LOCUS       NZ_CP035487             5591 bp    DNA     circular CON 18-JUN-2024
DEFINITION  Escherichia coli strain NissleGFP_pZE21 plasmid pMut2, complete
            sequence.
ACCESSION   NZ_CP035487
VERSION     NZ_CP035487.1
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 5591)
  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  JOURNAL   Unpublished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 5591)
  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
            CP035487.1.
            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..5591
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="NissleGFP_pZE21"
                     /isolation_source="cell culture"
                     /db_xref="taxon:562"
                     /plasmid="pMut2"
                     /geo_loc_name="USA:Missouri,Saint Louis"
                     /collection_date="2014"
     gene            join(4727..5591,1..2)
                     /locus_tag="EUJ32_RS24690"
                     /old_locus_tag="EUJ32_24690"
     CDS             join(4727..5591,1..2)
                     /locus_tag="EUJ32_RS24690"
                     /old_locus_tag="EUJ32_24690"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001517860.1"
                     /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_129552463.1"
                     /translation="MDNQALTLFNDRLPHKPYFSDDLQFGVRIAGKERALLAKYIQFNQ
                     PHAMYWLCFDVDRAGAAIDWADLGAPAPTLTIKNPENGHAHLLYALHTAVRTAPDGRAA
                     PLKYAAAIENALRKKLGADAGYSGLICKNPNHLHWQITVWQPELYTLDWLADYLDLGAA
                     NDREILPDYGLGRNCTLFDKTRKWAYRAIRQGWPQYDQWLQACIERAKAYNLQFSAPLD
                     ENEVMGIAKSVAKWTSKNLTELGFEEYVKQTHTSEIQRQRGKKSSGGGRPKVRDGEWIS
                     LGISRST"
                     /name="replication initiation protein"
     gene            99..746
                     /gene="kwaA"
                     /locus_tag="EUJ32_RS24695"
                     /old_locus_tag="EUJ32_24695"
     CDS             99..746
                     /gene="kwaA"
                     /locus_tag="EUJ32_RS24695"
                     /old_locus_tag="EUJ32_24695"
                     /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            749..1891
                     /locus_tag="EUJ32_RS24700"
                     /old_locus_tag="EUJ32_24700"
     CDS             749..1891
                     /locus_tag="EUJ32_RS24700"
                     /old_locus_tag="EUJ32_24700"
                     /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            2118..2444
                     /locus_tag="EUJ32_RS24705"
                     /old_locus_tag="EUJ32_24705"
     CDS             2118..2444
                     /locus_tag="EUJ32_RS24705"
                     /old_locus_tag="EUJ32_24705"
                     /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            2602..>3072
                     /locus_tag="EUJ32_RS25475"
                     /pseudo=""
     CDS             2602..>3072
                     /locus_tag="EUJ32_RS25475"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /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            3122..3607
                     /locus_tag="EUJ32_RS25715"
     CDS             3122..3607
                     /locus_tag="EUJ32_RS25715"
                     /inference="COORDINATES: protein motif:HMM:NF016710.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_001554707.1"
                     /translation="MSEILNLAREFESKSKQQAKTTATSVANAFEKHEKRITEALKLSS
                     GNIQTAIQEENDSQLKQIHRLVGMTWLYSLALSGILFAILIGVAWYLGTIVVERQNEIS
                     EQSQILQDLKSQTGAGVSIIHDSKNKSVYYLILPQGAKKIDEYKNAQHRQVIKYSAK"
                     /name="MbeB family mobilization protein"
     gene            3677..3901
                     /locus_tag="EUJ32_RS24715"
                     /old_locus_tag="EUJ32_24715"
     CDS             3677..3901
                     /locus_tag="EUJ32_RS24715"
                     /old_locus_tag="EUJ32_24715"
                     /inference="COORDINATES: protein motif:HMM:NF016769.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_223938297.1"
                     /translation="MEQQLLSALESLQRHYEQQQQAWQDSYANLQRMFEVTSQELAKND
                     RVCQALSMQVTGLAQQVESLNRTVRRLSN"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(3946..4230)
                     /locus_tag="EUJ32_RS24720"
                     /old_locus_tag="EUJ32_24720"
     CDS             complement(3946..4230)
                     /locus_tag="EUJ32_RS24720"
                     /old_locus_tag="EUJ32_24720"
                     /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"
     gene            complement(4220..4462)
                     /locus_tag="EUJ32_RS24725"
                     /old_locus_tag="EUJ32_24725"
     CDS             complement(4220..4462)
                     /locus_tag="EUJ32_RS24725"
                     /old_locus_tag="EUJ32_24725"
                     /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"
     Typing          4590..5591
                     /name="rep_cluster_2486"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2435..3948
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.802"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 aaaaaaaagc tctggtggtg gaaggccgaa agttagagat ggagaatgga tttctttagg
       61 aataagtaga tcaacgtggt acaggaaatt ttacaaaaat gaaaattaga atgtatctct
      121 tatcaatgtt gtttttattt ataccgataa caatatattt ttctggtatt gataacgtat
      181 ggtctgtttt agataaggcc atgtcttcgt gttctggcgc ggatggaaaa tttcaatgcg
      241 tactcgacta ttcaaatagc agattaacat tttctgtatt gaggtcagtg atctgcgggg
      301 ctttgatttt aacttgttct tatacataca tttggtatcg atgggttttg aaaaacttag
      361 actccggtgc ggtgtcaaga aagttaaagg tcgtttcatg taaaaaagaa tccggtgagt
      421 atctttcttt tttatcaacg tacataatgc cgttggtctt tactgattta agcaaaccat
      481 caaatatagt taattttttg tttgttttga ttatcgtcgg ttttttgcac atcaaaacaa
      541 aaagaattca ctgcaaccca acattgtcat tatttaatgt ttctgcctat aagattactt
      601 acagtgtggt agctaatgga agggaaaaaa cgcaagacgg tgagttgata gttttatcta
      661 aagatttaat aaaagaaaat gattttatca gagttataaa tcatgatgat tatttaacgt
      721 tcgcgaaaaa aatcatagag gaatgatgat gagtgacgat gccttagatc ttgatgcttt
      781 ggagcataat gaagaaaaag cacaagagct tttagaactg tataagcatt ttgattgtga
      841 tattaacgat gttacattgc acacttactt taactttaaa aataaaggta aagcgggtgc
      901 taaggactct tttagctata aaattgccat ccttaaaaat gacagtgagc taaaacagtc
      961 cattattgat aatgtgataa agaaaactat atctgattta gaaaatcggg ttgtgatagt
     1021 atcagatgtt aatacactaa gtgaccgcac caacaccatt tcatttttaa atgatgctga
     1081 gcagtatgat aatgagcaaa tgaagtttct gactggcatt gtgtttgatg ctgggtttgg
     1141 tggtgatggc aatgaaaata tcccaattgt tgattttgac agtgtggatc taatatcaaa
     1201 agttgactca atcattttcg ttttgagtaa gaataatgac gacaattgta taaccatata
     1261 caagaagcaa tatccagttc aaaacttatc aagaaagaaa aataattttt atgggtttag
     1321 caaaaaagaa ctatctcgag tagatcaaga tatgatttct attgatggta aggcatctct
     1381 tgtttttgct ggcgatacgg tatttatcta cgaccaaaat gttttcgagc gtttttttgg
     1441 ctataaagca tggataaaaa atgctgccac tgattttgtt aacaatatgt ccactcgttt
     1501 taagggattt gttgacttaa gcaaatttat tgagcgagta aataaagata gtcatgatgc
     1561 ggatgctttt tctcggaagc tagctaaggc gtatgctcga agcgaaacaa agcaaacgct
     1621 acaaacaata acaaatgaac atcttaagag tgttctagat gaaaatggat atttagcagg
     1681 tgttttaaag tataaaaaag gtgatgctac gatttgcatc gcaagccata accagcaaga
     1741 tacgtttatc gctatggtat ccgaaggcgt attgagatcg ttgattacag gcattgatta
     1801 tttaagcctt gggtcaaagc ggaaaatatc gtcagcagca tccaatacta ctaccagtac
     1861 cacttcggat tcctcttccg ctgccgtgtg agacaaaaca acctatatca gataacagcc
     1921 ctgcttttgc ggggcttttt gtttgtgcgt gatgcgacct cgatgtacga tagatgctgt
     1981 actaagccag tacacacagc gtcccctctt cgaggtgccg tctgtgactg tttcaggggg
     2041 ctcgccgccc cccgaaaccc cttgcatcca ctgcgaaaat tcgcactttg ggtgcgaaac
     2101 tttctcagcg gattctcatg gaaaagcgca ccaaagagat caaaatcaga ctcaccgaag
     2161 cggagcatca gcggctactt gaacgctgtg accgtaagca tttggccgag tggttacgag
     2221 ccgttggctt aggcgaatcg cgtacagctc ggcgtcgtcc gctacctacc gtagacccga
     2281 ccttgttacg tcaggtcagc gggatcggta ataacctcaa tcaaatagcc cgttacttga
     2341 atcagcatgg cttaccgccg caagaacggg tgtcgttgtt agcggtgctc aatagcattg
     2401 accaacatct tgccgaactg ctggagcaac atcgtgatcg ttaagattca tggtcgtggt
     2461 gccggtggcg ggagtggtcc tgtcgattac cttctgggcc ctgatcgtca gcgcgaacaa
     2521 gcgacggtgt tacggggtaa ccctgagcac gtcaaagagc tgattgatgg ctgcgaattt
     2581 gcccgaactt atacctctgg cgtgctctct tttcaggaga gtgatttacc cgaaggcgaa
     2641 aagcagcgat tgatggatga atgggagcag acattgatga ccggtctaga taaagaccag
     2701 tatgcctgcc tctgggttca acatcaggac aaagggcgtc ttgaattgaa ttttgttatc
     2761 ccgaacatcg aattgcagag cggaaaacgg ctacaacctt actttgatcg ggctgaccgg
     2821 cctcgtgtta acgcatggca aaccctcacc aatgaccggc ttgggttacg cgacccgaat
     2881 gaccctgcta atcgccgagc attaaccccc tctaatgacc ttcctcgcaa caaacagcag
     2941 gcagcggaag ccattaccaa agggctaatc agcttgattg agcagggaga aattacggat
     3001 cgtaaagggg tgatttccca ccttaccgat gccggattgt cggtcgtacg ggaaaccaaa
     3061 tccagtatca gtattgctga tccggcaggt ggcccgaata ttcgcttaaa aggagtgctg
     3121 tatgagcgag attttaaatt tagcgcggga gttcgagagc aaatcgaagc agcaagccaa
     3181 gactaccgca acgagcgtcg cgaacgcatt cgagaagcac gagaaacgta tcaccgaggc
     3241 cttgaaatta agctcaggga acatacagac cgctatccaa gaagagaacg acagccagct
     3301 aaaacagata caccgcttag tcggaatgac atggctgtac agcctggcat taagtgggat
     3361 cctgtttgcg atattgattg gagtagcttg gtatctcggg actatcgtgg tcgaacgcca
     3421 gaacgaaatc agcgagcaga gccagatcct gcaggactta aagagccaga ccggagccgg
     3481 cgtatcgata attcacgatt ccaagaacaa gagcgtgtat tacctgatcc ttccgcaggg
     3541 ggcgaagaag atcgacgagt acaagaacgc tcaacatcgt caggtcatca agtacagcgc
     3601 caaataacct catcagacgc cacagaatcg attctgggcg gttttatcta tcagggtgaa
     3661 gagattcatg accgaaatgg agcagcagct tctgagcgca ttagagagct tacagaggca
     3721 ctacgaacaa cagcagcaag cgtggcagga cagctacgcc aacttacagc gcatgttcga
     3781 ggttacctcg caggagttgg cgaaaaacga cagggtttgt caggccttga gcatgcaagt
     3841 caccggcttg gcgcagcaag tcgagagctt aaacagaaca gtgcgccgct tgagcaatta
     3901 gccaagcggc acgaacagcg gtattctcgc ggtcacggca tgagtttata agcgtttatc
     3961 ggccgcatcg taagcggcag aacgctcgcg cttaccgacc gccaccacga ataccgtaat
     4021 ggtttgatcg cgaacctgat agaccaagcg ataaccggat gcacggagct tgattttgta
     4081 gcagtcatgc agctctcgca ggcgattttt atcgatccgc gggtgttgta gaacctgctc
     4141 gagttttttc ttgaactgca gacggacatc atccccgagc ttgcgccatt ccttcagggc
     4201 tcggggatca aattcaaggt tatagctcat ccagtgacac ctttacgccc gcctgtgggt
     4261 tttccagacg atcccgaacg atagccatca aatcggcatc atcctcggtc agcaaaacct
     4321 gctggaacgg caaacgtccg ctttgggcca catattccag tgtttggcgc agaacctcgg
     4381 acggcgttac gcccagcttt tccagtgcgg cataagagcg gcttttcagc tcgtcatcga
     4441 tccgaatatt aatcgtggcc atcatctcac ctcttgatgt agtgacaagt gtatctacaa
     4501 gaagtagtat gagcgtaaag ccgtgcgaga acaagcagga ataacggatt gtcggggatg
     4561 acaaaaaccg ttgttgaggt gtaacttagt ggcagaaaaa acaaagcccc gaaatcatgc
     4621 tctactttgg cgagcggaca tgacattcag ggctaggtcg aaacctagaa aggatattag
     4681 cacatgcagc gtgcaaaaca acagccccgc cataaggctg ggagccttgg ataatcaggc
     4741 tttaacgctt tttaacgacc ggttacccca caagccgtac ttctccgatg atttacagtt
     4801 tggtgttcgc attgccggta aagagcgtgc tctcctcgca aaatacatcc agtttaatca
     4861 gcctcacgcc atgtactggc tttgctttga cgtggacaga gccggagccg cgattgattg
     4921 ggccgatctg ggggcacctg cgcccacact caccatcaaa aaccccgaga acggacatgc
     4981 tcacctgttg tatgccttgc atacggcggt acgtaccgcg ccggatggtc gagctgcccc
     5041 ccttaaatac gccgccgcca tcgagaatgc gctgcgtaaa aaattgggcg cagatgcggg
     5101 gtattcaggg ctaatttgca agaatccgaa ccacctgcac tggcagatca ccgtctggca
     5161 gccagagctc tatacccttg actggttagc cgattacctc gaccttggcg cagccaatga
     5221 ccgcgaaatc ctgccggact acggtttagg ccgtaactgc accctcttcg ataaaacccg
     5281 caagtgggct taccgcgcta tccgccaagg ctggccgcag tatgaccaat ggctacaagc
     5341 ctgcattgaa cgcgctaaag cctacaacct gcagttctcc gcacctttag acgagaacga
     5401 agtcatggga attgctaaaa gtgtggctaa gtggacaagt aagaacctta cagagcttgg
     5461 ctttgaagag tatgttaaac aaacacatac ttctgaaatt cagcgtcaac gtggaaaaaa
     5521 aagctctggt ggtggaaggc cgaaagttag agatggagaa tggatttctt taggaataag
     5581 tagatcaacg t
//
