LOCUS       CP134922                2462 bp    DNA     circular BCT 27-SEP-2023
DEFINITION  Escherichia coli strain 1588 plasmid pMB8775_4, complete sequence.
ACCESSION   CP134922
VERSION     CP134922.1
DBLINK      BioProject: PRJNA924946
            BioSample: SAMN32977864
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 2462)
  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  JOURNAL   Unpublished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 2462)
  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                   :: 106x
            Sequencing Technology             :: Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 09/21/2023 12:35:31
            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)                     :: 4,943
            CDSs (total)                      :: 4,816
            Genes (coding)                    :: 4,592
            CDSs (with protein)               :: 4,592
            Genes (RNA)                       :: 127
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 90
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 224
            CDSs (without protein)            :: 224
            Pseudo Genes (ambiguous residues) :: 0 of 224
            Pseudo Genes (frameshifted)       :: 67 of 224
            Pseudo Genes (incomplete)         :: 152 of 224
            Pseudo Genes (internal stop)      :: 43 of 224
            Pseudo Genes (multiple problems)  :: 38 of 224
            Pseudo Genes (short protein)      :: 4 of 224
            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..2462
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="1588"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pMB8775_4"
                     /geo_loc_name="USA: Houston"
                     /lat_lon="29.7068 N 95.3971 W"
                     /collection_date="2019-07-29"
                     /collected_by="MDACC"
                     /note="genotype: ST167"
     gene            234..317
                     /locus_tag="RNO65_24710"
     CDS             234..317
                     /locus_tag="RNO65_24710"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WNL93879.1"
                     /translation="MHEPPVQSDRCALSGNYRLESNPDRHD"
                     /name="replication initiation protein"
     gene            complement(863..1405)
                     /locus_tag="RNO65_24715"
     CDS             complement(863..1405)
                     /locus_tag="RNO65_24715"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001632013.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="stationary phase growth adaptation protein"
                     /protein_id="WNL93878.1"
                     /translation="MNIDEVAKWRPFTDQDGNIWDLSFLDAHEVSYTHCSPGKPDIVYK
                     FTVSYSFHCFCKDYPEQTEEEKLSLMYDAGKDSRPFCKVRYALARDKLRAIIEGLGNAK
                     VIHAGYGSYAFVEITVDEGESEFYFVPFKVYRERKKLRLHVTSAYPVKERPSGKPVSFF
                     KIAHNLLRGKPLPKPHM"
                     /name="stationary phase growth adaptation protein"
     Typing          53..534
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="86.706"
                     /coverage="94.0"
                     /evalue="1.33e-148"
ORIGIN
        1 ccataggctc cgcccccctg acaagcatca cgaaatctga cgctcaaatc agtggtggcg
       61 aaacccgaca ggactataaa gataccaggc gtttccccct ggtggctccc tcgtgcgctc
      121 tcctgttcct gcctttcggt ttaccggtgt cattccgctg ttatggccgc gtttatctca
      181 ttccacgcct gacactcagt tccgggtagg cagttcgctc caagctggac tgtatgcacg
      241 aaccccccgt tcagtccgac cgctgcgcct tgtccggtaa ctatcgtctt gagtccaacc
      301 cggatagaca cgactaatcg ccattggcaa cggccactgg taagcaggat gtgcgagaga
      361 tgtaacgaga gttcttgaag tggcggccta actgaggcta cactgaaagg acagtatttg
      421 gtgacatgtc tcgcacaaga ctgttaccac ggttagagaa tctgccagga ttaactaacc
      481 ttcggaaaaa ccacctgcca gggtggtttt ttcgtttctg agcaagagac tacgacgagc
      541 cactgatgat ctcaagtgtt catttctgat atccacagca gaataactgt taggatatag
      601 ggtatctata gtcaggagct tcaagaaagc cagacacagc aatggattcc ggcattatcg
      661 agaaaaatta gtatataggt tgcaaccaaa atgttggttg caaatctaca tcacactacc
      721 tacaattgct ttaaggatgc agcagactgg taacaccaga catcccacta ccaataacaa
      781 tgttggtcga ggccaagccc ggtaaaggtg ttctgaatac cagaagaaat ttctggcgaa
      841 gcccgcaact aagcgggctt tgttacatat gaggtttagg taatggcttc ccgcgcagga
      901 gattgtgagc tatcttgaaa aagctaactg gcttacctga cggtctctcc ttgacaggat
      961 aagcacttgt tacatgcaag cgcagctttt tacgctcacg atatacctta aaaggcacaa
     1021 agtagaactc actttcacct tcatctacag taatctctac aaaagcataa ctaccatatc
     1081 cagcatggat aaccttcgcg ttacccaatc cttcaatgat ggctctcagc ttgtctcgag
     1141 caagggcata tcggacctta caaaatggcc tcgagtcttt gcctgcatca tacatcaacg
     1201 ataatttttc ttcctcagtc tgctctggat aatccttgca aaaacaatga aatgagtaag
     1261 aaacagtgaa cttatacaca atatcaggtt taccaggaga acaatgagta taagaaacct
     1321 catgtgcatc aagaaatgac agatcccata tattgccatc ctgatccgta aaaggacgcc
     1381 acttagcaac ttcatcaatg ttcacgaaaa aacctcaata tccggatggc agaatccgca
     1441 cattctacca gagaagaaac aagcggaagg agcgtggcaa aataagagct aggcctttta
     1501 cagaagactt cgccacaacc tttcatggat acattggtaa tgattaagtg ttatttacca
     1561 taacatccgt tgcgtgcacc gccgcagagg ccctcagcgc gtttctgagg cctccgacct
     1621 gaaacacaca cctttctgtg cccatatcga gaaaaaacgc ccctgatgat tctggcgcga
     1681 ctgcatggct atgcacggac atacctggcc gggattttag cggctaaaat ccgatgaacg
     1741 ccctgaaagc caccacgaac caccccgata acgcctcacg ggtgcgcagt ttactgtgcg
     1801 gccgtgaggc gttggccagg ccgtcaggca tggctggatt tattgctaag ggggtcggat
     1861 ttaacgtgga tgaatcagca cgcagtgatg aacgggattc ggaaggggca cccttgcggc
     1921 gcggcgatgt atacatcgct aacgtgcctt ggtcatttat tgcaagaagg gagaggtagc
     1981 attttgatag caaaaaagta gcaaaaggat agcaaccgaa agaccagaag actctggaga
     2041 tagcaaaaaa gtagcaaaat ggtagcaaaa agatagcaaa aagatagcaa acatgcggga
     2101 gctaaccagg agtctttagc gggccggcgg tactccaaaa acacatcttg tcccgctgtt
     2161 ttgtgaataa gccagcatag ctgtgggcac aaaacatttc ctgtccgctg ctttaacctt
     2221 tgtaatccag gaacgtcagg tgacgtcact ttgcggcgtt cgccctatcc tgcatcgtat
     2281 taaaaaatgc agctatggcg cgtacggtgc caaagagaag cccgcagata ttccgcttcc
     2341 tcgctcactg actcgctccg ctcggtcgtt cggctgcggc gagcgttacc tgcacacgga
     2401 taaggacaaa ggcatacggc gtgacaggca gggcaggaaa aggatgcggc gctgccgttt
     2461 tt
//
