LOCUS       NZ_CP058218             3173 bp    DNA     circular CON 18-DEC-2023
DEFINITION  Escherichia coli Nissle 1917 plasmid pMUT1, complete sequence.
ACCESSION   NZ_CP058218
VERSION     NZ_CP058218.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15325684
            Assembly: GCF_021559835.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli Nissle 1917
  ORGANISM  Escherichia coli Nissle 1917
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3173)
  AUTHORS   Sproer,C., Tegelkamp,K., Wami,H., Bunk,B., Overmann,J. and
            Dobrindt,U.
  TITLE     Comparison three closely relates ST73 Escherichia coli strains
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3173)
  AUTHORS   Sproer,C., Tegelkamp,K., Wami,H., Bunk,B., Overmann,J. and
            Dobrindt,U.
  TITLE     Direct Submission
  JOURNAL   Submitted (19-JUN-2020) Institute of Hygiene, University of
            Muenster, Mendelstrasse 7, Muenster 48149, Germany
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 11-JUL-2019
            Assembly Method :: RS_HGAP_Assembly.3 protocol v. 2.2.0; BWA v.
            07.7.17; Unicycler v. 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 112x
            Sequencing Technology :: Illumina MiSeq, Oxford Nanopore Minion and
            PacBio RSII
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 12/17/2023 05:03:09
            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)                     :: 4,863
            CDSs (total)                      :: 4,749
            Genes (coding)                    :: 4,530
            CDSs (with protein)               :: 4,530
            Genes (RNA)                       :: 114
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 219
            CDSs (without protein)            :: 219
            Pseudo Genes (ambiguous residues) :: 0 of 219
            Pseudo Genes (frameshifted)       :: 94 of 219
            Pseudo Genes (incomplete)         :: 137 of 219
            Pseudo Genes (internal stop)      :: 51 of 219
            Pseudo Genes (multiple problems)  :: 54 of 219
            Pseudo Genes (short protein)      :: 4 of 219
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP058218.1.
            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 Nissle 1917"
                     /mol_type="genomic DNA"
                     /strain="Nissle 1917"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:316435"
                     /plasmid="pMUT1"
                     /geo_loc_name="Germany"
                     /collection_date="1917"
     gene            194..325
                     /locus_tag="HW372_RS24175"
                     /old_locus_tag="HW372_23980"
     CDS             194..325
                     /locus_tag="HW372_RS24175"
                     /old_locus_tag="HW372_23980"
                     /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"
     gene            complement(541..969)
                     /locus_tag="HW372_RS24180"
                     /old_locus_tag="HW372_23985"
     CDS             complement(541..969)
                     /locus_tag="HW372_RS24180"
                     /old_locus_tag="HW372_23985"
                     /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(933..1103)
                     /locus_tag="HW372_RS24185"
                     /old_locus_tag="HW372_23990"
     CDS             complement(933..1103)
                     /locus_tag="HW372_RS24185"
                     /old_locus_tag="HW372_23990"
                     /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            1261..1689
                     /locus_tag="HW372_RS24190"
                     /old_locus_tag="HW372_23995"
     CDS             1261..1689
                     /locus_tag="HW372_RS24190"
                     /old_locus_tag="HW372_23995"
                     /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(2078..2401)
                     /gene="mobA"
                     /locus_tag="HW372_RS24195"
                     /old_locus_tag="HW372_24000"
     CDS             complement(2078..2401)
                     /gene="mobA"
                     /locus_tag="HW372_RS24195"
                     /old_locus_tag="HW372_24000"
                     /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            2685..2879
                     /locus_tag="HW372_RS24200"
                     /old_locus_tag="HW372_24005"
     CDS             2685..2879
                     /locus_tag="HW372_RS24200"
                     /old_locus_tag="HW372_24005"
                     /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"
     Typing          complement(2411..2647)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.49e-121"
     Typing          2..321
                     /name="rep_cluster_2370"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.639"
                     /coverage="99.0"
                     /evalue="3.9e-143"
     Typing          2915..3173
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="90.875"
                     /coverage="95.0"
                     /evalue="5.42e-93"
     Typing          complement(2082..2401)
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="2.23e-62"
ORIGIN
        1 gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct ccctcgtgcg
       61 ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc cttcgggaag
      121 cgtggcgctt tctcatagct cacgctgttg gtatctcggt tcggtgtagg tcgttcgctc
      181 caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct tatccggtaa
      241 ctatcgtctt gagtccaacc cggtaagaca cgacttaacg ccactggcaa cggccactgg
      301 taagcaggat gtgcgagaga tgtaacgaga gttcttgaag tggcggccta actgaggcta
      361 cactgaaagg acagtatttg gtgacatgtc tcgcacaaga ctgttaccac ggttagagaa
      421 tctgccagga ttaactaacc ttcgaaaaac cacctgccag ggtggttttt tcgtttttac
      481 aatagtgaga ttacgacgag actgaatgaa tctcaagatt tcatttagcc tgccgctcga
      541 tcattcaaag ttttgaggta gcttcattgg gtcatggtat ccaagctcta aaagctttat
      601 atggttcggt gtcagccgct ggaaatgaat aacccagtca gaaaccttgt atttcccatg
      661 aaacgtatct ttaaaaaccg gatcgcctaa atgagcatgc cataatttgt tagctctagc
      721 atacttctca atagcttctt tgttttcgta atgatcaggc actttccacg atggcgatac
      781 tttgccagtc caagctggat atccttttaa aggatcgcca aagagattgt atttttcaaa
      841 atgctcaatg aaatcatcga ttttatcgag tgtttttgca gaatatctgg atgtgtaata
      901 aaggttgaag gtctcagaga atgagacaat attcaattgt ggattttgcg cgcctgctcc
      961 gctgcccatg ctcttctctg ctcccgactt agaccagatg gcattgtaac agacttctca
     1021 ttcgctctgg aaatcaacag agacaaggat acgccaaaaa cctcaatatc tttaacaaga
     1081 tcatgacgtt gttcggtttt catatcgcta actccgtatc taattcaggc aggaaaaaat
     1141 cttttcctcg ttttcagagt agtctttttt ggttgcacaa taatggcgcc agtgtcaccc
     1201 tattcatatg aatataccat ataatatata ctttaaatat tttggggctt aggaaaatca
     1261 atgacttact ccgttaagaa taaatggaaa gctggcggtt tgtctcttgg ctggacagca
     1321 gtgcctaccg tattgttttt tatacaaaac gagaaaaagc taacttcagt ggcctttaac
     1381 acactactta acctgatcgt tcactggtgg agtttgcaag agtggccgca tccgtcaatg
     1441 gaaagtctag ccatacgtat gggggtttct gtacggactg ttcagagagc tatcaatgat
     1501 cttgaaaaag ctaatctctt ggacaagaaa ccaacatcga agagtgatcg ccgatatggt
     1561 ggtcgcaata tttatgatct aacaaagcta gttgactacc tagatacaat gggtccatca
     1621 gtagctgaac aagttaagaa accacgccat aaaaaaccgg tatataccgt aagaaaaacg
     1681 acagcttaaa aaagcacaat ggaactgagc gcgagcgatg cacgatagca aaacgatata
     1741 ttacttattg cattggtctt ggtagccctg cttctggcta aaccactgtc aggagtaatt
     1801 ggctttgcct gtaatgggtt catcgcttca cagttaaagt tatcgcatag ctcatatatt
     1861 taccataatc ccttaattgt acgcaccact gaaacgcgct gaacgcgatt ctgacgcaga
     1921 caccgcaaaa agagatgttt taccccggaa aaacaggaag gatgcgtcag gatcgttttc
     1981 agctcgctgc atagctatgc atgaaagcga atggtgatca ctttgggagc ttacggtgtt
     2041 cataccgtca gttttcgaca gttttctctc cgggaagcta atctgccata agcctggata
     2101 acagggcacg gtgatactcc gtaatagcga tcagcacctc cgcatactcc ctgtccccga
     2161 cacgcttgcc gtcgataaag agttttttct gtaacgcccc cagtctcata acttctttca
     2221 gtacccgatc atcagtcagt gagttaactt tcttaccgag agctgccgcc cgtaaaaaac
     2281 cggaaacggt cttgccgcat tcagcagccc tttttctgat ttcctggtct tcttctgccg
     2341 tcagacgaac agggcgactg atagcccgcc tgcgcgtatt acttccactt cgttttgtca
     2401 taaaacatgg ctccgtatct gacatgggtg tcggggcaaa gccctgacca gggcaattgt
     2461 aatagcgtgc atgtatgcgc ggtataacaa ttgcacatcc tgtcctgtca gcaagctcga
     2521 attaccgaca aaggcacggc agttttttgg cagtgacagt gttgtctgac agaaatgccc
     2581 gtcaaaaagc caagcggcag aatagcggca gcaaaacagt cgaaaagtgg tacgcgatat
     2641 aatcacacaa cgcagatgac agacagaacg gagaaaacga aaagatgaat aagcagcagc
     2701 aagccgtact caacatggcg ggattcataa aaagtcagag cctgacgctg ctcgaaaaac
     2761 tggacgcact caatgccgac gaacaggccg ccatgtgtga gaaactgcac gaactcgcag
     2821 aagaactcca gaacagcata cagacacgct ttgaagcgga aaatcttacc gggatataac
     2881 gcatccggac aggatgcaga acggcataga ggagcgtaag gagaaaatgt cacataaggc
     2941 gctcttccgc ttcctcgctc actgactcgc tacgctcggt cgttcgactg cggcgagcgg
     3001 tgtcagctca ctcaaaggcg gtaatacggt tatccacaga atcgggggat aaaaccggaa
     3061 agaacatgtg agcaaaagac aaagacccag aagaagggcg cgcgggaggc gtttttccat
     3121 aggctccgcc cccctgacga gcatcacaaa aatcgacgct caagtcagag gtg
//
