Query gi|254780693|ref|YP_003065106.1| transcriptional regulator protein [Candidatus Liberibacter asiaticus str. psy62] Match_columns 235 No_of_seqs 120 out of 7465 Neff 9.5 Searched_HMMs 39220 Date Mon May 30 02:40:04 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780693.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 PRK13870 transcriptional regul 100.0 3.1E-36 7.8E-41 277.5 25.2 215 12-234 16-234 (234) 2 PRK10188 DNA-binding transcrip 100.0 1.1E-35 2.9E-40 273.5 23.0 219 8-234 17-240 (240) 3 TIGR03541 reg_near_HchA LuxR f 100.0 1.2E-34 3.1E-39 266.1 25.3 222 7-234 10-232 (232) 4 TIGR03020 EpsA transcriptional 99.9 2.6E-19 6.7E-24 156.8 19.6 214 9-230 17-247 (247) 5 PRK04841 transcriptional regul 99.8 7.7E-19 2E-23 153.5 8.5 60 172-231 837-896 (903) 6 PRK09483 response regulator; P 99.8 5.8E-18 1.5E-22 147.2 9.7 66 169-234 144-209 (216) 7 PRK09935 transcriptional regul 99.7 1.8E-17 4.5E-22 143.8 9.6 63 172-234 148-210 (210) 8 PRK10100 DNA-binding transcrip 99.7 2.9E-17 7.3E-22 142.3 10.4 62 170-231 152-213 (216) 9 PRK10840 transcriptional regul 99.7 4.6E-17 1.2E-21 140.8 10.6 64 171-234 148-211 (216) 10 PRK10651 transcriptional regul 99.7 5.7E-17 1.5E-21 140.1 10.7 63 171-233 153-215 (216) 11 PRK09390 fixJ response regulat 99.7 3.4E-17 8.7E-22 141.7 8.7 63 172-234 140-202 (202) 12 COG2197 CitB Response regulato 99.7 3.7E-17 9.5E-22 141.4 8.8 63 172-234 147-209 (211) 13 PRK09958 DNA-binding transcrip 99.7 1.1E-16 2.9E-21 138.0 10.5 63 171-233 141-203 (204) 14 PRK10403 transcriptional regul 99.7 1.1E-16 2.7E-21 138.2 9.0 62 170-231 150-211 (215) 15 PRK10360 DNA-binding transcrip 99.7 2.1E-16 5.4E-21 136.1 9.0 62 171-233 135-196 (196) 16 COG2909 MalT ATP-dependent tra 99.7 6.4E-17 1.6E-21 139.8 6.1 62 173-234 831-892 (894) 17 pfam00196 GerE Bacterial regul 99.6 4.2E-15 1.1E-19 126.8 7.5 57 172-228 2-58 (58) 18 cd06170 LuxR_C_like C-terminal 99.6 1.1E-14 2.9E-19 123.7 7.9 57 174-230 1-57 (57) 19 smart00421 HTH_LUXR helix_turn 99.5 3.2E-14 8.1E-19 120.6 7.3 57 172-228 2-58 (58) 20 PRK11475 DNA-binding transcrip 99.5 2.7E-13 6.9E-18 114.0 10.8 62 170-231 131-192 (205) 21 COG4566 TtrR Response regulato 99.4 2.4E-12 6.2E-17 107.1 8.8 63 171-233 140-202 (202) 22 COG2771 CsgD DNA-binding HTH d 99.4 2.4E-12 6E-17 107.2 8.4 63 172-234 3-65 (65) 23 pfam03472 Autoind_bind Autoind 99.3 2.6E-10 6.7E-15 92.7 15.4 129 13-147 1-129 (146) 24 TIGR02985 Sig70_bacteroi1 RNA 98.5 3.7E-07 9.5E-12 70.2 5.8 46 172-217 118-164 (167) 25 PRK06930 positive control sigm 98.2 3.2E-06 8.2E-11 63.5 5.7 46 173-218 114-160 (170) 26 pfam07638 Sigma70_ECF ECF sigm 98.2 5.4E-06 1.4E-10 61.9 6.2 45 173-217 135-180 (185) 27 PRK12523 RNA polymerase sigma 98.2 5.6E-06 1.4E-10 61.8 6.3 45 172-216 118-163 (172) 28 TIGR02937 sigma70-ECF RNA poly 98.1 8.4E-06 2.1E-10 60.5 6.1 45 173-217 114-159 (162) 29 PRK08295 RNA polymerase factor 98.1 4.6E-05 1.2E-09 55.3 9.6 45 173-217 155-199 (209) 30 PRK12527 RNA polymerase sigma 98.1 1E-05 2.6E-10 59.9 6.2 46 173-218 105-151 (159) 31 PRK07037 extracytoplasmic-func 98.1 1E-05 2.6E-10 59.9 6.1 45 172-216 122-167 (183) 32 PRK12525 RNA polymerase sigma 98.1 1.2E-05 3E-10 59.5 6.2 44 173-216 118-162 (168) 33 PRK09646 RNA polymerase sigma 98.0 1.1E-05 2.7E-10 59.8 5.8 45 172-216 141-186 (194) 34 PRK09637 RNA polymerase sigma 98.0 1.6E-05 4.2E-10 58.5 6.2 46 172-217 105-151 (181) 35 PRK11922 RNA polymerase sigma 98.0 1.6E-05 4.1E-10 58.5 6.2 44 173-216 149-193 (231) 36 PRK13919 putative RNA polymera 98.0 2E-05 5.1E-10 57.9 6.3 45 173-217 136-181 (187) 37 PRK09645 RNA polymerase sigma 98.0 1.9E-05 4.9E-10 58.0 6.2 46 172-217 115-161 (171) 38 PRK09047 RNA polymerase factor 98.0 1.8E-05 4.7E-10 58.1 6.0 45 173-217 106-151 (161) 39 PRK12519 RNA polymerase sigma 98.0 2E-05 5E-10 57.9 5.9 46 172-217 140-186 (194) 40 PRK09651 RNA polymerase sigma 98.0 2.2E-05 5.7E-10 57.5 6.2 45 172-216 118-163 (172) 41 PRK09652 RNA polymerase sigma 98.0 2.1E-05 5.5E-10 57.6 6.0 45 173-217 137-182 (192) 42 PRK09638 RNA polymerase sigma 97.9 2.5E-05 6.4E-10 57.2 6.2 46 172-217 126-172 (177) 43 PRK09639 RNA polymerase sigma 97.9 2.3E-05 5.9E-10 57.4 6.0 45 173-217 112-156 (166) 44 PRK12515 RNA polymerase sigma 97.9 3.8E-05 9.7E-10 55.9 7.0 57 173-233 131-188 (189) 45 PRK12526 RNA polymerase sigma 97.9 2.8E-05 7.2E-10 56.8 6.3 45 173-217 153-198 (206) 46 PRK05602 RNA polymerase sigma 97.9 2.6E-05 6.7E-10 57.0 6.1 46 172-217 127-173 (186) 47 PRK12524 RNA polymerase sigma 97.9 2.7E-05 6.8E-10 56.9 6.1 46 172-217 135-181 (196) 48 PRK12537 RNA polymerase sigma 97.9 2.6E-05 6.7E-10 57.0 6.0 45 173-217 135-180 (184) 49 pfam08281 Sigma70_r4_2 Sigma-7 97.9 2.3E-05 5.8E-10 57.4 5.7 45 172-216 9-54 (54) 50 PRK12516 RNA polymerase sigma 97.9 3E-05 7.6E-10 56.6 6.1 45 173-217 119-164 (190) 51 PRK12529 RNA polymerase sigma 97.9 3.1E-05 8E-10 56.5 6.2 44 172-215 126-170 (178) 52 PRK12512 RNA polymerase sigma 97.9 3.2E-05 8.2E-10 56.4 6.2 46 173-218 131-177 (184) 53 PRK12541 RNA polymerase sigma 97.9 3.3E-05 8.5E-10 56.3 6.2 45 173-217 112-157 (161) 54 PRK12543 RNA polymerase sigma 97.9 3.6E-05 9.1E-10 56.1 6.3 44 173-216 129-173 (190) 55 PRK12514 RNA polymerase sigma 97.9 3.3E-05 8.4E-10 56.3 6.0 45 173-217 129-174 (179) 56 cd06171 Sigma70_r4 Sigma70, re 97.9 3.7E-05 9.4E-10 55.9 6.2 46 172-217 9-55 (55) 57 PRK09641 RNA polymerase sigma 97.9 3.9E-05 1E-09 55.8 6.0 45 173-217 136-181 (187) 58 PRK09643 RNA polymerase sigma 97.9 4.4E-05 1.1E-09 55.4 6.2 45 173-217 131-176 (197) 59 PRK12547 RNA polymerase sigma 97.9 4.5E-05 1.1E-09 55.3 6.2 45 173-217 112-157 (164) 60 PRK12528 RNA polymerase sigma 97.8 4.7E-05 1.2E-09 55.2 6.2 45 172-216 118-163 (167) 61 PRK12534 RNA polymerase sigma 97.8 4.8E-05 1.2E-09 55.1 6.2 45 173-217 137-182 (187) 62 PRK12538 RNA polymerase sigma 97.8 4.8E-05 1.2E-09 55.1 6.2 45 173-217 171-216 (233) 63 PRK12517 RNA polymerase sigma 97.8 5.7E-05 1.5E-09 54.6 6.3 45 173-217 128-173 (188) 64 PRK12513 RNA polymerase sigma 97.8 5.7E-05 1.5E-09 54.6 6.2 45 173-217 139-184 (194) 65 PRK12542 RNA polymerase sigma 97.8 5.4E-05 1.4E-09 54.8 6.1 44 173-216 122-166 (185) 66 PRK11924 RNA polymerase sigma 97.8 5.5E-05 1.4E-09 54.7 6.1 45 173-217 125-170 (180) 67 PRK09648 RNA polymerase sigma 97.8 6E-05 1.5E-09 54.4 6.3 46 172-217 136-182 (187) 68 PRK11923 algU RNA polymerase s 97.8 6E-05 1.5E-09 54.4 6.3 45 173-217 138-183 (193) 69 PRK09647 RNA polymerase sigma 97.8 6.1E-05 1.6E-09 54.4 6.2 46 172-217 156-202 (222) 70 PRK12531 RNA polymerase sigma 97.8 6.6E-05 1.7E-09 54.2 6.2 46 172-217 140-186 (194) 71 PRK06811 RNA polymerase factor 97.8 7.2E-05 1.8E-09 53.9 6.3 45 172-216 127-172 (185) 72 PRK12539 RNA polymerase sigma 97.8 7.9E-05 2E-09 53.6 6.2 46 172-217 130-176 (184) 73 PRK12533 RNA polymerase sigma 97.8 8E-05 2E-09 53.6 6.2 45 173-217 137-182 (217) 74 PRK12522 RNA polymerase sigma 97.8 8.5E-05 2.2E-09 53.4 6.3 45 173-217 119-164 (173) 75 PRK09644 RNA polymerase sigma 97.8 7.3E-05 1.9E-09 53.8 5.9 45 173-217 108-153 (165) 76 PRK12520 RNA polymerase sigma 97.7 7.8E-05 2E-09 53.6 5.9 45 173-217 131-176 (191) 77 PRK12536 RNA polymerase sigma 97.7 9.4E-05 2.4E-09 53.1 6.3 45 173-217 126-171 (178) 78 PRK12546 RNA polymerase sigma 97.7 9.1E-05 2.3E-09 53.1 6.2 45 173-217 113-158 (188) 79 PRK12511 RNA polymerase sigma 97.7 3.6E-05 9.1E-10 56.0 4.0 45 173-217 111-156 (182) 80 PRK12518 RNA polymerase sigma 97.7 9.8E-05 2.5E-09 52.9 6.2 45 173-217 120-165 (175) 81 PRK09640 RNA polymerase sigma 97.7 0.00012 2.9E-09 52.4 6.2 45 173-217 134-179 (188) 82 PRK12540 RNA polymerase sigma 97.7 0.00011 2.9E-09 52.4 6.2 45 173-217 111-156 (181) 83 PRK09415 RNA polymerase factor 97.7 0.00012 3.1E-09 52.3 6.3 45 173-217 127-172 (177) 84 PRK06759 RNA polymerase factor 97.7 0.00013 3.3E-09 52.0 6.4 45 173-217 106-151 (154) 85 PRK09642 RNA polymerase sigma 97.7 0.00014 3.6E-09 51.8 6.2 45 173-217 106-151 (160) 86 PRK12535 RNA polymerase sigma 97.6 0.00014 3.7E-09 51.7 6.1 45 173-217 132-177 (195) 87 PRK12532 RNA polymerase sigma 97.6 0.00018 4.6E-09 51.0 6.2 45 173-217 136-181 (195) 88 PRK09649 RNA polymerase sigma 97.6 0.00019 4.8E-09 50.9 6.3 46 173-218 130-176 (185) 89 PRK12544 RNA polymerase sigma 97.6 0.00018 4.6E-09 51.0 6.1 45 173-217 149-194 (207) 90 PRK12530 RNA polymerase sigma 97.6 0.00025 6.5E-09 50.0 6.3 45 173-217 136-181 (191) 91 COG3413 Predicted DNA binding 97.6 0.0009 2.3E-08 46.1 9.1 45 172-216 154-206 (215) 92 COG1595 RpoE DNA-directed RNA 97.5 0.00028 7.1E-09 49.7 6.1 45 173-217 127-172 (182) 93 pfam04545 Sigma70_r4 Sigma-70, 97.4 0.0003 7.7E-09 49.4 5.6 46 172-217 3-49 (50) 94 pfam04967 HTH_10 HTH DNA bindi 97.4 0.00064 1.6E-08 47.1 6.3 43 174-216 1-51 (53) 95 PRK12545 RNA polymerase sigma 97.2 0.0057 1.4E-07 40.4 10.1 45 173-217 139-184 (201) 96 PRK09636 RNA polymerase sigma 97.2 0.0042 1.1E-07 41.3 9.0 49 172-220 110-159 (289) 97 PRK13558 bacterio-opsin activa 97.1 0.00088 2.2E-08 46.1 5.2 44 173-216 616-667 (674) 98 TIGR02983 SigE-fam_strep RNA p 97.1 0.00046 1.2E-08 48.2 3.7 45 173-218 113-159 (165) 99 PRK08583 RNA polymerase sigma 97.1 0.0015 3.8E-08 44.5 6.0 46 172-217 204-250 (257) 100 PRK07408 RNA polymerase sigma 97.0 0.0019 5E-08 43.7 6.1 46 172-217 202-248 (256) 101 TIGR02999 Sig-70_X6 RNA polyme 97.0 0.0015 3.9E-08 44.4 5.5 46 173-218 145-191 (194) 102 PRK07670 RNA polymerase sigma 97.0 0.0084 2.1E-07 39.2 8.9 45 173-217 197-242 (250) 103 PRK07122 RNA polymerase sigma 97.0 0.0025 6.3E-08 42.9 6.0 45 173-217 214-259 (263) 104 PRK12427 flagellar biosynthesi 96.9 0.0022 5.7E-08 43.2 5.7 47 172-218 180-227 (229) 105 TIGR01884 cas_HTH CRISPR locus 96.8 0.003 7.7E-08 42.3 5.7 47 169-215 162-211 (231) 106 PRK08215 sporulation sigma fac 96.8 0.0037 9.4E-08 41.7 6.0 45 173-217 209-254 (257) 107 TIGR02952 Sig70_famx2 RNA poly 96.8 0.0066 1.7E-07 39.9 7.2 45 173-217 123-168 (171) 108 PRK05572 sporulation sigma fac 96.8 0.0038 9.8E-08 41.6 6.0 45 173-217 201-246 (251) 109 PRK07500 rpoH2 RNA polymerase 96.8 0.018 4.5E-07 36.8 9.1 45 173-217 227-274 (289) 110 PRK06288 RNA polymerase sigma 96.7 0.0041 1E-07 41.4 5.7 45 173-217 208-253 (261) 111 PRK08301 sporulation sigma fac 96.7 0.0041 1E-07 41.4 5.7 45 172-216 182-231 (239) 112 PRK05803 sporulation sigma fac 96.7 0.0048 1.2E-07 40.9 5.7 46 172-217 173-223 (228) 113 PRK06596 RNA polymerase factor 96.7 0.027 6.8E-07 35.6 9.5 45 173-217 230-277 (284) 114 PRK09635 sigI RNA polymerase s 96.7 0.024 6.2E-07 35.9 9.2 48 173-220 118-166 (290) 115 PRK06986 fliA flagellar biosyn 96.7 0.0058 1.5E-07 40.3 6.0 45 173-217 183-228 (234) 116 PRK10336 DNA-binding transcrip 96.6 0.0048 1.2E-07 40.9 5.1 48 172-219 148-204 (219) 117 PRK03975 tfx putative transcri 96.6 0.0034 8.8E-08 41.9 4.4 56 173-228 4-59 (139) 118 PRK08241 RNA polymerase factor 96.6 0.017 4.3E-07 37.0 7.9 46 173-218 156-202 (341) 119 PRK05911 RNA polymerase sigma 96.4 0.008 2E-07 39.3 5.5 46 172-217 204-250 (257) 120 PRK12423 LexA repressor; Provi 96.3 0.0064 1.6E-07 40.0 4.6 43 173-215 3-53 (202) 121 PRK00215 LexA repressor; Valid 96.3 0.0084 2.1E-07 39.2 5.2 42 174-215 2-51 (204) 122 PRK05949 RNA polymerase sigma 96.3 0.054 1.4E-06 33.4 9.4 47 173-219 266-317 (327) 123 PRK05657 RNA polymerase sigma 96.3 0.048 1.2E-06 33.8 9.0 48 173-220 265-317 (328) 124 pfam01726 LexA_DNA_bind LexA D 96.3 0.0098 2.5E-07 38.7 5.4 44 172-215 2-53 (65) 125 pfam02001 DUF134 Protein of un 96.3 0.012 3E-07 38.1 5.8 45 172-216 35-80 (100) 126 PRK07921 RNA polymerase sigma 96.2 0.091 2.3E-06 31.8 10.0 51 173-223 258-313 (320) 127 PRK13413 mpi multiple promoter 96.1 0.017 4.4E-07 36.9 5.8 41 174-214 158-198 (200) 128 PRK05901 RNA polymerase sigma 96.1 0.024 6.1E-07 35.9 6.4 52 173-224 335-391 (398) 129 PRK09210 RNA polymerase sigma 96.0 0.11 2.9E-06 31.1 9.7 52 173-224 306-362 (368) 130 PRK07598 RNA polymerase sigma 96.0 0.031 8E-07 35.1 6.8 53 173-225 345-402 (410) 131 PRK07406 RNA polymerase sigma 95.9 0.034 8.6E-07 34.8 6.7 54 172-225 322-380 (385) 132 COG1191 FliA DNA-directed RNA 95.9 0.023 5.8E-07 36.1 5.7 45 173-217 196-241 (247) 133 PRK04217 hypothetical protein; 95.8 0.027 6.8E-07 35.5 5.7 45 172-216 41-86 (110) 134 PRK07405 RNA polymerase sigma 95.8 0.028 7E-07 35.5 5.8 47 172-218 256-307 (318) 135 pfam09862 DUF2089 Protein of u 95.7 0.091 2.3E-06 31.8 8.2 64 171-234 31-103 (113) 136 TIGR02984 Sig-70_plancto1 RNA 95.7 0.12 3.1E-06 30.9 8.7 45 173-217 141-186 (190) 137 PRK10710 DNA-binding transcrip 95.6 0.028 7.2E-07 35.4 5.3 48 172-219 159-215 (240) 138 TIGR02997 Sig70-cyanoRpoD RNA 95.5 0.12 3.1E-06 30.8 8.3 44 173-216 287-335 (336) 139 pfam08279 HTH_11 HTH domain. T 95.5 0.035 8.8E-07 34.8 5.3 41 177-218 1-44 (55) 140 COG0856 Orotate phosphoribosyl 95.2 0.033 8.5E-07 34.9 4.4 41 180-220 10-50 (203) 141 cd00090 HTH_ARSR Arsenical Res 95.2 0.059 1.5E-06 33.1 5.7 41 174-214 4-46 (78) 142 TIGR02954 Sig70_famx3 RNA poly 95.1 0.015 3.7E-07 37.4 2.4 37 181-218 132-168 (173) 143 COG1342 Predicted DNA-binding 95.1 0.056 1.4E-06 33.2 5.4 46 171-216 31-77 (99) 144 TIGR02479 FliA_WhiG RNA polyme 95.0 0.065 1.7E-06 32.8 5.4 47 172-218 177-224 (227) 145 PRK00118 putative DNA-binding 94.9 0.099 2.5E-06 31.5 6.1 45 173-217 17-62 (105) 146 PRK13719 conjugal transfer tra 94.7 0.04 1E-06 34.3 3.8 60 175-234 147-206 (220) 147 pfam04297 UPF0122 Putative hel 94.7 0.11 2.8E-06 31.2 6.0 44 173-216 17-61 (101) 148 TIGR02980 SigBFG RNA polymeras 94.6 0.022 5.7E-07 36.1 2.3 45 173-217 180-225 (229) 149 COG0568 RpoD DNA-directed RNA 94.6 0.099 2.5E-06 31.5 5.5 50 174-223 280-335 (342) 150 cd00569 HTH_Hin_like Helix-tur 94.5 0.063 1.6E-06 32.9 4.4 38 172-209 4-42 (42) 151 TIGR02989 Sig-70_gvs1 RNA poly 94.4 0.1 2.6E-06 31.4 5.4 45 173-217 115-160 (163) 152 cd00383 trans_reg_C Effector d 94.4 0.093 2.4E-06 31.7 5.1 49 172-220 22-79 (95) 153 TIGR02960 SigX5 RNA polymerase 94.4 0.087 2.2E-06 31.9 4.8 47 173-219 143-190 (329) 154 TIGR02959 SigZ RNA polymerase 94.3 0.079 2E-06 32.2 4.5 44 173-216 100-144 (170) 155 COG3415 Transposase and inacti 94.2 0.11 2.7E-06 31.3 5.0 41 174-214 7-47 (138) 156 PRK10766 DNA-binding transcrip 94.2 0.14 3.6E-06 30.4 5.6 46 173-218 162-216 (224) 157 pfam00486 Trans_reg_C Transcri 94.2 0.12 2.9E-06 31.0 5.1 48 172-219 4-60 (77) 158 COG3355 Predicted transcriptio 94.1 0.16 4.2E-06 29.9 5.9 43 173-215 24-69 (126) 159 PRK09468 ompR osmolarity respo 94.1 0.11 2.8E-06 31.1 5.0 47 173-219 161-216 (239) 160 COG1710 Uncharacterized protei 94.1 0.09 2.3E-06 31.8 4.5 42 174-215 94-136 (139) 161 TIGR02859 spore_sigH RNA polym 94.0 0.16 4.1E-06 30.0 5.6 90 118-217 105-194 (198) 162 COG1318 Predicted transcriptio 93.9 0.035 8.9E-07 34.7 2.1 37 181-217 54-90 (182) 163 pfam02796 HTH_7 Helix-turn-hel 93.8 0.12 3.2E-06 30.8 4.7 39 172-210 4-43 (45) 164 smart00862 Trans_reg_C Transcr 93.7 0.15 3.9E-06 30.2 5.1 48 172-219 4-61 (78) 165 PRK09836 DNA-binding transcrip 93.7 0.15 3.7E-06 30.3 4.9 48 173-220 150-206 (226) 166 PRK11517 transcriptional regul 93.7 0.15 3.9E-06 30.2 5.0 47 173-219 147-202 (223) 167 PRK10701 DNA-binding transcrip 93.7 0.13 3.4E-06 30.6 4.7 47 173-219 161-216 (240) 168 PRK06704 RNA polymerase factor 93.6 0.15 3.8E-06 30.2 4.9 58 173-230 116-185 (228) 169 pfam03444 DUF293 Domain of unk 93.6 0.13 3.2E-06 30.7 4.5 45 173-218 1-52 (79) 170 PRK10643 DNA-binding transcrip 93.6 0.17 4.4E-06 29.8 5.2 47 172-218 148-203 (222) 171 PRK10955 DNA-binding transcrip 93.5 0.15 3.8E-06 30.2 4.7 47 173-219 156-211 (232) 172 smart00344 HTH_ASNC helix_turn 93.4 0.22 5.6E-06 29.1 5.4 48 176-224 3-52 (108) 173 COG2390 DeoR Transcriptional r 93.3 0.11 2.9E-06 31.1 3.9 37 198-234 261-303 (321) 174 PRK11083 DNA-binding response 93.3 0.2 5.2E-06 29.3 5.2 48 173-220 155-211 (229) 175 COG5625 Predicted transcriptio 93.1 0.094 2.4E-06 31.7 3.2 43 173-215 18-63 (113) 176 TIGR02941 Sigma_B RNA polymera 93.1 0.12 3.1E-06 30.9 3.7 45 173-217 206-251 (256) 177 PRK02277 orotate phosphoribosy 93.0 0.099 2.5E-06 31.5 3.2 30 182-211 12-41 (201) 178 PRK10161 transcriptional regul 93.0 0.23 5.7E-06 29.0 5.0 47 173-219 154-209 (229) 179 TIGR03001 Sig-70_gmx1 RNA poly 92.9 0.2 5.1E-06 29.3 4.6 56 172-227 165-221 (249) 180 PRK09191 two-component respons 92.8 0.3 7.6E-06 28.1 5.4 46 173-218 88-134 (261) 181 CHL00148 orf27 Ycf27; Reviewed 92.8 0.25 6.3E-06 28.7 5.0 47 173-219 161-218 (240) 182 PRK11557 putative DNA-binding 92.8 0.33 8.4E-06 27.8 5.6 19 20-38 50-68 (282) 183 COG0745 OmpR Response regulato 92.7 0.21 5.3E-06 29.2 4.5 48 173-220 153-209 (229) 184 TIGR02846 spore_sigmaK RNA pol 92.7 0.17 4.2E-06 29.9 4.0 45 173-217 175-224 (228) 185 TIGR00721 tfx DNA-binding prot 92.6 0.23 5.9E-06 28.8 4.7 46 172-217 5-50 (142) 186 pfam01978 TrmB Sugar-specific 92.5 0.46 1.2E-05 26.7 6.0 44 172-215 4-49 (68) 187 PRK11886 biotin--protein ligas 92.5 0.34 8.6E-06 27.7 5.3 37 4-40 17-54 (319) 188 pfam01371 Trp_repressor Trp re 92.4 0.22 5.5E-06 29.1 4.3 38 173-210 26-71 (88) 189 COG1356 tfx Transcriptional re 92.4 0.082 2.1E-06 32.1 2.1 52 171-222 6-57 (143) 190 COG3398 Uncharacterized protei 92.4 0.27 6.9E-06 28.4 4.7 35 179-213 177-213 (240) 191 PRK10816 DNA-binding transcrip 92.3 0.2 5E-06 29.4 3.9 47 173-219 149-204 (223) 192 pfam03811 Ins_element1 Inserti 92.2 0.19 4.8E-06 29.5 3.7 36 177-212 52-87 (88) 193 PRK11337 DNA-binding transcrip 92.0 0.47 1.2E-05 26.7 5.6 18 20-37 63-80 (293) 194 COG1737 RpiR Transcriptional r 92.0 0.45 1.1E-05 26.8 5.4 19 20-38 52-70 (281) 195 PRK10529 DNA-binding transcrip 91.9 0.34 8.6E-06 27.7 4.7 47 173-219 151-206 (225) 196 pfam01022 HTH_5 Bacterial regu 91.9 0.55 1.4E-05 26.2 5.8 38 177-214 3-41 (47) 197 smart00347 HTH_MARR helix_turn 91.6 0.55 1.4E-05 26.2 5.5 45 171-215 5-51 (101) 198 COG1522 Lrp Transcriptional re 91.3 0.68 1.7E-05 25.5 5.8 43 172-214 4-48 (154) 199 pfam01047 MarR MarR family. Th 91.1 0.69 1.8E-05 25.5 5.7 42 174-215 1-44 (59) 200 COG3877 Uncharacterized protei 91.0 0.56 1.4E-05 26.1 5.2 51 169-219 37-88 (122) 201 TIGR02957 SigX4 RNA polymerase 90.6 1.3 3.4E-05 23.5 8.7 48 173-220 109-158 (287) 202 PRK11179 DNA-binding transcrip 90.6 0.99 2.5E-05 24.4 6.0 40 174-213 7-48 (153) 203 COG2865 Predicted transcriptio 90.5 0.53 1.4E-05 26.3 4.6 42 173-214 399-442 (467) 204 PRK11173 two-component respons 90.4 0.59 1.5E-05 26.0 4.8 48 173-220 160-216 (237) 205 TIGR02233 Myxo_sigma_rel Myxoc 90.4 0.53 1.4E-05 26.3 4.5 56 172-227 23-79 (106) 206 COG2522 Predicted transcriptio 90.3 0.54 1.4E-05 26.3 4.5 35 177-211 11-45 (119) 207 pfam03965 Pencillinase_R Penic 90.2 0.78 2E-05 25.1 5.2 13 173-185 100-112 (115) 208 pfam08461 HTH_12 Ribonuclease 90.0 0.56 1.4E-05 26.2 4.4 34 180-213 2-43 (66) 209 pfam00126 HTH_1 Bacterial regu 89.9 0.97 2.5E-05 24.4 5.6 43 177-219 2-44 (60) 210 PRK05658 RNA polymerase sigma 89.7 1.6 4E-05 23.0 10.3 52 173-224 557-613 (620) 211 PRK11242 DNA-binding transcrip 89.6 1.1 2.8E-05 24.1 5.6 19 13-31 28-46 (292) 212 PRK11074 putative DNA-binding 89.5 1.4 3.5E-05 23.3 6.1 14 17-30 33-46 (300) 213 PRK13856 two-component respons 89.5 0.31 7.9E-06 28.0 2.8 48 172-219 154-210 (241) 214 pfam01418 HTH_6 Helix-turn-hel 89.2 1.1 2.8E-05 24.0 5.4 49 172-224 12-66 (106) 215 COG1654 BirA Biotin operon rep 89.0 0.86 2.2E-05 24.8 4.7 39 175-214 5-45 (79) 216 PRK12683 transcriptional regul 88.7 1.6 4.1E-05 22.9 6.0 26 173-198 279-304 (308) 217 smart00418 HTH_ARSR helix_turn 88.7 0.88 2.3E-05 24.7 4.6 34 181-214 2-36 (66) 218 COG1846 MarR Transcriptional r 88.6 1.2 3.1E-05 23.8 5.3 42 174-215 20-63 (126) 219 COG5484 Uncharacterized conser 88.6 0.79 2E-05 25.1 4.3 19 172-190 152-170 (279) 220 pfam09339 HTH_IclR IclR helix- 88.3 1.5 3.9E-05 23.0 5.6 38 177-214 4-44 (52) 221 PRK12679 cbl transcriptional r 88.2 2 5E-05 22.3 6.2 25 174-198 280-304 (316) 222 TIGR02702 SufR_cyano iron-sulf 88.2 0.67 1.7E-05 25.6 3.7 28 185-212 11-39 (215) 223 COG1321 TroR Mn-dependent tran 87.9 1.4 3.5E-05 23.3 5.2 39 174-212 4-48 (154) 224 CHL00180 rbcR LysR transcripti 87.9 1.9 4.8E-05 22.4 5.9 19 13-31 32-50 (307) 225 PRK03573 transcriptional regul 87.7 2.1 5.4E-05 22.0 8.3 44 172-215 27-73 (144) 226 PRK11302 DNA-binding transcrip 87.5 1.7 4.4E-05 22.6 5.5 21 19-39 49-69 (284) 227 PRK10341 DNA-binding transcrip 87.5 1.8 4.7E-05 22.5 5.7 17 15-31 36-52 (312) 228 pfam06056 Terminase_5 Putative 87.2 0.94 2.4E-05 24.5 4.0 31 181-211 6-36 (58) 229 PRK12684 transcriptional regul 87.1 2.2 5.7E-05 21.8 5.9 25 174-198 280-304 (313) 230 cd04762 HTH_MerR-trunc Helix-T 87.1 0.61 1.6E-05 25.9 3.0 23 189-211 1-23 (49) 231 PRK11139 DNA-binding transcrip 86.5 2.4 6.2E-05 21.6 5.9 12 18-29 38-49 (295) 232 PRK10046 dpiA two-component re 86.4 1.1 2.7E-05 24.1 4.0 38 177-214 166-203 (225) 233 pfam11268 DUF3071 Protein of u 86.1 1.9 4.9E-05 22.4 5.1 42 170-213 52-93 (169) 234 PRK11013 DNA-binding transcrip 86.1 2.5 6.5E-05 21.5 6.0 17 15-31 33-49 (309) 235 TIGR02950 SigM_subfam RNA poly 86.0 0.72 1.8E-05 25.3 2.9 45 174-218 114-159 (162) 236 pfam07750 GcrA GcrA cell cycle 86.0 0.83 2.1E-05 24.9 3.2 19 120-140 120-138 (162) 237 PRK09801 transcriptional activ 86.0 2.6 6.6E-05 21.4 6.1 13 174-186 281-293 (310) 238 pfam07900 DUF1670 Protein of u 85.9 1.4 3.6E-05 23.3 4.4 30 180-209 189-218 (220) 239 COG1497 Predicted transcriptio 85.8 1.6 4.2E-05 22.8 4.6 15 198-212 231-245 (260) 240 PRK11151 DNA-binding transcrip 85.7 2.7 6.8E-05 21.3 5.9 17 15-31 30-46 (305) 241 pfam01527 Transposase_8 Transp 85.6 1.7 4.4E-05 22.7 4.7 38 180-217 14-52 (75) 242 PRK01381 Trp operon repressor; 85.3 0.99 2.5E-05 24.4 3.3 35 173-207 32-74 (99) 243 PRK09791 putative DNA-binding 85.2 2.8 7.1E-05 21.2 6.1 18 14-31 33-50 (302) 244 smart00346 HTH_ICLR helix_turn 84.9 2.9 7.3E-05 21.1 5.9 57 176-232 5-69 (91) 245 COG2739 Uncharacterized protei 84.9 2.5 6.3E-05 21.5 5.2 44 173-216 17-61 (105) 246 pfam07374 DUF1492 Protein of u 84.8 1.5 3.9E-05 23.0 4.1 42 176-217 58-100 (100) 247 PRK12680 transcriptional regul 84.4 3 7.7E-05 20.9 5.8 19 13-31 29-47 (327) 248 COG4565 CitB Response regulato 84.2 2 5E-05 22.2 4.5 41 173-213 154-198 (224) 249 PRK11169 leucine-responsive tr 84.2 1.5 3.9E-05 23.0 3.9 39 174-212 12-52 (164) 250 TIGR03298 argP transcriptional 84.2 3.1 7.8E-05 20.9 5.7 19 13-31 28-46 (292) 251 smart00419 HTH_CRP helix_turn_ 84.0 1.5 3.7E-05 23.2 3.7 26 189-214 9-34 (48) 252 COG2964 Uncharacterized protei 83.8 1.2 3.1E-05 23.8 3.2 38 176-213 174-216 (220) 253 PRK10141 DNA-binding transcrip 83.4 2.9 7.5E-05 21.0 5.1 38 177-214 15-54 (106) 254 smart00550 Zalpha Z-DNA-bindin 83.3 2.8 7.3E-05 21.1 5.0 42 178-219 8-53 (68) 255 PRK10430 DNA-binding transcrip 83.3 1.8 4.6E-05 22.5 3.9 42 173-214 158-204 (239) 256 PRK13348 chromosome replicatio 82.9 3.4 8.8E-05 20.5 6.1 20 13-32 29-48 (294) 257 PRK11233 nitrogen assimilation 82.2 3.6 9.3E-05 20.3 6.0 12 19-30 34-45 (305) 258 PRK03635 chromosome replicatio 82.1 3.7 9.4E-05 20.3 6.1 19 13-31 29-47 (295) 259 PRK04172 pheS phenylalanyl-tRN 82.1 3.7 9.4E-05 20.3 5.5 14 187-200 449-462 (501) 260 PRK09834 DNA-binding transcrip 82.1 3.7 9.4E-05 20.3 5.4 29 116-144 206-234 (264) 261 smart00354 HTH_LACI helix_turn 82.0 0.93 2.4E-05 24.6 2.1 44 190-234 2-45 (70) 262 PRK09906 DNA-binding transcrip 81.9 3.7 9.5E-05 20.3 5.5 18 14-31 29-46 (296) 263 COG0583 LysR Transcriptional r 81.9 3.8 9.6E-05 20.3 5.9 11 178-188 222-232 (297) 264 pfam01710 Transposase_14 Trans 81.7 3.3 8.4E-05 20.7 4.8 24 188-211 71-94 (120) 265 PRK10163 DNA-binding transcrip 81.7 3.8 9.7E-05 20.2 5.9 27 116-142 216-243 (271) 266 pfam10668 Phage_terminase Phag 81.6 1 2.7E-05 24.2 2.2 21 188-208 22-42 (60) 267 PRK00423 tfb transcription ini 81.5 3.8 9.8E-05 20.2 5.1 39 181-219 269-307 (310) 268 PRK10086 DNA-binding transcrip 81.5 3.9 9.9E-05 20.2 5.8 17 15-31 43-59 (311) 269 pfam04218 CENP-B_N CENP-B N-te 81.4 3.3 8.4E-05 20.6 4.7 43 173-215 6-49 (53) 270 pfam00376 MerR MerR family reg 81.1 1.7 4.3E-05 22.7 3.1 22 190-211 1-22 (38) 271 smart00420 HTH_DEOR helix_turn 81.0 3 7.7E-05 20.9 4.4 39 177-215 1-41 (53) 272 PRK11512 DNA-binding transcrip 80.9 4 0.0001 20.0 6.8 43 173-215 37-81 (144) 273 pfam00356 LacI Bacterial regul 80.8 1.2 3E-05 23.8 2.2 44 190-234 1-44 (46) 274 PRK03601 transcriptional regul 80.3 4.2 0.00011 19.9 5.7 18 14-31 29-46 (275) 275 PRK10082 putative DNA-binding 79.9 4.3 0.00011 19.8 5.6 16 16-31 41-56 (303) 276 COG2524 Predicted transcriptio 79.9 2.2 5.6E-05 21.9 3.4 29 179-207 221-249 (294) 277 PRK13509 transcriptional repre 79.8 4.4 0.00011 19.8 4.9 12 13-24 32-43 (251) 278 COG3711 BglG Transcriptional a 79.8 2.8 7.1E-05 21.2 3.9 28 189-216 101-128 (491) 279 PRK10632 putative DNA-binding 79.3 4.5 0.00012 19.7 5.8 14 174-187 277-290 (309) 280 pfam01325 Fe_dep_repress Iron 79.3 2 5.1E-05 22.2 3.0 26 189-214 21-46 (58) 281 PRK12681 cysB transcriptional 79.2 4.6 0.00012 19.6 5.8 27 174-200 280-306 (324) 282 PRK10411 DNA-binding transcrip 78.9 4.6 0.00012 19.6 4.8 13 13-25 31-43 (240) 283 PRK10837 putative DNA-binding 78.6 4.7 0.00012 19.5 6.3 20 13-32 30-49 (291) 284 TIGR01764 excise DNA binding d 78.3 1.9 4.9E-05 22.3 2.7 23 189-211 2-24 (49) 285 PRK12682 transcriptional regul 77.9 5 0.00013 19.4 6.0 18 174-191 280-297 (309) 286 cd00092 HTH_CRP helix_turn_hel 77.6 3.5 8.8E-05 20.5 3.8 28 187-214 24-51 (67) 287 COG1349 GlpR Transcriptional r 77.4 4.6 0.00012 19.6 4.4 11 11-21 19-29 (253) 288 cd04768 HTH_BmrR-like Helix-Tu 77.1 2.4 6.2E-05 21.6 2.9 29 181-209 50-78 (96) 289 pfam00440 TetR_N Bacterial reg 77.1 1.6 4.1E-05 22.9 2.0 27 186-212 14-40 (47) 290 cd04769 HTH_MerR2 Helix-Turn-H 76.6 2.6 6.5E-05 21.4 2.9 12 187-198 55-66 (116) 291 PRK00876 nadE NAD synthetase; 76.4 5.4 0.00014 19.1 5.3 46 174-219 263-309 (325) 292 pfam08220 HTH_DeoR DeoR-like h 76.3 5 0.00013 19.4 4.4 38 177-214 1-40 (57) 293 PRK11569 transcriptional repre 75.9 5.6 0.00014 19.0 5.7 26 116-141 221-247 (274) 294 pfam05043 Mga Mga helix-turn-h 75.5 5.2 0.00013 19.2 4.3 32 186-217 28-59 (87) 295 cd04761 HTH_MerR-SF Helix-Turn 75.5 2.8 7.1E-05 21.2 2.9 23 189-211 1-23 (49) 296 smart00422 HTH_MERR helix_turn 75.4 2.9 7.3E-05 21.1 2.9 15 185-199 54-68 (70) 297 pfam00325 Crp Bacterial regula 75.3 3.5 9E-05 20.4 3.4 27 189-215 3-29 (32) 298 cd01107 HTH_BmrR Helix-Turn-He 75.2 2.9 7.4E-05 21.0 2.9 17 183-199 53-69 (108) 299 TIGR02393 RpoD_Cterm RNA polym 75.1 5.8 0.00015 18.9 8.8 85 130-224 144-234 (240) 300 cd04787 HTH_HMRTR_unk Helix-Tu 74.9 3 7.7E-05 20.9 2.9 14 205-218 84-97 (133) 301 cd04776 HTH_GnyR Helix-Turn-He 74.9 3 7.6E-05 21.0 2.9 15 186-200 53-67 (118) 302 cd04774 HTH_YfmP Helix-Turn-He 74.8 3 7.6E-05 20.9 2.9 43 174-216 38-85 (96) 303 cd04781 HTH_MerR-like_sg6 Heli 74.7 3 7.6E-05 21.0 2.8 31 186-216 54-90 (120) 304 COG0789 SoxR Predicted transcr 74.7 3.1 7.8E-05 20.9 2.9 15 186-200 55-69 (124) 305 cd04764 HTH_MlrA-like_sg1 Heli 74.3 3.1 7.9E-05 20.8 2.9 26 174-199 38-67 (67) 306 TIGR02835 spore_sigmaE RNA pol 74.0 4.6 0.00012 19.6 3.7 46 172-217 177-227 (234) 307 PRK09430 djlA Dna-J like membr 73.9 6.2 0.00016 18.7 4.9 17 171-187 142-158 (269) 308 cd04789 HTH_Cfa Helix-Turn-Hel 73.8 3.2 8.3E-05 20.7 2.9 33 183-215 52-86 (102) 309 cd04770 HTH_HMRTR Helix-Turn-H 73.8 3.3 8.5E-05 20.6 2.9 37 181-217 50-96 (123) 310 COG2512 Predicted membrane-ass 73.7 6.3 0.00016 18.6 5.7 44 171-214 190-236 (258) 311 cd01106 HTH_TipAL-Mta Helix-Tu 73.6 3.4 8.7E-05 20.6 2.9 41 174-214 39-83 (103) 312 COG3682 Predicted transcriptio 73.4 6.4 0.00016 18.6 5.2 14 173-186 103-116 (123) 313 PRK04140 hypothetical protein; 73.2 3.7 9.4E-05 20.3 3.0 25 186-210 136-160 (319) 314 pfam01381 HTH_3 Helix-turn-hel 73.2 6.5 0.00017 18.6 5.0 43 186-232 7-49 (55) 315 PRK10094 DNA-binding transcrip 72.9 6.6 0.00017 18.5 6.1 18 14-31 30-47 (308) 316 cd04782 HTH_BltR Helix-Turn-He 72.8 3.7 9.3E-05 20.3 2.9 27 174-200 39-69 (97) 317 PRK10820 DNA-binding transcrip 72.5 6.7 0.00017 18.4 4.9 40 178-221 469-509 (513) 318 smart00529 HTH_DTXR Helix-turn 72.5 4 0.0001 20.0 3.1 19 193-211 4-22 (96) 319 cd04783 HTH_MerR1 Helix-Turn-H 72.4 3.7 9.5E-05 20.3 2.9 19 182-200 51-69 (126) 320 COG2973 TrpR Trp operon repres 72.4 6.2 0.00016 18.7 4.0 36 174-209 38-81 (103) 321 pfam08784 RPA_C Replication pr 72.2 6.8 0.00017 18.4 5.9 40 173-212 44-90 (103) 322 cd04766 HTH_HspR Helix-Turn-He 72.1 3.7 9.5E-05 20.3 2.8 43 174-216 39-88 (91) 323 cd04773 HTH_TioE_rpt2 Second H 72.0 3.9 1E-04 20.1 2.9 20 181-200 50-69 (108) 324 smart00530 HTH_XRE Helix-turn- 71.8 4.6 0.00012 19.6 3.2 28 185-212 7-34 (56) 325 PRK10668 DNA-binding transcrip 71.7 2.5 6.4E-05 21.5 1.9 17 19-35 15-31 (216) 326 cd01111 HTH_MerD Helix-Turn-He 71.5 4.4 0.00011 19.7 3.1 15 186-200 55-69 (107) 327 TIGR02947 SigH_actino RNA poly 71.4 7.1 0.00018 18.3 5.4 49 181-233 140-188 (193) 328 TIGR03384 betaine_BetI transcr 71.4 3 7.5E-05 21.0 2.2 14 21-34 14-27 (189) 329 cd01109 HTH_YyaN Helix-Turn-He 71.2 4.1 0.00011 19.9 2.9 27 174-200 39-69 (113) 330 COG1414 IclR Transcriptional r 71.1 7.2 0.00018 18.2 5.8 28 115-142 194-222 (246) 331 cd01108 HTH_CueR Helix-Turn-He 71.0 4.2 0.00011 19.9 2.9 18 183-200 52-69 (127) 332 PHA01976 helix-turn-helix prot 70.8 5.1 0.00013 19.3 3.3 27 183-209 10-36 (67) 333 pfam02787 CPSase_L_D3 Carbamoy 70.7 7.3 0.00019 18.2 4.9 42 173-220 58-99 (122) 334 cd04785 HTH_CadR-PbrR-like Hel 70.2 4.5 0.00011 19.7 2.9 20 181-200 50-69 (126) 335 PRK13752 putative transcriptio 70.2 4.1 0.00011 20.0 2.7 10 189-198 65-74 (144) 336 cd04775 HTH_Cfa-like Helix-Tur 70.1 4.5 0.00011 19.7 2.9 36 181-216 50-87 (102) 337 cd04763 HTH_MlrA-like Helix-Tu 69.9 4.1 0.0001 20.0 2.7 25 174-198 39-67 (68) 338 cd04780 HTH_MerR-like_sg5 Heli 69.8 5.5 0.00014 19.1 3.3 45 174-218 39-90 (95) 339 pfam08535 KorB KorB domain. Th 69.7 5.3 0.00014 19.2 3.2 24 187-210 2-25 (93) 340 COG4496 Uncharacterized protei 69.6 6.7 0.00017 18.5 3.7 40 178-221 46-85 (100) 341 cd04777 HTH_MerR-like_sg1 Heli 69.5 4.7 0.00012 19.6 2.9 21 180-200 47-67 (107) 342 PRK11161 fumarate/nitrate redu 68.8 7 0.00018 18.3 3.6 27 189-215 185-211 (235) 343 cd00592 HTH_MerR-like Helix-Tu 68.7 5 0.00013 19.3 2.9 29 174-202 38-70 (100) 344 COG1405 SUA7 Transcription ini 68.6 4.9 0.00013 19.4 2.8 34 187-220 250-283 (285) 345 pfam11662 DUF3263 Protein of u 68.6 8.1 0.00021 17.9 4.5 41 173-213 2-47 (77) 346 cd04786 HTH_MerR-like_sg7 Heli 68.3 5.2 0.00013 19.2 2.9 17 184-200 53-69 (131) 347 PHA00542 putative Cro-like pro 68.3 7 0.00018 18.3 3.6 37 173-210 17-53 (82) 348 PRK09975 DNA-binding transcrip 68.2 3.2 8.3E-05 20.7 1.8 16 20-35 16-31 (213) 349 PRK06266 transcription initiat 68.0 7.1 0.00018 18.3 3.5 13 193-205 41-53 (178) 350 cd01392 HTH_LacI Helix-turn-he 67.7 2.6 6.5E-05 21.4 1.2 41 192-233 1-41 (52) 351 PRK13824 replication initiatio 67.7 8 0.0002 17.9 3.8 33 191-227 324-356 (404) 352 cd04779 HTH_MerR-like_sg4 Heli 67.6 5.4 0.00014 19.2 2.9 11 188-198 56-66 (134) 353 cd04788 HTH_NolA-AlbR Helix-Tu 67.4 5.5 0.00014 19.1 2.9 30 174-203 39-72 (96) 354 PRK00767 transcriptional regul 67.2 4.4 0.00011 19.8 2.3 42 177-218 151-196 (197) 355 cd01282 HTH_MerR-like_sg3 Heli 66.8 5.9 0.00015 18.9 2.9 19 181-199 49-67 (112) 356 pfam04552 Sigma54_DBD Sigma-54 66.7 6.7 0.00017 18.5 3.2 28 190-221 123-155 (160) 357 cd04784 HTH_CadR-PbrR Helix-Tu 66.4 6 0.00015 18.8 2.9 34 184-217 53-96 (127) 358 PRK09514 zntR zinc-responsive 66.3 6 0.00015 18.8 2.9 11 188-198 58-68 (140) 359 TIGR03418 chol_sulf_TF putativ 66.3 9 0.00023 17.6 6.2 17 15-31 30-46 (291) 360 cd01104 HTH_MlrA-CarA Helix-Tu 66.0 6 0.00015 18.8 2.9 24 174-197 39-66 (68) 361 COG0640 ArsR Predicted transcr 65.1 9.4 0.00024 17.4 4.9 38 177-214 26-65 (110) 362 pfam00046 Homeobox Homeobox do 64.9 9.5 0.00024 17.4 5.1 44 173-216 6-55 (57) 363 cd01105 HTH_GlnR-like Helix-Tu 64.7 7.1 0.00018 18.3 3.0 27 174-200 40-70 (88) 364 KOG0489 consensus 64.6 5.8 0.00015 18.9 2.6 30 192-221 190-219 (261) 365 cd00093 HTH_XRE Helix-turn-hel 64.4 9.7 0.00025 17.3 3.9 44 185-232 9-52 (58) 366 pfam05263 DUF722 Protein of un 64.2 9.8 0.00025 17.3 5.6 44 173-216 81-127 (130) 367 COG3677 Transposase and inacti 64.0 9.8 0.00025 17.3 3.8 45 173-217 74-118 (129) 368 PRK10072 putative transcriptio 64.0 7.5 0.00019 18.1 3.0 32 178-210 37-68 (96) 369 TIGR02939 RpoE_Sigma70 RNA pol 63.4 3.8 9.7E-05 20.2 1.4 34 174-214 149-182 (192) 370 TIGR01369 CPSaseII_lrg carbamo 63.1 10 0.00026 17.2 3.8 43 176-218 489-534 (1089) 371 PRK11477 carbohydrate diacid t 63.0 10 0.00026 17.1 5.0 42 180-221 326-367 (385) 372 PRK09508 leuO leucine transcri 62.3 11 0.00027 17.1 5.4 12 19-30 55-66 (314) 373 PRK11753 cAMP-regulatory prote 62.2 11 0.00027 17.0 3.7 27 189-215 169-195 (211) 374 PRK09480 slmA nucleoid occlusi 62.1 5.3 0.00014 19.2 2.0 14 20-33 15-28 (194) 375 PRK09392 ftrB transcriptional 61.9 11 0.00027 17.0 3.6 30 189-219 174-203 (236) 376 PRK13756 tetracycline represso 61.6 4.6 0.00012 19.6 1.6 14 205-218 190-203 (205) 377 smart00351 PAX Paired Box doma 61.4 11 0.00028 16.9 4.6 38 179-216 24-61 (125) 378 COG3177 Fic family protein [Fu 61.3 11 0.00028 16.9 3.6 28 187-214 303-330 (348) 379 TIGR02612 mob_myst_A mobile my 61.1 6.2 0.00016 18.7 2.2 16 188-203 38-53 (150) 380 PRK00135 scpB segregation and 60.9 11 0.00028 16.9 4.3 28 13-40 26-55 (182) 381 TIGR02607 antidote_HigA addict 60.8 7.9 0.0002 17.9 2.7 26 185-210 17-42 (81) 382 KOG0723 consensus 60.6 5.7 0.00015 18.9 1.9 33 189-221 53-85 (112) 383 cd00086 homeodomain Homeodomai 60.2 11 0.00029 16.8 3.4 29 190-218 29-57 (59) 384 PRK09706 transcriptional repre 60.1 10 0.00025 17.2 3.1 35 173-208 84-118 (135) 385 COG2469 Uncharacterized conser 60.0 7.8 0.0002 18.0 2.5 52 164-215 204-255 (284) 386 TIGR02850 spore_sigG RNA polym 59.8 12 0.0003 16.8 3.9 45 173-217 206-251 (254) 387 pfam08069 Ribosomal_S13_N Ribo 59.6 9.3 0.00024 17.4 2.9 27 173-199 27-55 (60) 388 smart00345 HTH_GNTR helix_turn 59.6 12 0.0003 16.7 3.5 25 190-214 22-46 (60) 389 cd04765 HTH_MlrA-like_sg2 Heli 59.1 9.7 0.00025 17.3 2.9 28 173-200 38-70 (99) 390 cd04767 HTH_HspR-like_MBC Heli 58.1 9.8 0.00025 17.3 2.8 20 181-200 49-69 (120) 391 TIGR03613 RutR pyrimidine util 58.0 7.2 0.00018 18.2 2.1 16 174-189 184-199 (202) 392 COG3093 VapI Plasmid maintenan 57.7 9.9 0.00025 17.2 2.7 24 188-211 23-46 (104) 393 PRK03887 methylated-DNA--prote 57.6 13 0.00032 16.5 4.7 41 170-210 86-132 (172) 394 pfam04539 Sigma70_r3 Sigma-70 57.5 12 0.0003 16.7 3.1 34 179-212 11-44 (78) 395 COG1476 Predicted transcriptio 57.4 10 0.00025 17.2 2.7 25 185-209 11-35 (68) 396 pfam00392 GntR Bacterial regul 56.3 13 0.00034 16.4 3.3 24 190-213 26-49 (64) 397 pfam08280 HTH_Mga M protein tr 55.9 13 0.00034 16.3 3.6 41 176-216 5-47 (59) 398 pfam10078 DUF2316 Uncharacteri 55.8 13 0.00034 16.3 3.4 24 184-207 19-42 (89) 399 cd01279 HTH_HspR-like Helix-Tu 55.8 12 0.0003 16.7 2.9 31 174-204 39-74 (98) 400 smart00389 HOX Homeodomain. DN 55.7 13 0.00033 16.4 3.1 43 174-216 7-55 (56) 401 pfam06970 RepA_N Replication i 55.7 11 0.00029 16.8 2.8 22 189-210 53-74 (76) 402 PRK11388 DNA-binding transcrip 55.6 14 0.00034 16.3 5.4 35 177-211 593-627 (639) 403 KOG2581 consensus 55.4 14 0.00035 16.3 3.2 25 190-214 379-404 (493) 404 KOG0848 consensus 54.7 9.8 0.00025 17.3 2.3 27 191-217 229-255 (317) 405 pfam02954 HTH_8 Bacterial regu 53.8 14 0.00037 16.1 5.2 31 181-211 11-41 (42) 406 pfam05344 DUF746 Domain of Unk 53.6 14 0.00037 16.1 4.7 48 177-224 2-52 (65) 407 PRK09940 transcriptional regul 53.6 14 0.00037 16.1 3.1 26 186-211 148-173 (253) 408 KOG0709 consensus 53.4 15 0.00037 16.0 4.5 53 165-220 233-285 (472) 409 COG2378 Predicted transcriptio 53.1 15 0.00038 16.0 4.9 10 12-21 23-32 (311) 410 pfam05331 DUF742 Protein of un 52.8 15 0.00038 16.0 3.2 44 171-214 38-81 (114) 411 pfam06322 Phage_NinH Phage Nin 52.8 9 0.00023 17.5 1.9 26 190-215 18-43 (64) 412 PRK11062 nhaR transcriptional 52.7 15 0.00038 16.0 6.1 17 15-31 33-49 (296) 413 COG1395 Predicted transcriptio 52.7 13 0.00034 16.4 2.7 28 184-211 134-161 (313) 414 COG4197 Uncharacterized protei 52.5 13 0.00033 16.4 2.6 38 191-230 15-52 (96) 415 PRK10402 DNA-binding transcrip 52.2 15 0.00039 15.9 3.6 26 189-214 157-182 (213) 416 COG1974 LexA SOS-response tran 51.1 16 0.0004 15.8 4.4 14 12-25 38-51 (201) 417 cd07377 WHTH_GntR Winged helix 50.9 16 0.0004 15.8 3.6 24 190-213 27-50 (66) 418 pfam04233 Phage_Mu_F Phage Mu 50.0 16 0.00041 15.7 2.8 11 116-126 83-93 (110) 419 PRK09391 fixK transcriptional 49.1 17 0.00043 15.6 3.7 27 189-215 174-200 (224) 420 pfam04492 Phage_rep_O Bacterio 49.1 17 0.00043 15.6 4.8 41 173-213 29-79 (100) 421 PRK05932 RNA polymerase factor 48.3 14 0.00036 16.1 2.3 26 188-213 349-374 (461) 422 pfam01498 Transposase_5 Transp 48.3 15 0.00039 15.9 2.5 23 189-211 14-41 (72) 423 PRK11202 DNA-binding transcrip 47.8 9.2 0.00023 17.5 1.3 18 21-38 17-35 (203) 424 COG1725 Predicted transcriptio 47.3 18 0.00046 15.4 3.4 15 181-195 99-113 (125) 425 smart00342 HTH_ARAC helix_turn 46.9 18 0.00046 15.4 3.5 28 176-203 37-65 (84) 426 pfam07022 Phage_CI_repr Bacter 46.7 18 0.00047 15.3 2.9 22 189-210 13-34 (65) 427 pfam07037 DUF1323 Putative tra 45.7 19 0.00048 15.2 3.1 16 173-188 92-109 (122) 428 KOG2252 consensus 44.6 20 0.0005 15.1 3.2 43 173-215 426-474 (558) 429 TIGR01817 nifA Nif-specific re 44.5 20 0.0005 15.1 4.9 37 173-209 528-564 (574) 430 PRK13918 CRP/FNR family transc 43.8 20 0.00052 15.0 3.6 26 189-214 146-171 (201) 431 TIGR02943 Sig70_famx1 RNA poly 43.6 20 0.00052 15.0 3.2 37 174-217 146-182 (194) 432 pfam11740 KfrA_N Plasmid repli 43.1 21 0.00053 15.0 4.7 37 183-219 12-51 (120) 433 pfam12116 SpoIIID Stage III sp 43.0 21 0.00053 14.9 5.3 42 176-217 6-48 (82) 434 KOG0843 consensus 43.0 18 0.00047 15.3 2.2 45 172-216 107-157 (197) 435 PRK13832 plasmid partitioning 42.8 21 0.00053 14.9 4.6 30 179-208 109-138 (518) 436 PTZ00100 DnaJ chaperone protei 42.2 18 0.00045 15.5 2.0 31 188-218 59-89 (114) 437 TIGR00738 rrf2_super rrf2 fami 41.8 22 0.00055 14.8 3.1 41 85-128 24-64 (133) 438 pfam07453 NUMOD1 NUMOD1 domain 41.7 13 0.00032 16.5 1.2 21 189-209 17-37 (37) 439 PRK05782 precorrin-8X methylmu 41.6 19 0.00049 15.2 2.1 59 172-230 161-219 (332) 440 KOG0487 consensus 41.4 9.5 0.00024 17.4 0.5 50 174-224 247-298 (308) 441 PRK12469 RNA polymerase factor 41.0 17 0.00044 15.5 1.8 40 174-213 346-388 (475) 442 PRK08561 rps15p 30S ribosomal 40.9 20 0.0005 15.1 2.1 16 143-158 85-100 (151) 443 pfam02082 Rrf2 Transcriptional 40.7 22 0.00057 14.7 4.7 25 189-213 25-49 (82) 444 KOG1597 consensus 40.5 23 0.00058 14.7 3.3 35 182-216 254-288 (308) 445 TIGR03070 couple_hipB transcri 40.4 23 0.00058 14.7 3.1 25 184-208 11-35 (58) 446 pfam06971 Put_DNA-bind_N Putat 40.1 22 0.00057 14.7 2.3 19 190-208 29-47 (49) 447 PRK10870 transcriptional repre 39.5 23 0.0006 14.6 6.6 12 174-185 143-154 (176) 448 pfam08765 Mor Mor transcriptio 39.5 23 0.0006 14.6 5.2 43 173-216 57-99 (107) 449 pfam04936 DUF658 Protein of un 39.5 23 0.00058 14.7 2.2 44 184-229 84-127 (134) 450 KOG0484 consensus 39.4 23 0.0006 14.6 3.0 40 186-225 42-81 (125) 451 PRK10856 hypothetical protein; 39.4 23 0.0006 14.6 5.8 52 13-80 29-83 (332) 452 TIGR01610 phage_O_Nterm phage 39.1 24 0.0006 14.5 4.4 45 171-215 20-81 (104) 453 TIGR02154 PhoB phosphate regul 38.4 2.9 7.3E-05 21.1 -2.5 52 173-224 154-214 (226) 454 PTZ00072 40S ribosomal protein 38.1 19 0.00049 15.2 1.7 19 142-160 81-99 (148) 455 pfam10252 PP28 Casein kinase s 37.8 25 0.00063 14.4 3.6 28 170-197 21-58 (82) 456 PRK11608 pspF phage shock prot 37.6 25 0.00064 14.4 5.3 36 176-211 285-322 (325) 457 PRK04158 transcriptional repre 36.2 26 0.00067 14.2 4.7 101 116-220 111-229 (256) 458 COG3284 AcoR Transcriptional a 35.2 27 0.00069 14.1 5.2 36 176-211 566-601 (606) 459 PRK13626 transcriptional regul 35.2 27 0.00069 14.1 3.4 15 13-27 197-211 (551) 460 COG4533 ABC-type uncharacteriz 35.2 27 0.00069 14.1 4.7 14 14-27 200-213 (564) 461 pfam02042 RWP-RK RWP-RK domain 35.1 27 0.00069 14.1 3.7 29 188-220 15-43 (52) 462 pfam09012 FeoC FeoC like trans 35.1 27 0.00069 14.1 3.5 30 188-217 14-43 (68) 463 TIGR02948 SigW_bacill RNA poly 34.9 15 0.00037 16.1 0.6 36 177-213 142-177 (187) 464 cd06571 Bac_DnaA_C C-terminal 34.9 27 0.0007 14.1 6.3 54 174-229 29-86 (90) 465 COG1961 PinR Site-specific rec 34.9 21 0.00054 14.9 1.5 44 174-217 162-206 (222) 466 PRK05629 hypothetical protein; 34.7 28 0.0007 14.1 4.5 40 174-213 245-286 (331) 467 PRK11552 putative DNA-binding 34.6 24 0.00062 14.4 1.8 18 17-34 15-32 (224) 468 PTZ00037 DnaJ_C chaperone prot 34.4 18 0.00045 15.4 1.0 17 173-189 349-365 (422) 469 PRK10130 transcriptional regul 34.3 28 0.00071 14.0 3.4 31 181-211 249-279 (350) 470 cd00131 PAX Paired Box domain 34.2 28 0.00072 14.0 4.6 32 180-211 25-56 (128) 471 COG3655 Predicted transcriptio 34.0 28 0.00072 14.0 2.4 27 183-209 10-36 (73) 472 TIGR02392 rpoH_proteo alternat 34.0 28 0.00072 14.0 4.6 44 173-216 226-273 (279) 473 COG2944 Predicted transcriptio 33.9 28 0.00072 14.0 5.1 39 168-207 38-76 (104) 474 pfam06627 DUF1153 Protein of u 33.7 21 0.00054 14.9 1.3 17 218-234 34-50 (90) 475 pfam00382 TFIIB Transcription 33.7 21 0.00054 14.9 1.3 25 181-205 47-71 (71) 476 pfam07508 Recombinase Recombin 33.2 29 0.00074 13.9 2.8 33 179-211 8-51 (101) 477 COG3088 CcmH Uncharacterized p 33.1 29 0.00075 13.9 2.3 16 179-194 68-83 (153) 478 pfam11994 DUF3489 Protein of u 33.0 29 0.00075 13.9 3.8 29 187-215 23-51 (72) 479 COG5407 SEC63 Preprotein trans 33.0 21 0.00052 15.0 1.2 39 181-219 74-125 (610) 480 COG4941 Predicted RNA polymera 32.7 30 0.00076 13.9 4.1 32 185-216 133-164 (415) 481 COG3710 CadC DNA-binding winge 32.3 10 0.00027 17.1 -0.4 59 174-233 32-100 (148) 482 pfam04182 B-block_TFIIIC B-blo 31.9 30 0.00078 13.8 4.1 41 175-215 1-45 (73) 483 COG2344 AT-rich DNA-binding pr 31.8 31 0.00078 13.8 2.5 18 190-207 34-51 (211) 484 pfam04703 FaeA FaeA-like prote 31.7 31 0.00078 13.7 4.1 33 180-212 4-39 (61) 485 TIGR01321 TrpR trp operon repr 31.7 31 0.00078 13.7 3.0 32 174-205 42-73 (95) 486 pfam00292 PAX 'Paired box' dom 31.7 31 0.00078 13.7 4.6 36 179-214 24-59 (125) 487 TIGR03192 benz_CoA_bzdQ benzoy 31.6 31 0.00079 13.7 3.6 40 178-220 202-241 (293) 488 TIGR02748 GerC3_HepT heptapren 30.8 31 0.0008 13.7 1.8 22 205-233 161-182 (325) 489 PRK11014 transcriptional repre 30.7 32 0.00081 13.6 3.5 26 190-215 27-52 (141) 490 smart00531 TFIIE Transcription 30.6 32 0.00081 13.6 3.8 25 190-214 17-41 (147) 491 TIGR02698 CopY_TcrY copper tra 30.4 32 0.00082 13.6 3.4 41 175-215 3-49 (130) 492 PRK05022 anaerobic nitric oxid 30.2 32 0.00083 13.6 5.8 41 176-220 470-510 (510) 493 COG2508 Regulator of polyketid 30.1 33 0.00083 13.6 5.8 45 175-219 353-397 (421) 494 COG1378 Predicted transcriptio 30.0 33 0.00083 13.5 5.0 43 173-215 13-57 (247) 495 TIGR02395 rpoN_sigma RNA polym 29.9 21 0.00054 14.9 0.8 17 189-205 366-382 (477) 496 COG3311 AlpA Predicted transcr 29.5 33 0.00085 13.5 2.6 19 192-210 17-35 (70) 497 pfam03918 CcmH Cytochrome C bi 29.3 34 0.00086 13.5 2.4 16 179-194 61-76 (145) 498 PHA00675 hypothetical protein 29.2 34 0.00086 13.5 4.7 40 166-205 15-56 (78) 499 TIGR02047 CadR-PbrR Cd(II)/Pb( 28.5 26 0.00066 14.3 1.1 16 193-208 5-20 (127) 500 PRK12815 carB carbamoyl phosph 28.0 35 0.0009 13.3 4.5 31 181-211 484-514 (1068) No 1 >PRK13870 transcriptional regulator TraR; Provisional Probab=100.00 E-value=3.1e-36 Score=277.51 Aligned_cols=215 Identities=20% Similarity=0.156 Sum_probs=169.7 Q ss_pred CCHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCEEEECCCCCHHHHHHHHHHHHHCCCHHHHHHHHCCCCEEECC Q ss_conf 25999999999999985837858998417778731025044227877899962487444120879999961799837310 Q gi|254780693|r 12 SSLQELSPRLHLIQNRIKARNFALYTINSALDFPRRQQLICELHNYDLDSGDIPNILIETYGDDFLFHFNSGLLPIIWQS 91 (235) Q Consensus 12 ~sl~dl~~~l~~l~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dp~~~~~~~~~~p~~~~~ 91 (235) ..-..+...|..+.+.+++++|+|..+ ..+.+...+|||.+|.++|....|..+||++.++..+..|+.|+. T Consensus 16 ~de~~~~~~l~~~a~~~gf~~~ayl~~--------~~~~~~~isnYP~eW~~~Y~~~~Y~~iDPVv~~a~~~~~Pf~Ws~ 87 (234) T PRK13870 16 GDECILKTGLADIAEHFGFTGYAYLHI--------QHRHITAVTNYHREWQSTYFDKKFDALDPVVKRARSRKHIFTWSG 87 (234) T ss_pred CCHHHHHHHHHHHHHHCCCCCEEEEEE--------CCCCEEEEECCCHHHHHHHHHCCCEEECHHHHHHHCCCCCEEECC T ss_conf 539999999999999839985798750--------799757872799999999998889030879998834898976087 Q ss_pred HHHHCCCCCHHHHHHHHHHHCCCCCEEEEEEECCCCCCEEEEECCCCCCCCHHHHHHHHHHHH---HHHHHHHHHCCCCC Q ss_conf 133146672136789965425855358997216887523454105887899899999999999---99999985124678 Q gi|254780693|r 92 IQEETVIESSGQLSVRLEGGLLPFAGIAFPVRLGFHKNGYVIFTSEFLMLANEVIIEAHGACY---QVITDFLELFKKRS 168 (235) Q Consensus 92 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~pv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~ 168 (235) ..+.........-+......+|+++|+++|++++.+..+++++++..+..+.+...+...... .++.....+..... T Consensus 88 ~~~~~~~~~~~r~f~~eA~~~Gl~~G~tiPi~~~~G~~~~lSlas~~~~~~~~~~~~~~~~~~~~~~~h~~~~~l~~~~~ 167 (234) T PRK13870 88 EQERPSLSKDERAFYAHAADFGIRSGITIPIKTANGSMSMFTLASEKPVIDLDREIDAVAAAATIGQIHARISFLRTTPT 167 (234) T ss_pred CCCCCCCCHHHHHHHHHHHHCCCCCEEEEEEECCCCCEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCC T ss_conf 65544348689999999998599966999888799998999981399842167889999999999999999986204888 Q ss_pred -CCCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCC Q ss_conf -874449989999999998799978999994999889999999999980799789999999976999 Q gi|254780693|r 169 -SAARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFGYI 234 (235) Q Consensus 169 -~~~~~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~~~Gli 234 (235) .+...||+||+|||+|+|+|||++|||.+||||++||++|++|+++||||.||+|||++|+++||| T Consensus 168 ~~~~~~LT~RE~E~L~W~A~GKT~~EIA~ILgISe~TV~fHl~na~~KL~a~nr~qAVa~Ai~~gLI 234 (234) T PRK13870 168 AEDAAWLDPKEATYLRWIAVGMTMEEIADVEGVKYNSVRVKLREAMKRFDVRSKAHLTALAIRRKLI 234 (234) T ss_pred CCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCC T ss_conf 8776679979999999997899899999997988999999999999995899899999999985899 No 2 >PRK10188 DNA-binding transcriptional activator SdiA; Provisional Probab=100.00 E-value=1.1e-35 Score=273.47 Aligned_cols=219 Identities=18% Similarity=0.115 Sum_probs=175.7 Q ss_pred HHHHCCHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCEEEECCCCCHHHHHHHHHHHHHCCCHHHHHHHHCCCCE Q ss_conf 98622599999999999998583785899841777873102504422787789996248744412087999996179983 Q gi|254780693|r 8 GKKSSSLQELSPRLHLIQNRIKARNFALYTINSALDFPRRQQLICELHNYDLDSGDIPNILIETYGDDFLFHFNSGLLPI 87 (235) Q Consensus 8 ~~~~~sl~dl~~~l~~l~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dp~~~~~~~~~~p~ 87 (235) -+++.+.++++..+....+.+++++|+|. ...+.|..++.+...+|||..|.++|...+|...||++.++..+..|+ T Consensus 17 ~~~a~~~~~~~~~l~~~~~~lGFey~~~~---~~~p~p~~~p~~~l~snYP~~W~~~Y~~~~y~~iDPvv~~~~~s~~P~ 93 (240) T PRK10188 17 FQEMAAAEEVYHELQLQTQQLEYDYYSLC---VRHPVPFTRPKVAFYTTYPEAWVSHYQAENYLAIDPVLKPENFSQGHL 93 (240) T ss_pred HHHCCCHHHHHHHHHHHHHHCCCCEEEEE---EECCCCCCCCCEEEECCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCE T ss_conf 98479999999999999997598258988---742688888766887289999999999877914495102444689873 Q ss_pred EECCHHHHCCCCCHHHHHHHHHHHCCCCCEEEEEEECCCCCCEEEEECCCCCCCCH---HH-HHHHHHHHHHHHHHHHHH Q ss_conf 73101331466721367899654258553589972168875234541058878998---99-999999999999999851 Q gi|254780693|r 88 IWQSIQEETVIESSGQLSVRLEGGLLPFAGIAFPVRLGFHKNGYVIFTSEFLMLAN---EV-IIEAHGACYQVITDFLEL 163 (235) Q Consensus 88 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~pv~~~~~~~~~~~~~~~~~~~~~---~~-~~~~~~~~~~~~~~~~~~ 163 (235) .|++.... ....+++....+|++.|+++|++.+.+..+++++++....... .+ ...+...+...+....+. T Consensus 94 ~W~~~l~~-----~~~~~~~eA~~~Gl~~G~t~p~~~~~g~~g~lSla~~~~~~~~~~~~~~~l~l~~l~~~~~~~~~~~ 168 (240) T PRK10188 94 MWNDDLFS-----EAQALWDAARAHGLRRGVTQCLMLPNRALGFLSFSRSSLREIPILSDELELRLQLLVRESLMALMRL 168 (240) T ss_pred ECCCCHHH-----HHHHHHHHHHHCCCCCCEEEEEECCCCCEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH T ss_conf 07840124-----2099999999829867617888727998389998547887775435599999999999999999864 Q ss_pred CCC-CCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCC Q ss_conf 246-78874449989999999998799978999994999889999999999980799789999999976999 Q gi|254780693|r 164 FKK-RSSAARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFGYI 234 (235) Q Consensus 164 ~~~-~~~~~~~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~~~Gli 234 (235) ... ..++...||+||+|||+|+|+|||++|||.+|+||++||++|++|+++||||.||+|||++|+++||| T Consensus 169 ~~~~~~~~~~~LT~RE~E~L~W~A~GKTs~EIa~IL~ISe~TV~fHl~na~~KL~a~Nr~qAva~A~~~GLI 240 (240) T PRK10188 169 EDEMVMTPEMNFSKREKEILKWTAEGKTSAEIAMILSISENTVNFHQKNMQKKFNAPNKTQIACYAAATGLI 240 (240) T ss_pred CCCCCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCC T ss_conf 044457987889989999999997799999999883999999999999999995899899999999985899 No 3 >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=100.00 E-value=1.2e-34 Score=266.10 Aligned_cols=222 Identities=23% Similarity=0.222 Sum_probs=174.7 Q ss_pred CHHHHCCHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCEEEECCCCCHHHHHHHHHHHHHCCCHHHHHHHHCCCC Q ss_conf 19862259999999999999858378589984177787310250442278778999624874441208799999617998 Q gi|254780693|r 7 TGKKSSSLQELSPRLHLIQNRIKARNFALYTINSALDFPRRQQLICELHNYDLDSGDIPNILIETYGDDFLFHFNSGLLP 86 (235) Q Consensus 7 ~~~~~~sl~dl~~~l~~l~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dp~~~~~~~~~~p 86 (235) .-++++|++++...+..+.+.+++++|.|+.......... .......+.|.. +...|....|...||++.++.....| T Consensus 10 ~l~~a~t~~~l~~~l~~~~~~~Gfd~~~y~~~~~~~~~~~-~~~~~~~~~w~~-~~~~y~~~~Y~~~DPvv~~~~~~~~P 87 (232) T TIGR03541 10 QIEQASTLEAIQDAVREFAQNLGYDRFVLFSAHSAKDELI-ERIFWVEGDWFD-DGNAVDAQTYLRHCPVTRHILEADEP 87 (232) T ss_pred HHHHCCCHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCCC-CCEECCCCCHHH-HHHHHHHCCCCCCCCHHHHHHHCCCC T ss_conf 9984899999999999999984998899963477766556-400037874577-89999883991069899999857999 Q ss_pred EEECCHHHHCCCCCHHHHHHHHHHHCCCCCEEEEEEECCCCCCEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCC Q ss_conf 37310133146672136789965425855358997216887523454105887899899999999999999999851246 Q gi|254780693|r 87 IIWQSIQEETVIESSGQLSVRLEGGLLPFAGIAFPVRLGFHKNGYVIFTSEFLMLANEVIIEAHGACYQVITDFLELFKK 166 (235) Q Consensus 87 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~pv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 166 (235) +.|+...... .+...+.+.....|. .|+++|++.+.+..+++++++...+..+.....+...+..++....++... T Consensus 88 f~Ws~~~~~~---~~~~~~~~~a~~~G~-~G~tvPi~~~~G~~g~~s~a~~~~d~~~~~~~~l~l~~~~a~~~~~~l~~~ 163 (232) T TIGR03541 88 FFWSKTPNEN---GERYRVVRNPSGRGV-HGLQVPVFGRTGLEGAVSLGGKLIDLSARFRLALQLLCVTAFFAARRLLEA 163 (232) T ss_pred EECCCCCCCC---HHHHHHHHHHHHCCC-CEEEEEEECCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCC T ss_conf 6238887668---778999999986399-589998888999868998416877789999999999999999999997358 Q ss_pred CCC-CCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCC Q ss_conf 788-74449989999999998799978999994999889999999999980799789999999976999 Q gi|254780693|r 167 RSS-AARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFGYI 234 (235) Q Consensus 167 ~~~-~~~~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~~~Gli 234 (235) ..+ +...||+||+|||+|+|+|||++|||.+|+||++||++|++|+++||||.||+|||++|+++|+| T Consensus 164 ~~~~~~~~LT~RE~E~L~w~A~Gkt~~eIa~iL~iSe~TV~~hl~~a~~KLga~nr~qAVa~Ai~~GlI 232 (232) T TIGR03541 164 PLLREAGVLSEREREVLAWTALGRRQADIAAILGISERTVENHLRSARRKLGVATTAQAIAIALRKGDI 232 (232) T ss_pred CCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCC T ss_conf 998889998989999999998799999999996989999999999999984899999999999987999 No 4 >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=99.85 E-value=2.6e-19 Score=156.78 Aligned_cols=214 Identities=19% Similarity=0.027 Sum_probs=120.2 Q ss_pred HHHCCHHHHHHHHH-HHHHHHCCCCEEEEEECCCCCCCCCCCEEEECCCCCHHHHHHHHHHHHHCCCHHHH-----HHHH Q ss_conf 86225999999999-99998583785899841777873102504422787789996248744412087999-----9961 Q gi|254780693|r 9 KKSSSLQELSPRLH-LIQNRIKARNFALYTINSALDFPRRQQLICELHNYDLDSGDIPNILIETYGDDFLF-----HFNS 82 (235) Q Consensus 9 ~~~~sl~dl~~~l~-~l~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dp~~~-----~~~~ 82 (235) -+..+--+++..++ .++..++.+-+.- .+.........-..+............ ......++++. +... T Consensus 17 l~v~~~~~ff~WlQg~~Q~lLPHeill~-~~g~~~~g~i~~d~~S~~~~~~~~~~~----~~~~~~~~l~~~~~~~W~~~ 91 (247) T TIGR03020 17 LRIRRRHQFFSWLQGEVQSLLPHEILLC-GWADFEGGNVLHERFSPLRYVRDAQYS----RAIHPPDGLLHRLTNAWGAG 91 (247) T ss_pred HHHHHHHHHHHHHHHHHHHCCCHHHEEE-EEECCCCCCEEEEEEECCCCCCHHHHH----HCCCCCCCHHHHHHHHHHHC T ss_conf 8677889999999986653066021145-565056771799987358887617676----21267520459999999974 Q ss_pred CCCCEEECCHHHHCCCCCHHHHHHHHHHHCCCCCEEEEEEECCCCCC-EEEEECCCCCCCCHHHHHHHHHHHHHHHHHHH Q ss_conf 79983731013314667213678996542585535899721688752-34541058878998999999999999999998 Q gi|254780693|r 83 GLLPIIWQSIQEETVIESSGQLSVRLEGGLLPFAGIAFPVRLGFHKN-GYVIFTSEFLMLANEVIIEAHGACYQVITDFL 161 (235) Q Consensus 83 ~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~pv~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 161 (235) ...|+.-............ +.... ...-.+...+..+.+..+.. -+.+|.+.....++.....+.....++...+. T Consensus 92 ~r~P~~l~~~~~~~~~~~~--~~~~~-~~~~l~~~~~hGi~D~~g~~~cl~~f~~~~~~~~~~~~~~LelL~P~Lh~AL~ 168 (247) T TIGR03020 92 KRQPRLVCALTLDDDGWLR--FSVNL-LLLNLKNIAFHGLSDVDGRHDCLYSFSRSSVPLDARHAYFLELLLPYLDSALR 168 (247) T ss_pred CCCCEEECCCCCCCCCHHH--HHHHH-HHHHHHHHHHEECCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHH T ss_conf 9986785377777663034--30067-89887667520012678985559999715889987799999976889999999 Q ss_pred HHCCCC----CCC------CCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHH Q ss_conf 512467----887------444998999999999879997899999499988999999999998079978999999997 Q gi|254780693|r 162 ELFKKR----SSA------ARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIR 230 (235) Q Consensus 162 ~~~~~~----~~~------~~~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~~ 230 (235) +..... ..+ ...||+||.|||+|+++|+||+|||.+|+||++||++|+++|++||||+||+|||++|+. T Consensus 169 rv~~l~~q~~~~~~~~~~~~glLT~RE~EVL~~va~G~sn~eIA~~L~iS~~TVk~H~~~i~~KL~v~nR~qAV~kAla 247 (247) T TIGR03020 169 RVLFLPNQHRTRPLGERHSAGLITAREAEILAWVRDGKTNEEIAAILGISSLTVKNHLQHIFKKLDVRNRAQAVAKAIA 247 (247) T ss_pred HHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHC T ss_conf 8631643354555556776789998999999999879999999999497999999999999998099989999999859 No 5 >PRK04841 transcriptional regulator MalT; Provisional Probab=99.78 E-value=7.7e-19 Score=153.47 Aligned_cols=60 Identities=30% Similarity=0.406 Sum_probs=57.8 Q ss_pred CCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHC Q ss_conf 449989999999998799978999994999889999999999980799789999999976 Q gi|254780693|r 172 RNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRF 231 (235) Q Consensus 172 ~~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~~~ 231 (235) ..||+||.|||+++++|+||||||..|+||++|||+|++|||+||||+||+|||++|..+ T Consensus 837 ~~LT~RE~eVL~lLa~GlSNkeIA~~L~IS~~TVK~HlrnIy~KLgV~sR~~AV~~AreL 896 (903) T PRK04841 837 SPLTQREWQVLGLIYSGYSNEQIAGELDVAATTIKTHIRNLYQKLGIAHRQEAVQLAQQL 896 (903) T ss_pred CCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHH T ss_conf 897999999999997689999999881998769999999998565999899999999999 No 6 >PRK09483 response regulator; Provisional Probab=99.75 E-value=5.8e-18 Score=147.22 Aligned_cols=66 Identities=32% Similarity=0.413 Sum_probs=63.1 Q ss_pred CCCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCC Q ss_conf 874449989999999998799978999994999889999999999980799789999999976999 Q gi|254780693|r 169 SAARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFGYI 234 (235) Q Consensus 169 ~~~~~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~~~Gli 234 (235) .+...||+||.|||+|+++|+||+|||..|+||++||++|+++|++|||++||+|++.+|++.||| T Consensus 144 ~~~~~LT~RE~eVl~ll~~G~snkeIA~~L~iS~~TV~~h~~~i~~KL~v~~r~el~~~A~~~gli 209 (216) T PRK09483 144 NPFASLSERELQIMLMITKGQKVNEISEQLNLSPKTVNSYRYRMFSKLNISGDVELTHLAIRHGLL 209 (216) T ss_pred CCCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCC T ss_conf 654568999999999998799999999996989999999999999980999999999999995991 No 7 >PRK09935 transcriptional regulator FimZ; Provisional Probab=99.73 E-value=1.8e-17 Score=143.79 Aligned_cols=63 Identities=29% Similarity=0.318 Sum_probs=61.5 Q ss_pred CCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCC Q ss_conf 449989999999998799978999994999889999999999980799789999999976999 Q gi|254780693|r 172 RNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFGYI 234 (235) Q Consensus 172 ~~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~~~Gli 234 (235) ..||+||.|||+++++|+||+|||..|+||++||++|+++|++||||+||+|+|.+|.+.||| T Consensus 148 ~~Lt~RE~eVL~ll~~G~snkeIA~~L~iS~~TV~~h~~~I~~KL~v~nr~elv~~A~~~~Li 210 (210) T PRK09935 148 MPLSNREVTVLRYLANGLSNKEIAEQLLLSNKTISAHKSNIYGKLGLHSIVELIDYAKSHELL 210 (210) T ss_pred CCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCC T ss_conf 899989999999998699999999894988999999999999981999999999999985999 No 8 >PRK10100 DNA-binding transcriptional regulator CsgD; Provisional Probab=99.73 E-value=2.9e-17 Score=142.25 Aligned_cols=62 Identities=32% Similarity=0.242 Sum_probs=58.4 Q ss_pred CCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHC Q ss_conf 74449989999999998799978999994999889999999999980799789999999976 Q gi|254780693|r 170 AARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRF 231 (235) Q Consensus 170 ~~~~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~~~ 231 (235) +...||+||+|||+++++|+||+|||..|+||++||++|+.+|++|||++||+|||.+|... T Consensus 152 ~~~~LT~RE~eIL~lla~G~sNkEIA~~L~iSe~TVk~H~~~I~~KL~v~~R~qav~~A~~n 213 (216) T PRK10100 152 ESALLTHREKEILNKLRIGASNNEIARSLFISENTVKTHLYNLFKKIAVKNRTQAVSWANDN 213 (216) T ss_pred CCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHH T ss_conf 77899989999999998799999999894988989999999999980999999999999986 No 9 >PRK10840 transcriptional regulator RcsB; Provisional Probab=99.72 E-value=4.6e-17 Score=140.79 Aligned_cols=64 Identities=28% Similarity=0.377 Sum_probs=62.0 Q ss_pred CCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCC Q ss_conf 4449989999999998799978999994999889999999999980799789999999976999 Q gi|254780693|r 171 ARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFGYI 234 (235) Q Consensus 171 ~~~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~~~Gli 234 (235) ...||+||.|||+++++|+||+|||..|+||++||++|+++|++|||++||+|+|.+|.+.||+ T Consensus 148 ~~~LT~RE~eVL~lla~G~snkeIA~~L~iS~~TV~~h~~~i~~KLgv~n~~eLv~ya~~~gl~ 211 (216) T PRK10840 148 DKRLSPKESEVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVENDIALLNYLSSVTLS 211 (216) T ss_pred CCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCC T ss_conf 7899989999999998699999999896989999999999999982999899999999986999 No 10 >PRK10651 transcriptional regulator NarL; Provisional Probab=99.72 E-value=5.7e-17 Score=140.12 Aligned_cols=63 Identities=24% Similarity=0.298 Sum_probs=60.5 Q ss_pred CCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCC Q ss_conf 444998999999999879997899999499988999999999998079978999999997699 Q gi|254780693|r 171 ARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFGY 233 (235) Q Consensus 171 ~~~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~~~Gl 233 (235) ...||+||.|||+++++|+||+|||.+|+||++||++|+++|++|||++||+||+.+|++.+| T Consensus 153 ~~~LT~RE~eVL~ll~~G~snkeIA~~L~iS~~TV~~h~~~i~~KLgv~nr~ea~~~a~~~~l 215 (216) T PRK10651 153 VNQLTPRERDILKLIAQGLSNKMIARRLDITESTVKVHVKHMLKKMKLKSRVEAAVWVHQERI 215 (216) T ss_pred CCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCC T ss_conf 234898999999999859999999999697899999999999998489999999999998369 No 11 >PRK09390 fixJ response regulator FixJ; Provisional Probab=99.71 E-value=3.4e-17 Score=141.74 Aligned_cols=63 Identities=27% Similarity=0.363 Sum_probs=61.6 Q ss_pred CCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCC Q ss_conf 449989999999998799978999994999889999999999980799789999999976999 Q gi|254780693|r 172 RNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFGYI 234 (235) Q Consensus 172 ~~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~~~Gli 234 (235) ..||+||+|||+++++|+||+|||..|+||++||++|++||++|||+.||+|+|.+|++.|+| T Consensus 140 ~~LT~RE~eVL~ll~~G~snkeIA~~L~iS~~TV~~h~~~I~~KL~v~~~~elv~~A~~~Gll 202 (202) T PRK09390 140 ASLSERERQVMDGLVAGLSNKVIARDLDISPRTVEVYRANVMTKMQAGSLSELVRMALRAGAL 202 (202) T ss_pred CCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCC T ss_conf 669989999999998389689999997987889999999999996889889999999985999 No 12 >COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription] Probab=99.71 E-value=3.7e-17 Score=141.44 Aligned_cols=63 Identities=40% Similarity=0.538 Sum_probs=61.4 Q ss_pred CCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCC Q ss_conf 449989999999998799978999994999889999999999980799789999999976999 Q gi|254780693|r 172 RNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFGYI 234 (235) Q Consensus 172 ~~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~~~Gli 234 (235) ..||+||.+||+++++|+||+|||..|+||++||++|+.||++|||++||+||+.+|.+.|++ T Consensus 147 ~~LT~RE~eVl~lla~G~snkeIA~~L~iS~~TVk~h~~~i~~KL~v~~Rtea~~~a~~~g~~ 209 (211) T COG2197 147 ELLTPRELEVLRLLAEGLSNKEIAEELNLSEKTVKTHVSNILRKLGVRNRTEAAIRALRLGLI 209 (211) T ss_pred CCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCC T ss_conf 789989999999998799889999997878989999999999983999899999999982675 No 13 >PRK09958 DNA-binding transcriptional activator EvgA; Provisional Probab=99.71 E-value=1.1e-16 Score=138.02 Aligned_cols=63 Identities=27% Similarity=0.297 Sum_probs=60.8 Q ss_pred CCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCC Q ss_conf 444998999999999879997899999499988999999999998079978999999997699 Q gi|254780693|r 171 ARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFGY 233 (235) Q Consensus 171 ~~~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~~~Gl 233 (235) ...||+||+|||+++++|+||+|||.+|+||++||++|+++|++||||+||+|++.+|.+.|| T Consensus 141 ~~~Lt~RE~eVL~ll~~G~snkeIA~~L~iS~~TV~~h~~~i~~KL~v~~r~el~~~A~~~~l 203 (204) T PRK09958 141 LDSLSKQEISVMRYILDGKDNNDIAEKMFISNKTVSTYKSRLMEKLECKSLMDLYTFAQRNKI 203 (204) T ss_pred CCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCC T ss_conf 256899999999999869999999989788999999999999998489999999999998289 No 14 >PRK10403 transcriptional regulator NarP; Provisional Probab=99.69 E-value=1.1e-16 Score=138.21 Aligned_cols=62 Identities=27% Similarity=0.315 Sum_probs=58.3 Q ss_pred CCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHC Q ss_conf 74449989999999998799978999994999889999999999980799789999999976 Q gi|254780693|r 170 AARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRF 231 (235) Q Consensus 170 ~~~~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~~~ 231 (235) +...||+||.|||+++++|+||+|||..|+||++||++|++||++|||++||+|||.+|++. T Consensus 150 ~~~~LT~RE~eVL~lla~G~snkeIA~~L~iS~~TV~~h~~~I~~KLgv~nR~ea~~~~~~~ 211 (215) T PRK10403 150 PFSVLTERELDVLHELAQGLSNKQIASVLNISEQTVKVHIRNLLRKLNVRSRVAATILFLQQ 211 (215) T ss_pred CCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHH T ss_conf 44568999999999998699999999997982999999999999986899899999999998 No 15 >PRK10360 DNA-binding transcriptional activator UhpA; Provisional Probab=99.68 E-value=2.1e-16 Score=136.06 Aligned_cols=62 Identities=29% Similarity=0.395 Sum_probs=59.0 Q ss_pred CCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCC Q ss_conf 444998999999999879997899999499988999999999998079978999999997699 Q gi|254780693|r 171 ARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFGY 233 (235) Q Consensus 171 ~~~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~~~Gl 233 (235) ...||+||+|||+++++|+||+|||..|+||++||++|+++|++|||++||+|++-+|.. || T Consensus 135 ~~~LT~RE~eVL~lia~G~snkeIA~~L~IS~~TVk~h~~~i~~KL~v~~r~el~r~a~~-~~ 196 (196) T PRK10360 135 QDPLTKRERQVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKLGVSNDVELARRMFD-GW 196 (196) T ss_pred CCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHC-CC T ss_conf 689997999999999879999999999699999999999999998199999999999970-69 No 16 >COG2909 MalT ATP-dependent transcriptional regulator [Transcription] Probab=99.68 E-value=6.4e-17 Score=139.78 Aligned_cols=62 Identities=35% Similarity=0.505 Sum_probs=60.6 Q ss_pred CCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCC Q ss_conf 49989999999998799978999994999889999999999980799789999999976999 Q gi|254780693|r 173 NLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFGYI 234 (235) Q Consensus 173 ~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~~~Gli 234 (235) +||.||.|||.++++|.||+|||.+|.||.+|||+|+.|||.||||+||+|||.+|-.+|++ T Consensus 831 ~Ls~RE~eVL~Lia~G~SN~eIa~~L~isl~TVKtH~rniy~KLgV~~RtqAV~rAk~L~lL 892 (894) T COG2909 831 PLSQRELEVLGLIAQGLSNEEIAQELFISLTTVKTHIRNIYQKLGVANRTQAVQRAKELGLL 892 (894) T ss_pred CCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHH T ss_conf 76388999999998257778999998898988999999999884821589999999998754 No 17 >pfam00196 GerE Bacterial regulatory proteins, luxR family. Probab=99.59 E-value=4.2e-15 Score=126.84 Aligned_cols=57 Identities=33% Similarity=0.446 Sum_probs=55.4 Q ss_pred CCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHH Q ss_conf 449989999999998799978999994999889999999999980799789999999 Q gi|254780693|r 172 RNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKA 228 (235) Q Consensus 172 ~~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A 228 (235) +.|||||.+||.|+++|+|++|||..|+||++||++|+++|++||||+||+|+|.+| T Consensus 2 ~~LT~RE~~il~~l~~G~s~~eIA~~L~is~~TV~~h~~~i~~Kl~v~nr~elv~~A 58 (58) T pfam00196 2 DSLSPREREVLRLLAAGKSNKEIADILGISEKTVKVHRSNIMRKLNVHSRVELIRLA 58 (58) T ss_pred CCCCHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHC T ss_conf 977999999999998079999999997888999999999999980999999999559 No 18 >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=99.56 E-value=1.1e-14 Score=123.73 Aligned_cols=57 Identities=44% Similarity=0.539 Sum_probs=55.9 Q ss_pred CCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHH Q ss_conf 998999999999879997899999499988999999999998079978999999997 Q gi|254780693|r 174 LTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIR 230 (235) Q Consensus 174 LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~~ 230 (235) |||||.+||.|+++|+|++|||..|+||++||++|++++++|||+.||+|+|.+|++ T Consensus 1 LT~rE~~il~~~~~G~s~~eIA~~L~is~~TV~~~~~~i~~Kl~~~~r~elv~~A~r 57 (57) T cd06170 1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAYAIR 57 (57) T ss_pred CCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHC T ss_conf 988999999999807999999999897899999999999998689999999998729 No 19 >smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon Probab=99.52 E-value=3.2e-14 Score=120.57 Aligned_cols=57 Identities=42% Similarity=0.546 Sum_probs=55.2 Q ss_pred CCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHH Q ss_conf 449989999999998799978999994999889999999999980799789999999 Q gi|254780693|r 172 RNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKA 228 (235) Q Consensus 172 ~~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A 228 (235) ..||+||.+||.|+++|+|++|||..|+||++||++|+++|++|||+.||+|+|++| T Consensus 2 ~~LT~rE~~il~~l~~G~s~~eIA~~L~is~~TV~~~~~~i~~Kl~v~~r~elv~~A 58 (58) T smart00421 2 ASLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRLA 58 (58) T ss_pred CCCCHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHC T ss_conf 761899999999998179999999898978989999999999984899999999549 No 20 >PRK11475 DNA-binding transcriptional activator BglJ; Provisional Probab=99.50 E-value=2.7e-13 Score=113.95 Aligned_cols=62 Identities=24% Similarity=0.286 Sum_probs=57.4 Q ss_pred CCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHC Q ss_conf 74449989999999998799978999994999889999999999980799789999999976 Q gi|254780693|r 170 AARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRF 231 (235) Q Consensus 170 ~~~~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~~~ 231 (235) ....|||||+|||+++++|+|++|||..|+||.+||++|.+|+++|||++|.+++|-.|--+ T Consensus 131 ~~~~Lt~rE~eVl~l~a~G~s~~eIA~~L~~S~kTv~thr~~~m~KLgv~s~a~Li~~a~~~ 192 (205) T PRK11475 131 QSRMLSPTEREILRFMSRGYSMPQIAEQLERNIKTIRAHKFNVMSKLGVSSDAGLLDAADIL 192 (205) T ss_pred CCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHH T ss_conf 67889858999999997699999999997888889999999999982999879999999999 No 21 >COG4566 TtrR Response regulator [Signal transduction mechanisms] Probab=99.38 E-value=2.4e-12 Score=107.14 Aligned_cols=63 Identities=29% Similarity=0.351 Sum_probs=60.0 Q ss_pred CCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCC Q ss_conf 444998999999999879997899999499988999999999998079978999999997699 Q gi|254780693|r 171 ARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFGY 233 (235) Q Consensus 171 ~~~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~~~Gl 233 (235) ...|||||+|||..+.+|+.||+||..||||++||+.|..|+++|+++.|-.+.|-.|...|. T Consensus 140 l~tLT~RERqVl~~vV~G~~NKqIA~dLgiS~rTVe~HRanvM~Km~a~SlaeLvr~a~~~~~ 202 (202) T COG4566 140 LATLTPRERQVLDLVVRGLMNKQIAFDLGISERTVELHRANVMEKMQARSLAELVRMALSLGL 202 (202) T ss_pred HHHCCHHHHHHHHHHHCCCCCHHHHHHCCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHCCC T ss_conf 986698899999999837630899998398664599999999999733319999999985459 No 22 >COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription] Probab=99.38 E-value=2.4e-12 Score=107.24 Aligned_cols=63 Identities=40% Similarity=0.553 Sum_probs=60.7 Q ss_pred CCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCC Q ss_conf 449989999999998799978999994999889999999999980799789999999976999 Q gi|254780693|r 172 RNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFGYI 234 (235) Q Consensus 172 ~~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~~~Gli 234 (235) ..||+||.+|++|++.|++++|||..|+||++||++|+.++++|||+.||+++++++.+.|.+ T Consensus 3 ~~Lt~rE~~~~~l~~~G~s~~eia~~l~is~~tV~~h~~~i~~Kl~~~~r~~~~~~~~~~~~~ 65 (65) T COG2771 3 ADLTPREREILRLVAQGKSNKEIARILGISEETVKTHLRNIYRKLGVKNRVELVALALRLGLI 65 (65) T ss_pred CCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCC T ss_conf 113888999999998699899999998779999999999999997758699999999985449 No 23 >pfam03472 Autoind_bind Autoinducer binding domain. This domain is found a a large family of transcriptional regulators. This domain specifically binds to autoinducer molecules. Probab=99.31 E-value=2.6e-10 Score=92.66 Aligned_cols=129 Identities=16% Similarity=0.052 Sum_probs=103.6 Q ss_pred CHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCEEEECCCCCHHHHHHHHHHHHHCCCHHHHHHHHCCCCEEECCH Q ss_conf 59999999999999858378589984177787310250442278778999624874441208799999617998373101 Q gi|254780693|r 13 SLQELSPRLHLIQNRIKARNFALYTINSALDFPRRQQLICELHNYDLDSGDIPNILIETYGDDFLFHFNSGLLPIIWQSI 92 (235) Q Consensus 13 sl~dl~~~l~~l~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dp~~~~~~~~~~p~~~~~~ 92 (235) +.+++...+..+.+.+++++|+|..... ...........+||+.+|.+.|....+...||++.++..+..|+.|+.. T Consensus 1 ~~~~l~~~l~~~~~~lGf~~~~y~~~~~---~~~~~~~~~~~~~yP~~W~~~Y~~~~y~~~DPv~~~~~~~~~p~~W~~~ 77 (146) T pfam03472 1 SEEELWDLLERLAAALGFDYFAYGLLPP---SPGSRPDVLLLSNYPAEWVERYVEEGYYRIDPVVRHALRSSTPFSWSDL 77 (146) T ss_pred CHHHHHHHHHHHHHHCCCCEEEEEEECC---CCCCCCCEEEEECCCHHHHHHHHHCCCEECCHHHHHHHCCCCCEECCCC T ss_conf 9799999999999976998799974358---9899876799708999999999977955508799998628999887768 Q ss_pred HHHCCCCCHHHHHHHHHHHCCCCCEEEEEEECCCCCCEEEEECCCCCCCCHHHHH Q ss_conf 3314667213678996542585535899721688752345410588789989999 Q gi|254780693|r 93 QEETVIESSGQLSVRLEGGLLPFAGIAFPVRLGFHKNGYVIFTSEFLMLANEVII 147 (235) Q Consensus 93 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~pv~~~~~~~~~~~~~~~~~~~~~~~~~ 147 (235) .. .......++.....+|++.|+++|++.+.+..+++++++......+.+.. T Consensus 78 ~~---~~~~~~~~~~~a~~~Gl~~G~~~pv~~~~g~~g~~s~a~~~~~~~~~~~~ 129 (146) T pfam03472 78 DL---ASPRARRVFDEARDFGLRAGYTVPVHGPNGRLGALSLAGDGRDLDAVELI 129 (146) T ss_pred CC---CCHHHHHHHHHHHHCCCCCEEEEEEECCCCCEEEEEEECCCCCCCHHHHH T ss_conf 66---79779999999998599625899988799988999985699998989999 No 24 >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=98.46 E-value=3.7e-07 Score=70.16 Aligned_cols=46 Identities=35% Similarity=0.406 Sum_probs=43.3 Q ss_pred CCCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 4499899999999-987999789999949998899999999999807 Q gi|254780693|r 172 RNLTERETSCLQL-AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 172 ~~LT~RE~evL~l-~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) +.|.++-++|-.+ --+|+|++|||..||||++||++|++.++++|- T Consensus 118 ~~LPe~~R~iF~lsr~eg~s~~EIA~~L~iS~~TVe~hi~~ALk~LR 164 (167) T TIGR02985 118 EKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKALKFLR 164 (167) T ss_pred HHCCHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 75689899999998861798678998848988899999999999998 No 25 >PRK06930 positive control sigma-like factor; Validated Probab=98.20 E-value=3.2e-06 Score=63.50 Aligned_cols=46 Identities=35% Similarity=0.405 Sum_probs=42.4 Q ss_pred CCCHHHHHH-HHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCC Q ss_conf 499899999-9999879997899999499988999999999998079 Q gi|254780693|r 173 NLTERETSC-LQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDA 218 (235) Q Consensus 173 ~LT~RE~ev-L~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~ 218 (235) .||+||++| +-.-.+|+|..|||..||||..||+.|+.++.+|+.- T Consensus 114 ~Lt~rErevfll~~~~glsy~EIA~~L~Is~~tV~~~l~RA~~Ki~~ 160 (170) T PRK06930 114 VLTEREKEVYLMHRGYGLSYSEIAAYLNIKKSTVQSMIERAEKKIAK 160 (170) T ss_pred HCCHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH T ss_conf 56988889998897618889999999798899999999999999999 No 26 >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=98.16 E-value=5.4e-06 Score=61.91 Aligned_cols=45 Identities=33% Similarity=0.443 Sum_probs=42.0 Q ss_pred CCCHHHHHHHHHHH-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 49989999999998-7999789999949998899999999999807 Q gi|254780693|r 173 NLTERETSCLQLAG-DGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 173 ~LT~RE~evL~l~a-~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) .|.|++++|+.|-- +|+|++|||..||||++||+.++..++++|. T Consensus 135 ~Lpp~~r~v~~L~~~eglS~~EIAe~Lgis~~TVk~rl~~Ar~~Lr 180 (185) T pfam07638 135 SLSPRQARLVELRFFAGLSNDEIAERLGVSERTVERNWALARAWLH 180 (185) T ss_pred CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 4899888898889975999999999979699899999999999999 No 27 >PRK12523 RNA polymerase sigma factor; Reviewed Probab=98.16 E-value=5.6e-06 Score=61.81 Aligned_cols=45 Identities=31% Similarity=0.459 Sum_probs=41.9 Q ss_pred CCCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHC Q ss_conf 4499899999999-98799978999994999889999999999980 Q gi|254780693|r 172 RNLTERETSCLQL-AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKL 216 (235) Q Consensus 172 ~~LT~RE~evL~l-~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL 216 (235) ..|++++++|+.| --+|+|.+|||.+||||++||+.|+.++++++ T Consensus 118 ~~Lp~~~R~v~~L~~~eGls~~EIA~~LgiS~~tVk~~l~rAl~~~ 163 (172) T PRK12523 118 GKLSSKARAAFLYNRLDGMGHAEIAERLGVSVSRVRQYLAQGLRQC 163 (172) T ss_pred HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH T ss_conf 6499999999999999399999999998939999999999999999 No 28 >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=98.10 E-value=8.4e-06 Score=60.54 Aligned_cols=45 Identities=44% Similarity=0.507 Sum_probs=42.8 Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 4998999999999-87999789999949998899999999999807 Q gi|254780693|r 173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) .|+++|++|+.+- -+|+|.+|||.+||||+.||+.++.++++||- T Consensus 114 ~Lp~~~r~~~~l~~~~~~s~~eIA~~lg~s~~~v~~~~~ra~~~L~ 159 (162) T TIGR02937 114 KLPEREREVLVLRYLEGLSYKEIAEILGISEGTVKSRLKRARKKLR 159 (162) T ss_pred HCCHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 4799899999999971899889999868999999999999999998 No 29 >PRK08295 RNA polymerase factor sigma-70; Validated Probab=98.08 E-value=4.6e-05 Score=55.28 Aligned_cols=45 Identities=33% Similarity=0.420 Sum_probs=43.2 Q ss_pred CCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 499899999999987999789999949998899999999999807 Q gi|254780693|r 173 NLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 173 ~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) .|+++|++|+.+--+|+|.+|||.+||||+.||+.-+.++++||- T Consensus 155 ~l~~~e~~V~~~~~eg~s~~EIA~~l~is~~tV~~~l~RarkkLr 199 (209) T PRK08295 155 LLSDLEKEVLELYLDGKSYQEIAEELNRHVKSIDNALQRVKRKLE 199 (209) T ss_pred CCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 691899999999986999999999989299999999999999999 No 30 >PRK12527 RNA polymerase sigma factor; Reviewed Probab=98.07 E-value=1e-05 Score=59.89 Aligned_cols=46 Identities=24% Similarity=0.265 Sum_probs=42.8 Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCC Q ss_conf 4998999999999-879997899999499988999999999998079 Q gi|254780693|r 173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDA 218 (235) Q Consensus 173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~ 218 (235) .|+|++++|+.+- -+|+|.+|||..||||++||+.|+.+++++|-. T Consensus 105 ~Lp~~~R~v~~L~~~egls~~EIA~~lgis~~tVk~~l~rA~k~Lr~ 151 (159) T PRK12527 105 ELPPICRESFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAMKHCRV 151 (159) T ss_pred HCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH T ss_conf 69999989998898739799999999891999999999999999999 No 31 >PRK07037 extracytoplasmic-function sigma-70 factor; Validated Probab=98.07 E-value=1e-05 Score=59.94 Aligned_cols=45 Identities=24% Similarity=0.296 Sum_probs=41.6 Q ss_pred CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHC Q ss_conf 44998999999999-8799978999994999889999999999980 Q gi|254780693|r 172 RNLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKL 216 (235) Q Consensus 172 ~~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL 216 (235) ..|.+++++|+.+. -+|+|.+|||.+||||++||+.|+.+++++| T Consensus 122 ~~LP~~~R~v~~L~~~eg~s~~EIAe~LgiS~~tVk~~l~rAl~~L 167 (183) T PRK07037 122 DELPARTRAAFEMVRLRGETLQDIARELNVSQTLVNFMIRDALRHC 167 (183) T ss_pred HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH T ss_conf 8199999999898987398999999998929999999999999999 No 32 >PRK12525 RNA polymerase sigma factor; Provisional Probab=98.05 E-value=1.2e-05 Score=59.47 Aligned_cols=44 Identities=25% Similarity=0.405 Sum_probs=40.9 Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHC Q ss_conf 4998999999999-8799978999994999889999999999980 Q gi|254780693|r 173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKL 216 (235) Q Consensus 173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL 216 (235) .|+|+.++|+.+- -+|+|.+|||.+||||++||+.|+.++++.. T Consensus 118 ~LP~~~R~vflL~~~eGlsy~EIAe~LgIS~~tV~~~l~rAl~~c 162 (168) T PRK12525 118 GLSGKARAAFLMSQLEGLTYVEIGERLGVSLSRIHQYMVEAFKCC 162 (168) T ss_pred CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH T ss_conf 399999999999999299999999998979999999999999999 No 33 >PRK09646 RNA polymerase sigma factor SigK; Reviewed Probab=98.04 E-value=1.1e-05 Score=59.80 Aligned_cols=45 Identities=29% Similarity=0.428 Sum_probs=41.4 Q ss_pred CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHC Q ss_conf 44998999999999-8799978999994999889999999999980 Q gi|254780693|r 172 RNLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKL 216 (235) Q Consensus 172 ~~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL 216 (235) ..|++++++|+.+. -+|+|.+|||.+||||+.||+.|+.++++|| T Consensus 141 ~~Lp~~~R~vi~L~~~~g~s~~EIA~~Lgis~~TVk~rl~rA~~~L 186 (194) T PRK09646 141 DALTDTQREAITLAYYGGLTYREVAERLAVPLGTVKTRMRDGLRRL 186 (194) T ss_pred HHCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH T ss_conf 8678157899999999399999999998919999999999999999 No 34 >PRK09637 RNA polymerase sigma factor SigZ; Provisional Probab=98.01 E-value=1.6e-05 Score=58.46 Aligned_cols=46 Identities=37% Similarity=0.527 Sum_probs=42.6 Q ss_pred CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 44998999999999-87999789999949998899999999999807 Q gi|254780693|r 172 RNLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 172 ~~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) ..|++++++|+.+- -+|+|.+|||.+||||+.||+.++.++++||- T Consensus 105 ~~Lp~~~R~v~~L~~~eg~s~~EIA~~L~is~~tVksrl~RAr~~Lr 151 (181) T PRK09637 105 DALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRGRVKLK 151 (181) T ss_pred HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 76999998997999885999999999989499999999999999999 No 35 >PRK11922 RNA polymerase sigma factor; Provisional Probab=98.01 E-value=1.6e-05 Score=58.51 Aligned_cols=44 Identities=30% Similarity=0.302 Sum_probs=42.1 Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHC Q ss_conf 4998999999999-8799978999994999889999999999980 Q gi|254780693|r 173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKL 216 (235) Q Consensus 173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL 216 (235) .|++.+++|+.+- -+|+|.+|||.+||||++||+.++.++++|| T Consensus 149 ~Lp~~~R~v~~L~~~eglS~~EIA~~Lgis~~TVKsrL~RArk~L 193 (231) T PRK11922 149 ALPDAFRAVFVLRVVEELSVEETAQALGLPEETVKTRLHRARRLL 193 (231) T ss_pred HCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH T ss_conf 099999999999999399999999998939999999999999999 No 36 >PRK13919 putative RNA polymerase sigma E protein; Provisional Probab=97.99 E-value=2e-05 Score=57.86 Aligned_cols=45 Identities=31% Similarity=0.449 Sum_probs=41.4 Q ss_pred CCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 499899999999-987999789999949998899999999999807 Q gi|254780693|r 173 NLTERETSCLQL-AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 173 ~LT~RE~evL~l-~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) .|+|++++|+.+ --+|+|.+|||.+||||++||+.|+.++++||. T Consensus 136 ~L~~~~r~vi~L~~~~g~s~~EIA~~L~is~~TVk~~l~rA~k~Lr 181 (187) T PRK13919 136 ALSPEERRVIEVLYYQGYTHREAARLLGLPLGTLKTWARRALSKLK 181 (187) T ss_pred CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 4999999999999985999999999989399999999999999999 No 37 >PRK09645 RNA polymerase sigma factor SigL; Provisional Probab=97.98 E-value=1.9e-05 Score=57.99 Aligned_cols=46 Identities=26% Similarity=0.343 Sum_probs=42.7 Q ss_pred CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 44998999999999-87999789999949998899999999999807 Q gi|254780693|r 172 RNLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 172 ~~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) ..|++++++|+.+. -+|+|.+|||.+||||++||+.|+.++++||- T Consensus 115 ~~L~~~~r~v~~l~~~~g~s~~EIA~~l~is~~tVk~~l~ra~~~Lr 161 (171) T PRK09645 115 AQLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRLHYAVRALR 161 (171) T ss_pred HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 75999988798999986999999999989299999999999999999 No 38 >PRK09047 RNA polymerase factor sigma-70; Validated Probab=97.98 E-value=1.8e-05 Score=58.10 Aligned_cols=45 Identities=24% Similarity=0.257 Sum_probs=42.3 Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 4998999999999-87999789999949998899999999999807 Q gi|254780693|r 173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) .|++++++|+.|- -+|+|.+|||.+||||+.||+.|+.++++||- T Consensus 106 ~Lp~~qR~vl~L~~~egls~~EIA~~l~is~~tVk~~l~RAr~~Lr 151 (161) T PRK09047 106 KLPARQREAFLLRYWEDMDVAETAAAMGCSEGSVKTHCSRATHTLA 151 (161) T ss_pred HCCHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 1999999998999998779999999989699999999999999999 No 39 >PRK12519 RNA polymerase sigma factor; Provisional Probab=97.96 E-value=2e-05 Score=57.89 Aligned_cols=46 Identities=33% Similarity=0.474 Sum_probs=42.6 Q ss_pred CCCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 4499899999999-987999789999949998899999999999807 Q gi|254780693|r 172 RNLTERETSCLQL-AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 172 ~~LT~RE~evL~l-~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) ..|++++++|+.+ .-+|+|.+|||.+||||++||+.++.++++||- T Consensus 140 ~~Lp~~~R~v~~L~~~eg~s~~EIA~~lgis~~tVk~rl~rA~~~Lr 186 (194) T PRK12519 140 AQLPESQRQVLELAYYEGLSQSEIAKRLGIPLGTVKARARQGLLKLR 186 (194) T ss_pred HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 81998875688999981999999999989499999999999999999 No 40 >PRK09651 RNA polymerase sigma factor FecI; Provisional Probab=97.96 E-value=2.2e-05 Score=57.48 Aligned_cols=45 Identities=33% Similarity=0.482 Sum_probs=41.2 Q ss_pred CCCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHC Q ss_conf 4499899999999-98799978999994999889999999999980 Q gi|254780693|r 172 RNLTERETSCLQL-AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKL 216 (235) Q Consensus 172 ~~LT~RE~evL~l-~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL 216 (235) ..|++++++|+.+ --+|+|.+|||.+||||++||+.|+.++.+.+ T Consensus 118 ~~Lp~~~R~v~~L~~~egls~~EIA~~lgiS~~tVk~~l~rAlk~c 163 (172) T PRK09651 118 DGLNGKTREAFLLSQLDGLTYSEIAHKLGVSISSVKKYVAKAVEHC 163 (172) T ss_pred HHCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH T ss_conf 7099999999999988399999999998939999999999999999 No 41 >PRK09652 RNA polymerase sigma factor RpoE; Provisional Probab=97.96 E-value=2.1e-05 Score=57.63 Aligned_cols=45 Identities=31% Similarity=0.373 Sum_probs=42.6 Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 4998999999999-87999789999949998899999999999807 Q gi|254780693|r 173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) .|++++++|+.+. -+|+|.+|||.+||||+.||+.|+.++++||. T Consensus 137 ~L~~~~r~v~~l~~~~~~s~~EIA~~lgis~~tVk~~l~Ra~~~Lr 182 (192) T PRK09652 137 SLPEELRTAITLREIEGLSYEEIAEIMGCPIGTVRSRIFRAREALR 182 (192) T ss_pred HCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 3999999888899972999999999989399999999999999999 No 42 >PRK09638 RNA polymerase sigma factor SigY; Reviewed Probab=97.94 E-value=2.5e-05 Score=57.15 Aligned_cols=46 Identities=30% Similarity=0.315 Sum_probs=42.6 Q ss_pred CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 44998999999999-87999789999949998899999999999807 Q gi|254780693|r 172 RNLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 172 ~~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) ..|++++++|+.+- -+|+|.+|||.+||||++||+.++.++++||- T Consensus 126 ~~Lp~~~r~v~~L~~~eg~s~~EIA~~l~is~~tVk~~l~rA~~~Lr 172 (177) T PRK09638 126 MKLPPELRAPFILKHYYGYTYEEIAKMLGIPEGTVKSRVHHGLKKIR 172 (177) T ss_pred HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 75999898999999991999999999989399999999999999999 No 43 >PRK09639 RNA polymerase sigma factor SigX; Provisional Probab=97.94 E-value=2.3e-05 Score=57.39 Aligned_cols=45 Identities=36% Similarity=0.519 Sum_probs=42.4 Q ss_pred CCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 499899999999987999789999949998899999999999807 Q gi|254780693|r 173 NLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 173 ~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) .|++++++|+.+--+|+|.+|||.+||||+.||+.++.++++||- T Consensus 112 ~Lp~~~r~v~~l~~~g~s~~EIA~~l~is~~tVk~~l~RA~~~Lr 156 (166) T PRK09639 112 KMTERDRTVLLLRFSGYSYKEIAQALGIDESSVGTTLHRAKKKFR 156 (166) T ss_pred HCCHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 399999999999993899999999989199999999999999999 No 44 >PRK12515 RNA polymerase sigma factor; Provisional Probab=97.94 E-value=3.8e-05 Score=55.87 Aligned_cols=57 Identities=23% Similarity=0.236 Sum_probs=50.0 Q ss_pred CCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCC Q ss_conf 499899999999-9879997899999499988999999999998079978999999997699 Q gi|254780693|r 173 NLTERETSCLQL-AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFGY 233 (235) Q Consensus 173 ~LT~RE~evL~l-~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~~~Gl 233 (235) .|++++++|+.+ .-+|+|.+|||.+||||++||+.++.++++|| |.++-+..+..|| T Consensus 131 ~L~~~~R~vi~l~~~e~~s~~EIA~~lgis~~tV~~~l~RAr~~L----r~~L~~~g~~~g~ 188 (189) T PRK12515 131 KLSPAHREIIDLVYYHEKSVEEVGEIVGIPESTVKTRMFYARKKL----AELLKAAGVERGW 188 (189) T ss_pred CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH----HHHHHHHCCCCCC T ss_conf 599999999999998499999999998929999999999999999----9999972833589 No 45 >PRK12526 RNA polymerase sigma factor; Provisional Probab=97.93 E-value=2.8e-05 Score=56.79 Aligned_cols=45 Identities=24% Similarity=0.330 Sum_probs=42.1 Q ss_pred CCCHHHHHHHHHHH-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 49989999999998-7999789999949998899999999999807 Q gi|254780693|r 173 NLTERETSCLQLAG-DGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 173 ~LT~RE~evL~l~a-~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) .|.+.+++|+.+.- +|+|.+|||.+||||++||+.|+.++++||. T Consensus 153 ~LP~~~R~vi~L~~~egls~~EIA~~l~is~~TVksrl~rAlk~LR 198 (206) T PRK12526 153 KLPEAQQTVVKGVYFQELSQEQLAQQLNVPLGTVKSRLRLALAKLK 198 (206) T ss_pred CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 6899988898999985999999999989399999999999999999 No 46 >PRK05602 RNA polymerase sigma factor; Reviewed Probab=97.93 E-value=2.6e-05 Score=56.99 Aligned_cols=46 Identities=30% Similarity=0.403 Sum_probs=42.4 Q ss_pred CCCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 4499899999999-987999789999949998899999999999807 Q gi|254780693|r 172 RNLTERETSCLQL-AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 172 ~~LT~RE~evL~l-~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) ..|++++++|+.+ .-+|+|.+|||.+||||++||+.++.++++||- T Consensus 127 ~~Lp~~~R~v~~L~~~~g~s~~EIA~~l~is~~tVk~~l~RAr~~Lr 173 (186) T PRK05602 127 AALPERQREAIVLQYYQGLSNIEAARVMGLSVDALESLLARARRALR 173 (186) T ss_pred HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 75998788999999863899999999989399999999999999999 No 47 >PRK12524 RNA polymerase sigma factor; Provisional Probab=97.93 E-value=2.7e-05 Score=56.95 Aligned_cols=46 Identities=26% Similarity=0.376 Sum_probs=42.6 Q ss_pred CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 44998999999999-87999789999949998899999999999807 Q gi|254780693|r 172 RNLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 172 ~~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) ..|++++++|+.|- -+|+|.+|||.+||||+.||+.++.++++||- T Consensus 135 ~~Lp~~~R~vi~L~~~eg~s~~EIA~~lgis~~tVk~~l~Rark~Lr 181 (196) T PRK12524 135 AALPERQRQAVVLRHIEGLSNPEIAEVMQIGVEAVESLTARGKRALA 181 (196) T ss_pred HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 85999999998999980899999999989299999999999999999 No 48 >PRK12537 RNA polymerase sigma factor; Provisional Probab=97.93 E-value=2.6e-05 Score=56.99 Aligned_cols=45 Identities=31% Similarity=0.499 Sum_probs=41.0 Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 4998999999999-87999789999949998899999999999807 Q gi|254780693|r 173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) .|+|.+++|+.+. -+|+|.+|||.+||||++||+.|+.++++||- T Consensus 135 ~L~~~~r~~i~l~~~eg~s~~EIA~~l~is~~TVk~rl~rA~~~LR 180 (184) T PRK12537 135 QLEPARRNCILHAYVDGCSHAEIAQRLGAPLGTVKAWIKRSLKALR 180 (184) T ss_pred HCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 0999899999998843999999999989299999999999999999 No 49 >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=97.92 E-value=2.3e-05 Score=57.43 Aligned_cols=45 Identities=38% Similarity=0.455 Sum_probs=42.3 Q ss_pred CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHC Q ss_conf 44998999999999-8799978999994999889999999999980 Q gi|254780693|r 172 RNLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKL 216 (235) Q Consensus 172 ~~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL 216 (235) ..|++++++++.+- -+|+|.+|||.+||+|++||+.++.++++|| T Consensus 9 ~~Lp~~~r~~~~l~~~~~~s~~eIA~~lg~s~~tVk~~l~RA~~~L 54 (54) T pfam08281 9 EELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54 (54) T ss_pred HCCCHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHCC T ss_conf 8599999989687998785999999998949999999999999719 No 50 >PRK12516 RNA polymerase sigma factor; Provisional Probab=97.91 E-value=3e-05 Score=56.61 Aligned_cols=45 Identities=27% Similarity=0.451 Sum_probs=41.9 Q ss_pred CCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 499899999999-987999789999949998899999999999807 Q gi|254780693|r 173 NLTERETSCLQL-AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 173 ~LT~RE~evL~l-~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) .|++.+++|+.+ --+|+|.+|||.+||||+.||+.++.++++||- T Consensus 119 ~Lp~~~R~vl~L~~~egls~~EIAe~Lgis~~TVksrl~RAr~~Lr 164 (190) T PRK12516 119 QLPDDQREAIILIGASGFAYEEAAEICGCAVGTIKSRVSRARARLQ 164 (190) T ss_pred CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 1999998999989982999999999989499999999999999999 No 51 >PRK12529 RNA polymerase sigma factor; Provisional Probab=97.91 E-value=3.1e-05 Score=56.45 Aligned_cols=44 Identities=30% Similarity=0.453 Sum_probs=39.6 Q ss_pred CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHH Q ss_conf 44998999999999-879997899999499988999999999998 Q gi|254780693|r 172 RNLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVK 215 (235) Q Consensus 172 ~~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~K 215 (235) ..|+||.++|..+- .+|+|.+|||..||||++||+.|+.+++.. T Consensus 126 ~~Lp~r~R~vF~L~r~eGls~~EIAe~LgiS~~tV~~~l~rAl~~ 170 (178) T PRK12529 126 DTLRPRVKQAFLMATLDGMKQKDIAQALDIALPTVKKYIHQAYVT 170 (178) T ss_pred HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHH T ss_conf 569978889987998829999999999895999999999999999 No 52 >PRK12512 RNA polymerase sigma factor; Provisional Probab=97.91 E-value=3.2e-05 Score=56.36 Aligned_cols=46 Identities=30% Similarity=0.325 Sum_probs=42.6 Q ss_pred CCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCC Q ss_conf 499899999999-9879997899999499988999999999998079 Q gi|254780693|r 173 NLTERETSCLQL-AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDA 218 (235) Q Consensus 173 ~LT~RE~evL~l-~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~ 218 (235) .|++++++|+.+ --+|+|.+|||.+||||+.||+.++.++++||.. T Consensus 131 ~Lp~~~R~vi~L~~~~g~s~~EIA~~lgis~~tVk~~l~RA~~~Lr~ 177 (184) T PRK12512 131 TLPPRQRDVVQSIAVEGASIKETAAKLSMSEGAVRVALHRGLAALAA 177 (184) T ss_pred CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH T ss_conf 89999999999998559799999999891999999999999999999 No 53 >PRK12541 RNA polymerase sigma factor; Provisional Probab=97.90 E-value=3.3e-05 Score=56.27 Aligned_cols=45 Identities=29% Similarity=0.313 Sum_probs=42.3 Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 4998999999999-87999789999949998899999999999807 Q gi|254780693|r 173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) .|++.+++|+.|- -+|+|.+|||.+||||+.||+.++.++++||- T Consensus 112 ~Lp~~~R~v~~L~~~~g~s~~EIA~~lgis~~tVk~~l~RArk~Lr 157 (161) T PRK12541 112 SLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKETK 157 (161) T ss_pred CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 1999999999989974999999999989399999999999999998 No 54 >PRK12543 RNA polymerase sigma factor; Provisional Probab=97.90 E-value=3.6e-05 Score=56.05 Aligned_cols=44 Identities=27% Similarity=0.359 Sum_probs=41.9 Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHC Q ss_conf 4998999999999-8799978999994999889999999999980 Q gi|254780693|r 173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKL 216 (235) Q Consensus 173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL 216 (235) .|++++++|+.+- -+|+|.+|||.+||||++||+.++.++++|| T Consensus 129 ~Lp~~~R~vi~L~~~~g~s~~EIA~~l~is~~tVk~rl~rA~k~L 173 (190) T PRK12543 129 KLPYKLKQVIILRYLHDYSQEEVAQILHIPIGTVKSRIHAALKKL 173 (190) T ss_pred CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH T ss_conf 499999999999998599999999998939999999999999999 No 55 >PRK12514 RNA polymerase sigma factor; Provisional Probab=97.89 E-value=3.3e-05 Score=56.29 Aligned_cols=45 Identities=22% Similarity=0.419 Sum_probs=41.6 Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 4998999999999-87999789999949998899999999999807 Q gi|254780693|r 173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) .|++++++|+.+. -+|+|.+|||.+||||++||+.++.++++||- T Consensus 129 ~Lp~~~r~~~~l~~~eg~s~~EIA~~l~is~~tVk~~l~rA~~~Lr 174 (179) T PRK12514 129 ELEKDRAAAVRRAYLEGLSYKELAERHDVPLNTMRTWLRRSLLKLR 174 (179) T ss_pred HCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 7559999999999606998999999889099999999999999999 No 56 >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=97.88 E-value=3.7e-05 Score=55.94 Aligned_cols=46 Identities=43% Similarity=0.481 Sum_probs=43.0 Q ss_pred CCCCHHHHHHHHHHH-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 449989999999998-7999789999949998899999999999807 Q gi|254780693|r 172 RNLTERETSCLQLAG-DGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 172 ~~LT~RE~evL~l~a-~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) ..|++++++|+.|-- +|+|.+|||.+||||+.||+.++.++++||- T Consensus 9 ~~L~~~~r~vl~l~y~~~~s~~EIa~~lgis~~tVk~~l~rA~~~Lr 55 (55) T cd06171 9 DKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55 (55) T ss_pred HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC T ss_conf 83999998989999980999999999989599999999999998758 No 57 >PRK09641 RNA polymerase sigma factor SigW; Provisional Probab=97.86 E-value=3.9e-05 Score=55.76 Aligned_cols=45 Identities=24% Similarity=0.304 Sum_probs=42.4 Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 4998999999999-87999789999949998899999999999807 Q gi|254780693|r 173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) .|++++++|+.|- -+|+|.+|||.+||||+.||+.++.++++||- T Consensus 136 ~Lp~~~r~v~~L~~~~~~s~~EIA~~l~is~~tVk~~l~RAr~~Lr 181 (187) T PRK09641 136 QLPDKYRTVIVLKYIEELSLKEISEILDLPVGTVKTRIHRGREALR 181 (187) T ss_pred HCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 2898888999999982998999999989399999999999999999 No 58 >PRK09643 RNA polymerase sigma factor SigM; Reviewed Probab=97.86 E-value=4.4e-05 Score=55.38 Aligned_cols=45 Identities=22% Similarity=0.332 Sum_probs=42.2 Q ss_pred CCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 499899999999-987999789999949998899999999999807 Q gi|254780693|r 173 NLTERETSCLQL-AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 173 ~LT~RE~evL~l-~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) .|++.+++|+.| .-+|+|.+|||.+||||+.||+.++.++++||- T Consensus 131 ~Lp~~~R~vl~L~~~eg~s~~EIA~~lgis~~tVKsrl~RAr~~Lr 176 (197) T PRK09643 131 RLPVEQRAALVAVDMQGYSVADTARMLGVAEGTVKSRCARGRARLA 176 (197) T ss_pred CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 6999887999999981999999999989399999999999999999 No 59 >PRK12547 RNA polymerase sigma factor; Provisional Probab=97.86 E-value=4.5e-05 Score=55.33 Aligned_cols=45 Identities=27% Similarity=0.384 Sum_probs=42.4 Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 4998999999999-87999789999949998899999999999807 Q gi|254780693|r 173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) .|++.+++|+.+. -+|+|.+|||.+||||++||+.++.++++||- T Consensus 112 ~Lp~~~r~v~~L~~~~g~s~~EIA~~lgis~~tVksrl~rAr~~Lr 157 (164) T PRK12547 112 LLPADQREAIILIGASGFSYEEAAEICGCAVGTIKSRVSRARNRLQ 157 (164) T ss_pred HCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 5899999999989984999999999989399999999999999999 No 60 >PRK12528 RNA polymerase sigma factor; Provisional Probab=97.85 E-value=4.7e-05 Score=55.23 Aligned_cols=45 Identities=33% Similarity=0.448 Sum_probs=40.5 Q ss_pred CCCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHC Q ss_conf 4499899999999-98799978999994999889999999999980 Q gi|254780693|r 172 RNLTERETSCLQL-AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKL 216 (235) Q Consensus 172 ~~LT~RE~evL~l-~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL 216 (235) ..|.++.++|+.+ --+|+|.+|||.+||||+.||+.|+.+++..- T Consensus 118 ~~LP~~~R~vf~L~r~~gls~~EIA~~LgiS~~tVk~~l~rA~~~c 163 (167) T PRK12528 118 DGLPPLVKRAFLLAQVDGLGYGEIATELGISLATVKRYLNKAAMRC 163 (167) T ss_pred HCCCHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHH T ss_conf 7099999999999998298999999997979999999999999999 No 61 >PRK12534 RNA polymerase sigma factor; Provisional Probab=97.85 E-value=4.8e-05 Score=55.15 Aligned_cols=45 Identities=24% Similarity=0.361 Sum_probs=41.9 Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 4998999999999-87999789999949998899999999999807 Q gi|254780693|r 173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) .|+|.+++|+.+. -+|+|.+|||.+||||++||+.++.++++||- T Consensus 137 ~L~~~~r~vi~l~~~eg~s~~EIA~~l~i~~gTVksrl~ra~~~Lr 182 (187) T PRK12534 137 ELEPPRSELIRTAFFEGITYEELAARTDTPIGTVKSWIRRGLAKLK 182 (187) T ss_pred HCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 6899899999999984999999999989199999999999999999 No 62 >PRK12538 RNA polymerase sigma factor; Provisional Probab=97.85 E-value=4.8e-05 Score=55.12 Aligned_cols=45 Identities=24% Similarity=0.338 Sum_probs=42.1 Q ss_pred CCCHHHHHHHHHHH-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 49989999999998-7999789999949998899999999999807 Q gi|254780693|r 173 NLTERETSCLQLAG-DGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 173 ~LT~RE~evL~l~a-~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) .|.+++++|+.|.- +|+|.+|||.+||||+.||+.++.++++||- T Consensus 171 ~Lp~~~R~vl~L~~~egls~~EIA~~Lgis~~TVKsrL~RAr~~LR 216 (233) T PRK12538 171 RLPEQQRIAVILSYHENMSNGEIAEVMDTTVAAVESLLKRGRQQLR 216 (233) T ss_pred CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 5999999999999984999999999989299999999999999999 No 63 >PRK12517 RNA polymerase sigma factor; Provisional Probab=97.82 E-value=5.7e-05 Score=54.59 Aligned_cols=45 Identities=36% Similarity=0.335 Sum_probs=42.1 Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 4998999999999-87999789999949998899999999999807 Q gi|254780693|r 173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) .|++.+++|+.|- -+|+|.+|||.+||||+.||+.++.++++||. T Consensus 128 ~Lp~~~R~vi~L~~~eg~s~~EIA~~Lgis~~tVksrl~RAr~~Lr 173 (188) T PRK12517 128 KLDPEYREPLLLQVIGGFSGEEIAEILDLNKNTVMTRLFRARNQLK 173 (188) T ss_pred CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 6999999999999983999999999989399999999999999999 No 64 >PRK12513 RNA polymerase sigma factor; Provisional Probab=97.82 E-value=5.7e-05 Score=54.60 Aligned_cols=45 Identities=29% Similarity=0.361 Sum_probs=42.2 Q ss_pred CCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 499899999999-987999789999949998899999999999807 Q gi|254780693|r 173 NLTERETSCLQL-AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 173 ~LT~RE~evL~l-~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) .|++++++|+.+ .-+|+|.+|||.+||+|++||+.++.++++||- T Consensus 139 ~Lp~~~r~il~L~~~~g~s~~EIA~~l~is~~tVk~~l~rA~~~Lr 184 (194) T PRK12513 139 TLPDEQREVFLLREHGDLSLEEIAQLTGVPLETVKSRLRYALQKLR 184 (194) T ss_pred CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 2998999999999984999999999989499999999999999999 No 65 >PRK12542 RNA polymerase sigma factor; Provisional Probab=97.81 E-value=5.4e-05 Score=54.75 Aligned_cols=44 Identities=18% Similarity=0.272 Sum_probs=41.8 Q ss_pred CCCHHHHHHHHHHH-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHC Q ss_conf 49989999999998-799978999994999889999999999980 Q gi|254780693|r 173 NLTERETSCLQLAG-DGYTSEEIAEKLGLSVHTVNAYLGSATVKL 216 (235) Q Consensus 173 ~LT~RE~evL~l~a-~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL 216 (235) .|++++++|+.+-- +|+|.+|||.+||||+.||+.++.++++|| T Consensus 122 ~Lp~~~R~v~~L~~~~gls~~EIA~~L~is~~tVk~rl~RArk~L 166 (185) T PRK12542 122 ELNESNRQVFKYKVFYNLTYQEISSVMGITEANVRKQFERARKRV 166 (185) T ss_pred HCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH T ss_conf 299988899767998399999999998929999999999999999 No 66 >PRK11924 RNA polymerase sigma factor; Provisional Probab=97.81 E-value=5.5e-05 Score=54.73 Aligned_cols=45 Identities=33% Similarity=0.495 Sum_probs=42.5 Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 4998999999999-87999789999949998899999999999807 Q gi|254780693|r 173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) .|+|++++|+.+. .+|++.+|||.+||||++||+.|+.++++||- T Consensus 125 ~L~~~~r~il~l~~~~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr 170 (180) T PRK11924 125 ALPEKQREVFLLRYVEGLSYQEIADQLGVPLGTVKSRLRRARQKLR 170 (180) T ss_pred HCCHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 5999999999999996859999999989499999999999999999 No 67 >PRK09648 RNA polymerase sigma factor SigD; Reviewed Probab=97.81 E-value=6e-05 Score=54.43 Aligned_cols=46 Identities=28% Similarity=0.287 Sum_probs=42.8 Q ss_pred CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 44998999999999-87999789999949998899999999999807 Q gi|254780693|r 172 RNLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 172 ~~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) ..|++++++|+.+- -+|+|.+|||.+||+|+.||+.++.++++||. T Consensus 136 ~~Lp~~~R~vl~L~~~~g~s~~EIA~~lg~s~~tVk~~l~RA~~~Lr 182 (187) T PRK09648 136 EILPEKQREILILRVVVGLSAEETAEAVGSTPGAVRVAQHRALSRLR 182 (187) T ss_pred HHCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 83999999999999984999999999989399999999999999999 No 68 >PRK11923 algU RNA polymerase sigma factor AlgU; Provisional Probab=97.81 E-value=6e-05 Score=54.45 Aligned_cols=45 Identities=31% Similarity=0.330 Sum_probs=42.5 Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 4998999999999-87999789999949998899999999999807 Q gi|254780693|r 173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) .|++.+++|+.+- -+|+|.+|||.+||||++||+.++.++++||. T Consensus 138 ~Lp~~~R~v~~L~~~egls~~EIA~~l~is~~tVk~rl~RAr~~Lr 183 (193) T PRK11923 138 QLPEDLRTALTLREFDGLSYEDIASVMQCPVGTVRSRIFRAREAID 183 (193) T ss_pred CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 1789899999999994999999999989299999999999999999 No 69 >PRK09647 RNA polymerase sigma factor SigE; Reviewed Probab=97.80 E-value=6.1e-05 Score=54.40 Aligned_cols=46 Identities=26% Similarity=0.340 Sum_probs=42.8 Q ss_pred CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 44998999999999-87999789999949998899999999999807 Q gi|254780693|r 172 RNLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 172 ~~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) ..|++++++|+.|. -+|+|.+|||.+||||+.||+.++.++++||- T Consensus 156 ~~Lp~~qR~vl~Lr~~eglS~~EIAe~Lgis~gTVKsrl~RAr~~LR 202 (222) T PRK09647 156 DSLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRSRIHRGRQALR 202 (222) T ss_pred HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 82999998899879963999999999989399999999999999999 No 70 >PRK12531 RNA polymerase sigma factor; Provisional Probab=97.79 E-value=6.6e-05 Score=54.17 Aligned_cols=46 Identities=24% Similarity=0.302 Sum_probs=41.6 Q ss_pred CCCCHHHHHHHH-HHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 449989999999-9987999789999949998899999999999807 Q gi|254780693|r 172 RNLTERETSCLQ-LAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 172 ~~LT~RE~evL~-l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) ..|++.+++|+. ..-+|+|.+|||.+|+||++||+.|+.++++||- T Consensus 140 ~~Lp~~~R~vi~L~~~e~~s~~EIAe~l~is~~TVKsrl~rA~k~LR 186 (194) T PRK12531 140 DRLPKAQRDVLQAVYLEELPHQQVAEMFDIPLGTVKSRLRLAVEKLR 186 (194) T ss_pred HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 86999999999999886999999999989299999999999999999 No 71 >PRK06811 RNA polymerase factor sigma-70; Validated Probab=97.78 E-value=7.2e-05 Score=53.89 Aligned_cols=45 Identities=29% Similarity=0.338 Sum_probs=41.8 Q ss_pred CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHC Q ss_conf 44998999999999-8799978999994999889999999999980 Q gi|254780693|r 172 RNLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKL 216 (235) Q Consensus 172 ~~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL 216 (235) ..|++.+++|+.+- -+|+|.+|||.+||||+.||+.++.++++|| T Consensus 127 ~~L~~~~r~v~~l~~~~~~s~~EIA~~l~is~~tVk~rl~Rar~~L 172 (185) T PRK06811 127 NDLKKLDREIFIKRYLLGESIEEIAKKLGLTRSAIDNRLSRGRKKL 172 (185) T ss_pred HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH T ss_conf 4899999999999999499999999998929999999999999999 No 72 >PRK12539 RNA polymerase sigma factor; Provisional Probab=97.76 E-value=7.9e-05 Score=53.57 Aligned_cols=46 Identities=24% Similarity=0.268 Sum_probs=42.7 Q ss_pred CCCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 4499899999999-987999789999949998899999999999807 Q gi|254780693|r 172 RNLTERETSCLQL-AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 172 ~~LT~RE~evL~l-~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) ..|.+++++|+.+ -.+|+|.+|||.+||||+.||+.++.++++||. T Consensus 130 ~~Lp~~~r~v~~L~~~eg~s~~EIA~~lgis~~tVks~l~Rark~Lr 176 (184) T PRK12539 130 ARLPEKMRLAIQAVKLDGLSVAEAATRSGMSESAVKVSVHRGLKALA 176 (184) T ss_pred HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 84999999999999994999999999989199999999999999999 No 73 >PRK12533 RNA polymerase sigma factor; Provisional Probab=97.76 E-value=8e-05 Score=53.56 Aligned_cols=45 Identities=27% Similarity=0.222 Sum_probs=42.2 Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 4998999999999-87999789999949998899999999999807 Q gi|254780693|r 173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) .|++.+++|+.|- -+|+|.+|||.+|||++.|||.++.++++||- T Consensus 137 ~Lp~~~R~vl~Lr~~eglS~~EIAeiLgip~gTVKSRL~RAR~~Lr 182 (217) T PRK12533 137 KLPVEYREVLVLRELEDMSYREIAAIADVPVGTVMSRLARARRRLA 182 (217) T ss_pred CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 0999886899999980999999999989499999999999999999 No 74 >PRK12522 RNA polymerase sigma factor; Provisional Probab=97.76 E-value=8.5e-05 Score=53.37 Aligned_cols=45 Identities=27% Similarity=0.337 Sum_probs=42.1 Q ss_pred CCCHHHHHHHHHHH-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 49989999999998-7999789999949998899999999999807 Q gi|254780693|r 173 NLTERETSCLQLAG-DGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 173 ~LT~RE~evL~l~a-~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) .|++.+++|+.|.- +|+|.+|||.+||||++||+.++.++++||- T Consensus 119 ~L~~~~R~vi~L~~~~~~s~~EIA~~l~is~~tVksrl~rAr~~Lr 164 (173) T PRK12522 119 LLNEKYKTVLVLYYYEQYSYKEMSEILNIPIGTVKYRLNYAKKQMR 164 (173) T ss_pred CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 1999999999999983999999999989399999999999999999 No 75 >PRK09644 RNA polymerase sigma factor SigM; Provisional Probab=97.75 E-value=7.3e-05 Score=53.83 Aligned_cols=45 Identities=27% Similarity=0.210 Sum_probs=42.3 Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 4998999999999-87999789999949998899999999999807 Q gi|254780693|r 173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) .|++.+++|+.+- -+|+|.+|||.+||||+.||+.++.++++||- T Consensus 108 ~Lp~~~r~v~~L~~~~~~s~~EIA~~l~is~~tVk~rl~RAr~~Lr 153 (165) T PRK09644 108 TLPVIEAQAILLCDVHELTYEEAASVLDLKENTYKSHLFRGRKRLK 153 (165) T ss_pred CCCHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 2999999999999998889999999989399999999999999999 No 76 >PRK12520 RNA polymerase sigma factor; Provisional Probab=97.74 E-value=7.8e-05 Score=53.61 Aligned_cols=45 Identities=20% Similarity=0.273 Sum_probs=42.5 Q ss_pred CCCHHHHHHHHHHH-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 49989999999998-7999789999949998899999999999807 Q gi|254780693|r 173 NLTERETSCLQLAG-DGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 173 ~LT~RE~evL~l~a-~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) .|++++++|+.+-- +|+|.+|||..||+|+.||+.++.+++++|- T Consensus 131 ~Lp~~~R~v~~Lr~~~~ls~~EIA~~l~~s~~tVk~~l~RAR~~Lr 176 (191) T PRK12520 131 RLPARTGRVFMMREWLELETEEICKELQITATNLWVMLYRARLRLR 176 (191) T ss_pred HCCHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 7749999999999993899999999989499999999999999999 No 77 >PRK12536 RNA polymerase sigma factor; Provisional Probab=97.73 E-value=9.4e-05 Score=53.06 Aligned_cols=45 Identities=24% Similarity=0.256 Sum_probs=41.7 Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 4998999999999-87999789999949998899999999999807 Q gi|254780693|r 173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) .|++++++++.+. -+|+|.+|||.+||||+.||+.++.+++++|- T Consensus 126 ~Lp~~~R~~~~l~~~eg~s~~EIA~~lgis~~tVk~rl~Ra~k~Lr 171 (178) T PRK12536 126 QLPDRQRLPIVHVKLEGLSVEETAQLTGLSESAVKVGIHRGLKALA 171 (178) T ss_pred HCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 6999899999999885999999999989299999999999999999 No 78 >PRK12546 RNA polymerase sigma factor; Provisional Probab=97.73 E-value=9.1e-05 Score=53.15 Aligned_cols=45 Identities=31% Similarity=0.470 Sum_probs=42.4 Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 4998999999999-87999789999949998899999999999807 Q gi|254780693|r 173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) .|.+.+++|+.|. -+|+|.+|||.+||||+.||+.++.++++||- T Consensus 113 ~LP~~~R~vl~L~~~egls~~EIAe~Lgis~gTVKsRL~RAR~~Lr 158 (188) T PRK12546 113 QLPDEQREALILVGASGFSYEEAAEMCGVAVGTVKSRANRARARLA 158 (188) T ss_pred CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 6999998895879982989999999989399999999999999999 No 79 >PRK12511 RNA polymerase sigma factor; Provisional Probab=97.73 E-value=3.6e-05 Score=56.04 Aligned_cols=45 Identities=29% Similarity=0.482 Sum_probs=42.2 Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 4998999999999-87999789999949998899999999999807 Q gi|254780693|r 173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) .|++.+++|+.|. -+|+|.+|||.+||||+.||+.++.+++++|- T Consensus 111 ~Lp~~~R~vl~L~~~egls~~EIAe~Lgis~gTVKsrl~RAr~~LR 156 (182) T PRK12511 111 DLPEEQRAALHLVAIEGLSYQEAANVLGIPIGTLMSRIGRARAALR 156 (182) T ss_pred CCCHHHHHHEEEEEECCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 6999895011241007999999999989399999999999999999 No 80 >PRK12518 RNA polymerase sigma factor; Provisional Probab=97.72 E-value=9.8e-05 Score=52.92 Aligned_cols=45 Identities=31% Similarity=0.301 Sum_probs=42.0 Q ss_pred CCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 499899999999-987999789999949998899999999999807 Q gi|254780693|r 173 NLTERETSCLQL-AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 173 ~LT~RE~evL~l-~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) .|++.+++|+.+ .-+|+|.+|||.+||||++||+.++.++++||- T Consensus 120 ~Lp~~~r~vi~l~~~~~~s~~EIA~~l~is~~tVk~~l~Ra~k~Lr 165 (175) T PRK12518 120 TLSLEHRAVLVLHDLEDLPQKEIAEILNIPVGTVKSRLFYARRQLR 165 (175) T ss_pred CCCHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 6999999999999992999999999989599999999999999999 No 81 >PRK09640 RNA polymerase sigma factor SigX; Reviewed Probab=97.70 E-value=0.00012 Score=52.41 Aligned_cols=45 Identities=18% Similarity=0.152 Sum_probs=41.8 Q ss_pred CCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 499899999999-987999789999949998899999999999807 Q gi|254780693|r 173 NLTERETSCLQL-AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 173 ~LT~RE~evL~l-~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) .|+|.+++|+.+ .-+|+|.+|||.+||+|+.||+.++.++++||- T Consensus 134 ~L~~~~R~vl~L~~~~~ls~~EIA~~l~is~~tVksrl~RAr~~Lr 179 (188) T PRK09640 134 HVNPIDREILVLRFVAELEFQEIADIMHMGLSATKMRYKRALDKLR 179 (188) T ss_pred HCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 4899999999999992999999999989299999999999999999 No 82 >PRK12540 RNA polymerase sigma factor; Provisional Probab=97.69 E-value=0.00011 Score=52.43 Aligned_cols=45 Identities=27% Similarity=0.417 Sum_probs=42.8 Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 4998999999999-87999789999949998899999999999807 Q gi|254780693|r 173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) .|++.+++|+.|. -+|+|.+|||.+||||+.||+..+.++++||- T Consensus 111 ~Lp~~~R~vl~L~~~egls~~EIA~iL~is~gTVKsRL~RAr~kLr 156 (181) T PRK12540 111 KLPQDQREALILVGASGFSYEDAAAICGCAVGTIKSRVNRARSKLS 156 (181) T ss_pred CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 1999998998879980999999999989499999999999999999 No 83 >PRK09415 RNA polymerase factor sigma C; Reviewed Probab=97.69 E-value=0.00012 Score=52.26 Aligned_cols=45 Identities=22% Similarity=0.228 Sum_probs=42.4 Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 4998999999999-87999789999949998899999999999807 Q gi|254780693|r 173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) .|++++++|+.+- -+|+|.+|||.+||||++||+.++.++++||. T Consensus 127 ~L~~~~r~ii~l~~~~~~s~~EIA~~l~is~~tV~~rl~Rark~Lr 172 (177) T PRK09415 127 SLPIKYREVIYLFYYEELSIKEIATVTGVNENTIKTRLKKAKELLK 172 (177) T ss_pred CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 6999999999999980998999999889299999999999999999 No 84 >PRK06759 RNA polymerase factor sigma-70; Validated Probab=97.68 E-value=0.00013 Score=52.03 Aligned_cols=45 Identities=24% Similarity=0.099 Sum_probs=42.9 Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 4998999999999-87999789999949998899999999999807 Q gi|254780693|r 173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) .|++||+.++.+. -.|+|-+|||.+||||..||+...+++.+||- T Consensus 106 ~L~~re~~ii~~~~~~g~t~~EIA~~~gis~~~Vk~~~r~Al~KLR 151 (154) T PRK06759 106 VLDEKEKYIIFERFFVGKTMGEIALETEMTYYQVRWIYRQALEKMR 151 (154) T ss_pred HCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 4999999999999996998999999989899999999999999987 No 85 >PRK09642 RNA polymerase sigma factor SigW; Reviewed Probab=97.66 E-value=0.00014 Score=51.79 Aligned_cols=45 Identities=22% Similarity=0.141 Sum_probs=42.2 Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 4998999999999-87999789999949998899999999999807 Q gi|254780693|r 173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) .|++.+++|+.+- -+|+|.+|||.+||||++||+.++.+++++|- T Consensus 106 ~Lp~~~R~v~~L~~~e~~s~~EIA~~l~is~~tVk~~l~RArk~Lk 151 (160) T PRK09642 106 ELPENYRDVVLAHYLEEKSYQEIALQENIEVKTVEMKLYRARKWIK 151 (160) T ss_pred HCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 7999999997999982999999999989199999999999999999 No 86 >PRK12535 RNA polymerase sigma factor; Provisional Probab=97.64 E-value=0.00014 Score=51.74 Aligned_cols=45 Identities=29% Similarity=0.302 Sum_probs=42.3 Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 4998999999999-87999789999949998899999999999807 Q gi|254780693|r 173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) .|.+.+++|+.|. -+|+|.+|||.+||||+.||+..+.++++||- T Consensus 132 ~Lp~~~R~~l~L~~~~g~s~~EIA~ilgi~~gTVKsRl~RAr~~Lr 177 (195) T PRK12535 132 ALPPERREALILTQVLGYTYEEAAKIADVRVGTIRSRVARARADLV 177 (195) T ss_pred CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 4999887999999982998999999989399999999999999999 No 87 >PRK12532 RNA polymerase sigma factor; Provisional Probab=97.61 E-value=0.00018 Score=51.02 Aligned_cols=45 Identities=27% Similarity=0.377 Sum_probs=42.4 Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 4998999999999-87999789999949998899999999999807 Q gi|254780693|r 173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) .|.+++++|+.+- -+|+|.+|||.+||||+.||+.++.++++||- T Consensus 136 ~Lp~~~R~vl~L~~~egls~~EIA~~lgis~~tVks~l~RAR~~Lr 181 (195) T PRK12532 136 NLPENTARVFTLKEILGFSSDEIQQMCGISTSNYHTIMHRARESLR 181 (195) T ss_pred HCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 5999998999999981999999999989599999999999999999 No 88 >PRK09649 RNA polymerase sigma factor SigC; Reviewed Probab=97.61 E-value=0.00019 Score=50.92 Aligned_cols=46 Identities=26% Similarity=0.237 Sum_probs=42.8 Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCC Q ss_conf 4998999999999-879997899999499988999999999998079 Q gi|254780693|r 173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDA 218 (235) Q Consensus 173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~ 218 (235) .|++.+++|+.|. -+|+|.+|||.+||||+.|||.++.++++||-+ T Consensus 130 ~Lp~~~R~vl~L~~~egls~~EIA~~lg~~~gTVKsRl~RAR~~L~a 176 (185) T PRK09649 130 DLTTDQREALLLTQLLGLSYADAAAVCGCPVGTIRSRVARARDALLA 176 (185) T ss_pred CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH T ss_conf 49999999999899729999999999893999999999999999997 No 89 >PRK12544 RNA polymerase sigma factor; Provisional Probab=97.61 E-value=0.00018 Score=51.04 Aligned_cols=45 Identities=18% Similarity=0.214 Sum_probs=42.4 Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 4998999999999-87999789999949998899999999999807 Q gi|254780693|r 173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) .|++.+++|+.+- -+|+|.+|||.+||||+.||+..+.++++||- T Consensus 149 ~Lp~~~R~vl~Lr~~eglS~~EIAe~Lgis~~tVks~L~RAR~~Lr 194 (207) T PRK12544 149 ALPAKYARVFMMREFIELETPEICHNEDLTVSNLNVMLYRSRLRLR 194 (207) T ss_pred HCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 3999999999999981999999999979799999999999999999 No 90 >PRK12530 RNA polymerase sigma factor; Provisional Probab=97.55 E-value=0.00025 Score=49.98 Aligned_cols=45 Identities=16% Similarity=0.247 Sum_probs=41.9 Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 4998999999999-87999789999949998899999999999807 Q gi|254780693|r 173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) .|++++++|+.+- -+|+|.+|||.+||||+.||+.++.+++++|. T Consensus 136 ~LP~~~R~v~~Lr~~~~ls~~EIA~~l~is~~tVksrL~RAR~~Lr 181 (191) T PRK12530 136 KLPAQQARVFMMREFLELSSEQICQECHITTSNLHVLLYRARLQLQ 181 (191) T ss_pred HCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 6999999999999992999999999989699999999999999999 No 91 >COG3413 Predicted DNA binding protein [General function prediction only] Probab=97.55 E-value=0.0009 Score=46.05 Aligned_cols=45 Identities=33% Similarity=0.448 Sum_probs=40.6 Q ss_pred CCCCHHHHHHHHHHH--------CCCCHHHHHHHHCCCHHHHHHHHHHHHHHC Q ss_conf 449989999999998--------799978999994999889999999999980 Q gi|254780693|r 172 RNLTERETSCLQLAG--------DGYTSEEIAEKLGLSVHTVNAYLGSATVKL 216 (235) Q Consensus 172 ~~LT~RE~evL~l~a--------~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL 216 (235) ..||+||+++|+..- +.-+-+++|.+||||..|+..|++++-+|| T Consensus 154 ~~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLRrAe~Kl 206 (215) T COG3413 154 NDLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLRRAERKL 206 (215) T ss_pred CCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH T ss_conf 46999999999999985898887658999999995998889999999999999 No 92 >COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription] Probab=97.51 E-value=0.00028 Score=49.68 Aligned_cols=45 Identities=42% Similarity=0.504 Sum_probs=41.7 Q ss_pred CCCHHHHHHHHHHH-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 49989999999998-7999789999949998899999999999807 Q gi|254780693|r 173 NLTERETSCLQLAG-DGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 173 ~LT~RE~evL~l~a-~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) .|++++++|+.+.- +|+|.+|||..||||..||+.++.++++||. T Consensus 127 ~Lp~~~R~~~~l~~~~gls~~EIA~~l~i~~~tVks~l~ra~~~l~ 172 (182) T COG1595 127 RLPPRQREAFLLRYLEGLSYEEIAEILGISVGTVKSRLHRARKKLR 172 (182) T ss_pred CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 3999999999999985999999998959999999999999999999 No 93 >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=97.45 E-value=0.0003 Score=49.44 Aligned_cols=46 Identities=41% Similarity=0.515 Sum_probs=42.3 Q ss_pred CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 44998999999999-87999789999949998899999999999807 Q gi|254780693|r 172 RNLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 172 ~~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) ..|+++|++|+.+. -+|+|-.|||..||||+.||+..+.++.+||- T Consensus 3 ~~L~~~~r~ii~l~y~~~~t~~EIA~~lgis~~~V~~~~~ral~~LR 49 (50) T pfam04545 3 ASLPPREREVLVLRFGEGLTLEEIGERLGISRERVRQIEKRALRKLR 49 (50) T ss_pred HHCCHHHHHHHHHHCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHC T ss_conf 66899999999987068824999999989799999999999999862 No 94 >pfam04967 HTH_10 HTH DNA binding domain. Probab=97.35 E-value=0.00064 Score=47.12 Aligned_cols=43 Identities=37% Similarity=0.465 Sum_probs=39.7 Q ss_pred CCHHHHHHHHHHH--------CCCCHHHHHHHHCCCHHHHHHHHHHHHHHC Q ss_conf 9989999999998--------799978999994999889999999999980 Q gi|254780693|r 174 LTERETSCLQLAG--------DGYTSEEIAEKLGLSVHTVNAYLGSATVKL 216 (235) Q Consensus 174 LT~RE~evL~l~a--------~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL 216 (235) ||+||++||...- ++-+-+|||.+||||..|+..|++++-+|+ 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 95 >PRK12545 RNA polymerase sigma factor; Provisional Probab=97.24 E-value=0.0057 Score=40.36 Aligned_cols=45 Identities=18% Similarity=0.250 Sum_probs=40.6 Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 4998999999999-87999789999949998899999999999807 Q gi|254780693|r 173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) .|.+.+++|+.+- -+|++.+|||.+||||+.||+..+.+++++|- T Consensus 139 ~LP~~~R~v~~Lr~~egls~~EIA~~L~is~~tVksrL~RAR~~LR 184 (201) T PRK12545 139 HLPEQIGRVFMMREFLDFEIDDICTELTLTANHCSVLLYRARTRLR 184 (201) T ss_pred HCCHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 5999998898999992898999999989699999999999999999 No 96 >PRK09636 RNA polymerase sigma factor SigJ; Provisional Probab=97.19 E-value=0.0042 Score=41.27 Aligned_cols=49 Identities=24% Similarity=0.227 Sum_probs=43.7 Q ss_pred CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCC Q ss_conf 44998999999999-87999789999949998899999999999807997 Q gi|254780693|r 172 RNLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVN 220 (235) Q Consensus 172 ~~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~n 220 (235) +.|+|+|+.|+-|- ..|++..|||.+||+|+.||+..+.++++||.... T Consensus 110 ~~L~p~qRav~vLrdv~g~s~~EIA~iLg~s~~avR~~l~RAR~~l~~~~ 159 (289) T PRK09636 110 ERLSPLERAAFLLHDVFGVPFDEIASTLGRSEAACRQLASRARKHVRAAR 159 (289) T ss_pred HHCCHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHCCC T ss_conf 73999896254049860999999999981799999999999999873448 No 97 >PRK13558 bacterio-opsin activator; Provisional Probab=97.14 E-value=0.00088 Score=46.14 Aligned_cols=44 Identities=30% Similarity=0.345 Sum_probs=40.6 Q ss_pred CCCHHHHHHHHHHH--------CCCCHHHHHHHHCCCHHHHHHHHHHHHHHC Q ss_conf 49989999999998--------799978999994999889999999999980 Q gi|254780693|r 173 NLTERETSCLQLAG--------DGYTSEEIAEKLGLSVHTVNAYLGSATVKL 216 (235) Q Consensus 173 ~LT~RE~evL~l~a--------~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL 216 (235) .||+||+++|+..= +.-|-+|||..|+||+.|.+.|++.+-+|| T Consensus 616 ~LTDRQ~eaLqtAY~sGyFEwPR~sTGeElAesLgIS~pTfhqHLRaaerKL 667 (674) T PRK13558 616 DLTDRQLTALQKAYVSGYFEWPRRAEGKQLAESMDIVPSTYHQHLQAAKQKL 667 (674) T ss_pred HHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHCCCCHHHHHHHHHHHHHHH T ss_conf 6049899999999864757788778789999870988388999999999999 No 98 >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=97.14 E-value=0.00046 Score=48.16 Aligned_cols=45 Identities=33% Similarity=0.476 Sum_probs=36.8 Q ss_pred CCCHHHHHH--HHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCC Q ss_conf 499899999--9999879997899999499988999999999998079 Q gi|254780693|r 173 NLTERETSC--LQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDA 218 (235) Q Consensus 173 ~LT~RE~ev--L~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~ 218 (235) .|.+||+.| |+. -+++|.+|||.+||||..|||.|+.+..++|.- T Consensus 113 ~LP~rQR~vvVLRY-~eDlSe~~~A~~LG~SvGTVKS~~sRal~~LR~ 159 (165) T TIGR02983 113 RLPARQRAVVVLRY-YEDLSEAEVAEVLGISVGTVKSRLSRALARLRE 159 (165) T ss_pred HCCHHCCEEEEEEC-CCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHH T ss_conf 35641236723204-578986899988199932289989999999887 No 99 >PRK08583 RNA polymerase sigma factor SigB; Validated Probab=97.10 E-value=0.0015 Score=44.45 Aligned_cols=46 Identities=30% Similarity=0.373 Sum_probs=42.6 Q ss_pred CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 44998999999999-87999789999949998899999999999807 Q gi|254780693|r 172 RNLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 172 ~~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) ..|++||++|+.+. -+|+|-+|||..||||...|+...+++.+||- T Consensus 204 ~~L~erEr~Ii~lry~~~~t~~eIa~~lGiS~eRVrQi~~~Al~kLR 250 (257) T PRK08583 204 PVLSDREKSIIQCTFIENLSQKETGERLGISQMHVSRLQRQAIKKLR 250 (257) T ss_pred HCCCHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 54999999999999579999999999989699999999999999987 No 100 >PRK07408 RNA polymerase sigma factor SigF; Reviewed Probab=97.04 E-value=0.0019 Score=43.67 Aligned_cols=46 Identities=30% Similarity=0.380 Sum_probs=42.5 Q ss_pred CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 44998999999999-87999789999949998899999999999807 Q gi|254780693|r 172 RNLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 172 ~~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) ..|++||+.|+.+- -.++|-+|||..||||...|....+++.+||- T Consensus 202 ~~L~eREr~Il~~ry~~~~tl~EIa~~lgvS~~rVsqi~~~AL~kLR 248 (256) T PRK07408 202 AQLEERTREVLEFVFLHDLTQKEAAERLGISPVTVSRRVKKGLQQLK 248 (256) T ss_pred HCCCHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 56999999999999637998999998979899999999999999999 No 101 >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=97.02 E-value=0.0015 Score=44.40 Aligned_cols=46 Identities=37% Similarity=0.362 Sum_probs=41.2 Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCC Q ss_conf 4998999999999-879997899999499988999999999998079 Q gi|254780693|r 173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDA 218 (235) Q Consensus 173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~ 218 (235) ...||..+|+.|= =-|+|++|||..|+||++||+.+.+-++..|.. T Consensus 145 ~~~Pr~a~~veLr~F~Gl~~~E~A~~L~~S~~Tv~Rdw~~ARaWL~~ 191 (194) T TIGR02999 145 QVDPRQAEVVELRFFAGLTVEEIAELLGVSVRTVERDWRFARAWLLD 191 (194) T ss_pred HCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH T ss_conf 00678899885311048898999998688887899879999999987 No 102 >PRK07670 RNA polymerase sigma factor SigD; Validated Probab=96.97 E-value=0.0084 Score=39.16 Aligned_cols=45 Identities=29% Similarity=0.356 Sum_probs=41.6 Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 4998999999999-87999789999949998899999999999807 Q gi|254780693|r 173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) .|++||+.|+.+. -+++|-+|||.+||||...|+...+++.+||- T Consensus 197 ~L~~rEr~Vl~l~y~e~~Tl~eIa~~lgvS~erVrQi~~~AL~kLr 242 (250) T PRK07670 197 ELNEKEQLVISLFYKEELTLTEIGQVLNLSTSRISQIHSKALFKLK 242 (250) T ss_pred CCCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 5899999999997489868999999989799999999999999999 No 103 >PRK07122 RNA polymerase sigma factor SigF; Reviewed Probab=96.96 E-value=0.0025 Score=42.92 Aligned_cols=45 Identities=33% Similarity=0.464 Sum_probs=42.5 Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 4998999999999-87999789999949998899999999999807 Q gi|254780693|r 173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) .|++||++|+.+- -+|+|-+|||.+||||...|+.-.+++.+||- T Consensus 214 ~L~eREr~Vi~lry~e~~Tl~EIa~~lGiSreRVrQIe~~AL~KLR 259 (263) T PRK07122 214 ALPERERTVLVLRFFESMTQTQIAERVGISQMHVSRLLAKSLARLR 259 (263) T ss_pred CCCHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 5999999999999569998999999989799999999999999999 No 104 >PRK12427 flagellar biosynthesis sigma factor; Provisional Probab=96.94 E-value=0.0022 Score=43.23 Aligned_cols=47 Identities=26% Similarity=0.285 Sum_probs=43.3 Q ss_pred CCCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCC Q ss_conf 4499899999999-9879997899999499988999999999998079 Q gi|254780693|r 172 RNLTERETSCLQL-AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDA 218 (235) Q Consensus 172 ~~LT~RE~evL~l-~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~ 218 (235) ..|++||+.|+.+ --+|+|-+|||.+||||+..|..-.+++.+||-. T Consensus 180 ~~L~erEr~Vi~l~y~e~ltlkEIa~~LgvS~~RVsQi~~kal~kLR~ 227 (229) T PRK12427 180 SQLDEREQMILHLYYQQELSMKEIAQVLDLTEARICQLNKKLVQKIKS 227 (229) T ss_pred HHCCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH T ss_conf 719999999999980589989999999798899999999999999884 No 105 >TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein; InterPro: IPR010163 Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity.. Probab=96.84 E-value=0.003 Score=42.32 Aligned_cols=47 Identities=28% Similarity=0.336 Sum_probs=41.7 Q ss_pred CCCCCCCHHHHHHHHHHHC--C-CCHHHHHHHHCCCHHHHHHHHHHHHHH Q ss_conf 8744499899999999987--9-997899999499988999999999998 Q gi|254780693|r 169 SAARNLTERETSCLQLAGD--G-YTSEEIAEKLGLSVHTVNAYLGSATVK 215 (235) Q Consensus 169 ~~~~~LT~RE~evL~l~a~--G-~t~~eIA~~L~iS~~TV~~hl~~i~~K 215 (235) ++..++|.+|.+||..+.. | ++.+.||..||+|+.|+..|++...+| T Consensus 162 ~~~~~~s~~~~~vL~~L~~~~Ge~~v~~iA~~lg~s~~T~~~~~~~Lek~ 211 (231) T TIGR01884 162 PLLAGLSREELKVLEALKAEKGEKSVKNIAKKLGKSLSTISRHLAELEKK 211 (231) T ss_pred CCCCCCCHHHHHHHHHHHCCCCEECHHHHHHHHCCCHHHHHHHHHHHHHC T ss_conf 44678889999999998507880528779988578887999999988744 No 106 >PRK08215 sporulation sigma factor SigG; Reviewed Probab=96.81 E-value=0.0037 Score=41.68 Aligned_cols=45 Identities=29% Similarity=0.378 Sum_probs=42.2 Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 4998999999999-87999789999949998899999999999807 Q gi|254780693|r 173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) .|++||++|+.+- -+|+|-.|||.+||||...|+.--+++..||- T Consensus 209 ~L~~REr~Ii~~ry~~~~Tl~eIa~~lGvSreRVrQie~~AL~kLR 254 (257) T PRK08215 209 RLNDREKMILNLRFFQGKTQMEVADEIGISQAQVSRLEKAALKHMR 254 (257) T ss_pred CCCHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 4999999999999479998999999989699999999999999998 No 107 >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=96.80 E-value=0.0066 Score=39.87 Aligned_cols=45 Identities=27% Similarity=0.281 Sum_probs=42.3 Q ss_pred CCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 499899999999-987999789999949998899999999999807 Q gi|254780693|r 173 NLTERETSCLQL-AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 173 ~LT~RE~evL~l-~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) .|||.|.+|+.| -++|++++|||++||+.++.|+.-.-++.++|. T Consensus 123 ~L~p~qq~viaLrF~~~L~~~EvA~ilGk~~gavk~Lq~rAv~~L~ 168 (171) T TIGR02952 123 KLTPKQQEVIALRFAQNLPIAEVARILGKTEGAVKALQFRAVKKLA 168 (171) T ss_pred HCCHHHHHHHHHHHCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHH T ss_conf 1083231203332116883878998726897468999999999987 No 108 >PRK05572 sporulation sigma factor SigF; Validated Probab=96.80 E-value=0.0038 Score=41.56 Aligned_cols=45 Identities=27% Similarity=0.299 Sum_probs=42.0 Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 4998999999999-87999789999949998899999999999807 Q gi|254780693|r 173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) .|++||+.|+.+- -.++|-+|||.+||||...|+...+++.+||- T Consensus 201 ~L~~rEr~Vi~~ry~~~~tl~EIa~~lgiS~eRVrQI~~~Al~kLR 246 (251) T PRK05572 201 ELDERERLIIYLRYFKDKTQSEVAKRLGISQVQVSRLEKKILKQMK 246 (251) T ss_pred CCCHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 2899999999998178988999999979799999999999999999 No 109 >PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed Probab=96.76 E-value=0.018 Score=36.81 Aligned_cols=45 Identities=36% Similarity=0.398 Sum_probs=40.4 Q ss_pred CCCHHHHHHHHH---HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 499899999999---987999789999949998899999999999807 Q gi|254780693|r 173 NLTERETSCLQL---AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 173 ~LT~RE~evL~l---~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) .|++||+.|+.+ --+|+|-+|||..||||..-|+.--+++.+||- T Consensus 227 ~L~eREr~Ii~~r~~~~e~~TL~EIg~~lgvSreRVRQIe~kAL~KLR 274 (289) T PRK07500 227 TLNERELFIIRERRLREDGATLEALGEELGISKERVRQIEARALEKLR 274 (289) T ss_pred CCCHHHHHHHHHHCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 499999999999766899858999999979799999999999999999 No 110 >PRK06288 RNA polymerase sigma factor WhiG; Reviewed Probab=96.74 E-value=0.0041 Score=41.36 Aligned_cols=45 Identities=29% Similarity=0.393 Sum_probs=42.2 Q ss_pred CCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 499899999999-987999789999949998899999999999807 Q gi|254780693|r 173 NLTERETSCLQL-AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 173 ~LT~RE~evL~l-~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) .|++||++|+.+ --+|+|-+|||.+||||...|+.--+++.+||- T Consensus 208 ~L~erEr~Il~lry~e~~Tl~eIa~~lgiS~eRVrQie~~AL~kLR 253 (261) T PRK06288 208 TLPEREKKVITLYYYEDLTLKEIGEVLGVTESRISQIHTKAVLQLR 253 (261) T ss_pred CCCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 0899999999998079988999999979789999999999999999 No 111 >PRK08301 sporulation sigma factor SigE; Reviewed Probab=96.74 E-value=0.0041 Score=41.38 Aligned_cols=45 Identities=27% Similarity=0.458 Sum_probs=41.8 Q ss_pred CCCCHHHHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHC Q ss_conf 44998999999999-----8799978999994999889999999999980 Q gi|254780693|r 172 RNLTERETSCLQLA-----GDGYTSEEIAEKLGLSVHTVNAYLGSATVKL 216 (235) Q Consensus 172 ~~LT~RE~evL~l~-----a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL 216 (235) ..|++||++|+.+- -..+|-+|||..||||...|+.--+++.+|| T Consensus 182 ~~L~eREr~Ii~lRfGL~~~~~~Tl~EIa~~lgISrerVrQIe~~AL~KL 231 (239) T PRK08301 182 KKLNDREKQIMELRFGLAGGEEKTQKEVADMLGISQSYISRLEKRIIKRL 231 (239) T ss_pred HCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH T ss_conf 64899999999999578899840699999998978999999999999999 No 112 >PRK05803 sporulation sigma factor SigK; Reviewed Probab=96.68 E-value=0.0048 Score=40.87 Aligned_cols=46 Identities=33% Similarity=0.339 Sum_probs=42.4 Q ss_pred CCCCHHHHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 44998999999999-----87999789999949998899999999999807 Q gi|254780693|r 172 RNLTERETSCLQLA-----GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 172 ~~LT~RE~evL~l~-----a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) ..|++||++|+.+- -+.+|-+|||..||||...|+..-+++++||. T Consensus 173 ~~L~~REr~II~~RfGL~~~~~~Tl~eIg~~lgiSrERVRQIe~~Al~KLr 223 (228) T PRK05803 173 DILDPREKEVIEMRYGLGDGKEKTQREIAKALGISRSYVSRIEKKALKKLF 223 (228) T ss_pred HCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 518988999999986478999715999999989799999999999999999 No 113 >PRK06596 RNA polymerase factor sigma-32; Reviewed Probab=96.67 E-value=0.027 Score=35.55 Aligned_cols=45 Identities=27% Similarity=0.319 Sum_probs=40.6 Q ss_pred CCCHHHHHHHHHHH---CCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 49989999999998---7999789999949998899999999999807 Q gi|254780693|r 173 NLTERETSCLQLAG---DGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 173 ~LT~RE~evL~l~a---~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) .|++||++|+.+-= +++|-+|||..||||...|+.--+++++||- T Consensus 230 ~L~~REr~Il~~Ry~~d~~~TL~EIg~~lgiSrERVRQIe~kAL~KLR 277 (284) T PRK06596 230 TLDERSRDIIEARWLDDDKSTLQELAAEYGVSAERIRQIEKNAMKKLK 277 (284) T ss_pred HCCHHHHHHHHHHCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 099999999999767999948999999979799999999999999999 No 114 >PRK09635 sigI RNA polymerase sigma factor SigI; Provisional Probab=96.66 E-value=0.024 Score=35.85 Aligned_cols=48 Identities=21% Similarity=0.207 Sum_probs=43.0 Q ss_pred CCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCC Q ss_conf 499899999999-987999789999949998899999999999807997 Q gi|254780693|r 173 NLTERETSCLQL-AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVN 220 (235) Q Consensus 173 ~LT~RE~evL~l-~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~n 220 (235) .|||.|+.|+-| =..|++..|||.+||+|+.+|+..+.++++||.... T Consensus 118 ~L~P~eRaa~vLrdvfg~~~~EIA~~Lg~s~~a~Rqll~RAR~~l~~~~ 166 (290) T PRK09635 118 RLGPAERVVFVLHEIFGLPYQQIATTIGSQASTCRQLAHRARRKINESR 166 (290) T ss_pred CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHCCC T ss_conf 2998685455269860898899999968998999999999999873238 No 115 >PRK06986 fliA flagellar biosynthesis sigma factor; Validated Probab=96.66 E-value=0.0058 Score=40.31 Aligned_cols=45 Identities=31% Similarity=0.338 Sum_probs=41.0 Q ss_pred CCCHHHHHHHHHHH-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 49989999999998-7999789999949998899999999999807 Q gi|254780693|r 173 NLTERETSCLQLAG-DGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 173 ~LT~RE~evL~l~a-~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) .|++||+.|+.+-- +++|-+|||..||||...|+.-.+++.+||- T Consensus 183 ~L~~rEr~Ii~l~y~~~~tl~eIa~~lgiS~eRVrQie~~AL~kLR 228 (234) T PRK06986 183 KLPEREQLVLSLYYDEELNLKEIGAVLGVSESRVSQIHSQAIKRLR 228 (234) T ss_pred HCCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 0999999999987389989999999979789999999999999999 No 116 >PRK10336 DNA-binding transcriptional regulator QseB; Provisional Probab=96.57 E-value=0.0048 Score=40.85 Aligned_cols=48 Identities=23% Similarity=0.199 Sum_probs=43.0 Q ss_pred CCCCHHHHHHHHHHHCC----CCHHHHHHHHC-----CCHHHHHHHHHHHHHHCCCC Q ss_conf 44998999999999879----99789999949-----99889999999999980799 Q gi|254780693|r 172 RNLTERETSCLQLAGDG----YTSEEIAEKLG-----LSVHTVNAYLGSATVKLDAV 219 (235) Q Consensus 172 ~~LT~RE~evL~l~a~G----~t~~eIA~~L~-----iS~~TV~~hl~~i~~KLg~~ 219 (235) -.||++|.++|.++++. .|.++|...+. ++.+||+.|+.++++||+.. T Consensus 148 i~LT~~E~~lL~~L~~~~g~vvsre~l~~~vw~~~~~~~~~~vdv~I~rLRkKl~~~ 204 (219) T PRK10336 148 LTLKPKEFALLELLMRNAGRVLPRKLIEEKLYTWDEEVTSNAVEVHVHHLRRKLGSD 204 (219) T ss_pred EEECHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHCCCC T ss_conf 983789999999999689963979999999628898888581999999999767988 No 117 >PRK03975 tfx putative transcriptional regulator; Provisional Probab=96.56 E-value=0.0034 Score=41.90 Aligned_cols=56 Identities=29% Similarity=0.332 Sum_probs=47.2 Q ss_pred CCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHH Q ss_conf 49989999999998799978999994999889999999999980799789999999 Q gi|254780693|r 173 NLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKA 228 (235) Q Consensus 173 ~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A 228 (235) -||+||.+||++=.+|+|-.|||..||.|...|-.--++++++..=.-.|=+...+ T Consensus 4 ~Lt~~q~~vL~lR~~G~tQ~eIA~~lgTSraNvs~iEk~A~eNIekAreTl~~~~~ 59 (139) T PRK03975 4 FLTERQIEVLRLRKRGLTQQEIADILGTSRANISIIEKRARENIEKARNTLAFWNT 59 (139) T ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 56899999999998289799999997732889999999999999999999999996 No 118 >PRK08241 RNA polymerase factor sigma-70; Validated Probab=96.56 E-value=0.017 Score=36.96 Aligned_cols=46 Identities=35% Similarity=0.454 Sum_probs=42.0 Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCC Q ss_conf 4998999999999-879997899999499988999999999998079 Q gi|254780693|r 173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDA 218 (235) Q Consensus 173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~ 218 (235) .|+|+|+.|+-|- ..|++.+|||.+||+|+.+||..+.++++.|.. T Consensus 156 ~Lpp~QRavlvLRdV~g~s~~EiAe~Lg~S~aAVks~L~RARa~L~~ 202 (341) T PRK08241 156 HLPPRQRAVLLLRDVLGWSAAEVAEALGTSTAAVNSALQRARATLAE 202 (341) T ss_pred HCCHHHHEEEEHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH T ss_conf 39997902001297529988999999789999999999999999986 No 119 >PRK05911 RNA polymerase sigma factor sigma-28; Reviewed Probab=96.43 E-value=0.008 Score=39.29 Aligned_cols=46 Identities=28% Similarity=0.320 Sum_probs=42.1 Q ss_pred CCCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 4499899999999-987999789999949998899999999999807 Q gi|254780693|r 172 RNLTERETSCLQL-AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 172 ~~LT~RE~evL~l-~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) ..|++||+.|+.+ --+++|-+|||.+||||...|+.-.+++.+||- T Consensus 204 ~~L~erEr~Ii~lry~e~~Tl~EIg~~lgvS~eRVrQi~~~AL~kLR 250 (257) T PRK05911 204 LALEEKERKVMALYYYEELVLKEIGKILGVSESRVSQIHSKALLKLR 250 (257) T ss_pred HCCCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 65899999999987489878999998979889999999999999999 No 120 >PRK12423 LexA repressor; Provisional Probab=96.34 E-value=0.0064 Score=40.00 Aligned_cols=43 Identities=21% Similarity=0.311 Sum_probs=35.2 Q ss_pred CCCHHHHHHHHHHHC-----CC--CHHHHHHHHCC-CHHHHHHHHHHHHHH Q ss_conf 499899999999987-----99--97899999499-988999999999998 Q gi|254780693|r 173 NLTERETSCLQLAGD-----GY--TSEEIAEKLGL-SVHTVNAYLGSATVK 215 (235) Q Consensus 173 ~LT~RE~evL~l~a~-----G~--t~~eIA~~L~i-S~~TV~~hl~~i~~K 215 (235) .||+||.+||.++.+ |+ |-+||+..+|+ |..||..|++.+-+| T Consensus 3 ~LT~kQ~~iL~fI~~~~~~~G~~Pt~rEI~~~~g~~S~~~v~~hl~~L~~k 53 (202) T PRK12423 3 TLTPKRAAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARKHVQALAEA 53 (202) T ss_pred CCCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHC T ss_conf 208999999999999999629898899999982999867899999999988 No 121 >PRK00215 LexA repressor; Validated Probab=96.34 E-value=0.0084 Score=39.15 Aligned_cols=42 Identities=38% Similarity=0.484 Sum_probs=28.8 Q ss_pred CCHHHHHHHHHHHC-----C--CCHHHHHHHHCC-CHHHHHHHHHHHHHH Q ss_conf 99899999999987-----9--997899999499-988999999999998 Q gi|254780693|r 174 LTERETSCLQLAGD-----G--YTSEEIAEKLGL-SVHTVNAYLGSATVK 215 (235) Q Consensus 174 LT~RE~evL~l~a~-----G--~t~~eIA~~L~i-S~~TV~~hl~~i~~K 215 (235) ||+||.+||.++.+ | =|-+|||..+|+ |..||..|++.+-+| T Consensus 2 LT~kQ~~il~fI~~~~~~~g~~Ps~rEI~~~~g~~S~~tV~~~l~~Le~k 51 (204) T PRK00215 2 LTARQQEILDFIKDRIEETGYPPSRREIADALGLRSPSAVHEHLKALERK 51 (204) T ss_pred CCHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHC T ss_conf 89899999999999999748899899999980999818999999999879 No 122 >PRK05949 RNA polymerase sigma factor; Validated Probab=96.34 E-value=0.054 Score=33.36 Aligned_cols=47 Identities=21% Similarity=0.227 Sum_probs=41.6 Q ss_pred CCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCC Q ss_conf 49989999999998-----799978999994999889999999999980799 Q gi|254780693|r 173 NLTERETSCLQLAG-----DGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAV 219 (235) Q Consensus 173 ~LT~RE~evL~l~a-----~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~ 219 (235) .|++||++|+.+-= +-+|-+|||.+||||.--|+.--+++++||--+ T Consensus 266 ~L~~REr~Ii~~RfGl~~~~~~TL~EIg~~lgiSrERVRQIE~rAL~KLR~~ 317 (327) T PRK05949 266 ELTPQQREVLTLRFGLEDGKELSLAKVGQRLNLSRERVRQLEHQALAHLRRR 317 (327) T ss_pred CCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHC T ss_conf 6999999999997189996985799999998959999999999999998625 No 123 >PRK05657 RNA polymerase sigma factor RpoS; Validated Probab=96.31 E-value=0.048 Score=33.77 Aligned_cols=48 Identities=21% Similarity=0.298 Sum_probs=42.4 Q ss_pred CCCHHHHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCC Q ss_conf 4998999999999-----87999789999949998899999999999807997 Q gi|254780693|r 173 NLTERETSCLQLA-----GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVN 220 (235) Q Consensus 173 ~LT~RE~evL~l~-----a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~n 220 (235) .|++||++|+.+= -+.+|-+|||..||||.--|+.--+++.+||--.- T Consensus 265 ~L~~REr~II~~RfGL~~~e~~TL~EIg~~lgvSRERVRQIE~~AL~KLR~~l 317 (328) T PRK05657 265 ELNDKQREVIERRFGLNGYEAATLEEVAREIGLTRERVRQIQVEALRRLREIL 317 (328) T ss_pred CCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH T ss_conf 69999999999980889989605999998969799999999999999987999 No 124 >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=96.30 E-value=0.0098 Score=38.65 Aligned_cols=44 Identities=36% Similarity=0.530 Sum_probs=38.0 Q ss_pred CCCCHHHHHHHHHHHC-----CC--CHHHHHHHHCC-CHHHHHHHHHHHHHH Q ss_conf 4499899999999987-----99--97899999499-988999999999998 Q gi|254780693|r 172 RNLTERETSCLQLAGD-----GY--TSEEIAEKLGL-SVHTVNAYLGSATVK 215 (235) Q Consensus 172 ~~LT~RE~evL~l~a~-----G~--t~~eIA~~L~i-S~~TV~~hl~~i~~K 215 (235) ..||+||.+||.++.. |+ |-+||+..+|+ |..||..|++.+-+| T Consensus 2 ~~LT~rQ~~il~~I~~~~~~~G~~Pt~rEI~~~~g~~S~s~v~~~l~~Le~k 53 (65) T pfam01726 2 KPLTERQREVLDFIKASIEETGYPPSRREIAQALGLRSPNAAEEHLKALERK 53 (65) T ss_pred CCCCHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHC T ss_conf 6337999999999999999828898799999993899809999999999998 No 125 >pfam02001 DUF134 Protein of unknown function DUF134. This family of archaeal proteins has no known function. Probab=96.29 E-value=0.012 Score=38.10 Aligned_cols=45 Identities=36% Similarity=0.382 Sum_probs=42.6 Q ss_pred CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHC Q ss_conf 44998999999999-8799978999994999889999999999980 Q gi|254780693|r 172 RNLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKL 216 (235) Q Consensus 172 ~~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL 216 (235) ..||.-|.|.++|+ -+|++-.|.|..||||..|+..-+.++++|+ T Consensus 35 v~L~~dE~EAiRL~D~egl~QeeaA~~MgVSR~Tf~ril~~ARkKv 80 (100) T pfam02001 35 VIITLDEFEAIRLVDYEDYTQEEAAKLMGISRRTVWRLLTSARKKI 80 (100) T ss_pred EEECHHHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHHHHHHHH T ss_conf 8734999999998736079899999884976999999999999999 No 126 >PRK07921 RNA polymerase sigma factor SigB; Reviewed Probab=96.23 E-value=0.091 Score=31.78 Aligned_cols=51 Identities=27% Similarity=0.290 Sum_probs=44.5 Q ss_pred CCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHH Q ss_conf 49989999999998-----7999789999949998899999999999807997899 Q gi|254780693|r 173 NLTERETSCLQLAG-----DGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQ 223 (235) Q Consensus 173 ~LT~RE~evL~l~a-----~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~q 223 (235) .|++||++|+.+-= +-+|-+|||.+||||.--|+.--+++++||--..|.+ T Consensus 258 ~L~eREr~IL~~RfGl~~~~~~TL~EIg~~lgvSrERVRQIE~~AL~KLR~~~~~~ 313 (320) T PRK07921 258 TLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRHGERAD 313 (320) T ss_pred CCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHHH T ss_conf 59999999999974899989747999998979699999999999999970728888 No 127 >PRK13413 mpi multiple promoter invertase; Provisional Probab=96.09 E-value=0.017 Score=36.94 Aligned_cols=41 Identities=29% Similarity=0.306 Sum_probs=37.2 Q ss_pred CCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHH Q ss_conf 99899999999987999789999949998899999999999 Q gi|254780693|r 174 LTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATV 214 (235) Q Consensus 174 LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~ 214 (235) +...+..+..|+..|+|..+||..+|||..||..|++.+.. T Consensus 158 ~~~~~~~i~~~~~~g~s~~~iak~~gvsrsTvyR~lK~~~e 198 (200) T PRK13413 158 LHGKEEVITKELKKGTTKSEIAKKLKVSRTTLARFLKTMYE 198 (200) T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHC T ss_conf 47999999999988899999999989299999999974410 No 128 >PRK05901 RNA polymerase sigma factor; Provisional Probab=96.07 E-value=0.024 Score=35.91 Aligned_cols=52 Identities=25% Similarity=0.371 Sum_probs=46.7 Q ss_pred CCCHHHHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHH Q ss_conf 4998999999999-----879997899999499988999999999998079978999 Q gi|254780693|r 173 NLTERETSCLQLA-----GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQA 224 (235) Q Consensus 173 ~LT~RE~evL~l~-----a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qa 224 (235) .|++||+.|+.+- -+-+|-+|||..||||.--|+.--+++++||--.+|.+- T Consensus 335 ~L~~REr~Ii~~RyGL~~~~~~TL~eIg~~lgvSrERVRQIE~kAL~KLR~~~~~~~ 391 (398) T PRK05901 335 TLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTMRKLRHPSRSQV 391 (398) T ss_pred CCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCHHHHH T ss_conf 899999999999758999896039999989796999999999999999678378879 No 129 >PRK09210 RNA polymerase sigma factor RpoD; Validated Probab=96.04 E-value=0.11 Score=31.10 Aligned_cols=52 Identities=27% Similarity=0.315 Sum_probs=45.4 Q ss_pred CCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHH Q ss_conf 49989999999998-----79997899999499988999999999998079978999 Q gi|254780693|r 173 NLTERETSCLQLAG-----DGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQA 224 (235) Q Consensus 173 ~LT~RE~evL~l~a-----~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qa 224 (235) .|++||+.|+++-= +-+|-+|||..+|||.--|+.--+++++||-=.+|..- T Consensus 306 ~L~~REr~Il~~RfGL~~~~~~TLeEIg~~lgvSRERVRQIE~kAL~KLR~~~~~~~ 362 (368) T PRK09210 306 TLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQ 362 (368) T ss_pred CCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCHHHHH T ss_conf 799999999999759996896149999989697989999999999999767368789 No 130 >PRK07598 RNA polymerase sigma factor SigC; Validated Probab=96.02 E-value=0.031 Score=35.06 Aligned_cols=53 Identities=32% Similarity=0.412 Sum_probs=46.0 Q ss_pred CCCHHHHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHH Q ss_conf 4998999999999-----8799978999994999889999999999980799789999 Q gi|254780693|r 173 NLTERETSCLQLA-----GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAI 225 (235) Q Consensus 173 ~LT~RE~evL~l~-----a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qav 225 (235) .|++||++|+.+- -+-+|-+|||..||||.--|+.--+++++||--..|.+.. T Consensus 345 ~L~~REr~IL~lRfGL~dg~~~TL~EIG~~lgISRERVRQIE~kAL~KLR~p~r~~~L 402 (410) T PRK07598 345 DLTSRERDVIRMRFGLADGRTYSLAEIGRALDLSRERVRQIEAKALQKLRQPKRRNRI 402 (410) T ss_pred CCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCHHHHHH T ss_conf 6999999999996489997966899999897969999999999999996773778999 No 131 >PRK07406 RNA polymerase sigma factor RpoD; Validated Probab=95.93 E-value=0.034 Score=34.83 Aligned_cols=54 Identities=30% Similarity=0.345 Sum_probs=47.0 Q ss_pred CCCCHHHHHHHHHHH---CC--CCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHH Q ss_conf 449989999999998---79--9978999994999889999999999980799789999 Q gi|254780693|r 172 RNLTERETSCLQLAG---DG--YTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAI 225 (235) Q Consensus 172 ~~LT~RE~evL~l~a---~G--~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qav 225 (235) ..|++||++|+.+== .| +|-+|||.+||||.--|+.--+++++||--.+|.+.. T Consensus 322 ~~L~eREr~II~lRfGL~dg~~~TL~EIg~~lgISRERVRQIE~rAL~KLR~p~r~~~L 380 (385) T PRK07406 322 ATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSVL 380 (385) T ss_pred HCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCHHHHHH T ss_conf 64999999999997589999964699999897959999999999999996771778999 No 132 >COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription] Probab=95.92 E-value=0.023 Score=36.08 Aligned_cols=45 Identities=40% Similarity=0.400 Sum_probs=41.1 Q ss_pred CCCHHHHHHHHHHH-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 49989999999998-7999789999949998899999999999807 Q gi|254780693|r 173 NLTERETSCLQLAG-DGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 173 ~LT~RE~evL~l~a-~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) .|++||+.|+.+.= +++|-+|||..||||+-+|-.-.+.+..||- T Consensus 196 ~L~EREk~Vl~l~y~eelt~kEI~~~LgISes~VSql~kkai~kLr 241 (247) T COG1191 196 PLPEREKLVLVLRYKEELTQKEIAEVLGISESRVSRLHKKAIKKLR 241 (247) T ss_pred CCCHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 6689999999999970157999999949149899999999999999 No 133 >PRK04217 hypothetical protein; Provisional Probab=95.81 E-value=0.027 Score=35.54 Aligned_cols=45 Identities=36% Similarity=0.360 Sum_probs=42.2 Q ss_pred CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHC Q ss_conf 44998999999999-8799978999994999889999999999980 Q gi|254780693|r 172 RNLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKL 216 (235) Q Consensus 172 ~~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL 216 (235) ..||.-|.|.++|+ -+|++-.|.|..|+||..|+..-+.++++|+ T Consensus 41 V~LtvdE~EaiRL~D~egl~qeeaA~~M~VSR~Tf~ril~~AR~Kv 86 (110) T PRK04217 41 IIMTYEEFEALRLVDYEGLTQEEAGKRMGVSRGTVWRALTSARKKV 86 (110) T ss_pred EEECHHHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHHHHHHHH T ss_conf 5611999999998736079899999884976999999999999999 No 134 >PRK07405 RNA polymerase sigma factor SigD; Validated Probab=95.81 E-value=0.028 Score=35.47 Aligned_cols=47 Identities=26% Similarity=0.264 Sum_probs=40.8 Q ss_pred CCCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCC Q ss_conf 449989999999998-----79997899999499988999999999998079 Q gi|254780693|r 172 RNLTERETSCLQLAG-----DGYTSEEIAEKLGLSVHTVNAYLGSATVKLDA 218 (235) Q Consensus 172 ~~LT~RE~evL~l~a-----~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~ 218 (235) ..|++||++|+.+-= +-+|-+|||.+||||..-|+.--+++++||-= T Consensus 256 ~~L~eREr~II~lRfGl~~~~~~TL~EIg~~lgvSrERVRQIE~~AL~KLR~ 307 (318) T PRK07405 256 ADLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLRK 307 (318) T ss_pred HCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH T ss_conf 6299989999999807789897479999989795999999999999999987 No 135 >pfam09862 DUF2089 Protein of unknown function(DUF2089). This domain, found in various hypothetical prokaryotic proteins, has no known function. Probab=95.74 E-value=0.091 Score=31.77 Aligned_cols=64 Identities=22% Similarity=0.190 Sum_probs=51.8 Q ss_pred CCCCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCC--------CHHHHHHHHHHCCCC Q ss_conf 44499899999999-98799978999994999889999999999980799--------789999999976999 Q gi|254780693|r 171 ARNLTERETSCLQL-AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAV--------NRIQAIAKAIRFGYI 234 (235) Q Consensus 171 ~~~LT~RE~evL~l-~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~--------nR~qava~A~~~Gli 234 (235) -..||+-+.+.++. +....+-++++..||||..||+..+.++.+|||-. .+..-|..++..|-| T Consensus 31 f~~L~~E~l~Fi~~fi~~~Gnlke~~~~lgiSYpTvR~rLd~ii~~lGy~~~~~~~~~~~~~eIL~~Le~GEI 103 (113) T pfam09862 31 FCRLTPEQLEFVELFIKCRGNIKEVEKELGISYPTVRNRLDEIIAALGYEEEPEPEKRVDKKEILDKLEKGEI 103 (113) T ss_pred HHCCCHHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHCCCC T ss_conf 5238999999999999916889999999788818899999999998089877777776229999999984997 No 136 >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=95.68 E-value=0.12 Score=30.89 Aligned_cols=45 Identities=24% Similarity=0.269 Sum_probs=39.3 Q ss_pred CCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 499899999999-987999789999949998899999999999807 Q gi|254780693|r 173 NLTERETSCLQL-AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 173 ~LT~RE~evL~l-~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) .|.+-.+||+.+ -.+|+|++|||..|+.|+.+|.--.-+..+||- T Consensus 141 ~L~e~~REvi~LR~~EGLS~~EvA~~Md~~~~av~~l~~Ral~~Lr 186 (190) T TIGR02984 141 KLPEDYREVILLRHLEGLSFAEVAERMDRSEGAVSMLWVRALARLR 186 (190) T ss_pred HCCHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 4792258999998760355589998707975898758999999998 No 137 >PRK10710 DNA-binding transcriptional regulator BaeR; Provisional Probab=95.65 E-value=0.028 Score=35.39 Aligned_cols=48 Identities=19% Similarity=0.297 Sum_probs=41.3 Q ss_pred CCCCHHHHHHHHHHHCC----CCHHHHHHHHC-----CCHHHHHHHHHHHHHHCCCC Q ss_conf 44998999999999879----99789999949-----99889999999999980799 Q gi|254780693|r 172 RNLTERETSCLQLAGDG----YTSEEIAEKLG-----LSVHTVNAYLGSATVKLDAV 219 (235) Q Consensus 172 ~~LT~RE~evL~l~a~G----~t~~eIA~~L~-----iS~~TV~~hl~~i~~KLg~~ 219 (235) ..||++|.++|.+++.. .|.++|...+. ++.+||+.|+.++++||... T Consensus 159 i~LT~~E~~lL~~L~~~~g~vvSre~L~~~vw~~~~~~~~rsid~~I~rLRkKl~~~ 215 (240) T PRK10710 159 LDLTPAEFRLLKTLSHEPGKVFSREQLLNHLYDDYRVVTDRTIDSHIKNLRRKLESL 215 (240) T ss_pred EECCHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHCCC T ss_conf 855899999999999779973989999999628888888465999999999960106 No 138 >TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family. Probab=95.54 E-value=0.12 Score=30.83 Aligned_cols=44 Identities=41% Similarity=0.475 Sum_probs=39.5 Q ss_pred CCCHHHHHHHHH-----HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHC Q ss_conf 499899999999-----98799978999994999889999999999980 Q gi|254780693|r 173 NLTERETSCLQL-----AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKL 216 (235) Q Consensus 173 ~LT~RE~evL~l-----~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL 216 (235) .|||||++||.| =-+.+|=.|||..||||..=|+.==+.+++|| T Consensus 287 ~L~p~e~~VL~LRfGL~~~~~~TL~eiG~~l~lSRERVRQiE~~AL~kL 335 (336) T TIGR02997 287 ELTPRERQVLRLRFGLDDGEPLTLAEIGERLNLSRERVRQIEAKALRKL 335 (336) T ss_pred HCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHC T ss_conf 3798899999985789989753278999883883688889999997534 No 139 >pfam08279 HTH_11 HTH domain. This family includes helix-turn-helix domains in a wide variety of proteins. Probab=95.49 E-value=0.035 Score=34.76 Aligned_cols=41 Identities=29% Similarity=0.344 Sum_probs=32.5 Q ss_pred HHHHHHHHHH--CC-CCHHHHHHHHCCCHHHHHHHHHHHHHHCCC Q ss_conf 9999999998--79-997899999499988999999999998079 Q gi|254780693|r 177 RETSCLQLAG--DG-YTSEEIAEKLGLSVHTVNAYLGSATVKLDA 218 (235) Q Consensus 177 RE~evL~l~a--~G-~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~ 218 (235) |..++|.++. ++ .|.+++|..|+||.+||..+++.+. ..|+ T Consensus 1 R~~~il~~L~~~~~~vt~~~La~~l~VSr~TV~rdi~~L~-~~G~ 44 (55) T pfam08279 1 RLLQILELLLQAREPISGQELAEKLGVSRRTIRRDIKALE-ALGV 44 (55) T ss_pred CHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHH-HCCC T ss_conf 9899999999769991899999996988999999999999-8899 No 140 >COG0856 Orotate phosphoribosyltransferase homologs [Nucleotide transport and metabolism] Probab=95.17 E-value=0.033 Score=34.86 Aligned_cols=41 Identities=29% Similarity=0.284 Sum_probs=32.8 Q ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCC Q ss_conf 99999987999789999949998899999999999807997 Q gi|254780693|r 180 SCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVN 220 (235) Q Consensus 180 evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~n 220 (235) ....|-..|+|..|||.+|++|..|+.+.+.+..++..+.. T Consensus 10 kA~eLk~~Glt~gEIAdELNvSreTa~WL~~r~~~~~~~~~ 50 (203) T COG0856 10 KARELKSKGLTTGEIADELNVSRETATWLLTRAFKKESVPA 50 (203) T ss_pred HHHHHHHCCCCHHHHHHHHCCHHHHHHHHHHHHHHCCCCCC T ss_conf 99999877985777676641048778888754431147888 No 141 >cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions. Probab=95.17 E-value=0.059 Score=33.12 Aligned_cols=41 Identities=37% Similarity=0.420 Sum_probs=36.2 Q ss_pred CC-HHHHHHHHHHHCC-CCHHHHHHHHCCCHHHHHHHHHHHHH Q ss_conf 99-8999999999879-99789999949998899999999999 Q gi|254780693|r 174 LT-ERETSCLQLAGDG-YTSEEIAEKLGLSVHTVNAYLGSATV 214 (235) Q Consensus 174 LT-~RE~evL~l~a~G-~t~~eIA~~L~iS~~TV~~hl~~i~~ 214 (235) |+ +.-.+++..+.+| ++..|||..++||..||..|++.+.+ T Consensus 4 l~~~~r~~Il~~L~~~~~~~~eia~~l~is~~~vs~hL~~L~~ 46 (78) T cd00090 4 LSDPTRLRILRLLLEGPLTVSELAERLGLSQSTVSRHLKKLEE 46 (78) T ss_pred CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHH T ss_conf 2799999999999848906999987778487899999999998 No 142 >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=95.12 E-value=0.015 Score=37.45 Aligned_cols=37 Identities=35% Similarity=0.372 Sum_probs=32.0 Q ss_pred HHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCC Q ss_conf 99999879997899999499988999999999998079 Q gi|254780693|r 181 CLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDA 218 (235) Q Consensus 181 vL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~ 218 (235) ||+.--+ ++-+|||..|.++++||++|++++..+|+. T Consensus 132 IL~Yy~D-L~I~eIa~vM~~P~gTvKtyl~Ra~~~lk~ 168 (173) T TIGR02954 132 ILRYYHD-LKIKEIAEVMNKPEGTVKTYLRRAKKKLKK 168 (173) T ss_pred HHHHCCC-CCHHHHHHHCCCCCCCHHHHHHHHHHHHHH T ss_conf 4332179-984259985168985178999999999888 No 143 >COG1342 Predicted DNA-binding proteins [General function prediction only] Probab=95.10 E-value=0.056 Score=33.24 Aligned_cols=46 Identities=37% Similarity=0.375 Sum_probs=42.2 Q ss_pred CCCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHC Q ss_conf 444998999999999-8799978999994999889999999999980 Q gi|254780693|r 171 ARNLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKL 216 (235) Q Consensus 171 ~~~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL 216 (235) ...||.-|.|.++|+ -.|++-+|.|.+||||..|+-.-++++++|. T Consensus 31 ~V~lt~eElEAlRLvD~~~l~QeeAA~rMgISr~Tfwr~l~sAR~Kv 77 (99) T COG1342 31 PVILTIEELEALRLVDYEGLTQEEAALRMGISRQTFWRLLTSARKKV 77 (99) T ss_pred CEEECHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHH T ss_conf 43522999889998868610578999984642999999999999999 No 144 >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=94.96 E-value=0.065 Score=32.79 Aligned_cols=47 Identities=38% Similarity=0.394 Sum_probs=43.0 Q ss_pred CCCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCC Q ss_conf 44998999999999-879997899999499988999999999998079 Q gi|254780693|r 172 RNLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDA 218 (235) Q Consensus 172 ~~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~ 218 (235) ..||+||+-|+.|- -+|+|-||||..|||||.=|-.--+.+..||.. T Consensus 177 ~~L~eRE~LVl~LYY~eELnLKEIg~VL~lsESRvSQiHs~A~~~Lr~ 224 (227) T TIGR02479 177 EKLSEREKLVLSLYYYEELNLKEIGEVLGLSESRVSQIHSQALKKLRA 224 (227) T ss_pred HHCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH T ss_conf 406855788888864127668899988378705799999999999987 No 145 >PRK00118 putative DNA-binding protein; Validated Probab=94.86 E-value=0.099 Score=31.50 Aligned_cols=45 Identities=29% Similarity=0.379 Sum_probs=40.4 Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 4998999999999-87999789999949998899999999999807 Q gi|254780693|r 173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) -||+++++++.+- -+-+|-.|||..++||...|..+++++.++|. T Consensus 17 LLT~kQ~~~~~lyy~~DlSl~EIAe~~~iSRQaV~D~ikr~~~~L~ 62 (105) T PRK00118 17 LLTEKQRNYMELYYLDDYSLGEIAEEFNVSRQAVYDNIKRTEKLLE 62 (105) T ss_pred HCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 7559999999999885499999989969859999999999999999 No 146 >PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional Probab=94.73 E-value=0.04 Score=34.34 Aligned_cols=60 Identities=13% Similarity=0.093 Sum_probs=54.7 Q ss_pred CHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCC Q ss_conf 989999999998799978999994999889999999999980799789999999976999 Q gi|254780693|r 175 TERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFGYI 234 (235) Q Consensus 175 T~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~~~Gli 234 (235) |.=|.+|.-+-+-|.+-+.||..|+|+..|=+.++.++++++|.+||-++.-....-|+| T Consensus 147 ~~~~~~vf~~Ys~G~SH~~ia~~L~It~~sSkn~~s~i~k~~gissrde~l~~l~~s~~~ 206 (220) T PRK13719 147 TSIQYDVFILYSFGFSHNSIASLLNITNGSSKNKISEILKFFGISSRDELLIILHTSEMI 206 (220) T ss_pred EEEEEEEEEEEECCCCHHHHHHHHCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHH T ss_conf 200466898875242468899884741354077999999972988599999999997689 No 147 >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=94.73 E-value=0.11 Score=31.21 Aligned_cols=44 Identities=25% Similarity=0.311 Sum_probs=40.0 Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHC Q ss_conf 4998999999999-8799978999994999889999999999980 Q gi|254780693|r 173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKL 216 (235) Q Consensus 173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL 216 (235) -||+++++++.+- -+-.|-.|||..+|||...|..+++++.++| T Consensus 17 LLT~KQ~~~~~lyy~eDlSL~EIAe~~~iSRQaV~D~ikR~~~~L 61 (101) T pfam04297 17 LLTDKQKNYFELYYLDDLSLSEIAEEFNVSRQAVYDNIKRTEKML 61 (101) T ss_pred HCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH T ss_conf 765999999999987639899999881985999999999999999 No 148 >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=94.63 E-value=0.022 Score=36.14 Aligned_cols=45 Identities=40% Similarity=0.442 Sum_probs=41.4 Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 4998999999999-87999789999949998899999999999807 Q gi|254780693|r 173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) .|.+||++||.|- -++||-+|||.+||||.==|-.-++++.+||- T Consensus 180 ~LpeRER~il~lRFf~~~TQ~eiA~~lGiSQMhVSRl~~~~L~~LR 225 (229) T TIGR02980 180 ALPERERRILLLRFFEDKTQSEIAERLGISQMHVSRLLRRALKRLR 225 (229) T ss_pred HCCHHHCEEEEEEEECCCCHHHHHHHCCCCHHHHHHHHHHHHHHHH T ss_conf 0790270761000106977899997818436788999999999999 No 149 >COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription] Probab=94.55 E-value=0.099 Score=31.50 Aligned_cols=50 Identities=36% Similarity=0.444 Sum_probs=42.7 Q ss_pred CCHHHHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC-CCCHHH Q ss_conf 998999999999-----87999789999949998899999999999807-997899 Q gi|254780693|r 174 LTERETSCLQLA-----GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD-AVNRIQ 223 (235) Q Consensus 174 LT~RE~evL~l~-----a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg-~~nR~q 223 (235) ||+||+.|+++- -.++|-.|||.+++||.--|+.--+++++||- ..++.. T Consensus 280 Lt~rE~~Vi~~R~gl~~~~~~TLeevg~~~~vsrERvRQIE~kAl~KLr~~~~~~~ 335 (342) T COG0568 280 LTERERRVIRLRFGLDDGEPKTLEELGEEFGISRERVRQIEAKALRKLRRHPERSA 335 (342) T ss_pred CCHHHHHHHHHHHCCCCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 99999999999955679995519999989598699999999999999987063222 No 150 >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=94.53 E-value=0.063 Score=32.90 Aligned_cols=38 Identities=34% Similarity=0.483 Sum_probs=32.4 Q ss_pred CCCCHHH-HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH Q ss_conf 4499899-9999999879997899999499988999999 Q gi|254780693|r 172 RNLTERE-TSCLQLAGDGYTSEEIAEKLGLSVHTVNAYL 209 (235) Q Consensus 172 ~~LT~RE-~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl 209 (235) ..||+-+ .++.++++.|.|-.+||..+|||..|+..|+ T Consensus 4 ~~lt~~q~~~ar~l~~~G~~~~~iA~~~GVsr~Tiyr~l 42 (42) T cd00569 4 PKLTPEQIEEARRLLAAGESVAEIARRLGVSRSTLYRYL 42 (42) T ss_pred CCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHC T ss_conf 869999999999999978989999999797999998659 No 151 >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=94.43 E-value=0.1 Score=31.38 Aligned_cols=45 Identities=38% Similarity=0.493 Sum_probs=43.4 Q ss_pred CCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 499899999999-987999789999949998899999999999807 Q gi|254780693|r 173 NLTERETSCLQL-AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 173 ~LT~RE~evL~l-~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) +|.++++++|.+ --+|.+..+||..+|.|+++|..-+.+|+.+|. T Consensus 115 ~L~~~~R~Ll~~rY~~G~~~~~~A~~~g~~~~A~~~~L~R~R~~L~ 160 (163) T TIGR02989 115 KLPERQRELLQLRYQRGVSLEALAEQLGRTVNAVYKALSRLRVRLR 160 (163) T ss_pred HCCHHHHHHHHHHHCCCCCHHHHHHHHCCHHHHHHHHHHHHHHHHH T ss_conf 3597889999998227978789998847138999999999999975 No 152 >cd00383 trans_reg_C Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and a response regulator. The former autophosphorylates in a histidine residue on detecting an external stimulus. The phosphate is then transferred to an invariant aspartate residue in a highly conserved receiver domain of the response regulator. Phosphorylation activates a variable effector domain of the response regulator, which triggers the cellular response. The C-terminal effector domain contains DNA and RNA polymerase binding sites. Several dimers or monomers bind head to tail to small tandem repeats upstream of the genes. The RNA polymerase binding sites interact with the alpha or sigma subunite of RNA polymerase. Probab=94.41 E-value=0.093 Score=31.71 Aligned_cols=49 Identities=22% Similarity=0.258 Sum_probs=41.5 Q ss_pred CCCCHHHHHHHHHHHCC----CCHHHHHHHHC-----CCHHHHHHHHHHHHHHCCCCC Q ss_conf 44998999999999879----99789999949-----998899999999999807997 Q gi|254780693|r 172 RNLTERETSCLQLAGDG----YTSEEIAEKLG-----LSVHTVNAYLGSATVKLDAVN 220 (235) Q Consensus 172 ~~LT~RE~evL~l~a~G----~t~~eIA~~L~-----iS~~TV~~hl~~i~~KLg~~n 220 (235) -.||++|.++|.++..- .|-.+|...+. .+.++|+.|+.++++||+-.. T Consensus 22 i~Lt~~E~~lL~~L~~~~~~vvsr~~l~~~vw~~~~~~~~~~l~~~I~rLRkkl~~~~ 79 (95) T cd00383 22 VELTPKEFELLELLARNPGRVLSREQLLEAVWGDDYDVDDRTVDVHISRLRKKLEDDP 79 (95) T ss_pred EECCHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHCC T ss_conf 8779999999999987799745699999985397645574549999999999975268 No 153 >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=94.35 E-value=0.087 Score=31.92 Aligned_cols=47 Identities=36% Similarity=0.416 Sum_probs=43.5 Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCC Q ss_conf 4998999999999-8799978999994999889999999999980799 Q gi|254780693|r 173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAV 219 (235) Q Consensus 173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~ 219 (235) .|+|||+-||-|- +-|....|+|..||.|.-.||.-+++++..|+.. T Consensus 143 ~LpPrQRAvL~LRdvlGw~A~E~A~~L~~s~ASVnSaLQRARAtL~~~ 190 (329) T TIGR02960 143 LLPPRQRAVLLLRDVLGWKAAEVAELLGTSVASVNSALQRARATLAES 190 (329) T ss_pred CCCCHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHC T ss_conf 488145789998988355556899874383267865888878866531 No 154 >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=94.27 E-value=0.079 Score=32.22 Aligned_cols=44 Identities=32% Similarity=0.480 Sum_probs=40.5 Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHC Q ss_conf 4998999999999-8799978999994999889999999999980 Q gi|254780693|r 173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKL 216 (235) Q Consensus 173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL 216 (235) .|.+-.++.+.|+ -+|.|-+|||..||+|-.++|.=+++.+.|| T Consensus 100 ~LP~~~r~a~~L~el~G~sQ~e~A~kLGlSlSGaKSRVQRGR~~L 144 (170) T TIGR02959 100 ELPDEYREAIRLTELEGLSQKEIAEKLGLSLSGAKSRVQRGRKKL 144 (170) T ss_pred HCCHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCHHHHHHHHHHHH T ss_conf 569867889888750799827998761753351567889999999 No 155 >COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair] Probab=94.21 E-value=0.11 Score=31.30 Aligned_cols=41 Identities=24% Similarity=0.374 Sum_probs=35.3 Q ss_pred CCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHH Q ss_conf 99899999999987999789999949998899999999999 Q gi|254780693|r 174 LTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATV 214 (235) Q Consensus 174 LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~ 214 (235) .-.|++-+-..+.+|+|.+|||.++|+|..||...+++-.+ T Consensus 7 ~~~R~~~~~~~~~~G~S~re~Ak~~gvs~sTvy~wv~r~~e 47 (138) T COG3415 7 NDLRERVVDAVVGEGLSCREAAKRFGVSISTVYRWVRRYRE 47 (138) T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHCC T ss_conf 89999999999976854999999969229999999987333 No 156 >PRK10766 DNA-binding transcriptional regulator TorR; Provisional Probab=94.17 E-value=0.14 Score=30.44 Aligned_cols=46 Identities=20% Similarity=0.194 Sum_probs=38.9 Q ss_pred CCCHHHHHHHHHHHCC----CCHHHHHHHH-----CCCHHHHHHHHHHHHHHCCC Q ss_conf 4998999999999879----9978999994-----99988999999999998079 Q gi|254780693|r 173 NLTERETSCLQLAGDG----YTSEEIAEKL-----GLSVHTVNAYLGSATVKLDA 218 (235) Q Consensus 173 ~LT~RE~evL~l~a~G----~t~~eIA~~L-----~iS~~TV~~hl~~i~~KLg~ 218 (235) .||++|.++|.+++.. .|-++|-..+ ..+.+||+.|+.++++||+- T Consensus 162 ~LT~~E~~lL~~L~~~~g~vvsre~L~~~vw~~~~~~~~~sid~~I~rLRkKl~~ 216 (224) T PRK10766 162 KLTKAEYELLVAFVTNPGQVLSRERLLRMLSHRVEDPNDRTIDVLIRRLRHKLNP 216 (224) T ss_pred ECCHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHCCC T ss_conf 6789999999999967997396999999964888788847299999999976798 No 157 >pfam00486 Trans_reg_C Transcriptional regulatory protein, C terminal. Probab=94.15 E-value=0.12 Score=31.04 Aligned_cols=48 Identities=25% Similarity=0.321 Sum_probs=41.2 Q ss_pred CCCCHHHHHHHHHHHCC----CCHHHHHHHH-----CCCHHHHHHHHHHHHHHCCCC Q ss_conf 44998999999999879----9978999994-----999889999999999980799 Q gi|254780693|r 172 RNLTERETSCLQLAGDG----YTSEEIAEKL-----GLSVHTVNAYLGSATVKLDAV 219 (235) Q Consensus 172 ~~LT~RE~evL~l~a~G----~t~~eIA~~L-----~iS~~TV~~hl~~i~~KLg~~ 219 (235) -.||++|.++|..+.+- .|..+|...+ .++.++|+.|+.++++||+.. T Consensus 4 i~Lt~~E~~lL~~L~~~~~~~vsr~~l~~~iw~~~~~~~~~sl~~~I~rLR~kl~~~ 60 (77) T pfam00486 4 VELTPKEFDLLELLARNPGRVVSREELLEEVWGEDFDVDDNTVDVHISRLRKKLEDD 60 (77) T ss_pred EECCHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHC T ss_conf 233899999999999679971979999999638766655330999999999987544 No 158 >COG3355 Predicted transcriptional regulator [Transcription] Probab=94.14 E-value=0.16 Score=29.93 Aligned_cols=43 Identities=26% Similarity=0.166 Sum_probs=38.9 Q ss_pred CCCHHHHHHHHHHH---CCCCHHHHHHHHCCCHHHHHHHHHHHHHH Q ss_conf 49989999999998---79997899999499988999999999998 Q gi|254780693|r 173 NLTERETSCLQLAG---DGYTSEEIAEKLGLSVHTVNAYLGSATVK 215 (235) Q Consensus 173 ~LT~RE~evL~l~a---~G~t~~eIA~~L~iS~~TV~~hl~~i~~K 215 (235) +||+.+.+|+.-+. .++|..+||.+|++|..||+.-++|...+ T Consensus 24 GLs~~Dv~v~~~LL~~~~~~tvdelae~lnr~rStv~rsl~~L~~~ 69 (126) T COG3355 24 GLSELDVEVYKALLEENGPLTVDELAEILNRSRSTVYRSLQNLLEA 69 (126) T ss_pred CCCHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC T ss_conf 8968899999999864699579999999783199999999999985 No 159 >PRK09468 ompR osmolarity response regulator; Provisional Probab=94.13 E-value=0.11 Score=31.15 Aligned_cols=47 Identities=9% Similarity=0.088 Sum_probs=39.6 Q ss_pred CCCHHHHHHHHHHHCC----CCHHHHHHHH-----CCCHHHHHHHHHHHHHHCCCC Q ss_conf 4998999999999879----9978999994-----999889999999999980799 Q gi|254780693|r 173 NLTERETSCLQLAGDG----YTSEEIAEKL-----GLSVHTVNAYLGSATVKLDAV 219 (235) Q Consensus 173 ~LT~RE~evL~l~a~G----~t~~eIA~~L-----~iS~~TV~~hl~~i~~KLg~~ 219 (235) .||++|.++|.+++.. .|-++|-..+ ..+.+||+.|+.++++||+.. T Consensus 161 ~LT~~E~~LL~~L~~~~g~vvsre~Ll~~vwg~~~~~~~rtidv~I~rLRkKl~~~ 216 (239) T PRK09468 161 PLTTGEFAVLKALVRHPREPLSRDKLMNLARGREYSAMERSIDVQISRLRRLIEPD 216 (239) T ss_pred ECCHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHCC T ss_conf 76789999999999779966769999999629887888483999999999975207 No 160 >COG1710 Uncharacterized protein conserved in archaea [Function unknown] Probab=94.09 E-value=0.09 Score=31.81 Aligned_cols=42 Identities=24% Similarity=0.317 Sum_probs=33.1 Q ss_pred CCHHHHH-HHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHH Q ss_conf 9989999-99999879997899999499988999999999998 Q gi|254780693|r 174 LTERETS-CLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVK 215 (235) Q Consensus 174 LT~RE~e-vL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~K 215 (235) -+.+-+. |=.++-.|++.+||+..|||--+||.+|+++..+| T Consensus 94 yd~~t~~~i~emlr~gk~preIsk~lGIpirTvyY~l~k~k~~ 136 (139) T COG1710 94 YDRNTLLRIREMLRNGKTPREISKDLGIPIRTVYYLLKKLKKK 136 (139) T ss_pred CCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHH T ss_conf 3454899999999849987788886098622069999987665 No 161 >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=93.98 E-value=0.16 Score=30.01 Aligned_cols=90 Identities=22% Similarity=0.207 Sum_probs=60.0 Q ss_pred EEEEEECCCCCCEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHH Q ss_conf 89972168875234541058878998999999999999999998512467887444998999999999879997899999 Q gi|254780693|r 118 IAFPVRLGFHKNGYVIFTSEFLMLANEVIIEAHGACYQVITDFLELFKKRSSAARNLTERETSCLQLAGDGYTSEEIAEK 197 (235) Q Consensus 118 ~~~pv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~LT~RE~evL~l~a~G~t~~eIA~~ 197 (235) +.-|+.+.......+-..+.....+++++.-..-....+-.. -..-||.-|.+||..-.+|++..|||.. T Consensus 105 l~kPiy~~~sdrtl~d~~~~~~~~dP~~l~i~~e~~~~~~~~----------~~~~ls~le~~vl~~yl~G~~yqei~~~ 174 (198) T TIGR02859 105 LNKPIYDEESDRTLLDVVSEAKVADPEELIISKEEYEKIESK----------LEELLSDLELKVLVLYLDGKSYQEIAED 174 (198) T ss_pred CCCCCCCCCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHH----------HHHHHHHHHHHHHHHHHCCCHHHHHHHH T ss_conf 256525452014799988544322527776316889999999----------9999999999999998457407889988 Q ss_pred HCCCHHHHHHHHHHHHHHCC Q ss_conf 49998899999999999807 Q gi|254780693|r 198 LGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 198 L~iS~~TV~~hl~~i~~KLg 217 (235) |+-..+.+.+-++++.+||. T Consensus 175 l~r~~ksidnalqrvkrkle 194 (198) T TIGR02859 175 LNRHVKSIDNALQRVKRKLE 194 (198) T ss_pred HHHHHHHHHHHHHHHHHHHH T ss_conf 64566789999999999997 No 162 >COG1318 Predicted transcriptional regulators [Transcription] Probab=93.93 E-value=0.035 Score=34.73 Aligned_cols=37 Identities=35% Similarity=0.325 Sum_probs=29.9 Q ss_pred HHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 9999987999789999949998899999999999807 Q gi|254780693|r 181 CLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 181 vL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) ++-.--.|+|..+||..||+++.||++|++.--++.+ T Consensus 54 a~arekag~Ti~EIAeelG~TeqTir~hlkgetkAG~ 90 (182) T COG1318 54 ALAREKAGMTISEIAEELGRTEQTVRNHLKGETKAGQ 90 (182) T ss_pred HHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCHHHHH T ss_conf 9999870374999999968779999999751403316 No 163 >pfam02796 HTH_7 Helix-turn-helix domain of resolvase. Probab=93.78 E-value=0.12 Score=30.81 Aligned_cols=39 Identities=31% Similarity=0.469 Sum_probs=33.4 Q ss_pred CCCCH-HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHH Q ss_conf 44998-9999999998799978999994999889999999 Q gi|254780693|r 172 RNLTE-RETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLG 210 (235) Q Consensus 172 ~~LT~-RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~ 210 (235) ..|++ .-.++.+|+..|.+-++||.+.+||..||..++. T Consensus 4 ~kl~~~~~~~v~~L~~~G~~i~~IA~~~~vsrsTvYRyl~ 43 (45) T pfam02796 4 PKLNEEDINEVITLLEEGISIKQIAKIFGISRSTVYRYLA 43 (45) T ss_pred CCCCHHHHHHHHHHHHCCCCHHHHHHHHCCHHHHHHHHCC T ss_conf 1038999999999998799499999998600888876445 No 164 >smart00862 Trans_reg_C Transcriptional regulatory protein, C terminal. This domain is almost always found associated with the response regulator receiver domain. It may play a role in DNA binding. Probab=93.72 E-value=0.15 Score=30.18 Aligned_cols=48 Identities=23% Similarity=0.257 Sum_probs=40.0 Q ss_pred CCCCHHHHHHHHHHHCC----CCHHHHHHHH------CCCHHHHHHHHHHHHHHCCCC Q ss_conf 44998999999999879----9978999994------999889999999999980799 Q gi|254780693|r 172 RNLTERETSCLQLAGDG----YTSEEIAEKL------GLSVHTVNAYLGSATVKLDAV 219 (235) Q Consensus 172 ~~LT~RE~evL~l~a~G----~t~~eIA~~L------~iS~~TV~~hl~~i~~KLg~~ 219 (235) ..||++|.++|.++++- .|-++|...+ ..+.++++.|+.++++||+-. T Consensus 4 v~Lt~~e~~lL~~L~~~~~~~vs~~~l~~~lw~~~~~~~~~~~l~~~I~~LR~kl~~~ 61 (78) T smart00862 4 IKLTPKEFRLLELLLRNPGRVVSREELLEAVWGDDDDDVDDNTLDVHISRLRKKLEDD 61 (78) T ss_pred EECCHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHC T ss_conf 3248999999999984799629699999876288878888602789999999997645 No 165 >PRK09836 DNA-binding transcriptional activator CusR; Provisional Probab=93.69 E-value=0.15 Score=30.29 Aligned_cols=48 Identities=17% Similarity=0.123 Sum_probs=40.4 Q ss_pred CCCHHHHHHHHHHHCC----CCHHHHHHHHC-----CCHHHHHHHHHHHHHHCCCCC Q ss_conf 4998999999999879----99789999949-----998899999999999807997 Q gi|254780693|r 173 NLTERETSCLQLAGDG----YTSEEIAEKLG-----LSVHTVNAYLGSATVKLDAVN 220 (235) Q Consensus 173 ~LT~RE~evL~l~a~G----~t~~eIA~~L~-----iS~~TV~~hl~~i~~KLg~~n 220 (235) .||++|.++|.+++.- .|-++|...+. .+.+||+.|+.++++||+... T Consensus 150 ~LT~~E~~lL~~L~~~~g~vvsre~l~~~vw~~~~~~~~~~vdv~I~rLR~Kl~~~~ 206 (226) T PRK09836 150 TLTSKEFTLLEFFLRHQGEVLPRSLIASQVWDMNFDSDTNAIDVAVKRLRGKIDNDF 206 (226) T ss_pred ECCHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCC T ss_conf 568899999999986899648799999996288878885889999999999857889 No 166 >PRK11517 transcriptional regulatory protein YedW; Provisional Probab=93.69 E-value=0.15 Score=30.18 Aligned_cols=47 Identities=23% Similarity=0.226 Sum_probs=40.3 Q ss_pred CCCHHHHHHHHHHHCC----CCHHHHHHHHC-----CCHHHHHHHHHHHHHHCCCC Q ss_conf 4998999999999879----99789999949-----99889999999999980799 Q gi|254780693|r 173 NLTERETSCLQLAGDG----YTSEEIAEKLG-----LSVHTVNAYLGSATVKLDAV 219 (235) Q Consensus 173 ~LT~RE~evL~l~a~G----~t~~eIA~~L~-----iS~~TV~~hl~~i~~KLg~~ 219 (235) .||++|.++|..++.- .|-.+|...+. .+.+||+.|+.++++||+-. T Consensus 147 ~LT~~E~~LL~~L~~~~g~vvsre~l~~~vwg~~~~~~~~~idv~I~rLRkKl~~~ 202 (223) T PRK11517 147 TLTRKEFQLLWLLASRAGEIIPRTVIASEIWGINFDSDTNTVDVAIRRLRAKVDDP 202 (223) T ss_pred CCCHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCC T ss_conf 29999999999998689985989999999629887888587999999999985788 No 167 >PRK10701 DNA-binding transcriptional regulator RstA; Provisional Probab=93.67 E-value=0.13 Score=30.56 Aligned_cols=47 Identities=13% Similarity=0.046 Sum_probs=39.3 Q ss_pred CCCHHHHHHHHHHHCCC----CHHHHHHHH-----CCCHHHHHHHHHHHHHHCCCC Q ss_conf 49989999999998799----978999994-----999889999999999980799 Q gi|254780693|r 173 NLTERETSCLQLAGDGY----TSEEIAEKL-----GLSVHTVNAYLGSATVKLDAV 219 (235) Q Consensus 173 ~LT~RE~evL~l~a~G~----t~~eIA~~L-----~iS~~TV~~hl~~i~~KLg~~ 219 (235) .||++|.++|..++.-. |-++|-..+ ..+.+||+.|+.++++||+-. T Consensus 161 ~LT~~E~~lL~~L~~~~g~vvsre~L~~~vwg~~~~~~~rtvdv~I~rLRkKl~~~ 216 (240) T PRK10701 161 SLSTADFELLWELATHAGQIMDRDALLKNLRGVSYDGLDRSVDVAISRLRKKLLDN 216 (240) T ss_pred ECCHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHC T ss_conf 76789999999999779987389999998539887888678999999999987528 No 168 >PRK06704 RNA polymerase factor sigma-70; Validated Probab=93.65 E-value=0.15 Score=30.21 Aligned_cols=58 Identities=24% Similarity=0.305 Sum_probs=47.2 Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCC-----------HHHHHHHHHH Q ss_conf 4998999999999-87999789999949998899999999999807997-----------8999999997 Q gi|254780693|r 173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVN-----------RIQAIAKAIR 230 (235) Q Consensus 173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~n-----------R~qava~A~~ 230 (235) .|||++.-|+.+- .-+++..|||.++++||.+|+.-+.+.+.+|.-.| -.++++.|++ T Consensus 116 ~L~p~Q~vIfLLkDVF~ys~~eiAe~~s~sEGaVKasLfRsR~RLK~~~ee~~~~~~~~~D~e~~V~air 185 (228) T PRK06704 116 SLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASLFRSRNRLKTVSEEGIEIVEFTDDMEVVVTSIR 185 (228) T ss_pred HCCHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCHHHCCCCCCCCCHHHHHHHHH T ss_conf 2588889999999998755999999955663499999999999987338531245666776279999998 No 169 >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=93.60 E-value=0.13 Score=30.73 Aligned_cols=45 Identities=31% Similarity=0.303 Sum_probs=35.5 Q ss_pred CCCHHHHHHHHHHHC-----C--CCHHHHHHHHCCCHHHHHHHHHHHHHHCCC Q ss_conf 499899999999987-----9--997899999499988999999999998079 Q gi|254780693|r 173 NLTERETSCLQLAGD-----G--YTSEEIAEKLGLSVHTVNAYLGSATVKLDA 218 (235) Q Consensus 173 ~LT~RE~evL~l~a~-----G--~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~ 218 (235) .||++++++|+-+.+ | -.+++||..+++|+.||++-+... +.||- T Consensus 1 ~LT~~Qr~IL~aLI~lY~~~~~pVks~~IAe~l~~spgTIRN~M~~L-~~LGL 52 (79) T pfam03444 1 ELTPVQKEILQALINLYRKKGRAVKGEEIADIIGRNPGTVRNQMQSL-KALGL 52 (79) T ss_pred CCCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHH-HHCCC T ss_conf 97789999999999999972998667999999878908899999999-98588 No 170 >PRK10643 DNA-binding transcriptional regulator BasR; Provisional Probab=93.59 E-value=0.17 Score=29.79 Aligned_cols=47 Identities=17% Similarity=0.047 Sum_probs=38.1 Q ss_pred CCCCHHHHHHHHHHHCCC----CHHHHHHHH-----CCCHHHHHHHHHHHHHHCCC Q ss_conf 449989999999998799----978999994-----99988999999999998079 Q gi|254780693|r 172 RNLTERETSCLQLAGDGY----TSEEIAEKL-----GLSVHTVNAYLGSATVKLDA 218 (235) Q Consensus 172 ~~LT~RE~evL~l~a~G~----t~~eIA~~L-----~iS~~TV~~hl~~i~~KLg~ 218 (235) ..||++|.++|.++..-. |-++|...+ ..+.+||+.|+.++++||+= T Consensus 148 i~LT~~E~~lL~~L~~~~g~vvsre~L~~~v~~~~~~~~~~~ld~~I~rLRkKl~~ 203 (222) T PRK10643 148 LILTPKEYALLSRLMLKAGSPVHREILYNDIYNWDNEPSTNTLEVHIHNLRDKVGK 203 (222) T ss_pred EEECHHHHHHHHHHHHCCCCCCCHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHCCC T ss_conf 87087999999999967999868999999960878888867699999999976699 No 171 >PRK10955 DNA-binding transcriptional regulator CpxR; Provisional Probab=93.48 E-value=0.15 Score=30.22 Aligned_cols=47 Identities=17% Similarity=0.180 Sum_probs=38.2 Q ss_pred CCCHHHHHHHHHHHCC----CCHHHHHHHH-----CCCHHHHHHHHHHHHHHCCCC Q ss_conf 4998999999999879----9978999994-----999889999999999980799 Q gi|254780693|r 173 NLTERETSCLQLAGDG----YTSEEIAEKL-----GLSVHTVNAYLGSATVKLDAV 219 (235) Q Consensus 173 ~LT~RE~evL~l~a~G----~t~~eIA~~L-----~iS~~TV~~hl~~i~~KLg~~ 219 (235) .||++|.++|.++++- .|-++|...+ ..+.+||+.|+.++++||+-. T Consensus 156 ~LT~~E~~lL~~L~~~~g~vvsre~L~~~vwg~~~~~~~rtidv~I~rLRkKL~~~ 211 (232) T PRK10955 156 ELTGTEFTLLYLLAQHLGQVVSREHLSQEVLGKRLTPFDRAIDMHISNLRRKLPDR 211 (232) T ss_pred ECCHHHHHHHHHHHHCCCCEECHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHCCCC T ss_conf 66899999999999789950979999999718898888582999999999954116 No 172 >smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli Probab=93.38 E-value=0.22 Score=29.05 Aligned_cols=48 Identities=23% Similarity=0.251 Sum_probs=35.3 Q ss_pred HHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHH Q ss_conf 8999999999879--997899999499988999999999998079978999 Q gi|254780693|r 176 ERETSCLQLAGDG--YTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQA 224 (235) Q Consensus 176 ~RE~evL~l~a~G--~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qa 224 (235) +-.+++|+.+.+. .|..+||+.+|+|+.||...++++. +-|+=.++.+ T Consensus 3 ~~D~~Il~~L~~n~R~s~~~iA~~lg~S~~tv~~Ri~~L~-~~GiI~~~~~ 52 (108) T smart00344 3 EIDRKILEELQKDARISLAELAKKVGLSPSTVHNRVKRLE-EEGVIKGYTA 52 (108) T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHH-HCCCCCEEEE T ss_conf 8999999999982899999999998939999999999996-0897320289 No 173 >COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription] Probab=93.33 E-value=0.11 Score=31.11 Aligned_cols=37 Identities=24% Similarity=0.258 Sum_probs=26.1 Q ss_pred HCCCHHHHHHHHHHHHHHC------CCCCHHHHHHHHHHCCCC Q ss_conf 4999889999999999980------799789999999976999 Q gi|254780693|r 198 LGLSVHTVNAYLGSATVKL------DAVNRIQAIAKAIRFGYI 234 (235) Q Consensus 198 L~iS~~TV~~hl~~i~~KL------g~~nR~qava~A~~~Gli 234 (235) ..+..+|+---+..+.++= |=.++++|+.-|++-|+| T Consensus 261 ~~ln~r~igl~L~~l~~ip~vI~vAgG~~K~~AI~aaL~gg~~ 303 (321) T COG2390 261 TPLNDRVIGLSLDDLRQIPKVIAVAGGESKAEAILAALRGGYI 303 (321) T ss_pred CCCCCCEECCCHHHHHCCCCEEEEECCCCCHHHHHHHHHCCCC T ss_conf 5565716437788973278389995786028999999847998 No 174 >PRK11083 DNA-binding response regulator CreB; Provisional Probab=93.31 E-value=0.2 Score=29.26 Aligned_cols=48 Identities=21% Similarity=0.192 Sum_probs=39.4 Q ss_pred CCCHHHHHHHHHHHCC----CCHHHHHHHHC-----CCHHHHHHHHHHHHHHCCCCC Q ss_conf 4998999999999879----99789999949-----998899999999999807997 Q gi|254780693|r 173 NLTERETSCLQLAGDG----YTSEEIAEKLG-----LSVHTVNAYLGSATVKLDAVN 220 (235) Q Consensus 173 ~LT~RE~evL~l~a~G----~t~~eIA~~L~-----iS~~TV~~hl~~i~~KLg~~n 220 (235) .||++|.++|.+++.- .|-++|-..+. .+.+||+.|+.++++||...+ T Consensus 155 ~LT~~E~~LL~~L~~~~g~vvsr~~L~~~vw~~~~~~~~rtidv~I~rLR~KL~~~~ 211 (229) T PRK11083 155 SLTRYEFLLLKTLLLSPGRVFSRQQLMDIVWEDAQDSYDRTVDTHIKTLRAKLRAIN 211 (229) T ss_pred CCCHHHHHHHHHHHHCCCCEECHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHCC T ss_conf 599999999999986799409699999985599888884669999999999875268 No 175 >COG5625 Predicted transcription regulator containing HTH domain [Transcription] Probab=93.12 E-value=0.094 Score=31.65 Aligned_cols=43 Identities=28% Similarity=0.320 Sum_probs=36.0 Q ss_pred CCCHHHHHHHHHHH---CCCCHHHHHHHHCCCHHHHHHHHHHHHHH Q ss_conf 49989999999998---79997899999499988999999999998 Q gi|254780693|r 173 NLTERETSCLQLAG---DGYTSEEIAEKLGLSVHTVNAYLGSATVK 215 (235) Q Consensus 173 ~LT~RE~evL~l~a---~G~t~~eIA~~L~iS~~TV~~hl~~i~~K 215 (235) +|-+-|..|-.|+. .|+...||+.+|+||++||+.|+.+.++| T Consensus 18 glk~~eI~IY~lLve~~~~mri~ei~rEl~is~rtvr~~v~~l~rr 63 (113) T COG5625 18 GLKKNEIRIYSLLVEKGRGMRIREIQRELGISERTVRAAVAVLLRR 63 (113) T ss_pred CCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 7783300155689884677417899999829999999999999985 No 176 >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=93.11 E-value=0.12 Score=30.90 Aligned_cols=45 Identities=29% Similarity=0.371 Sum_probs=42.2 Q ss_pred CCCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 4998999999999-87999789999949998899999999999807 Q gi|254780693|r 173 NLTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 173 ~LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) -||+||++|+.++ -+|++-||.+..||||.==|-.--+.+.+||. T Consensus 206 iLserE~~ii~c~f~enlsQKeTGErlGiSQMHVSRl~R~ai~KL~ 251 (256) T TIGR02941 206 ILSEREKEIIECTFIENLSQKETGERLGISQMHVSRLQRRAIKKLK 251 (256) T ss_pred HCCHHHHHHHHHHHHCCCCCCHHHHHCCHHHHHHHHHHHHHHHHHH T ss_conf 0054456766655314787300232224035567788899999999 No 177 >PRK02277 orotate phosphoribosyltransferase-like protein; Provisional Probab=93.05 E-value=0.099 Score=31.51 Aligned_cols=30 Identities=33% Similarity=0.489 Sum_probs=11.8 Q ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHHHH Q ss_conf 999987999789999949998899999999 Q gi|254780693|r 182 LQLAGDGYTSEEIAEKLGLSVHTVNAYLGS 211 (235) Q Consensus 182 L~l~a~G~t~~eIA~~L~iS~~TV~~hl~~ 211 (235) ..|-..|++..|||.+|++|..||.+.+.+ T Consensus 12 ~eL~~~Gls~geIAdELnvS~eT~~WLl~~ 41 (201) T PRK02277 12 LELRSEGLSTGEIADELNVSRETATWLLTR 41 (201) T ss_pred HHHHHCCCCHHHHHHHHHHHHHHHHHHHHC T ss_conf 999986997666355540269999999834 No 178 >PRK10161 transcriptional regulator PhoB; Provisional Probab=92.99 E-value=0.23 Score=28.96 Aligned_cols=47 Identities=13% Similarity=0.100 Sum_probs=39.5 Q ss_pred CCCHHHHHHHHHHHCCC----CHHHHHHHHC-----CCHHHHHHHHHHHHHHCCCC Q ss_conf 49989999999998799----9789999949-----99889999999999980799 Q gi|254780693|r 173 NLTERETSCLQLAGDGY----TSEEIAEKLG-----LSVHTVNAYLGSATVKLDAV 219 (235) Q Consensus 173 ~LT~RE~evL~l~a~G~----t~~eIA~~L~-----iS~~TV~~hl~~i~~KLg~~ 219 (235) .||++|.++|.+++... |-++|-..+. ++.+||+.|+.++++||.-. T Consensus 154 ~LT~~E~~LL~~L~~~~g~vvsr~~L~~~vwg~~~~~~~rtldv~I~rLRkKl~~~ 209 (229) T PRK10161 154 EMGPTEFKLLHFFMTHPERVYSREQLLNHVWGTNVYVEDRTVDVHIRRLRKALEPG 209 (229) T ss_pred ECCHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCC T ss_conf 70689999999999779987979999998639998988473999999999974567 No 179 >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=92.92 E-value=0.2 Score=29.35 Aligned_cols=56 Identities=21% Similarity=0.310 Sum_probs=50.7 Q ss_pred CCCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHH Q ss_conf 4499899999999-9879997899999499988999999999998079978999999 Q gi|254780693|r 172 RNLTERETSCLQL-AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAK 227 (235) Q Consensus 172 ~~LT~RE~evL~l-~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~ 227 (235) ..||+||+..|+| .-+|+|..+||.-=+.|..||-.+++.++.++=-.+|.++..+ T Consensus 165 ~~L~~rER~LLRLHfv~~Ls~~r~g~my~~~~STvsR~~~~ARe~lle~Tr~~La~R 221 (249) T TIGR03001 165 AALSERERTLLRLHFVEGLSMDRLGAMYQVHRSTVSRWVAQARERLLERTRRRLAER 221 (249) T ss_pred HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 328986876555688203329999877457750789999999999999999999997 No 180 >PRK09191 two-component response regulator; Provisional Probab=92.81 E-value=0.3 Score=28.08 Aligned_cols=46 Identities=28% Similarity=0.432 Sum_probs=40.9 Q ss_pred CCCHHHHHHHHHHH-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCC Q ss_conf 49989999999998-79997899999499988999999999998079 Q gi|254780693|r 173 NLTERETSCLQLAG-DGYTSEEIAEKLGLSVHTVNAYLGSATVKLDA 218 (235) Q Consensus 173 ~LT~RE~evL~l~a-~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~ 218 (235) .|||+.++.+.|.+ +|.+..|+|.+|++++..|..-+..+++-+.. T Consensus 88 ~ltp~~RqAlLL~alEgFs~~eaA~Il~v~~~e~~~l~~~A~~ei~~ 134 (261) T PRK09191 88 AITPLPRQAFLLTALEGFSEEEAAEILGVDPAEVAALLDDASREIAR 134 (261) T ss_pred HCCCHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH T ss_conf 48930349999898828988999999789999999999999999973 No 181 >CHL00148 orf27 Ycf27; Reviewed Probab=92.80 E-value=0.25 Score=28.67 Aligned_cols=47 Identities=21% Similarity=0.202 Sum_probs=38.7 Q ss_pred CCCHHHHHHHHHHHCCC----CHHHHHHHHC-------CCHHHHHHHHHHHHHHCCCC Q ss_conf 49989999999998799----9789999949-------99889999999999980799 Q gi|254780693|r 173 NLTERETSCLQLAGDGY----TSEEIAEKLG-------LSVHTVNAYLGSATVKLDAV 219 (235) Q Consensus 173 ~LT~RE~evL~l~a~G~----t~~eIA~~L~-------iS~~TV~~hl~~i~~KLg~~ 219 (235) .||++|.++|..++.-. |-++|-..+. .+.+||+.|+.++++||+.. T Consensus 161 ~LT~~E~~lL~~L~~~~g~vvsre~L~~~vWg~~~~~~~~~r~vdv~I~rLRkKl~~~ 218 (240) T CHL00148 161 RLTGMEFSLLELLISESGEIFSRATILKEVWGYTPERHIDTRVVDVHISRLRAKLEDD 218 (240) T ss_pred ECCHHHHHHHHHHHHCCCCCCCHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHC T ss_conf 6589999999999967997496999999972888766787557999999999974107 No 182 >PRK11557 putative DNA-binding transcriptional regulator; Provisional Probab=92.80 E-value=0.33 Score=27.76 Aligned_cols=19 Identities=5% Similarity=0.235 Sum_probs=11.9 Q ss_pred HHHHHHHHHCCCCEEEEEE Q ss_conf 9999999858378589984 Q gi|254780693|r 20 RLHLIQNRIKARNFALYTI 38 (235) Q Consensus 20 ~l~~l~~~~~~~~f~~~~~ 38 (235) .+..+++.+++.||.-|.. T Consensus 50 TVvRf~kkLGf~Gf~efK~ 68 (282) T PRK11557 50 SVVKFAQKLGYKGFPALKL 68 (282) T ss_pred HHHHHHHHHCCCCHHHHHH T ss_conf 9999999938998999999 No 183 >COG0745 OmpR Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription] Probab=92.75 E-value=0.21 Score=29.20 Aligned_cols=48 Identities=23% Similarity=0.253 Sum_probs=40.1 Q ss_pred CCCHHHHHHHHHHHCCC----CHHHHHHHHC-----CCHHHHHHHHHHHHHHCCCCC Q ss_conf 49989999999998799----9789999949-----998899999999999807997 Q gi|254780693|r 173 NLTERETSCLQLAGDGY----TSEEIAEKLG-----LSVHTVNAYLGSATVKLDAVN 220 (235) Q Consensus 173 ~LT~RE~evL~l~a~G~----t~~eIA~~L~-----iS~~TV~~hl~~i~~KLg~~n 220 (235) .||++|.++|..+++-. |-.+|-..+. ...+||+.|++++++||+... T Consensus 153 ~Lt~~Ef~lL~~L~~~~g~v~sR~~L~~~vw~~~~~~~~rtvdvhI~rLR~Kl~~~~ 209 (229) T COG0745 153 TLTPKEFELLELLARHPGRVLSREQLLEAVWGYDFEVDSRTVDVHISRLRKKLEKDP 209 (229) T ss_pred CCCHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCEEHHHHHHHHHHHCCCC T ss_conf 178899999999996699526899999986086668764330599889999733567 No 184 >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=92.74 E-value=0.17 Score=29.90 Aligned_cols=45 Identities=33% Similarity=0.346 Sum_probs=37.7 Q ss_pred CCCHHHHHHHHH-----HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 499899999999-----987999789999949998899999999999807 Q gi|254780693|r 173 NLTERETSCLQL-----AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 173 ~LT~RE~evL~l-----~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) .|++||++|+.. -..-+|-+|||..||||..=|-.==+++..||- T Consensus 175 ~L~~rE~~vi~~RyGL~~~~~~tQREIA~~LgISRSYVSRIEK~Al~Kl~ 224 (228) T TIGR02846 175 VLKGREREVIEMRYGLKDGREKTQREIAKILGISRSYVSRIEKKALKKLY 224 (228) T ss_pred HHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHH T ss_conf 74088899998743668889541789987708650045488899999998 No 185 >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=92.64 E-value=0.23 Score=28.85 Aligned_cols=46 Identities=28% Similarity=0.318 Sum_probs=40.9 Q ss_pred CCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 4499899999999987999789999949998899999999999807 Q gi|254780693|r 172 RNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 172 ~~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) .-||++|..||.|=..|.+-++||..|+-|...|-.-=++++.+.. T Consensus 5 tFLTe~Q~kVL~lR~kGl~Q~eIAk~LkTtRaNvS~iEkrA~EnIe 50 (142) T TIGR00721 5 TFLTERQIKVLELREKGLKQKEIAKILKTTRANVSIIEKRALENIE 50 (142) T ss_pred CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHH T ss_conf 4340656899998633888788987726720137898887443237 No 186 >pfam01978 TrmB Sugar-specific transcriptional regulator TrmB. One member of this family, TrmB, has been shown to be a sugar-specific transcriptional regulator of the trehalose/maltose ABC transporter in Thermococcus litoralis. Probab=92.51 E-value=0.46 Score=26.74 Aligned_cols=44 Identities=30% Similarity=0.227 Sum_probs=37.8 Q ss_pred CCCCHHHHHHHHHHH--CCCCHHHHHHHHCCCHHHHHHHHHHHHHH Q ss_conf 449989999999998--79997899999499988999999999998 Q gi|254780693|r 172 RNLTERETSCLQLAG--DGYTSEEIAEKLGLSVHTVNAYLGSATVK 215 (235) Q Consensus 172 ~~LT~RE~evL~l~a--~G~t~~eIA~~L~iS~~TV~~hl~~i~~K 215 (235) -+||+.|.+|-..+. -..|..|||..++|+..+|...+++..+| T Consensus 4 ~Gls~~E~~vY~~Ll~~g~~t~~eia~~~~i~r~~vY~~L~~L~~k 49 (68) T pfam01978 4 LGLSEYEAKVYLALLKLGPATADEIAEESGVPRSKVYEVLRSLEKK 49 (68) T ss_pred CCCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC T ss_conf 3989999999999998199889999999598898999999999988 No 187 >PRK11886 biotin--protein ligase; Provisional Probab=92.48 E-value=0.34 Score=27.71 Aligned_cols=37 Identities=5% Similarity=0.190 Sum_probs=21.0 Q ss_pred HHCCHHHHCCHHHHHH-HHHHHHHHHCCCCEEEEEECC Q ss_conf 0211986225999999-999999985837858998417 Q gi|254780693|r 4 NTLTGKKSSSLQELSP-RLHLIQNRIKARNFALYTINS 40 (235) Q Consensus 4 ~~~~~~~~~sl~dl~~-~l~~l~~~~~~~~f~~~~~~~ 40 (235) +.+||++.+..-.+.+ .++..-+.+...||.+.+... T Consensus 17 ~~~SGe~la~~LgvSR~aVwK~i~~L~~~G~~I~s~~~ 54 (319) T PRK11886 17 DFHSGEQLAEELGISRAAIWKHIQTLEEWGLDIFSVKG 54 (319) T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEECC T ss_conf 92969999998798899999999999977973999789 No 188 >pfam01371 Trp_repressor Trp repressor protein. This protein binds to tryptophan and represses transcription of the Trp operon. Probab=92.42 E-value=0.22 Score=29.10 Aligned_cols=38 Identities=29% Similarity=0.311 Sum_probs=30.4 Q ss_pred CCCHHHHH-------HHH-HHHCCCCHHHHHHHHCCCHHHHHHHHH Q ss_conf 49989999-------999-998799978999994999889999999 Q gi|254780693|r 173 NLTERETS-------CLQ-LAGDGYTSEEIAEKLGLSVHTVNAYLG 210 (235) Q Consensus 173 ~LT~RE~e-------vL~-l~a~G~t~~eIA~~L~iS~~TV~~hl~ 210 (235) -+||.|.+ |++ ++..|+|-.+|+..+|+|..||-.=-+ T Consensus 26 l~T~~E~~ala~R~~va~~LL~~~~syreI~~~~g~S~aTItRvsr 71 (88) T pfam01371 26 LLTPDEREALAQRLRIAKELLRGELSQREIAQELGASIATITRGSN 71 (88) T ss_pred HCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHH T ss_conf 3999999999999999999997899899999985985231478899 No 189 >COG1356 tfx Transcriptional regulator [DNA replication, recombination and repair] Probab=92.40 E-value=0.082 Score=32.09 Aligned_cols=52 Identities=27% Similarity=0.261 Sum_probs=41.8 Q ss_pred CCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHH Q ss_conf 4449989999999998799978999994999889999999999980799789 Q gi|254780693|r 171 ARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRI 222 (235) Q Consensus 171 ~~~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~ 222 (235) ..-||+++.+||.+=.+|.|-+|||.+|+-+...|..-=++++.+..-.-+| T Consensus 6 dtflte~qikvl~lRekG~tQ~eIA~~L~TTraNvSaIEkrA~enIekarnT 57 (143) T COG1356 6 DTFLTEQQIKVLVLREKGLTQSEIARILKTTRANVSAIEKRALENIEKARNT 57 (143) T ss_pred HCEEEHHHEEEEEHHHCCCCHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHH T ss_conf 1110023023565264056489999997545101799999999989999889 No 190 >COG3398 Uncharacterized protein conserved in archaea [Function unknown] Probab=92.36 E-value=0.27 Score=28.38 Aligned_cols=35 Identities=29% Similarity=0.165 Sum_probs=28.5 Q ss_pred HHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHH Q ss_conf 9999999879--9978999994999889999999999 Q gi|254780693|r 179 TSCLQLAGDG--YTSEEIAEKLGLSVHTVNAYLGSAT 213 (235) Q Consensus 179 ~evL~l~a~G--~t~~eIA~~L~iS~~TV~~hl~~i~ 213 (235) +.+...+-++ .|+.+||..+++|..||.+|++++- T Consensus 177 k~I~~eiq~~~~~t~~~ia~~l~ls~aTV~~~lk~l~ 213 (240) T COG3398 177 KAIIYEIQENKCNTNLLIAYELNLSVATVAYHLKKLE 213 (240) T ss_pred HHHHHHHHCCCCCHHHHHHHHCCCCHHHHHHHHHHHH T ss_conf 8999998628741599998870865999999999898 No 191 >PRK10816 DNA-binding transcriptional regulator PhoP; Provisional Probab=92.31 E-value=0.2 Score=29.40 Aligned_cols=47 Identities=19% Similarity=0.234 Sum_probs=40.5 Q ss_pred CCCHHHHHHHHHHHCC----CCHHHHHHHHC-----CCHHHHHHHHHHHHHHCCCC Q ss_conf 4998999999999879----99789999949-----99889999999999980799 Q gi|254780693|r 173 NLTERETSCLQLAGDG----YTSEEIAEKLG-----LSVHTVNAYLGSATVKLDAV 219 (235) Q Consensus 173 ~LT~RE~evL~l~a~G----~t~~eIA~~L~-----iS~~TV~~hl~~i~~KLg~~ 219 (235) .||++|.++|.++... .|-++|-..+. .+.+||+.|+.++++||... T Consensus 149 ~LT~~E~~LL~~L~~~~~~vvsre~l~~~vw~~~~~~~~~sld~~I~rLRkKl~~~ 204 (223) T PRK10816 149 KLTAFEYTIMETLIRNNGKVVSKDSLMLQLYPDAELRESHTIDVLMGRLRKKIQAQ 204 (223) T ss_pred EECHHHHHHHHHHHHCCCEEECHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCC T ss_conf 70689999999999879923839999998549987888677999999999974335 No 192 >pfam03811 Ins_element1 Insertion element protein. Probab=92.21 E-value=0.19 Score=29.51 Aligned_cols=36 Identities=19% Similarity=0.242 Sum_probs=32.6 Q ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHH Q ss_conf 999999999879997899999499988999999999 Q gi|254780693|r 177 RETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSA 212 (235) Q Consensus 177 RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i 212 (235) -..+|+.+...|.--++||+.|+||.+||=.+|++. T Consensus 52 vkeqiv~m~~nG~GiRdtaRvl~Is~nTVlrtLK~s 87 (88) T pfam03811 52 TKEQIVDMAMNGAGCRYTARTLKIGINTVIRTLKNS 87 (88) T ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCC T ss_conf 789999997679854044787375689999987535 No 193 >PRK11337 DNA-binding transcriptional repressor RpiR; Provisional Probab=92.00 E-value=0.47 Score=26.69 Aligned_cols=18 Identities=6% Similarity=0.026 Sum_probs=11.1 Q ss_pred HHHHHHHHHCCCCEEEEE Q ss_conf 999999985837858998 Q gi|254780693|r 20 RLHLIQNRIKARNFALYT 37 (235) Q Consensus 20 ~l~~l~~~~~~~~f~~~~ 37 (235) .+..+++.+++.||.-|. T Consensus 63 TVvRf~kkLGf~Gf~efK 80 (293) T PRK11337 63 MIVKVAKLLGFSGFRNLR 80 (293) T ss_pred HHHHHHHHHCCCCHHHHH T ss_conf 999999995789789999 No 194 >COG1737 RpiR Transcriptional regulators [Transcription] Probab=91.97 E-value=0.45 Score=26.83 Aligned_cols=19 Identities=5% Similarity=0.259 Sum_probs=11.3 Q ss_pred HHHHHHHHHCCCCEEEEEE Q ss_conf 9999999858378589984 Q gi|254780693|r 20 RLHLIQNRIKARNFALYTI 38 (235) Q Consensus 20 ~l~~l~~~~~~~~f~~~~~ 38 (235) .+..+++.++++||.-|.. T Consensus 52 Tv~Rf~~kLGf~Gf~efk~ 70 (281) T COG1737 52 TVVRFARKLGFEGFSEFKL 70 (281) T ss_pred HHHHHHHHCCCCCHHHHHH T ss_conf 9999999859998899999 No 195 >PRK10529 DNA-binding transcriptional activator KdpE; Provisional Probab=91.91 E-value=0.34 Score=27.72 Aligned_cols=47 Identities=21% Similarity=0.241 Sum_probs=38.9 Q ss_pred CCCHHHHHHHHHHHCCC----CHHHHHHHHC-----CCHHHHHHHHHHHHHHCCCC Q ss_conf 49989999999998799----9789999949-----99889999999999980799 Q gi|254780693|r 173 NLTERETSCLQLAGDGY----TSEEIAEKLG-----LSVHTVNAYLGSATVKLDAV 219 (235) Q Consensus 173 ~LT~RE~evL~l~a~G~----t~~eIA~~L~-----iS~~TV~~hl~~i~~KLg~~ 219 (235) .||++|.++|.+++.-. |-++|-..+. .+.+||+.|++++++||+.. T Consensus 151 ~LT~~E~~lL~~L~~~~g~vvsre~L~~~vw~~~~~~~~~~idv~I~rLRkKl~~~ 206 (225) T PRK10529 151 HLTPIEFRLLAVLLNNAGKVLTQRQLLNQVWGPNAVEHSHYLRIYMGHLRQKLEQD 206 (225) T ss_pred CCCHHHHHHHHHHHHCCCCEECHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCC T ss_conf 13668999999999779961969999999649998988687999999999972007 No 196 >pfam01022 HTH_5 Bacterial regulatory protein, arsR family. Members of this family contains a DNA binding 'helix-turn-helix' motif. This family includes other proteins which are not included in the Prosite definition. Probab=91.91 E-value=0.55 Score=26.19 Aligned_cols=38 Identities=34% Similarity=0.327 Sum_probs=31.5 Q ss_pred HHHHHHHHHHCC-CCHHHHHHHHCCCHHHHHHHHHHHHH Q ss_conf 999999999879-99789999949998899999999999 Q gi|254780693|r 177 RETSCLQLAGDG-YTSEEIAEKLGLSVHTVNAYLGSATV 214 (235) Q Consensus 177 RE~evL~l~a~G-~t~~eIA~~L~iS~~TV~~hl~~i~~ 214 (235) --.+|+.++++| ++..||+..+++|+.||..|++..+. T Consensus 3 ~Rl~Il~~L~~~~~~v~el~~~l~~sq~~vS~HL~~L~~ 41 (47) T pfam01022 3 TRLKILYLLSEGELCVCELAEILGLSQSTVSHHLKKLRE 41 (47) T ss_pred HHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHH T ss_conf 899999999808996999999989588699999999989 No 197 >smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein. Probab=91.56 E-value=0.55 Score=26.19 Aligned_cols=45 Identities=27% Similarity=0.284 Sum_probs=38.8 Q ss_pred CCCCCHHHHHHHHHHH--CCCCHHHHHHHHCCCHHHHHHHHHHHHHH Q ss_conf 4449989999999998--79997899999499988999999999998 Q gi|254780693|r 171 ARNLTERETSCLQLAG--DGYTSEEIAEKLGLSVHTVNAYLGSATVK 215 (235) Q Consensus 171 ~~~LT~RE~evL~l~a--~G~t~~eIA~~L~iS~~TV~~hl~~i~~K 215 (235) .-+||+.|..||..+. .|.|..+||..++++..||...++++-+| T Consensus 5 ~~glt~~q~~vL~~l~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~ 51 (101) T smart00347 5 PLGLTPTQFLVLRILYEEGPLSVSELAKRLGVSPSTVTRVLDRLEKK 51 (101) T ss_pred HCCCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHCC T ss_conf 13949999999999997699799999999896887999999999458 No 198 >COG1522 Lrp Transcriptional regulators [Transcription] Probab=91.32 E-value=0.68 Score=25.52 Aligned_cols=43 Identities=26% Similarity=0.322 Sum_probs=31.9 Q ss_pred CCCCHHHHHHHHHHHCCC--CHHHHHHHHCCCHHHHHHHHHHHHH Q ss_conf 449989999999998799--9789999949998899999999999 Q gi|254780693|r 172 RNLTERETSCLQLAGDGY--TSEEIAEKLGLSVHTVNAYLGSATV 214 (235) Q Consensus 172 ~~LT~RE~evL~l~a~G~--t~~eIA~~L~iS~~TV~~hl~~i~~ 214 (235) ..|++-+.++|..+..+. +..+||..+|+|+.||...++++-+ T Consensus 4 ~~lD~~D~~IL~~L~~d~r~~~~eia~~lglS~~~v~~Ri~~L~~ 48 (154) T COG1522 4 MKLDDIDRRILRLLQEDARISNAELAERVGLSPSTVLRRIKRLEE 48 (154) T ss_pred CCCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHH T ss_conf 553799999999999727657999999979798999999999998 No 199 >pfam01047 MarR MarR family. The Mar proteins are involved in the multiple antibiotic resistance, a non-specific resistance system. The expression of the mar operon is controlled by a repressor, MarR. A large number of compounds induce transcription of the mar operon. This is thought to be due to the compound binding to MarR, and the resulting complex stops MarR binding to the DNA. With the MarR repression lost, transcription of the operon proceeds. The structure of MarR is known and shows MarR as a dimer with each subunit containing a winged-helix DNA binding motif. Probab=91.12 E-value=0.69 Score=25.47 Aligned_cols=42 Identities=33% Similarity=0.320 Sum_probs=36.7 Q ss_pred CCHHHHHHHHHHH--CCCCHHHHHHHHCCCHHHHHHHHHHHHHH Q ss_conf 9989999999998--79997899999499988999999999998 Q gi|254780693|r 174 LTERETSCLQLAG--DGYTSEEIAEKLGLSVHTVNAYLGSATVK 215 (235) Q Consensus 174 LT~RE~evL~l~a--~G~t~~eIA~~L~iS~~TV~~hl~~i~~K 215 (235) ||.-|..||..+. .|.+..+||..++++..||-.-++++-+| T Consensus 1 lT~~Q~~vL~~l~~~~~~s~~~la~~~~~~~~~vs~~i~~Le~~ 44 (59) T pfam01047 1 LTLTQFHILRILYEHGPLTVSELAEKLGVDRSTVTRVLDRLEKK 44 (59) T ss_pred CCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC T ss_conf 98999999999994699299999999885865499999999889 No 200 >COG3877 Uncharacterized protein conserved in bacteria [Function unknown] Probab=91.03 E-value=0.56 Score=26.12 Aligned_cols=51 Identities=22% Similarity=0.168 Sum_probs=41.6 Q ss_pred CCCCCCCHHHHHHHHHHHC-CCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCC Q ss_conf 8744499899999999987-99978999994999889999999999980799 Q gi|254780693|r 169 SAARNLTERETSCLQLAGD-GYTSEEIAEKLGLSVHTVNAYLGSATVKLDAV 219 (235) Q Consensus 169 ~~~~~LT~RE~evL~l~a~-G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~ 219 (235) .+-+.||+-|.+.+.+.-+ -..-|||-+.||+|..||+..+..+.+++|-. T Consensus 37 s~F~~Lt~d~LeFv~lf~r~RGnlKEvEr~lg~sYptvR~kld~vlramgy~ 88 (122) T COG3877 37 SKFEYLTSDQLEFVELFLRCRGNLKEVERELGISYPTVRTKLDEVLRAMGYN 88 (122) T ss_pred CCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHHHHHCCCC T ss_conf 6332358757689999999725799999997776178998999999980899 No 201 >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=90.63 E-value=1.3 Score=23.48 Aligned_cols=48 Identities=27% Similarity=0.248 Sum_probs=42.9 Q ss_pred CCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHC-CCCC Q ss_conf 499899999999-98799978999994999889999999999980-7997 Q gi|254780693|r 173 NLTERETSCLQL-AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKL-DAVN 220 (235) Q Consensus 173 ~LT~RE~evL~l-~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL-g~~n 220 (235) .|||-|+-|.-| =+-++.-+|||.++|.|+..++.-..++++|| ...- T Consensus 109 rL~P~ERAVF~LREVF~y~Y~EIA~~v~kS~ancRQl~~RAr~~lr~~~r 158 (287) T TIGR02957 109 RLSPLERAVFLLREVFDYDYEEIASIVGKSEANCRQLVSRARRHLRAARR 158 (287) T ss_pred HCCHHHHHHHHHHHHHCCCCHHHHHHCCCCHHHHHHHHHHHHHHHHHCCC T ss_conf 07978999999998745882678976068957999999999999975288 No 202 >PRK11179 DNA-binding transcriptional regulator AsnC; Provisional Probab=90.56 E-value=0.99 Score=24.38 Aligned_cols=40 Identities=15% Similarity=0.243 Sum_probs=21.4 Q ss_pred CCHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHH Q ss_conf 998999999999879--9978999994999889999999999 Q gi|254780693|r 174 LTERETSCLQLAGDG--YTSEEIAEKLGLSVHTVNAYLGSAT 213 (235) Q Consensus 174 LT~RE~evL~l~a~G--~t~~eIA~~L~iS~~TV~~hl~~i~ 213 (235) |.+--+.+|+.+.+- .|+.|||..+|+|+.||...++++. T Consensus 7 lD~~D~~IL~~Lq~d~R~s~~eiA~~lglS~stv~~Ri~rLe 48 (153) T PRK11179 7 IDNLDRGILEALMENARTPYAELAKQFGVSPGTIHVRVEKMK 48 (153) T ss_pred CCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHH T ss_conf 789999999999984899999999998929999999999999 No 203 >COG2865 Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Transcription] Probab=90.45 E-value=0.53 Score=26.31 Aligned_cols=42 Identities=29% Similarity=0.435 Sum_probs=38.4 Q ss_pred CCCHHHHHHHHHHHC--CCCHHHHHHHHCCCHHHHHHHHHHHHH Q ss_conf 499899999999987--999789999949998899999999999 Q gi|254780693|r 173 NLTERETSCLQLAGD--GYTSEEIAEKLGLSVHTVNAYLGSATV 214 (235) Q Consensus 173 ~LT~RE~evL~l~a~--G~t~~eIA~~L~iS~~TV~~hl~~i~~ 214 (235) .++.|+..|+.|+.+ =.|+++++.+|++|..|+..++.+..+ T Consensus 399 ~~~~~~~~il~~~~en~~~T~~~L~~~l~is~~~i~r~i~~Lv~ 442 (467) T COG2865 399 SLSERQEKILELIKENGKVTARELREILGISSETIRRRIANLVK 442 (467) T ss_pred CHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHC T ss_conf 76677899999975266558899998857564569999999844 No 204 >PRK11173 two-component response regulator; Provisional Probab=90.40 E-value=0.59 Score=25.98 Aligned_cols=48 Identities=13% Similarity=0.143 Sum_probs=38.1 Q ss_pred CCCHHHHHHHHHHHCCC----CHHHHHHHH-----CCCHHHHHHHHHHHHHHCCCCC Q ss_conf 49989999999998799----978999994-----9998899999999999807997 Q gi|254780693|r 173 NLTERETSCLQLAGDGY----TSEEIAEKL-----GLSVHTVNAYLGSATVKLDAVN 220 (235) Q Consensus 173 ~LT~RE~evL~l~a~G~----t~~eIA~~L-----~iS~~TV~~hl~~i~~KLg~~n 220 (235) .||++|.++|.+++.-. |-++|-..+ ..+.+||+.|+.++++||+... T Consensus 160 ~Lt~~E~~lL~~L~~~~~~vvsR~~L~~~vwg~~~~~~~r~ld~~I~rLRkKl~~~~ 216 (237) T PRK11173 160 KLPRSEFRAMLHFCENPGKIQSRAELLKKMTGRELKPHDRTVDVTIRRIRKHFESTP 216 (237) T ss_pred ECCHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHCC T ss_conf 769999999999986799876899999996198878885869999999999765279 No 205 >TIGR02233 Myxo_sigma_rel Myxococcus probable DNA-binding regulatory protein. Probab=90.36 E-value=0.53 Score=26.30 Aligned_cols=56 Identities=23% Similarity=0.325 Sum_probs=49.7 Q ss_pred CCCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHH Q ss_conf 4499899999999-9879997899999499988999999999998079978999999 Q gi|254780693|r 172 RNLTERETSCLQL-AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAK 227 (235) Q Consensus 172 ~~LT~RE~evL~l-~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~ 227 (235) ..|++||+++|++ .-+|.|-+.||..=+.+..||-.++..+...|--.+|-....+ T Consensus 23 a~L~~~eR~lLRLH~~~gLsldR~~~lY~~hrStvaR~v~~are~Ll~~Tr~~LaeR 79 (106) T TIGR02233 23 AALSERERTLLRLHHVEGLSLDRLGTLYGVHRSTVARWVAGARELLLERTRQELAER 79 (106) T ss_pred HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 528963335666776236558999988478861699999999999999989987674 No 206 >COG2522 Predicted transcriptional regulator [General function prediction only] Probab=90.29 E-value=0.54 Score=26.27 Aligned_cols=35 Identities=31% Similarity=0.469 Sum_probs=30.5 Q ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH Q ss_conf 99999999987999789999949998899999999 Q gi|254780693|r 177 RETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGS 211 (235) Q Consensus 177 RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~ 211 (235) |-.-...|+-+|+|-.+||..||||+..|..|++. T Consensus 11 Ra~lA~~L~eeG~Sq~~iA~LLGltqaAVS~Yls~ 45 (119) T COG2522 11 RALLAKELIEEGLSQYRIAKLLGLTQAAVSQYLSG 45 (119) T ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCC T ss_conf 99999999995886999999968889999999736 No 207 >pfam03965 Pencillinase_R Penicillinase repressor. The penicillinase repressor negatively regulates expression of the penicillinase gene. The N-terminal region of this protein is involved in operator recognition, while the C-terminal is responsible for dimerization of the protein. Probab=90.16 E-value=0.78 Score=25.11 Aligned_cols=13 Identities=15% Similarity=0.164 Sum_probs=7.1 Q ss_pred CCCHHHHHHHHHH Q ss_conf 4998999999999 Q gi|254780693|r 173 NLTERETSCLQLA 185 (235) Q Consensus 173 ~LT~RE~evL~l~ 185 (235) .||+-|.+-|+-+ T Consensus 100 ~ls~~el~~L~~~ 112 (115) T pfam03965 100 KLSPDDIEELREL 112 (115) T ss_pred CCCHHHHHHHHHH T ss_conf 9999999999998 No 208 >pfam08461 HTH_12 Ribonuclease R winged-helix domain. This domain is found at the amino terminus of Ribonuclease R and a number of presumed transcriptional regulatory proteins from archaebacteria. Probab=90.02 E-value=0.56 Score=26.17 Aligned_cols=34 Identities=21% Similarity=0.244 Sum_probs=27.0 Q ss_pred HHHHHHHCC---CCHHHHHHHH-----CCCHHHHHHHHHHHH Q ss_conf 999999879---9978999994-----999889999999999 Q gi|254780693|r 180 SCLQLAGDG---YTSEEIAEKL-----GLSVHTVNAYLGSAT 213 (235) Q Consensus 180 evL~l~a~G---~t~~eIA~~L-----~iS~~TV~~hl~~i~ 213 (235) |||+.++.- .++++||..| .|+++||++|++.+= T Consensus 2 eILriL~~~~~Pigak~ia~~L~~rG~~i~eRaVRYhL~~Ld 43 (66) T pfam08461 2 EILRILAESDKPIGAKIIAEELNLRGYDIGERAVRYHLRILD 43 (66) T ss_pred HHHHHHHHCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHH T ss_conf 789999985998649999999998285840899999999998 No 209 >pfam00126 HTH_1 Bacterial regulatory helix-turn-helix protein, lysR family. Probab=89.95 E-value=0.97 Score=24.43 Aligned_cols=43 Identities=21% Similarity=0.218 Sum_probs=39.6 Q ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCC Q ss_conf 9999999998799978999994999889999999999980799 Q gi|254780693|r 177 RETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAV 219 (235) Q Consensus 177 RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~ 219 (235) +..+++..+++=.+-...|..|+||+.||-.+++++-..||+. T Consensus 2 ~~l~~f~~v~~~gs~~~AA~~l~isqs~vs~~i~~LE~~lg~~ 44 (60) T pfam00126 2 RQLRVFVAVAEEGSFTAAAERLGLSQPAVSRQIKRLEEELGVP 44 (60) T ss_pred HHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCE T ss_conf 7799999999809999999997989889999999999995997 No 210 >PRK05658 RNA polymerase sigma factor RpoD; Validated Probab=89.72 E-value=1.6 Score=22.97 Aligned_cols=52 Identities=23% Similarity=0.309 Sum_probs=45.8 Q ss_pred CCCHHHHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHH Q ss_conf 4998999999999-----879997899999499988999999999998079978999 Q gi|254780693|r 173 NLTERETSCLQLA-----GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQA 224 (235) Q Consensus 173 ~LT~RE~evL~l~-----a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qa 224 (235) .|||||.+||++= ..-+|=+|++...+|+.-=|+.-=+++.+||--.+|... T Consensus 557 ~Lt~rE~~vl~~RfGi~~~~~~TLeevg~~f~vtRERiRQIEakalrklrhp~r~~~ 613 (620) T PRK05658 557 SLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSRK 613 (620) T ss_pred CCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHH T ss_conf 799999999999579999996789999988297689899999999998568725788 No 211 >PRK11242 DNA-binding transcriptional regulator CynR; Provisional Probab=89.58 E-value=1.1 Score=24.08 Aligned_cols=19 Identities=16% Similarity=0.319 Sum_probs=9.2 Q ss_pred CHHHHHHHHHHHHHHHCCC Q ss_conf 5999999999999985837 Q gi|254780693|r 13 SLQELSPRLHLIQNRIKAR 31 (235) Q Consensus 13 sl~dl~~~l~~l~~~~~~~ 31 (235) |-..+...+..+.+.++.. T Consensus 28 sQ~avS~~i~~LE~~lg~~ 46 (292) T PRK11242 28 SQPTLSQQIRQLEESLGVQ 46 (292) T ss_pred CHHHHHHHHHHHHHHHCCE T ss_conf 9899999999999996987 No 212 >PRK11074 putative DNA-binding transcriptional regulator; Provisional Probab=89.53 E-value=1.4 Score=23.35 Aligned_cols=14 Identities=7% Similarity=0.188 Sum_probs=5.0 Q ss_pred HHHHHHHHHHHHCC Q ss_conf 99999999998583 Q gi|254780693|r 17 LSPRLHLIQNRIKA 30 (235) Q Consensus 17 l~~~l~~l~~~~~~ 30 (235) +...+..+.+.++. T Consensus 33 VS~~I~~LE~~LG~ 46 (300) T PRK11074 33 VSYTVRQLEEWLAV 46 (300) T ss_pred HHHHHHHHHHHHCC T ss_conf 99999999999599 No 213 >PRK13856 two-component response regulator VirG; Provisional Probab=89.49 E-value=0.31 Score=27.95 Aligned_cols=48 Identities=15% Similarity=0.047 Sum_probs=37.1 Q ss_pred CCCCHHHHHHHHHHHCCC----CHHHHHHHH-----CCCHHHHHHHHHHHHHHCCCC Q ss_conf 449989999999998799----978999994-----999889999999999980799 Q gi|254780693|r 172 RNLTERETSCLQLAGDGY----TSEEIAEKL-----GLSVHTVNAYLGSATVKLDAV 219 (235) Q Consensus 172 ~~LT~RE~evL~l~a~G~----t~~eIA~~L-----~iS~~TV~~hl~~i~~KLg~~ 219 (235) ..||++|.++|.+++... |-.+|-..+ .++.+||+.|+.++++||.-. T Consensus 154 v~LT~~E~~lL~~L~~~~~~vvsRe~L~~~~~~~~~~~~~r~id~~I~rLRkKL~~~ 210 (241) T PRK13856 154 VKLTAGEFNLLVAFLEKPRDVLSREQLLIASRVREEEVYDRSIDVLILRLRRKLEQD 210 (241) T ss_pred EECCHHHHHHHHHHHHCCCCEEEHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCC T ss_conf 867889999999998769943819999998445677888686999999999973138 No 214 >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=89.16 E-value=1.1 Score=24.03 Aligned_cols=49 Identities=20% Similarity=0.126 Sum_probs=40.5 Q ss_pred CCCCHHHHHHHHHHHCC------CCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHH Q ss_conf 44998999999999879------997899999499988999999999998079978999 Q gi|254780693|r 172 RNLTERETSCLQLAGDG------YTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQA 224 (235) Q Consensus 172 ~~LT~RE~evL~l~a~G------~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qa 224 (235) +.||+.|+.|+.++..- +|..++|...|+|+.||- +..+|||..+=.+. T Consensus 12 ~~lt~~e~~ia~yil~~~~~~~~~si~~lA~~~~vS~atv~----Rf~kklG~~Gf~ef 66 (106) T pfam01418 12 SKLTKSEKKIADYILASPDNAIHLSIAELAKAAGVSEASVV----RFCRKLGFSGFSDL 66 (106) T ss_pred HHCCHHHHHHHHHHHHCHHHHHHCCHHHHHHHHCCCHHHHH----HHHHHHCCCCHHHH T ss_conf 76499999999999929999988339999989699899999----99999589989999 No 215 >COG1654 BirA Biotin operon repressor [Transcription] Probab=89.00 E-value=0.86 Score=24.81 Aligned_cols=39 Identities=26% Similarity=0.239 Sum_probs=29.5 Q ss_pred CHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHH Q ss_conf 98999999999879--99789999949998899999999999 Q gi|254780693|r 175 TERETSCLQLAGDG--YTSEEIAEKLGLSVHTVNAYLGSATV 214 (235) Q Consensus 175 T~RE~evL~l~a~G--~t~~eIA~~L~iS~~TV~~hl~~i~~ 214 (235) +.+...++.+ +.| .|-.+||..||||+.+|..|++.++. T Consensus 5 ~~~~~~ll~~-~~~~~~SGe~La~~LgiSRtaVwK~Iq~Lr~ 45 (79) T COG1654 5 SQMLLLLLLL-LTGNFVSGEKLAEELGISRTAVWKHIQQLRE 45 (79) T ss_pred HHHHHHHHHH-CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH T ss_conf 8999999997-3799666899999978659999999999998 No 216 >PRK12683 transcriptional regulator CysB-like protein; Reviewed Probab=88.72 E-value=1.6 Score=22.88 Aligned_cols=26 Identities=19% Similarity=0.192 Sum_probs=16.9 Q ss_pred CCCHHHHHHHHHHHCCCCHHHHHHHH Q ss_conf 49989999999998799978999994 Q gi|254780693|r 173 NLTERETSCLQLAGDGYTSEEIAEKL 198 (235) Q Consensus 173 ~LT~RE~evL~l~a~G~t~~eIA~~L 198 (235) .||+.-...+.++..-.+-.+|+..| T Consensus 279 ~Ls~~a~~Fie~l~~~l~~~~~~~~~ 304 (308) T PRK12683 279 YLRGYAYRFIEMFAPHLSEAEIAGAL 304 (308) T ss_pred CCCHHHHHHHHHHHHHHCHHHHHHHH T ss_conf 57999999999988862989999987 No 217 >smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor. Probab=88.65 E-value=0.88 Score=24.73 Aligned_cols=34 Identities=35% Similarity=0.335 Sum_probs=26.8 Q ss_pred HHHHHHC-CCCHHHHHHHHCCCHHHHHHHHHHHHH Q ss_conf 9999987-999789999949998899999999999 Q gi|254780693|r 181 CLQLAGD-GYTSEEIAEKLGLSVHTVNAYLGSATV 214 (235) Q Consensus 181 vL~l~a~-G~t~~eIA~~L~iS~~TV~~hl~~i~~ 214 (235) ++.++.+ .++..||+..+++|+.||..|++.+.+ T Consensus 2 Il~~L~~~~~~~~ela~~l~is~~tvs~HL~~L~~ 36 (66) T smart00418 2 ILKLLAEGELCVCELAEILGLSQSTVSHHLKKLRE 36 (66) T ss_pred HHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHH T ss_conf 58897739966999999988298888799999998 No 218 >COG1846 MarR Transcriptional regulators [Transcription] Probab=88.61 E-value=1.2 Score=23.76 Aligned_cols=42 Identities=31% Similarity=0.272 Sum_probs=36.4 Q ss_pred CCHHHHHHHHHHHCCCCH--HHHHHHHCCCHHHHHHHHHHHHHH Q ss_conf 998999999999879997--899999499988999999999998 Q gi|254780693|r 174 LTERETSCLQLAGDGYTS--EEIAEKLGLSVHTVNAYLGSATVK 215 (235) Q Consensus 174 LT~RE~evL~l~a~G~t~--~eIA~~L~iS~~TV~~hl~~i~~K 215 (235) ||+.|..+|..+...... .+||..|+++..||..+++++-+| T Consensus 20 l~~~q~~~L~~l~~~~~~~~~~la~~l~~~~~~vt~~l~~Le~~ 63 (126) T COG1846 20 LTPPQYQVLLALYEAGGITVKELAERLGLDRSTVTRLLKRLEDK 63 (126) T ss_pred CCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC T ss_conf 99899999999998489999999999787888899999999988 No 219 >COG5484 Uncharacterized conserved protein [Function unknown] Probab=88.58 E-value=0.79 Score=25.08 Aligned_cols=19 Identities=16% Similarity=0.001 Sum_probs=13.6 Q ss_pred CCCCHHHHHHHHHHHCCCC Q ss_conf 4499899999999987999 Q gi|254780693|r 172 RNLTERETSCLQLAGDGYT 190 (235) Q Consensus 172 ~~LT~RE~evL~l~a~G~t 190 (235) .-+|.||..+..++..|-- T Consensus 152 ~~~s~~E~~i~k~~~~~e~ 170 (279) T COG5484 152 TWYSAREAFIDKLTTKQEM 170 (279) T ss_pred HHHHHHHHHHHHHHHHHHH T ss_conf 1246788888876521356 No 220 >pfam09339 HTH_IclR IclR helix-turn-helix domain. Probab=88.29 E-value=1.5 Score=23.01 Aligned_cols=38 Identities=26% Similarity=0.364 Sum_probs=31.6 Q ss_pred HHHHHHHHHHC---CCCHHHHHHHHCCCHHHHHHHHHHHHH Q ss_conf 99999999987---999789999949998899999999999 Q gi|254780693|r 177 RETSCLQLAGD---GYTSEEIAEKLGLSVHTVNAYLGSATV 214 (235) Q Consensus 177 RE~evL~l~a~---G~t~~eIA~~L~iS~~TV~~hl~~i~~ 214 (235) |=.+||.+++. +.+.+|||..+|++..||..++....+ T Consensus 4 r~l~iL~~~~~~~~~~~l~eia~~~gl~kstv~RlL~tL~~ 44 (52) T pfam09339 4 RALAILEALAEAPGGLSLTEIARRTGLPKSTAHRLLQTLVE 44 (52) T ss_pred HHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH T ss_conf 99999999862899989999999989199999999999998 No 221 >PRK12679 cbl transcriptional regulator Cbl; Reviewed Probab=88.21 E-value=2 Score=22.27 Aligned_cols=25 Identities=20% Similarity=0.294 Sum_probs=18.7 Q ss_pred CCHHHHHHHHHHHCCCCHHHHHHHH Q ss_conf 9989999999998799978999994 Q gi|254780693|r 174 LTERETSCLQLAGDGYTSEEIAEKL 198 (235) Q Consensus 174 LT~RE~evL~l~a~G~t~~eIA~~L 198 (235) |++-=.+.+.+.+...|.++|.+.+ T Consensus 280 l~~~~~~Fi~~~~~~l~~~~~~~~~ 304 (316) T PRK12679 280 QRNYVWRFLELCNAGLSVEDIKRQV 304 (316) T ss_pred CHHHHHHHHHHHHCCCCHHHHHHHH T ss_conf 5699999999752028999999998 No 222 >TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR; InterPro: IPR014075 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 members of the SufR cyanobacterial protein family of transcriptional regulators that control the SUF system. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.. Probab=88.17 E-value=0.67 Score=25.59 Aligned_cols=28 Identities=25% Similarity=0.325 Sum_probs=18.7 Q ss_pred HHCC-CCHHHHHHHHCCCHHHHHHHHHHH Q ss_conf 9879-997899999499988999999999 Q gi|254780693|r 185 AGDG-YTSEEIAEKLGLSVHTVNAYLGSA 212 (235) Q Consensus 185 ~a~G-~t~~eIA~~L~iS~~TV~~hl~~i 212 (235) +.+| .|+-+||..|+||+-.|+.|+|.. T Consensus 11 L~~Gq~sA~~lA~~L~iSpQAvRrHLKDL 39 (215) T TIGR02702 11 LKEGQASALALAEELAISPQAVRRHLKDL 39 (215) T ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHHHHH T ss_conf 86004889999997278867887654332 No 223 >COG1321 TroR Mn-dependent transcriptional regulator [Transcription] Probab=87.92 E-value=1.4 Score=23.35 Aligned_cols=39 Identities=31% Similarity=0.390 Sum_probs=18.1 Q ss_pred CCHHHHHHHHHHH-----CC-CCHHHHHHHHCCCHHHHHHHHHHH Q ss_conf 9989999999998-----79-997899999499988999999999 Q gi|254780693|r 174 LTERETSCLQLAG-----DG-YTSEEIAEKLGLSVHTVNAYLGSA 212 (235) Q Consensus 174 LT~RE~evL~l~a-----~G-~t~~eIA~~L~iS~~TV~~hl~~i 212 (235) +|+++-+.|.-+- .| -..++||..|+||+.||...+++. T Consensus 4 ~s~~~edYL~~Iy~l~~~~~~~~~~diA~~L~Vsp~sVt~ml~rL 48 (154) T COG1321 4 LSETEEDYLETIYELLEEKGFARTKDIAERLKVSPPSVTEMLKRL 48 (154) T ss_pred CCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCCHHHHHHHHHH T ss_conf 421689999999999843687519999998589927899999999 No 224 >CHL00180 rbcR LysR transcriptional regulator; Provisional Probab=87.90 E-value=1.9 Score=22.38 Aligned_cols=19 Identities=11% Similarity=0.235 Sum_probs=9.1 Q ss_pred CHHHHHHHHHHHHHHHCCC Q ss_conf 5999999999999985837 Q gi|254780693|r 13 SLQELSPRLHLIQNRIKAR 31 (235) Q Consensus 13 sl~dl~~~l~~l~~~~~~~ 31 (235) |-..+...+..+.+.++.. T Consensus 32 sQpavS~~I~~LE~~lg~~ 50 (307) T CHL00180 32 SQPAVSLQIQNLEKQLNIP 50 (307) T ss_pred CHHHHHHHHHHHHHHHCCE T ss_conf 8789999999999986999 No 225 >PRK03573 transcriptional regulator SlyA; Provisional Probab=87.68 E-value=2.1 Score=22.05 Aligned_cols=44 Identities=16% Similarity=0.160 Sum_probs=37.1 Q ss_pred CCCCHHHHHHHHHHHC---CCCHHHHHHHHCCCHHHHHHHHHHHHHH Q ss_conf 4499899999999987---9997899999499988999999999998 Q gi|254780693|r 172 RNLTERETSCLQLAGD---GYTSEEIAEKLGLSVHTVNAYLGSATVK 215 (235) Q Consensus 172 ~~LT~RE~evL~l~a~---G~t~~eIA~~L~iS~~TV~~hl~~i~~K 215 (235) -+||+-+..||..+.+ |.|.+|+|..++|...||-..++++-+| T Consensus 27 ~gLt~~q~~~L~~L~~~~~g~tq~eLa~~l~v~~~t~tr~ld~LE~~ 73 (144) T PRK03573 27 LELTQTHWVTLHNIHQLPPDQSQIQLAKAIGIEQPSLVRTLDQLEEK 73 (144) T ss_pred CCCCHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC T ss_conf 69982599999999973989899999999798783699999999988 No 226 >PRK11302 DNA-binding transcriptional regulator HexR; Provisional Probab=87.55 E-value=1.7 Score=22.65 Aligned_cols=21 Identities=10% Similarity=0.420 Sum_probs=12.7 Q ss_pred HHHHHHHHHHCCCCEEEEEEC Q ss_conf 999999998583785899841 Q gi|254780693|r 19 PRLHLIQNRIKARNFALYTIN 39 (235) Q Consensus 19 ~~l~~l~~~~~~~~f~~~~~~ 39 (235) +.+..+++.+++.||.-|... T Consensus 49 aTV~Rf~kkLGf~Gf~efK~~ 69 (284) T PRK11302 49 PTVNRFCRSLDTKGFPDFKLH 69 (284) T ss_pred HHHHHHHHHHCCCCHHHHHHH T ss_conf 899999999578978999999 No 227 >PRK10341 DNA-binding transcriptional activator TdcA; Provisional Probab=87.53 E-value=1.8 Score=22.46 Aligned_cols=17 Identities=12% Similarity=0.145 Sum_probs=7.4 Q ss_pred HHHHHHHHHHHHHHCCC Q ss_conf 99999999999985837 Q gi|254780693|r 15 QELSPRLHLIQNRIKAR 31 (235) Q Consensus 15 ~dl~~~l~~l~~~~~~~ 31 (235) ..+...+..+.+.++.. T Consensus 36 pavS~~I~~LE~eLG~~ 52 (312) T PRK10341 36 PAVSKIINDIEDYFGVE 52 (312) T ss_pred HHHHHHHHHHHHHHCCE T ss_conf 89999999999984985 No 228 >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=87.16 E-value=0.94 Score=24.52 Aligned_cols=31 Identities=35% Similarity=0.511 Sum_probs=25.6 Q ss_pred HHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH Q ss_conf 9999987999789999949998899999999 Q gi|254780693|r 181 CLQLAGDGYTSEEIAEKLGLSVHTVNAYLGS 211 (235) Q Consensus 181 vL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~ 211 (235) .-.|--+|.+.+|||..||++++||.+-.++ T Consensus 6 Ar~LY~qg~~~~eIA~~Lg~~~~tVysWk~r 36 (58) T pfam06056 6 ARTLYWQGYRPAEIAQELGLKARTVYSWKDR 36 (58) T ss_pred HHHHHHCCCCHHHHHHHHCCCCCHHHHHHHH T ss_conf 9999996898999999978993145658652 No 229 >PRK12684 transcriptional regulator CysB-like protein; Reviewed Probab=87.15 E-value=2.2 Score=21.84 Aligned_cols=25 Identities=12% Similarity=0.135 Sum_probs=13.3 Q ss_pred CCHHHHHHHHHHHCCCCHHHHHHHH Q ss_conf 9989999999998799978999994 Q gi|254780693|r 174 LTERETSCLQLAGDGYTSEEIAEKL 198 (235) Q Consensus 174 LT~RE~evL~l~a~G~t~~eIA~~L 198 (235) ||+.-+..+.++.+-++-+-+-..| T Consensus 280 ls~~~r~FIe~l~e~l~r~~~~~~~ 304 (313) T PRK12684 280 LRGYVYTFIELFSPTLNRKLVEQAL 304 (313) T ss_pred CCHHHHHHHHHHHHHCCHHHHHHHH T ss_conf 6899999999987465989999998 No 230 >cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles. Probab=87.05 E-value=0.61 Score=25.88 Aligned_cols=23 Identities=35% Similarity=0.486 Sum_probs=20.9 Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH Q ss_conf 99789999949998899999999 Q gi|254780693|r 189 YTSEEIAEKLGLSVHTVNAYLGS 211 (235) Q Consensus 189 ~t~~eIA~~L~iS~~TV~~hl~~ 211 (235) +|.+|.|..||||+.|++...++ T Consensus 1 lt~~e~A~~lgVs~~TlrrW~~~ 23 (49) T cd04762 1 LTTKEAAELLGVSPSTLRRWVKE 23 (49) T ss_pred CCHHHHHHHHCCCHHHHHHHHHC T ss_conf 98899999979899999999987 No 231 >PRK11139 DNA-binding transcriptional activator GcvA; Provisional Probab=86.53 E-value=2.4 Score=21.61 Aligned_cols=12 Identities=8% Similarity=0.279 Sum_probs=4.2 Q ss_pred HHHHHHHHHHHC Q ss_conf 999999999858 Q gi|254780693|r 18 SPRLHLIQNRIK 29 (235) Q Consensus 18 ~~~l~~l~~~~~ 29 (235) ..++..+.+.++ T Consensus 38 S~~I~~LE~~lG 49 (295) T PRK11139 38 SHQIKALEDFLG 49 (295) T ss_pred HHHHHHHHHHHC T ss_conf 999999999859 No 232 >PRK10046 dpiA two-component response regulator DpiA; Provisional Probab=86.45 E-value=1.1 Score=24.13 Aligned_cols=38 Identities=24% Similarity=0.251 Sum_probs=30.2 Q ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHH Q ss_conf 99999999987999789999949998899999999999 Q gi|254780693|r 177 RETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATV 214 (235) Q Consensus 177 RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~ 214 (235) +=.++|+-...+.|..|||..+|||.-|++.|+.-.-. T Consensus 166 ~v~~~l~~~~~~~ta~eva~~~giSrvTaRRYLe~L~~ 203 (225) T PRK10046 166 AVRKLFKEPGVQHTAETVAQALTISRTTARRYLEYCAS 203 (225) T ss_pred HHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH T ss_conf 99999971799868999999858519999999999986 No 233 >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=86.15 E-value=1.9 Score=22.35 Aligned_cols=42 Identities=26% Similarity=0.385 Sum_probs=33.9 Q ss_pred CCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHH Q ss_conf 74449989999999998799978999994999889999999999 Q gi|254780693|r 170 AARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSAT 213 (235) Q Consensus 170 ~~~~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~ 213 (235) ....|||||.| ..|..|.|..|||...|+++.-|+.|-.-+. T Consensus 52 ~~~~lspreIQ--arIRaGas~eevA~~~g~~~~rVerfa~PVl 93 (169) T pfam11268 52 VDPTLSPREIQ--ARIRAGASAEEVAEAAGVPEERVERFEGPVL 93 (169) T ss_pred CCCCCCHHHHH--HHHHCCCCHHHHHHHHCCCHHHHHHCCCHHH T ss_conf 47888989999--9988799999999995999999874223388 No 234 >PRK11013 DNA-binding transcriptional regulator LysR; Provisional Probab=86.09 E-value=2.5 Score=21.46 Aligned_cols=17 Identities=18% Similarity=0.141 Sum_probs=6.9 Q ss_pred HHHHHHHHHHHHHHCCC Q ss_conf 99999999999985837 Q gi|254780693|r 15 QELSPRLHLIQNRIKAR 31 (235) Q Consensus 15 ~dl~~~l~~l~~~~~~~ 31 (235) ..+...+..+.+.++.. T Consensus 33 pavS~~I~~LE~~LG~~ 49 (309) T PRK11013 33 PTVSRELARFEQVIGLT 49 (309) T ss_pred HHHHHHHHHHHHHHCCE T ss_conf 89999999999997999 No 235 >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=86.00 E-value=0.72 Score=25.34 Aligned_cols=45 Identities=33% Similarity=0.320 Sum_probs=36.8 Q ss_pred CCHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCC Q ss_conf 998999999999-879997899999499988999999999998079 Q gi|254780693|r 174 LTERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDA 218 (235) Q Consensus 174 LT~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~ 218 (235) |-.-.++||-|. -.|.|-+|||..||+|..-||.-+=++++.|.. T Consensus 114 Lpe~yr~vl~Lr~~~efSYkEia~~~n~sl~~vK~~LfRaR~eLk~ 159 (162) T TIGR02950 114 LPENYRTVLLLREFKEFSYKEIAELLNLSLAKVKSELFRARKELKK 159 (162) T ss_pred CHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH T ss_conf 7087656567543126688899998456022100444487799987 No 236 >pfam07750 GcrA GcrA cell cycle regulator. GcrA is a master cell cycle regulator that, together with CtrA (see pfam00072 and pfam00486), is involved in controlling cell cycle progression and asymmetric polar morphogenesis. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery. Probab=86.00 E-value=0.83 Score=24.92 Aligned_cols=19 Identities=11% Similarity=0.111 Sum_probs=8.2 Q ss_pred EEEECCCCCCEEEEECCCCCC Q ss_conf 972168875234541058878 Q gi|254780693|r 120 FPVRLGFHKNGYVIFTSEFLM 140 (235) Q Consensus 120 ~pv~~~~~~~~~~~~~~~~~~ 140 (235) .|+.++.. --+.|++.... T Consensus 120 WPiGdP~~--~dF~FCG~~~~ 138 (162) T pfam07750 120 WPIGDPLS--EDFAFCGNKSS 138 (162) T ss_pred CCCCCCCC--CCCCCCCCCCC T ss_conf 88889898--88654288898 No 237 >PRK09801 transcriptional activator TtdR; Provisional Probab=85.95 E-value=2.6 Score=21.41 Aligned_cols=13 Identities=8% Similarity=0.317 Sum_probs=6.3 Q ss_pred CCHHHHHHHHHHH Q ss_conf 9989999999998 Q gi|254780693|r 174 LTERETSCLQLAG 186 (235) Q Consensus 174 LT~RE~evL~l~a 186 (235) +++|=+-++.|+. T Consensus 281 ~~~rvr~fidfl~ 293 (310) T PRK09801 281 RSMKLRVCVEFLA 293 (310) T ss_pred CCHHHHHHHHHHH T ss_conf 7879999999999 No 238 >pfam07900 DUF1670 Protein of unknown function (DUF1670). The hypothetical eukaryotic proteins found in this family are of unknown function. Probab=85.90 E-value=1.4 Score=23.25 Aligned_cols=30 Identities=30% Similarity=0.427 Sum_probs=19.3 Q ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHH Q ss_conf 999999879997899999499988999999 Q gi|254780693|r 180 SCLQLAGDGYTSEEIAEKLGLSVHTVNAYL 209 (235) Q Consensus 180 evL~l~a~G~t~~eIA~~L~iS~~TV~~hl 209 (235) +|..++..|++.+|||...|+|++.|.-|. T Consensus 189 rV~~l~~kg~~~~ei~~~tG~s~~lv~eY~ 218 (220) T pfam07900 189 RVEKLTEKGMSEEEIRYITGISERLVEEYV 218 (220) T ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHH T ss_conf 999999867879999999776589999997 No 239 >COG1497 Predicted transcriptional regulator [Transcription] Probab=85.79 E-value=1.6 Score=22.82 Aligned_cols=15 Identities=7% Similarity=0.060 Sum_probs=5.7 Q ss_pred HCCCHHHHHHHHHHH Q ss_conf 499988999999999 Q gi|254780693|r 198 LGLSVHTVNAYLGSA 212 (235) Q Consensus 198 L~iS~~TV~~hl~~i 212 (235) +-++.+-.+.+++++ T Consensus 231 vv~t~~ml~~~~~~l 245 (260) T COG1497 231 VVITRRMLRYLLRKL 245 (260) T ss_pred EEEEHHHHHHHHHHH T ss_conf 997077799999888 No 240 >PRK11151 DNA-binding transcriptional regulator OxyR; Provisional Probab=85.68 E-value=2.7 Score=21.32 Aligned_cols=17 Identities=12% Similarity=0.282 Sum_probs=7.2 Q ss_pred HHHHHHHHHHHHHHCCC Q ss_conf 99999999999985837 Q gi|254780693|r 15 QELSPRLHLIQNRIKAR 31 (235) Q Consensus 15 ~dl~~~l~~l~~~~~~~ 31 (235) ..+...+..+.+.++.. T Consensus 30 pavS~~I~~LE~~LG~~ 46 (305) T PRK11151 30 PTLSGQIRKLEDELGVM 46 (305) T ss_pred HHHHHHHHHHHHHHCCC T ss_conf 89999999999997986 No 241 >pfam01527 Transposase_8 Transposase. Transposase proteins are necessary for efficient DNA transposition. This family consists of various E. coli insertion elements and other bacterial transposases some of which are members of the IS3 family. Probab=85.58 E-value=1.7 Score=22.67 Aligned_cols=38 Identities=18% Similarity=0.145 Sum_probs=29.9 Q ss_pred HHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 99999-987999789999949998899999999999807 Q gi|254780693|r 180 SCLQL-AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 180 evL~l-~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) +++.+ +..|+|..+||..+|||+.|+..-++....-+. T Consensus 14 ~~V~~~~~~g~sv~~var~~gi~~~~l~~W~k~~~~g~~ 52 (75) T pfam01527 14 RAVKESLEPGASVSELAREHGVSPATLYKWRKKYRGGLL 52 (75) T ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCC T ss_conf 999999809984999999989599999999999846898 No 242 >PRK01381 Trp operon repressor; Provisional Probab=85.30 E-value=0.99 Score=24.38 Aligned_cols=35 Identities=26% Similarity=0.377 Sum_probs=27.8 Q ss_pred CCCHHHHH-------HHHHHHCC-CCHHHHHHHHCCCHHHHHH Q ss_conf 49989999-------99999879-9978999994999889999 Q gi|254780693|r 173 NLTERETS-------CLQLAGDG-YTSEEIAEKLGLSVHTVNA 207 (235) Q Consensus 173 ~LT~RE~e-------vL~l~a~G-~t~~eIA~~L~iS~~TV~~ 207 (235) -|||.|++ |.+.+..| +|-+|||..||+|.-||-. T Consensus 32 lLTp~Er~al~~R~~I~~~Ll~ge~sQReIa~~lgvsiAtITR 74 (99) T PRK01381 32 LLTPDEREALGTRVRIVEELLRGELSQREIKQELGVGIATITR 74 (99) T ss_pred HCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCEECCC T ss_conf 7899999999999999999994876499999984974020000 No 243 >PRK09791 putative DNA-binding transcriptional regulator; Provisional Probab=85.25 E-value=2.8 Score=21.18 Aligned_cols=18 Identities=17% Similarity=0.289 Sum_probs=8.1 Q ss_pred HHHHHHHHHHHHHHHCCC Q ss_conf 999999999999985837 Q gi|254780693|r 14 LQELSPRLHLIQNRIKAR 31 (235) Q Consensus 14 l~dl~~~l~~l~~~~~~~ 31 (235) -..+...+..+.+.++.. T Consensus 33 QpavS~~I~~LE~~lg~~ 50 (302) T PRK09791 33 QPALSKSIQELEEGLAAQ 50 (302) T ss_pred HHHHHHHHHHHHHHHCCE T ss_conf 799999999999995996 No 244 >smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation. Probab=84.90 E-value=2.9 Score=21.08 Aligned_cols=57 Identities=30% Similarity=0.374 Sum_probs=39.5 Q ss_pred HHHHHHHHHHHC---CCCHHHHHHHHCCCHHHHHHHHHHHHHH-----CCCCCHHHHHHHHHHCC Q ss_conf 899999999987---9997899999499988999999999998-----07997899999999769 Q gi|254780693|r 176 ERETSCLQLAGD---GYTSEEIAEKLGLSVHTVNAYLGSATVK-----LDAVNRIQAIAKAIRFG 232 (235) Q Consensus 176 ~RE~evL~l~a~---G~t~~eIA~~L~iS~~TV~~hl~~i~~K-----Lg~~nR~qava~A~~~G 232 (235) .|=.+||..+++ +.|..|||..+|++..||..+++..... -....++....+..++| T Consensus 5 ~ral~IL~~l~~~~~~~sl~eia~~~~l~ksT~~RlL~tL~~~G~l~~~~~~~~Y~lG~~~~~lg 69 (91) T smart00346 5 ERGLAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQDGQNGRYRLGPKVLELG 69 (91) T ss_pred HHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCCCEEEECHHHHHHH T ss_conf 99999999997289998999999998909999999999999889968849999775309999999 No 245 >COG2739 Uncharacterized protein conserved in bacteria [Function unknown] Probab=84.87 E-value=2.5 Score=21.53 Aligned_cols=44 Identities=25% Similarity=0.307 Sum_probs=38.9 Q ss_pred CCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHC Q ss_conf 499899999999-98799978999994999889999999999980 Q gi|254780693|r 173 NLTERETSCLQL-AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKL 216 (235) Q Consensus 173 ~LT~RE~evL~l-~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL 216 (235) -||.++...+.+ ..+-+|-.|||...+||...|..++++--..| T Consensus 17 LLT~KQ~~Y~~lyy~dDlSl~EIAee~~VSRqAIyDnIKr~~~~L 61 (105) T COG2739 17 LLTKKQKNYLELYYLDDLSLSEIAEEFNVSRQAIYDNIKRTEKIL 61 (105) T ss_pred HHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHH T ss_conf 986889999999998116699999995750999999999999999 No 246 >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=84.78 E-value=1.5 Score=23.05 Aligned_cols=42 Identities=24% Similarity=0.200 Sum_probs=35.9 Q ss_pred HHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 8999999999-87999789999949998899999999999807 Q gi|254780693|r 176 ERETSCLQLA-GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 176 ~RE~evL~l~-a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) |-++-||++. -++++.++|+.+|++|..|+...++.+.+-|| T Consensus 58 p~~RtvL~m~Yid~~~~~~v~e~l~~Sr~Tyyr~~r~Ai~~L~ 100 (100) T pfam07374 58 PDSRTILRMVYIDKMTVWQVCDKLNCSRTTYYRKLRVAIKELN 100 (100) T ss_pred HHHHHHHEEEEECCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC T ss_conf 0221311143443474999999976666789999999998529 No 247 >PRK12680 transcriptional regulator CysB-like protein; Reviewed Probab=84.40 E-value=3 Score=20.93 Aligned_cols=19 Identities=16% Similarity=0.235 Sum_probs=8.4 Q ss_pred CHHHHHHHHHHHHHHHCCC Q ss_conf 5999999999999985837 Q gi|254780693|r 13 SLQELSPRLHLIQNRIKAR 31 (235) Q Consensus 13 sl~dl~~~l~~l~~~~~~~ 31 (235) |-.-+...+..+.+.++.. T Consensus 29 SQPaVSkqIk~LE~eLGv~ 47 (327) T PRK12680 29 TQPGLSKQLKQLEDELGFL 47 (327) T ss_pred CHHHHHHHHHHHHHHHCCE T ss_conf 7679999999999985996 No 248 >COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms] Probab=84.23 E-value=2 Score=22.24 Aligned_cols=41 Identities=29% Similarity=0.329 Sum_probs=32.4 Q ss_pred CCCH-HHHHHHHHHH---CCCCHHHHHHHHCCCHHHHHHHHHHHH Q ss_conf 4998-9999999998---799978999994999889999999999 Q gi|254780693|r 173 NLTE-RETSCLQLAG---DGYTSEEIAEKLGLSVHTVNAYLGSAT 213 (235) Q Consensus 173 ~LT~-RE~evL~l~a---~G~t~~eIA~~L~iS~~TV~~hl~~i~ 213 (235) +|++ -...|..|+. +++|..|.|..+|||.-|++.|+.=.- T Consensus 154 Gi~~~Tl~~i~~~~~~~~~~~Taeela~~~giSRvTaRRYLeyl~ 198 (224) T COG4565 154 GLDELTLQKVREALKEPDQELTAEELAQALGISRVTARRYLEYLV 198 (224) T ss_pred CCCHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH T ss_conf 767999999999986757764799999883721999999999998 No 249 >PRK11169 leucine-responsive transcriptional regulator; Provisional Probab=84.21 E-value=1.5 Score=23.03 Aligned_cols=39 Identities=18% Similarity=0.254 Sum_probs=17.9 Q ss_pred CCHHHHHHHHHHHC-C-CCHHHHHHHHCCCHHHHHHHHHHH Q ss_conf 99899999999987-9-997899999499988999999999 Q gi|254780693|r 174 LTERETSCLQLAGD-G-YTSEEIAEKLGLSVHTVNAYLGSA 212 (235) Q Consensus 174 LT~RE~evL~l~a~-G-~t~~eIA~~L~iS~~TV~~hl~~i 212 (235) |-+--+.+|..+-+ | .|+.|||..+|+|+.||...++++ T Consensus 12 LD~~D~~IL~~Lq~daR~s~~eLA~~vglS~stv~~RikrL 52 (164) T PRK11169 12 LDRIDRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRL 52 (164) T ss_pred HHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHH T ss_conf 51999999999998489999999999892999999999999 No 250 >TIGR03298 argP transcriptional regulator, ArgP family. ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (PMID:10589831). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity (PMID: 15150242). Probab=84.20 E-value=3.1 Score=20.87 Aligned_cols=19 Identities=16% Similarity=0.366 Sum_probs=8.7 Q ss_pred CHHHHHHHHHHHHHHHCCC Q ss_conf 5999999999999985837 Q gi|254780693|r 13 SLQELSPRLHLIQNRIKAR 31 (235) Q Consensus 13 sl~dl~~~l~~l~~~~~~~ 31 (235) |-..+..++..+.+.++.. T Consensus 28 sqsaVS~~I~~LE~~LG~~ 46 (292) T TIGR03298 28 TPSAVSQRIKALEERLGQP 46 (292) T ss_pred CHHHHHHHHHHHHHHHCCH T ss_conf 8789999999999982962 No 251 >smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein. Probab=83.96 E-value=1.5 Score=23.16 Aligned_cols=26 Identities=42% Similarity=0.437 Sum_probs=23.1 Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH Q ss_conf 99789999949998899999999999 Q gi|254780693|r 189 YTSEEIAEKLGLSVHTVNAYLGSATV 214 (235) Q Consensus 189 ~t~~eIA~~L~iS~~TV~~hl~~i~~ 214 (235) +|.+|||..+|+|+.||...++...+ T Consensus 9 lt~~~iA~~lG~tretvsR~l~~l~~ 34 (48) T smart00419 9 LTRQEIAELLGLTRETVSRTLKRLEK 34 (48) T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH T ss_conf 79999999979979999999999998 No 252 >COG2964 Uncharacterized protein conserved in bacteria [Function unknown] Probab=83.80 E-value=1.2 Score=23.77 Aligned_cols=38 Identities=29% Similarity=0.398 Sum_probs=30.3 Q ss_pred HHHHHHHHHHHCCC-----CHHHHHHHHCCCHHHHHHHHHHHH Q ss_conf 89999999998799-----978999994999889999999999 Q gi|254780693|r 176 ERETSCLQLAGDGY-----TSEEIAEKLGLSVHTVNAYLGSAT 213 (235) Q Consensus 176 ~RE~evL~l~a~G~-----t~~eIA~~L~iS~~TV~~hl~~i~ 213 (235) .+-.-|..|-..|. ....+|..|+||++||..|++.+. T Consensus 174 ~~reiV~~L~EkGiF~lK~Ai~~VA~~L~iSr~TVY~YL~~~k 216 (220) T COG2964 174 KNREIVKALYEKGIFNLKDAINIVADRLGISRHTVYRYLRKFK 216 (220) T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHH T ss_conf 7899999998667641144899999996887589999999865 No 253 >PRK10141 DNA-binding transcriptional repressor ArsR; Provisional Probab=83.45 E-value=2.9 Score=21.02 Aligned_cols=38 Identities=13% Similarity=0.116 Sum_probs=30.4 Q ss_pred HHHHHHHHHHC-C-CCHHHHHHHHCCCHHHHHHHHHHHHH Q ss_conf 99999999987-9-99789999949998899999999999 Q gi|254780693|r 177 RETSCLQLAGD-G-YTSEEIAEKLGLSVHTVNAYLGSATV 214 (235) Q Consensus 177 RE~evL~l~a~-G-~t~~eIA~~L~iS~~TV~~hl~~i~~ 214 (235) -=..|+.++.+ | ++.-||+..|++|..||-.|++-+.. T Consensus 15 tRl~Il~lL~~~gelcV~eL~~~l~~sQs~vS~HL~~L~~ 54 (106) T PRK10141 15 TRLGIVLLLRESGELCVCDLCTALDQSQPKISRHLALLRE 54 (106) T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHH T ss_conf 9999999998749956999998869988899999999998 No 254 >smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab. Probab=83.28 E-value=2.8 Score=21.10 Aligned_cols=42 Identities=31% Similarity=0.302 Sum_probs=31.7 Q ss_pred HHHHHHHHH---CC-CCHHHHHHHHCCCHHHHHHHHHHHHHHCCCC Q ss_conf 999999998---79-9978999994999889999999999980799 Q gi|254780693|r 178 ETSCLQLAG---DG-YTSEEIAEKLGLSVHTVNAYLGSATVKLDAV 219 (235) Q Consensus 178 E~evL~l~a---~G-~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~ 219 (235) |.-||..+. .+ -|..+||..|||+.+.||.++-++.++=.|. T Consensus 8 eqkil~~L~~~g~~~~tA~~lak~lg~~Kk~vN~~LY~L~k~g~v~ 53 (68) T smart00550 8 EEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKGKVC 53 (68) T ss_pred HHHHHHHHHHCCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHCCCEE T ss_conf 9999999997488640399999994998999999999999748831 No 255 >PRK10430 DNA-binding transcriptional activator DcuR; Provisional Probab=83.27 E-value=1.8 Score=22.53 Aligned_cols=42 Identities=21% Similarity=0.262 Sum_probs=30.1 Q ss_pred CCCHHHH-HHHHHH---HCC-CCHHHHHHHHCCCHHHHHHHHHHHHH Q ss_conf 4998999-999999---879-99789999949998899999999999 Q gi|254780693|r 173 NLTERET-SCLQLA---GDG-YTSEEIAEKLGLSVHTVNAYLGSATV 214 (235) Q Consensus 173 ~LT~RE~-evL~l~---a~G-~t~~eIA~~L~iS~~TV~~hl~~i~~ 214 (235) +|++--. .|...+ ..| .|..|||..+|||.-|++.|+.-.-. T Consensus 158 Gl~~~TL~~i~~~l~~~~~~~~sa~eva~~~giSRvTaRRYLe~L~~ 204 (239) T PRK10430 158 GLTPQTLRTLCQWIDAHQDYEFSTDELANEVNISRVSCRKYLIWLVN 204 (239) T ss_pred CCCHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH T ss_conf 99999999999999827999846999998858529889999999986 No 256 >PRK13348 chromosome replication initiation inhibitor protein; Provisional Probab=82.91 E-value=3.4 Score=20.51 Aligned_cols=20 Identities=10% Similarity=0.218 Sum_probs=11.2 Q ss_pred CHHHHHHHHHHHHHHHCCCC Q ss_conf 59999999999999858378 Q gi|254780693|r 13 SLQELSPRLHLIQNRIKARN 32 (235) Q Consensus 13 sl~dl~~~l~~l~~~~~~~~ 32 (235) |-..+..++..+.+.++..- T Consensus 29 sqsavS~~I~~LE~~LG~~L 48 (294) T PRK13348 29 TRSAVSQRIKALEESLGQPL 48 (294) T ss_pred CHHHHHHHHHHHHHHHCCEE T ss_conf 87899999999999839843 No 257 >PRK11233 nitrogen assimilation transcriptional regulator; Provisional Probab=82.22 E-value=3.6 Score=20.34 Aligned_cols=12 Identities=0% Similarity=0.271 Sum_probs=4.3 Q ss_pred HHHHHHHHHHCC Q ss_conf 999999998583 Q gi|254780693|r 19 PRLHLIQNRIKA 30 (235) Q Consensus 19 ~~l~~l~~~~~~ 30 (235) ..+..+.+.++. T Consensus 34 ~~I~~LE~~LG~ 45 (305) T PRK11233 34 QQVATLEGELNQ 45 (305) T ss_pred HHHHHHHHHHCC T ss_conf 999999999699 No 258 >PRK03635 chromosome replication initiation inhibitor protein; Validated Probab=82.10 E-value=3.7 Score=20.31 Aligned_cols=19 Identities=16% Similarity=0.384 Sum_probs=9.2 Q ss_pred CHHHHHHHHHHHHHHHCCC Q ss_conf 5999999999999985837 Q gi|254780693|r 13 SLQELSPRLHLIQNRIKAR 31 (235) Q Consensus 13 sl~dl~~~l~~l~~~~~~~ 31 (235) |-..+..++..+.+.++.. T Consensus 29 tqsaVS~~I~~LE~~LG~~ 47 (295) T PRK03635 29 TQSAVSQRIKALEERVGQP 47 (295) T ss_pred CHHHHHHHHHHHHHHHCCC T ss_conf 8669999999999994972 No 259 >PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional Probab=82.07 E-value=3.7 Score=20.30 Aligned_cols=14 Identities=36% Similarity=0.629 Sum_probs=5.2 Q ss_pred CCCCHHHHHHHHCC Q ss_conf 79997899999499 Q gi|254780693|r 187 DGYTSEEIAEKLGL 200 (235) Q Consensus 187 ~G~t~~eIA~~L~i 200 (235) .|+-..|+=.-+|| T Consensus 449 ~G~~~pevl~~~g~ 462 (501) T PRK04172 449 AGIFRPEVTEPLGI 462 (501) T ss_pred CCCCCHHHHHHCCC T ss_conf 75788899975599 No 260 >PRK09834 DNA-binding transcriptional activator MhpR; Provisional Probab=82.05 E-value=3.7 Score=20.30 Aligned_cols=29 Identities=28% Similarity=0.218 Sum_probs=15.7 Q ss_pred CEEEEEEECCCCCCEEEEECCCCCCCCHH Q ss_conf 35899721688752345410588789989 Q gi|254780693|r 116 AGIAFPVRLGFHKNGYVIFTSEFLMLANE 144 (235) Q Consensus 116 ~~~~~pv~~~~~~~~~~~~~~~~~~~~~~ 144 (235) .++..|++.+..-.+.++..+.......+ T Consensus 206 ~~vAvPi~~~g~vvaalsvs~p~~r~~~~ 234 (264) T PRK09834 206 ASIAVPVRSGQRVLACLNLVYIASAMSIE 234 (264) T ss_pred EEEEEEECCCCEEEEEEEEEEECCCCCHH T ss_conf 99999971799299999996531229999 No 261 >smart00354 HTH_LACI helix_turn _helix lactose operon repressor. Probab=82.02 E-value=0.93 Score=24.56 Aligned_cols=44 Identities=27% Similarity=0.388 Sum_probs=29.5 Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCC Q ss_conf 978999994999889999999999980799789999999976999 Q gi|254780693|r 190 TSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFGYI 234 (235) Q Consensus 190 t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~~~Gli 234 (235) |-++||...|+|..||-..+.+- .+....+|..--..|-.+||. T Consensus 2 Ti~dvA~~aGVS~sTVSr~ln~~-~~Vs~~tr~rV~~~a~~lgY~ 45 (70) T smart00354 2 TIKDVARLAGVSKATVSRVLNGN-GRVSEETREKVLAAMEELGYI 45 (70) T ss_pred CHHHHHHHHCCCHHHHHHHHCCC-CCCCHHHHHHHHHHHHHHCCC T ss_conf 89999999895999999997799-989999999999999997899 No 262 >PRK09906 DNA-binding transcriptional regulator HcaR; Provisional Probab=81.90 E-value=3.7 Score=20.26 Aligned_cols=18 Identities=17% Similarity=0.235 Sum_probs=7.7 Q ss_pred HHHHHHHHHHHHHHHCCC Q ss_conf 999999999999985837 Q gi|254780693|r 14 LQELSPRLHLIQNRIKAR 31 (235) Q Consensus 14 l~dl~~~l~~l~~~~~~~ 31 (235) -..+...+..+.+.++.. T Consensus 29 QpalS~~I~~LE~~lG~~ 46 (296) T PRK09906 29 QPSLSQQIKDLENCVGVP 46 (296) T ss_pred HHHHHHHHHHHHHHHCCE T ss_conf 789999999999985988 No 263 >COG0583 LysR Transcriptional regulator [Transcription] Probab=81.86 E-value=3.8 Score=20.25 Aligned_cols=11 Identities=27% Similarity=0.362 Sum_probs=7.9 Q ss_pred HHHHHHHHHCC Q ss_conf 99999999879 Q gi|254780693|r 178 ETSCLQLAGDG 188 (235) Q Consensus 178 E~evL~l~a~G 188 (235) -..++.++..| T Consensus 222 ~~~~~~~v~~g 232 (297) T COG0583 222 AEALLQAVAAG 232 (297) T ss_pred HHHHHHHHHHC T ss_conf 99999999969 No 264 >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=81.69 E-value=3.3 Score=20.67 Aligned_cols=24 Identities=21% Similarity=0.243 Sum_probs=19.0 Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHH Q ss_conf 999789999949998899999999 Q gi|254780693|r 188 GYTSEEIAEKLGLSVHTVNAYLGS 211 (235) Q Consensus 188 G~t~~eIA~~L~iS~~TV~~hl~~ 211 (235) ..+-.|+|..+|||+.||...+++ T Consensus 71 D~tl~E~A~~~gVs~~tI~~aLkr 94 (120) T pfam01710 71 DAYLKERAKKFGVTPSSIHYALKK 94 (120) T ss_pred CCHHHHHHHHCCCCHHHHHHHHHH T ss_conf 720999999839879999999999 No 265 >PRK10163 DNA-binding transcriptional repressor AllR; Provisional Probab=81.67 E-value=3.8 Score=20.20 Aligned_cols=27 Identities=11% Similarity=-0.052 Sum_probs=13.0 Q ss_pred CEEEEEEECCCCCC-EEEEECCCCCCCC Q ss_conf 35899721688752-3454105887899 Q gi|254780693|r 116 AGIAFPVRLGFHKN-GYVIFTSEFLMLA 142 (235) Q Consensus 116 ~~~~~pv~~~~~~~-~~~~~~~~~~~~~ 142 (235) .++..||++..+.. +.++..+...... T Consensus 216 ~~iaaPV~d~~G~~vaAisv~gp~~r~~ 243 (271) T PRK10163 216 NCIASAIYDDVGSVVAAISISGPSSRLT 243 (271) T ss_pred EEEEEEEECCCCCEEEEEEEEEEHHHCC T ss_conf 8999989889999999999976856579 No 266 >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=81.58 E-value=1 Score=24.20 Aligned_cols=21 Identities=24% Similarity=0.390 Sum_probs=18.6 Q ss_pred CCCHHHHHHHHCCCHHHHHHH Q ss_conf 999789999949998899999 Q gi|254780693|r 188 GYTSEEIAEKLGLSVHTVNAY 208 (235) Q Consensus 188 G~t~~eIA~~L~iS~~TV~~h 208 (235) .+++++||.+|++|+.||+.- T Consensus 22 ~~~l~~IA~~L~vs~~~IrkW 42 (60) T pfam10668 22 TMKLKDIANKLNVSESQIRKW 42 (60) T ss_pred CEEHHHHHHHHCCCHHHHHHC T ss_conf 644999999968798887603 No 267 >PRK00423 tfb transcription initiation factor IIB; Reviewed Probab=81.53 E-value=3.8 Score=20.17 Aligned_cols=39 Identities=31% Similarity=0.312 Sum_probs=34.0 Q ss_pred HHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCC Q ss_conf 999998799978999994999889999999999980799 Q gi|254780693|r 181 CLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAV 219 (235) Q Consensus 181 vL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~ 219 (235) +.++.-.+.|-++||..-+||+-|++.-.+.+.+.|+.. T Consensus 269 a~~~~~~~~t~~~Ia~v~~vsevTIr~~ykel~~~l~~~ 307 (310) T PRK00423 269 ASLLEGERRTQREVAEVAGVTEVTVRNRYKELAEKLDIK 307 (310) T ss_pred HHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCC T ss_conf 999948898999999896988999999999999984872 No 268 >PRK10086 DNA-binding transcriptional regulator DsdC; Provisional Probab=81.47 E-value=3.9 Score=20.16 Aligned_cols=17 Identities=12% Similarity=0.386 Sum_probs=7.1 Q ss_pred HHHHHHHHHHHHHHCCC Q ss_conf 99999999999985837 Q gi|254780693|r 15 QELSPRLHLIQNRIKAR 31 (235) Q Consensus 15 ~dl~~~l~~l~~~~~~~ 31 (235) ..+..++..+.+.++.. T Consensus 43 saVS~~I~~LE~~LG~~ 59 (311) T PRK10086 43 SAVSHRINQLEEELGIK 59 (311) T ss_pred HHHHHHHHHHHHHHCCC T ss_conf 99999999999985984 No 269 >pfam04218 CENP-B_N CENP-B N-terminal DNA-binding domain. Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure. Probab=81.40 E-value=3.3 Score=20.64 Aligned_cols=43 Identities=21% Similarity=0.298 Sum_probs=36.2 Q ss_pred CCCHHH-HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHH Q ss_conf 499899-9999999879997899999499988999999999998 Q gi|254780693|r 173 NLTERE-TSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVK 215 (235) Q Consensus 173 ~LT~RE-~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~K 215 (235) .||-.| .+|++-+-+|.+..++|...||.+.||+.-++|--+- T Consensus 6 ~LTl~eKi~iI~~~e~G~s~~~lar~~gi~~STl~~I~Knkeki 49 (53) T pfam04218 6 SLTLREKIEVIQRSEEGESKASLARRFNVPRSTLRDILKNKEKL 49 (53) T ss_pred EECHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHH T ss_conf 41699999999999858968899999698797999999809999 No 270 >pfam00376 MerR MerR family regulatory protein. Probab=81.14 E-value=1.7 Score=22.72 Aligned_cols=22 Identities=36% Similarity=0.395 Sum_probs=19.6 Q ss_pred CHHHHHHHHCCCHHHHHHHHHH Q ss_conf 9789999949998899999999 Q gi|254780693|r 190 TSEEIAEKLGLSVHTVNAYLGS 211 (235) Q Consensus 190 t~~eIA~~L~iS~~TV~~hl~~ 211 (235) |..|+|..+|||++|++++-+. T Consensus 1 ti~e~A~~~gvs~~tlR~ye~~ 22 (38) T pfam00376 1 TIGEVAKLLGVSPRTLRYYEKI 22 (38) T ss_pred CHHHHHHHHCCCHHHHHHHHHC T ss_conf 9899999988799999999986 No 271 >smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor. Probab=80.96 E-value=3 Score=20.94 Aligned_cols=39 Identities=31% Similarity=0.381 Sum_probs=30.5 Q ss_pred HHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHH Q ss_conf 999999999879--997899999499988999999999998 Q gi|254780693|r 177 RETSCLQLAGDG--YTSEEIAEKLGLSVHTVNAYLGSATVK 215 (235) Q Consensus 177 RE~evL~l~a~G--~t~~eIA~~L~iS~~TV~~hl~~i~~K 215 (235) |..+++.++.+- .+..+++..++||+.||+.-+..+-.+ T Consensus 1 R~~~Il~~l~~~~~~~i~~La~~~~VS~~TiRRDl~~L~~~ 41 (53) T smart00420 1 RQQQILELLAQQGKVSVEELAELLGVSEMTIRRDLNKLEEQ 41 (53) T ss_pred CHHHHHHHHHHCCCEEHHHHHHHHCCCHHHHHHHHHHHHHC T ss_conf 98999999998697979999999897999999969999988 No 272 >PRK11512 DNA-binding transcriptional repressor MarR; Provisional Probab=80.88 E-value=4 Score=20.02 Aligned_cols=43 Identities=16% Similarity=0.179 Sum_probs=29.9 Q ss_pred CCCHHHHHHHHHHH--CCCCHHHHHHHHCCCHHHHHHHHHHHHHH Q ss_conf 49989999999998--79997899999499988999999999998 Q gi|254780693|r 173 NLTERETSCLQLAG--DGYTSEEIAEKLGLSVHTVNAYLGSATVK 215 (235) Q Consensus 173 ~LT~RE~evL~l~a--~G~t~~eIA~~L~iS~~TV~~hl~~i~~K 215 (235) +||+.|..||..+. .|.|..|+|..+++...||-..+.++-+| T Consensus 37 gLt~~Q~~vL~~L~~~~~~t~~eLa~~l~id~~tvt~~ldrLe~~ 81 (144) T PRK11512 37 DITAAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVCK 81 (144) T ss_pred CCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC T ss_conf 999999999999998699799999999788887899999999978 No 273 >pfam00356 LacI Bacterial regulatory proteins, lacI family. Probab=80.82 E-value=1.2 Score=23.84 Aligned_cols=44 Identities=25% Similarity=0.358 Sum_probs=31.9 Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCC Q ss_conf 978999994999889999999999980799789999999976999 Q gi|254780693|r 190 TSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFGYI 234 (235) Q Consensus 190 t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~~~Gli 234 (235) |-++||...|+|..||-..+.+- .+..-.+|..--..|-.+||. T Consensus 1 Ti~DIA~~agVS~~TVSr~ln~~-~~vs~~tr~rI~~~a~~lgY~ 44 (46) T pfam00356 1 TIKDVARLAGVSKATVSRVLNNP-ERVSEETREKVEAAMEELGYV 44 (46) T ss_pred CHHHHHHHHCCCHHHHHHHHCCC-CCCCHHHHHHHHHHHHHHCCC T ss_conf 99999999897999999998797-989999999999999997899 No 274 >PRK03601 transcriptional regulator HdfR; Provisional Probab=80.30 E-value=4.2 Score=19.89 Aligned_cols=18 Identities=17% Similarity=0.320 Sum_probs=8.4 Q ss_pred HHHHHHHHHHHHHHHCCC Q ss_conf 999999999999985837 Q gi|254780693|r 14 LQELSPRLHLIQNRIKAR 31 (235) Q Consensus 14 l~dl~~~l~~l~~~~~~~ 31 (235) -..+..++..+.+.++.. T Consensus 29 QsavS~~Ik~LE~~LG~~ 46 (275) T PRK03601 29 QSAVSFRIRQLENQLGVN 46 (275) T ss_pred HHHHHHHHHHHHHHHCCE T ss_conf 789999999999996983 No 275 >PRK10082 putative DNA-binding transcriptional regulator; Provisional Probab=79.91 E-value=4.3 Score=19.80 Aligned_cols=16 Identities=19% Similarity=0.380 Sum_probs=6.3 Q ss_pred HHHHHHHHHHHHHCCC Q ss_conf 9999999999985837 Q gi|254780693|r 16 ELSPRLHLIQNRIKAR 31 (235) Q Consensus 16 dl~~~l~~l~~~~~~~ 31 (235) .+..++..+.+.++.. T Consensus 41 avS~~I~~LE~~LGv~ 56 (303) T PRK10082 41 AFSRRIRALEQAIGVE 56 (303) T ss_pred HHHHHHHHHHHHHCCE T ss_conf 9999999999996995 No 276 >COG2524 Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription] Probab=79.88 E-value=2.2 Score=21.91 Aligned_cols=29 Identities=14% Similarity=0.272 Sum_probs=22.7 Q ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHH Q ss_conf 99999998799978999994999889999 Q gi|254780693|r 179 TSCLQLAGDGYTSEEIAEKLGLSVHTVNA 207 (235) Q Consensus 179 ~evL~l~a~G~t~~eIA~~L~iS~~TV~~ 207 (235) .+|...+|+|.-+......|--..-||+. T Consensus 221 ~dI~~aia~g~~~~kV~~~M~k~vitI~e 249 (294) T COG2524 221 SDIAKAIANGNLDAKVSDYMRKNVITINE 249 (294) T ss_pred HHHHHHHHCCCCCCCHHHHHCCCCCEECC T ss_conf 99999997689654388875057704757 No 277 >PRK13509 transcriptional repressor UlaR; Provisional Probab=79.83 E-value=4.4 Score=19.78 Aligned_cols=12 Identities=8% Similarity=0.050 Sum_probs=4.1 Q ss_pred CHHHHHHHHHHH Q ss_conf 599999999999 Q gi|254780693|r 13 SLQELSPRLHLI 24 (235) Q Consensus 13 sl~dl~~~l~~l 24 (235) |.+.+..-|..+ T Consensus 32 S~~TIRRDL~~L 43 (251) T PRK13509 32 SPATARRDINKL 43 (251) T ss_pred CHHHHHHHHHHH T ss_conf 998999839999 No 278 >COG3711 BglG Transcriptional antiterminator [Transcription] Probab=79.76 E-value=2.8 Score=21.19 Aligned_cols=28 Identities=29% Similarity=0.304 Sum_probs=17.8 Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHC Q ss_conf 9978999994999889999999999980 Q gi|254780693|r 189 YTSEEIAEKLGLSVHTVNAYLGSATVKL 216 (235) Q Consensus 189 ~t~~eIA~~L~iS~~TV~~hl~~i~~KL 216 (235) .+..+.|..|++|..||..+++++..++ T Consensus 101 ~~l~~La~~l~vs~~ti~~dl~~v~~~l 128 (491) T COG3711 101 LSLHELADELFVSKSTIINDLKDVRLKL 128 (491) T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHH T ss_conf 5799999998466999999999899999 No 279 >PRK10632 putative DNA-binding transcriptional regulator; Provisional Probab=79.33 E-value=4.5 Score=19.68 Aligned_cols=14 Identities=14% Similarity=0.169 Sum_probs=8.0 Q ss_pred CCHHHHHHHHHHHC Q ss_conf 99899999999987 Q gi|254780693|r 174 LTERETSCLQLAGD 187 (235) Q Consensus 174 LT~RE~evL~l~a~ 187 (235) +++|=+-++.++.+ T Consensus 277 ~~~rvr~fidfl~e 290 (309) T PRK10632 277 LPLKVQVVINYLTD 290 (309) T ss_pred CCHHHHHHHHHHHH T ss_conf 48999999999999 No 280 >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=79.33 E-value=2 Score=22.21 Aligned_cols=26 Identities=27% Similarity=0.372 Sum_probs=21.9 Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH Q ss_conf 99789999949998899999999999 Q gi|254780693|r 189 YTSEEIAEKLGLSVHTVNAYLGSATV 214 (235) Q Consensus 189 ~t~~eIA~~L~iS~~TV~~hl~~i~~ 214 (235) -++.+||..|++|+.||...++++-. T Consensus 21 v~~~~iA~~L~Vs~~SVt~mlkkL~~ 46 (58) T pfam01325 21 VKTKDLAERLNVSPSTVSEMLKKLEK 46 (58) T ss_pred EEHHHHHHHHCCCCHHHHHHHHHHHH T ss_conf 12999999959992529999999998 No 281 >PRK12681 cysB transcriptional regulator CysB; Reviewed Probab=79.16 E-value=4.6 Score=19.64 Aligned_cols=27 Identities=11% Similarity=0.122 Sum_probs=16.7 Q ss_pred CCHHHHHHHHHHHCCCCHHHHHHHHCC Q ss_conf 998999999999879997899999499 Q gi|254780693|r 174 LTERETSCLQLAGDGYTSEEIAEKLGL 200 (235) Q Consensus 174 LT~RE~evL~l~a~G~t~~eIA~~L~i 200 (235) |++--.+..++.+..+|-+.|-.-+.. T Consensus 280 l~~~~~~Fi~~~~p~l~~~~~~~~~~~ 306 (324) T PRK12681 280 LRSYMYDFIERFAPHLTRDVVEKAVAL 306 (324) T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHHC T ss_conf 579999999986120489999999834 No 282 >PRK10411 DNA-binding transcriptional activator FucR; Provisional Probab=78.88 E-value=4.6 Score=19.59 Aligned_cols=13 Identities=23% Similarity=0.284 Sum_probs=4.6 Q ss_pred CHHHHHHHHHHHH Q ss_conf 5999999999999 Q gi|254780693|r 13 SLQELSPRLHLIQ 25 (235) Q Consensus 13 sl~dl~~~l~~l~ 25 (235) |.+.+..-|..+. T Consensus 31 S~~TIRRDL~~Le 43 (240) T PRK10411 31 SKETIRRDLNELQ 43 (240) T ss_pred CHHHHHHHHHHHH T ss_conf 9989998299897 No 283 >PRK10837 putative DNA-binding transcriptional regulator; Provisional Probab=78.59 E-value=4.7 Score=19.53 Aligned_cols=20 Identities=15% Similarity=0.184 Sum_probs=9.4 Q ss_pred CHHHHHHHHHHHHHHHCCCC Q ss_conf 59999999999999858378 Q gi|254780693|r 13 SLQELSPRLHLIQNRIKARN 32 (235) Q Consensus 13 sl~dl~~~l~~l~~~~~~~~ 32 (235) |-..+..++..+.+.++..- T Consensus 30 sQpavS~~I~~LE~~Lg~~L 49 (291) T PRK10837 30 SQSAVSAALTDLEGQLGVQL 49 (291) T ss_pred CHHHHHHHHHHHHHHHCCCC T ss_conf 87899999999999969922 No 284 >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=78.29 E-value=1.9 Score=22.31 Aligned_cols=23 Identities=43% Similarity=0.445 Sum_probs=20.4 Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH Q ss_conf 99789999949998899999999 Q gi|254780693|r 189 YTSEEIAEKLGLSVHTVNAYLGS 211 (235) Q Consensus 189 ~t~~eIA~~L~iS~~TV~~hl~~ 211 (235) +|.+|+|.-||||..||..-+.+ T Consensus 2 lTv~EaA~yLgv~~~t~~~l~~~ 24 (49) T TIGR01764 2 LTVEEAAEYLGVSKSTVYRLIEE 24 (49) T ss_pred CCHHHHHHHCCCCHHHHHHHHHC T ss_conf 87788997719990578999971 No 285 >PRK12682 transcriptional regulator CysB-like protein; Reviewed Probab=77.87 E-value=5 Score=19.38 Aligned_cols=18 Identities=11% Similarity=0.110 Sum_probs=9.9 Q ss_pred CCHHHHHHHHHHHCCCCH Q ss_conf 998999999999879997 Q gi|254780693|r 174 LTERETSCLQLAGDGYTS 191 (235) Q Consensus 174 LT~RE~evL~l~a~G~t~ 191 (235) ||+.-+..+.++++-.+- T Consensus 280 l~~~~~~FId~l~e~l~~ 297 (309) T PRK12682 280 LRNYVYDFIELLAPHLSR 297 (309) T ss_pred CCHHHHHHHHHHHHHCCH T ss_conf 189999999999987298 No 286 >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=77.63 E-value=3.5 Score=20.49 Aligned_cols=28 Identities=36% Similarity=0.331 Sum_probs=24.0 Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHH Q ss_conf 7999789999949998899999999999 Q gi|254780693|r 187 DGYTSEEIAEKLGLSVHTVNAYLGSATV 214 (235) Q Consensus 187 ~G~t~~eIA~~L~iS~~TV~~hl~~i~~ 214 (235) --+|-+|||..+|+|..||...++...+ T Consensus 24 l~ltr~eiA~~lG~t~eTVsR~l~~l~~ 51 (67) T cd00092 24 LPLTRQEIADYLGLTRETVSRTLKELEE 51 (67) T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHH T ss_conf 1779999999978909999999999998 No 287 >COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism] Probab=77.44 E-value=4.6 Score=19.60 Aligned_cols=11 Identities=27% Similarity=0.389 Sum_probs=4.3 Q ss_pred HCCHHHHHHHH Q ss_conf 22599999999 Q gi|254780693|r 11 SSSLQELSPRL 21 (235) Q Consensus 11 ~~sl~dl~~~l 21 (235) .-+++||...+ T Consensus 19 ~v~v~eLa~~~ 29 (253) T COG1349 19 KVSVEELAELF 29 (253) T ss_pred CEEHHHHHHHH T ss_conf 69799999885 No 288 >cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They 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 HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins 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=77.11 E-value=2.4 Score=21.61 Aligned_cols=29 Identities=31% Similarity=0.370 Sum_probs=17.4 Q ss_pred HHHHHHCCCCHHHHHHHHCCCHHHHHHHH Q ss_conf 99999879997899999499988999999 Q gi|254780693|r 181 CLQLAGDGYTSEEIAEKLGLSVHTVNAYL 209 (235) Q Consensus 181 vL~l~a~G~t~~eIA~~L~iS~~TV~~hl 209 (235) |..+-..|.+-+||...|.-+...+...+ T Consensus 50 I~~lr~~G~~L~eIk~~l~~~~~~~~~~l 78 (96) T cd04768 50 ILFLRELGFSLAEIKELLDTEMEELTAML 78 (96) T ss_pred HHHHHHCCCCHHHHHHHHCCCCHHHHHHH T ss_conf 99999979999999999939969999999 No 289 >pfam00440 TetR_N Bacterial regulatory proteins, tetR family. Probab=77.05 E-value=1.6 Score=22.86 Aligned_cols=27 Identities=30% Similarity=0.252 Sum_probs=23.5 Q ss_pred HCCCCHHHHHHHHCCCHHHHHHHHHHH Q ss_conf 879997899999499988999999999 Q gi|254780693|r 186 GDGYTSEEIAEKLGLSVHTVNAYLGSA 212 (235) Q Consensus 186 a~G~t~~eIA~~L~iS~~TV~~hl~~i 212 (235) -+|.|..+||...|||..|+.+|.++- T Consensus 14 ~~~~s~~~Ia~~agvs~~~iy~~F~~K 40 (47) T pfam00440 14 YDATTVREIAKEAGVSKGALYRHFPSK 40 (47) T ss_pred CCCCCHHHHHHHHCCCHHHHHHHCCCH T ss_conf 150779999999796988999887699 No 290 >cd04769 HTH_MerR2 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription by reconfiguring the spacer 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=76.56 E-value=2.6 Score=21.43 Aligned_cols=12 Identities=25% Similarity=0.390 Sum_probs=4.2 Q ss_pred CCCCHHHHHHHH Q ss_conf 799978999994 Q gi|254780693|r 187 DGYTSEEIAEKL 198 (235) Q Consensus 187 ~G~t~~eIA~~L 198 (235) -|.|-+||...| T Consensus 55 ~GfsL~eI~~ll 66 (116) T cd04769 55 LGFTLAELKAIF 66 (116) T ss_pred CCCCHHHHHHHH T ss_conf 799999999999 No 291 >PRK00876 nadE NAD synthetase; Reviewed Probab=76.43 E-value=5.4 Score=19.11 Aligned_cols=46 Identities=24% Similarity=0.303 Sum_probs=36.4 Q ss_pred CCHHHHH-HHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCC Q ss_conf 9989999-999998799978999994999889999999999980799 Q gi|254780693|r 174 LTERETS-CLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAV 219 (235) Q Consensus 174 LT~RE~e-vL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~ 219 (235) ++=.+.+ ||...-.|.+.++||..|||+..+|+.-.+.|-+|=... T Consensus 263 ~~Y~~lD~~L~~~~~~~~~~~~~~~~g~~~e~v~~v~~~i~~kr~~t 309 (325) T PRK00876 263 LPYDIMDLCLYAQNHGVPAEVVAAALGLTPEQVERVWRDIEAKRRTT 309 (325) T ss_pred CCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHC T ss_conf 98899999999876499999999883989999999999999875302 No 292 >pfam08220 HTH_DeoR DeoR-like helix-turn-helix domain. Probab=76.35 E-value=5 Score=19.37 Aligned_cols=38 Identities=32% Similarity=0.336 Sum_probs=29.8 Q ss_pred HHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHH Q ss_conf 999999999879--99789999949998899999999999 Q gi|254780693|r 177 RETSCLQLAGDG--YTSEEIAEKLGLSVHTVNAYLGSATV 214 (235) Q Consensus 177 RE~evL~l~a~G--~t~~eIA~~L~iS~~TV~~hl~~i~~ 214 (235) |..+++.++.+- .+.+|++..+++|+-||+.-+..+-. T Consensus 1 R~~~Il~~l~~~~~v~i~~La~~f~VS~~TiRRDl~~L~~ 40 (57) T pfam08220 1 RIQQILELLKQQGTLSVEELAELLGVSEMTIRRDLNELEE 40 (57) T ss_pred CHHHHHHHHHHCCCEEHHHHHHHHCCCHHHHHHHHHHHHH T ss_conf 9899999999869797999999989599999996999998 No 293 >PRK11569 transcriptional repressor IclR; Provisional Probab=75.86 E-value=5.6 Score=19.01 Aligned_cols=26 Identities=4% Similarity=-0.060 Sum_probs=12.5 Q ss_pred CEEEEEEECCCCCC-EEEEECCCCCCC Q ss_conf 35899721688752-345410588789 Q gi|254780693|r 116 AGIAFPVRLGFHKN-GYVIFTSEFLML 141 (235) Q Consensus 116 ~~~~~pv~~~~~~~-~~~~~~~~~~~~ 141 (235) .++..|+++..+.. +.+++++..... T Consensus 221 ~~iAaPV~d~~g~~vaAlsv~gp~~r~ 247 (274) T PRK11569 221 RCLAACIFDEHREPFAAISISGPISRI 247 (274) T ss_pred EEEEEEEECCCCCEEEEEEEEEEHHHC T ss_conf 899998988999899999998885868 No 294 >pfam05043 Mga Mga helix-turn-helix domain. M regulator protein trans-acting positive regulator (Mga) is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions. This domain is found in the centre of the Mga proteins. This family also contains a number of bacterial RofA transcriptional regulators that seem to be largely restricted to streptococci. These proteins have been shown to regulate the expression of important bacterial adhesins. This is presumably a DNA-binding domain. Probab=75.50 E-value=5.2 Score=19.21 Aligned_cols=32 Identities=19% Similarity=0.175 Sum_probs=27.6 Q ss_pred HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 87999789999949998899999999999807 Q gi|254780693|r 186 GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 186 a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) ....|..+.|..+.||+.|+..+++.+..-|. T Consensus 28 ~~~~s~~~~a~~l~iS~sTl~R~ik~l~~~L~ 59 (87) T pfam05043 28 HEFFSLTSLAQKLFISESTLYRLIKKLNKLLK 59 (87) T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 89998999999978899999999999999999 No 295 >cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer 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=75.48 E-value=2.8 Score=21.18 Aligned_cols=23 Identities=35% Similarity=0.400 Sum_probs=19.8 Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH Q ss_conf 99789999949998899999999 Q gi|254780693|r 189 YTSEEIAEKLGLSVHTVNAYLGS 211 (235) Q Consensus 189 ~t~~eIA~~L~iS~~TV~~hl~~ 211 (235) +|-.|+|..+|||++|++++-+. T Consensus 1 ytI~eva~~~gvs~~tlR~ye~~ 23 (49) T cd04761 1 YTIGELAKLTGVSPSTLRYYERI 23 (49) T ss_pred CCHHHHHHHHCCCHHHHHHHHHC T ss_conf 95889999989399999999997 No 296 >smart00422 HTH_MERR helix_turn_helix, mercury resistance. Probab=75.42 E-value=2.9 Score=21.09 Aligned_cols=15 Identities=40% Similarity=0.477 Sum_probs=7.2 Q ss_pred HHCCCCHHHHHHHHC Q ss_conf 987999789999949 Q gi|254780693|r 185 AGDGYTSEEIAEKLG 199 (235) Q Consensus 185 ~a~G~t~~eIA~~L~ 199 (235) -..|.+-++|...|. T Consensus 54 r~~G~~l~~Ik~~l~ 68 (70) T smart00422 54 KELGFSLEEIKELLE 68 (70) T ss_pred HHCCCCHHHHHHHHH T ss_conf 997899999999996 No 297 >pfam00325 Crp Bacterial regulatory proteins, crp family. Probab=75.35 E-value=3.5 Score=20.43 Aligned_cols=27 Identities=37% Similarity=0.454 Sum_probs=23.4 Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHH Q ss_conf 997899999499988999999999998 Q gi|254780693|r 189 YTSEEIAEKLGLSVHTVNAYLGSATVK 215 (235) Q Consensus 189 ~t~~eIA~~L~iS~~TV~~hl~~i~~K 215 (235) +|..+||.-||.+..||..-+++..+| T Consensus 3 msrqdIadylGlt~ETVsR~l~~L~~~ 29 (32) T pfam00325 3 MSRQEIADYLGLTRETVSRLLKRLREK 29 (32) T ss_pred CCHHHHHHHHCCHHHHHHHHHHHHHHC T ss_conf 658899998472599999999999985 No 298 >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=75.24 E-value=2.9 Score=21.03 Aligned_cols=17 Identities=41% Similarity=0.470 Sum_probs=9.7 Q ss_pred HHHHCCCCHHHHHHHHC Q ss_conf 99987999789999949 Q gi|254780693|r 183 QLAGDGYTSEEIAEKLG 199 (235) Q Consensus 183 ~l~a~G~t~~eIA~~L~ 199 (235) .+-..|.|-+||...|. T Consensus 53 ~lr~~G~sL~eI~~~l~ 69 (108) T cd01107 53 YLRDLGFPLEEIKEILD 69 (108) T ss_pred HHHHCCCCHHHHHHHHH T ss_conf 99997999999999981 No 299 >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=75.13 E-value=5.8 Score=18.88 Aligned_cols=85 Identities=24% Similarity=0.225 Sum_probs=58.5 Q ss_pred EEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHH---HHCC---CCHHHHHHHHCCCHH Q ss_conf 3454105887899899999999999999999851246788744499899999999---9879---997899999499988 Q gi|254780693|r 130 GYVIFTSEFLMLANEVIIEAHGACYQVITDFLELFKKRSSAARNLTERETSCLQL---AGDG---YTSEEIAEKLGLSVH 203 (235) Q Consensus 130 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~LT~RE~evL~l---~a~G---~t~~eIA~~L~iS~~ 203 (235) .+.-|..+.....+.+...-......+ ...+. ..||+||..||++ +.+| +|=+|++..++|+.- T Consensus 144 ~l~DFi~D~~~~~P~~~~~~~~l~~~l-~~vL~---------~~L~~rE~~Vl~~RyGL~d~~~~~TLEEVG~~f~VTRE 213 (240) T TIGR02393 144 SLGDFIEDESIESPEDAAAKELLREQL-EEVLE---------NTLTERERKVLRMRYGLLDGEKPKTLEEVGKEFNVTRE 213 (240) T ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHH-HHHHH---------CCCCHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCCH T ss_conf 442652574446858999999999999-99986---------01788899999874389988765337888765178711 Q ss_pred HHHHHHHHHHHHCCCCCHHHH Q ss_conf 999999999998079978999 Q gi|254780693|r 204 TVNAYLGSATVKLDAVNRIQA 224 (235) Q Consensus 204 TV~~hl~~i~~KLg~~nR~qa 224 (235) =|+.-=.+|.|||--.+|..- T Consensus 214 RIRQIE~KALRKLrhp~r~~~ 234 (240) T TIGR02393 214 RIRQIESKALRKLRHPSRSKK 234 (240) T ss_pred HHHHHHHHHHHHCCCHHHHHH T ss_conf 456888999885028436677 No 300 >cd04787 HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators. Putative helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR), unknown subgroup. Based on sequence similarity, these proteins are predicted to function as transcription regulators that 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. This subgroup lacks one of the c Probab=74.92 E-value=3 Score=20.94 Aligned_cols=14 Identities=7% Similarity=0.268 Sum_probs=6.9 Q ss_pred HHHHHHHHHHHCCC Q ss_conf 99999999998079 Q gi|254780693|r 205 VNAYLGSATVKLDA 218 (235) Q Consensus 205 V~~hl~~i~~KLg~ 218 (235) ++.|+..+-+|+.- T Consensus 84 l~~~l~~i~~kI~e 97 (133) T cd04787 84 IEQRLAETERRIKE 97 (133) T ss_pred HHHHHHHHHHHHHH T ss_conf 99999999999999 No 301 >cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR. Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. These proteins 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. A typical MerR regulator is comprised of 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 dissimilar C-terminal domains bind specific coactivator molecules. Probab=74.90 E-value=3 Score=20.95 Aligned_cols=15 Identities=47% Similarity=0.585 Sum_probs=8.0 Q ss_pred HCCCCHHHHHHHHCC Q ss_conf 879997899999499 Q gi|254780693|r 186 GDGYTSEEIAEKLGL 200 (235) Q Consensus 186 a~G~t~~eIA~~L~i 200 (235) .-|.|-+||...|.+ T Consensus 53 ~~G~sL~eI~~~L~l 67 (118) T cd04776 53 RLGFSLEEIRELLDL 67 (118) T ss_pred HCCCCHHHHHHHHHH T ss_conf 829989999999964 No 302 >cd04774 HTH_YfmP Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator. Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Probab=74.83 E-value=3 Score=20.95 Aligned_cols=43 Identities=19% Similarity=0.248 Sum_probs=29.3 Q ss_pred CCHHHH----HHHHHHH-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHC Q ss_conf 998999----9999998-799978999994999889999999999980 Q gi|254780693|r 174 LTERET----SCLQLAG-DGYTSEEIAEKLGLSVHTVNAYLGSATVKL 216 (235) Q Consensus 174 LT~RE~----evL~l~a-~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL 216 (235) -|+... .|..+-. .|.|-+||...|..-...++...+.+..|| T Consensus 38 Y~~~dl~rL~~I~~l~~~lGfsL~eIk~lL~~~~~p~~~~~~~~~e~L 85 (96) T cd04774 38 YSEEDLKRLERILRLREVLGFSLQEVTHFLERPLEPVDGGHRYSAESL 85 (96) T ss_pred CCHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCCCCHHHHHHHHHHH T ss_conf 599999999999999995799899999998198883045999999999 No 303 >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=74.71 E-value=3 Score=20.97 Aligned_cols=31 Identities=16% Similarity=0.269 Sum_probs=12.8 Q ss_pred HCCCCHHHHHHHHCCC------HHHHHHHHHHHHHHC Q ss_conf 8799978999994999------889999999999980 Q gi|254780693|r 186 GDGYTSEEIAEKLGLS------VHTVNAYLGSATVKL 216 (235) Q Consensus 186 a~G~t~~eIA~~L~iS------~~TV~~hl~~i~~KL 216 (235) ..|.|-+||...|... ...++.|+..+-.|. T Consensus 54 ~lGfsL~EI~~ll~~~~~~~~~~~~l~~~~~~i~~~I 90 (120) T cd04781 54 AAGFSLDEIQAMLSHDGKPPIDRQLLKAKAAELDQQI 90 (120) T ss_pred HCCCCHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHH T ss_conf 9599999999988426898379999999999999999 No 304 >COG0789 SoxR Predicted transcriptional regulators [Transcription] Probab=74.71 E-value=3.1 Score=20.88 Aligned_cols=15 Identities=40% Similarity=0.514 Sum_probs=7.2 Q ss_pred HCCCCHHHHHHHHCC Q ss_conf 879997899999499 Q gi|254780693|r 186 GDGYTSEEIAEKLGL 200 (235) Q Consensus 186 a~G~t~~eIA~~L~i 200 (235) ..|.+-++|...|.. T Consensus 55 ~~G~sL~eI~~~l~~ 69 (124) T COG0789 55 ELGFSLAEIKELLDL 69 (124) T ss_pred HCCCCHHHHHHHHHH T ss_conf 869989999999985 No 305 >cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins. Probab=74.28 E-value=3.1 Score=20.83 Aligned_cols=26 Identities=31% Similarity=0.450 Sum_probs=12.6 Q ss_pred CCHHHHHHHH----HHHCCCCHHHHHHHHC Q ss_conf 9989999999----9987999789999949 Q gi|254780693|r 174 LTERETSCLQ----LAGDGYTSEEIAEKLG 199 (235) Q Consensus 174 LT~RE~evL~----l~a~G~t~~eIA~~L~ 199 (235) -|+...+-|+ |...|+|-++|...|+ T Consensus 38 Ys~~di~~l~~I~~l~~~G~sl~~Ik~~LN 67 (67) T cd04764 38 YTDEDIELLKKIKTLLEKGLSIKEIKEILN 67 (67) T ss_pred CCHHHHHHHHHHHHHHHCCCCHHHHHHHHC T ss_conf 399999999999999996998999999859 No 306 >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=73.96 E-value=4.6 Score=19.62 Aligned_cols=46 Identities=26% Similarity=0.421 Sum_probs=38.9 Q ss_pred CCCCHHHHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 44998999999999-----87999789999949998899999999999807 Q gi|254780693|r 172 RNLTERETSCLQLA-----GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 172 ~~LT~RE~evL~l~-----a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) ..|+.||++++.+- ..-+|.+++|..||||..-+...=++|.++|. T Consensus 177 ~~l~~re~~i~~lrfGl~~~~e~tqk~vad~lGisqsyisrlek~i~krl~ 227 (234) T TIGR02835 177 KKLNDREKKIMELRFGLAGGTEKTQKEVADLLGISQSYISRLEKRILKRLK 227 (234) T ss_pred HHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 987676787667630436772146788898862468999999999999999 No 307 >PRK09430 djlA Dna-J like membrane chaperone protein; Provisional Probab=73.90 E-value=6.2 Score=18.67 Aligned_cols=17 Identities=18% Similarity=0.260 Sum_probs=12.2 Q ss_pred CCCCCHHHHHHHHHHHC Q ss_conf 44499899999999987 Q gi|254780693|r 171 ARNLTERETSCLQLAGD 187 (235) Q Consensus 171 ~~~LT~RE~evL~l~a~ 187 (235) ...+++.|.++|+-++. T Consensus 142 DG~l~~~E~~~L~~Ia~ 158 (269) T PRK09430 142 DGSLHPNERQVLYVIAE 158 (269) T ss_pred CCCCCHHHHHHHHHHHH T ss_conf 58999999999999999 No 308 >cd04789 HTH_Cfa Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator. Putative helix-turn-helix (HTH) MerR-like transcription regulator; the N-terminal domain of Cfa, a cyclopropane fatty acid synthase and other related methyltransferases. 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=73.77 E-value=3.2 Score=20.70 Aligned_cols=33 Identities=21% Similarity=0.123 Sum_probs=14.2 Q ss_pred HHHHCCCCHHHHHHHHCC--CHHHHHHHHHHHHHH Q ss_conf 999879997899999499--988999999999998 Q gi|254780693|r 183 QLAGDGYTSEEIAEKLGL--SVHTVNAYLGSATVK 215 (235) Q Consensus 183 ~l~a~G~t~~eIA~~L~i--S~~TV~~hl~~i~~K 215 (235) .+-..|.|-+||...|.- +......++..+-++ T Consensus 52 ~lr~~G~sL~eI~~~l~~~~~~~~l~~~~~~l~~~ 86 (102) T cd04789 52 QLQAGGLSLKECLACLQGKLTRSLLLERLSSLAEQ 86 (102) T ss_pred HHHHCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHH T ss_conf 99997998999999985985569999999999999 No 309 >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=73.76 E-value=3.3 Score=20.62 Aligned_cols=37 Identities=22% Similarity=0.247 Sum_probs=19.0 Q ss_pred HHHHHHCCCCHHHHHHHHCCCH----------HHHHHHHHHHHHHCC Q ss_conf 9999987999789999949998----------899999999999807 Q gi|254780693|r 181 CLQLAGDGYTSEEIAEKLGLSV----------HTVNAYLGSATVKLD 217 (235) Q Consensus 181 vL~l~a~G~t~~eIA~~L~iS~----------~TV~~hl~~i~~KLg 217 (235) |..+-..|.|-+||...|.... ..++.|+..+-+|.. T Consensus 50 I~~lr~~G~sL~eI~~ll~~~~~~~~~~~~~~~~l~~~~~~i~~~i~ 96 (123) T cd04770 50 IRRAQALGFSLAEIRELLSLRDDGAAPCAEVRALLEEKLAEVEAKIA 96 (123) T ss_pred HHHHHHCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHH T ss_conf 99999869999999999852506999889999999999999999999 No 310 >COG2512 Predicted membrane-associated trancriptional regulator [Transcription] Probab=73.73 E-value=6.3 Score=18.64 Aligned_cols=44 Identities=34% Similarity=0.420 Sum_probs=37.4 Q ss_pred CCCCCHHHHHHHHHHHC-C--CCHHHHHHHHCCCHHHHHHHHHHHHH Q ss_conf 44499899999999987-9--99789999949998899999999999 Q gi|254780693|r 171 ARNLTERETSCLQLAGD-G--YTSEEIAEKLGLSVHTVNAYLGSATV 214 (235) Q Consensus 171 ~~~LT~RE~evL~l~a~-G--~t~~eIA~~L~iS~~TV~~hl~~i~~ 214 (235) ...|++-|++|+..+.. | -+-+|+.+.||+|+.||-.++++.=+ T Consensus 190 ~~~L~~~e~~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L~~LEk 236 (258) T COG2512 190 EYDLNEDEKEILDLIRERGGRITQAELRRALGLSKTTVSRILRRLEK 236 (258) T ss_pred CCCCCHHHHHHHHHHHHHCCEEEHHHHHHHHCCCHHHHHHHHHHHHH T ss_conf 57899789999999998589786999888609976779999999986 No 311 >cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip Probab=73.56 E-value=3.4 Score=20.56 Aligned_cols=41 Identities=24% Similarity=0.203 Sum_probs=22.5 Q ss_pred CCHHHHH----HHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHH Q ss_conf 9989999----9999987999789999949998899999999999 Q gi|254780693|r 174 LTERETS----CLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATV 214 (235) Q Consensus 174 LT~RE~e----vL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~ 214 (235) .|+.+.+ |..+-..|.+-++|...|.-+.......+..-.+ T Consensus 39 Y~~~~i~~l~~I~~lr~~G~~l~eI~~~l~~~~~~~~~~L~~~~~ 83 (103) T cd01106 39 YTEEDLERLQQILFLKELGFSLKEIKELLKDPSEDLLEALREQKE 83 (103) T ss_pred CCHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCCCHHHHHHHHHH T ss_conf 689999999999999997999999999980897119999999999 No 312 >COG3682 Predicted transcriptional regulator [Transcription] Probab=73.38 E-value=6.4 Score=18.59 Aligned_cols=14 Identities=29% Similarity=0.235 Sum_probs=7.5 Q ss_pred CCCHHHHHHHHHHH Q ss_conf 49989999999998 Q gi|254780693|r 173 NLTERETSCLQLAG 186 (235) Q Consensus 173 ~LT~RE~evL~l~a 186 (235) .||+-|.+-|+-+. T Consensus 103 ~l~~~eie~L~~il 116 (123) T COG3682 103 KLTADEIEALKAIL 116 (123) T ss_pred CCCHHHHHHHHHHH T ss_conf 79999999999999 No 313 >PRK04140 hypothetical protein; Provisional Probab=73.22 E-value=3.7 Score=20.31 Aligned_cols=25 Identities=32% Similarity=0.468 Sum_probs=20.2 Q ss_pred HCCCCHHHHHHHHCCCHHHHHHHHH Q ss_conf 8799978999994999889999999 Q gi|254780693|r 186 GDGYTSEEIAEKLGLSVHTVNAYLG 210 (235) Q Consensus 186 a~G~t~~eIA~~L~iS~~TV~~hl~ 210 (235) -.|+|-.+.|..||+|.+||..|=+ T Consensus 136 ~~g~SlG~LA~~LGVSRrtv~~YE~ 160 (319) T PRK04140 136 KLGLSLGELASELGVSRRTISKYEN 160 (319) T ss_pred HCCCCHHHHHHHHCCCHHHHHHHHH T ss_conf 8198888999984986999999970 No 314 >pfam01381 HTH_3 Helix-turn-helix. This large family of DNA binding helix-turn helix proteins includes Cro and CI. Probab=73.17 E-value=6.5 Score=18.55 Aligned_cols=43 Identities=28% Similarity=0.251 Sum_probs=29.7 Q ss_pred HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCC Q ss_conf 87999789999949998899999999999807997899999999769 Q gi|254780693|r 186 GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFG 232 (235) Q Consensus 186 a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~~~G 232 (235) ..|+|-++.|..+|||+.||..+-+. -...+-..+...|-.+| T Consensus 7 ~~g~tq~~lA~~~gis~~~is~~E~g----~~~p~~~~l~~ia~~l~ 49 (55) T pfam01381 7 ELGLSQEELAEKLGVSRSTISKIENG----KREPSLETLKKLAEALG 49 (55) T ss_pred HCCCCHHHHHHHHCCCHHHHHHHHCC----CCCCCHHHHHHHHHHHC T ss_conf 82998999999989699999999879----99999999999999978 No 315 >PRK10094 DNA-binding transcriptional activator AllS; Provisional Probab=72.86 E-value=6.6 Score=18.50 Aligned_cols=18 Identities=17% Similarity=0.296 Sum_probs=7.8 Q ss_pred HHHHHHHHHHHHHHHCCC Q ss_conf 999999999999985837 Q gi|254780693|r 14 LQELSPRLHLIQNRIKAR 31 (235) Q Consensus 14 l~dl~~~l~~l~~~~~~~ 31 (235) -..+...+..+.+.++.. T Consensus 30 qsavS~~I~~LE~~LGv~ 47 (308) T PRK10094 30 TATISYRIKLLEENTGVA 47 (308) T ss_pred HHHHHHHHHHHHHHHCCE T ss_conf 789999999999996996 No 316 >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=72.79 E-value=3.7 Score=20.33 Aligned_cols=27 Identities=26% Similarity=0.175 Sum_probs=14.0 Q ss_pred CCHHHHHH----HHHHHCCCCHHHHHHHHCC Q ss_conf 99899999----9999879997899999499 Q gi|254780693|r 174 LTERETSC----LQLAGDGYTSEEIAEKLGL 200 (235) Q Consensus 174 LT~RE~ev----L~l~a~G~t~~eIA~~L~i 200 (235) -|.....- ..+-..|.+-+||...+.- T Consensus 39 Y~~~~~~~l~~I~~~r~lG~sL~eI~~~~~~ 69 (97) T cd04782 39 YTLEQFEQLDIILLLKELGISLKEIKDYLDN 69 (97) T ss_pred CCHHHHHHHHHHHHHHHCCCCHHHHHHHHHC T ss_conf 7999999999999999969999999999827 No 317 >PRK10820 DNA-binding transcriptional regulator TyrR; Provisional Probab=72.50 E-value=6.7 Score=18.45 Aligned_cols=40 Identities=23% Similarity=0.310 Sum_probs=29.4 Q ss_pred HHHHHH-HHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCH Q ss_conf 999999-99879997899999499988999999999998079978 Q gi|254780693|r 178 ETSCLQ-LAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNR 221 (235) Q Consensus 178 E~evL~-l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR 221 (235) |+++++ +.....+.++.|..||||..|+..-+ +|+|...+ T Consensus 469 Er~~l~~l~~~~~~~~kaAk~LGISrttL~~Kl----kkyGI~~k 509 (513) T PRK10820 469 ERSVLTQLYRNYPSTRKLAKRLGVSHTAIANKL----REYGLSQK 509 (513) T ss_pred HHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHH----HHCCCCCC T ss_conf 999999999878899999999799899999999----98089987 No 318 >smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor Probab=72.50 E-value=4 Score=20.04 Aligned_cols=19 Identities=47% Similarity=0.541 Sum_probs=7.0 Q ss_pred HHHHHHCCCHHHHHHHHHH Q ss_conf 9999949998899999999 Q gi|254780693|r 193 EIAEKLGLSVHTVNAYLGS 211 (235) Q Consensus 193 eIA~~L~iS~~TV~~hl~~ 211 (235) +||..|++|+.||...+++ T Consensus 4 diA~~L~vs~~sVs~~l~~ 22 (96) T smart00529 4 EIAERLNVSPPTVTQMLKK 22 (96) T ss_pred HHHHHHCCCCHHHHHHHHH T ss_conf 8998849991679999999 No 319 >cd04783 HTH_MerR1 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator. Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines that define a mercury binding site. These proteins 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=72.37 E-value=3.7 Score=20.29 Aligned_cols=19 Identities=42% Similarity=0.469 Sum_probs=9.2 Q ss_pred HHHHHCCCCHHHHHHHHCC Q ss_conf 9999879997899999499 Q gi|254780693|r 182 LQLAGDGYTSEEIAEKLGL 200 (235) Q Consensus 182 L~l~a~G~t~~eIA~~L~i 200 (235) ..+-..|.|-+||...|.. T Consensus 51 ~~~r~~G~sL~eI~~ll~~ 69 (126) T cd04783 51 KRAQELGFTLDEIAELLEL 69 (126) T ss_pred HHHHHCCCCHHHHHHHHCC T ss_conf 9999879989999999742 No 320 >COG2973 TrpR Trp operon repressor [Transcription] Probab=72.36 E-value=6.2 Score=18.68 Aligned_cols=36 Identities=33% Similarity=0.396 Sum_probs=28.0 Q ss_pred CCHHHHH--------HHHHHHCCCCHHHHHHHHCCCHHHHHHHH Q ss_conf 9989999--------99999879997899999499988999999 Q gi|254780693|r 174 LTERETS--------CLQLAGDGYTSEEIAEKLGLSVHTVNAYL 209 (235) Q Consensus 174 LT~RE~e--------vL~l~a~G~t~~eIA~~L~iS~~TV~~hl 209 (235) |||-|++ |-.++---+|-+||+..||+|..|+..-- T Consensus 38 LTpdEReal~~Rv~Iv~eLL~ge~sQREi~~~LgvsiAtITRGS 81 (103) T COG2973 38 LTPDEREALGTRVRIVEELLRGELSQREIAQKLGVSIATITRGS 81 (103) T ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHCCCH T ss_conf 68768999999999999999563539999998586256550444 No 321 >pfam08784 RPA_C Replication protein A C terminal. This domain corresponds to the C terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. Probab=72.17 E-value=6.8 Score=18.40 Aligned_cols=40 Identities=28% Similarity=0.429 Sum_probs=34.5 Q ss_pred CCCHHHHHHHHHHH------CCCCHHHHHHHH-CCCHHHHHHHHHHH Q ss_conf 49989999999998------799978999994-99988999999999 Q gi|254780693|r 173 NLTERETSCLQLAG------DGYTSEEIAEKL-GLSVHTVNAYLGSA 212 (235) Q Consensus 173 ~LT~RE~evL~l~a------~G~t~~eIA~~L-~iS~~TV~~hl~~i 212 (235) .||+-.++|+.++. +|....||+.+| ++++..|+.-+..+ T Consensus 44 ~ls~~~~~V~~~i~~~~~~~eG~h~~~l~~~l~~~~~~~i~~a~d~L 90 (103) T pfam08784 44 GLTPLQDQVLNLIKQSCPGEEGVHVDELAAQLNGLPVNDIRQAVDFL 90 (103) T ss_pred CCCHHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCCHHHHHHHHHHH T ss_conf 87899999999999548898872799999998299999999999999 No 322 >cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins 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. A typical MerR regulator is comprised of 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 dissimilar C-terminal domains bind specific coactivator molecules. Probab=72.09 E-value=3.7 Score=20.28 Aligned_cols=43 Identities=21% Similarity=0.227 Sum_probs=31.0 Q ss_pred CCHHHHHHHHHH-----HCCCCHHHHHHHHCCCHH--HHHHHHHHHHHHC Q ss_conf 998999999999-----879997899999499988--9999999999980 Q gi|254780693|r 174 LTERETSCLQLA-----GDGYTSEEIAEKLGLSVH--TVNAYLGSATVKL 216 (235) Q Consensus 174 LT~RE~evL~l~-----a~G~t~~eIA~~L~iS~~--TV~~hl~~i~~KL 216 (235) .|+.+.+-|+.+ ..|.|-++|...|..-+. ....+++.+..|+ T Consensus 39 Ys~~di~~l~~I~~L~~~~G~sl~~I~~~L~l~~~~~~l~a~~~~l~~r~ 88 (91) T cd04766 39 YSERDIERLRRIQRLTQELGVNLAGVKRILELEEELAELRAELDELRARL 88 (91) T ss_pred CCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 47999999999999999869989999999980844999999999999998 No 323 >cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins 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. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins. Probab=71.98 E-value=3.9 Score=20.12 Aligned_cols=20 Identities=30% Similarity=0.305 Sum_probs=12.8 Q ss_pred HHHHHHCCCCHHHHHHHHCC Q ss_conf 99999879997899999499 Q gi|254780693|r 181 CLQLAGDGYTSEEIAEKLGL 200 (235) Q Consensus 181 vL~l~a~G~t~~eIA~~L~i 200 (235) |..+-..|.|-++|...|.. T Consensus 50 I~~lr~~G~sl~eI~~~l~~ 69 (108) T cd04773 50 IHLLRRGGYLLEQIATVVEQ 69 (108) T ss_pred HHHHHHCCCCHHHHHHHHHH T ss_conf 99999969999999999987 No 324 >smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins. Probab=71.81 E-value=4.6 Score=19.63 Aligned_cols=28 Identities=39% Similarity=0.502 Sum_probs=23.7 Q ss_pred HHCCCCHHHHHHHHCCCHHHHHHHHHHH Q ss_conf 9879997899999499988999999999 Q gi|254780693|r 185 AGDGYTSEEIAEKLGLSVHTVNAYLGSA 212 (235) Q Consensus 185 ~a~G~t~~eIA~~L~iS~~TV~~hl~~i 212 (235) ...|+|-++.|..+|||+.||..+.+.- T Consensus 7 ~~~glsq~~lA~~~gis~~~is~~E~g~ 34 (56) T smart00530 7 EEKGLTQEELAEKLGVSRSTLSRIENGK 34 (56) T ss_pred HHCCCCHHHHHHHHCCCHHHHHHHHCCC T ss_conf 7729999999999895999999999799 No 325 >PRK10668 DNA-binding transcriptional repressor AcrR; Provisional Probab=71.71 E-value=2.5 Score=21.50 Aligned_cols=17 Identities=6% Similarity=0.026 Sum_probs=8.0 Q ss_pred HHHHHHHHHHCCCCEEE Q ss_conf 99999999858378589 Q gi|254780693|r 19 PRLHLIQNRIKARNFAL 35 (235) Q Consensus 19 ~~l~~l~~~~~~~~f~~ 35 (235) ..+++..+.+.-.||.- T Consensus 15 ~Il~AA~~lFaekGy~~ 31 (216) T PRK10668 15 HILDVALRLFSQQGVSA 31 (216) T ss_pred HHHHHHHHHHHHHCCCC T ss_conf 99999999999849351 No 326 >cd01111 HTH_MerD Helix-Turn-Helix DNA binding domain of the MerD transcription regulator. Helix-turn-helix (HTH) transcription regulator MerD. The putative secondary regulator of mercury resistance (mer) operons, MerD, has been shown to down-regulate the expression of this operon in gram-negative bacteria. It binds to the same operator DNA as MerR that activates transcription of the operon in the presence of mercury ions. The MerD protein shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily, which promote transcription by reconfiguring the spacer 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 conserved and contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules such as metal ions, drugs, Probab=71.48 E-value=4.4 Score=19.72 Aligned_cols=15 Identities=20% Similarity=0.173 Sum_probs=8.5 Q ss_pred HCCCCHHHHHHHHCC Q ss_conf 879997899999499 Q gi|254780693|r 186 GDGYTSEEIAEKLGL 200 (235) Q Consensus 186 a~G~t~~eIA~~L~i 200 (235) ..|++-+||...|.. T Consensus 55 ~~G~sl~eI~~lL~~ 69 (107) T cd01111 55 EAGIGLDELARLCRA 69 (107) T ss_pred HCCCCHHHHHHHHHH T ss_conf 879999999999960 No 327 >TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family; InterPro: IPR014293 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). They and appear by homology, tree building, bidirectional best hits and (with one exception, a paralog in Thermobifida fusca strain YX) their one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor (see IPR014295 from INTERPRO) in an apparent operon.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent. Probab=71.45 E-value=7.1 Score=18.29 Aligned_cols=49 Identities=27% Similarity=0.300 Sum_probs=41.8 Q ss_pred HHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCC Q ss_conf 99999879997899999499988999999999998079978999999997699 Q gi|254780693|r 181 CLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFGY 233 (235) Q Consensus 181 vL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~~~Gl 233 (235) |+--=.+|...|||+.+|+.-..||-.-+.+.++.| |.+++-.|..+|+ T Consensus 140 v~~adveGf~ykei~~im~tP~Gtvmsrl~r~rk~l----~~~l~d~a~~rG~ 188 (193) T TIGR02947 140 VYFADVEGFAYKEIAEIMGTPIGTVMSRLHRGRKQL----RDLLADVAAERGF 188 (193) T ss_pred HHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH----HHHHHHHHHHCCC T ss_conf 887620353157799885474779999989999999----9999988874054 No 328 >TIGR03384 betaine_BetI transcriptional repressor BetI. BetI is a DNA-binding transcriptional repressor of the bet (betaine) regulon. In sequence, it is related to TetR (pfam00440). Choline, through BetI, induces the expression of the betaine biosynthesis genes betA and betB by derepression. The choline porter gene betT is also part of this regulon in Escherichia coli. Note that a different transcriptional regulator, ArcA, controls the expression of bet regulon genes in response to oxygen, as BetA is an oxygen-dependent enzyme. Probab=71.43 E-value=3 Score=20.99 Aligned_cols=14 Identities=14% Similarity=0.102 Sum_probs=6.1 Q ss_pred HHHHHHHHCCCCEE Q ss_conf 99999985837858 Q gi|254780693|r 21 LHLIQNRIKARNFA 34 (235) Q Consensus 21 l~~l~~~~~~~~f~ 34 (235) +++..+.+.-.||. T Consensus 14 l~Aa~~~i~~~G~~ 27 (189) T TIGR03384 14 IDATIESIGERGSL 27 (189) T ss_pred HHHHHHHHHHHCCC T ss_conf 99999999984935 No 329 >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=71.16 E-value=4.1 Score=19.94 Aligned_cols=27 Identities=26% Similarity=0.417 Sum_probs=13.2 Q ss_pred CCHHHHHHHHH----HHCCCCHHHHHHHHCC Q ss_conf 99899999999----9879997899999499 Q gi|254780693|r 174 LTERETSCLQL----AGDGYTSEEIAEKLGL 200 (235) Q Consensus 174 LT~RE~evL~l----~a~G~t~~eIA~~L~i 200 (235) .|+...+.|.. -..|.|-+||...|.. T Consensus 39 Y~~~~v~rl~~I~~lr~lG~sL~eI~~~l~~ 69 (113) T cd01109 39 FTEEDLEWLEFIKCLRNTGMSIKDIKEYAEL 69 (113) T ss_pred CCHHHHHHHHHHHHHHHCCCCHHHHHHHHHH T ss_conf 3498989999797599879989999999988 No 330 >COG1414 IclR Transcriptional regulator [Transcription] Probab=71.05 E-value=7.2 Score=18.23 Aligned_cols=28 Identities=14% Similarity=-0.026 Sum_probs=15.8 Q ss_pred CCEEEEEEECCCCC-CEEEEECCCCCCCC Q ss_conf 53589972168875-23454105887899 Q gi|254780693|r 115 FAGIAFPVRLGFHK-NGYVIFTSEFLMLA 142 (235) Q Consensus 115 ~~~~~~pv~~~~~~-~~~~~~~~~~~~~~ 142 (235) ..++..|+++..+. .+.++......... T Consensus 194 v~~iAaPi~~~~g~v~aaisv~~p~~r~~ 222 (246) T COG1414 194 VRCIAAPIFDAGGEVVAAISVSGPASRLT 222 (246) T ss_pred CEEEEEEEECCCCCEEEEEEEECHHHHCC T ss_conf 56999889869997899999626166509 No 331 >cd01108 HTH_CueR Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators. Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins 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 winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion binding site. These proteins 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=70.98 E-value=4.2 Score=19.87 Aligned_cols=18 Identities=39% Similarity=0.510 Sum_probs=9.9 Q ss_pred HHHHCCCCHHHHHHHHCC Q ss_conf 999879997899999499 Q gi|254780693|r 183 QLAGDGYTSEEIAEKLGL 200 (235) Q Consensus 183 ~l~a~G~t~~eIA~~L~i 200 (235) .+-..|.|-+||...|.+ T Consensus 52 ~~r~~G~sL~eI~~ll~~ 69 (127) T cd01108 52 RARDLGFSLEEIRELLAL 69 (127) T ss_pred HHHHCCCCHHHHHHHHHH T ss_conf 999879989999999853 No 332 >PHA01976 helix-turn-helix protein Probab=70.83 E-value=5.1 Score=19.29 Aligned_cols=27 Identities=7% Similarity=0.273 Sum_probs=23.2 Q ss_pred HHHHCCCCHHHHHHHHCCCHHHHHHHH Q ss_conf 999879997899999499988999999 Q gi|254780693|r 183 QLAGDGYTSEEIAEKLGLSVHTVNAYL 209 (235) Q Consensus 183 ~l~a~G~t~~eIA~~L~iS~~TV~~hl 209 (235) .--+.|.|-.|.|..+|||..||..+= T Consensus 10 lR~~~g~sQ~eLA~~lGVs~~~is~wE 36 (67) T PHA01976 10 ARNARAWSAPELSRRAGVRHSLIYDFE 36 (67) T ss_pred HHHHCCCCHHHHHHHHCCCHHHHHHHH T ss_conf 999869999999999499899999998 No 333 >pfam02787 CPSase_L_D3 Carbamoyl-phosphate synthetase large chain, oligomerisation domain. Carbamoyl-phosphate synthase catalyses the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate. The carbamoyl-phosphate synthase (CPS) enzyme in prokaryotes is a heterodimer of a small and large chain. Probab=70.75 E-value=7.3 Score=18.18 Aligned_cols=42 Identities=21% Similarity=0.306 Sum_probs=31.6 Q ss_pred CCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCC Q ss_conf 499899999999987999789999949998899999999999807997 Q gi|254780693|r 173 NLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVN 220 (235) Q Consensus 173 ~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~n 220 (235) .+++- ...+.-..|-|+++||..+++|+..|+.. ++++|+.- T Consensus 58 ~~~~~--~l~~aK~~GFSD~~IA~l~~~~e~~Ir~~----R~~~~i~P 99 (122) T pfam02787 58 PLSDD--LLLKAKKLGFSDAQIAKLLGVTEEEVRKL----RKELGIRP 99 (122) T ss_pred CCCHH--HHHHHHHHCCCHHHHHHHHCCCHHHHHHH----HHHCCCCC T ss_conf 99999--99999994999899998839869999999----99879912 No 334 >cd04785 HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators. Helix-turn-helix (HTH) CadR- and PbrR-like transcription regulators. CadR and PbrR regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of 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 have three conserved cysteines which comprise a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins 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=70.20 E-value=4.5 Score=19.71 Aligned_cols=20 Identities=30% Similarity=0.345 Sum_probs=10.5 Q ss_pred HHHHHHCCCCHHHHHHHHCC Q ss_conf 99999879997899999499 Q gi|254780693|r 181 CLQLAGDGYTSEEIAEKLGL 200 (235) Q Consensus 181 vL~l~a~G~t~~eIA~~L~i 200 (235) |..+-..|.|-+||...|.+ T Consensus 50 I~~~r~~GfsL~eI~~ll~l 69 (126) T cd04785 50 IRRARDLGFSLEEIRALLAL 69 (126) T ss_pred HHHHHHCCCCHHHHHHHHCC T ss_conf 99999879989999999713 No 335 >PRK13752 putative transcriptional regulator MerR; Provisional Probab=70.19 E-value=4.1 Score=19.96 Aligned_cols=10 Identities=50% Similarity=0.757 Sum_probs=3.1 Q ss_pred CCHHHHHHHH Q ss_conf 9978999994 Q gi|254780693|r 189 YTSEEIAEKL 198 (235) Q Consensus 189 ~t~~eIA~~L 198 (235) .|-+||...| T Consensus 65 fsL~eI~~LL 74 (144) T PRK13752 65 FSLDEIAELL 74 (144) T ss_pred CCHHHHHHHH T ss_conf 9899999997 No 336 >cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, 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 dissimil Probab=70.14 E-value=4.5 Score=19.70 Aligned_cols=36 Identities=25% Similarity=0.232 Sum_probs=19.8 Q ss_pred HHHHHHCCCCHHHHHHHHCCC--HHHHHHHHHHHHHHC Q ss_conf 999998799978999994999--889999999999980 Q gi|254780693|r 181 CLQLAGDGYTSEEIAEKLGLS--VHTVNAYLGSATVKL 216 (235) Q Consensus 181 vL~l~a~G~t~~eIA~~L~iS--~~TV~~hl~~i~~KL 216 (235) |..+-..|.|-+||...|.-. ....+.+++.+-++. T Consensus 50 I~~lr~~G~sL~eIk~lL~~~~~~~~l~~~~~~i~~~I 87 (102) T cd04775 50 IVFLQAGGLPLEEIAGCLAQPHVQAILEERLQSLNREI 87 (102) T ss_pred HHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHH T ss_conf 99999969999999999859957999999999999999 No 337 >cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen Probab=69.92 E-value=4.1 Score=19.97 Aligned_cols=25 Identities=8% Similarity=0.242 Sum_probs=14.1 Q ss_pred CCHHHHH----HHHHHHCCCCHHHHHHHH Q ss_conf 9989999----999998799978999994 Q gi|254780693|r 174 LTERETS----CLQLAGDGYTSEEIAEKL 198 (235) Q Consensus 174 LT~RE~e----vL~l~a~G~t~~eIA~~L 198 (235) .|+.+.+ |-.|...|+|-++|+..| T Consensus 39 Ys~~di~~l~~I~~l~~~G~~i~~i~~lL 67 (68) T cd04763 39 FNDADIDRILEIKRWIDNGVQVSKVKKLL 67 (68) T ss_pred CCHHHHHHHHHHHHHHHCCCCHHHHHHHH T ss_conf 49999999999999999799899999972 No 338 >cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), 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 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=69.76 E-value=5.5 Score=19.09 Aligned_cols=45 Identities=20% Similarity=0.236 Sum_probs=26.3 Q ss_pred CCHHHHHHHHHH---H--CCCCHHHHHHHHCC--CHHHHHHHHHHHHHHCCC Q ss_conf 998999999999---8--79997899999499--988999999999998079 Q gi|254780693|r 174 LTERETSCLQLA---G--DGYTSEEIAEKLGL--SVHTVNAYLGSATVKLDA 218 (235) Q Consensus 174 LT~RE~evL~l~---a--~G~t~~eIA~~L~i--S~~TV~~hl~~i~~KLg~ 218 (235) -++...+-|+++ . .|.+-+||...|.. -+.+-+.-+..+..+++. T Consensus 39 Y~~~~v~rL~~Ir~l~~~lG~sL~eIr~lL~~~~d~~~p~~l~~~~~~~~~~ 90 (95) T cd04780 39 YSEAHVERLRLIRALQQEGGLPISQIKEVLDAIADASLPSTLLALAVQRFGL 90 (95) T ss_pred CCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCCCCHHHHHHHHHHHCC T ss_conf 4999999999999999936999999999984368899951799999999557 No 339 >pfam08535 KorB KorB domain. This family consists of several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon. This domain includes the DNA-binding HTH motif. Probab=69.69 E-value=5.3 Score=19.16 Aligned_cols=24 Identities=42% Similarity=0.469 Sum_probs=13.3 Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHH Q ss_conf 799978999994999889999999 Q gi|254780693|r 187 DGYTSEEIAEKLGLSVHTVNAYLG 210 (235) Q Consensus 187 ~G~t~~eIA~~L~iS~~TV~~hl~ 210 (235) .|++-.+||..||-|..=|-.|+. T Consensus 2 ~G~kk~~IAk~LGks~s~VS~hla 25 (93) T pfam08535 2 KGVKQAEIAKKLGKSKSFVSQHLA 25 (93) T ss_pred CCCCHHHHHHHHCCCHHHHHHHHH T ss_conf 987799999997889889999999 No 340 >COG4496 Uncharacterized protein conserved in bacteria [Function unknown] Probab=69.60 E-value=6.7 Score=18.46 Aligned_cols=40 Identities=20% Similarity=0.253 Sum_probs=31.2 Q ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCH Q ss_conf 99999999879997899999499988999999999998079978 Q gi|254780693|r 178 ETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNR 221 (235) Q Consensus 178 E~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR 221 (235) -.+|.+++.+|+|...|..+-|+|..|+.. +.+-|+-.|- T Consensus 46 RlqVa~mL~eg~tY~~I~~eTGaStaTIsR----VkRcl~yGnd 85 (100) T COG4496 46 RLQVAKMLKEGRTYRDIEDETGASTATISR----VKRCLNYGND 85 (100) T ss_pred HHHHHHHHHCCCCCCHHHHCCCCCHHHHHH----HHHHHHCCCC T ss_conf 999999997689722466414840555999----9999980770 No 341 >cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), 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 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=69.48 E-value=4.7 Score=19.55 Aligned_cols=21 Identities=29% Similarity=0.403 Sum_probs=14.8 Q ss_pred HHHHHHHCCCCHHHHHHHHCC Q ss_conf 999999879997899999499 Q gi|254780693|r 180 SCLQLAGDGYTSEEIAEKLGL 200 (235) Q Consensus 180 evL~l~a~G~t~~eIA~~L~i 200 (235) -|+.+=.-|.|-+||...|.+ T Consensus 47 ~I~~~k~lgfsL~eIk~ll~l 67 (107) T cd04777 47 FILELKGLGFSLIEIQKIFSY 67 (107) T ss_pred HHHHHHHCCCCHHHHHHHHHH T ss_conf 999998889989999999962 No 342 >PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional Probab=68.76 E-value=7 Score=18.32 Aligned_cols=27 Identities=33% Similarity=0.490 Sum_probs=23.9 Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHH Q ss_conf 997899999499988999999999998 Q gi|254780693|r 189 YTSEEIAEKLGLSVHTVNAYLGSATVK 215 (235) Q Consensus 189 ~t~~eIA~~L~iS~~TV~~hl~~i~~K 215 (235) +|.+|||..+|.|+.||...++...++ T Consensus 185 lt~~dLA~~lG~trEtVsR~L~~L~~~ 211 (235) T PRK11161 185 MTRGDIGNYLGLTVETISRLLGRFQKS 211 (235) T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHC T ss_conf 789999988789899999999999978 No 343 >cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer 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=68.71 E-value=5 Score=19.34 Aligned_cols=29 Identities=24% Similarity=0.225 Sum_probs=17.2 Q ss_pred CCHHHHH----HHHHHHCCCCHHHHHHHHCCCH Q ss_conf 9989999----9999987999789999949998 Q gi|254780693|r 174 LTERETS----CLQLAGDGYTSEEIAEKLGLSV 202 (235) Q Consensus 174 LT~RE~e----vL~l~a~G~t~~eIA~~L~iS~ 202 (235) .|+...+ |..+-..|.|-++|...|.... T Consensus 38 Y~~~~i~~l~~I~~lr~~G~sl~~I~~~l~~~~ 70 (100) T cd00592 38 YSEEDLERLRLIRRLRELGLSLKEIRELLDARD 70 (100) T ss_pred CCHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCC T ss_conf 569999999999999997999999999983557 No 344 >COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription] Probab=68.60 E-value=4.9 Score=19.42 Aligned_cols=34 Identities=21% Similarity=0.198 Sum_probs=30.4 Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCC Q ss_conf 7999789999949998899999999999807997 Q gi|254780693|r 187 DGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVN 220 (235) Q Consensus 187 ~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~n 220 (235) .=.|-+|||...++++-|++++.+.+...++..+ T Consensus 250 ~~~tq~eva~v~~vtevTIrnrykel~~~~~i~~ 283 (285) T COG1405 250 ERRTQKEVAKVAGVTEVTIRNRYKELADALDIEV 283 (285) T ss_pred CCHHHHHHHHHHCCEEEHHHHHHHHHHHHHCCCC T ss_conf 7027999998838722079988999877322556 No 345 >pfam11662 DUF3263 Protein of unknown function (DUF3263). This family of proteins with unknown function appears to be restricted to Actinobacteria. Probab=68.60 E-value=8.1 Score=17.87 Aligned_cols=41 Identities=29% Similarity=0.375 Sum_probs=32.5 Q ss_pred CCCHHHHHHHH-----HHHCCCCHHHHHHHHCCCHHHHHHHHHHHH Q ss_conf 49989999999-----998799978999994999889999999999 Q gi|254780693|r 173 NLTERETSCLQ-----LAGDGYTSEEIAEKLGLSVHTVNAYLGSAT 213 (235) Q Consensus 173 ~LT~RE~evL~-----l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~ 213 (235) .||+||..||. |-..|-....|-..+|+|+---..-+..+. T Consensus 2 ~Ls~rd~~IL~fEr~ww~~~GaKe~AIRe~fglS~~rYYQ~LN~Li 47 (77) T pfam11662 2 ELTERDRAILDFERQWWKHAGAKEQAIRELFGLSSTRYYQLLNALI 47 (77) T ss_pred CCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCHHHHHHHHHHHH T ss_conf 8889999999999873368781899999997888899999999986 No 346 >cd04786 HTH_MerR-like_sg7 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 7) with a conserved cysteine 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, and organic su Probab=68.32 E-value=5.2 Score=19.25 Aligned_cols=17 Identities=24% Similarity=0.372 Sum_probs=8.9 Q ss_pred HHHCCCCHHHHHHHHCC Q ss_conf 99879997899999499 Q gi|254780693|r 184 LAGDGYTSEEIAEKLGL 200 (235) Q Consensus 184 l~a~G~t~~eIA~~L~i 200 (235) +-.-|.|-+||...|.+ T Consensus 53 ~r~lGfsL~eI~~ll~~ 69 (131) T cd04786 53 AQQAGFSLDEIRQLLPA 69 (131) T ss_pred HHHCCCCHHHHHHHHCC T ss_conf 99969999999998684 No 347 >PHA00542 putative Cro-like protein Probab=68.30 E-value=7 Score=18.33 Aligned_cols=37 Identities=22% Similarity=0.271 Sum_probs=29.3 Q ss_pred CCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHH Q ss_conf 49989999999998799978999994999889999999 Q gi|254780693|r 173 NLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLG 210 (235) Q Consensus 173 ~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~ 210 (235) .-+|-|. |..+++.|+|-.||+..-||+..++..-+. T Consensus 17 ~k~P~E~-V~aLi~~G~tQ~qI~~~tgv~QpsisRils 53 (82) T PHA00542 17 TQRPDEL-VCALIRAGWSQEQIADATDVSQPTICRIYS 53 (82) T ss_pred HCCHHHH-HHHHHHCCCCHHHHHHHHCCCCHHHHHHHC T ss_conf 3298999-999998225699999860877036899980 No 348 >PRK09975 DNA-binding transcriptional regulator EnvR; Provisional Probab=68.23 E-value=3.2 Score=20.70 Aligned_cols=16 Identities=13% Similarity=0.048 Sum_probs=7.5 Q ss_pred HHHHHHHHHCCCCEEE Q ss_conf 9999999858378589 Q gi|254780693|r 20 RLHLIQNRIKARNFAL 35 (235) Q Consensus 20 ~l~~l~~~~~~~~f~~ 35 (235) .+.+..+.+.-.||.- T Consensus 16 Il~AA~~lFae~G~~~ 31 (213) T PRK09975 16 LIETAIAQFALRGVAN 31 (213) T ss_pred HHHHHHHHHHHHCCCC T ss_conf 9999999999859455 No 349 >PRK06266 transcription initiation factor E subunit alpha; Validated Probab=67.99 E-value=7.1 Score=18.29 Aligned_cols=13 Identities=54% Similarity=0.825 Sum_probs=4.0 Q ss_pred HHHHHHCCCHHHH Q ss_conf 9999949998899 Q gi|254780693|r 193 EIAEKLGLSVHTV 205 (235) Q Consensus 193 eIA~~L~iS~~TV 205 (235) +||..+||..++| T Consensus 41 eiAe~~gi~lN~V 53 (178) T PRK06266 41 EIAEQTGIKLNTV 53 (178) T ss_pred HHHHHHCCCHHHH T ss_conf 9999969978999 No 350 >cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre Probab=67.71 E-value=2.6 Score=21.43 Aligned_cols=41 Identities=32% Similarity=0.492 Sum_probs=24.5 Q ss_pred HHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCC Q ss_conf 899999499988999999999998079978999999997699 Q gi|254780693|r 192 EEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFGY 233 (235) Q Consensus 192 ~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~~~Gl 233 (235) ++||..+|+|..||...+.+=- ...-.+|-.--..|..+|| T Consensus 1 ~diA~~~gvS~~TVSr~ln~~~-~Vs~~tr~~I~~~~~elgY 41 (52) T cd01392 1 KDIARAAGVSVATVSRVLNGKP-RVSEETRERVLAAAEELGY 41 (52) T ss_pred CHHHHHHCCCHHHHHHHHCCCC-CCCHHHHHHHHHHHHHHCC T ss_conf 9288887859999999987989-8999999999999999888 No 351 >PRK13824 replication initiation protein RepC; Provisional Probab=67.69 E-value=8 Score=17.92 Aligned_cols=33 Identities=21% Similarity=0.158 Sum_probs=20.7 Q ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHH Q ss_conf 7899999499988999999999998079978999999 Q gi|254780693|r 191 SEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAK 227 (235) Q Consensus 191 ~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~ 227 (235) ...+...||||+.+.. .+.+.+|-.+=+-+|+. T Consensus 324 A~~lr~mlGIS~saw~----eA~~~mG~~~AAvaiA~ 356 (404) T PRK13824 324 AVVVRSMLGVSPSAYQ----EACEVMGPENAAIVIAC 356 (404) T ss_pred HHHHHHHHCCCHHHHH----HHHHHHCHHHHHHHHHH T ss_conf 9999987098999999----99998696889999999 No 352 >cd04779 HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). 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, and organic substrates. Probab=67.63 E-value=5.4 Score=19.15 Aligned_cols=11 Identities=27% Similarity=0.419 Sum_probs=3.6 Q ss_pred CCCHHHHHHHH Q ss_conf 99978999994 Q gi|254780693|r 188 GYTSEEIAEKL 198 (235) Q Consensus 188 G~t~~eIA~~L 198 (235) |.|-+||-..| T Consensus 56 g~sL~eIk~lL 66 (134) T cd04779 56 RLSLAEIKDQL 66 (134) T ss_pred CCCHHHHHHHH T ss_conf 99899999998 No 353 >cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR. Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of 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=67.35 E-value=5.5 Score=19.07 Aligned_cols=30 Identities=17% Similarity=0.205 Sum_probs=19.4 Q ss_pred CCHHHHH----HHHHHHCCCCHHHHHHHHCCCHH Q ss_conf 9989999----99999879997899999499988 Q gi|254780693|r 174 LTERETS----CLQLAGDGYTSEEIAEKLGLSVH 203 (235) Q Consensus 174 LT~RE~e----vL~l~a~G~t~~eIA~~L~iS~~ 203 (235) -|..+.+ |..+-..|.+-+||...|.-+.. T Consensus 39 Y~~~~i~~l~~I~~lr~~G~sl~eI~~~l~~~~~ 72 (96) T cd04788 39 YDRADIRRLHQIIALRRLGFSLREIGRALDGPDF 72 (96) T ss_pred CCHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCC T ss_conf 8999999999999999979999999999808981 No 354 >PRK00767 transcriptional regulator BetI; Validated Probab=67.17 E-value=4.4 Score=19.76 Aligned_cols=42 Identities=10% Similarity=0.002 Sum_probs=18.9 Q ss_pred HHHHHHHHHHCCCCHHHHHHHHCC----CHHHHHHHHHHHHHHCCC Q ss_conf 999999999879997899999499----988999999999998079 Q gi|254780693|r 177 RETSCLQLAGDGYTSEEIAEKLGL----SVHTVNAYLGSATVKLDA 218 (235) Q Consensus 177 RE~evL~l~a~G~t~~eIA~~L~i----S~~TV~~hl~~i~~KLg~ 218 (235) +..+.|.-+.+|++-...-.-=.. ....+..|+.+.+.+.|. T Consensus 151 ~~A~~L~AliDGL~l~~~l~p~~~~~e~~~~~~~~~l~~~l~~~~~ 196 (197) T PRK00767 151 EAAEGLAALIDGLWLRGALSGDPEDTEAARALAKDYIDQQLAQYGS 196 (197) T ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCC T ss_conf 9999999999899999986689999999999999999999886379 No 355 >cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). 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, and organic substrates. Probab=66.82 E-value=5.9 Score=18.87 Aligned_cols=19 Identities=42% Similarity=0.378 Sum_probs=11.3 Q ss_pred HHHHHHCCCCHHHHHHHHC Q ss_conf 9999987999789999949 Q gi|254780693|r 181 CLQLAGDGYTSEEIAEKLG 199 (235) Q Consensus 181 vL~l~a~G~t~~eIA~~L~ 199 (235) |..+-..|+|-+||...|. T Consensus 49 I~~lr~~G~sl~eI~~~l~ 67 (112) T cd01282 49 IRRLLAAGLTLEEIREFLP 67 (112) T ss_pred HHHHHHCCCCHHHHHHHHH T ss_conf 9999996999999999998 No 356 >pfam04552 Sigma54_DBD Sigma-54, DNA binding domain. This DNA binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore this region contains a putative helix-turn-helix motif. At the C-terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins. Probab=66.67 E-value=6.7 Score=18.47 Aligned_cols=28 Identities=25% Similarity=0.382 Sum_probs=17.3 Q ss_pred CHHHHHHHH-----CCCHHHHHHHHHHHHHHCCCCCH Q ss_conf 978999994-----99988999999999998079978 Q gi|254780693|r 190 TSEEIAEKL-----GLSVHTVNAYLGSATVKLDAVNR 221 (235) Q Consensus 190 t~~eIA~~L-----~iS~~TV~~hl~~i~~KLg~~nR 221 (235) |+.+|+..| .||.|||..|.. .||..+- T Consensus 123 SD~~I~~~L~~~Gi~IaRRTVaKYR~----~L~Ip~s 155 (160) T pfam04552 123 SDDKIVELLKEQGIDIARRTVAKYRE----ALNIPSS 155 (160) T ss_pred CHHHHHHHHHHCCCCEEHHHHHHHHH----HCCCCCH T ss_conf 99999999997799521461999998----8399966 No 357 >cd04784 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators. Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of 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 have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins 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=66.36 E-value=6 Score=18.81 Aligned_cols=34 Identities=15% Similarity=0.158 Sum_probs=15.9 Q ss_pred HHHCCCCHHHHHHHHCCCH----------HHHHHHHHHHHHHCC Q ss_conf 9987999789999949998----------899999999999807 Q gi|254780693|r 184 LAGDGYTSEEIAEKLGLSV----------HTVNAYLGSATVKLD 217 (235) Q Consensus 184 l~a~G~t~~eIA~~L~iS~----------~TV~~hl~~i~~KLg 217 (235) +-..|.|-+||...|.+.. ..+..|+..+-+|+. T Consensus 53 lr~~GfsL~eI~~ll~l~~~~~~~~~~~~~ll~~kl~~i~~~I~ 96 (127) T cd04784 53 CRSLDMSLDEIRTLLQLQDDPEASCAEVNALIDEHLAHVRARIA 96 (127) T ss_pred HHHCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHH T ss_conf 98649879999999977728999899999999999999999999 No 358 >PRK09514 zntR zinc-responsive transcriptional regulator; Provisional Probab=66.29 E-value=6 Score=18.78 Aligned_cols=11 Identities=64% Similarity=0.854 Sum_probs=3.6 Q ss_pred CCCHHHHHHHH Q ss_conf 99978999994 Q gi|254780693|r 188 GYTSEEIAEKL 198 (235) Q Consensus 188 G~t~~eIA~~L 198 (235) |.|-+||...| T Consensus 58 GfsL~eI~~ll 68 (140) T PRK09514 58 GFTLEEIRELL 68 (140) T ss_pred CCCHHHHHHHH T ss_conf 99999999998 No 359 >TIGR03418 chol_sulf_TF putative choline sulfate-utilization transcription factor. Members of this protein family are transcription factors of the LysR family. Their genes typically are divergently transcribed from choline-sulfatase genes. That enzyme makes choline, a precursor to the osmoprotectant glycine-betaine, available by hydrolysis of choline sulfate. Probab=66.26 E-value=9 Score=17.56 Aligned_cols=17 Identities=6% Similarity=0.247 Sum_probs=7.2 Q ss_pred HHHHHHHHHHHHHHCCC Q ss_conf 99999999999985837 Q gi|254780693|r 15 QELSPRLHLIQNRIKAR 31 (235) Q Consensus 15 ~dl~~~l~~l~~~~~~~ 31 (235) ..+..++..+.+.++.. T Consensus 30 savS~~I~~LE~~lG~~ 46 (291) T TIGR03418 30 PAVSQQVKRLEEELGTP 46 (291) T ss_pred HHHHHHHHHHHHHHCCC T ss_conf 89999999999996996 No 360 >cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i Probab=66.02 E-value=6 Score=18.79 Aligned_cols=24 Identities=21% Similarity=0.338 Sum_probs=11.5 Q ss_pred CCHHHHHHHHH----HHCCCCHHHHHHH Q ss_conf 99899999999----9879997899999 Q gi|254780693|r 174 LTERETSCLQL----AGDGYTSEEIAEK 197 (235) Q Consensus 174 LT~RE~evL~l----~a~G~t~~eIA~~ 197 (235) .|+.+.+.|++ ...|.+-++|+.. T Consensus 39 Ys~~dv~~l~~I~~l~~~G~~l~~I~~l 66 (68) T cd01104 39 YSEADVARLRLIRRLTSEGVRISQAAAL 66 (68) T ss_pred CCHHHHHHHHHHHHHHHCCCCHHHHHHH T ss_conf 4999999999999999978999999987 No 361 >COG0640 ArsR Predicted transcriptional regulators [Transcription] Probab=65.14 E-value=9.4 Score=17.41 Aligned_cols=38 Identities=34% Similarity=0.331 Sum_probs=29.8 Q ss_pred HHHHHHHHHHC--CCCHHHHHHHHCCCHHHHHHHHHHHHH Q ss_conf 99999999987--999789999949998899999999999 Q gi|254780693|r 177 RETSCLQLAGD--GYTSEEIAEKLGLSVHTVNAYLGSATV 214 (235) Q Consensus 177 RE~evL~l~a~--G~t~~eIA~~L~iS~~TV~~hl~~i~~ 214 (235) -=.+++..+.+ ..+..+|+..+++|..||..|+..... T Consensus 26 ~r~~il~~l~~~~~~~~~~l~~~~~~~~~~v~~hL~~L~~ 65 (110) T COG0640 26 TRLEILSLLAEGGELTVGELAEALGLSQSTVSHHLKVLRE 65 (110) T ss_pred HHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHH T ss_conf 8999999998735137999998857678899999999987 No 362 >pfam00046 Homeobox Homeobox domain. Probab=64.93 E-value=9.5 Score=17.38 Aligned_cols=44 Identities=25% Similarity=0.329 Sum_probs=33.2 Q ss_pred CCCHHHHHHHHHHHCC------CCHHHHHHHHCCCHHHHHHHHHHHHHHC Q ss_conf 4998999999999879------9978999994999889999999999980 Q gi|254780693|r 173 NLTERETSCLQLAGDG------YTSEEIAEKLGLSVHTVNAYLGSATVKL 216 (235) Q Consensus 173 ~LT~RE~evL~l~a~G------~t~~eIA~~L~iS~~TV~~hl~~i~~KL 216 (235) .+|+.|.++|.-.=.- ..-.+||..||+++..|+.-..|-+.|. T Consensus 6 ~ft~~Q~~~Le~~F~~~~~P~~~~~~~LA~~l~l~~~~V~~WFqNrR~k~ 55 (57) T pfam00046 6 TFTPEQLEELEKEFEKNRYPSAEEREELAKKLGLTERQVKVWFQNRRAKW 55 (57) T ss_pred CCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHC T ss_conf 79999999999999857999989999999983999899789768758633 No 363 >cd01105 HTH_GlnR-like Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. These proteins 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. A typical MerR regulator is 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 dissimilar C-terminal domains bind specific coactivator molecules. Probab=64.73 E-value=7.1 Score=18.29 Aligned_cols=27 Identities=26% Similarity=0.364 Sum_probs=18.6 Q ss_pred CCHHHHHHH----HHHHCCCCHHHHHHHHCC Q ss_conf 998999999----999879997899999499 Q gi|254780693|r 174 LTERETSCL----QLAGDGYTSEEIAEKLGL 200 (235) Q Consensus 174 LT~RE~evL----~l~a~G~t~~eIA~~L~i 200 (235) .|+...+.| .|...|.+-++|...|.- T Consensus 40 Ys~~dl~~l~~I~~l~~~G~sl~~i~~~L~~ 70 (88) T cd01105 40 YSLADVDRLLVIKELLDEGFTLAAAVEKLRR 70 (88) T ss_pred CCHHHHHHHHHHHHHHHCCCCHHHHHHHHHH T ss_conf 7999999999999999979989999999998 No 364 >KOG0489 consensus Probab=64.65 E-value=5.8 Score=18.91 Aligned_cols=30 Identities=23% Similarity=0.368 Sum_probs=26.2 Q ss_pred HHHHHHHCCCHHHHHHHHHHHHHHCCCCCH Q ss_conf 899999499988999999999998079978 Q gi|254780693|r 192 EEIAEKLGLSVHTVNAYLGSATVKLDAVNR 221 (235) Q Consensus 192 ~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR 221 (235) -|||..|.++|+-||...+|.+.|-.-.++ T Consensus 190 iEiA~~L~LtErQIKIWFQNRRMK~Kk~~k 219 (261) T KOG0489 190 IEIAHALNLTERQIKIWFQNRRMKWKKENK 219 (261) T ss_pred HHHHHCCHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 998740100688999999888999987631 No 365 >cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators. Probab=64.39 E-value=9.7 Score=17.32 Aligned_cols=44 Identities=30% Similarity=0.294 Sum_probs=29.4 Q ss_pred HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCC Q ss_conf 987999789999949998899999999999807997899999999769 Q gi|254780693|r 185 AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFG 232 (235) Q Consensus 185 ~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~~~G 232 (235) ...|+|-.++|..+|||+.+|..+.+.-. ..+-..+...|-.+| T Consensus 9 ~~~~ls~~~lA~~~gis~~~l~~~e~g~~----~p~~~~l~~la~~~~ 52 (58) T cd00093 9 KEKGLTQEELAEKLGVSRSTISRIENGKR----NPSLETLEKLAKALG 52 (58) T ss_pred HHCCCCHHHHHHHCCCCHHHHHHHHCCCC----CCCHHHHHHHHHHHC T ss_conf 97599999995714999999999987998----999999999999938 No 366 >pfam05263 DUF722 Protein of unknown function (DUF722). This family contains several bacteriophage proteins of unknown function. Probab=64.16 E-value=9.8 Score=17.29 Aligned_cols=44 Identities=25% Similarity=0.237 Sum_probs=37.5 Q ss_pred CCCHHHHHHHHHHHCCC---CHHHHHHHHCCCHHHHHHHHHHHHHHC Q ss_conf 49989999999998799---978999994999889999999999980 Q gi|254780693|r 173 NLTERETSCLQLAGDGY---TSEEIAEKLGLSVHTVNAYLGSATVKL 216 (235) Q Consensus 173 ~LT~RE~evL~l~a~G~---t~~eIA~~L~iS~~TV~~hl~~i~~KL 216 (235) .|++-|++|+++=-.|. |=-+||..|.||++|++....+....+ T Consensus 81 ~~~~~~k~ii~lrY~~r~~~sW~~Va~~l~i~er~~~~~~~~FK~~i 127 (130) T pfam05263 81 VLTEEEKRIIELRYKGRNGMTWYQVAQELDISEKKAKRIYYSFKNDI 127 (130) T ss_pred HHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH T ss_conf 85189999999986764675499999996511999999999998876 No 367 >COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair] Probab=64.02 E-value=9.8 Score=17.27 Aligned_cols=45 Identities=24% Similarity=0.324 Sum_probs=38.2 Q ss_pred CCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 499899999999987999789999949998899999999999807 Q gi|254780693|r 173 NLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 173 ~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) .|-+.-..+..++-.|..-..||+.++|+..||...+.+...+.. T Consensus 74 ~~~~~~~~~~~~~~~~~~i~~~a~~l~i~~~~v~r~~~r~~~~~~ 118 (129) T COG3677 74 ALYKIKLQAVTLYMLGLGIRDIARTLGISINTVNRWSKRFGSRVE 118 (129) T ss_pred CCHHHHHHHHHHHHCCCCCCCHHHHHCCCHHHHHHHHHHCCCHHC T ss_conf 327799999999864999666999955469999999996031000 No 368 >PRK10072 putative transcriptional regulator; Provisional Probab=64.01 E-value=7.5 Score=18.09 Aligned_cols=32 Identities=31% Similarity=0.478 Sum_probs=24.7 Q ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHH Q ss_conf 999999998799978999994999889999999 Q gi|254780693|r 178 ETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLG 210 (235) Q Consensus 178 E~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~ 210 (235) |.+-++ -..|++-.|-|..||+|..||+.-=. T Consensus 37 dvkaIR-~~tgl~q~eFA~~lGvSv~tvksWEq 68 (96) T PRK10072 37 EFEQLR-KGTGLKIDDFARVLGVSVAMVKEWES 68 (96) T ss_pred CHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHH T ss_conf 399999-88099999999997777999999996 No 369 >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=63.40 E-value=3.8 Score=20.19 Aligned_cols=34 Identities=35% Similarity=0.389 Sum_probs=28.7 Q ss_pred CCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHH Q ss_conf 99899999999987999789999949998899999999999 Q gi|254780693|r 174 LTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATV 214 (235) Q Consensus 174 LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~ 214 (235) .|=||. +|+|-+|||.+|.+=..||+.-+=+++. T Consensus 149 i~LREl-------eGLSYe~IA~~MdCPvGTVRSRIFRARE 182 (192) T TIGR02939 149 ITLREL-------EGLSYEDIAEIMDCPVGTVRSRIFRARE 182 (192) T ss_pred HHHHHC-------CCCCHHHHHHHCCCCCCCCCCHHHHHHH T ss_conf 446512-------6878788873306998862114677589 No 370 >TIGR01369 CPSaseII_lrg carbamoyl-phosphate synthase, large subunit; InterPro: IPR006275 Carbamoyl phosphate synthase (CPSase) is a heterodimeric enzyme composed of a small and a large subunit (with the exception of CPSase III, see below). CPSase catalyses the synthesis of carbamoyl phosphate from biocarbonate, ATP and glutamine (6.3.5.5 from EC) or ammonia (6.3.4.16 from EC), and represents the first committed step in pyrimidine and arginine biosynthesis in prokaryotes and eukaryotes, and in the urea cycle in most terrestrial vertebrates , . CPSase has three active sites, one in the small subunit and two in the large subunit. The small subunit contains the glutamine binding site and catalyses the hydrolysis of glutamine to glutamate and ammonia. The large subunit has two homologous carboxy phosphate domains, both of which have ATP-binding sites; however, the N-terminal carboxy phosphate domain catalyses the phosphorylation of biocarbonate, while the C-terminal domain catalyses the phosphorylation of the carbamate intermediate . The carboxy phosphate domain found duplicated in the large subunit of CPSase is also present as a single copy in the biotin-dependent enzymes acetyl-CoA carboxylase (6.4.1.2 from EC) (ACC), propionyl-CoA carboxylase (6.4.1.3 from EC) (PCCase), pyruvate carboxylase (6.4.1.1 from EC) (PC) and urea carboxylase (6.3.4.6 from EC). Most prokaryotes carry one form of CPSase that participates in both arginine and pyrimidine biosynthesis, however certain bacteria can have separate forms. The large subunit in bacterial CPSase has four structural domains: the carboxy phosphate domain 1, the oligomerisation domain, the carbamoyl phosphate domain 2 and the allosteric domain . CPSase heterodimers from Escherichia coli contain two molecular tunnels: an ammonia tunnel and a carbamate tunnel. These inter-domain tunnels connect the three distinct active sites, and function as conduits for the transport of unstable reaction intermediates (ammonia and carbamate) between successive active sites . The catalytic mechanism of CPSase involves the diffusion of carbamate through the interior of the enzyme from the site of synthesis within the N-terminal domain of the large subunit to the site of phosphorylation within the C-terminal domain. Eukaryotes have two distinct forms of CPSase: a mitochondrial enzyme (CPSase I) that participates in both arginine biosynthesis and the urea cycle; and a cytosolic enzyme (CPSase II) involved in pyrimidine biosynthesis. CPSase II occurs as part of a multi-enzyme complex along with aspartate transcarbamoylase and dihydroorotase; this complex is referred to as the CAD protein . The hepatic expression of CPSase is transcriptionally regulated by glucocorticoids and/or cAMP . There is a third form of the enzyme, CPSase III, found in fish, which uses glutamine as a nitrogen source instead of ammonia . CPSase III is closely related to CPSase I, and is composed of a single polypeptide that may have arisen from gene fusion of the glutaminase and synthetase domains . This entry represents glutamine-dependent CPSase (6.3.5.5 from EC) from prokaryotes and eukaryotes (CPSase II). ; GO: 0004086 carbamoyl-phosphate synthase activity, 0006807 nitrogen compound metabolic process. Probab=63.09 E-value=10 Score=17.15 Aligned_cols=43 Identities=14% Similarity=0.172 Sum_probs=29.9 Q ss_pred HHHHHHHH-HHHCCCCHHHHHHHHCCCHHH--HHHHHHHHHHHCCC Q ss_conf 89999999-998799978999994999889--99999999998079 Q gi|254780693|r 176 ERETSCLQ-LAGDGYTSEEIAEKLGLSVHT--VNAYLGSATVKLDA 218 (235) Q Consensus 176 ~RE~evL~-l~a~G~t~~eIA~~L~iS~~T--V~~hl~~i~~KLg~ 218 (235) +--.|.|+ .=..|.|+++||..++.++.+ -...++++++.+|+ T Consensus 489 ~~~~e~L~~aK~lGFSD~~iA~~~~~~~~~~~~~~~vR~~R~~~gi 534 (1089) T TIGR01369 489 ELDKELLRKAKKLGFSDAQIARLVNVTEAESIEELEVRKLRKELGI 534 (1089) T ss_pred CCCHHHHHHHHHCCCCHHHHHHHHCCCHHHCCCHHHHHHHHHHCCC T ss_conf 4898899998641888789999868974442006899999984697 No 371 >PRK11477 carbohydrate diacid transcriptional activator CdaR; Provisional Probab=63.02 E-value=10 Score=17.15 Aligned_cols=42 Identities=7% Similarity=-0.103 Sum_probs=37.2 Q ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCH Q ss_conf 999999879997899999499988999999999998079978 Q gi|254780693|r 180 SCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNR 221 (235) Q Consensus 180 evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR 221 (235) .+-.|...+.+-.+.|..|.|=.+|+.+.+++|.+..|..=| T Consensus 326 TL~~yfe~n~si~~tA~~L~IHRNTL~YRL~KI~~lTGldpr 367 (385) T PRK11477 326 TLAAWFRHNVQPLATSKALFIHRNTLEYRLNRISELTGLDLG 367 (385) T ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCC T ss_conf 999999809999999998486450699999999999781977 No 372 >PRK09508 leuO leucine transcriptional activator; Reviewed Probab=62.27 E-value=11 Score=17.05 Aligned_cols=12 Identities=0% Similarity=-0.020 Sum_probs=4.2 Q ss_pred HHHHHHHHHHCC Q ss_conf 999999998583 Q gi|254780693|r 19 PRLHLIQNRIKA 30 (235) Q Consensus 19 ~~l~~l~~~~~~ 30 (235) ..+..+.+.++. T Consensus 55 ~aL~rLr~~~gd 66 (314) T PRK09508 55 NAVARLKVMFND 66 (314) T ss_pred HHHHHHHHHHCC T ss_conf 999999998199 No 373 >PRK11753 cAMP-regulatory protein; Provisional Probab=62.17 E-value=11 Score=17.04 Aligned_cols=27 Identities=26% Similarity=0.218 Sum_probs=22.9 Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHH Q ss_conf 997899999499988999999999998 Q gi|254780693|r 189 YTSEEIAEKLGLSVHTVNAYLGSATVK 215 (235) Q Consensus 189 ~t~~eIA~~L~iS~~TV~~hl~~i~~K 215 (235) .|-.|||..+|+|..||+.-++...++ T Consensus 169 lt~~eLA~~lG~sretvsR~L~~L~~~ 195 (211) T PRK11753 169 ITRQEIGRIVGCSREMVGRVLKMLEDQ 195 (211) T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHC T ss_conf 699999988699899999999999988 No 374 >PRK09480 slmA nucleoid occlusion protein; Provisional Probab=62.11 E-value=5.3 Score=19.16 Aligned_cols=14 Identities=7% Similarity=0.031 Sum_probs=6.4 Q ss_pred HHHHHHHHHCCCCE Q ss_conf 99999998583785 Q gi|254780693|r 20 RLHLIQNRIKARNF 33 (235) Q Consensus 20 ~l~~l~~~~~~~~f 33 (235) .++++.+.+...++ T Consensus 15 Il~a~~~ll~~~~~ 28 (194) T PRK09480 15 ILQTLAQMLESPPG 28 (194) T ss_pred HHHHHHHHHHHCCC T ss_conf 99999999862797 No 375 >PRK09392 ftrB transcriptional activator FtrB; Provisional Probab=61.85 E-value=11 Score=17.00 Aligned_cols=30 Identities=13% Similarity=0.292 Sum_probs=25.3 Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHCCCC Q ss_conf 9978999994999889999999999980799 Q gi|254780693|r 189 YTSEEIAEKLGLSVHTVNAYLGSATVKLDAV 219 (235) Q Consensus 189 ~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~ 219 (235) .|-.+||..||+|+.||...++...++ |+. T Consensus 174 ~t~~~lA~~lG~tretvsR~L~~L~~~-GI~ 203 (236) T PRK09392 174 YEKRTLASYLGMTPENLSRAFAALASH-GVH 203 (236) T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHC-CCE T ss_conf 789999998789899999999999979-968 No 376 >PRK13756 tetracycline repressor protein TetR; Provisional Probab=61.63 E-value=4.6 Score=19.62 Aligned_cols=14 Identities=7% Similarity=0.133 Sum_probs=5.1 Q ss_pred HHHHHHHHHHHCCC Q ss_conf 99999999998079 Q gi|254780693|r 205 VNAYLGSATVKLDA 218 (235) Q Consensus 205 V~~hl~~i~~KLg~ 218 (235) .+.-+.-+..+|.+ T Consensus 190 L~llL~Gle~rL~~ 203 (205) T PRK13756 190 LELIICGLEKQLKC 203 (205) T ss_pred HHHHHHHHHHHHHH T ss_conf 99999999999751 No 377 >smart00351 PAX Paired Box domain. Probab=61.40 E-value=11 Score=16.95 Aligned_cols=38 Identities=24% Similarity=0.244 Sum_probs=32.1 Q ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHC Q ss_conf 99999998799978999994999889999999999980 Q gi|254780693|r 179 TSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKL 216 (235) Q Consensus 179 ~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL 216 (235) .+++.|...|...-+|+++|.||-..|..-+.+.++.- T Consensus 24 ~kIveLa~~G~rpcdISr~L~VShGCVSKIL~Ry~etG 61 (125) T smart00351 24 QRIVELAQNGVRPCDISRQLCVSHGCVSKILGRYYETG 61 (125) T ss_pred HHHHHHHHCCCCHHHHHHHHCCCCCHHHHHHHHHHHCC T ss_conf 99999998599899987564577106999999997138 No 378 >COG3177 Fic family protein [Function unknown] Probab=61.28 E-value=11 Score=16.94 Aligned_cols=28 Identities=29% Similarity=0.189 Sum_probs=25.5 Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHH Q ss_conf 7999789999949998899999999999 Q gi|254780693|r 187 DGYTSEEIAEKLGLSVHTVNAYLGSATV 214 (235) Q Consensus 187 ~G~t~~eIA~~L~iS~~TV~~hl~~i~~ 214 (235) .+.|.++++.+.+||..|++.+++...+ T Consensus 303 ~~~t~~~~~~~~~~s~~Ta~r~l~~l~~ 330 (348) T COG3177 303 GYLTAAEIEAILGVSKATATRDLKELLE 330 (348) T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHH T ss_conf 7645999999828988889999999974 No 379 >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=61.12 E-value=6.2 Score=18.70 Aligned_cols=16 Identities=25% Similarity=0.650 Sum_probs=5.0 Q ss_pred CCCHHHHHHHHCCCHH Q ss_conf 9997899999499988 Q gi|254780693|r 188 GYTSEEIAEKLGLSVH 203 (235) Q Consensus 188 G~t~~eIA~~L~iS~~ 203 (235) |+|-.+.|.+|||.+. T Consensus 38 Gms~~QLA~RlGV~p~ 53 (150) T TIGR02612 38 GMSGAQLAARLGVTPQ 53 (150) T ss_pred CCCHHHHHHHCCCCHH T ss_conf 5157887665289737 No 380 >PRK00135 scpB segregation and condensation protein B; Reviewed Probab=60.91 E-value=11 Score=16.89 Aligned_cols=28 Identities=18% Similarity=0.281 Sum_probs=14.8 Q ss_pred CHHHHHHHHHHHHHHHCC--CCEEEEEECC Q ss_conf 599999999999998583--7858998417 Q gi|254780693|r 13 SLQELSPRLHLIQNRIKA--RNFALYTINS 40 (235) Q Consensus 13 sl~dl~~~l~~l~~~~~~--~~f~~~~~~~ 40 (235) +.+++...+..+.+.+.. .+|.+..... T Consensus 26 ~~~~i~~~l~~L~~~Y~~~~~gi~l~~~~~ 55 (182) T PRK00135 26 EPTEVKQLLEELQEKYEGDDRGLKLIEFAE 55 (182) T ss_pred CHHHHHHHHHHHHHHHCCCCCCEEEEEECC T ss_conf 989999999999999624897379999999 No 381 >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=60.75 E-value=7.9 Score=17.95 Aligned_cols=26 Identities=23% Similarity=0.340 Sum_probs=21.7 Q ss_pred HHCCCCHHHHHHHHCCCHHHHHHHHH Q ss_conf 98799978999994999889999999 Q gi|254780693|r 185 AGDGYTSEEIAEKLGLSVHTVNAYLG 210 (235) Q Consensus 185 ~a~G~t~~eIA~~L~iS~~TV~~hl~ 210 (235) ---|.|..+.|+.||||+.|++.=+. T Consensus 17 ~PLg~s~~~LA~~LgVsr~~~sriv~ 42 (81) T TIGR02607 17 EPLGLSVRALAKALGVSRSTLSRIVN 42 (81) T ss_pred HCCCHHHHHHHHHCCCCHHHHHHHHH T ss_conf 10470689999870999788888874 No 382 >KOG0723 consensus Probab=60.64 E-value=5.7 Score=18.95 Aligned_cols=33 Identities=18% Similarity=0.161 Sum_probs=28.0 Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCH Q ss_conf 997899999499988999999999998079978 Q gi|254780693|r 189 YTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNR 221 (235) Q Consensus 189 ~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR 221 (235) +|.+|-+.+|+||+.+.+.-++.+-+|.=+.|. T Consensus 53 Msr~EA~lIL~v~~s~~k~KikeaHrriM~~NH 85 (112) T KOG0723 53 MSRREAALILGVTPSLDKDKIKEAHRRIMLANH 85 (112) T ss_pred CCHHHHHHHHCCCCCCCHHHHHHHHHHHHHCCC T ss_conf 156889988278754568899999999998079 No 383 >cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner. Probab=60.15 E-value=11 Score=16.80 Aligned_cols=29 Identities=31% Similarity=0.519 Sum_probs=24.8 Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHCCC Q ss_conf 97899999499988999999999998079 Q gi|254780693|r 190 TSEEIAEKLGLSVHTVNAYLGSATVKLDA 218 (235) Q Consensus 190 t~~eIA~~L~iS~~TV~~hl~~i~~KLg~ 218 (235) .-.+||..+|+|+..|+....|-+.+..- T Consensus 29 ~~~~La~~~~l~~~qV~~WF~nrR~~~~~ 57 (59) T cd00086 29 EREELAKELGLTERQVKIWFQNRRAKLKR 57 (59) T ss_pred HHHHHHHHHCCCHHHHHHHHHHHHHHHHH T ss_conf 99999999792999999999989988873 No 384 >PRK09706 transcriptional repressor DicA; Reviewed Probab=60.08 E-value=10 Score=17.23 Aligned_cols=35 Identities=20% Similarity=0.263 Sum_probs=20.5 Q ss_pred CCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH Q ss_conf 499899999999987999789999949998899999 Q gi|254780693|r 173 NLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAY 208 (235) Q Consensus 173 ~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~h 208 (235) .||++|.+.|.+.-+ +...|-=..|..=+-.++.+ T Consensus 84 ~L~~~q~~LLeLf~~-LP~sEq~~~l~el~~r~~~~ 118 (135) T PRK09706 84 ELSEDQKELLELFDA-LPESEQEAQLSEMRARVENF 118 (135) T ss_pred CCCHHHHHHHHHHHH-CCHHHHHHHHHHHHHHHHHH T ss_conf 589999999999997-88999999999999999999 No 385 >COG2469 Uncharacterized conserved protein [Function unknown] Probab=59.97 E-value=7.8 Score=17.98 Aligned_cols=52 Identities=19% Similarity=0.141 Sum_probs=44.9 Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHH Q ss_conf 2467887444998999999999879997899999499988999999999998 Q gi|254780693|r 164 FKKRSSAARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVK 215 (235) Q Consensus 164 ~~~~~~~~~~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~K 215 (235) ......+...||+-|.++|-++--|..+-++...||++..-++....++..| T Consensus 204 ~eKe~k~~~~LsE~E~qiLvalYSg~~~~sl~~~lG~~~~el~~l~drlI~~ 255 (284) T COG2469 204 KEKEIKEKETLSEIEKQILVALYSGGDSASLELFLGVDTDELEILYDRLIDK 255 (284) T ss_pred HHHHHCCCCCCCHHHHEEEEEEECCCCCHHHHHHHCCCHHHHHHHHHHHHHH T ss_conf 8753332223330312113667528982303567487699999999999873 No 386 >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=59.77 E-value=12 Score=16.76 Aligned_cols=45 Identities=33% Similarity=0.393 Sum_probs=39.7 Q ss_pred CCCHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 499899999999-987999789999949998899999999999807 Q gi|254780693|r 173 NLTERETSCLQL-AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 173 ~LT~RE~evL~l-~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) .|..||+-+|.. .-+|+|.-|+|.+.|||...|...=+.+..++. T Consensus 206 ~l~~re~~il~~rff~G~tqmeva~eiGisqaqvsrlek~a~~~~~ 251 (254) T TIGR02850 206 RLNEREKLILKLRFFEGKTQMEVAEEIGISQAQVSRLEKAALKHMR 251 (254) T ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHH T ss_conf 8766788777755314631334565403016888888899999975 No 387 >pfam08069 Ribosomal_S13_N Ribosomal S13/S15 N-terminal domain. This domain is found at the N-terminus of ribosomal S13 and S15 proteins. This domain is also identified as NUC021. Probab=59.62 E-value=9.3 Score=17.44 Aligned_cols=27 Identities=26% Similarity=0.299 Sum_probs=21.8 Q ss_pred CCCH--HHHHHHHHHHCCCCHHHHHHHHC Q ss_conf 4998--99999999987999789999949 Q gi|254780693|r 173 NLTE--RETSCLQLAGDGYTSEEIAEKLG 199 (235) Q Consensus 173 ~LT~--RE~evL~l~a~G~t~~eIA~~L~ 199 (235) ..|+ =|..|+++..+|+|..+|+.+|- T Consensus 27 ~~~~~eve~~I~klakkG~~pSqIG~iLR 55 (60) T pfam08069 27 KYSPEEVEELIVKLAKKGLTPSQIGVILR 55 (60) T ss_pred CCCHHHHHHHHHHHHHCCCCHHHHHHHHH T ss_conf 68999999999999987998889735653 No 388 >smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor. Probab=59.57 E-value=12 Score=16.73 Aligned_cols=25 Identities=32% Similarity=0.424 Sum_probs=19.7 Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH Q ss_conf 9789999949998899999999999 Q gi|254780693|r 190 TSEEIAEKLGLSVHTVNAYLGSATV 214 (235) Q Consensus 190 t~~eIA~~L~iS~~TV~~hl~~i~~ 214 (235) |.+++|.++++|..||+.-++.+.. T Consensus 22 s~~~la~~~~vSr~tvr~A~~~L~~ 46 (60) T smart00345 22 SERELAAQLGVSRTTVREALSRLEA 46 (60) T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH T ss_conf 0999999989499999999999998 No 389 >cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Probab=59.09 E-value=9.7 Score=17.30 Aligned_cols=28 Identities=25% Similarity=0.300 Sum_probs=20.7 Q ss_pred CCCHHHHHHHHHHH-----CCCCHHHHHHHHCC Q ss_conf 49989999999998-----79997899999499 Q gi|254780693|r 173 NLTERETSCLQLAG-----DGYTSEEIAEKLGL 200 (235) Q Consensus 173 ~LT~RE~evL~l~a-----~G~t~~eIA~~L~i 200 (235) .-|+...+.++++. +|+|-+.|-..|.= T Consensus 38 ~Ys~~di~~l~~Ik~Ll~~~G~ti~~~k~~L~~ 70 (99) T cd04765 38 YYRPKDVELLLLIKHLLYEKGYTIEGAKQALKE 70 (99) T ss_pred CCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHH T ss_conf 068999999999999999879879999999983 No 390 >cd04767 HTH_HspR-like_MBC Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators. Putative helix-turn-helix (HTH) transcription regulator HspR-like proteins. Unlike the characterized HspR, these proteins have a C-terminal domain with putative metal binding cysteines (MBC). Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins 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. A typical MerR regulator is comprised of 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 dissimilar C-terminal domains bind spe Probab=58.10 E-value=9.8 Score=17.27 Aligned_cols=20 Identities=15% Similarity=0.255 Sum_probs=9.8 Q ss_pred HHHHH-HCCCCHHHHHHHHCC Q ss_conf 99999-879997899999499 Q gi|254780693|r 181 CLQLA-GDGYTSEEIAEKLGL 200 (235) Q Consensus 181 vL~l~-a~G~t~~eIA~~L~i 200 (235) |.+|+ ..|.+-.+|..+|.+ T Consensus 49 IkrL~~e~G~nlagI~~iLsl 69 (120) T cd04767 49 IKKLINEKGLNIAGVKQILSM 69 (120) T ss_pred HHHHHHHCCCCHHHHHHHHHC T ss_conf 999999759689999999806 No 391 >TIGR03613 RutR pyrimidine utilization regulatory protein R. This protein is observed in operons extremely similar to that characterized in E. coli K-12 responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the TetR family of transcriptional regulators defined by the N-teminal model pfam00440 and the C-terminal model pfam08362 (YcdC-like protein, C-terminal region). Probab=57.96 E-value=7.2 Score=18.24 Aligned_cols=16 Identities=13% Similarity=0.262 Sum_probs=7.9 Q ss_pred CCHHHHHHHHHHHCCC Q ss_conf 9989999999998799 Q gi|254780693|r 174 LTERETSCLQLAGDGY 189 (235) Q Consensus 174 LT~RE~evL~l~a~G~ 189 (235) ...+-..|..++..|. T Consensus 184 ~~~~~~~v~~lvL~Gl 199 (202) T TIGR03613 184 FNETVANVQRIVLEGI 199 (202) T ss_pred HHHHHHHHHHHHHHHC T ss_conf 9999999999998302 No 392 >COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only] Probab=57.65 E-value=9.9 Score=17.24 Aligned_cols=24 Identities=33% Similarity=0.617 Sum_probs=19.8 Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHH Q ss_conf 999789999949998899999999 Q gi|254780693|r 188 GYTSEEIAEKLGLSVHTVNAYLGS 211 (235) Q Consensus 188 G~t~~eIA~~L~iS~~TV~~hl~~ 211 (235) |+|..+.|..|||+++||+.-+.. T Consensus 23 glt~~~lA~~lgV~r~~is~ling 46 (104) T COG3093 23 GLTQTELAEALGVTRNTISELING 46 (104) T ss_pred CCCHHHHHHHHCCCHHHHHHHHCC T ss_conf 698999999939989999999837 No 393 >PRK03887 methylated-DNA--protein-cysteine methyltransferase; Provisional Probab=57.60 E-value=13 Score=16.51 Aligned_cols=41 Identities=24% Similarity=0.233 Sum_probs=32.4 Q ss_pred CCCCCCHHHHHHHHHHHC----C--CCHHHHHHHHCCCHHHHHHHHH Q ss_conf 744499899999999987----9--9978999994999889999999 Q gi|254780693|r 170 AARNLTERETSCLQLAGD----G--YTSEEIAEKLGLSVHTVNAYLG 210 (235) Q Consensus 170 ~~~~LT~RE~evL~l~a~----G--~t~~eIA~~L~iS~~TV~~hl~ 210 (235) ..+.+||=|+.|-.++.+ | .|..+||..|+.|+|.|-.-+. T Consensus 86 ~~~g~T~FqrkVy~~L~k~IP~G~t~TYgeiAk~lgts~RAVG~A~~ 132 (172) T PRK03887 86 SFEGLTKFERKVYEWLVKNVKRGEVITYGELAKALNTSPRAVGGAMK 132 (172) T ss_pred CCCCCCHHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHC T ss_conf 42579979999999997108998749499999997887789999975 No 394 >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=57.45 E-value=12 Score=16.67 Aligned_cols=34 Identities=41% Similarity=0.409 Sum_probs=23.5 Q ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHH Q ss_conf 9999999879997899999499988999999999 Q gi|254780693|r 179 TSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSA 212 (235) Q Consensus 179 ~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i 212 (235) .+..+-+-+-=|..|||..|++|+..|+..+... T Consensus 11 ~~L~q~lgR~Pt~eEiA~~l~~s~~~v~~~~~~~ 44 (78) T pfam04539 11 RELEQELGREPTPEEIAEELGISEEKVREVLEAA 44 (78) T ss_pred HHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHC T ss_conf 9999998889999999999694999999999875 No 395 >COG1476 Predicted transcriptional regulators [Transcription] Probab=57.43 E-value=10 Score=17.23 Aligned_cols=25 Identities=40% Similarity=0.424 Sum_probs=21.1 Q ss_pred HHCCCCHHHHHHHHCCCHHHHHHHH Q ss_conf 9879997899999499988999999 Q gi|254780693|r 185 AGDGYTSEEIAEKLGLSVHTVNAYL 209 (235) Q Consensus 185 ~a~G~t~~eIA~~L~iS~~TV~~hl 209 (235) .-.|+|-.+.|..+|||..|+..-= T Consensus 11 ~~~~ltQ~elA~~vgVsRQTi~~iE 35 (68) T COG1476 11 AELGLTQEELAKLVGVSRQTIIAIE 35 (68) T ss_pred HHHCCCHHHHHHHCCCCHHHHHHHH T ss_conf 9828589999999195799999999 No 396 >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=56.29 E-value=13 Score=16.36 Aligned_cols=24 Identities=29% Similarity=0.389 Sum_probs=18.8 Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHH Q ss_conf 978999994999889999999999 Q gi|254780693|r 190 TSEEIAEKLGLSVHTVNAYLGSAT 213 (235) Q Consensus 190 t~~eIA~~L~iS~~TV~~hl~~i~ 213 (235) |-+++|..+++|..||+.-++... T Consensus 26 s~~~La~~~~vSr~tvr~Al~~L~ 49 (64) T pfam00392 26 SERELAAEFGVSRTTVREALRRLE 49 (64) T ss_pred HHHHHHHHHCCCHHHHHHHHHHHH T ss_conf 799999997969999999999999 No 397 >pfam08280 HTH_Mga M protein trans-acting positive regulator (MGA) HTH domain. Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions. Probab=55.94 E-value=13 Score=16.32 Aligned_cols=41 Identities=29% Similarity=0.446 Sum_probs=31.6 Q ss_pred HHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHC Q ss_conf 8999999999879--9978999994999889999999999980 Q gi|254780693|r 176 ERETSCLQLAGDG--YTSEEIAEKLGLSVHTVNAYLGSATVKL 216 (235) Q Consensus 176 ~RE~evL~l~a~G--~t~~eIA~~L~iS~~TV~~hl~~i~~KL 216 (235) .|+.+.+.++-+- .+-.|+|..||+|+.|++.++..+..=+ T Consensus 5 ~rk~~Ll~lL~~~~~~~l~el~~~l~ls~~tl~~~i~~L~~~f 47 (59) T pfam08280 5 KRKLKLLELLTENKSITLDELAKQLGLSELTLKSYIHELNELF 47 (59) T ss_pred HHHHHHHHHHHCCCCEEHHHHHHHCCCCHHHHHHHHHHHHHHC T ss_conf 8999999999808836499999880997999999999999873 No 398 >pfam10078 DUF2316 Uncharacterized protein conserved in bacteria (DUF2316). Members of this family of hypothetical bacterial proteins have no known function. Probab=55.83 E-value=13 Score=16.31 Aligned_cols=24 Identities=29% Similarity=0.389 Sum_probs=18.1 Q ss_pred HHHCCCCHHHHHHHHCCCHHHHHH Q ss_conf 998799978999994999889999 Q gi|254780693|r 184 LAGDGYTSEEIAEKLGLSVHTVNA 207 (235) Q Consensus 184 l~a~G~t~~eIA~~L~iS~~TV~~ 207 (235) .--.|+|-++||..|++|+.-|+. T Consensus 19 f~~~~ls~~~iA~dL~~s~~~ve~ 42 (89) T pfam10078 19 FELSGLTIEQVAKDLNTTPEKVEA 42 (89) T ss_pred HHHCCCCHHHHHHHHCCCHHHHHH T ss_conf 988389899999894999999999 No 399 >cd01279 HTH_HspR-like Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator HspR and related proteins, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins 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. A typical MerR regulator is 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 dissimilar C-terminal domains bind specific coactivator molecules. Probab=55.78 E-value=12 Score=16.72 Aligned_cols=31 Identities=16% Similarity=0.334 Sum_probs=21.2 Q ss_pred CCHHHHHHHH----HH-HCCCCHHHHHHHHCCCHHH Q ss_conf 9989999999----99-8799978999994999889 Q gi|254780693|r 174 LTERETSCLQ----LA-GDGYTSEEIAEKLGLSVHT 204 (235) Q Consensus 174 LT~RE~evL~----l~-a~G~t~~eIA~~L~iS~~T 204 (235) -|+...+-|+ |+ ..|.|-..|-.+|.+.... T Consensus 39 Ys~~Dl~~L~~I~~L~~~~G~~l~gik~iL~l~~q~ 74 (98) T cd01279 39 YSNNDLELLRQVQRLSQDEGFNLAGIKRIIELYPQV 74 (98) T ss_pred CCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHH T ss_conf 499999999999999995898899999999989999 No 400 >smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes Probab=55.69 E-value=13 Score=16.43 Aligned_cols=43 Identities=28% Similarity=0.315 Sum_probs=30.4 Q ss_pred CCHHHHHHHHHHHCC------CCHHHHHHHHCCCHHHHHHHHHHHHHHC Q ss_conf 998999999999879------9978999994999889999999999980 Q gi|254780693|r 174 LTERETSCLQLAGDG------YTSEEIAEKLGLSVHTVNAYLGSATVKL 216 (235) Q Consensus 174 LT~RE~evL~l~a~G------~t~~eIA~~L~iS~~TV~~hl~~i~~KL 216 (235) +|+.+..+|.-.=.= ..-.+||..||+|+.+|+.-..|-+.|. T Consensus 7 ~s~~q~~~L~~~f~~~~~P~~~~~~~La~~l~l~~~~I~~WF~NrR~r~ 55 (56) T smart00389 7 FTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKW 55 (56) T ss_pred CCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHCC T ss_conf 9999999999999877999989999999996949999999878540256 No 401 >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=55.68 E-value=11 Score=16.82 Aligned_cols=22 Identities=32% Similarity=0.309 Sum_probs=18.8 Q ss_pred CCHHHHHHHHCCCHHHHHHHHH Q ss_conf 9978999994999889999999 Q gi|254780693|r 189 YTSEEIAEKLGLSVHTVNAYLG 210 (235) Q Consensus 189 ~t~~eIA~~L~iS~~TV~~hl~ 210 (235) .|++|++..|++|..||-.-.+ T Consensus 53 ft~~el~~~L~~s~~~v~k~~k 74 (76) T pfam06970 53 FTNEELMELLNCSKQKVIKIKK 74 (76) T ss_pred EEHHHHHHHHCCCHHHHHHHHH T ss_conf 6499999997878889999996 No 402 >PRK11388 DNA-binding transcriptional regulator DhaR; Provisional Probab=55.57 E-value=14 Score=16.28 Aligned_cols=35 Identities=17% Similarity=0.108 Sum_probs=26.1 Q ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH Q ss_conf 99999999987999789999949998899999999 Q gi|254780693|r 177 RETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGS 211 (235) Q Consensus 177 RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~ 211 (235) |+.=+-.|-..|..-.+.|+.||||..|...+++. T Consensus 593 r~~I~~aL~~~~gN~s~aA~~LGIsR~TLYRKlk~ 627 (639) T PRK11388 593 KQAIINAAQVCGGRIQEMAALLGIGRTTLWRKMKQ 627 (639) T ss_pred HHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHH T ss_conf 99999999994997999999989899999999999 No 403 >KOG2581 consensus Probab=55.42 E-value=14 Score=16.27 Aligned_cols=25 Identities=32% Similarity=0.404 Sum_probs=16.3 Q ss_pred CHHHHHHHHCC-CHHHHHHHHHHHHH Q ss_conf 97899999499-98899999999999 Q gi|254780693|r 190 TSEEIAEKLGL-SVHTVNAYLGSATV 214 (235) Q Consensus 190 t~~eIA~~L~i-S~~TV~~hl~~i~~ 214 (235) +-++||.+|+| |+.+|++-++++.+ T Consensus 379 Sl~DIA~kL~l~Seed~EyiVakAIR 404 (493) T KOG2581 379 SLQDIAKKLGLNSEEDAEYIVAKAIR 404 (493) T ss_pred CHHHHHHHHCCCCCHHHHHHHHHHHH T ss_conf 59999999669982027999999987 No 404 >KOG0848 consensus Probab=54.69 E-value=9.8 Score=17.27 Aligned_cols=27 Identities=30% Similarity=0.415 Sum_probs=22.6 Q ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 789999949998899999999999807 Q gi|254780693|r 191 SEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 191 ~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) -.|.|..|++|||-||.-.+|-+.|=- T Consensus 229 KSELA~~LgLsERQVKIWFQNRRAKER 255 (317) T KOG0848 229 KSELAATLGLSERQVKIWFQNRRAKER 255 (317) T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 678877607117666676541027777 No 405 >pfam02954 HTH_8 Bacterial regulatory protein, Fis family. Probab=53.82 E-value=14 Score=16.09 Aligned_cols=31 Identities=26% Similarity=0.222 Sum_probs=24.2 Q ss_pred HHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH Q ss_conf 9999987999789999949998899999999 Q gi|254780693|r 181 CLQLAGDGYTSEEIAEKLGLSVHTVNAYLGS 211 (235) Q Consensus 181 vL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~ 211 (235) .-.|-..|..-.+.|..||||..|...-++. T Consensus 11 ~~aL~~~~gn~~~aA~~LGisr~tL~~kmkk 41 (42) T pfam02954 11 EAALERTGGNKSKAARLLGISRRTLYRKLKK 41 (42) T ss_pred HHHHHHHCCCHHHHHHHHCCCHHHHHHHHHH T ss_conf 9999994997999999979699999999973 No 406 >pfam05344 DUF746 Domain of Unknown Function (DUF746). This is a short conserved region found in some transposons. Probab=53.65 E-value=14 Score=16.07 Aligned_cols=48 Identities=15% Similarity=0.225 Sum_probs=37.0 Q ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHH---CCCCCHHHH Q ss_conf 999999999879997899999499988999999999998---079978999 Q gi|254780693|r 177 RETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVK---LDAVNRIQA 224 (235) Q Consensus 177 RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~K---Lg~~nR~qa 224 (235) |..+..+++++-.+-.|.|.+||.++.+|..-++.-++- |+-+.+-++ T Consensus 2 r~~~~IrlLs~p~s~~qaa~~lg~~~~~i~~wv~~fr~~ll~LDPSG~~e~ 52 (65) T pfam05344 2 RMRLFIRLLSQPISCAQAADQLGTDEGIIRKWVRMFRRWLLQLDPSGHLER 52 (65) T ss_pred CHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCCHHH T ss_conf 387999982666659999999787888999999999999986198877188 No 407 >PRK09940 transcriptional regulator YdeO; Provisional Probab=53.60 E-value=14 Score=16.07 Aligned_cols=26 Identities=15% Similarity=0.188 Sum_probs=15.8 Q ss_pred HCCCCHHHHHHHHCCCHHHHHHHHHH Q ss_conf 87999789999949998899999999 Q gi|254780693|r 186 GDGYTSEEIAEKLGLSVHTVNAYLGS 211 (235) Q Consensus 186 a~G~t~~eIA~~L~iS~~TV~~hl~~ 211 (235) +.-=+-++||..|.+||.|++.++++ T Consensus 148 s~~W~L~dIA~~L~mSEStLkRkLk~ 173 (253) T PRK09940 148 AHPWKLKDICDCLYISESLLKKKLKQ 173 (253) T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHH T ss_conf 00460999998874589999999998 No 408 >KOG0709 consensus Probab=53.43 E-value=15 Score=16.05 Aligned_cols=53 Identities=15% Similarity=0.157 Sum_probs=41.9 Q ss_pred CCCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCC Q ss_conf 46788744499899999999987999789999949998899999999999807997 Q gi|254780693|r 165 KKRSSAARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVN 220 (235) Q Consensus 165 ~~~~~~~~~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~n 220 (235) ....+..-.||++|-++|+-+.+=..||++|.+ |.++=|-|+...-.|.++.+ T Consensus 233 G~slPs~lPLTKaEEriLKrvRRKIrNK~SAQE---SRrkKkeYid~LE~rv~~~t 285 (472) T KOG0709 233 GYSLPSKLPLTKAEERILKRVRRKIRNKRSAQE---SRRKKKEYIDGLESRVSAFT 285 (472) T ss_pred CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHCC T ss_conf 676722377508899999999999876566677---77767667888764221024 No 409 >COG2378 Predicted transcriptional regulator [Transcription] Probab=53.12 E-value=15 Score=16.02 Aligned_cols=10 Identities=20% Similarity=0.318 Sum_probs=3.7 Q ss_pred CCHHHHHHHH Q ss_conf 2599999999 Q gi|254780693|r 12 SSLQELSPRL 21 (235) Q Consensus 12 ~sl~dl~~~l 21 (235) .|..++...+ T Consensus 23 vta~~lA~~~ 32 (311) T COG2378 23 VTAAELADEF 32 (311) T ss_pred CHHHHHHHHH T ss_conf 4599999872 No 410 >pfam05331 DUF742 Protein of unknown function (DUF742). This family consists of several uncharacterized Streptomyces proteins as well as one from Mycobacterium tuberculosis. The function of these proteins is unknown. Probab=52.83 E-value=15 Score=15.98 Aligned_cols=44 Identities=25% Similarity=0.280 Sum_probs=37.2 Q ss_pred CCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHH Q ss_conf 44499899999999987999789999949998899999999999 Q gi|254780693|r 171 ARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATV 214 (235) Q Consensus 171 ~~~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~ 214 (235) ...|++=+..|+.+...-.|..|||..|++-...|+.-+..+.. T Consensus 38 ~~~l~pE~~~Il~lC~~p~SVAEiAA~L~LPl~VvrVLl~DL~~ 81 (114) T pfam05331 38 PPTLQPEHRRILRLCRAPLSVAEIAARLDLPVGVVRVLLSDLLD 81 (114) T ss_pred CCCCCHHHHHHHHHHCCCCCHHHHHHHHCCCCEEEEEEHHHHHH T ss_conf 88889799999999558520999997318984023015876875 No 411 >pfam06322 Phage_NinH Phage NinH protein. This family consists of several phage NinH proteins. The function of this family is unknown. Probab=52.77 E-value=9 Score=17.54 Aligned_cols=26 Identities=31% Similarity=0.368 Sum_probs=19.9 Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHH Q ss_conf 97899999499988999999999998 Q gi|254780693|r 190 TSEEIAEKLGLSVHTVNAYLGSATVK 215 (235) Q Consensus 190 t~~eIA~~L~iS~~TV~~hl~~i~~K 215 (235) -..|.|+.|++|..||+.|....-.| T Consensus 18 N~teVaR~L~c~R~TVrkY~~D~~~k 43 (64) T pfam06322 18 NQTEVARRLNCSRNTVRKYAEDKEGK 43 (64) T ss_pred CHHHHHHHHCCHHHHHHHHHCCCCCC T ss_conf 79999788511088899872355562 No 412 >PRK11062 nhaR transcriptional activator NhaR; Provisional Probab=52.73 E-value=15 Score=15.97 Aligned_cols=17 Identities=12% Similarity=0.522 Sum_probs=7.4 Q ss_pred HHHHHHHHHHHHHHCCC Q ss_conf 99999999999985837 Q gi|254780693|r 15 QELSPRLHLIQNRIKAR 31 (235) Q Consensus 15 ~dl~~~l~~l~~~~~~~ 31 (235) ..+...+..+.+.++.. T Consensus 33 ~~vS~qi~~LE~~lg~~ 49 (296) T PRK11062 33 QTITGQIKALEERLQGK 49 (296) T ss_pred HHHHHHHHHHHHHHCCC T ss_conf 79999999999995991 No 413 >COG1395 Predicted transcriptional regulator [Transcription] Probab=52.69 E-value=13 Score=16.36 Aligned_cols=28 Identities=29% Similarity=0.325 Sum_probs=21.4 Q ss_pred HHHCCCCHHHHHHHHCCCHHHHHHHHHH Q ss_conf 9987999789999949998899999999 Q gi|254780693|r 184 LAGDGYTSEEIAEKLGLSVHTVNAYLGS 211 (235) Q Consensus 184 l~a~G~t~~eIA~~L~iS~~TV~~hl~~ 211 (235) --.+|+|-.+.|..||+|.+||..|=+- T Consensus 134 Ree~glSlG~lA~~lgVSRktV~~YE~G 161 (313) T COG1395 134 REEMGLSLGDLATMLGVSRKTVYKYEKG 161 (313) T ss_pred HHHCCCCHHHHHHHHCCCHHHHHHHCCC T ss_conf 9980867878898838468889876247 No 414 >COG4197 Uncharacterized protein conserved in bacteria, prophage-related [Function unknown] Probab=52.50 E-value=13 Score=16.42 Aligned_cols=38 Identities=29% Similarity=0.374 Sum_probs=15.8 Q ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHH Q ss_conf 7899999499988999999999998079978999999997 Q gi|254780693|r 191 SEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIR 230 (235) Q Consensus 191 ~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~~ 230 (235) .+..|..||||+.+|+...+..++ .+..|.-+|.+|.. T Consensus 15 q~a~a~LLgvsp~~vnQw~~g~r~--~~a~r~~aIerAt~ 52 (96) T COG4197 15 QKALARLLGVSPPSVNQWIKGRRQ--VAAERALAIERATS 52 (96) T ss_pred HHHHHHHHCCCCHHHHHHHHHEEE--CCCCCCHHHHHHHC T ss_conf 899999972681478877652010--47553328999853 No 415 >PRK10402 DNA-binding transcriptional activator YeiL; Provisional Probab=52.23 E-value=15 Score=15.92 Aligned_cols=26 Identities=23% Similarity=0.151 Sum_probs=21.9 Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH Q ss_conf 99789999949998899999999999 Q gi|254780693|r 189 YTSEEIAEKLGLSVHTVNAYLGSATV 214 (235) Q Consensus 189 ~t~~eIA~~L~iS~~TV~~hl~~i~~ 214 (235) .+..|||..+|+|.+||...++...+ T Consensus 157 ~~~~elA~~lG~Sretl~R~L~~f~~ 182 (213) T PRK10402 157 EKHTQAAEYLGVSYRHLLYVLAQFCQ 182 (213) T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH T ss_conf 67999999979889999999999998 No 416 >COG1974 LexA SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms] Probab=51.10 E-value=16 Score=15.80 Aligned_cols=14 Identities=14% Similarity=0.304 Sum_probs=6.0 Q ss_pred CCHHHHHHHHHHHH Q ss_conf 25999999999999 Q gi|254780693|r 12 SSLQELSPRLHLIQ 25 (235) Q Consensus 12 ~sl~dl~~~l~~l~ 25 (235) .|-+.+..++..+. T Consensus 38 ~s~~~~~~~l~~L~ 51 (201) T COG1974 38 ASPSAIHSHLKALE 51 (201) T ss_pred CCHHHHHHHHHHHH T ss_conf 98489999999973 No 417 >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=50.93 E-value=16 Score=15.78 Aligned_cols=24 Identities=38% Similarity=0.472 Sum_probs=19.1 Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHH Q ss_conf 978999994999889999999999 Q gi|254780693|r 190 TSEEIAEKLGLSVHTVNAYLGSAT 213 (235) Q Consensus 190 t~~eIA~~L~iS~~TV~~hl~~i~ 213 (235) |-.++|..+++|..||+.-++... T Consensus 27 s~~~La~~~~vSr~tvr~Al~~L~ 50 (66) T cd07377 27 SERELAEELGVSRTTVREALRELE 50 (66) T ss_pred CHHHHHHHHCCCHHHHHHHHHHHH T ss_conf 799999997988899999999999 No 418 >pfam04233 Phage_Mu_F Phage Mu protein F like protein. Members of this family are found in double-stranded DNA bacteriophages, and in some bacteria. A member of this family is required for viral head morphogenesis in bacteriophage SPP1. This family is possibly a minor head protein. This family may be related to the family TT_ORF1 (pfam02956). Probab=50.02 E-value=16 Score=15.73 Aligned_cols=11 Identities=36% Similarity=0.434 Sum_probs=5.4 Q ss_pred CEEEEEEECCC Q ss_conf 35899721688 Q gi|254780693|r 116 AGIAFPVRLGF 126 (235) Q Consensus 116 ~~~~~pv~~~~ 126 (235) +|..|++..+. T Consensus 83 dGkv~~~dd~~ 93 (110) T pfam04233 83 DGKIFKVDDPF 93 (110) T ss_pred CCEEEECCCCC T ss_conf 89699678887 No 419 >PRK09391 fixK transcriptional regulator FixK; Provisional Probab=49.13 E-value=17 Score=15.59 Aligned_cols=27 Identities=30% Similarity=0.471 Sum_probs=23.4 Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHH Q ss_conf 997899999499988999999999998 Q gi|254780693|r 189 YTSEEIAEKLGLSVHTVNAYLGSATVK 215 (235) Q Consensus 189 ~t~~eIA~~L~iS~~TV~~hl~~i~~K 215 (235) .|-++||..+|+|+.||...++...++ T Consensus 174 lT~~dLA~~lG~trETVsR~L~~L~~e 200 (224) T PRK09391 174 MSRRDIADYLGLTIETVSRALSQLKDR 200 (224) T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHC T ss_conf 799999988799799999999999988 No 420 >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=49.08 E-value=17 Score=15.59 Aligned_cols=41 Identities=32% Similarity=0.261 Sum_probs=32.1 Q ss_pred CCCHHHHHHHHHHHC----------CCCHHHHHHHHCCCHHHHHHHHHHHH Q ss_conf 499899999999987----------99978999994999889999999999 Q gi|254780693|r 173 NLTERETSCLQLAGD----------GYTSEEIAEKLGLSVHTVNAYLGSAT 213 (235) Q Consensus 173 ~LT~RE~evL~l~a~----------G~t~~eIA~~L~iS~~TV~~hl~~i~ 213 (235) .||.||..|+..+.+ =-|+.+|+...|+++..|..-++... T Consensus 29 ~lt~rq~kv~~aV~RkTyG~nK~~d~I~~sqi~~mtgi~~~~Vs~a~~~Li 79 (100) T pfam04492 29 DLSGRQLKVLLAVIRKTYGWNKPMDRVTNEQIAELTGLSRTHVSEAKKSLV 79 (100) T ss_pred CCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHH T ss_conf 887889999999999860778503362299999997888545999999999 No 421 >PRK05932 RNA polymerase factor sigma-54; Reviewed Probab=48.33 E-value=14 Score=16.11 Aligned_cols=26 Identities=23% Similarity=0.268 Sum_probs=16.8 Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHH Q ss_conf 99978999994999889999999999 Q gi|254780693|r 188 GYTSEEIAEKLGLSVHTVNAYLGSAT 213 (235) Q Consensus 188 G~t~~eIA~~L~iS~~TV~~hl~~i~ 213 (235) -++-++||..||+++.||-.-+++=| T Consensus 349 PL~lkdiA~~lglheSTVSRav~~Ky 374 (461) T PRK05932 349 PLVLKDIAEALGMHESTISRATTNKY 374 (461) T ss_pred CCCHHHHHHHCCCCHHHHHHHHHCCE T ss_conf 76399999873998125889871661 No 422 >pfam01498 Transposase_5 Transposase. Transposase proteins are necessary for efficient DNA transposition. This family includes the amino-terminal region of Tc1, Tc1A, Tc1B and Tc2B transposases of C.elegans. The region encompasses the specific DNA binding and second DNA recognition domains as well as an amino-terminal region of the catalytic domain of Tc3 as described in. Tc3 is a member of the Tc1/mariner family of transposable elements. Probab=48.32 E-value=15 Score=15.91 Aligned_cols=23 Identities=26% Similarity=0.327 Sum_probs=15.6 Q ss_pred CCHHHHHHHH-----CCCHHHHHHHHHH Q ss_conf 9978999994-----9998899999999 Q gi|254780693|r 189 YTSEEIAEKL-----GLSVHTVNAYLGS 211 (235) Q Consensus 189 ~t~~eIA~~L-----~iS~~TV~~hl~~ 211 (235) .|..+|+.+| .||+.||+..+.+ T Consensus 14 ~T~~~i~~~l~~~g~~vS~~Tvrr~L~~ 41 (72) T pfam01498 14 ITLRDLANELQEIGKSVSRSTIRRRLHK 41 (72) T ss_pred CCHHHHHHHHHHCCCCCCHHHHHHHHHH T ss_conf 4699999999985997279999999998 No 423 >PRK11202 DNA-binding transcriptional repressor FabR; Provisional Probab=47.76 E-value=9.2 Score=17.47 Aligned_cols=18 Identities=11% Similarity=0.368 Sum_probs=7.5 Q ss_pred HHHHHHHHC-CCCEEEEEE Q ss_conf 999999858-378589984 Q gi|254780693|r 21 LHLIQNRIK-ARNFALYTI 38 (235) Q Consensus 21 l~~l~~~~~-~~~f~~~~~ 38 (235) +.+..+.+. -.+|.-.++ T Consensus 17 ldAAl~~l~~~~gf~~lsl 35 (203) T PRK11202 17 IDAAFSQLSAERSFSSLSL 35 (203) T ss_pred HHHHHHHHHCCCCCCCCCH T ss_conf 9999999860489330679 No 424 >COG1725 Predicted transcriptional regulators [Transcription] Probab=47.31 E-value=18 Score=15.40 Aligned_cols=15 Identities=27% Similarity=0.195 Sum_probs=6.0 Q ss_pred HHHHHHCCCCHHHHH Q ss_conf 999998799978999 Q gi|254780693|r 181 CLQLAGDGYTSEEIA 195 (235) Q Consensus 181 vL~l~a~G~t~~eIA 195 (235) |....+.|.+.+||= T Consensus 99 I~~~~~~G~s~eei~ 113 (125) T COG1725 99 IEEAKALGLSLEEIL 113 (125) T ss_pred HHHHHHCCCCHHHHH T ss_conf 999998699899999 No 425 >smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein. Probab=46.92 E-value=18 Score=15.36 Aligned_cols=28 Identities=29% Similarity=0.362 Sum_probs=19.0 Q ss_pred HHHHHHHHHHHCC-CCHHHHHHHHCCCHH Q ss_conf 8999999999879-997899999499988 Q gi|254780693|r 176 ERETSCLQLAGDG-YTSEEIAEKLGLSVH 203 (235) Q Consensus 176 ~RE~evL~l~a~G-~t~~eIA~~L~iS~~ 203 (235) -|=..+..++..+ .+..+||..+|.+-. T Consensus 37 ~Rl~~a~~~L~~~~~~i~~ia~~~Gy~~~ 65 (84) T smart00342 37 RRLERARRLLRDTDLSVTEIALRVGFSSQ 65 (84) T ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCCCH T ss_conf 99999999998576349999888199999 No 426 >pfam07022 Phage_CI_repr Bacteriophage CI repressor helix-turn-helix domain. This family consists of several phage CI repressor proteins and related bacterial sequences. The CI repressor is known to function as a transcriptional switch, determining whether transcription is lytic or lysogenic. Probab=46.74 E-value=18 Score=15.34 Aligned_cols=22 Identities=27% Similarity=0.501 Sum_probs=17.4 Q ss_pred CCHHHHHHHHCCCHHHHHHHHH Q ss_conf 9978999994999889999999 Q gi|254780693|r 189 YTSEEIAEKLGLSVHTVNAYLG 210 (235) Q Consensus 189 ~t~~eIA~~L~iS~~TV~~hl~ 210 (235) +|..|-|..||||..||..-.+ T Consensus 13 ~t~~eLA~~LgI~~stis~w~~ 34 (65) T pfam07022 13 KSRSELADHLGVSKSTLSTWYK 34 (65) T ss_pred CCHHHHHHHHCCCHHHHHHHHH T ss_conf 8699999996988888999998 No 427 >pfam07037 DUF1323 Putative transcription regulator (DUF1323). This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length. This family appears to have an HTH domain and is therefore likely to act as a transcriptional regulator. Probab=45.68 E-value=19 Score=15.23 Aligned_cols=16 Identities=31% Similarity=0.472 Sum_probs=8.0 Q ss_pred CCCHHHHHHH--HHHHCC Q ss_conf 4998999999--999879 Q gi|254780693|r 173 NLTERETSCL--QLAGDG 188 (235) Q Consensus 173 ~LT~RE~evL--~l~a~G 188 (235) .||+-|++=| -++.+| T Consensus 92 ~mT~~Eqekl~~lLlREG 109 (122) T pfam07037 92 EMTPSEQKQLTSLLSREG 109 (122) T ss_pred HCCHHHHHHHHHHHHHHH T ss_conf 839999999999999982 No 428 >KOG2252 consensus Probab=44.59 E-value=20 Score=15.12 Aligned_cols=43 Identities=23% Similarity=0.260 Sum_probs=35.9 Q ss_pred CCCHHHHHHHHHHHCCC------CHHHHHHHHCCCHHHHHHHHHHHHHH Q ss_conf 49989999999998799------97899999499988999999999998 Q gi|254780693|r 173 NLTERETSCLQLAGDGY------TSEEIAEKLGLSVHTVNAYLGSATVK 215 (235) Q Consensus 173 ~LT~RE~evL~l~a~G~------t~~eIA~~L~iS~~TV~~hl~~i~~K 215 (235) -||+-|++-|+-+=+-- .-..|+..|++...||-+..-|++++ T Consensus 426 VfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRR 474 (558) T KOG2252 426 VFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRR 474 (558) T ss_pred EECHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHH T ss_conf 6458899999999861789879999999998587688899987766651 No 429 >TIGR01817 nifA Nif-specific regulatory protein; InterPro: IPR010113 This entry represents NifA, a DNA-binding regulatory protein for nitrogen fixation. Not included in this group are: the homologue in Aquifex aeolicus (which lacks nitrogenase), transcriptional activators of alternative nitrogenases (VFe or FeFe instead of MoFe), and truncated forms. In diazotrophic proteobacteria, the sigma54-dependent activator NifA activates transcription of the nif (nitrogen fixation) genes by a conserved mechanism common to members of the enhancer binding protein family. Although NifA proteins have similar domain structures, both transcriptional regulation of nifA expression and posttranslational regulation of NifA activity by oxygen and fixed nitrogen vary significantly from one organism to another. In Klebsiella pneumoniae and Azotobacter vinelandii, nifA is co-ordinately transcribed with a second gene, nifL, whose product inhibits NifA activity in response to oxygen and fixed nitrogen .; GO: 0003677 DNA binding, 0016563 transcription activator activity, 0009399 nitrogen fixation. Probab=44.52 E-value=20 Score=15.11 Aligned_cols=37 Identities=32% Similarity=0.416 Sum_probs=17.2 Q ss_pred CCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH Q ss_conf 4998999999999879997899999499988999999 Q gi|254780693|r 173 NLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYL 209 (235) Q Consensus 173 ~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl 209 (235) .|++||+=|-.|=--|=--.=-|+.||+|||=|-|-| T Consensus 528 ~l~eRERli~AlE~aGWVQAKAARlLg~TPRQVgYal 564 (574) T TIGR01817 528 TLSERERLIAALEKAGWVQAKAARLLGLTPRQVGYAL 564 (574) T ss_pred CCCCHHHHHHHHHHCCHHHHHHHHHHCCCHHHHHHHH T ss_conf 7231789999997515379999997378655899999 No 430 >PRK13918 CRP/FNR family transcriptional regulator; Provisional Probab=43.81 E-value=20 Score=15.04 Aligned_cols=26 Identities=27% Similarity=0.344 Sum_probs=23.3 Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH Q ss_conf 99789999949998899999999999 Q gi|254780693|r 189 YTSEEIAEKLGLSVHTVNAYLGSATV 214 (235) Q Consensus 189 ~t~~eIA~~L~iS~~TV~~hl~~i~~ 214 (235) .|.+|||..+|.|.-||...++...+ T Consensus 146 lT~~eLA~~iGttREtVsR~L~~l~~ 171 (201) T PRK13918 146 ATHDELAAAVGSVRETVTKVVGELSR 171 (201) T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH T ss_conf 79999998859868999999999998 No 431 >TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family; InterPro: IPR014289 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 part of the larger sigma-70 family. From homology, tree building, bidirectional best hits and their one-to-a-genome distribution, they appear to represent a conserved family.. Probab=43.58 E-value=20 Score=15.01 Aligned_cols=37 Identities=32% Similarity=0.448 Sum_probs=31.7 Q ss_pred CCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 99899999999987999789999949998899999999999807 Q gi|254780693|r 174 LTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 174 LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) ++=||. -|+...||=..|+||...+..-+-+++.+|- T Consensus 146 F~MRE~-------L~~~~~eIC~~l~is~~N~~VlLyRAR~~LR 182 (194) T TIGR02943 146 FMMREV-------LGFESEEICQELEISASNCHVLLYRARLSLR 182 (194) T ss_pred HHHHHH-------HCCCHHHHHHHCCCHHHHHHHHHHHHHHHHH T ss_conf 555654-------2486688753003137679999999999999 No 432 >pfam11740 KfrA_N Plasmid replication region DNA-binding N-term. The broad host-range plasmid RK2 is able to replicate in and be inherited in a stable manner in diverse Gram-negative bacterial species. It encodes a number of co-ordinately regulated operons including a central control korF1 operon that represses the kfrA operon. The KfrA polypeptide is a site-specific DNA-binding protein whose operator overlaps the kfrA promoter. The N-terminus, containing an helix-turn-helix motif, is essential for function. Downstream from this family is an extended coiled-coil domain containing a heptad repeat segment which is probably responsible for formation of multimers, and may provide an example of a bridge to host structures required for plasmid partitioning. Probab=43.08 E-value=21 Score=14.96 Aligned_cols=37 Identities=30% Similarity=0.340 Sum_probs=18.8 Q ss_pred HHHHCCC--CHHHHHHHHC-CCHHHHHHHHHHHHHHCCCC Q ss_conf 9998799--9789999949-99889999999999980799 Q gi|254780693|r 183 QLAGDGY--TSEEIAEKLG-LSVHTVNAYLGSATVKLDAV 219 (235) Q Consensus 183 ~l~a~G~--t~~eIA~~L~-iS~~TV~~hl~~i~~KLg~~ 219 (235) .+++.|. |...|=..|| =|..||..|++.-....+.. T Consensus 12 ~L~~~G~~PTv~~VR~~lG~GS~stI~~~L~~w~~~~~~~ 51 (120) T pfam11740 12 ALLAAGERPTVDAVREELGTGSPTTISKYLKEWREEQRAA 51 (120) T ss_pred HHHHCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHC T ss_conf 9987489995999999977978888999999999986501 No 433 >pfam12116 SpoIIID Stage III sporulation protein D. This stage III sporulation protein is a small DNA-binding family that is essential for gene expression of the mother-cell compartment during sporulation. The domain is found in bacteria and viruses, and is about 40 amino acids in length. It has a conserved RGG sequence motif. Probab=42.95 E-value=21 Score=14.95 Aligned_cols=42 Identities=21% Similarity=0.181 Sum_probs=32.3 Q ss_pred HHHHHHHHHHHC-CCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 899999999987-999789999949998899999999999807 Q gi|254780693|r 176 ERETSCLQLAGD-GYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 176 ~RE~evL~l~a~-G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) .|-.++...+.+ ..|.++.|...|||..||..-+..-..+++ T Consensus 6 eR~~~i~~YIi~~~aTVR~tAk~FGvSKSTVHkDvTeRL~~in 48 (82) T pfam12116 6 ERVLEIANYIIENKATVRQAAKVFGVSKSTVHKDVTERLPKIN 48 (82) T ss_pred HHHHHHHHHHHHCCHHHHHHHHHHCCCHHHHHHHHHHHHHHCC T ss_conf 9999999999962628999999969609889887999998739 No 434 >KOG0843 consensus Probab=42.95 E-value=18 Score=15.31 Aligned_cols=45 Identities=22% Similarity=0.271 Sum_probs=36.2 Q ss_pred CCCCHHHHHHHHHHHC------CCCHHHHHHHHCCCHHHHHHHHHHHHHHC Q ss_conf 4499899999999987------99978999994999889999999999980 Q gi|254780693|r 172 RNLTERETSCLQLAGD------GYTSEEIAEKLGLSVHTVNAYLGSATVKL 216 (235) Q Consensus 172 ~~LT~RE~evL~l~a~------G~t~~eIA~~L~iS~~TV~~hl~~i~~KL 216 (235) ..+|+-+..-|...=+ |..-++.|..|++|+.-|+.-.+|-+.|. T Consensus 107 T~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~ 157 (197) T KOG0843 107 TAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKH 157 (197) T ss_pred CCCCHHHHHHHHHHHHCCCEEECHHHHHHHHHCCCCHHHHHHHHHHHHHHH T ss_conf 235899999999998408735236899999972987568123433003788 No 435 >PRK13832 plasmid partitioning protein; Provisional Probab=42.83 E-value=21 Score=14.93 Aligned_cols=30 Identities=30% Similarity=0.402 Sum_probs=17.5 Q ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHHH Q ss_conf 999999987999789999949998899999 Q gi|254780693|r 179 TSCLQLAGDGYTSEEIAEKLGLSVHTVNAY 208 (235) Q Consensus 179 ~evL~l~a~G~t~~eIA~~L~iS~~TV~~h 208 (235) +-|-++++.|.|.++|+.-|.++++-|+.. T Consensus 109 RaierlvalGwTeeaIa~ALal~vrqiRkL 138 (518) T PRK13832 109 RAIERLVALGWTEEAIAVALALPVRQIRKL 138 (518) T ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHHH T ss_conf 999999984998899999966899999999 No 436 >PTZ00100 DnaJ chaperone protein; Provisional Probab=42.22 E-value=18 Score=15.46 Aligned_cols=31 Identities=10% Similarity=0.080 Sum_probs=20.6 Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHCCC Q ss_conf 9997899999499988999999999998079 Q gi|254780693|r 188 GYTSEEIAEKLGLSVHTVNAYLGSATVKLDA 218 (235) Q Consensus 188 G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~ 218 (235) -+|-+|-..+||+++..-+.-++.+++||=. T Consensus 59 ~Mt~~EA~~ILGl~~~as~~~I~~ahrkLM~ 89 (114) T PTZ00100 59 KMSKSEACKILNIPPTANKERIREVHKQLML 89 (114) T ss_pred CCCHHHHHHHHCCCCCCCHHHHHHHHHHHHH T ss_conf 8599999998199999999999999999999 No 437 >TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator); InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulphovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis strain PCC 6803 hypothetical protein slr0846. These are small proteins of 12 to 18 kD which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.. Probab=41.82 E-value=22 Score=14.83 Aligned_cols=41 Identities=22% Similarity=0.043 Sum_probs=19.1 Q ss_pred CCEEECCHHHHCCCCCHHHHHHHHHHHCCCCCEEEEEEECCCCC Q ss_conf 98373101331466721367899654258553589972168875 Q gi|254780693|r 85 LPIIWQSIQEETVIESSGQLSVRLEGGLLPFAGIAFPVRLGFHK 128 (235) Q Consensus 85 ~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~pv~~~~~~ 128 (235) .|+-..++.+...... .|... --....++|++-+++++.|| T Consensus 24 ~~v~~~~ia~~~~Is~--~yL~K-~l~~L~~~GlV~S~rG~~GG 64 (133) T TIGR00738 24 GPVSVKEIAERQGISR--SYLEK-VLRTLRKAGLVESVRGPGGG 64 (133) T ss_pred CCCCHHHHHHHHCCCH--HHHHH-HHHHHHHCCCEECCCCCCCC T ss_conf 7607899998848998--79999-99988770764211589856 No 438 >pfam07453 NUMOD1 NUMOD1 domain. This domain probably represents a DNA-binding helix-turn-helix based on its similarity to other families (Bateman A pers obs). Probab=41.72 E-value=13 Score=16.48 Aligned_cols=21 Identities=43% Similarity=0.597 Sum_probs=17.4 Q ss_pred CCHHHHHHHHCCCHHHHHHHH Q ss_conf 997899999499988999999 Q gi|254780693|r 189 YTSEEIAEKLGLSVHTVNAYL 209 (235) Q Consensus 189 ~t~~eIA~~L~iS~~TV~~hl 209 (235) .|..|.|+.|++|.+|++.|+ T Consensus 17 ~Si~~aa~~L~i~~~tI~~~~ 37 (37) T pfam07453 17 SSIREAARALGISHSTINKYL 37 (37) T ss_pred HHHHHHHHHHCCCHHHHHCCC T ss_conf 679999998476465665029 No 439 >PRK05782 precorrin-8X methylmutase; Validated Probab=41.60 E-value=19 Score=15.17 Aligned_cols=59 Identities=20% Similarity=0.219 Sum_probs=50.4 Q ss_pred CCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHH Q ss_conf 44998999999999879997899999499988999999999998079978999999997 Q gi|254780693|r 172 RNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIR 230 (235) Q Consensus 172 ~~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~~ 230 (235) ....++|++|++-+-.---+-|++..|..|+..|+.=++.+.+.-.+-.-++.|.-.+. T Consensus 161 ~~~~~~e~~Vv~R~IHaTgDfe~a~~l~fs~~Av~aGi~AL~~G~~IvtDv~Mv~aGI~ 219 (332) T PRK05782 161 SNWRDREKEIIARAVYASGNLELAKYVYISNDLLDAGIEALKAGIPIVADVKMVAAGIR 219 (332) T ss_pred CCCCHHHHHHHHHHEECCCCCCHHHHEEECHHHHHHHHHHHHCCCCEEECHHHHHHHCC T ss_conf 47994550037764122667212853678905999999999869999982589985377 No 440 >KOG0487 consensus Probab=41.43 E-value=9.5 Score=17.38 Aligned_cols=50 Identities=22% Similarity=0.221 Sum_probs=34.9 Q ss_pred CCHHHHHHHH--HHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHH Q ss_conf 9989999999--99879997899999499988999999999998079978999 Q gi|254780693|r 174 LTERETSCLQ--LAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQA 224 (235) Q Consensus 174 LT~RE~evL~--l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qa 224 (235) +-+-|+|.|- .|-. ..-+||++.|++|+|-|+.-.+|=+-|+.--||-+. T Consensus 247 tlELEkEFlfN~Yitk-eKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~r 298 (308) T KOG0487 247 TLELEKEFLFNMYITK-EKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRENR 298 (308) T ss_pred HHHHHHHHHHHHHHHH-HHHHHHHHHCCCCHHHEEEEEEHHHHHHHHHHHHHH T ss_conf 9999999999877728-899999986275123213211010567665407664 No 441 >PRK12469 RNA polymerase factor sigma-54; Provisional Probab=40.99 E-value=17 Score=15.50 Aligned_cols=40 Identities=25% Similarity=0.340 Sum_probs=24.9 Q ss_pred CCHHHHHHHHH---HHCCCCHHHHHHHHCCCHHHHHHHHHHHH Q ss_conf 99899999999---98799978999994999889999999999 Q gi|254780693|r 174 LTERETSCLQL---AGDGYTSEEIAEKLGLSVHTVNAYLGSAT 213 (235) Q Consensus 174 LT~RE~evL~l---~a~G~t~~eIA~~L~iS~~TV~~hl~~i~ 213 (235) +=.++.+.+.. --.-++-++||..||+++.||-.-+++=| T Consensus 346 Iv~~Q~~Ff~~G~~~lkPL~lkdiA~~lglheSTVSRav~~Ky 388 (475) T PRK12469 346 IVARQRDFFRYGEIALKPLVLRDVAEELGLHESTVSRATGNKY 388 (475) T ss_pred HHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCCCHHHHHHCCCE T ss_conf 9999999984785003673499999981998203768862750 No 442 >PRK08561 rps15p 30S ribosomal protein S15P; Reviewed Probab=40.87 E-value=20 Score=15.12 Aligned_cols=16 Identities=6% Similarity=0.017 Sum_probs=6.8 Q ss_pred HHHHHHHHHHHHHHHH Q ss_conf 8999999999999999 Q gi|254780693|r 143 NEVIIEAHGACYQVIT 158 (235) Q Consensus 143 ~~~~~~~~~~~~~~~~ 158 (235) +++++.+...+..+.. T Consensus 85 PEDL~~LikkAv~lrk 100 (151) T PRK08561 85 PEDLMNLIKKAVNLRK 100 (151) T ss_pred CHHHHHHHHHHHHHHH T ss_conf 6799999999999999 No 443 >pfam02082 Rrf2 Transcriptional regulator. This family is related to pfam001022 and other transcription regulation families (personal obs: Yeats C). Probab=40.73 E-value=22 Score=14.71 Aligned_cols=25 Identities=36% Similarity=0.345 Sum_probs=17.5 Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH Q ss_conf 9978999994999889999999999 Q gi|254780693|r 189 YTSEEIAEKLGLSVHTVNAYLGSAT 213 (235) Q Consensus 189 ~t~~eIA~~L~iS~~TV~~hl~~i~ 213 (235) .|.++||..+++++..++.-++... T Consensus 25 ~s~~~iA~~~~i~~~~l~kil~~L~ 49 (82) T pfam02082 25 VTSEEIAERQNISPVYLRKILAKLR 49 (82) T ss_pred ECHHHHHHHHCCCHHHHHHHHHHHH T ss_conf 9599999878909999999999810 No 444 >KOG1597 consensus Probab=40.46 E-value=23 Score=14.69 Aligned_cols=35 Identities=23% Similarity=0.203 Sum_probs=25.1 Q ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHC Q ss_conf 99998799978999994999889999999999980 Q gi|254780693|r 182 LQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKL 216 (235) Q Consensus 182 L~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL 216 (235) .++-.+-+|-+||....|+++.|++.-.+-+|..+ T Consensus 254 sqls~~kkt~keI~~vtgVaE~TIr~sYK~Lyp~~ 288 (308) T KOG1597 254 SQLSDEKKTQKEIGEVTGVAEVTIRNSYKDLYPHA 288 (308) T ss_pred HHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCH T ss_conf 98504765488898885344888998899873046 No 445 >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=40.41 E-value=23 Score=14.68 Aligned_cols=25 Identities=16% Similarity=0.294 Sum_probs=21.2 Q ss_pred HHHCCCCHHHHHHHHCCCHHHHHHH Q ss_conf 9987999789999949998899999 Q gi|254780693|r 184 LAGDGYTSEEIAEKLGLSVHTVNAY 208 (235) Q Consensus 184 l~a~G~t~~eIA~~L~iS~~TV~~h 208 (235) --+.|.|-.+.|...|+|.++|..- T Consensus 11 Rk~~glTQ~~LA~~aGvs~~~Is~i 35 (58) T TIGR03070 11 RKALGLTQADLADLAGVGLRFIRDI 35 (58) T ss_pred HHHCCCCHHHHHHHHCCCHHHHHHH T ss_conf 9994998999998819989999999 No 446 >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=40.08 E-value=22 Score=14.74 Aligned_cols=19 Identities=21% Similarity=0.489 Sum_probs=16.6 Q ss_pred CHHHHHHHHCCCHHHHHHH Q ss_conf 9789999949998899999 Q gi|254780693|r 190 TSEEIAEKLGLSVHTVNAY 208 (235) Q Consensus 190 t~~eIA~~L~iS~~TV~~h 208 (235) +++|+|..+||++.+|+.- T Consensus 29 SS~eLa~~~gv~~aqiRKD 47 (49) T pfam06971 29 SSKELSEAIGIDAAQIRKD 47 (49) T ss_pred CHHHHHHHHCCCHHHHHCC T ss_conf 7999999979399996142 No 447 >PRK10870 transcriptional repressor MprA; Provisional Probab=39.53 E-value=23 Score=14.59 Aligned_cols=12 Identities=25% Similarity=0.288 Sum_probs=5.4 Q ss_pred CCHHHHHHHHHH Q ss_conf 998999999999 Q gi|254780693|r 174 LTERETSCLQLA 185 (235) Q Consensus 174 LT~RE~evL~l~ 185 (235) ||+-|++.|.-+ T Consensus 143 Ls~eE~~qL~~L 154 (176) T PRK10870 143 LSTTEKDQLEQI 154 (176) T ss_pred CCHHHHHHHHHH T ss_conf 999999999999 No 448 >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=39.48 E-value=23 Score=14.58 Aligned_cols=43 Identities=19% Similarity=0.194 Sum_probs=36.3 Q ss_pred CCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHC Q ss_conf 49989999999998799978999994999889999999999980 Q gi|254780693|r 173 NLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKL 216 (235) Q Consensus 173 ~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL 216 (235) ..+.|..+|-.=- .|..-.|.|.+=++|+++|..-++++++-. T Consensus 57 ~~~~Rd~~I~~eF-nG~N~~eLArkY~ls~~~i~~ii~~~rk~~ 99 (107) T pfam08765 57 RLALRDLEIYNEF-NGNNHAELARKYGVSEQWIYKIIKRVRKLE 99 (107) T ss_pred HHHHHHHHHHHHH-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHH T ss_conf 8999999999980-798799999996988999999999999999 No 449 >pfam04936 DUF658 Protein of unknown function (DUF658). Protein of unknown function found in Lactococcus lactis bacteriophages. Probab=39.46 E-value=23 Score=14.66 Aligned_cols=44 Identities=16% Similarity=0.032 Sum_probs=19.8 Q ss_pred HHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHH Q ss_conf 9987999789999949998899999999999807997899999999 Q gi|254780693|r 184 LAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAI 229 (235) Q Consensus 184 l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~ 229 (235) |.-.|.|..+|+.++ .++--+.|-+.--++|--.-|+|.+.-+. T Consensus 84 ~fim~GtareIS~e~--k~k~rrkhetkeerrlrrniraqmaie~~ 127 (134) T pfam04936 84 EFIMGGSAREISDEI--KDKDRRKHETKEERRLRRNIRAQMAIEAA 127 (134) T ss_pred CCCCCCCHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 413466266665888--88887512038899999988999988852 No 450 >KOG0484 consensus Probab=39.44 E-value=23 Score=14.58 Aligned_cols=40 Identities=30% Similarity=0.365 Sum_probs=30.9 Q ss_pred HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHH Q ss_conf 8799978999994999889999999999980799789999 Q gi|254780693|r 186 GDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAI 225 (235) Q Consensus 186 a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qav 225 (235) -+=+|-+|||..+.+++.-|....+|-+.|+----|...+ T Consensus 42 PDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a~~ 81 (125) T KOG0484 42 PDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAAIA 81 (125) T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 7403189998862056889999998668888888999998 No 451 >PRK10856 hypothetical protein; Provisional Probab=39.39 E-value=23 Score=14.57 Aligned_cols=52 Identities=13% Similarity=0.008 Sum_probs=29.1 Q ss_pred CHHHHHHHHH---HHHHHHCCCCEEEEEECCCCCCCCCCCEEEECCCCCHHHHHHHHHHHHHCCCHHHHHH Q ss_conf 5999999999---9999858378589984177787310250442278778999624874441208799999 Q gi|254780693|r 13 SLQELSPRLH---LIQNRIKARNFALYTINSALDFPRRQQLICELHNYDLDSGDIPNILIETYGDDFLFHF 80 (235) Q Consensus 13 sl~dl~~~l~---~l~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dp~~~~~ 80 (235) |++|+..+|+ ...+.++.+.|..+ ....|...++..|..+.....++++... T Consensus 29 Si~dvA~~LkL~~~~ieALE~dd~~~L----------------p~~tF~RGylRsYAr~LglD~~~ll~~~ 83 (332) T PRK10856 29 SQQAVAERLCLKVSTVRDIEEDKAPAD----------------LASTFLRGYIRSYARLVHIPEEELLPGL 83 (332) T ss_pred CHHHHHHHHCCCHHHHHHHHCCCHHCC----------------CCHHHHHHHHHHHHHHHCCCHHHHHHHH T ss_conf 999999870898999999857822108----------------7036479999999999788979965421 No 452 >TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain; InterPro: IPR006497 This set of protein sequences, defined by an N-terminal domain, represent phage lambda replication protein O and other homologous phage and prophage proteins. ; GO: 0006260 DNA replication. Probab=39.08 E-value=24 Score=14.54 Aligned_cols=45 Identities=29% Similarity=0.260 Sum_probs=34.1 Q ss_pred CCCCCHHHHHHHHHHHC---C-------CCHHHHHHHHC-------CCHHHHHHHHHHHHHH Q ss_conf 44499899999999987---9-------99789999949-------9988999999999998 Q gi|254780693|r 171 ARNLTERETSCLQLAGD---G-------YTSEEIAEKLG-------LSVHTVNAYLGSATVK 215 (235) Q Consensus 171 ~~~LT~RE~evL~l~a~---G-------~t~~eIA~~L~-------iS~~TV~~hl~~i~~K 215 (235) ...||.||.+|+.-|.. | -|+.+||...+ ++...|..-+.++.++ T Consensus 20 ~~~L~~Ref~v~~Ai~R~T~Gyn~~~~rvt~~~ia~lt~Pdeakaal~~~~vs~A~~~L~~~ 81 (104) T TIGR01610 20 GADLSGREFRVLLAILRLTYGYNKEADRVTASEIAELTKPDEAKAALERKRVSEAIKSLVRR 81 (104) T ss_pred CCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCHHHHHHCCHHHHHHHHHHHHHH T ss_conf 48784357999999998741566603566688888532831355521344788999998875 No 453 >TIGR02154 PhoB phosphate regulon transcriptional regulatory protein PhoB; InterPro: IPR011879 PhoB is a DNA-binding response regulator protein acting with PhoR in a 2-component system responding to phosphate ion. PhoB acts as a positive regulator of gene expression for phosphate-related genes such as phoA, phoS, phoE and ugpAB as well as itself . It is often found proximal to genes for the high-affinity phosphate ABC transporter (pstSCAB; GenProp0190) and presumably regulates these as well.; GO: 0000156 two-component response regulator activity, 0003677 DNA binding, 0000160 two-component signal transduction system (phosphorelay), 0006817 phosphate transport. Probab=38.43 E-value=2.9 Score=21.10 Aligned_cols=52 Identities=12% Similarity=0.015 Sum_probs=36.7 Q ss_pred CCCHHHHHHHHHHHC---------CCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHH Q ss_conf 499899999999987---------9997899999499988999999999998079978999 Q gi|254780693|r 173 NLTERETSCLQLAGD---------GYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQA 224 (235) Q Consensus 173 ~LT~RE~evL~l~a~---------G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qa 224 (235) .|+|-|-.-|...=+ =+=|.-=+....|=+|||..|+++.+|.|+....... T Consensus 154 ~lGPTEfRLL~FFM~HPeRV~SReQLLD~VWG~dvyVE~RTVDVHIRRLRKaL~~~g~~~~ 214 (226) T TIGR02154 154 ELGPTEFRLLHFFMTHPERVYSREQLLDRVWGRDVYVEERTVDVHIRRLRKALEPGGLEDL 214 (226) T ss_pred CCCCHHHHHHHHHHHCCCCEEEHHHHHHHHCCCCEEEECCCEEEEECCHHHHCCCCCCCCC T ss_conf 4687047889998623773440423201105894325135000322000542387888871 No 454 >PTZ00072 40S ribosomal protein S13; Provisional Probab=38.06 E-value=19 Score=15.18 Aligned_cols=19 Identities=11% Similarity=-0.066 Sum_probs=9.4 Q ss_pred CHHHHHHHHHHHHHHHHHH Q ss_conf 9899999999999999999 Q gi|254780693|r 142 ANEVIIEAHGACYQVITDF 160 (235) Q Consensus 142 ~~~~~~~~~~~~~~~~~~~ 160 (235) -++++..+...+..+..++ T Consensus 81 iPEDL~~LikKAv~irkHL 99 (148) T PTZ00072 81 IPEDLYFLIKKAVQMRKHL 99 (148) T ss_pred CCHHHHHHHHHHHHHHHHH T ss_conf 9589999999999999999 No 455 >pfam10252 PP28 Casein kinase substrate phosphoprotein PP28. This domain is a region of 70 residues conserved in proteins from plants to humans and contains a serine/arginine rich motif. In rats the full protein is a casein kinase substrate, and this region contains phosphorylation sites for both cAMP-dependent protein kinase and casein kinase II. Probab=37.80 E-value=25 Score=14.41 Aligned_cols=28 Identities=25% Similarity=0.392 Sum_probs=22.2 Q ss_pred CCCCCCHHHHH----------HHHHHHCCCCHHHHHHH Q ss_conf 74449989999----------99999879997899999 Q gi|254780693|r 170 AARNLTERETS----------CLQLAGDGYTSEEIAEK 197 (235) Q Consensus 170 ~~~~LT~RE~e----------vL~l~a~G~t~~eIA~~ 197 (235) ....||.||+| ..+|-++|+|...-|.. T Consensus 21 ~~~eLSRREREeiekQ~a~~rY~KLh~~GKT~eAraDL 58 (82) T pfam10252 21 DPVELSRREREEIEKQKARERYMKLHAEGKTEQARADL 58 (82) T ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHH T ss_conf 75321578899999889999999999825808899889 No 456 >PRK11608 pspF phage shock protein operon transcriptional activator; Provisional Probab=37.55 E-value=25 Score=14.38 Aligned_cols=36 Identities=33% Similarity=0.473 Sum_probs=27.1 Q ss_pred HHHHHHHH--HHHCCCCHHHHHHHHCCCHHHHHHHHHH Q ss_conf 89999999--9987999789999949998899999999 Q gi|254780693|r 176 ERETSCLQ--LAGDGYTSEEIAEKLGLSVHTVNAYLGS 211 (235) Q Consensus 176 ~RE~evL~--l~a~G~t~~eIA~~L~iS~~TV~~hl~~ 211 (235) .-|++++. |-..|..-...|..||||.+|....+++ T Consensus 285 ~~Ek~~I~~aL~~~~gn~~~aA~~LGIsR~tL~~klkk 322 (325) T PRK11608 285 QQEKELLQRSLQQAKFNQKRAAELLGLTYHQFRALLKK 322 (325) T ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHH T ss_conf 99999999999993998999999988899999999997 No 457 >PRK04158 transcriptional repressor CodY; Validated Probab=36.17 E-value=26 Score=14.23 Aligned_cols=101 Identities=17% Similarity=0.178 Sum_probs=64.9 Q ss_pred CEEEEEEECCCCCCEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCC---------CC--CCCCCCCHHHHHHHHH Q ss_conf 358997216887523454105887899899999999999999999851246---------78--8744499899999999 Q gi|254780693|r 116 AGIAFPVRLGFHKNGYVIFTSEFLMLANEVIIEAHGACYQVITDFLELFKK---------RS--SAARNLTERETSCLQL 184 (235) Q Consensus 116 ~~~~~pv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---------~~--~~~~~LT~RE~evL~l 184 (235) ....+|+..+..+.|.+.+...+.....+++......+.-+....++.... .. -+...||=-|.|.... T Consensus 111 ~ttIvPI~g~GeRLGTLil~r~~~~F~ddDLILaEy~ATVVGmEiLr~~~e~iEeeaRkka~VqmAi~tLSYSEleAv~h 190 (256) T PRK04158 111 LTTIVPIVGGGERLGTLILARNDKEFTDDDLILAEYSATVVGMEILREKAEEIEEEARKKAAVQMAINTLSYSELEAVEH 190 (256) T ss_pred CEEEEEEECCCCEEEEEEEEECCCCCCCCCEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHH T ss_conf 38999552277335899999637998866351112567999999999989988999999999999998637878999999 Q ss_pred HHCCC-------CHHHHHHHHCCCHHHHHHHHHHHHHHCCCCC Q ss_conf 98799-------9789999949998899999999999807997 Q gi|254780693|r 185 AGDGY-------TSEEIAEKLGLSVHTVNAYLGSATVKLDAVN 220 (235) Q Consensus 185 ~a~G~-------t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~n 220 (235) +-+-+ ...-||.+-||+.. -+-|+.|||.... T Consensus 191 If~EL~G~EGlLVASkIADrvGITRS----VIVNALRKlESAG 229 (256) T PRK04158 191 IFEELDGNEGLLVASKIADRVGITRS----VIVNALRKLESAG 229 (256) T ss_pred HHHHCCCCCCEEEEHHHHHHHCCCHH----HHHHHHHHHHHCC T ss_conf 99962897552754333443087156----7787777653146 No 458 >COG3284 AcoR Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription] Probab=35.24 E-value=27 Score=14.13 Aligned_cols=36 Identities=25% Similarity=0.199 Sum_probs=28.0 Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH Q ss_conf 899999999987999789999949998899999999 Q gi|254780693|r 176 ERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGS 211 (235) Q Consensus 176 ~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~ 211 (235) .++.=+..+-+.+--..+.|+.||||..|+..-+++ T Consensus 566 ~~~~l~~al~~~~~~is~aa~~lgi~R~T~yrklk~ 601 (606) T COG3284 566 EKAALLAALQATNGNISEAARLLGISRSTLYRKLKR 601 (606) T ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH T ss_conf 799999999980897999999859978889999997 No 459 >PRK13626 transcriptional regulator SgrR; Provisional Probab=35.21 E-value=27 Score=14.13 Aligned_cols=15 Identities=13% Similarity=0.251 Sum_probs=8.1 Q ss_pred CHHHHHHHHHHHHHH Q ss_conf 599999999999998 Q gi|254780693|r 13 SLQELSPRLHLIQNR 27 (235) Q Consensus 13 sl~dl~~~l~~l~~~ 27 (235) +.+|+...|..+... T Consensus 197 ta~dV~~sl~rl~~~ 211 (551) T PRK13626 197 EMDDVIASLTRINTL 211 (551) T ss_pred CHHHHHHHHHHHHCC T ss_conf 799999999987326 No 460 >COG4533 ABC-type uncharacterized transport system, periplasmic component [General function prediction only] Probab=35.15 E-value=27 Score=14.12 Aligned_cols=14 Identities=7% Similarity=0.036 Sum_probs=6.1 Q ss_pred HHHHHHHHHHHHHH Q ss_conf 99999999999998 Q gi|254780693|r 14 LQELSPRLHLIQNR 27 (235) Q Consensus 14 l~dl~~~l~~l~~~ 27 (235) .+|+...|..+.+. T Consensus 200 a~dV~~sL~r~~~l 213 (564) T COG4533 200 ASDVIASLLRLLQL 213 (564) T ss_pred HHHHHHHHHHHHCC T ss_conf 99999999998527 No 461 >pfam02042 RWP-RK RWP-RK domain. This domain is named RWP-RK after a conserved motif at the C terminus of the presumed domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development. Probab=35.13 E-value=27 Score=14.12 Aligned_cols=29 Identities=21% Similarity=0.263 Sum_probs=23.2 Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCC Q ss_conf 999789999949998899999999999807997 Q gi|254780693|r 188 GYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVN 220 (235) Q Consensus 188 G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~n 220 (235) -++-+|.|..|||+..+ ++++.+++|+.. T Consensus 15 ~lpi~~AA~~Lgv~~T~----LKk~CR~~gI~R 43 (52) T pfam02042 15 HLPIKEAAKELGVCLTV----LKKICRQLGIPR 43 (52) T ss_pred CCCHHHHHHHHCCCHHH----HHHHHHHCCCCC T ss_conf 87599999996877999----999999879987 No 462 >pfam09012 FeoC FeoC like transcriptional regulator. This family contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependant transcriptional repressor. Probab=35.07 E-value=27 Score=14.11 Aligned_cols=30 Identities=23% Similarity=0.145 Sum_probs=24.0 Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 999789999949998899999999999807 Q gi|254780693|r 188 GYTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 188 G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) --|-.||+..+.+|+.+|+-.+....+|=- T Consensus 14 ~~s~~~Ls~~f~~~~~~v~~ML~~wi~kGk 43 (68) T pfam09012 14 RASLAELARHFKMSPDAVEAMLEVWIRKGK 43 (68) T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHCCC T ss_conf 847999998979399999999999998797 No 463 >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=34.95 E-value=15 Score=16.05 Aligned_cols=36 Identities=31% Similarity=0.373 Sum_probs=28.2 Q ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHH Q ss_conf 9999999998799978999994999889999999999 Q gi|254780693|r 177 RETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSAT 213 (235) Q Consensus 177 RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~ 213 (235) |-.=||+.+-+ +|=+||+.+|++-..||++-+-+=+ T Consensus 142 R~~ivLKY~ed-LSL~EIS~IL~lPVgTVKTRiHRGR 177 (187) T TIGR02948 142 RSVIVLKYMED-LSLKEISEILDLPVGTVKTRIHRGR 177 (187) T ss_pred CEEHHHHHHHH-HHHHHHHHHHCCCCCCEECCCCCCH T ss_conf 12224544444-2188899985789431002430245 No 464 >cd06571 Bac_DnaA_C C-terminal domain of bacterial DnaA proteins. The DNA-binding C-terminal domain of DnaA contains a helix-turn-helix motif that specifically interacts with the DnaA box, a 9-mer motif that occurs repetitively in the replication origin oriC. Multiple copies of DnaA, which is an ATPase, bind to 9-mers at the origin and form an initial complex in which the DNA strands are being separated in an ATP-dependent step. Probab=34.92 E-value=27 Score=14.10 Aligned_cols=54 Identities=15% Similarity=0.138 Sum_probs=39.0 Q ss_pred CCHHHHHHHHHHH---CCCCHHHHHHHHC-CCHHHHHHHHHHHHHHCCCCCHHHHHHHHH Q ss_conf 9989999999998---7999789999949-998899999999999807997899999999 Q gi|254780693|r 174 LTERETSCLQLAG---DGYTSEEIAEKLG-LSVHTVNAYLGSATVKLDAVNRIQAIAKAI 229 (235) Q Consensus 174 LT~RE~evL~l~a---~G~t~~eIA~~L~-iS~~TV~~hl~~i~~KLg~~nR~qava~A~ 229 (235) -.+|+ |+-+++ .|+|..+||..+| -.-.||-+-++++-+++............+ T Consensus 29 ~~aR~--ia~yL~r~~~~~s~~~Ig~~fg~rdHsTV~~a~~kv~~~~~~d~~~~~~v~~i 86 (90) T cd06571 29 ALARQ--IAMYLARELTGLSLPEIGRAFGGRDHSTVLHAVRKIEELLEEDPELKEDVEEL 86 (90) T ss_pred HHHHH--HHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCHHHHHHHHHH T ss_conf 89999--99999999978899999999589971499999999999998399999999999 No 465 >COG1961 PinR Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair] Probab=34.90 E-value=21 Score=14.91 Aligned_cols=44 Identities=30% Similarity=0.319 Sum_probs=35.9 Q ss_pred CCHHHHHHHHHHHCC-CCHHHHHHHHCCCHHHHHHHHHHHHHHCC Q ss_conf 998999999999879-99789999949998899999999999807 Q gi|254780693|r 174 LTERETSCLQLAGDG-YTSEEIAEKLGLSVHTVNAYLGSATVKLD 217 (235) Q Consensus 174 LT~RE~evL~l~a~G-~t~~eIA~~L~iS~~TV~~hl~~i~~KLg 217 (235) -......|..+...| .+..+||..++||..||.....+...+-+ T Consensus 162 ~~~~~~~v~~l~~~~~~~~~~~a~~~~i~~~t~~r~~~~~~~~~~ 206 (222) T COG1961 162 AEEQAAAVRRLLADGLGSYSEIARALGISRSTVYRILNKLKKRGG 206 (222) T ss_pred CHHHHHHHHHHHHHCCCCHHHHHHHHCCCCEEEEECCCCCCCCCC T ss_conf 367799999999834634999999817774144400122222210 No 466 >PRK05629 hypothetical protein; Validated Probab=34.68 E-value=28 Score=14.07 Aligned_cols=40 Identities=20% Similarity=0.192 Sum_probs=28.5 Q ss_pred CCHHHHHHHHHH--HCCCCHHHHHHHHCCCHHHHHHHHHHHH Q ss_conf 998999999999--8799978999994999889999999999 Q gi|254780693|r 174 LTERETSCLQLA--GDGYTSEEIAEKLGLSVHTVNAYLGSAT 213 (235) Q Consensus 174 LT~RE~evL~l~--a~G~t~~eIA~~L~iS~~TV~~hl~~i~ 213 (235) |+-+=++++++. ..|.+..+||..|||.+=-|+.+...++ T Consensus 245 L~~~~r~l~~~~~~~~~~~~~~iA~~Lgv~P~~vkk~~~qar 286 (331) T PRK05629 245 LSMKVGQIARLYSTRGRINGFELAKELGMPPFVVEKTAKVAR 286 (331) T ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHH T ss_conf 999999999999751699989999883999899999999982 No 467 >PRK11552 putative DNA-binding transcriptional regulator; Provisional Probab=34.56 E-value=24 Score=14.44 Aligned_cols=18 Identities=0% Similarity=-0.090 Sum_probs=10.5 Q ss_pred HHHHHHHHHHHHCCCCEE Q ss_conf 999999999985837858 Q gi|254780693|r 17 LSPRLHLIQNRIKARNFA 34 (235) Q Consensus 17 l~~~l~~l~~~~~~~~f~ 34 (235) -...+.+..+.+.-.||. T Consensus 15 r~~ll~aA~~~F~~~G~~ 32 (224) T PRK11552 15 KQQLIAAALAQFGEYGLH 32 (224) T ss_pred HHHHHHHHHHHHHHHCCC T ss_conf 999999999999884914 No 468 >PTZ00037 DnaJ_C chaperone protein; Provisional Probab=34.43 E-value=18 Score=15.43 Aligned_cols=17 Identities=18% Similarity=0.045 Sum_probs=11.3 Q ss_pred CCCHHHHHHHHHHHCCC Q ss_conf 49989999999998799 Q gi|254780693|r 173 NLTERETSCLQLAGDGY 189 (235) Q Consensus 173 ~LT~RE~evL~l~a~G~ 189 (235) .|++.+.+.|+-+.-.. T Consensus 349 ~~~~~~~~~l~~~lp~~ 365 (422) T PTZ00037 349 KFTNEEKELLKELFPQN 365 (422) T ss_pred CCCHHHHHHHHHHCCCC T ss_conf 88999999999848998 No 469 >PRK10130 transcriptional regulator EutR; Provisional Probab=34.26 E-value=28 Score=14.03 Aligned_cols=31 Identities=16% Similarity=0.205 Sum_probs=24.0 Q ss_pred HHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH Q ss_conf 9999987999789999949998899999999 Q gi|254780693|r 181 CLQLAGDGYTSEEIAEKLGLSVHTVNAYLGS 211 (235) Q Consensus 181 vL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~ 211 (235) ++....+-.|..+|+..++||.+|..+..+. T Consensus 249 i~~~~~~pltv~~lc~~~~vS~RtLq~~F~~ 279 (350) T PRK10130 249 VLENMSEPVTVLDLCNQLHVSRRTLQNAFHA 279 (350) T ss_pred HHHCCCCCCCHHHHHHHHCCCHHHHHHHHHH T ss_conf 9848679999999998859779999999998 No 470 >cd00131 PAX Paired Box domain Probab=34.18 E-value=28 Score=14.02 Aligned_cols=32 Identities=25% Similarity=0.328 Sum_probs=19.5 Q ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH Q ss_conf 99999987999789999949998899999999 Q gi|254780693|r 180 SCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGS 211 (235) Q Consensus 180 evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~ 211 (235) .+++|..+|...-+|+++|.||-.-|-.-+.+ T Consensus 25 kIVeLa~~G~RpcdISR~L~VShGCVSKIL~R 56 (128) T cd00131 25 RIVELAQSGIRPCDISRQLRVSHGCVSKILNR 56 (128) T ss_pred HHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHH T ss_conf 99999985997888887637772168999998 No 471 >COG3655 Predicted transcriptional regulator [Transcription] Probab=34.00 E-value=28 Score=14.00 Aligned_cols=27 Identities=26% Similarity=0.352 Sum_probs=21.9 Q ss_pred HHHHCCCCHHHHHHHHCCCHHHHHHHH Q ss_conf 999879997899999499988999999 Q gi|254780693|r 183 QLAGDGYTSEEIAEKLGLSVHTVNAYL 209 (235) Q Consensus 183 ~l~a~G~t~~eIA~~L~iS~~TV~~hl 209 (235) -|+..+.+.++-+...|||+.|+..-- T Consensus 10 ~l~~r~~~~~eLa~~igis~~~ls~l~ 36 (73) T COG3655 10 MLADRKISLKELAEAIGISEANLSKLK 36 (73) T ss_pred HHHHHHHHHHHHHHHHCCCHHHHHHHH T ss_conf 999975017789999843698999997 No 472 >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=33.99 E-value=28 Score=14.00 Aligned_cols=44 Identities=25% Similarity=0.336 Sum_probs=0.0 Q ss_pred CCCHHHHHHH--HHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHC Q ss_conf 4998999999--999879--9978999994999889999999999980 Q gi|254780693|r 173 NLTERETSCL--QLAGDG--YTSEEIAEKLGLSVHTVNAYLGSATVKL 216 (235) Q Consensus 173 ~LT~RE~evL--~l~a~G--~t~~eIA~~L~iS~~TV~~hl~~i~~KL 216 (235) .|-.||+.|+ +|+.+- .|=.++|.+.|||.-=|+.-=+++++|+ T Consensus 226 ~Ld~RsR~I~~~RwL~d~~~~TL~~LA~eygvSaERiRQiE~~Am~K~ 273 (279) T TIGR02392 226 SLDARSRRIIEARWLDDDGKLTLHELAAEYGVSAERIRQIEKNAMKKL 273 (279) T ss_pred HHHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH T ss_conf 522887999987302788996478999884874667999999999999 No 473 >COG2944 Predicted transcriptional regulator [Transcription] Probab=33.86 E-value=28 Score=13.98 Aligned_cols=39 Identities=26% Similarity=0.322 Sum_probs=0.0 Q ss_pred CCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHH Q ss_conf 8874449989999999998799978999994999889999 Q gi|254780693|r 168 SSAARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNA 207 (235) Q Consensus 168 ~~~~~~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~ 207 (235) ......||+-|...++ -..|+|-.+-|+.||+|..||+. T Consensus 38 l~~~~~ls~~eIk~iR-e~~~lSq~vFA~~L~vs~~Tv~~ 76 (104) T COG2944 38 LLKVKTLSPTEIKAIR-EKLGLSQPVFARYLGVSVSTVRK 76 (104) T ss_pred HCCCCCCCHHHHHHHH-HHHCCCHHHHHHHHCCCHHHHHH T ss_conf 2367899889999999-98288899999998887999999 No 474 >pfam06627 DUF1153 Protein of unknown function (DUF1153). This family consists of several short, hypothetical bacterial proteins of unknown function. Probab=33.73 E-value=21 Score=14.91 Aligned_cols=17 Identities=29% Similarity=0.454 Sum_probs=0.0 Q ss_pred CCCHHHHHHHHHHCCCC Q ss_conf 99789999999976999 Q gi|254780693|r 218 AVNRIQAIAKAIRFGYI 234 (235) Q Consensus 218 ~~nR~qava~A~~~Gli 234 (235) |.+|-.+|++|+..||| T Consensus 34 VasRKA~VV~aV~~GLi 50 (90) T pfam06627 34 VASRKAAVVAAVRGGLL 50 (90) T ss_pred HHHHHHHHHHHHHHCCC T ss_conf 68888899999981777 No 475 >pfam00382 TFIIB Transcription factor TFIIB repeat. Probab=33.68 E-value=21 Score=14.88 Aligned_cols=25 Identities=24% Similarity=0.173 Sum_probs=0.0 Q ss_pred HHHHHHCCCCHHHHHHHHCCCHHHH Q ss_conf 9999987999789999949998899 Q gi|254780693|r 181 CLQLAGDGYTSEEIAEKLGLSVHTV 205 (235) Q Consensus 181 vL~l~a~G~t~~eIA~~L~iS~~TV 205 (235) +.+..-..+|-+||+...+||+.|+ T Consensus 47 Acr~~~~~rt~~eia~v~~vs~~tI 71 (71) T pfam00382 47 ACRLEEVKRTLKEISSVAQVSEKTI 71 (71) T ss_pred HHHHCCCCCCHHHHHHHHCCCCCCC T ss_conf 9998089989999999968987869 No 476 >pfam07508 Recombinase Recombinase. This domain is usually found associated with pfam00239 in putative integrases/recombinases of mobile genetic elements of diverse bacteria and phages. Probab=33.16 E-value=29 Score=13.90 Aligned_cols=33 Identities=27% Similarity=0.254 Sum_probs=0.0 Q ss_pred HHHHHHHHCCCCHHHHHHHHC-----------CCHHHHHHHHHH Q ss_conf 999999987999789999949-----------998899999999 Q gi|254780693|r 179 TSCLQLAGDGYTSEEIAEKLG-----------LSVHTVNAYLGS 211 (235) Q Consensus 179 ~evL~l~a~G~t~~eIA~~L~-----------iS~~TV~~hl~~ 211 (235) +++-.+.++|++..+||..|+ -+..||..-++| T Consensus 8 r~if~~~~~g~s~~~Ia~~Ln~~g~~~~~~~~w~~~~I~~iL~N 51 (101) T pfam07508 8 RLIFELYLEGKSLREIARYLNERGIPTPRGKKWTKSTVRRILTN 51 (101) T ss_pred HHHHHHHHCCCCHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHCC T ss_conf 99999998389999999999874996778982464435566208 No 477 >COG3088 CcmH Uncharacterized protein involved in biosynthesis of c-type cytochromes [Posttranslational modification, protein turnover, chaperones] Probab=33.06 E-value=29 Score=13.89 Aligned_cols=16 Identities=19% Similarity=0.418 Sum_probs=0.0 Q ss_pred HHHHHHHHCCCCHHHH Q ss_conf 9999999879997899 Q gi|254780693|r 179 TSCLQLAGDGYTSEEI 194 (235) Q Consensus 179 ~evL~l~a~G~t~~eI 194 (235) .+|..++.+|+|+.|| T Consensus 68 ~~V~e~l~eGkS~~qI 83 (153) T COG3088 68 HQVYELLQEGKSDQQI 83 (153) T ss_pred HHHHHHHHCCCCHHHH T ss_conf 9999999857868999 No 478 >pfam11994 DUF3489 Protein of unknown function (DUF3489). This family of proteins is functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 84 to 211 amino acids in length. This protein has a single completely conserved residue W that may be functionally important. Probab=33.05 E-value=29 Score=13.89 Aligned_cols=29 Identities=34% Similarity=0.386 Sum_probs=0.0 Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHH Q ss_conf 79997899999499988999999999998 Q gi|254780693|r 187 DGYTSEEIAEKLGLSVHTVNAYLGSATVK 215 (235) Q Consensus 187 ~G~t~~eIA~~L~iS~~TV~~hl~~i~~K 215 (235) +|-|..||...+|=-+|||+--+..+.+| T Consensus 23 ~Gati~~i~~atGWq~HTvRgalaG~lkK 51 (72) T pfam11994 23 EGATIAAISEATGWQPHTVRGALAGLLKK 51 (72) T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHH T ss_conf 89879999998687403589999888886 No 479 >COG5407 SEC63 Preprotein translocase subunit Sec63 [Intracellular trafficking and secretion] Probab=32.96 E-value=21 Score=14.98 Aligned_cols=39 Identities=15% Similarity=0.070 Sum_probs=0.0 Q ss_pred HHHHHHCCCCHHHHHH-------------HHCCCHHHHHHHHHHHHHHCCCC Q ss_conf 9999987999789999-------------94999889999999999980799 Q gi|254780693|r 181 CLQLAGDGYTSEEIAE-------------KLGLSVHTVNAYLGSATVKLDAV 219 (235) Q Consensus 181 vL~l~a~G~t~~eIA~-------------~L~iS~~TV~~hl~~i~~KLg~~ 219 (235) ++-|++-|.-..-|+. +|||+..|-..-+++.|+||-++ T Consensus 74 ivgWl~i~~L~~~I~~~k~~~~~~fDPyEILGI~~~ts~rdik~~yr~Ls~K 125 (610) T COG5407 74 IVGWLVISYLISNIRTLKIEYRRGFDPYEILGIDQDTSERDIKKRYRMLSMK 125 (610) T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHCCCCCCCHHHHHHHHHHHEEE T ss_conf 8999999999998777789987088818861246787577899999866240 No 480 >COG4941 Predicted RNA polymerase sigma factor containing a TPR repeat domain [Transcription] Probab=32.69 E-value=30 Score=13.85 Aligned_cols=32 Identities=16% Similarity=0.206 Sum_probs=0.0 Q ss_pred HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHC Q ss_conf 98799978999994999889999999999980 Q gi|254780693|r 185 AGDGYTSEEIAEKLGLSVHTVNAYLGSATVKL 216 (235) Q Consensus 185 ~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KL 216 (235) +.-|+|.+|||+--=+|+.|...-+.++.+|+ T Consensus 133 ~v~GLs~~eIArAFLv~e~am~QRivRAK~ri 164 (415) T COG4941 133 LVGGLSTAEIARAFLVPEAAMAQRIVRAKARI 164 (415) T ss_pred HHCCCCHHHHHHHHCCCCHHHHHHHHHHHHHH T ss_conf 98287599999998078078999999999999 No 481 >COG3710 CadC DNA-binding winged-HTH domains [Transcription] Probab=32.30 E-value=10 Score=17.07 Aligned_cols=59 Identities=24% Similarity=0.274 Sum_probs=0.0 Q ss_pred CCHHHHHHHHHHHCCCCHHHHHHHH---------CCCHHHHHHHHHHHHHHCCCCCH-HHHHHHHHHCCC Q ss_conf 9989999999998799978999994---------99988999999999998079978-999999997699 Q gi|254780693|r 174 LTERETSCLQLAGDGYTSEEIAEKL---------GLSVHTVNAYLGSATVKLDAVNR-IQAIAKAIRFGY 233 (235) Q Consensus 174 LT~RE~evL~l~a~G~t~~eIA~~L---------~iS~~TV~~hl~~i~~KLg~~nR-~qava~A~~~Gl 233 (235) |++||..||.++.+ .-.+-|++.- .++++|+..++..+++-|+-.+. .+.|+-=-+.|| T Consensus 32 l~~~~~~lL~~L~e-~~geVvsk~eL~~~VW~~~~v~~~~Ltq~I~~LRr~L~d~~~~~~~I~TvPrrGy 100 (148) T COG3710 32 LGPRELKLLSLLLE-RAGEVVSKDELLDAVWPGRIVTVNTLTQAISALRRALRDIGDGHRLIATVPRRGY 100 (148) T ss_pred ECHHHHHHHHHHHH-CCCCEECHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCE T ss_conf 66678899999985-4686052999999857996264454999999999986346876638998378546 No 482 >pfam04182 B-block_TFIIIC B-block binding subunit of TFIIIC. Yeast transcription factor IIIC (TFIIIC) is a multi-subunit protein complex that interacts with two control elements of class III promoters called the A and B blocks. This family represents the subunit within TFIIIC involved in B-block binding. Probab=31.93 E-value=30 Score=13.77 Aligned_cols=41 Identities=20% Similarity=0.161 Sum_probs=0.0 Q ss_pred CHHHHHHHHHHH----CCCCHHHHHHHHCCCHHHHHHHHHHHHHH Q ss_conf 989999999998----79997899999499988999999999998 Q gi|254780693|r 175 TERETSCLQLAG----DGYTSEEIAEKLGLSVHTVNAYLGSATVK 215 (235) Q Consensus 175 T~RE~evL~l~a----~G~t~~eIA~~L~iS~~TV~~hl~~i~~K 215 (235) ++-|.++|.++| .|-+..+.+...|+-+++|-.|+++...+ T Consensus 1 ~~~~~~lL~~Ia~~r~~Gi~q~dL~k~~~~D~rs~~~~~k~L~~~ 45 (73) T pfam04182 1 PALQFELLEEIARSRYNGITQSDLAKLTGQDPRSVFYRLKKLEDK 45 (73) T ss_pred CCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCHHHHHHHHHC T ss_conf 924899999999517688018999999689964317989999878 No 483 >COG2344 AT-rich DNA-binding protein [General function prediction only] Probab=31.82 E-value=31 Score=13.76 Aligned_cols=18 Identities=33% Similarity=0.593 Sum_probs=0.0 Q ss_pred CHHHHHHHHCCCHHHHHH Q ss_conf 978999994999889999 Q gi|254780693|r 190 TSEEIAEKLGLSVHTVNA 207 (235) Q Consensus 190 t~~eIA~~L~iS~~TV~~ 207 (235) |++|||+.++|...||+. T Consensus 34 sS~els~~~~vdsatIRr 51 (211) T COG2344 34 SSKELSEALGVDSATIRR 51 (211) T ss_pred CHHHHHHHHCCCHHHHHH T ss_conf 689999986899999863 No 484 >pfam04703 FaeA FaeA-like protein. This family represents a number of fimbrial protein transcription regulators found in Gram-negative bacteria. These proteins are thought to facilitate binding of the leucine-rich regulatory protein to regulatory elements, possibly by inhibiting deoxyadenosine methylation of these elements by deoxyadenosine methylase. Probab=31.75 E-value=31 Score=13.75 Aligned_cols=33 Identities=33% Similarity=0.428 Sum_probs=0.0 Q ss_pred HHHHHHHC---CCCHHHHHHHHCCCHHHHHHHHHHH Q ss_conf 99999987---9997899999499988999999999 Q gi|254780693|r 180 SCLQLAGD---GYTSEEIAEKLGLSVHTVNAYLGSA 212 (235) Q Consensus 180 evL~l~a~---G~t~~eIA~~L~iS~~TV~~hl~~i 212 (235) +||..+-. +-...|||.-+|+|.--+++|+... T Consensus 4 ~Il~~i~~i~~p~~T~eIAda~gls~YQaR~YL~~L 39 (61) T pfam04703 4 SILTFINSIGAPCKTREIADALGLSAYQARYYLEQL 39 (61) T ss_pred HHHHHHHHCCCCCCHHHHHHHHCCHHHHHHHHHHHH T ss_conf 899999874898418899998550799999999999 No 485 >TIGR01321 TrpR trp operon repressor; InterPro: IPR013335 The Trp repressor (TrpR) binds to at least five operators in the Escherichia coli genome, repressing gene expression. The operators at which it binds vary considerably in DNA sequence and location within the promoter; when bound to the Trp operon it recognises the sequence 5'-ACTAGT-3' and acts to prevent the initiation of transcription. The TrpR controls the trpEDCBA (trpO) operon and the genes for trpR, aroH, mtr and aroL, which are involved in the biosynthesis and uptake of the amino acid tryptophan . The repressor binds to the operators only in the presence of L-tryptophan, thereby controlling the intracellular level of its effector; the complex also regulates Trp repressor biosynthesis by binding to its own regulatory region. TrpR acts as a dimer that is composed of identical 6-helical subunits, where four of the helices form the core of the protein and intertwine with the corresponding helices from the other subunit. This entry represents Trp repressors found in proteobacterial and chlamydial species.; GO: 0016564 transcription repressor activity, 0006355 regulation of transcription DNA-dependent. Probab=31.66 E-value=31 Score=13.74 Aligned_cols=32 Identities=38% Similarity=0.473 Sum_probs=0.0 Q ss_pred CCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHH Q ss_conf 99899999999987999789999949998899 Q gi|254780693|r 174 LTERETSCLQLAGDGYTSEEIAEKLGLSVHTV 205 (235) Q Consensus 174 LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV 205 (235) |-.|=+=|=.|+-.-+|-+||+..||+|.-|+ T Consensus 42 l~~R~~I~~~LL~~~~~QREi~~~lG~SiA~I 73 (95) T TIGR01321 42 LGSRVRIVEELLEGEMSQREIAEKLGVSIATI 73 (95) T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHH T ss_conf 98799999999614897478888637616678 No 486 >pfam00292 PAX 'Paired box' domain. Probab=31.65 E-value=31 Score=13.74 Aligned_cols=36 Identities=25% Similarity=0.307 Sum_probs=0.0 Q ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHH Q ss_conf 999999987999789999949998899999999999 Q gi|254780693|r 179 TSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATV 214 (235) Q Consensus 179 ~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~ 214 (235) ..+++|...|...-+|+++|.||-.-|-.-+.+.++ T Consensus 24 ~kIVeLa~~G~RpCdISR~L~VShGCVSKIL~Ry~e 59 (125) T pfam00292 24 QKIVELAHSGVRPCDISRQLRVSHGCVSKILGRYQE 59 (125) T ss_pred HHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHH T ss_conf 999999984997888877626762168999998872 No 487 >TIGR03192 benz_CoA_bzdQ benzoyl-CoA reductase, bzd-type, Q subunit. Members of this family are the Q subunit of one of two related types of four-subunit ATP-dependent benzoyl-CoA reductase. This enzyme system catalyzes the dearomatization of benzoyl-CoA, a common intermediate in pathways for the degradation for a number of different aromatic compounds, such as phenol and toluene. Probab=31.57 E-value=31 Score=13.73 Aligned_cols=40 Identities=15% Similarity=0.229 Sum_probs=0.0 Q ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCC Q ss_conf 9999999987999789999949998899999999999807997 Q gi|254780693|r 178 ETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVN 220 (235) Q Consensus 178 E~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~n 220 (235) |.||..++++|.+..+|+. ||...-++..+ ++.+|++... T Consensus 202 ESevis~l~~G~~~edI~a--Gl~~sia~rv~-~l~~r~~~~~ 241 (293) T TIGR03192 202 KSEALGLLKAGYTKNMVIA--AYCQAMAERVV-SLLERIGVEE 241 (293) T ss_pred EHHHHHHHHCCCCHHHHHH--HHHHHHHHHHH-HHHHHCCCCC T ss_conf 1769999986998999999--99999999999-9976338899 No 488 >TIGR02748 GerC3_HepT heptaprenyl diphosphate synthase component II; InterPro: IPR014119 The proteins in this entry are component II of the heterodimeric heptaprenyl diphosphate synthase. They are found proximate to the gene for component I (IPR009920 from INTERPRO). This enzyme acts in menaquinone-7 isoprenoid side chain biosynthesis.. Probab=30.82 E-value=31 Score=13.67 Aligned_cols=22 Identities=23% Similarity=0.214 Sum_probs=0.0 Q ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHCCC Q ss_conf 99999999998079978999999997699 Q gi|254780693|r 205 VNAYLGSATVKLDAVNRIQAIAKAIRFGY 233 (235) Q Consensus 205 V~~hl~~i~~KLg~~nR~qava~A~~~Gl 233 (235) ++.|+++|.||. |--+|+.++| T Consensus 161 lR~YLRRIKRKT-------ALLIA~SCqL 182 (325) T TIGR02748 161 LRTYLRRIKRKT-------ALLIAASCQL 182 (325) T ss_pred HHHHHHHHHHHH-------HHHHHHHHHH T ss_conf 003665666889-------9999987765 No 489 >PRK11014 transcriptional repressor NsrR; Provisional Probab=30.69 E-value=32 Score=13.63 Aligned_cols=26 Identities=15% Similarity=0.235 Sum_probs=0.0 Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHH Q ss_conf 97899999499988999999999998 Q gi|254780693|r 190 TSEEIAEKLGLSVHTVNAYLGSATVK 215 (235) Q Consensus 190 t~~eIA~~L~iS~~TV~~hl~~i~~K 215 (235) +.+|||...+||++.+..-++...++ T Consensus 27 ~~~eIae~~~Ip~~~L~KIl~~L~~a 52 (141) T PRK11014 27 SISEVTEVYGVSRNHMVKIINQLSRA 52 (141) T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHC T ss_conf 49999998794999999999999887 No 490 >smart00531 TFIIE Transcription initiation factor IIE. Probab=30.63 E-value=32 Score=13.62 Aligned_cols=25 Identities=28% Similarity=0.284 Sum_probs=0.0 Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH Q ss_conf 9789999949998899999999999 Q gi|254780693|r 190 TSEEIAEKLGLSVHTVNAYLGSATV 214 (235) Q Consensus 190 t~~eIA~~L~iS~~TV~~hl~~i~~ 214 (235) |..+||..||++.+.|+.-+..++. T Consensus 17 ~dedLa~~l~~~~n~vRkiL~~L~e 41 (147) T smart00531 17 TEEDLAELLGIKQKQLRKILYLLYD 41 (147) T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH T ss_conf 7999999979999999999999997 No 491 >TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family; InterPro: IPR014071 This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferable copper resistance) of an Enterococcus faecium (Streptococcus faecium) plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this entry are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.. Probab=30.36 E-value=32 Score=13.59 Aligned_cols=41 Identities=22% Similarity=0.218 Sum_probs=0.0 Q ss_pred CHHHHHHHH--HHHCCCCHHHHHHHHCC----CHHHHHHHHHHHHHH Q ss_conf 989999999--99879997899999499----988999999999998 Q gi|254780693|r 175 TERETSCLQ--LAGDGYTSEEIAEKLGL----SVHTVNAYLGSATVK 215 (235) Q Consensus 175 T~RE~evL~--l~a~G~t~~eIA~~L~i----S~~TV~~hl~~i~~K 215 (235) |+-|-||++ |.-.--|+++|-.+|.= +..||++-+.+.-.| T Consensus 3 sDaEWEVMRvvW~~g~~~S~~~i~~L~~k~DW~~STiKTLl~RLV~K 49 (130) T TIGR02698 3 SDAEWEVMRVVWTLGETTSKDIISVLAEKKDWKDSTIKTLLGRLVDK 49 (130) T ss_pred CCHHHHHHHHHCCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHH T ss_conf 74232433421048872778999986055776267899999765441 No 492 >PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional Probab=30.21 E-value=32 Score=13.57 Aligned_cols=41 Identities=17% Similarity=0.116 Sum_probs=0.0 Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCC Q ss_conf 899999999987999789999949998899999999999807997 Q gi|254780693|r 176 ERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVN 220 (235) Q Consensus 176 ~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~n 220 (235) +|+.=.-.+-..|..-.+.|+.||||..|.. +.++|||.+. T Consensus 470 Er~lI~~AL~~~~GN~s~AAr~LGIsRstLy----Rk~KrLGIk~ 510 (510) T PRK05022 470 QRQLIRQALAQHNGNWAAAARALELDRANLH----RLAKRLGLKD 510 (510) T ss_pred HHHHHHHHHHHHCCCHHHHHHHHCCCHHHHH----HHHHHHCCCC T ss_conf 9999999999919989999999798999999----9999808999 No 493 >COG2508 Regulator of polyketide synthase expression [Signal transduction mechanisms / Secondary metabolites biosynthesis, transport, and catabolism] Probab=30.12 E-value=33 Score=13.56 Aligned_cols=45 Identities=13% Similarity=-0.050 Sum_probs=0.0 Q ss_pred CHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCC Q ss_conf 989999999998799978999994999889999999999980799 Q gi|254780693|r 175 TERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAV 219 (235) Q Consensus 175 T~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~ 219 (235) |+=...+...+-.+....+.|+.|+|=++|+++-+++|...+|.. T Consensus 353 teLl~TL~~yl~~~~ni~~tAk~L~iHRNTL~YRi~kieEltg~d 397 (421) T COG2508 353 TELLETLRAYLKNNGNISATAKRLFVHRNTLRYRLKKIEELTGID 397 (421) T ss_pred HHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCC T ss_conf 679999999998489799999983745423999999999994879 No 494 >COG1378 Predicted transcriptional regulators [Transcription] Probab=29.99 E-value=33 Score=13.55 Aligned_cols=43 Identities=30% Similarity=0.194 Sum_probs=0.0 Q ss_pred CCCHHHHHHHHHHHC--CCCHHHHHHHHCCCHHHHHHHHHHHHHH Q ss_conf 499899999999987--9997899999499988999999999998 Q gi|254780693|r 173 NLTERETSCLQLAGD--GYTSEEIAEKLGLSVHTVNAYLGSATVK 215 (235) Q Consensus 173 ~LT~RE~evL~l~a~--G~t~~eIA~~L~iS~~TV~~hl~~i~~K 215 (235) +||+.|..|-.-+.. ..|.+||+...||-..-|..-++++-.| T Consensus 13 Glt~yEa~vY~aLl~~g~~tA~eis~~sgvP~~kvY~vl~sLe~k 57 (247) T COG1378 13 GLTEYEAKVYLALLCLGEATAKEISEASGVPRPKVYDVLRSLEKK 57 (247) T ss_pred CCCHHHHHHHHHHHHHCCCCHHHHHHHCCCCCHHHHHHHHHHHHC T ss_conf 997889999999998188779999986599932299999999878 No 495 >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=29.94 E-value=21 Score=14.90 Aligned_cols=17 Identities=47% Similarity=0.640 Sum_probs=0.0 Q ss_pred CCHHHHHHHHCCCHHHH Q ss_conf 99789999949998899 Q gi|254780693|r 189 YTSEEIAEKLGLSVHTV 205 (235) Q Consensus 189 ~t~~eIA~~L~iS~~TV 205 (235) +|-++||..|++++.|| T Consensus 366 L~L~~vA~el~~heSTi 382 (477) T TIGR02395 366 LTLREVAEELGLHESTI 382 (477) T ss_pred CCHHHHHHHHCCCCCCE T ss_conf 63899998858898724 No 496 >COG3311 AlpA Predicted transcriptional regulator [Transcription] Probab=29.54 E-value=33 Score=13.49 Aligned_cols=19 Identities=32% Similarity=0.401 Sum_probs=0.0 Q ss_pred HHHHHHHCCCHHHHHHHHH Q ss_conf 8999994999889999999 Q gi|254780693|r 192 EEIAEKLGLSVHTVNAYLG 210 (235) Q Consensus 192 ~eIA~~L~iS~~TV~~hl~ 210 (235) +|++..+|+|..|+..+++ T Consensus 17 ~ev~~~~GlSrstiYr~i~ 35 (70) T COG3311 17 PEVAQLTGLSRSTIYRLIK 35 (70) T ss_pred HHHHHHHCCCHHHHHHHHC T ss_conf 9999997766899999980 No 497 >pfam03918 CcmH Cytochrome C biogenesis protein. Members of this family include NrfF, CcmH, CycL, Ccl2. Probab=29.30 E-value=34 Score=13.47 Aligned_cols=16 Identities=25% Similarity=0.358 Sum_probs=0.0 Q ss_pred HHHHHHHHCCCCHHHH Q ss_conf 9999999879997899 Q gi|254780693|r 179 TSCLQLAGDGYTSEEI 194 (235) Q Consensus 179 ~evL~l~a~G~t~~eI 194 (235) .+|-+.+.+|+|++|| T Consensus 61 ~~i~~~i~~G~sd~eI 76 (145) T pfam03918 61 LEVREMLVEGKSDEEI 76 (145) T ss_pred HHHHHHHHCCCCHHHH T ss_conf 9999999859999999 No 498 >PHA00675 hypothetical protein Probab=29.21 E-value=34 Score=13.46 Aligned_cols=40 Identities=20% Similarity=0.253 Sum_probs=0.0 Q ss_pred CCCCCCCCCCHHHHHHHHHHHC--CCCHHHHHHHHCCCHHHH Q ss_conf 6788744499899999999987--999789999949998899 Q gi|254780693|r 166 KRSSAARNLTERETSCLQLAGD--GYTSEEIAEKLGLSVHTV 205 (235) Q Consensus 166 ~~~~~~~~LT~RE~evL~l~a~--G~t~~eIA~~L~iS~~TV 205 (235) +.......||.-+.|..+-+.+ |++--.+|...+++..|| T Consensus 15 G~~Hhna~ltd~~Vd~IR~LrE~~gl~Yg~La~~f~~pkgtI 56 (78) T PHA00675 15 GEDHPNAKLTDAEVERIRELHEVEGMSYAVLAEKFEQSKGAI 56 (78) T ss_pred CCCCCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHH T ss_conf 675755657789999999999872843899999972756899 No 499 >TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator; InterPro: IPR011791 This entry represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal efflux system , . This protein is a member of the MerR family of transcriptional activators and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix .. Probab=28.50 E-value=26 Score=14.25 Aligned_cols=16 Identities=50% Similarity=0.785 Sum_probs=0.0 Q ss_pred HHHHHHCCCHHHHHHH Q ss_conf 9999949998899999 Q gi|254780693|r 193 EIAEKLGLSVHTVNAY 208 (235) Q Consensus 193 eIA~~L~iS~~TV~~h 208 (235) |-|..-|+|..|++|| T Consensus 5 eLA~~t~v~v~TIRFY 20 (127) T TIGR02047 5 ELAKKTGVSVETIRFY 20 (127) T ss_pred HHHHHHCCCCCHHHHH T ss_conf 4545533440022464 No 500 >PRK12815 carB carbamoyl phosphate synthase large subunit; Reviewed Probab=28.03 E-value=35 Score=13.32 Aligned_cols=31 Identities=19% Similarity=0.246 Sum_probs=0.0 Q ss_pred HHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH Q ss_conf 9999987999789999949998899999999 Q gi|254780693|r 181 CLQLAGDGYTSEEIAEKLGLSVHTVNAYLGS 211 (235) Q Consensus 181 vL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~ 211 (235) .+++-..|.|+++||..+++|+..|+.+.++ T Consensus 484 l~~aK~~GFSD~~Ia~l~~~~e~~vr~~R~~ 514 (1068) T PRK12815 484 LRKAKEKGFSDRLIAELTGVTEEDVRELRKK 514 (1068) T ss_pred HHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH T ss_conf 9999984999999997709999999999997 Done!