LOCUS       NZ_CP035489             1978 bp    DNA     circular CON 18-JUN-2024
DEFINITION  Escherichia coli strain NissleGFP_pZE21 plasmid pZE21, complete
            sequence.
ACCESSION   NZ_CP035489
VERSION     NZ_CP035489.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN10824104
            Assembly: GCF_004135125.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 1978)
  AUTHORS   Crook,N.C., Ferreiro,A., Gasparrini,A.J., Pesesky,M.W., Gibson,M.K.,
            Wang,B., Sun,X., Condiotte,Z., Dobrowolski,S., Peterson,D. and
            Dantas,G.
  TITLE     Adaptive strategies of the candidate probiotic E. coli Nissle in the
            mammalian gut
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 1978)
  AUTHORS   Crook,N.C., Ferreiro,A., Gasparrini,A.J., Pesesky,M.W., Gibson,M.K.,
            Wang,B., Sun,X., Condiotte,Z. and Dantas,G.
  TITLE     Direct Submission
  JOURNAL   Submitted (26-JAN-2019) Pathology and Immunology, Washington
            University in Saint Louis, 4515 McKinley Ave, Saint Louis, MO 63108,
            USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 31-DEC-2017
            Assembly Method                   :: SPAdes v. 3.11.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 60.0x
            Sequencing Technology :: Illumina NextSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_004135125.1-RS_2024_06_18
            Annotation Date                   :: 06/18/2024 04:23:19
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,870
            CDSs (total)                      :: 4,758
            Genes (coding)                    :: 4,539
            CDSs (with protein)               :: 4,539
            Genes (RNA)                       :: 112
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 219
            CDSs (without protein)            :: 219
            Pseudo Genes (ambiguous residues) :: 0 of 219
            Pseudo Genes (frameshifted)       :: 97 of 219
            Pseudo Genes (incomplete)         :: 137 of 219
            Pseudo Genes (internal stop)      :: 53 of 219
            Pseudo Genes (multiple problems)  :: 56 of 219
            Pseudo Genes (short protein)      :: 2 of 219
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP035489.1.
            Bacteria and source DNA available from Gautam Dantas,
            dantas@wustl.edu.
            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..1978
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="NissleGFP_pZE21"
                     /isolation_source="cell culture"
                     /db_xref="taxon:562"
                     /plasmid="pZE21"
                     /geo_loc_name="USA:Missouri,Saint Louis"
                     /collection_date="2014"
     gene            <353..424
                     /locus_tag="EUJ32_RS25480"
                     /pseudo=""
     CDS             <353..424
                     /locus_tag="EUJ32_RS25480"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_308303.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /name="hypothetical protein"
     gene            complement(484..1278)
                     /locus_tag="EUJ32_RS24765"
                     /old_locus_tag="EUJ32_24765"
     CDS             complement(484..1278)
                     /locus_tag="EUJ32_RS24765"
                     /old_locus_tag="EUJ32_24765"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000572405.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="aminoglycoside O-phosphotransferase APH(3')-IIa"
                     /protein_id="WP_000572405.1"
                     /translation="MIEQDGLHAGSPAAWVERLFGYDWAQQTIGCSDAAVFRLSAQGRP
                     VLFVKTDLSGALNELQDEAARLSWLATTGVPCAAVLDVVTEAGRDWLLLGEVPGQDLLS
                     SHLAPAEKVSIMADAMRRLHTLDPATCPFDHQAKHRIERARTRMEAGLVDQDDLDEEHQ
                     GLAPAELFARLKARMPDGEDLVVTHGDACLPNIMVENGRFSGFIDCGRLGVADRYQDIA
                     LATRDIAEELGGEWADRFLVLYGIAAPDSQRIAFYRLLDEFF"
                     /name="aminoglycoside O-phosphotransferase APH(3')-IIa"
     ARG             complement(488..1278)
                     /name="aph(3')-IIa"
                     /gene="aph(3')-IIa"
                     /gene_name="aminoglycoside O-phosphotransferase
                     APH(3')-IIa"
                     /tool="amrfinderplus"
                     /drug_class="AMINOGLYCOSIDE"
                     /identity="100.0"
                     /coverage="100.0"
ORIGIN
        1 cccggtaaga cacgacttat cgccactggc agcagccact ggtaacagga ttagcagagc
       61 gaggtatgta ggcggtgcta cagagttctt gaagtggtgg cctaactacg gctacactag
      121 aaggacagta tttggtatct gcgctctgct gaagccagtt accttcggaa aaagagttgg
      181 tagctcttga tccggcaaac aaaccaccgc tggtagcggt ggtttttttg tttgcaagca
      241 gcagattacg cgcagaaaaa aaggatctca agaagatcct ttgatctttt ctacggggtc
      301 tgacgctcag tggaacgaaa actcacgtta agggattttg gtcatgacta gtgcttggat
      361 tctcaccaat aaaaaacgcc cggcggcaac cgagcgttct gaacaaatcc agatggagtt
      421 ctgaggtcat tactggatct atcaacagga gtccaagcga gctctcgaac cccagagtcc
      481 cgctcagaag aactcgtcaa gaaggcgata gaaggcgatg cgctgcgaat cgggagcggc
      541 gataccgtaa agcacgagga agcggtcagc ccattcgccg ccaagctctt cagcaatatc
      601 acgggtagcc aacgctatgt cctgatagcg gtccgccaca cccagccggc cacagtcgat
      661 gaatccagaa aagcggccat tttccaccat gatattcggc aagcaggcat cgccatgggt
      721 cacgacgaga tcctcgccgt cgggcatgcg cgccttgagc ctggcgaaca gttcggctgg
      781 cgcgagcccc tgatgctctt cgtccagatc atcctgatcg acaagaccgg cttccatccg
      841 agtacgtgct cgctcgatgc gatgtttcgc ttggtggtcg aatgggcagg tagccggatc
      901 aagcgtatgc agccgccgca ttgcatcagc catgatggat actttctcgg caggagcaag
      961 gtgagatgac aggagatcct gccccggcac ttcgcccaat agcagccagt cccttcccgc
     1021 ttcagtgaca acgtcgagca cagctgcgca aggaacgccc gtcgtggcca gccacgatag
     1081 ccgcgctgcc tcgtcctgca gttcattcag ggcaccggac aggtcggtct tgacaaaaag
     1141 aaccgggcgc ccctgcgctg acagccggaa cacggcggca tcagagcagc cgattgtctg
     1201 ttgtgcccag tcatagccga atagcctctc cacccaagcg gccggagaac ctgcgtgcaa
     1261 tccatcttgt tcaatcatgc gaaacgatcc tcatcctgtc tcttgatcag atcttgatcc
     1321 cctgcgccat cagatccttg gcggcaagaa agccatccag tttactttgc agggcttccc
     1381 aaccttacca gagggcgccc cagctggcaa ttccgacgtc taagaaacca ttattatcat
     1441 gacattaacc tataaaaata ggcgtatcac gaggcccttt cgtcttcacc tcgagtccct
     1501 atcagtgata gagattgaca tccctatcag tgatagagat actgagcaca tcagcaggac
     1561 gcactgaccg aattcattaa agaggagaaa ggtaccgggc cccccctcga ggtcgacggt
     1621 atcgataagc ttgatatcga attcctgcag cccgggggat cccatggtac gcgtgctaga
     1681 ggcatcaaat aaaacgaaag gctcagtcga aagactgggc ctttcgtttt atctgttgtt
     1741 tgtcggtgaa cgctctcctg agtaggacaa atccgccgcc ctagacctag ggcgttcggc
     1801 tgcggcgagc ggtatcagct cactcaaagg cggtaatacg gttatccaca gaatcagggg
     1861 ataacgcagg aaagaacatg tgagcaaaag gccagcaaaa ggccaggaac cgtaaaaagg
     1921 ccgcgttgct ggcgtttttc cataggctcc gcccccctga cgagcatcac aaaaatcg
//
