LOCUS       sequence-330760-        9144 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  CodA-based mutagenesis vector for C. difficile.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 9144)
  AUTHORS   Fuchs M, Lamm-Schmidt V, Sulzer J, Ponath F, Jenniches L, Kirk JA, 
            Fagan RP, Barquist L, Vogel J, Faber F
  TITLE     An RNA-centric global view of Clostridioides difficile reveals broad
            activity of Hfq in a clinically important gram-positive bacterium.
  JOURNAL   Proc Natl Acad Sci U S A. 2021 Jun 22;118(25). pii: 2103579118. doi:
            10.1073/pnas.2103579118.
  PUBMED    34131082
REFERENCE   2  (bases 1 to 9144)
  AUTHORS   .
  TITLE     Direct Submission
  JOURNAL   Exported Dec 15, 2025 from SnapGene Server 8.0.1
            https://www.snapgene.com
COMMENT     SGRef: number: 1; type: "Journal Article"; journalName: "Proc Natl 
            Acad Sci U S A."; date: "2021-06-22"; volume: "118(25). pii: 
            2103579118. doi"; pages: " 10.1073/pnas.2103579118"
COMMENT     Sequence Label: pJAK112
FEATURES             Location/Qualifiers
     source          1..9144
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     primer_bind     108..124
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     108..124
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     protein_bind    299..323
                     /label=lac operator
                     /bound_moiety="lac repressor encoded by lacI"
                     /note="The lac repressor binds to the lac operator to 
                     inhibit transcription in E. coli. This inhibition can be 
                     relieved by adding lactose or 
                     isopropyl-beta-D-thiogalactopyranoside (IPTG)."
     RBS             342..350
                     /label=Shine-Dalgarno sequence
                     /note="full consensus sequence for ribosome-binding sites 
                     upstream of start codons in E. coli; complementary to a 
                     region in the 3' end of the 16S rRNA (Chen et al., 1994)"
     CDS             366..1646
                     /codon_start=1
                     /gene="codA"
                     /product="E. coli cytosine deaminase"
                     /label=codA
                     /note="confers sensitivity to 5-fluorocytosine"
                     /translation="SNNALQTIINARLPGEEGLWQIHLQDGKISAIDAQSGVMPITENS
                     LDAEQGLVIPPFVEPHIHLDTTQTAGQPNWNQSGTLFEGIERWAERKALLTHDDVKQRA
                     WQTLKWQIANGIQHVRTHVDVSDATLTALKAMLEVKQEVAPWIDLQIVAFPQEGILSYP
                     NGEALLEEALRLGADVVGAIPHFEFTREYGVESLHKTFALAQKYDRLIDVHCDEIDDEQ
                     SRFVETVAALAHHEGMGARVTASHTTAMHSYNGAYTSRLFRLLKMSGINFVANPLVNIH
                     LQGRFDTYPKRRGITRVKEMLESGINVCFGHDDVFDPWYPLGTANMLQVLHMGLHVCQL
                     MGYGQINDGLNLITHHSARTLNLQDYGIAAGNSANLIILPAENGFDALRRQVPVRYSVR
                     GGKVIASTQPAQTTVYLEQPEAIDYKR"
     primer_bind     complement(1746..1763)
                     /label=M13 Forward
                     /note="In lacZ gene. Also called M13-F20 or M13 (-21) 
                     Forward"
     primer_bind     complement(1746..1762)
                     /label=M13 fwd
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(1755..1777)
                     /label=M13/pUC Forward
                     /note="In lacZ gene"
     rep_origin      7633..8221
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     8122..8141
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     primer_bind     8375..8392
                     /label=L4440
                     /note="L4440 vector, forward primer"
     oriT            8542..8651
                     /note="incP origin of transfer"
     CDS             8684..9055
                     /codon_start=1
                     /gene="traJ"
                     /product="oriT-recognizing protein"
                     /label=traJ
                     /translation="MADETKPTRKGSPPIKVYCLPDERRAIEEKAAAAGMSLSAYLLAV
                     GQGYKITGVVDYEHVRELARINGDLGRLGGLLKLWLTDDPRTARFGDATILALLAKIEE
                     KQDELGKVMMGVVRPRAEP"
ORIGIN
        1 tggtgaagta catcaccgac gagcaaggca agaccgatcg ggccccctgc aggataaaaa
       61 aattgtagat aaattttata aaatagtttt atctacaatt tttttatcag gaaacagcta
      121 tgaccgcggc cgctgtatcc atatgaccat gattacgaat tccccggatc gagatagtat
      181 atgatgcata ttctttaaat atagataaag ttatagaagc aatagaagat ttaggattta
      241 ctgtaatata aattacactt ttaaaaagtt taaaaacatg atacaataag ttatggttgg
      301 aattgttatc cgctcacaat tccaacttat gattaaaatt ttaaggaggt gtatttcata
      361 atgtgtcgaa taacgcttta caaacaatta ttaacgcccg gttaccaggc gaagaggggc
      421 tgtggcagat tcatctgcag gacggaaaaa tcagcgccat tgatgcgcaa tccggcgtga
      481 tgcccataac tgaaaacagc ctggatgccg aacaaggttt agttataccg ccgtttgtgg
      541 agccacatat tcacctggac accacgcaaa ccgccggaca accgaactgg aatcagtccg
      601 gcacgctgtt tgaaggcatt gaacgctggg ccgagcgcaa agcgttatta acccatgacg
      661 atgtgaaaca acgcgcatgg caaacgctga aatggcagat tgccaacggc attcagcatg
      721 tgcgtaccca tgtcgatgtt tcggatgcaa cgctaactgc gctgaaagca atgctggaag
      781 tgaagcagga agtcgcgccg tggattgatc tgcaaatcgt cgccttccct caggaaggga
      841 ttttgtcgta tcccaacggt gaagcgttgc tggaagaggc gttacgctta ggggcagatg
      901 tagtgggggc gattccgcat tttgaattta cccgtgaata cggcgtggag tcgctgcata
      961 aaaccttcgc cctggcgcaa aaatacgacc gtctcatcga cgttcactgt gatgagatcg
     1021 atgacgagca gtcgcgcttt gtcgaaaccg ttgctgccct ggcgcaccat gaaggcatgg
     1081 gcgcacgagt caccgccagc cacaccacgg caatgcactc ctataacggg gcgtatacct
     1141 cacgcctgtt ccgcttgctg aaaatgtccg gtattaactt tgtcgccaac ccgctggtca
     1201 atattcatct gcaaggacgt ttcgatacgt atccaaaacg tcgcggcatc acgcgcgtta
     1261 aagagatgct ggagtccggc attaacgtct gctttggtca cgatgatgtc ttcgatccgt
     1321 ggtatccgct gggaacggcg aatatgctgc aagtgctgca tatggggctg catgtttgcc
     1381 agttgatggg ctacgggcag attaacgatg gcctgaattt aatcacccac cacagcgcaa
     1441 ggacgttgaa tttgcaggat tacggcattg ccgccggaaa cagcgccaac ctgattatcc
     1501 tgccggctga aaatgggttt gatgcgctgc gccgtcaggt tccggtacgt tattcggtac
     1561 gtggcggcaa ggtgattgcc agcacacaac cggcacaaac caccgtatat ctggagcagc
     1621 cagaagccat cgattacaaa cgttgaacga ctgggttaca gcgagcttag tttaaagggc
     1681 gaattcctag agtcgacgtc acgcgtccat ggagatctcg aggcctgcag acatgcaagc
     1741 ttggcactgg ccgtcgtttt acaacgtcgt gactgggaaa accctggcgt tacccaactt
     1801 aatcgccttg cagcacatcc ccctttcgcc agctggcgta atagcgaaga ggcccgcacc
     1861 gatcgccctt cccaacagtt gcgcagcctg aatggcgaat ggcgctagca taaaaataag
     1921 aagcctgcat ttgcaggctt cttattttta tggcgcgccg ttctgaatcc ttagctaatg
     1981 gttcaacagg taactatgac gaagatagca ccctggataa gtctgtaatg gattctaagg
     2041 catttaatga agacgtgtat ataaaatgtg ctaatgaaaa agaaaatgcg ttaaaagagc
     2101 ctaaaatgag ttcaaatggt tttgaaattg attggtagtt taatttaata tattttttct
     2161 attggctatc tcgataccta tagaatcttc tgttcacttt tgtttttgaa atataaaaag
     2221 gggcttttta gccccttttt tttaaaactc cggaggagtt tcttcattct tgatactata
     2281 cgtaactatt tcgatttgac ttcattgtca attaagctag taaaatcaat ggttaaaaaa
     2341 caaaaaactt gcatttttct acctagtaat ttataatttt aagtgtcgag tttaaaagta
     2401 taatttacca ggaaaggagc aagtttttta ataaggaaaa atttttcctt ttaaaattct
     2461 atttcgttat atgactaatt ataatcaaaa aaatgaaaat aaacaagagg taaaaactgc
     2521 tttagagaaa tgtactgata aaaaaagaaa aaatcctaga tttacgtcat acatagcacc
     2581 tttaactact aagaaaaata ttgaaaggac ttccacttgt ggagattatt tgtttatgtt
     2641 gagtgatgca gacttagaac attttaaatt acataaaggt aatttttgcg gtaatagatt
     2701 ttgtccaatg tgtagttggc gacttgcttg taaggatagt ttagaaatat ctattcttat
     2761 ggagcattta agaaaagaag aaaataaaga gtttatattt ttaactctta caactccaaa
     2821 tgtaaaaagt tatgatctta attattctat taaacaatat aataaatctt ttaaaaaatt
     2881 aatggagcgt aaggaagtta aggatataac taaaggttat ataagaaaat tagaagtaac
     2941 ttaccaaaag gaaaaataca taacaaagga tttatggaaa ataaaaaaag attattatca
     3001 aaaaaaagga cttgaaattg gtgatttaga acctaatttt gatacttata atcctcattt
     3061 tcatgtagtt attgcagtta ataaaagtta ttttacagat aaaaattatt atataaatcg
     3121 agaaagatgg ttggaattat ggaagtttgc tactaaggat gattctataa ctcaagttga
     3181 tgttagaaaa gcaaaaatta atgattataa agaggtttac gaacttgcga aatattcagc
     3241 taaagacact gattatttaa tatcgaggcc agtatttgaa attttttata aagcattaaa
     3301 aggcaagcag gtattagttt ttagtggatt ttttaaagat gcacacaaat tgtacaagca
     3361 aggaaaactt gatgtttata aaaagaaaga tgaaattaaa tatgtctata tagtttatta
     3421 taattggtgc aaaaaacaat atgaaaaaac tagaataagg gaacttacgg aagatgaaaa
     3481 agaagaatta aatcaagatt taatagatgg aatagaaata gattaaagtg taactatact
     3541 ttatatatat atgattaaaa aaataaaaaa caacagccta ttaggttgtt gttttttatt
     3601 ttctttatta atttttttaa tttttagttt ttagttcttt tttaaaataa gtttcagcct
     3661 ctttttcaat attttttaaa gaaggagtat ttgcatgaat tgcctttttt ctaacagact
     3721 taggaaatat tttaacagta tcttcttgcg ccggtgattt tggaacttca taacttacta
     3781 atttataatt attattttct tttttaattg taacagttgc aaaagaagct gaacctgttc
     3841 cttcaactag tttatcatct tcaatataat attcttgacc tatatagtat aaatatattt
     3901 ttattatatt tttacttttt tctgaatcta ttattttata atcataaaaa gttttaccac
     3961 caaaagaagg ttgtactcct tctggtccaa catatttttt tactatatta tctaaataat
     4021 ttttgggaac tggtgttgta atttgattaa tcgaacaacc agttatactt aaaggaatta
     4081 taactataaa aatatatagg attatctttt taaatttcat tattggcctc ctttttatta
     4141 aatttatgtt accataaaaa ggacataacg ggaatatgta gaatattttt aatgtagaca
     4201 aaattttaca taaatataaa gaaaggaagt gtttgtttaa attttatagc aaactatcaa
     4261 aaattagggg gataaaaatt tatgaaaaaa aggttttcga tgttattttt atgtttaact
     4321 ttaatagttt gtggtttatt tacaaattcg gccggccagt gggcaagttg aaaaattcac
     4381 aaaaatgtgg tataatatct ttgttcatta gagcgataaa cttgaatttg agagggaact
     4441 tagatggtat ttgaaaaaat tgataaaaat agttggaaca gaaaagagta ttttgaccac
     4501 tactttgcaa gtgtaccttg tacctacagc atgaccgtta aagtggatat cacacaaata
     4561 aaggaaaagg gaatgaaact atatcctgca atgctttatt atattgcaat gattgtaaac
     4621 cgccattcag agtttaggac ggcaatcaat caagatggtg aattggggat atatgatgag
     4681 atgataccaa gctatacaat atttcacaat gatactgaaa cattttccag cctttggact
     4741 gagtgtaagt ctgactttaa atcattttta gcagattatg aaagtgatac gcaacggtat
     4801 ggaaacaatc atagaatgga aggaaagcca aatgctccgg aaaacatttt taatgtatct
     4861 atgataccgt ggtcaacctt cgatggcttt aatctgaatt tgcagaaagg atatgattat
     4921 ttgattccta tttttactat ggggaaatat tataaagaag ataacaaaat tatacttcct
     4981 ttggcaattc aagttcatca cgcagtatgt gacggatttc acatttgccg ttttgtaaac
     5041 gaattgcagg aattgataaa tagttaactt caggtttgtc tgtaactaaa aacaagtatt
     5101 taagcaaaaa catcgtagaa atacggtgtt ttttgttacc ctagagctct atacaggtga
     5161 agcagatgct atgagtgcgt catcagtagc atcaagagat ggatcaccta taattttaac
     5221 taatggtaaa aatgttccat ttgagaaaaa agaaggtgtg caatgttatg ctcttggttc
     5281 agaggagata ataagtaatg atttagttaa aaaaactaat gcagttagat tagctggaga
     5341 agatagattt gagactaata aaaaagttat aaaacatttt tatagttcgg caaaagaatt
     5401 ttatctttct aaaggttatc aattagtaga tgcagttgct ggttcttcta tagcaaaaaa
     5461 tgcacctatt gtattagttg acggaaatag tgataagtct gtacttagaa gtgctgataa
     5521 gattacagca ctaggaggaa tagatgaaaa gacactagaa caatgtttaa gtgcatcatc
     5581 actggatgca agtgcaccaa caataactgt tggaaattta aatatttatc aaggtgataa
     5641 gtttgatata agtaaactga atatcgtagc aaaggatagc aatggtaacg atttgacacc
     5701 agagcttata ggaaatattg atactgataa ggtgggtaaa tacaaagtta ctataaaagc
     5761 tactgatatt ggtggaaaga ctacatcaat aagtgtagaa gtaaatgtac ttgaatataa
     5821 gactaatgat atgaatagta gtgagtttaa aagaatggtt tctagtgaaa tgtatagttt
     5881 ggtaaattca tatagaaaag aaaaaggtaa agagccatta caagtttcta aaaacttaga
     5941 aggactttct aattcctggt ctaagtacat ggcagataaa ggtcagtttt cacatgtaat
     6001 aaatggtaag aaatctgttg aagtatttac tggatatggc ttgagaagtg aagaaaatat
     6061 agcttttgta ccacttgtta caaaaagtac ttatacaaca aaggatgcta gagaagtagc
     6121 aaatgtaata tttacagttt ggaaaaagtc agataaatat aatgaaaata tgttaaatag
     6181 tgattttgta tatactgggt ttggattata tatattgcct aatggagaag tgtatgctac
     6241 acaagaattt ttaaataagt aatttaaata agtaaaatca aattttttaa gttattaaat
     6301 attggagttt aagggtataa aaactcatat gcttgggtat aaatataata atataaaaag
     6361 gcttcttata tgagaagtct ttttatatta tgttttcgaa tacaaaaaaa gagactaaat
     6421 ttagtctctt ttttatgtga gaaatactta aatatataaa gatgtaattt atttaagtat
     6481 gattattata ctatacaata aaataattgt ctactattct ataattttaa ggtataataa
     6541 taattgtatg ataaaagagg aggtcaaaaa atatgtcagt tttagatgca atcttagata
     6601 aagcggatga acaagaaatt aaaaaattaa atttaatagt agataaaata gaatctttag
     6661 aaaaagatat ggaaatcaaa gagaatgaac aattaaaaga aatgacaaat acttttagac
     6721 ttagattaga caaaggtgaa agtttggatg atatacttcc agaagcattt gctgttgtta
     6781 gagaggtctc aaaaagagtt ttaggaatgc gtcaatataa agttcagtta attggaggta
     6841 tagtaattca tcaaggaaag atagctgaga tgaagactgg tgaggggaaa actttagttg
     6901 aggtagctcc agtatatcta aatgctttaa caggaaaagg tgtacatgta attacagtaa
     6961 atgattattt ggcagaacgt gataaagaac ttatgcgtcc agtatatgaa tttttaggat
     7021 tgactgtagg tgtaatttta tctaaccaag acccaagtat aagaaaagaa caatataaat
     7081 gtgatataac ttatggaaca aatagtgaat ttggatttga ctatttaaga gataatatgg
     7141 tgccagattt gtctcataaa gtacaaaggg aactaaactt tgccatagta gatgagatag
     7201 actcaatatt aatagatgaa gctagaactc cacttattat tgcaggagat ggtgatgaag
     7261 atttaaaact ttatgagtta gcaaataact ttgtaaaaac tgttaaagaa gaagactttg
     7321 agatggatag aaaagataaa actatagcat taacagcaag tggtataagc aaagctgagt
     7381 cattttttgg tataacaaac cttactgata taaagaatat agaattatat catcatataa
     7441 atcaagcttt aagaggtcat aagcttatgg aaaaagatgt tgactatgtt atctcaaatg
     7501 gagaagtaat gatagttgac gaatttacag gaagagggat cccctttttg ataatctcat
     7561 gaccaaaatc ccttaacgtg agttttcgtt ccactgagcg tcagaccccg tagaaaagat
     7621 caaaggatct tcttgagatc ctttttttct gcgcgtaatc tgctgcttgc aaacaaaaaa
     7681 accaccgcta ccagcggtgg tttgtttgcc ggatcaagag ctaccaactc tttttccgaa
     7741 ggtaactggc ttcagcagag cgcagatacc aaatactgtt cttctagtgt agccgtagtt
     7801 aggccaccac ttcaagaact ctgtagcacc gcctacatac ctcgctctgc taatcctgtt
     7861 accagtggct gctgccagtg gcgataagtc gtgtcttacc gggttggact caagacgata
     7921 gttaccggat aaggcgcagc ggtcgggctg aacggggggt tcgtgcacac agcccagctt
     7981 ggagcgaacg acctacaccg aactgagata cctacagcgt gagctatgag aaagcgccac
     8041 gcttcccgaa gggagaaagg cggacaggta tccggtaagc ggcagggtcg gaacaggaga
     8101 gcgcacgagg gagcttccag ggggaaacgc ctggtatctt tatagtcctg tcgggtttcg
     8161 ccacctctga cttgagcgtc gatttttgtg atgctcgtca ggggggcgga gcctatggaa
     8221 aaacgccagc aacgcggcct ttttacggtt cctggccttt tgctggcctt ttgctcacat
     8281 gttctttcct gcgttatccc ctgattctgt ggataaccgt attaccgcct ttgagtgagc
     8341 tgataccgct cgccgcagcc gaacgaccga gcgcagcgag tcagtgagcg aggaagcgga
     8401 agagcgccca atacgcaggg ccccctgctt cggggtcatt atagcgattt tttcggtata
     8461 tccatccttt ttcgcacgat atacaggatt ttgccaaagg gttcgtgtag actttccttg
     8521 gtgtatccaa cggcgtcagc cgggcaggat aggtgaagta ggcccacccg cgagcgggtg
     8581 ttccttcttc actgtccctt attcgcacct ggcggtgctc aacgggaatc ctgctctgcg
     8641 aggctggccg gctaccgccg gcgtaacaga tgagggcaag cggatggctg atgaaaccaa
     8701 gccaaccagg aagggcagcc cacctatcaa ggtgtactgc cttccagacg aacgaagagc
     8761 gattgaggaa aaggcggcgg cggccggcat gagcctgtcg gcctacctgc tggccgtcgg
     8821 ccagggctac aaaatcacgg gcgtcgtgga ctatgagcac gtccgcgagc tggcccgcat
     8881 caatggcgac ctgggccgcc tgggcggcct gctgaaactc tggctcaccg acgacccgcg
     8941 cacggcgcgg ttcggtgatg ccacgatcct cgccctgctg gcgaagatcg aagagaagca
     9001 ggacgagctt ggcaaggtca tgatgggcgt ggtccgcccg agggcagagc catgactttt
     9061 ttagccgcta aaacggccgg ggggtgcgcg tgattgccaa gcacgtcccc atgcgctcca
     9121 tcaagaagag cgacttcgcg gagc
//
