LOCUS       NZ_CP103761             3173 bp    DNA     circular CON 21-SEP-2023
DEFINITION  Escherichia coli strain p10B plasmid unnamed3, complete sequence.
ACCESSION   NZ_CP103761
VERSION     NZ_CP103761.1
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 3173)
  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 3173)
  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
            CP103761.1.
            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..3173
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="p10B"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="unnamed3"
                     /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(793..987)
                     /locus_tag="NYO15_RS23945"
                     /old_locus_tag="NYO15_23945"
     CDS             complement(793..987)
                     /locus_tag="NYO15_RS23945"
                     /old_locus_tag="NYO15_23945"
                     /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_001041619.1"
                     /translation="MNKQQQAVLNMAGFIKSQSLTLLEKLDALDADEQAAMCEKLHELA
                     EELQNSIQTRFEAENRTGI"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1271..1594
                     /gene="mobA"
                     /locus_tag="NYO15_RS23950"
                     /old_locus_tag="NYO15_23950"
     CDS             1271..1594
                     /gene="mobA"
                     /locus_tag="NYO15_RS23950"
                     /old_locus_tag="NYO15_23950"
                     /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            complement(1983..2411)
                     /locus_tag="NYO15_RS23955"
                     /old_locus_tag="NYO15_23955"
     CDS             complement(1983..2411)
                     /locus_tag="NYO15_RS23955"
                     /old_locus_tag="NYO15_23955"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000222531.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_000222531.1"
                     /translation="MTYSVKNKWKAGGLSLGWTAVPTVLFFIQNEKKLTSVAFNTLLNL
                     IVHWWSLQEWPHPSMESLAIRMGVSVRTVQRAINDLEKANLLDKKPTSKSDRRYGGRNI
                     YDLTKLVDYLDTMGPSVAEQVKKPRHKKPVYTVRKTTA"
                     /name="helix-turn-helix domain-containing protein"
     gene            2569..2739
                     /locus_tag="NYO15_RS23960"
                     /old_locus_tag="NYO15_23960"
     CDS             2569..2739
                     /locus_tag="NYO15_RS23960"
                     /old_locus_tag="NYO15_23960"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001531327.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001531327.1"
                     /translation="MKTEQRHDLVKDIEVFGVSLSLLISRANEKSVTMPSGLSREQRRA
                     WAAEQARKIHN"
                     /name="hypothetical protein"
     gene            2703..3131
                     /locus_tag="NYO15_RS23965"
                     /old_locus_tag="NYO15_23965"
     CDS             2703..3131
                     /locus_tag="NYO15_RS23965"
                     /old_locus_tag="NYO15_23965"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000534558.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_004029842.1"
                     /translation="MGSGAGAQNPQLNIVSFSETFNLYYTSRYSAKTLDKIDDFIEHFE
                     KYNLFGDPLKGYPAWTGKVSPSWKVPDHYENKEAIEMYARANKLWHAHLGDPVFKDTFH
                     GKYKVSDWVIHFQRLTPNHIKLLELGYHDPMKLPQNFE"
                     /name="hypothetical protein"
     Typing          1023..1262
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.585"
                     /coverage="100.0"
                     /evalue="3.54e-121"
     Typing          complement(234..758)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.34"
                     /coverage="95.0"
                     /evalue="0.0"
     Typing          1272..1591
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="2.23e-62"
ORIGIN
        1 cgtcgtaatc tcactattgt aaaaacgaaa aaaccaccct ggcaggtggt ttttcgaagg
       61 ttagttaatc ctggcagatt ctctaaccgt ggtaacagtc ttgtgcgaga catgtcacca
      121 aatactgtcc tttcagtgta gcctcagtta ggccgccact tcaagaactc tcgttacatc
      181 tctcgcacat cctgcttacc agtggccgtt gccagtggcg ttaagtcgtg tcttaccggg
      241 ttggattcaa gacgatagtt accggataag gcgcagcggt cgggctgaac ggggggttcg
      301 tgcacacagc ccagcttgga gcgaacgacc tacaccgggc cgagatacca acagcgtgag
      361 ctatgagaaa gcgccacgct tcccgaaggg agaaaggcgg acaggtatcc ggtaagcggc
      421 agggtcggaa caggagagcg cacgagggag cttccagggg gaaacgcctg gtatctttat
      481 agtcctgtcg ggtttcgcca cctctggctt gagcgtcgat ttttgtgatg ctcgtcaggg
      541 gggcggagcc tatggaaaaa cgcctgcggc gctggcttct tccggtgctt tgctttttgc
      601 tcacatgttc tttccggctt tatcccctga ttctgtggat aaccgtatta ccgcttttga
      661 gtgagcttac accgctcgcc gcagtcgaac gaccgagcgt agcgagtcag tgagcgagga
      721 agcggaagag cgccttatgt gacattttct ccttacgctc ctctatgccg ttctgcatcc
      781 tgtccggatg cgttatatcc cggtgcgatt ttccgcttca aagcgtgtct gtatgctgtt
      841 ctgaagttct tccgcgagtt cgtgcagctt ctcacacatg gcggcctgtt cgtcagcatc
      901 gagtgcgtcc agtttttcga gcagcgtcag gctctggctt tttatgaatc ctgccatgtt
      961 gagtacggct tgctgctgct tgttcatctt ttcgttttct ccgttctgtc tgtcatctgc
     1021 gttgtgtgat tatatcgcgt accacttttc gactgtttta ccgccggtat tctgccgtct
     1081 gacgctttga cgggtatttc tgcctgacaa tactgtcact gccaaaaaac tgccgtgtct
     1141 ttgtcggtaa ttcgaacttg ctgacaggac aggatgtgta attgttatac cgcgcatgca
     1201 tgcacgctat tacaattacc ctggtcaggg ctttgccccg acacccatgt cagatacgga
     1261 gccatgtttt atgacaaaac gaagtggaag taatacgcgc aggcgggcta tcagtcgccc
     1321 tgttcgtctg acggcagaag aagaccagga aatcagaaaa agggctgctg aatgcggcaa
     1381 gaccgtttcc ggttttttac gggcggcagc tctcggtaag aaagttaact cactgactga
     1441 tgatcgggta ctgaaagaag ttatgagact gggggcgtta cagaaaaaac tctttatcga
     1501 cggcaagcgt gtcggggaca gggaatatgc ggaggtgctg atcgctatta cggagtatca
     1561 ccgtgccctg ttatccaggc ttatggcaga ttagcttccc ggagagaaaa ctgtcgaaaa
     1621 cagacggtat gaacaccgta agctcccaaa gtgatcacca ttcgctttca tgcatagcta
     1681 tgcagcgagc tgaaaacgat cctgacgcat ccttcctgtt ttcccggggt aaaacatctc
     1741 tttttgcggt gtctgcgtca gaatcgcgtt cagcgcgttt cagtggtgcg tacaattaag
     1801 ggattatggt aaatatatga gctatgcgat aactttaact gtgaagcgat gaacccatta
     1861 caggcaaagc caattactcc tgacagtggt ttagccagaa gcagggctac caagaccaat
     1921 gcaataagta atatatcgtt ttgctatcgt gcatcgctcg cgctcagttc cattgtgctt
     1981 ttttaagctg tcgtttttct tacggtatat accggttttt tatggcgtgg tttcttaact
     2041 tgttcagcta ctgatggacc cattgtatct aggtagtcaa ctagctttgt tagatcataa
     2101 atattgcgac caccatatcg gcgatcactc ttcgatgttg gtttcttgtc caagagatta
     2161 gctttttcaa gatcattgat agctctctga acagtccgta cagaaacccc catacgtatg
     2221 gctagacttt ccattgacgg atgcggccac tcttgcaaac tccaccagtg aacgatcagg
     2281 ttaagtagtg tgttaaaggc cactgaagtt agctttttct cgttttgtat aaaaaacaat
     2341 acggtaggca ctgccgtcca gccaagagac aaaccgccag ctttccattt attcttaacg
     2401 gagtaagtca ttgattttcc taagccccaa aatatttaaa gtatatatta tatggtatat
     2461 tcatatgaat agggtgacac tggcgccatt attgtgcaac caaaaaagac tactctgaaa
     2521 acgaggaaaa gattttttcc tgcctgaatt agatacggag ttagcgatat gaaaaccgaa
     2581 caacgtcatg atcttgttaa agatattgag gtttttggcg tatccttgtc tctgttgatt
     2641 tccagagcga atgagaagtc tgttacaatg ccatctggtc taagtcggga gcagagaaga
     2701 gcatgggcag cggagcaggc gcgcaaaatc cacaattgaa tattgtctca ttctctgaga
     2761 ccttcaacct ttattacaca tccagatatt ctgcaaaaac actcgataaa atcgatgatt
     2821 tcattgagca ttttgaaaaa tacaatctct ttggcgatcc tttaaaagga tatccagctt
     2881 ggactggcaa agtatcgcca tcgtggaaag tgcctgatca ttacgaaaac aaagaagcta
     2941 ttgagatgta tgctagagct aacaaattat ggcatgctca tttaggcgat ccggttttta
     3001 aagatacgtt tcatgggaaa tacaaggttt ctgactgggt tattcatttc cagcggctga
     3061 caccgaacca tataaagctt ttagagcttg gataccatga cccaatgaag ctacctcaaa
     3121 actttgaatg atcgagcggc aggctaaatg aaatcttgag attcattcag tct
//
