AlignACE 3.0 10/20/99 AlignACE2 -i MJ/MJ_profile017_300.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944243008 numcols = 10 undersample = 1 oversample = 1 Input sequences: #0 MJ0034 141 conserved hypothetical protein #1 MJ0035 269 ABC transporter subunit #2 MJ0189 300 SSU ribosomal protein S13P (rpsM) #3 MJ0190 57 SSU ribosomal protein S4P (rpsD) #4 MJ0191 25 SSU ribosomal protein S11P (rpsK) #5 MJ0193 77 LSU ribosomal protein L18E #6 MJ0194 31 LSU ribosomal protein L13P (rplM) #7 MJ0196 57 DNA-directed RNA polymerase, subunit N (rpoN) #8 MJ0197 140 DNA-directed RNA polymerase, subunit K (rpoK) #9 MJ0198 200 M. jannaschii predicted coding region MJ0198 #10 MJ0623 300 conserved hypothetical protein #11 MJ0823 300 CODH nickel-insertion accessory protein CooC (cooC) Motif 1 ATAGGTATCGCAATAGGAGTTTCTCCTATGC 0 54 1 ATTCCCTCTCCTCTGGGACTTTTTTGTAGCA 0 94 0 TTCTCTCCCTCTGGGATTTTAATTTTATT 0 122 0 TTTTTTATTTCCATAGGGCTTCGCCCTATTG 1 51 1 TACTAGACTACAGTGGGGCTGAACGTAGTGA 1 85 1 TGAGATACCCGAGTGGGGCTTCACTACGTTC 1 105 0 TCGGGTATCTCAATAGGGGTTTCCCTATGGG 1 124 1 AGGGGTTTCCCTATGGGTCTGAAGAGACCTG 1 138 1 CCCGGCCAAGGCGTGGGACTGGAGATCCCAT 2 165 1 ACTGGAGATCCCATGGGGCTTTGCCCCGCGG 2 182 1 GGGCTTTGCCCCGCGGGGGTTCAAATCCCCC 2 197 1 AAGTGGCGCGGAGGGGGGGATTTGAACCCCC 2 211 0 TTTAACGGGGCCGTGGGGTAGCCTGGATATC 8 35 1 ATGGTGGGGCCGCCGGGACTTGAACCCGGGT 8 88 0 TTTTTAACTACAGTGGGGCTGAACGTAGTGA 9 13 1 CTATACCTCAGAGTGGAGCTTCACTACGTTC 9 33 0 TTTGTTAAATCCGTAGGATTTCATCTGATAG 9 126 1 CATGGCTAGGCCGGGGGGTTGGGCGTCCCCT 10 67 1 GAAGGAAGGACTGGAGGACATGCCGCCCCCA 10 135 0 AGGTCTCGTCCCGTGGGGCTCGGCGGTGGGG 10 181 1 TGGGGCTCGGCGGTGGGGGAGCATCTCCTGT 10 194 1 GGAGCATCTCCTGTAGGGGAGATGTAACCCC 10 211 1 CCTTCCGGGCCTGGCGGGGTTCGGCAGGTAA 10 244 0 TTATAAAAATATGTGGGGGTTTATAATGAAT 11 243 1 * ********* MAP Score: 35.6679 Motif 2 AATAGATATTAAAAAATAAAAAGAAGTGGCGC 2 233 0 TCGCTCTATTAAAAAATAAAAAAAGTTACAAA 11 148 1 ATATAAAAAGAATATATAAAAAATGAAACACG 2 111 1 AACTTTTTTAAATGGATAAAAATTAATTTTGA 11 187 1 GTATTGTGGGAATATATAAAAAGAATATATAA 2 98 1 TCACCTCTGAAATATATAAAATATCAAATGGT 8 114 0 GCCCCGTTAAAAAGAATAATAAGTTTAAAAAT 8 14 0 TTAATAGCTCATACAATAAAAAGATTACCATA 1 198 0 TACCATATCGATAAAATAAAAATAACAAAAAC 1 173 0 AAAATAAAAGAAAAGATAATATCTTTCCAAAA 7 24 0 TACAAAATTTAATTTATAATATCGCTCTATTA 11 127 1 CATGCACACCAATTAATAATATAATAGGACTT 10 39 0 AACCGAAAATAATATATAATATGGTATCCATT 2 52 1 ATTTAGTAGAAACTTATAAAAATATGTGGGGG 11 230 1 TATAACAAAGATATAATAAAATTTTTCATTCA 11 97 0 GAGAAGGCATAAACAATTAAATTATAATTATT 9 157 1 AAAAATTTCTAATTCATTATAAACCCCCACAT 11 253 0 AAATTATAAATAGGTCTTTTGT 1 257 0 CACCACAAACTATATATAAAAAGTCCTATTAT 10 19 1 AGGAGAGGGAATAAAATTAAAATCCCAGAGGG 0 113 1 CACCTCAATTAAAAAATAATTATAATTTAATT 9 171 0 *** ******* MAP Score: 25.1928 Motif 3 TAAAAAACATGCCAGGTCTCTTTGGACTGGCGACC 1 23 0 ATCCCAATAGGGCGAAGCCCTATGGAAATAAAAAA 1 51 0 TGAACGTAGTGAAGCCCCACTCGGGTATCTCAATA 1 104 1 GCCCGGCCAAGGCGTGGGACTGGAGATCCCATGGG 2 164 1 CCCCCGCGGGGCAAAGCCCCATGGGATCTCCAGTC 2 181 0 AAAAAGAAGTGGCGCGGAGGGGGGGATTTGAACCC 2 213 0 TATTCTTTTTAACGGGGCCGTGGGGTAGCCTGGAT 8 28 1 AGCCTGGATATCCTGTGCGCTTGGGGGGCGTGCGA 8 54 1 GCGCTTGGGGGGCGTGCGACCCGGGTTCAAGTCCC 8 70 1 AATATCAAATGGTGGGGCCGCCGGGACTTGAACCC 8 92 0 CTGAGGTATAGTAATCGCCCATGGGCGAGTAATGA 9 53 1 TGGTGTGCATGGCTAGGCCGGGGGGTTGGGCGTCC 10 60 1 CTCCCCCACCGCCGAGCCCCACGGGACGAGACCTC 10 180 0 CGGTGGGGGAGCATCTCCTGTAGGGGAGATGTAAC 10 204 1 GTTGCTCCCTTCCGGGCCTGGCGGGGTTCGGCAGG 10 247 0 TAGGCAGGACGTCGGCGCTCACGGGG 10 284 1 * ** *** * *** MAP Score: 22.5613 Motif 4 ATAATTTACACCTCCGAGCGAAGCGAGGAGGTGTTATAGGTAT 0 19 1 ATAGGTATCGCAATAGGAGTTTCTCCTATGCTGAGGAAAATGC 0 54 1 TTTTTTATTTCCATAGGGCTTCGCCCTATTGGGATACTAGACT 1 51 1 TACTAGACTACAGTGGGGCTGAACGTAGTGAAGCCCCACTCGG 1 85 1 TAGGGAAACCCCTATTGAGATACCCGAGTGGGGCTTCACTACG 1 108 0 ACTGGAGATCCCATGGGGCTTTGCCCCGCGGGGGTTCAAATCC 2 182 1 ATATCCTGTGCGCTTGGGGGGCGTGCGACCCGGGTTCAAGTCC 8 61 1 GGGTTCAAGTCCCGGCGGCCCCACCATTTGATATTTTATATAT 8 92 1 TTTTTAACTACAGTGGGGCTGAACGTAGTGAAGCTCCACTCTG 9 13 1 TCGGCCCCCGCATAAGGGCGATTTCGGGTTACAGGGGACGCCC 10 87 0 GGGCCGAAAACTTGGGGGCGGCATGTCCTCCAGTCCTTCCTTC 10 123 1 CCGCCGAGCCCCACGGGACGAGACCTCATCGAGGAGTCTGGGA 10 164 0 TGGGGCTCGGCGGTGGGGGAGCATCTCCTGTAGGGGAGATGTA 10 194 1 CCGTTGCTCCCTTCCGGGCCTGGCGGGGTTCGGCAGGTAAAGG 10 241 0 * **** ** ** * MAP Score: 18.6616 Motif 5 GAATGAAAAATTTTATTATATCTTTGTTATA 11 98 1 ATAATAGGACTTTTTATATATAGTTTGTGGT 10 20 0 TTATATATTCTTTTTATATATTCCCACAATA 2 99 0 CGTGTTTCATTTTTTATATATTCTTTTTATA 2 112 0 TAAAAATTAATTTTGATATATCCAAATATTT 11 203 1 AGATATTATCTTTTCTTTTATTTTGGGTGAG 7 32 1 TTTTTGTTATTTTTATTTTATCGATATGGTA 1 174 1 ATGGTAATCTTTTTATTGTATGAGCTATTAA 1 199 1 ATCCAAAGGATTTTGTTAAATCCGTAGGATT 9 115 1 CATTTGTAACTTTTTTTATTTTTTAATAGAG 11 151 0 ACCATTTGATATTTTATATATTTCAGAGGTG 8 114 1 CGCCACTTCTTTTTATTTTTTAATATCTATT 2 234 1 TTCAATAATTTTTTGTTGAATGTTATGCTAA 3 27 0 AGTGTTTCACCTTTAATTTATATTT 4 4 0 GTTATACAAAATTTAATTTATAATATCGCTC 11 123 1 ATGTTTGCAACTTTTTTAAATGGATAAAAAT 11 179 1 AATTATAATTATTTTTTAATTGAGGTGGATG 9 176 1 TCCTTCAAACCTTTTATAATTATTATAAGGT 5 40 0 **** ****** MAP Score: 18.583 Motif 6 TTTAATTTTATTCCCTCTCCTCTGGGACTTTTTTGT 0 98 0 GGGAATAAAATTAAAATCCCAGAGGGAGAGAA 0 119 1 ATCCCAATAGGGCGAAGCCCTATGGAAATAAAAAAC 1 50 0 GCTGAACGTAGTGAAGCCCCACTCGGGTATCTCAAT 1 102 1 TATCTCAATAGGGGTTTCCCTATGGGTCTGAAGAGA 1 129 1 GGAGGTAGCCTAGCCCGGCCAAGGCGTGGGACTGGA 2 152 1 GGCGTGGGACTGGAGATCCCATGGGGCTTTGCCCCG 2 174 1 AGGGGGGGATTTGAACCCCCGCGGGGCAAAGCCCCA 2 195 0 AAAATAAAAAGAAGTGGCGCGGAGGGGGGGATTTGA 2 217 0 TTATTCTTTTTAACGGGGCCGTGGGGTAGCCTGGAT 8 27 1 AGCCTGGATATCCTGTGCGCTTGGGGGGCGTGCGAC 8 54 1 AAATATCAAATGGTGGGGCCGCCGGGACTTGAACCC 8 92 0 CTGAGGTATAGTAATCGCCCATGGGCGAGTAATGAA 9 53 1 TTGGTGTGCATGGCTAGGCCGGGGGGTTGGGCGTCC 10 59 1 CCTCGATGAGGTCTCGTCCCGTGGGGCTCGGCGGTG 10 173 1 CGTTGCTCCCTTCCGGGCCTGGCGGGGTTCGGCAGG 10 247 0 TAGGCAGGACGTCGGCGCTCACGGGG 10 284 1 * * **** **** MAP Score: 17.3047 Motif 7 GTTTTATAGTAAATAGATATTAAAAAATAAAAAGAAGT 2 238 0 TTTGTATAACAAAGATATAATAAAATTTTTCATTCAGA 11 95 0 TTATTAAATGAAACACTTAGCATAACATTCAACAAAAA 3 11 1 TGATATATCCAAATATTTAGTAGAAACTTATAAAAATA 11 216 1 CACCTCAATTAAAAAATAATTATAATTTAATTGTTTAT 9 165 0 ATCGCTCTATTAAAAAATAAAAAAAGTTACAAATGTTT 11 147 1 TCACCCAAAATAAAAGAAAAGATAATATCTTTCCAAAA 7 24 0 ACGGCCCCGTTAAAAAGAATAATAAGTTTAAAAATCTA 8 11 0 ATCGATAAAATAAAAATAACAAAAACATGCCAGGTCTC 1 161 0 GAATATATAAAAAGAATATATAAAAAATGAAACACGTT 2 107 1 TAACCTTACTAAAAACCGAAAATAATATATAATATGGT 2 39 1 TATGCTGAGGAAAATGCTACAAAAAAGTCCCAGAGGAG 0 80 1 TTCAAACCTTTTATAATTATTATAAGGTTTGACAAATA 5 30 0 TGTGGGGGTTTATAATGAATTAGAAATTTTTTCTTTAA 11 254 1 CTAATCACCTTCAATAATTTTTTGTTGAAT 3 37 0 GATTGACGGTATATACCTTCGACAAACTACTATATAAA 11 25 1 GCACCACCACAAACTATATATAAAAAGTCCTATTATAT 10 15 1 TTGTTATACAAAATTTAATTTATAATATCGCTCTATTA 11 121 1 *** * ** * ** * MAP Score: 17.2001 Motif 8 CTTTTTAACGGGGCCGTGGGGTAGCCTGGATATCCTGTG 8 32 1 CGTGCGACCCGGGTTCAAGTCCCGGCGGCCCCACCATTT 8 82 1 TCGGCGGTGGGGGAGCATCTCCTGTAGGGGAGATGTAAC 10 200 1 AGGCCCGGAAGGGAGCAACGGTAGGCAGGACGTCGGCGC 10 263 1 TGCTCCCTTCCGGGCCTGGCGGGGTTCGGCAGGTAAAGG 10 241 0 ACTCCTCGATGAGGTCTCGTCCCGTGGGGCTCGGCGGTG 10 170 1 CGTTTCAGAGCGGAGGTAGCCTAGCCCGGCCAAGGCGTG 2 141 1 TTATTAATTGGTGTGCATGGCTAGGCCGGGGGGTTGGGC 10 52 1 GAGATCCCATGGGGCTTTGCCCCGCGGGGGTTCAAATCC 2 186 1 TGGATATCCTGTGCGCTTGGGGGGCGTGCGACCCGGGTT 8 58 1 AAAGCCCCATGGGATCTCCAGTCCCACGCCTTGGCCGGG 2 165 0 CCTTATGCGGGGGCCGAAAACTTGGGGGCGGCATGTCCT 10 113 1 AAAAAATAAAAAGAAGTGGCGCGGAGGGGGGGATTTGAA 2 216 0 CGCCCTATTGGGATACTAGACTACAGTGGGGCTGAACGT 1 72 1 *** ** * * * ** MAP Score: 16.5331 Motif 9 CCTCCTCGCTTCGCTCGGAGGTGTAAATTATT 0 18 0 CCTCCGAGCGAAGCGAGGAGGTGTTATAGGTA 0 29 1 TTCTCTCCCTCTGGGATTTTAATTTTA 0 124 0 TCTATCACCCGATGGTCGCCAGTCCA 1 4 1 CTACGTTCAGCCCCACTGTAGTCTAGTATCCC 1 81 0 CGTAGTGAAGCCCCACTCGGGTATCTCAATAG 1 108 1 GGACTGGAGATCCCATGGGGCTTTGCCCCGCG 2 180 1 TGGGGCTTTGCCCCGCGGGGGTTCAAATCCCC 2 195 1 GTTTGAAGGAAAACACGGTGATATAT 5 61 1 AACTGGATTAAAACACGGTGATAGTT 6 15 1 TATCTCACCTCTGAAATATATAAAATA 8 123 0 CTACGTTCAGCCCCACTGTAGTTAAAAACAA 9 9 0 TAGTGAAGCTCCACTCTGAGGTATAGTAATCG 9 38 1 CACCGCCGAGCCCCACGGGACGAGACCTCATC 10 177 0 **** *** *** MAP Score: 6.0146 Motif 10 AGCATAGGAGAAACTCCTATTGCGATACCT 0 56 0 ATGCTACAAAAAAGTCCCAGAGGAGAGGGA 0 93 1 CCAATAGGGCGAAGCCCTATGGAAATAAAA 1 53 0 ACCCATAGGGAAACCCCTATTGAGATACCC 1 126 0 AACATTCACAAAAGACCTATTTATAATTT 1 250 1 CCCGCGGGGCAAAGCCCCATGGGATCTCCA 2 184 0 CGGATTTAACAAAATCCTTTGGATTTTGTA 9 109 0 CCTATCAGATGAAATCCTACGGATTTAACA 9 128 0 CTATATATAAAAAGTCCTATTATATTATTA 10 28 1 ********** MAP Score: 4.69349 Motif 11 TTGAGATACCCGAGTGGGGCTTCACTACGTT 1 106 0 GACTGGAGATCCCATGGGGCTTTGCCCCGCG 2 181 1 GGGGCTTTGCCCCGCGGGGGTTCAAATCCCC 2 196 1 AGAAGTGGCGCGGAGGGGGGGATTTGAACCC 2 213 0 ATATCCTGTGCGCTTGGGGGGCGTGCGACCC 8 61 1 ATGGTGGGGCCGCCGGGACTTGAACCCGGGT 8 88 0 CTAGGCCGGGGGGTTGGGCGTCCCCTGTAAC 10 72 1 GAGGTCTCGTCCCGTGGGGCTCGGCGGTGGG 10 180 1 CTCCCTTCCGGGCCTGGCGGGGTTCGGCAGG 10 247 0 *** ******* MAP Score: 1.71404 Motif 12 CACCTCCTCGCTTCGCTCGGAGGTGTAAATT 0 21 0 ATAGGGCTTCGCCCTATTGGGATACTAGACT 1 63 1 GGATACTAGACTACAGTGGGGCTGAACGTAG 1 82 1 CGTAGTGAAGCCCCACTCGGGTATCTCAATA 1 108 1 ATGGGGCTTTGCCCCGCGGGGGTTCAAATCC 2 194 1 CTTTTTAACGGGGCCGTGGGGTAGCCTGGAT 8 32 1 TGGATATCCTGTGCGCTTGGGGGGCGTGCGA 8 58 1 CCGGGTTCAAGTCCCGGCGGCCCCACCATTT 8 90 1 TTGTTTTTAACTACAGTGGGGCTGAACGTAG 9 10 1 TAGTGAAGCTCCACTCTGAGGTATAGTAATC 9 38 1 GTGTGCATGGCTAGGCCGGGGGGTTGGGCGT 10 62 1 ATGAGGTCTCGTCCCGTGGGGCTCGGCGGTG 10 178 1 GGGGGAGCATCTCCTGTAGGGGAGATGTAAC 10 208 1 ACCCCGCCAGGCCCGGAAGGGAGCAACGGTA 10 255 1 **** ****** MAP Score: 1.58549