LOCUS       NZ_CP035488             3250 bp    DNA     circular CON 18-JUN-2024
DEFINITION  Escherichia coli strain NissleGFP_pZE21 plasmid pMut1, complete
            sequence.
ACCESSION   NZ_CP035488
VERSION     NZ_CP035488.1
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 3250)
  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  JOURNAL   Unpublished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 3250)
  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
            CP035488.1.
            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..3250
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="NissleGFP_pZE21"
                     /isolation_source="cell culture"
                     /db_xref="taxon:562"
                     /plasmid="pMut1"
                     /geo_loc_name="USA:Missouri,Saint Louis"
                     /collection_date="2014"
     gene            complement(283..711)
                     /locus_tag="EUJ32_RS24735"
                     /old_locus_tag="EUJ32_24735"
     CDS             complement(283..711)
                     /locus_tag="EUJ32_RS24735"
                     /old_locus_tag="EUJ32_24735"
                     /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_000534558.1"
                     /translation="MGSGAGAQNPQLNIVSFSETFNLYYTSRYSAKTLDKIDDFIEHFE
                     KYNLFGDPLKGYPAWTGKVSPSWKVPDHYENKEAIEKYARANKLWHAHLGDPVFKDTFH
                     GKYKVSDWVIHFQRLTPNHIKLLELGYHDPMKLPQNFE"
                     /name="hypothetical protein"
     gene            complement(675..845)
                     /locus_tag="EUJ32_RS24905"
     CDS             complement(675..845)
                     /locus_tag="EUJ32_RS24905"
                     /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            1003..1431
                     /locus_tag="EUJ32_RS24740"
                     /old_locus_tag="EUJ32_24740"
     CDS             1003..1431
                     /locus_tag="EUJ32_RS24740"
                     /old_locus_tag="EUJ32_24740"
                     /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            complement(1820..2143)
                     /gene="mobA"
                     /locus_tag="EUJ32_RS24745"
                     /old_locus_tag="EUJ32_24745"
     CDS             complement(1820..2143)
                     /gene="mobA"
                     /locus_tag="EUJ32_RS24745"
                     /old_locus_tag="EUJ32_24745"
                     /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            2427..2621
                     /locus_tag="EUJ32_RS24750"
                     /old_locus_tag="EUJ32_24750"
     CDS             2427..2621
                     /locus_tag="EUJ32_RS24750"
                     /old_locus_tag="EUJ32_24750"
                     /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_001041622.1"
                     /translation="MNKQQQAVLNMAGFIKSQSLTLLEKLDALNADEQAAMCEKLHELA
                     EELQNSIQTRFEAENLTGI"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            3109..3240
                     /locus_tag="EUJ32_RS25055"
     CDS             3109..3240
                     /locus_tag="EUJ32_RS25055"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005019281.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_023151671.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHDLTPLATATGKQDVREM"
                     /name="hypothetical protein"
     Typing          complement(2153..2389)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.49e-121"
     Typing          2657..3181
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.085"
                     /coverage="95.0"
                     /evalue="0.0"
     Typing          complement(1824..2143)
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="2.4e-62"
ORIGIN
        1 cccggtaaga cacgacttaa cgccactggc aacggccact ggtaagcagg atgtgcgaga
       61 gatgtaacga gagttcttga agtggcggcc taactgaggc tacactgaaa ggacagtatt
      121 tggtgacatg tctcgcacaa gactgttacc acggttagag aatctgccag gattaactaa
      181 ccttcgaaaa accacctgcc agggtggttt tttcgttttt acaatagtga gattacgacg
      241 agactgaatg aatctcaaga tttcatttag cctgccgctc gatcattcaa agttttgagg
      301 tagcttcatt gggtcatggt atccaagctc taaaagcttt atatggttcg gtgtcagccg
      361 ctggaaatga ataacccagt cagaaacctt gtatttccca tgaaacgtat ctttaaaaac
      421 cggatcgcct aaatgagcat gccataattt gttagctcta gcatacttct caatagcttc
      481 tttgttttcg taatgatcag gcactttcca cgatggcgat actttgccag tccaagctgg
      541 atatcctttt aaaggatcgc caaagagatt gtatttttca aaatgctcaa tgaaatcatc
      601 gattttatcg agtgtttttg cagaatatct ggatgtgtaa taaaggttga aggtctcaga
      661 gaatgagaca atattcaatt gtggattttg cgcgcctgct ccgctgccca tgctcttctc
      721 tgctcccgac ttagaccaga tggcattgta acagacttct cattcgctct ggaaatcaac
      781 agagacaagg atacgccaaa aacctcaata tctttaacaa gatcatgacg ttgttcggtt
      841 ttcatatcgc taactccgta tctaattcag gcaggaaaaa atcttttcct cgttttcaga
      901 gtagtctttt ttggttgcac aataatggcg ccagtgtcac cctattcata tgaatatacc
      961 atataatata tactttaaat attttggggc ttaggaaaat caatgactta ctccgttaag
     1021 aataaatgga aagctggcgg tttgtctctt ggctggacag cagtgcctac cgtattgttt
     1081 tttatacaaa acgagaaaaa gctaacttca gtggccttta acacactact taacctgatc
     1141 gttcactggt ggagtttgca agagtggccg catccgtcaa tggaaagtct agccatacgt
     1201 atgggggttt ctgtacggac tgttcagaga gctatcaatg atcttgaaaa agctaatctc
     1261 ttggacaaga aaccaacatc gaagagtgat cgccgatatg gtggtcgcaa tatttatgat
     1321 ctaacaaagc tagttgacta cctagataca atgggtccat cagtagctga acaagttaag
     1381 aaaccacgcc ataaaaaacc ggtatatacc gtaagaaaaa cgacagctta aaaaagcaca
     1441 atggaactga gcgcgagcga tgcacgatag caaaacgata tattacttat tgcattggtc
     1501 ttggtagccc tgcttctggc taaaccactg tcaggagtaa ttggctttgc ctgtaatggg
     1561 ttcatcgctt cacagttaaa gttatcgcat agctcatata tttaccataa tcccttaatt
     1621 gtacgcacca ctgaaacgcg ctgaacgcga ttctgacgca gacaccgcaa aaagagatgt
     1681 tttaccccgg aaaaacagga aggatgcgtc aggatcgttt tcagctcgct gcatagctat
     1741 gcatgaaagc gaatggtgat cactttggga gcttacggtg ttcataccgt cagttttcga
     1801 cagttttctc tccgggaagc taatctgcca taagcctgga taacagggca cggtgatact
     1861 ccgtaatagc gatcagcacc tccgcatact ccctgtcccc gacacgcttg ccgtcgataa
     1921 agagtttttt ctgtaacgcc cccagtctca taacttcttt cagtacccga tcatcagtca
     1981 gtgagttaac tttcttaccg agagctgccg cccgtaaaaa accggaaacg gtcttgccgc
     2041 attcagcagc cctttttctg atttcctggt cttcttctgc cgtcagacga acagggcgac
     2101 tgatagcccg cctgcgcgta ttacttccac ttcgttttgt cataaaacat ggctccgtat
     2161 ctgacatggg tgtcggggca aagccctgac cagggcaatt gtaatagcgt gcatgtatgc
     2221 gcggtataac aattgcacat cctgtcctgt cagcaagctc gaattaccga caaaggcacg
     2281 gcagtttttt ggcagtgaca gtgttgtctg acagaaatgc ccgtcaaaaa gccaagcggc
     2341 agaatagcgg cagcaaaaca gtcgaaaagt ggtacgcgat ataatcacac aacgcagatg
     2401 acagacagaa cggagaaaac gaaaagatga ataagcagca gcaagccgta ctcaacatgg
     2461 cgggattcat aaaaagtcag agcctgacgc tgctcgaaaa actggacgca ctcaatgccg
     2521 acgaacaggc cgccatgtgt gagaaactgc acgaactcgc agaagaactc cagaacagca
     2581 tacagacacg ctttgaagcg gaaaatctta ccgggatata acgcatccgg acaggatgca
     2641 gaacggcata gaggagcgta aggagaaaat gtcacataag gcgctcttcc gcttcctcgc
     2701 tcactgactc gctacgctcg gtcgttcgac tgcggcgagc ggtgtcagct cactcaaagg
     2761 cggtaatacg gttatccaca gaatcggggg ataaaaccgg aaagaacatg tgagcaaaag
     2821 acaaagaccc agaagaaggg cgcgcgggag gcgtttttcc ataggctccg cccccctgac
     2881 gagcatcaca aaaatcgacg ctcaagtcag aggtggcgaa acccgacagg actataaaga
     2941 taccaggcgt ttccccctgg aagctccctc gtgcgctctc ctgttccgac cctgccgctt
     3001 accggatacc tgtccgcctt tctcccttcg ggaagcgtgg cgctttctca tagctcacgc
     3061 tgttggtatc tcggttcggt gtaggtcgtt cgctccaagc tgggctgtgt gcacgaaccc
     3121 cccgttcagc ccgaccgctg cgccttatcc ggtaactatc gtcttgagtc caacccggta
     3181 agacacgact taacgccact ggcaacggcc actggtaagc aggatgtgcg agagatgtaa
     3241 cgagagttct
//
