LOCUS T7.1-beta_as_built 3368 bp DNA PHG 13-AUG-2004 DEFINITION Sequence of section alpha of T7.1 (Revision 1) as constructed by the Endy Group. ACCESSION # VERSION # GI:# KEYWORDS Bacteriophage; T7; refactored; synthetic; engineered; parts. SOURCE Endy Group, MIT. http://web.mit.edu/endy/ ORGANISM Enterobacteria phage T7 Viruses; dsDNA viruses, no RNA stage; Caudovirales; Podoviridae; T7-like viruses. REFERENCE 1 (bases 1 to 3368) AUTHORS Chan,L., Kosuri,S. and Endy,D. TITLE Refactoring Bacteriophage T7 JOURNAL MEDLINE REFERENCE 2 (bases 1 to 3368, partial) AUTHORS Dunn,J.J. and Studier,F.W. TITLE Complete nucleotide sequence of bacteriophage T7 DNA and the locations of T7 genetic elements JOURNAL J. Mol. Biol. 166 (4), 477-535 (1983) MEDLINE 83241725 REMARK complete genome REFERENCE 3 (bases 1 to 3368, partial) AUTHORS Dunn,J.J. and Studier,F.W. TITLE Direct Submission JOURNAL Submitted (23-NOV-1993) Dunn J.J REMARK complete genome COMMENT This is the DNA sequence of the "as-built" section beta of T7.1 (ACCESSION#). Differences between the design and as-built sequence are annotated here. When combined with the remainder of the wild-type genome (1..8311,11516..39938), the resulting chimeric genome codes for a viable bacteriophage. The chimera of section alpha (ACCESSION#) with beta (this section) and the remaining wild-type genome (11516..39938) also codes for a viable bacteriphage. COMMENT The design of T7.1 does not intentionally include any genetic functions different from those found on wild-type T7. Based on initial laboratory characterization, Chan, Kosuri, and Endy assert that the same precautions and safety measures that apply to wild-type T7 should also apply to T7.1. FEATURES Location/Qualifiers CDS 1..446 /codon_start=1 /transl_table=11 /protein_id="NP_041967.1" /db_xref="GI:9627439" /db_xref="SWISS-PROT:P03781" /label=gene\1.7\fragment /note="gene 1.7" CDS 483..629 /codon_start=1 /transl_table=11 /protein_id="NP_041968.1" /db_xref="GI:9627440" /db_xref="SWISS-PROT:P03794" /label=gene\1.8 /note="gene 1.8" CDS 666..860 /codon_start=1 /transl_table=11 /protein_id="NP_041969.1" /db_xref="GI:9627441" /db_xref="SWISS-PROT:P03704" /label=gene\2 /note="gene 2, inhibits E. coli RNA polymerase" promoter 872..906 /standard_name="phi2.5" /function="gp1 promoter" /label=phi2.5 /note="T7 promoter phi2.5 -- Differs from 23bp at four positions (-1 1 4 5)" misc_structure 899..899 /standard_name="S_phi2.5" /function="mRNA start site" /label=S_phi2.5 CDS 942..1639 /codon_start=1 /transl_table=11 /protein_id="NP_041970.1" /db_xref="GI:9627442" /db_xref="SWISS-PROT:P03696" /label=gene\2.5 /note="gene 2.5, single-stranded DNA-binding protein" promoter 944..1007 /standard_name="S2" /citation=[8] /function="putative RNAP promoter" /label=S2 misc_structure 948..948 /standard_name="-45_S2" /function="-45 conserved base" /label=-45_S2 -35_signal 957..961 /standard_name="-35_S2" /label=-35_S2 -10_signal 981..986 /standard_name="-10_S2" /label=-10_S2 misc_structure 993..993 /standard_name="S_S2" /function="putative mRNA start site" /label=S_S2 CDS 1668..2005 /codon_start=1 /transl_table=11 /protein_id="NP_041971.1" /db_xref="GI:9627443" /db_xref="SWISS-PROT:P03795" /label=gene\2.8 /note="gene 2.8" CDS 2026..2475 /codon_start=1 /transl_table=11 /protein_id="NP_041972.1" /db_xref="GI:9627444" /db_xref="SWISS-PROT:P00641" /label=gene\3 /note="gene 3, endonuclease" CDS 2510..2965 /codon_start=1 /transl_table=11 /protein_id="NP_041973.1" /db_xref="GI:9627445" /db_xref="SWISS-PROT:P00806" /label=gene\3.5 /note="gene 3.5, lysozyme/inhibits T7 RNA polymerase [7]" promoter 2619..2682 /standard_name="S3" /citation=[8] /function="putative RNAP promoter" /label=S3 misc_structure 2623..2623 /standard_name="-45_S3" /function="-45 conserved base" /label=-45_S3 -35_signal 2632..2636 /standard_name="-35_S3" /label=-35_S3 -10_signal 2656..2661 /standard_name="10_S3" /label=10_S3 misc_structure 2668..2668 /standard_name="S_S3" /function="putative mRNA start site" /label=S_S3 promoter 2957..3012 /standard_name="phi3.8" /function="gp1 promoter" /label=phi3.8 /note="T7 promoter phi3.8 -- Differs from 23bp consensus sequence at 4 positions (-13 -12 -11 -2)" misc_binding 2958..3075 /bound_moiety="RNase III" /function="R3.8" /label=Bind_Site_6 /note="possible RNase III site R3.8" stem_loop 2989..3037 /standard_name="RSL_R3.8" /label=RSL_R3.8 misc_structure 3005..3005 /standard_name="C_R3.8" /function="RNaseIII cut site" /label=C_R3.8 misc_structure 3005..3005 /standard_name="S_phi3.8" /function="mRNA start site" /label=S_phi3.8 CDS 3073..3368 /codon_start=1 /transl_table=11 /protein_id="NP_041974.1" /db_xref="GI:9627446" /db_xref="SWISS-PROT:P03797" /label=gene\3.8 /note="gene 3.8" misc_feature 447..451 /label=D23-R /note="D21-R AgeI" misc_feature 449..455 /label=D24-L misc_feature 630..636 /label=D24-R /note="D-22R" misc_feature 635..641 /label=D25-L misc_feature 865..871 /label=D26-L misc_feature 907..914 /label=D26-R misc_feature 912..917 /label=D27-L misc_feature 1640..1645 /label=D27-R misc_feature 1644..1649 /label=D28-L misc_feature 2482..2487 /label=D30-L misc_feature 2966..2971 /label=D30-R misc_feature 2972..2977 /label=D31-L misc_feature 3052..3057 /label=D31-R misc_feature 3056..3061 /label=D32-L misc_difference 83..83 /label=C->T /note="silent" misc_difference 534..534 /label=A->G /note="Thr->Ala" misc_difference 736..736 /label=A->T /note="Glu->Val" misc_difference 1639..1640 /label=deleted\base\between /note="adds Tyr-Pro-Gly-Ser-Glu-Asp-Gly-Asp-Phe" misc_difference 1915..1915 /label=A->G /note="Asp->Gly" misc_difference 2127..2127 /label=C->T /note="silent" misc_difference 2005..2006 /label=87\deleted\bases\between /note="now terminates 20 bases into 3.0" misc_feature 861..866 /label=D25-R misc_feature 2006..2011 /label=D29-L misc_feature 2476..2481 /label=D-29R BASE COUNT 982 a 734 c 879 g 773 t ORIGIN 1 tgatcattaa gttgatagac aataatgaag gtcgcccaga tgatttgaat ggctgcggta 61 ttctctgctc caatgtccct tgtcacctct gccccgcaaa taacgatcaa aagataacct 121 taggtgaaat ccgagcgatg gacccacgta aaccacatct gaataaacct gaggtaactc 181 ctacagatga ccagccttcc gctgagacaa tcgaaggtgt cactaagcct tcccactaca 241 tgctgtttga cgacattgag gctatcgaag tgattgctcg ttcaatgacc gttgagcagt 301 tcaagggata ctgcttcggt aacatcttaa agtacagact acgtgctggt aagaagtcag 361 agttagcgta cttagagaaa gacctagcga aagcagactt ctataaagaa ctctttgaga 421 aacataagga taaatgttat gcataaccgg tgacctcttt gagaaacata aggataaatg 481 ttatgcataa cttcaagtca accccacctg ccgacagcct atctgatgac ttcgcatctt 541 gctcagagtg gtgccgaaag atgtgggaag agacattcga cgatgcgtac atcaagctgt 601 atgaactttg gaaatcgaga ggtcaatgag gtcaccgtac gttggaaatc gagaggtcaa 661 tgactatgtc aaacgtaaat acaggttcac ttagtgtgga caataagaag ttttgggcta 721 ccgtagagtc ctcggtgcat tccttcgagg ttccaatcta cgctgagacc ctagacgaag 781 ctctggagtt agccgaatgg caatacgttc cggctggctt tgaggttact cgtgtgcgtc 841 cttgtgtagc accgaagtaa cgtacgaatt cagcaccgaa gtaatacgac tcactattag 901 ggaagagaat tcccgggcga aacctaaagg agattaacat tatggctaag aagattttca 961 cctctgcgct gggtaccgct gaaccttacg cttacatcgc caagccggac tacggcaacg 1021 aagagcgtgg ctttgggaac cctcgtggtg tctataaagt tgacctgact attcccaaca 1081 aagacccgcg ctgccagcgt atggtcgatg aaatcgtgaa gtgtcacgaa gaggcttatg 1141 ctgctgccgt tgaggaatac gaagctaatc cacctgctgt agctcgtggt aagaaaccgc 1201 tgaaaccgta tgagggtgac atgccgttct tcgataacgg tgacggtacg actaccttta 1261 agttcaaatg ctacgcgtct ttccaagaca agaagaccaa agagaccaag cacatcaatc 1321 tggttgtggt tgactcaaaa ggtaagaaga tggaagacgt tccgattatc ggtggtggct 1381 ctaagctgaa agttaaatat tctctggttc catacaagtg gaacactgct gtaggtgcga 1441 gcgttaagct gcaactggaa tccgtgatgc tggtcgaact ggctaccttt ggtggcggtg 1501 aagacgattg ggctgacgaa gttgaagaga acggctatgt tgcctctggt tctgccaaag 1561 cgagcaaacc acgcgacgaa gaaagctggg acgaagacga cgaagagtcc gaggaagcag 1621 acgaagacgg ggacttctac ccgggatccg aagacggaga cttctaagtg gaactgcggg 1681 agaaaatcct tgagcgaatc aaggtgactt cctctgggtg ttgggagtgg cagggcgcta 1741 cgaacaataa agggtacggg caggtgtggt gcagcaatac cggaaaggtt gtctactgtc 1801 atcgcgtaat gtctaatgct ccgaaaggtt ctaccgtcct gcactcctgt gataatccat 1861 tatgttgtaa ccctgaacac ctatccatag gaactccaaa agagaactcc actggcatgg 1921 taaataaggg tcgctcacac aaggggtata aactttcaga cgaagacgta atggcaatca 1981 tggagtccag cgagtccaat gtatccggcc gcaaagggag gcgacatggc aggttacggc 2041 gctaaaggaa tccgaaaggt tggagcgttt cgctctggcc tagaggacaa ggtttcaaag 2101 cagttggaat caaaaggtat taaatttgag tatgaagagt ggaaagtgcc ttatgtaatt 2161 ccggcgagca atcacactta cactccagac ttcttacttc caaacggtat attcgttgag 2221 acaaagggtc tgtgggaaag cgatgataga aagaagcact tattaattag ggagcagcac 2281 cccgagctag acatccgtat tgtcttctca agctcacgta ctaagttata caaaggttct 2341 ccaacgtctt atggagagtt ctgcgaaaag catggtatta agttcgctga taaactgata 2401 cctgctgagt ggataaagga acccaagaag gaggtcccct ttgatagatt aaaacgcaag 2461 ggggggaaga aataacggcc gccgcggaaa ggaaaggagg aaagaaataa tggctcgtgt 2521 acagtttaaa caacgtgaat ctactgacgc aatctttgtt cactgctcgg ctaccaagcc 2581 aagtcagaat gttggtgtcc gtgagattcg ccagtggcac aaagagcagg gttggctcga 2641 tgtgggatac cactttatca tcaagcgaga cggtactgtg gaggcaggac gagatgagat 2701 ggctgtaggc tctcacgcta agggttacaa ccacaactct atcggcgtct gccttgttgg 2761 tggtatcgac gataaaggta agttcgacgc taactttacg ccagcccaaa tgcaatccct 2821 tcgctcactg cttgtcacac tgctggctaa gtacgaaggc gctgtgcttc gcgcccatca 2881 tgaggtggcg ccgaaggctt gcccttcgtt cgaccttaag cgttggtggg agaagaacga 2941 actggtcact tctgaccgtg gataaccgcg gacatgtcgt ggataattaa ttgaactcac 3001 taaagggaga ccacagcggt ttccctttgt tcgcattgga ggtcaaataa tacatgtcga 3061 cgaggtcaaa taatgcgcaa gtcttataaa caattctata aggctccgag gaggcatatc 3121 caagtgtggg aggcagccaa tgggcctata ccaaaaggtt attatataga ccacattgac 3181 ggcaatccac tcaacgacgc cttagacaat ctccgtctgg ctctcccaaa agaaaactca 3241 tggaacatga agactccaaa gagcaatacc tcaggactaa agggactgag ttggagcaag 3301 gaaagggaga tgtggagagg cactgtaaca gctgagggta aacagcataa ctttcgtagt 3361 agagatct //