Query gi|254780289|ref|YP_003064702.1| RNA polymerase sigma factor RpoD [Candidatus Liberibacter asiaticus str. psy62] Match_columns 682 No_of_seqs 267 out of 2830 Neff 7.9 Searched_HMMs 39220 Date Sun May 29 16:46:22 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780289.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 PRK05658 RNA polymerase sigma 100.0 0 0 1529.1 62.2 618 19-682 1-620 (620) 2 PRK05901 RNA polymerase sigma 100.0 0 0 878.3 41.3 384 22-681 14-397 (398) 3 PRK09210 RNA polymerase sigma 100.0 0 0 823.7 38.7 357 28-681 12-368 (368) 4 TIGR02997 Sig70-cyanoRpoD RNA 100.0 0 0 821.6 31.0 246 415-668 90-336 (336) 5 TIGR02393 RpoD_Cterm RNA polym 100.0 0 0 831.2 24.2 238 444-681 1-240 (240) 6 PRK07598 RNA polymerase sigma 100.0 0 0 732.4 38.6 254 421-682 155-408 (410) 7 PRK07406 RNA polymerase sigma 100.0 0 0 706.4 34.7 246 430-680 139-384 (385) 8 PRK07921 RNA polymerase sigma 100.0 0 0 668.4 34.6 240 441-680 80-319 (320) 9 COG0568 RpoD DNA-directed RNA 100.0 0 0 669.6 30.7 267 414-681 74-342 (342) 10 PRK05949 RNA polymerase sigma 100.0 0 0 650.0 34.4 245 430-681 82-326 (327) 11 PRK07405 RNA polymerase sigma 100.0 0 0 645.6 34.0 239 440-681 79-317 (318) 12 PRK05657 RNA polymerase sigma 100.0 0 0 645.0 27.6 234 444-677 90-323 (328) 13 TIGR02394 rpoS_proteo RNA poly 100.0 0 0 646.6 20.5 231 443-673 46-283 (292) 14 PRK06596 RNA polymerase factor 100.0 0 0 510.8 27.9 226 443-673 48-282 (284) 15 PRK07500 rpoH2 RNA polymerase 100.0 0 0 478.1 27.6 236 442-680 39-288 (289) 16 PRK07122 RNA polymerase sigma 100.0 0 0 478.3 24.9 236 425-669 21-260 (263) 17 PRK08583 RNA polymerase sigma 100.0 0 0 466.2 25.7 248 414-673 2-255 (257) 18 PRK08215 sporulation sigma fac 100.0 0 0 459.2 26.9 240 417-669 14-255 (257) 19 PRK07408 RNA polymerase sigma 100.0 0 0 455.4 25.1 234 428-670 12-250 (256) 20 PRK05572 sporulation sigma fac 100.0 0 0 448.8 25.0 235 421-669 11-247 (251) 21 PRK05911 RNA polymerase sigma 100.0 0 0 444.0 26.5 242 425-680 7-257 (257) 22 PRK06288 RNA polymerase sigma 100.0 0 0 438.7 26.4 239 421-669 7-254 (261) 23 PRK07670 RNA polymerase sigma 100.0 0 0 427.9 24.1 222 441-669 16-243 (250) 24 PRK06986 fliA flagellar biosyn 100.0 0 0 417.4 25.5 221 439-669 4-229 (234) 25 TIGR02392 rpoH_proteo alternat 100.0 0 0 419.0 21.2 252 414-669 8-275 (279) 26 PRK05803 sporulation sigma fac 100.0 0 0 406.9 21.8 209 405-669 13-224 (228) 27 PRK08301 sporulation sigma fac 100.0 0 0 403.0 20.5 192 422-669 39-233 (239) 28 PRK12427 flagellar biosynthesi 100.0 1.4E-45 0 378.8 22.7 221 432-669 2-227 (229) 29 TIGR02980 SigBFG RNA polymeras 100.0 0 0 387.1 13.1 219 442-669 2-226 (229) 30 TIGR02885 spore_sigF RNA polym 100.0 2.4E-39 6E-44 329.6 12.7 220 440-669 8-229 (231) 31 COG1191 FliA DNA-directed RNA 100.0 2.9E-36 7.4E-41 305.2 24.3 235 422-670 6-243 (247) 32 TIGR02479 FliA_WhiG RNA polyme 100.0 4.5E-36 1.2E-40 303.7 18.1 215 448-669 1-224 (227) 33 TIGR02850 spore_sigG RNA polym 100.0 4E-28 1E-32 241.0 21.5 235 422-669 16-252 (254) 34 TIGR02846 spore_sigmaK RNA pol 100.0 2.1E-28 5.4E-33 243.1 12.1 192 422-669 30-225 (228) 35 pfam04546 Sigma70_ner Sigma-70 99.9 2.4E-24 6.2E-29 211.1 20.2 209 160-417 1-210 (210) 36 TIGR02941 Sigma_B RNA polymera 99.9 1.5E-25 3.7E-30 220.7 14.0 240 422-671 10-254 (256) 37 TIGR02835 spore_sigmaE RNA pol 99.8 3.4E-20 8.5E-25 178.4 13.9 193 422-670 34-229 (234) 38 PRK08295 RNA polymerase factor 99.8 6.7E-19 1.7E-23 168.2 19.1 194 422-670 6-201 (209) 39 TIGR02937 sigma70-ECF RNA poly 99.8 1.9E-17 4.9E-22 156.7 14.8 159 444-669 2-160 (162) 40 PRK06759 RNA polymerase factor 99.7 1.8E-15 4.6E-20 141.1 15.7 149 444-670 5-153 (154) 41 pfam03979 Sigma70_r1_1 Sigma-7 99.5 3.4E-14 8.6E-19 131.1 7.2 63 24-86 2-64 (79) 42 pfam04539 Sigma70_r3 Sigma-70 99.5 1.3E-13 3.3E-18 126.4 6.4 77 527-603 1-77 (78) 43 PRK09652 RNA polymerase sigma 99.2 3.5E-09 8.8E-14 91.5 17.0 184 428-681 7-190 (192) 44 PRK09641 RNA polymerase sigma 99.2 7.5E-09 1.9E-13 88.8 17.4 180 425-669 3-182 (187) 45 PRK12519 RNA polymerase sigma 99.2 9.3E-09 2.4E-13 88.1 17.0 184 422-681 11-194 (194) 46 PRK11923 algU RNA polymerase s 99.1 3.5E-08 8.9E-13 83.6 17.0 188 423-681 3-191 (193) 47 PRK13919 putative RNA polymera 99.1 1.7E-08 4.3E-13 86.0 15.2 172 428-669 11-182 (187) 48 PRK09648 RNA polymerase sigma 99.0 7.6E-08 1.9E-12 80.9 17.7 175 423-669 5-183 (187) 49 PRK12513 RNA polymerase sigma 99.0 9.4E-08 2.4E-12 80.2 18.0 172 428-669 14-185 (194) 50 PRK11922 RNA polymerase sigma 99.0 1E-07 2.7E-12 79.8 17.9 186 420-669 10-195 (231) 51 PRK09646 RNA polymerase sigma 99.0 3.8E-08 9.6E-13 83.3 15.6 177 422-669 12-188 (194) 52 PRK12543 RNA polymerase sigma 99.0 1.3E-07 3.2E-12 79.1 18.0 171 426-669 5-175 (190) 53 PRK06811 RNA polymerase factor 99.0 1.3E-07 3.4E-12 79.0 17.5 168 428-669 4-174 (185) 54 PRK12534 RNA polymerase sigma 99.0 2E-07 5.1E-12 77.5 17.3 177 421-669 6-183 (187) 55 PRK05602 RNA polymerase sigma 98.9 2.2E-07 5.7E-12 77.2 16.9 168 427-669 7-174 (186) 56 PRK11924 RNA polymerase sigma 98.9 2.8E-07 7.1E-12 76.5 16.3 170 429-669 2-171 (180) 57 PRK12522 RNA polymerase sigma 98.9 3.3E-07 8.3E-12 75.9 16.4 172 441-681 1-172 (173) 58 PRK12514 RNA polymerase sigma 98.9 3.6E-07 9.2E-12 75.5 16.2 174 423-669 2-175 (179) 59 PRK12531 RNA polymerase sigma 98.9 5.1E-07 1.3E-11 74.4 16.9 178 423-669 10-187 (194) 60 PRK12515 RNA polymerase sigma 98.9 4.7E-07 1.2E-11 74.7 16.6 169 427-669 9-177 (189) 61 PRK12520 RNA polymerase sigma 98.9 2.2E-07 5.6E-12 77.3 14.7 171 448-669 7-177 (191) 62 PRK12524 RNA polymerase sigma 98.9 8.4E-07 2.2E-11 72.6 17.2 169 428-669 14-182 (196) 63 PRK09640 RNA polymerase sigma 98.8 7.2E-07 1.8E-11 73.2 16.2 177 428-681 11-187 (188) 64 PRK09647 RNA polymerase sigma 98.8 6.4E-07 1.6E-11 73.6 15.7 171 429-669 33-203 (222) 65 PRK12544 RNA polymerase sigma 98.8 8.4E-07 2.1E-11 72.7 16.2 170 447-669 23-195 (207) 66 PRK12537 RNA polymerase sigma 98.8 5.9E-07 1.5E-11 73.9 15.3 176 423-669 6-181 (184) 67 TIGR02394 rpoS_proteo RNA poly 98.8 3.6E-08 9.2E-13 83.5 8.8 124 115-238 9-144 (292) 68 PRK09643 RNA polymerase sigma 98.8 9.1E-07 2.3E-11 72.4 15.9 170 427-677 14-183 (197) 69 PRK12538 RNA polymerase sigma 98.8 2.4E-06 6.1E-11 69.1 17.7 171 425-670 48-218 (233) 70 PRK09638 RNA polymerase sigma 98.8 1E-06 2.7E-11 71.9 15.7 168 427-669 6-173 (177) 71 PRK12512 RNA polymerase sigma 98.8 6.2E-07 1.6E-11 73.7 14.4 169 423-669 5-177 (184) 72 TIGR02859 spore_sigH RNA polym 98.8 2E-07 5.1E-12 77.6 11.9 182 428-668 7-190 (198) 73 PRK12533 RNA polymerase sigma 98.8 1.7E-06 4.4E-11 70.2 16.4 164 442-669 20-183 (217) 74 pfam00140 Sigma70_r1_2 Sigma-7 98.8 6.8E-09 1.7E-13 89.2 4.0 35 118-152 1-35 (37) 75 PRK07500 rpoH2 RNA polymerase 98.7 2.6E-06 6.6E-11 68.8 16.4 84 117-200 4-97 (289) 76 PRK12526 RNA polymerase sigma 98.7 2E-06 5E-11 69.8 14.9 174 428-669 26-199 (206) 77 PRK12536 RNA polymerase sigma 98.7 2.7E-06 6.8E-11 68.7 15.5 170 424-669 2-172 (178) 78 TIGR02984 Sig-70_plancto1 RNA 98.7 4.6E-07 1.2E-11 74.7 11.4 167 450-669 17-187 (190) 79 PRK09415 RNA polymerase factor 98.7 4.7E-06 1.2E-10 66.7 16.4 159 442-669 15-173 (177) 80 PRK12542 RNA polymerase sigma 98.7 3.4E-06 8.6E-11 67.9 15.5 162 442-670 8-169 (185) 81 PRK09644 RNA polymerase sigma 98.7 2.7E-06 6.8E-11 68.7 14.8 152 446-670 4-155 (165) 82 COG1595 RpoE DNA-directed RNA 98.7 5.3E-06 1.3E-10 66.4 16.3 164 439-670 11-174 (182) 83 PRK12532 RNA polymerase sigma 98.7 4.5E-06 1.1E-10 66.9 15.9 172 447-669 10-182 (195) 84 PRK12518 RNA polymerase sigma 98.6 3.8E-06 9.6E-11 67.5 14.5 165 431-669 2-166 (175) 85 PRK12545 RNA polymerase sigma 98.6 7.7E-06 2E-10 65.1 16.0 176 447-671 12-187 (201) 86 pfam07638 Sigma70_ECF ECF sigm 98.6 3.8E-06 9.7E-11 67.5 14.3 175 425-669 2-181 (185) 87 PRK12539 RNA polymerase sigma 98.6 1.3E-05 3.3E-10 63.3 16.2 171 422-669 3-177 (184) 88 PRK08311 putative RNA polymera 98.6 3.9E-07 9.8E-12 75.3 8.0 93 427-522 5-99 (237) 89 pfam04542 Sigma70_r2 Sigma-70 98.5 2.1E-07 5.4E-12 77.4 6.4 71 448-518 1-71 (71) 90 PRK09639 RNA polymerase sigma 98.5 1.4E-05 3.7E-10 62.9 15.2 157 441-669 1-157 (166) 91 PRK09642 RNA polymerase sigma 98.5 1.3E-05 3.3E-10 63.3 15.0 148 453-669 5-152 (160) 92 PRK12517 RNA polymerase sigma 98.5 2.7E-05 6.8E-10 60.8 16.5 155 440-669 20-174 (188) 93 PRK12530 RNA polymerase sigma 98.5 1.9E-05 4.9E-10 61.9 15.7 160 455-669 21-182 (191) 94 PRK09651 RNA polymerase sigma 98.5 2.2E-05 5.7E-10 61.4 15.0 156 442-668 9-164 (172) 95 PRK09637 RNA polymerase sigma 98.5 1.6E-05 4.1E-10 62.6 14.2 149 446-669 4-152 (181) 96 PRK09047 RNA polymerase factor 98.5 9.9E-06 2.5E-10 64.2 13.1 74 592-669 79-152 (161) 97 PRK12541 RNA polymerase sigma 98.4 2.6E-05 6.7E-10 60.9 14.9 155 442-669 4-158 (161) 98 PRK07037 extracytoplasmic-func 98.4 2.6E-05 6.6E-10 60.9 14.8 159 442-669 11-169 (183) 99 pfam04545 Sigma70_r4 Sigma-70, 98.4 4.5E-07 1.2E-11 74.8 5.7 50 616-669 1-50 (50) 100 TIGR02948 SigW_bacill RNA poly 98.4 3.2E-06 8.3E-11 68.0 9.2 161 427-652 5-165 (187) 101 PRK12535 RNA polymerase sigma 98.4 0.0001 2.6E-09 56.2 16.6 170 423-669 9-178 (195) 102 PRK09645 RNA polymerase sigma 98.4 4.8E-05 1.2E-09 58.8 14.7 157 442-669 6-162 (171) 103 PRK12546 RNA polymerase sigma 98.3 5.8E-05 1.5E-09 58.1 14.7 153 442-669 7-159 (188) 104 PRK12547 RNA polymerase sigma 98.3 0.00011 2.9E-09 55.8 15.9 155 441-669 4-158 (164) 105 PRK12527 RNA polymerase sigma 98.3 0.0001 2.7E-09 56.1 14.7 154 454-682 6-159 (159) 106 PRK09649 RNA polymerase sigma 98.3 0.00011 2.9E-09 55.8 14.7 171 422-669 6-176 (185) 107 PRK12516 RNA polymerase sigma 98.3 0.00013 3.2E-09 55.5 14.8 155 441-669 11-165 (190) 108 PRK08241 RNA polymerase factor 98.2 0.0002 5E-09 53.9 14.6 186 429-669 11-202 (341) 109 PRK12523 RNA polymerase sigma 98.2 0.00017 4.4E-09 54.4 14.2 155 444-669 11-165 (172) 110 TIGR02952 Sig70_famx2 RNA poly 98.2 8.4E-05 2.1E-09 56.9 12.5 131 468-669 36-169 (171) 111 PRK12540 RNA polymerase sigma 98.1 0.00039 9.9E-09 51.6 15.3 155 443-671 5-159 (181) 112 cd06171 Sigma70_r4 Sigma70, re 98.1 1.5E-05 3.8E-10 62.8 6.7 55 610-668 1-55 (55) 113 PRK12511 RNA polymerase sigma 98.0 0.00036 9.2E-09 51.9 13.1 150 446-669 8-157 (182) 114 PRK12525 RNA polymerase sigma 97.9 0.00083 2.1E-08 49.0 14.0 152 446-668 12-163 (168) 115 PRK09636 RNA polymerase sigma 97.9 0.0011 2.7E-08 48.2 14.5 153 448-670 5-158 (289) 116 PRK05803 sporulation sigma fac 97.9 0.00012 3E-09 55.7 8.4 67 121-187 17-92 (228) 117 PRK12529 RNA polymerase sigma 97.8 0.0046 1.2E-07 43.2 15.4 155 444-666 14-170 (178) 118 PRK12528 RNA polymerase sigma 97.7 0.0049 1.2E-07 42.9 14.2 154 444-668 11-164 (167) 119 TIGR02985 Sig70_bacteroi1 RNA 97.6 0.0043 1.1E-07 43.4 13.6 164 444-669 2-165 (167) 120 PRK09635 sigI RNA polymerase s 97.5 0.014 3.6E-07 39.3 16.5 155 447-669 9-164 (290) 121 PRK06930 positive control sigm 97.4 0.0006 1.5E-08 50.1 7.1 61 605-669 100-160 (170) 122 TIGR03001 Sig-70_gmx1 RNA poly 97.4 0.0038 9.7E-08 43.8 11.0 143 498-656 37-199 (249) 123 PRK08301 sporulation sigma fac 97.4 0.0016 4E-08 46.8 8.8 56 132-187 37-101 (239) 124 COG0568 RpoD DNA-directed RNA 97.3 0.0031 7.9E-08 44.5 9.1 26 543-568 296-321 (342) 125 PRK05658 RNA polymerase sigma 97.1 0.0011 2.7E-08 48.1 5.3 229 314-574 344-609 (620) 126 pfam08281 Sigma70_r4_2 Sigma-7 96.8 0.0051 1.3E-07 42.8 6.6 53 611-667 2-54 (54) 127 TIGR02393 RpoD_Cterm RNA polym 96.7 0.0013 3.2E-08 47.6 2.8 190 161-358 15-224 (240) 128 TIGR02957 SigX4 RNA polymerase 96.6 0.014 3.6E-07 39.3 7.5 71 597-671 86-157 (287) 129 TIGR02983 SigE-fam_strep RNA p 96.5 0.0015 3.9E-08 46.9 2.3 150 447-670 10-160 (165) 130 TIGR02233 Myxo_sigma_rel Myxoc 96.5 0.0054 1.4E-07 42.6 5.0 59 603-665 8-70 (106) 131 PRK08215 sporulation sigma fac 96.3 0.0055 1.4E-07 42.5 4.3 62 128-189 13-83 (257) 132 pfam00196 GerE Bacterial regul 95.9 0.028 7.1E-07 37.0 6.3 56 617-677 1-56 (58) 133 PRK10360 DNA-binding transcrip 95.8 0.045 1.1E-06 35.4 7.0 60 618-682 136-195 (196) 134 PRK08583 RNA polymerase sigma 95.8 0.0099 2.5E-07 40.5 3.6 62 125-186 1-72 (257) 135 PRK03975 tfx putative transcri 95.8 0.029 7.5E-07 36.8 5.8 46 619-669 4-49 (139) 136 TIGR02392 rpoH_proteo alternat 95.7 0.11 2.9E-06 32.2 8.5 68 121-188 3-80 (279) 137 PRK00118 putative DNA-binding 95.6 0.04 1E-06 35.7 5.9 47 619-669 17-63 (105) 138 PRK10188 DNA-binding transcrip 95.5 0.06 1.5E-06 34.3 6.5 52 619-675 179-230 (240) 139 smart00421 HTH_LUXR helix_turn 95.5 0.055 1.4E-06 34.7 6.2 56 617-677 1-56 (58) 140 PRK09958 DNA-binding transcrip 95.4 0.065 1.7E-06 34.1 6.6 56 617-677 141-196 (204) 141 pfam04297 UPF0122 Putative hel 95.2 0.063 1.6E-06 34.2 5.9 47 619-669 17-63 (101) 142 PRK10403 transcriptional regul 95.1 0.1 2.6E-06 32.5 6.8 58 618-680 152-209 (215) 143 PRK09390 fixJ response regulat 95.0 0.19 4.7E-06 30.5 7.8 59 614-677 136-194 (202) 144 PRK09483 response regulator; P 95.0 0.11 2.8E-06 32.3 6.6 55 618-677 147-201 (216) 145 PRK10840 transcriptional regul 94.9 0.12 3E-06 32.1 6.6 54 619-677 150-203 (216) 146 PRK05572 sporulation sigma fac 94.9 0.031 7.9E-07 36.6 3.6 59 130-188 8-75 (251) 147 COG3413 Predicted DNA binding 94.8 0.11 2.9E-06 32.1 6.3 51 618-668 154-207 (215) 148 PRK05949 RNA polymerase sigma 94.7 0.41 1E-05 27.8 9.1 39 112-150 11-49 (327) 149 cd06170 LuxR_C_like C-terminal 94.6 0.15 3.9E-06 31.1 6.6 53 620-677 1-53 (57) 150 PRK07406 RNA polymerase sigma 94.5 0.44 1.1E-05 27.5 9.3 38 113-150 69-106 (385) 151 PRK11475 DNA-binding transcrip 94.3 0.19 4.9E-06 30.3 6.5 52 619-675 134-185 (205) 152 TIGR03020 EpsA transcriptional 94.2 0.51 1.3E-05 27.0 11.2 85 587-676 137-242 (247) 153 COG2771 CsgD DNA-binding HTH d 94.2 0.25 6.3E-06 29.5 6.9 58 618-680 3-60 (65) 154 PRK10651 transcriptional regul 94.2 0.2 5E-06 30.3 6.3 54 618-676 154-207 (216) 155 TIGR02939 RpoE_Sigma70 RNA pol 94.2 0.52 1.3E-05 27.0 12.5 159 428-651 9-168 (192) 156 PRK13870 transcriptional regul 94.1 0.53 1.4E-05 26.9 11.4 51 620-675 174-224 (234) 157 PRK09935 transcriptional regul 94.0 0.24 6.2E-06 29.5 6.6 54 619-677 149-202 (210) 158 PRK07405 RNA polymerase sigma 94.0 0.47 1.2E-05 27.3 7.9 37 115-151 5-41 (318) 159 TIGR03541 reg_near_HchA LuxR f 93.9 0.58 1.5E-05 26.6 11.5 53 618-675 170-222 (232) 160 pfam04967 HTH_10 HTH DNA bindi 93.7 0.28 7.2E-06 29.1 6.4 48 620-667 1-51 (53) 161 COG2197 CitB Response regulato 93.0 0.46 1.2E-05 27.3 6.6 56 618-678 147-202 (211) 162 COG4566 TtrR Response regulato 92.9 0.8 2E-05 25.5 8.6 68 608-680 131-198 (202) 163 TIGR02997 Sig70-cyanoRpoD RNA 92.8 0.6 1.5E-05 26.4 7.0 29 119-147 1-29 (336) 164 TIGR00721 tfx DNA-binding prot 92.7 0.2 5.1E-06 30.2 4.4 45 620-669 7-51 (142) 165 TIGR02989 Sig-70_gvs1 RNA poly 92.4 0.92 2.4E-05 25.0 16.0 135 467-667 25-159 (163) 166 TIGR02950 SigM_subfam RNA poly 92.0 0.62 1.6E-05 26.3 6.2 77 587-667 81-157 (162) 167 TIGR02895 spore_sigI RNA polym 91.2 0.69 1.7E-05 26.0 5.7 77 442-518 8-87 (225) 168 TIGR02960 SigX5 RNA polymerase 90.6 1.4 3.5E-05 23.6 8.2 155 465-663 27-183 (329) 169 TIGR02954 Sig70_famx3 RNA poly 90.4 1.4 3.6E-05 23.5 13.5 162 431-669 7-168 (173) 170 PRK10100 DNA-binding transcrip 90.1 1.5 3.7E-05 23.4 6.6 54 619-677 155-208 (216) 171 TIGR02999 Sig-70_X6 RNA polyme 88.7 1.9 4.8E-05 22.6 11.7 161 426-657 3-179 (194) 172 pfam01726 LexA_DNA_bind LexA D 88.0 1.7 4.4E-05 22.8 5.8 37 531-567 10-47 (65) 173 PRK12423 LexA repressor; Provi 87.6 1 2.6E-05 24.7 4.3 41 527-567 6-47 (202) 174 PRK04841 transcriptional regul 87.5 2.2 5.5E-05 22.0 6.4 54 619-677 838-891 (903) 175 COG1356 tfx Transcriptional re 86.5 0.49 1.3E-05 27.1 2.3 12 572-583 66-77 (143) 176 TIGR03209 P21_Cbot clostridium 86.3 0.33 8.4E-06 28.5 1.3 41 612-656 100-140 (142) 177 PRK00215 LexA repressor; Valid 85.7 2.4 6E-05 21.8 5.4 41 528-568 5-46 (204) 178 COG2739 Uncharacterized protei 84.2 2.6 6.6E-05 21.4 5.1 36 620-659 18-53 (105) 179 PRK10869 recombination and rep 84.0 3.1 7.9E-05 20.8 17.0 109 313-454 276-384 (553) 180 pfam02650 HTH_WhiA Sporulation 82.2 3.1 7.9E-05 20.8 4.8 42 617-661 141-188 (191) 181 COG1809 (2R)-phospho-3-sulfola 82.1 3.1 7.9E-05 20.8 4.8 24 56-79 55-78 (258) 182 PRK00286 xseA exodeoxyribonucl 81.8 3.7 9.5E-05 20.2 6.7 13 61-73 147-159 (443) 183 PRK09954 hypothetical protein; 80.4 4.1 0.00011 19.8 5.3 43 30-75 4-46 (362) 184 PRK13239 alkylmercury lyase; P 79.8 4.1 0.00011 19.8 4.8 28 543-570 33-60 (206) 185 COG1570 XseA Exonuclease VII, 79.6 4.3 0.00011 19.7 5.6 46 558-605 212-257 (440) 186 PRK09191 two-component respons 79.5 4.4 0.00011 19.6 5.0 124 448-574 6-132 (261) 187 pfam07374 DUF1492 Protein of u 77.7 4.9 0.00013 19.2 6.3 55 609-667 44-99 (100) 188 pfam04963 Sigma54_CBD Sigma-54 76.8 5.2 0.00013 19.1 7.8 129 507-668 16-148 (195) 189 PRK13558 bacterio-opsin activa 76.3 5.3 0.00014 19.0 6.9 55 613-667 610-667 (674) 190 COG4367 Uncharacterized protei 74.4 5.9 0.00015 18.6 5.3 39 535-573 10-50 (97) 191 TIGR02612 mob_myst_A mobile my 73.2 2.7 7E-05 21.3 2.4 41 618-662 21-61 (150) 192 PRK09247 ATP-dependent DNA lig 73.1 3.8 9.7E-05 20.1 3.1 27 623-649 507-533 (537) 193 COG1802 GntR Transcriptional r 72.3 5.2 0.00013 19.1 3.6 38 424-464 185-222 (230) 194 pfam05263 DUF722 Protein of un 71.5 6.8 0.00017 18.1 6.1 51 608-660 70-120 (130) 195 KOG0996 consensus 71.1 6.9 0.00018 18.1 16.5 54 26-79 139-224 (1293) 196 PRK13869 plasmid-partitioning 71.0 7 0.00018 18.1 4.2 13 470-482 155-167 (405) 197 COG1481 Uncharacterized protei 70.8 7 0.00018 18.0 5.3 45 617-664 251-301 (308) 198 pfam02601 Exonuc_VII_L Exonucl 70.1 7.3 0.00018 17.9 7.1 45 29-73 26-70 (295) 199 cd04981 IgV_H Immunoglobulin ( 68.9 0.31 7.9E-06 28.7 -3.2 21 492-512 22-42 (117) 200 TIGR02168 SMC_prok_B chromosom 68.6 7.8 0.0002 17.7 18.3 28 427-454 468-495 (1191) 201 cd00228 eu-GS Eukaryotic Gluta 67.0 5.4 0.00014 18.9 2.8 128 484-632 257-398 (471) 202 PRK11414 putative DNA-binding 66.6 7.9 0.0002 17.6 3.6 16 446-461 129-144 (221) 203 cd00569 HTH_Hin_like Helix-tur 65.2 8.9 0.00023 17.2 4.3 35 619-657 5-39 (42) 204 pfam06971 Put_DNA-bind_N Putat 64.4 9.2 0.00023 17.1 4.2 47 520-566 1-47 (49) 205 PRK06266 transcription initiat 63.6 7.7 0.0002 17.7 3.0 24 545-568 35-58 (178) 206 PRK05932 RNA polymerase factor 63.6 9.5 0.00024 17.0 9.3 68 545-619 348-415 (461) 207 TIGR01637 phage_arpU phage tra 63.5 9.5 0.00024 17.0 7.5 56 611-668 75-130 (139) 208 pfam02001 DUF134 Protein of un 61.7 10 0.00026 16.7 5.6 46 619-668 36-81 (100) 209 pfam04748 Polysacc_deac_2 Dive 61.5 10 0.00026 16.7 3.4 141 17-180 62-204 (213) 210 TIGR02395 rpoN_sigma RNA polym 61.0 10 0.00027 16.7 3.4 267 315-618 134-431 (477) 211 COG2856 Predicted Zn peptidase 59.5 10 0.00026 16.7 3.1 16 359-374 112-127 (213) 212 TIGR02147 Fsuc_second hypothet 57.5 12 0.0003 16.2 6.2 118 536-662 132-260 (281) 213 COG3824 Predicted Zn-dependent 57.3 4.6 0.00012 19.5 1.0 27 637-663 108-135 (136) 214 KOG2727 consensus 57.0 12 0.00031 16.2 8.6 54 502-567 922-975 (1244) 215 pfam10078 DUF2316 Uncharacteri 57.0 12 0.00031 16.2 4.6 37 535-571 10-48 (89) 216 pfam12324 HTH_15 Helix-turn-he 56.8 12 0.00031 16.1 6.8 36 536-571 26-63 (77) 217 PRK09943 DNA-binding transcrip 56.7 12 0.00031 16.1 3.9 22 451-475 47-68 (185) 218 COG2186 FadR Transcriptional r 55.9 11 0.00029 16.3 2.8 19 446-464 145-163 (241) 219 pfam01698 FLO_LFY Floricaula / 55.8 12 0.00031 16.1 2.9 43 29-73 44-94 (382) 220 COG1476 Predicted transcriptio 55.4 13 0.00033 16.0 3.9 21 641-661 16-36 (68) 221 KOG2773 consensus 55.2 13 0.00033 16.0 12.5 171 345-551 193-367 (483) 222 pfam08279 HTH_11 HTH domain. T 53.9 13 0.00034 15.8 4.0 22 547-568 16-37 (55) 223 PRK11564 stationary phase indu 53.6 14 0.00034 15.8 4.6 48 32-79 19-68 (426) 224 TIGR01764 excise DNA binding d 53.3 14 0.00035 15.7 3.0 25 547-571 2-26 (49) 225 PRK07023 short chain dehydroge 53.3 14 0.00035 15.7 6.6 89 454-554 133-221 (243) 226 PRK04424 fatty acid biosynthes 52.9 14 0.00035 15.7 4.8 19 544-562 19-37 (185) 227 pfam02885 Glycos_trans_3N Glyc 52.6 14 0.00036 15.6 3.7 47 31-77 2-51 (66) 228 pfam06239 ECSIT Evolutionarily 52.0 14 0.00036 15.6 3.8 27 408-434 122-148 (229) 229 TIGR02607 antidote_HigA addict 52.0 13 0.00033 15.9 2.6 40 537-579 13-52 (81) 230 PRK02842 light-independent pro 51.7 11 0.00029 16.4 2.2 45 622-666 232-277 (425) 231 COG1510 Predicted transcriptio 51.6 12 0.0003 16.2 2.3 26 544-569 39-64 (177) 232 PRK01381 Trp operon repressor; 50.5 15 0.00038 15.4 4.3 42 612-653 24-69 (99) 233 PRK01388 arginine deiminase; P 50.3 12 0.0003 16.3 2.1 42 38-79 24-69 (410) 234 TIGR02865 spore_II_E stage II 50.0 15 0.00039 15.4 6.9 64 572-635 590-660 (794) 235 pfam10668 Phage_terminase Phag 50.0 15 0.00039 15.4 3.4 32 535-566 11-42 (60) 236 pfam11913 DUF3431 Protein of u 49.4 2.8 7E-05 21.2 -1.2 24 646-669 158-181 (222) 237 KOG3099 consensus 49.3 16 0.0004 15.3 3.0 11 375-385 109-119 (340) 238 pfam12128 DUF3584 Protein of u 48.5 16 0.00041 15.2 23.9 16 478-493 907-922 (1192) 239 pfam02682 AHS1 Allophanate hyd 48.3 16 0.00041 15.2 3.2 47 513-575 82-128 (202) 240 TIGR03338 phnR_burk phosphonat 48.0 16 0.00042 15.1 2.9 46 28-76 17-64 (212) 241 TIGR01026 fliI_yscN ATPase Fli 47.5 17 0.00042 15.1 3.9 41 506-549 253-293 (455) 242 TIGR02546 III_secr_ATP type II 47.5 17 0.00042 15.1 3.5 43 506-551 232-274 (430) 243 PRK05472 redox-sensing transcr 47.0 17 0.00043 15.0 5.4 24 473-496 89-112 (211) 244 pfam04760 IF2_N Translation in 46.2 17 0.00044 14.9 2.8 34 547-580 4-37 (52) 245 COG2316 Predicted hydrolase (H 45.0 14 0.00035 15.7 1.8 19 645-663 171-189 (212) 246 PRK04217 hypothetical protein; 44.6 18 0.00046 14.8 5.6 45 620-668 43-87 (110) 247 COG1342 Predicted DNA-binding 44.3 18 0.00047 14.7 5.2 45 619-667 33-77 (99) 248 PRK06704 RNA polymerase factor 44.2 18 0.00047 14.7 7.8 40 468-507 42-81 (228) 249 PRK09863 putative frv operon r 44.2 18 0.00047 14.7 4.0 49 28-79 3-54 (585) 250 TIGR01632 L11_bact ribosomal p 44.1 18 0.00047 14.7 2.6 38 42-79 99-144 (144) 251 pfam02638 DUF187 Uncharacteriz 44.0 13 0.00034 15.9 1.6 20 58-77 56-75 (394) 252 COG1654 BirA Biotin operon rep 44.0 19 0.00047 14.7 4.4 33 539-571 12-44 (79) 253 pfam01371 Trp_repressor Trp re 43.9 19 0.00047 14.7 3.4 44 613-656 19-66 (88) 254 pfam04931 DNA_pol_phi DNA poly 43.8 19 0.00048 14.7 11.5 16 604-619 699-714 (784) 255 TIGR00169 leuB 3-isopropylmala 43.7 8.2 0.00021 17.5 0.5 82 506-599 171-262 (370) 256 COG2188 PhnF Transcriptional r 43.4 19 0.00048 14.6 3.4 26 544-569 29-54 (236) 257 pfam11268 DUF3071 Protein of u 42.9 19 0.00049 14.6 3.4 67 492-566 22-88 (169) 258 COG2390 DeoR Transcriptional r 42.7 19 0.00049 14.6 4.8 25 636-660 255-279 (321) 259 pfam09339 HTH_IclR IclR helix- 42.6 19 0.00049 14.5 4.0 30 540-569 12-41 (52) 260 PRK04483 threonyl-tRNA synthet 42.3 11 0.00027 16.6 0.9 36 127-172 53-88 (634) 261 TIGR00373 TIGR00373 conserved 42.0 20 0.0005 14.5 2.6 46 546-591 30-75 (168) 262 TIGR02169 SMC_prok_A chromosom 41.7 20 0.00051 14.4 21.7 51 133-183 239-292 (1202) 263 PRK12444 threonyl-tRNA synthet 41.7 12 0.0003 16.3 1.0 22 493-514 265-286 (639) 264 TIGR03070 couple_hipB transcri 41.1 20 0.00052 14.4 3.4 23 640-662 16-38 (58) 265 TIGR02959 SigZ RNA polymerase 41.0 20 0.00052 14.4 3.9 43 606-652 87-129 (170) 266 PRK09392 ftrB transcriptional 40.5 21 0.00053 14.3 3.4 18 551-568 178-195 (236) 267 cd02758 MopB_Tetrathionate-Ra 40.2 21 0.00053 14.3 3.6 22 414-435 342-363 (735) 268 pfam11633 Nsp3 Replicase polyp 40.1 17 0.00045 14.9 1.7 39 16-54 10-53 (142) 269 COG0856 Orotate phosphoribosyl 40.0 21 0.00054 14.3 3.7 30 453-500 87-116 (203) 270 PRK04140 hypothetical protein; 40.0 21 0.00054 14.2 4.1 15 63-77 6-20 (319) 271 pfam09286 Pro-kuma_activ Pro-k 39.9 21 0.00054 14.2 4.3 37 41-80 45-81 (141) 272 smart00531 TFIIE Transcription 39.6 21 0.00054 14.2 2.9 100 546-652 15-121 (147) 273 COG2049 DUR1 Allophanate hydro 39.6 21 0.00054 14.2 2.4 42 517-574 84-125 (223) 274 TIGR01279 DPOR_bchN light-inde 39.4 6 0.00015 18.6 -0.7 58 612-669 242-305 (458) 275 TIGR00223 panD aspartate 1-dec 39.1 5.8 0.00015 18.7 -0.9 53 447-507 14-67 (127) 276 PRK10286 O-6-alkylguanine-DNA: 38.6 22 0.00056 14.1 6.2 78 502-581 60-140 (171) 277 cd06569 GH20_Sm-chitobiase-lik 38.6 22 0.00056 14.1 3.7 50 31-81 56-117 (445) 278 pfam01381 HTH_3 Helix-turn-hel 38.6 22 0.00056 14.1 2.8 23 640-662 10-32 (55) 279 pfam05049 IIGP Interferon-indu 38.5 22 0.00056 14.1 4.0 36 113-148 95-139 (375) 280 CHL00059 atpA ATP synthase CF1 38.1 22 0.00057 14.0 3.9 49 499-550 237-285 (501) 281 cd00092 HTH_CRP helix_turn_hel 37.8 23 0.00058 14.0 3.5 22 547-568 26-47 (67) 282 smart00787 Spc7 Spc7 kinetocho 37.7 23 0.00058 14.0 20.7 36 121-156 51-89 (312) 283 PRK11637 hypothetical protein; 37.7 23 0.00058 14.0 17.2 26 331-356 77-102 (404) 284 pfam00392 GntR Bacterial regul 37.7 23 0.00058 14.0 2.6 27 544-570 22-48 (64) 285 KOG0976 consensus 37.4 23 0.00058 14.0 17.7 55 403-457 374-428 (1265) 286 COG5174 TFA2 Transcription ini 37.4 23 0.00058 14.0 4.1 41 533-573 85-126 (285) 287 smart00796 AHS1 Allophanate hy 37.1 13 0.00034 15.9 0.7 48 511-574 81-128 (201) 288 PRK11920 rirA iron-responsive 37.0 23 0.00059 13.9 5.2 29 542-570 20-48 (153) 289 pfam06953 ArsD Arsenical resis 36.7 19 0.00049 14.6 1.5 21 542-562 84-104 (119) 290 TIGR02237 recomb_radB DNA repa 36.6 17 0.00044 14.9 1.3 22 442-463 127-148 (223) 291 PRK09990 DNA-binding transcrip 36.3 24 0.00061 13.8 3.3 56 21-79 6-64 (251) 292 PRK04184 DNA topoisomerase VI 36.2 24 0.00061 13.8 3.7 48 473-520 381-454 (533) 293 TIGR01436 glu_cys_lig_pln glut 35.6 24 0.00062 13.8 2.1 87 544-648 284-382 (446) 294 PRK10225 DNA-binding transcrip 35.4 24 0.00062 13.7 3.5 19 447-465 143-161 (257) 295 COG0853 PanD Aspartate 1-decar 35.3 4.9 0.00012 19.3 -1.7 50 448-505 14-63 (126) 296 PRK09526 lacI lac repressor; R 35.1 25 0.00063 13.7 2.8 29 47-75 20-49 (342) 297 PRK11886 biotin--protein ligas 35.0 25 0.00063 13.7 2.9 49 28-79 3-51 (319) 298 PRK10430 DNA-binding transcrip 34.9 25 0.00064 13.7 5.9 79 501-582 135-216 (239) 299 PRK11753 cAMP-regulatory prote 34.7 25 0.00064 13.7 3.4 26 639-668 168-193 (211) 300 pfam01325 Fe_dep_repress Iron 34.4 25 0.00065 13.6 3.0 29 542-570 16-44 (58) 301 cd07377 WHTH_GntR Winged helix 33.9 26 0.00066 13.6 3.2 26 545-570 24-49 (66) 302 PRK13752 putative transcriptio 33.8 22 0.00056 14.1 1.4 25 546-570 7-31 (144) 303 PRK13394 3-hydroxybutyrate deh 33.2 26 0.00067 13.5 4.1 110 439-556 121-237 (262) 304 TIGR02018 his_ut_repres histid 33.1 26 0.00068 13.5 5.1 68 503-600 5-75 (234) 305 COG1522 Lrp Transcriptional re 32.7 27 0.00068 13.4 4.2 36 532-568 9-44 (154) 306 cd06919 Asp_decarbox Aspartate 32.6 4.7 0.00012 19.4 -2.2 35 471-505 29-63 (111) 307 TIGR02513 type_III_yscB type I 32.3 10 0.00026 16.8 -0.5 103 537-652 5-117 (140) 308 TIGR02267 TIGR02267 Myxococcus 32.2 27 0.0007 13.4 2.6 24 427-450 62-85 (123) 309 cd01107 HTH_BmrR Helix-Turn-He 32.1 27 0.0007 13.3 2.2 23 548-570 2-24 (108) 310 pfam12129 Phtf-FEM1B_bdg Male 31.9 20 0.0005 14.5 0.9 57 442-512 42-98 (159) 311 pfam00325 Crp Bacterial regula 31.7 28 0.00071 13.3 2.4 21 548-568 4-24 (32) 312 PRK00876 nadE NAD synthetase; 31.7 28 0.00071 13.3 8.3 35 638-673 277-311 (325) 313 PRK03837 transcriptional regul 31.6 28 0.00071 13.3 3.0 51 23-76 15-68 (243) 314 COG1649 Uncharacterized protei 31.5 27 0.00069 13.4 1.6 23 55-77 58-80 (418) 315 COG1318 Predicted transcriptio 31.4 28 0.00072 13.3 2.8 22 547-568 62-83 (182) 316 pfam00382 TFIIB Transcription 31.2 28 0.00072 13.2 1.7 67 550-653 2-68 (71) 317 PRK00413 thrS threonyl-tRNA sy 31.1 19 0.0005 14.5 0.8 10 129-138 53-62 (639) 318 KOG1495 consensus 30.8 14 0.00036 15.6 0.0 62 443-505 79-151 (332) 319 COG4977 Transcriptional regula 30.8 29 0.00073 13.2 5.1 40 530-569 220-259 (328) 320 smart00345 HTH_GNTR helix_turn 30.6 29 0.00074 13.2 2.9 27 544-570 18-44 (60) 321 KOG4021 consensus 30.6 24 0.00062 13.8 1.2 13 492-504 176-188 (239) 322 smart00530 HTH_XRE Helix-turn- 30.3 29 0.00074 13.1 3.9 23 640-662 11-33 (56) 323 TIGR03337 phnR transcriptional 30.3 29 0.00074 13.1 3.4 45 418-468 19-63 (231) 324 PRK13890 conjugal transfer pro 30.2 29 0.00075 13.1 3.5 29 545-573 17-45 (119) 325 cd02986 DLP Dim1 family, Dim1- 30.0 28 0.00072 13.2 1.5 18 111-128 18-35 (114) 326 TIGR02404 trehalos_R_Bsub treh 30.0 30 0.00075 13.1 2.7 33 541-573 19-51 (236) 327 PRK09973 putative outer membra 29.7 30 0.00076 13.1 4.0 28 330-357 21-48 (85) 328 PRK12824 acetoacetyl-CoA reduc 29.6 30 0.00076 13.0 3.7 99 441-556 119-220 (245) 329 pfam02969 TAF TATA box binding 29.6 30 0.00076 13.0 2.7 46 626-674 10-55 (66) 330 KOG0697 consensus 29.6 30 0.00076 13.0 2.2 35 27-61 81-123 (379) 331 pfam05635 Ribosomal_S23p S23 r 29.6 30 0.00076 13.0 4.6 13 422-434 88-100 (110) 332 TIGR01942 pcnB poly(A) polymer 29.5 18 0.00047 14.7 0.4 12 493-504 392-403 (448) 333 PRK04406 hypothetical protein; 29.4 30 0.00077 13.0 7.6 52 313-364 5-56 (75) 334 PRK13209 L-xylulose 5-phosphat 29.1 31 0.00078 13.0 2.3 48 30-77 22-73 (283) 335 PRK05557 fabG 3-ketoacyl-(acyl 28.8 31 0.00079 12.9 3.2 97 441-556 122-223 (248) 336 pfam01710 Transposase_14 Trans 28.7 31 0.00079 12.9 4.8 23 546-568 18-40 (120) 337 pfam04100 Vps53_N Vps53-like, 28.3 31 0.0008 12.9 11.4 28 45-73 6-33 (375) 338 smart00346 HTH_ICLR helix_turn 28.3 31 0.0008 12.9 4.0 31 540-570 14-44 (91) 339 PRK09391 fixK transcriptional 28.2 32 0.0008 12.9 3.4 18 639-656 173-190 (224) 340 PRK10219 DNA-binding transcrip 28.1 32 0.00081 12.9 5.3 37 533-569 8-44 (107) 341 pfam02261 Asp_decarbox Asparta 28.1 6.4 0.00016 18.4 -2.1 35 472-506 31-65 (116) 342 PRK11161 fumarate/nitrate redu 28.0 32 0.00081 12.8 8.2 37 629-669 168-210 (235) 343 cd01667 TGS_ThrRS_N TGS _ThrRS 27.9 9.3 0.00024 17.1 -1.3 47 543-589 13-59 (61) 344 pfam09413 DUF2007 Protein of u 27.9 25 0.00064 13.6 0.9 11 67-77 16-26 (68) 345 COG3711 BglG Transcriptional a 27.8 32 0.00082 12.8 6.4 54 29-82 5-59 (491) 346 PRK05629 hypothetical protein; 27.6 32 0.00082 12.8 6.2 43 528-571 244-286 (331) 347 KOG2822 consensus 27.5 12 0.00031 16.2 -0.8 28 457-485 203-230 (407) 348 pfam02082 Rrf2 Transcriptional 27.5 32 0.00082 12.8 5.5 46 544-589 22-67 (82) 349 TIGR03324 alt_F1F0_F1_al alter 27.3 33 0.00083 12.8 3.9 50 499-551 236-285 (497) 350 cd00907 Bacterioferritin Bacte 27.2 33 0.00083 12.7 1.7 14 353-366 55-68 (153) 351 pfam02271 UCR_14kD Ubiquinol-c 27.1 33 0.00084 12.7 3.7 45 445-490 7-51 (105) 352 pfam03917 GSH_synth_ATP Eukary 26.9 33 0.00084 12.7 5.3 128 484-632 256-397 (469) 353 pfam03444 DUF293 Domain of unk 26.9 33 0.00084 12.7 6.5 43 529-571 6-48 (79) 354 PRK06200 2,3-dihydroxy-2,3-dih 26.8 33 0.00085 12.7 1.5 94 452-555 137-233 (263) 355 PRK02119 hypothetical protein; 26.7 33 0.00085 12.7 7.1 50 315-364 5-54 (73) 356 smart00491 HELICc2 helicase su 26.6 33 0.00085 12.7 1.4 48 467-514 77-126 (142) 357 TIGR02470 sucr_synth sucrose s 26.3 29 0.00074 13.2 1.0 62 514-575 343-432 (790) 358 COG3355 Predicted transcriptio 26.2 34 0.00087 12.6 6.5 26 543-568 39-64 (126) 359 TIGR01572 A_thl_para_3677 Arab 26.2 8.5 0.00022 17.4 -1.8 42 458-500 46-87 (290) 360 TIGR02944 suf_reg_Xantho FeS a 26.1 34 0.00087 12.6 2.5 52 538-589 17-68 (130) 361 PRK00901 methylated-DNA--prote 25.9 34 0.00088 12.6 5.0 75 505-581 48-124 (155) 362 TIGR01097 3A0109s02M phosphona 25.6 22 0.00056 14.1 0.3 12 501-512 37-48 (192) 363 PTZ00183 centrin; Provisional 25.6 35 0.00089 12.5 6.1 54 21-74 16-76 (168) 364 cd04781 HTH_MerR-like_sg6 Heli 25.5 33 0.00085 12.7 1.2 23 548-570 2-24 (120) 365 pfam08726 efhand_Ca_insen Ca2+ 25.5 35 0.00089 12.5 2.3 27 28-57 9-35 (69) 366 pfam09184 PPP4R2 PPP4R2. PPP4R 25.2 35 0.0009 12.5 4.6 11 321-331 89-99 (285) 367 PRK09764 DNA-binding transcrip 25.0 35 0.0009 12.5 4.1 35 419-453 24-58 (239) 368 PRK12469 RNA polymerase factor 25.0 36 0.00091 12.5 6.8 110 533-651 347-466 (475) 369 TIGR01736 FGAM_synth_II phosph 25.0 36 0.00091 12.5 1.5 18 540-557 13-30 (763) 370 cd04782 HTH_BltR Helix-Turn-He 24.9 36 0.00091 12.4 2.1 23 548-570 2-24 (97) 371 TIGR00270 TIGR00270 conserved 24.8 36 0.00091 12.4 4.6 63 525-592 80-165 (169) 372 COG3904 Predicted periplasmic 24.7 25 0.00064 13.6 0.4 29 636-666 202-230 (245) 373 pfam10500 SR-25 Nuclear RNA-sp 24.7 36 0.00092 12.4 2.0 47 606-665 14-60 (74) 374 KOG4697 consensus 24.6 36 0.00092 12.4 2.0 26 489-514 107-132 (160) 375 PRK10857 DNA-binding transcrip 24.6 36 0.00092 12.4 5.1 22 547-568 26-47 (164) 376 PRK05449 aspartate alpha-decar 24.5 8.1 0.00021 17.5 -2.2 35 472-506 31-65 (126) 377 KOG3361 consensus 24.3 36 0.00093 12.4 2.3 80 452-565 39-132 (157) 378 PRK08643 acetoin reductase; Va 24.3 37 0.00093 12.4 4.4 107 441-556 118-231 (256) 379 smart00492 HELICc3 helicase su 24.2 35 0.0009 12.5 1.1 30 485-514 94-125 (141) 380 smart00342 HTH_ARAC helix_turn 24.1 37 0.00094 12.3 3.7 23 546-568 1-23 (84) 381 PRK10703 DNA-binding transcrip 24.0 37 0.00094 12.3 2.8 47 470-523 246-294 (335) 382 COG2344 AT-rich DNA-binding pr 23.9 37 0.00095 12.3 5.2 29 473-503 89-117 (211) 383 PRK09281 F0F1 ATP synthase sub 23.8 37 0.00095 12.3 4.2 45 501-548 238-282 (502) 384 PRK13805 bifunctional acetalde 23.6 38 0.00096 12.3 11.4 137 422-567 677-829 (862) 385 smart00419 HTH_CRP helix_turn_ 23.6 38 0.00096 12.3 2.9 21 548-568 10-30 (48) 386 COG4477 EzrA Negative regulato 23.2 38 0.00097 12.2 16.2 22 467-488 440-463 (570) 387 PRK08219 short chain dehydroge 23.1 38 0.00098 12.2 3.5 81 453-555 123-203 (226) 388 TIGR01004 PulS_OutS lipoprotei 23.0 39 0.00098 12.2 3.4 61 460-552 56-116 (136) 389 PRK09464 pdhR transcriptional 23.0 39 0.00098 12.2 5.2 51 24-77 12-65 (254) 390 PRK12274 serine/threonine prot 22.9 39 0.00098 12.2 5.6 52 579-631 104-163 (198) 391 pfam10498 IFT57 Intra-flagella 22.9 39 0.00099 12.2 12.8 28 331-358 235-262 (355) 392 TIGR03103 trio_acet_GNAT GNAT- 22.8 31 0.00078 13.0 0.6 62 408-470 278-349 (547) 393 PRK00509 argininosuccinate syn 22.8 39 0.00099 12.1 3.9 33 113-145 117-161 (398) 394 pfam06056 Terminase_5 Putative 22.7 39 0.00099 12.1 1.7 30 534-566 4-33 (58) 395 COG4473 EcsB Predicted ABC-typ 22.7 39 0.00099 12.1 1.6 30 117-146 72-101 (379) 396 smart00803 TAF TATA box bindin 22.7 39 0.00099 12.1 2.7 21 653-673 33-53 (65) 397 KOG0464 consensus 22.7 33 0.00085 12.7 0.7 26 56-81 69-94 (753) 398 PRK02793 hypothetical protein; 22.7 39 0.001 12.1 7.1 49 316-364 5-53 (72) 399 TIGR02485 CobZ_N-term precorri 22.6 39 0.001 12.1 3.5 44 545-593 327-371 (467) 400 TIGR03653 arch_L6P archaeal ri 22.4 37 0.00094 12.3 0.9 32 649-682 133-164 (170) 401 pfam10566 Glyco_hydro_97 Glyco 22.4 39 0.001 12.1 2.7 40 443-482 402-453 (643) 402 pfam02002 TFIIE_alpha TFIIE al 22.4 40 0.001 12.1 2.8 27 545-571 26-52 (105) 403 PRK08359 transcription factor; 22.4 40 0.001 12.1 5.7 23 545-567 95-117 (175) 404 PRK08217 fabG 3-ketoacyl-(acyl 22.3 40 0.001 12.1 5.7 96 443-556 132-231 (253) 405 TIGR02617 tnaA_trp_ase tryptop 22.3 40 0.001 12.1 1.5 19 448-466 201-219 (468) 406 PRK03501 ppnK inorganic polyph 22.2 40 0.001 12.1 2.7 32 56-87 12-43 (264) 407 cd01109 HTH_YyaN Helix-Turn-He 22.2 40 0.001 12.1 2.3 23 548-570 2-24 (113) 408 pfam01418 HTH_6 Helix-turn-hel 22.2 40 0.001 12.1 3.4 18 548-565 36-53 (106) 409 pfam07455 Psu Phage polarity s 22.1 38 0.00096 12.3 0.9 73 501-582 60-139 (188) 410 pfam04433 SWIRM SWIRM domain. 22.0 40 0.001 12.0 3.8 33 40-75 49-81 (84) 411 PRK10014 DNA-binding transcrip 22.0 40 0.001 12.0 3.1 19 478-496 166-184 (342) 412 pfam04492 Phage_rep_O Bacterio 21.9 40 0.001 12.0 5.4 40 618-657 28-72 (100) 413 pfam08765 Mor Mor transcriptio 21.9 40 0.001 12.0 4.6 41 621-668 59-99 (107) 414 smart00344 HTH_ASNC helix_turn 21.8 40 0.001 12.0 4.2 37 533-570 5-41 (108) 415 cd02844 PAZ_CAF_like PAZ domai 21.3 41 0.0011 11.9 1.6 24 482-505 53-76 (135) 416 PRK12429 3-hydroxybutyrate deh 21.3 41 0.0011 11.9 2.7 106 442-556 121-233 (258) 417 TIGR00370 TIGR00370 conserved 21.1 38 0.00098 12.2 0.8 23 639-661 105-127 (217) 418 PRK07740 hypothetical protein; 21.1 25 0.00063 13.7 -0.2 14 640-653 185-198 (240) 419 COG0411 LivG ABC-type branched 21.1 23 0.00058 14.0 -0.4 60 417-479 175-234 (250) 420 TIGR02104 pulA_typeI pullulana 21.0 42 0.0011 11.9 1.7 20 67-86 188-207 (655) 421 PRK02234 recU Holliday junctio 21.0 42 0.0011 11.9 1.2 16 463-478 25-40 (199) 422 COG4809 Archaeal ADP-dependent 21.0 33 0.00084 12.7 0.4 116 412-562 288-403 (466) 423 COG1904 UxaC Glucuronate isome 20.9 42 0.0011 11.9 3.0 95 421-523 244-341 (463) 424 pfam11503 DUF3215 Protein of u 20.9 26 0.00067 13.5 -0.1 44 39-82 9-56 (77) 425 COG1675 TFA1 Transcription ini 20.9 42 0.0011 11.9 5.6 34 543-577 30-65 (176) 426 cd05133 RasGAP_IQGAP1 IQGAP1 i 20.7 42 0.0011 11.8 1.8 43 142-185 18-60 (360) 427 PRK09706 transcriptional repre 20.5 43 0.0011 11.8 4.1 24 545-568 17-40 (135) 428 pfam06970 RepA_N Replication i 20.5 43 0.0011 11.8 2.7 19 548-566 54-72 (76) 429 TIGR01752 flav_long flavodoxin 20.5 39 0.001 12.1 0.7 19 550-568 18-37 (176) 430 KOG1389 consensus 20.4 43 0.0011 11.8 1.6 25 554-582 358-382 (435) 431 TIGR00624 tag DNA-3-methyladen 20.3 43 0.0011 11.8 1.3 31 474-508 141-172 (185) 432 TIGR02881 spore_V_K stage V sp 20.1 44 0.0011 11.7 2.7 55 468-528 173-233 (261) 433 cd04770 HTH_HMRTR Helix-Turn-H 20.0 44 0.0011 11.7 1.8 23 548-570 2-24 (123) No 1 >PRK05658 RNA polymerase sigma factor RpoD; Validated Probab=100.00 E-value=0 Score=1529.11 Aligned_cols=618 Identities=53% Similarity=0.785 Sum_probs=564.3 Q ss_pred CCCCCHHCCHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCEEECCCCCCCCCCCCCCC-CCCH Q ss_conf 554430202899999999787848867899975268435998889999999984797783278410000123643-2110 Q gi|254780289|r 19 DDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSL-DLAS 97 (682) Q Consensus 19 ~~~~~~d~~~~~ik~LI~~gke~GylTydeIn~~LP~d~~~~e~ie~i~~~L~~~GI~Vve~~~~~~~~~~~~~~-~~~~ 97 (682) +|+|++|.+++.||+||++||+||||||+|||++||++.++|||||+|+++|++|||+|+|++++++.....+.. ..++ T Consensus 1 ~~~~~~~~~~~~ik~LI~~GKe~GyLTy~EInd~LP~d~~~~eqId~ii~~L~~~GI~Vve~~~~~~~~~~~~~~~~~d~ 80 (620) T PRK05658 1 GDSPLLKNQQSALKLLIKRGKERGYLTYAELNDHLPEDIVDSEQIEDIISMINDMGIQVVESAPDADDLLLADNAAESDE 80 (620) T ss_pred CCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCEEEECCCCCCHHCCCCCCCCCCH T ss_conf 99525654789999999985416826599999768998999899999999999779737506864200001445443204 Q ss_pred HHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCC Q ss_conf 11122334444200345777728999999856976889788999999999889999999872823899999999873117 Q gi|254780289|r 98 SASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDG 177 (682) Q Consensus 98 ~~~~e~~~~~~~~~~e~~rtdDPVRMYLREMG~V~LLTREgEIeIAKRIE~G~~~i~~al~~~P~ti~~il~~~e~i~~g 177 (682) +..+++..+++.+++++|||||||||||||||+||||||||||+||||||+|+++|+++||+||++++++++|++.|.+| T Consensus 81 ~~~ee~~~~l~~~~~e~grTdDPVRMYLREMG~V~LLTREGEIeIAKRIE~G~~~~~~ai~~~P~~i~~il~~~e~l~~g 160 (620) T PRK05658 81 EAEEEAAAALSSVESEIGRTDDPVRMYLREMGTVELLTREGEIEIAKRIEDGENIMIAALCESPLTIDAILEWYDRLENE 160 (620) T ss_pred HHHHHHHHHCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCC T ss_conf 56655443102210125888980999999728876788074999999999999999999962969999999999999828 Q ss_pred CHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCHHHHHH Q ss_conf 10367876421013543333333433333211000111000100000000122100001111101356666530344310 Q gi|254780289|r 178 TTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERN 257 (682) Q Consensus 178 e~~LrdIIDld~t~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~e~~~e~~~~~~~~~~~~~~~~~~e~e~~~~~ 257 (682) +++++|||+.+.+...... ....... ...........+.. T Consensus 161 e~rl~diIdg~~d~~~~~~-----------~~~~~~~-----------------------------~~~~~~~~~~~~~~ 200 (620) T PRK05658 161 EIRLRELIDGFVDPNAEEA-----------PTATHVG-----------------------------SELSEEDEDDDEEE 200 (620) T ss_pred CEEHHHHHHCCCCCCCCCC-----------CCCCCCC-----------------------------CCCCCCCCCCCCCC T ss_conf 7139999842468432223-----------1101233-----------------------------33322221111112 Q ss_pred HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 00222334555564442102347987668999999999999987521012000799999999999999862100577887 Q gi|254780289|r 258 LDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDL 337 (682) Q Consensus 258 ~e~e~de~~~sla~~e~eLk~~v~e~l~~i~~~~~kl~k~~~~~~~~~~~~~~~kk~~kl~~eL~e~~~~lkl~~k~iE~ 337 (682) .+.+.+....+++.+...+++.+.+.|..+.+.|.++.++..+... ...+++.+++.+|.+.|..|+|++++|+. T Consensus 201 ~~~~~d~~~~~~~~~~~~~~~~v~e~f~~i~k~~~k~~k~~~k~~~-----~~~k~~~k~~~~L~~~~~~lkl~~k~ie~ 275 (620) T PRK05658 201 DEEDDDEAAKSLAADEAILPEKVLEKFKALAKQYKKLRKAQKKKGR-----EQEKKYAKLREKLKEELKSLRLTSKQIEE 275 (620) T ss_pred CCCCCCCCCHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCH-----HHHHHHHHHHHHHHHHHHHCCCCHHHHHH T ss_conf 2222220003257660756899999999999999999999997332-----40499999999999999845898899999 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH-HHHCCCHHHHHHHCCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 89999999999999999999999-97125357777631677689899999861355106765543456776532233332 Q gi|254780289|r 338 LVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSI 416 (682) Q Consensus 338 L~~~l~~~~k~Ir~~Er~L~rl~-~k~~i~R~~Fi~~f~gnEt~~~wl~~~~~~~~~~~~~~l~~~~~eI~~~q~kL~~i 416 (682) |++.++..+++|+.+|+.|+++| .++||||++|++.|++|++++.|+.+.... .+.|+.++.....+|..+|++|..+ T Consensus 276 L~~~l~~~~~~Ir~~Er~I~rl~v~~~~m~R~~Fi~~f~g~e~~~~W~~k~~~~-~k~~~~~l~~~~~~I~~~q~kL~~i 354 (620) T PRK05658 276 LVDQMRDINKRVRTLERQILRLAVERCKMPRKDFLRLFPGNETDITWLEKEIAS-GKPWSEFLKRVYDEIQRLQQELEAI 354 (620) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHCCCCCCCHHHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHHH T ss_conf 999999999999999999999999871999999998732443435689999884-3436999998699999999999999 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEE Q ss_conf 22221126889999998765332112468999875557899988752235677788754436799998874385457312 Q gi|254780289|r 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496 (682) Q Consensus 417 e~~~gl~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f 496 (682) +..+|+++.+||+++++|++|++++++||++||+|||||||||||||+||||+|+|||||||||||||||||||+||||| T Consensus 355 e~~~gl~i~elK~i~r~I~~Ge~~a~~AKkeMiEANLRLVISIAKKYtNRGLqFLDLIQEGNiGLMkAVdKFeyrrGyKF 434 (620) T PRK05658 355 EEETGLTIEELKEINRQISKGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 434 (620) T ss_pred HHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCHHHHHHHHHCCCCCCCCH T ss_conf 99849799999999999999877789999999986189999999983148998789987440799999986284559713 Q ss_pred EHHHHHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCC Q ss_conf 01028989999999997228704614205889899999999987760889997899987099989999999860898755 Q gi|254780289|r 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576 (682) Q Consensus 497 ~tya~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl 576 (682) |||||||||||||||||||||||||||||+++|||++|++|++.|++||+|||+|||++||||++||+++|+++++|||| T Consensus 435 STYATWWIRQAITRaIaDqaRTIRiPVHmietinkl~r~~r~l~qe~Grept~eEia~~~~~~~~kvr~vlki~~epiSl 514 (620) T PRK05658 435 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERLGMPEDKVRKVLKIAKEPISL 514 (620) T ss_pred HHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHCCCCCCC T ss_conf 57799999999999998617740151889999999999999999982899999999989498999999999864898024 Q ss_pred CCCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHH Q ss_conf 36358899860475623898899899999999999999997329988999999981879867468899989966789999 Q gi|254780289|r 577 ETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656 (682) Q Consensus 577 ~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~ 656 (682) +||||+++||+|||||+|+++.+|.+++...+|++++.+||++|+|||++||+||||||++++|||||||++|+|||||| T Consensus 515 e~pig~~~ds~lgdfied~~~~~p~~~~~~~~l~~~~~~vl~~Lt~rE~~vl~~RfGi~~~~~~TLeevg~~f~vtRERi 594 (620) T PRK05658 515 ETPIGDDEDSHLGDFIEDKNAELPIDAATQESLREQTTDVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERI 594 (620) T ss_pred CCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHH T ss_conf 38878888764001016899998799999999999999998479999999999957999999678999998829768989 Q ss_pred HHHHHHHHHHHCCHHHHHHHHHHHCC Q ss_conf 99999999983296777875665179 Q gi|254780289|r 657 RQIEAKAIRKLKHPSRSKKLRSFLDG 682 (682) Q Consensus 657 rqi~~~a~~~l~~~~~~~~l~~~~~~ 682 (682) ||||+|||||||||+|+++||+|||- T Consensus 595 RQIEakalrklrhp~r~~~l~~fl~~ 620 (620) T PRK05658 595 RQIEAKALRKLRHPSRSRKLRSFLDD 620 (620) T ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCC T ss_conf 99999999985687257888876049 No 2 >PRK05901 RNA polymerase sigma factor; Provisional Probab=100.00 E-value=0 Score=878.34 Aligned_cols=384 Identities=47% Similarity=0.755 Sum_probs=343.8 Q ss_pred CCHHCCHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCEEECCCCCCCCCCCCCCCCCCHHHHH Q ss_conf 43020289999999978784886789997526843599888999999998479778327841000012364321101112 Q gi|254780289|r 22 LVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASN 101 (682) Q Consensus 22 ~~~d~~~~~ik~LI~~gke~GylTydeIn~~LP~d~~~~e~ie~i~~~L~~~GI~Vve~~~~~~~~~~~~~~~~~~~~~~ 101 (682) ......+..+|+||.+||++|||||+|||++||++.+++|+||+|+.+|++|||+|++..+............ ...+ T Consensus 14 ~~~~~~~~~lk~Li~~gKe~G~lTy~EIn~~Lp~~~~~~e~id~i~~~l~d~gi~v~~~~~~~~~~~~~~~~~---~~~~ 90 (398) T PRK05901 14 AAKKKKQKKAKELKALAKEDGDITYEEIDEDLDLDFDEDEDIDDVIIFLDDLDEDVENEADVDEDKEDDEDDE---IAEK 90 (398) T ss_pred HHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCEECCCCCCCCCCCCCCCCC---CCCC T ss_conf 4057899999999998862798369999975898679989999999999977973046763111233343332---1210 Q ss_pred HHHHHHHHHCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCHHH Q ss_conf 23344442003457777289999998569768897889999999998899999998728238999999998731171036 Q gi|254780289|r 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL 181 (682) Q Consensus 102 e~~~~~~~~~~e~~rtdDPVRMYLREMG~V~LLTREgEIeIAKRIE~G~~~i~~al~~~P~ti~~il~~~e~i~~ge~~L 181 (682) .........+++.++|||||||||||||+||||||++||+||||||+|... . T Consensus 91 ~~~~~~~~~~~~~~~tdd~v~~yl~~~g~~~ll~~~~e~~~a~~~~~~~~~------------~---------------- 142 (398) T PRK05901 91 SEKDRQARKDAELTATADPVKAYLKQIGKVKLLNAEEEVELAKRIEAGLYA------------E---------------- 142 (398) T ss_pred HHHHHHHCCCCCCCCCCCCHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHH------------H---------------- T ss_conf 234444113333688897199999862755488879999999999840456------------7---------------- Q ss_pred HHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCHHHHHHHHHH Q ss_conf 78764210135433333334333332110001110001000000001221000011111013566665303443100022 Q gi|254780289|r 182 REIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDED 261 (682) Q Consensus 182 rdIIDld~t~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~e~~~e~~~~~~~~~~~~~~~~~~e~e~~~~~~e~e 261 (682) + T Consensus 143 -~------------------------------------------------------------------------------ 143 (398) T PRK05901 143 -E------------------------------------------------------------------------------ 143 (398) T ss_pred -H------------------------------------------------------------------------------ T ss_conf -6------------------------------------------------------------------------------ Q ss_pred HHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 23345555644421023479876689999999999999875210120007999999999999998621005778878999 Q gi|254780289|r 262 EDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341 (682) Q Consensus 262 ~de~~~sla~~e~eLk~~v~e~l~~i~~~~~kl~k~~~~~~~~~~~~~~~kk~~kl~~eL~e~~~~lkl~~k~iE~L~~~ 341 (682) .+ + T Consensus 144 ----------------------------------------------------------~~--------------~----- 146 (398) T PRK05901 144 ----------------------------------------------------------LL--------------E----- 146 (398) T ss_pred ----------------------------------------------------------HH--------------H----- T ss_conf ----------------------------------------------------------67--------------6----- Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999999999999999999712535777763167768989999986135510676554345677653223333222221 Q gi|254780289|r 342 LYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG 421 (682) Q Consensus 342 l~~~~k~Ir~~Er~L~rl~~k~~i~R~~Fi~~f~gnEt~~~wl~~~~~~~~~~~~~~l~~~~~eI~~~q~kL~~ie~~~g 421 (682) + . ...| T Consensus 147 ------------~-------------~-----------~~~~-------------------------------------- 152 (398) T PRK05901 147 ------------K-------------R-----------DLRW-------------------------------------- 152 (398) T ss_pred ------------H-------------H-----------HHHH-------------------------------------- T ss_conf ------------7-------------7-----------7777-------------------------------------- Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHH Q ss_conf 12688999999876533211246899987555789998875223567778875443679999887438545731201028 Q gi|254780289|r 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501 (682) Q Consensus 422 l~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~ 501 (682) ..+..++||++||+|||||||||||+|.|+|++|+|||||||+|||+||+||||.|||||||||+ T Consensus 153 ---------------~~~~~~~Ar~~Li~aNLRLVvsIAkkY~~~Gl~l~DLIQEGniGLirAvekFDp~rG~rFSTYA~ 217 (398) T PRK05901 153 ---------------IARDGKRAKNHLLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYAT 217 (398) T ss_pred ---------------HHHCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHH T ss_conf ---------------53053999999999706999999976468998988999986899999999719777995421149 Q ss_pred HHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCC Q ss_conf 98999999999722870461420588989999999998776088999789998709998999999986089875536358 Q gi|254780289|r 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG 581 (682) Q Consensus 502 ~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~ 581 (682) |||||+|+|||++|+|+||+|+||.+++|++.++.+++.+++||+||++|||+.||+|+++|+.++++++.|+|||+|+| T Consensus 218 wWIRqaI~rai~~~~r~IRiP~h~~e~~~k~~r~~~~l~~~~gr~Pt~eEiA~~lg~~~~~v~~~~~~~~~~~SLd~~vg 297 (398) T PRK05901 218 WWIRQAITRAMADQARTIRIPVHMVETINKLGRIERELLQELGREPTPEELAEEMDFTPEKVREIQKYAREPISLDKTIG 297 (398) T ss_pred HHHHHHHHHHHHHCCCEEECCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCC T ss_conf 99999999999966873523323999999999999999998489999999998819999999999997289855678778 Q ss_pred CCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHH Q ss_conf 89986047562389889989999999999999999732998899999998187986746889998996678999999999 Q gi|254780289|r 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661 (682) Q Consensus 582 ~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~ 661 (682) ++++++|+|+++|.++.+|++.+....+++.|..+|.+|+|||+.||++||||+++.|+||+|||+.||||||||||||. T Consensus 298 ~d~~~~l~d~i~D~~~~~p~~~~~~~~l~~~l~~~L~~L~~REr~Ii~~RyGL~~~~~~TL~eIg~~lgvSrERVRQIE~ 377 (398) T PRK05901 298 DEGDSQFGDFIEDSEAVSPVDAVSFTLLQDQLQEVLETLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIES 377 (398) T ss_pred CCCCCCHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHH T ss_conf 99865186641699999999999999999999999838999999999997589998960399999897969999999999 Q ss_pred HHHHHHCCHHHHHHHHHHHC Q ss_conf 99998329677787566517 Q gi|254780289|r 662 KAIRKLKHPSRSKKLRSFLD 681 (682) Q Consensus 662 ~a~~~l~~~~~~~~l~~~~~ 681 (682) +||+|||||+|+..|++||| T Consensus 378 kAL~KLR~~~~~~~l~~~l~ 397 (398) T PRK05901 378 KTMRKLRHPSRSQVLRDFLD 397 (398) T ss_pred HHHHHHCCCHHHHHHHHHHC T ss_conf 99999678378879999857 No 3 >PRK09210 RNA polymerase sigma factor RpoD; Validated Probab=100.00 E-value=0 Score=823.65 Aligned_cols=357 Identities=53% Similarity=0.843 Sum_probs=328.4 Q ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHH Q ss_conf 89999999978784886789997526843599888999999998479778327841000012364321101112233444 Q gi|254780289|r 28 DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQ 107 (682) Q Consensus 28 ~~~ik~LI~~gke~GylTydeIn~~LP~d~~~~e~ie~i~~~L~~~GI~Vve~~~~~~~~~~~~~~~~~~~~~~e~~~~~ 107 (682) .+.++.||++||++|||||+||+++||+..++++++|.|+..|.+.||.|++..+..............+ .... T Consensus 12 ~~~~~~l~~~~~~~g~~~~~ei~~~~~~~~~~~~~~~~~~~~l~~~~i~i~~~~~~~~~~~~~~~~~~~~------~~~~ 85 (368) T PRK09210 12 EVVVKELIEKGKKRGTLTYDEIAEKLQPFELDSDQIDDLYERLEDAGISIVDENGNPSSKALQEEKKEEE------LEDE 85 (368) T ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCEEECCCCCCCCCCCCCCCCCCC------HHHH T ss_conf 9999999999987697559999987043489999999999999987898847877642100001111100------0000 Q ss_pred HHHCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCHHHHHHHHH Q ss_conf 42003457777289999998569768897889999999998899999998728238999999998731171036787642 Q gi|254780289|r 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDL 187 (682) Q Consensus 108 ~~~~~e~~rtdDPVRMYLREMG~V~LLTREgEIeIAKRIE~G~~~i~~al~~~P~ti~~il~~~e~i~~ge~~LrdIIDl 187 (682) .....+...++|||||||+|||++||||+|+|+++||||++|- T Consensus 86 ~~~~~~~~~~~d~v~~YL~eI~~~pLLt~eEE~~La~r~~~GD------------------------------------- 128 (368) T PRK09210 86 DLSVPPGVKINDPVRMYLKEIGRVPLLTAEEEIELAKRIEEGD------------------------------------- 128 (368) T ss_pred CCCCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHCC------------------------------------- T ss_conf 0132114655858999999956788999999999999988157------------------------------------- Q ss_pred HHCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHH Q ss_conf 10135433333334333332110001110001000000001221000011111013566665303443100022233455 Q gi|254780289|r 188 EACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267 (682) Q Consensus 188 d~t~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~e~~~e~~~~~~~~~~~~~~~~~~e~e~~~~~~e~e~de~~~ 267 (682) T Consensus 129 -------------------------------------------------------------------------------- 128 (368) T PRK09210 129 -------------------------------------------------------------------------------- 128 (368) T ss_pred -------------------------------------------------------------------------------- T ss_conf -------------------------------------------------------------------------------- Q ss_pred HHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 55644421023479876689999999999999875210120007999999999999998621005778878999999999 Q gi|254780289|r 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISK 347 (682) Q Consensus 268 sla~~e~eLk~~v~e~l~~i~~~~~kl~k~~~~~~~~~~~~~~~kk~~kl~~eL~e~~~~lkl~~k~iE~L~~~l~~~~k 347 (682) T Consensus 129 -------------------------------------------------------------------------------- 128 (368) T PRK09210 129 -------------------------------------------------------------------------------- 128 (368) T ss_pred -------------------------------------------------------------------------------- T ss_conf -------------------------------------------------------------------------------- Q ss_pred HHHHHHHHHHHHHHHHCCCHHHHHHHCCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999999999999712535777763167768989999986135510676554345677653223333222221126889 Q gi|254780289|r 348 RIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427 (682) Q Consensus 348 ~Ir~~Er~L~rl~~k~~i~R~~Fi~~f~gnEt~~~wl~~~~~~~~~~~~~~l~~~~~eI~~~q~kL~~ie~~~gl~i~El 427 (682) T Consensus 129 -------------------------------------------------------------------------------- 128 (368) T PRK09210 129 -------------------------------------------------------------------------------- 128 (368) T ss_pred -------------------------------------------------------------------------------- T ss_conf -------------------------------------------------------------------------------- Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHH Q ss_conf 99999876533211246899987555789998875223567778875443679999887438545731201028989999 Q gi|254780289|r 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507 (682) Q Consensus 428 K~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~ 507 (682) ..||++||+|||||||||||+|.|+|++|+|||||||+|||+||+||||+|||||||||+|||||+ T Consensus 129 --------------~~Ar~~Li~aNLRLVVsIAkkY~~~Gl~l~DLIQEGNiGLmkAVeKFDp~rG~RFSTYA~WWIRqa 194 (368) T PRK09210 129 --------------EEAKQRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQA 194 (368) T ss_pred --------------HHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHH T ss_conf --------------999999999838999999986668998989999986799999999729877995334669999999 Q ss_pred HHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCE Q ss_conf 99999722870461420588989999999998776088999789998709998999999986089875536358899860 Q gi|254780289|r 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587 (682) Q Consensus 508 i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~ 587 (682) |+|||++||||||+|+||.+++||+.++.+++.+++||+||++|||+.||+|+++|+.++++++.|+|||+|+|++++++ T Consensus 195 I~raI~~q~r~IRiPvh~~e~~~kl~r~~r~L~q~lGrePt~eEIA~~lgi~~e~V~~i~~~~~~~~SLd~pvg~e~~s~ 274 (368) T PRK09210 195 ITRAIADQARTIRIPVHMVETINKLIRVQRQLLQELGRDPTPEEIAEEMDMPPEKVREILKIAQEPVSLETPIGEEDDSH 274 (368) T ss_pred HHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCH T ss_conf 99999982785135424999999999999999998389998899998949989999999985388856688678877552 Q ss_pred EEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH Q ss_conf 47562389889989999999999999999732998899999998187986746889998996678999999999999983 Q gi|254780289|r 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667 (682) Q Consensus 588 ~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l 667 (682) ++|+++|.++.+|.+.+....+++.|..+|.+|+|||+.||++||||+++.|+||+|||+.||||||||||||.+||+|| T Consensus 275 l~d~i~D~~~~~p~e~~~~~~l~~~l~~~L~~L~~REr~Il~~RfGL~~~~~~TLeEIg~~lgvSRERVRQIE~kAL~KL 354 (368) T PRK09210 275 LGDFIEDQDATSPADHAAYELLKEQLEEVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 354 (368) T ss_pred HHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH T ss_conf 87552489999989999999999999999817999999999997599968961499999896979899999999999997 Q ss_pred CCHHHHHHHHHHHC Q ss_conf 29677787566517 Q gi|254780289|r 668 KHPSRSKKLRSFLD 681 (682) Q Consensus 668 ~~~~~~~~l~~~~~ 681 (682) |||+|+++|++||| T Consensus 355 R~~~~~~~l~~~l~ 368 (368) T PRK09210 355 RHPSRSKQLKDFLE 368 (368) T ss_pred CCCHHHHHHHHHHC T ss_conf 67368789888739 No 4 >TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family. Probab=100.00 E-value=0 Score=821.59 Aligned_cols=246 Identities=48% Similarity=0.826 Sum_probs=236.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCC Q ss_conf 32222211268899999987653321124689998755578999887522356777887544367999988743854573 Q gi|254780289|r 415 SISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494 (682) Q Consensus 415 ~ie~~~gl~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~ 494 (682) ...+.+.++. ||+.+ .+..++||.+||+|||||||||||||.|||++|+||||||+|||.+||+||||.||| T Consensus 90 aWA~~a~l~l-eLk~~-------~r~G~RAK~kMi~ANLRLVVSvAKKYq~RglElLDLIQEG~lGL~RAVEKFDPtrGY 161 (336) T TIGR02997 90 AWAEAAQLEL-ELKLV-------LRQGQRAKEKMIKANLRLVVSVAKKYQNRGLELLDLIQEGTLGLERAVEKFDPTRGY 161 (336) T ss_pred HHHHHHHHHH-HHHHH-------HHHHHHHHHHHHHHCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCCCCCCCC T ss_conf 8899842258-99999-------997899999998760226889999851368833568876343122112335777788 Q ss_pred EEEHHHHHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCC Q ss_conf 12010289899999999972287046142058898999999999877608899978999870999899999998608987 Q gi|254780289|r 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI 574 (682) Q Consensus 495 ~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ 574 (682) ||||||+|||||+||||||.||||||+|+||.|++||+.|++|++.|++||.||.+|||+.|+|++++|+.++..++.|+ T Consensus 162 KFSTYAYWWIRQ~ITRAIA~qSRTIRLPiH~~EKLnkiKK~qReL~q~lGR~Ps~~EiAe~lel~~~qvR~~l~~~~~p~ 241 (336) T TIGR02997 162 KFSTYAYWWIRQGITRAIANQSRTIRLPIHITEKLNKIKKVQRELSQKLGRRPSEAEIAEALELEPEQVRELLQRARQPV 241 (336) T ss_pred CCCCHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCC T ss_conf 63301246875688999843688324741076666899899899999838897868999883889889999999707874 Q ss_pred CCCCCC-CCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCH Q ss_conf 553635-8899860475623898899899999999999999997329988999999981879867468899989966789 Q gi|254780289|r 575 SLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTR 653 (682) Q Consensus 575 sl~~~~-~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~ 653 (682) |||+|| |+++||.|||+|+|++..+|++.+.+.+|+..|..+|+.|+|||++||+|||||+++.++||.|||+.||||| T Consensus 242 SLd~~VrG~e~dt~LgdLl~d~~~~~P~~~~~~~~l~~dL~~lL~~L~p~e~~VL~LRfGL~~~~~~TL~eiG~~l~lSR 321 (336) T TIGR02997 242 SLDTRVRGDEEDTELGDLLEDEDGESPEEQVEQESLRQDLESLLAELTPRERQVLRLRFGLDDGEPLTLAEIGERLNLSR 321 (336) T ss_pred CCCCCCCCCCCCCHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCH T ss_conf 45773268885422654326888998278999999999999988637988999999857899897532789998838836 Q ss_pred HHHHHHHHHHHHHHC Q ss_conf 999999999999832 Q gi|254780289|r 654 ERIRQIEAKAIRKLK 668 (682) Q Consensus 654 er~rqi~~~a~~~l~ 668 (682) |||||||++||+||| T Consensus 322 ERVRQiE~~AL~kLR 336 (336) T TIGR02997 322 ERVRQIEAKALRKLR 336 (336) T ss_pred HHHHHHHHHHHHHCC T ss_conf 888899999975349 No 5 >TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD; InterPro: IPR012760 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This entry represents the C-terminal region of sigma 70 (RpoD) which contains the well-conserved regions 2, 3 and 4. Region 2 of sigma-70 is the most conserved region of the entire protein. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core-binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime , . The aromatic residues of the recognition helix, found at the C terminus of this domain are thought to mediate strand separation, thereby allowing transcription initiation , . Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme .Region 4 is involved in binding to the -35 promoter element via a helix-turn-helix motif .; GO: 0003677 DNA binding, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent. Probab=100.00 E-value=0 Score=831.21 Aligned_cols=238 Identities=65% Similarity=1.022 Sum_probs=236.7 Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCC Q ss_conf 68999875557899988752235677788754436799998874385457312010289899999999972287046142 Q gi|254780289|r 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523 (682) Q Consensus 444 AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~ 523 (682) ||++||+|||||||||||||.||||+|+|||||||+||||||+||||++||||||||||||||||||||||||||||||| T Consensus 1 Ak~~l~~sNLRLVvSIAKkY~nRGL~F~DLIQEGn~GL~KAv~KFdy~kGyKFSTYATWWIRQAITRAIADQARtIRiPV 80 (240) T TIGR02393 1 AKKKLVESNLRLVVSIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPV 80 (240) T ss_pred CHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCH T ss_conf 93568873014666676663047863343676523578988776213578865511578999999998875137201103 Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHH Q ss_conf 05889899999999987760889997899987099989999999860898755363588998604756238988998999 Q gi|254780289|r 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603 (682) Q Consensus 524 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~ 603 (682) ||+|||||+.++.|++.|++||+||+||||+.||++++||+.+.+++++|||||+|||+|+||.|+|||+|+++.+|.+. T Consensus 81 Hm~ETINk~~~~~R~l~Q~~Gr~Pt~EelAe~~g~~~~Kv~~i~~~~~~PiSLe~piG~e~dS~l~DFi~D~~~~~P~~~ 160 (240) T TIGR02393 81 HMVETINKLIKAERKLLQELGREPTDEELAERMGLPVEKVREIKKIAQEPISLETPIGEEEDSSLGDFIEDESIESPEDA 160 (240) T ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHH T ss_conf 26678889999989999872889987789987089989999999862488656667788777744265257444685899 Q ss_pred HHHHHHHHHHHHHHH-CCCHHHHHHHHHHHCCCCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHC Q ss_conf 999999999999973-2998899999998187986-74688999899667899999999999998329677787566517 Q gi|254780289|r 604 AIQANLRETTTRVLA-SLTPREERVLRMRFGIGMN-TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681 (682) Q Consensus 604 ~~~~~~~~~~~~~l~-~l~~re~~v~~~r~g~~~~-~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~~~~~l~~~~~ 681 (682) +....|+++|..||. +|++||+.||+|||||.++ +++||||||+.|+||||||||||+|||||||||+|++.||+|++ T Consensus 161 ~~~~~l~~~l~~vL~~~L~~rE~~Vl~~RyGL~d~~~~~TLEEVG~~f~VTRERIRQIE~KALRKLrhp~r~~~Lk~f~~ 240 (240) T TIGR02393 161 AAKELLREQLEEVLENTLTERERKVLRMRYGLLDGEKPKTLEEVGKEFNVTRERIRQIESKALRKLRHPSRSKKLKDFLD 240 (240) T ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHCC T ss_conf 99999999999998601788899999874389988765337888765178711456888999885028436677776419 No 6 >PRK07598 RNA polymerase sigma factor SigC; Validated Probab=100.00 E-value=0 Score=732.38 Aligned_cols=254 Identities=46% Similarity=0.789 Sum_probs=241.3 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHH Q ss_conf 11268899999987653321124689998755578999887522356777887544367999988743854573120102 Q gi|254780289|r 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500 (682) Q Consensus 421 gl~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya 500 (682) +++..++..+ + +..++||++||+|||||||||||+|.|+|++|+|||||||+|||+||+||||+||||||||| T Consensus 155 ~~~~~el~~~---~----~~G~~Ar~kLI~aNLRLVVsIAkkY~~rGl~l~DLIQEGniGLirAVEKFDp~rG~RFSTYA 227 (410) T PRK07598 155 KLTVEELEQI---Q----KQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYA 227 (410) T ss_pred CCCHHHHHHH---H----HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEE T ss_conf 1469999999---9----99999999999998999999998657899898999987489999999970965597257621 Q ss_pred HHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCC Q ss_conf 89899999999972287046142058898999999999877608899978999870999899999998608987553635 Q gi|254780289|r 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580 (682) Q Consensus 501 ~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~ 580 (682) +|||||+|+|||++|+||||+|+|+.+.+||+.++.+++.+++||.||.+|||+.||+++++|+.++.....|+|||+|+ T Consensus 228 ~WWIRQaI~RaI~~~~r~IRlP~h~~e~l~ki~r~~r~L~q~lGR~Pt~eEIA~~lg~s~e~V~~~l~~~~~~vSLd~pv 307 (410) T PRK07598 228 YWWIRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREVLLRVPRSVSLETKV 307 (410) T ss_pred HHHHHHHHHHHHHHHCCEECCCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHCCCCCCCCCCC T ss_conf 89999999999998088020460299999999999999998759999799999880999999999998727885536788 Q ss_pred CCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHH Q ss_conf 88998604756238988998999999999999999973299889999999818798674688999899667899999999 Q gi|254780289|r 581 GDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660 (682) Q Consensus 581 ~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~ 660 (682) |+|++++++|+++|.+ .+|++.+....++..|..+|..|+|||+.||++||||+++.|+||+|||+.|||||||||||| T Consensus 308 g~d~d~~l~dll~~~~-~~pee~~~~~~l~~~L~~lL~~L~~REr~IL~lRfGL~dg~~~TL~EIG~~lgISRERVRQIE 386 (410) T PRK07598 308 GKDKDTELGDLLETDD-VSPEEMLMRESLQRDLQQLLADLTSRERDVIRMRFGLADGRTYSLAEIGRALDLSRERVRQIE 386 (410) T ss_pred CCCCCCCHHHHHCCCC-CCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHH T ss_conf 8888641888744589-998999999999999999983699999999999648999796689999989796999999999 Q ss_pred HHHHHHHCCHHHHHHHHHHHCC Q ss_conf 9999983296777875665179 Q gi|254780289|r 661 AKAIRKLKHPSRSKKLRSFLDG 682 (682) Q Consensus 661 ~~a~~~l~~~~~~~~l~~~~~~ 682 (682) .+||+|||||+|+..|++|||. T Consensus 387 ~kAL~KLR~p~r~~~Lr~yl~~ 408 (410) T PRK07598 387 AKALQKLRQPKRRNRIRDYLEL 408 (410) T ss_pred HHHHHHHCCCHHHHHHHHHHHH T ss_conf 9999996773778999999872 No 7 >PRK07406 RNA polymerase sigma factor RpoD; Validated Probab=100.00 E-value=0 Score=706.36 Aligned_cols=246 Identities=54% Similarity=0.874 Sum_probs=237.6 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHH Q ss_conf 99987653321124689998755578999887522356777887544367999988743854573120102898999999 Q gi|254780289|r 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509 (682) Q Consensus 430 i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~ 509 (682) +.+.+..| ++||++||+|||||||||||+|.|+|++|+|||||||+|||+||+||||.|||||||||+|||||+|+ T Consensus 139 l~~~~~~g----~~Ar~~LI~aNLRLVVsIAkkY~~rGl~l~DLIQEGniGLirAvEKFDp~rG~RFSTYA~WWIRqaI~ 214 (385) T PRK07406 139 FRRRLMLG----RRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAIT 214 (385) T ss_pred HHHHHHHH----HHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCEEEHHHHHHHHHHH T ss_conf 99999879----99999999998999999998656899898899998589999999981965488221102999999999 Q ss_pred HHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEE Q ss_conf 99972287046142058898999999999877608899978999870999899999998608987553635889986047 Q gi|254780289|r 510 RSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589 (682) Q Consensus 510 ~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~ 589 (682) |||++|+|+||+|+|+.+.++++.++.+.+.+++||.||++|||+.+++++++|+.+++.++.|+|||+|+|++++++++ T Consensus 215 RaI~~~sr~IRlP~h~~e~l~ki~k~~~~L~~~lGr~Pt~eEIA~~l~i~~e~v~~~~~~~~~~vSLD~pvg~~~ds~l~ 294 (385) T PRK07406 215 RAIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLG 294 (385) T ss_pred HHHHHCCCEECCHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCHH T ss_conf 99997386120208999999999999999998708998699999993999999999998548986545888876533188 Q ss_pred EEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC Q ss_conf 56238988998999999999999999973299889999999818798674688999899667899999999999998329 Q gi|254780289|r 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669 (682) Q Consensus 590 ~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~ 669 (682) |++++ +..+|++.+....+++.|..+|++|+|||+.||++||||+++.|+||+|||+.||||||||||||.+||+|||| T Consensus 295 D~i~~-d~~~pe~~~~~~~lr~~L~~~L~~L~eREr~II~lRfGL~dg~~~TL~EIg~~lgISRERVRQIE~rAL~KLR~ 373 (385) T PRK07406 295 DFIEA-DGETPEDDVSKNLLREDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRH 373 (385) T ss_pred HHHHC-CCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC T ss_conf 89863-59999999999999999999986499999999999758999996469999989795999999999999999677 Q ss_pred HHHHHHHHHHH Q ss_conf 67778756651 Q gi|254780289|r 670 PSRSKKLRSFL 680 (682) Q Consensus 670 ~~~~~~l~~~~ 680 (682) |+|+..|+.|| T Consensus 374 p~r~~~L~~yl 384 (385) T PRK07406 374 PNRNSVLKEYI 384 (385) T ss_pred CHHHHHHHHHH T ss_conf 17789999974 No 8 >PRK07921 RNA polymerase sigma factor SigB; Reviewed Probab=100.00 E-value=0 Score=668.40 Aligned_cols=240 Identities=47% Similarity=0.854 Sum_probs=236.8 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEE Q ss_conf 12468999875557899988752235677788754436799998874385457312010289899999999972287046 Q gi|254780289|r 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520 (682) Q Consensus 441 ~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r 520 (682) ..+||++||+|||||||||||+|.|+|++|.|||||||||||+||+||||+|||||||||+|||||+|+|+|.+|+|+|| T Consensus 80 g~~A~~~lI~aNLRLVvsIAk~Y~~~Gl~~~DLIQEGniGLirAvekFDp~rG~rFSTYA~wWIRq~I~r~i~~~~r~IR 159 (320) T PRK07921 80 GEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIR 159 (320) T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCC T ss_conf 69999999998189999999856589999899999838999988851689999812877799999999999997086214 Q ss_pred CCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCH Q ss_conf 14205889899999999987760889997899987099989999999860898755363588998604756238988998 Q gi|254780289|r 521 IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600 (682) Q Consensus 521 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~ 600 (682) +|+|+.+.++++.++.+++.+++||+||++|||+.+|+|+++|..++..++.|+|||.|+|+|++++++|+++|.+..+| T Consensus 160 lP~~~~~~~~ki~~~~~~l~~~lGR~Pt~eEIA~~lgi~~~~v~~~l~~~~~~~SLD~~vg~d~~~~l~d~i~D~~~~~~ 239 (320) T PRK07921 160 LPVHLVEQVNKLARIKREMHQHLGREATDEELAEESGIPEEKINDLLEHSRDPVSLDMPVGSDEEAPLGDFIEDAEAMSA 239 (320) T ss_pred CCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHCCCCCCH T ss_conf 71889999999999999999983899989999988199999999999972888366776688875303324405678998 Q ss_pred HHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHH Q ss_conf 99999999999999997329988999999981879867468899989966789999999999999832967778756651 Q gi|254780289|r 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680 (682) Q Consensus 601 ~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~~~~~l~~~~ 680 (682) ++.+....++..|..+|++|+|||+.||++||||+++.|+||+|||+.||||||||||||.+||+|||||.|+..|++|. T Consensus 240 e~~~~~~~l~~~L~~~L~~L~eREr~IL~~RfGl~~~~~~TL~EIg~~lgvSrERVRQIE~~AL~KLR~~~~~~~L~~y~ 319 (320) T PRK07921 240 ENAVIAELLHTDIRSVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRHGERADRLRSYA 319 (320) T ss_pred HHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHH T ss_conf 99999999999999999759999999999974899989747999998979699999999999999970728888887542 No 9 >COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription] Probab=100.00 E-value=0 Score=669.59 Aligned_cols=267 Identities=56% Similarity=0.881 Sum_probs=258.6 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCC Q ss_conf 33222221126889999998765332112468999875557899988752235677788754436799998874385457 Q gi|254780289|r 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493 (682) Q Consensus 414 ~~ie~~~gl~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g 493 (682) ..++....++..|.+.+...+..|++ ...||++||+|||||||||||+|.|+||+|+|||||||+||||||+||||.|| T Consensus 74 ~~~~~~~~l~~~Ee~~la~~~~~g~~-~~~Ak~klv~snLRlVvsIAk~Y~~rGL~~~DLIQEGniGLmkAVekFdp~rG 152 (342) T COG0568 74 RAIEAAPLLTPEEEKALARRLKRGER-DLDAKKKLVESNLRLVVSIAKKYTGRGLPFLDLIQEGNIGLMKAVEKFDPEKG 152 (342) T ss_pred HHHHHCCCCCHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHCCCHHHHHHHHHCCCCCC T ss_conf 88764001597899999999985885-59999999999889999999986337986889885250999999996296668 Q ss_pred CEEEHHHHHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCC Q ss_conf 31201028989999999997228704614205889899999999987760889997899987099989999999860898 Q gi|254780289|r 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573 (682) Q Consensus 494 ~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~ 573 (682) |||||||||||||+|+|+|++||||||+|+||++++|++.|+.+++.|++||+|+++|||+.||++.++|+.+++.++.| T Consensus 153 ~kFsTYA~wWIrqaI~raI~~q~rtIRipvh~~e~~nkl~r~~r~l~q~~~r~p~~eeia~~l~~~~~~V~~m~~~~~~~ 232 (342) T COG0568 153 FKFSTYATWWIRQAITRAIADQARTIRIPVHQVELINKLRRVKRELLQELGREPTPEEIAEELGVSPDKVREMLKRASEP 232 (342) T ss_pred CCCHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHCCCC T ss_conf 72110999999999999999742346576999999999999999999984589979999999599999999999865367 Q ss_pred CCCCCCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHC-CCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCC Q ss_conf 7553635889986047562389889989999999999999999732-998899999998187986746889998996678 Q gi|254780289|r 574 ISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652 (682) Q Consensus 574 ~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~-l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~ 652 (682) +|||+|+|+|+|+.++||++|.+..+|++.+.+.++++.+..+|++ |+|||+.||++|||++++.|+||+|||+.|||| T Consensus 233 ~SLd~~ig~ded~~l~d~leD~~~~~p~~~~~~~~~~~~~~~~L~~~Lt~rE~~Vi~~R~gl~~~~~~TLeevg~~~~vs 312 (342) T COG0568 233 ISLDTPIGDDEDSELGDFLEDDKSVSPEDAVERESLKEDLNEVLAEALTERERRVIRLRFGLDDGEPKTLEELGEEFGIS 312 (342) T ss_pred CCCCCCCCCCCCCHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCHHHHHHHHHCCC T ss_conf 67678488885207888764268789899999888999999998715999999999999556799955199999895986 Q ss_pred HHHHHHHHHHHHHHHC-CHHHHHHHHHHHC Q ss_conf 9999999999999832-9677787566517 Q gi|254780289|r 653 RERIRQIEAKAIRKLK-HPSRSKKLRSFLD 681 (682) Q Consensus 653 ~er~rqi~~~a~~~l~-~~~~~~~l~~~~~ 681 (682) ||||||||++||+||| ||.++..|++|++ T Consensus 313 rERvRQIE~kAl~KLr~~~~~~~~~~~~l~ 342 (342) T COG0568 313 RERVRQIEAKALRKLRRHPERSALLRSYLD 342 (342) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHC T ss_conf 999999999999999870632227777539 No 10 >PRK05949 RNA polymerase sigma factor; Validated Probab=100.00 E-value=0 Score=650.02 Aligned_cols=245 Identities=43% Similarity=0.793 Sum_probs=235.3 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHH Q ss_conf 99987653321124689998755578999887522356777887544367999988743854573120102898999999 Q gi|254780289|r 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAIT 509 (682) Q Consensus 430 i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~ 509 (682) +.+.+..| ++||++||+|||||||||||+|.|+|++|.|||||||+|||+||+||||.|||||||||+|||||+|+ T Consensus 82 l~~~~~~g----~~A~~~LI~sNLRLVvsIAkrY~~~Gl~~~DLIQEGniGLirAvekFDp~rG~RFSTYA~wWIRq~I~ 157 (327) T PRK05949 82 LKQALKQG----KRAKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAIT 157 (327) T ss_pred HHHHHHHH----HHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEHHHHHHHHHH T ss_conf 99998758----99999999981999999998643699898999998589999999980965597134200999989999 Q ss_pred HHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEE Q ss_conf 99972287046142058898999999999877608899978999870999899999998608987553635889986047 Q gi|254780289|r 510 RSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589 (682) Q Consensus 510 ~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~ 589 (682) |||.+|+|+||+|+|+.+.++++.++.+++.+++||.||++|||+.||+++++|+.++.+++.|+|||.|+|++++++++ T Consensus 158 r~i~~~~r~IRlP~~~~~~~~ki~~~~~~l~~~lgr~pt~~EiA~~l~i~~~~v~~~l~~~~~~~SLD~~v~d~~~~~l~ 237 (327) T PRK05949 158 RAIAQQARTIRLPIHITEKLNKIKKTQRELSQKLGRSATPAEIAKALELEPSQIREYLSMARQPISLDVRVGDNQDTELS 237 (327) T ss_pred HHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHH T ss_conf 99998288744637899999999999999999818899889999894999999999998418872236746999740266 Q ss_pred EEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC Q ss_conf 56238988998999999999999999973299889999999818798674688999899667899999999999998329 Q gi|254780289|r 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669 (682) Q Consensus 590 ~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~ 669 (682) |+++|.+ .+|++.+....+++.+..+|+.|+|||+.||++||||+++.|+||+|||+.||||||||||||.+||+|||| T Consensus 238 dll~d~~-~~pe~~~~~~~lr~~l~~~L~~L~~REr~Ii~~RfGl~~~~~~TL~EIg~~lgiSrERVRQIE~rAL~KLR~ 316 (327) T PRK05949 238 ELLEDEG-VSPDQYITQELLRQDLNNLLAELTPQQREVLTLRFGLEDGKELSLAKVGQRLNLSRERVRQLEHQALAHLRR 316 (327) T ss_pred HHHCCCC-CCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH T ss_conf 6733688-999999999999999999985699999999999718999698579999999895999999999999999862 Q ss_pred HHHHHHHHHHHC Q ss_conf 677787566517 Q gi|254780289|r 670 PSRSKKLRSFLD 681 (682) Q Consensus 670 ~~~~~~l~~~~~ 681 (682) |+..|+.||- T Consensus 317 --~~~~l~~y~~ 326 (327) T PRK05949 317 --RRANVKEYIA 326 (327) T ss_pred --CHHHHHHHHC T ss_conf --5788899865 No 11 >PRK07405 RNA polymerase sigma factor SigD; Validated Probab=100.00 E-value=0 Score=645.57 Aligned_cols=239 Identities=44% Similarity=0.798 Sum_probs=232.3 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEE Q ss_conf 11246899987555789998875223567778875443679999887438545731201028989999999997228704 Q gi|254780289|r 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519 (682) Q Consensus 440 e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~ 519 (682) ...+||.+||+|||||||||||+|.|+|++|.|||||||+|||+||+||||.|||||||||+|||||+|+|+|.+++|+| T Consensus 79 ~g~~A~~~lv~~NLRLVv~iAk~y~~~gl~~~DLIQEGniGLi~AvekFDp~rG~rFSTYA~wWIrq~I~r~i~~~~r~I 158 (318) T PRK07405 79 EGEAAKRKMVEANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTI 158 (318) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEHHHHHHHHHHHHHHHCCCCC T ss_conf 27999999999819999999986657997988999986899999999709765980222009999999999999769851 Q ss_pred ECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCC Q ss_conf 61420588989999999998776088999789998709998999999986089875536358899860475623898899 Q gi|254780289|r 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599 (682) Q Consensus 520 r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~ 599 (682) |+|+|+.+.++++.++.+++.+++||+||++|||+.+|+++++|..++..++.|+|||.|+|++++++++|+++|.+ .+ T Consensus 159 RlP~~~~~~~~ki~~~~~~L~~~lGr~Pt~~EIAe~lgi~~e~V~~~l~~~~~~~SLD~~v~d~~~~~l~dll~D~~-~~ 237 (318) T PRK07405 159 RLPIHITEKLNKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERARQPLSLDLRVGDNQDTELGELLEDDG-AS 237 (318) T ss_pred CCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHCCCC-CC T ss_conf 68778999999999999999987189864899998859999999999998078867688889998640566754788-98 Q ss_pred HHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHHHHHH Q ss_conf 89999999999999999732998899999998187986746889998996678999999999999983296777875665 Q gi|254780289|r 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679 (682) Q Consensus 600 ~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~~~~~l~~~ 679 (682) |++.+....++..+..+|+.|+|||+.||++||||+++.|+||+|||+.||||||||||||.+||.|||+ |+..|++| T Consensus 238 pe~~~~~~~l~~~L~~~L~~L~eREr~II~lRfGl~~~~~~TL~EIg~~lgvSrERVRQIE~~AL~KLR~--~~~~l~~y 315 (318) T PRK07405 238 PEDFATQSSLRRDLERLMADLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLRK--RKANIQEY 315 (318) T ss_pred HHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH--HHHHHHHH T ss_conf 7999999999999999996299989999999807789897479999989795999999999999999987--28888998 Q ss_pred HC Q ss_conf 17 Q gi|254780289|r 680 LD 681 (682) Q Consensus 680 ~~ 681 (682) |- T Consensus 316 l~ 317 (318) T PRK07405 316 LA 317 (318) T ss_pred HC T ss_conf 63 No 12 >PRK05657 RNA polymerase sigma factor RpoS; Validated Probab=100.00 E-value=0 Score=645.02 Aligned_cols=234 Identities=41% Similarity=0.739 Sum_probs=229.4 Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCC Q ss_conf 68999875557899988752235677788754436799998874385457312010289899999999972287046142 Q gi|254780289|r 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523 (682) Q Consensus 444 AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~ 523 (682) |+++||+|||||||||||+|.|+|++|.|||||||+|||+||+||||.|||||||||+|||||+|.|||.+|+|+||+|+ T Consensus 90 Ar~~LI~sNLRLVvsIAkkY~~~Gl~l~DLIQEGniGLikAveKFDp~rG~RFSTYA~WWIRq~I~raI~~~~r~IRlP~ 169 (328) T PRK05657 90 ARQRMIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPV 169 (328) T ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEHHHHHHHHHHHHHHCCCCCCCCC T ss_conf 99999998189999999855689989899998868999999997197669984230099999999999996577777561 Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHH Q ss_conf 05889899999999987760889997899987099989999999860898755363588998604756238988998999 Q gi|254780289|r 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603 (682) Q Consensus 524 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~ 603 (682) |+.+.+|++.++.+++.+.+||+||++|||+.+|+++++|..++..++.++|||+|+|.|++.+++|+++|.+..+|++. T Consensus 170 ~~~~~l~~i~ra~~~l~~~~gr~pt~eEIA~~lg~~~~~v~~~l~~~~~~~SLD~pv~~d~~~tl~d~l~D~~~~~pd~~ 249 (328) T PRK05657 170 HVVKELNVYLRAARELEHKLDHEPSAEEIAELLDKPVDDVSRMLALNERITSLDAPLGGDPEKSLLDILADDQENGPEDT 249 (328) T ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHCCCCCCCHHHH T ss_conf 19999999999999999984899989999999695999999999745876344453589985117888627789999999 Q ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHHHH Q ss_conf 99999999999997329988999999981879867468899989966789999999999999832967778756 Q gi|254780289|r 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677 (682) Q Consensus 604 ~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~~~~~l~ 677 (682) +....++..+..+|+.|+|||+.||++||||+++.|+||+|||+.||||||||||||.+||+|||++.++..|. T Consensus 250 ~~~~~l~~~l~~~L~~L~~REr~II~~RfGL~~~e~~TL~EIg~~lgvSRERVRQIE~~AL~KLR~~l~~~~l~ 323 (328) T PRK05657 250 TQDDDLKQSIVKWLFELNDKQREVIERRFGLNGYEAATLEEVAREIGLTRERVRQIQVEALRRLREILQTQGLS 323 (328) T ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCC T ss_conf 99999999999998069999999999980889989605999998969799999999999999987999986997 No 13 >TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS; InterPro: IPR012761 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This entry represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second principal sigma factor at that time.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent. Probab=100.00 E-value=0 Score=646.57 Aligned_cols=231 Identities=45% Similarity=0.742 Sum_probs=226.2 Q ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECC Q ss_conf 46899987555789998875223567778875443679999887438545731201028989999999997228704614 Q gi|254780289|r 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522 (682) Q Consensus 443 ~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~ 522 (682) .||+.|||+||||||||||+|.|||+||+|||-|||+|||+||+||||.|||||||||||||||+|-|||-.||||||+| T Consensus 46 eAR~~MIE~NLRLVV~IAk~Y~nRGlpLlDLIEEGNLGLm~AvEKFDPeRGFRFSTYATWWIRQtIERAIMNQaRTiRLP 125 (292) T TIGR02394 46 EARKKMIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVEKFDPERGFRFSTYATWWIRQTIERAIMNQARTIRLP 125 (292) T ss_pred HHHHHHHHHHCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCEECC T ss_conf 89888776401267678644047651457777653356654210458899984430111366532786531354411053 Q ss_pred CHHHHHHHHHHHHHHHHHH---HCC---CCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCC-CCEEEEEECCC Q ss_conf 2058898999999999877---608---8999789998709998999999986089875536358899-86047562389 Q gi|254780289|r 523 VHMRDKIHKVVRTARRMSN---KIK---REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED-TSHLGDFIEDK 595 (682) Q Consensus 523 ~~~~~~~~~~~~~~~~~~~---~~~---~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~-~~~~~~~~~d~ 595 (682) ||++.-+|.+.|++|+|.+ ..| ||||+||||+.++=|+++|.++|..+-.++|||+|++.|. ..+++|+|+|. T Consensus 126 vHV~kELNv~LRa~r~L~~ns~~~~E~~~EpS~eeiA~~~~kpvedv~~~L~Lne~~~S~D~Pl~~D~n~~Sl~d~~ADe 205 (292) T TIGR02394 126 VHVVKELNVYLRAARQLEKNSAKLDEEEREPSVEEIAELLDKPVEDVSKVLALNERIASLDAPLDEDSNSKSLLDTIADE 205 (292) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHCCCCEEEECCCCCCCCCHHHHHCCCCC T ss_conf 14346777999988876556763373357788789998838988899999841799525305778774301210004788 Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHH Q ss_conf 889989999999999999999732998899999998187986746889998996678999999999999983296777 Q gi|254780289|r 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673 (682) Q Consensus 596 ~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~~~ 673 (682) +..+|+..+....|+..+...|+.|+.|++.||..||||.+.++.|||+||..+|+||||||||..-||.||||--.. T Consensus 206 ~~~~P~~~~~~~~l~~~~~~~L~~Lne~~R~V~~rRFGL~g~E~~TLE~va~~~gLTRERvRQIQ~eaL~~Lr~~L~~ 283 (292) T TIGR02394 206 QSIDPESLVQNDDLKQLIEAWLAELNERQREVLARRFGLRGYEKATLEEVAKELGLTRERVRQIQVEALKKLRRILER 283 (292) T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHCHHHHEEHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH T ss_conf 877807642189999999998861063211210100376654266699999872881047899889999999999986 No 14 >PRK06596 RNA polymerase factor sigma-32; Reviewed Probab=100.00 E-value=0 Score=510.83 Aligned_cols=226 Identities=32% Similarity=0.506 Sum_probs=192.7 Q ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECC Q ss_conf 46899987555789998875223567778875443679999887438545731201028989999999997228704614 Q gi|254780289|r 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522 (682) Q Consensus 443 ~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~ 522 (682) .|+++||+|||||||||||+|.|+|+++.|||||||||||+||+||||+|||||||||+|||||+|+|+|.++||+||+| T Consensus 48 ~A~~~Li~sNLRLVvsiAkky~~~gl~l~DLIQEGniGLikAvekFDp~kG~rFSTYA~wWIrq~I~r~i~~~~r~Vrip 127 (284) T PRK06596 48 EAAKQLVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIHEYILRNWRIVKVA 127 (284) T ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHH T ss_conf 99999999867999999984678999989999998999999997058998998186799999999999998745613788 Q ss_pred CHHHHHHHHHHHHHHHHHH--HCCCCCCHHHHHHHCCCCHHHHHHHH-HHHCCCCCCCCCCCCCCCC--EEEEEECCCCC Q ss_conf 2058898999999999877--60889997899987099989999999-8608987553635889986--04756238988 Q gi|254780289|r 523 VHMRDKIHKVVRTARRMSN--KIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTS--HLGDFIEDKNA 597 (682) Q Consensus 523 ~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~sl~~~~~~~~~~--~~~~~~~d~~~ 597 (682) +|..+. ++....++..+ ...++|+.++||+.||++.++|..+. +++..++|||+|++++++. .+.|+++|.. T Consensus 128 ~~~~~r--kl~~~lr~~~~~~~~~~~~~~~eiA~~l~~~~~~v~~~~~~l~~~~~SLd~~~~~~~~~~~~~~d~l~d~~- 204 (284) T PRK06596 128 TTKAQR--KLFFNLRKAKKRLGWLNPEEVEMIAEELGVSEEEVREMESRLSGQDASLDAPIDDDDGESGAPQDYLEDKS- 204 (284) T ss_pred HHHHHH--HHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHHCCCC- T ss_conf 899999--99999999999871459862999999979199999999998537982023788888777542466514678- Q ss_pred CCHHHHHHHH----HHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHH Q ss_conf 9989999999----999999999732998899999998187986746889998996678999999999999983296777 Q gi|254780289|r 598 VSPLDSAIQA----NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673 (682) Q Consensus 598 ~~~~~~~~~~----~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~~~ 673 (682) .+|++.+... .++..|..+|+.|+|||+.||++|||. +.|+||+|||+.||||||||||||.+||+|||+.-++ T Consensus 205 ~~~~~~~~~~~~~~~~~~~L~~al~~L~~REr~Il~~Ry~~--d~~~TL~EIg~~lgiSrERVRQIe~kAL~KLR~~L~~ 282 (284) T PRK06596 205 SDPAAVLEEDNWEDQRRELLADALETLDERSRDIIEARWLD--DDKSTLQELAAEYGVSAERIRQIEKNAMKKLKAAIEA 282 (284) T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHCCC--CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH T ss_conf 98678999999999999999999860999999999997679--9994899999997979999999999999999999880 No 15 >PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed Probab=100.00 E-value=0 Score=478.08 Aligned_cols=236 Identities=32% Similarity=0.483 Sum_probs=202.5 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEEC Q ss_conf 24689998755578999887522356777887544367999988743854573120102898999999999722870461 Q gi|254780289|r 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521 (682) Q Consensus 442 ~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~ 521 (682) ..|+++||++|||||+|||++|.|+|+++.|||||||+|||+||+||||+|||||||||+|||||+|.|+|.+++++||+ T Consensus 39 ~~Ar~~LI~~NLRLV~~iA~ry~~~g~~l~DLIQeG~iGLi~AvekFDp~rG~rFSTYA~wWIr~aI~r~i~~~~~~iR~ 118 (289) T PRK07500 39 EDALHRIISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFDPDRDVRFSTYATWWIRASIQDYILRNWSIVRG 118 (289) T ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCEEEHHHHHHHHHHHHHHHHCCCCCCC T ss_conf 99999999985899999998745899897899998699999999736988899721101999999998877736651000 Q ss_pred CCHHHHHH--HHHHHHHHHH---HHHCCCCCCHHHHHHHCCCCHHHHHHHH-HHHCCCCCCCCCCCCCCCCE--EEEEEC Q ss_conf 42058898--9999999998---7760889997899987099989999999-86089875536358899860--475623 Q gi|254780289|r 522 PVHMRDKI--HKVVRTARRM---SNKIKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIGDEDTSH--LGDFIE 593 (682) Q Consensus 522 ~~~~~~~~--~~~~~~~~~~---~~~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~sl~~~~~~~~~~~--~~~~~~ 593 (682) |+|..+.. .++.+...++ ...+++.|+.+|||+.||+|+++|..+. ++...++||+.|++++++.+ +.|++. T Consensus 119 p~~~~~~~l~~~~~~~~~~l~~~~~~~~~~~~~~eiA~~l~~~~~~v~~~~~~~~~~~~SL~~~~~~d~~~~~~~~d~l~ 198 (289) T PRK07500 119 GTSSAQKALFFNLRRLRARLAQSDEQLTKHEIHREIATALGVSLSDVEMMDARLSGPDSSLNAPQSEEDEGRSERMDFLV 198 (289) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHC T ss_conf 03887899999999999999986154565543999998809999999999999737986666806787777401555404 Q ss_pred CCCCCCHHHHHH----HHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC Q ss_conf 898899899999----9999999999973299889999999818798674688999899667899999999999998329 Q gi|254780289|r 594 DKNAVSPLDSAI----QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669 (682) Q Consensus 594 d~~~~~~~~~~~----~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~ 669 (682) |.. +.|++.+. ...++..|..+|+.|++||+.||++|||. +.|.||.|||+.|||||||||||+.+||+|||+ T Consensus 199 d~~-~~p~~~~e~~~~~~~~~~~L~~~l~~L~eREr~Ii~~r~~~--~e~~TL~EIg~~lgvSreRVRQIe~kAL~KLR~ 275 (289) T PRK07500 199 DDS-PLPDEIVESSIDGERRRQWLTQALQTLNERELFIIRERRLR--EDGATLEALGEELGISKERVRQIEARALEKLRR 275 (289) T ss_pred CCC-CCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCC--CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH T ss_conf 688-98389999999999999999999854999999999997668--998589999999797999999999999999999 Q ss_pred H--HHHHHHHHHH Q ss_conf 6--7778756651 Q gi|254780289|r 670 P--SRSKKLRSFL 680 (682) Q Consensus 670 ~--~~~~~l~~~~ 680 (682) . +++.-++.|+ T Consensus 276 ~L~~~~~e~~~~~ 288 (289) T PRK07500 276 ALLSQSPEAAYFL 288 (289) T ss_pred HHHHHCHHHHHHH T ss_conf 9998477988863 No 16 >PRK07122 RNA polymerase sigma factor SigF; Reviewed Probab=100.00 E-value=0 Score=478.33 Aligned_cols=236 Identities=24% Similarity=0.382 Sum_probs=216.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHH Q ss_conf 88999999876533211246899987555789998875223567778875443679999887438545731201028989 Q gi|254780289|r 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504 (682) Q Consensus 425 ~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i 504 (682) ..|..-+..|-.|..+.++||++||++|||||++||++|.|+|+++.||||+||+|||+||+||||+|||||||||+||| T Consensus 21 ~~~~~~~~~~~~~~~~~~~aR~~lI~~nLrLV~~iA~ry~~rGl~~~DLiQeG~iGLi~A~ekFDp~rG~rFsTYA~~wI 100 (263) T PRK07122 21 PEMFRELAGLPAGSPEFQRQRDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVEAGSDFVSFAVPTI 100 (263) T ss_pred HHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHH T ss_conf 99999998568999899999999999909999999987216898888999999999999999719877998599999999 Q ss_pred HHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHH--HCCCCCCCCCCCC Q ss_conf 99999999722870461420588989999999998776088999789998709998999999986--0898755363588 Q gi|254780289|r 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGD 582 (682) Q Consensus 505 ~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~--~~~~~sl~~~~~~ 582 (682) ||+|.+++.+++|+||+|+|+.+...++.++..++.+++||+||++|||+.||++.++|..++.. ...|+|||.|+++ T Consensus 101 rgaI~r~lr~~~~~IRlP~~~~~~~~ki~~~~~~l~~~~gr~Pt~~EiA~~lg~~~~~v~~~l~~~~~~~~~SlD~~~~~ 180 (263) T PRK07122 101 MGEVRRHFRDNSWSVKVPRRLKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVVEGLVAGSSYNTLSIDSGGGS 180 (263) T ss_pred HHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCCCC T ss_conf 99999999982875465799999989999999999998688999999998969399999999987335898778788888 Q ss_pred CCCC--EEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHH Q ss_conf 9986--04756238988998999999999999999973299889999999818798674688999899667899999999 Q gi|254780289|r 583 EDTS--HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660 (682) Q Consensus 583 ~~~~--~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~ 660 (682) +++. .+.|.+.|.+ ........++.+..+|+.|++||+.||++||| .++||.|||+.||||+||||||+ T Consensus 181 ~~~~~~~l~d~~~d~~-----~~~e~~~~~~~L~~~l~~L~eREr~Vi~lry~----e~~Tl~EIa~~lGiSreRVrQIe 251 (263) T PRK07122 181 GDDDARAIADTLGDVD-----AGLDHIENREALRPLLAALPERERTVLVLRFF----ESMTQTQIAERVGISQMHVSRLL 251 (263) T ss_pred CCCCCCHHHHHCCCCC-----HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHC----CCCCHHHHHHHHCCCHHHHHHHH T ss_conf 8865203546416976-----42899999999999997599999999999956----99989999999897999999999 Q ss_pred HHHHHHHCC Q ss_conf 999998329 Q gi|254780289|r 661 AKAIRKLKH 669 (682) Q Consensus 661 ~~a~~~l~~ 669 (682) .+||.|||. T Consensus 252 ~~AL~KLR~ 260 (263) T PRK07122 252 AKSLARLRD 260 (263) T ss_pred HHHHHHHHH T ss_conf 999999999 No 17 >PRK08583 RNA polymerase sigma factor SigB; Validated Probab=100.00 E-value=0 Score=466.21 Aligned_cols=248 Identities=21% Similarity=0.398 Sum_probs=221.0 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCC Q ss_conf 33222221126889999998765-33211246899987555789998875223567778875443679999887438545 Q gi|254780289|r 414 KSISVETGISISEFRHIVSMVRK-GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCL 492 (682) Q Consensus 414 ~~ie~~~gl~i~ElK~i~r~I~~-ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~ 492 (682) .++.+..-|+..|..++.++.+. |. ..|+++||++|||||++||++|.++|+++.|||||||+|||+||+||||+| T Consensus 2 ~~~~~~~~Lt~eee~~L~~~~~~~gd---~~Ar~~Li~~nlrLV~~iA~~y~~~g~~~~DLiQeG~iGLi~AiekFDp~r 78 (257) T PRK08583 2 KESSQPTKLTKEDVNQWIAEYQENQD---EEAQEKLVKHYKNLVESLAYKYSKGQSHHEDLVQVGMVGLLGAIRRYDYSF 78 (257) T ss_pred CCCCCCCCCCHHHHHHHHHHHHHCCC---HHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCCCCC T ss_conf 86768999999999999999988199---999999999849999999998626898861799999999999987069865 Q ss_pred CCEEEHHHHHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHC- Q ss_conf 7312010289899999999972287046142058898999999999877608899978999870999899999998608- Q gi|254780289|r 493 GYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK- 571 (682) Q Consensus 493 g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~- 571 (682) ||||||||+|||||+|.+++.+++|+||+|+|+.+.++++.++..++.+++||.||++|||+.||++.++|..++.... T Consensus 79 G~rFsTYA~~wIr~~I~~~lr~~~~~ir~P~~~~~~~~ki~~~~~~l~~~~~r~pt~~eiA~~l~~s~e~v~~~l~~~~~ 158 (257) T PRK08583 79 GRSFEAFAVPTIIGEIKRYLRDKTWSVHVPRRIKELGPKIKKAVDELTDELQRSPKISEIADRLGVSEEEVLEAMEMGKS 158 (257) T ss_pred CCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHCC T ss_conf 88839878999999999999964871135499999988899999999998089987999998959599999999997516 Q ss_pred -CCCCCCCCCCCCCCC---EEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHH Q ss_conf -987553635889986---0475623898899899999999999999997329988999999981879867468899989 Q gi|254780289|r 572 -EPISLETPIGDEDTS---HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGK 647 (682) Q Consensus 572 -~~~sl~~~~~~~~~~---~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~ 647 (682) .++|||.|++++++. ++.|.+.+ |++.......+..+..++..|++||+.||.+||| .+.|+.|||+ T Consensus 159 ~~~~Sld~~~~~d~d~~~~~~~d~~~~-----~e~~~e~~e~~~~l~~~l~~L~erEr~Ii~lry~----~~~t~~eIa~ 229 (257) T PRK08583 159 YQALSVDHSIEADSDGSTVTLLDIVGQ-----QEDGYELTEQRMILEKILPVLSDREKSIIQCTFI----ENLSQKETGE 229 (257) T ss_pred CCCCCCCCCCCCCCCCCCCCHHHCCCC-----CCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHC----CCCCHHHHHH T ss_conf 897027888877888771204330489-----6624789999999999995499999999999957----9999999999 Q ss_pred HHCCCHHHHHHHHHHHHHHHCCHHHH Q ss_conf 96678999999999999983296777 Q gi|254780289|r 648 QFCVTRERIRQIEAKAIRKLKHPSRS 673 (682) Q Consensus 648 ~~~~~~er~rqi~~~a~~~l~~~~~~ 673 (682) .||||+||||||+.+||.|||++.+. T Consensus 230 ~lGiS~eRVrQi~~~Al~kLR~~~~~ 255 (257) T PRK08583 230 RLGISQMHVSRLQRQAIKKLREAAFL 255 (257) T ss_pred HHCCCHHHHHHHHHHHHHHHHHHHCC T ss_conf 98969999999999999998777505 No 18 >PRK08215 sporulation sigma factor SigG; Reviewed Probab=100.00 E-value=0 Score=459.20 Aligned_cols=240 Identities=30% Similarity=0.456 Sum_probs=213.8 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEE Q ss_conf 22221126889999998765332112468999875557899988752235677788754436799998874385457312 Q gi|254780289|r 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496 (682) Q Consensus 417 e~~~gl~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f 496 (682) ...--|+..|.+++.++++.|. ..|+++||++|||||+|||++|.|+|+++.|||||||+|||+||+||||.||||| T Consensus 14 ~k~PlLt~EEe~~L~~~~~~gD---~~Ar~~LI~~nLrLV~~iA~ky~~~g~~~~DLiQeG~iGLi~AiekFDp~rG~rF 90 (257) T PRK08215 14 SKLPVLKNEEMKELFRRMQNGD---TSAREKLINGNLRLVLSVIQRFNNRGEYVDDLFQVGCIGLMKAIDNFDLSQNVKF 90 (257) T ss_pred CCCCCCCHHHHHHHHHHHHHCC---HHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCE T ss_conf 2489999999999999999388---9999999998789999999876589989889999879999999997097679954 Q ss_pred EHHHHHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCC Q ss_conf 01028989999999997228704614205889899999999987760889997899987099989999999860898755 Q gi|254780289|r 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISL 576 (682) Q Consensus 497 ~tya~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl 576 (682) ||||+|||||+|.++|.++ ++||+|.|+....+++.+...++.+++||+||++|||+.||++.++|..++...+.|+|| T Consensus 91 sTYA~~wIr~~I~~~i~~~-~~irip~~~~~~~~k~~~~~~~l~~~~~r~pt~~eiA~~l~i~~~~v~~~l~~~~~~~SL 169 (257) T PRK08215 91 STYAVPMIIGEIRRYLRDN-NPIRVSRSLRDIAYKALQVREKLIKENSKEPTVSEIAKELEVPREEVVFALDAIQDPVSL 169 (257) T ss_pred EEHHHHHHHHHHHHHHHHC-CCCEEEHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHCCCCCCC T ss_conf 3211999999999999967-985100999999999999999999983899999999988098999999999863898667 Q ss_pred CCCCCCCCCC--EEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHH Q ss_conf 3635889986--04756238988998999999999999999973299889999999818798674688999899667899 Q gi|254780289|r 577 ETPIGDEDTS--HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRE 654 (682) Q Consensus 577 ~~~~~~~~~~--~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~e 654 (682) +.|+++|++. ++.|.+.|..... ...+. ...+.++|+.|+|||+.||++||+ .++|+.|||+.|||||| T Consensus 170 ~~~~~~d~~d~~~~~d~~~d~~~~~-~~~~~----~~~l~~~l~~L~~REr~Ii~~ry~----~~~Tl~eIa~~lGvSre 240 (257) T PRK08215 170 FEPIYHDGGDPIFVMDQISDEKNKD-EQWLE----EIALKEAMKRLNDREKMILNLRFF----QGKTQMEVADEIGISQA 240 (257) T ss_pred CCCCCCCCCCCHHHHHCCCCCCCCC-HHHHH----HHHHHHHHHCCCHHHHHHHHHHHC----CCCCHHHHHHHHCCCHH T ss_conf 6855578997104422147976550-89999----999999996499999999999947----99989999999896999 Q ss_pred HHHHHHHHHHHHHCC Q ss_conf 999999999998329 Q gi|254780289|r 655 RIRQIEAKAIRKLKH 669 (682) Q Consensus 655 r~rqi~~~a~~~l~~ 669 (682) ||||||.+||.|||. T Consensus 241 RVrQie~~AL~kLR~ 255 (257) T PRK08215 241 QVSRLEKAALKHMRK 255 (257) T ss_pred HHHHHHHHHHHHHHH T ss_conf 999999999999985 No 19 >PRK07408 RNA polymerase sigma factor SigF; Reviewed Probab=100.00 E-value=0 Score=455.36 Aligned_cols=234 Identities=25% Similarity=0.401 Sum_probs=205.5 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-CCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHH Q ss_conf 999998765332112468999875557899988752235-6777887544367999988743854573120102898999 Q gi|254780289|r 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR-GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506 (682) Q Consensus 428 K~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~-~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~ 506 (682) .++.++.+. ..-.+|+++||++|||||++||++|.++ |+++.||||+||+|||+||+||||.+||||||||+||||| T Consensus 12 ~eL~~~y~~--~gd~~ar~~LI~~nlrLV~~iA~ry~~~~~~~~~DLiQeG~iGLi~AvekFDp~kG~rFsTYA~~wIr~ 89 (256) T PRK07408 12 MELLRAYQQ--TPSIALRNQLVELNLGLVRKEAHRWSNQCSEPYEDLEQVGYLGLIRAIERFDPSKGHAFSSFAVPYIRG 89 (256) T ss_pred HHHHHHHHH--CCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHH T ss_conf 999999988--499999999999809999999998615799987899999999999999973973389889999999999 Q ss_pred HHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHH--HHCCCCCCCCCCCCCC Q ss_conf 99999972287046142058898999999999877608899978999870999899999998--6089875536358899 Q gi|254780289|r 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDED 584 (682) Q Consensus 507 ~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~sl~~~~~~~~ 584 (682) +|.++|.+++|+||+|+|+.+..+++.++...+.+++||+||.+|||+.||+|+++|..++. .+..|+|||.|+++++ T Consensus 90 ~I~~~lr~~~~~iRiP~~~~~~~~ki~~~~~~l~~~~gr~pt~~EiA~~l~is~~~v~~~~~~~~~~~~~SLd~~~~~~~ 169 (256) T PRK07408 90 EIQHYLRDKSPTVRIPRRWLELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIKLALQNRMPLSLDAPVSQDE 169 (256) T ss_pred HHHHHHHHHCCCEECCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCEECCCCCCCCC T ss_conf 99999998089741369999999999999999999878999899999895969999999999872788730566477999 Q ss_pred C--CEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHH Q ss_conf 8--60475623898899899999999999999997329988999999981879867468899989966789999999999 Q gi|254780289|r 585 T--SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662 (682) Q Consensus 585 ~--~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~ 662 (682) + .+++|.++|++...+..... .+..+.++|..|++||+.||++|||.+ .||.|||+.||||++|||||+.+ T Consensus 170 d~~~~l~d~l~d~~~~~~~~~~e---~~~~L~~~l~~L~eREr~Il~~ry~~~----~tl~EIa~~lgvS~~rVsqi~~~ 242 (256) T PRK07408 170 DGSTSLGDLLPDPRYRSFQLAQE---DRIRLQQALAQLEERTREVLEFVFLHD----LTQKEAAERLGISPVTVSRRVKK 242 (256) T ss_pred CCCCHHHHHCCCCCCCHHHHHHH---HHHHHHHHHHCCCHHHHHHHHHHHCCC----CCHHHHHHHHCCCHHHHHHHHHH T ss_conf 87611777558999753889999---999999998569999999999996379----98999998979899999999999 Q ss_pred HHHHHCCH Q ss_conf 99983296 Q gi|254780289|r 663 AIRKLKHP 670 (682) Q Consensus 663 a~~~l~~~ 670 (682) ||.|||+- T Consensus 243 AL~kLR~~ 250 (256) T PRK07408 243 GLQQLKKL 250 (256) T ss_pred HHHHHHHH T ss_conf 99999997 No 20 >PRK05572 sporulation sigma factor SigF; Validated Probab=100.00 E-value=0 Score=448.79 Aligned_cols=235 Identities=29% Similarity=0.452 Sum_probs=210.0 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHH Q ss_conf 11268899999987653321124689998755578999887522356777887544367999988743854573120102 Q gi|254780289|r 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500 (682) Q Consensus 421 gl~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya 500 (682) .|+..|-.++.++++.|.. +|+++||++|||||+|||++|.|+|+++.|||||||+|||+||+||||++|||||||| T Consensus 11 ~Ls~eee~~L~~~~~~Gd~---~Ar~~Li~~nlrLV~siA~ry~~~g~~~~DLiQeG~iGLi~A~ekFDp~~G~rFsTYA 87 (251) T PRK05572 11 QLKDEENKELIKKAQDGDK---EARDKLVEKNLRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYA 87 (251) T ss_pred CCCHHHHHHHHHHHHCCCH---HHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHH T ss_conf 9999999999999980799---9999999985999999998775899998899999999999996225989898402200 Q ss_pred HHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCC Q ss_conf 89899999999972287046142058898999999999877608899978999870999899999998608987553635 Q gi|254780289|r 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580 (682) Q Consensus 501 ~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~ 580 (682) +|||||+|.++|.+++ +||+|.|+.+..+++.++...+.+.+||.||.+|||+.+|++.++|..++.....+.|++.++ T Consensus 88 ~~wIr~~I~~~ir~~~-~irvp~~~~~~~~ki~~~~~~l~~~~~r~ps~~eia~~lg~~~~~v~~~~~~~~~~~sl~~~~ 166 (251) T PRK05572 88 VPMIIGEIQRFLRDDG-IIKVSRSLKELANKIRKDKEELSKELGRAPTIEELAEYLGVTPEEVVLAQEASRSPQSIHETV 166 (251) T ss_pred HHHHHHHHHHHHHHCC-CCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCC T ss_conf 9999999999998578-766868899999889999999999878899899999997939999999998817987534666 Q ss_pred CCCCCC--EEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHH Q ss_conf 889986--047562389889989999999999999999732998899999998187986746889998996678999999 Q gi|254780289|r 581 GDEDTS--HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658 (682) Q Consensus 581 ~~~~~~--~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rq 658 (682) +++++. ++.|.++|.... ..... +..+.++|..|++||+.||.+||| .++||.|||+.||||+||||| T Consensus 167 ~~~d~~~~~l~d~~~~~~~~--~~~~~----~~~L~~~l~~L~~rEr~Vi~~ry~----~~~tl~EIa~~lgiS~eRVrQ 236 (251) T PRK05572 167 HENDGDPITLLDQIADQSEE--DDWFD----KIALKEAIRELDERERLIIYLRYF----KDKTQSEVAKRLGISQVQVSR 236 (251) T ss_pred CCCCCCHHHHHHHCCCCCHH--HHHHH----HHHHHHHHHCCCHHHHHHHHHHHC----CCCCHHHHHHHHCCCHHHHHH T ss_conf 67899715665412687346--89999----999999997289999999999817----898899999997979999999 Q ss_pred HHHHHHHHHCC Q ss_conf 99999998329 Q gi|254780289|r 659 IEAKAIRKLKH 669 (682) Q Consensus 659 i~~~a~~~l~~ 669 (682) |+.+||+|||. T Consensus 237 I~~~Al~kLR~ 247 (251) T PRK05572 237 LEKKILKQMKE 247 (251) T ss_pred HHHHHHHHHHH T ss_conf 99999999999 No 21 >PRK05911 RNA polymerase sigma factor sigma-28; Reviewed Probab=100.00 E-value=0 Score=444.03 Aligned_cols=242 Identities=24% Similarity=0.377 Sum_probs=213.0 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC---CCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHH Q ss_conf 88999999876533211246899987555789998875223---567778875443679999887438545731201028 Q gi|254780289|r 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501 (682) Q Consensus 425 ~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~---~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~ 501 (682) .++.++.++-. +..-..|+++||++|||||++||++|.+ .|+++.||||+||+|||+||+||||+|||||||||+ T Consensus 7 ~~~~~lw~~y~--~~~d~~ar~~LI~~nLrLV~~iA~r~~~~~p~~v~~~DLiQeG~iGLi~AiekFDp~kG~rFsTYA~ 84 (257) T PRK05911 7 QNIAETWQLYW--ETQEIEYRDVLIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYAL 84 (257) T ss_pred HHHHHHHHHHH--HCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHH T ss_conf 78999999998--8399999999999839999999999864699999889999999999999998329866999488769 Q ss_pred HHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCC--CCCCCCC Q ss_conf 98999999999722870461420588989999999998776088999789998709998999999986089--8755363 Q gi|254780289|r 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE--PISLETP 579 (682) Q Consensus 502 ~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~--~~sl~~~ 579 (682) |||||+|.+++..+.| +|+|+.+.++++.++.+.+.+++||+||.+|||+.||+++++|..++..... .+||+.+ T Consensus 85 ~wIr~aI~~~lr~~~~---lpr~~~~~~~ki~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~~~sl~~~ 161 (257) T PRK05911 85 FLIKAAIIDDLRKQDW---VPRSVHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFSSARPALILSLNEE 161 (257) T ss_pred HHHHHHHHHHHHHCCC---CCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHCCCCCEECCCCC T ss_conf 9989999999987162---5579999999999999999998688999999998839799999999985355222305788 Q ss_pred CCC--CCC--CEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHH Q ss_conf 588--998--6047562389889989999999999999999732998899999998187986746889998996678999 Q gi|254780289|r 580 IGD--EDT--SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655 (682) Q Consensus 580 ~~~--~~~--~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er 655 (682) .+. |++ .++.|.++|+...+|.+.+....++..+.++|..|+|||+.||.+|| +.++||.|||+.||||||| T Consensus 162 ~~~~~d~~~~~~l~d~i~d~~~~~~~~~~~~~~~~~~L~~al~~L~erEr~Ii~lry----~e~~Tl~EIg~~lgvS~eR 237 (257) T PRK05911 162 FPSQSDDEAGLALEERIADERAETGYDVVDKKEFSSILANAILALEEKERKVMALYY----YEELVLKEIGKILGVSESR 237 (257) T ss_pred CCCCCCCCCCCCHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHC----CCCCCHHHHHHHHCCCHHH T ss_conf 887888876530777467988899899999999999999998658999999999874----8987899999897988999 Q ss_pred HHHHHHHHHHHHCCHHHHHHHHHHH Q ss_conf 9999999999832967778756651 Q gi|254780289|r 656 IRQIEAKAIRKLKHPSRSKKLRSFL 680 (682) Q Consensus 656 ~rqi~~~a~~~l~~~~~~~~l~~~~ 680 (682) ||||+.+||.|||. .|.+|+ T Consensus 238 VrQi~~~AL~kLR~-----~L~a~~ 257 (257) T PRK05911 238 VSQIHSKALLKLRA-----ALSAFL 257 (257) T ss_pred HHHHHHHHHHHHHH-----HHHHCC T ss_conf 99999999999999-----998609 No 22 >PRK06288 RNA polymerase sigma factor WhiG; Reviewed Probab=100.00 E-value=0 Score=438.67 Aligned_cols=239 Identities=28% Similarity=0.401 Sum_probs=215.5 Q ss_pred HHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHC---CCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEE Q ss_conf 1126889999998765-3321124689998755578999887522---35677788754436799998874385457312 Q gi|254780289|r 421 GISISEFRHIVSMVRK-GECEASIAKKEMVEANLRLVISVAKKYT---NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKF 496 (682) Q Consensus 421 gl~i~ElK~i~r~I~~-ge~e~~~AK~~l~~anlr~v~~~~~~~~---~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f 496 (682) .++..|-+++.++.+. |. ..|+++||++|||||++||++|. ++|+++.|||||||+|||+||+||||++|||| T Consensus 7 ~~s~eee~eL~~~~~~~gd---~~ar~~LI~~nlrLV~~iA~~~~~~~~~~~~~~DLiQeG~iGLi~AvekFDp~rG~rF 83 (261) T PRK06288 7 KYAQQDETELWKSYKETGD---AKIREYLILKYSPLVKYVAGRVAVGMPQNVEFDDLVSYGVFGLLDAIEKFDPEREIKF 83 (261) T ss_pred CCCHHHHHHHHHHHHHCCC---HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCC T ss_conf 2386999999999988199---9999999998599999999998457999999999999999999999996599878883 Q ss_pred EHHHHHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHH--HHCCCC Q ss_conf 010289899999999972287046142058898999999999877608899978999870999899999998--608987 Q gi|254780289|r 497 STYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPI 574 (682) Q Consensus 497 ~tya~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~ 574 (682) ||||+|||||+|..++.... ++|+|+.+..+++.++...+.+++||.||.+|||+.||+++++|..++. ....++ T Consensus 84 sTYA~~wIr~aI~~~lR~~~---~~pr~~~~~~~ki~~~~~~l~~~~gr~pt~~eia~~lg~~~~~v~~~~~~~~~~~~~ 160 (261) T PRK06288 84 ETYAITRIRGAIFDELRSID---WIPRSVRQKARQVERAIAMLEAKLGRTPTDDEIAKELGISLEEYHSLLSKVSGTSVV 160 (261) T ss_pred HHHHHHHHHHHHHHHHHHHH---HCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHCCCCHHHHHHHHHHHHCCCCC T ss_conf 98799999999999999860---031999999999999999999986899987888878199999999999997269974 Q ss_pred CCCCCCCC---CCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCC Q ss_conf 55363588---998604756238988998999999999999999973299889999999818798674688999899667 Q gi|254780289|r 575 SLETPIGD---EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651 (682) Q Consensus 575 sl~~~~~~---~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~ 651 (682) |||.|+.. +++.+++|.++|+...+|+..+....++..+..+|..|++||+.||.+||| .++||.|||+.||| T Consensus 161 SLd~~~~~~~~~~~~~~~d~l~d~~~~~p~~~~e~~~~~~~l~~~l~~L~erEr~Il~lry~----e~~Tl~eIa~~lgi 236 (261) T PRK06288 161 SLNDLLFLGDENDEVSLMDTLEDPAAMNPDEIIEKEEIKRVIVEAINTLPEREKKVITLYYY----EDLTLKEIGEVLGV 236 (261) T ss_pred CCCCCCCCCCCCCCCCHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCC----CCCCHHHHHHHHCC T ss_conf 76777657999864308787058898999999999999999999987089999999999807----99889999999797 Q ss_pred CHHHHHHHHHHHHHHHCC Q ss_conf 899999999999998329 Q gi|254780289|r 652 TRERIRQIEAKAIRKLKH 669 (682) Q Consensus 652 ~~er~rqi~~~a~~~l~~ 669 (682) |+||||||+.+||.|||. T Consensus 237 S~eRVrQie~~AL~kLR~ 254 (261) T PRK06288 237 TESRISQIHTKAVLQLRA 254 (261) T ss_pred CHHHHHHHHHHHHHHHHH T ss_conf 899999999999999999 No 23 >PRK07670 RNA polymerase sigma factor SigD; Validated Probab=100.00 E-value=0 Score=427.92 Aligned_cols=222 Identities=27% Similarity=0.433 Sum_probs=207.3 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHCC---CCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCC Q ss_conf 1246899987555789998875223---5677788754436799998874385457312010289899999999972287 Q gi|254780289|r 441 ASIAKKEMVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517 (682) Q Consensus 441 ~~~AK~~l~~anlr~v~~~~~~~~~---~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~ 517 (682) -..|+++||++|||||++||++|.+ +|+++.||||+||+|||+||+||||++||||||||+|||||+|.+++.+++ T Consensus 16 D~~Ar~~LV~~nl~LV~~ia~r~~~~~~~~v~~eDLiQeG~iGLi~AiekFDp~~G~rFsTYA~~wIr~aI~~~lr~~~- 94 (250) T PRK07670 16 DPEAADDLIRRYMPLVTYHVQRISAGLPKSVSKDDLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIRGAIIDGLRKED- 94 (250) T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHCC- T ss_conf 9999999999819999999999970489999888999999999999999609866999077219999999999987425- Q ss_pred EEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHH--HHCCCCCCCCCCCCC-CCCEEEEEECC Q ss_conf 046142058898999999999877608899978999870999899999998--608987553635889-98604756238 Q gi|254780289|r 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDE-DTSHLGDFIED 594 (682) Q Consensus 518 ~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~sl~~~~~~~-~~~~~~~~~~d 594 (682) |+|+|+.+..+++.++..++.+++||.||++|||+.||+++++|..++. ....++|||.+++++ ++.++.+.+.| T Consensus 95 --~lpr~~~~~~~ki~~~~~~l~~~~gr~ps~~eia~~lg~s~~~v~~~~~~~~~~~~~Sld~~~~~~~~~~~~~~~~~d 172 (250) T PRK07670 95 --WLPRSSREKTKKVEAAIEKLEQRYMRNVTPSEVAAELGMSEEEVVTTMNEGFFANLLSIDEKLHDQDDGENVQVMIRD 172 (250) T ss_pred --CCHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHC T ss_conf --400999999999999999999983899988899877199999999999987547980367777788885047788852 Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC Q ss_conf 988998999999999999999973299889999999818798674688999899667899999999999998329 Q gi|254780289|r 595 KNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669 (682) Q Consensus 595 ~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~ 669 (682) +...+|++.+....++..|..+|+.|++||+.||.+|| +.++||.|||+.||||+||||||+.+||.|||. T Consensus 173 ~~~~~pe~~~~~~~~~~~L~~~l~~L~~rEr~Vl~l~y----~e~~Tl~eIa~~lgvS~erVrQi~~~AL~kLr~ 243 (250) T PRK07670 173 DKAVTPEEKLVKEELIEQLAEKIKELNEKEQLVISLFY----KEELTLTEIGQVLNLSTSRISQIHSKALFKLKK 243 (250) T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHC----CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH T ss_conf 46799999999999999999998558999999999974----898689999999897999999999999999999 No 24 >PRK06986 fliA flagellar biosynthesis sigma factor; Validated Probab=100.00 E-value=0 Score=417.42 Aligned_cols=221 Identities=27% Similarity=0.453 Sum_probs=198.5 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCCC---CCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHC Q ss_conf 2112468999875557899988752235---6777887544367999988743854573120102898999999999722 Q gi|254780289|r 439 CEASIAKKEMVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQ 515 (682) Q Consensus 439 ~e~~~AK~~l~~anlr~v~~~~~~~~~~---~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~ 515 (682) .+.++||++||++|||||++||++|.++ |+++.|||||||+|||+||+||||++||||||||+|||||+|..++... T Consensus 4 ~~g~~Ar~~Lv~~nl~LV~~iA~r~~~r~~~~v~~~DLiQeG~iGLi~AvekFDp~~G~rFsTYA~~~Ir~aI~~~~r~~ 83 (234) T PRK06986 4 AQGKMSQDSLVEQYAPLVKRIALRLKARLPASVDLDDLIQAGMIGLLEASRRYDGEQGASFETYAGQRIRGAMLDELRSG 83 (234) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHC T ss_conf 76899999999981999999999997338999988999999999999999981886699969999999999999999854 Q ss_pred CCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHH--HCCCCCCCCCCCCCCCCEEEEEEC Q ss_conf 870461420588989999999998776088999789998709998999999986--089875536358899860475623 Q gi|254780289|r 516 SCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTSHLGDFIE 593 (682) Q Consensus 516 ~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~--~~~~~sl~~~~~~~~~~~~~~~~~ 593 (682) .+ +|.++.....++.++.+.+.+++||+||.+|||+.||+++++|..++.. ...++|+|.+..+++ + +.+. . T Consensus 84 ~~---~~r~~~~~~~~i~~~~~~l~~~~~r~pt~~eia~~l~~s~e~v~~~~~~~~~~~~~sld~~~~~~~-~-~~~~-~ 157 (234) T PRK06986 84 DW---VPRSVRRNAREVADAIRELEQELGREPTDTEVAEKLGLSLEEYREMLLDTNISQLFSIDDLGESGE-L-LTDE-D 157 (234) T ss_pred CC---CCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCCCCCC-C-CCCC-C T ss_conf 56---649999999999999999999878799899999895949999999999850577868776776643-1-1122-2 Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC Q ss_conf 8988998999999999999999973299889999999818798674688999899667899999999999998329 Q gi|254780289|r 594 DKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669 (682) Q Consensus 594 d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~ 669 (682) +....+|.+.+....++..|..+|+.|+|||+.||.+|| +.++||.|||+.|||||||||||+.+||.|||. T Consensus 158 ~~~~~~~~~~~~~~~~~~~l~~~l~~L~~rEr~Ii~l~y----~~~~tl~eIa~~lgiS~eRVrQie~~AL~kLR~ 229 (234) T PRK06986 158 QSEHEDPLQQLEDEELREALVEAIEKLPEREQLVLSLYY----DEELNLKEIGAVLGVSESRVSQIHSQAIKRLRA 229 (234) T ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHC----CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH T ss_conf 457899999999999999999999809999999999873----899899999999797899999999999999999 No 25 >TIGR02392 rpoH_proteo alternative sigma factor RpoH; InterPro: IPR012759 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This entry represents the proteobacterial clade of sigma factors called RpoH. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0008270 zinc ion binding, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent, 0009408 response to heat. Probab=100.00 E-value=0 Score=418.99 Aligned_cols=252 Identities=28% Similarity=0.429 Sum_probs=216.8 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCC Q ss_conf 33222221126889999998765332112468999875557899988752235677788754436799998874385457 Q gi|254780289|r 414 KSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLG 493 (682) Q Consensus 414 ~~ie~~~gl~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g 493 (682) ..+...--|++.|-..+.++++.... ..|=++||-+||||||+||+.|.|+|||..||||||||||||||.||||.+| T Consensus 8 ~~vn~~P~L~~EEE~~LA~r~r~~~D--l~AA~~Lv~SHLRfVv~iArgY~GYGL~~aDLIQEGNIGLMkAVkRFdP~~G 85 (279) T TIGR02392 8 RAVNRIPMLTAEEEQELAKRLREEGD--LDAAKKLVLSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPERG 85 (279) T ss_pred HHHHHCCCCCHHHHHHHHHHHHHCCC--HHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCC T ss_conf 99971789998899999998654237--7899987466247875532036777744244342222665533442178987 Q ss_pred CEEEHHHHHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHH-HHHHHHHHHC-CCCCCH---HHHHHHCCCCHHHHHHHH- Q ss_conf 3120102898999999999722870461420588989999-9999987760-889997---899987099989999999- Q gi|254780289|r 494 YKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV-RTARRMSNKI-KREPTP---EEIAKKLAMPVEGVRKVL- 567 (682) Q Consensus 494 ~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~-~~~~~~~~~~-~~~~~~---~~~a~~~~~~~~~~~~~~- 567 (682) +|++|||+||||.+|+.||-.+||+|+|.+...|...+|+ |-.+...+.+ +.--++ +-||+.||++..+|..|- T Consensus 86 vRLvSfAvHWIkAeIHEyILrnWRlVKvATTkaQrKLFFNLRk~K~ki~~l~~gw~~~~e~~~~A~~L~V~~~eV~eMe~ 165 (279) T TIGR02392 86 VRLVSFAVHWIKAEIHEYILRNWRLVKVATTKAQRKLFFNLRKMKKKITRLQDGWLNPEEVEAIAEELGVSEEEVLEMES 165 (279) T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCHHHHHHHHH T ss_conf 22047888999999866899755598885277678887658889998631015798989999999763898889988751 Q ss_pred HHHCCCCCCCCCCCCCCCC-----EEEEEECCCCCCCHHHHHHHHH----HHHHHHHHHHCCCHHHHHHHHHHHCCCCCC Q ss_conf 8608987553635889986-----0475623898899899999999----999999997329988999999981879867 Q gi|254780289|r 568 KITKEPISLETPIGDEDTS-----HLGDFIEDKNAVSPLDSAIQAN----LRETTTRVLASLTPREERVLRMRFGIGMNT 638 (682) Q Consensus 568 ~~~~~~~sl~~~~~~~~~~-----~~~~~~~d~~~~~~~~~~~~~~----~~~~~~~~l~~l~~re~~v~~~r~g~~~~~ 638 (682) +++...+|||.|+.+++++ ...+++.|+...+|...+.... .+..|..+|.+|+.|++.||..|+ ..+. T Consensus 166 RlsG~D~~L~~~~~~~~~~~~~~~~~~~yL~D~~~~~~~~~l~~~~~~~~~~~~L~~AL~~Ld~RsR~I~~~Rw--L~d~ 243 (279) T TIGR02392 166 RLSGRDISLNASIDDDEDDGGSDFAPIAYLADKATSDPEATLEEEQWEELQTQKLANALESLDARSRRIIEARW--LDDD 243 (279) T ss_pred CCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC--CCCC T ss_conf 45537733478876553456311457886304777788899999899999999999998852288799998730--2788 Q ss_pred -CCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC Q ss_conf -4688999899667899999999999998329 Q gi|254780289|r 639 -DHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669 (682) Q Consensus 639 -~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~ 669 (682) |.||+++|..||||+|||||||+.|+.|||. T Consensus 244 ~~~TL~~LA~eygvSaERiRQiE~~Am~K~k~ 275 (279) T TIGR02392 244 GKLTLHELAAEYGVSAERIRQIEKNAMKKLKA 275 (279) T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH T ss_conf 99647899988487466799999999999999 No 26 >PRK05803 sporulation sigma factor SigK; Reviewed Probab=100.00 E-value=0 Score=406.88 Aligned_cols=209 Identities=31% Similarity=0.477 Sum_probs=180.6 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHH Q ss_conf 77653223333222221126889999998765332112468999875557899988752235677788754436799998 Q gi|254780289|r 405 SILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484 (682) Q Consensus 405 eI~~~q~kL~~ie~~~gl~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a 484 (682) ++.-++.-|.++....-|+..|-..+.++++.|. ..|+++||+|||||||||||+|.|+|+++.|||||||+|||+| T Consensus 13 ~~~~l~syl~~i~~~~~Ls~eEE~~La~~~~~GD---~~Ar~~LI~~NLRLVvsIAkky~~~g~~l~DLIQEGniGLi~A 89 (228) T PRK05803 13 EVLFLVSYVKNNSFPQPLSEEEERKYLELMKQGD---EEARNILIERNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKA 89 (228) T ss_pred HHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHCCC---HHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHH T ss_conf 8999999997478899999999999999998468---9999999998779999999627799989899999999999999 Q ss_pred HHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHH Q ss_conf 87438545731201028989999999997228704614205889899999999987760889997899987099989999 Q gi|254780289|r 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564 (682) Q Consensus 485 ~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~ 564 (682) |+||||+|||||||||+||||++|.+++.... T Consensus 90 vekFDp~rG~rFSTYA~~wIr~~I~~~lr~~k------------------------------------------------ 121 (228) T PRK05803 90 IDSFDAGKGTKLATYAARCIENEILMHLRNLK------------------------------------------------ 121 (228) T ss_pred HHHHCCCCCCCCHHCCHHHHHHHHHHHHHHHH------------------------------------------------ T ss_conf 99848998997052009999999999999988------------------------------------------------ Q ss_pred HHHHHHCCCCCCCCCCCCCCC---CEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCC Q ss_conf 999860898755363588998---60475623898899899999999999999997329988999999981879867468 Q gi|254780289|r 565 KVLKITKEPISLETPIGDEDT---SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHT 641 (682) Q Consensus 565 ~~~~~~~~~~sl~~~~~~~~~---~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~t 641 (682) ..+.++|++.|+|.|.+ .++.|++.+... ++.+.+........+..+|+.|+|||+.||++||||+++.|+| T Consensus 122 ----k~~~~~sl~~~i~~d~e~~e~~l~d~l~~~~~-~~~e~~~~~~~~~~l~~~l~~L~~REr~II~~RfGL~~~~~~T 196 (228) T PRK05803 122 ----KTKGEVSLQDPIGVDKEGNEISLIDILKSESD-DVIEMVELSMEVEKLYKKIDILDPREKEVIEMRYGLGDGKEKT 196 (228) T ss_pred ----HHCCCCCCCCCCCCCCCCCCCHHHHHCCCCCC-CHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCC T ss_conf ----75355012374466878983224343168899-8799999999899999998518988999999986478999715 Q ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHCC Q ss_conf 8999899667899999999999998329 Q gi|254780289|r 642 LEEVGKQFCVTRERIRQIEAKAIRKLKH 669 (682) Q Consensus 642 l~e~~~~~~~~~er~rqi~~~a~~~l~~ 669 (682) |+|||+.||||||||||||.+||.|||. T Consensus 197 l~eIg~~lgiSrERVRQIe~~Al~KLrk 224 (228) T PRK05803 197 QREIAKALGISRSYVSRIEKKALKKLFK 224 (228) T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHH T ss_conf 9999999897999999999999999999 No 27 >PRK08301 sporulation sigma factor SigE; Reviewed Probab=100.00 E-value=0 Score=403.01 Aligned_cols=192 Identities=26% Similarity=0.419 Sum_probs=164.0 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHH Q ss_conf 12688999999876533211246899987555789998875223567778875443679999887438545731201028 Q gi|254780289|r 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501 (682) Q Consensus 422 l~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~ 501 (682) |+..|-.++.++++.|.. .|+++||+|||||||||||+|.|+|+++.|||||||+|||+||+||||.|||||||||+ T Consensus 39 Ls~eeE~~l~~~~~~GD~---~Ar~~LI~~NLRLVv~IAkky~~~G~~l~DLIqEGniGLikAvekFDp~kG~rFSTYA~ 115 (239) T PRK08301 39 LSKEEEEVLLNKLPKGDE---AVRSILIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYAS 115 (239) T ss_pred CCHHHHHHHHHHHHHCCH---HHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHH T ss_conf 899999999999983469---99999999878999999975768997989999985899999999649888997163019 Q ss_pred HHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCC Q ss_conf 98999999999722870461420588989999999998776088999789998709998999999986089875536358 Q gi|254780289|r 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG 581 (682) Q Consensus 502 ~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~ 581 (682) |||+|+|.+++..+.++ +.++|++.|++ T Consensus 116 ~~I~~eI~~~lr~~~~~----------------------------------------------------r~evsl~epl~ 143 (239) T PRK08301 116 RCIENEILMYLRRNNKV----------------------------------------------------RSEVSFDEPLN 143 (239) T ss_pred HHHHHHHHHHHHHHHHH----------------------------------------------------HCCCHHCCCCC T ss_conf 99999999999970424----------------------------------------------------22400015368 Q ss_pred CCCC---CEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHH Q ss_conf 8998---6047562389889989999999999999999732998899999998187986746889998996678999999 Q gi|254780289|r 582 DEDT---SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658 (682) Q Consensus 582 ~~~~---~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rq 658 (682) -+.+ ..+.|++.+.+ ..+.+.......+..+..+|+.|+|||+.||++||||+++.|+||+|||+.|||||||||| T Consensus 144 ~d~d~~e~~l~D~l~~d~-d~~~~~~e~~~~~~~L~~al~~L~eREr~Ii~lRfGL~~~~~~Tl~EIa~~lgISrerVrQ 222 (239) T PRK08301 144 IDWDGNELLLSDVLGTDN-DIIYKDIEDEVDKKLLLKALKKLNDREKQIMELRFGLAGGEEKTQKEVADMLGISQSYISR 222 (239) T ss_pred CCCCCCHHHHHHCCCCCC-CHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHH T ss_conf 776656224301148987-5066789999999999999964899999999999578899840699999998978999999 Q ss_pred HHHHHHHHHCC Q ss_conf 99999998329 Q gi|254780289|r 659 IEAKAIRKLKH 669 (682) Q Consensus 659 i~~~a~~~l~~ 669 (682) ||.+||+|||. T Consensus 223 Ie~~AL~KLR~ 233 (239) T PRK08301 223 LEKRIIKRLKK 233 (239) T ss_pred HHHHHHHHHHH T ss_conf 99999999999 No 28 >PRK12427 flagellar biosynthesis sigma factor; Provisional Probab=100.00 E-value=1.4e-45 Score=378.77 Aligned_cols=221 Identities=19% Similarity=0.336 Sum_probs=193.2 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC---CCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHH Q ss_conf 987653321124689998755578999887522356---77788754436799998874385457312010289899999 Q gi|254780289|r 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG---LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508 (682) Q Consensus 432 r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~---~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i 508 (682) +++..+..-+.++|++||++||+||.+||++|.+++ +++.||+|+|++|||+|++|||+++| +|||||+|||||+| T Consensus 2 ~~~~~~~~~~~~~k~~lV~~~L~LV~~ia~r~~~~~~~~vd~dDLiq~G~iGLi~Ai~rFD~~~g-~F~tYA~~rIrGaI 80 (229) T PRK12427 2 REFEACLTLTAAEEGKYLNAYLPLVKRIVRQLSFQADSVIGKEDMQQIALMGLLEALRRYGHPDG-QFAAYAVHRIRGSI 80 (229) T ss_pred CCCHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCC-CHHHHHHHHHHHHH T ss_conf 65220356899999999999599999999999742877798888999999999999984499898-85999999999999 Q ss_pred HHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHH--HCCCCCCCCCCCCCCCC Q ss_conf 9999722870461420588989999999998776088999789998709998999999986--08987553635889986 Q gi|254780289|r 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTS 586 (682) Q Consensus 509 ~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~--~~~~~sl~~~~~~~~~~ 586 (682) .+++.++.| +|+++.+..+++..+.+++.+++||+||++|||+.||+++++|..++.. +..++|||.++++++.. T Consensus 81 ~d~lR~~~~---~pR~~r~~~~ki~~a~~~l~~~lgr~Pt~~EiA~~l~is~~~v~~~~~~~~~~~~~sld~~~~~e~~~ 157 (229) T PRK12427 81 LDQLREHDW---RPRRLRQKTHKTNEAIRQIAKRLGHEPNFEEISAELNLTADEYQEYLLLENAGAMESLDEILALEAHN 157 (229) T ss_pred HHHHHHHCC---CCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCC T ss_conf 999987213---75999999999999999999985889999999989199999999999987366875723344578876 Q ss_pred EEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH Q ss_conf 04756238988998999999999999999973299889999999818798674688999899667899999999999998 Q gi|254780289|r 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666 (682) Q Consensus 587 ~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~ 666 (682) . .+.+ .++. ....++..|..+|++|++||+.||.||| ..+.||.|||+.||||++|||||+.+||.| T Consensus 158 ~---~~~~---~~~~---e~~~~~~~L~~al~~L~erEr~Vi~l~y----~e~ltlkEIa~~LgvS~~RVsQi~~kal~k 224 (229) T PRK12427 158 D---ILQS---RDLE---ENIIIEDNLKQAISQLDEREQMILHLYY----QQELSMKEIAQVLDLTEARICQLNKKLVQK 224 (229) T ss_pred C---CCCC---CCHH---HHHHHHHHHHHHHHHCCHHHHHHHHHHC----CCCCCHHHHHHHHCCCHHHHHHHHHHHHHH T ss_conf 5---4567---6646---7899999999999719999999999980----589989999999798899999999999999 Q ss_pred HCC Q ss_conf 329 Q gi|254780289|r 667 LKH 669 (682) Q Consensus 667 l~~ 669 (682) ||. T Consensus 225 LR~ 227 (229) T PRK12427 225 IKS 227 (229) T ss_pred HHH T ss_conf 884 No 29 >TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily; InterPro: IPR014322 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:IPR014236 from INTERPRO and SigG:IPR014212 from INTERPRO as well as SigB:IPR014288 from INTERPRO), and the high GC Gram-positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent. Probab=100.00 E-value=0 Score=387.09 Aligned_cols=219 Identities=31% Similarity=0.507 Sum_probs=205.4 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCCC-HHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEE Q ss_conf 2468999875557899988752235677-788754436799998874385457312010289899999999972287046 Q gi|254780289|r 442 SIAKKEMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520 (682) Q Consensus 442 ~~AK~~l~~anlr~v~~~~~~~~~~~~~-~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r 520 (682) .+|+.+||++||+||-|||+||.|||.+ +.||+|-|+|||||||||||+++|.+|||||+|.|.++|.||+.|++|+|| T Consensus 2 ~~~R~~Lv~~nlpLv~~~A~RF~~RGe~~~EDL~QVG~iGL~kAidrFD~~~g~~F~tyAVPtI~GEIkR~fRD~~W~vr 81 (229) T TIGR02980 2 KEAREKLVELNLPLVESIARRFRSRGEPHLEDLVQVGTIGLVKAIDRFDPSYGVKFSTYAVPTIMGEIKRFFRDDTWAVR 81 (229) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHCHHCCCCCCCCCCCCEEEEEEEEEECCCCEEE T ss_conf 67889999961279999999851378874311578888888877753011116986641046023323133424873266 Q ss_pred CCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCC--CCCCCCCCC-C-CCC-CEEEEEECCC Q ss_conf 1420588989999999998776088999789998709998999999986089--875536358-8-998-6047562389 Q gi|254780289|r 521 IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKE--PISLETPIG-D-EDT-SHLGDFIEDK 595 (682) Q Consensus 521 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~--~~sl~~~~~-~-~~~-~~~~~~~~d~ 595 (682) ||....|.-++++++...|.+++||.||+.|||+.|++|.++|..+|.+.+. |.|||+|++ + ||+ .+|+|.|.+. T Consensus 82 VPRrlkEl~~~~~~a~eeL~~~lgR~Pt~~EiAe~L~~s~EEv~~aleA~~~Y~~~Sld~~~~a~~dg~~~~L~D~lG~~ 161 (229) T TIGR02980 82 VPRRLKELRLKINKATEELTQRLGRSPTVAEIAEELGVSEEEVVEALEAGNSYSALSLDATIEADDDGDPIALLDTLGDE 161 (229) T ss_pred CCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHCCC T ss_conf 05138988999999999999982889887899988588999999999865417861120004558888424566444022 Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC Q ss_conf 88998999999999999999973299889999999818798674688999899667899999999999998329 Q gi|254780289|r 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669 (682) Q Consensus 596 ~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~ 669 (682) +.......-+.+|..+|+.|||||+.||.||| -...|=.|||+++|||==-|=-|+++||.|||. T Consensus 162 -----D~~~e~~~~~~aLk~~l~~LpeRER~il~lRF----f~~~TQ~eiA~~lGiSQMhVSRl~~~~L~~LR~ 226 (229) T TIGR02980 162 -----DDALETVEDRLALKPLLAALPERERRILLLRF----FEDKTQSEIAERLGISQMHVSRLLRRALKRLRE 226 (229) T ss_pred -----CCHHHHHHHHHHHHHHHHHCCHHHCEEEEEEE----ECCCCHHHHHHHCCCCHHHHHHHHHHHHHHHHH T ss_conf -----43267899999999998507902707610001----069778999978184367889999999999998 No 30 >TIGR02885 spore_sigF RNA polymerase sigma-F factor; InterPro: IPR014236 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . Members of this entry represent RNA polymerase sigma factor F. Within the Firmicutes, Sigma-F is specifically, and universally, a component of the endospore formation program, and is expressed in the forespore to turn on the expression of dozens of genes. It is closely related to sigma-G, which is also expressed in the forespore.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent. Probab=100.00 E-value=2.4e-39 Score=329.58 Aligned_cols=220 Identities=30% Similarity=0.482 Sum_probs=200.8 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEE Q ss_conf 11246899987555789998875223567778875443679999887438545731201028989999999997228704 Q gi|254780289|r 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519 (682) Q Consensus 440 e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~ 519 (682) -=..|.++||+.|+|||.||.+||.|||++..||+|-|||||+|||+|||-+...||||||+|.|.++|.|++.|. +.| T Consensus 8 GDk~A~dkLi~~N~~LV~siv~rF~nRGYe~eDlFQIGciGLvKAidkFD~~y~VKFSTYAVPmI~GEIkRFLRDD-G~i 86 (231) T TIGR02885 8 GDKEARDKLIEENLRLVSSIVKRFLNRGYEYEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEIKRFLRDD-GII 86 (231) T ss_pred HHHHHHHHHHHHCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHCCC-CCE T ss_conf 0489999998723346899999852068870000222115566655421767770155212220221222310268-855 Q ss_pred ECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCC--EEEEEECCCCC Q ss_conf 6142058898999999999877608899978999870999899999998608987553635889986--04756238988 Q gi|254780289|r 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDFIEDKNA 597 (682) Q Consensus 520 r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~--~~~~~~~d~~~ 597 (682) ||..++.++-+|+.+....|..++||+||++|||+.+|++.++|-.++..++.|-||-.-|++|++. +|.|-|.|+.. T Consensus 87 kVSRSlK~la~k~~~~kE~L~~~l~R~PTi~Elae~lg~~~EEiv~A~Es~~~~~sly~tvh~dDGdPi~LlD~i~d~~~ 166 (231) T TIGR02885 87 KVSRSLKELARKIRYEKEELTKKLGREPTINELAEALGVSPEEIVMALESARSLQSLYDTVHEDDGDPILLLDQIADKGS 166 (231) T ss_pred EEEHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCHHCCEEECCCCCHHHHHHHHCCCCC T ss_conf 75152789999998779999998389988899988758788786644202576101100114179464467665212577 Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC Q ss_conf 998999999999999999973299889999999818798674688999899667899999999999998329 Q gi|254780289|r 598 VSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669 (682) Q Consensus 598 ~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~ 669 (682) .+ .+....- +|.++|..|+|||+.||.+|| -.+.|=-|||..+|+|===|--||.|+|.++|. T Consensus 167 ~~-~~~~~ki----~Lke~i~~Ld~rer~ii~LRY----FKDkTQ~eVA~~LGISQVQVSRlEkk~L~~~k~ 229 (231) T TIGR02885 167 ED-SDLLEKI----ALKEAISKLDERERQIIMLRY----FKDKTQTEVAKMLGISQVQVSRLEKKVLKKMKE 229 (231) T ss_pred CH-HHHHHHH----HHHHHHHHCCCCCCEEEEEEC----CCCCHHHHHHHHCCCCCCHHHHHHHHHHHHHHH T ss_conf 13-6899989----999998612522678977410----140017999977185700122789999999874 No 31 >COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription] Probab=100.00 E-value=2.9e-36 Score=305.21 Aligned_cols=235 Identities=29% Similarity=0.485 Sum_probs=210.7 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHH Q ss_conf 12688999999876533211246899987555789998875223567-77887544367999988743854573120102 Q gi|254780289|r 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL-QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500 (682) Q Consensus 422 l~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~-~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya 500 (682) ++-.++.......+.|. ..|+ .+|+.||+||.+||.+|.|+|. .+.||||.|++||++||+|||+.+|.+|+||| T Consensus 6 ~~~~e~~~~~~~~~~g~---~~~~-~Li~~ylpLV~~ia~k~~~r~~~~~dDLiqiG~iGLi~Aieryd~~kg~kF~tyA 81 (247) T COG1191 6 LSKEEEEKLLEYYAEGD---EEAR-RLIERYLPLVKSIARKFENRGPSEYDDLIQIGMIGLIKAIERYDPSKGTKFSTYA 81 (247) T ss_pred CCHHHHHHHHHHHHHCC---HHHH-HHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHH T ss_conf 24689999999998458---9999-9999978999999999980599854389997899999999974931286148889 Q ss_pred HHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHC--CCCCCCC Q ss_conf 89899999999972287046142058898999999999877608899978999870999899999998608--9875536 Q gi|254780289|r 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLET 578 (682) Q Consensus 501 ~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~--~~~sl~~ 578 (682) .+.|+++|.+++.++. +|++|+...+..+++..+..++.+++||+||.+|||+.||++.++|..++.... .++|++. T Consensus 82 ~~~I~Gei~d~LR~~~-~v~vpR~~~~~~~~i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~~~~~~~~sld~ 160 (247) T COG1191 82 VRRIRGEILDYLRKND-SVKVPRSLRELGRRIEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAINGSQLLSLDE 160 (247) T ss_pred HHHHHHHHHHHHHHCC-CCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCC T ss_conf 9999999999998478-746768998887788999999999847998689999896989999999998730124541100 Q ss_pred CCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHH Q ss_conf 35889986047562389889989999999999999999732998899999998187986746889998996678999999 Q gi|254780289|r 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658 (682) Q Consensus 579 ~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rq 658 (682) .+..++|.. .+....+|.+......+...+.+++..|++||+.|+.+|| ..+.|+-|||+.+|||.-||-| T Consensus 161 ~~~~~~d~~-----~~~~~~~~~~~~~~~~~~~~l~~~i~~L~EREk~Vl~l~y----~eelt~kEI~~~LgISes~VSq 231 (247) T COG1191 161 DVLKDDDDD-----VDDQIENPDDGVEKEELLEILKEAIEPLPEREKLVLVLRY----KEELTQKEIAEVLGISESRVSR 231 (247) T ss_pred CCCCCCCCC-----HHHCCCCCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----HHCCCHHHHHHHHCCCHHHHHH T ss_conf 001356520-----2202356035778899999999998766899999999999----7015799999994914989999 Q ss_pred HHHHHHHHHCCH Q ss_conf 999999983296 Q gi|254780289|r 659 IEAKAIRKLKHP 670 (682) Q Consensus 659 i~~~a~~~l~~~ 670 (682) |+.+||.|||+- T Consensus 232 l~kkai~kLr~~ 243 (247) T COG1191 232 LHKKAIKKLRKE 243 (247) T ss_pred HHHHHHHHHHHH T ss_conf 999999999998 No 32 >TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family; InterPro: IPR012845 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0045449 regulation of transcription. Probab=100.00 E-value=4.5e-36 Score=303.68 Aligned_cols=215 Identities=30% Similarity=0.514 Sum_probs=201.0 Q ss_pred HHHHHHHHHHHHHHHHCCC---CCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCCH Q ss_conf 9875557899988752235---6777887544367999988743854573120102898999999999722870461420 Q gi|254780289|r 448 MVEANLRLVISVAKKYTNR---GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH 524 (682) Q Consensus 448 l~~anlr~v~~~~~~~~~~---~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~ 524 (682) +|...+.||-.+|.+-..+ .+++.||||.|.+|||.|++|||+.+|.+|.|||+.|||+||--.....-| +|.. T Consensus 1 l~~~Y~pLVk~~a~rl~~~~P~~v~~~DL~q~G~~GL~dA~~ryd~~~g~~F~TyA~~RIRGAmlDELR~~DW---~PRs 77 (227) T TIGR02479 1 LIKKYLPLVKRIAGRLVVQLPSSVELDDLIQAGMIGLLDAIERYDPSKGVKFETYAVQRIRGAMLDELRKLDW---VPRS 77 (227) T ss_pred CCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHCCCCHHHHHHHHHHCCC---CCHH T ss_conf 9001268999988664310488234875898889999999983188888944100011130205788753066---7836 Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHH--HHCCCCCCCCCCCCCCCC----EEEEEECCCCCC Q ss_conf 58898999999999877608899978999870999899999998--608987553635889986----047562389889 Q gi|254780289|r 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTS----HLGDFIEDKNAV 598 (682) Q Consensus 525 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~sl~~~~~~~~~~----~~~~~~~d~~~~ 598 (682) ..+..+++.++.+++.+.+||.||.+|||+.|||++++|+.++. .+..-+|||.-.-+++++ ++.|.|.+++.. T Consensus 78 ~R~~~~~~~~a~~~Le~~LgR~P~~~EiA~~Lg~~~~e~~~~~~~~~~~~~~SLd~~~~~~~~~~~~~~~~~~~~~~~~~ 157 (227) T TIGR02479 78 LRQKARKLEEAIEELEARLGREPTEEEIAEELGMDLKEVRQALNEINAESLVSLDELLESGDDGGAEGSLIDLIEDDKSE 157 (227) T ss_pred HHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHEECCCCCC T ss_conf 89998689999999999869898888999983999989999999988998764899984146322345323100143576 Q ss_pred CHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC Q ss_conf 98999999999999999973299889999999818798674688999899667899999999999998329 Q gi|254780289|r 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669 (682) Q Consensus 599 ~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~ 669 (682) +|+..+.+..|+..|.++|.+||+||+-||.|+| .++.||-|||..+|||--||.||+++|+.|||. T Consensus 158 ~P~~~~~~~~L~~~l~~ai~~L~eRE~LVl~LYY----~eELnLKEIg~VL~lsESRvSQiHs~A~~~Lr~ 224 (227) T TIGR02479 158 DPEEELEREELREALAEAIEKLSEREKLVLSLYY----YEELNLKEIGEVLGLSESRVSQIHSQALKKLRA 224 (227) T ss_pred CHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH T ss_conf 8135899999999999997406855788888864----127668899988378705799999999999987 No 33 >TIGR02850 spore_sigG RNA polymerase sigma-G factor; InterPro: IPR014212 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . Members of this entry comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also designated stage III sporulation protein G (SpoIIIG). Members of this entry are closely related to sigma-F (SpoIIAC), another sporulation sigma factor.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent. Probab=99.97 E-value=4e-28 Score=240.97 Aligned_cols=235 Identities=31% Similarity=0.499 Sum_probs=209.5 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHH Q ss_conf 12688999999876533211246899987555789998875223567778875443679999887438545731201028 Q gi|254780289|r 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501 (682) Q Consensus 422 l~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~ 501 (682) +...+.+++..+++.|+. .|+.++|.+|||||.||..+|.|||-...||+|-||+|||||+|-||.....||||||+ T Consensus 16 l~~~~~~~l~~~~~~G~~---~ar~~l~~~nlrlvlsviqrf~nrGe~~ddlfqvGCiGl~k~idnfdl~~nv~fstyav 92 (254) T TIGR02850 16 LKNEEMRELFVRMKSGDK---SAREKLINGNLRLVLSVIQRFNNRGEYVDDLFQVGCIGLIKSIDNFDLSQNVKFSTYAV 92 (254) T ss_pred CCHHHHHHHHHHHHCCHH---HHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHH T ss_conf 354789999999851207---89999875226888888887511454034567632577777655310111320011346 Q ss_pred HHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCC Q ss_conf 98999999999722870461420588989999999998776088999789998709998999999986089875536358 Q gi|254780289|r 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG 581 (682) Q Consensus 502 ~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~ 581 (682) +.|-+.|.|++.|+ ..||+...+.+...+-......+..+..++||..+||..|++|.++|-.++...++||||=.|+. T Consensus 93 PmiiGeirrylrdn-~~irvsrslrd~ay~alqvr~~l~~~~~~eP~~~~ia~~l~~~~~~~v~aldaiq~PvslfeP~y 171 (254) T TIGR02850 93 PMIIGEIRRYLRDN-NPIRVSRSLRDIAYKALQVRDKLVSKNSKEPTVSEIAKELDVPKEEVVFALDAIQDPVSLFEPIY 171 (254) T ss_pred HHHHHHHHHHHHCC-CCEEEHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHH T ss_conf 67889889985248-74130355889999999999999853125875889998734755787765664216423431001 Q ss_pred CCCCC--EEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHH Q ss_conf 89986--0475623898899899999999999999997329988999999981879867468899989966789999999 Q gi|254780289|r 582 DEDTS--HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659 (682) Q Consensus 582 ~~~~~--~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi 659 (682) .|++. ...|-+.|.... +...-..+ .+.++|..|+.||+-||.+|| -...|--||+...|+|.-.|-.+ T Consensus 172 ~d~Gd~i~vmdq~~d~~~~---d~~W~~~~--~l~~~~~~l~~re~~il~~rf----f~G~tqmeva~eiGisqaqvsrl 242 (254) T TIGR02850 172 NDGGDPIYVMDQISDEKNK---DEQWLEEI--ALKEALKRLNEREKLILKLRF----FEGKTQMEVAEEIGISQAQVSRL 242 (254) T ss_pred CCCCCEEEEEECCCCHHHH---HHHHHHHH--HHHHHHHHHHHHHHHHHHHHH----HCCCHHHHHHHHHCCHHHHHHHH T ss_conf 3799748874010020345---69999888--999999987667887777553----14631334565403016888888 Q ss_pred HHHHHHHHCC Q ss_conf 9999998329 Q gi|254780289|r 660 EAKAIRKLKH 669 (682) Q Consensus 660 ~~~a~~~l~~ 669 (682) |..||..++. T Consensus 243 ek~a~~~~~k 252 (254) T TIGR02850 243 EKAALKHMRK 252 (254) T ss_pred HHHHHHHHHH T ss_conf 8999999751 No 34 >TIGR02846 spore_sigmaK RNA polymerase sigma-K factor; InterPro: IPR014209 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homologue sigma-E (sigma-29, see IPR014200 from INTERPRO), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note: that in Bacillus subtilis (and apparently also in Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K .; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent. Probab=99.96 E-value=2.1e-28 Score=243.13 Aligned_cols=192 Identities=30% Similarity=0.447 Sum_probs=166.0 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHH Q ss_conf 12688999999876533211246899987555789998875223567778875443679999887438545731201028 Q gi|254780289|r 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501 (682) Q Consensus 422 l~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~ 501 (682) |+..|-+.-..+++.|.. .||+.|||.|||||-+|.|||.+.|-+..|||+-|+|||+||||.|++.+|.|++|||. T Consensus 30 Ls~~eE~~YL~~l~~GD~---~Ar~~LiErNLRLVAHiVKKf~~~G~~~dDLISIGTiGLIKAidsf~~~KGt~LATYAA 106 (228) T TIGR02846 30 LSEEEEKKYLERLKEGDE---EARNVLIERNLRLVAHIVKKFSNTGEDVDDLISIGTIGLIKAIDSFDPEKGTRLATYAA 106 (228) T ss_pred CCHHHHHHHHHHHHHHHH---HHHHHHHHHCCCEEEEEEECCCCCCCCCCCHHCCCCHHEECCEECCCCCCCCHHHHHHH T ss_conf 986689999999873159---99999776333000215651178874100001002201000110224787731566786 Q ss_pred HHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCC Q ss_conf 98999999999722870461420588989999999998776088999789998709998999999986089875536358 Q gi|254780289|r 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG 581 (682) Q Consensus 502 ~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~ 581 (682) --|-.+|.=++... +-++.-|||..||| T Consensus 107 rCiENEILM~lR~~----------------------------------------------------KK~k~eV~L~DPIG 134 (228) T TIGR02846 107 RCIENEILMHLRAL----------------------------------------------------KKTKGEVSLQDPIG 134 (228) T ss_pred HHHHHHHHHHHHHC----------------------------------------------------CCCCCCEEECCCCC T ss_conf 65347899999743----------------------------------------------------67478332107888 Q ss_pred CCCC---CEEEEEECCCCCCCHHHHHHHHHHHHHHHHHH-HCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHH Q ss_conf 8998---60475623898899899999999999999997-3299889999999818798674688999899667899999 Q gi|254780289|r 582 DEDT---SHLGDFIEDKNAVSPLDSAIQANLRETTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657 (682) Q Consensus 582 ~~~~---~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l-~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~r 657 (682) -|-+ -+|.|++...+-.-+ +.+....--..+..-| ..|.+||+.||.+||||.++.+.|=.|||+.+|+||-=|- T Consensus 135 ~DKEGNEIsL~DiL~~~~d~v~-e~v~~~~~~~~l~~~~~~~L~~rE~~vi~~RyGL~~~~~~tQREIA~~LgISRSYVS 213 (228) T TIGR02846 135 VDKEGNEISLIDILGSDEDSVI-EQVEKKLEIKKLYKKLNSVLKGREREVIEMRYGLKDGREKTQREIAKILGISRSYVS 213 (228) T ss_pred CCCCCCEEEEEECCCCCCCHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCCHHHH T ss_conf 6767642300000168873168-888864459999999998740888999987436688895417899877086500454 Q ss_pred HHHHHHHHHHCC Q ss_conf 999999998329 Q gi|254780289|r 658 QIEAKAIRKLKH 669 (682) Q Consensus 658 qi~~~a~~~l~~ 669 (682) -||.|||.||-| T Consensus 214 RIEK~Al~Kl~~ 225 (228) T TIGR02846 214 RIEKKALKKLYK 225 (228) T ss_pred HHHHHHHHHHHH T ss_conf 888999999986 No 35 >pfam04546 Sigma70_ner Sigma-70, non-essential region. The domain is found in the primary vegetative sigma factor. The function of this domain is unclear and can be removed without loss of function. Probab=99.94 E-value=2.4e-24 Score=211.13 Aligned_cols=209 Identities=17% Similarity=0.252 Sum_probs=160.9 Q ss_pred CCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHH Q ss_conf 82389999999987311710367876421013543333333433333211000111000100000000122100001111 Q gi|254780289|r 160 SPLTFQALIIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKD 239 (682) Q Consensus 160 ~P~ti~~il~~~e~i~~ge~~LrdIIDld~t~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~e~~~e~~~~~~~~ 239 (682) ||.++.+++.+|++|.+|+++|.|+|+++ .++.+..+..............+.. T Consensus 1 yP~ti~~ll~~y~~v~~ge~rl~dli~Gf-----------~Dp~~~~~~~~~~~~~~~~~~~~~~--------------- 54 (210) T pfam04546 1 YPGAIAYLLEQYDRVEAGEGRLSDLISGF-----------IDPNADAAAATAPAIESELDEEDLE--------------- 54 (210) T ss_pred CCHHHHHHHHHHHHHHCCCCCHHHHHHHC-----------CCCCCCCCCCCCCCCCCCCCCCCCC--------------- T ss_conf 97799999999999981886289998734-----------7987556655555544432111113--------------- Q ss_pred HHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHH Q ss_conf 10135666653034431000222334555564442102347987668999999999999987521012000799999999 Q gi|254780289|r 240 DRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKE 319 (682) Q Consensus 240 ~~~~~~~~~~e~e~~~~~~e~e~de~~~sla~~e~eLk~~v~e~l~~i~~~~~kl~k~~~~~~~~~~~~~~~kk~~kl~~ 319 (682) .+.+.+.+.............++.+.++|..+.+.|.++.+... ++|..++++.+.+. T Consensus 55 ----------------~~~~~~~~~~~~~~~~d~gpdpeea~~rf~~l~~~~~~~~~a~~------k~G~~~~~~~k~~~ 112 (210) T pfam04546 55 ----------------DDDDDDDEDDDEEEEADLGPDPEEARERFAELREQYEKTRKAIE------KHGRGSKKAQKARE 112 (210) T ss_pred ----------------CCCCCCCCCCCHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHH------HCCCCHHHHHHHHH T ss_conf ----------------33334565542021665389999999999999999999999998------63987199999999 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHCCCHHHHHHHCCCCCCCHHHHHHHHHCCCCHHHHH Q ss_conf 99999986210057788789999999999999999999999-97125357777631677689899999861355106765 Q gi|254780289|r 320 KLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLA-QSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNF 398 (682) Q Consensus 320 eL~e~~~~lkl~~k~iE~L~~~l~~~~k~Ir~~Er~L~rl~-~k~~i~R~~Fi~~f~gnEt~~~wl~~~~~~~~~~~~~~ 398 (682) +|++.|+.|+|+|++|+.|++.++..+..||.+||.|+++| .++||||+.|++.|+|||||+.|++...+.+ +.|+.. T Consensus 113 ~l~e~f~~~Kl~pk~~d~L~~~lR~~v~~IR~~ER~I~~lcV~~a~MpRk~Fik~F~gnEtn~~W~~~~~k~~-k~~s~~ 191 (210) T pfam04546 113 ALAEEFKQFRLVPKQFDRLVDNLRGMVDRVRAQERQIMKLCVERAKMPRKDFIKSFPGNETNLDWLDELLAAK-KPYAEA 191 (210) T ss_pred HHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHCCCCCCCHHHHHHHHHCC-CHHHHH T ss_conf 9999999861768999999999999999999999999999999818998999988678888889999998739-648999 Q ss_pred HHHHHHHHHHHHHHHHHHH Q ss_conf 5434567765322333322 Q gi|254780289|r 399 VACEVDSILKIRNEIKSIS 417 (682) Q Consensus 399 l~~~~~eI~~~q~kL~~ie 417 (682) +..++++|.++|++|..|+ T Consensus 192 L~~~~~~I~~~Q~kL~~iE 210 (210) T pfam04546 192 LERVKPDIQRAQQKLIDIE 210 (210) T ss_pred HHHHHHHHHHHHHHHHHCC T ss_conf 9996999999999998619 No 36 >TIGR02941 Sigma_B RNA polymerase sigma-B factor; InterPro: IPR014288 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This entry represents the sigma factor, sigmaB. It is restricted to certain species within the order Bacillales including Staphylococcus aureus , Listeria monocytogenes and Bacillus cereus (strain ATCC 14579 / DSM 31) .. Probab=99.94 E-value=1.5e-25 Score=220.74 Aligned_cols=240 Identities=22% Similarity=0.422 Sum_probs=207.0 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHH Q ss_conf 12688999999876533211246899987555789998875223567778875443679999887438545731201028 Q gi|254780289|r 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501 (682) Q Consensus 422 l~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~ 501 (682) ++..++-.+....+.-- ....|-.+||..-=.||-|||.||...+---.||||.|-+||+-||.||||+.|-+|-.||. T Consensus 10 ~~~e~v~~wI~e~Q~nP-~n~eaQeklV~hY~~Lv~SiAykYSKg~~~HEDlvQVGM~GLlgAirRyD~s~g~~FE~Fai 88 (256) T TIGR02941 10 LTKEDVIQWIKEFQKNP-KNEEAQEKLVKHYQDLVESIAYKYSKGSAIHEDLVQVGMVGLLGAIRRYDYSYGKAFEAFAI 88 (256) T ss_pred CCHHHHHHHHHHHCCCC-CCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCC T ss_conf 78878999999963699-83257899999998999988754048788333045676899999986511000456566236 Q ss_pred HHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHC--CCCCCCCC Q ss_conf 9899999999972287046142058898999999999877608899978999870999899999998608--98755363 Q gi|254780289|r 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLETP 579 (682) Q Consensus 502 ~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~--~~~sl~~~ 579 (682) |.|-+.|.|+++|.+|-|+||....+.=.|+.++.-+|..++.|-|++.|||++||+|+++|..+|.+.+ ...|+|.. T Consensus 89 PTiiGEIKrylRDKTWsvHVPRRIKelGpkIkk~~dELT~~lqrSP~i~EIA~~lg~SEEEVLE~Me~g~sY~alSvD~~ 168 (256) T TIGR02941 89 PTIIGEIKRYLRDKTWSVHVPRRIKELGPKIKKAVDELTDELQRSPKIAEIADRLGVSEEEVLEIMEMGQSYKALSVDDK 168 (256) T ss_pred CCHHHHHHHHHCCCCCCCCCCCCHHCCCCCCHHHHHHHHHHHCCCCCHHHHHHHCCCCHHHHHHHHHCCCCCCEEECCCC T ss_conf 61001011211156430015741100377201455664444214870654641217748889877614777433322530 Q ss_pred CCCCCC-CE--EEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHH Q ss_conf 588998-60--475623898899899999999999999997329988999999981879867468899989966789999 Q gi|254780289|r 580 IGDEDT-SH--LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656 (682) Q Consensus 580 ~~~~~~-~~--~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~ 656 (682) |=.|.| || +.|++... ++......-|--|..+|..|++||+.||..-| -...+=-|-|..+|+|-=-| T Consensus 169 iEadsDGStVa~ld~vG~~-----edgYd~tE~Rm~LekIlpiLserE~~ii~c~f----~enlsQKeTGErlGiSQMHV 239 (256) T TIGR02941 169 IEADSDGSTVALLDLVGEV-----EDGYDQTEKRMVLEKILPILSEREKEIIECTF----IENLSQKETGERLGISQMHV 239 (256) T ss_pred CCCCCCCCCCHHHHHHCCC-----CCCHHHHHHHHHHHHHHHHCCHHHHHHHHHHH----HCCCCCCHHHHHCCHHHHHH T ss_conf 0036888511111121676-----66545788888888741000544567666553----14787300232224035567 Q ss_pred HHHHHHHHHHHCCHH Q ss_conf 999999999832967 Q gi|254780289|r 657 RQIEAKAIRKLKHPS 671 (682) Q Consensus 657 rqi~~~a~~~l~~~~ 671 (682) --|..+||+|||... T Consensus 240 SRl~R~ai~KL~eAa 254 (256) T TIGR02941 240 SRLQRRAIKKLKEAA 254 (256) T ss_pred HHHHHHHHHHHHHHH T ss_conf 788899999999972 No 37 >TIGR02835 spore_sigmaE RNA polymerase sigma-E factor; InterPro: IPR014200 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . Members of this entry represent the endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. In Bacillus subtilis, sigma-29 is synthesized as a precursor (P31), specifically in the mother cell compartment, and is activated by a cleavage that removes the N-terminal 29 amino acids .; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent. Probab=99.85 E-value=3.4e-20 Score=178.43 Aligned_cols=193 Identities=26% Similarity=0.440 Sum_probs=165.2 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHH Q ss_conf 12688999999876533211246899987555789998875223567778875443679999887438545731201028 Q gi|254780289|r 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501 (682) Q Consensus 422 l~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~ 501 (682) ++..|-..+..++..|.. .+|.-||+-||||||.||+||-|.|+...|||+-|++||+|||.-|+|.+-.|++|||. T Consensus 34 l~~eee~~l~~~l~~Gd~---~~~~~liernlrlvvyia~kf~ntG~~~edl~s~GtiGlikav~tf~P~k~iklatyas 110 (234) T TIGR02835 34 LTKEEEEALLEKLEKGDE---AAKSILIERNLRLVVYIARKFENTGINIEDLVSIGTIGLIKAVNTFNPEKKIKLATYAS 110 (234) T ss_pred CCHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHCCCCCEEEHHHHHHHHHHHHHHHHCCCCHHHHHHHHHH T ss_conf 871579999999875479---99999886222431121012202562110222221478887765227301103556776 Q ss_pred HHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCC Q ss_conf 98999999999722870461420588989999999998776088999789998709998999999986089875536358 Q gi|254780289|r 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG 581 (682) Q Consensus 502 ~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~ 581 (682) -.|-..|.-++..+.+ .+.-||++.|+. T Consensus 111 ~Cieneilmylrr~~~----------------------------------------------------~~~evsf~ePln 138 (234) T TIGR02835 111 RCIENEILMYLRRNNK----------------------------------------------------IRSEVSFDEPLN 138 (234) T ss_pred HHHHHHHHHHHHHHCC----------------------------------------------------CCCEEEECCCCC T ss_conf 7678889998875112----------------------------------------------------100000025546 Q ss_pred CCCCCE---EEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHH Q ss_conf 899860---47562389889989999999999999999732998899999998187986746889998996678999999 Q gi|254780289|r 582 DEDTSH---LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658 (682) Q Consensus 582 ~~~~~~---~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rq 658 (682) -|+|++ +.|++.-.+ ..-........-+..+..+|..|+.||++|+.+||||.++...|-.+|+..+|+|..-|-. T Consensus 139 ~dW~Gnelllsd~lGt~~-~~~~~~~e~~v~~~ll~~al~~l~~re~~i~~lrfGl~~~~e~tqk~vad~lGisqsyisr 217 (234) T TIGR02835 139 VDWDGNELLLSDVLGTDS-DIVYKVLEEEVDRELLKKALKKLNDREKKIMELRFGLAGGTEKTQKEVADLLGISQSYISR 217 (234) T ss_pred CCCCCCHHHHHHHHCCCH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHH T ss_conf 566762114344414742-6889999999999999999998767678766763043677214678889886246899999 Q ss_pred HHHHHHHHHCCH Q ss_conf 999999983296 Q gi|254780289|r 659 IEAKAIRKLKHP 670 (682) Q Consensus 659 i~~~a~~~l~~~ 670 (682) +|.+-+++|+.- T Consensus 218 lek~i~krl~ke 229 (234) T TIGR02835 218 LEKRILKRLKKE 229 (234) T ss_pred HHHHHHHHHHHH T ss_conf 999999999999 No 38 >PRK08295 RNA polymerase factor sigma-70; Validated Probab=99.84 E-value=6.7e-19 Score=168.17 Aligned_cols=194 Identities=24% Similarity=0.320 Sum_probs=161.2 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHH Q ss_conf 12688999999876533211246899987555789998875223567778875443679999887438545731201028 Q gi|254780289|r 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501 (682) Q Consensus 422 l~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~ 501 (682) +...+=.+++.+++.|.. .|...|+..+.++|.++|++|.+.+....||+|||.|++++|+++|++.+|.+|+||+. T Consensus 6 ~~~~~d~~Li~~~~~GD~---~Af~~L~~~y~~~v~~~~~~~~~~~~d~EDlvQe~~i~l~kai~~f~~~k~~~F~t~~~ 82 (209) T PRK08295 6 LRDKEDEELVELAQSGDT---EALEYLIEKYKNFVRAKARSYFLIGAEREDIVQEGMIGLYKAIRDYDEDKLSSFKSFAE 82 (209) T ss_pred CCHHHHHHHHHHHHHCCH---HHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHH T ss_conf 872019999999991679---99999999989999999999828987799999999999999998568654872899999 Q ss_pred HHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCC Q ss_conf 98999999999722870461420588989999999998776088999789998709998999999986089875536358 Q gi|254780289|r 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG 581 (682) Q Consensus 502 ~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~ 581 (682) +||+..|..++....|--+.|. ...+|||.|+. T Consensus 83 ~~i~~~i~~~ir~~~r~k~~~~-----------------------------------------------~~~~sld~~~~ 115 (209) T PRK08295 83 LCITRQIITAIKTANRQKHIPL-----------------------------------------------NSYVSLDKPIY 115 (209) T ss_pred HHHHHHHHHHHHHHHCCCCCCC-----------------------------------------------CHHHCCCCCCC T ss_conf 9999999999999833045452-----------------------------------------------02414566645 Q ss_pred CCC-CCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHH-HCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHH Q ss_conf 899-860475623898899899999999999999997-329988999999981879867468899989966789999999 Q gi|254780289|r 582 DED-TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL-ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659 (682) Q Consensus 582 ~~~-~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l-~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi 659 (682) +++ +.++.+++.+....+|++..........+.+.+ ..|+|+++.|+.++| ..+|+.|||+.+|+|-..|+.. T Consensus 116 ~~~~~~~~~~~~~~~~~~~pe~~~~~~e~~~~i~~~i~~~l~~~e~~V~~~~~-----eg~s~~EIA~~l~is~~tV~~~ 190 (209) T PRK08295 116 DEESDRTLLDVISGAKVTDPEELIISKEELEIIEEKILELLSDLEKEVLELYL-----DGKSYQEIAEELNRHVKSIDNA 190 (209) T ss_pred CCCCHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHH T ss_conf 55420356543046778999999999999999999998469189999999998-----6999999999989299999999 Q ss_pred HHHHHHHHCCH Q ss_conf 99999983296 Q gi|254780289|r 660 EAKAIRKLKHP 670 (682) Q Consensus 660 ~~~a~~~l~~~ 670 (682) -.+|.+|||.- T Consensus 191 l~RarkkLr~~ 201 (209) T PRK08295 191 LQRVKRKLEKY 201 (209) T ss_pred HHHHHHHHHHH T ss_conf 99999999999 No 39 >TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family; InterPro: IPR014284 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This entry is found in all varieties of the sigma-70 type sigma factors, including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (IPR000394 from INTERPRO) are included within this entry. ; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent. Probab=99.77 E-value=1.9e-17 Score=156.68 Aligned_cols=159 Identities=23% Similarity=0.290 Sum_probs=135.7 Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCC Q ss_conf 68999875557899988752235677788754436799998874385457312010289899999999972287046142 Q gi|254780289|r 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523 (682) Q Consensus 444 AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~ 523 (682) |-.+++..|.++|.++|++|++.+.+..||+|||.++|++++++|++. |..|+||+.+|+|..|..++..+.+..+.+. T Consensus 2 a~~~l~~~~~~~~~~~a~~~~~~~~~aeDl~Qe~~~~~~~~~~~~~~~-~~~f~~wl~~~~~n~~~d~~R~~~~~~~~~~ 80 (162) T TIGR02937 2 AFEELVERYLPLLYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPE-GGSFKAWLFRIARNLILDYLRRKRRRVRRLR 80 (162) T ss_pred HHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 788999999999999999971787579999999999999878624878-7653899999999999999998664420014 Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHH Q ss_conf 05889899999999987760889997899987099989999999860898755363588998604756238988998999 Q gi|254780289|r 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603 (682) Q Consensus 524 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~ 603 (682) ...... +. ..-. . .++|++ T Consensus 81 ~~~~~~-----------------------------------------------------~~-----~~~~-~-~~~~~~- 99 (162) T TIGR02937 81 VELDED-----------------------------------------------------DE-----LEEL-E-DPSPEE- 99 (162) T ss_pred HHHCCH-----------------------------------------------------HH-----HHHH-C-CCCHHH- T ss_conf 541221-----------------------------------------------------34-----4321-3-578778- Q ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC Q ss_conf 999999999999973299889999999818798674688999899667899999999999998329 Q gi|254780289|r 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669 (682) Q Consensus 604 ~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~ 669 (682) +. ......|.++|..|||+++.||.+|| ....|+.|||+.+|+|...|+++-.+|++||+. T Consensus 100 ~~-~~~~~~l~~al~~Lp~~~r~~~~l~~----~~~~s~~eIA~~lg~s~~~v~~~~~ra~~~L~~ 160 (162) T TIGR02937 100 LE-EEEREALREALEKLPEREREVLVLRY----LEGLSYKEIAEILGISEGTVKSRLKRARKKLRE 160 (162) T ss_pred HH-HHHHHHHHHHHHHCCHHHHHHHHHHH----HHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH T ss_conf 99-99999999998747998999999999----718998899998689999999999999999985 No 40 >PRK06759 RNA polymerase factor sigma-70; Validated Probab=99.70 E-value=1.8e-15 Score=141.11 Aligned_cols=149 Identities=22% Similarity=0.271 Sum_probs=114.8 Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCC Q ss_conf 68999875557899988752235677788754436799998874385457312010289899999999972287046142 Q gi|254780289|r 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523 (682) Q Consensus 444 AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~ 523 (682) +-.++++..=.+|++++|+|.-. -.+.|++|+|.|||.+|+++||+.+| .|||||..+||..+...+..+.+. T Consensus 5 sFee~~~~Y~pmI~~~lkkl~i~-~d~dd~~Q~g~i~Lw~a~~~yd~~kg-~fstya~~~ir~~~ld~lrKe~~~----- 77 (154) T PRK06759 5 TFTEAVVLYEGLIVNQIKKLGIY-QDYEEYYQCGLIGLWHAYERYDEKKG-SFPAYAVVTVRGYILERLKKEFAV----- 77 (154) T ss_pred CHHHHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHHHHHHCCCCCC-CHHHHHHHHHHHHHHHHHHHCCCC----- T ss_conf 59999999878999999993673-33899999999999999997694347-669999999999999999863143----- Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHH Q ss_conf 05889899999999987760889997899987099989999999860898755363588998604756238988998999 Q gi|254780289|r 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603 (682) Q Consensus 524 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~ 603 (682) .+ .. .++++ |++. T Consensus 78 --------------------------~e----------------------~~--~~~~~-----------------~ed~ 90 (154) T PRK06759 78 --------------------------QE----------------------KC--VCVGE-----------------YEDH 90 (154) T ss_pred --------------------------CC----------------------CC--CCCCC-----------------CHHH T ss_conf --------------------------34----------------------33--35565-----------------2255 Q ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCH Q ss_conf 9999999999999732998899999998187986746889998996678999999999999983296 Q gi|254780289|r 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670 (682) Q Consensus 604 ~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~ 670 (682) .........+.++|+.|+|||+.||.++| -..+|..||+..+|||...|+++..+||.|||+. T Consensus 91 ~~~~d~~~~l~~~l~~L~~re~~ii~~~~----~~g~t~~EIA~~~gis~~~Vk~~~r~Al~KLR~~ 153 (154) T PRK06759 91 FHFEDVEMKVKDFMSVLDEKEKYIIFERF----FVGKTMGEIALETEMTYYQVRWIYRQALEKMRNS 153 (154) T ss_pred HHHCHHHHHHHHHHHHCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHC T ss_conf 51011889999999849999999999999----9699899999998989999999999999998733 No 41 >pfam03979 Sigma70_r1_1 Sigma-70 factor, region 1.1. Region 1.1 modulates DNA binding by region 2 and 4 when sigma is unbound by the core RNA polymerase. Region 1.1 is also involved in promoter binding. Probab=99.52 E-value=3.4e-14 Score=131.06 Aligned_cols=63 Identities=46% Similarity=0.780 Sum_probs=58.3 Q ss_pred HHCCHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCEEECCCCCCCC Q ss_conf 020289999999978784886789997526843599888999999998479778327841000 Q gi|254780289|r 24 FDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDE 86 (682) Q Consensus 24 ~d~~~~~ik~LI~~gke~GylTydeIn~~LP~d~~~~e~ie~i~~~L~~~GI~Vve~~~~~~~ 86 (682) .|++++.||+||.+||+||||||++||++||++.++|++||+||++|++|||.|+++++..+. T Consensus 2 ~d~~~~~ik~LI~~GK~~GylTy~eIn~~Lp~~~~~~d~ie~i~~~L~~~gI~Vve~~~~~e~ 64 (79) T pfam03979 2 EDLSQAQVKKLIEQGKKRGYLTYDEINEALPPDDVDSEQIDDIISMLEDMGIEVVEEADSEEL 64 (79) T ss_pred CHHHHHHHHHHHHHHHHCCEEEHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCEEEECCCCCCC T ss_conf 304799999999987645836399999768876799999999999999889968527972212 No 42 >pfam04539 Sigma70_r3 Sigma-70 region 3. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but as some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme. Probab=99.46 E-value=1.3e-13 Score=126.44 Aligned_cols=77 Identities=44% Similarity=0.821 Sum_probs=74.7 Q ss_pred HHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHH Q ss_conf 89899999999987760889997899987099989999999860898755363588998604756238988998999 Q gi|254780289|r 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603 (682) Q Consensus 527 ~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~ 603 (682) ++|||+.|+.++|.|++||+||.+|||+.||||+++|+.++..++.|+|||+|+|++++++|+||++|.+.++|++. T Consensus 1 E~i~ki~ka~~~L~q~lgR~Pt~eEiA~~l~~s~~~v~~~~~~~~~~~SLd~p~~~~~~~~l~d~i~D~~~~~P~e~ 77 (78) T pfam04539 1 ELLNKIKRAQRELEQELGREPTPEEIAEELGISEEKVREVLEAAREPVSLDLPVGEEEDGELGDLLEDDDAESPEDA 77 (78) T ss_pred CHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHCCCCEEEECCCCCCCCCCHHHHCCCCCCCCHHHH T ss_conf 97799999999999998889999999999694999999999875898661067688998628662059999881010 No 43 >PRK09652 RNA polymerase sigma factor RpoE; Provisional Probab=99.21 E-value=3.5e-09 Score=91.50 Aligned_cols=184 Identities=20% Similarity=0.235 Sum_probs=130.0 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHH Q ss_conf 99999876533211246899987555789998875223567778875443679999887438545731201028989999 Q gi|254780289|r 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507 (682) Q Consensus 428 K~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~ 507 (682) .+++.+++.|... |=..++..+..+|.++|.+|.+..-.-.|++|+.-+.|.+.+.+|++.. .|.+|...-.|.. T Consensus 7 ~~Li~~~~~Gd~~---A~~~L~~~y~~~l~~~~~~~~~~~~~aeDv~Qe~fl~l~~~~~~~~~~~--~~~~wL~~iarn~ 81 (192) T PRK09652 7 QELVERVQQGDRA---AFELLVRKYQPRLYRLLSRLVRDPADAEDLAQETFIKAYRALPSFRGGA--AFYTWLYRIAVNT 81 (192) T ss_pred HHHHHHHHHCCHH---HHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCCCCH--HHHHHHHHHHHHH T ss_conf 9999999838899---9999999999999999999969999999987599999887113457711--7999999999999 Q ss_pred HHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCE Q ss_conf 99999722870461420588989999999998776088999789998709998999999986089875536358899860 Q gi|254780289|r 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587 (682) Q Consensus 508 i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~ 587 (682) + ++.+.+..+ .+... +.+.+ ++.... T Consensus 82 ~--------------------~d~~r~~~r--------~~~~~------------------------~~~~~--~~~~~~ 107 (192) T PRK09652 82 A--------------------INYLRKQGR--------RPPES------------------------DLDAE--DAEYFE 107 (192) T ss_pred H--------------------HHHHHHHHC--------CCCCC------------------------CCCHH--HHHHHC T ss_conf 9--------------------999999716--------56655------------------------40023--454300 Q ss_pred EEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH Q ss_conf 47562389889989999999999999999732998899999998187986746889998996678999999999999983 Q gi|254780289|r 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667 (682) Q Consensus 588 ~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l 667 (682) ..+. .....+|++.+....+...|..+|..|||+++.|+.++| -...|..|||..+|+|..-|++.=.+|+++| T Consensus 108 ~~~~--~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~----~~~~s~~EIA~~lgis~~tVk~~l~Ra~~~L 181 (192) T PRK09652 108 DADA--LREISSPEEELLSQELEQRVRRAIESLPEELRTAITLRE----IEGLSYEEIAEIMGCPIGTVRSRIFRAREAL 181 (192) T ss_pred CCCC--CCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH T ss_conf 0003--555576799999999999999999839999998888999----7299999999998939999999999999999 Q ss_pred CCHHHHHHHHHHHC Q ss_conf 29677787566517 Q gi|254780289|r 668 KHPSRSKKLRSFLD 681 (682) Q Consensus 668 ~~~~~~~~l~~~~~ 681 (682) | +.|+.||+ T Consensus 182 r-----~~L~~~~~ 190 (192) T PRK09652 182 R-----AKLQPLLD 190 (192) T ss_pred H-----HHHHHHHH T ss_conf 9-----99898771 No 44 >PRK09641 RNA polymerase sigma factor SigW; Provisional Probab=99.18 E-value=7.5e-09 Score=88.84 Aligned_cols=180 Identities=16% Similarity=0.246 Sum_probs=131.0 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHH Q ss_conf 88999999876533211246899987555789998875223567778875443679999887438545731201028989 Q gi|254780289|r 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504 (682) Q Consensus 425 ~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i 504 (682) ..+++++++++.|.. .|-.++++..-..|..+|.+|++..-.-.|++|+.-+.+.+..++|++... |+| |-. T Consensus 3 ~~i~~Li~~~~~GD~---~Af~~L~~~y~~~l~~~~~~~~~~~~~AeD~vQe~flk~~~~~~~~~~~~~--~~~---WL~ 74 (187) T PRK09641 3 TLIKKRIKQVKKGDQ---NAFADIVDLYKDKIYQLCYRMLGNRHEAEDIAQEAFIRAYVNIDSFDINRK--FST---WLY 74 (187) T ss_pred HHHHHHHHHHHHCCH---HHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCCCCCC--HHH---HHH T ss_conf 899999999993889---999999999999999999999099999999999999999984612574134--999---999 Q ss_pred HHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCC Q ss_conf 99999999722870461420588989999999998776088999789998709998999999986089875536358899 Q gi|254780289|r 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584 (682) Q Consensus 505 ~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~ 584 (682) +-+...++ |. +.+.. ...+++.++...+ T Consensus 75 ~Ia~N~~~-d~----------------~Rk~~-----------------------------------~~~~~~~~~~~~~ 102 (187) T PRK09641 75 RIATNLTI-DR----------------LRKKK-----------------------------------PDYYLDAEVAGTE 102 (187) T ss_pred HHHHHHHH-HH----------------HHHHC-----------------------------------CCCCHHHHHCCCC T ss_conf 99999999-99----------------99726-----------------------------------5343126540310 Q ss_pred CCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH Q ss_conf 86047562389889989999999999999999732998899999998187986746889998996678999999999999 Q gi|254780289|r 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664 (682) Q Consensus 585 ~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~ 664 (682) +..+.+.+.+ ...+|++.+....+...+..+|..|||+.+.|+.||| -..+|..||+..+|+|-.-|+..=.+|+ T Consensus 103 ~~~~~~~~~~-~~~~~~~~~~~~e~~~~l~~al~~Lp~~~r~v~~L~~----~~~~s~~EIA~~l~is~~tVk~~l~RAr 177 (187) T PRK09641 103 GLTMYSQLAA-DEALPEDQVESLELQETIQEEILQLPDKYRTVIVLKY----IEELSLKEISEILDLPVGTVKTRIHRGR 177 (187) T ss_pred CCHHHHHCCC-CCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHH T ss_conf 0004430356-6798478999999999999999828988889999999----8299899999998939999999999999 Q ss_pred HHHCC Q ss_conf 98329 Q gi|254780289|r 665 RKLKH 669 (682) Q Consensus 665 ~~l~~ 669 (682) ++||. T Consensus 178 ~~Lr~ 182 (187) T PRK09641 178 EALRK 182 (187) T ss_pred HHHHH T ss_conf 99999 No 45 >PRK12519 RNA polymerase sigma factor; Provisional Probab=99.15 E-value=9.3e-09 Score=88.11 Aligned_cols=184 Identities=18% Similarity=0.276 Sum_probs=129.7 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHH Q ss_conf 12688999999876533211246899987555789998875223567778875443679999887438545731201028 Q gi|254780289|r 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501 (682) Q Consensus 422 l~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~ 501 (682) |+...=.+++..++.|.. .|-.+|+...-+.|..+|.+|.+..-.-.|++|+.-+.+.+... |+..+| .|+||.. T Consensus 11 m~~~tD~eLi~~~~~GD~---~Af~~L~~ry~~~l~~~a~~~~~~~~~AeDlvQe~fl~~~~~~~-~~~~~~-~~~~wL~ 85 (194) T PRK12519 11 LSSRSDAELFSALKAGQS---AALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRKSS-YDPKRG-SLSSYLL 85 (194) T ss_pred CCCCCHHHHHHHHHHCCH---HHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH-CCCCCC-CHHHHHH T ss_conf 999609999999993859---99999999999999999999939999999999999999998633-166624-2999999 Q ss_pred HHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCC Q ss_conf 98999999999722870461420588989999999998776088999789998709998999999986089875536358 Q gi|254780289|r 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG 581 (682) Q Consensus 502 ~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~ 581 (682) -..|..+...+..+.+..+ ..+. .+ T Consensus 86 ~ia~n~~~d~~R~~~~~~~---------------------------~~~~----------------------------~~ 110 (194) T PRK12519 86 TLTRSRAIDRLRSRRSRQR---------------------------LLER----------------------------WQ 110 (194) T ss_pred HHHHHHHHHHHHHHHCCCC---------------------------HHHH----------------------------HH T ss_conf 9999999999998632012---------------------------2444----------------------------44 Q ss_pred CCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHH Q ss_conf 89986047562389889989999999999999999732998899999998187986746889998996678999999999 Q gi|254780289|r 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661 (682) Q Consensus 582 ~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~ 661 (682) . +...+.....|.+.+........|..+|..|||+.+.|+.||| -..+|..||++.+|+|.--|+.--. T Consensus 111 ~-------~~~~~~~~~~~~~~~~~~e~~~~l~~al~~Lp~~~R~v~~L~~----~eg~s~~EIA~~lgis~~tVk~rl~ 179 (194) T PRK12519 111 Q-------ELLGEASEDTPLEQASLAERSQRVQTALAQLPESQRQVLELAY----YEGLSQSEIAKRLGIPLGTVKARAR 179 (194) T ss_pred H-------HHCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHH T ss_conf 5-------4114677898588998999999999999819988756889999----8199999999998949999999999 Q ss_pred HHHHHHCCHHHHHHHHHHHC Q ss_conf 99998329677787566517 Q gi|254780289|r 662 KAIRKLKHPSRSKKLRSFLD 681 (682) Q Consensus 662 ~a~~~l~~~~~~~~l~~~~~ 681 (682) +|+.+|| +.|+.||| T Consensus 180 rA~~~Lr-----~~L~e~le 194 (194) T PRK12519 180 QGLLKLR-----ELLQDLLE 194 (194) T ss_pred HHHHHHH-----HHHHHHHC T ss_conf 9999999-----99898739 No 46 >PRK11923 algU RNA polymerase sigma factor AlgU; Provisional Probab=99.07 E-value=3.5e-08 Score=83.56 Aligned_cols=188 Identities=19% Similarity=0.271 Sum_probs=134.4 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHH Q ss_conf 26889999998765332112468999875557899988752235677788754436799998874385457312010289 Q gi|254780289|r 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502 (682) Q Consensus 423 ~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~ 502 (682) +..+-.+++.+++.|... |=..++...-+.|..+|.+|++..-.-.|++|+.-+.+.+..++|+... .|.| | T Consensus 3 t~~~D~~Li~~~~~GD~~---Af~~L~~~y~~~l~~~~~~~~~d~~~AeDi~Qe~f~~~~~~~~~~~~~~--~f~~---W 74 (193) T PRK11923 3 TQEEDQQLVERVQRGDKR---AFDLLVLKYQHKILGLIVRFVHDTHEAQDVAQEAFIKAYRALGNFRGDS--AFYT---W 74 (193) T ss_pred CCCCHHHHHHHHHHCCHH---HHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCCCCH--HHHH---H T ss_conf 871099999999948699---9999999999999999999909999999999999999986132126504--6899---9 Q ss_pred HHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCC-CCCC Q ss_conf 899999999972287046142058898999999999877608899978999870999899999998608987553-6358 Q gi|254780289|r 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE-TPIG 581 (682) Q Consensus 503 ~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~-~~~~ 581 (682) -.|-++..++ +.+.+. .|.+...+ ++.+ .+.. T Consensus 75 L~~Ia~n~~~-----------------~~~~~~--------~rr~~~~~----------------------~~~~~~~~~ 107 (193) T PRK11923 75 LYRIAINTAK-----------------NHLVSR--------GRRPPDSD----------------------VSSEDAEFY 107 (193) T ss_pred HHHHHHHHHH-----------------HHHHHH--------HCCCCCCC----------------------CCHHHHHHC T ss_conf 9999999999-----------------999998--------65575333----------------------453466522 Q ss_pred CCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHH Q ss_conf 89986047562389889989999999999999999732998899999998187986746889998996678999999999 Q gi|254780289|r 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661 (682) Q Consensus 582 ~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~ 661 (682) +.+ +.+. +..+|+..+....+...|..+|..|||+.+.|+.||| -..+|..|||..+|+|-.-|+.-=. T Consensus 108 ~~~-----~~~~--~~~~~e~~~~~~e~~~~i~~~l~~Lp~~~R~v~~L~~----~egls~~EIA~~l~is~~tVk~rl~ 176 (193) T PRK11923 108 DGD-----HALK--DIESPERALLRDEIEATVHRTIQQLPEDLRTALTLRE----FDGLSYEDIASVMQCPVGTVRSRIF 176 (193) T ss_pred CCC-----CCCC--CCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHH T ss_conf 554-----3223--4488889999999999999999817898999999999----9499999999998929999999999 Q ss_pred HHHHHHCCHHHHHHHHHHHC Q ss_conf 99998329677787566517 Q gi|254780289|r 662 KAIRKLKHPSRSKKLRSFLD 681 (682) Q Consensus 662 ~a~~~l~~~~~~~~l~~~~~ 681 (682) +|..+||. .|+.|+. T Consensus 177 RAr~~Lr~-----~L~~ll~ 191 (193) T PRK11923 177 RAREAIDK-----ALQPLLQ 191 (193) T ss_pred HHHHHHHH-----HHHHHHH T ss_conf 99999999-----9899873 No 47 >PRK13919 putative RNA polymerase sigma E protein; Provisional Probab=99.07 E-value=1.7e-08 Score=86.02 Aligned_cols=172 Identities=20% Similarity=0.283 Sum_probs=117.3 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHH Q ss_conf 99999876533211246899987555789998875223567778875443679999887438545731201028989999 Q gi|254780289|r 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507 (682) Q Consensus 428 K~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~ 507 (682) .+++.+++.|.. .|-..++.-.-..|.++|.+|++..-.-.|++||.-+.+.+..++|++.+| .|+|| -.+=+ T Consensus 11 ~eLi~~~~~GD~---~Af~~L~~ry~~~l~~~~~~~~~d~~~AEDivQe~flki~~~~~~~~~~~~-~~~~w---L~~ia 83 (187) T PRK13919 11 EALLALVARGDE---EAFRALFRRYAGSFLALARRMGLDGAAAEDVVQEAMIRVWQKAKEFDPRRG-SARAF---LLTLG 83 (187) T ss_pred HHHHHHHHHCCH---HHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCCC-CHHHH---HHHHH T ss_conf 999999994779---999999999999999999999099999999999999999999987687646-49999---99999 Q ss_pred HHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCE Q ss_conf 99999722870461420588989999999998776088999789998709998999999986089875536358899860 Q gi|254780289|r 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587 (682) Q Consensus 508 i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~ 587 (682) ...++ +.+.+ -.+.|++++.-.. ..+.. T Consensus 84 ~n~~~-----------------d~~Rk----------------------------------~~~~~~~~~~~~~-~~~~~ 111 (187) T PRK13919 84 HHAAV-----------------DEVRR----------------------------------RAARPLPLEPDPE-REEEA 111 (187) T ss_pred HHHHH-----------------HHHHH----------------------------------HHCCCCCCCCCCH-HHHHH T ss_conf 99999-----------------99997----------------------------------6267787776610-11332 Q ss_pred EEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH Q ss_conf 47562389889989999999999999999732998899999998187986746889998996678999999999999983 Q gi|254780289|r 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667 (682) Q Consensus 588 ~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l 667 (682) + + .+.|.........+..+..+|..|||+.+.|+.|+| -..+|..||++.+|+|---|+..-.+|+++| T Consensus 112 ~-~------~~~~~~~~e~~~~~~~l~~al~~L~~~~r~vi~L~~----~~g~s~~EIA~~L~is~~TVk~~l~rA~k~L 180 (187) T PRK13919 112 F-D------LPGPGLDEEGHLDRTRLGRALKALSPEERRVIEVLY----YQGYTHREAARLLGLPLGTLKTWARRALSKL 180 (187) T ss_pred C-C------CCCCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH T ss_conf 0-4------688640278789999999999849999999999999----8599999999998939999999999999999 Q ss_pred CC Q ss_conf 29 Q gi|254780289|r 668 KH 669 (682) Q Consensus 668 ~~ 669 (682) |. T Consensus 181 r~ 182 (187) T PRK13919 181 KE 182 (187) T ss_pred HH T ss_conf 99 No 48 >PRK09648 RNA polymerase sigma factor SigD; Reviewed Probab=99.04 E-value=7.6e-08 Score=80.91 Aligned_cols=175 Identities=19% Similarity=0.263 Sum_probs=125.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC----CCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEH Q ss_conf 26889999998765332112468999875557899988752235----67778875443679999887438545731201 Q gi|254780289|r 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR----GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498 (682) Q Consensus 423 ~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~----~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~t 498 (682) ...++.+++.+...|... |-.+|+...-..|...|.+..++ ...-.|++||.-+.+.+++.+|.. .|-.|+| T Consensus 5 ~~~~l~~Li~~a~~GD~~---Af~~L~~~~~~~v~r~~~~~l~~~~~~~~dAeDl~Qe~fl~~~~~l~~f~~-~~~~f~~ 80 (187) T PRK09648 5 AGEELDALVAEAVAGDRR---ALREVLETIHPLVVRYCRARLGTVERSGLSADDVAQEVCLAVITALPRYRD-QGRPFLA 80 (187) T ss_pred CHHHHHHHHHHHHHCCHH---HHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCCC-CCCCHHH T ss_conf 217899999999845899---999999999999999999997144587643999999999999983766266-7784999 Q ss_pred HHHHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCC Q ss_conf 02898999999999722870461420588989999999998776088999789998709998999999986089875536 Q gi|254780289|r 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578 (682) Q Consensus 499 ya~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~ 578 (682) |+. .|.+.. .++.+.+.. |.+. . T Consensus 81 ----Wl~-~Ia~n~---------------~~d~~R~~~--------r~~~-----------------------~------ 103 (187) T PRK09648 81 ----FVY-GIAAHK---------------VADAHRAAG--------RDKA-----------------------Y------ 103 (187) T ss_pred ----HHH-HHHHHH---------------HHHHHHHHH--------CCCC-----------------------C------ T ss_conf ----999-999999---------------999999874--------6764-----------------------3------ Q ss_pred CCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHH Q ss_conf 35889986047562389889989999999999999999732998899999998187986746889998996678999999 Q gi|254780289|r 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658 (682) Q Consensus 579 ~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rq 658 (682) |..+ +.+.. ....+|++.+........+..+|+.|||+.+.||.||| -..+|..|||+.+|+|---|+. T Consensus 104 ~~~~-----~~~~~--~~~~~pe~~~~~~e~~~~l~~~l~~Lp~~~R~vl~L~~----~~g~s~~EIA~~lg~s~~tVk~ 172 (187) T PRK09648 104 PTEE-----VPERP--SDEAGPEQRALEAESSARMRELLEILPEKQREILILRV----VVGLSAEETAEAVGSTPGAVRV 172 (187) T ss_pred CCCC-----CCCCC--CCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHH T ss_conf 2112-----33347--87788589999899999999999839999999999999----8499999999998939999999 Q ss_pred HHHHHHHHHCC Q ss_conf 99999998329 Q gi|254780289|r 659 IEAKAIRKLKH 669 (682) Q Consensus 659 i~~~a~~~l~~ 669 (682) .-.+|+.+||. T Consensus 173 ~l~RA~~~Lr~ 183 (187) T PRK09648 173 AQHRALSRLRA 183 (187) T ss_pred HHHHHHHHHHH T ss_conf 99999999999 No 49 >PRK12513 RNA polymerase sigma factor; Provisional Probab=99.04 E-value=9.4e-08 Score=80.16 Aligned_cols=172 Identities=15% Similarity=0.205 Sum_probs=126.2 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHH Q ss_conf 99999876533211246899987555789998875223567778875443679999887438545731201028989999 Q gi|254780289|r 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507 (682) Q Consensus 428 K~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~ 507 (682) .+++.+++.|... |=.+++...-..|..++.+|++.--.-.|++|+.-+-+.+...+|++. ..|.||...-.|.. T Consensus 14 ~eL~~~~~~GD~~---Af~~L~~~y~~~l~~~~~~~~~d~~~AeDl~Qevfl~~~~~~~~~~~~--~~~~~wL~~ia~n~ 88 (194) T PRK12513 14 EALMLRYRAGDAA---AFEALYARHRTGLYRFLLRLARDPALADDIFQETWLRVIRARSQWQPR--ARFRTWLYQIARNR 88 (194) T ss_pred HHHHHHHHHCCHH---HHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCC--CCHHHHHHHHHHHH T ss_conf 9999999946299---999999999999999999996999999999989999999887616975--45999999999999 Q ss_pred HHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCE Q ss_conf 99999722870461420588989999999998776088999789998709998999999986089875536358899860 Q gi|254780289|r 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587 (682) Q Consensus 508 i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~ 587 (682) +..++..+.+ . .+. +.+.+ . T Consensus 89 ~~~~~R~~~~--------------------~-------~~~------------------------~~~~~--------~- 108 (194) T PRK12513 89 LIDHWRKHGA--------------------R-------QAP------------------------SLDAD--------E- 108 (194) T ss_pred HHHHHHHHHC--------------------C-------CCC------------------------CCCHH--------H- T ss_conf 9999998744--------------------3-------775------------------------31103--------6- Q ss_pred EEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH Q ss_conf 47562389889989999999999999999732998899999998187986746889998996678999999999999983 Q gi|254780289|r 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667 (682) Q Consensus 588 ~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l 667 (682) ...... ....+|+..+........|..+|+.|||+.+.|+.||| -..+|..||+..+|+|--=|+..=.+|+++| T Consensus 109 ~~~~~~-~~~~~~e~~~~~~e~~~~l~~~l~~Lp~~~r~il~L~~----~~g~s~~EIA~~l~is~~tVk~~l~rA~~~L 183 (194) T PRK12513 109 LAHALA-DDGAGPEQQLSLFRDRRRLQAALETLPDEQREVFLLRE----HGDLSLEEIAQLTGVPLETVKSRLRYALQKL 183 (194) T ss_pred HHHCCC-CCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH T ss_conf 650367-78899999999999999999999729989999999999----8499999999998949999999999999999 Q ss_pred CC Q ss_conf 29 Q gi|254780289|r 668 KH 669 (682) Q Consensus 668 ~~ 669 (682) |. T Consensus 184 r~ 185 (194) T PRK12513 184 RE 185 (194) T ss_pred HH T ss_conf 99 No 50 >PRK11922 RNA polymerase sigma factor; Provisional Probab=99.03 E-value=1e-07 Score=79.79 Aligned_cols=186 Identities=18% Similarity=0.259 Sum_probs=136.6 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHH Q ss_conf 21126889999998765332112468999875557899988752235677788754436799998874385457312010 Q gi|254780289|r 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499 (682) Q Consensus 420 ~gl~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~ty 499 (682) ..++-.+-.+++.+++.|.. .|=..++...-+.|..+|.++++..-.-.|++|+--+-+.+..++|+.... |. T Consensus 10 ~~~~~~~D~eLi~~~~~GD~---~Af~~L~~ry~~~ly~~a~~~~~~~~dAEDlvQevFlk~~~~l~~f~~~~~--f~-- 82 (231) T PRK11922 10 TPLSAADDAELVARVLAGDE---AAFEQLMRRHNRRLYRLARAILRDDAEAEDVVQEAYLRAFRALARFRGDAS--LS-- 82 (231) T ss_pred CCCCCCCHHHHHHHHHHCCH---HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHCCCCCCC--HH-- T ss_conf 99999759999999995659---999999999999999999999299999999999999999987530577565--99-- Q ss_pred HHHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCC Q ss_conf 28989999999997228704614205889899999999987760889997899987099989999999860898755363 Q gi|254780289|r 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579 (682) Q Consensus 500 a~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~ 579 (682) +|-.+-+...++ +.+.+..+.. ..+... T Consensus 83 -tWL~~Ia~N~~l-----------------d~lRk~~~~~---------------------------------~~~~~~- 110 (231) T PRK11922 83 -TWLSRIVLNEAL-----------------GRLRRRRRDV---------------------------------IELRLA- 110 (231) T ss_pred -HHHHHHHHHHHH-----------------HHHHHHHCCC---------------------------------CCCCCC- T ss_conf -999999999999-----------------9999874122---------------------------------311000- Q ss_pred CCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHH Q ss_conf 58899860475623898899899999999999999997329988999999981879867468899989966789999999 Q gi|254780289|r 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659 (682) Q Consensus 580 ~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi 659 (682) ....+.....+..+....+|+.......+...+..+|+.|||+.+.|+.||| -..+|..||++.+|+|---|+.. T Consensus 111 -~~~~~~~~~~~~~~~~~~~pe~~~~~~E~~~~l~~al~~Lp~~~R~v~~L~~----~eglS~~EIA~~Lgis~~TVKsr 185 (231) T PRK11922 111 -TESEEGEEIEFPDADPAEDPEDAAARREIRALLERAIDALPDAFRAVFVLRV----VEELSVEETAQALGLPEETVKTR 185 (231) T ss_pred -CCCCCCHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHH T ss_conf -1233210100233567899999999999999999999809999999999999----93999999999989399999999 Q ss_pred HHHHHHHHCC Q ss_conf 9999998329 Q gi|254780289|r 660 EAKAIRKLKH 669 (682) Q Consensus 660 ~~~a~~~l~~ 669 (682) =.+|.++||. T Consensus 186 L~RArk~LRe 195 (231) T PRK11922 186 LHRARRLLRE 195 (231) T ss_pred HHHHHHHHHH T ss_conf 9999999999 No 51 >PRK09646 RNA polymerase sigma factor SigK; Reviewed Probab=99.03 E-value=3.8e-08 Score=83.29 Aligned_cols=177 Identities=16% Similarity=0.237 Sum_probs=125.2 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHH Q ss_conf 12688999999876533211246899987555789998875223567778875443679999887438545731201028 Q gi|254780289|r 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501 (682) Q Consensus 422 l~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~ 501 (682) .+..+..+++.+++.|... |=.+|+...-+.|..+|.+|++.--.-.|++|+.-+-+.+...+|++.+| .|. + T Consensus 12 ~~~~d~~~Li~~~~~GD~~---Af~~Ly~~y~~~l~~~~~~~~~d~~~AeDivQevFl~~~~~~~~~~~~~~-~~~---~ 84 (194) T PRK09646 12 APSPDLDALLRRVARGDQD---AFAELYDRTASRVYGLVRRVLRDPGYSEETTQEVYLEVWRTASRFDPARG-SAL---A 84 (194) T ss_pred CCCCCHHHHHHHHHHCCHH---HHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCC-CHH---H T ss_conf 3796699999999936799---99999999999999999999299999999999999999997521475426-599---9 Q ss_pred HHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCC Q ss_conf 98999999999722870461420588989999999998776088999789998709998999999986089875536358 Q gi|254780289|r 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG 581 (682) Q Consensus 502 ~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~ 581 (682) |-.+-+..+++ +.+.+..... .+ +...+ T Consensus 85 WL~~Ia~n~~~-----------------d~~R~~~~~~----~~-------------------------------~~~~~ 112 (194) T PRK09646 85 WLLTLAHRRAV-----------------DRVRSEQAAS----QR-------------------------------EVRYG 112 (194) T ss_pred HHHHHHHHHHH-----------------HHHHHHHHHH----HH-------------------------------HHHHC T ss_conf 99999999999-----------------9999987413----24-------------------------------43200 Q ss_pred CCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHH Q ss_conf 89986047562389889989999999999999999732998899999998187986746889998996678999999999 Q gi|254780289|r 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661 (682) Q Consensus 582 ~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~ 661 (682) ..+.. .....+.+.+........|..+|..|||+.+.||.||| -..+|.+||++.+|+|-.-|+.-=. T Consensus 113 ~~~~~--------~~~~~~~e~~~~~~~~~~l~~~l~~Lp~~~R~vi~L~~----~~g~s~~EIA~~Lgis~~TVk~rl~ 180 (194) T PRK09646 113 ARNVD--------PAFDQVAEEVEARLERERVRGCLDALTDTQREAITLAY----YGGLTYREVAERLAVPLGTVKTRMR 180 (194) T ss_pred CCCCC--------CCCCCCHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHH T ss_conf 02368--------87553147899899999999999867815789999999----9399999999998919999999999 Q ss_pred HHHHHHCC Q ss_conf 99998329 Q gi|254780289|r 662 KAIRKLKH 669 (682) Q Consensus 662 ~a~~~l~~ 669 (682) +|+++||. T Consensus 181 rA~~~LR~ 188 (194) T PRK09646 181 DGLRRLRD 188 (194) T ss_pred HHHHHHHH T ss_conf 99999999 No 52 >PRK12543 RNA polymerase sigma factor; Provisional Probab=99.02 E-value=1.3e-07 Score=79.13 Aligned_cols=171 Identities=16% Similarity=0.258 Sum_probs=125.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHH Q ss_conf 89999998765332112468999875557899988752235677788754436799998874385457312010289899 Q gi|254780289|r 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505 (682) Q Consensus 426 ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~ 505 (682) ..++++.+++.|... |=.++++..-+.|..+|.++++..-.-.|++||.-+-+.+...+|++... |.| |+. T Consensus 5 d~~~Li~~~~~Gd~~---Af~~Ly~~y~~~l~~~~~~~~~d~~~AeD~vQe~Flk~~~~~~~~~~~~~--~~~----WL~ 75 (190) T PRK12543 5 DYKHLIQLTLSGNKE---AYSELYDVTIQEVYKTVHFLIEDKTDVDDVVQEVYIQLYESLRKYDSEKP--FRP----WLI 75 (190) T ss_pred CHHHHHHHHHHCCHH---HHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCC--HHH----HHH T ss_conf 899999999956699---99999999999999999999099999999999999999999987188886--899----999 Q ss_pred HHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCC Q ss_conf 99999997228704614205889899999999987760889997899987099989999999860898755363588998 Q gi|254780289|r 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDT 585 (682) Q Consensus 506 ~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~ 585 (682) .-..+.+.+..| +..+.. ..++. . T Consensus 76 ~ia~n~~~~~~r----------------~~~~~~----------------------------------~~~~~-----~- 99 (190) T PRK12543 76 GLVIKQIHSYRR----------------KRWMRL----------------------------------RIFKK-----A- 99 (190) T ss_pred HHHHHHHHHHHH----------------HHHHHC----------------------------------CCCCC-----H- T ss_conf 999999999999----------------875003----------------------------------41220-----0- Q ss_pred CEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH Q ss_conf 60475623898899899999999999999997329988999999981879867468899989966789999999999999 Q gi|254780289|r 586 SHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665 (682) Q Consensus 586 ~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~ 665 (682) +....+....|++.+........+..+|..|||+.+.|+.||| -..+|..|||..+|+|-.-|+--=.+|++ T Consensus 100 ----~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~R~vi~L~~----~~g~s~~EIA~~l~is~~tVk~rl~rA~k 171 (190) T PRK12543 100 ----EEQRKPVQIDFSNDLLSKISNQKLIELIHKLPYKLKQVIILRY----LHDYSQEEVAQILHIPIGTVKSRIHAALK 171 (190) T ss_pred ----HHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHH T ss_conf ----1001555688268999999999999999849999999999999----85999999999989399999999999999 Q ss_pred HHCC Q ss_conf 8329 Q gi|254780289|r 666 KLKH 669 (682) Q Consensus 666 ~l~~ 669 (682) +||. T Consensus 172 ~LR~ 175 (190) T PRK12543 172 KLRQ 175 (190) T ss_pred HHHH T ss_conf 9999 No 53 >PRK06811 RNA polymerase factor sigma-70; Validated Probab=99.00 E-value=1.3e-07 Score=78.96 Aligned_cols=168 Identities=15% Similarity=0.216 Sum_probs=121.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC---HHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHH Q ss_conf 999998765332112468999875557899988752235677---78875443679999887438545731201028989 Q gi|254780289|r 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ---FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504 (682) Q Consensus 428 K~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~---~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i 504 (682) .+++.+++.|.. .|-.++++..-++|.+++.++.+.... -.|++|+.-+-+.+...+|++.+| +|+|| -. T Consensus 4 ~~Li~~~~~GD~---~Af~~l~~~y~~~v~~~~~~~l~~~~~~~~aeD~vQevFi~~~~~~~~~~~~~~-~f~~W---L~ 76 (185) T PRK06811 4 DNFIKELKKKNE---KALEFIIDTYGNLIKKIVHKVLGTDQYKQLIEECVNDIFLSIWNNIDKFDEEKG-SFKNW---IA 76 (185) T ss_pred HHHHHHHHHCCH---HHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCHHCCCCCC-CHHHH---HH T ss_conf 999999982789---999999999999999999999677688989999999999999983700388645-29999---99 Q ss_pred HHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCC Q ss_conf 99999999722870461420588989999999998776088999789998709998999999986089875536358899 Q gi|254780289|r 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584 (682) Q Consensus 505 ~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~ 584 (682) +=+..+++ +.+.+..+ .. .++.+ + T Consensus 77 ~Ia~n~~~-----------------d~~Rk~~r--------~~-------------------------~~~~~------~ 100 (185) T PRK06811 77 AISKYKAI-----------------DYKRKLTK--------NN-------------------------NIDSD------E 100 (185) T ss_pred HHHHHHHH-----------------HHHHHHCC--------CC-------------------------CCCHH------H T ss_conf 99999999-----------------99997426--------56-------------------------66456------5 Q ss_pred CCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH Q ss_conf 86047562389889989999999999999999732998899999998187986746889998996678999999999999 Q gi|254780289|r 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664 (682) Q Consensus 585 ~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~ 664 (682) .......+|++.......+..+..+|..|||+.+.|+.||| -..+|.+|||+.+|+|.--|+..=.+|+ T Consensus 101 -------~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~----~~~~s~~EIA~~l~is~~tVk~rl~Rar 169 (185) T PRK06811 101 -------FILISEESIENEIILKENKEEIIKLINDLKKLDREIFIKRY----LLGESIEEIAKKLGLTRSAIDNRLSRGR 169 (185) T ss_pred -------HCCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHH T ss_conf -------21355588788999999999999998489999999999999----9499999999998929999999999999 Q ss_pred HHHCC Q ss_conf 98329 Q gi|254780289|r 665 RKLKH 669 (682) Q Consensus 665 ~~l~~ 669 (682) ++||. T Consensus 170 ~~Lr~ 174 (185) T PRK06811 170 KKLKN 174 (185) T ss_pred HHHHH T ss_conf 99999 No 54 >PRK12534 RNA polymerase sigma factor; Provisional Probab=98.96 E-value=2e-07 Score=77.55 Aligned_cols=177 Identities=18% Similarity=0.255 Sum_probs=131.9 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHH Q ss_conf 11268899999987653321124689998755578999887522356777887544367999988743854573120102 Q gi|254780289|r 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500 (682) Q Consensus 421 gl~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya 500 (682) |.+-.+...++..++.|... |=..|+...-+.|.+++.+|++..-.-.|++|+.-+-+.+..++|++.+|+-+ T Consensus 6 ~~~~de~~~Li~~~~~GD~~---Af~~Ly~~y~~~l~~~~~~~~~~~~~AeDv~Qe~Fl~vw~~~~~~~~~~~~~~---- 78 (187) T PRK12534 6 GHDDDETGRLLTATAGGDRH---AFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFDPSRARGL---- 78 (187) T ss_pred CCCCHHHHHHHHHHHHCCHH---HHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCHH---- T ss_conf 99962899999999936899---99999999999999999998699999999999999999987533687522189---- Q ss_pred HHHHHH-HHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCC Q ss_conf 898999-9999997228704614205889899999999987760889997899987099989999999860898755363 Q gi|254780289|r 501 MWWVKQ-AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579 (682) Q Consensus 501 ~~~i~~-~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~ 579 (682) +|+.. +...|+ |..| +.. ..+..++++.. T Consensus 79 -tWl~~IarN~~~-d~lR----------------~~~--------------------------------~~~~~~~~~~~ 108 (187) T PRK12534 79 -TWLAMIARNKAI-DHLR----------------ANA--------------------------------PQRRNVALDDA 108 (187) T ss_pred -HHHHHHHHHHHH-HHHH----------------HCC--------------------------------CCCCCCCCCCC T ss_conf -999999999999-9999----------------624--------------------------------41357773411 Q ss_pred CCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHH Q ss_conf 58899860475623898899899999999999999997329988999999981879867468899989966789999999 Q gi|254780289|r 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659 (682) Q Consensus 580 ~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi 659 (682) . . +. ....+|.+.......+..|..+|..|+|..+.|+.++| -..+|++||++.+|+|---|+.- T Consensus 109 ------~---~-~~-~~~~~~~e~~~~~~~~~~l~~al~~L~~~~r~vi~l~~----~eg~s~~EIA~~l~i~~gTVksr 173 (187) T PRK12534 109 ------G---E-LR-AADASPLERTERASTRRRIDHCLAELEPPRSELIRTAF----FEGITYEELAARTDTPIGTVKSW 173 (187) T ss_pred ------C---C-CC-CCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHH T ss_conf ------0---0-13-56898277899999999999999868998999999999----84999999999989199999999 Q ss_pred HHHHHHHHCC Q ss_conf 9999998329 Q gi|254780289|r 660 EAKAIRKLKH 669 (682) Q Consensus 660 ~~~a~~~l~~ 669 (682) =.+|+++||. T Consensus 174 l~ra~~~Lr~ 183 (187) T PRK12534 174 IRRGLAKLKA 183 (187) T ss_pred HHHHHHHHHH T ss_conf 9999999999 No 55 >PRK05602 RNA polymerase sigma factor; Reviewed Probab=98.94 E-value=2.2e-07 Score=77.22 Aligned_cols=168 Identities=17% Similarity=0.265 Sum_probs=124.8 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHH Q ss_conf 99999987653321124689998755578999887522356777887544367999988743854573120102898999 Q gi|254780289|r 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506 (682) Q Consensus 427 lK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~ 506 (682) =.+++..++.|... |-.+|+...-..|.++|.++++..-.-.|++|+.-+.+.+...+|++..+ +|.| |-.+- T Consensus 7 D~eLi~~~~~Gd~~---Af~~L~~~y~~~l~~~~~~~~~d~~~AeDivQe~fl~~~~~~~~~~~~~~-~~~~---wL~~i 79 (186) T PRK05602 7 DAELMARVGAGDAS---AFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWNQAPSWRPGEA-RFDT---WLHRV 79 (186) T ss_pred HHHHHHHHHHCCHH---HHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCCCCCH-HHHH---HHHHH T ss_conf 99999999928899---99999999999999999999299999999999999999987222588620-3999---99999 Q ss_pred HHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCC Q ss_conf 99999972287046142058898999999999877608899978999870999899999998608987553635889986 Q gi|254780289|r 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586 (682) Q Consensus 507 ~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~ 586 (682) +...++ +.+.+ .+ .++++.+ T Consensus 80 a~n~~~-----------------d~~Rk-~~-----------------------------------~~~~~~~------- 99 (186) T PRK05602 80 VLNLCY-----------------DRLRR-RR-----------------------------------EVPVEDA------- 99 (186) T ss_pred HHHHHH-----------------HHHHH-HH-----------------------------------CCCCCCC------- T ss_conf 999999-----------------99987-14-----------------------------------1573222------- Q ss_pred EEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH Q ss_conf 04756238988998999999999999999973299889999999818798674688999899667899999999999998 Q gi|254780289|r 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666 (682) Q Consensus 587 ~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~ 666 (682) .+. .+ ...+|++..........+..+|..|||+.+.|+.|+| -..+|..||+..+|+|---|+..=.+|+++ T Consensus 100 --~~~-~~-~~~~~~~~~~~~e~~~~l~~al~~Lp~~~R~v~~L~~----~~g~s~~EIA~~l~is~~tVk~~l~RAr~~ 171 (186) T PRK05602 100 --PEV-PD-PAPGPDERLEARQRARRVEQALAALPERQREAIVLQY----YQGLSNIEAARVMGLSVDALESLLARARRA 171 (186) T ss_pred --CCC-CC-CCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHH T ss_conf --000-34-6898778999999999999999759987889999998----638999999999893999999999999999 Q ss_pred HCC Q ss_conf 329 Q gi|254780289|r 667 LKH 669 (682) Q Consensus 667 l~~ 669 (682) ||. T Consensus 172 Lr~ 174 (186) T PRK05602 172 LRA 174 (186) T ss_pred HHH T ss_conf 999 No 56 >PRK11924 RNA polymerase sigma factor; Provisional Probab=98.91 E-value=2.8e-07 Score=76.46 Aligned_cols=170 Identities=17% Similarity=0.207 Sum_probs=122.5 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHH Q ss_conf 99998765332112468999875557899988752235677788754436799998874385457312010289899999 Q gi|254780289|r 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508 (682) Q Consensus 429 ~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i 508 (682) +++...+.|.. .|=.++....-.+|.++|.++++..-.-.|++|+.-+.+++..+.|+....++ + |+..-. T Consensus 2 ~l~~~a~~Gd~---~Af~~ly~~y~~~l~~~~~~~~~d~~~AeDi~Qe~fi~l~~~~~~~~~~~~~~--~----wL~~ia 72 (180) T PRK11924 2 QLPAVAASGDK---EAFSELFLPHAPDLLRYARRQLGNRALAEDAVQEAFLRAWRKADLFNGKGSAR--T----WLLTIA 72 (180) T ss_pred HHHHHHHHCCH---HHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCHH--H----HHHHHH T ss_conf 88899995599---99999999999999999999929999999999999999988632235434799--9----999999 Q ss_pred HHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEE Q ss_conf 99997228704614205889899999999987760889997899987099989999999860898755363588998604 Q gi|254780289|r 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588 (682) Q Consensus 509 ~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~ 588 (682) .+.+.+..| +..+. ...+.+.+.+ T Consensus 73 rn~~~d~~r----------------k~~~~-------------------------------~~~~~~~~~~--------- 96 (180) T PRK11924 73 RNKCYDMLR----------------RRRRE-------------------------------RKEAAEDEDL--------- 96 (180) T ss_pred HHHHHHHHH----------------HHHHH-------------------------------CCCCCCHHHC--------- T ss_conf 999999999----------------97201-------------------------------0223311001--------- Q ss_pred EEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC Q ss_conf 75623898899899999999999999997329988999999981879867468899989966789999999999999832 Q gi|254780289|r 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668 (682) Q Consensus 589 ~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~ 668 (682) .++ .....+|.+..........|..+|..|+|+++.|+.|+| -..++++|||+.+|+|..-|++.=.+|.++|| T Consensus 97 ~~~--~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~----~~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr 170 (180) T PRK11924 97 APL--SAEFETPEAALLAKDDLARIDRCLDALPEKQREVFLLRY----VEGLSYQEIADQLGVPLGTVKSRLRRARQKLR 170 (180) T ss_pred CCC--CCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH----HHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 333--446698589999999999999999859999999999999----96859999999989499999999999999999 Q ss_pred C Q ss_conf 9 Q gi|254780289|r 669 H 669 (682) Q Consensus 669 ~ 669 (682) - T Consensus 171 ~ 171 (180) T PRK11924 171 E 171 (180) T ss_pred H T ss_conf 9 No 57 >PRK12522 RNA polymerase sigma factor; Provisional Probab=98.90 E-value=3.3e-07 Score=75.90 Aligned_cols=172 Identities=15% Similarity=0.200 Sum_probs=120.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEE Q ss_conf 12468999875557899988752235677788754436799998874385457312010289899999999972287046 Q gi|254780289|r 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520 (682) Q Consensus 441 ~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r 520 (682) +++|=.+|++..-+.|..+|.++++..-.-.|++|+.-+-+.+..++|+... .|. +|-.+=+...++ | T Consensus 1 ~Eeafe~L~~~y~~~l~~~~~~~~~~~~~AeDl~Qe~flk~~~~~~~~~~~~--~~~---~WL~~Ia~N~~~-d------ 68 (173) T PRK12522 1 MEEKVEELIDIYKDQIYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSYVE--NYK---KWITTICVRTFY-D------ 68 (173) T ss_pred CHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCC--CHH---HHHHHHHHHHHH-H------ T ss_conf 9799999999999999999999919999999999999999999777668854--489---999999999999-9------ Q ss_pred CCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCH Q ss_conf 14205889899999999987760889997899987099989999999860898755363588998604756238988998 Q gi|254780289|r 521 IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600 (682) Q Consensus 521 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~ 600 (682) .+.+..+.. ....+.. +..+ +..+..++..+| T Consensus 69 ----------~~Rk~~r~~---------------------------------~~~~~~~--~~~~---~~~~~~~~~~~~ 100 (173) T PRK12522 69 ----------FYRKKKRWK---------------------------------DRILDLF--HKED---GGEIEFADDVNI 100 (173) T ss_pred ----------HHHHHCCCC---------------------------------CCCCCCC--CHHH---HHCCCCCCCCCC T ss_conf ----------999863412---------------------------------1110100--0100---001235677885 Q ss_pred HHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHH Q ss_conf 99999999999999997329988999999981879867468899989966789999999999999832967778756651 Q gi|254780289|r 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680 (682) Q Consensus 601 ~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~~~~~l~~~~ 680 (682) .+..........+..+|..|||+.+.|+.|+| -...|..||++.+|+|---|+--=.+|.++|| ..|++|+ T Consensus 101 ~~~~~~~~~~~~l~~~l~~L~~~~R~vi~L~~----~~~~s~~EIA~~l~is~~tVksrl~rAr~~Lr-----~~Le~~~ 171 (173) T PRK12522 101 SEEFIQKVEAEMIREVIQLLNEKYKTVLVLYY----YEQYSYKEMSEILNIPIGTVKYRLNYAKKQMR-----EHLEGFV 171 (173) T ss_pred HHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH-----HHHHCCC T ss_conf 29999999999999999819999999999999----83999999999989399999999999999999-----9875651 Q ss_pred C Q ss_conf 7 Q gi|254780289|r 681 D 681 (682) Q Consensus 681 ~ 681 (682) . T Consensus 172 ~ 172 (173) T PRK12522 172 H 172 (173) T ss_pred C T ss_conf 3 No 58 >PRK12514 RNA polymerase sigma factor; Provisional Probab=98.89 E-value=3.6e-07 Score=75.54 Aligned_cols=174 Identities=14% Similarity=0.243 Sum_probs=127.9 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHH Q ss_conf 26889999998765332112468999875557899988752235677788754436799998874385457312010289 Q gi|254780289|r 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502 (682) Q Consensus 423 ~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~ 502 (682) .+.+...++.+++.|... |=..|+..+-+.|..+|.+|++..-.-.|++|+.-+-+.+..++|.... ..|+| | T Consensus 2 ~p~d~~~Li~~~~~GD~~---Af~~L~~~y~~~l~~~a~~~~~d~~~AeDi~Qe~fl~~~~~~~~~~~~~-~~~~~---w 74 (179) T PRK12514 2 QPDDIEKLIVRVSLGDRD---AFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAVSG-LSPMT---W 74 (179) T ss_pred CCCCHHHHHHHHHHCCHH---HHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCC-CCHHH---H T ss_conf 971099999999965899---9999999999999999999909999999999999999998875157665-53999---9 Q ss_pred HHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCC Q ss_conf 89999999997228704614205889899999999987760889997899987099989999999860898755363588 Q gi|254780289|r 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582 (682) Q Consensus 503 ~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~ 582 (682) -.+-+...++ |. +.+ +.+. ...++. T Consensus 75 L~~iarN~~i-d~----------------~R~----------~~~~------------------------~~~~~~---- 99 (179) T PRK12514 75 LITIARNHAI-DR----------------LRA----------RKAV------------------------AVDIDE---- 99 (179) T ss_pred HHHHHHHHHH-HH----------------HHH----------CCCC------------------------CCCHHH---- T ss_conf 9999999999-99----------------986----------3777------------------------787456---- Q ss_pred CCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHH Q ss_conf 99860475623898899899999999999999997329988999999981879867468899989966789999999999 Q gi|254780289|r 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662 (682) Q Consensus 583 ~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~ 662 (682) ..++. + ..++|+..+........+..+|..|||+.+.|+.|+| -..+|..||++.+|+|---|+.-=.+ T Consensus 100 -----~~~~~-~-~~~~~e~~~~~~~~~~~l~~~l~~Lp~~~r~~~~l~~----~eg~s~~EIA~~l~is~~tVk~~l~r 168 (179) T PRK12514 100 -----AHDLA-D-PSPGPEAEVIAGDEGQRIDACLEELEKDRAAAVRRAY----LEGLSYKELAERHDVPLNTMRTWLRR 168 (179) T ss_pred -----HHHHC-C-CCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHH T ss_conf -----76512-4-6898699999889999999999875599999999996----06998999999889099999999999 Q ss_pred HHHHHCC Q ss_conf 9998329 Q gi|254780289|r 663 AIRKLKH 669 (682) Q Consensus 663 a~~~l~~ 669 (682) |+++||. T Consensus 169 A~~~Lr~ 175 (179) T PRK12514 169 SLLKLRE 175 (179) T ss_pred HHHHHHH T ss_conf 9999999 No 59 >PRK12531 RNA polymerase sigma factor; Provisional Probab=98.88 E-value=5.1e-07 Score=74.38 Aligned_cols=178 Identities=17% Similarity=0.174 Sum_probs=122.3 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHH Q ss_conf 26889999998765332112468999875557899988752235677788754436799998874385457312010289 Q gi|254780289|r 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502 (682) Q Consensus 423 ~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~ 502 (682) +-.+-.+++.+++.|..+ |=.+|++..-..|.+.|.++++..-.-.|++|+.-+.+.+....|++.++ .|+||..= T Consensus 10 ~~~~~~eLi~r~~~GD~~---Af~~Ly~~y~~~l~~~~~~~~~d~~~AeDlvQe~Flk~~~~~~~~~~~~s-~f~tWl~~ 85 (194) T PRK12531 10 GRQEWLECMEKVKSRDKQ---AFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKAHLFDGQKS-ALSTWIYT 85 (194) T ss_pred CCHHHHHHHHHHHHCCHH---HHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCC-CHHHHHHH T ss_conf 516699999999958899---99999999999999999999399999999999999999998886676536-09999999 Q ss_pred HHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCC Q ss_conf 89999999997228704614205889899999999987760889997899987099989999999860898755363588 Q gi|254780289|r 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582 (682) Q Consensus 503 ~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~ 582 (682) -.+..+..++..+. ++.. .++.+.... T Consensus 86 Ia~N~~~d~lRk~~---------------------------~~~~-------------------------~~~~~~~~~- 112 (194) T PRK12531 86 IIRNLCFDLLRKQK---------------------------GKDL-------------------------HIHADDIWP- 112 (194) T ss_pred HHHHHHHHHHHHHC---------------------------CCCC-------------------------CCCHHHCCC- T ss_conf 99999999999740---------------------------4343-------------------------432111142- Q ss_pred CCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHH Q ss_conf 99860475623898899899999999999999997329988999999981879867468899989966789999999999 Q gi|254780289|r 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662 (682) Q Consensus 583 ~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~ 662 (682) . +....+.+ +..+|+ ...+++++..+|..||++.+.|+.|+| -..+|..||++.+|+|-.-|+--=.+ T Consensus 113 ~-~~~~~~~~---~~~~~e----~~~~~~~~~~~l~~Lp~~~R~vi~L~~----~e~~s~~EIAe~l~is~~TVKsrl~r 180 (194) T PRK12531 113 S-DYYPPDLV---DHYSPE----QDMLKEQVMKFLDRLPKAQRDVLQAVY----LEELPHQQVAEMFDIPLGTVKSRLRL 180 (194) T ss_pred C-CCCCCCCC---CCCCHH----HHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHH T ss_conf 2-24783000---125879----999999999999869999999999998----86999999999989299999999999 Q ss_pred HHHHHCC Q ss_conf 9998329 Q gi|254780289|r 663 AIRKLKH 669 (682) Q Consensus 663 a~~~l~~ 669 (682) |+++||. T Consensus 181 A~k~LR~ 187 (194) T PRK12531 181 AVEKLRH 187 (194) T ss_pred HHHHHHH T ss_conf 9999999 No 60 >PRK12515 RNA polymerase sigma factor; Provisional Probab=98.88 E-value=4.7e-07 Score=74.68 Aligned_cols=169 Identities=18% Similarity=0.261 Sum_probs=124.3 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHH Q ss_conf 99999987653321124689998755578999887522356777887544367999988743854573120102898999 Q gi|254780289|r 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506 (682) Q Consensus 427 lK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~ 506 (682) =..++.+++.|.. .|=.+|+...-..|...|.+|++..-.-.|++|+.-+.+.+..++|++... |.| |-.+- T Consensus 9 D~~Lv~~~~~gd~---~Af~~L~~ry~~~l~~~~~~~~~~~~~AeDivQe~Fl~~~~~~~~~~~~~~--~~~---WL~~I 80 (189) T PRK12515 9 DEMLLARIAQGDR---TAMHTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEGRSQ--VST---WLLSI 80 (189) T ss_pred HHHHHHHHHHCCH---HHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCH--HHH---HHHHH T ss_conf 9999999993779---999999999999999999999299999999999999999986510253022--999---99999 Q ss_pred HHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCC Q ss_conf 99999972287046142058898999999999877608899978999870999899999998608987553635889986 Q gi|254780289|r 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586 (682) Q Consensus 507 ~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~ 586 (682) +..+++ +.+.+.. + .++ ..++.. T Consensus 81 arn~~~-----------------~~~r~~~--------~--------------------------~~~------~~~~~~ 103 (189) T PRK12515 81 ARFKAL-----------------SALRQRK--------D--------------------------EEI------DDEAAA 103 (189) T ss_pred HHHHHH-----------------HHHHHCC--------C--------------------------CCC------CHHHHH T ss_conf 999999-----------------9998513--------3--------------------------666------545676 Q ss_pred EEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH Q ss_conf 04756238988998999999999999999973299889999999818798674688999899667899999999999998 Q gi|254780289|r 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666 (682) Q Consensus 587 ~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~ 666 (682) . +.| ...+|+...........+..+|..|||+.+.||.||| -...|+.|||..+|+|---|+..=.+|+++ T Consensus 104 ~----~~~-~~~~~e~~~~~~~~~~~l~~~l~~L~~~~R~vi~l~~----~e~~s~~EIA~~lgis~~tV~~~l~RAr~~ 174 (189) T PRK12515 104 A----IED-GSDTPEVALQKKDTSAILRACIAKLSPAHREIIDLVY----YHEKSVEEVGEIVGIPESTVKTRMFYARKK 174 (189) T ss_pred H----CCC-CCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHH T ss_conf 3----367-7899889998999999999998759999999999999----849999999999892999999999999999 Q ss_pred HCC Q ss_conf 329 Q gi|254780289|r 667 LKH 669 (682) Q Consensus 667 l~~ 669 (682) ||- T Consensus 175 Lr~ 177 (189) T PRK12515 175 LAE 177 (189) T ss_pred HHH T ss_conf 999 No 61 >PRK12520 RNA polymerase sigma factor; Provisional Probab=98.87 E-value=2.2e-07 Score=77.25 Aligned_cols=171 Identities=17% Similarity=0.204 Sum_probs=117.8 Q ss_pred HHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCCHHHH Q ss_conf 98755578999887522356777887544367999988743854573120102898999999999722870461420588 Q gi|254780289|r 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527 (682) Q Consensus 448 l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~~~ 527 (682) .+++.=+.+...|.+|++..-.-.|++|+--+.++...++|... .+|.||.+=-.|..+.-++..+.|..+++.. T Consensus 7 ~le~~r~~L~r~A~~~v~d~~~AEDvvQetfl~~~~~~~~f~~~--~~~~tWL~~IarN~~id~lR~~~r~~~~~~~--- 81 (191) T PRK12520 7 QLEALRPYLLRFARLQLRDEAWAEDAVSETLLAALEKPERFAGQ--SQLKTYLVGILKHKIIDALRSGRREVRLSLD--- 81 (191) T ss_pred HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCC--CCHHHHHHHHHHHHHHHHHHHHCCCCCCCCC--- T ss_conf 99999999999999994999999999999999999817642765--4559899999999999999983675555433--- Q ss_pred HHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHHHH Q ss_conf 98999999999877608899978999870999899999998608987553635889986047562389889989999999 Q gi|254780289|r 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQA 607 (682) Q Consensus 528 ~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~ 607 (682) .....+.+.+.. .+ .+ .+++..+. .....+|+..+.+. T Consensus 82 ---------------~~~~~~~~~~~~-----------~~------~~--------~~~~~~~~--p~~~~~Pe~~l~~~ 119 (191) T PRK12520 82 ---------------EGDEQSDDDLFD-----------AL------FT--------ADGHYREP--PSDWGDPEATLQRR 119 (191) T ss_pred ---------------CCCCCCHHHHHH-----------HH------HC--------CCCCCCCC--CCCCCCHHHHHHHH T ss_conf ---------------456554046777-----------76------22--------34432358--76659999999999 Q ss_pred HHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC Q ss_conf 99999999973299889999999818798674688999899667899999999999998329 Q gi|254780289|r 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669 (682) Q Consensus 608 ~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~ 669 (682) .+...+..+|+.|||+.+.|+.||| ....+..|||..+|+|..-|++.=.+|..+||- T Consensus 120 e~~~~l~~aL~~Lp~~~R~v~~Lr~----~~~ls~~EIA~~l~~s~~tVk~~l~RAR~~Lr~ 177 (191) T PRK12520 120 QFFEVLQACVERLPARTGRVFMMRE----WLELETEEICKELQITATNLWVMLYRARLRLRE 177 (191) T ss_pred HHHHHHHHHHHHCCHHHHHHHHHHH----HHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH T ss_conf 9999999999877499999999999----938999999999894999999999999999999 No 62 >PRK12524 RNA polymerase sigma factor; Provisional Probab=98.85 E-value=8.4e-07 Score=72.64 Aligned_cols=169 Identities=16% Similarity=0.235 Sum_probs=124.8 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHH Q ss_conf 99999876533211246899987555789998875223567778875443679999887438545731201028989999 Q gi|254780289|r 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507 (682) Q Consensus 428 K~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~ 507 (682) .+++..++.|.. .|=.+|+...-+.|.++|.++.+.--.-.|++|+.-+-+.+....|...++ +|+| |-.+-+ T Consensus 14 ~~Lv~~~~~GD~---~Af~~L~~ry~~~l~~~a~~~l~d~~~AEDlvQe~Fl~~~~~~~~~~~~~~-~~~t---WL~~Ia 86 (196) T PRK12524 14 EALLVLFANGDP---AAARALTLRLAPRALAVATRVLGNRAEAEDVTQEAMLRLWRIAPDWRQGEA-RVST---WLYRVV 86 (196) T ss_pred HHHHHHHHHCCH---HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCC-HHHH---HHHHHH T ss_conf 999999992889---999999999999999999999199999999999999999997466156520-7999---999999 Q ss_pred HHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCE Q ss_conf 99999722870461420588989999999998776088999789998709998999999986089875536358899860 Q gi|254780289|r 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587 (682) Q Consensus 508 i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~ 587 (682) ...++. .+.+.. + ...+++ +... T Consensus 87 ~N~~~d-----------------~~R~~~--------~--------------------------~~~~~~------~~~~ 109 (196) T PRK12524 87 CNLCTD-----------------RLRRQR--------R--------------------------ASVDLD------DAPE 109 (196) T ss_pred HHHHHH-----------------HHHHHH--------C--------------------------CCCCCC------CCCC T ss_conf 999999-----------------999850--------5--------------------------677611------2433 Q ss_pred EEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH Q ss_conf 47562389889989999999999999999732998899999998187986746889998996678999999999999983 Q gi|254780289|r 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667 (682) Q Consensus 588 ~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l 667 (682) .. ...++|++.+........|..+|..|||+.+.|+.||| -..+|..||+..+|+|-.-|+..=.+|+++| T Consensus 110 ----~~-~~~~~~e~~~~~~~~~~~l~~al~~Lp~~~R~vi~L~~----~eg~s~~EIA~~lgis~~tVk~~l~Rark~L 180 (196) T PRK12524 110 ----PA-DAAPGAEEALQEGDRMRALDAALAALPERQRQAVVLRH----IEGLSNPEIAEVMQIGVEAVESLTARGKRAL 180 (196) T ss_pred ----CC-CCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH T ss_conf ----24-56898879999899999999999859999999989999----8089999999998929999999999999999 Q ss_pred CC Q ss_conf 29 Q gi|254780289|r 668 KH 669 (682) Q Consensus 668 ~~ 669 (682) |. T Consensus 181 r~ 182 (196) T PRK12524 181 AA 182 (196) T ss_pred HH T ss_conf 99 No 63 >PRK09640 RNA polymerase sigma factor SigX; Reviewed Probab=98.83 E-value=7.2e-07 Score=73.17 Aligned_cols=177 Identities=18% Similarity=0.287 Sum_probs=122.9 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHH Q ss_conf 99999876533211246899987555789998875223567778875443679999887438545731201028989999 Q gi|254780289|r 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507 (682) Q Consensus 428 K~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~ 507 (682) .+++.+++.|..-=++|=.+++...-..|.+.+.++++.--.-.|++||.-+-+.+..++|+.. .+|. +|-.+=+ T Consensus 11 ~eLv~~~~~g~~gD~~AF~~L~~~y~~~v~~~~~~~~~~~~dAEDl~Qe~flk~~~~l~~~~~~--~~f~---~WL~~Ia 85 (188) T PRK09640 11 EELVARVHVELFHVTRAYEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGK--SKFK---TWLYSIT 85 (188) T ss_pred HHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCC--CCHH---HHHHHHH T ss_conf 9999999827963899999999999999999999990999999999999999999988765898--8789---9999999 Q ss_pred HHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCE Q ss_conf 99999722870461420588989999999998776088999789998709998999999986089875536358899860 Q gi|254780289|r 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587 (682) Q Consensus 508 i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~ 587 (682) ...++. .+.+.. |.+.. ....+++. +.+ T Consensus 86 ~N~~~d-----------------~~Rk~~--------r~~~~---------------------~~~~~~~~-~~~----- 113 (188) T PRK09640 86 YNECIT-----------------QYRKER--------RKRRL---------------------MDALSLDP-LEE----- 113 (188) T ss_pred HHHHHH-----------------HHHHHC--------CCCCC---------------------CCCCCCCC-CCC----- T ss_conf 999999-----------------999861--------54555---------------------43000244-456----- Q ss_pred EEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH Q ss_conf 47562389889989999999999999999732998899999998187986746889998996678999999999999983 Q gi|254780289|r 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667 (682) Q Consensus 588 ~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l 667 (682) .+.+.......+..+..+|..|+|.++.|+.||| -..+|..||+..+|+|---|+.-=.+|+.+| T Consensus 114 -----------~~~~~~~~~e~~~~l~~~l~~L~~~~R~vl~L~~----~~~ls~~EIA~~l~is~~tVksrl~RAr~~L 178 (188) T PRK09640 114 -----------ASEEKAPKPEERGGLDRWLVHVNPIDREILVLRF----VAELEFQEIADIMHMGLSATKMRYKRALDKL 178 (188) T ss_pred -----------CCCCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH T ss_conf -----------8631002489999999999848999999999999----9299999999998929999999999999999 Q ss_pred CCHHHHHHHHHHHC Q ss_conf 29677787566517 Q gi|254780289|r 668 KHPSRSKKLRSFLD 681 (682) Q Consensus 668 ~~~~~~~~l~~~~~ 681 (682) | +.|++|.| T Consensus 179 r-----~~L~~~~e 187 (188) T PRK09640 179 R-----EKFAGLAE 187 (188) T ss_pred H-----HHHHCCCC T ss_conf 9-----98645146 No 64 >PRK09647 RNA polymerase sigma factor SigE; Reviewed Probab=98.82 E-value=6.4e-07 Score=73.61 Aligned_cols=171 Identities=18% Similarity=0.223 Sum_probs=126.4 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHH Q ss_conf 99998765332112468999875557899988752235677788754436799998874385457312010289899999 Q gi|254780289|r 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508 (682) Q Consensus 429 ~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i 508 (682) ...-..+.|.+.-..|-.+|++..-+.|...|.++++.--.-.||+||.-+-+.+..++|++ | .|+| |-.|=+. T Consensus 33 ~~~~~~~~~~~~d~~AF~eLv~rh~~~vy~~a~r~~gn~~dAEDlvQEtFlka~r~l~~f~~--~-sf~t---WL~rIA~ 106 (222) T PRK09647 33 GTAVFDATGDKATMPSWEELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSLQNYQP--G-TFEG---WLHRITT 106 (222) T ss_pred CHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCC--C-CHHH---HHHHHHH T ss_conf 44888741452458999999999999999999998599989999999999999986222477--3-0899---9999999 Q ss_pred HHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEE Q ss_conf 99997228704614205889899999999987760889997899987099989999999860898755363588998604 Q gi|254780289|r 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHL 588 (682) Q Consensus 509 ~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~ 588 (682) ..++. . +.|.. | +..+ .+.++. T Consensus 107 N~~iD-~----------------~Rr~~--------r----------------------------~~~~-~~~e~~---- 128 (222) T PRK09647 107 NLFLD-M----------------VRRRQ--------R----------------------------IRME-ALPEDY---- 128 (222) T ss_pred HHHHH-H----------------HHHCC--------C----------------------------CCCC-CCCCHH---- T ss_conf 99999-9----------------98112--------4----------------------------6655-561134---- Q ss_pred EEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC Q ss_conf 75623898899899999999999999997329988999999981879867468899989966789999999999999832 Q gi|254780289|r 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668 (682) Q Consensus 589 ~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~ 668 (682) +.+.+ ..++|+..+....+...|..+|..|+|+.+.||.||| -..+|.+||++.+|+|---|+.-=.+|+++|| T Consensus 129 -e~~~~-~~~~pe~~~~~~~~~~~L~~al~~Lp~~qR~vl~Lr~----~eglS~~EIAe~Lgis~gTVKsrl~RAr~~LR 202 (222) T PRK09647 129 -DRVPA-DEPNPEQIYHDARLDPDLQAALDSLPPEFRAAVVLCD----IEGLSYEEIAATLGVKLGTVRSRIHRGRQALR 202 (222) T ss_pred -HHCCC-CCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf -42566-7899789999999999999999829999988998799----63999999999989399999999999999999 Q ss_pred C Q ss_conf 9 Q gi|254780289|r 669 H 669 (682) Q Consensus 669 ~ 669 (682) . T Consensus 203 ~ 203 (222) T PRK09647 203 A 203 (222) T ss_pred H T ss_conf 9 No 65 >PRK12544 RNA polymerase sigma factor; Provisional Probab=98.82 E-value=8.4e-07 Score=72.67 Aligned_cols=170 Identities=16% Similarity=0.153 Sum_probs=114.2 Q ss_pred HHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHH---HHCCCEEECCC Q ss_conf 998755578999887522356777887544367999988743854573120102898999999999---72287046142 Q gi|254780289|r 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI---ADQSCTIRIPV 523 (682) Q Consensus 447 ~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~---~~~~~~~r~~~ 523 (682) .||+..=+-.+..|.++.+.--.-.|++||.-+-..+..++|+.+. +|+| |-.|=+...++ ..+.|...++ T Consensus 23 ~l~e~y~~~L~r~A~r~l~d~~~AEDlvQEtFlka~~~l~~F~g~s--~f~t---WL~~Ia~N~~iD~lRk~~r~~~~~- 96 (207) T PRK12544 23 VFLEDLRAQMLKFAKLQLRDNHLAEDAVQEALFSAYQNADSFAGRA--AFKT---WVFAILKNKIIDLLRQKKRHVSAS- 96 (207) T ss_pred HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCC--CHHH---HHHHHHHHHHHHHHHHHCCCCCCC- T ss_conf 9999999999999999949999999999999999998177438888--6098---999999999999999851656521- Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHH Q ss_conf 05889899999999987760889997899987099989999999860898755363588998604756238988998999 Q gi|254780289|r 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603 (682) Q Consensus 524 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~ 603 (682) .+-..+...+ .++ ++.+ +.+++...-.......|++. T Consensus 97 ------------------~~~~~~~~~~-----------------------~~~-~~~d-~~g~~~~~e~p~~~~~pee~ 133 (207) T PRK12544 97 ------------------QLEDGDEGEA-----------------------LIE-ALFD-ESGHWQKDERPQKWDQPEEG 133 (207) T ss_pred ------------------CCCCCCCHHH-----------------------HHH-HHHC-CCCCCCCCCCCCCCCCHHHH T ss_conf ------------------0134541013-----------------------466-6511-12343333465333898999 Q ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC Q ss_conf 999999999999973299889999999818798674688999899667899999999999998329 Q gi|254780289|r 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669 (682) Q Consensus 604 ~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~ 669 (682) +....+...+..+|..|||+.+.|+.||| -...+..||++.+|+|-.-|+..=.+|-.+||. T Consensus 134 l~~~e~~~~l~~aL~~Lp~~~R~vl~Lr~----~eglS~~EIAe~Lgis~~tVks~L~RAR~~Lr~ 195 (207) T PRK12544 134 VEQEQFWRIFDACLDALPAKYARVFMMRE----FIELETPEICHNEDLTVSNLNVMLYRSRLRLRE 195 (207) T ss_pred HHHHHHHHHHHHHHHHCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH T ss_conf 99999999999999839999999999999----819999999999797999999999999999999 No 66 >PRK12537 RNA polymerase sigma factor; Provisional Probab=98.81 E-value=5.9e-07 Score=73.87 Aligned_cols=176 Identities=12% Similarity=0.185 Sum_probs=119.3 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHH Q ss_conf 26889999998765332112468999875557899988752235677788754436799998874385457312010289 Q gi|254780289|r 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502 (682) Q Consensus 423 ~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~ 502 (682) ++.+...+++.+++|.. .|-.+++...-..|..+|.+|++.--.-.|++|+.-+-+.+..++|++.+|. |. + T Consensus 6 ~p~d~e~ll~~~~~GD~---~Af~~Ly~~y~~~l~~~~~~~~~d~~~AeDivQe~Fl~~~~~~~~~~~~~~~-~~---~- 77 (184) T PRK12537 6 APFDYEACLQACARGER---RALQRLYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTKAASFDAARGS-AR---G- 77 (184) T ss_pred CCCCHHHHHHHHHHCCH---HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCCCCCCCC-HH---H- T ss_conf 99999999999995889---9999999999999999999992999999999999999999860416844263-99---9- Q ss_pred HHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCC Q ss_conf 89999999997228704614205889899999999987760889997899987099989999999860898755363588 Q gi|254780289|r 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582 (682) Q Consensus 503 ~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~ 582 (682) |+..-..+.. +|.+.+..+. .+..+... ...+.+ T Consensus 78 WL~~Iarn~~----------------~~~lR~~~r~-------~~~~~~~~------------------~~~~~~----- 111 (184) T PRK12537 78 WIYSVTRHLA----------------LNTLRDTRRE-------VVLDDDAS------------------EQATAQ----- 111 (184) T ss_pred HHHHHHHHHH----------------HHHHHHHCCC-------CCCCCHHH------------------HHCCCC----- T ss_conf 9999999999----------------9999985065-------66651002------------------101346----- Q ss_pred CCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHH Q ss_conf 99860475623898899899999999999999997329988999999981879867468899989966789999999999 Q gi|254780289|r 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662 (682) Q Consensus 583 ~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~ 662 (682) ......+ ..........|..+|..|+|+.+.|+.++| -..+|..||++.+|+|-.-|+..=.+ T Consensus 112 ----------~~~~~~~---~~~~~~~~~~l~~~l~~L~~~~r~~i~l~~----~eg~s~~EIA~~l~is~~TVk~rl~r 174 (184) T PRK12537 112 ----------GWQEIID---DFDLWVNSGKIHRCLEQLEPARRNCILHAY----VDGCSHAEIAQRLGAPLGTVKAWIKR 174 (184) T ss_pred ----------CCCCCCC---HHHHHHHHHHHHHHHHHCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHH T ss_conf ----------7777556---798999999999999809998999999988----43999999999989299999999999 Q ss_pred HHHHHCC Q ss_conf 9998329 Q gi|254780289|r 663 AIRKLKH 669 (682) Q Consensus 663 a~~~l~~ 669 (682) |+.+||. T Consensus 175 A~~~LR~ 181 (184) T PRK12537 175 SLKALRE 181 (184) T ss_pred HHHHHHH T ss_conf 9999998 No 67 >TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS; InterPro: IPR012761 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This entry represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second principal sigma factor at that time.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent. Probab=98.80 E-value=3.6e-08 Score=83.47 Aligned_cols=124 Identities=21% Similarity=0.154 Sum_probs=93.2 Q ss_pred CCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHH------------HHHHHHHHHHCCHHHHHHHHHHHHHHCCCHHHH Q ss_conf 77772899999985697688978899999999988------------999999987282389999999987311710367 Q gi|254780289|r 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG------------RAMMMASLCESPLTFQALIIWRDELNDGTTLLR 182 (682) Q Consensus 115 ~rtdDPVRMYLREMG~V~LLTREgEIeIAKRIE~G------------~~~i~~al~~~P~ti~~il~~~e~i~~ge~~Lr 182 (682) ..+-||+.+||||+|.-||||.++|+.+|.|--+| .+-|.++--+|-.-.-.++|+.++-+=|=|..- T Consensus 9 ~~~~D~~Q~YL~eIg~~PLLt~~EE~~~Arra~~GD~eAR~~MIE~NLRLVV~IAk~Y~nRGlpLlDLIEEGNLGLm~Av 88 (292) T TIGR02394 9 TRVADVTQLYLREIGFKPLLTAEEELAYARRALAGDFEARKKMIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAV 88 (292) T ss_pred HHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHH T ss_conf 23302688878886015588988999998886507888988877640126767864404765145777765335665421 Q ss_pred HHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHH Q ss_conf 87642101354333333343333321100011100010000000012210000111 Q gi|254780289|r 183 EIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSK 238 (682) Q Consensus 183 dIIDld~t~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~e~~~e~~~~~~~ 238 (682) +-+|-.-.|.+.++.+||..+..+-.-.++..+...+.+.+.+.+........... T Consensus 89 EKFDPeRGFRFSTYATWWIRQtIERAIMNQaRTiRLPvHV~kELNv~LRa~r~L~~ 144 (292) T TIGR02394 89 EKFDPERGFRFSTYATWWIRQTIERAIMNQARTIRLPVHVVKELNVYLRAARQLEK 144 (292) T ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCEECCHHHHHHHHHHHHHHHHHHH T ss_conf 04588999844301113665327865313544110531434677799998887655 No 68 >PRK09643 RNA polymerase sigma factor SigM; Reviewed Probab=98.80 E-value=9.1e-07 Score=72.38 Aligned_cols=170 Identities=14% Similarity=0.165 Sum_probs=119.9 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHH Q ss_conf 99999987653321124689998755578999887522356777887544367999988743854573120102898999 Q gi|254780289|r 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506 (682) Q Consensus 427 lK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~ 506 (682) =.+++.+++.|.. .|=.+|+...-..|..+|.++++..-.-.|++|+--+-+.+...+|+... .|. +|-.+= T Consensus 14 D~eLi~~~~~GD~---~Af~~L~~ry~~~l~~~a~~~~~~~~~AeDvvQe~flk~~~~~~~~~~~~--~f~---~WL~~I 85 (197) T PRK09643 14 DAELLAAHVAGDR---YAFGELFRRHHRQLWRLARRTSGTREDAADALQDAMLSAHRGAGSFRGDA--AVS---SWLHRI 85 (197) T ss_pred HHHHHHHHHHCCH---HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCC--HHH---HHHHHH T ss_conf 9999999992779---99999999999999999999919999999999999999999886338863--499---999999 Q ss_pred HHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCC Q ss_conf 99999972287046142058898999999999877608899978999870999899999998608987553635889986 Q gi|254780289|r 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586 (682) Q Consensus 507 ~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~ 586 (682) +...++ +.+.+.. +.+ .++++. .. T Consensus 86 a~N~~~-----------------d~~Rk~~--------~~~-------------------------~~~~~~----~~-- 109 (197) T PRK09643 86 VVNACL-----------------DRLRRAK--------ARP-------------------------TVPLED----VY-- 109 (197) T ss_pred HHHHHH-----------------HHHHHHC--------CCC-------------------------CCCCCC----CC-- T ss_conf 999999-----------------9999851--------467-------------------------788665----67-- Q ss_pred EEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH Q ss_conf 04756238988998999999999999999973299889999999818798674688999899667899999999999998 Q gi|254780289|r 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666 (682) Q Consensus 587 ~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~ 666 (682) ..+.+..........+.++|..|||..+.||.|+| -..+|+.||++.+|+|-.-|+..-.+|+.+ T Consensus 110 -----------~~~~~~~~~~e~~~~l~~al~~Lp~~~R~vl~L~~----~eg~s~~EIA~~lgis~~tVKsrl~RAr~~ 174 (197) T PRK09643 110 -----------PVADRETARVETAIAVQRALMRLPVEQRAALVAVD----MQGYSVADTARMLGVAEGTVKSRCARGRAR 174 (197) T ss_pred -----------CCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHH T ss_conf -----------78652031389999999999769998879999999----819999999999893999999999999999 Q ss_pred HCCHHHHHHHH Q ss_conf 32967778756 Q gi|254780289|r 667 LKHPSRSKKLR 677 (682) Q Consensus 667 l~~~~~~~~l~ 677 (682) ||. .-..|+ T Consensus 175 Lr~--~L~~l~ 183 (197) T PRK09643 175 LAE--LLGYLR 183 (197) T ss_pred HHH--HHHHHH T ss_conf 999--999884 No 69 >PRK12538 RNA polymerase sigma factor; Provisional Probab=98.79 E-value=2.4e-06 Score=69.08 Aligned_cols=171 Identities=13% Similarity=0.238 Sum_probs=128.2 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHH Q ss_conf 88999999876533211246899987555789998875223567778875443679999887438545731201028989 Q gi|254780289|r 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504 (682) Q Consensus 425 ~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i 504 (682) .+-.+++.+++.|.. .|-..|++..-..|..+|.++++.--.-.|++||--+-+.+..++|++.+ .+|+ ||-. T Consensus 48 d~D~eLv~R~~~GD~---~AF~~Ly~ry~~~l~~~a~r~l~d~~dAEDvvQEvFlk~w~~~~~f~~g~-s~f~---tWL~ 120 (233) T PRK12538 48 DEDEELLDRLATDDE---AAFRLLVERHIDRAYAIALRIVGNRADAEDVVQDTMLKVWTHRGRWQHGR-AKFS---TWLY 120 (233) T ss_pred CCHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHCCCCCC-CHHH---HHHH T ss_conf 978999999996029---99999999999999999999959999999999999999999884477786-7399---9999 Q ss_pred HHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCC Q ss_conf 99999999722870461420588989999999998776088999789998709998999999986089875536358899 Q gi|254780289|r 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDED 584 (682) Q Consensus 505 ~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~ 584 (682) +-+..+++. . .| + .|. +.+ +. +.+ T Consensus 121 ~IA~N~~id-~-----------------~R---k-----~r~-------------------------~~~--d~-~~e-- 144 (233) T PRK12538 121 RVVSNRCID-L-----------------RR---K-----PRT-------------------------ENV--DA-VPE-- 144 (233) T ss_pred HHHHHHHHH-H-----------------HH---H-----HCC-------------------------CCC--CC-CCC-- T ss_conf 999999999-9-----------------97---4-----145-------------------------652--23-444-- Q ss_pred CCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH Q ss_conf 86047562389889989999999999999999732998899999998187986746889998996678999999999999 Q gi|254780289|r 585 TSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAI 664 (682) Q Consensus 585 ~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~ 664 (682) +.| ..+++...+....+...|..+|..|||+.+.|+.|+| ...+|.+||+..+|+|---|+..=.+|+ T Consensus 145 -------~~d-~~~~~~~~l~~~e~~~~L~~aL~~Lp~~~R~vl~L~~----~egls~~EIA~~Lgis~~TVKsrL~RAr 212 (233) T PRK12538 145 -------VAD-GKPDAVSVIERNELSDLLEAAMQRLPEQQRIAVILSY----HENMSNGEIAEVMDTTVAAVESLLKRGR 212 (233) T ss_pred -------CCC-CCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHH T ss_conf -------456-8988878999999999999999759999999999999----8499999999998929999999999999 Q ss_pred HHHCCH Q ss_conf 983296 Q gi|254780289|r 665 RKLKHP 670 (682) Q Consensus 665 ~~l~~~ 670 (682) ++||.- T Consensus 213 ~~LR~~ 218 (233) T PRK12538 213 QQLRDL 218 (233) T ss_pred HHHHHH T ss_conf 999999 No 70 >PRK09638 RNA polymerase sigma factor SigY; Reviewed Probab=98.78 E-value=1e-06 Score=71.90 Aligned_cols=168 Identities=17% Similarity=0.256 Sum_probs=113.5 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHH Q ss_conf 99999987653321124689998755578999887522356777887544367999988743854573120102898999 Q gi|254780289|r 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506 (682) Q Consensus 427 lK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~ 506 (682) -.+++.+++.|.. .|-.+++...-..|...|.++++..-.-.|++|+.-+.+.+..++|++... | .+|-.+- T Consensus 6 d~~Li~~~~~GD~---~Af~~L~~~y~~~l~~~~~~~~~~~~~AeDivQe~fl~~~~~~~~~~~~~~--~---~~wL~~i 77 (177) T PRK09638 6 EKELIRRAKKGND---AALTKLLQQHYNFLYGYVLKLTLNPDLAEDLVQETMLKAIENIHQFQGRSK--F---STWLISI 77 (177) T ss_pred HHHHHHHHHHCCH---HHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCHH--H---HHHHHHH T ss_conf 9999999994779---999999999999999999999199999999999999999998877065007--9---9999999 Q ss_pred HHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCC Q ss_conf 99999972287046142058898999999999877608899978999870999899999998608987553635889986 Q gi|254780289|r 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586 (682) Q Consensus 507 ~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~ 586 (682) +...++ |. +.+.. |.....+ ...+.+. T Consensus 78 a~n~~~-d~----------------~Rk~~--------r~~~~~~----------------------~~~~~~~------ 104 (177) T PRK09638 78 ASRLYL-DH----------------LRKRK--------REELREE----------------------AATEETL------ 104 (177) T ss_pred HHHHHH-HH----------------HHHHC--------CCCCCCC----------------------CCCCCCC------ T ss_conf 999999-99----------------99860--------3011000----------------------2333355------ Q ss_pred EEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH Q ss_conf 04756238988998999999999999999973299889999999818798674688999899667899999999999998 Q gi|254780289|r 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666 (682) Q Consensus 587 ~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~ 666 (682) .... .+..........+..+|..|||+.+.|+.||| -..+|..|||+.+|+|-.-|+..=.+|+++ T Consensus 105 ---------~~~~-~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~L~~----~eg~s~~EIA~~l~is~~tVk~~l~rA~~~ 170 (177) T PRK09638 105 ---------RKEK-WETAISGHEWSELLDLLMKLPPELRAPFILKH----YYGYTYEEIAKMLGIPEGTVKSRVHHGLKK 170 (177) T ss_pred ---------CCCC-CCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHH T ss_conf ---------6676-11465379999999999759998989999999----919999999999893999999999999999 Q ss_pred HCC Q ss_conf 329 Q gi|254780289|r 667 LKH 669 (682) Q Consensus 667 l~~ 669 (682) ||. T Consensus 171 Lr~ 173 (177) T PRK09638 171 IRK 173 (177) T ss_pred HHH T ss_conf 999 No 71 >PRK12512 RNA polymerase sigma factor; Provisional Probab=98.78 E-value=6.2e-07 Score=73.68 Aligned_cols=169 Identities=14% Similarity=0.244 Sum_probs=115.3 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-CC---CHHHHHHHHHHHHHHHHHHCCCCCCCEEEH Q ss_conf 26889999998765332112468999875557899988752235-67---778875443679999887438545731201 Q gi|254780289|r 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNR-GL---QFLDLIQEGNIGLMKAAEKFDWCLGYKFST 498 (682) Q Consensus 423 ~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~-~~---~~~~~~~~~~~~l~~a~~~~~~~~g~~f~t 498 (682) ...++.++++.++.|... |=.+|++.....|.++|.+++.+ |. .-.|++|+--+-+.+...+|++. ..|.| T Consensus 5 ~~~e~~~Li~~~~~GD~~---Af~~L~~~~~~~l~~~~~~~l~~~~~~~~dAeDlvQevfl~~~~~~~~~~~~--~~f~~ 79 (184) T PRK12512 5 REDEWTDLMRSANAGDAA---AYRRLLKAVTPVLRAAARRGLARAGQPADQAEDIVQEILLAVHLKRHTWDPG--APFAP 79 (184) T ss_pred CHHHHHHHHHHHHHCCHH---HHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCC--CCHHH T ss_conf 528799999999827899---9999999999999999999988468998899999999999999872314888--85899 Q ss_pred HHHHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCC Q ss_conf 02898999999999722870461420588989999999998776088999789998709998999999986089875536 Q gi|254780289|r 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLET 578 (682) Q Consensus 499 ya~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~ 578 (682) |-.--.|..+..++..+ ++.+. ++.+.+ T Consensus 80 WL~~Iarn~~~d~~Rk~----------------------------~~~~~---------~~~~~~--------------- 107 (184) T PRK12512 80 WLFAIARNKLIDALRRR----------------------------GRRVF---------VDIDDF--------------- 107 (184) T ss_pred HHHHHHHHHHHHHHHHH----------------------------CCCCC---------CCHHHH--------------- T ss_conf 99999999999999974----------------------------37778---------983444--------------- Q ss_pred CCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHH Q ss_conf 35889986047562389889989999999999999999732998899999998187986746889998996678999999 Q gi|254780289|r 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658 (682) Q Consensus 579 ~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rq 658 (682) .+.+.+.... +.. ....+..+|..|||+.+.||.|+| -..+|..||++.+|+|---|+. T Consensus 108 ----------~~~~~~~~~~---~~~----~~~~l~~~L~~Lp~~~R~vi~L~~----~~g~s~~EIA~~lgis~~tVk~ 166 (184) T PRK12512 108 ----------AETLPSEPAA---ETL----PAGDVGRHLETLPPRQRDVVQSIA----VEGASIKETAAKLSMSEGAVRV 166 (184) T ss_pred ----------HHCCCCCCCC---CHH----HHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHH T ss_conf ----------2216788876---426----899999999689999999999998----5597999999998919999999 Q ss_pred HHHHHHHHHCC Q ss_conf 99999998329 Q gi|254780289|r 659 IEAKAIRKLKH 669 (682) Q Consensus 659 i~~~a~~~l~~ 669 (682) .-.+|+++||. T Consensus 167 ~l~RA~~~Lr~ 177 (184) T PRK12512 167 ALHRGLAALAA 177 (184) T ss_pred HHHHHHHHHHH T ss_conf 99999999999 No 72 >TIGR02859 spore_sigH RNA polymerase sigma-H factor; InterPro: IPR014218 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . Members of this entry represent the RNA polymerase sigma-H factor required for sporulation in endospore-forming bacteria. These proteins are also called Sigma-30 and SigH. Related sequences exist in Listeria, but as Listeria does not form spores the role of these related sigma factors in that genus is in doubt.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent. Probab=98.78 E-value=2e-07 Score=77.61 Aligned_cols=182 Identities=26% Similarity=0.365 Sum_probs=150.0 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHH Q ss_conf 99999876533211246899987555789998875223567778875443679999887438545731201028989999 Q gi|254780289|r 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507 (682) Q Consensus 428 K~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~ 507 (682) .+++..++.|.. .|..-+|.-.-.+|-+-|+.|---|-+-.|.+|||.+||.||+.-|...+=..|-.||-..|... T Consensus 7 ~~~~~~~~~G~~---~a~~~~i~~y~~fv~ak~~~yfl~Gad~edi~qeGmiGlyka~rd~~~~~l~sf~afaelC~trq 83 (198) T TIGR02859 7 EEIVELAREGDE---KALEYLIEKYKNFVKAKARSYFLVGADKEDIIQEGMIGLYKAIRDYKEDKLSSFKAFAELCVTRQ 83 (198) T ss_pred HHHHHHHHCCHH---HHHHHHHHHHHHHHHHHHHHHEEEECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 899999970118---89999999999998775311013206456566611689999997531567899999999999999 Q ss_pred HHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCC-CCCC Q ss_conf 999997228704614205889899999999987760889997899987099989999999860898755363588-9986 Q gi|254780289|r 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD-EDTS 586 (682) Q Consensus 508 i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~-~~~~ 586 (682) |..+|..-+|--+||.. .-|||+.||.+ +.|. T Consensus 84 iitaiktatrqkhiPln-----------------------------------------------~y~sl~kPiy~~~sdr 116 (198) T TIGR02859 84 IITAIKTATRQKHIPLN-----------------------------------------------SYVSLNKPIYDEESDR 116 (198) T ss_pred HHHHHHHHHHHCCCCCH-----------------------------------------------HHEECCCCCCCCCCHH T ss_conf 99998876520246520-----------------------------------------------0000256525452014 Q ss_pred EEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHC-CCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH Q ss_conf 047562389889989999999999999999732-9988999999981879867468899989966789999999999999 Q gi|254780289|r 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665 (682) Q Consensus 587 ~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~-l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~ 665 (682) +|.|++......+|.+.+....--..+...+.. |+.=|..||.... +| .++.||+..++- .+.-|.+ ||. T Consensus 117 tl~d~~~~~~~~dP~~l~i~~e~~~~~~~~~~~~ls~le~~vl~~yl---~G--~~yqei~~~l~r---~~ksidn-alq 187 (198) T TIGR02859 117 TLLDVVSEAKVADPEELIISKEEYEKIESKLEELLSDLELKVLVLYL---DG--KSYQEIAEDLNR---HVKSIDN-ALQ 187 (198) T ss_pred HHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---CC--CHHHHHHHHHHH---HHHHHHH-HHH T ss_conf 79998854432252777631688999999999999999999999984---57--407889988645---6678999-999 Q ss_pred HHC Q ss_conf 832 Q gi|254780289|r 666 KLK 668 (682) Q Consensus 666 ~l~ 668 (682) +.+ T Consensus 188 rvk 190 (198) T TIGR02859 188 RVK 190 (198) T ss_pred HHH T ss_conf 999 No 73 >PRK12533 RNA polymerase sigma factor; Provisional Probab=98.76 E-value=1.7e-06 Score=70.16 Aligned_cols=164 Identities=16% Similarity=0.136 Sum_probs=115.8 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEEC Q ss_conf 24689998755578999887522356777887544367999988743854573120102898999999999722870461 Q gi|254780289|r 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521 (682) Q Consensus 442 ~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~ 521 (682) .+|-.+||..+.+.|..+|.++++.--.-.|++||.-+-..+..++|.. -.++ +|-.+=+...++ T Consensus 20 ~eaF~~Lv~rh~~~lyr~a~r~~gn~~dAEDlvQEtFlra~r~l~~frg---~~~~---tWL~rIa~N~~~--------- 84 (217) T PRK12533 20 GERFRALVLPHLDAAYNLARWLCGNASDADDVVQEACMRALRFFDSCRG---DNAR---PWLLAIVRHTWY--------- 84 (217) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCC---CCHH---HHHHHHHHHHHH--------- T ss_conf 9999999999999999999999699999999999999999986776234---4248---999999999999--------- Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHH Q ss_conf 42058898999999999877608899978999870999899999998608987553635889986047562389889989 Q gi|254780289|r 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601 (682) Q Consensus 522 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~ 601 (682) +.+.+..+ .. .+..... .+.+..+.++. ....+|. T Consensus 85 --------~~~Rrr~~--~~-------------------------------~~~~~~~--~~~~~~~~~~~--~~~~~pe 119 (217) T PRK12533 85 --------SEWRRRAN--AH-------------------------------EVAYPDT--LDDADSPDDWQ--PAVEDPL 119 (217) T ss_pred --------HHHHHHHC--CC-------------------------------CCCCCCC--CCCCCCCCCCC--CCCCCHH T ss_conf --------99997411--23-------------------------------3442111--34432343346--7879999 Q ss_pred HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC Q ss_conf 99999999999999973299889999999818798674688999899667899999999999998329 Q gi|254780289|r 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669 (682) Q Consensus 602 ~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~ 669 (682) ..+........|..+|..|||..+.||.||| -..+|++||++.+|++---|+.-=.+|-++||. T Consensus 120 ~~~~~~e~~~~l~~AL~~Lp~~~R~vl~Lr~----~eglS~~EIAeiLgip~gTVKSRL~RAR~~Lr~ 183 (217) T PRK12533 120 ALLLRGEDVRLVNAALAKLPVEYREVLVLRE----LEDMSYREIAAIADVPVGTVMSRLARARRRLAA 183 (217) T ss_pred HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH T ss_conf 9999889999999999809998868999999----809999999999894999999999999999999 No 74 >pfam00140 Sigma70_r1_2 Sigma-70 factor, region 1.2. Probab=98.76 E-value=6.8e-09 Score=89.15 Aligned_cols=35 Identities=51% Similarity=0.935 Sum_probs=33.1 Q ss_pred CCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHH Q ss_conf 72899999985697688978899999999988999 Q gi|254780289|r 118 DDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAM 152 (682) Q Consensus 118 dDPVRMYLREMG~V~LLTREgEIeIAKRIE~G~~~ 152 (682) +|||++||||||++||||+|+||++||+|+.|... T Consensus 1 ~D~v~~YL~eIg~~pLLt~eEEi~LA~~i~~g~~~ 35 (37) T pfam00140 1 SDSVRLYLREIGRVPLLTAEEEVELARRIEAGDEL 35 (37) T ss_pred CCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHCCHH T ss_conf 97099999983776789989999999999816373 No 75 >PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed Probab=98.73 E-value=2.6e-06 Score=68.81 Aligned_cols=84 Identities=17% Similarity=0.088 Sum_probs=54.6 Q ss_pred CCCHHHHHHHHHCCCCCCCHHHHHHHHHHHH-HHHHHHHHHHHHC--CHHHHHH-------HHHHHHHHCCCHHHHHHHH Q ss_conf 7728999999856976889788999999999-8899999998728--2389999-------9999873117103678764 Q gi|254780289|r 117 TDDPVRMYLREMGSIELLSREGEIAIAKRIE-AGRAMMMASLCES--PLTFQAL-------IIWRDELNDGTTLLREIID 186 (682) Q Consensus 117 tdDPVRMYLREMG~V~LLTREgEIeIAKRIE-~G~~~i~~al~~~--P~ti~~i-------l~~~e~i~~ge~~LrdIID 186 (682) -.|.||+|||+++++||||+|+|+++|+|+- .|......-+..+ ++++... +.+-|.|++|.+.|-.-|+ T Consensus 4 ~~~~~~~y~~~~~~~plLt~eeE~~L~~~~~~~gD~~Ar~~LI~~NLRLV~~iA~ry~~~g~~l~DLIQeG~iGLi~Ave 83 (289) T PRK07500 4 DASADRSMIRSAMKAPYLEREEEHALAYRWKDTRDEDALHRIISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAA 83 (289) T ss_pred CCHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHH T ss_conf 53468999999633799999999999999987779999999999858999999987458998978999986999999997 Q ss_pred HHHCCCCCCCCCCC Q ss_conf 21013543333333 Q gi|254780289|r 187 LEACIGPESKGGFF 200 (682) Q Consensus 187 ld~t~~~~~~~~~~ 200 (682) .|..-....+++|. T Consensus 84 kFDp~rG~rFSTYA 97 (289) T PRK07500 84 RFDPDRDVRFSTYA 97 (289) T ss_pred CCCCCCCCCEEEHH T ss_conf 36988899721101 No 76 >PRK12526 RNA polymerase sigma factor; Provisional Probab=98.70 E-value=2e-06 Score=69.77 Aligned_cols=174 Identities=14% Similarity=0.162 Sum_probs=117.7 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHH Q ss_conf 99999876533211246899987555789998875223567778875443679999887438545731201028989999 Q gi|254780289|r 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507 (682) Q Consensus 428 K~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~ 507 (682) ..++++.+.|. ++|-.+|++..=..|..+|.++.+.--.-.|++|+--+-+.+..++|++.+| +|+|| +-.- T Consensus 26 ~~Lv~~A~~GD---~~AF~~Ly~~y~~~l~~~~~r~l~d~~~AEDvvQetFlkvw~~~~~~~~~~~-~f~tW----L~~I 97 (206) T PRK12526 26 QWLILVAISRD---KQAFTHLFQFFAPKIKRFGIKQLGNEAQANELVQETMSNVWRKAHLYNGDKG-AATTW----VYTV 97 (206) T ss_pred HHHHHHHHHCC---HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCC-HHHHH----HHHH T ss_conf 99999999658---9999999999999999999999199999999999999999983876586425-29999----9999 Q ss_pred HHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCE Q ss_conf 99999722870461420588989999999998776088999789998709998999999986089875536358899860 Q gi|254780289|r 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587 (682) Q Consensus 508 i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~ 587 (682) ......|. +.+.... ...++ ++ +... T Consensus 98 arN~~~d~----------------lRk~~~~---------------------------------~~~~~----~~-d~~~ 123 (206) T PRK12526 98 MRNAAFDM----------------LRKIKAK---------------------------------KEQNL----GD-DIWP 123 (206) T ss_pred HHHHHHHH----------------HHHHHCC---------------------------------CCCCC----CC-HHCH T ss_conf 99999999----------------9865312---------------------------------22232----10-0000 Q ss_pred EEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH Q ss_conf 47562389889989999999999999999732998899999998187986746889998996678999999999999983 Q gi|254780289|r 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667 (682) Q Consensus 588 ~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l 667 (682) +.+...+ .. .+.+......+...|..+|..||++.+.|+.|+| -..+|.+||+..+|+|---|+.-=.+|+.+| T Consensus 124 ~~~~~~~-~~-~~~~~~~~~~~~~~l~~~l~~LP~~~R~vi~L~~----~egls~~EIA~~l~is~~TVksrl~rAlk~L 197 (206) T PRK12526 124 IEQALAE-SQ-SESEEFSDHLMDKQILSYIEKLPEAQQTVVKGVY----FQELSQEQLAQQLNVPLGTVKSRLRLALAKL 197 (206) T ss_pred HHHCCCC-CC-CCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH T ss_conf 4430145-78-8357899899999999999868999888989999----8599999999998939999999999999999 Q ss_pred CC Q ss_conf 29 Q gi|254780289|r 668 KH 669 (682) Q Consensus 668 ~~ 669 (682) |- T Consensus 198 R~ 199 (206) T PRK12526 198 KV 199 (206) T ss_pred HH T ss_conf 99 No 77 >PRK12536 RNA polymerase sigma factor; Provisional Probab=98.69 E-value=2.7e-06 Score=68.71 Aligned_cols=170 Identities=16% Similarity=0.209 Sum_probs=114.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC-CCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHH Q ss_conf 68899999987653321124689998755578999887522356-77788754436799998874385457312010289 Q gi|254780289|r 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG-LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502 (682) Q Consensus 424 i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~-~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~ 502 (682) ..+++.++.++..|... |=.+++...-+.|...+.++.+.. -.-.|++||.-+-+.+...+|++.. .|+| T Consensus 2 ~~~l~~Ll~~~~~GD~~---Af~~l~~~y~~~l~~~~~~~l~~~~~~AEDl~Qe~fl~~~~~~~~~~~~~--~~~~---- 72 (178) T PRK12536 2 ESRLKALLLRGLAGDAA---AYRQFLTELARHLRAFLRRRLPQLPDEVEDLVQEILLAVHNARHTYRPDQ--PLTA---- 72 (178) T ss_pred HHHHHHHHHHHHHCCHH---HHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCCCC--CHHH---- T ss_conf 48899999999815699---99999999999999999999099876899999999999999787669999--6899---- Q ss_pred HHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCC Q ss_conf 89999999997228704614205889899999999987760889997899987099989999999860898755363588 Q gi|254780289|r 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582 (682) Q Consensus 503 ~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~ 582 (682) |+. .|.+.. .++.+.+.. |.+... .++.+ T Consensus 73 WL~-~Ia~n~---------------~~d~~R~~~--------r~~~~~---------------------------~~~~~ 101 (178) T PRK12536 73 WVQ-AIARYK---------------LADFLRRRA--------RREALH---------------------------DPLDD 101 (178) T ss_pred HHH-HHHHHH---------------HHHHHHHHH--------CCCCCC---------------------------CCCHH T ss_conf 999-999999---------------999999874--------645445---------------------------75112 Q ss_pred CCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHH Q ss_conf 99860475623898899899999999999999997329988999999981879867468899989966789999999999 Q gi|254780289|r 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662 (682) Q Consensus 583 ~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~ 662 (682) .. +....+. ..| ...+..+..+|..|||+.+.||.|+| -..+|..||++.+|+|..-|+.-=.+ T Consensus 102 ~~-----~~~~~~~-~~~------~~~~~~l~~~l~~Lp~~~R~~~~l~~----~eg~s~~EIA~~lgis~~tVk~rl~R 165 (178) T PRK12536 102 EA-----ELFATSD-DEA------AEARRDLGKLLEQLPDRQRLPIVHVK----LEGLSVEETAQLTGLSESAVKVGIHR 165 (178) T ss_pred HH-----HCCCCCC-CCH------HHHHHHHHHHHHHCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHH T ss_conf 32-----0247886-358------99999999999869998999999998----85999999999989299999999999 Q ss_pred HHHHHCC Q ss_conf 9998329 Q gi|254780289|r 663 AIRKLKH 669 (682) Q Consensus 663 a~~~l~~ 669 (682) |+++||. T Consensus 166 a~k~Lr~ 172 (178) T PRK12536 166 GLKALAA 172 (178) T ss_pred HHHHHHH T ss_conf 9999999 No 78 >TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1; InterPro: IPR014326 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This group of sigma factors are members of the sigma-70 family (IPR014284 from INTERPRO) and are apparently found only in the Planctomycetaceae family including the genus s Gemmata and Pirellula, in which seven sequences are found.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent. Probab=98.69 E-value=4.6e-07 Score=74.73 Aligned_cols=167 Identities=23% Similarity=0.355 Sum_probs=120.5 Q ss_pred HHHHHHH--HHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCCHHHH Q ss_conf 7555789--99887522356777887544367999988743854573120102898999999999722870461420588 Q gi|254780289|r 450 EANLRLV--ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527 (682) Q Consensus 450 ~anlr~v--~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~~~ 527 (682) ..-||++ +-|..++.+| ++-.|++||. +|.|...|+-=||--=.-++. |-|+=..+.|++. T Consensus 17 ~~yLr~La~~~L~~~L~~r-~dpSD~VQe~---~l~A~~~~~~fRG~t~~Ef~~-WLR~IL~~~l~~~------------ 79 (190) T TIGR02984 17 RNYLRLLARVQLDRRLRRR-VDPSDVVQET---LLEAHRDFDQFRGKTEGEFAG-WLRQILANVLADA------------ 79 (190) T ss_pred HHHHHHHHHHHHHHHHHCC-CCHHHHHHHH---HHHHHHHHHHHCCCCHHHHHH-HHHHHHHHHHHHH------------ T ss_conf 2499999999760884001-5754589999---999998887532898578999-9999999999999------------ Q ss_pred HHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCC--EEEEEECCCCCCCHHHHHH Q ss_conf 98999999999877608899978999870999899999998608987553635889986--0475623898899899999 Q gi|254780289|r 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS--HLGDFIEDKNAVSPLDSAI 605 (682) Q Consensus 528 ~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~--~~~~~~~d~~~~~~~~~~~ 605 (682) .+.+.+.--|. .+.=+||+++-+-.++| .|.-++.+ +..+|...+. T Consensus 80 --------~~~h~~~qkRD-----------------------~rrE~~l~~~~~~~~~Ss~~L~~~Laa-~~~sPS~~a~ 127 (190) T TIGR02984 80 --------LRRHLGAQKRD-----------------------IRREQSLDAGAARVDESSVRLEAQLAA-DGPSPSQAAA 127 (190) T ss_pred --------HHHHHHHHCCC-----------------------CHHCCCCCCCCCCHHHHHHHHHHHHCC-CCCCCHHHHH T ss_conf --------99886642026-----------------------201012012457658879999997518-9998558999 Q ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC Q ss_conf 9999999999973299889999999818798674688999899667899999999999998329 Q gi|254780289|r 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669 (682) Q Consensus 606 ~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~ 669 (682) +...-..+..+|+.|||..++||.||| -+.+++.|||..||.|.-=|+-.-.+||+|||. T Consensus 128 r~E~~~~L~~AL~~L~e~~REvi~LR~----~EGLS~~EvA~~Md~~~~av~~l~~Ral~~Lr~ 187 (190) T TIGR02984 128 RRESAVRLAQALAKLPEDYREVILLRH----LEGLSFAEVAERMDRSEGAVSMLWVRALARLRQ 187 (190) T ss_pred HHHHHHHHHHHHHHCCHHHHHHHHHHH----HHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH T ss_conf 977999999999647922589999987----603555899987079758987589999999987 No 79 >PRK09415 RNA polymerase factor sigma C; Reviewed Probab=98.68 E-value=4.7e-06 Score=66.73 Aligned_cols=159 Identities=17% Similarity=0.155 Sum_probs=114.8 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEEC Q ss_conf 24689998755578999887522356777887544367999988743854573120102898999999999722870461 Q gi|254780289|r 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521 (682) Q Consensus 442 ~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~ 521 (682) .+|=.+++..+-..|..+|.++++.--.-.|++|+.-+-+++...+|.... .|. +|-.+-+...++ T Consensus 15 e~Af~~L~~~y~~~v~~~~~~~~~d~~~AeD~~Qe~fl~~~~~~~~~~~~~--~~~---~Wl~~ia~N~~~--------- 80 (177) T PRK09415 15 EDLIDEIMNKYGQEVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYKGKS--NLK---TWLYRIAINHCK--------- 80 (177) T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCC--CHH---HHHHHHHHHHHH--------- T ss_conf 999999999999999999999909999999999999999999874558855--499---999999999999--------- Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHH Q ss_conf 42058898999999999877608899978999870999899999998608987553635889986047562389889989 Q gi|254780289|r 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601 (682) Q Consensus 522 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~ 601 (682) +.+.+..+ +...+.+ .+ . +.+. ....+|. T Consensus 81 --------d~~R~~~~-------~~~~~~~--------------------------~~-----~----~~~~-~~~~~~~ 109 (177) T PRK09415 81 --------DYLKSWHN-------KKVIVTE--------------------------DI-----F----TYME-SQKESVE 109 (177) T ss_pred --------HHHHHHHC-------CCCCCCH--------------------------HH-----H----HHCC-CCCCCHH T ss_conf --------99999871-------3556303--------------------------56-----6----4025-5579989 Q ss_pred HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC Q ss_conf 99999999999999973299889999999818798674688999899667899999999999998329 Q gi|254780289|r 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669 (682) Q Consensus 602 ~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~ 669 (682) +..........+..+|..|||+.+.|+.+|| -...|..|||..+|+|-.-|+..=.+|.++||. T Consensus 110 ~~~~~~~~~~~l~~~l~~L~~~~r~ii~l~~----~~~~s~~EIA~~l~is~~tV~~rl~Rark~Lr~ 173 (177) T PRK09415 110 EEVIQNAEDERLASAVMSLPIKYREVIYLFY----YEELSIKEIATVTGVNENTIKTRLKKAKELLKK 173 (177) T ss_pred HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH T ss_conf 9999999999999999769999999999999----809989999998892999999999999999998 No 80 >PRK12542 RNA polymerase sigma factor; Provisional Probab=98.67 E-value=3.4e-06 Score=67.90 Aligned_cols=162 Identities=19% Similarity=0.155 Sum_probs=113.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEEC Q ss_conf 24689998755578999887522356777887544367999988743854573120102898999999999722870461 Q gi|254780289|r 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521 (682) Q Consensus 442 ~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~ 521 (682) ..|=.+|++..-..|.++|.++++.--.-.|++|+.=+-+.+..++|+...+-+|+| |..|=+..++|. T Consensus 8 ~~afe~Ly~~y~~~ly~~a~~~~~d~~~AEDivQe~Flk~~~~~~~~~~~~~~~~~~---wL~rIa~N~~id-------- 76 (185) T PRK12542 8 YEKMEELYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKNLEKLHSLNTQELKR---YILRVAKNKAID-------- 76 (185) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHH---HHHHHHHHHHHH-------- T ss_conf 999999999999999999999949999999999999999999888716655267999---999999999999-------- Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHH Q ss_conf 42058898999999999877608899978999870999899999998608987553635889986047562389889989 Q gi|254780289|r 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601 (682) Q Consensus 522 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~ 601 (682) .+.+.. +.++. ++... .+. + +....++. T Consensus 77 ---------~~Rk~k--------~~~~~--------------------------~~~~~--~~~------~-~~~~~~~e 104 (185) T PRK12542 77 ---------SYRKNK--------RHETF--------------------------LEEYE--RES------I-EAVDENIE 104 (185) T ss_pred ---------HHHHHC--------CCCCC--------------------------HHHHH--CCC------C-CCCCCCHH T ss_conf ---------999732--------43442--------------------------01321--023------3-56787743 Q ss_pred HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCH Q ss_conf 999999999999999732998899999998187986746889998996678999999999999983296 Q gi|254780289|r 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670 (682) Q Consensus 602 ~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~ 670 (682) +..........|..+|..|||+.+.|+.||| -..+|..||+..+|+|---|+..=.+|+++||.- T Consensus 105 ~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~----~~gls~~EIA~~L~is~~tVk~rl~RArk~Lr~~ 169 (185) T PRK12542 105 EWEKRKMSEVQIDTLLKELNESNRQVFKYKV----FYNLTYQEISSVMGITEANVRKQFERARKRVQNM 169 (185) T ss_pred HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH T ss_conf 7999998999999999829998889976799----8399999999998929999999999999999998 No 81 >PRK09644 RNA polymerase sigma factor SigM; Provisional Probab=98.66 E-value=2.7e-06 Score=68.70 Aligned_cols=152 Identities=20% Similarity=0.183 Sum_probs=107.6 Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCCHH Q ss_conf 99987555789998875223567778875443679999887438545731201028989999999997228704614205 Q gi|254780289|r 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525 (682) Q Consensus 446 ~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~ 525 (682) .++....-..|...|.++++.--.-.|++|+.-+-+.+..+.|+.+ +|.| |-.+=+...++ T Consensus 4 E~ly~~y~~~l~~~~~~~~~d~~~AeDl~Qe~flk~~~~~~~~~~~---~~~~---WL~~Ia~n~~~------------- 64 (165) T PRK09644 4 EEIYKMYINDVYRYLFSLTKSHHLAEDLLQETFYRAYIYLEDYDNQ---KVKP---WLFKVAYHTFI------------- 64 (165) T ss_pred HHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCC---CHHH---HHHHHHHHHHH------------- T ss_conf 9999999999999999990999999999999999999988766813---1899---99999999999------------- Q ss_pred HHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHH Q ss_conf 88989999999998776088999789998709998999999986089875536358899860475623898899899999 Q gi|254780289|r 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605 (682) Q Consensus 526 ~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~~~ 605 (682) +.+.+. .|.+. + +++. +++....+|.+.+. T Consensus 65 ----d~~Rk~--------~r~~~-------------------------~------~~~~-------~~~~~~~~~~~~~~ 94 (165) T PRK09644 65 ----DFVRKE--------KKVVF-------------------------V------GTDE-------IETIQAESTEEYAV 94 (165) T ss_pred ----HHHHHH--------CCCCC-------------------------C------CHHH-------HCCCCCCCHHHHHH T ss_conf ----999974--------47577-------------------------6------5211-------00113588014999 Q ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCH Q ss_conf 99999999999732998899999998187986746889998996678999999999999983296 Q gi|254780289|r 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670 (682) Q Consensus 606 ~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~ 670 (682) .......+..+|..|||+.+.|+.||| -...|..|||..+|+|-.-|+..=.+|..+||.- T Consensus 95 ~~e~~~~l~~~l~~Lp~~~r~v~~L~~----~~~~s~~EIA~~l~is~~tVk~rl~RAr~~Lr~~ 155 (165) T PRK09644 95 AKNSYEKLIQIIHTLPVIEAQAILLCD----VHELTYEEAASVLDLKENTYKSHLFRGRKRLKAL 155 (165) T ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHH----HHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH T ss_conf 899999999998729999999999999----9888999999998939999999999999999999 No 82 >COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription] Probab=98.66 E-value=5.3e-06 Score=66.36 Aligned_cols=164 Identities=18% Similarity=0.201 Sum_probs=111.9 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCE Q ss_conf 21124689998755578999887522356777887544367999988743854573120102898999999999722870 Q gi|254780289|r 439 CEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518 (682) Q Consensus 439 ~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~ 518 (682) ...+.+-.+++..+.+.+...+.++++..-.-.||+||..+.++++...| .-+..|.||. .+=+...+| T Consensus 11 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~dAeDlvQE~~lr~~~~~~~~--~~~~~~~~wl---~~Ia~n~~i------ 79 (182) T COG1595 11 RGDRAAFEELLERLRPRLRRLARRLLGDRADAEDLVQETFLRAWRAIDSF--RGRSSFKAWL---YRIARNLAI------ 79 (182) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCHHC--CCCCCHHHHH---HHHHHHHHH------ T ss_conf 75178899999999999999999996884309999999999999733311--6788789999---999999999------ Q ss_pred EECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCC Q ss_conf 46142058898999999999877608899978999870999899999998608987553635889986047562389889 Q gi|254780289|r 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598 (682) Q Consensus 519 ~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~ 598 (682) +.+.+..+.... ..+.. . . +...+.... T Consensus 80 -----------D~~R~~~r~~~~---------------------------------~~~~~----~-~---~~~~~~~~~ 107 (182) T COG1595 80 -----------DRLRKRKRRRAR---------------------------------VEEAD----L-L---PEEADPAPD 107 (182) T ss_pred -----------HHHHHHHHHCCH---------------------------------HHHCC----C-C---CCCCCCCCH T ss_conf -----------999976101320---------------------------------01000----2-4---543456702 Q ss_pred CHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCH Q ss_conf 989999999999999999732998899999998187986746889998996678999999999999983296 Q gi|254780289|r 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670 (682) Q Consensus 599 ~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~ 670 (682) .+ +.+........+.++|..|||+++.|+.|+| -..+|..||++.+|||---|+..-.+|+.+|+.. T Consensus 108 ~~-~~~~~~~~~~~l~~al~~Lp~~~R~~~~l~~----~~gls~~EIA~~l~i~~~tVks~l~ra~~~l~~~ 174 (182) T COG1595 108 LA-ELLLAEEELERLRRALARLPPRQREAFLLRY----LEGLSYEEIAEILGISVGTVKSRLHRARKKLREQ 174 (182) T ss_pred HH-HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH T ss_conf 67-8887678999999999839999999999999----8599999999895999999999999999999998 No 83 >PRK12532 RNA polymerase sigma factor; Provisional Probab=98.66 E-value=4.5e-06 Score=66.92 Aligned_cols=172 Identities=14% Similarity=0.177 Sum_probs=106.9 Q ss_pred HHHHHHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCCHH Q ss_conf 9987555789998875223567-778875443679999887438545731201028989999999997228704614205 Q gi|254780289|r 447 EMVEANLRLVISVAKKYTNRGL-QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525 (682) Q Consensus 447 ~l~~anlr~v~~~~~~~~~~~~-~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~ 525 (682) +|+ .+.+-.+..|.......- .-.|++||.-+-..++.+.|+. +.+|+||..==.|..+..++...+|..++.... T Consensus 10 ~l~-~~r~~L~~fa~~~L~~~~d~AEDlvQEtflka~~~~~~f~~--~s~f~tWL~~IarN~~id~lR~~~r~~~~~~~~ 86 (195) T PRK12532 10 ELI-ESRKLLLHFARLQLPDHPDLAEDLVQETLLSAYSAGDSFQG--RALVNSWLFAILKNKIIDALRQIGRQRKVFTAL 86 (195) T ss_pred HHH-HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCC--CCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC T ss_conf 999-98999999999980898757999999999999986874589--887888999999999999999862766767532 Q ss_pred HHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHH Q ss_conf 88989999999998776088999789998709998999999986089875536358899860475623898899899999 Q gi|254780289|r 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605 (682) Q Consensus 526 ~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~~~ 605 (682) .++. ++ -+.+..+..++..+ .--...+..+|++.+. T Consensus 87 -----------------------~~e~---~d----------------~~~~~~~~~~~~~~--~~~~p~~~~~pe~~~~ 122 (195) T PRK12532 87 -----------------------DDEL---LD----------------EAFESHFSQNGHWT--PEGQPQHWNTPEKSLN 122 (195) T ss_pred -----------------------CHHH---HH----------------HHHHHHHCCCCCCC--CCCCCCCCCCHHHHHH T ss_conf -----------------------0233---32----------------56665420134457--5446555499999999 Q ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC Q ss_conf 9999999999973299889999999818798674688999899667899999999999998329 Q gi|254780289|r 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669 (682) Q Consensus 606 ~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~ 669 (682) ...+...+..+|..||++.+.|+.||| -..++++|||+.+|+|-.-|+..=.+|-.+||. T Consensus 123 ~~e~~~~l~~~l~~Lp~~~R~vl~L~~----~egls~~EIA~~lgis~~tVks~l~RAR~~Lr~ 182 (195) T PRK12532 123 NNEFQKILQSCLYNLPENTARVFTLKE----ILGFSSDEIQQMCGISTSNYHTIMHRARESLRQ 182 (195) T ss_pred HHHHHHHHHHHHHHCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH T ss_conf 899999999999859999989999999----819999999999895999999999999999999 No 84 >PRK12518 RNA polymerase sigma factor; Provisional Probab=98.62 E-value=3.8e-06 Score=67.52 Aligned_cols=165 Identities=18% Similarity=0.200 Sum_probs=109.5 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHH Q ss_conf 99876533211246899987555789998875223567778875443679999887438545731201028989999999 Q gi|254780289|r 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510 (682) Q Consensus 431 ~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~ 510 (682) +++++.|.. .|=.++++..-+.|..++.++++.. .-.|++|+.-+.+.+..++|+.. ..|+| |+-.-... T Consensus 2 i~~~~~Gd~---~Af~~ly~~y~~~l~~~~~~~~~~~-~AEDi~Qd~fik~~~~~~~~~~~--~~~~~----wl~~ia~N 71 (175) T PRK12518 2 IQRCQRGDR---QAFRQLYRRYQQKVRSTLYQLCGRE-LLDDLVQEVFLRVWKGLPKLRNP--AYFST----WLYRITWN 71 (175) T ss_pred HHHHHHCCH---HHHHHHHHHHHHHHHHHHHHHCCHH-HHHHHHHHHHHHHHHCCCCCCCC--CHHHH----HHHHHHHH T ss_conf 898986589---9999999999999999999977998-89999999999998711127982--35999----99999999 Q ss_pred HHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEE Q ss_conf 99722870461420588989999999998776088999789998709998999999986089875536358899860475 Q gi|254780289|r 511 SIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590 (682) Q Consensus 511 ~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~ 590 (682) .. ++.+.+..+ .+...+.+...+. T Consensus 72 ~~----------------~d~~Rk~~r----------------------------------~~~~~~~~~~~~~------ 95 (175) T PRK12518 72 VA----------------TDARRQFAK----------------------------------RPSRIQQDSSLDQ------ 95 (175) T ss_pred HH----------------HHHHHHHHC----------------------------------CCCCCCCCCCCCC------ T ss_conf 99----------------999999870----------------------------------2432332100024------ Q ss_pred EECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC Q ss_conf 6238988998999999999999999973299889999999818798674688999899667899999999999998329 Q gi|254780289|r 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669 (682) Q Consensus 591 ~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~ 669 (682) .......| ..........+..+|..|||+.+.|+.|+| -...|+.|||+.+|+|-.-|+..=.+|+++||. T Consensus 96 --~~~~~~~~--~~~~~~~~~~l~~~l~~Lp~~~r~vi~l~~----~~~~s~~EIA~~l~is~~tVk~~l~Ra~k~Lr~ 166 (175) T PRK12518 96 --PSRPSDEP--DLMQLHYQDLVQQGLATLSLEHRAVLVLHD----LEDLPQKEIAEILNIPVGTVKSRLFYARRQLRK 166 (175) T ss_pred --CCCCCCCH--HHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----HHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH T ss_conf --56788976--999999999999999769999999999999----929999999999895999999999999999999 No 85 >PRK12545 RNA polymerase sigma factor; Provisional Probab=98.61 E-value=7.7e-06 Score=65.08 Aligned_cols=176 Identities=14% Similarity=0.114 Sum_probs=115.1 Q ss_pred HHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCCHHH Q ss_conf 99875557899988752235677788754436799998874385457312010289899999999972287046142058 Q gi|254780289|r 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526 (682) Q Consensus 447 ~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~~ 526 (682) .+|+-.=+-++..|..+.+.--.-.|++||.-+...++.++|+.+..| -||-.+=+...|+. T Consensus 12 ~~~~~~r~~L~r~A~~~l~d~~~AEDlvQEtflka~~~~~~F~g~ss~-----~TWL~~Ia~N~~id------------- 73 (201) T PRK12545 12 AYLAQLRHDLLRFARLQLRDADAAEDAVQEALAAAWSQAGRFAGQSAH-----KTWVFGILRNKLID------------- 73 (201) T ss_pred HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHH-----HHHHHHHHHHHHHH------------- T ss_conf 999999999999999990999899999999999999854045875238-----99999999999999------------- Q ss_pred HHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHHH Q ss_conf 89899999999987760889997899987099989999999860898755363588998604756238988998999999 Q gi|254780289|r 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606 (682) Q Consensus 527 ~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~ 606 (682) .+.+. .|......+...+ ...-.+|..+..+. +.+.........+.|+..+.. T Consensus 74 ----~lRkr--------~r~~~~~~~d~~~--------------d~e~~~d~~~~~d~-g~w~~~~~p~~~~~Pe~~l~~ 126 (201) T PRK12545 74 ----TLRAR--------RRTINLSALDAEL--------------DGESLLDRELFKDN-GHWAAHAKPRPWPKPETILQQ 126 (201) T ss_pred ----HHHHH--------CCCCCCCCCCCCC--------------CCCCCCHHHHHCCC-CCCCCCCCCCCCCCHHHHHHH T ss_conf ----99961--------5778855344454--------------63211105540344-543233578889998999999 Q ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHH Q ss_conf 99999999997329988999999981879867468899989966789999999999999832967 Q gi|254780289|r 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671 (682) Q Consensus 607 ~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~ 671 (682) ..+...+..+|..|||+.+.|+.||+ -...+.+||+..+|+|-.-|+..=.+|-.+||.-- T Consensus 127 ~e~~~~l~~aL~~LP~~~R~v~~Lr~----~egls~~EIA~~L~is~~tVksrL~RAR~~LR~~L 187 (201) T PRK12545 127 QQFWTLFETCLDHLPEQIGRVFMMRE----FLDFEIDDICTELTLTANHCSVLLYRARTRLRTCL 187 (201) T ss_pred HHHHHHHHHHHHHCCHHHHHHHHHHH----HHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH T ss_conf 99999999999959999988989999----92898999999989699999999999999999999 No 86 >pfam07638 Sigma70_ECF ECF sigma factor. These proteins are probably RNA polymerase sigma factors belonging to the extra-cytoplasmic function (ECF) subfamily and show sequence similarity to pfam04542 and pfam04545. Probab=98.61 E-value=3.8e-06 Score=67.48 Aligned_cols=175 Identities=17% Similarity=0.212 Sum_probs=113.3 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHH-----HHHHHHHHHHHHHHHCCCCCCCEEEHH Q ss_conf 889999998765332112468999875557899988752235677788-----754436799998874385457312010 Q gi|254780289|r 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD-----LIQEGNIGLMKAAEKFDWCLGYKFSTY 499 (682) Q Consensus 425 ~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~-----~~~~~~~~l~~a~~~~~~~~g~~f~ty 499 (682) .++-+++++++.|.. .|-.+|++..-.-+..+|.+|.+.-..-.| ++|+.-+-|.+.-+.+++.....|.|| T Consensus 2 ~~~teLi~~~k~GD~---~Af~~L~~~y~~~l~r~a~~~l~~~~~~ed~~~~~lvqe~Flrl~~~~~~~~~~~~~~f~~~ 78 (185) T pfam07638 2 QEVTQLLQQVKDGDA---AATEQLLPLVYDELRRLAGSKLQNERRGHTLQPTALVHEAFVRLVDTEDFPDWSGRGHFFAA 78 (185) T ss_pred CHHHHHHHHHHCCCH---HHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHH T ss_conf 479999999986779---99999999999999999999963532101677899999999999840202367756899999 Q ss_pred HHHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCC Q ss_conf 28989999999997228704614205889899999999987760889997899987099989999999860898755363 Q gi|254780289|r 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579 (682) Q Consensus 500 a~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~ 579 (682) +.-|+|.-+..+...+.+.-|. + ... ..+++ T Consensus 79 l~~i~~~~~id~~R~~~~~~~~----------------------~---~~~----------------------~~~~~-- 109 (185) T pfam07638 79 AAEAMRRILIDHARRRQRQKRG----------------------G---DVQ----------------------RRELD-- 109 (185) T ss_pred HHHHHHHHHHHHHHHHHHHHCC----------------------C---CCH----------------------HCCHH-- T ss_conf 9999999999999988866126----------------------6---410----------------------10101-- Q ss_pred CCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHH Q ss_conf 58899860475623898899899999999999999997329988999999981879867468899989966789999999 Q gi|254780289|r 580 IGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659 (682) Q Consensus 580 ~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi 659 (682) ++ ......++|+.... +.+.+ +.|.+|||+.+.|+.||| ....|..|||+.+|+|---|+-= T Consensus 110 --~~--------~~~~~~~~~~~~~~---l~~~~-~~l~~Lpp~~r~v~~L~~----~eglS~~EIAe~Lgis~~TVk~r 171 (185) T pfam07638 110 --EV--------VDNGDSPNPDLLLD---LDEAL-EQLFSLSPRQARLVELRF----FAGLSNDEIAERLGVSERTVERN 171 (185) T ss_pred --HH--------CCCCCCCCHHHHHH---HHHHH-HHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHH T ss_conf --10--------01456898788999---99999-998648998888988899----75999999999979699899999 Q ss_pred HHHHHHHHCC Q ss_conf 9999998329 Q gi|254780289|r 660 EAKAIRKLKH 669 (682) Q Consensus 660 ~~~a~~~l~~ 669 (682) =.+|..+||. T Consensus 172 l~~Ar~~Lr~ 181 (185) T pfam07638 172 WALARAWLHR 181 (185) T ss_pred HHHHHHHHHH T ss_conf 9999999998 No 87 >PRK12539 RNA polymerase sigma factor; Provisional Probab=98.57 E-value=1.3e-05 Score=63.27 Aligned_cols=171 Identities=15% Similarity=0.187 Sum_probs=112.0 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC----CCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEE Q ss_conf 12688999999876533211246899987555789998875223----56777887544367999988743854573120 Q gi|254780289|r 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTN----RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS 497 (682) Q Consensus 422 l~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~----~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~ 497 (682) .+..+++.++.....|...+- ..++...-+.+.+++..+.. ..-.-.|++|+.-+-+.+...+|++.. .|+ T Consensus 3 ~~~~~~~~Lv~~~~~GD~~Af---~~L~~r~~~~l~~~~~~~l~r~~~~~~dAeDlvQe~fl~~~~~~~~~~~~~--~~~ 77 (184) T PRK12539 3 SKENELKALMLASLDGDAAAH---RALLERLSGHLRAYYKGKLARIGRGAEEAEDLVQEALMAIHTRRHTYDPEQ--PLT 77 (184) T ss_pred CCHHHHHHHHHHHHCCCHHHH---HHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCC--CHH T ss_conf 977999999999980889999---999999899999999999998439998999999999999998377559998--579 Q ss_pred HHHHHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCC Q ss_conf 10289899999999972287046142058898999999999877608899978999870999899999998608987553 Q gi|254780289|r 498 TYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLE 577 (682) Q Consensus 498 tya~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~ 577 (682) +|-.+=+...++ +.+.+.. +. ...+ T Consensus 78 ---~WL~~Ia~n~~~-----------------d~~R~~~--------~~------------------------~~~~--- 102 (184) T PRK12539 78 ---PWVYAIARYKLI-----------------DHLRRTR--------AS------------------------LADV--- 102 (184) T ss_pred ---HHHHHHHHHHHH-----------------HHHHHCC--------CC------------------------CCCC--- T ss_conf ---999999999999-----------------9998514--------55------------------------3448--- Q ss_pred CCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHH Q ss_conf 63588998604756238988998999999999999999973299889999999818798674688999899667899999 Q gi|254780289|r 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657 (682) Q Consensus 578 ~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~r 657 (682) |+.+.+ +.........++ ....+..+|+.|||+.+.|+.|+| -...|..||+..+|+|-.-|+ T Consensus 103 -~~~~~~-----~~~~~~~~~~~e-------~~~~l~~~l~~Lp~~~r~v~~L~~----~eg~s~~EIA~~lgis~~tVk 165 (184) T PRK12539 103 -PIDDAD-----ELVAHDDAAAVE-------STLDLGRLLARLPEKMRLAIQAVK----LDGLSVAEAATRSGMSESAVK 165 (184) T ss_pred -CCCCCC-----CCCCCCCHHHHH-------HHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHH T ss_conf -844344-----456785133188-------999999999849999999999999----949999999999891999999 Q ss_pred HHHHHHHHHHCC Q ss_conf 999999998329 Q gi|254780289|r 658 QIEAKAIRKLKH 669 (682) Q Consensus 658 qi~~~a~~~l~~ 669 (682) --=.+|+++||. T Consensus 166 s~l~Rark~Lr~ 177 (184) T PRK12539 166 VSVHRGLKALAA 177 (184) T ss_pred HHHHHHHHHHHH T ss_conf 999999999999 No 88 >PRK08311 putative RNA polymerase sigma factor SigI; Reviewed Probab=98.56 E-value=3.9e-07 Score=75.33 Aligned_cols=93 Identities=17% Similarity=0.285 Sum_probs=80.3 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC--HHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHH Q ss_conf 9999998765332112468999875557899988752235677--78875443679999887438545731201028989 Q gi|254780289|r 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQ--FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504 (682) Q Consensus 427 lK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~--~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i 504 (682) +..++..++.|. ..|+.++|+.+.+||..++.+++++-+. -.|+++.|-+|+..|+++||+.+|..|.+||.+-| T Consensus 5 le~~l~~i~~Gd---~~~re~lI~~y~pfI~k~~s~~~~r~~~~e~DDe~SIgliAfneAI~~y~~~kg~~F~~fA~~vI 81 (237) T PRK08311 5 IEDILEKIQNGD---EELREELIEEYKPFILKVVSSVCGRYIDWENDDELSIGLIAFNEAIDSYDEEKGKSFLSFAELVI 81 (237) T ss_pred HHHHHHHHHCCC---HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHH T ss_conf 999999988678---99999999992789999999996777898878299899999999998628335986599999999 Q ss_pred HHHHHHHHHHCCCEEECC Q ss_conf 999999997228704614 Q gi|254780289|r 505 KQAITRSIADQSCTIRIP 522 (682) Q Consensus 505 ~~~i~~~~~~~~~~~r~~ 522 (682) +..+.-++..+.+.-..+ T Consensus 82 k~rliDy~Rke~k~~~~~ 99 (237) T PRK08311 82 KRRLIDYIRKEKKHSKVV 99 (237) T ss_pred HHHHHHHHHHHCCCCCCC T ss_conf 999999999740444568 No 89 >pfam04542 Sigma70_r2 Sigma-70 region 2. Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime. The aromatic residues of the recognition helix, found at the C-terminus of this domain are though to mediate strand separation, thereby allowing transcription initiation. Probab=98.54 E-value=2.1e-07 Score=77.40 Aligned_cols=71 Identities=39% Similarity=0.570 Sum_probs=67.3 Q ss_pred HHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCE Q ss_conf 98755578999887522356777887544367999988743854573120102898999999999722870 Q gi|254780289|r 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518 (682) Q Consensus 448 l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~ 518 (682) |++.+.++|.++|++|.+.+....|++||+.+++++++++|++.+|.+|+||+.++++..+..++..+.|+ T Consensus 1 L~~~y~~~l~~~~~~~~~~~~~aeDl~Qe~f~~~~~~~~~~~~~~~~~f~~wl~~i~~n~~~d~~Rk~~r~ 71 (71) T pfam04542 1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLLRAVERFDPERGVSFSTWLYTIIRNAIIDALRKQRRT 71 (71) T ss_pred CHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCC T ss_conf 99989999999999883986029999999999999998757961366099899999999999999973999 No 90 >PRK09639 RNA polymerase sigma factor SigX; Provisional Probab=98.52 E-value=1.4e-05 Score=62.93 Aligned_cols=157 Identities=18% Similarity=0.218 Sum_probs=108.6 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEE Q ss_conf 12468999875557899988752235677788754436799998874385457312010289899999999972287046 Q gi|254780289|r 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520 (682) Q Consensus 441 ~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r 520 (682) +.+|=.++...+-+.|...+.++++.--.-.|++|+.-+-+.+. .|.... .|. +|-.+-+...++ |. T Consensus 1 meeAF~~ly~~y~~~l~~~~~~~~~d~~~AeDl~Qe~flk~~~~--~~~~~~--~~~---~wL~~ia~n~~~-d~----- 67 (166) T PRK09639 1 MEETFEDLFKQYYQDVVQQIIYIVKDRTQAEDLAQEVFLRLLRS--DWKGIE--NEK---GWLIKSARNVAY-NY----- 67 (166) T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHC--CCCCCC--CHH---HHHHHHHHHHHH-HH----- T ss_conf 98999999999999999999999299999999999999999872--635446--789---999999999999-99----- Q ss_pred CCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCH Q ss_conf 14205889899999999987760889997899987099989999999860898755363588998604756238988998 Q gi|254780289|r 521 IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600 (682) Q Consensus 521 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~ 600 (682) +.+..+... ...+ ... ........+| T Consensus 68 -----------~R~~~~~~~---------------------------------~~~~-~~~---------~~~~~~~~~~ 93 (166) T PRK09639 68 -----------FRSEKRHRA---------------------------------RILG-EFQ---------WQEEQIDSSP 93 (166) T ss_pred -----------HHHHHHHHH---------------------------------HHCC-CHH---------CCCCCCCCCH T ss_conf -----------998840201---------------------------------0000-100---------0134557997 Q ss_pred HHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC Q ss_conf 999999999999999973299889999999818798674688999899667899999999999998329 Q gi|254780289|r 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669 (682) Q Consensus 601 ~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~ 669 (682) ++.+........+..+|..|||+.+.|+.+|| . | +|..||+..+|+|-.-|+..=.+|+++||. T Consensus 94 e~~~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~--~-g--~s~~EIA~~l~is~~tVk~~l~RA~~~Lr~ 157 (166) T PRK09639 94 EEIWIRKEEITKVQEVLAKMTERDRTVLLLRF--S-G--YSYKEIAQALGIDESSVGTTLHRAKKKFRK 157 (166) T ss_pred HHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH--H-C--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH T ss_conf 89999899999999998839999999999999--3-8--999999999891999999999999999999 No 91 >PRK09642 RNA polymerase sigma factor SigW; Reviewed Probab=98.52 E-value=1.3e-05 Score=63.29 Aligned_cols=148 Identities=17% Similarity=0.201 Sum_probs=109.9 Q ss_pred HHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCCHHHHHHHHH Q ss_conf 57899988752235677788754436799998874385457312010289899999999972287046142058898999 Q gi|254780289|r 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532 (682) Q Consensus 453 lr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~ 532 (682) =+.|.++|-++++..-.-.|++|+.-+-+.+..++|+. +| | .+|-.|=+...|+. . + T Consensus 5 ~~~ly~~~~~~~~n~~dAeDi~QevFik~~~~~~~~~~-~~--~---~~WL~~Ia~N~~~d-~----------------~ 61 (160) T PRK09642 5 RHYIFQVIFSILRHEEDAKDVTQEVFVKIHASLPNYQF-RG--L---KTWMARIATNHAID-Y----------------K 61 (160) T ss_pred HHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCC-CC--H---HHHHHHHHHHHHHH-H----------------H T ss_conf 89999999999099999999999999999984503362-44--9---99999999999999-9----------------9 Q ss_pred HHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHH Q ss_conf 99999987760889997899987099989999999860898755363588998604756238988998999999999999 Q gi|254780289|r 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612 (682) Q Consensus 533 ~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~ 612 (682) .+.. |.+ ..+|+. .+.+ +.+ ....+|++.+........ T Consensus 62 Rk~~--------r~~------------------------~~~~~~----~~~~----~~~--~~~~~~e~~~~~~e~~~~ 99 (160) T PRK09642 62 RKKA--------REN------------------------EELSLC----KETE----ENI--KSSHNIEDLLLTKEQKLL 99 (160) T ss_pred HHHH--------CCC------------------------CCCCCC----HHHH----HCC--CCCCCHHHHHHHHHHHHH T ss_conf 9872--------455------------------------312200----0112----115--677998999998999999 Q ss_pred HHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC Q ss_conf 999973299889999999818798674688999899667899999999999998329 Q gi|254780289|r 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669 (682) Q Consensus 613 ~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~ 669 (682) +.++|..|||+.+.|+.||| -...|+.||+..+|+|-.-|+.-=.+|.++||. T Consensus 100 l~~~l~~Lp~~~R~v~~L~~----~e~~s~~EIA~~l~is~~tVk~~l~RArk~Lkk 152 (160) T PRK09642 100 IAQKLRELPENYRDVVLAHY----LEEKSYQEIALQENIEVKTVEMKLYRARKWIKK 152 (160) T ss_pred HHHHHHHCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH T ss_conf 99999979999999979999----829999999999891999999999999999999 No 92 >PRK12517 RNA polymerase sigma factor; Provisional Probab=98.51 E-value=2.7e-05 Score=60.79 Aligned_cols=155 Identities=18% Similarity=0.168 Sum_probs=108.5 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEE Q ss_conf 11246899987555789998875223567778875443679999887438545731201028989999999997228704 Q gi|254780289|r 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTI 519 (682) Q Consensus 440 e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~ 519 (682) .-++|=.+|++.+-..|.+.|-++++.--.-.|++||.-+-+.+..++|+....|+ +|-.+-+ +. T Consensus 20 ~~~~AFe~L~~~y~~~ly~~a~~~~~d~~~AeDl~QEtFlk~~~~~~~~~~~~~~~-----tWL~~I~--~~-------- 84 (188) T PRK12517 20 SKQRRYEALVKALHADIYRYAYWLCKDKHIAEDLVQETFLRAWRSLDSLKDEKAAK-----AWLITIL--RR-------- 84 (188) T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCCHH-----HHHHHHH--HH-------- T ss_conf 35999999999999999999999949999999999999999999887647963189-----9999999--99-------- Q ss_pred ECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCC Q ss_conf 61420588989999999998776088999789998709998999999986089875536358899860475623898899 Q gi|254780289|r 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599 (682) Q Consensus 520 r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~ 599 (682) ....++. +. .+ ..+.++. ..+.+..... T Consensus 85 -------~~~~r~~---r~-------~~------------------------~~~~~~~-----------~~~~~~~~~~ 112 (188) T PRK12517 85 -------ENARRFE---RK-------QF------------------------DLVDIED-----------DSIEDDLSSS 112 (188) T ss_pred -------HHHHHHH---HC-------CC------------------------CCCCCCC-----------CCCCCCCCCC T ss_conf -------9889998---61-------57------------------------7565220-----------0024666788 Q ss_pred HHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC Q ss_conf 8999999999999999973299889999999818798674688999899667899999999999998329 Q gi|254780289|r 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669 (682) Q Consensus 600 ~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~ 669 (682) |++.... ..|..+|..|||+.+.||.||| -...|..|||..+|+|-.-|+..=.+|..+||. T Consensus 113 ~e~~~~~----~~l~~~l~~Lp~~~R~vi~L~~----~eg~s~~EIA~~Lgis~~tVksrl~RAr~~Lr~ 174 (188) T PRK12517 113 SEEEMEQ----YWLRRQIAKLDPEYREPLLLQV----IGGFSGEEIAEILDLNKNTVMTRLFRARNQLKE 174 (188) T ss_pred CHHHHHH----HHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH T ss_conf 1689999----9999999769999999999999----839999999999893999999999999999999 No 93 >PRK12530 RNA polymerase sigma factor; Provisional Probab=98.51 E-value=1.9e-05 Score=61.90 Aligned_cols=160 Identities=16% Similarity=0.140 Sum_probs=101.7 Q ss_pred HHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHH Q ss_conf 89998875223567778875443679999887438545731201028989999999997228704614205889899999 Q gi|254780289|r 455 LVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVR 534 (682) Q Consensus 455 ~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~ 534 (682) -+...|.++++.--.-.|++||.-+-..+..+.|+... +|+ ||-.|=+...++. .+.+ T Consensus 21 ~L~~fa~~~l~d~~~AEDlvQEtFlka~~~~~~f~~~~--~f~---tWL~~Ia~N~~id-----------------~lRk 78 (191) T PRK12530 21 QMLKFATLQLKDADLAEDVVQEAFTSALKNIDSFKGQS--ALK---TWIFAILKNKIID-----------------YIRQ 78 (191) T ss_pred HHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCC--CHH---HHHHHHHHHHHHH-----------------HHHH T ss_conf 99999999939999999999999999998688637877--299---9999999999999-----------------9998 Q ss_pred HHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCC--CCCCCCEEEEEECCCCCCCHHHHHHHHHHHHH Q ss_conf 9999877608899978999870999899999998608987553635--88998604756238988998999999999999 Q gi|254780289|r 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQANLRET 612 (682) Q Consensus 535 ~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~--~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~ 612 (682) .+|.+...++. .-+.|. .++....-.+..+......|...+....+... T Consensus 79 --------~~r~~~~~~~~---------------------~~~~~~~~~d~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~ 129 (191) T PRK12530 79 --------RKRFVNESELI---------------------EEESPNSFFDEKGHWKPETYEPSELQDVEQTVYSEEFWLI 129 (191) T ss_pred --------HCCCCCCCCCC---------------------CCCCCHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHH T ss_conf --------46667721001---------------------2224100101112234333683021689999999999999 Q ss_pred HHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC Q ss_conf 999973299889999999818798674688999899667899999999999998329 Q gi|254780289|r 613 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669 (682) Q Consensus 613 ~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~ 669 (682) +..+|..|||+.+.|+.||| -...|.+||++.+|+|-.-|+..=.+|-.+||. T Consensus 130 l~~~l~~LP~~~R~v~~Lr~----~~~ls~~EIA~~l~is~~tVksrL~RAR~~Lr~ 182 (191) T PRK12530 130 FEICLNKLPAQQARVFMMRE----FLELSSEQICQECHITTSNLHVLLYRARLQLQA 182 (191) T ss_pred HHHHHHHCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH T ss_conf 99999869999999999999----929999999999896999999999999999999 No 94 >PRK09651 RNA polymerase sigma factor FecI; Provisional Probab=98.46 E-value=2.2e-05 Score=61.41 Aligned_cols=156 Identities=13% Similarity=0.124 Sum_probs=112.2 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEEC Q ss_conf 24689998755578999887522356777887544367999988743854573120102898999999999722870461 Q gi|254780289|r 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521 (682) Q Consensus 442 ~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~ 521 (682) .-|=..+.+.+-+.+...+.++++..-.-.|++|+.=+-+.+. +++..-. .+.+|-.++.|..+..++..+ T Consensus 9 ~~AFe~Ly~~~~~~l~~~~~~~~~~~~~AeDivQe~Flr~~~~-~~~~~~~--~~~a~L~~iarn~~id~~Rr~------ 79 (172) T PRK09651 9 SLTFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVS-ETLSTIR--DPRSFLCTIAKRVMVDLFRRN------ 79 (172) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHC-CCCCCCC--CHHHHHHHHHHHHHHHHHHHH------ T ss_conf 6699999999999999999999598868999999999999863-8523346--889999999999999999998------ Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHH Q ss_conf 42058898999999999877608899978999870999899999998608987553635889986047562389889989 Q gi|254780289|r 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601 (682) Q Consensus 522 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~ 601 (682) .... ...+.+ .. +.+...++|+ T Consensus 80 --------------~~~~-------~~~~~~-----------------~~--------------------~~~~~~~~~e 101 (172) T PRK09651 80 --------------ALEK-------AYLEML-----------------AL--------------------MPEGGAPSPE 101 (172) T ss_pred --------------HHHH-------HHHHHH-----------------HH--------------------CCCCCCCCHH T ss_conf --------------8888-------788888-----------------74--------------------7554599988 Q ss_pred HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC Q ss_conf 9999999999999997329988999999981879867468899989966789999999999999832 Q gi|254780289|r 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668 (682) Q Consensus 602 ~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~ 668 (682) ...........+..+|+.|||+.+.|+.|++ -...|..||+..+|+|-.-|+.-=.+||+.++ T Consensus 102 ~~~~~~e~~~~l~~~l~~Lp~~~R~v~~L~~----~egls~~EIA~~lgiS~~tVk~~l~rAlk~c~ 164 (172) T PRK09651 102 ERESQLETLQLLDSMLDGLNGKTREAFLLSQ----LDGLTYSEIAHKLGVSISSVKKYVAKAVEHCL 164 (172) T ss_pred HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 9999999999999998709999999999998----83999999999989399999999999999999 No 95 >PRK09637 RNA polymerase sigma factor SigZ; Provisional Probab=98.46 E-value=1.6e-05 Score=62.57 Aligned_cols=149 Identities=13% Similarity=0.128 Sum_probs=101.3 Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCCHH Q ss_conf 99987555789998875223567778875443679999887438545731201028989999999997228704614205 Q gi|254780289|r 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525 (682) Q Consensus 446 ~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~ 525 (682) .++...+-+.|...+.++++..-.-.|++|+.-+-+.+..++|+... .|.| |-.+-+...++ |..| T Consensus 4 E~Ly~~y~~~l~~~~~~~~~d~~~AEDivQe~flk~~~~~~~~~~~~--~~~~---WL~~IarN~~i-d~~R-------- 69 (181) T PRK09637 4 ESIWSEYKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLKDGS--SIKS---WLYQIANNTII-DFYR-------- 69 (181) T ss_pred HHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCC--CHHH---HHHHHHHHHHH-HHHH-------- T ss_conf 99999999999999999959999999999999999998522058823--4999---99999999999-9998-------- Q ss_pred HHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHH Q ss_conf 88989999999998776088999789998709998999999986089875536358899860475623898899899999 Q gi|254780289|r 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605 (682) Q Consensus 526 ~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~~~ 605 (682) +. .|.... + +.....+ .|.+... T Consensus 70 --------k~--------~r~~~~---------~-----------------~~~~~~~---------------~~~~~~~ 92 (181) T PRK09637 70 --------KK--------NRSEEL---------P-----------------DDLLFED---------------EEREENA 92 (181) T ss_pred --------HH--------CCCCCC---------C-----------------HHHCCCC---------------CCCCHHH T ss_conf --------61--------555677---------4-----------------2221467---------------9832249 Q ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC Q ss_conf 9999999999973299889999999818798674688999899667899999999999998329 Q gi|254780289|r 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669 (682) Q Consensus 606 ~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~ 669 (682) ...+...+..+|+.|||+.+.|+.|+| -..+|..||+..+|+|-.-|+.-=.+|..+||. T Consensus 93 ~~e~~~~l~~~l~~Lp~~~R~v~~L~~----~eg~s~~EIA~~L~is~~tVksrl~RAr~~Lr~ 152 (181) T PRK09637 93 KKELAPCLRPFIDALPEKYAEALRLTE----LEGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKE 152 (181) T ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH T ss_conf 999999999999769999989979998----859999999999894999999999999999999 No 96 >PRK09047 RNA polymerase factor sigma-70; Validated Probab=98.46 E-value=9.9e-06 Score=64.19 Aligned_cols=74 Identities=18% Similarity=0.287 Sum_probs=67.1 Q ss_pred ECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC Q ss_conf 238988998999999999999999973299889999999818798674688999899667899999999999998329 Q gi|254780289|r 592 IEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669 (682) Q Consensus 592 ~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~ 669 (682) ..+....+|.+.+.+......+..+|..||++.+.|+.||| -...|.+||++.+|+|---|+-.=.+|+++||. T Consensus 79 ~~~~~~~~p~~~~~~~e~~~~l~~ai~~Lp~~qR~vl~L~~----~egls~~EIA~~l~is~~tVk~~l~RAr~~Lr~ 152 (161) T PRK09047 79 ADDDGAESPEDRLERAQVLQLIEEAIQKLPARQREAFLLRY----WEDMDVAETAAAMGCSEGSVKTHCSRATHTLAK 152 (161) T ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH----HHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH T ss_conf 56766899999999999999999999819999999989999----987799999999896999999999999999999 No 97 >PRK12541 RNA polymerase sigma factor; Provisional Probab=98.44 E-value=2.6e-05 Score=60.87 Aligned_cols=155 Identities=15% Similarity=0.156 Sum_probs=102.7 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEEC Q ss_conf 24689998755578999887522356777887544367999988743854573120102898999999999722870461 Q gi|254780289|r 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521 (682) Q Consensus 442 ~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~ 521 (682) ++|=.+++..+-+.|...+.++++.--.-.|++||.-+-+++..+.|. |-.|.| |-.+=+...++ |. T Consensus 4 r~afe~ly~~~~~~l~~~~~~~~~d~~~AeDl~QetFlk~~~~~~~~~---~~~~~~---WL~~Ia~N~~~-d~------ 70 (161) T PRK12541 4 KQSLEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYK---GEEIRP---WLFTIAYNAFI-DW------ 70 (161) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCC---CCCHHH---HHHHHHHHHHH-HH------ T ss_conf 999999999999999999999939999999999999999998361316---675689---99999999999-99------ Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHH Q ss_conf 42058898999999999877608899978999870999899999998608987553635889986047562389889989 Q gi|254780289|r 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601 (682) Q Consensus 522 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~ 601 (682) +.+.. +.++ .+++ +.. + ++.++|+ T Consensus 71 ----------~Rk~~--------~~~~-------------------------~~~~-------~~~----~--~~~~~~~ 94 (161) T PRK12541 71 ----------YRKEK--------KYKT-------------------------TTVE-------EFH----L--PNVPSTE 94 (161) T ss_pred ----------HHHHH--------CCCC-------------------------CCHH-------HHC----C--CCCCCCH T ss_conf ----------99860--------4465-------------------------5255-------540----4--6899962 Q ss_pred HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC Q ss_conf 99999999999999973299889999999818798674688999899667899999999999998329 Q gi|254780289|r 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669 (682) Q Consensus 602 ~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~ 669 (682) +..........+.++|..|||..+.|+.||| -..+|..|||+.+|+|-.-|+..=.+|.++||. T Consensus 95 ~~~~~~~~~~~~~~~l~~Lp~~~R~v~~L~~----~~g~s~~EIA~~lgis~~tVk~~l~RArk~Lr~ 158 (161) T PRK12541 95 HEYFVKHEIASWLDSLSSLPLERRNVLLLRD----YYGFSYKEIAEMTGLSLAKVKIELHRGRKETKS 158 (161) T ss_pred HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH T ss_conf 7789999999999999819999999999899----749999999999893999999999999999987 No 98 >PRK07037 extracytoplasmic-function sigma-70 factor; Validated Probab=98.44 E-value=2.6e-05 Score=60.92 Aligned_cols=159 Identities=18% Similarity=0.244 Sum_probs=111.2 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEEC Q ss_conf 24689998755578999887522356777887544367999988743854573120102898999999999722870461 Q gi|254780289|r 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521 (682) Q Consensus 442 ~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~ 521 (682) ..|=.++...+=.-+...|.+|++..-.-.|++|+.=+-|...-+.|++..- -+ |+..-+.....|+ T Consensus 11 e~al~elf~~~~~~L~~~a~r~~~~~~~AEDivQe~Flkl~~~~~~~~~~~~------~a-wL~~iarN~~id~------ 77 (183) T PRK07037 11 DGALLDVFVDNRSMLVKIARGIVGCASRAEDVVQDAFVKLVEAPNQDAVKQP------VA-YLFQMVRNLAIDH------ 77 (183) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCCCCH------HH-HHHHHHHHHHHHH------ T ss_conf 8999999999999999999999799988999999999999974543441369------99-9999999999999------ Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHH Q ss_conf 42058898999999999877608899978999870999899999998608987553635889986047562389889989 Q gi|254780289|r 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601 (682) Q Consensus 522 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~ 601 (682) +.+.... .. .+ +++++. .+ +.+ ...+|+ T Consensus 78 ----------lRr~~~~--~~-------------------------------~~-----~~~~~~--~~-~~~-~~~~pe 105 (183) T PRK07037 78 ----------CRRQSLE--NK-------------------------------YH-----GDEDDG--LD-VPS-PEASPE 105 (183) T ss_pred ----------HHHHHHH--HH-------------------------------CC-----CCHHHH--CC-CCC-CCCCHH T ss_conf ----------9977766--50-------------------------------13-----424442--12-678-899989 Q ss_pred HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC Q ss_conf 99999999999999973299889999999818798674688999899667899999999999998329 Q gi|254780289|r 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669 (682) Q Consensus 602 ~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~ 669 (682) +.+........|..+|..|||+.+.|+.|++ -...|..||++.+|||---|+--=.+|+++||. T Consensus 106 ~~~~~~e~~~~l~~ai~~LP~~~R~v~~L~~----~eg~s~~EIAe~LgiS~~tVk~~l~rAl~~LR~ 169 (183) T PRK07037 106 AALINRDTLRHVADALDELPARTRAAFEMVR----LRGETLQDIARELNVSQTLVNFMIRDALRHCRK 169 (183) T ss_pred HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH T ss_conf 9999999999999999819999999989898----739899999999892999999999999999999 No 99 >pfam04545 Sigma70_r4 Sigma-70, region 4. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives. Probab=98.43 E-value=4.5e-07 Score=74.77 Aligned_cols=50 Identities=54% Similarity=0.882 Sum_probs=46.4 Q ss_pred HHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC Q ss_conf 973299889999999818798674688999899667899999999999998329 Q gi|254780289|r 616 VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669 (682) Q Consensus 616 ~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~ 669 (682) +|+.|||+++.||.||| ..+.|+.|||+.+|+|..+|+|+..+||.|||. T Consensus 1 Al~~L~~~~r~ii~l~y----~~~~t~~EIA~~lgis~~~V~~~~~ral~~LR~ 50 (50) T pfam04545 1 ALASLPPREREVLVLRF----GEGLTLEEIGERLGISRERVRQIEKRALRKLRK 50 (50) T ss_pred CHHHCCHHHHHHHHHHC----CCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHCC T ss_conf 97668999999999870----688249999999897999999999999998629 No 100 >TIGR02948 SigW_bacill RNA polymerase sigma-W factor; InterPro: IPR014294 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This entry represents sigmaW, which is restricted to certain lineages of the order Bacillales.. Probab=98.39 E-value=3.2e-06 Score=68.02 Aligned_cols=161 Identities=19% Similarity=0.318 Sum_probs=131.8 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHH Q ss_conf 99999987653321124689998755578999887522356777887544367999988743854573120102898999 Q gi|254780289|r 427 FRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506 (682) Q Consensus 427 lK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~ 506 (682) .|..++.|++|...+- -+||+--===|..++=+-.|....-.|.-||+-|-----+|.||+.| |||| |--|= T Consensus 5 ~Kk~ik~v~~GD~~Af---AdlVdlYKDKiY~l~YRMlGN~HEA~D~AQEAF~RAY~~IDtyd~~~--KFST---WLyRI 76 (187) T TIGR02948 5 IKKRIKEVKKGDENAF---ADLVDLYKDKIYQLCYRMLGNVHEAEDVAQEAFIRAYVNIDTYDIER--KFST---WLYRI 76 (187) T ss_pred HHHHHHHHHHCHHHHH---HHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCC--CHHH---HHHHH T ss_conf 6889999860217888---99999964247777776506743055688888888654114316664--3147---89999 Q ss_pred HHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCC Q ss_conf 99999972287046142058898999999999877608899978999870999899999998608987553635889986 Q gi|254780289|r 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586 (682) Q Consensus 507 ~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~ 586 (682) | +.+ +|-++. --+..+.||.||+.-++- T Consensus 77 A---------------TNl--~IDrlR-----------------------------------KrKPD~yLd~~V~G~dGL 104 (187) T TIGR02948 77 A---------------TNL--TIDRLR-----------------------------------KRKPDFYLDDEVAGTDGL 104 (187) T ss_pred H---------------HHH--HHHHHH-----------------------------------CCCCCCCCCCCCCCCCCC T ss_conf 9---------------877--886541-----------------------------------348886436755786774 Q ss_pred EEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCC Q ss_conf 047562389889989999999999999999732998899999998187986746889998996678 Q gi|254780289|r 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652 (682) Q Consensus 587 ~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~ 652 (682) |+..-++. ....|++.+..-.+++.+.+.+..|||+-|.|+.|.| =.+.+|.||...+++. T Consensus 105 T~~sQlaa-~~~~~~d~V~~lE~~~~iQ~~I~~LP~KYR~~ivLKY----~edLSL~EIS~IL~lP 165 (187) T TIGR02948 105 TMESQLAA-DEASPEDEVVSLELRDTIQEEIEALPEKYRSVIVLKY----MEDLSLKEISEILDLP 165 (187) T ss_pred HHHHCCCC-CCCCCHHHHHHHHHHHHHHHHHHHCCHHHCEEHHHHH----HHHHHHHHHHHHHCCC T ss_conf 00100110-1246214655535678999999743433512224544----4442188899985789 No 101 >PRK12535 RNA polymerase sigma factor; Provisional Probab=98.37 E-value=0.0001 Score=56.19 Aligned_cols=170 Identities=19% Similarity=0.136 Sum_probs=109.0 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHH Q ss_conf 26889999998765332112468999875557899988752235677788754436799998874385457312010289 Q gi|254780289|r 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502 (682) Q Consensus 423 ~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~ 502 (682) +-..+.+++.+.+.|.+.+ -..+++.+-..|..++.+..|. -.-.|++||--+-+.+...+|.... .|+ || T Consensus 9 ~da~~~~Lv~~a~~GD~~A---f~~L~~r~~~~v~r~~~~l~~~-~~AeDl~QEtflk~~~~l~~f~~~~--~f~---tW 79 (195) T PRK12535 9 NDAHVTELALAAGRGDRAA---LTEFIRATQDDVWRLLAHLGGH-DIADDLTQETYLRVMSALPRFAARS--SAR---TW 79 (195) T ss_pred CHHHHHHHHHHHHHCCHHH---HHHHHHHHHHHHHHHHHHHCCH-HHHHHHHHHHHHHHHHHHHHCCCCC--CHH---HH T ss_conf 8488999999998220999---9999999999999999893799-7799999999999999887707888--799---99 Q ss_pred HHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCC Q ss_conf 89999999997228704614205889899999999987760889997899987099989999999860898755363588 Q gi|254780289|r 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582 (682) Q Consensus 503 ~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~ 582 (682) -++=+...++ |+.| + ... .|-....++ T Consensus 80 L~~Ia~n~~~-d~~R----------------~---~~~-------------------------------~~~~~~~~~-- 106 (195) T PRK12535 80 LLSLARRVWV-DNIR----------------H---DMA-------------------------------RPRKSAVEY-- 106 (195) T ss_pred HHHHHHHHHH-HHHH----------------H---HHC-------------------------------CCCCCCCCC-- T ss_conf 9999999999-9999----------------8---851-------------------------------666553332-- Q ss_pred CCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHH Q ss_conf 99860475623898899899999999999999997329988999999981879867468899989966789999999999 Q gi|254780289|r 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662 (682) Q Consensus 583 ~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~ 662 (682) ++... .| ...+..... ...+..+|..|||..+.||.|+| -..+|.+||+..+|++---|+--=.+ T Consensus 107 -~~~~~----~d--~~~~~~~~~----~~~l~~~l~~Lp~~~R~~l~L~~----~~g~s~~EIA~ilgi~~gTVKsRl~R 171 (195) T PRK12535 107 -EDTGA----TD--ATNAGIWSE----WIDVRTLIDALPPERREALILTQ----VLGYTYEEAAKIADVRVGTIRSRVAR 171 (195) T ss_pred -CCCCC----CC--CCCCHHHHH----HHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHH T ss_conf -23566----77--764035777----99999999849998879999999----82998999999989399999999999 Q ss_pred HHHHHCC Q ss_conf 9998329 Q gi|254780289|r 663 AIRKLKH 669 (682) Q Consensus 663 a~~~l~~ 669 (682) |..+||- T Consensus 172 Ar~~Lr~ 178 (195) T PRK12535 172 ARADLVA 178 (195) T ss_pred HHHHHHH T ss_conf 9999999 No 102 >PRK09645 RNA polymerase sigma factor SigL; Provisional Probab=98.36 E-value=4.8e-05 Score=58.82 Aligned_cols=157 Identities=13% Similarity=0.148 Sum_probs=103.4 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEEC Q ss_conf 24689998755578999887522356777887544367999988743854573120102898999999999722870461 Q gi|254780289|r 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521 (682) Q Consensus 442 ~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~ 521 (682) ..|=..|...+-+.|...+.++++.-..-.|++|+--+-+.+..+.|+. .+-.|.| |+..-....+.|+ T Consensus 6 ~~af~~Ly~~~~~~l~~~~~~~~~d~~~AeDivQe~F~k~~~~~~~~~~-~~~~~~~----wL~~Ia~n~~~d~------ 74 (171) T PRK09645 6 AALMRALYDEHAAALWRYALRLTGDRARAEDVVQETLLRAWQHPEVLAD-PTRSARA----WLFTVARNLVIDE------ 74 (171) T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCC-CCCCHHH----HHHHHHHHHHHHH------ T ss_conf 9999999999999999999999099999999999999999985887066-4141999----9999999999999------ Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHH Q ss_conf 42058898999999999877608899978999870999899999998608987553635889986047562389889989 Q gi|254780289|r 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601 (682) Q Consensus 522 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~ 601 (682) +.+.... .....+... ...+...++.. T Consensus 75 ----------~R~~~~~---------------------------------~~~~~~~~~----------~~~~~~~~~~~ 101 (171) T PRK09645 75 ----------RRSARAR---------------------------------PVEGSPDVL----------GVPEQSTPDEV 101 (171) T ss_pred ----------HHHHHCC---------------------------------CCCCCCCHH----------HHCCCCCCCHH T ss_conf ----------9987547---------------------------------543444233----------20256883168 Q ss_pred HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC Q ss_conf 99999999999999973299889999999818798674688999899667899999999999998329 Q gi|254780289|r 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669 (682) Q Consensus 602 ~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~ 669 (682) + .......+..+|..|||+.+.|+.||| -..+|++|||+.+|+|-.-|+.-=.+|+++||. T Consensus 102 ~---~~~~~~~l~~ai~~L~~~~r~v~~l~~----~~g~s~~EIA~~l~is~~tVk~~l~ra~~~Lr~ 162 (171) T PRK09645 102 D---AALDRLLIADALAQLSPEHRAVLVRSY----YRGWSTAQIAADLGIPEGTVKSRLHYAVRALRL 162 (171) T ss_pred H---HHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH T ss_conf 8---999999999999759999887989999----869999999999892999999999999999999 No 103 >PRK12546 RNA polymerase sigma factor; Provisional Probab=98.34 E-value=5.8e-05 Score=58.12 Aligned_cols=153 Identities=16% Similarity=0.134 Sum_probs=100.7 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEEC Q ss_conf 24689998755578999887522356777887544367999988743854573120102898999999999722870461 Q gi|254780289|r 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521 (682) Q Consensus 442 ~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~ 521 (682) ...++++++ +..-+...|.++++..-.-.|++|+.-+-+.+..++|++.. +|.| |..+=+...++ T Consensus 7 ~~~~~~l~e-H~p~L~~fa~r~~~~~~~AEDlvQEtflk~~~~l~~~~~~~--~~~t---WL~~IarN~~~--------- 71 (188) T PRK12546 7 RDPRDELVE-HLPALRAFAISLTRNVAAADDLVQDTVVKAWTNFDKFQEGT--NLRA---WLFTILRNTFY--------- 71 (188) T ss_pred HHHHHHHHH-HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCC--CHHH---HHHHHHHHHHH--------- T ss_conf 629999999-99999999999919999999999999999999787647653--1388---99999999999--------- Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHH Q ss_conf 42058898999999999877608899978999870999899999998608987553635889986047562389889989 Q gi|254780289|r 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601 (682) Q Consensus 522 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~ 601 (682) + ..|+ .+|.. ...+.... + ....+ +.++ T Consensus 72 --------d----~~Rk----~~r~~--------------------------~~~~~~~~---~----~~~~~---~~~~ 99 (188) T PRK12546 72 --------S----DRRK----HKREV--------------------------EDPEGVHA---A----SLAVK---PAHD 99 (188) T ss_pred --------H----HHHH----HCCCC--------------------------CCCCCCCC---C----CCCCC---CCCH T ss_conf --------9----9997----44777--------------------------76421112---3----34689---8700 Q ss_pred HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC Q ss_conf 99999999999999973299889999999818798674688999899667899999999999998329 Q gi|254780289|r 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669 (682) Q Consensus 602 ~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~ 669 (682) ... ....+..+|..|||+.+.||.|+| -..+|+.||++.+|+|---|+.-=.+|.++||. T Consensus 100 ~~~----~~~~l~~aL~~LP~~~R~vl~L~~----~egls~~EIAe~Lgis~gTVKsRL~RAR~~Lr~ 159 (188) T PRK12546 100 GRL----AMSDFRAAFAQLPDEQREALILVG----ASGFSYEEAAEMCGVAVGTVKSRANRARARLAE 159 (188) T ss_pred HHH----HHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH T ss_conf 689----999999999869999988958799----829899999999893999999999999999999 No 104 >PRK12547 RNA polymerase sigma factor; Provisional Probab=98.32 E-value=0.00011 Score=55.82 Aligned_cols=155 Identities=12% Similarity=0.091 Sum_probs=103.4 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEE Q ss_conf 12468999875557899988752235677788754436799998874385457312010289899999999972287046 Q gi|254780289|r 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520 (682) Q Consensus 441 ~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r 520 (682) ..++=.+++.+...-+...|.++++..-.-.|++|+.-+-+.+..++|++. .+|.||. .+=+...++ T Consensus 4 ~~~~F~~l~~~~~p~L~~~a~~l~~~~~~AeDlvQe~flk~~~~~~~~~~~--~~~~~Wl---~~IarN~~~-------- 70 (164) T PRK12547 4 TSKNFKQELLAALPSLRAFAVSLSSKHDKADDLVQDTLMKAWAKQDSFQPG--TNLKAWL---FTILRNEFY-------- 70 (164) T ss_pred CHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCC--CCHHHHH---HHHHHHHHH-------- T ss_conf 799999999998999999999994999999999999999999988876998--8699999---999999999-------- Q ss_pred CCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCH Q ss_conf 14205889899999999987760889997899987099989999999860898755363588998604756238988998 Q gi|254780289|r 521 IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600 (682) Q Consensus 521 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~ 600 (682) +.+.+ .+|+....+ .. +.++....++ T Consensus 71 ---------d~~Rk--------~~r~~~~~~----------------------------------~~---~~~~~~~~~~ 96 (164) T PRK12547 71 ---------SQMRK--------RGREVQDSD----------------------------------GV---FTARLAVHPA 96 (164) T ss_pred ---------HHHHH--------HCCCCCCCC----------------------------------CC---CCCCCCCCCH T ss_conf ---------99997--------278776521----------------------------------01---1012568940 Q ss_pred HHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC Q ss_conf 999999999999999973299889999999818798674688999899667899999999999998329 Q gi|254780289|r 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669 (682) Q Consensus 601 ~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~ 669 (682) .... .. ...+..+|..||+..+.|+.|+| -..+|..||+..+|+|-.-|+.-=.+|..+||. T Consensus 97 ~~~~--~~-~~~l~~al~~Lp~~~r~v~~L~~----~~g~s~~EIA~~lgis~~tVksrl~rAr~~Lr~ 158 (164) T PRK12547 97 QYGS--LD-LQDFRKALNLLPADQREAIILIG----ASGFSYEEAAEICGCAVGTIKSRVSRARNRLQE 158 (164) T ss_pred HHHH--HH-HHHHHHHHHHCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH T ss_conf 2436--89-99999999858999999999899----849999999999893999999999999999999 No 105 >PRK12527 RNA polymerase sigma factor; Reviewed Probab=98.27 E-value=0.0001 Score=56.11 Aligned_cols=154 Identities=12% Similarity=0.156 Sum_probs=101.0 Q ss_pred HHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHH Q ss_conf 78999887522356777887544367999988743854573120102898999999999722870461420588989999 Q gi|254780289|r 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533 (682) Q Consensus 454 r~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~ 533 (682) +-+...+.++++.--.-.|++|+.-+-+.+ +++....-.+ -+|..|-+...++. . +. T Consensus 6 ~~L~~~~~~~~~~~~~AeDivQd~F~k~~~---~~~~~~~~~~---~a~L~~ia~N~~~d-~----------------~R 62 (159) T PRK12527 6 RELLRFLSARLGNRQAAEDVAHDAYLRVLE---RSSSAQIEHP---RAFLYRTALNLVVD-R----------------HR 62 (159) T ss_pred HHHHHHHHHHHCCHHHHHHHHHHHHHHHHH---HCCCCCCCCH---HHHHHHHHHHHHHH-H----------------HH T ss_conf 999999999969999999999999999998---6663554569---99999999999999-9----------------99 Q ss_pred HHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHH Q ss_conf 99999877608899978999870999899999998608987553635889986047562389889989999999999999 Q gi|254780289|r 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETT 613 (682) Q Consensus 534 ~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~ 613 (682) +.. .+...+++.. .+ ......++|++.+........+ T Consensus 63 ~~~---------------------------------~~~~~~~~~~-~~---------~~~~~~~~~~~~~~~~e~~~~l 99 (159) T PRK12527 63 RHR---------------------------------VRQAEPLEVL-DE---------EERLHSPSPQTRLDLGQRLALL 99 (159) T ss_pred HHH---------------------------------HCCCCCHHHH-CC---------CCCCCCCCHHHHHHHHHHHHHH T ss_conf 987---------------------------------5145530211-10---------1012489869999999999999 Q ss_pred HHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHCC Q ss_conf 999732998899999998187986746889998996678999999999999983296777875665179 Q gi|254780289|r 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682 (682) Q Consensus 614 ~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~~~~~l~~~~~~ 682 (682) ..+|+.|||+.+.|+.|+| -...|..||++.+|+|..-|+.-=.+|+++||. .|+.|-.| T Consensus 100 ~~al~~Lp~~~R~v~~L~~----~egls~~EIA~~lgis~~tVk~~l~rA~k~Lr~-----~L~~~e~g 159 (159) T PRK12527 100 QRALAELPPICRESFLLRK----LEGLSHQQIAEHLGISRSLVEKHIVNAMKHCRV-----RMRQWESG 159 (159) T ss_pred HHHHHHCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH-----HHHHHHCC T ss_conf 9999869999989998898----739799999999891999999999999999999-----99977673 No 106 >PRK09649 RNA polymerase sigma factor SigC; Reviewed Probab=98.26 E-value=0.00011 Score=55.84 Aligned_cols=171 Identities=18% Similarity=0.132 Sum_probs=112.8 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHH Q ss_conf 12688999999876533211246899987555789998875223567778875443679999887438545731201028 Q gi|254780289|r 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501 (682) Q Consensus 422 l~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~ 501 (682) .+..++-+++.+.+.|..+ |=..|+..+-+-|...+. |.+..-.-.|++||--+-..++..+|+.+. +|+ | T Consensus 6 ~dd~~l~aLv~~a~~GD~~---Af~~L~~~~~~~v~r~~~-~l~d~~~AeDl~QEtFlka~~~l~~f~~~s--~f~---t 76 (185) T PRK09649 6 SDDEAVTALALSAAKGNGR---ALEAFIKATQQDVWRFVA-YLSDVGSADDLTQETFLRAIGAIPRFSARS--SAR---T 76 (185) T ss_pred CCHHHHHHHHHHHHHCCHH---HHHHHHHHHHHHHHHHHH-HHCCHHHHHHHHHHHHHHHHHHHHHCCCCC--CHH---H T ss_conf 4609999999999944799---999999999999999999-938998999999999999999887628876--189---9 Q ss_pred HHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCC Q ss_conf 98999999999722870461420588989999999998776088999789998709998999999986089875536358 Q gi|254780289|r 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG 581 (682) Q Consensus 502 ~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~ 581 (682) |-.+=+...++. .+.+.. +.|.. +. + T Consensus 77 WL~~IA~N~~~d-----------------~~Rk~~--------~~~~~-------------------------~~----~ 102 (185) T PRK09649 77 WLLAIARHVVAD-----------------HIRHVR--------SRPRT-------------------------TR----G 102 (185) T ss_pred HHHHHHHHHHHH-----------------HHHHHH--------CCCCC-------------------------CC----C T ss_conf 999999999999-----------------999874--------37764-------------------------34----4 Q ss_pred CCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHH Q ss_conf 89986047562389889989999999999999999732998899999998187986746889998996678999999999 Q gi|254780289|r 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661 (682) Q Consensus 582 ~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~ 661 (682) .+.+. +.+ .+......++ ...+..+|..|||..+.||.||| -..+|++||+..+|++---|+--=. T Consensus 103 ~~~e~-~~~--~~~~~~~~e~-------~~~l~~al~~Lp~~~R~vl~L~~----~egls~~EIA~~lg~~~gTVKsRl~ 168 (185) T PRK09649 103 ARPEH-LID--GDRHARGFED-------LVEVTTMIADLTTDQREALLLTQ----LLGLSYADAAAVCGCPVGTIRSRVA 168 (185) T ss_pred CCHHH-CCC--CCCCCCCHHH-------HHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHH T ss_conf 57231-158--4311023788-------99999999849999999999899----7299999999998939999999999 Q ss_pred HHHHHHCC Q ss_conf 99998329 Q gi|254780289|r 662 KAIRKLKH 669 (682) Q Consensus 662 ~a~~~l~~ 669 (682) +|..+|+- T Consensus 169 RAR~~L~a 176 (185) T PRK09649 169 RARDALLA 176 (185) T ss_pred HHHHHHHH T ss_conf 99999997 No 107 >PRK12516 RNA polymerase sigma factor; Provisional Probab=98.25 E-value=0.00013 Score=55.48 Aligned_cols=155 Identities=14% Similarity=0.119 Sum_probs=103.3 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEE Q ss_conf 12468999875557899988752235677788754436799998874385457312010289899999999972287046 Q gi|254780289|r 441 ASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520 (682) Q Consensus 441 ~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r 520 (682) ...|-.+++.+.+.-+...|.++++.--.-.|++|+.-+-+.+..++|... -.|.| |-.+=+..+++ T Consensus 11 ~~~~F~~l~~~~~p~L~~~a~~l~~~~~dAEDlvQetflk~~~~~~~~~~~--~~~~a---WL~~IarN~~~-------- 77 (190) T PRK12516 11 GTPPFKRELLASLPSLRAFAVSLIGQHDRADDLVQDTIMKAWAKQESFEVG--TNMKA---WLFTILRNEFY-------- 77 (190) T ss_pred CCHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCC--CCHHH---HHHHHHHHHHH-------- T ss_conf 872099999998999999999990999999999999999999998635656--77999---99999999999-------- Q ss_pred CCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCH Q ss_conf 14205889899999999987760889997899987099989999999860898755363588998604756238988998 Q gi|254780289|r 521 IPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600 (682) Q Consensus 521 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~ 600 (682) +.+.+. ++... ..+.. +. +..+..| T Consensus 78 ---------d~~Rk~--------~r~~~--------------------------~~d~~--------~~----e~~~~~~ 102 (190) T PRK12516 78 ---------TQMRKR--------GREVQ--------------------------DTDGM--------FS----EQLAVHP 102 (190) T ss_pred ---------HHHHHC--------CCCCC--------------------------CCCCC--------CC----CCCCCCC T ss_conf ---------999961--------68666--------------------------53222--------33----3346895 Q ss_pred HHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC Q ss_conf 999999999999999973299889999999818798674688999899667899999999999998329 Q gi|254780289|r 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669 (682) Q Consensus 601 ~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~ 669 (682) ... .......+..+|..|||+.+.|+.|+| -..+|.+||+..+|+|---|+.-=.+|.++||. T Consensus 103 ~~~--~~~~~~~l~~al~~Lp~~~R~vl~L~~----~egls~~EIAe~Lgis~~TVksrl~RAr~~Lr~ 165 (190) T PRK12516 103 SQY--GTLDLQDFRAALDQLPDDQREAIILIG----ASGFAYEEAAEICGCAVGTIKSRVSRARARLQE 165 (190) T ss_pred CCC--CHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH T ss_conf 420--207799999999819999989999899----829999999999894999999999999999999 No 108 >PRK08241 RNA polymerase factor sigma-70; Validated Probab=98.18 E-value=0.0002 Score=53.93 Aligned_cols=186 Identities=16% Similarity=0.211 Sum_probs=123.2 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHH Q ss_conf 99998765332112468999875557899988752235677788754436799998874385457312010289899999 Q gi|254780289|r 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508 (682) Q Consensus 429 ~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i 508 (682) ......+.|. ..|-.++++..-+-+...+.+..+..-+-.|++||.-+-..++.++|+.+. ...||-.|=+. T Consensus 11 ~~~a~a~~GD---~~Af~~Lv~~~r~~L~~~cyRmlGs~~dAED~vQEt~lrawr~~~~f~~~~-----~~rtWL~rIat 82 (341) T PRK08241 11 AGLAAAADGD---RDAFLALAEPHRRELLAHCYRMLGSLHDAEDLVQETLLRAWRSYDRFEGRS-----SLRTWLYRIAT 82 (341) T ss_pred HHHHHHHCCC---HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCCCC-----CCCEEEHHHHH T ss_conf 9999997479---999999999999999999999809998999999999999985132226556-----64131019899 Q ss_pred HHHHHHCCCEEECCCHHHHHHHHHH-HHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCE Q ss_conf 9999722870461420588989999-999998776088999789998709998999999986089875536358899860 Q gi|254780289|r 509 TRSIADQSCTIRIPVHMRDKIHKVV-RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587 (682) Q Consensus 509 ~~~~~~~~~~~r~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~ 587 (682) ..|+. .+. +..|.....+|...... ..+.....+.. T Consensus 83 n~cLd-----------------~Lr~r~RR~~~~~l~~~~~~~--------------------------~~~~~~~~~~~ 119 (341) T PRK08241 83 NVCLD-----------------ALEGRARRPLPTGLGPPSADP--------------------------SAALVERPEVP 119 (341) T ss_pred HHHHH-----------------HHHHHHCCCCCCCCCCCCCCC--------------------------CCCCCCCCCCC T ss_conf 99999-----------------998742446744456665665--------------------------44555555666 Q ss_pred ----EEEEECCCCCCCHHHHHH-HHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHH Q ss_conf ----475623898899899999-999999999997329988999999981879867468899989966789999999999 Q gi|254780289|r 588 ----LGDFIEDKNAVSPLDSAI-QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662 (682) Q Consensus 588 ----~~~~~~d~~~~~~~~~~~-~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~ 662 (682) +-|-.-+....+|.+.+. +..++-++..+|..|+|+++.|+.||--+ .++..||+..+|+|-.=|+|.=.+ T Consensus 120 WleP~Pd~~~~~~~~dP~~~~~~rEsv~lA~laaLq~Lpp~QRavlvLRdV~----g~s~~EiAe~Lg~S~aAVks~L~R 195 (341) T PRK08241 120 WLEPLPDALLDPAAADPAAIVVARESVRLAFVAALQHLPPRQRAVLLLRDVL----GWSAAEVAEALGTSTAAVNSALQR 195 (341) T ss_pred CCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCHHHHEEEEHHHHC----CCCHHHHHHHHCCCHHHHHHHHHH T ss_conf 5466775345667799889988877899999999983999790200129752----998899999978999999999999 Q ss_pred HHHHHCC Q ss_conf 9998329 Q gi|254780289|r 663 AIRKLKH 669 (682) Q Consensus 663 a~~~l~~ 669 (682) |=..|+. T Consensus 196 ARa~L~~ 202 (341) T PRK08241 196 ARATLAE 202 (341) T ss_pred HHHHHHH T ss_conf 9999986 No 109 >PRK12523 RNA polymerase sigma factor; Reviewed Probab=98.18 E-value=0.00017 Score=54.39 Aligned_cols=155 Identities=14% Similarity=0.134 Sum_probs=104.7 Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCC Q ss_conf 68999875557899988752235677788754436799998874385457312010289899999999972287046142 Q gi|254780289|r 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523 (682) Q Consensus 444 AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~ 523 (682) +=..+.+-+-..|...+.++.+.--.-.|++|+.-+-|++. ..|... .+..+|..+-+-..++ |+ T Consensus 11 ~~~~Ly~~~~~~L~~~~~r~~~~~e~AEDivQd~Flrl~~~-~~~~~~-----~~~~a~Lf~iarNl~~-D~-------- 75 (172) T PRK12523 11 LVGALYRDHRGWLLAWLRRNLACRQRAEDLSQDTFVRLLGR-PELPTP-----REPRAFLAAVAKGLMF-DH-------- 75 (172) T ss_pred HHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHC-CCCCCC-----CCHHHHHHHHHHHHHH-HH-------- T ss_conf 99999999999999999999498868999999999999827-765673-----4599999999999999-99-------- Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHH Q ss_conf 05889899999999987760889997899987099989999999860898755363588998604756238988998999 Q gi|254780289|r 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603 (682) Q Consensus 524 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~ 603 (682) +.+..++.. ..++++ .+.+...++|++. T Consensus 76 --------~Rr~~~~~~-------~~~~~~-------------------------------------~~~~~~~~~~e~~ 103 (172) T PRK12523 76 --------FRRAALEQA-------YLAELA-------------------------------------LVPEAEQPSPEEQ 103 (172) T ss_pred --------HHHHHHHHH-------HHHHHH-------------------------------------CCCCCCCCCHHHH T ss_conf --------998998850-------088886-------------------------------------2665468997999 Q ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC Q ss_conf 999999999999973299889999999818798674688999899667899999999999998329 Q gi|254780289|r 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669 (682) Q Consensus 604 ~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~ 669 (682) .........|..+|+.|||+.+.|+.|++ -..+|..||+..+|+|---|++-=.+||+.++. T Consensus 104 ~~~~e~~~~l~~al~~Lp~~~R~v~~L~~----~eGls~~EIA~~LgiS~~tVk~~l~rAl~~~~~ 165 (172) T PRK12523 104 HLILEDLKAIDRLLGKLSSKARAAFLYNR----LDGMGHAEIAERLGVSVSRVRQYLAQGLRQCYI 165 (172) T ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH T ss_conf 99999999999998649999999999999----939999999999893999999999999999999 No 110 >TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family; InterPro: IPR014298 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This group of sigma factors appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent. Probab=98.17 E-value=8.4e-05 Score=56.89 Aligned_cols=131 Identities=18% Similarity=0.354 Sum_probs=98.4 Q ss_pred CCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHH---HHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCC Q ss_conf 77788754436799998874385457312010289899---999999972287046142058898999999999877608 Q gi|254780289|r 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK---QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544 (682) Q Consensus 468 ~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~---~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~ 544 (682) ..-.||+|+==.-.|+.++.|-+.....|+. |-.+ .-|.-|+....| T Consensus 36 ~tAEDL~s~vF~~~L~~i~~f~~~~~t~f~~---WLf~iA~N~v~Dyfr~~~r--------------------------- 85 (171) T TIGR02952 36 YTAEDLTSEVFLRVLRKIDSFKEQKNTDFEA---WLFTIARNVVADYFRKSKR--------------------------- 85 (171) T ss_pred EEHHHHHHHHHHHHHHHHHHHCCCCCCCCHH---HHHHHHHHHHHHHHHCCCC--------------------------- T ss_conf 3114647899999973122101257877224---7899999999988511345--------------------------- Q ss_pred CCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHH Q ss_conf 89997899987099989999999860898755363588998604756238988998999999999999999973299889 Q gi|254780289|r 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPRE 624 (682) Q Consensus 545 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re 624 (682) .+.++.+.+..++ ...++|.+.+....--+.+..++..|+|.+ T Consensus 86 ----------~~~~~~~~~~~l~---------------------------~~e~~P~e~~~~~~~n~~L~~a~~~L~p~q 128 (171) T TIGR02952 86 ----------RPLLSLDVVKELL---------------------------SAEPSPEEAVLKELANEKLLEAVKKLTPKQ 128 (171) T ss_pred ----------CCCCCHHHHHHHH---------------------------HCCCCHHHHHHHHHHHHHHHHHHHHCCHHH T ss_conf ----------5210099989887---------------------------348981789998888999999996108323 Q ss_pred HHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC Q ss_conf 999999818798674688999899667899999999999998329 Q gi|254780289|r 625 ERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669 (682) Q Consensus 625 ~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~ 669 (682) ++||.||| +....-.||++.+|.+--=|.+|..+|+++|+. T Consensus 129 q~viaLrF----~~~L~~~EvA~ilGk~~gavk~Lq~rAv~~L~r 169 (171) T TIGR02952 129 QEVIALRF----AQNLPIAEVARILGKTEGAVKALQFRAVKKLAR 169 (171) T ss_pred HHHHHHHH----CCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHH T ss_conf 12033321----168838789987268974689999999999873 No 111 >PRK12540 RNA polymerase sigma factor; Provisional Probab=98.14 E-value=0.00039 Score=51.63 Aligned_cols=155 Identities=14% Similarity=0.104 Sum_probs=100.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECC Q ss_conf 46899987555789998875223567778875443679999887438545731201028989999999997228704614 Q gi|254780289|r 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIP 522 (682) Q Consensus 443 ~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~ 522 (682) .|-++.+.+-..=+...|-++++..-.-.||+||.-+-+.+..++|++. .+|.|| -.+ |.|..+ T Consensus 5 ~~f~~~~l~~~P~L~~fa~~l~~n~~dAEDlvQEtflk~~~~~~~~~~~--~~~~tW---L~~--IarN~~--------- 68 (181) T PRK12540 5 DSLRDDILAAVPSLRAFAISLSGNGDRADDLVQETLLRALANIDSFQPG--SNLPAW---LFT--ILRNLF--------- 68 (181) T ss_pred HHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCC--CCHHHH---HHH--HHHHHH--------- T ss_conf 8899999998799999999993999999999999999999849875987--624899---999--999999--------- Q ss_pred CHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHH Q ss_conf 20588989999999998776088999789998709998999999986089875536358899860475623898899899 Q gi|254780289|r 523 VHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLD 602 (682) Q Consensus 523 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~ 602 (682) ++.+.+. .+..... +..+...+.. .+.... T Consensus 69 ------~~~~Rk~--------~r~~~~~----------------------------------~~~~~~~~~~--~~~~~~ 98 (181) T PRK12540 69 ------RSDYRKR--------RREVEDA----------------------------------DGSYAKTLKS--QPGQNA 98 (181) T ss_pred ------HHHHHHH--------CCCCCCC----------------------------------CCCCCCCCCC--CCCHHH T ss_conf ------9999983--------5766643----------------------------------2110001468--997356 Q ss_pred HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHH Q ss_conf 999999999999997329988999999981879867468899989966789999999999999832967 Q gi|254780289|r 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671 (682) Q Consensus 603 ~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~ 671 (682) .. ..+.+..+|..||+..+.||.|+| -..+|.+||++.+|+|---|+--=.+|.+|||--- T Consensus 99 ~~----~~~~l~~al~~Lp~~~R~vl~L~~----~egls~~EIA~iL~is~gTVKsRL~RAr~kLr~~L 159 (181) T PRK12540 99 HL----EFEEFRAALEKLPQDQREALILVG----ASGFSYEDAAAICGCAVGTIKSRVNRARSKLSALL 159 (181) T ss_pred HH----HHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH T ss_conf 77----899999999819999989988799----80999999999989499999999999999999998 No 112 >cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas Probab=98.05 E-value=1.5e-05 Score=62.80 Aligned_cols=55 Identities=31% Similarity=0.526 Sum_probs=51.2 Q ss_pred HHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC Q ss_conf 99999997329988999999981879867468899989966789999999999999832 Q gi|254780289|r 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668 (682) Q Consensus 610 ~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~ 668 (682) ++.|.++|+.|||+++.|+.||| -..+|+.|||..+|+|...|++.-.+|+.+|| T Consensus 1 r~~l~~al~~L~~~~r~vl~l~y----~~~~s~~EIa~~lgis~~tVk~~l~rA~~~Lr 55 (55) T cd06171 1 RERLEEALDKLPEREREVILLRF----GEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55 (55) T ss_pred CHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC T ss_conf 98999999839999989899999----80999999999989599999999999998758 No 113 >PRK12511 RNA polymerase sigma factor; Provisional Probab=98.01 E-value=0.00036 Score=51.89 Aligned_cols=150 Identities=12% Similarity=0.124 Sum_probs=96.8 Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCCHH Q ss_conf 99987555789998875223567778875443679999887438545731201028989999999997228704614205 Q gi|254780289|r 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525 (682) Q Consensus 446 ~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~ 525 (682) ..++. ++.=+...|.++++.--.-.|++|+.-+-+.+..++|+.... +.+|+.+-+...+|. ..| T Consensus 8 ~~~~~-~~P~L~rfa~~l~~d~~dAEDlvQetflk~~~~~~~~~~~~~-----~~~WL~~IarN~~id-~~R-------- 72 (182) T PRK12511 8 FDVID-QLVPLRRYARSLTRDSAEAEDLVHDALVRALERRASFRSGGN-----LRTWLMSILHNAFID-ELR-------- 72 (182) T ss_pred HHHHH-HHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCC-----HHHHHHHHHHHHHHH-HHH-------- T ss_conf 99999-899999999999299999999999999999999886688664-----999999999999999-998-------- Q ss_pred HHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHH Q ss_conf 88989999999998776088999789998709998999999986089875536358899860475623898899899999 Q gi|254780289|r 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605 (682) Q Consensus 526 ~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~~~ 605 (682) +.. +. +...+. +.. ..+.....+.+... T Consensus 73 --------r~~--------~~--------------------------~~~~~~-~~~---------~~~~~~~~~~e~~~ 100 (182) T PRK12511 73 --------RRR--------AE--------------------------ARRADE-LVV---------EADASAPAGQEHAV 100 (182) T ss_pred --------HCC--------CC--------------------------CCCCCC-CCC---------CCCCCCCCCHHHHH T ss_conf --------433--------44--------------------------343331-012---------35556896356899 Q ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC Q ss_conf 9999999999973299889999999818798674688999899667899999999999998329 Q gi|254780289|r 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669 (682) Q Consensus 606 ~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~ 669 (682) . ...+..+|..|||+.+.||.|+| -..+|..|||+.+|+|---|+.-=.+|..+||. T Consensus 101 ~---~~~l~~al~~Lp~~~R~vl~L~~----~egls~~EIAe~Lgis~gTVKsrl~RAr~~LR~ 157 (182) T PRK12511 101 R---LAQIRDAFFDLPEEQRAALHLVA----IEGLSYQEAANVLGIPIGTLMSRIGRARAALRA 157 (182) T ss_pred H---HHHHHHHHHCCCHHHHHHEEEEE----ECCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH T ss_conf 9---99999999869998950112410----079999999999893999999999999999999 No 114 >PRK12525 RNA polymerase sigma factor; Provisional Probab=97.95 E-value=0.00083 Score=49.04 Aligned_cols=152 Identities=14% Similarity=0.102 Sum_probs=98.0 Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCCHH Q ss_conf 99987555789998875223567778875443679999887438545731201028989999999997228704614205 Q gi|254780289|r 446 KEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525 (682) Q Consensus 446 ~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~ 525 (682) .+|-..+-+-++.-+.++.+.--.-.|++||--+-+...-+..+. ..-. .|+.....+...|++| T Consensus 12 ~~Lf~~~y~~L~~~~~r~lg~~~~AeDivQe~Flr~~~~~~~~~~------~~~~-a~L~~iArnl~~d~~R-------- 76 (168) T PRK12525 12 GQMFQQDYDWLCKKLSRQLGCPHSAEDIASETFLQVLALPDPASI------REPR-ALLTTIARRLMYEGWR-------- 76 (168) T ss_pred HHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCC------CCHH-HHHHHHHHHHHHHHHH-------- T ss_conf 999999999999999999498857999999999999867774554------5889-9999999999999999-------- Q ss_pred HHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHH Q ss_conf 88989999999998776088999789998709998999999986089875536358899860475623898899899999 Q gi|254780289|r 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605 (682) Q Consensus 526 ~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~~~ 605 (682) |..... +..+ ++ .+ ..+...++|++.+. T Consensus 77 --------r~~~~~-------~~~~------------------------~~----~~---------~~~~~~~~pe~~~~ 104 (168) T PRK12525 77 --------RQDLER-------AYLQ------------------------SL----AE---------APEAVQPSPEEQWM 104 (168) T ss_pred --------HHHHHH-------HHHH------------------------HH----HC---------CCCCCCCCHHHHHH T ss_conf --------999999-------8888------------------------88----51---------66656898678999 Q ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC Q ss_conf 999999999997329988999999981879867468899989966789999999999999832 Q gi|254780289|r 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668 (682) Q Consensus 606 ~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~ 668 (682) .......+..+|+.|||+.+.|+.|++ -..+|..|||+.+|||.--|..-=.+||+..+ T Consensus 105 ~~e~~~~l~~al~~LP~~~R~vflL~~----~eGlsy~EIAe~LgIS~~tV~~~l~rAl~~c~ 163 (168) T PRK12525 105 VIETLLAIDRLLDGLSGKARAAFLMSQ----LEGLTYVEIGERLGVSLSRIHQYMVEAFKCCY 163 (168) T ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 999999999998639999999999999----92999999999989799999999999999999 No 115 >PRK09636 RNA polymerase sigma factor SigJ; Provisional Probab=97.94 E-value=0.0011 Score=48.17 Aligned_cols=153 Identities=14% Similarity=0.190 Sum_probs=99.6 Q ss_pred HHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCCHHHH Q ss_conf 98755578999887522356777887544367999988743854573120102898999999999722870461420588 Q gi|254780289|r 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRD 527 (682) Q Consensus 448 l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~~~ 527 (682) --++.=+.+.++|.+..+..-.-.|++||.-+-+.++ +++ ..+.-.+|-.|-+...|+. T Consensus 5 ~fe~~R~~L~~~AyRmlGs~~DAEDvvQEt~lr~~~~-~~~------~~~~~~aWL~rI~~n~~ld-------------- 63 (289) T PRK09636 5 EFEPLRPHLLSVAYRMLGSVADAEDIVQEAWLRWNNA-DRA------EIRDPRAFLTRVVTRLCLD-------------- 63 (289) T ss_pred HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHCC-CCC------CCCCHHHHHHHHHHHHHHH-------------- T ss_conf 8998799999999998099978999999999998506-842------2347899999999999999-------------- Q ss_pred HHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHH-HHHHH Q ss_conf 98999999999877608899978999870999899999998608987553635889986047562389889989-99999 Q gi|254780289|r 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL-DSAIQ 606 (682) Q Consensus 528 ~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~-~~~~~ 606 (682) .+.+..+....-.| . -|..|+- + ...+|. ..... T Consensus 64 ---~LR~ar~rre~~~g-------------~----------------wlpep~~------------~-~~~~p~~~~~~~ 98 (289) T PRK09636 64 ---RLRSARHRRETYVG-------------P----------------WLPEPVV------------E-DSDDPLEAVVAA 98 (289) T ss_pred ---HHHHHHCCCCCCCC-------------C----------------CCCCCCC------------C-CCCCCHHHHHHH T ss_conf ---99854016554678-------------7----------------7887667------------8-889935678877 Q ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCH Q ss_conf 9999999999732998899999998187986746889998996678999999999999983296 Q gi|254780289|r 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670 (682) Q Consensus 607 ~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~ 670 (682) ..+..++..+|..|||+++.|+.||.-. .++++||+..+|+|-.=|||+-.+|=++|+.. T Consensus 99 e~~~~al~~~L~~L~p~qRav~vLrdv~----g~s~~EIA~iLg~s~~avR~~l~RAR~~l~~~ 158 (289) T PRK09636 99 EDLSLALMLALERLSPLERAAFLLHDVF----GVPFDEIASTLGRSEAACRQLASRARKHVRAA 158 (289) T ss_pred HHHHHHHHHHHHHCCHHHHHHHHHHHHH----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHCC T ss_conf 8899999999973999896254049860----99999999998179999999999999987344 No 116 >PRK05803 sporulation sigma factor SigK; Reviewed Probab=97.85 E-value=0.00012 Score=55.66 Aligned_cols=67 Identities=22% Similarity=0.145 Sum_probs=46.3 Q ss_pred HHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHC--CHHHHHH-------HHHHHHHHCCCHHHHHHHHH Q ss_conf 9999998569768897889999999998899999998728--2389999-------99998731171036787642 Q gi|254780289|r 121 VRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCES--PLTFQAL-------IIWRDELNDGTTLLREIIDL 187 (682) Q Consensus 121 VRMYLREMG~V~LLTREgEIeIAKRIE~G~~~i~~al~~~--P~ti~~i-------l~~~e~i~~ge~~LrdIIDl 187 (682) .-.||+++...+|||+|+|+++|.|+.+|.......+..+ .+++... +.+-|.|++|.+.|-.-|+. T Consensus 17 l~syl~~i~~~~~Ls~eEE~~La~~~~~GD~~Ar~~LI~~NLRLVvsIAkky~~~g~~l~DLIQEGniGLi~Avek 92 (228) T PRK05803 17 LVSYVKNNSFPQPLSEEEERKYLELMKQGDEEARNILIERNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIDS 92 (228) T ss_pred HHHHHHCCCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHH T ss_conf 9999974788999999999999999984689999999998779999999627799989899999999999999998 No 117 >PRK12529 RNA polymerase sigma factor; Provisional Probab=97.77 E-value=0.0046 Score=43.16 Aligned_cols=155 Identities=10% Similarity=0.080 Sum_probs=95.2 Q ss_pred HHHHHHHHHHHHH-HHHHHHHCCCCC-CHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEEC Q ss_conf 6899987555789-998875223567-77887544367999988743854573120102898999999999722870461 Q gi|254780289|r 444 AKKEMVEANLRLV-ISVAKKYTNRGL-QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRI 521 (682) Q Consensus 444 AK~~l~~anlr~v-~~~~~~~~~~~~-~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~ 521 (682) |=..|...+=.++ -.+.++..+.|- .-.||+|+--+-|.++.+...+.-.-.| .+|--|-+ .....|+ T Consensus 14 a~~~Ly~~h~~~L~~~l~~Rl~~~~~~~AeDl~QDvFlrl~~~~~~~~~~~i~~p---~a~L~rIA-~Nl~id~------ 83 (178) T PRK12529 14 KVATLYRENHAWLRNWLAYRLRSWGRGVADDLAHDIFLRILASRDGGQREAIRQP---RAYLARIA-NCVLVSW------ 83 (178) T ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHCCCCCCCHHHHH---HHHHHHHH-HHHHHHH------ T ss_conf 9999999999999999999828998354699999999999973444564323348---99999999-9999999------ Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHH Q ss_conf 42058898999999999877608899978999870999899999998608987553635889986047562389889989 Q gi|254780289|r 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601 (682) Q Consensus 522 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~ 601 (682) ..|...... ..+++ . + +.++..++|+ T Consensus 84 ----------~Rr~~~~~~-------~le~~-----------------~-------------------~-~~~~~~pspE 109 (178) T PRK12529 84 ----------RRRQSLELA-------WLEAL-----------------A-------------------T-LPEPLHPSPE 109 (178) T ss_pred ----------HHHHHHHHH-------HHHHH-----------------H-------------------C-CCCCCCCCHH T ss_conf ----------998888987-------89988-----------------6-------------------4-7866689989 Q ss_pred HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH Q ss_conf 99999999999999973299889999999818798674688999899667899999999999998 Q gi|254780289|r 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666 (682) Q Consensus 602 ~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~ 666 (682) ..+........|..+|+.||||-+.|+.|++ -..+|..||++.+|||.--|.+-=.+||.. T Consensus 110 ~~~~~~e~l~~l~~al~~Lp~r~R~vF~L~r----~eGls~~EIAe~LgiS~~tV~~~l~rAl~~ 170 (178) T PRK12529 110 QQSVILETLHEIDALLDTLRPRVKQAFLMAT----LDGMKQKDIAQALDIALPTVKKYIHQAYVT 170 (178) T ss_pred HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHH T ss_conf 9999999999999998569978889987998----829999999999895999999999999999 No 118 >PRK12528 RNA polymerase sigma factor; Provisional Probab=97.66 E-value=0.0049 Score=42.95 Aligned_cols=154 Identities=14% Similarity=0.133 Sum_probs=98.6 Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCC Q ss_conf 68999875557899988752235677788754436799998874385457312010289899999999972287046142 Q gi|254780289|r 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523 (682) Q Consensus 444 AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~ 523 (682) |=.++-..+-..+...+.++.+..-.-.|++|+--+-|+..-+..+. .+-.. |+.+...+.+.|+.| T Consensus 11 ~~e~ly~~~~~~L~~~~~r~~g~~~~AEDivQd~Flrl~~~~~~~~~------~~~~a-yL~~iA~n~~id~~R------ 77 (167) T PRK12528 11 TVEGLYSAHHHWLTGWLRRRLGCPQSAADLAQDTFVKVLVARETAQI------IEPRA-FLTTIAKRVLCNHYR------ 77 (167) T ss_pred HHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCC------CCHHH-HHHHHHHHHHHHHHH------ T ss_conf 99999999999999999999398857999999999999965654465------67999-999999999999999------ Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHH Q ss_conf 05889899999999987760889997899987099989999999860898755363588998604756238988998999 Q gi|254780289|r 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603 (682) Q Consensus 524 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~ 603 (682) +...... ..+.+ .. ..+...++|++. T Consensus 78 ----------~~~~~~~-------~~~~~-----------------~~--------------------~~~~~~~~~e~~ 103 (167) T PRK12528 78 ----------RQDLERA-------YLEAL-----------------AQ--------------------LPERVAPSEEER 103 (167) T ss_pred ----------HHHHHHH-------HHHHH-----------------HC--------------------CCCCCCCCHHHH T ss_conf ----------9998998-------99887-----------------63--------------------653246985789 Q ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC Q ss_conf 99999999999997329988999999981879867468899989966789999999999999832 Q gi|254780289|r 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668 (682) Q Consensus 604 ~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~ 668 (682) +........+..+|+.|||+.+.|+.|+. -...|..||++.+|+|-.-|+.-=.+|+.... T Consensus 104 ~~~~e~~~~l~~~l~~LP~~~R~vf~L~r----~~gls~~EIA~~LgiS~~tVk~~l~rA~~~c~ 164 (167) T PRK12528 104 AIILETLVELDRLLDGLPPLVKRAFLLAQ----VDGLGYGEIATELGISLATVKRYLNKAAMRCY 164 (167) T ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHHHHH----HHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 99999999999998709999999999999----82989999999979799999999999999999 No 119 >TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; InterPro: IPR014327 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This group of sigma factors are members of the sigma-70 family and are found primarily in the genus Bacteroides. This appears to have resulted from a lineage-specific expansion as Bacteroides thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037 (Tannerella forsythensis ATCC 43037), Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currently only two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent. Probab=97.64 E-value=0.0043 Score=43.39 Aligned_cols=164 Identities=13% Similarity=0.194 Sum_probs=122.0 Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCC Q ss_conf 68999875557899988752235677788754436799998874385457312010289899999999972287046142 Q gi|254780289|r 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523 (682) Q Consensus 444 AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~ 523 (682) |=+.|....=+-+...|.+|++..-.-.|++|+-=+.|..-=+.++... .|.+|=.=+||..+..++..+.- T Consensus 2 aF~~ly~~Yy~~l~~fA~~yv~~~e~AEdIVqdvF~~lWe~r~~l~~~~--~~~~YL~~~v~N~~ln~Lr~~~~------ 73 (167) T TIGR02985 2 AFEQLYRRYYPKLCAFARRYVKDEEDAEDIVQDVFLKLWENRESLEESE--SIKAYLFTIVKNRCLNYLRHKQV------ 73 (167) T ss_pred HHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCCCC--CCCHHHHHHHHHHHHHHHHHHHH------ T ss_conf 4889999987999999999836899999999999999973145256213--52179999999989989988999------ Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHH Q ss_conf 05889899999999987760889997899987099989999999860898755363588998604756238988998999 Q gi|254780289|r 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS 603 (682) Q Consensus 524 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~ 603 (682) ...... ++.+ . .+..++.-+. ....+|.+. T Consensus 74 ---------~~~~~~------------~~~~--------------~--~~~~~~~~~~-------------~l~~~~~~~ 103 (167) T TIGR02985 74 ---------EEKYQE------------ELSE--------------I--EEDEIELRLQ-------------SLEADPEED 103 (167) T ss_pred ---------HHHHHH------------HHHH--------------H--HHHHHHHHHH-------------HCCCCCHHH T ss_conf ---------999999------------9998--------------6--5567876310-------------036897457 Q ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC Q ss_conf 999999999999973299889999999818798674688999899667899999999999998329 Q gi|254780289|r 604 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669 (682) Q Consensus 604 ~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~ 669 (682) .....|...|..+|+.|||+-|.|+.|-+ -+.+|-.|||..+|||--=|.--=.+||+.||+ T Consensus 104 ~~~~El~~~i~~~~~~LPe~~R~iF~lsr----~eg~s~~EIA~~L~iS~~TVe~hi~~ALk~LR~ 165 (167) T TIGR02985 104 IYSKELEEIIEEAIEKLPEQCREIFILSR----FEGLSNKEIAEELGISVKTVEYHITKALKFLRK 165 (167) T ss_pred HHHHHHHHHHHHHHHHCCHHHHHHHHHHH----HHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH T ss_conf 87999999999998756898999999988----617986789988489888999999999999987 No 120 >PRK09635 sigI RNA polymerase sigma factor SigI; Provisional Probab=97.50 E-value=0.014 Score=39.31 Aligned_cols=155 Identities=19% Similarity=0.247 Sum_probs=100.7 Q ss_pred HHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCCHHH Q ss_conf 99875557899988752235677788754436799998874385457312010289899999999972287046142058 Q gi|254780289|r 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMR 526 (682) Q Consensus 447 ~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~~ 526 (682) +-.+++=+..+++|-+..+..-+-.|++||.-+-+.++- +.. ...--+|-.|-.-..||. T Consensus 9 ~~fe~hR~~L~~~ayRmlGs~~dAED~VQEa~lr~~~~~--~~~-----~~~~~awL~ri~tn~cld------------- 68 (290) T PRK09635 9 AAWRAHRAYLVDLAFRMVGDIGVAEDMVQEAFSRLLRAP--VGD-----IDDERGWLIVVTSRLCLD------------- 68 (290) T ss_pred HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCC--CCC-----CCCHHHHHHHHHHHHHHH------------- T ss_conf 999998999999999980898789999999999997477--312-----357888999999999999------------- Q ss_pred HHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHH-HH Q ss_conf 89899999999987760889997899987099989999999860898755363588998604756238988998999-99 Q gi|254780289|r 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDS-AI 605 (682) Q Consensus 527 ~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~-~~ 605 (682) .+.+.... |+ .|.. +|..... + ..+...+|.+. .. T Consensus 69 ----~LR~~r~r------re-------------------------~~~~----~~~~~~~---~--~~~~~~dp~~~~~~ 104 (290) T PRK09635 69 ----HIKSASTR------RE-------------------------RPQD----IAAWHDG---D--ASVSSVDPADRVTL 104 (290) T ss_pred ----HHHHHHHC------CC-------------------------CCCC----CCCCCCC---C--CCCCCCCHHHHHHH T ss_conf ----98766522------67-------------------------8766----6777876---7--77888982889887 Q ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC Q ss_conf 9999999999973299889999999818798674688999899667899999999999998329 Q gi|254780289|r 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669 (682) Q Consensus 606 ~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~ 669 (682) ...+..++..+|..|+|+|+.|+.||--+| ++++||+..+|.|-.=+||+=.+|=++|+. T Consensus 105 ~~~v~~All~~Le~L~P~eRaa~vLrdvfg----~~~~EIA~~Lg~s~~a~Rqll~RAR~~l~~ 164 (290) T PRK09635 105 DDEVRLALLIMLERLGPAERVVFVLHEIFG----LPYQQIATTIGSQASTCRQLAHRARRKINE 164 (290) T ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHHHCC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHC T ss_conf 778999999998629986854552698608----988999999689989999999999998732 No 121 >PRK06930 positive control sigma-like factor; Validated Probab=97.45 E-value=0.0006 Score=50.11 Aligned_cols=61 Identities=18% Similarity=0.242 Sum_probs=54.1 Q ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC Q ss_conf 99999999999973299889999999818798674688999899667899999999999998329 Q gi|254780289|r 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669 (682) Q Consensus 605 ~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~ 669 (682) ....-+..|.++|+.|+|||++|+.|.. ++..|..|||..+|||+--|.+.=.+|..|++. T Consensus 100 ~se~d~~~iedALs~Lt~rErevfll~~----~~glsy~EIA~~L~Is~~tV~~~l~RA~~Ki~~ 160 (170) T PRK06930 100 ISEWDKIRIEDALSVLTEREKEVYLMHR----GYGLSYSEIAAYLNIKKSTVQSMIERAEKKIAK 160 (170) T ss_pred CCHHHHHHHHHHHHHCCHHHHHHHHHHH----HHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH T ss_conf 0389998899999856988889998897----618889999999798899999999999999999 No 122 >TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1; InterPro: IPR011745 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This entry describes sigma-70 factors in Myxococcus xanthus DK 1622 and in other members of the Mycococcales. Each of the six members in M. xanthusis is encoded near a gene for a predicted serine/threonine kinase. Members of this family show sequence similarity to members of Pfam family IPR007630 from INTERPRO (region 4 of sigma-70 like sigma-factors), a helix-turn-helix family in which trusted and noise cutoffs deliberately are set artificially high and which therefore has many false negatives.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent. Probab=97.42 E-value=0.0038 Score=43.79 Aligned_cols=143 Identities=20% Similarity=0.342 Sum_probs=92.8 Q ss_pred HHHHHHHHHHHHHHHHHCCCE----EECCCHHHHHHHHHHHHHHHHHHH--CCCCCCHHHHHHHCC-------CCHHHHH Q ss_conf 102898999999999722870----461420588989999999998776--088999789998709-------9989999 Q gi|254780289|r 498 TYAMWWVKQAITRSIADQSCT----IRIPVHMRDKIHKVVRTARRMSNK--IKREPTPEEIAKKLA-------MPVEGVR 564 (682) Q Consensus 498 tya~~~i~~~i~~~~~~~~~~----~r~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~a~~~~-------~~~~~~~ 564 (682) |-+.+|=.++.-|+|-.+... +|-|.-|++-.-...| +. .|+.-+|.-||++.| +.+-=+| T Consensus 37 ~~G~p~Al~~lErhvL~k~~~~L~~~r~~~~~vdEV~Q~lR------~rLLl~~~~~ppriaeY~GrGpL~~WvR~~A~R 110 (249) T TIGR03001 37 AQGEPAALAALERHVLSKVPARLARLRPPEAFVDEVLQRLR------QRLLLPRAEAPPRIAEYSGRGPLLSWVRIVAVR 110 (249) T ss_pred HHCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHH------HHCCCCCCCCCHHHHHHCCCCHHHHHHHHHHHH T ss_conf 61228999999999998735523788998642776579977------642689888621244211652469999999999 Q ss_pred HHHHHHC---CCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHHH----HHHHHHHHHHHHCCCHHHHHHHHHHHCCCCC Q ss_conf 9998608---98755363588998604756238988998999999----9999999999732998899999998187986 Q gi|254780289|r 565 KVLKITK---EPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ----ANLRETTTRVLASLTPREERVLRMRFGIGMN 637 (682) Q Consensus 565 ~~~~~~~---~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~----~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~ 637 (682) -+++..+ ..... +.++.+.++..-....+|+-...+ ..+++++.++|++||+|||..||+.| = T Consensus 111 ~A~~L~~~~~~~~~~------e~~~~~~~~~~~~~maDpEl~llr~~~r~~f~~Al~~Al~~L~~rER~LLRLHf----v 180 (249) T TIGR03001 111 IALELQAQERRHSHL------EEETELAALPAPGSMADPELDLLRERYRQEFRAALREALAALSERERTLLRLHF----V 180 (249) T ss_pred HHHHHHHHCCCCCCC------CCCCCHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----H T ss_conf 999987512444520------023314544068874117899999999999999999987328986876555688----2 Q ss_pred CCCCHHHHHHHHCCCHHHH Q ss_conf 7468899989966789999 Q gi|254780289|r 638 TDHTLEEVGKQFCVTRERI 656 (682) Q Consensus 638 ~~~tl~e~~~~~~~~~er~ 656 (682) ...|+++||..|+++|-=| T Consensus 181 ~~Ls~~r~g~my~~~~STv 199 (249) T TIGR03001 181 EGLSMDRLGAMYQVHRSTV 199 (249) T ss_pred CCCCHHHHHHHHCCCCHHH T ss_conf 0332999987745775078 No 123 >PRK08301 sporulation sigma factor SigE; Reviewed Probab=97.41 E-value=0.0016 Score=46.85 Aligned_cols=56 Identities=23% Similarity=0.235 Sum_probs=36.1 Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHCC--HHHHHH-------HHHHHHHHCCCHHHHHHHHH Q ss_conf 688978899999999988999999987282--389999-------99998731171036787642 Q gi|254780289|r 132 ELLSREGEIAIAKRIEAGRAMMMASLCESP--LTFQAL-------IIWRDELNDGTTLLREIIDL 187 (682) Q Consensus 132 ~LLTREgEIeIAKRIE~G~~~i~~al~~~P--~ti~~i-------l~~~e~i~~ge~~LrdIIDl 187 (682) ||||+|+|+++|+||.+|......-+..+- +++... +.+-|.|++|.+.|-.-|+. T Consensus 37 p~Ls~eeE~~l~~~~~~GD~~Ar~~LI~~NLRLVv~IAkky~~~G~~l~DLIqEGniGLikAvek 101 (239) T PRK08301 37 PPLSKEEEEVLLNKLPKGDEAVRSILIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNT 101 (239) T ss_pred CCCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHH T ss_conf 99899999999999983469999999998789999999757689979899999858999999996 No 124 >COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription] Probab=97.27 E-value=0.0031 Score=44.49 Aligned_cols=26 Identities=23% Similarity=0.296 Sum_probs=22.9 Q ss_pred CCCCCCHHHHHHHCCCCHHHHHHHHH Q ss_conf 08899978999870999899999998 Q gi|254780289|r 543 IKREPTPEEIAKKLAMPVEGVRKVLK 568 (682) Q Consensus 543 ~~~~~~~~~~a~~~~~~~~~~~~~~~ 568 (682) .|.+.|.++|++.+|+|.++||.+.. T Consensus 296 ~~~~~TLeevg~~~~vsrERvRQIE~ 321 (342) T COG0568 296 DGEPKTLEELGEEFGISRERVRQIEA 321 (342) T ss_pred CCCCCHHHHHHHHHCCCHHHHHHHHH T ss_conf 99955199999895986999999999 No 125 >PRK05658 RNA polymerase sigma factor RpoD; Validated Probab=97.10 E-value=0.0011 Score=48.14 Aligned_cols=229 Identities=19% Similarity=0.234 Sum_probs=94.4 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------HHHHHHHCCCHHHHHHHCCCCCCCHHHHH Q ss_conf 9999999999998621005778878999999999999999999--------99999712535777763167768989999 Q gi|254780289|r 314 CKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGEL--------LRLAQSYGIKRDVFLERHQGRELDPHWVS 385 (682) Q Consensus 314 ~~kl~~eL~e~~~~lkl~~k~iE~L~~~l~~~~k~Ir~~Er~L--------~rl~~k~~i~R~~Fi~~f~gnEt~~~wl~ 385 (682) ...++.+|..+-....++...|..++..+..-..+.+..-+++ ..+|++|-----.|+.+.+ |-|..... T Consensus 344 I~~~q~kL~~ie~~~gl~i~elK~i~r~I~~Ge~~a~~AKkeMiEANLRLVISIAKKYtNRGLqFLDLIQ--EGNiGLMk 421 (620) T PRK05658 344 IQRLQQELEAIEEETGLTIEELKEINRQISKGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ--EGNIGLMK 421 (620) T ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHH--HCCHHHHH T ss_conf 9999999999999849799999999999999877789999999986189999999983148998789987--44079999 Q ss_pred HHHHCCCCHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----------HHHHHHHHHH Q ss_conf 9861355106765543456776532-233332222211268899999987653321124-----------6899987555 Q gi|254780289|r 386 YAKDFPEGEWKNFVACEVDSILKIR-NEIKSISVETGISISEFRHIVSMVRKGECEASI-----------AKKEMVEANL 453 (682) Q Consensus 386 ~~~~~~~~~~~~~l~~~~~eI~~~q-~kL~~ie~~~gl~i~ElK~i~r~I~~ge~e~~~-----------AK~~l~~anl 453 (682) .+.+.....-..|..-.-..|..+. +.|++=..-+.+|++=+-.|++-++....-.+. .+-.|-.--. T Consensus 422 AVdKFeyrrGyKFSTYATWWIRQAITRaIaDqaRTIRiPVHmietinkl~r~~r~l~qe~Grept~eEia~~~~~~~~kv 501 (620) T PRK05658 422 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERLGMPEDKV 501 (620) T ss_pred HHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHH T ss_conf 99862845597135779999999999999861774015188999999999999999998289999999998949899999 Q ss_pred HHHHHHHHHHCCC----C----CCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCCHH Q ss_conf 7899988752235----6----7778875443679999887438545731201028989999999997228704614205 Q gi|254780289|r 454 RLVISVAKKYTNR----G----LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525 (682) Q Consensus 454 r~v~~~~~~~~~~----~----~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~ 525 (682) |=|..|||-=.-- | -.|.|.|...|.-- -+-.++...+.++.+ T Consensus 502 r~vlki~~epiSle~pig~~~ds~lgdfied~~~~~---------------------p~~~~~~~~l~~~~~-------- 552 (620) T PRK05658 502 RKVLKIAKEPISLETPIGDDEDSHLGDFIEDKNAEL---------------------PIDAATQESLREQTT-------- 552 (620) T ss_pred HHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC---------------------HHHHHHHHHHHHHHH-------- T ss_conf 999986489802438878888764001016899998---------------------799999999999999-------- Q ss_pred HHHHHHH-HHHHHHHHHH----CCCCCCHHHHHHHCCCCHHHHHHH----HHHHCCCC Q ss_conf 8898999-9999998776----088999789998709998999999----98608987 Q gi|254780289|r 526 RDKIHKV-VRTARRMSNK----IKREPTPEEIAKKLAMPVEGVRKV----LKITKEPI 574 (682) Q Consensus 526 ~~~~~~~-~~~~~~~~~~----~~~~~~~~~~a~~~~~~~~~~~~~----~~~~~~~~ 574 (682) +.+..+ -|-.+-+... .|.+.|.||+...++++.++||.+ ++-.++|. T Consensus 553 -~vl~~Lt~rE~~vl~~RfGi~~~~~~TLeevg~~f~vtRERiRQIEakalrklrhp~ 609 (620) T PRK05658 553 -DVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 609 (620) T ss_pred -HHHHCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCC T ss_conf -998479999999999957999999678999998829768989999999999856872 No 126 >pfam08281 Sigma70_r4_2 Sigma-70, region 4. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif. Probab=96.79 E-value=0.0051 Score=42.78 Aligned_cols=53 Identities=23% Similarity=0.424 Sum_probs=48.0 Q ss_pred HHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH Q ss_conf 999999732998899999998187986746889998996678999999999999983 Q gi|254780289|r 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667 (682) Q Consensus 611 ~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l 667 (682) +.+.++|+.|||+.+.|+.|+| -...|..||++.+|+|---|+..=.+|+++| T Consensus 2 ~~l~~ai~~Lp~~~r~~~~l~~----~~~~s~~eIA~~lg~s~~tVk~~l~RA~~~L 54 (54) T pfam08281 2 EALLRALEELPPRQREVFLLRY----LEGLSYAEIAELLGISEGTVKSRLSRARKKL 54 (54) T ss_pred HHHHHHHHCCCHHHHHHHHHHH----HHCCCHHHHHHHHCCCHHHHHHHHHHHHHCC T ss_conf 8999999859999998968799----8785999999998949999999999999719 No 127 >TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD; InterPro: IPR012760 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This entry represents the C-terminal region of sigma 70 (RpoD) which contains the well-conserved regions 2, 3 and 4. Region 2 of sigma-70 is the most conserved region of the entire protein. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core-binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime , . The aromatic residues of the recognition helix, found at the C terminus of this domain are thought to mediate strand separation, thereby allowing transcription initiation , . Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme .Region 4 is involved in binding to the -35 promoter element via a helix-turn-helix motif .; GO: 0003677 DNA binding, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent. Probab=96.69 E-value=0.0013 Score=47.57 Aligned_cols=190 Identities=11% Similarity=0.052 Sum_probs=117.2 Q ss_pred CHHHHHH---HHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCHHHHH Q ss_conf 2389999---9999873117103678764210135433333334333332110001110001000000001221000011 Q gi|254780289|r 161 PLTFQAL---IIWRDELNDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVS 237 (682) Q Consensus 161 P~ti~~i---l~~~e~i~~ge~~LrdIIDld~t~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~e~~~e~~~~~~ 237 (682) +++-+|+ |.+.|.|++|++.|=.-|+.|..-.++.+++++.||-.++.....+++......+++..+.-+.-....- T Consensus 15 SIAKkY~nRGL~F~DLIQEGn~GL~KAv~KFdy~kGyKFSTYATWWIRQAITRAIADQARtIRiPVHm~ETINk~~~~~R 94 (240) T TIGR02393 15 SIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIKAER 94 (240) T ss_pred HHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHH T ss_conf 67666304786334367652357898877621357886551157899999999887513720110326678889999989 Q ss_pred HHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHH Q ss_conf 11101356666530344310002223345555644421023479876689999999999999875210120007999999 Q gi|254780289|r 238 KDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVL 317 (682) Q Consensus 238 ~~~~~~~~~~~~e~e~~~~~~e~e~de~~~sla~~e~eLk~~v~e~l~~i~~~~~kl~k~~~~~~~~~~~~~~~kk~~kl 317 (682) .....-..++..+.-.+..+...+.-.....++..--+|...+-+--+.--..|-+-. ............-+ T Consensus 95 ~l~Q~~Gr~Pt~EelAe~~g~~~~Kv~~i~~~~~~PiSLe~piG~e~dS~l~DFi~D~--------~~~~P~~~~~~~~l 166 (240) T TIGR02393 95 KLLQELGREPTDEELAERMGLPVEKVREIKKIAQEPISLETPIGEEEDSSLGDFIEDE--------SIESPEDAAAKELL 166 (240) T ss_pred HHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCC--------CCCCHHHHHHHHHH T ss_conf 9998728899877899870899899999998624886566677887777442652574--------44685899999999 Q ss_pred HHHHHHHHH-HH---------------HH-HHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 999999998-62---------------10-0577887899999999999999999999 Q gi|254780289|r 318 KEKLVKLVG-SL---------------SL-NQSRIDLLVEQLYDISKRIMHNEGELLR 358 (682) Q Consensus 318 ~~eL~e~~~-~l---------------kl-~~k~iE~L~~~l~~~~k~Ir~~Er~L~r 358 (682) .++|.+.+. .| .. .++.+|++...+.....+||++|.+.+| T Consensus 167 ~~~l~~vL~~~L~~rE~~Vl~~RyGL~d~~~~~TLEEVG~~f~VTRERIRQIE~KALR 224 (240) T TIGR02393 167 REQLEEVLENTLTERERKVLRMRYGLLDGEKPKTLEEVGKEFNVTRERIRQIESKALR 224 (240) T ss_pred HHHHHHHHHCCCCHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHH T ss_conf 9999999860178889999987438998876533788876517871145688899988 No 128 >TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family; InterPro: IPR014303 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This group of sigma factors appear by homology, tree building and bidirectional best hits, to represent a conserved family. This entry is found in a limited number of bacterial lineages and ncludes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis str. MC2 155, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM 10152.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent. Probab=96.57 E-value=0.014 Score=39.33 Aligned_cols=71 Identities=23% Similarity=0.285 Sum_probs=58.3 Q ss_pred CCCHHHHHH-HHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHH Q ss_conf 899899999-999999999997329988999999981879867468899989966789999999999999832967 Q gi|254780289|r 597 AVSPLDSAI-QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPS 671 (682) Q Consensus 597 ~~~~~~~~~-~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~ 671 (682) ..+|.+.++ ..+|.-+.--+|..|+|-||.|+.||==.+ +.++||+...|.|--=.|||-.+|=+|||.-. T Consensus 86 ~~dP~e~~E~~eslS~A~L~lLErL~P~ERAVF~LREVF~----y~Y~EIA~~v~kS~ancRQl~~RAr~~lr~~~ 157 (287) T TIGR02957 86 SADPAESVELAESLSMAYLLLLERLSPLERAVFLLREVFD----YDYEEIASIVGKSEANCRQLVSRARRHLRAAR 157 (287) T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHC----CCCHHHHHHCCCCHHHHHHHHHHHHHHHHHCC T ss_conf 5553889988753779999987307978999999998745----88267897606895799999999999997528 No 129 >TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family; InterPro: IPR014325 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor . The protein appears to include a paralogous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.. Probab=96.51 E-value=0.0015 Score=46.93 Aligned_cols=150 Identities=18% Similarity=0.253 Sum_probs=101.3 Q ss_pred HHHHHHHHHHHHHHHHHC-CCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCCHH Q ss_conf 998755578999887522-3567778875443679999887438545731201028989999999997228704614205 Q gi|254780289|r 447 EMVEANLRLVISVAKKYT-NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHM 525 (682) Q Consensus 447 ~l~~anlr~v~~~~~~~~-~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~ 525 (682) +.+.+.-+=.+-.|.-.+ +--..-.||+|+.=+-+-.+=+++ +=.-=+--|+|+.+.+.-...||-=|+ T Consensus 10 ~f~~~r~~~L~r~A~lLt~GD~~~AEDLvQ~Al~~~y~rW~Ri------~~~~~~~aYvR~vl~n~~~s~wRrR~~---- 79 (165) T TIGR02983 10 AFVAARYPRLLRTAYLLTAGDPHEAEDLVQEALVRTYVRWDRI------RDADAPDAYVRRVLVNLAISRWRRRRV---- 79 (165) T ss_pred HHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCC------CCCCCCHHHHHHHHHHHHHHHHHHHHH---- T ss_conf 9999999999999999827887569999999999998862215------882540578999999999999998876---- Q ss_pred HHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHH Q ss_conf 88989999999998776088999789998709998999999986089875536358899860475623898899899999 Q gi|254780289|r 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605 (682) Q Consensus 526 ~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~~~ 605 (682) ..++ |..+ ++|.. +-.+... T Consensus 80 ----------~~e~---------------------------------------~~~~---------~Pd~~--ga~d~~~ 99 (165) T TIGR02983 80 ----------RLEL---------------------------------------PTEE---------LPDAA--GAPDPAA 99 (165) T ss_pred ----------HHHC---------------------------------------CCCC---------CCCCC--CCCCCCC T ss_conf ----------4421---------------------------------------4668---------64888--8987531 Q ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCH Q ss_conf 99999999999732998899999998187986746889998996678999999999999983296 Q gi|254780289|r 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHP 670 (682) Q Consensus 606 ~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~ 670 (682) ...++..|.++|..||+|.+.||.||| ..+.|=+||+..+|+|-==|+=-=.+||.+||+- T Consensus 100 ~~~~r~~l~~AL~~LP~rQR~vvVLRY----~eDlSe~~~A~~LG~SvGTVKS~~sRal~~LR~~ 160 (165) T TIGR02983 100 DVALRAALARALRRLPARQRAVVVLRY----YEDLSEAEVAEVLGISVGTVKSRLSRALARLREL 160 (165) T ss_pred CHHHHHHHHHHHHHCCHHCCEEEEEEC----CCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHH T ss_conf 122699999999735641236723204----5789868999881999322899899999998873 No 130 >TIGR02233 Myxo_sigma_rel Myxococcus probable DNA-binding regulatory protein. Probab=96.50 E-value=0.0054 Score=42.61 Aligned_cols=59 Identities=20% Similarity=0.369 Sum_probs=47.2 Q ss_pred HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHH----HHHHHHHHH Q ss_conf 999999999999997329988999999981879867468899989966789999----999999999 Q gi|254780289|r 603 SAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI----RQIEAKAIR 665 (682) Q Consensus 603 ~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~----rqi~~~a~~ 665 (682) .-.+..+++++..++++|+|||+.|||+.| =...||+-||..||+.|-=| -+....++. T Consensus 8 ~~~R~~~~~al~~Ala~L~~~eR~lLRLH~----~~gLsldR~~~lY~~hrStvaR~v~~are~Ll~ 70 (106) T TIGR02233 8 EEARQHLSAALSEALAALSERERTLLRLHH----VEGLSLDRLGTLYGVHRSTVARWVAGARELLLE 70 (106) T ss_pred HHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHH T ss_conf 999999999999997528963335666776----236558999988478861699999999999999 No 131 >PRK08215 sporulation sigma factor SigG; Reviewed Probab=96.34 E-value=0.0055 Score=42.53 Aligned_cols=62 Identities=18% Similarity=0.191 Sum_probs=41.0 Q ss_pred HCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHC--CHHHHHH-------HHHHHHHHCCCHHHHHHHHHHH Q ss_conf 569768897889999999998899999998728--2389999-------9999873117103678764210 Q gi|254780289|r 128 MGSIELLSREGEIAIAKRIEAGRAMMMASLCES--PLTFQAL-------IIWRDELNDGTTLLREIIDLEA 189 (682) Q Consensus 128 MG~V~LLTREgEIeIAKRIE~G~~~i~~al~~~--P~ti~~i-------l~~~e~i~~ge~~LrdIIDld~ 189 (682) ..+.||||+|+|+++|+|+.+|.......|..+ ++++... +.+-|.+++|.+.|-.-++.|. T Consensus 13 ~~k~PlLt~EEe~~L~~~~~~gD~~Ar~~LI~~nLrLV~~iA~ky~~~g~~~~DLiQeG~iGLi~AiekFD 83 (257) T PRK08215 13 TSKLPVLKNEEMKELFRRMQNGDTSAREKLINGNLRLVLSVIQRFNNRGEYVDDLFQVGCIGLMKAIDNFD 83 (257) T ss_pred CCCCCCCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHC T ss_conf 22489999999999999999388999999999878999999987658998988999987999999999709 No 132 >pfam00196 GerE Bacterial regulatory proteins, luxR family. Probab=95.94 E-value=0.028 Score=36.96 Aligned_cols=56 Identities=29% Similarity=0.474 Sum_probs=49.2 Q ss_pred HHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHHHH Q ss_conf 7329988999999981879867468899989966789999999999999832967778756 Q gi|254780289|r 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677 (682) Q Consensus 617 l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~~~~~l~ 677 (682) |++|+|||.+|+++-. ..+|-.|||..+|||.--|+..-..+++||.-.+|....+ T Consensus 1 l~~LT~RE~~il~~l~-----~G~s~~eIA~~L~is~~TV~~h~~~i~~Kl~v~nr~elv~ 56 (58) T pfam00196 1 LDSLSPREREVLRLLA-----AGKSNKEIADILGISEKTVKVHRSNIMRKLNVHSRVELIR 56 (58) T ss_pred CCCCCHHHHHHHHHHH-----HCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHH T ss_conf 9977999999999998-----0799999999978889999999999999809999999995 No 133 >PRK10360 DNA-binding transcriptional activator UhpA; Provisional Probab=95.84 E-value=0.045 Score=35.35 Aligned_cols=60 Identities=20% Similarity=0.312 Sum_probs=54.1 Q ss_pred HCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHCC Q ss_conf 32998899999998187986746889998996678999999999999983296777875665179 Q gi|254780289|r 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682 (682) Q Consensus 618 ~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~~~~~l~~~~~~ 682 (682) ..|+|||++||++= ...+|-.|||..+++|---|+-.-...++||.-.+|....|--.|| T Consensus 136 ~~LT~RE~eVL~li-----a~G~snkeIA~~L~IS~~TVk~h~~~i~~KL~v~~r~el~r~a~~~ 195 (196) T PRK10360 136 DPLTKRERQVAEKL-----AQGMAVKEIAAELGLSPKTVHVHRANLMEKLGVSNDVELARRMFDG 195 (196) T ss_pred CCCCHHHHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHCC T ss_conf 89997999999999-----8799999999996999999999999999981999999999999706 No 134 >PRK08583 RNA polymerase sigma factor SigB; Validated Probab=95.84 E-value=0.0099 Score=40.52 Aligned_cols=62 Identities=15% Similarity=0.081 Sum_probs=40.3 Q ss_pred HHHHCCCCCCCHHHHHHHHHHHHH-HHHHHHHHHHHC--CHHHHHHHHH-------HHHHHCCCHHHHHHHH Q ss_conf 998569768897889999999998-899999998728--2389999999-------9873117103678764 Q gi|254780289|r 125 LREMGSIELLSREGEIAIAKRIEA-GRAMMMASLCES--PLTFQALIIW-------RDELNDGTTLLREIID 186 (682) Q Consensus 125 LREMG~V~LLTREgEIeIAKRIE~-G~~~i~~al~~~--P~ti~~il~~-------~e~i~~ge~~LrdIID 186 (682) |+|++++|+||+|+|.+++++.-. |.......|..+ |+++.....+ -|.+++|.+.|-.-++ T Consensus 1 ~~~~~~~~~Lt~eee~~L~~~~~~~gd~~Ar~~Li~~nlrLV~~iA~~y~~~g~~~~DLiQeG~iGLi~Aie 72 (257) T PRK08583 1 MKESSQPTKLTKEDVNQWIAEYQENQDEEAQEKLVKHYKNLVESLAYKYSKGQSHHEDLVQVGMVGLLGAIR 72 (257) T ss_pred CCCCCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHH T ss_conf 986768999999999999999988199999999999849999999998626898861799999999999987 No 135 >PRK03975 tfx putative transcriptional regulator; Provisional Probab=95.77 E-value=0.029 Score=36.78 Aligned_cols=46 Identities=30% Similarity=0.423 Sum_probs=42.4 Q ss_pred CCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC Q ss_conf 299889999999818798674688999899667899999999999998329 Q gi|254780289|r 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669 (682) Q Consensus 619 ~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~ 669 (682) -|+.|...||++| ...+|..||+..+|.||--|--||.+|+.+++. T Consensus 4 ~Lt~~q~~vL~lR-----~~G~tQ~eIA~~lgTSraNvs~iEk~A~eNIek 49 (139) T PRK03975 4 FLTERQIEVLRLR-----KRGLTQQEIADILGTSRANISIIEKRARENIEK 49 (139) T ss_pred HHHHHHHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH T ss_conf 5689999999999-----828979999999773288999999999999999 No 136 >TIGR02392 rpoH_proteo alternative sigma factor RpoH; InterPro: IPR012759 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This entry represents the proteobacterial clade of sigma factors called RpoH. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0008270 zinc ion binding, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent, 0009408 response to heat. Probab=95.67 E-value=0.11 Score=32.20 Aligned_cols=68 Identities=21% Similarity=0.315 Sum_probs=47.9 Q ss_pred HHHHHHHHCCCCCCCHHHHHHHHHHH------HHHHHHHHHHHHHC-CHHHHHH---HHHHHHHHCCCHHHHHHHHHH Q ss_conf 99999985697688978899999999------98899999998728-2389999---999987311710367876421 Q gi|254780289|r 121 VRMYLREMGSIELLSREGEIAIAKRI------EAGRAMMMASLCES-PLTFQAL---IIWRDELNDGTTLLREIIDLE 188 (682) Q Consensus 121 VRMYLREMG~V~LLTREgEIeIAKRI------E~G~~~i~~al~~~-P~ti~~i---l~~~e~i~~ge~~LrdIIDld 188 (682) .--|++.+-..|+||.|+|-.+|+|- +|+++.|++=|=.. .++..|- |...|.|++|++.|=--|.-| T Consensus 3 L~~Yi~~vn~~P~L~~EEE~~LA~r~r~~~Dl~AA~~Lv~SHLRfVv~iArgY~GYGL~~aDLIQEGNIGLMkAVkRF 80 (279) T TIGR02392 3 LDAYIRAVNRIPMLTAEEEQELAKRLREEGDLDAAKKLVLSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRF 80 (279) T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHC T ss_conf 788999997178999889999999865423778999874662478755320367777442443422226655334421 No 137 >PRK00118 putative DNA-binding protein; Validated Probab=95.58 E-value=0.04 Score=35.72 Aligned_cols=47 Identities=19% Similarity=0.359 Sum_probs=42.3 Q ss_pred CCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC Q ss_conf 299889999999818798674688999899667899999999999998329 Q gi|254780289|r 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669 (682) Q Consensus 619 ~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~ 669 (682) -|+++.+.++.+.| ..+.+|.|||..+||||.-|...=.+|...|.. T Consensus 17 LLT~kQ~~~~~lyy----~~DlSl~EIAe~~~iSRQaV~D~ikr~~~~L~~ 63 (105) T PRK00118 17 LLTEKQRNYMELYY----LDDYSLGEIAEEFNVSRQAVYDNIKRTEKLLED 63 (105) T ss_pred HCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH T ss_conf 75599999999998----854999999899698599999999999999999 No 138 >PRK10188 DNA-binding transcriptional activator SdiA; Provisional Probab=95.47 E-value=0.06 Score=34.33 Aligned_cols=52 Identities=13% Similarity=0.340 Sum_probs=46.9 Q ss_pred CCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHH Q ss_conf 299889999999818798674688999899667899999999999998329677787 Q gi|254780289|r 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675 (682) Q Consensus 619 ~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~~~~~ 675 (682) .|++||++||++= ....|-.|||..+|||..-|..-=..|.+||.-++|... T Consensus 179 ~LT~RE~E~L~W~-----A~GKTs~EIa~IL~ISe~TV~fHl~na~~KL~a~Nr~qA 230 (240) T PRK10188 179 NFSKREKEILKWT-----AEGKTSAEIAMILSISENTVNFHQKNMQKKFNAPNKTQI 230 (240) T ss_pred CCCHHHHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHH T ss_conf 8998999999999-----779999999988399999999999999999589989999 No 139 >smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon Probab=95.45 E-value=0.055 Score=34.66 Aligned_cols=56 Identities=34% Similarity=0.520 Sum_probs=48.9 Q ss_pred HHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHHHH Q ss_conf 7329988999999981879867468899989966789999999999999832967778756 Q gi|254780289|r 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677 (682) Q Consensus 617 l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~~~~~l~ 677 (682) ++.|+|||.+|+.+- ...+|-.+|+..+|+|..-|+..-.++++||.-.+|....+ T Consensus 1 l~~LT~rE~~il~~l-----~~G~s~~eIA~~L~is~~TV~~~~~~i~~Kl~v~~r~elv~ 56 (58) T smart00421 1 LASLTPREREVLRLL-----AEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVR 56 (58) T ss_pred CCCCCHHHHHHHHHH-----HHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHH T ss_conf 976189999999999-----81799999998989789899999999999848999999995 No 140 >PRK09958 DNA-binding transcriptional activator EvgA; Provisional Probab=95.44 E-value=0.065 Score=34.06 Aligned_cols=56 Identities=16% Similarity=0.268 Sum_probs=48.9 Q ss_pred HHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHHHH Q ss_conf 7329988999999981879867468899989966789999999999999832967778756 Q gi|254780289|r 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677 (682) Q Consensus 617 l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~~~~~l~ 677 (682) +..|+|||++||++= ...+|-.|||+.+++|..-|+..-...++||.-.+|..... T Consensus 141 ~~~Lt~RE~eVL~ll-----~~G~snkeIA~~L~iS~~TV~~h~~~i~~KL~v~~r~el~~ 196 (204) T PRK09958 141 LDSLSKQEISVMRYI-----LDGKDNNDIAEKMFISNKTVSTYKSRLMEKLECKSLMDLYT 196 (204) T ss_pred CCCCCHHHHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHH T ss_conf 256899999999999-----86999999998978899999999999999848999999999 No 141 >pfam04297 UPF0122 Putative helix-turn-helix protein, YlxM / p13 like. Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13. Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway. Probab=95.20 E-value=0.063 Score=34.18 Aligned_cols=47 Identities=19% Similarity=0.368 Sum_probs=41.7 Q ss_pred CCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC Q ss_conf 299889999999818798674688999899667899999999999998329 Q gi|254780289|r 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669 (682) Q Consensus 619 ~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~ 669 (682) -||++.+.++.+.| ..+.+|.|||..+||||.-|...=.+|-..|.. T Consensus 17 LLT~KQ~~~~~lyy----~eDlSL~EIAe~~~iSRQaV~D~ikR~~~~L~~ 63 (101) T pfam04297 17 LLTDKQKNYFELYY----LDDLSLSEIAEEFNVSRQAVYDNIKRTEKMLES 63 (101) T ss_pred HCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH T ss_conf 76599999999998----763989999988198599999999999999999 No 142 >PRK10403 transcriptional regulator NarP; Provisional Probab=95.14 E-value=0.1 Score=32.54 Aligned_cols=58 Identities=22% Similarity=0.258 Sum_probs=50.8 Q ss_pred HCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHH Q ss_conf 329988999999981879867468899989966789999999999999832967778756651 Q gi|254780289|r 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680 (682) Q Consensus 618 ~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~~~~~l~~~~ 680 (682) ..|++||.+||++- ...+|-.|||..+++|..-|+-.-...++||.-.+|....--|+ T Consensus 152 ~~LT~RE~eVL~ll-----a~G~snkeIA~~L~iS~~TV~~h~~~I~~KLgv~nR~ea~~~~~ 209 (215) T PRK10403 152 SVLTERELDVLHEL-----AQGLSNKQIASVLNISEQTVKVHIRNLLRKLNVRSRVAATILFL 209 (215) T ss_pred CCCCHHHHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHH T ss_conf 56899999999999-----86999999999979829999999999999868998999999999 No 143 >PRK09390 fixJ response regulator FixJ; Provisional Probab=94.98 E-value=0.19 Score=30.47 Aligned_cols=59 Identities=19% Similarity=0.253 Sum_probs=49.9 Q ss_pred HHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHHHH Q ss_conf 9997329988999999981879867468899989966789999999999999832967778756 Q gi|254780289|r 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677 (682) Q Consensus 614 ~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~~~~~l~ 677 (682) ..-+..|+|||++||++= ...+|-.|||..+++|.--|.-.-..-++||.-.+|....+ T Consensus 136 ~~~~~~LT~RE~eVL~ll-----~~G~snkeIA~~L~iS~~TV~~h~~~I~~KL~v~~~~elv~ 194 (202) T PRK09390 136 RARIASLSERERQVMDGL-----VAGLSNKVIARDLDISPRTVEVYRANVMTKMQAGSLSELVR 194 (202) T ss_pred HHHHCCCCHHHHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHH T ss_conf 740066998999999999-----83896899999979878899999999999968898899999 No 144 >PRK09483 response regulator; Provisional Probab=94.97 E-value=0.11 Score=32.30 Aligned_cols=55 Identities=18% Similarity=0.299 Sum_probs=48.7 Q ss_pred HCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHHHH Q ss_conf 329988999999981879867468899989966789999999999999832967778756 Q gi|254780289|r 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677 (682) Q Consensus 618 ~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~~~~~l~ 677 (682) ..|+|||++|+++- ...+|-.||+..+++|.--|+-.-...++||.-.+|....+ T Consensus 147 ~~LT~RE~eVl~ll-----~~G~snkeIA~~L~iS~~TV~~h~~~i~~KL~v~~r~el~~ 201 (216) T PRK09483 147 ASLSERELQIMLMI-----TKGQKVNEISEQLNLSPKTVNSYRYRMFSKLNISGDVELTH 201 (216) T ss_pred CCCCHHHHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHH T ss_conf 56899999999999-----87999999999969899999999999999809999999999 No 145 >PRK10840 transcriptional regulator RcsB; Provisional Probab=94.93 E-value=0.12 Score=32.05 Aligned_cols=54 Identities=24% Similarity=0.323 Sum_probs=47.7 Q ss_pred CCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHHHH Q ss_conf 29988999999981879867468899989966789999999999999832967778756 Q gi|254780289|r 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677 (682) Q Consensus 619 ~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~~~~~l~ 677 (682) .|+|||.+||++= ...+|-.|||..+++|.--|+-.-...++||.-.+|....+ T Consensus 150 ~LT~RE~eVL~ll-----a~G~snkeIA~~L~iS~~TV~~h~~~i~~KLgv~n~~eLv~ 203 (216) T PRK10840 150 RLSPKESEVLRLF-----AEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVENDIALLN 203 (216) T ss_pred CCCHHHHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHH T ss_conf 9998999999999-----86999999998969899999999999999829998999999 No 146 >PRK05572 sporulation sigma factor SigF; Validated Probab=94.89 E-value=0.031 Score=36.61 Aligned_cols=59 Identities=20% Similarity=0.159 Sum_probs=39.3 Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHC--CHHHHHHH-------HHHHHHHCCCHHHHHHHHHH Q ss_conf 9768897889999999998899999998728--23899999-------99987311710367876421 Q gi|254780289|r 130 SIELLSREGEIAIAKRIEAGRAMMMASLCES--PLTFQALI-------IWRDELNDGTTLLREIIDLE 188 (682) Q Consensus 130 ~V~LLTREgEIeIAKRIE~G~~~i~~al~~~--P~ti~~il-------~~~e~i~~ge~~LrdIIDld 188 (682) .-|+||+|+|.++|+++.+|.......|..+ ++++...- .+-|.+++|.+.|-.-++.| T Consensus 8 ~~~~Ls~eee~~L~~~~~~Gd~~Ar~~Li~~nlrLV~siA~ry~~~g~~~~DLiQeG~iGLi~A~ekF 75 (251) T PRK05572 8 KKEQLKDEENKELIKKAQDGDKEARDKLVEKNLRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKF 75 (251) T ss_pred CCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCC T ss_conf 68999999999999999807999999999985999999998775899998899999999999996225 No 147 >COG3413 Predicted DNA binding protein [General function prediction only] Probab=94.82 E-value=0.11 Score=32.13 Aligned_cols=51 Identities=25% Similarity=0.449 Sum_probs=41.7 Q ss_pred HCCCHHHHHHHHHHHCCC---CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC Q ss_conf 329988999999981879---867468899989966789999999999999832 Q gi|254780289|r 618 ASLTPREERVLRMRFGIG---MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668 (682) Q Consensus 618 ~~l~~re~~v~~~r~g~~---~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~ 668 (682) ..|+|||.+||+.=|-.| ..+..||.++++.||||+-=+-|.=.+|.+||= T Consensus 154 ~~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLRrAe~Kl~ 207 (215) T COG3413 154 NDLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLRRAERKLI 207 (215) T ss_pred CCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 469999999999999858988876589999999959988899999999999999 No 148 >PRK05949 RNA polymerase sigma factor; Validated Probab=94.69 E-value=0.41 Score=27.78 Aligned_cols=39 Identities=36% Similarity=0.525 Sum_probs=35.0 Q ss_pred CCCCCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHH Q ss_conf 345777728999999856976889788999999999889 Q gi|254780289|r 112 SADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150 (682) Q Consensus 112 ~e~~rtdDPVRMYLREMG~V~LLTREgEIeIAKRIE~G~ 150 (682) .....|.|||++||+|||.+||||+|+||.+|++|..+. T Consensus 11 ~~~~~~~D~~~~YL~ei~~~pLLt~eeE~~La~~iq~~~ 49 (327) T PRK05949 11 TQPTFTADMVRTYLHEIGRVPLLTHEQEIVYGKQVQQMM 49 (327) T ss_pred CCCCCCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHH T ss_conf 999899881999999827866889999999999999999 No 149 >cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental Probab=94.61 E-value=0.15 Score=31.10 Aligned_cols=53 Identities=28% Similarity=0.433 Sum_probs=47.0 Q ss_pred CCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHHHH Q ss_conf 9988999999981879867468899989966789999999999999832967778756 Q gi|254780289|r 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677 (682) Q Consensus 620 l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~~~~~l~ 677 (682) |+|||.+||.+- ...+|-.||++.+|+|..-|+-.-..+++||.-.+|..... T Consensus 1 LT~rE~~il~~~-----~~G~s~~eIA~~L~is~~TV~~~~~~i~~Kl~~~~r~elv~ 53 (57) T cd06170 1 LTPREREVLRLL-----AEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVA 53 (57) T ss_pred CCHHHHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHH T ss_conf 988999999999-----80799999999989789999999999999868999999999 No 150 >PRK07406 RNA polymerase sigma factor RpoD; Validated Probab=94.53 E-value=0.44 Score=27.51 Aligned_cols=38 Identities=37% Similarity=0.613 Sum_probs=34.5 Q ss_pred CCCCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHH Q ss_conf 45777728999999856976889788999999999889 Q gi|254780289|r 113 ADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGR 150 (682) Q Consensus 113 e~~rtdDPVRMYLREMG~V~LLTREgEIeIAKRIE~G~ 150 (682) ....|+|||||||||+|+|||||.++||++||+|+.|. T Consensus 69 ~~~~t~D~vr~YL~eIg~~~LLt~~eEi~La~~i~~~~ 106 (385) T PRK07406 69 KGVYTEDSIRVYLQEIGRIRLLRPDEEIELARKIADLL 106 (385) T ss_pred CCCCCCCCHHHHHHHCCCCCCCCHHHHHHHHHHHHHHH T ss_conf 66888884999998627767999999999999999999 No 151 >PRK11475 DNA-binding transcriptional activator BglJ; Provisional Probab=94.31 E-value=0.19 Score=30.32 Aligned_cols=52 Identities=21% Similarity=0.309 Sum_probs=45.2 Q ss_pred CCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHH Q ss_conf 299889999999818798674688999899667899999999999998329677787 Q gi|254780289|r 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675 (682) Q Consensus 619 ~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~~~~~ 675 (682) .|+|||++||++- ...+|..||+.++++|-.-|.--...+++||--.+...- T Consensus 134 ~Lt~rE~eVl~l~-----a~G~s~~eIA~~L~~S~kTv~thr~~~m~KLgv~s~a~L 185 (205) T PRK11475 134 MLSPTEREILRFM-----SRGYSMPQIAEQLERNIKTIRAHKFNVMSKLGVSSDAGL 185 (205) T ss_pred CCCHHHHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHH T ss_conf 8985899999999-----769999999999788888999999999998299987999 No 152 >TIGR03020 EpsA transcriptional regulator EpsA. Proteins in this family include a C-terminal LuxR transcriptional regulator domain (pfam00196). These proteins are positioned proximal to either EpsH-containing exopolysaccharide biosynthesis operons of the Methylobacillus type, or the associated PEP-CTERM-containing genes. Probab=94.19 E-value=0.51 Score=27.00 Aligned_cols=85 Identities=16% Similarity=0.201 Sum_probs=61.3 Q ss_pred EEEEEECCCCCCCHHHHHHHHHH----HHHHHH-----------------HHHCCCHHHHHHHHHHHCCCCCCCCCHHHH Q ss_conf 04756238988998999999999----999999-----------------973299889999999818798674688999 Q gi|254780289|r 587 HLGDFIEDKNAVSPLDSAIQANL----RETTTR-----------------VLASLTPREERVLRMRFGIGMNTDHTLEEV 645 (682) Q Consensus 587 ~~~~~~~d~~~~~~~~~~~~~~~----~~~~~~-----------------~l~~l~~re~~v~~~r~g~~~~~~~tl~e~ 645 (682) ++--|..-....+|-....-..| ..++.+ .++.|+|||.+||++= ....|-.|| T Consensus 137 cl~~f~~~~~~~~~~~~~~LelL~P~Lh~AL~rv~~l~~q~~~~~~~~~~~~glLT~RE~EVL~~v-----a~G~sn~eI 211 (247) T TIGR03020 137 CLYSFSRSSVPLDARHAYFLELLLPYLDSALRRVLFLPNQHRTRPLGERHSAGLITAREAEILAWV-----RDGKTNEEI 211 (247) T ss_pred EEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHH-----HCCCCHHHH T ss_conf 599997158899877999999768899999998631643354555556776789998999999999-----879999999 Q ss_pred HHHHCCCHHHHHHHHHHHHHHHCCHHHHHHH Q ss_conf 8996678999999999999983296777875 Q gi|254780289|r 646 GKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676 (682) Q Consensus 646 ~~~~~~~~er~rqi~~~a~~~l~~~~~~~~l 676 (682) |..++||..-|+.--..+++||.-.+|.... T Consensus 212 A~~L~iS~~TVk~H~~~i~~KL~v~nR~qAV 242 (247) T TIGR03020 212 AAILGISSLTVKNHLQHIFKKLDVRNRAQAV 242 (247) T ss_pred HHHHCCCHHHHHHHHHHHHHHCCCCCHHHHH T ss_conf 9994979999999999999980999899999 No 153 >COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription] Probab=94.19 E-value=0.25 Score=29.49 Aligned_cols=58 Identities=26% Similarity=0.373 Sum_probs=49.8 Q ss_pred HCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHH Q ss_conf 329988999999981879867468899989966789999999999999832967778756651 Q gi|254780289|r 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680 (682) Q Consensus 618 ~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~~~~~l~~~~ 680 (682) ..|++||..|+++-- .| +|..||+..+++|..-|+..-..+.+||...+|...+.-+. T Consensus 3 ~~Lt~rE~~~~~l~~---~G--~s~~eia~~l~is~~tV~~h~~~i~~Kl~~~~r~~~~~~~~ 60 (65) T COG2771 3 ADLTPREREILRLVA---QG--KSNKEIARILGISEETVKTHLRNIYRKLGVKNRVELVALAL 60 (65) T ss_pred CCCCHHHHHHHHHHH---CC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHH T ss_conf 113888999999998---69--98999999987799999999999999977586999999999 No 154 >PRK10651 transcriptional regulator NarL; Provisional Probab=94.18 E-value=0.2 Score=30.29 Aligned_cols=54 Identities=20% Similarity=0.361 Sum_probs=47.7 Q ss_pred HCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHHH Q ss_conf 32998899999998187986746889998996678999999999999983296777875 Q gi|254780289|r 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKL 676 (682) Q Consensus 618 ~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~~~~~l 676 (682) ..|+|||.+||++- ...+|-.|||..+++|-.-|+-.-...++||.-.+|.... T Consensus 154 ~~LT~RE~eVL~ll-----~~G~snkeIA~~L~iS~~TV~~h~~~i~~KLgv~nr~ea~ 207 (216) T PRK10651 154 NQLTPRERDILKLI-----AQGLSNKMIARRLDITESTVKVHVKHMLKKMKLKSRVEAA 207 (216) T ss_pred CCCCHHHHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHH T ss_conf 34898999999999-----8599999999996978999999999999984899999999 No 155 >TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE; InterPro: IPR014286 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This entry represents the clade of sigma factors called RpoE. These proteins are variously annotated as sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent. Probab=94.17 E-value=0.52 Score=26.96 Aligned_cols=159 Identities=19% Similarity=0.276 Sum_probs=120.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHH Q ss_conf 99999876533211246899987555789998875223567778875443679999887438545731201028989999 Q gi|254780289|r 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507 (682) Q Consensus 428 K~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~ 507 (682) ..+++++++|+. +|-+=||.=-=+=|+++.-+|....-...|.-||.=|-=-+|+..|=-. |.|=||--|=| T Consensus 9 ~~Lv~RVQrG~k---~AF~lLV~KYQ~kv~~Lv~Ryv~~~~e~~DVAQe~FvkAYRAl~~FRGd-----saFYTWLyRIa 80 (192) T TIGR02939 9 LELVERVQRGEK---QAFDLLVRKYQHKVVSLVGRYVRDSEEVEDVAQEAFVKAYRALASFRGD-----SAFYTWLYRIA 80 (192) T ss_pred HHHHHHHHCCCH---HHHHHHHHHHHHHHHHHHHHHHCCHHCCCCHHHHHHHHHHHHHCCCCCC-----HHHHHHHHHHH T ss_conf 899888733223---5677788999999999998761481003401477899999751235551-----36789999999 Q ss_pred HHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHH-HHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCC Q ss_conf 99999722870461420588989999999998776088999789-99870999899999998608987553635889986 Q gi|254780289|r 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE-IAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTS 586 (682) Q Consensus 508 i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~ 586 (682) |. +++.++-..||.|.... + | ..+-+.. T Consensus 81 vN-------------------------TAKNyLVaq~Rr~p~~dg~------------------------~--~edAE~F 109 (192) T TIGR02939 81 VN-------------------------TAKNYLVAQGRRPPTSDGV------------------------E--AEDAEQF 109 (192) T ss_pred HH-------------------------HHHHHHHHCCCCCCCCCCC------------------------C--CHHHHCC T ss_conf 98-------------------------8777664247988744567------------------------6--0433120 Q ss_pred EEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCC Q ss_conf 04756238988998999999999999999973299889999999818798674688999899667 Q gi|254780289|r 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651 (682) Q Consensus 587 ~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~ 651 (682) .-+|-+- +..+|+..++...|...+..+|..||+-=+.=|.||= -...++|||++.|+- T Consensus 110 ~~a~~Lr--~~~tPE~~ll~~el~~~v~~a~~aLPE~Lr~Ai~LRE----leGLSYe~IA~~MdC 168 (192) T TIGR02939 110 EEADALR--DIDTPERLLLSRELEQTVNKALEALPEDLRTAITLRE----LEGLSYEDIAEIMDC 168 (192) T ss_pred CCCCCCC--CCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH----CCCCCHHHHHHHCCC T ss_conf 0267665--5666167999999999999998617267874544651----268787888733069 No 156 >PRK13870 transcriptional regulator TraR; Provisional Probab=94.10 E-value=0.53 Score=26.86 Aligned_cols=51 Identities=24% Similarity=0.318 Sum_probs=45.7 Q ss_pred CCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHH Q ss_conf 99889999999818798674688999899667899999999999998329677787 Q gi|254780289|r 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675 (682) Q Consensus 620 l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~~~~~ 675 (682) |+|||+++|+.= ....|-.|||..+|||..-|+-.=..|.+||.-.+|... T Consensus 174 LT~RE~E~L~W~-----A~GKT~~EIA~ILgISe~TV~fHl~na~~KL~a~nr~qA 224 (234) T PRK13870 174 LDPKEATYLRWI-----AVGMTMEEIADVEGVKYNSVRVKLREAMKRFDVRSKAHL 224 (234) T ss_pred CCHHHHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHH T ss_conf 997999999999-----789989999999798899999999999999589989999 No 157 >PRK09935 transcriptional regulator FimZ; Provisional Probab=94.03 E-value=0.24 Score=29.53 Aligned_cols=54 Identities=22% Similarity=0.253 Sum_probs=47.6 Q ss_pred CCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHHHH Q ss_conf 29988999999981879867468899989966789999999999999832967778756 Q gi|254780289|r 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677 (682) Q Consensus 619 ~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~~~~~l~ 677 (682) .|+|||.+|+++- ...+|-.|||..+++|.--|+-.-...++||.-.+|....+ T Consensus 149 ~Lt~RE~eVL~ll-----~~G~snkeIA~~L~iS~~TV~~h~~~I~~KL~v~nr~elv~ 202 (210) T PRK09935 149 PLSNREVTVLRYL-----ANGLSNKEIAEQLLLSNKTISAHKSNIYGKLGLHSIVELID 202 (210) T ss_pred CCCHHHHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHH T ss_conf 9998999999999-----86999999998949889999999999999819999999999 No 158 >PRK07405 RNA polymerase sigma factor SigD; Validated Probab=93.96 E-value=0.47 Score=27.29 Aligned_cols=37 Identities=41% Similarity=0.636 Sum_probs=33.6 Q ss_pred CCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHH Q ss_conf 7777289999998569768897889999999998899 Q gi|254780289|r 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRA 151 (682) Q Consensus 115 ~rtdDPVRMYLREMG~V~LLTREgEIeIAKRIE~G~~ 151 (682) ..++|||++||+|+|.+||||+|+|+.+|++|+.|.. T Consensus 5 ~~~~d~~~~Yl~ei~~~~LLt~eeE~~la~~i~~~~~ 41 (318) T PRK07405 5 KTATDLVRTYLREIGRVPLLTHEEEILYGKQVQRLMA 41 (318) T ss_pred CCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHH T ss_conf 7898759999998177679999999999999999988 No 159 >TIGR03541 reg_near_HchA LuxR family transcriptional regulatory, chaperone HchA-associated. Members of this protein family belong to the LuxR transcriptional regulator family, and contain both autoinducer binding (pfam03472) and transcriptional regulator (pfam00196) domains. Members, however, occur only in a few members of the Gammaproteobacteria that have the chaperone/aminopeptidase HchA, and are always encoded by the adjacent gene. Probab=93.90 E-value=0.58 Score=26.59 Aligned_cols=53 Identities=17% Similarity=0.235 Sum_probs=46.7 Q ss_pred HCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHH Q ss_conf 3299889999999818798674688999899667899999999999998329677787 Q gi|254780289|r 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKK 675 (682) Q Consensus 618 ~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~~~~~ 675 (682) ..|+|||++||++= ...+|--|||..+|||..-|+..=..|.+||.-.+|... T Consensus 170 ~~LT~RE~E~L~w~-----A~Gkt~~eIa~iL~iSe~TV~~hl~~a~~KLga~nr~qA 222 (232) T TIGR03541 170 GVLSEREREVLAWT-----ALGRRQADIAAILGISERTVENHLRSARRKLGVATTAQA 222 (232) T ss_pred CCCCHHHHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHH T ss_conf 99898999999999-----879999999999698999999999999998489999999 No 160 >pfam04967 HTH_10 HTH DNA binding domain. Probab=93.67 E-value=0.28 Score=29.05 Aligned_cols=48 Identities=25% Similarity=0.484 Sum_probs=37.0 Q ss_pred CCHHHHHHHHHHHCCC---CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH Q ss_conf 9988999999981879---86746889998996678999999999999983 Q gi|254780289|r 620 LTPREERVLRMRFGIG---MNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667 (682) Q Consensus 620 l~~re~~v~~~r~g~~---~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l 667 (682) |++|+++||..=|-.| ..+..|+.||+..||||+--+-..=.+|.+|+ T Consensus 1 LT~rQ~evl~~A~~~GYfd~PR~~~l~elA~~lgis~sT~~~hLr~ae~ki 51 (53) T pfam04967 1 LTDRQREILRLAYKMGYFDYPRRVTLKDLAKELGISKSTLSEHLRRAESKL 51 (53) T ss_pred CCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH T ss_conf 988999999999986897788768899999996989999999999999987 No 161 >COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription] Probab=93.04 E-value=0.46 Score=27.34 Aligned_cols=56 Identities=23% Similarity=0.363 Sum_probs=48.8 Q ss_pred HCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHHHHH Q ss_conf 3299889999999818798674688999899667899999999999998329677787566 Q gi|254780289|r 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRS 678 (682) Q Consensus 618 ~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~~~~~l~~ 678 (682) ..|+|||..|+++- ...+|-.|||.++++|---|+-.-...++||.-.+|.....- T Consensus 147 ~~LT~RE~eVl~ll-----a~G~snkeIA~~L~iS~~TVk~h~~~i~~KL~v~~Rtea~~~ 202 (211) T COG2197 147 ELLTPRELEVLRLL-----AEGLSNKEIAEELNLSEKTVKTHVSNILRKLGVRNRTEAAIR 202 (211) T ss_pred CCCCHHHHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHH T ss_conf 78998999999999-----879988999999787898999999999998399989999999 No 162 >COG4566 TtrR Response regulator [Signal transduction mechanisms] Probab=92.92 E-value=0.8 Score=25.46 Aligned_cols=68 Identities=21% Similarity=0.304 Sum_probs=54.0 Q ss_pred HHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHH Q ss_conf 9999999997329988999999981879867468899989966789999999999999832967778756651 Q gi|254780289|r 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680 (682) Q Consensus 608 ~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~~~~~l~~~~ 680 (682) .....+...|++|+|||++|+..=- ..++=-+|+..+|+|---|--..+..++|++.-+-+..++-++ T Consensus 131 ~~~~~~~~~l~tLT~RERqVl~~vV-----~G~~NKqIA~dLgiS~rTVe~HRanvM~Km~a~SlaeLvr~a~ 198 (202) T COG4566 131 DRQAAIRARLATLTPRERQVLDLVV-----RGLMNKQIAFDLGISERTVELHRANVMEKMQARSLAELVRMAL 198 (202) T ss_pred HHHHHHHHHHHHCCHHHHHHHHHHH-----CCCCCHHHHHHCCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHH T ss_conf 7899999999866988999999998-----3763089999839866459999999999973331999999998 No 163 >TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family. Probab=92.81 E-value=0.6 Score=26.42 Aligned_cols=29 Identities=45% Similarity=0.861 Sum_probs=28.5 Q ss_pred CHHHHHHHHHCCCCCCCHHHHHHHHHHHH Q ss_conf 28999999856976889788999999999 Q gi|254780289|r 119 DPVRMYLREMGSIELLSREGEIAIAKRIE 147 (682) Q Consensus 119 DPVRMYLREMG~V~LLTREgEIeIAKRIE 147 (682) |+||.||+|||.|||||.|+||++|++|- T Consensus 1 D~Vr~YL~eIGRvPLLt~eEEI~LArqVQ 29 (336) T TIGR02997 1 DLVRLYLQEIGRVPLLTPEEEIELARQVQ 29 (336) T ss_pred CCCHHHHHHCCCCCCCCHHHHHHHHHHHH T ss_conf 92004445056678987688999989999 No 164 >TIGR00721 tfx DNA-binding protein, Tfx family; InterPro: IPR004645 This is a family of Tfx DNA-binding proteins, which is restricted to the archaea. Homology among the members is strongest in the helix-turn-helix-containing N-terminal region. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.; GO: 0003677 DNA binding. Probab=92.74 E-value=0.2 Score=30.24 Aligned_cols=45 Identities=29% Similarity=0.473 Sum_probs=41.7 Q ss_pred CCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC Q ss_conf 99889999999818798674688999899667899999999999998329 Q gi|254780289|r 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669 (682) Q Consensus 620 l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~ 669 (682) |+++...||.|| ....+=+|||+.++-||.=|--||.+|+.+..- T Consensus 7 LTe~Q~kVL~lR-----~kGl~Q~eIAk~LkTtRaNvS~iEkrA~EnIeK 51 (142) T TIGR00721 7 LTERQIKVLELR-----EKGLKQKEIAKILKTTRANVSIIEKRALENIEK 51 (142) T ss_pred CHHHHHHHHHHH-----HCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHH T ss_conf 406568999986-----338887889877267201378988874432377 No 165 >TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; InterPro: IPR014331 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This entry of sigma factors are members of the sigma-70 family and are abundantly found in the species Rhodopirellula baltica, and Verrucomicrobium spinosum and to a lesser extent in Gemmata obscuriglobus.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent. Probab=92.42 E-value=0.92 Score=24.98 Aligned_cols=135 Identities=19% Similarity=0.252 Sum_probs=77.1 Q ss_pred CCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCC Q ss_conf 67778875443679999887438545731201028989999999997228704614205889899999999987760889 Q gi|254780289|r 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKRE 546 (682) Q Consensus 467 ~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~ 546 (682) --+-.|++||.++-++.-.+.|++..+| ..|.++ || .|++.. .....||. T Consensus 25 ~~dadDv~QEt~v~~~~k~~~f~~~~~F------~aWa~~-----iA---------------rn~vl~----~~r~~~R~ 74 (163) T TIGR02989 25 RDDADDVLQETFVTAWRKFDEFDPGTDF------GAWARG-----IA---------------RNKVLN----HRRKLGRD 74 (163) T ss_pred CCCHHHHHHHHHHHHHHHHHHHCCCCCC------HHHHHH-----HH---------------HHHHHH----HHHHCCCC T ss_conf 5658889999999998607751789897------678999-----99---------------999999----98730244 Q ss_pred CCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHH Q ss_conf 99789998709998999999986089875536358899860475623898899899999999999999997329988999 Q gi|254780289|r 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREER 626 (682) Q Consensus 547 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~ 626 (682) +.. +..--+++-..|.. .++.+.-.+. .+.-..+|..=|..||++.+. T Consensus 75 ~~~------l~~f~D~l~e~lA~-----~~~~~~~~~~---------------------~~~~~~AL~~C~~~L~~~~R~ 122 (163) T TIGR02989 75 RER------LVVFDDELLEALAA-----ELEEAEEADR---------------------SEDELQALEGCLEKLPERQRE 122 (163) T ss_pred CHH------HHHHHHHHHHHHHH-----HHHHHHCCCC---------------------CHHHHHHHHHHHHHCCHHHHH T ss_conf 127------77625999999999-----8755522788---------------------178999999878635978899 Q ss_pred HHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH Q ss_conf 99998187986746889998996678999999999999983 Q gi|254780289|r 627 VLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667 (682) Q Consensus 627 v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l 667 (682) +|.+||+= ..+++.|+.+.|.|-..|+|-=.+.-..| T Consensus 123 Ll~~rY~~----G~~~~~~A~~~g~~~~A~~~~L~R~R~~L 159 (163) T TIGR02989 123 LLQLRYQR----GVSLEALAEQLGRTVNAVYKALSRLRVRL 159 (163) T ss_pred HHHHHHCC----CCCHHHHHHHHCCHHHHHHHHHHHHHHHH T ss_conf 99998227----97878999884713899999999999997 No 166 >TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family; InterPro: IPR014296 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This family of RNA polymerase sigma factors is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors, as two proteins from this family are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these do not apparently represent the same two sigma factors in each species). One of these proteins is designated as SigM in B. subtilis (SP: SIGM_BACSU) and is activated by various stressors , .; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent. Probab=91.97 E-value=0.62 Score=26.32 Aligned_cols=77 Identities=18% Similarity=0.210 Sum_probs=59.6 Q ss_pred EEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH Q ss_conf 04756238988998999999999999999973299889999999818798674688999899667899999999999998 Q gi|254780289|r 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666 (682) Q Consensus 587 ~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~ 666 (682) .+|++--=++...|+.........+.+...|+.||+--|.||.||. -.+.+..||+..+|+|--.|--.==+|=+. T Consensus 81 ~~~~~~~l~~~~~pE~~~~~K~~~e~~~~~l~~Lpe~yr~vl~Lr~----~~efSYkEia~~~n~sl~~vK~~LfRaR~e 156 (162) T TIGR02950 81 LIGELELLDPVESPEHELLIKEELEELTKHLSSLPENYRTVLLLRE----FKEFSYKEIAELLNLSLAKVKSELFRARKE 156 (162) T ss_pred HHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHH T ss_conf 2000131276441089999999999999998527087656567543----126688899998456022100444487799 Q ss_pred H Q ss_conf 3 Q gi|254780289|r 667 L 667 (682) Q Consensus 667 l 667 (682) | T Consensus 157 L 157 (162) T TIGR02950 157 L 157 (162) T ss_pred H T ss_conf 9 No 167 >TIGR02895 spore_sigI RNA polymerase sigma-I factor; InterPro: IPR014244 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This entry represents the transcription factor Sigma-I. This protein is found in endospore-forming species in the Firmicutes lineage of bacteria, such as Bacillus subtilis, but is not universally present among such species. Sigma-I was shown to be induced by heat shock in B. subtilis and is suggested by its phylogenetic profile to be connected to the program of sporulation .; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent. Probab=91.22 E-value=0.69 Score=25.99 Aligned_cols=77 Identities=17% Similarity=0.236 Sum_probs=66.6 Q ss_pred HHH-HHHHHHHHHHHHHHHHHHHCCCCC--CHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCE Q ss_conf 246-899987555789998875223567--77887544367999988743854573120102898999999999722870 Q gi|254780289|r 442 SIA-KKEMVEANLRLVISVAKKYTNRGL--QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518 (682) Q Consensus 442 ~~A-K~~l~~anlr~v~~~~~~~~~~~~--~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~ 518 (682) ..+ +.+||+-.=.|.++++-+.|+|=+ .-.|=.+-|-+.+=-||++|++.+|-.|-.+|.--|+--+--++..+.++ T Consensus 8 ~~~l~e~LI~~Y~PFI~k~vs~~~~ryId~~~DDE~SIGL~AFnEAI~sY~~~KG~sFL~FA~l~IkRr~IDy~R~n~k~ 87 (225) T TIGR02895 8 NEELREELIRQYKPFIAKLVSSVCKRYIDTKEDDELSIGLIAFNEAIESYDLNKGKSFLSFAKLIIKRRVIDYIRKNQKY 87 (225) T ss_pred CHHHHHHHHHHHCHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 06899999885146899999998633068888832558899999899873143562169999998899988888741112 No 168 >TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family; InterPro: IPR014305 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This group of sigma factors appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution and represent a conserved family.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent. Probab=90.64 E-value=1.4 Score=23.64 Aligned_cols=155 Identities=23% Similarity=0.287 Sum_probs=92.7 Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHH-HHHHHHHHHC Q ss_conf 356777887544367999988743854573120102898999999999722870461420588989999-9999987760 Q gi|254780289|r 465 NRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV-RTARRMSNKI 543 (682) Q Consensus 465 ~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~-~~~~~~~~~~ 543 (682) |.-.+-.|||||--+===++-++||-+-|+| +|--|=|-.-|+ +-+. |..+...-+. T Consensus 27 GS~~eAeDlVQeTllrAW~~~~~FeGrSS~R-----~WLYrIATN~CL-----------------~~L~~R~~r~~~~~~ 84 (329) T TIGR02960 27 GSLHEAEDLVQETLLRAWRAREKFEGRSSLR-----AWLYRIATNACL-----------------DALKARRRRARPLEL 84 (329) T ss_pred CCCCCHHHHHHHHHHHHHHHCCCCCCCCCCC-----HHHHHHHHHHHH-----------------HHHHCCCCCCCCCCC T ss_conf 6521144678999999731003315776630-----678898999999-----------------987423224653347 Q ss_pred CCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHH-HHHHHHHHHHHHHCCCH Q ss_conf 88999789998709998999999986089875536358899860475623898899899999-99999999999732998 Q gi|254780289|r 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI-QANLRETTTRVLASLTP 622 (682) Q Consensus 544 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~~~-~~~~~~~~~~~l~~l~~ 622 (682) +-.|+++--|+ +....+.-=|+ |. -|..|-+ .++.+..|+..+. +++.+-+-.-+|.-||| T Consensus 85 ~~rp~~~~~Aa------------~~~~~e~~WLe-P~---Pd~~L~~--~~p~aa~P~~~~~~~EsvrLAF~AAlQ~LpP 146 (329) T TIGR02960 85 SARPSAEGRAA------------LSLAAEVTWLE-PL---PDVELDL--VLPAAADPEAAAVARESVRLAFVAALQLLPP 146 (329) T ss_pred CCCCCCCCCCC------------CCCCCCCCCCC-CC---CCCCCCC--CCCCCCCHHHHHHHHHHHHHHHHHHHHCCCC T ss_conf 78747887744------------20367887667-88---6021752--3688887112332114689999999874881 Q ss_pred HHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHH Q ss_conf 89999999818798674688999899667899999999999 Q gi|254780289|r 623 REERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663 (682) Q Consensus 623 re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a 663 (682) |.|.||.||=-+| ..=.||++-+|-|--=|.=.=.+| T Consensus 147 rQRAvL~LRdvlG----w~A~E~A~~L~~s~ASVnSaLQRA 183 (329) T TIGR02960 147 RQRAVLLLRDVLG----WKAAEVAELLGTSVASVNSALQRA 183 (329) T ss_pred HHHHHHHHHHHHC----CCHHHHHHHHCCCHHHHHHHHHHH T ss_conf 4578999898835----555689987438326786588887 No 169 >TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family; InterPro: IPR014300 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This group of sigma factors appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This entry is found in certain Bacillus and Clostridium species.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent. Probab=90.40 E-value=1.4 Score=23.49 Aligned_cols=162 Identities=19% Similarity=0.259 Sum_probs=110.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHH Q ss_conf 99876533211246899987555789998875223567778875443679999887438545731201028989999999 Q gi|254780289|r 431 VSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITR 510 (682) Q Consensus 431 ~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~ 510 (682) +++--+|. ..|=..||+.|==-...+|=.|++.--+-+|.|||...==-.+++|- +.-+| +-||-+|==|.. T Consensus 7 v~~a~~Gn---~~aF~~Li~~~ke~LYk~Af~Yvkne~DALd~i~EtvyKAY~sI~kL---k~~~Y--F~TW~trILIn~ 78 (173) T TIGR02954 7 VKKAIRGN---KEAFESLIKKNKEKLYKTAFIYVKNEHDALDVIQETVYKAYLSIEKL---KHPEY--FNTWLTRILINE 78 (173) T ss_pred HHHHHHCC---HHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHH---CCCCC--CHHHHHHHHHHH T ss_conf 99987249---34789999984366857665440673405899999999999989983---36100--025678999999 Q ss_pred HHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEE Q ss_conf 99722870461420588989999999998776088999789998709998999999986089875536358899860475 Q gi|254780289|r 511 SIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGD 590 (682) Q Consensus 511 ~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~ 590 (682) ||. .++| -+.-|-++.+....+. T Consensus 79 ci~--------------lL~K--------------------------------------~kk~i~~~~~~~~~~~----- 101 (173) T TIGR02954 79 CID--------------LLKK--------------------------------------KKKVILFDKNTKIEKK----- 101 (173) T ss_pred HHH--------------HHHC--------------------------------------CCCEEECCCCCCHHHH----- T ss_conf 999--------------9843--------------------------------------8975306887101223----- Q ss_pred EECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC Q ss_conf 6238988998999999999999999973299889999999818798674688999899667899999999999998329 Q gi|254780289|r 591 FIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669 (682) Q Consensus 591 ~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~ 669 (682) ....+-.+.++. ..|-.||.+|.+.++.+|.||| -.+.|-.||++.|+.+--=|---=.||+.+||. T Consensus 102 ----~~~~~~~~~lef----~dLy~Ai~~L~~~~~t~IIL~Y----y~DL~I~eIa~vM~~P~gTvKtyl~Ra~~~lk~ 168 (173) T TIGR02954 102 ----ECEVDADERLEF----EDLYKAIDTLNDKYKTAIILRY----YHDLKIKEIAEVMNKPEGTVKTYLRRAKKKLKK 168 (173) T ss_pred ----HCCCCHHHHHCH----HHHHHHHHHHHHHHHHHHHHHH----CCCCCHHHHHHHCCCCCCCHHHHHHHHHHHHHH T ss_conf ----216686886258----6899999731145440264332----179984259985168985178999999999888 No 170 >PRK10100 DNA-binding transcriptional regulator CsgD; Provisional Probab=90.10 E-value=1.5 Score=23.43 Aligned_cols=54 Identities=15% Similarity=0.292 Sum_probs=46.9 Q ss_pred CCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHHHH Q ss_conf 29988999999981879867468899989966789999999999999832967778756 Q gi|254780289|r 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677 (682) Q Consensus 619 ~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~~~~~l~ 677 (682) .|++||++||++= ....|=.||++.+.||---|+-.-..-++||.--+|..... T Consensus 155 ~LT~RE~eIL~ll-----a~G~sNkEIA~~L~iSe~TVk~H~~~I~~KL~v~~R~qav~ 208 (216) T PRK10100 155 LLTHREKEILNKL-----RIGASNNEIARSLFISENTVKTHLYNLFKKIAVKNRTQAVS 208 (216) T ss_pred CCCHHHHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHH T ss_conf 9998999999999-----87999999998949889899999999999809999999999 No 171 >TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family; InterPro: IPR011517 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This entry represents a group of sigma factors that are able to regulate extra cellular function (ECF) . Eubacteria display considerable genetic diversity between ECF-sigma factors, but all retain two features: the ability to respond to extra-cytoplasmic functions; and regulation by anti-sigma and anti-anti-sigma factors . This family show sequence similarity to IPR007627 from INTERPRO and IPR007630 from INTERPRO.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent. Probab=88.68 E-value=1.9 Score=22.56 Aligned_cols=161 Identities=20% Similarity=0.298 Sum_probs=88.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HCCCCCC----------HHHHHHHHHHHHHHHHHHCCC Q ss_conf 8999999876533211246899987555789998875-----2235677----------788754436799998874385 Q gi|254780289|r 426 EFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKK-----YTNRGLQ----------FLDLIQEGNIGLMKAAEKFDW 490 (682) Q Consensus 426 ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~-----~~~~~~~----------~~~~~~~~~~~l~~a~~~~~~ 490 (682) .+.+|....+.|...+. ++|...----.-.||.+ -.|.+|+ --+||.|.-+=|+...+.=.+ T Consensus 3 ~vt~ll~~~~~Gd~~A~---~~L~~~~Y~~LR~~A~~~~~~~~~~~~Lq~~~~~~ci~stT~LV~EAylrL~~t~~~~~~ 79 (194) T TIGR02999 3 PVTELLQQWQNGDQAAR---DQLFPALYQELRRIARRELRRERSGQTLQVEVLAVCIDSTTALVHEAYLRLVDTQDEQEW 79 (194) T ss_pred HHHHHHHHHHCCCHHHH---HHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCHHHHHHHHHHHHHCCCCHHHH T ss_conf 59999998836458899---999999999999999999985103665204467751046678899876642123202322 Q ss_pred C-CCCEEEHHHHHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHH Q ss_conf 4-573120102898999999999722870461420588989999999998776088999789998709998999999986 Q gi|254780289|r 491 C-LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI 569 (682) Q Consensus 491 ~-~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~ 569 (682) . |++=|+.=| +++.|=+-||+| ++..++-| - T Consensus 80 ~~r~HF~~~AA-----~aMRrIL~D~AR-------------------~~~~~KRG------------------------g 111 (194) T TIGR02999 80 SDRRHFFAAAA-----KAMRRILVDHAR-------------------RRRAQKRG------------------------G 111 (194) T ss_pred CCHHHHHHHHH-----HHHHHHHHHHHH-------------------HHHHHCCC------------------------C T ss_conf 25088999999-----999999999999-------------------99874136------------------------7 Q ss_pred HCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHH Q ss_conf 08987553635889986047562389889989999999999999999732998899999998187986746889998996 Q gi|254780289|r 570 TKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649 (682) Q Consensus 570 ~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~ 649 (682) ...-++| ++.. + ...|+....-..| +..-.-|+...||-.+|+.||| -+| +|.+|||..+ T Consensus 112 ~~~~~~l----~~~~--------~---~~~~~~~~~L~~L-d~aL~~L~~~~Pr~a~~veLr~--F~G--l~~~E~A~~L 171 (194) T TIGR02999 112 GAVRVSL----DEVL--------P---DAEADADEELLDL-DDALDKLAQVDPRQAEVVELRF--FAG--LTVEEIAELL 171 (194) T ss_pred CCCCCCC----CCCC--------C---CCCCCCHHHHHHH-HHHHHHHHHCCHHHHHHHHHHH--HCC--CCHHHHHHHH T ss_conf 7633552----0000--------1---3577740359999-9999877400678899885311--048--8989999986 Q ss_pred CCCHHHHH Q ss_conf 67899999 Q gi|254780289|r 650 CVTRERIR 657 (682) Q Consensus 650 ~~~~er~r 657 (682) +||.-=|. T Consensus 172 ~~S~~Tv~ 179 (194) T TIGR02999 172 GVSVRTVE 179 (194) T ss_pred CCCHHHHH T ss_conf 88887899 No 172 >pfam01726 LexA_DNA_bind LexA DNA binding domain. This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins. The aligned region contains a variant form of the helix-turn-helix DNA binding motif. This domain is found associated with pfam00717 the auto-proteolytic domain of LexA EC:3.4.21.88. Probab=87.98 E-value=1.7 Score=22.80 Aligned_cols=37 Identities=19% Similarity=0.279 Sum_probs=18.4 Q ss_pred HHHHHHHHHHHHCCCCCCHHHHHHHCCC-CHHHHHHHH Q ss_conf 9999999987760889997899987099-989999999 Q gi|254780289|r 531 KVVRTARRMSNKIKREPTPEEIAKKLAM-PVEGVRKVL 567 (682) Q Consensus 531 ~~~~~~~~~~~~~~~~~~~~~~a~~~~~-~~~~~~~~~ 567 (682) ++...-+.+..++|..||..||++.+|+ |..-|...+ T Consensus 10 ~il~~I~~~~~~~G~~Pt~rEI~~~~g~~S~s~v~~~l 47 (65) T pfam01726 10 EVLDFIKASIEETGYPPSRREIAQALGLRSPNAAEEHL 47 (65) T ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHHCCCCHHHHHHHH T ss_conf 99999999999828898799999993899809999999 No 173 >PRK12423 LexA repressor; Provisional Probab=87.57 E-value=1 Score=24.66 Aligned_cols=41 Identities=20% Similarity=0.223 Sum_probs=28.5 Q ss_pred HHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCC-CHHHHHHHH Q ss_conf 89899999999987760889997899987099-989999999 Q gi|254780289|r 527 DKIHKVVRTARRMSNKIKREPTPEEIAKKLAM-PVEGVRKVL 567 (682) Q Consensus 527 ~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~-~~~~~~~~~ 567 (682) ..-.++...-+++..++|..||..|||+.+|+ |..-|..-+ T Consensus 6 ~kQ~~iL~fI~~~~~~~G~~Pt~rEI~~~~g~~S~~~v~~hl 47 (202) T PRK12423 6 PKRAAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARKHV 47 (202) T ss_pred HHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCCCHHHHHHH T ss_conf 999999999999999629898899999982999867899999 No 174 >PRK04841 transcriptional regulator MalT; Provisional Probab=87.53 E-value=2.2 Score=22.05 Aligned_cols=54 Identities=22% Similarity=0.258 Sum_probs=47.1 Q ss_pred CCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHHHHH Q ss_conf 29988999999981879867468899989966789999999999999832967778756 Q gi|254780289|r 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLR 677 (682) Q Consensus 619 ~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~~~~~l~ 677 (682) .|++||.+||++= ....|=.||+..++||-.-|.-.=..-.+||.-.+|...+. T Consensus 838 ~LT~RE~eVL~lL-----a~GlSNkeIA~~L~IS~~TVK~HlrnIy~KLgV~sR~~AV~ 891 (903) T PRK04841 838 PLTQREWQVLGLI-----YSGYSNEQIAGELDVAATTIKTHIRNLYQKLGIAHRQEAVQ 891 (903) T ss_pred CCCHHHHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHH T ss_conf 9799999999999-----76899999998819987699999999985659998999999 No 175 >COG1356 tfx Transcriptional regulator [DNA replication, recombination and repair] Probab=86.54 E-value=0.49 Score=27.14 Aligned_cols=12 Identities=25% Similarity=0.733 Sum_probs=5.1 Q ss_pred CCCCCCCCCCCC Q ss_conf 987553635889 Q gi|254780289|r 572 EPISLETPIGDE 583 (682) Q Consensus 572 ~~~sl~~~~~~~ 583 (682) .|||...|-|++ T Consensus 66 spv~i~v~aGe~ 77 (143) T COG1356 66 SPVSITVKAGED 77 (143) T ss_pred CCEEEEECCCCC T ss_conf 975898558884 No 176 >TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR. Similarly, tetanus toxin production of Clostridium tetani is regulated by TetR which is a very close relative of BotR. Both BotR and TetR are members of the TIGR02937 subfamily of sigma-70 RNA polymerase sigma factors. Functional complementation experiments have been done for botR and tetR in highly transformable strain of Clostridium perfringens host cells to assess functional interchangeability of sigma factors and it has been confirmed that they are interchangeable in vivo. Probab=86.27 E-value=0.33 Score=28.49 Aligned_cols=41 Identities=15% Similarity=0.422 Sum_probs=34.3 Q ss_pred HHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHH Q ss_conf 999997329988999999981879867468899989966789999 Q gi|254780289|r 612 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656 (682) Q Consensus 612 ~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~ 656 (682) ...++++.|||++++|+-|+| -....--|||+.+.+||.-| T Consensus 100 eF~DLISiL~~~QKkIIYmKF----f~~~kdieIak~L~ISRQsV 140 (142) T TIGR03209 100 EFNDLISILPNKQKKIIYMKF----FEDMKEIDIAKKLHISRQSV 140 (142) T ss_pred HHHHHHHHCCCCHHEEEHHHH----HHHHHHHHHHHHHCCHHHHH T ss_conf 298899857940010115899----87777857999953028751 No 177 >PRK00215 LexA repressor; Validated Probab=85.71 E-value=2.4 Score=21.76 Aligned_cols=41 Identities=20% Similarity=0.306 Sum_probs=29.9 Q ss_pred HHHHHHHHHHHHHHHCCCCCCHHHHHHHCCC-CHHHHHHHHH Q ss_conf 9899999999987760889997899987099-9899999998 Q gi|254780289|r 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAM-PVEGVRKVLK 568 (682) Q Consensus 528 ~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~-~~~~~~~~~~ 568 (682) ...++..--+++..++|+.||..|||+.+|+ |..-|...++ T Consensus 5 kQ~~il~fI~~~~~~~g~~Ps~rEI~~~~g~~S~~tV~~~l~ 46 (204) T PRK00215 5 RQQEILDFIKDRIEETGYPPSRREIADALGLRSPSAVHEHLK 46 (204) T ss_pred HHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCHHHHHHHH T ss_conf 999999999999997488998999999809998189999999 No 178 >COG2739 Uncharacterized protein conserved in bacteria [Function unknown] Probab=84.17 E-value=2.6 Score=21.42 Aligned_cols=36 Identities=28% Similarity=0.492 Sum_probs=21.6 Q ss_pred CCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHH Q ss_conf 9988999999981879867468899989966789999999 Q gi|254780289|r 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659 (682) Q Consensus 620 l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi 659 (682) |+.+....+.+.| .-+.+|.||+..|+|||.-|-+- T Consensus 18 LT~KQ~~Y~~lyy----~dDlSl~EIAee~~VSRqAIyDn 53 (105) T COG2739 18 LTKKQKNYLELYY----LDDLSLSEIAEEFNVSRQAIYDN 53 (105) T ss_pred HHHHHHHHHHHHH----HHHCCHHHHHHHHCCCHHHHHHH T ss_conf 8688999999999----81166999999957509999999 No 179 >PRK10869 recombination and repair protein; Provisional Probab=84.01 E-value=3.1 Score=20.80 Aligned_cols=109 Identities=10% Similarity=0.181 Sum_probs=52.4 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCCCCCCHHHHHHHHHCCC Q ss_conf 99999999999998621005778878999999999999999999999997125357777631677689899999861355 Q gi|254780289|r 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPE 392 (682) Q Consensus 313 k~~kl~~eL~e~~~~lkl~~k~iE~L~~~l~~~~k~Ir~~Er~L~rl~~k~~i~R~~Fi~~f~gnEt~~~wl~~~~~~~~ 392 (682) ...++...|......+.+.|.+++.+-+.+. .|.++++|++++-++.+..+.. T Consensus 276 ~l~e~~~~L~~~~~~le~Dp~~Le~ie~RL~-----------~i~~L~RKyg~~~eeLl~~~~~---------------- 328 (553) T PRK10869 276 QIQEASDELRHYLDRLDLDPNRLFELEQRLS-----------KQISLARKHHVSPEELPQHHQS---------------- 328 (553) T ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHHHHH-----------HHHHHHHHHCCCHHHHHHHHHH---------------- T ss_conf 9999999999998735688476899999999-----------9999998839999999999999---------------- Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 10676554345677653223333222221126889999998765332112468999875557 Q gi|254780289|r 393 GEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLR 454 (682) Q Consensus 393 ~~~~~~l~~~~~eI~~~q~kL~~ie~~~gl~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr 454 (682) +......+......+..++.+......++......++..++++-..=.+-|...|. T Consensus 329 ------l~~eL~~l~~~~~~l~~L~~~~~~~~~~~~~~A~~Ls~~R~~aA~~L~~~I~~~L~ 384 (553) T PRK10869 329 ------LLEEQQQLDDQEDKLETLALAVEKHHQQALETARKLHQSRQRYAKELAKLITQSMH 384 (553) T ss_pred ------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf ------99999863087999999999999999999999999999999999999999999986 No 180 >pfam02650 HTH_WhiA Sporulation Regulator WhiA C terminal domain. This domain is found at the C terminal of the sporulation regulator WhiA. It is predicted to form a DNA binding helix-turn-helix structure. WhiA is a distant homologue of LAGLIDADG homing endonucleases. Probab=82.23 E-value=3.1 Score=20.81 Aligned_cols=42 Identities=29% Similarity=0.579 Sum_probs=33.3 Q ss_pred HHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHC--CCHH----HHHHHHH Q ss_conf 7329988999999981879867468899989966--7899----9999999 Q gi|254780289|r 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFC--VTRE----RIRQIEA 661 (682) Q Consensus 617 l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~--~~~e----r~rqi~~ 661 (682) +..||+..+.+..+|. ...+.||.|+|+.+. ||+- |.|.|+. T Consensus 141 l~~Lp~~l~~~a~lRl---~~Pd~SL~ELgell~p~isKSgvnhRlrKi~~ 188 (191) T pfam02650 141 LDNLPEKLREIAQLRL---ENPDASLKELGELLDPPITKSGVNHRLRKLEK 188 (191) T ss_pred CCCCCHHHHHHHHHHH---HCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHH T ss_conf 1219999999999999---69656799999883799788999899999998 No 181 >COG1809 (2R)-phospho-3-sulfolactate synthase (PSL synthase, CoM biosynthesis) [Coenzyme transport and metabolism] Probab=82.06 E-value=3.1 Score=20.81 Aligned_cols=24 Identities=17% Similarity=0.332 Sum_probs=18.6 Q ss_pred CCCCHHHHHHHHHHHHHCCCEEEC Q ss_conf 359988899999999847977832 Q gi|254780289|r 56 DEVSSEQMEDTVAMLSNMGINVVD 79 (682) Q Consensus 56 d~~~~e~ie~i~~~L~~~GI~Vve 79 (682) ...+.|++..-+++..+.||.|+- T Consensus 55 ~Li~kd~V~ekid~y~e~~i~v~p 78 (258) T COG1809 55 SLIDKDQVKEKIDMYKENDIYVFP 78 (258) T ss_pred CCCCHHHHHHHHHHHHHCCCEECC T ss_conf 466289999999999975935657 No 182 >PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed Probab=81.76 E-value=3.7 Score=20.18 Aligned_cols=13 Identities=23% Similarity=0.401 Sum_probs=6.1 Q ss_pred HHHHHHHHHHHHC Q ss_conf 8899999999847 Q gi|254780289|r 61 EQMEDTVAMLSNM 73 (682) Q Consensus 61 e~ie~i~~~L~~~ 73 (682) .-+.||+..+... T Consensus 147 Aa~~Di~~~~~~R 159 (443) T PRK00286 147 AAIRDILTVLSRR 159 (443) T ss_pred HHHHHHHHHHHCC T ss_conf 8999999998504 No 183 >PRK09954 hypothetical protein; Provisional Probab=80.39 E-value=4.1 Score=19.84 Aligned_cols=43 Identities=16% Similarity=0.288 Sum_probs=29.3 Q ss_pred HHHHHHHHHHHCCCCCHHHHHHHCCCCCCCHHHHHHHHHHHHHCCC Q ss_conf 9999999787848867899975268435998889999999984797 Q gi|254780289|r 30 SWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGI 75 (682) Q Consensus 30 ~ik~LI~~gke~GylTydeIn~~LP~d~~~~e~ie~i~~~L~~~GI 75 (682) .=|+++++=|+..|++..||-+.|. .+-.-+=.-++-|..-|+ T Consensus 4 re~~il~~i~~~p~i~q~ela~~lg---isrs~va~hi~~l~~kg~ 46 (362) T PRK09954 4 REKEILAILRRNPLIQQNEIADILQ---ISRSRVAAHIMDLMRKGR 46 (362) T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHC---CCHHHHHHHHHHHHHCCE T ss_conf 8999999998789958999999979---879999999998875476 No 184 >PRK13239 alkylmercury lyase; Provisional Probab=79.79 E-value=4.1 Score=19.83 Aligned_cols=28 Identities=36% Similarity=0.406 Sum_probs=25.9 Q ss_pred CCCCCCHHHHHHHCCCCHHHHHHHHHHH Q ss_conf 0889997899987099989999999860 Q gi|254780289|r 543 IKREPTPEEIAKKLAMPVEGVRKVLKIT 570 (682) Q Consensus 543 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~ 570 (682) .|++.|++.||+.+|+|+++|+.+|... T Consensus 33 ~G~PVs~~~LA~~~g~~~e~v~~~L~~~ 60 (206) T PRK13239 33 KGRPVSRETLAGALGWPVEEVAAVLEQA 60 (206) T ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHHHC T ss_conf 6999999999988699999999999857 No 185 >COG1570 XseA Exonuclease VII, large subunit [DNA replication, recombination, and repair] Probab=79.62 E-value=4.3 Score=19.66 Aligned_cols=46 Identities=26% Similarity=0.415 Sum_probs=26.1 Q ss_pred CCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHH Q ss_conf 998999999986089875536358899860475623898899899999 Q gi|254780289|r 558 MPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI 605 (682) Q Consensus 558 ~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~~~ 605 (682) ...+.|..+.-.++-|| =.-||-+-|.++.||++|--+++|..+++ T Consensus 212 FNdE~vaRAi~~s~iPv--ISAVGHEtD~tL~DfVAD~RApTPTaAAE 257 (440) T COG1570 212 FNDEIVARAIAASRIPV--ISAVGHETDFTLADFVADLRAPTPTAAAE 257 (440) T ss_pred CCHHHHHHHHHHCCCCE--EEECCCCCCCCHHHHHHHCCCCCCHHHHH T ss_conf 58099999998079985--84066677752877643134799668788 No 186 >PRK09191 two-component response regulator; Provisional Probab=79.50 E-value=4.4 Score=19.63 Aligned_cols=124 Identities=14% Similarity=0.103 Sum_probs=62.7 Q ss_pred HHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCC--HH Q ss_conf 9875557899988752235677788754436799998874385457312010289899999999972287046142--05 Q gi|254780289|r 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPV--HM 525 (682) Q Consensus 448 l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~--~~ 525 (682) -|-.||.++---|+--+|.--.=..+++.---.|+-.-+.|+...+-|..-|..+ +.|-....-+.....-|. .. T Consensus 6 ~ia~~LPyLRRYARALTGsQ~~GD~yV~a~LEallad~~~~~~~~~~Rv~Ly~~f---~~iw~s~~~~~~~~~~~~~~~~ 82 (261) T PRK09191 6 RIAPHLPYLRRYARALTGSQSSGDAYVAATLEALLADPSIFPEASSPRVGLYRLF---HRIWSSAGANDPEPESPFEARA 82 (261) T ss_pred HHHHHCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCHHCCCCCCHHHHHHHHH---HHHHHHCCCCCCCCCCCCHHHH T ss_conf 8887583999999986178201899999999999809220267775589999999---9999725999888876300689 Q ss_pred HHHHHHHHHHHHHHHH-HCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCC Q ss_conf 8898999999999877-608899978999870999899999998608987 Q gi|254780289|r 526 RDKIHKVVRTARRMSN-KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI 574 (682) Q Consensus 526 ~~~~~~~~~~~~~~~~-~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ 574 (682) ...+.++....|+.+- -.=-.=+.+|+|+.||++.+++...+..++.-+ T Consensus 83 ~~~L~~ltp~~RqAlLL~alEgFs~~eaA~Il~v~~~e~~~l~~~A~~ei 132 (261) T PRK09191 83 ERRLSAITPLPRQAFLLTALEGFSEEEAAEILGVDPAEVAALLDDASREI 132 (261) T ss_pred HHHHHHCCCHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHH T ss_conf 99987489303499998988289889999997899999999999999999 No 187 >pfam07374 DUF1492 Protein of unknown function (DUF1492). This family consists of several hypothetical, highly conserved Streptococcal and related phage proteins of around 100 residues in length. The function of this family is unknown. It appears to be distantly related to pfam08281. Probab=77.68 E-value=4.9 Score=19.24 Aligned_cols=55 Identities=22% Similarity=0.301 Sum_probs=45.3 Q ss_pred HHHHHHHHHHCC-CHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH Q ss_conf 999999997329-98899999998187986746889998996678999999999999983 Q gi|254780289|r 609 LRETTTRVLASL-TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667 (682) Q Consensus 609 ~~~~~~~~l~~l-~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l 667 (682) -+..+.++++.| +|-++.||+|.| -...+.-+|+..++.||.-+--+-.+|++-| T Consensus 44 ~r~El~rlI~~l~np~~RtvL~m~Y----id~~~~~~v~e~l~~Sr~Tyyr~~r~Ai~~L 99 (100) T pfam07374 44 RKLELGRLIDKLENPDSRTILRMVY----IDKMTVWQVCDKLNCSRTTYYRKLRVAIKEL 99 (100) T ss_pred HHHHHHHHHHHCCCHHHHHHHEEEE----ECCCCHHHHHHHHCCCHHHHHHHHHHHHHHC T ss_conf 9999999998457802213111434----4347499999997666678999999999852 No 188 >pfam04963 Sigma54_CBD Sigma-54 factor, core binding domain. This domain makes a direct interaction with the core RNA polymerase, to form an enhancer dependent holoenzyme. The centre of this domain contains a very weak similarity to a helix-turn-helix motif which may represent the other DNA binding domain. Probab=76.78 E-value=5.2 Score=19.06 Aligned_cols=129 Identities=16% Similarity=0.194 Sum_probs=59.9 Q ss_pred HHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHH---HCCC-CCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCC Q ss_conf 99999972287046142058898999999999877---6088-9997899987099989999999860898755363588 Q gi|254780289|r 507 AITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN---KIKR-EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582 (682) Q Consensus 507 ~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~---~~~~-~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~ 582 (682) +...++..|-+...++-.. ..++..+.. +.|. .-+.++||..++++.++|..+++..+ +|| |.|= T Consensus 16 sL~e~L~~Ql~~~~l~~~e-------~~ia~~iI~~LD~~GyL~~~~~eia~~~~~~~~~ie~~l~~iQ---~le-P~GI 84 (195) T pfam04963 16 SLRDHLLEQLELAPFSDAD-------RLIALALIDALDDTGYLQASLEEIAESLGVELDEVEAVLAVLQ---QFD-PAGV 84 (195) T ss_pred CHHHHHHHHHCCCCCCHHH-------HHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH---CCC-CCCC T ss_conf 9999999998146999999-------9999999962697776387999999880878999999999997---489-9823 Q ss_pred CCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHH Q ss_conf 99860475623898899899999999999999997329988999999981879867468899989966789999999999 Q gi|254780289|r 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662 (682) Q Consensus 583 ~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~ 662 (682) . +.+ ...+|.-++... ..-.+--..|+.-.|..- ..+.+..|.+.+|+|.+.|+..-.. T Consensus 85 g-------------Arn-----L~EcL~lQL~~~-~~~~~~a~~ii~~~le~l--~~~~~~~i~k~l~~s~~~i~~a~~~ 143 (195) T pfam04963 85 G-------------ARD-----LSECLLLQLRQL-DRWLDPAMEALVDHLELL--ARRDFATLKRICGVDEEDLREMIEE 143 (195) T ss_pred C-------------CCC-----HHHHHHHHHHHC-CCCHHHHHHHHHHHHHHH--HCCCHHHHHHHHCCCHHHHHHHHHH T ss_conf 5-------------088-----999999998652-865689999999889998--5268999999969199999999999 Q ss_pred HHHHHC Q ss_conf 999832 Q gi|254780289|r 663 AIRKLK 668 (682) Q Consensus 663 a~~~l~ 668 (682) +++|. T Consensus 144 -I~~Ln 148 (195) T pfam04963 144 -IRSLN 148 (195) T ss_pred -HHHCC T ss_conf -99679 No 189 >PRK13558 bacterio-opsin activator; Provisional Probab=76.28 E-value=5.3 Score=18.97 Aligned_cols=55 Identities=15% Similarity=0.108 Sum_probs=44.9 Q ss_pred HHHHHHCCCHHHHHHHHHHHCC---CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH Q ss_conf 9999732998899999998187---986746889998996678999999999999983 Q gi|254780289|r 613 TTRVLASLTPREERVLRMRFGI---GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667 (682) Q Consensus 613 ~~~~l~~l~~re~~v~~~r~g~---~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l 667 (682) ...+...|++|.+.+|+.=|== .-.++.|=+||+..+|||+--.-|.=.+|-+|| T Consensus 610 ~~aL~e~LTDRQ~eaLqtAY~sGyFEwPR~sTGeElAesLgIS~pTfhqHLRaaerKL 667 (674) T PRK13558 610 REELRNDLTDRQLTALQKAYVSGYFEWPRRAEGKQLAESMDIVPSTYHQHLQAAKQKL 667 (674) T ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHCCCCHHHHHHHHHHHHHHH T ss_conf 9999876049899999999864757788778789999870988388999999999999 No 190 >COG4367 Uncharacterized protein conserved in bacteria [Function unknown] Probab=74.42 E-value=5.9 Score=18.62 Aligned_cols=39 Identities=23% Similarity=0.307 Sum_probs=29.7 Q ss_pred HHHHHHHH-C-CCCCCHHHHHHHCCCCHHHHHHHHHHHCCC Q ss_conf 99998776-0-889997899987099989999999860898 Q gi|254780289|r 535 TARRMSNK-I-KREPTPEEIAKKLAMPVEGVRKVLKITKEP 573 (682) Q Consensus 535 ~~~~~~~~-~-~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~ 573 (682) .+++-+|+ + --.-|.++||+.|+++..++.+++.+.++| T Consensus 10 ~Tk~elqan~el~~LS~~~iA~~Ln~t~~~lekil~~tqr~ 50 (97) T COG4367 10 RTKQELQANFELCPLSDEEIATALNWTEVKLEKILQVTQRP 50 (97) T ss_pred HHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHCC T ss_conf 88999997544064529999999588799999999885064 No 191 >TIGR02612 mob_myst_A mobile mystery protein A; InterPro: IPR013435 Proteins in this entry are more often encoded within mobilisation-related contexts than not. This includes a CRISPR-associated gene region in Geobacter sulfurreducens PCA, and plasmids in Agrobacterium tumefaciens and Coxiella burnetii. They are found together with mobile mystery protein B, a member of the Fic protein family (IPR003812 from INTERPRO). Mobile mystery protein A is encoded by the upstream member of the gene pair and contains a helix-turn-helix domain.. Probab=73.17 E-value=2.7 Score=21.26 Aligned_cols=41 Identities=29% Similarity=0.430 Sum_probs=21.6 Q ss_pred HCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHH Q ss_conf 329988999999981879867468899989966789999999999 Q gi|254780289|r 618 ASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662 (682) Q Consensus 618 ~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~ 662 (682) ...+|..-.|=.+|--||. |...+|.++||++.||-+||.- T Consensus 21 ~~~~P~~GWvR~~R~ALGm----s~~QLA~RlGV~p~Rv~~~E~~ 61 (150) T TIGR02612 21 ALKTPKKGWVRAIRKALGM----SGAQLAARLGVTPQRVEAIEKS 61 (150) T ss_pred CCCCCCCCCHHHHHHHHCC----CHHHHHHHCCCCHHHHHHHHHH T ss_conf 5387688616889877251----5788766528973779998888 No 192 >PRK09247 ATP-dependent DNA ligase; Validated Probab=73.15 E-value=3.8 Score=20.12 Aligned_cols=27 Identities=26% Similarity=0.342 Sum_probs=13.1 Q ss_pred HHHHHHHHHHCCCCCCCCCHHHHHHHH Q ss_conf 899999998187986746889998996 Q gi|254780289|r 623 REERVLRMRFGIGMNTDHTLEEVGKQF 649 (682) Q Consensus 623 re~~v~~~r~g~~~~~~~tl~e~~~~~ 649 (682) |=-+|+|.|.--.-..--|+++|-+.| T Consensus 507 RFPR~~r~R~DK~~~ea~t~~~~~~l~ 533 (537) T PRK09247 507 RFPRILRWRWDKPAAEADRLETLQALL 533 (537) T ss_pred ECCCEEEECCCCCHHHCCCHHHHHHHH T ss_conf 747210452999936683999999999 No 193 >COG1802 GntR Transcriptional regulators [Transcription] Probab=72.26 E-value=5.2 Score=19.06 Aligned_cols=38 Identities=26% Similarity=0.288 Sum_probs=17.7 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC Q ss_conf 68899999987653321124689998755578999887522 Q gi|254780289|r 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYT 464 (682) Q Consensus 424 i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~ 464 (682) +.+-..|...|..+..+.- .+++..+++.+.+...++. T Consensus 185 ~~eH~~il~ai~~~d~~~A---~~~m~~Hl~~~~~~~~~~~ 222 (230) T COG1802 185 IDEHRAILEALEARDAEAA---AEAMRQHLRRARSRLLEAL 222 (230) T ss_pred HHHHHHHHHHHHCCCHHHH---HHHHHHHHHHHHHHHHHHH T ss_conf 9999999999993999999---9999999999999999985 No 194 >pfam05263 DUF722 Protein of unknown function (DUF722). This family contains several bacteriophage proteins of unknown function. Probab=71.50 E-value=6.8 Score=18.13 Aligned_cols=51 Identities=18% Similarity=0.343 Sum_probs=40.2 Q ss_pred HHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHH Q ss_conf 99999999973299889999999818798674688999899667899999999 Q gi|254780289|r 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660 (682) Q Consensus 608 ~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~ 660 (682) ..++.+.....+|.+-+++||.+||| .....|--.|+..++|+--.++-+. T Consensus 70 ~qk~~id~~~~~~~~~~k~ii~lrY~--~r~~~sW~~Va~~l~i~er~~~~~~ 120 (130) T pfam05263 70 RQKEILDNFYKVLTEEEKRIIELRYK--GRNGMTWYQVAQELDISEKKAKRIY 120 (130) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHC--CCCCCCHHHHHHHHCCCHHHHHHHH T ss_conf 99999999999851899999999867--6467549999999651199999999 No 195 >KOG0996 consensus Probab=71.09 E-value=6.9 Score=18.06 Aligned_cols=54 Identities=13% Similarity=0.314 Sum_probs=33.6 Q ss_pred CCHHHHHHHHHHHHHCCCC-------CHHHHH-------HHCCCCCCC------------------HHHHHHHHHHHHHC Q ss_conf 0289999999978784886-------789997-------526843599------------------88899999999847 Q gi|254780289|r 26 FSDDSWKKMIKLARQRGYV-------TIEELN-------AFLPPDEVS------------------SEQMEDTVAMLSNM 73 (682) Q Consensus 26 ~~~~~ik~LI~~gke~Gyl-------TydeIn-------~~LP~d~~~------------------~e~ie~i~~~L~~~ 73 (682) ++..++-.||..+-..+-+ +|..|. +.+|+..|. +...-+|...|... T Consensus 139 iR~~klS~LIh~S~~~~~l~SCsV~vhFq~iiD~~~~~~E~vp~s~~~ItRtA~~~NsSkY~Ingk~as~~~V~~lLk~~ 218 (1293) T KOG0996 139 IRSKKLSALIHKSDGHPNLQSCSVEVHFQKIIDKPGGTYEVVPDSEFTITRTAFRDNSSKYYINGKEASFKDVTKLLKSH 218 (1293) T ss_pred HHHHHHHHHHHCCCCCCCCCCEEEEEEEEEEECCCCCCEEECCCCEEEEEEHHHHCCCCEEEECCCCCCHHHHHHHHHHC T ss_conf 76778999883447899876304887643323168986221379705897435407873276778504299999999866 Q ss_pred CCEEEC Q ss_conf 977832 Q gi|254780289|r 74 GINVVD 79 (682) Q Consensus 74 GI~Vve 79 (682) ||++-. T Consensus 219 gIDleH 224 (1293) T KOG0996 219 GIDLEH 224 (1293) T ss_pred CCCCCC T ss_conf 978766 No 196 >PRK13869 plasmid-partitioning protein RepA; Provisional Probab=71.02 E-value=7 Score=18.05 Aligned_cols=13 Identities=15% Similarity=0.312 Sum_probs=5.9 Q ss_pred HHHHHHHHHHHHH Q ss_conf 7887544367999 Q gi|254780289|r 470 FLDLIQEGNIGLM 482 (682) Q Consensus 470 ~~~~~~~~~~~l~ 482 (682) +.||=..||+..+ T Consensus 155 lIDLDPQgnlS~~ 167 (405) T PRK13869 155 AVDLDPQASLSAL 167 (405) T ss_pred EEECCHHHHHHHH T ss_conf 9964561788898 No 197 >COG1481 Uncharacterized protein conserved in bacteria [Function unknown] Probab=70.77 E-value=7 Score=18.01 Aligned_cols=45 Identities=24% Similarity=0.409 Sum_probs=34.7 Q ss_pred HHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCC--CHH----HHHHHHHHHH Q ss_conf 73299889999999818798674688999899667--899----9999999999 Q gi|254780289|r 617 LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV--TRE----RIRQIEAKAI 664 (682) Q Consensus 617 l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~--~~e----r~rqi~~~a~ 664 (682) |..||++.+++..+|- ..++.||+|+|+.+.. |+- |.|.|..-|- T Consensus 251 l~~lpe~l~e~a~LRl---~hpd~SLeeLg~~l~~~iSKSGvnHrlrkl~kia~ 301 (308) T COG1481 251 LEKLPEKLREAALLRL---EHPDASLEELGELLEPPISKSGVNHRLRKLKKIAE 301 (308) T ss_pred HHHCCHHHHHHHHHHH---CCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHH T ss_conf 3117988999999973---38051099999985584368888889999999999 No 198 >pfam02601 Exonuc_VII_L Exonuclease VII, large subunit. This family consist of exonuclease VII, large subunit EC:3.1.11.6 This enzyme catalyses exonucleolytic cleavage in either 5'-3' or 3'-5' direction to yield 5'-phosphomononucleotides. This exonuclease VII enzyme is composed of one large subunit and 4 small ones. Probab=70.09 E-value=7.3 Score=17.91 Aligned_cols=45 Identities=16% Similarity=0.277 Sum_probs=18.4 Q ss_pred HHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCHHHHHHHHHHHHHC Q ss_conf 999999997878488678999752684359988899999999847 Q gi|254780289|r 29 DSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNM 73 (682) Q Consensus 29 ~~ik~LI~~gke~GylTydeIn~~LP~d~~~~e~ie~i~~~L~~~ 73 (682) ..++..+..-+++++...=.|.-+.-++.-.+..|=..+..++.+ T Consensus 26 Aa~~Di~~~~~~r~p~~~i~l~p~~VQG~~a~~~I~~ai~~~~~~ 70 (295) T pfam02601 26 AAYQDFLRTARRRGPLVEIEIYPTLVQGDGAAESIVSALERANER 70 (295) T ss_pred HHHHHHHHHHHHHCCCCEEEEECCCCCCCHHHHHHHHHHHHHHHC T ss_conf 899999999998199967999473576504899999999999846 No 199 >cd04981 IgV_H Immunoglobulin (Ig) heavy chain (H), variable (V) domain. IgV_H: Immunoglobulin (Ig) heavy chain (H), variable (V) domain. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. In Ig, each chain is composed of one variable domain (IgV) and one or more constant domains (IgC); these names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. There are five types of heavy chains (alpha, gamma, delta, epsilon, and mu), which determine the type of immunoglobulin: IgA, IgG, IgD, IgE, and IgM, respectively. In higher vertebrates, there are two types of light chain, designated kappa and lambda, which can associate with any of the heavy chains. This family includes alpha, gamma, delta, epsilon, and mu heavy chains. Probab=68.95 E-value=0.31 Score=28.70 Aligned_cols=21 Identities=33% Similarity=0.851 Sum_probs=17.6 Q ss_pred CCCEEEHHHHHHHHHHHHHHH Q ss_conf 573120102898999999999 Q gi|254780289|r 492 LGYKFSTYAMWWVKQAITRSI 512 (682) Q Consensus 492 ~g~~f~tya~~~i~~~i~~~~ 512 (682) .||-|++|+..||||+=-+.+ T Consensus 22 SGftf~~y~m~WVRQaPGkgL 42 (117) T cd04981 22 SGFTFTSYGVNWVRQAPGKGL 42 (117) T ss_pred CCCCHHHCEEEEEEECCCCCE T ss_conf 066966691689985899982 No 200 >TIGR02168 SMC_prok_B chromosome segregation protein SMC; InterPro: IPR011890 The SMC (structural maintenance of chromosomes) family of proteins, exist in virtually all organisms including both bacteria and archaea. The SMC proteins are essential for successful chromosome transmission during replication and segregation of the genome in all organisms and form three types of heterodimer (SMC1SMC3, SMC2SMC4, SMC5SMC6), which are core components of large multiprotein complexes. The best known complexes are cohesin, which is responsible for sister-chromatid cohesion, and condensin, which is required for full chromosome condensation in mitosis. SMCs are generally present as single proteins in bacteria, and as at least six distinct proteins in eukaryotes. The proteins range in size from approximately 110 to 170 kDa, and share a five-domain structure, with globular N- and C-terminal (IPR003395 from INTERPRO) domains separated by a long (circa 100 nm or 900 residues) coiled coil segment in the centre of which is a globular ''hinge'' domain, characterised by a set of four highly conserved glycine residues that are typical of flexible regions in a protein. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif (XXXXD, where X is any hydrophobic residue), and a LSGG motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases . All SMC proteins appear to form dimers, either forming homodimers with themselves, as in the case of prokaryotic SMC proteins, or heterodimers between different but related SMC proteins. The dimers are arranged in an antiparallel alignment. This orientation brings the N- and C-terminal globular domains (from either different or identical protamers) together, which unites an ATP binding site (Walker A motif) within the N-terminal domain with a Walker B motif (DA box) within the C-terminal domain, to form a potentially functional ATPase. Protein interaction and microscopy data suggest that SMC dimers form a ring-like structure which might embrace DNA molecules. Non-SMC subunits associate with the SMC amino- and carboxy-terminal domains. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. SMCs share not only sequence similarity but also structural similarity with ABC proteins. SMC proteins function together with other proteins in a range of chromosomal transactions, including chromosome condensation, sister-chromatid cohesion, recombination, DNA repair and epigenetic silencing of gene expression . The smc gene is often associated with scpB (IPR005234 from INTERPRO) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle , , .; GO: 0005515 protein binding, 0005524 ATP binding, 0005694 chromosome. Probab=68.56 E-value=7.8 Score=17.68 Aligned_cols=28 Identities=18% Similarity=0.298 Sum_probs=9.9 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 9999998765332112468999875557 Q gi|254780289|r 427 FRHIVSMVRKGECEASIAKKEMVEANLR 454 (682) Q Consensus 427 lK~i~r~I~~ge~e~~~AK~~l~~anlr 454 (682) +..+-.++...+.....|+.++-+++=| T Consensus 468 l~~~~~~~~~~~~~~~~~~~~l~~~~~r 495 (1191) T TIGR02168 468 LEELREELEEAEQALDAAKRELAQLQAR 495 (1191) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 9999999999999999999999999999 No 201 >cd00228 eu-GS Eukaryotic Glutathione Synthetase (eu-GS); catalyses the production of glutathione from gamma-glutamylcysteine and glycine in an ATP-dependent manner. Belongs to the ATP-grasp superfamily. Probab=67.05 E-value=5.4 Score=18.94 Aligned_cols=128 Identities=16% Similarity=0.235 Sum_probs=70.1 Q ss_pred HHHHCCCCCCCEEEHH---HHHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCH Q ss_conf 8874385457312010---2898999999999722870461420588989999999998776088999789998709998 Q gi|254780289|r 484 AAEKFDWCLGYKFSTY---AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560 (682) Q Consensus 484 a~~~~~~~~g~~f~ty---a~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~ 560 (682) .|.-.=+|-||-.+-| +.|=.|- .-.+++.|+||.-..+ .-.+++..|.+-. |.-|...+ -.. T Consensus 257 eVavVYfRaGY~P~dY~se~~W~aRl-----~lE~S~AIKcPsi~~q-----LaGtKKVQQ~La~---p~vLerFl-~~~ 322 (471) T cd00228 257 EVAVVYFRAGYTPDDYPSESEWEARL-----LMERSSAIKCPSISTQ-----LAGTKKIQQELAE---PGVLERFL-PNP 322 (471) T ss_pred EEEEEEECCCCCCCCCCCHHHHHHHH-----HHHHCCCCCCCCHHHH-----HHCCHHHHHHHCC---HHHHHHHC-CCH T ss_conf 99999973777802389878889999-----9986377148899998-----6242999998668---30998870-899 Q ss_pred HHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHH--------HHHHHHHHHHHHHCCCH---HHHHHHH Q ss_conf 999999986089875536358899860475623898899899999--------99999999999732998---8999999 Q gi|254780289|r 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI--------QANLRETTTRVLASLTP---REERVLR 629 (682) Q Consensus 561 ~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~~~--------~~~~~~~~~~~l~~l~~---re~~v~~ 629 (682) +++..+.+....-.|||.. +.++.....- ..+|+..+. ...-.+.|...|..|++ |.+-||. T Consensus 323 ~~~~~lr~tFa~ly~Ld~~--~~g~~~~~~A-----~~~P~~yVLKPQREGGGNNiyg~dI~~~L~~l~~~ee~~ayILM 395 (471) T cd00228 323 EEVAKLRATFAGLYSLDDT--EEGDEIVRKA-----LEKPELFVLKPQREGGGNNIYGEEMREALLKLQGSEERAAYILM 395 (471) T ss_pred HHHHHHHHHHHCCCCCCCC--CCHHHHHHHH-----HHCHHHEEECCCCCCCCCCHHHHHHHHHHHHCCCHHHHCCEEEE T ss_conf 9999999973114047874--0128999998-----83913125647465760001108999999856982441530165 Q ss_pred HHH Q ss_conf 981 Q gi|254780289|r 630 MRF 632 (682) Q Consensus 630 ~r~ 632 (682) -|. T Consensus 396 erI 398 (471) T cd00228 396 EKI 398 (471) T ss_pred ECC T ss_conf 145 No 202 >PRK11414 putative DNA-binding transcriptional regulator; Provisional Probab=66.64 E-value=7.9 Score=17.63 Aligned_cols=16 Identities=13% Similarity=0.347 Sum_probs=7.5 Q ss_pred HHHHHHHHHHHHHHHH Q ss_conf 9998755578999887 Q gi|254780289|r 446 KEMVEANLRLVISVAK 461 (682) Q Consensus 446 ~~l~~anlr~v~~~~~ 461 (682) ..++++|..+=..|+. T Consensus 129 ~~~~~~d~~FH~~i~~ 144 (221) T PRK11414 129 EQIINANRLFRLAIYH 144 (221) T ss_pred HHHHHHHHHHHHHHHH T ss_conf 9999999999999998 No 203 >cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D Probab=65.23 E-value=8.9 Score=17.20 Aligned_cols=35 Identities=20% Similarity=0.378 Sum_probs=23.5 Q ss_pred CCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHH Q ss_conf 299889999999818798674688999899667899999 Q gi|254780289|r 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657 (682) Q Consensus 619 ~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~r 657 (682) .|++-...-++-++ ..| .|..+|+..|||||.-|- T Consensus 5 ~lt~~q~~~ar~l~--~~G--~~~~~iA~~~GVsr~Tiy 39 (42) T cd00569 5 KLTPEQIEEARRLL--AAG--ESVAEIARRLGVSRSTLY 39 (42) T ss_pred CCCHHHHHHHHHHH--HCC--CCHHHHHHHHCCCHHHHH T ss_conf 69999999999999--978--989999999797999998 No 204 >pfam06971 Put_DNA-bind_N Putative DNA-binding protein N-terminus. This family represents the N-terminus (approximately 50 residues) of a number of putative bacterial DNA-binding proteins. Probab=64.41 E-value=9.2 Score=17.09 Aligned_cols=47 Identities=13% Similarity=0.221 Sum_probs=34.0 Q ss_pred ECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHH Q ss_conf 61420588989999999998776088999789998709998999999 Q gi|254780289|r 520 RIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566 (682) Q Consensus 520 r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~ 566 (682) +||-..+..+-...|.-.++...--.--+-+|||+.+|++...||+= T Consensus 1 kIP~ati~RLp~Y~R~L~~L~~~g~~~vSS~eLa~~~gv~~aqiRKD 47 (49) T pfam06971 1 KIPEATIKRLPLYYRYLEELLEEGVERVSSKELSEAIGIDAAQIRKD 47 (49) T ss_pred CCCHHHHHHHHHHHHHHHHHHHCCCCEECHHHHHHHHCCCHHHHHCC T ss_conf 98889999999999999999985990497999999979399996142 No 205 >PRK06266 transcription initiation factor E subunit alpha; Validated Probab=63.62 E-value=7.7 Score=17.69 Aligned_cols=24 Identities=42% Similarity=0.527 Sum_probs=19.4 Q ss_pred CCCCHHHHHHHCCCCHHHHHHHHH Q ss_conf 899978999870999899999998 Q gi|254780289|r 545 REPTPEEIAKKLAMPVEGVRKVLK 568 (682) Q Consensus 545 ~~~~~~~~a~~~~~~~~~~~~~~~ 568 (682) -+.|.++||+.+|+.+..||++|- T Consensus 35 ~evTDEeiAe~~gi~lN~VRk~LY 58 (178) T PRK06266 35 GEVTDEEIAEQTGIKLNTVRKILY 58 (178) T ss_pred CCCCHHHHHHHHCCCHHHHHHHHH T ss_conf 657899999996997899999999 No 206 >PRK05932 RNA polymerase factor sigma-54; Reviewed Probab=63.56 E-value=9.5 Score=16.98 Aligned_cols=68 Identities=18% Similarity=0.217 Sum_probs=42.6 Q ss_pred CCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHC Q ss_conf 899978999870999899999998608987553635889986047562389889989999999999999999732 Q gi|254780289|r 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619 (682) Q Consensus 545 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~ 619 (682) ++-|..+||+.+|+.+..|..+.+- -.+.||.|- ..|-.|....-.......++....+..|.++++. T Consensus 348 kPL~lkdiA~~lglheSTVSRav~~----Kyi~tp~G~---~~lk~fFs~~~~~~~g~~~S~~~ik~~i~~lI~~ 415 (461) T PRK05932 348 KPLVLKDIAEALGMHESTISRATTN----KYMATPRGI---FELKYFFSSAVSTDSGGEASSTAIRALIKKLIAA 415 (461) T ss_pred CCCCHHHHHHHCCCCHHHHHHHHHC----CEECCCCCE---EEHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHH T ss_conf 6763999998739981258898716----611489744---6699974230578886201399999999999984 No 207 >TIGR01637 phage_arpU phage transcriptional regulator, ArpU family; InterPro: IPR006524 These sequences represent a family of phage proteins, including ArpU, called a putative autolysin regulatory protein. ArpU was described as a regulator of cellular muramidase-2 of Enterococcus hirae but appears to have been cloned from a prophage. This family appears related to the RinA family of bacteriophage transcriptional activators and to some sporulation-specific sigma factors. This group of sequences could be a phage transcriptional activator family.. Probab=63.54 E-value=9.5 Score=16.98 Aligned_cols=56 Identities=9% Similarity=0.207 Sum_probs=43.9 Q ss_pred HHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC Q ss_conf 9999997329988999999981879867468899989966789999999999999832 Q gi|254780289|r 611 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668 (682) Q Consensus 611 ~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~ 668 (682) ..+..++..|++++|.||...| -......=-.|-..+|+|.-..-.+-.+|+-+|- T Consensus 75 ~~v~~~~~~L~~~~R~Il~~~Y--~~~~~~~D~~i~~el~~s~~~Yy~~K~rA~l~lA 130 (139) T TIGR01637 75 NAVSKAINQLDEISRQILYDKY--LEEDKKSDYQIMNELGYSHSQYYRIKKRALLRLA 130 (139) T ss_pred HHHHHHHHCCCHHHHHHHHHHH--HCHHHHCCHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 9999998408888999999971--0455303788888743777899999999999999 No 208 >pfam02001 DUF134 Protein of unknown function DUF134. This family of archaeal proteins has no known function. Probab=61.73 E-value=10 Score=16.74 Aligned_cols=46 Identities=24% Similarity=0.272 Sum_probs=38.9 Q ss_pred CCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC Q ss_conf 29988999999981879867468899989966789999999999999832 Q gi|254780289|r 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668 (682) Q Consensus 619 ~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~ 668 (682) .|++-|-+.|||-. ...+|-+|-+..+||||--+--|-..|-+|+- T Consensus 36 ~L~~dE~EAiRL~D----~egl~QeeaA~~MgVSR~Tf~ril~~ARkKvA 81 (100) T pfam02001 36 IITLDEFEAIRLVD----YEDYTQEEAAKLMGISRRTVWRLLTSARKKIA 81 (100) T ss_pred EECHHHHHHHHHHH----HCCCCHHHHHHHCCCCHHHHHHHHHHHHHHHH T ss_conf 73499999999873----60798999998849769999999999999999 No 209 >pfam04748 Polysacc_deac_2 Divergent polysaccharide deacetylase. This family is divergently related to pfam01522 (personal obs:Yeats C). Probab=61.54 E-value=10 Score=16.72 Aligned_cols=141 Identities=21% Similarity=0.237 Sum_probs=76.0 Q ss_pred CCCCCCCHHCCHHHHHHHHHHHHHC-CCCCHHHHHHHCCCCCCCHHH-HHHHHHHHHHCCCEEECCCCCCCCCCCCCCCC Q ss_conf 6555443020289999999978784-886789997526843599888-99999999847977832784100001236432 Q gi|254780289|r 17 DSDDSLVFDFSDDSWKKMIKLARQR-GYVTIEELNAFLPPDEVSSEQ-MEDTVAMLSNMGINVVDGDDLEDEEGSEDSLD 94 (682) Q Consensus 17 ~~~~~~~~d~~~~~ik~LI~~gke~-GylTydeIn~~LP~d~~~~e~-ie~i~~~L~~~GI~Vve~~~~~~~~~~~~~~~ 94 (682) .+......++..+.++..+.....+ .+... +|+|..+.....++ |..++..|.+.|.-.+|+..........-... T Consensus 62 ~gp~~L~~~~~~~~i~~~l~~~l~~~p~avG--vnNhmGS~~t~~~~~m~~vl~~l~~~gl~fvDS~Tt~~S~a~~~A~~ 139 (213) T pfam04748 62 PGPGTLTVGMSAEEIEKRLEAALSRVPYAVG--VNNHMGSRFTADRAAMRWVMEELKKRGLFFVDSRTSGRSVAPKLAKE 139 (213) T ss_pred CCCCCCCCCCCHHHHHHHHHHHHHHCCCCEE--EECCCCCCCCCCHHHHHHHHHHHHHCCCEEEECCCCCCCHHHHHHHH T ss_conf 9977588899999999999999987888489--95466755416999999999999877988991477766589999998 Q ss_pred CCHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHH Q ss_conf 11011122334444200345777728999999856976889788999999999889999999872823899999999873 Q gi|254780289|r 95 LASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDEL 174 (682) Q Consensus 95 ~~~~~~~e~~~~~~~~~~e~~rtdDPVRMYLREMG~V~LLTREgEIeIAKRIE~G~~~i~~al~~~P~ti~~il~~~e~i 174 (682) ..-....- ....| ...+.+.|+-+|++. +.+||+ .|. ++..-.-+|.|+..+..|...+ T Consensus 140 ~gvp~~~r----dvfLD--~~~~~~~I~~ql~~~-----------~~~A~~--~G~--aI~Igh~~p~Tl~~L~~~~~~l 198 (213) T pfam04748 140 LGVPAAKR----DVFLD--NEQTEAAIRRQLDQA-----------AALARK--EGS--AIAIGHPHPETIAALKEWLPEL 198 (213) T ss_pred CCCCEEEE----EEECC--CCCCHHHHHHHHHHH-----------HHHHHH--CCC--EEEEECCCHHHHHHHHHHHHHH T ss_conf 39986761----03147--999999999999999-----------999986--395--7999779989999999986577 Q ss_pred HCCCHH Q ss_conf 117103 Q gi|254780289|r 175 NDGTTL 180 (682) Q Consensus 175 ~~ge~~ 180 (682) ....+. T Consensus 199 ~~~gi~ 204 (213) T pfam04748 199 RARGIE 204 (213) T ss_pred HHCCEE T ss_conf 658879 No 210 >TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor; InterPro: IPR000394 Sigma factors are bacterial transcription initiation factors that promote the attachment of the core RNA polymerase to specific initiation sites and are then released. They alter the specificity of promoter recognition. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma- 70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes: the sigma-54 and sigma-70 families. The sigma-70 family has many different sigma factors (see the relevant entry IPR000943 from INTERPRO). The sigma-54 family consists exclusively of sigma-54 factor , required for the transcription of promoters that have a characteristic -24 and -12 consensus recognition element but which are devoid of the typical -10, -35 sequences recognized by the major sigma factors. The sigma-54 factor is also characterised by its interaction with ATP-dependent positive regulatory proteins that bind to upstream activating sequences. Structurally sigma-54 factors consist of three distinct regions: A relatively well conserved N-terminal glutamine-rich region of about 50 residues that contains a potential leucine zipper motif. A region of variable length which is not well conserved. A well conserved C-terminal region of about 350 residues that contains a second potential leucine zipper, a potential DNA-binding 'helix-turn-helix' motif and a perfectly conserved octapeptide whose function is not known. ; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0003899 DNA-directed RNA polymerase activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent. Probab=60.98 E-value=10 Score=16.65 Aligned_cols=267 Identities=16% Similarity=0.187 Sum_probs=130.2 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHCCCHHHHHHH-----CC-CCCCCHHHHHH Q ss_conf 99999999999862100577887899999--999999999999999999712535777763-----16-77689899999 Q gi|254780289|r 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLY--DISKRIMHNEGELLRLAQSYGIKRDVFLER-----HQ-GRELDPHWVSY 386 (682) Q Consensus 315 ~kl~~eL~e~~~~lkl~~k~iE~L~~~l~--~~~k~Ir~~Er~L~rl~~k~~i~R~~Fi~~-----f~-gnEt~~~wl~~ 386 (682) +.+-..|.+.+..=.+-..-++.+.+.+. .-...+...-..|.++ +=.||--.++.+- -. -...++.|... T Consensus 134 ~~ia~~iI~~Ld~~GYL~~~~e~~~~~~~~~~~~~~v~~vl~~~Q~L-dP~GvgAr~L~EcL~LQl~~~~~~~~~~~~~~ 212 (477) T TIGR02395 134 RKIALYIIDALDEDGYLEEDLEEIADELEIEVSEEEVEKVLELIQRL-DPAGVGARDLQECLLLQLERRLDEDDTPLREL 212 (477) T ss_pred HHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHCC-CCCCCCCCCHHHHHHHHHHHHCCCCCCHHHHH T ss_conf 99999998501788852578899999728898888999999998423-88850117889999999865338998789999 Q ss_pred HHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHH-----HHHHHHHHHHHHHH--H------- Q ss_conf 8613551067655434567765322333322222112-6889999998765-----33211246899987--5------- Q gi|254780289|r 387 AKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS-ISEFRHIVSMVRK-----GECEASIAKKEMVE--A------- 451 (682) Q Consensus 387 ~~~~~~~~~~~~l~~~~~eI~~~q~kL~~ie~~~gl~-i~ElK~i~r~I~~-----ge~e~~~AK~~l~~--a------- 451 (682) ....-...... + +.+++..+...++++ ..+++....-|+. |..=........|- . T Consensus 213 a~~i~~~~~~~--------L--~~~~~~~l~~~~~~~~~~~~~~a~~~i~~L~P~Pg~~f~~~~~~~y~~~~PD~~v~~~ 282 (477) T TIGR02395 213 ALNILLEHLEL--------L--AEKDFKRLAKKLGLSSEEELKEALDLIKSLSPKPGKEFADPEEEEYVIVKPDVIVTKK 282 (477) T ss_pred HHHHHHHHHHH--------H--HHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCCCHHHHCCCCCCEEEEECCEEEEEEE T ss_conf 99998755679--------9--9853555798707998899999999997079986032236777603787364899883 Q ss_pred HHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCCHHHHHHHH Q ss_conf 55789998875223567778875443679999887438545731201028989999999997228704614205889899 Q gi|254780289|r 452 NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531 (682) Q Consensus 452 nlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~ 531 (682) |=.|+| ...++++|-..+-+.+.-.+-+ .++=+ +.-|+++...+|= |.|+.=--=.+|+.| T Consensus 283 ~~~~~~----~l~~~~~P~~~~~~~y~~~~~~-~~~~~----------~~~yl~~k~~eA~----wL~~~l~~R~~TL~~ 343 (477) T TIGR02395 283 NGEWVV----ELNKRSLPELRINEEYFKLLKK-AEKEA----------AQQYLKEKLQEAR----WLIKALEQREETLLR 343 (477) T ss_pred CCEEEE----EECCCCCCEEEECHHHHHHHHH-HHHHH----------HHHHHHHHHHHHH----HHHHHHHHHHHHHHH T ss_conf 878899----8737777614431868899874-22357----------8899999999999----999999998999999 Q ss_pred HH----HHHHHHHH---HCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCC-CCCHHHH Q ss_conf 99----99999877---6088999789998709998999999986089875536358899860475623898-8998999 Q gi|254780289|r 532 VV----RTARRMSN---KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKN-AVSPLDS 603 (682) Q Consensus 532 ~~----~~~~~~~~---~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~-~~~~~~~ 603 (682) +. ...+.++. ..=|+-|..+||+.+|+.+..|..+-+ -=+|.||.|= ..|-.|....- ...+... T Consensus 344 v~~~Iv~~Q~~FF~~g~~~LkPL~L~~vA~el~~heSTiSRai~----~KYl~T~~G~---f~Lk~FFS~~v~~~~~~~~ 416 (477) T TIGR02395 344 VAEAIVERQKDFFEGGPAALKPLTLREVAEELGLHESTISRAIN----NKYLQTPRGV---FELKYFFSSGVSTESAEGE 416 (477) T ss_pred HHHHHHHHHHHHHHCCHHCCCCCCHHHHHHHHCCCCCCEEEEEC----CCEEECCCCC---HHHHHHCCHHHCCCCCCHH T ss_conf 99999999999841452006886389999885889872463317----7357607640---3365431201203456503 Q ss_pred HHHHHHHHHHHHHHH Q ss_conf 999999999999973 Q gi|254780289|r 604 AIQANLRETTTRVLA 618 (682) Q Consensus 604 ~~~~~~~~~~~~~l~ 618 (682) ++....|..|.++++ T Consensus 417 ~S~~~ik~~~~~lI~ 431 (477) T TIGR02395 417 ASSTAIKALIKELIA 431 (477) T ss_pred HHHHHHHHHHHHHHH T ss_conf 469999999999997 No 211 >COG2856 Predicted Zn peptidase [Amino acid transport and metabolism] Probab=59.49 E-value=10 Score=16.73 Aligned_cols=16 Identities=25% Similarity=0.306 Sum_probs=5.6 Q ss_pred HHHHHCCCHHHHHHHC Q ss_conf 9997125357777631 Q gi|254780289|r 359 LAQSYGIKRDVFLERH 374 (682) Q Consensus 359 l~~k~~i~R~~Fi~~f 374 (682) .+...-||...|.+.| T Consensus 112 FAa~lLmP~~~l~~~~ 127 (213) T COG2856 112 FAAELLMPEEVLRERL 127 (213) T ss_pred HHHHHHCCHHHHHHHH T ss_conf 9999837849998632 No 212 >TIGR02147 Fsuc_second hypothetical protein, TIGR02147; InterPro: IPR011873 This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterised.. Probab=57.50 E-value=12 Score=16.22 Aligned_cols=118 Identities=24% Similarity=0.366 Sum_probs=76.2 Q ss_pred HHHHHHHCCCCC-CHHHHHHHCC--CCHHHHHHHHHHHCCCCCCCCCCCCCC-CCEEEEEECCCCCC-CHHHHH------ Q ss_conf 999877608899-9789998709--998999999986089875536358899-86047562389889-989999------ Q gi|254780289|r 536 ARRMSNKIKREP-TPEEIAKKLA--MPVEGVRKVLKITKEPISLETPIGDED-TSHLGDFIEDKNAV-SPLDSA------ 604 (682) Q Consensus 536 ~~~~~~~~~~~~-~~~~~a~~~~--~~~~~~~~~~~~~~~~~sl~~~~~~~~-~~~~~~~~~d~~~~-~~~~~~------ 604 (682) .|.+..-.+-.| .+++||..+. +|+..|+..+...-+ ++| |-.++ +.... ..|+.+. ++.+.. T Consensus 132 iRe~~~~~~~~~~~~~~la~~~~P~IS~~qvk~sl~LL~~-l~l---i~K~~q~G~y~--~~~~~vs~~g~e~~~~av~~ 205 (281) T TIGR02147 132 IRELVAVMPFADDDPEELAKRLKPKISAEQVKESLDLLER-LGL---IKKNEQDGFYK--QTDKAVSMTGSEVIPLAVRQ 205 (281) T ss_pred HHHHHHHCCCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHH-CCC---CEEECCCCCEE--EECCCEEECCHHHHHHHHHH T ss_conf 9999875489999868999870798578999999999862-332---01103058767--60760660746568999999 Q ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHH Q ss_conf 9999999999997329988999999981879867468899989966789999999999 Q gi|254780289|r 605 IQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662 (682) Q Consensus 605 ~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~ 662 (682) -...+-+.=.++|..+|+-+|.|=-+=||+... |+.+|-+....=|-.|..|=++ T Consensus 206 y~~Q~~~La~~al~~~~~~~R~~S~~T~g~~~~---~y~~i~~~i~~fR~~~~~~~~~ 260 (281) T TIGR02147 206 YQKQMIDLAKEALDALPPEERDVSTVTLGISEE---AYKEIVKKIQEFRKEVLAIAAK 260 (281) T ss_pred HHHHHHHHHHHHHHHCCCCCCCEEEEEECCCHH---HHHHHHHHHHHHHHHHHHHHHC T ss_conf 879999999999971789876313003233599---9999999999999999999841 No 213 >COG3824 Predicted Zn-dependent protease [General function prediction only] Probab=57.33 E-value=4.6 Score=19.48 Aligned_cols=27 Identities=26% Similarity=0.570 Sum_probs=22.1 Q ss_pred CCCCC-HHHHHHHHCCCHHHHHHHHHHH Q ss_conf 67468-8999899667899999999999 Q gi|254780289|r 637 NTDHT-LEEVGKQFCVTRERIRQIEAKA 663 (682) Q Consensus 637 ~~~~t-l~e~~~~~~~~~er~rqi~~~a 663 (682) .-.|| ++|||-.||+|-+++-|||..| T Consensus 108 ~vthvliHEIgHhFGLsDdd~~rie~~a 135 (136) T COG3824 108 QVTHVLIHEIGHHFGLSDDDLERIEWAA 135 (136) T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHHCC T ss_conf 7443023532212387776898754303 No 214 >KOG2727 consensus Probab=57.03 E-value=12 Score=16.17 Aligned_cols=54 Identities=22% Similarity=0.324 Sum_probs=40.0 Q ss_pred HHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHH Q ss_conf 989999999997228704614205889899999999987760889997899987099989999999 Q gi|254780289|r 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVL 567 (682) Q Consensus 502 ~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~ 567 (682) |-+|+.|.|-|-+ .++-+...++-.+.+..||-|-..+--+.+||+..++...+ T Consensus 922 ~~l~hGIa~miWn------------~fl~~~fqaa~~lv~KvGr~PkDk~crkdigms~~k~~eFL 975 (1244) T KOG2727 922 PRLRHGIARMIWN------------KFLFMVFQAAVNLVEKVGRRPKDKECRKDIGMSEVKLEEFL 975 (1244) T ss_pred HHHHCCHHHHHHH------------HHHHHHHHHHHHHHHHHCCCCCCHHHHHHCCCCCCHHHHHH T ss_conf 6886214999998------------89999999999999984789732677874175400079999 No 215 >pfam10078 DUF2316 Uncharacterized protein conserved in bacteria (DUF2316). Members of this family of hypothetical bacterial proteins have no known function. Probab=57.03 E-value=12 Score=16.17 Aligned_cols=37 Identities=24% Similarity=0.306 Sum_probs=27.1 Q ss_pred HHHHHHHH-C-CCCCCHHHHHHHCCCCHHHHHHHHHHHC Q ss_conf 99998776-0-8899978999870999899999998608 Q gi|254780289|r 535 TARRMSNK-I-KREPTPEEIAKKLAMPVEGVRKVLKITK 571 (682) Q Consensus 535 ~~~~~~~~-~-~~~~~~~~~a~~~~~~~~~~~~~~~~~~ 571 (682) ++++-+|+ + --.-|.+++|..|++|+++|..+|.+.+ T Consensus 10 ~T~~ELqeNf~~~~ls~~~iA~dL~~s~~~ve~vL~m~~ 48 (89) T pfam10078 10 ATRKELQANFELSGLTIEQVAKDLNTTPEKVEALLQLKQ 48 (89) T ss_pred HHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCC T ss_conf 999999999988389899999894999999999997346 No 216 >pfam12324 HTH_15 Helix-turn-helix domain of alkylmercury lyase. Alkylmercury lyase (EC:4.99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. This is the N terminal helix-turn-helix domain associated with pfam03243. Probab=56.81 E-value=12 Score=16.14 Aligned_cols=36 Identities=33% Similarity=0.304 Sum_probs=28.8 Q ss_pred HHHHHHH--CCCCCCHHHHHHHCCCCHHHHHHHHHHHC Q ss_conf 9998776--08899978999870999899999998608 Q gi|254780289|r 536 ARRMSNK--IKREPTPEEIAKKLAMPVEGVRKVLKITK 571 (682) Q Consensus 536 ~~~~~~~--~~~~~~~~~~a~~~~~~~~~~~~~~~~~~ 571 (682) .+-+++. .|++-|++.||..+|.|+++|+.+|.... T Consensus 26 ~~~LLr~La~G~PVt~~~LA~a~g~~~e~V~~~L~~~p 63 (77) T pfam12324 26 FRPLLRMLADGRPVTREDLAGATGKPVERVAKVLAQAP 63 (77) T ss_pred HHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHCC T ss_conf 99999999479986899999896989999999998588 No 217 >PRK09943 DNA-binding transcriptional repressor PuuR; Provisional Probab=56.67 E-value=12 Score=16.13 Aligned_cols=22 Identities=18% Similarity=0.422 Sum_probs=9.2 Q ss_pred HHHHHHHHHHHHHCCCCCCHHHHHH Q ss_conf 5557899988752235677788754 Q gi|254780289|r 451 ANLRLVISVAKKYTNRGLQFLDLIQ 475 (682) Q Consensus 451 anlr~v~~~~~~~~~~~~~~~~~~~ 475 (682) +.|..+..||+-+ |+++.+|+. T Consensus 47 PSl~tL~kIa~aL---~v~l~~lf~ 68 (185) T PRK09943 47 PAISTLQKLLKVY---GLSLSEFFS 68 (185) T ss_pred CCHHHHHHHHHHH---CCCHHHHHC T ss_conf 9999999999984---999999827 No 218 >COG2186 FadR Transcriptional regulators [Transcription] Probab=55.86 E-value=11 Score=16.34 Aligned_cols=19 Identities=21% Similarity=0.382 Sum_probs=8.0 Q ss_pred HHHHHHHHHHHHHHHHHHC Q ss_conf 9998755578999887522 Q gi|254780289|r 446 KEMVEANLRLVISVAKKYT 464 (682) Q Consensus 446 ~~l~~anlr~v~~~~~~~~ 464 (682) ....++.+.|-..||.--. T Consensus 145 ~~~~~aD~~FH~aIa~as~ 163 (241) T COG2186 145 EAFAEADLAFHLAIAEASG 163 (241) T ss_pred HHHHHHHHHHHHHHHHHCC T ss_conf 1207889999999999839 No 219 >pfam01698 FLO_LFY Floricaula / Leafy protein. This family consists of various plant development proteins which are homologues of floricaula (FLO) and Leafy (LFY) proteins which are floral meristem identity proteins. Mutations in the sequences of these proteins affect flower and leaf development. Probab=55.78 E-value=12 Score=16.12 Aligned_cols=43 Identities=21% Similarity=0.410 Sum_probs=22.7 Q ss_pred HHHHHHHHHHHHCC--CCCHHHHHHH------CCCCCCCHHHHHHHHHHHHHC Q ss_conf 99999999787848--8678999752------684359988899999999847 Q gi|254780289|r 29 DSWKKMIKLARQRG--YVTIEELNAF------LPPDEVSSEQMEDTVAMLSNM 73 (682) Q Consensus 29 ~~ik~LI~~gke~G--ylTydeIn~~------LP~d~~~~e~ie~i~~~L~~~ 73 (682) -.++.|=.+-+.=| |.|-+-|.+. | -.+.-+.+|+.|..|.+. T Consensus 44 ~~l~gLEdLF~~YGVRy~TaAKIaELGFTasTL--v~MkdeELDdMM~sLs~i 94 (382) T pfam01698 44 RKLRGLEELFQAYGVRYYTAAKIAELGFTVSTL--VNMKDEELDDMMNSLSHI 94 (382) T ss_pred CCCCCHHHHHHHCCCHHHHHHHHHHHCCHHHHH--HCCCHHHHHHHHHHHHHH T ss_conf 553449999884285199999999715449876--467688999999999976 No 220 >COG1476 Predicted transcriptional regulators [Transcription] Probab=55.37 E-value=13 Score=15.97 Aligned_cols=21 Identities=43% Similarity=0.474 Sum_probs=10.8 Q ss_pred CHHHHHHHHCCCHHHHHHHHH Q ss_conf 889998996678999999999 Q gi|254780289|r 641 TLEEVGKQFCVTRERIRQIEA 661 (682) Q Consensus 641 tl~e~~~~~~~~~er~rqi~~ 661 (682) |=++.|+..||||.-|-.||. T Consensus 16 tQ~elA~~vgVsRQTi~~iEk 36 (68) T COG1476 16 TQEELAKLVGVSRQTIIAIEK 36 (68) T ss_pred CHHHHHHHCCCCHHHHHHHHC T ss_conf 899999991957999999991 No 221 >KOG2773 consensus Probab=55.19 E-value=13 Score=15.95 Aligned_cols=171 Identities=15% Similarity=0.138 Sum_probs=82.5 Q ss_pred HHHHHHHHHHHHHHHHH-HHCCCHHHHHHHCCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999999999999999-71253577776316776898999998613551067655434567765322333322222112 Q gi|254780289|r 345 ISKRIMHNEGELLRLAQ-SYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGIS 423 (682) Q Consensus 345 ~~k~Ir~~Er~L~rl~~-k~~i~R~~Fi~~f~gnEt~~~wl~~~~~~~~~~~~~~l~~~~~eI~~~q~kL~~ie~~~gl~ 423 (682) +-..|......+.+-|. -..+|..+.+..|..-.. ...+..+.........+.+.|..+...+-.. T Consensus 193 lwD~ile~Ri~lQKa~~~anqLP~~ev~~lf~sd~~-------------ee~st~lke~~k~l~kll~~ll~lr~~ll~~ 259 (483) T KOG2773 193 LWDNILELRIKLQKADDDANQLPQPEVLSLFKSDDE-------------EELSTALKELAKNLKKLLQSLLKLREALLTK 259 (483) T ss_pred HHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCC-------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC T ss_conf 999899888888875555530787066787631663-------------6677899999999999999999999998623 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHCCCCC-CHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHH Q ss_conf 6889999998765332112468999875557899--98875223567-77887544367999988743854573120102 Q gi|254780289|r 424 ISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI--SVAKKYTNRGL-QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500 (682) Q Consensus 424 i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~--~~~~~~~~~~~-~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya 500 (682) ...-..++..=+.-+.. .-+..|-+--++.+- +--..|+|..| .|.|.+|-.+-|...--.+|-.- T Consensus 260 ~~~~~~~v~~k~~~E~~--~~~~~l~~~~~~i~sl~~~~~~yrN~~L~KW~dkt~~~sg~a~~~~~kf~~~--------- 328 (483) T KOG2773 260 YPNTTKIVNAKKSFESG--KFKRSLKEFSLEINSLDFFLLEYRNKVLRKWHDKTQLASGGAAPKCKKFLIP--------- 328 (483) T ss_pred CCHHHHHHHCCCCCCCC--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHCC--------- T ss_conf 73045564057742245--3016688999999888999999989999987412453166322110234054--------- Q ss_pred HHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHH Q ss_conf 898999999999722870461420588989999999998776088999789 Q gi|254780289|r 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551 (682) Q Consensus 501 ~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 551 (682) +-|-+.|..+..+..|.++ -+++.|..+.-+++-|-+.. T Consensus 329 -~~i~~Qi~~~l~d~erl~~-----------rtq~~r~~~~v~~~~pe~a~ 367 (483) T KOG2773 329 -FSINFQIEHFLDDPERLVK-----------RTQTMRRKFSVLARFPENAQ 367 (483) T ss_pred -CHHHHHHHHHHHCHHHHHH-----------HHHHCCCCCCCCCCCCCHHC T ss_conf -3178999998618999998-----------75321331232345760210 No 222 >pfam08279 HTH_11 HTH domain. This family includes helix-turn-helix domains in a wide variety of proteins. Probab=53.92 E-value=13 Score=15.80 Aligned_cols=22 Identities=27% Similarity=0.450 Sum_probs=12.5 Q ss_pred CCHHHHHHHCCCCHHHHHHHHH Q ss_conf 9978999870999899999998 Q gi|254780289|r 547 PTPEEIAKKLAMPVEGVRKVLK 568 (682) Q Consensus 547 ~~~~~~a~~~~~~~~~~~~~~~ 568 (682) -|..+||+.|++|..-|..-++ T Consensus 16 vt~~~La~~l~VSr~TV~rdi~ 37 (55) T pfam08279 16 ISGQELAEKLGVSRRTIRRDIK 37 (55) T ss_pred CCHHHHHHHHCCCHHHHHHHHH T ss_conf 1899999996988999999999 No 223 >PRK11564 stationary phase inducible protein CsiE; Provisional Probab=53.61 E-value=14 Score=15.77 Aligned_cols=48 Identities=13% Similarity=0.263 Sum_probs=24.5 Q ss_pred HHHHHHHHHCCCCCHHHHHHHCC-CCCCCHHHHHHHHHHHHHC-CCEEEC Q ss_conf 99999787848867899975268-4359988899999999847-977832 Q gi|254780289|r 32 KKMIKLARQRGYVTIEELNAFLP-PDEVSSEQMEDTVAMLSNM-GINVVD 79 (682) Q Consensus 32 k~LI~~gke~GylTydeIn~~LP-~d~~~~e~ie~i~~~L~~~-GI~Vve 79 (682) -=|+.+--....||-+.+.+.|- +...-..++.++-.-|..- ++.+.- T Consensus 19 ~ill~Ll~~~e~vtl~~L~~~l~VSr~Ti~~DLk~l~~~L~~y~~L~L~~ 68 (426) T PRK11564 19 QILLMLFQPGLTVTLETISQLNGVDDDIARQDIAETAREIQRYHHLTLTT 68 (426) T ss_pred HHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCEEEEE T ss_conf 99999977999734999999969988899999999999983008869998 No 224 >TIGR01764 excise DNA binding domain, excisionase family; InterPro: IPR010093 An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This entry represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This entry identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (IPR000551 from INTERPRO).; GO: 0003677 DNA binding. Probab=53.28 E-value=14 Score=15.73 Aligned_cols=25 Identities=24% Similarity=0.238 Sum_probs=20.3 Q ss_pred CCHHHHHHHCCCCHHHHHHHHHHHC Q ss_conf 9978999870999899999998608 Q gi|254780289|r 547 PTPEEIAKKLAMPVEGVRKVLKITK 571 (682) Q Consensus 547 ~~~~~~a~~~~~~~~~~~~~~~~~~ 571 (682) -|++|.|+.||+|...|.++.+-.. T Consensus 2 lTv~EaA~yLgv~~~t~~~l~~~g~ 26 (49) T TIGR01764 2 LTVEEAAEYLGVSKSTVYRLIEEGE 26 (49) T ss_pred CCHHHHHHHCCCCHHHHHHHHHCCC T ss_conf 8778899771999057899997189 No 225 >PRK07023 short chain dehydrogenase; Provisional Probab=53.27 E-value=14 Score=15.73 Aligned_cols=89 Identities=16% Similarity=0.034 Sum_probs=56.1 Q ss_pred HHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHH Q ss_conf 78999887522356777887544367999988743854573120102898999999999722870461420588989999 Q gi|254780289|r 454 RLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVV 533 (682) Q Consensus 454 r~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~ 533 (682) -.+.|++-.....|...-----.|-.|++++.-.- ..+|.|..+.+--||.-.+++.+...... +..+. T Consensus 133 InisS~a~~~~~~~~~~Y~aSKaal~~~t~sla~E-~~~~IrVn~V~PG~v~T~m~~~~~~~~~~---~~~~~------- 201 (243) T PRK07023 133 LHISSGAARNAYAGWSVYCATKAALDHHARAVALE-ANRALRIVSLAPGVVDTGMQATIRATDEE---RFPMR------- 201 (243) T ss_pred EEEECHHHCCCCCCCHHHHHHHHHHHHHHHHHHHH-CCCCCEEEEEECCCCCCHHHHHHHHCCCC---CHHHH------- T ss_conf 57833111678999668999999999999999986-79998899996377977466787545830---07999------- Q ss_pred HHHHHHHHHCCCCCCHHHHHH Q ss_conf 999998776088999789998 Q gi|254780289|r 534 RTARRMSNKIKREPTPEEIAK 554 (682) Q Consensus 534 ~~~~~~~~~~~~~~~~~~~a~ 554 (682) ..-.-.+.+||-.||+|+|. T Consensus 202 -~~~~~~~p~GR~g~PedVA~ 221 (243) T PRK07023 202 -ERFRQLKASGALSTPEDAAR 221 (243) T ss_pred -HHHHHCCCCCCCCCHHHHHH T ss_conf -99870688899768999999 No 226 >PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional Probab=52.94 E-value=14 Score=15.69 Aligned_cols=19 Identities=26% Similarity=0.356 Sum_probs=13.7 Q ss_pred CCCCCHHHHHHHCCCCHHH Q ss_conf 8899978999870999899 Q gi|254780289|r 544 KREPTPEEIAKKLAMPVEG 562 (682) Q Consensus 544 ~~~~~~~~~a~~~~~~~~~ 562 (682) ..--|.||||+.+|+|+.. T Consensus 19 nPF~TDeeLa~~f~VSiqT 37 (185) T PRK04424 19 NPFITDEELAEKFGVSIQT 37 (185) T ss_pred CCCCCHHHHHHHCCCEEEE T ss_conf 8998779999860957778 No 227 >pfam02885 Glycos_trans_3N Glycosyl transferase family, helical bundle domain. This family includes anthranilate phosphoribosyltransferase (TrpD), thymidine phosphorylase. All these proteins can transfer a phosphorylated ribose substrate. Probab=52.56 E-value=14 Score=15.65 Aligned_cols=47 Identities=23% Similarity=0.218 Sum_probs=37.0 Q ss_pred HHHHHHHHHHCCCCCHHHHHHHCC---CCCCCHHHHHHHHHHHHHCCCEE Q ss_conf 999999787848867899975268---43599888999999998479778 Q gi|254780289|r 31 WKKMIKLARQRGYVTIEELNAFLP---PDEVSSEQMEDTVAMLSNMGINV 77 (682) Q Consensus 31 ik~LI~~gke~GylTydeIn~~LP---~d~~~~e~ie~i~~~L~~~GI~V 77 (682) ++.+|++=...+-||++|+..++- ++.+++.|+-.+...|...|... T Consensus 2 ~~~~l~kl~~g~~Ls~~e~~~~~~~i~~g~~s~~qi~afL~al~~kget~ 51 (66) T pfam02885 2 IKELIKKLLRGEDLSREEAEALMDAIMSGEASDAQIAAFLMALRIKGETP 51 (66) T ss_pred HHHHHHHHHCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCH T ss_conf 89999999859997999999999999869999999999999999839999 No 228 >pfam06239 ECSIT Evolutionarily conserved signalling intermediate in Toll pathway. Activation of NF-kappaB as a consequence of signaling through the Toll and IL-1 receptors is a major element of innate immune responses. ECSIT plays an important role in signalling to NF-kappaB, functioning as the intermediate in the signaling pathways between TRAF-6 and MEKK-1. Probab=52.02 E-value=14 Score=15.59 Aligned_cols=27 Identities=4% Similarity=0.007 Sum_probs=14.3 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 532233332222211268899999987 Q gi|254780289|r 408 KIRNEIKSISVETGISISEFRHIVSMV 434 (682) Q Consensus 408 ~~q~kL~~ie~~~gl~i~ElK~i~r~I 434 (682) -+..-|..+|.+--+|-.|...+.-.| T Consensus 122 cai~vLeqME~~gV~Pd~E~~~ll~~i 148 (229) T pfam06239 122 CAIDVLEQMENHGVMPDKETEFLLVNI 148 (229) T ss_pred HHHHHHHHHHHCCCCCCHHHHHHHHHH T ss_conf 999999999983888958999999999 No 229 >TIGR02607 antidote_HigA addiction module antidote protein, HigA family; InterPro: IPR013430 Proteins in this entry form a distinct group of helix-turn-helix proteins, which are strictly bacterial and nearly always shorter than 110 amino acids. They include the characterised member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is encoded by the upstream member of the gene pair.; GO: 0003677 DNA binding. Probab=51.96 E-value=13 Score=15.90 Aligned_cols=40 Identities=10% Similarity=0.244 Sum_probs=26.4 Q ss_pred HHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCC Q ss_conf 9987760889997899987099989999999860898755363 Q gi|254780289|r 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP 579 (682) Q Consensus 537 ~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~ 579 (682) .+++..+ .-|..++|+.||+|...+..+.. .+.+||-|+- T Consensus 13 eEfL~PL--g~s~~~LA~~LgVsr~~~sriv~-~~~~iT~dmA 52 (81) T TIGR02607 13 EEFLEPL--GLSVRALAKALGVSRSTLSRIVN-GRRGITADMA 52 (81) T ss_pred HHHHHCC--CHHHHHHHHHCCCCHHHHHHHHH-CCCCCCHHHH T ss_conf 7752104--70689999870999788888874-4899888899 No 230 >PRK02842 light-independent protochlorophyllide reductase subunit N; Provisional Probab=51.71 E-value=11 Score=16.41 Aligned_cols=45 Identities=27% Similarity=0.378 Sum_probs=30.8 Q ss_pred HHHHHHHHHHHCCC-CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH Q ss_conf 88999999981879-8674688999899667899999999999998 Q gi|254780289|r 622 PREERVLRMRFGIG-MNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666 (682) Q Consensus 622 ~re~~v~~~r~g~~-~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~ 666 (682) .|-.++|..-|-+| +|+..-++.++..|||+.++++..++.+..+ T Consensus 232 ~RGa~~i~ApFP~G~eGT~~Wl~aiA~~fgv~~~~~~~~~~~~~aR 277 (425) T PRK02842 232 ERGAKVLTAPFPLGPEGTRAWLEAAAAAFGIDPDGLEEREAPAWER 277 (425) T ss_pred HCCCCEECCCCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH T ss_conf 5298310578987840169999999998499888899888878888 No 231 >COG1510 Predicted transcriptional regulators [Transcription] Probab=51.57 E-value=12 Score=16.22 Aligned_cols=26 Identities=35% Similarity=0.360 Sum_probs=14.7 Q ss_pred CCCCCHHHHHHHCCCCHHHHHHHHHH Q ss_conf 88999789998709998999999986 Q gi|254780289|r 544 KREPTPEEIAKKLAMPVEGVRKVLKI 569 (682) Q Consensus 544 ~~~~~~~~~a~~~~~~~~~~~~~~~~ 569 (682) ..+-|..||++.+|||...|..+++- T Consensus 39 ~~Pmtl~Ei~E~lg~Sks~vS~~lkk 64 (177) T COG1510 39 RKPLTLDEIAEALGMSKSNVSMGLKK 64 (177) T ss_pred CCCCCHHHHHHHHCCCCCHHHHHHHH T ss_conf 99966999999977780128899999 No 232 >PRK01381 Trp operon repressor; Provisional Probab=50.53 E-value=15 Score=15.42 Aligned_cols=42 Identities=24% Similarity=0.261 Sum_probs=24.2 Q ss_pred HHHHHHHC-CCHHHHHHHHHHHCCCC---CCCCCHHHHHHHHCCCH Q ss_conf 99999732-99889999999818798---67468899989966789 Q gi|254780289|r 612 TTTRVLAS-LTPREERVLRMRFGIGM---NTDHTLEEVGKQFCVTR 653 (682) Q Consensus 612 ~~~~~l~~-l~~re~~v~~~r~g~~~---~~~~tl~e~~~~~~~~~ 653 (682) ....+|.. |+|.|+.-|..|+-|-. ...++-.||++.+||+= T Consensus 24 ~~~~ll~~lLTp~Er~al~~R~~I~~~Ll~ge~sQReIa~~lgvsi 69 (99) T PRK01381 24 LHLPLLTLLLTPDEREALGTRVRIVEELLRGELSQREIKQELGVGI 69 (99) T ss_pred HHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCC T ss_conf 6999999978999999999999999999948764999999849740 No 233 >PRK01388 arginine deiminase; Provisional Probab=50.34 E-value=12 Score=16.27 Aligned_cols=42 Identities=17% Similarity=0.135 Sum_probs=35.5 Q ss_pred HHHCCCCCHHHHHHHCCCCCCCHHHH----HHHHHHHHHCCCEEEC Q ss_conf 87848867899975268435998889----9999999847977832 Q gi|254780289|r 38 ARQRGYVTIEELNAFLPPDEVSSEQM----EDTVAMLSNMGINVVD 79 (682) Q Consensus 38 gke~GylTydeIn~~LP~d~~~~e~i----e~i~~~L~~~GI~Vve 79 (682) |.|-.+||-+-+.+.|=+|++..+.. +.....|.+.||+|+. T Consensus 24 G~El~~ltP~~~~~lLFddi~~l~~A~~EHd~f~~~Lr~~GveV~~ 69 (410) T PRK01388 24 GLELERLTPSNCDELLFDDVPWVERAQKEHDAFAQTLRERGVEVLY 69 (410) T ss_pred CHHHHHCCCCCHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCCEEEE T ss_conf 5898855911146651055658999999999999999868988998 No 234 >TIGR02865 spore_II_E stage II sporulation protein E; InterPro: IPR014221 This entry contains the stage II sporulation protein E (SpoIIE), which is a multiple membrane spanning protein with two separable functions. It plays a role in the switch to polar cell division during sporulation and it has phosphatase activity, located in the C-terminal region, which is required to activate sigma-F. All members of this entry are found in endospore-forming Gram-positive bacteria. A homologous protein, not a member of this entry, is found in the Cyanobacterium-like (and presumably non-spore-forming) photosynthesizer Heliobacillus mobilis.. Probab=50.05 E-value=15 Score=15.37 Aligned_cols=64 Identities=17% Similarity=0.213 Sum_probs=31.8 Q ss_pred CCCCCCC-CCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHC-CCHHHH-----HHHHHHHCCC Q ss_conf 9875536-35889986047562389889989999999999999999732-998899-----9999981879 Q gi|254780289|r 572 EPISLET-PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS-LTPREE-----RVLRMRFGIG 635 (682) Q Consensus 572 ~~~sl~~-~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~-l~~re~-----~v~~~r~g~~ 635 (682) +.||=|. ..|+=.+..+.-.|.|-=..-|.-..+....=..|.+.+.. +++.=+ -||.+||+=+ T Consensus 590 e~vSGDSY~~~~L~~Gky~~~iSDGMG~G~~A~~ES~a~~~LlEk~l~~Gf~~~~AI~tvNSil~LrF~~~ 660 (794) T TIGR02865 590 ELVSGDSYSFGKLSAGKYAVAISDGMGSGPEAAQESSACVRLLEKFLESGFDREVAIKTVNSILSLRFSED 660 (794) T ss_pred CCCCCCEEEEEECCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCCCC T ss_conf 94016556776317970799985479981889999999999999999707887689999889973148998 No 235 >pfam10668 Phage_terminase Phage terminase small subunit. This family of small highly conserved proteins come from a subset of Firmicute species. Its putative function is as a phage terminase small subunit. Probab=50.04 E-value=15 Score=15.36 Aligned_cols=32 Identities=25% Similarity=0.269 Sum_probs=22.1 Q ss_pred HHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHH Q ss_conf 99998776088999789998709998999999 Q gi|254780289|r 535 TARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566 (682) Q Consensus 535 ~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~ 566 (682) .+.++..+.|-.-+.-+||+.|++|...|+.= T Consensus 11 kA~eiy~~s~G~~~l~~IA~~L~vs~~~IrkW 42 (60) T pfam10668 11 KAKEMWKESGGTMKLKDIANKLNVSESQIRKW 42 (60) T ss_pred HHHHHHHHCCCCEEHHHHHHHHCCCHHHHHHC T ss_conf 99999998289644999999968798887603 No 236 >pfam11913 DUF3431 Protein of unknown function (DUF3431). This family of proteins are functionally uncharacterized. This protein is found in eukaryotes. Proteins in this family are typically between 291 to 390 amino acids in length. This protein has a conserved NLRC sequence motif. Probab=49.36 E-value=2.8 Score=21.22 Aligned_cols=24 Identities=33% Similarity=0.517 Sum_probs=18.5 Q ss_pred HHHHCCCHHHHHHHHHHHHHHHCC Q ss_conf 899667899999999999998329 Q gi|254780289|r 646 GKQFCVTRERIRQIEAKAIRKLKH 669 (682) Q Consensus 646 ~~~~~~~~er~rqi~~~a~~~l~~ 669 (682) +.+|.||||||||.-..-..++|. T Consensus 158 CaQFaVsre~Ir~rP~~~Y~~~r~ 181 (222) T pfam11913 158 CAQFAVSRERIRKRPREDYVRYRQ 181 (222) T ss_pred EEEEEEEHHHHHHCCHHHHHHHHH T ss_conf 342326399998689999999999 No 237 >KOG3099 consensus Probab=49.30 E-value=16 Score=15.28 Aligned_cols=11 Identities=18% Similarity=0.425 Sum_probs=4.0 Q ss_pred CCCCCCHHHHH Q ss_conf 67768989999 Q gi|254780289|r 375 QGRELDPHWVS 385 (682) Q Consensus 375 ~gnEt~~~wl~ 385 (682) .+|+....|+. T Consensus 109 ~~~~va~e~la 119 (340) T KOG3099 109 SGNEVAAEILA 119 (340) T ss_pred CCCCHHHHHHH T ss_conf 77621499987 No 238 >pfam12128 DUF3584 Protein of unknown function (DUF3584). This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 943 to 1234 amino acids in length. There are two conserved sequence motifs: GKT and YLP. Probab=48.51 E-value=16 Score=15.19 Aligned_cols=16 Identities=31% Similarity=0.364 Sum_probs=10.3 Q ss_pred HHHHHHHHHHCCCCCC Q ss_conf 6799998874385457 Q gi|254780289|r 478 NIGLMKAAEKFDWCLG 493 (682) Q Consensus 478 ~~~l~~a~~~~~~~~g 493 (682) --.+.+++++|+.--. T Consensus 907 ~~~~~~~~~~f~~~~~ 922 (1192) T pfam12128 907 SGDLKKFVERFDGVIA 922 (1192) T ss_pred HHHHHHHHHHHHHHHH T ss_conf 9999999999899998 No 239 >pfam02682 AHS1 Allophanate hydrolase subunit 1. This family is the first subunit of allophanate hydrolase. Probab=48.27 E-value=16 Score=15.17 Aligned_cols=47 Identities=28% Similarity=0.317 Sum_probs=33.7 Q ss_pred HHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCC Q ss_conf 722870461420588989999999998776088999789998709998999999986089875 Q gi|254780289|r 513 ADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPIS 575 (682) Q Consensus 513 ~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~s 575 (682) ...+++++|||.--.. --|..+++|+..|++.++|-++.....-.|. T Consensus 82 ~~~~~~~~IPV~Yd~~----------------~gpDL~~va~~~gLs~~evI~~Hs~~~y~V~ 128 (202) T pfam02682 82 AAPSRIIEIPVCYGGE----------------FGPDLEEVAEHNGLSVEEVIRLHSAAEYRVY 128 (202) T ss_pred CCCCCEEEEEEEECCC----------------CCCCHHHHHHHHCCCHHHHHHHHHCCCEEEE T ss_conf 6898489997688996----------------6879999999839499999999856787999 No 240 >TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Polaromonas, Burkholderia, Ralstonia and Verminephrobacter. Probab=47.98 E-value=16 Score=15.13 Aligned_cols=46 Identities=20% Similarity=0.267 Sum_probs=18.9 Q ss_pred HHHHHHHHHHHHHC-C-CCCHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCE Q ss_conf 89999999978784-8-8678999752684359988899999999847977 Q gi|254780289|r 28 DDSWKKMIKLARQR-G-YVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGIN 76 (682) Q Consensus 28 ~~~ik~LI~~gke~-G-ylTydeIn~~LP~d~~~~e~ie~i~~~L~~~GI~ 76 (682) -+.|+..|--|.=. | .|+-.+|.+-|. ++---+=+.+..|...|+- T Consensus 17 ~~~lr~~I~~g~l~pG~~L~E~~La~~~g---VSRtpvREAL~~L~~eGlv 64 (212) T TIGR03338 17 QDEIERAILSGELPPGAKLNESDIAARLG---VSRGPVREAFRALEEAGLV 64 (212) T ss_pred HHHHHHHHHCCCCCCCCCCCHHHHHHHHC---CCHHHHHHHHHHHHHCCCH T ss_conf 99999999839999909818999999889---6949999999999986963 No 241 >TIGR01026 fliI_yscN ATPase FliI/YscN family; InterPro: IPR005714 Proteins in this entry show extensive homology to the ATP synthase F1 beta subunit, and are involved in type III protein secretion. They fall into the two separate functional groups outlined below. The first group, exemplified by the Salmonella typhimurium FliI protein (P26465 from SWISSPROT), is needed for flagellar assembly. Most structural components of the bacterial flagellum are translocated through the central channel of the growing flagellar structure by the type III flagellar protein-export apparatus in an ATPase-driven manner, to be assembled at the growing end. FliI is the ATPase that couples ATP hydrolysis to the translocation reaction , . The second group couples ATP hydrolysis to protein translocation in non-flagellar type III secretion systems. Often these systems are involved in virulence and pathogenicity. YscN (P40290 from SWISSPROT) from pathogenic Yersinia species, for example, energises the injection of antihost factors directly into eukaryotic cells, thus overcoming host defences .; GO: 0016887 ATPase activity, 0009058 biosynthetic process, 0015031 protein transport, 0005737 cytoplasm. Probab=47.46 E-value=17 Score=15.08 Aligned_cols=41 Identities=17% Similarity=0.293 Sum_probs=33.8 Q ss_pred HHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCH Q ss_conf 99999997228704614205889899999999987760889997 Q gi|254780289|r 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549 (682) Q Consensus 506 ~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 549 (682) -+|-.|++||...|=+ |.+.+.++-++.|++--..|-+||. T Consensus 253 t~iAEYFrdqGk~VlL---lmDSvTRfA~AqREiGLA~GEPP~~ 293 (455) T TIGR01026 253 TAIAEYFRDQGKDVLL---LMDSVTRFAMAQREIGLAAGEPPAT 293 (455) T ss_pred HHHHHHHHHCCCEEEE---EHHHHHHHHHHHHHHHHHCCCCCCC T ss_conf 2543546521870562---0202789988988998743777777 No 242 >TIGR02546 III_secr_ATP type III secretion apparatus H+-transporting two-sector ATPase; InterPro: IPR013380 Proteins in this entry are found in a variety of bacteria, and are predicted to be ATPases involved in type III secretion systems. One example is YscN (P40290 from SWISSPROT) from Yersinia enterocolitica, which is thought to energise the YOP (Yersinia outer protein) secretion system .; GO: 0046961 hydrogen ion transporting ATPase activity rotational mechanism, 0030254 protein secretion by the type III secretion system. Probab=47.46 E-value=17 Score=15.08 Aligned_cols=43 Identities=21% Similarity=0.318 Sum_probs=35.6 Q ss_pred HHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHH Q ss_conf 9999999722870461420588989999999998776088999789 Q gi|254780289|r 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551 (682) Q Consensus 506 ~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 551 (682) -+|-.|+.||.+.|=+ |.+++.++-|+.|+.--..|-+|+-.. T Consensus 232 TaIAEYFRDQGk~VlL---mmDSlTRfARA~REiGLAaGEP~aR~G 274 (430) T TIGR02546 232 TAIAEYFRDQGKRVLL---MMDSLTRFARALREIGLAAGEPPARRG 274 (430) T ss_pred HHHHHHHHHCCCEEEE---EEECHHHHHHHHHHHHHHCCCCCCCCC T ss_conf 7999999973990798---840277999998778875378400257 No 243 >PRK05472 redox-sensing transcriptional repressor Rex; Provisional Probab=47.04 E-value=17 Score=15.03 Aligned_cols=24 Identities=25% Similarity=0.213 Sum_probs=13.0 Q ss_pred HHHHHHHHHHHHHHHCCCCCCCEE Q ss_conf 754436799998874385457312 Q gi|254780289|r 473 LIQEGNIGLMKAAEKFDWCLGYKF 496 (682) Q Consensus 473 ~~~~~~~~l~~a~~~~~~~~g~~f 496 (682) ||-.||+|-.=+--.+=.++||+. T Consensus 89 lvGaGnLG~AL~~y~gf~~~gf~I 112 (211) T PRK05472 89 LVGAGNLGRALLNYNGFKKRGFKI 112 (211) T ss_pred EECCCHHHHHHHHCCCHHHCCCEE T ss_conf 988877999998487623189789 No 244 >pfam04760 IF2_N Translation initiation factor IF-2, N-terminal region. This conserved feature at the N-terminus of bacterial translation initiation factor IF2 has recently had its structure solved. It shows structural similarity to the tRNA anticodon Stem Contact Fold domains of the methionyl-tRNA and glutaminyl-tRNA synthetases, and a similar fold is also found in the B5 domain of the phenylalanine-tRNA synthetase. Probab=46.22 E-value=17 Score=14.94 Aligned_cols=34 Identities=18% Similarity=0.067 Sum_probs=23.3 Q ss_pred CCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCC Q ss_conf 9978999870999899999998608987553635 Q gi|254780289|r 547 PTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI 580 (682) Q Consensus 547 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~ 580 (682) -|+.|+|+.||++..+|-+.+-...-.+|.+..+ T Consensus 4 itV~elA~~l~~~~~~vi~~L~~~Gi~~~~n~~l 37 (52) T pfam04760 4 IRVYELAKELGVSSKELIKKLFKLGIMKTHNSTL 37 (52) T ss_pred EEHHHHHHHHCCCHHHHHHHHHHCCCEECCCCCC T ss_conf 7399999998888999999999879855677745 No 245 >COG2316 Predicted hydrolase (HD superfamily) [General function prediction only] Probab=45.02 E-value=14 Score=15.75 Aligned_cols=19 Identities=32% Similarity=0.361 Sum_probs=11.0 Q ss_pred HHHHHCCCHHHHHHHHHHH Q ss_conf 9899667899999999999 Q gi|254780289|r 645 VGKQFCVTRERIRQIEAKA 663 (682) Q Consensus 645 ~~~~~~~~~er~rqi~~~a 663 (682) -|=--|++|++|||+|.-. T Consensus 171 K~FAaG~~Rd~vR~~E~lG 189 (212) T COG2316 171 KGFAAGVNRDEVRQAEELG 189 (212) T ss_pred HHHHCCCCHHHHHHHHHHC T ss_conf 5554158899999999919 No 246 >PRK04217 hypothetical protein; Provisional Probab=44.60 E-value=18 Score=14.76 Aligned_cols=45 Identities=29% Similarity=0.295 Sum_probs=36.9 Q ss_pred CCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC Q ss_conf 9988999999981879867468899989966789999999999999832 Q gi|254780289|r 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668 (682) Q Consensus 620 l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~ 668 (682) |+.-|-+.|||-. ...+|-+|-+..+||||--+--|-..|-+|+- T Consensus 43 LtvdE~EaiRL~D----~egl~qeeaA~~M~VSR~Tf~ril~~AR~KvA 87 (110) T PRK04217 43 MTYEEFEALRLVD----YEGLTQEEAGKRMGVSRGTVWRALTSARKKVA 87 (110) T ss_pred ECHHHHHHHHHHH----HCCCCHHHHHHHCCCCHHHHHHHHHHHHHHHH T ss_conf 1199999999873----60798999998849769999999999999999 No 247 >COG1342 Predicted DNA-binding proteins [General function prediction only] Probab=44.32 E-value=18 Score=14.73 Aligned_cols=45 Identities=24% Similarity=0.248 Sum_probs=35.1 Q ss_pred CCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH Q ss_conf 2998899999998187986746889998996678999999999999983 Q gi|254780289|r 619 SLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667 (682) Q Consensus 619 ~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l 667 (682) .|+.-|-+.|||.+ ....|-+|-|.++||||--+--+=..|..|. T Consensus 33 ~lt~eElEAlRLvD----~~~l~QeeAA~rMgISr~Tfwr~l~sAR~Kv 77 (99) T COG1342 33 ILTIEELEALRLVD----YEGLTQEEAALRMGISRQTFWRLLTSARKKV 77 (99) T ss_pred EECHHHHHHHHHHH----HHHCCHHHHHHHHCCCHHHHHHHHHHHHHHH T ss_conf 52299988999886----8610578999984642999999999999999 No 248 >PRK06704 RNA polymerase factor sigma-70; Validated Probab=44.25 E-value=18 Score=14.72 Aligned_cols=40 Identities=20% Similarity=0.276 Sum_probs=20.3 Q ss_pred CCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHH Q ss_conf 7778875443679999887438545731201028989999 Q gi|254780289|r 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507 (682) Q Consensus 468 ~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~ 507 (682) -+-.||.||...-+|.++.+=|..--|-|----.-||-|. T Consensus 42 WDaEDLaQet~~Kviq~~~~k~~~~a~l~kIArNqW~Dql 81 (228) T PRK06704 42 WDGEDLAQETVCKVLQKYSNKDICMTLVYKIARNRWLDQI 81 (228) T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 6578899999999999987622179999999998999998 No 249 >PRK09863 putative frv operon regulatory protein; Provisional Probab=44.17 E-value=18 Score=14.71 Aligned_cols=49 Identities=16% Similarity=0.093 Sum_probs=32.6 Q ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCC---HHHHHHHHHHHHHCCCEEEC Q ss_conf 89999999978784886789997526843599---88899999999847977832 Q gi|254780289|r 28 DDSWKKMIKLARQRGYVTIEELNAFLPPDEVS---SEQMEDTVAMLSNMGINVVD 79 (682) Q Consensus 28 ~~~ik~LI~~gke~GylTydeIn~~LP~d~~~---~e~ie~i~~~L~~~GI~Vve 79 (682) |+...+|+.+=.+ ..+|-+||...|. +.+ -..|..|=..|.+.+|-.+. T Consensus 3 n~Rq~~il~lL~~-~~lt~~eLA~~L~--VS~RTIR~DI~~iN~~L~~~~i~~~~ 54 (585) T PRK09863 3 NERELKIVDLLEQ-QDRSGGELAQQLG--VSRRTIVRDIAYINFTLNGKAIGSIS 54 (585) T ss_pred CHHHHHHHHHHHC-CCCCHHHHHHHCC--CCCHHHHHHHHHHHHHHHHCCEEEEE T ss_conf 6799999999975-9999899998749--97117899999999998418518984 No 250 >TIGR01632 L11_bact ribosomal protein L11; InterPro: IPR006519 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , . Ribosomal protein L11 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L11 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities , groups bacterial, chloroplast, cyanelle, and most mitochondrial forms of ribosomal protein L11. L11 is a protein of 140 to 165 amino-acid residues. In E. coli, the C-terminal half of L11 has been shown to be in an extended and loosely folded conformation and is likely to be buried within the ribosomal structure. This entry represents the bacterial, chloroplast and mitochondrial forms. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome. Probab=44.07 E-value=18 Score=14.70 Aligned_cols=38 Identities=21% Similarity=0.549 Sum_probs=20.5 Q ss_pred CCCCHHHHHHH----CCCCCCCHHHHHHHHHHH----HHCCCEEEC Q ss_conf 88678999752----684359988899999999----847977832 Q gi|254780289|r 42 GYVTIEELNAF----LPPDEVSSEQMEDTVAML----SNMGINVVD 79 (682) Q Consensus 42 GylTydeIn~~----LP~d~~~~e~ie~i~~~L----~~~GI~Vve 79 (682) |-||..+|.+. ++|+.++.-.||.++-++ -.|||+|++ T Consensus 99 G~it~~q~~eIA~~K~~D~~ln~~~~EaA~k~I~GtAkSMGi~v~~ 144 (144) T TIGR01632 99 GKITRKQVREIAEIKMSDERLNTKDLEAAMKIIAGTAKSMGIEVVG 144 (144) T ss_pred EEECHHHHHHHHHHHCCCCCCCHHCHHHHHHHHCCCCCCCCEEECC T ss_conf 2012788899998616898888102553154300000218615259 No 251 >pfam02638 DUF187 Uncharacterized BCR, COG1649. Probab=43.99 E-value=13 Score=15.87 Aligned_cols=20 Identities=20% Similarity=0.513 Sum_probs=12.4 Q ss_pred CCHHHHHHHHHHHHHCCCEE Q ss_conf 99888999999998479778 Q gi|254780289|r 58 VSSEQMEDTVAMLSNMGINV 77 (682) Q Consensus 58 ~~~e~ie~i~~~L~~~GI~V 77 (682) .++.++.+.+..|.++|++- T Consensus 56 ~~~~q~~e~i~~L~~lnfNt 75 (394) T pfam02638 56 PDPVQLQEAIALLDDLNFNT 75 (394) T ss_pred CCHHHHHHHHHHHHHCCCCE T ss_conf 89899999999999869987 No 252 >COG1654 BirA Biotin operon repressor [Transcription] Probab=43.97 E-value=19 Score=14.69 Aligned_cols=33 Identities=15% Similarity=0.138 Sum_probs=21.8 Q ss_pred HHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHC Q ss_conf 877608899978999870999899999998608 Q gi|254780289|r 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK 571 (682) Q Consensus 539 ~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~ 571 (682) +....++.-+-++||+.||+|..-|-+..+..+ T Consensus 12 l~~~~~~~~SGe~La~~LgiSRtaVwK~Iq~Lr 44 (79) T COG1654 12 LLLLTGNFVSGEKLAEELGISRTAVWKHIQQLR 44 (79) T ss_pred HHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH T ss_conf 997379966689999997865999999999999 No 253 >pfam01371 Trp_repressor Trp repressor protein. This protein binds to tryptophan and represses transcription of the Trp operon. Probab=43.86 E-value=19 Score=14.68 Aligned_cols=44 Identities=23% Similarity=0.345 Sum_probs=22.9 Q ss_pred HHHHHHC-CCHHHHHHHHHHHCCCC---CCCCCHHHHHHHHCCCHHHH Q ss_conf 9999732-99889999999818798---67468899989966789999 Q gi|254780289|r 613 TTRVLAS-LTPREERVLRMRFGIGM---NTDHTLEEVGKQFCVTRERI 656 (682) Q Consensus 613 ~~~~l~~-l~~re~~v~~~r~g~~~---~~~~tl~e~~~~~~~~~er~ 656 (682) +...+.. ++|.|..-+..||-+-. ...+|..+|.+..|+|---| T Consensus 19 ~~~f~~dl~T~~E~~ala~R~~va~~LL~~~~syreI~~~~g~S~aTI 66 (88) T pfam01371 19 CYAFLTDLLTPDEREALAQRLRIAKELLRGELSQREIAQELGASIATI 66 (88) T ss_pred HHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHH T ss_conf 999999839999999999999999999978998999999859852314 No 254 >pfam04931 DNA_pol_phi DNA polymerase phi. This family includes the fifth essential DNA polymerase in yeast EC:2.7.7.7. Pol5p is localized exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units. Probab=43.77 E-value=19 Score=14.67 Aligned_cols=16 Identities=25% Similarity=0.387 Sum_probs=7.9 Q ss_pred HHHHHHHHHHHHHHHC Q ss_conf 9999999999999732 Q gi|254780289|r 604 AIQANLRETTTRVLAS 619 (682) Q Consensus 604 ~~~~~~~~~~~~~l~~ 619 (682) ......+.++..+|.. T Consensus 699 ~~d~~~~~aL~~al~~ 714 (784) T pfam04931 699 PIDKAVRRALPKVLNL 714 (784) T ss_pred HHHHHHHHHHHHHCCC T ss_conf 6679999999984068 No 255 >TIGR00169 leuB 3-isopropylmalate dehydrogenase; InterPro: IPR004429 Several NAD- or NADP-dependent dehydrogenases, including 3-isopropylmalate dehydrogenase, tartrate dehydrogenase, and the dimeric forms of isocitrate dehydrogenase, share a nucleotide binding domain unrelated to that of lactate dehydrogenase and its homologs. These enzymes dehydrogenate their substates at a H-C-OH site adjacent to a H-C-COOH site; the latter carbon, now adjacent to a carbonyl group, readily decarboxylates. Among these decarboxylating dehydrogenases of hydroxyacids, overall sequence homology indicates evolutionary history rather than actual substrate or cofactor specifity, which may be toggled experimentally by replacement of just a few amino acids. 3-isopropylmalate dehydrogenase is an NAD-dependent enzyme and should have a sequence resembling HGSAPDI around residue 340. The subtrate binding loop should include a sequence resembling E[KQR]X(0,1)LLXXR around residue 115.; GO: 0003862 3-isopropylmalate dehydrogenase activity, 0009098 leucine biosynthetic process, 0005737 cytoplasm. Probab=43.71 E-value=8.2 Score=17.50 Aligned_cols=82 Identities=23% Similarity=0.337 Sum_probs=52.5 Q ss_pred HHHHHHHHHCCCEEEC--CCHHHHHHHHHH--HHHHHHHHHCCCCCCHHHHHH-HC-CCCHHHH---HHHHHHHCCCCCC Q ss_conf 9999999722870461--420588989999--999998776088999789998-70-9998999---9999860898755 Q gi|254780289|r 506 QAITRSIADQSCTIRI--PVHMRDKIHKVV--RTARRMSNKIKREPTPEEIAK-KL-AMPVEGV---RKVLKITKEPISL 576 (682) Q Consensus 506 ~~i~~~~~~~~~~~r~--~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~a~-~~-~~~~~~~---~~~~~~~~~~~sl 576 (682) +-|.|.=+.-|+.-|- ||.-+++.|-+. +.+|+... |+++ .. ++.+++. -.+|...+.|-++ T Consensus 171 ~RIaR~AFe~A~kr~~P~~vTSvDKANVL~sS~LWR~~V~---------e~~~~eYPdv~L~H~yiDnAAM~Lvk~P~~f 241 (370) T TIGR00169 171 ERIARVAFEMARKRRKPLKVTSVDKANVLESSRLWRKTVE---------EIAKEEYPDVELEHQYIDNAAMQLVKSPRQF 241 (370) T ss_pred HHHHHHHHHHHHHCCCCCCEEEECHHHHHHHHHHHHHHHH---------HHHHCCCCCEEECCCHHHHHHHHHHCCCCCC T ss_conf 7899999999985488985321001204554378999999---------9984688805730215878876753286504 Q ss_pred C-CCCCCCCCCEEEEEECCCCCCC Q ss_conf 3-6358899860475623898899 Q gi|254780289|r 577 E-TPIGDEDTSHLGDFIEDKNAVS 599 (682) Q Consensus 577 ~-~~~~~~~~~~~~~~~~d~~~~~ 599 (682) | .-|-+ --|||+|.|..+.- T Consensus 242 DGV~vT~---N~FGDIlSDeAsvi 262 (370) T TIGR00169 242 DGVVVTG---NLFGDILSDEASVI 262 (370) T ss_pred CCEEEEC---CCCCHHHHHHHHHH T ss_conf 8667726---53300688888763 No 256 >COG2188 PhnF Transcriptional regulators [Transcription] Probab=43.39 E-value=19 Score=14.63 Aligned_cols=26 Identities=27% Similarity=0.431 Sum_probs=15.4 Q ss_pred CCCCCHHHHHHHCCCCHHHHHHHHHH Q ss_conf 88999789998709998999999986 Q gi|254780289|r 544 KREPTPEEIAKKLAMPVEGVRKVLKI 569 (682) Q Consensus 544 ~~~~~~~~~a~~~~~~~~~~~~~~~~ 569 (682) .+-|+-.|||+.+|+|.-.|++++.. T Consensus 29 ~~LPsE~eLa~~f~VSR~TvRkAL~~ 54 (236) T COG2188 29 DKLPSERELAEQFGVSRMTVRKALDE 54 (236) T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHH T ss_conf 95959899999979889999999999 No 257 >pfam11268 DUF3071 Protein of unknown function (DUF3071). Some members in this family of proteins are annotated as DNA-binding proteins however this cannot be confirmed. Currently no function is known. Probab=42.86 E-value=19 Score=14.57 Aligned_cols=67 Identities=18% Similarity=0.288 Sum_probs=38.3 Q ss_pred CCCEEEHHHHHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHH Q ss_conf 573120102898999999999722870461420588989999999998776088999789998709998999999 Q gi|254780289|r 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566 (682) Q Consensus 492 ~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~ 566 (682) -|-+|.--..=-.|.++.+..... -.++.-+..++ .-+++....---.|++++|+..|+|+++|+.. T Consensus 22 ~G~~f~l~idd~LRaAvr~~~~~~---~~~~~e~~~~l-----spreIQarIRaGas~eevA~~~g~~~~rVerf 88 (169) T pfam11268 22 DGERFRLPVDDRLRAALRGDRARL---GQVEIEVDPTL-----SPREIQARIRAGASAEEVAEAAGVPEERVERF 88 (169) T ss_pred CCCEEEEECCHHHHHHHCCCCCCC---CCCCCCCCCCC-----CHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHC T ss_conf 999898874879999873566666---76643447888-----98999999887999999999959999998742 No 258 >COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription] Probab=42.72 E-value=19 Score=14.55 Aligned_cols=25 Identities=12% Similarity=0.085 Sum_probs=14.8 Q ss_pred CCCCCCHHHHHHHHCCCHHHHHHHH Q ss_conf 8674688999899667899999999 Q gi|254780289|r 636 MNTDHTLEEVGKQFCVTRERIRQIE 660 (682) Q Consensus 636 ~~~~~tl~e~~~~~~~~~er~rqi~ 660 (682) .|.+....-=.+.+|++-+..|||. T Consensus 255 ~G~~~~~~ln~r~igl~L~~l~~ip 279 (321) T COG2390 255 NGQPVDTPLNDRVIGLSLDDLRQIP 279 (321) T ss_pred CCCCCCCCCCCCEECCCHHHHHCCC T ss_conf 9988555565716437788973278 No 259 >pfam09339 HTH_IclR IclR helix-turn-helix domain. Probab=42.64 E-value=19 Score=14.54 Aligned_cols=30 Identities=17% Similarity=0.278 Sum_probs=23.2 Q ss_pred HHHCCCCCCHHHHHHHCCCCHHHHHHHHHH Q ss_conf 776088999789998709998999999986 Q gi|254780289|r 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKI 569 (682) Q Consensus 540 ~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~ 569 (682) ....+++.+..|||..+|+|...|..++.. T Consensus 12 ~~~~~~~~~l~eia~~~gl~kstv~RlL~t 41 (52) T pfam09339 12 LAEAPGGLSLTEIARRTGLPKSTAHRLLQT 41 (52) T ss_pred HHHCCCCCCHHHHHHHHCCCHHHHHHHHHH T ss_conf 862899989999999989199999999999 No 260 >PRK04483 threonyl-tRNA synthetase; Validated Probab=42.28 E-value=11 Score=16.61 Aligned_cols=36 Identities=14% Similarity=0.158 Sum_probs=18.2 Q ss_pred HHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH Q ss_conf 8569768897889999999998899999998728238999999998 Q gi|254780289|r 127 EMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRD 172 (682) Q Consensus 127 EMG~V~LLTREgEIeIAKRIE~G~~~i~~al~~~P~ti~~il~~~e 172 (682) +=|+|++||.+.+ +|...+.+..+. +....+..+|- T Consensus 53 ~D~~leiiT~~d~--------egl~v~rHS~AH--vla~Av~~l~p 88 (634) T PRK04483 53 HDASLRIITAKDA--------EGVEIIRHSCAH--LVGHAVKQLYP 88 (634) T ss_pred CCCEEEEECCCCH--------HHHHHHHHHHHH--HHHHHHHHHCC T ss_conf 9978999569997--------899999999999--99999999779 No 261 >TIGR00373 TIGR00373 conserved hypothetical protein TIGR00373; InterPro: IPR005241 This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain. . Probab=42.01 E-value=20 Score=14.47 Aligned_cols=46 Identities=26% Similarity=0.300 Sum_probs=27.2 Q ss_pred CCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEE Q ss_conf 9997899987099989999999860898755363588998604756 Q gi|254780289|r 546 EPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDF 591 (682) Q Consensus 546 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~ 591 (682) +-|.++||..||+.+.-||++|=..=+.--.|=--.-|+++.+... T Consensus 30 e~Tdeeis~elg~klN~vRk~Ly~LYdagladYkR~kD~eT~Wy~Y 75 (168) T TIGR00373 30 EVTDEEISKELGIKLNVVRKLLYKLYDAGLADYKRRKDDETNWYEY 75 (168) T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHCCEEEEEEECCCCCCCCEEE T ss_conf 7477888888384055788999987303010002136898885236 No 262 >TIGR02169 SMC_prok_A chromosome segregation protein SMC; InterPro: IPR011891 The SMC (structural maintenance of chromosomes) family of proteins, exist in virtually all organisms including both bacteria and archaea. The SMC proteins are essential for successful chromosome transmission during replication and segregation of the genome in all organisms and form three types of heterodimer (SMC1SMC3, SMC2SMC4, SMC5SMC6), which are core components of large multiprotein complexes. The best known complexes are cohesin, which is responsible for sister-chromatid cohesion, and condensin, which is required for full chromosome condensation in mitosis. SMCs are generally present as single proteins in bacteria, and as at least six distinct proteins in eukaryotes. The proteins range in size from approximately 110 to 170 kDa, and share a five-domain structure, with globular N- and C-terminal (IPR003395 from INTERPRO) domains separated by a long (circa 100 nm or 900 residues) coiled coil segment in the centre of which is a globular ''hinge'' domain, characterised by a set of four highly conserved glycine residues that are typical of flexible regions in a protein. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif (XXXXD, where X is any hydrophobic residue), and a LSGG motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases . All SMC proteins appear to form dimers, either forming homodimers with themselves, as in the case of prokaryotic SMC proteins, or heterodimers between different but related SMC proteins. The dimers are arranged in an antiparallel alignment. This orientation brings the N- and C-terminal globular domains (from either different or identical protamers) together, which unites an ATP binding site (Walker A motif) within the N-terminal domain with a Walker B motif (DA box) within the C-terminal domain, to form a potentially functional ATPase. Protein interaction and microscopy data suggest that SMC dimers form a ring-like structure which might embrace DNA molecules. Non-SMC subunits associate with the SMC amino- and carboxy-terminal domains. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. SMCs share not only sequence similarity but also structural similarity with ABC proteins. SMC proteins function together with other proteins in a range of chromosomal transactions, including chromosome condensation, sister-chromatid cohesion, recombination, DNA repair and epigenetic silencing of gene expression . This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by IPR011890 from INTERPRO. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent .. Probab=41.71 E-value=20 Score=14.44 Aligned_cols=51 Identities=20% Similarity=0.039 Sum_probs=22.0 Q ss_pred CCCHHHHH---HHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCHHHHH Q ss_conf 88978899---9999999889999999872823899999999873117103678 Q gi|254780289|r 133 LLSREGEI---AIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLRE 183 (682) Q Consensus 133 LLTREgEI---eIAKRIE~G~~~i~~al~~~P~ti~~il~~~e~i~~ge~~Lrd 183 (682) |+++-+|+ .+++.+++-..+....-.+-...=..+-.+-.++..-..++.. T Consensus 239 L~~~k~e~e~~~ll~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~ 292 (1202) T TIGR02169 239 LKKEKREYEGYLLLKEKEALEKQKEAIEKQLAELEEELEKLTEEIEELEKRLEE 292 (1202) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 999988899999999999999999999999999999999999999999999999 No 263 >PRK12444 threonyl-tRNA synthetase; Reviewed Probab=41.67 E-value=12 Score=16.30 Aligned_cols=22 Identities=9% Similarity=0.135 Sum_probs=9.5 Q ss_pred CCEEEHHHHHHHHHHHHHHHHH Q ss_conf 7312010289899999999972 Q gi|254780289|r 493 GYKFSTYAMWWVKQAITRSIAD 514 (682) Q Consensus 493 g~~f~tya~~~i~~~i~~~~~~ 514 (682) |.-|=.---|.|++.+..++.+ T Consensus 265 G~~fwlP~G~~i~~~le~~~r~ 286 (639) T PRK12444 265 GMPFYLPKGQIIRNELEAFLRE 286 (639) T ss_pred CCEEEECCHHHHHHHHHHHHHH T ss_conf 7447846786999999999999 No 264 >TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems. Probab=41.15 E-value=20 Score=14.38 Aligned_cols=23 Identities=26% Similarity=0.170 Sum_probs=14.7 Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH Q ss_conf 68899989966789999999999 Q gi|254780289|r 640 HTLEEVGKQFCVTRERIRQIEAK 662 (682) Q Consensus 640 ~tl~e~~~~~~~~~er~rqi~~~ 662 (682) .|.++++..-|||+-.|.+||.- T Consensus 16 lTQ~~LA~~aGvs~~~Is~iE~G 38 (58) T TIGR03070 16 LTQADLADLAGVGLRFIRDIEKG 38 (58) T ss_pred CCHHHHHHHHCCCHHHHHHHHCC T ss_conf 98999998819989999999789 No 265 >TIGR02959 SigZ RNA polymerase sigma factor, SigZ family; InterPro: IPR014304 This entry is a group of RNA polymerase sigma factors where one of the members is designated as SigZ in Bacillus subtilis . This group has a very sporadic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member Dechloromonas aromatica (strain RCB), that appears to have two of these sigma factors. A member of which appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri (strain ATCC 700601 / ES114), where a second one is chromosomally encoded.. Probab=41.03 E-value=20 Score=14.37 Aligned_cols=43 Identities=9% Similarity=0.198 Sum_probs=23.8 Q ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCC Q ss_conf 99999999999732998899999998187986746889998996678 Q gi|254780289|r 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVT 652 (682) Q Consensus 606 ~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~ 652 (682) ...+...|..+|..||...++-|++- +-+..|=-||++.+||| T Consensus 87 ~~e~~~Cl~~~i~~LP~~~r~a~~L~----el~G~sQ~e~A~kLGlS 129 (170) T TIGR02959 87 VKELSQCLRPMIKELPDEYREAIRLT----ELEGLSQKEIAEKLGLS 129 (170) T ss_pred HHHHHHHHHHHHHHCCHHHHHHHHHH----HCCCCCHHHHHHHCCCC T ss_conf 45688888998875698678898887----50799827998761753 No 266 >PRK09392 ftrB transcriptional activator FtrB; Provisional Probab=40.55 E-value=21 Score=14.31 Aligned_cols=18 Identities=22% Similarity=0.375 Sum_probs=8.0 Q ss_pred HHHHHCCCCHHHHHHHHH Q ss_conf 999870999899999998 Q gi|254780289|r 551 EIAKKLAMPVEGVRKVLK 568 (682) Q Consensus 551 ~~a~~~~~~~~~~~~~~~ 568 (682) +||..+|++.+.|..+++ T Consensus 178 ~lA~~lG~tretvsR~L~ 195 (236) T PRK09392 178 TLASYLGMTPENLSRAFA 195 (236) T ss_pred HHHHHHCCCHHHHHHHHH T ss_conf 999987898999999999 No 267 >cd02758 MopB_Tetrathionate-Ra The MopB_Tetrathionate-Ra CD contains tetrathionate reductase, subunit A, (TtrA) and other related proteins. The Salmonella enterica tetrathionate reductase catalyses the reduction of trithionate but not sulfur or thiosulfate. Members of this CD belong to the molybdopterin_binding (MopB) superfamily of proteins. Probab=40.22 E-value=21 Score=14.28 Aligned_cols=22 Identities=5% Similarity=0.098 Sum_probs=10.0 Q ss_pred HHHHHHHHHHHHHHHHHHHHHH Q ss_conf 3322222112688999999876 Q gi|254780289|r 414 KSISVETGISISEFRHIVSMVR 435 (682) Q Consensus 414 ~~ie~~~gl~i~ElK~i~r~I~ 435 (682) ....+.+|++...+.++.+++. T Consensus 342 e~~AeitGVpa~~I~~lArEfa 363 (735) T cd02758 342 EEYAEICGVPEAKIIELAKEFT 363 (735) T ss_pred HHHHHHHCCCHHHHHHHHHHHH T ss_conf 9999886989999999999998 No 268 >pfam11633 Nsp3 Replicase polyprotein 1ab. This family of proteins represents Nsp3, the product of ORF1a in group 2 coronavirus.This is the largest replicase subunit. Probab=40.08 E-value=17 Score=14.89 Aligned_cols=39 Identities=13% Similarity=0.311 Sum_probs=26.2 Q ss_pred CCCCCCCCHHCCHHHHHHHHHHHHHCCCCC-----HHHHHHHCC Q ss_conf 465554430202899999999787848867-----899975268 Q gi|254780289|r 16 EDSDDSLVFDFSDDSWKKMIKLARQRGYVT-----IEELNAFLP 54 (682) Q Consensus 16 ~~~~~~~~~d~~~~~ik~LI~~gke~GylT-----ydeIn~~LP 54 (682) .+.....+++..-..++.++.-||++|+++ |.-+++.|- T Consensus 10 a~~~~~~~l~~v~~~~r~mv~hake~g~l~pIc~Dy~A~~k~Lk 53 (142) T pfam11633 10 APPAKPELLGVVSESFRAMVRHAKETGLLCPICIDYPAFMKVLK 53 (142) T ss_pred CCCCCCCEEEEEEHHHHHHHHHHHHCCCEEEEEECCHHHHHHHH T ss_conf 89999776777633189999866632835579965288999998 No 269 >COG0856 Orotate phosphoribosyltransferase homologs [Nucleotide transport and metabolism] Probab=39.99 E-value=21 Score=14.25 Aligned_cols=30 Identities=20% Similarity=0.531 Sum_probs=18.8 Q ss_pred HHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHH Q ss_conf 578999887522356777887544367999988743854573120102 Q gi|254780289|r 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500 (682) Q Consensus 453 lr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya 500 (682) .-.||-|| ..|.|+.-|+. |..|.-|.+|- T Consensus 87 vDvVvGIa----~sGvPlAt~vA--------------~elg~elaiY~ 116 (203) T COG0856 87 VDVVVGIA----ISGVPLATMVA--------------YELGKELAIYH 116 (203) T ss_pred EEEEEEEE----ECCCCHHHHHH--------------HHHCCCEEEEE T ss_conf 46899885----06862899999--------------97378469981 No 270 >PRK04140 hypothetical protein; Provisional Probab=39.98 E-value=21 Score=14.25 Aligned_cols=15 Identities=20% Similarity=0.605 Sum_probs=5.7 Q ss_pred HHHHHHHHHHCCCEE Q ss_conf 999999998479778 Q gi|254780289|r 63 MEDTVAMLSNMGINV 77 (682) Q Consensus 63 ie~i~~~L~~~GI~V 77 (682) |++++.+|...|..| T Consensus 6 i~~v~~~L~~~gf~v 20 (319) T PRK04140 6 ISEVIDLLESAGFKV 20 (319) T ss_pred HHHHHHHHHHCCCEE T ss_conf 999999999879579 No 271 >pfam09286 Pro-kuma_activ Pro-kumamolisin, activation domain. Members of this family are found in various subtilase propeptides, and adopt a ferredoxin-like fold, with an alpha+beta sandwich. Cleavage of the domain results in activation of the peptide. Probab=39.94 E-value=21 Score=14.24 Aligned_cols=37 Identities=30% Similarity=0.417 Sum_probs=29.8 Q ss_pred CCCCCHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCEEECC Q ss_conf 4886789997526843599888999999998479778327 Q gi|254780289|r 41 RGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDG 80 (682) Q Consensus 41 ~GylTydeIn~~LP~d~~~~e~ie~i~~~L~~~GI~Vve~ 80 (682) ..|||.+|+.+.+.+ +.+.++.|...|...||.+... T Consensus 45 g~~Lt~~e~~~~~~p---s~~~~~~V~~wL~~~g~~~~~~ 81 (141) T pfam09286 45 GKHLSREEVAALFAP---SQETVDAVRAWLESAGITVERA 81 (141) T ss_pred CCCCCHHHHHHHHCC---CHHHHHHHHHHHHHCCCCEEEE T ss_conf 666899999988789---9999999999999869954885 No 272 >smart00531 TFIIE Transcription initiation factor IIE. Probab=39.59 E-value=21 Score=14.21 Aligned_cols=100 Identities=12% Similarity=0.133 Sum_probs=51.7 Q ss_pred CCCHHHHHHHCCCCHHHHHHHHHHHCC--CCCCCCCCCCCCCC--EEE-EEECCCCCCCHHHHHHHHHHHHHHHHHHHCC Q ss_conf 999789998709998999999986089--87553635889986--047-5623898899899999999999999997329 Q gi|254780289|r 546 EPTPEEIAKKLAMPVEGVRKVLKITKE--PISLETPIGDEDTS--HLG-DFIEDKNAVSPLDSAIQANLRETTTRVLASL 620 (682) Q Consensus 546 ~~~~~~~a~~~~~~~~~~~~~~~~~~~--~~sl~~~~~~~~~~--~~~-~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l 620 (682) .-|.++||+.||++...||+++....+ -++-..--..++++ ..- -+-- + .......++..+..++..| T Consensus 15 ~v~dedLa~~l~~~~n~vRkiL~~L~e~~lv~~~~~rek~~~~~~~~~yyw~i-----~--y~~~~~~vk~k~~~~~~~L 87 (147) T smart00531 15 CVTEEDLAELLGIKQKQLRKILYLLYDEKLIKIDYKREKDPETKTWYRYYWYI-----N--YDTLLDVVKYKLDKMRKRL 87 (147) T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEEEEEECCCCCEEEEEEEEE-----C--HHHHHHHHHHHHHHHHHHH T ss_conf 70799999997999999999999999779646899987758886599999997-----7--9999999999999999999 Q ss_pred CHHHHHHH-HHHHC-CCCCCCCCHHHHHHHHCCC Q ss_conf 98899999-99818-7986746889998996678 Q gi|254780289|r 621 TPREERVL-RMRFG-IGMNTDHTLEEVGKQFCVT 652 (682) Q Consensus 621 ~~re~~v~-~~r~g-~~~~~~~tl~e~~~~~~~~ 652 (682) ..|.+.=. ...|- -.++..+|..|+.+.++.+ T Consensus 88 ~~~l~~e~~~~~Y~C~~C~~ryt~~eA~~l~~~~ 121 (147) T smart00531 88 EDKLEDETNNAYYKCPNCQSKYTFLEANQLLDMD 121 (147) T ss_pred HHHHHHCCCCCEEECCCCCCEECHHHHHHHCCCC T ss_conf 9998627489878899999786299998841899 No 273 >COG2049 DUR1 Allophanate hydrolase subunit 1 [Amino acid transport and metabolism] Probab=39.58 E-value=21 Score=14.21 Aligned_cols=42 Identities=26% Similarity=0.316 Sum_probs=31.5 Q ss_pred CEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCC Q ss_conf 7046142058898999999999877608899978999870999899999998608987 Q gi|254780289|r 517 CTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI 574 (682) Q Consensus 517 ~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ 574 (682) |+|.|||+--. ..-|..+++|+.-|+++++|-.+.....--| T Consensus 84 ~~IeIPV~Y~~----------------~~GpDL~~va~~~gls~~evI~~Hs~~~Y~V 125 (223) T COG2049 84 RLIEIPVVYGG----------------EYGPDLAEVARHNGLSVEEVIELHSSTEYRV 125 (223) T ss_pred CEEEEEEEECC----------------CCCCCHHHHHHHCCCCHHHHHHHHCCCCEEE T ss_conf 76997007689----------------8898899999881999999999725785599 No 274 >TIGR01279 DPOR_bchN light-independent protochlorophyllide reductase, N subunit; InterPro: IPR005970 Synonym: dark protochlorophyllide reductase Protochlorophyllide reductase catalyzes the reductive formation of chlorophyllide from protochlorophyllide during biosynthesis of chlorophylls and bacteriochlorophylls. The light-independent (dark) form of protochlorophyllide reductase plays a key role in the ability of gymnosperms, algae, and photosynthetic bacteria to form chlorophyll in the dark. Genetic and sequence analyses have indicated that dark protochlorophyllide reductase consists of three protein subunits that exhibit significant sequence similarity to the three subunits of nitrogenase, which catalyzes the reductive formation of ammonia from dinitrogen. Dark protochlorophyllide reductase activity was shown to be dependent on the presence of all three subunits, ATP, and the reductant dithionite. This enzyme describes the N subunit of the dark form protochlorophyllide reductase, a nitrogenase-like enzyme . ; GO: 0016730 oxidoreductase activity acting on iron-sulfur proteins as donors, 0015995 chlorophyll biosynthetic process, 0019685 photosynthesis dark reaction. Probab=39.43 E-value=6 Score=18.57 Aligned_cols=58 Identities=26% Similarity=0.381 Sum_probs=32.4 Q ss_pred HHHHHHHCCCH-HHHHHHHHHHCCC-CCCCCCHHHHHHHHCCCHHHHHHHHH----HHHHHHCC Q ss_conf 99999732998-8999999981879-86746889998996678999999999----99998329 Q gi|254780289|r 612 TTTRVLASLTP-REERVLRMRFGIG-MNTDHTLEEVGKQFCVTRERIRQIEA----KAIRKLKH 669 (682) Q Consensus 612 ~~~~~l~~l~~-re~~v~~~r~g~~-~~~~~tl~e~~~~~~~~~er~rqi~~----~a~~~l~~ 669 (682) .|.+...+|.- |-.+||--=|=+| +|+..=||.|+..|||.-.|+..=++ +|-++|+| T Consensus 242 yL~~ta~~L~~eR~~~~L~~~FPfGPDGT~~f~e~ia~~fG~~~~~l~er~aPrre~aW~~l~~ 305 (458) T TIGR01279 242 YLSDTATTLRRERGAKVLSALFPFGPDGTRRFLEAIAAEFGIEVDKLSEREAPRREQAWRALEP 305 (458) T ss_pred HHHHHHHHHHHHCCCEEECCCCCCCCCHHHHHHHHHHHHHCCCCCCCCHHHCHHHHHHHHHHHH T ss_conf 1889999998502665611578988516899999999985982122001101028999999888 No 275 >TIGR00223 panD aspartate 1-decarboxylase; InterPro: IPR003190 Decarboxylation of aspartate is the major route of alanine production in bacteria, and is catalysed by the enzyme aspartate decarboxylase. The enzyme is translated as an inactive proenzyme of two chains, A and B. This family contains both chains of aspartate decarboxylase.; GO: 0004068 aspartate 1-decarboxylase activity, 0006523 alanine biosynthetic process. Probab=39.11 E-value=5.8 Score=18.70 Aligned_cols=53 Identities=25% Similarity=0.235 Sum_probs=33.8 Q ss_pred HHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHH-HHH Q ss_conf 9987555789998875223567778875443679999887438545731201028989-999 Q gi|254780289|r 447 EMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV-KQA 507 (682) Q Consensus 447 ~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i-~~~ 507 (682) ...+|||-+|=||+ ==.||+...-+===.+|+=.+..=|-|||||+..-= |++ T Consensus 14 ~vT~AnLnY~GSit--------IDeDl~daag~lenekv~IvnvnNG~RfsTY~I~gkkRGs 67 (127) T TIGR00223 14 TVTEANLNYVGSIT--------IDEDLLDAAGLLENEKVDIVNVNNGKRFSTYVIAGKKRGS 67 (127) T ss_pred EEEECCCCEEEEEE--------HHHHHHHHHHCCCCCEEEEEECCCCCCEEEEEECCCCCCC T ss_conf 76323674365332--------5467999851289984899866899712346651423587 No 276 >PRK10286 O-6-alkylguanine-DNA:cysteine-protein methyltransferase; Provisional Probab=38.64 E-value=22 Score=14.10 Aligned_cols=78 Identities=15% Similarity=0.111 Sum_probs=56.6 Q ss_pred HHHHHHHHHHHHHCCCEE-ECCCHHHHHHHHHHHHHHHHHHH-CCCCCCHHHHHHHCCCCHHHHHHHH-HHHCCCCCCCC Q ss_conf 989999999997228704-61420588989999999998776-0889997899987099989999999-86089875536 Q gi|254780289|r 502 WWVKQAITRSIADQSCTI-RIPVHMRDKIHKVVRTARRMSNK-IKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLET 578 (682) Q Consensus 502 ~~i~~~i~~~~~~~~~~~-r~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~sl~~ 578 (682) -+|.+.+..+++-.-... -+|+++..+- +-.++...+.+- .|.--|-.+||+.+|.|.. +|.+- .+.+.|+++-. T Consensus 60 ~~i~~~l~~YF~G~~~~f~~~pl~~~gt~-Fq~~Vw~~l~~Ip~G~t~sY~~lA~~~g~p~a-~RAVg~A~~~Np~~i~i 137 (171) T PRK10286 60 GGLSDKLRDYFAGNLSIIDTLPTATGGTP-FQREVWQTLRTIPCGQVMHYGQLAEQLGRPGA-ARAVGAANGSNPISIVV 137 (171) T ss_pred HHHHHHHHHHHCCCCCCCCCCCCCCCCCH-HHHHHHHHHHCCCCCCCCCHHHHHHHHCCCCH-HHHHHHHHHCCCCCCCC T ss_conf 78999999998789776785675789999-99999999955899886729999999679854-89999998429988736 Q ss_pred CCC Q ss_conf 358 Q gi|254780289|r 579 PIG 581 (682) Q Consensus 579 ~~~ 581 (682) |-+ T Consensus 138 PCH 140 (171) T PRK10286 138 PCH 140 (171) T ss_pred CCC T ss_conf 884 No 277 >cd06569 GH20_Sm-chitobiase-like The chitobiase of Serratia marcescens is a beta-N-1,4-acetylhexosaminidase with a glycosyl hydrolase family 20 (GH20) domain that hydrolyzes the beta-1,4-glycosidic linkages in oligomers derived from chitin. Chitin is degraded by a two step process: i) a chitinase hydrolyzes the chitin to oligosaccharides and disaccharides such as di-N-acetyl-D-glucosamine and chitobiose, ii) chitobiase then further degrades these oligomers into monomers. The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by solvent or the enzyme, but by the substrate itself. Probab=38.62 E-value=22 Score=14.10 Aligned_cols=50 Identities=14% Similarity=0.192 Sum_probs=36.7 Q ss_pred HHHHHHHHHHCCCCCHHHHHHHCC------------CCCCCHHHHHHHHHHHHHCCCEEECCC Q ss_conf 999999787848867899975268------------435998889999999984797783278 Q gi|254780289|r 31 WKKMIKLARQRGYVTIEELNAFLP------------PDEVSSEQMEDTVAMLSNMGINVVDGD 81 (682) Q Consensus 31 ik~LI~~gke~GylTydeIn~~LP------------~d~~~~e~ie~i~~~L~~~GI~Vve~~ 81 (682) .=+|-+.|-.+|| +..|....+| .+.++.++|-+|+.+=...||.|+-+. T Consensus 56 yP~Lt~~Ga~r~~-~~~e~~~~~p~~~~~~~~~~~~~g~YT~~di~eiV~YA~~RgI~VIPEI 117 (445) T cd06569 56 LPELTEVGAKRCH-DLSETTCLLPQLGSGPDTNNSGSGYYSRADYIEILKYAKARHIEVIPEI 117 (445) T ss_pred CCHHHHHHCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCEEEECC T ss_conf 8526565120566-6433334464336787777776884689999999999997599886506 No 278 >pfam01381 HTH_3 Helix-turn-helix. This large family of DNA binding helix-turn helix proteins includes Cro and CI. Probab=38.60 E-value=22 Score=14.09 Aligned_cols=23 Identities=30% Similarity=0.455 Sum_probs=17.2 Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH Q ss_conf 68899989966789999999999 Q gi|254780289|r 640 HTLEEVGKQFCVTRERIRQIEAK 662 (682) Q Consensus 640 ~tl~e~~~~~~~~~er~rqi~~~ 662 (682) .|..++|+..|||+..|.++|.. T Consensus 10 ~tq~~lA~~~gis~~~is~~E~g 32 (55) T pfam01381 10 LSQEELAEKLGVSRSTISKIENG 32 (55) T ss_pred CCHHHHHHHHCCCHHHHHHHHCC T ss_conf 98999999989699999999879 No 279 >pfam05049 IIGP Interferon-inducible GTPase (IIGP). Interferon-inducible GTPase (IIGP) is thought to play a role in in intracellular defence. IIGP is predominantly associated with the Golgi apparatus and also localizes to the endoplasmic reticulum and exerts a distinct role in IFN-induced intracellular membrane trafficking or processing. Probab=38.55 E-value=22 Score=14.09 Aligned_cols=36 Identities=28% Similarity=0.314 Sum_probs=23.1 Q ss_pred CCCCCCCHHHHHHHHHCCCCC-----C----CHHHHHHHHHHHHH Q ss_conf 457777289999998569768-----8----97889999999998 Q gi|254780289|r 113 ADRSTDDPVRMYLREMGSIEL-----L----SREGEIAIAKRIEA 148 (682) Q Consensus 113 e~~rtdDPVRMYLREMG~V~L-----L----TREgEIeIAKRIE~ 148 (682) ..|.++=|..-||.+|+=-.- . =++-.|.+||.|.. T Consensus 95 G~gt~~f~~~~Yl~~~~f~~yDfFiiiss~rf~~n~v~LAk~i~~ 139 (375) T pfam05049 95 GLGATNFTVETYLEEMKFSEYDFFIIISSERFSLNDVKLAKAIQR 139 (375) T ss_pred CCCCCCCCHHHHHHHCCCCCCCEEEEEECCCCCHHHHHHHHHHHH T ss_conf 999899898999987485647789999677543201899999998 No 280 >CHL00059 atpA ATP synthase CF1 alpha subunit Probab=38.14 E-value=22 Score=14.04 Aligned_cols=49 Identities=22% Similarity=0.291 Sum_probs=31.4 Q ss_pred HHHHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHH Q ss_conf 0289899999999972287046142058898999999999877608899978 Q gi|254780289|r 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPE 550 (682) Q Consensus 499 ya~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 550 (682) |.++|.-.+|-.++.||.+-+=+ +.+.+.|+-.+.|++.--+||+|+-+ T Consensus 237 ~~Apyaa~aIAEyFrdqGkdVLl---v~DdLTr~A~A~REisLllgrPPgre 285 (501) T CHL00059 237 YLAPYTGAALAEYFMYRERHTLI---IYDDLSKQAQAYRQMSLLLRRPPGRE 285 (501) T ss_pred HHHHHHHHHHHHHHHHCCCEEEE---EEECCHHHHHHHHHHHHHCCCCCCCC T ss_conf 99999999999999977982899---98682698899999898648999766 No 281 >cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family. Probab=37.84 E-value=23 Score=14.01 Aligned_cols=22 Identities=41% Similarity=0.462 Sum_probs=10.9 Q ss_pred CCHHHHHHHCCCCHHHHHHHHH Q ss_conf 9978999870999899999998 Q gi|254780289|r 547 PTPEEIAKKLAMPVEGVRKVLK 568 (682) Q Consensus 547 ~~~~~~a~~~~~~~~~~~~~~~ 568 (682) .|-++||+.+|++.+.|..+++ T Consensus 26 ltr~eiA~~lG~t~eTVsR~l~ 47 (67) T cd00092 26 LTRQEIADYLGLTRETVSRTLK 47 (67) T ss_pred CCHHHHHHHHCCCHHHHHHHHH T ss_conf 7999999997890999999999 No 282 >smart00787 Spc7 Spc7 kinetochore protein. This domain is found in cell division proteins which are required for kinetochore-spindle association. Probab=37.75 E-value=23 Score=14.00 Aligned_cols=36 Identities=19% Similarity=0.219 Sum_probs=24.2 Q ss_pred HHHHHHHH-CCCCCCCHHHHH--HHHHHHHHHHHHHHHH Q ss_conf 99999985-697688978899--9999999889999999 Q gi|254780289|r 121 VRMYLREM-GSIELLSREGEI--AIAKRIEAGRAMMMAS 156 (682) Q Consensus 121 VRMYLREM-G~V~LLTREgEI--eIAKRIE~G~~~i~~a 156 (682) .-=|..-+ .+||+|.=-.-. ++-|+|+.|+..+... T Consensus 51 l~d~v~A~~~~iP~LELY~~sC~EL~~~I~egr~~~~~~ 89 (312) T smart00787 51 LDQYVVAGYCTVPLLELYQFSCKELKKYISEGRDLFKEI 89 (312) T ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 999999715886099999999999999999889999999 No 283 >PRK11637 hypothetical protein; Provisional Probab=37.67 E-value=23 Score=13.99 Aligned_cols=26 Identities=15% Similarity=0.220 Sum_probs=8.9 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 05778878999999999999999999 Q gi|254780289|r 331 NQSRIDLLVEQLYDISKRIMHNEGEL 356 (682) Q Consensus 331 ~~k~iE~L~~~l~~~~k~Ir~~Er~L 356 (682) ....|+.+...+.....++......+ T Consensus 77 ~~~eI~~l~~~i~~l~~~~~~~~~~l 102 (404) T PRK11637 77 LNKQIDEMNASIAKLEQQKAAQERSL 102 (404) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 99999999999999999999999999 No 284 >pfam00392 GntR Bacterial regulatory proteins, gntR family. This family of regulatory proteins consists of the N-terminal HTH region of GntR-like bacterial transcription factors. At the C-terminus there is usually an effector-binding/oligomerisation domain. The GntR-like proteins include the following sub-families: MocR, YtrR, FadR, AraR, HutC and PlmA, DevA, DasR. Many of these proteins have been shown experimentally to be autoregulatory, enabling the prediction of operator sites and the discovery of cis/trans relationships. The DasR regulator has been shown to be a global regulator of primary metabolism and development in Streptomyces coelicolor. Probab=37.65 E-value=23 Score=13.99 Aligned_cols=27 Identities=22% Similarity=0.405 Sum_probs=19.5 Q ss_pred CCCCCHHHHHHHCCCCHHHHHHHHHHH Q ss_conf 889997899987099989999999860 Q gi|254780289|r 544 KREPTPEEIAKKLAMPVEGVRKVLKIT 570 (682) Q Consensus 544 ~~~~~~~~~a~~~~~~~~~~~~~~~~~ 570 (682) .+-|+..+||+.++++..-|+++++.. T Consensus 22 ~~LPs~~~La~~~~vSr~tvr~Al~~L 48 (64) T pfam00392 22 DKLPSERELAAEFGVSRTTVREALRRL 48 (64) T ss_pred CCCHHHHHHHHHHCCCHHHHHHHHHHH T ss_conf 998479999999796999999999999 No 285 >KOG0976 consensus Probab=37.45 E-value=23 Score=13.97 Aligned_cols=55 Identities=18% Similarity=0.255 Sum_probs=36.0 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 5677653223333222221126889999998765332112468999875557899 Q gi|254780289|r 403 VDSILKIRNEIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVI 457 (682) Q Consensus 403 ~~eI~~~q~kL~~ie~~~gl~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~ 457 (682) ++.+....+.|..+..+..--+.++|.-+-++..|.+.-..||++|-+|-=||-. T Consensus 374 k~nve~elqsL~~l~aerqeQidelKn~if~~e~~~~dhe~~kneL~~a~ekld~ 428 (1265) T KOG0976 374 KENVEEELQSLLELQAERQEQIDELKNHIFRLEQGKKDHEAAKNELQEALEKLDL 428 (1265) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHH T ss_conf 9879999999999999999999999875554664110267788899999999988 No 286 >COG5174 TFA2 Transcription initiation factor IIE, beta subunit [Transcription] Probab=37.44 E-value=23 Score=13.97 Aligned_cols=41 Identities=20% Similarity=0.183 Sum_probs=26.8 Q ss_pred HHHHHHHHHHCCCCCCHHHHHHHCCCCHH-HHHHHHHHHCCC Q ss_conf 99999987760889997899987099989-999999860898 Q gi|254780289|r 533 VRTARRMSNKIKREPTPEEIAKKLAMPVE-GVRKVLKITKEP 573 (682) Q Consensus 533 ~~~~~~~~~~~~~~~~~~~~a~~~~~~~~-~~~~~~~~~~~~ 573 (682) ...+-++++++||+-+.+||+..|.|+.. .+..+++..+++ T Consensus 85 lh~aieylk~~~~P~~~eEi~dyls~~l~~~~v~Llkk~~ri 126 (285) T COG5174 85 LHAAIEYLKQHDRPLSFEEIKDYLSIDLHNNYVLLLKKKRRI 126 (285) T ss_pred HHHHHHHHHHCCCCCCHHHHHHHHCCCCCHHHHHHHHHCCCC T ss_conf 999999999718965599998886476654699998650472 No 287 >smart00796 AHS1 Allophanate hydrolase subunit 1. This domain represents subunit 1 of allophanate hydrolase (AHS1). Probab=37.07 E-value=13 Score=15.86 Aligned_cols=48 Identities=19% Similarity=0.256 Sum_probs=34.2 Q ss_pred HHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCC Q ss_conf 9972287046142058898999999999877608899978999870999899999998608987 Q gi|254780289|r 511 SIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPI 574 (682) Q Consensus 511 ~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ 574 (682) .....+++++|||.--.. --|..+.+|+..|+++++|.+......--| T Consensus 81 ~~~~~~r~~~IPV~Yd~~----------------~gpDL~~va~~~gls~~evI~~H~~~~y~V 128 (201) T smart00796 81 ALEVPGRIIEIPVCYGGE----------------FGPDLEFVARHNGLSVDEVIRLHSAAEYRV 128 (201) T ss_pred CCCCCCCEEEEEEEECCC----------------CCCCHHHHHHHHCCCHHHHHHHHHCCCEEE T ss_conf 357898389998587998----------------777999999884959999999973689899 No 288 >PRK11920 rirA iron-responsive transcriptional regulator; Reviewed Probab=37.01 E-value=23 Score=13.92 Aligned_cols=29 Identities=17% Similarity=0.052 Sum_probs=21.8 Q ss_pred HCCCCCCHHHHHHHCCCCHHHHHHHHHHH Q ss_conf 60889997899987099989999999860 Q gi|254780289|r 542 KIKREPTPEEIAKKLAMPVEGVRKVLKIT 570 (682) Q Consensus 542 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~ 570 (682) .-|+..+..+||+..++|..-+.++++.. T Consensus 20 ~~~~~~~~~~Ia~~~~is~~~l~kIl~~L 48 (153) T PRK11920 20 NDGKLSRIPEIARAYGVSELFLFKILQPL 48 (153) T ss_pred CCCCCCCHHHHHHHHCCCHHHHHHHHHHH T ss_conf 89997679999988891999999999999 No 289 >pfam06953 ArsD Arsenical resistance operon trans-acting repressor ArsD. This family consists of several bacterial arsenical resistance operon trans-acting repressor ArsD proteins. ArsD is a trans-acting repressor of the arsRDABC operon that confers resistance to arsenicals and antimonials in Escherichia coli. It possesses two-pairs of vicinal cysteine residues, Cys(12)-Cys(13) and Cys(112)-Cys(113), that potentially form separate binding sites for the metalloids that trigger dissociation of ArsD from the operon. However, as a homodimer it has four vicinal cysteine pairs. Probab=36.75 E-value=19 Score=14.56 Aligned_cols=21 Identities=33% Similarity=0.423 Sum_probs=17.7 Q ss_pred HCCCCCCHHHHHHHCCCCHHH Q ss_conf 608899978999870999899 Q gi|254780289|r 542 KIKREPTPEEIAKKLAMPVEG 562 (682) Q Consensus 542 ~~~~~~~~~~~a~~~~~~~~~ 562 (682) ..||.||-+|+|+.+|++... T Consensus 84 ~~G~YPt~eEla~w~gi~~~~ 104 (119) T pfam06953 84 KTGRYPTREELARWAGITLSP 104 (119) T ss_pred EECCCCCHHHHHHHHCCCCCC T ss_conf 815699999999996998776 No 290 >TIGR02237 recomb_radB DNA repair and recombination protein RadB; InterPro: IPR011939 This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA, eukaryotic RAD51 (IPR011941 from INTERPRO) and DMC1 (IPR011940 from INTERPRO), and archaeal RadA (IPR011938 from INTERPRO) ,, .; GO: 0003684 damaged DNA binding, 0005524 ATP binding, 0008094 DNA-dependent ATPase activity, 0006281 DNA repair, 0006310 DNA recombination. Probab=36.64 E-value=17 Score=14.90 Aligned_cols=22 Identities=27% Similarity=0.409 Sum_probs=12.7 Q ss_pred HHHHHHHHHHHHHHHHHHHHHH Q ss_conf 2468999875557899988752 Q gi|254780289|r 442 SIAKKEMVEANLRLVISVAKKY 463 (682) Q Consensus 442 ~~AK~~l~~anlr~v~~~~~~~ 463 (682) ......++..=|.+..++|+|+ T Consensus 127 ~~~~~~~l~~Ql~~Ll~lArk~ 148 (223) T TIGR02237 127 QISLNRELARQLTLLLSLARKK 148 (223) T ss_pred HHHHHHHHHHHHHHHHHHHHHC T ss_conf 6799999999999999998764 No 291 >PRK09990 DNA-binding transcriptional regulator GlcC; Provisional Probab=36.28 E-value=24 Score=13.83 Aligned_cols=56 Identities=18% Similarity=0.227 Sum_probs=40.7 Q ss_pred CCCHHCCHHHHHHHHHHHHHC-C-CC-CHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCEEEC Q ss_conf 443020289999999978784-8-86-78999752684359988899999999847977832 Q gi|254780289|r 21 SLVFDFSDDSWKKMIKLARQR-G-YV-TIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD 79 (682) Q Consensus 21 ~~~~d~~~~~ik~LI~~gke~-G-yl-TydeIn~~LP~d~~~~e~ie~i~~~L~~~GI~Vve 79 (682) .++-|..-+.|+..|--|.=+ | -| |-.+|.+.|. +|---+=..+..|...|+-.+. T Consensus 6 ~~l~e~V~~~ir~~I~~g~l~pG~~LP~E~eLae~~g---VSR~~VREAL~~L~~~GlV~~~ 64 (251) T PRK09990 6 RPIADVVAERIERLIVDGVLKVGQALPSERRLTEKLG---VSRSALREGLKVLRGRGIIETA 64 (251) T ss_pred CCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHC---CCHHHHHHHHHHHHHCCCEEEE T ss_conf 7399999999999998099999297923999999989---7959999999999988997985 No 292 >PRK04184 DNA topoisomerase VI subunit B; Validated Probab=36.16 E-value=24 Score=13.82 Aligned_cols=48 Identities=19% Similarity=0.315 Sum_probs=36.2 Q ss_pred HHHHHHHHHHHHHHHCCCCC-CCEEEHH-------------------------HHHHHHHHHHHHHHHCCCEEE Q ss_conf 75443679999887438545-7312010-------------------------289899999999972287046 Q gi|254780289|r 473 LIQEGNIGLMKAAEKFDWCL-GYKFSTY-------------------------AMWWVKQAITRSIADQSCTIR 520 (682) Q Consensus 473 ~~~~~~~~l~~a~~~~~~~~-g~~f~ty-------------------------a~~~i~~~i~~~~~~~~~~~r 520 (682) |.|+|.-.+-+||...+|++ |.+++.- ...=|..+|..|+.+-+|-++ T Consensus 381 ly~~g~caitkav~~inWr~Ygl~q~p~gP~~v~VhvaSt~VPftsesKEaIAd~pEI~~EIrlAl~e~~R~L~ 454 (533) T PRK04184 381 LYDEGACVITKAVESINWKRYGLSQPPDAPLVVLVHVASTKVPYTSEGKEAIADVPEIEKEIRLALMEAARKLK 454 (533) T ss_pred EECCCCCHHHHHHHHCCHHHCCCCCCCCCCEEEEEEEEECCCCCCCCCHHHHCCCHHHHHHHHHHHHHHHHHHH T ss_conf 21266417888877478565187899998789999962068896774355433778999999999999999999 No 293 >TIGR01436 glu_cys_lig_pln glutamate--cysteine ligase; InterPro: IPR011556 These sequences represent one of two highly dissimilar forms of glutamate--cysteine ligase (gamma-glutamylcysteine synthetase), an enzyme of glutathione biosynthesis. The other group is represented by IPR006335 from INTERPRO. This form is found in plants (with a probable transit peptide), root nodule and other bacteria, but not Escherichia coli and closely related species. ; GO: 0004357 glutamate-cysteine ligase activity, 0006750 glutathione biosynthetic process, 0009507 chloroplast. Probab=35.62 E-value=24 Score=13.76 Aligned_cols=87 Identities=15% Similarity=0.266 Sum_probs=44.2 Q ss_pred CCCCCHHHHHHHCCC--CHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHHH-----HHHHHHHHHH Q ss_conf 889997899987099--989999999860898755363588998604756238988998999999-----9999999999 Q gi|254780289|r 544 KREPTPEEIAKKLAM--PVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ-----ANLRETTTRV 616 (682) Q Consensus 544 ~~~~~~~~~a~~~~~--~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~-----~~~~~~~~~~ 616 (682) |-.|+...=..+|.. |.-+.+.-|.+- |-|+.+. ...+..-+... ..+-.++.++ T Consensus 284 ge~P~l~DW~~HLsT~FPeVRLK~YLEmR----------GADgg~~--------~~lcAlpAfW~glLyD~~~L~aa~D~ 345 (446) T TIGR01436 284 GELPILSDWEDHLSTLFPEVRLKRYLEMR----------GADGGSA--------RRLCALPAFWVGLLYDEEALDAALDL 345 (446) T ss_pred CCCCCCCCHHHHHHCCCCCHHHHHHHHCC----------CCCCCCC--------CCCCHHHHHHHHHHHHHHHHHHHHHH T ss_conf 88876544143540247511211122112----------6675443--------21311367777786336789999988 Q ss_pred HHCCCHHHHHHHHH---HHCCCCC--CCCCHHHHHHH Q ss_conf 73299889999999---8187986--74688999899 Q gi|254780289|r 617 LASLTPREERVLRM---RFGIGMN--TDHTLEEVGKQ 648 (682) Q Consensus 617 l~~l~~re~~v~~~---r~g~~~~--~~~tl~e~~~~ 648 (682) ++.=++-|++-||. |-||-+- ...+|..||.+ T Consensus 346 ~k~Ws~~er~~lrnevP~~gLkTl~~~g~sl~~lg~~ 382 (446) T TIGR01436 346 VKDWSMEERERLRNEVPKKGLKTLIRDGISLKDLGRD 382 (446) T ss_pred HHCCCHHHHHHHHHHCCHHHHCCCCCCCHHHHHHHHH T ss_conf 6238988998776521421311668762679999999 No 294 >PRK10225 DNA-binding transcriptional repressor UxuR; Provisional Probab=35.43 E-value=24 Score=13.74 Aligned_cols=19 Identities=11% Similarity=0.281 Sum_probs=10.2 Q ss_pred HHHHHHHHHHHHHHHHHCC Q ss_conf 9987555789998875223 Q gi|254780289|r 447 EMVEANLRLVISVAKKYTN 465 (682) Q Consensus 447 ~l~~anlr~v~~~~~~~~~ 465 (682) ....++..|-..||.--.| T Consensus 143 ~~~~~D~~FH~~Ia~AsgN 161 (257) T PRK10225 143 SSESGDMQFHLAIAEATHN 161 (257) T ss_pred HHHHHHHHHHHHHHHHCCC T ss_conf 6999999999999998599 No 295 >COG0853 PanD Aspartate 1-decarboxylase [Coenzyme metabolism] Probab=35.25 E-value=4.9 Score=19.26 Aligned_cols=50 Identities=26% Similarity=0.244 Sum_probs=29.9 Q ss_pred HHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHH Q ss_conf 9875557899988752235677788754436799998874385457312010289899 Q gi|254780289|r 448 MVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505 (682) Q Consensus 448 l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~ 505 (682) ..+|||-+|=||+ ==.||.....|==...|+=++..-|-|||||+..-=| T Consensus 14 VT~A~L~Y~GSit--------ID~dlldaagile~EkV~I~N~nNGaRf~TYvI~g~r 63 (126) T COG0853 14 VTEADLNYVGSIT--------IDEDLLDAAGILENEKVDIVNVNNGARFSTYVIAGER 63 (126) T ss_pred EEECCCCEEEEEE--------ECHHHHHHCCCCCCCEEEEEECCCCCEEEEEEEECCC T ss_conf 8502330477688--------8999996538987766899988888378999987268 No 296 >PRK09526 lacI lac repressor; Reviewed Probab=35.14 E-value=25 Score=13.70 Aligned_cols=29 Identities=17% Similarity=0.295 Sum_probs=16.2 Q ss_pred HHHHHHCC-CCCCCHHHHHHHHHHHHHCCC Q ss_conf 99975268-435998889999999984797 Q gi|254780289|r 47 EELNAFLP-PDEVSSEQMEDTVAMLSNMGI 75 (682) Q Consensus 47 deIn~~LP-~d~~~~e~ie~i~~~L~~~GI 75 (682) .-++.+|- ...++++--+.|.....++|. T Consensus 20 sTVSrvLn~~~~vs~~tr~rV~~~a~elgY 49 (342) T PRK09526 20 QTVSRVLNQASHVSAKTREKVEAAMAELNY 49 (342) T ss_pred HHHHHHHCCCCCCCHHHHHHHHHHHHHHCC T ss_conf 999999789799999999999999998399 No 297 >PRK11886 biotin--protein ligase; Provisional Probab=35.05 E-value=25 Score=13.69 Aligned_cols=49 Identities=14% Similarity=0.266 Sum_probs=39.3 Q ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCEEEC Q ss_conf 8999999997878488678999752684359988899999999847977832 Q gi|254780289|r 28 DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVD 79 (682) Q Consensus 28 ~~~ik~LI~~gke~GylTydeIn~~LP~d~~~~e~ie~i~~~L~~~GI~Vve 79 (682) .+++-+|+++=+...|++=++|.+.|. ++-..+=+-+..|.++|+.|.- T Consensus 3 ~~~~~~lL~~L~~g~~~SGe~la~~Lg---vSR~aVwK~i~~L~~~G~~I~s 51 (319) T PRK11886 3 YEKMLQLLSLLADGDFHSGEQLAEELG---ISRAAIWKHIQTLEEWGLDIFS 51 (319) T ss_pred HHHHHHHHHHHHCCCCCCHHHHHHHHC---CCHHHHHHHHHHHHHCCCEEEE T ss_conf 789999999973799296999999879---8899999999999977973999 No 298 >PRK10430 DNA-binding transcriptional activator DcuR; Provisional Probab=34.86 E-value=25 Score=13.67 Aligned_cols=79 Identities=15% Similarity=0.167 Sum_probs=38.8 Q ss_pred HHHHHHHHHHHHHHCCCEEECCCHHH-HHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHH--HHCCCCCCC Q ss_conf 89899999999972287046142058-898999999999877608899978999870999899999998--608987553 Q gi|254780289|r 501 MWWVKQAITRSIADQSCTIRIPVHMR-DKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLE 577 (682) Q Consensus 501 ~~~i~~~i~~~~~~~~~~~r~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~sl~ 577 (682) --+|-+.+.+........-++|-.+. .|+. ++...+....|.+-|.+|+|+.+|+|.-.+++-|. ....-+..+ T Consensus 135 Q~~iD~l~~~~~~~~~~~~~lPKGl~~~TL~---~i~~~l~~~~~~~~sa~eva~~~giSRvTaRRYLe~L~~~g~~~~~ 211 (239) T PRK10430 135 QAELDQLIHGSSSNEQDPRRLPKGLTPQTLR---TLCQWIDAHQDYEFSTDELANEVNISRVSCRKYLIWLVNCHILFTS 211 (239) T ss_pred HHHHHHHHHCCCCCCCCCCCCCCCCCHHHHH---HHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEEE T ss_conf 9999999850578888766699999999999---9999998279998469999988585298899999999868958998 Q ss_pred CCCCC Q ss_conf 63588 Q gi|254780289|r 578 TPIGD 582 (682) Q Consensus 578 ~~~~~ 582 (682) .-.|. T Consensus 212 ~~YG~ 216 (239) T PRK10430 212 IHYGV 216 (239) T ss_pred ECCCC T ss_conf 35789 No 299 >PRK11753 cAMP-regulatory protein; Provisional Probab=34.72 E-value=25 Score=13.65 Aligned_cols=26 Identities=23% Similarity=0.447 Sum_probs=15.3 Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHC Q ss_conf 468899989966789999999999999832 Q gi|254780289|r 639 DHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668 (682) Q Consensus 639 ~~tl~e~~~~~~~~~er~rqi~~~a~~~l~ 668 (682) +.|-+|+|..+|+|||.|- ++|++|+ T Consensus 168 ~lt~~eLA~~lG~sretvs----R~L~~L~ 193 (211) T PRK11753 168 KITRQEIGRIVGCSREMVG----RVLKMLE 193 (211) T ss_pred CCCHHHHHHHHCCCHHHHH----HHHHHHH T ss_conf 4699999988699899999----9999999 No 300 >pfam01325 Fe_dep_repress Iron dependent repressor, N-terminal DNA binding domain. This family includes the Diphtheria toxin repressor. DNA binding is through a helix-turn-helix motif. Probab=34.36 E-value=25 Score=13.61 Aligned_cols=29 Identities=21% Similarity=0.266 Sum_probs=22.6 Q ss_pred HCCCCCCHHHHHHHCCCCHHHHHHHHHHH Q ss_conf 60889997899987099989999999860 Q gi|254780289|r 542 KIKREPTPEEIAKKLAMPVEGVRKVLKIT 570 (682) Q Consensus 542 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~ 570 (682) +.+..++..+||+.||++..-|..+++-. T Consensus 16 ~~~~~v~~~~iA~~L~Vs~~SVt~mlkkL 44 (58) T pfam01325 16 EEKGVVKTKDLAERLNVSPSTVSEMLKKL 44 (58) T ss_pred CCCCCEEHHHHHHHHCCCCHHHHHHHHHH T ss_conf 26996129999999599925299999999 No 301 >cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is Probab=33.87 E-value=26 Score=13.56 Aligned_cols=26 Identities=31% Similarity=0.482 Sum_probs=17.9 Q ss_pred CCCCHHHHHHHCCCCHHHHHHHHHHH Q ss_conf 89997899987099989999999860 Q gi|254780289|r 545 REPTPEEIAKKLAMPVEGVRKVLKIT 570 (682) Q Consensus 545 ~~~~~~~~a~~~~~~~~~~~~~~~~~ 570 (682) +-|+..+||+.+|+|..-|+.++... T Consensus 24 ~LPs~~~La~~~~vSr~tvr~Al~~L 49 (66) T cd07377 24 RLPSERELAEELGVSRTTVREALREL 49 (66) T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH T ss_conf 99279999999798889999999999 No 302 >PRK13752 putative transcriptional regulator MerR; Provisional Probab=33.75 E-value=22 Score=14.11 Aligned_cols=25 Identities=24% Similarity=0.125 Sum_probs=14.4 Q ss_pred CCCHHHHHHHCCCCHHHHHHHHHHH Q ss_conf 9997899987099989999999860 Q gi|254780289|r 546 EPTPEEIAKKLAMPVEGVRKVLKIT 570 (682) Q Consensus 546 ~~~~~~~a~~~~~~~~~~~~~~~~~ 570 (682) .-++-|+|+..|++++.||..-++. T Consensus 7 ~m~IgelAk~~gvs~~tIRyYE~~G 31 (144) T PRK13752 7 NLTIGVFAKAAGVNVETIRFYQRKG 31 (144) T ss_pred CCCHHHHHHHHCCCHHHHHHHHHCC T ss_conf 3829999999789845667987259 No 303 >PRK13394 3-hydroxybutyrate dehydrogenase; Provisional Probab=33.25 E-value=26 Score=13.48 Aligned_cols=110 Identities=15% Similarity=0.061 Sum_probs=61.5 Q ss_pred HHHHHHHHHHHHHH----HHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHH-H Q ss_conf 21124689998755----578999887522356777887544367999988743854573120102898999999999-7 Q gi|254780289|r 439 CEASIAKKEMVEAN----LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI-A 513 (682) Q Consensus 439 ~e~~~AK~~l~~an----lr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~-~ 513 (682) .-++.+-..|++.+ .-.+.|++-.....+...------|.+||.|++-+-=-..|.+.-+.+--||+-.+.... . T Consensus 121 ~~~~~~~p~M~k~~~~G~IVnisS~~~~~~~~~~~~Y~asKaal~~ltk~lA~E~a~~gIrVN~V~PG~i~T~~~~~~~~ 200 (262) T PRK13394 121 LTTKAALKHMYKDDRGGVVIYMGSVHSHEASPLKSAYVTAKHGLLGLARVLAKEGAKHNVRSHVVCPGFVRTPLVDKQIP 200 (262) T ss_pred HHHHHHHHHHHHHCCCCEEEEECCHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCEEEEEEEECCCCCCHHHHHCH T ss_conf 99999999999837996899974577676799976899999999999999999852319699999758788702331365 Q ss_pred HCCCEEECCCHHHHHHHHHHHHHHHHH--HHCCCCCCHHHHHHHC Q ss_conf 228704614205889899999999987--7608899978999870 Q gi|254780289|r 514 DQSCTIRIPVHMRDKIHKVVRTARRMS--NKIKREPTPEEIAKKL 556 (682) Q Consensus 514 ~~~~~~r~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~a~~~ 556 (682) +.+.-..+. .- ....+.+. .-.||-.+|+|+|... T Consensus 201 ~~~~~~~~~--~~------~~~~~~~~~~~p~~r~g~p~dvA~~v 237 (262) T PRK13394 201 EQAKELGIS--EE------EVVKKVMLGKTVDGVFTTVEDVAQTV 237 (262) T ss_pred HHHHHCCCC--HH------HHHHHHHHCCCCCCCCCCHHHHHHHH T ss_conf 578763788--58------99999986179988972999999999 No 304 >TIGR02018 his_ut_repres histidine utilization repressor; InterPro: IPR010248 This entry represents a proteobacterial histidine utilization repressor. It is usually found clustered with the enzymes HutUHIG so that it can regulate its own expression as well. A number of species have several paralogs and may fine-tune the regulation according to levels of degradation intermediates such as urocanate. This family belongs to the larger GntR family of transcriptional regulators.; GO: 0003677 DNA binding, 0016564 transcription repressor activity, 0006547 histidine metabolic process, 0045892 negative regulation of transcription DNA-dependent. Probab=33.08 E-value=26 Score=13.46 Aligned_cols=68 Identities=25% Similarity=0.354 Sum_probs=47.3 Q ss_pred HHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHH-HHCCCCCCCCCCC Q ss_conf 899999999972287046142058898999999999877608899978999870999899999998-6089875536358 Q gi|254780289|r 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK-ITKEPISLETPIG 581 (682) Q Consensus 503 ~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~sl~~~~~ 581 (682) =|||.|.+.|.-..| -| .-|-|+-.||++.+|+|.=.|.++|+ .+..- -|.--= T Consensus 5 rik~~I~~~I~SG~W---~~--------------------g~R~PsE~EL~~~~G~SRMTvnrALreLt~~G-~l~R~q- 59 (234) T TIGR02018 5 RIKQDILERIRSGEW---PP--------------------GHRIPSENELVAQFGVSRMTVNRALRELTDAG-LLERRQ- 59 (234) T ss_pred HHHHHHHHCCCCCCC---CC--------------------CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCC-CEEEEC- T ss_conf 899999962578888---87--------------------67568779999774872335789999887568-188127- Q ss_pred CCCCCEEEEEECC--CCCCCH Q ss_conf 8998604756238--988998 Q gi|254780289|r 582 DEDTSHLGDFIED--KNAVSP 600 (682) Q Consensus 582 ~~~~~~~~~~~~d--~~~~~~ 600 (682) -+|.||.- +...++ T Consensus 60 -----g~GTFVA~ae~k~~s~ 75 (234) T TIGR02018 60 -----GVGTFVARAEPKAQSA 75 (234) T ss_pred -----CCEEEECCCCCCCCCH T ss_conf -----8500441777653101 No 305 >COG1522 Lrp Transcriptional regulators [Transcription] Probab=32.69 E-value=27 Score=13.42 Aligned_cols=36 Identities=19% Similarity=0.288 Sum_probs=24.2 Q ss_pred HHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHH Q ss_conf 9999999877608899978999870999899999998 Q gi|254780289|r 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK 568 (682) Q Consensus 532 ~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~ 568 (682) +.+..-..+|..+| -+..+||+.+|+|...|..-.+ T Consensus 9 ~D~~IL~~L~~d~r-~~~~eia~~lglS~~~v~~Ri~ 44 (154) T COG1522 9 IDRRILRLLQEDAR-ISNAELAERVGLSPSTVLRRIK 44 (154) T ss_pred HHHHHHHHHHHCCC-CCHHHHHHHHCCCHHHHHHHHH T ss_conf 99999999997276-5799999997979899999999 No 306 >cd06919 Asp_decarbox Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production. Decarboxylation of aspartate is the major route of beta-alanine production in bacteria, and is catalyzed by the enzyme L-aspartate decarboxylase (ADC), EC:4.1.1.11 which requires a pyruvoyl group for its activity. The pyruvoyl cofactor is covalently bound to the enzyme. The protein is synthesized as a proenzyme and cleaved via self-processing at Gly23-Ser24 to yield an alpha chain (C-terminal fragment) and beta chain (N-terminal fragment), and the pyruvoyl group. Beta-alanine is required for the biosynthesis of pantothenate, in which the enzyme plays a critical regulatory role. The active site of the tetrameric enzyme is located at the interface of two subunits, with a Lysine and a Histidine from the beta chain of one subunit forming the active site with residues from the alpha chain of the adjacent subunit. This alignment Probab=32.59 E-value=4.7 Score=19.38 Aligned_cols=35 Identities=20% Similarity=0.180 Sum_probs=23.0 Q ss_pred HHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHH Q ss_conf 88754436799998874385457312010289899 Q gi|254780289|r 471 LDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505 (682) Q Consensus 471 ~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~ 505 (682) .||+...+|---.-|+=++..-|-||+|||.+--| T Consensus 29 ~~Lm~aa~i~~~E~V~V~N~~NG~Rf~TYvI~g~~ 63 (111) T cd06919 29 EDLLEAAGILPYEKVLVVNVNNGARFETYVIPGER 63 (111) T ss_pred HHHHHHCCCCCCCEEEEEECCCCCEEEEEEEECCC T ss_conf 99998759998988999989899478999986468 No 307 >TIGR02513 type_III_yscB type III secretion system chaperone, YscB family; InterPro: IPR013353 Members of this family include YscB of Yersinia and functionally equivalent (but differently named) proteins from type III secretion systems of other pathogens that affect animal cells. YscB acts, along with SycN (IPR012673 from INTERPRO), as a chaperone for YopN, a key part of a complex that regulates type III secretion so that it responds to contact with the eukaryotic target cell.. Probab=32.30 E-value=10 Score=16.78 Aligned_cols=103 Identities=18% Similarity=0.301 Sum_probs=68.9 Q ss_pred HHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHH Q ss_conf 99877608899978999870999899999998608987553635889986047562389889989999999999999999 Q gi|254780289|r 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRV 616 (682) Q Consensus 537 ~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~ 616 (682) +.+...+|+.|-+..=--...+.+++..-+++--..-+-|++|+. .....|-+......||..+..+ T Consensus 5 ~~LA~~LG~gPFvAd~~G~Y~l~iD~~~l~l~~~g~~lll~tpL~-------------~~~~~~~~~~~~~lLk~llq~~ 71 (140) T TIGR02513 5 KSLAERLGQGPFVADRQGAYHLEIDKLTLLLKQHGSELLLETPLE-------------LRFLEPKDDQQVELLKRLLQQV 71 (140) T ss_pred HHHHHHCCCCCCEECCCCCEEEEECCEEEEEECCCCHHHHHCCCC-------------CCCCCCCCHHHHHHHHHHHHHH T ss_conf 899987289983107986157878363566201363442405456-------------3214757704789999999999 Q ss_pred HH---------CCCHHHHHHHHHHHCCCCCCCCCHHHH-HHHHCCC Q ss_conf 73---------299889999999818798674688999-8996678 Q gi|254780289|r 617 LA---------SLTPREERVLRMRFGIGMNTDHTLEEV-GKQFCVT 652 (682) Q Consensus 617 l~---------~l~~re~~v~~~r~g~~~~~~~tl~e~-~~~~~~~ 652 (682) ++ +|+.-++-||..|.+|..-.++.|+++ +++.+|- T Consensus 72 ~~w~r~~P~~L~ld~~~~LiL~arl~l~~ld~~~L~~~L~~~~~ll 117 (140) T TIGR02513 72 LKWLRRYPQALVLDADGQLILEARLRLDELDNDQLEELLAKHVNLL 117 (140) T ss_pred HHHHHCCCCEEEECCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHH T ss_conf 9875138836866553111888655211589889999999999999 No 308 >TIGR02267 TIGR02267 Myxococcus xanthus paralogous family TIGR02267; InterPro: IPR011753 This family consists of at least 7 paralogs in Myxococcus xanthus, a member of the Deltaproteobacteria. The function is unknown.. Probab=32.20 E-value=27 Score=13.36 Aligned_cols=24 Identities=29% Similarity=0.361 Sum_probs=13.6 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 999999876533211246899987 Q gi|254780289|r 427 FRHIVSMVRKGECEASIAKKEMVE 450 (682) Q Consensus 427 lK~i~r~I~~ge~e~~~AK~~l~~ 450 (682) |+++.++|+.|=.+.-+|=.+|++ T Consensus 62 L~e~~~RIr~GS~RL~rAL~~a~~ 85 (123) T TIGR02267 62 LKEISRRIREGSRRLSRALTEAVR 85 (123) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 999988865644899999999986 No 309 >cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Probab=32.08 E-value=27 Score=13.35 Aligned_cols=23 Identities=30% Similarity=0.265 Sum_probs=17.0 Q ss_pred CHHHHHHHCCCCHHHHHHHHHHH Q ss_conf 97899987099989999999860 Q gi|254780289|r 548 TPEEIAKKLAMPVEGVRKVLKIT 570 (682) Q Consensus 548 ~~~~~a~~~~~~~~~~~~~~~~~ 570 (682) |+.|+|+.+|+|+..++---+.. T Consensus 2 tIgevAk~~gvs~~TlRyYE~~G 24 (108) T cd01107 2 TIGEFAKLSNLSIKALRYYDKIG 24 (108) T ss_pred CHHHHHHHHCCCHHHHHHHHHCC T ss_conf 78999999895999999999859 No 310 >pfam12129 Phtf-FEM1B_bdg Male germ-cell putative homeodomain transcription factor. This domain is found in bacteria and eukaryotes, and is typically between 101 and 140 amino acids in length. Phtf proteins do not display any sequence similarity to known or predicted proteins, but their conservation among species suggests an essential function. The 84 kDa Phtf1 protein is an integral membrane protein, anchored to a cell membrane by six to eight trans-membrane domains, that is associated with a domain of the endoplasmic reticulum (ER) juxtaposed to the Golgi apparatus. It is present during meiosis and spermiogenesis, and, by the end of spermiogenesis, is released from the mature spermatozoon within the residual bodies. Phtf1 enhances the binding of FEM1B -feminisation homologue 1B - to cell membranes. Fem-1 was initially identified in the signaling pathway for sex determination, as well as being implicated in apoptosis, but its biochemical role is still unclear, and neither FEM1B nor PHT Probab=31.91 E-value=20 Score=14.51 Aligned_cols=57 Identities=21% Similarity=0.347 Sum_probs=29.6 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHH Q ss_conf 24689998755578999887522356777887544367999988743854573120102898999999999 Q gi|254780289|r 442 SIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI 512 (682) Q Consensus 442 ~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~ 512 (682) ..-|.++|--.|--=.+-+|- -|..-+..-...|+++.+ =|.-|+-|||.|--.+.+ T Consensus 42 ~~lK~dLIDVDLVRGStF~KA-----KP~~~w~svtr~gi~Rvl---------f~P~y~~WWiQqTS~~iF 98 (159) T pfam12129 42 GHLKPDLIDVDLVRGSTFAKA-----KPELPWTSLTRKGAVRVV---------FFPIFAKWWVQVTSPRIF 98 (159) T ss_pred CCCCCCCEEEEEECCCCCCCC-----CCCCCHHHHHHHHHHHHH---------HHHHHHHHHHHHCCHHHH T ss_conf 788800133320126665666-----887749999999999999---------999999999985227899 No 311 >pfam00325 Crp Bacterial regulatory proteins, crp family. Probab=31.75 E-value=28 Score=13.31 Aligned_cols=21 Identities=38% Similarity=0.532 Sum_probs=11.8 Q ss_pred CHHHHHHHCCCCHHHHHHHHH Q ss_conf 978999870999899999998 Q gi|254780289|r 548 TPEEIAKKLAMPVEGVRKVLK 568 (682) Q Consensus 548 ~~~~~a~~~~~~~~~~~~~~~ 568 (682) +-.+||..+|++.+.|..++. T Consensus 4 srqdIadylGlt~ETVsR~l~ 24 (32) T pfam00325 4 SRQEIADYLGLTRETVSRLLK 24 (32) T ss_pred CHHHHHHHHCCHHHHHHHHHH T ss_conf 588999984725999999999 No 312 >PRK00876 nadE NAD synthetase; Reviewed Probab=31.67 E-value=28 Score=13.30 Aligned_cols=35 Identities=17% Similarity=0.226 Sum_probs=24.9 Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHH Q ss_conf 746889998996678999999999999983296777 Q gi|254780289|r 638 TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673 (682) Q Consensus 638 ~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~~~ 673 (682) ...+.+++++.+|+|.|.|..+-.. +..-||.+|- T Consensus 277 ~~~~~~~~~~~~g~~~e~v~~v~~~-i~~kr~~t~~ 311 (325) T PRK00876 277 HGVPAEVVAAALGLTPEQVERVWRD-IEAKRRTTRY 311 (325) T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH-HHHHHHHCCC T ss_conf 4999999998839899999999999-9987530210 No 313 >PRK03837 transcriptional regulator NanR; Provisional Probab=31.65 E-value=28 Score=13.29 Aligned_cols=51 Identities=20% Similarity=0.335 Sum_probs=25.6 Q ss_pred CHHCCHHHHHHHHHHHHHC-C-CC-CHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCE Q ss_conf 3020289999999978784-8-86-78999752684359988899999999847977 Q gi|254780289|r 23 VFDFSDDSWKKMIKLARQR-G-YV-TIEELNAFLPPDEVSSEQMEDTVAMLSNMGIN 76 (682) Q Consensus 23 ~~d~~~~~ik~LI~~gke~-G-yl-TydeIn~~LP~d~~~~e~ie~i~~~L~~~GI~ 76 (682) +-|.--+.|+..|--|.=+ | -| |-.+|.+-|. ++---+=+.+..|...|+- T Consensus 15 l~e~V~~~lr~~I~~g~l~pG~rLp~E~eLae~lg---VSRtpVREAL~~L~~~GlV 68 (243) T PRK03837 15 LSEEVEERLEQMIRSGEFGPGEQLPSERELMAFFG---VGRPSVREALQALKRKGLV 68 (243) T ss_pred HHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHC---CCHHHHHHHHHHHHHCCCE T ss_conf 99999999999998399999497935999999979---6978999999999988998 No 314 >COG1649 Uncharacterized protein conserved in bacteria [Function unknown] Probab=31.50 E-value=27 Score=13.39 Aligned_cols=23 Identities=13% Similarity=0.241 Sum_probs=15.2 Q ss_pred CCCCCHHHHHHHHHHHHHCCCEE Q ss_conf 43599888999999998479778 Q gi|254780289|r 55 PDEVSSEQMEDTVAMLSNMGINV 77 (682) Q Consensus 55 ~d~~~~e~ie~i~~~L~~~GI~V 77 (682) ...++..++-+++..|..||++= T Consensus 58 ~v~~~~~el~~~ld~l~~ln~NT 80 (418) T COG1649 58 RVLFQRQELKDILDDLQKLNFNT 80 (418) T ss_pred CCCCCHHHHHHHHHHHHHCCCCE T ss_conf 41036999999999999709852 No 315 >COG1318 Predicted transcriptional regulators [Transcription] Probab=31.43 E-value=28 Score=13.27 Aligned_cols=22 Identities=41% Similarity=0.392 Sum_probs=13.0 Q ss_pred CCHHHHHHHCCCCHHHHHHHHH Q ss_conf 9978999870999899999998 Q gi|254780289|r 547 PTPEEIAKKLAMPVEGVRKVLK 568 (682) Q Consensus 547 ~~~~~~a~~~~~~~~~~~~~~~ 568 (682) -|..|||+.+|.+...|++.++ T Consensus 62 ~Ti~EIAeelG~TeqTir~hlk 83 (182) T COG1318 62 MTISEIAEELGRTEQTVRNHLK 83 (182) T ss_pred CCHHHHHHHHCCCHHHHHHHHH T ss_conf 7499999996877999999975 No 316 >pfam00382 TFIIB Transcription factor TFIIB repeat. Probab=31.24 E-value=28 Score=13.25 Aligned_cols=67 Identities=18% Similarity=0.169 Sum_probs=35.7 Q ss_pred HHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHH Q ss_conf 89998709998999999986089875536358899860475623898899899999999999999997329988999999 Q gi|254780289|r 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLR 629 (682) Q Consensus 550 ~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~ 629 (682) ..++..||+|..-...+..+.+.......- ..-+|.-.+.-... +. T Consensus 2 ~r~~~~L~L~~~i~~~A~~i~~~~~~~~~~----------------~Grs~~~iaaA~iY------------------~A 47 (71) T pfam00382 2 KRFADALELPKKVADAANELAKLALDDNLL----------------KGRSPESIAAACLY------------------IA 47 (71) T ss_pred HHHHHHCCCCHHHHHHHHHHHHHHHHCCCC----------------CCCCHHHHHHHHHH------------------HH T ss_conf 688977799889999999999999885874----------------69989999999999------------------99 Q ss_pred HHHCCCCCCCCCHHHHHHHHCCCH Q ss_conf 981879867468899989966789 Q gi|254780289|r 630 MRFGIGMNTDHTLEEVGKQFCVTR 653 (682) Q Consensus 630 ~r~g~~~~~~~tl~e~~~~~~~~~ 653 (682) -| ..+.|+|+.||+..+|||. T Consensus 48 cr---~~~~~rt~~eia~v~~vs~ 68 (71) T pfam00382 48 CR---LEEVKRTLKEISSVAQVSE 68 (71) T ss_pred HH---HCCCCCCHHHHHHHHCCCC T ss_conf 99---8089989999999968987 No 317 >PRK00413 thrS threonyl-tRNA synthetase; Reviewed Probab=31.10 E-value=19 Score=14.52 Aligned_cols=10 Identities=10% Similarity=0.567 Sum_probs=3.9 Q ss_pred CCCCCCCHHH Q ss_conf 6976889788 Q gi|254780289|r 129 GSIELLSREG 138 (682) Q Consensus 129 G~V~LLTREg 138 (682) |+++++|-+. T Consensus 53 ~~leiit~~d 62 (639) T PRK00413 53 ATVEIVTADD 62 (639) T ss_pred CEEEEECCCC T ss_conf 7899946999 No 318 >KOG1495 consensus Probab=30.83 E-value=14 Score=15.61 Aligned_cols=62 Identities=31% Similarity=0.397 Sum_probs=41.9 Q ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHH--HCCCCCCCEE---------EHHHHHHHH Q ss_conf 46899987555789998875223567778875443679999887--4385457312---------010289899 Q gi|254780289|r 443 IAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAE--KFDWCLGYKF---------STYAMWWVK 505 (682) Q Consensus 443 ~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~--~~~~~~g~~f---------~tya~~~i~ 505 (682) ..|+=-+.||-++|+--|-.-..-|-..+||+|- |+-++|++= --.|+..+.| -||+||-+- T Consensus 79 ~~~Dy~~sa~S~lvIiTAGarq~~gesRL~lvQr-NV~ifK~iip~lv~ySpd~~llvvSNPVDilTYv~wKLS 151 (332) T KOG1495 79 ASKDYSVSANSKLVIITAGARQSEGESRLDLVQR-NVDIFKAIIPALVKYSPDCILLVVSNPVDILTYVTWKLS 151 (332) T ss_pred ECCCCCCCCCCCEEEEECCCCCCCCCHHHHHHHH-HHHHHHHHHHHHHHCCCCEEEEEECCCHHHHHHHHHHHC T ss_conf 6676323479868999567778987178999998-899999987888504887089996580378888889871 No 319 >COG4977 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription] Probab=30.82 E-value=29 Score=13.19 Aligned_cols=40 Identities=13% Similarity=0.333 Sum_probs=32.6 Q ss_pred HHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHH Q ss_conf 9999999998776088999789998709998999999986 Q gi|254780289|r 530 HKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI 569 (682) Q Consensus 530 ~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~ 569 (682) -++.++...+.+.++++-+.++||..+|||...+....+. T Consensus 220 ~~l~~~i~~me~nle~plsl~~LA~~~~~S~R~leRlF~~ 259 (328) T COG4977 220 PRLLRAIELMEANLEEPLSLEELADRAGLSRRQLERLFRA 259 (328) T ss_pred HHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHH T ss_conf 7899999999986538868999999968788789999999 No 320 >smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor. Probab=30.65 E-value=29 Score=13.17 Aligned_cols=27 Identities=26% Similarity=0.401 Sum_probs=20.3 Q ss_pred CCCCCHHHHHHHCCCCHHHHHHHHHHH Q ss_conf 889997899987099989999999860 Q gi|254780289|r 544 KREPTPEEIAKKLAMPVEGVRKVLKIT 570 (682) Q Consensus 544 ~~~~~~~~~a~~~~~~~~~~~~~~~~~ 570 (682) .+-|+..+||+.+++|..-|+++++.. T Consensus 18 ~~LPs~~~la~~~~vSr~tvr~A~~~L 44 (60) T smart00345 18 DKLPSERELAAQLGVSRTTVREALSRL 44 (60) T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHH T ss_conf 988109999999894999999999999 No 321 >KOG4021 consensus Probab=30.61 E-value=24 Score=13.78 Aligned_cols=13 Identities=15% Similarity=0.524 Sum_probs=7.3 Q ss_pred CCCEEEHHHHHHH Q ss_conf 5731201028989 Q gi|254780289|r 492 LGYKFSTYAMWWV 504 (682) Q Consensus 492 ~g~~f~tya~~~i 504 (682) |.|-||+|---|- T Consensus 176 R~~Dys~~yg~~t 188 (239) T KOG4021 176 RNFDYSQWYGSWT 188 (239) T ss_pred CCCCHHHHCCCCC T ss_conf 4475677515122 No 322 >smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins. Probab=30.35 E-value=29 Score=13.14 Aligned_cols=23 Identities=30% Similarity=0.452 Sum_probs=12.7 Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH Q ss_conf 68899989966789999999999 Q gi|254780289|r 640 HTLEEVGKQFCVTRERIRQIEAK 662 (682) Q Consensus 640 ~tl~e~~~~~~~~~er~rqi~~~ 662 (682) .|..++|+..|+|.-.|.++|.- T Consensus 11 lsq~~lA~~~gis~~~is~~E~g 33 (56) T smart00530 11 LTQEELAEKLGVSRSTLSRIENG 33 (56) T ss_pred CCHHHHHHHHCCCHHHHHHHHCC T ss_conf 99999999989599999999979 No 323 >TIGR03337 phnR transcriptional regulator protein. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Salmonella, Vibrio Aeromonas hydrophila, Hahella chejuensis and Psychromonas ingrahamii. Probab=30.29 E-value=29 Score=13.13 Aligned_cols=45 Identities=13% Similarity=0.135 Sum_probs=25.6 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC Q ss_conf 222112688999999876533211246899987555789998875223567 Q gi|254780289|r 418 VETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGL 468 (682) Q Consensus 418 ~~~gl~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~ 468 (682) -..|-.+.--.++.++..-...-+++|=+.|+...|-- +..++|. T Consensus 19 ~~~G~~LPsE~eLa~~~~VSR~TvR~Al~~L~~eGli~------r~~G~GT 63 (231) T TIGR03337 19 LLPGDKLPSERDLGERFNTTRVTIREALQQLEAEGLIY------REDRRGW 63 (231) T ss_pred CCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE------EECCCEE T ss_conf 99959785899999997979999999999999879969------9668667 No 324 >PRK13890 conjugal transfer protein TrbA; Provisional Probab=30.23 E-value=29 Score=13.12 Aligned_cols=29 Identities=14% Similarity=0.248 Sum_probs=17.7 Q ss_pred CCCCHHHHHHHCCCCHHHHHHHHHHHCCC Q ss_conf 89997899987099989999999860898 Q gi|254780289|r 545 REPTPEEIAKKLAMPVEGVRKVLKITKEP 573 (682) Q Consensus 545 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~ 573 (682) |.-|..|+|+..|+|+.-+..+-+-...| T Consensus 17 rGmT~~eLAe~AGIS~s~LSqIE~Gk~NP 45 (119) T PRK13890 17 RHMTKKELSDRSGVSISFLSDLTTGKANP 45 (119) T ss_pred CCCCHHHHHHHHCCCHHHHHHHHCCCCCC T ss_conf 59979999988298899999997799898 No 325 >cd02986 DLP Dim1 family, Dim1-like protein (DLP) subfamily; DLP is a novel protein which shares 38% sequence identity to Dim1. Like Dim1, it is also implicated in pre-mRNA splicing and cell cycle progression. DLP is located in the nucleus and has been shown to interact with the U5 small nuclear ribonucleoprotein particle (snRNP)-specific 102kD protein (or Prp6). Dim1 protein, also known as U5 snRNP-specific 15kD protein is a component of U5 snRNP, which pre-assembles with U4/U6 snRNPs to form a [U4/U6:U5] tri-snRNP complex required for pre-mRNA splicing. Dim1 adopts a thioredoxin fold but does not contain the redox active CXXC motif. Probab=30.01 E-value=28 Score=13.23 Aligned_cols=18 Identities=17% Similarity=0.143 Sum_probs=15.5 Q ss_pred CCCCCCCCCHHHHHHHHH Q ss_conf 034577772899999985 Q gi|254780289|r 111 DSADRSTDDPVRMYLREM 128 (682) Q Consensus 111 ~~e~~rtdDPVRMYLREM 128 (682) -.-+||..||+.|.|-|+ T Consensus 18 ViRFGr~~d~~Cm~mDei 35 (114) T cd02986 18 VLRFGRDEDAVCLQLDDI 35 (114) T ss_pred EEEECCCCCCHHHHHHHH T ss_conf 998469999349889899 No 326 >TIGR02404 trehalos_R_Bsub trehalose operon repressor; InterPro: IPR012770 This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from Escherichia coli.. Probab=29.96 E-value=30 Score=13.09 Aligned_cols=33 Identities=24% Similarity=0.333 Sum_probs=25.1 Q ss_pred HHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCC Q ss_conf 760889997899987099989999999860898 Q gi|254780289|r 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP 573 (682) Q Consensus 541 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~ 573 (682) +.--.=||-.+|++..+.|.+.||+|+....+. T Consensus 19 k~G~~LPSE~~L~~~Y~~SReTvRKAL~~L~~~ 51 (236) T TIGR02404 19 KEGDLLPSEHELMEQYGASRETVRKALNLLTEA 51 (236) T ss_pred CCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC T ss_conf 887738887899986068745889999999857 No 327 >PRK09973 putative outer membrane lipoprotein; Provisional Probab=29.72 E-value=30 Score=13.06 Aligned_cols=28 Identities=14% Similarity=0.381 Sum_probs=15.3 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 0057788789999999999999999999 Q gi|254780289|r 330 LNQSRIDLLVEQLYDISKRIMHNEGELL 357 (682) Q Consensus 330 l~~k~iE~L~~~l~~~~k~Ir~~Er~L~ 357 (682) -++.++++|...+..+|.+|.+++..+. T Consensus 21 sn~~kv~qLsSdVqtLN~KVdqLs~Dv~ 48 (85) T PRK09973 21 VNEQKVNQLASNVQTLNAKIARLEQDMK 48 (85) T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 5558899998889999999999998899 No 328 >PRK12824 acetoacetyl-CoA reductase; Provisional Probab=29.61 E-value=30 Score=13.05 Aligned_cols=99 Identities=20% Similarity=0.153 Sum_probs=61.1 Q ss_pred HHHHHHHHHHHH---HHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCC Q ss_conf 124689998755---57899988752235677788754436799998874385457312010289899999999972287 Q gi|254780289|r 441 ASIAKKEMVEAN---LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517 (682) Q Consensus 441 ~~~AK~~l~~an---lr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~ 517 (682) ++.+-..|.+.+ .-.+.|++-.....|..------.|-+||.|..-+-=..+|.+.-+.+--||.-.+.... T Consensus 119 ~~~~~~~m~~~~~G~IVnisS~~~~~~~~~~~~Y~asKaal~~ltk~lA~E~a~~gIrvN~I~PG~i~T~~~~~~----- 193 (245) T PRK12824 119 TQPLFPAMCEQGYGRIINISSVNGLKGQFGQTNYSAAKAGMIGFTKALASEGARYGITVNCIAPGYIATPMVEQA----- 193 (245) T ss_pred HHHHHHHHHHCCCCEEEEECCHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCEEEEEEEECCCCCCCCHHC----- T ss_conf 999999999839955999746775778899689999999999999999999725491999997446878210005----- Q ss_pred EEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHC Q ss_conf 046142058898999999999877608899978999870 Q gi|254780289|r 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556 (682) Q Consensus 518 ~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~ 556 (682) +-...+. ... ..-+||-.+|+|+|... T Consensus 194 ----~~e~~~~------~~~--~~Pl~R~g~peevA~~v 220 (245) T PRK12824 194 ----GPEVLQS------IKN--QIPMKRLGTPEEIAAAV 220 (245) T ss_pred ----CHHHHHH------HHH--CCCCCCCCCHHHHHHHH T ss_conf ----9999999------985--69988987899999999 No 329 >pfam02969 TAF TATA box binding protein associated factor (TAF). TAF proteins adopt a histone-like fold. Probab=29.57 E-value=30 Score=13.04 Aligned_cols=46 Identities=22% Similarity=0.386 Sum_probs=22.9 Q ss_pred HHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHH Q ss_conf 9999981879867468899989966789999999999999832967778 Q gi|254780289|r 626 RVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674 (682) Q Consensus 626 ~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~~~~~~ 674 (682) +++.--.||+.-.+-....++.. ..-|||||=..|++=+||..|.+ T Consensus 10 k~iAeS~Gi~~l~de~a~~La~d---veyRl~eiiqeA~KFMrhskR~~ 55 (66) T pfam02969 10 KVIAESLGITNLSDEAAALLAED---VEYRLKEIVQDAAKFMRHSKRQK 55 (66) T ss_pred HHHHHHCCCCCCCHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHCCCC T ss_conf 99999949888999999998999---99999999999999999867577 No 330 >KOG0697 consensus Probab=29.57 E-value=30 Score=13.04 Aligned_cols=35 Identities=17% Similarity=0.354 Sum_probs=27.5 Q ss_pred CHHHHHH--------HHHHHHHCCCCCHHHHHHHCCCCCCCHH Q ss_conf 2899999--------9997878488678999752684359988 Q gi|254780289|r 27 SDDSWKK--------MIKLARQRGYVTIEELNAFLPPDEVSSE 61 (682) Q Consensus 27 ~~~~ik~--------LI~~gke~GylTydeIn~~LP~d~~~~e 61 (682) +++.++. .++.|-..|||.+||+-..|++..-.+| T Consensus 81 sse~F~~~~k~gsv~~~~~GIrtGFL~iDE~mr~~~~~~~~~d 123 (379) T KOG0697 81 SSEEFRGMTKNGSVENVEKGIRTGFLSIDEIMRTLSDISKGSD 123 (379) T ss_pred HHHHHHHHCCCCCHHHHHHHHHHCCEEHHHHHHHHHHHHCCCC T ss_conf 3587763124785889986676340018888765155421344 No 331 >pfam05635 Ribosomal_S23p S23 ribosomal protein. This family consists of bacterial 23S rRNA proteins. Probab=29.56 E-value=30 Score=13.04 Aligned_cols=13 Identities=23% Similarity=0.457 Sum_probs=4.6 Q ss_pred HHHHHHHHHHHHH Q ss_conf 1268899999987 Q gi|254780289|r 422 ISISEFRHIVSMV 434 (682) Q Consensus 422 l~i~ElK~i~r~I 434 (682) ++..++..+...+ T Consensus 88 i~~~~~~~l~~~~ 100 (110) T pfam05635 88 ISEEEYEELLEEL 100 (110) T ss_pred CCHHHHHHHHHHH T ss_conf 9999999999999 No 332 >TIGR01942 pcnB poly(A) polymerase; InterPro: IPR010206 This entry describes the pcnB family of poly(A) polymerases (also known as plasmid copy number protein). These enzymes sequentially add adenosine nucleotides to the 3' end of RNAs, targeting them for degradation by the cell , . This was originally described for anti-sense RNAs, but was later demonstrated for mRNAs as well . Members of this family are as yet limited to the gamma- and beta-proteobacteria, with putative members in the Chlamydiacae and spirochetes. This family has homology to tRNA nucleotidyltransferase.; GO: 0003723 RNA binding, 0004652 polynucleotide adenylyltransferase activity, 0006378 mRNA polyadenylation. Probab=29.53 E-value=18 Score=14.70 Aligned_cols=12 Identities=33% Similarity=0.883 Sum_probs=7.2 Q ss_pred CCEEEHHHHHHH Q ss_conf 731201028989 Q gi|254780289|r 493 GYKFSTYAMWWV 504 (682) Q Consensus 493 g~~f~tya~~~i 504 (682) |-.-.+||.||- T Consensus 392 g~~~~~~~~W~~ 403 (448) T TIGR01942 392 GKEEAKLAEWWT 403 (448) T ss_pred CCCCHHHHHHHH T ss_conf 430012544456 No 333 >PRK04406 hypothetical protein; Provisional Probab=29.44 E-value=30 Score=13.03 Aligned_cols=52 Identities=15% Similarity=0.190 Sum_probs=42.5 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC Q ss_conf 9999999999999862100577887899999999999999999999999712 Q gi|254780289|r 313 KCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG 364 (682) Q Consensus 313 k~~kl~~eL~e~~~~lkl~~k~iE~L~~~l~~~~k~Ir~~Er~L~rl~~k~~ 364 (682) ....+...|.++-+.+-|--..|+.|.+.+......|..+...+.-++.+.+ T Consensus 5 ~~~~Le~Ri~eLE~rlAFQE~tIeeLN~~v~~qq~~i~~lq~qlr~L~~klk 56 (75) T PRK04406 5 TIEQLEERINDLECQLAFQEQTIEELNDALSQQQLLITKMQDQMKYVVGKVK 56 (75) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 8999999999999999978999999999999999999999999999999998 No 334 >PRK13209 L-xylulose 5-phosphate 3-epimerase; Reviewed Probab=29.07 E-value=31 Score=12.98 Aligned_cols=48 Identities=25% Similarity=0.455 Sum_probs=20.6 Q ss_pred HHHHHHHHHHHCCC----CCHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCEE Q ss_conf 99999997878488----6789997526843599888999999998479778 Q gi|254780289|r 30 SWKKMIKLARQRGY----VTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV 77 (682) Q Consensus 30 ~ik~LI~~gke~Gy----lTydeIn~~LP~d~~~~e~ie~i~~~L~~~GI~V 77 (682) .+++-+.++|+=|| ++.||=.+.++.=..+.+++..|...+.+.||.| T Consensus 22 sw~e~~~~ak~~Gfd~iElsiDe~d~~~~rL~w~~~~~~~ir~~~~~~gi~i 73 (283) T PRK13209 22 CWLEKLRIAKTAGFDFVEMSVDETDERLARLDWSREQRLALVNALVETGFRV 73 (283) T ss_pred CHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCC T ss_conf 9999999999859987998426853100358999999999999999819986 No 335 >PRK05557 fabG 3-ketoacyl-(acyl-carrier-protein) reductase; Validated Probab=28.81 E-value=31 Score=12.95 Aligned_cols=97 Identities=20% Similarity=0.237 Sum_probs=58.7 Q ss_pred HHHHHHHHHHHH---HHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCC Q ss_conf 124689998755---57899988752235677788754436799998874385457312010289899999999972287 Q gi|254780289|r 441 ASIAKKEMVEAN---LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSC 517 (682) Q Consensus 441 ~~~AK~~l~~an---lr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~ 517 (682) ++.+-..|.+.+ .-.+-|++-.+...+...-----.|-.||+|+.-+.=-.+|.|..+-+-=||.-.+++.+ T Consensus 122 ~~~~~p~m~~~~~G~IVnisS~~~~~~~~~~~~Y~asKaal~~lt~~lA~e~~~~gIrvN~V~PG~i~T~~~~~~----- 196 (248) T PRK05557 122 TKAVARPMMKQRSGRIINISSVVGLMGNPGQANYAASKAGVIGFTKSLARELASRGITVNAVAPGFIETDMTDAL----- 196 (248) T ss_pred HHHHHHHHHHCCCCEEEEECCHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCEEEEEEEECCCCCCCCCCC----- T ss_conf 999999999706971899804665678999555699999999999999998533194999997488877542117----- Q ss_pred EEECCCHHHHHHHHHHHHHHHH--HHHCCCCCCHHHHHHHC Q ss_conf 0461420588989999999998--77608899978999870 Q gi|254780289|r 518 TIRIPVHMRDKIHKVVRTARRM--SNKIKREPTPEEIAKKL 556 (682) Q Consensus 518 ~~r~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~a~~~ 556 (682) +-. ....+ ..-++|-.+|+|+|... T Consensus 197 ----~~~----------~~~~~~~~~pl~R~~~p~dva~~v 223 (248) T PRK05557 197 ----PED----------VKEAILAQIPLGRLGQPEEIASAV 223 (248) T ss_pred ----CHH----------HHHHHHHCCCCCCCCCHHHHHHHH T ss_conf ----999----------999998579999980999999999 No 336 >pfam01710 Transposase_14 Transposase. Transposase proteins are necessary for efficient DNA transposition. This family includes insertion sequences from Synechocystis PCC 6803 three of which are characterized as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily. Probab=28.73 E-value=31 Score=12.94 Aligned_cols=23 Identities=17% Similarity=0.147 Sum_probs=16.6 Q ss_pred CCCHHHHHHHCCCCHHHHHHHHH Q ss_conf 99978999870999899999998 Q gi|254780289|r 546 EPTPEEIAKKLAMPVEGVRKVLK 568 (682) Q Consensus 546 ~~~~~~~a~~~~~~~~~~~~~~~ 568 (682) ..+..+.|..++++..-|..-++ T Consensus 18 G~S~~eaA~~F~Is~~Tv~rWlk 40 (120) T pfam01710 18 GGSITEASKVFQIGRATIYRWLK 40 (120) T ss_pred CCCHHHHHHHHCCCHHHHHHHHH T ss_conf 99999999993702999999985 No 337 >pfam04100 Vps53_N Vps53-like, N-terminal. Vps53 complexes with Vps52 and Vps54 to form a multi- subunit complex involved in regulating membrane trafficking events. Probab=28.30 E-value=31 Score=12.88 Aligned_cols=28 Identities=14% Similarity=0.421 Sum_probs=17.4 Q ss_pred CHHHHHHHCCCCCCCHHHHHHHHHHHHHC Q ss_conf 78999752684359988899999999847 Q gi|254780289|r 45 TIEELNAFLPPDEVSSEQMEDTVAMLSNM 73 (682) Q Consensus 45 TydeIn~~LP~d~~~~e~ie~i~~~L~~~ 73 (682) .-+-||..||++. +...|++++..++.- T Consensus 6 pv~~iN~lFp~e~-SL~~id~~i~~l~~~ 33 (375) T pfam04100 6 ALEYINQLFPTEQ-SLTNIDSLIQKIQEE 33 (375) T ss_pred HHHHHHHHCCCHH-HHHHHHHHHHHHHHH T ss_conf 8999988599968-886179999999999 No 338 >smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation. Probab=28.26 E-value=31 Score=12.88 Aligned_cols=31 Identities=16% Similarity=0.190 Sum_probs=25.5 Q ss_pred HHHCCCCCCHHHHHHHCCCCHHHHHHHHHHH Q ss_conf 7760889997899987099989999999860 Q gi|254780289|r 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKIT 570 (682) Q Consensus 540 ~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~ 570 (682) ....+++.+..|||+.+|+|...+..++... T Consensus 14 l~~~~~~~sl~eia~~~~l~ksT~~RlL~tL 44 (91) T smart00346 14 LAEEPGGLTLAELAERLGLSKSTAHRLLNTL 44 (91) T ss_pred HHHCCCCCCHHHHHHHHCCCHHHHHHHHHHH T ss_conf 9728999899999999890999999999999 No 339 >PRK09391 fixK transcriptional regulator FixK; Provisional Probab=28.18 E-value=32 Score=12.87 Aligned_cols=18 Identities=11% Similarity=0.209 Sum_probs=9.6 Q ss_pred CCCHHHHHHHHCCCHHHH Q ss_conf 468899989966789999 Q gi|254780289|r 639 DHTLEEVGKQFCVTRERI 656 (682) Q Consensus 639 ~~tl~e~~~~~~~~~er~ 656 (682) |.|=+++|...|+|||.| T Consensus 173 ~lT~~dLA~~lG~trETV 190 (224) T PRK09391 173 PMSRRDIADYLGLTIETV 190 (224) T ss_pred CCCHHHHHHHHCCCHHHH T ss_conf 579999998879979999 No 340 >PRK10219 DNA-binding transcriptional regulator SoxS; Provisional Probab=28.10 E-value=32 Score=12.86 Aligned_cols=37 Identities=11% Similarity=0.116 Sum_probs=27.9 Q ss_pred HHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHH Q ss_conf 9999998776088999789998709998999999986 Q gi|254780289|r 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI 569 (682) Q Consensus 533 ~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~ 569 (682) .++...+.+.+..+.|.++||+.+|+|......+.+. T Consensus 8 ~~~~~yI~~h~~~~i~l~~lA~~~~~S~~~l~r~Fk~ 44 (107) T PRK10219 8 QTLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRT 44 (107) T ss_pred HHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH T ss_conf 9999999986699999999998989399999999999 No 341 >pfam02261 Asp_decarbox Aspartate decarboxylase. Decarboxylation of aspartate is the major route of beta-alanine production in bacteria, and is catalysed by the enzyme aspartate decarboxylase EC:4.1.1.11 which requires a pyruvoyl group for its activity. It is synthesized initially as a proenzyme which is then proteolytically cleaved to an alpha (C-terminal) and beta (N-terminal) subunit and a pyruvoyl group. This family contains both chains of aspartate decarboxylase. Probab=28.07 E-value=6.4 Score=18.36 Aligned_cols=35 Identities=20% Similarity=0.219 Sum_probs=21.6 Q ss_pred HHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHH Q ss_conf 87544367999988743854573120102898999 Q gi|254780289|r 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506 (682) Q Consensus 472 ~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~ 506 (682) ||+...+|---.-|+=++..-|-||+|||.+--+. T Consensus 31 ~Lm~aagi~~~E~V~V~Nv~NG~R~~TYvI~g~~g 65 (116) T pfam02261 31 DLLDAAGILEYEKVQIVNVNNGERFETYVIPGERG 65 (116) T ss_pred HHHHHCCCCCCCEEEEEECCCCCEEEEEEEECCCC T ss_conf 99987599989889999898996899998864799 No 342 >PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional Probab=28.00 E-value=32 Score=12.85 Aligned_cols=37 Identities=19% Similarity=0.261 Sum_probs=22.7 Q ss_pred HHHHCCCCC------CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC Q ss_conf 998187986------74688999899667899999999999998329 Q gi|254780289|r 629 RMRFGIGMN------TDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669 (682) Q Consensus 629 ~~r~g~~~~------~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~~ 669 (682) .-+||-.+. -|.|-+++|...|+|||.|- +.|++|+. T Consensus 168 ~~~~g~~~~~~~~i~l~lt~~dLA~~lG~trEtVs----R~L~~L~~ 210 (235) T PRK11161 168 SRRFAQRGFSPREFRLTMTRGDIGNYLGLTVETIS----RLLGRFQK 210 (235) T ss_pred HHHHCCCCCCCCEEEECCCHHHHHHHHCCCHHHHH----HHHHHHHH T ss_conf 99838778888779823789999988789899999----99999997 No 343 >cd01667 TGS_ThrRS_N TGS _ThrRS_N: ThrRS (threonyl-tRNA Synthetase) is a class II tRNA synthetase that couples threonine to its cognate tRNA. In addition to its catalytic and anticodon-binding domains, ThrRS has an N-terminal TGS domain, named after the ThrRS, GTPase, and SpoT proteins where it occurs. The TGS domain is thought to interact with the tRNA acceptor arm along with an adjacent N-terminal domain. The specific function of TGS is not well understood. Probab=27.90 E-value=9.3 Score=17.06 Aligned_cols=47 Identities=19% Similarity=0.289 Sum_probs=36.5 Q ss_pred CCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEE Q ss_conf 08899978999870999899999998608987553635889986047 Q gi|254780289|r 543 IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589 (682) Q Consensus 543 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~ 589 (682) +....|+.++|+.++-+..+-.-+.+++.+.+-|..|+.+|..-.+. T Consensus 13 ~~~~~T~~eiA~~i~~~l~k~~vaa~vng~l~DL~~~i~~d~~v~~i 59 (61) T cd01667 13 FPKGTTPLDIAKSISPGLAKKAVAAKVNGELVDLSRPLEEDCELEII 59 (61) T ss_pred CCCCCCHHHHHHHHCHHHHCCEEEEEECCEEECCCCCCCCCCEEEEE T ss_conf 78998999999985966341379999999998357412699999998 No 344 >pfam09413 DUF2007 Protein of unknown function (DUF2007). This is a family of proteins with unknown function. Probab=27.90 E-value=25 Score=13.64 Aligned_cols=11 Identities=36% Similarity=0.579 Sum_probs=4.0 Q ss_pred HHHHHHCCCEE Q ss_conf 99998479778 Q gi|254780289|r 67 VAMLSNMGINV 77 (682) Q Consensus 67 ~~~L~~~GI~V 77 (682) -+.|.+.||.. T Consensus 16 ~aLL~~agI~~ 26 (68) T pfam09413 16 QALLKGAGIEA 26 (68) T ss_pred HHHHHHCCCCE T ss_conf 99971279977 No 345 >COG3711 BglG Transcriptional antiterminator [Transcription] Probab=27.77 E-value=32 Score=12.82 Aligned_cols=54 Identities=17% Similarity=0.175 Sum_probs=40.2 Q ss_pred HHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCH-HHHHHHHHHHHHCCCEEECCCC Q ss_conf 99999999787848867899975268435998-8899999999847977832784 Q gi|254780289|r 29 DSWKKMIKLARQRGYVTIEELNAFLPPDEVSS-EQMEDTVAMLSNMGINVVDGDD 82 (682) Q Consensus 29 ~~ik~LI~~gke~GylTydeIn~~LP~d~~~~-e~ie~i~~~L~~~GI~Vve~~~ 82 (682) ..-.-|..+--+++++|-.++.+.|.=.--+. -.|..|-..|.+-|+.++.... T Consensus 5 ~~~~~l~~l~~~~~~~~~~~la~~l~vS~Rti~~~i~~In~~l~~~~~~~~~~~~ 59 (491) T COG3711 5 RREQLLLLLLLKNPLLTIKELAEQLGVSRRTIRYDIKKINESLEEGGIPIIKRKG 59 (491) T ss_pred HHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCEEEECCC T ss_conf 7899999987346886999999996976744988899999888618850244378 No 346 >PRK05629 hypothetical protein; Validated Probab=27.62 E-value=32 Score=12.80 Aligned_cols=43 Identities=28% Similarity=0.283 Sum_probs=28.2 Q ss_pred HHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHC Q ss_conf 98999999999877608899978999870999899999998608 Q gi|254780289|r 528 KIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK 571 (682) Q Consensus 528 ~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~ 571 (682) .+....|.-.++.+..|+ .+..+||..||+++=.|+.++.-++ T Consensus 244 ~L~~~~r~l~~~~~~~~~-~~~~~iA~~Lgv~P~~vkk~~~qar 286 (331) T PRK05629 244 ALSMKVGQIARLYSTRGR-INGFELAKELGMPPFVVEKTAKVAR 286 (331) T ss_pred HHHHHHHHHHHHHHHHCC-CCHHHHHHHHCCCHHHHHHHHHHHH T ss_conf 999999999999975169-9989999883999899999999982 No 347 >KOG2822 consensus Probab=27.52 E-value=12 Score=16.16 Aligned_cols=28 Identities=18% Similarity=0.323 Sum_probs=19.4 Q ss_pred HHHHHHHCCCCCCHHHHHHHHHHHHHHHH Q ss_conf 99887522356777887544367999988 Q gi|254780289|r 457 ISVAKKYTNRGLQFLDLIQEGNIGLMKAA 485 (682) Q Consensus 457 ~~~~~~~~~~~~~~~~~~~~~~~~l~~a~ 485 (682) +..-+=|++. ..++|++.-+-+|.+-++ T Consensus 203 v~lgRiY~GM-HgvlDi~sG~ligvl~~~ 230 (407) T KOG2822 203 VCLGRIYCGM-HGVLDIVSGLLIGVLILI 230 (407) T ss_pred HHHHHHHHCC-HHHHHHHHHHHHHHHHHH T ss_conf 9987787041-488898740698887855 No 348 >pfam02082 Rrf2 Transcriptional regulator. This family is related to pfam001022 and other transcription regulation families (personal obs: Yeats C). Probab=27.49 E-value=32 Score=12.78 Aligned_cols=46 Identities=22% Similarity=0.218 Sum_probs=32.6 Q ss_pred CCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEE Q ss_conf 8899978999870999899999998608987553635889986047 Q gi|254780289|r 544 KREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589 (682) Q Consensus 544 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~ 589 (682) +..-+..+||+.+++|..-++++++..+..--+.+--|-.|+..|. T Consensus 22 ~~~~s~~~iA~~~~i~~~~l~kil~~L~~~gli~s~rG~~GGy~L~ 67 (82) T pfam02082 22 EGPVTSEEIAERQNISPVYLRKILAKLRKAGLVKSVRGPGGGYRLA 67 (82) T ss_pred CCEECHHHHHHHHCCCHHHHHHHHHHHHCCCCEEECCCCCCCCCCC T ss_conf 9849599999878909999999999810279825658999881134 No 349 >TIGR03324 alt_F1F0_F1_al alternate F1F0 ATPase, F1 subunit alpha. A small number of taxonomically diverse prokaryotic species, including Methanosarcina barkeri, have what appears to be a second ATP synthase, in addition to the normal F1F0 ATPase in bacteria and A1A0 ATPase in archaea. These enzymes use ion gradients to synthesize ATP, and in principle may run in either direction. This model represents the F1 alpha subunit of this apparent second ATP synthase. Probab=27.25 E-value=33 Score=12.75 Aligned_cols=50 Identities=22% Similarity=0.349 Sum_probs=30.5 Q ss_pred HHHHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHH Q ss_conf 02898999999999722870461420588989999999998776088999789 Q gi|254780289|r 499 YAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEE 551 (682) Q Consensus 499 ya~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 551 (682) |-++|.-.+|-.++.||.+-+=+ +.+.+.|+-.+.|++.-.+||+|+-+- T Consensus 236 ~~Apyaa~aiAEyFrd~G~dVLl---v~DdLTr~A~A~REisLll~rpPgrea 285 (497) T TIGR03324 236 YIAPYAATSIGEHFMEQGRDVLI---VYDDLTQHARAYRELSLLLRRPPGREA 285 (497) T ss_pred HHHHHHHHHHHHHHHHCCCEEEE---EEECHHHHHHHHHHHHHHCCCCCCCCC T ss_conf 88789999999999968974899---997806999999999986489998778 No 350 >cd00907 Bacterioferritin Bacterioferritin, ferritin-like diiron-binding domain. Bacterioferritins, also known as cytochrome b1, are members of a broad superfamily of ferritin-like diiron-carboxylate proteins. Similar to ferritin in architecture, Bfr forms an oligomer of 24 subunits that assembles to form a hollow sphere with 432 symmetry. Up to 12 heme cofactor groups (iron protoporphyrin IX or coproporphyrin III) are bound between dimer pairs. The role of the heme is unknown, although it may be involved in mediating iron-core reduction and iron release. Each subunit is composed of a four-helix bundle which carries a diiron ferroxidase center; it is here that initial oxidation of ferrous iron by molecular oxygen occurs, facilitating the detoxification of iron, protection against dioxygen and radical products, and storage of ferric-hydroxyphosphate at the core. Some bacterioferritins are composed of two subunit types, one conferring heme-binding ability (alpha) and the other (beta) best Probab=27.23 E-value=33 Score=12.75 Aligned_cols=14 Identities=14% Similarity=0.157 Sum_probs=5.1 Q ss_pred HHHHHHHHHHHCCC Q ss_conf 99999999971253 Q gi|254780289|r 353 EGELLRLAQSYGIK 366 (682) Q Consensus 353 Er~L~rl~~k~~i~ 366 (682) +.-+.|+..-.|.| T Consensus 55 ~~l~~rIl~LgG~P 68 (153) T cd00907 55 DKLIERILFLEGLP 68 (153) T ss_pred HHHHHHHHHCCCCC T ss_conf 99999999839998 No 351 >pfam02271 UCR_14kD Ubiquinol-cytochrome C reductase complex 14kD subunit. The ubiquinol-cytochrome C reductase complex (cytochrome bc1 complex) is a respiratory multienzyme complex. This Pfam family represents the 14kD (or VI) subunit of the complex which is not directly involved in electron transfer, but has a role in assembly of the complex. Probab=27.08 E-value=33 Score=12.73 Aligned_cols=45 Identities=20% Similarity=0.330 Sum_probs=31.9 Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCC Q ss_conf 8999875557899988752235677788754436799998874385 Q gi|254780289|r 445 KKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDW 490 (682) Q Consensus 445 K~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~ 490 (682) ...++..-=+|-++. -.|...||-+.||+-|-|--.-+|+.|--. T Consensus 7 l~~~~~p~a~w~~na-sgyrk~GL~~DDll~ee~~~v~eAL~RLP~ 51 (105) T pfam02271 7 LSKLLKPLAKWYFNA-AGYRQLGLRYDDLIPEENPDVQEALRRLPR 51 (105) T ss_pred HHHHHHHHHHHHHHH-HCHHHCCCCHHHCCCCCCHHHHHHHHHCCH T ss_conf 999999999999998-452221663864568799899999986899 No 352 >pfam03917 GSH_synth_ATP Eukaryotic glutathione synthase, ATP binding domain. Probab=26.94 E-value=33 Score=12.71 Aligned_cols=128 Identities=17% Similarity=0.255 Sum_probs=72.4 Q ss_pred HHHHCCCCCCCEEEHH---HHHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCH Q ss_conf 8874385457312010---2898999999999722870461420588989999999998776088999789998709998 Q gi|254780289|r 484 AAEKFDWCLGYKFSTY---AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPV 560 (682) Q Consensus 484 a~~~~~~~~g~~f~ty---a~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~ 560 (682) .|.-.=+|-||-.+-| +.|=. |-.-.+++.|++|.- .--.-.+++..|.+-. |.-|. ++.-.. T Consensus 256 eVavVYfRaGY~P~dY~se~~W~a-----Rl~lE~S~AIKcPsi-----~~qLaGtKKVQQ~La~---p~vLe-rFl~~~ 321 (469) T pfam03917 256 EVAVVYFRAGYTPDDYPSESEWEA-----RLLMEQSSAIKCPSI-----STQLAGTKKIQQELAK---PGVLE-RFLENK 321 (469) T ss_pred EEEEEEEECCCCCCCCCCHHHHHH-----HHHHHHCCCCCCCCH-----HHHHHCCHHHHHHHCC---HHHHH-HHCCCH T ss_conf 899999707768133798788999-----999986377148899-----9986242999998668---54998-872999 Q ss_pred HHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHH--------HHHHHHHHHHHHHCCCH---HHHHHHH Q ss_conf 999999986089875536358899860475623898899899999--------99999999999732998---8999999 Q gi|254780289|r 561 EGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAI--------QANLRETTTRVLASLTP---REERVLR 629 (682) Q Consensus 561 ~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~~~--------~~~~~~~~~~~l~~l~~---re~~v~~ 629 (682) +++..+.+....-.|||.. +.++..... ....|+..+. ...-.+.|...|..|++ |.+-||. T Consensus 322 ~~~~~lr~tFa~ly~Ld~~--~~g~~~v~~-----A~~~P~~yVLKPQREGGGNNiyg~dI~~~L~~l~~~ee~~ayILM 394 (469) T pfam03917 322 EDIAKLRKTFAGLWSLDDT--EEGDEIVKL-----AIEKPELFVLKPQREGGGNNIYGDDMREALLKLQKSEERAAYILM 394 (469) T ss_pred HHHHHHHHHHCCCCCCCCC--CCCHHHHHH-----HHHCHHHEEECCCCCCCHHHHHHHHHHHHHHHCCCHHHHHHHEEE T ss_conf 9999999972346306875--121999999-----874945246647676760001107999999856881231101043 Q ss_pred HHH Q ss_conf 981 Q gi|254780289|r 630 MRF 632 (682) Q Consensus 630 ~r~ 632 (682) -|. T Consensus 395 erI 397 (469) T pfam03917 395 ERI 397 (469) T ss_pred ECC T ss_conf 035 No 353 >pfam03444 DUF293 Domain of unknown function. This domain is always found with a pair of CBS domains pfam00571. this region may be distantly related to the HrcA proteins of prokaryotes (Bateman A pers. obs.). Probab=26.92 E-value=33 Score=12.71 Aligned_cols=43 Identities=21% Similarity=0.211 Sum_probs=34.8 Q ss_pred HHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHC Q ss_conf 8999999999877608899978999870999899999998608 Q gi|254780289|r 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITK 571 (682) Q Consensus 529 ~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~ 571 (682) -..+.++--.++.+.|++-.-++||+.++.+...||+.|...+ T Consensus 6 Qr~IL~aLI~lY~~~~~pVks~~IAe~l~~spgTIRN~M~~L~ 48 (79) T pfam03444 6 QKEILQALINLYRKKGRAVKGEEIADIIGRNPGTVRNQMQSLK 48 (79) T ss_pred HHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHH T ss_conf 9999999999999729986679999998789088999999999 No 354 >PRK06200 2,3-dihydroxy-2,3-dihydrophenylpropionate dehydrogenase; Provisional Probab=26.81 E-value=33 Score=12.69 Aligned_cols=94 Identities=13% Similarity=0.173 Sum_probs=48.6 Q ss_pred HHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCCHHHHH-HH Q ss_conf 55789998875223567778875443679999887438545731201028989999999997228704614205889-89 Q gi|254780289|r 452 NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDK-IH 530 (682) Q Consensus 452 nlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~~~~-~~ 530 (682) ..-++.|++-.+...|.+.------|-.||.|+.-. ++..+.|.-+-+-.||.-.+..... . .+.+. .. T Consensus 137 ~iI~~~S~~~~~~~~~~~~Y~asKaal~~ltr~lA~-ela~~IrVN~I~PG~i~T~~~~~~~-------~--~~~~~~~~ 206 (263) T PRK06200 137 SIIFTLSNSSFYPGGGGPLYTASKHAVVGLVRQLAY-ELAPKIRVNGVAPGGTVTDLRGPAS-------L--GQGETSIS 206 (263) T ss_pred EEEEECCHHHCCCCCCCHHHHHHHHHHHHHHHHHHH-HHCCCCEEEEEECCCCCCCCCCCCC-------C--CHHHHHHC T ss_conf 799982202125889856789999999999999999-9779988999962889888644211-------2--14665420 Q ss_pred HHHHHHHHHH--HHCCCCCCHHHHHHH Q ss_conf 9999999987--760889997899987 Q gi|254780289|r 531 KVVRTARRMS--NKIKREPTPEEIAKK 555 (682) Q Consensus 531 ~~~~~~~~~~--~~~~~~~~~~~~a~~ 555 (682) ........+. .-+||-++|+|+|.. T Consensus 207 ~~~~~~~~~~~~~Pl~R~g~p~dia~~ 233 (263) T PRK06200 207 DVPGLADMIAAITPLQFAPQPEDHTGP 233 (263) T ss_pred CCHHHHHHHHHCCCCCCCCCHHHHHHH T ss_conf 468899999717998998399999999 No 355 >PRK02119 hypothetical protein; Provisional Probab=26.74 E-value=33 Score=12.69 Aligned_cols=50 Identities=14% Similarity=0.213 Sum_probs=40.9 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC Q ss_conf 99999999999862100577887899999999999999999999999712 Q gi|254780289|r 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG 364 (682) Q Consensus 315 ~kl~~eL~e~~~~lkl~~k~iE~L~~~l~~~~k~Ir~~Er~L~rl~~k~~ 364 (682) ..+...|.++-.++-|--..|+.|-+.+......|..+...+.-++.+.+ T Consensus 5 ~~Le~Ri~~LE~rlAFQe~tIe~LNq~v~~Qq~~i~~l~~ql~~L~~rlk 54 (73) T PRK02119 5 QMLENRIAELEMKIAFQENLLEELNQALIQQQFVIDKMQVQLRHMANKLK 54 (73) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 99999999999999978989999999999999999999999999999998 No 356 >smart00491 HELICc2 helicase superfamily c-terminal domain. Probab=26.59 E-value=33 Score=12.67 Aligned_cols=48 Identities=19% Similarity=0.049 Sum_probs=23.6 Q ss_pred CCCHHHHHHHHHHHHHHHHHHCCCCCCCEEE--HHHHHHHHHHHHHHHHH Q ss_conf 6777887544367999988743854573120--10289899999999972 Q gi|254780289|r 467 GLQFLDLIQEGNIGLMKAAEKFDWCLGYKFS--TYAMWWVKQAITRSIAD 514 (682) Q Consensus 467 ~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~--tya~~~i~~~i~~~~~~ 514 (682) |+||.-.-..=..--+.-.++.-...|+++. .=|...++|+|-|.|.. T Consensus 77 glP~p~~~d~~~~~r~~y~~~~~~~~~~~~~y~~~a~~~v~QaiGR~IR~ 126 (142) T smart00491 77 GIPFPNPDSPILRARLEYLDEKGGIRPFDEVYLFDAMRALAQAIGRAIRH 126 (142) T ss_pred ECCCCCCCCHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHCCCCCC T ss_conf 08999999999999999999864899833112589999999982967546 No 357 >TIGR02470 sucr_synth sucrose synthase; InterPro: IPR012820 This entry represents sucrose synthase an enzyme that despite its name, generally uses rather produces sucrose. Sucrose plus UDP (or ADP) becomes D-fructose plus UDP-glucose (or ADP-glucose), which is then available for cell wall (or starch) biosynthesis. The enzyme is homologous to sucrose phosphate synthase, which catalyses the penultimate step in sucrose synthesis. Sucrose synthase is found, so far, exclusively in plants and cyanobacteria.; GO: 0016157 sucrose synthase activity. Probab=26.28 E-value=29 Score=13.17 Aligned_cols=62 Identities=19% Similarity=0.345 Sum_probs=44.9 Q ss_pred HCCCEEECCCHHHHH------HH---------HH-HHHHHHHHHHCCCCCCH------------HHHHHHCCCCHHHHHH Q ss_conf 228704614205889------89---------99-99999987760889997------------8999870999899999 Q gi|254780289|r 514 DQSCTIRIPVHMRDK------IH---------KV-VRTARRMSNKIKREPTP------------EEIAKKLAMPVEGVRK 565 (682) Q Consensus 514 ~~~~~~r~~~~~~~~------~~---------~~-~~~~~~~~~~~~~~~~~------------~~~a~~~~~~~~~~~~ 565 (682) +++++.|||...-.- |+ .+ .-+.+++..+++-.|.. -=||.+||++--.|.. T Consensus 343 ~~~~ILRVPFr~~nG~~~~~WISRFeiWPYLE~FA~D~~~e~~~el~g~PDLIIGNYSDGNLVA~LLA~kLgVTQC~IAH 422 (790) T TIGR02470 343 EHAHILRVPFRTENGIILRKWISRFEIWPYLETFAEDAEKEILAELQGKPDLIIGNYSDGNLVASLLARKLGVTQCTIAH 422 (790) T ss_pred CCCEEEECCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEECCCCHHHHHHHHHHHCCCCCCCHHH T ss_conf 85316421664347730036633012472045668999999999846899706732563589999998533622220333 Q ss_pred HHHHHCCCCC Q ss_conf 9986089875 Q gi|254780289|r 566 VLKITKEPIS 575 (682) Q Consensus 566 ~~~~~~~~~s 575 (682) +|.-++.|-| T Consensus 423 ALEKtKY~~S 432 (790) T TIGR02470 423 ALEKTKYPDS 432 (790) T ss_pred HCCCCCCCCC T ss_conf 1334367664 No 358 >COG3355 Predicted transcriptional regulator [Transcription] Probab=26.19 E-value=34 Score=12.61 Aligned_cols=26 Identities=23% Similarity=0.180 Sum_probs=21.8 Q ss_pred CCCCCCHHHHHHHCCCCHHHHHHHHH Q ss_conf 08899978999870999899999998 Q gi|254780289|r 543 IKREPTPEEIAKKLAMPVEGVRKVLK 568 (682) Q Consensus 543 ~~~~~~~~~~a~~~~~~~~~~~~~~~ 568 (682) ...+-|.++||+.|+.+...|.++++ T Consensus 39 ~~~~~tvdelae~lnr~rStv~rsl~ 64 (126) T COG3355 39 ENGPLTVDELAEILNRSRSTVYRSLQ 64 (126) T ss_pred HCCCCCHHHHHHHHCCCHHHHHHHHH T ss_conf 46995799999997831999999999 No 359 >TIGR01572 A_thl_para_3677 Arabidopsis paralogous family TIGR01572; InterPro: IPR006462 These sequences comprise a paralogous family of hypothetical proteins in Arabidopsis thaliana. No homologs are detected from other species. Length heterogeneity within the family is attributable partly to a 21-residue repeat present in from zero to three tandem copies. The proteins have no known function.. Probab=26.17 E-value=8.5 Score=17.35 Aligned_cols=42 Identities=29% Similarity=0.415 Sum_probs=35.7 Q ss_pred HHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHH Q ss_conf 9887522356777887544367999988743854573120102 Q gi|254780289|r 458 SVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500 (682) Q Consensus 458 ~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya 500 (682) ++.|-|..-||..--..+--|+-|| +|+||+.++-+-.|||= T Consensus 46 ~lVk~yA~~GLHrYN~l~G~nl~L~-~v~kFNm~~~~~~s~Yy 87 (290) T TIGR01572 46 DLVKLYALVGLHRYNVLEGTNLELD-AVKKFNMKLMCALSSYY 87 (290) T ss_pred CEEEEEEECCCHHHHHCCCCCCCCC-CHHHHHHHHHHHCCCCE T ss_conf 2153320002200000268752000-02245578764027421 No 360 >TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator; InterPro: IPR014290 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] . FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins , . It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly . The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA . SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA , acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins . Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen . This entry represents proteins belonging to the Rtf2 family of transcriptional regulators and are found, typically, as the first gene of the SUF operon. They are found only in a subset of the genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.. Probab=26.14 E-value=34 Score=12.61 Aligned_cols=52 Identities=19% Similarity=0.207 Sum_probs=31.5 Q ss_pred HHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEE Q ss_conf 9877608899978999870999899999998608987553635889986047 Q gi|254780289|r 538 RMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLG 589 (682) Q Consensus 538 ~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~ 589 (682) .+.+.-...=++.+||+..|+....|+++|+...+.-=.+-.=|=.|+..|. T Consensus 17 ~lA~~~~~~ySAA~lA~~tgL~~pTvsK~Lk~L~~A~lV~S~RGv~GGY~La 68 (130) T TIGR02944 17 VLAQADEQTYSAAELAEQTGLEAPTVSKILKALSEAGLVTSKRGVEGGYTLA 68 (130) T ss_pred HHHCCCCCHHHHHHHHHHCCCCCCHHHHHHHHHHCCCCCCCCCCCCHHHHHH T ss_conf 9852899700688878645988604789988764287532434643004620 No 361 >PRK00901 methylated-DNA--protein-cysteine methyltransferase; Provisional Probab=25.88 E-value=34 Score=12.57 Aligned_cols=75 Identities=16% Similarity=0.213 Sum_probs=54.8 Q ss_pred HHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHH-CCCCCCHHHHHHHCCCCHHHHHHHH-HHHCCCCCCCCCCC Q ss_conf 99999999722870461420588989999999998776-0889997899987099989999999-86089875536358 Q gi|254780289|r 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNK-IKREPTPEEIAKKLAMPVEGVRKVL-KITKEPISLETPIG 581 (682) Q Consensus 505 ~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~sl~~~~~ 581 (682) .+.+..+++......-+|.++..| .+-.++.+.+.+- .|.--|-.+||+.+|-|. -+|.+- .+.+.|+++=-|-+ T Consensus 48 ~~qL~~YF~g~~~~f~lpl~~~GT-~FQ~~VW~~L~~IP~G~t~sY~~lA~~ig~p~-a~RAVG~A~g~Npi~iiIPCH 124 (155) T PRK00901 48 NKQLEEYFRGKRKKFDLPLAPQGT-EFQKKVWKALQEIPYGETRSYGEIAKNIGNPK-ACRAVGLANNKNPIPIFIPCH 124 (155) T ss_pred HHHHHHHHCCCCCCCCCCCCCCCC-HHHHHHHHHHCCCCCCCCEEHHHHHHHHCCCC-CCHHHHHHHHCCCCCCCCCCC T ss_conf 999999985998655521268999-99999999748479976300999999938996-217999998309977536897 No 362 >TIGR01097 3A0109s02M phosphonate ABC transporter, permease protein; InterPro: IPR005769 Bacterial binding protein-dependent transport systems , are multicomponent systems typically composed of a periplasmic substrate-binding protein, one or two reciprocally homologous integral inner-membrane proteins and one or two peripheral membrane ATP-binding proteins that couple energy to the active transport system. The integral inner-membrane proteins translocate the substrate across the membrane. It has been shown , that most of these proteins contain a conserved region located about 80 to 100 residues from their C-terminal extremity. This region seems to be located in a cytoplasmic loop between two transmembrane domains. Apart from the conserved region, the sequence of these proteins is quite divergent, and they have a variable number of transmembrane helices. These proteins represent a family of phosphonate uptake transporters., probably responsible for the transport of phosphonate across the inner membrane. ; GO: 0015604 phosphonate transmembrane transporter activity, 0015716 phosphonate transport, 0005887 integral to plasma membrane. Probab=25.60 E-value=22 Score=14.10 Aligned_cols=12 Identities=33% Similarity=0.639 Sum_probs=8.8 Q ss_pred HHHHHHHHHHHH Q ss_conf 898999999999 Q gi|254780289|r 501 MWWVKQAITRSI 512 (682) Q Consensus 501 ~~~i~~~i~~~~ 512 (682) .|||||-++|-. T Consensus 37 n~W~~~~VRRLM 48 (192) T TIGR01097 37 NPWVRQIVRRLM 48 (192) T ss_pred CCCCCHHHHHHH T ss_conf 842104789999 No 363 >PTZ00183 centrin; Provisional Probab=25.60 E-value=35 Score=12.54 Aligned_cols=54 Identities=15% Similarity=0.270 Sum_probs=30.2 Q ss_pred CCCHHCCHHHHHHHHHHHH-----HCCCCCHHHHHHHCCCCC--CCHHHHHHHHHHHHHCC Q ss_conf 4430202899999999787-----848867899975268435--99888999999998479 Q gi|254780289|r 21 SLVFDFSDDSWKKMIKLAR-----QRGYVTIEELNAFLPPDE--VSSEQMEDTVAMLSNMG 74 (682) Q Consensus 21 ~~~~d~~~~~ik~LI~~gk-----e~GylTydeIn~~LP~d~--~~~e~ie~i~~~L~~~G 74 (682) ...-+.+.+.+++|-+.-+ ..|+|+..|+-.+|..-. .+.+.+..++..+...| T Consensus 16 ~~~~~ls~eq~~elke~F~~~D~d~dG~Is~~El~~~L~~lG~~~t~~el~~i~~~~D~d~ 76 (168) T PTZ00183 16 SIRPELNEEQKLEIREAFDLFDTDGTGYIDVKELKVAMRALGFEPKKEEIKRMIADVDKDG 76 (168) T ss_pred HHCCCCCHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCC T ss_conf 2002699999999999999986998696979999999999089999999999998628789 No 364 >cd04781 HTH_MerR-like_sg6 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 6) with at least two conserved cysteines present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, an Probab=25.50 E-value=33 Score=12.66 Aligned_cols=23 Identities=17% Similarity=0.251 Sum_probs=14.6 Q ss_pred CHHHHHHHCCCCHHHHHHHHHHH Q ss_conf 97899987099989999999860 Q gi|254780289|r 548 TPEEIAKKLAMPVEGVRKVLKIT 570 (682) Q Consensus 548 ~~~~~a~~~~~~~~~~~~~~~~~ 570 (682) |+.|+|+.+|+|+..++.--++. T Consensus 2 tIgelA~~~gvs~~TiRyYE~~G 24 (120) T cd04781 2 DIAEVARQSGLPASTLRYYEEKG 24 (120) T ss_pred CHHHHHHHHCCCHHHHHHHHHCC T ss_conf 68999999886889898999649 No 365 >pfam08726 efhand_Ca_insen Ca2+ insensitive EF hand. EF hands are helix-loop-helix binding motifs involved in the regulation of many cellular processes. EF hands usually bind to Ca2+ ions which causes a major conformational change that allows the protein to interact with its designated targets. This domain corresponds to an EF hand which has partially or entirely lost its calcium-binding properties. The calcium insensitive EF hand is still able to mediate protein-protein recognition. Probab=25.47 E-value=35 Score=12.52 Aligned_cols=27 Identities=33% Similarity=0.645 Sum_probs=21.0 Q ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHCCCCC Q ss_conf 899999999787848867899975268435 Q gi|254780289|r 28 DDSWKKMIKLARQRGYVTIEELNAFLPPDE 57 (682) Q Consensus 28 ~~~ik~LI~~gke~GylTydeIn~~LP~d~ 57 (682) .+.+|.| +..+.|||-.||..+||++. T Consensus 9 ~~sFr~l---A~~KpYVT~~dLr~~L~pdq 35 (69) T pfam08726 9 EQSFRAL---AEGKPYVTEEDLRRALTPEQ 35 (69) T ss_pred HHHHHHH---HCCCCCCCHHHHHHHCCHHH T ss_conf 9999998---48998107999997689999 No 366 >pfam09184 PPP4R2 PPP4R2. PPP4R2 (protein phosphatase 4 core regulatory subunit R2) is the regulatory subunit of the histone H2A phosphatase complex. It has been shown to confer resistance to the anticancer drug cisplatin in yeast, and may confer resistance in higher eukaryotes. Probab=25.17 E-value=35 Score=12.48 Aligned_cols=11 Identities=9% Similarity=0.301 Sum_probs=3.6 Q ss_pred HHHHHHHHHHH Q ss_conf 99999862100 Q gi|254780289|r 321 LVKLVGSLSLN 331 (682) Q Consensus 321 L~e~~~~lkl~ 331 (682) +.+.|..+-|+ T Consensus 89 ~~~~F~~~PFT 99 (285) T pfam09184 89 IVTNFNGIPFT 99 (285) T ss_pred HHHHCCCCCHH T ss_conf 99743688718 No 367 >PRK09764 DNA-binding transcriptional repressor MngR; Provisional Probab=25.05 E-value=35 Score=12.46 Aligned_cols=35 Identities=11% Similarity=0.174 Sum_probs=19.0 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 22112688999999876533211246899987555 Q gi|254780289|r 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANL 453 (682) Q Consensus 419 ~~gl~i~ElK~i~r~I~~ge~e~~~AK~~l~~anl 453 (682) ..|-.+.--.++.++......-+++|=+.|+...| T Consensus 24 ~~G~~LPsE~eLa~~~~VSR~TvR~Al~~L~~eGl 58 (239) T PRK09764 24 KPGDALPTESALQTEFGVSRVTVRQALRQLVEQQI 58 (239) T ss_pred CCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCC T ss_conf 99599929999999979799999999999997899 No 368 >PRK12469 RNA polymerase factor sigma-54; Provisional Probab=25.00 E-value=36 Score=12.46 Aligned_cols=110 Identities=17% Similarity=0.182 Sum_probs=55.5 Q ss_pred HHHHHHHHHH---CCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHHHHHH Q ss_conf 9999998776---0889997899987099989999999860898755363588998604756238988998999999999 Q gi|254780289|r 533 VRTARRMSNK---IKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANL 609 (682) Q Consensus 533 ~~~~~~~~~~---~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~ 609 (682) .+....++.. .-++-|..+||+.+|+.+..|..+.+- -.+.+|.|= ..|-.|....-........+.... T Consensus 347 v~~Q~~Ff~~G~~~lkPL~lkdiA~~lglheSTVSRav~~----Kyi~tp~Gi---~~lk~FFs~~~~~~~g~~~S~~~i 419 (475) T PRK12469 347 VARQRDFFRYGEIALKPLVLRDVAEELGLHESTVSRATGN----KYMATPRGT---FEFKHFFPRKLEAAGGGECSAAAV 419 (475) T ss_pred HHHHHHHHHCCCCCCCCCCHHHHHHHHCCCCCHHHHHHCC----CEECCCCCE---EEHHHHHHHCCCCCCCCCCCHHHH T ss_conf 9999999847850036734999999819982037688627----502379854---669986232056899741149999 Q ss_pred HHHHHHHHH------CCCHHHH-HHHHHHHCCCCCCCCCHHHHHHHHCC Q ss_conf 999999973------2998899-99999818798674688999899667 Q gi|254780289|r 610 RETTTRVLA------SLTPREE-RVLRMRFGIGMNTDHTLEEVGKQFCV 651 (682) Q Consensus 610 ~~~~~~~l~------~l~~re~-~v~~~r~g~~~~~~~tl~e~~~~~~~ 651 (682) +..|.+++. .|+...= .+|.-+ ||..-+ +|-.--=..+|+ T Consensus 420 k~~I~~lI~~Ed~~kPlSD~~I~~~L~~~-Gi~IaR-RTVAKYRe~L~I 466 (475) T PRK12469 420 RALIKDMIAAEQATDPLSDVALAERLAGR-GILLAR-RTVAKYRQAMKI 466 (475) T ss_pred HHHHHHHHHHCCCCCCCCHHHHHHHHHHC-CCCEEE-CCHHHHHHHCCC T ss_conf 99999999844899998999999999977-998763-257999987399 No 369 >TIGR01736 FGAM_synth_II phosphoribosylformylglycinamidine synthase II; InterPro: IPR010074 Phosphoribosylformylglycinamidine synthase is a single, long polypeptide in most bacteria. Three proteins are required in Bacillus subtilis and many other species. This is the longest of the three and is designated PurL, phosphoribosylformylglycinamidine synthase II, or FGAM synthase II.; GO: 0004642 phosphoribosylformylglycinamidine synthase activity, 0006189 'de novo' IMP biosynthetic process, 0005737 cytoplasm. Probab=24.99 E-value=36 Score=12.46 Aligned_cols=18 Identities=33% Similarity=0.375 Sum_probs=11.4 Q ss_pred HHHCCCCCCHHHHHHHCC Q ss_conf 776088999789998709 Q gi|254780289|r 540 SNKIKREPTPEEIAKKLA 557 (682) Q Consensus 540 ~~~~~~~~~~~~~a~~~~ 557 (682) +..+||+|+.-|+|-.-. T Consensus 13 F~~LGRePn~~E~~~f~~ 30 (763) T TIGR01736 13 FKELGREPNDTELAMFEA 30 (763) T ss_pred HHHHCCCHHHHHHHHHHH T ss_conf 997388834899999985 No 370 >cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Probab=24.87 E-value=36 Score=12.44 Aligned_cols=23 Identities=26% Similarity=0.160 Sum_probs=17.0 Q ss_pred CHHHHHHHCCCCHHHHHHHHHHH Q ss_conf 97899987099989999999860 Q gi|254780289|r 548 TPEEIAKKLAMPVEGVRKVLKIT 570 (682) Q Consensus 548 ~~~~~a~~~~~~~~~~~~~~~~~ 570 (682) |+-|+|+.+|+|+..++---++. T Consensus 2 ~Ige~Ak~~gvs~~TLRyYe~~G 24 (97) T cd04782 2 TTGEFAKLCGISKQTLFHYDKIG 24 (97) T ss_pred CHHHHHHHHCCCHHHHHHHHHCC T ss_conf 78999999896999999999669 No 371 >TIGR00270 TIGR00270 conserved hypothetical protein TIGR00270; InterPro: IPR004451 This family of conserved hypothetical proteins includes proteins of unknown function from archaebacteria.. Probab=24.81 E-value=36 Score=12.43 Aligned_cols=63 Identities=30% Similarity=0.478 Sum_probs=35.5 Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCC-------------CCCCCCCC---------- Q ss_conf 5889899999999987760889997899987099989999999860898-------------75536358---------- Q gi|254780289|r 525 MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEP-------------ISLETPIG---------- 581 (682) Q Consensus 525 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~-------------~sl~~~~~---------- 581 (682) ++|-...+.|..|+ =|.-+.|+||+.+.+-+.-+.++-+.--+| ++|--.|+ T Consensus 80 lvEdyg~iIR~eRE-----KRgwS~E~LAkki~eK~S~i~kiE~~e~eP~~k~~~kLEkllkIkL~E~~~e~~~ekseG~ 154 (169) T TIGR00270 80 LVEDYGRIIREERE-----KRGWSREELAKKIKEKASVIKKIEREELEPEEKVVKKLEKLLKIKLLEKVEEEKLEKSEGR 154 (169) T ss_pred HHHHHHHHHHHHCC-----CCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCCCCCCEECCCCC T ss_conf 66432254220001-----4687878999987410678888754037988899999888835010023571000015788 Q ss_pred CCCCCEEEEEE Q ss_conf 89986047562 Q gi|254780289|r 582 DEDTSHLGDFI 592 (682) Q Consensus 582 ~~~~~~~~~~~ 592 (682) +....|||||+ T Consensus 155 ~~~g~TlGD~~ 165 (169) T TIGR00270 155 DERGATLGDVV 165 (169) T ss_pred CCCCCCCCCEE T ss_conf 76787423466 No 372 >COG3904 Predicted periplasmic protein [Function unknown] Probab=24.75 E-value=25 Score=13.64 Aligned_cols=29 Identities=21% Similarity=0.126 Sum_probs=13.6 Q ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH Q ss_conf 8674688999899667899999999999998 Q gi|254780289|r 636 MNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666 (682) Q Consensus 636 ~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~ 666 (682) +|-+.+|-+..+...- -|||||-.|-+-- T Consensus 202 MgigpgLlq~ml~tpp--~dir~l~~kem~~ 230 (245) T COG3904 202 MGIGPGLLQMMLATPP--SDIRQLGLKEMTA 230 (245) T ss_pred CCCCHHHHHHHHCCCH--HHHHHHHHHHHHH T ss_conf 0898799999860894--7655513778765 No 373 >pfam10500 SR-25 Nuclear RNA-splicing-associated protein. SR-25, otherwise known as ADP-ribosylation factor-like factor 6-interacting protein 4, is expressed in virtually all tissues. At the N-terminus there is a repeat of serine-arginine (SR repeat), and towards the middle of the protein there are clusters of both serines and of basic amino acids. The presence of many nuclear localisation signals strongly implies that this is a nuclear protein that may contribute to RNA splicing. SR-25 is also implicated, along with heat-shock-protein-27, as a mediator in the Rac1 (GTPase ras-related C3 botulinum toxin substrate 1) signalling pathway. Probab=24.71 E-value=36 Score=12.42 Aligned_cols=47 Identities=28% Similarity=0.390 Sum_probs=24.7 Q ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH Q ss_conf 999999999997329988999999981879867468899989966789999999999999 Q gi|254780289|r 606 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIR 665 (682) Q Consensus 606 ~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~ 665 (682) ...-...+..+.+.-+-|-+-|- |+|+ -|||| |||||-.+|-.+|-+ T Consensus 14 ~e~rQsviRrv~DpeTGR~RLIk------GdgE--ilEEi-----VsrerHk~INkqaT~ 60 (74) T pfam10500 14 YEARQSVIRKVVDPETGRTRLIK------GDGE--ILEEI-----VSKERHKEINKQATR 60 (74) T ss_pred HHHHHHHHHHHCCCCCCCEEEEC------CCHH--HHHHH-----HHHHHHHHHHHHHHC T ss_conf 99999889885076657542441------7628--99999-----828889999887421 No 374 >KOG4697 consensus Probab=24.64 E-value=36 Score=12.41 Aligned_cols=26 Identities=27% Similarity=0.507 Sum_probs=20.4 Q ss_pred CCCCCCEEEHHHHHHHHHHHHHHHHH Q ss_conf 85457312010289899999999972 Q gi|254780289|r 489 DWCLGYKFSTYAMWWVKQAITRSIAD 514 (682) Q Consensus 489 ~~~~g~~f~tya~~~i~~~i~~~~~~ 514 (682) -+-.+-+|.|-++||+-|-|+--|.- T Consensus 107 ~~~Ynr~fPsqfsWw~LqVis~tI~~ 132 (160) T KOG4697 107 VFLYNRKFPSQFSWWFLQVISSTILI 132 (160) T ss_pred HHHCCCCCCCHHHHHHHHHHHHHHHH T ss_conf 01123568750179999999887998 No 375 >PRK10857 DNA-binding transcriptional regulator IscR; Provisional Probab=24.57 E-value=36 Score=12.40 Aligned_cols=22 Identities=5% Similarity=0.231 Sum_probs=11.6 Q ss_pred CCHHHHHHHCCCCHHHHHHHHH Q ss_conf 9978999870999899999998 Q gi|254780289|r 547 PTPEEIAKKLAMPVEGVRKVLK 568 (682) Q Consensus 547 ~~~~~~a~~~~~~~~~~~~~~~ 568 (682) -+..+||+..++|..-+.+++. T Consensus 26 vsi~eIAe~~~Is~~~LekIl~ 47 (164) T PRK10857 26 VPLADISERQGISLSYLEQLFS 47 (164) T ss_pred ECHHHHHHHHCCCHHHHHHHHH T ss_conf 9499999887919999999999 No 376 >PRK05449 aspartate alpha-decarboxylase; Provisional Probab=24.45 E-value=8.1 Score=17.54 Aligned_cols=35 Identities=20% Similarity=0.229 Sum_probs=19.2 Q ss_pred HHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHH Q ss_conf 87544367999988743854573120102898999 Q gi|254780289|r 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQ 506 (682) Q Consensus 472 ~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~ 506 (682) ||....+|---..|+=++..-|-||+|||.+--+. T Consensus 31 ~Lm~aagi~~~E~V~V~Nv~NG~Rf~TYvI~g~~G 65 (126) T PRK05449 31 DLLDAAGILENEKVDIVNVNNGARFETYVIKGERG 65 (126) T ss_pred HHHHHCCCCCCCEEEEEECCCCCEEEEEEEECCCC T ss_conf 99987599989889999898995899999864798 No 377 >KOG3361 consensus Probab=24.35 E-value=36 Score=12.37 Aligned_cols=80 Identities=34% Similarity=0.344 Sum_probs=39.8 Q ss_pred HHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCC---CCCEE-----------EHHHHHHHHHHHHHHHHHCCC Q ss_conf 5578999887522356777887544367999988743854---57312-----------010289899999999972287 Q gi|254780289|r 452 NLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC---LGYKF-----------STYAMWWVKQAITRSIADQSC 517 (682) Q Consensus 452 nlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~---~g~~f-----------~tya~~~i~~~i~~~~~~~~~ 517 (682) |-|-|-|.-|+-+|-|.-+----+-| -+||--=|+|-. -..|| |.|||-||+.--. T Consensus 39 nPRNVGSldK~dpnVGtGlVGAPACG--DVMkLqIkvd~~g~I~dakFKTFGCGSAIASSS~aTewvkgkt~-------- 108 (157) T KOG3361 39 NPRNVGSLDKNDPNVGTGLVGAPACG--DVMKLQIKVDDSGVIEDAKFKTFGCGSAIASSSLATEWVKGKTL-------- 108 (157) T ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCC--CEEEEEEEECCCCCEEEEEEEECCCCHHHHHHHHHHHHHCCCCH-------- T ss_conf 86555766789997655553576522--00048889779982887665211563476666889999835628-------- Q ss_pred EEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHH Q ss_conf 046142058898999999999877608899978999870999899999 Q gi|254780289|r 518 TIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565 (682) Q Consensus 518 ~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~ 565 (682) +...++ ...|||++|.+|.-|..- T Consensus 109 ---------dea~kI---------------kNteIAKeL~LPPVKLHC 132 (157) T KOG3361 109 ---------DEALKI---------------KNTEIAKELSLPPVKLHC 132 (157) T ss_pred ---------HHHHHC---------------CCHHHHHHCCCCCHHHHH T ss_conf ---------897711---------------318889761699601346 No 378 >PRK08643 acetoin reductase; Validated Probab=24.32 E-value=37 Score=12.36 Aligned_cols=107 Identities=21% Similarity=0.200 Sum_probs=59.4 Q ss_pred HHHHHHHHHHHH--HHHH--HHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCC Q ss_conf 124689998755--5789--998875223567778875443679999887438545731201028989999999997228 Q gi|254780289|r 441 ASIAKKEMVEAN--LRLV--ISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQS 516 (682) Q Consensus 441 ~~~AK~~l~~an--lr~v--~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~ 516 (682) ++.+-+.|.+.+ -+.| .|++-.....+...------|-+||.|+.-+-=-.+|.|.-.-+-.||+-.+...+.++. T Consensus 118 ~~~~~~~m~~~~~~G~IVnisS~~~~~~~~~~~~Y~asKaav~~ltkslA~ela~~gIrVN~V~PG~i~T~~~~~~~~~~ 197 (256) T PRK08643 118 IQAAQEQFKKLGHGGKIINATSQAGVEGNPGLSVYGSTKFAVRGLTQTAARDLASEGITVNAYAPGIVKTPMMFDIAHEV 197 (256) T ss_pred HHHHHHHHHHHCCCCEEEEEECCHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCEEEEEEECCCCCCHHHHHHHHH T ss_conf 99999999982899279998321013589984899999999999999999998775918999960668870456677887 Q ss_pred CE-EECCCHHHHHHHHHHHHHHHHHH--HCCCCCCHHHHHHHC Q ss_conf 70-46142058898999999999877--608899978999870 Q gi|254780289|r 517 CT-IRIPVHMRDKIHKVVRTARRMSN--KIKREPTPEEIAKKL 556 (682) Q Consensus 517 ~~-~r~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~a~~~ 556 (682) .. ...|. .....++.. -+||..+|+|+|... T Consensus 198 ~~~~~~~~---------~~~~~~~~~~ipl~R~g~pedia~~v 231 (256) T PRK08643 198 GENAGKPD---------EWGMEQFAKDITLKRLSEPEDVANVV 231 (256) T ss_pred HHHCCCCH---------HHHHHHHHHCCCCCCCCCHHHHHHHH T ss_conf 87628975---------89999998359999986899999999 No 379 >smart00492 HELICc3 helicase superfamily c-terminal domain. Probab=24.18 E-value=35 Score=12.46 Aligned_cols=30 Identities=20% Similarity=0.149 Sum_probs=14.6 Q ss_pred HHHCCCCCCCEEEH-H-HHHHHHHHHHHHHHH Q ss_conf 87438545731201-0-289899999999972 Q gi|254780289|r 485 AEKFDWCLGYKFST-Y-AMWWVKQAITRSIAD 514 (682) Q Consensus 485 ~~~~~~~~g~~f~t-y-a~~~i~~~i~~~~~~ 514 (682) .+++....+|.+.. + |.-.++|++-|+|.. T Consensus 94 ~~~~~~~~~~~~~~~~~A~r~v~Qa~GR~IR~ 125 (141) T smart00492 94 LRDKGQIRPFDFVSLPDAMRTLAQCVGRLIRG 125 (141) T ss_pred HHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCC T ss_conf 99856998424665899999999986875457 No 380 >smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein. Probab=24.08 E-value=37 Score=12.33 Aligned_cols=23 Identities=26% Similarity=0.423 Sum_probs=13.8 Q ss_pred CCCHHHHHHHCCCCHHHHHHHHH Q ss_conf 99978999870999899999998 Q gi|254780289|r 546 EPTPEEIAKKLAMPVEGVRKVLK 568 (682) Q Consensus 546 ~~~~~~~a~~~~~~~~~~~~~~~ 568 (682) +.|.++||+.+++|...+....+ T Consensus 1 plsl~~lA~~~~~S~~~l~~~f~ 23 (84) T smart00342 1 PLTLEDLAEALGMSPRHLQRLFK 23 (84) T ss_pred CCCHHHHHHHHCCCHHHHHHHHH T ss_conf 98999999988909999999999 No 381 >PRK10703 DNA-binding transcriptional repressor PurR; Provisional Probab=24.03 E-value=37 Score=12.33 Aligned_cols=47 Identities=17% Similarity=0.126 Sum_probs=20.9 Q ss_pred HHHHHHHHHHHHHHHHHHCCCC--CCCEEEHHHHHHHHHHHHHHHHHCCCEEECCC Q ss_conf 7887544367999988743854--57312010289899999999972287046142 Q gi|254780289|r 470 FLDLIQEGNIGLMKAAEKFDWC--LGYKFSTYAMWWVKQAITRSIADQSCTIRIPV 523 (682) Q Consensus 470 ~~~~~~~~~~~l~~a~~~~~~~--~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~ 523 (682) .-|.+. +|+|+|.....++ .-+....|--+++-+- +.-.--||+.|. T Consensus 246 ~nD~~A---~g~~~~l~~~g~~VP~DisvigfDd~~~~~~----~~P~LTtv~~~~ 294 (335) T PRK10703 246 GGDIMA---MGAICAADEMGLRVPQDISVIGYDNVRNARY----FTPALTTIHQPK 294 (335) T ss_pred CCHHHH---HHHHHHHHHCCCCCCCCEEEEEECCCHHHHH----CCCCCEEEECCH T ss_conf 875999---9999999971999999749999888289982----589827998299 No 382 >COG2344 AT-rich DNA-binding protein [General function prediction only] Probab=23.87 E-value=37 Score=12.30 Aligned_cols=29 Identities=17% Similarity=0.347 Sum_probs=13.6 Q ss_pred HHHHHHHHHHHHHHHCCCCCCCEEEHHHHHH Q ss_conf 7544367999988743854573120102898 Q gi|254780289|r 473 LIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503 (682) Q Consensus 473 ~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~ 503 (682) +|-.||+| +|+=-|......+|---+.+= T Consensus 89 iVG~GnlG--~All~Y~f~~~~~~~iv~~FD 117 (211) T COG2344 89 IVGVGNLG--RALLNYNFSKKNGMKIVAAFD 117 (211) T ss_pred EECCCHHH--HHHHCCCCHHHCCCEEEEEEC T ss_conf 99057088--898607423326935999961 No 383 >PRK09281 F0F1 ATP synthase subunit alpha; Validated Probab=23.78 E-value=37 Score=12.29 Aligned_cols=45 Identities=20% Similarity=0.222 Sum_probs=18.0 Q ss_pred HHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCC Q ss_conf 898999999999722870461420588989999999998776088999 Q gi|254780289|r 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548 (682) Q Consensus 501 ~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 548 (682) ++|.--+|-.++.||.+-+=+ +.+.+.|+-.+.|++.--+||+|+ T Consensus 238 Apyaa~aIAEyFrd~G~dVLl---v~DdLtr~A~A~REisLll~rPPg 282 (502) T PRK09281 238 APYAGCAMGEYFMDNGKDALI---VYDDLSKQAVAYRQLSLLLRRPPG 282 (502) T ss_pred HHHHHHHHHHHHHHCCCCEEE---EEECHHHHHHHHHHHHHHCCCCCC T ss_conf 999999999999967994899---985568999999888986279987 No 384 >PRK13805 bifunctional acetaldehyde-CoA/alcohol dehydrogenase; Provisional Probab=23.62 E-value=38 Score=12.27 Aligned_cols=137 Identities=12% Similarity=0.164 Sum_probs=82.4 Q ss_pred HHHHHHHHHHHHHHHHHHHH---HHHHHHHH-----------HHHHHHHHHHHHHHCCC-CCCHHHHHHHHHHHHHHHHH Q ss_conf 12688999999876533211---24689998-----------75557899988752235-67778875443679999887 Q gi|254780289|r 422 ISISEFRHIVSMVRKGECEA---SIAKKEMV-----------EANLRLVISVAKKYTNR-GLQFLDLIQEGNIGLMKAAE 486 (682) Q Consensus 422 l~i~ElK~i~r~I~~ge~e~---~~AK~~l~-----------~anlr~v~~~~~~~~~~-~~~~~~~~~~~~~~l~~a~~ 486 (682) +...-++-+.+.+.+..... ..|+..|. .|.|-+|.++|....+. +++ .-.+|--|+-.|= T Consensus 677 ~Al~Ai~li~~~L~~a~~~g~~d~eARe~M~~As~~AG~AF~na~lG~~HamaH~lG~~~~ip----HG~aNAilLP~Vi 752 (862) T PRK13805 677 LALQAIKLVFEYLPRSYKNGAKDPEAREKMHNAATIAGMAFANAFLGICHSMAHKLGAEFHIP----HGRANAILIPHVI 752 (862) T ss_pred HHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCC----HHHHHHHHHHHHH T ss_conf 999999999999999996899889999999999999999996851788788624751486865----5889999989999 Q ss_pred HCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCCH-HHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHH Q ss_conf 43854573120102898999999999722870461420-58898999999999877608899978999870999899999 Q gi|254780289|r 487 KFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVH-MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRK 565 (682) Q Consensus 487 ~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~ 565 (682) +|....-.||.++..|-.-.+..|+ ++-++.+-++.+ ..+...++...-++|...+|=+.+..+ +|++.++... T Consensus 753 ~fNa~~p~k~~~~p~y~~~~a~ery-a~iA~~lGl~~~s~~e~~~~li~ai~~L~~~lgiP~~L~e----~GV~e~df~~ 827 (862) T PRK13805 753 RYNATDPTKQAAFPQYEYPRADERY-AEIARHLGLPGDTTEEKVESLIKAIEELKAELGIPMSIKE----AGVDEADFLA 827 (862) T ss_pred HHHCCCCCCCCCCCCCCCCCHHHHH-HHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCHHH----CCCCHHHHHH T ss_conf 9745575322333212333168999-9999983999999899999999999999997699998898----2989899886 Q ss_pred HH Q ss_conf 99 Q gi|254780289|r 566 VL 567 (682) Q Consensus 566 ~~ 567 (682) .+ T Consensus 828 ~l 829 (862) T PRK13805 828 KV 829 (862) T ss_pred HH T ss_conf 69 No 385 >smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein. Probab=23.58 E-value=38 Score=12.26 Aligned_cols=21 Identities=43% Similarity=0.531 Sum_probs=11.6 Q ss_pred CHHHHHHHCCCCHHHHHHHHH Q ss_conf 978999870999899999998 Q gi|254780289|r 548 TPEEIAKKLAMPVEGVRKVLK 568 (682) Q Consensus 548 ~~~~~a~~~~~~~~~~~~~~~ 568 (682) |-++||+.+|++.+-|..+++ T Consensus 10 t~~~iA~~lG~tretvsR~l~ 30 (48) T smart00419 10 TRQEIAELLGLTRETVSRTLK 30 (48) T ss_pred CHHHHHHHHCCCHHHHHHHHH T ss_conf 999999997997999999999 No 386 >COG4477 EzrA Negative regulator of septation ring formation [Cell division and chromosome partitioning] Probab=23.20 E-value=38 Score=12.21 Aligned_cols=22 Identities=23% Similarity=0.409 Sum_probs=9.5 Q ss_pred CCC--HHHHHHHHHHHHHHHHHHC Q ss_conf 677--7887544367999988743 Q gi|254780289|r 467 GLQ--FLDLIQEGNIGLMKAAEKF 488 (682) Q Consensus 467 ~~~--~~~~~~~~~~~l~~a~~~~ 488 (682) |+| |++|.-.+---+--.+.+| T Consensus 440 GlPe~~l~l~~~~~~~i~~l~~eL 463 (570) T COG4477 440 GLPETFLSLFFTAGHEIQDLMKEL 463 (570) T ss_pred CCCHHHHHHHHHHHHHHHHHHHHH T ss_conf 995999999971006899999998 No 387 >PRK08219 short chain dehydrogenase; Provisional Probab=23.13 E-value=38 Score=12.20 Aligned_cols=81 Identities=14% Similarity=0.033 Sum_probs=42.2 Q ss_pred HHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCCHHHHHHHHH Q ss_conf 57899988752235677788754436799998874385457312010289899999999972287046142058898999 Q gi|254780289|r 453 LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKV 532 (682) Q Consensus 453 lr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~ 532 (682) .-.|.|++-....-|...------|-.||+++.-. ++..|.|..+-+--||+-.+++.+.++.. T Consensus 123 IV~isS~~g~~~~~~~~~Y~aSKaAl~~l~~~L~~-e~~~~IrVn~I~PG~v~T~m~~~~~~~~~--------------- 186 (226) T PRK08219 123 VVFINSGAGLNASPGWASYAASKFALRALADALRE-EEAGNVRVTSVHPGRTATDMQRELVAQEG--------------- 186 (226) T ss_pred EEEEECHHHCCCCCCCHHHHHHHHHHHHHHHHHHH-HCCCCEEEEEEEECCCCCCCCHHHHHHHH--------------- T ss_conf 99994767648899974799999999999999998-66998499999708997865355676543--------------- Q ss_pred HHHHHHHHHHCCCCCCHHHHHHH Q ss_conf 99999987760889997899987 Q gi|254780289|r 533 VRTARRMSNKIKREPTPEEIAKK 555 (682) Q Consensus 533 ~~~~~~~~~~~~~~~~~~~~a~~ 555 (682) .....||-.+|+|+|+. T Consensus 187 ------~~~~~~r~~~PedVA~~ 203 (226) T PRK08219 187 ------REYDPARFLRPETVAAA 203 (226) T ss_pred ------CCCCCCCCCCHHHHHHH T ss_conf ------03787679699999999 No 388 >TIGR01004 PulS_OutS lipoprotein, PulS/OutS family; InterPro: IPR005699 This family comprises lipoproteins from four gamma proteobacterial species: PulS protein of Klebsiella pneumoniae (P20440 from SWISSPROT), the OutS protein of Erwinia chrysanthemi (Q01567 from SWISSPROT) and Pectobacterium chrysanthemi, and the functionally uncharacterised E. coli protein EtpO. PulS and OutS have been shown to interact with and facilitate insertion of secretins into the outer membrane, suggesting a chaperone-like, or piloting function for members of this family.; GO: 0008565 protein transporter activity, 0006886 intracellular protein transport. Probab=23.01 E-value=39 Score=12.18 Aligned_cols=61 Identities=16% Similarity=0.286 Sum_probs=42.8 Q ss_pred HHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHH Q ss_conf 87522356777887544367999988743854573120102898999999999722870461420588989999999998 Q gi|254780289|r 460 AKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539 (682) Q Consensus 460 ~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~ 539 (682) |-||...-|.-.||=.+|.| . +.||.=++...|-+++ .+.+.+.+.++ T Consensus 56 a~rYLk~~CnRSDLPdd~~I--l----------------------~~A~nva~~kGW~~~~--------~~~l~q~S~~l 103 (136) T TIGR01004 56 AARYLKVKCNRSDLPDDEAI--L----------------------KVAVNVAVKKGWDSLD--------AEDLSQRSEDL 103 (136) T ss_pred HHHHHHHCCCCCCCCCHHHH--H----------------------HHHHHHHHHHCCCCCC--------HHHHHHHHHHH T ss_conf 98886420677899700579--9----------------------9999987563124500--------56688878999 Q ss_pred HHHCCCCCCHHHH Q ss_conf 7760889997899 Q gi|254780289|r 540 SNKIKREPTPEEI 552 (682) Q Consensus 540 ~~~~~~~~~~~~~ 552 (682) ++.+-++-||+.+ T Consensus 104 Y~~L~~DsTPea~ 116 (136) T TIGR01004 104 YQRLLKDSTPEAT 116 (136) T ss_pred HHHHHCCCCCCCC T ss_conf 9886148886630 No 389 >PRK09464 pdhR transcriptional regulator PdhR; Reviewed Probab=23.00 E-value=39 Score=12.18 Aligned_cols=51 Identities=20% Similarity=0.261 Sum_probs=30.1 Q ss_pred HHCCHHHHHHHHHHHHHC-C-CC-CHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCEE Q ss_conf 020289999999978784-8-86-789997526843599888999999998479778 Q gi|254780289|r 24 FDFSDDSWKKMIKLARQR-G-YV-TIEELNAFLPPDEVSSEQMEDTVAMLSNMGINV 77 (682) Q Consensus 24 ~d~~~~~ik~LI~~gke~-G-yl-TydeIn~~LP~d~~~~e~ie~i~~~L~~~GI~V 77 (682) .|..-+.|++.|--|.=+ | .| +-.+|.+.|. ++---+=+.+..|..+|+-. T Consensus 12 ~e~V~~~L~~~I~~G~l~pGd~LPsE~eLA~~lg---VSR~~VREAL~~L~~~GlV~ 65 (254) T PRK09464 12 SDVIEQQLEFLILEGTLRPGEKLPPERELAKQFD---VSRPSLREAIQRLEAKGLLL 65 (254) T ss_pred HHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHC---CCCHHHHHHHHHHHHCCCEE T ss_conf 9999999999998499999396936999999868---99559999999999889989 No 390 >PRK12274 serine/threonine protein kinase; Provisional Probab=22.95 E-value=39 Score=12.17 Aligned_cols=52 Identities=27% Similarity=0.326 Sum_probs=36.3 Q ss_pred CCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHH--------HCCCHHHHHHHHHH Q ss_conf 358899860475623898899899999999999999997--------32998899999998 Q gi|254780289|r 579 PIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVL--------ASLTPREERVLRMR 631 (682) Q Consensus 579 ~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l--------~~l~~re~~v~~~r 631 (682) .+|+|+...+.||-- .....|--...+..-++.+..+| +.|+|+|+.+|.-. T Consensus 104 L~~~dg~p~liDFQl-A~~~~rr~~~~Rila~eDlrhllK~kr~y~~e~Ltp~e~~~L~r~ 163 (198) T PRK12274 104 LVQEDGSPAVIDFQL-AVRGNPRARWMRLLAREDLRHLLKHKRMYCPAALTPVERRVLKRT 163 (198) T ss_pred EECCCCCEEEEEEEE-CCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHH T ss_conf 887999978897441-002363038999999998999999888638988998999999840 No 391 >pfam10498 IFT57 Intra-flagellar transport protein 57. Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans. Probab=22.90 E-value=39 Score=12.17 Aligned_cols=28 Identities=18% Similarity=0.213 Sum_probs=16.2 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 0577887899999999999999999999 Q gi|254780289|r 331 NQSRIDLLVEQLYDISKRIMHNEGELLR 358 (682) Q Consensus 331 ~~k~iE~L~~~l~~~~k~Ir~~Er~L~r 358 (682) ....++.|...+-....+|.+.|+.|.. T Consensus 235 ~~~~L~kl~~d~~~~LekI~sREk~lN~ 262 (355) T pfam10498 235 TKQYLKKLSQDLSKALEKISSREKHLNN 262 (355) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 8999999999999999999889999987 No 392 >TIGR03103 trio_acet_GNAT GNAT-family acetyltransferase TIGR03103. Members of this protein family belong to the GNAT family of acetyltransferases. Each is part of a conserved three-gene cassette sparsely distributed across at least twenty different species known so far, including alpha, beta, and gamma Proteobacteria, Mycobacterium, and Prosthecochloris, which is a member of the Chlorobi. The other two members of the cassette are a probable protease and an asparagine synthetase family protein. Probab=22.85 E-value=31 Score=12.95 Aligned_cols=62 Identities=8% Similarity=0.234 Sum_probs=36.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----------HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCH Q ss_conf 5322333322222112688999999876533----------21124689998755578999887522356777 Q gi|254780289|r 408 KIRNEIKSISVETGISISEFRHIVSMVRKGE----------CEASIAKKEMVEANLRLVISVAKKYTNRGLQF 470 (682) Q Consensus 408 ~~q~kL~~ie~~~gl~i~ElK~i~r~I~~ge----------~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~ 470 (682) .++..|.++...+.|++-.=|.+.+++-..- .....|-.=+-+.. ++||.=+..-.++|... T Consensus 278 ~creslSelTSAvAms~c~DK~lT~rll~~AG~~VP~~~~~~~~~~~~~fl~~~G-~VVVKP~dGnqGrGVtv 349 (547) T TIGR03103 278 RCRESLSELTSAVAMSLCDDKRLTRRLVSEAGLQVPEQQLAGNGEAVEAFLAEHG-AVVVKPVRGEQGKGISV 349 (547) T ss_pred EEECHHHHHHHHHHHHHHCCHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHCC-CEEECCCCCCCCCCEEE T ss_conf 8612025788899988740499999999973998999745699899999998739-99977687888861587 No 393 >PRK00509 argininosuccinate synthase; Provisional Probab=22.76 E-value=39 Score=12.15 Aligned_cols=33 Identities=30% Similarity=0.435 Sum_probs=22.4 Q ss_pred CCCCCCCHHHH--HHHHHC-C---------CCCCCHHHHHHHHHH Q ss_conf 45777728999--999856-9---------768897889999999 Q gi|254780289|r 113 ADRSTDDPVRM--YLREMG-S---------IELLSREGEIAIAKR 145 (682) Q Consensus 113 e~~rtdDPVRM--YLREMG-~---------V~LLTREgEIeIAKR 145 (682) .+|+-+|-||. +.+-++ . -.+.||++||+.|+. T Consensus 117 ~TGkGNDQvRFe~~~~aL~P~l~iiaP~Rd~~~~sR~~~i~ya~~ 161 (398) T PRK00509 117 CTGKGNDQVRFELAIAALAPDLKVIAPWREWDLMSREELIAYAEE 161 (398) T ss_pred CCCCCCCHHHHHHHHHHHCCCCEEEEEEECCCCCCHHHHHHHHHH T ss_conf 556786089999999985999768611321341689999999998 No 394 >pfam06056 Terminase_5 Putative ATPase subunit of terminase (gpP-like). This family of proteins are annotated as ATPase subunits of phage terminase after. Terminases are viral proteins that are involved in packaging viral DNA into the capsid. Probab=22.73 E-value=39 Score=12.14 Aligned_cols=30 Identities=30% Similarity=0.355 Sum_probs=18.7 Q ss_pred HHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHH Q ss_conf 999998776088999789998709998999999 Q gi|254780289|r 534 RTARRMSNKIKREPTPEEIAKKLAMPVEGVRKV 566 (682) Q Consensus 534 ~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~ 566 (682) +.++.|+- +.=++.|||+.||+|..-|..= T Consensus 4 ~~Ar~LY~---qg~~~~eIA~~Lg~~~~tVysW 33 (58) T pfam06056 4 RQARTLYW---QGYRPAEIAQELGLKARTVYSW 33 (58) T ss_pred HHHHHHHH---CCCCHHHHHHHHCCCCCHHHHH T ss_conf 99999999---6898999999978993145658 No 395 >COG4473 EcsB Predicted ABC-type exoprotein transport system, permease component [Intracellular trafficking and secretion] Probab=22.71 E-value=39 Score=12.14 Aligned_cols=30 Identities=30% Similarity=0.402 Sum_probs=25.7 Q ss_pred CCCHHHHHHHHHCCCCCCCHHHHHHHHHHH Q ss_conf 772899999985697688978899999999 Q gi|254780289|r 117 TDDPVRMYLREMGSIELLSREGEIAIAKRI 146 (682) Q Consensus 117 tdDPVRMYLREMG~V~LLTREgEIeIAKRI 146 (682) +.-|||-||+|--+|-||..|.|+.-=+|= T Consensus 72 ~~g~vrT~LkeaDkVFLL~~E~~m~~y~r~ 101 (379) T COG4473 72 SIGSVRTFLKEADKVFLLPKEEEMDQYLRQ 101 (379) T ss_pred HHHHHHHHHHCCCEEEEECCHHHHHHHHHH T ss_conf 986388898377878871448899999999 No 396 >smart00803 TAF TATA box binding protein associated factor. TAFs (TATA box binding protein associated factors) are part of the transcription initiation factor TFIID multimeric protein complex. TFIID is composed of the TATA box binding protein (TBP) and a number of TAFs. The TAFs provide binding sites for many different transcriptional activators and co-activators that modulate transcription initiation by Pol II. TAF proteins adopt a histone-like fold. Probab=22.69 E-value=39 Score=12.14 Aligned_cols=21 Identities=29% Similarity=0.583 Sum_probs=11.9 Q ss_pred HHHHHHHHHHHHHHHCCHHHH Q ss_conf 999999999999983296777 Q gi|254780289|r 653 RERIRQIEAKAIRKLKHPSRS 673 (682) Q Consensus 653 ~er~rqi~~~a~~~l~~~~~~ 673 (682) .-|||||=..|++=++|..|. T Consensus 33 eyRlkei~q~A~Kfm~hskR~ 53 (65) T smart00803 33 EYRIKEIVQEALKFMRHSKRT 53 (65) T ss_pred HHHHHHHHHHHHHHHHHHCCC T ss_conf 999999999999999975767 No 397 >KOG0464 consensus Probab=22.69 E-value=33 Score=12.68 Aligned_cols=26 Identities=19% Similarity=0.307 Sum_probs=18.6 Q ss_pred CCCCHHHHHHHHHHHHHCCCEEECCC Q ss_conf 35998889999999984797783278 Q gi|254780289|r 56 DEVSSEQMEDTVAMLSNMGINVVDGD 81 (682) Q Consensus 56 d~~~~e~ie~i~~~L~~~GI~Vve~~ 81 (682) ++-+.+.+-+++..=.+.||.|...+ T Consensus 69 ~vddgdtvtdfla~erergitiqsaa 94 (753) T KOG0464 69 DVDDGDTVTDFLAIERERGITIQSAA 94 (753) T ss_pred CCCCCCHHHHHHHHHHHCCCEEEEEE T ss_conf 56788537788888886483665404 No 398 >PRK02793 hypothetical protein; Provisional Probab=22.66 E-value=39 Score=12.13 Aligned_cols=49 Identities=16% Similarity=0.184 Sum_probs=38.7 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC Q ss_conf 9999999999862100577887899999999999999999999999712 Q gi|254780289|r 316 VLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYG 364 (682) Q Consensus 316 kl~~eL~e~~~~lkl~~k~iE~L~~~l~~~~k~Ir~~Er~L~rl~~k~~ 364 (682) .+...|.++-..+-|--..|+.|.+.+......|..+.+.+..++.+.+ T Consensus 5 ~le~Ri~~LE~rlAfQe~tIe~LN~~v~~Qq~~i~~L~~ql~~L~~rLk 53 (72) T PRK02793 5 SLEARLAELESRLAFQEITIEELNLTVTAHEMEMAKLRDHLRLLTEKLK 53 (72) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 8999999999999968999999999999999999999999999999998 No 399 >TIGR02485 CobZ_N-term precorrin 3B synthase CobZ; InterPro: IPR012831 Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt. Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase . In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase . There are at least two distinct cobalamin biosynthetic pathways in bacteria : Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway ; found in Pseudomonas denitrificans and Rhodobacter capsulatus. Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis ; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii shermanii. Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) . There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans. This entry represents CobZ, which is essential for cobalamin biosynthesis and is complemented by precorrin 3B synthase CobG (1.3.99.1 from EC). The enzyme has been shown to contain flavin, haem and Fe-S cluster cofactors, and is believed to require dioxygen as a substrate. In Rhodobacter capsulatus, CobZ is found as a N-terminal domain, whereas in other species it exists as a separate protein. The C-terminal portion is homologous to the 2-component signal transduction system protein CitB (IPR012830 from INTERPRO).. Probab=22.59 E-value=39 Score=12.12 Aligned_cols=44 Identities=27% Similarity=0.428 Sum_probs=31.2 Q ss_pred CCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCC-CCCCCCCEEEEEEC Q ss_conf 89997899987099989999999860898755363-58899860475623 Q gi|254780289|r 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETP-IGDEDTSHLGDFIE 593 (682) Q Consensus 545 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~-~~~~~~~~~~~~~~ 593 (682) .-||++|||..|+++++-....+..-. +.| +|.=+.++|-|.-. T Consensus 327 ~Adtl~eLA~~lgidp~~l~~tld~~n-----aaprvGqfdhttlddCht 371 (467) T TIGR02485 327 KADTLEELAAKLGIDPDALAETLDAYN-----AAPRVGQFDHTTLDDCHT 371 (467) T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHCCC-----CCCCCCCCCCCCHHCCCC T ss_conf 888879999985888889998650678-----787666555531000013 No 400 >TIGR03653 arch_L6P archaeal ribosomal protein L6P. Members of this protein family are the archaeal ribosomal protein L6P. The top-scoring proteins not selected by this model are eukaryotic cytosolic ribosomal protein L9. Bacterial ribosomal protein L6 scores lower and is described by a distinct model. Probab=22.43 E-value=37 Score=12.33 Aligned_cols=32 Identities=25% Similarity=0.421 Sum_probs=15.1 Q ss_pred HCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHCC Q ss_conf 6678999999999999983296777875665179 Q gi|254780289|r 649 FCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLDG 682 (682) Q Consensus 649 ~~~~~er~rqi~~~a~~~l~~~~~~~~l~~~~~~ 682 (682) -|..+|.|-|.-|. +|+++. .+.+-.|-|+|| T Consensus 133 ~G~DKq~VGq~AA~-Ir~~~k-~k~kd~R~f~dG 164 (170) T TIGR03653 133 TGIDKEDVGQTAAN-IEQATR-IKGRDPRVFQDG 164 (170) T ss_pred EECCHHHHHHHHHH-HHHHCC-CCCCCCCEEECC T ss_conf 97789998699987-466255-689977684156 No 401 >pfam10566 Glyco_hydro_97 Glycoside hydrolase 97. This is the 97th family of glycosidases, in this case bacterial. The central part of the GH97 family protein sequences represents a typical and complete (beta/alpha)8-barrel or catalytic TIM-barrel type domain. The N- and C-terminal parts of the sequences, mainly consisting of beta-strands, most probably form two additional non-catalytic domains with as yet unknown functions. The non-catalytic domains of glycosidases from the alpha-galactosidase and alpha-glucosidase superfamilies are also predominantly composed of beta-strands, and at least some of these domains are involved in oligomerisation and carbohydrate binding. In all known glycosidases with the (beta-alpha)8-barrel fold, the amino acid residues at the active site are located on the C-termini of the beta-strands. Probab=22.42 E-value=39 Score=12.10 Aligned_cols=40 Identities=33% Similarity=0.240 Sum_probs=21.0 Q ss_pred HHHHHHHHHHHHHHHHHHHH---------HCCCCCCH--H-HHHHHHHHHHH Q ss_conf 46899987555789998875---------22356777--8-87544367999 Q gi|254780289|r 443 IAKKEMVEANLRLVISVAKK---------YTNRGLQF--L-DLIQEGNIGLM 482 (682) Q Consensus 443 ~AK~~l~~anlr~v~~~~~~---------~~~~~~~~--~-~~~~~~~~~l~ 482 (682) +..++||....+.+---|+. |.-+|+.- . =+-+||..|.= T Consensus 402 ~d~Q~~v~~y~~i~~~AA~~~L~V~fHg~~kPtG~~RTYPN~~t~Egv~G~E 453 (643) T pfam10566 402 RDDQEMVRWVYEALEKAAKYKLLVDFHGEYKPTGLSRTYPNLLTQEGVRGNE 453 (643) T ss_pred CCCHHHHHHHHHHHHHHHHCCCEEEECCCCCCCCCCCCCCCHHHHHHHCCEE T ss_conf 6528999999999999987794699268716986530275366665533232 No 402 >pfam02002 TFIIE_alpha TFIIE alpha subunit. The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation together with RNA polymerase II and other general factors. Human TFIIE consists of two subunits TFIIE-alpha and TFIIE-beta, and joins the preinitiation complex after RNA polymerase II and TFIIF. This family consists of the conserved amino terminal region of eukaryotic TFIIE-alpha and proteins from archaebacteria that are presumed to be TFIIE-alpha subunits. Probab=22.36 E-value=40 Score=12.09 Aligned_cols=27 Identities=30% Similarity=0.362 Sum_probs=22.8 Q ss_pred CCCCHHHHHHHCCCCHHHHHHHHHHHC Q ss_conf 899978999870999899999998608 Q gi|254780289|r 545 REPTPEEIAKKLAMPVEGVRKVLKITK 571 (682) Q Consensus 545 ~~~~~~~~a~~~~~~~~~~~~~~~~~~ 571 (682) ..-|.++||+.+|+....|++++-... T Consensus 26 ~~v~dedLa~~l~~~~n~vRkiL~~L~ 52 (105) T pfam02002 26 GEVTEEDLAELLGIDLNELRKLLYRLY 52 (105) T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHH T ss_conf 883899999997898889999999998 No 403 >PRK08359 transcription factor; Validated Probab=22.36 E-value=40 Score=12.09 Aligned_cols=23 Identities=22% Similarity=0.450 Sum_probs=12.5 Q ss_pred CCCCHHHHHHHCCCCHHHHHHHH Q ss_conf 89997899987099989999999 Q gi|254780289|r 545 REPTPEEIAKKLAMPVEGVRKVL 567 (682) Q Consensus 545 ~~~~~~~~a~~~~~~~~~~~~~~ 567 (682) +.-|-+|||..+++.+.-++++- T Consensus 95 ~GlSqeeLA~ki~ek~nvI~kiE 117 (175) T PRK08359 95 SGLSYEELSHKVGLSVNDLRRIA 117 (175) T ss_pred CCCCHHHHHHHHCCHHHHHHHHH T ss_conf 59999999999722299999998 No 404 >PRK08217 fabG 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional Probab=22.29 E-value=40 Score=12.08 Aligned_cols=96 Identities=19% Similarity=0.173 Sum_probs=51.7 Q ss_pred HHHHHHHHHH----HHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHHCCCE Q ss_conf 4689998755----578999887522356777887544367999988743854573120102898999999999722870 Q gi|254780289|r 443 IAKKEMVEAN----LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCT 518 (682) Q Consensus 443 ~AK~~l~~an----lr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~~~~~ 518 (682) .+-..|.+.+ .-.+.|++ .+.+.|..------.|-.||+|+.-+.=...|.|..+-+-.||.-.++..+ T Consensus 132 ~~~~~m~~~~~~g~Ii~isS~~-~~~~~~~~~Y~asKaal~~ltk~lA~el~~~gIrVN~I~PG~i~T~~~~~~------ 204 (253) T PRK08217 132 EAAAKMIESGSKGVIINISSIA-RAGNMGQTNYSASKAGVAAMTVTWAKELARYGIRVAAIAPGVIETEMTAAM------ 204 (253) T ss_pred HHHHHHHHHCCCEEEEEECCHH-CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCEEEEEEEECCCCCCCCCCC------ T ss_conf 9999999848972799963311-138888616899999999999999999532195999997388987331117------ Q ss_pred EECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHC Q ss_conf 46142058898999999999877608899978999870 Q gi|254780289|r 519 IRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKL 556 (682) Q Consensus 519 ~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~ 556 (682) +-. ...+ -.-..-+||-.+|+|+|... T Consensus 205 ---~~~---~~~~-----~~~~~pl~R~g~p~dva~~v 231 (253) T PRK08217 205 ---KPE---ALER-----LEKMIPVGRLGEPEEIAHTV 231 (253) T ss_pred ---CHH---HHHH-----HHHCCCCCCCCCHHHHHHHH T ss_conf ---999---9999-----98579999984999999999 No 405 >TIGR02617 tnaA_trp_ase tryptophanase; InterPro: IPR013440 Proteins in this entry belong to the beta-eliminating lyase family and are thought to act as tryptophanases (4.1.99.1 from EC) (also known as L-tryptophan indole-lyases). The genes encoding these proteins are, as a rule, found with a tryptophanase leader peptide TnaC (IPR013439 from INTERPRO) encoded upstream. ; GO: 0009034 tryptophanase activity, 0006568 tryptophan metabolic process. Probab=22.25 E-value=40 Score=12.07 Aligned_cols=19 Identities=42% Similarity=0.499 Sum_probs=14.1 Q ss_pred HHHHHHHHHHHHHHHHCCC Q ss_conf 9875557899988752235 Q gi|254780289|r 448 MVEANLRLVISVAKKYTNR 466 (682) Q Consensus 448 l~~anlr~v~~~~~~~~~~ 466 (682) .--|||+=|.+|||+|--- T Consensus 201 vSlANlKAvY~IAk~yDIP 219 (468) T TIGR02617 201 VSLANLKAVYEIAKKYDIP 219 (468) T ss_pred HHHHHHHHHHHHHHHCCCC T ss_conf 6788889999998645998 No 406 >PRK03501 ppnK inorganic polyphosphate/ATP-NAD kinase; Provisional Probab=22.21 E-value=40 Score=12.07 Aligned_cols=32 Identities=19% Similarity=0.192 Sum_probs=23.9 Q ss_pred CCCCHHHHHHHHHHHHHCCCEEECCCCCCCCC Q ss_conf 35998889999999984797783278410000 Q gi|254780289|r 56 DEVSSEQMEDTVAMLSNMGINVVDGDDLEDEE 87 (682) Q Consensus 56 d~~~~e~ie~i~~~L~~~GI~Vve~~~~~~~~ 87 (682) +.-..|..+.++..++++|+.++|..+++|.. T Consensus 12 ~~~~~e~~~~~~~~~~~~g~~~vdd~~~aDli 43 (264) T PRK03501 12 DKELVEKVKPLKKIAEENGFTVVDDPKNANII 43 (264) T ss_pred CHHHHHHHHHHHHHHHHCCCEEECCCCCCCEE T ss_conf 87899999999999998798884898898999 No 407 >cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates. Probab=22.21 E-value=40 Score=12.07 Aligned_cols=23 Identities=26% Similarity=0.271 Sum_probs=18.8 Q ss_pred CHHHHHHHCCCCHHHHHHHHHHH Q ss_conf 97899987099989999999860 Q gi|254780289|r 548 TPEEIAKKLAMPVEGVRKVLKIT 570 (682) Q Consensus 548 ~~~~~a~~~~~~~~~~~~~~~~~ 570 (682) |+.|+|+.+|+|+..++---+.. T Consensus 2 tIgelA~~~gvs~~tlRyYe~~G 24 (113) T cd01109 2 TIKEVAEKTGLSADTLRYYEKEG 24 (113) T ss_pred CHHHHHHHHCCCHHHHHHHHHCC T ss_conf 78899999895999999999838 No 408 >pfam01418 HTH_6 Helix-turn-helix domain, rpiR family. This domain contains a helix-turn-helix motif. The best characterized member of this family is RpiR, a regulator of the expression of rpiB gene. Probab=22.15 E-value=40 Score=12.06 Aligned_cols=18 Identities=22% Similarity=0.268 Sum_probs=7.2 Q ss_pred CHHHHHHHCCCCHHHHHH Q ss_conf 978999870999899999 Q gi|254780289|r 548 TPEEIAKKLAMPVEGVRK 565 (682) Q Consensus 548 ~~~~~a~~~~~~~~~~~~ 565 (682) |..+||+..|+|..-|.+ T Consensus 36 si~~lA~~~~vS~atv~R 53 (106) T pfam01418 36 SIAELAKAAGVSEASVVR 53 (106) T ss_pred CHHHHHHHHCCCHHHHHH T ss_conf 399999896998999999 No 409 >pfam07455 Psu Phage polarity suppression protein (Psu). This family contains a number of phage polarity suppression proteins (Psu) (approximately 190 residues long). The Psu protein of bacteriophage P4 causes suppression of transcriptional polarity in Escherichia coli by overcoming Rho termination factor activity. Probab=22.05 E-value=38 Score=12.27 Aligned_cols=73 Identities=14% Similarity=0.193 Sum_probs=35.3 Q ss_pred HHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCC-------HHHHHHHHHHHCCC Q ss_conf 89899999999972287046142058898999999999877608899978999870999-------89999999860898 Q gi|254780289|r 501 MWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP-------VEGVRKVLKITKEP 573 (682) Q Consensus 501 ~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~-------~~~~~~~~~~~~~~ 573 (682) -|=|-|+-.|+|.-| |.+..++ +....+.|.|.+|-+-+..---+.||++ ..-+...+.+.++. T Consensus 60 kWeiNqaAgryI~SH--------e~vq~is-ir~~L~~FMQ~hG~~L~aaLAPeLmg~~~q~~~~~~~aldra~~yLReA 130 (188) T pfam07455 60 KWEINQAAGRYIRSH--------EEVQHIS-IRDRLNDFMQQHGAELAAALAPELMGYSEQTAAVKRCAMQRSVDYLREA 130 (188) T ss_pred HHHHHHHHHHHHHHH--------HHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHH T ss_conf 999847888887889--------9999999-9999999999827999997659970853250888876789999999999 Q ss_pred CCCCCCCCC Q ss_conf 755363588 Q gi|254780289|r 574 ISLETPIGD 582 (682) Q Consensus 574 ~sl~~~~~~ 582 (682) +|.-..+|+ T Consensus 131 L~~~la~g~ 139 (188) T pfam07455 131 LSVWLAAGE 139 (188) T ss_pred HHHHHHHCC T ss_conf 999997178 No 410 >pfam04433 SWIRM SWIRM domain. This SWIRM domain is a small alpha-helical domain of about 85 amino acid residues found in chromosomal proteins. It contains a helix-turn helix motif and binds to DNA. Probab=22.04 E-value=40 Score=12.04 Aligned_cols=33 Identities=15% Similarity=0.286 Sum_probs=18.5 Q ss_pred HCCCCCHHHHHHHCCCCCCCHHHHHHHHHHHHHCCC Q ss_conf 848867899975268435998889999999984797 Q gi|254780289|r 40 QRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGI 75 (682) Q Consensus 40 e~GylTydeIn~~LP~d~~~~e~ie~i~~~L~~~GI 75 (682) ..+|||..+.-..++. +...+-.|+.+|+..|+ T Consensus 49 p~~~Lt~t~~r~~~~~---D~~~i~ri~~FL~~~G~ 81 (84) T pfam04433 49 PGKYLTKTDARRLLKG---DVNKVSRVHDFLERWGL 81 (84) T ss_pred CCEEEEHHHHHHHHCC---CHHHHHHHHHHHHHCCC T ss_conf 8704649999998458---89999999999998083 No 411 >PRK10014 DNA-binding transcriptional repressor MalI; Provisional Probab=22.03 E-value=40 Score=12.04 Aligned_cols=19 Identities=11% Similarity=-0.081 Sum_probs=6.9 Q ss_pred HHHHHHHHHHCCCCCCCEE Q ss_conf 6799998874385457312 Q gi|254780289|r 478 NIGLMKAAEKFDWCLGYKF 496 (682) Q Consensus 478 ~~~l~~a~~~~~~~~g~~f 496 (682) |..-++.+-+|=..+|+|= T Consensus 166 ~~~~~~~a~~~L~~~Ghr~ 184 (342) T PRK10014 166 NMQAAQLLTEHLIRNGHQR 184 (342) T ss_pred HHHHHHHHHHHHHHCCCCE T ss_conf 6999999999998759986 No 412 >pfam04492 Phage_rep_O Bacteriophage replication protein O. Replication protein O is necessary for the initiation of bacteriophage DNA replication. Protein O interacts with the lambda replication origin, and also with replication protein P to form an oligomer. It is speculated that the N-terminal half interacts with the replication origin while the C terminal half mediates protein-protein interaction. Probab=21.93 E-value=40 Score=12.03 Aligned_cols=40 Identities=28% Similarity=0.409 Sum_probs=28.9 Q ss_pred HCCCHHHHHHH----HHHHCCCCCCC-CCHHHHHHHHCCCHHHHH Q ss_conf 32998899999----99818798674-688999899667899999 Q gi|254780289|r 618 ASLTPREERVL----RMRFGIGMNTD-HTLEEVGKQFCVTRERIR 657 (682) Q Consensus 618 ~~l~~re~~v~----~~r~g~~~~~~-~tl~e~~~~~~~~~er~r 657 (682) ..|+.||..|+ |+-||.+-..+ -|..+++..-|+++-.|. T Consensus 28 ~~lt~rq~kv~~aV~RkTyG~nK~~d~I~~sqi~~mtgi~~~~Vs 72 (100) T pfam04492 28 ADLSGRQLKVLLAVIRKTYGWNKPMDRVTNEQIAELTGLSRTHVS 72 (100) T ss_pred CCCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCHHHHH T ss_conf 888788999999999986077850336229999999788854599 No 413 >pfam08765 Mor Mor transcription activator family. Mor (Middle operon regulator) is a sequence specific DNA binding protein. It mediates transcription activation through its interactions with the C-terminal domains of the alpha and sigma subunits of bacterial RNA polymerase. The N terminal region of Mor is the dimerization region, and the C terminal contains a helix-turn-helix motif which binds DNA. Probab=21.91 E-value=40 Score=12.03 Aligned_cols=41 Identities=20% Similarity=0.332 Sum_probs=29.2 Q ss_pred CHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC Q ss_conf 988999999981879867468899989966789999999999999832 Q gi|254780289|r 621 TPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668 (682) Q Consensus 621 ~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l~ 668 (682) +.|...|..-.- | ....|++..||+|--+|++|=.+ .+|+. T Consensus 59 ~~Rd~~I~~eFn----G--~N~~eLArkY~ls~~~i~~ii~~-~rk~~ 99 (107) T pfam08765 59 ALRDLEIYNEFN----G--NNHAELARKYGVSEQWIYKIIKR-VRKLE 99 (107) T ss_pred HHHHHHHHHHHC----C--CCHHHHHHHHCCCHHHHHHHHHH-HHHHH T ss_conf 999999999807----9--87999999969889999999999-99999 No 414 >smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli Probab=21.82 E-value=40 Score=12.01 Aligned_cols=37 Identities=24% Similarity=0.166 Sum_probs=26.5 Q ss_pred HHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHH Q ss_conf 99999987760889997899987099989999999860 Q gi|254780289|r 533 VRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT 570 (682) Q Consensus 533 ~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~ 570 (682) .+.--..+|+.||. +..+||+.+|+|...|+.-++.. T Consensus 5 D~~Il~~L~~n~R~-s~~~iA~~lg~S~~tv~~Ri~~L 41 (108) T smart00344 5 DRKILEELQKDARI-SLAELAKKVGLSPSTVHNRVKRL 41 (108) T ss_pred HHHHHHHHHHCCCC-CHHHHHHHHCCCHHHHHHHHHHH T ss_conf 99999999982899-99999999893999999999999 No 415 >cd02844 PAZ_CAF_like PAZ domain, CAF_like subfamily. CAF (for carpel factory) is a plant homolog of Dicer. CAF has been implicated in flower morphogenesis and in early Arabidopsis development and might function through posttranscriptional regulation of specific mRNA molecules. PAZ domains are named after the proteins Piwi, Argonaut, and Zwille. PAZ is found in two families of proteins that are essential components of RNA-mediated gene-silencing pathways, including RNA interference, the Piwi and Dicer families. PAZ functions as a nucleic-acid binding domain, with a strong preference for single-stranded nucleic acids (RNA or DNA) or RNA duplexes with single-stranded 3' overhangs. It has been suggested that the PAZ domain provides a unique mode for the recognition of the two 3'-terminal nucleotides in single-stranded nucleic acids and buries the 3' OH group, and that it might recognize characteristic 3' overhangs in siRNAs within RISC (RNA-induced silencing) and other complexes. Probab=21.32 E-value=41 Score=11.94 Aligned_cols=24 Identities=25% Similarity=0.450 Sum_probs=19.3 Q ss_pred HHHHHHCCCCCCCEEEHHHHHHHH Q ss_conf 998874385457312010289899 Q gi|254780289|r 482 MKAAEKFDWCLGYKFSTYAMWWVK 505 (682) Q Consensus 482 ~~a~~~~~~~~g~~f~tya~~~i~ 505 (682) |-|-..|+.+.|.+|+||+.++-. T Consensus 53 ln~~S~f~~~~g~~~~SY~eYykk 76 (135) T cd02844 53 LNANSSFPGKEGLGYATYAEYFKE 76 (135) T ss_pred CCCCCCCCCCCCCCCCCHHHHHHH T ss_conf 898886876578771439999999 No 416 >PRK12429 3-hydroxybutyrate dehydrogenase; Provisional Probab=21.31 E-value=41 Score=11.94 Aligned_cols=106 Identities=21% Similarity=0.099 Sum_probs=50.9 Q ss_pred HHHHHHHHHHH---HHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHH-HHCCC Q ss_conf 24689998755---578999887522356777887544367999988743854573120102898999999999-72287 Q gi|254780289|r 442 SIAKKEMVEAN---LRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSI-ADQSC 517 (682) Q Consensus 442 ~~AK~~l~~an---lr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~-~~~~~ 517 (682) +.+-..|.+.+ .-.+.|++-.....|...-----.|..||.|+.-+---.+|.|.-+-+-=||.-.+.+.. .+.+. T Consensus 121 ~~~~p~m~~~~~G~Iv~isS~~~~~~~~~~~~Y~asKaal~~lt~~lA~e~~~~gIrvN~V~PG~i~T~~~~~~~~~~~~ 200 (258) T PRK12429 121 KAALPHMKAQKWGRIINMASVHGLVGSAGKAAYVSAKHGLIGLTKVVALEGATHGVTVNAICPGYVDTPLVRKQIPDLAK 200 (258) T ss_pred HHHHHHHHHCCCCEEEEECCHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCEEEEEEEECCCCCCCHHHHHHHHHH T ss_conf 67777664359928999877554668999758999999999999999998532097999997487987102213367897 Q ss_pred EEECCCHHHHHHHHHHHHHHHHH---HHCCCCCCHHHHHHHC Q ss_conf 04614205889899999999987---7608899978999870 Q gi|254780289|r 518 TIRIPVHMRDKIHKVVRTARRMS---NKIKREPTPEEIAKKL 556 (682) Q Consensus 518 ~~r~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~a~~~ 556 (682) .-.++. ....++.. .-+||-.+|+|+|... T Consensus 201 ~~~~~~---------~~~~~~~~~~~~P~~R~g~p~dia~~v 233 (258) T PRK12429 201 ERGISE---------EEVLEDVLLPLVPQKRFTTVEEIADLA 233 (258) T ss_pred HCCCCH---------HHHHHHHHHHCCCCCCCCCHHHHHHHH T ss_conf 739997---------999999997279989984999999999 No 417 >TIGR00370 TIGR00370 conserved hypothetical protein TIGR00370; InterPro: IPR010016 This is an uncharacterised family of proteins of unknown function.. Probab=21.06 E-value=38 Score=12.19 Aligned_cols=23 Identities=26% Similarity=0.313 Sum_probs=14.9 Q ss_pred CCCHHHHHHHHCCCHHHHHHHHH Q ss_conf 46889998996678999999999 Q gi|254780289|r 639 DHTLEEVGKQFCVTRERIRQIEA 661 (682) Q Consensus 639 ~~tl~e~~~~~~~~~er~rqi~~ 661 (682) ..-|++|++.-++|-|+|=||++ T Consensus 105 GpDL~~VAk~~qlspe~vi~~Hs 127 (217) T TIGR00370 105 GPDLEEVAKFNQLSPEEVIDLHS 127 (217) T ss_pred CCCHHHHHHHHCCCHHHEEEECC T ss_conf 98989999771788457344047 No 418 >PRK07740 hypothetical protein; Provisional Probab=21.06 E-value=25 Score=13.72 Aligned_cols=14 Identities=21% Similarity=0.245 Sum_probs=6.0 Q ss_pred CCHHHHHHHHCCCH Q ss_conf 68899989966789 Q gi|254780289|r 640 HTLEEVGKQFCVTR 653 (682) Q Consensus 640 ~tl~e~~~~~~~~~ 653 (682) ++|+.+...||++- T Consensus 185 ~sL~~l~~~fgI~~ 198 (240) T PRK07740 185 PTLDDALACYGITC 198 (240) T ss_pred CCHHHHHHHCCCCC T ss_conf 78999999769999 No 419 >COG0411 LivG ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism] Probab=21.05 E-value=23 Score=14.00 Aligned_cols=60 Identities=18% Similarity=0.381 Sum_probs=39.4 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHH Q ss_conf 222211268899999987653321124689998755578999887522356777887544367 Q gi|254780289|r 417 SVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479 (682) Q Consensus 417 e~~~gl~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~ 479 (682) |--.||+..|-.++...|......... -==|||+++.+|..++.+-. .+.+-..|.+|.- T Consensus 175 EPaAGln~~e~~~l~~~i~~i~~~~g~-tillIEHdM~~Vm~l~dri~--Vl~~G~~IAeG~P 234 (250) T COG0411 175 EPAAGLNPEETEELAELIRELRDRGGV-TILLIEHDMKLVMGLADRIV--VLNYGEVIAEGTP 234 (250) T ss_pred CCCCCCCHHHHHHHHHHHHHHHHCCCC-EEEEEEECCHHHHHHCCEEE--ECCCCCCCCCCCH T ss_conf 765798989999999999998854896-89999742078862266999--5018838441898 No 420 >TIGR02104 pulA_typeI pullulanase, type I; InterPro: IPR011840 Pullulan is an unusual, industrially important polysaccharide in which short alpha-1,4 chains (maltotriose) are connected in alpha-1,6 linkages. Enzymes that cleave alpha-1,6 linkages in pullulan and release maltotriose are called pullulanases although pullulan itself may not be the natural substrate. This family consists of pullulanases related to the entries in IPR011838 from INTERPRO and IPR011839 from INTERPRO but having a different domain architecture with shorter sequences. Members are called type I pullulanases .. Probab=21.02 E-value=42 Score=11.89 Aligned_cols=20 Identities=20% Similarity=0.189 Sum_probs=11.7 Q ss_pred HHHHHHCCCEEECCCCCCCC Q ss_conf 99998479778327841000 Q gi|254780289|r 67 VAMLSNMGINVVDGDDLEDE 86 (682) Q Consensus 67 ~~~L~~~GI~Vve~~~~~~~ 86 (682) ++.|.+|||.=|+=.|..|- T Consensus 188 l~y~keLGVTHVqLLP~fDf 207 (655) T TIGR02104 188 LDYLKELGVTHVQLLPVFDF 207 (655) T ss_pred HHHHHHCCCCEEEECCCCCC T ss_conf 35554336535654341122 No 421 >PRK02234 recU Holliday junction-specific endonuclease; Reviewed Probab=20.99 E-value=42 Score=11.89 Aligned_cols=16 Identities=44% Similarity=0.692 Sum_probs=5.9 Q ss_pred HCCCCCCHHHHHHHHH Q ss_conf 2235677788754436 Q gi|254780289|r 463 YTNRGLQFLDLIQEGN 478 (682) Q Consensus 463 ~~~~~~~~~~~~~~~~ 478 (682) |.|||+.|.++|.+.| T Consensus 25 y~nRGM~LE~~IN~tN 40 (199) T PRK02234 25 YANRGMSLEKDINETN 40 (199) T ss_pred CCCCCCHHHHHHHHHH T ss_conf 2446605999999999 No 422 >COG4809 Archaeal ADP-dependent phosphofructokinase/glucokinase [Carbohydrate transport and metabolism] Probab=20.99 E-value=33 Score=12.71 Aligned_cols=116 Identities=16% Similarity=0.239 Sum_probs=50.5 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCC Q ss_conf 33332222211268899999987653321124689998755578999887522356777887544367999988743854 Q gi|254780289|r 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWC 491 (682) Q Consensus 412 kL~~ie~~~gl~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~ 491 (682) .+..+...+||+..|+..+..-+- +++ +|++....+ ...|+| .|+|+-.++|+.. T Consensus 288 ~il~~v~SvGldE~ElA~vl~vlG--~~e------------------La~~I~~~~-~~~avi----eg~~~L~~e~~~e 342 (466) T COG4809 288 NILSIVYSVGLDEVELANVLNVLG--YRE------------------LADRIISKD-DIEAVI----EGAMILLDELGLE 342 (466) T ss_pred HHHHHHHHCCCCHHHHHHHHHHHC--HHH------------------HHHHHHCCC-CHHHHH----HHHHHHHHHCCCC T ss_conf 998664404878999999998607--699------------------987664134-388999----9999999863950 Q ss_pred CCCEEEHHHHHHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHH Q ss_conf 57312010289899999999972287046142058898999999999877608899978999870999899 Q gi|254780289|r 492 LGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEG 562 (682) Q Consensus 492 ~g~~f~tya~~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~ 562 (682) |=+ |-||..+. +|++ +++. . -.-|..+.+.+-. ..-.-...+|+--.+.++-+-|.+|... T Consensus 343 ~i~-vHT~~y~l---~i~~--~~np--l-~~Ee~~daL~Fs~-~lAa~~A~~GnIe~~~d~~~glkvp~~~ 403 (466) T COG4809 343 RIH-VHTYGYYL---AITK--RGNP--L-SGEELRDALLFST-LLAAAKAMLGNIERLDDLKEGLKVPISE 403 (466) T ss_pred EEE-EEEEEEEE---EEEC--CCCC--C-CHHHHHHHHHHHH-HHHHHHHHCCCCCCHHHHHHHCCCCCHH T ss_conf 899-98755788---8864--8995--4-3899999888888-9999998607866635677650488102 No 423 >COG1904 UxaC Glucuronate isomerase [Carbohydrate transport and metabolism] Probab=20.92 E-value=42 Score=11.88 Aligned_cols=95 Identities=14% Similarity=0.155 Sum_probs=56.2 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHH---HHHHHHHHHHHHHHHCCCCCCCEEE Q ss_conf 1126889999998765332112468999875557899988752235677788---7544367999988743854573120 Q gi|254780289|r 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLD---LIQEGNIGLMKAAEKFDWCLGYKFS 497 (682) Q Consensus 421 gl~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~---~~~~~~~~l~~a~~~~~~~~g~~f~ 497 (682) .++..+...|..+...|+.-. ....++-+|++ .+-+||.|..+|+-++= -...-|. ++..||-+..||--+ T Consensus 244 ~~~~~~a~~if~k~l~G~~lt-~~E~~~f~a~~--l~~l~km~~~~gwVmQiH~ga~RN~n~---~~~~k~G~D~GfDi~ 317 (463) T COG1904 244 ELSEADADAIFDKRLAGEALS-TEEAEQFKAAM--LTELAKMSAEDGWVMQIHPGALRNHNP---RMFKKLGPDTGFDIP 317 (463) T ss_pred CCCHHHHHHHHHHHHCCCCCC-HHHHHHHHHHH--HHHHHHHHHHCCEEEEECCCCCCCCCH---HHHHHHCCCCCCCCC T ss_conf 578899999999986478788-89999999999--999998644168268851461036788---999973898777887 Q ss_pred HHHHHHHHHHHHHHHHHCCCEEECCC Q ss_conf 10289899999999972287046142 Q gi|254780289|r 498 TYAMWWVKQAITRSIADQSCTIRIPV 523 (682) Q Consensus 498 tya~~~i~~~i~~~~~~~~~~~r~~~ 523 (682) +=-- |-.+.++.+....-.=++|+ T Consensus 318 ~~~~--~a~~L~~LLd~~~~~~~L~k 341 (463) T COG1904 318 NDTE--IAEGLKPLLDAFGEDNDLPK 341 (463) T ss_pred CCCH--HHHHHHHHHHHHCCCCCCCE T ss_conf 8404--67889999875402578754 No 424 >pfam11503 DUF3215 Protein of unknown function (DUF3215). This family of proteins with unknown function appears to be restricted to Saccharomycetaceae. Probab=20.90 E-value=26 Score=13.50 Aligned_cols=44 Identities=20% Similarity=0.353 Sum_probs=34.7 Q ss_pred HHCCCCCHHHHHHHCCCCCCCHHHHHHHHHH----HHHCCCEEECCCC Q ss_conf 7848867899975268435998889999999----9847977832784 Q gi|254780289|r 39 RQRGYVTIEELNAFLPPDEVSSEQMEDTVAM----LSNMGINVVDGDD 82 (682) Q Consensus 39 ke~GylTydeIn~~LP~d~~~~e~ie~i~~~----L~~~GI~Vve~~~ 82 (682) +--|-||||+=|..+-......+.+++|+.. |.+.|..|++... T Consensus 9 ~aiGtlaFDen~nlv~stGigk~rveDI~~lS~~eld~eG~~v~~d~~ 56 (77) T pfam11503 9 RAVGTLAFDENYNVVDSTGVGKSRIEDIIRLSNAELDREGYAVYQDAQ 56 (77) T ss_pred CCEEEEEECCCCCEEEECCCCHHHHHHHHHHHHHHHCCCCEEEEECCC T ss_conf 632589984899899702432566777887756443665337985696 No 425 >COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription] Probab=20.85 E-value=42 Score=11.87 Aligned_cols=34 Identities=32% Similarity=0.308 Sum_probs=26.0 Q ss_pred CCCCCCHHHHHHHCCCCHHHHHHHHHHHC--CCCCCC Q ss_conf 08899978999870999899999998608--987553 Q gi|254780289|r 543 IKREPTPEEIAKKLAMPVEGVRKVLKITK--EPISLE 577 (682) Q Consensus 543 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~--~~~sl~ 577 (682) .| +-|.++||+.+|+....|+.+|.... ..++.. T Consensus 30 kg-e~tDeela~~l~i~~~~vrriL~~L~e~~li~~~ 65 (176) T COG1675 30 KG-ELTDEELAELLGIKKNEVRRILYALYEDGLISYR 65 (176) T ss_pred CC-CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEE T ss_conf 27-7674899888676399999999999857926888 No 426 >cd05133 RasGAP_IQGAP1 IQGAP1 is a homodimeric protein that is widely expressed among vertebrate cell types from early embryogenesis. Mammalian IQGAP1 protein is the best characterized member of the IQGAP family, and contains several protein-interacting domains. Human IQGAP1 is most similar to mouse Iqgap1 (94% identity) and has 62% identity to human IQGAP2. IQGAP1 binds and cross-links actin filaments in vitro and has been implicated in Ca2+/calmodulin signaling, E-cadherin-dependent cell adhesion, cell motility, and invasion. Yeast IQGAP homologues have a role in the recruitment of actin filaments, are components of the spindle pole body, and are required for actomyosin ring assembly and cytokinesis. Furthermore, IQGAP1 over-expression has also been detected in gastric and colorectal carcinomas and gastric cancer cell lines. Probab=20.71 E-value=42 Score=11.85 Aligned_cols=43 Identities=14% Similarity=0.312 Sum_probs=25.3 Q ss_pred HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCHHHHHHH Q ss_conf 99999988999999987282389999999987311710367876 Q gi|254780289|r 142 IAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREII 185 (682) Q Consensus 142 IAKRIE~G~~~i~~al~~~P~ti~~il~~~e~i~~ge~~LrdII 185 (682) +...|+.....+...+-..|..++.+..++. -..|..-|++++ T Consensus 18 l~~Ei~s~~~~~~d~lr~N~~~~km~~~y~R-~~~g~~~Lk~iL 60 (360) T cd05133 18 LQEEIKSKVDQIQEIVTGNPTVIKMVVSFNR-GARGQNALRQIL 60 (360) T ss_pred HHHHHHHCCCCHHHHHHCCCHHHHHHHHHHC-CCCCHHHHHHHH T ss_conf 9999986037899997458099999999854-875359999999 No 427 >PRK09706 transcriptional repressor DicA; Reviewed Probab=20.55 E-value=43 Score=11.82 Aligned_cols=24 Identities=8% Similarity=0.126 Sum_probs=14.8 Q ss_pred CCCCHHHHHHHCCCCHHHHHHHHH Q ss_conf 899978999870999899999998 Q gi|254780289|r 545 REPTPEEIAKKLAMPVEGVRKVLK 568 (682) Q Consensus 545 ~~~~~~~~a~~~~~~~~~~~~~~~ 568 (682) +.-|-.++|+.+|++..-|...-+ T Consensus 17 ~glTQ~eLA~~~Gvs~~tVs~wE~ 40 (135) T PRK09706 17 LKLSQRALAKAVGVSHVSISQWER 40 (135) T ss_pred CCCCHHHHHHHHCCCHHHHHHHHC T ss_conf 599999999996988999999982 No 428 >pfam06970 RepA_N Replication initiator protein A (RepA) N-terminus. This of family of predicted proteins represents the N-terminus (approximately 80 residues) of replication initiator protein A (RepA), a DNA replication initiator in plasmids. Most proteins in this family are bacterial, but archaeal and eukaryotic members are also included. Probab=20.53 E-value=43 Score=11.82 Aligned_cols=19 Identities=32% Similarity=0.342 Sum_probs=7.5 Q ss_pred CHHHHHHHCCCCHHHHHHH Q ss_conf 9789998709998999999 Q gi|254780289|r 548 TPEEIAKKLAMPVEGVRKV 566 (682) Q Consensus 548 ~~~~~a~~~~~~~~~~~~~ 566 (682) |.+|+++.|+++..+|.++ T Consensus 54 t~~el~~~L~~s~~~v~k~ 72 (76) T pfam06970 54 TNEELMELLNCSKQKVIKI 72 (76) T ss_pred EHHHHHHHHCCCHHHHHHH T ss_conf 4999999978788899999 No 429 >TIGR01752 flav_long flavodoxin; InterPro: IPR010086 Flavodoxins are small redox-active proteins with a flavin mononucleotide (FMN) prosthetic group. They function as electron transfer agents in a variety of microbial metabolic processes, including nitrogen fixation by nitrogenase , sulphite reduction , and light-dependent NADP+ reduction during photosynthesis . This entry describes the long chain type, typical for nitrogen fixation but associated with pyruvate formate-lyase activation and cobalamin-dependent methionine synthase activity in Escherichia coli .; GO: 0010181 FMN binding, 0006118 electron transport. Probab=20.52 E-value=39 Score=12.11 Aligned_cols=19 Identities=37% Similarity=0.351 Sum_probs=9.8 Q ss_pred HHHHHHCC-CCHHHHHHHHH Q ss_conf 89998709-99899999998 Q gi|254780289|r 550 EEIAKKLA-MPVEGVRKVLK 568 (682) Q Consensus 550 ~~~a~~~~-~~~~~~~~~~~ 568 (682) +.|+..|| -+..+|..+-+ T Consensus 18 e~I~~~lG~~~~~d~~ni~~ 37 (176) T TIGR01752 18 EKIAKELGKESDVDVFNIAK 37 (176) T ss_pred HHHHHHHCCCCCCCCCCCCC T ss_conf 99999818886621013231 No 430 >KOG1389 consensus Probab=20.40 E-value=43 Score=11.80 Aligned_cols=25 Identities=32% Similarity=0.563 Sum_probs=14.0 Q ss_pred HHCCCCHHHHHHHHHHHCCCCCCCCCCCC Q ss_conf 87099989999999860898755363588 Q gi|254780289|r 554 KKLAMPVEGVRKVLKITKEPISLETPIGD 582 (682) Q Consensus 554 ~~~~~~~~~~~~~~~~~~~~~sl~~~~~~ 582 (682) +.|+++.+|| ....-.+-|-.|+|- T Consensus 358 ~KL~ld~ekV----N~~GGaiAlGHPlGa 382 (435) T KOG1389 358 NKLGLDPEKV----NVNGGAIALGHPLGA 382 (435) T ss_pred HHHCCCHHHC----CCCCCEEECCCCCCC T ss_conf 8738988884----888862330687577 No 431 >TIGR00624 tag DNA-3-methyladenine glycosylase I; InterPro: IPR004597 One common form of damage to DNA occurs when alkyl groups become covalently linked to DNA, leading to the formation of mutagenic or toxic lesions. Alkylating agents are ubiquitous in the environment and can also exist endogenously; for example S-adenosylmethionine, a commonly used methyl donor in many cellualr pathways, can produce methylation damage. Given the prevalence of alkylating agents it is not surprising that all cellular organisms studied so far have developed repair systems to deal with DNA alkylation . DNA-3-methyladenine glycosylase I (also known as TagI) is part of the broader helix-hairpin-helix DNA repair glycosylase supefamily. It specifically catalyses the release of 3-methylated adenine and, to a lesser extent, guanosine bases from DNA by hydrolysis of the deoxyribose N-glycosidic bond , . A phylogenomic study suggests that TagI evolved in, and is specific to, the bacteria .; GO: 0008725 DNA-3-methyladenine glycosylase I activity, 0006284 base-excision repair. Probab=20.33 E-value=43 Score=11.79 Aligned_cols=31 Identities=19% Similarity=0.253 Sum_probs=18.9 Q ss_pred HHHHHHHHHHHHHHCCCCCCCEEE-HHHHHHHHHHH Q ss_conf 544367999988743854573120-10289899999 Q gi|254780289|r 474 IQEGNIGLMKAAEKFDWCLGYKFS-TYAMWWVKQAI 508 (682) Q Consensus 474 ~~~~~~~l~~a~~~~~~~~g~~f~-tya~~~i~~~i 508 (682) +.-....|-|+.. +|||||. |=-.|-..||. T Consensus 141 ~t~ea~Amsk~LK----krGF~FVGpTicYalMQA~ 172 (185) T TIGR00624 141 ITSEAKAMSKELK----KRGFRFVGPTICYALMQAT 172 (185) T ss_pred CCHHHHHHHHHHH----HCCCCCCCHHHHHHHHHHH T ss_conf 6767899999987----5688300168999988641 No 432 >TIGR02881 spore_V_K stage V sporulation protein K; InterPro: IPR014232 Proteins in this entry include the stage V sporulation protein K (SpoVK), a close homologue of the Rubisco expression protein CbbX (IPR000470 from INTERPRO), and are members of an ATPase family associated with various cellular activities. These proteins are strictly limited to bacterial endospore-forming species, but are not found universally among members of this group; they are missing from the Clostridium species.. Probab=20.06 E-value=44 Score=11.75 Aligned_cols=55 Identities=24% Similarity=0.359 Sum_probs=40.9 Q ss_pred CCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHH------CCCEEECCCHHHHH Q ss_conf 77788754436799998874385457312010289899999999972------28704614205889 Q gi|254780289|r 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIAD------QSCTIRIPVHMRDK 528 (682) Q Consensus 468 ~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i~~~~~~------~~~~~r~~~~~~~~ 528 (682) +.|.|---+ -||.=+.+|=-.|-|+||.-|.|-+|+-+.+.-.. |+|.|| .|+|. T Consensus 173 i~FPdY~~e---eL~~Ia~~m~~~ReY~Lt~~A~~~lr~~l~~~~~~~~~~~sNaR~vR---N~iE~ 233 (261) T TIGR02881 173 IDFPDYTVE---ELMEIAERMVKEREYKLTEEAKWKLREHLAKVDQLSSREFSNARYVR---NIIEK 233 (261) T ss_pred EECCCCCHH---HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHH---HHHHH T ss_conf 418899888---99999999986464225788999999997412444210057620124---28899 No 433 >cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates. Probab=20.00 E-value=44 Score=11.74 Aligned_cols=23 Identities=22% Similarity=0.245 Sum_probs=15.9 Q ss_pred CHHHHHHHCCCCHHHHHHHHHHH Q ss_conf 97899987099989999999860 Q gi|254780289|r 548 TPEEIAKKLAMPVEGVRKVLKIT 570 (682) Q Consensus 548 ~~~~~a~~~~~~~~~~~~~~~~~ 570 (682) |+.|+|+.+|+|+..++.--+.. T Consensus 2 ~Ige~A~~~gvs~~tlR~Ye~~G 24 (123) T cd04770 2 KIGELAKAAGVSPDTIRYYERIG 24 (123) T ss_pred CHHHHHHHHCCCHHHHHHHHHCC T ss_conf 68999999895999999999818 Done!