AlignACE 3.0 10/20/99 AlignACE2 -i BS/BS_fusions045_300.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944242221 numcols = 10 undersample = 1 oversample = 1 Input sequences: #0 flgB 300 flagellar basal-body rod protein #1 fliF 45 flagellar basal-body M-ring protein #2 fliH 117 flagellar assembly protein #3 fliK 160 fliK #4 flgE 21 flagellar hook protein #5 fliL 251 flagellar protein #6 fliM 33 flagellar motor switch protein #7 cheY 25 two-component response regulator #8 flhA 32 flagella-associated protein #9 cheW 21 cheW #10 sigD 22 RNA polymerase sigma-28 factor (sigma-D) #11 ylxL 28 ylxL #12 rpsB 143 ribosomal protein S2 #13 tsf 101 elongation factor Ts #14 panB 245 ketopantoate hydroxymethyltransferase #15 ypjH 31 alternate gene name: jojH; similar to lipopolysaccharide biosynthesis-related protein #16 ypjD 300 alternate gene name: jojD #17 ypfD 232 alternate gene name: jofD; similar to ribosomal protein S1 homolog #18 cmk 78 cytidylate kinase #19 ypfB 44 alternate gene name: jofB #20 ypfA 92 alternate gene name: jofA #21 ypeB 34 alternate gene name: joeB, yzuA; similar to hypothetical proteins #22 sleB 138 spore cortex-lytic enzyme #23 ypdC 119 similar to hypothetical proteins #24 ypdA 108 similar to thioredoxin reductase #25 ypcA 155 similar to glutamate dehydrogenase #26 ypbH 158 similar to negative regulation of competence MecA homolog #27 ypbG 85 similar to hypothetical proteins #28 ypbF 62 ypbF #29 ypbD 59 ypbD #30 ypbB 265 ypbB Motif 1 GCCGAAAAGAAAGGAGAAAAAACAGAAATT 0 70 1 TTCTCCACAAAAGGAAAAAAGAAAACTTTC 2 34 1 CAGCCTGCAAAAGGTGAGAATGATCAATAC 2 78 0 CTTTCAGAACAAGGAAAGGGAACTCCTAAT 3 118 1 GCAATGGATCAAGGAATAGAGGAACCGGA 5 232 1 ACAGAATACGGAGGTGAGGAAA 6 21 1 CGAAACACAAGGAGAGAGATAGATT 7 8 1 TTCGATTTAAAAGGAGAGAAAAAACAGC 8 14 1 GACCTAAGCGGAGGAAAAAAACCATTATAT 12 109 1 ATTATATTAGGAGGAAATAAC 12 132 1 CCTATTCAAAAGGTGATAAGAGGGACTGC 13 9 1 TTCTTGAAAAAAGGTGATAAAAGGCAGTCC 13 32 0 CTCATGTTTAGAGGAGATGATCTGCCGTTT 14 214 0 TAAACATGAGGAGGAGAAAAC 14 234 1 TATCTAATGGAAGGAAAAGGGGTTTTGTGT 16 172 0 ACAATCCTTAGAGGAGAAAAGAGCAAGGAG 18 51 1 AGAAAAGAGCAAGGAGAGGAATT 18 65 1 AAACAGGAGGAAAGGACTAAATGTCT 20 6 1 TAATGAAAAAAAGGAAAAGACATTTAGTCC 20 23 0 GAGGGATAACAAGGAAAGAGTGTATAAAAA 22 59 1 TAGGAATATAAAGGAAAGAGGTTGCCTG 23 101 1 GAAAATGGACAAGGTGTGAAGCGT 28 48 1 CAATAAGTAAGAGGAATAGGTGTTAAATTG 30 68 0 ********** MAP Score: 35.9641 Motif 2 TTTAATAAATTTTGCATTTTTCTTCAAAAAGT 0 29 1 GGCTTTTTTGTGTGCAGTTTTTATGTTCTGAG 22 30 1 TTTAAGCACGTTTGCTGTTTTCTTTTTCATCC 16 218 0 AAACAGAAATTCTGCTATTTTCAGGCTTATAT 0 89 1 GATGCATTCGTATGCTCTTTTTGTTTTTTTAA 23 25 1 AAATCGTTGATTTGCTCTTTTTATTTTAACAG 30 216 0 GTATAGAAAGTTTTCTTTTTTCCTTTTGTGGA 2 37 0 GAGGAGATGATCTGCCGTTTTCTTCTGCAAGC 14 202 0 ACTTTTGCTTTATGCCCTTTTCCACATCAGCC 16 14 0 ACTGCTGAAATCAGCAGTTTTCCGTTGCATTC 25 10 0 ACTAAATGTCTTTTCCTTTTTTTCATTACGTG 20 25 1 ACTGCTGATTTCAGCAGTTTTTTTTCGTTAAA 25 24 1 GCATGTTATATGTTCAGCTTTCAAACCGTTTT 17 171 1 AATTTCTGTTTTTTCTCCTTTCTTTTCGGCAT 0 68 0 TTATTCATCAATTTTTCACCCTTTTT 18 4 1 CGAGAAGGATTCTTCACTTTCTAAAGTTCGGC 14 150 0 TCACTTCATATTTTCTATTTCCGAATAAAAAA 24 60 0 CCTCCTAGAATCTTCTGTTTCTCACATGCTCC 25 124 0 AGACAAGCACAATGCAGTTTTTATTGCCATAC 26 30 0 GGACTGCCTTTTATCACCTTTTTTCAAGAAAA 13 32 1 GCAGTCCCTCTTATCACCTTTTGAATAGG 13 7 0 AACAGCTTCTTCATCTTCTTTTACTACAAACT 5 158 0 ACTTACCTCCATTTCAGTTTTTTTCACCCTCA 0 274 0 TAAACAAGAATCATCTATTTCTCCACAAAAGG 2 16 1 GGATGGCAAATGCCACTTTTTTTGAATTTT 17 8 1 CAGAATTAGGAGTTCCCTTTCCTTGTTCTGAA 3 120 0 CTAATTCTGAAGATCAGCTTTTAGCAG 3 143 1 * **** ***** MAP Score: 26.7959 Motif 3 GAAAGTTTTCTTTTTTCCTTTTGTGGAGAAAT 2 32 0 GGACTAAATGTCTTTTCCTTTTTTTCATTACG 20 23 1 GCACGTTTGCTGTTTTCTTTTTCATCCACTAT 16 213 0 ATTCGTATGCTCTTTTTGTTTTTTTAAGTGCA 23 30 1 GGTATTATTTTTATTTTACGTTCATAT 28 5 1 GTTGATTTGCTCTTTTTATTTTAACAGATTTC 30 211 0 GCCATACGGATTTTTGCTTTTTAGAAG 26 5 0 ATCATAGGAGATTTTTTATTTTTATGCAAATC 24 16 0 TAAAAAACATATTTTTTATTTTAATCGGAGCG 16 120 0 ATTTTAATAAATTTTGCATTTTTCTTCAAAAA 0 27 1 CCATTGCAAATATTTGTATTTTTCGGTAGAAA 5 207 0 ACTCCTGGCTACTTTTCATGTTTTTAGCGGCA 3 47 0 TTTCACTTCATATTTTCTATTTCCGAATAAAA 24 62 0 TTTTGTGTGCAGTTTTTATGTTCTGAGGGATA 22 35 1 AAACGTTATGTTTTTCCATGTTTTTTAACGAA 25 47 0 TTTTATACACTCTTTCCTTGTTATCCCTCAGA 22 56 0 AAAATAGCAGAATTTCTGTTTTTTCTCCTTTC 0 78 0 ATTTTTCGATTTAAAAGGAGAG 8 0 1 CGGAGCGGCAATTTTTTCATTTGGCTTGGTTC 16 95 0 GATAGAAACGTCTTTTTTTATTGTCCGTCTTA 27 30 1 * ***** **** MAP Score: 22.4218 Motif 4 TTAGAGGAGAAAAGAGCAAGGAGAGGAATT 18 58 1 CAAAAATGCCGAAAAGAAAGGAGAAAAAACAGA 0 63 1 CTCTTGTTTAAACATATAAGGAGGAATACAA 13 80 1 TCTGAGGGATAACAAGGAAAGAGTGTATAAAAA 22 56 1 CTATCTAATGGAAGGAAAAGGGGTTTTGTGTGA 16 170 0 CGAAACACAAGGAGAGAGATAGAT 7 1 1 GAACTTTCAGAACAAGGAAAGGGAACTCCTAAT 3 115 1 TGCACTTAAAAAAACAAAAAGAGCATACGAATG 23 29 0 GAAATCTGTTAAAATAAAAAGAGCAAATCAACG 30 211 1 TGAATTAGCTAACATGTAAGAGGATGATAGGAG 16 267 1 ACATCATTACAATAAGTAAGAGGAATAGGTGTT 30 74 0 GATAAGTTCTAAAAAGAATGGAGAGTTTTTT 27 64 1 ATTTCTCCACAAAAGGAAAAAAGAAAACTTTCT 2 32 1 CCTATTCAAAAGGTGATAAGAGGGACTGCCTT 13 9 1 CAGATATGAGAAAGCATAAAAAGAGGTGTGATA 21 10 1 TTAAGGTATTAGGGGGATAACA 10 2 1 GAGGGGCTGATGTGGAAAAGGGCATAAAGCA 16 8 1 TAAAGCACGTAATGAAAAAAAGGAAAAGACATT 20 29 0 ATTTTTCGATTTAAAAGGAGAGAAAAAACA 8 7 1 AATCTCCTATGATAAAATAGGAGATTTTTTTAT 24 35 1 TTACTCTGTCAAATGGTAAGAAGTTTGTAGTAA 5 137 1 GTTTGTAGTAAAAGAAGATGAAGAAGCTGTTCT 5 159 1 TTCTTGAAAAAAGGTGATAAAAGGCAGTCCCTC 13 29 0 TAGCAATGAAAATGGACAAGGTGTGAAGCGT 28 41 1 TGTAAGAAATAACAGGCATAAAGTCTATGAAGT 0 205 0 GCTTGATCATGATGTGCTTGGGGGCGAACA 15 11 1 GGGTGAAAAAAACTGAAATGGAGGTAAGTGGAT 0 277 1 TTCGTTGAAAAATTCAAAAAAAGTGGCATTTGC 17 15 0 ** * * ****** MAP Score: 21.2191 Motif 5 ACGCTTCACACCTTGTCCATTTTCATTGCTACA 28 39 0 TTATTCATCAATTTTTCACCCTTTTTCATAAAGTT 18 5 1 GAGTTTCATCCCTCTGTCCCAGTCCTTTTTTGGATCAAGG 14 110 0 CAACGGAAAACTGCTGATTTCAGCAGTTTTTTTTCGTTAA 25 15 1 TTTCTCCAAGCATCACACAAAACCCCTTTTCCTTCCATTA 16 158 1 TGGTTTTTTTCCTCCGCTTAGGTCATTTTTGTACAGAACT 12 93 0 ATAAGAGGGACTGCCTTTTATCACCTTTTTTCAAGAAAAA 13 25 1 GGAGCATATGATGCATTCGTATGCTCTTTTTGTTTTTTTA 23 16 1 GGAGGCGAGTAATCGCTTCTCCGCTGTTTTATGATTAAAG 5 19 1 AGGCAGACTGCTGCAATGTCTATCTATTTTAATAATAGGT 14 73 0 CTTATGTGATAAGCATTCTCAATCATTTTTCTGTTGAAAT 30 116 0 TTCAATCCAGCCTCAGACATAAGCCAGTTTTGAAAACTCC 3 74 0 GAAAGCTGAACATATAACATGCCCGCTTTTAGCCGAATAT 17 153 0 AATTCCTCTCCTTGCTCTTTTCTCCTCTAAG 18 57 0 AAGCCGCACAGCAACCGTGCGGCTTTTTTGTGTGCAGT 22 8 1 TCAATACGCACCTCTTGTATAGAAAGTTTTCTTTTTTCCT 2 45 0 TCCTGACAAAAATCGTTGATTTGCTCTTTTTATTTTAACA 30 217 0 CCTTTCTTTTCGGCATTTTTGAAACTTTTTGAAGAAAAAT 0 44 0 AGGTATTACACTTTTGCTTTATGCCCTTTTCCACATCAGC 16 15 0 ATCCACTTACCTCCATTTCAGTTTTTTTCACCCTC 0 275 0 TGTATTAAAGAATCATCCAAAAAAGTTTTTTGAATGATCA 17 114 0 * ** * * * **** MAP Score: 18.0792 Motif 6 TTTTTGAAGAAAAATGCAAAATTTATTAAAAT 0 27 0 AAAATGCCGAAAAGAAAGGAGAAAAAACAGAA 0 65 1 CGATTTAGAGAAAGAGTGGAATGACCGGGGGT 1 19 1 ATTTCTCCACAAAAGGAAAAAAGAAAACTTTC 2 32 1 TCTGCCGCTAAAAACATGAAAAGTAGCCAGGA 3 45 1 AGGAACTTTCAGAACAAGGAAAGGGAACTCCT 3 113 1 TTGTAGTAAAAGAAGATGAAGAAGCTGTTCTG 5 161 1 CGAAACACAAGGAGAGAGATAGATT 7 3 1 TTTCGATTTAAAAGGAGAGAAAAAACAGC 8 13 1 AAATGACCTAAGCGGAGGAAAAAAACCATTAT 12 105 1 CCTATTCAAAAGGTGATAAGAGGGACTGC 13 7 1 TTTTCTTGAAAAAAGGTGATAAAAGGCAGTCC 13 32 0 GCCGAACTTTAGAAAGTGAAGAATCCTTCTCG 14 150 1 ACTTTATGAAAAAGGGTGAAAAATTGATGAAT 18 12 0 AGAGGAGAAAAGAGCAAGGAGAGGAATT 18 60 1 AAACAGGAGGAAAGGACTAAATG 20 1 1 CACGTAATGAAAAAAAGGAAAAGACATTTAGT 20 25 0 ATTGAATGCGAAAGAGTGAAGTCA 20 78 1 GATATGAGAAAGCATAAAAAGAGGTGTGATAA 21 12 1 GTTATCCCTCAGAACATAAAAACTGCACACAA 22 37 0 TCTGAGGGATAACAAGGAAAGAGTGTATAAAA 22 56 1 TGCACTTAAAAAAACAAAAAGAGCATACGAAT 23 30 0 TCGGAAATAGAAAATATGAAGTGAAATGCCAA 24 68 1 TTTTCGTTAAAAAACATGGAAAAACATAACGT 25 45 1 CTTCTAAAAAGCAAAAATCCGTATGGC 26 5 1 TAAGTTCTAAAAAGAATGGAGAGTTTTTT 27 66 1 TTAAATTGATTAAATATAAAGATTGATCCATT 30 44 0 GAAATCTGTTAAAATAAAAAGAGCAAATCAAC 30 211 1 **** * ***** MAP Score: 13.4903 Motif 7 AAAAAAACTGAAATGGAGGTAAGTGGAT 0 282 1 AAACATCTGGGGGAATATATT 4 4 1 GGAGGGAGGGGAGGCGAGTAATCGCTTCTC 5 5 1 ATTTGACAGAATACGGAGGTGAGGAAA 6 16 1 CGAAACACAAGGAGAGAGATAGATT 7 6 1 TTTCGATTTAAAAGGAGAGAAAAAACAGC 8 13 1 TTAAGGTATTAGGGGGATAACA 10 7 1 AAAATGACCTAAGCGGAGGAAAAAAACCATTATAT 12 104 1 AAACCATTATATTAGGAGGAAATAAC 12 127 1 GTTTAAACATATAAGGAGGAATACAA 13 85 1 TCCTCTAAACATGAGGAGGAGAAAAC 14 229 1 ATCATGATGTGCTTGGGGGCGAACA 15 16 1 AACGCTATCTAATGGAAGGAAAAGGGGTTTTGTGT 16 172 0 AAACAGGAGGAAAGGACTAAATGTCT 20 1 1 AAAAATTTGCAGTAGGAGGCTTGAAAAG 22 120 1 TGCACAGATCATATGAAGGTGTATACTATTCTCTG 25 85 1 * ***** *** * MAP Score: 8.69174 Motif 8 TTTTATCACCTTTTTTCAAGAAAAATGTGTAATA 13 40 1 ATTTTTGAAACTTTTTGAAGAAAAATGCAAAATT 0 36 0 TTTTTCCATGTTTTTTAACGAAAAAAAACTGCTG 25 35 0 AAGATCGCAGCTTTCTACCGAAAAATACAAATAT 5 196 1 CTTAGGTCATTTTTGTACAGAACTGCCGCCTGCA 12 83 0 TCTTTTTTCCTTTTGTGGAGAAATAGATGATTCT 2 22 0 TTTTCTCTCCTTTTAAATCGAAAAAT 8 2 0 AACATGCCCGCTTTTAGCCGAATATGTATTAAAG 17 144 0 AATCAACGATTTTTGTCAGGAAGAATGTAGGTGG 30 236 1 CAAACCTGTCCTTTTATTAGAAGTTAATACTAAT 17 68 1 TGAGGACATTTTTTTACACGAACTTCATAGACTT 0 184 1 TAGGAGATTTTTTTATTCGGAAATAGAAAATATG 24 52 1 AAAGCTGCGATCTTTTCCAGAACAGCTTCTTCAT 5 176 0 CCCTCAATATCCTTGTCGAGAATTGTAAAACTAT 0 246 0 AAACTCTCCATTCTTTTTAGAACTTATCAATAAG 27 58 0 AAAAAGAAAACTTTCTATACAAGAGGTGCGTATT 2 49 1 **** * **** * MAP Score: 8.39331 Motif 9 AATAAATTTTGCATTTTTCTTCAAAAAGTTTC 0 32 1 ATAATTGTGAGGACATTTTTTTACACGAACTT 0 177 1 CCCGGTCATTCCACTCTTTCTCTAAATCGTCA 1 16 0 ATTAGCCGGACCTTTCGTCGAGACCGACG 3 7 1 GGAAAAGATCGCAGCTTTCTACCGAAAAATAC 5 192 1 CTGCCTTTTATCACCTTTTTTCAAGAAAAATG 13 35 1 CCTGCGAACTGCACCTATTATTAAAATAGATA 14 61 1 GAGATGATCTGCCGTTTTCTTCTGCAAGCCAA 14 199 0 TCACACAAAACCCCTTTTCCTTCCATTAGATA 16 170 1 AAGCACGTTTGCTGTTTTCTTTTTCATCCACT 16 215 0 GAGGATGATAGGAGGTTTCGTTCA 16 286 1 ATGGCAAATGCCACTTTTTTTGAATTTTTCAA 17 12 1 CAGCAACCGTGCGGCTTTTTTGTGTGCAGTTT 22 18 1 TTTTTTGTGTGCAGTTTTTATGTTCTGAGGGA 22 33 1 GCATTCGTATGCTCTTTTTGTTTTTTTAAGTG 23 28 1 TGATAAAATAGGAGATTTTTTTATTCGGAAAT 24 44 1 GCTGATTTCAGCAGTTTTTTTTCGTTAAAAAA 25 27 1 CAAGCACAATGCAGTTTTTATTGCCATACGGA 26 27 0 AATGGGGCGTTTTCTCAAACGATAGA 27 4 1 TAAAAAGAATGGAGAGTTTTTT 27 73 1 GAACAATCTGGGAGGTTTTATTC 30 1 0 GATGTTGCTGCCACATTTCAACAGAAAAATGA 30 102 1 **** **** ** MAP Score: 4.38091