ID AF306799; SV 1; circular; genomic DNA; STD; UNC; 6094 BP. XX AC AF306799; XX DT 21-APR-2001 (Rel. 67, Created) DT 13-MAR-2011 (Rel. 108, Last updated, Version 10) XX DE Plasmid pCD4, complete sequence. XX KW . XX OS Plasmid pCD4 OC other sequences; plasmids. OG Plasmid pCD4 XX RN [1] RP 1-6094 RX DOI; 10.1128/AEM.67.4.1700-1709.2001. RX PUBMED; 11282624. RA Emond E., Lavallee R., Drolet G., Moineau S., LaPointe G.; RT "Molecular characterization of a theta replication plasmid and its use for RT development of a two-component food-grade cloning system for Lactococcus RT lactis"; RL Appl. Environ. Microbiol. 67(4):1700-1709(2001). XX RN [2] RP 1-6094 RA Emond E., Lavallee R., Drolet G., Moineau S., LaPointe G.; RT ; RL Submitted (19-SEP-2000) to the INSDC. RL STELA Dairy Research Centre, Universite Laval, Pavillon Paul-Comtois, Cite RL Universitaire, Quebec, QC G1K 7P4, Canada XX DR RFAM; RF00238; ctRNA_pND324. XX FH Key Location/Qualifiers FH FT source 1..6094 FT /organism="Plasmid pCD4" FT /plasmid="pCD4" FT /host="Lactococcus lactis subsp. lactis MJC15" FT /mol_type="genomic DNA" FT /db_xref="taxon:157539" FT gene join(6078..6094,1..591) FT /gene="orfA" FT CDS 1..591 FT /codon_start=1 FT /transl_table=11 FT /gene="orfA" FT /product="tyrosine family DNA recombinase OrfA" FT /db_xref="GOA:Q7BI07" FT /db_xref="InterPro:IPR002104" FT /db_xref="InterPro:IPR011010" FT /db_xref="InterPro:IPR013762" FT /db_xref="UniProtKB/TrEMBL:Q7BI07" FT /protein_id="AAK38198.1" FT /translation="MVKQIVLPIKDSNILKMVQDTLLDSFRAGRRNYTIFQVGKATLLR FT VSDVMKLKKTDVFNLDGTVKQTAFIHDQKTGKGNTLYLKPVQQDLMLYHAWLIQQNMNS FT EWLFPSTSRPDRPITEKQFYKIMARVGDLLGINYLGTHTMRKTGAYRVYTQSNYNIGLV FT MHLLNHSSEAMTLTYLGLDQASRETMLDQIDFG" FT terminator 608..631 FT terminator 637..664 FT oriT 716..1179 FT stem_loop 720..764 FT stem_loop 772..822 FT stem_loop 820..843 FT stem_loop 850..881 FT stem_loop 923..951 FT stem_loop 958..997 FT rep_origin 1399..2101 FT misc_feature 1806..1846 FT /note="AT-rich region" FT repeat_region 1807..1829 FT /rpt_unit_seq="atatctattt" FT /note="contains DRIa and DRIb" FT protein_bind 1889..1968 FT /bound_moiety="Rep initiator" FT repeat_region 1889..1968 FT /function="replication control" FT /rpt_unit_seq="taaggacagaaaaatcgatgta" FT /note="contains DRIIa, DRIIb, DRIIc and DRIId" FT protein_bind 1955..1987 FT /bound_moiety="Rep initiator" FT stem_loop 1955..1987 FT /function="autoregulation" FT gene 1970..3235 FT /gene="repB" FT -35_signal 1970..1975 FT /gene="repB" FT -10_signal 1993..1998 FT /gene="repB" FT misc_RNA complement(1996..2073) FT /product="counter transcript" FT stem_loop 2003..2040 FT terminator complement(2003..2040) FT RBS 2059..2065 FT /gene="repB" FT CDS 2075..3235 FT /codon_start=1 FT /transl_table=11 FT /gene="repB" FT /product="replication initiator protein RepB" FT /db_xref="GOA:Q9AC99" FT /db_xref="InterPro:IPR000525" FT /db_xref="InterPro:IPR010931" FT /db_xref="InterPro:IPR011991" FT /db_xref="UniProtKB/TrEMBL:Q9AC99" FT /protein_id="AAK38199.1" FT /translation="MPIITEKQENKKQVLTLNELEKRKVVEHNALITSVAKMQKTALKM FT FELAVSCIDTENLPKNNMVYLSKKELFSFFEVSSNSKHSQFKEAIEFMQKQAYFKIKSN FT KALGIEYESIVPIPYVKWNDYNDEVTIQFSEHIMPYLINLKAEFTQYKISELQKLNSKY FT SIILYRWLAMNYNQYEHYSNKGGRRAEQVESYRNPSITVKELREITDTIKDYQKMSHFT FT TWVLEKPLEEINAHTSFNVSYEKVKKGRSVDSIVFHITKKPVARNDFYKLEEQDPIYLK FT DKANKEQAEELLAGKALKSKYTKLLFHNMLLSPYEMTDTSLMAGLQAHVYPLYDELKAL FT RGLNGVKDHLSYVRAKQEAYSKRNIAKYLKKAIEQYLPTVKRQDLS" FT -10_signal complement(2081..2087) FT -35_signal complement(2101..2106) FT gene 3216..3861 FT /gene="orfX" FT RBS 3216..3220 FT /gene="orfX" FT CDS 3232..3861 FT /codon_start=1 FT /transl_table=11 FT /gene="orfX" FT /product="OrfX" FT /db_xref="InterPro:IPR007489" FT /db_xref="InterPro:IPR011991" FT /db_xref="InterPro:IPR013196" FT /db_xref="UniProtKB/TrEMBL:Q9AC98" FT /protein_id="AAK38200.1" FT /translation="MSENLKTIKELADELGVSKQTIRNKIDKDFREKFVQTIKIKGNNT FT LVINNAGYSLLKKTLQNDTAQTAKTLQNDTAQTAKTLQNDTAQTKLICFLEEQLDKKEQ FT QLSVKDKQLENKDTQISQMQNLLDQQQRLALQDKKLLEEYKAENDSLKALNVPSQETEF FT KHLDNQYKDEVNALKEKLENLQEQIKDQKRIEEQEKPRKWWGLWRK" FT gene 3821..5021 FT /gene="hsdS" FT RBS 3821..3825 FT /gene="hsdS" FT CDS 3837..5021 FT /codon_start=1 FT /transl_table=11 FT /gene="hsdS" FT /product="HsdS" FT /db_xref="GOA:Q9AC97" FT /db_xref="InterPro:IPR000055" FT /db_xref="UniProtKB/TrEMBL:Q9AC97" FT /protein_id="AAK38201.1" FT /translation="MVGTMAKIDDSVKKKVPELRFPGFTDDWEERKAKEMIKTHHFRSY FT LAEPNDVGNYEVIQQGDKPIAGYANGEPFEYFYDVTLFGDHTVSLFKPTKPFFIATDGV FT KIISADEFDGRYFYVTLERYKPASQGYKRHFTILKNEDIWFTTNKDEQVKIGTFFKQLD FT DTIALHQRKLDLLKEQKKGYLQKMFPKNGAKVPELRFAGFADDWEQRKLKDVTERVRSN FT DGRMDLPTLTMSASSGWLDQKDRFSGDISGKEKKNYTLLKKGELSYNHGNSKLAKYGVV FT FSLTNYEEALVPRVYHSFKALENTSADFIEYMFSTKLPDRELGKLVSSGARMDGLLNIN FT YDDFMNIHISIPNYEEQILMSTFFRKLDDTIALHQRKLDLLKEQKKGFLQKMFV" FT terminator 5413..5459 FT gene 5463..6079 FT /gene="orf1" FT -10_signal 5463..5468 FT /gene="orf1" FT RBS 5484..5489 FT /gene="orf1" FT CDS 5498..6079 FT /codon_start=1 FT /transl_table=11 FT /gene="orf1" FT /product="Orf1" FT /db_xref="InterPro:IPR002798" FT /db_xref="UniProtKB/TrEMBL:Q9AC96" FT /protein_id="AAK38202.1" FT /translation="MNNVFKPIKYLSIIMLVVIISAVITYIVNPNFSDTLNSVPSNISK FT SVSQKSGLNLVVAYIFNNGFKVPMGMLFFSIIPIRFLYWIQPLFTAILPGILFGIAFRY FT SVAKAFIILISSLPHMLLEIFAFCLWMVALDRFNKWIRYKISRKKQTSTKLFYEFKLIL FT ISYVKYVLPLIVIAAFTETYVADWISRILS" FT RBS 6078..6086 FT /gene="orfA" XX SQ Sequence 6094 BP; 2201 A; 926 C; 1111 G; 1855 T; 1 other; atggttaaac aaatcgttct acccatcaaa gattcaaaca tcttaaaaat ggtgcaggat 60 acactacttg atagttttcg tgctggtcgt cgcaactata caattttcca agttgggaaa 120 gcgaccttgc tacgtgtgag tgacgtcatg aaattaaaga aaacagatgt ctttaatctt 180 gatggaacag tcaaacaaac tgcatttatt catgatcaaa aaacaggtaa gggaaatacg 240 ttatatttaa aacctgtcca acaagattta atgctttatc atgcatggct aatccaacaa 300 aacatgaatt cagagtggtt atttccttca acttctcgtc ctgatcgtcc tattaccgag 360 aaacagtttt ataagattat ggcacgagtt ggagatcttt taggaattaa ctatctagga 420 acgcatacca tgcgtaaaac aggcgcttat cgggtctata cccagtcaaa ctataatatt 480 ggcttagtga tgcatttatt aaaccattca agtgaagcca tgaccttaac gtatcttgga 540 ttagatcaag ctagtcgaga aacgatgtta gaccaaattg attttgggta atgaatgttt 600 agaacttagt agtcgtccaa aaacgactac tttttttgtt gaatcgtcct tggacgattc 660 gatgcttttg acttgtaaga acaggattga atgaagccat actgttcgca tatttttagt 720 ggatgaacaa acaaaatacg agagattttt tgttcgttca tccatggttt taggaaaaag 780 agggacgatt tcggaagaag aaarctcgtc tctttttttc ttctttttgt atgacaaaaa 840 gaaagatctt ttgcccattt tatttttata aaatgggtag gtggcgtttg cgtaaagcaa 900 atcgacacaa tccaaagggg ataaaagggg aaagtgaaac ttcccccttt tcaagcaaca 960 ttgtaataca agaacgaagt gatttgtatt acaatgtgat agcttgcagt atttatggtt 1020 ttatatggtc tattttgtta taatgattgt aaccgaatag ggcgcaatac ttataacaaa 1080 atcaatgaca aagggcgatt gagaaatgag cgctggggca ttttatattt gagtaagtta 1140 ttgatggatc agaaaaatgt atcacaaatt taaacaaaga ctcactcatt taagagacgc 1200 tactagcatg aaattttgtt gttgcgataa gcaacttctg atacaggttt ttaggggtta 1260 gcacgacatc aatttatttg atgtgtaagt gcgcattgca ctcttttttt acgaaacaag 1320 ccgaccagcg tttgaaactt tttagttttt catcattcta ttttaaaacg ttctaaaact 1380 cgatttaagc gactttaatt cgaaactgtc tatttgttca aaggaagcat taagaatgct 1440 taaacgagct tttaagtggg tttaaattga ttttgaattg aatagcttgt tgtaagttgt 1500 aaaaaaacaa gttaaacaaa gtatcagttt tccatttaag ggttgttagg gcttgccctg 1560 accgtctgta agacgcttga ttgcatgata tgagtattta gctagtcaaa cagttaaaac 1620 agcttatatg agaaattaga gggaatccaa taaattccta aaagcggttt tgatcttttc 1680 ttttagcgag tgaacgaagt gaacgctgca agtaaaatgt gagcgtggtt ttcgctcact 1740 cctttttttg atgactttga cctttggttt taaatttttg aaaaaaataa aaaataggcg 1800 aagcctatat ctatttatca tatatatttt aatcttttgt tcttttgcgt gaaaaaaatg 1860 tcagtggtag taaggctata aagattttta aggacagaaa aatcgatgta taaggacaga 1920 aaaatcgatg tataaggaca gaaaaatcga tgtataagga cagaaaaagt tgaattactg 1980 tccttatttt gatataataa aagcatagag aaatttactc gctaaagtct ttctctatgc 2040 ctacttaaaa tcactcacaa aggagtaact ctctatgcct attataacag aaaaacaaga 2100 aaacaaaaag caggtgctga ccttgaatga acttgaaaaa cgaaaagtag tggagcataa 2160 cgctttaatt actagcgtgg ctaaaatgca aaagaccgct ttaaaaatgt ttgagttggc 2220 ggtatcttgc attgatacgg aaaacctacc taaaaataat atggtttatc tgtcaaagaa 2280 agagttgttt tctttctttg aagtatcttc taatagtaag catagtcaat tcaaagaagc 2340 cattgaattt atgcagaagc aagcatattt taaaatcaag tccaataaag cattaggtat 2400 tgagtatgaa agcattgtgc ctatccctta tgtaaaatgg aacgattata atgatgaagt 2460 aacgatacaa tttagcgagc atattatgcc ctatctgatt aacttaaagg cagaatttac 2520 tcaatataaa atttctgaat tacagaaatt gaatagcaag tatagcatta tcttgtatcg 2580 ttggttagcc atgaattaca accaatacga gcattacagc aataagggcg ggcggagagc 2640 cgaacaagtg gaaagctatc gcaatccctc aatcacagtc aaagaattgc gagaaatcac 2700 tgatacgatt aaagactatc aaaaaatgtc acactttact acatgggtac tagaaaaacc 2760 attggaagaa atcaacgctc acacctcttt taacgtgtct tacgagaaag tcaaaaaagg 2820 gcgaagcgtt gattctattg tctttcatat cacgaagaaa ccagtcgcac gaaatgactt 2880 ctacaagctg gaagaacaag accctattta tttgaaggat aaagcaaata aagaacaagc 2940 agaagaactt ttagcaggga aagcattaaa aagtaaatac acgaaacttt tgttccataa 3000 tatgctatta agtccttatg aaatgaccga tacgtcactt atggcaggat tgcaggcgca 3060 cgtgtaccct ctctatgacg agctgaaagc cttacgaggg ttgaatgggg tcaaagacca 3120 cctctcttat gtgagagcta aacaagaagc ctattcaaaa cgcaatatag ccaagtacct 3180 caaaaaagca attgaacaat acctaccaac ggttaaaagg caggacttat catgagtgag 3240 aatttaaaaa ccataaaaga acttgcggac gagttaggcg tatcaaaaca gacgataaga 3300 aataaaatag ataaagattt tagagaaaag tttgttcaaa caataaaaat taaaggtaat 3360 aataccttag taattaataa cgcagggtac tctttactaa aaaaaacact gcaaaatgat 3420 actgcacaaa ctgcaaaaac actgcaaaat gatactgcac agactgcaaa aacactgcaa 3480 aatgatactg cacagactaa attaatatgt tttttagaag aacaattaga taaaaaggaa 3540 cagcaattat ctgttaaaga taagcaacta gaaaataaag acactcaaat ctcacaaatg 3600 caaaatttgt tagaccagca acagcgatta gctttgcaag ataaaaagct actggaagaa 3660 tacaaggcag aaaacgacag tctaaaagcc cttaatgtgc cgtcacagga aacagaattc 3720 aaacacttag acaatcaata taaagatgaa gtgaacgctc ttaaagagaa gttggaaaat 3780 ttgcaggaac aaatcaaaga tcaaaaaagg atagaagaac aagaaaaacc aagaaaatgg 3840 tggggactat ggcgaaaata gatgattcag ttaaaaagaa agttccagaa ttaaggtttc 3900 cgggatttac ggatgattgg gaagagcgta aggctaagga aatgataaaa actcatcatt 3960 ttcgttcata tttagcagag cccaatgatg ttggaaatta tgaagttatt caacaaggag 4020 acaaacctat tgctggatat gctaatggag aaccgtttga atatttttac gatgtaactt 4080 tatttggaga ccatactgtt tctctattca aaccaacaaa accgttcttt atagctactg 4140 atggagtaaa aatcattagt gcggatgaat ttgatggcag atatttttat gtgacattag 4200 aacgatataa gccagcatca cagggataca agcgccactt tacgatacta aagaatgaag 4260 atatttggtt tacaacaaac aaagatgaac aggtcaaaat cggaaccttc ttcaaacaac 4320 tcgacgacac tatcgctctt catcaacgta agttagatct tctcaaagag cagaaaaaag 4380 gctacttgca aaagatgttc cctaaaaatg gtgccaaagt tcctgaattg cgatttgcgg 4440 ggtttgctga cgattgggaa cagcgtaagt taaaagatgt tactgagcga gtaagatcta 4500 atgacgggag aatggattta cctacactaa ccatgtctgc tagtagtggt tggttagacc 4560 aaaaagatag attctctgga gacatttcag gtaaagagaa aaagaattat actttattga 4620 aaaagggaga attatcgtat aatcacggaa attctaagct agctaaatac ggagttgtat 4680 tcagtctaac aaattatgaa gaagcacttg tcccaagggt ttaccatagt tttaaagcgt 4740 tagagaatac gtcggctgac ttcattgagt atatgttttc aactaaacta cctgatagag 4800 aactaggaaa attagtatct tctggggctc gtatggatgg actgttaaat attaactatg 4860 atgatttcat gaatattcat atatctatcc ctaattatga agaacaaatt ttgatgtcta 4920 ctttctttag aaaattagat gacactatcg ctcttcatca acgtaagtta gatttgttga 4980 aagaacagaa aaaaggcttt ttacaaaaga tgtttgtttg atattttaaa tagaaaagag 5040 agataaagtg aagtttttaa attttttgaa ctataaatat ttaaactggg tattatatgc 5100 tattacatta ttttttattg tttattactt ttttaccgat gataatattt ttttaatttt 5160 agcaatactt tttcttgttt catctatttt tcgtaatagc ttcattgaag ttcttacaga 5220 accagaagtt cggtctatga cggatgagga acaacaagtt attaaagcta tgattttggc 5280 aaatgagaaa gacgttgtag ttatcaaaaa gattagagag tatacaaatt taggtctttt 5340 acaagcaaaa aaagtatatg aaaaaataaa aaagggtcta taattagata ataacccctc 5400 acaaatccca ttaaaatagc ccctaagata taaaggttat atcttagggg ctattttttt 5460 gttataatga tataataact ctaaaaggag taagcaaatg aataatgttt ttaaacccat 5520 taagtattta agtatcatta tgcttgttgt tattatctcg gctgtaataa cttatattgt 5580 caatcctaat ttctcagata cattaaattc tgtaccaagt aatatttcca aatcggtctc 5640 acagaaatca ggattaaatt tagttgttgc ttatattttt aacaatggat ttaaagtccc 5700 aatggggatg ttattttttt caattatacc tattcgattt ttatattgga ttcagccact 5760 tttcacagcc atattacctg gaattttatt tgggatagca tttagatact cggttgcaaa 5820 agcttttatt atattaattt cttcgctacc tcatatgtta ttagagatat tcgcattttg 5880 cttatggatg gtcgctcttg atcgttttaa caaatggatt agatacaaaa tatctaggaa 5940 aaaacaaaca agtactaagt tattttatga attcaagtta atattaatct catatgttaa 6000 atacgttctc ccattaattg ttatcgcagc tttcaccgaa acttacgttg ctgattggat 6060 tagtcgtata ttaagttaaa ggaggagtac taac 6094 //