Query 008556
Match_columns 561
No_of_seqs 402 out of 2366
Neff 5.9
Searched_HMMs 46136
Date Thu Mar 28 13:39:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008556.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008556hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK07598 RNA polymerase sigma 100.0 7.3E-65 1.6E-69 540.8 38.7 315 245-560 58-414 (415)
2 PRK07406 RNA polymerase sigma 100.0 5.5E-62 1.2E-66 515.0 38.7 312 245-557 61-372 (373)
3 PRK05949 RNA polymerase sigma 100.0 2E-61 4.2E-66 504.4 39.1 311 245-558 16-326 (327)
4 TIGR02997 Sig70-cyanoRpoD RNA 100.0 1.2E-60 2.6E-65 492.7 37.2 298 247-545 1-298 (298)
5 PRK07405 RNA polymerase sigma 100.0 2.6E-60 5.6E-65 494.3 38.7 310 246-558 7-316 (317)
6 PRK05901 RNA polymerase sigma 100.0 2.9E-59 6.4E-64 508.7 33.7 301 245-558 209-509 (509)
7 COG0568 RpoD DNA-directed RNA 100.0 4.2E-59 9.1E-64 482.8 32.5 314 245-558 7-342 (342)
8 PRK07921 RNA polymerase sigma 100.0 5.7E-58 1.2E-62 477.5 36.3 300 245-557 24-323 (324)
9 PRK09210 RNA polymerase sigma 100.0 1.5E-54 3.2E-59 459.4 33.4 276 243-558 92-367 (367)
10 PRK05658 RNA polymerase sigma 100.0 1.3E-51 2.7E-56 463.2 31.2 274 248-558 345-618 (619)
11 TIGR02393 RpoD_Cterm RNA polym 100.0 8.5E-48 1.8E-52 384.6 28.7 238 321-558 1-238 (238)
12 PRK05657 RNA polymerase sigma 100.0 1E-44 2.2E-49 378.5 33.6 272 245-556 51-322 (325)
13 PRK06596 RNA polymerase factor 100.0 2E-44 4.4E-49 369.8 32.9 262 245-550 12-282 (284)
14 PRK07500 rpoH2 RNA polymerase 100.0 2.4E-44 5.3E-49 370.1 32.9 264 247-552 6-281 (289)
15 TIGR02392 rpoH_proteo alternat 100.0 8.2E-44 1.8E-48 362.6 32.0 258 248-549 2-269 (270)
16 PRK07122 RNA polymerase sigma 100.0 3.7E-43 8E-48 357.0 28.6 220 320-548 40-263 (264)
17 PRK07408 RNA polymerase sigma 100.0 2.5E-41 5.4E-46 342.0 30.7 228 317-551 22-254 (256)
18 TIGR02394 rpoS_proteo RNA poly 100.0 5.6E-41 1.2E-45 344.1 33.7 274 241-554 7-280 (285)
19 TIGR02850 spore_sigG RNA polym 100.0 8.6E-40 1.9E-44 330.0 31.1 243 256-548 10-254 (254)
20 PRK05911 RNA polymerase sigma 100.0 1.2E-39 2.6E-44 330.0 28.8 227 317-550 20-255 (257)
21 PRK08215 sporulation sigma fac 100.0 2.1E-38 4.6E-43 320.4 31.5 243 256-548 13-257 (258)
22 COG1191 FliA DNA-directed RNA 100.0 1.8E-38 3.9E-43 318.0 28.9 223 317-550 21-246 (247)
23 PRK06288 RNA polymerase sigma 100.0 5.4E-37 1.2E-41 312.0 30.6 250 256-551 6-263 (268)
24 TIGR02941 Sigma_B RNA polymera 100.0 3E-36 6.6E-41 303.9 31.0 244 260-548 8-253 (255)
25 TIGR02885 spore_sigF RNA polym 100.0 2.5E-36 5.4E-41 299.9 28.9 223 316-548 7-231 (231)
26 TIGR02980 SigBFG RNA polymeras 100.0 6.9E-36 1.5E-40 295.8 28.2 221 319-548 2-226 (227)
27 PRK07670 RNA polymerase sigma 100.0 3.8E-35 8.1E-40 295.6 31.0 226 317-549 19-250 (251)
28 PRK05572 sporulation sigma fac 100.0 1.9E-34 4.2E-39 290.7 31.0 244 254-549 6-251 (252)
29 PRK08583 RNA polymerase sigma 100.0 2.5E-34 5.3E-39 290.3 31.0 243 260-550 8-255 (257)
30 TIGR02479 FliA_WhiG RNA polyme 100.0 1.5E-34 3.2E-39 286.1 27.1 217 325-548 1-223 (224)
31 PRK12427 flagellar biosynthesi 100.0 2.8E-34 6.1E-39 286.6 28.3 209 322-547 17-230 (231)
32 PRK06986 fliA flagellar biosyn 100.0 4.1E-33 8.8E-38 278.1 28.4 225 317-550 5-234 (236)
33 PRK05803 sporulation sigma fac 100.0 3.5E-28 7.6E-33 242.3 25.9 210 248-550 17-229 (233)
34 PRK08301 sporulation sigma fac 99.9 2.1E-24 4.6E-29 214.9 25.2 181 317-550 49-232 (234)
35 TIGR02846 spore_sigmaK RNA pol 99.9 2.3E-24 5.1E-29 214.2 25.5 199 257-548 25-226 (227)
36 TIGR02835 spore_sigmaE RNA pol 99.9 1.5E-23 3.3E-28 209.3 25.2 181 317-550 49-232 (234)
37 PRK08295 RNA polymerase factor 99.9 1.2E-22 2.5E-27 197.5 22.6 195 306-552 9-206 (208)
38 PRK05602 RNA polymerase sigma 99.9 4E-22 8.6E-27 191.2 20.6 176 306-553 5-181 (186)
39 TIGR02859 spore_sigH RNA polym 99.9 8.6E-22 1.9E-26 189.8 21.3 191 306-548 4-197 (198)
40 PRK09646 RNA polymerase sigma 99.9 1E-21 2.2E-26 190.2 20.5 175 308-550 17-192 (194)
41 PRK12513 RNA polymerase sigma 99.9 8.2E-22 1.8E-26 190.2 19.2 181 306-553 11-192 (194)
42 PRK09641 RNA polymerase sigma 99.9 1.5E-21 3.3E-26 186.2 20.8 180 308-549 5-185 (187)
43 TIGR02948 SigW_bacill RNA poly 99.9 1.4E-21 3E-26 186.5 20.3 178 310-549 7-185 (187)
44 PRK09648 RNA polymerase sigma 99.9 2.9E-21 6.3E-26 185.7 21.8 171 310-549 13-188 (189)
45 TIGR02952 Sig70_famx2 RNA poly 99.9 7.2E-21 1.6E-25 178.7 19.8 164 316-548 7-170 (170)
46 PRK09652 RNA polymerase sigma 99.9 7.5E-21 1.6E-25 179.5 19.9 172 316-549 6-177 (182)
47 PRK13919 putative RNA polymera 99.9 7.1E-21 1.5E-25 182.2 19.9 176 307-550 9-185 (186)
48 PRK12519 RNA polymerase sigma 99.9 7.2E-21 1.6E-25 183.5 19.5 175 307-549 15-190 (194)
49 PRK12514 RNA polymerase sigma 99.9 9.8E-21 2.1E-25 180.3 20.1 173 307-549 5-178 (179)
50 PRK06811 RNA polymerase factor 99.9 1.2E-20 2.7E-25 181.8 20.6 174 306-549 3-180 (189)
51 TIGR02939 RpoE_Sigma70 RNA pol 99.9 1.5E-20 3.2E-25 179.8 20.6 181 307-549 6-187 (190)
52 PRK06759 RNA polymerase factor 99.9 6.8E-21 1.5E-25 176.5 17.6 151 319-547 3-153 (154)
53 PRK11922 RNA polymerase sigma 99.9 1.3E-20 2.8E-25 187.7 20.7 173 317-550 27-199 (231)
54 PRK12524 RNA polymerase sigma 99.9 1.7E-20 3.6E-25 181.9 20.7 177 306-552 11-188 (196)
55 PRK12537 RNA polymerase sigma 99.9 1.7E-20 3.8E-25 179.6 19.9 172 307-548 9-181 (182)
56 PRK11923 algU RNA polymerase s 99.9 2.9E-20 6.3E-25 179.1 21.3 180 308-549 7-187 (193)
57 PRK12538 RNA polymerase sigma 99.9 1.7E-20 3.7E-25 187.7 20.0 174 307-552 49-223 (233)
58 PRK09640 RNA polymerase sigma 99.9 1.1E-20 2.4E-25 181.8 17.0 173 305-549 7-183 (188)
59 PRK12534 RNA polymerase sigma 99.9 3E-20 6.4E-25 178.2 19.5 172 310-549 14-186 (187)
60 TIGR02984 Sig-70_plancto1 RNA 99.9 7.8E-20 1.7E-24 174.5 21.7 180 317-548 4-188 (189)
61 PRK12526 RNA polymerase sigma 99.9 5.7E-20 1.2E-24 180.0 20.8 171 316-551 34-204 (206)
62 PRK12515 RNA polymerase sigma 99.8 7.9E-20 1.7E-24 175.9 20.8 177 306-553 7-184 (189)
63 PRK12542 RNA polymerase sigma 99.8 3.3E-20 7.1E-25 178.0 17.8 175 316-557 5-179 (185)
64 PRK11924 RNA polymerase sigma 99.8 7.8E-20 1.7E-24 172.1 20.0 168 316-551 9-176 (179)
65 PRK09638 RNA polymerase sigma 99.8 8.6E-20 1.9E-24 173.0 18.3 172 306-549 3-175 (176)
66 PRK09643 RNA polymerase sigma 99.8 1.5E-19 3.3E-24 175.0 20.4 172 306-550 12-184 (192)
67 TIGR02954 Sig70_famx3 RNA poly 99.8 1.2E-19 2.7E-24 171.2 19.2 167 306-549 1-168 (169)
68 TIGR02937 sigma70-ECF RNA poly 99.8 2.1E-19 4.6E-24 162.5 19.1 157 321-548 2-158 (158)
69 PRK12531 RNA polymerase sigma 99.8 1.4E-19 2.9E-24 175.3 18.7 176 311-552 17-193 (194)
70 PRK12543 RNA polymerase sigma 99.8 1.9E-19 4.1E-24 172.0 19.1 165 317-551 4-168 (179)
71 TIGR02985 Sig70_bacteroi1 RNA 99.8 1.9E-19 4.2E-24 166.3 18.0 160 321-548 2-161 (161)
72 PRK09645 RNA polymerase sigma 99.8 3.1E-19 6.7E-24 168.9 19.3 165 317-552 6-170 (173)
73 PRK12536 RNA polymerase sigma 99.8 2.5E-19 5.3E-24 171.5 17.7 169 310-551 10-180 (181)
74 PRK09415 RNA polymerase factor 99.8 4.1E-19 9E-24 169.8 18.9 164 318-550 14-177 (179)
75 PRK12522 RNA polymerase sigma 99.8 5.3E-19 1.1E-23 167.7 19.4 167 320-550 3-169 (173)
76 TIGR02989 Sig-70_gvs1 RNA poly 99.8 3.1E-19 6.7E-24 166.0 17.5 158 321-548 2-159 (159)
77 TIGR03001 Sig-70_gmx1 RNA poly 99.8 5.4E-19 1.2E-23 178.2 20.6 181 304-553 22-214 (244)
78 PRK12520 RNA polymerase sigma 99.8 4.4E-19 9.6E-24 171.0 18.8 182 321-553 3-184 (191)
79 PRK12539 RNA polymerase sigma 99.8 7.3E-19 1.6E-23 168.7 19.4 169 308-550 8-181 (184)
80 TIGR02999 Sig-70_X6 RNA polyme 99.8 7.9E-19 1.7E-23 167.4 18.8 171 309-548 5-182 (183)
81 PRK12512 RNA polymerase sigma 99.8 1.3E-18 2.8E-23 166.4 20.2 166 311-551 12-182 (184)
82 PRK12533 RNA polymerase sigma 99.8 1.6E-18 3.4E-23 171.7 20.7 172 316-551 14-185 (216)
83 PRK12529 RNA polymerase sigma 99.8 1.2E-18 2.6E-23 166.6 18.7 166 316-549 9-176 (178)
84 COG1595 RpoE DNA-directed RNA 99.8 2.2E-18 4.7E-23 165.3 20.3 171 313-551 8-178 (182)
85 PRK12518 RNA polymerase sigma 99.8 1.1E-18 2.3E-23 165.3 17.8 166 316-552 7-172 (175)
86 PRK09649 RNA polymerase sigma 99.8 1.4E-18 3.1E-23 167.2 17.9 169 310-552 13-182 (185)
87 PRK09642 RNA polymerase sigma 99.8 1.3E-18 2.9E-23 162.5 17.0 157 327-552 2-158 (160)
88 PRK12516 RNA polymerase sigma 99.8 1.9E-18 4E-23 167.1 18.0 162 317-552 7-168 (187)
89 TIGR02947 SigH_actino RNA poly 99.8 1E-18 2.2E-23 168.7 16.2 172 319-550 10-181 (193)
90 PRK09647 RNA polymerase sigma 99.8 4E-18 8.6E-23 167.1 20.2 166 318-553 26-191 (203)
91 PRK12523 RNA polymerase sigma 99.8 2.5E-18 5.4E-23 163.1 17.9 163 317-550 7-169 (172)
92 PRK09644 RNA polymerase sigma 99.8 2.8E-18 6.1E-23 161.5 18.0 158 322-552 3-160 (165)
93 TIGR02983 SigE-fam_strep RNA p 99.8 2.6E-18 5.7E-23 160.7 17.4 158 317-550 3-160 (162)
94 TIGR02895 spore_sigI RNA polym 99.8 7.5E-18 1.6E-22 167.2 20.4 118 315-432 4-126 (218)
95 PRK12528 RNA polymerase sigma 99.8 7E-18 1.5E-22 158.0 18.5 157 320-547 4-160 (161)
96 PRK12547 RNA polymerase sigma 99.8 8.9E-18 1.9E-22 158.3 19.1 159 319-551 5-163 (164)
97 PRK12532 RNA polymerase sigma 99.8 8.4E-18 1.8E-22 162.6 18.8 181 323-553 8-189 (195)
98 PRK12545 RNA polymerase sigma 99.8 9E-18 2E-22 163.8 18.9 181 324-553 12-192 (201)
99 PRK12541 RNA polymerase sigma 99.8 1.2E-17 2.5E-22 156.5 18.7 157 318-547 3-159 (161)
100 PRK12530 RNA polymerase sigma 99.8 1.1E-17 2.3E-22 161.7 18.8 176 323-551 10-185 (189)
101 PRK12544 RNA polymerase sigma 99.8 1.7E-17 3.8E-22 162.9 20.4 180 322-551 20-199 (206)
102 TIGR02943 Sig70_famx1 RNA poly 99.8 1E-17 2.2E-22 161.9 18.2 178 323-551 5-182 (188)
103 PRK08241 RNA polymerase factor 99.8 1.4E-17 3E-22 174.5 20.5 187 310-547 8-200 (339)
104 PRK09639 RNA polymerase sigma 99.8 1.8E-17 4E-22 155.4 19.1 160 319-550 2-161 (166)
105 PRK12535 RNA polymerase sigma 99.8 1.8E-17 4E-22 161.4 19.3 169 311-551 15-184 (196)
106 TIGR02960 SigX5 RNA polymerase 99.8 1.7E-17 3.6E-22 172.5 20.2 183 317-550 2-192 (324)
107 TIGR02950 SigM_subfam RNA poly 99.8 7E-18 1.5E-22 156.1 14.4 152 327-548 2-153 (154)
108 PRK07037 extracytoplasmic-func 99.8 2.8E-17 6.1E-22 153.9 18.5 159 324-551 2-160 (163)
109 PRK12540 RNA polymerase sigma 99.8 2.9E-17 6.3E-22 158.1 18.6 160 320-553 5-164 (182)
110 PRK12527 RNA polymerase sigma 99.8 2.6E-17 5.7E-22 153.8 17.7 155 327-551 2-156 (159)
111 PRK09651 RNA polymerase sigma 99.8 5.4E-17 1.2E-21 154.3 18.5 164 318-552 8-171 (172)
112 PRK12517 RNA polymerase sigma 99.7 4.3E-17 9.4E-22 157.6 18.0 161 315-550 18-178 (188)
113 PRK09637 RNA polymerase sigma 99.7 7.4E-17 1.6E-21 155.1 19.0 154 322-550 3-156 (181)
114 PRK12546 RNA polymerase sigma 99.7 1.1E-16 2.3E-21 155.2 18.4 156 320-550 8-163 (188)
115 TIGR02959 SigZ RNA polymerase 99.7 1.1E-16 2.3E-21 152.0 17.6 148 327-549 2-149 (170)
116 PRK12511 RNA polymerase sigma 99.7 1.2E-16 2.7E-21 153.8 17.3 157 322-551 6-162 (182)
117 PRK12525 RNA polymerase sigma 99.7 3.2E-16 6.8E-21 148.3 18.9 160 319-549 8-167 (168)
118 PRK09047 RNA polymerase factor 99.7 4.3E-16 9.4E-21 145.2 16.6 156 342-553 2-159 (161)
119 PRK09636 RNA polymerase sigma 99.7 6.9E-16 1.5E-20 159.0 17.7 160 320-549 4-164 (293)
120 PRK06704 RNA polymerase factor 99.7 3.6E-15 7.7E-20 149.1 17.8 158 311-550 9-166 (228)
121 TIGR02957 SigX4 RNA polymerase 99.6 4.7E-15 1E-19 152.3 17.5 156 324-549 1-157 (281)
122 PRK09635 sigI RNA polymerase s 99.6 7.3E-15 1.6E-19 151.8 17.8 161 320-548 5-166 (290)
123 TIGR03209 P21_Cbot clostridium 99.5 2E-13 4.3E-18 125.4 13.7 136 322-534 1-141 (142)
124 PRK09191 two-component respons 99.5 1.4E-13 3.1E-18 137.1 13.0 137 321-550 2-138 (261)
125 PRK08311 putative RNA polymera 99.5 4.3E-12 9.4E-17 127.7 19.8 88 308-395 5-95 (237)
126 PF07638 Sigma70_ECF: ECF sigm 99.4 3.7E-11 8E-16 116.2 19.0 174 309-549 5-184 (185)
127 PF04542 Sigma70_r2: Sigma-70 99.2 2.5E-11 5.5E-16 97.7 8.0 70 325-394 1-70 (71)
128 PF04545 Sigma70_r4: Sigma-70, 99.2 2.4E-11 5.1E-16 93.1 7.2 50 493-546 1-50 (50)
129 PF04539 Sigma70_r3: Sigma-70 99.0 6.5E-10 1.4E-14 92.5 7.4 77 404-480 1-77 (78)
130 PF08281 Sigma70_r4_2: Sigma-7 98.9 3E-09 6.6E-14 82.4 7.2 54 487-544 1-54 (54)
131 PRK06930 positive control sigm 98.7 1.1E-07 2.5E-12 91.3 9.7 71 477-551 95-165 (170)
132 PRK00118 putative DNA-binding 98.4 8.8E-07 1.9E-11 78.5 8.9 61 489-553 10-70 (104)
133 cd06171 Sigma70_r4 Sigma70, re 98.3 2.2E-06 4.7E-11 64.3 6.8 54 488-545 2-55 (55)
134 TIGR00721 tfx DNA-binding prot 98.2 3.8E-06 8.2E-11 78.0 6.9 57 495-556 5-61 (137)
135 PRK03975 tfx putative transcri 98.1 5.6E-06 1.2E-10 77.2 7.2 51 495-550 5-55 (141)
136 PRK04217 hypothetical protein; 98.1 7.1E-06 1.5E-10 73.5 6.6 56 495-554 41-96 (110)
137 PF00140 Sigma70_r1_2: Sigma-7 98.0 1.5E-06 3.3E-11 62.9 0.8 34 246-279 1-34 (37)
138 PRK05658 RNA polymerase sigma 98.0 0.0022 4.8E-08 73.4 25.8 34 245-278 102-135 (619)
139 PF04297 UPF0122: Putative hel 98.0 3.4E-05 7.4E-10 68.0 8.3 58 489-550 9-67 (101)
140 TIGR01636 phage_rinA phage tra 97.9 4.4E-05 9.6E-10 70.6 8.9 62 485-548 71-132 (134)
141 smart00421 HTH_LUXR helix_turn 97.8 4.7E-05 1E-09 58.1 5.7 46 495-545 2-47 (58)
142 PF00196 GerE: Bacterial regul 97.6 0.00012 2.5E-09 57.7 5.9 46 495-545 2-47 (58)
143 cd06170 LuxR_C_like C-terminal 97.6 0.00015 3.3E-09 55.4 6.1 45 497-546 1-45 (57)
144 PF07374 DUF1492: Protein of u 97.6 0.00033 7.1E-09 61.6 8.7 55 486-544 44-99 (100)
145 TIGR03879 near_KaiC_dom probab 97.6 0.00016 3.4E-09 60.2 6.1 47 489-539 8-55 (73)
146 PF04967 HTH_10: HTH DNA bindi 97.5 0.0003 6.6E-09 55.0 6.8 48 497-544 1-51 (53)
147 TIGR01321 TrpR trp operon repr 97.5 0.00017 3.8E-09 62.7 5.1 49 488-536 23-75 (94)
148 PRK15201 fimbriae regulatory p 97.3 0.00049 1.1E-08 66.3 6.5 47 495-546 132-178 (198)
149 PRK15411 rcsA colanic acid cap 97.3 0.00045 9.9E-09 68.1 6.3 46 496-546 137-182 (207)
150 PRK10840 transcriptional regul 97.2 0.00055 1.2E-08 66.8 6.2 46 495-545 149-194 (216)
151 PRK13870 transcriptional regul 97.2 0.00054 1.2E-08 69.1 6.2 45 496-545 173-217 (234)
152 TIGR03020 EpsA transcriptional 97.2 0.00057 1.2E-08 69.6 6.4 48 494-546 188-235 (247)
153 PRK13719 conjugal transfer tra 97.2 0.0006 1.3E-08 67.9 6.2 50 491-545 138-187 (217)
154 TIGR03541 reg_near_HchA LuxR f 97.2 0.00058 1.3E-08 68.6 6.2 48 494-546 169-216 (232)
155 PRK11475 DNA-binding transcrip 97.2 0.00064 1.4E-08 67.3 6.4 46 495-545 133-178 (207)
156 PRK10188 DNA-binding transcrip 97.2 0.00073 1.6E-08 68.3 6.4 45 496-545 179-223 (240)
157 PRK10100 DNA-binding transcrip 97.2 0.00076 1.7E-08 67.2 6.3 48 494-546 153-200 (216)
158 PF02001 DUF134: Protein of un 97.0 0.0017 3.7E-08 57.9 6.5 53 496-552 41-93 (106)
159 COG2197 CitB Response regulato 97.0 0.0011 2.4E-08 65.7 6.0 46 495-545 147-192 (211)
160 COG4566 TtrR Response regulato 97.0 0.003 6.5E-08 61.6 8.2 59 485-548 131-189 (202)
161 COG2771 CsgD DNA-binding HTH d 97.0 0.0026 5.6E-08 50.1 6.5 47 495-546 3-49 (65)
162 PF13936 HTH_38: Helix-turn-he 96.9 0.0011 2.4E-08 49.7 4.0 41 495-539 3-43 (44)
163 PRK09483 response regulator; P 96.9 0.0019 4.2E-08 61.7 6.1 46 495-545 147-192 (217)
164 PRK15369 two component system 96.7 0.003 6.5E-08 59.0 6.3 46 495-545 148-193 (211)
165 TIGR01637 phage_arpU phage tra 96.7 0.0096 2.1E-07 54.5 9.4 63 485-549 67-130 (132)
166 COG3413 Predicted DNA binding 96.7 0.004 8.6E-08 61.8 6.8 53 496-548 155-210 (215)
167 PRK01381 Trp operon repressor; 96.5 0.003 6.5E-08 55.5 4.0 48 488-535 23-74 (99)
168 PRK10651 transcriptional regul 96.5 0.0052 1.1E-07 58.1 5.9 46 495-545 154-199 (216)
169 COG1356 tfx Transcriptional re 96.4 0.0026 5.6E-08 57.9 3.2 48 496-548 8-55 (143)
170 PRK09390 fixJ response regulat 96.4 0.0094 2E-07 55.3 7.1 53 489-546 134-186 (202)
171 COG2739 Uncharacterized protei 96.3 0.015 3.3E-07 51.1 7.4 48 495-546 16-63 (105)
172 COG1342 Predicted DNA-binding 96.1 0.017 3.7E-07 50.3 6.3 52 496-551 33-84 (99)
173 PRK15320 transcriptional activ 95.9 0.014 3.1E-07 57.3 5.9 47 494-545 162-208 (251)
174 PRK10403 transcriptional regul 95.9 0.016 3.5E-07 54.6 5.9 46 495-545 152-197 (215)
175 COG4941 Predicted RNA polymera 95.5 0.32 6.8E-06 51.6 14.2 159 323-547 8-167 (415)
176 PRK09935 transcriptional regul 95.4 0.031 6.7E-07 52.8 6.1 45 496-545 149-193 (210)
177 PRK09958 DNA-binding transcrip 95.4 0.031 6.8E-07 52.8 6.1 47 494-545 141-187 (204)
178 PRK10360 DNA-binding transcrip 95.3 0.027 5.8E-07 52.9 5.2 46 495-545 136-181 (196)
179 PRK13558 bacterio-opsin activa 95.3 0.033 7.1E-07 63.7 6.8 55 494-548 605-662 (665)
180 PRK04841 transcriptional regul 95.2 0.031 6.7E-07 66.0 6.5 46 495-545 837-882 (903)
181 PF00325 Crp: Bacterial regula 95.0 0.032 7E-07 39.3 3.4 27 516-546 2-28 (32)
182 PF12645 HTH_16: Helix-turn-he 94.9 0.11 2.5E-06 42.3 6.9 56 311-366 4-65 (65)
183 PF01726 LexA_DNA_bind: LexA D 94.5 0.057 1.2E-06 44.0 4.4 45 494-538 1-48 (65)
184 TIGR02531 yecD_yerC TrpR-relat 94.5 0.079 1.7E-06 45.8 5.5 37 495-537 35-71 (88)
185 PF13412 HTH_24: Winged helix- 94.5 0.11 2.3E-06 39.1 5.6 40 497-539 1-40 (48)
186 PF13613 HTH_Tnp_4: Helix-turn 94.4 0.1 2.2E-06 40.5 5.5 50 496-548 2-51 (53)
187 PF13384 HTH_23: Homeodomain-l 94.3 0.039 8.5E-07 41.7 2.8 32 504-540 10-41 (50)
188 PF06530 Phage_antitermQ: Phag 94.1 0.29 6.2E-06 44.8 8.7 55 494-552 60-114 (125)
189 PRK15418 transcriptional regul 94.1 0.07 1.5E-06 56.4 5.2 36 503-542 20-55 (318)
190 PF05263 DUF722: Protein of un 94.0 0.21 4.5E-06 46.3 7.4 53 486-540 71-123 (130)
191 PF04539 Sigma70_r3: Sigma-70 93.7 0.13 2.9E-06 42.4 5.2 38 278-315 4-41 (78)
192 cd00569 HTH_Hin_like Helix-tur 93.5 0.17 3.7E-06 33.7 4.6 36 497-536 6-41 (42)
193 TIGR02393 RpoD_Cterm RNA polym 93.5 0.97 2.1E-05 45.4 11.9 35 279-313 88-122 (238)
194 PF02796 HTH_7: Helix-turn-hel 93.4 0.1 2.3E-06 39.1 3.6 32 501-537 11-42 (45)
195 PRK09210 RNA polymerase sigma 93.3 1.1 2.4E-05 48.2 12.8 129 280-445 218-347 (367)
196 PRK07921 RNA polymerase sigma 93.2 1.5 3.2E-05 46.7 13.2 35 279-313 174-208 (324)
197 PRK05901 RNA polymerase sigma 93.1 1.2 2.6E-05 50.1 13.1 130 279-445 359-489 (509)
198 PRK10430 DNA-binding transcrip 92.1 0.29 6.4E-06 48.5 6.0 47 496-542 158-204 (239)
199 COG1191 FliA DNA-directed RNA 92.0 4.4 9.6E-05 41.6 14.4 147 248-445 88-234 (247)
200 PF13730 HTH_36: Helix-turn-he 91.8 0.59 1.3E-05 35.9 6.1 47 496-546 2-51 (55)
201 PF13404 HTH_AsnC-type: AsnC-t 91.7 0.49 1.1E-05 35.2 5.3 40 497-539 1-40 (42)
202 PHA00675 hypothetical protein 91.5 0.35 7.7E-06 40.6 4.8 40 495-538 21-61 (78)
203 PRK07598 RNA polymerase sigma 91.3 4.5 9.8E-05 44.5 14.5 37 408-444 112-148 (415)
204 COG2390 DeoR Transcriptional r 91.0 0.3 6.4E-06 51.8 4.9 35 504-542 18-52 (321)
205 PF09862 DUF2089: Protein of u 90.8 0.65 1.4E-05 42.0 6.2 50 493-546 30-79 (113)
206 PF13518 HTH_28: Helix-turn-he 90.8 0.43 9.4E-06 35.9 4.4 27 515-541 11-37 (52)
207 smart00351 PAX Paired Box doma 90.6 0.66 1.4E-05 42.4 6.2 41 497-541 18-58 (125)
208 PF04218 CENP-B_N: CENP-B N-te 90.1 0.38 8.2E-06 37.5 3.5 40 496-539 6-45 (53)
209 PF08279 HTH_11: HTH domain; 90.0 0.56 1.2E-05 36.0 4.4 38 500-539 1-38 (55)
210 PF10668 Phage_terminase: Phag 89.8 0.59 1.3E-05 37.6 4.5 35 503-539 11-45 (60)
211 PF06056 Terminase_5: Putative 89.8 0.66 1.4E-05 37.0 4.8 26 515-540 12-37 (58)
212 COG2909 MalT ATP-dependent tra 89.8 0.38 8.3E-06 56.4 4.7 45 496-545 831-875 (894)
213 PRK00423 tfb transcription ini 89.5 17 0.00038 38.2 16.6 178 323-544 119-304 (310)
214 TIGR02395 rpoN_sigma RNA polym 89.5 16 0.00035 40.4 16.9 46 493-538 283-340 (429)
215 PRK05932 RNA polymerase factor 89.4 11 0.00025 41.9 15.7 46 493-538 308-365 (455)
216 PHA02547 55 RNA polymerase sig 89.3 1.4 2.9E-05 42.6 7.2 64 327-390 44-110 (179)
217 PF02650 HTH_WhiA: WhiA C-term 89.3 0.79 1.7E-05 39.4 5.2 44 494-540 35-80 (85)
218 PRK05911 RNA polymerase sigma 89.2 2.8 6E-05 42.8 10.1 34 280-313 112-145 (257)
219 PRK07406 RNA polymerase sigma 89.2 5.8 0.00013 43.0 13.0 34 279-312 224-257 (373)
220 PF12802 MarR_2: MarR family; 89.1 0.83 1.8E-05 35.6 4.9 43 496-539 2-44 (62)
221 PHA02591 hypothetical protein; 89.0 0.78 1.7E-05 38.7 4.7 24 515-538 58-81 (83)
222 COG3355 Predicted transcriptio 88.9 1.5 3.1E-05 40.5 6.9 53 488-546 16-68 (126)
223 PRK11083 DNA-binding response 88.5 0.66 1.4E-05 44.3 4.8 50 496-546 154-208 (228)
224 PRK06288 RNA polymerase sigma 88.3 9 0.0002 39.2 13.2 35 279-313 119-153 (268)
225 PRK07408 RNA polymerase sigma 88.3 1.3 2.9E-05 45.1 7.1 34 280-313 115-148 (256)
226 PRK07122 RNA polymerase sigma 88.0 7.7 0.00017 39.8 12.5 34 280-313 129-162 (264)
227 PF01325 Fe_dep_repress: Iron 87.8 0.8 1.7E-05 36.6 4.0 46 497-546 2-48 (60)
228 PF01022 HTH_5: Bacterial regu 87.6 1.4 3E-05 33.1 5.1 36 499-538 2-37 (47)
229 PRK10710 DNA-binding transcrip 87.5 0.84 1.8E-05 44.1 4.8 50 496-546 160-214 (240)
230 PRK05949 RNA polymerase sigma 87.2 8.3 0.00018 41.0 12.5 35 279-313 179-213 (327)
231 PF03444 HrcA_DNA-bdg: Winged 87.1 1.4 2.9E-05 37.4 5.1 42 496-537 1-44 (78)
232 cd00131 PAX Paired Box domain 87.1 1.6 3.5E-05 40.1 6.1 41 497-541 18-58 (128)
233 PF01371 Trp_repressor: Trp re 87.0 1.3 2.7E-05 38.4 5.1 46 496-542 26-74 (87)
234 PRK07670 RNA polymerase sigma 87.0 9 0.0002 38.7 12.2 35 280-314 111-145 (251)
235 TIGR02885 spore_sigF RNA polym 86.6 2.6 5.6E-05 41.9 7.9 32 282-313 101-132 (231)
236 PF12840 HTH_20: Helix-turn-he 86.5 2.3 5.1E-05 33.5 6.0 35 499-537 10-45 (61)
237 PRK12423 LexA repressor; Provi 86.4 1.3 2.8E-05 43.7 5.5 47 496-546 3-52 (202)
238 PRK15479 transcriptional regul 86.1 1.2 2.7E-05 42.1 5.1 49 496-545 148-201 (221)
239 PRK10336 DNA-binding transcrip 86.0 1.1 2.4E-05 42.4 4.8 49 496-545 149-202 (219)
240 TIGR02850 spore_sigG RNA polym 86.0 9 0.0002 38.8 11.6 34 281-314 123-156 (254)
241 TIGR02997 Sig70-cyanoRpoD RNA 85.9 12 0.00027 38.9 12.8 35 279-313 162-196 (298)
242 PRK12469 RNA polymerase factor 85.9 38 0.00083 38.1 17.2 46 493-538 334-391 (481)
243 PRK07500 rpoH2 RNA polymerase 85.3 16 0.00036 37.9 13.4 25 422-446 244-268 (289)
244 PF13463 HTH_27: Winged helix 85.3 1.5 3.3E-05 34.7 4.5 41 497-539 1-41 (68)
245 smart00344 HTH_ASNC helix_turn 85.2 2 4.4E-05 37.4 5.6 41 497-540 1-41 (108)
246 smart00550 Zalpha Z-DNA-bindin 85.0 1.9 4.2E-05 35.1 5.0 23 516-538 22-44 (68)
247 TIGR02154 PhoB phosphate regul 84.9 0.69 1.5E-05 43.9 2.8 49 496-545 154-207 (226)
248 PRK07405 RNA polymerase sigma 84.7 13 0.00028 39.4 12.3 34 279-312 169-202 (317)
249 PF13542 HTH_Tnp_ISL3: Helix-t 84.6 2.3 5E-05 32.2 5.0 33 503-540 19-51 (52)
250 PF09339 HTH_IclR: IclR helix- 84.4 1.3 2.9E-05 33.9 3.6 34 505-538 7-40 (52)
251 PRK10046 dpiA two-component re 84.3 1.1 2.4E-05 44.1 3.9 39 496-538 161-199 (225)
252 PF13744 HTH_37: Helix-turn-he 84.2 2 4.3E-05 36.1 4.9 38 515-552 30-72 (80)
253 PF01710 HTH_Tnp_IS630: Transp 84.2 10 0.00022 34.2 9.9 28 515-546 70-97 (119)
254 TIGR02147 Fsuc_second hypothet 84.1 23 0.00051 36.8 13.7 87 423-511 137-227 (271)
255 PF12728 HTH_17: Helix-turn-he 83.5 1.2 2.7E-05 33.6 3.1 24 517-540 2-25 (51)
256 TIGR01610 phage_O_Nterm phage 83.5 4.6 9.9E-05 35.1 7.0 49 494-546 20-73 (95)
257 smart00345 HTH_GNTR helix_turn 83.3 2 4.3E-05 32.7 4.2 30 513-546 16-46 (60)
258 PF00356 LacI: Bacterial regul 83.3 1.2 2.6E-05 33.8 2.8 22 518-539 1-22 (46)
259 TIGR00498 lexA SOS regulatory 83.0 2 4.3E-05 41.9 5.0 43 495-537 2-47 (199)
260 PF01726 LexA_DNA_bind: LexA D 82.9 3.7 7.9E-05 33.4 5.7 40 407-446 9-49 (65)
261 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 82.5 3.2 6.9E-05 32.3 4.9 39 496-538 4-42 (50)
262 COG1508 RpoN DNA-directed RNA 82.3 35 0.00075 38.0 14.6 48 491-538 293-352 (444)
263 PF01978 TrmB: Sugar-specific 82.0 1.4 3E-05 35.4 3.0 44 496-546 5-48 (68)
264 TIGR03787 marine_sort_RR prote 81.9 2 4.4E-05 41.2 4.6 49 496-545 156-206 (227)
265 COG3415 Transposase and inacti 81.9 2.6 5.7E-05 39.4 5.1 27 515-541 20-46 (138)
266 TIGR02479 FliA_WhiG RNA polyme 81.7 19 0.00042 35.5 11.7 35 279-313 84-118 (224)
267 PRK11179 DNA-binding transcrip 81.6 3.1 6.8E-05 39.0 5.7 41 496-539 6-46 (153)
268 smart00342 HTH_ARAC helix_turn 81.4 25 0.00054 27.9 10.3 23 423-445 1-23 (84)
269 TIGR01764 excise DNA binding d 81.3 1.8 3.8E-05 31.7 3.1 24 517-540 2-25 (49)
270 PRK00215 LexA repressor; Valid 81.2 2.8 6.1E-05 41.0 5.4 43 497-539 2-47 (205)
271 PF01047 MarR: MarR family; I 80.9 3.1 6.8E-05 32.1 4.6 41 497-540 1-41 (59)
272 CHL00148 orf27 Ycf27; Reviewed 80.8 2.2 4.9E-05 41.1 4.5 50 496-546 161-217 (240)
273 PRK13413 mpi multiple promoter 80.6 2.9 6.2E-05 40.9 5.2 34 501-539 162-195 (200)
274 cd04762 HTH_MerR-trunc Helix-T 80.4 2 4.4E-05 31.1 3.2 25 517-541 1-25 (49)
275 PF13022 HTH_Tnp_1_2: Helix-tu 80.2 7 0.00015 36.8 7.2 64 490-553 4-73 (142)
276 PF01418 HTH_6: Helix-turn-hel 80.0 3.5 7.5E-05 34.3 4.8 49 487-537 4-55 (77)
277 COG1522 Lrp Transcriptional re 79.2 4 8.7E-05 37.6 5.5 42 495-539 4-45 (154)
278 PRK11564 stationary phase indu 79.0 4.8 0.0001 43.9 6.9 51 496-546 10-60 (426)
279 PF13011 LZ_Tnp_IS481: leucine 78.8 4.8 0.0001 34.7 5.3 44 495-541 7-50 (85)
280 PF13551 HTH_29: Winged helix- 78.6 3.8 8.3E-05 35.4 4.9 26 515-540 10-36 (112)
281 PRK12427 flagellar biosynthesi 78.6 26 0.00056 35.2 11.5 34 280-313 103-136 (231)
282 PRK11169 leucine-responsive tr 78.2 3.6 7.7E-05 39.1 4.9 40 497-539 12-51 (164)
283 PHA01976 helix-turn-helix prot 77.3 4.2 9.1E-05 32.3 4.4 25 515-539 14-38 (67)
284 PF01381 HTH_3: Helix-turn-hel 77.3 2.5 5.4E-05 32.1 2.9 25 515-539 8-32 (55)
285 COG0856 Orotate phosphoribosyl 77.2 3.1 6.6E-05 40.6 4.0 39 503-546 10-48 (203)
286 PRK05572 sporulation sigma fac 76.4 27 0.00058 35.3 11.0 32 281-312 121-152 (252)
287 cd04761 HTH_MerR-SF Helix-Turn 76.3 2.1 4.5E-05 31.7 2.2 25 517-541 1-25 (49)
288 PHA00542 putative Cro-like pro 75.9 4.3 9.4E-05 34.3 4.3 26 515-540 30-55 (82)
289 smart00420 HTH_DEOR helix_turn 75.8 6.8 0.00015 28.8 4.9 25 515-539 13-37 (53)
290 PF08220 HTH_DeoR: DeoR-like h 75.7 4.7 0.0001 31.6 4.2 24 515-538 13-36 (57)
291 cd06571 Bac_DnaA_C C-terminal 75.5 8.9 0.00019 32.8 6.2 31 515-545 43-74 (90)
292 COG1654 BirA Biotin operon rep 75.5 7.2 0.00016 33.1 5.4 32 512-547 15-46 (79)
293 cd00092 HTH_CRP helix_turn_hel 75.0 7.8 0.00017 30.3 5.4 28 515-546 24-51 (67)
294 TIGR03697 NtcA_cyano global ni 75.0 3.6 7.9E-05 39.0 4.0 29 515-547 142-170 (193)
295 PF13560 HTH_31: Helix-turn-he 74.9 3.8 8.2E-05 32.5 3.5 25 515-539 13-37 (64)
296 PF14394 DUF4423: Domain of un 74.8 7.9 0.00017 37.4 6.3 110 422-550 38-154 (171)
297 TIGR03070 couple_hipB transcri 74.8 5.4 0.00012 30.1 4.2 25 515-539 14-38 (58)
298 cd07377 WHTH_GntR Winged helix 74.8 5.9 0.00013 30.7 4.5 26 517-546 26-51 (66)
299 smart00419 HTH_CRP helix_turn_ 74.6 4.4 9.5E-05 29.6 3.6 28 515-546 7-34 (48)
300 TIGR00122 birA_repr_reg BirA b 74.5 6.9 0.00015 31.5 5.0 25 515-539 12-36 (69)
301 TIGR02787 codY_Gpos GTP-sensin 74.5 14 0.00029 37.9 8.0 55 488-546 168-224 (251)
302 smart00418 HTH_ARSR helix_turn 74.2 5.4 0.00012 30.2 4.2 25 515-539 9-33 (66)
303 PF08822 DUF1804: Protein of u 74.1 6.9 0.00015 37.7 5.6 41 499-542 5-45 (165)
304 TIGR02941 Sigma_B RNA polymera 74.1 30 0.00066 34.9 10.7 34 280-313 118-151 (255)
305 PF08765 Mor: Mor transcriptio 73.7 6.7 0.00015 34.8 5.1 42 499-546 61-102 (108)
306 PF02954 HTH_8: Bacterial regu 73.6 5.9 0.00013 29.1 4.0 37 499-538 4-40 (42)
307 PF00046 Homeobox: Homeobox do 73.5 6 0.00013 30.4 4.2 51 496-546 6-57 (57)
308 TIGR03830 CxxCG_CxxCG_HTH puta 73.4 11 0.00024 33.7 6.6 48 487-540 55-102 (127)
309 COG1476 Predicted transcriptio 73.3 5.3 0.00012 33.0 4.0 25 515-539 13-37 (68)
310 COG2522 Predicted transcriptio 73.1 6.1 0.00013 36.2 4.7 24 515-538 21-44 (119)
311 PRK10072 putative transcriptio 72.7 5.5 0.00012 35.0 4.2 32 504-539 38-69 (96)
312 PF13545 HTH_Crp_2: Crp-like h 72.5 4.1 9E-05 33.0 3.3 28 515-546 27-54 (76)
313 COG5625 Predicted transcriptio 72.4 5.5 0.00012 35.4 4.0 70 488-557 8-79 (113)
314 TIGR02337 HpaR homoprotocatech 72.3 17 0.00037 32.2 7.5 41 495-538 24-64 (118)
315 TIGR02844 spore_III_D sporulat 72.0 8 0.00017 32.9 4.9 24 515-538 18-41 (80)
316 TIGR02612 mob_myst_A mobile my 71.9 8.5 0.00018 36.6 5.6 49 498-550 24-78 (150)
317 PRK08215 sporulation sigma fac 71.8 49 0.0011 33.5 11.6 33 281-313 126-158 (258)
318 PF07750 GcrA: GcrA cell cycle 71.7 4.9 0.00011 38.6 4.0 35 501-539 7-42 (162)
319 PRK06986 fliA flagellar biosyn 71.6 57 0.0012 32.5 11.9 33 281-313 98-130 (236)
320 COG1510 Predicted transcriptio 71.5 4.4 9.6E-05 39.3 3.6 29 514-546 39-67 (177)
321 PF13551 HTH_29: Winged helix- 71.1 12 0.00026 32.2 6.0 24 425-448 14-37 (112)
322 smart00346 HTH_ICLR helix_turn 71.0 9.7 0.00021 31.8 5.3 26 515-540 19-44 (91)
323 PF13411 MerR_1: MerR HTH fami 70.4 2.2 4.8E-05 34.1 1.2 25 517-541 1-25 (69)
324 PRK09954 putative kinase; Prov 70.3 8.4 0.00018 40.9 5.9 42 497-541 1-42 (362)
325 PRK03573 transcriptional regul 70.2 13 0.00028 34.1 6.4 49 489-539 19-69 (144)
326 PF08280 HTH_Mga: M protein tr 69.8 5.2 0.00011 31.6 3.1 36 500-538 6-41 (59)
327 COG5484 Uncharacterized conser 69.5 5.8 0.00013 40.7 4.1 25 515-539 18-42 (279)
328 TIGR02980 SigBFG RNA polymeras 69.3 38 0.00083 33.4 10.0 31 282-312 94-124 (227)
329 COG2973 TrpR Trp operon repres 69.3 10 0.00023 33.5 5.1 39 496-534 37-78 (103)
330 PF00392 GntR: Bacterial regul 69.2 5.6 0.00012 31.6 3.3 30 513-546 20-50 (64)
331 cd00090 HTH_ARSR Arsenical Res 69.1 13 0.00028 28.8 5.4 23 517-539 21-43 (78)
332 PRK13918 CRP/FNR family transc 68.3 6.1 0.00013 37.8 3.9 28 515-546 148-175 (202)
333 PF08535 KorB: KorB domain; I 68.0 5 0.00011 34.5 2.9 24 515-538 2-25 (93)
334 PRK11337 DNA-binding transcrip 67.9 9.2 0.0002 39.4 5.4 52 486-539 15-69 (292)
335 PF06971 Put_DNA-bind_N: Putat 67.4 15 0.00032 28.6 5.1 45 398-442 3-47 (50)
336 PRK11302 DNA-binding transcrip 67.0 9.3 0.0002 39.0 5.2 51 487-539 4-57 (284)
337 cd01104 HTH_MlrA-CarA Helix-Tu 66.2 7.4 0.00016 30.9 3.4 23 517-539 1-23 (68)
338 PF12116 SpoIIID: Stage III sp 66.2 8.9 0.00019 32.7 3.9 44 501-546 6-49 (82)
339 PRK06030 hypothetical protein; 65.6 18 0.00038 33.4 6.1 40 515-558 68-107 (124)
340 PRK10870 transcriptional repre 65.4 34 0.00074 32.9 8.4 50 489-539 43-94 (176)
341 COG2944 Predicted transcriptio 65.2 17 0.00038 32.5 5.8 40 494-539 41-80 (104)
342 PF11662 DUF3263: Protein of u 65.1 23 0.00049 30.1 6.1 47 496-542 2-48 (77)
343 TIGR01884 cas_HTH CRISPR locus 64.9 16 0.00035 35.8 6.2 45 492-539 136-180 (203)
344 smart00347 HTH_MARR helix_turn 64.8 16 0.00035 30.4 5.5 44 496-546 7-50 (101)
345 PRK15482 transcriptional regul 64.4 11 0.00024 38.8 5.1 50 488-539 5-57 (285)
346 PF00376 MerR: MerR family reg 64.3 4.3 9.4E-05 29.5 1.5 23 518-540 1-23 (38)
347 PF05043 Mga: Mga helix-turn-h 64.2 5.5 0.00012 33.5 2.4 31 515-545 29-59 (87)
348 TIGR00647 MG103 conserved hypo 64.2 14 0.00031 38.5 5.9 44 494-540 225-274 (279)
349 PF02082 Rrf2: Transcriptional 64.0 12 0.00026 31.4 4.4 24 515-538 24-47 (83)
350 COG2345 Predicted transcriptio 63.8 13 0.00027 37.6 5.2 25 515-539 24-48 (218)
351 PF14493 HTH_40: Helix-turn-he 63.7 11 0.00023 32.3 4.1 29 515-543 12-40 (91)
352 PRK11161 fumarate/nitrate redu 63.6 8.2 0.00018 38.0 3.9 27 516-546 184-210 (235)
353 PRK11512 DNA-binding transcrip 63.4 40 0.00086 31.0 8.2 48 489-539 28-77 (144)
354 PRK11753 DNA-binding transcrip 63.1 36 0.00077 32.7 8.2 27 516-546 168-194 (211)
355 PF01527 HTH_Tnp_1: Transposas 62.5 8.3 0.00018 31.2 3.1 27 515-541 22-48 (76)
356 TIGR02607 antidote_HigA addict 62.4 16 0.00035 29.7 4.9 25 515-539 17-41 (78)
357 cd04764 HTH_MlrA-like_sg1 Heli 62.0 10 0.00022 30.3 3.5 23 517-539 1-23 (67)
358 KOG0484 Transcription factor P 61.9 12 0.00026 33.5 4.1 50 495-548 27-76 (125)
359 smart00354 HTH_LACI helix_turn 61.6 8.2 0.00018 31.4 2.9 23 517-539 1-23 (70)
360 smart00422 HTH_MERR helix_turn 61.5 6.3 0.00014 31.3 2.2 25 517-541 1-25 (70)
361 PRK09413 IS2 repressor TnpA; R 61.4 18 0.00039 32.6 5.4 34 504-541 21-54 (121)
362 PRK09726 antitoxin HipB; Provi 60.5 14 0.0003 31.4 4.3 25 515-539 24-48 (88)
363 PF08784 RPA_C: Replication pr 59.6 15 0.00032 32.0 4.3 42 496-537 44-86 (102)
364 PRK11557 putative DNA-binding 59.3 19 0.00041 36.8 5.8 48 490-539 3-53 (278)
365 PRK04984 fatty acid metabolism 59.1 14 0.0003 36.8 4.6 30 513-546 27-57 (239)
366 PRK10161 transcriptional regul 58.9 11 0.00024 36.1 3.8 50 496-546 154-208 (229)
367 cd04763 HTH_MlrA-like Helix-Tu 58.8 12 0.00026 29.9 3.4 23 517-539 1-23 (68)
368 PRK01905 DNA-binding protein F 58.4 42 0.0009 28.0 6.7 36 501-539 38-73 (77)
369 PRK09391 fixK transcriptional 58.3 12 0.00026 37.2 4.0 28 516-547 179-206 (230)
370 COG1318 Predicted transcriptio 57.8 10 0.00022 36.8 3.3 28 515-542 60-87 (182)
371 TIGR01889 Staph_reg_Sar staphy 57.7 68 0.0015 28.2 8.3 44 496-539 22-66 (109)
372 smart00342 HTH_ARAC helix_turn 57.6 17 0.00036 29.0 4.1 26 516-541 1-26 (84)
373 PRK09863 putative frv operon r 57.3 36 0.00078 38.9 8.1 102 423-545 17-121 (584)
374 cd00086 homeodomain Homeodomai 57.2 27 0.00058 26.5 5.0 51 496-546 6-57 (59)
375 PF12085 DUF3562: Protein of u 57.1 21 0.00044 29.5 4.4 40 518-560 9-48 (66)
376 PRK11050 manganese transport r 57.1 17 0.00038 34.1 4.7 26 514-539 49-74 (152)
377 PF00165 HTH_AraC: Bacterial r 56.9 16 0.00034 26.5 3.5 25 515-539 7-31 (42)
378 TIGR02702 SufR_cyano iron-sulf 56.8 22 0.00048 34.9 5.6 26 515-540 14-39 (203)
379 PF08006 DUF1700: Protein of u 56.7 28 0.0006 33.5 6.1 57 483-539 3-63 (181)
380 PRK10402 DNA-binding transcrip 56.3 26 0.00056 34.6 6.0 47 497-547 149-196 (226)
381 PF05225 HTH_psq: helix-turn-h 55.6 29 0.00063 26.1 4.7 22 517-538 17-38 (45)
382 PRK10955 DNA-binding transcrip 55.4 8.8 0.00019 36.7 2.5 49 496-545 156-209 (232)
383 PF06413 Neugrin: Neugrin; In 55.1 19 0.00042 36.4 4.9 42 496-538 10-51 (225)
384 COG2512 Predicted membrane-ass 55.1 17 0.00037 37.6 4.6 46 495-546 191-236 (258)
385 PF04703 FaeA: FaeA-like prote 54.9 12 0.00027 30.3 2.8 24 515-538 14-37 (62)
386 PRK09863 putative frv operon r 54.7 25 0.00054 40.2 6.3 46 497-546 2-47 (584)
387 TIGR01387 cztR_silR_copR heavy 54.6 19 0.00041 33.8 4.6 49 496-545 147-200 (218)
388 PRK10411 DNA-binding transcrip 54.6 23 0.00049 36.0 5.4 41 499-542 4-44 (240)
389 PRK03902 manganese transport t 54.5 23 0.00051 32.6 5.0 25 514-538 20-44 (142)
390 PF13556 HTH_30: PucR C-termin 54.4 35 0.00076 26.8 5.3 35 515-549 11-45 (59)
391 COG3093 VapI Plasmid maintenan 54.4 19 0.00042 32.2 4.1 35 503-539 12-46 (104)
392 COG1405 SUA7 Transcription ini 54.3 2.8E+02 0.0062 29.1 15.2 25 515-539 250-274 (285)
393 PRK11511 DNA-binding transcrip 54.1 1.7E+02 0.0037 26.4 10.5 38 409-446 11-48 (127)
394 TIGR02395 rpoN_sigma RNA polym 53.8 1.1E+02 0.0025 33.8 11.0 35 412-446 304-341 (429)
395 PRK14082 hypothetical protein; 53.8 42 0.00092 27.5 5.6 56 319-376 8-63 (65)
396 PF01710 HTH_Tnp_IS630: Transp 53.7 18 0.00039 32.6 4.0 24 515-538 17-40 (119)
397 COG4709 Predicted membrane pro 53.4 26 0.00057 34.5 5.3 59 483-541 3-65 (195)
398 PF12324 HTH_15: Helix-turn-he 53.3 37 0.00081 28.8 5.5 29 420-448 35-63 (77)
399 PF06322 Phage_NinH: Phage Nin 53.3 20 0.00043 29.1 3.6 27 504-537 11-37 (64)
400 PRK06266 transcription initiat 53.0 41 0.00088 32.8 6.6 47 489-539 13-59 (178)
401 PRK09706 transcriptional repre 52.9 20 0.00044 32.7 4.3 25 515-539 17-41 (135)
402 PRK04158 transcriptional repre 52.4 23 0.0005 36.5 5.0 58 485-546 168-227 (256)
403 smart00530 HTH_XRE Helix-turn- 52.1 24 0.00053 24.8 3.9 25 515-539 9-33 (56)
404 PF09012 FeoC: FeoC like trans 51.9 11 0.00024 30.6 2.1 25 515-539 13-37 (69)
405 PF12844 HTH_19: Helix-turn-he 51.9 24 0.00051 27.6 4.0 25 515-539 11-35 (64)
406 PRK09392 ftrB transcriptional 51.9 16 0.00035 36.0 3.7 27 516-546 173-199 (236)
407 TIGR02394 rpoS_proteo RNA poly 51.6 2.3E+02 0.0049 29.2 12.3 30 285-314 140-169 (285)
408 PRK11517 transcriptional regul 51.5 27 0.00059 33.0 5.2 49 496-545 147-200 (223)
409 TIGR02812 fadR_gamma fatty aci 51.3 22 0.00048 35.3 4.6 31 512-546 25-56 (235)
410 smart00352 POU Found in Pit-Oc 50.7 29 0.00062 29.3 4.4 31 504-538 16-52 (75)
411 PRK13509 transcriptional repre 50.7 25 0.00055 35.8 5.0 25 515-539 18-42 (251)
412 COG1846 MarR Transcriptional r 50.3 33 0.00072 29.4 5.1 40 497-539 20-59 (126)
413 TIGR02944 suf_reg_Xantho FeS a 50.2 26 0.00057 31.7 4.6 26 513-538 22-47 (130)
414 cd01392 HTH_LacI Helix-turn-he 50.0 10 0.00022 28.4 1.6 21 520-540 1-21 (52)
415 cd00093 HTH_XRE Helix-turn-hel 49.9 32 0.00069 24.4 4.2 25 515-539 11-35 (58)
416 smart00389 HOX Homeodomain. DN 49.6 28 0.0006 26.3 4.0 47 497-543 7-54 (56)
417 TIGR00738 rrf2_super rrf2 fami 49.4 32 0.00069 30.9 5.0 25 514-538 23-47 (132)
418 TIGR00180 parB_part ParB-like 49.4 30 0.00065 33.5 5.1 43 495-539 101-143 (187)
419 PF14502 HTH_41: Helix-turn-he 49.1 32 0.00069 26.6 4.0 29 515-547 5-33 (48)
420 smart00862 Trans_reg_C Transcr 48.8 51 0.0011 26.3 5.7 50 496-546 5-60 (78)
421 PRK10225 DNA-binding transcrip 48.8 25 0.00054 35.5 4.6 37 504-546 22-59 (257)
422 PRK10141 DNA-binding transcrip 48.7 44 0.00095 30.4 5.7 49 491-546 7-56 (117)
423 COG1321 TroR Mn-dependent tran 48.7 32 0.00068 32.8 5.0 42 497-538 4-46 (154)
424 PRK14101 bifunctional glucokin 48.6 32 0.00069 39.8 6.0 52 486-539 343-397 (638)
425 PRK06424 transcription factor; 48.1 26 0.00057 33.1 4.3 25 515-539 96-120 (144)
426 PRK11014 transcriptional repre 48.0 36 0.00078 31.4 5.2 30 513-546 22-51 (141)
427 PF00292 PAX: 'Paired box' dom 47.8 39 0.00085 31.2 5.2 32 503-539 25-56 (125)
428 PF13443 HTH_26: Cro/C1-type H 47.7 18 0.0004 28.2 2.7 26 515-540 9-34 (63)
429 PRK05657 RNA polymerase sigma 47.7 2.3E+02 0.005 30.0 11.9 33 282-314 177-209 (325)
430 cd04768 HTH_BmrR-like Helix-Tu 47.7 14 0.0003 32.1 2.2 26 517-542 1-26 (96)
431 PF12298 Bot1p: Eukaryotic mit 47.5 38 0.00082 33.0 5.4 38 497-537 17-54 (172)
432 COG4465 CodY Pleiotropic trans 47.4 69 0.0015 32.5 7.2 55 489-547 175-231 (261)
433 TIGR02431 pcaR_pcaU beta-ketoa 47.4 32 0.0007 34.6 5.2 35 504-538 12-46 (248)
434 PRK10643 DNA-binding transcrip 47.4 24 0.00051 33.3 4.0 49 496-545 149-202 (222)
435 PRK09834 DNA-binding transcrip 47.1 31 0.00067 35.2 5.0 37 502-538 12-48 (263)
436 PRK15340 transcriptional regul 46.8 3.2E+02 0.007 27.6 12.9 31 416-446 118-148 (216)
437 COG0568 RpoD DNA-directed RNA 46.7 29 0.00064 37.3 4.9 34 245-278 65-98 (342)
438 PRK13890 conjugal transfer pro 46.6 29 0.00064 31.5 4.3 25 515-539 17-41 (120)
439 PRK12469 RNA polymerase factor 46.5 1.9E+02 0.0041 32.7 11.4 25 422-446 368-392 (481)
440 cd00383 trans_reg_C Effector d 46.3 45 0.00098 27.7 5.2 49 496-545 23-76 (95)
441 PF07900 DUF1670: Protein of u 46.3 1.9E+02 0.0042 29.3 10.2 36 411-447 94-129 (220)
442 COG1737 RpiR Transcriptional r 46.2 45 0.00097 34.5 6.1 51 486-538 5-58 (281)
443 PHA00738 putative HTH transcri 45.9 39 0.00085 30.5 4.8 36 499-537 12-47 (108)
444 PRK08583 RNA polymerase sigma 45.8 1.6E+02 0.0035 29.6 10.0 30 283-312 121-150 (257)
445 PF07037 DUF1323: Putative tra 45.7 23 0.0005 32.5 3.3 23 517-539 1-23 (122)
446 TIGR02698 CopY_TcrY copper tra 45.0 56 0.0012 30.0 5.9 45 496-543 1-49 (130)
447 cd04775 HTH_Cfa-like Helix-Tur 44.9 16 0.00034 32.1 2.1 26 517-542 2-27 (102)
448 PF09012 FeoC: FeoC like trans 44.9 31 0.00067 27.9 3.8 25 423-447 14-38 (69)
449 PRK13239 alkylmercury lyase; P 44.9 42 0.00092 33.6 5.4 29 420-448 33-61 (206)
450 cd01105 HTH_GlnR-like Helix-Tu 44.5 17 0.00038 30.9 2.3 25 517-541 2-26 (88)
451 PRK09943 DNA-binding transcrip 44.3 31 0.00068 33.1 4.4 25 515-539 19-43 (185)
452 PRK09744 DNA-binding transcrip 44.2 31 0.00066 29.1 3.6 19 518-536 12-30 (75)
453 PF04552 Sigma54_DBD: Sigma-54 44.2 7.5 0.00016 37.3 0.0 48 489-538 24-71 (160)
454 PRK00082 hrcA heat-inducible t 44.0 35 0.00076 36.5 5.0 65 495-560 2-80 (339)
455 PRK11414 colanic acid/biofilm 43.9 25 0.00054 34.6 3.7 31 512-546 30-60 (221)
456 PRK08359 transcription factor; 43.8 32 0.00069 33.6 4.2 35 515-549 97-138 (176)
457 cd04773 HTH_TioE_rpt2 Second H 43.7 17 0.00037 32.2 2.2 25 517-541 1-25 (108)
458 TIGR00373 conserved hypothetic 43.7 40 0.00086 32.2 4.8 24 515-538 27-50 (158)
459 PRK15044 transcriptional regul 43.5 1.3E+02 0.0028 31.8 9.0 60 249-317 172-231 (295)
460 PRK05932 RNA polymerase factor 43.4 2.3E+02 0.005 31.7 11.4 25 422-446 342-366 (455)
461 PRK11512 DNA-binding transcrip 43.3 2.6E+02 0.0057 25.5 10.4 24 423-446 54-77 (144)
462 PRK10219 DNA-binding transcrip 43.2 58 0.0013 28.2 5.5 26 515-540 20-45 (107)
463 COG1349 GlpR Transcriptional r 43.1 29 0.00063 35.4 4.1 36 498-536 4-39 (253)
464 TIGR03338 phnR_burk phosphonat 43.1 26 0.00057 34.0 3.7 30 513-546 31-60 (212)
465 cd01107 HTH_BmrR Helix-Turn-He 43.1 18 0.00039 32.0 2.3 26 517-542 1-26 (108)
466 PRK10906 DNA-binding transcrip 42.7 36 0.00079 34.7 4.7 37 499-538 5-41 (252)
467 cd04782 HTH_BltR Helix-Turn-He 42.5 19 0.0004 31.3 2.2 25 517-541 1-25 (97)
468 cd04772 HTH_TioE_rpt1 First He 42.4 19 0.00041 31.4 2.3 26 517-542 1-26 (99)
469 PF10078 DUF2316: Uncharacteri 42.3 53 0.0012 28.6 4.9 24 515-538 22-45 (89)
470 TIGR03826 YvyF flagellar opero 42.3 76 0.0017 29.8 6.3 42 411-452 34-75 (137)
471 COG3711 BglG Transcriptional a 42.2 31 0.00067 38.2 4.5 47 499-546 84-130 (491)
472 PF02787 CPSase_L_D3: Carbamoy 42.1 2.5E+02 0.0054 25.7 9.6 43 489-538 52-94 (123)
473 COG3877 Uncharacterized protei 42.0 60 0.0013 29.3 5.2 47 494-544 39-85 (122)
474 PRK10870 transcriptional repre 42.0 2.8E+02 0.0062 26.6 10.6 24 423-446 71-94 (176)
475 PF04963 Sigma54_CBD: Sigma-54 41.9 47 0.001 32.6 5.2 60 495-558 28-94 (194)
476 cd01106 HTH_TipAL-Mta Helix-Tu 41.8 19 0.00042 31.4 2.2 25 517-541 1-25 (103)
477 PF13412 HTH_24: Winged helix- 41.8 73 0.0016 23.5 5.1 23 423-445 17-39 (48)
478 cd00592 HTH_MerR-like Helix-Tu 41.8 19 0.00042 30.9 2.2 25 517-541 1-25 (100)
479 TIGR00270 conserved hypothetic 41.7 37 0.00081 32.3 4.3 25 515-539 81-105 (154)
480 cd04765 HTH_MlrA-like_sg2 Heli 41.7 30 0.00066 30.2 3.5 23 517-539 1-23 (99)
481 cd04766 HTH_HspR Helix-Turn-He 41.6 19 0.00041 30.7 2.1 26 517-542 2-27 (91)
482 PRK11534 DNA-binding transcrip 41.4 33 0.00072 33.7 4.1 38 503-546 19-56 (224)
483 PRK03837 transcriptional regul 41.2 35 0.00075 33.9 4.2 30 513-546 33-63 (241)
484 PRK10434 srlR DNA-bindng trans 41.0 35 0.00075 34.9 4.3 38 499-539 5-42 (256)
485 cd04768 HTH_BmrR-like Helix-Tu 41.0 2.3E+02 0.005 24.4 8.8 35 515-549 56-90 (96)
486 cd04780 HTH_MerR-like_sg5 Heli 40.8 20 0.00044 31.1 2.2 25 517-541 1-25 (95)
487 cd04788 HTH_NolA-AlbR Helix-Tu 40.7 20 0.00044 31.0 2.1 26 517-542 1-26 (96)
488 TIGR02018 his_ut_repres histid 40.6 41 0.00088 33.4 4.6 28 515-546 23-51 (230)
489 PF10668 Phage_terminase: Phag 40.5 56 0.0012 26.4 4.4 29 417-445 16-44 (60)
490 KOG1597 Transcription initiati 40.5 4.3E+02 0.0093 28.1 11.9 126 418-546 159-290 (308)
491 cd04789 HTH_Cfa Helix-Turn-Hel 40.4 21 0.00045 31.3 2.2 26 517-542 2-27 (102)
492 PRK11511 DNA-binding transcrip 40.4 57 0.0012 29.5 5.2 33 504-540 17-49 (127)
493 PRK10163 DNA-binding transcrip 40.3 44 0.00096 34.3 5.0 25 514-538 38-62 (271)
494 cd01109 HTH_YyaN Helix-Turn-He 40.1 21 0.00046 31.7 2.3 26 517-542 1-26 (113)
495 PRK13777 transcriptional regul 39.9 62 0.0014 31.7 5.7 41 495-538 41-81 (185)
496 PF05930 Phage_AlpA: Prophage 39.8 34 0.00074 26.1 3.1 24 517-540 4-27 (51)
497 COG1481 Uncharacterized protei 39.8 56 0.0012 34.6 5.6 43 494-539 251-295 (308)
498 PHA02943 hypothetical protein; 39.7 46 0.001 31.9 4.4 24 515-538 23-46 (165)
499 TIGR02325 C_P_lyase_phnF phosp 39.5 34 0.00075 33.8 3.9 26 517-546 33-58 (238)
500 cd04774 HTH_YfmP Helix-Turn-He 39.4 22 0.00047 31.0 2.1 26 517-542 1-26 (96)
No 1
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=100.00 E-value=7.3e-65 Score=540.80 Aligned_cols=315 Identities=38% Similarity=0.651 Sum_probs=299.0
Q ss_pred CChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHH--------------------HHHHHHHHhhhhCCCCcHHHHHHHc
Q 008556 245 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIR--------------------LEKEKSKLQSQFGREPTLIEWAKAI 304 (561)
Q Consensus 245 ~~d~l~~Yl~~i~~~~lLT~eEE~eL~~~i~~~~~--------------------le~~~~~l~~~~g~~pt~~ewA~a~ 304 (561)
..|+++.||++|++.||||++||++|+++||.++. |++++..|++.+|++||..|||.++
T Consensus 58 ~~d~v~~yl~~igr~~lL~~~eEv~l~~~vq~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~g~~pt~~ewa~~~ 137 (415)
T PRK07598 58 STDLVRLYLQEIGRVRLLGRDEEVSEAQKVQRYMKLIVLANAAKEGDEVIKPYLRLIEVRERLTSELGHRPSLERWAKTA 137 (415)
T ss_pred CCChHHHHHHhcccccCCCHHHHHHHHHHHHHHHHHhhhhhhhhcccchhhhHHHHHHHHHHHHHHhCCCCCHHHHHHHh
Confidence 57899999999999999999999999999999999 8999999999999999999999554
Q ss_pred ----------------------cCCHHHHHHHHhhcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhh
Q 008556 305 ----------------------GLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSV 362 (561)
Q Consensus 305 ----------------------g~~~~eL~~~l~~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAi 362 (561)
||++++|+..++.|..|+++||.+|+++|++||++|.++|++++||||||++|||+|+
T Consensus 138 ~~~~~~l~~~l~~~~~~~~~~~~l~~~eL~~~l~~G~~A~e~LI~~nlrLVvsiAkky~~~g~~~eDLiQEG~iGL~rav 217 (415)
T PRK07598 138 DISLADLKPTLAEGKRRWAEIAKLTVEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAV 217 (415)
T ss_pred CCcHHHHHHhhhhhhhhhhhhccCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHH
Confidence 5566677777788999999999999999999999999999999999999999999999
Q ss_pred hhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHH
Q 008556 363 EKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLER 442 (561)
Q Consensus 363 ekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ 442 (561)
++|||++|++|+|||+||||++|.+++++++++||+|.|+...+++++++.+.+.+++||.|+.+|||+.+|+++++|+.
T Consensus 218 ekFDp~rG~rFSTYa~wwIRqaI~r~i~~~srtIrlP~~i~e~l~~lrk~~r~L~~~lgR~pt~~EiA~~l~is~~~vr~ 297 (415)
T PRK07598 218 EKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVRE 297 (415)
T ss_pred HHcCcccCCCHHHHHHHHHHHHHHHHHHHcCCceehhHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHH
Q 008556 443 LIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEV 522 (561)
Q Consensus 443 ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EI 522 (561)
++.....++|||.+++++++..+.+.+.++. .+|++.+....+...|..+|..||++||.||.|||||+||+++|++||
T Consensus 298 ~l~~~~~~~SLd~~vg~~~d~~l~d~l~~~~-~~pee~~~~~~l~~~L~~~L~~L~~reR~VI~LRygl~d~~~~Tl~EI 376 (415)
T PRK07598 298 VLLRVPRSVSLETKVGKDKDTELGDLLETDD-ISPEEMLMRESLQRDLQHLLADLTSRERDVIRMRFGLADGHTYSLAEI 376 (415)
T ss_pred HHHHccCCcccccccCCCccccHHHhccCCC-CCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCCCCCCCHHHH
Confidence 9999999999999999888888888876543 578888888899999999999999999999999999999999999999
Q ss_pred HHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhhhh
Q 008556 523 GNIFGLSKERVRQLESRALYRLKQSLGGKASYGYADLL 560 (561)
Q Consensus 523 Ae~LGISrerVRqie~RALkKLR~~l~~~~l~~yldll 560 (561)
|+.||||+++||+++++|++|||+.-....+++|++.|
T Consensus 377 A~~LGvS~erVRqie~rAl~KLR~~~~~~~l~~y~~~~ 414 (415)
T PRK07598 377 GRALDLSRERVRQIESKALQKLRQPKRRNRIRDYLELL 414 (415)
T ss_pred HHHHCcCHHHHHHHHHHHHHHHhchhHHHHHHHHHHhc
Confidence 99999999999999999999999999999999999764
No 2
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=5.5e-62 Score=515.00 Aligned_cols=312 Identities=37% Similarity=0.728 Sum_probs=299.9
Q ss_pred CChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHH
Q 008556 245 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK 324 (561)
Q Consensus 245 ~~d~l~~Yl~~i~~~~lLT~eEE~eL~~~i~~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~~l~~G~~Are~ 324 (561)
..|++..||++|+++|+||++||++|+++|++++.+++++.+|+...|++|+..+||.++|++..+|..+++.|..|++.
T Consensus 61 ~~d~l~~Yl~~i~~~~lLt~eEE~~La~~i~~~~~~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~ 140 (373)
T PRK07406 61 TEDSIRVYLQEIGRIRLLRPDEEIELARKIADLLELEELREQFESELGREPSDKEWAELVDMPLPKFRRRLMLGRRAKEK 140 (373)
T ss_pred CCCHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccchhhHhhhccccHHHHHHHHhcCHHHHHH
Confidence 35789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHH
Q 008556 325 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT 404 (561)
Q Consensus 325 LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~~ 404 (561)
||..|+++|+++|++|.++|.+++||+|||+||||+|+++|||.+|++|+|||+||||++|.++|++++++||+|.|+..
T Consensus 141 Li~~~l~lV~~iA~ry~~~~~~~eDLiQEG~igL~~Ai~kFd~~kg~~FsTYA~wWIRqaI~~~I~~~~r~IRlP~~~~~ 220 (373)
T PRK07406 141 MVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYE 220 (373)
T ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhcCCceeCCHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHHHHHH
Q 008556 405 LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQ 484 (561)
Q Consensus 405 ~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~le~~ 484 (561)
.+++++++...+.+++|+.||.+|||+.+|+++++|..++.....++|||.+++++++..+.+++++.. .+|++.+...
T Consensus 221 ~~~~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~~~~~~~~~~~SLd~~i~~~~~~~l~d~l~d~~-~~pee~~~~~ 299 (373)
T PRK07406 221 TISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIEADG-ETPEDDVAKN 299 (373)
T ss_pred HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCcccHHHhcCCCC-CCHHHHHHHH
Confidence 999999999999999999999999999999999999999888889999999998777778888888763 4788888888
Q ss_pred HHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhh
Q 008556 485 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYA 557 (561)
Q Consensus 485 e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~l~~yl 557 (561)
.+...|..+|..||++||.||.+|||++|++++|++|||+.||||++||||++.+|++|||+......++.|+
T Consensus 300 ~~~~~L~~aL~~L~~rEr~IL~lrygl~~~~~~Tl~EIA~~lgiS~eRVRQie~rAL~KLR~~~~~~~l~~~~ 372 (373)
T PRK07406 300 LLREDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSVLKEYI 372 (373)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHhchhHHHHHHHHh
Confidence 8999999999999999999999999999889999999999999999999999999999999999888898886
No 3
>PRK05949 RNA polymerase sigma factor; Validated
Probab=100.00 E-value=2e-61 Score=504.39 Aligned_cols=311 Identities=40% Similarity=0.676 Sum_probs=297.5
Q ss_pred CChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHH
Q 008556 245 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK 324 (561)
Q Consensus 245 ~~d~l~~Yl~~i~~~~lLT~eEE~eL~~~i~~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~~l~~G~~Are~ 324 (561)
..|++..||++|+++|+||++||++|+++|+.++.+++.+..|+..+|++|+..+|+.+++|++.+|+..++.|+.|++.
T Consensus 16 ~~d~~~~yl~~i~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~eL~~~~~~g~~A~~~ 95 (327)
T PRK05949 16 SADMVRTYLHEIGRVPLLTHEQEIVYGKQVQQMMSLLEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGKRAKQK 95 (327)
T ss_pred CCCHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCchHHHHHhccCCHHHHHHHHHccHHHHHH
Confidence 46899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHH
Q 008556 325 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT 404 (561)
Q Consensus 325 LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~~ 404 (561)
||..|+++|+++|++|.+++.+++|||||||+|||+++++|||++|++|+|||+||||++|.++|.+++++||+|.|+..
T Consensus 96 Li~~~~~~V~~iA~~y~~~~~~~eDLvQEg~igL~~a~~kfd~~~G~rFsTYa~wwIrq~I~r~i~~~~r~iRlP~~~~~ 175 (327)
T PRK05949 96 MIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHITE 175 (327)
T ss_pred HHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHhcCCcCCCChhhhhHHHHHHHHHHHHHHcCCceeCCHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHHHHHH
Q 008556 405 LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQ 484 (561)
Q Consensus 405 ~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~le~~ 484 (561)
.+++++++.+.+..++|++|+.+|||+.+|+++++|..++.....++|||.+++++++..+.+++.|.. .+|++.+...
T Consensus 176 ~~~~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~~~l~d~~-~~pe~~~~~~ 254 (327)
T PRK05949 176 KLNKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMARQPISLDVRVGDNQDTELSELLEDEG-PSPDQYITQE 254 (327)
T ss_pred HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhccccccCCCcCCCCCccHHhhcCCCC-CCHHHHHHHH
Confidence 999999999999999999999999999999999999999998899999999998777777888888765 5789889988
Q ss_pred HHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhh
Q 008556 485 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD 558 (561)
Q Consensus 485 e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~l~~yld 558 (561)
.+...|..+|+.||++||.||.+||||+|++++|++|||+.||||+++|||++.+|++|||+. ...++.|+.
T Consensus 255 ~~~~~L~~~L~~L~~rer~Vi~lr~gl~~~e~~Tl~EIa~~lgiS~erVrq~~~rAl~kLr~~--~~~l~~~~~ 326 (327)
T PRK05949 255 LLRQDLNNLLAELTPQQREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHLRRR--RANVKEYLA 326 (327)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH--HHHHHHHHh
Confidence 999999999999999999999999999999999999999999999999999999999999994 456777764
No 4
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family. This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).
Probab=100.00 E-value=1.2e-60 Score=492.69 Aligned_cols=298 Identities=44% Similarity=0.755 Sum_probs=285.6
Q ss_pred hHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHHH
Q 008556 247 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLI 326 (561)
Q Consensus 247 d~l~~Yl~~i~~~~lLT~eEE~eL~~~i~~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~~l~~G~~Are~LI 326 (561)
|++..||++|+++|+||++||.+|+++++.++.++..+..|+.+.|++||..+||+++|+++.+|...++.|..|++.||
T Consensus 1 ~~~~~yl~~~~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~Lv 80 (298)
T TIGR02997 1 DLVRLYLQEIGRVPLLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQRAKEKMI 80 (298)
T ss_pred CcHHHHHHHccccCCCCHHHHHHHHHHHHHHhHHHHHHHHHHHhhcCCCcHHHHHHhccCCHHHHHHHHhccHHHHHHHH
Confidence 36788999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHHHH
Q 008556 327 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLL 406 (561)
Q Consensus 327 ~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~~~l 406 (561)
.+|+++|++||++|.++|.+++|||||||+|||+|+++|||.+|++|+|||+||||++|.+++.+++++||+|.++...+
T Consensus 81 ~~~lrlV~~iA~~y~~~~~~~eDLiQEg~igL~~a~~kfd~~~g~rFsTya~~wIr~~I~r~i~~~~r~vr~p~~~~~~~ 160 (298)
T TIGR02997 81 KANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWWIRQGITRAIANQSRTIRLPIHITEKL 160 (298)
T ss_pred HHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCccCCCChHHHHHHHHHHHHHHHHHhcCCCeeCcHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHHHHHHHH
Q 008556 407 SKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLM 486 (561)
Q Consensus 407 ~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~le~~e~ 486 (561)
++++++...+.+.+|+.|+.+|||+.+|+++++|..++.....++|||.+++++++..+.+.+.+. ..+|++.+...+.
T Consensus 161 ~~~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~~~~~~~~~-~~~pe~~~~~~~~ 239 (298)
T TIGR02997 161 NKIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPVGDEEDTELGDLLEDD-GESPEEQVERESL 239 (298)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHcccCcccCCCcCCCCcchHHHhccCC-CCCHHHHHHHHHH
Confidence 999999999999999999999999999999999999999888999999998776666777777774 4578888998889
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556 487 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 545 (561)
Q Consensus 487 ~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 545 (561)
...|..+|+.||++||+||.+||||+|++++|++|||+.||||++||||++++|++|||
T Consensus 240 ~~~L~~~L~~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVrq~~~rAl~kLr 298 (298)
T TIGR02997 240 RQDLESLLAELTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRKLR 298 (298)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence 99999999999999999999999999989999999999999999999999999999996
No 5
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=100.00 E-value=2.6e-60 Score=494.27 Aligned_cols=310 Identities=38% Similarity=0.644 Sum_probs=296.1
Q ss_pred ChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHH
Q 008556 246 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKL 325 (561)
Q Consensus 246 ~d~l~~Yl~~i~~~~lLT~eEE~eL~~~i~~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~~l~~G~~Are~L 325 (561)
+|++..||++|+++|+||++||.+|+++|++++.+++++..|+.++|++|+..+||.++++++.+|+..++.|..|+++|
T Consensus 7 ~~~~~~yl~~i~~~~lLt~eeE~~La~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~g~~A~~~L 86 (317)
T PRK07405 7 TDLVRTYLREIGRVPLLTHEEEILYGKQVQRLVALQEIREELAEELGREPTDAEWAKAAKLSEEELRSAIAEGEAAKRKM 86 (317)
T ss_pred CcHHHHHHHHccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccchHHHhhhccCCHHHHHHHHhccHHHHHHH
Confidence 57899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHHH
Q 008556 326 INANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTL 405 (561)
Q Consensus 326 I~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~~~ 405 (561)
|..|+++|+++|++|.+++.+++||+||||+|||+++++|||++|++|+|||+||||++|.++|.+++++||+|.|+...
T Consensus 87 ~~~~~~~V~~~a~~~~~~~~~~eDLvQEg~i~L~~a~~~fd~~~g~rf~tYa~~wIR~~I~~~i~~~~~~ir~p~~~~~~ 166 (317)
T PRK07405 87 VEANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEK 166 (317)
T ss_pred HHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcCCCCChHHHHHHHHHHHHHHHHHhcCCCccCChHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHHHHHHH
Q 008556 406 LSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQL 485 (561)
Q Consensus 406 l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~le~~e 485 (561)
+++++++...+...+|+.|+.+|||+.+|+++++|..++......+|||.+++++.+..+.++++++. ..|++.+...+
T Consensus 167 ~~~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~~~~~d~~-~~pe~~~~~~~ 245 (317)
T PRK07405 167 LNKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERARQPLSLDLRVGDNQDTELGELLEDTG-ASPEDFATQSS 245 (317)
T ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCeeecCCCCCCCCccHHHhhcCCC-CCHHHHHHHHH
Confidence 99999999999999999999999999999999999999988888999999998777777888887764 57888899889
Q ss_pred HHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhh
Q 008556 486 MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD 558 (561)
Q Consensus 486 ~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~l~~yld 558 (561)
+...|..+|+.||++||.||.+||||+|++++|++|||+.||||++||||++.+|++|||+. ...+..|+.
T Consensus 246 ~~~~l~~al~~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVRqi~~rAl~kLr~~--~~~l~~~~~ 316 (317)
T PRK07405 246 LQLDLERLMEDLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLRKR--KANIQEYLA 316 (317)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHhhcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH--HHHHHHHHh
Confidence 99999999999999999999999999999999999999999999999999999999999995 456777764
No 6
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=100.00 E-value=2.9e-59 Score=508.70 Aligned_cols=301 Identities=35% Similarity=0.613 Sum_probs=277.2
Q ss_pred CChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHH
Q 008556 245 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK 324 (561)
Q Consensus 245 ~~d~l~~Yl~~i~~~~lLT~eEE~eL~~~i~~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~~l~~G~~Are~ 324 (561)
..|++..||++|+++|+||++||++|+++|+.+..++.. +. ...+|+. ....+|.+.++.|..|+++
T Consensus 209 ~~d~l~~YL~~i~~~~lLt~eEE~~La~~i~~g~~~~~~---~~-------~~~~~~~---~~~~~l~~~~~~g~~Ar~~ 275 (509)
T PRK05901 209 TADPVKAYLKQIGKVKLLNAEEEVELAKRIEAGLYAEEL---LA-------EGEKLDP---ELRRDLQWIGRDGKRAKNH 275 (509)
T ss_pred cccHHHHHHHHhccCCCCCHHHHHHHHHHHHhCCchhhh---hh-------hcccchh---hhhhhhhhhccchHHHHHH
Confidence 568999999999999999999999999999875433321 11 1123442 2457788889999999999
Q ss_pred HHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHH
Q 008556 325 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT 404 (561)
Q Consensus 325 LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~~ 404 (561)
||.+|+|||++||++|.++|++++||||||+||||+|+++|||++|++|+|||+||||++|.++|++++|+||+|.|+..
T Consensus 276 LI~sNLrLVvsIAkrY~~~Gl~~eDLIQEGnIGLikAvekFDp~rG~rFSTYA~wWIRqaI~raI~d~~r~IRvP~~~~e 355 (509)
T PRK05901 276 LLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE 355 (509)
T ss_pred HHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCchhhhHHHHHHHHHHHHHHcCCceecCHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHHHHHH
Q 008556 405 LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQ 484 (561)
Q Consensus 405 ~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~le~~ 484 (561)
.++++.++.+.+.+.+||.|+.+|||+.+|+++++|..++.....++|||.+++++++..+.+++.|.....|++.+...
T Consensus 356 ~i~kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~~p~~~~~~~ 435 (509)
T PRK05901 356 TINKLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQKYNREPISLDKTIGKEGDSQFGDFIEDSEAVSPVDAVSFT 435 (509)
T ss_pred HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccccccccCCcccHHHhccCCCCCCHHHHHHHH
Confidence 99999999999999999999999999999999999999999888999999999877777888999988777899999999
Q ss_pred HHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhh
Q 008556 485 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD 558 (561)
Q Consensus 485 e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~l~~yld 558 (561)
.++..|..+|..|++|||.||.+||||++++++|++|||+.||||++|||||+.+||+|||.......|+.|++
T Consensus 436 ~l~~~L~~aL~~L~eREr~VI~lRyGL~~~e~~TL~EIa~~lGVSrERVRQIe~kAL~KLR~~~~~~~l~~~l~ 509 (509)
T PRK05901 436 LLQDQLQEVLETLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKLRHPSRSQVLRDFLD 509 (509)
T ss_pred HHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999974
No 7
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=100.00 E-value=4.2e-59 Score=482.84 Aligned_cols=314 Identities=36% Similarity=0.654 Sum_probs=289.1
Q ss_pred CChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhh-hhCCCCcHH---------------HHHHHccCCH
Q 008556 245 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQS-QFGREPTLI---------------EWAKAIGLSC 308 (561)
Q Consensus 245 ~~d~l~~Yl~~i~~~~lLT~eEE~eL~~~i~~~~~le~~~~~l~~-~~g~~pt~~---------------ewA~a~g~~~ 308 (561)
..|.+..|+.+++..+++++++|.++.+.++....+......|.. ..+..|+.. +|+..+..++
T Consensus 7 ~~d~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~E 86 (342)
T COG0568 7 SADAVRAYLDEIGRIPLLVREAEVELAKQLEDEQLLVELGEDLTDLKLGREPSERARRPAGRLSFYIRAIEAAPLLTPEE 86 (342)
T ss_pred chhHHHHHHHHhcchhhhhHHHHHHHHHHHhHhhhhhHHHHHHHhcccccccchhhhhhhhhHHHHHHHHhhhcccChHH
Confidence 357889999999999999999999999999887777667777776 677888876 6666555554
Q ss_pred -HHHHHHHhhcH---HHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHH
Q 008556 309 -RDLKSELHSGN---SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 384 (561)
Q Consensus 309 -~eL~~~l~~G~---~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqa 384 (561)
..|..++..|. .|+.+||.+|+|||++||++|.|+|+++.|||||||||||+|+++|||++||+|||||+||||++
T Consensus 87 e~~la~~~~~g~~~~~Ak~klv~snLRlVvsIAk~Y~~rGL~~~DLIQEGniGLmkAVekFdp~rG~kFsTYA~wWIrqa 166 (342)
T COG0568 87 EKALARRLKRGERDLDAKKKLVESNLRLVVSIAKKYTGRGLPFLDLIQEGNIGLMKAVEKFDPEKGFKFSTYATWWIRQA 166 (342)
T ss_pred HHHHHHHHHcCCccHHHHHHHHHHHHHHHHHHHHHhhcCCCcHHHHHhcccHHHHHHHHhcCcccCCcchhHHHHHHHHH
Confidence 66777777663 69999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCch
Q 008556 385 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT 464 (561)
Q Consensus 385 I~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~ 464 (561)
|.++|.+++|+||+|.|+...+++++++.+.+.+++|++|+.+|||+.+|+++++|..++.....++|||.|++++++..
T Consensus 167 I~raI~~q~rtIRipvh~~e~~nkl~r~~r~l~q~~~r~p~~eeia~~l~~~~~~V~~m~~~~~~~~SLd~~ig~ded~~ 246 (342)
T COG0568 167 ITRAIADQARTIRIPVHQVELINKLRRVKRELLQELGREPTPEEIAEELGVSPDKVREMLKRASEPISLDTPIGDDEDSE 246 (342)
T ss_pred HHHHHHHhcchhhHhHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHhCCCHHHHHHHHHhcccCcccCCcCCCCcccH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999998889
Q ss_pred hhhhcccCCCCChhHHHHHHHHHHHHHHHHhc-CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 008556 465 FQEITADTGVEIPDISVQKQLMRQHVRNLLTL-LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYR 543 (561)
Q Consensus 465 l~d~l~d~~~~~pee~le~~e~~e~L~~aL~~-L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkK 543 (561)
+.|++.|+...+|++.+.+..+.+.+...|.. |++||+.||++|||++|+++.|++|||+.+|||++|||||+.+|++|
T Consensus 247 l~d~leD~~~~~p~~~~~~~~~~~~~~~~L~~~Lt~rE~~Vi~~R~gl~~~~~~TLeevg~~~~isrERvRQIE~kAl~K 326 (342)
T COG0568 247 LGDFLEDDKSVSPEDAVERESLKEDLNEVLAEALTERERRVIRLRFGLDDGEPKTLEELGEEFGISRERVRQIEAKALRK 326 (342)
T ss_pred HHHHhhcCCcCCHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCcchHHHHHHHhCCcHHHHHHHHHHHHHH
Confidence 99999999877999999999999999999999 99999999999999999999999999999999999999999999999
Q ss_pred HHH-HhhcCchhhhhh
Q 008556 544 LKQ-SLGGKASYGYAD 558 (561)
Q Consensus 544 LR~-~l~~~~l~~yld 558 (561)
||. ......+++|++
T Consensus 327 Lr~~~~~~~~~~~~l~ 342 (342)
T COG0568 327 LRRHPERSALLRSYLD 342 (342)
T ss_pred HHHhhhhhhHHHHhhC
Confidence 994 444555677764
No 8
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=100.00 E-value=5.7e-58 Score=477.52 Aligned_cols=300 Identities=36% Similarity=0.629 Sum_probs=275.5
Q ss_pred CChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHH
Q 008556 245 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK 324 (561)
Q Consensus 245 ~~d~l~~Yl~~i~~~~lLT~eEE~eL~~~i~~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~~l~~G~~Are~ 324 (561)
.+|++..||++|+++|+||++||.+|+++|+.+..++.. |...+|.... ...+|...++.|..|+++
T Consensus 24 ~~~~~~~Yl~~i~~~~lLt~eeE~~La~~~~~g~~~~~~-----------~~~~~~~~~~--~~~~l~~~~~~~~~A~~~ 90 (324)
T PRK07921 24 AADLVRVYLNGIGKTALLTAADEVELAKRIEAGLYAEHL-----------LETRKRLSEA--RKRDLAAVVRDGEAARRH 90 (324)
T ss_pred CCChHHHHHHHhcccCCCCHHHHHHHHHHHHhhhhhhhh-----------hccccccchh--HHHHHHHHHhcCHHHHHH
Confidence 357899999999999999999999999999986655543 2223332111 456788899999999999
Q ss_pred HHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHH
Q 008556 325 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT 404 (561)
Q Consensus 325 LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~~ 404 (561)
||..|+++|+++|++|.++|.+++||+|||+||||+|+++|||++|++|+|||+||||++|.++|++++++||+|.|+..
T Consensus 91 Lv~~~~~lV~~iA~r~~~~~~~~eDLvQEg~igL~~a~~~fdp~~G~rFsTYA~~wIr~aI~~~i~~~~r~vrlP~~~~~ 170 (324)
T PRK07921 91 LLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVE 170 (324)
T ss_pred HHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHcCCCccCCHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHHHHHH
Q 008556 405 LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQ 484 (561)
Q Consensus 405 ~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~le~~ 484 (561)
.+++++++...+.+++|+.||.+|||+.+|+++++|..++.....++|||.+++++++.++.++++|+...+|++.+...
T Consensus 171 ~~~~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~l~d~~~~~pe~~~~~~ 250 (324)
T PRK07921 171 QVNKLARIKRELHQQLGREATDEELAEESGIPEEKIADLLEHSRDPVSLDMPVGSDEEAPLGDFIEDSEATSAENAVIAG 250 (324)
T ss_pred HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCceecCCCCCCCCchHHHHhcCCCCCCHHHHHHHH
Confidence 99999999999999999999999999999999999999998888899999999877777888999887666888888888
Q ss_pred HHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhh
Q 008556 485 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYA 557 (561)
Q Consensus 485 e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~l~~yl 557 (561)
+++..|..+|..|++|||.||.+||||+||+++|++|||+.||||++|||||+.+|++|||.......++.|+
T Consensus 251 ~~~~~l~~~L~~L~eREr~Vl~~rygl~~~~~~Tl~eIa~~lgvS~eRVrQIe~~Al~KLr~~~~~~~l~~~~ 323 (324)
T PRK07921 251 LLHTDIRSVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRNGERADRLRSYA 323 (324)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHHHHHHHHhh
Confidence 9999999999999999999999999999989999999999999999999999999999999998888888885
No 9
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=1.5e-54 Score=459.37 Aligned_cols=276 Identities=36% Similarity=0.704 Sum_probs=262.6
Q ss_pred CCCChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHH
Q 008556 243 FDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSR 322 (561)
Q Consensus 243 ~~~~d~l~~Yl~~i~~~~lLT~eEE~eL~~~i~~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~~l~~G~~Ar 322 (561)
....|+++.||++|+++|+||++||.+|+.+++. |+..|+
T Consensus 92 ~~~~d~~~~yl~~i~~~~~l~~~ee~~L~~~~~~----------------------------------------Gd~~A~ 131 (367)
T PRK09210 92 VKINDPVRMYLKEIGRVPLLTAEEEIELAKRIEE----------------------------------------GDEEAK 131 (367)
T ss_pred cccCcHHHHHHHHhhccCCCCHHHHHHHHHHHHh----------------------------------------hHHHHH
Confidence 3457899999999999999999999999988764 345899
Q ss_pred HHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhH
Q 008556 323 EKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENI 402 (561)
Q Consensus 323 e~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~ 402 (561)
+.||..|+++|+++|++|.+++.+++||+|||+||||+|+++|||.+|++|+|||+||||++|.++|++++|+||+|.|+
T Consensus 132 ~~Li~~~~~lV~~iA~~~~~~~~~~eDLiQEg~igL~~a~~~fd~~~g~~FsTyA~~wIr~aI~~~i~~~~r~irip~~~ 211 (367)
T PRK09210 132 QRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHM 211 (367)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHcCCceeccHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHHHH
Q 008556 403 YTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQ 482 (561)
Q Consensus 403 ~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~le 482 (561)
...++++.++.+.+.+++||.||.+|||+.+|+++++|..++.....++|||.+++.+++..+.+++.|....+|++.+.
T Consensus 212 ~~~~~~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~i~d~~~~~p~~~~~ 291 (367)
T PRK09210 212 VETINKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPADHAA 291 (367)
T ss_pred HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCCcCCCCCCCCcchhhhhccCCCCCCHHHHHH
Confidence 99999999999999999999999999999999999999999998888999999998877778899999887778999999
Q ss_pred HHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhh
Q 008556 483 KQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD 558 (561)
Q Consensus 483 ~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~l~~yld 558 (561)
...++..|..+|..||++||.||.+||||+||+++|++|||+.||||++||||++.+||+|||+......|+.|++
T Consensus 292 ~~~~~~~l~~~l~~L~~rEr~Vl~lrygl~~~~~~tl~EIa~~lgvs~erVrQi~~~Al~kLr~~~~~~~l~~~~~ 367 (367)
T PRK09210 292 YELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 367 (367)
T ss_pred HHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhChHHHhHHHHhhC
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999874
No 10
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=1.3e-51 Score=463.18 Aligned_cols=274 Identities=34% Similarity=0.633 Sum_probs=252.6
Q ss_pred HHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHHHH
Q 008556 248 PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLIN 327 (561)
Q Consensus 248 ~l~~Yl~~i~~~~lLT~eEE~eL~~~i~~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~~l~~G~~Are~LI~ 327 (561)
.+..||.++...+.||++|+.+++++++. |. .....|+++||.
T Consensus 345 ~lq~~L~~ie~~~~Ls~eElk~l~~~i~~---------------g~----------------------~~~~~a~~~Li~ 387 (619)
T PRK05658 345 KLQQELEAIEEETGLTIEELKEINRQISK---------------GE----------------------AKARRAKKEMVE 387 (619)
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHHHHHhc---------------cc----------------------hhhhHHHHHHHH
Confidence 44556777777777777777777766654 21 011368999999
Q ss_pred HHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHHHHH
Q 008556 328 ANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLS 407 (561)
Q Consensus 328 ~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~~~l~ 407 (561)
+|+|||++||++|.++|++++||||||+||||+|+++|||.+|++|+|||+||||++|.++|++++|+||+|.|+...++
T Consensus 388 ~nlrlV~~iA~ky~~~gl~~~DLiQeG~iGL~~Av~kfd~~~G~~FstYA~~wIr~aI~~~i~~~~r~irip~~~~~~~~ 467 (619)
T PRK05658 388 ANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN 467 (619)
T ss_pred HHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHHHHHhcCccCCCchHHHhHHHHHHHHHHHHHHcCCceecCHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHHHHHHHHH
Q 008556 408 KVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMR 487 (561)
Q Consensus 408 ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~le~~e~~ 487 (561)
+++++...+.+++||.||.+|||+.+|+++++|..++.....++|||.|++++++..+.+++.|....+|++.+....++
T Consensus 468 k~~~~~~~~~~~~gr~pt~~eiA~~l~~~~~~v~~~~~~~~~~~Sld~~i~~~~~~~l~d~i~d~~~~~p~~~~~~~~~~ 547 (619)
T PRK05658 468 KLNRISRQMLQEIGREPTPEELAERLGMPEDKVRKVLKIAKEPISLETPIGDDEDSHLGDFIEDKNAELPIDAAIQESLR 547 (619)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCCcCCCCCCCCCCCchhhhcCCCCCCChHHHHHHHHHH
Confidence 99999999999999999999999999999999999999888999999999888888899999998777899989899999
Q ss_pred HHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhh
Q 008556 488 QHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD 558 (561)
Q Consensus 488 e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~l~~yld 558 (561)
..|..+|..||+|||.||++||||+++.++|++|||+.||||++||||++.+|++|||+......|+.|+|
T Consensus 548 ~~l~~~l~~L~~rE~~Vl~~r~g~~~~~~~tl~ei~~~lgvs~eRVrQie~~al~kLr~~~~~~~l~~~~~ 618 (619)
T PRK05658 548 EATTDVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSRKLRSFLD 618 (619)
T ss_pred HHHHHHHHcCCHHHHHHHHHhcCCCCCCCccHHHHHHHhCCCHHHHHHHHHHHHHHHhchHHHHHHHHHhc
Confidence 99999999999999999999999998899999999999999999999999999999999999999999987
No 11
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain. This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.
Probab=100.00 E-value=8.5e-48 Score=384.61 Aligned_cols=238 Identities=39% Similarity=0.753 Sum_probs=227.2
Q ss_pred HHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccch
Q 008556 321 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPE 400 (561)
Q Consensus 321 Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~ 400 (561)
|+++||..|+++|+++|++|.++|.+++||+|||++||++|+++|||++|++|+|||+||||++|.++++++.+.+|+|.
T Consensus 1 a~~~Li~~~~~lv~~ia~~~~~~~~~~eDLiQeG~igL~~A~~~fd~~~g~~FstYA~~~Ir~~I~~~l~~~~~~vrip~ 80 (238)
T TIGR02393 1 AKKQLVESNLRLVVSIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPV 80 (238)
T ss_pred CHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCCCCCChHHHhHHHHHHHHHHHHHHcCCcEEeCH
Confidence 57899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHH
Q 008556 401 NIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDIS 480 (561)
Q Consensus 401 ~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~ 480 (561)
++...++++.++...+.+++|++||.+|||+.+|+++++|..++......+|||.+++.+++.++.+.+.|+...+|++.
T Consensus 81 ~~~~~~~~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~l~d~~~~~p~~~ 160 (238)
T TIGR02393 81 HMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVREIKKIAQEPISLETPIGEEEDSFLGDFIEDTSIESPDDY 160 (238)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCCcCCCCCCCCcccHHHHhcCCCCCChHHH
Confidence 99999999999999999999999999999999999999999998888889999999877766678888888877788888
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhh
Q 008556 481 VQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD 558 (561)
Q Consensus 481 le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~l~~yld 558 (561)
+...++...|..+|..||++||.||.++|||++++++|++|||+.||||+++|+|++.+|++|||+.+....++.|+|
T Consensus 161 ~~~~~~~~~l~~~l~~L~~~er~vl~l~ygl~~~~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~~~~~~~~~~~~~ 238 (238)
T TIGR02393 161 AAKELLREQLDEVLETLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRKLRHPSRSKKLKSFLD 238 (238)
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhhhHHHhHHHHhhC
Confidence 888889999999999999999999999999998899999999999999999999999999999999999999999975
No 12
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=100.00 E-value=1e-44 Score=378.52 Aligned_cols=272 Identities=35% Similarity=0.567 Sum_probs=253.7
Q ss_pred CChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHH
Q 008556 245 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK 324 (561)
Q Consensus 245 ~~d~l~~Yl~~i~~~~lLT~eEE~eL~~~i~~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~~l~~G~~Are~ 324 (561)
..|.++.|+.+|+..|+||+++|.+|+.+++. |+..|++.
T Consensus 51 ~~~~~~~y~~~~~~~~~l~~~ee~~li~~~~~----------------------------------------Gd~~A~~~ 90 (325)
T PRK05657 51 VLDATQLYLNEIGYSPLLTAEEEVYFARRALR----------------------------------------GDFAARQR 90 (325)
T ss_pred cccHHHHHHHHHhcCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHH
Confidence 46788999999999999999999999987654 45689999
Q ss_pred HHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHH
Q 008556 325 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT 404 (561)
Q Consensus 325 LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~~ 404 (561)
||..|.++|+++|++|.+++.+++||+|||++|+|+++++||+.+|++|+||++||||++|.++++++.+.|++|.++..
T Consensus 91 Li~~y~~~V~~~a~~~~~~~~~aeDLvQE~fi~l~~ai~~fd~~rg~~Fstyatw~iR~ai~~~i~~~~r~ir~p~~~~~ 170 (325)
T PRK05657 91 MIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPVHVVK 170 (325)
T ss_pred HHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCccCCCHHHHHHHHHHHHHHHHHHHcCCccccCHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHHHHHH
Q 008556 405 LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQ 484 (561)
Q Consensus 405 ~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~le~~ 484 (561)
.++++.++...+.+.+|+.|+.+|||+.+|+++++|..++.......|+|.++..+...++.+.+.+....+|+..+...
T Consensus 171 ~l~~~~R~~~~l~~~l~r~~t~~eiA~~l~~~~~~v~~~l~~~~~~~sld~~~~~~~~~~l~d~l~d~~~~~pe~~~~~~ 250 (325)
T PRK05657 171 ELNVYLRAARELEHKLDHEPSAEEIAELLDKPVDDVSRMLALNERITSLDTPLGGDPEKSLLDILADEQENGPEDTTQDD 250 (325)
T ss_pred HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhccCCcccCCCCCCCCCcchhhhccCCCCCCHHHHHHHH
Confidence 99988899999999999999999999999999999999998888889999998777666778888877666888888888
Q ss_pred HHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhh
Q 008556 485 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGY 556 (561)
Q Consensus 485 e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~l~~y 556 (561)
+....|..+|..||+++|.||.+||||.+.+++|++|||+.||||+++|++++++|+++||+.+...++..+
T Consensus 251 e~~~~L~~aL~~L~~~~R~vl~lrygL~~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l~~~~~~~~ 322 (325)
T PRK05657 251 DMKQSIVKWLFELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLREILQTQGLSIE 322 (325)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhCccchh
Confidence 888999999999999999999999999888999999999999999999999999999999999998887644
No 13
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=100.00 E-value=2e-44 Score=369.84 Aligned_cols=262 Identities=27% Similarity=0.470 Sum_probs=223.8
Q ss_pred CChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHH
Q 008556 245 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK 324 (561)
Q Consensus 245 ~~d~l~~Yl~~i~~~~lLT~eEE~eL~~~i~~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~~l~~G~~Are~ 324 (561)
+.+.+..|++++++.|+||.++|.+|+.+++. .|+..|++.
T Consensus 12 ~~~~~~~y~~~~~~~~~l~~~~e~~l~~~~~~---------------------------------------~Gd~~a~~~ 52 (284)
T PRK06596 12 PEGNLDAYIQAVNKIPMLTAEEEYMLAKRLRE---------------------------------------HGDLEAAKQ 52 (284)
T ss_pred CccHHHHHHHHHhccCCCCHHHHHHHHHHHHH---------------------------------------cCCHHHHHH
Confidence 45789999999999999999999999887532 245689999
Q ss_pred HHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHH
Q 008556 325 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT 404 (561)
Q Consensus 325 LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~~ 404 (561)
||..|+++|+++|++|.+++.+++||+|||++||++|+++|||++|++|+|||+|||+++|.+++++++++|++|.+...
T Consensus 53 Lv~~~~~lV~~ia~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~~~FstYA~~~Ir~~i~~~l~~~~~~vr~p~~~~~ 132 (284)
T PRK06596 53 LVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIHEYILRNWRIVKVATTKAQ 132 (284)
T ss_pred HHHHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHHcCCeeeccchHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999888999987642
Q ss_pred --HHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHh-cCCCccCCCCCCCCCC--chhhhhcccCCCCChhH
Q 008556 405 --LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI-TRMPLSMQQPVWADQD--TTFQEITADTGVEIPDI 479 (561)
Q Consensus 405 --~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~-~~~~~SLD~~v~~d~~--~~l~d~l~d~~~~~pee 479 (561)
...++.+....+. .+++|+.+|||+.+|+++++|..++.. ....+|||.+++++++ .++.+.+.|+. .+|++
T Consensus 133 ~~~~~~~~~~~~~l~--~~~~~t~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~~~~~~~l~~~l~d~~-~~p~~ 209 (284)
T PRK06596 133 RKLFFNLRKAKKRLG--WLNPEEVEMVAEELGVSEEEVREMESRLSGQDASLDAPIDDDDEESGAPQDYLEDKS-SDPAD 209 (284)
T ss_pred HHHHHHHHHHHHHhc--cCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCcCcCCCCCCCCCCcchHHHHcCCCC-CCchH
Confidence 2334444444443 358999999999999999999998753 3478999999865532 45778887764 46776
Q ss_pred HHHHH----HHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008556 480 SVQKQ----LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 550 (561)
Q Consensus 480 ~le~~----e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 550 (561)
.++.. ++...|..+|+.||++||.||.+||+. + +++|++|||+.||||++||||++++|++|||..+..
T Consensus 210 ~~~~~~~~~~~~~~L~~al~~L~~rEr~VL~lry~~-~-~~~Tl~EIA~~lgvS~~rVrqi~~~Al~kLR~~l~~ 282 (284)
T PRK06596 210 VLEEDNWEDQRRALLADALEGLDERSRDIIEARWLD-D-DKSTLQELAAEYGVSAERVRQIEKNAMKKLKAAIEA 282 (284)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcC-C-CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 66654 357789999999999999999999973 2 689999999999999999999999999999998754
No 14
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=100.00 E-value=2.4e-44 Score=370.14 Aligned_cols=264 Identities=26% Similarity=0.451 Sum_probs=226.2
Q ss_pred hHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHHH
Q 008556 247 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLI 326 (561)
Q Consensus 247 d~l~~Yl~~i~~~~lLT~eEE~eL~~~i~~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~~l~~G~~Are~LI 326 (561)
+.++.||++++++|+||+++|.+|+.+++. .|+..|+++||
T Consensus 6 ~~~~~y~~~~~~~~~l~~~~e~~L~~~~~~---------------------------------------~gd~~A~~~Lv 46 (289)
T PRK07500 6 SADRSMIRSAMKAPYLEREEEHALAYRWKD---------------------------------------HRDEDALHRII 46 (289)
T ss_pred hHHHHHHHHHhcCCCCCHHHHHHHHHHHHH---------------------------------------CCCHHHHHHHH
Confidence 467789999999999999999999987642 14568999999
Q ss_pred HHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHH--
Q 008556 327 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT-- 404 (561)
Q Consensus 327 ~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~~-- 404 (561)
..|+++|+++|++|.+++.+++||+||||+|||+++++|||.+|.+|+|||+||||++|.++|+++++++|+|.+...
T Consensus 47 ~~~~~lV~~~a~~~~~~~~~~eDLvQeg~i~L~~a~~~fd~~~~~~f~tya~~~Ir~~I~~~lr~~~~~iR~p~~~~~~~ 126 (289)
T PRK07500 47 SAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQKA 126 (289)
T ss_pred HHhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHHCCCceecCccHHHHH
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999988654
Q ss_pred HHHHHHHHHHHHHH---hCCCCCCHHHHHHHhCCCHHHHHHHHH-hcCCCccCCCCCCCCCCc--hhhhhcccCCCCChh
Q 008556 405 LLSKVLEAKRLYIQ---EGNHSPDKEDLARRVGITVEKLERLIF-ITRMPLSMQQPVWADQDT--TFQEITADTGVEIPD 478 (561)
Q Consensus 405 ~l~ki~ka~~~l~~---e~gr~Pt~eEIA~~lgis~e~v~~ll~-~~~~~~SLD~~v~~d~~~--~l~d~l~d~~~~~pe 478 (561)
...++++....+.+ .+|+.|+.+|||+.||+++++|..+.. ....++|||.+++++++. ++.+.+.++.. +|+
T Consensus 127 ~~~~~~~~~~~~~~~~~~l~~~pt~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~~~~~~~l~d~i~d~~~-~pe 205 (289)
T PRK07500 127 LFFNLRRLRARLAQADEELTKQEIHREIATALGVSLSDVEMMDARLSGPDASLNAPQSEEDEGRSERMDFLVDDSP-LPD 205 (289)
T ss_pred HHHHHHHHHHHHHhhhcccCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCccccCCCCCCCCCcccHHHhccCCCC-Cch
Confidence 33444445444444 689999999999999999999988753 355799999998765443 57788877643 566
Q ss_pred HHHHH----HHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 008556 479 ISVQK----QLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA 552 (561)
Q Consensus 479 e~le~----~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~ 552 (561)
+.+.. .+....|..+|..||++||.||.+||+. ++++|++|||+.||||+++|+|++++|++|||..+....
T Consensus 206 ~~~~~~~~~~~~~~~l~~al~~L~~rer~vl~lr~~~--~~~~t~~EIa~~lgvs~~~V~q~~~~Al~kLr~~l~~~~ 281 (289)
T PRK07500 206 EQVESSIDGERRRRWLTQALQTLNERELRIIRERRLR--EDGATLEALGEELGISKERVRQIEARALEKLRRALLSQS 281 (289)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcC--CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhcC
Confidence 55443 3456779999999999999999999962 378999999999999999999999999999999987544
No 15
>TIGR02392 rpoH_proteo alternative sigma factor RpoH. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. 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.
Probab=100.00 E-value=8.2e-44 Score=362.57 Aligned_cols=258 Identities=28% Similarity=0.501 Sum_probs=217.0
Q ss_pred HHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHHHH
Q 008556 248 PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLIN 327 (561)
Q Consensus 248 ~l~~Yl~~i~~~~lLT~eEE~eL~~~i~~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~~l~~G~~Are~LI~ 327 (561)
++..||++++++|+|++++|.+|+.++.. .++..|++.||.
T Consensus 2 ~~~~yl~~~~~~~~l~~~~e~~l~~~~~~---------------------------------------~gd~~a~~~Lv~ 42 (270)
T TIGR02392 2 SLDAYIRAVNRIPMLTPEEEYQLAKRLRE---------------------------------------HGDLDAAKKLVL 42 (270)
T ss_pred hHHHHHHHHhcCCCCCHHHHHHHHHHHHH---------------------------------------CCCHHHHHHHHH
Confidence 57789999999999999999999886432 245689999999
Q ss_pred HHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHH--HH
Q 008556 328 ANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIY--TL 405 (561)
Q Consensus 328 ~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~--~~ 405 (561)
.|+++|+++|++|.+++.+++||+|||++|||+|+++|||++|++|+|||+||||++|.+++++.++++|+|.+.. ..
T Consensus 43 ~~~~lV~~~a~~~~~~~~~~eDLvQeg~igl~~a~~~fd~~~~~~FsTYA~~~Ir~~i~~~l~~~~~~ir~p~~~~~~~~ 122 (270)
T TIGR02392 43 SHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEYILRNWRLVKVATTKAQRKL 122 (270)
T ss_pred HhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCChHHhhHHHHHHHHHHHHHHcCCceecCchHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999999999999988899997653 33
Q ss_pred HHHHHHHHHHHHHhCCCCC-CHHHHHHHhCCCHHHHHHHHHhc-CCCccCCCCCCCCCC--chhhhhcccCCCCChhHHH
Q 008556 406 LSKVLEAKRLYIQEGNHSP-DKEDLARRVGITVEKLERLIFIT-RMPLSMQQPVWADQD--TTFQEITADTGVEIPDISV 481 (561)
Q Consensus 406 l~ki~ka~~~l~~e~gr~P-t~eEIA~~lgis~e~v~~ll~~~-~~~~SLD~~v~~d~~--~~l~d~l~d~~~~~pee~l 481 (561)
..++.++...+. +++.| +.+|||+.+|+++++|..++... ....|||.+++++++ ..+.+.+.|.. .+|++.+
T Consensus 123 ~~~~~~~~~~~~--~~~~~~~~~eiA~~l~~~~~~v~~~~~~~~~~~~Sld~~~~~~~~~~~~~~~~l~d~~-~~pe~~~ 199 (270)
T TIGR02392 123 FFNLRKMKKRLQ--GWLNPEEVEAIAEELGVSEREVREMESRLSGQDMSLNASIDDDEDDGGAPIAYLVDKT-SDPEDTL 199 (270)
T ss_pred HHHHHHHHHHHh--cCCCCCCHHHHHHHhCCCHHHHHHHHHHccCCCccCCCCCCCCCCccccHHHHhcCCC-CChHHHH
Confidence 444444444432 32455 69999999999999999986533 348999999866543 25667777764 3677666
Q ss_pred HHH----HHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008556 482 QKQ----LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 549 (561)
Q Consensus 482 e~~----e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 549 (561)
+.. .+...|..+|..||++||.||.+||+. ++++|++|||+.||||+++|+|++++|++|||..+.
T Consensus 200 ~~~~~~~~~~~~L~~al~~L~~rer~vl~l~y~~--~~~~t~~eIA~~lgvS~~~V~q~~~~Al~kLr~~l~ 269 (270)
T TIGR02392 200 EEEQWEELQRQALANALGSLDARSRRIIEARWLD--DDKLTLQELAAEYGVSAERIRQIEKNAMKKLKAALA 269 (270)
T ss_pred HHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhcC--CCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Confidence 543 356789999999999999999999962 368999999999999999999999999999998764
No 16
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=100.00 E-value=3.7e-43 Score=357.03 Aligned_cols=220 Identities=24% Similarity=0.393 Sum_probs=200.9
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccc
Q 008556 320 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP 399 (561)
Q Consensus 320 ~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP 399 (561)
.++++||.+|++||++||++|.++|++++||||||+|||++|+++|||++|++|+|||+||||++|.++++++.++||+|
T Consensus 40 ~~r~~Lv~~~l~LV~~iA~~y~~~g~~~~DLiQeG~iGLi~AierFDp~~G~~FsTYA~~~Irg~I~~~lr~~~~~ir~P 119 (264)
T PRK07122 40 RQRDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGEVRRHFRDNSWSVKVP 119 (264)
T ss_pred HHHHHHHHHhHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHHcCCccccC
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHh--cCCCccCCCCCCCCCCc--hhhhhcccCCCC
Q 008556 400 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI--TRMPLSMQQPVWADQDT--TFQEITADTGVE 475 (561)
Q Consensus 400 ~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~--~~~~~SLD~~v~~d~~~--~l~d~l~d~~~~ 475 (561)
+++...+++++++...+.+++|+.||.+|||+.+|+++++|.+++.. ...+.|||.+++++++. .+.+.++
T Consensus 120 r~~~~~~~~i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~~~~~d~~~----- 194 (264)
T PRK07122 120 RRLKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVVEGLVAGSAYNTLSIDSGGGSGDDDARAIADTLG----- 194 (264)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhhcCCCCcccccccCCCCCcccchhccC-----
Confidence 99999999999999999999999999999999999999999998864 45689999998654322 3333332
Q ss_pred ChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008556 476 IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 548 (561)
Q Consensus 476 ~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 548 (561)
.++..++..+....|..+|..||++||.||.++|+ +++|++|||+.||||.++|++++++|+++||..+
T Consensus 195 ~~~~~~e~~~~~~~l~~~l~~L~~rer~vl~l~y~----~~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~l 263 (264)
T PRK07122 195 DVDAGLDQIENREALRPLLAALPERERTVLVLRFF----ESMTQTQIAERVGISQMHVSRLLAKTLARLRDQL 263 (264)
T ss_pred CcHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhc----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHc
Confidence 34555666777888999999999999999999998 8999999999999999999999999999999876
No 17
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=100.00 E-value=2.5e-41 Score=342.01 Aligned_cols=228 Identities=25% Similarity=0.408 Sum_probs=201.7
Q ss_pred hcHHHHHHHHHHHHHHHHHHHHhhhCC-CCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccc
Q 008556 317 SGNSSREKLINANLRLVVHVAKQYQGR-GISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT 395 (561)
Q Consensus 317 ~G~~Are~LI~~nlrLV~sIArrY~~~-g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~ 395 (561)
++..|+++||..|+++|+++|++|.+. +.+++||+|||+||||+|+++|||++|++|+|||+|||+++|.++++++.++
T Consensus 22 gd~~a~~~Lv~~~~~lV~~ia~~~~~~~~~~~eDL~Qeg~igL~~a~~~fd~~~g~~F~tya~~~Ir~~i~~~lr~~~~~ 101 (256)
T PRK07408 22 PSIALRNQLVELNLGLVRKEAHRWSNQCSEPYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLRDKSPT 101 (256)
T ss_pred CCHHHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHHcCCe
Confidence 445899999999999999999999876 6679999999999999999999999999999999999999999999999999
Q ss_pred cccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHH--hcCCCccCCCCCCCCCCc--hhhhhccc
Q 008556 396 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIF--ITRMPLSMQQPVWADQDT--TFQEITAD 471 (561)
Q Consensus 396 IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~--~~~~~~SLD~~v~~d~~~--~l~d~l~d 471 (561)
||+|+++...+++++++...+.+++|++|+.+|||+.+|+++++|..++. ......|||.++..+++. .+.+.+++
T Consensus 102 vr~pr~~~~~~~~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~~~l~d~~~d 181 (256)
T PRK07408 102 VRIPRRWQELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIKLALQNRTPLSLDAPVNQDEDGSTSLGDLLPD 181 (256)
T ss_pred eeeCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHhhccCCccccccCCCCCCCccccccccCC
Confidence 99999999999999999999999999999999999999999999999865 345689999987554332 45566655
Q ss_pred CCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008556 472 TGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 551 (561)
Q Consensus 472 ~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 551 (561)
+... +. ....+....|..+|..||+++|.||.++|+ +++|++|||+.||||.++|++++++|++|||+.+...
T Consensus 182 ~~~~-~~--~~~~~~~~~l~~~l~~L~~~~r~vl~l~y~----~~~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~l~~~ 254 (256)
T PRK07408 182 PRYR-SF--QLAQEDRIRLQQALAQLEERTREVLEFVFL----HDLTQKEAAERLGISPVTVSRRVKKGLDQLKKLLQPE 254 (256)
T ss_pred cccc-hh--hhhHHHHHHHHHHHHcCCHHHHHHHHHHHH----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhhcc
Confidence 4322 11 123345677999999999999999999998 8999999999999999999999999999999988653
No 18
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).
Probab=100.00 E-value=5.6e-41 Score=344.13 Aligned_cols=274 Identities=35% Similarity=0.553 Sum_probs=249.3
Q ss_pred CCCCCChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHH
Q 008556 241 EGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNS 320 (561)
Q Consensus 241 ~~~~~~d~l~~Yl~~i~~~~lLT~eEE~eL~~~i~~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~~l~~G~~ 320 (561)
......|.+++||.+|+.+|.||.++|.+|+.+++. |+..
T Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~----------------------------------------gd~~ 46 (285)
T TIGR02394 7 TETRVADVTQLYLREIGFKPLLTAEEEIAYARRALA----------------------------------------GDFE 46 (285)
T ss_pred cccCcchHHHHHHHHHhccCCCCHHHHHHHHHHHHc----------------------------------------CCHH
Confidence 334467899999999999999999999999887654 4568
Q ss_pred HHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccch
Q 008556 321 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPE 400 (561)
Q Consensus 321 Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~ 400 (561)
|++.||..|.++|+++|++|.+++.+++||+|||+||||+|+++||+.+|++|+||+.|||+.+|.+++.++.+.+++|.
T Consensus 47 a~~~L~~~y~~~v~~~a~~~~~~~~~aeDLvQe~~i~l~~a~~~fd~~~g~~f~tya~w~i~~ain~~i~~~~~~~~~p~ 126 (285)
T TIGR02394 47 ARKVMIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVEKFDPERGFRFSTYATWWIRQTIERAIMNQARTIRLPV 126 (285)
T ss_pred HHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCCCCCCcHhhhHHHHHHHHHHHHHHcCCceeCcH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHH
Q 008556 401 NIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDIS 480 (561)
Q Consensus 401 ~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~ 480 (561)
++...++.+.+..+.+.+..|+.|+.+++|..+|++++++..++.......|+|.++..++...+.+.+.++...+|++.
T Consensus 127 ~~~~~~~~~~r~~~~l~~~~~r~~~~~e~a~~l~~~~~~~~~~~~~~~~~~sld~~~~~~~~~~~~~~~~~~~~~~pe~~ 206 (285)
T TIGR02394 127 HVIKELNVYLRAARQLEKKLGREPSVEEIAELLDKPVEDVSRVLALNERITSLDAPLDDDSSKSLLDTIADEQSIDPESL 206 (285)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhhcCCCcCCCCCCCCCCcchhhhhcCCCCCCHHHH
Confidence 99999999888888788888999999999999999999999999888889999988766555556666666655678888
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchh
Q 008556 481 VQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASY 554 (561)
Q Consensus 481 le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~l~ 554 (561)
+...+....|..+|..||+++|.||.++|||.+.+++|++|||+.||||.++|++++++|+++||+.+...++.
T Consensus 207 ~~~~e~~~~L~~al~~Lp~~~R~Vl~l~ygL~~~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~l~~~~~~ 280 (285)
T TIGR02394 207 VQNDDLKQLIEAWLAELNERQREVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQVEALKKLRRILERDGVD 280 (285)
T ss_pred HHHHHHHHHHHHHHHcCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 99889999999999999999999999999887779999999999999999999999999999999999865553
No 19
>TIGR02850 spore_sigG RNA polymerase sigma-G factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also desginated stage III sporulation protein G (SpoIIIG). This protein is rather closely related to sigma-F (SpoIIAC), another sporulation sigma factor.
Probab=100.00 E-value=8.6e-40 Score=330.04 Aligned_cols=243 Identities=27% Similarity=0.443 Sum_probs=215.8
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHHHHHHHHHHHH
Q 008556 256 PETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVH 335 (561)
Q Consensus 256 i~~~~lLT~eEE~eL~~~i~~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~~l~~G~~Are~LI~~nlrLV~s 335 (561)
.+++|+||++||.+|+.+++. ++..|++.|+..|+++|++
T Consensus 10 ~~~~~~l~~~~~~~li~~~~~----------------------------------------gd~~a~~~L~~~~~~~v~~ 49 (254)
T TIGR02850 10 TSKLPVLKNQEMRELFIRMQS----------------------------------------GDTTAREKLINGNLRLVLS 49 (254)
T ss_pred ccCCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHHHhHHHHHH
Confidence 468899999999998877653 3468999999999999999
Q ss_pred HHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHH
Q 008556 336 VAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRL 415 (561)
Q Consensus 336 IArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~ 415 (561)
+|++|.+++.+++||+|||++|||+++++|||.+|.+|+||++|||++.|.++++++. .||+|+++...++++.++...
T Consensus 50 ~a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~tyl~~~irn~~~~~lr~~~-~ir~p~~~~~~~~~~~~~~~~ 128 (254)
T TIGR02850 50 VIQRFNNRGEYVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVRDK 128 (254)
T ss_pred HHHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHHHHHHhCC-CccCchHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999965 889999999999999999999
Q ss_pred HHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCC--chhhhhcccCCCCChhHHHHHHHHHHHHHHH
Q 008556 416 YIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQD--TTFQEITADTGVEIPDISVQKQLMRQHVRNL 493 (561)
Q Consensus 416 l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~--~~l~d~l~d~~~~~pee~le~~e~~e~L~~a 493 (561)
+..++|+.|+.+|||+.+|+++++|..++.....+.|||.++.++++ ..+.+.+.|+.. .++ ....+..|..+
T Consensus 129 l~~~l~~~pt~~elA~~l~~~~e~v~~~~~~~~~~~Sld~~~~~~~~~~~~~~~~~~d~~~-~~~----~~~~~~~l~~~ 203 (254)
T TIGR02850 129 LISENSKEPTVSEIAKELKVPQEEVVFALDAIQDPVSLFEPIYNDGGDPIYVMDQISDEKN-KDS----QWLEGIALKEA 203 (254)
T ss_pred HHHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCCcccCCCCCCCCCcchhhhhcCCccc-cHH----HHHhHHHHHHH
Confidence 99999999999999999999999999999888889999998754443 245666665432 122 22344578999
Q ss_pred HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008556 494 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 548 (561)
Q Consensus 494 L~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 548 (561)
+..|++++|.||.+||+ +++|++|||+.||||+++|++++++|++|||+.+
T Consensus 204 l~~L~~rer~vi~~~~~----~~~t~~eIA~~lgis~~~V~~~~~ral~kLr~~~ 254 (254)
T TIGR02850 204 MKRLNEREKMILNMRFF----EGKTQMEVAEEIGISQAQVSRLEKAALKHMRKYV 254 (254)
T ss_pred HHcCCHHHHHHHHHHHc----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhhC
Confidence 99999999999999997 8899999999999999999999999999999853
No 20
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=100.00 E-value=1.2e-39 Score=330.02 Aligned_cols=227 Identities=26% Similarity=0.391 Sum_probs=204.6
Q ss_pred hcHHHHHHHHHHHHHHHHHHHHhhhC---CCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcc
Q 008556 317 SGNSSREKLINANLRLVVHVAKQYQG---RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHS 393 (561)
Q Consensus 317 ~G~~Are~LI~~nlrLV~sIArrY~~---~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~s 393 (561)
++..|+++||..|+++|+++|++|.+ .+++++||+|||+||||+|+++|||++|++|+|||.||||++|.+++++..
T Consensus 20 ~~~~ar~~Li~~~~~lV~~ia~~~~~~~~~~~~~eDL~QeG~igL~~ai~~fd~~~g~~F~tya~~~Ir~~i~~~lr~~~ 99 (257)
T PRK05911 20 QEIEYRDVLIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAIIDDLRKQD 99 (257)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhcC
Confidence 45589999999999999999999852 356899999999999999999999999999999999999999999999987
Q ss_pred cccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcC--CCccCCCCCCC--CC--Cchhhh
Q 008556 394 RTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITR--MPLSMQQPVWA--DQ--DTTFQE 467 (561)
Q Consensus 394 r~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~--~~~SLD~~v~~--d~--~~~l~d 467 (561)
+ +|+++...++++.++...+.+++|+.|+.+|||+.+|+++++|..++.... .++|||.++.. ++ +.++.+
T Consensus 100 ~---~pr~~~~~~~~l~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~~~Sld~~~~~~~~~~~~~~l~~ 176 (257)
T PRK05911 100 W---VPRSVHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFSSARPALILSLNEEFPCQSDDEAGLALEE 176 (257)
T ss_pred C---CCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHHhhccceeeccccCCCCCCCccccchhh
Confidence 5 899999999999999999999999999999999999999999999887553 46899987643 21 235677
Q ss_pred hcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008556 468 ITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 547 (561)
Q Consensus 468 ~l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 547 (561)
.++|.....|++.+...+....|..+|..||++||.||.++|+ +++|++|||+.||||.++|++++.+|+++||+.
T Consensus 177 ~l~d~~~~~~~~~~~~~~~~~~l~~al~~L~~~er~vi~l~y~----e~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~ 252 (257)
T PRK05911 177 RIADERAETGYDVVDKKEFSSILAEAILALEEKERKVMALYYY----EELVLKEIGKILGVSESRVSQIHSKALLKLRAT 252 (257)
T ss_pred hccCCCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 8888766678888888888899999999999999999999998 899999999999999999999999999999998
Q ss_pred hhc
Q 008556 548 LGG 550 (561)
Q Consensus 548 l~~ 550 (561)
+..
T Consensus 253 l~~ 255 (257)
T PRK05911 253 LSA 255 (257)
T ss_pred HHh
Confidence 754
No 21
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=100.00 E-value=2.1e-38 Score=320.43 Aligned_cols=243 Identities=27% Similarity=0.463 Sum_probs=214.8
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHHHHHHHHHHHH
Q 008556 256 PETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVH 335 (561)
Q Consensus 256 i~~~~lLT~eEE~eL~~~i~~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~~l~~G~~Are~LI~~nlrLV~s 335 (561)
..++|+|+++|+..|+.+++. ++..|+++||..|.++|++
T Consensus 13 ~~~~~~l~~~~~~~l~~~~~~----------------------------------------gd~~a~~~l~~~~~~~v~~ 52 (258)
T PRK08215 13 TSKLPVLKNEEMRELFERMQN----------------------------------------GDKEAREKLINGNLRLVLS 52 (258)
T ss_pred CCCCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHHHHHHHHHH
Confidence 467789999999988877653 4568999999999999999
Q ss_pred HHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHH
Q 008556 336 VAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRL 415 (561)
Q Consensus 336 IArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~ 415 (561)
+|++|.+++.+++||+|||++|||+++++|||.+|++|+||+++||+++|.++++++. .+|+|+++.....++.++...
T Consensus 53 ~a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~t~l~~~ir~~i~~~lr~~~-~vrip~~~~~~~~~~~~~~~~ 131 (258)
T PRK08215 53 VIQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVREK 131 (258)
T ss_pred HHHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHhCC-ceEecHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999885 889999999999999999999
Q ss_pred HHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCc--hhhhhcccCCCCChhHHHHHHHHHHHHHHH
Q 008556 416 YIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDT--TFQEITADTGVEIPDISVQKQLMRQHVRNL 493 (561)
Q Consensus 416 l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~--~l~d~l~d~~~~~pee~le~~e~~e~L~~a 493 (561)
+.+++|+.|+.+|||+.+|+++++|..++.....+.|||.++.++++. ++.+.+.++.. .++ .......|..+
T Consensus 132 l~~~~~r~p~~~eia~~l~v~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~~~~~~-~~~----~~~~~~~l~~~ 206 (258)
T PRK08215 132 LINENSKEPTVEEIAKELEVPREEVVFALDAIQDPVSLFEPIYHDGGDPIYVMDQISDEKN-KDE----NWLEEIALKEA 206 (258)
T ss_pred HHHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCccccCCCCCCCCcchhhhhhccCccc-cHH----HHHhHHHHHHH
Confidence 999999999999999999999999999988877888999988655432 34555554431 222 22334578899
Q ss_pred HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008556 494 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 548 (561)
Q Consensus 494 L~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 548 (561)
|..||+++|.||.++|+ +++|++|||+.||||.++|++++++|++|||+.+
T Consensus 207 l~~L~~~er~vi~~~~~----~~~t~~eIA~~lgis~~~V~~~~~~al~kLr~~l 257 (258)
T PRK08215 207 MKKLNDREKLILNLRFF----QGKTQMEVAEEIGISQAQVSRLEKAALKHMRKYI 257 (258)
T ss_pred HHcCCHHHHHHHHHHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 99999999999999997 8899999999999999999999999999999876
No 22
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=100.00 E-value=1.8e-38 Score=318.03 Aligned_cols=223 Identities=27% Similarity=0.504 Sum_probs=202.7
Q ss_pred hcHHHHHHHHHHHHHHHHHHHHhhhCCCC-CHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccc
Q 008556 317 SGNSSREKLINANLRLVVHVAKQYQGRGI-SLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT 395 (561)
Q Consensus 317 ~G~~Are~LI~~nlrLV~sIArrY~~~g~-~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~ 395 (561)
++..++ .||+.|+|||.+||++|.+++. +++||+|-|+|||++|+++|||++|.+|+|||...|+++|.+++|++. .
T Consensus 21 g~~~~~-~Li~~ylpLV~~ia~k~~~r~~~~~dDLiqiG~iGLi~Aieryd~~kg~kF~tyA~~~I~Gei~d~LR~~~-~ 98 (247)
T COG1191 21 GDEEAR-RLIERYLPLVKSIARKFENRGPSEYDDLIQIGMIGLIKAIERYDPSKGTKFSTYAVRRIRGEILDYLRKND-S 98 (247)
T ss_pred cCHHHH-HHHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHHHHcCcccCcchHHHHHHHHHHHHHHHHHhCC-C
Confidence 345888 9999999999999999998877 999999999999999999999999999999999999999999999999 9
Q ss_pred cccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcC--CCccCCCCCCCCCCchhhhhcccCC
Q 008556 396 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITR--MPLSMQQPVWADQDTTFQEITADTG 473 (561)
Q Consensus 396 IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~--~~~SLD~~v~~d~~~~l~d~l~d~~ 473 (561)
+++|+.+....+++..+...+.+++||+||.+|||+.+|++.+++..++.... ..+|+|..+..+++.. .++.
T Consensus 99 v~vpR~~~~~~~~i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~~~~~~~~sld~~~~~~~d~~-----~~~~ 173 (247)
T COG1191 99 VKVPRSLRELGRRIEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAINGSQLLSLDEDVLKDDDDD-----VDDQ 173 (247)
T ss_pred ccCcHHHHHHHHHHHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHHhccccccchhhhhccccccc-----hhhc
Confidence 99999999999999999999999999999999999999999999999887654 6788887665444333 2233
Q ss_pred CCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008556 474 VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 550 (561)
Q Consensus 474 ~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 550 (561)
..+|...+++.+..+.|.+++..|++|||.|+.+||. +++|++|||+.||||..+|+|++++|++|||..+..
T Consensus 174 ~~~~~~~~~~~~~~~~l~~ai~~L~EREk~Vl~l~y~----eelt~kEI~~~LgISes~VSql~kkai~kLr~~l~~ 246 (247)
T COG1191 174 IENPDDGVEKEELLEILKEAIEPLPEREKLVLVLRYK----EELTQKEIAEVLGISESRVSRLHKKAIKKLRKELNK 246 (247)
T ss_pred cccchhHHHHHHHHHHHHHHHHccCHHHHHHHHHHHH----hccCHHHHHHHhCccHHHHHHHHHHHHHHHHHHhcc
Confidence 4467778888888889999999999999999999998 999999999999999999999999999999998753
No 23
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=100.00 E-value=5.4e-37 Score=311.99 Aligned_cols=250 Identities=20% Similarity=0.359 Sum_probs=221.4
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHHHHHHHHHHHH
Q 008556 256 PETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVH 335 (561)
Q Consensus 256 i~~~~lLT~eEE~eL~~~i~~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~~l~~G~~Are~LI~~nlrLV~s 335 (561)
.+++|+||.++|.+|+.+++. .++..+++.|+..|.++|+.
T Consensus 6 ~~~~~~~~~~~e~~l~~~~~~---------------------------------------~~d~~a~~~l~~~y~~lv~~ 46 (268)
T PRK06288 6 SGKIPKYAQQDETELWREYKK---------------------------------------TGDPKIREYLILKYSPLVKY 46 (268)
T ss_pred cCCCccccchHHHHHHHHHHH---------------------------------------cCCHHHHHHHHHHHHHHHHH
Confidence 378999999999999987653 13468999999999999999
Q ss_pred HHHhhh-C--CCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHH
Q 008556 336 VAKQYQ-G--RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEA 412 (561)
Q Consensus 336 IArrY~-~--~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~~~l~ki~ka 412 (561)
+|++|. + .+.+++||+|||++|||+++++||+.+|++|+||++||||+.|.+++++.. ++|+++....++++++
T Consensus 47 ~a~~~~~~~~~~~~~eDl~Qeg~l~L~~a~~~fd~~~~~~f~ty~~~~ir~~i~d~~R~~~---~~p~~~~~~~~~i~~~ 123 (268)
T PRK06288 47 VAGRIAVGMPQNVEFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAIFDELRSID---WIPRSVRQKARQIERA 123 (268)
T ss_pred HHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhcC---ccCHHHHHHHHHHHHH
Confidence 999986 3 467899999999999999999999999999999999999999999998654 6899999999999999
Q ss_pred HHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhc--CCCccCCCCCCCCC---CchhhhhcccCCCCChhHHHHHHHHH
Q 008556 413 KRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT--RMPLSMQQPVWADQ---DTTFQEITADTGVEIPDISVQKQLMR 487 (561)
Q Consensus 413 ~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~--~~~~SLD~~v~~d~---~~~l~d~l~d~~~~~pee~le~~e~~ 487 (561)
...+.+++|+.|+.+|||+.+|++.+++..++... ....|||..+..++ ..++.+.++++...+|+..+...+..
T Consensus 124 ~~~l~~~~~~~pt~~eia~~lg~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~l~~~~~~~~~~~pe~~~~~~e~~ 203 (268)
T PRK06288 124 IAMLEARLGRTPSDEEIADELGISLEEYNSLLSKLSGTSVVSLNDLWFGGDEGDEVSLMDTLESPAALNPDEIAEREEIK 203 (268)
T ss_pred HHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhcccccchhhhhccCCCcccchhhhhccCCCCCCHHHHHHHHHHH
Confidence 99999999999999999999999999999988643 45789988763222 23466777776667888888888888
Q ss_pred HHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008556 488 QHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 551 (561)
Q Consensus 488 e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 551 (561)
..|..+|..||+++|.||.++|+ +++|++|||+.||+|.++|++++.+|+++||.++...
T Consensus 204 ~~l~~~l~~L~~~~r~vl~l~~~----~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l~~~ 263 (268)
T PRK06288 204 RVIVEAIKTLPEREKKVLILYYY----EDLTLKEIGKVLGVTESRISQLHTKAVLQLRAKLAEI 263 (268)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999998 8999999999999999999999999999999988643
No 24
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=100.00 E-value=3e-36 Score=303.89 Aligned_cols=244 Identities=23% Similarity=0.358 Sum_probs=215.0
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHHHHHHHHHHHHHHHh
Q 008556 260 KLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQ 339 (561)
Q Consensus 260 ~lLT~eEE~eL~~~i~~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~~l~~G~~Are~LI~~nlrLV~sIArr 339 (561)
|.||+++|.+|+.+++. .++..|+++|+..|.++|+.+|++
T Consensus 8 ~~l~~~~~~~li~~~~~---------------------------------------~gd~~a~~~l~~~y~~~v~~~a~~ 48 (255)
T TIGR02941 8 TNLTKEDVIQWIAEFQQ---------------------------------------NQNGEAQEKLVDHYQNLVYSIAYK 48 (255)
T ss_pred CCCCHHHHHHHHHHHHH---------------------------------------CCCHHHHHHHHHHhHHHHHHHHHH
Confidence 66899999888877653 134689999999999999999999
Q ss_pred hhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHHHHh
Q 008556 340 YQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQE 419 (561)
Q Consensus 340 Y~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e 419 (561)
|.+++.+++||+|||++|||+++++||+..|.+|.||+++||++.|.++++++.+.+++|.++....++++++...+.+.
T Consensus 49 ~~~~~~~aeDlvQe~~i~l~~a~~~~~~~~~~~f~tyl~~~i~n~~~~~lr~~~~~iri~~~~~~~~~~~~~~~~~l~~~ 128 (255)
T TIGR02941 49 YSKGGPMHEDLVQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIIGEIKRYLRDKTWSVHVPRRIKELGPKIKKAIDELTDH 128 (255)
T ss_pred HhcCCCCHHHHHHHHHHHHHHHHHHcCCcCCCCcHhHHHHHHHHHHHHHHHHcCCCcCCCHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHhc--CCCccCCCCCCCCCCchhhhhcccCCCCChhHHHHHHHHHHHHHHHHhcC
Q 008556 420 GNHSPDKEDLARRVGITVEKLERLIFIT--RMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLL 497 (561)
Q Consensus 420 ~gr~Pt~eEIA~~lgis~e~v~~ll~~~--~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~le~~e~~e~L~~aL~~L 497 (561)
+|+.|+.+|+|+.+|++.+++..++... ....|||.++..+++......+ +. ...|++.+...+....|..+|+.|
T Consensus 129 ~~r~p~~~eia~~l~i~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~-~~-~~~~~~~~~~~e~~~~l~~~l~~L 206 (255)
T TIGR02941 129 LQRSPKIIEIADHLGLSEEEVLEIMEMGQSYRALSVDDVIEADSDGSTVARL-DS-VGEVEDGYDQTERRMVLEKILPIL 206 (255)
T ss_pred hCCCCCHHHHHHHhCCCHHHHHHHHHHHhccCCccccccccCCCCCcccccc-cc-cCCcchHHHHHHHHHHHHHHHHcC
Confidence 9999999999999999999998887653 4578999888655443222221 11 124666677777778899999999
Q ss_pred CHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008556 498 NPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 548 (561)
Q Consensus 498 ~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 548 (561)
|+++|.||.++|+ +++|++|||+.||||.++|++++.+|+++||+.+
T Consensus 207 ~~~~r~ii~l~~~----~g~s~~eIA~~lgis~~~V~~~~~ra~~~Lr~~~ 253 (255)
T TIGR02941 207 SEREKSIIHCTFE----ENLSQKETGERLGISQMHVSRLQRQAISKLKEAA 253 (255)
T ss_pred CHHHHHHHHHHHc----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 9999999999998 8999999999999999999999999999999865
No 25
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=100.00 E-value=2.5e-36 Score=299.91 Aligned_cols=223 Identities=29% Similarity=0.469 Sum_probs=199.1
Q ss_pred hhcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccc
Q 008556 316 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT 395 (561)
Q Consensus 316 ~~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~ 395 (561)
.++..|+++|+..|.++|+++|++|.+++.+++||+|||++|||+++++|||.+|.+|+||++|||++.|.++++++. .
T Consensus 7 ~gd~~a~~~l~~~y~~~v~~~a~~~~~~~~~aeDl~Qe~~i~l~~a~~~f~~~~~~~f~tyl~~~i~~~i~~~lr~~~-~ 85 (231)
T TIGR02885 7 NGDKEARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEIKRFLRDDG-I 85 (231)
T ss_pred cCCHHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHhCC-C
Confidence 355699999999999999999999999999999999999999999999999999999999999999999999999986 8
Q ss_pred cccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCc--hhhhhcccCC
Q 008556 396 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDT--TFQEITADTG 473 (561)
Q Consensus 396 IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~--~l~d~l~d~~ 473 (561)
|++|+++...++++.++...+..++|+.|+.+|||+.+|++++++..++.......|||.++.++++. ++.+.+.++.
T Consensus 86 i~~p~~~~~~~~~~~~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~d~~~~~~ 165 (231)
T TIGR02885 86 IKVSRSLKELARKIRYMKEELSKELGREPTINELAEALGVSPEEIVMALESARSPQSLYDTVHQDDGDPIYLLDQIADKG 165 (231)
T ss_pred eECCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHHHccCCcCcccCCCCCCCCcchhhhhcCCCC
Confidence 89999999999999999999999999999999999999999999999988888889999888655432 3456665543
Q ss_pred CCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008556 474 VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 548 (561)
Q Consensus 474 ~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 548 (561)
. ++. ....+..|..++..||++|++||.++|+ +++|++|||+.||||+++|++++++|++|||..|
T Consensus 166 ~--~~~---~~~~~~~l~~~l~~L~~~e~~i~~~~~~----~~~t~~eIA~~lgis~~~V~~~~~~al~~Lr~~l 231 (231)
T TIGR02885 166 S--EDS---DWLEKIALKEAISKLDERERQIIMLRYF----KDKTQTEVANMLGISQVQVSRLEKKVLKKMKEKL 231 (231)
T ss_pred c--cHH---hHHHHHHHHHHHHcCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHhC
Confidence 2 222 2223557889999999999999999998 8999999999999999999999999999999864
No 26
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily. This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.
Probab=100.00 E-value=6.9e-36 Score=295.77 Aligned_cols=221 Identities=28% Similarity=0.452 Sum_probs=198.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhccccccc
Q 008556 319 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL 398 (561)
Q Consensus 319 ~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRl 398 (561)
..|++.||..|.++|+++|++|.+++.+.+||+|||++|||+|+++||+.+|.+|+||++|||++.|.++++++.+.+++
T Consensus 2 ~~a~~~lv~~y~~~v~~~a~~~~~~~~~~eDl~Qe~~i~l~~a~~~f~~~~~~~F~ty~~~~i~~~~~~~~r~~~~~~ri 81 (227)
T TIGR02980 2 KEAREKLVELNLPLVRSIARRFRNRGEPHEDLVQVGTIGLVKAIDRFDPSYGVKFSTFAVPTIMGEIKRFFRDDTWAVRV 81 (227)
T ss_pred HHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCCcHHHHHHHHHHHHHHHHHHcCCceec
Confidence 46899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred chhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCC--CccCCCCCCCCCC--chhhhhcccCCC
Q 008556 399 PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRM--PLSMQQPVWADQD--TTFQEITADTGV 474 (561)
Q Consensus 399 P~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~--~~SLD~~v~~d~~--~~l~d~l~d~~~ 474 (561)
|.++...+++++++...+.+.+|+.|+.+|+|+.+|++++++..++..... ..|||.++.++++ ..+.+.+.
T Consensus 82 ~~~~~~~~~~~~~~~~~l~~~~~~~p~~~ela~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~~d~~~---- 157 (227)
T TIGR02980 82 PRRLKELGLKINKATEELTQRLGRSPTIAEIAEELGVSEEEVVEALEAGNSYSALSLDAPIEDDDGDPIALLDTLG---- 157 (227)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCCeeccccCCCCCCCCcccccccC----
Confidence 999999999999999999999999999999999999999999998876654 8999988763222 12223322
Q ss_pred CChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008556 475 EIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 548 (561)
Q Consensus 475 ~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 548 (561)
+++..++..+....|..+|..||+++|+||.++|+ +++|++|||+.||+|.++|++++++|+++||+.+
T Consensus 158 -~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~y~----~~~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~~l 226 (227)
T TIGR02980 158 -DEDDALETVEDRLALKPLLAALPERERRILLLRFF----EDKTQSEIAERLGISQMHVSRLLRRALKKLREQL 226 (227)
T ss_pred -CcchHHHhHHHHHHHHHHHHcCCHHHHHHHHHHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 34455556667778999999999999999999998 8999999999999999999999999999999865
No 27
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=100.00 E-value=3.8e-35 Score=295.65 Aligned_cols=226 Identities=23% Similarity=0.367 Sum_probs=202.3
Q ss_pred hcHHHHHHHHHHHHHHHHHHHHhhhC---CCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcc
Q 008556 317 SGNSSREKLINANLRLVVHVAKQYQG---RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHS 393 (561)
Q Consensus 317 ~G~~Are~LI~~nlrLV~sIArrY~~---~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~s 393 (561)
++..|++.||..|.++|+++|++|.+ ++.+.+||+|||++|||+++++||+.+|.+|+||+++||++.|.++++++.
T Consensus 19 ~d~~a~~~L~~~y~~~v~~~~~~~~~~~~~~~~~eDl~Qe~~i~l~~~~~~f~~~~~~~f~tyl~~~irn~~~d~lR~~~ 98 (251)
T PRK07670 19 RDPDAADELIRRYMPLVHYHVQRISVGLPKSVSKDDLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIRGAIIDGLRKED 98 (251)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhcC
Confidence 34589999999999999999999965 678999999999999999999999999999999999999999999999876
Q ss_pred cccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHH--hcCCCccCCCCCCCCCCc-hhhhhcc
Q 008556 394 RTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIF--ITRMPLSMQQPVWADQDT-TFQEITA 470 (561)
Q Consensus 394 r~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~--~~~~~~SLD~~v~~d~~~-~l~d~l~ 470 (561)
++|.++...+++++++...+.+.+|+.|+.+|||+.+|+++++|..++. ......|||.++.++++. .+.+.+.
T Consensus 99 ---~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~~~~~ 175 (251)
T PRK07670 99 ---WLPRSMREKTKKVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATMNEGFFANLLSIDEKTHDQDDGENVSVTIR 175 (251)
T ss_pred ---CCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHHHHHHhccCccccCccccCCCCcchhhhhhc
Confidence 6999999999999999999999999999999999999999999999976 356789999988654432 2334444
Q ss_pred cCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008556 471 DTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 549 (561)
Q Consensus 471 d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 549 (561)
+....++++.+...+....|..+|..||+++|+||.++|+ +++|++|||+.||+|.++|+++++||+++||.++.
T Consensus 176 ~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~~~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l~ 250 (251)
T PRK07670 176 DDKTPTPEEKLLKEELIEELAEKIKQLSEKEQLVISLFYK----EELTLTEIGQVLNLSTSRISQIHSKALFKLKKLLE 250 (251)
T ss_pred CcCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence 5555577878888888889999999999999999999998 89999999999999999999999999999999875
No 28
>PRK05572 sporulation sigma factor SigF; Validated
Probab=100.00 E-value=1.9e-34 Score=290.66 Aligned_cols=244 Identities=28% Similarity=0.430 Sum_probs=213.1
Q ss_pred hcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHHHHHHHHHH
Q 008556 254 WGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLV 333 (561)
Q Consensus 254 ~~i~~~~lLT~eEE~eL~~~i~~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~~l~~G~~Are~LI~~nlrLV 333 (561)
+.-+..|.||.+++.+|..+++. ++..|++.|+..|.++|
T Consensus 6 ~~~~~~~~l~~~~~~~li~~~~~----------------------------------------gd~~a~~~L~~~y~~~v 45 (252)
T PRK05572 6 KNKKKKPQLKDEENKELIKKSQD----------------------------------------GDQEARDTLVEKNLRLV 45 (252)
T ss_pred ccCcCCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHHHhHHHH
Confidence 44567899999999888766442 44689999999999999
Q ss_pred HHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHH
Q 008556 334 VHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAK 413 (561)
Q Consensus 334 ~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~~~l~ki~ka~ 413 (561)
+++|++|.+++.+++||+|||++++|+++++||+.+|.+|.||+++||++.|.+++++.. .+++|+++....++++++.
T Consensus 46 ~~~a~~~~~~~~~aeDl~Qe~~l~l~~~~~~f~~~~~~~f~twl~~~i~~~i~~~lr~~~-~~r~~~~~~~~~~~~~~~~ 124 (252)
T PRK05572 46 WSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSLKETANKIRKDK 124 (252)
T ss_pred HHHHHHHccCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHhCC-CCCCCHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999998889999999999999999999884 7899999999999999999
Q ss_pred HHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCc--hhhhhcccCCCCChhHHHHHHHHHHHHH
Q 008556 414 RLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDT--TFQEITADTGVEIPDISVQKQLMRQHVR 491 (561)
Q Consensus 414 ~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~--~l~d~l~d~~~~~pee~le~~e~~e~L~ 491 (561)
..+..++|+.|+.+|+|+.+|++++++..++.....+.|++.++.+++.. ++.+.+.++.. + .......|.
T Consensus 125 ~~l~~~~~r~p~~~eia~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~d~~~~~~~---~----~~~~~~~l~ 197 (252)
T PRK05572 125 DELSKELGREPTIEELAEYLGVTPEEVVLAQEASRSPQSIHETVHENDGDPITLLDQIADQSE---E----DWFDKIALK 197 (252)
T ss_pred HHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHhcCCCcCcccCcccCCCCcchhhhhcCCCch---h----hHHHHHHHH
Confidence 99999999999999999999999999999888878889999887654322 23344433321 1 123356789
Q ss_pred HHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008556 492 NLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 549 (561)
Q Consensus 492 ~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 549 (561)
.+|..||+++++||.++|+ +++|++|||+.+|+|.++|++++++|+++||..+.
T Consensus 198 ~~l~~L~~~~~~v~~l~~~----~~~s~~eIA~~lgis~~~V~~~~~ral~kLr~~l~ 251 (252)
T PRK05572 198 EAIRELDERERLIVYLRYF----KDKTQSEVAKRLGISQVQVSRLEKKILKQMKEKLD 251 (252)
T ss_pred HHHHcCCHHHHHHHHHHHh----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhc
Confidence 9999999999999999998 89999999999999999999999999999998774
No 29
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=100.00 E-value=2.5e-34 Score=290.34 Aligned_cols=243 Identities=24% Similarity=0.355 Sum_probs=213.9
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHHHHHHHHHHHHHHHh
Q 008556 260 KLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQ 339 (561)
Q Consensus 260 ~lLT~eEE~eL~~~i~~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~~l~~G~~Are~LI~~nlrLV~sIArr 339 (561)
|.|+++||.+|..+++. .++..|++.||..|.++|+++|++
T Consensus 8 ~~l~~~e~~~li~~~~~---------------------------------------~gd~~a~~~l~~~~~~~v~~~a~~ 48 (257)
T PRK08583 8 TKLTKEEVNKWIAEYQE---------------------------------------NQDEEAQEKLVKHYKNLVESLAYK 48 (257)
T ss_pred CcCChHHHHHHHHHHHH---------------------------------------cCCHHHHHHHHHHHHHHHHHHHHH
Confidence 77999999888776543 134689999999999999999999
Q ss_pred hhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHHHHh
Q 008556 340 YQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQE 419 (561)
Q Consensus 340 Y~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e 419 (561)
|.+++.+++||+||||+|||+++++||+.+|.+|.||+++||++.|.++++++.+.+++|+++....++++++...+...
T Consensus 49 ~~~~~~~aeDlvQe~~l~l~~~~~~f~~~~~~~f~tyl~~~i~n~~~~~lr~~~~~~~i~r~~~~~~~~~~~~~~~~~~~ 128 (257)
T PRK08583 49 YSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPTIIGEIKRYLRDKTWSVHVPRRIKELGPKIKKAVDELTTE 128 (257)
T ss_pred HhcCCCCHHHHHHHHHHHHHHHHHHcCccCCCChHHHHHHHHHHHHHHHHHhcCCCcCCCHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999998999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHhc--CCCccCCCCCCCCCCc---hhhhhcccCCCCChhHHHHHHHHHHHHHHHH
Q 008556 420 GNHSPDKEDLARRVGITVEKLERLIFIT--RMPLSMQQPVWADQDT---TFQEITADTGVEIPDISVQKQLMRQHVRNLL 494 (561)
Q Consensus 420 ~gr~Pt~eEIA~~lgis~e~v~~ll~~~--~~~~SLD~~v~~d~~~---~l~d~l~d~~~~~pee~le~~e~~e~L~~aL 494 (561)
.++.|+.+++|+.+|++.+++..++... ....|+|.+++.+++. .+.+.. ..|+..+...+....|..+|
T Consensus 129 ~~r~~~~~e~a~~~~~~~~~~~~~~~~~~~~~~~sld~~~~~~~~~~~~~~~~~~-----~~~e~~~~~~~~~~~l~~~l 203 (257)
T PRK08583 129 LQRSPKISEIADRLGVSEEEVLEAMEMGKSYQALSVDHSIEADSDGSTVTLLDIV-----GQQEDGYELTEQRMILEKIL 203 (257)
T ss_pred hCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceecCccccCCCCCccchHhhhc-----CCcchhHHHHHHHHHHHHHH
Confidence 9999999999999999999998876643 3578888887654332 122222 24556666677778899999
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008556 495 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 550 (561)
Q Consensus 495 ~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 550 (561)
..||+++|+||.++|+ +++|++|||+.||||.++|++++++|+++||..+..
T Consensus 204 ~~L~~~~r~vl~l~~~----~g~s~~eIA~~l~is~~tV~~~~~ra~~kLr~~l~~ 255 (257)
T PRK08583 204 PVLSDREKSIIQCTFI----ENLSQKETGERLGISQMHVSRLQRQAIKKLREAAFL 255 (257)
T ss_pred HhCCHHHHHHHHHHHh----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhcc
Confidence 9999999999999998 899999999999999999999999999999998764
No 30
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. 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.
Probab=100.00 E-value=1.5e-34 Score=286.14 Aligned_cols=217 Identities=23% Similarity=0.419 Sum_probs=195.5
Q ss_pred HHHHHHHHHHHHHHhhhC---CCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchh
Q 008556 325 LINANLRLVVHVAKQYQG---RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN 401 (561)
Q Consensus 325 LI~~nlrLV~sIArrY~~---~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~ 401 (561)
|+..|.++|+++|++|.+ ++.+++||+|||++|||+++++|||.+|++|+||+++||++.|.+++++.. ++|.+
T Consensus 1 L~~~~~~lv~~~a~~~~~~~~~~~~~eDl~Qe~~~~l~~a~~~fd~~~~~~f~t~~~~~i~~~~~~~lr~~~---~~p~~ 77 (224)
T TIGR02479 1 LIRRYLPLVKRIAGRLSVGLPSSVELDDLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAMLDELRRLD---WVPRS 77 (224)
T ss_pred CHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHHcC---ccCHH
Confidence 688999999999999986 789999999999999999999999999999999999999999999999865 58999
Q ss_pred HHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHh--cCCCccCCCCCCCC-CCchhhhhcccCCCCChh
Q 008556 402 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI--TRMPLSMQQPVWAD-QDTTFQEITADTGVEIPD 478 (561)
Q Consensus 402 ~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~--~~~~~SLD~~v~~d-~~~~l~d~l~d~~~~~pe 478 (561)
....++++.++...+.+.+|+.|+.+|+|+.+|+++++|..++.. .....|+|....++ +...+.+.++++...+|+
T Consensus 78 ~~~~~~~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~~~~~~~~~ 157 (224)
T TIGR02479 78 LRQKARKLERAIRELEARLGREPTEEEIAEELGMDLKEYRQALNEINALSLVSLDELLESGDDGGSLIDRIEDDKSEDPE 157 (224)
T ss_pred HHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHHHHHHHhcCCccccCCcccCCCccchhhhhccccccCCHH
Confidence 999999999999999999999999999999999999999999864 34567888766443 234566666655556788
Q ss_pred HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008556 479 ISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 548 (561)
Q Consensus 479 e~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 548 (561)
+.+...+....|..+|..||+++|+||.++|+ +++|++|||+.||+|.++|++++++|+++||+++
T Consensus 158 ~~~~~~~~~~~l~~~l~~L~~~~r~il~l~y~----~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l 223 (224)
T TIGR02479 158 EELEREELREALAEAIESLSEREQLVLSLYYY----EELNLKEIGEVLGLTESRVSQIHSQALKKLRAKL 223 (224)
T ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHh----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHc
Confidence 88888888899999999999999999999998 8999999999999999999999999999999875
No 31
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=100.00 E-value=2.8e-34 Score=286.60 Aligned_cols=209 Identities=21% Similarity=0.327 Sum_probs=179.7
Q ss_pred HHHHHHHHHHHHHHHHHhhhC---CCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhccccccc
Q 008556 322 REKLINANLRLVVHVAKQYQG---RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL 398 (561)
Q Consensus 322 re~LI~~nlrLV~sIArrY~~---~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRl 398 (561)
...|+..|+++|.++|++|.+ .+.+.+||+|||++|||+|+++|||.+| +|+||++||||++|.+++++..+ +
T Consensus 17 ~~~lv~~y~~lV~~la~~~~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~-~F~tYa~~~Ir~~il~~lr~~~~---~ 92 (231)
T PRK12427 17 EGKYLNAYLPLVKKVVRQLAFQADSVIDREDMEQIALMGLLEALRRYGHPDE-QFAAYAVHRIRGAILDELRELDW---R 92 (231)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHhcCCCCC-ChHHHHHHHHHHHHHHHHHhcCC---C
Confidence 356788899999999999875 4679999999999999999999998666 89999999999999999998653 6
Q ss_pred chhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHh--cCCCccCCCCCCCCCCchhhhhcccCCCCC
Q 008556 399 PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI--TRMPLSMQQPVWADQDTTFQEITADTGVEI 476 (561)
Q Consensus 399 P~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~--~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~ 476 (561)
|+++....++++++...+.+++|+.|+.+|||+.+|+++++|.+++.. .....|||.+++++++.. .+.+ ..
T Consensus 93 ~r~vr~~~~~i~~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~---~~~~---~~ 166 (231)
T PRK12427 93 PRRLRQKTHKTNDAIREIAKRLGHEPNFEEISAELNLTAEEYQEYLLLENAGTLESLDELLALEAHND---ILQS---RD 166 (231)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceeccCcccCCCccc---ccCC---CC
Confidence 888889999999999999999999999999999999999999998764 456899999886654322 2221 12
Q ss_pred hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008556 477 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 547 (561)
Q Consensus 477 pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 547 (561)
+++. ......|..++..||+++|.||.++|+ +++|++|||+.||||.++|+|++++|++|||..
T Consensus 167 ~~~~---~~~~~~l~~~l~~L~~~er~vi~l~~~----~~~t~~EIA~~lgis~~~V~q~~~~~~~kLr~~ 230 (231)
T PRK12427 167 LEEN---IIIEDNLKQALSQLDEREQLILHLYYQ----HEMSLKEIALVLDLTEARICQLNKKIAQKIKSF 230 (231)
T ss_pred HHHH---HHHHHHHHHHHHcCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhh
Confidence 3322 234557899999999999999999998 899999999999999999999999999999964
No 32
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=100.00 E-value=4.1e-33 Score=278.14 Aligned_cols=225 Identities=23% Similarity=0.406 Sum_probs=197.9
Q ss_pred hcHHHHHHHHHHHHHHHHHHHHhhh---CCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcc
Q 008556 317 SGNSSREKLINANLRLVVHVAKQYQ---GRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHS 393 (561)
Q Consensus 317 ~G~~Are~LI~~nlrLV~sIArrY~---~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~s 393 (561)
.|.-++++|+..|.++|+++|++|. +++.+++||+|||++|||+++++|||.+|.+|+||+++||++.|.++++++.
T Consensus 5 ~~~~~~~~L~~~~~~~v~~~a~~~~~~~~~~~~aeDlvQe~~i~l~~~~~~f~~~~~~~f~tyl~~~irn~~~~~lR~~~ 84 (236)
T PRK06986 5 EGKMDQDELVEQYAPLVKRIALRLKARLPASVDLDDLIQAGMIGLLEAARRYDGEQGASFETYAGQRIRGAMLDELRSLD 84 (236)
T ss_pred cccccHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhcCcccCCChHHHHHHHHHHHHHHHHHHcC
Confidence 4678999999999999999999997 6789999999999999999999999999999999999999999999999986
Q ss_pred cccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHh--cCCCccCCCCCCCCCCchhhhhccc
Q 008556 394 RTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI--TRMPLSMQQPVWADQDTTFQEITAD 471 (561)
Q Consensus 394 r~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~--~~~~~SLD~~v~~d~~~~l~d~l~d 471 (561)
+ +|.++....+++.++...+.+.+|++|+.+|||+.+|++.++|..++.. .....|++..++++++. +.. ..+
T Consensus 85 ~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ela~~l~i~~~~v~~~~~~~~~~~~~sl~~~~~~~~~~-~~~-~~~ 159 (236)
T PRK06986 85 W---VPRSVRRNAREVAQAIRQLEQELGREPTDTEVAEKLGLSLEEYREMLLDTNISQLFSIDELRGEHGDS-ILV-TED 159 (236)
T ss_pred C---CCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhccCCccccccccCCCcc-ccc-ccC
Confidence 4 6888888888888888999999999999999999999999999998874 34567888876554442 222 223
Q ss_pred CCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008556 472 TGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 550 (561)
Q Consensus 472 ~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 550 (561)
+...+|++.+...+....|..+|..||+++|.||.++|. +++|++|||+.||||.++|++++.+|+++||+.+..
T Consensus 160 ~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l~~ 234 (236)
T PRK06986 160 HQDEDPLQQLEDEELREALVEAIESLPEREQLVLSLYYQ----EELNLKEIGAVLGVSESRVSQIHSQAIKRLRARLGE 234 (236)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHhHhc----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 334467778888888889999999999999999999998 899999999999999999999999999999998754
No 33
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=99.96 E-value=3.5e-28 Score=242.35 Aligned_cols=210 Identities=25% Similarity=0.451 Sum_probs=171.1
Q ss_pred HHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHHHH
Q 008556 248 PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLIN 327 (561)
Q Consensus 248 ~l~~Yl~~i~~~~lLT~eEE~eL~~~i~~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~~l~~G~~Are~LI~ 327 (561)
.+..|+.+++..|+||+++|..|+..++. ++..|++.|+.
T Consensus 17 ~~~~~~~~~~~~~~~~~~~e~~l~~~~~~----------------------------------------gd~~a~~~l~~ 56 (233)
T PRK05803 17 FLVSYVKNNSFPQPLSEEEERKYLELMKE----------------------------------------GDEEARNILIE 56 (233)
T ss_pred HHHHHHHHhcccCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHH
Confidence 46789999999999999999888776543 44689999999
Q ss_pred HHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHHHHH
Q 008556 328 ANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLS 407 (561)
Q Consensus 328 ~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~~~l~ 407 (561)
.|.++|+++|.+|.+++.+.+||+|||++++|+++++||+++|.+|.||+++|+++.+.+++++..+..
T Consensus 57 ~y~~~l~~~a~~~~~~~~daeDlvQE~fi~l~~~~~~f~~~~~~~f~~wl~~i~rn~~id~~Rk~~~~~----------- 125 (233)
T PRK05803 57 RNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYAARCIENEILMHLRNLKKTK----------- 125 (233)
T ss_pred HhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCChHHHHHHHHHHHHHHHHHHHhccc-----------
Confidence 999999999999999999999999999999999999999998999999999999999999998754210
Q ss_pred HHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCC---CCchhhhhcccCCCCChhHHHHHH
Q 008556 408 KVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWAD---QDTTFQEITADTGVEIPDISVQKQ 484 (561)
Q Consensus 408 ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d---~~~~l~d~l~d~~~~~pee~le~~ 484 (561)
...+++.....+ ....+.+...+. .+++++.+..+
T Consensus 126 -----------------------------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~ 163 (233)
T PRK05803 126 -----------------------------------------KEVSLQDPIGVDKEGNEISLIDILGSE-EDDVIEQVELK 163 (233)
T ss_pred -----------------------------------------cCCCccccccCCCCcCcccHHHHccCC-CCCHHHHHHHH
Confidence 011111111111 112233333332 23567777777
Q ss_pred HHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008556 485 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 550 (561)
Q Consensus 485 e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 550 (561)
...+.|..+|..||+++|+||.++|++++.+++|++|||+.||||.++|+++++||+++||+.+..
T Consensus 164 ~~~~~l~~~l~~Lp~~~R~i~~l~y~~~~~e~~S~~EIA~~lgis~~tV~~~~~rA~~kLr~~l~~ 229 (233)
T PRK05803 164 MEVEKLYKKIDILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKKLFKELYR 229 (233)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHhCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 777889999999999999999999977666899999999999999999999999999999998754
No 34
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=99.93 E-value=2.1e-24 Score=214.86 Aligned_cols=181 Identities=28% Similarity=0.533 Sum_probs=140.0
Q ss_pred hcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhccccc
Q 008556 317 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI 396 (561)
Q Consensus 317 ~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~I 396 (561)
++..|++.|+..|.++|+.+|++|.+++.+++|++||+++++|+++++|++..+++|.||++++++|.+.++++++.+..
T Consensus 49 gd~~af~~l~~~y~~~l~~~a~~~~~~~~~AeDlvQevfl~l~~~~~~f~~~~~~~f~twl~~iarn~~~d~lRk~~~~~ 128 (234)
T PRK08301 49 GDEAVRSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEILMYLRRNNKVK 128 (234)
T ss_pred cCHHHHHHHHHHhHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHHHHHHhccc
Confidence 44689999999999999999999999999999999999999999999999988889999999999999999998764210
Q ss_pred ccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCC--CCC-chhhhhcccCC
Q 008556 397 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWA--DQD-TTFQEITADTG 473 (561)
Q Consensus 397 RlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~--d~~-~~l~d~l~d~~ 473 (561)
...+++.+... ++. ..+.+...+.
T Consensus 129 ----------------------------------------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~- 155 (234)
T PRK08301 129 ----------------------------------------------------AEVSFDEPLNIDWDGNELLLSDVLGTD- 155 (234)
T ss_pred ----------------------------------------------------cccccccccccccCCCcccHHHhccCc-
Confidence 00111111100 000 1111222211
Q ss_pred CCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008556 474 VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 550 (561)
Q Consensus 474 ~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 550 (561)
...++..+........|..+|+.||+++|+||.++|+|...+++|++|||+.||||.++|+++++||+++||+.+..
T Consensus 156 ~~~~~~~~~~~~~~~~l~~al~~Lp~~~R~v~~L~y~l~~~eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~l~~ 232 (234)
T PRK08301 156 NDIIYKDIEDEVDRKLLKKALKKLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEKRIIKRLKKEINK 232 (234)
T ss_pred ccchHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 11233344455556679999999999999999999965444899999999999999999999999999999998753
No 35
>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor. 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 homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also 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.
Probab=99.93 E-value=2.3e-24 Score=214.19 Aligned_cols=199 Identities=28% Similarity=0.527 Sum_probs=155.9
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHHHHHHHHHHHHH
Q 008556 257 ETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHV 336 (561)
Q Consensus 257 ~~~~lLT~eEE~eL~~~i~~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~~l~~G~~Are~LI~~nlrLV~sI 336 (561)
+..+.|++.+|.+|..+++. ++..|++.|+..|.++|+++
T Consensus 25 ~~~~~~~~~~~~~li~~~~~----------------------------------------gd~~af~~l~~~y~~~v~~~ 64 (227)
T TIGR02846 25 SFPQPLSEEEEKKYLDRLKE----------------------------------------GDEEARNVLIERNLRLVAHI 64 (227)
T ss_pred hCCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHHHhHHHHHHH
Confidence 45567888888888776543 44689999999999999999
Q ss_pred HHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHH
Q 008556 337 AKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLY 416 (561)
Q Consensus 337 ArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l 416 (561)
|.+|.++..+++||+||+++++|+++++|+++++.+|.||+++|+++.|.+++++..+..+
T Consensus 65 ~~~~~~~~~dAEDlvQevfi~l~~~~~~~~~~~~~~f~twl~~i~rN~~~d~~Rk~~r~~~------------------- 125 (227)
T TIGR02846 65 VKKFSNTGEDVDDLISIGTIGLIKAIDSFDPDKGTRLATYAARCIENEILMHLRALKKTKG------------------- 125 (227)
T ss_pred HHHhcCCCCCHHHHHHHHHHHHHHHHHhCCcccCCChHHHHHHHHHHHHHHHHHHHhcccc-------------------
Confidence 9999999999999999999999999999999888899999999999999999987642100
Q ss_pred HHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCC---CCchhhhhcccCCCCChhHHHHHHHHHHHHHHH
Q 008556 417 IQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWAD---QDTTFQEITADTGVEIPDISVQKQLMRQHVRNL 493 (561)
Q Consensus 417 ~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d---~~~~l~d~l~d~~~~~pee~le~~e~~e~L~~a 493 (561)
..+++.....+ ....+.+...+. ...+++.+...+..+.|..+
T Consensus 126 ---------------------------------~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~l~~~ 171 (227)
T TIGR02846 126 ---------------------------------EVSLQDPIGVDKEGNEISLIDILGSD-GDSVIEQVELNLEIKKLYKK 171 (227)
T ss_pred ---------------------------------ceeccccccCCcccCcccHHHHhcCC-CCChHHHHHHHHHHHHHHHH
Confidence 00111111000 011122222221 23456666666666789999
Q ss_pred HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008556 494 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 548 (561)
Q Consensus 494 L~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 548 (561)
|+.||+++|+||.++|.++..+++|++|||+.||+|.++|++++++|+++||+.+
T Consensus 172 i~~L~~~~r~il~l~y~~~~~e~~S~~EIAe~lgis~~tV~~~~~rAl~~Lr~~~ 226 (227)
T TIGR02846 172 LSVLDGREREVIEMRYGLGDGRRKTQREIAKILGISRSYVSRIEKRALMKLYKEL 226 (227)
T ss_pred HHhCCHHHHHHHHHHHcCCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 9999999999999999765557899999999999999999999999999999865
No 36
>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. As characterized in Bacillus subtilis, this protein is synthesized as a precursor, specifically in the mother cell compartment, and must cleaved by the SpoIIGA protein to be made active.
Probab=99.92 E-value=1.5e-23 Score=209.30 Aligned_cols=181 Identities=30% Similarity=0.540 Sum_probs=141.2
Q ss_pred hcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhccccc
Q 008556 317 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI 396 (561)
Q Consensus 317 ~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~I 396 (561)
++..|++.|+..|.+.|+.+|++|.+++.+.+|++||+++++|+++++|++..+++|.||++.++++.+.++++++.+..
T Consensus 49 ~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~AEDlvQE~fl~l~~~~~~f~~~~~~~f~~wl~~iarN~~~d~~Rk~~r~~ 128 (234)
T TIGR02835 49 GDESAKSTLIERNLRLVVYIARKFENTGIGIEDLVSIGTIGLIKAVNTFNPSKKIKLATYASRCIENEILMYLRRNNKTR 128 (234)
T ss_pred CCHHHHHHHHHHhHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHHhcccc
Confidence 45689999999999999999999999999999999999999999999999988889999999999999999998765310
Q ss_pred ccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCC---CCCCchhhhhcccCC
Q 008556 397 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVW---ADQDTTFQEITADTG 473 (561)
Q Consensus 397 RlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~---~d~~~~l~d~l~d~~ 473 (561)
...+++..+. .+......+.. ++.
T Consensus 129 ----------------------------------------------------~~~~~~~~~~~~~~~~~~~~~~~~-~~~ 155 (234)
T TIGR02835 129 ----------------------------------------------------SEVSFDEPLNVDWDGNELLLSDVL-GTD 155 (234)
T ss_pred ----------------------------------------------------CcccccccccCCCCCCcchHHHhc-CCC
Confidence 0011111110 00001111111 111
Q ss_pred CCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008556 474 VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 550 (561)
Q Consensus 474 ~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 550 (561)
.+.++..+........|..+|+.||+++|+||.++|++.+++++|++|||+.||||..+|+++.+||+++||+.+..
T Consensus 156 ~~~~~~~~~~~~~~~~l~~ai~~Lp~~~R~ii~L~~~l~~~eg~s~~EIA~~Lgis~~tV~~~l~ra~~~LR~~l~~ 232 (234)
T TIGR02835 156 SDIVYKYLEEEVDRELLRKALAKLNDREKKIMELRFGLVGGTEKTQKEVADMLGISQSYISRLEKRILKRLKKEINR 232 (234)
T ss_pred CCcHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhhc
Confidence 12333444555566789999999999999999999976555899999999999999999999999999999998754
No 37
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=99.91 E-value=1.2e-22 Score=197.55 Aligned_cols=195 Identities=22% Similarity=0.329 Sum_probs=149.5
Q ss_pred CCHHHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHH
Q 008556 306 LSCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 384 (561)
Q Consensus 306 ~~~~eL~~~l~~G-~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqa 384 (561)
++++.|...++.| ..|++.|+..|.++|+.+|++|.+++.+++|++||++++||+++.+||+.+|.+|.||++.++++.
T Consensus 9 ~~~~~l~~~~~~~d~~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~~~~f~twl~~i~~n~ 88 (208)
T PRK08295 9 LEDEELVELARSGDKEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAELCITRQ 88 (208)
T ss_pred CChHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHH
Confidence 4556666666544 599999999999999999999999999999999999999999999999988789999999999999
Q ss_pred HHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCC-CCCc
Q 008556 385 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWA-DQDT 463 (561)
Q Consensus 385 I~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~-d~~~ 463 (561)
+.+++++..+..+.+. ....|.+.++.. +.+.
T Consensus 89 ~~d~~r~~~r~~~~~~-----------------------------------------------~~~~s~~~~~~~~~~~~ 121 (208)
T PRK08295 89 IITAIKTANRQKHIPL-----------------------------------------------NSYVSLDKPIYDEESDR 121 (208)
T ss_pred HHHHHHHhhhhccccc-----------------------------------------------cceeecCCcccCCccch
Confidence 9998876432111100 011233332221 1222
Q ss_pred hhhhhcccCCCCChhHHHHHHHHHHHH-HHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008556 464 TFQEITADTGVEIPDISVQKQLMRQHV-RNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 542 (561)
Q Consensus 464 ~l~d~l~d~~~~~pee~le~~e~~e~L-~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALk 542 (561)
.+.+.+.++...+|+..+...+....+ ..++..||+++|+||.+ |. +++|++|||+.||||.++|+..+.||++
T Consensus 122 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~L~~~~r~vl~l-~~----e~~s~~EIA~~lgis~~tV~~~l~rar~ 196 (208)
T PRK08295 122 TLLDVISEAKVTDPEELIISKEELEDIEEKIEELLSELEKEVLEL-YL----DGKSYQEIAEELNRHVKSIDNALQRVKR 196 (208)
T ss_pred hHHHHhcCcccCCHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHH-HH----ccCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 344444444444677666555555555 45679999999999999 77 8999999999999999999999999999
Q ss_pred HHHHHhhcCc
Q 008556 543 RLKQSLGGKA 552 (561)
Q Consensus 543 KLR~~l~~~~ 552 (561)
+||+++....
T Consensus 197 ~Lr~~l~~~~ 206 (208)
T PRK08295 197 KLEKYLENRE 206 (208)
T ss_pred HHHHHHHhhc
Confidence 9999886543
No 38
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=99.90 E-value=4e-22 Score=191.19 Aligned_cols=176 Identities=16% Similarity=0.250 Sum_probs=143.5
Q ss_pred CCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHH
Q 008556 306 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 384 (561)
Q Consensus 306 ~~~~eL~~~l~~G~-~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqa 384 (561)
++++.|+..+..|+ .|++.|+..|.++|+.+|++|.+++.+.+|++||+++++|+++.+|++. +..|.+|++..+++.
T Consensus 5 ~~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~f~~wl~~ia~n~ 83 (186)
T PRK05602 5 DPDEELLARVAAGDPAAFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRPG-EARFDTWLHRVVLNL 83 (186)
T ss_pred ccHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHhhhcCCC-CCcHHHHHHHHHHHH
Confidence 45666777665555 9999999999999999999999999999999999999999999999986 457999999999999
Q ss_pred HHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCch
Q 008556 385 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT 464 (561)
Q Consensus 385 I~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~ 464 (561)
+.++++++... +.+. .
T Consensus 84 ~~d~~R~~~~~--------------------------------------------------------~~~~-~------- 99 (186)
T PRK05602 84 CYDRLRRRREV--------------------------------------------------------PVED-A------- 99 (186)
T ss_pred HHHHHHhcCCC--------------------------------------------------------Cccc-c-------
Confidence 99998765310 0000 0
Q ss_pred hhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008556 465 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 544 (561)
Q Consensus 465 l~d~l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKL 544 (561)
.+ ..+. ...++..+...+....+..+|..||+++|+||.++|. +++|++|||+.||+|..+|++.++||+++|
T Consensus 100 -~~-~~~~-~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Rar~~L 172 (186)
T PRK05602 100 -PD-VPDP-APGPDAGLEARQRARRVEQALAALPERQREAIVLQYY----QGLSNIEAAAVMDISVDALESLLARGRRAL 172 (186)
T ss_pred -cc-cCCC-CCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhHHHh----cCCCHHHHHHHhCcCHHHHHHHHHHHHHHH
Confidence 00 0011 1134555555666678999999999999999999998 899999999999999999999999999999
Q ss_pred HHHhhcCch
Q 008556 545 KQSLGGKAS 553 (561)
Q Consensus 545 R~~l~~~~l 553 (561)
|+.+...+.
T Consensus 173 r~~l~~~~~ 181 (186)
T PRK05602 173 RAQLADLPG 181 (186)
T ss_pred HHHHHhccc
Confidence 999876553
No 39
>TIGR02859 spore_sigH RNA polymerase sigma-H factor. Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs are detected in Listeria, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt.
Probab=99.89 E-value=8.6e-22 Score=189.83 Aligned_cols=191 Identities=23% Similarity=0.325 Sum_probs=145.1
Q ss_pred CCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHH
Q 008556 306 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 384 (561)
Q Consensus 306 ~~~~eL~~~l~~G~-~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqa 384 (561)
|++..|+..+..|+ .|++.|+..|.+.|+.+|+++.++..+++||+||+++++|+++.+|++..+..|.||++.+|++.
T Consensus 4 ~~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~a~~~~~~~~~aeDlvQe~fl~~~~~~~~~~~~~~~~f~~wl~~~~~~~ 83 (198)
T TIGR02859 4 LEDEEIVELARQGNTHALEYLINKYKNFVRAKARSYFLIGADKEDIIQEGMIGLYKAIRDFRPDKLSSFKAFAELCVTRQ 83 (198)
T ss_pred cchHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHccccCcHHHHHHHHHHHHHHHHHHhCcccCCChHHHHHHHHHHH
Confidence 45667777776665 99999999999999999999999999999999999999999999999988779999999999999
Q ss_pred HHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCC-CCCc
Q 008556 385 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWA-DQDT 463 (561)
Q Consensus 385 I~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~-d~~~ 463 (561)
+.++++...+..+.+ .....|++.+... +++.
T Consensus 84 ~~~~~r~~~~~~~~~-----------------------------------------------~~~~~~~~~~~~~~~~~~ 116 (198)
T TIGR02859 84 IITAIKTATRQKHIP-----------------------------------------------LNSYVSLNKPIYDEESDR 116 (198)
T ss_pred HHHHHHHHHHhcccc-----------------------------------------------hhhhcCcccccccccccc
Confidence 988886532110000 0011233322211 1122
Q ss_pred hhhhhcccCCCCChhHHHHHHHHHHHHHHHHhcC-CHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008556 464 TFQEITADTGVEIPDISVQKQLMRQHVRNLLTLL-NPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 542 (561)
Q Consensus 464 ~l~d~l~d~~~~~pee~le~~e~~e~L~~aL~~L-~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALk 542 (561)
++.+.+.+....+|+..+...+....|.++|..| ++.++.|+. +|. +++|++|||+.||+|.++|+..++||++
T Consensus 117 ~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~Ll~~~~~~i~~-~~~----~~~s~~eIA~~l~~s~~tV~~~l~r~r~ 191 (198)
T TIGR02859 117 TLLDVISGAKVTDPEELIISQEEYGDIESKMNELLSDLEWKVLQ-SYL----DGKSYQEIACDLNRHVKSIDNALQRVKR 191 (198)
T ss_pred hHHHHhhccccCCHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHH-HHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 2333333222346777777777778899999995 566666665 566 8999999999999999999999999999
Q ss_pred HHHHHh
Q 008556 543 RLKQSL 548 (561)
Q Consensus 543 KLR~~l 548 (561)
+||+.+
T Consensus 192 ~L~~~l 197 (198)
T TIGR02859 192 KLEKYL 197 (198)
T ss_pred HHHHhc
Confidence 999875
No 40
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=99.89 E-value=1e-21 Score=190.16 Aligned_cols=175 Identities=17% Similarity=0.196 Sum_probs=139.1
Q ss_pred HHHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHH
Q 008556 308 CRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIR 386 (561)
Q Consensus 308 ~~eL~~~l~~G-~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~ 386 (561)
...|+..+..| ..++++|+..|.++|+++|.+|.++..+.+|++||+++++|+++++||+.+| .|.+|++..+++.+.
T Consensus 17 ~~~li~~~~~g~~~a~~~l~~~y~~~l~~~~~~~~~~~~dAeDivQe~fi~l~~~~~~~~~~~~-~~~~wl~~ia~n~~~ 95 (194)
T PRK09646 17 LDALLRRVARGDQDAFAELYDRTSSRVYGLVRRVLRDPGYSEETTQEVYLEVWRTASRFDPARG-SALAWLLTLAHRRAV 95 (194)
T ss_pred HHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhhcCcccc-cHHHHHHHHHHHHHH
Confidence 44555655544 5999999999999999999999999999999999999999999999998766 699999999999999
Q ss_pred HHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhh
Q 008556 387 KAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQ 466 (561)
Q Consensus 387 ~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~ 466 (561)
++++++.+..+. ... ... .
T Consensus 96 d~~r~~~~~~~~---------------------------------------------------~~~----~~~-~----- 114 (194)
T PRK09646 96 DRVRSEQAASQR---------------------------------------------------EVR----YGA-R----- 114 (194)
T ss_pred HHHHhhcccccc---------------------------------------------------ccc----ccc-c-----
Confidence 999876421100 000 000 0
Q ss_pred hhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556 467 EITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 546 (561)
Q Consensus 467 d~l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 546 (561)
+. +.....+++.+...+..+.|..+|..||+++|+||.++|. +++|++|||+.||+|..+|+++++||+++||.
T Consensus 115 ~~--~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~~~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~ 188 (194)
T PRK09646 115 NV--DPAFDQVAEEVEARLERERVRDCLDALTDTQRESVTLAYY----GGLTYREVAERLAVPLGTVKTRMRDGLIRLRD 188 (194)
T ss_pred cc--cccccchHHHHHHHhHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCCChHhHHHHHHHHHHHHHH
Confidence 00 0001123344444555678999999999999999999998 89999999999999999999999999999999
Q ss_pred Hhhc
Q 008556 547 SLGG 550 (561)
Q Consensus 547 ~l~~ 550 (561)
.+..
T Consensus 189 ~l~~ 192 (194)
T PRK09646 189 CLGV 192 (194)
T ss_pred Hhcc
Confidence 8854
No 41
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=99.89 E-value=8.2e-22 Score=190.25 Aligned_cols=181 Identities=19% Similarity=0.254 Sum_probs=145.5
Q ss_pred CCHHHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHH
Q 008556 306 LSCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 384 (561)
Q Consensus 306 ~~~~eL~~~l~~G-~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqa 384 (561)
++++.++..+..| ..|++.|+..|.+.|+++|+++.++..+.+|++||+++++|+++++|++.. .|.+|++.++++.
T Consensus 11 ~~~~~l~~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~fi~l~~~~~~~~~~~--~f~~wl~~i~~n~ 88 (194)
T PRK12513 11 ASDEALMLRYRAGDAAAFEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRARAQYQPRA--RFRTWLYQIARNL 88 (194)
T ss_pred CCHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCCC--chHHHHHHHHHHH
Confidence 3456666666655 599999999999999999999999999999999999999999999999753 6999999999999
Q ss_pred HHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCch
Q 008556 385 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT 464 (561)
Q Consensus 385 I~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~ 464 (561)
+.+++++..+....+ .+. +. .
T Consensus 89 ~~~~~R~~~~~~~~~-----------------------------------------------------~~~----~~--~ 109 (194)
T PRK12513 89 LIDHWRRHGARQAPS-----------------------------------------------------LDA----DE--Q 109 (194)
T ss_pred HHHHHHHhccccccc-----------------------------------------------------ccc----ch--h
Confidence 999998765321110 000 00 0
Q ss_pred hhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008556 465 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 544 (561)
Q Consensus 465 l~d~l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKL 544 (561)
. ....+ ....|+..++..+....|..+|+.||+++|.||.++|. +++|++|||+.||||.++|++++.||+++|
T Consensus 110 ~-~~~~~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~ra~~~L 183 (194)
T PRK12513 110 L-HALAD-DGAAPEQQLSLFRDRRRLQAALETLPDEQREVFLLREH----GDLELEEIAELTGVPEETVKSRLRYALQKL 183 (194)
T ss_pred h-hhcCC-CCCCHHHHHHHHHHHHHHHHHHHhCCHhHhhheeeehc----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 0 00011 12256666666677788999999999999999999998 899999999999999999999999999999
Q ss_pred HHHhhcCch
Q 008556 545 KQSLGGKAS 553 (561)
Q Consensus 545 R~~l~~~~l 553 (561)
|..+...++
T Consensus 184 r~~l~~~~~ 192 (194)
T PRK12513 184 RELLAEEVA 192 (194)
T ss_pred HHHHHHhhc
Confidence 999876554
No 42
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=99.89 E-value=1.5e-21 Score=186.20 Aligned_cols=180 Identities=15% Similarity=0.234 Sum_probs=141.4
Q ss_pred HHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHH
Q 008556 308 CRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIR 386 (561)
Q Consensus 308 ~~eL~~~l~~G~-~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~ 386 (561)
.+.|+..++.|+ .+++.|+..|.++|+++|+++.++..+++|++||++++||+++.+|++.. .|.+|++..+++.+.
T Consensus 5 ~~~li~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~~--~~~~wl~~iarn~~~ 82 (187)
T PRK09641 5 IKRLIKQVKKGDQNAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINR--KFSTWLYRIATNLTI 82 (187)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhhCCCc--chhHHHHHHHHHHHH
Confidence 344555555554 99999999999999999999999999999999999999999999999853 699999999999999
Q ss_pred HHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhh
Q 008556 387 KAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQ 466 (561)
Q Consensus 387 ~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~ 466 (561)
++++++.+.. +++.....++.....
T Consensus 83 d~~R~~~~~~-------------------------------------------------------~~~~~~~~~~~~~~~ 107 (187)
T PRK09641 83 DRLRKRKPDY-------------------------------------------------------YLDAEVAGTEGLTMY 107 (187)
T ss_pred HHHHhcCccc-------------------------------------------------------cccccccCCcchhhh
Confidence 9988754210 000000011111111
Q ss_pred hhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556 467 EITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 546 (561)
Q Consensus 467 d~l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 546 (561)
+.+.+. ..+|++.+...+....+..+|..||+++|+||.++|. ++++++|||+.||||.++|++.++||+++||+
T Consensus 108 ~~~~~~-~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~~----~~~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 182 (187)
T PRK09641 108 SQLAAD-DALPEEQVVSLELQETIQEAILQLPEKYRTVIVLKYI----EDLSLKEISEILDLPVGTVKTRIHRGREALRK 182 (187)
T ss_pred cccccC-cCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHHh----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 111111 2246666777777788999999999999999999998 89999999999999999999999999999999
Q ss_pred Hhh
Q 008556 547 SLG 549 (561)
Q Consensus 547 ~l~ 549 (561)
.+.
T Consensus 183 ~l~ 185 (187)
T PRK09641 183 QLR 185 (187)
T ss_pred HHh
Confidence 875
No 43
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=99.88 E-value=1.4e-21 Score=186.52 Aligned_cols=178 Identities=16% Similarity=0.241 Sum_probs=139.0
Q ss_pred HHHHHHh-hcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHH
Q 008556 310 DLKSELH-SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKA 388 (561)
Q Consensus 310 eL~~~l~-~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~ 388 (561)
.|+..+. ++..++++|+..|.++|+.+|++|.+++.+++|++||+++++|+++.+|++.. .|.+|++..+++.+.++
T Consensus 7 ~li~~~~~gd~~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~~~~ 84 (187)
T TIGR02948 7 KRIKEVRKGDENAFADLVDLYKDKIYQLCYRMLGNVHEAEDVAQEAFIRAYTNIDTYDIQR--KFSTWLYRIATNLTIDR 84 (187)
T ss_pred HHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCCC--chHHHHHHHHHHHHHHH
Confidence 3444444 45599999999999999999999999999999999999999999999999865 59999999999999999
Q ss_pred HHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhh
Q 008556 389 IFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEI 468 (561)
Q Consensus 389 Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~ 468 (561)
+++..+... ++.....++.....+.
T Consensus 85 ~rk~~~~~~-------------------------------------------------------~~~~~~~~~~~~~~~~ 109 (187)
T TIGR02948 85 LRKRKPDFY-------------------------------------------------------LDDEVQGTDGLTMESQ 109 (187)
T ss_pred HHhhccccc-------------------------------------------------------ccccccCccccccccc
Confidence 876431100 0000000000011111
Q ss_pred cccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008556 469 TADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 548 (561)
Q Consensus 469 l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 548 (561)
..+. .+.|++.+...+....+..+|..||+++|.||.++|. +++|++|||+.||+|.++|++.+.||+++||..+
T Consensus 110 ~~~~-~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l 184 (187)
T TIGR02948 110 LAAD-EAPPEDQVISLELRDTIQQEIQALPPKYRMVIVLKYM----EDLSLKEISEILDLPVGTVKTRIHRGREALRKQL 184 (187)
T ss_pred cccC-cCCHHHHHHHHHHHHHHHHHHHhCCHHHhHHhhhHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 1111 1256666666677778999999999999999999998 8999999999999999999999999999999987
Q ss_pred h
Q 008556 549 G 549 (561)
Q Consensus 549 ~ 549 (561)
.
T Consensus 185 ~ 185 (187)
T TIGR02948 185 R 185 (187)
T ss_pred h
Confidence 5
No 44
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=99.88 E-value=2.9e-21 Score=185.68 Aligned_cols=171 Identities=23% Similarity=0.325 Sum_probs=137.4
Q ss_pred HHHHHHhhc-HHHHHHHHHHHHHHHHHHHHhhhCC----CCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHH
Q 008556 310 DLKSELHSG-NSSREKLINANLRLVVHVAKQYQGR----GISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 384 (561)
Q Consensus 310 eL~~~l~~G-~~Are~LI~~nlrLV~sIArrY~~~----g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqa 384 (561)
.|+..+..| ..|+++|+..|.+.|+.+|.++.++ +.+++|++||+++++|+++.+|++. +..|.+|++..+++.
T Consensus 13 ~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~~~~wl~~i~~n~ 91 (189)
T PRK09648 13 ALVAEAVAGDRRALREVLEIIRPLVVRYCRARLGGVERPGLSADDVAQEVCLAVITALPRYRDQ-GRPFLAFVYGIAAHK 91 (189)
T ss_pred HHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhcccccCCCCHHHHHHHHHHHHHHHHHHHhcc-CCcHHHHHHHHHHHH
Confidence 355555545 5999999999999999999998765 3689999999999999999999864 457999999999999
Q ss_pred HHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCch
Q 008556 385 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT 464 (561)
Q Consensus 385 I~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~ 464 (561)
+.++++++.+....+ .+.
T Consensus 92 ~~d~~r~~~r~~~~~-----------------------------------------------------~~~--------- 109 (189)
T PRK09648 92 VADAHRAAGRDKAVP-----------------------------------------------------TEE--------- 109 (189)
T ss_pred HHHHHHHhCCCcccc-----------------------------------------------------ccc---------
Confidence 999988765311000 000
Q ss_pred hhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008556 465 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 544 (561)
Q Consensus 465 l~d~l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKL 544 (561)
..+... ...+|++.+...+..+.|..+|..||+++|+||.++|+ +++|++|||+.||||..+|++.++||+++|
T Consensus 110 ~~~~~~--~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Ra~~~L 183 (189)
T PRK09648 110 VPERPS--DDAGPEERALRSESSNRMRELLDTLPEKQREILILRVV----VGLSAEETAEAVGSTPGAVRVAQHRALARL 183 (189)
T ss_pred cccccc--cCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 000000 11256666666777788999999999999999999998 899999999999999999999999999999
Q ss_pred HHHhh
Q 008556 545 KQSLG 549 (561)
Q Consensus 545 R~~l~ 549 (561)
|+.+.
T Consensus 184 r~~l~ 188 (189)
T PRK09648 184 RAEIE 188 (189)
T ss_pred HHHhc
Confidence 99764
No 45
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and 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.
Probab=99.87 E-value=7.2e-21 Score=178.68 Aligned_cols=164 Identities=20% Similarity=0.343 Sum_probs=134.8
Q ss_pred hhcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccc
Q 008556 316 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT 395 (561)
Q Consensus 316 ~~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~ 395 (561)
.++..|++.|+..|.+.+++++.++.++..+++|++||+++++|+++++|+...+ .|.+|++.++++.+.++++++.+.
T Consensus 7 ~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~-~~~~wl~~i~~n~~~d~~R~~~~~ 85 (170)
T TIGR02952 7 DREEDAFARIYETYSDRVYRYIYYRVGCKYTAEDLTSEVFERVLRKIDSFKEQKN-SFEAWLFTIARNVVNDYFRGSKRH 85 (170)
T ss_pred ccCHHHHHHHHHHHHHHHHHHHHHHHCChhhHHHHHHHHHHHHHHhHHhcccccc-cHHHHHHHHHHHHHHHHHHhcCCC
Confidence 3456999999999999999999999998899999999999999999999997555 799999999999999999876521
Q ss_pred cccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCC
Q 008556 396 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVE 475 (561)
Q Consensus 396 IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~ 475 (561)
... +.+. ..+... ...
T Consensus 86 ~~~-----------------------------------------------------~~~~---------~~~~~~--~~~ 101 (170)
T TIGR02952 86 PLF-----------------------------------------------------SLDV---------FKELLS--NEP 101 (170)
T ss_pred CCC-----------------------------------------------------cHHH---------HhhcCC--CCC
Confidence 100 0000 000000 112
Q ss_pred ChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008556 476 IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 548 (561)
Q Consensus 476 ~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 548 (561)
.|++.+...+..+.+..+|..|||++|+||.++|. +|+|++|||+.||||..+|++.+.||+++||+.+
T Consensus 102 ~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~g~s~~eIA~~l~is~~tv~~~l~ra~~~Lr~~l 170 (170)
T TIGR02952 102 NPEEAILKEEANEKLLKALKILTPKQQHVIALRFG----QNLPIAEVARILGKTEGAVKILQFRAIKKLARQM 170 (170)
T ss_pred CHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhC
Confidence 45666666667788999999999999999999998 8999999999999999999999999999999864
No 46
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=99.87 E-value=7.5e-21 Score=179.47 Aligned_cols=172 Identities=19% Similarity=0.236 Sum_probs=136.9
Q ss_pred hhcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccc
Q 008556 316 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT 395 (561)
Q Consensus 316 ~~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~ 395 (561)
.++..|+++|+..|.++|+.++++|.+++.+.+|++||++++||+++++|+ .+.+|.+|++.++++.+.+++++..+.
T Consensus 6 ~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~r~~~~~ 83 (182)
T PRK09652 6 RGDRAAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFR--GGAAFYTWLYRIARNTAINYLRKQGRR 83 (182)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHhcC--CCcchHHHHHHHHHHHHHHHHHcccCC
Confidence 455699999999999999999999999999999999999999999999999 445899999999999999998775421
Q ss_pred cccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCC
Q 008556 396 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVE 475 (561)
Q Consensus 396 IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~ 475 (561)
...+ +++ ..+.++....+...+ ..
T Consensus 84 ~~~~----------------------------------------------------~~~--~~~~~~~~~~~~~~~--~~ 107 (182)
T PRK09652 84 PPAS----------------------------------------------------DVD--AEEAEDFDLADALRD--IS 107 (182)
T ss_pred CCcc----------------------------------------------------ccc--ccccccccccccccc--cc
Confidence 1000 000 000000011111111 12
Q ss_pred ChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008556 476 IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 549 (561)
Q Consensus 476 ~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 549 (561)
+|+..+...+....+..+|..||+++|+||.++|. .++|++|||+.||+|..+|++.+.||+++||+.+.
T Consensus 108 ~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 177 (182)
T PRK09652 108 TPENELLSAELEQRVRAAIESLPEELRTAITLREI----EGLSYEEIAEIMGCPIGTVRSRIFRAREALRAKLQ 177 (182)
T ss_pred ChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 46666666677788999999999999999999998 89999999999999999999999999999999875
No 47
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=99.87 E-value=7.1e-21 Score=182.15 Aligned_cols=176 Identities=19% Similarity=0.286 Sum_probs=135.1
Q ss_pred CHHHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHH
Q 008556 307 SCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI 385 (561)
Q Consensus 307 ~~~eL~~~l~~G-~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI 385 (561)
++..+...+..| ..|++.|+..|.+.|+.++++|.+++.+++|++||+++++|+++++|++..+ .|.+|++..+++.+
T Consensus 9 ~~~~l~~~~~~~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~~i~l~~~~~~~~~~~~-~~~~wl~~ia~n~~ 87 (186)
T PRK13919 9 SDEALLALVARGEEEALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKKAKEFDPRRG-SARAWLLALAHHAA 87 (186)
T ss_pred CHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhhhccCcccc-chHHHHHHHHHHHH
Confidence 456666666544 5999999999999999999999999899999999999999999999997643 69999999999999
Q ss_pred HHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchh
Q 008556 386 RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF 465 (561)
Q Consensus 386 ~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l 465 (561)
.+++++..+..+ ....+ ......
T Consensus 88 ~d~~rk~~~~~~----------------------------------------------------~~~~~-----~~~~~~ 110 (186)
T PRK13919 88 VDHVRRRAARPQ----------------------------------------------------PLEPD-----EREPEA 110 (186)
T ss_pred HHHHHhhhcccc----------------------------------------------------ccccc-----cccccc
Confidence 999976542100 00000 000000
Q ss_pred hhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556 466 QEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 545 (561)
Q Consensus 466 ~d~l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 545 (561)
.+ .. .+..........+.|..+|..||+++|+||.++|. +++|++|||+.||||..+|+..++||+++||
T Consensus 111 ~~-~~-----~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~~~s~~eIA~~lgis~~~V~~~l~ra~~~Lr 180 (186)
T PRK13919 111 FD-LP-----GPGLDEEGHLDRTRLGRALKALSPEERRVIEVLYY----QGYTHREAAQLLGLPLGTLKTRARRALSRLK 180 (186)
T ss_pred cc-CC-----CccccHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 00 00 11111122233456899999999999999999998 8999999999999999999999999999999
Q ss_pred HHhhc
Q 008556 546 QSLGG 550 (561)
Q Consensus 546 ~~l~~ 550 (561)
..+..
T Consensus 181 ~~l~~ 185 (186)
T PRK13919 181 EVLRE 185 (186)
T ss_pred HHhcC
Confidence 98753
No 48
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=99.87 E-value=7.2e-21 Score=183.49 Aligned_cols=175 Identities=22% Similarity=0.276 Sum_probs=137.6
Q ss_pred CHHHHHHHHhh-cHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHH
Q 008556 307 SCRDLKSELHS-GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI 385 (561)
Q Consensus 307 ~~~eL~~~l~~-G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI 385 (561)
++.+|...+.. +..+++.|+..|.+.|+.+++++.++..+.+|++||+++++|+. ..|++..+ .|.||++.++++.+
T Consensus 15 ~~~~l~~~~~~gd~~a~~~L~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~l~~~-~~~~~~~~-~f~~wl~~iarn~~ 92 (194)
T PRK12519 15 SDAELFSALKAGQSAALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRK-SSYDPKRG-SLSSYLLTLTRSRA 92 (194)
T ss_pred cHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHh-cCCCcccc-cHHHHHHHHHHHHH
Confidence 34556665554 45999999999999999999999999899999999999999976 67887655 79999999999999
Q ss_pred HHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchh
Q 008556 386 RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF 465 (561)
Q Consensus 386 ~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l 465 (561)
.++++++.+..+.. .+. + .
T Consensus 93 ~d~~Rk~~~~~~~~---------------------------~~~------------------------~--------~-- 111 (194)
T PRK12519 93 IDRLRSRRSRQRLL---------------------------ERW------------------------Q--------Q-- 111 (194)
T ss_pred HHHHHhcccccchh---------------------------hhh------------------------h--------h--
Confidence 99998764210000 000 0 0
Q ss_pred hhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556 466 QEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 545 (561)
Q Consensus 466 ~d~l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 545 (561)
+...+.....+++.+...+....|..+|..||+++++||.++|. +++|++|||+.||+|..+|++++.||+++||
T Consensus 112 -~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~~~v~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr 186 (194)
T PRK12519 112 -ELLGEASEDTPLEQASLAERSQRVQTALAQLPESQRQVLELAYY----EGLSQSEIAKRLGIPLGTVKARARQGLLKLR 186 (194)
T ss_pred -hhcccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhhhhh----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 00000011245555555666677999999999999999999998 8999999999999999999999999999999
Q ss_pred HHhh
Q 008556 546 QSLG 549 (561)
Q Consensus 546 ~~l~ 549 (561)
+.+.
T Consensus 187 ~~l~ 190 (194)
T PRK12519 187 ELLQ 190 (194)
T ss_pred HHHH
Confidence 9874
No 49
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=99.87 E-value=9.8e-21 Score=180.28 Aligned_cols=173 Identities=14% Similarity=0.146 Sum_probs=137.6
Q ss_pred CHHHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHH
Q 008556 307 SCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI 385 (561)
Q Consensus 307 ~~~eL~~~l~~G-~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI 385 (561)
+...|+..+..| ..++..|+..|.+.|+.+|.+|.++..+.+|++||+++++|+++++|++..+ .|.||++..++|.+
T Consensus 5 ~~~~li~~~~~g~~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~fl~~~~~~~~~~~~~~-~~~~wl~~ia~n~~ 83 (179)
T PRK12514 5 DIEKLIVRVSLGDRDAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAVSGL-SPMTWLITIARNHA 83 (179)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHHHhHHhcCcccc-cHHHHHHHHHHHHH
Confidence 344555555444 5899999999999999999999999999999999999999999999997544 69999999999999
Q ss_pred HHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchh
Q 008556 386 RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF 465 (561)
Q Consensus 386 ~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l 465 (561)
.++++++.+.. .+ ++ . .
T Consensus 84 ~d~~R~~~~~~-~~-----------------------------------------------------~~------~---~ 100 (179)
T PRK12514 84 IDRLRARKAVA-VD-----------------------------------------------------ID------E---A 100 (179)
T ss_pred HHHHHhcCCcc-cc-----------------------------------------------------cc------c---c
Confidence 99998654210 00 00 0 0
Q ss_pred hhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556 466 QEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 545 (561)
Q Consensus 466 ~d~l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 545 (561)
.+ ..+. ...|++.+...+....|..+|..||+++|+||.++|. +|+|++|||+.||||..+|++.+.||+++||
T Consensus 101 ~~-~~~~-~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr 174 (179)
T PRK12514 101 HD-LADP-SPGPEAEVIAGDEGQRIDACLEELEKDRAAAVRRAYL----EGLSYKELAERHDVPLNTMRTWLRRSLLKLR 174 (179)
T ss_pred hh-cccc-CCCHHHHHHhHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCChHHHHHHHHHHHHHHH
Confidence 00 0011 1245555554555567899999999999999999998 8999999999999999999999999999999
Q ss_pred HHhh
Q 008556 546 QSLG 549 (561)
Q Consensus 546 ~~l~ 549 (561)
+++.
T Consensus 175 ~~l~ 178 (179)
T PRK12514 175 ECLS 178 (179)
T ss_pred HHhc
Confidence 9874
No 50
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=99.87 E-value=1.2e-20 Score=181.84 Aligned_cols=174 Identities=14% Similarity=0.192 Sum_probs=141.1
Q ss_pred CCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHhhhCCC---CCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHH
Q 008556 306 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRG---ISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWV 381 (561)
Q Consensus 306 ~~~~eL~~~l~~G~-~Are~LI~~nlrLV~sIArrY~~~g---~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wI 381 (561)
++++.|+..+..|+ .|++.|+..|.+.|+.++.++.+++ .+++|++||+++++|+++++|++..+ .|.||++..+
T Consensus 3 ~~~~~li~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~~~daeDi~Qe~~i~l~~~~~~~~~~~~-~~~~wl~~ia 81 (189)
T PRK06811 3 INEDNFIKELKKKNEKALEFIVDTYGNLVKKIVHKVLGTVNYSQLIEECVNDIFLSIWNNIDKFDEEKG-SFKKWIAAIS 81 (189)
T ss_pred CcHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHHcccCchhHHHHHHHHHHHHHHHhHHHhccccc-cHHHHHHHHH
Confidence 56677777777665 8999999999999999999998863 46899999999999999999997655 7999999999
Q ss_pred HHHHHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCC
Q 008556 382 RQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQ 461 (561)
Q Consensus 382 RqaI~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~ 461 (561)
++.+.++++++.+.... .+.+.
T Consensus 82 rn~~~d~~rk~~~~~~~----------------------------------------------------~~~~~------ 103 (189)
T PRK06811 82 KYKAIDYKRKLTKNNEI----------------------------------------------------DSIDE------ 103 (189)
T ss_pred HHHHHHHHHHhcccccc----------------------------------------------------ccchh------
Confidence 99999999876521100 00000
Q ss_pred CchhhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 008556 462 DTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL 541 (561)
Q Consensus 462 ~~~l~d~l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RAL 541 (561)
... ....++++.+...+....|..+|..||+++|.||.++|. +++|++|||+.||+|..+|++.+.||+
T Consensus 104 ------~~~-~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIAe~lgis~~~V~~~l~Ra~ 172 (189)
T PRK06811 104 ------FIL-ISEESIENEIILKENKEEILKLINDLEKLDREIFIRRYL----LGEKIEEIAKKLGLTRSAIDNRLSRGR 172 (189)
T ss_pred ------hhh-cccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----ccCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 000 011245566666677778999999999999999999998 899999999999999999999999999
Q ss_pred HHHHHHhh
Q 008556 542 YRLKQSLG 549 (561)
Q Consensus 542 kKLR~~l~ 549 (561)
++||...-
T Consensus 173 ~~Lr~~~~ 180 (189)
T PRK06811 173 KKLQKNKL 180 (189)
T ss_pred HHHHHccc
Confidence 99998643
No 51
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.
Probab=99.87 E-value=1.5e-20 Score=179.84 Aligned_cols=181 Identities=16% Similarity=0.210 Sum_probs=140.9
Q ss_pred CHHHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHH
Q 008556 307 SCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI 385 (561)
Q Consensus 307 ~~~eL~~~l~~G-~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI 385 (561)
++..|+..+..| ..+++.|+..|.+.|+.+|+++.++..+++|++||+++++|+++.+|++. ..|.+|++...++.+
T Consensus 6 ~d~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~--~~~~~wl~~iarn~~ 83 (190)
T TIGR02939 6 LDLELVERVQRGEKQAFDLLVRKYQHKVVALVGRYVRDSSEVEDVAQEAFVKAYRALSSFRGD--SAFYTWLYRIAVNTA 83 (190)
T ss_pred cHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCC--CccHhHHHHHHHHHH
Confidence 455666666655 48999999999999999999999999999999999999999999999975 369999999999999
Q ss_pred HHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchh
Q 008556 386 RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF 465 (561)
Q Consensus 386 ~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l 465 (561)
.++++++.+..... ..+.+. ....
T Consensus 84 ~~~~r~~~r~~~~~--------------------------------------------------~~~~~~------~~~~ 107 (190)
T TIGR02939 84 KNHLVAQGRRPPTS--------------------------------------------------DVEIED------AEHF 107 (190)
T ss_pred HHHHHHhccCCCcc--------------------------------------------------cccccc------hhhh
Confidence 99887554211000 000000 0000
Q ss_pred hhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556 466 QEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 545 (561)
Q Consensus 466 ~d~l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 545 (561)
.+........+|++.+...+....|..+|..||+++|+||.++|. ++++++|||+.||+|..+|++.++||+++||
T Consensus 108 ~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~~~s~~EIA~~lgis~~tv~~~l~rar~~Lr 183 (190)
T TIGR02939 108 EGADRLREIDTPERLLLSRELEQTVMRAVEALPEDLRTAITLREL----EGLSYEDIARIMDCPVGTVRSRIFRAREAIA 183 (190)
T ss_pred cccccccccCChHHHHHHHHHHHHHHHHHHcCCHHHhhhhhhhhh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 000000011246666666777788999999999999999999998 8999999999999999999999999999999
Q ss_pred HHhh
Q 008556 546 QSLG 549 (561)
Q Consensus 546 ~~l~ 549 (561)
+++.
T Consensus 184 ~~l~ 187 (190)
T TIGR02939 184 IRLR 187 (190)
T ss_pred HHhh
Confidence 9885
No 52
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=99.86 E-value=6.8e-21 Score=176.52 Aligned_cols=151 Identities=21% Similarity=0.253 Sum_probs=123.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhccccccc
Q 008556 319 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL 398 (561)
Q Consensus 319 ~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRl 398 (561)
..|++.|+..|.++|+.+++++ +...+++|++|||++++|+++++|++..| .|.+|++..+++.+.++++++.+..
T Consensus 3 ~~af~~l~~~y~~~l~~~~~~~-~~~~~aeDi~Qe~~l~l~~~~~~~~~~~~-~f~~wl~~i~~n~~ld~~rk~~~~~-- 78 (154)
T PRK06759 3 PATFTEAVVLYEGLIVNQIKKL-GIYQDYEEYYQCGLIGLWHAYERYDEKKG-SFPAYAVVTVRGYILERLKKEFAVQ-- 78 (154)
T ss_pred cccHHHHHHHHHHHHHHHHHHh-CCcccHHHHHHHHHHHHHHHHHHhCccCC-chHHHHHHHHHHHHHHHHHHHHhhc--
Confidence 4689999999999999999886 56678999999999999999999998776 6999999999999999998753100
Q ss_pred chhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChh
Q 008556 399 PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPD 478 (561)
Q Consensus 399 P~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pe 478 (561)
. ... .+ +.|+
T Consensus 79 ----------------------~---------------------------------~~~-~~--------------~~~~ 88 (154)
T PRK06759 79 ----------------------E---------------------------------KCV-CV--------------GEYE 88 (154)
T ss_pred ----------------------c---------------------------------ccc-cc--------------CCCc
Confidence 0 000 00 0111
Q ss_pred HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008556 479 ISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 547 (561)
Q Consensus 479 e~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 547 (561)
+.+...+....|..+|..||+++|+||.++|+ +++|.+|||+.||+|..+|++++.||+++||+.
T Consensus 89 ~~~~~~~~~~~l~~~l~~L~~~~r~ii~l~~~----~~~s~~EIA~~l~is~~tV~~~~~ra~~~Lr~~ 153 (154)
T PRK06759 89 DHFHFEDVEMKVKDFMSVLDEKEKYIIFERFF----VGKTMGEIALETEMTYYQVRWIYRQALEKMRNS 153 (154)
T ss_pred ccccHHHHHHHHHHHHHhCCHHHHHHHHHHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHhhc
Confidence 12223334567999999999999999999998 899999999999999999999999999999974
No 53
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=99.86 E-value=1.3e-20 Score=187.71 Aligned_cols=173 Identities=19% Similarity=0.245 Sum_probs=137.9
Q ss_pred hcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhccccc
Q 008556 317 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI 396 (561)
Q Consensus 317 ~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~I 396 (561)
++..|++.|+..|.+.|+++|+++.+++.+++|++||+++++|+++++|++. ..|.+|++..+++.+.+++++..+..
T Consensus 27 gd~~a~~~l~~~y~~~l~~~a~~~~~~~~~AEDlvQE~fi~l~~~~~~~~~~--~~~~~wL~~iarn~~~d~~Rk~~r~~ 104 (231)
T PRK11922 27 GDEAAFEALMRRHNRRLYRTARAILRNDAEAEDVVQEAYLRAFRALGTFRGD--ASLSTWLSRIVLNEALGRLRRRRRLV 104 (231)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHhcCCC--chhHHHHHHHHHHHHHHHHHhhcccc
Confidence 4568999999999999999999999999999999999999999999999986 36999999999999999988765321
Q ss_pred ccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCC
Q 008556 397 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEI 476 (561)
Q Consensus 397 RlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~ 476 (561)
.++. . ..+. ... ++ ...... ....+
T Consensus 105 ~~~~----------------------------~----------------------~~~~-~~~-~~--~~~~~~-~~~~~ 129 (231)
T PRK11922 105 NLAE----------------------------M----------------------VMAS-TIA-GG--ERTPLA-DPAED 129 (231)
T ss_pred cchh----------------------------c----------------------cccc-ccc-cc--cccccC-cccCC
Confidence 1100 0 0000 000 00 000001 11235
Q ss_pred hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008556 477 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 550 (561)
Q Consensus 477 pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 550 (561)
|++.+...+..+.|..+|..||+++|+||.++|. +++|++|||+.||+|.++|++++.||+++||+.+..
T Consensus 130 ~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l~~ 199 (231)
T PRK11922 130 PERAAARREIRALLERAIDALPDAFRAVFVLRVV----EELSVEETAQALGLPEETVKTRLHRARRLLRESLAR 199 (231)
T ss_pred hHHHHHHHHHHHHHHHHHHhCCHHHhhhheeehh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 6677777778888999999999999999999987 899999999999999999999999999999998864
No 54
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=99.86 E-value=1.7e-20 Score=181.90 Aligned_cols=177 Identities=19% Similarity=0.206 Sum_probs=142.8
Q ss_pred CCHHHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHH
Q 008556 306 LSCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 384 (561)
Q Consensus 306 ~~~~eL~~~l~~G-~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqa 384 (561)
+++..|+..+..| ..|++.|+..|.+.|+.+|.++.++..+++|++||+++++|+.+.+|++.. ..|.+|++..+++.
T Consensus 11 ~~~~~li~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~~-~~~~~wl~~ia~n~ 89 (196)
T PRK12524 11 VSDEALLVLYANGDPAAARALTLRLAPRALAVATRVLGDRAEAEDVTQEAMLRLWRIAPDWRQGE-ARVSTWLYRVVCNL 89 (196)
T ss_pred cCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhcccccc-chHHHHHHHHHHHH
Confidence 4566777776665 499999999999999999999999999999999999999999999998533 46999999999999
Q ss_pred HHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCch
Q 008556 385 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT 464 (561)
Q Consensus 385 I~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~ 464 (561)
+.++++++.+.. ..++. . .
T Consensus 90 ~~d~~Rk~~~~~------------------------------------------------------~~~~~-~-~----- 108 (196)
T PRK12524 90 CTDRLRRRRRAS------------------------------------------------------VDLDD-A-P----- 108 (196)
T ss_pred HHHHHHhhcCCC------------------------------------------------------CCccc-c-c-----
Confidence 999987653100 00000 0 0
Q ss_pred hhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008556 465 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 544 (561)
Q Consensus 465 l~d~l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKL 544 (561)
+. .+. ...+++.+...+....|..+|..||+++|+||.|+|. ++++++|||+.||||..+|+++++||+++|
T Consensus 109 --~~-~~~-~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~L~~~----~g~s~~eIA~~lgis~~tV~~~l~Ra~~~L 180 (196)
T PRK12524 109 --EP-ADA-APGAEEALIEGDRMRALDAALAALPERQRQAVVLRHI----EGLSNPEIAEVMEIGVEAVESLTARGKRAL 180 (196)
T ss_pred --cc-ccc-CCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 00 011 1235555666677778999999999999999999998 899999999999999999999999999999
Q ss_pred HHHhhcCc
Q 008556 545 KQSLGGKA 552 (561)
Q Consensus 545 R~~l~~~~ 552 (561)
|.++...+
T Consensus 181 r~~l~~~~ 188 (196)
T PRK12524 181 AALLAGQR 188 (196)
T ss_pred HHHHHhcc
Confidence 99987543
No 55
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=99.86 E-value=1.7e-20 Score=179.58 Aligned_cols=172 Identities=14% Similarity=0.177 Sum_probs=137.0
Q ss_pred CHHHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHH
Q 008556 307 SCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI 385 (561)
Q Consensus 307 ~~~eL~~~l~~G-~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI 385 (561)
+...|+..+.+| ..|++.|+..|.+.++.++.++.++..+.+|++||+++.+|+.+++|++..+ .|.+|++..+++.+
T Consensus 9 ~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~~-~~~~wL~~iarn~~ 87 (182)
T PRK12537 9 DYEACLLACARGDRRALQALYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTGAASFDPARG-SARGWIYSVTRHLA 87 (182)
T ss_pred hHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhccccCCcccc-cHHHHHHHHHHHHH
Confidence 445566666555 4999999999999999999999999999999999999999999999986443 69999999999999
Q ss_pred HHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchh
Q 008556 386 RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF 465 (561)
Q Consensus 386 ~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l 465 (561)
.+++++..+...+ +. ..
T Consensus 88 ~d~~r~~~~~~~~-------------------------------------------------------~~-----~~--- 104 (182)
T PRK12537 88 LNVLRDTRREVVL-------------------------------------------------------DD-----DA--- 104 (182)
T ss_pred HHHHHhccccCcc-------------------------------------------------------cc-----ch---
Confidence 9999876421100 00 00
Q ss_pred hhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556 466 QEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 545 (561)
Q Consensus 466 ~d~l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 545 (561)
.+...+ ...+++..+..+....|..+|+.||+++|+||.++|. +++|++|||+.||||.++|+..+.||+++||
T Consensus 105 ~~~~~~--~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr 178 (182)
T PRK12537 105 EETAQT--LHEIIDDFDLWANSGKIHRCLEQLEPARRNCILHAYV----DGCSHAEIAQRLGAPLGTVKAWIKRSLKALR 178 (182)
T ss_pred hhhccc--ccchHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCChhhHHHHHHHHHHHHH
Confidence 000000 1123333444455667899999999999999999998 8999999999999999999999999999999
Q ss_pred HHh
Q 008556 546 QSL 548 (561)
Q Consensus 546 ~~l 548 (561)
.++
T Consensus 179 ~~l 181 (182)
T PRK12537 179 ECM 181 (182)
T ss_pred HHh
Confidence 876
No 56
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=99.86 E-value=2.9e-20 Score=179.09 Aligned_cols=180 Identities=15% Similarity=0.203 Sum_probs=140.2
Q ss_pred HHHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHH
Q 008556 308 CRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIR 386 (561)
Q Consensus 308 ~~eL~~~l~~G-~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~ 386 (561)
++.|+..++.| ..+++.|+..|.+.|+.+++++.++..+.+|++||+++++|+++.+|++.. .|.+|++..+++.+.
T Consensus 7 ~~~ll~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~~i~l~~~~~~~~~~~--~~~~wl~~ia~n~~~ 84 (193)
T PRK11923 7 DQQLVERVQRGDKRAFDLLVLKYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYRALGNFRGDS--AFYTWLYRIAINTAK 84 (193)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHhCcCCCC--ccHhHHHHHHHHHHH
Confidence 44555555554 599999999999999999999999989999999999999999999999874 499999999999999
Q ss_pred HHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhh
Q 008556 387 KAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQ 466 (561)
Q Consensus 387 ~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~ 466 (561)
++++++.+.... ....++.....++.
T Consensus 85 d~~rk~~~~~~~--------------------------------------------------~~~~~~~~~~~~~~---- 110 (193)
T PRK11923 85 NHLVSRGRRPPD--------------------------------------------------SDVSSEDAEFYDGD---- 110 (193)
T ss_pred HHHHHhcCCCcc--------------------------------------------------ccccccchhhhccc----
Confidence 998765421100 00000000000000
Q ss_pred hhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556 467 EITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 546 (561)
Q Consensus 467 d~l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 546 (561)
..+. ....|+..+...+..+.+..+|..||+++|+||.++|. +|+|++|||+.||+|..+|++.+.||+++||.
T Consensus 111 ~~~~--~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~ 184 (193)
T PRK11923 111 HALK--DIESPERALLRDEIEGTVHRTIQQLPEDLRTALTLREF----DGLSYEDIASVMQCPVGTVRSRIFRAREAIDK 184 (193)
T ss_pred cccc--CcCCHHHHHHHHHHHHHHHHHHHhCCHHHhHHHhhHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 0011 12356666666777788999999999999999999998 89999999999999999999999999999999
Q ss_pred Hhh
Q 008556 547 SLG 549 (561)
Q Consensus 547 ~l~ 549 (561)
++.
T Consensus 185 ~l~ 187 (193)
T PRK11923 185 ALQ 187 (193)
T ss_pred HHH
Confidence 885
No 57
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=99.86 E-value=1.7e-20 Score=187.70 Aligned_cols=174 Identities=15% Similarity=0.223 Sum_probs=139.9
Q ss_pred CHHHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHH
Q 008556 307 SCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI 385 (561)
Q Consensus 307 ~~~eL~~~l~~G-~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI 385 (561)
++..|+..+..| ..+++.|+..|.+.|+.+++++.++..+.+|++||+|+++|+++++|++..+ .|.+|++..+++.+
T Consensus 49 ~d~~Li~~~~~gd~~af~~L~~~y~~~l~~~~~~~~~d~~dAEDivQEvfl~l~~~~~~~~~~~~-~f~~WL~~IarN~~ 127 (233)
T PRK12538 49 EDEELLDRLATDDEAAFRLLVERHIDRAYAIALRIVGNRADAEDVVQDTMLKVWTHRGRWQHGRA-KFSTWLYRVVSNRC 127 (233)
T ss_pred cHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHcccccc-cHHHHHHHHHHHHH
Confidence 455666666555 5899999999999999999999999999999999999999999999987554 79999999999999
Q ss_pred HHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchh
Q 008556 386 RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF 465 (561)
Q Consensus 386 ~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l 465 (561)
.++++++.+. . ++. . .
T Consensus 128 id~~Rk~~~~-~-------------------------------------------------------~~~-~-~------ 143 (233)
T PRK12538 128 IDLRRKPRTE-N-------------------------------------------------------VDA-V-P------ 143 (233)
T ss_pred HHHHHhhccc-c-------------------------------------------------------ccc-c-c------
Confidence 9988753210 0 000 0 0
Q ss_pred hhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556 466 QEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 545 (561)
Q Consensus 466 ~d~l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 545 (561)
+. .+ ....+++.+...+....|..+|..||+++|+||.|+|. +++|++|||+.||+|.++|+++++||+++||
T Consensus 144 -~~-~~-~~~~~~~~~~~~e~~~~l~~~L~~Lp~~~R~v~~L~~~----eg~s~~EIA~~Lgis~~tVk~~l~RAr~kLr 216 (233)
T PRK12538 144 -EV-AD-GKPDAVSVIERNELSDLLEAAMQRLPEQQRIAVILSYH----ENMSNGEIAEVMDTTVAAVESLLKRGRQQLR 216 (233)
T ss_pred -cc-cc-CCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 00 00 01133444555666678999999999999999999998 9999999999999999999999999999999
Q ss_pred HHhhcCc
Q 008556 546 QSLGGKA 552 (561)
Q Consensus 546 ~~l~~~~ 552 (561)
+.+...+
T Consensus 217 ~~l~~~~ 223 (233)
T PRK12538 217 DLLRRHE 223 (233)
T ss_pred HHHHHhh
Confidence 9987544
No 58
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=99.86 E-value=1.1e-20 Score=181.84 Aligned_cols=173 Identities=20% Similarity=0.286 Sum_probs=136.5
Q ss_pred cCCHHHHHHHHhh----cHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHH
Q 008556 305 GLSCRDLKSELHS----GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWW 380 (561)
Q Consensus 305 g~~~~eL~~~l~~----G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~w 380 (561)
.++++.|+..++. +..|++.|+..|.+.|+++|.+|.++..+.+|++||+++.+|+++++|++. ..|.+|++.+
T Consensus 7 ~~~~~~li~~~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~f~~l~~~~~~~~~~--~~~~~wl~~i 84 (188)
T PRK09640 7 ELNDEELVARVHVELFHVTRAYEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGK--SKFKTWLYSI 84 (188)
T ss_pred CCCHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHHHhcCC--CcchHHHHHH
Confidence 4667778777763 569999999999999999999999999999999999999999999999963 4699999999
Q ss_pred HHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCC
Q 008556 381 VRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWAD 460 (561)
Q Consensus 381 IRqaI~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d 460 (561)
+++.+.+++++..+.... ..+..
T Consensus 85 a~n~~~d~~R~~~~~~~~-----------------------------------------------------~~~~~---- 107 (188)
T PRK09640 85 TYNECITQYRKERRKRRL-----------------------------------------------------MDALS---- 107 (188)
T ss_pred HHHHHHHHHHHhcccccC-----------------------------------------------------cchhh----
Confidence 999999999864321000 00000
Q ss_pred CCchhhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008556 461 QDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA 540 (561)
Q Consensus 461 ~~~~l~d~l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RA 540 (561)
.+...++. +......+....|..+|..||+++|+||.++|. +++|++|||+.||||..+|+..+.||
T Consensus 108 -----~~~~~~~~----~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Ra 174 (188)
T PRK09640 108 -----LDPLEEAS----EEKAPKPEERGGLDRWLVHVNPIDREILVLRFV----AELEFQEIADIMHMGLSATKMRYKRA 174 (188)
T ss_pred -----hccccccc----ccccccHHHHHHHHHHHHhcChhheeeeeeHHh----cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 00000000 001112234456899999999999999999998 89999999999999999999999999
Q ss_pred HHHHHHHhh
Q 008556 541 LYRLKQSLG 549 (561)
Q Consensus 541 LkKLR~~l~ 549 (561)
+++||+.+.
T Consensus 175 ~~~Lr~~l~ 183 (188)
T PRK09640 175 LDKLREKFA 183 (188)
T ss_pred HHHHHHHHH
Confidence 999999874
No 59
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=99.85 E-value=3e-20 Score=178.20 Aligned_cols=172 Identities=15% Similarity=0.160 Sum_probs=136.2
Q ss_pred HHHHH-HhhcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHH
Q 008556 310 DLKSE-LHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKA 388 (561)
Q Consensus 310 eL~~~-l~~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~ 388 (561)
.+... ..++..+++.|+..|.++|+.+|+++.++..+.+|++||+++++|+++++|++.++ .|.+|++..+++.+.++
T Consensus 14 ~l~~~~~~~~~~~~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~~~~~~~~~~~~~~-~~~~wl~~I~~n~~~d~ 92 (187)
T PRK12534 14 RLLTATAGGDRHAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFDPSRA-RGLTWLAMIARNKAIDH 92 (187)
T ss_pred HHHHHHHcCCHHHHHHHHHHhhHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccCCcccc-cHHHHHHHHHHHHHHHH
Confidence 34444 34555999999999999999999999999999999999999999999999998655 58899999999999999
Q ss_pred HHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhh
Q 008556 389 IFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEI 468 (561)
Q Consensus 389 Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~ 468 (561)
++++.+... ..+.+. ..+.
T Consensus 93 ~R~~~~~~~----------------------------------------------------~~~~~~---------~~~~ 111 (187)
T PRK12534 93 LRANAPQRR----------------------------------------------------NVALDD---------AGEL 111 (187)
T ss_pred HHhcccccc----------------------------------------------------cccccc---------hhhh
Confidence 876542100 000000 0000
Q ss_pred cccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008556 469 TADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 548 (561)
Q Consensus 469 l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 548 (561)
. ++ ..++++.....+....|..+|..||+++++||.++|. +++|++|||+.||||..+|+++++||+++||..+
T Consensus 112 ~-~~-~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l 185 (187)
T PRK12534 112 R-AA-DASPLERTERASTRRRIDHCLAELEPPRSELIRTAFF----EGITYEELAARTDTPIGTVKSWIRRGLAKLKACL 185 (187)
T ss_pred c-cc-cCChhhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCCChhHHHHHHHHHHHHHHHHH
Confidence 0 00 1123344455566778999999999999999999998 8999999999999999999999999999999987
Q ss_pred h
Q 008556 549 G 549 (561)
Q Consensus 549 ~ 549 (561)
.
T Consensus 186 ~ 186 (187)
T PRK12534 186 E 186 (187)
T ss_pred c
Confidence 4
No 60
>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are apparently found only in the Planctomycetaceae family including the genuses Gemmata and Pirellula (in which seven sequences are found).
Probab=99.85 E-value=7.8e-20 Score=174.51 Aligned_cols=180 Identities=18% Similarity=0.203 Sum_probs=138.1
Q ss_pred hcHHHHHHHHHHHHHHHHHHHHhhhC----CCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhc
Q 008556 317 SGNSSREKLINANLRLVVHVAKQYQG----RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQH 392 (561)
Q Consensus 317 ~G~~Are~LI~~nlrLV~sIArrY~~----~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~ 392 (561)
++..|++.|+..|.+.|+.+|++|.+ +..+.+|++||+++.+|+++.+|++..+..|.+|++..+++.+.+++++.
T Consensus 4 ~~~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~~~~~~wl~~i~~n~~~d~~r~~ 83 (189)
T TIGR02984 4 GDQEALGELLDRYRNYLRLLARVQLDPRLRRRVDPSDLVQETLLEAHRRFDQFRGKTEGEFAGWLRGILSNVLADALRRH 83 (189)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHhhhhcCCccCHHHHHHHHHHHHHHHHHhccCcccchHHHHHHHHHHHHHHHHHHHH
Confidence 45699999999999999999999853 56789999999999999999999986666899999999999999998764
Q ss_pred ccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCC-CCCCchhhhhccc
Q 008556 393 SRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVW-ADQDTTFQEITAD 471 (561)
Q Consensus 393 sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~-~d~~~~l~d~l~d 471 (561)
.+. .+ +.+ ....+++.... .+....+.+.+.+
T Consensus 84 ~~~-----------------~~-------r~~-----------------------~~~~~~~~~~~~~~~~~~~~~~~~~ 116 (189)
T TIGR02984 84 LGA-----------------QK-------RDI-----------------------RREQSLDAGGRLDESSVRLAAQLAA 116 (189)
T ss_pred HHH-----------------Hh-------hhc-----------------------ccccCCCcccccCCcchhHHHHccC
Confidence 200 00 000 00112221111 1111123333333
Q ss_pred CCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008556 472 TGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 548 (561)
Q Consensus 472 ~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 548 (561)
. ..+|++.+...+....|..+|..||+++|+||.++|. +|++++|||+.||||.++|++.++||+++||+.+
T Consensus 117 ~-~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~vi~l~~~----~g~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~~l 188 (189)
T TIGR02984 117 D-GPSPSQVAARREAAVRLAQALAKLPEDYREVILLRHL----EGLSFAEVAERMDRSEGAVSMLWVRGLARLRQIL 188 (189)
T ss_pred C-CCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 2 2356777777777788999999999999999999998 8999999999999999999999999999999876
No 61
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=99.85 E-value=5.7e-20 Score=179.96 Aligned_cols=171 Identities=12% Similarity=0.165 Sum_probs=133.2
Q ss_pred hhcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccc
Q 008556 316 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT 395 (561)
Q Consensus 316 ~~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~ 395 (561)
.++..++++|+..|.+.|+.++.++.++..+++|++||+++.+|+++.+|++.++ .|.||++.++++.+.++++++.+.
T Consensus 34 ~~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~~-~~~~wl~~I~rn~~~d~~Rk~~~~ 112 (206)
T PRK12526 34 SRDKQAFTHLFQFFAPKIKRFGIKQLGNEAQANELVQETMSNVWRKAHLYNGDKG-AATTWVYTVMRNAAFDMLRKIKAK 112 (206)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCccc-chhHHHHHHHHHHHHHHHHHhccc
Confidence 3556999999999999999999999999889999999999999999999998765 599999999999999999876421
Q ss_pred cccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCC
Q 008556 396 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVE 475 (561)
Q Consensus 396 IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~ 475 (561)
.... .+ ++...+.+.+.+. ..
T Consensus 113 ~~~~-----------------------------------------------------~~-----~~~~~~~~~~~~~-~~ 133 (206)
T PRK12526 113 KEQN-----------------------------------------------------LG-----DDIWPIEQALAES-QS 133 (206)
T ss_pred cccc-----------------------------------------------------cc-----cccchhhhhcccc-cC
Confidence 1000 00 0000000111111 11
Q ss_pred ChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008556 476 IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 551 (561)
Q Consensus 476 ~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 551 (561)
.+. ..........|..+|..||+++|+||.++|+ +++|++|||+.||||..+|+..++||+++||+.+...
T Consensus 134 ~~~-~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~~~ 204 (206)
T PRK12526 134 ESE-EFSDHLMDKQILSYIEKLPEAQQTVVKGVYF----QELSQEQLAQQLNVPLGTVKSRLRLALAKLKVQMGEQ 204 (206)
T ss_pred chH-HHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhhc
Confidence 122 2223334457899999999999999999998 8999999999999999999999999999999998654
No 62
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=99.85 E-value=7.9e-20 Score=175.89 Aligned_cols=177 Identities=19% Similarity=0.266 Sum_probs=142.9
Q ss_pred CCHHHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHH
Q 008556 306 LSCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 384 (561)
Q Consensus 306 ~~~~eL~~~l~~G-~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqa 384 (561)
++++.|...+..| ..|++.|+..|.+.++.++.++.++..+.+|++||+++.+|+++++|++. ..|.+|++..+++.
T Consensus 7 ~~~~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~l~~~~~~~~~~--~~~~~wl~~i~~n~ 84 (189)
T PRK12515 7 TTDEMLLARIAQGDRTAMQTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEGR--SQVSTWLLSIARFK 84 (189)
T ss_pred cCHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCC--CChHHHHHHHHHHH
Confidence 4666777766655 58999999999999999999999999999999999999999999999964 36999999999999
Q ss_pred HHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCch
Q 008556 385 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT 464 (561)
Q Consensus 385 I~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~ 464 (561)
+.+++++..+.. +.. +.
T Consensus 85 ~~d~~r~~~~~~--------------------------------------------------------~~~----~~--- 101 (189)
T PRK12515 85 ALSALRRRKHEE--------------------------------------------------------IDD----EA--- 101 (189)
T ss_pred HHHHHHccCCCC--------------------------------------------------------Ccc----cc---
Confidence 999987643100 000 00
Q ss_pred hhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008556 465 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 544 (561)
Q Consensus 465 l~d~l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKL 544 (561)
.....+ ...+++......+....+..+|+.||+++|+||.++|. ++++++|||+.||||..+|++++.||+++|
T Consensus 102 -~~~~~~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~~~s~~eIA~~lgis~~tV~~~l~Rar~~L 175 (189)
T PRK12515 102 -AAAIED-GADTPEVALQKSDTSAALRACLAKLSPAHREIIDLVYY----HEKSVEEVGEIVGIPESTVKTRMFYARKKL 175 (189)
T ss_pred -ccccCC-CCCCHHHHHHhHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 000111 12245555566666778999999999999999999998 899999999999999999999999999999
Q ss_pred HHHhhcCch
Q 008556 545 KQSLGGKAS 553 (561)
Q Consensus 545 R~~l~~~~l 553 (561)
|..+...+.
T Consensus 176 r~~l~~~~~ 184 (189)
T PRK12515 176 AELLKAAGV 184 (189)
T ss_pred HHHHHHhcc
Confidence 999876543
No 63
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=99.85 E-value=3.3e-20 Score=177.95 Aligned_cols=175 Identities=17% Similarity=0.201 Sum_probs=138.7
Q ss_pred hhcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccc
Q 008556 316 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT 395 (561)
Q Consensus 316 ~~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~ 395 (561)
.++..|++.|+..|.+.++.+|.++.++..+++|++||+++.+|+++++|++..+..|.||++..+++.+.++++++.+.
T Consensus 5 ~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~~~~~~~~wL~~Iarn~~~d~~Rk~~~~ 84 (185)
T PRK12542 5 NNDYEKMEELYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKNLEKLHSLNTQELKRYILRVAKNKAIDSYRKNKRH 84 (185)
T ss_pred ccCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 35569999999999999999999999999999999999999999999999875445799999999999999999876421
Q ss_pred cccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCC
Q 008556 396 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVE 475 (561)
Q Consensus 396 IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~ 475 (561)
... . +. . .. +.... ..+
T Consensus 85 ~~~------------------~------------------------------------~~-~---~~----~~~~~-~~~ 101 (185)
T PRK12542 85 ETF------------------L------------------------------------EE-Y---ER----ESIEA-VDE 101 (185)
T ss_pred hhh------------------h------------------------------------hh-c---cc----cchhh-hhc
Confidence 000 0 00 0 00 00000 001
Q ss_pred ChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhh
Q 008556 476 IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYG 555 (561)
Q Consensus 476 ~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~l~~ 555 (561)
.+++.....+....|..+|..||+++|+||.|+|. +++|++|||+.||+|..+|+..+.||+++||+.+.......
T Consensus 102 ~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~~~~~ 177 (185)
T PRK12542 102 NIEEWEKRKMSEVQIDTLLKELNESNRQVFKYKVF----YNLTYQEISSVMGITEANVRKQFERARKRVQNMIGGIQHDE 177 (185)
T ss_pred cHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHcccchHH
Confidence 23333334444567999999999999999999998 89999999999999999999999999999999998877766
Q ss_pred hh
Q 008556 556 YA 557 (561)
Q Consensus 556 yl 557 (561)
|+
T Consensus 178 ~~ 179 (185)
T PRK12542 178 FK 179 (185)
T ss_pred HH
Confidence 64
No 64
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=99.85 E-value=7.8e-20 Score=172.08 Aligned_cols=168 Identities=16% Similarity=0.176 Sum_probs=138.7
Q ss_pred hhcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccc
Q 008556 316 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT 395 (561)
Q Consensus 316 ~~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~ 395 (561)
.++..|++.|+..|.+.|+++|+++.+++.+.+|++||++++||+++++|+ .+..|.+|++..+++.+.+++++..+.
T Consensus 9 ~~~~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDl~qe~~~~l~~~~~~~~--~~~~~~~~l~~i~~~~~~d~~r~~~~~ 86 (179)
T PRK11924 9 TGDKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFN--GKGSARTWLLTIARNVCYDLLRRRRRE 86 (179)
T ss_pred ccCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHhhcC--CcchHHHHHHHHHHHHHHHHHHhcccc
Confidence 455699999999999999999999999999999999999999999999998 345799999999999999998765421
Q ss_pred cccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCC
Q 008556 396 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVE 475 (561)
Q Consensus 396 IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~ 475 (561)
... ..+ .. .+...+....
T Consensus 87 ~~~-----------------------------------------------------~~~-~~--------~~~~~~~~~~ 104 (179)
T PRK11924 87 KAV-----------------------------------------------------LSD-DA--------LEPEFAETAE 104 (179)
T ss_pred ccc-----------------------------------------------------Ccc-cc--------cccccCCccC
Confidence 100 000 00 0000000223
Q ss_pred ChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008556 476 IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 551 (561)
Q Consensus 476 ~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 551 (561)
+|+..+...+....|..+|..||+++++||.++|. ++++.+|||+.||+|+.+|++.+.||+++||+.+...
T Consensus 105 ~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~~~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l~~~ 176 (179)
T PRK11924 105 TPEAALLAKDDLARIDRCLDALPVKQREVFLLRYV----EGLSYREIAEILGVPVGTVKSRLRRARQLLRECLEAQ 176 (179)
T ss_pred CHHHHHhhHHHHHHHHHHHHhCCHHHHHHhhHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 67777888888889999999999999999999998 8999999999999999999999999999999988654
No 65
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=99.84 E-value=8.6e-20 Score=172.97 Aligned_cols=172 Identities=13% Similarity=0.188 Sum_probs=134.2
Q ss_pred CCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHH
Q 008556 306 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 384 (561)
Q Consensus 306 ~~~~eL~~~l~~G~-~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqa 384 (561)
|++..+...+..|+ .|++.|+..|.+.|+.+|++|.++..+.+|++||+++++|+++++|++. .+|.+|++..+++.
T Consensus 3 ~~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~--~~~~~wl~~i~~n~ 80 (176)
T PRK09638 3 MDEKELIQKAKKGDDAALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSFQGR--SKFSTWLISIASRL 80 (176)
T ss_pred ccHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHH
Confidence 45566666655554 9999999999999999999999998999999999999999999999874 47999999999999
Q ss_pred HHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCch
Q 008556 385 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT 464 (561)
Q Consensus 385 I~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~ 464 (561)
+.+++++..+..... +.+ .+.
T Consensus 81 ~~d~~r~~~~~~~~~---------------------------~~~-----------------------~~~--------- 101 (176)
T PRK09638 81 YKDHLRKQKREKLRL---------------------------QRA-----------------------KEE--------- 101 (176)
T ss_pred HHHHHHHhccccchh---------------------------hhc-----------------------ccc---------
Confidence 999998754211000 000 000
Q ss_pred hhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008556 465 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 544 (561)
Q Consensus 465 l~d~l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKL 544 (561)
..+ .... +..........|..+|..||+++|+||.++|. +|++++|||+.||+|..+|++.+.||+++|
T Consensus 102 ----~~~--~~~~-~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~l~is~~~V~~~l~ra~~~l 170 (176)
T PRK09638 102 ----TLR--KEKW-EAAIKGAEWSEMLDALSKLDPEFRAPVILKHY----YGYTYEEIAKMLNIPEGTVKSRVHHGIKQL 170 (176)
T ss_pred ----cCC--ccch-HHHHHhhhHHHHHHHHHcCCHHHhheeeehhh----cCCCHHHHHHHHCCChhHHHHHHHHHHHHH
Confidence 000 0000 11122233456889999999999999999988 899999999999999999999999999999
Q ss_pred HHHhh
Q 008556 545 KQSLG 549 (561)
Q Consensus 545 R~~l~ 549 (561)
|+.+.
T Consensus 171 ~~~l~ 175 (176)
T PRK09638 171 RKEWG 175 (176)
T ss_pred HHHhc
Confidence 99763
No 66
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=99.84 E-value=1.5e-19 Score=174.97 Aligned_cols=172 Identities=17% Similarity=0.174 Sum_probs=138.5
Q ss_pred CCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHH
Q 008556 306 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 384 (561)
Q Consensus 306 ~~~~eL~~~l~~G~-~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqa 384 (561)
+++..+...+..|+ .+++.|+..|.+.|++++.++.++..+++|++||+++.+|+++++|++.. .|.+|++..+++.
T Consensus 12 ~~~~~l~~~~~~gd~~~~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQEvfl~l~~~~~~~~~~~--~f~~wL~~i~rn~ 89 (192)
T PRK09643 12 RSDAELLAAHVAGDRYAFGELFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHRAAGSFRGDA--AVSSWLHRIVVNA 89 (192)
T ss_pred cCHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCCCC--ccHHHHHHHHHHH
Confidence 35666666665554 99999999999999999999999999999999999999999999999753 5999999999999
Q ss_pred HHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCch
Q 008556 385 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT 464 (561)
Q Consensus 385 I~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~ 464 (561)
+.+++++..+..+. +++ +..
T Consensus 90 ~~d~~Rk~~~~~~~-----------------------------------------------------~~~-----~~~-- 109 (192)
T PRK09643 90 CLDRLRRAKARPTV-----------------------------------------------------PLD-----DVY-- 109 (192)
T ss_pred HHHHHHccccCCCC-----------------------------------------------------Ccc-----ccc--
Confidence 99999875421100 000 000
Q ss_pred hhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008556 465 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 544 (561)
Q Consensus 465 l~d~l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKL 544 (561)
+. . ..+++.+...+....|..+|..||+++|+||.|+|. +++|++|||+.||+|..+|+..+.||+++|
T Consensus 110 --~~-~----~~~~~~~~~~e~~~~l~~~l~~Lp~~~r~i~~l~~~----~g~s~~EIA~~lg~s~~tV~~rl~rar~~L 178 (192)
T PRK09643 110 --PV-A----QLERDPTARVETALAVQRALMRLPVEQRAALVAVDM----QGYSVADAARMLGVAEGTVKSRCARGRARL 178 (192)
T ss_pred --cc-c----CCcccHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 00 0 012223444455667999999999999999999998 899999999999999999999999999999
Q ss_pred HHHhhc
Q 008556 545 KQSLGG 550 (561)
Q Consensus 545 R~~l~~ 550 (561)
|+.+..
T Consensus 179 r~~l~~ 184 (192)
T PRK09643 179 AELLGY 184 (192)
T ss_pred HHHHHH
Confidence 998864
No 67
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=99.84 E-value=1.2e-19 Score=171.19 Aligned_cols=167 Identities=18% Similarity=0.230 Sum_probs=132.1
Q ss_pred CCHHHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHH
Q 008556 306 LSCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 384 (561)
Q Consensus 306 ~~~~eL~~~l~~G-~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqa 384 (561)
|+++.+...+..| ..|++.++..|.+.|++++.++.++..+++|++||+++.+|+++++|++.. .|.||++..+++.
T Consensus 1 ~~~~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~l~~~~~~~~~~~~~--~~~~wl~~i~~n~ 78 (169)
T TIGR02954 1 MNDEELVKKAKRGNKPAFESLIKKHKEKLYKTAFIYVKNEHDALDVIQETVYKAYLSIDKLKHPK--YFNTWLTRILINE 78 (169)
T ss_pred CCHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhccCcc--ccHHHHHHHHHHH
Confidence 3455666665555 599999999999999999999999999999999999999999999999753 6999999999999
Q ss_pred HHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCch
Q 008556 385 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT 464 (561)
Q Consensus 385 I~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~ 464 (561)
+.+++++..+.. | ++.....+
T Consensus 79 ~~d~~R~~~~~~--~-----------------------------------------------------~~~~~~~~---- 99 (169)
T TIGR02954 79 CIDLLKKKKKVI--P-----------------------------------------------------FDPNTSIE---- 99 (169)
T ss_pred HHHHHHhcCCcC--c-----------------------------------------------------cccccccc----
Confidence 999987654210 0 00000000
Q ss_pred hhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008556 465 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 544 (561)
Q Consensus 465 l~d~l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKL 544 (561)
+. .++ ... .....+..+|..||+++|+||.++|. +|+|.+|||+.||||..+|+..+.||+++|
T Consensus 100 ------~~---~~~--~~~-~~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~eiA~~lgis~~tv~~~l~Ra~~~L 163 (169)
T TIGR02954 100 ------KG---ECE--THA-DSRLDLYKAIDTLNDKYQTAIILRYY----HDLTIKEIAEVMNKPEGTVKTYLHRALKKL 163 (169)
T ss_pred ------cc---hhh--hch-HHHHHHHHHHHhCCHHHhHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 00 000 001 11236889999999999999999998 899999999999999999999999999999
Q ss_pred HHHhh
Q 008556 545 KQSLG 549 (561)
Q Consensus 545 R~~l~ 549 (561)
|..+.
T Consensus 164 r~~l~ 168 (169)
T TIGR02954 164 KKRLE 168 (169)
T ss_pred HHHhc
Confidence 99874
No 68
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=99.84 E-value=2.1e-19 Score=162.50 Aligned_cols=157 Identities=24% Similarity=0.383 Sum_probs=131.2
Q ss_pred HHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccch
Q 008556 321 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPE 400 (561)
Q Consensus 321 Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~ 400 (561)
|++.++..|.++|.++++++.+++.+.+|++|||++++|++++.|++. .+|.+|+.+++++.+.++++++.+ . +.
T Consensus 2 a~~~l~~~~~~~v~~~~~~~~~~~~~~~D~~qe~~~~l~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~rk~~~-~--~~ 76 (158)
T TIGR02937 2 AFEELYERYLPLLYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPE--GSFKAWLFRIARNLILDYLRRKRR-L--RR 76 (158)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCCc--chHHHHHHHHHHHHHHHHHHHhcc-C--Cc
Confidence 789999999999999999999999999999999999999999999998 589999999999999999987763 1 10
Q ss_pred hHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHH
Q 008556 401 NIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDIS 480 (561)
Q Consensus 401 ~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~ 480 (561)
.. . .. ... ......++..
T Consensus 77 ~~---------------------------------------------------~------~~----~~~-~~~~~~~~~~ 94 (158)
T TIGR02937 77 EL---------------------------------------------------D------LL----EEL-LDSDPSPEEE 94 (158)
T ss_pred ch---------------------------------------------------h------hh----hhc-ccccCCHHHH
Confidence 00 0 00 000 0111245556
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008556 481 VQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 548 (561)
Q Consensus 481 le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 548 (561)
.........|..++..||++++.||.++|+ .|+|..|||+.+|+|+.+|+++..+++++||+.+
T Consensus 95 ~~~~~~~~~l~~~l~~L~~~~~~ii~~~~~----~g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~~l 158 (158)
T TIGR02937 95 LEQEEEREALREALEKLPEREREVLVLRYL----EGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158 (158)
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHhhHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence 666677788999999999999999999987 7899999999999999999999999999999754
No 69
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=99.83 E-value=1.4e-19 Score=175.29 Aligned_cols=176 Identities=11% Similarity=0.145 Sum_probs=133.8
Q ss_pred HHHHHh-hcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHH
Q 008556 311 LKSELH-SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAI 389 (561)
Q Consensus 311 L~~~l~-~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~I 389 (561)
++..+. ++..+++.|+..|.+.|+.+|.++.++..+++|++||+++.+|+.+++|++.++ .|.+|++..++|.+.+++
T Consensus 17 li~~~~~~d~~af~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQev~l~l~~~~~~~~~~~~-~~~~wL~~iarn~~ld~~ 95 (194)
T PRK12531 17 CMEKVKSRDKQAFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKAHLFDGQKS-ALSTWIYTIIRNLCFDLL 95 (194)
T ss_pred HHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCcccc-hHHHHHHHHHHHHHHHHH
Confidence 445554 445999999999999999999999999889999999999999999999997554 699999999999999999
Q ss_pred HhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhc
Q 008556 390 FQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEIT 469 (561)
Q Consensus 390 r~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l 469 (561)
++..+.... . ..+... .+.. ....+
T Consensus 96 Rk~~~~~~~-------------------------~---------------------------~~~~~~-~~~~--~~~~~ 120 (194)
T PRK12531 96 RKQKGKDLH-------------------------I---------------------------HADDIW-PSDY--YPPDL 120 (194)
T ss_pred HHhcccccc-------------------------c---------------------------chhhcc-cccc--ccccc
Confidence 875421000 0 000000 0000 00000
Q ss_pred ccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008556 470 ADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 549 (561)
Q Consensus 470 ~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 549 (561)
.+ ...++.. ...+.+..+|..||+++|+||.++|. +++|.+|||+.||||.++|+..++||+++||..+.
T Consensus 121 ~~--~~~~e~~----~~~~~l~~~l~~Lp~~~r~v~~l~~~----eg~s~~EIA~~lgis~~tVk~rl~ra~~~Lr~~l~ 190 (194)
T PRK12531 121 VD--HYSPEQD----MLKEQVMKFLDRLPKAQRDVLQAVYL----EELPHQQVAEMFDIPLGTVKSRLRLAVEKLRHSMD 190 (194)
T ss_pred cc--ccCHHHH----HHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHhh
Confidence 00 0122221 23356889999999999999999998 89999999999999999999999999999999987
Q ss_pred cCc
Q 008556 550 GKA 552 (561)
Q Consensus 550 ~~~ 552 (561)
...
T Consensus 191 ~~~ 193 (194)
T PRK12531 191 AES 193 (194)
T ss_pred hcc
Confidence 654
No 70
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=99.83 E-value=1.9e-19 Score=172.00 Aligned_cols=165 Identities=16% Similarity=0.196 Sum_probs=132.8
Q ss_pred hcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhccccc
Q 008556 317 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI 396 (561)
Q Consensus 317 ~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~I 396 (561)
++..|++.|+..|.+.|+.++++|.++..+.+|++||+++.+|+++.+|++.. .|.+|++..+++.+.++++...+..
T Consensus 4 ~d~~af~~l~~~~~~~l~~~~~~~~~~~~daeDl~Qevfl~l~~~~~~~~~~~--~f~~wl~~iarn~~~~~~r~~~~~~ 81 (179)
T PRK12543 4 GDQEAFSEIYDVTIQEVYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKYDSNR--PFRFWLIGLVIKQIHSWRRKRWRRF 81 (179)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHcCCCC--ChHHHHHHHHHHHHHHHHHhhcccc
Confidence 44589999999999999999999999999999999999999999999999864 5999999999999988876543110
Q ss_pred ccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCC
Q 008556 397 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEI 476 (561)
Q Consensus 397 RlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~ 476 (561)
+. ++... + ..+ ......
T Consensus 82 ~~------------------------------------------------------~~~~~--~----~~~---~~~~~~ 98 (179)
T PRK12543 82 RI------------------------------------------------------FEKAE--E----QRK---PVSIDF 98 (179)
T ss_pred cc------------------------------------------------------ccccc--c----ccc---cccccC
Confidence 00 00000 0 000 001113
Q ss_pred hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008556 477 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 551 (561)
Q Consensus 477 pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 551 (561)
|+. +...+....|..+|..||+++|+||.++|. +++|++|||+.||||..+|+..++||+++||+.+...
T Consensus 99 ~~~-~~~~~~~~~l~~~l~~Lp~~~r~i~~l~~~----e~~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~ 168 (179)
T PRK12543 99 SED-VLSKESNQELIELIHKLPYKLRQVIILRYL----HDYSQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQIE 168 (179)
T ss_pred hHH-HHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----ccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 444 556666778999999999999999999998 8999999999999999999999999999999988654
No 71
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=99.83 E-value=1.9e-19 Score=166.26 Aligned_cols=160 Identities=18% Similarity=0.183 Sum_probs=129.2
Q ss_pred HHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccch
Q 008556 321 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPE 400 (561)
Q Consensus 321 Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~ 400 (561)
|+++|+..|.+.|+++++++.++..+.+|++||+++++|+++.+|++. .+|.+|++.++++.+.+++++..+...
T Consensus 2 a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~~~~~~~~~~~~--~~~~~wl~~i~r~~~~d~~r~~~~~~~--- 76 (161)
T TIGR02985 2 AFEQLYRRYYPKLCAFAYRYVKDEEEAEDIVQDVFVKLWENRETLEEV--ESFKAYLFTIVKNRSLNYLRHKQVEEK--- 76 (161)
T ss_pred hHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcccc--ccHHHHHHHHHHHHHHHHHHHHHhHhH---
Confidence 789999999999999999999998999999999999999999999874 369999999999999999876542100
Q ss_pred hHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHH
Q 008556 401 NIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDIS 480 (561)
Q Consensus 401 ~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~ 480 (561)
.. ..+ . .+.. .......+++.
T Consensus 77 -----------~~-------------~~~------------------------~----~~~~-------~~~~~~~~~~~ 97 (161)
T TIGR02985 77 -----------YQ-------------EEI------------------------L----EIEV-------DELSENDPEEE 97 (161)
T ss_pred -----------HH-------------HHH------------------------H----hhcc-------cccCCCCcHHH
Confidence 00 000 0 0000 00011245555
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008556 481 VQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 548 (561)
Q Consensus 481 le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 548 (561)
+...+....|..++..||+++++||.++|. +++|..|||+.||+|+++|++++.+|+++||+.|
T Consensus 98 ~~~~e~~~~l~~~l~~L~~~~r~il~l~~~----~~~~~~eIA~~lgis~~tv~~~~~ra~~~Lr~~l 161 (161)
T TIGR02985 98 LEAKELQLIIYKAIEKLPEQCRKIFILSRF----EGKSYKEIAEELGISVKTVEYHISKALKELRKEL 161 (161)
T ss_pred HHHHHHHHHHHHHHHHCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence 666677778999999999999999999998 8999999999999999999999999999999864
No 72
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=99.83 E-value=3.1e-19 Score=168.92 Aligned_cols=165 Identities=14% Similarity=0.133 Sum_probs=131.2
Q ss_pred hcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhccccc
Q 008556 317 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI 396 (561)
Q Consensus 317 ~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~I 396 (561)
++..+++.|+..|.+.|+.+|.++.++..+++|++||.|+.+|+..++|++.. ..|.+|++..++|.+.++++++.+..
T Consensus 6 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~~~AeD~vQevfl~~~~~~~~~~~~~-~~~~~wL~~iarn~~~d~~Rk~~~~~ 84 (173)
T PRK09645 6 AEAALMRALYDEHAAPLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLADTG-RSARAWLFTVARNLVIDERRSARARP 84 (173)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCccc-ccHHHHHHHHHHHHHHHHHHhhcccc
Confidence 35689999999999999999999999888999999999999999999997533 36999999999999999998654210
Q ss_pred ccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCC
Q 008556 397 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEI 476 (561)
Q Consensus 397 RlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~ 476 (561)
.. ..+ +.. +. .+. .
T Consensus 85 ~~-----------------------------------------------------~~~------~~~---~~-~~~---~ 98 (173)
T PRK09645 85 VE-----------------------------------------------------GGD------DVL---GV-PEQ---S 98 (173)
T ss_pred cc-----------------------------------------------------ccc------ccc---cC-CCC---C
Confidence 00 000 000 00 000 1
Q ss_pred hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 008556 477 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA 552 (561)
Q Consensus 477 pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~ 552 (561)
+++.+........|..+|+.||+++|+||.|+|. +++|++|||+.||+|..+|+..++||+++||+.+...+
T Consensus 99 ~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~L~~~----~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~ 170 (173)
T PRK09645 99 APDEVDRALDRLLVADALAQLSPEHRAVLVRSYY----RGWSTAQIAADLGIPEGTVKSRLHYALRALRLALQERG 170 (173)
T ss_pred CchHHHHHhHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhhccc
Confidence 2222333344457899999999999999999998 89999999999999999999999999999999987544
No 73
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=99.82 E-value=2.5e-19 Score=171.50 Aligned_cols=169 Identities=15% Similarity=0.128 Sum_probs=129.9
Q ss_pred HHHHHH-hhcHHHHHHHHHHHHHHHHHHHHhhhC-CCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHH
Q 008556 310 DLKSEL-HSGNSSREKLINANLRLVVHVAKQYQG-RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRK 387 (561)
Q Consensus 310 eL~~~l-~~G~~Are~LI~~nlrLV~sIArrY~~-~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~ 387 (561)
.++..+ .++..|++.|+..|.+.|+.++.++.+ ...+.+|++||+++.||+.++.|++. ..|.+|++..++|.+.+
T Consensus 10 ~~~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~~aeDlvQevfl~l~~~~~~~~~~--~~~~~wl~~iarN~~~d 87 (181)
T PRK12536 10 ALLLRGLAGDAAAYRQFLSELAAHLRGFLRRRLPQLPDEVEDLVQEILLAVHNARHTYRAD--QPLTAWVHAIARYKLMD 87 (181)
T ss_pred HHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCChhhHHHHHHHHHHHHHHhHHhcCCC--CchHHHHHHHHHHHHHH
Confidence 344444 455699999999999999999998764 57899999999999999999999974 36999999999999999
Q ss_pred HHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhh
Q 008556 388 AIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQE 467 (561)
Q Consensus 388 ~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d 467 (561)
+++++.+.... ..+++ . ..+
T Consensus 88 ~~Rk~~~~~~~---------------------------------------------------~~~~~----~-----~~~ 107 (181)
T PRK12536 88 FLRSRARREAL---------------------------------------------------HDPLD----D-----ESE 107 (181)
T ss_pred HHHHHhccccc---------------------------------------------------cCCcc----c-----hhh
Confidence 99875421000 00000 0 000
Q ss_pred hcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008556 468 ITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 547 (561)
Q Consensus 468 ~l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 547 (561)
...+. .++. .+....+..+|..||+++|.||.++|. +++|.+|||+.||||.++|+..++||+++||+.
T Consensus 108 ~~~~~---~~~~----~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~EIA~~l~is~~tV~~~l~rar~~Lr~~ 176 (181)
T PRK12536 108 LFATS---DDEA----AEARRDLGKLLEQLPDRQRLPIVHVKL----EGLSVAETAQLTGLSESAVKVGIHRGLKALAAK 176 (181)
T ss_pred hcCCC---Ccch----HHHHHHHHHHHHHCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 00011 1111 123446899999999999999999998 899999999999999999999999999999998
Q ss_pred hhcC
Q 008556 548 LGGK 551 (561)
Q Consensus 548 l~~~ 551 (561)
+...
T Consensus 177 l~~~ 180 (181)
T PRK12536 177 IRGE 180 (181)
T ss_pred hcCC
Confidence 7643
No 74
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=99.82 E-value=4.1e-19 Score=169.80 Aligned_cols=164 Identities=16% Similarity=0.180 Sum_probs=133.8
Q ss_pred cHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccc
Q 008556 318 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR 397 (561)
Q Consensus 318 G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IR 397 (561)
+..|+++|+..|.+.|+++|.++.++..+.+|++||+++.+|+++++|++. ..|.+|++..+++.+.+++++..+...
T Consensus 14 ~~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQd~fl~l~~~~~~~~~~--~~~~awl~~ia~n~~~d~~Rk~~~~~~ 91 (179)
T PRK09415 14 KEDLIDEIMNEYGQEVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYKGK--SSLKTWLYRIAINHCKDYLKSWHNKKV 91 (179)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcCCC--cccHHHHHHHHHHHHHHHHHhhccccc
Confidence 358999999999999999999999999999999999999999999999874 369999999999999999876431100
Q ss_pred cchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCCh
Q 008556 398 LPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIP 477 (561)
Q Consensus 398 lP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~p 477 (561)
. ..+. ...... ....+|
T Consensus 92 ~-----------------------------------------------------~~~~--------~~~~~~--~~~~~~ 108 (179)
T PRK09415 92 I-----------------------------------------------------VTED--------IFTYME--SQKESV 108 (179)
T ss_pred c-----------------------------------------------------cccc--------cccccc--ccccCc
Confidence 0 0000 000000 011245
Q ss_pred hHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008556 478 DISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 550 (561)
Q Consensus 478 ee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 550 (561)
++.+...+....|..+|..||+++|+||.++|. +|+|++|||+.||||.++|++.+.||+++||+.+..
T Consensus 109 e~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~l~~ 177 (179)
T PRK09415 109 EEEVIQNAEDERLASAVMSLPIKYREVIYLFYY----EELSIKEIAEVTGVNENTVKTRLKKAKELLKKGLEE 177 (179)
T ss_pred HHHHHHHHHHHHHHHHHHhCCHHHhhHhHhHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 666666677778999999999999999999998 899999999999999999999999999999998764
No 75
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=99.82 E-value=5.3e-19 Score=167.69 Aligned_cols=167 Identities=16% Similarity=0.193 Sum_probs=130.6
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccc
Q 008556 320 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP 399 (561)
Q Consensus 320 ~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP 399 (561)
..+++|+..|.++|+.+|++|.++..+++|++||+++.+|+++++|++.. +|.+|++..+++.+.++++++.+....+
T Consensus 3 ~~~~~l~~~y~~~i~~~~~~~~~~~~daeDvvQe~~i~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~Rk~~~~~~~~ 80 (173)
T PRK12522 3 EKVEELIDIYKQQIYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSYVE--NYKKWITTICVRTFYDFYRKKKRWKDRI 80 (173)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHcCCcc--chHHHHHHHHHHHHHHHHHHhccccccc
Confidence 45899999999999999999999999999999999999999999999754 6999999999999999998765311000
Q ss_pred hhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhH
Q 008556 400 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDI 479 (561)
Q Consensus 400 ~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee 479 (561)
... .+ .+ ...+.........++.
T Consensus 81 ~~~--------------------------------------------------~~------~~-~~~~~~~~~~~~~~~~ 103 (173)
T PRK12522 81 LDL--------------------------------------------------FH------KE-DGGEIEFADDVNISEE 103 (173)
T ss_pred ccc--------------------------------------------------cc------hh-hhhhhccccCCCChHH
Confidence 000 00 00 0000000001112333
Q ss_pred HHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008556 480 SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 550 (561)
Q Consensus 480 ~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 550 (561)
....+..+.|..+|..||+++++||.|+|. ++++++|||+.||||.++|+..+.||+++||+.+..
T Consensus 104 -~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~~~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~~ 169 (173)
T PRK12522 104 -FIQKVEAEMIREVIQLLNEKYKTVLVLYYY----EQYSYKEMSEILNIPIGTVKYRLNYAKKQMREHLEG 169 (173)
T ss_pred -HHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 444556778999999999999999999998 899999999999999999999999999999998753
No 76
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=99.82 E-value=3.1e-19 Score=166.03 Aligned_cols=158 Identities=18% Similarity=0.214 Sum_probs=125.6
Q ss_pred HHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccch
Q 008556 321 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPE 400 (561)
Q Consensus 321 Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~ 400 (561)
+++.++..|.+.|+.+|+++.++..+.+|++||+++.+|+++++|++.. .|.+|++..+++.+.++++++.+.-.. .
T Consensus 2 ~~~~~~~~~~~~l~~~~~~~~~~~~~aEDivQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~r~~~~~~~~-~ 78 (159)
T TIGR02989 2 AFAALLQRHQRSLRAFVRSLVPDRDDADDVLQETFVTAWRKFDEFDPGT--DFGAWARGIARNKVLNHRRKLGRDRLV-F 78 (159)
T ss_pred HHHHHHHHhHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHHhCCCCC--chHHHHHHHHHHHHHHHHHHhcccccc-c
Confidence 7899999999999999999999999999999999999999999999764 599999999999999999876521100 0
Q ss_pred hHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHH
Q 008556 401 NIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDIS 480 (561)
Q Consensus 401 ~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~ 480 (561)
.++ ..+.+.+.. .+.+.
T Consensus 79 -------------------------~~~------------------------------------~~~~~~~~~--~~~~~ 95 (159)
T TIGR02989 79 -------------------------DDE------------------------------------LLEALAAEA--EATEA 95 (159)
T ss_pred -------------------------CHH------------------------------------HHHHHHhhc--ccchH
Confidence 000 000000000 11112
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008556 481 VQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 548 (561)
Q Consensus 481 le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 548 (561)
....+....|..+++.||++++.||.++|. +|++.+|||+.||||..+|+..++||+++||+++
T Consensus 96 ~~~~~~~~~l~~~i~~L~~~~r~v~~l~~~----~g~~~~eIA~~l~is~~tv~~~l~Rar~~Lr~~~ 159 (159)
T TIGR02989 96 DRSEDELQALEGCLEKLPERQRELLQLRYQ----RGVSLTALAEQLGRTVNAVYKALSRLRVRLRDCV 159 (159)
T ss_pred hhHHHHHHHHHHHHHHCCHHHHHHHHHHHh----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhcC
Confidence 222334567899999999999999999998 8999999999999999999999999999999853
No 77
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.
Probab=99.82 E-value=5.4e-19 Score=178.18 Aligned_cols=181 Identities=16% Similarity=0.201 Sum_probs=141.6
Q ss_pred ccCCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHH-------hhhhcCCCCCCchhH
Q 008556 304 IGLSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMK-------SVEKFKPQAGCRFAS 375 (561)
Q Consensus 304 ~g~~~~eL~~~l~~G~-~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLir-------AiekFDp~kG~rFST 375 (561)
++.++..|...+++|+ .|++.|+..|.+.|+.+++++.++..+++|++||.|+.+|. .+.+|++. ..|.|
T Consensus 22 ~~~~d~~Li~~~~~gd~~Af~~L~~~y~~~l~~~~~~~~~~~~dAEDivQEvFlkl~~~~~~~~~~~~~~~~~--~~~~t 99 (244)
T TIGR03001 22 LHAADLYLACACAQGEPAALAALERHVLSKVPARLAGLRPPTAFVDEVLQRLRQRLLVPRAERPPRIAEYSGR--GPLLS 99 (244)
T ss_pred ccccHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhccchhhhhhccCCC--CchHh
Confidence 4456777888877666 99999999999999999999999999999999999999994 78889864 36999
Q ss_pred HHHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCC
Q 008556 376 YAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQ 455 (561)
Q Consensus 376 YA~~wIRqaI~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~ 455 (561)
|++.+++|.+.++++++.+...+ +
T Consensus 100 WL~~Ia~N~~id~lRk~~r~~~~-------------------------------------------------------~- 123 (244)
T TIGR03001 100 WVRIVATRIALELQAQERRHSPV-------------------------------------------------------E- 123 (244)
T ss_pred HHHHHHHHHHHHHHHHhcccCcc-------------------------------------------------------c-
Confidence 99999999999999765421000 0
Q ss_pred CCCCCCCchhhhhcccCCCCChhHHHHH----HHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHH
Q 008556 456 PVWADQDTTFQEITADTGVEIPDISVQK----QLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKE 531 (561)
Q Consensus 456 ~v~~d~~~~l~d~l~d~~~~~pee~le~----~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISre 531 (561)
.+. ...+. .+. ...|++.+.. .+..+.|..+|+.||+++|+||.|+|. +++|++|||++||||.+
T Consensus 124 ---~~~--~~~~~-~~~-~~~~e~~~~~~e~~~e~~~~l~~aL~~Lp~~~R~v~~L~~~----eg~S~~EIA~~Lgis~~ 192 (244)
T TIGR03001 124 ---EPT--ELAAL-PAP-GSDPELDLLRERYRQDFRQALREALAALSERERHLLRLHFV----DGLSMDRIGAMYQVHRS 192 (244)
T ss_pred ---ccc--ccccc-cCC-CCCHHHHHHHHhhHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHH
Confidence 000 00000 011 1133433332 235567999999999999999999998 89999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhhcCch
Q 008556 532 RVRQLESRALYRLKQSLGGKAS 553 (561)
Q Consensus 532 rVRqie~RALkKLR~~l~~~~l 553 (561)
+|+..+.||+++||+.+.....
T Consensus 193 TVk~rl~RAr~~Lr~~l~~~~~ 214 (244)
T TIGR03001 193 TVSRWVAQARERLLERTRRRLA 214 (244)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999876543
No 78
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=99.82 E-value=4.4e-19 Score=170.97 Aligned_cols=182 Identities=16% Similarity=0.178 Sum_probs=136.6
Q ss_pred HHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccch
Q 008556 321 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPE 400 (561)
Q Consensus 321 Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~ 400 (561)
+++.|+..|.+.|+.+|+++.++..+.+|++||.++.+|+.+++|++.. +|.+|++..++|.+.++++++.+......
T Consensus 3 ~~~~l~~~~~~~l~~~a~~~~~~~~~AeDivQevfl~~~~~~~~~~~~~--~~~~WL~~ia~n~~~d~~Rk~~r~~~~~~ 80 (191)
T PRK12520 3 IAPAQLEALRPHLLRFARLQLRDPALAEDAVSETLLAVLEHPERFAGQS--SLKTYLVGILKHKIIDAIRSGRREVRLSL 80 (191)
T ss_pred chHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhcccc--cHHHHHHHHHHHHHHHHHHhhcCcCcccc
Confidence 6899999999999999999999999999999999999999999998643 69999999999999999987653211100
Q ss_pred hHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHH
Q 008556 401 NIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDIS 480 (561)
Q Consensus 401 ~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~ 480 (561)
.. .......++ ++. ... .+. .....++. ..+|++.
T Consensus 81 ~~------------------~~~~~~~~~-----------------------~~~-~~~-~~~-~~~~~~~~-~~~~~~~ 115 (191)
T PRK12520 81 DD------------------ADEQSDDDL-----------------------FDA-LFA-ADG-HYREPPSD-WGDPDAA 115 (191)
T ss_pred cc------------------cccchhhhh-----------------------hhh-hcc-ccc-ccccCccc-cCCHHHH
Confidence 00 000000000 000 000 000 00001111 2356666
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 008556 481 VQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS 553 (561)
Q Consensus 481 le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~l 553 (561)
+...+....|..+|..||+++|+||.|+|. +++|++|||+.||+|.++|++.+.||+++||+++...+.
T Consensus 116 ~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~~ 184 (191)
T PRK12520 116 LSRREFFEVLQACVDRLPPRTGRVFMMREW----LELETEEICQELQITATNAWVLLYRARMRLRECLDLHWF 184 (191)
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 777777788999999999999999999998 899999999999999999999999999999999987653
No 79
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=99.82 E-value=7.3e-19 Score=168.66 Aligned_cols=169 Identities=15% Similarity=0.157 Sum_probs=130.1
Q ss_pred HHHHHHHHhh-cHHHHHHHHHHHHHHHHHHHHh----hhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHH
Q 008556 308 CRDLKSELHS-GNSSREKLINANLRLVVHVAKQ----YQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVR 382 (561)
Q Consensus 308 ~~eL~~~l~~-G~~Are~LI~~nlrLV~sIArr----Y~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIR 382 (561)
...|+..+.. +..|++.|+..|.+.|+.+|++ +.++..+.+|++||+++.+|++++.|++.. .|.+|++..++
T Consensus 8 ~~~l~~~~~~gd~~af~~l~~~~~~~l~~~~~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~~--~f~~wl~~i~~ 85 (184)
T PRK12539 8 LKALMLASLDGDAAAHRALLERLSGHLRAYYKGKLARIGRGAEEAEDLVQEALMAIHTRRHTYDPEQ--PLTPWVYAIAR 85 (184)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHhhcCCCC--ChHHHHHHHHH
Confidence 3445555544 4599999999999999999874 557788999999999999999999999753 59999999999
Q ss_pred HHHHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCC
Q 008556 383 QTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQD 462 (561)
Q Consensus 383 qaI~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~ 462 (561)
+.+.+++++..+.. . ....+ +.
T Consensus 86 n~~~d~~R~~~~~~-~---------------------------------------------------~~~~~------~~ 107 (184)
T PRK12539 86 YKLIDHLRRTRASL-A---------------------------------------------------DVPID------DA 107 (184)
T ss_pred HHHHHHHHHHhccc-c---------------------------------------------------ccChh------hh
Confidence 99999988653100 0 00000 00
Q ss_pred chhhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008556 463 TTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 542 (561)
Q Consensus 463 ~~l~d~l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALk 542 (561)
. ... +.+.....+....|..++..||+++|+||.++|. +|++++|||+.||||..+|+..+.||++
T Consensus 108 ~---~~~-------~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~lgis~~tV~~~l~ra~~ 173 (184)
T PRK12539 108 D---ELV-------AHDDHAAVESTLDLGRLLARLPEKMRLAIQAVKL----EGLSVAEAATRSGMSESAVKVSVHRGLK 173 (184)
T ss_pred c---ccc-------CCcHHhhHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 0 000 0001112233457899999999999999999998 8999999999999999999999999999
Q ss_pred HHHHHhhc
Q 008556 543 RLKQSLGG 550 (561)
Q Consensus 543 KLR~~l~~ 550 (561)
+||+.+..
T Consensus 174 ~Lr~~l~~ 181 (184)
T PRK12539 174 ALAALIGR 181 (184)
T ss_pred HHHHHHhh
Confidence 99998754
No 80
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=99.82 E-value=7.9e-19 Score=167.39 Aligned_cols=171 Identities=19% Similarity=0.264 Sum_probs=125.2
Q ss_pred HHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHhhhCCCC-----CHHHHHHHHHHHHHH-hhhhcCCCCCCchhHHHHHHH
Q 008556 309 RDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGI-----SLHDLLQEGSMGLMK-SVEKFKPQAGCRFASYAYWWV 381 (561)
Q Consensus 309 ~eL~~~l~~G~-~Are~LI~~nlrLV~sIArrY~~~g~-----~~eDLIQEG~IGLir-AiekFDp~kG~rFSTYA~~wI 381 (561)
..|+..+..|+ .|++.|+..|.+.++.+|++|.++.. +.+|++||+|+.+|+ ...+|++. ..|.+|++.++
T Consensus 5 ~~li~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~AeDlvQevfl~~~~~~~~~~~~~--~~~~~wl~~i~ 82 (183)
T TIGR02999 5 TELLQQWQNGDAAARDQLFPQLYQELRRIARRQLRRERSGQTLQTTALVHEAYLRLSDQDEQKWDDR--AHFFAAAAKAM 82 (183)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhhcccccccchHHHHHHHHHHHHhhcccCCCCch--HHHHHHHHHHH
Confidence 34555555554 89999999999999999999998877 899999999999998 78889754 36999999999
Q ss_pred HHHHHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCC
Q 008556 382 RQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQ 461 (561)
Q Consensus 382 RqaI~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~ 461 (561)
++.+.++++++.+..+. . ...+..
T Consensus 83 ~n~~~d~~R~~~~~~~~----------------------~-----------------------------~~~~~~----- 106 (183)
T TIGR02999 83 RRILVDHARRRRAQKRG----------------------G-----------------------------GAVRVP----- 106 (183)
T ss_pred HHHHHHHHHHHHHHhcc----------------------C-----------------------------Cccccc-----
Confidence 99999998764311000 0 000000
Q ss_pred CchhhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 008556 462 DTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL 541 (561)
Q Consensus 462 ~~~l~d~l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RAL 541 (561)
+.+..++. .++.. +.....+.+...|..||+++|+||.|+|. +|+|++|||+.||||..+|+..+.||+
T Consensus 107 ---~~~~~~~~---~~~~~-~~~~~l~~~~~~l~~Lp~~~r~v~~l~~~----~g~s~~EIA~~lgis~~tVk~~l~Rar 175 (183)
T TIGR02999 107 ---LDEVLPDA---EADLD-EELLDLDDALDKLAQVDPRQAEVVELRFF----AGLTVEEIAELLGVSVRTVERDWRFAR 175 (183)
T ss_pred ---cccccCCC---CccHH-HHHHHHHHHHHHhhcCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 00000000 11111 11111223444567799999999999998 999999999999999999999999999
Q ss_pred HHHHHHh
Q 008556 542 YRLKQSL 548 (561)
Q Consensus 542 kKLR~~l 548 (561)
++||+.+
T Consensus 176 ~~Lr~~l 182 (183)
T TIGR02999 176 AWLADEL 182 (183)
T ss_pred HHHHHHh
Confidence 9999876
No 81
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=99.81 E-value=1.3e-18 Score=166.40 Aligned_cols=166 Identities=19% Similarity=0.239 Sum_probs=128.4
Q ss_pred HHHHHh-hcHHHHHHHHHHHHHHHHHHHHhhhCC----CCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHH
Q 008556 311 LKSELH-SGNSSREKLINANLRLVVHVAKQYQGR----GISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI 385 (561)
Q Consensus 311 L~~~l~-~G~~Are~LI~~nlrLV~sIArrY~~~----g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI 385 (561)
+...+. ++..|++.|+..|.+.|+.+|+++.++ ..+++|++||+++.+|...++|+.. ..|.+|++..+++.+
T Consensus 12 l~~~~~~gd~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeDlvQe~fl~l~~~~~~~~~~--~~~~~wl~~i~rn~~ 89 (184)
T PRK12512 12 LMRSANAGDAAAYRRLLKAVTPVLRAAARRGLARAGQPADQAEDIVQEILLAVHLKRHTWDPG--APFAPWLFAIARNKL 89 (184)
T ss_pred HHHHHHccCHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccHHHHHHHHHHHHHHhHHhcCcc--ccHHHHHHHHHHHHH
Confidence 334443 556999999999999999999998753 3689999999999999999999874 469999999999999
Q ss_pred HHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchh
Q 008556 386 RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF 465 (561)
Q Consensus 386 ~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l 465 (561)
.++++++.+...+ .++. +
T Consensus 90 ~d~~Rr~~~~~~~-----------------------------------------------------~~~~---------~ 107 (184)
T PRK12512 90 IDALRRRGRRVFV-----------------------------------------------------DIDD---------F 107 (184)
T ss_pred HHHHHhhcccccC-----------------------------------------------------Cchh---------c
Confidence 9998765421110 0000 0
Q ss_pred hhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556 466 QEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 545 (561)
Q Consensus 466 ~d~l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 545 (561)
.+.+++. .+.. ....+.+..+|..||+++|+||.++|. +++|++|||+.||+|..+|+..+.||+++||
T Consensus 108 ~~~~~~~---~~~~----~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~l~is~~tV~~~l~ra~~~Lr 176 (184)
T PRK12512 108 AETLPAE---PATE----TLPAGDVGRHLETLPPRQRDVVQSISV----EGASIKETAAKLSMSEGAVRVALHRGLAALA 176 (184)
T ss_pred ccccccc---chhh----HHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 0001110 0001 122346788999999999999999998 8999999999999999999999999999999
Q ss_pred HHhhcC
Q 008556 546 QSLGGK 551 (561)
Q Consensus 546 ~~l~~~ 551 (561)
..+...
T Consensus 177 ~~l~~~ 182 (184)
T PRK12512 177 AKFRSE 182 (184)
T ss_pred HHhhcC
Confidence 988754
No 82
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=99.81 E-value=1.6e-18 Score=171.74 Aligned_cols=172 Identities=18% Similarity=0.165 Sum_probs=136.7
Q ss_pred hhcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccc
Q 008556 316 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT 395 (561)
Q Consensus 316 ~~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~ 395 (561)
.....+++.|+..|.+.++.+++++.++..+.+|++||+++.+|+.+++|++. .|.+|++.+++|.+.++++++.+.
T Consensus 14 ~~~~~~f~~l~~~~~~~l~~~~~~~~~d~~dAEDlvQEvflkl~~~~~~~~~~---~~~aWL~~IarN~~~d~~Rk~~~~ 90 (216)
T PRK12533 14 AARGERFRQLVLPHLDAAYNLARWLCGNASDADDVVQEACMRALRFFDSFRGD---NARPWLLAIVRHTWYSEWRRRANA 90 (216)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCcc---chHhHHHHHHHHHHHHHHHhhccc
Confidence 34568999999999999999999999999999999999999999999999853 499999999999999998875421
Q ss_pred cccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCC
Q 008556 396 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVE 475 (561)
Q Consensus 396 IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~ 475 (561)
.... .......+ ..... . ++...
T Consensus 91 ~~~~-----------------------------------------------------~~~~~~~~--~~~~~-~-~~~~~ 113 (216)
T PRK12533 91 HEVA-----------------------------------------------------APDTLDDA--DSLDD-W-QPAGE 113 (216)
T ss_pred cccc-----------------------------------------------------cccccccc--ccccc-c-ccCCC
Confidence 0000 00000000 00000 0 11123
Q ss_pred ChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008556 476 IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 551 (561)
Q Consensus 476 ~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 551 (561)
+|++.+...+....|..+|..||+++|+||.|+|. +++|++|||+.||||.++|+++++||+++||+.+...
T Consensus 114 ~~e~~~~~~e~~~~l~~al~~Lp~~~R~v~~L~y~----eg~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l~~~ 185 (216)
T PRK12533 114 DPLALLLRAEDVRLVNAALAKLPVEYREVLVLREL----EDMSYREIAAIADVPVGTVMSRLARARRRLAALLGGA 185 (216)
T ss_pred CHHHHHHHHHHHHHHHHHHHcCCHHHHhHhhhHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHccc
Confidence 56667777777788999999999999999999998 8999999999999999999999999999999998653
No 83
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=99.81 E-value=1.2e-18 Score=166.60 Aligned_cols=166 Identities=9% Similarity=0.032 Sum_probs=130.2
Q ss_pred hhcHHHHHHHHHHHHHHHHHHHHhhhC--CCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcc
Q 008556 316 HSGNSSREKLINANLRLVVHVAKQYQG--RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHS 393 (561)
Q Consensus 316 ~~G~~Are~LI~~nlrLV~sIArrY~~--~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~s 393 (561)
.++..+++.|+..|.+.|+.++.++.+ +..+++|++||.|+.+|+..++|++.....|.||++.++++.+.++++++.
T Consensus 9 ~~d~~af~~ly~~~~~~l~~~~~~~~~~~~~~~AeDivQevFl~~~~~~~~~~~~~~~~~~~wL~~ia~n~~~d~~Rk~~ 88 (178)
T PRK12529 9 SADRDKVATLYRENHAWLRNWLAYRLRSWGRGVADDLAHDIFLRILASRDGGQREAIRQPRAYLARIANCVLVSWRRRQS 88 (178)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHhcccccccccccCHHHHHHHHHHHHHHHHHHHHH
Confidence 456699999999999999998766665 357899999999999999999998544457999999999999999887542
Q ss_pred cccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCC
Q 008556 394 RTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTG 473 (561)
Q Consensus 394 r~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~ 473 (561)
+.. .. .+. ..+. .+..
T Consensus 89 ~~~------------------~~------------------------------------~~~---------~~~~-~~~~ 104 (178)
T PRK12529 89 LEL------------------AW------------------------------------LEA---------LATL-PEPL 104 (178)
T ss_pred HHh------------------hh------------------------------------hhH---------hhhc-cCcC
Confidence 100 00 000 0000 0011
Q ss_pred CCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008556 474 VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 549 (561)
Q Consensus 474 ~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 549 (561)
..+|++.+...+....|..+|..||+++|.||.|+|. +++|++|||+.||||.++|+..+.||+.+|++.+.
T Consensus 105 ~~~~e~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~----~g~s~~EIA~~lgis~~tVk~~l~rAl~~~~~~~~ 176 (178)
T PRK12529 105 HPSPEQQSVILETLHEIDALLDTLRPRVKQAFLMATL----DGMKQKDIAQALDIALPTVKKYIHQAYVTCLSLMP 176 (178)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhCC
Confidence 1245655665666678999999999999999999998 89999999999999999999999999999998753
No 84
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=99.81 E-value=2.2e-18 Score=165.26 Aligned_cols=171 Identities=20% Similarity=0.286 Sum_probs=136.3
Q ss_pred HHHhhcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhc
Q 008556 313 SELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQH 392 (561)
Q Consensus 313 ~~l~~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~ 392 (561)
....++..+++.++..|.+.++.+|+++.++..+.+||+||+++.+|+++..| ... ..|.||++.+++|.+.+++++.
T Consensus 8 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~dAeDlvQE~~lr~~~~~~~~-~~~-~~~~~wl~~Ia~n~~iD~~R~~ 85 (182)
T COG1595 8 EALRGDRAAFEELLERLRPRLRRLARRLLGDRADAEDLVQETFLRAWRAIDSF-RGR-SSFKAWLYRIARNLAIDRLRKR 85 (182)
T ss_pred HHHhcchHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhc-CCC-CchHHHHHHHHHHHHHHHHHHh
Confidence 34456679999999999999999999999988899999999999999999999 433 4799999999999999999876
Q ss_pred ccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccC
Q 008556 393 SRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADT 472 (561)
Q Consensus 393 sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~ 472 (561)
.+.... .+ +.+ ..+...+.
T Consensus 86 ~r~~~~------------------------------------------------------~~-----~~~--~~~~~~~~ 104 (182)
T COG1595 86 KRRRAR------------------------------------------------------VE-----EAD--LLPEEADP 104 (182)
T ss_pred cccccc------------------------------------------------------cc-----ccc--ccccccCc
Confidence 643211 00 000 00000011
Q ss_pred CCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008556 473 GVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 551 (561)
Q Consensus 473 ~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 551 (561)
..+.. +.+...+....|..+|..||+++|+||.|+|. +|+|++|||+.||||.++|+..++||+++||+.+...
T Consensus 105 ~~~~~-~~~~~~~~~~~l~~al~~Lp~~~R~~~~l~~~----~gls~~EIA~~l~i~~~tVks~l~ra~~~l~~~l~~~ 178 (182)
T COG1595 105 APDLA-ELLLAEEELERLRRALARLPPRQREAFLLRYL----EGLSYEEIAEILGISVGTVKSRLHRARKKLREQLEEA 178 (182)
T ss_pred ccccc-hHHHHHHHHHHHHHHHHhCCHHHhHHhhhHhh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhhc
Confidence 10011 24555667788999999999999999999999 9999999999999999999999999999999988754
No 85
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=99.81 E-value=1.1e-18 Score=165.34 Aligned_cols=166 Identities=17% Similarity=0.153 Sum_probs=128.0
Q ss_pred hhcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccc
Q 008556 316 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT 395 (561)
Q Consensus 316 ~~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~ 395 (561)
.++..+++.|+..|.+.|+.+++++.+ ..+++|++||+++.+|+.++.|++. ..|.+|++..+++.+.+++++..+.
T Consensus 7 ~gd~~a~~~l~~~~~~~l~~~~~~~~~-~~~aeDivQe~~l~l~~~~~~~~~~--~~~~~wl~~ia~n~~~d~~R~~~~~ 83 (175)
T PRK12518 7 RGDRQSFRQLYRRYQQKVRSTLYQLCG-RELLDDLVQEVFLRVWKGLPKLRNP--AYFSTWLYRITWNVATDARRQFAQR 83 (175)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHHHcC-HhHHHHHHHHHHHHHHHhHHhhCCc--ccHHHHHHHHHHHHHHHHHHHhhcc
Confidence 455699999999999999999999875 3689999999999999999999974 4699999999999999998764311
Q ss_pred cccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCC
Q 008556 396 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVE 475 (561)
Q Consensus 396 IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~ 475 (561)
-.. .+... ... . ....
T Consensus 84 ~~~------------------------------------------------------~~~~~-~~~-----~-~~~~--- 99 (175)
T PRK12518 84 PSR------------------------------------------------------IQDDS-LND-----Q-PSRP--- 99 (175)
T ss_pred ccc------------------------------------------------------hhccc-ccc-----c-ccCC---
Confidence 000 00000 000 0 0000
Q ss_pred ChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 008556 476 IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA 552 (561)
Q Consensus 476 ~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~ 552 (561)
.++......+....+..+|+.||+++|+||.++|. +|+|++|||+.||+|..+|++.+.||+++||+.+...+
T Consensus 100 ~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l~~~~ 172 (175)
T PRK12518 100 SDTPDLMQLHYQDLVQQGLQTLSLEHRAVLVLHDL----EDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFLQQQG 172 (175)
T ss_pred CCcHHHHHHHHHHHHHHHHHhCCHHHeeeeeehHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhcc
Confidence 11112222334456889999999999999999998 89999999999999999999999999999999987644
No 86
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=99.80 E-value=1.4e-18 Score=167.20 Aligned_cols=169 Identities=17% Similarity=0.111 Sum_probs=128.2
Q ss_pred HHHHHHh-hcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHH
Q 008556 310 DLKSELH-SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKA 388 (561)
Q Consensus 310 eL~~~l~-~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~ 388 (561)
.|+..+. ++..|++.|+..|.+.++.+++ +.++..+.+|++||.|+.+|+.+++|++. ..|.+|++.++++.+.++
T Consensus 13 ~l~~~~~~gd~~af~~l~~~~~~~l~~~~~-~~~~~~~AeDivQe~flkl~~~~~~~~~~--~~~~~Wl~~Iarn~~~d~ 89 (185)
T PRK09649 13 ALALSAAKGNGRALEAFIKATQQDVWRFVA-YLSDVGSADDLTQETFLRAIGAIPRFSAR--SSARTWLLAIARHVVADH 89 (185)
T ss_pred HHHHHHHccCHHHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHhccccCcc--chHHHHHHHHHHHHHHHH
Confidence 3444444 4559999999999999999995 67888899999999999999999999964 369999999999999999
Q ss_pred HHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhh
Q 008556 389 IFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEI 468 (561)
Q Consensus 389 Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~ 468 (561)
+++..+..+. +.+. . .+.
T Consensus 90 ~Rk~~~~~~~-----------------------------------------------------~~~~-----~----~~~ 107 (185)
T PRK09649 90 IRHVRSRPRT-----------------------------------------------------TRGA-----R----PEH 107 (185)
T ss_pred HHHhcccccc-----------------------------------------------------cccc-----c----hhh
Confidence 9875421000 0000 0 000
Q ss_pred cccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008556 469 TADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 548 (561)
Q Consensus 469 l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 548 (561)
..+. +......+....|..+|..||+++|+||.|+|. +++|++|||+.||+|.++|++.+.||+++||+.+
T Consensus 108 ~~~~-----~~~~~~~e~~~~l~~~l~~Lp~~~r~v~~L~~~----~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~~ 178 (185)
T PRK09649 108 LIDG-----DRHARGFEDLVEVTTMIADLTTDQREALLLTQL----LGLSYADAAAVCGCPVGTIRSRVARARDALLADA 178 (185)
T ss_pred ccCh-----hhhhhhHHHHHHHHHHHHhCCHHHhHHhhhHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence 0000 000011112245788999999999999999998 8999999999999999999999999999999966
Q ss_pred hcCc
Q 008556 549 GGKA 552 (561)
Q Consensus 549 ~~~~ 552 (561)
....
T Consensus 179 ~~~~ 182 (185)
T PRK09649 179 EPDD 182 (185)
T ss_pred Cccc
Confidence 5443
No 87
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=99.80 E-value=1.3e-18 Score=162.55 Aligned_cols=157 Identities=13% Similarity=0.041 Sum_probs=125.8
Q ss_pred HHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHHHH
Q 008556 327 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLL 406 (561)
Q Consensus 327 ~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~~~l 406 (561)
..|.+.|+.+|.++.++..+++|++||+++.+|+++++|++. .|.+|++..++|.+.++++++.+..+.
T Consensus 2 ~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~---~~~~wl~~ia~n~~~d~~Rk~~~~~~~-------- 70 (160)
T PRK09642 2 QTYRHYIFQVIFSILRHEEDAKDVTQEVFVKIHASLPNYQFR---GLKTWMARIATNHAIDYKRKKARENEE-------- 70 (160)
T ss_pred chHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcccccccc---hhHHHHHHHHHHHHHHHHHHhcccccc--------
Confidence 568999999999999999999999999999999999999963 499999999999999999875421000
Q ss_pred HHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHHHHHHHH
Q 008556 407 SKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLM 486 (561)
Q Consensus 407 ~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~le~~e~ 486 (561)
..+. +. ..+... ...++++.+...+.
T Consensus 71 --------------------------------------------~~~~-----~~---~~~~~~--~~~~~~~~~~~~e~ 96 (160)
T PRK09642 71 --------------------------------------------LSLC-----KE---TEENIK--SSHNIEDLLLTKEQ 96 (160)
T ss_pred --------------------------------------------cccc-----hh---hhhhcc--CCCChHHHHHHHHH
Confidence 0000 00 000000 11245556666677
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 008556 487 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA 552 (561)
Q Consensus 487 ~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~ 552 (561)
...|..+|..||+++|+||.|+|. +|+|++|||+.||||..+|++++.||+++||+.+....
T Consensus 97 ~~~l~~~l~~Lp~~~r~v~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~ 158 (160)
T PRK09642 97 KLLIAQKLRELPENYRDVVLAHYL----EEKSYQEIALQEKIEVKTVEMKLYRARKWIKKHWKEEE 158 (160)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHH----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhhhc
Confidence 778999999999999999999998 99999999999999999999999999999999986543
No 88
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=99.80 E-value=1.9e-18 Score=167.06 Aligned_cols=162 Identities=20% Similarity=0.193 Sum_probs=128.8
Q ss_pred hcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhccccc
Q 008556 317 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI 396 (561)
Q Consensus 317 ~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~I 396 (561)
++..++..|+..|.+.++.+|.++.++..+.+|++||.++.+|+..++|+... .|.+|++..++|.+.++++++.+..
T Consensus 7 ~~~~~f~~l~~~~~~~L~~~a~~~~~~~~~AEDivQevfl~~~~~~~~~~~~~--~~~awL~~Ia~n~~~d~~R~~~~~~ 84 (187)
T PRK12516 7 EGTPPFKRELLAALPSLRAFAVSLIGRHDRADDLVQDTIMKAWAKQDHFEVGT--NMKAWLFTILRNEFYSQMRKRGREV 84 (187)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHhhhccCCcc--cHHHHHHHHHHHHHHHHHHhhcCCc
Confidence 34689999999999999999999999999999999999999999999998643 5999999999999999988754210
Q ss_pred ccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCC
Q 008556 397 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEI 476 (561)
Q Consensus 397 RlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~ 476 (561)
.. .+.. +.+.... .
T Consensus 85 ~~------------------------------------------------------~~~~--------~~~~~~~----~ 98 (187)
T PRK12516 85 QD------------------------------------------------------TDGM--------FTEQLAV----H 98 (187)
T ss_pred cc------------------------------------------------------cccc--------cccccCC----C
Confidence 00 0000 0000000 0
Q ss_pred hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 008556 477 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA 552 (561)
Q Consensus 477 pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~ 552 (561)
++. ........|..+|..||+++|+||.|+|. +++|++|||+.||||.++|+.++.||+++||+.+...+
T Consensus 99 ~~~--~~~~~~~~l~~~L~~Lp~~~r~i~~L~~~----~g~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~~~~ 168 (187)
T PRK12516 99 PSQ--YGTLDLQDFRAALDQLPDDQREAIILVGA----SGFAYEEAAEICGCAVGTIKSRVNRARQRLQEILQIEG 168 (187)
T ss_pred cch--hhHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhc
Confidence 110 11122346889999999999999999998 89999999999999999999999999999999987654
No 89
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) 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 in an apparent operon.
Probab=99.80 E-value=1e-18 Score=168.69 Aligned_cols=172 Identities=18% Similarity=0.199 Sum_probs=130.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhccccccc
Q 008556 319 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL 398 (561)
Q Consensus 319 ~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRl 398 (561)
..+++.|+..|.+.|+.+|.++.++..+.+|++||.|+.+|+.+.+|++. ..|.+|++..++|.+.++++++.+....
T Consensus 10 ~~~f~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQevfl~~~~~~~~~~~~--~~~~~wL~~iarN~~~d~~Rk~~~~~~~ 87 (193)
T TIGR02947 10 AQRFERDALEYLDQLYGAALRMTRNPADAEDLVQEAYAKAFSSFHQFKPG--TNLKAWLYRILTNTYINSYRKAQRRPQQ 87 (193)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhcccCCC--CcchHHHHHHHHHHHHHHHHHhcCCccc
Confidence 48999999999999999999999998999999999999999999999864 3699999999999999999876521100
Q ss_pred chhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChh
Q 008556 399 PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPD 478 (561)
Q Consensus 399 P~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pe 478 (561)
. ..+++. .. .+. .... ........++
T Consensus 88 ~-------------------------~~~~~~-----------~~--------~~~----~~~~------~~~~~~~~~e 113 (193)
T TIGR02947 88 S-------------------------DDDDIE-----------DW--------QLA----KAAS------HTSNGLRSAE 113 (193)
T ss_pred c-------------------------cchhhh-----------hh--------hhc----cccc------cccccccchh
Confidence 0 000000 00 000 0000 0000011233
Q ss_pred HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008556 479 ISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 550 (561)
Q Consensus 479 e~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 550 (561)
......+....|..+|..||+++|+||.|+|. +++|++|||+.||||..+|+.++.||+++||+.+..
T Consensus 114 ~~~~~~~~~~~l~~~l~~Lp~~~r~i~~L~~~----~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~ 181 (193)
T TIGR02947 114 LEALDGLPDQDIKDALQGLPEEFRQAVYLADV----EGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQLVD 181 (193)
T ss_pred HHHHhhhhHHHHHHHHHhCCHHHhhheeehhh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 33333344567899999999999999999998 899999999999999999999999999999998864
No 90
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=99.80 E-value=4e-18 Score=167.09 Aligned_cols=166 Identities=20% Similarity=0.287 Sum_probs=135.8
Q ss_pred cHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccc
Q 008556 318 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR 397 (561)
Q Consensus 318 G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IR 397 (561)
+..++++|+..|.+.++.++.++.++..+.+|++||+++.+|+...+|++ + .|.+|++..+|+.+.+++++..+ .+
T Consensus 26 d~~a~~~l~~~~~~~L~~~~~~~~~~~~~AEDivQEvflkl~~~~~~~~~--~-~~~~wL~~iarn~~~d~~Rk~~~-~~ 101 (203)
T PRK09647 26 TMPSWEELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSLQNYQP--G-TFEGWLHRITTNLFLDMVRRRAR-IR 101 (203)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCC--c-ccHHHHHHHHHHHHHHHHHhccc-Cc
Confidence 45899999999999999999999999999999999999999999999985 3 59999999999999999987542 00
Q ss_pred cchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCCh
Q 008556 398 LPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIP 477 (561)
Q Consensus 398 lP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~p 477 (561)
. ..++ ++ + +.... ...+|
T Consensus 102 ~----------------------------------------------------~~~~-----~~---~-~~~~~-~~~~~ 119 (203)
T PRK09647 102 M----------------------------------------------------EALP-----ED---Y-DRVPG-DEPNP 119 (203)
T ss_pred c----------------------------------------------------cccc-----cc---c-cccCC-CCCCH
Confidence 0 0000 00 0 00011 12245
Q ss_pred hHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 008556 478 DISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS 553 (561)
Q Consensus 478 ee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~l 553 (561)
+..+...+....|..+|..||+++|+||.|+|. ++++++|||+.||||..+|++.+.||+++||+.+...+-
T Consensus 120 ~~~~~~~~~~~~l~~~L~~L~~~~r~v~~L~~~----~g~s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l~~~~~ 191 (203)
T PRK09647 120 EQIYHDARLDPDLQAALDSLPPEFRAAVVLCDI----EGLSYEEIAATLGVKLGTVRSRIHRGRQQLRAALAAHAP 191 (203)
T ss_pred HHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhch
Confidence 556666777778999999999999999999998 899999999999999999999999999999999876543
No 91
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=99.80 E-value=2.5e-18 Score=163.11 Aligned_cols=163 Identities=14% Similarity=0.092 Sum_probs=127.7
Q ss_pred hcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhccccc
Q 008556 317 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI 396 (561)
Q Consensus 317 ~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~I 396 (561)
++..++..|+..|.+.|+.+|.++.++..+.+|++||+++.+|+. ..|+.. ..|.+|++.+++|.+.++++++.+..
T Consensus 7 ~~~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQevflk~~~~-~~~~~~--~~~~~wL~~Iarn~~~d~~Rk~~~~~ 83 (172)
T PRK12523 7 PHSELVGALYRDHRGWLLAWLRRNVACRQRAEDLSQDTFVRLLGR-PELPTP--REPRAFLAAVAKGLMFDHFRRAALEQ 83 (172)
T ss_pred CCcHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHcc-cccCcc--hhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334999999999999999999999999999999999999999987 446543 36999999999999999998753100
Q ss_pred ccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCC
Q 008556 397 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEI 476 (561)
Q Consensus 397 RlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~ 476 (561)
... .++ . . ........
T Consensus 84 ------------------~~~---------~~~------------------------~------------~-~~~~~~~~ 99 (172)
T PRK12523 84 ------------------AYL---------AEL------------------------A------------L-VPEAEQPS 99 (172)
T ss_pred ------------------HHH---------HHH------------------------h------------h-cccccCCC
Confidence 000 000 0 0 00000113
Q ss_pred hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008556 477 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 550 (561)
Q Consensus 477 pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 550 (561)
|+......+....|..+|..||+++|+||.|+|. +++|++|||+.||||.++|++.+.||+++||..+..
T Consensus 100 ~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~L~~~----~g~s~~EIA~~lgis~~tV~~~l~ra~~~~~~~l~~ 169 (172)
T PRK12523 100 PEEQHLILEDLKAIDRLLGKLSSKARAAFLYNRL----DGMGHAEIAERLGVSVSRVRQYLAQGLRQCYIALYG 169 (172)
T ss_pred hHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhcC
Confidence 4444444444567999999999999999999998 899999999999999999999999999999998754
No 92
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=99.80 E-value=2.8e-18 Score=161.49 Aligned_cols=158 Identities=15% Similarity=0.107 Sum_probs=130.2
Q ss_pred HHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchh
Q 008556 322 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN 401 (561)
Q Consensus 322 re~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~ 401 (561)
++.|+..|.+.|+.+|+++.++..+.+|++||+++.+|+++++|++. .|.+|++..+++.+.+++++..+....
T Consensus 3 ~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~---~~~~wL~~i~~n~~~d~~R~~~~~~~~--- 76 (165)
T PRK09644 3 IEEIYKMYINDVYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDYDNQ---KVKPWLFKVAYHTFIDFVRKEKKVSFV--- 76 (165)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcccc---chHHHHHHHHHHHHHHHHHhhhhcccc---
Confidence 57899999999999999999999999999999999999999999863 599999999999999999875421100
Q ss_pred HHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHHH
Q 008556 402 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISV 481 (561)
Q Consensus 402 ~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~l 481 (561)
..+++ +.+.+ ..|++.+
T Consensus 77 -----------------------~~~~~-------------------------------------~~~~~---~~~~~~~ 93 (165)
T PRK09644 77 -----------------------GTDEI-------------------------------------EAIQA---ESTEEYV 93 (165)
T ss_pred -----------------------chhHH-------------------------------------hhhcc---cChHHHH
Confidence 00000 00000 1345555
Q ss_pred HHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 008556 482 QKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA 552 (561)
Q Consensus 482 e~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~ 552 (561)
...+....|..+|..||+++|+||.++|. ++++++|||+.||+|.++|+..+.||+++||+.+....
T Consensus 94 ~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~~~~ 160 (165)
T PRK09644 94 VAKNSYEKLIQIIHTLPVIEAQAILLCDV----HELTYEEAASVLDLKLNTYKSHLFRGRKRLKALLKEEK 160 (165)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHHHhHHH----hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhh
Confidence 55666678999999999999999999998 89999999999999999999999999999999987543
No 93
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=99.79 E-value=2.6e-18 Score=160.69 Aligned_cols=158 Identities=19% Similarity=0.211 Sum_probs=127.8
Q ss_pred hcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhccccc
Q 008556 317 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI 396 (561)
Q Consensus 317 ~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~I 396 (561)
|+..+++.|+..|.+.|+.+|.++.++..+.+|++||+++.+|++.++|+. ...|.+|++..+++.+.+++++..+.
T Consensus 3 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~~~~~~~~~~~--~~~~~~wl~~i~~n~~~d~~rk~~~~- 79 (162)
T TIGR02983 3 ATEEEFTAFVAARYPRLLRTAYLLTGDPHEAEDLVQEALVRTYVRWDRIRD--PDAPDAYVRRVLVNLARSRWRRRRLL- 79 (162)
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhcCC--cccHHHHHHHHHHHHHHHHHHhhccc-
Confidence 566999999999999999999999999999999999999999999999964 34799999999999999998765410
Q ss_pred ccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCC
Q 008556 397 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEI 476 (561)
Q Consensus 397 RlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~ 476 (561)
.+ . +... .+..
T Consensus 80 ~~-----------------------------------------------------~-~~~~------------~~~~--- 90 (162)
T TIGR02983 80 EL-----------------------------------------------------P-TREL------------PDAA--- 90 (162)
T ss_pred cc-----------------------------------------------------c-cccc------------Cccc---
Confidence 00 0 0000 0000
Q ss_pred hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008556 477 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 550 (561)
Q Consensus 477 pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 550 (561)
+.......+..+.|..+|..||+++|+||.|+|. +++|.+|||+.||+|.++|++.+.||+++||+.+..
T Consensus 91 ~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~~ 160 (162)
T TIGR02983 91 APDPAPDVALRAALARALRRLPARQRAVVVLRYY----EDLSEAQVAEALGISVGTVKSRLSRALARLRELLEE 160 (162)
T ss_pred CCccchhHHHHHHHHHHHHhCCHHHHHHhhhHHH----hcCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhcC
Confidence 0001122344567889999999999999999998 899999999999999999999999999999998754
No 94
>TIGR02895 spore_sigI RNA polymerase sigma-I factor. Members of this sigma factor protein family are strictly limited to endospore-forming species in the Firmicutes lineage of bacteria, but are not universally present among such species. Sigma-I was shown to be induced by heat shock (PubMed:11157964) in Bacillus subtilis and is suggested by its phylogenetic profile to be connected to the program of sporulation (PubMed:16311624).
Probab=99.79 E-value=7.5e-18 Score=167.16 Aligned_cols=118 Identities=18% Similarity=0.265 Sum_probs=104.0
Q ss_pred HhhcHHHHHHHHHHHHHHHHHHHHhhhCCC--CCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhc
Q 008556 315 LHSGNSSREKLINANLRLVVHVAKQYQGRG--ISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQH 392 (561)
Q Consensus 315 l~~G~~Are~LI~~nlrLV~sIArrY~~~g--~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~ 392 (561)
++.|+..+++||..|.|+|.++|++|.++. .+.+|++|+|+||||+|+++|||++|.+|.|||.+||++.|.+++|+.
T Consensus 4 ~~~gd~~~e~LI~~Y~plI~~~a~~~~~~~~~~e~dDlvQ~glial~eAi~~yd~~kg~~F~sya~~~Ir~~i~dylRk~ 83 (218)
T TIGR02895 4 IQPGNEEREELIRQYKPFIAKIVSSVCGRYIDTKSDDELSIGLIAFNEAIESYDSNKGKSFLSFAKLIIKRRLIDYIRKN 83 (218)
T ss_pred hhcCChHHHHHHHHhHHHHHHHHHHHHccCCCCChhHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHhc
Confidence 345554599999999999999999998765 589999999999999999999999999999999999999999999988
Q ss_pred c---cccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHH
Q 008556 393 S---RTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARR 432 (561)
Q Consensus 393 s---r~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~ 432 (561)
. +.+++|.........+..+...+..+.++.|+.+||+..
T Consensus 84 ~k~~~~v~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~eEI~~~ 126 (218)
T TIGR02895 84 QKYQNLLYLDEDYDENPLEFNKSMEEYRNEIENENRRLEILEY 126 (218)
T ss_pred ccccCeeeCCchHHHHHHHHHHHHHHHHHHHccccHHHHHHHH
Confidence 7 577899766666667777778888899999999999754
No 95
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=99.78 E-value=7e-18 Score=158.00 Aligned_cols=157 Identities=15% Similarity=0.099 Sum_probs=124.1
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccc
Q 008556 320 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP 399 (561)
Q Consensus 320 ~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP 399 (561)
.|+++|+..|.+.|+.++.++.++..+.+|++||+++.+|+..+.|++ ..|.+|.+.++++.+.+++++..+.
T Consensus 4 ~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~flk~~~~~~~~~~---~~~~~wl~~i~~n~~~d~~R~~~~~---- 76 (161)
T PRK12528 4 ATVEGLYSAHHHWLTGWLRRRLGCPQSAADLAQDTFVKVLVARETAQI---IEPRAFLTTIAKRVLCNHYRRQDLE---- 76 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHhccccccc---cCHHHHHHHHHHHHHHHHHHHHHHH----
Confidence 689999999999999999999999999999999999999999988864 2599999999999999998764310
Q ss_pred hhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhH
Q 008556 400 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDI 479 (561)
Q Consensus 400 ~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee 479 (561)
... ..++ + + ..+.....++.
T Consensus 77 --------------~~~---------~~~~------------------------~------------~-~~~~~~~~~~~ 96 (161)
T PRK12528 77 --------------RAY---------LEAL------------------------A------------Q-LPERVAPSEEE 96 (161)
T ss_pred --------------Hhh---------HHHh------------------------h------------c-cccccCCCHHH
Confidence 000 0000 0 0 00000112333
Q ss_pred HHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008556 480 SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 547 (561)
Q Consensus 480 ~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 547 (561)
.....+....|..+|..||+++|+||.|+|. +|+|++|||+.||+|.++|+..+.||+++||..
T Consensus 97 ~~~~~~~~~~l~~~l~~L~~~~r~v~~L~~~----~g~s~~EIA~~l~is~~tV~~~l~ra~~~~~~~ 160 (161)
T PRK12528 97 RAIILETLVELDQLLDGLPPLVKRAFLLAQV----DGLGYGEIATELGISLATVKRYLNKAAMRCYFA 160 (161)
T ss_pred HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhc
Confidence 3333344567899999999999999999998 899999999999999999999999999999864
No 96
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=99.78 E-value=8.9e-18 Score=158.27 Aligned_cols=159 Identities=16% Similarity=0.158 Sum_probs=126.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhccccccc
Q 008556 319 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL 398 (561)
Q Consensus 319 ~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRl 398 (561)
...+..++..|.+.|+.+|+++.++..+++|++||+++.+|+..++|++.. .|.+|++..++|.+.+++++..+....
T Consensus 5 ~~~f~~~~~~~~~~l~~~a~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~R~~~~~~~~ 82 (164)
T PRK12547 5 SKNFKQELLLALPALRAFAVSLSSKHDKAEDLVQDTLMKAWAKQDSFEMGT--NLKAWLFTILRNEFYSQMRKRGREVQD 82 (164)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHhhhhcCCcc--cHHHHHHHHHHHHHHHHHHhhcccccc
Confidence 468899999999999999999999999999999999999999999998643 599999999999999998865421000
Q ss_pred chhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChh
Q 008556 399 PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPD 478 (561)
Q Consensus 399 P~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pe 478 (561)
.+... .. . .+ ..++
T Consensus 83 ------------------------------------------------------~~~~~--~~-----~--~~---~~~~ 96 (164)
T PRK12547 83 ------------------------------------------------------SDGVF--TA-----R--VA---VHPA 96 (164)
T ss_pred ------------------------------------------------------ccccc--cc-----c--CC---CCch
Confidence 00000 00 0 00 0111
Q ss_pred HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008556 479 ISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 551 (561)
Q Consensus 479 e~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 551 (561)
. ........|..+|..||+++|+||.|+|. +++|++|||+.||||.++|++.+.||+++||..+.-.
T Consensus 97 ~--~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~ 163 (164)
T PRK12547 97 Q--YGSLDLQDFKKALNLLSADQREAIILIGA----SGFSYEDAAAICGCAVGTIKSRVSRARNRLQELLKVD 163 (164)
T ss_pred h--hhHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHhcc
Confidence 1 11122456889999999999999999998 8999999999999999999999999999999987643
No 97
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=99.78 E-value=8.4e-18 Score=162.59 Aligned_cols=181 Identities=18% Similarity=0.160 Sum_probs=132.2
Q ss_pred HHHHHHHHHHHHHHHHhhhCCCCC-HHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchh
Q 008556 323 EKLINANLRLVVHVAKQYQGRGIS-LHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN 401 (561)
Q Consensus 323 e~LI~~nlrLV~sIArrY~~~g~~-~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~ 401 (561)
+..+..|.+.|+.+|+++.++..+ .+|++||+++.+|+++++|++. ..|.+|++..+++.+.++++++.+.......
T Consensus 8 ~~~~~~~~~~l~~~a~~~~~~~~~~AEDivQevfl~~~~~~~~~~~~--~~~~~wL~~Ia~n~~~d~~Rk~~~~~~~~~~ 85 (195)
T PRK12532 8 DAELIESRKLLLHFARLQLPDHPDLAEDLVQETLLSAYSAGDSFQGR--ALVNSWLFAILKNKIIDALRQIGRQRKVFTL 85 (195)
T ss_pred hhhHHHHHHHHHHHHHHHcCChhhhHHHHHHHHHHHHHHhccccccc--chHHHHHHHHHHHHHHHHHHHhccccccccc
Confidence 456778999999999999998888 9999999999999999999864 3799999999999999999876532110000
Q ss_pred HHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHHH
Q 008556 402 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISV 481 (561)
Q Consensus 402 ~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~l 481 (561)
. ..+.+ .... ... ...+ .....+... ....+|+..+
T Consensus 86 ~----------------------~~~~~-----------~~~~------~~~---~~~~-~~~~~~~~~-~~~~~~e~~~ 121 (195)
T PRK12532 86 L----------------------DDELL-----------DEAF------ESH---FSQN-GHWTPEGQP-QHWNTPEKSL 121 (195)
T ss_pred c----------------------ccccc-----------chhh------hhh---hccc-cccccccCc-cccCCHHHHH
Confidence 0 00000 0000 000 0000 000000000 1123567777
Q ss_pred HHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 008556 482 QKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS 553 (561)
Q Consensus 482 e~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~l 553 (561)
...+....+..+|..||+++|+||.|+|. +++|++|||+.||+|..+|++.++||+++||+++....+
T Consensus 122 ~~~e~~~~l~~~l~~L~~~~r~i~~L~~~----~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~~~ 189 (195)
T PRK12532 122 NNNEFQKILQSCLYNLPENTARVFTLKEI----LGFSSDEIQQMCGISTSNYHTIMHRARESLRQCLQIKWF 189 (195)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHhhhHHH----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 77777788999999999999999999998 899999999999999999999999999999999876543
No 98
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=99.78 E-value=9e-18 Score=163.83 Aligned_cols=181 Identities=14% Similarity=0.141 Sum_probs=130.6
Q ss_pred HHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHH
Q 008556 324 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIY 403 (561)
Q Consensus 324 ~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~ 403 (561)
.++..|.+.++.+|+++.++..+.+|++||.|+.+|+.+++|++.. .|.+|++.+++|.+.++++++.+...++..
T Consensus 12 ~~~~~~~~~l~~~~~~~~~d~~~AEDivQe~fl~~~~~~~~~~~~~--~~~~WL~~IarN~~~d~~Rk~~r~~~~~~~-- 87 (201)
T PRK12545 12 AYLAQLRHDLLRFARLQLRDADAAEDAVQEALAAAWSQAGRFAGQS--AHKTWVFGILRNKLIDTLRARQRTVNLSAL-- 87 (201)
T ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhccccc--hHHHHHHHHHHHHHHHHHHhhccccccccc--
Confidence 4588999999999999999999999999999999999999999753 599999999999999999876532111000
Q ss_pred HHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHHHHH
Q 008556 404 TLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQK 483 (561)
Q Consensus 404 ~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~le~ 483 (561)
..++. . ...++............+..++ ....++.....
T Consensus 88 ----------------------~~~~~------~------------~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~ 126 (201)
T PRK12545 88 ----------------------DAELD------G------------EALLDRELFKDNGHWAAHAKPR-PWPKPETILQQ 126 (201)
T ss_pred ----------------------ccccc------h------------hhhhhhhhhcccccccccccCc-CCCCHHHHHHH
Confidence 00000 0 0000000000000000000011 11245555555
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 008556 484 QLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS 553 (561)
Q Consensus 484 ~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~l 553 (561)
.+....|..+|..||+++|+||.|+|+ +++|++|||+.||+|.++|+..+.||+++||+++...++
T Consensus 127 ~~~~~~l~~~L~~Lp~~~r~v~~L~~~----eg~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~~~~ 192 (201)
T PRK12545 127 QQFWTLFETCLDHLPEQIGRVFMMREF----LDFEIDDICTELTLTANHCSVLLYRARTRLRTCLSEKGL 192 (201)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 566677899999999999999999998 899999999999999999999999999999999975544
No 99
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=99.78 E-value=1.2e-17 Score=156.52 Aligned_cols=157 Identities=15% Similarity=0.120 Sum_probs=124.1
Q ss_pred cHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccc
Q 008556 318 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR 397 (561)
Q Consensus 318 G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IR 397 (561)
...+++.++..|.+.|+.+|.++.++..+++|++||+++.+|+..++|++. .|.||++..+++.+.+++++..+...
T Consensus 3 ~~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDv~Qe~f~~~~~~~~~~~~~---~~~~wl~~i~~n~~~d~~R~~~~~~~ 79 (161)
T PRK12541 3 RKQSLEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYKGE---EIRPWLFTIAYNAFIDWYRKEKKYKT 79 (161)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhHHHccCC---ChHHHHHHHHHHHHHHHHHhcccccc
Confidence 357899999999999999999999999999999999999999999999863 49999999999999999987652100
Q ss_pred cchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCCh
Q 008556 398 LPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIP 477 (561)
Q Consensus 398 lP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~p 477 (561)
+ ..+ +.........+
T Consensus 80 ~-----------------------------------------------------~~~------------~~~~~~~~~~~ 94 (161)
T PRK12541 80 T-----------------------------------------------------TIE------------EFHLPNVPSTE 94 (161)
T ss_pred c-----------------------------------------------------chh------------hhhccCCCCcH
Confidence 0 000 00000000112
Q ss_pred hHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008556 478 DISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 547 (561)
Q Consensus 478 ee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 547 (561)
+......+. ..+..+|..||+++|.||.|+|. +++|++|||+.||+|..+|++.+.||+++||+.
T Consensus 95 ~~~~~~~~~-~~~~~~l~~L~~~~r~v~~l~~~----~~~s~~eIA~~lgis~~tv~~~l~Rar~~L~~~ 159 (161)
T PRK12541 95 HEYFIKHEI-ASWLDSLSSLPLERRNVLLLRDY----YGFSYKEIAEMTGLSLAKVKIELHRGRKETKSI 159 (161)
T ss_pred HHHHHHhHH-HHHHHHHHHCCHHHHHHhhhHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 222222233 34567899999999999999998 899999999999999999999999999999974
No 100
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=99.78 E-value=1.1e-17 Score=161.68 Aligned_cols=176 Identities=16% Similarity=0.118 Sum_probs=130.7
Q ss_pred HHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhH
Q 008556 323 EKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENI 402 (561)
Q Consensus 323 e~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~ 402 (561)
+.-|..|.+.++.+|.++.++..+++|++||.|+.+|+.+++|++.. +|.+|++..++|.+.++++++.+...... .
T Consensus 10 ~~~~~~~~~~l~~~~~~~~~d~~~AeDivQe~flk~~~~~~~~~~~~--~~~~wL~~Ia~n~~~d~~Rk~~~~~~~~~-~ 86 (189)
T PRK12530 10 SLEIEEIRLQMLKFATLQLKDADLAEDVVQEALVSAYKNADSFKGQS--ALKTWIFAILKNKIIDLIRYRKRFVNESE-L 86 (189)
T ss_pred HHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHhchhccCCc--cHHHHHHHHHHHHHHHHHHhhccCCCccc-c
Confidence 34577889999999999999989999999999999999999998653 69999999999999999987653211000 0
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHHHH
Q 008556 403 YTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQ 482 (561)
Q Consensus 403 ~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~le 482 (561)
. .+. .+.... +.......+.........|+..+.
T Consensus 87 ------------------~-----~~~-------------------~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~ 120 (189)
T PRK12530 87 ------------------I-----EED-------------------SPNSFF----DEKGHWKPEYYEPSEWQEVENTVY 120 (189)
T ss_pred ------------------c-----ccc-------------------cchhhh----cccccccccccCCccccCHHHHHH
Confidence 0 000 000000 000000000000111235666677
Q ss_pred HHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008556 483 KQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 551 (561)
Q Consensus 483 ~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 551 (561)
..+....|..+|+.||+++|+||.|+|. +++|++|||+.||+|.++|+.+++||+++||+++...
T Consensus 121 ~~~~~~~l~~~l~~Lp~~~R~v~~L~~~----~g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~~ 185 (189)
T PRK12530 121 KEEFWLIFEACLNHLPAQQARVFMMREY----LELSSEQICQECDISTSNLHVLLYRARLQLQACLSKN 185 (189)
T ss_pred HHHHHHHHHHHHHhCCHHHHHHHhHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 7777788999999999999999999998 8999999999999999999999999999999998654
No 101
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=99.78 E-value=1.7e-17 Score=162.94 Aligned_cols=180 Identities=18% Similarity=0.215 Sum_probs=133.6
Q ss_pred HHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchh
Q 008556 322 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN 401 (561)
Q Consensus 322 re~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~ 401 (561)
-..++..|.+.|+.+|+++.++..+.+|++||+++.+|+.+.+|++. .+|.+|++.++++.+.+++++..+....+..
T Consensus 20 ~~~~~~~~~~~l~~~~~~~~~d~~~AEDivQEvfikl~~~~~~~~~~--~~~~~WL~~IarN~~~d~~Rk~~~~~~~~~~ 97 (206)
T PRK12544 20 DPVFLEDLRKQMIKFATLQLSDLHLAEDAVQEALIGALKNADSFAGR--AAFKTWVFAILKNKIIDLLRQKKRHVSASSL 97 (206)
T ss_pred hHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHHHHHHHHhhccccccccc
Confidence 46789999999999999999999999999999999999999999864 4699999999999999999876532111100
Q ss_pred HHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHHH
Q 008556 402 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISV 481 (561)
Q Consensus 402 ~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~l 481 (561)
. . .... ...+..+. + ................|+..+
T Consensus 98 ~------------------~--~~~~---------~~~~~~~~--------------~-~~~~~~~~~~~~~~~~~e~~~ 133 (206)
T PRK12544 98 L------------------R--DEEE---------EEDFEELF--------------D-ESGHWQKDERPQAWGNPEESL 133 (206)
T ss_pred c------------------c--ccch---------hhHHHHhh--------------c-ccccccccccccccCCHHHHH
Confidence 0 0 0000 00000000 0 000000000001113566667
Q ss_pred HHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008556 482 QKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 551 (561)
Q Consensus 482 e~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 551 (561)
...+....+..+|..||+++|+||.|+|. ++++++|||+.||+|..+|++.+.||+++||+.+...
T Consensus 134 ~~~e~~~~l~~~L~~L~~~~r~v~~L~~~----~g~s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l~~~ 199 (206)
T PRK12544 134 EQEQFWRIFEACLDGLPAKYARVFMMREF----IELETNEICHAVDLSVSNLNVLLYRARLRLRECLENK 199 (206)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHH
Confidence 77777778999999999999999999998 8999999999999999999999999999999998754
No 102
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=99.78 E-value=1e-17 Score=161.89 Aligned_cols=178 Identities=12% Similarity=0.132 Sum_probs=132.7
Q ss_pred HHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhH
Q 008556 323 EKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENI 402 (561)
Q Consensus 323 e~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~ 402 (561)
.+.+..|.+.|+.+|+++.++..+.+|++||+++.+|+...+|++. .+|.+|++..+++.+.++++++.+....+. +
T Consensus 5 ~~~~~~~~~~l~~~~~~~~~~~~dAeDivQevfl~l~~~~~~~~~~--~~~~~wL~~iarn~~~d~~R~~~r~~~~~~-~ 81 (188)
T TIGR02943 5 PQELEQLRRDLLRFARLQLRDRDLAEDAVQETLLAALSHRDSFAGR--SALKTWLFAILKNKIIDALRAKGREVKVSD-L 81 (188)
T ss_pred HHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhccc--cHHHHHHHHHHHHHHHHHHHhhcccCCccc-c
Confidence 4578889999999999999999999999999999999999999965 479999999999999999987653211100 0
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHHHH
Q 008556 403 YTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQ 482 (561)
Q Consensus 403 ~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~le 482 (561)
. .+. ..-.++... ...+....+...+ ....|+..+.
T Consensus 82 ------------------~-----~~~-------------------~~~~~~~~~-~~~~~~~~~~~~~-~~~~~e~~~~ 117 (188)
T TIGR02943 82 ------------------D-----DEL-------------------DDEAFNALF-TQNGHWAQHGQPQ-HWNTPEKQLE 117 (188)
T ss_pred ------------------c-----ccc-------------------ccchhhhhh-ccccchhcccccc-ccCCHHHHHH
Confidence 0 000 000000000 0000000011111 1235666777
Q ss_pred HHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008556 483 KQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 551 (561)
Q Consensus 483 ~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 551 (561)
..+....+..+|..||+++|+||.++|. ++++++|||+.||+|.++|++++.||+++||+++...
T Consensus 118 ~~e~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l~~~ 182 (188)
T TIGR02943 118 NKEFWEVFEACLYHLPEQTARVFMMREV----LGFESDEICQELEISTSNCHVLLYRARLSLRACLSIN 182 (188)
T ss_pred HHHHHHHHHHHHHhCCHHHHHHHHHHHH----hCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 7777788999999999999999999998 8999999999999999999999999999999998754
No 103
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=99.77 E-value=1.4e-17 Score=174.48 Aligned_cols=187 Identities=18% Similarity=0.211 Sum_probs=135.3
Q ss_pred HHHHHHhhc-HHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHH
Q 008556 310 DLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKA 388 (561)
Q Consensus 310 eL~~~l~~G-~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~ 388 (561)
+|+..+..| ..++++|+..|.+.|+.+|+++.++..+.+|++||.++.+|+.+++|++. ..|.+|++.+++|.+.++
T Consensus 8 ~l~~~~~~gd~~af~~l~~~y~~~l~~~~~~~~~~~~dAEDivQevfl~~~~~~~~~~~~--~~~~~wL~~Ia~n~~~d~ 85 (339)
T PRK08241 8 ALLARAAAGDRDAFAALVEPHRRELLAHCYRMLGSVHDAEDAVQETLLRAWRGYDRFEGR--SSLRTWLYRIATNVCLDA 85 (339)
T ss_pred HHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHhhhhccccc--cchHHHHHHHHHHHHHHH
Confidence 455555544 59999999999999999999999998999999999999999999999853 369999999999999999
Q ss_pred HHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhh
Q 008556 389 IFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEI 468 (561)
Q Consensus 389 Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~ 468 (561)
++++.+.. .+.. .+ .+. .........+......+.
T Consensus 86 ~Rk~~~~~-~~~~------------------~~-~~~-------------------------~~~~~~~~~~~~~~~~~~ 120 (339)
T PRK08241 86 LEGRARRP-LPTD------------------LG-APA-------------------------ADPVDELVERPEVPWLEP 120 (339)
T ss_pred HHhhcccc-Cccc------------------cC-CCc-------------------------CcccccccccccccccCC
Confidence 98754210 0000 00 000 000000000000000011
Q ss_pred cccC----CCCChhHHHHHHH-HHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 008556 469 TADT----GVEIPDISVQKQL-MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYR 543 (561)
Q Consensus 469 l~d~----~~~~pee~le~~e-~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkK 543 (561)
+.+. ...+|++.+...+ ....|..+|..||+++|+||.|+|. +++|++|||++||+|..+|++++.||+++
T Consensus 121 ~~~~~~~~~~~~~e~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L~~~----~g~s~~EIA~~lgis~~tVk~~l~RAr~~ 196 (339)
T PRK08241 121 YPDALLDPAAADPAARVVARESVRLAFVAALQHLPPRQRAVLILRDV----LGWSAAEVAELLDTSVAAVNSALQRARAT 196 (339)
T ss_pred CCcccccccCCChHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhhHHh----hCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 1110 1235665555444 3456899999999999999999998 89999999999999999999999999999
Q ss_pred HHHH
Q 008556 544 LKQS 547 (561)
Q Consensus 544 LR~~ 547 (561)
||+.
T Consensus 197 Lr~~ 200 (339)
T PRK08241 197 LAER 200 (339)
T ss_pred Hhhc
Confidence 9983
No 104
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=99.77 E-value=1.8e-17 Score=155.37 Aligned_cols=160 Identities=19% Similarity=0.183 Sum_probs=128.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhccccccc
Q 008556 319 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL 398 (561)
Q Consensus 319 ~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRl 398 (561)
+.+++.|+..|.+.|+.+|+++.++..+.+|++||+++.+|++ .|+. +..|.+|++..+++.+.+++++..+..+.
T Consensus 2 ~~~f~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fi~~~~~--~~~~--~~~~~~wl~~i~rn~~~d~~rk~~~~~~~ 77 (166)
T PRK09639 2 DETFEDLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLYRS--DFKG--IENEKGWLIKSARNVAYNYLRSEKRRRAR 77 (166)
T ss_pred chHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH--hccc--ccchHHHHHHHHHHHHHHHHHHhcccccc
Confidence 3689999999999999999999999999999999999999999 6764 34699999999999999999875421100
Q ss_pred chhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChh
Q 008556 399 PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPD 478 (561)
Q Consensus 399 P~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pe 478 (561)
. +. .....+. + ....|+
T Consensus 78 ~------------------------------------------------------~~------~~~~~~~--~-~~~~~e 94 (166)
T PRK09639 78 I------------------------------------------------------LG------EFQWQEV--D-NEPSPE 94 (166)
T ss_pred c------------------------------------------------------cc------hhhhhhc--c-CCCChH
Confidence 0 00 0000000 1 122566
Q ss_pred HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008556 479 ISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 550 (561)
Q Consensus 479 e~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 550 (561)
+.....+....|..+|..||+++|.||.++| +|++++|||+.||+|..+|+..+.||+++||+.+..
T Consensus 95 ~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~-----~g~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l~~ 161 (166)
T PRK09639 95 EIWIRKEEITKVQEVLAKMTERDRTVLLLRF-----SGYSYKEIAEALGIKESSVGTTLARAKKKFRKIYEQ 161 (166)
T ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 6666666777899999999999999999999 479999999999999999999999999999998864
No 105
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=99.77 E-value=1.8e-17 Score=161.40 Aligned_cols=169 Identities=17% Similarity=0.099 Sum_probs=128.8
Q ss_pred HHHHHh-hcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHH
Q 008556 311 LKSELH-SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAI 389 (561)
Q Consensus 311 L~~~l~-~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~I 389 (561)
|+..+. ++..+++.|+..|.+.++.+++ +.++..+.+|++||.++.+|+..++|++. ..|.+|++..+++.+.+++
T Consensus 15 l~~~~~~~d~~a~~~l~~~y~~~l~~~~~-~~~~~~~AEDivQevflkl~~~~~~~~~~--~~~~~WL~~Iarn~~id~~ 91 (196)
T PRK12535 15 LALAAGRGDRAALTEFIRETQDDVWRLLA-HLGGHDIADDLTQETYLRVMSALPRFAAR--SSARTWLLSLARRVWVDNI 91 (196)
T ss_pred HHHHHHcCCHHHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHHhhhcCCc--ccHHHHHHHHHHHHHHHHH
Confidence 444443 4559999999999999999975 57888899999999999999999999864 3699999999999999999
Q ss_pred HhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhc
Q 008556 390 FQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEIT 469 (561)
Q Consensus 390 r~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l 469 (561)
+++.+..+. ..+ .. . ...+
T Consensus 92 Rk~~~~~~~-----------------------------------------------------~~~-~~-~----~~~~-- 110 (196)
T PRK12535 92 RHDMARPRK-----------------------------------------------------SAT-EY-E----DAAA-- 110 (196)
T ss_pred HhhccCCCc-----------------------------------------------------ccc-cc-c----cccc--
Confidence 875421100 000 00 0 0000
Q ss_pred ccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008556 470 ADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 549 (561)
Q Consensus 470 ~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 549 (561)
.. ..++..... .....|..+|..||+++|+||.|+|. +++|++|||+.||+|.++|++.+.||+++||+.+.
T Consensus 111 --~~-~~~~~~~~~-~~~~~l~~~l~~Lp~~~r~v~~l~~~----~g~s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~ 182 (196)
T PRK12535 111 --TT-ASNETTGSW-SEWIDVRTLIDALPPERREALILTQV----LGYTYEEAAKIADVRVGTIRSRVARARADLIAATA 182 (196)
T ss_pred --cc-CCcchhHHH-HHHHHHHHHHHcCCHHHHHHhhhHHH----hCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhc
Confidence 00 111111111 12346889999999999999999998 89999999999999999999999999999999886
Q ss_pred cC
Q 008556 550 GK 551 (561)
Q Consensus 550 ~~ 551 (561)
..
T Consensus 183 ~~ 184 (196)
T PRK12535 183 TG 184 (196)
T ss_pred cc
Confidence 54
No 106
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=99.77 E-value=1.7e-17 Score=172.46 Aligned_cols=183 Identities=16% Similarity=0.171 Sum_probs=134.2
Q ss_pred hcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhccccc
Q 008556 317 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI 396 (561)
Q Consensus 317 ~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~I 396 (561)
|+..+++.|+..|.+.++.+|.++.++..+.+|++||.++.+|+.+++|++. ..|.+|++.+++|.+.++++++.+..
T Consensus 2 gd~~af~~l~~~~~~~l~~~a~~~~~~~~~AEDivQe~fl~~~~~~~~~~~~--~~~~~WL~~Ia~n~~~d~~Rk~~~~~ 79 (324)
T TIGR02960 2 VDGAAFTALAEPHRRELLAHCYRMLGSLHEAEDLVQETLLRAWRARDRFEGR--SSVRTWLYRIATNACLDALEARQRRP 79 (324)
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHHHhhhhccCcc--cchHHHHHHHHHHHHHHHHHhccCCc
Confidence 3468999999999999999999999999999999999999999999999964 36999999999999999998764211
Q ss_pred ccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcc------
Q 008556 397 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITA------ 470 (561)
Q Consensus 397 RlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~------ 470 (561)
.... ... . ........ ..+......+.+.
T Consensus 80 ~~~~------------------~~~-~-------------------------~~~~~~~~-~~~~~~~~~~~~~~~~~~~ 114 (324)
T TIGR02960 80 RPVG------------------LGA-P-------------------------SADGTAAA-SEAAEVTWLEPLPDLTLDL 114 (324)
T ss_pred Cccc------------------cCC-C-------------------------CCcccccc-cccccccccCCCCcccccc
Confidence 0000 000 0 00000000 0000000000000
Q ss_pred -cCCCCChhHHHHHHH-HHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008556 471 -DTGVEIPDISVQKQL-MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 548 (561)
Q Consensus 471 -d~~~~~pee~le~~e-~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 548 (561)
.....+|++.+...+ +...+..+|..||+++|+||.|+|. +++|++|||+.||||.++|++++.||+++||+++
T Consensus 115 ~~~~~~~~~~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L~~~----~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 190 (324)
T TIGR02960 115 DDPAAADPSVAAGSRESVRLAFVAAIQYLPPRQRAVLLLRDV----LGWRAAETAELLGTSTASVNSALQRARATLDEVG 190 (324)
T ss_pred ccCCCCCHHHHHHHHHHHHHHHHHHHHhCCHHHhhHhhhHHH----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhc
Confidence 011124565555444 4557889999999999999999998 8999999999999999999999999999999988
Q ss_pred hc
Q 008556 549 GG 550 (561)
Q Consensus 549 ~~ 550 (561)
..
T Consensus 191 ~~ 192 (324)
T TIGR02960 191 PS 192 (324)
T ss_pred cc
Confidence 74
No 107
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=99.76 E-value=7e-18 Score=156.10 Aligned_cols=152 Identities=18% Similarity=0.206 Sum_probs=122.4
Q ss_pred HHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHHHH
Q 008556 327 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLL 406 (561)
Q Consensus 327 ~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~~~l 406 (561)
..|.+.|+.++.++.++..+.+|++||+++.+|+++++|++ .+|.+|++..+++.+.++++++.+.....
T Consensus 2 ~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~l~~~~~~~~~---~~f~~wl~~i~~~~~~d~~r~~~~~~~~~------- 71 (154)
T TIGR02950 2 REYMHDVFRYLYRLTKDKHLAEDLLQETFLKAYIHLHSFKD---SSIKPWLFRIARNAFIDWYRKDKKIQTID------- 71 (154)
T ss_pred chHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHhcC---CchHHHHHHHHHHHHHHHHHHhhhhcccc-------
Confidence 57899999999999998889999999999999999999997 37999999999999999987654210000
Q ss_pred HHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHHHHHHHH
Q 008556 407 SKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLM 486 (561)
Q Consensus 407 ~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~le~~e~ 486 (561)
.+. +.+... .....|++.+...+.
T Consensus 72 -------------------~~~------------------------------------~~~~~~-~~~~~~~~~~~~~~~ 95 (154)
T TIGR02950 72 -------------------DDA------------------------------------IGDLEQ-HPVESPEHHLLIKIE 95 (154)
T ss_pred -------------------Hhh------------------------------------hhhccc-cccCChhHHHHHHHH
Confidence 000 000000 011245555565666
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008556 487 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 548 (561)
Q Consensus 487 ~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 548 (561)
...|..+|..||+++++||.++|+ +|+|++|||+.||||..+|++.+.||+++||+.+
T Consensus 96 ~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~~l 153 (154)
T TIGR02950 96 QEEITHHLSRLPENYRTVLILREF----KEFSYKEIAELLNLSLAKVKSNLFRARKELKKLL 153 (154)
T ss_pred HHHHHHHHHhCCHhheeeeeehhh----ccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 678999999999999999999998 8999999999999999999999999999999865
No 108
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=99.76 E-value=2.8e-17 Score=153.88 Aligned_cols=159 Identities=14% Similarity=0.214 Sum_probs=125.2
Q ss_pred HHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHH
Q 008556 324 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIY 403 (561)
Q Consensus 324 ~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~ 403 (561)
.++..|.+.++.+|.++.++..+.+|++||+++++|+....|++. .|.+|++..+++.+.++++++.+....
T Consensus 2 ~~~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~---~~~~wl~~iarn~~~d~~R~~~~~~~~----- 73 (163)
T PRK07037 2 DVFVDNRSMLVKIAARIVGCRSRAEDVVQDAFVKLVEAPNQDAVK---QPVAYLFRIVRNLAIDHYRRQALENKY----- 73 (163)
T ss_pred hHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhccccCCcc---cHHHHHHHHHHHHHHHHHHhhcccccc-----
Confidence 367789999999999999999999999999999999998877753 488999999999999999875421000
Q ss_pred HHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHHHHH
Q 008556 404 TLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQK 483 (561)
Q Consensus 404 ~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~le~ 483 (561)
. ..+.... +. .+. ..+++..+..
T Consensus 74 ------------------------------------------------~------~~~~~~~-~~-~~~-~~~~~~~~~~ 96 (163)
T PRK07037 74 ------------------------------------------------H------GDEEDGL-DV-PSP-EASPEAALIN 96 (163)
T ss_pred ------------------------------------------------c------ccccccc-cc-CCC-CCCHHHHHHH
Confidence 0 0000000 00 011 1245555555
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008556 484 QLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 551 (561)
Q Consensus 484 ~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 551 (561)
.+..+.|..+|..||+++|+||.++|. +++|.+|||+.||||.++|+..+.||+++||+.+...
T Consensus 97 ~~~~~~l~~~l~~L~~~~r~v~~l~~~----~~~s~~EIA~~lgis~~tV~~~l~ra~~~lr~~l~~~ 160 (163)
T PRK07037 97 RDTLRHVADALSELPARTRYAFEMYRL----HGETQKDIARELGVSPTLVNFMIRDALVHCRKCLDAC 160 (163)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhcc
Confidence 666678999999999999999999998 8999999999999999999999999999999988654
No 109
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=99.76 E-value=2.9e-17 Score=158.10 Aligned_cols=160 Identities=18% Similarity=0.222 Sum_probs=126.7
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccc
Q 008556 320 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP 399 (561)
Q Consensus 320 ~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP 399 (561)
.++..++..|.+.|+.+|.++.++..+++|++||.++.+|+..++|++.. .|.+|++..++|.+.++++++.+....
T Consensus 5 ~~~~~~~~~~~~~l~~~~~~~~~~~~~AEDivQevflkl~~~~~~~~~~~--~~~~WL~~Ia~n~~~d~~Rk~~~~~~~- 81 (182)
T PRK12540 5 DSLRDDILAAVPSLRAFAISLSGNGDRADDLVQETLLRALANIDSFQPGS--NLPAWLFTILRNLFRSDYRKRRREVED- 81 (182)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCCc--hHHHHHHHHHHHHHHHHHHhccccccc-
Confidence 46788999999999999999999999999999999999999999998653 599999999999999998765421000
Q ss_pred hhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhH
Q 008556 400 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDI 479 (561)
Q Consensus 400 ~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee 479 (561)
.+. ...+.. +. .++.
T Consensus 82 -----------------------------------------------------~~~--------~~~~~~-~~---~~~~ 96 (182)
T PRK12540 82 -----------------------------------------------------ADG--------SYAKTL-KS---QPGQ 96 (182)
T ss_pred -----------------------------------------------------ccc--------cccccc-cC---CCch
Confidence 000 000000 00 1111
Q ss_pred HHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 008556 480 SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS 553 (561)
Q Consensus 480 ~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~l 553 (561)
.. ......|..+|..||+++|+||.|+|. +++|++|||+.||||..+|++.++||+++||+.+.....
T Consensus 97 ~~--~~~~~~l~~~l~~Lp~~~R~v~~L~~~----~g~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~~~~~ 164 (182)
T PRK12540 97 NA--HLEFEEFRAALDKLPQDQREALILVGA----SGFSYEDAAAICGCAVGTIKSRVNRARSKLSALLYVDGA 164 (182)
T ss_pred HH--HHHHHHHHHHHHhCCHHHHHHhhHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhccc
Confidence 11 112346899999999999999999998 899999999999999999999999999999999986553
No 110
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=99.76 E-value=2.6e-17 Score=153.81 Aligned_cols=155 Identities=12% Similarity=0.100 Sum_probs=123.9
Q ss_pred HHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHHHH
Q 008556 327 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLL 406 (561)
Q Consensus 327 ~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~~~l 406 (561)
..|.+.++.++.++.++..+.+|++||.++.+|+..+.|++. +|.||++..+++.+.++++++.+...
T Consensus 2 ~~~~~~l~~~~~~~~~~~~~aeDi~Qevf~~l~~~~~~~~~~---~~~~wL~~ia~n~~~d~~R~~~~~~~--------- 69 (159)
T PRK12527 2 ENYYRELVRFLSARLGNRQAAEDVAHDAYLRVLERSSSAQIE---HPRAFLYRTALNLVVDRHRRHRVRQA--------- 69 (159)
T ss_pred hhHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHhcccccccc---chHHHHHHHHHHHHHHHHHHHhcccc---------
Confidence 568889999999999988899999999999999999998752 69999999999999999876531000
Q ss_pred HHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHHHHHHHH
Q 008556 407 SKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLM 486 (561)
Q Consensus 407 ~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~le~~e~ 486 (561)
..++. . .+. .......|++.+..++.
T Consensus 70 --------------------------------------------~~~~~-~-~~~--------~~~~~~~~~~~~~~~~~ 95 (159)
T PRK12527 70 --------------------------------------------EPLEV-L-DEE--------ERLHSPSPQTRLDLGQR 95 (159)
T ss_pred --------------------------------------------cchhh-h-hcc--------ccccCCCHHHHHHHHHH
Confidence 00000 0 000 00011246666666677
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008556 487 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 551 (561)
Q Consensus 487 ~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 551 (561)
...|..+|..||+++++||.|+|+ +++|.+|||+.||+|.++|+..+.||+++||+.+...
T Consensus 96 ~~~l~~~l~~L~~~~r~v~~l~~~----~~~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l~~~ 156 (159)
T PRK12527 96 LALLQRALAELPPACRDSFLLRKL----EGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVRMRQW 156 (159)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHhc
Confidence 778999999999999999999998 8999999999999999999999999999999998753
No 111
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=99.75 E-value=5.4e-17 Score=154.26 Aligned_cols=164 Identities=16% Similarity=0.094 Sum_probs=126.9
Q ss_pred cHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccc
Q 008556 318 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR 397 (561)
Q Consensus 318 G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IR 397 (561)
+..|++.++..|.+.++.++.++.++..+.+|++||.++.+|+. ..|++-. .|.+|++..+++.+.++++++.+..
T Consensus 8 ~~~af~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQe~flkl~~~-~~~~~~~--~~~~wL~~iarn~~~d~~R~~~~~~- 83 (172)
T PRK09651 8 ASLTFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVS-ETLSTIR--DPRSFLCTIAKRVMVDLFRRNALEK- 83 (172)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhh-ccccccc--CHHHHHHHHHHHHHHHHHHHHHHHh-
Confidence 35899999999999999999999999999999999999999998 3565433 5899999999999999987643100
Q ss_pred cchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCCh
Q 008556 398 LPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIP 477 (561)
Q Consensus 398 lP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~p 477 (561)
.. ...+ + + +.+....+|
T Consensus 84 -----------------~~---------~~~~------------------------~------------~-~~~~~~~~~ 100 (172)
T PRK09651 84 -----------------AY---------LEML------------------------A------------L-MPEGGAPSP 100 (172)
T ss_pred -----------------hh---------hhHH------------------------h------------h-ccccCCCCh
Confidence 00 0000 0 0 000011133
Q ss_pred hHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 008556 478 DISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA 552 (561)
Q Consensus 478 ee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~ 552 (561)
+......+....|..+|..||+++|+||.++|+ +++|++|||+.||+|.++|+..+.||+++|+...-..|
T Consensus 101 ~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Ra~~~~~~~~~~~~ 171 (172)
T PRK09651 101 EERESQLETLQLLDSMLDGLNGKTREAFLLSQL----DGLTYSEIAHKLGVSVSSVKKYVAKATEHCLLFRLEYG 171 (172)
T ss_pred HHHHHHHHHHHHHHHHHHhCCHHHhHHhhhhhc----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHcC
Confidence 344444455567999999999999999999998 89999999999999999999999999999998765443
No 112
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=99.75 E-value=4.3e-17 Score=157.55 Aligned_cols=161 Identities=19% Similarity=0.162 Sum_probs=125.7
Q ss_pred HhhcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhccc
Q 008556 315 LHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSR 394 (561)
Q Consensus 315 l~~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr 394 (561)
+..+..+++.++..|.+.|+.+|+++.++..+++|++||.|+.+|+.++.|++. ..|.+|++..+++.+.+.++++.+
T Consensus 18 ~~~~~~~f~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQdvflkl~~~~~~~~~~--~~~~~wL~~Iarn~~~~~~r~~~~ 95 (188)
T PRK12517 18 MLSKQRRYEALVKALHADIYRYAYWLCKDKHIAEDLVQETFLRAWRSLDSLKDE--KAAKAWLITILRRENARRFERKQF 95 (188)
T ss_pred hhccHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhhcCc--cchHHHHHHHHHHHHHHHHHHhcc
Confidence 345679999999999999999999999999999999999999999999999865 369999999999876655432210
Q ss_pred ccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCC
Q 008556 395 TIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGV 474 (561)
Q Consensus 395 ~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~ 474 (561)
. ....+ . +...+...
T Consensus 96 ~------------------------------------------------------~~~~~-------~----~~~~~~~~ 110 (188)
T PRK12517 96 D------------------------------------------------------LVDIE-------D----DSIEDDAS 110 (188)
T ss_pred C------------------------------------------------------ccCcc-------c----ccccCccc
Confidence 0 00000 0 00011111
Q ss_pred CChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008556 475 EIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 550 (561)
Q Consensus 475 ~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 550 (561)
..++.. ...+.|..+|..||+++|.||.++|. ++++++|||+.||||..+|+.++.||+++||..+..
T Consensus 111 ~~~e~~----~~~~~l~~~l~~Lp~~~r~v~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 178 (188)
T PRK12517 111 HSSEEE----MEQEWLRRQIAKLDPEYREPLLLQVI----GGFSGEEIAEILDLNKNTVMTRLFRARNQLKEALEK 178 (188)
T ss_pred cChhHH----HHHHHHHHHHHhCCHHHHHHHHHHHH----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 123322 22356899999999999999999998 899999999999999999999999999999999864
No 113
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=99.75 E-value=7.4e-17 Score=155.05 Aligned_cols=154 Identities=21% Similarity=0.194 Sum_probs=125.9
Q ss_pred HHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchh
Q 008556 322 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN 401 (561)
Q Consensus 322 re~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~ 401 (561)
++.|+..|.+.|+.+|.++.++..+++|++||.++.+|+.+..|++. ..|.+|++..+++.+.++++++.+...++
T Consensus 3 ~~~l~~~y~~~l~~~~~~~~~~~~~aeDi~QEvflkl~~~~~~~~~~--~~~~~wL~~i~~n~~~d~~Rk~~~~~~~~-- 78 (181)
T PRK09637 3 LESIWSEYKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLKDG--SSIKSWLYQIANNTIIDFYRKKNRSEELP-- 78 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHhHHHhccc--cchHHHHHHHHHHHHHHHHHhccccCCcc--
Confidence 57899999999999999999999999999999999999999999853 47999999999999999998764211000
Q ss_pred HHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHHH
Q 008556 402 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISV 481 (561)
Q Consensus 402 ~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~l 481 (561)
.+ +...+ .+++..
T Consensus 79 ---------------------------------------------------------~~------~~~~~----~~~~~~ 91 (181)
T PRK09637 79 ---------------------------------------------------------DD------LLFED----EEREEN 91 (181)
T ss_pred ---------------------------------------------------------hh------hhccC----CChhHH
Confidence 00 00000 111222
Q ss_pred HHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008556 482 QKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 550 (561)
Q Consensus 482 e~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 550 (561)
...+....+..+|..||+++|+||.++|. +|++.+|||+.||+|..+|+..+.||+++||+.+..
T Consensus 92 ~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~g~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 156 (181)
T PRK09637 92 AKKELAPCLRPFIDALPEKYAEALRLTEL----EGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKELLEG 156 (181)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHHHHHHh----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 33445667899999999999999999998 899999999999999999999999999999998764
No 114
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=99.74 E-value=1.1e-16 Score=155.16 Aligned_cols=156 Identities=19% Similarity=0.200 Sum_probs=121.7
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccc
Q 008556 320 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP 399 (561)
Q Consensus 320 ~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP 399 (561)
.+++.|.. |.+.|+.+|+++.++..+.+|++||.++.+|+.+..|+.. ..|.+|++..++|.+.+++++..+...
T Consensus 8 ~~~~~l~~-~~~~l~~~a~~~l~~~~~AEDivQevfl~l~~~~~~~~~~--~~~~awL~~ia~n~~~d~~Rk~~r~~~-- 82 (188)
T PRK12546 8 DPRDELVE-HLPALRAFAISLTRNVAVADDLVQDTIVKAWTNFDKFQEG--TNLRAWLFTILRNTFYSDRRKHKREVP-- 82 (188)
T ss_pred hHHHHHHH-HHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHhccCCC--cchHHHHHHHHHHHHHHHHHHhccccc--
Confidence 56666766 7799999999999999999999999999999999999864 369999999999999998877542100
Q ss_pred hhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhH
Q 008556 400 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDI 479 (561)
Q Consensus 400 ~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee 479 (561)
..+. ...+...+.. ..+
T Consensus 83 ----------------------------------------------------~~~~--------~~~~~~~~~~--~~~- 99 (188)
T PRK12546 83 ----------------------------------------------------DPEG--------VHAASLAVKP--AHD- 99 (188)
T ss_pred ----------------------------------------------------Cccc--------ccccccccCC--cch-
Confidence 0000 0000000000 011
Q ss_pred HHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008556 480 SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 550 (561)
Q Consensus 480 ~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 550 (561)
.......+..+|..||+++|+||.|+|. +++|.+|||+.||||..+|+..+.||+++||+.+..
T Consensus 100 ---~~~~~~~l~~~L~~Lp~~~r~v~~L~~~----~g~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l~~ 163 (188)
T PRK12546 100 ---GRLAMSDFRAAFAQLPDEQREALILVGA----SGFSYEEAAEMCGVAVGTVKSRANRARARLAELLQL 163 (188)
T ss_pred ---hHHHHHHHHHHHHhCCHHHhHHhhhHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 1122346889999999999999999998 899999999999999999999999999999998865
No 115
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=99.73 E-value=1.1e-16 Score=152.05 Aligned_cols=148 Identities=21% Similarity=0.220 Sum_probs=120.6
Q ss_pred HHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHHHH
Q 008556 327 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLL 406 (561)
Q Consensus 327 ~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~~~l 406 (561)
..|.+.++.++.++.++..+++|++||+++.+|+++++|++. .+|.+|++..+++.+.+++++..+...++
T Consensus 2 ~~~~~~l~~~~~~~~~~~~~AeDlvQe~fl~l~~~~~~~~~~--~~f~~wl~~iarn~~~d~~Rk~~~~~~~~------- 72 (170)
T TIGR02959 2 DEFRSELKAFIKSRVSDASDVEDLLQEVFIKIHRNLPSLKDG--QKIQSWLYQIARNTIIDFYRSKSRSVELP------- 72 (170)
T ss_pred chHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHHHHHHHHhccCccccc-------
Confidence 468889999999999999999999999999999999999963 47999999999999999998765211000
Q ss_pred HHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHHHHHHHH
Q 008556 407 SKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLM 486 (561)
Q Consensus 407 ~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~le~~e~ 486 (561)
+ + .... ..+++.....+.
T Consensus 73 -----------------------------------------------~-----~-------~~~~---~~~~~~~~~~e~ 90 (170)
T TIGR02959 73 -----------------------------------------------E-----S-------LLAA---DSAREETFVKEL 90 (170)
T ss_pred -----------------------------------------------h-----h-------hccc---CCccHHHHHHHH
Confidence 0 0 0000 011222333445
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008556 487 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 549 (561)
Q Consensus 487 ~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 549 (561)
...|..+|..||+++|+||.++|. ++++++|||+.||+|..+|++.+.||+++||..+.
T Consensus 91 ~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 149 (170)
T TIGR02959 91 SQCIPPMIKELPDEYREAIRLTEL----EGLSQQEIAEKLGLSLSGAKSRVQRGRKKLKELLE 149 (170)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 567899999999999999999998 89999999999999999999999999999999885
No 116
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=99.73 E-value=1.2e-16 Score=153.84 Aligned_cols=157 Identities=13% Similarity=0.167 Sum_probs=122.4
Q ss_pred HHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchh
Q 008556 322 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN 401 (561)
Q Consensus 322 re~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~ 401 (561)
.+..+..+++.|+.+|.++.++..+.+|++||.|+.+|+.+..|++. ..|.+|++.++++.+.++++++.+.....
T Consensus 6 ~~~~~~~~~~~l~~~~~~~~~~~~dAEDivQe~flkl~~~~~~~~~~--~~~~~WL~~Iarn~~id~~Rk~~~~~~~~-- 81 (182)
T PRK12511 6 KRFDVLDQLVPLRRYARSLTRDSAEAEDLVHDALVRALERRASFRSG--GNLRTWLMSILHNAFIDELRRRRVEARRA-- 81 (182)
T ss_pred hhhhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCc--cchHHHHHHHHHHHHHHHHHhhccccccc--
Confidence 45557889999999999999998999999999999999999999864 36999999999999999998764211000
Q ss_pred HHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHHH
Q 008556 402 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISV 481 (561)
Q Consensus 402 ~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~l 481 (561)
+++ .+. .+.....+.
T Consensus 82 -------------------------~~~------------------------------------~~~-~~~~~~~~~--- 96 (182)
T PRK12511 82 -------------------------DEL------------------------------------AVL-ADASLPAAQ--- 96 (182)
T ss_pred -------------------------cch------------------------------------hhc-cccCCCcch---
Confidence 000 000 000000111
Q ss_pred HHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008556 482 QKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 551 (561)
Q Consensus 482 e~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 551 (561)
........|..+|..||+++|+||.|+|. +++|++|||+.||||.++|++.+.||+++||..+...
T Consensus 97 ~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~----eg~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~~~~ 162 (182)
T PRK12511 97 EHAVRLAQIRDAFFDLPEEQRAALHLVAI----EGLSYQEAAAVLGIPIGTLMSRIGRARAALRAFEEGT 162 (182)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHHhc
Confidence 11223456889999999999999999998 8999999999999999999999999999999988754
No 117
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=99.72 E-value=3.2e-16 Score=148.29 Aligned_cols=160 Identities=14% Similarity=0.116 Sum_probs=126.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhccccccc
Q 008556 319 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL 398 (561)
Q Consensus 319 ~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRl 398 (561)
..++.+++..|.+.++.+|.++.++..+.+|++||.++.+|+..+.++. ..|.+|++..++|.+.+++++...
T Consensus 8 ~~~~~~~~~~~~~~l~~~~~~~~~~~~~aeDlvQevf~~l~~~~~~~~~---~~~~~wl~~Iarn~~~d~~Rr~~~---- 80 (168)
T PRK12525 8 NTLIGQMFQQDYDWLCKKLSRQLGCPHSAEDIASETFLQVLALPDPASI---REPRALLTTIARRLMYEGWRRQDL---- 80 (168)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCcCcHHHHHHHHHHHHHhCCCcccc---cCHHHHHHHHHHHHHHHHHHHHHH----
Confidence 3789999999999999999999999999999999999999986665542 269999999999999998875320
Q ss_pred chhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChh
Q 008556 399 PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPD 478 (561)
Q Consensus 399 P~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pe 478 (561)
.+ ... ..+ + + ........|+
T Consensus 81 --------~~------~~~---------~~~------------------------~------------~-~~~~~~~~~~ 100 (168)
T PRK12525 81 --------ER------AYL---------QSL------------------------A------------E-APEAVQPSPE 100 (168)
T ss_pred --------HH------HHH---------HHH------------------------h------------c-ccccccCChH
Confidence 00 000 000 0 0 0000112455
Q ss_pred HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008556 479 ISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 549 (561)
Q Consensus 479 e~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 549 (561)
......+....|..+|..||+++|+||.|+|. +++|++|||+.||+|..+|+..+.+|+++||..+.
T Consensus 101 ~~~~~~~~~~~l~~~l~~L~~~~r~v~~L~~~----eg~s~~EIA~~l~is~~tV~~~l~ra~~~~~~~~~ 167 (168)
T PRK12525 101 EQWMVIETLLAIDRLLDGLSGKARAAFLMSQL----EGLTYVEIGERLGVSLSRIHQYMVEAFKCCYQGFQ 167 (168)
T ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhhc
Confidence 55555666678999999999999999999998 99999999999999999999999999999998764
No 118
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=99.70 E-value=4.3e-16 Score=145.18 Aligned_cols=156 Identities=17% Similarity=0.183 Sum_probs=113.0
Q ss_pred CCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCC
Q 008556 342 GRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGN 421 (561)
Q Consensus 342 ~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~g 421 (561)
++..+++|++||+|+.+|+..+. ++ +..|.+|++..++|.+.++++++.+..+...
T Consensus 2 ~~~~~AeDivQe~fl~~~~~~~~-~~--~~~~~~wl~~ia~n~~~d~~Rk~~~~~~~~~--------------------- 57 (161)
T PRK09047 2 RDDDAALDIVQDAMIKLAEKYGD-RP--AAEWPPLFQRILQNRIHDWFRRQKVRNTWVS--------------------- 57 (161)
T ss_pred CCHHHHHHHHHHHHHHHHHHHhh-cc--cCchHHHHHHHHHHHHHHHHHhhcccccccc---------------------
Confidence 34457899999999999999886 33 3469999999999999999987542110000
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCC--CCChhHHHHHHHHHHHHHHHHhcCCH
Q 008556 422 HSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTG--VEIPDISVQKQLMRQHVRNLLTLLNP 499 (561)
Q Consensus 422 r~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~--~~~pee~le~~e~~e~L~~aL~~L~e 499 (561)
...++.... .+++....+.+.+.. ...|+..+...+....|..+|..||+
T Consensus 58 ---------------------------~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~ 109 (161)
T PRK09047 58 ---------------------------LFSSFSDDD-DDDDFDPLETLDSADEGAESPADKLERAQVLQLIEEAIQKLPA 109 (161)
T ss_pred ---------------------------ccccccccc-ccccccHHHHhccccccCCCHHHHHHHHHHHHHHHHHHHhCCH
Confidence 000000000 000111112222211 23577777777788889999999999
Q ss_pred HHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 008556 500 KERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS 553 (561)
Q Consensus 500 rER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~l 553 (561)
++|+||.|+|+ +++|++|||+.||||..+|+.++.||+++||+++...++
T Consensus 110 ~~r~v~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~~ 159 (161)
T PRK09047 110 RQREAFLLRYW----EDMDVAETAAAMGCSEGSVKTHCSRATHALAKALEAKGI 159 (161)
T ss_pred HHHHHHHHHHH----hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhcCc
Confidence 99999999998 899999999999999999999999999999999976553
No 119
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=99.69 E-value=6.9e-16 Score=159.04 Aligned_cols=160 Identities=16% Similarity=0.120 Sum_probs=123.1
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccc
Q 008556 320 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP 399 (561)
Q Consensus 320 ~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP 399 (561)
....+++..|.+.++.+|+++.++..+.+|++||.++. |.....|+. ..|.+|++..++|.+.+++++..+....
T Consensus 4 ~~~~~l~~~~~~~l~~~a~~~~~~~~dAEDlvQe~fl~-~~~~~~~~~---~~~~~WL~~Ia~n~~~d~lR~~~~~~~~- 78 (293)
T PRK09636 4 ADAAAEFEPLRPHLLSVAYRMLGSVADAEDIVQEAWLR-WNNADRAQI---RDPRAWLTRVVTRLCLDRLRSARHRRET- 78 (293)
T ss_pred cHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH-HHhcccccc---cCHHHHHHHHHHHHHHHHHHhhhccccc-
Confidence 34678999999999999999999999999999999999 666677762 4699999999999999999865310000
Q ss_pred hhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhH
Q 008556 400 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDI 479 (561)
Q Consensus 400 ~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee 479 (561)
. .+ ..+..+ ..+.. ..|++
T Consensus 79 ----------------~---~~-----------------------------~~~~e~------------~~~~~-~~~~~ 97 (293)
T PRK09636 79 ----------------Y---VG-----------------------------PWLPEP------------VVEEL-DDPLE 97 (293)
T ss_pred ----------------c---cC-----------------------------CcCCcC------------CCCCC-CChHH
Confidence 0 00 000000 00111 12333
Q ss_pred H-HHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008556 480 S-VQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 549 (561)
Q Consensus 480 ~-le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 549 (561)
. .........+..+|+.|||++|.||.|+|. ++++++|||+.||+|..+|+++++||+++||+.+.
T Consensus 98 ~~~~~~~~~~~l~~~l~~L~~~~R~v~~L~~~----~g~s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~~~ 164 (293)
T PRK09636 98 AVVAAEDLSLALMLALERLSPLERAAFLLHDV----FGVPFDEIASTLGRSPAACRQLASRARKHVRAARP 164 (293)
T ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCC
Confidence 3 334455567899999999999999999998 89999999999999999999999999999999765
No 120
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=99.66 E-value=3.6e-15 Score=149.15 Aligned_cols=158 Identities=19% Similarity=0.189 Sum_probs=122.5
Q ss_pred HHHHHhhcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHH
Q 008556 311 LKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIF 390 (561)
Q Consensus 311 L~~~l~~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir 390 (561)
|.+.+.++..+++.+++.| +.++.+|.++.++..+.+||+||.++.+|+. |+.. ..|.+|++.+++|.+.++++
T Consensus 9 ~~~~~~~~~~~~~~l~~~y-~~L~r~~~~~~~d~~dAEDlvQE~flk~~~~---~~~~--~~~~~WL~~IarN~~id~~R 82 (228)
T PRK06704 9 LKNHIDMNHSNINFLIEQY-GELKRYCTFLTKNKWDGEDLAQETVCKVLQK---YSNK--DICMTLVYKIARNRWLDQIK 82 (228)
T ss_pred HhcccCCCHHHHHHHHHHH-HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH---cCcc--ccHHHHHHHHHHHHHHHHHh
Confidence 4445556668888888877 7899999999999999999999999999986 5543 24999999999999999988
Q ss_pred hcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcc
Q 008556 391 QHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITA 470 (561)
Q Consensus 391 ~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~ 470 (561)
++.+.-. + .+ + ...
T Consensus 83 k~k~~~~-------------------------------~-----------------------~~-----~--~~~----- 96 (228)
T PRK06704 83 SKSVHEK-------------------------------I-----------------------RD-----Q--ITF----- 96 (228)
T ss_pred ccccccc-------------------------------c-----------------------cc-----c--ccc-----
Confidence 6542000 0 00 0 000
Q ss_pred cCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008556 471 DTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 550 (561)
Q Consensus 471 d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 550 (561)
..+.... .+..+.+..+|..||+++|.||.|+|. +++|++|||+.||+|.++|++.+.||+++||+.+..
T Consensus 97 ----~~~~~~~--~~~~~~l~~~L~~Lp~~~R~v~lL~~~----eg~S~~EIAe~LgiS~~tVksrL~Rark~Lr~~l~~ 166 (228)
T PRK06704 97 ----EEPHEKI--ADLHEMVGKVLSSLNVQQSAILLLKDV----FQYSIADIAKVCSVSEGAVKASLFRSRNRLKTVSEE 166 (228)
T ss_pred ----CChHHHH--HHHHHHHHHHHHhCCHHHhhHhhhHHh----hCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHh
Confidence 0111111 123356889999999999999999998 899999999999999999999999999999998865
No 121
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.
Probab=99.64 E-value=4.7e-15 Score=152.26 Aligned_cols=156 Identities=22% Similarity=0.164 Sum_probs=118.8
Q ss_pred HHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHH
Q 008556 324 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIY 403 (561)
Q Consensus 324 ~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~ 403 (561)
+++..|.+.++.+|+++.++..+.+|++||+++.+++. .|+.. ..|.+|++.+++|.+.+++++..+.-..
T Consensus 1 ~l~~~~~~~l~~~a~r~lg~~~dAEDvvQE~flk~~~~--~~~~~--~~~~awL~~Ia~n~~ld~lR~~~~~~~~----- 71 (281)
T TIGR02957 1 EEFEALRPLLFSLAYRMLGSVADAEDIVQETFLRWQEA--DRAQI--ENPKAYLTKVVTRRCIDVLRSARARREV----- 71 (281)
T ss_pred ChHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhC--Ccccc--cCHHHHHHHHHHHHHHHHHHHhhhcccc-----
Confidence 37889999999999999999999999999999997775 45432 3699999999999999999764310000
Q ss_pred HHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHHHHH
Q 008556 404 TLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQK 483 (561)
Q Consensus 404 ~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~le~ 483 (561)
+ .+ .-+..+ ..+. ...|++.+..
T Consensus 72 ------------~---~~-----------------------------~~~~e~------------~~~~-~~~~~~~~~~ 94 (281)
T TIGR02957 72 ------------Y---VG-----------------------------PWLPEP------------LLTT-SADPAESVEL 94 (281)
T ss_pred ------------c---CC-----------------------------CCCCcc------------cCCC-CCChHHHHHH
Confidence 0 00 000000 0000 1234444433
Q ss_pred -HHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008556 484 -QLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 549 (561)
Q Consensus 484 -~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 549 (561)
+.+...+..+|+.||++||.||.|+|. .++|++|||+.||+|..+|+++++||+++||+...
T Consensus 95 ~e~~~~~l~~~l~~L~~~~R~v~~L~~~----~g~s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~~~ 157 (281)
T TIGR02957 95 AESLSMAYLLLLERLSPLERAVFVLREV----FDYPYEEIASIVGKSEANCRQLVSRARRHLDARRP 157 (281)
T ss_pred HHHHHHHHHHHHhhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCC
Confidence 345567889999999999999999998 89999999999999999999999999999999754
No 122
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=99.63 E-value=7.3e-15 Score=151.80 Aligned_cols=161 Identities=17% Similarity=0.133 Sum_probs=123.3
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccc
Q 008556 320 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP 399 (561)
Q Consensus 320 ~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP 399 (561)
..+..++..|.+.++.+|+++.++..+.||++||.++.+|++...+ . ..|.+|++...+|.+.+++++..+.-..
T Consensus 5 ~~~~~l~~~~~~~L~~~a~r~lgs~~dAEDvvQE~flr~~~~~~~~-~---~~~~aWL~~Ia~n~~id~lRk~~~rr~~- 79 (290)
T PRK09635 5 DPVSAAWRAHRAYLVDLAFRMVGDIGVAEDMVQEAFSRLLRAPVGD-I---DDERGWLIVVTSRLCLDHIKSASTRRER- 79 (290)
T ss_pred cHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCccc-c---ccHHHHHHHHHHHHHHHHHhhhhccCcC-
Confidence 5678899999999999999999999999999999999999987543 1 2599999999999999999864310000
Q ss_pred hhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhH
Q 008556 400 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDI 479 (561)
Q Consensus 400 ~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee 479 (561)
....+. +..+ +...+ ..+|++
T Consensus 80 --------------------------------------------------~~~~~~--~~~~-----~~~~~--~~~~~~ 100 (290)
T PRK09635 80 --------------------------------------------------PQDIAA--WHDG-----DASVS--SVDPAD 100 (290)
T ss_pred --------------------------------------------------cccccc--cCcc-----ccCCC--CCCcHH
Confidence 000000 0000 00001 112333
Q ss_pred -HHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008556 480 -SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 548 (561)
Q Consensus 480 -~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 548 (561)
.....+....+..+|..|||++|.||.|+|. .+++++|||+.||+|..+|+++++||+++||+..
T Consensus 101 ~~~~~~e~~~al~~~L~~L~p~~R~vf~L~~~----~g~s~~EIA~~Lgis~~tVr~~l~RAr~~Lr~~~ 166 (290)
T PRK09635 101 RVTLDDEVRLALLIMLERLGPAERVVFVLHEI----FGLPYQQIATTIGSQASTCRQLAHRARRKINESR 166 (290)
T ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHhhHHHH----hCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhhC
Confidence 3345556678999999999999999999998 8999999999999999999999999999999864
No 123
>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR. Similarly, tetanus toxin production of Clostridium tetani is regulated by TetR which is a very close relative of BotR. Both BotR and TetR are members of the TIGR02937 subfamily of sigma-70 RNA polymerase sigma factors. Functional complementation experiments have been done for botR and tetR in highly transformable strain of Clostridium perfringens host cells to assess functional interchangeability of sigma factors and it has been confirmed that they are interchangeable in vivo.
Probab=99.51 E-value=2e-13 Score=125.43 Aligned_cols=136 Identities=12% Similarity=0.130 Sum_probs=99.7
Q ss_pred HHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhh-----cCCCCCCchhHHHHHHHHHHHHHHHHhccccc
Q 008556 322 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEK-----FKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI 396 (561)
Q Consensus 322 re~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiek-----FDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~I 396 (561)
++.++..|.++++.+|++|... +| +||.++.+|..+.+ |++. ..|.||++..++|.+.++++++.+..
T Consensus 1 f~~~~~~y~~~l~~~~~~~~~~----~~-~qdvf~~~w~~~~~~~~~~~~~~--~~~~~wL~~iarN~~id~~Rk~~~~~ 73 (142)
T TIGR03209 1 FEEIYMNFKNTIDIFTRKYNLY----YD-YNDILYHLWIILKKIDLNKFNTE--NDLEKYISTSLKRYCLDICNKKNRDK 73 (142)
T ss_pred ChHHHHHHHHHHHHHHHHhcch----hh-HHHHHHHHHHHHHHhhhhhcCch--hHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 3679999999999999999662 34 49999999999875 5543 46999999999999999998654110
Q ss_pred ccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCC
Q 008556 397 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEI 476 (561)
Q Consensus 397 RlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~ 476 (561)
+. . . ..++ + + .. ..
T Consensus 74 ~~-----------------~-~-------~~~~------------------------~-----~-----------~~-~~ 87 (142)
T TIGR03209 74 KI-----------------I-Y-------NSEI------------------------T-----D-----------IK-LS 87 (142)
T ss_pred hh-----------------h-h-------hhhh------------------------h-----c-----------cc-cc
Confidence 00 0 0 0000 0 0 00 01
Q ss_pred hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHH
Q 008556 477 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVR 534 (561)
Q Consensus 477 pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVR 534 (561)
+.+.+...+....|..+|+.||+++|+||.|+|. +++|++|||+.||||.++|+
T Consensus 88 ~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~~----~~~s~~EIA~~l~is~~tV~ 141 (142)
T TIGR03209 88 LINVYSSNDLEFEFNDLISILPNKQKKIIYMKFF----EDMKEIDIAKKLHISRQSVY 141 (142)
T ss_pred hhHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHhhc
Confidence 1122333344557889999999999999999998 99999999999999999997
No 124
>PRK09191 two-component response regulator; Provisional
Probab=99.51 E-value=1.4e-13 Score=137.13 Aligned_cols=137 Identities=16% Similarity=0.124 Sum_probs=111.1
Q ss_pred HHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccch
Q 008556 321 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPE 400 (561)
Q Consensus 321 Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~ 400 (561)
++..|+..|.+.++.+|.++.++..+.+|++||+++.+|+...+|++. ..|.+|++.++++..... .
T Consensus 2 ~~~~l~~~~~~~l~~~~~~~~~~~~~aeDi~qd~~~~~~~~~~~~~~~--~~~~~wl~~~~~~~~~~~----~------- 68 (261)
T PRK09191 2 SLSQRIAPHLPYLRRYARALTGSQSSGDAYVAATLEALLADPSIFPEA--SSPRVGLYRLFHRLWSSA----G------- 68 (261)
T ss_pred chHHHHHHHhHHHHHHHHHhcCChhhHHHHHHHHHHHHHHhHHhcCCC--cchhhHHHHHHHHHhccc----c-------
Confidence 578999999999999999999999999999999999999999999874 358999998765321100 0
Q ss_pred hHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHH
Q 008556 401 NIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDIS 480 (561)
Q Consensus 401 ~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~ 480 (561)
. +.. .. ..+..
T Consensus 69 --------------------------------------------------------~--~~~--------~~--~~~~~- 79 (261)
T PRK09191 69 --------------------------------------------------------A--NDP--------EP--GSPFE- 79 (261)
T ss_pred --------------------------------------------------------c--cCC--------CC--CCCch-
Confidence 0 000 00 01111
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008556 481 VQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 550 (561)
Q Consensus 481 le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 550 (561)
..+..+|..||+++|+||.|+|. +++|++|||+.||+|.++|+.+..+|+++||..+..
T Consensus 80 -------~~l~~~l~~L~~~~r~v~~l~~~----~~~s~~eIA~~l~~s~~tV~~~l~ra~~~l~~~~~~ 138 (261)
T PRK09191 80 -------ARAERRLAGLTPLPRQAFLLTAL----EGFSVEEAAEILGVDPAEAEALLDDARAEIARQVAT 138 (261)
T ss_pred -------HHHHHHHHhCCHHHhHHHHHHHH----hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHhccCCC
Confidence 15889999999999999999998 899999999999999999999999999999987653
No 125
>PRK08311 putative RNA polymerase sigma factor SigI; Reviewed
Probab=99.46 E-value=4.3e-12 Score=127.72 Aligned_cols=88 Identities=20% Similarity=0.354 Sum_probs=77.7
Q ss_pred HHHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHhhhCCCC--CHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHH
Q 008556 308 CRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGI--SLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 384 (561)
Q Consensus 308 ~~eL~~~l~~G-~~Are~LI~~nlrLV~sIArrY~~~g~--~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqa 384 (561)
.+.++..++.| ..|++.|+..|.++|+++|.++.++.. +.+|++|||++++|+++++|++.+|..|.+|+..+|++.
T Consensus 5 ~~~Li~~~~~gD~~AfeeLi~~Y~p~I~~~a~~~~~~~~~~eaeDlvQe~fi~l~eai~~y~~~kg~sF~awl~~Iirn~ 84 (237)
T PRK08311 5 LEDILEKIKNGDEELREELIEEYKPFIAKVVSSVCGRYIDWENDDELSIGLIAFNEAIDSYDEEKGKSFLSFAELVIKRR 84 (237)
T ss_pred HHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhcccCCCCchHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHH
Confidence 34455555555 589999999999999999999998765 589999999999999999999999888999999999999
Q ss_pred HHHHHHhcccc
Q 008556 385 IRKAIFQHSRT 395 (561)
Q Consensus 385 I~~~Ir~~sr~ 395 (561)
+.++++++.+.
T Consensus 85 ~iDylRk~~~~ 95 (237)
T PRK08311 85 LIDYFRKESKH 95 (237)
T ss_pred HHHHHHHhhcc
Confidence 99999987664
No 126
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=99.37 E-value=3.7e-11 Score=116.22 Aligned_cols=174 Identities=20% Similarity=0.300 Sum_probs=118.3
Q ss_pred HHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHhhhCC---CCCHHH--HHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHH
Q 008556 309 RDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGR---GISLHD--LLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVR 382 (561)
Q Consensus 309 ~eL~~~l~~G~-~Are~LI~~nlrLV~sIArrY~~~---g~~~eD--LIQEG~IGLirAiekFDp~kG~rFSTYA~~wIR 382 (561)
.+|+..++.|+ .|.+.|+..|++-++.+|+++.+. +.+.+| |++|.++.+++.-...+...-..|-.|+...++
T Consensus 5 t~ll~~~~~GD~~A~~~L~~~~y~~L~~~a~~~l~~~~~~~~~~~~~lv~ea~lrl~~~~~~~~~~~~~~f~~~~~~~~r 84 (185)
T PF07638_consen 5 TELLDRWRQGDEAALDQLFERYYPELRRLARRRLRRERRGHDLQDTALVHEAFLRLARRGRFVQFSDRRHFWALLARIMR 84 (185)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHhccccCCchhHHHHHHHHHHHHhccccccCCCCHHHHHHHHHHHHH
Confidence 34555665555 999999999999999999987633 334554 477888877774333233333458888899999
Q ss_pred HHHHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCC
Q 008556 383 QTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQD 462 (561)
Q Consensus 383 qaI~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~ 462 (561)
+.+.++.+++.+.. .+|.. ...+|+...
T Consensus 85 r~lid~~R~~~a~K----------------------Rg~~~-------------------------~~~~l~~~~----- 112 (185)
T PF07638_consen 85 RKLIDHARRRQAQK----------------------RGGDQ-------------------------VRVELDERA----- 112 (185)
T ss_pred HHHHHHHHHHHHHh----------------------cCCCC-------------------------cccchhhhh-----
Confidence 88888887654211 11100 001111111
Q ss_pred chhhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008556 463 TTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 542 (561)
Q Consensus 463 ~~l~d~l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALk 542 (561)
.+...+.|+..+ ++.+.+..+.. |+|++++||.++|. .|+|.+|||+.||||..+|++....|..
T Consensus 113 -------~~~~~~~~~~~~---~l~e~l~~L~~-l~~~~~~~v~l~~~----~Gls~~EIA~~lgiS~~tV~r~l~~aR~ 177 (185)
T PF07638_consen 113 -------DSGDEPSPEELL---ELEEALERLLA-LDPRQRRVVELRFF----EGLSVEEIAERLGISERTVRRRLRRARA 177 (185)
T ss_pred -------ccccCCCHHHHH---HHHHHHHHHHc-cCHHHHHHHHHHHH----CCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 011112444433 23445555555 99999999999998 8999999999999999999999999999
Q ss_pred HHHHHhh
Q 008556 543 RLKQSLG 549 (561)
Q Consensus 543 KLR~~l~ 549 (561)
+|+..+.
T Consensus 178 ~l~~~l~ 184 (185)
T PF07638_consen 178 WLRRELR 184 (185)
T ss_pred HHHHHhc
Confidence 9998764
No 127
>PF04542 Sigma70_r2: Sigma-70 region 2 ; InterPro: IPR007627 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 recognised by the major sigma factors [, ]. Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core-binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime [, ]. The aromatic residues of the recognition helix, found at the C terminus of this domain are thought to mediate strand separation, thereby allowing transcription initiation [, ].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1OR7_B 1H3L_B 2Z2S_C 2Q1Z_C 2O7G_B 1SMY_F 1IW7_P 2BE5_F 2A6E_F 2CW0_F ....
Probab=99.24 E-value=2.5e-11 Score=97.69 Aligned_cols=70 Identities=23% Similarity=0.432 Sum_probs=67.0
Q ss_pred HHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhccc
Q 008556 325 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSR 394 (561)
Q Consensus 325 LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr 394 (561)
|++.|.++|+++|++|.+++.+.+|++||++++||+++++||+++|..|.+|++..+++.+.++++++.|
T Consensus 1 L~~~~~~~l~~~~~~~~~~~~~~eD~~qe~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~r~~~r 70 (71)
T PF04542_consen 1 LYERYYPLLYRYARRYTGDPEDAEDLVQEAFIKLWRAIDSYDPDRGDSFRAWLFRIARNRILDYLRKRRR 70 (71)
T ss_dssp HHHHTHHHHHHHHHTCTTCSSHHHHHHHHHHHHHHHHHHHTSTTSSSHHHHHHHHHHHHHHHHHHHCSSS
T ss_pred CHHHHHHHHHHHHHHHhCCHhhHHHHhhHHHHHHHhhhhcccccccCCHHHHHHHHHHHHHHHHHHHhcC
Confidence 6899999999999999999999999999999999999999999999899999999999999999998764
No 128
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 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 recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is 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.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=99.24 E-value=2.4e-11 Score=93.11 Aligned_cols=50 Identities=36% Similarity=0.628 Sum_probs=46.3
Q ss_pred HHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556 493 LLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 546 (561)
Q Consensus 493 aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 546 (561)
+|+.||++||+||.++|+ +++|++|||+.||+|+++|+++..+|++|||+
T Consensus 1 Al~~L~~~er~vi~~~y~----~~~t~~eIa~~lg~s~~~V~~~~~~al~kLR~ 50 (50)
T PF04545_consen 1 ALDQLPPREREVIRLRYF----EGLTLEEIAERLGISRSTVRRILKRALKKLRK 50 (50)
T ss_dssp HHCTS-HHHHHHHHHHHT----ST-SHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred ChhhCCHHHHHHHHHHhc----CCCCHHHHHHHHCCcHHHHHHHHHHHHHHhcC
Confidence 588999999999999998 99999999999999999999999999999985
No 129
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 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 recognised by the major sigma factors [, ]. 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 [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=99.03 E-value=6.5e-10 Score=92.47 Aligned_cols=77 Identities=30% Similarity=0.491 Sum_probs=66.1
Q ss_pred HHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHH
Q 008556 404 TLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDIS 480 (561)
Q Consensus 404 ~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~ 480 (561)
+.+++|.+++..|.+++||.||.+|||+.|||++++|..++...+..+||+.+++.+++.++.+++.|+...+|++.
T Consensus 1 E~l~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~~~~~~~Sl~~~~~~~~~~~l~~~i~d~~~~~P~e~ 77 (78)
T PF04539_consen 1 EKLRKIERARRELEQELGREPTDEEIAEELGISVEEVRELLQASRRPVSLDLPVGDEDDSTLGDFIEDDDAPSPEEE 77 (78)
T ss_dssp HHHHHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHHHHSCCEESSHCCSSSSSEEGGGSSB-SSS--HHHH
T ss_pred ChHHHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHHhCCCCeEEeeeecCCCCCchhheecCCCCCChhhc
Confidence 35789999999999999999999999999999999999999999999999999998888899999999988788764
No 130
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 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 recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=98.93 E-value=3e-09 Score=82.42 Aligned_cols=54 Identities=30% Similarity=0.440 Sum_probs=46.4
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008556 487 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 544 (561)
Q Consensus 487 ~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKL 544 (561)
++.|..+|..||+++|.||.++|. +++|++|||+.+|+|.++|++.+.+|+++|
T Consensus 1 r~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~eIa~~l~~s~~~v~~~l~ra~~~L 54 (54)
T PF08281_consen 1 REALQQALAQLPERQREIFLLRYF----QGMSYAEIAEILGISESTVKRRLRRARKKL 54 (54)
T ss_dssp HHHHHHHHHCS-HHHHHHHHHHHT----S---HHHHHHHCTS-HHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHH----HCcCHHHHHHHHCcCHHHHHHHHHHHHhhC
Confidence 357899999999999999999999 899999999999999999999999999987
No 131
>PRK06930 positive control sigma-like factor; Validated
Probab=98.66 E-value=1.1e-07 Score=91.26 Aligned_cols=71 Identities=18% Similarity=0.285 Sum_probs=62.3
Q ss_pred hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008556 477 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 551 (561)
Q Consensus 477 pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 551 (561)
+.+.....+....|..++..||+++|+||.++|+ +++|++|||+.||+|..+|++++.||+++|+..+...
T Consensus 95 ~~~~~~~~e~~~~l~~al~~L~~rer~V~~L~~~----eg~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l~~~ 165 (170)
T PRK06930 95 EPESVISEWDKIRIEDALSVLTEREKEVYLMHRG----YGLSYSEIADYLNIKKSTVQSMIERAEKKIARQINES 165 (170)
T ss_pred ChhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHh
Confidence 3334444556678999999999999999999998 8999999999999999999999999999999988644
No 132
>PRK00118 putative DNA-binding protein; Validated
Probab=98.45 E-value=8.8e-07 Score=78.51 Aligned_cols=61 Identities=21% Similarity=0.146 Sum_probs=55.2
Q ss_pred HHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 008556 489 HVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS 553 (561)
Q Consensus 489 ~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~l 553 (561)
.+.-+...||+++++|+.++|. +++|..|||+.+|+|+.+|++++.||+++||+++..-++
T Consensus 10 l~d~~~~~L~ekqRevl~L~y~----eg~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~~~~~~ 70 (104)
T PRK00118 10 LFDFYGSLLTEKQRNYMELYYL----DDYSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEEKLHL 70 (104)
T ss_pred HHHHHhccCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHCh
Confidence 4455668999999999999998 899999999999999999999999999999999876543
No 133
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=98.30 E-value=2.2e-06 Score=64.30 Aligned_cols=54 Identities=37% Similarity=0.589 Sum_probs=49.8
Q ss_pred HHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556 488 QHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 545 (561)
Q Consensus 488 e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 545 (561)
+.+..++..|++.++.++.++|. +++|..+||+.+|+|..+|+++..++..+||
T Consensus 2 ~~~~~~~~~l~~~~~~~~~~~~~----~~~~~~~ia~~~~~s~~~i~~~~~~~~~~l~ 55 (55)
T cd06171 2 ERLEEALDKLPEREREVILLRFG----EGLSYEEIAEILGISRSTVRQRLHRALKKLR 55 (55)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence 35778899999999999999997 7899999999999999999999999988874
No 134
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=98.18 E-value=3.8e-06 Score=77.99 Aligned_cols=57 Identities=19% Similarity=0.269 Sum_probs=49.2
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhh
Q 008556 495 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGY 556 (561)
Q Consensus 495 ~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~l~~y 556 (561)
..|+++|++||.+++ +|+|++|||+.||+|+.+|++++++|+++|+.......+-.+
T Consensus 5 ~~Lte~qr~VL~Lr~-----~GlTq~EIAe~LgiS~stV~~~e~ra~kkLr~a~~~~~l~~~ 61 (137)
T TIGR00721 5 TFLTERQIKVLELRE-----KGLSQKEIAKELKTTRANVSAIEKRAMENIEKARNTLDFVKF 61 (137)
T ss_pred CCCCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHhHHHHHHHHhhHHHHHHH
Confidence 359999999999975 799999999999999999999999999999986554444443
No 135
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=98.14 E-value=5.6e-06 Score=77.22 Aligned_cols=51 Identities=24% Similarity=0.399 Sum_probs=46.8
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008556 495 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 550 (561)
Q Consensus 495 ~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 550 (561)
..|+++|++||.+++ +++|++|||+.||+|+.+|++++++|+++||+...-
T Consensus 5 ~~Lt~rqreVL~lr~-----~GlTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~t 55 (141)
T PRK03975 5 SFLTERQIEVLRLRE-----RGLTQQEIADILGTSRANVSSIEKRARENIEKARET 55 (141)
T ss_pred cCCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 469999999999965 799999999999999999999999999999987644
No 136
>PRK04217 hypothetical protein; Provisional
Probab=98.09 E-value=7.1e-06 Score=73.47 Aligned_cols=56 Identities=20% Similarity=0.134 Sum_probs=51.2
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchh
Q 008556 495 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASY 554 (561)
Q Consensus 495 ~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~l~ 554 (561)
..|++.|++||.++|. +++|++|||+.||||+.+|++++.+|+++|++.+......
T Consensus 41 ~~Lt~eereai~l~~~----eGlS~~EIAk~LGIS~sTV~r~L~RArkkLre~L~~~~~~ 96 (110)
T PRK04217 41 IFMTYEEFEALRLVDY----EGLTQEEAGKRMGVSRGTVWRALTSARKKVAQMLVEGREL 96 (110)
T ss_pred ccCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhccce
Confidence 5689999999999998 8999999999999999999999999999999998765543
No 137
>PF00140 Sigma70_r1_2: Sigma-70 factor, region 1.2; InterPro: IPR009042 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 recognised by the major sigma factors [, ]. ; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1SMY_F 1IW7_P 1SIG_A 3IYD_F 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P 3DXJ_P ....
Probab=98.03 E-value=1.5e-06 Score=62.93 Aligned_cols=34 Identities=41% Similarity=0.464 Sum_probs=30.1
Q ss_pred ChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHH
Q 008556 246 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIR 279 (561)
Q Consensus 246 ~d~l~~Yl~~i~~~~lLT~eEE~eL~~~i~~~~~ 279 (561)
+|+++.||++|+++|+||++||++|+++|+.+..
T Consensus 1 ~D~l~~Yl~ei~~~~LLt~eeE~~LA~~i~~g~~ 34 (37)
T PF00140_consen 1 SDSLRLYLKEIGRYPLLTAEEEIELARRIRKGDE 34 (37)
T ss_dssp HHHHHHHHHHHHHS-EETTHHHHHHHHHHHHHHH
T ss_pred CcHHHHHHHHHcCCCCCCHHHHHHHHHHHHHhHH
Confidence 3789999999999999999999999999998554
No 138
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=97.98 E-value=0.0022 Score=73.37 Aligned_cols=34 Identities=32% Similarity=0.493 Sum_probs=31.5
Q ss_pred CChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHH
Q 008556 245 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLI 278 (561)
Q Consensus 245 ~~d~l~~Yl~~i~~~~lLT~eEE~eL~~~i~~~~ 278 (561)
.+||+++||++|+..||||+|+|+++|++|..+.
T Consensus 102 t~DPVRMYLREMG~V~LLTREgEIeIAKRIE~G~ 135 (619)
T PRK05658 102 TDDPVRMYLREMGTVELLTREGEIEIAKRIEAGE 135 (619)
T ss_pred CCChHHHHHHHhccCcCCCcHHHHHHHHHHHHHH
Confidence 5799999999999999999999999999998743
No 139
>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT). 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 [].; PDB: 1S7O_A 1XSV_B.
Probab=97.96 E-value=3.4e-05 Score=68.00 Aligned_cols=58 Identities=28% Similarity=0.350 Sum_probs=45.1
Q ss_pred HHHHHH-hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008556 489 HVRNLL-TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 550 (561)
Q Consensus 489 ~L~~aL-~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 550 (561)
.|.++. .-|+++|++++.++|. +++|+.|||+.+|||+..|...++||.++|...=..
T Consensus 9 ~L~d~Yg~LLT~kQ~~~l~lyy~----eDlSlsEIAe~~~iSRqaV~d~ikr~~~~L~~yE~k 67 (101)
T PF04297_consen 9 LLFDFYGELLTEKQREILELYYE----EDLSLSEIAEELGISRQAVYDSIKRAEKKLEEYEEK 67 (101)
T ss_dssp HHHHHHGGGS-HHHHHHHHHHCT----S---HHHHHHHCTS-HHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHCCHHHHHHHHHHHc----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 344444 4599999999999998 999999999999999999999999999999775433
No 140
>TIGR01636 phage_rinA phage transcriptional activator, RinA family. This model represents a family of phage proteins, including RinA, a transcriptional activator in staphylococcal phage phi 11. This family shows similarity to ArpU, a phage-related putative autolysin regulator, and to some sporulation-specific sigma factors.
Probab=97.93 E-value=4.4e-05 Score=70.59 Aligned_cols=62 Identities=18% Similarity=0.264 Sum_probs=55.0
Q ss_pred HHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008556 485 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 548 (561)
Q Consensus 485 e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 548 (561)
...+.|..+|+.|++.+|.||.++|+ .+..+|..+||..||+|+.+|.++..+|+.+|+..+
T Consensus 71 ~~~~~I~~~l~~Ld~~er~II~~rY~--~~~~~t~~~Ia~~l~iS~~t~~r~r~~~l~kla~~l 132 (134)
T TIGR01636 71 RNRDAIENCLNEADEQTRVIIQELYM--KKRPLTLVGLAQQLFISKSTAYRLRNHIIEAVAEEL 132 (134)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHc--cCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 44577899999999999999999996 223469999999999999999999999999999865
No 141
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=97.80 E-value=4.7e-05 Score=58.07 Aligned_cols=46 Identities=26% Similarity=0.400 Sum_probs=41.2
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556 495 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 545 (561)
Q Consensus 495 ~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 545 (561)
..|+++|+.|+.+.+ .+++.+|||+.+|||+.+|+++..++++||+
T Consensus 2 ~~l~~~e~~i~~~~~-----~g~s~~eia~~l~is~~tv~~~~~~~~~kl~ 47 (58)
T smart00421 2 ASLTPREREVLRLLA-----EGLTNKEIAERLGISEKTVKTHLSNIMRKLG 47 (58)
T ss_pred CCCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Confidence 468999999997743 6899999999999999999999999988885
No 142
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=97.65 E-value=0.00012 Score=57.70 Aligned_cols=46 Identities=24% Similarity=0.335 Sum_probs=40.9
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556 495 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 545 (561)
Q Consensus 495 ~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 545 (561)
..|+++|.+|+.+.. .|++.+|||+.+|||..+|+....++++||.
T Consensus 2 ~~LT~~E~~vl~~l~-----~G~~~~eIA~~l~is~~tV~~~~~~i~~Kl~ 47 (58)
T PF00196_consen 2 PSLTERELEVLRLLA-----QGMSNKEIAEELGISEKTVKSHRRRIMKKLG 47 (58)
T ss_dssp GSS-HHHHHHHHHHH-----TTS-HHHHHHHHTSHHHHHHHHHHHHHHHHT
T ss_pred CccCHHHHHHHHHHH-----hcCCcchhHHhcCcchhhHHHHHHHHHHHhC
Confidence 479999999999887 6999999999999999999999999999985
No 143
>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=97.62 E-value=0.00015 Score=55.44 Aligned_cols=45 Identities=29% Similarity=0.487 Sum_probs=40.2
Q ss_pred CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556 497 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 546 (561)
Q Consensus 497 L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 546 (561)
|+++|++|+.+.+ .++|.+|||+.+|+|+.+|++..++++++|+.
T Consensus 1 l~~~e~~i~~~~~-----~~~s~~eia~~l~~s~~tv~~~~~~~~~~l~~ 45 (57)
T cd06170 1 LTPREREVLRLLA-----EGKTNKEIADILGISEKTVKTHLRNIMRKLGV 45 (57)
T ss_pred CCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHhCC
Confidence 6899999998854 58999999999999999999999999888764
No 144
>PF07374 DUF1492: Protein of unknown function (DUF1492); InterPro: IPR010861 This entry is represented by Streptococcus phage 7201, Orf19. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several hypothetical, highly conserved Streptococcal and related phage proteins. The function of this family is unknown.
Probab=97.60 E-value=0.00033 Score=61.63 Aligned_cols=55 Identities=22% Similarity=0.439 Sum_probs=49.6
Q ss_pred HHHHHHHHHhcCC-HHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008556 486 MRQHVRNLLTLLN-PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 544 (561)
Q Consensus 486 ~~e~L~~aL~~L~-erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKL 544 (561)
.+..+..+++.|+ +.+|.||.++|. .+++..+|++.||+|+.++-.+.++|++.|
T Consensus 44 ~k~ei~~~I~~l~d~~~r~iL~~~Yi----~~~~~~~I~~~l~~S~~t~yr~~~~Al~~L 99 (100)
T PF07374_consen 44 EKLEIRRAINKLEDPDERLILRMRYI----NKLTWEQIAEELNISRRTYYRIHKKALKEL 99 (100)
T ss_pred HHHHHHHHHHHccChhHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHhc
Confidence 3456788888886 899999999998 789999999999999999999999999876
No 145
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=97.59 E-value=0.00016 Score=60.21 Aligned_cols=47 Identities=19% Similarity=0.213 Sum_probs=41.7
Q ss_pred HHHHHHhcCCHHHHHHHHHH-hcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556 489 HVRNLLTLLNPKERCIVRLR-FGIEDGKPKSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 489 ~L~~aL~~L~erER~VL~LR-yGL~d~e~~Tl~EIAe~LGISrerVRqie~R 539 (561)
.+.+-|+.||++.+.++.|. |. +++|++|||+.||||..+|+.++++
T Consensus 8 ~~~~~l~~l~~~~r~af~L~R~~----eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 8 KLAERLTWVDSLAEAAAALAREE----AGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred hHHHHHhcCCHHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 46677899999999999995 55 7999999999999999999998775
No 146
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=97.54 E-value=0.0003 Score=55.02 Aligned_cols=48 Identities=27% Similarity=0.428 Sum_probs=42.0
Q ss_pred CCHHHHHHHHHHhccc--C-CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008556 497 LNPKERCIVRLRFGIE--D-GKPKSLSEVGNIFGLSKERVRQLESRALYRL 544 (561)
Q Consensus 497 L~erER~VL~LRyGL~--d-~e~~Tl~EIAe~LGISrerVRqie~RALkKL 544 (561)
|+++|++||..-|-.+ + ...-|+.|||+.||||+.+|..++.+|.+||
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~LRrae~kl 51 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSEHLRRAERKL 51 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 7899999999866533 3 4678999999999999999999999999987
No 147
>TIGR01321 TrpR trp operon repressor, proteobacterial. This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis.
Probab=97.48 E-value=0.00017 Score=62.70 Aligned_cols=49 Identities=22% Similarity=0.244 Sum_probs=42.7
Q ss_pred HHHHHHH-hcCCHHHHHHHHHHhcccC---CCCCCHHHHHHHhCCCHHHHHHH
Q 008556 488 QHVRNLL-TLLNPKERCIVRLRFGIED---GKPKSLSEVGNIFGLSKERVRQL 536 (561)
Q Consensus 488 e~L~~aL-~~L~erER~VL~LRyGL~d---~e~~Tl~EIAe~LGISrerVRqi 536 (561)
+.+..+| ..|+|+|+.+|.+||++.+ ..++|++|||+.+|||+.+|.+.
T Consensus 23 ~~l~~~l~~lLTp~E~~~l~~R~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~ 75 (94)
T TIGR01321 23 DDMQLLLELILTRSEREDLGDRIRIVNELLNGNMSQREIASKLGVSIATITRG 75 (94)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHhCCChhhhhHH
Confidence 3566677 5599999999999999987 67899999999999999999764
No 148
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=97.31 E-value=0.00049 Score=66.34 Aligned_cols=47 Identities=23% Similarity=0.352 Sum_probs=43.6
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556 495 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 546 (561)
Q Consensus 495 ~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 546 (561)
..|+++|++||.+.- +|+|.+|||+.||+|..||+....++++||.-
T Consensus 132 ~~LSpRErEVLrLLA-----qGkTnKEIAe~L~IS~rTVkth~srImkKLgV 178 (198)
T PRK15201 132 RHFSVTERHLLKLIA-----SGYHLSETAALLSLSEEQTKSLRRSIMRKLHV 178 (198)
T ss_pred CCCCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 469999999999986 79999999999999999999999999999954
No 149
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=97.28 E-value=0.00045 Score=68.10 Aligned_cols=46 Identities=11% Similarity=0.237 Sum_probs=43.2
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556 496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 546 (561)
Q Consensus 496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 546 (561)
.|++||++||.+.- +|+|.+|||+.||||..||+....+.++||.-
T Consensus 137 ~LT~RE~eVL~lla-----~G~snkeIA~~L~iS~~TVk~h~~~I~~KL~v 182 (207)
T PRK15411 137 SLSRTESSMLRMWM-----AGQGTIQISDQMNIKAKTVSSHKGNIKRKIKT 182 (207)
T ss_pred cCCHHHHHHHHHHH-----cCCCHHHHHHHcCCCHHHHHHHHHHHHHHhCC
Confidence 49999999999986 79999999999999999999999999999963
No 150
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=97.23 E-value=0.00055 Score=66.76 Aligned_cols=46 Identities=22% Similarity=0.291 Sum_probs=43.0
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556 495 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 545 (561)
Q Consensus 495 ~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 545 (561)
..|++||++|+.+.- +|+|.+|||+.||||..||+.+..+.++||-
T Consensus 149 ~~Lt~rE~evl~~~~-----~G~s~~eIA~~l~iS~~TV~~h~~~i~~Kl~ 194 (216)
T PRK10840 149 KRLSPKESEVLRLFA-----EGFLVTEIAKKLNRSIKTISSQKKSAMMKLG 194 (216)
T ss_pred ccCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence 469999999999986 6999999999999999999999999999994
No 151
>PRK13870 transcriptional regulator TraR; Provisional
Probab=97.23 E-value=0.00054 Score=69.09 Aligned_cols=45 Identities=27% Similarity=0.383 Sum_probs=42.5
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556 496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 545 (561)
Q Consensus 496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 545 (561)
.|++||++||.+-= +|+|..|||.+||||..||...+++|++||-
T Consensus 173 ~LT~RE~E~L~W~A-----~GKT~~EIa~ILgISe~TV~~Hl~na~~KLg 217 (234)
T PRK13870 173 WLDPKEATYLRWIA-----VGKTMEEIADVEGVKYNSVRVKLREAMKRFD 217 (234)
T ss_pred CCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence 59999999999976 7999999999999999999999999999994
No 152
>TIGR03020 EpsA transcriptional regulator EpsA. Proteins in this family include a C-terminal LuxR transcriptional regulator domain (pfam00196). These proteins are positioned proximal to either EpsH-containing exopolysaccharide biosynthesis operons of the Methylobacillus type, or the associated PEP-CTERM-containing genes.
Probab=97.23 E-value=0.00057 Score=69.61 Aligned_cols=48 Identities=21% Similarity=0.261 Sum_probs=44.3
Q ss_pred HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556 494 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 546 (561)
Q Consensus 494 L~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 546 (561)
+..|+++|++|+.+.. +|+|.+|||+.||||..||+...+++++||.-
T Consensus 188 ~~~LT~RE~evl~l~a-----~G~s~~eIA~~L~IS~~TVk~hl~~i~~KL~v 235 (247)
T TIGR03020 188 AGLITAREAEILAWVR-----DGKTNEEIAAILGISSLTVKNHLQHIFKKLDV 235 (247)
T ss_pred ccCCCHHHHHHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHhCC
Confidence 4579999999999965 79999999999999999999999999999964
No 153
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=97.21 E-value=0.0006 Score=67.86 Aligned_cols=50 Identities=8% Similarity=-0.050 Sum_probs=46.3
Q ss_pred HHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556 491 RNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 545 (561)
Q Consensus 491 ~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 545 (561)
.++...|++||++||.+.- +|+|.+|||+.|+||..||+....+.++||.
T Consensus 138 ~~~~~~LS~RE~eVL~Lia-----~G~SnkEIA~~L~IS~~TVk~hvs~I~~KLg 187 (217)
T PRK13719 138 LEAKNKVTKYQNDVFILYS-----FGFSHEYIAQLLNITVGSSKNKISEILKFFG 187 (217)
T ss_pred hhccCCCCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 5667899999999999976 7999999999999999999999999999994
No 154
>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=97.21 E-value=0.00058 Score=68.59 Aligned_cols=48 Identities=19% Similarity=0.267 Sum_probs=44.3
Q ss_pred HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556 494 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 546 (561)
Q Consensus 494 L~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 546 (561)
...|+++|++||.+.. +|+|..|||++||||..+|+..+.++++||+.
T Consensus 169 ~~~Lt~re~evl~~~a-----~G~t~~eIa~~l~is~~Tv~~~l~~~~~kl~~ 216 (232)
T TIGR03541 169 AGVLSEREREVLAWTA-----LGRRQADIAAILGISERTVENHLRSARRKLGV 216 (232)
T ss_pred hccCCHHHHHHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCC
Confidence 3579999999999964 79999999999999999999999999999974
No 155
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=97.20 E-value=0.00064 Score=67.29 Aligned_cols=46 Identities=20% Similarity=0.342 Sum_probs=43.2
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556 495 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 545 (561)
Q Consensus 495 ~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 545 (561)
..|++||++||.+.- +|+|.+|||+.|+||..||+....+.++||.
T Consensus 133 ~~LT~RE~eVL~ll~-----~G~snkeIA~~L~iS~~TV~~h~~~I~~KLg 178 (207)
T PRK11475 133 RMLSPTEREILRFMS-----RGYSMPQIAEQLERNIKTIRAHKFNVMSKLG 178 (207)
T ss_pred CCCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence 469999999999986 6999999999999999999999999999994
No 156
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=97.16 E-value=0.00073 Score=68.34 Aligned_cols=45 Identities=16% Similarity=0.258 Sum_probs=42.8
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556 496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 545 (561)
Q Consensus 496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 545 (561)
.|++||++||.+-. +|+|..|||++||||..||+..+.++++||-
T Consensus 179 ~LT~rE~evl~~~a-----~G~t~~eIa~~l~is~~TV~~h~~~~~~KL~ 223 (240)
T PRK10188 179 NFSKREKEILKWTA-----EGKTSAEIAMILSISENTVNFHQKNMQKKFN 223 (240)
T ss_pred CCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 69999999999986 7999999999999999999999999999995
No 157
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=97.15 E-value=0.00076 Score=67.17 Aligned_cols=48 Identities=17% Similarity=0.127 Sum_probs=44.2
Q ss_pred HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556 494 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 546 (561)
Q Consensus 494 L~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 546 (561)
+..|++||++|+.+.+ +|+|.+|||+.|++|..+|+....++++||.-
T Consensus 153 ~~~Lt~rE~~Vl~l~~-----~G~s~~eIA~~L~iS~~TVk~~~~~i~~Kl~v 200 (216)
T PRK10100 153 SALLTHREKEILNKLR-----IGASNNEIARSLFISENTVKTHLYNLFKKIAV 200 (216)
T ss_pred cCCCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 3469999999999998 68999999999999999999999999999953
No 158
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=97.02 E-value=0.0017 Score=57.89 Aligned_cols=53 Identities=19% Similarity=0.164 Sum_probs=48.4
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 008556 496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA 552 (561)
Q Consensus 496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~ 552 (561)
.|+..|-+.|+|.+. +++|++|-|+.||||+.|+-.++..|.+|+-..|....
T Consensus 41 ~L~~dElEAiRL~D~----egl~QeeaA~~MgVSR~T~~ril~~ARkKiA~ALv~Gk 93 (106)
T PF02001_consen 41 VLTVDELEAIRLVDY----EGLSQEEAAERMGVSRPTFQRILESARKKIADALVEGK 93 (106)
T ss_pred EeeHHHHHHHHHHHH----cCCCHHHHHHHcCCcHHHHHHHHHHHHHHHHHHHHCCC
Confidence 478888999999998 89999999999999999999999999999999886543
No 159
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=97.02 E-value=0.0011 Score=65.73 Aligned_cols=46 Identities=30% Similarity=0.371 Sum_probs=43.0
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556 495 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 545 (561)
Q Consensus 495 ~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 545 (561)
..|++||++|+++-- +|+|.+|||+.|++|..||+.+..+.++||.
T Consensus 147 ~~LT~RE~eVL~lla-----~G~snkeIA~~L~iS~~TVk~h~~~i~~KL~ 192 (211)
T COG2197 147 ELLTPRELEVLRLLA-----EGLSNKEIAEELNLSEKTVKTHVSNILRKLG 192 (211)
T ss_pred CCCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHhHHHHHHHHHHHHcC
Confidence 469999999999875 7999999999999999999999999999994
No 160
>COG4566 TtrR Response regulator [Signal transduction mechanisms]
Probab=96.96 E-value=0.003 Score=61.62 Aligned_cols=59 Identities=17% Similarity=0.260 Sum_probs=52.5
Q ss_pred HHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008556 485 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 548 (561)
Q Consensus 485 e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 548 (561)
.....+...+.+|++|||+|+..-- .|+..++||..||||.-||..+-.+.++||+..-
T Consensus 131 ~~~~~~~~~l~tLT~RERqVl~~vV-----~G~~NKqIA~dLgiS~rTVe~HRanvM~Km~a~S 189 (202)
T COG4566 131 DRQAAIRARLATLTPRERQVLDLVV-----RGLMNKQIAFDLGISERTVELHRANVMEKMQARS 189 (202)
T ss_pred HHHHHHHHHHHhcCHHHHHHHHHHH-----cCcccHHHHHHcCCchhhHHHHHHHHHHHHhhcc
Confidence 4456788999999999999999876 6899999999999999999999999999997643
No 161
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=96.96 E-value=0.0026 Score=50.11 Aligned_cols=47 Identities=34% Similarity=0.441 Sum_probs=42.6
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556 495 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 546 (561)
Q Consensus 495 ~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 546 (561)
..|+++|++|+.+.- .|++..|||..+|+|..+|+....++.+||.-
T Consensus 3 ~~Lt~rE~~v~~l~~-----~G~s~~eia~~l~is~~tV~~h~~~i~~Kl~~ 49 (65)
T COG2771 3 ADLTPREREILRLVA-----QGKSNKEIARILGISEETVKTHLRNIYRKLGV 49 (65)
T ss_pred ccCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Confidence 368999999998876 57999999999999999999999999999864
No 162
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=96.95 E-value=0.0011 Score=49.70 Aligned_cols=41 Identities=24% Similarity=0.339 Sum_probs=24.3
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556 495 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 495 ~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R 539 (561)
..|++.||..|...+- +|+|..+||+.||+|+.||...++|
T Consensus 3 ~~Lt~~eR~~I~~l~~----~G~s~~~IA~~lg~s~sTV~relkR 43 (44)
T PF13936_consen 3 KHLTPEERNQIEALLE----QGMSIREIAKRLGRSRSTVSRELKR 43 (44)
T ss_dssp ---------HHHHHHC----S---HHHHHHHTT--HHHHHHHHHH
T ss_pred cchhhhHHHHHHHHHH----cCCCHHHHHHHHCcCcHHHHHHHhc
Confidence 4689999999988776 8899999999999999999988776
No 163
>PRK09483 response regulator; Provisional
Probab=96.86 E-value=0.0019 Score=61.73 Aligned_cols=46 Identities=22% Similarity=0.300 Sum_probs=42.2
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556 495 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 545 (561)
Q Consensus 495 ~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 545 (561)
..|++||++||.+.. +|+|.+|||+.|++|..||+.+..+.++||-
T Consensus 147 ~~Lt~rE~~vl~~~~-----~G~~~~~Ia~~l~is~~TV~~~~~~i~~Kl~ 192 (217)
T PRK09483 147 ASLSERELQIMLMIT-----KGQKVNEISEQLNLSPKTVNSYRYRMFSKLN 192 (217)
T ss_pred cccCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 469999999998764 7899999999999999999999999999983
No 164
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=96.75 E-value=0.003 Score=58.97 Aligned_cols=46 Identities=22% Similarity=0.382 Sum_probs=42.3
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556 495 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 545 (561)
Q Consensus 495 ~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 545 (561)
..|+++|++||.+ +. ++++.+|||+.+++|..||+....++++||.
T Consensus 148 ~~lt~~e~~vl~l-~~----~g~~~~~Ia~~l~~s~~tv~~~~~~~~~kl~ 193 (211)
T PRK15369 148 PLLTPRERQILKL-IT----EGYTNRDIAEQLSISIKTVETHRLNMMRKLD 193 (211)
T ss_pred cCCCHHHHHHHHH-HH----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 4599999999998 44 7899999999999999999999999999995
No 165
>TIGR01637 phage_arpU phage transcriptional regulator, ArpU family. This model represents a family of phage proteins, including ArpU, called a putative autolysin regulatory protein. ArpU was described as a regulator of cellular muramidase-2 of Enterococcus hirae but appears to have been cloned from a prophage. This family appears related to the RinA family of bacteriophage transcriptional activators and to some sporulation-specific sigma factors. We propose that this is a phage transcriptional activator family.
Probab=96.74 E-value=0.0096 Score=54.55 Aligned_cols=63 Identities=21% Similarity=0.231 Sum_probs=53.7
Q ss_pred HHHHHHHHHH-hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008556 485 LMRQHVRNLL-TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 549 (561)
Q Consensus 485 e~~e~L~~aL-~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 549 (561)
.....+..++ ..|++.+|+||..+|. . .++++..+|+..+|+|+.+...+.++|+.++-..+.
T Consensus 67 ~~~~~i~~ai~~~l~~~~r~Il~~~Yl-~-~~~~~~~~I~~~l~~s~~~~y~~k~~Al~~fA~~l~ 130 (132)
T TIGR01637 67 QEARAIVNAIVNQLDEISRQILYDKYL-E-PDQKYDYQIMMELGYSHRQYYRIKKRALLRFATLYG 130 (132)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHHc-C-ccccchHHHHHHhCCcHHHHHHHHHHHHHHHHHHhC
Confidence 3345677777 9999999999999997 2 137899999999999999999999999999987654
No 166
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=96.67 E-value=0.004 Score=61.84 Aligned_cols=53 Identities=23% Similarity=0.350 Sum_probs=45.9
Q ss_pred cCCHHHHHHHHHHhccc--C-CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008556 496 LLNPKERCIVRLRFGIE--D-GKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 548 (561)
Q Consensus 496 ~L~erER~VL~LRyGL~--d-~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 548 (561)
.|+++|++||+.-|-+| | ....+++|||+.||||+.++.+++.+|.+||=..+
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLRrAe~Kl~~~~ 210 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLRRAERKLIEAY 210 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 69999999999876543 3 36789999999999999999999999999996643
No 167
>PRK01381 Trp operon repressor; Provisional
Probab=96.50 E-value=0.003 Score=55.50 Aligned_cols=48 Identities=27% Similarity=0.320 Sum_probs=40.4
Q ss_pred HHHHHHHhc-CCHHHHHHHHHHhcccC---CCCCCHHHHHHHhCCCHHHHHH
Q 008556 488 QHVRNLLTL-LNPKERCIVRLRFGIED---GKPKSLSEVGNIFGLSKERVRQ 535 (561)
Q Consensus 488 e~L~~aL~~-L~erER~VL~LRyGL~d---~e~~Tl~EIAe~LGISrerVRq 535 (561)
+.+..+|.. |+|+|+.+|..||++.. ..++|++||++.+|||..+|.+
T Consensus 23 ~~~~~~l~~llTp~Er~al~~R~~I~~~L~~g~~sQREIa~~lGvSiaTITR 74 (99)
T PRK01381 23 DLHLPLLTLLLTPDEREALGTRVRIVEELLRGELSQREIKQELGVGIATITR 74 (99)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHHHHHHHcCCcCHHHHHHHhCCceeeehh
Confidence 456666655 99999999999999875 4579999999999999988853
No 168
>PRK10651 transcriptional regulator NarL; Provisional
Probab=96.47 E-value=0.0052 Score=58.12 Aligned_cols=46 Identities=20% Similarity=0.294 Sum_probs=42.4
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556 495 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 545 (561)
Q Consensus 495 ~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 545 (561)
..|+++|++|+.+.. ++++.++||+.+++|..||+....++++||.
T Consensus 154 ~~Lt~rE~~vl~~l~-----~g~~~~~ia~~l~is~~tV~~~~~~l~~Kl~ 199 (216)
T PRK10651 154 NQLTPRERDILKLIA-----QGLPNKMIARRLDITESTVKVHVKHMLKKMK 199 (216)
T ss_pred ccCCHHHHHHHHHHH-----cCCCHHHHHHHcCCCHHHHHHHHHHHHHHcC
Confidence 459999999999865 6899999999999999999999999999995
No 169
>COG1356 tfx Transcriptional regulator [DNA replication, recombination and repair]
Probab=96.41 E-value=0.0026 Score=57.89 Aligned_cols=48 Identities=25% Similarity=0.359 Sum_probs=44.1
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008556 496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 548 (561)
Q Consensus 496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 548 (561)
-|+++|-.||.||- +|+|++|||++||-|+..|+-++++|+.++.+.-
T Consensus 8 flte~qikvl~lRe-----kG~tQ~eIA~~L~TTraNvSaIEkrA~enIekar 55 (143)
T COG1356 8 FLTEQQIKVLVLRE-----KGLTQSEIARILKTTRANVSAIEKRALENIEKAR 55 (143)
T ss_pred eeehhheeeeehhh-----ccccHHHHHHHHccchhhHHHHHHHHHHHHHHHH
Confidence 48899999999997 7999999999999999999999999999997753
No 170
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=96.39 E-value=0.0094 Score=55.32 Aligned_cols=53 Identities=13% Similarity=0.190 Sum_probs=46.7
Q ss_pred HHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556 489 HVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 546 (561)
Q Consensus 489 ~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 546 (561)
.+...+..|+++|++||.+.+ .+++.++||+.+|+|..+|+....++++||+.
T Consensus 134 ~~~~~~~~l~~~e~~vl~~~~-----~~~~~~~ia~~l~~s~~tv~~~~~~~~~kl~~ 186 (202)
T PRK09390 134 DIRARIASLSERERQVMDGLV-----AGLSNKVIARDLDISPRTVEVYRANVMTKMQA 186 (202)
T ss_pred HHHHHHHhhhhhHHHHHHHHH-----ccCchHHHHHHcCCCHHHHHHHHHHHHHHHcc
Confidence 455667889999999999744 57899999999999999999999999999964
No 171
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=96.34 E-value=0.015 Score=51.12 Aligned_cols=48 Identities=25% Similarity=0.328 Sum_probs=43.7
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556 495 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 546 (561)
Q Consensus 495 ~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 546 (561)
.-|+.+|+..+.++|. .++|+.|||+.++||+..|...++|.-+.|-.
T Consensus 16 sLLT~KQ~~Y~~lyy~----dDlSl~EIAee~~VSRqAIyDnIKr~~~~L~~ 63 (105)
T COG2739 16 SLLTKKQKNYLELYYL----DDLSLSEIAEEFNVSRQAIYDNIKRTEKILED 63 (105)
T ss_pred HHHhHHHHHHHHHHHH----hhccHHHHHHHhCccHHHHHHHHHHHHHHHHH
Confidence 4589999999999998 89999999999999999999999998777644
No 172
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=96.07 E-value=0.017 Score=50.31 Aligned_cols=52 Identities=19% Similarity=0.148 Sum_probs=46.8
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008556 496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 551 (561)
Q Consensus 496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 551 (561)
.|+..|-+.|+|... ++++++|-|..||||+.|+-..++.|++|+-.++...
T Consensus 33 ~lt~eElEAlRLvD~----~~l~QeeAA~rMgISr~Tfwr~l~sAR~KvA~aLveG 84 (99)
T COG1342 33 ILTIEELEALRLVDY----EGLTQEEAALRMGISRQTFWRLLTSARKKVADALVEG 84 (99)
T ss_pred eecHHHHHHHHHHhH----hhccHHHHHHHhcccHHHHHHHHHHHHHHHHHHHhcC
Confidence 367778889999988 8999999999999999999999999999999887654
No 173
>PRK15320 transcriptional activator SprB; Provisional
Probab=95.93 E-value=0.014 Score=57.34 Aligned_cols=47 Identities=19% Similarity=0.280 Sum_probs=43.1
Q ss_pred HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556 494 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 545 (561)
Q Consensus 494 L~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 545 (561)
--.|+++|.+|+.+-- +|+|.+|||+.|++|..+|+....+.+.||.
T Consensus 162 ~~~LSdREIEVL~LLA-----kG~SNKEIAekL~LS~KTVSTYKnRLLeKLg 208 (251)
T PRK15320 162 PPGVTQAKYALLILLS-----SGHPAIELAKKFGLGTKTVSIYRKKVMYRLG 208 (251)
T ss_pred CCCCCHHHHHHHHHHH-----cCCCHHHHHHHhccchhhHHHHHHHHHHHcC
Confidence 3679999999999876 7999999999999999999999999999985
No 174
>PRK10403 transcriptional regulator NarP; Provisional
Probab=95.86 E-value=0.016 Score=54.57 Aligned_cols=46 Identities=15% Similarity=0.230 Sum_probs=42.0
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556 495 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 545 (561)
Q Consensus 495 ~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 545 (561)
..|+++|.+|+.+.. +++|.++||+.+|+|..+|+....+.++||.
T Consensus 152 ~~Lt~~e~~vl~~~~-----~g~s~~~ia~~l~~s~~tv~~~~~~i~~kl~ 197 (215)
T PRK10403 152 SVLTERELDVLHELA-----QGLSNKQIASVLNISEQTVKVHIRNLLRKLN 197 (215)
T ss_pred ccCCHHHHHHHHHHH-----CCCCHHHHHHHcCCCHHHHHHHHHHHHHHcC
Confidence 459999999998765 6899999999999999999999999999984
No 175
>COG4941 Predicted RNA polymerase sigma factor containing a TPR repeat domain [Transcription]
Probab=95.53 E-value=0.32 Score=51.65 Aligned_cols=159 Identities=18% Similarity=0.137 Sum_probs=96.6
Q ss_pred HHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhH
Q 008556 323 EKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENI 402 (561)
Q Consensus 323 e~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~ 402 (561)
+..+..-.+-++.---+|.++=.-.||.+||.|+.-.+.-.+=-|-++ -..|.+..-|+.-.+.++++.+.-..|.+
T Consensus 8 e~~~r~~~~r~~a~L~r~~rd~dlAEEa~~dA~~~Ale~WPr~G~P~~--PaAWL~~v~R~~aiD~~Rr~~~~~~~~~e- 84 (415)
T COG4941 8 EAAARIERPRAMAALARYLRDLDLAEEALQDAFAAALERWPRAGPPRN--PAAWLIAVGRNRAIDRVRRRARRDAAPPE- 84 (415)
T ss_pred HHHHHHhhhHHHHHHHHHhcccchHHHHHHHHHHHHHHhCcccCCCCC--hHHHHHHHHhhhHHHHHHHHHHhccCChh-
Confidence 334444444444444556666556799999999865555444333332 56788877888888888776533222211
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHHHH
Q 008556 403 YTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQ 482 (561)
Q Consensus 403 ~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~le 482 (561)
+ .++ . ++.+..+. +.+++...
T Consensus 85 --------------------------l--------------------~~~------~-e~~e~~~a------~~~~d~~i 105 (415)
T COG4941 85 --------------------------L--------------------LLS------D-EDEEMEEA------EALDDEHI 105 (415)
T ss_pred --------------------------h--------------------ccc------c-cchhhhcc------cccccccc
Confidence 1 000 0 00000000 00111111
Q ss_pred HHHHHHHHHHHH-hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008556 483 KQLMRQHVRNLL-TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 547 (561)
Q Consensus 483 ~~e~~e~L~~aL-~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 547 (561)
.++....|--|. -.|++.+|-.|.||.. -|+|..|||..|=|+..++-|.+.||.++++..
T Consensus 106 ~Dd~LRLiFvccHPal~~~~riALtLR~v----~GLs~~eIArAFLv~e~am~QRivRAK~ri~~a 167 (415)
T COG4941 106 RDDRLRLIFVCCHPALPPEQRIALTLRLV----GGLSTAEIARAFLVPEAAMAQRIVRAKARIREA 167 (415)
T ss_pred chhhHHhhhhhcCCCCChhhHHHHHHHHH----cCCcHHHHHHHHcCCcHHHHHHHHHHHHHHHhc
Confidence 111112222222 5699999999999988 789999999999999999999999999999874
No 176
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=95.44 E-value=0.031 Score=52.76 Aligned_cols=45 Identities=24% Similarity=0.242 Sum_probs=40.2
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556 496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 545 (561)
Q Consensus 496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 545 (561)
.|+++|.+|+.+.. +++|.+|||+.+++|..+|+....++++||.
T Consensus 149 ~lt~re~~vl~~l~-----~g~s~~eIa~~l~~s~~tv~~~~~~~~~kl~ 193 (210)
T PRK09935 149 VLSNREVTILRYLV-----SGLSNKEIADQLLLSNKTVSAHKSNIYGKLG 193 (210)
T ss_pred cCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 48899999887644 5799999999999999999999999999984
No 177
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=95.42 E-value=0.031 Score=52.80 Aligned_cols=47 Identities=21% Similarity=0.320 Sum_probs=42.5
Q ss_pred HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556 494 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 545 (561)
Q Consensus 494 L~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 545 (561)
+..|+++|++|+.+.. .+.+.+|||+.+++|..+|+....+.++||.
T Consensus 141 ~~~lt~~E~~vl~~l~-----~g~~~~~I~~~l~~s~~tv~~~~~~l~~Kl~ 187 (204)
T PRK09958 141 LDSLSKQEISVMRYIL-----DGKDNNDIAEKMFISNKTVSTYKSRLMEKLE 187 (204)
T ss_pred cccCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 3569999999998876 5789999999999999999999999999983
No 178
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=95.30 E-value=0.027 Score=52.94 Aligned_cols=46 Identities=20% Similarity=0.255 Sum_probs=42.1
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556 495 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 545 (561)
Q Consensus 495 ~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 545 (561)
..|+++|++|+.+.. ++++.++||+.+++|..+|+.+..+.++||.
T Consensus 136 ~~Lt~~E~~il~~l~-----~g~~~~~Ia~~l~~s~~tv~~~~~~l~~Kl~ 181 (196)
T PRK10360 136 DPLTKRERQVAEKLA-----QGMAVKEIAAELGLSPKTVHVHRANLMEKLG 181 (196)
T ss_pred cCCCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 469999999999865 5799999999999999999999999999985
No 179
>PRK13558 bacterio-opsin activator; Provisional
Probab=95.30 E-value=0.033 Score=63.71 Aligned_cols=55 Identities=13% Similarity=0.070 Sum_probs=45.7
Q ss_pred HhcCCHHHHHHHHHHhccc---CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008556 494 LTLLNPKERCIVRLRFGIE---DGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 548 (561)
Q Consensus 494 L~~L~erER~VL~LRyGL~---d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 548 (561)
...|+++|+++|..-|..+ -..+-|.+|||+.||||+.++.+++.+|.+||=..+
T Consensus 605 ~~~lt~~q~e~l~~a~~~gyf~~pr~~~~~e~a~~l~is~~t~~~~lr~a~~~l~~~~ 662 (665)
T PRK13558 605 ENDLTDRQLTALQKAYVSGYFEWPRRVEGEELAESMGISRSTFHQHLRAAERKLVGAF 662 (665)
T ss_pred hhhCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 4679999999999988721 113349999999999999999999999999986543
No 180
>PRK04841 transcriptional regulator MalT; Provisional
Probab=95.21 E-value=0.031 Score=65.95 Aligned_cols=46 Identities=11% Similarity=0.172 Sum_probs=43.0
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556 495 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 545 (561)
Q Consensus 495 ~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 545 (561)
..|+++|++|+.+.. +|+|.+|||+.|+||..||+..+++.++||.
T Consensus 837 ~~lt~~e~~v~~~~~-----~g~~~~~ia~~l~~s~~tv~~h~~~~~~kl~ 882 (903)
T PRK04841 837 SPLTQREWQVLGLIY-----SGYSNEQIAGELDVAATTIKTHIRNLYQKLG 882 (903)
T ss_pred CCCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 449999999999976 7999999999999999999999999999995
No 181
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=94.97 E-value=0.032 Score=39.25 Aligned_cols=27 Identities=30% Similarity=0.643 Sum_probs=19.8
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556 516 PKSLSEVGNIFGLSKERVRQLESRALYRLKQ 546 (561)
Q Consensus 516 ~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 546 (561)
++|.+|||+.+|+|+|+|. |++++|++
T Consensus 2 ~mtr~diA~~lG~t~ETVS----R~l~~l~~ 28 (32)
T PF00325_consen 2 PMTRQDIADYLGLTRETVS----RILKKLER 28 (32)
T ss_dssp E--HHHHHHHHTS-HHHHH----HHHHHHHH
T ss_pred CcCHHHHHHHhCCcHHHHH----HHHHHHHH
Confidence 4789999999999999996 56666664
No 182
>PF12645 HTH_16: Helix-turn-helix domain; InterPro: IPR024760 This domain appears to be a helix-turn-helix domain, suggesting a transcriptional regulatory protein. Some proteins with this domain are annotated as conjugative transposon proteins.
Probab=94.87 E-value=0.11 Score=42.25 Aligned_cols=56 Identities=18% Similarity=0.286 Sum_probs=45.1
Q ss_pred HHHHHhhcHHHHHHHHHHHHHHHHHHHHhh----hC--CCCCHHHHHHHHHHHHHHhhhhcC
Q 008556 311 LKSELHSGNSSREKLINANLRLVVHVAKQY----QG--RGISLHDLLQEGSMGLMKSVEKFK 366 (561)
Q Consensus 311 L~~~l~~G~~Are~LI~~nlrLV~sIArrY----~~--~g~~~eDLIQEG~IGLirAiekFD 366 (561)
+.++.+|+..|.++++..|.+++.+.+.+- .+ ++.-=+|+-|+-...|++++-+|+
T Consensus 4 I~~A~~GD~~A~~~IL~~y~~yI~kls~r~~~d~~g~~~~~vDedl~q~l~~kLi~~I~~F~ 65 (65)
T PF12645_consen 4 IKAAKQGDPEAMEEILKHYEPYISKLSTRTLYDEYGNVYGYVDEDLKQRLEIKLIEAILKFE 65 (65)
T ss_pred HHHHHcCCHHHHHHHHHHHHHHHHHHHHhhcccccCCcCceeCHHHHHHHHHHHHHHHHccC
Confidence 445556677999999999999999998772 22 133349999999999999999996
No 183
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=94.53 E-value=0.057 Score=44.00 Aligned_cols=45 Identities=18% Similarity=0.417 Sum_probs=29.4
Q ss_pred HhcCCHHHHHHHHH--HhcccCCCCCCHHHHHHHhCCC-HHHHHHHHH
Q 008556 494 LTLLNPKERCIVRL--RFGIEDGKPKSLSEVGNIFGLS-KERVRQLES 538 (561)
Q Consensus 494 L~~L~erER~VL~L--RyGL~d~e~~Tl~EIAe~LGIS-rerVRqie~ 538 (561)
+..|+++|++||.. .|.-..|-+-|.+|||+.||++ ..+|.+.+.
T Consensus 1 M~~LT~rQ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~ 48 (65)
T PF01726_consen 1 MKELTERQKEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLK 48 (65)
T ss_dssp -----HHHHHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHH
Confidence 35799999999886 3333456788999999999997 999987654
No 184
>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD. This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.
Probab=94.52 E-value=0.079 Score=45.82 Aligned_cols=37 Identities=14% Similarity=0.220 Sum_probs=30.8
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHH
Q 008556 495 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLE 537 (561)
Q Consensus 495 ~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie 537 (561)
..|++| ..|+.+.- .++|..+||+.+|||+.||..+.
T Consensus 35 ~~Ls~R-~~I~~ll~-----~G~S~~eIA~~LgISrsTIyRi~ 71 (88)
T TIGR02531 35 QSLAQR-LQVAKMLK-----QGKTYSDIEAETGASTATISRVK 71 (88)
T ss_pred HhhhHH-HHHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHH
Confidence 458888 77877754 57999999999999999998833
No 185
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=94.51 E-value=0.11 Score=39.10 Aligned_cols=40 Identities=18% Similarity=0.271 Sum_probs=28.9
Q ss_pred CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556 497 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 497 L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R 539 (561)
|++.++.||..-+- +.+.|..|||+.+|+|..+|++++++
T Consensus 1 l~~~~~~Il~~l~~---~~~~t~~ela~~~~is~~tv~~~l~~ 40 (48)
T PF13412_consen 1 LDETQRKILNYLRE---NPRITQKELAEKLGISRSTVNRYLKK 40 (48)
T ss_dssp --HHHHHHHHHHHH---CTTS-HHHHHHHHTS-HHHHHHHHHH
T ss_pred CCHHHHHHHHHHHH---cCCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 56778888866543 35699999999999999999876554
No 186
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=94.44 E-value=0.1 Score=40.50 Aligned_cols=50 Identities=18% Similarity=0.242 Sum_probs=42.1
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008556 496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 548 (561)
Q Consensus 496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 548 (561)
+|+..++-++.+.|. ..+.++++||..+|||+.+|.++.+..+.-|...+
T Consensus 2 kLs~~d~lll~L~~L---R~~~~~~~La~~FgIs~stvsri~~~~~~~L~~~l 51 (53)
T PF13613_consen 2 KLSLEDQLLLTLMYL---RLNLTFQDLAYRFGISQSTVSRIFHEWIPLLYQVL 51 (53)
T ss_pred CCCHHHHHHHHHHHH---HcCCcHhHHhhheeecHHHHHHHHHHHHHHHHHhc
Confidence 578888888888665 26789999999999999999999999888776543
No 187
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=94.27 E-value=0.039 Score=41.69 Aligned_cols=32 Identities=28% Similarity=0.361 Sum_probs=22.6
Q ss_pred HHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008556 504 IVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA 540 (561)
Q Consensus 504 VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RA 540 (561)
||.+.. +++|..+||+.||||+.+|+++.++-
T Consensus 10 ii~l~~-----~G~s~~~ia~~lgvs~~Tv~~w~kr~ 41 (50)
T PF13384_consen 10 IIRLLR-----EGWSIREIAKRLGVSRSTVYRWIKRY 41 (50)
T ss_dssp HHHHHH-----HT--HHHHHHHHTS-HHHHHHHHT--
T ss_pred HHHHHH-----CCCCHHHHHHHHCcCHHHHHHHHHHc
Confidence 555554 58999999999999999999887653
No 188
>PF06530 Phage_antitermQ: Phage antitermination protein Q; InterPro: IPR010534 This entry is represented by Bacteriophage 933W, GpQ. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several phage antitermination protein Q and related bacterial sequences. Phage 993W gene Q encodes a phage-specific positive regulator of late gene expression, thought, by analogy to the corresponding gene of phage lambda, to be a transcription antiterminator. GpQ positively regulates expression of the phage late gene operons. Bacterial host RNA polymerase modified by antitermination proteins transcribes through termination sites that otherwise prevent expression of the regulated genes [, ].; GO: 0003677 DNA binding, 0060567 negative regulation of transcription termination, DNA-dependent
Probab=94.13 E-value=0.29 Score=44.84 Aligned_cols=55 Identities=18% Similarity=0.123 Sum_probs=49.1
Q ss_pred HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 008556 494 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA 552 (561)
Q Consensus 494 L~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~ 552 (561)
|..-.+.+-+||.++|. .++|...||..+++|...||+.+.+|-..+..++.-.+
T Consensus 60 L~~~~~~~~~ll~~~Yv----~g~s~r~IA~~~~~s~~~ir~~l~~ae~~i~g~l~~~~ 114 (125)
T PF06530_consen 60 LKKRDPEEYDLLILYYV----YGWSKRQIARKLKCSEGKIRKRLQRAEGFIDGCLSMLT 114 (125)
T ss_pred HHccCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHhhhhHhhhhHHhh
Confidence 45578999999999999 89999999999999999999999999999988865443
No 189
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=94.10 E-value=0.07 Score=56.41 Aligned_cols=36 Identities=22% Similarity=0.344 Sum_probs=32.7
Q ss_pred HHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008556 503 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 542 (561)
Q Consensus 503 ~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALk 542 (561)
.|-.|||. +++|+.|||++|||||.+|.+++.+|++
T Consensus 20 ~vA~lYY~----~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~ 55 (318)
T PRK15418 20 RIAWFYYH----DGLTQSEIGERLGLTRLKVSRLLEKGRQ 55 (318)
T ss_pred HHHHHHHh----cCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 46678888 8999999999999999999999999975
No 190
>PF05263 DUF722: Protein of unknown function (DUF722); InterPro: IPR007927 This entry is represented by Bacteriophage bIL285, Orf38. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=93.96 E-value=0.21 Score=46.26 Aligned_cols=53 Identities=17% Similarity=0.356 Sum_probs=44.3
Q ss_pred HHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008556 486 MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA 540 (561)
Q Consensus 486 ~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RA 540 (561)
..+.|...++.|.+.++.||.+||+ ...++|..+||..|+||..+++.....-
T Consensus 71 ~k~~id~~~~~l~de~k~Ii~lry~--~r~~~TW~~IA~~l~i~erta~r~~~~f 123 (130)
T PF05263_consen 71 QKEAIDRWLETLIDEEKRIIKLRYD--RRSRRTWYQIAQKLHISERTARRWRDRF 123 (130)
T ss_pred HHHHHHHHHHhhCHHHHHHHHHHHc--ccccchHHHHHHHhCccHHHHHHHHHHH
Confidence 3456788889999999999999998 3346999999999999999998765443
No 191
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 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 recognised by the major sigma factors [, ]. 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 [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=93.74 E-value=0.13 Score=42.41 Aligned_cols=38 Identities=32% Similarity=0.613 Sum_probs=29.6
Q ss_pred HHHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHHHH
Q 008556 278 IRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSEL 315 (561)
Q Consensus 278 ~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~~l 315 (561)
.++.+++.+|+..+||+||.+|.|+.+|++.+.+...+
T Consensus 4 ~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l 41 (78)
T PF04539_consen 4 RKIERARRELEQELGREPTDEEIAEELGISVEEVRELL 41 (78)
T ss_dssp HHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHH
Confidence 35677889999999999999999999999988876443
No 192
>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=93.48 E-value=0.17 Score=33.67 Aligned_cols=36 Identities=19% Similarity=0.335 Sum_probs=27.8
Q ss_pred CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHH
Q 008556 497 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQL 536 (561)
Q Consensus 497 L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqi 536 (561)
+++.++..+...|. .+.+..+||+.+|+|+.+|..+
T Consensus 6 ~~~~~~~~i~~~~~----~~~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 6 LTPEQIEEARRLLA----AGESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred CCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHh
Confidence 45555665555554 5679999999999999999865
No 193
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain. This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.
Probab=93.47 E-value=0.97 Score=45.38 Aligned_cols=35 Identities=31% Similarity=0.574 Sum_probs=29.1
Q ss_pred HHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHH
Q 008556 279 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 313 (561)
Q Consensus 279 ~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~ 313 (561)
++.++...|...+|++||.+|.|+.+|++.+.+..
T Consensus 88 ~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~ 122 (238)
T TIGR02393 88 KLIKAERQLTQELGREPTDEELAERMGMPAEKVRE 122 (238)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence 34456777888899999999999999999887753
No 194
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=93.40 E-value=0.1 Score=39.08 Aligned_cols=32 Identities=25% Similarity=0.296 Sum_probs=23.4
Q ss_pred HHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHH
Q 008556 501 ERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLE 537 (561)
Q Consensus 501 ER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie 537 (561)
..+|+.|+- +|+|..+||+.+|||+.+|.+++
T Consensus 11 ~~~i~~l~~-----~G~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 11 IEEIKELYA-----EGMSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp HHHHHHHHH-----TT--HHHHHHHTTS-HHHHHHHH
T ss_pred HHHHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHH
Confidence 345666664 67999999999999999998765
No 195
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=93.32 E-value=1.1 Score=48.23 Aligned_cols=129 Identities=19% Similarity=0.273 Sum_probs=71.8
Q ss_pred HHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHH-HHHH
Q 008556 280 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEG-SMGL 358 (561)
Q Consensus 280 le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~~l~~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG-~IGL 358 (561)
+.++..+|...+|++||..|.|+.+|++.+.+...+... .. .+++++.+.++ -..|
T Consensus 218 ~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~~-------------------~~----~~SLd~~~~~~~~~~l 274 (367)
T PRK09210 218 LIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIA-------------------QE----PVSLETPIGEEDDSHL 274 (367)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHh-------------------cC----CCCcCCCCCCCCcchh
Confidence 455677888889999999999999999988775432211 11 11111111110 1111
Q ss_pred HHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHH
Q 008556 359 MKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVE 438 (561)
Q Consensus 359 irAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e 438 (561)
...+. |+.............++..+.+++. .+|..-...+.. .+.-..|.+.|.+|||+.+|+|.+
T Consensus 275 ~d~i~--d~~~~~p~~~~~~~~~~~~l~~~l~------~L~~rEr~Vl~l------rygl~~~~~~tl~EIa~~lgvs~e 340 (367)
T PRK09210 275 GDFIE--DQDATSPADHAAYELLKEQLEDVLD------TLTDREENVLRL------RFGLDDGRTRTLEEVGKVFGVTRE 340 (367)
T ss_pred hhhcc--CCCCCCHHHHHHHHHHHHHHHHHHH------hCCHHHHHHHHH------HhccCCCCCccHHHHHHHHCCCHH
Confidence 11111 2111223444455566666666663 233322111111 111123467899999999999999
Q ss_pred HHHHHHH
Q 008556 439 KLERLIF 445 (561)
Q Consensus 439 ~v~~ll~ 445 (561)
+|+.+..
T Consensus 341 rVrQi~~ 347 (367)
T PRK09210 341 RIRQIEA 347 (367)
T ss_pred HHHHHHH
Confidence 9998854
No 196
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=93.19 E-value=1.5 Score=46.66 Aligned_cols=35 Identities=31% Similarity=0.452 Sum_probs=29.5
Q ss_pred HHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHH
Q 008556 279 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 313 (561)
Q Consensus 279 ~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~ 313 (561)
++.+++.+|...+|++||..|.|..+|++.+.+..
T Consensus 174 ~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~ 208 (324)
T PRK07921 174 KLARIKRELHQQLGREATDEELAEESGIPEEKIAD 208 (324)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHH
Confidence 45567778888899999999999999999887753
No 197
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=93.15 E-value=1.2 Score=50.13 Aligned_cols=130 Identities=18% Similarity=0.320 Sum_probs=70.6
Q ss_pred HHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHH-HHHH
Q 008556 279 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQE-GSMG 357 (561)
Q Consensus 279 ~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~~l~~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQE-G~IG 357 (561)
++.+++.+|...+|++||.+|.|+.+|++.+.+....+ +....+++++.+.+ +...
T Consensus 359 kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~~-----------------------~~~~~~SLD~~i~~d~~~~ 415 (509)
T PRK05901 359 KLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQK-----------------------YNREPISLDKTIGKEGDSQ 415 (509)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHH-----------------------hcCCCcccccccccCCccc
Confidence 45567788888999999999999999999887754321 11112222322211 1111
Q ss_pred HHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCH
Q 008556 358 LMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITV 437 (561)
Q Consensus 358 LirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~ 437 (561)
|...+. |+........+..+..+..+..++.. ||..-...+.. + +.-..+.+.|..|||..+||+.
T Consensus 416 l~d~l~--D~~~~~p~~~~~~~~l~~~L~~aL~~------L~eREr~VI~l----R--yGL~~~e~~TL~EIa~~lGVSr 481 (509)
T PRK05901 416 FGDFIE--DSEAVSPVDAVSFTLLQDQLQEVLET------LSEREAGVIRM----R--FGLTDGQPKTLDEIGQVYGVTR 481 (509)
T ss_pred HHHhcc--CCCCCCHHHHHHHHHHHHHHHHHHhh------CCHHHHHHHHH----H--hhccCCCCCCHHHHHHHHCCCH
Confidence 222221 11111223334444455555555532 33222111111 1 1111246789999999999999
Q ss_pred HHHHHHHH
Q 008556 438 EKLERLIF 445 (561)
Q Consensus 438 e~v~~ll~ 445 (561)
++|+++..
T Consensus 482 ERVRQIe~ 489 (509)
T PRK05901 482 ERIRQIES 489 (509)
T ss_pred HHHHHHHH
Confidence 99998844
No 198
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=92.09 E-value=0.29 Score=48.53 Aligned_cols=47 Identities=15% Similarity=0.087 Sum_probs=36.2
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008556 496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 542 (561)
Q Consensus 496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALk 542 (561)
.|+++|.+++.....=..++|+|.+|||+.||+|..||+....++..
T Consensus 158 ~Lt~re~~~l~~~i~~~~~~g~s~~eIA~~l~iS~~Tv~~~~~~~~~ 204 (239)
T PRK10430 158 GLTPQTLRTLCQWIDAHQDYEFSTDELANAVNISRVSCRKYLIWLVN 204 (239)
T ss_pred CCCHHHHHHHHHHHHhCCCCCcCHHHHHHHhCchHHHHHHHHHHHHh
Confidence 48899987764433111237899999999999999999999887754
No 199
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=92.04 E-value=4.4 Score=41.55 Aligned_cols=147 Identities=20% Similarity=0.201 Sum_probs=81.8
Q ss_pred HHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHHHH
Q 008556 248 PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLIN 327 (561)
Q Consensus 248 ~l~~Yl~~i~~~~lLT~eEE~eL~~~i~~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~~l~~G~~Are~LI~ 327 (561)
.+-.||++-. +.--+.--.+++.+ +..+..+|+..+|++||..|.|+..|++.+++...+..+.
T Consensus 88 ei~d~LR~~~--~v~vpR~~~~~~~~------i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~~~-------- 151 (247)
T COG1191 88 EILDYLRKND--SVKVPRSLRELGRR------IEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAIN-------- 151 (247)
T ss_pred HHHHHHHhCC--CccCcHHHHHHHHH------HHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHHhc--------
Confidence 4556888877 22223334444444 4457788899999999999999999999888765433322
Q ss_pred HHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHHHHH
Q 008556 328 ANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLS 407 (561)
Q Consensus 328 ~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~~~l~ 407 (561)
.....++--.....+.+ + + +...+..+..+-.|-..+.+.+++.. +|..-.
T Consensus 152 --~~~~~sld~~~~~~~d~--~------------~---~~~~~~~~~~~~~~~~~~~l~~ai~~------L~EREk---- 202 (247)
T COG1191 152 --GSQLLSLDEDVLKDDDD--D------------V---DDQIENPDDGVEKEELLEILKEAIEP------LPEREK---- 202 (247)
T ss_pred --cccccchhhhhcccccc--c------------h---hhccccchhHHHHHHHHHHHHHHHHc------cCHHHH----
Confidence 11111111111111110 0 1 11122344455566666666666541 222110
Q ss_pred HHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008556 408 KVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIF 445 (561)
Q Consensus 408 ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~ 445 (561)
.| +.-...-+-|..|||+.||||..+|..+..
T Consensus 203 ~V------l~l~y~eelt~kEI~~~LgISes~VSql~k 234 (247)
T COG1191 203 LV------LVLRYKEELTQKEIAEVLGISESRVSRLHK 234 (247)
T ss_pred HH------HHHHHHhccCHHHHHHHhCccHHHHHHHHH
Confidence 00 011112256889999999999999988754
No 200
>PF13730 HTH_36: Helix-turn-helix domain
Probab=91.76 E-value=0.59 Score=35.90 Aligned_cols=47 Identities=17% Similarity=0.270 Sum_probs=33.8
Q ss_pred cCCHHHHHHHHHHhcccCCCC---CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556 496 LLNPKERCIVRLRFGIEDGKP---KSLSEVGNIFGLSKERVRQLESRALYRLKQ 546 (561)
Q Consensus 496 ~L~erER~VL~LRyGL~d~e~---~Tl~EIAe~LGISrerVRqie~RALkKLR~ 546 (561)
.|++.++.|+..-..+.++.+ .|.+.||+.+|+|+.+|++ +++.|.+
T Consensus 2 ~Ls~~~~~v~~~l~~~~~~~~~~~pS~~~la~~~g~s~~Tv~~----~i~~L~~ 51 (55)
T PF13730_consen 2 NLSPTAKLVYLYLASYANKNGGCFPSQETLAKDLGVSRRTVQR----AIKELEE 51 (55)
T ss_pred CCCHHHHHHHHHHHHhcCCCCCCCcCHHHHHHHHCcCHHHHHH----HHHHHHH
Confidence 588888888766444432222 2899999999999999964 5666654
No 201
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=91.74 E-value=0.49 Score=35.20 Aligned_cols=40 Identities=35% Similarity=0.460 Sum_probs=26.9
Q ss_pred CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556 497 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 497 L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R 539 (561)
|++-.+.||..--. | ...++.+||+.+|+|..+|.+.+.+
T Consensus 1 lD~~D~~Il~~Lq~--d-~r~s~~~la~~lglS~~~v~~Ri~r 40 (42)
T PF13404_consen 1 LDELDRKILRLLQE--D-GRRSYAELAEELGLSESTVRRRIRR 40 (42)
T ss_dssp --HHHHHHHHHHHH----TTS-HHHHHHHHTS-HHHHHHHHHH
T ss_pred CCHHHHHHHHHHHH--c-CCccHHHHHHHHCcCHHHHHHHHHH
Confidence 34556667765443 2 4689999999999999999887654
No 202
>PHA00675 hypothetical protein
Probab=91.54 E-value=0.35 Score=40.64 Aligned_cols=40 Identities=18% Similarity=0.089 Sum_probs=30.6
Q ss_pred hcCCHHHHHHHHHHh-cccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008556 495 TLLNPKERCIVRLRF-GIEDGKPKSLSEVGNIFGLSKERVRQLES 538 (561)
Q Consensus 495 ~~L~erER~VL~LRy-GL~d~e~~Tl~EIAe~LGISrerVRqie~ 538 (561)
..|++.+-+.|+.++ - .+.|+.+||+.||||+.+|.+|..
T Consensus 21 AKLt~~qV~~IR~l~~r----~G~s~~~IA~~fGVsrstV~~I~~ 61 (78)
T PHA00675 21 AKLTDAEVERIRELHEV----EGMSYAVLAEKFEQSKGAIAKICR 61 (78)
T ss_pred cccCHHHHHHHHHHHHh----cCccHHHHHHHhCCCHHHHHHHHc
Confidence 346666655555555 4 678999999999999999998864
No 203
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=91.34 E-value=4.5 Score=44.48 Aligned_cols=37 Identities=22% Similarity=0.399 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHH
Q 008556 408 KVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLI 444 (561)
Q Consensus 408 ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll 444 (561)
.+.+.+..+..++|++||.+|.|..+|+++..++..+
T Consensus 112 ~l~~~~~~l~~~~g~~pt~~ewa~~~~~~~~~l~~~l 148 (415)
T PRK07598 112 RLIEVRERLTSELGHRPSLERWAKTADISLADLKPTL 148 (415)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCcHHHHHHhh
Confidence 3455667888899999999999988887766666554
No 204
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=91.02 E-value=0.3 Score=51.84 Aligned_cols=35 Identities=23% Similarity=0.290 Sum_probs=31.2
Q ss_pred HHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008556 504 IVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 542 (561)
Q Consensus 504 VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALk 542 (561)
+-.+||. +++|..|||++||||+.+|+.++.+|.+
T Consensus 18 ~A~lYY~----~gltQ~eIA~~LgiSR~~v~rlL~~Ar~ 52 (321)
T COG2390 18 AAWLYYV----EGLTQSEIAERLGISRATVSRLLAKARE 52 (321)
T ss_pred HHHHHHh----cCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 5567887 8999999999999999999999988865
No 205
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=90.84 E-value=0.65 Score=42.03 Aligned_cols=50 Identities=20% Similarity=0.300 Sum_probs=41.7
Q ss_pred HHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556 493 LLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 546 (561)
Q Consensus 493 aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 546 (561)
.+..|++.+..-|....- . .=+++|+++.||||-.|||..+.+.+++|.-
T Consensus 30 ~~~~L~~E~~~Fi~~Fi~-~---rGnlKe~e~~lgiSYPTvR~rLd~ii~~lg~ 79 (113)
T PF09862_consen 30 WFARLSPEQLEFIKLFIK-N---RGNLKEMEKELGISYPTVRNRLDKIIEKLGY 79 (113)
T ss_pred hhhcCCHHHHHHHHHHHH-h---cCCHHHHHHHHCCCcHHHHHHHHHHHHHhCC
Confidence 367899888887766543 3 3399999999999999999999999999975
No 206
>PF13518 HTH_28: Helix-turn-helix domain
Probab=90.82 E-value=0.43 Score=35.92 Aligned_cols=27 Identities=26% Similarity=0.382 Sum_probs=22.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 008556 515 KPKSLSEVGNIFGLSKERVRQLESRAL 541 (561)
Q Consensus 515 e~~Tl~EIAe~LGISrerVRqie~RAL 541 (561)
++.|+.+||..+|||+.+|+++..+-.
T Consensus 11 ~g~s~~~~a~~~gis~~tv~~w~~~y~ 37 (52)
T PF13518_consen 11 EGESVREIAREFGISRSTVYRWIKRYR 37 (52)
T ss_pred cCCCHHHHHHHHCCCHhHHHHHHHHHH
Confidence 456999999999999999988876543
No 207
>smart00351 PAX Paired Box domain.
Probab=90.59 E-value=0.66 Score=42.40 Aligned_cols=41 Identities=15% Similarity=0.074 Sum_probs=32.1
Q ss_pred CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 008556 497 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL 541 (561)
Q Consensus 497 L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RAL 541 (561)
|+..+|.=|...|- ++.+..+||+.||||+.+|..++++..
T Consensus 18 ~s~~~R~riv~~~~----~G~s~~~iA~~~gvs~~tV~kwi~r~~ 58 (125)
T smart00351 18 LPDEERQRIVELAQ----NGVRPCDISRQLCVSHGCVSKILGRYY 58 (125)
T ss_pred CCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 45555554555554 678999999999999999999988864
No 208
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 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 [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=90.07 E-value=0.38 Score=37.50 Aligned_cols=40 Identities=20% Similarity=0.305 Sum_probs=27.0
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556 496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R 539 (561)
.|+..|+.=|.-+|- .|.+..+||..|||++.+|+.+...
T Consensus 6 ~LTl~eK~~iI~~~e----~g~s~~~ia~~fgv~~sTv~~I~K~ 45 (53)
T PF04218_consen 6 SLTLEEKLEIIKRLE----EGESKRDIAREFGVSRSTVSTILKN 45 (53)
T ss_dssp S--HHHHHHHHHHHH----CTT-HHHHHHHHT--CCHHHHHHHC
T ss_pred cCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHh
Confidence 466666664445554 6679999999999999999998765
No 209
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=89.95 E-value=0.56 Score=36.03 Aligned_cols=38 Identities=21% Similarity=0.438 Sum_probs=26.6
Q ss_pred HHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556 500 KERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 500 rER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R 539 (561)
|++.||.+-+ ..+.+.|.+|||+.||||+.+|++.++.
T Consensus 1 R~~~il~~L~--~~~~~it~~eLa~~l~vS~rTi~~~i~~ 38 (55)
T PF08279_consen 1 RQKQILKLLL--ESKEPITAKELAEELGVSRRTIRRDIKE 38 (55)
T ss_dssp HHHHHHHHHH--HTTTSBEHHHHHHHCTS-HHHHHHHHHH
T ss_pred CHHHHHHHHH--HcCCCcCHHHHHHHhCCCHHHHHHHHHH
Confidence 4556666542 2335699999999999999999865443
No 210
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=89.82 E-value=0.59 Score=37.64 Aligned_cols=35 Identities=17% Similarity=0.294 Sum_probs=26.5
Q ss_pred HHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556 503 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 503 ~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R 539 (561)
..+.++.. .+..+++.+||+.||||..+||....+
T Consensus 11 kA~e~y~~--~~g~i~lkdIA~~Lgvs~~tIr~WK~~ 45 (60)
T PF10668_consen 11 KAFEIYKE--SNGKIKLKDIAEKLGVSESTIRKWKSR 45 (60)
T ss_pred HHHHHHHH--hCCCccHHHHHHHHCCCHHHHHHHhhh
Confidence 34555432 235899999999999999999987554
No 211
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 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.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=89.79 E-value=0.66 Score=36.99 Aligned_cols=26 Identities=19% Similarity=0.331 Sum_probs=23.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008556 515 KPKSLSEVGNIFGLSKERVRQLESRA 540 (561)
Q Consensus 515 e~~Tl~EIAe~LGISrerVRqie~RA 540 (561)
+|++..|||+.||+++.+|.....+-
T Consensus 12 ~G~~~~eIA~~Lg~~~~TV~~W~~r~ 37 (58)
T PF06056_consen 12 QGWSIKEIAEELGVPRSTVYSWKDRY 37 (58)
T ss_pred cCCCHHHHHHHHCCChHHHHHHHHhh
Confidence 79999999999999999999887663
No 212
>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]
Probab=89.75 E-value=0.38 Score=56.40 Aligned_cols=45 Identities=18% Similarity=0.100 Sum_probs=42.4
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556 496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 545 (561)
Q Consensus 496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 545 (561)
-|+.||++|+.+-| .|+|.+|||+.+.||-.||+....+...||.
T Consensus 831 ~Ls~RE~eVL~Lia-----~G~SN~eIa~~L~isl~TVKtH~rniy~KLg 875 (894)
T COG2909 831 PLSQRELEVLGLIA-----QGLSNEEIAQELFISLTTVKTHIRNIYQKLG 875 (894)
T ss_pred CccHHHHHHHHHHH-----ccCCHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 38999999999999 6999999999999999999999999999984
No 213
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=89.49 E-value=17 Score=38.25 Aligned_cols=178 Identities=12% Similarity=0.143 Sum_probs=92.9
Q ss_pred HHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhH
Q 008556 323 EKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENI 402 (561)
Q Consensus 323 e~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~ 402 (561)
++-+...+..+..++.+. ++ -+-+.|....+++.+..-..-+|.....++.-.|.-+++.
T Consensus 119 er~l~~a~~~I~~~~~~L---~L--p~~v~e~A~~iyk~~~~~~~~rgrs~~~i~AAclYiACR~--------------- 178 (310)
T PRK00423 119 ERNLAFALSELDRIASQL---GL--PRSVREEAAVIYRKAVEKGLIRGRSIEGVVAAALYAACRR--------------- 178 (310)
T ss_pred hHHHHHHHHHHHHHHHHc---CC--CHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHH---------------
Confidence 334444556666666655 23 3667777777888777667778877666665555544332
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhh-hhcccCCCCChhHHH
Q 008556 403 YTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQ-EITADTGVEIPDISV 481 (561)
Q Consensus 403 ~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~-d~l~d~~~~~pee~l 481 (561)
.+-+-|..||+..++++..++..........+.++.+.. .-..+. .+...-.. +....
T Consensus 179 -----------------~~~prtl~eI~~~~~v~~k~i~~~~~~l~k~L~~~~~~~--~p~~~i~r~~~~L~L--~~~v~ 237 (310)
T PRK00423 179 -----------------CKVPRTLDEIAEVSRVSRKEIGRCYRFLLRELNLKLPPT--DPIDYVPRFASELGL--SGEVQ 237 (310)
T ss_pred -----------------cCCCcCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCCCC--CHHHHHHHHHHHcCC--CHHHH
Confidence 223557888899999988888765443322222222211 111111 11111111 11111
Q ss_pred HHHHHHHHHHHHHh-cC----CHHH--HHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008556 482 QKQLMRQHVRNLLT-LL----NPKE--RCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 544 (561)
Q Consensus 482 e~~e~~e~L~~aL~-~L----~erE--R~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKL 544 (561)
. .....+..+.+ .| +|.- --+|.+-.-+. |.+.|++|||...|||..+|++..+.-.+.|
T Consensus 238 ~--~A~~i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~~-g~~~t~keIa~v~~Vs~~tI~~~ykel~~~l 304 (310)
T PRK00423 238 K--KAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLL-GERRTQREVAEVAGVTEVTVRNRYKELAEKL 304 (310)
T ss_pred H--HHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHh-CCCCCHHHHHHHcCCCHHHHHHHHHHHHHHh
Confidence 1 11122222221 11 1111 11122211112 3789999999999999999998766655544
No 214
>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., PubMed:15231786). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations
Probab=89.49 E-value=16 Score=40.41 Aligned_cols=46 Identities=24% Similarity=0.453 Sum_probs=31.8
Q ss_pred HHhcCCHHHHHHHHH---------HhcccCC---CCCCHHHHHHHhCCCHHHHHHHHH
Q 008556 493 LLTLLNPKERCIVRL---------RFGIEDG---KPKSLSEVGNIFGLSKERVRQLES 538 (561)
Q Consensus 493 aL~~L~erER~VL~L---------RyGL~d~---e~~Tl~EIAe~LGISrerVRqie~ 538 (561)
++..|.-|.+.+++. -|+..|. .++|+++||+.+|++.+||++..+
T Consensus 283 li~~i~~R~~TL~~v~~~Iv~~Q~~Ff~~G~~~LkPLtlkdiA~~lglheSTVSRav~ 340 (429)
T TIGR02395 283 LIKALEQREETLLKVAEAIVEHQKDFFLGGPAALKPLTLREVAEELGLHESTISRAIN 340 (429)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccCcCCcHHHHHHHhCCCccchhhhhc
Confidence 345666666655432 2222232 799999999999999999987654
No 215
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=89.38 E-value=11 Score=41.90 Aligned_cols=46 Identities=15% Similarity=0.394 Sum_probs=32.2
Q ss_pred HHhcCCHHHHHHHHH---------HhcccCC---CCCCHHHHHHHhCCCHHHHHHHHH
Q 008556 493 LLTLLNPKERCIVRL---------RFGIEDG---KPKSLSEVGNIFGLSKERVRQLES 538 (561)
Q Consensus 493 aL~~L~erER~VL~L---------RyGL~d~---e~~Tl~EIAe~LGISrerVRqie~ 538 (561)
++..|..|.+.+++. -|+..|. .++|+++||+.+|+..+||++..+
T Consensus 308 li~~i~~R~~TL~~v~~~Iv~~Q~~Ff~~G~~~LkPLtlkdvAe~lglheSTVSRav~ 365 (455)
T PRK05932 308 LIKSLEQRKETLLKVARCIVEQQRDFFEHGEEALKPLVLKDIAEELGMHESTISRATT 365 (455)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccCcCccHHHHHHHhCCCccchhhhhc
Confidence 445666676665542 2322232 799999999999999999987653
No 216
>PHA02547 55 RNA polymerase sigma factor; Provisional
Probab=89.29 E-value=1.4 Score=42.59 Aligned_cols=64 Identities=13% Similarity=0.137 Sum_probs=46.9
Q ss_pred HHHHHHHHHHHHhhhCCCCC--H-HHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHH
Q 008556 327 NANLRLVVHVAKQYQGRGIS--L-HDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIF 390 (561)
Q Consensus 327 ~~nlrLV~sIArrY~~~g~~--~-eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir 390 (561)
.+-+..+..+.++|.-+|.. + +|.|.+|.-.+++.+..|||++...+-.|.+..+-++..+.|.
T Consensus 44 ~~imkIa~glS~r~nF~~Yt~~wKedMI~DgIe~~i~ylhNFD~~k~~Np~aYiT~~~~~AF~~RI~ 110 (179)
T PHA02547 44 LAIMKIAEGLSRRPNFSGYTQTWKEDMIADGIEACIKGLHNFDETKYKNPHAYITQACFNAFVQRIK 110 (179)
T ss_pred HHHHHHHhccccCCccccchHHHHHHHHHHHHHHHHHHhhcCCcccccChHHHHHHHHHHHHHHHHH
Confidence 34455555666666545555 4 8999999999999999999999887877777666655554443
No 217
>PF02650 HTH_WhiA: WhiA C-terminal HTH domain; InterPro: IPR023054 This domain is found at the C terminus of the sporulation regulator WhiA. It is predicted to form a DNA binding helix-turn-helix structure []. ; PDB: 3HYI_A.
Probab=89.26 E-value=0.79 Score=39.43 Aligned_cols=44 Identities=30% Similarity=0.363 Sum_probs=33.5
Q ss_pred HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHh--CCCHHHHHHHHHHH
Q 008556 494 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIF--GLSKERVRQLESRA 540 (561)
Q Consensus 494 L~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~L--GISrerVRqie~RA 540 (561)
++.||+..+++..+|.- ....|+.|+|+.| .||++.|..+..+.
T Consensus 35 ~~~l~~~l~~~a~lRl~---~Pd~SL~EL~~~~~~~iSKSgvnhrlrKl 80 (85)
T PF02650_consen 35 LDKLPEKLREFAELRLE---NPDASLKELGELLEPPISKSGVNHRLRKL 80 (85)
T ss_dssp GGGS-HHHHHHHHHHHH----TTS-HHHHHHTT--T--HHHHHHHHHHH
T ss_pred cccCCHHHHHHHHHHHH---CccccHHHHHHHHcCcCcHHHHHHHHHHH
Confidence 57899999999999875 3789999999999 99999998765543
No 218
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=89.19 E-value=2.8 Score=42.82 Aligned_cols=34 Identities=26% Similarity=0.423 Sum_probs=27.3
Q ss_pred HHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHH
Q 008556 280 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 313 (561)
Q Consensus 280 le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~ 313 (561)
+......|...+|++|+.+|.|+.+|++.+.+..
T Consensus 112 l~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~ 145 (257)
T PRK05911 112 LADAMDSLRQSLGKEPTDGELCEYLNISQQELSG 145 (257)
T ss_pred HHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHH
Confidence 3345556777889999999999999999887743
No 219
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=89.17 E-value=5.8 Score=43.04 Aligned_cols=34 Identities=32% Similarity=0.584 Sum_probs=28.7
Q ss_pred HHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHH
Q 008556 279 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK 312 (561)
Q Consensus 279 ~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~ 312 (561)
++.+....|...+|++||.+|.|+.+|++.+.+.
T Consensus 224 ~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~ 257 (373)
T PRK07406 224 RIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLR 257 (373)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHH
Confidence 4556677888889999999999999999987774
No 220
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=89.08 E-value=0.83 Score=35.62 Aligned_cols=43 Identities=23% Similarity=0.287 Sum_probs=31.6
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556 496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R 539 (561)
.|++.|..||..-+.-+ +.+.|..|||+.+|+++.+|.+++++
T Consensus 2 glt~~q~~vL~~l~~~~-~~~~t~~~la~~l~~~~~~vs~~v~~ 44 (62)
T PF12802_consen 2 GLTPSQFRVLMALARHP-GEELTQSELAERLGISKSTVSRIVKR 44 (62)
T ss_dssp TSTHHHHHHHHHHHHST-TSGEEHHHHHHHHTS-HHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHHCC-CCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 47788888887666522 23489999999999999999765544
No 221
>PHA02591 hypothetical protein; Provisional
Probab=88.98 E-value=0.78 Score=38.73 Aligned_cols=24 Identities=21% Similarity=0.436 Sum_probs=22.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 008556 515 KPKSLSEVGNIFGLSKERVRQLES 538 (561)
Q Consensus 515 e~~Tl~EIAe~LGISrerVRqie~ 538 (561)
.|+|.++||+.||||.++||+.++
T Consensus 58 qGlSqeqIA~~LGVsqetVrKYL~ 81 (83)
T PHA02591 58 KGFTVEKIASLLGVSVRKVRRYLE 81 (83)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHh
Confidence 689999999999999999999865
No 222
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=88.86 E-value=1.5 Score=40.55 Aligned_cols=53 Identities=21% Similarity=0.289 Sum_probs=41.7
Q ss_pred HHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556 488 QHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 546 (561)
Q Consensus 488 e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 546 (561)
..+..++-.|++.+-+|+..-. ..+.++|..|||+.+|+++.+| .||+++|=.
T Consensus 16 ~dvl~c~~GLs~~Dv~v~~~LL--~~~~~~tvdelae~lnr~rStv----~rsl~~L~~ 68 (126)
T COG3355 16 EDVLKCVYGLSELDVEVYKALL--EENGPLTVDELAEILNRSRSTV----YRSLQNLLE 68 (126)
T ss_pred HHHHHHHhCCcHHHHHHHHHHH--hhcCCcCHHHHHHHHCccHHHH----HHHHHHHHH
Confidence 3566788899999999887654 1236899999999999999999 467777744
No 223
>PRK11083 DNA-binding response regulator CreB; Provisional
Probab=88.54 E-value=0.66 Score=44.26 Aligned_cols=50 Identities=14% Similarity=0.050 Sum_probs=43.1
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCC-----HHHHHHHHHHHHHHHHH
Q 008556 496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLS-----KERVRQLESRALYRLKQ 546 (561)
Q Consensus 496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGIS-----rerVRqie~RALkKLR~ 546 (561)
.|+++|++|+.+-.. +.|.++|.+||++.++.+ ..+|+.+..+.++||..
T Consensus 154 ~Lt~~E~~il~~l~~-~~~~~~s~~~i~~~l~~~~~~~~~~tv~~~i~~l~~Kl~~ 208 (228)
T PRK11083 154 TLTRYEFLLLKTLLL-SPGRVFSRQQLMDIVWEDAQDSYDRTVDTHIKTLRAKLRA 208 (228)
T ss_pred ecCHHHHHHHHHHHh-CCCceECHHHHHHHhcCCCCCCCccCHHHHHHHHHHHhcc
Confidence 599999999988764 445679999999999986 78999999999999964
No 224
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=88.30 E-value=9 Score=39.16 Aligned_cols=35 Identities=29% Similarity=0.532 Sum_probs=28.9
Q ss_pred HHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHH
Q 008556 279 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 313 (561)
Q Consensus 279 ~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~ 313 (561)
.+.+....|+..+|++||.++.|...|++.+.+..
T Consensus 119 ~i~~~~~~l~~~~~~~pt~~eia~~lg~~~~~v~~ 153 (268)
T PRK06288 119 QIERAIAMLEARLGRTPSDEEIADELGISLEEYNS 153 (268)
T ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHH
Confidence 45556677888899999999999999999877653
No 225
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=88.29 E-value=1.3 Score=45.05 Aligned_cols=34 Identities=29% Similarity=0.497 Sum_probs=28.9
Q ss_pred HHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHH
Q 008556 280 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 313 (561)
Q Consensus 280 le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~ 313 (561)
+.++...|...+|++||.+|.|+.+|++.+++..
T Consensus 115 ~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~ 148 (256)
T PRK07408 115 AKKVRQELRQELGRQPTDQEIAQALDISLEEWQE 148 (256)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHH
Confidence 4556778888999999999999999999887743
No 226
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=88.00 E-value=7.7 Score=39.82 Aligned_cols=34 Identities=26% Similarity=0.524 Sum_probs=28.4
Q ss_pred HHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHH
Q 008556 280 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 313 (561)
Q Consensus 280 le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~ 313 (561)
+.+...+|...+|++||.+|.|+.+|++.+++..
T Consensus 129 i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~ 162 (264)
T PRK07122 129 LGRATAELSQRLGRAPTASELAAELGMDREEVVE 162 (264)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence 4456677888899999999999999999887754
No 227
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=87.82 E-value=0.8 Score=36.60 Aligned_cols=46 Identities=22% Similarity=0.416 Sum_probs=31.5
Q ss_pred CCHHHHHHHHHHhccc-CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556 497 LNPKERCIVRLRFGIE-DGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 546 (561)
Q Consensus 497 L~erER~VL~LRyGL~-d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 546 (561)
|++....-|..-|.|. ++...+..+||+.||||+.+|.. +++||.+
T Consensus 2 Lt~~~e~YL~~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~----ml~~L~~ 48 (60)
T PF01325_consen 2 LTESEEDYLKAIYELSEEGGPVRTKDIAERLGVSPPTVTE----MLKRLAE 48 (60)
T ss_dssp CSCHHHHHHHHHHHHHHCTSSBBHHHHHHHHTS-HHHHHH----HHHHHHH
T ss_pred CCcHHHHHHHHHHHHHcCCCCccHHHHHHHHCCChHHHHH----HHHHHHH
Confidence 4445555555555544 45788999999999999999975 5556654
No 228
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=87.58 E-value=1.4 Score=33.09 Aligned_cols=36 Identities=28% Similarity=0.376 Sum_probs=26.2
Q ss_pred HHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008556 499 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES 538 (561)
Q Consensus 499 erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~ 538 (561)
|.-..|+.+-.. .+++..||++.+|+|+.+|++.+.
T Consensus 2 ~~R~~Il~~L~~----~~~~~~el~~~l~~s~~~vs~hL~ 37 (47)
T PF01022_consen 2 PTRLRILKLLSE----GPLTVSELAEELGLSQSTVSHHLK 37 (47)
T ss_dssp HHHHHHHHHHTT----SSEEHHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHHHHh----CCCchhhHHHhccccchHHHHHHH
Confidence 334455554443 689999999999999999987654
No 229
>PRK10710 DNA-binding transcriptional regulator BaeR; Provisional
Probab=87.47 E-value=0.84 Score=44.09 Aligned_cols=50 Identities=18% Similarity=0.120 Sum_probs=44.3
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHHH
Q 008556 496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFG-----LSKERVRQLESRALYRLKQ 546 (561)
Q Consensus 496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LG-----ISrerVRqie~RALkKLR~ 546 (561)
.|+++|++|+.+... +.|++.|.++|++.+. ++..+|+....+.++||..
T Consensus 160 ~Lt~~e~~il~~l~~-~~~~~~s~~~i~~~~~~~~~~~~~~tv~~~i~~lr~kl~~ 214 (240)
T PRK10710 160 DLTPAEFRLLKTLSH-EPGKVFSREQLLNHLYDDYRVVTDRTIDSHIKNLRRKLES 214 (240)
T ss_pred ecCHHHHHHHHHHHh-CCCceEcHHHHHHHhcCcCcCCCccCHHHHHHHHHHHhhc
Confidence 599999999998764 5567899999999998 9999999999999999963
No 230
>PRK05949 RNA polymerase sigma factor; Validated
Probab=87.24 E-value=8.3 Score=41.02 Aligned_cols=35 Identities=26% Similarity=0.461 Sum_probs=28.3
Q ss_pred HHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHH
Q 008556 279 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 313 (561)
Q Consensus 279 ~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~ 313 (561)
++.+.+..+...+|++|+..|.|+.+|++.+.+..
T Consensus 179 ~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~ 213 (327)
T PRK05949 179 KIKKTQRELSQKLGRSATPAEIAKELELEPSQIRE 213 (327)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHH
Confidence 34456667778889999999999999999877754
No 231
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=87.07 E-value=1.4 Score=37.43 Aligned_cols=42 Identities=24% Similarity=0.400 Sum_probs=34.2
Q ss_pred cCCHHHHHHHHHHhc--ccCCCCCCHHHHHHHhCCCHHHHHHHH
Q 008556 496 LLNPKERCIVRLRFG--IEDGKPKSLSEVGNIFGLSKERVRQLE 537 (561)
Q Consensus 496 ~L~erER~VL~LRyG--L~d~e~~Tl~EIAe~LGISrerVRqie 537 (561)
.|++|+++||..-.- ...|++-.-++||+.+|+|..+||+..
T Consensus 1 ~Lt~rq~~IL~alV~~Y~~~~~PVgSk~ia~~l~~s~aTIRN~M 44 (78)
T PF03444_consen 1 MLTERQREILKALVELYIETGEPVGSKTIAEELGRSPATIRNEM 44 (78)
T ss_pred CCCHHHHHHHHHHHHHHHhcCCCcCHHHHHHHHCCChHHHHHHH
Confidence 388999998876322 346789999999999999999999754
No 232
>cd00131 PAX Paired Box domain
Probab=87.07 E-value=1.6 Score=40.14 Aligned_cols=41 Identities=12% Similarity=0.017 Sum_probs=30.8
Q ss_pred CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 008556 497 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL 541 (561)
Q Consensus 497 L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RAL 541 (561)
|+...|.-|...|. ++++..+||+.||||+.+|..+.++-.
T Consensus 18 lS~d~R~rIv~~~~----~G~s~~~iA~~~~Vs~~tV~r~i~r~~ 58 (128)
T cd00131 18 LPDSIRQRIVELAQ----SGIRPCDISRQLRVSHGCVSKILNRYY 58 (128)
T ss_pred CCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 44444443344454 689999999999999999999887754
No 233
>PF01371 Trp_repressor: Trp repressor protein; InterPro: IPR000831 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.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3FRW_H 3KOR_A 3SSW_N 1P6Z_N 1CO0_B 1JHG_A 1WRT_S 1WRS_R 1WRP_R 1RCS_B ....
Probab=87.04 E-value=1.3 Score=38.36 Aligned_cols=46 Identities=26% Similarity=0.372 Sum_probs=32.5
Q ss_pred cCCHHHHHHHHHHhcccC---CCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008556 496 LLNPKERCIVRLRFGIED---GKPKSLSEVGNIFGLSKERVRQLESRALY 542 (561)
Q Consensus 496 ~L~erER~VL~LRyGL~d---~e~~Tl~EIAe~LGISrerVRqie~RALk 542 (561)
-++|.|+.-|..|+-+-. .+++|+.||++.+|+|..+|.+. +|+|+
T Consensus 26 L~T~~E~~~l~~R~~va~~lL~~g~syreIa~~tgvS~aTItRv-sr~Lk 74 (87)
T PF01371_consen 26 LCTPDELEALAQRWQVAKELLDEGKSYREIAEETGVSIATITRV-SRCLK 74 (87)
T ss_dssp HSSHHHHHHHHHHHHHHHHHHHTTSSHHHHHHHHTSTHHHHHHH-HHHHH
T ss_pred hCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHH-HHHHH
Confidence 467777776666654332 15899999999999999999642 44444
No 234
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=87.03 E-value=9 Score=38.73 Aligned_cols=35 Identities=23% Similarity=0.363 Sum_probs=28.2
Q ss_pred HHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHHH
Q 008556 280 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSE 314 (561)
Q Consensus 280 le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~~ 314 (561)
+.++...+...+|++|+..++|+..|++.+.+...
T Consensus 111 ~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~ 145 (251)
T PRK07670 111 VEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEAT 145 (251)
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHH
Confidence 34455667778899999999999999998877543
No 235
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=86.58 E-value=2.6 Score=41.88 Aligned_cols=32 Identities=38% Similarity=0.579 Sum_probs=26.3
Q ss_pred HHHHHHhhhhCCCCcHHHHHHHccCCHHHHHH
Q 008556 282 KEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 313 (561)
Q Consensus 282 ~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~ 313 (561)
+....|...+|+.||..+.|+.+|++.+.+..
T Consensus 101 ~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~ 132 (231)
T TIGR02885 101 YMKEELSKELGREPTINELAEALGVSPEEIVM 132 (231)
T ss_pred HHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHH
Confidence 44566777889999999999999999877643
No 236
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=86.49 E-value=2.3 Score=33.52 Aligned_cols=35 Identities=29% Similarity=0.384 Sum_probs=26.7
Q ss_pred HHHHHHHHHH-hcccCCCCCCHHHHHHHhCCCHHHHHHHH
Q 008556 499 PKERCIVRLR-FGIEDGKPKSLSEVGNIFGLSKERVRQLE 537 (561)
Q Consensus 499 erER~VL~LR-yGL~d~e~~Tl~EIAe~LGISrerVRqie 537 (561)
|.-+.||.+- -. .++|..|||+.+|++..+|+..+
T Consensus 10 p~R~~Il~~L~~~----~~~t~~ela~~l~~~~~t~s~hL 45 (61)
T PF12840_consen 10 PTRLRILRLLASN----GPMTVSELAEELGISQSTVSYHL 45 (61)
T ss_dssp HHHHHHHHHHHHC----STBEHHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHHHhcC----CCCCHHHHHHHHCCCHHHHHHHH
Confidence 5556666655 33 79999999999999999998654
No 237
>PRK12423 LexA repressor; Provisional
Probab=86.42 E-value=1.3 Score=43.69 Aligned_cols=47 Identities=30% Similarity=0.478 Sum_probs=35.3
Q ss_pred cCCHHHHHHHHHHh--cccCCCCCCHHHHHHHhC-CCHHHHHHHHHHHHHHHHH
Q 008556 496 LLNPKERCIVRLRF--GIEDGKPKSLSEVGNIFG-LSKERVRQLESRALYRLKQ 546 (561)
Q Consensus 496 ~L~erER~VL~LRy--GL~d~e~~Tl~EIAe~LG-ISrerVRqie~RALkKLR~ 546 (561)
.|++++++|+..-- ...+|-+.|..|||+.|| +|+.+|+. +|++|++
T Consensus 3 ~lt~~q~~il~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~~----~l~~L~~ 52 (202)
T PRK12423 3 TLTPKRAAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARK----HVQALAE 52 (202)
T ss_pred cCCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHH----HHHHHHH
Confidence 48999999987632 222344679999999999 59999984 6666665
No 238
>PRK15479 transcriptional regulatory protein TctD; Provisional
Probab=86.06 E-value=1.2 Score=42.13 Aligned_cols=49 Identities=18% Similarity=0.233 Sum_probs=41.7
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHH
Q 008556 496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFG-----LSKERVRQLESRALYRLK 545 (561)
Q Consensus 496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LG-----ISrerVRqie~RALkKLR 545 (561)
.|+++|.+|+.+... +.|...|.++|++.+. +|..+|+....+.++||.
T Consensus 148 ~Lt~~E~~il~~l~~-~~~~~~~~~~i~~~l~~~~~~~~~~tv~~~i~~ir~kl~ 201 (221)
T PRK15479 148 ALTPREQALLTVLMY-RRTRPVSRQQLFEQVFSLNDEVSPESIELYIHRLRKKLQ 201 (221)
T ss_pred ecCHHHHHHHHHHHh-CCCCcCcHHHHHHHhcCCCCCCCcccHHHHHHHHHHhcC
Confidence 599999999987643 3346679999999986 999999999999999985
No 239
>PRK10336 DNA-binding transcriptional regulator QseB; Provisional
Probab=86.04 E-value=1.1 Score=42.44 Aligned_cols=49 Identities=16% Similarity=0.180 Sum_probs=41.9
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHH
Q 008556 496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFG-----LSKERVRQLESRALYRLK 545 (561)
Q Consensus 496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LG-----ISrerVRqie~RALkKLR 545 (561)
.|+++|.+|+.+..- +.|..+|.++|++.+. ++..+|+....+.++||.
T Consensus 149 ~Lt~~E~~il~~l~~-~~~~~~s~~~i~~~l~~~~~~~~~~tv~~~i~~lr~Kl~ 202 (219)
T PRK10336 149 TLKPKEFALLELLMR-NAGRVLPRKLIEEKLYTWDEEVTSNAVEVHVHHLRRKLG 202 (219)
T ss_pred ecCHHHHHHHHHHHh-CCCccCcHHHHHHHhcCCCCCCCccCHHHHHHHHHHhcC
Confidence 499999999987652 3446699999999996 999999999999999985
No 240
>TIGR02850 spore_sigG RNA polymerase sigma-G factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also desginated stage III sporulation protein G (SpoIIIG). This protein is rather closely related to sigma-F (SpoIIAC), another sporulation sigma factor.
Probab=86.01 E-value=9 Score=38.84 Aligned_cols=34 Identities=26% Similarity=0.317 Sum_probs=28.0
Q ss_pred HHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHHH
Q 008556 281 EKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSE 314 (561)
Q Consensus 281 e~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~~ 314 (561)
.++..++...+|++||.+|.|+.+|++.+.+...
T Consensus 123 ~~~~~~l~~~l~~~pt~~elA~~l~~~~e~v~~~ 156 (254)
T TIGR02850 123 LQVRDKLISENSKEPTVSEIAKELKVPQEEVVFA 156 (254)
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHH
Confidence 3456677788899999999999999998877544
No 241
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family. This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).
Probab=85.91 E-value=12 Score=38.89 Aligned_cols=35 Identities=26% Similarity=0.496 Sum_probs=28.5
Q ss_pred HHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHH
Q 008556 279 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 313 (561)
Q Consensus 279 ~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~ 313 (561)
++.+.+..+...+|++||..+.|..+|++.+.+..
T Consensus 162 ~~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~ 196 (298)
T TIGR02997 162 KIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRE 196 (298)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence 34455667777899999999999999999887753
No 242
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=85.86 E-value=38 Score=38.10 Aligned_cols=46 Identities=22% Similarity=0.284 Sum_probs=33.0
Q ss_pred HHhcCCHHHHHHHHH---------HhcccCC---CCCCHHHHHHHhCCCHHHHHHHHH
Q 008556 493 LLTLLNPKERCIVRL---------RFGIEDG---KPKSLSEVGNIFGLSKERVRQLES 538 (561)
Q Consensus 493 aL~~L~erER~VL~L---------RyGL~d~---e~~Tl~EIAe~LGISrerVRqie~ 538 (561)
++..|..|.+.+++. -|+..|. .++|+++||+.+|+..+||++..+
T Consensus 334 li~si~qR~~TllkV~~~Iv~~Q~~Ff~~G~~~LkPLtlkdVAe~lglHeSTVSRa~~ 391 (481)
T PRK12469 334 LIRNAQQRFDTIQRVAECIVARQRDFFRYGEIALKPLVLRDVAEELGLHESTISRATG 391 (481)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccCcCCcHHHHHHHhCCCcchhhHHhc
Confidence 456677777766542 2322222 799999999999999999987654
No 243
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=85.32 E-value=16 Score=37.94 Aligned_cols=25 Identities=20% Similarity=0.337 Sum_probs=21.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHh
Q 008556 422 HSPDKEDLARRVGITVEKLERLIFI 446 (561)
Q Consensus 422 r~Pt~eEIA~~lgis~e~v~~ll~~ 446 (561)
..-|.+|||+.+|++.++|..++..
T Consensus 244 ~~~t~~EIa~~lgvs~~~V~q~~~~ 268 (289)
T PRK07500 244 DGATLEALGEELGISKERVRQIEAR 268 (289)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 4678999999999999999988654
No 244
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=85.29 E-value=1.5 Score=34.67 Aligned_cols=41 Identities=20% Similarity=0.332 Sum_probs=25.6
Q ss_pred CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556 497 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 497 L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R 539 (561)
|+..|..||..-. ..+.+++..+|++.+|+++.+|...+++
T Consensus 1 lt~~q~~vL~~l~--~~~~~~t~~~l~~~~~~~~~~vs~~i~~ 41 (68)
T PF13463_consen 1 LTRPQWQVLRALA--HSDGPMTQSDLAERLGISKSTVSRIIKK 41 (68)
T ss_dssp --HHHHHHHHHHT----TS-BEHHHHHHHTT--HHHHHHHHHH
T ss_pred CCHHHHHHHHHHH--ccCCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 4566666665544 2447899999999999999999754443
No 245
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=85.18 E-value=2 Score=37.37 Aligned_cols=41 Identities=29% Similarity=0.289 Sum_probs=31.3
Q ss_pred CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008556 497 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA 540 (561)
Q Consensus 497 L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RA 540 (561)
|++.++.||..... + ...|..+||+.+|+|+.+|++.+.+-
T Consensus 1 ld~~D~~il~~L~~--~-~~~~~~~la~~l~~s~~tv~~~l~~L 41 (108)
T smart00344 1 LDEIDRKILEELQK--D-ARISLAELAKKVGLSPSTVHNRVKRL 41 (108)
T ss_pred CCHHHHHHHHHHHH--h-CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 46677888866543 2 46899999999999999998765443
No 246
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=84.99 E-value=1.9 Score=35.10 Aligned_cols=23 Identities=17% Similarity=0.299 Sum_probs=19.9
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHH
Q 008556 516 PKSLSEVGNIFGLSKERVRQLES 538 (561)
Q Consensus 516 ~~Tl~EIAe~LGISrerVRqie~ 538 (561)
+.|..|||+.+||++.+|++++.
T Consensus 22 ~~ta~eLa~~lgl~~~~v~r~L~ 44 (68)
T smart00550 22 TSTALQLAKNLGLPKKEVNRVLY 44 (68)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHH
Confidence 59999999999999999976543
No 247
>TIGR02154 PhoB phosphate regulon transcriptional regulatory protein PhoB. 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.
Probab=84.95 E-value=0.69 Score=43.92 Aligned_cols=49 Identities=16% Similarity=0.117 Sum_probs=42.1
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHH-----HHHhCCCHHHHHHHHHHHHHHHH
Q 008556 496 LLNPKERCIVRLRFGIEDGKPKSLSEV-----GNIFGLSKERVRQLESRALYRLK 545 (561)
Q Consensus 496 ~L~erER~VL~LRyGL~d~e~~Tl~EI-----Ae~LGISrerVRqie~RALkKLR 545 (561)
.|+++|++|+.+-.. +.|.++|.++| |..++++..+|+....+.++||.
T Consensus 154 ~Lt~~E~~il~~l~~-~~~~~~s~~~i~~~~~~~~~~~~~~tv~~~i~~l~~Kl~ 207 (226)
T TIGR02154 154 SLGPTEFRLLHFFMT-HPERVYSREQLLDRVWGRDVYVEERTVDVHIRRLRKALN 207 (226)
T ss_pred EcCHHHHHHHHHHHh-CCCceEcHHHHHHHhcCCCCCCCCccHHHHHHHHHHhhc
Confidence 599999999988764 34467888888 77899999999999999999996
No 248
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=84.67 E-value=13 Score=39.35 Aligned_cols=34 Identities=26% Similarity=0.522 Sum_probs=28.2
Q ss_pred HHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHH
Q 008556 279 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK 312 (561)
Q Consensus 279 ~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~ 312 (561)
++.+.+..+...+|+.||..+.|+++|++.+.+.
T Consensus 169 ~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~ 202 (317)
T PRK07405 169 KIKKAQRQLSQQLGRAATIGELAEELELTPKQVR 202 (317)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHH
Confidence 4556677788889999999999999999877664
No 249
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=84.62 E-value=2.3 Score=32.16 Aligned_cols=33 Identities=27% Similarity=0.405 Sum_probs=26.2
Q ss_pred HHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008556 503 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA 540 (561)
Q Consensus 503 ~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RA 540 (561)
.|+.+.. +..|.++||+.+|||-.+|+.+..+.
T Consensus 19 ~i~~~~~-----~~~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 19 YILKLLR-----ESRSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred HHHHHHh-----hcCCHHHHHHHHCCCHHHHHHHHHhh
Confidence 4555544 34699999999999999999988764
No 250
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=84.35 E-value=1.3 Score=33.86 Aligned_cols=34 Identities=35% Similarity=0.443 Sum_probs=24.5
Q ss_pred HHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008556 505 VRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES 538 (561)
Q Consensus 505 L~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~ 538 (561)
-.+.+.-..+.++|+.|||+.+|+++.+|..++.
T Consensus 7 ~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~ 40 (52)
T PF09339_consen 7 RILEALAESGGPLTLSEIARALGLPKSTVHRLLQ 40 (52)
T ss_dssp HHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3344444455778999999999999999976543
No 251
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=84.26 E-value=1.1 Score=44.06 Aligned_cols=39 Identities=18% Similarity=0.232 Sum_probs=28.6
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008556 496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES 538 (561)
Q Consensus 496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~ 538 (561)
.|+++ +|+.+-- .+..++|.+|||+.||||+.||+....
T Consensus 161 ~Lt~r--~Vl~~~~--~g~~g~s~~eIa~~l~iS~~Tv~~~~~ 199 (225)
T PRK10046 161 PLTLN--AVRKLFK--EPGVQHTAETVAQALTISRTTARRYLE 199 (225)
T ss_pred HHHHH--HHHHHHH--cCCCCcCHHHHHHHhCccHHHHHHHHH
Confidence 35554 5665442 222479999999999999999998764
No 252
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=84.25 E-value=2 Score=36.06 Aligned_cols=38 Identities=26% Similarity=0.347 Sum_probs=26.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH-----HHHHHHHHHhhcCc
Q 008556 515 KPKSLSEVGNIFGLSKERVRQLES-----RALYRLKQSLGGKA 552 (561)
Q Consensus 515 e~~Tl~EIAe~LGISrerVRqie~-----RALkKLR~~l~~~~ 552 (561)
.++|..|+|+.+|||+.+|.++++ -.+.+|...+..-+
T Consensus 30 ~~ltQ~e~A~~lgisq~~vS~l~~g~~~~~sl~~L~~~l~aLG 72 (80)
T PF13744_consen 30 RGLTQAELAERLGISQPRVSRLENGKIDDFSLDTLLRYLEALG 72 (80)
T ss_dssp CT--HHHHHHHHTS-HHHHHHHHTT-GCC--HHHHHHHHHHTT
T ss_pred cCCCHHHHHHHHCCChhHHHHHHcCcccCCCHHHHHHHHHHcC
Confidence 789999999999999999999985 23566666555443
No 253
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=84.20 E-value=10 Score=34.18 Aligned_cols=28 Identities=32% Similarity=0.432 Sum_probs=22.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556 515 KPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 546 (561)
Q Consensus 515 e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 546 (561)
.+.|+.|||+.||||..+|. ++|++|.-
T Consensus 70 pd~tl~Ela~~l~Vs~~ti~----~~Lkrlg~ 97 (119)
T PF01710_consen 70 PDATLRELAERLGVSPSTIW----RALKRLGI 97 (119)
T ss_pred CCcCHHHHHHHcCCCHHHHH----HHHHHcCc
Confidence 78999999999999999986 45666543
No 254
>TIGR02147 Fsuc_second hypothetical protein, TIGR02147. This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterized.
Probab=84.09 E-value=23 Score=36.77 Aligned_cols=87 Identities=22% Similarity=0.237 Sum_probs=46.9
Q ss_pred CCCHHHHHHHhC--CCHHHHHHHHHhcCCCccCCCCCCCCCCchhh-hhcccCCCCChh-HHHHHHHHHHHHHHHHhcCC
Q 008556 423 SPDKEDLARRVG--ITVEKLERLIFITRMPLSMQQPVWADQDTTFQ-EITADTGVEIPD-ISVQKQLMRQHVRNLLTLLN 498 (561)
Q Consensus 423 ~Pt~eEIA~~lg--is~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~-d~l~d~~~~~pe-e~le~~e~~e~L~~aL~~L~ 498 (561)
.+++++||+.++ |+.++|++.+..-...--+. ..+ ++.-... ..+.......+. -.-.+.++.+.-.++|+..|
T Consensus 137 ~~~~~~ia~~l~p~is~~ev~~sL~~L~~~glik-k~~-~g~y~~t~~~l~~~~~~~~~avr~~h~q~l~lA~~al~~~p 214 (271)
T TIGR02147 137 ADDPEELAKRCFPKISAEQVKESLDLLERLGLIK-KNE-DGFYKQTDKAVSTGDEVIPLAVRQYQKQMIDLAKEALDALP 214 (271)
T ss_pred CCCHHHHHHHhCCCCCHHHHHHHHHHHHHCCCee-ECC-CCcEEeecceeecCCccchHHHHHHHHHHHHHHHHHHHhCC
Confidence 567889999999 99999999876432111110 000 1100000 111111111121 11123344455677889999
Q ss_pred HHHHHHHHHHhcc
Q 008556 499 PKERCIVRLRFGI 511 (561)
Q Consensus 499 erER~VL~LRyGL 511 (561)
+.+|.+=-+-+|+
T Consensus 215 ~~eR~~S~lT~~i 227 (271)
T TIGR02147 215 PSERDVSTVTFGI 227 (271)
T ss_pred ccccccceeeEec
Confidence 9999977776664
No 255
>PF12728 HTH_17: Helix-turn-helix domain
Probab=83.50 E-value=1.2 Score=33.64 Aligned_cols=24 Identities=17% Similarity=0.376 Sum_probs=21.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHH
Q 008556 517 KSLSEVGNIFGLSKERVRQLESRA 540 (561)
Q Consensus 517 ~Tl~EIAe~LGISrerVRqie~RA 540 (561)
+|.+|+|+.||||+.+|+++..+.
T Consensus 2 lt~~e~a~~l~is~~tv~~~~~~g 25 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWIRQG 25 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcC
Confidence 689999999999999999987653
No 256
>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain. This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.
Probab=83.50 E-value=4.6 Score=35.07 Aligned_cols=49 Identities=18% Similarity=0.244 Sum_probs=36.2
Q ss_pred HhcCCHHHHHHHHHH----hccc-CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556 494 LTLLNPKERCIVRLR----FGIE-DGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 546 (561)
Q Consensus 494 L~~L~erER~VL~LR----yGL~-d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 546 (561)
...|++++..||..- ||.. ...+.|..|||+.+|+++++|. |++++|.+
T Consensus 20 ~~~l~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~sr~tVs----r~L~~Le~ 73 (95)
T TIGR01610 20 GADLSGREFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLSRTHVS----DAIKSLAR 73 (95)
T ss_pred hCCCCHHHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence 467899999877642 3322 2368999999999999999996 46666654
No 257
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=83.26 E-value=2 Score=32.74 Aligned_cols=30 Identities=37% Similarity=0.508 Sum_probs=23.8
Q ss_pred CCCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556 513 DGKPK-SLSEVGNIFGLSKERVRQLESRALYRLKQ 546 (561)
Q Consensus 513 d~e~~-Tl~EIAe~LGISrerVRqie~RALkKLR~ 546 (561)
.|..+ |..|||+.+|+|+.+|++ ++++|.+
T Consensus 16 ~~~~l~s~~~la~~~~vs~~tv~~----~l~~L~~ 46 (60)
T smart00345 16 PGDKLPSERELAAQLGVSRTTVRE----ALSRLEA 46 (60)
T ss_pred CCCcCcCHHHHHHHHCCCHHHHHH----HHHHHHH
Confidence 34556 899999999999999975 5666654
No 258
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=83.26 E-value=1.2 Score=33.85 Aligned_cols=22 Identities=18% Similarity=0.356 Sum_probs=19.9
Q ss_pred CHHHHHHHhCCCHHHHHHHHHH
Q 008556 518 SLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 518 Tl~EIAe~LGISrerVRqie~R 539 (561)
|++|||+..|||..+|+..++.
T Consensus 1 Ti~dIA~~agvS~~TVSr~ln~ 22 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRVLNG 22 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHHHTT
T ss_pred CHHHHHHHHCcCHHHHHHHHhC
Confidence 7899999999999999988764
No 259
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=82.99 E-value=2 Score=41.91 Aligned_cols=43 Identities=19% Similarity=0.285 Sum_probs=33.6
Q ss_pred hcCCHHHHHHHHHHhc--ccCCCCCCHHHHHHHhCCC-HHHHHHHH
Q 008556 495 TLLNPKERCIVRLRFG--IEDGKPKSLSEVGNIFGLS-KERVRQLE 537 (561)
Q Consensus 495 ~~L~erER~VL~LRyG--L~d~e~~Tl~EIAe~LGIS-rerVRqie 537 (561)
..|+++|++||..-.- ..++.+.|.+|||+.+|++ +.+|+.++
T Consensus 2 ~~lt~~q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l 47 (199)
T TIGR00498 2 KPLTARQQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHL 47 (199)
T ss_pred CccCHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHH
Confidence 3589999999887542 2245678999999999998 99997543
No 260
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=82.88 E-value=3.7 Score=33.44 Aligned_cols=40 Identities=28% Similarity=0.472 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHHhCCCCCCHHHHHHHhCCC-HHHHHHHHHh
Q 008556 407 SKVLEAKRLYIQEGNHSPDKEDLARRVGIT-VEKLERLIFI 446 (561)
Q Consensus 407 ~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis-~e~v~~ll~~ 446 (561)
.+|-.....+..+.|..||..|||+.+|++ ...|...+..
T Consensus 9 ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~ 49 (65)
T PF01726_consen 9 KEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKA 49 (65)
T ss_dssp HHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHH
Confidence 344455566677889999999999999997 8888877653
No 261
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=82.47 E-value=3.2 Score=32.27 Aligned_cols=39 Identities=21% Similarity=0.242 Sum_probs=25.2
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008556 496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES 538 (561)
Q Consensus 496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~ 538 (561)
.|++-||--|....- .++++.|||..+|-|+..|+..++
T Consensus 4 ~Lt~~Eqaqid~m~q----lG~s~~~isr~i~RSr~~Ir~yl~ 42 (50)
T PF11427_consen 4 TLTDAEQAQIDVMHQ----LGMSLREISRRIGRSRTCIRRYLK 42 (50)
T ss_dssp ---HHHHHHHHHHHH----TT--HHHHHHHHT--HHHHHHHHH
T ss_pred cCCHHHHHHHHHHHH----hchhHHHHHHHhCccHHHHHHHhc
Confidence 467777766666555 589999999999999999987653
No 262
>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]
Probab=82.26 E-value=35 Score=37.97 Aligned_cols=48 Identities=21% Similarity=0.439 Sum_probs=33.3
Q ss_pred HHHHhcCCHHHHHHHH-------HHhcc-cCC----CCCCHHHHHHHhCCCHHHHHHHHH
Q 008556 491 RNLLTLLNPKERCIVR-------LRFGI-EDG----KPKSLSEVGNIFGLSKERVRQLES 538 (561)
Q Consensus 491 ~~aL~~L~erER~VL~-------LRyGL-~d~----e~~Tl~EIAe~LGISrerVRqie~ 538 (561)
+.++..|..|++.++. .-+++ .+| .++++++||+.+|+..+||++...
T Consensus 293 ~wLiksL~qR~~TLlkV~~~Iv~~Q~~Ff~~g~~~l~PL~LrdvA~~i~~HESTISRai~ 352 (444)
T COG1508 293 KWLIKSLEQREETLLKVAEEIVEYQKAFFEGGEEALKPLVLRDVADEIGMHESTISRAIT 352 (444)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccCCcccHHHHHHHhCccHHHHHHHHh
Confidence 3345777777776654 22222 222 579999999999999999987654
No 263
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=82.01 E-value=1.4 Score=35.44 Aligned_cols=44 Identities=23% Similarity=0.344 Sum_probs=32.1
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556 496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 546 (561)
Q Consensus 496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 546 (561)
.|++.|..|+..-. .. .+.|..|||+.+|+++.+|+. ++++|.+
T Consensus 5 gLs~~E~~vy~~Ll--~~-~~~t~~eIa~~l~i~~~~v~~----~L~~L~~ 48 (68)
T PF01978_consen 5 GLSENEAKVYLALL--KN-GPATAEEIAEELGISRSTVYR----ALKSLEE 48 (68)
T ss_dssp CHHHHHHHHHHHHH--HH-CHEEHHHHHHHHTSSHHHHHH----HHHHHHH
T ss_pred CcCHHHHHHHHHHH--Hc-CCCCHHHHHHHHCcCHHHHHH----HHHHHHH
Confidence 46777777775432 11 589999999999999999975 5555543
No 264
>TIGR03787 marine_sort_RR proteobacterial dedicated sortase system response regulator. This model describes a family of DNA-binding response regulator proteins, associated with an adjacent histidine kinase (TIGR03785) to form a two-component system. This system co-occurs with, and often is adjacent to, a proteobacterial variant form of the protein sorting transpeptidase called sortase (TIGR03784), and a single target protein for the sortase. We give this protein the gene symbol pdsR, for Proteobacterial Dedicated Sortase system Response regulator.
Probab=81.87 E-value=2 Score=41.20 Aligned_cols=49 Identities=14% Similarity=0.090 Sum_probs=41.5
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHH--HHHhCCCHHHHHHHHHHHHHHHH
Q 008556 496 LLNPKERCIVRLRFGIEDGKPKSLSEV--GNIFGLSKERVRQLESRALYRLK 545 (561)
Q Consensus 496 ~L~erER~VL~LRyGL~d~e~~Tl~EI--Ae~LGISrerVRqie~RALkKLR 545 (561)
.|+++|.+||.+-.- +.|..+|.++| +..++++..+|+.+..+.++||.
T Consensus 156 ~Lt~~E~~il~~l~~-~~g~v~s~~~i~~~~~~~~~~~tv~~~v~rlr~Kl~ 206 (227)
T TIGR03787 156 DLTVTEFWMVHALAK-HPGHVKSRQQLMDAAKIVVDDSTITSHIKRIRKKFQ 206 (227)
T ss_pred cCCHHHHHHHHHHHh-CCCccccHHHHHHHhhhcCCccCHHHHHHHHHHHhc
Confidence 499999999988652 22355699999 88899999999999999999996
No 265
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=81.86 E-value=2.6 Score=39.45 Aligned_cols=27 Identities=26% Similarity=0.208 Sum_probs=24.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 008556 515 KPKSLSEVGNIFGLSKERVRQLESRAL 541 (561)
Q Consensus 515 e~~Tl~EIAe~LGISrerVRqie~RAL 541 (561)
+|+|.+|||++||||..+|....++-.
T Consensus 20 ~G~S~re~Ak~~gvs~sTvy~wv~r~~ 46 (138)
T COG3415 20 EGLSCREAAKRFGVSISTVYRWVRRYR 46 (138)
T ss_pred cCccHHHHHHHhCccHHHHHHHHHHhc
Confidence 699999999999999999998887754
No 266
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. 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.
Probab=81.66 E-value=19 Score=35.51 Aligned_cols=35 Identities=31% Similarity=0.635 Sum_probs=28.7
Q ss_pred HHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHH
Q 008556 279 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 313 (561)
Q Consensus 279 ~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~ 313 (561)
++.++..+|...+|++|+.+|.|+.+|++.+.+..
T Consensus 84 ~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~ 118 (224)
T TIGR02479 84 KLERAIRELEARLGREPTEEEIAEELGMDLKEYRQ 118 (224)
T ss_pred HHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHH
Confidence 35556677888899999999999999998877653
No 267
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=81.56 E-value=3.1 Score=39.01 Aligned_cols=41 Identities=15% Similarity=0.276 Sum_probs=32.0
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556 496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R 539 (561)
.|++.++.||..--. | ...|+.|||+.+|+|+.+|+.+.++
T Consensus 6 ~lD~~D~~Il~~Lq~--d-~R~s~~eiA~~lglS~~tV~~Ri~r 46 (153)
T PRK11179 6 QIDNLDRGILEALME--N-ARTPYAELAKQFGVSPGTIHVRVEK 46 (153)
T ss_pred ccCHHHHHHHHHHHH--c-CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 377888888876543 2 4689999999999999999865543
No 268
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=81.43 E-value=25 Score=27.92 Aligned_cols=23 Identities=35% Similarity=0.496 Sum_probs=19.9
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHH
Q 008556 423 SPDKEDLARRVGITVEKLERLIF 445 (561)
Q Consensus 423 ~Pt~eEIA~~lgis~e~v~~ll~ 445 (561)
+++.++||+.+|++...+..++.
T Consensus 1 ~~~~~~la~~~~~s~~~l~~~f~ 23 (84)
T smart00342 1 PLTLEDLAEALGMSPRHLQRLFK 23 (84)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHH
Confidence 36889999999999999988765
No 269
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model 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 model 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 (pfam00376).
Probab=81.33 E-value=1.8 Score=31.66 Aligned_cols=24 Identities=25% Similarity=0.407 Sum_probs=21.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHH
Q 008556 517 KSLSEVGNIFGLSKERVRQLESRA 540 (561)
Q Consensus 517 ~Tl~EIAe~LGISrerVRqie~RA 540 (561)
+|.+|+|+.||||+.+|+++.+..
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~~g 25 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIHEG 25 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHcC
Confidence 589999999999999999988654
No 270
>PRK00215 LexA repressor; Validated
Probab=81.21 E-value=2.8 Score=41.03 Aligned_cols=43 Identities=26% Similarity=0.306 Sum_probs=33.3
Q ss_pred CCHHHHHHHHHHh--cccCCCCCCHHHHHHHhCC-CHHHHHHHHHH
Q 008556 497 LNPKERCIVRLRF--GIEDGKPKSLSEVGNIFGL-SKERVRQLESR 539 (561)
Q Consensus 497 L~erER~VL~LRy--GL~d~e~~Tl~EIAe~LGI-SrerVRqie~R 539 (561)
|+++|++||.+-. ....+.+.|+.|||+.+|+ ++.+|..++.+
T Consensus 2 lt~~q~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~ 47 (205)
T PRK00215 2 LTKRQQEILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKA 47 (205)
T ss_pred CCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHH
Confidence 7889999986543 2334578899999999999 99999766544
No 271
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=80.89 E-value=3.1 Score=32.12 Aligned_cols=41 Identities=24% Similarity=0.416 Sum_probs=28.6
Q ss_pred CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008556 497 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA 540 (561)
Q Consensus 497 L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RA 540 (561)
|+..|-.||..-+- ..+.|..+||+.+|+++.+|.++.++-
T Consensus 1 lt~~q~~iL~~l~~---~~~~~~~~la~~~~~~~~~~t~~i~~L 41 (59)
T PF01047_consen 1 LTPSQFRILRILYE---NGGITQSELAEKLGISRSTVTRIIKRL 41 (59)
T ss_dssp STHHHHHHHHHHHH---HSSEEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHH---cCCCCHHHHHHHHCCChhHHHHHHHHH
Confidence 45555566655443 256999999999999999997665543
No 272
>CHL00148 orf27 Ycf27; Reviewed
Probab=80.76 E-value=2.2 Score=41.08 Aligned_cols=50 Identities=18% Similarity=0.115 Sum_probs=42.6
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHh-------CCCHHHHHHHHHHHHHHHHH
Q 008556 496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIF-------GLSKERVRQLESRALYRLKQ 546 (561)
Q Consensus 496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~L-------GISrerVRqie~RALkKLR~ 546 (561)
.|+++|.+|+.+... +.|.++|.+||++.+ +++..+|+.+..+.++||..
T Consensus 161 ~Lt~~E~~il~~l~~-~~~~~~s~~~i~~~l~~~~~~~~~~~~tv~~~i~~lr~KL~~ 217 (240)
T CHL00148 161 RLTGMEFSLLELLIS-KSGEIFSRATILKEVWGYTPERHIDTRVVDVHISRLRAKLED 217 (240)
T ss_pred EcCHHHHHHHHHHHH-CCCEEEcHHHHHHHhcCCCcccCCCcccHHHHHHHHHHHhcc
Confidence 499999999987653 345789999999999 48999999999999999964
No 273
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=80.56 E-value=2.9 Score=40.89 Aligned_cols=34 Identities=26% Similarity=0.293 Sum_probs=27.3
Q ss_pred HHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556 501 ERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 501 ER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R 539 (561)
++.|..++- .++|+.+||+.||||+.+|.++.+.
T Consensus 162 ~~~i~~~~~-----~g~s~~~iak~lgis~~Tv~r~~k~ 195 (200)
T PRK13413 162 EEKIKKLLD-----KGTSKSEIARKLGVSRTTLARFLKT 195 (200)
T ss_pred HHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHh
Confidence 345666643 5799999999999999999988763
No 274
>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=80.41 E-value=2 Score=31.11 Aligned_cols=25 Identities=16% Similarity=0.300 Sum_probs=22.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 008556 517 KSLSEVGNIFGLSKERVRQLESRAL 541 (561)
Q Consensus 517 ~Tl~EIAe~LGISrerVRqie~RAL 541 (561)
+|..|+|+.+|||+.+|++......
T Consensus 1 ~s~~e~a~~lgvs~~tl~~~~~~g~ 25 (49)
T cd04762 1 LTTKEAAELLGVSPSTLRRWVKEGK 25 (49)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCC
Confidence 5889999999999999999988754
No 275
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=80.25 E-value=7 Score=36.76 Aligned_cols=64 Identities=19% Similarity=0.326 Sum_probs=36.4
Q ss_pred HHHHHhcCCHHHHHHHHHH----hcccCCCCCCHHHHHHHhCCCHHHHHHHHH--HHHHHHHHHhhcCch
Q 008556 490 VRNLLTLLNPKERCIVRLR----FGIEDGKPKSLSEVGNIFGLSKERVRQLES--RALYRLKQSLGGKAS 553 (561)
Q Consensus 490 L~~aL~~L~erER~VL~LR----yGL~d~e~~Tl~EIAe~LGISrerVRqie~--RALkKLR~~l~~~~l 553 (561)
+..+=..|++.|+....+- |...+|+.+|+.|||+.+||++.+.-++.+ ++.....+.+....+
T Consensus 4 ~~~le~~L~~~Q~kAa~ll~~ne~~~~~~~r~T~~eiAee~Gis~~tLYrWr~~~~~Fiey~n~la~~~~ 73 (142)
T PF13022_consen 4 LKELEAKLTLQQRKAAQLLVENELMPENGERRTQAEIAEEVGISRSTLYRWRQQNKAFIEYKNELADRFL 73 (142)
T ss_dssp HHHHHTTS-HHHHHHHHHHHHHHHS------S-HHHHHHHHTS-HHHHHHHHHH-HHHHHHHHHHHHHHH
T ss_pred HHHHHHHcCHHHHHHHHHHHHHHHhhhccccchHHHHHHHhCCCHHHHHHHHhcCHHHHHHHHHHHHHHH
Confidence 4455578999998843332 222234789999999999999999998874 334444444443333
No 276
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=79.99 E-value=3.5 Score=34.30 Aligned_cols=49 Identities=22% Similarity=0.293 Sum_probs=34.1
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHhcccC---CCCCCHHHHHHHhCCCHHHHHHHH
Q 008556 487 RQHVRNLLTLLNPKERCIVRLRFGIED---GKPKSLSEVGNIFGLSKERVRQLE 537 (561)
Q Consensus 487 ~e~L~~aL~~L~erER~VL~LRyGL~d---~e~~Tl~EIAe~LGISrerVRqie 537 (561)
...|......|++.|+.|...- +.. -..+|..|||+..|||..+|-+..
T Consensus 4 ~~~i~~~~~~ls~~e~~Ia~yi--l~~~~~~~~~si~elA~~~~vS~sti~Rf~ 55 (77)
T PF01418_consen 4 LEKIRSQYNSLSPTEKKIADYI--LENPDEIAFMSISELAEKAGVSPSTIVRFC 55 (77)
T ss_dssp HHHHHHHGGGS-HHHHHHHHHH--HH-HHHHCT--HHHHHHHCTS-HHHHHHHH
T ss_pred HHHHHHHHhhCCHHHHHHHHHH--HhCHHHHHHccHHHHHHHcCCCHHHHHHHH
Confidence 3467777899999999987643 332 257999999999999999996543
No 277
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=79.21 E-value=4 Score=37.65 Aligned_cols=42 Identities=31% Similarity=0.285 Sum_probs=32.9
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556 495 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 495 ~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R 539 (561)
..|++.++.||..--. | ...++.|||+.+|+|..+|+.+..+
T Consensus 4 ~~lD~~D~~IL~~L~~--d-~r~~~~eia~~lglS~~~v~~Ri~~ 45 (154)
T COG1522 4 MKLDDIDRRILRLLQE--D-ARISNAELAERVGLSPSTVLRRIKR 45 (154)
T ss_pred ccccHHHHHHHHHHHH--h-CCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 4578888888876432 3 4599999999999999999876543
No 278
>PRK11564 stationary phase inducible protein CsiE; Provisional
Probab=79.03 E-value=4.8 Score=43.90 Aligned_cols=51 Identities=16% Similarity=0.203 Sum_probs=42.5
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556 496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 546 (561)
Q Consensus 496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 546 (561)
.+++.||..+.+.+.|...++.|+.++|+.|+||+.||.+-+++..+.|.+
T Consensus 10 ~~s~~ER~~~il~~LL~~~~~v~l~~Lae~l~VSrsTi~~DLk~l~~~L~~ 60 (426)
T PRK11564 10 VLSAPQRRCQILLMLFQPGLTVTLETFSQLNGVDDDTARQDIAETGREIQR 60 (426)
T ss_pred CCCHHHHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 478888888877777777789999999999999999999877766666655
No 279
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=78.85 E-value=4.8 Score=34.70 Aligned_cols=44 Identities=20% Similarity=0.243 Sum_probs=36.5
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 008556 495 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL 541 (561)
Q Consensus 495 ~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RAL 541 (561)
..|++.-|..|..+.. + ++++..++|+.||||+.+++++..|=.
T Consensus 7 A~Lt~~gR~~lv~~vv-~--~g~~~a~aA~~~gVS~~Ta~kW~~Ryr 50 (85)
T PF13011_consen 7 ARLTPRGRLRLVRRVV-E--QGWPVAHAAAEFGVSRRTAYKWLARYR 50 (85)
T ss_pred CCCCHHHHHHHHHHHH-H--cCCcHHHHHHHhCCCHHHHHHHHHHHH
Confidence 3588999988888763 2 579999999999999999998887643
No 280
>PF13551 HTH_29: Winged helix-turn helix
Probab=78.61 E-value=3.8 Score=35.35 Aligned_cols=26 Identities=19% Similarity=0.349 Sum_probs=22.9
Q ss_pred CCC-CHHHHHHHhCCCHHHHHHHHHHH
Q 008556 515 KPK-SLSEVGNIFGLSKERVRQLESRA 540 (561)
Q Consensus 515 e~~-Tl~EIAe~LGISrerVRqie~RA 540 (561)
++. |..+||+.+|||+.+|.+++++-
T Consensus 10 ~g~~~~~~ia~~lg~s~~Tv~r~~~~~ 36 (112)
T PF13551_consen 10 EGVSTIAEIARRLGISRRTVYRWLKRY 36 (112)
T ss_pred cCCCcHHHHHHHHCcCHHHHHHHHHHH
Confidence 567 69999999999999999888773
No 281
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=78.58 E-value=26 Score=35.19 Aligned_cols=34 Identities=15% Similarity=0.392 Sum_probs=28.3
Q ss_pred HHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHH
Q 008556 280 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 313 (561)
Q Consensus 280 le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~ 313 (561)
+.+....|...+|++|+.+|.|+.+|++.+++..
T Consensus 103 i~~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~ 136 (231)
T PRK12427 103 TNDAIREIAKRLGHEPNFEEISAELNLTAEEYQE 136 (231)
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHH
Confidence 4456677888899999999999999999887754
No 282
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=78.21 E-value=3.6 Score=39.14 Aligned_cols=40 Identities=23% Similarity=0.147 Sum_probs=30.7
Q ss_pred CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556 497 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 497 L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R 539 (561)
|++.++.||..-- .+...|+.|||+.+|+|+.+|+.+++|
T Consensus 12 lD~~D~~IL~~Lq---~d~R~s~~eiA~~lglS~~tv~~Ri~r 51 (164)
T PRK11169 12 LDRIDRNILNELQ---KDGRISNVELSKRVGLSPTPCLERVRR 51 (164)
T ss_pred HHHHHHHHHHHhc---cCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 5667788887432 235789999999999999999876543
No 283
>PHA01976 helix-turn-helix protein
Probab=77.30 E-value=4.2 Score=32.25 Aligned_cols=25 Identities=16% Similarity=0.238 Sum_probs=23.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556 515 KPKSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 515 e~~Tl~EIAe~LGISrerVRqie~R 539 (561)
.++|..|+|+.+|||+.+|.++++.
T Consensus 14 ~glt~~~lA~~~gvs~~~v~~~e~g 38 (67)
T PHA01976 14 RAWSAPELSRRAGVRHSLIYDFEAD 38 (67)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 6799999999999999999999864
No 284
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=77.30 E-value=2.5 Score=32.13 Aligned_cols=25 Identities=24% Similarity=0.426 Sum_probs=21.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556 515 KPKSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 515 e~~Tl~EIAe~LGISrerVRqie~R 539 (561)
.++|++|+|+.+|+|+.+|.++++.
T Consensus 8 ~gls~~~la~~~gis~~~i~~~~~g 32 (55)
T PF01381_consen 8 KGLSQKELAEKLGISRSTISRIENG 32 (55)
T ss_dssp TTS-HHHHHHHHTS-HHHHHHHHTT
T ss_pred cCCCHHHHHHHhCCCcchhHHHhcC
Confidence 6799999999999999999999875
No 285
>COG0856 Orotate phosphoribosyltransferase homologs [Nucleotide transport and metabolism]
Probab=77.17 E-value=3.1 Score=40.56 Aligned_cols=39 Identities=21% Similarity=0.202 Sum_probs=32.7
Q ss_pred HHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556 503 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 546 (561)
Q Consensus 503 ~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 546 (561)
..+.|+- .|+|..|||+.||+|++|++-+..|+.++...
T Consensus 10 kA~eLk~-----~Glt~gEIAdELNvSreTa~WL~~r~~~~~~~ 48 (203)
T COG0856 10 KARELKS-----KGLTTGEIADELNVSRETATWLLTRAFKKESV 48 (203)
T ss_pred HHHHHHH-----CCCcHHHhhhhhhhhHHHHHHHHhhhhhccCC
Confidence 3555664 68999999999999999999999998877643
No 286
>PRK05572 sporulation sigma factor SigF; Validated
Probab=76.42 E-value=27 Score=35.30 Aligned_cols=32 Identities=34% Similarity=0.640 Sum_probs=25.4
Q ss_pred HHHHHHHhhhhCCCCcHHHHHHHccCCHHHHH
Q 008556 281 EKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK 312 (561)
Q Consensus 281 e~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~ 312 (561)
.+....+....|+.|+..+.|+.+|++.+.+.
T Consensus 121 ~~~~~~l~~~~~r~p~~~eia~~l~~~~~~v~ 152 (252)
T PRK05572 121 RKDKDELSKELGREPTIEELAEYLGVTPEEVV 152 (252)
T ss_pred HHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHH
Confidence 34556667778999999999999999877663
No 287
>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=76.31 E-value=2.1 Score=31.69 Aligned_cols=25 Identities=24% Similarity=0.404 Sum_probs=22.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 008556 517 KSLSEVGNIFGLSKERVRQLESRAL 541 (561)
Q Consensus 517 ~Tl~EIAe~LGISrerVRqie~RAL 541 (561)
+|..|+|+.+|||..+|+..+.+.+
T Consensus 1 ~~~~e~a~~~gv~~~tlr~~~~~g~ 25 (49)
T cd04761 1 YTIGELAKLTGVSPSTLRYYERIGL 25 (49)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5889999999999999999988775
No 288
>PHA00542 putative Cro-like protein
Probab=75.92 E-value=4.3 Score=34.30 Aligned_cols=26 Identities=12% Similarity=0.102 Sum_probs=23.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008556 515 KPKSLSEVGNIFGLSKERVRQLESRA 540 (561)
Q Consensus 515 e~~Tl~EIAe~LGISrerVRqie~RA 540 (561)
.++|..++|+.+|||+.+|.++++..
T Consensus 30 ~glTq~elA~~lgIs~~tIsr~e~g~ 55 (82)
T PHA00542 30 AGWSQEQIADATDVSQPTICRIYSGR 55 (82)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHcCC
Confidence 67999999999999999999998654
No 289
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=75.81 E-value=6.8 Score=28.85 Aligned_cols=25 Identities=20% Similarity=0.376 Sum_probs=21.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556 515 KPKSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 515 e~~Tl~EIAe~LGISrerVRqie~R 539 (561)
.+.|..+|++.+|+|+.+|++.+..
T Consensus 13 ~~~s~~~l~~~l~~s~~tv~~~l~~ 37 (53)
T smart00420 13 GKVSVEELAELLGVSEMTIRRDLNK 37 (53)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 4699999999999999999776543
No 290
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=75.67 E-value=4.7 Score=31.65 Aligned_cols=24 Identities=25% Similarity=0.346 Sum_probs=21.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 008556 515 KPKSLSEVGNIFGLSKERVRQLES 538 (561)
Q Consensus 515 e~~Tl~EIAe~LGISrerVRqie~ 538 (561)
...|.+|+|+.||||..|||+-+.
T Consensus 13 ~~~s~~ela~~~~VS~~TiRRDl~ 36 (57)
T PF08220_consen 13 GKVSVKELAEEFGVSEMTIRRDLN 36 (57)
T ss_pred CCEEHHHHHHHHCcCHHHHHHHHH
Confidence 578999999999999999986543
No 291
>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=75.48 E-value=8.9 Score=32.84 Aligned_cols=31 Identities=26% Similarity=0.290 Sum_probs=24.2
Q ss_pred CCCCHHHHHHHhC-CCHHHHHHHHHHHHHHHH
Q 008556 515 KPKSLSEVGNIFG-LSKERVRQLESRALYRLK 545 (561)
Q Consensus 515 e~~Tl~EIAe~LG-ISrerVRqie~RALkKLR 545 (561)
-++|+.+||+.|| .+..+|.....+.-++|.
T Consensus 43 ~~~s~~~Ig~~fg~r~hStV~~a~~ri~~~~~ 74 (90)
T cd06571 43 TGLSLPEIGRAFGGRDHSTVLHAVRKIEELLE 74 (90)
T ss_pred hCCCHHHHHHHhCCCCHhHHHHHHHHHHHHHH
Confidence 4799999999999 999999875555444443
No 292
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=75.46 E-value=7.2 Score=33.14 Aligned_cols=32 Identities=19% Similarity=0.289 Sum_probs=26.0
Q ss_pred cCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008556 512 EDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 547 (561)
Q Consensus 512 ~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 547 (561)
.++...|-++||+.|||||.+| .+.+++||+.
T Consensus 15 ~~~~~~SGe~La~~LgiSRtaV----wK~Iq~Lr~~ 46 (79)
T COG1654 15 LTGNFVSGEKLAEELGISRTAV----WKHIQQLREE 46 (79)
T ss_pred cCCCcccHHHHHHHHCccHHHH----HHHHHHHHHh
Confidence 3447889999999999998888 4577788864
No 293
>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=75.02 E-value=7.8 Score=30.31 Aligned_cols=28 Identities=29% Similarity=0.552 Sum_probs=22.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556 515 KPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 546 (561)
Q Consensus 515 e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 546 (561)
.++|..|||+.+|+|+.+|++ .+++|++
T Consensus 24 ~~~s~~ela~~~g~s~~tv~r----~l~~L~~ 51 (67)
T cd00092 24 LPLTRQEIADYLGLTRETVSR----TLKELEE 51 (67)
T ss_pred CCcCHHHHHHHHCCCHHHHHH----HHHHHHH
Confidence 578999999999999999965 5555554
No 294
>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial. Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.
Probab=74.97 E-value=3.6 Score=38.96 Aligned_cols=29 Identities=17% Similarity=0.244 Sum_probs=24.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008556 515 KPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 547 (561)
Q Consensus 515 e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 547 (561)
-++|.+|||..+|+|+++|. |++++|++.
T Consensus 142 ~~~t~~~iA~~lG~tretvs----R~l~~l~~~ 170 (193)
T TIGR03697 142 LRLSHQAIAEAIGSTRVTIT----RLLGDLRKK 170 (193)
T ss_pred CCCCHHHHHHHhCCcHHHHH----HHHHHHHHC
Confidence 36899999999999999995 677888764
No 295
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=74.86 E-value=3.8 Score=32.49 Aligned_cols=25 Identities=20% Similarity=0.340 Sum_probs=20.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556 515 KPKSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 515 e~~Tl~EIAe~LGISrerVRqie~R 539 (561)
.++|..++|+.+|+|..+|+++++-
T Consensus 13 ~gls~~~lA~~~g~s~s~v~~iE~G 37 (64)
T PF13560_consen 13 AGLSQAQLADRLGVSQSTVSRIERG 37 (64)
T ss_dssp HTS-HHHHHHHHTS-HHHHHHHHTT
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHCC
Confidence 5799999999999999999999864
No 296
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=74.83 E-value=7.9 Score=37.41 Aligned_cols=110 Identities=16% Similarity=0.206 Sum_probs=59.2
Q ss_pred CCCCHHHHHHHh--CCCHHHHHHHHHhcCC--CccCCCCCCCCCCchhh-hhcccCCCCChhHHH--HHHHHHHHHHHHH
Q 008556 422 HSPDKEDLARRV--GITVEKLERLIFITRM--PLSMQQPVWADQDTTFQ-EITADTGVEIPDISV--QKQLMRQHVRNLL 494 (561)
Q Consensus 422 r~Pt~eEIA~~l--gis~e~v~~ll~~~~~--~~SLD~~v~~d~~~~l~-d~l~d~~~~~pee~l--e~~e~~e~L~~aL 494 (561)
-.++..+||+.+ +|+.+++++.+..-.. -+--+.. +.-... ..+. ...+.+...+ .+..+.+.-.++|
T Consensus 38 ~~~d~~~iak~l~p~is~~ev~~sL~~L~~~gli~k~~~----g~y~~t~~~l~-~~~~~~~~avr~~h~q~~~lA~~al 112 (171)
T PF14394_consen 38 FAPDPEWIAKRLRPKISAEEVRDSLEFLEKLGLIKKDGD----GKYVQTDKSLT-TSSEIPSEAVRSYHKQMLELAQEAL 112 (171)
T ss_pred CCCCHHHHHHHhcCCCCHHHHHHHHHHHHHCCCeEECCC----CcEEEecceee-CCCCCcHHHHHHHHHHHHHHHHHHH
Confidence 366899999999 9999999998764321 1111110 000000 1111 1111222111 2233444456677
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008556 495 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 550 (561)
Q Consensus 495 ~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 550 (561)
+..|+.+|.+=-+-++++. .++++ |+..+...++++......
T Consensus 113 ~~~p~~~R~~s~~T~~vs~---~~~~k-----------i~~~i~~fRk~i~~i~~~ 154 (171)
T PF14394_consen 113 DRVPPEERDFSGLTMSVSR---EDYEK-----------IKKEIREFRKKIIAIAEE 154 (171)
T ss_pred HhCCccccceeeeEEEeCH---HHHHH-----------HHHHHHHHHHHHHHHHhc
Confidence 8888999988777776432 23333 445556666666655544
No 297
>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=74.82 E-value=5.4 Score=30.09 Aligned_cols=25 Identities=12% Similarity=0.279 Sum_probs=22.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556 515 KPKSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 515 e~~Tl~EIAe~LGISrerVRqie~R 539 (561)
.++|..++|+.+|+|+.+|+.+++.
T Consensus 14 ~gltq~~lA~~~gvs~~~vs~~e~g 38 (58)
T TIGR03070 14 LGLTQADLADLAGVGLRFIRDVENG 38 (58)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHCC
Confidence 5799999999999999999999864
No 298
>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=74.79 E-value=5.9 Score=30.67 Aligned_cols=26 Identities=35% Similarity=0.482 Sum_probs=21.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556 517 KSLSEVGNIFGLSKERVRQLESRALYRLKQ 546 (561)
Q Consensus 517 ~Tl~EIAe~LGISrerVRqie~RALkKLR~ 546 (561)
.|..+||+.+|+|+++|++ ++++|.+
T Consensus 26 ~~~~~la~~~~is~~~v~~----~l~~L~~ 51 (66)
T cd07377 26 PSERELAEELGVSRTTVRE----ALRELEA 51 (66)
T ss_pred CCHHHHHHHHCCCHHHHHH----HHHHHHH
Confidence 3599999999999999974 6666655
No 299
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=74.56 E-value=4.4 Score=29.56 Aligned_cols=28 Identities=32% Similarity=0.627 Sum_probs=22.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556 515 KPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 546 (561)
Q Consensus 515 e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 546 (561)
-+.|..+||+.+|+|+.+|++ ++++|.+
T Consensus 7 ~~~s~~~la~~l~~s~~tv~~----~l~~L~~ 34 (48)
T smart00419 7 LPLTRQEIAELLGLTRETVSR----TLKRLEK 34 (48)
T ss_pred eccCHHHHHHHHCCCHHHHHH----HHHHHHH
Confidence 368999999999999999954 5555554
No 300
>TIGR00122 birA_repr_reg BirA biotin operon repressor domain. This model may recognize some other putative repressor proteins, such as DnrO of Streptomyces peucetius with scores below the noise cutoff but with significance shown by low E-value.
Probab=74.49 E-value=6.9 Score=31.53 Aligned_cols=25 Identities=24% Similarity=0.388 Sum_probs=20.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556 515 KPKSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 515 e~~Tl~EIAe~LGISrerVRqie~R 539 (561)
...+..|||+.+|+|+.+|++.+.+
T Consensus 12 ~~~~~~eLa~~l~vS~~tv~~~l~~ 36 (69)
T TIGR00122 12 NPFSGEKLGEALGMSRTAVNKHIQT 36 (69)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 3578999999999999999865443
No 301
>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY. This model represents the full length of CodY, a pleiotropic repressor in Bacillus subtilis and other Firmicutes (low-GC Gram-positive bacteria) that responds to intracellular levels of GTP and branched chain amino acids. The C-terminal helix-turn-helix DNA-binding region is modeled by pfam08222 in Pfam.
Probab=74.49 E-value=14 Score=37.95 Aligned_cols=55 Identities=22% Similarity=0.236 Sum_probs=43.6
Q ss_pred HHHHHHHhcCCHHHHHHHHHHhcccCC--CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556 488 QHVRNLLTLLNPKERCIVRLRFGIEDG--KPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 546 (561)
Q Consensus 488 e~L~~aL~~L~erER~VL~LRyGL~d~--e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 546 (561)
..++-++..|+--|.+.+...+-.-++ .-.+..+||+.+|||+..|+ +|+++|..
T Consensus 168 a~Vq~Ai~tLSySEleAv~~IL~~L~~~egrlse~eLAerlGVSRs~ir----eAlrkLE~ 224 (251)
T TIGR02787 168 AAVQMAINTLSYSELEAVEHIFEELDGNEGLLVASKIADRVGITRSVIV----NALRKLES 224 (251)
T ss_pred HHHHHHHHhccHhHHHHHHHHHHHhccccccccHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 457778999999999888876654444 36799999999999999887 46777755
No 302
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=74.25 E-value=5.4 Score=30.20 Aligned_cols=25 Identities=24% Similarity=0.373 Sum_probs=21.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556 515 KPKSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 515 e~~Tl~EIAe~LGISrerVRqie~R 539 (561)
++.|..+|++.+|+|+.+|+..+++
T Consensus 9 ~~~~~~~i~~~l~is~~~v~~~l~~ 33 (66)
T smart00418 9 GELCVCELAEILGLSQSTVSHHLKK 33 (66)
T ss_pred CCccHHHHHHHHCCCHHHHHHHHHH
Confidence 6789999999999999999876654
No 303
>PF08822 DUF1804: Protein of unknown function (DUF1804); InterPro: IPR014926 This entry is represented by Bacteriophage D3112, Orf24. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=74.11 E-value=6.9 Score=37.74 Aligned_cols=41 Identities=22% Similarity=0.214 Sum_probs=33.5
Q ss_pred HHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008556 499 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 542 (561)
Q Consensus 499 erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALk 542 (561)
+.-|.-++..|.+ +++|++.+|..+|||..|+|++..+|..
T Consensus 5 ~e~R~~~R~~YV~---~~~sLe~aA~~~gVs~~TarrWK~~Ak~ 45 (165)
T PF08822_consen 5 QETRDAVRRAYVF---DRLSLEQAAAKCGVSYATARRWKREAKA 45 (165)
T ss_pred HHHHHHHHHHHHh---CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4445666666763 5799999999999999999999998854
No 304
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=74.05 E-value=30 Score=34.89 Aligned_cols=34 Identities=29% Similarity=0.515 Sum_probs=26.9
Q ss_pred HHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHH
Q 008556 280 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 313 (561)
Q Consensus 280 le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~ 313 (561)
+......+...+|+.|+..+.|..+|++.+.+..
T Consensus 118 ~~~~~~~l~~~~~r~p~~~eia~~l~i~~~~~~~ 151 (255)
T TIGR02941 118 IKKAIDELTDHLQRSPKIIEIADHLGLSEEEVLE 151 (255)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence 3345667777889999999999999998876643
No 305
>PF08765 Mor: Mor transcription activator family; InterPro: IPR014875 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 dimerisation region, and the C-terminal contains a helix-turn-helix motif which binds DNA []. ; PDB: 1RR7_A.
Probab=73.65 E-value=6.7 Score=34.84 Aligned_cols=42 Identities=21% Similarity=0.311 Sum_probs=27.2
Q ss_pred HHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556 499 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 546 (561)
Q Consensus 499 erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 546 (561)
.|.++|...+ .|++..|+|..+|+|..+|++|+++..++-++
T Consensus 61 ~R~~~I~~~f------~G~n~~eLA~kyglS~r~I~~Ii~~~~~~~~~ 102 (108)
T PF08765_consen 61 LRNREIRREF------NGMNVRELARKYGLSERQIYRIIKRVRRRERR 102 (108)
T ss_dssp HHHHHHHHH--------SS-HHHHHHHHT--HHHHHHHHHHHHH----
T ss_pred HHHHHHHHHh------CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 3455566543 46899999999999999999999988777654
No 306
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=73.59 E-value=5.9 Score=29.15 Aligned_cols=37 Identities=14% Similarity=0.225 Sum_probs=24.1
Q ss_pred HHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008556 499 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES 538 (561)
Q Consensus 499 erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~ 538 (561)
+-|+.+|.-..-- .+.+..+.|+.||||+.+++..+.
T Consensus 4 ~~E~~~i~~aL~~---~~gn~~~aA~~Lgisr~tL~~klk 40 (42)
T PF02954_consen 4 EFEKQLIRQALER---CGGNVSKAARLLGISRRTLYRKLK 40 (42)
T ss_dssp HHHHHHHHHHHHH---TTT-HHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHHHHHH---hCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3456666554431 245889999999999999986554
No 307
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=73.45 E-value=6 Score=30.38 Aligned_cols=51 Identities=12% Similarity=0.137 Sum_probs=39.6
Q ss_pred cCCHHHHHHHHHHhcccCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556 496 LLNPKERCIVRLRFGIEDG-KPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 546 (561)
Q Consensus 496 ~L~erER~VL~LRyGL~d~-e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 546 (561)
.+++.+..+|.-.|..+.. ......+||..+||+...|......-..+.|+
T Consensus 6 ~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 6 RFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence 4678888899988875321 22356899999999999999999887777653
No 308
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=73.45 E-value=11 Score=33.67 Aligned_cols=48 Identities=21% Similarity=0.248 Sum_probs=35.6
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008556 487 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA 540 (561)
Q Consensus 487 ~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RA 540 (561)
.+.+...-..+.+.+-.-++..+ ++|..++|+.+|+|+.+|+++++..
T Consensus 55 ~~~~~~~~~~~~~~~i~~~r~~~------gltq~~lA~~lg~~~~tis~~e~g~ 102 (127)
T TIGR03830 55 ADFYRKVDGLLTPPEIRRIRKKL------GLSQREAAELLGGGVNAFSRYERGE 102 (127)
T ss_pred HHHHHHccCCcCHHHHHHHHHHc------CCCHHHHHHHhCCCHHHHHHHHCCC
Confidence 33344444667777665565555 5899999999999999999988743
No 309
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=73.28 E-value=5.3 Score=33.03 Aligned_cols=25 Identities=16% Similarity=0.331 Sum_probs=22.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556 515 KPKSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 515 e~~Tl~EIAe~LGISrerVRqie~R 539 (561)
.++|..|.|+.+|||+.||-.+++-
T Consensus 13 ~~ltQ~elA~~vgVsRQTi~~iEkg 37 (68)
T COG1476 13 LGLTQEELAKLVGVSRQTIIAIEKG 37 (68)
T ss_pred hCcCHHHHHHHcCcCHHHHHHHHcC
Confidence 4699999999999999999998864
No 310
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=73.09 E-value=6.1 Score=36.17 Aligned_cols=24 Identities=25% Similarity=0.336 Sum_probs=22.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 008556 515 KPKSLSEVGNIFGLSKERVRQLES 538 (561)
Q Consensus 515 e~~Tl~EIAe~LGISrerVRqie~ 538 (561)
+|+|..+||+.||+|+..|+|.++
T Consensus 21 eG~Sq~~iA~LLGltqaAVS~Yls 44 (119)
T COG2522 21 EGLSQYRIAKLLGLTQAAVSQYLS 44 (119)
T ss_pred cCCcHHHHHHHhCCCHHHHHHHHc
Confidence 579999999999999999999875
No 311
>PRK10072 putative transcriptional regulator; Provisional
Probab=72.69 E-value=5.5 Score=35.00 Aligned_cols=32 Identities=28% Similarity=0.479 Sum_probs=26.9
Q ss_pred HHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556 504 IVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 504 VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R 539 (561)
|-.+|.. .++|..|+|+.+|||..+|++++..
T Consensus 38 ik~LR~~----~glTQ~elA~~lGvS~~TVs~WE~G 69 (96)
T PRK10072 38 FEQLRKG----TGLKIDDFARVLGVSVAMVKEWESR 69 (96)
T ss_pred HHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 4455555 6899999999999999999999863
No 312
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=72.54 E-value=4.1 Score=32.98 Aligned_cols=28 Identities=39% Similarity=0.666 Sum_probs=23.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556 515 KPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 546 (561)
Q Consensus 515 e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 546 (561)
-++|.++||..+|+|+++|. +.+++|++
T Consensus 27 ~~lt~~~iA~~~g~sr~tv~----r~l~~l~~ 54 (76)
T PF13545_consen 27 LPLTQEEIADMLGVSRETVS----RILKRLKD 54 (76)
T ss_dssp EESSHHHHHHHHTSCHHHHH----HHHHHHHH
T ss_pred ecCCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 36899999999999999985 56666665
No 313
>COG5625 Predicted transcription regulator containing HTH domain [Transcription]
Probab=72.39 E-value=5.5 Score=35.39 Aligned_cols=70 Identities=23% Similarity=0.275 Sum_probs=50.2
Q ss_pred HHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHH--HHHHHHhhcCchhhhh
Q 008556 488 QHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL--YRLKQSLGGKASYGYA 557 (561)
Q Consensus 488 e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RAL--kKLR~~l~~~~l~~yl 557 (561)
..|..+|..+.-+--+|..+.+.+.-+.+|...||+..||||.-+||-...--+ --|+..+...++--|+
T Consensus 8 ~~l~~~L~~~glk~~eI~IY~lLve~~~~mri~ei~rEl~is~rtvr~~v~~l~rrGll~relvqkgWvGYi 79 (113)
T COG5625 8 RKLGKALEAIGLKKNEIRIYSLLVEKGRGMRIREIQRELGISERTVRAAVAVLLRRGLLARELVQKGWVGYI 79 (113)
T ss_pred HHHHHHHHHcCCCcchhhhhhHHHHhcCCchHHHHHHHHhHHHHHHHHHHHHHHHhhHHHHHHHhccceeeE
Confidence 345666766665555566666666666889999999999999999998777666 3466666666665553
No 314
>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR. This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.
Probab=72.33 E-value=17 Score=32.20 Aligned_cols=41 Identities=10% Similarity=0.110 Sum_probs=31.9
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008556 495 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES 538 (561)
Q Consensus 495 ~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~ 538 (561)
..|++.+..||..-+. +.+.|..|||+.+|+++.+|.+++.
T Consensus 24 ~~lt~~q~~iL~~l~~---~~~~t~~ela~~~~~~~~tvs~~l~ 64 (118)
T TIGR02337 24 HGLTEQQWRILRILAE---QGSMEFTQLANQACILRPSLTGILA 64 (118)
T ss_pred cCCCHHHHHHHHHHHH---cCCcCHHHHHHHhCCCchhHHHHHH
Confidence 4688888888865432 3579999999999999999965443
No 315
>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID. Members of this protein are the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if and only if the species is capable of endospore formation as occurs in the model species Bacillus subtilis. SpoIIID is a DNA binding protein that, in B. subtilis, downregulates many genes but also turns on ten genes.
Probab=71.96 E-value=8 Score=32.95 Aligned_cols=24 Identities=25% Similarity=0.447 Sum_probs=21.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 008556 515 KPKSLSEVGNIFGLSKERVRQLES 538 (561)
Q Consensus 515 e~~Tl~EIAe~LGISrerVRqie~ 538 (561)
...|+++||+.+|||+.||+..+.
T Consensus 18 ~~~ti~dvA~~~gvS~~TVsr~L~ 41 (80)
T TIGR02844 18 TKATVRETAKVFGVSKSTVHKDVT 41 (80)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHhc
Confidence 467999999999999999998665
No 316
>TIGR02612 mob_myst_A mobile mystery protein A. Members of this protein family are found in mobization-related contexts more often than not, including within a CRISPR-associated gene region in Geobacter sulfurreducens PCA, and on plasmids in Agrobacterium tumefaciens and Coxiella burnetii, always together with mobile mystery protein B, a member of the Fic protein family (pfam02661). This protein is encoded by the upstream member of the gene pair and belongs to a family of helix-turn-helix DNA binding proteins (pfam01381).
Probab=71.94 E-value=8.5 Score=36.56 Aligned_cols=49 Identities=24% Similarity=0.349 Sum_probs=35.7
Q ss_pred CHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH------HHHHHHHHhhc
Q 008556 498 NPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR------ALYRLKQSLGG 550 (561)
Q Consensus 498 ~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R------ALkKLR~~l~~ 550 (561)
+|..-.|=.+|-. .|+|..++|+.+|||+.+|.++++. .+..|.+....
T Consensus 24 ~p~~~~Ir~~R~~----lGmTq~eLAerlGVS~~tIs~iE~G~~~~~psl~~L~kIA~a 78 (150)
T TIGR02612 24 TPKEGWVRAIRKA----LGMSGAQLAGRLGVTPQRVEALEKSELSGTVTLKTLRAAAEA 78 (150)
T ss_pred cCcHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHcCCCCCCCCHHHHHHHHHH
Confidence 4444445556665 6899999999999999999999985 34455554443
No 317
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=71.84 E-value=49 Score=33.52 Aligned_cols=33 Identities=24% Similarity=0.307 Sum_probs=27.1
Q ss_pred HHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHH
Q 008556 281 EKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 313 (561)
Q Consensus 281 e~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~ 313 (561)
.+...++...+|++|+..|.|..+|++.+.+..
T Consensus 126 ~~~~~~l~~~~~r~p~~~eia~~l~v~~~~v~~ 158 (258)
T PRK08215 126 LQVREKLINENSKEPTVEEIAKELEVPREEVVF 158 (258)
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHH
Confidence 345566777889999999999999999888754
No 318
>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the 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=71.67 E-value=4.9 Score=38.57 Aligned_cols=35 Identities=20% Similarity=0.208 Sum_probs=27.6
Q ss_pred HHHHHHHHhcccCCCCCCHHHHHHHhC-CCHHHHHHHHHH
Q 008556 501 ERCIVRLRFGIEDGKPKSLSEVGNIFG-LSKERVRQLESR 539 (561)
Q Consensus 501 ER~VL~LRyGL~d~e~~Tl~EIAe~LG-ISrerVRqie~R 539 (561)
.-+.|.-.+. +|+|..|||+.|| ||++.|--..+|
T Consensus 7 ~~~~L~~lw~----~G~SasqIA~~lg~vsRnAViGk~hR 42 (162)
T PF07750_consen 7 RVERLRKLWA----EGLSASQIARQLGGVSRNAVIGKAHR 42 (162)
T ss_pred HHHHHHHHHH----cCCCHHHHHHHhCCcchhhhhhhhhc
Confidence 3344444555 8999999999999 999999877766
No 319
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=71.56 E-value=57 Score=32.48 Aligned_cols=33 Identities=33% Similarity=0.556 Sum_probs=26.2
Q ss_pred HHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHH
Q 008556 281 EKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 313 (561)
Q Consensus 281 e~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~ 313 (561)
.+....+....|++|+..++|+.+|++.+.+..
T Consensus 98 ~~~~~~~~~~~~~~~~~~ela~~l~i~~~~v~~ 130 (236)
T PRK06986 98 AQAIRQLEQELGREPTDTEVAEKLGLSLEEYRE 130 (236)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHH
Confidence 344556667789999999999999999877643
No 320
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=71.52 E-value=4.4 Score=39.29 Aligned_cols=29 Identities=34% Similarity=0.598 Sum_probs=25.1
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556 514 GKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 546 (561)
Q Consensus 514 ~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 546 (561)
.+++|+.||++.+|+|+.+|++ ++++|..
T Consensus 39 ~~Pmtl~Ei~E~lg~Sks~vS~----~lkkL~~ 67 (177)
T COG1510 39 RKPLTLDEIAEALGMSKSNVSM----GLKKLQD 67 (177)
T ss_pred CCCccHHHHHHHHCCCcchHHH----HHHHHHh
Confidence 4899999999999999999976 6777754
No 321
>PF13551 HTH_29: Winged helix-turn helix
Probab=71.07 E-value=12 Score=32.23 Aligned_cols=24 Identities=29% Similarity=0.426 Sum_probs=21.5
Q ss_pred CHHHHHHHhCCCHHHHHHHHHhcC
Q 008556 425 DKEDLARRVGITVEKLERLIFITR 448 (561)
Q Consensus 425 t~eEIA~~lgis~e~v~~ll~~~~ 448 (561)
+..++|+.+|++...|..++....
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~~~ 37 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKRYR 37 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHH
Confidence 799999999999999999987643
No 322
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=70.95 E-value=9.7 Score=31.78 Aligned_cols=26 Identities=27% Similarity=0.349 Sum_probs=22.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008556 515 KPKSLSEVGNIFGLSKERVRQLESRA 540 (561)
Q Consensus 515 e~~Tl~EIAe~LGISrerVRqie~RA 540 (561)
.++|..|||+.+|+++.+|++++..-
T Consensus 19 ~~~t~~~ia~~l~i~~~tv~r~l~~L 44 (91)
T smart00346 19 GGLTLAELAERLGLSKSTAHRLLNTL 44 (91)
T ss_pred CCcCHHHHHHHhCCCHHHHHHHHHHH
Confidence 57999999999999999998766543
No 323
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=70.41 E-value=2.2 Score=34.05 Aligned_cols=25 Identities=28% Similarity=0.514 Sum_probs=22.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 008556 517 KSLSEVGNIFGLSKERVRQLESRAL 541 (561)
Q Consensus 517 ~Tl~EIAe~LGISrerVRqie~RAL 541 (561)
||..|+|+.+|||..+||..+.+.+
T Consensus 1 yti~eva~~~gvs~~tlr~y~~~gl 25 (69)
T PF13411_consen 1 YTIKEVAKLLGVSPSTLRYYEREGL 25 (69)
T ss_dssp EEHHHHHHHTTTTHHHHHHHHHTTS
T ss_pred CcHHHHHHHHCcCHHHHHHHHHhcC
Confidence 5789999999999999999988766
No 324
>PRK09954 putative kinase; Provisional
Probab=70.29 E-value=8.4 Score=40.91 Aligned_cols=42 Identities=19% Similarity=0.279 Sum_probs=32.3
Q ss_pred CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 008556 497 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL 541 (561)
Q Consensus 497 L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RAL 541 (561)
|+++++.||.+..- + ...|..|||+.||||+.+|+.++++-.
T Consensus 1 ~~~~~~~il~~l~~--~-~~~s~~~la~~l~~s~~~v~~~i~~L~ 42 (362)
T PRK09954 1 MNNREKEILAILRR--N-PLIQQNEIADILQISRSRVAAHIMDLM 42 (362)
T ss_pred CChHHHHHHHHHHH--C-CCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 46677777766542 2 478999999999999999998776543
No 325
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=70.24 E-value=13 Score=34.12 Aligned_cols=49 Identities=8% Similarity=0.047 Sum_probs=34.6
Q ss_pred HHHHHH--hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556 489 HVRNLL--TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 489 ~L~~aL--~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R 539 (561)
.+...+ -.|++.+-.||..-+. .+++.|..|||+.+|+++.+|.++..+
T Consensus 19 ~~~~~l~~~glt~~q~~vL~~l~~--~~~~~t~~eLa~~l~~~~~tvt~~v~~ 69 (144)
T PRK03573 19 LIDHRLKPLELTQTHWVTLHNIHQ--LPPEQSQIQLAKAIGIEQPSLVRTLDQ 69 (144)
T ss_pred HHHHHHHhcCCCHHHHHHHHHHHH--cCCCCCHHHHHHHhCCChhhHHHHHHH
Confidence 344444 3588888777765542 225689999999999999999765443
No 326
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 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 [].; PDB: 2WTE_A 3SQN_A.
Probab=69.85 E-value=5.2 Score=31.62 Aligned_cols=36 Identities=14% Similarity=0.218 Sum_probs=25.7
Q ss_pred HHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008556 500 KERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES 538 (561)
Q Consensus 500 rER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~ 538 (561)
|+-++|.+-+. ...+|+.|||+.+|+|.-+|++.+.
T Consensus 6 rq~~Ll~~L~~---~~~~~~~ela~~l~~S~rti~~~i~ 41 (59)
T PF08280_consen 6 RQLKLLELLLK---NKWITLKELAKKLNISERTIKNDIN 41 (59)
T ss_dssp HHHHHHHHHHH---HTSBBHHHHHHHCTS-HHHHHHHHH
T ss_pred HHHHHHHHHHc---CCCCcHHHHHHHHCCCHHHHHHHHH
Confidence 34445555443 3689999999999999999986543
No 327
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=69.51 E-value=5.8 Score=40.66 Aligned_cols=25 Identities=20% Similarity=0.444 Sum_probs=23.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556 515 KPKSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 515 e~~Tl~EIAe~LGISrerVRqie~R 539 (561)
++|.+.+||++||||+.+|+....|
T Consensus 18 ~gmk~~dIAeklGvspntiksWKrr 42 (279)
T COG5484 18 KGMKLKDIAEKLGVSPNTIKSWKRR 42 (279)
T ss_pred hhccHHHHHHHhCCChHHHHHHHHh
Confidence 7899999999999999999998766
No 328
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily. This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.
Probab=69.30 E-value=38 Score=33.36 Aligned_cols=31 Identities=32% Similarity=0.592 Sum_probs=25.6
Q ss_pred HHHHHHhhhhCCCCcHHHHHHHccCCHHHHH
Q 008556 282 KEKSKLQSQFGREPTLIEWAKAIGLSCRDLK 312 (561)
Q Consensus 282 ~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~ 312 (561)
+....+....|++|+..|.|+.+|++.+.+.
T Consensus 94 ~~~~~l~~~~~~~p~~~ela~~l~~~~~~v~ 124 (227)
T TIGR02980 94 KATEELTQRLGRSPTIAEIAEELGVSEEEVV 124 (227)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHhCCCHHHHH
Confidence 3455677778999999999999999988764
No 329
>COG2973 TrpR Trp operon repressor [Transcription]
Probab=69.28 E-value=10 Score=33.46 Aligned_cols=39 Identities=28% Similarity=0.376 Sum_probs=31.1
Q ss_pred cCCHHHHHHHHHHhcccC---CCCCCHHHHHHHhCCCHHHHH
Q 008556 496 LLNPKERCIVRLRFGIED---GKPKSLSEVGNIFGLSKERVR 534 (561)
Q Consensus 496 ~L~erER~VL~LRyGL~d---~e~~Tl~EIAe~LGISrerVR 534 (561)
-|++.||+-+-.|+-+.. ...+|.+||+..||+|-.+|-
T Consensus 37 lLTpdEReal~~Rv~Iv~eLL~ge~sQREi~~~LgvsiAtIT 78 (103)
T COG2973 37 LLTPDEREALGTRVRIVEELLRGELSQREIAQKLGVSIATIT 78 (103)
T ss_pred HcCHhHHHHHHHHHHHHHHHHhccccHHHHHHHhCcchhhhc
Confidence 388889888877776432 147999999999999988873
No 330
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=69.15 E-value=5.6 Score=31.59 Aligned_cols=30 Identities=37% Similarity=0.547 Sum_probs=22.3
Q ss_pred CCCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556 513 DGKPK-SLSEVGNIFGLSKERVRQLESRALYRLKQ 546 (561)
Q Consensus 513 d~e~~-Tl~EIAe~LGISrerVRqie~RALkKLR~ 546 (561)
.|+.+ |..+||+.+|||+.+||. |+..|..
T Consensus 20 ~g~~lps~~~la~~~~vsr~tvr~----al~~L~~ 50 (64)
T PF00392_consen 20 PGDRLPSERELAERYGVSRTTVRE----ALRRLEA 50 (64)
T ss_dssp TTSBE--HHHHHHHHTS-HHHHHH----HHHHHHH
T ss_pred CCCEeCCHHHHHHHhccCCcHHHH----HHHHHHH
Confidence 44777 999999999999999975 6666644
No 331
>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=69.14 E-value=13 Score=28.84 Aligned_cols=23 Identities=26% Similarity=0.391 Sum_probs=19.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q 008556 517 KSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 517 ~Tl~EIAe~LGISrerVRqie~R 539 (561)
.+..||++.+|+++.+|+..+.+
T Consensus 21 ~~~~ei~~~~~i~~~~i~~~l~~ 43 (78)
T cd00090 21 LTVSELAERLGLSQSTVSRHLKK 43 (78)
T ss_pred cCHHHHHHHHCcCHhHHHHHHHH
Confidence 99999999999999999765443
No 332
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=68.32 E-value=6.1 Score=37.84 Aligned_cols=28 Identities=18% Similarity=0.237 Sum_probs=23.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556 515 KPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 546 (561)
Q Consensus 515 e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 546 (561)
-+.|.++||..+|+|+++|. |++++|++
T Consensus 148 ~~~t~~~iA~~lG~tretvs----R~l~~l~~ 175 (202)
T PRK13918 148 IYATHDELAAAVGSVRETVT----KVIGELSR 175 (202)
T ss_pred ecCCHHHHHHHhCccHHHHH----HHHHHHHH
Confidence 35799999999999999995 56777765
No 333
>PF08535 KorB: KorB domain; InterPro: IPR013741 This entry contains 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 []. ; PDB: 1R71_C.
Probab=67.95 E-value=5 Score=34.52 Aligned_cols=24 Identities=17% Similarity=0.108 Sum_probs=17.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 008556 515 KPKSLSEVGNIFGLSKERVRQLES 538 (561)
Q Consensus 515 e~~Tl~EIAe~LGISrerVRqie~ 538 (561)
.|+|..|||+.+|.|+..|.+++.
T Consensus 2 ~G~tq~eIA~~lGks~s~Vs~~l~ 25 (93)
T PF08535_consen 2 FGWTQEEIAKRLGKSRSWVSNHLA 25 (93)
T ss_dssp TT--HHHHHHHTT--HHHHHHHHG
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
Confidence 479999999999999999998764
No 334
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=67.92 E-value=9.2 Score=39.39 Aligned_cols=52 Identities=15% Similarity=0.311 Sum_probs=41.4
Q ss_pred HHHHHHHHHhcCCHHHHHHHHHHhcccCC---CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556 486 MRQHVRNLLTLLNPKERCIVRLRFGIEDG---KPKSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 486 ~~e~L~~aL~~L~erER~VL~LRyGL~d~---e~~Tl~EIAe~LGISrerVRqie~R 539 (561)
+...|+..+..|++.|+.|...- +++. ..+|..+||+..|||..+|-+..++
T Consensus 15 i~~~i~~~~~~Lt~~e~~Ia~yi--l~~~~~v~~~si~~lA~~~~vS~aTi~Rf~kk 69 (292)
T PRK11337 15 LGPYIRMKQEGLTPLESRVVEWL--LKPGDLSEATALKDIAEALAVSEAMIVKVAKK 69 (292)
T ss_pred HHHHHHHHHhhcCHHHHHHHHHH--HhCHHHHHhcCHHHHHHHhCCChHHHHHHHHH
Confidence 34478888999999999998754 4332 4589999999999999999776554
No 335
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=67.42 E-value=15 Score=28.56 Aligned_cols=45 Identities=22% Similarity=0.330 Sum_probs=31.1
Q ss_pred cchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHH
Q 008556 398 LPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLER 442 (561)
Q Consensus 398 lP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ 442 (561)
||......+-...+.-..+..++-...+-.+||+.+|+++..|+.
T Consensus 3 Ip~~ti~RL~~Y~r~L~~l~~~G~~~vSS~~La~~~gi~~~qVRK 47 (50)
T PF06971_consen 3 IPKATIRRLPLYLRYLEQLKEEGVERVSSQELAEALGITPAQVRK 47 (50)
T ss_dssp -SHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHTS-HHHHHH
T ss_pred CCHHHHHHHHHHHHHHHHHHHcCCeeECHHHHHHHHCCCHHHhcc
Confidence 555555555555666666777777778899999999999999975
No 336
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=67.01 E-value=9.3 Score=38.98 Aligned_cols=51 Identities=14% Similarity=0.230 Sum_probs=40.5
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHhcccCC---CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556 487 RQHVRNLLTLLNPKERCIVRLRFGIEDG---KPKSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 487 ~e~L~~aL~~L~erER~VL~LRyGL~d~---e~~Tl~EIAe~LGISrerVRqie~R 539 (561)
.+.|...+..|++.|+.|..+- ++.. ..+|..|||+..|+|..+|-+..++
T Consensus 4 ~~~i~~~~~~Lt~~e~~Ia~yi--l~n~~~v~~~si~~lA~~~~vS~aTv~Rf~kk 57 (284)
T PRK11302 4 LEKIQSRLEHLSKSERKVAEVI--LASPQTAIHSSIATLAKMANVSEPTVNRFCRS 57 (284)
T ss_pred HHHHHHHHhhCCHHHHHHHHHH--HhCHHHHHhcCHHHHHHHhCCCHHHHHHHHHH
Confidence 3467888899999999998753 4432 3589999999999999999776554
No 337
>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=66.25 E-value=7.4 Score=30.85 Aligned_cols=23 Identities=26% Similarity=0.488 Sum_probs=20.9
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q 008556 517 KSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 517 ~Tl~EIAe~LGISrerVRqie~R 539 (561)
+|..|+|+.+|||..++|..+++
T Consensus 1 ~s~~eva~~~gvs~~tlr~w~~~ 23 (68)
T cd01104 1 YTIGAVARLTGVSPDTLRAWERR 23 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHh
Confidence 57899999999999999998865
No 338
>PF12116 SpoIIID: Stage III sporulation protein D; InterPro: IPR014208 Members of this entry represent the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if, and only if, the species is capable of endospore formation. In Bacillus subtilis SpoIIID is a DNA binding protein that is involved in gene repression as well as activation [].; PDB: 2L0K_A.
Probab=66.24 E-value=8.9 Score=32.72 Aligned_cols=44 Identities=25% Similarity=0.398 Sum_probs=29.0
Q ss_pred HHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556 501 ERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 546 (561)
Q Consensus 501 ER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 546 (561)
||-|-.-.|.++ ...|.++.|..||||++||.+-...=|.++-.
T Consensus 6 eR~i~i~~yIi~--~~aTVR~~Ak~FGvSKSTVHkDvteRL~~in~ 49 (82)
T PF12116_consen 6 ERVIEIANYIIE--TKATVRQAAKVFGVSKSTVHKDVTERLPKINP 49 (82)
T ss_dssp HHHHHHHHHHHH--H---HHHHHHHHTS-HHHHHHHHTTHHHHH-H
T ss_pred HHHHHHHHHHHH--cccHHHHHHHHHCCcHHHHHHHHHHHHHhcCH
Confidence 555555667665 46899999999999999998876655555543
No 339
>PRK06030 hypothetical protein; Provisional
Probab=65.58 E-value=18 Score=33.41 Aligned_cols=40 Identities=15% Similarity=0.081 Sum_probs=28.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhh
Q 008556 515 KPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD 558 (561)
Q Consensus 515 e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~l~~yld 558 (561)
-++|+.+||+.||.+..||-.-.+ ++++.+.+..++..++
T Consensus 68 ~~~sl~~IG~~FGRDHSTV~haik----kIe~~~~d~~lk~~v~ 107 (124)
T PRK06030 68 LGWPMNEVALAFGRDRTTVGHACH----TVEDLRDDAAFDARVS 107 (124)
T ss_pred cCCCHHHHHHHHCCChhHHHHHHH----HHHHHhhCHHHHHHHH
Confidence 578999999999999999977555 4444444445554444
No 340
>PRK10870 transcriptional repressor MprA; Provisional
Probab=65.38 E-value=34 Score=32.94 Aligned_cols=50 Identities=12% Similarity=0.118 Sum_probs=35.8
Q ss_pred HHHHHHh--cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556 489 HVRNLLT--LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 489 ~L~~aL~--~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R 539 (561)
.+...+. .|++-+-.||..-+. .++.+.|..|||+.+|+++.+|.+++.+
T Consensus 43 ~~~~~l~~~gLt~~q~~iL~~L~~-~~~~~it~~eLa~~l~l~~~tvsr~v~r 94 (176)
T PRK10870 43 NRNKMLKAQGINETLFMALITLES-QENHSIQPSELSCALGSSRTNATRIADE 94 (176)
T ss_pred HHHHHHHHCCCCHHHHHHHHHHhc-CCCCCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 4455553 488887777766653 2235789999999999999999765544
No 341
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=65.19 E-value=17 Score=32.48 Aligned_cols=40 Identities=28% Similarity=0.392 Sum_probs=35.8
Q ss_pred HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556 494 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 494 L~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R 539 (561)
...|++.|-..|+-.++ +|..+-|..||+|..+|+.++..
T Consensus 41 ~~~ls~~eIk~iRe~~~------lSQ~vFA~~L~vs~~Tv~~WEqG 80 (104)
T COG2944 41 VKTLSPTEIKAIREKLG------LSQPVFARYLGVSVSTVRKWEQG 80 (104)
T ss_pred CCCCCHHHHHHHHHHhC------CCHHHHHHHHCCCHHHHHHHHcC
Confidence 36799999999888875 89999999999999999999975
No 342
>PF11662 DUF3263: Protein of unknown function (DUF3263); InterPro: IPR021678 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=65.12 E-value=23 Score=30.10 Aligned_cols=47 Identities=19% Similarity=0.135 Sum_probs=36.6
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008556 496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 542 (561)
Q Consensus 496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALk 542 (561)
.|+++++.||.+---.....|-+-+.|-+.||+|.-+--|.++..+.
T Consensus 2 ~Ls~~d~~iL~fE~~ww~~~GaKe~aIre~fGls~~rYyq~Ln~LiD 48 (77)
T PF11662_consen 2 GLSDRDRAILDFERRWWRHGGAKEEAIREEFGLSPTRYYQRLNALID 48 (77)
T ss_pred CCCHHHHHHHHHHHHhCcCCCCcHHHHHHHHCCCHHHHHHHHHHHhC
Confidence 68999999998632222224668899999999999999999887653
No 343
>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein. 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=64.95 E-value=16 Score=35.82 Aligned_cols=45 Identities=18% Similarity=0.178 Sum_probs=34.9
Q ss_pred HHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556 492 NLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 492 ~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R 539 (561)
.....|++++..|+.+-.. ..+.+..|||+.+|+|+.+|++.+.+
T Consensus 136 ~~~~~ls~~~~~IL~~l~~---~g~~s~~eia~~l~is~stv~r~L~~ 180 (203)
T TIGR01884 136 PLLAGLSREELKVLEVLKA---EGEKSVKNIAKKLGKSLSTISRHLRE 180 (203)
T ss_pred hhhcCCCHHHHHHHHHHHH---cCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 3456799999888866542 13679999999999999999866554
No 344
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=64.80 E-value=16 Score=30.37 Aligned_cols=44 Identities=30% Similarity=0.477 Sum_probs=32.8
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556 496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 546 (561)
Q Consensus 496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 546 (561)
.|+..+..||.+-+. ..++|..+|++.+++|+.+|++ ++++|.+
T Consensus 7 ~l~~~~~~il~~l~~---~~~~~~~~la~~~~~s~~~i~~----~l~~L~~ 50 (101)
T smart00347 7 GLTPTQFLVLRILYE---EGPLSVSELAKRLGVSPSTVTR----VLDRLEK 50 (101)
T ss_pred CCCHHHHHHHHHHHH---cCCcCHHHHHHHHCCCchhHHH----HHHHHHH
Confidence 467777777777654 1469999999999999999875 5555544
No 345
>PRK15482 transcriptional regulator MurR; Provisional
Probab=64.36 E-value=11 Score=38.80 Aligned_cols=50 Identities=16% Similarity=0.245 Sum_probs=40.0
Q ss_pred HHHHHHHhcCCHHHHHHHHHHhcccCC---CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556 488 QHVRNLLTLLNPKERCIVRLRFGIEDG---KPKSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 488 e~L~~aL~~L~erER~VL~LRyGL~d~---e~~Tl~EIAe~LGISrerVRqie~R 539 (561)
..|+.....|++.||.|..+ .|++. ..+|..|||+..|+|..+|-+.-++
T Consensus 5 ~~i~~~~~~Lt~~e~~Ia~y--Il~n~~~v~~~si~elA~~~~vS~aTv~Rf~kk 57 (285)
T PRK15482 5 TKIRNAESEFTENEQKIADF--LRANVSELKSVSSRKMAKQLGISQSSIVKFAQK 57 (285)
T ss_pred HHHHHHHhhcCHHHHHHHHH--HHhCHHHHHhcCHHHHHHHhCCCHHHHHHHHHH
Confidence 46778889999999999875 34432 3589999999999999999776554
No 346
>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....
Probab=64.28 E-value=4.3 Score=29.49 Aligned_cols=23 Identities=26% Similarity=0.538 Sum_probs=19.2
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHH
Q 008556 518 SLSEVGNIFGLSKERVRQLESRA 540 (561)
Q Consensus 518 Tl~EIAe~LGISrerVRqie~RA 540 (561)
|..|+|+.+|||..++|..+...
T Consensus 1 ti~e~A~~~gvs~~tlR~ye~~G 23 (38)
T PF00376_consen 1 TIGEVAKLLGVSPRTLRYYEREG 23 (38)
T ss_dssp EHHHHHHHHTS-HHHHHHHHHTT
T ss_pred CHHHHHHHHCCCHHHHHHHHHCC
Confidence 46799999999999999988765
No 347
>PF05043 Mga: Mga helix-turn-helix domain; InterPro: IPR007737 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 []. The family also contains VirR like proteins which match only at the C terminus of the alignment.; PDB: 3SQN_A.
Probab=64.24 E-value=5.5 Score=33.49 Aligned_cols=31 Identities=13% Similarity=0.081 Sum_probs=23.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556 515 KPKSLSEVGNIFGLSKERVRQLESRALYRLK 545 (561)
Q Consensus 515 e~~Tl~EIAe~LGISrerVRqie~RALkKLR 545 (561)
+..|+.++|+.++||+.+|.+..++.-+.|+
T Consensus 29 ~~~s~~~la~~~~iS~sti~~~i~~l~~~l~ 59 (87)
T PF05043_consen 29 EYVSIEDLAEELFISRSTIYRDIKKLNKYLK 59 (87)
T ss_dssp SEEEHHHHHHHHT--HHHHHHHHHHHHHHHH
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 7889999999999999999876655544444
No 348
>TIGR00647 MG103 conserved hypothetical protein.
Probab=64.23 E-value=14 Score=38.53 Aligned_cols=44 Identities=16% Similarity=0.231 Sum_probs=37.2
Q ss_pred HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhC------CCHHHHHHHHHHH
Q 008556 494 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFG------LSKERVRQLESRA 540 (561)
Q Consensus 494 L~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LG------ISrerVRqie~RA 540 (561)
++.||+.-+++..+|.- ..+.|++|+|+.|. ||++.|..+..+.
T Consensus 225 l~~Lp~~L~~~a~lRl~---~Pd~SL~ELgell~~~~~~~isKSgvnhRlrKl 274 (279)
T TIGR00647 225 FEKLPLNFQRICLLKID---HPDWSLEQIAEFFASKYKVKISRSGIQHRLRKL 274 (279)
T ss_pred cccCCHHHHHHHHHHHh---CcccCHHHHHHHhccCCCCCcCHHHHHHHHHHH
Confidence 57899999999999974 37899999999994 9999998766543
No 349
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio 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 sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=63.96 E-value=12 Score=31.35 Aligned_cols=24 Identities=29% Similarity=0.481 Sum_probs=19.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 008556 515 KPKSLSEVGNIFGLSKERVRQLES 538 (561)
Q Consensus 515 e~~Tl~EIAe~LGISrerVRqie~ 538 (561)
.+.|.+|||+.+|+|+..|+++..
T Consensus 24 ~~~s~~eiA~~~~i~~~~l~kil~ 47 (83)
T PF02082_consen 24 KPVSSKEIAERLGISPSYLRKILQ 47 (83)
T ss_dssp C-BEHHHHHHHHTS-HHHHHHHHH
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHH
Confidence 458999999999999999987543
No 350
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=63.78 E-value=13 Score=37.60 Aligned_cols=25 Identities=28% Similarity=0.347 Sum_probs=22.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556 515 KPKSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 515 e~~Tl~EIAe~LGISrerVRqie~R 539 (561)
.++|..|||++||||...||+.+..
T Consensus 24 g~~sa~elA~~Lgis~~avR~HL~~ 48 (218)
T COG2345 24 GPVSADELAEELGISPMAVRRHLDD 48 (218)
T ss_pred CCccHHHHHHHhCCCHHHHHHHHHH
Confidence 5899999999999999999987654
No 351
>PF14493 HTH_40: Helix-turn-helix domain
Probab=63.65 E-value=11 Score=32.33 Aligned_cols=29 Identities=21% Similarity=0.245 Sum_probs=26.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 008556 515 KPKSLSEVGNIFGLSKERVRQLESRALYR 543 (561)
Q Consensus 515 e~~Tl~EIAe~LGISrerVRqie~RALkK 543 (561)
+|+|+.|||+.-|++.+||..++.++...
T Consensus 12 ~G~si~eIA~~R~L~~sTI~~HL~~~~~~ 40 (91)
T PF14493_consen 12 KGLSIEEIAKIRGLKESTIYGHLAELIES 40 (91)
T ss_pred cCCCHHHHHHHcCCCHHHHHHHHHHHHHh
Confidence 68999999999999999999998887654
No 352
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=63.57 E-value=8.2 Score=38.00 Aligned_cols=27 Identities=26% Similarity=0.527 Sum_probs=22.6
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556 516 PKSLSEVGNIFGLSKERVRQLESRALYRLKQ 546 (561)
Q Consensus 516 ~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 546 (561)
++|.++||..+|+|+++|.+ .+++|++
T Consensus 184 ~lt~~~iA~~lG~sr~tvsR----~l~~l~~ 210 (235)
T PRK11161 184 TMTRGDIGNYLGLTVETISR----LLGRFQK 210 (235)
T ss_pred cccHHHHHHHhCCcHHHHHH----HHHHHHH
Confidence 58999999999999999964 5667765
No 353
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=63.38 E-value=40 Score=30.98 Aligned_cols=48 Identities=6% Similarity=0.020 Sum_probs=35.7
Q ss_pred HHHHHH--hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556 489 HVRNLL--TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 489 ~L~~aL--~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R 539 (561)
.+...+ ..|++.|-.||..-+. ..+.|..|||+.+|+++.+|..++.+
T Consensus 28 ~~~~~l~~~glt~~q~~vL~~l~~---~~~~t~~eLa~~l~i~~~tvsr~l~~ 77 (144)
T PRK11512 28 LLNEYLSPLDITAAQFKVLCSIRC---AACITPVELKKVLSVDLGALTRMLDR 77 (144)
T ss_pred HHHHHhcccCCCHHHHHHHHHHHH---cCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 344444 3588999888876542 25799999999999999999765443
No 354
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=63.11 E-value=36 Score=32.68 Aligned_cols=27 Identities=37% Similarity=0.493 Sum_probs=22.8
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556 516 PKSLSEVGNIFGLSKERVRQLESRALYRLKQ 546 (561)
Q Consensus 516 ~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 546 (561)
..|.++||..+|+|+++|. |++++|++
T Consensus 168 ~~t~~~lA~~lG~tr~tvs----R~l~~l~~ 194 (211)
T PRK11753 168 KITRQEIGRIVGCSREMVG----RVLKMLED 194 (211)
T ss_pred CCCHHHHHHHhCCCHHHHH----HHHHHHHH
Confidence 6889999999999999996 56667765
No 355
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=62.49 E-value=8.3 Score=31.23 Aligned_cols=27 Identities=22% Similarity=0.306 Sum_probs=23.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 008556 515 KPKSLSEVGNIFGLSKERVRQLESRAL 541 (561)
Q Consensus 515 e~~Tl~EIAe~LGISrerVRqie~RAL 541 (561)
.+.|..+||..+||++.++++......
T Consensus 22 ~g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 22 SGESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp HHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCceEeeecccccccccccHHHHHHh
Confidence 579999999999999999999988876
No 356
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized 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 uncoded by the upstream member of the gene pair.
Probab=62.42 E-value=16 Score=29.65 Aligned_cols=25 Identities=12% Similarity=0.275 Sum_probs=22.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556 515 KPKSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 515 e~~Tl~EIAe~LGISrerVRqie~R 539 (561)
.++|..++|+.+|+|+.+|.++++.
T Consensus 17 ~~~t~~~lA~~~gis~~tis~~~~g 41 (78)
T TIGR02607 17 LGLSIRALAKALGVSRSTLSRIVNG 41 (78)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 6789999999999999999999863
No 357
>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=61.98 E-value=10 Score=30.26 Aligned_cols=23 Identities=26% Similarity=0.473 Sum_probs=21.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q 008556 517 KSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 517 ~Tl~EIAe~LGISrerVRqie~R 539 (561)
+|..|+|+.+|||..++|..+.+
T Consensus 1 ~~i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 1 YTIKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHh
Confidence 57899999999999999999876
No 358
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=61.94 E-value=12 Score=33.53 Aligned_cols=50 Identities=14% Similarity=0.164 Sum_probs=44.4
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008556 495 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 548 (561)
Q Consensus 495 ~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 548 (561)
.+|.+-||-...-+|- +-+|-+|||-.+.++..||..+...-..|.|+.-
T Consensus 27 ~QLkELErvF~ETHYP----DIYTREEiA~kidLTEARVQVWFQNRRAKfRKQE 76 (125)
T KOG0484|consen 27 AQLKELERVFAETHYP----DIYTREEIALKIDLTEARVQVWFQNRRAKFRKQE 76 (125)
T ss_pred HHHHHHHHHHHhhcCC----cchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHH
Confidence 5788889999999997 8899999999999999999999988888888743
No 359
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=61.57 E-value=8.2 Score=31.40 Aligned_cols=23 Identities=22% Similarity=0.416 Sum_probs=20.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q 008556 517 KSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 517 ~Tl~EIAe~LGISrerVRqie~R 539 (561)
.|++|||+.+|||+.+|+.+++.
T Consensus 1 ~t~~~iA~~~gvS~~TVSr~ln~ 23 (70)
T smart00354 1 ATIKDVARLAGVSKATVSRVLNG 23 (70)
T ss_pred CCHHHHHHHHCCCHHHHHHHHCC
Confidence 37899999999999999987654
No 360
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=61.49 E-value=6.3 Score=31.34 Aligned_cols=25 Identities=28% Similarity=0.412 Sum_probs=21.9
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 008556 517 KSLSEVGNIFGLSKERVRQLESRAL 541 (561)
Q Consensus 517 ~Tl~EIAe~LGISrerVRqie~RAL 541 (561)
+|..|+|+.+|||..+||..+...+
T Consensus 1 ~s~~eva~~~gvs~~tlr~~~~~gl 25 (70)
T smart00422 1 YTIGEVAKLAGVSVRTLRYYERIGL 25 (70)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5889999999999999999877554
No 361
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=61.44 E-value=18 Score=32.63 Aligned_cols=34 Identities=18% Similarity=0.197 Sum_probs=27.4
Q ss_pred HHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 008556 504 IVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL 541 (561)
Q Consensus 504 VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RAL 541 (561)
++...+- .++|..+||..+|||..+|.+...+..
T Consensus 21 aV~~~~~----~g~sv~evA~e~gIs~~tl~~W~r~y~ 54 (121)
T PRK09413 21 IVQQSFE----PGMTVSLVARQHGVAASQLFLWRKQYQ 54 (121)
T ss_pred HHHHHHc----CCCCHHHHHHHHCcCHHHHHHHHHHHh
Confidence 4444444 689999999999999999999977643
No 362
>PRK09726 antitoxin HipB; Provisional
Probab=60.49 E-value=14 Score=31.40 Aligned_cols=25 Identities=16% Similarity=0.330 Sum_probs=23.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556 515 KPKSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 515 e~~Tl~EIAe~LGISrerVRqie~R 539 (561)
.++|..++|+.+|||+.+|+++++.
T Consensus 24 ~gltq~elA~~~gvs~~tis~~e~g 48 (88)
T PRK09726 24 NGWTQSELAKKIGIKQATISNFENN 48 (88)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHCC
Confidence 5799999999999999999999884
No 363
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein 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. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=59.57 E-value=15 Score=31.99 Aligned_cols=42 Identities=17% Similarity=0.246 Sum_probs=30.2
Q ss_pred cCCHHHHHHHHHHhc-ccCCCCCCHHHHHHHhCCCHHHHHHHH
Q 008556 496 LLNPKERCIVRLRFG-IEDGKPKSLSEVGNIFGLSKERVRQLE 537 (561)
Q Consensus 496 ~L~erER~VL~LRyG-L~d~e~~Tl~EIAe~LGISrerVRqie 537 (561)
.|++.++.||.+.-. -...+|.+..+|++.|+++...||+.+
T Consensus 44 ~~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al 86 (102)
T PF08784_consen 44 GLSPLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKAL 86 (102)
T ss_dssp -S-HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHH
T ss_pred CCCHHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHH
Confidence 688888888877554 334588999999999999999998754
No 364
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=59.34 E-value=19 Score=36.76 Aligned_cols=48 Identities=17% Similarity=0.227 Sum_probs=38.1
Q ss_pred HHHHHhcCCHHHHHHHHHHhcccCC---CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556 490 VRNLLTLLNPKERCIVRLRFGIEDG---KPKSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 490 L~~aL~~L~erER~VL~LRyGL~d~---e~~Tl~EIAe~LGISrerVRqie~R 539 (561)
|+.....|++.|+.|..+- ++.. ..+|..|+|+..|+|..+|-+..++
T Consensus 3 i~~~~~~Lt~~e~~ia~yi--l~n~~~v~~~si~elA~~~~vS~aTv~Rf~kk 53 (278)
T PRK11557 3 IRQRYPGLAQSDRKLADYL--LLQPDTARHLSSQQLANEAGVSQSSVVKFAQK 53 (278)
T ss_pred hhHhhhhCCHHHHHHHHHH--HhCHHHHHhcCHHHHHHHhCCCHHHHHHHHHH
Confidence 5567788999999998754 3332 3599999999999999999876654
No 365
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=59.14 E-value=14 Score=36.82 Aligned_cols=30 Identities=23% Similarity=0.474 Sum_probs=25.4
Q ss_pred CCCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556 513 DGKPK-SLSEVGNIFGLSKERVRQLESRALYRLKQ 546 (561)
Q Consensus 513 d~e~~-Tl~EIAe~LGISrerVRqie~RALkKLR~ 546 (561)
.|+.+ |-.|+|+.||||+.+||. ||+.|..
T Consensus 27 pG~~LPsE~eLae~~gVSRt~VRe----AL~~L~~ 57 (239)
T PRK04984 27 PGSILPAERELSELIGVTRTTLRE----VLQRLAR 57 (239)
T ss_pred CCCcCCCHHHHHHHHCCCHHHHHH----HHHHHHH
Confidence 45788 799999999999999985 7777765
No 366
>PRK10161 transcriptional regulator PhoB; Provisional
Probab=58.87 E-value=11 Score=36.14 Aligned_cols=50 Identities=14% Similarity=0.055 Sum_probs=40.0
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHH-----HhCCCHHHHHHHHHHHHHHHHH
Q 008556 496 LLNPKERCIVRLRFGIEDGKPKSLSEVGN-----IFGLSKERVRQLESRALYRLKQ 546 (561)
Q Consensus 496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe-----~LGISrerVRqie~RALkKLR~ 546 (561)
.|+++|.+||.+-. -+.|++.|.++|.. .++++..+|+....+.++||..
T Consensus 154 ~Lt~~E~~ll~~l~-~~~~~~~s~~~l~~~~~~~~~~~~~~tv~~~i~rlr~Kl~~ 208 (229)
T PRK10161 154 EMGPTEFKLLHFFM-THPERVYSREQLLNHVWGTNVYVEDRTVDVHIRRLRKALEP 208 (229)
T ss_pred EcCHHHHHHHHHHH-hCCCceEcHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhcc
Confidence 59999999987655 24457888777644 6678999999999999999963
No 367
>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=58.75 E-value=12 Score=29.95 Aligned_cols=23 Identities=22% Similarity=0.355 Sum_probs=20.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q 008556 517 KSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 517 ~Tl~EIAe~LGISrerVRqie~R 539 (561)
++..|+|+.+|||..++|..+..
T Consensus 1 ~~i~e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 1 YTIGEVALLTGIKPHVLRAWERE 23 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHh
Confidence 47899999999999999998765
No 368
>PRK01905 DNA-binding protein Fis; Provisional
Probab=58.39 E-value=42 Score=27.99 Aligned_cols=36 Identities=11% Similarity=0.222 Sum_probs=24.4
Q ss_pred HHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556 501 ERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 501 ER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R 539 (561)
|+.+|...+-- .+-+..+.|+.+|||+.+++...++
T Consensus 38 E~~~i~~aL~~---~~gn~s~aAr~LGIsrstL~rklkk 73 (77)
T PRK01905 38 EKPLLEVVMEQ---AGGNQSLAAEYLGINRNTLRKKLQQ 73 (77)
T ss_pred HHHHHHHHHHH---cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 55555444331 2347899999999999998765443
No 369
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=58.25 E-value=12 Score=37.17 Aligned_cols=28 Identities=36% Similarity=0.587 Sum_probs=23.4
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008556 516 PKSLSEVGNIFGLSKERVRQLESRALYRLKQS 547 (561)
Q Consensus 516 ~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 547 (561)
+.|.++||..+|+|+++|. |++++|++.
T Consensus 179 ~lt~~~IA~~lGisretls----R~L~~L~~~ 206 (230)
T PRK09391 179 PMSRRDIADYLGLTIETVS----RALSQLQDR 206 (230)
T ss_pred cCCHHHHHHHHCCCHHHHH----HHHHHHHHC
Confidence 5799999999999999995 567777763
No 370
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=57.84 E-value=10 Score=36.80 Aligned_cols=28 Identities=18% Similarity=0.227 Sum_probs=24.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008556 515 KPKSLSEVGNIFGLSKERVRQLESRALY 542 (561)
Q Consensus 515 e~~Tl~EIAe~LGISrerVRqie~RALk 542 (561)
-+||..|||+.+|.|..+||+++.-.-+
T Consensus 60 ag~Ti~EIAeelG~TeqTir~hlkgetk 87 (182)
T COG1318 60 AGMTISEIAEELGRTEQTVRNHLKGETK 87 (182)
T ss_pred ccCcHHHHHHHhCCCHHHHHHHHhcchh
Confidence 4699999999999999999998765433
No 371
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=57.73 E-value=68 Score=28.17 Aligned_cols=44 Identities=11% Similarity=0.064 Sum_probs=34.1
Q ss_pred cCCHHHHHHHHHHhcc-cCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556 496 LLNPKERCIVRLRFGI-EDGKPKSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 496 ~L~erER~VL~LRyGL-~d~e~~Tl~EIAe~LGISrerVRqie~R 539 (561)
.|+..|-.||..-+.+ ..+.+.|..+||+.+++++.+|.+++.+
T Consensus 22 ~ls~~q~~vL~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~ 66 (109)
T TIGR01889 22 NLSLEELLILYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKK 66 (109)
T ss_pred CCCHHHHHHHHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHHH
Confidence 6899999988765521 1235799999999999999999765544
No 372
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=57.59 E-value=17 Score=28.96 Aligned_cols=26 Identities=19% Similarity=0.471 Sum_probs=22.5
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHH
Q 008556 516 PKSLSEVGNIFGLSKERVRQLESRAL 541 (561)
Q Consensus 516 ~~Tl~EIAe~LGISrerVRqie~RAL 541 (561)
+.|+.+||+.+|+|...+.++..+..
T Consensus 1 ~~~~~~la~~~~~s~~~l~~~f~~~~ 26 (84)
T smart00342 1 PLTLEDLAEALGMSPRHLQRLFKKET 26 (84)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHh
Confidence 36899999999999999988887654
No 373
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=57.29 E-value=36 Score=38.87 Aligned_cols=102 Identities=15% Similarity=0.187 Sum_probs=57.8
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHhcCCC---ccCCCCCCCCCCchhhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCH
Q 008556 423 SPDKEDLARRVGITVEKLERLIFITRMP---LSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNP 499 (561)
Q Consensus 423 ~Pt~eEIA~~lgis~e~v~~ll~~~~~~---~SLD~~v~~d~~~~l~d~l~d~~~~~pee~le~~e~~e~L~~aL~~L~e 499 (561)
..|..+||+.+|+|...|++-+..-+.. ..+. .+....+..+ ... ++. .+...+..-++
T Consensus 17 ~~t~~~LA~~l~VS~RTIr~dI~~in~~l~~~~~~-~i~~~~Gy~l----~~~---~~~----------~~~~~~~~~~~ 78 (584)
T PRK09863 17 DRSGGELAQQLGVSRRTIVRDIAYINFTLNGKAIG-SISGSAKYHL----EIL---NRR----------SLFQLLQKSDN 78 (584)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhcchh-heecCCceEE----EeC---CHH----------HHHHHHhcCCH
Confidence 6789999999999999987655432110 0000 0000011111 000 111 11122222233
Q ss_pred HHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556 500 KERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 545 (561)
Q Consensus 500 rER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR 545 (561)
|+..+.++..+ + ++.++.++|+.|.||+.+|.+-+.+..+.+.
T Consensus 79 -e~~~il~~Ll~-~-~~~~~~~La~~l~vS~sTi~~dl~~v~~~l~ 121 (584)
T PRK09863 79 -EDRLLLLRLLL-N-TFTPMAQLASALNLSRTWVAERLPRLNQRYE 121 (584)
T ss_pred -HHHHHHHHHHH-c-CCccHHHHHHHhCCCHHHHHHHHHHHHHhhh
Confidence 44444444443 3 6899999999999999999988877777665
No 374
>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=57.17 E-value=27 Score=26.52 Aligned_cols=51 Identities=16% Similarity=0.198 Sum_probs=38.5
Q ss_pred cCCHHHHHHHHHHhcccCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556 496 LLNPKERCIVRLRFGIEDG-KPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 546 (561)
Q Consensus 496 ~L~erER~VL~LRyGL~d~-e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 546 (561)
.+++.+..+|.-.|..+.. ......+||..+|++...|+.....-..+.+.
T Consensus 6 ~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~ 57 (59)
T cd00086 6 RFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKR 57 (59)
T ss_pred cCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence 4667778888888875432 23457899999999999999998877766553
No 375
>PF12085 DUF3562: Protein of unknown function (DUF3562); InterPro: IPR021945 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 62 to 84 amino acids in length. This protein has two completely conserved residues (A and Y) that may be functionally important.
Probab=57.13 E-value=21 Score=29.46 Aligned_cols=40 Identities=20% Similarity=0.341 Sum_probs=33.4
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhhhh
Q 008556 518 SLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYADLL 560 (561)
Q Consensus 518 Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~l~~yldll 560 (561)
.+++||+..|++.+.|++.....+..|+. .....+|+-+|
T Consensus 9 ~i~~iA~~t~~P~e~V~~my~dt~~~l~~---~ARV~DYl~lf 48 (66)
T PF12085_consen 9 VIRSIAEETGTPAETVRRMYDDTMRELSS---GARVHDYLPLF 48 (66)
T ss_pred HHHHHHHHHCCCHHHHHHHHHHHHHHHHc---CCchhhhHHHH
Confidence 57899999999999999999999888875 44567777665
No 376
>PRK11050 manganese transport regulator MntR; Provisional
Probab=57.07 E-value=17 Score=34.13 Aligned_cols=26 Identities=15% Similarity=0.233 Sum_probs=21.7
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556 514 GKPKSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 514 ~e~~Tl~EIAe~LGISrerVRqie~R 539 (561)
+.+.+..|||+.+|||+.+|++.+.+
T Consensus 49 ~~~~t~~eLA~~l~is~stVsr~l~~ 74 (152)
T PRK11050 49 VGEARQVDIAARLGVSQPTVAKMLKR 74 (152)
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 36789999999999999999765443
No 377
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=56.88 E-value=16 Score=26.47 Aligned_cols=25 Identities=16% Similarity=0.274 Sum_probs=18.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556 515 KPKSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 515 e~~Tl~EIAe~LGISrerVRqie~R 539 (561)
.++|+.+||+.+|+|....+++.++
T Consensus 7 ~~~~l~~iA~~~g~S~~~f~r~Fk~ 31 (42)
T PF00165_consen 7 QKLTLEDIAEQAGFSPSYFSRLFKK 31 (42)
T ss_dssp SS--HHHHHHHHTS-HHHHHHHHHH
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 6799999999999998888766554
No 378
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR. All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the 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=56.85 E-value=22 Score=34.88 Aligned_cols=26 Identities=12% Similarity=0.176 Sum_probs=23.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008556 515 KPKSLSEVGNIFGLSKERVRQLESRA 540 (561)
Q Consensus 515 e~~Tl~EIAe~LGISrerVRqie~RA 540 (561)
.+.|..|||+.+||++.+|++++.+-
T Consensus 14 ~~~t~~eLA~~lgis~~tV~~~L~~L 39 (203)
T TIGR02702 14 GQATAAALAEALAISPQAVRRHLKDL 39 (203)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 46999999999999999999998875
No 379
>PF08006 DUF1700: Protein of unknown function (DUF1700); InterPro: IPR012963 This family contains many hypothetical bacterial proteins and two putative membrane proteins (Q6GFD0 from SWISSPROT and Q6G806 from SWISSPROT).
Probab=56.71 E-value=28 Score=33.52 Aligned_cols=57 Identities=23% Similarity=0.248 Sum_probs=44.1
Q ss_pred HHHHHHHHHHHHhcCCHHHHHHHHHHhc--ccC--CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556 483 KQLMRQHVRNLLTLLNPKERCIVRLRFG--IED--GKPKSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 483 ~~e~~e~L~~aL~~L~erER~VL~LRyG--L~d--~e~~Tl~EIAe~LGISrerVRqie~R 539 (561)
+++..+.|+..|..||+.|++=+.-.|- ++| .+|+|-+||.+.||=+++-++++...
T Consensus 3 k~efL~~L~~~L~~lp~~e~~e~l~~Y~e~f~d~~~~G~sEeeii~~LG~P~~iA~~i~~~ 63 (181)
T PF08006_consen 3 KNEFLNELEKYLKKLPEEEREEILEYYEEYFDDAGEEGKSEEEIIAELGSPKEIAREILAE 63 (181)
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhCCCCHHHHHHHcCCHHHHHHHHHHh
Confidence 4556678899999999998886555443 233 35789999999999999999988754
No 380
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=56.28 E-value=26 Score=34.58 Aligned_cols=47 Identities=15% Similarity=0.142 Sum_probs=31.4
Q ss_pred CCHHHHHHHHHHhccc-CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008556 497 LNPKERCIVRLRFGIE-DGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 547 (561)
Q Consensus 497 L~erER~VL~LRyGL~-d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 547 (561)
++.++|-+-.+...-+ +.-+.|.++||+.+|+|+++|. |+|++|++.
T Consensus 149 ~~~~~Rla~~L~~~~~~~~~~~t~~~lA~~lG~sretvs----R~L~~L~~~ 196 (226)
T PRK10402 149 FPLENRLAAFILLTQEGDLYHEKHTQAAEYLGVSYRHLL----YVLAQFIQD 196 (226)
T ss_pred ChHHHHHHHHHHhcccCCcccchHHHHHHHHCCcHHHHH----HHHHHHHHC
Confidence 3566665544432111 1234689999999999999995 577777763
No 381
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []. In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.
Probab=55.57 E-value=29 Score=26.08 Aligned_cols=22 Identities=14% Similarity=0.354 Sum_probs=16.9
Q ss_pred CCHHHHHHHhCCCHHHHHHHHH
Q 008556 517 KSLSEVGNIFGLSKERVRQLES 538 (561)
Q Consensus 517 ~Tl~EIAe~LGISrerVRqie~ 538 (561)
+|+.+.|+.+||++.+++...+
T Consensus 17 ~S~r~AA~~ygVp~sTL~~r~~ 38 (45)
T PF05225_consen 17 MSIRKAAKKYGVPRSTLRRRLR 38 (45)
T ss_dssp S-HHHHHHHHT--HHHHHHHHH
T ss_pred CCHHHHHHHHCcCHHHHHHHHc
Confidence 9999999999999999986554
No 382
>PRK10955 DNA-binding transcriptional regulator CpxR; Provisional
Probab=55.39 E-value=8.8 Score=36.70 Aligned_cols=49 Identities=16% Similarity=0.035 Sum_probs=37.5
Q ss_pred cCCHHHHHHHHHHhcccCCCCC-----CHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556 496 LLNPKERCIVRLRFGIEDGKPK-----SLSEVGNIFGLSKERVRQLESRALYRLK 545 (561)
Q Consensus 496 ~L~erER~VL~LRyGL~d~e~~-----Tl~EIAe~LGISrerVRqie~RALkKLR 545 (561)
.|+++|.+|+.+-.. +-|... ....||..++++..+|+.+..+.++||.
T Consensus 156 ~Lt~~E~~~l~~l~~-~~~~v~sr~~l~~~~~~~~~~~~~~tv~~~i~~lr~Kl~ 209 (232)
T PRK10955 156 ELTGTEFTLLYLLAQ-HLGQVVSREHLSQEVLGKRLTPFDRAIDMHISNLRRKLP 209 (232)
T ss_pred cCCHHHHHHHHHHHh-CCCceEcHHHHHHHHhCCCCCCCCcCHHHHHHHHHHhcc
Confidence 599999999988663 111111 2467888889999999999999999996
No 383
>PF06413 Neugrin: Neugrin; InterPro: IPR010487 This family contains mouse and human neugrin proteins. Neugrin and m-neugrin are mainly expressed in neurons in the nervous system, and are thought to play an important role in the process of neuronal differentiation []. Homologues of neugrin are found in fungi suggesting they have a alternative role or more than one function.
Probab=55.15 E-value=19 Score=36.44 Aligned_cols=42 Identities=14% Similarity=0.188 Sum_probs=32.9
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008556 496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES 538 (561)
Q Consensus 496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~ 538 (561)
.|+..+.+-|++-+-.+ -+.+|...+|+.|+||.+.||+|++
T Consensus 10 ~Ls~~~~~~ir~L~~~~-p~~~t~~~Lae~F~vspe~irrILk 51 (225)
T PF06413_consen 10 KLSREAMEQIRYLHKED-PEEWTVERLAESFKVSPEAIRRILK 51 (225)
T ss_pred CCCHHHHHHHHHHHHhC-ccccCHHHHHhhCCCCHHHHHHHHh
Confidence 56777777776655432 2568999999999999999999875
No 384
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=55.15 E-value=17 Score=37.57 Aligned_cols=46 Identities=33% Similarity=0.368 Sum_probs=35.4
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556 495 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 546 (561)
Q Consensus 495 ~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 546 (561)
..|++.|++||.+--+ .|...++.||-+.+|+|+.+|.. ++++|-+
T Consensus 191 ~~L~~~e~~il~~i~~--~GGri~Q~eL~r~lglsktTvsR----~L~~LEk 236 (258)
T COG2512 191 YDLNEDEKEILDLIRE--RGGRITQAELRRALGLSKTTVSR----ILRRLEK 236 (258)
T ss_pred CCCCHHHHHHHHHHHH--hCCEEeHHHHHHhhCCChHHHHH----HHHHHHh
Confidence 4689999999887544 33468999999999999999964 5555543
No 385
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=54.86 E-value=12 Score=30.27 Aligned_cols=24 Identities=25% Similarity=0.329 Sum_probs=19.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 008556 515 KPKSLSEVGNIFGLSKERVRQLES 538 (561)
Q Consensus 515 e~~Tl~EIAe~LGISrerVRqie~ 538 (561)
.+.+-.|||+.+|+|+.+||.++.
T Consensus 14 ~p~~T~eiA~~~gls~~~aR~yL~ 37 (62)
T PF04703_consen 14 GPLKTREIADALGLSIYQARYYLE 37 (62)
T ss_dssp S-EEHHHHHHHHTS-HHHHHHHHH
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Confidence 689999999999999999998754
No 386
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=54.70 E-value=25 Score=40.16 Aligned_cols=46 Identities=24% Similarity=0.266 Sum_probs=36.5
Q ss_pred CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556 497 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 546 (561)
Q Consensus 497 L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 546 (561)
|++|++++|.+-- + .+.|..++|+.||||.-|||+-+...=.-|++
T Consensus 2 l~~R~~~iL~~L~---~-~~~t~~~LA~~l~VS~RTIr~dI~~in~~l~~ 47 (584)
T PRK09863 2 LNERELKIVDLLE---Q-QDRSGGELAQQLGVSRRTIVRDIAYINFTLNG 47 (584)
T ss_pred hHHHHHHHHHHHH---c-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 5788888887542 2 57899999999999999999877766555555
No 387
>TIGR01387 cztR_silR_copR heavy metal response regulator. Members of this family contain a response regulator receiver domain (Pfam:PF00072) and an associated transcriptional regulatory region (Pfam:PF00486). This group is separated phylogenetically from related proteins with similar architecture and contains a number of proteins associated with heavy metal resistance efflux systems for copper, silver, cadmium, and/or zinc. Most members encoded by genes adjacent to genes for encoding a member of the heavy metal sensor histidine kinase family (TIGRFAMs:TIGR01386), its partner in the two-component response regulator system.
Probab=54.59 E-value=19 Score=33.84 Aligned_cols=49 Identities=14% Similarity=0.121 Sum_probs=40.6
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHh-----CCCHHHHHHHHHHHHHHHH
Q 008556 496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIF-----GLSKERVRQLESRALYRLK 545 (561)
Q Consensus 496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~L-----GISrerVRqie~RALkKLR 545 (561)
.|+++|.+|+.+-.. +.|+..|.++|.+.+ ..+..+|..++.+.++||.
T Consensus 147 ~Lt~~E~~il~~l~~-~~~~~~sr~~i~~~~~~~~~~~~~~~~~~~i~~lr~kl~ 200 (218)
T TIGR01387 147 TLTRKEFQLLWLLMR-RTGEVLPRTVIASLVWGMNFDSDTNVVDVAIRRLRAKVD 200 (218)
T ss_pred eCCHHHHHHHHHHHh-CCCeeEcHHHHHHHhcCCCCCCCcCCHHHHHHHHHHhhc
Confidence 599999999988764 445679999999998 4567889998888888885
No 388
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=54.57 E-value=23 Score=35.95 Aligned_cols=41 Identities=17% Similarity=0.236 Sum_probs=31.4
Q ss_pred HHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008556 499 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 542 (561)
Q Consensus 499 erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALk 542 (561)
+|++.|+.+-.. ....+..||++.||||..|||+-+..--.
T Consensus 4 ~R~~~Il~~l~~---~~~~~~~eLa~~l~VS~~TiRRdL~~L~~ 44 (240)
T PRK10411 4 ARQQAIVDLLLN---HTSLTTEALAEQLNVSKETIRRDLNELQT 44 (240)
T ss_pred HHHHHHHHHHHH---cCCCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 566666655332 25789999999999999999998886544
No 389
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=54.45 E-value=23 Score=32.58 Aligned_cols=25 Identities=8% Similarity=0.185 Sum_probs=21.1
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHH
Q 008556 514 GKPKSLSEVGNIFGLSKERVRQLES 538 (561)
Q Consensus 514 ~e~~Tl~EIAe~LGISrerVRqie~ 538 (561)
+...+..+||+.||||+.+|+..+.
T Consensus 20 ~~~~~~~ela~~l~vs~~svs~~l~ 44 (142)
T PRK03902 20 KGYARVSDIAEALSVHPSSVTKMVQ 44 (142)
T ss_pred CCCcCHHHHHHHhCCChhHHHHHHH
Confidence 3567999999999999999987553
No 390
>PF13556 HTH_30: PucR C-terminal helix-turn-helix domain; PDB: 3ONQ_B.
Probab=54.42 E-value=35 Score=26.80 Aligned_cols=35 Identities=11% Similarity=0.121 Sum_probs=26.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008556 515 KPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 549 (561)
Q Consensus 515 e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 549 (561)
.+.+..+.|+.|+|.++||+.++.|+-..+.-.+.
T Consensus 11 ~~~n~~~tA~~L~iHrNTl~yRl~ki~~l~g~dl~ 45 (59)
T PF13556_consen 11 NNGNISKTARALHIHRNTLRYRLKKIEELLGLDLD 45 (59)
T ss_dssp TTT-HHHHHHHHTS-HHHHHHHHHHHHHHHS--TT
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCcCCC
Confidence 56899999999999999999998888776654443
No 391
>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]
Probab=54.37 E-value=19 Score=32.19 Aligned_cols=35 Identities=17% Similarity=0.302 Sum_probs=27.4
Q ss_pred HHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556 503 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 503 ~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R 539 (561)
+||.-.|. +.-++|..+.|+.|||++.+|..+++-
T Consensus 12 EiL~eefl--ep~glt~~~lA~~lgV~r~~is~ling 46 (104)
T COG3093 12 EILREEFL--EPLGLTQTELAEALGVTRNTISELING 46 (104)
T ss_pred HHHHHHHh--ccccCCHHHHHHHhCCCHHHHHHHHcC
Confidence 46666665 213699999999999999999988764
No 392
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=54.31 E-value=2.8e+02 Score=29.12 Aligned_cols=25 Identities=16% Similarity=0.337 Sum_probs=22.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556 515 KPKSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 515 e~~Tl~EIAe~LGISrerVRqie~R 539 (561)
...|++|||+..|||..|||+..+.
T Consensus 250 ~~~tq~eva~v~~vtevTIrnryke 274 (285)
T COG1405 250 ERRTQKEVAKVAGVTEVTIRNRYKE 274 (285)
T ss_pred CchHHHHHHHHhCCeeeHHHHHHHH
Confidence 7899999999999999999998733
No 393
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=54.05 E-value=1.7e+02 Score=26.43 Aligned_cols=38 Identities=13% Similarity=0.095 Sum_probs=29.1
Q ss_pred HHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHh
Q 008556 409 VLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI 446 (561)
Q Consensus 409 i~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~ 446 (561)
+.++..-+......+++.++||+.+|+++..+..+...
T Consensus 11 i~~~~~~I~~~~~~~~sl~~lA~~~g~S~~~l~r~Fk~ 48 (127)
T PRK11511 11 IHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKK 48 (127)
T ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 34444555555666899999999999999999888653
No 394
>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., PubMed:15231786). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations
Probab=53.77 E-value=1.1e+02 Score=33.84 Aligned_cols=35 Identities=14% Similarity=0.263 Sum_probs=25.8
Q ss_pred HHHHHHHhCC---CCCCHHHHHHHhCCCHHHHHHHHHh
Q 008556 412 AKRLYIQEGN---HSPDKEDLARRVGITVEKLERLIFI 446 (561)
Q Consensus 412 a~~~l~~e~g---r~Pt~eEIA~~lgis~e~v~~ll~~ 446 (561)
....+...+. ++-+..+||+.+|+.+..|..+...
T Consensus 304 ~Q~~Ff~~G~~~LkPLtlkdiA~~lglheSTVSRav~~ 341 (429)
T TIGR02395 304 HQKDFFLGGPAALKPLTLREVAEELGLHESTISRAINN 341 (429)
T ss_pred HHHHHHhcCcccCcCCcHHHHHHHhCCCccchhhhhcC
Confidence 3344444442 5678999999999999999988653
No 395
>PRK14082 hypothetical protein; Provisional
Probab=53.76 E-value=42 Score=27.49 Aligned_cols=56 Identities=16% Similarity=0.100 Sum_probs=40.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHH
Q 008556 319 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASY 376 (561)
Q Consensus 319 ~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTY 376 (561)
....+.+|....+.+.+-...- .-.+-+||.||--|.+++.+..++...+--|--|
T Consensus 8 ~~e~e~ii~~FepkIkKsL~~T--~yqeREDLeQElk~Ki~eK~~~~~~~e~PGF~ef 63 (65)
T PRK14082 8 TEEIEHLIENFSPMIKKKLSNT--SYQEREDLEQELKIKIIEKADMLLCQEVPGFWEF 63 (65)
T ss_pred HHHHHHHHHHccHHHHHHHhcC--ChhhHHHHHHHHHHHHHHHHHHhhcccCCcHHHh
Confidence 3566778888888776544321 1245699999999999999999987766555444
No 396
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=53.73 E-value=18 Score=32.60 Aligned_cols=24 Identities=33% Similarity=0.458 Sum_probs=22.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 008556 515 KPKSLSEVGNIFGLSKERVRQLES 538 (561)
Q Consensus 515 e~~Tl~EIAe~LGISrerVRqie~ 538 (561)
.|.|..++|..||||+.+|..+..
T Consensus 17 ~g~s~~eaa~~F~VS~~Tv~~W~k 40 (119)
T PF01710_consen 17 KGKSIREAAKRFGVSRNTVYRWLK 40 (119)
T ss_pred ccchHHHHHHHhCcHHHHHHHHHH
Confidence 578999999999999999998876
No 397
>COG4709 Predicted membrane protein [Function unknown]
Probab=53.43 E-value=26 Score=34.53 Aligned_cols=59 Identities=20% Similarity=0.173 Sum_probs=45.6
Q ss_pred HHHHHHHHHHHHhcCCHHHHHHHHHHhc--cc--CCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 008556 483 KQLMRQHVRNLLTLLNPKERCIVRLRFG--IE--DGKPKSLSEVGNIFGLSKERVRQLESRAL 541 (561)
Q Consensus 483 ~~e~~e~L~~aL~~L~erER~VL~LRyG--L~--d~e~~Tl~EIAe~LGISrerVRqie~RAL 541 (561)
+.+....|+..|+.||+.+|.=+...|- ++ +..++|-+||++.||=+.+-.+++..+..
T Consensus 3 k~efL~eL~~yL~~Lp~~~r~e~m~dyeehF~~a~~~GksE~EI~~~LG~P~eiA~ei~s~~~ 65 (195)
T COG4709 3 KTEFLNELEQYLEGLPREERREIMYDYEEHFREAQEAGKSEEEIAKDLGDPKEIAAEILSERG 65 (195)
T ss_pred HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhhhhcCCCHHHHHHHhCCHHHHHHHHHHHcc
Confidence 3455667899999999999886665443 22 33688999999999999999988876654
No 398
>PF12324 HTH_15: Helix-turn-helix domain of alkylmercury lyase; InterPro: IPR024259 Alkylmercury lyase (EC:4.99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. This entry represents the N-terminal helix-turn-helix domain.; PDB: 3FN8_B 3F2G_B 3F0P_A 3F2F_B 3F2H_A 3F0O_B 1S6L_A.
Probab=53.26 E-value=37 Score=28.80 Aligned_cols=29 Identities=21% Similarity=0.239 Sum_probs=21.3
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHhcC
Q 008556 420 GNHSPDKEDLARRVGITVEKLERLIFITR 448 (561)
Q Consensus 420 ~gr~Pt~eEIA~~lgis~e~v~~ll~~~~ 448 (561)
.|++.+.++||..+|++.++|..++....
T Consensus 35 ~G~PVt~~~LA~a~g~~~e~v~~~L~~~p 63 (77)
T PF12324_consen 35 KGQPVTVEQLAAALGWPVEEVRAALAAMP 63 (77)
T ss_dssp TTS-B-HHHHHHHHT--HHHHHHHHHH-T
T ss_pred cCCCcCHHHHHHHHCCCHHHHHHHHHhCC
Confidence 37789999999999999999999987653
No 399
>PF06322 Phage_NinH: Phage NinH protein; InterPro: IPR010454 This entry is represented by Bacteriophage 933W, NinH. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=53.25 E-value=20 Score=29.10 Aligned_cols=27 Identities=22% Similarity=0.463 Sum_probs=22.9
Q ss_pred HHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHH
Q 008556 504 IVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLE 537 (561)
Q Consensus 504 VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie 537 (561)
+|.-.|| +..|+|..||+++.+||+..
T Consensus 11 lLi~~~G-------nqtEvaR~l~c~R~TVrKY~ 37 (64)
T PF06322_consen 11 LLIETYG-------NQTEVARRLGCNRATVRKYS 37 (64)
T ss_pred HHHHHhC-------cHHHHHHHhcccHHHHHHHh
Confidence 4666777 78999999999999998754
No 400
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=53.03 E-value=41 Score=32.79 Aligned_cols=47 Identities=11% Similarity=0.153 Sum_probs=30.3
Q ss_pred HHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556 489 HVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 489 ~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R 539 (561)
.|..++.. ++....||..- +.. ...|-+|||+.|||+...||+++.+
T Consensus 13 ~l~~~~~~-~~~~~~Vl~~L--~~~-g~~tdeeLA~~Lgi~~~~VRk~L~~ 59 (178)
T PRK06266 13 VLFEIMEG-DEEGFEVLKAL--IKK-GEVTDEEIAEQTGIKLNTVRKILYK 59 (178)
T ss_pred HHHHHhcC-CccHhHHHHHH--HHc-CCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 34444432 44444455432 122 3799999999999999999976543
No 401
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=52.94 E-value=20 Score=32.74 Aligned_cols=25 Identities=16% Similarity=0.104 Sum_probs=23.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556 515 KPKSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 515 e~~Tl~EIAe~LGISrerVRqie~R 539 (561)
.++|..++|+.+|||+.+|+++++.
T Consensus 17 ~gltq~~lA~~~gvs~~~is~~E~g 41 (135)
T PRK09706 17 LKLSQRSLAKAVKVSHVSISQWERD 41 (135)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 5799999999999999999999865
No 402
>PRK04158 transcriptional repressor CodY; Validated
Probab=52.36 E-value=23 Score=36.52 Aligned_cols=58 Identities=17% Similarity=0.236 Sum_probs=45.6
Q ss_pred HHHHHHHHHHhcCCHHHHHHHHHHhc-ccCCCC-CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556 485 LMRQHVRNLLTLLNPKERCIVRLRFG-IEDGKP-KSLSEVGNIFGLSKERVRQLESRALYRLKQ 546 (561)
Q Consensus 485 e~~e~L~~aL~~L~erER~VL~LRyG-L~d~e~-~Tl~EIAe~LGISrerVRqie~RALkKLR~ 546 (561)
..+..++.++..|+--|.+.+.+-|. |+|.+| +.-..||++.||||+=| -.||+||-.
T Consensus 168 Rk~~~V~~Ai~tLSySEleAv~hIf~eL~g~EG~lvASkiADrvgITRSVI----VNALRK~ES 227 (256)
T PRK04158 168 RKKAVVQMAINTLSYSELEAVEHIFEELDGNEGLLVASKIADRVGITRSVI----VNALRKLES 227 (256)
T ss_pred HHHHHHHHHHHhcCHhHHHHHHHHHHhcCCCcceEEeeecccccCCchhhh----hhhhhhhhc
Confidence 33456888999999999999999887 444455 47789999999996655 578888865
No 403
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=52.09 E-value=24 Score=24.82 Aligned_cols=25 Identities=20% Similarity=0.388 Sum_probs=22.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556 515 KPKSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 515 e~~Tl~EIAe~LGISrerVRqie~R 539 (561)
.++|..++|+.+|++..+|.+++..
T Consensus 9 ~~~s~~~la~~~~i~~~~i~~~~~~ 33 (56)
T smart00530 9 KGLTQEELAEKLGVSRSTLSRIENG 33 (56)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHCC
Confidence 5789999999999999999887664
No 404
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=51.92 E-value=11 Score=30.58 Aligned_cols=25 Identities=32% Similarity=0.446 Sum_probs=19.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556 515 KPKSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 515 e~~Tl~EIAe~LGISrerVRqie~R 539 (561)
...|+.|||..||+|++.|+.++..
T Consensus 13 ~~~S~~eLa~~~~~s~~~ve~mL~~ 37 (69)
T PF09012_consen 13 GRVSLAELAREFGISPEAVEAMLEQ 37 (69)
T ss_dssp -SEEHHHHHHHTT--HHHHHHHHHH
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 6789999999999999999877654
No 405
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=51.91 E-value=24 Score=27.59 Aligned_cols=25 Identities=16% Similarity=0.405 Sum_probs=20.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556 515 KPKSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 515 e~~Tl~EIAe~LGISrerVRqie~R 539 (561)
.++|+.++|+.+|+++.++.++++.
T Consensus 11 ~~lt~~~~a~~~~i~~~~i~~~e~g 35 (64)
T PF12844_consen 11 KGLTQKDLAEKLGISRSTISKIENG 35 (64)
T ss_dssp CT--HHHHHHHHTS-HHHHHHHHTT
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHCC
Confidence 5799999999999999999999864
No 406
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=51.86 E-value=16 Score=36.04 Aligned_cols=27 Identities=22% Similarity=0.395 Sum_probs=22.0
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556 516 PKSLSEVGNIFGLSKERVRQLESRALYRLKQ 546 (561)
Q Consensus 516 ~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 546 (561)
++|.++||..+|+++++|. |++++|++
T Consensus 173 ~~t~~~iA~~lG~tretvs----R~l~~L~~ 199 (236)
T PRK09392 173 PYEKRVLASYLGMTPENLS----RAFAALAS 199 (236)
T ss_pred eCCHHHHHHHhCCChhHHH----HHHHHHHh
Confidence 5778999999999999986 55666665
No 407
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).
Probab=51.62 E-value=2.3e+02 Score=29.20 Aligned_cols=30 Identities=27% Similarity=0.490 Sum_probs=23.6
Q ss_pred HHHhhhhCCCCcHHHHHHHccCCHHHHHHH
Q 008556 285 SKLQSQFGREPTLIEWAKAIGLSCRDLKSE 314 (561)
Q Consensus 285 ~~l~~~~g~~pt~~ewA~a~g~~~~eL~~~ 314 (561)
..+....|++|+..+.|...|++...+...
T Consensus 140 ~~l~~~~~r~~~~~e~a~~l~~~~~~~~~~ 169 (285)
T TIGR02394 140 RQLEKKLGREPSVEEIAELLDKPVEDVSRV 169 (285)
T ss_pred HHHHHHhCCCCCHHHHHHHhCcCHHHHHHH
Confidence 334556799999999999999998777543
No 408
>PRK11517 transcriptional regulatory protein YedW; Provisional
Probab=51.47 E-value=27 Score=33.04 Aligned_cols=49 Identities=14% Similarity=0.078 Sum_probs=40.2
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHh-----CCCHHHHHHHHHHHHHHHH
Q 008556 496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIF-----GLSKERVRQLESRALYRLK 545 (561)
Q Consensus 496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~L-----GISrerVRqie~RALkKLR 545 (561)
.|+++|.+|+.+-.- +.|+..|.++|.+.+ ..+..+|+.+..|.++||.
T Consensus 147 ~Lt~~E~~il~~l~~-~~g~~~s~~~i~~~~w~~~~~~~~~tv~~~i~rlr~Kl~ 200 (223)
T PRK11517 147 TLTRKEFQLLWLLAS-RAGEIIPRTVIASEIWGINFDSDTNTVDVAIRRLRAKVD 200 (223)
T ss_pred eCCHHHHHHHHHHHh-CCCccCCHHHHHHHhcCCCCCCCcCCHHHHHHHHHHhhc
Confidence 599999999987653 445778999999986 4577899999888888885
No 409
>TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR. Members of this family are FadR, a transcriptional regulator of fatty acid metabolism, including both biosynthesis and beta-oxidation. It is found exclusively in a subset of Gammaproteobacteria, with strictly one copy per genome. It has an N-terminal DNA-binding domain and a less well conserved C-terminal long chain acyl-CoA-binding domain. FadR from this family heterologously expressed in Escherichia coli show differences in regulatory response and fatty acid binding profiles. The family is nevertheless designated equivalog, as all member proteins have at least nominally the same function.
Probab=51.27 E-value=22 Score=35.30 Aligned_cols=31 Identities=23% Similarity=0.454 Sum_probs=26.1
Q ss_pred cCCCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556 512 EDGKPK-SLSEVGNIFGLSKERVRQLESRALYRLKQ 546 (561)
Q Consensus 512 ~d~e~~-Tl~EIAe~LGISrerVRqie~RALkKLR~ 546 (561)
..|+.+ |-.++|+.||||+..||. ||.+|..
T Consensus 25 ~pG~~LpsE~~La~~lgVSRtpVRE----AL~~Le~ 56 (235)
T TIGR02812 25 PPGSILPAERELSELIGVTRTTLRE----VLQRLAR 56 (235)
T ss_pred CCCCcCcCHHHHHHHHCcCHHHHHH----HHHHHHH
Confidence 356788 899999999999999985 7788765
No 410
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=50.68 E-value=29 Score=29.34 Aligned_cols=31 Identities=19% Similarity=0.315 Sum_probs=25.5
Q ss_pred HHHHHhcccCCCCCCHHHHHHHhC------CCHHHHHHHHH
Q 008556 504 IVRLRFGIEDGKPKSLSEVGNIFG------LSKERVRQLES 538 (561)
Q Consensus 504 VL~LRyGL~d~e~~Tl~EIAe~LG------ISrerVRqie~ 538 (561)
+...|-- -++|..++|+.+| +|+.+|.++++
T Consensus 16 lk~~R~~----lGLTQ~dvA~~lg~~~g~i~SQstISR~Es 52 (75)
T smart00352 16 FKQRRIK----LGFTQADVGLALGALYGPDFSQTTICRFEA 52 (75)
T ss_pred HHHHHHH----cCCCHHHHHHHhcccccCcCCHHHHHHHHh
Confidence 4445554 5799999999999 59999999886
No 411
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=50.68 E-value=25 Score=35.77 Aligned_cols=25 Identities=16% Similarity=0.155 Sum_probs=22.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556 515 KPKSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 515 e~~Tl~EIAe~LGISrerVRqie~R 539 (561)
...+.+||++.||||..|||+-+..
T Consensus 18 ~~~~~~ela~~l~vS~~TirRdL~~ 42 (251)
T PRK13509 18 GFVTVEKVIERLGISPATARRDINK 42 (251)
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 5789999999999999999987654
No 412
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=50.32 E-value=33 Score=29.37 Aligned_cols=40 Identities=20% Similarity=0.348 Sum_probs=30.9
Q ss_pred CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556 497 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 497 L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R 539 (561)
|++.|..||...+..+ +.+..+||+.+++++.+|.+++.+
T Consensus 20 lt~~q~~~L~~l~~~~---~~~~~~la~~l~i~~~~vt~~l~~ 59 (126)
T COG1846 20 LTPPQYQVLLALYEAG---GITVKELAERLGLDRSTVTRLLKR 59 (126)
T ss_pred CCHHHHHHHHHHHHhC---CCcHHHHHHHHCCCHHHHHHHHHH
Confidence 9999999998877622 222299999999999999765544
No 413
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial. The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.
Probab=50.16 E-value=26 Score=31.65 Aligned_cols=26 Identities=27% Similarity=0.429 Sum_probs=21.7
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008556 513 DGKPKSLSEVGNIFGLSKERVRQLES 538 (561)
Q Consensus 513 d~e~~Tl~EIAe~LGISrerVRqie~ 538 (561)
++.+.|..|||+.+|+|+..|++++.
T Consensus 22 ~~~~~s~~eia~~l~is~~~v~~~l~ 47 (130)
T TIGR02944 22 DSQPYSAAEIAEQTGLNAPTVSKILK 47 (130)
T ss_pred CCCCccHHHHHHHHCcCHHHHHHHHH
Confidence 34679999999999999999976543
No 414
>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=50.01 E-value=10 Score=28.38 Aligned_cols=21 Identities=14% Similarity=0.248 Sum_probs=18.2
Q ss_pred HHHHHHhCCCHHHHHHHHHHH
Q 008556 520 SEVGNIFGLSKERVRQLESRA 540 (561)
Q Consensus 520 ~EIAe~LGISrerVRqie~RA 540 (561)
++||+.+|||+.+|+++++.-
T Consensus 1 ~~lA~~~gvs~~tvs~~l~g~ 21 (52)
T cd01392 1 KDIARAAGVSVATVSRVLNGK 21 (52)
T ss_pred CcHHHHHCcCHHHHHHHHcCC
Confidence 379999999999999988754
No 415
>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=49.88 E-value=32 Score=24.38 Aligned_cols=25 Identities=20% Similarity=0.405 Sum_probs=22.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556 515 KPKSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 515 e~~Tl~EIAe~LGISrerVRqie~R 539 (561)
.++|..++|..+|+++.+|.+++..
T Consensus 11 ~~~s~~~~a~~~~~~~~~v~~~~~g 35 (58)
T cd00093 11 KGLTQEELAEKLGVSRSTISRIENG 35 (58)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHcC
Confidence 5689999999999999999987664
No 416
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=49.58 E-value=28 Score=26.29 Aligned_cols=47 Identities=15% Similarity=0.171 Sum_probs=36.1
Q ss_pred CCHHHHHHHHHHhcccCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 008556 497 LNPKERCIVRLRFGIEDG-KPKSLSEVGNIFGLSKERVRQLESRALYR 543 (561)
Q Consensus 497 L~erER~VL~LRyGL~d~-e~~Tl~EIAe~LGISrerVRqie~RALkK 543 (561)
+++.+..+|.-.|..+.. ......+||..+|++...|.........+
T Consensus 7 ~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~ 54 (56)
T smart00389 7 FTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAK 54 (56)
T ss_pred CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhc
Confidence 678888888888875432 23457899999999999999987766554
No 417
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=49.38 E-value=32 Score=30.92 Aligned_cols=25 Identities=20% Similarity=0.367 Sum_probs=21.4
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHH
Q 008556 514 GKPKSLSEVGNIFGLSKERVRQLES 538 (561)
Q Consensus 514 ~e~~Tl~EIAe~LGISrerVRqie~ 538 (561)
+.+.|.+|||+.+|+++..|++++.
T Consensus 23 ~~~~s~~eia~~~~i~~~~v~~il~ 47 (132)
T TIGR00738 23 EGPVSVKEIAERQGISRSYLEKILR 47 (132)
T ss_pred CCcCcHHHHHHHHCcCHHHHHHHHH
Confidence 3589999999999999999987554
No 418
>TIGR00180 parB_part ParB-like partition proteins. This model represents the most well-conserved core of a set of chromosomal and plasmid partition proteins related to ParB, including Spo0J, RepB, and SopB. Spo0J has been shown to bind a specific DNA sequence that, when introduced into a plasmid, can serve as partition site. Study of RepB, which has nicking-closing activity, suggests that it forms a transient protein-DNA covalent intermediate during the strand transfer reaction.
Probab=49.35 E-value=30 Score=33.53 Aligned_cols=43 Identities=19% Similarity=0.191 Sum_probs=31.8
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556 495 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 495 ~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R 539 (561)
..|++-|+-....+.. .. .++|.++||+.+|+|+.+|++++.-
T Consensus 101 ~~lt~~e~a~~~~~l~-~~-~g~s~~~iA~~lg~s~~~V~r~l~l 143 (187)
T TIGR00180 101 EDLSPIEEAQAYKRLL-EK-FSMTQEDLAKKIGKSRAHITNLLRL 143 (187)
T ss_pred cCCCHHHHHHHHHHHH-HH-hCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 4688888765544432 11 4689999999999999999987654
No 419
>PF14502 HTH_41: Helix-turn-helix domain
Probab=49.05 E-value=32 Score=26.62 Aligned_cols=29 Identities=28% Similarity=0.455 Sum_probs=24.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008556 515 KPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 547 (561)
Q Consensus 515 e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 547 (561)
.-.|..|.++.|++|+.+| ..||+.|.+.
T Consensus 5 Ri~tI~e~~~~~~vs~Gti----Q~Alk~Le~~ 33 (48)
T PF14502_consen 5 RIPTISEYSEKFGVSRGTI----QNALKFLEEN 33 (48)
T ss_pred ccCCHHHHHHHhCcchhHH----HHHHHHHHHC
Confidence 5679999999999999999 4688888763
No 420
>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=48.84 E-value=51 Score=26.28 Aligned_cols=50 Identities=22% Similarity=0.231 Sum_probs=35.9
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHh------CCCHHHHHHHHHHHHHHHHH
Q 008556 496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIF------GLSKERVRQLESRALYRLKQ 546 (561)
Q Consensus 496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~L------GISrerVRqie~RALkKLR~ 546 (561)
.|+++|..+|.+-. ...|...|.++|.+.+ +.+..+|++...+-.++|..
T Consensus 5 ~Lt~~e~~lL~~L~-~~~~~~vs~~~l~~~lw~~~~~~~~~~~l~~~i~~LR~~l~~ 60 (78)
T smart00862 5 KLTPKEFRLLELLL-RNPGRVVSREELLEAVWGDDDDDVDDNTLDVHISRLRKKLED 60 (78)
T ss_pred ecCHHHHHHHHHHH-hCCCCccCHHHHHHHHcCCCCCCCccchHHHHHHHHHHHHhc
Confidence 47889999775543 3455789999999975 35677777777777666654
No 421
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=48.81 E-value=25 Score=35.46 Aligned_cols=37 Identities=22% Similarity=0.436 Sum_probs=28.4
Q ss_pred HHHHHhcccCCCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556 504 IVRLRFGIEDGKPK-SLSEVGNIFGLSKERVRQLESRALYRLKQ 546 (561)
Q Consensus 504 VL~LRyGL~d~e~~-Tl~EIAe~LGISrerVRqie~RALkKLR~ 546 (561)
|+.-.|. .|+.+ |-.++|+.||||+..||. |+++|..
T Consensus 22 I~~g~l~--pG~~LpsE~eLa~~~gVSRtpVRE----AL~~L~~ 59 (257)
T PRK10225 22 IIKTPYN--PGERLPPEREIAEMLDVTRTVVRE----ALIMLEI 59 (257)
T ss_pred HHhCCCC--CCCcCcCHHHHHHHhCCCHHHHHH----HHHHHHH
Confidence 4444433 45788 699999999999999985 7777765
No 422
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=48.74 E-value=44 Score=30.42 Aligned_cols=49 Identities=16% Similarity=0.226 Sum_probs=33.7
Q ss_pred HHHHhcCCHHHH-HHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556 491 RNLLTLLNPKER-CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 546 (561)
Q Consensus 491 ~~aL~~L~erER-~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 546 (561)
.+.+..|.+.-| .||.+-. ++.+++..||++.+|+|+.+|.+.+ +.|++
T Consensus 7 ~~~fkaLadptRl~IL~~L~---~~~~~~v~ela~~l~lsqstvS~HL----~~L~~ 56 (117)
T PRK10141 7 LQLFKILSDETRLGIVLLLR---ESGELCVCDLCTALDQSQPKISRHL----ALLRE 56 (117)
T ss_pred HHHHHHhCCHHHHHHHHHHH---HcCCcCHHHHHHHHCcCHHHHHHHH----HHHHH
Confidence 355566665444 5665432 2257999999999999999998764 45554
No 423
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=48.71 E-value=32 Score=32.77 Aligned_cols=42 Identities=10% Similarity=0.127 Sum_probs=28.5
Q ss_pred CCHHHHHHHHHHhccc-CCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008556 497 LNPKERCIVRLRFGIE-DGKPKSLSEVGNIFGLSKERVRQLES 538 (561)
Q Consensus 497 L~erER~VL~LRyGL~-d~e~~Tl~EIAe~LGISrerVRqie~ 538 (561)
+++....-|..-|.+. ++......+||+.|||++.+|.++++
T Consensus 4 ~s~~~edYL~~Iy~l~~~~~~~~~~diA~~L~Vsp~sVt~ml~ 46 (154)
T COG1321 4 LSETEEDYLETIYELLEEKGFARTKDIAERLKVSPPSVTEMLK 46 (154)
T ss_pred cchHHHHHHHHHHHHHhccCcccHHHHHHHhCCCcHHHHHHHH
Confidence 3444444444444333 34568999999999999999976543
No 424
>PRK14101 bifunctional glucokinase/RpiR family transcriptional regulator; Provisional
Probab=48.65 E-value=32 Score=39.81 Aligned_cols=52 Identities=15% Similarity=0.278 Sum_probs=41.4
Q ss_pred HHHHHHHHHhcCCHHHHHHHHHHhcccCC---CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556 486 MRQHVRNLLTLLNPKERCIVRLRFGIEDG---KPKSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 486 ~~e~L~~aL~~L~erER~VL~LRyGL~d~---e~~Tl~EIAe~LGISrerVRqie~R 539 (561)
+.+.|+.....|++.||.|..+- |... ..+|..|||+..|+|..+|-+..++
T Consensus 343 l~~~I~~~~~~Lt~~E~~IA~yI--l~n~~~v~~~si~eLA~~~~vS~aTV~Rf~kk 397 (638)
T PRK14101 343 VFERIRQMRDALTPAERRVADLA--LNHPRSIINDPIVDIARKADVSQPTVIRFCRS 397 (638)
T ss_pred HHHHHHHHHhhcCHHHHHHHHHH--HhCHHHHHhccHHHHHHHhCCCHHHHHHHHHH
Confidence 44578888999999999998753 3332 3579999999999999999776554
No 425
>PRK06424 transcription factor; Provisional
Probab=48.07 E-value=26 Score=33.05 Aligned_cols=25 Identities=12% Similarity=0.056 Sum_probs=23.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556 515 KPKSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 515 e~~Tl~EIAe~LGISrerVRqie~R 539 (561)
.++|++|+|+.+|+++.+|.++++.
T Consensus 96 ~GLSQ~eLA~~iGvs~stIskiE~G 120 (144)
T PRK06424 96 LSMSQADLAAKIFERKNVIASIERG 120 (144)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHCC
Confidence 6899999999999999999999863
No 426
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=48.00 E-value=36 Score=31.40 Aligned_cols=30 Identities=27% Similarity=0.617 Sum_probs=24.5
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556 513 DGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 546 (561)
Q Consensus 513 d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 546 (561)
+|+..+.++||+.+|||+..||+ ++.+|++
T Consensus 22 ~g~~~s~~~ia~~~~is~~~vrk----~l~~L~~ 51 (141)
T PRK11014 22 EGRMTSISEVTEVYGVSRNHMVK----IINQLSR 51 (141)
T ss_pred CCCccCHHHHHHHHCcCHHHHHH----HHHHHHh
Confidence 45678999999999999999976 5666665
No 427
>PF00292 PAX: 'Paired box' domain; InterPro: IPR001523 The paired box is a conserved 124 amino acid N-terminal domain of unknown function that usually, but not always, precedes a homeobox domain (see IPR001356 from INTERPRO) [, ]. Paired box genes are expressed in alternate segments of the developing fruit fly, the observed grouping of segments into pairs depending on the position of the segment in the segmental array, and not on the identity of the segment as in the case of homeotic genes. This implies that the genes affect different processes from those altered by homeotic genes.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 6PAX_A 1K78_E 1MDM_A 2K27_A 1PDN_C.
Probab=47.84 E-value=39 Score=31.24 Aligned_cols=32 Identities=22% Similarity=0.210 Sum_probs=23.6
Q ss_pred HHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556 503 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 503 ~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R 539 (561)
.||.|.. .+..-.+||..|+||...|++++.|
T Consensus 25 rIvela~-----~G~rp~~Isr~l~Vs~gcVsKIl~R 56 (125)
T PF00292_consen 25 RIVELAK-----EGVRPCDISRQLRVSHGCVSKILSR 56 (125)
T ss_dssp HHHHHHH-----TT--HHHHHHHHT--HHHHHHHHHH
T ss_pred HHHHHhh-----hcCCHHHHHHHHccchhHHHHHHHH
Confidence 4666765 6899999999999999999998775
No 428
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=47.72 E-value=18 Score=28.15 Aligned_cols=26 Identities=8% Similarity=0.218 Sum_probs=19.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008556 515 KPKSLSEVGNIFGLSKERVRQLESRA 540 (561)
Q Consensus 515 e~~Tl~EIAe~LGISrerVRqie~RA 540 (561)
.++|..++|+..|||+.+|..+.+.-
T Consensus 9 ~~it~~~La~~~gis~~tl~~~~~~~ 34 (63)
T PF13443_consen 9 RGITQKDLARKTGISRSTLSRILNGK 34 (63)
T ss_dssp TT--HHHHHHHHT--HHHHHHHHTTT
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHhcc
Confidence 56899999999999999999988765
No 429
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=47.71 E-value=2.3e+02 Score=30.03 Aligned_cols=33 Identities=18% Similarity=0.318 Sum_probs=26.5
Q ss_pred HHHHHHhhhhCCCCcHHHHHHHccCCHHHHHHH
Q 008556 282 KEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSE 314 (561)
Q Consensus 282 ~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~~ 314 (561)
+....|+..+|++|+..+.|...|++.+++...
T Consensus 177 R~~~~l~~~l~r~~t~~eiA~~l~~~~~~v~~~ 209 (325)
T PRK05657 177 RAARELEHKLDHEPSAEEIAELLDKPVDDVSRM 209 (325)
T ss_pred HHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHH
Confidence 445567777899999999999999998777544
No 430
>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=47.67 E-value=14 Score=32.06 Aligned_cols=26 Identities=19% Similarity=0.448 Sum_probs=22.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008556 517 KSLSEVGNIFGLSKERVRQLESRALY 542 (561)
Q Consensus 517 ~Tl~EIAe~LGISrerVRqie~RALk 542 (561)
+|..|+|+.+|||..++|-.+...+-
T Consensus 1 ~ti~eva~~~gvs~~tLRyye~~Gll 26 (96)
T cd04768 1 LTIGEFAKLAGVSIRTLRHYDDIGLF 26 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 57899999999999999999887543
No 431
>PF12298 Bot1p: Eukaryotic mitochondrial regulator protein ; InterPro: IPR021036 This entry represents Ribosomal protein S35, which localises to the mitochondria in live cells and co-fractionates with purified mitochondrial ribosomes. This group of proteins have a novel function in the control of cell respiration by acting on the mitochondrial protein synthesis machinery and a role in mitochondrial integrity. Observations also indicate that in Schizosaccharomyces pombe (Fission yeast), alterations of mitochondrial function are linked to changes in cell cycle and cell morphology control mechanisms [].
Probab=47.53 E-value=38 Score=32.97 Aligned_cols=38 Identities=24% Similarity=0.280 Sum_probs=27.8
Q ss_pred CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHH
Q 008556 497 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLE 537 (561)
Q Consensus 497 L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie 537 (561)
|++.-|+-|...+. .+++|+++||..+||+..||.-|+
T Consensus 17 lse~~r~~Iy~~~~---~~~~sv~~vS~~ygi~~~RV~AIv 54 (172)
T PF12298_consen 17 LSEELREQIYEDVM---QDGKSVREVSQKYGIKIQRVEAIV 54 (172)
T ss_pred CCHHHHHHHHHHHH---hCCCCHHHHHHHhCCCHHHHHHHH
Confidence 55555555555443 157799999999999999997554
No 432
>COG4465 CodY Pleiotropic transcriptional repressor [Transcription]
Probab=47.44 E-value=69 Score=32.45 Aligned_cols=55 Identities=18% Similarity=0.268 Sum_probs=43.7
Q ss_pred HHHHHHhcCCHHHHHHHHHHhc-ccCCCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008556 489 HVRNLLTLLNPKERCIVRLRFG-IEDGKPK-SLSEVGNIFGLSKERVRQLESRALYRLKQS 547 (561)
Q Consensus 489 ~L~~aL~~L~erER~VL~LRyG-L~d~e~~-Tl~EIAe~LGISrerVRqie~RALkKLR~~ 547 (561)
.+.-++..|+--|.+.+..-|+ |+|.+|+ .-.-||++.||+|+-| -.||+||-..
T Consensus 175 ~V~mAi~tLSYSEleAve~I~eELdG~EG~lvASkiADrvGITRSVI----VNALRKlESA 231 (261)
T COG4465 175 VVQMAISTLSYSELEAVEHIFEELDGNEGLLVASKIADRVGITRSVI----VNALRKLESA 231 (261)
T ss_pred HHHHHHhhccHHHHHHHHHHHHhcCCccceeeehhhhhhhCchHHHH----HHHHHHhhhc
Confidence 4566789999999999999887 5555554 7889999999996654 6788998653
No 433
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family. Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.
Probab=47.42 E-value=32 Score=34.59 Aligned_cols=35 Identities=14% Similarity=0.186 Sum_probs=25.6
Q ss_pred HHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008556 504 IVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES 538 (561)
Q Consensus 504 VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~ 538 (561)
+-.|.+.-..+.++|+.|||+.+|+++.+|..++.
T Consensus 12 l~IL~~l~~~~~~~~l~eia~~lglpksT~~RlL~ 46 (248)
T TIGR02431 12 LAVIEAFGAERPRLTLTDVAEATGLTRAAARRFLL 46 (248)
T ss_pred HHHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 33343332334789999999999999999977654
No 434
>PRK10643 DNA-binding transcriptional regulator BasR; Provisional
Probab=47.39 E-value=24 Score=33.27 Aligned_cols=49 Identities=14% Similarity=0.059 Sum_probs=35.5
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHH-----HhCCCHHHHHHHHHHHHHHHH
Q 008556 496 LLNPKERCIVRLRFGIEDGKPKSLSEVGN-----IFGLSKERVRQLESRALYRLK 545 (561)
Q Consensus 496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe-----~LGISrerVRqie~RALkKLR 545 (561)
.|+++|.+|+.+..- ..|...+-++|.+ .++++..+|+.+.++.++||.
T Consensus 149 ~Lt~~E~~il~~l~~-~~g~~~~~~~~~~~~~~~~~~~~~~tv~~~i~~lr~Kl~ 202 (222)
T PRK10643 149 ILTPKEFALLSRLML-KAGSPVHREILYQDIYNWDDEPSSNTLEVHIHNLRDKVG 202 (222)
T ss_pred ecCHHHHHHHHHHHh-CCCceEcHHHHHHHhcCCCCCCCcCCHHHHHHHHHHhCC
Confidence 499999999987642 2223344455544 368999999999999999985
No 435
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=47.12 E-value=31 Score=35.19 Aligned_cols=37 Identities=22% Similarity=0.238 Sum_probs=25.8
Q ss_pred HHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008556 502 RCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES 538 (561)
Q Consensus 502 R~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~ 538 (561)
|-+-.|.+.-..+.++|+.||++.+|+++.+|.+++.
T Consensus 12 ral~iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~ 48 (263)
T PRK09834 12 RGLMVLRALNRLDGGATVGLLAELTGLHRTTVRRLLE 48 (263)
T ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3344444433334569999999999999999975543
No 436
>PRK15340 transcriptional regulator InvF; Provisional
Probab=46.78 E-value=3.2e+02 Score=27.56 Aligned_cols=31 Identities=13% Similarity=0.210 Sum_probs=24.8
Q ss_pred HHHhCCCCCCHHHHHHHhCCCHHHHHHHHHh
Q 008556 416 YIQEGNHSPDKEDLARRVGITVEKLERLIFI 446 (561)
Q Consensus 416 l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~ 446 (561)
+........+.++||+.+|+++..+..+...
T Consensus 118 Ll~~~~~~~sleeLA~~~gvS~r~f~RlFk~ 148 (216)
T PRK15340 118 LLAQSTSGNTMRMLGEDYGVSYTHFRRLCSR 148 (216)
T ss_pred HHhCccCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 3344556789999999999999999988653
No 437
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=46.71 E-value=29 Score=37.30 Aligned_cols=34 Identities=24% Similarity=0.290 Sum_probs=29.9
Q ss_pred CChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHH
Q 008556 245 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLI 278 (561)
Q Consensus 245 ~~d~l~~Yl~~i~~~~lLT~eEE~eL~~~i~~~~ 278 (561)
....+..|+..+...|+||++||.+|+.+++.+-
T Consensus 65 ~~~~~~~~~~~~~~~~~l~~~Ee~~la~~~~~g~ 98 (342)
T COG0568 65 PAGRLSFYIRAIEAAPLLTPEEEKALARRLKRGE 98 (342)
T ss_pred hhhhHHHHHHHHhhhcccChHHHHHHHHHHHcCC
Confidence 4457788999999999999999999999999863
No 438
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=46.63 E-value=29 Score=31.46 Aligned_cols=25 Identities=16% Similarity=0.183 Sum_probs=22.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556 515 KPKSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 515 e~~Tl~EIAe~LGISrerVRqie~R 539 (561)
.++|.+|+|+.+|||+.+|.++++.
T Consensus 17 ~Glsq~eLA~~~Gis~~~is~iE~g 41 (120)
T PRK13890 17 RHMTKKELSERSGVSISFLSDLTTG 41 (120)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHcC
Confidence 5799999999999999999999864
No 439
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=46.50 E-value=1.9e+02 Score=32.68 Aligned_cols=25 Identities=16% Similarity=0.149 Sum_probs=21.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHh
Q 008556 422 HSPDKEDLARRVGITVEKLERLIFI 446 (561)
Q Consensus 422 r~Pt~eEIA~~lgis~e~v~~ll~~ 446 (561)
++-+..+||+.+|+.+..|..+...
T Consensus 368 kPLtlkdVAe~lglHeSTVSRa~~~ 392 (481)
T PRK12469 368 KPLVLRDVAEELGLHESTISRATGN 392 (481)
T ss_pred cCCcHHHHHHHhCCCcchhhHHhcC
Confidence 5678999999999999999988653
No 440
>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=46.35 E-value=45 Score=27.74 Aligned_cols=49 Identities=22% Similarity=0.154 Sum_probs=35.5
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHH
Q 008556 496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFG-----LSKERVRQLESRALYRLK 545 (561)
Q Consensus 496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LG-----ISrerVRqie~RALkKLR 545 (561)
.|+++|..+|.+-+ ...|+..|.++|.+.+. .+...+++.+.+..+||.
T Consensus 23 ~Lt~~e~~lL~~L~-~~~~~~vs~~~l~~~lw~~~~~~~~~~l~~~I~rLRkkl~ 76 (95)
T cd00383 23 ELTPKEFELLELLA-RNPGRVLSREQLLEAVWGDDYDVDDRTVDVHISRLRKKLE 76 (95)
T ss_pred EeCHHHHHHHHHHH-hCCCCcCCHHHHHHHhcCCCCCCCcccHHHHHHHHHHHhc
Confidence 47889998887755 35568999999999884 566666666665555554
No 441
>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=46.30 E-value=1.9e+02 Score=29.26 Aligned_cols=36 Identities=22% Similarity=0.204 Sum_probs=26.7
Q ss_pred HHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhc
Q 008556 411 EAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT 447 (561)
Q Consensus 411 ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~ 447 (561)
+...+..+++| -.|.+++|-.||+|+..|...+...
T Consensus 94 Rl~~EAy~Qgg-lLT~~Dla~LL~~S~~TI~~~i~~y 129 (220)
T PF07900_consen 94 RLTNEAYDQGG-LLTQEDLAMLLGISPRTISKDIKEY 129 (220)
T ss_pred HHHHHHHHcCC-cccHHHHHHHHCCCHHHHHHHHHHH
Confidence 33334444455 8999999999999999998877643
No 442
>COG1737 RpiR Transcriptional regulators [Transcription]
Probab=46.22 E-value=45 Score=34.50 Aligned_cols=51 Identities=20% Similarity=0.260 Sum_probs=39.9
Q ss_pred HHHHHHHHHhcCCHHHHHHHHHHhcccCC---CCCCHHHHHHHhCCCHHHHHHHHH
Q 008556 486 MRQHVRNLLTLLNPKERCIVRLRFGIEDG---KPKSLSEVGNIFGLSKERVRQLES 538 (561)
Q Consensus 486 ~~e~L~~aL~~L~erER~VL~LRyGL~d~---e~~Tl~EIAe~LGISrerVRqie~ 538 (561)
+...|......|++.||.|-.+- |.+. ..+|.+|||+..|||+.+|-+..+
T Consensus 5 l~~~I~~~~~~Lt~~er~iA~yi--l~~~~~~~~~si~elA~~a~VS~aTv~Rf~~ 58 (281)
T COG1737 5 LLERIRERYDSLTKSERKIADYI--LANPDEVALLSIAELAERAGVSPATVVRFAR 58 (281)
T ss_pred HHHHHHHHHhcCCHHHHHHHHHH--HhCHHHHHHHHHHHHHHHhCCCHHHHHHHHH
Confidence 44578888999999999997643 4432 357999999999999999965543
No 443
>PHA00738 putative HTH transcription regulator
Probab=45.86 E-value=39 Score=30.48 Aligned_cols=36 Identities=22% Similarity=0.033 Sum_probs=26.7
Q ss_pred HHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHH
Q 008556 499 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLE 537 (561)
Q Consensus 499 erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie 537 (561)
|.-+.||.+-. ++++++..||++.+++|+.+|++.+
T Consensus 12 ptRr~IL~lL~---~~e~~~V~eLae~l~lSQptVS~HL 47 (108)
T PHA00738 12 ILRRKILELIA---ENYILSASLISHTLLLSYTTVLRHL 47 (108)
T ss_pred HHHHHHHHHHH---HcCCccHHHHHHhhCCCHHHHHHHH
Confidence 33455555432 2357999999999999999999865
No 444
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=45.77 E-value=1.6e+02 Score=29.63 Aligned_cols=30 Identities=23% Similarity=0.436 Sum_probs=23.0
Q ss_pred HHHHHhhhhCCCCcHHHHHHHccCCHHHHH
Q 008556 283 EKSKLQSQFGREPTLIEWAKAIGLSCRDLK 312 (561)
Q Consensus 283 ~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~ 312 (561)
....+....|+.|+..+.+...|++.+++.
T Consensus 121 ~~~~~~~~~~r~~~~~e~a~~~~~~~~~~~ 150 (257)
T PRK08583 121 AVDELTTELQRSPKISEIADRLGVSEEEVL 150 (257)
T ss_pred HHHHHHHHhCCCCCHHHHHHHhCCCHHHHH
Confidence 334456677999999999999998877664
No 445
>PF07037 DUF1323: Putative transcription regulator (DUF1323); InterPro: IPR010749 This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length. The function of this family is unknown.
Probab=45.66 E-value=23 Score=32.48 Aligned_cols=23 Identities=13% Similarity=0.338 Sum_probs=20.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q 008556 517 KSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 517 ~Tl~EIAe~LGISrerVRqie~R 539 (561)
||.+|+|+.+|+|+.+|.....+
T Consensus 1 MT~eELA~~tG~srQTINrWvRk 23 (122)
T PF07037_consen 1 MTPEELAELTGYSRQTINRWVRK 23 (122)
T ss_pred CCHHHHHHHhCccHHHHHHHHHh
Confidence 68999999999999999887654
No 446
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus 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 model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.
Probab=44.96 E-value=56 Score=30.03 Aligned_cols=45 Identities=13% Similarity=0.203 Sum_probs=33.9
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHh----CCCHHHHHHHHHHHHHH
Q 008556 496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIF----GLSKERVRQLESRALYR 543 (561)
Q Consensus 496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~L----GISrerVRqie~RALkK 543 (561)
.|++.|.+|+..-+. . .+.|..||.+.| |++..||..++.|-.+|
T Consensus 1 ~Lt~~E~~VM~vlW~--~-~~~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~K 49 (130)
T TIGR02698 1 SISDAEWEVMRVVWT--L-GETTSRDIIRILAEKKDWSDSTIKTLLGRLVDK 49 (130)
T ss_pred CCCHHHHHHHHHHHc--C-CCCCHHHHHHHHhhccCCcHHHHHHHHHHHHHC
Confidence 378889998866543 2 468999977776 79999998887776553
No 447
>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=44.95 E-value=16 Score=32.08 Aligned_cols=26 Identities=23% Similarity=0.384 Sum_probs=23.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008556 517 KSLSEVGNIFGLSKERVRQLESRALY 542 (561)
Q Consensus 517 ~Tl~EIAe~LGISrerVRqie~RALk 542 (561)
+|..|+|+.+|||..++|-.+..++-
T Consensus 2 ~~i~eva~~~gvs~~tLR~ye~~Gll 27 (102)
T cd04775 2 YTIGQMSRKFGVSRSTLLYYESIGLI 27 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 68999999999999999999988664
No 448
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=44.92 E-value=31 Score=27.89 Aligned_cols=25 Identities=28% Similarity=0.368 Sum_probs=20.2
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHhc
Q 008556 423 SPDKEDLARRVGITVEKLERLIFIT 447 (561)
Q Consensus 423 ~Pt~eEIA~~lgis~e~v~~ll~~~ 447 (561)
..+..+||..+|++++.|+.++...
T Consensus 14 ~~S~~eLa~~~~~s~~~ve~mL~~l 38 (69)
T PF09012_consen 14 RVSLAELAREFGISPEAVEAMLEQL 38 (69)
T ss_dssp SEEHHHHHHHTT--HHHHHHHHHHH
T ss_pred CcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 6789999999999999999998753
No 449
>PRK13239 alkylmercury lyase; Provisional
Probab=44.92 E-value=42 Score=33.58 Aligned_cols=29 Identities=21% Similarity=0.237 Sum_probs=26.0
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHhcC
Q 008556 420 GNHSPDKEDLARRVGITVEKLERLIFITR 448 (561)
Q Consensus 420 ~gr~Pt~eEIA~~lgis~e~v~~ll~~~~ 448 (561)
.|++|+..+||+.+|+++++|+.+|....
T Consensus 33 ~G~pvt~~~lA~~~~~~~~~v~~~L~~l~ 61 (206)
T PRK13239 33 KGRPVSVTTLAAALGWPVEEVEAVLEAMP 61 (206)
T ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHhCC
Confidence 56799999999999999999999988654
No 450
>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=44.49 E-value=17 Score=30.94 Aligned_cols=25 Identities=28% Similarity=0.498 Sum_probs=22.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 008556 517 KSLSEVGNIFGLSKERVRQLESRAL 541 (561)
Q Consensus 517 ~Tl~EIAe~LGISrerVRqie~RAL 541 (561)
+|..|+|+.+|||..++|..+.+.+
T Consensus 2 ~ti~evA~~~gvs~~tLR~ye~~Gl 26 (88)
T cd01105 2 IGIGEVSKLTGVSPRQLRYWEEKGL 26 (88)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 6899999999999999999988764
No 451
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=44.34 E-value=31 Score=33.13 Aligned_cols=25 Identities=16% Similarity=0.290 Sum_probs=23.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556 515 KPKSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 515 e~~Tl~EIAe~LGISrerVRqie~R 539 (561)
.++|++|+|+.+|||+.+|+++++.
T Consensus 19 ~glt~~elA~~~gis~~~is~~E~g 43 (185)
T PRK09943 19 QGLSQRRAAELSGLTHSAISTIEQD 43 (185)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHcC
Confidence 5799999999999999999999974
No 452
>PRK09744 DNA-binding transcriptional regulator DicC; Provisional
Probab=44.20 E-value=31 Score=29.09 Aligned_cols=19 Identities=21% Similarity=0.240 Sum_probs=18.3
Q ss_pred CHHHHHHHhCCCHHHHHHH
Q 008556 518 SLSEVGNIFGLSKERVRQL 536 (561)
Q Consensus 518 Tl~EIAe~LGISrerVRqi 536 (561)
+...+|+.||||.+.|+|+
T Consensus 12 s~~kvA~aLGIs~~AVsQW 30 (75)
T PRK09744 12 SKTKLANAAGVRLASVAAW 30 (75)
T ss_pred cHHHHHHHHCCCHHHHHHH
Confidence 8899999999999999998
No 453
>PF04552 Sigma54_DBD: Sigma-54, DNA binding domain; InterPro: IPR007634 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 [].; PDB: 2AHQ_A 2O9L_A 2O8K_A.
Probab=44.20 E-value=7.5 Score=37.30 Aligned_cols=48 Identities=13% Similarity=0.212 Sum_probs=0.0
Q ss_pred HHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008556 489 HVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES 538 (561)
Q Consensus 489 ~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~ 538 (561)
.|..+...|=.+|+.-|.. |-..-.++|+++||+.+|++.+||+...+
T Consensus 24 TL~~v~~~iv~~Q~~ff~~--g~~~l~PLt~~~iA~~lgl~~STVSRav~ 71 (160)
T PF04552_consen 24 TLLRVAQAIVERQKDFFLG--GPGALKPLTMKDIADELGLHESTVSRAVK 71 (160)
T ss_dssp --------------------------------------------------
T ss_pred HHHHHHHHHHHHHHHHHhc--CcccCcCCCHHHHHHHhCCCHhHHHHHHc
Confidence 4555556666666665542 11112799999999999999999987554
No 454
>PRK00082 hrcA heat-inducible transcription repressor; Provisional
Probab=44.04 E-value=35 Score=36.53 Aligned_cols=65 Identities=23% Similarity=0.283 Sum_probs=44.5
Q ss_pred hcCCHHHHHHHHH--HhcccCCCCCCHHHHHHH--hCCCHHHHHHHHHHHHHHHHHHhh----------cCchhhhhhhh
Q 008556 495 TLLNPKERCIVRL--RFGIEDGKPKSLSEVGNI--FGLSKERVRQLESRALYRLKQSLG----------GKASYGYADLL 560 (561)
Q Consensus 495 ~~L~erER~VL~L--RyGL~d~e~~Tl~EIAe~--LGISrerVRqie~RALkKLR~~l~----------~~~l~~yldll 560 (561)
..|++|+++|+.. ...+..+++.+.+++++. +|+|..|||+-.. .|.++--..+ ..+++.|+|-|
T Consensus 2 ~~l~~R~~~Il~~IV~~yi~~~~pv~s~~l~~~~~l~~S~aTIR~dm~-~Le~~G~l~~~h~sagrIPT~kGYR~YVd~L 80 (339)
T PRK00082 2 SMLDERQREILRAIVEDYIATGEPVGSKTLSKRYGLGVSSATIRNDMA-DLEELGLLEKPHTSSGRIPTDKGYRYFVDHL 80 (339)
T ss_pred CccCHHHHHHHHHHHHHHHhcCCCcCHHHHHHHhCCCCChHHHHHHHH-HHHhCCCcCCCcCCCCCCcCHHHHHHHHHHh
Confidence 3588999999962 112334589999999977 9999999998765 3555422111 23677777754
No 455
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=43.94 E-value=25 Score=34.63 Aligned_cols=31 Identities=29% Similarity=0.397 Sum_probs=26.2
Q ss_pred cCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556 512 EDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 546 (561)
Q Consensus 512 ~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 546 (561)
..|+.++..+||+.||||+..||. ||+.|..
T Consensus 30 ~pG~~L~e~~La~~lgVSRtpVRE----AL~~L~~ 60 (221)
T PRK11414 30 KPGARLITKNLAEQLGMSITPVRE----ALLRLVS 60 (221)
T ss_pred CCCCccCHHHHHHHHCCCchhHHH----HHHHHHH
Confidence 356888999999999999999985 7777765
No 456
>PRK08359 transcription factor; Validated
Probab=43.76 E-value=32 Score=33.63 Aligned_cols=35 Identities=20% Similarity=0.284 Sum_probs=27.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH-------HHHHHHHHhh
Q 008556 515 KPKSLSEVGNIFGLSKERVRQLESR-------ALYRLKQSLG 549 (561)
Q Consensus 515 e~~Tl~EIAe~LGISrerVRqie~R-------ALkKLR~~l~ 549 (561)
.++|++|+|+.+|+++.+|+.++.- .+.+|-+.+.
T Consensus 97 kglSQeeLA~~lgvs~stI~~iE~G~~~Ps~~~l~kLak~l~ 138 (176)
T PRK08359 97 SGLSYEELSHEVGLSVNDLRRIAHGEYEPTIKEAKKLERYFK 138 (176)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHCCCcCCCHHHHHHHHHHhC
Confidence 6899999999999999999998753 4455555443
No 457
>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=43.72 E-value=17 Score=32.24 Aligned_cols=25 Identities=20% Similarity=0.521 Sum_probs=22.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 008556 517 KSLSEVGNIFGLSKERVRQLESRAL 541 (561)
Q Consensus 517 ~Tl~EIAe~LGISrerVRqie~RAL 541 (561)
||..|+|+.+|||..++|..+...+
T Consensus 1 ~~i~eva~~~gvs~~tlR~ye~~Gl 25 (108)
T cd04773 1 MTIGELAHLLGVPPSTLRHWEKEGL 25 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5889999999999999999988765
No 458
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=43.71 E-value=40 Score=32.17 Aligned_cols=24 Identities=17% Similarity=0.122 Sum_probs=20.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 008556 515 KPKSLSEVGNIFGLSKERVRQLES 538 (561)
Q Consensus 515 e~~Tl~EIAe~LGISrerVRqie~ 538 (561)
..+|-+|||+.|||+...||.++.
T Consensus 27 ~~~tdEeLa~~Lgi~~~~VRk~L~ 50 (158)
T TIGR00373 27 GEFTDEEISLELGIKLNEVRKALY 50 (158)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
Confidence 479999999999999999986543
No 459
>PRK15044 transcriptional regulator SirC; Provisional
Probab=43.53 E-value=1.3e+02 Score=31.79 Aligned_cols=60 Identities=22% Similarity=0.198 Sum_probs=44.4
Q ss_pred HHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHHHHhh
Q 008556 249 LRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHS 317 (561)
Q Consensus 249 l~~Yl~~i~~~~lLT~eEE~eL~~~i~~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~~l~~ 317 (561)
+..|++..+..+.|..+..... .+++..-+....+++++.++||+.+||+...|.+.++.
T Consensus 172 Ls~~l~~~~~~~~L~~~~~is~---------~~kV~~~I~~nl~~~~SLeeLA~~lgmS~~tL~R~Fk~ 231 (295)
T PRK15044 172 ISAFVRKPGGFDFLERAIKITT---------KEKVYNIIISDLTRKWSQAEVAGKLFMSVSSLKRKLAA 231 (295)
T ss_pred HHHHHhcccchhhHHHHhhhhH---------HHHHHHHHHhCcccCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 6678887777776655544332 33445556677889999999999999999999888764
No 460
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=43.36 E-value=2.3e+02 Score=31.72 Aligned_cols=25 Identities=16% Similarity=0.209 Sum_probs=21.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHh
Q 008556 422 HSPDKEDLARRVGITVEKLERLIFI 446 (561)
Q Consensus 422 r~Pt~eEIA~~lgis~e~v~~ll~~ 446 (561)
++-+..+||+.+|+.+..|..+...
T Consensus 342 kPLtlkdvAe~lglheSTVSRav~~ 366 (455)
T PRK05932 342 KPLVLKDIAEELGMHESTISRATTN 366 (455)
T ss_pred cCccHHHHHHHhCCCccchhhhhcC
Confidence 4668999999999999999888653
No 461
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=43.28 E-value=2.6e+02 Score=25.51 Aligned_cols=24 Identities=13% Similarity=0.213 Sum_probs=20.7
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHh
Q 008556 423 SPDKEDLARRVGITVEKLERLIFI 446 (561)
Q Consensus 423 ~Pt~eEIA~~lgis~e~v~~ll~~ 446 (561)
..+..|||+.+|++...+..++..
T Consensus 54 ~~t~~eLa~~l~i~~~tvsr~l~~ 77 (144)
T PRK11512 54 CITPVELKKVLSVDLGALTRMLDR 77 (144)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHH
Confidence 468999999999999999888764
No 462
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=43.22 E-value=58 Score=28.17 Aligned_cols=26 Identities=19% Similarity=0.238 Sum_probs=23.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008556 515 KPKSLSEVGNIFGLSKERVRQLESRA 540 (561)
Q Consensus 515 e~~Tl~EIAe~LGISrerVRqie~RA 540 (561)
++.|+++||+.+|+|+.+..++.++.
T Consensus 20 ~~~~~~~lA~~~~~S~~~l~r~f~~~ 45 (107)
T PRK10219 20 QPLNIDVVAKKSGYSKWYLQRMFRTV 45 (107)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 78999999999999999998888776
No 463
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=43.15 E-value=29 Score=35.44 Aligned_cols=36 Identities=22% Similarity=0.347 Sum_probs=27.9
Q ss_pred CHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHH
Q 008556 498 NPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQL 536 (561)
Q Consensus 498 ~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqi 536 (561)
.+|.+.|+.+--- ..-.+.+|+++.||||..|||+=
T Consensus 4 ~eR~~~Il~~l~~---~g~v~v~eLa~~~~VS~~TIRRD 39 (253)
T COG1349 4 EERHQKILELLKE---KGKVSVEELAELFGVSEMTIRRD 39 (253)
T ss_pred HHHHHHHHHHHHH---cCcEEHHHHHHHhCCCHHHHHHh
Confidence 3577777776432 24679999999999999999973
No 464
>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Polaromonas, Burkholderia, Ralstonia and Verminephrobacter.
Probab=43.14 E-value=26 Score=34.04 Aligned_cols=30 Identities=27% Similarity=0.434 Sum_probs=25.5
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556 513 DGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 546 (561)
Q Consensus 513 d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 546 (561)
.|+.++..++|+.||||+..||. ||+.|..
T Consensus 31 pG~~L~e~~La~~lgVSRtpVRe----AL~~L~~ 60 (212)
T TIGR03338 31 PGAKLNESDIAARLGVSRGPVRE----AFRALEE 60 (212)
T ss_pred CCCEecHHHHHHHhCCChHHHHH----HHHHHHH
Confidence 45788999999999999999985 7777765
No 465
>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=43.11 E-value=18 Score=31.97 Aligned_cols=26 Identities=19% Similarity=0.273 Sum_probs=23.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008556 517 KSLSEVGNIFGLSKERVRQLESRALY 542 (561)
Q Consensus 517 ~Tl~EIAe~LGISrerVRqie~RALk 542 (561)
++..|+|+.+|||..++|-.+..++-
T Consensus 1 ~~i~eva~~~gis~~tlR~ye~~GLi 26 (108)
T cd01107 1 FTIGEFAKLSNLSIKALRYYDKIGLL 26 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCC
Confidence 57899999999999999999988654
No 466
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=42.68 E-value=36 Score=34.72 Aligned_cols=37 Identities=19% Similarity=0.190 Sum_probs=27.1
Q ss_pred HHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008556 499 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES 538 (561)
Q Consensus 499 erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~ 538 (561)
+|.+.|+.+-- .....+..||++.||||..|||+-+.
T Consensus 5 ~R~~~Il~~l~---~~~~~~~~ela~~l~vS~~TiRRdL~ 41 (252)
T PRK10906 5 QRHDAIIELVK---QQGYVSTEELVEHFSVSPQTIRRDLN 41 (252)
T ss_pred HHHHHHHHHHH---HcCCEeHHHHHHHhCCCHHHHHHHHH
Confidence 45555665532 22468999999999999999997543
No 467
>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=42.46 E-value=19 Score=31.29 Aligned_cols=25 Identities=20% Similarity=0.339 Sum_probs=22.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 008556 517 KSLSEVGNIFGLSKERVRQLESRAL 541 (561)
Q Consensus 517 ~Tl~EIAe~LGISrerVRqie~RAL 541 (561)
+|..|+|+.+|||..++|..+..++
T Consensus 1 ~~i~eva~~~gvs~~tlR~ye~~Gl 25 (97)
T cd04782 1 FTTGEFAKLCGISKQTLFHYDKIGL 25 (97)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999999988765
No 468
>cd04772 HTH_TioE_rpt1 First 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 contains the N-terminal or first repeat (rpt1) of these tandem MerR-like domain proteins.
Probab=42.39 E-value=19 Score=31.43 Aligned_cols=26 Identities=31% Similarity=0.396 Sum_probs=22.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008556 517 KSLSEVGNIFGLSKERVRQLESRALY 542 (561)
Q Consensus 517 ~Tl~EIAe~LGISrerVRqie~RALk 542 (561)
++..|+|+.+|||..++|..+...+-
T Consensus 1 y~i~e~A~~~gvs~~tlR~Ye~~Gll 26 (99)
T cd04772 1 YRTVDLARAIGLSPQTVRNYESLGLI 26 (99)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCC
Confidence 47899999999999999998876553
No 469
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=42.33 E-value=53 Score=28.64 Aligned_cols=24 Identities=25% Similarity=0.306 Sum_probs=21.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 008556 515 KPKSLSEVGNIFGLSKERVRQLES 538 (561)
Q Consensus 515 e~~Tl~EIAe~LGISrerVRqie~ 538 (561)
-++|.++||..||+|.+.|.+++.
T Consensus 22 ~~ls~~~ia~dL~~s~~~le~vL~ 45 (89)
T PF10078_consen 22 SGLSLEQIAADLGTSPEHLEQVLN 45 (89)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHc
Confidence 579999999999999999988764
No 470
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=42.28 E-value=76 Score=29.78 Aligned_cols=42 Identities=12% Similarity=0.271 Sum_probs=31.6
Q ss_pred HHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcc
Q 008556 411 EAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLS 452 (561)
Q Consensus 411 ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~S 452 (561)
+++.-|...-++..|+.||++.+|++++.|..++...+-.++
T Consensus 34 kV~~yLr~~p~~~ati~eV~e~tgVs~~~I~~~IreGRL~~~ 75 (137)
T TIGR03826 34 KVYKFLRKHENRQATVSEIVEETGVSEKLILKFIREGRLQLK 75 (137)
T ss_pred HHHHHHHHCCCCCCCHHHHHHHHCcCHHHHHHHHHcCCeecc
Confidence 333344444556789999999999999999999987765444
No 471
>COG3711 BglG Transcriptional antiterminator [Transcription]
Probab=42.16 E-value=31 Score=38.18 Aligned_cols=47 Identities=21% Similarity=0.138 Sum_probs=38.3
Q ss_pred HHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556 499 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 546 (561)
Q Consensus 499 erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 546 (561)
..||.++.+.+.+.+ +..++.++|..+++|+.+|.+-.+....+++.
T Consensus 84 ~~er~~~~ll~~~~~-~~~~l~~La~~l~vs~~ti~~dl~~v~~~l~~ 130 (491)
T COG3711 84 KDERIIIILLLLLLS-ELLSLHELADELFVSKSTIINDLKDVRLKLLL 130 (491)
T ss_pred hHHHHHHHHHHHHhc-ChhhHHHHHHHHHhHHHHHHHHHHHHHHHHHh
Confidence 677887777776655 68999999999999999999988876555554
No 472
>PF02787 CPSase_L_D3: Carbamoyl-phosphate synthetase large chain, oligomerisation domain; InterPro: IPR005480 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 the oligomerisation domain found in the large subunit of carbamoyl phosphate synthases as well as in certain other carboxy phsophate domain-containing enzymes.; GO: 0006807 nitrogen compound metabolic process; PDB: 1M6V_C 1CS0_C 1C30_E 1C3O_G 1BXR_A 1T36_E 1A9X_A 1KEE_G 1CE8_A 1JDB_H ....
Probab=42.07 E-value=2.5e+02 Score=25.66 Aligned_cols=43 Identities=23% Similarity=0.434 Sum_probs=24.4
Q ss_pred HHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008556 489 HVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES 538 (561)
Q Consensus 489 ~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~ 538 (561)
.|......|++. .+....- -|.|-+.||..+|++.+.||++..
T Consensus 52 ~L~~~~~~~~~~--~L~~aK~-----~GFsD~~IA~l~~~~e~~vr~~R~ 94 (123)
T PF02787_consen 52 ELKEYLNELDPE--LLRKAKR-----LGFSDRQIARLWGVSEEEVRELRK 94 (123)
T ss_dssp HHHHHGGG--HH--HHHHHHH-----TT--HHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHhhccchHH--HHHHHHH-----cCCCHHHHHhccCCCHHHHHHHHH
Confidence 344434445554 3333432 367889999999999999987543
No 473
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=42.04 E-value=60 Score=29.25 Aligned_cols=47 Identities=23% Similarity=0.241 Sum_probs=37.9
Q ss_pred HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008556 494 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 544 (561)
Q Consensus 494 L~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKL 544 (561)
.+.|++.+-+.+++.+- --=+++||-..+|+|--+||..+...|++|
T Consensus 39 F~~Lt~d~LeFv~lf~r----~RGnlKEvEr~lg~sYptvR~kld~vlram 85 (122)
T COG3877 39 FEYLTSDQLEFVELFLR----CRGNLKEVERELGISYPTVRTKLDEVLRAM 85 (122)
T ss_pred ccccCHhHhHHHHHHHH----HccCHHHHHHHHCCccHHHHHHHHHHHHHc
Confidence 35677777777777665 223899999999999999999988888776
No 474
>PRK10870 transcriptional repressor MprA; Provisional
Probab=42.03 E-value=2.8e+02 Score=26.56 Aligned_cols=24 Identities=17% Similarity=0.142 Sum_probs=20.0
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHh
Q 008556 423 SPDKEDLARRVGITVEKLERLIFI 446 (561)
Q Consensus 423 ~Pt~eEIA~~lgis~e~v~~ll~~ 446 (561)
..+..+||+.+|++...+..++..
T Consensus 71 ~it~~eLa~~l~l~~~tvsr~v~r 94 (176)
T PRK10870 71 SIQPSELSCALGSSRTNATRIADE 94 (176)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHH
Confidence 457799999999999998877653
No 475
>PF04963 Sigma54_CBD: Sigma-54 factor, core binding domain; InterPro: IPR007046 This domain makes a direct interaction with the core RNA polymerase, to form an enhancer dependent holoenzyme []. The centre of this domain contains a very weak similarity to a helix-turn-helix motif, which may represent a DNA binding domain.; GO: 0003677 DNA binding, 0006352 transcription initiation, DNA-dependent; PDB: 2K9L_A 2K9M_A.
Probab=41.91 E-value=47 Score=32.55 Aligned_cols=60 Identities=27% Similarity=0.322 Sum_probs=35.0
Q ss_pred hcCCHHHHHHHHHHhcccCCC---CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH----hhcCchhhhhh
Q 008556 495 TLLNPKERCIVRLRFGIEDGK---PKSLSEVGNIFGLSKERVRQLESRALYRLKQS----LGGKASYGYAD 558 (561)
Q Consensus 495 ~~L~erER~VL~LRyGL~d~e---~~Tl~EIAe~LGISrerVRqie~RALkKLR~~----l~~~~l~~yld 558 (561)
..|++.++.|...--+--|.. ..++++||+.+|++.+.|. ++++.|+.. +....++++|.
T Consensus 28 ~~l~~~~~~ia~~lI~~LD~~GyL~~~~~eia~~l~~~~~~v~----~~l~~lQ~leP~GigAr~l~EcLl 94 (194)
T PF04963_consen 28 SPLSEEEREIAEYLIDNLDDDGYLTESLEEIAEELGVSEEEVE----KALELLQSLEPAGIGARDLQECLL 94 (194)
T ss_dssp H---TCCHHHHHHHCCCBTTTSTCSS-HHHHHHHCTS-HHHHH----HHHHHHHTTSS--TTTS-TTHHHH
T ss_pred cccCHHHHHHHHHHHHcCCCCCccCCCHHHHHHHhCCCHHHHH----HHHHHHHcCCCCccCcCCHHHHHH
Confidence 468888888776544422323 4599999999999999985 466666642 22344555544
No 476
>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=41.82 E-value=19 Score=31.40 Aligned_cols=25 Identities=20% Similarity=0.339 Sum_probs=22.4
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 008556 517 KSLSEVGNIFGLSKERVRQLESRAL 541 (561)
Q Consensus 517 ~Tl~EIAe~LGISrerVRqie~RAL 541 (561)
+|..|+|+.+|||..++|..+...+
T Consensus 1 ~ti~eva~~~gvs~~tlR~ye~~Gl 25 (103)
T cd01106 1 YTVGEVAKLTGVSVRTLHYYDEIGL 25 (103)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999999988765
No 477
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=41.78 E-value=73 Score=23.49 Aligned_cols=23 Identities=22% Similarity=0.453 Sum_probs=18.7
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHH
Q 008556 423 SPDKEDLARRVGITVEKLERLIF 445 (561)
Q Consensus 423 ~Pt~eEIA~~lgis~e~v~~ll~ 445 (561)
..+..|||+.+|++...+...+.
T Consensus 17 ~~t~~ela~~~~is~~tv~~~l~ 39 (48)
T PF13412_consen 17 RITQKELAEKLGISRSTVNRYLK 39 (48)
T ss_dssp TS-HHHHHHHHTS-HHHHHHHHH
T ss_pred CCCHHHHHHHhCCCHHHHHHHHH
Confidence 48899999999999999988765
No 478
>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=41.78 E-value=19 Score=30.89 Aligned_cols=25 Identities=28% Similarity=0.542 Sum_probs=22.4
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 008556 517 KSLSEVGNIFGLSKERVRQLESRAL 541 (561)
Q Consensus 517 ~Tl~EIAe~LGISrerVRqie~RAL 541 (561)
+|..|+|+.+||+..+||..+...+
T Consensus 1 ~~~~eva~~~gi~~~tlr~~~~~Gl 25 (100)
T cd00592 1 YTIGEVAKLLGVSVRTLRYYEEKGL 25 (100)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999999987765
No 479
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=41.70 E-value=37 Score=32.33 Aligned_cols=25 Identities=8% Similarity=0.157 Sum_probs=23.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556 515 KPKSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 515 e~~Tl~EIAe~LGISrerVRqie~R 539 (561)
.++|++++|+.+|+++.+|+++++-
T Consensus 81 ~glSqeeLA~~lgvs~s~IsriE~G 105 (154)
T TIGR00270 81 RGWSQEQLAKKIQEKESLIKKIENA 105 (154)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHCC
Confidence 6899999999999999999999963
No 480
>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=41.68 E-value=30 Score=30.25 Aligned_cols=23 Identities=35% Similarity=0.507 Sum_probs=21.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q 008556 517 KSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 517 ~Tl~EIAe~LGISrerVRqie~R 539 (561)
+|..|+|+.+|||..++|..+..
T Consensus 1 yti~EvA~~~gVs~~tLR~ye~~ 23 (99)
T cd04765 1 FSIGEVAEILGLPPHVLRYWETE 23 (99)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHH
Confidence 57899999999999999999776
No 481
>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=41.64 E-value=19 Score=30.74 Aligned_cols=26 Identities=19% Similarity=0.286 Sum_probs=22.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008556 517 KSLSEVGNIFGLSKERVRQLESRALY 542 (561)
Q Consensus 517 ~Tl~EIAe~LGISrerVRqie~RALk 542 (561)
+|..|+|+.+|||..+||..+...+-
T Consensus 2 ~~i~e~A~~~gvs~~tLr~ye~~Gli 27 (91)
T cd04766 2 YVISVAAELSGMHPQTLRLYERLGLL 27 (91)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHCCCc
Confidence 68899999999999999999876544
No 482
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=41.42 E-value=33 Score=33.75 Aligned_cols=38 Identities=24% Similarity=0.310 Sum_probs=29.1
Q ss_pred HHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556 503 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 546 (561)
Q Consensus 503 ~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 546 (561)
.|+.-.| ..|+.++..++|+.||||+..||. ||.+|..
T Consensus 19 ~I~~g~l--~pG~~L~e~eLae~lgVSRtpVRE----AL~~L~~ 56 (224)
T PRK11534 19 DIIRGNF--QPDEKLRMSLLTSRYALGVGPLRE----ALSQLVA 56 (224)
T ss_pred HHHhCCC--CCCCcCCHHHHHHHHCCChHHHHH----HHHHHHH
Confidence 3555444 245888999999999999999985 7777754
No 483
>PRK03837 transcriptional regulator NanR; Provisional
Probab=41.16 E-value=35 Score=33.86 Aligned_cols=30 Identities=37% Similarity=0.511 Sum_probs=25.2
Q ss_pred CCCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556 513 DGKPK-SLSEVGNIFGLSKERVRQLESRALYRLKQ 546 (561)
Q Consensus 513 d~e~~-Tl~EIAe~LGISrerVRqie~RALkKLR~ 546 (561)
.|+.+ +..+||+.||||+..||. ||..|..
T Consensus 33 pG~~Lp~E~~Lae~~gVSRt~VRE----AL~~L~~ 63 (241)
T PRK03837 33 PGDQLPSERELMAFFGVGRPAVRE----ALQALKR 63 (241)
T ss_pred CCCCCCCHHHHHHHhCCCHHHHHH----HHHHHHH
Confidence 45778 899999999999999985 7777764
No 484
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=41.01 E-value=35 Score=34.88 Aligned_cols=38 Identities=13% Similarity=0.150 Sum_probs=28.4
Q ss_pred HHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556 499 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 539 (561)
Q Consensus 499 erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R 539 (561)
+|++.|+.+--- ....+..|+|+.||||+.|||+-+..
T Consensus 5 eR~~~Il~~L~~---~~~v~v~eLa~~l~VS~~TIRRDL~~ 42 (256)
T PRK10434 5 QRQAAILEYLQK---QGKTSVEELAQYFDTTGTTIRKDLVI 42 (256)
T ss_pred HHHHHHHHHHHH---cCCEEHHHHHHHHCCCHHHHHHHHHH
Confidence 455666655322 24689999999999999999987655
No 485
>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=40.96 E-value=2.3e+02 Score=24.37 Aligned_cols=35 Identities=14% Similarity=0.174 Sum_probs=26.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008556 515 KPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 549 (561)
Q Consensus 515 e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 549 (561)
-|+++++|.+.+......+..++..-+..|++.+.
T Consensus 56 ~G~~l~~I~~~l~~~~~~~~~~l~~~~~~l~~~i~ 90 (96)
T cd04768 56 LGFSLAEIKELLDTEMEELTAMLLEKKQAIQQKID 90 (96)
T ss_pred cCCCHHHHHHHHhcCcHHHHHHHHHHHHHHHHHHH
Confidence 47999999999998766777777777777666543
No 486
>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=40.75 E-value=20 Score=31.09 Aligned_cols=25 Identities=20% Similarity=0.262 Sum_probs=22.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 008556 517 KSLSEVGNIFGLSKERVRQLESRAL 541 (561)
Q Consensus 517 ~Tl~EIAe~LGISrerVRqie~RAL 541 (561)
|+..|+|+.+|||..+||-.+...+
T Consensus 1 m~I~eva~~~gvs~~tlR~Ye~~GL 25 (95)
T cd04780 1 MRMSELSKRSGVSVATIKYYLREGL 25 (95)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999999887665
No 487
>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=40.70 E-value=20 Score=31.02 Aligned_cols=26 Identities=19% Similarity=0.270 Sum_probs=22.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008556 517 KSLSEVGNIFGLSKERVRQLESRALY 542 (561)
Q Consensus 517 ~Tl~EIAe~LGISrerVRqie~RALk 542 (561)
|+..|+|+.+|||..++|..+...+-
T Consensus 1 m~i~eva~~~gvs~~tlR~ye~~Gll 26 (96)
T cd04788 1 WKIGELARRTGLSVRTLHHYDHIGLL 26 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 57899999999999999999886653
No 488
>TIGR02018 his_ut_repres histidine utilization repressor, proteobacterial. This model represents a proteobacterial histidine utilization repressor. It is usually found clustered with the enzymes HutUHIG so that it can regulate its own expression as well. A number of species have several paralogs and may fine-tune the regulation according to levels of degradation intermediates such as urocanate. This family belongs to the larger GntR family of transcriptional regulators.
Probab=40.65 E-value=41 Score=33.36 Aligned_cols=28 Identities=29% Similarity=0.297 Sum_probs=23.2
Q ss_pred CCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556 515 KPK-SLSEVGNIFGLSKERVRQLESRALYRLKQ 546 (561)
Q Consensus 515 e~~-Tl~EIAe~LGISrerVRqie~RALkKLR~ 546 (561)
+.+ |-.|+|+.+|||+.|||+ |+..|.+
T Consensus 23 ~~LPsE~eLa~~~~VSR~TVR~----Al~~L~~ 51 (230)
T TIGR02018 23 HRIPSEHELVAQYGCSRMTVNR----ALRELTD 51 (230)
T ss_pred CcCcCHHHHHHHHCCCHHHHHH----HHHHHHH
Confidence 444 899999999999999985 7777755
No 489
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=40.51 E-value=56 Score=26.43 Aligned_cols=29 Identities=17% Similarity=0.335 Sum_probs=23.2
Q ss_pred HHhCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008556 417 IQEGNHSPDKEDLARRVGITVEKLERLIF 445 (561)
Q Consensus 417 ~~e~gr~Pt~eEIA~~lgis~e~v~~ll~ 445 (561)
..+.+..-+..+||+.||++...|+..-.
T Consensus 16 y~~~~g~i~lkdIA~~Lgvs~~tIr~WK~ 44 (60)
T PF10668_consen 16 YKESNGKIKLKDIAEKLGVSESTIRKWKS 44 (60)
T ss_pred HHHhCCCccHHHHHHHHCCCHHHHHHHhh
Confidence 34445588999999999999999987743
No 490
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=40.48 E-value=4.3e+02 Score=28.10 Aligned_cols=126 Identities=9% Similarity=0.192 Sum_probs=64.8
Q ss_pred HhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchh-hhhcccCCCCChhHHHHHHHHHHHHHHHHhc
Q 008556 418 QEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF-QEITADTGVEIPDISVQKQLMRQHVRNLLTL 496 (561)
Q Consensus 418 ~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l-~d~l~d~~~~~pee~le~~e~~e~L~~aL~~ 496 (561)
.+.+-+.|..||+...+++..++-++.......+-.+.+...-...++ --+...-..+........+..+.. .-++.
T Consensus 159 Rq~~~pRT~kEI~~~anv~kKEIgr~~K~i~~~l~~s~~~~s~~t~~~m~RFCs~L~L~~~~q~aA~e~a~ka--~~~~~ 236 (308)
T KOG1597|consen 159 RQEDVPRTFKEISAVANVSKKEIGRCVKLIGEALETSVDLISISTGDFMPRFCSNLGLPKSAQEAATEIAEKA--EEMDI 236 (308)
T ss_pred HhcCCCchHHHHHHHHcCCHHHHHHHHHHHHHHHhccchhhhhhHHHHHHHHHHhcCCCHHHHHHHHHHHHHH--HHhcc
Confidence 345567899999999999999998876543322211111111001111 112222221111111111100000 11122
Q ss_pred C---CHH--HHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556 497 L---NPK--ERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 546 (561)
Q Consensus 497 L---~er--ER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 546 (561)
+ +|. ---+|.|--.|.+ +.+|++||++..||+..|||+-.+--+-.+-+
T Consensus 237 ~~gRsPiSIAAa~IYmisqls~-~kkt~keI~~vtgVaE~TIr~sYK~Lyp~~~~ 290 (308)
T KOG1597|consen 237 RAGRSPISIAAAAIYMISQLSD-EKKTQKEIGEVTGVAEVTIRNSYKDLYPHADK 290 (308)
T ss_pred ccCCCchhHHHHHHHHHHHhcc-CcccHHHHHHHhhhhHHHHHHHHHHHhhchhh
Confidence 2 222 2234545444555 89999999999999999999876655544433
No 491
>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=40.41 E-value=21 Score=31.33 Aligned_cols=26 Identities=23% Similarity=0.313 Sum_probs=23.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008556 517 KSLSEVGNIFGLSKERVRQLESRALY 542 (561)
Q Consensus 517 ~Tl~EIAe~LGISrerVRqie~RALk 542 (561)
+|..|+|+.+|||..++|..+...+-
T Consensus 2 ~~i~eva~~~gvs~~tlR~ye~~Gll 27 (102)
T cd04789 2 YTISELAEKAGISRSTLLYYEKLGLI 27 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 68999999999999999998887554
No 492
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=40.37 E-value=57 Score=29.54 Aligned_cols=33 Identities=21% Similarity=0.271 Sum_probs=27.0
Q ss_pred HHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008556 504 IVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA 540 (561)
Q Consensus 504 VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RA 540 (561)
.|.-.+. ++.|+.+||+.+|+|+.++.++.++.
T Consensus 17 ~I~~~~~----~~~sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 17 WIEDNLE----SPLSLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred HHHHhcC----CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 3444554 68999999999999999998888776
No 493
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=40.30 E-value=44 Score=34.27 Aligned_cols=25 Identities=20% Similarity=0.223 Sum_probs=21.5
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHH
Q 008556 514 GKPKSLSEVGNIFGLSKERVRQLES 538 (561)
Q Consensus 514 ~e~~Tl~EIAe~LGISrerVRqie~ 538 (561)
+.++|+.|||+.+|+++.+|..+++
T Consensus 38 ~~~~tl~eIa~~lglpkStv~RlL~ 62 (271)
T PRK10163 38 GGSSSVSDISLNLDLPLSTTFRLLK 62 (271)
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHH
Confidence 3679999999999999999976654
No 494
>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=40.13 E-value=21 Score=31.68 Aligned_cols=26 Identities=31% Similarity=0.446 Sum_probs=23.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008556 517 KSLSEVGNIFGLSKERVRQLESRALY 542 (561)
Q Consensus 517 ~Tl~EIAe~LGISrerVRqie~RALk 542 (561)
+|..|+|+.+|||..++|-.+..++-
T Consensus 1 ~~i~e~a~~~gvs~~tlr~ye~~gll 26 (113)
T cd01109 1 YTIKEVAEKTGLSADTLRYYEKEGLL 26 (113)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 57899999999999999999887664
No 495
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=39.95 E-value=62 Score=31.73 Aligned_cols=41 Identities=20% Similarity=0.152 Sum_probs=32.6
Q ss_pred hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008556 495 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES 538 (561)
Q Consensus 495 ~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~ 538 (561)
-.|++.|-.||..-+. ..+.|..+||+.+++++.+|.+++.
T Consensus 41 ~gLt~~q~~iL~~L~~---~~~itq~eLa~~l~l~~sTvtr~l~ 81 (185)
T PRK13777 41 YDLNINEHHILWIAYH---LKGASISEIAKFGVMHVSTAFNFSK 81 (185)
T ss_pred CCCCHHHHHHHHHHHh---CCCcCHHHHHHHHCCCHhhHHHHHH
Confidence 3689999988876553 3589999999999999999865443
No 496
>PF05930 Phage_AlpA: Prophage CP4-57 regulatory protein (AlpA); InterPro: IPR010260 This entry is represents phage P4, Orf88. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. In Escherichia coli phage P4 Orf 88 is similar to AlpA of the CP4-57 cryptic prophage []. AlpA acts as a positive transcriptional regulator of slpA, a gene linked to alpA and necessary for suppression of lon mutants [, ]. The sequence of slpA suggests that it encodes an integrase gene closely related to phage P4 int and that both alpA and slpA are part of a cryptic P4-like prophage. Increase in alpA expression increases SlpA synthesis. Increased SlpA leads, in turn, to the excision and loss of the cryptic prophage. ; PDB: 1Z4H_A.
Probab=39.85 E-value=34 Score=26.09 Aligned_cols=24 Identities=21% Similarity=0.439 Sum_probs=19.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHH
Q 008556 517 KSLSEVGNIFGLSKERVRQLESRA 540 (561)
Q Consensus 517 ~Tl~EIAe~LGISrerVRqie~RA 540 (561)
.+.+|+++.+|+|+.++....++.
T Consensus 4 l~~~ev~~~~g~s~~ti~~~~k~g 27 (51)
T PF05930_consen 4 LRIKEVAELLGVSRSTIYRLIKDG 27 (51)
T ss_dssp E-HHHHHHHHSS-HHHHHHHHHHH
T ss_pred ccHHHHHHHHCCCHHHHHHHHhcc
Confidence 478999999999999999887743
No 497
>COG1481 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=39.75 E-value=56 Score=34.63 Aligned_cols=43 Identities=30% Similarity=0.299 Sum_probs=35.9
Q ss_pred HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCC--CHHHHHHHHHH
Q 008556 494 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGL--SKERVRQLESR 539 (561)
Q Consensus 494 L~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGI--SrerVRqie~R 539 (561)
++.||+..+++-.+|.- ..+.|++|||+.+.. |+..|..+..|
T Consensus 251 l~~lpe~l~e~a~LRl~---hpd~SLeeLg~~l~~~iSKSGvnHrlrk 295 (308)
T COG1481 251 LEKLPEKLREAALLRLE---HPDASLEELGELLEPPISKSGVNHRLRK 295 (308)
T ss_pred hhhCCHHHHHHHHHhhc---ChhhhHHHHHHHhcCcccHHHHHHHHHH
Confidence 47899999999999864 478999999999987 88888765544
No 498
>PHA02943 hypothetical protein; Provisional
Probab=39.68 E-value=46 Score=31.91 Aligned_cols=24 Identities=25% Similarity=0.257 Sum_probs=20.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 008556 515 KPKSLSEVGNIFGLSKERVRQLES 538 (561)
Q Consensus 515 e~~Tl~EIAe~LGISrerVRqie~ 538 (561)
...|..|||+.||+|.+.|+-++.
T Consensus 23 G~~TtseIAkaLGlS~~qa~~~Ly 46 (165)
T PHA02943 23 GCKTTSRIANKLGVSHSMARNALY 46 (165)
T ss_pred CCccHHHHHHHHCCCHHHHHHHHH
Confidence 368899999999999999987653
No 499
>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF. All members of the seed alignment for this family are predicted helix-turn-helix transcriptional regulatory proteins of the broader gntR and are found associated with genes for the import and degradation of phosphonates and/or related compounds (e.g. phosphonites) with a direct C-P bond.
Probab=39.49 E-value=34 Score=33.80 Aligned_cols=26 Identities=23% Similarity=0.437 Sum_probs=22.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556 517 KSLSEVGNIFGLSKERVRQLESRALYRLKQ 546 (561)
Q Consensus 517 ~Tl~EIAe~LGISrerVRqie~RALkKLR~ 546 (561)
-|-.|+|+.+|||+.|||+ ||..|.+
T Consensus 33 PsE~eLa~~~~VSR~TvR~----Al~~L~~ 58 (238)
T TIGR02325 33 PAEMQLAERFGVNRHTVRR----AIAALVE 58 (238)
T ss_pred cCHHHHHHHHCCCHHHHHH----HHHHHHH
Confidence 3899999999999999985 7777765
No 500
>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=39.44 E-value=22 Score=30.98 Aligned_cols=26 Identities=27% Similarity=0.402 Sum_probs=22.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008556 517 KSLSEVGNIFGLSKERVRQLESRALY 542 (561)
Q Consensus 517 ~Tl~EIAe~LGISrerVRqie~RALk 542 (561)
|+..|+|+.+|||..++|..+...+-
T Consensus 1 ~~I~e~a~~~gvs~~tLR~ye~~Gll 26 (96)
T cd04774 1 YKVDEVAKRLGLTKRTLKYYEEIGLV 26 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 57899999999999999999876543
Done!