LOCUS       NZ_CP023342             5514 bp    DNA     circular CON 17-JUN-2024
DEFINITION  Escherichia coli Nissle 1917 plasmid pMUT2, complete sequence.
ACCESSION   NZ_CP023342
VERSION     NZ_CP023342.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN07451663
            Assembly: GCF_003546975.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli Nissle 1917
  ORGANISM  Escherichia coli Nissle 1917
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5514)
  AUTHORS   McClelland,M., Porwollik,S. and Chu,W.
  TITLE     Improved sequence of E. coli Nissle 117 genome
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5514)
  AUTHORS   McClelland,M., Porwollik,S. and Chu,W.
  TITLE     Direct Submission
  JOURNAL   Submitted (08-SEP-2017) Microbiology and Molecular Genetics,
            University of California, B240 Medical Sciences, Irvine, CA
            92697-4025, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: HGAP v. 2
            Genome Coverage                   :: 290.03
            Sequencing Technology             :: PacBio
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_003546975.1-RS_2024_06_17
            Annotation Date                   :: 06/17/2024 06:53:12
            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)                     :: 4,875
            CDSs (total)                      :: 4,761
            Genes (coding)                    :: 4,537
            CDSs (with protein)               :: 4,537
            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)              :: 224
            CDSs (without protein)            :: 224
            Pseudo Genes (ambiguous residues) :: 0 of 224
            Pseudo Genes (frameshifted)       :: 95 of 224
            Pseudo Genes (incomplete)         :: 141 of 224
            Pseudo Genes (internal stop)      :: 53 of 224
            Pseudo Genes (multiple problems)  :: 54 of 224
            Pseudo Genes (short protein)      :: 2 of 224
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP023342.1.
            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..5514
                     /organism="Escherichia coli Nissle 1917"
                     /mol_type="genomic DNA"
                     /strain="Nissle 1917"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:316435"
                     /plasmid="pMUT2"
                     /geo_loc_name="Germany: Freiburg"
                     /altitude="279 m"
                     /collection_date="1917"
                     /collected_by="Nissle"
     gene            complement(<612..1403)
                     /locus_tag="CIW80_RS25650"
                     /old_locus_tag="CIW80_25895"
                     /pseudo=""
     CDS             complement(<612..1403)
                     /locus_tag="CIW80_RS25650"
                     /old_locus_tag="CIW80_25895"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000635827.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            complement(1393..1719)
                     /locus_tag="CIW80_RS25655"
                     /old_locus_tag="CIW80_25900"
     CDS             complement(1393..1719)
                     /locus_tag="CIW80_RS25655"
                     /old_locus_tag="CIW80_25900"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_006674374.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_001554615.1"
                     /translation="MEKRTKEIKIRLTEAEHQRLLERCDRKHLAEWLRAVGLGESRTAR
                     RRPLPTVDPTLLRQVSGIGNNLNQIARYLNQHGLPPQERVSLLAVLNSIDQHLAELLEQ
                     HRDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            complement(1946..3088)
                     /locus_tag="CIW80_RS25660"
                     /old_locus_tag="CIW80_25905"
     CDS             complement(1946..3088)
                     /locus_tag="CIW80_RS25660"
                     /old_locus_tag="CIW80_25905"
                     /inference="COORDINATES: protein motif:HMM:NF027488.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Kiwa anti-phage protein KwaB-like
                     domain-containing protein"
                     /protein_id="WP_001704287.1"
                     /translation="MSDDALDLDALEHNEEKAQELLELYKHFDCDINDVTLHTYFNFKN
                     KGKAGAKDSFSYKIAILKNDSELKQSIIDNVIKKTISDLENRVVIVSDVNTLSDRTNTI
                     SFLNDAEQYDNEQMKFLTGIVFDAGFGGDGNENIPIVDFDSVDLISKVDSIIFVLSKNN
                     DDNCITIYKKQYPVQNLSRKKNNFYGFSKKELSRVDQDMISIDGKASLVFAGDTVFIYD
                     QNVFERFFGYKAWIKNAATDFVNNMSTRFKGFVDLSKFIERVNKDSHDADAFSRKLAKA
                     YARSETKQTLQTITNEHLKSVLDENGYLAGVLKYKKGDATICIASHNQQDTFIAMVSEG
                     VLRSLITGIDYLSLGSKRKISSAASNTTTSTTSDSSSAAV"
                     /name="Kiwa anti-phage protein KwaB-like domain-containing
                     protein"
     gene            complement(3091..3738)
                     /gene="kwaA"
                     /locus_tag="CIW80_RS25665"
                     /old_locus_tag="CIW80_25910"
     CDS             complement(3091..3738)
                     /gene="kwaA"
                     /locus_tag="CIW80_RS25665"
                     /old_locus_tag="CIW80_25910"
                     /inference="COORDINATES: protein motif:HMM:NF041622.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="anti-phage protein KwaA"
                     /protein_id="WP_024199421.1"
                     /translation="MKIRMYLLSMLFLFIPITIYFSGIDNVWSVLDKAMSSCSGADGKF
                     QCVLDYSNSRLTFSVLRSVICGALILTCSYTYIWYRWVLKNLDSGAVSRKLKVVSCKKE
                     SGEYLSFLSTYIMPLVFTDLSKPSNIVNFLFVLIIVGFLHIKTKRIHCNPTLSLFNVSA
                     YKITYSVVANGREKTQDGELIVLSKDLIKENDFIRVINHDDYLTFAKKIIEE"
                     /name="kwaA"
     gene            complement(3728..4624)
                     /locus_tag="CIW80_RS25670"
                     /old_locus_tag="CIW80_25915"
     CDS             complement(3728..4624)
                     /locus_tag="CIW80_RS25670"
                     /old_locus_tag="CIW80_25915"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_006674370.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_024199422.1"
                     /translation="MDNQALTLFNDRLPHKPYFSDDLQFGVRIAGKERALLAKYIQFNQ
                     PHAMYWLCFDVDRAGAAIDWADLGAPAPTLTIKNPENGHAHLLYALHTAVRTAPDGRAA
                     PLKYAAAIENALRKKLGADAGYSGLICKNPNHLHWQITVWQPELYTLDWLADYLDLGAA
                     NDREILPDYGLGRNCTLFDKTRKWAYRAIRQGWPQYDQWLQACIERAKAYNLQFSAPLD
                     ENEVMGIAKSVAKWTSKNLTELGFEEYVKQTHTSEIQRQRGKKSSGGGRPKVRDGEWIS
                     LGISRSTWYRKFYKNEN"
                     /name="replication initiation protein"
     gene            4889..5131
                     /locus_tag="CIW80_RS25675"
                     /old_locus_tag="CIW80_25920"
     CDS             4889..5131
                     /locus_tag="CIW80_RS25675"
                     /old_locus_tag="CIW80_25920"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_020301039.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RelB/DinJ family
                     antitoxin"
                     /protein_id="WP_001554710.1"
                     /translation="MATINIRIDDELKSRSYAALEKLGVTPSEVLRQTLEYVAQSGRLP
                     FQQVLLTEDDADLMAIVRDRLENPQAGVKVSLDEL"
                     /name="type II toxin-antitoxin system RelB/DinJ family
                     antitoxin"
     gene            5121..5405
                     /locus_tag="CIW80_RS25680"
                     /old_locus_tag="CIW80_25925"
     CDS             5121..5405
                     /locus_tag="CIW80_RS25680"
                     /old_locus_tag="CIW80_25925"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016149473.1"
                     /GO_function="GO:0008657 - DNA topoisomerase type II
                     (double strand cut, ATP-hydrolyzing) inhibitor activity
                     [Evidence IEA]; GO:0042803 - protein homodimerization
                     activity [Evidence IEA]"
                     /GO_process="GO:0030541 - plasmid partitioning [Evidence
                     IEA]; GO:0051290 - protein heterotetramerization [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RelE/ParE family
                     toxin"
                     /protein_id="WP_001554709.1"
                     /translation="MSYNLEFDPRALKEWRKLGDDVRLQFKKKLEQVLQHPRIDKNRLR
                     ELHDCYKIKLRASGYRLVYQVRDQTITVFVVAVGKRERSAAYDAADKRL"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     Typing          complement(3729..4762)
                     /name="rep_cluster_2486"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(4..1403)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.786"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 gcatgctcaa ggcctgacaa accctgtcgt ttttcgccaa ctcctgcgag gtaacctcga
       61 acatgcgctg taagttggcg tagctgtcct gccacgcttg ctgctgttgt tcgtagtgcc
      121 tctgtaagct ctctaatgcg ctcagaagct gctgctccat ttcggtcatg aatctcttca
      181 ccctgataga taaaaccgcc cagaatcgat tctgtggcgt ctgatgaggt tatttggcgc
      241 tgtacttgat gacctgacga tgttgagcgt tcttgtactc gtcgatcttc ttcgccccct
      301 gcggaaggat caggtaatac acgctcttgt tcttggaatc gtgaattatc gatacgccgg
      361 ctccggtctg gctctttaag tcctgcagga tctggctctg ctcgctgatt tcgttctggc
      421 gttcgaccac gatagtcccg agataccaag ctactccaat caatatcgca aacaggatcc
      481 cacttaatgc caggctgtac agccatgtca ttccgactaa gcggtgtatc tgttttagct
      541 ggctgtcgtt ctcttcttgg atagcggtct gtatgttccc tgagcttaat ttcaaggcct
      601 cggtgatacg tttctcgtgc ttctcgaatg cgttcgcgac gctcgttgcg gtagtcttgg
      661 cttgctgctt cgatttgctc tcgaactccc gcgctaaatt taaaatctcg ctcatacagc
      721 actcctttta agcgaatatt cgggccacct gccggatcag caatactgat actggatttg
      781 gtttcccgta cgaccgacaa tccggcatcg gtaaggtggg aaatcacccc tttacgatcc
      841 gtaatttctc cctgctcaat caagctgatt agccctttgg taatggcttc cgctgcctgc
      901 tgtttgttgc gaggaaggtc attagagggg gttaatgctc ggcgattagc agggtcattc
      961 gggtcgcgta acccaagccg gtcattggtg agggtttgcc atgcgttaac acgaggccgg
     1021 tcagcccgat caaagtaagg ttgtagccgt tttccgctct gcaattcgat gttcgggata
     1081 acaaaattca attcaagacg ccctttgtcc tgatgttgaa cccagaggca ggcatactgg
     1141 tctttatcta gaccggtcat caatgtctgc tcccattcat ccatcaatcg ctgcttttcg
     1201 ccttcgggta aatcactctc ctgaaaagag agcacgccag aggtataagt tcgggcaaat
     1261 tcgcagccat caatcagctc tttgacgtgc tcagggttac cccgtaacac cgtcgcttgt
     1321 tcgcgctgac gatcagggcc cagaaggtaa tcgacaggac cactcccgcc accggcacca
     1381 cgaccatgaa tcttaacgat cacgatgttg ctccagcagt tcggcaagat gttggtcaat
     1441 gctattgagc accgctaaca acgacacccg ttcttgcggc ggtaagccat gctgattcaa
     1501 gtaacgggct atttgattga ggttattacc gatcccgctg acctgacgta acaaggtcgg
     1561 gtctacggta ggtagcggac gacgccgagc tgtacgcgat tcgcctaagc caacggctcg
     1621 taaccactcg gccaaatgct tacggtcaca gcgttcaagt agccgctgat gctccgcttc
     1681 ggtgagtctg attttgatct ctttggtgcg cttttccatg agaatccgct gagaaagttt
     1741 cgcacccaaa gtgcgaattt tcgcagtgga tgcaaggggt ttcggggggc ggcgagcccc
     1801 ctgaaacagt cacagacggc acctcgaaga ggggacgctg tgtgtactgg cttagtacag
     1861 catctatcgt acatcgaggt cgcatcacgc acaaacaaaa agccccgcaa aagcagggct
     1921 gttatctgat ataggttgtt ttgtctcaca cggcagcgga agaggaatcc gaagtggtac
     1981 tggtagtagt attggatgct gctgacgata ttttccgctt tgacccaagg cttaaataat
     2041 caatgcctgt aatcaacgat ctcaatacgc cttcggatac catagcgata aacgtatctt
     2101 gctggttatg gcttgcgatg caaatcgtag catcaccttt tttatacttt aaaacacctg
     2161 ctaaatatcc attttcatct agaacactct taagatgttc atttgttatt gtttgtagcg
     2221 tttgctttgt ttcgcttcga gcatacgcct tagctagctt ccgagaaaaa gcatccgcat
     2281 catgactatc tttatttact cgctcaataa atttgcttaa gtcaacaaat cccttaaaac
     2341 gagtggacat attgttaaca aaatcagtgg cagcattttt tatccatgct ttatagccaa
     2401 aaaaacgctc gaaaacattt tggtcgtaga taaataccgt atcgccagca aaaacaagag
     2461 atgccttacc atcaatagaa atcatatctt gatctactcg agatagttct tttttgctaa
     2521 acccataaaa attatttttc tttcttgata agttttgaac tggatattgc ttcttgtata
     2581 tggttataca attgtcgtca ttattcttac tcaaaacgaa aatgattgag tcaacttttg
     2641 atattagatc cacactgtca aaatcaacaa ttgggatatt ttcattgcca tcaccaccaa
     2701 acccagcatc aaacacaatg ccagtcagaa acttcatttg ctcattatca tactgctcag
     2761 catcatttaa aaatgaaatg gtgttggtgc ggtcacttag tgtattaaca tctgatacta
     2821 tcacaacccg attttctaaa tcagatatag ttttctttat cacattatca ataatggact
     2881 gttttagctc actgtcattt ttaaggatgg caattttata gctaaaagag tccttagcac
     2941 ccgctttacc tttattttta aagttaaagt aagtgtgcaa tgtaacatcg ttaatatcac
     3001 aatcaaaatg cttatacagt tctaaaagct cttgtgcttt ttcttcatta tgctccaaag
     3061 catcaagatc taaggcatcg tcactcatca tcattcctct atgatttttt tcgcgaacgt
     3121 taaataatca tcatgattta taactctgat aaaatcattt tcttttatta aatctttaga
     3181 taaaactatc aactcaccgt cttgcgtttt ttcccttcca ttagctacca cactgtaagt
     3241 aatcttatag gcagaaacat taaataatga caatgttggg ttgcagtgaa ttctttttgt
     3301 tttgatgtgc aaaaaaccga cgataatcaa aacaaacaaa aaattaacta tatttgatgg
     3361 tttgcttaaa tcagtaaaga ccaacggcat tatgtacgtt gataaaaaag aaagatactc
     3421 accggattct tttttacatg aaacgacctt taactttctt gacaccgcac cggagtctaa
     3481 gtttttcaaa acccatcgat accaaatgta tgtataagaa caagttaaaa tcaaagcccc
     3541 gcagatcact gacctcaata cagaaaatgt taatctgcta tttgaatagt cgagtacgca
     3601 ttgaaatttt ccatccgcgc cagaacacga agacatggcc ttatctaaaa cagaccatac
     3661 gttatcaata ccagaaaaat atattgttat cggtataaat aaaaacaaca ttgataagag
     3721 atacattcta attttcattt ttgtaaaatt tcctgtacca cgttgatcta cttattccta
     3781 aagaaatcca ttctccatct ctaactttcg gccttccacc accagagctt ttttttccac
     3841 gttgacgctg aatttcagaa gtatgtgttt gtttaacata ctcttcaaag ccaagctctg
     3901 taaggttctt acttgtccac ttagccacac ttttagcaat tcccatgact tcgttctcgt
     3961 ctaaaggtgc ggagaactgc aggttgtagg ctttagcgcg ttcaatgcag gcttgtagcc
     4021 attggtcata ctgcggccag ccttggcgga tagcgcggta agcccacttg cgggttttat
     4081 cgaagagggt gcagttacgg cctaaaccgt agtccggcag gatttcgcgg tcattggctg
     4141 cgccaaggtc gaggtaatcg gctaaccagt caagggtata gagctctggc tgccagacgg
     4201 tgatctgcca gtgcaggtgg ttcggattct tgcaaattag ccctgaatac cccgcatctg
     4261 cgcccaattt tttacgcagc gcattctcga tggcggcggc gtatttaagg ggggcagctc
     4321 gaccatccgg cgcggtacgt accgccgtat gcaaggcata caacaggtga gcatgtccgt
     4381 tctcggggtt tttgatggtg agtgtgggcg caggtgcccc cagatcggcc caatcaatcg
     4441 cggctccggc tctgtccacg tcaaagcaaa gccagtacat ggcgtgaggc tgattaaact
     4501 ggatgtattt tgcgaggaga gcacgctctt taccggcaat gcgaacacca aactgtaaat
     4561 catcggagaa gtacggcttg tggggtaacc ggtcgttaaa aagcgttaaa gcctgattat
     4621 ccaaggctcc cagccttatg gcggggctgt tgttttgcac gctgcatgtg ctaatatcct
     4681 ttctaggttt cgacctagcc ctgaatgtca tgtccgctcg ccaaagtaga gcatgatttc
     4741 ggggctttgt tttttctgcc actaagttac acctcaacaa cggtttttgt catccccgac
     4801 aatccgttat tcctgcttgt tctcgcacgg ctttacgctc atactacttc ttgtagatac
     4861 acttgtcact acatcaagag gtgagatgat ggccacgatt aatattcgga tcgatgacga
     4921 gctgaaaagc cgctcttatg ccgcactgga aaagctgggc gtaacgccgt ccgaggttct
     4981 gcgccaaaca ctggaatatg tggcccaaag cggacgtttg ccgttccagc aggttttgct
     5041 gaccgaggat gatgccgatt tgatggctat cgttcgggat cgtctggaaa acccacaggc
     5101 gggcgtaaag gtgtcactgg atgagctata accttgaatt tgatccccga gccctgaagg
     5161 aatggcgcaa gctcggggat gatgtccgtc tgcagttcaa gaaaaaactc gagcaggttc
     5221 tacaacaccc gcggatcgat aaaaatcgcc tgcgagagct gcatgactgc tacaaaatca
     5281 agctccgtgc atccggttat cgcttggtct atcaggttcg cgatcaaacc attacggtat
     5341 tcgtggtggc ggtcggtaag cgcgagcgtt ctgccgctta cgatgcggcc gataaacgct
     5401 tataaactca tgccgtgacc gcgagaatac cgctgttcgt gccgcttggc taattgctca
     5461 agcggcgcac tgttctgttt aagctctcga cttgctgcgc caagccggtg actt
//
