggcgggagcg
     1201 taaccgcgaa ggcgcaacgg tgctccgggg taacccggaa gaagtgcggg aactcattga
     1261 ttccacgcca ttctcgaaga aatacacttc aggcgttctg tcgttcgcgg agaaggagtt
     1321 accgccgggt gaacgcgaaa gagtgatgac gagctttgag cgtgttctta tgcccggtct
     1381 cgaaaaagac cagtacagca ttctctgggt ggaacaccag gataaggggc ggctcgaact
     1441 gaattttgtc atcccgaaca tggagctaca gagcggtaag cgcctccagc cgtactacga
     1501 ccgcgcggac aggccgagga taaatgcctg gcagacgctg gttaatcatc attacgggct
     1561 gcgtgacccg aacgcaccgg agaacagacg gacgcttgtc acgccaaata atctgccaaa
     1621 agcgaaacag gaggccgcag aagcgattac acggggtctt gaggctcttt accatgccgg
     1681 agcaataaaa acgcgtcagg atgtcacaga ggcgcttaca gcggcaggtt ttgaggtggt
     1741 gaggacaacc aaaagcagca tcagtattgc cgacccggag ggggggcgga atctcaggct
     1801 aaagggggcg ctgtatgagc aatcttttac aaatgggaac agacttcgag aagaaactga
     1861 aagagcgagc cgcttctacc gagaacatgc tgaacagcga gttcaggaag ctcgaagagt
     1921 ctgtagacaa ggcattgagc ttaaacaggc agaaaatcag agacgctatc agcgaacata
     1981 caacatccgt gaaaaagcaa ctggatacgc tgagcaccac cgtgagcatg cagttcagca
     2041 ccacagaggc cgaactgtcc cggcagcaga aaaaactgct ctggcgggtg atcaaagggc
     2101 ggatactgtt tccggcgctg accgcgctca gcgtcacggg cggcattttc ctggggtgct
     2161 gggggctgat ggagtggcag gaaagcaaga ttgcgaaaaa tatcctgact atcagagagc
     2221 aggaaaacac gctggcgaaa ctcgaggcaa aaacctgggg ggtgacgttc gtcaatggcg
     2281 agaacgggaa atttctggtg ttgccggacg gggtgaaagg ggaaaacacc tggacggtgg
     2341 gcgacaagaa cgccgtgagg ctggtcaggg agtaaacgag tatgacggaa ctggaagggc
     2401 atttgctgaa cgccttagag catttgcaac aggactatat gcggcggctg aacgagtggg
     2461 agagcgcctt cgcggaattg cagaagatgc acgaggttac gcaacggaac aacgcgatac
     2521 tgaacgagcg cgtcgtgata ttgagtcagc aggtgcagag attagccggg caagtggatc
     2581 gcttgagtcg gttatttatc gcgaacaaca gctaagggat gaacaggagc gtgcccggta
     2641 cagacatgag gtacaggaac gcgcggcacg ggttcggagt gggccatcaa tggagatgtg
     2701 accggggaag tgacgaaatc ttgccatttt gaccagttcg acggctgggg cgagcgaaac
     2761 aaatcgtgtg ccgtatttgt gcatagctat gcaacatcct gaaaacgcat ttcacgcgtt
     2821 tttggggatt cagccagggg aaaacatggt ttttttactt tttgagcgta aagacgtgaa
     2881 aaatctcgtt attgcacttg cgatctttcg tcggcgggcg tagaacgaaa acagctcgcc
     2941 aggaaggcga gctgtttcgg gttcattgag gtctctgacc tcctcaatgt tcctgtggaa
     3001 actgttgaga tccacaacag aaaccagttc attcagtttg catgagcctt ctgtattctt
     3061 caagaatttt tcaacagcac agtctcccag gaaccccgaa aaaaacctgt ttttgcagat
     3121 acttgcgtat ttgcgagaat cgtttgcggt tgggggagct gtgacgacgg cgaccgcacg
     3181 cgtgagagtt ccgctaccgg cgcagagagt ttcatcgaca gcggacacct gatgagttgc
     3241 cacaaaaacc gtatgtagcg cggctagatt ggttgagtta gaccttggcg gcagttcccg
     3301 gtatgtggtg gcgtgacggg tgagatggtg cggcgaagac gcatacgtca cgcaggcgcg
     3361 ggttcttcca c
//
