LOCUS       NZ_CP058219             5514 bp    DNA     circular CON 18-DEC-2023
DEFINITION  Escherichia coli Nissle 1917 plasmid pMUT2, complete sequence.
ACCESSION   NZ_CP058219
VERSION     NZ_CP058219.1
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 5514)
  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  JOURNAL   Unpublished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 5514)
  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
            CP058219.1.
            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="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:316435"
                     /plasmid="pMUT2"
                     /geo_loc_name="Germany"
                     /collection_date="1917"
     gene            join(5121..5514,1..749)
                     /locus_tag="HW372_RS24205"
                     /old_locus_tag="HW372_24010"
     CDS             join(5121..5514,1..749)
                     /locus_tag="HW372_RS24205"
                     /old_locus_tag="HW372_24010"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /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            976..1302
                     /locus_tag="HW372_RS24210"
                     /old_locus_tag="HW372_24015"
     CDS             976..1302
                     /locus_tag="HW372_RS24210"
                     /old_locus_tag="HW372_24015"
                     /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            1511..>1876
                     /locus_tag="HW372_RS24215"
                     /pseudo=""
     CDS             1511..>1876
                     /locus_tag="HW372_RS24215"
                     /inference="COORDINATES: protein motif:HMM:NF015397.3"
                     /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            2535..2759
                     /locus_tag="HW372_RS24220"
                     /old_locus_tag="HW372_24025"
     CDS             2535..2759
                     /locus_tag="HW372_RS24220"
                     /old_locus_tag="HW372_24025"
                     /inference="COORDINATES: protein motif:HMM:NF016769.3"
                     /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(2804..3088)
                     /locus_tag="HW372_RS24225"
                     /old_locus_tag="HW372_24030"
     CDS             complement(2804..3088)
                     /locus_tag="HW372_RS24225"
                     /old_locus_tag="HW372_24030"
                     /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(3078..3320)
                     /locus_tag="HW372_RS24230"
                     /old_locus_tag="HW372_24035"
     CDS             complement(3078..3320)
                     /locus_tag="HW372_RS24230"
                     /old_locus_tag="HW372_24035"
                     /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            3585..4481
                     /locus_tag="HW372_RS24235"
                     /old_locus_tag="HW372_24040"
     CDS             3585..4481
                     /locus_tag="HW372_RS24235"
                     /old_locus_tag="HW372_24040"
                     /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            4471..5118
                     /gene="kwaA"
                     /locus_tag="HW372_RS24240"
                     /old_locus_tag="HW372_24045"
     CDS             4471..5118
                     /gene="kwaA"
                     /locus_tag="HW372_RS24240"
                     /old_locus_tag="HW372_24045"
                     /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"
     Typing          3448..4481
                     /name="rep_cluster_2486"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          1293..2806
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.802"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gtgatggcaa tgaaaatatc ccaattgttg attttgacag tgtggatcta atatcaaaag
       61 ttgactcaat cattttcgtt ttgagtaaga ataatgacga caattgtata accatataca
      121 agaagcaata tccagttcaa aacttatcaa gaaagaaaaa taatttttat gggtttagca
      181 aaaaagaact atctcgagta gatcaagata tgatttctat tgatggtaag gcatctcttg
      241 tttttgctgg cgatacggta tttatctacg accaaaatgt tttcgagcgt ttttttggct
      301 ataaagcatg gataaaaaat gctgccactg attttgttaa caatatgtcc actcgtttta
      361 agggatttgt tgacttaagc aaatttattg agcgagtaaa taaagatagt catgatgcgg
      421 atgctttttc tcggaagcta gctaaggcgt atgctcgaag cgaaacaaag caaacgctac
      481 aaacaataac aaatgaacat cttaagagtg ttctagatga aaatggatat ttagcaggtg
      541 ttttaaagta taaaaaaggt gatgctacga tttgcatcgc aagccataac cagcaagata
      601 cgtttatcgc tatggtatcc gaaggcgtat tgagatcgtt gattacaggc attgattatt
      661 taagccttgg gtcaaagcgg aaaatatcgt cagcagcatc caatactact accagtacca
      721 cttcggattc ctcttccgct gccgtgtgag acaaaacaac ctatatcaga taacagccct
      781 gcttttgcgg ggctttttgt ttgtgcgtga tgcgacctcg atgtacgata gatgctgtac
      841 taagccagta cacacagcgt cccctcttcg aggtgccgtc tgtgactgtt tcagggggct
      901 cgccgccccc cgaaacccct tgcatccact gcgaaaattc gcactttggg tgcgaaactt
      961 tctcagcgga ttctcatgga aaagcgcacc aaagagatca aaatcagact caccgaagcg
     1021 gagcatcagc ggctacttga acgctgtgac cgtaagcatt tggccgagtg gttacgagcc
     1081 gttggcttag gcgaatcgcg tacagctcgg cgtcgtccgc tacctaccgt agacccgacc
     1141 ttgttacgtc aggtcagcgg gatcggtaat aacctcaatc aaatagcccg ttacttgaat
     1201 cagcatggct taccgccgca agaacgggtg tcgttgttag cggtgctcaa tagcattgac
     1261 caacatcttg ccgaactgct ggagcaacat cgtgatcgtt aagattcatg gtcgtggtgc
     1321 cggtggcggg agtggtcctg tcgattacct tctgggccct gatcgtcagc gcgaacaagc
     1381 gacggtgtta cggggtaacc ctgagcacgt caaagagctg attgatggct gcgaatttgc
     1441 ccgaacttat acctctggcg tgctctcttt tcaggagagt gatttacccg aaggcgaaaa
     1501 gcagcgattg atggatgaat gggagcagac attgatgacc ggtctagata aagaccagta
     1561 tgcctgcctc tgggttcaac atcaggacaa agggcgtctt gaattgaatt ttgttatccc
     1621 gaacatcgaa ttgcagagcg gaaaacggct acaaccttac tttgatcggg ctgaccggcc
     1681 tcgtgttaac gcatggcaaa ccctcaccaa tgaccggctt gggttacgcg acccgaatga
     1741 ccctgctaat cgccgagcat taaccccctc taatgacctt cctcgcaaca aacagcaggc
     1801 agcggaagcc attaccaaag ggctaatcag cttgattgag cagggagaaa ttacggatcg
     1861 taaaggggtg atttcccacc ttaccgatgc cggattgtcg gtcgtacggg aaaccaaatc
     1921 cagtatcagt attgctgatc cggcaggtgg cccgaatatt cgcttaaaag gagtgctgta
     1981 tgagcgagat tttaaattta gcgcgggagt tcgagagcaa atcgaagcag caagccaaga
     2041 ctaccgcaac gagcgtcgcg aacgcattcg agaagcacga gaaacgtatc accgaggcct
     2101 tgaaattaag ctcagggaac atacagaccg ctatccaaga agagaacgac agccagctaa
     2161 aacagataca ccgcttagtc ggaatgacat ggctgtacag cctggcatta agtgggatcc
     2221 tgtttgcgat attgattgga gtagcttggt atctcgggac tatcgtggtc gaacgccaga
     2281 acgaaatcag cgagcagagc cagatcctgc aggacttaaa gagccagacc ggagccggcg
     2341 tatcgataat tcacgattcc aagaacaaga gcgtgtatta cctgatcctt ccgcaggggg
     2401 cgaagaagat cgacgagtac aagaacgctc aacatcgtca ggtcatcaag tacagcgcca
     2461 aataacctca tcagacgcca cagaatcgat tctgggcggt tttatctatc agggtgaaga
     2521 gattcatgac cgaaatggag cagcagcttc tgagcgcatt agagagctta cagaggcact
     2581 acgaacaaca gcagcaagcg tggcaggaca gctacgccaa cttacagcgc atgttcgagg
     2641 ttacctcgca ggagttggcg aaaaacgaca gggtttgtca ggccttgagc atgcaagtca
     2701 ccggcttggc gcagcaagtc gagagcttaa acagaacagt gcgccgcttg agcaattagc
     2761 caagcggcac gaacagcggt attctcgcgg tcacggcatg agtttataag cgtttatcgg
     2821 ccgcatcgta agcggcagaa cgctcgcgct taccgaccgc caccacgaat accgtaatgg
     2881 tttgatcgcg aacctgatag accaagcgat aaccggatgc acggagcttg attttgtagc
     2941 agtcatgcag ctctcgcagg cgatttttat cgatccgcgg gtgttgtaga acctgctcga
     3001 gttttttctt gaactgcaga cggacatcat ccccgagctt gcgccattcc ttcagggctc
     3061 ggggatcaaa ttcaaggtta tagctcatcc agtgacacct ttacgcccgc ctgtgggttt
     3121 tccagacgat cccgaacgat agccatcaaa tcggcatcat cctcggtcag caaaacctgc
     3181 tggaacggca aacgtccgct ttgggccaca tattccagtg tttggcgcag aacctcggac
     3241 ggcgttacgc ccagcttttc cagtgcggca taagagcggc ttttcagctc gtcatcgatc
     3301 cgaatattaa tcgtggccat catctcacct cttgatgtag tgacaagtgt atctacaaga
     3361 agtagtatga gcgtaaagcc gtgcgagaac aagcaggaat aacggattgt cggggatgac
     3421 aaaaaccgtt gttgaggtgt aacttagtgg cagaaaaaac aaagccccga aatcatgctc
     3481 tactttggcg agcggacatg acattcaggg ctaggtcgaa acctagaaag gatattagca
     3541 catgcagcgt gcaaaacaac agccccgcca taaggctggg agccttggat aatcaggctt
     3601 taacgctttt taacgaccgg ttaccccaca agccgtactt ctccgatgat ttacagtttg
     3661 gtgttcgcat tgccggtaaa gagcgtgctc tcctcgcaaa atacatccag tttaatcagc
     3721 ctcacgccat gtactggctt tgctttgacg tggacagagc cggagccgcg attgattggg
     3781 ccgatctggg ggcacctgcg cccacactca ccatcaaaaa ccccgagaac ggacatgctc
     3841 acctgttgta tgccttgcat acggcggtac gtaccgcgcc ggatggtcga gctgcccccc
     3901 ttaaatacgc cgccgccatc gagaatgcgc tgcgtaaaaa attgggcgca gatgcggggt
     3961 attcagggct aatttgcaag aatccgaacc acctgcactg gcagatcacc gtctggcagc
     4021 cagagctcta tacccttgac tggttagccg attacctcga ccttggcgca gccaatgacc
     4081 gcgaaatcct gccggactac ggtttaggcc gtaactgcac cctcttcgat aaaacccgca
     4141 agtgggctta ccgcgctatc cgccaaggct ggccgcagta tgaccaatgg ctacaagcct
     4201 gcattgaacg cgctaaagcc tacaacctgc agttctccgc acctttagac gagaacgaag
     4261 tcatgggaat tgctaaaagt gtggctaagt ggacaagtaa gaaccttaca gagcttggct
     4321 ttgaagagta tgttaaacaa acacatactt ctgaaattca gcgtcaacgt ggaaaaaaaa
     4381 gctctggtgg tggaaggccg aaagttagag atggagaatg gatttcttta ggaataagta
     4441 gatcaacgtg gtacaggaaa ttttacaaaa atgaaaatta gaatgtatct cttatcaatg
     4501 ttgtttttat ttataccgat aacaatatat ttttctggta ttgataacgt atggtctgtt
     4561 ttagataagg ccatgtcttc gtgttctggc gcggatggaa aatttcaatg cgtactcgac
     4621 tattcaaata gcagattaac attttctgta ttgaggtcag tgatctgcgg ggctttgatt
     4681 ttaacttgtt cttatacata catttggtat cgatgggttt tgaaaaactt agactccggt
     4741 gcggtgtcaa gaaagttaaa ggtcgtttca tgtaaaaaag aatccggtga gtatctttct
     4801 tttttatcaa cgtacataat gccgttggtc tttactgatt taagcaaacc atcaaatata
     4861 gttaattttt tgtttgtttt gattatcgtc ggttttttgc acatcaaaac aaaaagaatt
     4921 cactgcaacc caacattgtc attatttaat gtttctgcct ataagattac ttacagtgtg
     4981 gtagctaatg gaagggaaaa aacgcaagac ggtgagttga tagttttatc taaagattta
     5041 ataaaagaaa atgattttat cagagttata aatcatgatg attatttaac gttcgcgaaa
     5101 aaaatcatag aggaatgatg atgagtgacg atgccttaga tcttgatgct ttggagcata
     5161 atgaagaaaa agcacaagag cttttagaac tgtataagca ttttgattgt gatattaacg
     5221 atgttacatt gcacacttac tttaacttta aaaataaagg taaagcgggt gctaaggact
     5281 cttttagcta taaaattgcc atccttaaaa atgacagtga gctaaaacag tccattattg
     5341 ataatgtgat aaagaaaact atatctgatt tagaaaatcg ggttgtgata gtatcagatg
     5401 ttaatacact aagtgaccgc accaacacca tttcattttt aaatgatgct gagcagtatg
     5461 ataatgagca aatgaagttt ctgactggca ttgtgtttga tgctgggttt ggtg
//
