LOCUS       NZ_CP103760             3372 bp    DNA     circular CON 21-SEP-2023
DEFINITION  Escherichia coli strain p10B plasmid unnamed2, complete sequence.
ACCESSION   NZ_CP103760
VERSION     NZ_CP103760.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13948682
            Assembly: GCF_024918895.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3372)
  AUTHORS   Shropshire,W.C., Aitken,S.L., Pifer,R., Kim,J., Bhatti,M.M., Li,X.,
            Kalia,A., Galloway-Pena,J., Sahasrabhojane,P., Arias,C.A.,
            Greenberg,D.E., Hanson,B.M. and Shelburne,S.A.
  TITLE     IS26-mediated amplification of blaOXA-1 and blaCTX-M-15 with
            concurrent outer membrane porin disruption associated with de novo
            carbapenem resistance in a recurrent bacteraemia cohort
  JOURNAL   J Antimicrob Chemother 76 (2), 385-395 (2021)
   PUBMED   33164081
REFERENCE   2  (bases 1 to 3372)
  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, TEXAS 77054, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Flye v. 2.8.3-b1695
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 265x
            Sequencing Technology             :: Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 09/21/2023 03:54:23
            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)                     :: 4,815
            CDSs (total)                      :: 4,692
            Genes (coding)                    :: 4,447
            CDSs (with protein)               :: 4,447
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 14
            Pseudo Genes (total)              :: 245
            CDSs (without protein)            :: 245
            Pseudo Genes (ambiguous residues) :: 0 of 245
            Pseudo Genes (frameshifted)       :: 77 of 245
            Pseudo Genes (incomplete)         :: 174 of 245
            Pseudo Genes (internal stop)      :: 35 of 245
            Pseudo Genes (multiple problems)  :: 42 of 245
            Pseudo Genes (short protein)      :: 4 of 245
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP103760.1.
            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..3372
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="p10B"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="unnamed2"
                     /geo_loc_name="USA:Houston"
                     /lat_lon="29.7068 N 95.3971 W"
                     /collection_date="2015-01/2016-07"
                     /collected_by="MDACC"
                     /genotype="ST10"
     gene            complement(<92..559)
                     /locus_tag="NYO15_RS24110"
                     /pseudo=""
     CDS             complement(<92..559)
                     /locus_tag="NYO15_RS24110"
                     /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(549..872)
                     /locus_tag="NYO15_RS23925"
                     /old_locus_tag="NYO15_23925"
     CDS             complement(549..872)
                     /locus_tag="NYO15_RS23925"
                     /old_locus_tag="NYO15_23925"
                     /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_024132211.1"
                     /translation="MLTIRVTDEEHARLLERCEGKRLAEWMRRVCLGEPVARTGKLPTL
                     SPPLLRHLAAIGNNLNQTARKVNSGQWSSIDRVHVVAALMAIEGELRQLRQAVREQGVR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            936..1127
                     /locus_tag="NYO15_RS23930"
                     /old_locus_tag="NYO15_23930"
     CDS             936..1127
                     /locus_tag="NYO15_RS23930"
                     /old_locus_tag="NYO15_23930"
                     /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(2443..2676)
                     /locus_tag="NYO15_RS23935"
                     /old_locus_tag="NYO15_23935"
     CDS             complement(2443..2676)
                     /locus_tag="NYO15_RS23935"
                     /old_locus_tag="NYO15_23935"
                     /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(2683..3243)
                     /locus_tag="NYO15_RS23940"
                     /old_locus_tag="NYO15_23940"
     CDS             complement(2683..3243)
                     /locus_tag="NYO15_RS23940"
                     /old_locus_tag="NYO15_23940"
                     /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_000067487.1"
                     /translation="MSNLLQMGTDFEKKLKERAASTENMLNSEFRKLEESVDKALSLNR
                     QKIRDAISEHTTSVKKQLDTLSTTVSMQFSTTEAELSRQQKKLLWRVIKGRILFPALTA
                     LSVTGGIFLGCWGLMEWQESKIAKNILTIREQENTLAKLEAKTWGVTFVNGENGKFLVL
                     PDGVKGENTWTVGDKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     Typing          complement(1209..1289)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="87.805"
                     /coverage="93.0"
                     /evalue="8.68e-18"
     Typing          complement(3..559)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.387"
                     /coverage="99.0"
                     /evalue="1.05e-119"
     Typing          complement(2361..3370)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="90.058"
                     /coverage="99.0"
                     /evalue="6.89e-178"
ORIGIN
        1 ttgctccggc atggtaaaga gcctcaagac cccgtgtaat cgcttctgcg gcctcctgtt
       61 tcgcttttgg cagattattt ggcgtgacaa gcgtccgtct gttctccggt gcgttcgggt
      121 cacgcagccc gtaatgatga ttaaccagcg tctgccaggc atttatcctc ggcctgtccg
      181 cgcggtcgta gtacggctgg aggcgcttac cgctctgtag ctccatgttc gggatgacaa
      241 aattcagttc gagccgcccc ttatcctggt gttccaccca gagaatgctg tactggtctt
      301 tttcgagacc gggcataaga acacgctcaa agctcgtcat cactctttcg cgttcacccg
      361 gcggtaactc cttctccgcg aacgacagaa cgcctgaagt gtatttcttc gagaatggcg
      421 tggaatcaat gagttcccgc acttcttccg ggttaccccg gagcaccgtt gcgccttcgc
      481 ggttacgctc ccgccccagc aggtaatcga ccgggccact tccaccgcct ttccccctgg
      541 catgaaattt aactatcatc ccgtaccccc tgttccctga cagcctgccg caactggcgc
      601 aattcaccct cgatggccat cagtgcggcc accacatgaa cccggtcaat cgaagaccac
      661 tggccgctgt tcaccttccg ggctgtctgg ttcaggttgt tcccgatggc agccagatgc
      721 cgcagcaatg gcggcgatag tgtcggcagt tttcctgtgc gtgcaaccgg ctcccccaga
      781 cagacccgcc gcatccattc cgccagtcgt ttaccctcgc agcgttccag taaccgggcg
      841 tgctcctcat cggtaacccg tatcgtgagc atcttctcgc gtttcatcgg tatcattccc
      901 cctaacaaat cccccataca aggagcctta agaccatgac caaacaggaa aaaacagccc
      961 ttaacatggc tcgctttatc agaagccaga cgctaaccct gctggaaaaa ctcaacgatc
     1021 tggacgcgga cgaacaggca gacatctgcg aatcacttca cgaccacgcc gacgaactct
     1081 accgcagttg cctcgcacgc ttcggcgatg acggtgaaag caactgaaac atgcagctcc
     1141 cggagacgtt cacagcttgc ctgtgagcgg atgccgggag cagacaagcc cgccagggcg
     1201 cgtcagtgcg ggtgtcgggg cgcagccctg acccagttca cagagcgata gcgatgtgta
     1261 tactggctta tctcattttg catcggtgca gacatggatg ggaagtgcac catgtcagga
     1321 gtaaaaagcc gcacagatgt aaaaacagcg cacccgataa acagcacaca cgcggacact
     1381 ggcacaggcg cgtaagtgca caatgcttgc atctgtgact cttccgcttc ctcgcccact
     1441 cgctcactac gttcggtcgc tggggctgcg gcgagcggtg ggatcactct cgttgtgatg
     1501 cagatccgtt tttttttttg cactggagtt atcaggagtt gcggtgcaca tgggatcgtg
     1561 cgatatgccg gatggtgaaa ggttggaggg aacggcaaca actcacccct cccagtgaag
     1621 ggacgggtag tttgccgctc tcgatatgcc ggacggagcc aaggccatcg atcacggggc
     1681 gcgtcagtgg aagaacccgc gcctgcgtga cgtatgcgtc ttcgccgcac catctcaccc
     1741 gtcacgccac cacataccgg gaactgccgc caaggtctaa ctcaaccaat ctagccgcgc
     1801 tacatacggt ttttgtggca actcatcagg tgtccgctgt cgatgaaact ctctgcgccg
     1861 gtagcggaac tctcacgcgt gcggtcgccg tcgtcacagc tcccccaacc gcaaacgatt
     1921 ctcgcaaata cgcaagtatc tgcaaaaaca ggtttttttc ggggttcctg ggagactgtg
     1981 ctgttgaaaa attcttgaag aatacagaag gctcatgcaa actgaatgaa ctggtttctg
     2041 ttgtggatct caacagtttc cacaggaaca ttgaggaggt cagagacctc aatgaacccg
     2101 aaacagctcg ccttcctggc gagctgtttt cgttctacgc ccgccgacga aagatcgcaa
     2161 gtgcaataac gagatttttc acgtctttac gctcaaaaag taaaaaaacc atgttttccc
     2221 ctggctgaat ccccaaaaac gcgtgaaatg cgttttcagg atgttgcata gctatgcaca
     2281 aatacggcac acgatttgtt tcgctcgccc cagccgtcga actggtcaaa atggcaagat
     2341 ttcgtcactt ccccggtcac atctccattg atggcccact ccgaacccgt gccgcgcgtt
     2401 cctgtacctc atgtctgtac cgggcacgct cctgttcatc ccttagctgt tgttcgcgat
     2461 aaataaccga ctcaagcgat ccacttgccc ggctaatctc tgcacctgct gactcaatat
     2521 cacgacgcgc tcgttcagta tcgcgttgtt ccgttgcgta acctcgtgca tcttctgcaa
     2581 ttccgcgaag gcgctctccc actcgttcag ccgccgcata tagtcctgtt gcaaatgctc
     2641 taaggcgttc agcaaatgcc cttccagttc cgtcatactc gtttactccc tgaccagcct
     2701 cacggcgttc ttgtcgccca ccgtccaggt gttttcccct ttcaccccgt ccggcaacac
     2761 cagaaatttc ccgttctcgc cattgacgaa cgtcaccccc caggtttttg cctcgagttt
     2821 cgccagcgtg ttttcctgct ctctgatagt caggatattt ttcgcaatct tgctttcctg
     2881 ccactccatc agcccccagc accccaggaa aatgccgccc gtgacgctga gcgcggtcag
     2941 cgccggaaac agtatccgcc ctttgatcac ccgccagagc agttttttct gctgccggga
     3001 cagttcggcc tctgtggtgc tgaactgcat gctcacggtg gtgctcagcg tatccagttg
     3061 ctttttcacg gatgttgtat gttcgctgat agcgtctctg attttctgcc tgtttaagct
     3121 cagtgccttg tctacagact cttcgagctt cctgaactcg ctgttcagca tgttctcggt
     3181 agaagcggct cgctctttca gtttcttctc gaagtctgtt cccatttgta aaagattgct
     3241 catacagcgc cccctttagc ctgagattcc gccccccctc cgggtcggca atactgatgc
     3301 tgcttttggt tgtcctcacc acctcaaaac ctgccgctgt aagcgcctct gtgacatcct
     3361 gacgcgtttt ta
//
