LOCUS       NZ_CP148106             5514 bp    DNA     circular CON 05-APR-2024
DEFINITION  Escherichia coli strain Nissle plasmid pEcFELIX464.2, complete
            sequence.
ACCESSION   NZ_CP148106
VERSION     NZ_CP148106.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN40298380
            Assembly: GCF_037744325.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5514)
  AUTHORS   Wan,K.H., Park,S., Neff,M., Lawrence,Q., Egbert,R., Booth,B.W. and
            Celniker,S.E.
  TITLE     Complete Genome Sequence of the Escherichia coli FELIX_MS464
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5514)
  AUTHORS   Wan,K.H., Park,S., Neff,M., Lawrence,Q., Egbert,R., Booth,B.W. and
            Celniker,S.E.
  TITLE     Direct Submission
  JOURNAL   Submitted (14-MAR-2024) Life Sciences Division, Lawrence Berkeley
            National Lab, 717 Potter Street, Berkeley, CA 94720, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.4.9b
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 197.97x
            Sequencing Technology :: Illumina MiSeq, Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_037744325.1-RS_2024_04_05
            Annotation Date                   :: 04/05/2024 20:33:26
            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)                     :: 4,862
            CDSs (total)                      :: 4,748
            Genes (coding)                    :: 4,528
            CDSs (with protein)               :: 4,528
            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)              :: 220
            CDSs (without protein)            :: 220
            Pseudo Genes (ambiguous residues) :: 0 of 220
            Pseudo Genes (frameshifted)       :: 93 of 220
            Pseudo Genes (incomplete)         :: 139 of 220
            Pseudo Genes (internal stop)      :: 51 of 220
            Pseudo Genes (multiple problems)  :: 54 of 220
            Pseudo Genes (short protein)      :: 4 of 220
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP148106.1.
            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"
                     /mol_type="genomic DNA"
                     /strain="Nissle"
                     /db_xref="taxon:562"
                     /plasmid="pEcFELIX464.2"
     gene            join(4344..5514,1..347)
                     /locus_tag="WHM01_RS24250"
     CDS             join(4344..5514,1..347)
                     /locus_tag="WHM01_RS24250"
                     /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="relaxase/mobilization nuclease domain-containing
                     protein"
                     /protein_id="WP_001704286.1"
                     /translation="MIVKIHGRGAGGGSGPVDYLLGPDRQREQATVLRGNPEHVKELID
                     GCEFARTYTSGVLSFQESDLPEGEKQRLMDEWEQTLMTGLDKDQYACLWVQHQDKGRLE
                     LNFVIPNIELQSGKRLQPYFDRADRPRVNAWQTLTNDRLGLRDPNDPANRRALTPSNDL
                     PRNKQQAAEAITKGLISLIEQGEITDRKGVISHLTDAGLSVVRETKSSISIADPAGGPN
                     IRLKGVLYERDFKFSAGVREQIEAASQDYRNERRERIREARETYHRGLEIKLREHTDRY
                     PRRERQPAKTDTPLSRNDMAVQPGIKWDPVCDIDWSSLVSRDYRGRTPERNQRAEPDPA
                     GLKEPDRSRRIDNSRFQEQERVLPDPSAGGEEDRRVQERSTSSGHQVQRQITSSDATES
                     ILGGFIYQGEEIHDRNGAAASERIRELTEALRTTAASVAGQLRQLTAHVRGYLAGVGEK
                     RQGLSGLEHASHRLGAASRELKQNSAPLEQLAKRHEQRYSRGHGMSL"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            complement(342..626)
                     /locus_tag="WHM01_RS24255"
     CDS             complement(342..626)
                     /locus_tag="WHM01_RS24255"
                     /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(616..858)
                     /locus_tag="WHM01_RS24260"
     CDS             complement(616..858)
                     /locus_tag="WHM01_RS24260"
                     /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            1123..2019
                     /locus_tag="WHM01_RS24265"
     CDS             1123..2019
                     /locus_tag="WHM01_RS24265"
                     /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            2009..2656
                     /gene="kwaA"
                     /locus_tag="WHM01_RS24270"
     CDS             2009..2656
                     /gene="kwaA"
                     /locus_tag="WHM01_RS24270"
                     /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            2659..3801
                     /locus_tag="WHM01_RS24275"
     CDS             2659..3801
                     /locus_tag="WHM01_RS24275"
                     /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            4028..4354
                     /locus_tag="WHM01_RS24280"
     CDS             4028..4354
                     /locus_tag="WHM01_RS24280"
                     /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"
     Typing          986..2019
                     /name="rep_cluster_2486"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          4345..5513
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.744"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 taacctcatc agacgccaca gaatcgattc tgggcggttt tatctatcag ggtgaagaga
       61 ttcatgaccg aaatggagca gcagcttctg agcgcattag agagcttaca gaggcactac
      121 gaacaacagc agcaagcgtg gcaggacagc tacgccaact tacagcgcat gttcgaggtt
      181 acctcgcagg agttggcgaa aaacgacagg gtttgtcagg ccttgagcat gcaagtcacc
      241 ggcttggcgc agcaagtcga gagcttaaac agaacagtgc gccgcttgag caattagcca
      301 agcggcacga acagcggtat tctcgcggtc acggcatgag tttataagcg tttatcggcc
      361 gcatcgtaag cggcagaacg ctcgcgctta ccgaccgcca ccacgaatac cgtaatggtt
      421 tgatcgcgaa cctgatagac caagcgataa ccggatgcac ggagcttgat tttgtagcag
      481 tcatgcagct ctcgcaggcg atttttatcg atccgcgggt gttgtagaac ctgctcgagt
      541 tttttcttga actgcagacg gacatcatcc ccgagcttgc gccattcctt cagggctcgg
      601 ggatcaaatt caaggttata gctcatccag tgacaccttt acgcccgcct gtgggttttc
      661 cagacgatcc cgaacgatag ccatcaaatc ggcatcatcc tcggtcagca aaacctgctg
      721 gaacggcaaa cgtccgcttt gggccacata ttccagtgtt tggcgcagaa cctcggacgg
      781 cgttacgccc agcttttcca gtgcggcata agagcggctt ttcagctcgt catcgatccg
      841 aatattaatc gtggccatca tctcacctct tgatgtagtg acaagtgtat ctacaagaag
      901 tagtatgagc gtaaagccgt gcgagaacaa gcaggaataa cggattgtcg gggatgacaa
      961 aaaccgttgt tgaggtgtaa cttagtggca gaaaaaacaa agccccgaaa tcatgctcta
     1021 ctttggcgag cggacatgac attcagggct aggtcgaaac ctagaaagga tattagcaca
     1081 tgcagcgtgc aaaacaacag ccccgccata aggctgggag ccttggataa tcaggcttta
     1141 acgcttttta acgaccggtt accccacaag ccgtacttct ccgatgattt acagtttggt
     1201 gttcgcattg ccggtaaaga gcgtgctctc ctcgcaaaat acatccagtt taatcagcct
     1261 cacgccatgt actggctttg ctttgacgtg gacagagccg gagccgcgat tgattgggcc
     1321 gatctggggg cacctgcgcc cacactcacc atcaaaaacc ccgagaacgg acatgctcac
     1381 ctgttgtatg ccttgcatac ggcggtacgt accgcgccgg atggtcgagc tgcccccctt
     1441 aaatacgccg ccgccatcga gaatgcgctg cgtaaaaaat tgggcgcaga tgcggggtat
     1501 tcagggctaa tttgcaagaa tccgaaccac ctgcactggc agatcaccgt ctggcagcca
     1561 gagctctata cccttgactg gttagccgat tacctcgacc ttggcgcagc caatgaccgc
     1621 gaaatcctgc cggactacgg tttaggccgt aactgcaccc tcttcgataa aacccgcaag
     1681 tgggcttacc gcgctatccg ccaaggctgg ccgcagtatg accaatggct acaagcctgc
     1741 attgaacgcg ctaaagccta caacctgcag ttctccgcac ctttagacga gaacgaagtc
     1801 atgggaattg ctaaaagtgt ggctaagtgg acaagtaaga accttacaga gcttggcttt
     1861 gaagagtatg ttaaacaaac acatacttct gaaattcagc gtcaacgtgg aaaaaaaagc
     1921 tctggtggtg gaaggccgaa agttagagat ggagaatgga tttctttagg aataagtaga
     1981 tcaacgtggt acaggaaatt ttacaaaaat gaaaattaga atgtatctct tatcaatgtt
     2041 gtttttattt ataccgataa caatatattt ttctggtatt gataacgtat ggtctgtttt
     2101 agataaggcc atgtcttcgt gttctggcgc ggatggaaaa tttcaatgcg tactcgacta
     2161 ttcaaatagc agattaacat tttctgtatt gaggtcagtg atctgcgggg ctttgatttt
     2221 aacttgttct tatacataca tttggtatcg atgggttttg aaaaacttag actccggtgc
     2281 ggtgtcaaga aagttaaagg tcgtttcatg taaaaaagaa tccggtgagt atctttcttt
     2341 tttatcaacg tacataatgc cgttggtctt tactgattta agcaaaccat caaatatagt
     2401 taattttttg tttgttttga ttatcgtcgg ttttttgcac atcaaaacaa aaagaattca
     2461 ctgcaaccca acattgtcat tatttaatgt ttctgcctat aagattactt acagtgtggt
     2521 agctaatgga agggaaaaaa cgcaagacgg tgagttgata gttttatcta aagatttaat
     2581 aaaagaaaat gattttatca gagttataaa tcatgatgat tatttaacgt tcgcgaaaaa
     2641 aatcatagag gaatgatgat gagtgacgat gccttagatc ttgatgcttt ggagcataat
     2701 gaagaaaaag cacaagagct tttagaactg tataagcatt ttgattgtga tattaacgat
     2761 gttacattgc acacttactt taactttaaa aataaaggta aagcgggtgc taaggactct
     2821 tttagctata aaattgccat ccttaaaaat gacagtgagc taaaacagtc cattattgat
     2881 aatgtgataa agaaaactat atctgattta gaaaatcggg ttgtgatagt atcagatgtt
     2941 aatacactaa gtgaccgcac caacaccatt tcatttttaa atgatgctga gcagtatgat
     3001 aatgagcaaa tgaagtttct gactggcatt gtgtttgatg ctgggtttgg tggtgatggc
     3061 aatgaaaata tcccaattgt tgattttgac agtgtggatc taatatcaaa agttgactca
     3121 atcattttcg ttttgagtaa gaataatgac gacaattgta taaccatata caagaagcaa
     3181 tatccagttc aaaacttatc aagaaagaaa aataattttt atgggtttag caaaaaagaa
     3241 ctatctcgag tagatcaaga tatgatttct attgatggta aggcatctct tgtttttgct
     3301 ggcgatacgg tatttatcta cgaccaaaat gttttcgagc gtttttttgg ctataaagca
     3361 tggataaaaa atgctgccac tgattttgtt aacaatatgt ccactcgttt taagggattt
     3421 gttgacttaa gcaaatttat tgagcgagta aataaagata gtcatgatgc ggatgctttt
     3481 tctcggaagc tagctaaggc gtatgctcga agcgaaacaa agcaaacgct acaaacaata
     3541 acaaatgaac atcttaagag tgttctagat gaaaatggat atttagcagg tgttttaaag
     3601 tataaaaaag gtgatgctac gatttgcatc gcaagccata accagcaaga tacgtttatc
     3661 gctatggtat ccgaaggcgt attgagatcg ttgattacag gcattgatta tttaagcctt
     3721 gggtcaaagc ggaaaatatc gtcagcagca tccaatacta ctaccagtac cacttcggat
     3781 tcctcttccg ctgccgtgtg agacaaaaca acctatatca gataacagcc ctgcttttgc
     3841 ggggcttttt gtttgtgcgt gatgcgacct cgatgtacga tagatgctgt actaagccag
     3901 tacacacagc gtcccctctt cgaggtgccg tctgtgactg tttcaggggg ctcgccgccc
     3961 cccgaaaccc cttgcatcca ctgcgaaaat tcgcactttg ggtgcgaaac tttctcagcg
     4021 gattctcatg gaaaagcgca ccaaagagat caaaatcaga ctcaccgaag cggagcatca
     4081 gcggctactt gaacgctgtg accgtaagca tttggccgag tggttacgag ccgttggctt
     4141 aggcgaatcg cgtacagctc ggcgtcgtcc gctacctacc gtagacccga ccttgttacg
     4201 tcaggtcagc gggatcggta ataacctcaa tcaaatagcc cgttacttga atcagcatgg
     4261 cttaccgccg caagaacggg tgtcgttgtt agcggtgctc aatagcattg accaacatct
     4321 tgccgaactg ctggagcaac atcgtgatcg ttaagattca tggtcgtggt gccggtggcg
     4381 ggagtggtcc tgtcgattac cttctgggcc ctgatcgtca gcgcgaacaa gcgacggtgt
     4441 tacggggtaa ccctgagcac gtcaaagagc tgattgatgg ctgcgaattt gcccgaactt
     4501 atacctctgg cgtgctctct tttcaggaga gtgatttacc cgaaggcgaa aagcagcgat
     4561 tgatggatga atgggagcag acattgatga ccggtctaga taaagaccag tatgcctgcc
     4621 tctgggttca acatcaggac aaagggcgtc ttgaattgaa ttttgttatc ccgaacatcg
     4681 aattgcagag cggaaaacgg ctacaacctt actttgatcg ggctgaccgg cctcgtgtta
     4741 acgcatggca aaccctcacc aatgaccggc ttgggttacg cgacccgaat gaccctgcta
     4801 atcgccgagc attaaccccc tctaatgacc ttcctcgcaa caaacagcag gcagcggaag
     4861 ccattaccaa agggctaatc agcttgattg agcagggaga aattacggat cgtaaagggg
     4921 tgatttccca ccttaccgat gccggattgt cggtcgtacg ggaaaccaaa tccagtatca
     4981 gtattgctga tccggcaggt ggcccgaata ttcgcttaaa aggagtgctg tatgagcgag
     5041 attttaaatt tagcgcggga gttcgagagc aaatcgaagc agcaagccaa gactaccgca
     5101 acgagcgtcg cgaacgcatt cgagaagcac gagaaacgta tcaccgaggc cttgaaatta
     5161 agctcaggga acatacagac cgctatccaa gaagagaacg acagccagct aaaacagata
     5221 caccgcttag tcggaatgac atggctgtac agcctggcat taagtgggat cctgtttgcg
     5281 atattgattg gagtagcttg gtatctcggg actatcgtgg tcgaacgcca gaacgaaatc
     5341 agcgagcaga gccagatcct gcaggactta aagagccaga ccggagccgg cgtatcgata
     5401 attcacgatt ccaagaacaa gagcgtgtat tacctgatcc ttccgcaggg ggcgaagaag
     5461 atcgacgagt acaagaacgc tcaacatcgt caggtcatca agtacagcgc caaa
//
