Query psy15215
Match_columns 1432
No_of_seqs 837 out of 5615
Neff 7.9
Searched_HMMs 46136
Date Fri Aug 16 23:38:39 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15215.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15215hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK05658 RNA polymerase sigma 100.0 9E-110 2E-114 1048.4 65.6 601 827-1429 7-619 (619)
2 PRK05658 RNA polymerase sigma 100.0 1E-109 3E-114 1046.9 65.8 589 40-629 10-609 (619)
3 COG0568 RpoD DNA-directed RNA 100.0 2.3E-58 4.9E-63 520.0 34.0 337 1074-1428 3-342 (342)
4 COG0568 RpoD DNA-directed RNA 100.0 3.8E-55 8.2E-60 493.9 33.5 326 283-626 2-329 (342)
5 PRK09210 RNA polymerase sigma 100.0 5.4E-54 1.2E-58 508.6 40.0 359 827-1428 9-367 (367)
6 PRK07598 RNA polymerase sigma 100.0 8E-54 1.7E-58 501.3 39.0 250 1175-1429 164-413 (415)
7 PRK05901 RNA polymerase sigma 100.0 1.3E-53 2.9E-58 511.3 34.8 238 1191-1428 272-509 (509)
8 PRK09210 RNA polymerase sigma 100.0 5.9E-52 1.3E-56 491.2 39.5 347 39-628 11-357 (367)
9 PRK05901 RNA polymerase sigma 100.0 3.7E-51 7.9E-56 490.3 35.3 229 401-629 272-500 (509)
10 PRK07598 RNA polymerase sigma 100.0 3.2E-50 6.9E-55 471.0 41.1 239 385-628 164-402 (415)
11 PRK07406 RNA polymerase sigma 100.0 8.8E-49 1.9E-53 458.0 37.0 245 1178-1427 128-372 (373)
12 PRK05949 RNA polymerase sigma 100.0 6.2E-48 1.3E-52 448.1 35.6 247 1176-1429 81-327 (327)
13 PRK07406 RNA polymerase sigma 100.0 4.8E-46 1E-50 435.1 37.2 237 388-629 128-364 (373)
14 PRK07405 RNA polymerase sigma 100.0 3.1E-46 6.7E-51 433.8 35.3 246 1177-1429 72-317 (317)
15 PRK07921 RNA polymerase sigma 100.0 3.9E-46 8.5E-51 431.3 31.6 272 1156-1427 28-323 (324)
16 PRK05949 RNA polymerase sigma 100.0 1.8E-45 3.9E-50 427.5 36.5 238 386-628 81-318 (327)
17 TIGR02997 Sig70-cyanoRpoD RNA 100.0 1.2E-44 2.6E-49 419.7 34.0 235 1176-1415 64-298 (298)
18 PRK07405 RNA polymerase sigma 100.0 5.4E-44 1.2E-48 415.0 35.7 237 387-628 72-308 (317)
19 PRK07921 RNA polymerase sigma 100.0 6.3E-44 1.4E-48 412.9 31.8 260 366-628 28-314 (324)
20 TIGR02997 Sig70-cyanoRpoD RNA 100.0 5.1E-43 1.1E-47 406.1 35.1 235 386-625 64-298 (298)
21 TIGR02393 RpoD_Cterm RNA polym 100.0 6.6E-42 1.4E-46 385.1 27.2 238 1191-1428 1-238 (238)
22 TIGR02393 RpoD_Cterm RNA polym 100.0 1.8E-39 3.9E-44 365.3 27.5 230 401-630 1-230 (238)
23 PRK07122 RNA polymerase sigma 100.0 1.2E-38 2.7E-43 362.0 27.9 228 1182-1418 32-263 (264)
24 PRK07122 RNA polymerase sigma 100.0 8.1E-38 1.8E-42 355.3 29.2 227 393-628 33-263 (264)
25 PRK05657 RNA polymerase sigma 100.0 1.6E-37 3.6E-42 361.7 31.0 265 1156-1423 55-319 (325)
26 PRK06596 RNA polymerase factor 100.0 2.8E-37 6.1E-42 354.6 29.7 255 1158-1420 18-282 (284)
27 PRK05657 RNA polymerase sigma 100.0 7.2E-37 1.6E-41 356.3 32.1 261 366-629 55-315 (325)
28 PRK07500 rpoH2 RNA polymerase 100.0 4.8E-37 1E-41 353.2 29.3 259 1157-1421 9-280 (289)
29 PRK07408 RNA polymerase sigma 100.0 9.1E-37 2E-41 346.1 28.0 237 1173-1419 10-252 (256)
30 PRK06596 RNA polymerase factor 100.0 2E-36 4.4E-41 347.5 30.2 255 367-629 17-281 (284)
31 PRK07500 rpoH2 RNA polymerase 100.0 2.6E-36 5.7E-41 347.1 29.9 257 367-629 9-278 (289)
32 TIGR02392 rpoH_proteo alternat 100.0 3.2E-36 7E-41 344.6 29.2 253 1158-1418 5-268 (270)
33 PRK07408 RNA polymerase sigma 100.0 4.8E-36 1E-40 340.2 28.8 237 383-629 10-252 (256)
34 PRK05667 dnaG DNA primase; Val 100.0 3.2E-37 7E-42 381.5 19.9 203 618-820 107-370 (580)
35 TIGR02392 rpoH_proteo alternat 100.0 1.5E-35 3.3E-40 339.0 28.7 255 367-629 4-269 (270)
36 PRK05911 RNA polymerase sigma 100.0 3.6E-35 7.8E-40 333.0 28.6 233 1177-1419 12-254 (257)
37 PRK05911 RNA polymerase sigma 100.0 9.1E-35 2E-39 329.7 28.9 236 386-631 11-256 (257)
38 TIGR02850 spore_sigG RNA polym 100.0 9.3E-35 2E-39 330.1 28.5 237 1168-1417 15-253 (254)
39 TIGR02394 rpoS_proteo RNA poly 100.0 3E-34 6.6E-39 331.3 31.1 262 1157-1421 16-277 (285)
40 COG1191 FliA DNA-directed RNA 100.0 1.8E-34 4E-39 315.9 26.2 237 1168-1418 5-244 (247)
41 COG1191 FliA DNA-directed RNA 100.0 2.5E-34 5.4E-39 314.9 26.8 239 377-629 4-245 (247)
42 COG0358 DnaG DNA primase (bact 100.0 9.3E-36 2E-40 373.0 17.1 207 599-811 83-348 (568)
43 TIGR02394 rpoS_proteo RNA poly 100.0 8.1E-34 1.8E-38 327.7 31.8 262 366-630 15-276 (285)
44 TIGR02850 spore_sigG RNA polym 100.0 6.5E-34 1.4E-38 323.2 28.3 238 377-627 14-253 (254)
45 TIGR01391 dnaG DNA primase, ca 100.0 8.2E-35 1.8E-39 350.1 20.7 191 618-811 110-357 (415)
46 PRK08215 sporulation sigma fac 100.0 2.3E-33 5.1E-38 319.6 27.9 238 1168-1418 18-257 (258)
47 PRK08215 sporulation sigma fac 100.0 1.5E-32 3.3E-37 313.0 28.8 238 378-628 18-257 (258)
48 TIGR02885 spore_sigF RNA polym 100.0 1.1E-32 2.4E-37 309.5 26.3 227 1178-1417 2-230 (231)
49 TIGR02941 Sigma_B RNA polymera 100.0 2.3E-32 4.9E-37 311.4 28.8 242 1168-1418 9-253 (255)
50 TIGR02941 Sigma_B RNA polymera 100.0 1.2E-31 2.5E-36 305.6 29.3 242 378-628 9-253 (255)
51 TIGR02885 spore_sigF RNA polym 100.0 7.3E-32 1.6E-36 302.9 26.3 227 388-627 2-230 (231)
52 TIGR02980 SigBFG RNA polymeras 100.0 1.6E-31 3.5E-36 299.4 26.1 219 1190-1417 3-225 (227)
53 PRK07670 RNA polymerase sigma 100.0 2.8E-31 6.1E-36 301.3 28.2 236 1173-1418 7-249 (251)
54 PRK06288 RNA polymerase sigma 100.0 3.7E-31 8E-36 303.1 28.1 244 1167-1420 10-262 (268)
55 PRK06288 RNA polymerase sigma 100.0 1.3E-30 2.9E-35 298.5 29.4 244 377-630 10-262 (268)
56 PRK07670 RNA polymerase sigma 100.0 1.6E-30 3.4E-35 295.2 28.9 237 383-629 7-250 (251)
57 TIGR02980 SigBFG RNA polymeras 100.0 9.5E-31 2.1E-35 293.2 26.7 220 400-628 3-226 (227)
58 PRK05572 sporulation sigma fac 100.0 1.7E-30 3.7E-35 295.1 27.9 239 1165-1418 10-250 (252)
59 PRK08583 RNA polymerase sigma 100.0 2.2E-30 4.7E-35 295.5 27.8 243 1168-1419 9-254 (257)
60 TIGR02479 FliA_WhiG RNA polyme 100.0 1.3E-30 2.7E-35 291.3 25.4 217 1195-1418 1-223 (224)
61 PRK12427 flagellar biosynthesi 100.0 2.3E-30 5E-35 288.8 26.3 209 1192-1417 17-230 (231)
62 PRK05572 sporulation sigma fac 100.0 8.3E-30 1.8E-34 289.5 28.2 240 375-629 10-251 (252)
63 TIGR02479 FliA_WhiG RNA polyme 100.0 6.6E-30 1.4E-34 285.6 25.9 217 405-628 1-223 (224)
64 TIGR00646 MG010 DNA primase-re 100.0 3.2E-31 7E-36 281.3 12.9 124 674-805 52-206 (218)
65 PRK08583 RNA polymerase sigma 100.0 2.2E-29 4.8E-34 287.2 29.0 244 377-629 8-254 (257)
66 PRK12427 flagellar biosynthesi 100.0 1.7E-29 3.8E-34 281.7 26.5 209 402-627 17-230 (231)
67 PRK06986 fliA flagellar biosyn 100.0 2.5E-29 5.5E-34 283.0 26.7 221 1190-1419 8-233 (236)
68 PRK06986 fliA flagellar biosyn 100.0 1.2E-28 2.7E-33 277.4 27.5 221 401-630 9-234 (236)
69 PF04546 Sigma70_ner: Sigma-70 100.0 2.6E-31 5.6E-36 291.7 5.5 204 171-374 1-211 (211)
70 PF04546 Sigma70_ner: Sigma-70 100.0 3.8E-31 8.3E-36 290.3 5.3 204 961-1164 1-211 (211)
71 PHA02540 61 DNA primase; Provi 99.9 1.5E-27 3.3E-32 271.9 15.1 162 635-810 123-315 (337)
72 PHA02031 putative DnaG-like pr 99.9 1.3E-26 2.9E-31 251.2 11.8 123 674-810 111-262 (266)
73 PRK05803 sporulation sigma fac 99.9 1.5E-22 3.3E-27 227.4 25.3 214 1151-1420 13-229 (233)
74 PRK05803 sporulation sigma fac 99.9 4.4E-22 9.5E-27 223.7 25.5 214 360-629 12-228 (233)
75 PRK08624 hypothetical protein; 99.9 5.1E-23 1.1E-27 234.0 12.9 113 644-771 158-313 (373)
76 TIGR02846 spore_sigmaK RNA pol 99.9 2.6E-21 5.6E-26 216.5 22.6 193 1169-1417 30-225 (227)
77 PRK08301 sporulation sigma fac 99.9 4.7E-21 1E-25 215.9 21.9 194 1169-1418 34-230 (234)
78 TIGR02846 spore_sigmaK RNA pol 99.9 1.1E-20 2.4E-25 211.3 22.1 194 379-628 30-226 (227)
79 PRK08301 sporulation sigma fac 99.9 2.3E-20 5E-25 210.3 22.5 196 379-630 34-232 (234)
80 TIGR02835 spore_sigmaE RNA pol 99.9 2.8E-20 6.1E-25 209.1 22.1 191 1172-1418 37-230 (234)
81 TIGR02835 spore_sigmaE RNA pol 99.8 1.2E-19 2.7E-24 203.9 22.5 194 380-629 35-231 (234)
82 PRK08295 RNA polymerase factor 99.8 6.5E-20 1.4E-24 203.0 19.9 193 1174-1421 11-205 (208)
83 PRK09648 RNA polymerase sigma 99.8 1.7E-19 3.6E-24 196.6 20.8 178 1169-1418 6-187 (189)
84 PRK09646 RNA polymerase sigma 99.8 1.4E-19 3.1E-24 197.8 18.9 180 1169-1419 12-191 (194)
85 PRK05602 RNA polymerase sigma 99.8 1.9E-19 4.1E-24 195.6 18.9 172 1174-1420 7-178 (186)
86 PRK08295 RNA polymerase factor 99.8 3.8E-19 8.3E-24 196.9 20.6 191 384-629 11-203 (208)
87 PRK12519 RNA polymerase sigma 99.8 3.3E-19 7.1E-24 195.1 18.5 179 1169-1418 11-189 (194)
88 TIGR02859 spore_sigH RNA polym 99.8 4.1E-19 8.9E-24 195.1 19.3 190 1174-1418 6-197 (198)
89 PRK12513 RNA polymerase sigma 99.8 3.6E-19 7.7E-24 194.8 17.8 180 1173-1422 12-191 (194)
90 PRK09648 RNA polymerase sigma 99.8 1E-18 2.3E-23 190.3 20.9 179 379-629 6-188 (189)
91 TIGR02948 SigW_bacill RNA poly 99.8 6.7E-19 1.5E-23 191.5 19.1 180 1175-1419 6-185 (187)
92 PRK09641 RNA polymerase sigma 99.8 7.5E-19 1.6E-23 191.1 19.3 181 1174-1419 5-185 (187)
93 PRK09646 RNA polymerase sigma 99.8 8.2E-19 1.8E-23 191.8 19.4 181 378-629 11-191 (194)
94 TIGR02952 Sig70_famx2 RNA poly 99.8 8E-19 1.7E-23 187.8 18.2 168 1178-1417 2-169 (170)
95 PRK09652 RNA polymerase sigma 99.8 1E-18 2.2E-23 189.1 19.0 175 1179-1418 2-176 (182)
96 PRK11923 algU RNA polymerase s 99.8 1.8E-18 4E-23 189.1 20.9 184 1170-1419 3-187 (193)
97 PRK05602 RNA polymerase sigma 99.8 1.3E-18 2.9E-23 189.0 19.5 173 383-630 6-178 (186)
98 TIGR02859 spore_sigH RNA polym 99.8 1.5E-18 3.3E-23 190.5 19.4 190 384-628 6-197 (198)
99 PRK12514 RNA polymerase sigma 99.8 1.4E-18 3E-23 187.6 18.5 174 1172-1418 4-177 (179)
100 PRK11923 algU RNA polymerase s 99.8 2.7E-18 5.8E-23 187.8 20.6 190 379-634 2-192 (193)
101 PRK13919 putative RNA polymera 99.8 1.4E-18 3.1E-23 188.8 18.2 177 1171-1418 7-183 (186)
102 PRK06811 RNA polymerase factor 99.8 1.9E-18 4.2E-23 188.1 19.3 172 1175-1419 6-180 (189)
103 PRK12524 RNA polymerase sigma 99.8 2E-18 4.3E-23 189.1 19.3 175 1173-1420 12-186 (196)
104 PRK12542 RNA polymerase sigma 99.8 6.9E-19 1.5E-23 191.0 15.0 181 1181-1431 3-183 (185)
105 PRK09652 RNA polymerase sigma 99.8 2.2E-18 4.8E-23 186.4 18.7 179 389-632 2-180 (182)
106 PRK12538 RNA polymerase sigma 99.8 2.1E-18 4.6E-23 193.0 18.6 173 1174-1421 50-222 (233)
107 PRK11922 RNA polymerase sigma 99.8 2.2E-18 4.7E-23 193.5 18.8 189 1168-1420 11-199 (231)
108 PRK12519 RNA polymerase sigma 99.8 2.7E-18 5.9E-23 187.9 19.0 184 378-632 10-193 (194)
109 TIGR02939 RpoE_Sigma70 RNA pol 99.8 4E-18 8.7E-23 185.9 19.8 180 1175-1419 8-187 (190)
110 TIGR02948 SigW_bacill RNA poly 99.8 3.7E-18 8.1E-23 185.6 19.4 180 385-629 6-185 (187)
111 PRK12537 RNA polymerase sigma 99.8 3.5E-18 7.7E-23 184.9 18.4 173 1173-1418 9-181 (182)
112 PRK06759 RNA polymerase factor 99.8 2.6E-18 5.7E-23 180.7 17.0 150 1190-1417 4-153 (154)
113 PRK09641 RNA polymerase sigma 99.8 5.9E-18 1.3E-22 184.1 19.8 181 384-629 5-185 (187)
114 PRK12513 RNA polymerase sigma 99.8 4.1E-18 8.9E-23 186.5 18.5 178 382-629 11-188 (194)
115 PRK12534 RNA polymerase sigma 99.8 3.4E-18 7.3E-23 186.0 17.6 176 1172-1418 10-185 (187)
116 PRK12526 RNA polymerase sigma 99.8 5.5E-18 1.2E-22 186.9 19.1 179 1174-1420 25-203 (206)
117 TIGR02952 Sig70_famx2 RNA poly 99.8 6.6E-18 1.4E-22 180.7 18.2 169 387-627 1-169 (170)
118 PRK13919 putative RNA polymera 99.8 6.3E-18 1.4E-22 183.7 18.2 180 379-629 5-184 (186)
119 PRK12531 RNA polymerase sigma 99.8 5.2E-18 1.1E-22 185.5 17.6 182 1172-1422 12-193 (194)
120 PRK09643 RNA polymerase sigma 99.8 9.7E-18 2.1E-22 182.9 18.9 173 1170-1418 10-182 (192)
121 TIGR02984 Sig-70_plancto1 RNA 99.8 9.3E-18 2E-22 182.9 18.7 180 1183-1418 3-188 (189)
122 PRK12514 RNA polymerase sigma 99.8 1.2E-17 2.7E-22 180.2 19.2 176 381-629 3-178 (179)
123 PRK12524 RNA polymerase sigma 99.8 1.5E-17 3.2E-22 182.3 19.9 176 382-630 11-186 (196)
124 PRK11924 RNA polymerase sigma 99.8 1.3E-17 2.9E-22 179.8 19.3 174 1176-1420 2-175 (179)
125 PRK09640 RNA polymerase sigma 99.8 4.2E-18 9.1E-23 185.3 15.4 170 1174-1418 10-182 (188)
126 PRK11922 RNA polymerase sigma 99.8 1.3E-17 2.8E-22 187.2 19.4 190 377-630 10-199 (231)
127 PRK12538 RNA polymerase sigma 99.8 1.7E-17 3.8E-22 185.6 19.7 173 384-631 50-222 (233)
128 PRK12515 RNA polymerase sigma 99.8 1.9E-17 4.1E-22 180.4 19.0 174 1174-1421 9-182 (189)
129 TIGR02939 RpoE_Sigma70 RNA pol 99.8 2.1E-17 4.5E-22 180.3 19.4 182 384-630 7-188 (190)
130 PRK06811 RNA polymerase factor 99.8 2.2E-17 4.7E-22 179.8 19.2 170 385-627 6-178 (189)
131 PRK12537 RNA polymerase sigma 99.8 2.4E-17 5.3E-22 178.3 18.9 174 382-628 8-181 (182)
132 PRK12543 RNA polymerase sigma 99.8 1.8E-17 4E-22 178.8 17.8 167 1182-1421 2-168 (179)
133 TIGR03001 Sig-70_gmx1 RNA poly 99.8 3.5E-17 7.6E-22 184.0 20.4 181 1174-1426 26-217 (244)
134 PRK09649 RNA polymerase sigma 99.7 2.2E-17 4.8E-22 179.0 17.5 173 1168-1417 5-177 (185)
135 PRK12526 RNA polymerase sigma 99.7 4.4E-17 9.5E-22 179.8 20.0 179 383-629 24-202 (206)
136 PRK12536 RNA polymerase sigma 99.7 1.9E-17 4.2E-22 179.0 16.8 172 1172-1419 6-178 (181)
137 PRK12534 RNA polymerase sigma 99.7 3.1E-17 6.7E-22 178.4 18.3 178 381-629 9-186 (187)
138 PRK12539 RNA polymerase sigma 99.7 3.8E-17 8.3E-22 177.1 18.8 171 1173-1420 7-181 (184)
139 PRK12522 RNA polymerase sigma 99.7 2.7E-17 5.9E-22 176.5 17.3 165 1190-1418 3-167 (173)
140 PRK12520 RNA polymerase sigma 99.7 2.6E-17 5.7E-22 179.6 17.4 181 1191-1422 3-183 (191)
141 TIGR02954 Sig70_famx3 RNA poly 99.7 3.2E-17 6.8E-22 175.3 17.5 164 1175-1418 4-167 (169)
142 PRK06759 RNA polymerase factor 99.7 2.4E-17 5.2E-22 173.4 16.2 150 400-627 4-153 (154)
143 PRK09640 RNA polymerase sigma 99.7 1.8E-17 4E-22 180.3 15.7 174 384-632 10-186 (188)
144 PRK09643 RNA polymerase sigma 99.7 6.6E-17 1.4E-21 176.4 19.8 177 379-631 9-185 (192)
145 PRK09638 RNA polymerase sigma 99.7 2.3E-17 4.9E-22 177.7 15.8 170 1174-1418 5-174 (176)
146 PRK09645 RNA polymerase sigma 99.7 3.7E-17 8E-22 175.5 16.9 158 1191-1419 10-167 (173)
147 PRK12529 RNA polymerase sigma 99.7 2.6E-17 5.6E-22 177.4 15.6 166 1181-1417 7-174 (178)
148 PRK11924 RNA polymerase sigma 99.7 1E-16 2.2E-21 172.9 20.0 173 386-629 2-174 (179)
149 PRK09415 RNA polymerase factor 99.7 5.5E-17 1.2E-21 175.0 17.3 162 1189-1419 15-176 (179)
150 TIGR02984 Sig-70_plancto1 RNA 99.7 7.7E-17 1.7E-21 175.7 18.6 181 392-628 2-188 (189)
151 PRK12512 RNA polymerase sigma 99.7 7.3E-17 1.6E-21 175.0 18.0 172 1172-1421 7-182 (184)
152 TIGR02999 Sig-70_X6 RNA polyme 99.7 5.8E-17 1.2E-21 175.7 17.1 172 1174-1417 4-181 (183)
153 PRK12531 RNA polymerase sigma 99.7 8.3E-17 1.8E-21 176.0 18.4 180 381-629 11-190 (194)
154 TIGR02989 Sig-70_gvs1 RNA poly 99.7 4.2E-17 9E-22 172.5 15.5 157 1191-1417 2-158 (159)
155 PRK12542 RNA polymerase sigma 99.7 2.9E-17 6.2E-22 178.3 14.5 170 391-630 3-172 (185)
156 PRK12533 RNA polymerase sigma 99.7 9.1E-17 2E-21 177.5 18.4 168 1190-1421 18-185 (216)
157 PRK12518 RNA polymerase sigma 99.7 4.5E-17 9.8E-22 175.2 15.3 169 1178-1420 2-170 (175)
158 PRK12535 RNA polymerase sigma 99.7 1.2E-16 2.5E-21 174.7 18.5 179 1166-1419 4-182 (196)
159 PRK12543 RNA polymerase sigma 99.7 1.1E-16 2.5E-21 172.6 18.1 166 392-630 2-167 (179)
160 TIGR02985 Sig70_bacteroi1 RNA 99.7 5E-17 1.1E-21 172.1 15.0 159 1191-1417 2-160 (161)
161 PRK12515 RNA polymerase sigma 99.7 2E-16 4.3E-21 172.3 19.9 173 383-629 8-180 (189)
162 COG1595 RpoE DNA-directed RNA 99.7 1.9E-16 4.1E-21 171.3 18.8 170 1180-1420 8-177 (182)
163 TIGR02947 SigH_actino RNA poly 99.7 7E-17 1.5E-21 176.5 14.9 170 1190-1419 11-180 (193)
164 PRK12536 RNA polymerase sigma 99.7 1.6E-16 3.4E-21 171.8 17.3 173 381-629 5-178 (181)
165 PRK12522 RNA polymerase sigma 99.7 2E-16 4.2E-21 169.9 17.5 169 400-632 3-171 (173)
166 PF08275 Toprim_N: DNA primase 99.7 1.5E-18 3.3E-23 174.4 1.1 93 631-723 1-128 (128)
167 PRK09647 RNA polymerase sigma 99.7 2.3E-16 5E-21 173.1 18.4 162 1189-1420 27-188 (203)
168 PRK09642 RNA polymerase sigma 99.7 1E-16 2.2E-21 169.8 15.1 155 1197-1420 2-156 (160)
169 PRK08241 RNA polymerase factor 99.7 2.9E-16 6.4E-21 187.1 20.7 183 1174-1417 6-200 (339)
170 PRK12523 RNA polymerase sigma 99.7 7.4E-17 1.6E-21 173.0 13.9 164 1182-1419 5-168 (172)
171 PRK12539 RNA polymerase sigma 99.7 3.8E-16 8.2E-21 169.4 19.3 171 382-629 6-180 (184)
172 PRK09649 RNA polymerase sigma 99.7 2.2E-16 4.7E-21 171.3 17.3 174 378-628 5-178 (185)
173 PRK09638 RNA polymerase sigma 99.7 1.6E-16 3.5E-21 171.0 16.2 170 384-628 5-174 (176)
174 TIGR02954 Sig70_famx3 RNA poly 99.7 2.9E-16 6.2E-21 167.9 17.7 165 385-629 4-168 (169)
175 TIGR03001 Sig-70_gmx1 RNA poly 99.7 6.5E-16 1.4E-20 173.8 21.3 183 383-637 25-218 (244)
176 PRK12528 RNA polymerase sigma 99.7 2.2E-16 4.9E-21 167.3 16.6 157 1190-1417 4-160 (161)
177 TIGR02937 sigma70-ECF RNA poly 99.7 2.6E-16 5.6E-21 164.9 16.9 156 1191-1417 2-157 (158)
178 PRK12516 RNA polymerase sigma 99.7 2.3E-16 5E-21 171.1 16.7 159 1190-1422 10-168 (187)
179 TIGR02943 Sig70_famx1 RNA poly 99.7 3.4E-16 7.3E-21 170.1 18.0 177 1194-1421 6-182 (188)
180 PRK09644 RNA polymerase sigma 99.7 2.4E-16 5.3E-21 167.8 16.4 157 1192-1421 3-159 (165)
181 PRK09639 RNA polymerase sigma 99.7 3.1E-16 6.7E-21 167.2 17.2 158 1190-1419 3-160 (166)
182 PRK12529 RNA polymerase sigma 99.7 1.6E-16 3.5E-21 171.2 15.0 168 390-628 6-175 (178)
183 PRK12512 RNA polymerase sigma 99.7 5E-16 1.1E-20 168.5 18.6 170 382-629 7-180 (184)
184 TIGR02999 Sig-70_X6 RNA polyme 99.7 3.8E-16 8.3E-21 169.2 17.6 174 383-628 3-182 (183)
185 PRK12520 RNA polymerase sigma 99.7 4.7E-16 1E-20 169.7 18.0 179 401-630 3-181 (191)
186 TIGR02983 SigE-fam_strep RNA p 99.7 2.4E-16 5.1E-21 167.3 15.1 158 1183-1419 2-159 (162)
187 PRK12530 RNA polymerase sigma 99.7 4.4E-16 9.6E-21 169.5 17.4 174 1193-1419 10-183 (189)
188 PRK09645 RNA polymerase sigma 99.7 5.6E-16 1.2E-20 166.3 17.8 162 394-629 6-167 (173)
189 PRK09415 RNA polymerase factor 99.7 5.5E-16 1.2E-20 167.3 17.8 162 400-630 16-177 (179)
190 PRK12544 RNA polymerase sigma 99.7 4.2E-16 9.2E-21 171.5 17.0 177 1194-1420 22-198 (206)
191 PRK12545 RNA polymerase sigma 99.7 4.8E-16 1E-20 170.8 17.3 180 1194-1422 12-191 (201)
192 PRK12533 RNA polymerase sigma 99.7 5.9E-16 1.3E-20 171.1 18.0 178 401-642 19-196 (216)
193 PRK12518 RNA polymerase sigma 99.7 3.6E-16 7.9E-21 168.2 15.9 169 388-630 2-170 (175)
194 PRK12532 RNA polymerase sigma 99.7 4.7E-16 1E-20 170.3 16.9 180 1193-1422 8-188 (195)
195 PRK12547 RNA polymerase sigma 99.7 6.3E-16 1.4E-20 164.3 17.3 156 1190-1419 6-161 (164)
196 PRK12541 RNA polymerase sigma 99.7 6.1E-16 1.3E-20 164.0 17.1 154 1191-1417 6-159 (161)
197 PRK12535 RNA polymerase sigma 99.7 7.9E-16 1.7E-20 168.2 18.4 180 377-631 5-184 (196)
198 TIGR02960 SigX5 RNA polymerase 99.7 7.2E-16 1.6E-20 182.7 19.3 182 1184-1419 2-191 (324)
199 COG1595 RpoE DNA-directed RNA 99.7 1.2E-15 2.7E-20 165.0 19.4 172 388-630 6-177 (182)
200 TIGR02947 SigH_actino RNA poly 99.7 5.2E-16 1.1E-20 169.6 15.8 178 392-632 6-183 (193)
201 TIGR02985 Sig70_bacteroi1 RNA 99.7 5.8E-16 1.3E-20 163.9 15.6 159 401-627 2-160 (161)
202 TIGR02989 Sig-70_gvs1 RNA poly 99.7 4.7E-16 1E-20 164.5 14.6 157 401-627 2-158 (159)
203 PRK12540 RNA polymerase sigma 99.7 8.1E-16 1.8E-20 166.1 16.4 160 1190-1423 5-164 (182)
204 TIGR02895 spore_sigI RNA polym 99.7 1.9E-15 4.1E-20 165.1 18.8 118 1180-1301 3-125 (218)
205 PRK09647 RNA polymerase sigma 99.7 2.2E-15 4.7E-20 165.5 19.0 166 393-631 24-189 (203)
206 TIGR02937 sigma70-ECF RNA poly 99.7 1.6E-15 3.4E-20 159.0 16.6 156 401-627 2-157 (158)
207 PRK09637 RNA polymerase sigma 99.7 1.9E-15 4.1E-20 163.2 17.2 153 1192-1419 3-155 (181)
208 PRK12523 RNA polymerase sigma 99.7 1.2E-15 2.6E-20 163.6 15.5 164 392-629 5-168 (172)
209 PRK09639 RNA polymerase sigma 99.7 2.5E-15 5.4E-20 160.2 17.9 160 400-631 3-162 (166)
210 PRK09642 RNA polymerase sigma 99.7 1.6E-15 3.5E-20 160.6 15.7 154 407-629 2-155 (160)
211 PRK12527 RNA polymerase sigma 99.6 2.1E-15 4.5E-20 159.6 15.9 154 1196-1419 1-154 (159)
212 PRK08241 RNA polymerase factor 99.6 4.3E-15 9.3E-20 177.1 20.3 182 384-626 6-199 (339)
213 PRK07037 extracytoplasmic-func 99.6 3.1E-15 6.8E-20 158.9 17.1 158 1194-1420 2-159 (163)
214 PRK12530 RNA polymerase sigma 99.6 4.2E-15 9E-20 161.8 18.3 174 404-630 11-184 (189)
215 PRK09651 RNA polymerase sigma 99.6 2.7E-15 5.8E-20 160.8 16.4 158 1189-1417 9-166 (172)
216 PRK12532 RNA polymerase sigma 99.6 3.4E-15 7.4E-20 163.5 17.6 183 403-635 8-191 (195)
217 PRK12528 RNA polymerase sigma 99.6 2.6E-15 5.7E-20 159.1 16.2 157 400-627 4-160 (161)
218 PRK09644 RNA polymerase sigma 99.6 3.4E-15 7.3E-20 159.0 16.9 156 402-630 3-158 (165)
219 TIGR02950 SigM_subfam RNA poly 99.6 9E-16 1.9E-20 161.4 12.3 152 1196-1417 1-152 (154)
220 TIGR02895 spore_sigI RNA polym 99.6 4.8E-15 1E-19 162.0 18.2 119 389-511 2-125 (218)
221 PRK12516 RNA polymerase sigma 99.6 4.3E-15 9.4E-20 161.2 17.8 156 401-630 11-166 (187)
222 PRK12511 RNA polymerase sigma 99.6 2.2E-15 4.8E-20 162.6 15.2 156 1191-1419 5-160 (182)
223 TIGR02943 Sig70_famx1 RNA poly 99.6 5.1E-15 1.1E-19 160.9 18.1 176 404-630 6-181 (188)
224 PRK12517 RNA polymerase sigma 99.6 2.9E-15 6.3E-20 162.8 16.0 157 1190-1421 23-179 (188)
225 TIGR02983 SigE-fam_strep RNA p 99.6 3E-15 6.5E-20 158.9 15.4 158 393-629 2-159 (162)
226 PRK12546 RNA polymerase sigma 99.6 4.8E-15 1E-19 160.8 16.9 155 1191-1420 9-163 (188)
227 PRK12544 RNA polymerase sigma 99.6 7.3E-15 1.6E-19 161.7 17.9 178 403-630 21-198 (206)
228 PRK12547 RNA polymerase sigma 99.6 1E-14 2.2E-19 155.1 18.0 156 400-629 6-161 (164)
229 TIGR02959 SigZ RNA polymerase 99.6 5.6E-15 1.2E-19 158.0 16.0 148 1197-1419 2-149 (170)
230 PRK12541 RNA polymerase sigma 99.6 8.1E-15 1.8E-19 155.4 17.0 154 401-627 6-159 (161)
231 TIGR02960 SigX5 RNA polymerase 99.6 8.1E-15 1.8E-19 173.8 18.9 184 394-631 2-193 (324)
232 PRK12545 RNA polymerase sigma 99.6 1E-14 2.2E-19 160.3 18.1 178 404-630 12-189 (201)
233 PRK12525 RNA polymerase sigma 99.6 6.5E-15 1.4E-19 157.2 15.8 158 1190-1418 9-166 (168)
234 PRK09637 RNA polymerase sigma 99.6 2E-14 4.3E-19 155.2 18.1 159 402-635 3-161 (181)
235 PRK12527 RNA polymerase sigma 99.6 1.4E-14 3.1E-19 153.2 16.4 154 407-630 2-155 (159)
236 PRK12540 RNA polymerase sigma 99.6 2.2E-14 4.8E-19 155.0 17.4 159 400-632 5-163 (182)
237 TIGR02950 SigM_subfam RNA poly 99.6 7.8E-15 1.7E-19 154.3 12.5 152 407-628 2-153 (154)
238 PRK09651 RNA polymerase sigma 99.6 2.8E-14 6.2E-19 152.9 16.9 160 400-630 10-169 (172)
239 PRK07037 extracytoplasmic-func 99.6 3.7E-14 8E-19 150.7 17.6 158 404-630 2-159 (163)
240 PRK12517 RNA polymerase sigma 99.6 3E-14 6.6E-19 154.8 16.7 157 401-632 24-180 (188)
241 PRK09636 RNA polymerase sigma 99.6 3.1E-14 6.7E-19 165.9 17.3 159 1191-1419 5-164 (293)
242 PRK12511 RNA polymerase sigma 99.6 2.9E-14 6.3E-19 154.0 15.6 156 401-629 5-160 (182)
243 TIGR02959 SigZ RNA polymerase 99.6 4.6E-14 1E-18 150.9 16.9 149 407-630 2-150 (170)
244 PRK12546 RNA polymerase sigma 99.6 4.9E-14 1.1E-18 152.9 17.0 156 401-631 9-164 (188)
245 PRK09047 RNA polymerase factor 99.6 2.8E-14 6E-19 151.3 14.6 154 1212-1421 2-157 (161)
246 PRK06704 RNA polymerase factor 99.6 4.4E-14 9.4E-19 156.4 15.8 159 1177-1420 8-166 (228)
247 PRK12525 RNA polymerase sigma 99.6 5.4E-14 1.2E-18 150.2 15.5 158 401-629 10-167 (168)
248 PRK09635 sigI RNA polymerase s 99.5 6.9E-14 1.5E-18 161.5 17.0 160 1190-1417 5-165 (290)
249 TIGR02957 SigX4 RNA polymerase 99.5 1.3E-13 2.8E-18 159.4 17.1 155 1194-1418 1-156 (281)
250 PRK09047 RNA polymerase factor 99.5 3.4E-13 7.3E-18 143.0 15.4 152 423-630 3-156 (161)
251 PRK09636 RNA polymerase sigma 99.5 4E-13 8.7E-18 156.6 17.3 158 401-628 5-163 (293)
252 PRK06704 RNA polymerase factor 99.5 4.2E-13 9E-18 148.6 16.2 159 386-629 7-165 (228)
253 PRK09635 sigI RNA polymerase s 99.5 8.2E-13 1.8E-17 152.6 16.9 161 400-628 5-166 (290)
254 TIGR02957 SigX4 RNA polymerase 99.4 1.4E-12 3E-17 150.9 16.8 155 404-628 1-156 (281)
255 TIGR03209 P21_Cbot clostridium 99.4 2.6E-12 5.6E-17 133.2 13.4 138 1192-1404 1-141 (142)
256 PF03979 Sigma70_r1_1: Sigma-7 99.3 9.4E-13 2E-17 121.6 4.8 63 39-101 5-67 (82)
257 TIGR03209 P21_Cbot clostridium 99.3 1.5E-11 3.3E-16 127.4 13.2 138 402-614 1-141 (142)
258 PRK08311 putative RNA polymera 99.3 6.6E-11 1.4E-15 131.8 18.2 93 1173-1268 4-98 (237)
259 PRK09191 two-component respons 99.3 1.6E-11 3.4E-16 141.0 13.1 136 1191-1419 2-137 (261)
260 PF07638 Sigma70_ECF: ECF sigm 99.3 1.3E-10 2.9E-15 125.8 17.1 176 1173-1418 3-183 (185)
261 PRK08311 putative RNA polymera 99.2 4.1E-10 8.8E-15 125.6 17.9 92 383-477 4-97 (237)
262 PF07638 Sigma70_ECF: ECF sigm 99.2 3.9E-10 8.4E-15 122.2 17.3 177 383-629 3-184 (185)
263 PRK09191 two-component respons 99.2 1.8E-10 3.8E-15 132.3 12.7 135 401-628 2-136 (261)
264 PF04542 Sigma70_r2: Sigma-70 99.0 5.9E-10 1.3E-14 100.6 7.4 70 1195-1264 1-70 (71)
265 PF13155 Toprim_2: Toprim-like 99.0 4.6E-10 9.9E-15 108.0 6.9 68 733-800 1-96 (96)
266 TIGR02760 TraI_TIGR conjugativ 99.0 7.9E-10 1.7E-14 154.9 12.0 164 623-810 1667-1871(1960)
267 PF04545 Sigma70_r4: Sigma-70, 99.0 7.2E-10 1.6E-14 92.6 6.3 50 1363-1416 1-50 (50)
268 PF04539 Sigma70_r3: Sigma-70 99.0 7.8E-10 1.7E-14 102.0 7.0 78 1274-1351 1-78 (78)
269 PF04542 Sigma70_r2: Sigma-70 99.0 9.5E-10 2.1E-14 99.2 7.3 70 405-474 1-70 (71)
270 PF04539 Sigma70_r3: Sigma-70 99.0 1.1E-09 2.3E-14 101.1 7.0 78 484-561 1-78 (78)
271 PF03979 Sigma70_r1_1: Sigma-7 98.9 5.9E-10 1.3E-14 103.1 4.6 64 828-891 4-67 (82)
272 PRK04031 DNA primase; Provisio 98.9 1.2E-09 2.7E-14 125.8 7.1 85 720-811 160-263 (408)
273 PHA02415 DNA primase domain-co 98.9 5.2E-09 1.1E-13 127.7 10.4 172 638-810 120-346 (930)
274 PF00140 Sigma70_r1_2: Sigma-7 98.8 9.2E-10 2E-14 84.8 1.6 35 129-163 1-35 (37)
275 PF00140 Sigma70_r1_2: Sigma-7 98.8 9.2E-10 2E-14 84.8 1.2 35 919-953 1-35 (37)
276 cd03364 TOPRIM_DnaG_primases T 98.8 1.1E-08 2.4E-13 94.5 7.4 57 730-789 1-78 (79)
277 PF04545 Sigma70_r4: Sigma-70, 98.8 1E-08 2.3E-13 85.6 6.4 50 573-626 1-50 (50)
278 PF13662 Toprim_4: Toprim doma 98.7 1.4E-08 3E-13 94.3 5.4 52 730-781 1-76 (81)
279 PF08281 Sigma70_r4_2: Sigma-7 98.7 5.6E-08 1.2E-12 82.7 7.2 54 1357-1414 1-54 (54)
280 PF13362 Toprim_3: Toprim doma 98.5 3E-07 6.6E-12 88.4 8.0 73 731-806 1-96 (96)
281 PF08281 Sigma70_r4_2: Sigma-7 98.5 3.9E-07 8.4E-12 77.5 7.1 54 567-624 1-54 (54)
282 cd01027 TOPRIM_RNase_M5_like T 98.4 3.8E-07 8.3E-12 84.0 6.1 48 730-777 2-71 (81)
283 cd01029 TOPRIM_primases TOPRIM 98.4 6.5E-07 1.4E-11 82.7 7.1 52 730-781 1-73 (79)
284 PRK06930 positive control sigm 98.3 2.4E-06 5.3E-11 90.5 8.6 71 1347-1421 95-165 (170)
285 PRK06930 positive control sigm 98.1 1E-05 2.2E-10 85.8 9.4 70 557-630 95-164 (170)
286 PRK00118 putative DNA-binding 98.1 1.1E-05 2.4E-10 77.3 8.1 63 1356-1422 7-69 (104)
287 smart00493 TOPRIM topoisomeras 98.1 6E-06 1.3E-10 75.6 6.1 49 730-778 1-74 (76)
288 cd06171 Sigma70_r4 Sigma70, re 97.9 3.7E-05 8E-10 64.8 6.9 54 1358-1415 2-55 (55)
289 PRK00118 putative DNA-binding 97.9 8.7E-05 1.9E-09 71.2 9.7 66 566-635 7-74 (104)
290 TIGR00721 tfx DNA-binding prot 97.6 9.5E-05 2.1E-09 74.6 6.6 58 1365-1427 5-62 (137)
291 PRK04217 hypothetical protein; 97.6 8.4E-05 1.8E-09 72.1 5.6 61 1364-1428 40-100 (110)
292 PRK07078 hypothetical protein; 97.6 0.00014 3.1E-09 93.8 9.2 86 712-804 177-288 (759)
293 PRK03975 tfx putative transcri 97.6 0.00013 2.8E-09 74.1 6.8 51 1365-1420 5-55 (141)
294 PF04297 UPF0122: Putative hel 97.6 0.00028 6E-09 67.0 8.1 48 1366-1417 17-64 (101)
295 cd06171 Sigma70_r4 Sigma70, re 97.5 0.00022 4.8E-09 60.0 6.3 54 568-625 2-55 (55)
296 PF12965 DUF3854: Domain of un 97.5 0.00031 6.6E-09 71.0 8.1 76 730-808 11-130 (130)
297 PF04967 HTH_10: HTH DNA bindi 97.4 0.00047 1E-08 57.6 6.7 48 1367-1414 1-51 (53)
298 smart00421 HTH_LUXR helix_turn 97.2 0.0007 1.5E-08 57.8 6.3 51 1365-1420 2-52 (58)
299 PRK03975 tfx putative transcri 97.2 0.00076 1.6E-08 68.6 6.9 51 575-630 5-55 (141)
300 TIGR01636 phage_rinA phage tra 97.2 0.00098 2.1E-08 68.1 7.8 61 1355-1417 71-131 (134)
301 TIGR03879 near_KaiC_dom probab 97.2 0.00072 1.6E-08 60.2 5.8 47 1359-1409 8-55 (73)
302 PF04297 UPF0122: Putative hel 97.2 0.0016 3.5E-08 61.9 8.4 54 570-627 10-64 (101)
303 PRK04217 hypothetical protein; 97.2 0.00087 1.9E-08 65.1 6.7 55 574-632 40-94 (110)
304 PF07374 DUF1492: Protein of u 97.0 0.0024 5.3E-08 61.7 8.2 55 1356-1414 44-99 (100)
305 TIGR01636 phage_rinA phage tra 97.0 0.0023 4.9E-08 65.4 8.3 62 565-628 71-132 (134)
306 cd06170 LuxR_C_like C-terminal 97.0 0.0022 4.8E-08 54.7 7.0 50 1367-1421 1-50 (57)
307 TIGR01321 TrpR trp operon repr 96.9 0.0014 3.1E-08 61.2 5.6 68 567-635 22-93 (94)
308 TIGR00721 tfx DNA-binding prot 96.9 0.0016 3.5E-08 65.9 6.4 48 576-628 6-53 (137)
309 PF00196 GerE: Bacterial regul 96.9 0.0028 6E-08 54.7 6.4 53 1365-1422 2-54 (58)
310 cd00188 TOPRIM Topoisomerase-p 96.8 0.0036 7.7E-08 57.4 7.1 48 730-777 1-73 (83)
311 PF04967 HTH_10: HTH DNA bindi 96.8 0.004 8.7E-08 52.1 6.2 49 577-625 1-52 (53)
312 TIGR03879 near_KaiC_dom probab 96.7 0.0028 6.1E-08 56.5 5.4 47 569-619 8-55 (73)
313 PRK15201 fimbriae regulatory p 96.7 0.0039 8.4E-08 64.5 6.9 53 1365-1422 132-184 (198)
314 COG4941 Predicted RNA polymera 96.7 0.034 7.4E-07 63.0 14.7 161 1192-1417 7-167 (415)
315 COG4566 TtrR Response regulato 96.7 0.0073 1.6E-07 63.4 8.8 69 1354-1427 130-198 (202)
316 PF07374 DUF1492: Protein of u 96.6 0.0068 1.5E-07 58.6 7.8 55 566-624 44-99 (100)
317 PRK01381 Trp operon repressor; 96.5 0.0042 9.1E-08 58.5 5.5 75 563-638 18-96 (99)
318 smart00421 HTH_LUXR helix_turn 96.5 0.0044 9.6E-08 52.8 5.4 46 575-625 2-47 (58)
319 PRK13719 conjugal transfer tra 96.4 0.0064 1.4E-07 66.0 7.1 59 1361-1424 138-196 (217)
320 PF00196 GerE: Bacterial regul 96.4 0.0061 1.3E-07 52.6 5.5 46 575-625 2-47 (58)
321 TIGR01321 TrpR trp operon repr 96.3 0.0059 1.3E-07 57.2 5.1 55 1357-1412 22-80 (94)
322 PRK15201 fimbriae regulatory p 96.2 0.007 1.5E-07 62.6 5.6 46 576-626 133-178 (198)
323 TIGR03020 EpsA transcriptional 96.1 0.01 2.2E-07 67.0 6.9 54 1364-1422 188-241 (247)
324 PRK15411 rcsA colanic acid cap 96.1 0.0085 1.8E-07 66.3 6.1 51 1366-1421 137-187 (207)
325 PF13936 HTH_38: Helix-turn-he 96.1 0.0081 1.7E-07 48.6 4.2 41 1365-1409 3-43 (44)
326 TIGR03541 reg_near_HchA LuxR f 96.1 0.01 2.2E-07 66.9 6.5 54 1364-1422 169-222 (232)
327 PRK11475 DNA-binding transcrip 96.0 0.013 2.8E-07 64.8 6.7 55 1364-1423 132-186 (207)
328 PRK10100 DNA-binding transcrip 96.0 0.014 3.1E-07 64.9 7.1 55 1364-1423 153-207 (216)
329 PF02001 DUF134: Protein of un 96.0 0.014 3E-07 56.3 5.8 49 1366-1418 41-89 (106)
330 COG2739 Uncharacterized protei 96.0 0.013 2.7E-07 54.8 5.3 46 1366-1415 17-62 (105)
331 PRK13719 conjugal transfer tra 95.9 0.01 2.2E-07 64.4 5.5 50 571-625 138-187 (217)
332 COG4566 TtrR Response regulato 95.9 0.024 5.2E-07 59.6 7.9 59 564-627 130-188 (202)
333 cd06170 LuxR_C_like C-terminal 95.9 0.015 3.3E-07 49.4 5.5 45 577-626 1-45 (57)
334 COG2771 CsgD DNA-binding HTH d 95.9 0.025 5.5E-07 49.6 7.0 57 1365-1426 3-59 (65)
335 COG3413 Predicted DNA binding 95.8 0.015 3.3E-07 64.7 6.7 51 1366-1416 155-208 (215)
336 PRK15411 rcsA colanic acid cap 95.8 0.012 2.6E-07 65.2 5.6 45 576-625 137-181 (207)
337 COG2197 CitB Response regulato 95.8 0.017 3.7E-07 64.0 6.7 56 1365-1425 147-202 (211)
338 PRK01381 Trp operon repressor; 95.7 0.017 3.7E-07 54.5 5.3 61 1352-1413 17-81 (99)
339 COG4941 Predicted RNA polymera 95.7 0.22 4.7E-06 56.8 14.6 187 404-664 9-202 (415)
340 TIGR01637 phage_arpU phage tra 95.7 0.087 1.9E-06 53.8 10.8 63 565-629 67-130 (132)
341 PRK10840 transcriptional regul 95.7 0.019 4.2E-07 63.8 6.6 54 1365-1423 149-202 (216)
342 PF02001 DUF134: Protein of un 95.7 0.025 5.3E-07 54.5 6.2 48 577-628 42-89 (106)
343 PRK11475 DNA-binding transcrip 95.6 0.016 3.4E-07 64.1 5.3 47 574-625 132-178 (207)
344 TIGR01637 phage_arpU phage tra 95.6 0.095 2.1E-06 53.5 10.6 61 1355-1417 67-128 (132)
345 PRK13870 transcriptional regul 95.5 0.024 5.1E-07 63.9 6.5 52 1366-1422 173-224 (234)
346 PRK10188 DNA-binding transcrip 95.3 0.032 7E-07 63.2 6.8 52 1366-1422 179-230 (240)
347 COG2197 CitB Response regulato 95.2 0.023 4.9E-07 63.1 5.2 46 575-625 147-192 (211)
348 PRK10840 transcriptional regul 95.2 0.025 5.4E-07 62.9 5.4 46 575-625 149-194 (216)
349 PF13936 HTH_38: Helix-turn-he 95.1 0.026 5.5E-07 45.7 3.7 41 575-619 3-43 (44)
350 COG1356 tfx Transcriptional re 95.1 0.014 3E-07 56.4 2.5 49 1367-1420 9-57 (143)
351 PRK15369 two component system 95.0 0.048 1.1E-06 59.2 7.1 55 1365-1424 148-202 (211)
352 PRK13870 transcriptional regul 94.9 0.035 7.6E-07 62.6 5.4 46 576-626 173-218 (234)
353 TIGR03020 EpsA transcriptional 94.8 0.042 9.1E-07 62.1 5.8 47 574-625 188-234 (247)
354 PRK10100 DNA-binding transcrip 94.8 0.041 9E-07 61.2 5.7 47 574-625 153-199 (216)
355 COG2771 CsgD DNA-binding HTH d 94.6 0.069 1.5E-06 46.9 5.6 48 575-627 3-50 (65)
356 TIGR03541 reg_near_HchA LuxR f 94.6 0.048 1E-06 61.5 5.6 48 574-626 169-216 (232)
357 PRK09390 fixJ response regulat 94.5 0.091 2E-06 56.7 7.5 61 1359-1424 134-194 (202)
358 COG1342 Predicted DNA-binding 94.4 0.091 2E-06 48.7 5.8 48 577-628 34-81 (99)
359 COG3413 Predicted DNA binding 94.4 0.081 1.8E-06 58.9 6.8 53 576-628 155-210 (215)
360 PRK04017 hypothetical protein; 94.4 0.078 1.7E-06 53.3 5.9 53 728-780 21-94 (132)
361 COG1342 Predicted DNA-binding 94.4 0.082 1.8E-06 49.0 5.4 48 1367-1418 34-81 (99)
362 COG1356 tfx Transcriptional re 94.3 0.029 6.3E-07 54.3 2.6 49 577-630 9-57 (143)
363 COG2739 Uncharacterized protei 94.3 0.09 1.9E-06 49.3 5.5 47 576-626 17-63 (105)
364 PRK10651 transcriptional regul 94.2 0.09 1.9E-06 57.6 6.8 55 1365-1424 154-208 (216)
365 PF12645 HTH_16: Helix-turn-he 94.2 0.13 2.9E-06 45.3 6.3 58 386-446 2-65 (65)
366 PRK09483 response regulator; P 94.2 0.079 1.7E-06 58.5 6.2 53 1365-1422 147-199 (217)
367 PRK10188 DNA-binding transcrip 94.0 0.077 1.7E-06 60.1 5.7 46 576-626 179-224 (240)
368 PRK15320 transcriptional activ 93.9 0.098 2.1E-06 55.1 5.7 50 1363-1417 161-210 (251)
369 PRK10360 DNA-binding transcrip 93.9 0.13 2.8E-06 55.8 7.1 60 1365-1429 136-195 (196)
370 PF12645 HTH_16: Helix-turn-he 93.5 0.23 4.9E-06 43.9 6.5 58 1176-1236 2-65 (65)
371 PRK09483 response regulator; P 93.3 0.11 2.4E-06 57.3 5.3 46 575-625 147-192 (217)
372 PF01751 Toprim: Toprim domain 93.1 0.24 5.1E-06 48.0 6.6 49 731-779 1-88 (100)
373 PRK15320 transcriptional activ 93.0 0.15 3.2E-06 53.8 5.2 47 574-625 162-208 (251)
374 PF05263 DUF722: Protein of un 92.9 0.33 7.1E-06 48.8 7.4 58 1356-1415 71-128 (130)
375 PF09862 DUF2089: Protein of u 92.6 0.26 5.7E-06 48.1 6.0 50 1363-1416 30-79 (113)
376 PRK10403 transcriptional regul 92.6 0.25 5.4E-06 54.0 6.9 60 1365-1429 152-211 (215)
377 PRK15369 two component system 92.5 0.19 4.1E-06 54.5 5.7 46 575-625 148-193 (211)
378 PF01726 LexA_DNA_bind: LexA D 92.4 0.2 4.3E-06 44.2 4.6 45 1364-1408 1-48 (65)
379 PRK13558 bacterio-opsin activa 91.8 0.27 5.9E-06 64.6 7.0 53 1363-1415 604-659 (665)
380 TIGR02531 yecD_yerC TrpR-relat 91.7 0.29 6.3E-06 45.9 5.0 42 1364-1412 34-75 (88)
381 PRK10651 transcriptional regul 91.1 0.28 6.1E-06 53.7 5.2 46 575-625 154-199 (216)
382 PRK15418 transcriptional regul 91.1 0.26 5.6E-06 58.2 5.0 37 1372-1412 19-55 (318)
383 PF13613 HTH_Tnp_4: Helix-turn 90.9 0.56 1.2E-05 39.6 5.5 47 1366-1416 2-49 (53)
384 PF13384 HTH_23: Homeodomain-l 90.7 0.22 4.9E-06 41.3 3.0 32 1374-1410 10-41 (50)
385 PF09862 DUF2089: Protein of u 90.5 0.54 1.2E-05 46.0 5.7 50 573-626 30-79 (113)
386 PRK09935 transcriptional regul 90.3 0.54 1.2E-05 51.3 6.5 53 1366-1423 149-201 (210)
387 PF05263 DUF722: Protein of un 90.3 0.83 1.8E-05 46.0 7.0 51 567-619 72-122 (130)
388 COG1658 Small primase-like pro 90.2 0.5 1.1E-05 47.3 5.4 47 729-775 9-79 (127)
389 PRK09390 fixJ response regulat 90.2 0.59 1.3E-05 50.3 6.6 53 569-626 134-186 (202)
390 PHA00675 hypothetical protein 90.1 0.57 1.2E-05 41.9 4.9 40 1365-1408 21-61 (78)
391 PF00325 Crp: Bacterial regula 89.9 0.37 8E-06 36.0 3.1 23 1387-1409 3-25 (32)
392 PRK14719 bifunctional RNAse/5- 89.9 0.33 7.2E-06 58.0 4.5 54 728-781 22-97 (360)
393 PRK09958 DNA-binding transcrip 89.4 0.77 1.7E-05 49.9 6.8 54 1364-1422 141-194 (204)
394 PRK04841 transcriptional regul 89.0 0.6 1.3E-05 63.8 6.8 55 1365-1424 837-891 (903)
395 PF02796 HTH_7: Helix-turn-hel 88.5 0.52 1.1E-05 38.3 3.4 33 1371-1408 11-43 (45)
396 PF04218 CENP-B_N: CENP-B N-te 88.1 0.55 1.2E-05 39.7 3.4 40 1366-1409 6-45 (53)
397 TIGR02531 yecD_yerC TrpR-relat 87.6 0.77 1.7E-05 43.1 4.4 36 574-615 34-69 (88)
398 cd00569 HTH_Hin_like Helix-tur 87.5 1 2.2E-05 33.9 4.5 36 1367-1406 6-41 (42)
399 PF13412 HTH_24: Winged helix- 87.3 1.4 3.1E-05 36.2 5.4 41 1367-1410 1-41 (48)
400 PRK13558 bacterio-opsin activa 86.5 1.2 2.7E-05 58.5 7.2 56 573-628 604-662 (665)
401 PF13613 HTH_Tnp_4: Helix-turn 86.5 1.5 3.3E-05 37.0 5.2 48 576-626 2-49 (53)
402 PF10668 Phage_terminase: Phag 86.4 1.1 2.4E-05 38.7 4.2 24 1386-1409 22-45 (60)
403 PHA02547 55 RNA polymerase sig 86.2 3.6 7.8E-05 42.7 8.6 70 1195-1264 42-114 (179)
404 TIGR00334 5S_RNA_mat_M5 ribonu 85.7 1.4 2.9E-05 46.6 5.5 38 730-767 3-63 (174)
405 PRK10403 transcriptional regul 85.7 1.1 2.4E-05 48.7 5.3 46 575-625 152-197 (215)
406 PHA02547 55 RNA polymerase sig 85.6 4.4 9.5E-05 42.1 8.8 67 408-474 45-114 (179)
407 PF13404 HTH_AsnC-type: AsnC-t 85.3 2.1 4.6E-05 34.3 5.2 39 1368-1409 2-40 (42)
408 PF06530 Phage_antitermQ: Phag 84.9 3.5 7.6E-05 41.7 7.8 52 1363-1418 59-110 (125)
409 PF00325 Crp: Bacterial regula 84.8 1.1 2.4E-05 33.5 3.1 26 597-626 3-28 (32)
410 PF01726 LexA_DNA_bind: LexA D 84.8 2.2 4.8E-05 37.7 5.6 41 1277-1317 9-50 (65)
411 PF03444 HrcA_DNA-bdg: Winged 84.7 2 4.3E-05 39.1 5.2 43 1366-1408 1-45 (78)
412 PRK10360 DNA-binding transcrip 84.7 1.5 3.3E-05 47.3 5.7 46 575-625 136-181 (196)
413 PRK09935 transcriptional regul 84.7 1.4 3E-05 48.0 5.4 45 576-625 149-193 (210)
414 COG2390 DeoR Transcriptional r 84.6 1.1 2.4E-05 52.6 4.8 36 1373-1412 17-52 (321)
415 PRK15418 transcriptional regul 84.6 1 2.3E-05 53.1 4.6 37 582-622 19-55 (318)
416 PRK09958 DNA-binding transcrip 84.2 1.6 3.4E-05 47.4 5.6 47 574-625 141-187 (204)
417 PF13518 HTH_28: Helix-turn-he 84.1 1.5 3.3E-05 36.4 4.2 33 1374-1411 5-37 (52)
418 PRK10430 DNA-binding transcrip 83.7 1.8 4E-05 48.8 6.0 47 1366-1412 158-204 (239)
419 COG4026 Uncharacterized protei 83.1 4.8 0.0001 43.2 8.1 78 730-810 8-118 (290)
420 PF01371 Trp_repressor: Trp re 83.0 2.8 6E-05 39.3 5.7 58 569-627 18-79 (87)
421 PRK04841 transcriptional regul 82.9 1.5 3.2E-05 60.0 5.7 46 575-625 837-882 (903)
422 PHA00675 hypothetical protein 82.6 2.1 4.6E-05 38.4 4.4 40 575-618 21-61 (78)
423 smart00351 PAX Paired Box doma 82.5 2.7 5.9E-05 42.4 6.0 42 1367-1412 18-59 (125)
424 PF08279 HTH_11: HTH domain; 82.5 2.3 5E-05 36.0 4.7 39 1370-1410 1-39 (55)
425 PF13384 HTH_23: Homeodomain-l 81.2 1.4 2.9E-05 36.6 2.7 31 584-619 10-40 (50)
426 PF06056 Terminase_5: Putative 81.0 2.8 6E-05 36.2 4.6 26 1386-1411 13-38 (58)
427 PF13730 HTH_36: Helix-turn-he 80.5 4.7 0.0001 34.1 5.8 47 1366-1416 2-51 (55)
428 PF02796 HTH_7: Helix-turn-hel 80.1 2.1 4.6E-05 34.8 3.4 36 577-617 6-42 (45)
429 PHA02591 hypothetical protein; 80.0 2 4.4E-05 38.4 3.4 23 1386-1408 59-81 (83)
430 COG2909 MalT ATP-dependent tra 79.2 2.5 5.3E-05 54.6 5.3 52 1366-1422 831-882 (894)
431 PF04218 CENP-B_N: CENP-B N-te 78.8 2.9 6.4E-05 35.3 4.0 40 576-619 6-45 (53)
432 PF06530 Phage_antitermQ: Phag 78.1 9.5 0.0002 38.6 8.1 51 574-628 60-110 (125)
433 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 77.8 4.7 0.0001 33.6 4.7 38 1366-1407 4-41 (50)
434 PF13412 HTH_24: Winged helix- 77.8 5.1 0.00011 32.8 5.1 40 577-619 1-40 (48)
435 COG2909 MalT ATP-dependent tra 77.8 2.6 5.6E-05 54.4 4.8 47 576-627 831-877 (894)
436 cd00569 HTH_Hin_like Helix-tur 76.9 4.5 9.8E-05 30.1 4.4 36 577-616 6-41 (42)
437 PRK10430 DNA-binding transcrip 76.3 4.1 8.8E-05 46.0 5.6 47 576-622 158-204 (239)
438 cd00131 PAX Paired Box domain 75.9 5.8 0.00013 40.3 6.0 42 1367-1412 18-59 (128)
439 PF13730 HTH_36: Helix-turn-he 75.9 7.4 0.00016 32.8 5.8 46 576-625 2-50 (55)
440 PF01371 Trp_repressor: Trp re 75.8 4.9 0.00011 37.7 4.9 48 1367-1415 27-77 (87)
441 smart00342 HTH_ARAC helix_turn 75.2 31 0.00067 31.1 10.3 25 1293-1317 1-25 (84)
442 PF10668 Phage_terminase: Phag 74.8 4.4 9.5E-05 35.1 3.9 37 581-619 9-45 (60)
443 PF02650 HTH_WhiA: WhiA C-term 74.8 7.1 0.00015 36.5 5.7 45 1364-1411 35-81 (85)
444 PRK12423 LexA repressor; Provi 74.2 4.7 0.0001 44.4 5.2 48 1365-1416 2-52 (202)
445 PRK11083 DNA-binding response 73.6 3.9 8.4E-05 45.1 4.5 50 1366-1416 154-208 (228)
446 cd01025 TOPRIM_recR TOPRIM_rec 73.5 11 0.00024 37.1 7.0 62 730-793 1-98 (112)
447 PF13011 LZ_Tnp_IS481: leucine 73.5 7.5 0.00016 36.2 5.4 45 1365-1412 7-51 (85)
448 PF13404 HTH_AsnC-type: AsnC-t 73.2 8 0.00017 31.0 4.9 38 579-619 3-40 (42)
449 PF01418 HTH_6: Helix-turn-hel 72.7 8.3 0.00018 35.3 5.6 53 1356-1408 3-56 (77)
450 PRK15479 transcriptional regul 72.0 5 0.00011 44.0 4.9 50 1366-1416 148-202 (221)
451 PRK10336 DNA-binding transcrip 72.0 4.5 9.9E-05 44.3 4.6 50 1366-1416 149-203 (219)
452 COG3593 Predicted ATP-dependen 72.0 3.6 7.7E-05 51.9 4.0 80 689-774 362-471 (581)
453 PF12802 MarR_2: MarR family; 71.9 7.5 0.00016 33.6 5.0 44 1366-1410 2-45 (62)
454 COG3415 Transposase and inacti 71.7 6.4 0.00014 40.3 5.0 36 1372-1411 11-46 (138)
455 PF01325 Fe_dep_repress: Iron 71.4 6.4 0.00014 34.2 4.3 46 1367-1416 2-48 (60)
456 PF01710 HTH_Tnp_IS630: Transp 71.4 29 0.00064 34.7 9.7 88 1251-1409 7-94 (119)
457 COG2973 TrpR Trp operon repres 71.1 13 0.00029 35.0 6.4 60 577-637 38-100 (103)
458 COG2390 DeoR Transcriptional r 71.1 4.5 9.8E-05 47.6 4.3 35 583-621 17-51 (321)
459 PF00356 LacI: Bacterial regul 70.6 4.1 8.9E-05 33.4 2.7 22 1388-1409 1-22 (46)
460 PF01325 Fe_dep_repress: Iron 70.4 8.2 0.00018 33.6 4.7 45 577-625 2-47 (60)
461 PF01022 HTH_5: Bacterial regu 69.1 9.5 0.00021 31.2 4.7 37 1369-1409 2-38 (47)
462 smart00550 Zalpha Z-DNA-bindin 69.1 9.5 0.00021 34.0 5.0 24 1386-1409 22-45 (68)
463 PF12840 HTH_20: Helix-turn-he 68.9 15 0.00032 31.9 6.1 42 1361-1408 4-46 (61)
464 smart00352 POU Found in Pit-Oc 68.5 17 0.00037 33.0 6.3 49 582-634 14-73 (75)
465 PF08279 HTH_11: HTH domain; 68.1 12 0.00027 31.5 5.4 36 580-617 1-36 (55)
466 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 67.6 10 0.00022 31.6 4.4 38 576-617 4-41 (50)
467 PRK10710 DNA-binding transcrip 67.5 6.7 0.00014 43.7 4.7 50 1366-1416 160-214 (240)
468 PF13518 HTH_28: Helix-turn-he 67.0 7.6 0.00017 32.2 3.8 22 598-619 14-35 (52)
469 TIGR02154 PhoB phosphate regul 67.0 3.4 7.5E-05 45.4 2.2 52 1366-1418 154-210 (226)
470 PF06056 Terminase_5: Putative 66.8 9 0.0002 33.1 4.2 25 596-620 13-37 (58)
471 cd04762 HTH_MerR-trunc Helix-T 66.6 5.2 0.00011 32.3 2.7 25 1387-1411 1-25 (49)
472 TIGR02787 codY_Gpos GTP-sensin 66.5 20 0.00044 39.9 7.8 56 1356-1415 166-223 (251)
473 TIGR00498 lexA SOS regulatory 66.0 8.9 0.00019 42.1 5.2 44 1365-1408 2-48 (199)
474 PRK00423 tfb transcription ini 65.6 1.2E+02 0.0025 36.0 14.6 32 1384-1415 274-305 (310)
475 TIGR01610 phage_O_Nterm phage 65.4 14 0.0003 35.4 5.7 49 1364-1416 20-73 (95)
476 TIGR03787 marine_sort_RR prote 65.3 7.8 0.00017 42.8 4.7 50 1366-1416 156-207 (227)
477 PF12728 HTH_17: Helix-turn-he 65.2 6.4 0.00014 32.7 3.0 24 1387-1410 2-25 (51)
478 PF09339 HTH_IclR: IclR helix- 64.5 9.2 0.0002 32.0 3.8 37 1372-1408 4-40 (52)
479 smart00351 PAX Paired Box doma 64.3 13 0.00028 37.6 5.5 40 577-620 18-57 (125)
480 PRK00423 tfb transcription ini 64.1 1.4E+02 0.003 35.3 15.0 54 407-465 123-176 (310)
481 PF13551 HTH_29: Winged helix- 63.6 14 0.0003 36.0 5.6 103 1281-1410 1-111 (112)
482 PRK10046 dpiA two-component re 63.0 6.8 0.00015 43.8 3.6 40 1365-1408 160-199 (225)
483 TIGR01764 excise DNA binding d 62.7 6.7 0.00015 31.8 2.6 24 1387-1410 2-25 (49)
484 PF00046 Homeobox: Homeobox do 62.5 10 0.00022 32.3 3.8 50 1366-1415 6-56 (57)
485 cd04761 HTH_MerR-SF Helix-Turn 62.5 5.5 0.00012 32.6 2.1 25 1387-1411 1-25 (49)
486 PF08822 DUF1804: Protein of u 62.2 15 0.00033 38.6 5.6 41 1368-1412 4-45 (165)
487 smart00342 HTH_ARAC helix_turn 62.2 71 0.0015 28.7 9.8 24 503-526 1-24 (84)
488 PF06971 Put_DNA-bind_N: Putat 62.1 15 0.00033 30.7 4.5 48 1267-1314 2-49 (50)
489 PF13542 HTH_Tnp_ISL3: Helix-t 61.6 17 0.00037 30.2 5.0 23 1388-1410 29-51 (52)
490 PF02650 HTH_WhiA: WhiA C-term 61.3 18 0.00039 33.9 5.4 44 573-619 34-79 (85)
491 PF13463 HTH_27: Winged helix 61.3 15 0.00032 32.3 4.8 42 1367-1410 1-42 (68)
492 TIGR02787 codY_Gpos GTP-sensin 61.1 31 0.00067 38.5 8.0 55 567-625 167-223 (251)
493 PF02954 HTH_8: Bacterial regu 61.0 12 0.00027 29.8 3.7 38 1369-1409 4-41 (42)
494 PF01418 HTH_6: Helix-turn-hel 60.8 27 0.00059 32.0 6.5 51 566-616 3-54 (77)
495 PF06971 Put_DNA-bind_N: Putat 60.7 19 0.00041 30.1 4.8 48 477-524 2-49 (50)
496 cd06571 Bac_DnaA_C C-terminal 60.5 21 0.00045 33.8 5.9 44 1369-1416 31-75 (90)
497 COG1476 Predicted transcriptio 60.4 13 0.00027 33.2 3.9 33 1373-1409 5-37 (68)
498 PF01978 TrmB: Sugar-specific 60.3 8.9 0.00019 34.0 3.2 41 1366-1409 5-45 (68)
499 COG3877 Uncharacterized protei 60.2 19 0.00041 34.4 5.2 49 1364-1416 39-87 (122)
500 PRK11083 DNA-binding response 60.2 11 0.00023 41.5 4.6 49 576-625 154-207 (228)
No 1
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=9.3e-110 Score=1048.44 Aligned_cols=601 Identities=56% Similarity=0.871 Sum_probs=543.5
Q ss_pred HHHHHHHHHHHHhccccCccchHHHhhhCCCCCCCHHHHHHHHHHHHhcCccccccccchhhhhccCCCC----CchhHH
Q psy15215 827 ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNITS----DDDVEE 902 (1432)
Q Consensus 827 ~~~~~~~~~Li~~gk~~g~lT~~ei~~~lp~~~~~~e~ie~i~~~l~~~gI~v~e~~~~~e~~~~~~~~~----de~~~e 902 (1432)
...++.++.||..||++|||||+|||++||++.++++++++++.+|+++||+|+|.+++.+.+.+++... +++..+
T Consensus 7 ~~~~~~~~~li~~~k~~g~~t~~ei~~~lp~d~~~~d~~~~~~~~~~~~gi~v~~~~~~~~~~~~~~~~~~~~~~~~~~~ 86 (619)
T PRK05658 7 DNPQSQLKKLIKRGKERGYLTYAELNDHLPEDIVDSEQIEDIIAMLNDMGIQVVEEAPDADDLLLAENEADAQTDEDAEE 86 (619)
T ss_pred hhhHHHHHHHHHhCcccCCccHHHHHHhCCCcCCCHHHHHHHHHHHHHcCceEEecCcchhhhcccccccccccchhhhh
Confidence 3344579999999999999999999999999999999999999999999999999998866554444221 333344
Q ss_pred HHHhhhccCCCCCCCCCChHHHHHHccCCccCCCchHHHHHHHHHHHhHHHHHHHHhhChHHHHHHHHHHHHhhhcccch
Q psy15215 903 ATEAALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKI 982 (1432)
Q Consensus 903 ~~~~~~~~~~~~~grt~DPVRmYLREMG~v~LLTREgEIeIAKRIE~G~~~v~~al~~~P~~v~~il~~~e~l~~ge~~l 982 (1432)
+++.+++.+++++|+|||||||||||||+||||||||||+||||||+|+++|+++||.||+++++|++|+++|.+|+++|
T Consensus 87 ~~~~~~~~~~~~~~rt~DPVRMYLREMG~V~LLTREgEIeIAKRIE~G~~~v~~al~~~P~~i~~il~~~e~v~~ge~rl 166 (619)
T PRK05658 87 EAAAALSSVESEIGRTDDPVRMYLREMGTVELLTREGEIEIAKRIEAGENIMIAALCESPLTIDAILEWYDRLENGERRL 166 (619)
T ss_pred hhHHhhcccccccCCCCChHHHHHHHhccCcCCCcHHHHHHHHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHhCCCcH
Confidence 45556667788899999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhccccCCCCCCchh-h--c-cCCCCCchhhhhhhccCCCCCHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHh--CC
Q psy15215 983 DEIVDGLIDKNFSSNNR-V--I-KGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKE--GY 1056 (1432)
Q Consensus 983 ~dii~g~~d~~~~~~~~-~--~-~~~~~~e~~~d~~~~~~~~~~~~~l~~l~~~~~~~f~~l~~~~~~~~~~~~~~--~~ 1056 (1432)
+|||+||.||+.+...+ . + ++.++++++++ ++.............+++.+.++|..|++.|.++.+++.++ |.
T Consensus 167 ~diI~~~~d~~~~~~~~~~~~e~~~~~~d~de~~-~e~~~~~~~~~~~~~~~~~v~~~~~~i~~~~~~~~~~~~k~~~g~ 245 (619)
T PRK05658 167 RELIDGFVDPNAEEDPAHVGSELEELDDDEDEEE-EEDENDDSLAADESELPEKVLEKFKALAKQYKKLRKAQEKKVEGR 245 (619)
T ss_pred HHHHhcccCCCccccccccccccccccccccccc-cccccccchhcccccCHHHHHHHHHHHHHHHHHHHHHHHhhcccc
Confidence 99999999886321110 0 0 00000000000 00000001111223456888999999999999999999998 88
Q ss_pred C--cHHHHHHHHHHHHHhhccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCChHHHHHhcCCCccchhhHHH
Q psy15215 1057 N--SESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDN 1134 (1432)
Q Consensus 1057 ~--~~~~~k~~~~i~~~l~~irl~~k~i~~l~~~l~~~~~~ir~~Er~i~~~~~~~~~m~r~~fl~~f~~~e~~~~wl~~ 1134 (1432)
. ++.+.+.+..|++.|++|+|++++|++|++.|+..+++|+.+|+.|++ |++++||||++|++.|+||++|..|+.+
T Consensus 246 ~~~~~~~~~~r~~i~~~l~~lkL~~k~id~Lv~~lr~~~~rIr~~Er~i~~-~~~~~~m~R~~Fi~~f~gnEt~~~w~~~ 324 (619)
T PRK05658 246 LAQHKKYAKLREKLKEELKSLRLTSKQIDELVEQLRDINKRVRGQERELLR-LVERLKMPRKDFLKLFQGNELDITWLEK 324 (619)
T ss_pred chhhHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHcCCCHHHHHHHccCCcCCHHHHHH
Confidence 7 889999999999999999999999999999999999999999999999 9999999999999999999999999999
Q ss_pred HhhhcCchhHHHhhchHHHHHHHHHHHHhhhhcCCChhhHHHHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHhccCCC
Q psy15215 1135 ETKIQHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRG 1214 (1432)
Q Consensus 1135 ~~~~~~~~~~~L~~~~~~I~~~q~~L~~ie~~~~l~~~e~~~l~~~~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~ 1214 (1432)
.++.+++|++++.++.++|..+|++|.+++..+++++.+++.++++++.|+..+..|+++||.+|+|||++||++|.++|
T Consensus 325 ~~~~~~~~a~~l~~~~~~I~~lq~~L~~ie~~~~Ls~eElk~l~~~i~~g~~~~~~a~~~Li~~nlrlV~~iA~ky~~~g 404 (619)
T PRK05658 325 EIASGKPWSEFLVRVYDEIKKLQQELEAIEEETGLTIEELKEINRQISKGEAKARRAKKEMVEANLRLVISIAKKYTNRG 404 (619)
T ss_pred HHhccCchHHHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHhccchhhhHHHHHHHHHHHHHHHHHHHHHhhCC
Confidence 99989999999999999999999999999999999999999999999999988888999999999999999999999999
Q ss_pred CChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCC
Q psy15215 1215 LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEP 1294 (1432)
Q Consensus 1215 ~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~p 1294 (1432)
++++|||||||||||+|+++|||++|++|||||+||||++|+++|++++|+||+|+|+.+++++++++.+++.+++||+|
T Consensus 405 l~~~DLiQeG~iGL~~Av~kfd~~~G~~FstYA~~wIr~aI~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~gr~p 484 (619)
T PRK05658 405 LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEIGREP 484 (619)
T ss_pred CCHHHHHHHHHHHHHHHHHhcCccCCCchHHHhHHHHHHHHHHHHHHcCCceecCHHHHHHHHHHHHHHHHHHHHhCCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHH
Q psy15215 1295 DPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKV 1374 (1432)
Q Consensus 1295 t~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~~d~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~V 1374 (1432)
|++|||+.||+|+++|+.+++.+..++||+.|++++++++++++++|....+|.+.+....++..|..+|++||+||+.|
T Consensus 485 t~~eiA~~l~~~~~~v~~~~~~~~~~~Sld~~i~~~~~~~l~d~i~d~~~~~p~~~~~~~~~~~~l~~~l~~L~~rE~~V 564 (619)
T PRK05658 485 TPEELAERLGMPEDKVRKVLKIAKEPISLETPIGDDEDSHLGDFIEDKNAELPIDAAIQESLREATTDVLASLTPREAKV 564 (619)
T ss_pred CHHHHHHHhCCCHHHHHHHHHhcCCCCcCCCCCCCCCCCchhhhcCCCCCCChHHHHHHHHHHHHHHHHHHcCCHHHHHH
Confidence 99999999999999999999999999999999999988899999999988899999999999999999999999999999
Q ss_pred HHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchhhhhHHhhhcc
Q psy15215 1375 LRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429 (1432)
Q Consensus 1375 l~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~~~~l~~~~~~ 1429 (1432)
|++|||+++++++|++|||+.||||++||||++++|++|||++.++..|++||++
T Consensus 565 l~~r~g~~~~~~~tl~ei~~~lgvs~eRVrQie~~al~kLr~~~~~~~l~~~~~~ 619 (619)
T PRK05658 565 LRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSRKLRSFLDN 619 (619)
T ss_pred HHHhcCCCCCCCccHHHHHHHhCCCHHHHHHHHHHHHHHHhchHHHHHHHHHhcC
Confidence 9999999988999999999999999999999999999999999999999999973
No 2
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=1.4e-109 Score=1046.89 Aligned_cols=589 Identities=55% Similarity=0.859 Sum_probs=532.9
Q ss_pred HHHHHHHHHhccccCcccHHHHHhhCCCCCCCHHHHHHHHHHHhhCCCcccccCCchhhhhccCCCC----CchhhHHHH
Q psy15215 40 RKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNITS----DDDVEEATE 115 (1432)
Q Consensus 40 ~~~l~~Li~~Gke~G~lTy~EInd~LP~~~~~~d~id~ii~~L~~~gI~v~d~~~~~~~~~~~~~~~----de~~~~~~~ 115 (1432)
++.+++||++||++|||||+||||+||+++++||+||+|+.+|+++||+|+|.+++.+++.+++... +++..++++
T Consensus 10 ~~~~~~li~~~k~~g~~t~~ei~~~lp~d~~~~d~~~~~~~~~~~~gi~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 89 (619)
T PRK05658 10 QSQLKKLIKRGKERGYLTYAELNDHLPEDIVDSEQIEDIIAMLNDMGIQVVEEAPDADDLLLAENEADAQTDEDAEEEAA 89 (619)
T ss_pred HHHHHHHHHhCcccCCccHHHHHHhCCCcCCCHHHHHHHHHHHHHcCceEEecCcchhhhcccccccccccchhhhhhhH
Confidence 4579999999999999999999999999999999999999999999999999998876654444321 333444455
Q ss_pred hhhccCCCCCCCCCChHHHHHHhcCCccCCCchHHHHHHHHHHHHHHHHHHHHhhChHHHHHHHHHHHHhhhcccchhhh
Q psy15215 116 AALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEI 195 (1432)
Q Consensus 116 ~~l~~~~~~~grt~DPVRmYLREMG~V~LLTREgEIeIAKRIE~G~~~v~~al~~~P~~v~~il~~~e~l~~ge~rl~di 195 (1432)
.+++.+++++|+|||||||||||||+||||||||||+||||||+|+++|+++||.||+++.+|++|+++|.+|+++++||
T Consensus 90 ~~~~~~~~~~~rt~DPVRMYLREMG~V~LLTREgEIeIAKRIE~G~~~v~~al~~~P~~i~~il~~~e~v~~ge~rl~di 169 (619)
T PRK05658 90 AALSSVESEIGRTDDPVRMYLREMGTVELLTREGEIEIAKRIEAGENIMIAALCESPLTIDAILEWYDRLENGERRLREL 169 (619)
T ss_pred HhhcccccccCCCCChHHHHHHHhccCcCCCcHHHHHHHHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHhCCCcHHHH
Confidence 56677788899999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hccccCCCCCCcch---hccCCCCCChhhhhhhcCCCCCCHHHHHHhHHHHHHHHHhHHHHHHHHHHHHHHc--CCC--c
Q psy15215 196 VDGLIDKNFSSNNR---VIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKE--GYN--S 268 (1432)
Q Consensus 196 i~g~~d~~~~~~~~---~~~~~~~~~e~~d~~~~~~~~~~~~~~~~l~~~~~~~f~~l~~~~~~~~~~~~~~--g~~--~ 268 (1432)
|+||.||+.+.... .+.++.+++++++++++............+++.+.++|..|++.|.+++++++++ |.. +
T Consensus 170 I~~~~d~~~~~~~~~~~~e~~~~~~d~de~~~e~~~~~~~~~~~~~~~~~v~~~~~~i~~~~~~~~~~~~k~~~g~~~~~ 249 (619)
T PRK05658 170 IDGFVDPNAEEDPAHVGSELEELDDDEDEEEEEDENDDSLAADESELPEKVLEKFKALAKQYKKLRKAQEKKVEGRLAQH 249 (619)
T ss_pred HhcccCCCccccccccccccccccccccccccccccccchhcccccCHHHHHHHHHHHHHHHHHHHHHHHhhccccchhh
Confidence 99999886321110 0000000000100000000001112223466889999999999999999999998 888 8
Q ss_pred HHHHHHHHHHHHHhhcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCChHHHHHhcCCCccchhhhhhHhhh
Q psy15215 269 ESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKI 348 (1432)
Q Consensus 269 ~~~~k~~~~i~~~l~~ikl~~k~ie~l~~~l~~~~~~ir~~Er~i~~~~v~~~gmpr~~fi~~f~~~e~~~~wl~~~~~~ 348 (1432)
+.+.+.+.+|++.|++|+|++++|++|++.|+..+++|+.+|+.|++ |++++||||++|++.|+||++|+.|+.+..+.
T Consensus 250 ~~~~~~r~~i~~~l~~lkL~~k~id~Lv~~lr~~~~rIr~~Er~i~~-~~~~~~m~R~~Fi~~f~gnEt~~~w~~~~~~~ 328 (619)
T PRK05658 250 KKYAKLREKLKEELKSLRLTSKQIDELVEQLRDINKRVRGQERELLR-LVERLKMPRKDFLKLFQGNELDITWLEKEIAS 328 (619)
T ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHcCCCHHHHHHHccCCcCCHHHHHHHHhc
Confidence 99999999999999999999999999999999999999999999999 99999999999999999999999999999998
Q ss_pred cCchHHHHhhchHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHHhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChh
Q psy15215 349 QHDYNLILCRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFL 428 (1432)
Q Consensus 349 ~~~~~~~L~~~~~~i~~~q~~L~~iE~~~~l~~~e~~~l~~~i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~ 428 (1432)
+++|++.+....++|+.+|++|.+++..+++++.+++.++++++.|+..+..|+++||.+|+|||++||++|.++|++++
T Consensus 329 ~~~~a~~l~~~~~~I~~lq~~L~~ie~~~~Ls~eElk~l~~~i~~g~~~~~~a~~~Li~~nlrlV~~iA~ky~~~gl~~~ 408 (619)
T PRK05658 329 GKPWSEFLVRVYDEIKKLQQELEAIEEETGLTIEELKEINRQISKGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFL 408 (619)
T ss_pred cCchHHHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHhccchhhhHHHHHHHHHHHHHHHHHHHHHhhCCCCHH
Confidence 99999999999999999999999999999999999999999999999877789999999999999999999999999999
Q ss_pred hHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHHHHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHH
Q psy15215 429 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSV 508 (1432)
Q Consensus 429 DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~e 508 (1432)
|||||||||||+|+++|||.+|++|||||+||||++|+++|++++|+||+|+|+.+++++++++.+++.+++|++||++|
T Consensus 409 DLiQeG~iGL~~Av~kfd~~~G~~FstYA~~wIr~aI~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~gr~pt~~e 488 (619)
T PRK05658 409 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEIGREPTPEE 488 (619)
T ss_pred HHHHHHHHHHHHHHHhcCccCCCchHHHhHHHHHHHHHHHHHHcCCceecCHHHHHHHHHHHHHHHHHHHHhCCCCCHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHH
Q psy15215 509 IAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMR 588 (1432)
Q Consensus 509 ia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr 588 (1432)
||+.||+|+++|+.+++++..++||+.|+++++++++++++++....+|.+.+....+...|..+|++||+||+.||++|
T Consensus 489 iA~~l~~~~~~v~~~~~~~~~~~Sld~~i~~~~~~~l~d~i~d~~~~~p~~~~~~~~~~~~l~~~l~~L~~rE~~Vl~~r 568 (619)
T PRK05658 489 LAERLGMPEDKVRKVLKIAKEPISLETPIGDDEDSHLGDFIEDKNAELPIDAAIQESLREATTDVLASLTPREAKVLRMR 568 (619)
T ss_pred HHHHhCCCHHHHHHHHHhcCCCCcCCCCCCCCCCCchhhhcCCCCCCChHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHh
Confidence 99999999999999999999999999999998888999999998888999999999999999999999999999999999
Q ss_pred hhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHHH
Q psy15215 589 FGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLAH 629 (1432)
Q Consensus 589 ~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l~ 629 (1432)
||+|++.++|++|||+.||||+++|+|++.+|++|||++..
T Consensus 569 ~g~~~~~~~tl~ei~~~lgvs~eRVrQie~~al~kLr~~~~ 609 (619)
T PRK05658 569 FGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 609 (619)
T ss_pred cCCCCCCCccHHHHHHHhCCCHHHHHHHHHHHHHHHhchHH
Confidence 99998899999999999999999999999999999999864
No 3
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=100.00 E-value=2.3e-58 Score=520.01 Aligned_cols=337 Identities=45% Similarity=0.730 Sum_probs=307.2
Q ss_pred ccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCChHHHHHhcCCCccchhhHHHHhhhcCc-hhHHHhhchHH
Q psy15215 1074 GIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHD-YNLILCRNIPS 1152 (1432)
Q Consensus 1074 ~irl~~k~i~~l~~~l~~~~~~ir~~Er~i~~~~~~~~~m~r~~fl~~f~~~e~~~~wl~~~~~~~~~-~~~~L~~~~~~ 1152 (1432)
..++++..+..+++.+......++..+..+.+.+.....+ .|+...+...+. |..... ....
T Consensus 3 ~~~~~~d~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~----------------~~~~~~l~~~~~~~~~~~~-~~~~ 65 (342)
T COG0568 3 RVRLSADAVRAYLDEIGRIPLLVREAEVELAKQLEDEQLL----------------VELGEDLTDLKLGREPSER-ARRP 65 (342)
T ss_pred ccccchhHHHHHHHHhcchhhhhHHHHHHHHHHHhHhhhh----------------hHHHHHHHhcccccccchh-hhhh
Confidence 4678888899999999999999999998888776544333 344444443222 322222 4556
Q ss_pred HHHHHHHHHHhhhhcCCChhhHHHHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHH
Q psy15215 1153 IKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAV 1232 (1432)
Q Consensus 1153 I~~~q~~L~~ie~~~~l~~~e~~~l~~~~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav 1232 (1432)
+..++..+..++..+.+++++...+..++..|.. +..|+.+||++|+|+|++||++|.++|+++.|||||||||||+||
T Consensus 66 ~~~~~~~~~~~~~~~~l~~~Ee~~la~~~~~g~~-~~~Ak~klv~snLRlVvsIAk~Y~~rGL~~~DLIQEGniGLmkAV 144 (342)
T COG0568 66 AGRLSFYIRAIEAAPLLTPEEEKALARRLKRGER-DLDAKKKLVESNLRLVVSIAKKYTGRGLPFLDLIQEGNIGLMKAV 144 (342)
T ss_pred hhhHHHHHHHHhhhcccChHHHHHHHHHHHcCCc-cHHHHHHHHHHHHHHHHHHHHHhhcCCCcHHHHHhcccHHHHHHH
Confidence 7788899999999999999999999999999943 344999999999999999999999999999999999999999999
Q ss_pred HhccccCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHH
Q psy15215 1233 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRK 1312 (1432)
Q Consensus 1233 ~kfd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~ 1312 (1432)
++|||.+||+|||||+||||++|+++|.+|+|+||+|+||++++|+++|+.+++.|++|++||++|||+.+|+++++|+.
T Consensus 145 ekFdp~rG~kFsTYA~wWIrqaI~raI~~q~rtIRipvh~~e~~nkl~r~~r~l~q~~~r~p~~eeia~~l~~~~~~V~~ 224 (342)
T COG0568 145 EKFDPEKGFKFSTYATWWIRQAITRAIADQARTIRIPVHQVELINKLRRVKRELLQELGREPTPEEIAEELGVSPDKVRE 224 (342)
T ss_pred HhcCcccCCcchhHHHHHHHHHHHHHHHHhcchhhHhHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHhCCCHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHHHHHHHHHHHHHHHHcc-CCHHHHHHHHHHhcccCCCCCCHHH
Q psy15215 1313 IMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNS-LTPRESKVLRMRFGIEMSSDHTLEE 1391 (1432)
Q Consensus 1313 ~~~~~~~~~Sl~~~~~~~~~~~~~d~i~d~~~~~p~~~~~~~~~~~~l~~~L~~-L~~rer~Vl~lr~~~~~~~~~t~~E 1391 (1432)
+++.+..|+||++|+|+++++.++||++|....+|++.+....+...+...|+. |||||+.||++|||.+++.++|++|
T Consensus 225 m~~~~~~~~SLd~~ig~ded~~l~d~leD~~~~~p~~~~~~~~~~~~~~~~L~~~Lt~rE~~Vi~~R~gl~~~~~~TLee 304 (342)
T COG0568 225 MLKRASEPISLDTPIGDDEDSELGDFLEDDKSVSPEDAVERESLKEDLNEVLAEALTERERRVIRLRFGLDDGEPKTLEE 304 (342)
T ss_pred HHHhcccCcccCCcCCCCcccHHHHHhhcCCcCCHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCcchHHH
Confidence 999999999999999999999999999999988999999999999999999999 9999999999999999999999999
Q ss_pred HHHHhCCCHHHHHHHHHHHHHHhh-CchhhhhHHhhhc
Q psy15215 1392 VGKQFDVTRERIRQIEAKALRKLR-HPSRYYKLKIFLE 1428 (1432)
Q Consensus 1392 Ia~~l~vs~~~Vrq~~~rAl~kLr-~~~~~~~l~~~~~ 1428 (1432)
||..||||++|||||+.+|++||| |+.+...+++|++
T Consensus 305 vg~~~~isrERvRQIE~kAl~KLr~~~~~~~~~~~~l~ 342 (342)
T COG0568 305 LGEEFGISRERVRQIEAKALRKLRRHPERSALLRSYLD 342 (342)
T ss_pred HHHHhCCcHHHHHHHHHHHHHHHHHhhhhhhHHHHhhC
Confidence 999999999999999999999999 9999999999974
No 4
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=100.00 E-value=3.8e-55 Score=493.91 Aligned_cols=326 Identities=45% Similarity=0.722 Sum_probs=294.5
Q ss_pred hcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCChHHHHHhcCCCccchhhhhhHhhhcCc-hHHHHhhchH
Q psy15215 283 LGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHD-YNLILCRNIP 361 (1432)
Q Consensus 283 ~~ikl~~k~ie~l~~~l~~~~~~ir~~Er~i~~~~v~~~gmpr~~fi~~f~~~e~~~~wl~~~~~~~~~-~~~~L~~~~~ 361 (1432)
...++++..+..+++.+......++..+..+.+.+.....+ .|+...+...+. |..... ...
T Consensus 2 ~~~~~~~d~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~----------------~~~~~~l~~~~~~~~~~~~-~~~ 64 (342)
T COG0568 2 KRVRLSADAVRAYLDEIGRIPLLVREAEVELAKQLEDEQLL----------------VELGEDLTDLKLGREPSER-ARR 64 (342)
T ss_pred CccccchhHHHHHHHHhcchhhhhHHHHHHHHHHHhHhhhh----------------hHHHHHHHhcccccccchh-hhh
Confidence 34678888899999999998889999988887776444333 334443333221 222222 455
Q ss_pred HHHHHHHHHHhhhhccCCChhhHHHHHHHHHHhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHH
Q psy15215 362 SIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKA 441 (1432)
Q Consensus 362 ~i~~~q~~L~~iE~~~~l~~~e~~~l~~~i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~ka 441 (1432)
.+..++.++..++..+.+++++...+..++..|+. ...|+.+||++|+|+|++||++|.++|+++.|||||||||||+|
T Consensus 65 ~~~~~~~~~~~~~~~~~l~~~Ee~~la~~~~~g~~-~~~Ak~klv~snLRlVvsIAk~Y~~rGL~~~DLIQEGniGLmkA 143 (342)
T COG0568 65 PAGRLSFYIRAIEAAPLLTPEEEKALARRLKRGER-DLDAKKKLVESNLRLVVSIAKKYTGRGLPFLDLIQEGNIGLMKA 143 (342)
T ss_pred hhhhHHHHHHHHhhhcccChHHHHHHHHHHHcCCc-cHHHHHHHHHHHHHHHHHHHHHhhcCCCcHHHHHhcccHHHHHH
Confidence 67788899999999999999999999999999942 23399999999999999999999999999999999999999999
Q ss_pred HhhccccCCCccHHHHHHHHHHHHHHHHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHH
Q psy15215 442 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIR 521 (1432)
Q Consensus 442 v~~fd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~ 521 (1432)
|++|||.+||+|||||+||||++|+++|.+++|+||+|+||++++|+++|+.+++.|++|++||++|||+.+|+++++|+
T Consensus 144 VekFdp~rG~kFsTYA~wWIrqaI~raI~~q~rtIRipvh~~e~~nkl~r~~r~l~q~~~r~p~~eeia~~l~~~~~~V~ 223 (342)
T COG0568 144 VEKFDPEKGFKFSTYATWWIRQAITRAIADQARTIRIPVHQVELINKLRRVKRELLQELGREPTPEEIAEELGVSPDKVR 223 (342)
T ss_pred HHhcCcccCCcchhHHHHHHHHHHHHHHHHhcchhhHhHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHhCCCHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHHHHHHHHHHHHHHHHhc-CCHHHHHHHHHHhhcccCCCCcHH
Q psy15215 522 KIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNS-LTPRESKVLRMRFGIEMSSDHTLE 600 (1432)
Q Consensus 522 ~~~~~~~~~~sl~~~~~~~~~~~~~~~i~d~~~~~p~~~~~~~~~~~~l~~~L~~-L~~rer~Vl~lr~~~~~~~~~t~~ 600 (1432)
.++..+..|+||+.|+|+++++.++||++|....+|++.+....+.+.+...|+. |||||+.||++|||.+++.++|++
T Consensus 224 ~m~~~~~~~~SLd~~ig~ded~~l~d~leD~~~~~p~~~~~~~~~~~~~~~~L~~~Lt~rE~~Vi~~R~gl~~~~~~TLe 303 (342)
T COG0568 224 EMLKRASEPISLDTPIGDDEDSELGDFLEDDKSVSPEDAVERESLKEDLNEVLAEALTERERRVIRLRFGLDDGEPKTLE 303 (342)
T ss_pred HHHHhcccCcccCCcCCCCcccHHHHHhhcCCcCCHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCcchHH
Confidence 9999999999999999999999999999999888999999999999999999999 999999999999999999999999
Q ss_pred HHHhhcccchhHHHHHHHHHHHHHHH
Q psy15215 601 EVGKQFDVTRERIRQIEAKALRKLRP 626 (1432)
Q Consensus 601 EIa~~l~is~~~v~~~~~rAl~kLr~ 626 (1432)
|||+.+|||+++|||++.+|++|||.
T Consensus 304 evg~~~~isrERvRQIE~kAl~KLr~ 329 (342)
T COG0568 304 ELGEEFGISRERVRQIEAKALRKLRR 329 (342)
T ss_pred HHHHHhCCcHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999993
No 5
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=5.4e-54 Score=508.57 Aligned_cols=359 Identities=56% Similarity=0.889 Sum_probs=316.9
Q ss_pred HHHHHHHHHHHHhccccCccchHHHhhhCCCCCCCHHHHHHHHHHHHhcCccccccccchhhhhccCCCCCchhHHHHHh
Q psy15215 827 ENLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNITSDDDVEEATEA 906 (1432)
Q Consensus 827 ~~~~~~~~~Li~~gk~~g~lT~~ei~~~lp~~~~~~e~ie~i~~~l~~~gI~v~e~~~~~e~~~~~~~~~de~~~e~~~~ 906 (1432)
....+.++.++..|+.+|++|+++|.+++++...+++.++.++..|...||.|.+..++.+..... +++..++...
T Consensus 9 ~~~~~~l~~l~~~~~~~~~it~eei~~~~~~~~~~~~~~~~i~~~l~~~gi~v~~~~~~~~~~~~~----e~~~~~~~~~ 84 (367)
T PRK09210 9 TTLEQVVKELIEKGKKRGTLTYDEIAEKLIPFELDSDQIDDLYERLEDAGISIVDEEGNPSSAQVV----EEEEEEELDN 84 (367)
T ss_pred hhHHHHHHHHHHhhhccCCCCHHHHHHhhcccCCCHHHHHHHHHHHHHcCCcccCCCccccccccc----cccchhhhhh
Confidence 345567888999999999999999999999988899999999999999999998654322211100 0011111111
Q ss_pred hhccCCCCCCCCCChHHHHHHccCCccCCCchHHHHHHHHHHHhHHHHHHHHhhChHHHHHHHHHHHHhhhcccchhhhh
Q psy15215 907 ALSTVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIV 986 (1432)
Q Consensus 907 ~~~~~~~~~grt~DPVRmYLREMG~v~LLTREgEIeIAKRIE~G~~~v~~al~~~P~~v~~il~~~e~l~~ge~~l~dii 986 (1432)
.++. .+...++|||++||+|||.+||||.++|+++++++..|-
T Consensus 85 ~~~~--~~~~~~~d~~~~yl~~i~~~~~l~~~ee~~L~~~~~~Gd----------------------------------- 127 (367)
T PRK09210 85 DLSV--PPGVKINDPVRMYLKEIGRVPLLTAEEEIELAKRIEEGD----------------------------------- 127 (367)
T ss_pred hhhc--ccccccCcHHHHHHHHhhccCCCCHHHHHHHHHHHHhhH-----------------------------------
Confidence 1111 123467999999999999999999999988887765441
Q ss_pred ccccCCCCCCchhhccCCCCCchhhhhhhccCCCCCHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHhCCCcHHHHHHHH
Q psy15215 987 DGLIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHN 1066 (1432)
Q Consensus 987 ~g~~d~~~~~~~~~~~~~~~~e~~~d~~~~~~~~~~~~~l~~l~~~~~~~f~~l~~~~~~~~~~~~~~~~~~~~~~k~~~ 1066 (1432)
T Consensus 128 -------------------------------------------------------------------------------- 127 (367)
T PRK09210 128 -------------------------------------------------------------------------------- 127 (367)
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred HHHHHhhccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCChHHHHHhcCCCccchhhHHHHhhhcCchhHHH
Q psy15215 1067 NISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLIL 1146 (1432)
Q Consensus 1067 ~i~~~l~~irl~~k~i~~l~~~l~~~~~~ir~~Er~i~~~~~~~~~m~r~~fl~~f~~~e~~~~wl~~~~~~~~~~~~~L 1146 (1432)
T Consensus 128 -------------------------------------------------------------------------------- 127 (367)
T PRK09210 128 -------------------------------------------------------------------------------- 127 (367)
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred hhchHHHHHHHHHHHHhhhhcCCChhhHHHHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHH
Q psy15215 1147 CRNIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNI 1226 (1432)
Q Consensus 1147 ~~~~~~I~~~q~~L~~ie~~~~l~~~e~~~l~~~~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~i 1226 (1432)
.. |++.|+..|+++|+++|++|++++.+++||+||||+
T Consensus 128 ---------------------------------------~~---A~~~Li~~~~~lV~~iA~~~~~~~~~~eDLiQEg~i 165 (367)
T PRK09210 128 ---------------------------------------EE---AKQRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNM 165 (367)
T ss_pred ---------------------------------------HH---HHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHH
Confidence 11 677899999999999999999999999999999999
Q ss_pred HHHHHHHhccccCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCC
Q psy15215 1227 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMP 1306 (1432)
Q Consensus 1227 gl~kav~kfd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~ 1306 (1432)
|||+|+++|+|.+|++|+|||+||||++|.++|++++|++|+|+|+++.+|++.++.+.+.+++||+||++|||+.||++
T Consensus 166 gL~~a~~~fd~~~g~~FsTyA~~wIr~aI~~~i~~~~r~irip~~~~~~~~~~~~~~~~l~~~lgr~pt~~EiA~~l~~~ 245 (367)
T PRK09210 166 GLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQELGREPTPEEIAEEMDMP 245 (367)
T ss_pred HHHHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHcCCceeccHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCC
Q psy15215 1307 EEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSD 1386 (1432)
Q Consensus 1307 ~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~~d~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~ 1386 (1432)
+++|+.+++....++||+.|+++++++.++++++|....+|++.+....++..|..+|.+||++||.||.+|||+++|.+
T Consensus 246 ~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~i~d~~~~~p~~~~~~~~~~~~l~~~l~~L~~rEr~Vl~lrygl~~~~~ 325 (367)
T PRK09210 246 PEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRT 325 (367)
T ss_pred HHHHHHHHHHhcCCCCcCCCCCCCCcchhhhhccCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCC
Confidence 99999999999999999999998888889999999888899999999999999999999999999999999999988889
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchhhhhHHhhhc
Q psy15215 1387 HTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428 (1432)
Q Consensus 1387 ~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~~~~l~~~~~ 1428 (1432)
+|++|||+.||||++||||++.+||+|||++.++..|++|++
T Consensus 326 ~tl~EIa~~lgvs~erVrQi~~~Al~kLr~~~~~~~l~~~~~ 367 (367)
T PRK09210 326 RTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 367 (367)
T ss_pred ccHHHHHHHHCCCHHHHHHHHHHHHHHHhChHHHhHHHHhhC
Confidence 999999999999999999999999999999999999999974
No 6
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=100.00 E-value=8e-54 Score=501.29 Aligned_cols=250 Identities=46% Similarity=0.817 Sum_probs=238.4
Q ss_pred HHHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHH
Q psy15215 1175 RDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA 1254 (1432)
Q Consensus 1175 ~~l~~~~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~ 1254 (1432)
.+|.+.++.| .. |++.||.+|+++|+++|++|.++|+.++||||||++|||+|+++|||.+|++|||||+||||++
T Consensus 164 ~eL~~~l~~G-~~---A~e~LI~~nlrLVvsiAkky~~~g~~~eDLiQEG~iGL~ravekFDp~rG~rFSTYa~wwIRqa 239 (415)
T PRK07598 164 EELEQIQKQG-LR---AKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRQG 239 (415)
T ss_pred HHHHHHHHCC-HH---HHHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHH
Confidence 4567778888 34 9999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCC
Q psy15215 1255 ITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSH 1334 (1432)
Q Consensus 1255 i~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~ 1334 (1432)
|++++++++++||+|+|+.+.++++++..+++.+++||.||++|||+.+||++++|+.++..+..++||+.|++++++..
T Consensus 240 I~r~i~~~srtIrlP~~i~e~l~~lrk~~r~L~~~lgR~pt~~EiA~~l~is~~~vr~~l~~~~~~~SLd~~vg~~~d~~ 319 (415)
T PRK07598 240 ITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREVLLRVPRSVSLETKVGKDKDTE 319 (415)
T ss_pred HHHHHHHcCCceehhHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHccCCcccccccCCCcccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999998888
Q ss_pred cCcccccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Q psy15215 1335 LGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 1414 (1432)
Q Consensus 1335 ~~d~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kL 1414 (1432)
+.+++++. ..+|++.+....+...|..+|..|||+||.||.||||++.+.++|++|||+.||+|++||||++++|++||
T Consensus 320 l~d~l~~~-~~~pee~~~~~~l~~~L~~~L~~L~~reR~VI~LRygl~d~~~~Tl~EIA~~LGvS~erVRqie~rAl~KL 398 (415)
T PRK07598 320 LGDLLETD-DISPEEMLMRESLQRDLQHLLADLTSRERDVIRMRFGLADGHTYSLAEIGRALDLSRERVRQIESKALQKL 398 (415)
T ss_pred HHHhccCC-CCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 88888754 46899999999999999999999999999999999998888889999999999999999999999999999
Q ss_pred hCchhhhhHHhhhcc
Q psy15215 1415 RHPSRYYKLKIFLEG 1429 (1432)
Q Consensus 1415 r~~~~~~~l~~~~~~ 1429 (1432)
|+|.++..|++|+++
T Consensus 399 R~~~~~~~l~~y~~~ 413 (415)
T PRK07598 399 RQPKRRNRIRDYLEL 413 (415)
T ss_pred hchhHHHHHHHHHHh
Confidence 999999999999964
No 7
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=100.00 E-value=1.3e-53 Score=511.34 Aligned_cols=238 Identities=58% Similarity=0.983 Sum_probs=231.9
Q ss_pred hHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHHHHHHhcccccccc
Q psy15215 1191 AKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 1270 (1432)
Q Consensus 1191 A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~ 1270 (1432)
|++.||.+|+|||++||++|.++|++++||||||+||||+|+++|||.+|++|||||+||||++|.++|++++|+||+|+
T Consensus 272 Ar~~LI~sNLrLVvsIAkrY~~~Gl~~eDLIQEGnIGLikAvekFDp~rG~rFSTYA~wWIRqaI~raI~d~~r~IRvP~ 351 (509)
T PRK05901 272 AKNHLLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPV 351 (509)
T ss_pred HHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCchhhhHHHHHHHHHHHHHHcCCceecCH
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHH
Q psy15215 1271 HMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 1350 (1432)
Q Consensus 1271 ~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~~d~i~d~~~~~p~~~ 1350 (1432)
|+.+.++++.++.+++.+++||+||++|||+.||+++++|..+++....++||+.|+++++++.++++++|....+|++.
T Consensus 352 ~~~e~i~kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~~p~~~ 431 (509)
T PRK05901 352 HMVETINKLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQKYNREPISLDKTIGKEGDSQFGDFIEDSEAVSPVDA 431 (509)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccccccccCCcccHHHhccCCCCCCHHHH
Confidence 99999999999999999999999999999999999999999999999999999999998888889999999888899999
Q ss_pred HHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchhhhhHHhhhc
Q psy15215 1351 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428 (1432)
Q Consensus 1351 ~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~~~~l~~~~~ 1428 (1432)
+....++..|..+|..||+|||.||.+|||++.+.++|++|||+.||||++|||||+.+|++|||++.++..|+.|++
T Consensus 432 ~~~~~l~~~L~~aL~~L~eREr~VI~lRyGL~~~e~~TL~EIa~~lGVSrERVRQIe~kAL~KLR~~~~~~~l~~~l~ 509 (509)
T PRK05901 432 VSFTLLQDQLQEVLETLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKLRHPSRSQVLRDFLD 509 (509)
T ss_pred HHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 999999999999999999999999999999988889999999999999999999999999999999999999999984
No 8
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=5.9e-52 Score=491.19 Aligned_cols=347 Identities=55% Similarity=0.882 Sum_probs=307.2
Q ss_pred HHHHHHHHHHhccccCcccHHHHHhhCCCCCCCHHHHHHHHHHHhhCCCcccccCCchhhhhccCCCCCchhhHHHHhhh
Q psy15215 39 LRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLMLSNITSDDDVEEATEAAL 118 (1432)
Q Consensus 39 ~~~~l~~Li~~Gke~G~lTy~EInd~LP~~~~~~d~id~ii~~L~~~gI~v~d~~~~~~~~~~~~~~~de~~~~~~~~~l 118 (1432)
..+.++.|+..|+++|++|+++|++++++...++++++.++..|.+.||.|.+..++.+.... .+++..++....+
T Consensus 11 ~~~~l~~l~~~~~~~~~it~eei~~~~~~~~~~~~~~~~i~~~l~~~gi~v~~~~~~~~~~~~----~e~~~~~~~~~~~ 86 (367)
T PRK09210 11 LEQVVKELIEKGKKRGTLTYDEIAEKLIPFELDSDQIDDLYERLEDAGISIVDEEGNPSSAQV----VEEEEEEELDNDL 86 (367)
T ss_pred HHHHHHHHHHhhhccCCCCHHHHHHhhcccCCCHHHHHHHHHHHHHcCCcccCCCcccccccc----ccccchhhhhhhh
Confidence 456789999999999999999999999988789999999999999999999865433221110 0001111111111
Q ss_pred ccCCCCCCCCCChHHHHHHhcCCccCCCchHHHHHHHHHHHHHHHHHHHHhhChHHHHHHHHHHHHhhhcccchhhhhcc
Q psy15215 119 STVDSDFGRTKDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKDMIHAISSCPTTIMEILIAADKISKNEIKIDEIVDG 198 (1432)
Q Consensus 119 ~~~~~~~grt~DPVRmYLREMG~V~LLTREgEIeIAKRIE~G~~~v~~al~~~P~~v~~il~~~e~l~~ge~rl~dii~g 198 (1432)
.. .+...++|||+|||+|||.+||||.++|+++++++..|-
T Consensus 87 ~~--~~~~~~~d~~~~yl~~i~~~~~l~~~ee~~L~~~~~~Gd------------------------------------- 127 (367)
T PRK09210 87 SV--PPGVKINDPVRMYLKEIGRVPLLTAEEEIELAKRIEEGD------------------------------------- 127 (367)
T ss_pred hc--ccccccCcHHHHHHHHhhccCCCCHHHHHHHHHHHHhhH-------------------------------------
Confidence 11 123467999999999999999999999999888776551
Q ss_pred ccCCCCCCcchhccCCCCCChhhhhhhcCCCCCCHHHHHHhHHHHHHHHHhHHHHHHHHHHHHHHcCCCcHHHHHHHHHH
Q psy15215 199 LIDKNFSSNNRVIKGNKNNNEEKILIESSSADLSTEQLEKLKYESLIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNI 278 (1432)
Q Consensus 199 ~~d~~~~~~~~~~~~~~~~~e~~d~~~~~~~~~~~~~~~~l~~~~~~~f~~l~~~~~~~~~~~~~~g~~~~~~~k~~~~i 278 (1432)
T Consensus 128 -------------------------------------------------------------------------------- 127 (367)
T PRK09210 128 -------------------------------------------------------------------------------- 127 (367)
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred HHHhhcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCChHHHHHhcCCCccchhhhhhHhhhcCchHHHHhh
Q psy15215 279 SNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGMPRLHFIKVFPENEINLNWVDNETKIQHDYNLILCR 358 (1432)
Q Consensus 279 ~~~l~~ikl~~k~ie~l~~~l~~~~~~ir~~Er~i~~~~v~~~gmpr~~fi~~f~~~e~~~~wl~~~~~~~~~~~~~L~~ 358 (1432)
T Consensus 128 -------------------------------------------------------------------------------- 127 (367)
T PRK09210 128 -------------------------------------------------------------------------------- 127 (367)
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred chHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHHhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHH
Q psy15215 359 NIPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGL 438 (1432)
Q Consensus 359 ~~~~i~~~q~~L~~iE~~~~l~~~e~~~l~~~i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL 438 (1432)
.. |++.|+..|+++|+++|++|++++.+++||+|||||||
T Consensus 128 -------------------------------------~~---A~~~Li~~~~~lV~~iA~~~~~~~~~~eDLiQEg~igL 167 (367)
T PRK09210 128 -------------------------------------EE---AKQRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGL 167 (367)
T ss_pred -------------------------------------HH---HHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHH
Confidence 01 66789999999999999999999999999999999999
Q ss_pred HHHHhhccccCCCccHHHHHHHHHHHHHHHHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHH
Q psy15215 439 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEE 518 (1432)
Q Consensus 439 ~kav~~fd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~ 518 (1432)
|+|+++|+|.+|++|+|||+||||++|.++|+++.|++|+|+|+++.+|++.++.+++.+++|++||++|||+.||++++
T Consensus 168 ~~a~~~fd~~~g~~FsTyA~~wIr~aI~~~i~~~~r~irip~~~~~~~~~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~ 247 (367)
T PRK09210 168 MKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQELGREPTPEEIAEEMDMPPE 247 (367)
T ss_pred HHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHcCCceeccHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCc
Q psy15215 519 KIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHT 598 (1432)
Q Consensus 519 ~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t 598 (1432)
+|+.+++.+..++||+.|+++++++.+++++++....+|++.+....+...|..+|.+||++|+.||.||||++.|.++|
T Consensus 248 ~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~i~d~~~~~p~~~~~~~~~~~~l~~~l~~L~~rEr~Vl~lrygl~~~~~~t 327 (367)
T PRK09210 248 KVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRT 327 (367)
T ss_pred HHHHHHHHhcCCCCcCCCCCCCCcchhhhhccCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCcc
Confidence 99999999999999999999888888999999988889999999999999999999999999999999999998888999
Q ss_pred HHHHHhhcccchhHHHHHHHHHHHHHHHHH
Q psy15215 599 LEEVGKQFDVTRERIRQIEAKALRKLRPLA 628 (1432)
Q Consensus 599 ~~EIa~~l~is~~~v~~~~~rAl~kLr~~l 628 (1432)
++|||+.||+|+++|+|++.+||++||++.
T Consensus 328 l~EIa~~lgvs~erVrQi~~~Al~kLr~~~ 357 (367)
T PRK09210 328 LEEVGKVFGVTRERIRQIEAKALRKLRHPS 357 (367)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHhChH
Confidence 999999999999999999999999999886
No 9
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=100.00 E-value=3.7e-51 Score=490.31 Aligned_cols=229 Identities=58% Similarity=0.973 Sum_probs=222.3
Q ss_pred hHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHHHHHHhccccccch
Q psy15215 401 AKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 480 (1432)
Q Consensus 401 A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~ 480 (1432)
|++.||.+|+|||+++|++|.++|++++||||||+||||+|+++|||.+|++|||||+||||++|.++|++++|+||+|+
T Consensus 272 Ar~~LI~sNLrLVvsIAkrY~~~Gl~~eDLIQEGnIGLikAvekFDp~rG~rFSTYA~wWIRqaI~raI~d~~r~IRvP~ 351 (509)
T PRK05901 272 AKNHLLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPV 351 (509)
T ss_pred HHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCchhhhHHHHHHHHHHHHHHcCCceecCH
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHH
Q psy15215 481 HMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 560 (1432)
Q Consensus 481 ~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~i~d~~~~~p~~~ 560 (1432)
|+.+.++++.++.+++.+.+|++||++|||+.|||++++|..+++....++||+.|+++++++.+++++++....+|.+.
T Consensus 352 ~~~e~i~kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~~p~~~ 431 (509)
T PRK05901 352 HMVETINKLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQKYNREPISLDKTIGKEGDSQFGDFIEDSEAVSPVDA 431 (509)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccccccccCCcccHHHhccCCCCCCHHHH
Confidence 99999999999999999999999999999999999999999999999999999999998888889999999887899999
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHHH
Q psy15215 561 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLAH 629 (1432)
Q Consensus 561 ~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l~ 629 (1432)
+....+...|..+|.+|++||+.||++|||++.+.++|++|||+.||||+++|+|++.+|+.+||+...
T Consensus 432 ~~~~~l~~~L~~aL~~L~eREr~VI~lRyGL~~~e~~TL~EIa~~lGVSrERVRQIe~kAL~KLR~~~~ 500 (509)
T PRK05901 432 VSFTLLQDQLQEVLETLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKLRHPSR 500 (509)
T ss_pred HHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999988889999999999999999999999999999998753
No 10
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=100.00 E-value=3.2e-50 Score=471.00 Aligned_cols=239 Identities=46% Similarity=0.818 Sum_probs=227.0
Q ss_pred HHHHHHHHHhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHH
Q psy15215 385 RDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA 464 (1432)
Q Consensus 385 ~~l~~~i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~ 464 (1432)
..|...++.| .. |++.||.+|+++|+++|++|.++|++++||||||++|||+|+++|||.+|++|||||+||||++
T Consensus 164 ~eL~~~l~~G-~~---A~e~LI~~nlrLVvsiAkky~~~g~~~eDLiQEG~iGL~ravekFDp~rG~rFSTYa~wwIRqa 239 (415)
T PRK07598 164 EELEQIQKQG-LR---AKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRQG 239 (415)
T ss_pred HHHHHHHHCC-HH---HHHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHH
Confidence 3566778888 34 9999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCC
Q psy15215 465 ITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSH 544 (1432)
Q Consensus 465 i~~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~ 544 (1432)
|++++++++|+||+|+|+.+.+++++++.+++.+++||.||.+|||+.+||++++|+.++..+..++||+.++|++++..
T Consensus 240 I~r~i~~~srtIrlP~~i~e~l~~lrk~~r~L~~~lgR~pt~~EiA~~l~is~~~vr~~l~~~~~~~SLd~~vg~~~d~~ 319 (415)
T PRK07598 240 ITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREVLLRVPRSVSLETKVGKDKDTE 319 (415)
T ss_pred HHHHHHHcCCceehhHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHccCCcccccccCCCcccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999988888
Q ss_pred cCcccccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHH
Q psy15215 545 LGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 624 (1432)
Q Consensus 545 ~~~~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kL 624 (1432)
+.+++++. ..+|++.+....+...|..+|..|||+|+.||.||||++.+.++|++|||+.||+|+++|++++++|+++|
T Consensus 320 l~d~l~~~-~~~pee~~~~~~l~~~L~~~L~~L~~reR~VI~LRygl~d~~~~Tl~EIA~~LGvS~erVRqie~rAl~KL 398 (415)
T PRK07598 320 LGDLLETD-DISPEEMLMRESLQRDLQHLLADLTSRERDVIRMRFGLADGHTYSLAEIGRALDLSRERVRQIESKALQKL 398 (415)
T ss_pred HHHhccCC-CCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 88888754 46899999999999999999999999999999999998888889999999999999999999999999999
Q ss_pred HHHH
Q psy15215 625 RPLA 628 (1432)
Q Consensus 625 r~~l 628 (1432)
|++-
T Consensus 399 R~~~ 402 (415)
T PRK07598 399 RQPK 402 (415)
T ss_pred hchh
Confidence 9764
No 11
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=8.8e-49 Score=458.04 Aligned_cols=245 Identities=55% Similarity=0.910 Sum_probs=232.0
Q ss_pred HHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHH
Q psy15215 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITR 1257 (1432)
Q Consensus 1178 ~~~~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~ 1257 (1432)
.+++..| .. |++.||.+|+++|+++|++|.++|.+++||+||||+|||+|+++||+.+|++|+|||+||||++|.+
T Consensus 128 ~~~~~~g-~~---A~~~Li~~~l~lV~~iA~ry~~~~~~~eDLiQEG~igL~~Ai~kFd~~kg~~FsTYA~wWIRqaI~~ 203 (373)
T PRK07406 128 RRRLMLG-RR---AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITR 203 (373)
T ss_pred HHHHhcC-HH---HHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHH
Confidence 3444555 44 9999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCc
Q psy15215 1258 SIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGD 1337 (1432)
Q Consensus 1258 ~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~~d 1337 (1432)
+|++++++||+|+|+.+.+++++++.+.+.+++|++||++|||+.+|+++++|..++.....++||+.|+++++++.+.+
T Consensus 204 ~I~~~~r~IRlP~~~~~~~~~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~~~~~~~~~~~SLd~~i~~~~~~~l~d 283 (373)
T PRK07406 204 AIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGD 283 (373)
T ss_pred HHHhcCCceeCCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCcccHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999998888888999
Q ss_pred ccccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCc
Q psy15215 1338 FIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417 (1432)
Q Consensus 1338 ~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~ 1417 (1432)
++++. ..+|++.+....+...|..+|++||++||.||.+|||++.+.++|++|||+.||||++||||++.+|++|||++
T Consensus 284 ~l~d~-~~~pee~~~~~~~~~~L~~aL~~L~~rEr~IL~lrygl~~~~~~Tl~EIA~~lgiS~eRVRQie~rAL~KLR~~ 362 (373)
T PRK07406 284 FIEAD-GETPEDDVAKNLLREDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHP 362 (373)
T ss_pred hcCCC-CCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHhch
Confidence 99876 45899999999999999999999999999999999998777889999999999999999999999999999999
Q ss_pred hhhhhHHhhh
Q psy15215 1418 SRYYKLKIFL 1427 (1432)
Q Consensus 1418 ~~~~~l~~~~ 1427 (1432)
.+...|+.|+
T Consensus 363 ~~~~~l~~~~ 372 (373)
T PRK07406 363 NRNSVLKEYI 372 (373)
T ss_pred hHHHHHHHHh
Confidence 9999999986
No 12
>PRK05949 RNA polymerase sigma factor; Validated
Probab=100.00 E-value=6.2e-48 Score=448.14 Aligned_cols=247 Identities=45% Similarity=0.820 Sum_probs=232.3
Q ss_pred HHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHH
Q psy15215 1176 DINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 1255 (1432)
Q Consensus 1176 ~l~~~~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i 1255 (1432)
.++..++.|+ . |++.||..|+++|+++|++|.+++..++||+||||+|||+|+++|++.+|++|||||+||||++|
T Consensus 81 eL~~~~~~g~-~---A~~~Li~~~~~~V~~iA~~y~~~~~~~eDLvQEg~igL~~a~~kfd~~~G~rFsTYa~wwIrq~I 156 (327)
T PRK05949 81 ELKQTLKQGK-R---AKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAI 156 (327)
T ss_pred HHHHHHHccH-H---HHHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHhcCCcCCCChhhhhHHHHHHHH
Confidence 3555666774 4 89999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCc
Q psy15215 1256 TRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHL 1335 (1432)
Q Consensus 1256 ~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~ 1335 (1432)
.+++++++++||+|+|+.+.++++++..+++.+++|++||++|||+.+|+++++|..++.....++||+.|++++++..+
T Consensus 157 ~r~i~~~~r~iRlP~~~~~~~~~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l 236 (327)
T PRK05949 157 TRAIAQQARTIRLPIHITEKLNKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMARQPISLDVRVGDNQDTEL 236 (327)
T ss_pred HHHHHHcCCceeCCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhccccccCCCcCCCCCccH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999998887788
Q ss_pred CcccccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhh
Q psy15215 1336 GDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 1415 (1432)
Q Consensus 1336 ~d~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr 1415 (1432)
.+.+++.. .+|++.+....+...|..+|+.|||+||.||.+|||++.+.++|++|||+.||||++||||++++|++|||
T Consensus 237 ~~~l~d~~-~~pe~~~~~~~~~~~L~~~L~~L~~rer~Vi~lr~gl~~~e~~Tl~EIa~~lgiS~erVrq~~~rAl~kLr 315 (327)
T PRK05949 237 SELLEDEG-PSPDQYITQELLRQDLNNLLAELTPQQREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHLR 315 (327)
T ss_pred HhhcCCCC-CCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 88888765 68999999999999999999999999999999999988888999999999999999999999999999999
Q ss_pred CchhhhhHHhhhcc
Q psy15215 1416 HPSRYYKLKIFLEG 1429 (1432)
Q Consensus 1416 ~~~~~~~l~~~~~~ 1429 (1432)
+ +...|+.|+.+
T Consensus 316 ~--~~~~l~~~~~~ 327 (327)
T PRK05949 316 R--RRANVKEYLAS 327 (327)
T ss_pred H--HHHHHHHHHhC
Confidence 9 45678888753
No 13
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=4.8e-46 Score=435.09 Aligned_cols=237 Identities=55% Similarity=0.899 Sum_probs=223.5
Q ss_pred HHHHHHhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHH
Q psy15215 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITR 467 (1432)
Q Consensus 388 ~~~i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~ 467 (1432)
..++..| .. |++.||..|+++|+++|++|.++|.+++||+|||+||||+|+++|++.+|++|+|||+||||++|.+
T Consensus 128 ~~~~~~g-~~---A~~~Li~~~l~lV~~iA~ry~~~~~~~eDLiQEG~igL~~Ai~kFd~~kg~~FsTYA~wWIRqaI~~ 203 (373)
T PRK07406 128 RRRLMLG-RR---AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITR 203 (373)
T ss_pred HHHHhcC-HH---HHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHH
Confidence 3344555 44 9999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCc
Q psy15215 468 SIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGD 547 (1432)
Q Consensus 468 ~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~ 547 (1432)
+|++++++||+|+|+.+.+++++++.+.+.+++|++||.+|||+.||+++++|+.++..+..++||+.|+++++++.+.+
T Consensus 204 ~I~~~~r~IRlP~~~~~~~~~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~~~~~~~~~~~SLd~~i~~~~~~~l~d 283 (373)
T PRK07406 204 AIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGD 283 (373)
T ss_pred HHHhcCCceeCCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCcccHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999998888888899
Q ss_pred ccccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHH
Q psy15215 548 FIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPL 627 (1432)
Q Consensus 548 ~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~ 627 (1432)
++++. ..+|++.+....+...|..+|++||++|+.||.+|||++.+.++|++|||+.||+|+++|+|++.+|+++||++
T Consensus 284 ~l~d~-~~~pee~~~~~~~~~~L~~aL~~L~~rEr~IL~lrygl~~~~~~Tl~EIA~~lgiS~eRVRQie~rAL~KLR~~ 362 (373)
T PRK07406 284 FIEAD-GETPEDDVAKNLLREDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHP 362 (373)
T ss_pred hcCCC-CCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHhch
Confidence 99876 35899999999999999999999999999999999998777889999999999999999999999999999987
Q ss_pred HH
Q psy15215 628 AH 629 (1432)
Q Consensus 628 l~ 629 (1432)
..
T Consensus 363 ~~ 364 (373)
T PRK07406 363 NR 364 (373)
T ss_pred hH
Confidence 54
No 14
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=100.00 E-value=3.1e-46 Score=433.81 Aligned_cols=246 Identities=43% Similarity=0.789 Sum_probs=231.2
Q ss_pred HHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHH
Q psy15215 1177 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 1256 (1432)
Q Consensus 1177 l~~~~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~ 1256 (1432)
|+..++.|+ . |++.||.+|+++|+++|++|++++.+++||+||||+|||+++++|++.+|++|+|||+||||++|.
T Consensus 72 L~~~~~~g~-~---A~~~L~~~~~~~V~~~a~~~~~~~~~~eDLvQEg~i~L~~a~~~fd~~~g~rf~tYa~~wIR~~I~ 147 (317)
T PRK07405 72 LRSAIAEGE-A---AKRKMVEANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAIT 147 (317)
T ss_pred HHHHHhccH-H---HHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcCCCCChHHHHHHHHHHHHH
Confidence 455666674 4 999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcC
Q psy15215 1257 RSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLG 1336 (1432)
Q Consensus 1257 ~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~~ 1336 (1432)
++|++++++||+|+|+.+.++++++..+.+.+++|++||++|||+.+|+++++|..+++....++||+.|++++++..+.
T Consensus 148 ~~i~~~~~~ir~p~~~~~~~~~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~ 227 (317)
T PRK07405 148 RAIAEKSRTIRLPIHITEKLNKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERARQPLSLDLRVGDNQDTELG 227 (317)
T ss_pred HHHHhcCCCccCChHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCeeecCCCCCCCCccHH
Confidence 99999999999999999999999999999999999999999999999999999999999888999999999888777888
Q ss_pred cccccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhC
Q psy15215 1337 DFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 1416 (1432)
Q Consensus 1337 d~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~ 1416 (1432)
+++++.. .+|++.+....+...|..+|++|||+||.||.+|||++.+.++|++|||+.||||++||||++++|++|||+
T Consensus 228 ~~~~d~~-~~pe~~~~~~~~~~~l~~al~~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVRqi~~rAl~kLr~ 306 (317)
T PRK07405 228 ELLEDTG-ASPEDFATQSSLQLDLERLMEDLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLRK 306 (317)
T ss_pred HhhcCCC-CCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhhcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 8888764 689999999999999999999999999999999999887788999999999999999999999999999999
Q ss_pred chhhhhHHhhhcc
Q psy15215 1417 PSRYYKLKIFLEG 1429 (1432)
Q Consensus 1417 ~~~~~~l~~~~~~ 1429 (1432)
. ...|+.|+.+
T Consensus 307 ~--~~~l~~~~~~ 317 (317)
T PRK07405 307 R--KANIQEYLAS 317 (317)
T ss_pred H--HHHHHHHHhC
Confidence 4 5678888753
No 15
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=100.00 E-value=3.9e-46 Score=431.28 Aligned_cols=272 Identities=44% Similarity=0.807 Sum_probs=253.8
Q ss_pred HHHHHHHhhhhcCCChhhHHHHHHHHHhhhh------------------------hhhhhHHHHHHHHHHHHHHHHHhcc
Q psy15215 1156 LQQKLINLQTDIVLPLNDLRDINRKMIAGEM------------------------KARKAKREMTEANLRLVISIAKKYT 1211 (1432)
Q Consensus 1156 ~q~~L~~ie~~~~l~~~e~~~l~~~~~~g~~------------------------~~~~A~~~Li~~~~~lV~~ia~~y~ 1211 (1432)
+..+|.++.....+++++...|.++++.|.. ....|++.|+..|+++|+++|++|.
T Consensus 28 ~~~Yl~~i~~~~lLt~eeE~~La~~~~~g~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~A~~~Lv~~~~~lV~~iA~r~~ 107 (324)
T PRK07921 28 VRVYLNGIGKTALLTAADEVELAKRIEAGLYAEHLLETRKRLSEARKRDLAAVVRDGEAARRHLLEANLRLVVSLAKRYT 107 (324)
T ss_pred HHHHHHHhcccCCCCHHHHHHHHHHHHhhhhhhhhhccccccchhHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3457777888888888888888888887710 0234999999999999999999999
Q ss_pred CCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHHhC
Q psy15215 1212 DRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETG 1291 (1432)
Q Consensus 1212 ~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g 1291 (1432)
+++.+++||+||||+|||+|+++|+|.+|++|+|||+||||++|.+++++++++||+|+|+.+.+++++++.+.+.+++|
T Consensus 108 ~~~~~~eDLvQEg~igL~~a~~~fdp~~G~rFsTYA~~wIr~aI~~~i~~~~r~vrlP~~~~~~~~~l~~~~~~l~~~lg 187 (324)
T PRK07921 108 GRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKRELHQQLG 187 (324)
T ss_pred cCCCCHHHHHHHHHHHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHcCCCccCCHHHHHHHHHHHHHHHHHHHHhC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHHHHHHHHHHHHHHHHccCCHHH
Q psy15215 1292 SEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRE 1371 (1432)
Q Consensus 1292 ~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~~d~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~re 1371 (1432)
++||.+|||+.+|+++++|..++.....++|||.|++++++.++.+++++....+|++.+....+...|..+|+.||+||
T Consensus 188 r~pt~~EiA~~lgi~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~l~d~~~~~pe~~~~~~~~~~~l~~~L~~L~eRE 267 (324)
T PRK07921 188 REATDEELAEESGIPEEKIADLLEHSRDPVSLDMPVGSDEEAPLGDFIEDSEATSAENAVIAGLLHTDIRSVLATLDERE 267 (324)
T ss_pred CCCCHHHHHHHhCcCHHHHHHHHHHcCCCceecCCCCCCCCchHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHH
Confidence 99999999999999999999999988899999999988877788999998877789999999999999999999999999
Q ss_pred HHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchhhhhHHhhh
Q psy15215 1372 SKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFL 1427 (1432)
Q Consensus 1372 r~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~~~~l~~~~ 1427 (1432)
+.||.+|||++.+.++|++|||+.||||++|||||+.+|++|||++.+...|+.|+
T Consensus 268 r~Vl~~rygl~~~~~~Tl~eIa~~lgvS~eRVrQIe~~Al~KLr~~~~~~~l~~~~ 323 (324)
T PRK07921 268 QQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRNGERADRLRSYA 323 (324)
T ss_pred HHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHHHHHHHHhh
Confidence 99999999988778899999999999999999999999999999999999999986
No 16
>PRK05949 RNA polymerase sigma factor; Validated
Probab=100.00 E-value=1.8e-45 Score=427.51 Aligned_cols=238 Identities=45% Similarity=0.826 Sum_probs=225.3
Q ss_pred HHHHHHHHhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHH
Q psy15215 386 DINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 465 (1432)
Q Consensus 386 ~l~~~i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i 465 (1432)
.|+..++.|+ . |++.||..|+++|+++|++|.+++.+++|||||||+|||+|+++|++.+|++|||||+||||++|
T Consensus 81 eL~~~~~~g~-~---A~~~Li~~~~~~V~~iA~~y~~~~~~~eDLvQEg~igL~~a~~kfd~~~G~rFsTYa~wwIrq~I 156 (327)
T PRK05949 81 ELKQTLKQGK-R---AKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAI 156 (327)
T ss_pred HHHHHHHccH-H---HHHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHhcCCcCCCChhhhhHHHHHHHH
Confidence 4556677774 4 89999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCc
Q psy15215 466 TRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHL 545 (1432)
Q Consensus 466 ~~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~ 545 (1432)
.+++++++++||+|+|+.+.+++++++.+++.+++|++||++|||+.+|+++++|..++..+..++||+.|++++++..+
T Consensus 157 ~r~i~~~~r~iRlP~~~~~~~~~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l 236 (327)
T PRK05949 157 TRAIAQQARTIRLPIHITEKLNKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMARQPISLDVRVGDNQDTEL 236 (327)
T ss_pred HHHHHHcCCceeCCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhccccccCCCcCCCCCccH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999998877788
Q ss_pred CcccccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHH
Q psy15215 546 GDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625 (1432)
Q Consensus 546 ~~~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr 625 (1432)
.+.+++.. .+|++.+....+...|..+|++|||+||.||.||||++.+.++|++|||+.||+|+++|++++++|+++||
T Consensus 237 ~~~l~d~~-~~pe~~~~~~~~~~~L~~~L~~L~~rer~Vi~lr~gl~~~e~~Tl~EIa~~lgiS~erVrq~~~rAl~kLr 315 (327)
T PRK05949 237 SELLEDEG-PSPDQYITQELLRQDLNNLLAELTPQQREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHLR 315 (327)
T ss_pred HhhcCCCC-CCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 88888765 68999999999999999999999999999999999988888899999999999999999999999999999
Q ss_pred HHH
Q psy15215 626 PLA 628 (1432)
Q Consensus 626 ~~l 628 (1432)
+..
T Consensus 316 ~~~ 318 (327)
T PRK05949 316 RRR 318 (327)
T ss_pred HHH
Confidence 843
No 17
>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-44 Score=419.67 Aligned_cols=235 Identities=51% Similarity=0.912 Sum_probs=221.3
Q ss_pred HHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHH
Q psy15215 1176 DINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 1255 (1432)
Q Consensus 1176 ~l~~~~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i 1255 (1432)
+++.+++.| .. |++.||.+|+++|+++|++|.++|.+++||+||||+|||+|+++|||.+|++|+|||+||||++|
T Consensus 64 ~l~~~~~~g-~~---A~~~Lv~~~lrlV~~iA~~y~~~~~~~eDLiQEg~igL~~a~~kfd~~~g~rFsTya~~wIr~~I 139 (298)
T TIGR02997 64 ELRQRLRQG-QR---AKEKMIKANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWWIRQGI 139 (298)
T ss_pred HHHHHHhcc-HH---HHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCccCCCChHHHHHHHHHHHH
Confidence 455666677 35 99999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCc
Q psy15215 1256 TRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHL 1335 (1432)
Q Consensus 1256 ~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~ 1335 (1432)
.+++.++++++|+|.|+...++++++..+.+.+.+|++||.+|||+.+|+++++|..++.....++|||.|++++++..+
T Consensus 140 ~r~i~~~~r~vr~p~~~~~~~~~~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~~ 219 (298)
T TIGR02997 140 TRAIANQSRTIRLPIHITEKLNKIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPVGDEEDTEL 219 (298)
T ss_pred HHHHHhcCCCeeCcHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHcccCcccCCCcCCCCcchH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999987776677
Q ss_pred CcccccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhh
Q psy15215 1336 GDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 1415 (1432)
Q Consensus 1336 ~d~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr 1415 (1432)
.+.+++ ...+|++.+....+...|..+|++|||+||.||.+|||++.+.++|++|||+.||||++||||++++|++|||
T Consensus 220 ~~~~~~-~~~~pe~~~~~~~~~~~L~~~L~~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVrq~~~rAl~kLr 298 (298)
T TIGR02997 220 GDLLED-DGESPEEQVERESLRQDLESLLAELTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRKLR 298 (298)
T ss_pred HHhccC-CCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence 777777 4568999999999999999999999999999999999987778889999999999999999999999999997
No 18
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=100.00 E-value=5.4e-44 Score=415.04 Aligned_cols=237 Identities=44% Similarity=0.805 Sum_probs=224.4
Q ss_pred HHHHHHHhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHH
Q psy15215 387 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 466 (1432)
Q Consensus 387 l~~~i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~ 466 (1432)
|+..++.|+ . |++.||..|+++|+++|++|++++.+++||+||||+|||+++++|++.+|++|+|||+||||++|.
T Consensus 72 L~~~~~~g~-~---A~~~L~~~~~~~V~~~a~~~~~~~~~~eDLvQEg~i~L~~a~~~fd~~~g~rf~tYa~~wIR~~I~ 147 (317)
T PRK07405 72 LRSAIAEGE-A---AKRKMVEANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAIT 147 (317)
T ss_pred HHHHHhccH-H---HHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcCCCCChHHHHHHHHHHHHH
Confidence 455666774 5 999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcC
Q psy15215 467 RSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLG 546 (1432)
Q Consensus 467 ~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~ 546 (1432)
++|++++++||+|+|+.+.+++++++.+.+.+.+|++||.+|||+.+|+++++|..+++....++||+.|++++++..+.
T Consensus 148 ~~i~~~~~~ir~p~~~~~~~~~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~ 227 (317)
T PRK07405 148 RAIAEKSRTIRLPIHITEKLNKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERARQPLSLDLRVGDNQDTELG 227 (317)
T ss_pred HHHHhcCCCccCChHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCeeecCCCCCCCCccHH
Confidence 99999999999999999999999999999999999999999999999999999999999889999999999888777888
Q ss_pred cccccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHH
Q psy15215 547 DFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRP 626 (1432)
Q Consensus 547 ~~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~ 626 (1432)
+++++.. .+|++.+....+...|..+|++|||+||.||.+|||++.+.++|++|||+.||+|+++|+|++++|+++||+
T Consensus 228 ~~~~d~~-~~pe~~~~~~~~~~~l~~al~~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVRqi~~rAl~kLr~ 306 (317)
T PRK07405 228 ELLEDTG-ASPEDFATQSSLQLDLERLMEDLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLRK 306 (317)
T ss_pred HhhcCCC-CCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhhcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 8888764 689999999999999999999999999999999999887788999999999999999999999999999998
Q ss_pred HH
Q psy15215 627 LA 628 (1432)
Q Consensus 627 ~l 628 (1432)
..
T Consensus 307 ~~ 308 (317)
T PRK07405 307 RK 308 (317)
T ss_pred HH
Confidence 53
No 19
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=100.00 E-value=6.3e-44 Score=412.92 Aligned_cols=260 Identities=45% Similarity=0.821 Sum_probs=246.8
Q ss_pred HHHHHHhhhhccCCChhhHHHHHHHHHHh---------------------------HHHHHHhHHHHHHHHHHHHHHHHH
Q psy15215 366 LQQKLINLQTDIVLPLNDLRDINRKMIAG---------------------------EMKARKAKREMTEANLRLVISIAK 418 (1432)
Q Consensus 366 ~q~~L~~iE~~~~l~~~e~~~l~~~i~~g---------------------------d~~~~~A~~~li~~~~~lV~~ia~ 418 (1432)
+..+|.++.....+++++...|.++++.| +. .|++.|+..|+++|+++|+
T Consensus 28 ~~~Yl~~i~~~~lLt~eeE~~La~~~~~g~~~~~~~~~~~~~~~~~~~~l~~~~~~~~---~A~~~Lv~~~~~lV~~iA~ 104 (324)
T PRK07921 28 VRVYLNGIGKTALLTAADEVELAKRIEAGLYAEHLLETRKRLSEARKRDLAAVVRDGE---AARRHLLEANLRLVVSLAK 104 (324)
T ss_pred HHHHHHHhcccCCCCHHHHHHHHHHHHhhhhhhhhhccccccchhHHHHHHHHHhcCH---HHHHHHHHHHHHHHHHHHH
Confidence 44688888888999999999999999887 33 4999999999999999999
Q ss_pred hcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHHHHHHhccccccchhHHHHHHHHHHHHHHHHH
Q psy15215 419 KYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQ 498 (1432)
Q Consensus 419 ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~ 498 (1432)
+|.+++.+++||+|||+||||+|+++|+|.+|++|+|||+||||++|.++|++++++||+|+|+.+.+++++++.+.+.+
T Consensus 105 r~~~~~~~~eDLvQEg~igL~~a~~~fdp~~G~rFsTYA~~wIr~aI~~~i~~~~r~vrlP~~~~~~~~~l~~~~~~l~~ 184 (324)
T PRK07921 105 RYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKRELHQ 184 (324)
T ss_pred HHhcCCCCHHHHHHHHHHHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHcCCCccCCHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHHHHHHHHHHHHHHHHhcCC
Q psy15215 499 ETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLT 578 (1432)
Q Consensus 499 ~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~ 578 (1432)
++|++||.+|||+.||+++++|..++..+..++||+.|++++++.++.+++++....+|++.+....+...|..+|+.||
T Consensus 185 ~lgr~pt~~EiA~~lgi~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~l~d~~~~~pe~~~~~~~~~~~l~~~L~~L~ 264 (324)
T PRK07921 185 QLGREATDEELAEESGIPEEKIADLLEHSRDPVSLDMPVGSDEEAPLGDFIEDSEATSAENAVIAGLLHTDIRSVLATLD 264 (324)
T ss_pred HhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCceecCCCCCCCCchHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHHhCC
Confidence 99999999999999999999999999998999999999988877788999998777789999999999999999999999
Q ss_pred HHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHH
Q psy15215 579 PRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLA 628 (1432)
Q Consensus 579 ~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l 628 (1432)
++|+.||.+|||++.+.++|++|||+.||||+++|+|++.+|++|||...
T Consensus 265 eREr~Vl~~rygl~~~~~~Tl~eIa~~lgvS~eRVrQIe~~Al~KLr~~~ 314 (324)
T PRK07921 265 EREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRNGE 314 (324)
T ss_pred HHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Confidence 99999999999998778899999999999999999999999999999874
No 20
>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=5.1e-43 Score=406.08 Aligned_cols=235 Identities=51% Similarity=0.912 Sum_probs=221.1
Q ss_pred HHHHHHHHhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHH
Q psy15215 386 DINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 465 (1432)
Q Consensus 386 ~l~~~i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i 465 (1432)
.|+.+++.| .. |++.||.+|+++|+++|++|.++|.+++|||||||+|||+|+++|||.+|++|+|||+||||++|
T Consensus 64 ~l~~~~~~g-~~---A~~~Lv~~~lrlV~~iA~~y~~~~~~~eDLiQEg~igL~~a~~kfd~~~g~rFsTya~~wIr~~I 139 (298)
T TIGR02997 64 ELRQRLRQG-QR---AKEKMIKANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWWIRQGI 139 (298)
T ss_pred HHHHHHhcc-HH---HHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCccCCCChHHHHHHHHHHHH
Confidence 456667777 35 99999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCc
Q psy15215 466 TRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHL 545 (1432)
Q Consensus 466 ~~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~ 545 (1432)
.+++.+++++||+|.++...++++++..+.+.+.+|++||.+|||+.+|+++++|..++.....++||+.|++++++..+
T Consensus 140 ~r~i~~~~r~vr~p~~~~~~~~~~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~~ 219 (298)
T TIGR02997 140 TRAIANQSRTIRLPIHITEKLNKIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPVGDEEDTEL 219 (298)
T ss_pred HHHHHhcCCCeeCcHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHcccCcccCCCcCCCCcchH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999987766677
Q ss_pred CcccccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHH
Q psy15215 546 GDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625 (1432)
Q Consensus 546 ~~~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr 625 (1432)
.+.+++ ...+|++.+...++...|..+|++|||+|+.||.+|||++.+.++|++|||+.||+|+++|++++++|+++||
T Consensus 220 ~~~~~~-~~~~pe~~~~~~~~~~~L~~~L~~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVrq~~~rAl~kLr 298 (298)
T TIGR02997 220 GDLLED-DGESPEEQVERESLRQDLESLLAELTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRKLR 298 (298)
T ss_pred HHhccC-CCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence 777777 3568999999999999999999999999999999999987778889999999999999999999999999986
No 21
>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=6.6e-42 Score=385.06 Aligned_cols=238 Identities=67% Similarity=1.061 Sum_probs=228.3
Q ss_pred hHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHHHHHHhcccccccc
Q psy15215 1191 AKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 1270 (1432)
Q Consensus 1191 A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~ 1270 (1432)
|+++|+.+|+++|+++|++|.+++.+++||+|||++|||+|+++|||.+|++|+|||+||||++|.++++++.+++|+|.
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 cHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHH
Q psy15215 1271 HMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 1350 (1432)
Q Consensus 1271 ~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~~d~i~d~~~~~p~~~ 1350 (1432)
++.+.++++.++.+.+.+++|++||.+|||+.||+++++|..+++.....+||+.|++++++.++.++++|+...+|++.
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 99999999999999999999999999999999999999999999988889999999988777778889998887889999
Q ss_pred HHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchhhhhHHhhhc
Q psy15215 1351 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428 (1432)
Q Consensus 1351 ~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~~~~l~~~~~ 1428 (1432)
+....+...|..+|+.||++|+.||.+|||.+...++|++|||+.||||+++|+|++.+|++|||++.++..|+.|++
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 999999999999999999999999999998877788899999999999999999999999999999999999999975
No 22
>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=1.8e-39 Score=365.34 Aligned_cols=230 Identities=66% Similarity=1.040 Sum_probs=219.6
Q ss_pred hHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHHHHHHhccccccch
Q psy15215 401 AKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 480 (1432)
Q Consensus 401 A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~ 480 (1432)
|++.||..|+++|+++|++|.+++.+++||+|||++|||+|+++|||.+|++|+|||+||||++|.++++++.+.+|+|.
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 67899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHH
Q psy15215 481 HMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 560 (1432)
Q Consensus 481 ~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~i~d~~~~~p~~~ 560 (1432)
++.+.++++.++.+.+.+++|++||.+|||+.||+++++|+.+++....++||+.|++++++.++.++++++...+|++.
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 99999999999999999999999999999999999999999999888889999999987777778888988877889999
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHHHH
Q psy15215 561 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLAHD 630 (1432)
Q Consensus 561 ~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l~~ 630 (1432)
+...++...|..+|++||++|+.||.+|||.+...++|++|||+.||+|+++|++++.+|+++||+.+..
T Consensus 161 ~~~~~~~~~l~~~l~~L~~~er~vl~l~ygl~~~~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~~~~~ 230 (238)
T TIGR02393 161 AAKELLREQLDEVLETLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRKLRHPSRS 230 (238)
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhhhHHH
Confidence 9999999999999999999999999999988777888999999999999999999999999999988754
No 23
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=100.00 E-value=1.2e-38 Score=361.99 Aligned_cols=228 Identities=24% Similarity=0.392 Sum_probs=206.9
Q ss_pred HhhhhhhhhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHHHHHH
Q psy15215 1182 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIAD 1261 (1432)
Q Consensus 1182 ~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~~i~~ 1261 (1432)
..|+....++++.||.+|+|||+++|++|.++|.+++||||||+|||++|+++|||.+|++|+|||+||||++|.+++++
T Consensus 32 ~~~~~~~~~~r~~Lv~~~l~LV~~iA~~y~~~g~~~~DLiQeG~iGLi~AierFDp~~G~~FsTYA~~~Irg~I~~~lr~ 111 (264)
T PRK07122 32 PAGSPEFQRQRDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGEVRRHFRD 111 (264)
T ss_pred cCCCHHHHHHHHHHHHHhHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHH
Confidence 34566666799999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHH--ccCCCCCCCCCCCCCCC--CcCc
Q psy15215 1262 QARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKI--AKEPVSMESPVGDDEDS--HLGD 1337 (1432)
Q Consensus 1262 ~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~--~~~~~Sl~~~~~~~~~~--~~~d 1337 (1432)
+.++||+|+++.+.+++++++...+.+++|++||++|||+.||+++++|.+++.. ...++|||.|++++++. .+.+
T Consensus 112 ~~~~ir~Pr~~~~~~~~i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~~~~~d 191 (264)
T PRK07122 112 NSWSVKVPRRLKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVVEGLVAGSAYNTLSIDSGGGSGDDDARAIAD 191 (264)
T ss_pred cCCccccCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhhcCCCCcccccccCCCCCcccchh
Confidence 9999999999999999999999999999999999999999999999999999864 45789999998754332 3444
Q ss_pred ccccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCc
Q psy15215 1338 FIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417 (1432)
Q Consensus 1338 ~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~ 1417 (1432)
.++ +|...+........+..+|+.||++++.||.++|+.++ |++|||+.||+|+++|++++++|+++||..
T Consensus 192 ~~~-----~~~~~~e~~~~~~~l~~~l~~L~~rer~vl~l~y~~~~----t~~EIA~~lgis~~~V~~~~~ral~kLr~~ 262 (264)
T PRK07122 192 TLG-----DVDAGLDQIENREALRPLLAALPERERTVLVLRFFESM----TQTQIAERVGISQMHVSRLLAKTLARLRDQ 262 (264)
T ss_pred ccC-----CcHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhcCCC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 433 45566677778899999999999999999999998887 999999999999999999999999999985
Q ss_pred h
Q psy15215 1418 S 1418 (1432)
Q Consensus 1418 ~ 1418 (1432)
+
T Consensus 263 l 263 (264)
T PRK07122 263 L 263 (264)
T ss_pred c
Confidence 3
No 24
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=100.00 E-value=8.1e-38 Score=355.26 Aligned_cols=227 Identities=24% Similarity=0.390 Sum_probs=206.5
Q ss_pred HhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHHHHHHh
Q psy15215 393 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQ 472 (1432)
Q Consensus 393 ~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~~i~~~ 472 (1432)
.|+....++++.||.+|+|||+++|++|.++|.+++||||||+|||++|+++|||.+|++|+|||+||||++|.++++++
T Consensus 33 ~~~~~~~~~r~~Lv~~~l~LV~~iA~~y~~~g~~~~DLiQeG~iGLi~AierFDp~~G~~FsTYA~~~Irg~I~~~lr~~ 112 (264)
T PRK07122 33 AGSPEFQRQRDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGEVRRHFRDN 112 (264)
T ss_pred CCCHHHHHHHHHHHHHhHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHHc
Confidence 45666667999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHH--ccCCCCCCCCCCCCCCC--CcCcc
Q psy15215 473 ARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKI--AKEPVSMESPVGDDEDS--HLGDF 548 (1432)
Q Consensus 473 ~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~--~~~~~sl~~~~~~~~~~--~~~~~ 548 (1432)
.++||+|+++.+.+++++++...+.+++|++||++|||+.||+++++|..++.. ...++||+.|++++++. .+.+.
T Consensus 113 ~~~ir~Pr~~~~~~~~i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~~~~~d~ 192 (264)
T PRK07122 113 SWSVKVPRRLKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVVEGLVAGSAYNTLSIDSGGGSGDDDARAIADT 192 (264)
T ss_pred CCccccCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhhcCCCCcccccccCCCCCcccchhc
Confidence 999999999999999999999999999999999999999999999999999864 45789999998754332 33443
Q ss_pred cccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHH
Q psy15215 549 IEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLA 628 (1432)
Q Consensus 549 i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l 628 (1432)
+ .+|...+...+....+..+|+.||++++.||.++|+.++ |++|||+.||+|+++|+++.++|+.+|+..+
T Consensus 193 ~-----~~~~~~~e~~~~~~~l~~~l~~L~~rer~vl~l~y~~~~----t~~EIA~~lgis~~~V~~~~~ral~kLr~~l 263 (264)
T PRK07122 193 L-----GDVDAGLDQIENREALRPLLAALPERERTVLVLRFFESM----TQTQIAERVGISQMHVSRLLAKTLARLRDQL 263 (264)
T ss_pred c-----CCcHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhcCCC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHc
Confidence 3 245566677778889999999999999999999998887 9999999999999999999999999999865
No 25
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=100.00 E-value=1.6e-37 Score=361.67 Aligned_cols=265 Identities=38% Similarity=0.666 Sum_probs=249.5
Q ss_pred HHHHHHHhhhhcCCChhhHHHHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhc
Q psy15215 1156 LQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKF 1235 (1432)
Q Consensus 1156 ~q~~L~~ie~~~~l~~~e~~~l~~~~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kf 1235 (1432)
.+..+.+++..+.+++.+...++.+++.|+.. |++.||..|.++|+++|++|++++.+++||+||||+|+|+++++|
T Consensus 55 ~~~y~~~~~~~~~l~~~ee~~li~~~~~Gd~~---A~~~Li~~y~~~V~~~a~~~~~~~~~aeDLvQE~fi~l~~ai~~f 131 (325)
T PRK05657 55 TQLYLNEIGYSPLLTAEEEVYFARRALRGDFA---ARQRMIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKF 131 (325)
T ss_pred HHHHHHHHhcCCCCCHHHHHHHHHHHHcCCHH---HHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHh
Confidence 35678889999999999999999999999988 999999999999999999999999999999999999999999999
Q ss_pred cccCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHH
Q psy15215 1236 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMK 1315 (1432)
Q Consensus 1236 d~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~ 1315 (1432)
++.+|++|+||++||||++|.++++++.+++|+|+|++..++++.|..+.+.+.+|++||+++||+.+|+++++|..++.
T Consensus 132 d~~rg~~Fstyatw~iR~ai~~~i~~~~r~ir~p~~~~~~l~~~~R~~~~l~~~l~r~~t~~eiA~~l~~~~~~v~~~l~ 211 (325)
T PRK05657 132 DPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPVHVVKELNVYLRAARELEHKLDHEPSAEEIAELLDKPVDDVSRMLA 211 (325)
T ss_pred CCccCCCHHHHHHHHHHHHHHHHHHHcCCccccCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HccCCCCCCCCCCCCCCCCcCcccccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHH
Q psy15215 1316 IAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQ 1395 (1432)
Q Consensus 1316 ~~~~~~Sl~~~~~~~~~~~~~d~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~ 1395 (1432)
......||+.|+++++..++.+.+.+....+|++.+...++...|..+|..||+++|.||.+|||+....++|++|||+.
T Consensus 212 ~~~~~~sld~~~~~~~~~~l~d~l~d~~~~~pe~~~~~~e~~~~L~~aL~~L~~~~R~vl~lrygL~~~e~~s~~EIA~~ 291 (325)
T PRK05657 212 LNERITSLDTPLGGDPEKSLLDILADEQENGPEDTTQDDDMKQSIVKWLFELNDKQREVLARRFGLLGYEAATLEDVARE 291 (325)
T ss_pred hccCCcccCCCCCCCCCcchhhhccCCCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhccCCCCCcCHHHHHHH
Confidence 88888999999888777788888888777789999999999999999999999999999999998776678899999999
Q ss_pred hCCCHHHHHHHHHHHHHHhhCchhhhhH
Q psy15215 1396 FDVTRERIRQIEAKALRKLRHPSRYYKL 1423 (1432)
Q Consensus 1396 l~vs~~~Vrq~~~rAl~kLr~~~~~~~l 1423 (1432)
+|||++||++++++|+++||+.+....+
T Consensus 292 Lgis~~tV~~~~~rAl~kLr~~l~~~~~ 319 (325)
T PRK05657 292 IGLTRERVRQIQVEALRRLREILQTQGL 319 (325)
T ss_pred HCcCHHHHHHHHHHHHHHHHHHHHhCcc
Confidence 9999999999999999999997766544
No 26
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=100.00 E-value=2.8e-37 Score=354.59 Aligned_cols=255 Identities=26% Similarity=0.480 Sum_probs=217.9
Q ss_pred HHHHHhhhhcCCChhhHHHHHHHH-HhhhhhhhhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhcc
Q psy15215 1158 QKLINLQTDIVLPLNDLRDINRKM-IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 1236 (1432)
Q Consensus 1158 ~~L~~ie~~~~l~~~e~~~l~~~~-~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd 1236 (1432)
.++.++.....++..+...++.++ ..||.. |++.||..|+++|+++|++|.+++.+++||+||||+|||+|+++||
T Consensus 18 ~y~~~~~~~~~l~~~~e~~l~~~~~~~Gd~~---a~~~Lv~~~~~lV~~ia~~~~~~~~~~eDLvQeg~igL~~a~~~fd 94 (284)
T PRK06596 18 AYIQAVNKIPMLTAEEEYMLAKRLREHGDLE---AAKQLVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFD 94 (284)
T ss_pred HHHHHHhccCCCCHHHHHHHHHHHHHcCCHH---HHHHHHHHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHhC
Confidence 466677777788999899999995 589888 9999999999999999999999999999999999999999999999
Q ss_pred ccCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHHh--CCCCCHHHHHHHcCCCHHHHHHHH
Q psy15215 1237 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQET--GSEPDPSVIAIKMEMPEEKIRKIM 1314 (1432)
Q Consensus 1237 ~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~--g~~pt~~eia~~~~~~~~~v~~~~ 1314 (1432)
+.+|++|+|||+||||++|.++++++++++|+|.+... +++....+.+.+++ +++||.+|||+.||+++++|..++
T Consensus 95 ~~~~~~FstYA~~~Ir~~i~~~l~~~~~~vr~p~~~~~--~~~~~~~~~~~~~l~~~~~~t~~eiA~~l~~~~~~v~~~~ 172 (284)
T PRK06596 95 PEVGVRLVSFAVHWIKAEIHEYILRNWRIVKVATTKAQ--RKLFFNLRKAKKRLGWLNPEEVEMVAEELGVSEEEVREME 172 (284)
T ss_pred cccCCCHHHHHHHHHHHHHHHHHHHcCCeeeccchHHH--HHHHHHHHHHHHHhccCCCCCHHHHHHHhCcCHHHHHHHH
Confidence 99999999999999999999999999888999998642 23333333444444 499999999999999999999997
Q ss_pred H-HccCCCCCCCCCCCCCC--CCcCcccccCCCCChHHHHHHH----HHHHHHHHHHccCCHHHHHHHHHHhcccCCCCC
Q psy15215 1315 K-IAKEPVSMESPVGDDED--SHLGDFIEDENMLAPSDAALNA----SMRSVVKDILNSLTPRESKVLRMRFGIEMSSDH 1387 (1432)
Q Consensus 1315 ~-~~~~~~Sl~~~~~~~~~--~~~~d~i~d~~~~~p~~~~~~~----~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~ 1387 (1432)
. .....+||+.|++++++ .++.+++++. ..+|++.+... .+...|..+|+.||++|+.||.+||+.+ .++
T Consensus 173 ~~~~~~~~SLd~~~~~~~~~~~~l~~~l~d~-~~~p~~~~~~~~~~~~~~~~L~~al~~L~~rEr~VL~lry~~~--~~~ 249 (284)
T PRK06596 173 SRLSGQDASLDAPIDDDDEESGAPQDYLEDK-SSDPADVLEEDNWEDQRRALLADALEGLDERSRDIIEARWLDD--DKS 249 (284)
T ss_pred HHhcCCCcCcCCCCCCCCCCcchHHHHcCCC-CCCchHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcCC--CCc
Confidence 5 34578999999875533 3577888877 35787776654 3678899999999999999999999752 456
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHhhCchhh
Q psy15215 1388 TLEEVGKQFDVTRERIRQIEAKALRKLRHPSRY 1420 (1432)
Q Consensus 1388 t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~~ 1420 (1432)
|++|||+.||||++||||++++|++|||+...+
T Consensus 250 Tl~EIA~~lgvS~~rVrqi~~~Al~kLR~~l~~ 282 (284)
T PRK06596 250 TLQELAAEYGVSAERVRQIEKNAMKKLKAAIEA 282 (284)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 999999999999999999999999999996554
No 27
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=100.00 E-value=7.2e-37 Score=356.30 Aligned_cols=261 Identities=38% Similarity=0.683 Sum_probs=247.7
Q ss_pred HHHHHHhhhhccCCChhhHHHHHHHHHHhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhc
Q psy15215 366 LQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKF 445 (1432)
Q Consensus 366 ~q~~L~~iE~~~~l~~~e~~~l~~~i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~f 445 (1432)
.+.++.+++..+.++..+...++.+++.||.. |++.||..|.++|+++|++|++++.+++||+||||+|+|+++++|
T Consensus 55 ~~~y~~~~~~~~~l~~~ee~~li~~~~~Gd~~---A~~~Li~~y~~~V~~~a~~~~~~~~~aeDLvQE~fi~l~~ai~~f 131 (325)
T PRK05657 55 TQLYLNEIGYSPLLTAEEEVYFARRALRGDFA---ARQRMIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKF 131 (325)
T ss_pred HHHHHHHHhcCCCCCHHHHHHHHHHHHcCCHH---HHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHh
Confidence 46688899999999999999999999999999 999999999999999999999999999999999999999999999
Q ss_pred cccCCCccHHHHHHHHHHHHHHHHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHH
Q psy15215 446 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMK 525 (1432)
Q Consensus 446 d~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~ 525 (1432)
++.+|++|+|||+||||++|.+++.++.+++|+|+|++..++++.|+.+.+.+.+|++||+++||..+|+++++|..++.
T Consensus 132 d~~rg~~Fstyatw~iR~ai~~~i~~~~r~ir~p~~~~~~l~~~~R~~~~l~~~l~r~~t~~eiA~~l~~~~~~v~~~l~ 211 (325)
T PRK05657 132 DPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPVHVVKELNVYLRAARELEHKLDHEPSAEEIAELLDKPVDDVSRMLA 211 (325)
T ss_pred CCccCCCHHHHHHHHHHHHHHHHHHHcCCccccCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HccCCCCCCCCCCCCCCCCcCcccccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhh
Q psy15215 526 IAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQ 605 (1432)
Q Consensus 526 ~~~~~~sl~~~~~~~~~~~~~~~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~ 605 (1432)
......|++.|+++++..++.+.+++....+|++.+...+....|..+|.+||+++|.||.+|||+....++|++|||+.
T Consensus 212 ~~~~~~sld~~~~~~~~~~l~d~l~d~~~~~pe~~~~~~e~~~~L~~aL~~L~~~~R~vl~lrygL~~~e~~s~~EIA~~ 291 (325)
T PRK05657 212 LNERITSLDTPLGGDPEKSLLDILADEQENGPEDTTQDDDMKQSIVKWLFELNDKQREVLARRFGLLGYEAATLEDVARE 291 (325)
T ss_pred hccCCcccCCCCCCCCCcchhhhccCCCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhccCCCCCcCHHHHHHH
Confidence 88888999999887777778888888777789999999999999999999999999999999998776678899999999
Q ss_pred cccchhHHHHHHHHHHHHHHHHHH
Q psy15215 606 FDVTRERIRQIEAKALRKLRPLAH 629 (1432)
Q Consensus 606 l~is~~~v~~~~~rAl~kLr~~l~ 629 (1432)
+|+|+++|+++.++|+++||+.+.
T Consensus 292 Lgis~~tV~~~~~rAl~kLr~~l~ 315 (325)
T PRK05657 292 IGLTRERVRQIQVEALRRLREILQ 315 (325)
T ss_pred HCcCHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999998874
No 28
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=100.00 E-value=4.8e-37 Score=353.18 Aligned_cols=259 Identities=27% Similarity=0.424 Sum_probs=223.7
Q ss_pred HHHHHHhhhhcCCChhhHHHHHHHHH-hhhhhhhhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhc
Q psy15215 1157 QQKLINLQTDIVLPLNDLRDINRKMI-AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKF 1235 (1432)
Q Consensus 1157 q~~L~~ie~~~~l~~~e~~~l~~~~~-~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kf 1235 (1432)
..+|..+.....++..+...|++++. .|+.. |++.||..|+|+|+++|++|++++.+++||+||||+|||+|+++|
T Consensus 9 ~~y~~~~~~~~~l~~~~e~~L~~~~~~~gd~~---A~~~Lv~~~~~lV~~~a~~~~~~~~~~eDLvQeg~i~L~~a~~~f 85 (289)
T PRK07500 9 RSMIRSAMKAPYLEREEEHALAYRWKDHRDED---ALHRIISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARF 85 (289)
T ss_pred HHHHHHHhcCCCCCHHHHHHHHHHHHHCCCHH---HHHHHHHHhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHc
Confidence 34778888888899999999999974 78888 999999999999999999999999999999999999999999999
Q ss_pred cccCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHH--HHHHHHHHHHHHHH---HhCCCCCHHHHHHHcCCCHHHH
Q psy15215 1236 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE--TINKISRISRQILQ---ETGSEPDPSVIAIKMEMPEEKI 1310 (1432)
Q Consensus 1236 d~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~~~~~--~~~k~~~~~~~~~~---~~g~~pt~~eia~~~~~~~~~v 1310 (1432)
++.+|.+|+|||+||||++|.++++++.+++|+|++... ...+++++...+.+ .+|++||++|||+.||+++++|
T Consensus 86 d~~~~~~f~tya~~~Ir~~I~~~lr~~~~~iR~p~~~~~~~~~~~~~~~~~~~~~~~~~l~~~pt~~eiA~~l~~~~~~v 165 (289)
T PRK07500 86 EPDREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQKALFFNLRRLRARLAQADEELTKQEIHREIATALGVSLSDV 165 (289)
T ss_pred CCCCCCChHHHHHHHHHHHHHHHHHHCCCceecCccHHHHHHHHHHHHHHHHHHhhhcccCCCCCHHHHHHHhCcCHHHH
Confidence 999999999999999999999999999999999999765 44555555555555 6899999999999999999999
Q ss_pred HHHHH-HccCCCCCCCCCCCCCCC--CcCcccccCCCCChHHHHHH----HHHHHHHHHHHccCCHHHHHHHHHHhcccC
Q psy15215 1311 RKIMK-IAKEPVSMESPVGDDEDS--HLGDFIEDENMLAPSDAALN----ASMRSVVKDILNSLTPRESKVLRMRFGIEM 1383 (1432)
Q Consensus 1311 ~~~~~-~~~~~~Sl~~~~~~~~~~--~~~d~i~d~~~~~p~~~~~~----~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~ 1383 (1432)
..+.. ....++|||.|++++++. ++.+++++.. .+|++.+.. ..+...|..+|+.||++|+.||.+||+.
T Consensus 166 ~~~~~~~~~~~~SLd~~~~~~~~~~~~l~d~i~d~~-~~pe~~~~~~~~~~~~~~~l~~al~~L~~rer~vl~lr~~~-- 242 (289)
T PRK07500 166 EMMDARLSGPDASLNAPQSEEDEGRSERMDFLVDDS-PLPDEQVESSIDGERRRRWLTQALQTLNERELRIIRERRLR-- 242 (289)
T ss_pred HHHHHHhcCCCccccCCCCCCCCCcccHHHhccCCC-CCchHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcC--
Confidence 98763 455789999998766543 5778888764 467766543 4467789999999999999999999972
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchhhh
Q psy15215 1384 SSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYY 1421 (1432)
Q Consensus 1384 ~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~~~ 1421 (1432)
..++|++|||+.||||++||+|++++|++|||......
T Consensus 243 ~~~~t~~EIa~~lgvs~~~V~q~~~~Al~kLr~~l~~~ 280 (289)
T PRK07500 243 EDGATLEALGEELGISKERVRQIEARALEKLRRALLSQ 280 (289)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhc
Confidence 24559999999999999999999999999999876543
No 29
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=100.00 E-value=9.1e-37 Score=346.10 Aligned_cols=237 Identities=25% Similarity=0.451 Sum_probs=209.3
Q ss_pred hHHHHHHHHH-hhhhhhhhhHHHHHHHHHHHHHHHHHhccCC-CCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHH
Q psy15215 1173 DLRDINRKMI-AGEMKARKAKREMTEANLRLVISIAKKYTDR-GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 1250 (1432)
Q Consensus 1173 e~~~l~~~~~-~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~-~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ 1250 (1432)
+...++...+ .|+.. |+++||..|+|+|+++|++|.++ +.+++||+|||++|||+|+++|||.+|++|+|||+||
T Consensus 10 ~~~~~~~~~~~~gd~~---a~~~Lv~~~~~lV~~ia~~~~~~~~~~~eDL~Qeg~igL~~a~~~fd~~~g~~F~tya~~~ 86 (256)
T PRK07408 10 ETMELLRAYQQNPSIA---LRNQLVELNLGLVRKEAHRWSNQCSEPYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPY 86 (256)
T ss_pred HHHHHHHHHHHCCCHH---HHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHH
Confidence 5566666664 77777 99999999999999999999876 6679999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHH--HccCCCCCCCCCC
Q psy15215 1251 IRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMK--IAKEPVSMESPVG 1328 (1432)
Q Consensus 1251 ir~~i~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~--~~~~~~Sl~~~~~ 1328 (1432)
||++|.++++++.++||+|+++.+.+++++++..++.+++|++||++|||+.||+++++|..++. ....++||+.|++
T Consensus 87 Ir~~i~~~lr~~~~~vr~pr~~~~~~~~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~~~~~~~~~~~~SLd~~~~ 166 (256)
T PRK07408 87 IRGEIQHYLRDKSPTVRIPRRWQELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIKLALQNRTPLSLDAPVN 166 (256)
T ss_pred HHHHHHHHHHHcCCeeeeCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHhhccCCccccccCC
Confidence 99999999999999999999999999999999999999999999999999999999999999975 3456899999986
Q ss_pred CCCCC--CcCcccccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHH
Q psy15215 1329 DDEDS--HLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQI 1406 (1432)
Q Consensus 1329 ~~~~~--~~~d~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~ 1406 (1432)
++++. .+.+.++++... +.. ...+....|..+|.+||+++|.||.++|+.|+ |++|||+.||+|+++|+++
T Consensus 167 ~~~~~~~~l~d~~~d~~~~-~~~--~~~~~~~~l~~~l~~L~~~~r~vl~l~y~~~~----s~~eIA~~lgvs~~~V~~~ 239 (256)
T PRK07408 167 QDEDGSTSLGDLLPDPRYR-SFQ--LAQEDRIRLQQALAQLEERTREVLEFVFLHDL----TQKEAAERLGISPVTVSRR 239 (256)
T ss_pred CCCCCccccccccCCcccc-hhh--hhHHHHHHHHHHHHcCCHHHHHHHHHHHHCCC----CHHHHHHHHCcCHHHHHHH
Confidence 55443 566777665432 221 23345678999999999999999999998888 9999999999999999999
Q ss_pred HHHHHHHhhCchh
Q psy15215 1407 EAKALRKLRHPSR 1419 (1432)
Q Consensus 1407 ~~rAl~kLr~~~~ 1419 (1432)
+++|+++||..+.
T Consensus 240 ~~ra~~kLr~~l~ 252 (256)
T PRK07408 240 VKKGLDQLKKLLQ 252 (256)
T ss_pred HHHHHHHHHHHhh
Confidence 9999999998654
No 30
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=100.00 E-value=2e-36 Score=347.51 Aligned_cols=255 Identities=25% Similarity=0.487 Sum_probs=219.2
Q ss_pred HHHHHhhhhccCCChhhHHHHHHHH-HHhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhc
Q psy15215 367 QQKLINLQTDIVLPLNDLRDINRKM-IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKF 445 (1432)
Q Consensus 367 q~~L~~iE~~~~l~~~e~~~l~~~i-~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~f 445 (1432)
..++.++.....++..+...++.++ +.||.. |++.||..|+|+|+++|++|.+.+.+++||+|||++|||+|+++|
T Consensus 17 ~~y~~~~~~~~~l~~~~e~~l~~~~~~~Gd~~---a~~~Lv~~~~~lV~~ia~~~~~~~~~~eDLvQeg~igL~~a~~~f 93 (284)
T PRK06596 17 DAYIQAVNKIPMLTAEEEYMLAKRLREHGDLE---AAKQLVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRF 93 (284)
T ss_pred HHHHHHHhccCCCCHHHHHHHHHHHHHcCCHH---HHHHHHHHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHh
Confidence 3577788888889999999999995 589988 999999999999999999999999999999999999999999999
Q ss_pred cccCCCccHHHHHHHHHHHHHHHHHHhccccccchhHHH--HHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHH
Q psy15215 446 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE--TINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKI 523 (1432)
Q Consensus 446 d~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~~~~~--~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~ 523 (1432)
|+.+|++|+|||+|||+++|.++++++++++|+|.+... ...++.+...++. .+++||.+|||+.||+++++|..+
T Consensus 94 d~~~~~~FstYA~~~Ir~~i~~~l~~~~~~vr~p~~~~~~~~~~~~~~~~~~l~--~~~~~t~~eiA~~l~~~~~~v~~~ 171 (284)
T PRK06596 94 DPEVGVRLVSFAVHWIKAEIHEYILRNWRIVKVATTKAQRKLFFNLRKAKKRLG--WLNPEEVEMVAEELGVSEEEVREM 171 (284)
T ss_pred CcccCCCHHHHHHHHHHHHHHHHHHHcCCeeeccchHHHHHHHHHHHHHHHHhc--cCCCCCHHHHHHHhCcCHHHHHHH
Confidence 999999999999999999999999999888999998642 2334444443332 359999999999999999999999
Q ss_pred HH-HccCCCCCCCCCCCCCC--CCcCcccccCCCCChHHHHHHH----HHHHHHHHHHhcCCHHHHHHHHHHhhcccCCC
Q psy15215 524 MK-IAKEPVSMESPVGDDED--SHLGDFIEDENMLAPSDAALNA----SMRSVVKDILNSLTPRESKVLRMRFGIEMSSD 596 (1432)
Q Consensus 524 ~~-~~~~~~sl~~~~~~~~~--~~~~~~i~d~~~~~p~~~~~~~----~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~ 596 (1432)
+. .....+||+.|++++++ .++.+++++. ..+|++.+... .+...|..+++.||++|+.||++||+.+ .+
T Consensus 172 ~~~~~~~~~SLd~~~~~~~~~~~~l~~~l~d~-~~~p~~~~~~~~~~~~~~~~L~~al~~L~~rEr~VL~lry~~~--~~ 248 (284)
T PRK06596 172 ESRLSGQDASLDAPIDDDDEESGAPQDYLEDK-SSDPADVLEEDNWEDQRRALLADALEGLDERSRDIIEARWLDD--DK 248 (284)
T ss_pred HHHhcCCCcCcCCCCCCCCCCcchHHHHcCCC-CCCchHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcCC--CC
Confidence 75 34578999999875533 3577888876 35787776654 3578899999999999999999999752 46
Q ss_pred CcHHHHHhhcccchhHHHHHHHHHHHHHHHHHH
Q psy15215 597 HTLEEVGKQFDVTRERIRQIEAKALRKLRPLAH 629 (1432)
Q Consensus 597 ~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l~ 629 (1432)
+|++|||+.||+|+++|+|++++|+.+||+.+.
T Consensus 249 ~Tl~EIA~~lgvS~~rVrqi~~~Al~kLR~~l~ 281 (284)
T PRK06596 249 STLQELAAEYGVSAERVRQIEKNAMKKLKAAIE 281 (284)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 699999999999999999999999999998875
No 31
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=100.00 E-value=2.6e-36 Score=347.06 Aligned_cols=257 Identities=28% Similarity=0.434 Sum_probs=224.2
Q ss_pred HHHHHhhhhccCCChhhHHHHHHHHH-HhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhc
Q psy15215 367 QQKLINLQTDIVLPLNDLRDINRKMI-AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKF 445 (1432)
Q Consensus 367 q~~L~~iE~~~~l~~~e~~~l~~~i~-~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~f 445 (1432)
..+|.++-....++..+...|+.+++ .||.. |++.||..|+|+|+++|++|++++.+++||+||||+|||+|+++|
T Consensus 9 ~~y~~~~~~~~~l~~~~e~~L~~~~~~~gd~~---A~~~Lv~~~~~lV~~~a~~~~~~~~~~eDLvQeg~i~L~~a~~~f 85 (289)
T PRK07500 9 RSMIRSAMKAPYLEREEEHALAYRWKDHRDED---ALHRIISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARF 85 (289)
T ss_pred HHHHHHHhcCCCCCHHHHHHHHHHHHHCCCHH---HHHHHHHHhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHc
Confidence 44788898889999999999999975 79988 999999999999999999999999999999999999999999999
Q ss_pred cccCCCccHHHHHHHHHHHHHHHHHHhccccccchhHHH--HHHHHHHHHHHHHH---HhCCCCCHHHHHHHcCCCHHHH
Q psy15215 446 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE--TINKISRISRQILQ---ETGSEPDPSVIAIKMEMPEEKI 520 (1432)
Q Consensus 446 d~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~~~~~--~~~k~~r~~~~~~~---~~g~~pt~~eia~~~~~~~~~v 520 (1432)
++.+|.+|+|||+||||++|.++|+++++.+|+|++... ...++.++...+.+ .+|++||.+|||+.||+++++|
T Consensus 86 d~~~~~~f~tya~~~Ir~~I~~~lr~~~~~iR~p~~~~~~~~~~~~~~~~~~~~~~~~~l~~~pt~~eiA~~l~~~~~~v 165 (289)
T PRK07500 86 EPDREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQKALFFNLRRLRARLAQADEELTKQEIHREIATALGVSLSDV 165 (289)
T ss_pred CCCCCCChHHHHHHHHHHHHHHHHHHCCCceecCccHHHHHHHHHHHHHHHHHHhhhcccCCCCCHHHHHHHhCcCHHHH
Confidence 999999999999999999999999999999999998765 44566666655555 6899999999999999999999
Q ss_pred HHHH-HHccCCCCCCCCCCCCCCC--CcCcccccCCCCChHHHHHH----HHHHHHHHHHHhcCCHHHHHHHHHHhhccc
Q psy15215 521 RKIM-KIAKEPVSMESPVGDDEDS--HLGDFIEDENMLAPSDAALN----ASMRSVVKDILNSLTPRESKVLRMRFGIEM 593 (1432)
Q Consensus 521 ~~~~-~~~~~~~sl~~~~~~~~~~--~~~~~i~d~~~~~p~~~~~~----~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~ 593 (1432)
..+. .....++||+.|++++++. ++.+++++.. .+|++.+.. .++...|..+|+.||++|+.||.+||+.
T Consensus 166 ~~~~~~~~~~~~SLd~~~~~~~~~~~~l~d~i~d~~-~~pe~~~~~~~~~~~~~~~l~~al~~L~~rer~vl~lr~~~-- 242 (289)
T PRK07500 166 EMMDARLSGPDASLNAPQSEEDEGRSERMDFLVDDS-PLPDEQVESSIDGERRRRWLTQALQTLNERELRIIRERRLR-- 242 (289)
T ss_pred HHHHHHhcCCCccccCCCCCCCCCcccHHHhccCCC-CCchHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcC--
Confidence 9875 3456789999998765543 5778888764 467766543 3466789999999999999999999972
Q ss_pred CCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHHH
Q psy15215 594 SSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLAH 629 (1432)
Q Consensus 594 ~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l~ 629 (1432)
..++|++|||+.||+|+++|++++++|+++||..+.
T Consensus 243 ~~~~t~~EIa~~lgvs~~~V~q~~~~Al~kLr~~l~ 278 (289)
T PRK07500 243 EDGATLEALGEELGISKERVRQIEARALEKLRRALL 278 (289)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 245599999999999999999999999999998775
No 32
>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=3.2e-36 Score=344.61 Aligned_cols=253 Identities=26% Similarity=0.470 Sum_probs=213.6
Q ss_pred HHHHHhhhhcCCChhhHHHHHHH-HHhhhhhhhhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhcc
Q psy15215 1158 QKLINLQTDIVLPLNDLRDINRK-MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 1236 (1432)
Q Consensus 1158 ~~L~~ie~~~~l~~~e~~~l~~~-~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd 1236 (1432)
.+|.++.....++..+...|+.+ ...|+.. |++.|+..|+++|+++|++|.+++.+++||+||||+|||+|+++||
T Consensus 5 ~yl~~~~~~~~l~~~~e~~l~~~~~~~gd~~---a~~~Lv~~~~~lV~~~a~~~~~~~~~~eDLvQeg~igl~~a~~~fd 81 (270)
T TIGR02392 5 AYIRAVNRIPMLTPEEEYQLAKRLREHGDLD---AAKKLVLSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRFD 81 (270)
T ss_pred HHHHHHhcCCCCCHHHHHHHHHHHHHCCCHH---HHHHHHHHhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhC
Confidence 46777888888999999999998 4688888 9999999999999999999999999999999999999999999999
Q ss_pred ccCCCcchhHHHHHHHHHHHHHHHHhcccccccccHH--HHHHHHHHHHHHHHHHhCCCC-CHHHHHHHcCCCHHHHHHH
Q psy15215 1237 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI--ETINKISRISRQILQETGSEP-DPSVIAIKMEMPEEKIRKI 1313 (1432)
Q Consensus 1237 ~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~~~~--~~~~k~~~~~~~~~~~~g~~p-t~~eia~~~~~~~~~v~~~ 1313 (1432)
+.+|++|||||+||||++|.++++++++++|+|.+.. +..++++.+...+. .++.| |.+|||+.||+++++|..+
T Consensus 82 ~~~~~~FsTYA~~~Ir~~i~~~l~~~~~~ir~p~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~eiA~~l~~~~~~v~~~ 159 (270)
T TIGR02392 82 PERGVRLVSFAVHWIKAEIHEYILRNWRLVKVATTKAQRKLFFNLRKMKKRLQ--GWLNPEEVEAIAEELGVSEREVREM 159 (270)
T ss_pred cccCCChHHhhHHHHHHHHHHHHHHcCCceecCchHHHHHHHHHHHHHHHHHh--cCCCCCCHHHHHHHhCCCHHHHHHH
Confidence 9999999999999999999999999988899998754 33444444443332 22555 6999999999999999998
Q ss_pred HHH-ccCCCCCCCCCCCCCCC--CcCcccccCCCCChHHHHHHH----HHHHHHHHHHccCCHHHHHHHHHHhcccCCCC
Q psy15215 1314 MKI-AKEPVSMESPVGDDEDS--HLGDFIEDENMLAPSDAALNA----SMRSVVKDILNSLTPRESKVLRMRFGIEMSSD 1386 (1432)
Q Consensus 1314 ~~~-~~~~~Sl~~~~~~~~~~--~~~d~i~d~~~~~p~~~~~~~----~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~ 1386 (1432)
+.. ...++||+.|++++++. .+.+++++.. .+|++.+... .+...|..+|..||++||.||.+||+. +.+
T Consensus 160 ~~~~~~~~~Sld~~~~~~~~~~~~~~~~l~d~~-~~pe~~~~~~~~~~~~~~~L~~al~~L~~rer~vl~l~y~~--~~~ 236 (270)
T TIGR02392 160 ESRLSGQDMSLNASIDDDEDDGGAPIAYLVDKT-SDPEDTLEEEQWEELQRQALANALGSLDARSRRIIEARWLD--DDK 236 (270)
T ss_pred HHHccCCCccCCCCCCCCCCccccHHHHhcCCC-CChHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhcC--CCC
Confidence 753 34589999998775443 4667777764 4687766643 366889999999999999999999975 235
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHhhCch
Q psy15215 1387 HTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418 (1432)
Q Consensus 1387 ~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~ 1418 (1432)
+|++|||+.||||++||+|++++|++|||+..
T Consensus 237 ~t~~eIA~~lgvS~~~V~q~~~~Al~kLr~~l 268 (270)
T TIGR02392 237 LTLQELAAEYGVSAERIRQIEKNAMKKLKAAL 268 (270)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 59999999999999999999999999999854
No 33
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=100.00 E-value=4.8e-36 Score=340.19 Aligned_cols=237 Identities=26% Similarity=0.459 Sum_probs=209.3
Q ss_pred hHHHHHHHHH-HhHHHHHHhHHHHHHHHHHHHHHHHHhcccC-CCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHH
Q psy15215 383 DLRDINRKMI-AGEMKARKAKREMTEANLRLVISIAKKYTDR-GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 460 (1432)
Q Consensus 383 e~~~l~~~i~-~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~-~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ 460 (1432)
+...++...+ .|+.. |+++||..|+|+|+++|++|.++ +.+++||+|||+||||+|+++|||.+|++|+|||+||
T Consensus 10 ~~~~~~~~~~~~gd~~---a~~~Lv~~~~~lV~~ia~~~~~~~~~~~eDL~Qeg~igL~~a~~~fd~~~g~~F~tya~~~ 86 (256)
T PRK07408 10 ETMELLRAYQQNPSIA---LRNQLVELNLGLVRKEAHRWSNQCSEPYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPY 86 (256)
T ss_pred HHHHHHHHHHHCCCHH---HHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHH
Confidence 5566666665 78887 99999999999999999999876 6679999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHH--HccCCCCCCCCCC
Q psy15215 461 IRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMK--IAKEPVSMESPVG 538 (1432)
Q Consensus 461 ir~~i~~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~--~~~~~~sl~~~~~ 538 (1432)
|+|+|.++++++.++||+|+++.+.+++++++..++.+++|++||++|||+.||+++++|..+.. ....++||+.+++
T Consensus 87 Ir~~i~~~lr~~~~~vr~pr~~~~~~~~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~~~~~~~~~~~~SLd~~~~ 166 (256)
T PRK07408 87 IRGEIQHYLRDKSPTVRIPRRWQELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIKLALQNRTPLSLDAPVN 166 (256)
T ss_pred HHHHHHHHHHHcCCeeeeCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHhhccCCccccccCC
Confidence 99999999999999999999999999999999999999999999999999999999999999875 3456789999986
Q ss_pred CCCCC--CcCcccccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHH
Q psy15215 539 DDEDS--HLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQI 616 (1432)
Q Consensus 539 ~~~~~--~~~~~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~ 616 (1432)
++++. .+.+.+++.... +.. ...+....|..+|.+||++++.||.++|+.|+ |++|||+.+|+|+++|+++
T Consensus 167 ~~~~~~~~l~d~~~d~~~~-~~~--~~~~~~~~l~~~l~~L~~~~r~vl~l~y~~~~----s~~eIA~~lgvs~~~V~~~ 239 (256)
T PRK07408 167 QDEDGSTSLGDLLPDPRYR-SFQ--LAQEDRIRLQQALAQLEERTREVLEFVFLHDL----TQKEAAERLGISPVTVSRR 239 (256)
T ss_pred CCCCCccccccccCCcccc-hhh--hhHHHHHHHHHHHHcCCHHHHHHHHHHHHCCC----CHHHHHHHHCcCHHHHHHH
Confidence 54433 566777665432 211 23345678999999999999999999998888 9999999999999999999
Q ss_pred HHHHHHHHHHHHH
Q psy15215 617 EAKALRKLRPLAH 629 (1432)
Q Consensus 617 ~~rAl~kLr~~l~ 629 (1432)
.++|+.+|+..+.
T Consensus 240 ~~ra~~kLr~~l~ 252 (256)
T PRK07408 240 VKKGLDQLKKLLQ 252 (256)
T ss_pred HHHHHHHHHHHhh
Confidence 9999999998764
No 34
>PRK05667 dnaG DNA primase; Validated
Probab=100.00 E-value=3.2e-37 Score=381.48 Aligned_cols=203 Identities=36% Similarity=0.528 Sum_probs=172.1
Q ss_pred HHHHHHHHHHHHHHHHHhhh--hhhhhH-hhcC--CCcccccccccCCCCCchhhHHHHHHH----------------H-
Q psy15215 618 AKALRKLRPLAHDWLEQRTH--QNEKII-ACSS--DSSNHNEHVTNNNFPPGFNIFHKLLRI----------------L- 675 (1432)
Q Consensus 618 ~rAl~kLr~~l~~~~~~~l~--~~~~~~-~l~~--l~~~~~~~f~~Gyap~~~~~l~~~~~~----------------~- 675 (1432)
+..+..+...+..||+.++. .+..|+ ||.. ||+++|++|+|||||.+|+.|.+++.. .
T Consensus 107 ~~~l~~~~~~a~~~y~~~L~~~~~~~a~~YL~~RGls~~~i~~f~lGyap~~~~~L~~~l~~~~~~~~~l~~~GL~~~~~ 186 (580)
T PRK05667 107 RQRLYEIMELAAKFYQQQLRTPEGAEARQYLYKRGLSEETIERFGIGYAPDGWDALLKHLGGKGFSEKELEEAGLLIKNE 186 (580)
T ss_pred HHHHHHHHHHHHHHHHHHHcCccchHHHHHHHHcCCCHHHHHHhCCccCCChHHHHHHHHHhcCCCHHHHHHCCceEecC
Confidence 45577778888899999874 466777 9877 999999999999999999998776631 0
Q ss_pred --HHhhhcc--EEEEee-----eeeeeeeeeeCCCCC----CCCCCCcccCccccCchHhHHhhccCCeEEEEecchhHH
Q psy15215 676 --QEYLESF--LISFFL-----RNHGISGFLLTTPDP----VHETPLFHKSNELYGLFEAKNAIGKSGYVLITEGYMDVI 742 (1432)
Q Consensus 676 --~~~~~~f--ri~fpi-----r~igf~gR~~~~~~~----s~et~~f~K~~~Ly~~~~a~~~~~~~~~~~~vEG~~D~i 742 (1432)
..+++|| |||||| +||||+||.++++.| ||||++|+||++|||+|.|++.+++.+.+||||||||||
T Consensus 187 ~~~~~yd~Fr~RimfPI~d~~G~vigF~GR~l~~~~pKYlNSpet~iF~K~~~LYgl~~a~~~i~~~~~viivEG~~Dvi 266 (580)
T PRK05667 187 DGGGPYDRFRNRIMFPIRDLRGRVIGFGGRVLGDDKPKYLNSPETPLFHKGRVLYGLDEARKAIAKKKQVIVVEGYMDVI 266 (580)
T ss_pred CCCCcchhcCCeEEEEEECCCCcEEEEEeeecCCCCCeeeCCCCCCCccCCccccCccHHHHhcccCCeEEEEeeHHHHH
Confidence 2244445 599999 699999999987667 999999999999999999999999999999999999999
Q ss_pred HHhhhCC---------------------CCCeEEEEecCcHHHHHHHHHHHHHhhhhcCCCceEEEecCCCCCCHHHHHH
Q psy15215 743 GLSQFGF---------------------FANSSYTCFDGDQAGRRAARRALEVCLLYATDDKIIKFLFLPDKYDPDSYIR 801 (1432)
Q Consensus 743 a~~~~g~---------------------~~~~i~~~~D~D~aG~~a~~~~~~~~~~~~~~~~~~~~~~lp~~~Dpde~~~ 801 (1432)
++||+|+ ++.+||+|||||.||++||.|+++.+++....++.|+|+.+|+|+|||||++
T Consensus 267 sl~q~Gi~naVA~lGtalt~~~~~~L~r~~~~vil~~D~D~AG~~aa~r~~~~~~~l~~~g~~v~vv~lp~gkDpdd~l~ 346 (580)
T PRK05667 267 ALHQAGITNAVASLGTALTEEHLKLLRRLTDEVILCFDGDKAGRKAALRALELALPLLKDGRQVRVAFLPDGKDPDDLVR 346 (580)
T ss_pred HHHHcCCCcEEEeCCCCCCHHHHHHHHhcCCeEEEEeCCCHHHHHHHHHHHHHHHHHHhCCceEEEEECCCCCChHHHHH
Confidence 9999999 4679999999999999999999999555444455699999999999999999
Q ss_pred HhChhhhhhc-----cccchhhcc
Q psy15215 802 KFGYKIFSKK-----NAFSFDIKS 820 (1432)
Q Consensus 802 ~~g~~~~~~~-----~~~~f~~~~ 820 (1432)
++|+++|.+. +.++|.+..
T Consensus 347 ~~G~~~~~~~i~~a~~~~~f~~~~ 370 (580)
T PRK05667 347 KEGPEAFRALLEQAIPLSEFLIRR 370 (580)
T ss_pred HhCHHHHHHHHHcCCCHHHHHHHH
Confidence 9999999774 444444443
No 35
>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=1.5e-35 Score=339.03 Aligned_cols=255 Identities=26% Similarity=0.474 Sum_probs=215.9
Q ss_pred HHHHHhhhhccCCChhhHHHHHHH-HHHhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhc
Q psy15215 367 QQKLINLQTDIVLPLNDLRDINRK-MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKF 445 (1432)
Q Consensus 367 q~~L~~iE~~~~l~~~e~~~l~~~-i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~f 445 (1432)
..+|.++.....|+..+...|+.+ .+.||.. |++.|+..|+|+|+++|++|.+++.+++||+|||++|||+|+++|
T Consensus 4 ~~yl~~~~~~~~l~~~~e~~l~~~~~~~gd~~---a~~~Lv~~~~~lV~~~a~~~~~~~~~~eDLvQeg~igl~~a~~~f 80 (270)
T TIGR02392 4 DAYIRAVNRIPMLTPEEEYQLAKRLREHGDLD---AAKKLVLSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRF 80 (270)
T ss_pred HHHHHHHhcCCCCCHHHHHHHHHHHHHCCCHH---HHHHHHHHhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHh
Confidence 357888888888999999999998 5689988 999999999999999999999999999999999999999999999
Q ss_pred cccCCCccHHHHHHHHHHHHHHHHHHhccccccchhHH--HHHHHHHHHHHHHHHHhCCCC-CHHHHHHHcCCCHHHHHH
Q psy15215 446 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI--ETINKISRISRQILQETGSEP-DPSVIAIKMEMPEEKIRK 522 (1432)
Q Consensus 446 d~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~~~~--~~~~k~~r~~~~~~~~~g~~p-t~~eia~~~~~~~~~v~~ 522 (1432)
|+.+|++|+|||+||||++|.++++++++++|+|.+.. +..++++++...+. .++.| |.+|||+.||+++++|..
T Consensus 81 d~~~~~~FsTYA~~~Ir~~i~~~l~~~~~~ir~p~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~eiA~~l~~~~~~v~~ 158 (270)
T TIGR02392 81 DPERGVRLVSFAVHWIKAEIHEYILRNWRLVKVATTKAQRKLFFNLRKMKKRLQ--GWLNPEEVEAIAEELGVSEREVRE 158 (270)
T ss_pred CcccCCChHHhhHHHHHHHHHHHHHHcCCceecCchHHHHHHHHHHHHHHHHHh--cCCCCCCHHHHHHHhCCCHHHHHH
Confidence 99999999999999999999999999988899998754 34445555444332 22555 699999999999999999
Q ss_pred HHH-HccCCCCCCCCCCCCCCC--CcCcccccCCCCChHHHHHHH----HHHHHHHHHHhcCCHHHHHHHHHHhhcccCC
Q psy15215 523 IMK-IAKEPVSMESPVGDDEDS--HLGDFIEDENMLAPSDAALNA----SMRSVVKDILNSLTPRESKVLRMRFGIEMSS 595 (1432)
Q Consensus 523 ~~~-~~~~~~sl~~~~~~~~~~--~~~~~i~d~~~~~p~~~~~~~----~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~ 595 (1432)
++. ....++||+.|++++++. .+.+++++.. .+|++.+... .+...|..+|++||++|+.||.+||+. +.
T Consensus 159 ~~~~~~~~~~Sld~~~~~~~~~~~~~~~~l~d~~-~~pe~~~~~~~~~~~~~~~L~~al~~L~~rer~vl~l~y~~--~~ 235 (270)
T TIGR02392 159 MESRLSGQDMSLNASIDDDEDDGGAPIAYLVDKT-SDPEDTLEEEQWEELQRQALANALGSLDARSRRIIEARWLD--DD 235 (270)
T ss_pred HHHHccCCCccCCCCCCCCCCccccHHHHhcCCC-CChHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhcC--CC
Confidence 865 334579999998765443 4667777764 4687776643 356889999999999999999999965 23
Q ss_pred CCcHHHHHhhcccchhHHHHHHHHHHHHHHHHHH
Q psy15215 596 DHTLEEVGKQFDVTRERIRQIEAKALRKLRPLAH 629 (1432)
Q Consensus 596 ~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l~ 629 (1432)
++|++|||+.||||+++|++++++|+.+||+.+.
T Consensus 236 ~~t~~eIA~~lgvS~~~V~q~~~~Al~kLr~~l~ 269 (270)
T TIGR02392 236 KLTLQELAAEYGVSAERIRQIEKNAMKKLKAALA 269 (270)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Confidence 5599999999999999999999999999998763
No 36
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=100.00 E-value=3.6e-35 Score=332.98 Aligned_cols=233 Identities=24% Similarity=0.360 Sum_probs=209.2
Q ss_pred HHHHH-HhhhhhhhhhHHHHHHHHHHHHHHHHHhcc---CCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHH
Q psy15215 1177 INRKM-IAGEMKARKAKREMTEANLRLVISIAKKYT---DRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 1252 (1432)
Q Consensus 1177 l~~~~-~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~---~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir 1252 (1432)
++... ..|+.. |++.||..|+|+|+++|++|. ..+.+++||+|||++|||+|+++|||.+|++|+|||+||||
T Consensus 12 ~~~~~~~~~~~~---ar~~Li~~~~~lV~~ia~~~~~~~~~~~~~eDL~QeG~igL~~ai~~fd~~~g~~F~tya~~~Ir 88 (257)
T PRK05911 12 TWQLYWSTQEIE---YRDVLIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIK 88 (257)
T ss_pred HHHHHHhcCCHH---HHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHH
Confidence 44444 357776 999999999999999999985 23567999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHcc--CCCCCCCCCCC-
Q psy15215 1253 QAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAK--EPVSMESPVGD- 1329 (1432)
Q Consensus 1253 ~~i~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~--~~~Sl~~~~~~- 1329 (1432)
++|.++++++.+ +|+++.+.++++.++.+.+.+.+|++||.+|||+.+|+++++|..++.... .++||+.++..
T Consensus 89 ~~i~~~lr~~~~---~pr~~~~~~~~l~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~~~Sld~~~~~~ 165 (257)
T PRK05911 89 AAIIDDLRKQDW---VPRSVHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFSSARPALILSLNEEFPCQ 165 (257)
T ss_pred HHHHHHHHhcCC---CCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHHhhccceeeccccCCCC
Confidence 999999999876 899999999999999999999999999999999999999999999987654 46899987643
Q ss_pred -CC--CCCcCcccccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHH
Q psy15215 1330 -DE--DSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQI 1406 (1432)
Q Consensus 1330 -~~--~~~~~d~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~ 1406 (1432)
++ ..++.++++|....+|++.+....+...|..+|.+|||++|.||.++|+.++ |++|||+.||+|+++|+++
T Consensus 166 ~~~~~~~~l~~~l~d~~~~~~~~~~~~~~~~~~l~~al~~L~~~er~vi~l~y~e~~----t~~EIA~~lgis~~~V~~~ 241 (257)
T PRK05911 166 SDDEAGLALEERIADERAETGYDVVDKKEFSSILAEAILALEEKERKVMALYYYEEL----VLKEIGKILGVSESRVSQI 241 (257)
T ss_pred CCCccccchhhhccCCCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHhcCC----CHHHHHHHHCcCHHHHHHH
Confidence 22 2357788888877789999998999999999999999999999999998877 9999999999999999999
Q ss_pred HHHHHHHhhCchh
Q psy15215 1407 EAKALRKLRHPSR 1419 (1432)
Q Consensus 1407 ~~rAl~kLr~~~~ 1419 (1432)
+++|+++||+.+.
T Consensus 242 ~~ral~kLr~~l~ 254 (257)
T PRK05911 242 HSKALLKLRATLS 254 (257)
T ss_pred HHHHHHHHHHHHH
Confidence 9999999999553
No 37
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=100.00 E-value=9.1e-35 Score=329.66 Aligned_cols=236 Identities=24% Similarity=0.365 Sum_probs=211.8
Q ss_pred HHHHHH-HHhHHHHHHhHHHHHHHHHHHHHHHHHhcc---cCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHH
Q psy15215 386 DINRKM-IAGEMKARKAKREMTEANLRLVISIAKKYT---DRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 461 (1432)
Q Consensus 386 ~l~~~i-~~gd~~~~~A~~~li~~~~~lV~~ia~ky~---~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~i 461 (1432)
.++... ..|+.. |++.||..|+|+|+++|++|. ..+.+++||+|||+||||+|+++|||.+|++|+|||+|||
T Consensus 11 ~~~~~~~~~~~~~---ar~~Li~~~~~lV~~ia~~~~~~~~~~~~~eDL~QeG~igL~~ai~~fd~~~g~~F~tya~~~I 87 (257)
T PRK05911 11 ETWQLYWSTQEIE---YRDVLIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLI 87 (257)
T ss_pred HHHHHHHhcCCHH---HHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHH
Confidence 344444 357777 999999999999999999986 2356799999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHcc--CCCCCCCCCCC
Q psy15215 462 RQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAK--EPVSMESPVGD 539 (1432)
Q Consensus 462 r~~i~~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~--~~~sl~~~~~~ 539 (1432)
|++|.++++++.+ +|+++.+.++++.++.+.+.+.+|++||.+|||+.||+++++|..++..+. .++|++.++.+
T Consensus 88 r~~i~~~lr~~~~---~pr~~~~~~~~l~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~~~Sld~~~~~ 164 (257)
T PRK05911 88 KAAIIDDLRKQDW---VPRSVHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFSSARPALILSLNEEFPC 164 (257)
T ss_pred HHHHHHHHHhcCC---CCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHHhhccceeeccccCCC
Confidence 9999999999876 899999999999999999999999999999999999999999999987664 45899987643
Q ss_pred --CC--CCCcCcccccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHH
Q psy15215 540 --DE--DSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 615 (1432)
Q Consensus 540 --~~--~~~~~~~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~ 615 (1432)
++ ..++.+++++....+|.+.+...++...|..+|++|||+++.||.|+|+.++ |++|||+.||+|.++|++
T Consensus 165 ~~~~~~~~~l~~~l~d~~~~~~~~~~~~~~~~~~l~~al~~L~~~er~vi~l~y~e~~----t~~EIA~~lgis~~~V~~ 240 (257)
T PRK05911 165 QSDDEAGLALEERIADERAETGYDVVDKKEFSSILAEAILALEEKERKVMALYYYEEL----VLKEIGKILGVSESRVSQ 240 (257)
T ss_pred CCCCccccchhhhccCCCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHhcCC----CHHHHHHHHCcCHHHHHH
Confidence 21 2357788888777789999988899999999999999999999999998887 999999999999999999
Q ss_pred HHHHHHHHHHHHHHHH
Q psy15215 616 IEAKALRKLRPLAHDW 631 (1432)
Q Consensus 616 ~~~rAl~kLr~~l~~~ 631 (1432)
+.++|+.+|++.+..|
T Consensus 241 ~~~ral~kLr~~l~~~ 256 (257)
T PRK05911 241 IHSKALLKLRATLSAF 256 (257)
T ss_pred HHHHHHHHHHHHHHhh
Confidence 9999999999998764
No 38
>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=9.3e-35 Score=330.12 Aligned_cols=237 Identities=30% Similarity=0.477 Sum_probs=213.5
Q ss_pred CCChhhHHHHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHH
Q psy15215 1168 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 1247 (1432)
Q Consensus 1168 ~l~~~e~~~l~~~~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya 1247 (1432)
.|+.++...++.+++.|+.. |++.|+..|+++|+++|++|++++.+++||+||||+|||+++++|++.+|.+|+||+
T Consensus 15 ~l~~~~~~~li~~~~~gd~~---a~~~L~~~~~~~v~~~a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~tyl 91 (254)
T TIGR02850 15 VLKNQEMRELFIRMQSGDTT---AREKLINGNLRLVLSVIQRFNNRGEYVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYA 91 (254)
T ss_pred CCCHHHHHHHHHHHHcCCHH---HHHHHHHHhHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCChHHHH
Confidence 45667778899999999888 999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCC
Q psy15215 1248 TWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPV 1327 (1432)
Q Consensus 1248 ~~~ir~~i~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~ 1327 (1432)
+|||+|+|.++++++. ++|+|+++.+.++++.++...+.+++|++||++|||+.||+++++|..++.....++||+.|+
T Consensus 92 ~~~irn~~~~~lr~~~-~ir~p~~~~~~~~~~~~~~~~l~~~l~~~pt~~elA~~l~~~~e~v~~~~~~~~~~~Sld~~~ 170 (254)
T TIGR02850 92 VPMIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVRDKLISENSKEPTVSEIAKELKVPQEEVVFALDAIQDPVSLFEPI 170 (254)
T ss_pred HHHHHHHHHHHHHhCC-CccCchHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCCcccCCC
Confidence 9999999999999975 899999999999999999999999999999999999999999999999999998999999998
Q ss_pred CCCCC--CCcCcccccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHH
Q psy15215 1328 GDDED--SHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 1405 (1432)
Q Consensus 1328 ~~~~~--~~~~d~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq 1405 (1432)
.++++ ..+.+++++... +.+ .......+..++..||+++|.||.+||+.++ |++|||+.||+|+++|+|
T Consensus 171 ~~~~~~~~~~~~~~~d~~~--~~~---~~~~~~~l~~~l~~L~~rer~vi~~~~~~~~----t~~eIA~~lgis~~~V~~ 241 (254)
T TIGR02850 171 YNDGGDPIYVMDQISDEKN--KDS---QWLEGIALKEAMKRLNEREKMILNMRFFEGK----TQMEVAEEIGISQAQVSR 241 (254)
T ss_pred CCCCCCcchhhhhcCCccc--cHH---HHHhHHHHHHHHHcCCHHHHHHHHHHHcCCC----CHHHHHHHHCcCHHHHHH
Confidence 64443 246677766532 222 2234567899999999999999999998777 999999999999999999
Q ss_pred HHHHHHHHhhCc
Q psy15215 1406 IEAKALRKLRHP 1417 (1432)
Q Consensus 1406 ~~~rAl~kLr~~ 1417 (1432)
++++|++|||+.
T Consensus 242 ~~~ral~kLr~~ 253 (254)
T TIGR02850 242 LEKAALKHMRKY 253 (254)
T ss_pred HHHHHHHHHHhh
Confidence 999999999974
No 39
>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=3e-34 Score=331.28 Aligned_cols=262 Identities=42% Similarity=0.685 Sum_probs=243.5
Q ss_pred HHHHHHhhhhcCCChhhHHHHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhcc
Q psy15215 1157 QQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE 1236 (1432)
Q Consensus 1157 q~~L~~ie~~~~l~~~e~~~l~~~~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd 1236 (1432)
+.+|.+|+...+|+..+...++..++.|+.. |++.|+..|.++|+++|++|++++.+++||+||||+|||+|+++|+
T Consensus 16 ~~~~~~~~~~~~~~~~~~~~li~~~~~gd~~---a~~~L~~~y~~~v~~~a~~~~~~~~~aeDLvQe~~i~l~~a~~~fd 92 (285)
T TIGR02394 16 QLYLREIGFKPLLTAEEEIAYARRALAGDFE---ARKVMIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVEKFD 92 (285)
T ss_pred HHHHHHHhccCCCCHHHHHHHHHHHHcCCHH---HHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhC
Confidence 4578899999999999999999999999988 9999999999999999999999999999999999999999999999
Q ss_pred ccCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHH
Q psy15215 1237 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKI 1316 (1432)
Q Consensus 1237 ~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~ 1316 (1432)
+.+|++|+||++||++.++.++++++.+++|+|.++...+|.+.+..+.+.+.+|++||.+++|+.+|++++++..++..
T Consensus 93 ~~~g~~f~tya~w~i~~ain~~i~~~~~~~~~p~~~~~~~~~~~r~~~~l~~~~~r~~~~~e~a~~l~~~~~~~~~~~~~ 172 (285)
T TIGR02394 93 PERGFRFSTYATWWIRQTIERAIMNQARTIRLPVHVIKELNVYLRAARQLEKKLGREPSVEEIAELLDKPVEDVSRVLAL 172 (285)
T ss_pred CCCCCCcHhhhHHHHHHHHHHHHHHcCCceeCcHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHh
Confidence 99999999999999999999999999999999999999999999988888899999999999999999999999999999
Q ss_pred ccCCCCCCCCCCCCCCCCcCcccccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHh
Q psy15215 1317 AKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQF 1396 (1432)
Q Consensus 1317 ~~~~~Sl~~~~~~~~~~~~~d~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l 1396 (1432)
....+|++.++.+++...+.+.+.+....+|++.+...+....|..+|..||+++|.||.|+||+...+++|++|||+.|
T Consensus 173 ~~~~~sld~~~~~~~~~~~~~~~~~~~~~~pe~~~~~~e~~~~L~~al~~Lp~~~R~Vl~l~ygL~~~e~~s~~EIA~~L 252 (285)
T TIGR02394 173 NERITSLDAPLDDDSSKSLLDTIADEQSIDPESLVQNDDLKQLIEAWLAELNERQREVLARRFGLLGYEPATLEEVAAEV 252 (285)
T ss_pred hcCCCcCCCCCCCCCCcchhhhhcCCCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhCCCCCCCccHHHHHHHH
Confidence 88899999988766655566777777667899999999999999999999999999999999965545666999999999
Q ss_pred CCCHHHHHHHHHHHHHHhhCchhhh
Q psy15215 1397 DVTRERIRQIEAKALRKLRHPSRYY 1421 (1432)
Q Consensus 1397 ~vs~~~Vrq~~~rAl~kLr~~~~~~ 1421 (1432)
|||.+||++++++|+++||..+...
T Consensus 253 gis~~tVk~~l~rAlkkLr~~l~~~ 277 (285)
T TIGR02394 253 GLTRERVRQIQVEALKKLRRILERD 277 (285)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 9999999999999999999977643
No 40
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=100.00 E-value=1.8e-34 Score=315.92 Aligned_cols=237 Identities=28% Similarity=0.476 Sum_probs=216.2
Q ss_pred CCChhhHHHHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHhccCCCC-ChhHHHHHHHHHHHHHHHhccccCCCcchhH
Q psy15215 1168 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGL-QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 1246 (1432)
Q Consensus 1168 ~l~~~e~~~l~~~~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~-~~~DLiQEg~igl~kav~kfd~~~g~~Fsty 1246 (1432)
.++..+...+...++.|+.. +. .|++.|+|||.++|++|.+++. .++||+|-|++||++|+++||+.+|.+|+||
T Consensus 5 ~~~~~e~~~~~~~~~~g~~~---~~-~Li~~ylpLV~~ia~k~~~r~~~~~dDLiqiG~iGLi~Aieryd~~kg~kF~ty 80 (247)
T COG1191 5 PLSKEEEEKLLEYYAEGDEE---AR-RLIERYLPLVKSIARKFENRGPSEYDDLIQIGMIGLIKAIERYDPSKGTKFSTY 80 (247)
T ss_pred ccchHHHHHHHHHHHhcCHH---HH-HHHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHHHHcCcccCcchHHH
Confidence 45567788899999999988 88 9999999999999999999988 9999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHcc--CCCCCC
Q psy15215 1247 ATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAK--EPVSME 1324 (1432)
Q Consensus 1247 a~~~ir~~i~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~--~~~Sl~ 1324 (1432)
|...|+++|.+++|++. ++++|+.+.+..+++..+..++.+++||+||.+|||+.+|++.++|..++...+ ..+|++
T Consensus 81 A~~~I~Gei~d~LR~~~-~v~vpR~~~~~~~~i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~~~~~~~~sld 159 (247)
T COG1191 81 AVRRIRGEILDYLRKND-SVKVPRSLRELGRRIEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAINGSQLLSLD 159 (247)
T ss_pred HHHHHHHHHHHHHHhCC-CccCcHHHHHHHHHHHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHHhccccccchh
Confidence 99999999999999999 899999999999999999999999999999999999999999999999997764 778888
Q ss_pred CCCCCCCCCCcCcccccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHH
Q psy15215 1325 SPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIR 1404 (1432)
Q Consensus 1325 ~~~~~~~~~~~~d~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vr 1404 (1432)
..+..+++.. .+....+|.+.....++...+.+++..||+||+.|+.+||+.++ |++|||+.+|||+++|+
T Consensus 160 ~~~~~~~d~~-----~~~~~~~~~~~~~~~~~~~~l~~ai~~L~EREk~Vl~l~y~eel----t~kEI~~~LgISes~VS 230 (247)
T COG1191 160 EDVLKDDDDD-----VDDQIENPDDGVEKEELLEILKEAIEPLPEREKLVLVLRYKEEL----TQKEIAEVLGISESRVS 230 (247)
T ss_pred hhhccccccc-----hhhccccchhHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHhcc----CHHHHHHHhCccHHHHH
Confidence 7665444433 22334478888888899899999999999999999999999888 99999999999999999
Q ss_pred HHHHHHHHHhhCch
Q psy15215 1405 QIEAKALRKLRHPS 1418 (1432)
Q Consensus 1405 q~~~rAl~kLr~~~ 1418 (1432)
|++++|+++||+..
T Consensus 231 ql~kkai~kLr~~l 244 (247)
T COG1191 231 RLHKKAIKKLRKEL 244 (247)
T ss_pred HHHHHHHHHHHHHh
Confidence 99999999999854
No 41
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=100.00 E-value=2.5e-34 Score=314.89 Aligned_cols=239 Identities=28% Similarity=0.467 Sum_probs=218.5
Q ss_pred cCCChhhHHHHHHHHHHhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCC-ChhhHHHHHHHHHHHHHhhccccCCCccHH
Q psy15215 377 IVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGL-QFLDLIQEGNIGLMKAVDKFEYRRGYKFST 455 (1432)
Q Consensus 377 ~~l~~~e~~~l~~~i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~-~~~DLiQEg~igL~kav~~fd~~~g~~Fst 455 (1432)
+.++..+...++...+.|+.. +. .||+.|+|||.++|++|.+++. .++||+|-|+|||++|+++||+.+|.+|+|
T Consensus 4 ~~~~~~e~~~~~~~~~~g~~~---~~-~Li~~ylpLV~~ia~k~~~r~~~~~dDLiqiG~iGLi~Aieryd~~kg~kF~t 79 (247)
T COG1191 4 QPLSKEEEEKLLEYYAEGDEE---AR-RLIERYLPLVKSIARKFENRGPSEYDDLIQIGMIGLIKAIERYDPSKGTKFST 79 (247)
T ss_pred cccchHHHHHHHHHHHhcCHH---HH-HHHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHHHHcCcccCcchHH
Confidence 456677889999999999999 88 9999999999999999999988 999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHcc--CCCCC
Q psy15215 456 YATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAK--EPVSM 533 (1432)
Q Consensus 456 ya~~~ir~~i~~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~--~~~sl 533 (1432)
||...|+++|.+++|+.. .+++|+++.+..+++..+..++.+++||+||.+|||+.||++.++|..++.... ..+|+
T Consensus 80 yA~~~I~Gei~d~LR~~~-~v~vpR~~~~~~~~i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~~~~~~~~sl 158 (247)
T COG1191 80 YAVRRIRGEILDYLRKND-SVKVPRSLRELGRRIEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAINGSQLLSL 158 (247)
T ss_pred HHHHHHHHHHHHHHHhCC-CccCcHHHHHHHHHHHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHHhccccccch
Confidence 999999999999999999 899999999999999999999999999999999999999999999999987664 67888
Q ss_pred CCCCCCCCCCCcCcccccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHH
Q psy15215 534 ESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERI 613 (1432)
Q Consensus 534 ~~~~~~~~~~~~~~~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v 613 (1432)
+..+..+++.. .++...+|.+.....+....+.+++..|++||+.|+.+||..++ |++|||+.+|||.++|
T Consensus 159 d~~~~~~~d~~-----~~~~~~~~~~~~~~~~~~~~l~~ai~~L~EREk~Vl~l~y~eel----t~kEI~~~LgISes~V 229 (247)
T COG1191 159 DEDVLKDDDDD-----VDDQIENPDDGVEKEELLEILKEAIEPLPEREKLVLVLRYKEEL----TQKEIAEVLGISESRV 229 (247)
T ss_pred hhhhccccccc-----hhhccccchhHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHhcc----CHHHHHHHhCccHHHH
Confidence 77665444433 22334578888888889899999999999999999999999998 9999999999999999
Q ss_pred HHHHHHHHHHHHHHHH
Q psy15215 614 RQIEAKALRKLRPLAH 629 (1432)
Q Consensus 614 ~~~~~rAl~kLr~~l~ 629 (1432)
++++++|+.+|++.+.
T Consensus 230 Sql~kkai~kLr~~l~ 245 (247)
T COG1191 230 SRLHKKAIKKLRKELN 245 (247)
T ss_pred HHHHHHHHHHHHHHhc
Confidence 9999999999998875
No 42
>COG0358 DnaG DNA primase (bacterial type) [DNA replication, recombination, and repair]
Probab=100.00 E-value=9.3e-36 Score=372.95 Aligned_cols=207 Identities=29% Similarity=0.435 Sum_probs=177.7
Q ss_pred HHHHHhhcccchhHH---HHHHHHHHHHHHHHHHHHHHHhhh-hhhhhH-hhcC--CCcccccccccCCCCCchhhHHHH
Q psy15215 599 LEEVGKQFDVTRERI---RQIEAKALRKLRPLAHDWLEQRTH-QNEKII-ACSS--DSSNHNEHVTNNNFPPGFNIFHKL 671 (1432)
Q Consensus 599 ~~EIa~~l~is~~~v---~~~~~rAl~kLr~~l~~~~~~~l~-~~~~~~-~l~~--l~~~~~~~f~~Gyap~~~~~l~~~ 671 (1432)
..++|.+.|+..+.. +....+.+..+...+..||+..|. .+.+++ ||.. +|.+++++|+|||||++ +.+. .
T Consensus 83 v~~La~~~gi~~~~~~~~~~~~~~~l~~~~~~~~~fy~~~L~~~~~~a~~yL~~Rgls~~~i~~f~iG~ap~~-~~~~-~ 160 (568)
T COG0358 83 VLQLAGRAGIELPYEKGKRIEKRQKLYDGKEEAAIFYQSSLDPEGAAALKYLETRGLAAELIAHFRLGYAPPN-DSLL-P 160 (568)
T ss_pred HHHHHHHhCCCCCccccccchhHHHHHHHHHHHHHHHHHHHHhchHHHHHHHHHcCCCHHHHHHhCCCCCCCc-hHHH-H
Confidence 344555555443322 345567888899999999999987 455565 8887 89999999999999999 6666 3
Q ss_pred HH----------------------HHHHhhhccEEEEee-----eeeeeeeeeeCCCCC----CCCCCCcccCccccCch
Q psy15215 672 LR----------------------ILQEYLESFLISFFL-----RNHGISGFLLTTPDP----VHETPLFHKSNELYGLF 720 (1432)
Q Consensus 672 ~~----------------------~~~~~~~~fri~fpi-----r~igf~gR~~~~~~~----s~et~~f~K~~~Ly~~~ 720 (1432)
+. .||+|++ |||||| +|||||||.+++..| ||+|++|+||+.|||++
T Consensus 161 ~~~k~~~~~~~l~~~Gl~~~~~~~~ydrFr~--RImfPI~d~~g~vigFggR~l~~~~~KYlNspet~if~Kg~~Lyg~~ 238 (568)
T COG0358 161 FLAKKEYREEKLEDLGLLKRKEGKIYDRFRN--RIMFPIRDLRGDVIGFGGRVLGDDKPKYLNSPETELFKKGEELYGLD 238 (568)
T ss_pred HHhcCCcCHHHHHHCCCeecCCCceeehhcC--eeEEeccCCCCCEEeeeccccCCCCCcccCCCCCcCccCcHHhhCHH
Confidence 32 2444444 599999 699999999997666 99999999999999999
Q ss_pred HhHHhhccCCeEEEEecchhHHHHhhhCC---------------------CCCeEEEEecCcHHHHHHHHHHHHHhhhhc
Q psy15215 721 EAKNAIGKSGYVLITEGYMDVIGLSQFGF---------------------FANSSYTCFDGDQAGRRAARRALEVCLLYA 779 (1432)
Q Consensus 721 ~a~~~~~~~~~~~~vEG~~D~ia~~~~g~---------------------~~~~i~~~~D~D~aG~~a~~~~~~~~~~~~ 779 (1432)
+|+..+++.+.+|||||||||||||++|| ...+||||||||.||++||+|+++.++..+
T Consensus 239 ~a~~~~~~~~~iivVEGymDViaL~~aGi~naVA~lGTalt~ehi~~L~r~~~~vil~fDgD~AG~~Aa~ral~~~~~~~ 318 (568)
T COG0358 239 PARKKIAKADQIIVVEGYMDVIALHKAGIKNAVASLGTALTEEHIKLLSRGKKKVILCFDGDRAGRKAAKRALQLVLPLD 318 (568)
T ss_pred HHHHhhccCCeEEEEechHHHHHHHHcCCcceeecccccCCHHHHHHHHhcCCCEEEEeCChHHHHHHHHHHHHHhhhhc
Confidence 99999999999999999999999999999 578899999999999999999999999998
Q ss_pred CCCceEEEecCCCCCCHHHHHHHhChhhhhhc
Q psy15215 780 TDDKIIKFLFLPDKYDPDSYIRKFGYKIFSKK 811 (1432)
Q Consensus 780 ~~~~~~~~~~lp~~~Dpde~~~~~g~~~~~~~ 811 (1432)
..+ |.|+.+|+|+||||+++++|+++|.+.
T Consensus 319 ~~~--v~v~~~P~GkDpDel~~k~g~~al~~~ 348 (568)
T COG0358 319 FVG--VFVILLPDGKDPDELIRKEGAEALRKK 348 (568)
T ss_pred cCC--eEEEECCCCCChHHHHHHhChHHHHHH
Confidence 887 999999999999999999999998775
No 43
>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=8.1e-34 Score=327.70 Aligned_cols=262 Identities=42% Similarity=0.695 Sum_probs=243.9
Q ss_pred HHHHHHhhhhccCCChhhHHHHHHHHHHhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhc
Q psy15215 366 LQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKF 445 (1432)
Q Consensus 366 ~q~~L~~iE~~~~l~~~e~~~l~~~i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~f 445 (1432)
++.+|.+|+...+|+..+...|+..++.||.. |++.|+..|.++|+++|++|++++.+++||+||||||||+|+++|
T Consensus 15 ~~~~~~~~~~~~~~~~~~~~~li~~~~~gd~~---a~~~L~~~y~~~v~~~a~~~~~~~~~aeDLvQe~~i~l~~a~~~f 91 (285)
T TIGR02394 15 TQLYLREIGFKPLLTAEEEIAYARRALAGDFE---ARKVMIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVEKF 91 (285)
T ss_pred HHHHHHHHhccCCCCHHHHHHHHHHHHcCCHH---HHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHh
Confidence 35588999999999999999999999999999 999999999999999999999999999999999999999999999
Q ss_pred cccCCCccHHHHHHHHHHHHHHHHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHH
Q psy15215 446 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMK 525 (1432)
Q Consensus 446 d~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~ 525 (1432)
++.+|++|+||++||++.++.+++.++.+++++|.++.+.+|.+.+..+.+.+.+|++|+.+++|..+|++++.|..++.
T Consensus 92 d~~~g~~f~tya~w~i~~ain~~i~~~~~~~~~p~~~~~~~~~~~r~~~~l~~~~~r~~~~~e~a~~l~~~~~~~~~~~~ 171 (285)
T TIGR02394 92 DPERGFRFSTYATWWIRQTIERAIMNQARTIRLPVHVIKELNVYLRAARQLEKKLGREPSVEEIAELLDKPVEDVSRVLA 171 (285)
T ss_pred CCCCCCCcHhhhHHHHHHHHHHHHHHcCCceeCcHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999998888889999999999999999999999999999
Q ss_pred HccCCCCCCCCCCCCCCCCcCcccccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhh
Q psy15215 526 IAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQ 605 (1432)
Q Consensus 526 ~~~~~~sl~~~~~~~~~~~~~~~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~ 605 (1432)
.+...+|++.++.+++...+.+.+.+....+|++.+...+....|..+|.+||+++|.||.|+||+....++|++|||+.
T Consensus 172 ~~~~~~sld~~~~~~~~~~~~~~~~~~~~~~pe~~~~~~e~~~~L~~al~~Lp~~~R~Vl~l~ygL~~~e~~s~~EIA~~ 251 (285)
T TIGR02394 172 LNERITSLDAPLDDDSSKSLLDTIADEQSIDPESLVQNDDLKQLIEAWLAELNERQREVLARRFGLLGYEPATLEEVAAE 251 (285)
T ss_pred hhcCCCcCCCCCCCCCCcchhhhhcCCCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhCCCCCCCccHHHHHHH
Confidence 98889999988876655556667776666789999999999999999999999999999999996554566699999999
Q ss_pred cccchhHHHHHHHHHHHHHHHHHHH
Q psy15215 606 FDVTRERIRQIEAKALRKLRPLAHD 630 (1432)
Q Consensus 606 l~is~~~v~~~~~rAl~kLr~~l~~ 630 (1432)
||+|.++|+++.++|+++|+..+..
T Consensus 252 Lgis~~tVk~~l~rAlkkLr~~l~~ 276 (285)
T TIGR02394 252 VGLTRERVRQIQVEALKKLRRILER 276 (285)
T ss_pred HCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999998864
No 44
>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=6.5e-34 Score=323.19 Aligned_cols=238 Identities=29% Similarity=0.474 Sum_probs=214.5
Q ss_pred cCCChhhHHHHHHHHHHhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHH
Q psy15215 377 IVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 456 (1432)
Q Consensus 377 ~~l~~~e~~~l~~~i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fsty 456 (1432)
..|+.++...++.+++.||.. |++.|+..|+++|+++|++|++++.+++||+||||+|||+++++|++.+|.+|+||
T Consensus 14 ~~l~~~~~~~li~~~~~gd~~---a~~~L~~~~~~~v~~~a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~ty 90 (254)
T TIGR02850 14 PVLKNQEMRELFIRMQSGDTT---AREKLINGNLRLVLSVIQRFNNRGEYVDDLFQVGCIGLMKSIDNFDLSQNVKFSTY 90 (254)
T ss_pred CCCCHHHHHHHHHHHHcCCHH---HHHHHHHHhHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCChHHH
Confidence 456777888999999999988 99999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCC
Q psy15215 457 ATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESP 536 (1432)
Q Consensus 457 a~~~ir~~i~~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~ 536 (1432)
++|||+|+|.++++++. ++|+|+++.+.++++.++..++.+++|++||++|||+.||+++++|..++.....++||+.|
T Consensus 91 l~~~irn~~~~~lr~~~-~ir~p~~~~~~~~~~~~~~~~l~~~l~~~pt~~elA~~l~~~~e~v~~~~~~~~~~~Sld~~ 169 (254)
T TIGR02850 91 AVPMIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVRDKLISENSKEPTVSEIAKELKVPQEEVVFALDAIQDPVSLFEP 169 (254)
T ss_pred HHHHHHHHHHHHHHhCC-CccCchHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCCcccCC
Confidence 99999999999999975 89999999999999999999999999999999999999999999999999998899999998
Q ss_pred CCCCCC--CCcCcccccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHH
Q psy15215 537 VGDDED--SHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIR 614 (1432)
Q Consensus 537 ~~~~~~--~~~~~~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~ 614 (1432)
+.++++ ..+.+++++... +.+ .......+..++..||++++.||.+||+.++ |++|||+.+|+|+++|+
T Consensus 170 ~~~~~~~~~~~~~~~~d~~~--~~~---~~~~~~~l~~~l~~L~~rer~vi~~~~~~~~----t~~eIA~~lgis~~~V~ 240 (254)
T TIGR02850 170 IYNDGGDPIYVMDQISDEKN--KDS---QWLEGIALKEAMKRLNEREKMILNMRFFEGK----TQMEVAEEIGISQAQVS 240 (254)
T ss_pred CCCCCCCcchhhhhcCCccc--cHH---HHHhHHHHHHHHHcCCHHHHHHHHHHHcCCC----CHHHHHHHHCcCHHHHH
Confidence 854433 246677766532 222 2234567899999999999999999998777 99999999999999999
Q ss_pred HHHHHHHHHHHHH
Q psy15215 615 QIEAKALRKLRPL 627 (1432)
Q Consensus 615 ~~~~rAl~kLr~~ 627 (1432)
+++++|+.+|++.
T Consensus 241 ~~~~ral~kLr~~ 253 (254)
T TIGR02850 241 RLEKAALKHMRKY 253 (254)
T ss_pred HHHHHHHHHHHhh
Confidence 9999999999975
No 45
>TIGR01391 dnaG DNA primase, catalytic core. This protein contains a CHC2 zinc finger (Pfam:PF01807) and a Toprim domain (Pfam:PF01751).
Probab=100.00 E-value=8.2e-35 Score=350.11 Aligned_cols=191 Identities=36% Similarity=0.579 Sum_probs=165.8
Q ss_pred HHHHHHHHHHHHHHHHHhhhh---hhhhH-hhcC--CCcccccccccCCCCCchhhHHHHHHHH----------------
Q psy15215 618 AKALRKLRPLAHDWLEQRTHQ---NEKII-ACSS--DSSNHNEHVTNNNFPPGFNIFHKLLRIL---------------- 675 (1432)
Q Consensus 618 ~rAl~kLr~~l~~~~~~~l~~---~~~~~-~l~~--l~~~~~~~f~~Gyap~~~~~l~~~~~~~---------------- 675 (1432)
...+..+...+..||+.++.. +..|+ ||.. ||+++|++|+|||||.+|+.|.+++...
T Consensus 110 ~~~l~~~~~~a~~~y~~~L~~~~~~~~a~~YL~~RGis~e~i~~f~lGyap~~~~~l~~~l~~k~~~~~~~l~~~Gl~~~ 189 (415)
T TIGR01391 110 RKKLYELLELAAKFFKNQLKHTPENRAALDYLQSRGLSDETIDRFELGYAPNNWDFLFDFLQNKKGFDLELLAEAGLLVK 189 (415)
T ss_pred HHHHHHHHHHHHHHHHHHhccCccchHHHHHHHHcCCCHHHHHHcCCCCCCCcHHHHHHHHHhccCCCHHHHHHCCCeEE
Confidence 344566777788899998765 44566 8877 9999999999999999998876665321
Q ss_pred ---HHhhhcc--EEEEee-----eeeeeeeeeeCCCCC----CCCCCCcccCccccCchHhHHhhccCCeEEEEecchhH
Q psy15215 676 ---QEYLESF--LISFFL-----RNHGISGFLLTTPDP----VHETPLFHKSNELYGLFEAKNAIGKSGYVLITEGYMDV 741 (1432)
Q Consensus 676 ---~~~~~~f--ri~fpi-----r~igf~gR~~~~~~~----s~et~~f~K~~~Ly~~~~a~~~~~~~~~~~~vEG~~D~ 741 (1432)
..++++| |||||| +||||+||.++++.| ||+|++|+|+..|||+|.|++.+++.+.+|||||||||
T Consensus 190 ~~~g~~~d~Fr~RiifPi~d~~G~vvgf~gR~~~~~~pKYlNspet~~f~K~~~lygl~~a~~~~~~~~~viivEG~~Da 269 (415)
T TIGR01391 190 KENGKYYDRFRNRIMFPIHDPKGRVVGFGGRALGDEKPKYLNSPETPLFKKSELLYGLHKARKEIRKEKELILVEGYMDV 269 (415)
T ss_pred CCCCCeeeecCCeEEEEEECCCCCEEEEEeeecCCCCCceeCCCCCCCccCCccccCHhHHHHhhccCCcEEEEecHHHH
Confidence 1133444 599999 699999999987666 99999999999999999999999999999999999999
Q ss_pred HHHhhhCC---------------------CCCeEEEEecCcHHHHHHHHHHHHHhhhhcCCCceEEEecCCCCCCHHHHH
Q psy15215 742 IGLSQFGF---------------------FANSSYTCFDGDQAGRRAARRALEVCLLYATDDKIIKFLFLPDKYDPDSYI 800 (1432)
Q Consensus 742 ia~~~~g~---------------------~~~~i~~~~D~D~aG~~a~~~~~~~~~~~~~~~~~~~~~~lp~~~Dpde~~ 800 (1432)
||+||+|+ +..+||+|||||.||++||.|++..+.+.|+. |+|+.+|+|+|||||+
T Consensus 270 isl~~~G~~~aVA~~Gtalt~~~~~~l~r~~~~vvl~~D~D~aG~~aa~r~~~~l~~~g~~---v~v~~lp~gkDpdd~l 346 (415)
T TIGR01391 270 IALHQAGIKNAVASLGTALTEEHIKLLKRYADEIILCFDGDKAGRKAALRAIELLLPLGIN---VKVIKLPGGKDPDEYL 346 (415)
T ss_pred HHHHHCCCCcEEECCCCCCcHHHHHHHHhhCCeEEEEeCCCHHHHHHHHHHHHHHHHcCCe---EEEEECCCCCCHHHHH
Confidence 99999999 45799999999999999999999999988765 9999999999999999
Q ss_pred HHhChhhhhhc
Q psy15215 801 RKFGYKIFSKK 811 (1432)
Q Consensus 801 ~~~g~~~~~~~ 811 (1432)
+++|+++|.+.
T Consensus 347 ~~~g~~~~~~~ 357 (415)
T TIGR01391 347 RKEGVEALKKL 357 (415)
T ss_pred HHhCHHHHHHH
Confidence 99999999774
No 46
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=100.00 E-value=2.3e-33 Score=319.62 Aligned_cols=238 Identities=30% Similarity=0.484 Sum_probs=213.1
Q ss_pred CCChhhHHHHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHH
Q psy15215 1168 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 1247 (1432)
Q Consensus 1168 ~l~~~e~~~l~~~~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya 1247 (1432)
.+++++...++.+++.|+.. |++.|+..|.++|+++|++|++++.+++||+|||++|||+|+++|++.+|.+|+||+
T Consensus 18 ~l~~~~~~~l~~~~~~gd~~---a~~~l~~~~~~~v~~~a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~t~l 94 (258)
T PRK08215 18 VLKNEEMRELFERMQNGDKE---AREKLINGNLRLVLSVIQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYA 94 (258)
T ss_pred CCCHHHHHHHHHHHHcCCHH---HHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHH
Confidence 45667788899999999888 999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCC
Q psy15215 1248 TWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPV 1327 (1432)
Q Consensus 1248 ~~~ir~~i~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~ 1327 (1432)
+|||+++|.++++++. ++|+|+++.....++.++...+.+++|++||++|||+.||+++++|..++.....+.||+.|+
T Consensus 95 ~~~ir~~i~~~lr~~~-~vrip~~~~~~~~~~~~~~~~l~~~~~r~p~~~eia~~l~v~~~~v~~~~~~~~~~~sl~~~~ 173 (258)
T PRK08215 95 VPMIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVREKLINENSKEPTVEEIAKELEVPREEVVFALDAIQDPVSLFEPI 173 (258)
T ss_pred HHHHHHHHHHHHHhCC-ceEecHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCccccCCC
Confidence 9999999999999985 889999999999999999999999999999999999999999999999998888899999998
Q ss_pred CCCCCC--CcCcccccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHH
Q psy15215 1328 GDDEDS--HLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 1405 (1432)
Q Consensus 1328 ~~~~~~--~~~d~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq 1405 (1432)
+++++. ++.+.+++... .+. .......+..+|+.||++++.||.++|+.|+ |++|||+.||+|+++|++
T Consensus 174 ~~~~~~~~~~~~~~~~~~~-~~~----~~~~~~~l~~~l~~L~~~er~vi~~~~~~~~----t~~eIA~~lgis~~~V~~ 244 (258)
T PRK08215 174 YHDGGDPIYVMDQISDEKN-KDE----NWLEEIALKEAMKKLNDREKLILNLRFFQGK----TQMEVAEEIGISQAQVSR 244 (258)
T ss_pred CCCCCcchhhhhhccCccc-cHH----HHHhHHHHHHHHHcCCHHHHHHHHHHHhcCC----CHHHHHHHHCcCHHHHHH
Confidence 655432 35566665432 222 2234567899999999999999999998777 999999999999999999
Q ss_pred HHHHHHHHhhCch
Q psy15215 1406 IEAKALRKLRHPS 1418 (1432)
Q Consensus 1406 ~~~rAl~kLr~~~ 1418 (1432)
++++|+++||+.+
T Consensus 245 ~~~~al~kLr~~l 257 (258)
T PRK08215 245 LEKAALKHMRKYI 257 (258)
T ss_pred HHHHHHHHHHHHh
Confidence 9999999999743
No 47
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=100.00 E-value=1.5e-32 Score=313.00 Aligned_cols=238 Identities=30% Similarity=0.491 Sum_probs=213.5
Q ss_pred CCChhhHHHHHHHHHHhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHH
Q psy15215 378 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 457 (1432)
Q Consensus 378 ~l~~~e~~~l~~~i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya 457 (1432)
.++..+...++.+++.||.. |++.|+..|+++|+++|++|.+++.+++||+|||++|||+|+++|++.+|.+|+||+
T Consensus 18 ~l~~~~~~~l~~~~~~gd~~---a~~~l~~~~~~~v~~~a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~t~l 94 (258)
T PRK08215 18 VLKNEEMRELFERMQNGDKE---AREKLINGNLRLVLSVIQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYA 94 (258)
T ss_pred CCCHHHHHHHHHHHHcCCHH---HHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHH
Confidence 45677888899999999988 999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCC
Q psy15215 458 TWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPV 537 (1432)
Q Consensus 458 ~~~ir~~i~~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~ 537 (1432)
+|||+|+|.++++++. ++|+|+++.....++.++..++.+++|++||++|||+.||+++++|..++.....+.|++.|+
T Consensus 95 ~~~ir~~i~~~lr~~~-~vrip~~~~~~~~~~~~~~~~l~~~~~r~p~~~eia~~l~v~~~~v~~~~~~~~~~~sl~~~~ 173 (258)
T PRK08215 95 VPMIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVREKLINENSKEPTVEEIAKELEVPREEVVFALDAIQDPVSLFEPI 173 (258)
T ss_pred HHHHHHHHHHHHHhCC-ceEecHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCccccCCC
Confidence 9999999999999985 889999999999999999999999999999999999999999999999998888889999998
Q ss_pred CCCCCC--CcCcccccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHH
Q psy15215 538 GDDEDS--HLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 615 (1432)
Q Consensus 538 ~~~~~~--~~~~~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~ 615 (1432)
+++++. ++.+.+++... .+ + .......+..+|+.||++++.||.++|+.|+ |++|||+.+|+|+++|++
T Consensus 174 ~~~~~~~~~~~~~~~~~~~-~~-~---~~~~~~~l~~~l~~L~~~er~vi~~~~~~~~----t~~eIA~~lgis~~~V~~ 244 (258)
T PRK08215 174 YHDGGDPIYVMDQISDEKN-KD-E---NWLEEIALKEAMKKLNDREKLILNLRFFQGK----TQMEVAEEIGISQAQVSR 244 (258)
T ss_pred CCCCCcchhhhhhccCccc-cH-H---HHHhHHHHHHHHHcCCHHHHHHHHHHHhcCC----CHHHHHHHHCcCHHHHHH
Confidence 654432 34566655431 12 2 2234567899999999999999999998777 999999999999999999
Q ss_pred HHHHHHHHHHHHH
Q psy15215 616 IEAKALRKLRPLA 628 (1432)
Q Consensus 616 ~~~rAl~kLr~~l 628 (1432)
+.++|+.+|++.+
T Consensus 245 ~~~~al~kLr~~l 257 (258)
T PRK08215 245 LEKAALKHMRKYI 257 (258)
T ss_pred HHHHHHHHHHHHh
Confidence 9999999999875
No 48
>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=1.1e-32 Score=309.55 Aligned_cols=227 Identities=30% Similarity=0.449 Sum_probs=203.6
Q ss_pred HHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHH
Q psy15215 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITR 1257 (1432)
Q Consensus 1178 ~~~~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~ 1257 (1432)
+.+++.|+.. |++.|+..|.++|+++|++|.+++.+++||+||||+|||+++++|++.+|.+|+||++|||+|+|.+
T Consensus 2 i~~~~~gd~~---a~~~l~~~y~~~v~~~a~~~~~~~~~aeDl~Qe~~i~l~~a~~~f~~~~~~~f~tyl~~~i~~~i~~ 78 (231)
T TIGR02885 2 IKLAQNGDKE---ARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEIKR 78 (231)
T ss_pred hHHHHcCCHH---HHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHH
Confidence 3456678877 9999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCC--Cc
Q psy15215 1258 SIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDS--HL 1335 (1432)
Q Consensus 1258 ~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~--~~ 1335 (1432)
+++++. .+|+|+++.+..+++.++...+.+++|++||++|||+.+|+++++|..++.....+.||+.+++++++. ++
T Consensus 79 ~lr~~~-~i~~p~~~~~~~~~~~~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~ 157 (231)
T TIGR02885 79 FLRDDG-IIKVSRSLKELARKIRYMKEELSKELGREPTINELAEALGVSPEEIVMALESARSPQSLYDTVHQDDGDPIYL 157 (231)
T ss_pred HHHhCC-CeECCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHHHccCCcCcccCCCCCCCCcchh
Confidence 999986 799999999999999999999999999999999999999999999999998888899999988765432 35
Q ss_pred CcccccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhh
Q psy15215 1336 GDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 1415 (1432)
Q Consensus 1336 ~d~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr 1415 (1432)
.+.+.+... +++. ......+..+++.||++++.||.++|+.|+ |++|||+.||+|+++|++++++|+++||
T Consensus 158 ~d~~~~~~~--~~~~---~~~~~~l~~~l~~L~~~e~~i~~~~~~~~~----t~~eIA~~lgis~~~V~~~~~~al~~Lr 228 (231)
T TIGR02885 158 LDQIADKGS--EDSD---WLEKIALKEAISKLDERERQIIMLRYFKDK----TQTEVANMLGISQVQVSRLEKKVLKKMK 228 (231)
T ss_pred hhhcCCCCc--cHHh---HHHHHHHHHHHHcCCHHHHHHHHHHHHcCC----CHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 566665432 2222 234668899999999999999999998877 9999999999999999999999999999
Q ss_pred Cc
Q psy15215 1416 HP 1417 (1432)
Q Consensus 1416 ~~ 1417 (1432)
..
T Consensus 229 ~~ 230 (231)
T TIGR02885 229 EK 230 (231)
T ss_pred Hh
Confidence 73
No 49
>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=2.3e-32 Score=311.40 Aligned_cols=242 Identities=23% Similarity=0.367 Sum_probs=217.8
Q ss_pred CCChhhHHHHHHHHHh-hhhhhhhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhH
Q psy15215 1168 VLPLNDLRDINRKMIA-GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 1246 (1432)
Q Consensus 1168 ~l~~~e~~~l~~~~~~-g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fsty 1246 (1432)
.+++.+...++.+++. |+.. |++.|+..|.++|+++|++|++++.+++||+||||+|||+++++|++..|.+|+||
T Consensus 9 ~l~~~~~~~li~~~~~~gd~~---a~~~l~~~y~~~v~~~a~~~~~~~~~aeDlvQe~~i~l~~a~~~~~~~~~~~f~ty 85 (255)
T TIGR02941 9 NLTKEDVIQWIAEFQQNQNGE---AQEKLVDHYQNLVYSIAYKYSKGGPMHEDLVQVGMLGLLGAIRRYDYSIGNAFEPF 85 (255)
T ss_pred CCCHHHHHHHHHHHHHCCCHH---HHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCcCCCCcHhH
Confidence 4677788889999988 6777 99999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHc--cCCCCCC
Q psy15215 1247 ATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIA--KEPVSME 1324 (1432)
Q Consensus 1247 a~~~ir~~i~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~--~~~~Sl~ 1324 (1432)
+++||+|+|.++++++.+.+|+|+++.+..++++++...+.+.+|++||.+|+|+.+|++++++..++... ....||+
T Consensus 86 l~~~i~n~~~~~lr~~~~~iri~~~~~~~~~~~~~~~~~l~~~~~r~p~~~eia~~l~i~~~~~~~~~~~~~~~~~~sl~ 165 (255)
T TIGR02941 86 AIPTIIGEIKRYLRDKTWSVHVPRRIKELGPKIKKAIDELTDHLQRSPKIIEIADHLGLSEEEVLEIMEMGQSYRALSVD 165 (255)
T ss_pred HHHHHHHHHHHHHHHcCCCcCCCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHHhccCCcccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999988654 4678999
Q ss_pred CCCCCCCCCCcCcccccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHH
Q psy15215 1325 SPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIR 1404 (1432)
Q Consensus 1325 ~~~~~~~~~~~~d~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vr 1404 (1432)
.+++++++......+ + ...+|++.....+....+..+|+.|||++|.||.++|+.|+ |++|||+.+|+|+++|+
T Consensus 166 ~~~~~~~~~~~~~~~-~-~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~ii~l~~~~g~----s~~eIA~~lgis~~~V~ 239 (255)
T TIGR02941 166 DVIEADSDGSTVARL-D-SVGEVEDGYDQTERRMVLEKILPILSEREKSIIHCTFEENL----SQKETGERLGISQMHVS 239 (255)
T ss_pred ccccCCCCCcccccc-c-ccCCcchHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHcCCC----CHHHHHHHHCcCHHHHH
Confidence 998766544322222 1 12246777777788889999999999999999999998888 99999999999999999
Q ss_pred HHHHHHHHHhhCch
Q psy15215 1405 QIEAKALRKLRHPS 1418 (1432)
Q Consensus 1405 q~~~rAl~kLr~~~ 1418 (1432)
+++++|+++||+.+
T Consensus 240 ~~~~ra~~~Lr~~~ 253 (255)
T TIGR02941 240 RLQRQAISKLKEAA 253 (255)
T ss_pred HHHHHHHHHHHHHh
Confidence 99999999999853
No 50
>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=1.2e-31 Score=305.56 Aligned_cols=242 Identities=23% Similarity=0.363 Sum_probs=218.5
Q ss_pred CCChhhHHHHHHHHHH-hHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHH
Q psy15215 378 VLPLNDLRDINRKMIA-GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 456 (1432)
Q Consensus 378 ~l~~~e~~~l~~~i~~-gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fsty 456 (1432)
.+++.+...|+.+++. ||.. |+++|+..|.++|+++|++|++++.+++||+||||+|||+|+++|++..|.+|+||
T Consensus 9 ~l~~~~~~~li~~~~~~gd~~---a~~~l~~~y~~~v~~~a~~~~~~~~~aeDlvQe~~i~l~~a~~~~~~~~~~~f~ty 85 (255)
T TIGR02941 9 NLTKEDVIQWIAEFQQNQNGE---AQEKLVDHYQNLVYSIAYKYSKGGPMHEDLVQVGMLGLLGAIRRYDYSIGNAFEPF 85 (255)
T ss_pred CCCHHHHHHHHHHHHHCCCHH---HHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCcCCCCcHhH
Confidence 4678888999999998 6887 99999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHc--cCCCCCC
Q psy15215 457 ATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIA--KEPVSME 534 (1432)
Q Consensus 457 a~~~ir~~i~~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~--~~~~sl~ 534 (1432)
+++||+|.|.++++++.+.+|+|++..++.++++++...+.+.+|++||.+|+|+.+|++++++..++... ....||+
T Consensus 86 l~~~i~n~~~~~lr~~~~~iri~~~~~~~~~~~~~~~~~l~~~~~r~p~~~eia~~l~i~~~~~~~~~~~~~~~~~~sl~ 165 (255)
T TIGR02941 86 AIPTIIGEIKRYLRDKTWSVHVPRRIKELGPKIKKAIDELTDHLQRSPKIIEIADHLGLSEEEVLEIMEMGQSYRALSVD 165 (255)
T ss_pred HHHHHHHHHHHHHHHcCCCcCCCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHHhccCCcccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999987654 4578999
Q ss_pred CCCCCCCCCCcCcccccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHH
Q psy15215 535 SPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIR 614 (1432)
Q Consensus 535 ~~~~~~~~~~~~~~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~ 614 (1432)
.+++++++......+. ...+|.+.....+....+..+|+.|||++|.||.++|+.|+ |++|||+.+|+|+++|+
T Consensus 166 ~~~~~~~~~~~~~~~~--~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~ii~l~~~~g~----s~~eIA~~lgis~~~V~ 239 (255)
T TIGR02941 166 DVIEADSDGSTVARLD--SVGEVEDGYDQTERRMVLEKILPILSEREKSIIHCTFEENL----SQKETGERLGISQMHVS 239 (255)
T ss_pred ccccCCCCCccccccc--ccCCcchHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHcCCC----CHHHHHHHHCcCHHHHH
Confidence 9987655443222221 12356777777788889999999999999999999998888 99999999999999999
Q ss_pred HHHHHHHHHHHHHH
Q psy15215 615 QIEAKALRKLRPLA 628 (1432)
Q Consensus 615 ~~~~rAl~kLr~~l 628 (1432)
++.++|+.+||..+
T Consensus 240 ~~~~ra~~~Lr~~~ 253 (255)
T TIGR02941 240 RLQRQAISKLKEAA 253 (255)
T ss_pred HHHHHHHHHHHHHh
Confidence 99999999999865
No 51
>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=7.3e-32 Score=302.92 Aligned_cols=227 Identities=30% Similarity=0.445 Sum_probs=203.8
Q ss_pred HHHHHHhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHH
Q psy15215 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITR 467 (1432)
Q Consensus 388 ~~~i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~ 467 (1432)
+.+++.||.. |++.|+..|.++|+++|++|.+++.+++||+|||++|||+++++|++..|.+|+||++|||+|+|.+
T Consensus 2 i~~~~~gd~~---a~~~l~~~y~~~v~~~a~~~~~~~~~aeDl~Qe~~i~l~~a~~~f~~~~~~~f~tyl~~~i~~~i~~ 78 (231)
T TIGR02885 2 IKLAQNGDKE---ARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEIKR 78 (231)
T ss_pred hHHHHcCCHH---HHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHH
Confidence 4566788888 9999999999999999999999999999999999999999999999998999999999999999999
Q ss_pred HHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCC--Cc
Q psy15215 468 SIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDS--HL 545 (1432)
Q Consensus 468 ~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~--~~ 545 (1432)
+++++. .+|+|+++.+..+++.++...+.+++|++||.+|||+.||+++++|..++..+..+.||+.+++++++. ++
T Consensus 79 ~lr~~~-~i~~p~~~~~~~~~~~~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~ 157 (231)
T TIGR02885 79 FLRDDG-IIKVSRSLKELARKIRYMKEELSKELGREPTINELAEALGVSPEEIVMALESARSPQSLYDTVHQDDGDPIYL 157 (231)
T ss_pred HHHhCC-CeECCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHHHccCCcCcccCCCCCCCCcchh
Confidence 999986 799999999999999999999999999999999999999999999999998888889999988765432 35
Q ss_pred CcccccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHH
Q psy15215 546 GDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625 (1432)
Q Consensus 546 ~~~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr 625 (1432)
.+.+.+... +.+. ......+..+++.||++++.||.++|+.|+ |++|||+.+|+|+++|++++++|+.+|+
T Consensus 158 ~d~~~~~~~--~~~~---~~~~~~l~~~l~~L~~~e~~i~~~~~~~~~----t~~eIA~~lgis~~~V~~~~~~al~~Lr 228 (231)
T TIGR02885 158 LDQIADKGS--EDSD---WLEKIALKEAISKLDERERQIIMLRYFKDK----TQTEVANMLGISQVQVSRLEKKVLKKMK 228 (231)
T ss_pred hhhcCCCCc--cHHh---HHHHHHHHHHHHcCCHHHHHHHHHHHHcCC----CHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 566665432 2222 234668899999999999999999998877 9999999999999999999999999999
Q ss_pred HH
Q psy15215 626 PL 627 (1432)
Q Consensus 626 ~~ 627 (1432)
..
T Consensus 229 ~~ 230 (231)
T TIGR02885 229 EK 230 (231)
T ss_pred Hh
Confidence 75
No 52
>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=1.6e-31 Score=299.45 Aligned_cols=219 Identities=31% Similarity=0.498 Sum_probs=199.1
Q ss_pred hhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q psy15215 1190 KAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 1269 (1432)
Q Consensus 1190 ~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip 1269 (1432)
.|++.|+..|.++|+++|++|.+++.+++||+|||++|||+|+++|++.+|.+|+||++|||++.|.++++++.+++|+|
T Consensus 3 ~a~~~lv~~y~~~v~~~a~~~~~~~~~~eDl~Qe~~i~l~~a~~~f~~~~~~~F~ty~~~~i~~~~~~~~r~~~~~~ri~ 82 (227)
T TIGR02980 3 EAREKLVELNLPLVRSIARRFRNRGEPHEDLVQVGTIGLVKAIDRFDPSYGVKFSTFAVPTIMGEIKRFFRDDTWAVRVP 82 (227)
T ss_pred HHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCCcHHHHHHHHHHHHHHHHHHcCCceecC
Confidence 48999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccC--CCCCCCCCCCCCC--CCcCcccccCCCC
Q psy15215 1270 VHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKE--PVSMESPVGDDED--SHLGDFIEDENML 1345 (1432)
Q Consensus 1270 ~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~--~~Sl~~~~~~~~~--~~~~d~i~d~~~~ 1345 (1432)
+++.+.+++++.+...+.+++|++||.+|+|+.+|++++++..++..... +.||+.+++++++ ..+.+.+.
T Consensus 83 ~~~~~~~~~~~~~~~~l~~~~~~~p~~~ela~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~~d~~~----- 157 (227)
T TIGR02980 83 RRLKELGLKINKATEELTQRLGRSPTIAEIAEELGVSEEEVVEALEAGNSYSALSLDAPIEDDDGDPIALLDTLG----- 157 (227)
T ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCCeeccccCCCCCCCCcccccccC-----
Confidence 99999999999999999999999999999999999999999999887665 8999998873322 12333332
Q ss_pred ChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCc
Q psy15215 1346 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417 (1432)
Q Consensus 1346 ~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~ 1417 (1432)
+|++.+........+..+|..||++++.||.++|+.|+ |++|||+.+|+|+++|++++++|+++||..
T Consensus 158 ~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~y~~~~----s~~eIA~~lgis~~~v~~~~~ra~~~Lr~~ 225 (227)
T TIGR02980 158 DEDDALETVEDRLALKPLLAALPERERRILLLRFFEDK----TQSEIAERLGISQMHVSRLLRRALKKLREQ 225 (227)
T ss_pred CcchHHHhHHHHHHHHHHHHcCCHHHHHHHHHHHhcCC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 44555666677888999999999999999999998888 999999999999999999999999999974
No 53
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=100.00 E-value=2.8e-31 Score=301.29 Aligned_cols=236 Identities=24% Similarity=0.381 Sum_probs=210.6
Q ss_pred hHHHHHHHHH-hhhhhhhhhHHHHHHHHHHHHHHHHHhccC---CCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHH
Q psy15215 1173 DLRDINRKMI-AGEMKARKAKREMTEANLRLVISIAKKYTD---RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 1248 (1432)
Q Consensus 1173 e~~~l~~~~~-~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~---~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~ 1248 (1432)
+...|+++++ .|+.. |++.||..|.++|+++|++|++ ++..++||+||||+|||+++++|++.+|++|+||++
T Consensus 7 ~e~~l~~~~~~~~d~~---a~~~L~~~y~~~v~~~~~~~~~~~~~~~~~eDl~Qe~~i~l~~~~~~f~~~~~~~f~tyl~ 83 (251)
T PRK07670 7 EEQKLWDRWKEERDPD---AADELIRRYMPLVHYHVQRISVGLPKSVSKDDLKSLGMLGLYDALEKFDPSRDLKFDTYAS 83 (251)
T ss_pred HHHHHHHHHHHcCCHH---HHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHH
Confidence 3456777744 56877 9999999999999999999965 688999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHH--HccCCCCCCCC
Q psy15215 1249 WWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMK--IAKEPVSMESP 1326 (1432)
Q Consensus 1249 ~~ir~~i~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~--~~~~~~Sl~~~ 1326 (1432)
||++|.|.+++|++. ++|.++.+.+++++++...+.+.+|++||.+|||+.+|+++++|..++. ....++||+.|
T Consensus 84 ~~irn~~~d~lR~~~---~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~~~~~~~~~~~sld~~ 160 (251)
T PRK07670 84 FRIRGAIIDGLRKED---WLPRSMREKTKKVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATMNEGFFANLLSIDEK 160 (251)
T ss_pred HHHHHHHHHHHHhcC---CCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHHHHHHhccCccccCcc
Confidence 999999999999876 4899999999999999999999999999999999999999999999985 45678999999
Q ss_pred CCCCCCC-CcCcccccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHH
Q psy15215 1327 VGDDEDS-HLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 1405 (1432)
Q Consensus 1327 ~~~~~~~-~~~d~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq 1405 (1432)
+.++++. .+...+.+....+|++.....+....|..+|+.||+++|.||.|+|+.|+ |++|||+.||+|.++|++
T Consensus 161 ~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~~----s~~EIA~~lgis~~tV~~ 236 (251)
T PRK07670 161 THDQDDGENVSVTIRDDKTPTPEEKLLKEELIEELAEKIKQLSEKEQLVISLFYKEEL----TLTEIGQVLNLSTSRISQ 236 (251)
T ss_pred ccCCCCcchhhhhhcCcCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCC----CHHHHHHHHCcCHHHHHH
Confidence 8765543 23344455556688888888888999999999999999999999998888 999999999999999999
Q ss_pred HHHHHHHHhhCch
Q psy15215 1406 IEAKALRKLRHPS 1418 (1432)
Q Consensus 1406 ~~~rAl~kLr~~~ 1418 (1432)
++++|+++||...
T Consensus 237 ~~~ra~~~Lr~~l 249 (251)
T PRK07670 237 IHSKALFKLKKLL 249 (251)
T ss_pred HHHHHHHHHHHHh
Confidence 9999999999854
No 54
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=99.98 E-value=3.7e-31 Score=303.08 Aligned_cols=244 Identities=27% Similarity=0.366 Sum_probs=217.1
Q ss_pred cCCChhhHHHHHHHHH-hhhhhhhhhHHHHHHHHHHHHHHHHHhccC---CCCChhHHHHHHHHHHHHHHHhccccCCCc
Q psy15215 1167 IVLPLNDLRDINRKMI-AGEMKARKAKREMTEANLRLVISIAKKYTD---RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 1242 (1432)
Q Consensus 1167 ~~l~~~e~~~l~~~~~-~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~---~~~~~~DLiQEg~igl~kav~kfd~~~g~~ 1242 (1432)
..++..+...|+.+++ .|+.. |++.++..|.++|+.+|++|.. .+.+++||+||||+|||+|+++|++.+|++
T Consensus 10 ~~~~~~~e~~l~~~~~~~~d~~---a~~~l~~~y~~lv~~~a~~~~~~~~~~~~~eDl~Qeg~l~L~~a~~~fd~~~~~~ 86 (268)
T PRK06288 10 PKYAQQDETELWREYKKTGDPK---IREYLILKYSPLVKYVAGRIAVGMPQNVEFDDLVSYGVFGLIDAIEKFDPEREIK 86 (268)
T ss_pred ccccchHHHHHHHHHHHcCCHH---HHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCC
Confidence 3466677788888866 46777 9999999999999999999862 567899999999999999999999998999
Q ss_pred chhHHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHc--cCC
Q psy15215 1243 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIA--KEP 1320 (1432)
Q Consensus 1243 Fstya~~~ir~~i~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~--~~~ 1320 (1432)
|+||++|||||.|.+++|++. ++|.++....++++++...+.+++|++||.+|||+.+|++.+++..++... ..+
T Consensus 87 f~ty~~~~ir~~i~d~~R~~~---~~p~~~~~~~~~i~~~~~~l~~~~~~~pt~~eia~~lg~~~~~v~~~~~~~~~~~~ 163 (268)
T PRK06288 87 FKTYAVTRIRGAIFDELRSID---WIPRSVRQKARQIERAIAMLEARLGRTPSDEEIADELGISLEEYNSLLSKLSGTSV 163 (268)
T ss_pred HHHHHHHHHHHHHHHHHHhcC---ccCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhcccc
Confidence 999999999999999999765 489999999999999999999999999999999999999999999998654 467
Q ss_pred CCCCCCCC--CCC-CCCcCcccccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhC
Q psy15215 1321 VSMESPVG--DDE-DSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFD 1397 (1432)
Q Consensus 1321 ~Sl~~~~~--~~~-~~~~~d~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~ 1397 (1432)
+||+.+++ +++ ...+.+.+++....+|++.+...+....|..+|..|||++|.||.++|+.|+ |++|||+.||
T Consensus 164 ~sld~~~~~~~~~~~~~l~~~~~~~~~~~pe~~~~~~e~~~~l~~~l~~L~~~~r~vl~l~~~~~~----s~~eIA~~lg 239 (268)
T PRK06288 164 VSLNDLWFGGDEGDEVSLMDTLESPAALNPDEIAEREEIKRVIVEAIKTLPEREKKVLILYYYEDL----TLKEIGKVLG 239 (268)
T ss_pred cchhhhhccCCCcccchhhhhccCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHHC
Confidence 99998764 222 2246677877777899999999999999999999999999999999999888 9999999999
Q ss_pred CCHHHHHHHHHHHHHHhhCchhh
Q psy15215 1398 VTRERIRQIEAKALRKLRHPSRY 1420 (1432)
Q Consensus 1398 vs~~~Vrq~~~rAl~kLr~~~~~ 1420 (1432)
+|.++|++++++|+++||.....
T Consensus 240 is~~tV~~~~~ra~~~Lr~~l~~ 262 (268)
T PRK06288 240 VTESRISQLHTKAVLQLRAKLAE 262 (268)
T ss_pred cCHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999997643
No 55
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=99.98 E-value=1.3e-30 Score=298.51 Aligned_cols=244 Identities=27% Similarity=0.373 Sum_probs=217.9
Q ss_pred cCCChhhHHHHHHHHH-HhHHHHHHhHHHHHHHHHHHHHHHHHhccc---CCCChhhHHHHHHHHHHHHHhhccccCCCc
Q psy15215 377 IVLPLNDLRDINRKMI-AGEMKARKAKREMTEANLRLVISIAKKYTD---RGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 452 (1432)
Q Consensus 377 ~~l~~~e~~~l~~~i~-~gd~~~~~A~~~li~~~~~lV~~ia~ky~~---~~~~~~DLiQEg~igL~kav~~fd~~~g~~ 452 (1432)
+.++..+...|+.+++ .||.. |++.++..|.++|+.+|++|.. .+.+++||+||||+|||+|+++|++.+|++
T Consensus 10 ~~~~~~~e~~l~~~~~~~~d~~---a~~~l~~~y~~lv~~~a~~~~~~~~~~~~~eDl~Qeg~l~L~~a~~~fd~~~~~~ 86 (268)
T PRK06288 10 PKYAQQDETELWREYKKTGDPK---IREYLILKYSPLVKYVAGRIAVGMPQNVEFDDLVSYGVFGLIDAIEKFDPEREIK 86 (268)
T ss_pred ccccchHHHHHHHHHHHcCCHH---HHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCC
Confidence 4567788889999876 46887 9999999999999999999862 467899999999999999999999998999
Q ss_pred cHHHHHHHHHHHHHHHHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHc--cCC
Q psy15215 453 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIA--KEP 530 (1432)
Q Consensus 453 Fstya~~~ir~~i~~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~--~~~ 530 (1432)
|+||++|||||.|.+++|+.. ++|.++....++++++...+.+++|++||.+|||+.+|++.++|..++... ..+
T Consensus 87 f~ty~~~~ir~~i~d~~R~~~---~~p~~~~~~~~~i~~~~~~l~~~~~~~pt~~eia~~lg~~~~~v~~~~~~~~~~~~ 163 (268)
T PRK06288 87 FKTYAVTRIRGAIFDELRSID---WIPRSVRQKARQIERAIAMLEARLGRTPSDEEIADELGISLEEYNSLLSKLSGTSV 163 (268)
T ss_pred HHHHHHHHHHHHHHHHHHhcC---ccCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhcccc
Confidence 999999999999999999765 489999999999999999999999999999999999999999999998654 467
Q ss_pred CCCCCCCC--CCC-CCCcCcccccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcc
Q psy15215 531 VSMESPVG--DDE-DSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFD 607 (1432)
Q Consensus 531 ~sl~~~~~--~~~-~~~~~~~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~ 607 (1432)
+|++.+++ ++. ...+.+.+++....+|++.+...+....|..+|.+|||++|.||.++|+.|+ |++|||+.+|
T Consensus 164 ~sld~~~~~~~~~~~~~l~~~~~~~~~~~pe~~~~~~e~~~~l~~~l~~L~~~~r~vl~l~~~~~~----s~~eIA~~lg 239 (268)
T PRK06288 164 VSLNDLWFGGDEGDEVSLMDTLESPAALNPDEIAEREEIKRVIVEAIKTLPEREKKVLILYYYEDL----TLKEIGKVLG 239 (268)
T ss_pred cchhhhhccCCCcccchhhhhccCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHHC
Confidence 89988763 222 1246677777777889999999999999999999999999999999999888 9999999999
Q ss_pred cchhHHHHHHHHHHHHHHHHHHH
Q psy15215 608 VTRERIRQIEAKALRKLRPLAHD 630 (1432)
Q Consensus 608 is~~~v~~~~~rAl~kLr~~l~~ 630 (1432)
+|.++|+++.++|+++|+..+..
T Consensus 240 is~~tV~~~~~ra~~~Lr~~l~~ 262 (268)
T PRK06288 240 VTESRISQLHTKAVLQLRAKLAE 262 (268)
T ss_pred cCHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999998753
No 56
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=99.97 E-value=1.6e-30 Score=295.15 Aligned_cols=237 Identities=24% Similarity=0.389 Sum_probs=211.0
Q ss_pred hHHHHHHHHH-HhHHHHHHhHHHHHHHHHHHHHHHHHhccc---CCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHH
Q psy15215 383 DLRDINRKMI-AGEMKARKAKREMTEANLRLVISIAKKYTD---RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 458 (1432)
Q Consensus 383 e~~~l~~~i~-~gd~~~~~A~~~li~~~~~lV~~ia~ky~~---~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~ 458 (1432)
+...|+++++ .||.. |++.|+..|.++|+++|++|+. ++.+.+||+||||+|||+++++|++.+|.+|+||++
T Consensus 7 ~e~~l~~~~~~~~d~~---a~~~L~~~y~~~v~~~~~~~~~~~~~~~~~eDl~Qe~~i~l~~~~~~f~~~~~~~f~tyl~ 83 (251)
T PRK07670 7 EEQKLWDRWKEERDPD---AADELIRRYMPLVHYHVQRISVGLPKSVSKDDLKSLGMLGLYDALEKFDPSRDLKFDTYAS 83 (251)
T ss_pred HHHHHHHHHHHcCCHH---HHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHH
Confidence 4456666644 57888 9999999999999999999965 688999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHH--HccCCCCCCCC
Q psy15215 459 WWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMK--IAKEPVSMESP 536 (1432)
Q Consensus 459 ~~ir~~i~~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~--~~~~~~sl~~~ 536 (1432)
|||+|.|.++++++. ++|.++.+.+++++++..++.+.+|++|+.+|||..||+++++|+.++. ....+.|++.|
T Consensus 84 ~~irn~~~d~lR~~~---~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~~~~~~~~~~~sld~~ 160 (251)
T PRK07670 84 FRIRGAIIDGLRKED---WLPRSMREKTKKVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATMNEGFFANLLSIDEK 160 (251)
T ss_pred HHHHHHHHHHHHhcC---CCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHHHHHHhccCccccCcc
Confidence 999999999999876 4899999999999999999999999999999999999999999999985 45678999999
Q ss_pred CCCCCCC-CcCcccccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHH
Q psy15215 537 VGDDEDS-HLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 615 (1432)
Q Consensus 537 ~~~~~~~-~~~~~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~ 615 (1432)
++++++. .+...+.+....+|++.....+....|..+|+.||+++|.||.|+|+.|+ |++|||+.||+|.++|++
T Consensus 161 ~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~~----s~~EIA~~lgis~~tV~~ 236 (251)
T PRK07670 161 THDQDDGENVSVTIRDDKTPTPEEKLLKEELIEELAEKIKQLSEKEQLVISLFYKEEL----TLTEIGQVLNLSTSRISQ 236 (251)
T ss_pred ccCCCCcchhhhhhcCcCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCC----CHHHHHHHHCcCHHHHHH
Confidence 8765543 23344455556688888888888899999999999999999999998888 999999999999999999
Q ss_pred HHHHHHHHHHHHHH
Q psy15215 616 IEAKALRKLRPLAH 629 (1432)
Q Consensus 616 ~~~rAl~kLr~~l~ 629 (1432)
+.++|+++|+..+.
T Consensus 237 ~~~ra~~~Lr~~l~ 250 (251)
T PRK07670 237 IHSKALFKLKKLLE 250 (251)
T ss_pred HHHHHHHHHHHHhh
Confidence 99999999998763
No 57
>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=99.97 E-value=9.5e-31 Score=293.22 Aligned_cols=220 Identities=31% Similarity=0.494 Sum_probs=199.4
Q ss_pred HhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHHHHHHhccccccc
Q psy15215 400 KAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 479 (1432)
Q Consensus 400 ~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip 479 (1432)
.|++.|+..|.|+|+++|++|.+++.+++||+|||++|||+|+++|++.+|.+|+||++|||+|.|.++++++.+.+|+|
T Consensus 3 ~a~~~lv~~y~~~v~~~a~~~~~~~~~~eDl~Qe~~i~l~~a~~~f~~~~~~~F~ty~~~~i~~~~~~~~r~~~~~~ri~ 82 (227)
T TIGR02980 3 EAREKLVELNLPLVRSIARRFRNRGEPHEDLVQVGTIGLVKAIDRFDPSYGVKFSTFAVPTIMGEIKRFFRDDTWAVRVP 82 (227)
T ss_pred HHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCCcHHHHHHHHHHHHHHHHHHcCCceecC
Confidence 38999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccC--CCCCCCCCCCCCCC--CcCcccccCCCC
Q psy15215 480 VHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKE--PVSMESPVGDDEDS--HLGDFIEDENML 555 (1432)
Q Consensus 480 ~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~--~~sl~~~~~~~~~~--~~~~~i~d~~~~ 555 (1432)
+++.+.+++++++...+.+.+|++||.+|+|+.||++++++..++..... +.|++.+++++++. .+.+.+.
T Consensus 83 ~~~~~~~~~~~~~~~~l~~~~~~~p~~~ela~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~~d~~~----- 157 (227)
T TIGR02980 83 RRLKELGLKINKATEELTQRLGRSPTIAEIAEELGVSEEEVVEALEAGNSYSALSLDAPIEDDDGDPIALLDTLG----- 157 (227)
T ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCCeeccccCCCCCCCCcccccccC-----
Confidence 99999999999999999999999999999999999999999999887765 89999988633222 2333332
Q ss_pred ChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHH
Q psy15215 556 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLA 628 (1432)
Q Consensus 556 ~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l 628 (1432)
+|.+.+...+....+..+|..||++++.||.++|+.|+ |++|||+.+|+|+++|+++.++|+++|+..+
T Consensus 158 ~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~y~~~~----s~~eIA~~lgis~~~v~~~~~ra~~~Lr~~l 226 (227)
T TIGR02980 158 DEDDALETVEDRLALKPLLAALPERERRILLLRFFEDK----TQSEIAERLGISQMHVSRLLRRALKKLREQL 226 (227)
T ss_pred CcchHHHhHHHHHHHHHHHHcCCHHHHHHHHHHHhcCC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 34555566677888999999999999999999998888 9999999999999999999999999999764
No 58
>PRK05572 sporulation sigma factor SigF; Validated
Probab=99.97 E-value=1.7e-30 Score=295.07 Aligned_cols=239 Identities=28% Similarity=0.431 Sum_probs=213.3
Q ss_pred hhcCCChhhHHHHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcch
Q psy15215 1165 TDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 1244 (1432)
Q Consensus 1165 ~~~~l~~~e~~~l~~~~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fs 1244 (1432)
....++..+...++.++..|+.. |++.|+..|.++|+++|++|++++.+++||+||||+++|+++++|++.+|.+|+
T Consensus 10 ~~~~l~~~~~~~li~~~~~gd~~---a~~~L~~~y~~~v~~~a~~~~~~~~~aeDl~Qe~~l~l~~~~~~f~~~~~~~f~ 86 (252)
T PRK05572 10 KKPQLKDEENKELIKKSQDGDQE---ARDTLVEKNLRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFS 86 (252)
T ss_pred CCCCCCHHHHHHHHHHHHcCCHH---HHHHHHHHhHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChH
Confidence 35667888888899999999888 999999999999999999999999999999999999999999999998888999
Q ss_pred hHHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCC
Q psy15215 1245 TYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSME 1324 (1432)
Q Consensus 1245 tya~~~ir~~i~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~ 1324 (1432)
||+++||+++|.+++++.. .+|+|.++....++++++..++.+++|++||++|+|+.+|++++.|..++.....+.||+
T Consensus 87 twl~~~i~~~i~~~lr~~~-~~r~~~~~~~~~~~~~~~~~~l~~~~~r~p~~~eia~~l~~~~~~v~~~~~~~~~~~sl~ 165 (252)
T PRK05572 87 TYAVPMIIGEIQRFLRDDG-TVKVSRSLKETANKIRKDKDELSKELGREPTIEELAEYLGVTPEEVVLAQEASRSPQSIH 165 (252)
T ss_pred HHHHHHHHHHHHHHHHhCC-CCCCCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHhcCCCcCcc
Confidence 9999999999999999885 789999999999999999999999999999999999999999999999998888899999
Q ss_pred CCCCCCCCC--CcCcccccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHH
Q psy15215 1325 SPVGDDEDS--HLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRER 1402 (1432)
Q Consensus 1325 ~~~~~~~~~--~~~d~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~ 1402 (1432)
.++++++.. .+.+.+.+... . .......+..+++.||++++.||.++|+.|+ |++|||+.+|+|+++
T Consensus 166 ~~~~~~~~~~~~~~d~~~~~~~---~----~~~~~~~l~~~l~~L~~~~~~v~~l~~~~~~----s~~eIA~~lgis~~~ 234 (252)
T PRK05572 166 ETVHENDGDPITLLDQIADQSE---E----DWFDKIALKEAIRELDERERLIVYLRYFKDK----TQSEVAKRLGISQVQ 234 (252)
T ss_pred cCcccCCCCcchhhhhcCCCch---h----hHHHHHHHHHHHHcCCHHHHHHHHHHHhCCC----CHHHHHHHHCcCHHH
Confidence 988665432 23344443221 1 1334678899999999999999999998887 999999999999999
Q ss_pred HHHHHHHHHHHhhCch
Q psy15215 1403 IRQIEAKALRKLRHPS 1418 (1432)
Q Consensus 1403 Vrq~~~rAl~kLr~~~ 1418 (1432)
|+++.++|+++||..+
T Consensus 235 V~~~~~ral~kLr~~l 250 (252)
T PRK05572 235 VSRLEKKILKQMKEKL 250 (252)
T ss_pred HHHHHHHHHHHHHHHh
Confidence 9999999999999754
No 59
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=99.97 E-value=2.2e-30 Score=295.47 Aligned_cols=243 Identities=21% Similarity=0.350 Sum_probs=216.0
Q ss_pred CCChhhHHHHHHHHHh-hhhhhhhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhH
Q psy15215 1168 VLPLNDLRDINRKMIA-GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 1246 (1432)
Q Consensus 1168 ~l~~~e~~~l~~~~~~-g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fsty 1246 (1432)
.|++.+...++.+++. |+.. |++.|+..|.++|+++|++|++++.+++||+||||++||+++++|++..|.+|+||
T Consensus 9 ~l~~~e~~~li~~~~~~gd~~---a~~~l~~~~~~~v~~~a~~~~~~~~~aeDlvQe~~l~l~~~~~~f~~~~~~~f~ty 85 (257)
T PRK08583 9 KLTKEEVNKWIAEYQENQDEE---AQEKLVKHYKNLVESLAYKYSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAF 85 (257)
T ss_pred cCChHHHHHHHHHHHHcCCHH---HHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCccCCCChHHH
Confidence 3677778889999875 7877 99999999999999999999999999999999999999999999999988899999
Q ss_pred HHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHc--cCCCCCC
Q psy15215 1247 ATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIA--KEPVSME 1324 (1432)
Q Consensus 1247 a~~~ir~~i~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~--~~~~Sl~ 1324 (1432)
+++||+|.|.++++++.+.+++|++..+..++++++...+...+|+.|+.+++|+.+|++.+.+..++... ..+.|++
T Consensus 86 l~~~i~n~~~~~lr~~~~~~~i~r~~~~~~~~~~~~~~~~~~~~~r~~~~~e~a~~~~~~~~~~~~~~~~~~~~~~~sld 165 (257)
T PRK08583 86 AVPTIIGEIKRYLRDKTWSVHVPRRIKELGPKIKKAVDELTTELQRSPKISEIADRLGVSEEEVLEAMEMGKSYQALSVD 165 (257)
T ss_pred HHHHHHHHHHHHHHhcCCCcCCCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceecC
Confidence 99999999999999999999999999999999999999999999999999999999999999999988764 3678999
Q ss_pred CCCCCCCCCCcCcccccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHH
Q psy15215 1325 SPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIR 1404 (1432)
Q Consensus 1325 ~~~~~~~~~~~~d~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vr 1404 (1432)
.+++++++.....+. + ...+|++.....+....+..+|..|||++|.||.++|+.|+ |++|||+.||||+++|+
T Consensus 166 ~~~~~~~~~~~~~~~-~-~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~g~----s~~eIA~~l~is~~tV~ 239 (257)
T PRK08583 166 HSIEADSDGSTVTLL-D-IVGQQEDGYELTEQRMILEKILPVLSDREKSIIQCTFIENL----SQKETGERLGISQMHVS 239 (257)
T ss_pred ccccCCCCCccchHh-h-hcCCcchhHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhCCC----CHHHHHHHHCCCHHHHH
Confidence 988765443211111 1 12356677777778888999999999999999999998888 99999999999999999
Q ss_pred HHHHHHHHHhhCchh
Q psy15215 1405 QIEAKALRKLRHPSR 1419 (1432)
Q Consensus 1405 q~~~rAl~kLr~~~~ 1419 (1432)
+++++|+++||+.+.
T Consensus 240 ~~~~ra~~kLr~~l~ 254 (257)
T PRK08583 240 RLQRQAIKKLREAAF 254 (257)
T ss_pred HHHHHHHHHHHHHhc
Confidence 999999999998654
No 60
>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=99.97 E-value=1.3e-30 Score=291.31 Aligned_cols=217 Identities=29% Similarity=0.446 Sum_probs=197.6
Q ss_pred HHHHHHHHHHHHHHhccC---CCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHHHHHHhccccccccc
Q psy15215 1195 MTEANLRLVISIAKKYTD---RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 1271 (1432)
Q Consensus 1195 Li~~~~~lV~~ia~~y~~---~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~~ 1271 (1432)
|+..|.++|+++|++|.+ ++.+++||+||||+|||+|+++|++.+|++|+||+++||++.+.+++|+.. ++|.+
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 588999999999999986 789999999999999999999999999999999999999999999999875 48999
Q ss_pred HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHc--cCCCCCCCCCCCC-CCCCcCcccccCCCCChH
Q psy15215 1272 MIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIA--KEPVSMESPVGDD-EDSHLGDFIEDENMLAPS 1348 (1432)
Q Consensus 1272 ~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~--~~~~Sl~~~~~~~-~~~~~~d~i~d~~~~~p~ 1348 (1432)
+...+++++++.+++.+++|++||.+|+|+.+|++++.|..++... ...+|++.+..+. +...+.+++++....+|+
T Consensus 78 ~~~~~~~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~~~~~~~~~ 157 (224)
T TIGR02479 78 LRQKARKLERAIRELEARLGREPTEEEIAEELGMDLKEYRQALNEINALSLVSLDELLESGDDGGSLIDRIEDDKSEDPE 157 (224)
T ss_pred HHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHHHHHHHhcCCccccCCcccCCCccchhhhhccccccCCHH
Confidence 9999999999999999999999999999999999999999999644 4567888876553 234566667766667899
Q ss_pred HHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCch
Q psy15215 1349 DAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418 (1432)
Q Consensus 1349 ~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~ 1418 (1432)
+.+........+..+|+.||+++|.||.++|+.|+ |++|||+.+|+|.++|++++++|+++||..+
T Consensus 158 ~~~~~~~~~~~l~~~l~~L~~~~r~il~l~y~~~~----s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l 223 (224)
T TIGR02479 158 EELEREELREALAEAIESLSEREQLVLSLYYYEEL----NLKEIGEVLGLTESRVSQIHSQALKKLRAKL 223 (224)
T ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhCCC----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHc
Confidence 99999999999999999999999999999998888 9999999999999999999999999999753
No 61
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=99.97 E-value=2.3e-30 Score=288.76 Aligned_cols=209 Identities=21% Similarity=0.332 Sum_probs=182.7
Q ss_pred HHHHHHHHHHHHHHHHHhccC---CCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHHHHHHhcccccc
Q psy15215 1192 KREMTEANLRLVISIAKKYTD---RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI 1268 (1432)
Q Consensus 1192 ~~~Li~~~~~lV~~ia~~y~~---~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~~i~~~~r~iri 1268 (1432)
...|+..|+|+|+++|++|.. .+.+.+||+|||++|||+|+++|++..| +|+|||+|||||+|.+++++..+ .
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 457899999999999999875 4679999999999999999999997666 89999999999999999999776 6
Q ss_pred cccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHH--ccCCCCCCCCCCCCCCCCcCcccccCCCCC
Q psy15215 1269 PVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKI--AKEPVSMESPVGDDEDSHLGDFIEDENMLA 1346 (1432)
Q Consensus 1269 p~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~--~~~~~Sl~~~~~~~~~~~~~d~i~d~~~~~ 1346 (1432)
|+++....++++++.+.+.+++|++||++|||+.||+++++|..++.. ....+|||.+++++++.. .+++ .+
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 889999999999999999999999999999999999999999999864 457899999987765422 2221 23
Q ss_pred hHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCc
Q psy15215 1347 PSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417 (1432)
Q Consensus 1347 p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~ 1417 (1432)
|++.. .....+..++..||+++|.||.++|+.++ |++|||+.+|||+++|+|++++|+++||+.
T Consensus 167 ~~~~~---~~~~~l~~~l~~L~~~er~vi~l~~~~~~----t~~EIA~~lgis~~~V~q~~~~~~~kLr~~ 230 (231)
T PRK12427 167 LEENI---IIEDNLKQALSQLDEREQLILHLYYQHEM----SLKEIALVLDLTEARICQLNKKIAQKIKSF 230 (231)
T ss_pred HHHHH---HHHHHHHHHHHcCCHHHHHHHHHHHHcCC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHhh
Confidence 44332 24567899999999999999999998887 999999999999999999999999999963
No 62
>PRK05572 sporulation sigma factor SigF; Validated
Probab=99.97 E-value=8.3e-30 Score=289.47 Aligned_cols=240 Identities=28% Similarity=0.431 Sum_probs=214.7
Q ss_pred hccCCChhhHHHHHHHHHHhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccH
Q psy15215 375 TDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 454 (1432)
Q Consensus 375 ~~~~l~~~e~~~l~~~i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fs 454 (1432)
..+.++..+...++.+++.|+.. |++.|+..|.++|+++|++|++++.+++||+|||++++|+++++|++.+|.+|+
T Consensus 10 ~~~~l~~~~~~~li~~~~~gd~~---a~~~L~~~y~~~v~~~a~~~~~~~~~aeDl~Qe~~l~l~~~~~~f~~~~~~~f~ 86 (252)
T PRK05572 10 KKPQLKDEENKELIKKSQDGDQE---ARDTLVEKNLRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFS 86 (252)
T ss_pred CCCCCCHHHHHHHHHHHHcCCHH---HHHHHHHHhHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChH
Confidence 45678888889999999999988 999999999999999999999999999999999999999999999998888999
Q ss_pred HHHHHHHHHHHHHHHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCC
Q psy15215 455 TYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSME 534 (1432)
Q Consensus 455 tya~~~ir~~i~~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~ 534 (1432)
||+++||+++|.+++++.. .+|+|+++.+..++++++..++.+++|++||++|+|+.+|++++.|..+......+.|++
T Consensus 87 twl~~~i~~~i~~~lr~~~-~~r~~~~~~~~~~~~~~~~~~l~~~~~r~p~~~eia~~l~~~~~~v~~~~~~~~~~~sl~ 165 (252)
T PRK05572 87 TYAVPMIIGEIQRFLRDDG-TVKVSRSLKETANKIRKDKDELSKELGREPTIEELAEYLGVTPEEVVLAQEASRSPQSIH 165 (252)
T ss_pred HHHHHHHHHHHHHHHHhCC-CCCCCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHhcCCCcCcc
Confidence 9999999999999999885 789999999999999999999999999999999999999999999999998888899999
Q ss_pred CCCCCCCCC--CcCcccccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhH
Q psy15215 535 SPVGDDEDS--HLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRER 612 (1432)
Q Consensus 535 ~~~~~~~~~--~~~~~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~ 612 (1432)
.++++++.. ++.+.+.+... . .......+..+++.||++++.||.++|+.|+ |++|||+.+|+|+++
T Consensus 166 ~~~~~~~~~~~~~~d~~~~~~~----~---~~~~~~~l~~~l~~L~~~~~~v~~l~~~~~~----s~~eIA~~lgis~~~ 234 (252)
T PRK05572 166 ETVHENDGDPITLLDQIADQSE----E---DWFDKIALKEAIRELDERERLIVYLRYFKDK----TQSEVAKRLGISQVQ 234 (252)
T ss_pred cCcccCCCCcchhhhhcCCCch----h---hHHHHHHHHHHHHcCCHHHHHHHHHHHhCCC----CHHHHHHHHCcCHHH
Confidence 888655432 23344443221 1 1234678899999999999999999998887 999999999999999
Q ss_pred HHHHHHHHHHHHHHHHH
Q psy15215 613 IRQIEAKALRKLRPLAH 629 (1432)
Q Consensus 613 v~~~~~rAl~kLr~~l~ 629 (1432)
|+++.++|+.+|+..+.
T Consensus 235 V~~~~~ral~kLr~~l~ 251 (252)
T PRK05572 235 VSRLEKKILKQMKEKLD 251 (252)
T ss_pred HHHHHHHHHHHHHHHhc
Confidence 99999999999998764
No 63
>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=99.97 E-value=6.6e-30 Score=285.55 Aligned_cols=217 Identities=29% Similarity=0.446 Sum_probs=197.5
Q ss_pred HHHHHHHHHHHHHHhccc---CCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHHHHHHhccccccchh
Q psy15215 405 MTEANLRLVISIAKKYTD---RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 481 (1432)
Q Consensus 405 li~~~~~lV~~ia~ky~~---~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~~ 481 (1432)
|+..|.++|+++|++|.+ ++.+++||+|||++|||+|+++|++.+|++|+||+++||+|.+.+++++.. ++|.+
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 578999999999999986 689999999999999999999999999999999999999999999999875 48999
Q ss_pred HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHc--cCCCCCCCCCCCC-CCCCcCcccccCCCCChH
Q psy15215 482 MIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIA--KEPVSMESPVGDD-EDSHLGDFIEDENMLAPS 558 (1432)
Q Consensus 482 ~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~--~~~~sl~~~~~~~-~~~~~~~~i~d~~~~~p~ 558 (1432)
+...++++.++..++.+++|++||.+|+|+.||+++++|+.++..+ ...+|++.+.+++ +...+.++++++...+|+
T Consensus 78 ~~~~~~~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~~~~~~~~~ 157 (224)
T TIGR02479 78 LRQKARKLERAIRELEARLGREPTEEEIAEELGMDLKEYRQALNEINALSLVSLDELLESGDDGGSLIDRIEDDKSEDPE 157 (224)
T ss_pred HHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHHHHHHHhcCCccccCCcccCCCccchhhhhccccccCCHH
Confidence 9999999999999999999999999999999999999999998644 4567888876543 333566667766667899
Q ss_pred HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHH
Q psy15215 559 DAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLA 628 (1432)
Q Consensus 559 ~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l 628 (1432)
+.+...+....+..+|+.||++++.||.++|+.|+ |++|||+.+|+|.++|+++.++|+++|+..+
T Consensus 158 ~~~~~~~~~~~l~~~l~~L~~~~r~il~l~y~~~~----s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l 223 (224)
T TIGR02479 158 EELEREELREALAEAIESLSEREQLVLSLYYYEEL----NLKEIGEVLGLTESRVSQIHSQALKKLRAKL 223 (224)
T ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhCCC----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHc
Confidence 99999999999999999999999999999998888 9999999999999999999999999999865
No 64
>TIGR00646 MG010 DNA primase-related protein. The DNA primase DnaG of E. coli and its apparent orthologs in other eubacterial species are approximately 600 residues in length. Within this set, a conspicuous outlier in percent identity, as seen in a UPGMA difference tree, is the branch containing the Mycoplasmas. This lineage is also unique in containing the small, DNA primase-related protein modelled by this alignment, which is homologous to the central third of DNA primase. Several small regions of sequence similarity specifically to Mycoplasma sequences rather than to all DnaG homologs suggests that the divergence of this protein from DnaG post-dated the separation of bacterial lineages. The function of this DNA primase-related protein is unknown.
Probab=99.97 E-value=3.2e-31 Score=281.26 Aligned_cols=124 Identities=19% Similarity=0.133 Sum_probs=109.5
Q ss_pred HHHHhhhccEEEEee-----eeeeeeeeeeCCCCC---CCCCCCcccCccccCchHhHHhhccCCeEEEEecchhHHHHh
Q psy15215 674 ILQEYLESFLISFFL-----RNHGISGFLLTTPDP---VHETPLFHKSNELYGLFEAKNAIGKSGYVLITEGYMDVIGLS 745 (1432)
Q Consensus 674 ~~~~~~~~fri~fpi-----r~igf~gR~~~~~~~---s~et~~f~K~~~Ly~~~~a~~~~~~~~~~~~vEG~~D~ia~~ 745 (1432)
.|++|++| ||||| ||||||||.++++++ ||||++|+||++|||++.+ +++.+.+|||||||||||+|
T Consensus 52 ~y~~~~~R--imFPI~d~~G~vvgFgGR~l~~~~KYlNspet~~f~K~~~Lygl~~~---~~k~~~vilvEGymDVIsl~ 126 (218)
T TIGR00646 52 AYLGEKEW--LNLPLYNFDGNLIGFLNRKVGFEKEFLYLPFNKPPSKSEAFLGLKEL---PIEDNSIYLVEGDFDWLAFR 126 (218)
T ss_pred EecccCCE--EEEEEECCCCCEEEEeccCCCCCCCcccCCCCCCcccchhhcCcchh---hcCCCEEEEEecHHHHHHHH
Confidence 35666666 99999 799999999986433 9999999999999999765 56789999999999999999
Q ss_pred hhCC----------------------CCCeEEEEecCcHHHHHHHHHHHHHhhhhcCCCceEEEecCCCC-CCHHHHHHH
Q psy15215 746 QFGF----------------------FANSSYTCFDGDQAGRRAARRALEVCLLYATDDKIIKFLFLPDK-YDPDSYIRK 802 (1432)
Q Consensus 746 ~~g~----------------------~~~~i~~~~D~D~aG~~a~~~~~~~~~~~~~~~~~~~~~~lp~~-~Dpde~~~~ 802 (1432)
|+|+ .+++||+|||||.||++||.|+++++...|+. |+|+.+|++ ||+||+++.
T Consensus 127 qaGi~naVAslGTALT~~q~~lLkr~~~~~Iil~~D~D~AG~~Aa~r~~~~L~~~G~~---v~vv~lP~~~KDwNEllk~ 203 (218)
T TIGR00646 127 KAGILNCLPLCGLTISDKQMKFFKQKKIEKIFICFDNDFAGKNAAANLEEILKKAGFI---TKVIEIKAAAKDWNDLFLL 203 (218)
T ss_pred HCCCCeEEEcCchHhHHHHHHHHhccCCCEEEEEeCCCHHHHHHHHHHHHHHHHCCCe---EEEEeCCCcCCChhHHHHH
Confidence 9999 25799999999999999999999999887766 999999974 999999987
Q ss_pred hCh
Q psy15215 803 FGY 805 (1432)
Q Consensus 803 ~g~ 805 (1432)
+|.
T Consensus 204 ~~~ 206 (218)
T TIGR00646 204 NNK 206 (218)
T ss_pred hhh
Confidence 764
No 65
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=99.97 E-value=2.2e-29 Score=287.23 Aligned_cols=244 Identities=21% Similarity=0.348 Sum_probs=216.9
Q ss_pred cCCChhhHHHHHHHHHH-hHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHH
Q psy15215 377 IVLPLNDLRDINRKMIA-GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 455 (1432)
Q Consensus 377 ~~l~~~e~~~l~~~i~~-gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fst 455 (1432)
..|+..+...++.+++. ||.. |++.|+..|.++|+++|++|++++.+++||+||||++||+++++|++..|.+|+|
T Consensus 8 ~~l~~~e~~~li~~~~~~gd~~---a~~~l~~~~~~~v~~~a~~~~~~~~~aeDlvQe~~l~l~~~~~~f~~~~~~~f~t 84 (257)
T PRK08583 8 TKLTKEEVNKWIAEYQENQDEE---AQEKLVKHYKNLVESLAYKYSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEA 84 (257)
T ss_pred CcCChHHHHHHHHHHHHcCCHH---HHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCccCCCChHH
Confidence 34677788899999986 7888 9999999999999999999999999999999999999999999999998889999
Q ss_pred HHHHHHHHHHHHHHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHc--cCCCCC
Q psy15215 456 YATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIA--KEPVSM 533 (1432)
Q Consensus 456 ya~~~ir~~i~~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~--~~~~sl 533 (1432)
|+++||+|.|.++++++.+.+++|++..+..+++.++...+.+.+|+.|+.+++|+.+|++.+.+..+.... ..+.|+
T Consensus 85 yl~~~i~n~~~~~lr~~~~~~~i~r~~~~~~~~~~~~~~~~~~~~~r~~~~~e~a~~~~~~~~~~~~~~~~~~~~~~~sl 164 (257)
T PRK08583 85 FAVPTIIGEIKRYLRDKTWSVHVPRRIKELGPKIKKAVDELTTELQRSPKISEIADRLGVSEEEVLEAMEMGKSYQALSV 164 (257)
T ss_pred HHHHHHHHHHHHHHHhcCCCcCCCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceec
Confidence 999999999999999999999999999999999999999999999999999999999999999999887654 367899
Q ss_pred CCCCCCCCCCCcCcccccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHH
Q psy15215 534 ESPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERI 613 (1432)
Q Consensus 534 ~~~~~~~~~~~~~~~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v 613 (1432)
+.+++++++.....+.+ ...+|++.....+....+..+|..|||+++.||.|+|+.|+ |++|||+.||+|+++|
T Consensus 165 d~~~~~~~~~~~~~~~~--~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~g~----s~~eIA~~l~is~~tV 238 (257)
T PRK08583 165 DHSIEADSDGSTVTLLD--IVGQQEDGYELTEQRMILEKILPVLSDREKSIIQCTFIENL----SQKETGERLGISQMHV 238 (257)
T ss_pred CccccCCCCCccchHhh--hcCCcchhHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhCCC----CHHHHHHHHCCCHHHH
Confidence 98887654432111111 12356677777778888999999999999999999998888 9999999999999999
Q ss_pred HHHHHHHHHHHHHHHH
Q psy15215 614 RQIEAKALRKLRPLAH 629 (1432)
Q Consensus 614 ~~~~~rAl~kLr~~l~ 629 (1432)
+++.++|+++|+..+.
T Consensus 239 ~~~~~ra~~kLr~~l~ 254 (257)
T PRK08583 239 SRLQRQAIKKLREAAF 254 (257)
T ss_pred HHHHHHHHHHHHHHhc
Confidence 9999999999998764
No 66
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=99.97 E-value=1.7e-29 Score=281.69 Aligned_cols=209 Identities=21% Similarity=0.342 Sum_probs=181.9
Q ss_pred HHHHHHHHHHHHHHHHHhccc---CCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHHHHHHhcccccc
Q psy15215 402 KREMTEANLRLVISIAKKYTD---RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI 478 (1432)
Q Consensus 402 ~~~li~~~~~lV~~ia~ky~~---~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~~i~~~~r~iri 478 (1432)
...|+..|+|+|.++|++|.. .+.+.+||+|||+||||+|+++|++..| +|+|||+|||||+|.+++++..+ .
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 338999999999999999875 4679999999999999999999997666 89999999999999999999766 6
Q ss_pred chhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHH--ccCCCCCCCCCCCCCCCCcCcccccCCCCC
Q psy15215 479 PVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKI--AKEPVSMESPVGDDEDSHLGDFIEDENMLA 556 (1432)
Q Consensus 479 p~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~--~~~~~sl~~~~~~~~~~~~~~~i~d~~~~~ 556 (1432)
|+++....++++++.+.+.+++|++||.+|||+.||+++++|..++.. .....||+.+++++++.. .+++ .+
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 899999999999999999999999999999999999999999999864 456799999987654422 2221 23
Q ss_pred hHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHH
Q psy15215 557 PSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPL 627 (1432)
Q Consensus 557 p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~ 627 (1432)
|++.. .....+..++..||++++.||.++|+.|+ |++|||+.+|+|.++|+++.++++.+|+..
T Consensus 167 ~~~~~---~~~~~l~~~l~~L~~~er~vi~l~~~~~~----t~~EIA~~lgis~~~V~q~~~~~~~kLr~~ 230 (231)
T PRK12427 167 LEENI---IIEDNLKQALSQLDEREQLILHLYYQHEM----SLKEIALVLDLTEARICQLNKKIAQKIKSF 230 (231)
T ss_pred HHHHH---HHHHHHHHHHHcCCHHHHHHHHHHHHcCC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHhh
Confidence 44333 24667899999999999999999998887 999999999999999999999999999854
No 67
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=99.97 E-value=2.5e-29 Score=283.01 Aligned_cols=221 Identities=27% Similarity=0.417 Sum_probs=197.6
Q ss_pred hhHHHHHHHHHHHHHHHHHhcc---CCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHHHHHHhcccc
Q psy15215 1190 KAKREMTEANLRLVISIAKKYT---DRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTI 1266 (1432)
Q Consensus 1190 ~A~~~Li~~~~~lV~~ia~~y~---~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~~i~~~~r~i 1266 (1432)
-++++|+..|.++|+++|++|+ +++.+++||+||||+|||+++++|++..|.+|+||+++|++|.|.+++|++.+
T Consensus 8 ~~~~~L~~~~~~~v~~~a~~~~~~~~~~~~aeDlvQe~~i~l~~~~~~f~~~~~~~f~tyl~~~irn~~~~~lR~~~~-- 85 (236)
T PRK06986 8 MDQDELVEQYAPLVKRIALRLKARLPASVDLDDLIQAGMIGLLEAARRYDGEQGASFETYAGQRIRGAMLDELRSLDW-- 85 (236)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhcCcccCCChHHHHHHHHHHHHHHHHHHcCC--
Confidence 3789999999999999999997 67899999999999999999999999989999999999999999999999875
Q ss_pred cccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHc--cCCCCCCCCCCCCCCCCcCcccccCCC
Q psy15215 1267 RIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIA--KEPVSMESPVGDDEDSHLGDFIEDENM 1344 (1432)
Q Consensus 1267 rip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~--~~~~Sl~~~~~~~~~~~~~d~i~d~~~ 1344 (1432)
+|.++....+++.+....+.+.+|++||.++||+.+|+++++|..++... ..++|++.+++++++. +.. ..+...
T Consensus 86 -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ela~~l~i~~~~v~~~~~~~~~~~~~sl~~~~~~~~~~-~~~-~~~~~~ 162 (236)
T PRK06986 86 -VPRSVRRNAREVAQAIRQLEQELGREPTDTEVAEKLGLSLEEYREMLLDTNISQLFSIDELRGEHGDS-ILV-TEDHQD 162 (236)
T ss_pred -CCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhccCCccccccccCCCcc-ccc-ccCCCC
Confidence 68888888888999999999999999999999999999999999999754 3567898887665543 222 223345
Q ss_pred CChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchh
Q psy15215 1345 LAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 1419 (1432)
Q Consensus 1345 ~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~ 1419 (1432)
.+|++.+...+....|..+|+.|||++|.||.++|+.|+ |++|||+.+|+|.++|++++++|+++||+...
T Consensus 163 ~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~g~----s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l~ 233 (236)
T PRK06986 163 EDPLQQLEDEELREALVEAIESLPEREQLVLSLYYQEEL----NLKEIGAVLGVSESRVSQIHSQAIKRLRARLG 233 (236)
T ss_pred CCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHhHhccCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 678888888889999999999999999999999998888 99999999999999999999999999998543
No 68
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=99.97 E-value=1.2e-28 Score=277.39 Aligned_cols=221 Identities=27% Similarity=0.423 Sum_probs=198.1
Q ss_pred hHHHHHHHHHHHHHHHHHhcc---cCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHHHHHHhccccc
Q psy15215 401 AKREMTEANLRLVISIAKKYT---DRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIR 477 (1432)
Q Consensus 401 A~~~li~~~~~lV~~ia~ky~---~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~~i~~~~r~ir 477 (1432)
++++|+..|.++|+++|++|+ +.+.+++||+||||+|||+++++|++..|.+|+||+++|++|.|.++++++.+
T Consensus 9 ~~~~L~~~~~~~v~~~a~~~~~~~~~~~~aeDlvQe~~i~l~~~~~~f~~~~~~~f~tyl~~~irn~~~~~lR~~~~--- 85 (236)
T PRK06986 9 DQDELVEQYAPLVKRIALRLKARLPASVDLDDLIQAGMIGLLEAARRYDGEQGASFETYAGQRIRGAMLDELRSLDW--- 85 (236)
T ss_pred cHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhcCcccCCChHHHHHHHHHHHHHHHHHHcCC---
Confidence 789999999999999999997 67899999999999999999999999988999999999999999999999875
Q ss_pred cchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHc--cCCCCCCCCCCCCCCCCcCcccccCCCC
Q psy15215 478 IPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIA--KEPVSMESPVGDDEDSHLGDFIEDENML 555 (1432)
Q Consensus 478 ip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~--~~~~sl~~~~~~~~~~~~~~~i~d~~~~ 555 (1432)
+|.++....+++.++...+.+.+|++||.++||+.+|+++++|..++... ..++|++.+++++++. +.. ..+....
T Consensus 86 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ela~~l~i~~~~v~~~~~~~~~~~~~sl~~~~~~~~~~-~~~-~~~~~~~ 163 (236)
T PRK06986 86 VPRSVRRNAREVAQAIRQLEQELGREPTDTEVAEKLGLSLEEYREMLLDTNISQLFSIDELRGEHGDS-ILV-TEDHQDE 163 (236)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhccCCccccccccCCCcc-ccc-ccCCCCC
Confidence 68888888888999999999999999999999999999999999998754 4567888887665443 222 2233456
Q ss_pred ChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHHHH
Q psy15215 556 APSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLAHD 630 (1432)
Q Consensus 556 ~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l~~ 630 (1432)
+|++.+...+....|..+|+.||+++|.||.++|..|+ |++|||+.+|+|.++|+++.++|+++|++.+..
T Consensus 164 ~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~g~----s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l~~ 234 (236)
T PRK06986 164 DPLQQLEDEELREALVEAIESLPEREQLVLSLYYQEEL----NLKEIGAVLGVSESRVSQIHSQAIKRLRARLGE 234 (236)
T ss_pred CHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHhHhccCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 78888888889999999999999999999999998888 999999999999999999999999999988754
No 69
>PF04546 Sigma70_ner: Sigma-70, non-essential region; InterPro: IPR007631 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 [, ]. This domain is found in the primary vegetative sigma factor. Its function is unclear, and it can be removed without apparent loss of function [, ].; 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: 1SIG_A 3IYD_F.
Probab=99.97 E-value=2.6e-31 Score=291.66 Aligned_cols=204 Identities=29% Similarity=0.534 Sum_probs=154.0
Q ss_pred ChHHHHHHHHHHHHhhhcccchhhhhccccCCCCCCc---chhc---cCCCCCC-hhhhhhhcCCCCCCHHHHHHhHHHH
Q psy15215 171 CPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN---NRVI---KGNKNNN-EEKILIESSSADLSTEQLEKLKYES 243 (1432)
Q Consensus 171 ~P~~v~~il~~~e~l~~ge~rl~dii~g~~d~~~~~~---~~~~---~~~~~~~-e~~d~~~~~~~~~~~~~~~~l~~~~ 243 (1432)
||.||..||+||++|.+|+++|+|||+||+|++..+. .... ++.++++ ++++++++++..........+++.+
T Consensus 1 ~P~~v~~ll~~~~~v~~ge~rl~diI~gf~d~~~~~~~~~~~~~~~~~~~e~~~~dddd~d~d~~~~~~~~~~~~~~e~v 80 (211)
T PF04546_consen 1 YPGTVEELLEWYDRVEEGEIRLRDIIDGFIDPEAEEEEEAEEEEEDEDDEEDEEDDDDDEDDDEDDASEAADEGPDPEEV 80 (211)
T ss_dssp -HHHHHHHHHHHCCCCTTSS-GGGTEEEE-S-S--S--S-TTTT-SS-CCCT------------------------HHHH
T ss_pred CCHHHHHHHHHHHHHHcCCcchHHHHhhccccccccccccCcccccccccccccccccccccccccccchhhccCCHHHH
Confidence 8999999999999999999999999999999831111 1000 1111111 1111111111122334445678999
Q ss_pred HHHHHhHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHhhcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCC
Q psy15215 244 LIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGM 323 (1432)
Q Consensus 244 ~~~f~~l~~~~~~~~~~~~~~g~~~~~~~k~~~~i~~~l~~ikl~~k~ie~l~~~l~~~~~~ir~~Er~i~~~~v~~~gm 323 (1432)
+++|..|++.|.++.++++++|..++.|.+++.+|++.|+.|||+|++|++|++.||..+.+||.+||+||++||++|||
T Consensus 81 ~~~f~~i~~~~~~~~~~~~~~g~~~~~~~~~~~~l~~~~~~ikl~~k~id~L~~~lr~~~~~Ir~~Er~i~~l~v~~~gm 160 (211)
T PF04546_consen 81 LERFDEIRKLYEKLQKALKKHGRDSKKYQKLREELAEEFMEIKLSPKQIDRLVEQLREIVERIRQQERRIMRLCVRRAGM 160 (211)
T ss_dssp HHHHHHHCCCHHHHCCCTTT--S-SHHHHHHHHHHHHHHTTCEE-HHHHHHHCHHHHCCCHHHHHHHHHHHHCCCTTTT-
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHHHhhccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ChHHHHHhcCCCccchhhhhhHhhhcCchHHHHhhchHHHHHHHHHHHhhh
Q psy15215 324 PRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQ 374 (1432)
Q Consensus 324 pr~~fi~~f~~~e~~~~wl~~~~~~~~~~~~~L~~~~~~i~~~q~~L~~iE 374 (1432)
||++|++.|+|||||++|++++++.+++|+..|.++.+.|.++|++|.+||
T Consensus 161 pR~~Fi~~f~gnEtn~~Wl~~~~~~~~~~~~~l~~~~~~I~~~q~kL~~iE 211 (211)
T PF04546_consen 161 PRKEFIKSFPGNETNPNWLDKLIKAKKKWAEALERHAPEIREAQRKLAEIE 211 (211)
T ss_dssp -HHHCCCCCTTT-SSCCCTHHHHTT-SCCHHHGGGTHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHccCcccHHHHHHHHHHcCChHHHHHHHhHHHHHHHHHHHHHhC
Confidence 999999999999999999999999999999999999999999999999886
No 70
>PF04546 Sigma70_ner: Sigma-70, non-essential region; InterPro: IPR007631 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 [, ]. This domain is found in the primary vegetative sigma factor. Its function is unclear, and it can be removed without apparent loss of function [, ].; 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: 1SIG_A 3IYD_F.
Probab=99.96 E-value=3.8e-31 Score=290.27 Aligned_cols=204 Identities=29% Similarity=0.535 Sum_probs=153.9
Q ss_pred ChHHHHHHHHHHHHhhhcccchhhhhccccCCCCCCc---hhhc-cCC--CCCc-hhhhhhhccCCCCCHHHHHHhHHHH
Q psy15215 961 CPTTIMEILIAADKISKNEIKIDEIVDGLIDKNFSSN---NRVI-KGN--KNNN-EEKILIESSSADLSTEQLEKLKYES 1033 (1432)
Q Consensus 961 ~P~~v~~il~~~e~l~~ge~~l~dii~g~~d~~~~~~---~~~~-~~~--~~~e-~~~d~~~~~~~~~~~~~l~~l~~~~ 1033 (1432)
||.+|+.||+||++|.+|+++|+|||+||+|++.... .... +.+ +.++ +++|++++++..........+++.+
T Consensus 1 ~P~~v~~ll~~~~~v~~ge~rl~diI~gf~d~~~~~~~~~~~~~~~~~~~e~~~~dddd~d~d~~~~~~~~~~~~~~e~v 80 (211)
T PF04546_consen 1 YPGTVEELLEWYDRVEEGEIRLRDIIDGFIDPEAEEEEEAEEEEEDEDDEEDEEDDDDDEDDDEDDASEAADEGPDPEEV 80 (211)
T ss_dssp -HHHHHHHHHHHCCCCTTSS-GGGTEEEE-S-S--S--S-TTTT-SS-CCCT------------------------HHHH
T ss_pred CCHHHHHHHHHHHHHHcCCcchHHHHhhccccccccccccCcccccccccccccccccccccccccccchhhccCCHHHH
Confidence 8999999999999999999999999999999831111 0000 000 0011 1111111111123334445678999
Q ss_pred HHHHHHHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHhhccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q psy15215 1034 LIKFSNISFHFDKMRKAFEKEGYNSESYIKAHNNISNEMLGIRFTAKSIEKLCDTLRNQINQVTQIEKQILEIVVNKCGM 1113 (1432)
Q Consensus 1034 ~~~f~~l~~~~~~~~~~~~~~~~~~~~~~k~~~~i~~~l~~irl~~k~i~~l~~~l~~~~~~ir~~Er~i~~~~~~~~~m 1113 (1432)
+++|..|++.|+++.+++.++|..+++|.+++.+|++.|+.|||+|++|++|++.||..+++||.+||+||++||++|||
T Consensus 81 ~~~f~~i~~~~~~~~~~~~~~g~~~~~~~~~~~~l~~~~~~ikl~~k~id~L~~~lr~~~~~Ir~~Er~i~~l~v~~~gm 160 (211)
T PF04546_consen 81 LERFDEIRKLYEKLQKALKKHGRDSKKYQKLREELAEEFMEIKLSPKQIDRLVEQLREIVERIRQQERRIMRLCVRRAGM 160 (211)
T ss_dssp HHHHHHHCCCHHHHCCCTTT--S-SHHHHHHHHHHHHHHTTCEE-HHHHHHHCHHHHCCCHHHHHHHHHHHHCCCTTTT-
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHHHhhccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ChHHHHHhcCCCccchhhHHHHhhhcCchhHHHhhchHHHHHHHHHHHHhh
Q psy15215 1114 PRLHFIKVFPENEINLNWVDNETKIQHDYNLILCRNIPSIKELQQKLINLQ 1164 (1432)
Q Consensus 1114 ~r~~fl~~f~~~e~~~~wl~~~~~~~~~~~~~L~~~~~~I~~~q~~L~~ie 1164 (1432)
||++|++.|+|||||++|++++++.+++|+..|.++.+.|.++|++|.+||
T Consensus 161 pR~~Fi~~f~gnEtn~~Wl~~~~~~~~~~~~~l~~~~~~I~~~q~kL~~iE 211 (211)
T PF04546_consen 161 PRKEFIKSFPGNETNPNWLDKLIKAKKKWAEALERHAPEIREAQRKLAEIE 211 (211)
T ss_dssp -HHHCCCCCTTT-SSCCCTHHHHTT-SCCHHHGGGTHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHccCcccHHHHHHHHHHcCChHHHHHHHhHHHHHHHHHHHHHhC
Confidence 999999999999999999999999999999999999999999999999886
No 71
>PHA02540 61 DNA primase; Provisional
Probab=99.95 E-value=1.5e-27 Score=271.92 Aligned_cols=162 Identities=12% Similarity=0.096 Sum_probs=129.6
Q ss_pred hhhhhhhhH-hhcC--CCcccccccccCCCCCchhhHHHHHHH----HHHhhhccEEEEee-----eeeeeeeeeeCC-C
Q psy15215 635 RTHQNEKII-ACSS--DSSNHNEHVTNNNFPPGFNIFHKLLRI----LQEYLESFLISFFL-----RNHGISGFLLTT-P 701 (1432)
Q Consensus 635 ~l~~~~~~~-~l~~--l~~~~~~~f~~Gyap~~~~~l~~~~~~----~~~~~~~fri~fpi-----r~igf~gR~~~~-~ 701 (1432)
++..+..|+ ||+. ||+++++. ||+|++|+.|.+++.. ....++ |||||| |||||+||+|++ .
T Consensus 123 ~l~~~~~a~~YL~~RGi~~~~~~~---~~~~~~~~~l~~~l~~~~~~~~~d~~--RImFPI~d~~G~vigFgGR~l~~~~ 197 (337)
T PHA02540 123 TLPEDHPIIKYVENRCIPKDKWKL---LYFTREWQKLVNSIKPDTYKKEKPEP--RLVIPIFNKDGKIESFQGRALRKDA 197 (337)
T ss_pred hCcccHHHHHHHHHcCCCHHHHHh---cCCCccHHHHHHHHhhccCchhccCC--eeEEEEECCCCCEEEEEeEECCCCC
Confidence 355677788 9988 99998775 5778899999988851 112234 599999 799999999986 4
Q ss_pred CC-CCCCCCcccCccccCchHhHHhhccCCeEEEEecchhHHHHhhhCC-------------CCCeEEEEecCcHHHHHH
Q psy15215 702 DP-VHETPLFHKSNELYGLFEAKNAIGKSGYVLITEGYMDVIGLSQFGF-------------FANSSYTCFDGDQAGRRA 767 (1432)
Q Consensus 702 ~~-s~et~~f~K~~~Ly~~~~a~~~~~~~~~~~~vEG~~D~ia~~~~g~-------------~~~~i~~~~D~D~aG~~a 767 (1432)
.| --+||+|+|++.|||++.|+ +.+.+||||||||||++. +++ ++.+||+||||| ||++|
T Consensus 198 ~pKYlNSp~f~K~~~LYGl~~a~----~~~~vilvEGYmDvi~i~-naVAtlGTaLT~~~~~~~~~vvl~~D~D-a~~~a 271 (337)
T PHA02540 198 PQKYITIKADEEATKIYGLDRID----PGKTVYVVEGPIDSLFLP-NSIAITGGDLDLNEVPFKDTRVWVLDNE-PRHPD 271 (337)
T ss_pred CCCeeeCCcccccccccChhHhc----cCCEEEEEeCCcceeeec-cceeeCccccCHhHhCccceEEEEECCc-hhHHH
Confidence 55 34457999999999999765 468999999999999863 333 678999999999 88899
Q ss_pred HHHHHHHhhhhcCCCceEEEecCC--CCCCHHHHHHHhCh--hhhhh
Q psy15215 768 ARRALEVCLLYATDDKIIKFLFLP--DKYDPDSYIRKFGY--KIFSK 810 (1432)
Q Consensus 768 ~~~~~~~~~~~~~~~~~~~~~~lp--~~~Dpde~~~~~g~--~~~~~ 810 (1432)
|.|++++|+..|+. |.++..| ++||||||++++|+ +.|.+
T Consensus 272 t~r~~~~l~~~g~~---v~v~~~~~~~~kDpde~i~~~G~~~~~~~~ 315 (337)
T PHA02540 272 TIKRISKLIDAGEK---VVIWDKCPWPSKDINDMIMKGGATPEDIME 315 (337)
T ss_pred HHHHHHHHHHCCCe---EEEecCCCCCCcCHHHHHHhcCCCHHHHHH
Confidence 99999999988864 6665555 56999999999996 55544
No 72
>PHA02031 putative DnaG-like primase
Probab=99.94 E-value=1.3e-26 Score=251.16 Aligned_cols=123 Identities=18% Similarity=0.213 Sum_probs=105.6
Q ss_pred HHHHhhhccEEEEeeeeeeeeeeeeCCCCC----CCCCCCcccCccccCchHhHHhhccCCeEEEEecchhHHHHhh---
Q psy15215 674 ILQEYLESFLISFFLRNHGISGFLLTTPDP----VHETPLFHKSNELYGLFEAKNAIGKSGYVLITEGYMDVIGLSQ--- 746 (1432)
Q Consensus 674 ~~~~~~~~fri~fpir~igf~gR~~~~~~~----s~et~~f~K~~~Ly~~~~a~~~~~~~~~~~~vEG~~D~ia~~~--- 746 (1432)
.||+|++| |||||+. |||||.|++.+| |+ || +..|||++. ++++.+.+||||||||||++|+
T Consensus 111 ~yDrFr~R--imFPI~d-gFgGR~l~~~~PKYLN~~-SP----~~~l~~~~~---~~~~~~~vIlvEGYmDVI~l~~a~~ 179 (266)
T PHA02031 111 EYSERQGR--LIFRTDA-GWLGRATADQQPKWVGYG-YP----APDYVGWPP---ELSMPRPVVLTEDYLSALKVRWACN 179 (266)
T ss_pred ceeeeCCE--EEEeecc-ccccccCCCCCCCcCCCC-CC----cHHHhhchh---hhccCCeEEEEcCcHHHHHHHHHHh
Confidence 36777777 9999988 999999987766 22 22 346788765 4467899999999999999986
Q ss_pred hCC---------------------C-CCeEEEEecCcHHHHHHHHHHHHHhhhhcCCCceEEEecCCCCCCHHHHHHHhC
Q psy15215 747 FGF---------------------F-ANSSYTCFDGDQAGRRAARRALEVCLLYATDDKIIKFLFLPDKYDPDSYIRKFG 804 (1432)
Q Consensus 747 ~g~---------------------~-~~~i~~~~D~D~aG~~a~~~~~~~~~~~~~~~~~~~~~~lp~~~Dpde~~~~~g 804 (1432)
+|| . +++||||||||.||++||.|++.+++..++. ++|+.||+|+|||||+++.|
T Consensus 180 aG~~naVA~LGTALT~~q~~~L~r~~~~~Vil~fDgD~AG~~Aa~ra~~~l~~~~~~---v~vv~lP~g~DPDd~ir~~i 256 (266)
T PHA02031 180 KPEVFAVALLGTRLRDRLAAILLQQTCPRVLIFLDGDPAGVDGSAGAMRRLRPLLIE---GQVIITPDGFDPKDLEREQI 256 (266)
T ss_pred cCcceEEECCcccCCHHHHHHHHhcCCCCEEEEeCCCHHHHHHHHHHHHHHHHcCCc---eEEEECCCCCChHHHHHHHH
Confidence 688 3 7999999999999999999999999988876 99999999999999999999
Q ss_pred hhhhhh
Q psy15215 805 YKIFSK 810 (1432)
Q Consensus 805 ~~~~~~ 810 (1432)
.+++..
T Consensus 257 ~eal~~ 262 (266)
T PHA02031 257 RELLIG 262 (266)
T ss_pred HHHHhc
Confidence 988754
No 73
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=99.90 E-value=1.5e-22 Score=227.37 Aligned_cols=214 Identities=29% Similarity=0.390 Sum_probs=171.4
Q ss_pred HHHHHHHHHHHHhhhhcCCChhhHHHHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHH
Q psy15215 1151 PSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMK 1230 (1432)
Q Consensus 1151 ~~I~~~q~~L~~ie~~~~l~~~e~~~l~~~~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~k 1230 (1432)
.+|.=+.+.+..+.....+++.+...++..+..|+.. |++.|+..|.++|+++|.+|++++.+++||+||||+++|+
T Consensus 13 ~~~~~~~~~~~~~~~~~~~~~~~e~~l~~~~~~gd~~---a~~~l~~~y~~~l~~~a~~~~~~~~daeDlvQE~fi~l~~ 89 (233)
T PRK05803 13 KEILFLVSYVKNNSFPQPLSEEEERKYLELMKEGDEE---ARNILIERNLRLVAHIVKKFENTGEDVDDLISIGTIGLIK 89 (233)
T ss_pred HHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHcCCHH---HHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHH
Confidence 3455566677777555567788888999999999888 9999999999999999999999999999999999999999
Q ss_pred HHHhccccCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHH
Q psy15215 1231 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKI 1310 (1432)
Q Consensus 1231 av~kfd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v 1310 (1432)
++++|++.++.+|+||+++|+||.+.+++|+..+..
T Consensus 90 ~~~~f~~~~~~~f~~wl~~i~rn~~id~~Rk~~~~~-------------------------------------------- 125 (233)
T PRK05803 90 AIESFDAGKGTKLATYAARCIENEILMHLRNLKKTK-------------------------------------------- 125 (233)
T ss_pred HHHhcCcccCCChHHHHHHHHHHHHHHHHHHHhccc--------------------------------------------
Confidence 999999988889999999999999999999876410
Q ss_pred HHHHHHccCCCCCCCCCCCC---CCCCcCcccccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCC
Q psy15215 1311 RKIMKIAKEPVSMESPVGDD---EDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDH 1387 (1432)
Q Consensus 1311 ~~~~~~~~~~~Sl~~~~~~~---~~~~~~d~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~ 1387 (1432)
...+++.+.+.+ ...++.+..++. ..+|++..........+..+|+.|||++|.|+.++|+.+..+++
T Consensus 126 --------~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~l~~~l~~Lp~~~R~i~~l~y~~~~~e~~ 196 (233)
T PRK05803 126 --------KEVSLQDPIGVDKEGNEISLIDILGSE-EDDVIEQVELKMEVEKLYKKIDILDEREKEVIEMRYGLGNGKEK 196 (233)
T ss_pred --------cCCCccccccCCCCcCcccHHHHccCC-CCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCCCCCCc
Confidence 011222221111 111222333332 23577777777888899999999999999999999964434566
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHhhCchhh
Q psy15215 1388 TLEEVGKQFDVTRERIRQIEAKALRKLRHPSRY 1420 (1432)
Q Consensus 1388 t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~~ 1420 (1432)
|++|||+.+|+|+++|++++++|+++||..+..
T Consensus 197 S~~EIA~~lgis~~tV~~~~~rA~~kLr~~l~~ 229 (233)
T PRK05803 197 TQREIAKALGISRSYVSRIEKRALKKLFKELYR 229 (233)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999986543
No 74
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=99.90 E-value=4.4e-22 Score=223.71 Aligned_cols=214 Identities=29% Similarity=0.399 Sum_probs=174.4
Q ss_pred hHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHHhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHH
Q psy15215 360 IPSIKELQQKLINLQTDIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLM 439 (1432)
Q Consensus 360 ~~~i~~~q~~L~~iE~~~~l~~~e~~~l~~~i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~ 439 (1432)
..+|.-+.+++.++.....+++.+...++..++.|+.. |++.|+..|.++|+++|.+|++++.+++||+|||++++|
T Consensus 12 ~~~~~~~~~~~~~~~~~~~~~~~~e~~l~~~~~~gd~~---a~~~l~~~y~~~l~~~a~~~~~~~~daeDlvQE~fi~l~ 88 (233)
T PRK05803 12 VKEILFLVSYVKNNSFPQPLSEEEERKYLELMKEGDEE---ARNILIERNLRLVAHIVKKFENTGEDVDDLISIGTIGLI 88 (233)
T ss_pred HHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHcCCHH---HHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHH
Confidence 34566777888888666778888889999999999988 999999999999999999999999999999999999999
Q ss_pred HHHhhccccCCCccHHHHHHHHHHHHHHHHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHH
Q psy15215 440 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEK 519 (1432)
Q Consensus 440 kav~~fd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~ 519 (1432)
+++.+|++.++.+|.||+++|++|.+.+++|+..+..
T Consensus 89 ~~~~~f~~~~~~~f~~wl~~i~rn~~id~~Rk~~~~~------------------------------------------- 125 (233)
T PRK05803 89 KAIESFDAGKGTKLATYAARCIENEILMHLRNLKKTK------------------------------------------- 125 (233)
T ss_pred HHHHhcCcccCCChHHHHHHHHHHHHHHHHHHHhccc-------------------------------------------
Confidence 9999999988889999999999999999999775410
Q ss_pred HHHHHHHccCCCCCCCCCC-CC--CCCCcCcccccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCC
Q psy15215 520 IRKIMKIAKEPVSMESPVG-DD--EDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSD 596 (1432)
Q Consensus 520 v~~~~~~~~~~~sl~~~~~-~~--~~~~~~~~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~ 596 (1432)
...+++.+.+ ++ ...++.+..++. ..+|.+..........+..+|+.||+++|.|+.++|+.+...+
T Consensus 126 ---------~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~l~~~l~~Lp~~~R~i~~l~y~~~~~e~ 195 (233)
T PRK05803 126 ---------KEVSLQDPIGVDKEGNEISLIDILGSE-EDDVIEQVELKMEVEKLYKKIDILDEREKEVIEMRYGLGNGKE 195 (233)
T ss_pred ---------cCCCccccccCCCCcCcccHHHHccCC-CCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCCCCCC
Confidence 0112222211 11 111222333332 2357777777788889999999999999999999996443456
Q ss_pred CcHHHHHhhcccchhHHHHHHHHHHHHHHHHHH
Q psy15215 597 HTLEEVGKQFDVTRERIRQIEAKALRKLRPLAH 629 (1432)
Q Consensus 597 ~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l~ 629 (1432)
+|++|||+.+|+|+++|+++.++|+++|+..+.
T Consensus 196 ~S~~EIA~~lgis~~tV~~~~~rA~~kLr~~l~ 228 (233)
T PRK05803 196 KTQREIAKALGISRSYVSRIEKRALKKLFKELY 228 (233)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 699999999999999999999999999998875
No 75
>PRK08624 hypothetical protein; Provisional
Probab=99.89 E-value=5.1e-23 Score=234.05 Aligned_cols=113 Identities=19% Similarity=0.163 Sum_probs=94.3
Q ss_pred hhcC-CCcccccccccCCCCCchhhHHHHHHHHHHhhhccEEEEee-----eeeeeeeeeeCCCC---C----C--CCCC
Q psy15215 644 ACSS-DSSNHNEHVTNNNFPPGFNIFHKLLRILQEYLESFLISFFL-----RNHGISGFLLTTPD---P----V--HETP 708 (1432)
Q Consensus 644 ~l~~-l~~~~~~~f~~Gyap~~~~~l~~~~~~~~~~~~~fri~fpi-----r~igf~gR~~~~~~---~----s--~et~ 708 (1432)
|+.. +|++|+++|+|||+| |+|++| ||||| |||||+||++++.. | + .+|+
T Consensus 158 ~l~RGIs~etik~F~lGy~~-------------D~Fr~R--ImFPI~d~~GrvIGFgGR~l~~~~~~~~KY~p~y~Nst~ 222 (373)
T PRK08624 158 WLDEGISEKTQKYWEIKFYL-------------DVISQR--IIIPHRDESGELIGIRGRLLDKELVDKNKYFPIYVNDTG 222 (373)
T ss_pred HHHcCCCHHHHHHhCCCccc-------------cccCCe--eEEEEECCCCCEEEEeCeEcCCCccccccccccCCCCcc
Confidence 5544 999999999999997 567777 99999 79999999998642 2 2 2344
Q ss_pred C-cccCccccCchHhHHhhccCCeEEEEecchhHH---HHhhhCC--------------------C-CCeEEEEecC---
Q psy15215 709 L-FHKSNELYGLFEAKNAIGKSGYVLITEGYMDVI---GLSQFGF--------------------F-ANSSYTCFDG--- 760 (1432)
Q Consensus 709 ~-f~K~~~Ly~~~~a~~~~~~~~~~~~vEG~~D~i---a~~~~g~--------------------~-~~~i~~~~D~--- 760 (1432)
+ |+||++|||+|.|+.+|++.+.+|||||||||| ++|++|- + .++|||||||
T Consensus 223 ~~F~Kg~~LYGl~~Ak~~irk~~~vIivEGymDVI~~~a~~~~G~naVA~lGTalT~~q~~lL~r~~~~~Vil~~Dgd~~ 302 (373)
T PRK08624 223 YNHPKGKILYGLWQNKKYIKEKKKVIIVESEKSVLFSDKFYGEGNFVVAICGSNISEVQAEKLLRLGVEEVTIALDKEYM 302 (373)
T ss_pred cccccchhhcCHHHHHHHhccCCeEEEEeccHHHHHHHHHhcCCCcEEECChhhCCHHHHHHHHhcCCCcEEEEecCCcc
Confidence 4 999999999999999999999999999999999 8899983 3 4699999999
Q ss_pred cHHHHHHHHHH
Q psy15215 761 DQAGRRAARRA 771 (1432)
Q Consensus 761 D~aG~~a~~~~ 771 (1432)
|.+|-.+....
T Consensus 303 d~~~~~~~~~~ 313 (373)
T PRK08624 303 DVTEEEVYEYI 313 (373)
T ss_pred ccchHHHHHHH
Confidence 56666555444
No 76
>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=99.88 E-value=2.6e-21 Score=216.48 Aligned_cols=193 Identities=29% Similarity=0.435 Sum_probs=153.8
Q ss_pred CChhhHHHHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHH
Q psy15215 1169 LPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 1248 (1432)
Q Consensus 1169 l~~~e~~~l~~~~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~ 1248 (1432)
+++.+...++.+++.|+.. |++.|+..|.+.|+++|.+|++++.+++||+||+|+++|+++++|++..+.+|.||++
T Consensus 30 ~~~~~~~~li~~~~~gd~~---af~~l~~~y~~~v~~~~~~~~~~~~dAEDlvQevfi~l~~~~~~~~~~~~~~f~twl~ 106 (227)
T TIGR02846 30 LSEEEEKKYLDRLKEGDEE---ARNVLIERNLRLVAHIVKKFSNTGEDVDDLISIGTIGLIKAIDSFDPDKGTRLATYAA 106 (227)
T ss_pred CCHHHHHHHHHHHHcCCHH---HHHHHHHHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHhCCcccCCChHHHHH
Confidence 5566778888999999888 9999999999999999999999999999999999999999999999988888999999
Q ss_pred HHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCC
Q psy15215 1249 WWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVG 1328 (1432)
Q Consensus 1249 ~~ir~~i~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~ 1328 (1432)
+|++|.|.+++|+..+..+ ..+++.+.+
T Consensus 107 ~i~rN~~~d~~Rk~~r~~~----------------------------------------------------~~~~~~~~~ 134 (227)
T TIGR02846 107 RCIENEILMHLRALKKTKG----------------------------------------------------EVSLQDPIG 134 (227)
T ss_pred HHHHHHHHHHHHHHhcccc----------------------------------------------------ceecccccc
Confidence 9999999999998765210 011111111
Q ss_pred CCC---CCCcCcccccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHH
Q psy15215 1329 DDE---DSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 1405 (1432)
Q Consensus 1329 ~~~---~~~~~d~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq 1405 (1432)
.+. ...+.+...+ ...+|.+..........|..+|+.|||++|.|+.|+|+.+...++|++|||+.+|+|+++|++
T Consensus 135 ~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~l~~~i~~L~~~~r~il~l~y~~~~~e~~S~~EIAe~lgis~~tV~~ 213 (227)
T TIGR02846 135 VDKEGNEISLIDILGS-DGDSVIEQVELNLEIKKLYKKLSVLDGREREVIEMRYGLGDGRRKTQREIAKILGISRSYVSR 213 (227)
T ss_pred CCcccCcccHHHHhcC-CCCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHcCCCCCCcCHHHHHHHHCCCHHHHHH
Confidence 000 0111121111 123566777777777889999999999999999999974433445999999999999999999
Q ss_pred HHHHHHHHhhCc
Q psy15215 1406 IEAKALRKLRHP 1417 (1432)
Q Consensus 1406 ~~~rAl~kLr~~ 1417 (1432)
++++|+++||+.
T Consensus 214 ~~~rAl~~Lr~~ 225 (227)
T TIGR02846 214 IEKRALMKLYKE 225 (227)
T ss_pred HHHHHHHHHHHH
Confidence 999999999974
No 77
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=99.87 E-value=4.7e-21 Score=215.86 Aligned_cols=194 Identities=26% Similarity=0.449 Sum_probs=149.9
Q ss_pred CChhhHHHHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHH
Q psy15215 1169 LPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 1248 (1432)
Q Consensus 1169 l~~~e~~~l~~~~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~ 1248 (1432)
++......++.+++.|+.. |++.++..|.++|+++|++|++++.+++|++||+|+++|+++++|++..+.+|+||++
T Consensus 34 ~~~~~~~~L~~~~~~gd~~---af~~l~~~y~~~l~~~a~~~~~~~~~AeDlvQevfl~l~~~~~~f~~~~~~~f~twl~ 110 (234)
T PRK08301 34 LSKEEEEYLLNKLPKGDEA---VRSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYAS 110 (234)
T ss_pred CCHHHHHHHHHHHHccCHH---HHHHHHHHhHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCCHHHHHH
Confidence 4455677888999999988 9999999999999999999999999999999999999999999999887778999999
Q ss_pred HHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCC
Q psy15215 1249 WWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVG 1328 (1432)
Q Consensus 1249 ~~ir~~i~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~ 1328 (1432)
++++|.|.+++|++.+.. ...+++.+..
T Consensus 111 ~iarn~~~d~lRk~~~~~----------------------------------------------------~~~~~~~~~~ 138 (234)
T PRK08301 111 RCIENEILMYLRRNNKVK----------------------------------------------------AEVSFDEPLN 138 (234)
T ss_pred HHHHHHHHHHHHHHhccc----------------------------------------------------cccccccccc
Confidence 999999999999876410 0112222211
Q ss_pred CC--CC-CCcCcccccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHH
Q psy15215 1329 DD--ED-SHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 1405 (1432)
Q Consensus 1329 ~~--~~-~~~~d~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq 1405 (1432)
.+ +. ....+...+. ...+............+..+|++|||++|.|+.|+|+.....++|++|||+.||+|.+||++
T Consensus 139 ~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~l~~al~~Lp~~~R~v~~L~y~l~~~eg~s~~EIA~~lgis~~tVk~ 217 (234)
T PRK08301 139 IDWDGNELLLSDVLGTD-NDIIYKDIEDEVDRKLLKKALKKLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISR 217 (234)
T ss_pred cccCCCcccHHHhccCc-ccchHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCCCHHHHHH
Confidence 00 00 0011111111 12334445555567789999999999999999999943222334999999999999999999
Q ss_pred HHHHHHHHhhCch
Q psy15215 1406 IEAKALRKLRHPS 1418 (1432)
Q Consensus 1406 ~~~rAl~kLr~~~ 1418 (1432)
+++||+++||+..
T Consensus 218 ~~~rA~~~Lr~~l 230 (234)
T PRK08301 218 LEKRIIKRLKKEI 230 (234)
T ss_pred HHHHHHHHHHHHH
Confidence 9999999999854
No 78
>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=99.86 E-value=1.1e-20 Score=211.33 Aligned_cols=194 Identities=29% Similarity=0.424 Sum_probs=155.3
Q ss_pred CChhhHHHHHHHHHHhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHH
Q psy15215 379 LPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 458 (1432)
Q Consensus 379 l~~~e~~~l~~~i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~ 458 (1432)
+++.+...++.+++.|+.. |++.++..|.+.|+++|.+|.++..+++||+||+|+++|+++++|++..+.+|.||++
T Consensus 30 ~~~~~~~~li~~~~~gd~~---af~~l~~~y~~~v~~~~~~~~~~~~dAEDlvQevfi~l~~~~~~~~~~~~~~f~twl~ 106 (227)
T TIGR02846 30 LSEEEEKKYLDRLKEGDEE---ARNVLIERNLRLVAHIVKKFSNTGEDVDDLISIGTIGLIKAIDSFDPDKGTRLATYAA 106 (227)
T ss_pred CCHHHHHHHHHHHHcCCHH---HHHHHHHHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHhCCcccCCChHHHHH
Confidence 5677788899999999988 9999999999999999999999999999999999999999999999988889999999
Q ss_pred HHHHHHHHHHHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCC
Q psy15215 459 WWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVG 538 (1432)
Q Consensus 459 ~~ir~~i~~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~ 538 (1432)
+|++|.|.+++|+..+..+ ..+++...+
T Consensus 107 ~i~rN~~~d~~Rk~~r~~~----------------------------------------------------~~~~~~~~~ 134 (227)
T TIGR02846 107 RCIENEILMHLRALKKTKG----------------------------------------------------EVSLQDPIG 134 (227)
T ss_pred HHHHHHHHHHHHHHhcccc----------------------------------------------------ceecccccc
Confidence 9999999999998765210 011111111
Q ss_pred CC---CCCCcCcccccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHH
Q psy15215 539 DD---EDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 615 (1432)
Q Consensus 539 ~~---~~~~~~~~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~ 615 (1432)
.+ ....+.+...+ ...+|.+.....+....|..+++.|||++|.||.|+|+.+...++|++|||+.+|+|+++|++
T Consensus 135 ~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~l~~~i~~L~~~~r~il~l~y~~~~~e~~S~~EIAe~lgis~~tV~~ 213 (227)
T TIGR02846 135 VDKEGNEISLIDILGS-DGDSVIEQVELNLEIKKLYKKLSVLDGREREVIEMRYGLGDGRRKTQREIAKILGISRSYVSR 213 (227)
T ss_pred CCcccCcccHHHHhcC-CCCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHcCCCCCCcCHHHHHHHHCCCHHHHHH
Confidence 00 01111121111 123567777777777889999999999999999999974433445999999999999999999
Q ss_pred HHHHHHHHHHHHH
Q psy15215 616 IEAKALRKLRPLA 628 (1432)
Q Consensus 616 ~~~rAl~kLr~~l 628 (1432)
+.++|+++|++.+
T Consensus 214 ~~~rAl~~Lr~~~ 226 (227)
T TIGR02846 214 IEKRALMKLYKEL 226 (227)
T ss_pred HHHHHHHHHHHHh
Confidence 9999999999764
No 79
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=99.86 E-value=2.3e-20 Score=210.25 Aligned_cols=196 Identities=26% Similarity=0.443 Sum_probs=152.3
Q ss_pred CChhhHHHHHHHHHHhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHH
Q psy15215 379 LPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 458 (1432)
Q Consensus 379 l~~~e~~~l~~~i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~ 458 (1432)
++......++.+++.||.. |+..++..|.++|+++|++|++.+.+++|++||+|+++|+++++|++..+++|.||++
T Consensus 34 ~~~~~~~~L~~~~~~gd~~---af~~l~~~y~~~l~~~a~~~~~~~~~AeDlvQevfl~l~~~~~~f~~~~~~~f~twl~ 110 (234)
T PRK08301 34 LSKEEEEYLLNKLPKGDEA---VRSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYAS 110 (234)
T ss_pred CCHHHHHHHHHHHHccCHH---HHHHHHHHhHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCCHHHHHH
Confidence 5556778899999999998 9999999999999999999999999999999999999999999999887788999999
Q ss_pred HHHHHHHHHHHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCC
Q psy15215 459 WWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVG 538 (1432)
Q Consensus 459 ~~ir~~i~~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~ 538 (1432)
++++|.|.+++|++.+.. ...+++.+..
T Consensus 111 ~iarn~~~d~lRk~~~~~----------------------------------------------------~~~~~~~~~~ 138 (234)
T PRK08301 111 RCIENEILMYLRRNNKVK----------------------------------------------------AEVSFDEPLN 138 (234)
T ss_pred HHHHHHHHHHHHHHhccc----------------------------------------------------cccccccccc
Confidence 999999999999876420 0011222111
Q ss_pred CC--CC-CCcCcccccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHH
Q psy15215 539 DD--ED-SHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 615 (1432)
Q Consensus 539 ~~--~~-~~~~~~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~ 615 (1432)
.+ +. ..+.+..++. ...+............+..+|++||+++|.|+.|+|+.....++|++|||+.+|+|+++|++
T Consensus 139 ~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~l~~al~~Lp~~~R~v~~L~y~l~~~eg~s~~EIA~~lgis~~tVk~ 217 (234)
T PRK08301 139 IDWDGNELLLSDVLGTD-NDIIYKDIEDEVDRKLLKKALKKLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISR 217 (234)
T ss_pred cccCCCcccHHHhccCc-ccchHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCCCHHHHHH
Confidence 00 00 0111111111 12344445555567789999999999999999999953222334999999999999999999
Q ss_pred HHHHHHHHHHHHHHH
Q psy15215 616 IEAKALRKLRPLAHD 630 (1432)
Q Consensus 616 ~~~rAl~kLr~~l~~ 630 (1432)
+.++|+++||+.+..
T Consensus 218 ~~~rA~~~Lr~~l~~ 232 (234)
T PRK08301 218 LEKRIIKRLKKEINK 232 (234)
T ss_pred HHHHHHHHHHHHHHh
Confidence 999999999988753
No 80
>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=99.85 E-value=2.8e-20 Score=209.08 Aligned_cols=191 Identities=28% Similarity=0.472 Sum_probs=147.0
Q ss_pred hhHHHHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHH
Q psy15215 1172 NDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 1251 (1432)
Q Consensus 1172 ~e~~~l~~~~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~i 1251 (1432)
.+...++.++..|+.. |++.++..|.+.|+++|++|++++.+++|++||+|+++|+++++|++..+.+|+||+++++
T Consensus 37 ~~~~~l~~~~~~~d~~---a~~~l~~~y~~~l~~~~~~~~~~~~~AEDlvQE~fl~l~~~~~~f~~~~~~~f~~wl~~ia 113 (234)
T TIGR02835 37 EEEEALLQKLTQGDES---AKSTLIERNLRLVVYIARKFENTGIGIEDLVSIGTIGLIKAVNTFNPSKKIKLATYASRCI 113 (234)
T ss_pred HHHHHHHHHHHcCCHH---HHHHHHHHhHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHH
Confidence 3455677788889887 9999999999999999999999999999999999999999999999887778999999999
Q ss_pred HHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCC--
Q psy15215 1252 RQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGD-- 1329 (1432)
Q Consensus 1252 r~~i~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~-- 1329 (1432)
+|.+.+++|++.+.. ...+++.+...
T Consensus 114 rN~~~d~~Rk~~r~~----------------------------------------------------~~~~~~~~~~~~~ 141 (234)
T TIGR02835 114 ENEILMYLRRNNKTR----------------------------------------------------SEVSFDEPLNVDW 141 (234)
T ss_pred HHHHHHHHHHhcccc----------------------------------------------------CcccccccccCCC
Confidence 999999999876510 01111211110
Q ss_pred CCCC-CcCcccccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q psy15215 1330 DEDS-HLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEA 1408 (1432)
Q Consensus 1330 ~~~~-~~~d~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~ 1408 (1432)
++.. ...+.. +.....+.+..........+..+|+.||+++|.|+.|+|+.....++|++|||+.+|+|.+||+++++
T Consensus 142 ~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~l~~ai~~Lp~~~R~ii~L~~~l~~~eg~s~~EIA~~Lgis~~tV~~~l~ 220 (234)
T TIGR02835 142 DGNELLLSDVL-GTDSDIVYKYLEEEVDRELLRKALAKLNDREKKIMELRFGLVGGTEKTQKEVADMLGISQSYISRLEK 220 (234)
T ss_pred CCCcchHHHhc-CCCCCcHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 0000 001111 11112344455555667789999999999999999999963222344999999999999999999999
Q ss_pred HHHHHhhCch
Q psy15215 1409 KALRKLRHPS 1418 (1432)
Q Consensus 1409 rAl~kLr~~~ 1418 (1432)
+|+++||+..
T Consensus 221 ra~~~LR~~l 230 (234)
T TIGR02835 221 RILKRLKKEI 230 (234)
T ss_pred HHHHHHHHHh
Confidence 9999999854
No 81
>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=99.84 E-value=1.2e-19 Score=203.91 Aligned_cols=194 Identities=27% Similarity=0.451 Sum_probs=149.3
Q ss_pred ChhhHHHHHHHHHHhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHH
Q psy15215 380 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 459 (1432)
Q Consensus 380 ~~~e~~~l~~~i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~ 459 (1432)
+..+...++..+..|+.. |+..++..|.+.|+++|++|++++.+++||+||+++++|+++++|++..+++|+||++.
T Consensus 35 ~~~~~~~l~~~~~~~d~~---a~~~l~~~y~~~l~~~~~~~~~~~~~AEDlvQE~fl~l~~~~~~f~~~~~~~f~~wl~~ 111 (234)
T TIGR02835 35 TGEEEEALLQKLTQGDES---AKSTLIERNLRLVVYIARKFENTGIGIEDLVSIGTIGLIKAVNTFNPSKKIKLATYASR 111 (234)
T ss_pred CHHHHHHHHHHHHcCCHH---HHHHHHHHhHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHH
Confidence 344556778888999988 99999999999999999999999999999999999999999999998877889999999
Q ss_pred HHHHHHHHHHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCC
Q psy15215 460 WIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGD 539 (1432)
Q Consensus 460 ~ir~~i~~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~ 539 (1432)
+++|.+.++++++.+.. ...+++.++..
T Consensus 112 iarN~~~d~~Rk~~r~~----------------------------------------------------~~~~~~~~~~~ 139 (234)
T TIGR02835 112 CIENEILMYLRRNNKTR----------------------------------------------------SEVSFDEPLNV 139 (234)
T ss_pred HHHHHHHHHHHHhcccc----------------------------------------------------CcccccccccC
Confidence 99999999999876520 00111111110
Q ss_pred --CCC-CCcCcccccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHH
Q psy15215 540 --DED-SHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQI 616 (1432)
Q Consensus 540 --~~~-~~~~~~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~ 616 (1432)
++. ....+.. +.....+.+..........+..+|++||+++|.|+.|+|++....++|++|||+.+|+|+++|+++
T Consensus 140 ~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~l~~ai~~Lp~~~R~ii~L~~~l~~~eg~s~~EIA~~Lgis~~tV~~~ 218 (234)
T TIGR02835 140 DWDGNELLLSDVL-GTDSDIVYKYLEEEVDRELLRKALAKLNDREKKIMELRFGLVGGTEKTQKEVADMLGISQSYISRL 218 (234)
T ss_pred CCCCCcchHHHhc-CCCCCcHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHH
Confidence 000 0011111 111123344455555677899999999999999999999632223449999999999999999999
Q ss_pred HHHHHHHHHHHHH
Q psy15215 617 EAKALRKLRPLAH 629 (1432)
Q Consensus 617 ~~rAl~kLr~~l~ 629 (1432)
.++|+.+||+.+.
T Consensus 219 l~ra~~~LR~~l~ 231 (234)
T TIGR02835 219 EKRILKRLKKEIN 231 (234)
T ss_pred HHHHHHHHHHHhh
Confidence 9999999998764
No 82
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=99.84 E-value=6.5e-20 Score=203.02 Aligned_cols=193 Identities=22% Similarity=0.321 Sum_probs=152.4
Q ss_pred HHHHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHH
Q psy15215 1174 LRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 1253 (1432)
Q Consensus 1174 ~~~l~~~~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~ 1253 (1432)
...++..++.|+.. |++.|+..|.++|+++|.+|++++.+++|++||+|++||+++.+|++.++.+|.||++.++++
T Consensus 11 ~~~l~~~~~~~d~~---a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~~~~f~twl~~i~~n 87 (208)
T PRK08295 11 DEELVELARSGDKE---ALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAELCITR 87 (208)
T ss_pred hHHHHHHHHcCCHH---HHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHH
Confidence 34567788889888 999999999999999999999999999999999999999999999988777999999999999
Q ss_pred HHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCC-CCC
Q psy15215 1254 AITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGD-DED 1332 (1432)
Q Consensus 1254 ~i~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~-~~~ 1332 (1432)
.+.+++++..+..+.|. ....|++.+..+ +.+
T Consensus 88 ~~~d~~r~~~r~~~~~~-----------------------------------------------~~~~s~~~~~~~~~~~ 120 (208)
T PRK08295 88 QIITAIKTANRQKHIPL-----------------------------------------------NSYVSLDKPIYDEESD 120 (208)
T ss_pred HHHHHHHHhhhhccccc-----------------------------------------------cceeecCCcccCCccc
Confidence 99999997655222111 011233433222 222
Q ss_pred CCcCcccccCCCCChHHHHHHHHHHHHH-HHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q psy15215 1333 SHLGDFIEDENMLAPSDAALNASMRSVV-KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKAL 1411 (1432)
Q Consensus 1333 ~~~~d~i~d~~~~~p~~~~~~~~~~~~l-~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl 1411 (1432)
..+.+.+.+....+|++.+........+ ..+++.||++++.||.+ |+.|+ |++|||+.||+|+++|+++++||+
T Consensus 121 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~L~~~~r~vl~l-~~e~~----s~~EIA~~lgis~~tV~~~l~rar 195 (208)
T PRK08295 121 RTLLDVISEAKVTDPEELIISKEELEDIEEKIEELLSELEKEVLEL-YLDGK----SYQEIAEELNRHVKSIDNALQRVK 195 (208)
T ss_pred hhHHHHhcCcccCCHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHH-HHccC----CHHHHHHHHCCCHHHHHHHHHHHH
Confidence 2333334444445787777666555565 56779999999999999 88887 999999999999999999999999
Q ss_pred HHhhCchhhh
Q psy15215 1412 RKLRHPSRYY 1421 (1432)
Q Consensus 1412 ~kLr~~~~~~ 1421 (1432)
++||+.....
T Consensus 196 ~~Lr~~l~~~ 205 (208)
T PRK08295 196 RKLEKYLENR 205 (208)
T ss_pred HHHHHHHHhh
Confidence 9999966543
No 83
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=99.83 E-value=1.7e-19 Score=196.56 Aligned_cols=178 Identities=20% Similarity=0.313 Sum_probs=149.3
Q ss_pred CChhhHHHHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHhccCC----CCChhHHHHHHHHHHHHHHHhccccCCCcch
Q psy15215 1169 LPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDR----GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 1244 (1432)
Q Consensus 1169 l~~~e~~~l~~~~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~----~~~~~DLiQEg~igl~kav~kfd~~~g~~Fs 1244 (1432)
.++.++..++..++.|+.. |+..|+..|.+.|+++|.+++++ +.+++|++||+|+++|+++.+|+.. +.+|.
T Consensus 6 ~~~~~~~~l~~~~~~gd~~---a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~~~ 81 (189)
T PRK09648 6 DTGEELDALVAEAVAGDRR---ALREVLEIIRPLVVRYCRARLGGVERPGLSADDVAQEVCLAVITALPRYRDQ-GRPFL 81 (189)
T ss_pred CCchHHHHHHHHHHcCCHH---HHHHHHHHHHHHHHHHHHHHhcccccCCCCHHHHHHHHHHHHHHHHHHHhcc-CCcHH
Confidence 4667888999999999988 99999999999999999998765 4689999999999999999999864 45899
Q ss_pred hHHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCC
Q psy15215 1245 TYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSME 1324 (1432)
Q Consensus 1245 tya~~~ir~~i~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~ 1324 (1432)
||++.+++|.+.++++++.+....+ .+
T Consensus 82 ~wl~~i~~n~~~d~~r~~~r~~~~~-----------------------------------------------------~~ 108 (189)
T PRK09648 82 AFVYGIAAHKVADAHRAAGRDKAVP-----------------------------------------------------TE 108 (189)
T ss_pred HHHHHHHHHHHHHHHHHhCCCcccc-----------------------------------------------------cc
Confidence 9999999999999999877521100 00
Q ss_pred CCCCCCCCCCcCcccccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHH
Q psy15215 1325 SPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIR 1404 (1432)
Q Consensus 1325 ~~~~~~~~~~~~d~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vr 1404 (1432)
. ..+... ...+|++.....+....+..+|..|||++|+||.++|+.|+ |++|||+.||+|..+|+
T Consensus 109 ~---------~~~~~~--~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~----s~~EIA~~lgis~~tV~ 173 (189)
T PRK09648 109 E---------VPERPS--DDAGPEERALRSESSNRMRELLDTLPEKQREILILRVVVGL----SAEETAEAVGSTPGAVR 173 (189)
T ss_pred c---------cccccc--cCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHHCCCHHHHH
Confidence 0 000000 12367777777788888999999999999999999999888 99999999999999999
Q ss_pred HHHHHHHHHhhCch
Q psy15215 1405 QIEAKALRKLRHPS 1418 (1432)
Q Consensus 1405 q~~~rAl~kLr~~~ 1418 (1432)
++++||+++||+..
T Consensus 174 ~~l~Ra~~~Lr~~l 187 (189)
T PRK09648 174 VAQHRALARLRAEI 187 (189)
T ss_pred HHHHHHHHHHHHHh
Confidence 99999999999854
No 84
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=99.83 E-value=1.4e-19 Score=197.76 Aligned_cols=180 Identities=16% Similarity=0.187 Sum_probs=148.0
Q ss_pred CChhhHHHHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHH
Q psy15215 1169 LPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 1248 (1432)
Q Consensus 1169 l~~~e~~~l~~~~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~ 1248 (1432)
+...+...++..+.+|+.. |+++|+..|.++|+++|.+|+++..+++|++||+|+++|+++++|++.+| +|.+|++
T Consensus 12 ~~~~~~~~li~~~~~g~~~---a~~~l~~~y~~~l~~~~~~~~~~~~dAeDivQe~fi~l~~~~~~~~~~~~-~~~~wl~ 87 (194)
T PRK09646 12 AESPDLDALLRRVARGDQD---AFAELYDRTSSRVYGLVRRVLRDPGYSEETTQEVYLEVWRTASRFDPARG-SALAWLL 87 (194)
T ss_pred CCcccHHHHHHHHHccCHH---HHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhhcCcccc-cHHHHHH
Confidence 4446678899999999888 99999999999999999999999999999999999999999999998665 7999999
Q ss_pred HHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCC
Q psy15215 1249 WWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVG 1328 (1432)
Q Consensus 1249 ~~ir~~i~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~ 1328 (1432)
.+++|.+.+++|++.+..+.- .+. .
T Consensus 88 ~ia~n~~~d~~r~~~~~~~~~---------------------------------------------------~~~----~ 112 (194)
T PRK09646 88 TLAHRRAVDRVRSEQAASQRE---------------------------------------------------VRY----G 112 (194)
T ss_pred HHHHHHHHHHHHhhccccccc---------------------------------------------------ccc----c
Confidence 999999999999876421100 000 0
Q ss_pred CCCCCCcCcccccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q psy15215 1329 DDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEA 1408 (1432)
Q Consensus 1329 ~~~~~~~~d~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~ 1408 (1432)
.. +. .....++.+.....+....+..+|+.||+++|.||.|+|+.|+ |++|||+.||+|.++|+++++
T Consensus 113 ~~------~~--~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~~----s~~EIA~~Lgis~~tVk~~l~ 180 (194)
T PRK09646 113 AR------NV--DPAFDQVAEEVEARLERERVRDCLDALTDTQRESVTLAYYGGL----TYREVAERLAVPLGTVKTRMR 180 (194)
T ss_pred cc------cc--cccccchHHHHHHHhHHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHhCCChHhHHHHHH
Confidence 00 00 0011234445555566788999999999999999999999888 999999999999999999999
Q ss_pred HHHHHhhCchh
Q psy15215 1409 KALRKLRHPSR 1419 (1432)
Q Consensus 1409 rAl~kLr~~~~ 1419 (1432)
||+++||....
T Consensus 181 ra~~~Lr~~l~ 191 (194)
T PRK09646 181 DGLIRLRDCLG 191 (194)
T ss_pred HHHHHHHHHhc
Confidence 99999998653
No 85
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=99.82 E-value=1.9e-19 Score=195.63 Aligned_cols=172 Identities=16% Similarity=0.223 Sum_probs=144.8
Q ss_pred HHHHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHH
Q psy15215 1174 LRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 1253 (1432)
Q Consensus 1174 ~~~l~~~~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~ 1253 (1432)
...++..++.|+.. |++.|+..|.++|+++|++|++++.+++|++||+|+++|+++.+|++. +.+|.+|++.+++|
T Consensus 7 ~~~l~~~~~~~d~~---a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~f~~wl~~ia~n 82 (186)
T PRK05602 7 DEELLARVAAGDPA---AFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRPG-EARFDTWLHRVVLN 82 (186)
T ss_pred HHHHHHHHHCcCHH---HHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHhhhcCCC-CCcHHHHHHHHHHH
Confidence 45688889999888 999999999999999999999999999999999999999999999975 35899999999999
Q ss_pred HHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCC
Q psy15215 1254 AITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDS 1333 (1432)
Q Consensus 1254 ~i~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~ 1333 (1432)
.+.+++|++... + .+. . ..
T Consensus 83 ~~~d~~R~~~~~---~-----------------------------------------------------~~~-~---~~- 101 (186)
T PRK05602 83 LCYDRLRRRREV---P-----------------------------------------------------VED-A---PD- 101 (186)
T ss_pred HHHHHHHhcCCC---C-----------------------------------------------------ccc-c---cc-
Confidence 999999976531 0 000 0 00
Q ss_pred CcCcccccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q psy15215 1334 HLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRK 1413 (1432)
Q Consensus 1334 ~~~d~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~k 1413 (1432)
..+ ....|+..+...+....+..+|+.||+++|.||.|+|+.|+ |++|||+.||+|+.+|+++++||+++
T Consensus 102 -----~~~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~----s~~EIA~~lgis~~tV~~~l~Rar~~ 171 (186)
T PRK05602 102 -----VPD-PAPGPDAGLEARQRARRVEQALAALPERQREAIVLQYYQGL----SNIEAAAVMDISVDALESLLARGRRA 171 (186)
T ss_pred -----cCC-CCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhHHHhcCC----CHHHHHHHhCcCHHHHHHHHHHHHHH
Confidence 001 11245666666677788999999999999999999999888 99999999999999999999999999
Q ss_pred hhCchhh
Q psy15215 1414 LRHPSRY 1420 (1432)
Q Consensus 1414 Lr~~~~~ 1420 (1432)
||+....
T Consensus 172 Lr~~l~~ 178 (186)
T PRK05602 172 LRAQLAD 178 (186)
T ss_pred HHHHHHh
Confidence 9996554
No 86
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=99.82 E-value=3.8e-19 Score=196.89 Aligned_cols=191 Identities=23% Similarity=0.335 Sum_probs=151.3
Q ss_pred HHHHHHHHHHhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHH
Q psy15215 384 LRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 463 (1432)
Q Consensus 384 ~~~l~~~i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~ 463 (1432)
...++..++.||.. |+..|+..|.++|+++|.+|+++..+++||+||++++||+++.+|++.++.+|.||++.++++
T Consensus 11 ~~~l~~~~~~~d~~---a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~~~~f~twl~~i~~n 87 (208)
T PRK08295 11 DEELVELARSGDKE---ALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAELCITR 87 (208)
T ss_pred hHHHHHHHHcCCHH---HHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHH
Confidence 34567788899988 999999999999999999999999999999999999999999999988777999999999999
Q ss_pred HHHHHHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCC-CCC
Q psy15215 464 AITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGD-DED 542 (1432)
Q Consensus 464 ~i~~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~-~~~ 542 (1432)
.+.+++++..+..+.|. ....|.+.+..+ +.+
T Consensus 88 ~~~d~~r~~~r~~~~~~-----------------------------------------------~~~~s~~~~~~~~~~~ 120 (208)
T PRK08295 88 QIITAIKTANRQKHIPL-----------------------------------------------NSYVSLDKPIYDEESD 120 (208)
T ss_pred HHHHHHHHhhhhccccc-----------------------------------------------cceeecCCcccCCccc
Confidence 99999987655222111 011233333222 222
Q ss_pred CCcCcccccCCCCChHHHHHHHHHHHHH-HHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHH
Q psy15215 543 SHLGDFIEDENMLAPSDAALNASMRSVV-KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKAL 621 (1432)
Q Consensus 543 ~~~~~~i~d~~~~~p~~~~~~~~~~~~l-~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl 621 (1432)
..+.+.+.+....+|++.+...+....+ ..+++.||++++.||.+ |..|+ |++|||+.+|+|+++|+.+.+||+
T Consensus 121 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~L~~~~r~vl~l-~~e~~----s~~EIA~~lgis~~tV~~~l~rar 195 (208)
T PRK08295 121 RTLLDVISEAKVTDPEELIISKEELEDIEEKIEELLSELEKEVLEL-YLDGK----SYQEIAEELNRHVKSIDNALQRVK 195 (208)
T ss_pred hhHHHHhcCcccCCHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHH-HHccC----CHHHHHHHHCCCHHHHHHHHHHHH
Confidence 2333334443345787777666555555 56779999999999999 88888 999999999999999999999999
Q ss_pred HHHHHHHH
Q psy15215 622 RKLRPLAH 629 (1432)
Q Consensus 622 ~kLr~~l~ 629 (1432)
++|++.+.
T Consensus 196 ~~Lr~~l~ 203 (208)
T PRK08295 196 RKLEKYLE 203 (208)
T ss_pred HHHHHHHH
Confidence 99998775
No 87
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=99.81 E-value=3.3e-19 Score=195.12 Aligned_cols=179 Identities=20% Similarity=0.247 Sum_probs=145.2
Q ss_pred CChhhHHHHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHH
Q psy15215 1169 LPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 1248 (1432)
Q Consensus 1169 l~~~e~~~l~~~~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~ 1248 (1432)
++......++.+++.|+.. |+..|+..|.+.|+++|++++++..+++|++||+|+++|+. ..|++..+ +|.||++
T Consensus 11 ~~~~~~~~l~~~~~~gd~~---a~~~L~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~l~~~-~~~~~~~~-~f~~wl~ 85 (194)
T PRK12519 11 LSSRSDAELFSALKAGQSA---ALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRK-SSYDPKRG-SLSSYLL 85 (194)
T ss_pred CCcccHHHHHHHHHcCCHH---HHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHh-cCCCcccc-cHHHHHH
Confidence 4445567889999999888 99999999999999999999999999999999999999976 57876554 7999999
Q ss_pred HHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCC
Q psy15215 1249 WWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVG 1328 (1432)
Q Consensus 1249 ~~ir~~i~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~ 1328 (1432)
++++|.+.+++|++.+..+.. + ....
T Consensus 86 ~iarn~~~d~~Rk~~~~~~~~-~--------------------------------------------------~~~~--- 111 (194)
T PRK12519 86 TLTRSRAIDRLRSRRSRQRLL-E--------------------------------------------------RWQQ--- 111 (194)
T ss_pred HHHHHHHHHHHHhcccccchh-h--------------------------------------------------hhhh---
Confidence 999999999999876411000 0 0000
Q ss_pred CCCCCCcCcccccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q psy15215 1329 DDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEA 1408 (1432)
Q Consensus 1329 ~~~~~~~~d~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~ 1408 (1432)
.... +....+|.+.+...+....|..+|+.||++++.||.|+|+.|+ |++|||+.||+|+++|+++++
T Consensus 112 ----~~~~----~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~~~v~~l~~~~g~----s~~EIA~~lgis~~tV~~~l~ 179 (194)
T PRK12519 112 ----ELLG----EASEDTPLEQASLAERSQRVQTALAQLPESQRQVLELAYYEGL----SQSEIAKRLGIPLGTVKARAR 179 (194)
T ss_pred ----hhcc----cccCCCHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhhhhhcCC----CHHHHHHHhCCCHHHHHHHHH
Confidence 0000 0012346666666677778999999999999999999999888 999999999999999999999
Q ss_pred HHHHHhhCch
Q psy15215 1409 KALRKLRHPS 1418 (1432)
Q Consensus 1409 rAl~kLr~~~ 1418 (1432)
||+++||...
T Consensus 180 Ra~~~Lr~~l 189 (194)
T PRK12519 180 QGLLKLRELL 189 (194)
T ss_pred HHHHHHHHHH
Confidence 9999999843
No 88
>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=99.81 E-value=4.1e-19 Score=195.07 Aligned_cols=190 Identities=24% Similarity=0.303 Sum_probs=147.1
Q ss_pred HHHHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHH
Q psy15215 1174 LRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 1253 (1432)
Q Consensus 1174 ~~~l~~~~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~ 1253 (1432)
...++..++.|+.. |++.|+..|.+.|+++|.+++++..+++|++||+|+++|+++.+|++..+.+|+||++.++++
T Consensus 6 ~~~l~~~~~~~d~~---a~~~l~~~~~~~l~~~a~~~~~~~~~aeDlvQe~fl~~~~~~~~~~~~~~~~f~~wl~~~~~~ 82 (198)
T TIGR02859 6 DEEIVELARQGNTH---ALEYLINKYKNFVRAKARSYFLIGADKEDIIQEGMIGLYKAIRDFRPDKLSSFKAFAELCVTR 82 (198)
T ss_pred hHHHHHHHHcCCHH---HHHHHHHHHHHHHHHHHHHHccccCcHHHHHHHHHHHHHHHHHHhCcccCCChHHHHHHHHHH
Confidence 34677788899888 999999999999999999999999999999999999999999999998777999999999999
Q ss_pred HHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCC-CC
Q psy15215 1254 AITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDD-ED 1332 (1432)
Q Consensus 1254 ~i~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~-~~ 1332 (1432)
.+.+++++..+..+.+. ....|++.+..++ ++
T Consensus 83 ~~~~~~r~~~~~~~~~~-----------------------------------------------~~~~~~~~~~~~~~~~ 115 (198)
T TIGR02859 83 QIITAIKTATRQKHIPL-----------------------------------------------NSYVSLNKPIYDEESD 115 (198)
T ss_pred HHHHHHHHHHHhcccch-----------------------------------------------hhhcCccccccccccc
Confidence 99999886543111110 1123333332211 11
Q ss_pred CCcCcccccCCCCChHHHHHHHHHHHHHHHHHccC-CHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q psy15215 1333 SHLGDFIEDENMLAPSDAALNASMRSVVKDILNSL-TPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKAL 1411 (1432)
Q Consensus 1333 ~~~~d~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L-~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl 1411 (1432)
.++.+.+.+....+|++.+...+....+.++|+.| |+.++.|+ ++|..|+ |++|||+.||+|.++|++.++||+
T Consensus 116 ~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~Ll~~~~~~i~-~~~~~~~----s~~eIA~~l~~s~~tV~~~l~r~r 190 (198)
T TIGR02859 116 RTLLDVISGAKVTDPEELIISQEEYGDIESKMNELLSDLEWKVL-QSYLDGK----SYQEIACDLNRHVKSIDNALQRVK 190 (198)
T ss_pred chHHHHhhccccCCHHHHHHHHHHHHHHHHHHHHhcCHHHHHHH-HHHHcCC----CHHHHHHHHCCCHHHHHHHHHHHH
Confidence 12223332223357888888888888899999995 55555555 5687887 999999999999999999999999
Q ss_pred HHhhCch
Q psy15215 1412 RKLRHPS 1418 (1432)
Q Consensus 1412 ~kLr~~~ 1418 (1432)
++||...
T Consensus 191 ~~L~~~l 197 (198)
T TIGR02859 191 RKLEKYL 197 (198)
T ss_pred HHHHHhc
Confidence 9999753
No 89
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=99.81 E-value=3.6e-19 Score=194.82 Aligned_cols=180 Identities=17% Similarity=0.174 Sum_probs=149.3
Q ss_pred hHHHHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHH
Q psy15215 1173 DLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 1252 (1432)
Q Consensus 1173 e~~~l~~~~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir 1252 (1432)
....++..++.|+.. |++.|+..|.+.|+++|.+++++..+++|++||+|+++|++..+|+.. ..|.+|++++++
T Consensus 12 ~~~~l~~~~~~gd~~---a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~fi~l~~~~~~~~~~--~~f~~wl~~i~~ 86 (194)
T PRK12513 12 SDEALMLRYRAGDAA---AFEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRARAQYQPR--ARFRTWLYQIAR 86 (194)
T ss_pred CHHHHHHHHHcCCHH---HHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCC--CchHHHHHHHHH
Confidence 346788999999988 999999999999999999999999999999999999999999999964 379999999999
Q ss_pred HHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCC
Q psy15215 1253 QAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDED 1332 (1432)
Q Consensus 1253 ~~i~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~ 1332 (1432)
|.+.+++|++.+..+.+ .+. +. .
T Consensus 87 n~~~~~~R~~~~~~~~~-----------------------------------------------------~~~---~~-~ 109 (194)
T PRK12513 87 NLLIDHWRRHGARQAPS-----------------------------------------------------LDA---DE-Q 109 (194)
T ss_pred HHHHHHHHHhccccccc-----------------------------------------------------ccc---ch-h
Confidence 99999999887621111 000 00 0
Q ss_pred CCcCcccccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q psy15215 1333 SHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALR 1412 (1432)
Q Consensus 1333 ~~~~d~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~ 1412 (1432)
.. ... ....+|............+..+|+.||+++|.||.|+|+.|+ |++|||+.||+|+++|+++++||++
T Consensus 110 --~~-~~~-~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~----s~~EIA~~lgis~~tV~~~l~ra~~ 181 (194)
T PRK12513 110 --LH-ALA-DDGAAPEQQLSLFRDRRRLQAALETLPDEQREVFLLREHGDL----ELEEIAELTGVPEETVKSRLRYALQ 181 (194)
T ss_pred --hh-hcC-CCCCCHHHHHHHHHHHHHHHHHHHhCCHhHhhheeeehccCC----CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 00 000 112357777777778889999999999999999999998888 9999999999999999999999999
Q ss_pred HhhCchhhhh
Q psy15215 1413 KLRHPSRYYK 1422 (1432)
Q Consensus 1413 kLr~~~~~~~ 1422 (1432)
+||....+..
T Consensus 182 ~Lr~~l~~~~ 191 (194)
T PRK12513 182 KLRELLAEEV 191 (194)
T ss_pred HHHHHHHHhh
Confidence 9999766543
No 90
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=99.81 E-value=1e-18 Score=190.29 Aligned_cols=179 Identities=20% Similarity=0.313 Sum_probs=150.5
Q ss_pred CChhhHHHHHHHHHHhHHHHHHhHHHHHHHHHHHHHHHHHhcccC----CCChhhHHHHHHHHHHHHHhhccccCCCccH
Q psy15215 379 LPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDR----GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 454 (1432)
Q Consensus 379 l~~~e~~~l~~~i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~----~~~~~DLiQEg~igL~kav~~fd~~~g~~Fs 454 (1432)
.++.++..++..++.|+.. |+..|+..|.+.|+++|.++++. +.+++|++||+|+++|+++.+|+.. +.+|.
T Consensus 6 ~~~~~~~~l~~~~~~gd~~---a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~~~ 81 (189)
T PRK09648 6 DTGEELDALVAEAVAGDRR---ALREVLEIIRPLVVRYCRARLGGVERPGLSADDVAQEVCLAVITALPRYRDQ-GRPFL 81 (189)
T ss_pred CCchHHHHHHHHHHcCCHH---HHHHHHHHHHHHHHHHHHHHhcccccCCCCHHHHHHHHHHHHHHHHHHHhcc-CCcHH
Confidence 3677889999999999998 99999999999999999998765 4689999999999999999999864 45899
Q ss_pred HHHHHHHHHHHHHHHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCC
Q psy15215 455 TYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSME 534 (1432)
Q Consensus 455 tya~~~ir~~i~~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~ 534 (1432)
||++..++|.+.++++++.+....+ .+
T Consensus 82 ~wl~~i~~n~~~d~~r~~~r~~~~~-----------------------------------------------------~~ 108 (189)
T PRK09648 82 AFVYGIAAHKVADAHRAAGRDKAVP-----------------------------------------------------TE 108 (189)
T ss_pred HHHHHHHHHHHHHHHHHhCCCcccc-----------------------------------------------------cc
Confidence 9999999999999999876521100 00
Q ss_pred CCCCCCCCCCcCcccccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHH
Q psy15215 535 SPVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIR 614 (1432)
Q Consensus 535 ~~~~~~~~~~~~~~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~ 614 (1432)
.+ .+... ...+|.+.....+....+..+|..|||++|+||.|+|+.|+ |++|||+.||+|+++|+
T Consensus 109 -~~--------~~~~~--~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~----s~~EIA~~lgis~~tV~ 173 (189)
T PRK09648 109 -EV--------PERPS--DDAGPEERALRSESSNRMRELLDTLPEKQREILILRVVVGL----SAEETAEAVGSTPGAVR 173 (189)
T ss_pred -cc--------ccccc--cCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHHCCCHHHHH
Confidence 00 00000 12367777777788889999999999999999999999988 99999999999999999
Q ss_pred HHHHHHHHHHHHHHH
Q psy15215 615 QIEAKALRKLRPLAH 629 (1432)
Q Consensus 615 ~~~~rAl~kLr~~l~ 629 (1432)
++.+||+++|++.+.
T Consensus 174 ~~l~Ra~~~Lr~~l~ 188 (189)
T PRK09648 174 VAQHRALARLRAEIE 188 (189)
T ss_pred HHHHHHHHHHHHHhc
Confidence 999999999998763
No 91
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=99.81 E-value=6.7e-19 Score=191.52 Aligned_cols=180 Identities=14% Similarity=0.270 Sum_probs=145.4
Q ss_pred HHHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHH
Q psy15215 1175 RDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA 1254 (1432)
Q Consensus 1175 ~~l~~~~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~ 1254 (1432)
..++..+.+|+.. |+.+|+..|.+.|+++|.+|++++.+++|++||+|+++|+++.+|++.. +|.||++.+++|.
T Consensus 6 ~~li~~~~~gd~~---a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~ 80 (187)
T TIGR02948 6 KKRIKEVRKGDEN---AFADLVDLYKDKIYQLCYRMLGNVHEAEDVAQEAFIRAYTNIDTYDIQR--KFSTWLYRIATNL 80 (187)
T ss_pred HHHHHHHHcCCHH---HHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCCC--chHHHHHHHHHHH
Confidence 4578889999888 9999999999999999999999999999999999999999999999765 6999999999999
Q ss_pred HHHHHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCC
Q psy15215 1255 ITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSH 1334 (1432)
Q Consensus 1255 i~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~ 1334 (1432)
+.+++|+..+... ++......+...
T Consensus 81 ~~~~~rk~~~~~~-------------------------------------------------------~~~~~~~~~~~~ 105 (187)
T TIGR02948 81 TIDRLRKRKPDFY-------------------------------------------------------LDDEVQGTDGLT 105 (187)
T ss_pred HHHHHHhhccccc-------------------------------------------------------ccccccCccccc
Confidence 9999987553100 000000000001
Q ss_pred cCcccccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Q psy15215 1335 LGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 1414 (1432)
Q Consensus 1335 ~~d~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kL 1414 (1432)
..+...+ ..++|++.+...+....+..+|+.|||++|.|+.++|+.|+ |++|||+.||+|+++|+++++||+++|
T Consensus 106 ~~~~~~~-~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g~----s~~eIA~~lgis~~~v~~~l~Rar~~L 180 (187)
T TIGR02948 106 MESQLAA-DEAPPEDQVISLELRDTIQQEIQALPPKYRMVIVLKYMEDL----SLKEISEILDLPVGTVKTRIHRGREAL 180 (187)
T ss_pred ccccccc-CcCCHHHHHHHHHHHHHHHHHHHhCCHHHhHHhhhHHhcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 1111111 12357777777777888999999999999999999999888 999999999999999999999999999
Q ss_pred hCchh
Q psy15215 1415 RHPSR 1419 (1432)
Q Consensus 1415 r~~~~ 1419 (1432)
|..++
T Consensus 181 r~~l~ 185 (187)
T TIGR02948 181 RKQLR 185 (187)
T ss_pred HHHhh
Confidence 98554
No 92
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=99.81 E-value=7.5e-19 Score=191.13 Aligned_cols=181 Identities=13% Similarity=0.243 Sum_probs=146.7
Q ss_pred HHHHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHH
Q psy15215 1174 LRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 1253 (1432)
Q Consensus 1174 ~~~l~~~~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~ 1253 (1432)
...++..++.|+.. |+..++..|.++|+++|+++.++..+++|++||+|++||++..+|++.. +|.+|++.+++|
T Consensus 5 ~~~li~~~~~~d~~---a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~~--~~~~wl~~iarn 79 (187)
T PRK09641 5 IKRLIKQVKKGDQN---AFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINR--KFSTWLYRIATN 79 (187)
T ss_pred HHHHHHHHHcCCHH---HHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhhCCCc--chhHHHHHHHHH
Confidence 34678888899888 9999999999999999999999999999999999999999999998753 799999999999
Q ss_pred HHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCC
Q psy15215 1254 AITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDS 1333 (1432)
Q Consensus 1254 ~i~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~ 1333 (1432)
.+.+++|++.+.. +++.+...++..
T Consensus 80 ~~~d~~R~~~~~~-------------------------------------------------------~~~~~~~~~~~~ 104 (187)
T PRK09641 80 LTIDRLRKRKPDY-------------------------------------------------------YLDAEVAGTEGL 104 (187)
T ss_pred HHHHHHHhcCccc-------------------------------------------------------cccccccCCcch
Confidence 9999999865410 011111111111
Q ss_pred CcCcccccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q psy15215 1334 HLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRK 1413 (1432)
Q Consensus 1334 ~~~d~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~k 1413 (1432)
...+.+.+ ...+|++.....+....+..+|+.||++++.||.|+|+.|. |++|||+.||+|.++|++.++||+++
T Consensus 105 ~~~~~~~~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~~~~~----s~~eIA~~lgis~~~v~~~l~Rar~~ 179 (187)
T PRK09641 105 TMYSQLAA-DDALPEEQVVSLELQETIQEAILQLPEKYRTVIVLKYIEDL----SLKEISEILDLPVGTVKTRIHRGREA 179 (187)
T ss_pred hhhccccc-CcCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHHhhCC----CHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 11111111 22357777777778888999999999999999999998888 99999999999999999999999999
Q ss_pred hhCchh
Q psy15215 1414 LRHPSR 1419 (1432)
Q Consensus 1414 Lr~~~~ 1419 (1432)
||..++
T Consensus 180 Lr~~l~ 185 (187)
T PRK09641 180 LRKQLR 185 (187)
T ss_pred HHHHHh
Confidence 998553
No 93
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=99.81 E-value=8.2e-19 Score=191.83 Aligned_cols=181 Identities=15% Similarity=0.184 Sum_probs=149.0
Q ss_pred CCChhhHHHHHHHHHHhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHH
Q psy15215 378 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 457 (1432)
Q Consensus 378 ~l~~~e~~~l~~~i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya 457 (1432)
++...+...++..+..|+.. |+..++..|.++|+++|.+|+++..+++|++||+++++|+++++|++..| +|.+|+
T Consensus 11 ~~~~~~~~~li~~~~~g~~~---a~~~l~~~y~~~l~~~~~~~~~~~~dAeDivQe~fi~l~~~~~~~~~~~~-~~~~wl 86 (194)
T PRK09646 11 PAESPDLDALLRRVARGDQD---AFAELYDRTSSRVYGLVRRVLRDPGYSEETTQEVYLEVWRTASRFDPARG-SALAWL 86 (194)
T ss_pred CCCcccHHHHHHHHHccCHH---HHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhhcCcccc-cHHHHH
Confidence 44556788999999999988 99999999999999999999999999999999999999999999998655 799999
Q ss_pred HHHHHHHHHHHHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCC
Q psy15215 458 TWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPV 537 (1432)
Q Consensus 458 ~~~ir~~i~~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~ 537 (1432)
+..++|.+.++++++.+..+.- .+ .
T Consensus 87 ~~ia~n~~~d~~r~~~~~~~~~---------------------------------------------------~~----~ 111 (194)
T PRK09646 87 LTLAHRRAVDRVRSEQAASQRE---------------------------------------------------VR----Y 111 (194)
T ss_pred HHHHHHHHHHHHHhhccccccc---------------------------------------------------cc----c
Confidence 9999999999999876421100 00 0
Q ss_pred CCCCCCCcCcccccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHH
Q psy15215 538 GDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 617 (1432)
Q Consensus 538 ~~~~~~~~~~~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~ 617 (1432)
... .. .....++.+.....+....+..+|++||++++.||.|+|..|+ |++|||+.||+|.++|+++.
T Consensus 112 ~~~---~~-----~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~~----s~~EIA~~Lgis~~tVk~~l 179 (194)
T PRK09646 112 GAR---NV-----DPAFDQVAEEVEARLERERVRDCLDALTDTQRESVTLAYYGGL----TYREVAERLAVPLGTVKTRM 179 (194)
T ss_pred ccc---cc-----cccccchHHHHHHHhHHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHhCCChHhHHHHH
Confidence 000 00 0011234455555566788999999999999999999999888 99999999999999999999
Q ss_pred HHHHHHHHHHHH
Q psy15215 618 AKALRKLRPLAH 629 (1432)
Q Consensus 618 ~rAl~kLr~~l~ 629 (1432)
++|+++|+..+.
T Consensus 180 ~ra~~~Lr~~l~ 191 (194)
T PRK09646 180 RDGLIRLRDCLG 191 (194)
T ss_pred HHHHHHHHHHhc
Confidence 999999998874
No 94
>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=99.80 E-value=8e-19 Score=187.78 Aligned_cols=168 Identities=18% Similarity=0.272 Sum_probs=141.2
Q ss_pred HHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHH
Q psy15215 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITR 1257 (1432)
Q Consensus 1178 ~~~~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~ 1257 (1432)
+.++++||.. |+..|+..|.+.+++++.+++++..+++|++||+|+.+|++.++|+...+ +|.+|++.+++|.+.+
T Consensus 2 i~~~~~~d~~---a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~-~~~~wl~~i~~n~~~d 77 (170)
T TIGR02952 2 LERAQDREED---AFARIYETYSDRVYRYIYYRVGCKYTAEDLTSEVFERVLRKIDSFKEQKN-SFEAWLFTIARNVVND 77 (170)
T ss_pred hHHHHccCHH---HHHHHHHHHHHHHHHHHHHHHCChhhHHHHHHHHHHHHHHhHHhcccccc-cHHHHHHHHHHHHHHH
Confidence 5567788888 99999999999999999999998899999999999999999999997555 8999999999999999
Q ss_pred HHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCc
Q psy15215 1258 SIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGD 1337 (1432)
Q Consensus 1258 ~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~~d 1337 (1432)
++|++.+.... +++. ...
T Consensus 78 ~~R~~~~~~~~-----------------------------------------------------~~~~---------~~~ 95 (170)
T TIGR02952 78 YFRGSKRHPLF-----------------------------------------------------SLDV---------FKE 95 (170)
T ss_pred HHHhcCCCCCC-----------------------------------------------------cHHH---------Hhh
Confidence 99987652110 0000 000
Q ss_pred ccccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCc
Q psy15215 1338 FIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417 (1432)
Q Consensus 1338 ~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~ 1417 (1432)
... ...+|++.+...+....+..+|..|||++|.||.++|+.|+ |++|||+.||+|.++|+++++||+++||+.
T Consensus 96 ~~~--~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~g~----s~~eIA~~l~is~~tv~~~l~ra~~~Lr~~ 169 (170)
T TIGR02952 96 LLS--NEPNPEEAILKEEANEKLLKALKILTPKQQHVIALRFGQNL----PIAEVARILGKTEGAVKILQFRAIKKLARQ 169 (170)
T ss_pred cCC--CCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 000 11256777777777889999999999999999999999888 999999999999999999999999999974
No 95
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=99.80 E-value=1e-18 Score=189.07 Aligned_cols=175 Identities=20% Similarity=0.243 Sum_probs=142.1
Q ss_pred HHHHhhhhhhhhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHHH
Q psy15215 1179 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRS 1258 (1432)
Q Consensus 1179 ~~~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~~ 1258 (1432)
.+++.||.. |++.|+..|.++|+++|++|++++.+.+|++||++++||+++++|+ .+.+|.||++.++++.+.++
T Consensus 2 ~~~~~gd~~---a~~~l~~~~~~~l~~~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~--~~~~~~~~l~~~~~~~~~~~ 76 (182)
T PRK09652 2 ERVQRGDRA---AFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFR--GGAAFYTWLYRIARNTAINY 76 (182)
T ss_pred chhhcCCHH---HHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHhcC--CCcchHHHHHHHHHHHHHHH
Confidence 356788888 9999999999999999999999999999999999999999999999 44589999999999999999
Q ss_pred HHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcc
Q psy15215 1259 IADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDF 1338 (1432)
Q Consensus 1259 i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~~d~ 1338 (1432)
+++..+....+ +.. ..+.++....+.
T Consensus 77 ~r~~~~~~~~~----------------------------------------------------~~~--~~~~~~~~~~~~ 102 (182)
T PRK09652 77 LRKQGRRPPAS----------------------------------------------------DVD--AEEAEDFDLADA 102 (182)
T ss_pred HHcccCCCCcc----------------------------------------------------ccc--cccccccccccc
Confidence 98876521100 000 001111111111
Q ss_pred cccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCch
Q psy15215 1339 IEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418 (1432)
Q Consensus 1339 i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~ 1418 (1432)
+.+ ..+|++.+........+..+|..|||+++.||.++|+.|+ |++|||+.||+|+.+|++++++|+++||+.+
T Consensus 103 ~~~--~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~~----s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 176 (182)
T PRK09652 103 LRD--ISTPENELLSAELEQRVRAAIESLPEELRTAITLREIEGL----SYEEIAEIMGCPIGTVRSRIFRAREALRAKL 176 (182)
T ss_pred ccc--ccChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 111 2357777777778889999999999999999999998888 9999999999999999999999999999844
No 96
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=99.80 E-value=1.8e-18 Score=189.07 Aligned_cols=184 Identities=14% Similarity=0.184 Sum_probs=148.2
Q ss_pred ChhhHHHHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHH
Q psy15215 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 1249 (1432)
Q Consensus 1170 ~~~e~~~l~~~~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~ 1249 (1432)
++.....++..++.|+.. |+..|+..|.+.|+++|++++++..+++|++||+|+++|+++.+|++.. .|.+|++.
T Consensus 3 ~~~~~~~ll~~~~~gd~~---a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~~i~l~~~~~~~~~~~--~~~~wl~~ 77 (193)
T PRK11923 3 TQEEDQQLVERVQRGDKR---AFDLLVLKYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYRALGNFRGDS--AFYTWLYR 77 (193)
T ss_pred ccccHHHHHHHHHcCCHH---HHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHhCcCCCC--ccHhHHHH
Confidence 344456788888999888 9999999999999999999999999999999999999999999999764 59999999
Q ss_pred HHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCC-CC
Q psy15215 1250 WIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESP-VG 1328 (1432)
Q Consensus 1250 ~ir~~i~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~-~~ 1328 (1432)
+++|.+.++++++.+..... ..+++.. ..
T Consensus 78 ia~n~~~d~~rk~~~~~~~~--------------------------------------------------~~~~~~~~~~ 107 (193)
T PRK11923 78 IAINTAKNHLVSRGRRPPDS--------------------------------------------------DVSSEDAEFY 107 (193)
T ss_pred HHHHHHHHHHHHhcCCCccc--------------------------------------------------cccccchhhh
Confidence 99999999999876521000 0001100 00
Q ss_pred CCCCCCcCcccccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q psy15215 1329 DDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEA 1408 (1432)
Q Consensus 1329 ~~~~~~~~d~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~ 1408 (1432)
++ . ..+. ...+|++.+...+....+..+|..||+++|.|+.++|..|+ |++|||+.||+|..+|+++++
T Consensus 108 ~~-~----~~~~--~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~----s~~eIA~~lgis~~tv~~~l~ 176 (193)
T PRK11923 108 DG-D----HALK--DIESPERALLRDEIEGTVHRTIQQLPEDLRTALTLREFDGL----SYEDIASVMQCPVGTVRSRIF 176 (193)
T ss_pred cc-c----cccc--CcCCHHHHHHHHHHHHHHHHHHHhCCHHHhHHHhhHHhcCC----CHHHHHHHHCCCHHHHHHHHH
Confidence 00 0 0011 12357777777788889999999999999999999998888 999999999999999999999
Q ss_pred HHHHHhhCchh
Q psy15215 1409 KALRKLRHPSR 1419 (1432)
Q Consensus 1409 rAl~kLr~~~~ 1419 (1432)
||+++||...+
T Consensus 177 Rar~~Lr~~l~ 187 (193)
T PRK11923 177 RAREAIDKALQ 187 (193)
T ss_pred HHHHHHHHHHH
Confidence 99999999543
No 97
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=99.80 E-value=1.3e-18 Score=189.00 Aligned_cols=173 Identities=16% Similarity=0.234 Sum_probs=146.0
Q ss_pred hHHHHHHHHHHhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHH
Q psy15215 383 DLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 462 (1432)
Q Consensus 383 e~~~l~~~i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir 462 (1432)
....++..++.|+.. |+..|+..|.++|+++|.+|++++.+++|++||+|+++|+++.+|++. +.+|.+|++..++
T Consensus 6 ~~~~l~~~~~~~d~~---a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~f~~wl~~ia~ 81 (186)
T PRK05602 6 PDEELLARVAAGDPA---AFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRPG-EARFDTWLHRVVL 81 (186)
T ss_pred cHHHHHHHHHCcCHH---HHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHhhhcCCC-CCcHHHHHHHHHH
Confidence 345688899999998 999999999999999999999999999999999999999999999975 4589999999999
Q ss_pred HHHHHHHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCC
Q psy15215 463 QAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDED 542 (1432)
Q Consensus 463 ~~i~~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~ 542 (1432)
|.+.++++++... + .+. ..+
T Consensus 82 n~~~d~~R~~~~~---~-----------------------------------------------------~~~-~~~--- 101 (186)
T PRK05602 82 NLCYDRLRRRREV---P-----------------------------------------------------VED-APD--- 101 (186)
T ss_pred HHHHHHHHhcCCC---C-----------------------------------------------------ccc-ccc---
Confidence 9999999876431 0 000 000
Q ss_pred CCcCcccccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHH
Q psy15215 543 SHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALR 622 (1432)
Q Consensus 543 ~~~~~~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~ 622 (1432)
..+ ....|+..+...+....+..+|..||++++.||.|+|..|+ |++|||+.||+|+++|+++.++|+.
T Consensus 102 ------~~~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~----s~~EIA~~lgis~~tV~~~l~Rar~ 170 (186)
T PRK05602 102 ------VPD-PAPGPDAGLEARQRARRVEQALAALPERQREAIVLQYYQGL----SNIEAAAVMDISVDALESLLARGRR 170 (186)
T ss_pred ------cCC-CCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhHHHhcCC----CHHHHHHHhCcCHHHHHHHHHHHHH
Confidence 001 11245666666677788999999999999999999999888 9999999999999999999999999
Q ss_pred HHHHHHHH
Q psy15215 623 KLRPLAHD 630 (1432)
Q Consensus 623 kLr~~l~~ 630 (1432)
+|++.+..
T Consensus 171 ~Lr~~l~~ 178 (186)
T PRK05602 171 ALRAQLAD 178 (186)
T ss_pred HHHHHHHh
Confidence 99998864
No 98
>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=99.80 E-value=1.5e-18 Score=190.54 Aligned_cols=190 Identities=24% Similarity=0.308 Sum_probs=147.0
Q ss_pred HHHHHHHHHHhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHH
Q psy15215 384 LRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 463 (1432)
Q Consensus 384 ~~~l~~~i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~ 463 (1432)
...++..++.||.. |+..|+..|.+.|+++|.+++++..+++||+||+++.+|+++.+|++..+.+|+||++.++++
T Consensus 6 ~~~l~~~~~~~d~~---a~~~l~~~~~~~l~~~a~~~~~~~~~aeDlvQe~fl~~~~~~~~~~~~~~~~f~~wl~~~~~~ 82 (198)
T TIGR02859 6 DEEIVELARQGNTH---ALEYLINKYKNFVRAKARSYFLIGADKEDIIQEGMIGLYKAIRDFRPDKLSSFKAFAELCVTR 82 (198)
T ss_pred hHHHHHHHHcCCHH---HHHHHHHHHHHHHHHHHHHHccccCcHHHHHHHHHHHHHHHHHHhCcccCCChHHHHHHHHHH
Confidence 34677888999988 999999999999999999999999999999999999999999999987777999999999999
Q ss_pred HHHHHHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCC-CCC
Q psy15215 464 AITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGD-DED 542 (1432)
Q Consensus 464 ~i~~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~-~~~ 542 (1432)
.+.++++...+..+.++ ....|++.+..+ +++
T Consensus 83 ~~~~~~r~~~~~~~~~~-----------------------------------------------~~~~~~~~~~~~~~~~ 115 (198)
T TIGR02859 83 QIITAIKTATRQKHIPL-----------------------------------------------NSYVSLNKPIYDEESD 115 (198)
T ss_pred HHHHHHHHHHHhcccch-----------------------------------------------hhhcCccccccccccc
Confidence 99998886543211110 012233332211 111
Q ss_pred CCcCcccccCCCCChHHHHHHHHHHHHHHHHHhcC-CHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHH
Q psy15215 543 SHLGDFIEDENMLAPSDAALNASMRSVVKDILNSL-TPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKAL 621 (1432)
Q Consensus 543 ~~~~~~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L-~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl 621 (1432)
.++.+.+++....+|++.+...+....+.++|+.| ++.++.|+ ++|..|+ |++|||+.||+|.++|+...++++
T Consensus 116 ~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~Ll~~~~~~i~-~~~~~~~----s~~eIA~~l~~s~~tV~~~l~r~r 190 (198)
T TIGR02859 116 RTLLDVISGAKVTDPEELIISQEEYGDIESKMNELLSDLEWKVL-QSYLDGK----SYQEIACDLNRHVKSIDNALQRVK 190 (198)
T ss_pred chHHHHhhccccCCHHHHHHHHHHHHHHHHHHHHhcCHHHHHHH-HHHHcCC----CHHHHHHHHCCCHHHHHHHHHHHH
Confidence 12223332223357888888888888899999995 55555555 5687888 999999999999999999999999
Q ss_pred HHHHHHH
Q psy15215 622 RKLRPLA 628 (1432)
Q Consensus 622 ~kLr~~l 628 (1432)
++|+..+
T Consensus 191 ~~L~~~l 197 (198)
T TIGR02859 191 RKLEKYL 197 (198)
T ss_pred HHHHHhc
Confidence 9999765
No 99
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=99.80 E-value=1.4e-18 Score=187.63 Aligned_cols=174 Identities=14% Similarity=0.202 Sum_probs=144.0
Q ss_pred hhHHHHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHH
Q psy15215 1172 NDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 1251 (1432)
Q Consensus 1172 ~e~~~l~~~~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~i 1251 (1432)
.+...++..+..|+.. |+..|+..|.+.|+++|.+++++..+++|++||+|+++|+++++|++.. ..|.||++.++
T Consensus 4 ~~~~~li~~~~~g~~~---a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~fl~~~~~~~~~~~~~-~~~~~wl~~ia 79 (179)
T PRK12514 4 DDIEKLIVRVSLGDRD---AFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAVSG-LSPMTWLITIA 79 (179)
T ss_pred hHHHHHHHHHHcCCHH---HHHHHHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHHHhHHhcCccc-ccHHHHHHHHH
Confidence 4567788888999888 9999999999999999999999999999999999999999999998654 36999999999
Q ss_pred HHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCC
Q psy15215 1252 RQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDE 1331 (1432)
Q Consensus 1252 r~~i~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~ 1331 (1432)
+|.+.+++|++.+. ..+ .+.
T Consensus 80 ~n~~~d~~R~~~~~-~~~-----------------------------------------------------~~~------ 99 (179)
T PRK12514 80 RNHAIDRLRARKAV-AVD-----------------------------------------------------IDE------ 99 (179)
T ss_pred HHHHHHHHHhcCCc-ccc-----------------------------------------------------ccc------
Confidence 99999999976531 000 000
Q ss_pred CCCcCcccccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q psy15215 1332 DSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKAL 1411 (1432)
Q Consensus 1332 ~~~~~d~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl 1411 (1432)
..+. .+ ...+|++.....+....+..+|..||++++.||.++|+.|+ |++|||+.||+|..+|+++++||+
T Consensus 100 ---~~~~-~~-~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~----s~~eIA~~lgis~~tV~~~l~Rar 170 (179)
T PRK12514 100 ---AHDL-AD-PSPGPEAEVIAGDEGQRIDACLEELEKDRAAAVRRAYLEGL----SYKELAERHDVPLNTMRTWLRRSL 170 (179)
T ss_pred ---chhc-cc-cCCCHHHHHHhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHHCCChHHHHHHHHHHH
Confidence 0000 00 11256666655555677999999999999999999999888 999999999999999999999999
Q ss_pred HHhhCch
Q psy15215 1412 RKLRHPS 1418 (1432)
Q Consensus 1412 ~kLr~~~ 1418 (1432)
++||+..
T Consensus 171 ~~Lr~~l 177 (179)
T PRK12514 171 LKLRECL 177 (179)
T ss_pred HHHHHHh
Confidence 9999864
No 100
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=99.79 E-value=2.7e-18 Score=187.77 Aligned_cols=190 Identities=15% Similarity=0.190 Sum_probs=153.7
Q ss_pred CChhhHHHHHHHHHHhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHH
Q psy15215 379 LPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 458 (1432)
Q Consensus 379 l~~~e~~~l~~~i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~ 458 (1432)
+++.....++..++.||.. |+..|+..|.+.|+++|++++++..+++|++||+++++|+++.+|++.. .|.+|++
T Consensus 2 ~~~~~~~~ll~~~~~gd~~---a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~~i~l~~~~~~~~~~~--~~~~wl~ 76 (193)
T PRK11923 2 LTQEEDQQLVERVQRGDKR---AFDLLVLKYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYRALGNFRGDS--AFYTWLY 76 (193)
T ss_pred CccccHHHHHHHHHcCCHH---HHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHhCcCCCC--ccHhHHH
Confidence 3445566888899999988 9999999999999999999999999999999999999999999999753 6999999
Q ss_pred HHHHHHHHHHHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCC-CC
Q psy15215 459 WWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMES-PV 537 (1432)
Q Consensus 459 ~~ir~~i~~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~-~~ 537 (1432)
..++|.+.++++++.+.... ...+++. ..
T Consensus 77 ~ia~n~~~d~~rk~~~~~~~--------------------------------------------------~~~~~~~~~~ 106 (193)
T PRK11923 77 RIAINTAKNHLVSRGRRPPD--------------------------------------------------SDVSSEDAEF 106 (193)
T ss_pred HHHHHHHHHHHHHhcCCCcc--------------------------------------------------ccccccchhh
Confidence 99999999999876652100 0000000 00
Q ss_pred CCCCCCCcCcccccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHH
Q psy15215 538 GDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 617 (1432)
Q Consensus 538 ~~~~~~~~~~~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~ 617 (1432)
.++ . ..+. ...+|++.+...+....+..+|..||++++.|+.|+|..|+ |++|||+.||+|+.+|+++.
T Consensus 107 ~~~-~----~~~~--~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~----s~~eIA~~lgis~~tv~~~l 175 (193)
T PRK11923 107 YDG-D----HALK--DIESPERALLRDEIEGTVHRTIQQLPEDLRTALTLREFDGL----SYEDIASVMQCPVGTVRSRI 175 (193)
T ss_pred hcc-c----cccc--CcCCHHHHHHHHHHHHHHHHHHHhCCHHHhHHHhhHHhcCC----CHHHHHHHHCCCHHHHHHHH
Confidence 000 0 0011 12357777777788889999999999999999999999888 99999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHH
Q psy15215 618 AKALRKLRPLAHDWLEQ 634 (1432)
Q Consensus 618 ~rAl~kLr~~l~~~~~~ 634 (1432)
+||+++|+.++..++++
T Consensus 176 ~Rar~~Lr~~l~~~~~~ 192 (193)
T PRK11923 176 FRAREAIDKALQPLLQE 192 (193)
T ss_pred HHHHHHHHHHHHHHhcC
Confidence 99999999999887653
No 101
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=99.79 E-value=1.4e-18 Score=188.78 Aligned_cols=177 Identities=18% Similarity=0.228 Sum_probs=139.5
Q ss_pred hhhHHHHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHH
Q psy15215 1171 LNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 1250 (1432)
Q Consensus 1171 ~~e~~~l~~~~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ 1250 (1432)
......++..++.|+.. |+..++..|.+.|+++|++|.+++.+++|++||+|+++|++..+|++..+ .|.+|++++
T Consensus 7 ~~~~~~l~~~~~~~d~~---a~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~~i~l~~~~~~~~~~~~-~~~~wl~~i 82 (186)
T PRK13919 7 SLSDEALLALVARGEEE---ALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKKAKEFDPRRG-SARAWLLAL 82 (186)
T ss_pred ccCHHHHHHHHHcCcHH---HHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhhhccCcccc-chHHHHHHH
Confidence 34567888888999888 99999999999999999999999999999999999999999999987543 699999999
Q ss_pred HHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCC
Q psy15215 1251 IRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDD 1330 (1432)
Q Consensus 1251 ir~~i~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~ 1330 (1432)
++|.+.+++|++.+..+ ..+.+ .
T Consensus 83 a~n~~~d~~rk~~~~~~----------------------------------------------------~~~~~-----~ 105 (186)
T PRK13919 83 AHHAAVDHVRRRAARPQ----------------------------------------------------PLEPD-----E 105 (186)
T ss_pred HHHHHHHHHHhhhcccc----------------------------------------------------ccccc-----c
Confidence 99999999998764100 00000 0
Q ss_pred CCCCcCcccccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q psy15215 1331 EDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 1410 (1432)
Q Consensus 1331 ~~~~~~d~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rA 1410 (1432)
......+ .. +|............+..+++.||++++.||.|+|..|+ |++|||+.+|+|.++|+.+++||
T Consensus 106 ~~~~~~~-~~-----~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~~----s~~eIA~~lgis~~~V~~~l~ra 175 (186)
T PRK13919 106 REPEAFD-LP-----GPGLDEEGHLDRTRLGRALKALSPEERRVIEVLYYQGY----THREAAQLLGLPLGTLKTRARRA 175 (186)
T ss_pred ccccccc-CC-----CccccHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHHCcCHHHHHHHHHHH
Confidence 0000000 00 11111122233567899999999999999999999888 99999999999999999999999
Q ss_pred HHHhhCch
Q psy15215 1411 LRKLRHPS 1418 (1432)
Q Consensus 1411 l~kLr~~~ 1418 (1432)
+++||...
T Consensus 176 ~~~Lr~~l 183 (186)
T PRK13919 176 LSRLKEVL 183 (186)
T ss_pred HHHHHHHh
Confidence 99999854
No 102
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=99.79 E-value=1.9e-18 Score=188.06 Aligned_cols=172 Identities=14% Similarity=0.175 Sum_probs=143.7
Q ss_pred HHHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHhccCCC---CChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHH
Q psy15215 1175 RDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRG---LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 1251 (1432)
Q Consensus 1175 ~~l~~~~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~---~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~i 1251 (1432)
..|+.+++.|+.. |+..++..|.+.|+++|.++++++ .+++|++||+++++|+++.+|++..+ +|.||++.++
T Consensus 6 ~~li~~~~~gd~~---a~~~l~~~y~~~l~~~~~~~~~~~~~~~daeDi~Qe~~i~l~~~~~~~~~~~~-~~~~wl~~ia 81 (189)
T PRK06811 6 DNFIKELKKKNEK---ALEFIVDTYGNLVKKIVHKVLGTVNYSQLIEECVNDIFLSIWNNIDKFDEEKG-SFKKWIAAIS 81 (189)
T ss_pred HHHHHHHHccCHH---HHHHHHHHHHHHHHHHHHHHHcccCchhHHHHHHHHHHHHHHHhHHHhccccc-cHHHHHHHHH
Confidence 5788899999988 999999999999999999998753 47999999999999999999987554 7999999999
Q ss_pred HHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCC
Q psy15215 1252 RQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDE 1331 (1432)
Q Consensus 1252 r~~i~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~ 1331 (1432)
+|.+.+++|++.+.... .+.+.
T Consensus 82 rn~~~d~~rk~~~~~~~----------------------------------------------------~~~~~------ 103 (189)
T PRK06811 82 KYKAIDYKRKLTKNNEI----------------------------------------------------DSIDE------ 103 (189)
T ss_pred HHHHHHHHHHhcccccc----------------------------------------------------ccchh------
Confidence 99999999987752100 00000
Q ss_pred CCCcCcccccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q psy15215 1332 DSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKAL 1411 (1432)
Q Consensus 1332 ~~~~~d~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl 1411 (1432)
.. .....+|++.....+....+..+|..|||+++.||.|+|..|+ |++|||+.||+|+.+|+++++||+
T Consensus 104 ~~-------~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~----s~~EIAe~lgis~~~V~~~l~Ra~ 172 (189)
T PRK06811 104 FI-------LISEESIENEIILKENKEEILKLINDLEKLDREIFIRRYLLGE----KIEEIAKKLGLTRSAIDNRLSRGR 172 (189)
T ss_pred hh-------hcccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHccC----CHHHHHHHHCCCHHHHHHHHHHHH
Confidence 00 0011356677777777888999999999999999999999888 999999999999999999999999
Q ss_pred HHhhCchh
Q psy15215 1412 RKLRHPSR 1419 (1432)
Q Consensus 1412 ~kLr~~~~ 1419 (1432)
++||...-
T Consensus 173 ~~Lr~~~~ 180 (189)
T PRK06811 173 KKLQKNKL 180 (189)
T ss_pred HHHHHccc
Confidence 99998543
No 103
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=99.79 E-value=2e-18 Score=189.09 Aligned_cols=175 Identities=14% Similarity=0.170 Sum_probs=146.6
Q ss_pred hHHHHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHH
Q psy15215 1173 DLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 1252 (1432)
Q Consensus 1173 e~~~l~~~~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir 1252 (1432)
....++.++..|+.. |++.|+..|.+.|+.+|.+++++..+++|++||+++++|++..+|++.. ..|.||++..++
T Consensus 12 ~~~~li~~~~~gd~~---a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~~-~~~~~wl~~ia~ 87 (196)
T PRK12524 12 SDEALLVLYANGDPA---AARALTLRLAPRALAVATRVLGDRAEAEDVTQEAMLRLWRIAPDWRQGE-ARVSTWLYRVVC 87 (196)
T ss_pred CHHHHHHHHHCCCHH---HHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhcccccc-chHHHHHHHHHH
Confidence 356889999999988 9999999999999999999999999999999999999999999998533 479999999999
Q ss_pred HHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCC
Q psy15215 1253 QAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDED 1332 (1432)
Q Consensus 1253 ~~i~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~ 1332 (1432)
+.+.+++|++.+. . ..++. ..+
T Consensus 88 n~~~d~~Rk~~~~-~-----------------------------------------------------~~~~~-~~~--- 109 (196)
T PRK12524 88 NLCTDRLRRRRRA-S-----------------------------------------------------VDLDD-APE--- 109 (196)
T ss_pred HHHHHHHHhhcCC-C-----------------------------------------------------CCccc-ccc---
Confidence 9999999976541 0 00000 000
Q ss_pred CCcCcccccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q psy15215 1333 SHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALR 1412 (1432)
Q Consensus 1333 ~~~~d~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~ 1412 (1432)
..+ ...+|++.+...+....+..+|+.||+++|.||.|+|+.|. |++|||+.||+|..+|+++++||++
T Consensus 110 ------~~~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~L~~~~g~----s~~eIA~~lgis~~tV~~~l~Ra~~ 178 (196)
T PRK12524 110 ------PAD-AAPGAEEALIEGDRMRALDAALAALPERQRQAVVLRHIEGL----SNPEIAEVMEIGVEAVESLTARGKR 178 (196)
T ss_pred ------ccc-cCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 001 11346666777777888999999999999999999999888 9999999999999999999999999
Q ss_pred HhhCchhh
Q psy15215 1413 KLRHPSRY 1420 (1432)
Q Consensus 1413 kLr~~~~~ 1420 (1432)
+||.....
T Consensus 179 ~Lr~~l~~ 186 (196)
T PRK12524 179 ALAALLAG 186 (196)
T ss_pred HHHHHHHh
Confidence 99987654
No 104
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=99.79 E-value=6.9e-19 Score=190.99 Aligned_cols=181 Identities=15% Similarity=0.143 Sum_probs=145.0
Q ss_pred HHhhhhhhhhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHHHHH
Q psy15215 1181 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA 1260 (1432)
Q Consensus 1181 ~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~~i~ 1260 (1432)
+..|+.. |+..|+..|.+.|+++|.+++++..+++|++||+|+.+|++.++|++..+..|.||++.+++|.+.+++|
T Consensus 3 ~~~gd~~---a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~~~~~~~~wL~~Iarn~~~d~~R 79 (185)
T PRK12542 3 VTNNDYE---KMEELYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKNLEKLHSLNTQELKRYILRVAKNKAIDSYR 79 (185)
T ss_pred ccccCHH---HHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHH
Confidence 4467777 9999999999999999999999999999999999999999999998654458999999999999999999
Q ss_pred HhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccc
Q psy15215 1261 DQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIE 1340 (1432)
Q Consensus 1261 ~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~~d~i~ 1340 (1432)
++.+..... +. ... +...
T Consensus 80 k~~~~~~~~------------------------------------------------------~~-~~~-------~~~~ 97 (185)
T PRK12542 80 KNKRHETFL------------------------------------------------------EE-YER-------ESIE 97 (185)
T ss_pred Hhhhhhhhh------------------------------------------------------hh-ccc-------cchh
Confidence 876410000 00 000 0000
Q ss_pred cCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchhh
Q psy15215 1341 DENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRY 1420 (1432)
Q Consensus 1341 d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~~ 1420 (1432)
. ...+|.+..........|..+|..|||++|+||.|+|+.|+ |++|||+.||+|.++|+++++||+++||+....
T Consensus 98 ~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~----s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~ 172 (185)
T PRK12542 98 A-VDENIEEWEKRKMSEVQIDTLLKELNESNRQVFKYKVFYNL----TYQEISSVMGITEANVRKQFERARKRVQNMIGG 172 (185)
T ss_pred h-hhccHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHcc
Confidence 0 01123343334445567999999999999999999999998 999999999999999999999999999999888
Q ss_pred hhHHhhhcccC
Q psy15215 1421 YKLKIFLEGKK 1431 (1432)
Q Consensus 1421 ~~l~~~~~~~~ 1431 (1432)
.....|+...+
T Consensus 173 ~~~~~~~~~~~ 183 (185)
T PRK12542 173 IQHDEFKELQR 183 (185)
T ss_pred cchHHHHHHhc
Confidence 88888876543
No 105
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=99.79 E-value=2.2e-18 Score=186.39 Aligned_cols=179 Identities=20% Similarity=0.240 Sum_probs=146.0
Q ss_pred HHHHHhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHHH
Q psy15215 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRS 468 (1432)
Q Consensus 389 ~~i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~~ 468 (1432)
.+++.||.. |++.|+..|.++|+++|++|.+++.+.+|++||++++||+++++|+ .+.+|.||++.++++.+.++
T Consensus 2 ~~~~~gd~~---a~~~l~~~~~~~l~~~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~--~~~~~~~~l~~~~~~~~~~~ 76 (182)
T PRK09652 2 ERVQRGDRA---AFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFR--GGAAFYTWLYRIARNTAINY 76 (182)
T ss_pred chhhcCCHH---HHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHhcC--CCcchHHHHHHHHHHHHHHH
Confidence 457889988 9999999999999999999999999999999999999999999998 44589999999999999999
Q ss_pred HHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcc
Q psy15215 469 IADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDF 548 (1432)
Q Consensus 469 i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~ 548 (1432)
+++..+....+ +. ...+.++....+.
T Consensus 77 ~r~~~~~~~~~----------------------------------------------------~~--~~~~~~~~~~~~~ 102 (182)
T PRK09652 77 LRKQGRRPPAS----------------------------------------------------DV--DAEEAEDFDLADA 102 (182)
T ss_pred HHcccCCCCcc----------------------------------------------------cc--ccccccccccccc
Confidence 98876521110 00 0001111111111
Q ss_pred cccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHH
Q psy15215 549 IEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLA 628 (1432)
Q Consensus 549 i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l 628 (1432)
.++ ..+|++.+...+....+..+|..|||+++.||.++|+.|+ |++|||+.||+|+.+|+++.++|+++|++.+
T Consensus 103 ~~~--~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~~----s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 176 (182)
T PRK09652 103 LRD--ISTPENELLSAELEQRVRAAIESLPEELRTAITLREIEGL----SYEEIAEIMGCPIGTVRSRIFRAREALRAKL 176 (182)
T ss_pred ccc--ccChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 111 2357777777778889999999999999999999998888 9999999999999999999999999999988
Q ss_pred HHHH
Q psy15215 629 HDWL 632 (1432)
Q Consensus 629 ~~~~ 632 (1432)
..++
T Consensus 177 ~~~~ 180 (182)
T PRK09652 177 QPLL 180 (182)
T ss_pred HHHh
Confidence 7664
No 106
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=99.79 E-value=2.1e-18 Score=192.96 Aligned_cols=173 Identities=12% Similarity=0.171 Sum_probs=143.5
Q ss_pred HHHHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHH
Q psy15215 1174 LRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 1253 (1432)
Q Consensus 1174 ~~~l~~~~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~ 1253 (1432)
...|+..++.|+.. |+..|+..|.+.|++++++++++..+++|++||+|+.+|++.++|++..+ +|.+|++.+++|
T Consensus 50 d~~Li~~~~~gd~~---af~~L~~~y~~~l~~~~~~~~~d~~dAEDivQEvfl~l~~~~~~~~~~~~-~f~~WL~~IarN 125 (233)
T PRK12538 50 DEELLDRLATDDEA---AFRLLVERHIDRAYAIALRIVGNRADAEDVVQDTMLKVWTHRGRWQHGRA-KFSTWLYRVVSN 125 (233)
T ss_pred HHHHHHHHHhCCHH---HHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHcccccc-cHHHHHHHHHHH
Confidence 45678888999888 99999999999999999999999999999999999999999999986544 799999999999
Q ss_pred HHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCC
Q psy15215 1254 AITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDS 1333 (1432)
Q Consensus 1254 ~i~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~ 1333 (1432)
.+.+++|++.+. .. ..+. +.
T Consensus 126 ~~id~~Rk~~~~-~~----------------------------------------------------~~~~----~~--- 145 (233)
T PRK12538 126 RCIDLRRKPRTE-NV----------------------------------------------------DAVP----EV--- 145 (233)
T ss_pred HHHHHHHhhccc-cc----------------------------------------------------cccc----cc---
Confidence 999999875320 00 0000 00
Q ss_pred CcCcccccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q psy15215 1334 HLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRK 1413 (1432)
Q Consensus 1334 ~~~d~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~k 1413 (1432)
. + ...++++.+...+....+..+|..||+++|.||.|+|+.|+ |++|||+.||+|.++|+++++||+++
T Consensus 146 -----~-~-~~~~~~~~~~~~e~~~~l~~~L~~Lp~~~R~v~~L~~~eg~----s~~EIA~~Lgis~~tVk~~l~RAr~k 214 (233)
T PRK12538 146 -----A-D-GKPDAVSVIERNELSDLLEAAMQRLPEQQRIAVILSYHENM----SNGEIAEVMDTTVAAVESLLKRGRQQ 214 (233)
T ss_pred -----c-c-CCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHHhcCC----CHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 0 0 01234555566667788999999999999999999999998 99999999999999999999999999
Q ss_pred hhCchhhh
Q psy15215 1414 LRHPSRYY 1421 (1432)
Q Consensus 1414 Lr~~~~~~ 1421 (1432)
||+.....
T Consensus 215 Lr~~l~~~ 222 (233)
T PRK12538 215 LRDLLRRH 222 (233)
T ss_pred HHHHHHHh
Confidence 99866543
No 107
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=99.79 E-value=2.2e-18 Score=193.53 Aligned_cols=189 Identities=16% Similarity=0.219 Sum_probs=153.1
Q ss_pred CCChhhHHHHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHH
Q psy15215 1168 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 1247 (1432)
Q Consensus 1168 ~l~~~e~~~l~~~~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya 1247 (1432)
.++......++..+..|+.. |++.++..|.+.|+++|.++++.+.+++|++||+|+++|+++++|++. ..|.||+
T Consensus 11 ~~~~~~~~~l~~~~~~gd~~---a~~~l~~~y~~~l~~~a~~~~~~~~~AEDlvQE~fi~l~~~~~~~~~~--~~~~~wL 85 (231)
T PRK11922 11 PLSAASDRELVARVLAGDEA---AFEALMRRHNRRLYRTARAILRNDAEAEDVVQEAYLRAFRALGTFRGD--ASLSTWL 85 (231)
T ss_pred CcCcccHHHHHHHHHcCCHH---HHHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHhcCCC--chhHHHH
Confidence 34555667788899999988 999999999999999999999999999999999999999999999875 3799999
Q ss_pred HHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCC
Q psy15215 1248 TWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPV 1327 (1432)
Q Consensus 1248 ~~~ir~~i~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~ 1327 (1432)
+.+++|.+.+++|+..+..+.+.. ... ..
T Consensus 86 ~~iarn~~~d~~Rk~~r~~~~~~~--------------------------------------------------~~~-~~ 114 (231)
T PRK11922 86 SRIVLNEALGRLRRRRRLVNLAEM--------------------------------------------------VMA-ST 114 (231)
T ss_pred HHHHHHHHHHHHHhhcccccchhc--------------------------------------------------ccc-cc
Confidence 999999999999987752111000 000 00
Q ss_pred CCCCCCCcCcccccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHH
Q psy15215 1328 GDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 1407 (1432)
Q Consensus 1328 ~~~~~~~~~d~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~ 1407 (1432)
.. ++ ..... .....+|++.....+....+..+|+.||++++.||.|+|+.|+ |++|||+.||+|.++|++++
T Consensus 115 ~~-~~--~~~~~-~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~----s~~EIAe~lgis~~tVk~~l 186 (231)
T PRK11922 115 IA-GG--ERTPL-ADPAEDPERAAARREIRALLERAIDALPDAFRAVFVLRVVEEL----SVEETAQALGLPEETVKTRL 186 (231)
T ss_pred cc-cc--ccccc-CcccCChHHHHHHHHHHHHHHHHHHhCCHHHhhhheeehhcCC----CHHHHHHHHCcCHHHHHHHH
Confidence 00 00 00001 1123467888888888899999999999999999999998888 99999999999999999999
Q ss_pred HHHHHHhhCchhh
Q psy15215 1408 AKALRKLRHPSRY 1420 (1432)
Q Consensus 1408 ~rAl~kLr~~~~~ 1420 (1432)
+||+++||+....
T Consensus 187 ~Rar~kLr~~l~~ 199 (231)
T PRK11922 187 HRARRLLRESLAR 199 (231)
T ss_pred HHHHHHHHHHHHH
Confidence 9999999997654
No 108
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=99.79 E-value=2.7e-18 Score=187.88 Aligned_cols=184 Identities=21% Similarity=0.266 Sum_probs=149.3
Q ss_pred CCChhhHHHHHHHHHHhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHH
Q psy15215 378 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 457 (1432)
Q Consensus 378 ~l~~~e~~~l~~~i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya 457 (1432)
.++......++.+++.||.. |+..|+..|.+.|+++|++++++..+++|++||+|+++|+. ..|++..+ +|.||+
T Consensus 10 ~~~~~~~~~l~~~~~~gd~~---a~~~L~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~l~~~-~~~~~~~~-~f~~wl 84 (194)
T PRK12519 10 SLSSRSDAELFSALKAGQSA---ALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRK-SSYDPKRG-SLSSYL 84 (194)
T ss_pred CCCcccHHHHHHHHHcCCHH---HHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHh-cCCCcccc-cHHHHH
Confidence 34556677899999999998 99999999999999999999999999999999999999976 67876554 799999
Q ss_pred HHHHHHHHHHHHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCC
Q psy15215 458 TWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPV 537 (1432)
Q Consensus 458 ~~~ir~~i~~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~ 537 (1432)
+.+++|.+.++++++.+..+.. + .....
T Consensus 85 ~~iarn~~~d~~Rk~~~~~~~~-~--------------------------------------------------~~~~~- 112 (194)
T PRK12519 85 LTLTRSRAIDRLRSRRSRQRLL-E--------------------------------------------------RWQQE- 112 (194)
T ss_pred HHHHHHHHHHHHHhcccccchh-h--------------------------------------------------hhhhh-
Confidence 9999999999999876521000 0 00000
Q ss_pred CCCCCCCcCcccccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHH
Q psy15215 538 GDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 617 (1432)
Q Consensus 538 ~~~~~~~~~~~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~ 617 (1432)
...+ ....+|.+.+...+....|..+|+.||++++.||.|+|..|+ |++|||+.||+|+++|+++.
T Consensus 113 ------~~~~----~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~~~v~~l~~~~g~----s~~EIA~~lgis~~tV~~~l 178 (194)
T PRK12519 113 ------LLGE----ASEDTPLEQASLAERSQRVQTALAQLPESQRQVLELAYYEGL----SQSEIAKRLGIPLGTVKARA 178 (194)
T ss_pred ------hccc----ccCCCHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhhhhhcCC----CHHHHHHHhCCCHHHHHHHH
Confidence 0000 011346666666677778999999999999999999999888 99999999999999999999
Q ss_pred HHHHHHHHHHHHHHH
Q psy15215 618 AKALRKLRPLAHDWL 632 (1432)
Q Consensus 618 ~rAl~kLr~~l~~~~ 632 (1432)
+||+++|+..+..++
T Consensus 179 ~Ra~~~Lr~~l~~~~ 193 (194)
T PRK12519 179 RQGLLKLRELLQDLL 193 (194)
T ss_pred HHHHHHHHHHHHHHh
Confidence 999999999887654
No 109
>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=99.79 E-value=4e-18 Score=185.91 Aligned_cols=180 Identities=16% Similarity=0.199 Sum_probs=145.2
Q ss_pred HHHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHH
Q psy15215 1175 RDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA 1254 (1432)
Q Consensus 1175 ~~l~~~~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~ 1254 (1432)
..++..+..|+.. |+..|+..|.+.|+.+|++++++..+++|++||+|+++|+++++|++. .+|.+|++.+++|.
T Consensus 8 ~~l~~~~~~gd~~---a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~--~~~~~wl~~iarn~ 82 (190)
T TIGR02939 8 LELVERVQRGEKQ---AFDLLVRKYQHKVVALVGRYVRDSSEVEDVAQEAFVKAYRALSSFRGD--SAFYTWLYRIAVNT 82 (190)
T ss_pred HHHHHHHHcCCHH---HHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCC--CccHhHHHHHHHHH
Confidence 4678888899888 999999999999999999999999999999999999999999999865 37999999999999
Q ss_pred HHHHHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCC
Q psy15215 1255 ITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSH 1334 (1432)
Q Consensus 1255 i~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~ 1334 (1432)
+.++++++.+..... ..+.+.. ...+.
T Consensus 83 ~~~~~r~~~r~~~~~--------------------------------------------------~~~~~~~-~~~~~-- 109 (190)
T TIGR02939 83 AKNHLVAQGRRPPTS--------------------------------------------------DVEIEDA-EHFEG-- 109 (190)
T ss_pred HHHHHHHhccCCCcc--------------------------------------------------cccccch-hhhcc--
Confidence 999998766421100 0000000 00000
Q ss_pred cCcccccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Q psy15215 1335 LGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 1414 (1432)
Q Consensus 1335 ~~d~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kL 1414 (1432)
.+.+ ....+|++.+...+....+..+|..||++++.||.++|..|+ |++|||+.||+|.++|++.++||+++|
T Consensus 110 -~~~~--~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~~~----s~~EIA~~lgis~~tv~~~l~rar~~L 182 (190)
T TIGR02939 110 -ADRL--REIDTPERLLLSRELEQTVMRAVEALPEDLRTAITLRELEGL----SYEDIARIMDCPVGTVRSRIFRAREAI 182 (190)
T ss_pred -cccc--cccCChHHHHHHHHHHHHHHHHHHcCCHHHhhhhhhhhhcCC----CHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 0000 012357777777778888999999999999999999998888 999999999999999999999999999
Q ss_pred hCchh
Q psy15215 1415 RHPSR 1419 (1432)
Q Consensus 1415 r~~~~ 1419 (1432)
|+..+
T Consensus 183 r~~l~ 187 (190)
T TIGR02939 183 AIRLR 187 (190)
T ss_pred HHHhh
Confidence 99654
No 110
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=99.79 E-value=3.7e-18 Score=185.65 Aligned_cols=180 Identities=13% Similarity=0.259 Sum_probs=146.0
Q ss_pred HHHHHHHHHhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHH
Q psy15215 385 RDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA 464 (1432)
Q Consensus 385 ~~l~~~i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~ 464 (1432)
..++..+++||.. |+.+++..|.+.|+++|.+|++.+.+++|++||+++++|+++.+|++.. +|.||++..++|.
T Consensus 6 ~~li~~~~~gd~~---a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~ 80 (187)
T TIGR02948 6 KKRIKEVRKGDEN---AFADLVDLYKDKIYQLCYRMLGNVHEAEDVAQEAFIRAYTNIDTYDIQR--KFSTWLYRIATNL 80 (187)
T ss_pred HHHHHHHHcCCHH---HHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCCC--chHHHHHHHHHHH
Confidence 4578889999998 9999999999999999999999999999999999999999999999754 6999999999999
Q ss_pred HHHHHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCC
Q psy15215 465 ITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSH 544 (1432)
Q Consensus 465 i~~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~ 544 (1432)
+.+++++..+... ++......+...
T Consensus 81 ~~~~~rk~~~~~~-------------------------------------------------------~~~~~~~~~~~~ 105 (187)
T TIGR02948 81 TIDRLRKRKPDFY-------------------------------------------------------LDDEVQGTDGLT 105 (187)
T ss_pred HHHHHHhhccccc-------------------------------------------------------ccccccCccccc
Confidence 9999987543100 000000000001
Q ss_pred cCcccccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHH
Q psy15215 545 LGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 624 (1432)
Q Consensus 545 ~~~~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kL 624 (1432)
+.+...+ ..++|++.+...+....+..+|++|||+++.|+.|+|..|+ |++|||+.||+|+++|+++.+||+++|
T Consensus 106 ~~~~~~~-~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g~----s~~eIA~~lgis~~~v~~~l~Rar~~L 180 (187)
T TIGR02948 106 MESQLAA-DEAPPEDQVISLELRDTIQQEIQALPPKYRMVIVLKYMEDL----SLKEISEILDLPVGTVKTRIHRGREAL 180 (187)
T ss_pred ccccccc-CcCCHHHHHHHHHHHHHHHHHHHhCCHHHhHHhhhHHhcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 1111111 12367777777777888999999999999999999999888 999999999999999999999999999
Q ss_pred HHHHH
Q psy15215 625 RPLAH 629 (1432)
Q Consensus 625 r~~l~ 629 (1432)
+..+.
T Consensus 181 r~~l~ 185 (187)
T TIGR02948 181 RKQLR 185 (187)
T ss_pred HHHhh
Confidence 98774
No 111
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=99.78 E-value=3.5e-18 Score=184.87 Aligned_cols=173 Identities=12% Similarity=0.159 Sum_probs=141.8
Q ss_pred hHHHHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHH
Q psy15215 1173 DLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 1252 (1432)
Q Consensus 1173 e~~~l~~~~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir 1252 (1432)
....++..+..|+.. |+..|+..|.+.|+.+|.+++++..+++|++||+|+.+|++.++|++..+ +|.+|++.+++
T Consensus 9 ~~~~l~~~~~~~d~~---a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~~-~~~~wL~~iar 84 (182)
T PRK12537 9 DYEACLLACARGDRR---ALQALYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTGAASFDPARG-SARGWIYSVTR 84 (182)
T ss_pred hHHHHHHHHHcCCHH---HHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhccccCCcccc-cHHHHHHHHHH
Confidence 446788899999888 99999999999999999999999999999999999999999999986443 79999999999
Q ss_pred HHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCC
Q psy15215 1253 QAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDED 1332 (1432)
Q Consensus 1253 ~~i~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~ 1332 (1432)
|.+.++++++.+.... +.. .
T Consensus 85 n~~~d~~r~~~~~~~~-------------------------------------------------------~~~---~-- 104 (182)
T PRK12537 85 HLALNVLRDTRREVVL-------------------------------------------------------DDD---A-- 104 (182)
T ss_pred HHHHHHHHhccccCcc-------------------------------------------------------ccc---h--
Confidence 9999999987641100 000 0
Q ss_pred CCcCcccccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q psy15215 1333 SHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALR 1412 (1432)
Q Consensus 1333 ~~~~d~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~ 1412 (1432)
.+...+ ..++.+..........+..+|+.|||++|.|+.|+|..|+ |++|||+.||+|.++|+++++||++
T Consensus 105 ---~~~~~~--~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~~~----s~~eIA~~lgis~~tV~~~l~ra~~ 175 (182)
T PRK12537 105 ---EETAQT--LHEIIDDFDLWANSGKIHRCLEQLEPARRNCILHAYVDGC----SHAEIAQRLGAPLGTVKAWIKRSLK 175 (182)
T ss_pred ---hhhccc--ccchHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHHCCChhhHHHHHHHHHH
Confidence 000000 1123344444455678999999999999999999999999 9999999999999999999999999
Q ss_pred HhhCch
Q psy15215 1413 KLRHPS 1418 (1432)
Q Consensus 1413 kLr~~~ 1418 (1432)
+||...
T Consensus 176 ~Lr~~l 181 (182)
T PRK12537 176 ALRECM 181 (182)
T ss_pred HHHHHh
Confidence 999853
No 112
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=99.78 E-value=2.6e-18 Score=180.69 Aligned_cols=150 Identities=22% Similarity=0.259 Sum_probs=123.9
Q ss_pred hhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q psy15215 1190 KAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 1269 (1432)
Q Consensus 1190 ~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip 1269 (1432)
.||..|++.|.++|+++++++ +...+++|++|||++++|+++++|++..+ +|.+|++.+++|.+.+++|++.+...
T Consensus 4 ~af~~l~~~y~~~l~~~~~~~-~~~~~aeDi~Qe~~l~l~~~~~~~~~~~~-~f~~wl~~i~~n~~ld~~rk~~~~~~-- 79 (154)
T PRK06759 4 ATFTEAVVLYEGLIVNQIKKL-GIYQDYEEYYQCGLIGLWHAYERYDEKKG-SFPAYAVVTVRGYILERLKKEFAVQE-- 79 (154)
T ss_pred ccHHHHHHHHHHHHHHHHHHh-CCcccHHHHHHHHHHHHHHHHHHhCccCC-chHHHHHHHHHHHHHHHHHHHHhhcc--
Confidence 389999999999999999986 55679999999999999999999997666 79999999999999999998753100
Q ss_pred ccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHH
Q psy15215 1270 VHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349 (1432)
Q Consensus 1270 ~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~~d~i~d~~~~~p~~ 1349 (1432)
..+ . . .+|++
T Consensus 80 --------------------------------------------------~~~-~-----~--------------~~~~~ 89 (154)
T PRK06759 80 --------------------------------------------------KCV-C-----V--------------GEYED 89 (154)
T ss_pred --------------------------------------------------ccc-c-----c--------------CCCcc
Confidence 000 0 0 01111
Q ss_pred HHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCc
Q psy15215 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417 (1432)
Q Consensus 1350 ~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~ 1417 (1432)
.....+....+..+|..|||++|.||.++|+.|+ |++|||+.+|+|.++|+++++||+++||+.
T Consensus 90 ~~~~~~~~~~l~~~l~~L~~~~r~ii~l~~~~~~----s~~EIA~~l~is~~tV~~~~~ra~~~Lr~~ 153 (154)
T PRK06759 90 HFHFEDVEMKVKDFMSVLDEKEKYIIFERFFVGK----TMGEIALETEMTYYQVRWIYRQALEKMRNS 153 (154)
T ss_pred cccHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHhhc
Confidence 1222334567999999999999999999999888 999999999999999999999999999973
No 113
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=99.78 E-value=5.9e-18 Score=184.11 Aligned_cols=181 Identities=13% Similarity=0.233 Sum_probs=147.3
Q ss_pred HHHHHHHHHHhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHH
Q psy15215 384 LRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 463 (1432)
Q Consensus 384 ~~~l~~~i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~ 463 (1432)
...++..++.|+.. |+..++..|.++|+++|+++.+...+++|++||++++||++..+|++.. +|.+|++..++|
T Consensus 5 ~~~li~~~~~~d~~---a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~~--~~~~wl~~iarn 79 (187)
T PRK09641 5 IKRLIKQVKKGDQN---AFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINR--KFSTWLYRIATN 79 (187)
T ss_pred HHHHHHHHHcCCHH---HHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhhCCCc--chhHHHHHHHHH
Confidence 45778889999988 9999999999999999999999999999999999999999999998743 799999999999
Q ss_pred HHHHHHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCC
Q psy15215 464 AITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDS 543 (1432)
Q Consensus 464 ~i~~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~ 543 (1432)
.+.+++|++.+.. +++.+..+++..
T Consensus 80 ~~~d~~R~~~~~~-------------------------------------------------------~~~~~~~~~~~~ 104 (187)
T PRK09641 80 LTIDRLRKRKPDY-------------------------------------------------------YLDAEVAGTEGL 104 (187)
T ss_pred HHHHHHHhcCccc-------------------------------------------------------cccccccCCcch
Confidence 9999999765410 001111111111
Q ss_pred CcCcccccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHH
Q psy15215 544 HLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRK 623 (1432)
Q Consensus 544 ~~~~~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~k 623 (1432)
...+.+.+ ...+|++.....+....+..+|+.||++++.||.|+|..|. |++|||+.||+|.++|++..+||+.+
T Consensus 105 ~~~~~~~~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~~~~~----s~~eIA~~lgis~~~v~~~l~Rar~~ 179 (187)
T PRK09641 105 TMYSQLAA-DDALPEEQVVSLELQETIQEAILQLPEKYRTVIVLKYIEDL----SLKEISEILDLPVGTVKTRIHRGREA 179 (187)
T ss_pred hhhccccc-CcCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHHhhCC----CHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 11111111 12357777777777888999999999999999999998888 99999999999999999999999999
Q ss_pred HHHHHH
Q psy15215 624 LRPLAH 629 (1432)
Q Consensus 624 Lr~~l~ 629 (1432)
|+..+.
T Consensus 180 Lr~~l~ 185 (187)
T PRK09641 180 LRKQLR 185 (187)
T ss_pred HHHHHh
Confidence 998764
No 114
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=99.78 E-value=4.1e-18 Score=186.45 Aligned_cols=178 Identities=17% Similarity=0.201 Sum_probs=148.3
Q ss_pred hhHHHHHHHHHHhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHH
Q psy15215 382 NDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 461 (1432)
Q Consensus 382 ~e~~~l~~~i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~i 461 (1432)
.....++.+++.||.. |++.|+..|.+.|+++|.+++++..+++|++||+|+++|++..+|+.. .+|.+|+++++
T Consensus 11 ~~~~~l~~~~~~gd~~---a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~fi~l~~~~~~~~~~--~~f~~wl~~i~ 85 (194)
T PRK12513 11 ASDEALMLRYRAGDAA---AFEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRARAQYQPR--ARFRTWLYQIA 85 (194)
T ss_pred CCHHHHHHHHHcCCHH---HHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCC--CchHHHHHHHH
Confidence 3356789999999998 999999999999999999999999999999999999999999999864 37999999999
Q ss_pred HHHHHHHHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCC
Q psy15215 462 RQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDE 541 (1432)
Q Consensus 462 r~~i~~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~ 541 (1432)
+|.+.+++|++.+..+.+ .+. +.
T Consensus 86 ~n~~~~~~R~~~~~~~~~-----------------------------------------------------~~~---~~- 108 (194)
T PRK12513 86 RNLLIDHWRRHGARQAPS-----------------------------------------------------LDA---DE- 108 (194)
T ss_pred HHHHHHHHHHhccccccc-----------------------------------------------------ccc---ch-
Confidence 999999999887521110 000 00
Q ss_pred CCCcCcccccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHH
Q psy15215 542 DSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKAL 621 (1432)
Q Consensus 542 ~~~~~~~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl 621 (1432)
.+. ... ....+|.......+....+..+|+.||++++.||.|+|+.|+ |++|||+.||+|+++|+++.++|+
T Consensus 109 --~~~-~~~-~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~----s~~EIA~~lgis~~tV~~~l~ra~ 180 (194)
T PRK12513 109 --QLH-ALA-DDGAAPEQQLSLFRDRRRLQAALETLPDEQREVFLLREHGDL----ELEEIAELTGVPEETVKSRLRYAL 180 (194)
T ss_pred --hhh-hcC-CCCCCHHHHHHHHHHHHHHHHHHHhCCHhHhhheeeehccCC----CHHHHHHHHCCCHHHHHHHHHHHH
Confidence 000 000 112357777777778889999999999999999999998888 999999999999999999999999
Q ss_pred HHHHHHHH
Q psy15215 622 RKLRPLAH 629 (1432)
Q Consensus 622 ~kLr~~l~ 629 (1432)
++|+..+.
T Consensus 181 ~~Lr~~l~ 188 (194)
T PRK12513 181 QKLRELLA 188 (194)
T ss_pred HHHHHHHH
Confidence 99998875
No 115
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=99.78 E-value=3.4e-18 Score=186.01 Aligned_cols=176 Identities=16% Similarity=0.207 Sum_probs=143.6
Q ss_pred hhHHHHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHH
Q psy15215 1172 NDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 1251 (1432)
Q Consensus 1172 ~e~~~l~~~~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~i 1251 (1432)
.+...++..+..|+.. +++.++..|.++|+++|++++++..+++|++||+|+++|++.++|++.++ +|.||++.++
T Consensus 10 ~~~~~l~~~~~~~~~~---~~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~~~~~~~~~~~~~~-~~~~wl~~I~ 85 (187)
T PRK12534 10 DETGRLLTATAGGDRH---AFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFDPSRA-RGLTWLAMIA 85 (187)
T ss_pred chHHHHHHHHHcCCHH---HHHHHHHHhhHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccCCcccc-cHHHHHHHHH
Confidence 3456778888889887 99999999999999999999999999999999999999999999997654 6899999999
Q ss_pred HHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCC
Q psy15215 1252 RQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDE 1331 (1432)
Q Consensus 1252 r~~i~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~ 1331 (1432)
+|.+.+++|+..+..+. .+.+.
T Consensus 86 ~n~~~d~~R~~~~~~~~----------------------------------------------------~~~~~------ 107 (187)
T PRK12534 86 RNKAIDHLRANAPQRRN----------------------------------------------------VALDD------ 107 (187)
T ss_pred HHHHHHHHHhccccccc----------------------------------------------------ccccc------
Confidence 99999999876531000 00000
Q ss_pred CCCcCcccccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q psy15215 1332 DSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKAL 1411 (1432)
Q Consensus 1332 ~~~~~d~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl 1411 (1432)
...... ...+|.+.....+....+..+|..||++++.|+.++|..|+ |++|||+.||+|.++|+++++||+
T Consensus 108 ---~~~~~~--~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~----s~~eIA~~lgis~~~v~~~l~Rar 178 (187)
T PRK12534 108 ---AGELRA--ADASPLERTERASTRRRIDHCLAELEPPRSELIRTAFFEGI----TYEELAARTDTPIGTVKSWIRRGL 178 (187)
T ss_pred ---hhhhcc--ccCChhhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHhCCChhHHHHHHHHHH
Confidence 000000 01134555555677789999999999999999999998888 999999999999999999999999
Q ss_pred HHhhCch
Q psy15215 1412 RKLRHPS 1418 (1432)
Q Consensus 1412 ~kLr~~~ 1418 (1432)
++||+..
T Consensus 179 ~~Lr~~l 185 (187)
T PRK12534 179 AKLKACL 185 (187)
T ss_pred HHHHHHH
Confidence 9999854
No 116
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=99.78 E-value=5.5e-18 Score=186.95 Aligned_cols=179 Identities=13% Similarity=0.097 Sum_probs=140.0
Q ss_pred HHHHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHH
Q psy15215 1174 LRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 1253 (1432)
Q Consensus 1174 ~~~l~~~~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~ 1253 (1432)
...+...+.+|+.. |+..|+..|.+.|+++|.+++++..+++|++||+|+.+|+++++|++.++ .|.||+++++||
T Consensus 25 ~~~l~~~~~~~d~~---a~~~l~~~y~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~~-~~~~wl~~I~rn 100 (206)
T PRK12526 25 SQWLILVAISRDKQ---AFTHLFQFFAPKIKRFGIKQLGNEAQANELVQETMSNVWRKAHLYNGDKG-AATTWVYTVMRN 100 (206)
T ss_pred HHHHHHHHHcCCHH---HHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCccc-chhHHHHHHHHH
Confidence 44556667889888 99999999999999999999999899999999999999999999987655 699999999999
Q ss_pred HHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCC
Q psy15215 1254 AITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDS 1333 (1432)
Q Consensus 1254 ~i~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~ 1333 (1432)
.+.+++|++.+..... +. ++ ..
T Consensus 101 ~~~d~~Rk~~~~~~~~-----------------------------------------------------~~----~~-~~ 122 (206)
T PRK12526 101 AAFDMLRKIKAKKEQN-----------------------------------------------------LG----DD-IW 122 (206)
T ss_pred HHHHHHHHhccccccc-----------------------------------------------------cc----cc-cc
Confidence 9999999876521000 00 00 00
Q ss_pred CcCcccccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q psy15215 1334 HLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRK 1413 (1432)
Q Consensus 1334 ~~~d~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~k 1413 (1432)
...+.+.+. ...+. ..........|..+|++||++++.||.|+|+.|+ |++|||+.+|+|.++|+.+++||+++
T Consensus 123 ~~~~~~~~~-~~~~~-~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~g~----s~~EIA~~lgis~~tV~~~l~Ra~~~ 196 (206)
T PRK12526 123 PIEQALAES-QSESE-EFSDHLMDKQILSYIEKLPEAQQTVVKGVYFQEL----SQEQLAQQLNVPLGTVKSRLRLALAK 196 (206)
T ss_pred hhhhhcccc-cCchH-HHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 000001111 11222 2333344567999999999999999999999998 99999999999999999999999999
Q ss_pred hhCchhh
Q psy15215 1414 LRHPSRY 1420 (1432)
Q Consensus 1414 Lr~~~~~ 1420 (1432)
||.....
T Consensus 197 Lr~~l~~ 203 (206)
T PRK12526 197 LKVQMGE 203 (206)
T ss_pred HHHHHhh
Confidence 9986643
No 117
>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=99.77 E-value=6.6e-18 Score=180.71 Aligned_cols=169 Identities=18% Similarity=0.267 Sum_probs=141.9
Q ss_pred HHHHHHHhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHH
Q psy15215 387 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 466 (1432)
Q Consensus 387 l~~~i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~ 466 (1432)
|+.++++||.. |+..|+..|.+.+++++.++++...+++|++||+++.+|++.++|+...+ +|.+|++.+++|.+.
T Consensus 1 li~~~~~~d~~---a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~-~~~~wl~~i~~n~~~ 76 (170)
T TIGR02952 1 LLERAQDREED---AFARIYETYSDRVYRYIYYRVGCKYTAEDLTSEVFERVLRKIDSFKEQKN-SFEAWLFTIARNVVN 76 (170)
T ss_pred ChHHHHccCHH---HHHHHHHHHHHHHHHHHHHHHCChhhHHHHHHHHHHHHHHhHHhcccccc-cHHHHHHHHHHHHHH
Confidence 35678889988 99999999999999999999988899999999999999999999987555 899999999999999
Q ss_pred HHHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcC
Q psy15215 467 RSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLG 546 (1432)
Q Consensus 467 ~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~ 546 (1432)
+++|++.+....+ .+. ..
T Consensus 77 d~~R~~~~~~~~~-----------------------------------------------------~~~---------~~ 94 (170)
T TIGR02952 77 DYFRGSKRHPLFS-----------------------------------------------------LDV---------FK 94 (170)
T ss_pred HHHHhcCCCCCCc-----------------------------------------------------HHH---------Hh
Confidence 9999876521100 000 00
Q ss_pred cccccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHH
Q psy15215 547 DFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRP 626 (1432)
Q Consensus 547 ~~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~ 626 (1432)
.... ...+|++.+...+....+..+|..|||+++.||.|+|..|+ |++|||+.||+|.++|+++.+||+++|++
T Consensus 95 ~~~~--~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~g~----s~~eIA~~l~is~~tv~~~l~ra~~~Lr~ 168 (170)
T TIGR02952 95 ELLS--NEPNPEEAILKEEANEKLLKALKILTPKQQHVIALRFGQNL----PIAEVARILGKTEGAVKILQFRAIKKLAR 168 (170)
T ss_pred hcCC--CCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 0000 11256777777777889999999999999999999999888 99999999999999999999999999997
Q ss_pred H
Q psy15215 627 L 627 (1432)
Q Consensus 627 ~ 627 (1432)
.
T Consensus 169 ~ 169 (170)
T TIGR02952 169 Q 169 (170)
T ss_pred h
Confidence 5
No 118
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=99.77 E-value=6.3e-18 Score=183.72 Aligned_cols=180 Identities=17% Similarity=0.218 Sum_probs=141.9
Q ss_pred CChhhHHHHHHHHHHhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHH
Q psy15215 379 LPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 458 (1432)
Q Consensus 379 l~~~e~~~l~~~i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~ 458 (1432)
|.......++..++.||.. |+..++..|.+.|+.+|++|.+++.+++|++||+++++|++..+|++.. .+|.+|++
T Consensus 5 ~~~~~~~~l~~~~~~~d~~---a~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~~i~l~~~~~~~~~~~-~~~~~wl~ 80 (186)
T PRK13919 5 LESLSDEALLALVARGEEE---ALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKKAKEFDPRR-GSARAWLL 80 (186)
T ss_pred ccccCHHHHHHHHHcCcHH---HHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhhhccCccc-cchHHHHH
Confidence 4445567888999999988 9999999999999999999999999999999999999999999998654 37999999
Q ss_pred HHHHHHHHHHHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCC
Q psy15215 459 WWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVG 538 (1432)
Q Consensus 459 ~~ir~~i~~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~ 538 (1432)
+.++|.+.++++++.+..+ .++.+
T Consensus 81 ~ia~n~~~d~~rk~~~~~~----------------------------------------------------~~~~~---- 104 (186)
T PRK13919 81 ALAHHAAVDHVRRRAARPQ----------------------------------------------------PLEPD---- 104 (186)
T ss_pred HHHHHHHHHHHHhhhcccc----------------------------------------------------ccccc----
Confidence 9999999999988654100 00000
Q ss_pred CCCCCCcCcccccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHH
Q psy15215 539 DDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEA 618 (1432)
Q Consensus 539 ~~~~~~~~~~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~ 618 (1432)
.......+ .+ +|............+..+++.||++++.||.|+|..|+ |++|||+.+|+|+++|+.+.+
T Consensus 105 -~~~~~~~~-~~-----~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~~----s~~eIA~~lgis~~~V~~~l~ 173 (186)
T PRK13919 105 -EREPEAFD-LP-----GPGLDEEGHLDRTRLGRALKALSPEERRVIEVLYYQGY----THREAAQLLGLPLGTLKTRAR 173 (186)
T ss_pred -cccccccc-CC-----CccccHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHHCcCHHHHHHHHH
Confidence 00000000 00 11111122233567899999999999999999999888 999999999999999999999
Q ss_pred HHHHHHHHHHH
Q psy15215 619 KALRKLRPLAH 629 (1432)
Q Consensus 619 rAl~kLr~~l~ 629 (1432)
||+.+|+..+.
T Consensus 174 ra~~~Lr~~l~ 184 (186)
T PRK13919 174 RALSRLKEVLR 184 (186)
T ss_pred HHHHHHHHHhc
Confidence 99999998764
No 119
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=99.77 E-value=5.2e-18 Score=185.47 Aligned_cols=182 Identities=16% Similarity=0.141 Sum_probs=142.2
Q ss_pred hhHHHHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHH
Q psy15215 1172 NDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 1251 (1432)
Q Consensus 1172 ~e~~~l~~~~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~i 1251 (1432)
.++..++.++..|+.. |++.|+..|.+.|+.+|.+++++...++|++||+|+.+|++.++|++..+ +|.||++.++
T Consensus 12 ~~~~~li~~~~~~d~~---af~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQev~l~l~~~~~~~~~~~~-~~~~wL~~ia 87 (194)
T PRK12531 12 QEWLECMEKVKSRDKQ---AFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKAHLFDGQKS-ALSTWIYTII 87 (194)
T ss_pred HhHHHHHHHHHcCCHH---HHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCcccc-hHHHHHHHHH
Confidence 4567788889999888 99999999999999999999999899999999999999999999997544 7999999999
Q ss_pred HHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCC
Q psy15215 1252 RQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDE 1331 (1432)
Q Consensus 1252 r~~i~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~ 1331 (1432)
+|.+.+++|++.+..... +.+....++
T Consensus 88 rn~~ld~~Rk~~~~~~~~----------------------------------------------------~~~~~~~~~- 114 (194)
T PRK12531 88 RNLCFDLLRKQKGKDLHI----------------------------------------------------HADDIWPSD- 114 (194)
T ss_pred HHHHHHHHHHhccccccc----------------------------------------------------chhhccccc-
Confidence 999999999876410000 000000000
Q ss_pred CCCcCcccccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q psy15215 1332 DSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKAL 1411 (1432)
Q Consensus 1332 ~~~~~d~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl 1411 (1432)
.....+.+ ...|+.. .....+..++++||++++.||.|+|..|+ |++|||+.||+|.++|+.++++|+
T Consensus 115 --~~~~~~~~--~~~~e~~----~~~~~l~~~l~~Lp~~~r~v~~l~~~eg~----s~~EIA~~lgis~~tVk~rl~ra~ 182 (194)
T PRK12531 115 --YYPPDLVD--HYSPEQD----MLKEQVMKFLDRLPKAQRDVLQAVYLEEL----PHQQVAEMFDIPLGTVKSRLRLAV 182 (194)
T ss_pred --cccccccc--ccCHHHH----HHHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHhCcCHHHHHHHHHHHH
Confidence 00000000 1123322 23456888999999999999999999998 999999999999999999999999
Q ss_pred HHhhCchhhhh
Q psy15215 1412 RKLRHPSRYYK 1422 (1432)
Q Consensus 1412 ~kLr~~~~~~~ 1422 (1432)
++||+......
T Consensus 183 ~~Lr~~l~~~~ 193 (194)
T PRK12531 183 EKLRHSMDAES 193 (194)
T ss_pred HHHHHHhhhcc
Confidence 99999766543
No 120
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=99.77 E-value=9.7e-18 Score=182.92 Aligned_cols=173 Identities=12% Similarity=0.114 Sum_probs=142.5
Q ss_pred ChhhHHHHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHH
Q psy15215 1170 PLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 1249 (1432)
Q Consensus 1170 ~~~e~~~l~~~~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~ 1249 (1432)
.......++..+..|+.. ++..++..|.+.|+++|.+++++..+++|++||+|+.+|++.++|++.. +|.+|++.
T Consensus 10 ~~~~~~~l~~~~~~gd~~---~~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQEvfl~l~~~~~~~~~~~--~f~~wL~~ 84 (192)
T PRK09643 10 GERSDAELLAAHVAGDRY---AFGELFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHRAAGSFRGDA--AVSSWLHR 84 (192)
T ss_pred CCcCHHHHHHHHHCcCHH---HHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCCCC--ccHHHHHH
Confidence 334457788899999888 9999999999999999999999999999999999999999999999653 69999999
Q ss_pred HHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCC
Q psy15215 1250 WIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGD 1329 (1432)
Q Consensus 1250 ~ir~~i~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~ 1329 (1432)
+++|.+.+++|+..+..+. +++ +
T Consensus 85 i~rn~~~d~~Rk~~~~~~~-----------------------------------------------------~~~----~ 107 (192)
T PRK09643 85 IVVNACLDRLRRAKARPTV-----------------------------------------------------PLD----D 107 (192)
T ss_pred HHHHHHHHHHHccccCCCC-----------------------------------------------------Ccc----c
Confidence 9999999999986541100 000 0
Q ss_pred CCCCCcCcccccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q psy15215 1330 DEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409 (1432)
Q Consensus 1330 ~~~~~~~d~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~r 1409 (1432)
... .. .+|.+.+...+....+..+|..||+++|.|+.|+|..|+ |++|||+.||+|..+|+++++|
T Consensus 108 ~~~------~~----~~~~~~~~~~e~~~~l~~~l~~Lp~~~r~i~~l~~~~g~----s~~EIA~~lg~s~~tV~~rl~r 173 (192)
T PRK09643 108 VYP------VA----QLERDPTARVETALAVQRALMRLPVEQRAALVAVDMQGY----SVADAARMLGVAEGTVKSRCAR 173 (192)
T ss_pred ccc------cc----CCcccHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHHCcCHHHHHHHHHH
Confidence 000 00 012233444556778999999999999999999999888 9999999999999999999999
Q ss_pred HHHHhhCch
Q psy15215 1410 ALRKLRHPS 1418 (1432)
Q Consensus 1410 Al~kLr~~~ 1418 (1432)
|+++||...
T Consensus 174 ar~~Lr~~l 182 (192)
T PRK09643 174 GRARLAELL 182 (192)
T ss_pred HHHHHHHHH
Confidence 999999944
No 121
>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=99.77 E-value=9.3e-18 Score=182.87 Aligned_cols=180 Identities=17% Similarity=0.217 Sum_probs=139.6
Q ss_pred hhhhhhhhhHHHHHHHHHHHHHHHHHhccC----CCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHHH
Q psy15215 1183 AGEMKARKAKREMTEANLRLVISIAKKYTD----RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRS 1258 (1432)
Q Consensus 1183 ~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~----~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~~ 1258 (1432)
.|+.. |+..|+..|.+.|+++|++|+. +..+++|++||+|+.+|+++.+|+...+.+|.+|++..++|.+.++
T Consensus 3 ~~~~~---a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~~~~~~wl~~i~~n~~~d~ 79 (189)
T TIGR02984 3 GGDQE---ALGELLDRYRNYLRLLARVQLDPRLRRRVDPSDLVQETLLEAHRRFDQFRGKTEGEFAGWLRGILSNVLADA 79 (189)
T ss_pred CCCHH---HHHHHHHHHHHHHHHHHHHHhhhhcCCccCHHHHHHHHHHHHHHHHHhccCcccchHHHHHHHHHHHHHHHH
Confidence 56666 9999999999999999999753 5678999999999999999999987655689999999999999999
Q ss_pred HHHhcc-cccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCC-CCcC
Q psy15215 1259 IADQAR-TIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDED-SHLG 1336 (1432)
Q Consensus 1259 i~~~~r-~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~-~~~~ 1336 (1432)
++++.+ .-|.+ ....+++.+.+.++. ..+.
T Consensus 80 ~r~~~~~~~r~~------------------------------------------------~~~~~~~~~~~~~~~~~~~~ 111 (189)
T TIGR02984 80 LRRHLGAQKRDI------------------------------------------------RREQSLDAGGRLDESSVRLA 111 (189)
T ss_pred HHHHHHHHhhhc------------------------------------------------ccccCCCcccccCCcchhHH
Confidence 997631 00000 001222222111111 1122
Q ss_pred cccccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhC
Q psy15215 1337 DFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 1416 (1432)
Q Consensus 1337 d~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~ 1416 (1432)
+.+.+ ...+|++.....+....|..+|..|||+++.||.++|+.|+ |++|||+.||+|+++|++.++||+++||+
T Consensus 112 ~~~~~-~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~vi~l~~~~g~----s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~ 186 (189)
T TIGR02984 112 AQLAA-DGPSPSQVAARREAAVRLAQALAKLPEDYREVILLRHLEGL----SFAEVAERMDRSEGAVSMLWVRGLARLRQ 186 (189)
T ss_pred HHccC-CCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHhcCC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 22222 23467777777777889999999999999999999999888 99999999999999999999999999997
Q ss_pred ch
Q psy15215 1417 PS 1418 (1432)
Q Consensus 1417 ~~ 1418 (1432)
.+
T Consensus 187 ~l 188 (189)
T TIGR02984 187 IL 188 (189)
T ss_pred Hh
Confidence 43
No 122
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=99.77 E-value=1.2e-17 Score=180.20 Aligned_cols=176 Identities=14% Similarity=0.198 Sum_probs=145.3
Q ss_pred hhhHHHHHHHHHHhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHH
Q psy15215 381 LNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 460 (1432)
Q Consensus 381 ~~e~~~l~~~i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ 460 (1432)
+.+...++..+..|+.. |+..++..|.+.|+++|.+++++..+++|++||+|+++|+++++|++.. .+|.||++..
T Consensus 3 ~~~~~~li~~~~~g~~~---a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~fl~~~~~~~~~~~~~-~~~~~wl~~i 78 (179)
T PRK12514 3 PDDIEKLIVRVSLGDRD---AFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAVSG-LSPMTWLITI 78 (179)
T ss_pred chHHHHHHHHHHcCCHH---HHHHHHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHHHhHHhcCccc-ccHHHHHHHH
Confidence 35567788899999988 9999999999999999999999999999999999999999999998643 4799999999
Q ss_pred HHHHHHHHHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCC
Q psy15215 461 IRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDD 540 (1432)
Q Consensus 461 ir~~i~~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~ 540 (1432)
++|.+.+++|++.+. ..+ .+.
T Consensus 79 a~n~~~d~~R~~~~~-~~~-----------------------------------------------------~~~----- 99 (179)
T PRK12514 79 ARNHAIDRLRARKAV-AVD-----------------------------------------------------IDE----- 99 (179)
T ss_pred HHHHHHHHHHhcCCc-ccc-----------------------------------------------------ccc-----
Confidence 999999999876531 000 000
Q ss_pred CCCCcCcccccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHH
Q psy15215 541 EDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 620 (1432)
Q Consensus 541 ~~~~~~~~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rA 620 (1432)
..+. .+ ...+|++.+...+....+..+|..||++++.||.++|+.|+ |++|||+.||+|..+|+++.+||
T Consensus 100 ----~~~~-~~-~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~----s~~eIA~~lgis~~tV~~~l~Ra 169 (179)
T PRK12514 100 ----AHDL-AD-PSPGPEAEVIAGDEGQRIDACLEELEKDRAAAVRRAYLEGL----SYKELAERHDVPLNTMRTWLRRS 169 (179)
T ss_pred ----chhc-cc-cCCCHHHHHHhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHHCCChHHHHHHHHHH
Confidence 0000 00 11246666655555667999999999999999999999888 99999999999999999999999
Q ss_pred HHHHHHHHH
Q psy15215 621 LRKLRPLAH 629 (1432)
Q Consensus 621 l~kLr~~l~ 629 (1432)
+++|++++.
T Consensus 170 r~~Lr~~l~ 178 (179)
T PRK12514 170 LLKLRECLS 178 (179)
T ss_pred HHHHHHHhc
Confidence 999998763
No 123
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=99.77 E-value=1.5e-17 Score=182.26 Aligned_cols=176 Identities=15% Similarity=0.188 Sum_probs=147.1
Q ss_pred hhHHHHHHHHHHhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHH
Q psy15215 382 NDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 461 (1432)
Q Consensus 382 ~e~~~l~~~i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~i 461 (1432)
.+...++.++..||.. |+..|+..|.+.|+.+|.+++++..+++|++||+++++|+...+|++.. .+|.||++..+
T Consensus 11 ~~~~~li~~~~~gd~~---a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~~-~~~~~wl~~ia 86 (196)
T PRK12524 11 VSDEALLVLYANGDPA---AARALTLRLAPRALAVATRVLGDRAEAEDVTQEAMLRLWRIAPDWRQGE-ARVSTWLYRVV 86 (196)
T ss_pred cCHHHHHHHHHCCCHH---HHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhcccccc-chHHHHHHHHH
Confidence 3456889999999988 9999999999999999999999999999999999999999999998533 47999999999
Q ss_pred HHHHHHHHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCC
Q psy15215 462 RQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDE 541 (1432)
Q Consensus 462 r~~i~~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~ 541 (1432)
++.+.+++|++.+. . ..++. ..+
T Consensus 87 ~n~~~d~~Rk~~~~-~-----------------------------------------------------~~~~~-~~~-- 109 (196)
T PRK12524 87 CNLCTDRLRRRRRA-S-----------------------------------------------------VDLDD-APE-- 109 (196)
T ss_pred HHHHHHHHHhhcCC-C-----------------------------------------------------CCccc-ccc--
Confidence 99999999876541 0 00000 000
Q ss_pred CCCcCcccccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHH
Q psy15215 542 DSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKAL 621 (1432)
Q Consensus 542 ~~~~~~~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl 621 (1432)
..+ ...+|++.+...+....|..+|+.||++++.||.|+|..|+ |++|||+.||+|+++|+++.+||+
T Consensus 110 -------~~~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~L~~~~g~----s~~eIA~~lgis~~tV~~~l~Ra~ 177 (196)
T PRK12524 110 -------PAD-AAPGAEEALIEGDRMRALDAALAALPERQRQAVVLRHIEGL----SNPEIAEVMEIGVEAVESLTARGK 177 (196)
T ss_pred -------ccc-cCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHHCcCHHHHHHHHHHHH
Confidence 001 11246666777777888999999999999999999999888 999999999999999999999999
Q ss_pred HHHHHHHHH
Q psy15215 622 RKLRPLAHD 630 (1432)
Q Consensus 622 ~kLr~~l~~ 630 (1432)
++|+..+..
T Consensus 178 ~~Lr~~l~~ 186 (196)
T PRK12524 178 RALAALLAG 186 (196)
T ss_pred HHHHHHHHh
Confidence 999988753
No 124
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=99.77 E-value=1.3e-17 Score=179.76 Aligned_cols=174 Identities=14% Similarity=0.120 Sum_probs=145.5
Q ss_pred HHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHH
Q psy15215 1176 DINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 1255 (1432)
Q Consensus 1176 ~l~~~~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i 1255 (1432)
.+...+..|+.. |+..+++.|.+.|+++|++++++..+++|++||++++||++.++|+ .+.+|.+|++.++++.+
T Consensus 2 ~~~~~~~~~~~~---a~~~l~~~y~~~l~~~~~~~~~~~~~aeDl~qe~~~~l~~~~~~~~--~~~~~~~~l~~i~~~~~ 76 (179)
T PRK11924 2 QLMPVDATGDKE---AFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFN--GKGSARTWLLTIARNVC 76 (179)
T ss_pred hHHHHHHccCHH---HHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHhhcC--CcchHHHHHHHHHHHHH
Confidence 356677889888 9999999999999999999999999999999999999999999998 34589999999999999
Q ss_pred HHHHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCc
Q psy15215 1256 TRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHL 1335 (1432)
Q Consensus 1256 ~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~ 1335 (1432)
.+++++..+..+. +.. +..+
T Consensus 77 ~d~~r~~~~~~~~-----------------------------------------------------~~~-~~~~------ 96 (179)
T PRK11924 77 YDLLRRRRREKAV-----------------------------------------------------LSD-DALE------ 96 (179)
T ss_pred HHHHHhccccccc-----------------------------------------------------Ccc-cccc------
Confidence 9999876641100 000 0000
Q ss_pred CcccccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhh
Q psy15215 1336 GDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 1415 (1432)
Q Consensus 1336 ~d~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr 1415 (1432)
...+....+|++.+...+....+..+|..|||+++.|+.++|..|+ |.+|||+.||+|+.+|++++++|+++||
T Consensus 97 --~~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~~~----~~~eIA~~lgis~~tv~~~~~ra~~~lr 170 (179)
T PRK11924 97 --PEFAETAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGL----SYREIAEILGVPVGTVKSRLRRARQLLR 170 (179)
T ss_pred --cccCCccCCHHHHHhhHHHHHHHHHHHHhCCHHHHHHhhHHHHcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 0000023478888888889999999999999999999999998888 9999999999999999999999999999
Q ss_pred Cchhh
Q psy15215 1416 HPSRY 1420 (1432)
Q Consensus 1416 ~~~~~ 1420 (1432)
+....
T Consensus 171 ~~l~~ 175 (179)
T PRK11924 171 ECLEA 175 (179)
T ss_pred HHHHH
Confidence 86554
No 125
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=99.77 E-value=4.2e-18 Score=185.32 Aligned_cols=170 Identities=18% Similarity=0.236 Sum_probs=134.2
Q ss_pred HHHHHHHHHh---hhhhhhhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHH
Q psy15215 1174 LRDINRKMIA---GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 1250 (1432)
Q Consensus 1174 ~~~l~~~~~~---g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ 1250 (1432)
...++..++. |+.. |+..|+..|.+.|+++|.+|+++..+++|++||+|+.+|+++++|++. .+|+||++.+
T Consensus 10 ~~~li~~~~~~~~gd~~---a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~f~~l~~~~~~~~~~--~~~~~wl~~i 84 (188)
T PRK09640 10 DEELVARVHVELFHVTR---AYEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGK--SKFKTWLYSI 84 (188)
T ss_pred HHHHHHHHhcccCCCHH---HHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHHHhcCC--CcchHHHHHH
Confidence 4456667764 5666 999999999999999999999999999999999999999999999853 4799999999
Q ss_pred HHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCC
Q psy15215 1251 IRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDD 1330 (1432)
Q Consensus 1251 ir~~i~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~ 1330 (1432)
++|.+.+++|+..+..... .+...
T Consensus 85 a~n~~~d~~R~~~~~~~~~-----------------------------------------------------~~~~~--- 108 (188)
T PRK09640 85 TYNECITQYRKERRKRRLM-----------------------------------------------------DALSL--- 108 (188)
T ss_pred HHHHHHHHHHHhcccccCc-----------------------------------------------------chhhh---
Confidence 9999999999765411000 00000
Q ss_pred CCCCcCcccccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q psy15215 1331 EDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 1410 (1432)
Q Consensus 1331 ~~~~~~d~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rA 1410 (1432)
+...+.. .+.....+....|.++|+.||+++|.||.|+|..|+ |++|||+.||+|.++|+.+++||
T Consensus 109 ------~~~~~~~----~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~----s~~EIA~~lgis~~tV~~~l~Ra 174 (188)
T PRK09640 109 ------DPLEEAS----EEKAPKPEERGGLDRWLVHVNPIDREILVLRFVAEL----EFQEIADIMHMGLSATKMRYKRA 174 (188)
T ss_pred ------ccccccc----ccccccHHHHHHHHHHHHhcChhheeeeeeHHhcCC----CHHHHHHHHCCCHHHHHHHHHHH
Confidence 0000000 001112234567999999999999999999999888 99999999999999999999999
Q ss_pred HHHhhCch
Q psy15215 1411 LRKLRHPS 1418 (1432)
Q Consensus 1411 l~kLr~~~ 1418 (1432)
+++||...
T Consensus 175 ~~~Lr~~l 182 (188)
T PRK09640 175 LDKLREKF 182 (188)
T ss_pred HHHHHHHH
Confidence 99999943
No 126
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=99.76 E-value=1.3e-17 Score=187.25 Aligned_cols=190 Identities=16% Similarity=0.204 Sum_probs=155.0
Q ss_pred cCCChhhHHHHHHHHHHhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHH
Q psy15215 377 IVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 456 (1432)
Q Consensus 377 ~~l~~~e~~~l~~~i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fsty 456 (1432)
.+++......++.++..|+.. |+..++..|.+.|+++|.+++..+.+++||+||+|+++|+++++|++. .+|.+|
T Consensus 10 ~~~~~~~~~~l~~~~~~gd~~---a~~~l~~~y~~~l~~~a~~~~~~~~~AEDlvQE~fi~l~~~~~~~~~~--~~~~~w 84 (231)
T PRK11922 10 PPLSAASDRELVARVLAGDEA---AFEALMRRHNRRLYRTARAILRNDAEAEDVVQEAYLRAFRALGTFRGD--ASLSTW 84 (231)
T ss_pred CCcCcccHHHHHHHHHcCCHH---HHHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHhcCCC--chhHHH
Confidence 456667778899999999998 999999999999999999999999999999999999999999999875 479999
Q ss_pred HHHHHHHHHHHHHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCC
Q psy15215 457 ATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESP 536 (1432)
Q Consensus 457 a~~~ir~~i~~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~ 536 (1432)
++..++|.+.+++|++.+..+.+.. . +..
T Consensus 85 L~~iarn~~~d~~Rk~~r~~~~~~~--------------------------------------------------~-~~~ 113 (231)
T PRK11922 85 LSRIVLNEALGRLRRRRRLVNLAEM--------------------------------------------------V-MAS 113 (231)
T ss_pred HHHHHHHHHHHHHHhhcccccchhc--------------------------------------------------c-ccc
Confidence 9999999999999987763211000 0 000
Q ss_pred CCCCCCCCcCcccccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHH
Q psy15215 537 VGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQI 616 (1432)
Q Consensus 537 ~~~~~~~~~~~~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~ 616 (1432)
...+ + ..... .....+|++.+...+..+.+..+|+.||++++.||.|+|..|+ |++|||+.||+|.++|+++
T Consensus 114 ~~~~-~--~~~~~-~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~----s~~EIAe~lgis~~tVk~~ 185 (231)
T PRK11922 114 TIAG-G--ERTPL-ADPAEDPERAAARREIRALLERAIDALPDAFRAVFVLRVVEEL----SVEETAQALGLPEETVKTR 185 (231)
T ss_pred cccc-c--ccccc-CcccCChHHHHHHHHHHHHHHHHHHhCCHHHhhhheeehhcCC----CHHHHHHHHCcCHHHHHHH
Confidence 0000 0 00000 1123467788888888889999999999999999999998888 9999999999999999999
Q ss_pred HHHHHHHHHHHHHH
Q psy15215 617 EAKALRKLRPLAHD 630 (1432)
Q Consensus 617 ~~rAl~kLr~~l~~ 630 (1432)
.++|+.+||+.+..
T Consensus 186 l~Rar~kLr~~l~~ 199 (231)
T PRK11922 186 LHRARRLLRESLAR 199 (231)
T ss_pred HHHHHHHHHHHHHH
Confidence 99999999998864
No 127
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=99.76 E-value=1.7e-17 Score=185.59 Aligned_cols=173 Identities=12% Similarity=0.180 Sum_probs=143.9
Q ss_pred HHHHHHHHHHhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHH
Q psy15215 384 LRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 463 (1432)
Q Consensus 384 ~~~l~~~i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~ 463 (1432)
...|+..++.||.. |+..|+..|.+.|++++.+++++..+++|++||+|+.+|++.++|++..+ +|.+|++..++|
T Consensus 50 d~~Li~~~~~gd~~---af~~L~~~y~~~l~~~~~~~~~d~~dAEDivQEvfl~l~~~~~~~~~~~~-~f~~WL~~IarN 125 (233)
T PRK12538 50 DEELLDRLATDDEA---AFRLLVERHIDRAYAIALRIVGNRADAEDVVQDTMLKVWTHRGRWQHGRA-KFSTWLYRVVSN 125 (233)
T ss_pred HHHHHHHHHhCCHH---HHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHcccccc-cHHHHHHHHHHH
Confidence 45678889999988 99999999999999999999999999999999999999999999986444 799999999999
Q ss_pred HHHHHHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCC
Q psy15215 464 AITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDS 543 (1432)
Q Consensus 464 ~i~~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~ 543 (1432)
.+.+++|++.+. .+ ..+. +.
T Consensus 126 ~~id~~Rk~~~~-~~----------------------------------------------------~~~~----~~--- 145 (233)
T PRK12538 126 RCIDLRRKPRTE-NV----------------------------------------------------DAVP----EV--- 145 (233)
T ss_pred HHHHHHHhhccc-cc----------------------------------------------------cccc----cc---
Confidence 999999865320 00 0000 00
Q ss_pred CcCcccccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHH
Q psy15215 544 HLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRK 623 (1432)
Q Consensus 544 ~~~~~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~k 623 (1432)
. + ...++.+.+...+....+..+|..||+++|.||.|+|..|+ |++|||+.||+|.++|+++.+||+++
T Consensus 146 -----~-~-~~~~~~~~~~~~e~~~~l~~~L~~Lp~~~R~v~~L~~~eg~----s~~EIA~~Lgis~~tVk~~l~RAr~k 214 (233)
T PRK12538 146 -----A-D-GKPDAVSVIERNELSDLLEAAMQRLPEQQRIAVILSYHENM----SNGEIAEVMDTTVAAVESLLKRGRQQ 214 (233)
T ss_pred -----c-c-CCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHHhcCC----CHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 0 0 01234555566667778999999999999999999999999 99999999999999999999999999
Q ss_pred HHHHHHHH
Q psy15215 624 LRPLAHDW 631 (1432)
Q Consensus 624 Lr~~l~~~ 631 (1432)
|++.+...
T Consensus 215 Lr~~l~~~ 222 (233)
T PRK12538 215 LRDLLRRH 222 (233)
T ss_pred HHHHHHHh
Confidence 99988644
No 128
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=99.76 E-value=1.9e-17 Score=180.42 Aligned_cols=174 Identities=17% Similarity=0.208 Sum_probs=145.3
Q ss_pred HHHHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHH
Q psy15215 1174 LRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 1253 (1432)
Q Consensus 1174 ~~~l~~~~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~ 1253 (1432)
...++..++.|+.. |++.|+..|.+.|+.++.+++++..+++|++||+|+.+|++..+|++. .+|.||++..+++
T Consensus 9 ~~~l~~~~~~gd~~---a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~l~~~~~~~~~~--~~~~~wl~~i~~n 83 (189)
T PRK12515 9 DEMLLARIAQGDRT---AMQTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEGR--SQVSTWLLSIARF 83 (189)
T ss_pred HHHHHHHHHccCHH---HHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCC--CChHHHHHHHHHH
Confidence 45678888899888 999999999999999999999999999999999999999999999964 3799999999999
Q ss_pred HHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCC
Q psy15215 1254 AITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDS 1333 (1432)
Q Consensus 1254 ~i~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~ 1333 (1432)
.+.+++++..+. .+ + .+.
T Consensus 84 ~~~d~~r~~~~~-~~-----------------------------------------------------~------~~~-- 101 (189)
T PRK12515 84 KALSALRRRKHE-EI-----------------------------------------------------D------DEA-- 101 (189)
T ss_pred HHHHHHHccCCC-CC-----------------------------------------------------c------ccc--
Confidence 999999865431 00 0 000
Q ss_pred CcCcccccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q psy15215 1334 HLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRK 1413 (1432)
Q Consensus 1334 ~~~d~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~k 1413 (1432)
. ..+.+ ...+|+......+....+..+|+.||+++|.||.|+|..|+ |++|||+.||+|.++|+++++||+++
T Consensus 102 -~-~~~~~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~~----s~~eIA~~lgis~~tV~~~l~Rar~~ 174 (189)
T PRK12515 102 -A-AAIED-GADTPEVALQKSDTSAALRACLAKLSPAHREIIDLVYYHEK----SVEEVGEIVGIPESTVKTRMFYARKK 174 (189)
T ss_pred -c-cccCC-CCCCHHHHHHhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 0 00111 12356666666777888999999999999999999999998 99999999999999999999999999
Q ss_pred hhCchhhh
Q psy15215 1414 LRHPSRYY 1421 (1432)
Q Consensus 1414 Lr~~~~~~ 1421 (1432)
||+.....
T Consensus 175 Lr~~l~~~ 182 (189)
T PRK12515 175 LAELLKAA 182 (189)
T ss_pred HHHHHHHh
Confidence 99966544
No 129
>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=99.76 E-value=2.1e-17 Score=180.27 Aligned_cols=182 Identities=15% Similarity=0.179 Sum_probs=147.0
Q ss_pred HHHHHHHHHHhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHH
Q psy15215 384 LRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 463 (1432)
Q Consensus 384 ~~~l~~~i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~ 463 (1432)
...++..+..||.. |+..|+..|.+.|+.+|+++++...+++||+||+++++|+++++|++. .+|.+|++..++|
T Consensus 7 d~~l~~~~~~gd~~---a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~--~~~~~wl~~iarn 81 (190)
T TIGR02939 7 DLELVERVQRGEKQ---AFDLLVRKYQHKVVALVGRYVRDSSEVEDVAQEAFVKAYRALSSFRGD--SAFYTWLYRIAVN 81 (190)
T ss_pred HHHHHHHHHcCCHH---HHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCC--CccHhHHHHHHHH
Confidence 35678888999988 999999999999999999999999999999999999999999999864 4799999999999
Q ss_pred HHHHHHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCC
Q psy15215 464 AITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDS 543 (1432)
Q Consensus 464 ~i~~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~ 543 (1432)
.+.+++++..+..... ..+.+.. ....+
T Consensus 82 ~~~~~~r~~~r~~~~~--------------------------------------------------~~~~~~~-~~~~~- 109 (190)
T TIGR02939 82 TAKNHLVAQGRRPPTS--------------------------------------------------DVEIEDA-EHFEG- 109 (190)
T ss_pred HHHHHHHHhccCCCcc--------------------------------------------------cccccch-hhhcc-
Confidence 9999998765421100 0000000 00000
Q ss_pred CcCcccccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHH
Q psy15215 544 HLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRK 623 (1432)
Q Consensus 544 ~~~~~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~k 623 (1432)
...+. ...+|++.+...+....+..+|..||++++.||.|+|..|+ |++|||+.||+|.++|+++.++|+++
T Consensus 110 --~~~~~--~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~~~----s~~EIA~~lgis~~tv~~~l~rar~~ 181 (190)
T TIGR02939 110 --ADRLR--EIDTPERLLLSRELEQTVMRAVEALPEDLRTAITLRELEGL----SYEDIARIMDCPVGTVRSRIFRAREA 181 (190)
T ss_pred --ccccc--ccCChHHHHHHHHHHHHHHHHHHcCCHHHhhhhhhhhhcCC----CHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 00000 12357777777778888999999999999999999999888 99999999999999999999999999
Q ss_pred HHHHHHH
Q psy15215 624 LRPLAHD 630 (1432)
Q Consensus 624 Lr~~l~~ 630 (1432)
|++.+..
T Consensus 182 Lr~~l~~ 188 (190)
T TIGR02939 182 IAIRLRP 188 (190)
T ss_pred HHHHhhc
Confidence 9998864
No 130
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=99.76 E-value=2.2e-17 Score=179.83 Aligned_cols=170 Identities=14% Similarity=0.189 Sum_probs=142.6
Q ss_pred HHHHHHHHHhHHHHHHhHHHHHHHHHHHHHHHHHhcccCC---CChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHH
Q psy15215 385 RDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRG---LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 461 (1432)
Q Consensus 385 ~~l~~~i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~---~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~i 461 (1432)
..|+.+++.|+.. |+..++..|.+.|+++|.++++++ .+++|++||+++++|+++++|++..+ +|.||++..+
T Consensus 6 ~~li~~~~~gd~~---a~~~l~~~y~~~l~~~~~~~~~~~~~~~daeDi~Qe~~i~l~~~~~~~~~~~~-~~~~wl~~ia 81 (189)
T PRK06811 6 DNFIKELKKKNEK---ALEFIVDTYGNLVKKIVHKVLGTVNYSQLIEECVNDIFLSIWNNIDKFDEEKG-SFKKWIAAIS 81 (189)
T ss_pred HHHHHHHHccCHH---HHHHHHHHHHHHHHHHHHHHHcccCchhHHHHHHHHHHHHHHHhHHHhccccc-cHHHHHHHHH
Confidence 5788999999988 999999999999999999998853 47999999999999999999987544 8999999999
Q ss_pred HHHHHHHHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCC
Q psy15215 462 RQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDE 541 (1432)
Q Consensus 462 r~~i~~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~ 541 (1432)
+|.+.++++++.+.... .+.+..
T Consensus 82 rn~~~d~~rk~~~~~~~----------------------------------------------------~~~~~~----- 104 (189)
T PRK06811 82 KYKAIDYKRKLTKNNEI----------------------------------------------------DSIDEF----- 104 (189)
T ss_pred HHHHHHHHHHhcccccc----------------------------------------------------ccchhh-----
Confidence 99999999987652100 000000
Q ss_pred CCCcCcccccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHH
Q psy15215 542 DSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKAL 621 (1432)
Q Consensus 542 ~~~~~~~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl 621 (1432)
. . ....+|++.....+....+..+|..|||+++.||.|+|..|+ |++|||+.||+|..+|+++.+||+
T Consensus 105 -~-----~--~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~----s~~EIAe~lgis~~~V~~~l~Ra~ 172 (189)
T PRK06811 105 -I-----L--ISEESIENEIILKENKEEILKLINDLEKLDREIFIRRYLLGE----KIEEIAKKLGLTRSAIDNRLSRGR 172 (189)
T ss_pred -h-----h--cccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHccC----CHHHHHHHHCCCHHHHHHHHHHHH
Confidence 0 0 011356677777777888999999999999999999999888 999999999999999999999999
Q ss_pred HHHHHH
Q psy15215 622 RKLRPL 627 (1432)
Q Consensus 622 ~kLr~~ 627 (1432)
++|+..
T Consensus 173 ~~Lr~~ 178 (189)
T PRK06811 173 KKLQKN 178 (189)
T ss_pred HHHHHc
Confidence 999864
No 131
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=99.75 E-value=2.4e-17 Score=178.34 Aligned_cols=174 Identities=11% Similarity=0.144 Sum_probs=143.2
Q ss_pred hhHHHHHHHHHHhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHH
Q psy15215 382 NDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 461 (1432)
Q Consensus 382 ~e~~~l~~~i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~i 461 (1432)
.+...++..++.|+.. |+..|+..|.+.|+.+|.+++++..+++|++||+|+.+|+..++|++.. .+|.+|++..+
T Consensus 8 ~~~~~l~~~~~~~d~~---a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~-~~~~~wL~~ia 83 (182)
T PRK12537 8 FDYEACLLACARGDRR---ALQALYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTGAASFDPAR-GSARGWIYSVT 83 (182)
T ss_pred hhHHHHHHHHHcCCHH---HHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhccccCCccc-ccHHHHHHHHH
Confidence 3456789999999988 9999999999999999999999999999999999999999999998643 37999999999
Q ss_pred HHHHHHHHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCC
Q psy15215 462 RQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDE 541 (1432)
Q Consensus 462 r~~i~~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~ 541 (1432)
+|.+.++++++.+...+ ... ..
T Consensus 84 rn~~~d~~r~~~~~~~~-------------------------------------------------------~~~---~~ 105 (182)
T PRK12537 84 RHLALNVLRDTRREVVL-------------------------------------------------------DDD---AE 105 (182)
T ss_pred HHHHHHHHHhccccCcc-------------------------------------------------------ccc---hh
Confidence 99999999987642100 000 00
Q ss_pred CCCcCcccccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHH
Q psy15215 542 DSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKAL 621 (1432)
Q Consensus 542 ~~~~~~~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl 621 (1432)
+... ...++.+..........+..+|++|||+++.|+.|+|..|+ |++|||+.||+|.++|+.+.+||+
T Consensus 106 -----~~~~--~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~~~----s~~eIA~~lgis~~tV~~~l~ra~ 174 (182)
T PRK12537 106 -----ETAQ--TLHEIIDDFDLWANSGKIHRCLEQLEPARRNCILHAYVDGC----SHAEIAQRLGAPLGTVKAWIKRSL 174 (182)
T ss_pred -----hhcc--cccchHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHHCCChhhHHHHHHHHH
Confidence 0000 01123344444455678999999999999999999999999 999999999999999999999999
Q ss_pred HHHHHHH
Q psy15215 622 RKLRPLA 628 (1432)
Q Consensus 622 ~kLr~~l 628 (1432)
++|+..+
T Consensus 175 ~~Lr~~l 181 (182)
T PRK12537 175 KALRECM 181 (182)
T ss_pred HHHHHHh
Confidence 9999875
No 132
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=99.75 E-value=1.8e-17 Score=178.80 Aligned_cols=167 Identities=17% Similarity=0.262 Sum_probs=136.0
Q ss_pred HhhhhhhhhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHHHHHH
Q psy15215 1182 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIAD 1261 (1432)
Q Consensus 1182 ~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~~i~~ 1261 (1432)
..|+.. |+..++..|.+.|++++++|+++..+++|++||+|+.+|+++.+|++.. +|.+|++.+++|.+.+++++
T Consensus 2 ~~~d~~---af~~l~~~~~~~l~~~~~~~~~~~~daeDl~Qevfl~l~~~~~~~~~~~--~f~~wl~~iarn~~~~~~r~ 76 (179)
T PRK12543 2 LSGDQE---AFSEIYDVTIQEVYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKYDSNR--PFRFWLIGLVIKQIHSWRRK 76 (179)
T ss_pred cCchHH---HHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHcCCCC--ChHHHHHHHHHHHHHHHHHh
Confidence 456666 9999999999999999999999999999999999999999999999764 69999999999999998876
Q ss_pred hcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCccccc
Q psy15215 1262 QARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIED 1341 (1432)
Q Consensus 1262 ~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~~d~i~d 1341 (1432)
..+..+. ++. ..+.. + .
T Consensus 77 ~~~~~~~------------------------------------------------------~~~-~~~~~-----~---~ 93 (179)
T PRK12543 77 RWRRFRI------------------------------------------------------FEK-AEEQR-----K---P 93 (179)
T ss_pred hcccccc------------------------------------------------------ccc-ccccc-----c---c
Confidence 6531000 000 00000 0 0
Q ss_pred CCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchhhh
Q psy15215 1342 ENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYY 1421 (1432)
Q Consensus 1342 ~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~~~ 1421 (1432)
....+|+. ....+....+..+|..|||++|.|+.|+|+.|+ |++|||+.||+|.++|+..++||+++||+.+...
T Consensus 94 ~~~~~~~~-~~~~~~~~~l~~~l~~Lp~~~r~i~~l~~~e~~----s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~ 168 (179)
T PRK12543 94 VSIDFSED-VLSKESNQELIELIHKLPYKLRQVIILRYLHDY----SQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQIE 168 (179)
T ss_pred ccccChHH-HHHHHHHHHHHHHHHhCCHHHHHHHHHHHHccC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 01123444 566677788999999999999999999999998 9999999999999999999999999999977654
No 133
>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=99.75 E-value=3.5e-17 Score=183.95 Aligned_cols=181 Identities=16% Similarity=0.189 Sum_probs=145.7
Q ss_pred HHHHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHH-------HHHhccccCCCcchhH
Q psy15215 1174 LRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMK-------AVDKFEYRRGYKFSTY 1246 (1432)
Q Consensus 1174 ~~~l~~~~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~k-------av~kfd~~~g~~Fsty 1246 (1432)
...++..++.|+.. ||..|+..|.+.|+.++.+++++..+++|++||+|+.+|. ++++|++. .+|.||
T Consensus 26 d~~Li~~~~~gd~~---Af~~L~~~y~~~l~~~~~~~~~~~~dAEDivQEvFlkl~~~~~~~~~~~~~~~~~--~~~~tW 100 (244)
T TIGR03001 26 DLYLACACAQGEPA---ALAALERHVLSKVPARLAGLRPPTAFVDEVLQRLRQRLLVPRAERPPRIAEYSGR--GPLLSW 100 (244)
T ss_pred HHHHHHHHHcCcHH---HHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhccchhhhhhccCCC--CchHhH
Confidence 44678889999887 9999999999999999999999999999999999999994 78889864 379999
Q ss_pred HHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCC
Q psy15215 1247 ATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESP 1326 (1432)
Q Consensus 1247 a~~~ir~~i~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~ 1326 (1432)
++.+++|.+.++++++.+...+ +
T Consensus 101 L~~Ia~N~~id~lRk~~r~~~~-------------------------------------------------------~-- 123 (244)
T TIGR03001 101 VRIVATRIALELQAQERRHSPV-------------------------------------------------------E-- 123 (244)
T ss_pred HHHHHHHHHHHHHHHhcccCcc-------------------------------------------------------c--
Confidence 9999999999999976641100 0
Q ss_pred CCCCCCCCcCcccccCCCCChHHHHHH----HHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHH
Q psy15215 1327 VGDDEDSHLGDFIEDENMLAPSDAALN----ASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRER 1402 (1432)
Q Consensus 1327 ~~~~~~~~~~d~i~d~~~~~p~~~~~~----~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~ 1402 (1432)
+++. ..+. .+ ...+|++.... ......+..+|++||+++|.|+.|+|..|+ |++|||+.||||.++
T Consensus 124 --~~~~--~~~~-~~-~~~~~e~~~~~~e~~~e~~~~l~~aL~~Lp~~~R~v~~L~~~eg~----S~~EIA~~Lgis~~T 193 (244)
T TIGR03001 124 --EPTE--LAAL-PA-PGSDPELDLLRERYRQDFRQALREALAALSERERHLLRLHFVDGL----SMDRIGAMYQVHRST 193 (244)
T ss_pred --cccc--cccc-cC-CCCCHHHHHHHHhhHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHHCcCHHH
Confidence 0000 0000 00 11244444433 246678999999999999999999999998 999999999999999
Q ss_pred HHHHHHHHHHHhhCchhhhhHHhh
Q psy15215 1403 IRQIEAKALRKLRHPSRYYKLKIF 1426 (1432)
Q Consensus 1403 Vrq~~~rAl~kLr~~~~~~~l~~~ 1426 (1432)
|+.+++||+++||+.+++.....|
T Consensus 194 Vk~rl~RAr~~Lr~~l~~~~~~~~ 217 (244)
T TIGR03001 194 VSRWVAQARERLLERTRRRLAERL 217 (244)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhc
Confidence 999999999999999888776655
No 134
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=99.75 E-value=2.2e-17 Score=178.97 Aligned_cols=173 Identities=16% Similarity=0.098 Sum_probs=136.8
Q ss_pred CCChhhHHHHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHH
Q psy15215 1168 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 1247 (1432)
Q Consensus 1168 ~l~~~e~~~l~~~~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya 1247 (1432)
+........++.++..|+.. |+..|+..|.+.|+.+++ ++++..+++|++||+|+.+|+..++|++. .+|.+|+
T Consensus 5 ~~~~~~~~~l~~~~~~gd~~---af~~l~~~~~~~l~~~~~-~~~~~~~AeDivQe~flkl~~~~~~~~~~--~~~~~Wl 78 (185)
T PRK09649 5 ASDDEAVTALALSAAKGNGR---ALEAFIKATQQDVWRFVA-YLSDVGSADDLTQETFLRAIGAIPRFSAR--SSARTWL 78 (185)
T ss_pred ccccHHHHHHHHHHHccCHH---HHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHhccccCcc--chHHHHH
Confidence 44456677889999999988 999999999999999995 67888899999999999999999999864 3799999
Q ss_pred HHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCC
Q psy15215 1248 TWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPV 1327 (1432)
Q Consensus 1248 ~~~ir~~i~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~ 1327 (1432)
+.+++|.+.+++|++.+..+.. .+..
T Consensus 79 ~~Iarn~~~d~~Rk~~~~~~~~-----------------------------------------------------~~~~- 104 (185)
T PRK09649 79 LAIARHVVADHIRHVRSRPRTT-----------------------------------------------------RGAR- 104 (185)
T ss_pred HHHHHHHHHHHHHHhccccccc-----------------------------------------------------cccc-
Confidence 9999999999999865411100 0000
Q ss_pred CCCCCCCcCcccccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHH
Q psy15215 1328 GDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 1407 (1432)
Q Consensus 1328 ~~~~~~~~~d~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~ 1407 (1432)
.+ ... .+.......+....+..+|++|||++|.||.|+|+.|+ |++|||+.||+|.++|++++
T Consensus 105 --~~------~~~-----~~~~~~~~~e~~~~l~~~l~~Lp~~~r~v~~L~~~~g~----s~~EIA~~lgis~~tVk~~l 167 (185)
T PRK09649 105 --PE------HLI-----DGDRHARGFEDLVEVTTMIADLTTDQREALLLTQLLGL----SYADAAAVCGCPVGTIRSRV 167 (185)
T ss_pred --hh------hcc-----ChhhhhhhHHHHHHHHHHHHhCCHHHhHHhhhHHHcCC----CHHHHHHHHCCCHHHHHHHH
Confidence 00 000 00000111122345888999999999999999999999 99999999999999999999
Q ss_pred HHHHHHhhCc
Q psy15215 1408 AKALRKLRHP 1417 (1432)
Q Consensus 1408 ~rAl~kLr~~ 1417 (1432)
+||+++||+.
T Consensus 168 ~Rar~~Lr~~ 177 (185)
T PRK09649 168 ARARDALLAD 177 (185)
T ss_pred HHHHHHHHhh
Confidence 9999999983
No 135
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=99.75 E-value=4.4e-17 Score=179.77 Aligned_cols=179 Identities=13% Similarity=0.093 Sum_probs=140.6
Q ss_pred hHHHHHHHHHHhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHH
Q psy15215 383 DLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 462 (1432)
Q Consensus 383 e~~~l~~~i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir 462 (1432)
....+...+..||.. |+..|+..|.+.|+++|.+++++..+++|++||+|+.+|+++.+|++.++ .|.||++.++|
T Consensus 24 ~~~~l~~~~~~~d~~---a~~~l~~~y~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~~-~~~~wl~~I~r 99 (206)
T PRK12526 24 LSQWLILVAISRDKQ---AFTHLFQFFAPKIKRFGIKQLGNEAQANELVQETMSNVWRKAHLYNGDKG-AATTWVYTVMR 99 (206)
T ss_pred HHHHHHHHHHcCCHH---HHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCccc-chhHHHHHHHH
Confidence 345566778889988 99999999999999999999999899999999999999999999987655 69999999999
Q ss_pred HHHHHHHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCC
Q psy15215 463 QAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDED 542 (1432)
Q Consensus 463 ~~i~~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~ 542 (1432)
|.+.+++|++.+..... .. ++ .
T Consensus 100 n~~~d~~Rk~~~~~~~~-----------------------------------------------------~~----~~-~ 121 (206)
T PRK12526 100 NAAFDMLRKIKAKKEQN-----------------------------------------------------LG----DD-I 121 (206)
T ss_pred HHHHHHHHHhccccccc-----------------------------------------------------cc----cc-c
Confidence 99999999876521000 00 00 0
Q ss_pred CCcCcccccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHH
Q psy15215 543 SHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALR 622 (1432)
Q Consensus 543 ~~~~~~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~ 622 (1432)
....+.+.+. ...+. ..........|..+|++||++++.||.|+|+.|+ |++|||+.+|+|.++|+.+.++|++
T Consensus 122 ~~~~~~~~~~-~~~~~-~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~g~----s~~EIA~~lgis~~tV~~~l~Ra~~ 195 (206)
T PRK12526 122 WPIEQALAES-QSESE-EFSDHLMDKQILSYIEKLPEAQQTVVKGVYFQEL----SQEQLAQQLNVPLGTVKSRLRLALA 195 (206)
T ss_pred chhhhhcccc-cCchH-HHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 0000001111 11222 2333344567999999999999999999999999 9999999999999999999999999
Q ss_pred HHHHHHH
Q psy15215 623 KLRPLAH 629 (1432)
Q Consensus 623 kLr~~l~ 629 (1432)
+|+..+.
T Consensus 196 ~Lr~~l~ 202 (206)
T PRK12526 196 KLKVQMG 202 (206)
T ss_pred HHHHHHh
Confidence 9998874
No 136
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=99.75 E-value=1.9e-17 Score=178.96 Aligned_cols=172 Identities=15% Similarity=0.168 Sum_probs=136.6
Q ss_pred hhHHHHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHhccC-CCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHH
Q psy15215 1172 NDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTD-RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 1250 (1432)
Q Consensus 1172 ~e~~~l~~~~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~-~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ 1250 (1432)
..+..++.++..|+.. |++.++..|.+.|+.+|.++++ +..+++|++||+|+.+|++.++|++. .+|.+|++.+
T Consensus 6 ~~~~~~~~~~~~~d~~---a~~~l~~~~~~~l~~~~~~~~~~~~~~aeDlvQevfl~l~~~~~~~~~~--~~~~~wl~~i 80 (181)
T PRK12536 6 ARLRALLLRGLAGDAA---AYRQFLSELAAHLRGFLRRRLPQLPDEVEDLVQEILLAVHNARHTYRAD--QPLTAWVHAI 80 (181)
T ss_pred hHHHHHHHHHHcCCHH---HHHHHHHHHHHHHHHHHHHHcCCChhhHHHHHHHHHHHHHHhHHhcCCC--CchHHHHHHH
Confidence 3456788899999988 9999999999999999998764 57899999999999999999999964 3799999999
Q ss_pred HHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCC
Q psy15215 1251 IRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDD 1330 (1432)
Q Consensus 1251 ir~~i~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~ 1330 (1432)
++|.+.+++|++.+.... ..+..+.
T Consensus 81 arN~~~d~~Rk~~~~~~~-------------------------------------------------------~~~~~~~ 105 (181)
T PRK12536 81 ARYKLMDFLRSRARREAL-------------------------------------------------------HDPLDDE 105 (181)
T ss_pred HHHHHHHHHHHHhccccc-------------------------------------------------------cCCccch
Confidence 999999999987641000 0000000
Q ss_pred CCCCcCcccccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q psy15215 1331 EDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 1410 (1432)
Q Consensus 1331 ~~~~~~d~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rA 1410 (1432)
. +...+. ...+ .+....+.++|..||++++.|+.|+|..|+ |++|||+.||+|+++|++.+++|
T Consensus 106 ~-----~~~~~~-~~~~------~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~----s~~EIA~~l~is~~tV~~~l~ra 169 (181)
T PRK12536 106 S-----ELFATS-DDEA------AEARRDLGKLLEQLPDRQRLPIVHVKLEGL----SVAETAQLTGLSESAVKVGIHRG 169 (181)
T ss_pred h-----hhcCCC-Ccch------HHHHHHHHHHHHHCCHHHHHHHHHHHHcCC----CHHHHHHHHCCCHHHHHHHHHHH
Confidence 0 000000 0111 133456899999999999999999999998 99999999999999999999999
Q ss_pred HHHhhCchh
Q psy15215 1411 LRKLRHPSR 1419 (1432)
Q Consensus 1411 l~kLr~~~~ 1419 (1432)
+++||+.+.
T Consensus 170 r~~Lr~~l~ 178 (181)
T PRK12536 170 LKALAAKIR 178 (181)
T ss_pred HHHHHHHhc
Confidence 999998554
No 137
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=99.75 E-value=3.1e-17 Score=178.44 Aligned_cols=178 Identities=16% Similarity=0.205 Sum_probs=145.3
Q ss_pred hhhHHHHHHHHHHhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHH
Q psy15215 381 LNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 460 (1432)
Q Consensus 381 ~~e~~~l~~~i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ 460 (1432)
..+...++..+..|+.. |++.++..|.++|+++|.+++++..+++|++||+|+++|++.++|++.++ +|.||++..
T Consensus 9 ~~~~~~l~~~~~~~~~~---~~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~~~~~~~~~~~~~~-~~~~wl~~I 84 (187)
T PRK12534 9 DDETGRLLTATAGGDRH---AFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFDPSRA-RGLTWLAMI 84 (187)
T ss_pred cchHHHHHHHHHcCCHH---HHHHHHHHhhHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccCCcccc-cHHHHHHHH
Confidence 34567788888899988 99999999999999999999999999999999999999999999987644 689999999
Q ss_pred HHHHHHHHHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCC
Q psy15215 461 IRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDD 540 (1432)
Q Consensus 461 ir~~i~~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~ 540 (1432)
++|.+.++++++.+..+. .+.+.
T Consensus 85 ~~n~~~d~~R~~~~~~~~----------------------------------------------------~~~~~----- 107 (187)
T PRK12534 85 ARNKAIDHLRANAPQRRN----------------------------------------------------VALDD----- 107 (187)
T ss_pred HHHHHHHHHHhccccccc----------------------------------------------------ccccc-----
Confidence 999999999876531000 00000
Q ss_pred CCCCcCcccccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHH
Q psy15215 541 EDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 620 (1432)
Q Consensus 541 ~~~~~~~~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rA 620 (1432)
...... ...+|.+.....+....+..+|..||++++.|+.|+|..|+ |++|||+.||+|+++|+++.+||
T Consensus 108 ----~~~~~~--~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~----s~~eIA~~lgis~~~v~~~l~Ra 177 (187)
T PRK12534 108 ----AGELRA--ADASPLERTERASTRRRIDHCLAELEPPRSELIRTAFFEGI----TYEELAARTDTPIGTVKSWIRRG 177 (187)
T ss_pred ----hhhhcc--ccCChhhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHhCCChhHHHHHHHHH
Confidence 000000 01234455555667789999999999999999999999888 99999999999999999999999
Q ss_pred HHHHHHHHH
Q psy15215 621 LRKLRPLAH 629 (1432)
Q Consensus 621 l~kLr~~l~ 629 (1432)
+++|+..+.
T Consensus 178 r~~Lr~~l~ 186 (187)
T PRK12534 178 LAKLKACLE 186 (187)
T ss_pred HHHHHHHHc
Confidence 999998763
No 138
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=99.75 E-value=3.8e-17 Score=177.12 Aligned_cols=171 Identities=11% Similarity=0.131 Sum_probs=136.6
Q ss_pred hHHHHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHH----hccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHH
Q psy15215 1173 DLRDINRKMIAGEMKARKAKREMTEANLRLVISIAK----KYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 1248 (1432)
Q Consensus 1173 e~~~l~~~~~~g~~~~~~A~~~Li~~~~~lV~~ia~----~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~ 1248 (1432)
....++.+++.|+.. |+..|+..|.+.|+.+|+ ++.++..+++|++||+|+.+|++.++|++.. +|.+|++
T Consensus 7 ~~~~l~~~~~~gd~~---af~~l~~~~~~~l~~~~~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~~--~f~~wl~ 81 (184)
T PRK12539 7 ELKALMLASLDGDAA---AHRALLERLSGHLRAYYKGKLARIGRGAEEAEDLVQEALMAIHTRRHTYDPEQ--PLTPWVY 81 (184)
T ss_pred HHHHHHHHHHcCCHH---HHHHHHHHHHHHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHhhcCCCC--ChHHHHH
Confidence 356788889999988 999999999999999976 5667889999999999999999999998753 6999999
Q ss_pred HHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCC
Q psy15215 1249 WWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVG 1328 (1432)
Q Consensus 1249 ~~ir~~i~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~ 1328 (1432)
.+++|.+.+++|+..+. +.+ .+.+.
T Consensus 82 ~i~~n~~~d~~R~~~~~-~~~---------------------------------------------------~~~~~--- 106 (184)
T PRK12539 82 AIARYKLIDHLRRTRAS-LAD---------------------------------------------------VPIDD--- 106 (184)
T ss_pred HHHHHHHHHHHHHHhcc-ccc---------------------------------------------------cChhh---
Confidence 99999999999986541 000 00000
Q ss_pred CCCCCCcCcccccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q psy15215 1329 DDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEA 1408 (1432)
Q Consensus 1329 ~~~~~~~~d~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~ 1408 (1432)
.+ .. .. ..+ ....+....+..++..||+++|.|+.|+|+.|+ |++|||+.||+|..+|+++++
T Consensus 107 -~~--~~---~~----~~~---~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g~----s~~eIA~~lgis~~tV~~~l~ 169 (184)
T PRK12539 107 -AD--EL---VA----HDD---HAAVESTLDLGRLLARLPEKMRLAIQAVKLEGL----SVAEAATRSGMSESAVKVSVH 169 (184)
T ss_pred -hc--cc---cC----CcH---HhhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCC----cHHHHHHHHCcCHHHHHHHHH
Confidence 00 00 00 011 112234567999999999999999999999888 999999999999999999999
Q ss_pred HHHHHhhCchhh
Q psy15215 1409 KALRKLRHPSRY 1420 (1432)
Q Consensus 1409 rAl~kLr~~~~~ 1420 (1432)
||+++||+....
T Consensus 170 ra~~~Lr~~l~~ 181 (184)
T PRK12539 170 RGLKALAALIGR 181 (184)
T ss_pred HHHHHHHHHHhh
Confidence 999999986543
No 139
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=99.74 E-value=2.7e-17 Score=176.52 Aligned_cols=165 Identities=10% Similarity=0.170 Sum_probs=130.8
Q ss_pred hhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q psy15215 1190 KAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 1269 (1432)
Q Consensus 1190 ~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip 1269 (1432)
..+++|+..|.++|+++|++|+++..+++|++||+++.+|++.++|++.. +|.+|++.+++|.+.+++|++.+....+
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 46999999999999999999999999999999999999999999999754 7999999999999999999877521100
Q ss_pred ccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHH
Q psy15215 1270 VHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349 (1432)
Q Consensus 1270 ~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~~d~i~d~~~~~p~~ 1349 (1432)
.. ..+.. ...... ..+ ....|..
T Consensus 81 ~~--------------------------------------------------~~~~~----~~~~~~--~~~-~~~~~~~ 103 (173)
T PRK12522 81 LD--------------------------------------------------LFHKE----DGGEIE--FAD-DVNISEE 103 (173)
T ss_pred cc--------------------------------------------------ccchh----hhhhhc--ccc-CCCChHH
Confidence 00 00000 000000 000 1112333
Q ss_pred HHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCch
Q psy15215 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418 (1432)
Q Consensus 1350 ~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~ 1418 (1432)
....+..+.+..+|..||++++.|+.|+|..|+ |++|||+.||+|.++|+.+++||+++||..+
T Consensus 104 -~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~~~----s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 167 (173)
T PRK12522 104 -FIQKVEAEMIREVIQLLNEKYKTVLVLYYYEQY----SYKEMSEILNIPIGTVKYRLNYAKKQMREHL 167 (173)
T ss_pred -HHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 445567788999999999999999999999999 9999999999999999999999999999854
No 140
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=99.74 E-value=2.6e-17 Score=179.55 Aligned_cols=181 Identities=17% Similarity=0.199 Sum_probs=138.4
Q ss_pred hHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHHHHHHhcccccccc
Q psy15215 1191 AKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 1270 (1432)
Q Consensus 1191 A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~ 1270 (1432)
+++.|+..|.+.|+.+|.+++++..+++|++||+|+.+|+++++|+.. .+|.||++.+++|.+.+++|++.+..+.+.
T Consensus 3 ~~~~l~~~~~~~l~~~a~~~~~~~~~AeDivQevfl~~~~~~~~~~~~--~~~~~WL~~ia~n~~~d~~Rk~~r~~~~~~ 80 (191)
T PRK12520 3 IAPAQLEALRPHLLRFARLQLRDPALAEDAVSETLLAVLEHPERFAGQ--SSLKTYLVGILKHKIIDAIRSGRREVRLSL 80 (191)
T ss_pred chHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhccc--ccHHHHHHHHHHHHHHHHHHhhcCcCcccc
Confidence 789999999999999999999999999999999999999999999854 379999999999999999998775221110
Q ss_pred cHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHH
Q psy15215 1271 HMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 1350 (1432)
Q Consensus 1271 ~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~~d~i~d~~~~~p~~~ 1350 (1432)
.... ..... . .++. .... +.. ....++ ...+|++.
T Consensus 81 ~~~~------------------~~~~~-----------~------------~~~~-~~~~-~~~-~~~~~~-~~~~~~~~ 115 (191)
T PRK12520 81 DDAD------------------EQSDD-----------D------------LFDA-LFAA-DGH-YREPPS-DWGDPDAA 115 (191)
T ss_pred cccc------------------cchhh-----------h------------hhhh-hccc-ccc-cccCcc-ccCCHHHH
Confidence 0000 00000 0 0000 0000 000 000111 12367777
Q ss_pred HHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchhhhh
Q psy15215 1351 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYK 1422 (1432)
Q Consensus 1351 ~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~~~~ 1422 (1432)
+...+....|..+|..|||++|.|+.|+|+.|+ |++|||+.||+|.++|+++++||+++||+......
T Consensus 116 ~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~~~g~----s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~ 183 (191)
T PRK12520 116 LSRREFFEVLQACVDRLPPRTGRVFMMREWLEL----ETEEICQELQITATNAWVLLYRARMRLRECLDLHW 183 (191)
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 777788888999999999999999999999998 99999999999999999999999999999887765
No 141
>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=99.74 E-value=3.2e-17 Score=175.31 Aligned_cols=164 Identities=16% Similarity=0.241 Sum_probs=133.6
Q ss_pred HHHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHH
Q psy15215 1175 RDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA 1254 (1432)
Q Consensus 1175 ~~l~~~~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~ 1254 (1432)
..++..+.+|+.. |++.++..|.+.|+++|.+++++..+++|++||+|+.+|++.++|++.. +|.||++.+++|.
T Consensus 4 ~~l~~~~~~gd~~---a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~l~~~~~~~~~~~~~--~~~~wl~~i~~n~ 78 (169)
T TIGR02954 4 EELVKKAKRGNKP---AFESLIKKHKEKLYKTAFIYVKNEHDALDVIQETVYKAYLSIDKLKHPK--YFNTWLTRILINE 78 (169)
T ss_pred HHHHHHHHcCCHH---HHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhccCcc--ccHHHHHHHHHHH
Confidence 3567788899888 9999999999999999999999999999999999999999999998653 7999999999999
Q ss_pred HHHHHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCC
Q psy15215 1255 ITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSH 1334 (1432)
Q Consensus 1255 i~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~ 1334 (1432)
+.+++|+..+. .| ++.....+
T Consensus 79 ~~d~~R~~~~~--~~-----------------------------------------------------~~~~~~~~---- 99 (169)
T TIGR02954 79 CIDLLKKKKKV--IP-----------------------------------------------------FDPNTSIE---- 99 (169)
T ss_pred HHHHHHhcCCc--Cc-----------------------------------------------------cccccccc----
Confidence 99999876541 00 00000000
Q ss_pred cCcccccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Q psy15215 1335 LGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 1414 (1432)
Q Consensus 1335 ~~d~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kL 1414 (1432)
+ ..+.. .. .....+..+|..||+++++|+.|+|+.|+ |++|||+.||+|.++|+.+++||+++|
T Consensus 100 ------~---~~~~~--~~-~~~~~l~~~l~~L~~~~r~i~~l~~~~g~----s~~eiA~~lgis~~tv~~~l~Ra~~~L 163 (169)
T TIGR02954 100 ------K---GECET--HA-DSRLDLYKAIDTLNDKYQTAIILRYYHDL----TIKEIAEVMNKPEGTVKTYLHRALKKL 163 (169)
T ss_pred ------c---chhhh--ch-HHHHHHHHHHHhCCHHHhHHHHHHHHcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 0 00100 00 11236888999999999999999999888 999999999999999999999999999
Q ss_pred hCch
Q psy15215 1415 RHPS 1418 (1432)
Q Consensus 1415 r~~~ 1418 (1432)
|+.+
T Consensus 164 r~~l 167 (169)
T TIGR02954 164 KKRL 167 (169)
T ss_pred HHHh
Confidence 9854
No 142
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=99.74 E-value=2.4e-17 Score=173.41 Aligned_cols=150 Identities=23% Similarity=0.256 Sum_probs=123.3
Q ss_pred HhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHHHHHHhccccccc
Q psy15215 400 KAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 479 (1432)
Q Consensus 400 ~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip 479 (1432)
.|+..+++.|.++|+++++++ +...+++|++|||++++|+++++|++..+ +|.+|++..++|.+.++++++.+...
T Consensus 4 ~af~~l~~~y~~~l~~~~~~~-~~~~~aeDi~Qe~~l~l~~~~~~~~~~~~-~f~~wl~~i~~n~~ld~~rk~~~~~~-- 79 (154)
T PRK06759 4 ATFTEAVVLYEGLIVNQIKKL-GIYQDYEEYYQCGLIGLWHAYERYDEKKG-SFPAYAVVTVRGYILERLKKEFAVQE-- 79 (154)
T ss_pred ccHHHHHHHHHHHHHHHHHHh-CCcccHHHHHHHHHHHHHHHHHHhCccCC-chHHHHHHHHHHHHHHHHHHHHhhcc--
Confidence 389999999999999999986 45679999999999999999999997666 79999999999999999998743100
Q ss_pred hhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHH
Q psy15215 480 VHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 559 (1432)
Q Consensus 480 ~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~i~d~~~~~p~~ 559 (1432)
... + + .+|.+
T Consensus 80 -------------------------------------------------~~~----~--~---------------~~~~~ 89 (154)
T PRK06759 80 -------------------------------------------------KCV----C--V---------------GEYED 89 (154)
T ss_pred -------------------------------------------------ccc----c--c---------------CCCcc
Confidence 000 0 0 01111
Q ss_pred HHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHH
Q psy15215 560 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPL 627 (1432)
Q Consensus 560 ~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~ 627 (1432)
.....+....+..++.+|||+++.||.++|+.|+ |++|||+.+|+|.++|+++.++|+++||+.
T Consensus 90 ~~~~~~~~~~l~~~l~~L~~~~r~ii~l~~~~~~----s~~EIA~~l~is~~tV~~~~~ra~~~Lr~~ 153 (154)
T PRK06759 90 HFHFEDVEMKVKDFMSVLDEKEKYIIFERFFVGK----TMGEIALETEMTYYQVRWIYRQALEKMRNS 153 (154)
T ss_pred cccHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHhhc
Confidence 1222334567999999999999999999999988 999999999999999999999999999863
No 143
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=99.74 E-value=1.8e-17 Score=180.26 Aligned_cols=174 Identities=18% Similarity=0.246 Sum_probs=137.4
Q ss_pred HHHHHHHHHH---hHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHH
Q psy15215 384 LRDINRKMIA---GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 460 (1432)
Q Consensus 384 ~~~l~~~i~~---gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ 460 (1432)
...++..++. ||.. |+..|+..|.+.|+++|.+|++...+++|++||+|+.+|+++++|++ ..+|+||++.+
T Consensus 10 ~~~li~~~~~~~~gd~~---a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~f~~l~~~~~~~~~--~~~~~~wl~~i 84 (188)
T PRK09640 10 DEELVARVHVELFHVTR---AYEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEG--KSKFKTWLYSI 84 (188)
T ss_pred HHHHHHHHhcccCCCHH---HHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHHHhcC--CCcchHHHHHH
Confidence 4456667764 5787 99999999999999999999999999999999999999999999985 34799999999
Q ss_pred HHHHHHHHHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCC
Q psy15215 461 IRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDD 540 (1432)
Q Consensus 461 ir~~i~~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~ 540 (1432)
++|.+.+++++..+..... .. .+.+.
T Consensus 85 a~n~~~d~~R~~~~~~~~~-------------------------~~------------------------~~~~~----- 110 (188)
T PRK09640 85 TYNECITQYRKERRKRRLM-------------------------DA------------------------LSLDP----- 110 (188)
T ss_pred HHHHHHHHHHHhcccccCc-------------------------ch------------------------hhhcc-----
Confidence 9999999999765421100 00 00000
Q ss_pred CCCCcCcccccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHH
Q psy15215 541 EDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 620 (1432)
Q Consensus 541 ~~~~~~~~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rA 620 (1432)
..+. ..+.....+....|..+|++||++++.||.|+|..|+ |++|||+.||+|.++|+.+.+||
T Consensus 111 --------~~~~----~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~----s~~EIA~~lgis~~tV~~~l~Ra 174 (188)
T PRK09640 111 --------LEEA----SEEKAPKPEERGGLDRWLVHVNPIDREILVLRFVAEL----EFQEIADIMHMGLSATKMRYKRA 174 (188)
T ss_pred --------cccc----cccccccHHHHHHHHHHHHhcChhheeeeeeHHhcCC----CHHHHHHHHCCCHHHHHHHHHHH
Confidence 0000 0000111234567999999999999999999999888 99999999999999999999999
Q ss_pred HHHHHHHHHHHH
Q psy15215 621 LRKLRPLAHDWL 632 (1432)
Q Consensus 621 l~kLr~~l~~~~ 632 (1432)
+.+|+..+..+.
T Consensus 175 ~~~Lr~~l~~~~ 186 (188)
T PRK09640 175 LDKLREKFAGLA 186 (188)
T ss_pred HHHHHHHHHHHh
Confidence 999999886553
No 144
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=99.74 E-value=6.6e-17 Score=176.37 Aligned_cols=177 Identities=12% Similarity=0.115 Sum_probs=145.8
Q ss_pred CChhhHHHHHHHHHHhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHH
Q psy15215 379 LPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 458 (1432)
Q Consensus 379 l~~~e~~~l~~~i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~ 458 (1432)
........++..+..|+.. ++..++..|.+.|+++|.++++...+++|++||+|+.+|++.++|++. .+|.+|++
T Consensus 9 ~~~~~~~~l~~~~~~gd~~---~~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQEvfl~l~~~~~~~~~~--~~f~~wL~ 83 (192)
T PRK09643 9 FGERSDAELLAAHVAGDRY---AFGELFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHRAAGSFRGD--AAVSSWLH 83 (192)
T ss_pred CCCcCHHHHHHHHHCcCHH---HHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCCC--CccHHHHH
Confidence 3344567888999999998 999999999999999999999999999999999999999999999964 36999999
Q ss_pred HHHHHHHHHHHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCC
Q psy15215 459 WWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVG 538 (1432)
Q Consensus 459 ~~ir~~i~~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~ 538 (1432)
..++|.+.+++|+..+..+. +++
T Consensus 84 ~i~rn~~~d~~Rk~~~~~~~-----------------------------------------------------~~~---- 106 (192)
T PRK09643 84 RIVVNACLDRLRRAKARPTV-----------------------------------------------------PLD---- 106 (192)
T ss_pred HHHHHHHHHHHHccccCCCC-----------------------------------------------------Ccc----
Confidence 99999999999987542100 000
Q ss_pred CCCCCCcCcccccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHH
Q psy15215 539 DDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEA 618 (1432)
Q Consensus 539 ~~~~~~~~~~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~ 618 (1432)
+... .. .+|.+.+...+....+..+|++||+++|.|+.|+|..|+ |++|||+.+|+|.++|+.+.+
T Consensus 107 ~~~~------~~----~~~~~~~~~~e~~~~l~~~l~~Lp~~~r~i~~l~~~~g~----s~~EIA~~lg~s~~tV~~rl~ 172 (192)
T PRK09643 107 DVYP------VA----QLERDPTARVETALAVQRALMRLPVEQRAALVAVDMQGY----SVADAARMLGVAEGTVKSRCA 172 (192)
T ss_pred cccc------cc----CCcccHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHHCcCHHHHHHHHH
Confidence 0000 00 012233444556778999999999999999999999998 999999999999999999999
Q ss_pred HHHHHHHHHHHHH
Q psy15215 619 KALRKLRPLAHDW 631 (1432)
Q Consensus 619 rAl~kLr~~l~~~ 631 (1432)
+|+++|++.+..+
T Consensus 173 rar~~Lr~~l~~~ 185 (192)
T PRK09643 173 RGRARLAELLGYL 185 (192)
T ss_pred HHHHHHHHHHHHh
Confidence 9999999988654
No 145
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=99.74 E-value=2.3e-17 Score=177.67 Aligned_cols=170 Identities=18% Similarity=0.196 Sum_probs=136.6
Q ss_pred HHHHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHH
Q psy15215 1174 LRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 1253 (1432)
Q Consensus 1174 ~~~l~~~~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~ 1253 (1432)
...++..+.+|+.. |++.|+..|.+.|+.+|.+|+++..+++|++||+|+++|+++++|++. .+|.+|++.+++|
T Consensus 5 ~~~l~~~~~~~d~~---a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~--~~~~~wl~~i~~n 79 (176)
T PRK09638 5 EKELIQKAKKGDDA---ALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSFQGR--SKFSTWLISIASR 79 (176)
T ss_pred HHHHHHHHHCCCHH---HHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHH
Confidence 34678888899888 999999999999999999999999999999999999999999999864 4899999999999
Q ss_pred HHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCC
Q psy15215 1254 AITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDS 1333 (1432)
Q Consensus 1254 ~i~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~ 1333 (1432)
.+.+++++..+..... + ...+.
T Consensus 80 ~~~d~~r~~~~~~~~~------------------------------------------------------~-~~~~~--- 101 (176)
T PRK09638 80 LYKDHLRKQKREKLRL------------------------------------------------------Q-RAKEE--- 101 (176)
T ss_pred HHHHHHHHhccccchh------------------------------------------------------h-hcccc---
Confidence 9999999876421000 0 00000
Q ss_pred CcCcccccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q psy15215 1334 HLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRK 1413 (1432)
Q Consensus 1334 ~~~d~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~k 1413 (1432)
..+. ...+..........+..+|..||++++.||.++|+.|+ |++|||+.||+|.++|++.++||+++
T Consensus 102 -----~~~~---~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~----s~~eIA~~l~is~~~V~~~l~ra~~~ 169 (176)
T PRK09638 102 -----TLRK---EKWEAAIKGAEWSEMLDALSKLDPEFRAPVILKHYYGY----TYEEIAKMLNIPEGTVKSRVHHGIKQ 169 (176)
T ss_pred -----cCCc---cchHHHHHhhhHHHHHHHHHcCCHHHhheeeehhhcCC----CHHHHHHHHCCChhHHHHHHHHHHHH
Confidence 0000 00011222334566889999999999999999998888 99999999999999999999999999
Q ss_pred hhCch
Q psy15215 1414 LRHPS 1418 (1432)
Q Consensus 1414 Lr~~~ 1418 (1432)
||+..
T Consensus 170 l~~~l 174 (176)
T PRK09638 170 LRKEW 174 (176)
T ss_pred HHHHh
Confidence 99843
No 146
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=99.74 E-value=3.7e-17 Score=175.51 Aligned_cols=158 Identities=15% Similarity=0.110 Sum_probs=128.0
Q ss_pred hHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHHHHHHhcccccccc
Q psy15215 1191 AKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 1270 (1432)
Q Consensus 1191 A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~ 1270 (1432)
|+..|+..|.+.|+++|.+++++..+++|++||+|+.+|++.++|++.. ..|.+|++.+++|.+.+++|++.+....
T Consensus 10 ~~~~l~~~~~~~l~~~~~~~~~~~~~AeD~vQevfl~~~~~~~~~~~~~-~~~~~wL~~iarn~~~d~~Rk~~~~~~~-- 86 (173)
T PRK09645 10 LMRALYDEHAAPLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLADTG-RSARAWLFTVARNLVIDERRSARARPVE-- 86 (173)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCccc-ccHHHHHHHHHHHHHHHHHHhhcccccc--
Confidence 9999999999999999999999989999999999999999999997533 4799999999999999999986541000
Q ss_pred cHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHH
Q psy15215 1271 HMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 1350 (1432)
Q Consensus 1271 ~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~~d~i~d~~~~~p~~~ 1350 (1432)
..+ + .... .+ .++.+.
T Consensus 87 ---------------------------------------------------~~~-----~-~~~~----~~---~~~~~~ 102 (173)
T PRK09645 87 ---------------------------------------------------GGD-----D-VLGV----PE---QSAPDE 102 (173)
T ss_pred ---------------------------------------------------ccc-----c-cccC----CC---CCCchH
Confidence 000 0 0000 00 112223
Q ss_pred HHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchh
Q psy15215 1351 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 1419 (1432)
Q Consensus 1351 ~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~ 1419 (1432)
.........|..+|+.|||++|.||.|+|+.|+ |++|||+.||+|.++|+.+++||+++||+...
T Consensus 103 ~~~~~~~~~l~~~l~~L~~~~r~vl~L~~~~g~----s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 167 (173)
T PRK09645 103 VDRALDRLLVADALAQLSPEHRAVLVRSYYRGW----STAQIAADLGIPEGTVKSRLHYALRALRLALQ 167 (173)
T ss_pred HHHHhHHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence 333344567899999999999999999999988 99999999999999999999999999998654
No 147
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=99.74 E-value=2.6e-17 Score=177.37 Aligned_cols=166 Identities=10% Similarity=0.051 Sum_probs=132.9
Q ss_pred HHhhhhhhhhhHHHHHHHHHHHHHHHHHhccC--CCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHHH
Q psy15215 1181 MIAGEMKARKAKREMTEANLRLVISIAKKYTD--RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRS 1258 (1432)
Q Consensus 1181 ~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~--~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~~ 1258 (1432)
+..|+.. ||..|+..|.+.|++++.++++ +..+++|++||+|+.+|+..++|+......|.||++.+++|.+.++
T Consensus 7 ~~~~d~~---af~~ly~~~~~~l~~~~~~~~~~~~~~~AeDivQevFl~~~~~~~~~~~~~~~~~~~wL~~ia~n~~~d~ 83 (178)
T PRK12529 7 CLSADRD---KVATLYRENHAWLRNWLAYRLRSWGRGVADDLAHDIFLRILASRDGGQREAIRQPRAYLARIANCVLVSW 83 (178)
T ss_pred CCCCCHH---HHHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHhcccccccccccCHHHHHHHHHHHHHHHH
Confidence 4567777 9999999999999998766665 4678999999999999999999985444579999999999999999
Q ss_pred HHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcc
Q psy15215 1259 IADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDF 1338 (1432)
Q Consensus 1259 i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~~d~ 1338 (1432)
+|++.+. +.. .+.. ..
T Consensus 84 ~Rk~~~~---~~~---------------------------------------------------~~~~-~~--------- 99 (178)
T PRK12529 84 RRRQSLE---LAW---------------------------------------------------LEAL-AT--------- 99 (178)
T ss_pred HHHHHHH---hhh---------------------------------------------------hhHh-hh---------
Confidence 9876430 000 0000 00
Q ss_pred cccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCc
Q psy15215 1339 IEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417 (1432)
Q Consensus 1339 i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~ 1417 (1432)
......++|++.....+....|..+|.+|||++|.||.|+|..|+ |++|||+.||+|.++|+.++++|+.+++..
T Consensus 100 ~~~~~~~~~e~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~~g~----s~~EIA~~lgis~~tVk~~l~rAl~~~~~~ 174 (178)
T PRK12529 100 LPEPLHPSPEQQSVILETLHEIDALLDTLRPRVKQAFLMATLDGM----KQKDIAQALDIALPTVKKYIHQAYVTCLSL 174 (178)
T ss_pred ccCcCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 000112356666666677788999999999999999999999888 999999999999999999999999999874
No 148
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=99.73 E-value=1e-16 Score=172.89 Aligned_cols=173 Identities=15% Similarity=0.139 Sum_probs=145.8
Q ss_pred HHHHHHHHhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHH
Q psy15215 386 DINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 465 (1432)
Q Consensus 386 ~l~~~i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i 465 (1432)
.+...+..|+.. |+..+++.|.+.|+++|+++++...+++|++||++++||++.++|+ .+.+|.+|++..+++.+
T Consensus 2 ~~~~~~~~~~~~---a~~~l~~~y~~~l~~~~~~~~~~~~~aeDl~qe~~~~l~~~~~~~~--~~~~~~~~l~~i~~~~~ 76 (179)
T PRK11924 2 QLMPVDATGDKE---AFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFN--GKGSARTWLLTIARNVC 76 (179)
T ss_pred hHHHHHHccCHH---HHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHhhcC--CcchHHHHHHHHHHHHH
Confidence 356788899998 9999999999999999999999999999999999999999999998 34589999999999999
Q ss_pred HHHHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCc
Q psy15215 466 TRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHL 545 (1432)
Q Consensus 466 ~~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~ 545 (1432)
.+++++..+..+. .. .+..+
T Consensus 77 ~d~~r~~~~~~~~----------------------------------------------------~~--~~~~~------ 96 (179)
T PRK11924 77 YDLLRRRRREKAV----------------------------------------------------LS--DDALE------ 96 (179)
T ss_pred HHHHHhccccccc----------------------------------------------------Cc--ccccc------
Confidence 9999876652100 00 00000
Q ss_pred CcccccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHH
Q psy15215 546 GDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625 (1432)
Q Consensus 546 ~~~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr 625 (1432)
...+....+|++.+...+....+..+|.+||++++.|+.++|..|+ |++|||+.||+|+.+|+++.++|+.+|+
T Consensus 97 --~~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~~~----~~~eIA~~lgis~~tv~~~~~ra~~~lr 170 (179)
T PRK11924 97 --PEFAETAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGL----SYREIAEILGVPVGTVKSRLRRARQLLR 170 (179)
T ss_pred --cccCCccCCHHHHHhhHHHHHHHHHHHHhCCHHHHHHhhHHHHcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 0000023478888888889999999999999999999999998888 9999999999999999999999999999
Q ss_pred HHHH
Q psy15215 626 PLAH 629 (1432)
Q Consensus 626 ~~l~ 629 (1432)
+.+.
T Consensus 171 ~~l~ 174 (179)
T PRK11924 171 ECLE 174 (179)
T ss_pred HHHH
Confidence 8775
No 149
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=99.73 E-value=5.5e-17 Score=175.04 Aligned_cols=162 Identities=12% Similarity=0.093 Sum_probs=134.0
Q ss_pred hhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHHHHHHhcccccc
Q psy15215 1189 RKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI 1268 (1432)
Q Consensus 1189 ~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~~i~~~~r~iri 1268 (1432)
..|+++++..|.+.|+++|.+++++..+++|++||+|+.+|++.++|+.. .+|.+|++.+++|.+.+++|+..+....
T Consensus 15 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQd~fl~l~~~~~~~~~~--~~~~awl~~ia~n~~~d~~Rk~~~~~~~ 92 (179)
T PRK09415 15 EDLIDEIMNEYGQEVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYKGK--SSLKTWLYRIAINHCKDYLKSWHNKKVI 92 (179)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcCCC--cccHHHHHHHHHHHHHHHHHhhcccccc
Confidence 35999999999999999999999999999999999999999999999864 3799999999999999999986541000
Q ss_pred cccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChH
Q psy15215 1269 PVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPS 1348 (1432)
Q Consensus 1269 p~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~~d~i~d~~~~~p~ 1348 (1432)
+ .+. . ..... ....+|+
T Consensus 93 ~-----------------------------------------------------~~~----~----~~~~~--~~~~~~e 109 (179)
T PRK09415 93 V-----------------------------------------------------TED----I----FTYME--SQKESVE 109 (179)
T ss_pred c-----------------------------------------------------ccc----c----ccccc--ccccCcH
Confidence 0 000 0 00000 1123566
Q ss_pred HHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchh
Q psy15215 1349 DAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 1419 (1432)
Q Consensus 1349 ~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~ 1419 (1432)
+.....+....+..+|++||+++|.|+.|+|+.|+ |++|||+.||+|.++|+++++||+++||....
T Consensus 110 ~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g~----s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~l~ 176 (179)
T PRK09415 110 EEVIQNAEDERLASAVMSLPIKYREVIYLFYYEEL----SIKEIAEVTGVNENTVKTRLKKAKELLKKGLE 176 (179)
T ss_pred HHHHHHHHHHHHHHHHHhCCHHHhhHhHhHHhcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 66677777888999999999999999999999998 99999999999999999999999999998543
No 150
>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=99.73 E-value=7.7e-17 Score=175.65 Aligned_cols=181 Identities=17% Similarity=0.220 Sum_probs=139.9
Q ss_pred HHhHHHHHHhHHHHHHHHHHHHHHHHHhccc----CCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHH
Q psy15215 392 IAGEMKARKAKREMTEANLRLVISIAKKYTD----RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITR 467 (1432)
Q Consensus 392 ~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~----~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~ 467 (1432)
+.|+.. |+..|+..|.+.|+++|++|+. +..+++|++||+++.+|+++.+|+...+.+|.+|++..++|.+.+
T Consensus 2 ~~~~~~---a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~~~~~~wl~~i~~n~~~d 78 (189)
T TIGR02984 2 RGGDQE---ALGELLDRYRNYLRLLARVQLDPRLRRRVDPSDLVQETLLEAHRRFDQFRGKTEGEFAGWLRGILSNVLAD 78 (189)
T ss_pred CCCCHH---HHHHHHHHHHHHHHHHHHHHhhhhcCCccCHHHHHHHHHHHHHHHHHhccCcccchHHHHHHHHHHHHHHH
Confidence 357777 9999999999999999999753 567899999999999999999998765568999999999999999
Q ss_pred HHHHhcc-ccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCC-CCCc
Q psy15215 468 SIADQAR-TIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDE-DSHL 545 (1432)
Q Consensus 468 ~i~~~~r-~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~-~~~~ 545 (1432)
+++++.+ .-|.+ ....+++.+.+.++ ...+
T Consensus 79 ~~r~~~~~~~r~~------------------------------------------------~~~~~~~~~~~~~~~~~~~ 110 (189)
T TIGR02984 79 ALRRHLGAQKRDI------------------------------------------------RREQSLDAGGRLDESSVRL 110 (189)
T ss_pred HHHHHHHHHhhhc------------------------------------------------ccccCCCcccccCCcchhH
Confidence 9987631 00000 00112222111111 1112
Q ss_pred CcccccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHH
Q psy15215 546 GDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625 (1432)
Q Consensus 546 ~~~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr 625 (1432)
.+.+.+ ...+|++.+...+....|..+|.+|||+++.||.++|+.|+ |++|||..||+|+++|++..+||+++|+
T Consensus 111 ~~~~~~-~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~vi~l~~~~g~----s~~eIA~~lgis~~~v~~~l~Ra~~~Lr 185 (189)
T TIGR02984 111 AAQLAA-DGPSPSQVAARREAAVRLAQALAKLPEDYREVILLRHLEGL----SFAEVAERMDRSEGAVSMLWVRGLARLR 185 (189)
T ss_pred HHHccC-CCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHhcCC----CHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 222222 23467777777777889999999999999999999999888 9999999999999999999999999999
Q ss_pred HHH
Q psy15215 626 PLA 628 (1432)
Q Consensus 626 ~~l 628 (1432)
+.+
T Consensus 186 ~~l 188 (189)
T TIGR02984 186 QIL 188 (189)
T ss_pred HHh
Confidence 865
No 151
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=99.73 E-value=7.3e-17 Score=175.02 Aligned_cols=172 Identities=16% Similarity=0.216 Sum_probs=136.4
Q ss_pred hhHHHHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHhccCC----CCChhHHHHHHHHHHHHHHHhccccCCCcchhHH
Q psy15215 1172 NDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDR----GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 1247 (1432)
Q Consensus 1172 ~e~~~l~~~~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~----~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya 1247 (1432)
.++..++..+..|+.. |+..|+..|.+.|+.+|.+++++ ..+++|++||+|+.+|+..++|+.. .+|.+|+
T Consensus 7 ~~~~~l~~~~~~gd~~---a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeDlvQe~fl~l~~~~~~~~~~--~~~~~wl 81 (184)
T PRK12512 7 DEWTDLMRSANAGDAA---AYRRLLKAVTPVLRAAARRGLARAGQPADQAEDIVQEILLAVHLKRHTWDPG--APFAPWL 81 (184)
T ss_pred hHHHHHHHHHHccCHH---HHHHHHHHHHHHHHHHHHHHHHhccCCcccHHHHHHHHHHHHHHhHHhcCcc--ccHHHHH
Confidence 3466778888889888 99999999999999999998763 4689999999999999999999863 4799999
Q ss_pred HHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCC
Q psy15215 1248 TWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPV 1327 (1432)
Q Consensus 1248 ~~~ir~~i~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~ 1327 (1432)
+.++||.+.++++++.+....+ ++.
T Consensus 82 ~~i~rn~~~d~~Rr~~~~~~~~-----------------------------------------------------~~~-- 106 (184)
T PRK12512 82 FAIARNKLIDALRRRGRRVFVD-----------------------------------------------------IDD-- 106 (184)
T ss_pred HHHHHHHHHHHHHhhcccccCC-----------------------------------------------------chh--
Confidence 9999999999999876421110 000
Q ss_pred CCCCCCCcCcccccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHH
Q psy15215 1328 GDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 1407 (1432)
Q Consensus 1328 ~~~~~~~~~d~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~ 1407 (1432)
..+.+++.. +.+ ......+..+|+.||++++.||.++|..|+ |++|||+.||+|..+|+..+
T Consensus 107 -------~~~~~~~~~---~~~----~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~----s~~eIA~~l~is~~tV~~~l 168 (184)
T PRK12512 107 -------FAETLPAEP---ATE----TLPAGDVGRHLETLPPRQRDVVQSISVEGA----SIKETAAKLSMSEGAVRVAL 168 (184)
T ss_pred -------ccccccccc---hhh----HHHHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHhCCCHHHHHHHH
Confidence 000011100 001 122456788999999999999999999888 99999999999999999999
Q ss_pred HHHHHHhhCchhhh
Q psy15215 1408 AKALRKLRHPSRYY 1421 (1432)
Q Consensus 1408 ~rAl~kLr~~~~~~ 1421 (1432)
++|+++||..+++.
T Consensus 169 ~ra~~~Lr~~l~~~ 182 (184)
T PRK12512 169 HRGLAALAAKFRSE 182 (184)
T ss_pred HHHHHHHHHHhhcC
Confidence 99999999866553
No 152
>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=99.73 E-value=5.8e-17 Score=175.69 Aligned_cols=172 Identities=18% Similarity=0.211 Sum_probs=130.5
Q ss_pred HHHHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHhccCCCC-----ChhHHHHHHHHHHHH-HHHhccccCCCcchhHH
Q psy15215 1174 LRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGL-----QFLDLIQEGNIGLMK-AVDKFEYRRGYKFSTYA 1247 (1432)
Q Consensus 1174 ~~~l~~~~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~-----~~~DLiQEg~igl~k-av~kfd~~~g~~Fstya 1247 (1432)
+..++..++.|+.. |+..|+..|.+.|+++|++|+++.. +++|++||+|+.+|+ ..++|++. ..|.||+
T Consensus 4 ~~~li~~~~~gd~~---a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~AeDlvQevfl~~~~~~~~~~~~~--~~~~~wl 78 (183)
T TIGR02999 4 VTELLQQWQNGDAA---ARDQLFPQLYQELRRIARRQLRRERSGQTLQTTALVHEAYLRLSDQDEQKWDDR--AHFFAAA 78 (183)
T ss_pred HHHHHHHHHcCCHH---HHHHHHHHHHHHHHHHHHHHhhcccccccchHHHHHHHHHHHHhhcccCCCCch--HHHHHHH
Confidence 55678889999888 9999999999999999999998877 899999999999998 78888754 3699999
Q ss_pred HHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCC
Q psy15215 1248 TWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPV 1327 (1432)
Q Consensus 1248 ~~~ir~~i~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~ 1327 (1432)
+.+++|.+.+++|++.+..+... ....+.
T Consensus 79 ~~i~~n~~~d~~R~~~~~~~~~~---------------------------------------------------~~~~~~ 107 (183)
T TIGR02999 79 AKAMRRILVDHARRRRAQKRGGG---------------------------------------------------AVRVPL 107 (183)
T ss_pred HHHHHHHHHHHHHHHHHHhccCC---------------------------------------------------cccccc
Confidence 99999999999998654111000 000000
Q ss_pred CCCCCCCcCcccccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHH
Q psy15215 1328 GDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 1407 (1432)
Q Consensus 1328 ~~~~~~~~~d~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~ 1407 (1432)
+ +..++ . ++... ........+...|++|||++|.||.|+|+.|+ |++|||+.||+|.++|+.++
T Consensus 108 -~-------~~~~~-~--~~~~~-~~~~~l~~~~~~l~~Lp~~~r~v~~l~~~~g~----s~~EIA~~lgis~~tVk~~l 171 (183)
T TIGR02999 108 -D-------EVLPD-A--EADLD-EELLDLDDALDKLAQVDPRQAEVVELRFFAGL----TVEEIAELLGVSVRTVERDW 171 (183)
T ss_pred -c-------cccCC-C--CccHH-HHHHHHHHHHHHhhcCCHHHHHHHHHHHHcCC----CHHHHHHHhCCCHHHHHHHH
Confidence 0 00000 0 11111 11111233444567799999999999999999 99999999999999999999
Q ss_pred HHHHHHhhCc
Q psy15215 1408 AKALRKLRHP 1417 (1432)
Q Consensus 1408 ~rAl~kLr~~ 1417 (1432)
+||+++||+.
T Consensus 172 ~Rar~~Lr~~ 181 (183)
T TIGR02999 172 RFARAWLADE 181 (183)
T ss_pred HHHHHHHHHH
Confidence 9999999974
No 153
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=99.73 E-value=8.3e-17 Score=176.03 Aligned_cols=180 Identities=16% Similarity=0.132 Sum_probs=141.2
Q ss_pred hhhHHHHHHHHHHhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHH
Q psy15215 381 LNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 460 (1432)
Q Consensus 381 ~~e~~~l~~~i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ 460 (1432)
..++..++.++..||.. |+..|+..|.+.|+.+|.+++++..+++|++||+++.+|+..++|++..+ +|.+|++..
T Consensus 11 ~~~~~~li~~~~~~d~~---af~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQev~l~l~~~~~~~~~~~~-~~~~wL~~i 86 (194)
T PRK12531 11 RQEWLECMEKVKSRDKQ---AFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKAHLFDGQKS-ALSTWIYTI 86 (194)
T ss_pred cHhHHHHHHHHHcCCHH---HHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCcccc-hHHHHHHHH
Confidence 35677888999999998 99999999999999999999999889999999999999999999987544 799999999
Q ss_pred HHHHHHHHHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCC
Q psy15215 461 IRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDD 540 (1432)
Q Consensus 461 ir~~i~~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~ 540 (1432)
++|.+.+++++..+..... +.+....++
T Consensus 87 arn~~ld~~Rk~~~~~~~~----------------------------------------------------~~~~~~~~~ 114 (194)
T PRK12531 87 IRNLCFDLLRKQKGKDLHI----------------------------------------------------HADDIWPSD 114 (194)
T ss_pred HHHHHHHHHHHhccccccc----------------------------------------------------chhhccccc
Confidence 9999999999876410000 000000000
Q ss_pred CCCCcCcccccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHH
Q psy15215 541 EDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 620 (1432)
Q Consensus 541 ~~~~~~~~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rA 620 (1432)
.....+.+ ...|+.. .....+..++.+||++++.||.|+|..|+ |++|||+.||+|.++|+.+.++|
T Consensus 115 ---~~~~~~~~--~~~~e~~----~~~~~l~~~l~~Lp~~~r~v~~l~~~eg~----s~~EIA~~lgis~~tVk~rl~ra 181 (194)
T PRK12531 115 ---YYPPDLVD--HYSPEQD----MLKEQVMKFLDRLPKAQRDVLQAVYLEEL----PHQQVAEMFDIPLGTVKSRLRLA 181 (194)
T ss_pred ---cccccccc--ccCHHHH----HHHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHhCcCHHHHHHHHHHH
Confidence 00000000 1123322 23456888999999999999999999999 99999999999999999999999
Q ss_pred HHHHHHHHH
Q psy15215 621 LRKLRPLAH 629 (1432)
Q Consensus 621 l~kLr~~l~ 629 (1432)
+++|+..+.
T Consensus 182 ~~~Lr~~l~ 190 (194)
T PRK12531 182 VEKLRHSMD 190 (194)
T ss_pred HHHHHHHhh
Confidence 999998774
No 154
>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=99.73 E-value=4.2e-17 Score=172.53 Aligned_cols=157 Identities=15% Similarity=0.193 Sum_probs=126.6
Q ss_pred hHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHHHHHHhcccccccc
Q psy15215 1191 AKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 1270 (1432)
Q Consensus 1191 A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~ 1270 (1432)
|++.++..|.+.|+++|+++.++..+++|++||+++.+|++.++|++.. .|.+|++..++|.+.++++++.+.-+ +.
T Consensus 2 ~~~~~~~~~~~~l~~~~~~~~~~~~~aEDivQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~r~~~~~~~-~~ 78 (159)
T TIGR02989 2 AFAALLQRHQRSLRAFVRSLVPDRDDADDVLQETFVTAWRKFDEFDPGT--DFGAWARGIARNKVLNHRRKLGRDRL-VF 78 (159)
T ss_pred HHHHHHHHhHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHHhCCCCC--chHHHHHHHHHHHHHHHHHHhccccc-cc
Confidence 7999999999999999999999999999999999999999999999754 69999999999999999999875210 00
Q ss_pred cHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHH
Q psy15215 1271 HMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 1350 (1432)
Q Consensus 1271 ~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~~d~i~d~~~~~p~~~ 1350 (1432)
. ++. .+.+.+. .+|.+.
T Consensus 79 ~-------------------------~~~------------------------------------~~~~~~~--~~~~~~ 95 (159)
T TIGR02989 79 D-------------------------DEL------------------------------------LEALAAE--AEATEA 95 (159)
T ss_pred C-------------------------HHH------------------------------------HHHHHhh--cccchH
Confidence 0 000 0000000 011122
Q ss_pred HHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCc
Q psy15215 1351 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417 (1432)
Q Consensus 1351 ~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~ 1417 (1432)
.........+..+++.||++++.|+.++|..|+ |.+|||+.||+|+++|++.++||+++||..
T Consensus 96 ~~~~~~~~~l~~~i~~L~~~~r~v~~l~~~~g~----~~~eIA~~l~is~~tv~~~l~Rar~~Lr~~ 158 (159)
T TIGR02989 96 DRSEDELQALEGCLEKLPERQRELLQLRYQRGV----SLTALAEQLGRTVNAVYKALSRLRVRLRDC 158 (159)
T ss_pred hhHHHHHHHHHHHHHHCCHHHHHHHHHHHhcCC----CHHHHHHHhCCCHHHHHHHHHHHHHHHHhc
Confidence 223344567899999999999999999999888 999999999999999999999999999974
No 155
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=99.73 E-value=2.9e-17 Score=178.30 Aligned_cols=170 Identities=15% Similarity=0.156 Sum_probs=136.4
Q ss_pred HHHhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHHHHH
Q psy15215 391 MIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA 470 (1432)
Q Consensus 391 i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~~i~ 470 (1432)
+..||.. |+..|+..|.+.|+.+|.++++...+++|++||+|+.+|+++.+|+...+.+|.||++..++|.+.+++|
T Consensus 3 ~~~gd~~---a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~~~~~~~~wL~~Iarn~~~d~~R 79 (185)
T PRK12542 3 VTNNDYE---KMEELYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKNLEKLHSLNTQELKRYILRVAKNKAIDSYR 79 (185)
T ss_pred ccccCHH---HHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHH
Confidence 4568877 9999999999999999999999999999999999999999999998644458999999999999999999
Q ss_pred HhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccc
Q psy15215 471 DQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIE 550 (1432)
Q Consensus 471 ~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~i~ 550 (1432)
++.+..... + .... +..+
T Consensus 80 k~~~~~~~~------------------------------------------------------~-~~~~-------~~~~ 97 (185)
T PRK12542 80 KNKRHETFL------------------------------------------------------E-EYER-------ESIE 97 (185)
T ss_pred Hhhhhhhhh------------------------------------------------------h-hccc-------cchh
Confidence 876410000 0 0000 0000
Q ss_pred cCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHHHH
Q psy15215 551 DENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLAHD 630 (1432)
Q Consensus 551 d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l~~ 630 (1432)
. ...+|.+.....+....|..+|.+|||++|.||.|+|..|+ |++|||+.||+|.++|+++.+||+++|+..+..
T Consensus 98 ~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~----s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~ 172 (185)
T PRK12542 98 A-VDENIEEWEKRKMSEVQIDTLLKELNESNRQVFKYKVFYNL----TYQEISSVMGITEANVRKQFERARKRVQNMIGG 172 (185)
T ss_pred h-hhccHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHcc
Confidence 0 01133343334445567999999999999999999999998 999999999999999999999999999998854
No 156
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=99.73 E-value=9.1e-17 Score=177.55 Aligned_cols=168 Identities=18% Similarity=0.167 Sum_probs=136.0
Q ss_pred hhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q psy15215 1190 KAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 1269 (1432)
Q Consensus 1190 ~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip 1269 (1432)
.+|..|+..|.+.|+.+|.+++++..+++|++||+|+.+|+.+++|+. + .|.+|++++++|.+.++++++.+.....
T Consensus 18 ~~f~~l~~~~~~~l~~~~~~~~~d~~dAEDlvQEvflkl~~~~~~~~~--~-~~~aWL~~IarN~~~d~~Rk~~~~~~~~ 94 (216)
T PRK12533 18 ERFRQLVLPHLDAAYNLARWLCGNASDADDVVQEACMRALRFFDSFRG--D-NARPWLLAIVRHTWYSEWRRRANAHEVA 94 (216)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCc--c-chHhHHHHHHHHHHHHHHHhhccccccc
Confidence 389999999999999999999999999999999999999999999984 2 5999999999999999999876410000
Q ss_pred ccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHH
Q psy15215 1270 VHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349 (1432)
Q Consensus 1270 ~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~~d~i~d~~~~~p~~ 1349 (1432)
..+. .... . .... . +....+|++
T Consensus 95 ----------------------------------------------------~~~~-~~~~-~-~~~~-~-~~~~~~~e~ 117 (216)
T PRK12533 95 ----------------------------------------------------APDT-LDDA-D-SLDD-W-QPAGEDPLA 117 (216)
T ss_pred ----------------------------------------------------cccc-cccc-c-cccc-c-ccCCCCHHH
Confidence 0000 0000 0 0000 0 111236777
Q ss_pred HHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchhhh
Q psy15215 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYY 1421 (1432)
Q Consensus 1350 ~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~~~ 1421 (1432)
.+...+....|..+|..||+++|.||.|+|+.|+ |++|||+.||||.++|+++++||+++||+.+...
T Consensus 118 ~~~~~e~~~~l~~al~~Lp~~~R~v~~L~y~eg~----s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l~~~ 185 (216)
T PRK12533 118 LLLRAEDVRLVNAALAKLPVEYREVLVLRELEDM----SYREIAAIADVPVGTVMSRLARARRRLAALLGGA 185 (216)
T ss_pred HHHHHHHHHHHHHHHHcCCHHHHhHhhhHHhcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHccc
Confidence 7888888899999999999999999999999988 9999999999999999999999999999976544
No 157
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=99.72 E-value=4.5e-17 Score=175.17 Aligned_cols=169 Identities=15% Similarity=0.132 Sum_probs=132.7
Q ss_pred HHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHH
Q psy15215 1178 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITR 1257 (1432)
Q Consensus 1178 ~~~~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~ 1257 (1432)
+..++.|+.. |+..++..|.+.|+.+|+++.+ ..+++|++||+|+.+|++.++|++. ..|.+|++.+++|.+.+
T Consensus 2 ~~~~~~gd~~---a~~~l~~~~~~~l~~~~~~~~~-~~~aeDivQe~~l~l~~~~~~~~~~--~~~~~wl~~ia~n~~~d 75 (175)
T PRK12518 2 ILRCQRGDRQ---SFRQLYRRYQQKVRSTLYQLCG-RELLDDLVQEVFLRVWKGLPKLRNP--AYFSTWLYRITWNVATD 75 (175)
T ss_pred hhHHHcCCHH---HHHHHHHHHHHHHHHHHHHHcC-HhHHHHHHHHHHHHHHHhHHhhCCc--ccHHHHHHHHHHHHHHH
Confidence 4567788888 9999999999999999999875 4789999999999999999999964 47999999999999999
Q ss_pred HHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCc
Q psy15215 1258 SIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGD 1337 (1432)
Q Consensus 1258 ~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~~d 1337 (1432)
++|++.+.-. . .... .....
T Consensus 76 ~~R~~~~~~~---~---------------------------------------------------~~~~-~~~~~----- 95 (175)
T PRK12518 76 ARRQFAQRPS---R---------------------------------------------------IQDD-SLNDQ----- 95 (175)
T ss_pred HHHHhhcccc---c---------------------------------------------------hhcc-ccccc-----
Confidence 9997654100 0 0000 00000
Q ss_pred ccccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCc
Q psy15215 1338 FIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417 (1432)
Q Consensus 1338 ~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~ 1417 (1432)
.......| ..........+..+|+.||+++|.||.|+|+.|+ |++|||+.||+|.++|++.++||+++||..
T Consensus 96 --~~~~~~~~--~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~g~----s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~ 167 (175)
T PRK12518 96 --PSRPSDTP--DLMQLHYQDLVQQGLQTLSLEHRAVLVLHDLEDL----PQKEIAEILNIPVGTVKSRLFYARRQLRKF 167 (175)
T ss_pred --ccCCCCcH--HHHHHHHHHHHHHHHHhCCHHHeeeeeehHhcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 00001122 2222344567899999999999999999999998 999999999999999999999999999997
Q ss_pred hhh
Q psy15215 1418 SRY 1420 (1432)
Q Consensus 1418 ~~~ 1420 (1432)
..+
T Consensus 168 l~~ 170 (175)
T PRK12518 168 LQQ 170 (175)
T ss_pred HHh
Confidence 654
No 158
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=99.72 E-value=1.2e-16 Score=174.71 Aligned_cols=179 Identities=20% Similarity=0.126 Sum_probs=141.0
Q ss_pred hcCCChhhHHHHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchh
Q psy15215 1166 DIVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 1245 (1432)
Q Consensus 1166 ~~~l~~~e~~~l~~~~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fst 1245 (1432)
..+++..++.+++.++..|+.. |+..++..|.+.++.+++ ++++..+++|++||+|+.+|+..++|++. .+|.+
T Consensus 4 ~~~~~~~~~~~l~~~~~~~d~~---a~~~l~~~y~~~l~~~~~-~~~~~~~AEDivQevflkl~~~~~~~~~~--~~~~~ 77 (196)
T PRK12535 4 SSERDDAHVTDLALAAGRGDRA---ALTEFIRETQDDVWRLLA-HLGGHDIADDLTQETYLRVMSALPRFAAR--SSART 77 (196)
T ss_pred ccccccHHHHHHHHHHHcCCHH---HHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHHhhhcCCc--ccHHH
Confidence 3456667788899999999988 999999999999999975 56888899999999999999999999864 37999
Q ss_pred HHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCC
Q psy15215 1246 YATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMES 1325 (1432)
Q Consensus 1246 ya~~~ir~~i~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~ 1325 (1432)
|++.+++|.+.+++|++.+..+. +.+
T Consensus 78 WL~~Iarn~~id~~Rk~~~~~~~-----------------------------------------------------~~~- 103 (196)
T PRK12535 78 WLLSLARRVWVDNIRHDMARPRK-----------------------------------------------------SAT- 103 (196)
T ss_pred HHHHHHHHHHHHHHHhhccCCCc-----------------------------------------------------ccc-
Confidence 99999999999999987642110 000
Q ss_pred CCCCCCCCCcCcccccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHH
Q psy15215 1326 PVGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 1405 (1432)
Q Consensus 1326 ~~~~~~~~~~~d~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq 1405 (1432)
...+ ..+ ...+|+.... ......+..+|+.|||++++||.|+|+.|+ |++|||+.||+|.++|++
T Consensus 104 ~~~~-----~~~-----~~~~~~~~~~-~~~~~~l~~~l~~Lp~~~r~v~~l~~~~g~----s~~EIAe~lgis~~tV~~ 168 (196)
T PRK12535 104 EYED-----AAA-----TTASNETTGS-WSEWIDVRTLIDALPPERREALILTQVLGY----TYEEAAKIADVRVGTIRS 168 (196)
T ss_pred cccc-----ccc-----ccCCcchhHH-HHHHHHHHHHHHcCCHHHHHHhhhHHHhCC----CHHHHHHHhCCCHHHHHH
Confidence 0000 000 0011221111 122357899999999999999999999999 999999999999999999
Q ss_pred HHHHHHHHhhCchh
Q psy15215 1406 IEAKALRKLRHPSR 1419 (1432)
Q Consensus 1406 ~~~rAl~kLr~~~~ 1419 (1432)
+++||+++||....
T Consensus 169 ~l~Rar~~Lr~~l~ 182 (196)
T PRK12535 169 RVARARADLIAATA 182 (196)
T ss_pred HHHHHHHHHHHHhc
Confidence 99999999998543
No 159
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=99.72 E-value=1.1e-16 Score=172.63 Aligned_cols=166 Identities=17% Similarity=0.253 Sum_probs=135.6
Q ss_pred HHhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHHHHHH
Q psy15215 392 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIAD 471 (1432)
Q Consensus 392 ~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~~i~~ 471 (1432)
+.|+.. |+..++..|.+.|+++|++|+++..+++|++||+++.+|+++.+|++.. +|.+|++..+++.+.+++++
T Consensus 2 ~~~d~~---af~~l~~~~~~~l~~~~~~~~~~~~daeDl~Qevfl~l~~~~~~~~~~~--~f~~wl~~iarn~~~~~~r~ 76 (179)
T PRK12543 2 LSGDQE---AFSEIYDVTIQEVYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKYDSNR--PFRFWLIGLVIKQIHSWRRK 76 (179)
T ss_pred cCchHH---HHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHcCCCC--ChHHHHHHHHHHHHHHHHHh
Confidence 457777 9999999999999999999999999999999999999999999999753 79999999999999998876
Q ss_pred hccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCccccc
Q psy15215 472 QARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIED 551 (1432)
Q Consensus 472 ~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~i~d 551 (1432)
..+..+. ++. ..+. .+ .
T Consensus 77 ~~~~~~~------------------------------------------------------~~~-~~~~-----~~---~ 93 (179)
T PRK12543 77 RWRRFRI------------------------------------------------------FEK-AEEQ-----RK---P 93 (179)
T ss_pred hcccccc------------------------------------------------------ccc-cccc-----cc---c
Confidence 5431000 000 0000 00 0
Q ss_pred CCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHHHH
Q psy15215 552 ENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLAHD 630 (1432)
Q Consensus 552 ~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l~~ 630 (1432)
....+|+. ....+....+..+|..|||++|.|+.|+|..|+ |++|||+.||+|.++|+.+.++|+.+|++.+..
T Consensus 94 ~~~~~~~~-~~~~~~~~~l~~~l~~Lp~~~r~i~~l~~~e~~----s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~ 167 (179)
T PRK12543 94 VSIDFSED-VLSKESNQELIELIHKLPYKLRQVIILRYLHDY----SQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQI 167 (179)
T ss_pred ccccChHH-HHHHHHHHHHHHHHHhCCHHHHHHHHHHHHccC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 01123444 566677788999999999999999999999999 999999999999999999999999999998864
No 160
>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=99.72 E-value=5e-17 Score=172.05 Aligned_cols=159 Identities=13% Similarity=0.164 Sum_probs=130.7
Q ss_pred hHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHHHHHHhcccccccc
Q psy15215 1191 AKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 1270 (1432)
Q Consensus 1191 A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~ 1270 (1432)
|+++|+..|.+.|+++|+++.++..+++|++||+++++|+++++|++. .+|.+|++.++|+.+.+++++..+.-..
T Consensus 2 a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~~~~~~~~~~~~--~~~~~wl~~i~r~~~~d~~r~~~~~~~~-- 77 (161)
T TIGR02985 2 AFEQLYRRYYPKLCAFAYRYVKDEEEAEDIVQDVFVKLWENRETLEEV--ESFKAYLFTIVKNRSLNYLRHKQVEEKY-- 77 (161)
T ss_pred hHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcccc--ccHHHHHHHHHHHHHHHHHHHHHhHhHH--
Confidence 899999999999999999999999999999999999999999999864 3799999999999999999987641000
Q ss_pred cHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHH
Q psy15215 1271 HMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 1350 (1432)
Q Consensus 1271 ~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~~d~i~d~~~~~p~~~ 1350 (1432)
...+ .+.... .....+|++.
T Consensus 78 ------------~~~~-----------------------------------------~~~~~~-------~~~~~~~~~~ 97 (161)
T TIGR02985 78 ------------QEEI-----------------------------------------LEIEVD-------ELSENDPEEE 97 (161)
T ss_pred ------------HHHH-----------------------------------------Hhhccc-------ccCCCCcHHH
Confidence 0000 000000 0011245666
Q ss_pred HHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCc
Q psy15215 1351 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417 (1432)
Q Consensus 1351 ~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~ 1417 (1432)
+...+....+..++..||++++.||.++|..|. |..|||+.+|+|+++|++++++|+++||+.
T Consensus 98 ~~~~e~~~~l~~~l~~L~~~~r~il~l~~~~~~----~~~eIA~~lgis~~tv~~~~~ra~~~Lr~~ 160 (161)
T TIGR02985 98 LEAKELQLIIYKAIEKLPEQCRKIFILSRFEGK----SYKEIAEELGISVKTVEYHISKALKELRKE 160 (161)
T ss_pred HHHHHHHHHHHHHHHHCCHHHHHHHHHHHHcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 666777888999999999999999999998888 999999999999999999999999999974
No 161
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=99.72 E-value=2e-16 Score=172.34 Aligned_cols=173 Identities=18% Similarity=0.226 Sum_probs=144.9
Q ss_pred hHHHHHHHHHHhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHH
Q psy15215 383 DLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 462 (1432)
Q Consensus 383 e~~~l~~~i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir 462 (1432)
....++..++.||.. |+..++..|.+.|+.++.+++++..+++|++||+|+.+|++..+|++. .+|.+|++..++
T Consensus 8 ~~~~l~~~~~~gd~~---a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~l~~~~~~~~~~--~~~~~wl~~i~~ 82 (189)
T PRK12515 8 TDEMLLARIAQGDRT---AMQTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEGR--SQVSTWLLSIAR 82 (189)
T ss_pred CHHHHHHHHHccCHH---HHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCC--CChHHHHHHHHH
Confidence 345678888999998 999999999999999999999999999999999999999999999963 479999999999
Q ss_pred HHHHHHHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCC
Q psy15215 463 QAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDED 542 (1432)
Q Consensus 463 ~~i~~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~ 542 (1432)
+.+.+++++..+. .+ + .+.
T Consensus 83 n~~~d~~r~~~~~-~~-----------------------------------------------------~------~~~- 101 (189)
T PRK12515 83 FKALSALRRRKHE-EI-----------------------------------------------------D------DEA- 101 (189)
T ss_pred HHHHHHHHccCCC-CC-----------------------------------------------------c------ccc-
Confidence 9999999865431 00 0 000
Q ss_pred CCcCcccccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHH
Q psy15215 543 SHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALR 622 (1432)
Q Consensus 543 ~~~~~~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~ 622 (1432)
. ..+.+ ...+|+......+....+..+|+.||+++|.||.|+|..|+ |++|||+.||+|+++|+++.+||+.
T Consensus 102 --~-~~~~~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~~----s~~eIA~~lgis~~tV~~~l~Rar~ 173 (189)
T PRK12515 102 --A-AAIED-GADTPEVALQKSDTSAALRACLAKLSPAHREIIDLVYYHEK----SVEEVGEIVGIPESTVKTRMFYARK 173 (189)
T ss_pred --c-cccCC-CCCCHHHHHHhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 0 00111 12356666666777788999999999999999999999999 9999999999999999999999999
Q ss_pred HHHHHHH
Q psy15215 623 KLRPLAH 629 (1432)
Q Consensus 623 kLr~~l~ 629 (1432)
+|++.+.
T Consensus 174 ~Lr~~l~ 180 (189)
T PRK12515 174 KLAELLK 180 (189)
T ss_pred HHHHHHH
Confidence 9998765
No 162
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=99.72 E-value=1.9e-16 Score=171.32 Aligned_cols=170 Identities=17% Similarity=0.182 Sum_probs=136.1
Q ss_pred HHHhhhhhhhhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHHHH
Q psy15215 1180 KMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSI 1259 (1432)
Q Consensus 1180 ~~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~~i 1259 (1432)
....|+.. ++..++..|.+.++.+|++++++..+++||+||+|+.+|+++..| . .+.+|.||++.+++|.+.+++
T Consensus 8 ~~~~~~~~---~~~~~~~~~~~~l~~~~~~~~~~~~dAeDlvQE~~lr~~~~~~~~-~-~~~~~~~wl~~Ia~n~~iD~~ 82 (182)
T COG1595 8 EALRGDRA---AFEELLERLRPRLRRLARRLLGDRADAEDLVQETFLRAWRAIDSF-R-GRSSFKAWLYRIARNLAIDRL 82 (182)
T ss_pred HHHhcchH---HHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhc-C-CCCchHHHHHHHHHHHHHHHH
Confidence 34455555 999999999999999999999998899999999999999999999 3 334899999999999999999
Q ss_pred HHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCccc
Q psy15215 1260 ADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFI 1339 (1432)
Q Consensus 1260 ~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~~d~i 1339 (1432)
|++.+..... .+ .+. .+..
T Consensus 83 R~~~r~~~~~-----------------------------------------------------~~-----~~~---~~~~ 101 (182)
T COG1595 83 RKRKRRRARV-----------------------------------------------------EE-----ADL---LPEE 101 (182)
T ss_pred HHhccccccc-----------------------------------------------------cc-----ccc---cccc
Confidence 9988632210 00 000 0000
Q ss_pred ccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchh
Q psy15215 1340 EDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 1419 (1432)
Q Consensus 1340 ~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~ 1419 (1432)
.+.....+ +.+...+....+..+|..||+++|.+|.|+|+.|. |++|||+.+|||.+||+.++++|+++||....
T Consensus 102 ~~~~~~~~-~~~~~~~~~~~l~~al~~Lp~~~R~~~~l~~~~gl----s~~EIA~~l~i~~~tVks~l~ra~~~l~~~l~ 176 (182)
T COG1595 102 ADPAPDLA-ELLLAEEELERLRRALARLPPRQREAFLLRYLEGL----SYEEIAEILGISVGTVKSRLHRARKKLREQLE 176 (182)
T ss_pred cCcccccc-hHHHHHHHHHHHHHHHHhCCHHHhHHhhhHhhcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 00000011 25666778899999999999999999999999888 99999999999999999999999999998654
Q ss_pred h
Q psy15215 1420 Y 1420 (1432)
Q Consensus 1420 ~ 1420 (1432)
.
T Consensus 177 ~ 177 (182)
T COG1595 177 E 177 (182)
T ss_pred h
Confidence 3
No 163
>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=99.71 E-value=7e-17 Score=176.52 Aligned_cols=170 Identities=12% Similarity=0.079 Sum_probs=130.8
Q ss_pred hhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q psy15215 1190 KAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 1269 (1432)
Q Consensus 1190 ~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip 1269 (1432)
.+|..|+..|.+.|+.+|.+++++..+++|++||+|+.+|++.++|++. .+|.+|++.+++|.+.+++|++.+.....
T Consensus 11 ~~f~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQevfl~~~~~~~~~~~~--~~~~~wL~~iarN~~~d~~Rk~~~~~~~~ 88 (193)
T TIGR02947 11 QRFERDALEYLDQLYGAALRMTRNPADAEDLVQEAYAKAFSSFHQFKPG--TNLKAWLYRILTNTYINSYRKAQRRPQQS 88 (193)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhcccCCC--CcchHHHHHHHHHHHHHHHHHhcCCcccc
Confidence 3899999999999999999999999999999999999999999999854 47999999999999999999876521100
Q ss_pred ccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHH
Q psy15215 1270 VHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349 (1432)
Q Consensus 1270 ~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~~d~i~d~~~~~p~~ 1349 (1432)
. .+++.. ..+. +.... .......|+.
T Consensus 89 ~-------------------------~~~~~~-------------------~~~~----~~~~~------~~~~~~~~e~ 114 (193)
T TIGR02947 89 D-------------------------DDDIED-------------------WQLA----KAASH------TSNGLRSAEL 114 (193)
T ss_pred c-------------------------chhhhh-------------------hhhc----ccccc------ccccccchhH
Confidence 0 000000 0000 00000 0000113444
Q ss_pred HHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchh
Q psy15215 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 1419 (1432)
Q Consensus 1350 ~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~ 1419 (1432)
..........|..+|++||+++|.|+.|+|..|+ |++|||+.||+|.++|+.+++||+++||+.+.
T Consensus 115 ~~~~~~~~~~l~~~l~~Lp~~~r~i~~L~~~~g~----s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~ 180 (193)
T TIGR02947 115 EALDGLPDQDIKDALQGLPEEFRQAVYLADVEGF----AYKEIAEIMGTPIGTVMSRLHRGRKQLRKQLV 180 (193)
T ss_pred HHHhhhhHHHHHHHHHhCCHHHhhheeehhhcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 4444455678999999999999999999999998 99999999999999999999999999998654
No 164
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=99.71 E-value=1.6e-16 Score=171.85 Aligned_cols=173 Identities=14% Similarity=0.155 Sum_probs=138.0
Q ss_pred hhhHHHHHHHHHHhHHHHHHhHHHHHHHHHHHHHHHHHhccc-CCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHH
Q psy15215 381 LNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTD-RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 459 (1432)
Q Consensus 381 ~~e~~~l~~~i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~-~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~ 459 (1432)
...+..++.++..||.. |+..++..|.+.|+.+|.++++ ...+++|++||+++.||++.+.|++. .+|.+|++.
T Consensus 5 ~~~~~~~~~~~~~~d~~---a~~~l~~~~~~~l~~~~~~~~~~~~~~aeDlvQevfl~l~~~~~~~~~~--~~~~~wl~~ 79 (181)
T PRK12536 5 EARLRALLLRGLAGDAA---AYRQFLSELAAHLRGFLRRRLPQLPDEVEDLVQEILLAVHNARHTYRAD--QPLTAWVHA 79 (181)
T ss_pred HhHHHHHHHHHHcCCHH---HHHHHHHHHHHHHHHHHHHHcCCChhhHHHHHHHHHHHHHHhHHhcCCC--CchHHHHHH
Confidence 34567789999999998 9999999999999999988764 57899999999999999999999974 479999999
Q ss_pred HHHHHHHHHHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCC
Q psy15215 460 WIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGD 539 (1432)
Q Consensus 460 ~ir~~i~~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~ 539 (1432)
.++|.+.+++|++.+.... ..+..+
T Consensus 80 iarN~~~d~~Rk~~~~~~~-------------------------------------------------------~~~~~~ 104 (181)
T PRK12536 80 IARYKLMDFLRSRARREAL-------------------------------------------------------HDPLDD 104 (181)
T ss_pred HHHHHHHHHHHHHhccccc-------------------------------------------------------cCCccc
Confidence 9999999999987642000 000000
Q ss_pred CCCCCcCcccccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHH
Q psy15215 540 DEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 619 (1432)
Q Consensus 540 ~~~~~~~~~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~r 619 (1432)
.. +...+. ...+ .+....+..+|..||++++.|+.|+|..|+ |++|||+.||+|+++|+.+.++
T Consensus 105 ~~-----~~~~~~-~~~~------~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~----s~~EIA~~l~is~~tV~~~l~r 168 (181)
T PRK12536 105 ES-----ELFATS-DDEA------AEARRDLGKLLEQLPDRQRLPIVHVKLEGL----SVAETAQLTGLSESAVKVGIHR 168 (181)
T ss_pred hh-----hhcCCC-Ccch------HHHHHHHHHHHHHCCHHHHHHHHHHHHcCC----CHHHHHHHHCCCHHHHHHHHHH
Confidence 00 000000 0011 134456899999999999999999999998 9999999999999999999999
Q ss_pred HHHHHHHHHH
Q psy15215 620 ALRKLRPLAH 629 (1432)
Q Consensus 620 Al~kLr~~l~ 629 (1432)
|+++|++.+.
T Consensus 169 ar~~Lr~~l~ 178 (181)
T PRK12536 169 GLKALAAKIR 178 (181)
T ss_pred HHHHHHHHhc
Confidence 9999998764
No 165
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=99.71 E-value=2e-16 Score=169.88 Aligned_cols=169 Identities=10% Similarity=0.190 Sum_probs=133.7
Q ss_pred HhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHHHHHHhccccccc
Q psy15215 400 KAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 479 (1432)
Q Consensus 400 ~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip 479 (1432)
..+.+|+..|.++|+.+|++|++...+++|++||+++.+|++.++|++.. +|.+|++..++|.+.+++|++.+....+
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 36899999999999999999999999999999999999999999999743 7999999999999999999876521000
Q ss_pred hhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHH
Q psy15215 480 VHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 559 (1432)
Q Consensus 480 ~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~i~d~~~~~p~~ 559 (1432)
.+ . .+. +....+. ..+ ....|..
T Consensus 81 ~~-------------------------------------------------~-~~~----~~~~~~~--~~~-~~~~~~~ 103 (173)
T PRK12522 81 LD-------------------------------------------------L-FHK----EDGGEIE--FAD-DVNISEE 103 (173)
T ss_pred cc-------------------------------------------------c-cch----hhhhhhc--ccc-CCCChHH
Confidence 00 0 000 0000000 000 1112333
Q ss_pred HHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHHHHHH
Q psy15215 560 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLAHDWL 632 (1432)
Q Consensus 560 ~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l~~~~ 632 (1432)
....+..+.+..+|..||++++.|+.|+|..|+ |++|||+.||+|.++|+.+.+||+++|+..+..+.
T Consensus 104 -~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~~~----s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~~~~ 171 (173)
T PRK12522 104 -FIQKVEAEMIREVIQLLNEKYKTVLVLYYYEQY----SYKEMSEILNIPIGTVKYRLNYAKKQMREHLEGFV 171 (173)
T ss_pred -HHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHh
Confidence 455567788999999999999999999999999 99999999999999999999999999999887653
No 166
>PF08275 Toprim_N: DNA primase catalytic core, N-terminal domain; InterPro: IPR013264 This is the N-terminal, catalytic core domain of DNA primases. DNA primase (2.7.7 from EC) is a nucleotidyltransferase which synthesizes the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork. It can also prime the leading strand and has been implicated in cell division []. ; PDB: 1EQN_E 1DD9_A 3B39_B 1DDE_A 2AU3_A.
Probab=99.71 E-value=1.5e-18 Score=174.40 Aligned_cols=93 Identities=27% Similarity=0.366 Sum_probs=67.0
Q ss_pred HHHHhhhhhhh--hH-hhcC--CCcccccccccCCCCCchhhHHHHHH------------------HHHHhhhcc--EEE
Q psy15215 631 WLEQRTHQNEK--II-ACSS--DSSNHNEHVTNNNFPPGFNIFHKLLR------------------ILQEYLESF--LIS 685 (1432)
Q Consensus 631 ~~~~~l~~~~~--~~-~l~~--l~~~~~~~f~~Gyap~~~~~l~~~~~------------------~~~~~~~~f--ri~ 685 (1432)
||++++..+.. |+ ||.. +|+++|+.|+|||||.+|..|.+++. ....++++| |||
T Consensus 1 fy~~~L~~~~~~~a~~YL~~Rgl~~e~i~~F~lGyap~~~~~l~~~l~~~~~~~~~l~~~GL~~~~~~~~~~d~F~~Rii 80 (128)
T PF08275_consen 1 FYHKQLKNNPGKEALEYLKKRGLSDETIKKFQLGYAPGNWDSLLEYLKKKGFSLEELLEAGLIRKNENGGYYDFFRGRII 80 (128)
T ss_dssp HHHHHCCCGHHHHHHHHHHHTT--HHHHHHTT-EEE-SCSCHHHHHHCCCCHHHHHHCCTTCEECCTTTEEEETTTTEEE
T ss_pred CchHHHcCCchHHHHHHHHHcCCCHHHHHHhCCCcccCcHHHHHHHHHhccccHHHHHHCCCcEEcCCCCcccccCCeEE
Confidence 68888776555 77 8877 89999999999999999999988773 112334445 699
Q ss_pred Eee-----eeeeeeeeeeCCC-CC----CCCCCCcccCccccCchHhH
Q psy15215 686 FFL-----RNHGISGFLLTTP-DP----VHETPLFHKSNELYGLFEAK 723 (1432)
Q Consensus 686 fpi-----r~igf~gR~~~~~-~~----s~et~~f~K~~~Ly~~~~a~ 723 (1432)
||| +||||+||.+++. .| ||||++|+|+++|||++.||
T Consensus 81 fPI~d~~G~vvgF~gR~l~~~~~pKYlNs~et~if~K~~~Lyg~~~Ak 128 (128)
T PF08275_consen 81 FPIRDERGRVVGFGGRRLDDENPPKYLNSPETPIFKKSRILYGLDQAK 128 (128)
T ss_dssp EEEE-TTS-EEEEEEEESSSSSS-SEEE---BTTB-GGG-EETHHHHH
T ss_pred EEEEcCCCCEEEEecccCCCCCCCceECCCCCccccCCceecCccccC
Confidence 999 6999999999765 34 99999999999999999996
No 167
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=99.71 E-value=2.3e-16 Score=173.13 Aligned_cols=162 Identities=17% Similarity=0.233 Sum_probs=134.3
Q ss_pred hhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHHHHHHhcccccc
Q psy15215 1189 RKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI 1268 (1432)
Q Consensus 1189 ~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~~i~~~~r~iri 1268 (1432)
..|+..|+..|.+.|+.++.+++++...++|++||+|+.+|++..+|++ + +|.+|++.++||.+.+++|+..+ .+.
T Consensus 27 ~~a~~~l~~~~~~~L~~~~~~~~~~~~~AEDivQEvflkl~~~~~~~~~--~-~~~~wL~~iarn~~~d~~Rk~~~-~~~ 102 (203)
T PRK09647 27 MPSWEELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSLQNYQP--G-TFEGWLHRITTNLFLDMVRRRAR-IRM 102 (203)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCC--c-ccHHHHHHHHHHHHHHHHHhccc-Ccc
Confidence 3499999999999999999999999999999999999999999999974 3 69999999999999999998653 110
Q ss_pred cccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChH
Q psy15215 1269 PVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPS 1348 (1432)
Q Consensus 1269 p~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~~d~i~d~~~~~p~ 1348 (1432)
. .++ ++ . +... ....+|.
T Consensus 103 --~--------------------------------------------------~~~-----~~---~-~~~~-~~~~~~~ 120 (203)
T PRK09647 103 --E--------------------------------------------------ALP-----ED---Y-DRVP-GDEPNPE 120 (203)
T ss_pred --c--------------------------------------------------ccc-----cc---c-cccC-CCCCCHH
Confidence 0 000 00 0 0001 1123566
Q ss_pred HHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchhh
Q psy15215 1349 DAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRY 1420 (1432)
Q Consensus 1349 ~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~~ 1420 (1432)
.......+...|..+|+.||++++.|+.|+|+.|+ |++|||+.||+|.++|++.++||+++||+.+..
T Consensus 121 ~~~~~~~~~~~l~~~L~~L~~~~r~v~~L~~~~g~----s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l~~ 188 (203)
T PRK09647 121 QIYHDARLDPDLQAALDSLPPEFRAAVVLCDIEGL----SYEEIAATLGVKLGTVRSRIHRGRQQLRAALAA 188 (203)
T ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 66777777888999999999999999999999888 999999999999999999999999999986654
No 168
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=99.71 E-value=1e-16 Score=169.76 Aligned_cols=155 Identities=12% Similarity=0.123 Sum_probs=126.3
Q ss_pred HHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHH
Q psy15215 1197 EANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 1276 (1432)
Q Consensus 1197 ~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~~~~~~~ 1276 (1432)
+.|.+.|+.+|.+++++..+++|++||+|+.+|++.++|++. .|.||++.+++|.+.+++|++.+..+.
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 578999999999999999999999999999999999999853 599999999999999999987641100
Q ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHHHHHHHH
Q psy15215 1277 NKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 1356 (1432)
Q Consensus 1277 ~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~~d~i~d~~~~~p~~~~~~~~~ 1356 (1432)
.++. ++. .+.+. ...+|++.....+.
T Consensus 71 --------------------------------------------~~~~----~~~----~~~~~--~~~~~~~~~~~~e~ 96 (160)
T PRK09642 71 --------------------------------------------LSLC----KET----EENIK--SSHNIEDLLLTKEQ 96 (160)
T ss_pred --------------------------------------------cccc----hhh----hhhcc--CCCChHHHHHHHHH
Confidence 0000 000 00000 11246666666777
Q ss_pred HHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchhh
Q psy15215 1357 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRY 1420 (1432)
Q Consensus 1357 ~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~~ 1420 (1432)
...+..+|++|||++|.|+.|+|..|+ |++|||+.||+|.++|+++++||+++||...+.
T Consensus 97 ~~~l~~~l~~Lp~~~r~v~~l~~~~g~----s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 156 (160)
T PRK09642 97 KLLIAQKLRELPENYRDVVLAHYLEEK----SYQEIALQEKIEVKTVEMKLYRARKWIKKHWKE 156 (160)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHhCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhh
Confidence 888999999999999999999999999 999999999999999999999999999996643
No 169
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=99.71 E-value=2.9e-16 Score=187.08 Aligned_cols=183 Identities=18% Similarity=0.221 Sum_probs=143.2
Q ss_pred HHHHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHH
Q psy15215 1174 LRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 1253 (1432)
Q Consensus 1174 ~~~l~~~~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~ 1253 (1432)
-.+|+.+++.|+.. |+.+|+..|.+.|+++|.+++++..+++|++||+|+.+|+..++|+.. .+|.+|++.+++|
T Consensus 6 ~~~l~~~~~~gd~~---af~~l~~~y~~~l~~~~~~~~~~~~dAEDivQevfl~~~~~~~~~~~~--~~~~~wL~~Ia~n 80 (339)
T PRK08241 6 AAALLARAAAGDRD---AFAALVEPHRRELLAHCYRMLGSVHDAEDAVQETLLRAWRGYDRFEGR--SSLRTWLYRIATN 80 (339)
T ss_pred HHHHHHHhhcCCHH---HHHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHhhhhccccc--cchHHHHHHHHHH
Confidence 35688899999988 999999999999999999999999999999999999999999999843 4799999999999
Q ss_pred HHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCC--
Q psy15215 1254 AITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDE-- 1331 (1432)
Q Consensus 1254 ~i~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~-- 1331 (1432)
.+.+++|++.+.. .+ .....+..+..
T Consensus 81 ~~~d~~Rk~~~~~-~~---------------------------------------------------~~~~~~~~~~~~~ 108 (339)
T PRK08241 81 VCLDALEGRARRP-LP---------------------------------------------------TDLGAPAADPVDE 108 (339)
T ss_pred HHHHHHHhhcccc-Cc---------------------------------------------------cccCCCcCccccc
Confidence 9999999876410 00 00000000000
Q ss_pred -----CCCcCccccc----CCCCChHHHHHHHH-HHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHH
Q psy15215 1332 -----DSHLGDFIED----ENMLAPSDAALNAS-MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRE 1401 (1432)
Q Consensus 1332 -----~~~~~d~i~d----~~~~~p~~~~~~~~-~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~ 1401 (1432)
.....+.+.+ ....+|++.....+ ....+..+|.+||+++|.||.|+|+.|+ |++|||+.||+|.+
T Consensus 109 ~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L~~~~g~----s~~EIA~~lgis~~ 184 (339)
T PRK08241 109 LVERPEVPWLEPYPDALLDPAAADPAARVVARESVRLAFVAALQHLPPRQRAVLILRDVLGW----SAAEVAELLDTSVA 184 (339)
T ss_pred ccccccccccCCCCcccccccCCChHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhhHHhhCC----CHHHHHHHhCCCHH
Confidence 0000111111 11346776665544 4567899999999999999999999999 99999999999999
Q ss_pred HHHHHHHHHHHHhhCc
Q psy15215 1402 RIRQIEAKALRKLRHP 1417 (1432)
Q Consensus 1402 ~Vrq~~~rAl~kLr~~ 1417 (1432)
+|+++++||+++||+.
T Consensus 185 tVk~~l~RAr~~Lr~~ 200 (339)
T PRK08241 185 AVNSALQRARATLAER 200 (339)
T ss_pred HHHHHHHHHHHHHhhc
Confidence 9999999999999993
No 170
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=99.71 E-value=7.4e-17 Score=172.95 Aligned_cols=164 Identities=13% Similarity=0.108 Sum_probs=130.7
Q ss_pred HhhhhhhhhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHHHHHH
Q psy15215 1182 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIAD 1261 (1432)
Q Consensus 1182 ~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~~i~~ 1261 (1432)
++|+.. |+..|+..|.+.|+.+|.+++++..+++|++||+|+.+|+. .+|... ..|.+|++.+++|.+.+++|+
T Consensus 5 ~~~~~~---a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQevflk~~~~-~~~~~~--~~~~~wL~~Iarn~~~d~~Rk 78 (172)
T PRK12523 5 QSPHSE---LVGALYRDHRGWLLAWLRRNVACRQRAEDLSQDTFVRLLGR-PELPTP--REPRAFLAAVAKGLMFDHFRR 78 (172)
T ss_pred CCCCcH---HHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHcc-cccCcc--hhHHHHHHHHHHHHHHHHHHH
Confidence 567777 99999999999999999999999999999999999999986 456543 379999999999999999998
Q ss_pred hcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCccccc
Q psy15215 1262 QARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIED 1341 (1432)
Q Consensus 1262 ~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~~d~i~d 1341 (1432)
+.+... ...+ +.. . . .
T Consensus 79 ~~~~~~------------------~~~~---------------------------------~~~-~-~-----------~ 94 (172)
T PRK12523 79 AALEQA------------------YLAE---------------------------------LAL-V-P-----------E 94 (172)
T ss_pred HHHHHH------------------HHHH---------------------------------Hhh-c-c-----------c
Confidence 763100 0000 000 0 0 0
Q ss_pred CCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchh
Q psy15215 1342 ENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 1419 (1432)
Q Consensus 1342 ~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~ 1419 (1432)
....+|+......+....+..+|+.||+++|.||.|+|+.|+ |++|||+.||+|.++|++++++|+++||....
T Consensus 95 ~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~L~~~~g~----s~~EIA~~lgis~~tV~~~l~ra~~~~~~~l~ 168 (172)
T PRK12523 95 AEQPSPEEQHLILEDLKAIDRLLGKLSSKARAAFLYNRLDGM----GHAEIAERLGVSVSRVRQYLAQGLRQCYIALY 168 (172)
T ss_pred ccCCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Confidence 011245555544555568999999999999999999999988 99999999999999999999999999987543
No 171
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=99.70 E-value=3.8e-16 Score=169.37 Aligned_cols=171 Identities=13% Similarity=0.164 Sum_probs=136.8
Q ss_pred hhHHHHHHHHHHhHHHHHHhHHHHHHHHHHHHHHHHH----hcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHH
Q psy15215 382 NDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAK----KYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 457 (1432)
Q Consensus 382 ~e~~~l~~~i~~gd~~~~~A~~~li~~~~~lV~~ia~----ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya 457 (1432)
.....++.+++.||.. |+..++..|.+.|+.+|+ +|.++..+++|++||+++.+|++.++|++. .+|.+|+
T Consensus 6 ~~~~~l~~~~~~gd~~---af~~l~~~~~~~l~~~~~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~--~~f~~wl 80 (184)
T PRK12539 6 NELKALMLASLDGDAA---AHRALLERLSGHLRAYYKGKLARIGRGAEEAEDLVQEALMAIHTRRHTYDPE--QPLTPWV 80 (184)
T ss_pred hHHHHHHHHHHcCCHH---HHHHHHHHHHHHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHhhcCCC--CChHHHH
Confidence 3467788999999998 999999999999999986 455778899999999999999999999874 3699999
Q ss_pred HHHHHHHHHHHHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCC
Q psy15215 458 TWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPV 537 (1432)
Q Consensus 458 ~~~ir~~i~~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~ 537 (1432)
+..++|.+.+++|+..+. +.+ .+.+
T Consensus 81 ~~i~~n~~~d~~R~~~~~-~~~---------------------------------------------------~~~~--- 105 (184)
T PRK12539 81 YAIARYKLIDHLRRTRAS-LAD---------------------------------------------------VPID--- 105 (184)
T ss_pred HHHHHHHHHHHHHHHhcc-ccc---------------------------------------------------cChh---
Confidence 999999999999986531 000 0000
Q ss_pred CCCCCCCcCcccccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHH
Q psy15215 538 GDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 617 (1432)
Q Consensus 538 ~~~~~~~~~~~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~ 617 (1432)
+. . .. .. ..+ ....+....+..++.+||++++.|+.|+|..|+ |++|||+.||+|+++|+++.
T Consensus 106 -~~-~-~~---~~----~~~---~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g~----s~~eIA~~lgis~~tV~~~l 168 (184)
T PRK12539 106 -DA-D-EL---VA----HDD---HAAVESTLDLGRLLARLPEKMRLAIQAVKLEGL----SVAEAATRSGMSESAVKVSV 168 (184)
T ss_pred -hh-c-cc---cC----CcH---HhhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCC----cHHHHHHHHCcCHHHHHHHH
Confidence 00 0 00 00 011 112234567899999999999999999999888 99999999999999999999
Q ss_pred HHHHHHHHHHHH
Q psy15215 618 AKALRKLRPLAH 629 (1432)
Q Consensus 618 ~rAl~kLr~~l~ 629 (1432)
++|+++|++.+.
T Consensus 169 ~ra~~~Lr~~l~ 180 (184)
T PRK12539 169 HRGLKALAALIG 180 (184)
T ss_pred HHHHHHHHHHHh
Confidence 999999998774
No 172
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=99.70 E-value=2.2e-16 Score=171.26 Aligned_cols=174 Identities=17% Similarity=0.113 Sum_probs=137.2
Q ss_pred CCChhhHHHHHHHHHHhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHH
Q psy15215 378 VLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 457 (1432)
Q Consensus 378 ~l~~~e~~~l~~~i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya 457 (1432)
+........++.++..||.. |+..|+..|.+.|+.++. ++++..+++|++||+|+.+|+..++|++. .+|.+|+
T Consensus 5 ~~~~~~~~~l~~~~~~gd~~---af~~l~~~~~~~l~~~~~-~~~~~~~AeDivQe~flkl~~~~~~~~~~--~~~~~Wl 78 (185)
T PRK09649 5 ASDDEAVTALALSAAKGNGR---ALEAFIKATQQDVWRFVA-YLSDVGSADDLTQETFLRAIGAIPRFSAR--SSARTWL 78 (185)
T ss_pred ccccHHHHHHHHHHHccCHH---HHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHhccccCcc--chHHHHH
Confidence 34456678899999999998 999999999999999995 67778899999999999999999999864 4799999
Q ss_pred HHHHHHHHHHHHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCC
Q psy15215 458 TWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPV 537 (1432)
Q Consensus 458 ~~~ir~~i~~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~ 537 (1432)
+.+++|.+.+++|++.+..+. +.+..
T Consensus 79 ~~Iarn~~~d~~Rk~~~~~~~-----------------------------------------------------~~~~~- 104 (185)
T PRK09649 79 LAIARHVVADHIRHVRSRPRT-----------------------------------------------------TRGAR- 104 (185)
T ss_pred HHHHHHHHHHHHHHhcccccc-----------------------------------------------------ccccc-
Confidence 999999999999986541110 00000
Q ss_pred CCCCCCCcCcccccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHH
Q psy15215 538 GDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 617 (1432)
Q Consensus 538 ~~~~~~~~~~~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~ 617 (1432)
. . .. . .+.......+....+..+|++|||++|.||.|+|+.|+ |++|||+.||+|+++|+++.
T Consensus 105 --~-~-~~----~-----~~~~~~~~~e~~~~l~~~l~~Lp~~~r~v~~L~~~~g~----s~~EIA~~lgis~~tVk~~l 167 (185)
T PRK09649 105 --P-E-HL----I-----DGDRHARGFEDLVEVTTMIADLTTDQREALLLTQLLGL----SYADAAAVCGCPVGTIRSRV 167 (185)
T ss_pred --h-h-hc----c-----ChhhhhhhHHHHHHHHHHHHhCCHHHhHHhhhHHHcCC----CHHHHHHHHCCCHHHHHHHH
Confidence 0 0 00 0 00000111122345888999999999999999999999 99999999999999999999
Q ss_pred HHHHHHHHHHH
Q psy15215 618 AKALRKLRPLA 628 (1432)
Q Consensus 618 ~rAl~kLr~~l 628 (1432)
++|+++|++.+
T Consensus 168 ~Rar~~Lr~~~ 178 (185)
T PRK09649 168 ARARDALLADA 178 (185)
T ss_pred HHHHHHHHhhC
Confidence 99999999743
No 173
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=99.70 E-value=1.6e-16 Score=171.04 Aligned_cols=170 Identities=18% Similarity=0.169 Sum_probs=137.1
Q ss_pred HHHHHHHHHHhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHH
Q psy15215 384 LRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 463 (1432)
Q Consensus 384 ~~~l~~~i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~ 463 (1432)
...++..+.+||.. |+..++..|.+.|+.+|.+|.++..+++|++||+|+++|+++++|++. .+|.+|++..++|
T Consensus 5 ~~~l~~~~~~~d~~---a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~--~~~~~wl~~i~~n 79 (176)
T PRK09638 5 EKELIQKAKKGDDA---ALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSFQGR--SKFSTWLISIASR 79 (176)
T ss_pred HHHHHHHHHCCCHH---HHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHH
Confidence 34678888999998 999999999999999999999999999999999999999999999863 4899999999999
Q ss_pred HHHHHHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCC
Q psy15215 464 AITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDS 543 (1432)
Q Consensus 464 ~i~~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~ 543 (1432)
.+.+++++..+.... . ....+.
T Consensus 80 ~~~d~~r~~~~~~~~--~-----------------------------------------------------~~~~~~--- 101 (176)
T PRK09638 80 LYKDHLRKQKREKLR--L-----------------------------------------------------QRAKEE--- 101 (176)
T ss_pred HHHHHHHHhccccch--h-----------------------------------------------------hhcccc---
Confidence 999999987642100 0 000000
Q ss_pred CcCcccccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHH
Q psy15215 544 HLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRK 623 (1432)
Q Consensus 544 ~~~~~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~k 623 (1432)
..+ ...+ +..........|..+|..||++++.||.++|..|+ |++|||+.||+|+++|+.+.++|+.+
T Consensus 102 -~~~------~~~~-~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~----s~~eIA~~l~is~~~V~~~l~ra~~~ 169 (176)
T PRK09638 102 -TLR------KEKW-EAAIKGAEWSEMLDALSKLDPEFRAPVILKHYYGY----TYEEIAKMLNIPEGTVKSRVHHGIKQ 169 (176)
T ss_pred -cCC------ccch-HHHHHhhhHHHHHHHHHcCCHHHhheeeehhhcCC----CHHHHHHHHCCChhHHHHHHHHHHHH
Confidence 000 0000 11222234466889999999999999999998888 99999999999999999999999999
Q ss_pred HHHHH
Q psy15215 624 LRPLA 628 (1432)
Q Consensus 624 Lr~~l 628 (1432)
|++.+
T Consensus 170 l~~~l 174 (176)
T PRK09638 170 LRKEW 174 (176)
T ss_pred HHHHh
Confidence 99865
No 174
>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=99.70 E-value=2.9e-16 Score=167.93 Aligned_cols=165 Identities=16% Similarity=0.227 Sum_probs=134.8
Q ss_pred HHHHHHHHHhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHH
Q psy15215 385 RDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA 464 (1432)
Q Consensus 385 ~~l~~~i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~ 464 (1432)
..++..+..||.. |+..++..|.+.|+++|.+++++..+++|++||+++.+|++.++|++. .+|.||++..++|.
T Consensus 4 ~~l~~~~~~gd~~---a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~l~~~~~~~~~~~~--~~~~~wl~~i~~n~ 78 (169)
T TIGR02954 4 EELVKKAKRGNKP---AFESLIKKHKEKLYKTAFIYVKNEHDALDVIQETVYKAYLSIDKLKHP--KYFNTWLTRILINE 78 (169)
T ss_pred HHHHHHHHcCCHH---HHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhccCc--cccHHHHHHHHHHH
Confidence 3667788999988 999999999999999999999999999999999999999999999864 37999999999999
Q ss_pred HHHHHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCC
Q psy15215 465 ITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSH 544 (1432)
Q Consensus 465 i~~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~ 544 (1432)
+.+++|+..+. .| ++.....+
T Consensus 79 ~~d~~R~~~~~--~~-----------------------------------------------------~~~~~~~~---- 99 (169)
T TIGR02954 79 CIDLLKKKKKV--IP-----------------------------------------------------FDPNTSIE---- 99 (169)
T ss_pred HHHHHHhcCCc--Cc-----------------------------------------------------cccccccc----
Confidence 99999876541 00 00000000
Q ss_pred cCcccccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHH
Q psy15215 545 LGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 624 (1432)
Q Consensus 545 ~~~~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kL 624 (1432)
. ..+.. .. .....+..+|+.||+++++|+.|+|+.|+ |++|||+.||+|+++|+.+.++|+.+|
T Consensus 100 ------~---~~~~~--~~-~~~~~l~~~l~~L~~~~r~i~~l~~~~g~----s~~eiA~~lgis~~tv~~~l~Ra~~~L 163 (169)
T TIGR02954 100 ------K---GECET--HA-DSRLDLYKAIDTLNDKYQTAIILRYYHDL----TIKEIAEVMNKPEGTVKTYLHRALKKL 163 (169)
T ss_pred ------c---chhhh--ch-HHHHHHHHHHHhCCHHHhHHHHHHHHcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 0 00100 01 11237889999999999999999999998 999999999999999999999999999
Q ss_pred HHHHH
Q psy15215 625 RPLAH 629 (1432)
Q Consensus 625 r~~l~ 629 (1432)
++.+.
T Consensus 164 r~~l~ 168 (169)
T TIGR02954 164 KKRLE 168 (169)
T ss_pred HHHhc
Confidence 98763
No 175
>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=99.70 E-value=6.5e-16 Score=173.76 Aligned_cols=183 Identities=16% Similarity=0.198 Sum_probs=145.6
Q ss_pred hHHHHHHHHHHhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHH-------HHhhccccCCCccHH
Q psy15215 383 DLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMK-------AVDKFEYRRGYKFST 455 (1432)
Q Consensus 383 e~~~l~~~i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~k-------av~~fd~~~g~~Fst 455 (1432)
+...|+..++.||.. |+..|+..|.+.|+.++.+++++..+++|++||+|+.+|. ++.+|+.. .+|.|
T Consensus 25 ~d~~Li~~~~~gd~~---Af~~L~~~y~~~l~~~~~~~~~~~~dAEDivQEvFlkl~~~~~~~~~~~~~~~~~--~~~~t 99 (244)
T TIGR03001 25 ADLYLACACAQGEPA---ALAALERHVLSKVPARLAGLRPPTAFVDEVLQRLRQRLLVPRAERPPRIAEYSGR--GPLLS 99 (244)
T ss_pred cHHHHHHHHHcCcHH---HHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhccchhhhhhccCCC--CchHh
Confidence 345688889999988 9999999999999999999999999999999999999994 78888853 47999
Q ss_pred HHHHHHHHHHHHHHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCC
Q psy15215 456 YATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMES 535 (1432)
Q Consensus 456 ya~~~ir~~i~~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~ 535 (1432)
|++.+++|.+.++++++.+...+ +
T Consensus 100 WL~~Ia~N~~id~lRk~~r~~~~-------------------------------------------------------~- 123 (244)
T TIGR03001 100 WVRIVATRIALELQAQERRHSPV-------------------------------------------------------E- 123 (244)
T ss_pred HHHHHHHHHHHHHHHHhcccCcc-------------------------------------------------------c-
Confidence 99999999999999976541100 0
Q ss_pred CCCCCCCCCcCcccccCCCCChHHHHHH----HHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchh
Q psy15215 536 PVGDDEDSHLGDFIEDENMLAPSDAALN----ASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRE 611 (1432)
Q Consensus 536 ~~~~~~~~~~~~~i~d~~~~~p~~~~~~----~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~ 611 (1432)
+++. ..+. .+ ...+|++.... .+....|..+|++||+++|.|+.|+|..|+ |++|||+.||+|.+
T Consensus 124 ---~~~~--~~~~-~~-~~~~~e~~~~~~e~~~e~~~~l~~aL~~Lp~~~R~v~~L~~~eg~----S~~EIA~~Lgis~~ 192 (244)
T TIGR03001 124 ---EPTE--LAAL-PA-PGSDPELDLLRERYRQDFRQALREALAALSERERHLLRLHFVDGL----SMDRIGAMYQVHRS 192 (244)
T ss_pred ---cccc--cccc-cC-CCCCHHHHHHHHhhHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHHCcCHH
Confidence 0000 0000 00 11244444433 235678999999999999999999999998 99999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhh
Q psy15215 612 RIRQIEAKALRKLRPLAHDWLEQRTH 637 (1432)
Q Consensus 612 ~v~~~~~rAl~kLr~~l~~~~~~~l~ 637 (1432)
+|+.+.++|+++|++.+..-+-.++.
T Consensus 193 TVk~rl~RAr~~Lr~~l~~~~~~~~~ 218 (244)
T TIGR03001 193 TVSRWVAQARERLLERTRRRLAERLK 218 (244)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 99999999999999998765555543
No 176
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=99.70 E-value=2.2e-16 Score=167.32 Aligned_cols=157 Identities=10% Similarity=0.110 Sum_probs=126.2
Q ss_pred hhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q psy15215 1190 KAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 1269 (1432)
Q Consensus 1190 ~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip 1269 (1432)
.|+.+|+..|.+.|+++|.+++++..+++|++||+|+.+|+..++|++ ..|.+|++++++|.+.+++|++.+. +
T Consensus 4 ~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~flk~~~~~~~~~~---~~~~~wl~~i~~n~~~d~~R~~~~~---~ 77 (161)
T PRK12528 4 ATVEGLYSAHHHWLTGWLRRRLGCPQSAADLAQDTFVKVLVARETAQI---IEPRAFLTTIAKRVLCNHYRRQDLE---R 77 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHhccccccc---cCHHHHHHHHHHHHHHHHHHHHHHH---H
Confidence 389999999999999999999999999999999999999999888764 2699999999999999999976531 0
Q ss_pred ccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHH
Q psy15215 1270 VHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349 (1432)
Q Consensus 1270 ~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~~d~i~d~~~~~p~~ 1349 (1432)
.. . + .++ + ..+....+++.
T Consensus 78 ~~---------------~---------~------------------------~~~----~---------~~~~~~~~~~~ 96 (161)
T PRK12528 78 AY---------------L---------E------------------------ALA----Q---------LPERVAPSEEE 96 (161)
T ss_pred hh---------------H---------H------------------------Hhh----c---------cccccCCCHHH
Confidence 00 0 0 000 0 00001123444
Q ss_pred HHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCc
Q psy15215 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417 (1432)
Q Consensus 1350 ~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~ 1417 (1432)
.....+....+..+|..||+++|.||.|+|+.|+ |++|||+.||+|.++|++++++|+++||..
T Consensus 97 ~~~~~~~~~~l~~~l~~L~~~~r~v~~L~~~~g~----s~~EIA~~l~is~~tV~~~l~ra~~~~~~~ 160 (161)
T PRK12528 97 RAIILETLVELDQLLDGLPPLVKRAFLLAQVDGL----GYGEIATELGISLATVKRYLNKAAMRCYFA 160 (161)
T ss_pred HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHhc
Confidence 4444455678999999999999999999999999 999999999999999999999999999863
No 177
>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=99.70 E-value=2.6e-16 Score=164.92 Aligned_cols=156 Identities=22% Similarity=0.333 Sum_probs=132.6
Q ss_pred hHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHHHHHHhcccccccc
Q psy15215 1191 AKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 1270 (1432)
Q Consensus 1191 A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~ 1270 (1432)
|++.++..|.++|+++++++..++.+++|++|||++++|+++++|++. .+|.||+.+++++.+.++++++.+ .+.
T Consensus 2 a~~~l~~~~~~~v~~~~~~~~~~~~~~~D~~qe~~~~l~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~rk~~~---~~~ 76 (158)
T TIGR02937 2 AFEELYERYLPLLYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPE--GSFKAWLFRIARNLILDYLRRKRR---LRR 76 (158)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCCc--chHHHHHHHHHHHHHHHHHHHhcc---CCc
Confidence 789999999999999999999999999999999999999999999988 589999999999999999998875 111
Q ss_pred cHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHH
Q psy15215 1271 HMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 1350 (1432)
Q Consensus 1271 ~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~~d~i~d~~~~~p~~~ 1350 (1432)
.+ ..+. .. .....+|.+.
T Consensus 77 ~~---------------------------------------------------~~~~------~~-----~~~~~~~~~~ 94 (158)
T TIGR02937 77 EL---------------------------------------------------DLLE------EL-----LDSDPSPEEE 94 (158)
T ss_pred ch---------------------------------------------------hhhh------hc-----ccccCCHHHH
Confidence 00 0000 00 0011256667
Q ss_pred HHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCc
Q psy15215 1351 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417 (1432)
Q Consensus 1351 ~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~ 1417 (1432)
.........+..++++||++++.||.++|+.|. |..|||+.+|+|+.+|+++..+++++||+.
T Consensus 95 ~~~~~~~~~l~~~l~~L~~~~~~ii~~~~~~g~----s~~eIA~~l~~s~~~v~~~~~~~~~kl~~~ 157 (158)
T TIGR02937 95 LEQEEEREALREALEKLPEREREVLVLRYLEGL----SYKEIAEILGISVGTVKRRLKRARKKLREL 157 (158)
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHhhHHhcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 777777888999999999999999999998888 999999999999999999999999999974
No 178
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=99.70 E-value=2.3e-16 Score=171.11 Aligned_cols=159 Identities=12% Similarity=0.092 Sum_probs=127.5
Q ss_pred hhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q psy15215 1190 KAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 1269 (1432)
Q Consensus 1190 ~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip 1269 (1432)
.++..++..|.+.|+.+|.+++++..+++|++||+|+.+|+..++|+.. ..|.+|++.+++|.+.+++|++.+...
T Consensus 10 ~~f~~l~~~~~~~L~~~a~~~~~~~~~AEDivQevfl~~~~~~~~~~~~--~~~~awL~~Ia~n~~~d~~R~~~~~~~-- 85 (187)
T PRK12516 10 PPFKRELLAALPSLRAFAVSLIGRHDRADDLVQDTIMKAWAKQDHFEVG--TNMKAWLFTILRNEFYSQMRKRGREVQ-- 85 (187)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHhhhccCCc--ccHHHHHHHHHHHHHHHHHHhhcCCcc--
Confidence 4999999999999999999999999999999999999999999999854 369999999999999999998764100
Q ss_pred ccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHH
Q psy15215 1270 VHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349 (1432)
Q Consensus 1270 ~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~~d~i~d~~~~~p~~ 1349 (1432)
. .+... . +.... .+.+.
T Consensus 86 -~---------------------------------------------------~~~~~-~-------~~~~~--~~~~~- 102 (187)
T PRK12516 86 -D---------------------------------------------------TDGMF-T-------EQLAV--HPSQY- 102 (187)
T ss_pred -c---------------------------------------------------ccccc-c-------cccCC--Ccchh-
Confidence 0 00000 0 00000 00111
Q ss_pred HHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchhhhh
Q psy15215 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYK 1422 (1432)
Q Consensus 1350 ~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~~~~ 1422 (1432)
.......+..+|..||+++|.||.|+|+.|+ |++|||+.||+|.++|+++++||+++||+.+....
T Consensus 103 ---~~~~~~~l~~~L~~Lp~~~r~i~~L~~~~g~----s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~~~~ 168 (187)
T PRK12516 103 ---GTLDLQDFRAALDQLPDDQREAIILVGASGF----AYEEAAEICGCAVGTIKSRVNRARQRLQEILQIEG 168 (187)
T ss_pred ---hHHHHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhc
Confidence 1122356899999999999999999999998 99999999999999999999999999999776543
No 179
>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=99.70 E-value=3.4e-16 Score=170.14 Aligned_cols=177 Identities=15% Similarity=0.147 Sum_probs=133.7
Q ss_pred HHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHHHHHHhcccccccccHH
Q psy15215 1194 EMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 1273 (1432)
Q Consensus 1194 ~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~~~~ 1273 (1432)
+.+..|.+.|+.+|++++++..+++|++||+|+.+|+...+|++. .+|.+|++.+++|.+.+++|++.+....+.- .
T Consensus 6 ~~~~~~~~~l~~~~~~~~~~~~dAeDivQevfl~l~~~~~~~~~~--~~~~~wL~~iarn~~~d~~R~~~r~~~~~~~-~ 82 (188)
T TIGR02943 6 QELEQLRRDLLRFARLQLRDRDLAEDAVQETLLAALSHRDSFAGR--SALKTWLFAILKNKIIDALRAKGREVKVSDL-D 82 (188)
T ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhccc--cHHHHHHHHHHHHHHHHHHHhhcccCCcccc-c
Confidence 578899999999999999999999999999999999999999864 3799999999999999999987652111100 0
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHHHHH
Q psy15215 1274 ETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALN 1353 (1432)
Q Consensus 1274 ~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~~d~i~d~~~~~p~~~~~~ 1353 (1432)
. ++. .-.+....... +....... ....++|+..+..
T Consensus 83 ~------------------~~~------------------------~~~~~~~~~~~-~~~~~~~~-~~~~~~~e~~~~~ 118 (188)
T TIGR02943 83 D------------------ELD------------------------DEAFNALFTQN-GHWAQHGQ-PQHWNTPEKQLEN 118 (188)
T ss_pred c------------------ccc------------------------cchhhhhhccc-cchhcccc-ccccCCHHHHHHH
Confidence 0 000 00000000000 00000111 1122467777777
Q ss_pred HHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchhhh
Q psy15215 1354 ASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYY 1421 (1432)
Q Consensus 1354 ~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~~~ 1421 (1432)
.+....+..+|.+||+++|+||.|+|+.|+ |++|||+.||+|.++|+++++||+++||+.....
T Consensus 119 ~e~~~~l~~~l~~L~~~~r~v~~l~~~~g~----s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l~~~ 182 (188)
T TIGR02943 119 KEFWEVFEACLYHLPEQTARVFMMREVLGF----ESDEICQELEISTSNCHVLLYRARLSLRACLSIN 182 (188)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHHHhCC----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 788889999999999999999999999999 9999999999999999999999999999966543
No 180
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=99.70 E-value=2.4e-16 Score=167.77 Aligned_cols=157 Identities=11% Similarity=0.093 Sum_probs=131.2
Q ss_pred HHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHHHHHHhccccccccc
Q psy15215 1192 KREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 1271 (1432)
Q Consensus 1192 ~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~~ 1271 (1432)
++.|+..|.+.|+++|++++++..+++|++||+|+.+|+++++|++. .|.+|++.+++|.+.+++|+..+.....
T Consensus 3 ~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~---~~~~wL~~i~~n~~~d~~R~~~~~~~~~-- 77 (165)
T PRK09644 3 IEEIYKMYINDVYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDYDNQ---KVKPWLFKVAYHTFIDFVRKEKKVSFVG-- 77 (165)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcccc---chHHHHHHHHHHHHHHHHHhhhhccccc--
Confidence 67899999999999999999999999999999999999999999852 6999999999999999999876411000
Q ss_pred HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHHH
Q psy15215 1272 MIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAA 1351 (1432)
Q Consensus 1272 ~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~~d~i~d~~~~~p~~~~ 1351 (1432)
.++ + +.+. ..+|++..
T Consensus 78 ------------------------~~~------------------------~-------------~~~~---~~~~~~~~ 93 (165)
T PRK09644 78 ------------------------TDE------------------------I-------------EAIQ---AESTEEYV 93 (165)
T ss_pred ------------------------hhH------------------------H-------------hhhc---ccChHHHH
Confidence 000 0 0000 12455666
Q ss_pred HHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchhhh
Q psy15215 1352 LNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYY 1421 (1432)
Q Consensus 1352 ~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~~~ 1421 (1432)
...+....+..+|..||+++++|+.|+|+.|. |++|||..||+|.++|+++++||+++||+..+..
T Consensus 94 ~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~----s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~~~ 159 (165)
T PRK09644 94 VAKNSYEKLIQIIHTLPVIEAQAILLCDVHEL----TYEEAASVLDLKLNTYKSHLFRGRKRLKALLKEE 159 (165)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHHHhHHHhcC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhh
Confidence 66677788999999999999999999999998 9999999999999999999999999999976544
No 181
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=99.70 E-value=3.1e-16 Score=167.16 Aligned_cols=158 Identities=16% Similarity=0.180 Sum_probs=130.9
Q ss_pred hhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q psy15215 1190 KAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 1269 (1432)
Q Consensus 1190 ~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip 1269 (1432)
.|++.++..|.+.|+.+|++++++..+++|++||+|+.+|++ +|+. +..|.||++.+++|.+.+++++..+..+..
T Consensus 3 ~~f~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fi~~~~~--~~~~--~~~~~~wl~~i~rn~~~d~~rk~~~~~~~~ 78 (166)
T PRK09639 3 ETFEDLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLYRS--DFKG--IENEKGWLIKSARNVAYNYLRSEKRRRARI 78 (166)
T ss_pred hHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH--hccc--ccchHHHHHHHHHHHHHHHHHHhccccccc
Confidence 489999999999999999999999999999999999999999 6764 347999999999999999999876521100
Q ss_pred ccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHH
Q psy15215 1270 VHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349 (1432)
Q Consensus 1270 ~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~~d~i~d~~~~~p~~ 1349 (1432)
. ... + ..+. ...++|++
T Consensus 79 ~------------------------------------------------------~~~-~-----~~~~---~~~~~~e~ 95 (166)
T PRK09639 79 L------------------------------------------------------GEF-Q-----WQEV---DNEPSPEE 95 (166)
T ss_pred c------------------------------------------------------chh-h-----hhhc---cCCCChHH
Confidence 0 000 0 0000 11236777
Q ss_pred HHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchh
Q psy15215 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 1419 (1432)
Q Consensus 1350 ~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~ 1419 (1432)
.....+....+..+|.+||+++|.||.++| .|+ |++|||+.||+|.++|++.++||+++||..+.
T Consensus 96 ~~~~~~~~~~l~~~l~~L~~~~r~il~l~~-~g~----s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l~ 160 (166)
T PRK09639 96 IWIRKEEITKVQEVLAKMTERDRTVLLLRF-SGY----SYKEIAEALGIKESSVGTTLARAKKKFRKIYE 160 (166)
T ss_pred HHHHHHHHHHHHHHHHcCCHHHHHHHHHHH-cCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 777777788899999999999999999999 999 99999999999999999999999999999654
No 182
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=99.70 E-value=1.6e-16 Score=171.23 Aligned_cols=168 Identities=10% Similarity=0.072 Sum_probs=134.1
Q ss_pred HHHHhHHHHHHhHHHHHHHHHHHHHHHHHhccc--CCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHH
Q psy15215 390 KMIAGEMKARKAKREMTEANLRLVISIAKKYTD--RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITR 467 (1432)
Q Consensus 390 ~i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~--~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~ 467 (1432)
.+..||.. |+..|+..|.+.|++++.++++ ...+++|++||+|+.+|+..++|+.....+|.||++.+++|.+.+
T Consensus 6 ~~~~~d~~---af~~ly~~~~~~l~~~~~~~~~~~~~~~AeDivQevFl~~~~~~~~~~~~~~~~~~~wL~~ia~n~~~d 82 (178)
T PRK12529 6 SCLSADRD---KVATLYRENHAWLRNWLAYRLRSWGRGVADDLAHDIFLRILASRDGGQREAIRQPRAYLARIANCVLVS 82 (178)
T ss_pred cCCCCCHH---HHHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHhcccccccccccCHHHHHHHHHHHHHHH
Confidence 34578877 9999999999999998766665 357899999999999999999997544457999999999999999
Q ss_pred HHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCc
Q psy15215 468 SIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGD 547 (1432)
Q Consensus 468 ~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~ 547 (1432)
+++++.+... . .+.. .+
T Consensus 83 ~~Rk~~~~~~---~---------------------------------------------------~~~~-~~-------- 99 (178)
T PRK12529 83 WRRRQSLELA---W---------------------------------------------------LEAL-AT-------- 99 (178)
T ss_pred HHHHHHHHhh---h---------------------------------------------------hhHh-hh--------
Confidence 9887543100 0 0000 00
Q ss_pred ccccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHH
Q psy15215 548 FIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPL 627 (1432)
Q Consensus 548 ~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~ 627 (1432)
.......+|++.....+....|..+|.+|||++|.||.|+|..|+ |++|||+.||+|+++|+.+.++|+.++++.
T Consensus 100 -~~~~~~~~~e~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~~g~----s~~EIA~~lgis~~tVk~~l~rAl~~~~~~ 174 (178)
T PRK12529 100 -LPEPLHPSPEQQSVILETLHEIDALLDTLRPRVKQAFLMATLDGM----KQKDIAQALDIALPTVKKYIHQAYVTCLSL 174 (178)
T ss_pred -ccCcCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 000112356666666677788999999999999999999999998 999999999999999999999999999876
Q ss_pred H
Q psy15215 628 A 628 (1432)
Q Consensus 628 l 628 (1432)
+
T Consensus 175 ~ 175 (178)
T PRK12529 175 M 175 (178)
T ss_pred C
Confidence 4
No 183
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=99.69 E-value=5e-16 Score=168.52 Aligned_cols=170 Identities=16% Similarity=0.220 Sum_probs=135.9
Q ss_pred hhHHHHHHHHHHhHHHHHHhHHHHHHHHHHHHHHHHHhcccC----CCChhhHHHHHHHHHHHHHhhccccCCCccHHHH
Q psy15215 382 NDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDR----GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 457 (1432)
Q Consensus 382 ~e~~~l~~~i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~----~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya 457 (1432)
.++..++..+..||.. |+..|+..|.+.|+.+|.+++++ ..+++|++||+++.+|+..++|+.. .+|.+|+
T Consensus 7 ~~~~~l~~~~~~gd~~---a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeDlvQe~fl~l~~~~~~~~~~--~~~~~wl 81 (184)
T PRK12512 7 DEWTDLMRSANAGDAA---AYRRLLKAVTPVLRAAARRGLARAGQPADQAEDIVQEILLAVHLKRHTWDPG--APFAPWL 81 (184)
T ss_pred hHHHHHHHHHHccCHH---HHHHHHHHHHHHHHHHHHHHHHhccCCcccHHHHHHHHHHHHHHhHHhcCcc--ccHHHHH
Confidence 4566788888899988 99999999999999999998863 4689999999999999999999863 4799999
Q ss_pred HHHHHHHHHHHHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCC
Q psy15215 458 TWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPV 537 (1432)
Q Consensus 458 ~~~ir~~i~~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~ 537 (1432)
+..++|.+.++++++.+....+ ++.
T Consensus 82 ~~i~rn~~~d~~Rr~~~~~~~~-----------------------------------------------------~~~-- 106 (184)
T PRK12512 82 FAIARNKLIDALRRRGRRVFVD-----------------------------------------------------IDD-- 106 (184)
T ss_pred HHHHHHHHHHHHHhhcccccCC-----------------------------------------------------chh--
Confidence 9999999999998765421110 000
Q ss_pred CCCCCCCcCcccccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHH
Q psy15215 538 GDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 617 (1432)
Q Consensus 538 ~~~~~~~~~~~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~ 617 (1432)
..+.+++.. +.+ ......+..+|++||++++.||.|+|..|+ |++|||+.||+|..+|+.+.
T Consensus 107 -------~~~~~~~~~---~~~----~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~----s~~eIA~~l~is~~tV~~~l 168 (184)
T PRK12512 107 -------FAETLPAEP---ATE----TLPAGDVGRHLETLPPRQRDVVQSISVEGA----SIKETAAKLSMSEGAVRVAL 168 (184)
T ss_pred -------ccccccccc---hhh----HHHHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHhCCCHHHHHHHH
Confidence 000011100 001 122356788999999999999999999988 99999999999999999999
Q ss_pred HHHHHHHHHHHH
Q psy15215 618 AKALRKLRPLAH 629 (1432)
Q Consensus 618 ~rAl~kLr~~l~ 629 (1432)
++|+++|+..+.
T Consensus 169 ~ra~~~Lr~~l~ 180 (184)
T PRK12512 169 HRGLAALAAKFR 180 (184)
T ss_pred HHHHHHHHHHhh
Confidence 999999998874
No 184
>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=99.69 E-value=3.8e-16 Score=169.24 Aligned_cols=174 Identities=17% Similarity=0.193 Sum_probs=131.8
Q ss_pred hHHHHHHHHHHhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCC-----ChhhHHHHHHHHHHH-HHhhccccCCCccHHH
Q psy15215 383 DLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGL-----QFLDLIQEGNIGLMK-AVDKFEYRRGYKFSTY 456 (1432)
Q Consensus 383 e~~~l~~~i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~-----~~~DLiQEg~igL~k-av~~fd~~~g~~Fsty 456 (1432)
.+..++..++.||.. |+..|+..|.+.|+.+|.+|+++.. +++|++||+|+.+|+ ...+|++. ..|.+|
T Consensus 3 ~~~~li~~~~~gd~~---a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~AeDlvQevfl~~~~~~~~~~~~~--~~~~~w 77 (183)
T TIGR02999 3 PVTELLQQWQNGDAA---ARDQLFPQLYQELRRIARRQLRRERSGQTLQTTALVHEAYLRLSDQDEQKWDDR--AHFFAA 77 (183)
T ss_pred cHHHHHHHHHcCCHH---HHHHHHHHHHHHHHHHHHHHhhcccccccchHHHHHHHHHHHHhhcccCCCCch--HHHHHH
Confidence 356678899999988 9999999999999999999999877 899999999999998 78888753 379999
Q ss_pred HHHHHHHHHHHHHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCC
Q psy15215 457 ATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESP 536 (1432)
Q Consensus 457 a~~~ir~~i~~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~ 536 (1432)
++.+++|.+.+++|++.+..+.. . ....+
T Consensus 78 l~~i~~n~~~d~~R~~~~~~~~~-------------------------------------------------~--~~~~~ 106 (183)
T TIGR02999 78 AAKAMRRILVDHARRRRAQKRGG-------------------------------------------------G--AVRVP 106 (183)
T ss_pred HHHHHHHHHHHHHHHHHHHhccC-------------------------------------------------C--ccccc
Confidence 99999999999998765410000 0 00000
Q ss_pred CCCCCCCCcCcccccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHH
Q psy15215 537 VGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQI 616 (1432)
Q Consensus 537 ~~~~~~~~~~~~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~ 616 (1432)
..+ ..+. .++... ........+...|++|||++|.||.|+|..|+ |++|||+.||+|+++|+.+
T Consensus 107 ~~~--------~~~~---~~~~~~-~~~~~l~~~~~~l~~Lp~~~r~v~~l~~~~g~----s~~EIA~~lgis~~tVk~~ 170 (183)
T TIGR02999 107 LDE--------VLPD---AEADLD-EELLDLDDALDKLAQVDPRQAEVVELRFFAGL----TVEEIAELLGVSVRTVERD 170 (183)
T ss_pred ccc--------ccCC---CCccHH-HHHHHHHHHHHHhhcCCHHHHHHHHHHHHcCC----CHHHHHHHhCCCHHHHHHH
Confidence 000 0000 011111 11111233444567799999999999999999 9999999999999999999
Q ss_pred HHHHHHHHHHHH
Q psy15215 617 EAKALRKLRPLA 628 (1432)
Q Consensus 617 ~~rAl~kLr~~l 628 (1432)
.+||+.+|++.+
T Consensus 171 l~Rar~~Lr~~l 182 (183)
T TIGR02999 171 WRFARAWLADEL 182 (183)
T ss_pred HHHHHHHHHHHh
Confidence 999999999875
No 185
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=99.69 E-value=4.7e-16 Score=169.70 Aligned_cols=179 Identities=17% Similarity=0.211 Sum_probs=136.9
Q ss_pred hHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHHHHHHhccccccch
Q psy15215 401 AKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 480 (1432)
Q Consensus 401 A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~ 480 (1432)
++..|+..|.+.|+.+|.+++++..+++|++||.|+.+|+.+++|+.. .+|.||++..++|.+.+++|++.+....+.
T Consensus 3 ~~~~l~~~~~~~l~~~a~~~~~~~~~AeDivQevfl~~~~~~~~~~~~--~~~~~WL~~ia~n~~~d~~Rk~~r~~~~~~ 80 (191)
T PRK12520 3 IAPAQLEALRPHLLRFARLQLRDPALAEDAVSETLLAVLEHPERFAGQ--SSLKTYLVGILKHKIIDAIRSGRREVRLSL 80 (191)
T ss_pred chHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhccc--ccHHHHHHHHHHHHHHHHHHhhcCcCcccc
Confidence 789999999999999999999999999999999999999999999854 379999999999999999998765321110
Q ss_pred hHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHH
Q psy15215 481 HMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 560 (1432)
Q Consensus 481 ~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~i~d~~~~~p~~~ 560 (1432)
... ......++ ++..... +.. ....++ ...+|++.
T Consensus 81 ~~~------------------~~~~~~~~-----------------------~~~~~~~--~~~-~~~~~~-~~~~~~~~ 115 (191)
T PRK12520 81 DDA------------------DEQSDDDL-----------------------FDALFAA--DGH-YREPPS-DWGDPDAA 115 (191)
T ss_pred ccc------------------ccchhhhh-----------------------hhhhccc--ccc-cccCcc-ccCCHHHH
Confidence 000 00000000 0000000 000 000111 12367777
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHHHH
Q psy15215 561 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLAHD 630 (1432)
Q Consensus 561 ~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l~~ 630 (1432)
+...+....|..+|.+|||++|.|+.|+|..|+ |++|||+.||+|.++|+++.+||+++|++.+..
T Consensus 116 ~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~~~g~----s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 181 (191)
T PRK12520 116 LSRREFFEVLQACVDRLPPRTGRVFMMREWLEL----ETEEICQELQITATNAWVLLYRARMRLRECLDL 181 (191)
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 777788888999999999999999999999998 999999999999999999999999999998864
No 186
>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=99.69 E-value=2.4e-16 Score=167.34 Aligned_cols=158 Identities=15% Similarity=0.195 Sum_probs=128.4
Q ss_pred hhhhhhhhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHHHHHHh
Q psy15215 1183 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQ 1262 (1432)
Q Consensus 1183 ~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~~i~~~ 1262 (1432)
+|+.. |++.++..|.+.|+++|.+++++..+++|++||+|+.+|.+.++|+. ...|.+|++.+++|.+.+++++.
T Consensus 2 ~~~~~---~~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~~~~~~~~~~~--~~~~~~wl~~i~~n~~~d~~rk~ 76 (162)
T TIGR02983 2 SATEE---EFTAFVAARYPRLLRTAYLLTGDPHEAEDLVQEALVRTYVRWDRIRD--PDAPDAYVRRVLVNLARSRWRRR 76 (162)
T ss_pred CCcHH---HHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhcCC--cccHHHHHHHHHHHHHHHHHHhh
Confidence 46666 99999999999999999999999999999999999999999999964 34899999999999999999976
Q ss_pred cccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccC
Q psy15215 1263 ARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDE 1342 (1432)
Q Consensus 1263 ~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~~d~i~d~ 1342 (1432)
.+. ..+ .....+. .
T Consensus 77 ~~~-~~~------------------------------------------------------~~~~~~~-~---------- 90 (162)
T TIGR02983 77 RLL-ELP------------------------------------------------------TRELPDA-A---------- 90 (162)
T ss_pred ccc-ccc------------------------------------------------------ccccCcc-c----------
Confidence 531 000 0000000 0
Q ss_pred CCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchh
Q psy15215 1343 NMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 1419 (1432)
Q Consensus 1343 ~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~ 1419 (1432)
+.+..........|..+|..||++++.|+.|+|..|+ |.+|||+.||+|.++|+++++||+++||+...
T Consensus 91 ----~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~----s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 159 (162)
T TIGR02983 91 ----APDPAPDVALRAALARALRRLPARQRAVVVLRYYEDL----SEAQVAEALGISVGTVKSRLSRALARLRELLE 159 (162)
T ss_pred ----CCccchhHHHHHHHHHHHHhCCHHHHHHhhhHHHhcC----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhc
Confidence 0001112344567889999999999999999999888 99999999999999999999999999998553
No 187
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=99.69 E-value=4.4e-16 Score=169.46 Aligned_cols=174 Identities=17% Similarity=0.208 Sum_probs=131.8
Q ss_pred HHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHHHHHHhcccccccccH
Q psy15215 1193 REMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 1272 (1432)
Q Consensus 1193 ~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~~~ 1272 (1432)
...+..|.+.|+.+|.+++++..+++|++||+|+.+|++.++|++.. +|.+|++.+++|.+.+++|++.+..... ..
T Consensus 10 ~~~~~~~~~~l~~~~~~~~~d~~~AeDivQe~flk~~~~~~~~~~~~--~~~~wL~~Ia~n~~~d~~Rk~~~~~~~~-~~ 86 (189)
T PRK12530 10 SLEIEEIRLQMLKFATLQLKDADLAEDVVQEALVSAYKNADSFKGQS--ALKTWIFAILKNKIIDLIRYRKRFVNES-EL 86 (189)
T ss_pred HHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHhchhccCCc--cHHHHHHHHHHHHHHHHHHhhccCCCcc-cc
Confidence 34688899999999999999999999999999999999999998653 6999999999999999999876521110 00
Q ss_pred HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHHHH
Q psy15215 1273 IETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAAL 1352 (1432)
Q Consensus 1273 ~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~~d~i~d~~~~~p~~~~~ 1352 (1432)
.. ...+.... +.......+........+|++...
T Consensus 87 ~~------------------------------------------~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~ 120 (189)
T PRK12530 87 IE------------------------------------------EDSPNSFF----DEKGHWKPEYYEPSEWQEVENTVY 120 (189)
T ss_pred cc------------------------------------------cccchhhh----cccccccccccCCccccCHHHHHH
Confidence 00 00000000 000000000000111235677777
Q ss_pred HHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchh
Q psy15215 1353 NASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 1419 (1432)
Q Consensus 1353 ~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~ 1419 (1432)
..+....+..+|++||+++|.||.|+|..|+ |++|||+.||+|.++|+++++||+++||..+.
T Consensus 121 ~~~~~~~l~~~l~~Lp~~~R~v~~L~~~~g~----s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~ 183 (189)
T PRK12530 121 KEEFWLIFEACLNHLPAQQARVFMMREYLEL----SSEQICQECDISTSNLHVLLYRARLQLQACLS 183 (189)
T ss_pred HHHHHHHHHHHHHhCCHHHHHHHhHHHHcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 7788889999999999999999999999998 99999999999999999999999999999764
No 188
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=99.69 E-value=5.6e-16 Score=166.33 Aligned_cols=162 Identities=15% Similarity=0.111 Sum_probs=130.1
Q ss_pred hHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHHHHHHhc
Q psy15215 394 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 473 (1432)
Q Consensus 394 gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~~i~~~~ 473 (1432)
++.. |+..++..|.+.|+++|.+++++..+++|++||.|+.+|+..++|++.. .+|.+|++..++|.+.+++|++.
T Consensus 6 ~~~~---~~~~l~~~~~~~l~~~~~~~~~~~~~AeD~vQevfl~~~~~~~~~~~~~-~~~~~wL~~iarn~~~d~~Rk~~ 81 (173)
T PRK09645 6 AEAA---LMRALYDEHAAPLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLADTG-RSARAWLFTVARNLVIDERRSAR 81 (173)
T ss_pred chHH---HHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCccc-ccHHHHHHHHHHHHHHHHHHhhc
Confidence 4555 9999999999999999999999989999999999999999999997533 47999999999999999999765
Q ss_pred cccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCC
Q psy15215 474 RTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDEN 553 (1432)
Q Consensus 474 r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~i~d~~ 553 (1432)
+.... ..+ + .... ++
T Consensus 82 ~~~~~-----------------------------------------------------~~~-----~-~~~~----~~-- 96 (173)
T PRK09645 82 ARPVE-----------------------------------------------------GGD-----D-VLGV----PE-- 96 (173)
T ss_pred ccccc-----------------------------------------------------ccc-----c-cccC----CC--
Confidence 41000 000 0 0000 00
Q ss_pred CCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHHH
Q psy15215 554 MLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLAH 629 (1432)
Q Consensus 554 ~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l~ 629 (1432)
.++.+..........+..+|+.||++++.||.|+|+.|+ |++|||+.||+|+++|+.+.++|+++|++.+.
T Consensus 97 -~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~L~~~~g~----s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 167 (173)
T PRK09645 97 -QSAPDEVDRALDRLLVADALAQLSPEHRAVLVRSYYRGW----STAQIAADLGIPEGTVKSRLHYALRALRLALQ 167 (173)
T ss_pred -CCCchHHHHHhHHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence 112223333344567899999999999999999999998 99999999999999999999999999998875
No 189
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=99.69 E-value=5.5e-16 Score=167.30 Aligned_cols=162 Identities=13% Similarity=0.106 Sum_probs=134.7
Q ss_pred HhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHHHHHHhccccccc
Q psy15215 400 KAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 479 (1432)
Q Consensus 400 ~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip 479 (1432)
.|+.+++..|.+.|+++|.+++++..+++|++||+++.+|+++++|+.. .+|.+|++..++|.+.+++|+..+....+
T Consensus 16 ~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQd~fl~l~~~~~~~~~~--~~~~awl~~ia~n~~~d~~Rk~~~~~~~~ 93 (179)
T PRK09415 16 DLIDEIMNEYGQEVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYKGK--SSLKTWLYRIAINHCKDYLKSWHNKKVIV 93 (179)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcCCC--cccHHHHHHHHHHHHHHHHHhhccccccc
Confidence 4999999999999999999999999999999999999999999999864 37999999999999999999865411000
Q ss_pred hhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHH
Q psy15215 480 VHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 559 (1432)
Q Consensus 480 ~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~i~d~~~~~p~~ 559 (1432)
.+. . ... .. ....+|++
T Consensus 94 -----------------------------------------------------~~~----~----~~~-~~-~~~~~~e~ 110 (179)
T PRK09415 94 -----------------------------------------------------TED----I----FTY-ME-SQKESVEE 110 (179)
T ss_pred -----------------------------------------------------ccc----c----ccc-cc-ccccCcHH
Confidence 000 0 000 00 01235667
Q ss_pred HHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHHHH
Q psy15215 560 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLAHD 630 (1432)
Q Consensus 560 ~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l~~ 630 (1432)
.+...+....+..+|++||+++|.|+.|+|+.|+ |++|||+.||+|.++|+++.+||+++|++.+..
T Consensus 111 ~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g~----s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~l~~ 177 (179)
T PRK09415 111 EVIQNAEDERLASAVMSLPIKYREVIYLFYYEEL----SIKEIAEVTGVNENTVKTRLKKAKELLKKGLEE 177 (179)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHhhHhHhHHhcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 7777778888999999999999999999999998 999999999999999999999999999987753
No 190
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=99.69 E-value=4.2e-16 Score=171.48 Aligned_cols=177 Identities=19% Similarity=0.218 Sum_probs=133.4
Q ss_pred HHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHHHHHHhcccccccccHH
Q psy15215 1194 EMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 1273 (1432)
Q Consensus 1194 ~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~~~~ 1273 (1432)
.++..|.+.|+++|++++++...++|++||+|+.+|+.+.+|+.. .+|++|++.+++|.+.+++|++.+....+...
T Consensus 22 ~~~~~~~~~l~~~~~~~~~d~~~AEDivQEvfikl~~~~~~~~~~--~~~~~WL~~IarN~~~d~~Rk~~~~~~~~~~~- 98 (206)
T PRK12544 22 VFLEDLRKQMIKFATLQLSDLHLAEDAVQEALIGALKNADSFAGR--AAFKTWVFAILKNKIIDLLRQKKRHVSASSLL- 98 (206)
T ss_pred HHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHHHHHHHHhhcccccccccc-
Confidence 589999999999999999999999999999999999999999854 37999999999999999999877521111000
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHHHHH
Q psy15215 1274 ETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALN 1353 (1432)
Q Consensus 1274 ~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~~d~i~d~~~~~p~~~~~~ 1353 (1432)
+...+. ..+..+ . +.......... .....+|+..+..
T Consensus 99 -----------------~~~~~~-----------~~~~~~---~-----------~~~~~~~~~~~-~~~~~~~e~~~~~ 135 (206)
T PRK12544 99 -----------------RDEEEE-----------EDFEEL---F-----------DESGHWQKDER-PQAWGNPEESLEQ 135 (206)
T ss_pred -----------------cccchh-----------hHHHHh---h-----------ccccccccccc-ccccCCHHHHHHH
Confidence 000000 000000 0 00000000000 0112367777777
Q ss_pred HHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchhh
Q psy15215 1354 ASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRY 1420 (1432)
Q Consensus 1354 ~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~~ 1420 (1432)
.+....+..+|..|||++|.||.|+|+.|+ |++|||+.||+|.++|+++++||+++||+.+..
T Consensus 136 ~e~~~~l~~~L~~L~~~~r~v~~L~~~~g~----s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l~~ 198 (206)
T PRK12544 136 EQFWRIFEACLDGLPAKYARVFMMREFIEL----ETNEICHAVDLSVSNLNVLLYRARLRLRECLEN 198 (206)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 778888999999999999999999999999 999999999999999999999999999997764
No 191
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=99.69 E-value=4.8e-16 Score=170.80 Aligned_cols=180 Identities=11% Similarity=0.124 Sum_probs=132.5
Q ss_pred HHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHHHHHHhcccccccccHH
Q psy15215 1194 EMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 1273 (1432)
Q Consensus 1194 ~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~~~~ 1273 (1432)
.++..|.+.|+.+|.+++++..+++|++||+|+.+|+..++|++.. +|.||++.+++|.+.+++|++.+...++..
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 4589999999999999999999999999999999999999998653 699999999999999999987752111100
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHHHHH
Q psy15215 1274 ETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALN 1353 (1432)
Q Consensus 1274 ~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~~d~i~d~~~~~p~~~~~~ 1353 (1432)
..++. ....++............+...+ ...+|.+....
T Consensus 88 ----------------------~~~~~------------------~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~ 126 (201)
T PRK12545 88 ----------------------DAELD------------------GEALLDRELFKDNGHWAAHAKPR-PWPKPETILQQ 126 (201)
T ss_pred ----------------------ccccc------------------hhhhhhhhhhcccccccccccCc-CCCCHHHHHHH
Confidence 00000 00000000000000000000001 12356666666
Q ss_pred HHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchhhhh
Q psy15215 1354 ASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYK 1422 (1432)
Q Consensus 1354 ~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~~~~ 1422 (1432)
.+....+..+|..|||++|.||.|+|+.|+ |++|||+.||+|.++|+++++||+++||+......
T Consensus 127 ~~~~~~l~~~L~~Lp~~~r~v~~L~~~eg~----s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~~~ 191 (201)
T PRK12545 127 QQFWTLFETCLDHLPEQIGRVFMMREFLDF----EIDDICTELTLTANHCSVLLYRARTRLRTCLSEKG 191 (201)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHh
Confidence 677778999999999999999999999998 99999999999999999999999999999876544
No 192
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=99.69 E-value=5.9e-16 Score=171.11 Aligned_cols=178 Identities=19% Similarity=0.177 Sum_probs=141.4
Q ss_pred hHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHHHHHHhccccccch
Q psy15215 401 AKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 480 (1432)
Q Consensus 401 A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~ 480 (1432)
++..|+..|.+.|+.+|.++++...+++|++||+|+.+|+.+++|+. + +|.+|++.+++|.+.++++++.+....
T Consensus 19 ~f~~l~~~~~~~l~~~~~~~~~d~~dAEDlvQEvflkl~~~~~~~~~--~-~~~aWL~~IarN~~~d~~Rk~~~~~~~-- 93 (216)
T PRK12533 19 RFRQLVLPHLDAAYNLARWLCGNASDADDVVQEACMRALRFFDSFRG--D-NARPWLLAIVRHTWYSEWRRRANAHEV-- 93 (216)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCc--c-chHhHHHHHHHHHHHHHHHhhcccccc--
Confidence 89999999999999999999999999999999999999999999974 2 599999999999999999987541000
Q ss_pred hHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHH
Q psy15215 481 HMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 560 (1432)
Q Consensus 481 ~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~i~d~~~~~p~~~ 560 (1432)
. ......+. . .... . +....+|++.
T Consensus 94 --------------------------------------------------~-~~~~~~~~-~-~~~~-~-~~~~~~~e~~ 118 (216)
T PRK12533 94 --------------------------------------------------A-APDTLDDA-D-SLDD-W-QPAGEDPLAL 118 (216)
T ss_pred --------------------------------------------------c-cccccccc-c-cccc-c-ccCCCCHHHH
Confidence 0 00000000 0 0000 0 0112367788
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHHHHHHHHhhhhhh
Q psy15215 561 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLAHDWLEQRTHQNE 640 (1432)
Q Consensus 561 ~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l~~~~~~~l~~~~ 640 (1432)
+...+....|..+|.+||++++.||.|+|..|+ |++|||+.||+|+++|+++.+||+++|++.+.+--..+-.|+.
T Consensus 119 ~~~~e~~~~l~~al~~Lp~~~R~v~~L~y~eg~----s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l~~~~~~~~~~~~ 194 (216)
T PRK12533 119 LLRAEDVRLVNAALAKLPVEYREVLVLRELEDM----SYREIAAIADVPVGTVMSRLARARRRLAALLGGASAAQAAPGE 194 (216)
T ss_pred HHHHHHHHHHHHHHHcCCHHHHhHhhhHHhcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHcccchhhcCCcc
Confidence 888888899999999999999999999999998 9999999999999999999999999999998765444444444
Q ss_pred hh
Q psy15215 641 KI 642 (1432)
Q Consensus 641 ~~ 642 (1432)
.+
T Consensus 195 ~~ 196 (216)
T PRK12533 195 RA 196 (216)
T ss_pred cc
Confidence 43
No 193
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=99.68 E-value=3.6e-16 Score=168.15 Aligned_cols=169 Identities=15% Similarity=0.147 Sum_probs=132.8
Q ss_pred HHHHHHhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHH
Q psy15215 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITR 467 (1432)
Q Consensus 388 ~~~i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~ 467 (1432)
+..++.||.. |+..++..|.+.|+.+|.++.+ ..+++|++||+|+.+|+..++|++. .+|.+|++..++|.+.+
T Consensus 2 ~~~~~~gd~~---a~~~l~~~~~~~l~~~~~~~~~-~~~aeDivQe~~l~l~~~~~~~~~~--~~~~~wl~~ia~n~~~d 75 (175)
T PRK12518 2 ILRCQRGDRQ---SFRQLYRRYQQKVRSTLYQLCG-RELLDDLVQEVFLRVWKGLPKLRNP--AYFSTWLYRITWNVATD 75 (175)
T ss_pred hhHHHcCCHH---HHHHHHHHHHHHHHHHHHHHcC-HhHHHHHHHHHHHHHHHhHHhhCCc--ccHHHHHHHHHHHHHHH
Confidence 5577889988 9999999999999999999875 4789999999999999999999964 47999999999999999
Q ss_pred HHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCc
Q psy15215 468 SIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGD 547 (1432)
Q Consensus 468 ~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~ 547 (1432)
++|++.+.-. . .... .+....
T Consensus 76 ~~R~~~~~~~---~---------------------------------------------------~~~~-~~~~~~---- 96 (175)
T PRK12518 76 ARRQFAQRPS---R---------------------------------------------------IQDD-SLNDQP---- 96 (175)
T ss_pred HHHHhhcccc---c---------------------------------------------------hhcc-cccccc----
Confidence 9987654100 0 0000 000000
Q ss_pred ccccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHH
Q psy15215 548 FIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPL 627 (1432)
Q Consensus 548 ~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~ 627 (1432)
.. ...+| .....+....+..+|+.||++++.||.|+|+.|+ |++|||+.||+|.++|++..+||+++|++.
T Consensus 97 --~~-~~~~~--~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~g~----s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~ 167 (175)
T PRK12518 97 --SR-PSDTP--DLMQLHYQDLVQQGLQTLSLEHRAVLVLHDLEDL----PQKEIAEILNIPVGTVKSRLFYARRQLRKF 167 (175)
T ss_pred --cC-CCCcH--HHHHHHHHHHHHHHHHhCCHHHeeeeeehHhcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 00 01122 2222334567899999999999999999999998 999999999999999999999999999988
Q ss_pred HHH
Q psy15215 628 AHD 630 (1432)
Q Consensus 628 l~~ 630 (1432)
+..
T Consensus 168 l~~ 170 (175)
T PRK12518 168 LQQ 170 (175)
T ss_pred HHh
Confidence 753
No 194
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=99.68 E-value=4.7e-16 Score=170.33 Aligned_cols=180 Identities=14% Similarity=0.156 Sum_probs=133.8
Q ss_pred HHHHHHHHHHHHHHHHhccCCCCC-hhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHHHHHHhccccccccc
Q psy15215 1193 REMTEANLRLVISIAKKYTDRGLQ-FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 1271 (1432)
Q Consensus 1193 ~~Li~~~~~lV~~ia~~y~~~~~~-~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~~ 1271 (1432)
++.+..|.+.|+++|.+++++..+ ++|++||+|+.+|++.++|+.. .+|.+|++.+++|.+.+++|++.+.......
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 467888999999999999999888 9999999999999999999864 3799999999999999999987652111000
Q ss_pred HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHHH
Q psy15215 1272 MIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAA 1351 (1432)
Q Consensus 1272 ~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~~d~i~d~~~~~p~~~~ 1351 (1432)
. ..+.+. .. ..+... .+ .....+... ....+|+..+
T Consensus 86 ~----------------------~~~~~~-----------~~------~~~~~~---~~-~~~~~~~~~-~~~~~~e~~~ 121 (195)
T PRK12532 86 L----------------------DDELLD-----------EA------FESHFS---QN-GHWTPEGQP-QHWNTPEKSL 121 (195)
T ss_pred c----------------------cccccc-----------hh------hhhhhc---cc-cccccccCc-cccCCHHHHH
Confidence 0 000000 00 000000 00 000000000 1124678888
Q ss_pred HHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchhhhh
Q psy15215 1352 LNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYK 1422 (1432)
Q Consensus 1352 ~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~~~~ 1422 (1432)
...+....+..+|..||+++|.||.|+|..|+ |++|||+.||+|.++|+++++||+++||+......
T Consensus 122 ~~~e~~~~l~~~l~~L~~~~r~i~~L~~~~g~----s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~~ 188 (195)
T PRK12532 122 NNNEFQKILQSCLYNLPENTARVFTLKEILGF----SSDEIQQMCGISTSNYHTIMHRARESLRQCLQIKW 188 (195)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHhhhHHHhCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhh
Confidence 77788889999999999999999999999998 99999999999999999999999999999775543
No 195
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=99.68 E-value=6.3e-16 Score=164.35 Aligned_cols=156 Identities=13% Similarity=0.134 Sum_probs=124.9
Q ss_pred hhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q psy15215 1190 KAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 1269 (1432)
Q Consensus 1190 ~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip 1269 (1432)
+.|.+++..|.+.|+.+|++++++..+++|++||+|+.+|+..++|+.. ..|.+|++..++|.+.+++|++.+...
T Consensus 6 ~~f~~~~~~~~~~l~~~a~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~R~~~~~~~-- 81 (164)
T PRK12547 6 KNFKQELLLALPALRAFAVSLSSKHDKAEDLVQDTLMKAWAKQDSFEMG--TNLKAWLFTILRNEFYSQMRKRGREVQ-- 81 (164)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHhhhhcCCc--ccHHHHHHHHHHHHHHHHHHhhccccc--
Confidence 4799999999999999999999999999999999999999999999753 369999999999999999998764100
Q ss_pred ccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHH
Q psy15215 1270 VHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349 (1432)
Q Consensus 1270 ~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~~d~i~d~~~~~p~~ 1349 (1432)
. .......+ . ..++..
T Consensus 82 -~-----------------------------------------------~~~~~~~~-------------~---~~~~~~ 97 (164)
T PRK12547 82 -D-----------------------------------------------SDGVFTAR-------------V---AVHPAQ 97 (164)
T ss_pred -c-----------------------------------------------cccccccc-------------C---CCCchh
Confidence 0 00000000 0 001111
Q ss_pred HHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchh
Q psy15215 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 1419 (1432)
Q Consensus 1350 ~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~ 1419 (1432)
. .......+..+|+.|||++|+|+.|+|..|+ |++|||+.||+|+++|+++++||+++||....
T Consensus 98 ~--~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~----s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 161 (164)
T PRK12547 98 Y--GSLDLQDFKKALNLLSADQREAIILIGASGF----SYEDAAAICGCAVGTIKSRVSRARNRLQELLK 161 (164)
T ss_pred h--hHHHHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHh
Confidence 1 1122457889999999999999999999888 99999999999999999999999999998543
No 196
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=99.68 E-value=6.1e-16 Score=163.98 Aligned_cols=154 Identities=12% Similarity=0.113 Sum_probs=123.5
Q ss_pred hHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHHHHHHhcccccccc
Q psy15215 1191 AKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 1270 (1432)
Q Consensus 1191 A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~ 1270 (1432)
|+..++..|.+.|+.+|.+++++..+++|++||+|+.+|+..++|++. .|.||++.+++|.+.+++|++.+....
T Consensus 6 a~~~l~~~~~~~l~~~~~~~~~~~~~AeDv~Qe~f~~~~~~~~~~~~~---~~~~wl~~i~~n~~~d~~R~~~~~~~~-- 80 (161)
T PRK12541 6 SLEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYKGE---EIRPWLFTIAYNAFIDWYRKEKKYKTT-- 80 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhHHHccCC---ChHHHHHHHHHHHHHHHHHhccccccc--
Confidence 899999999999999999999999999999999999999999999853 599999999999999999987651000
Q ss_pred cHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHH
Q psy15215 1271 HMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 1350 (1432)
Q Consensus 1271 ~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~~d~i~d~~~~~p~~~ 1350 (1432)
..+. ... ......+...
T Consensus 81 ---------------------------------------------------~~~~-------~~~-----~~~~~~~~~~ 97 (161)
T PRK12541 81 ---------------------------------------------------TIEE-------FHL-----PNVPSTEHEY 97 (161)
T ss_pred ---------------------------------------------------chhh-------hhc-----cCCCCcHHHH
Confidence 0000 000 0000012222
Q ss_pred HHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCc
Q psy15215 1351 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417 (1432)
Q Consensus 1351 ~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~ 1417 (1432)
....+. ..+..+|..||+++|.||.|+|..|. |++|||+.||+|.++|+++++||+++||..
T Consensus 98 ~~~~~~-~~~~~~l~~L~~~~r~v~~l~~~~~~----s~~eIA~~lgis~~tv~~~l~Rar~~L~~~ 159 (161)
T PRK12541 98 FIKHEI-ASWLDSLSSLPLERRNVLLLRDYYGF----SYKEIAEMTGLSLAKVKIELHRGRKETKSI 159 (161)
T ss_pred HHHhHH-HHHHHHHHHCCHHHHHHhhhHHhcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 333333 44557899999999999999999888 999999999999999999999999999974
No 197
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=99.68 E-value=7.9e-16 Score=168.16 Aligned_cols=180 Identities=19% Similarity=0.116 Sum_probs=142.8
Q ss_pred cCCChhhHHHHHHHHHHhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHH
Q psy15215 377 IVLPLNDLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 456 (1432)
Q Consensus 377 ~~l~~~e~~~l~~~i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fsty 456 (1432)
.+++..++.+++.++..|+.. |+..++..|.+.++.++. ++++..+++|++||.|+.+|+..++|++. .+|.+|
T Consensus 5 ~~~~~~~~~~l~~~~~~~d~~---a~~~l~~~y~~~l~~~~~-~~~~~~~AEDivQevflkl~~~~~~~~~~--~~~~~W 78 (196)
T PRK12535 5 SERDDAHVTDLALAAGRGDRA---ALTEFIRETQDDVWRLLA-HLGGHDIADDLTQETYLRVMSALPRFAAR--SSARTW 78 (196)
T ss_pred cccccHHHHHHHHHHHcCCHH---HHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHHhhhcCCc--ccHHHH
Confidence 456667788999999999999 999999999999999975 56778899999999999999999999863 379999
Q ss_pred HHHHHHHHHHHHHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCC
Q psy15215 457 ATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESP 536 (1432)
Q Consensus 457 a~~~ir~~i~~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~ 536 (1432)
++.+++|.+.+++|++.+..+. ..+ .
T Consensus 79 L~~Iarn~~id~~Rk~~~~~~~-----------------------------------------------------~~~-~ 104 (196)
T PRK12535 79 LLSLARRVWVDNIRHDMARPRK-----------------------------------------------------SAT-E 104 (196)
T ss_pred HHHHHHHHHHHHHHhhccCCCc-----------------------------------------------------ccc-c
Confidence 9999999999999987642110 000 0
Q ss_pred CCCCCCCCcCcccccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHH
Q psy15215 537 VGDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQI 616 (1432)
Q Consensus 537 ~~~~~~~~~~~~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~ 616 (1432)
..+. .+ ...+|..... ......+..+|+.|||++++||.|+|..|+ |++|||+.||+|+++|+++
T Consensus 105 ~~~~-----~~-----~~~~~~~~~~-~~~~~~l~~~l~~Lp~~~r~v~~l~~~~g~----s~~EIAe~lgis~~tV~~~ 169 (196)
T PRK12535 105 YEDA-----AA-----TTASNETTGS-WSEWIDVRTLIDALPPERREALILTQVLGY----TYEEAAKIADVRVGTIRSR 169 (196)
T ss_pred cccc-----cc-----ccCCcchhHH-HHHHHHHHHHHHcCCHHHHHHhhhHHHhCC----CHHHHHHHhCCCHHHHHHH
Confidence 0000 00 0011221111 122357899999999999999999999999 9999999999999999999
Q ss_pred HHHHHHHHHHHHHHH
Q psy15215 617 EAKALRKLRPLAHDW 631 (1432)
Q Consensus 617 ~~rAl~kLr~~l~~~ 631 (1432)
.+||+++||+.+..+
T Consensus 170 l~Rar~~Lr~~l~~~ 184 (196)
T PRK12535 170 VARARADLIAATATG 184 (196)
T ss_pred HHHHHHHHHHHhccc
Confidence 999999999888654
No 198
>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=99.68 E-value=7.2e-16 Score=182.75 Aligned_cols=182 Identities=17% Similarity=0.138 Sum_probs=135.8
Q ss_pred hhhhhhhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHHHHHHhc
Q psy15215 1184 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 1263 (1432)
Q Consensus 1184 g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~~i~~~~ 1263 (1432)
|+.. |+..|+..|.+.|+++|.+++++..+++|++||+|+.+|+..++|+.. .+|.||++.+++|.|.+++|++.
T Consensus 2 gd~~---af~~l~~~~~~~l~~~a~~~~~~~~~AEDivQe~fl~~~~~~~~~~~~--~~~~~WL~~Ia~n~~~d~~Rk~~ 76 (324)
T TIGR02960 2 VDGA---AFTALAEPHRRELLAHCYRMLGSLHEAEDLVQETLLRAWRARDRFEGR--SSVRTWLYRIATNACLDALEARQ 76 (324)
T ss_pred CcHH---HHHHHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHHHhhhhccCcc--cchHHHHHHHHHHHHHHHHHhcc
Confidence 6666 999999999999999999999999999999999999999999999864 37999999999999999999876
Q ss_pred ccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccc---
Q psy15215 1264 RTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIE--- 1340 (1432)
Q Consensus 1264 r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~~d~i~--- 1340 (1432)
+....... .. ....+...+ .++......+.+.
T Consensus 77 ~~~~~~~~------------------~~--------------------------~~~~~~~~~-~~~~~~~~~~~~~~~~ 111 (324)
T TIGR02960 77 RRPRPVGL------------------GA--------------------------PSADGTAAA-SEAAEVTWLEPLPDLT 111 (324)
T ss_pred CCcCcccc------------------CC--------------------------CCCcccccc-cccccccccCCCCccc
Confidence 41100000 00 000000000 0000000000000
Q ss_pred ----cCCCCChHHHHHHHH-HHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhh
Q psy15215 1341 ----DENMLAPSDAALNAS-MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 1415 (1432)
Q Consensus 1341 ----d~~~~~p~~~~~~~~-~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr 1415 (1432)
.....+|++.....+ +...+..+|.+|||++|.||.|+|+.|+ |++|||+.||+|.++|+++++||+++||
T Consensus 112 ~~~~~~~~~~~~~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L~~~~g~----s~~EIA~~lgis~~tV~~~l~Rar~~Lr 187 (324)
T TIGR02960 112 LDLDDPAAADPSVAAGSRESVRLAFVAAIQYLPPRQRAVLLLRDVLGW----RAAETAELLGTSTASVNSALQRARATLD 187 (324)
T ss_pred cccccCCCCCHHHHHHHHHHHHHHHHHHHHhCCHHHhhHhhhHHHhCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 112236776665554 5567899999999999999999999999 9999999999999999999999999999
Q ss_pred Cchh
Q psy15215 1416 HPSR 1419 (1432)
Q Consensus 1416 ~~~~ 1419 (1432)
+...
T Consensus 188 ~~l~ 191 (324)
T TIGR02960 188 EVGP 191 (324)
T ss_pred Hhcc
Confidence 8665
No 199
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=99.68 E-value=1.2e-15 Score=164.98 Aligned_cols=172 Identities=17% Similarity=0.201 Sum_probs=138.2
Q ss_pred HHHHHHhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHH
Q psy15215 388 NRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITR 467 (1432)
Q Consensus 388 ~~~i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~ 467 (1432)
......|+.. ++..++..|.+.++.+|++++++..+++||+||+|+.+|+++..| . .+.+|.||++.+++|.+.+
T Consensus 6 ~~~~~~~~~~---~~~~~~~~~~~~l~~~~~~~~~~~~dAeDlvQE~~lr~~~~~~~~-~-~~~~~~~wl~~Ia~n~~iD 80 (182)
T COG1595 6 LAEALRGDRA---AFEELLERLRPRLRRLARRLLGDRADAEDLVQETFLRAWRAIDSF-R-GRSSFKAWLYRIARNLAID 80 (182)
T ss_pred HHHHHhcchH---HHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhc-C-CCCchHHHHHHHHHHHHHH
Confidence 3445566666 999999999999999999999998899999999999999999999 3 3458999999999999999
Q ss_pred HHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCc
Q psy15215 468 SIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGD 547 (1432)
Q Consensus 468 ~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~ 547 (1432)
++|++.+.... +.+.+.....
T Consensus 81 ~~R~~~r~~~~----------------------------------------------------------~~~~~~~~~~- 101 (182)
T COG1595 81 RLRKRKRRRAR----------------------------------------------------------VEEADLLPEE- 101 (182)
T ss_pred HHHHhcccccc----------------------------------------------------------cccccccccc-
Confidence 99988763211 0000000000
Q ss_pred ccccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHH
Q psy15215 548 FIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPL 627 (1432)
Q Consensus 548 ~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~ 627 (1432)
.+.....+ +.+...+....+..+|..||+++|.+|.|+|+.|. |++|||+.+|+|.++|+.+.++|+.+|++.
T Consensus 102 --~~~~~~~~-~~~~~~~~~~~l~~al~~Lp~~~R~~~~l~~~~gl----s~~EIA~~l~i~~~tVks~l~ra~~~l~~~ 174 (182)
T COG1595 102 --ADPAPDLA-ELLLAEEELERLRRALARLPPRQREAFLLRYLEGL----SYEEIAEILGISVGTVKSRLHRARKKLREQ 174 (182)
T ss_pred --cCcccccc-hHHHHHHHHHHHHHHHHhCCHHHhHHhhhHhhcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 00000011 35666778899999999999999999999999998 999999999999999999999999999988
Q ss_pred HHH
Q psy15215 628 AHD 630 (1432)
Q Consensus 628 l~~ 630 (1432)
+..
T Consensus 175 l~~ 177 (182)
T COG1595 175 LEE 177 (182)
T ss_pred Hhh
Confidence 754
No 200
>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=99.67 E-value=5.2e-16 Score=169.64 Aligned_cols=178 Identities=12% Similarity=0.077 Sum_probs=135.2
Q ss_pred HHhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHHHHHH
Q psy15215 392 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIAD 471 (1432)
Q Consensus 392 ~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~~i~~ 471 (1432)
..++.. ++..|+..|.+.|+.+|.+++++..+++|++||+|+.+|+++.+|++. .+|.+|++..++|.+.+++|+
T Consensus 6 ~~~~~~---~f~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQevfl~~~~~~~~~~~~--~~~~~wL~~iarN~~~d~~Rk 80 (193)
T TIGR02947 6 KTQRAQ---RFERDALEYLDQLYGAALRMTRNPADAEDLVQEAYAKAFSSFHQFKPG--TNLKAWLYRILTNTYINSYRK 80 (193)
T ss_pred hhhhHH---HHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhcccCCC--CcchHHHHHHHHHHHHHHHHH
Confidence 344445 999999999999999999999999999999999999999999999853 479999999999999999998
Q ss_pred hccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCccccc
Q psy15215 472 QARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIED 551 (1432)
Q Consensus 472 ~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~i~d 551 (1432)
+.+...... .+++. . .... +.... ..
T Consensus 81 ~~~~~~~~~-------------------------~~~~~-----------~--------~~~~----~~~~~------~~ 106 (193)
T TIGR02947 81 AQRRPQQSD-------------------------DDDIE-----------D--------WQLA----KAASH------TS 106 (193)
T ss_pred hcCCccccc-------------------------chhhh-----------h--------hhhc----ccccc------cc
Confidence 765211000 00000 0 0000 00000 00
Q ss_pred CCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHHHHH
Q psy15215 552 ENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLAHDW 631 (1432)
Q Consensus 552 ~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l~~~ 631 (1432)
.....|+...........|..+|++||+++|.|+.|+|..|+ |++|||+.||+|.++|+.+.+||+++|++.+..+
T Consensus 107 ~~~~~~e~~~~~~~~~~~l~~~l~~Lp~~~r~i~~L~~~~g~----s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~ 182 (193)
T TIGR02947 107 NGLRSAELEALDGLPDQDIKDALQGLPEEFRQAVYLADVEGF----AYKEIAEIMGTPIGTVMSRLHRGRKQLRKQLVDV 182 (193)
T ss_pred ccccchhHHHHhhhhHHHHHHHHHhCCHHHhhheeehhhcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 001133334444455678999999999999999999999999 9999999999999999999999999999988754
Q ss_pred H
Q psy15215 632 L 632 (1432)
Q Consensus 632 ~ 632 (1432)
.
T Consensus 183 ~ 183 (193)
T TIGR02947 183 A 183 (193)
T ss_pred H
Confidence 3
No 201
>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=99.67 E-value=5.8e-16 Score=163.89 Aligned_cols=159 Identities=13% Similarity=0.159 Sum_probs=130.8
Q ss_pred hHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHHHHHHhccccccch
Q psy15215 401 AKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 480 (1432)
Q Consensus 401 A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~ 480 (1432)
|+.+++..|.+.|+.+|+++.++..+++|++||+++++|+++++|++. .+|.+|++.++|+.+.+++++..+.-..
T Consensus 2 a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~~~~~~~~~~~~--~~~~~wl~~i~r~~~~d~~r~~~~~~~~-- 77 (161)
T TIGR02985 2 AFEQLYRRYYPKLCAFAYRYVKDEEEAEDIVQDVFVKLWENRETLEEV--ESFKAYLFTIVKNRSLNYLRHKQVEEKY-- 77 (161)
T ss_pred hHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcccc--ccHHHHHHHHHHHHHHHHHHHHHhHhHH--
Confidence 899999999999999999999998999999999999999999999863 4799999999999999999987641000
Q ss_pred hHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHH
Q psy15215 481 HMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 560 (1432)
Q Consensus 481 ~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~i~d~~~~~p~~~ 560 (1432)
... + .+.... .....+|++.
T Consensus 78 ----------------~~~---------~----------------------------~~~~~~-------~~~~~~~~~~ 97 (161)
T TIGR02985 78 ----------------QEE---------I----------------------------LEIEVD-------ELSENDPEEE 97 (161)
T ss_pred ----------------HHH---------H----------------------------Hhhccc-------ccCCCCcHHH
Confidence 000 0 000000 0011246666
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHH
Q psy15215 561 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPL 627 (1432)
Q Consensus 561 ~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~ 627 (1432)
+...+....+..++..||++++.||.++|..|+ |..|||+.+|+|+++|+++.++|+++|++.
T Consensus 98 ~~~~e~~~~l~~~l~~L~~~~r~il~l~~~~~~----~~~eIA~~lgis~~tv~~~~~ra~~~Lr~~ 160 (161)
T TIGR02985 98 LEAKELQLIIYKAIEKLPEQCRKIFILSRFEGK----SYKEIAEELGISVKTVEYHISKALKELRKE 160 (161)
T ss_pred HHHHHHHHHHHHHHHHCCHHHHHHHHHHHHcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 667777888999999999999999999998888 999999999999999999999999999875
No 202
>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=99.67 E-value=4.7e-16 Score=164.51 Aligned_cols=157 Identities=15% Similarity=0.194 Sum_probs=126.4
Q ss_pred hHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHHHHHHhccccccch
Q psy15215 401 AKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 480 (1432)
Q Consensus 401 A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~ 480 (1432)
|+..++..|.+.|+++|+++.++..+++|++||+++.+|+++++|++.. .|.+|++..++|.+.++++++.+.-+ +.
T Consensus 2 ~~~~~~~~~~~~l~~~~~~~~~~~~~aEDivQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~r~~~~~~~-~~ 78 (159)
T TIGR02989 2 AFAALLQRHQRSLRAFVRSLVPDRDDADDVLQETFVTAWRKFDEFDPGT--DFGAWARGIARNKVLNHRRKLGRDRL-VF 78 (159)
T ss_pred HHHHHHHHhHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHHhCCCCC--chHHHHHHHHHHHHHHHHHHhccccc-cc
Confidence 7899999999999999999999999999999999999999999999753 69999999999999999998765210 00
Q ss_pred hHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHH
Q psy15215 481 HMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 560 (1432)
Q Consensus 481 ~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~i~d~~~~~p~~~ 560 (1432)
. ++. .+.+.+. .+|.+.
T Consensus 79 ~-------------------------~~~------------------------------------~~~~~~~--~~~~~~ 95 (159)
T TIGR02989 79 D-------------------------DEL------------------------------------LEALAAE--AEATEA 95 (159)
T ss_pred C-------------------------HHH------------------------------------HHHHHhh--cccchH
Confidence 0 000 0000000 011122
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHH
Q psy15215 561 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPL 627 (1432)
Q Consensus 561 ~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~ 627 (1432)
....+....+..+++.||++++.|+.|+|..|+ |++|||+.||+|+++|+.+.+||+.+|++.
T Consensus 96 ~~~~~~~~~l~~~i~~L~~~~r~v~~l~~~~g~----~~~eIA~~l~is~~tv~~~l~Rar~~Lr~~ 158 (159)
T TIGR02989 96 DRSEDELQALEGCLEKLPERQRELLQLRYQRGV----SLTALAEQLGRTVNAVYKALSRLRVRLRDC 158 (159)
T ss_pred hhHHHHHHHHHHHHHHCCHHHHHHHHHHHhcCC----CHHHHHHHhCCCHHHHHHHHHHHHHHHHhc
Confidence 223344567899999999999999999999888 999999999999999999999999999875
No 203
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=99.67 E-value=8.1e-16 Score=166.13 Aligned_cols=160 Identities=14% Similarity=0.131 Sum_probs=127.8
Q ss_pred hhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q psy15215 1190 KAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 1269 (1432)
Q Consensus 1190 ~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip 1269 (1432)
+++..++..|.+.|+++|.+++++..+++|++||+|+.+|+..++|++.. .|.+|++.+++|.+.++++++.+....
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 47889999999999999999999999999999999999999999998653 699999999999999999987641000
Q ss_pred ccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHH
Q psy15215 1270 VHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349 (1432)
Q Consensus 1270 ~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~~d~i~d~~~~~p~~ 1349 (1432)
. +... .+... .+|..
T Consensus 82 ----------------------------------------------------~-~~~~--------~~~~~----~~~~~ 96 (182)
T PRK12540 82 ----------------------------------------------------A-DGSY--------AKTLK----SQPGQ 96 (182)
T ss_pred ----------------------------------------------------c-cccc--------ccccc----CCCch
Confidence 0 0000 00000 01111
Q ss_pred HHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchhhhhH
Q psy15215 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKL 1423 (1432)
Q Consensus 1350 ~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~~~~l 1423 (1432)
.. ......+..+|+.||+++|.||.|+|..|+ |++|||+.||+|.++|+++++||+++||+.+.....
T Consensus 97 ~~--~~~~~~l~~~l~~Lp~~~R~v~~L~~~~g~----s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~~~~~ 164 (182)
T PRK12540 97 NA--HLEFEEFRAALDKLPQDQREALILVGASGF----SYEDAAAICGCAVGTIKSRVNRARSKLSALLYVDGA 164 (182)
T ss_pred HH--HHHHHHHHHHHHhCCHHHHHHhhHHHHcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhccc
Confidence 11 112356899999999999999999999888 999999999999999999999999999998776553
No 204
>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=99.67 E-value=1.9e-15 Score=165.13 Aligned_cols=118 Identities=14% Similarity=0.194 Sum_probs=106.9
Q ss_pred HHHhhhhhhhhhHHHHHHHHHHHHHHHHHhccCCC--CChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHH
Q psy15215 1180 KMIAGEMKARKAKREMTEANLRLVISIAKKYTDRG--LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITR 1257 (1432)
Q Consensus 1180 ~~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~--~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~ 1257 (1432)
.++.|+.. +++|+..|.|+|.++|++|+++. .+.+|++|+|++|||+|+++||+.+|.+|+|||.+||++.+.+
T Consensus 3 ~~~~gd~~----~e~LI~~Y~plI~~~a~~~~~~~~~~e~dDlvQ~glial~eAi~~yd~~kg~~F~sya~~~Ir~~i~d 78 (218)
T TIGR02895 3 PIQPGNEE----REELIRQYKPFIAKIVSSVCGRYIDTKSDDELSIGLIAFNEAIESYDSNKGKSFLSFAKLIIKRRLID 78 (218)
T ss_pred hhhcCChH----HHHHHHHhHHHHHHHHHHHHccCCCCChhHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHH
Confidence 46677654 99999999999999999998774 5899999999999999999999999999999999999999999
Q ss_pred HHHHhc---ccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHH
Q psy15215 1258 SIADQA---RTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 1301 (1432)
Q Consensus 1258 ~i~~~~---r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~ 1301 (1432)
++|++. +.+++|....+.......+..++.++.++.|+.+||+.
T Consensus 79 ylRk~~k~~~~v~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~eEI~~ 125 (218)
T TIGR02895 79 YIRKNQKYQNLLYLDEDYDENPLEFNKSMEEYRNEIENENRRLEILE 125 (218)
T ss_pred HHHhcccccCeeeCCchHHHHHHHHHHHHHHHHHHHccccHHHHHHH
Confidence 999987 67789987777777888888899999999999999987
No 205
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=99.66 E-value=2.2e-15 Score=165.50 Aligned_cols=166 Identities=17% Similarity=0.246 Sum_probs=137.2
Q ss_pred HhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHHHHHHh
Q psy15215 393 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQ 472 (1432)
Q Consensus 393 ~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~~i~~~ 472 (1432)
.|+.. |+..++..|.+.|+.++.++++...+.+|++||+++.+|+...+|++ + +|.+|++..+||.+.+++|+.
T Consensus 24 ~~d~~---a~~~l~~~~~~~L~~~~~~~~~~~~~AEDivQEvflkl~~~~~~~~~--~-~~~~wL~~iarn~~~d~~Rk~ 97 (203)
T PRK09647 24 KATMP---SWEELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSLQNYQP--G-TFEGWLHRITTNLFLDMVRRR 97 (203)
T ss_pred CCCHH---HHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCC--c-ccHHHHHHHHHHHHHHHHHhc
Confidence 45666 99999999999999999999999999999999999999999999974 3 699999999999999999976
Q ss_pred ccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccC
Q psy15215 473 ARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDE 552 (1432)
Q Consensus 473 ~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~i~d~ 552 (1432)
.+ .+. . .++ ++ . +... .
T Consensus 98 ~~-~~~--~--------------------------------------------------~~~----~~----~-~~~~-~ 114 (203)
T PRK09647 98 AR-IRM--E--------------------------------------------------ALP----ED----Y-DRVP-G 114 (203)
T ss_pred cc-Ccc--c--------------------------------------------------ccc----cc----c-cccC-C
Confidence 53 110 0 000 00 0 0000 1
Q ss_pred CCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHHHHH
Q psy15215 553 NMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLAHDW 631 (1432)
Q Consensus 553 ~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l~~~ 631 (1432)
...+|.......++...|..+|.+||++++.|+.|+|+.|+ |++|||+.||+|+++|++..+||+++|++.+...
T Consensus 115 ~~~~~~~~~~~~~~~~~l~~~L~~L~~~~r~v~~L~~~~g~----s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l~~~ 189 (203)
T PRK09647 115 DEPNPEQIYHDARLDPDLQAALDSLPPEFRAAVVLCDIEGL----SYEEIAATLGVKLGTVRSRIHRGRQQLRAALAAH 189 (203)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 12356666777777888999999999999999999999888 9999999999999999999999999999888653
No 206
>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=99.66 E-value=1.6e-15 Score=158.97 Aligned_cols=156 Identities=22% Similarity=0.347 Sum_probs=132.2
Q ss_pred hHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHHHHHHhccccccch
Q psy15215 401 AKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 480 (1432)
Q Consensus 401 A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~ 480 (1432)
|++.++..|.++|+++++++..++.+++|++|||++++|++++.|++. .+|.+|+.+++++.+.++++++.+ .+.
T Consensus 2 a~~~l~~~~~~~v~~~~~~~~~~~~~~~D~~qe~~~~l~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~rk~~~---~~~ 76 (158)
T TIGR02937 2 AFEELYERYLPLLYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPE--GSFKAWLFRIARNLILDYLRRKRR---LRR 76 (158)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCCc--chHHHHHHHHHHHHHHHHHHHhcc---CCc
Confidence 789999999999999999999999999999999999999999999987 689999999999999999998875 111
Q ss_pred hHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHH
Q psy15215 481 HMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 560 (1432)
Q Consensus 481 ~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~i~d~~~~~p~~~ 560 (1432)
.+ ..+. .. . ....+|.+.
T Consensus 77 ~~---------------------------------------------------~~~~------~~----~-~~~~~~~~~ 94 (158)
T TIGR02937 77 EL---------------------------------------------------DLLE------EL----L-DSDPSPEEE 94 (158)
T ss_pred ch---------------------------------------------------hhhh------hc----c-cccCCHHHH
Confidence 10 0000 00 0 011256666
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHH
Q psy15215 561 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPL 627 (1432)
Q Consensus 561 ~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~ 627 (1432)
.........+..++++||+.++.||.++|..|. |..|||+.+|+|+.+|+++..+++.+|++.
T Consensus 95 ~~~~~~~~~l~~~l~~L~~~~~~ii~~~~~~g~----s~~eIA~~l~~s~~~v~~~~~~~~~kl~~~ 157 (158)
T TIGR02937 95 LEQEEEREALREALEKLPEREREVLVLRYLEGL----SYKEIAEILGISVGTVKRRLKRARKKLREL 157 (158)
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHhhHHhcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 677777888999999999999999999998887 999999999999999999999999999875
No 207
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=99.66 E-value=1.9e-15 Score=163.20 Aligned_cols=153 Identities=11% Similarity=0.126 Sum_probs=126.8
Q ss_pred HHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHHHHHHhccccccccc
Q psy15215 1192 KREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 1271 (1432)
Q Consensus 1192 ~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~~ 1271 (1432)
++.+++.|.+.|+++|.+++++..+++|++||+|+.+|+.+.+|++. .+|.+|++.+++|.+.+++|++.+....+
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 67899999999999999999999999999999999999999999853 47999999999999999999876521000
Q ss_pred HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHHH
Q psy15215 1272 MIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAA 1351 (1432)
Q Consensus 1272 ~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~~d~i~d~~~~~p~~~~ 1351 (1432)
.+ .. .. .++.+..
T Consensus 79 ---------------------------------------------------------~~-~~-----~~----~~~~~~~ 91 (181)
T PRK09637 79 ---------------------------------------------------------DD-LL-----FE----DEEREEN 91 (181)
T ss_pred ---------------------------------------------------------hh-hh-----cc----CCChhHH
Confidence 00 00 00 0112233
Q ss_pred HHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchh
Q psy15215 1352 LNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 1419 (1432)
Q Consensus 1352 ~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~ 1419 (1432)
...+....+..+|+.||+++|.||.|+|+.|+ +.+|||+.||+|..+|+.+++||+++||+...
T Consensus 92 ~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~----~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 155 (181)
T PRK09637 92 AKKELAPCLRPFIDALPEKYAEALRLTELEGL----SQKEIAEKLGLSLSGAKSRVQRGRVKLKELLE 155 (181)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCC----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 34456778999999999999999999999998 99999999999999999999999999998554
No 208
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=99.65 E-value=1.2e-15 Score=163.56 Aligned_cols=164 Identities=12% Similarity=0.097 Sum_probs=131.0
Q ss_pred HHhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHHHHHH
Q psy15215 392 IAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIAD 471 (1432)
Q Consensus 392 ~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~~i~~ 471 (1432)
++|+.. |+..++..|.+.|+.+|.++++...+++|++||+|+.+|+. .+|... .+|.+|++.+++|.+.+++|+
T Consensus 5 ~~~~~~---a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQevflk~~~~-~~~~~~--~~~~~wL~~Iarn~~~d~~Rk 78 (172)
T PRK12523 5 QSPHSE---LVGALYRDHRGWLLAWLRRNVACRQRAEDLSQDTFVRLLGR-PELPTP--REPRAFLAAVAKGLMFDHFRR 78 (172)
T ss_pred CCCCcH---HHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHcc-cccCcc--hhHHHHHHHHHHHHHHHHHHH
Confidence 568877 99999999999999999999999999999999999999986 456532 479999999999999999998
Q ss_pred hccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCccccc
Q psy15215 472 QARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIED 551 (1432)
Q Consensus 472 ~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~i~d 551 (1432)
+.+.... . .++ .. . . .
T Consensus 79 ~~~~~~~------------------~---------~~~------------------------~~-~-~-----------~ 94 (172)
T PRK12523 79 AALEQAY------------------L---------AEL------------------------AL-V-P-----------E 94 (172)
T ss_pred HHHHHHH------------------H---------HHH------------------------hh-c-c-----------c
Confidence 7531000 0 000 00 0 0 0
Q ss_pred CCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHHH
Q psy15215 552 ENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLAH 629 (1432)
Q Consensus 552 ~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l~ 629 (1432)
....+|.......+....+..+|..||+++|.||.|+|..|+ |++|||+.||+|.++|+++.++|+++|+..+.
T Consensus 95 ~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~L~~~~g~----s~~EIA~~lgis~~tV~~~l~ra~~~~~~~l~ 168 (172)
T PRK12523 95 AEQPSPEEQHLILEDLKAIDRLLGKLSSKARAAFLYNRLDGM----GHAEIAERLGVSVSRVRQYLAQGLRQCYIALY 168 (172)
T ss_pred ccCCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Confidence 011245555444455568999999999999999999999998 99999999999999999999999999987763
No 209
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=99.65 E-value=2.5e-15 Score=160.16 Aligned_cols=160 Identities=16% Similarity=0.177 Sum_probs=132.3
Q ss_pred HhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHHHHHHhccccccc
Q psy15215 400 KAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 479 (1432)
Q Consensus 400 ~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip 479 (1432)
.|+..++..|.+.|+.+|.+++++..+++|++||+|+.+|++ +|+. +.+|.+|++..++|.+.+++++..+..+..
T Consensus 3 ~~f~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fi~~~~~--~~~~--~~~~~~wl~~i~rn~~~d~~rk~~~~~~~~ 78 (166)
T PRK09639 3 ETFEDLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLYRS--DFKG--IENEKGWLIKSARNVAYNYLRSEKRRRARI 78 (166)
T ss_pred hHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH--hccc--ccchHHHHHHHHHHHHHHHHHHhccccccc
Confidence 489999999999999999999999999999999999999999 6764 457999999999999999999876521100
Q ss_pred hhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHH
Q psy15215 480 VHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 559 (1432)
Q Consensus 480 ~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~i~d~~~~~p~~ 559 (1432)
. ... +. .+. ....+|++
T Consensus 79 ~------------------------------------------------------~~~-~~-----~~~---~~~~~~e~ 95 (166)
T PRK09639 79 L------------------------------------------------------GEF-QW-----QEV---DNEPSPEE 95 (166)
T ss_pred c------------------------------------------------------chh-hh-----hhc---cCCCChHH
Confidence 0 000 00 000 11236777
Q ss_pred HHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHHHHH
Q psy15215 560 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLAHDW 631 (1432)
Q Consensus 560 ~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l~~~ 631 (1432)
.....+....+..+|.+||++++.||.|+| .|+ |++|||+.||+|.++|+.+.++|+.+|+..+...
T Consensus 96 ~~~~~~~~~~l~~~l~~L~~~~r~il~l~~-~g~----s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l~~~ 162 (166)
T PRK09639 96 IWIRKEEITKVQEVLAKMTERDRTVLLLRF-SGY----SYKEIAEALGIKESSVGTTLARAKKKFRKIYEQM 162 (166)
T ss_pred HHHHHHHHHHHHHHHHcCCHHHHHHHHHHH-cCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 777777788899999999999999999999 999 9999999999999999999999999999988643
No 210
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=99.65 E-value=1.6e-15 Score=160.61 Aligned_cols=154 Identities=12% Similarity=0.120 Sum_probs=126.0
Q ss_pred HHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHHHHHHhccccccchhHHHHH
Q psy15215 407 EANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 486 (1432)
Q Consensus 407 ~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~~~~~~~ 486 (1432)
+.|.+.|+.+|.+++++..+++|++||+|+.+|++.++|++. .|.+|++..++|.+.+++|++.+..+.
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 579999999999999999999999999999999999999852 599999999999999999987541000
Q ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHHHHHHHH
Q psy15215 487 NKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 566 (1432)
Q Consensus 487 ~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~i~d~~~~~p~~~~~~~~~ 566 (1432)
.+.. ++. .+.+. ...+|++.....+.
T Consensus 71 --------------------------------------------~~~~----~~~----~~~~~--~~~~~~~~~~~~e~ 96 (160)
T PRK09642 71 --------------------------------------------LSLC----KET----EENIK--SSHNIEDLLLTKEQ 96 (160)
T ss_pred --------------------------------------------cccc----hhh----hhhcc--CCCChHHHHHHHHH
Confidence 0000 000 00000 11246666666777
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHHH
Q psy15215 567 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLAH 629 (1432)
Q Consensus 567 ~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l~ 629 (1432)
...+..+|++||+++|.|+.|+|..|+ |++|||+.||+|.++|+++.++|+.+|++.+.
T Consensus 97 ~~~l~~~l~~Lp~~~r~v~~l~~~~g~----s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 155 (160)
T PRK09642 97 KLLIAQKLRELPENYRDVVLAHYLEEK----SYQEIALQEKIEVKTVEMKLYRARKWIKKHWK 155 (160)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHhCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 888999999999999999999999999 99999999999999999999999999998875
No 211
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=99.65 E-value=2.1e-15 Score=159.56 Aligned_cols=154 Identities=10% Similarity=0.120 Sum_probs=125.5
Q ss_pred HHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHH
Q psy15215 1196 TEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET 1275 (1432)
Q Consensus 1196 i~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~~~~~~ 1275 (1432)
+..|.+.++.+|.+++++..+++|++||+|+.+|+..++|++ + +|.||++.+++|.+.+++|++.+...
T Consensus 1 ~~~~~~~l~~~~~~~~~~~~~aeDi~Qevf~~l~~~~~~~~~--~-~~~~wL~~ia~n~~~d~~R~~~~~~~-------- 69 (159)
T PRK12527 1 MENYYRELVRFLSARLGNRQAAEDVAHDAYLRVLERSSSAQI--E-HPRAFLYRTALNLVVDRHRRHRVRQA-------- 69 (159)
T ss_pred ChhHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHhccccccc--c-chHHHHHHHHHHHHHHHHHHHhcccc--------
Confidence 357889999999999999899999999999999999999864 3 79999999999999999997653100
Q ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHHHHHHH
Q psy15215 1276 INKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNAS 1355 (1432)
Q Consensus 1276 ~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~~d~i~d~~~~~p~~~~~~~~ 1355 (1432)
.+++. . ++. .....++|++.+....
T Consensus 70 ---------------------------------------------~~~~~-~-~~~--------~~~~~~~~~~~~~~~~ 94 (159)
T PRK12527 70 ---------------------------------------------EPLEV-L-DEE--------ERLHSPSPQTRLDLGQ 94 (159)
T ss_pred ---------------------------------------------cchhh-h-hcc--------ccccCCCHHHHHHHHH
Confidence 00000 0 000 0011235777777777
Q ss_pred HHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchh
Q psy15215 1356 MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 1419 (1432)
Q Consensus 1356 ~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~ 1419 (1432)
....+..+|.+|||+++.||.|+|+.|+ |++|||+.||+|.++|++++.||+++||....
T Consensus 95 ~~~~l~~~l~~L~~~~r~v~~l~~~~~~----s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l~ 154 (159)
T PRK12527 95 RLALLQRALAELPPACRDSFLLRKLEGL----SHQQIAEHLGISRSLVEKHIVNAMKHCRVRMR 154 (159)
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 7888999999999999999999999999 99999999999999999999999999998654
No 212
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=99.64 E-value=4.3e-15 Score=177.11 Aligned_cols=182 Identities=18% Similarity=0.213 Sum_probs=143.0
Q ss_pred HHHHHHHHHHhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHH
Q psy15215 384 LRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 463 (1432)
Q Consensus 384 ~~~l~~~i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~ 463 (1432)
-.+|+.+++.||.. |+.+|+..|.+.|+++|.+++++..+++|++||+|+.+|+.+++|+. ..+|.+|++.+++|
T Consensus 6 ~~~l~~~~~~gd~~---af~~l~~~y~~~l~~~~~~~~~~~~dAEDivQevfl~~~~~~~~~~~--~~~~~~wL~~Ia~n 80 (339)
T PRK08241 6 AAALLARAAAGDRD---AFAALVEPHRRELLAHCYRMLGSVHDAEDAVQETLLRAWRGYDRFEG--RSSLRTWLYRIATN 80 (339)
T ss_pred HHHHHHHhhcCCHH---HHHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHhhhhcccc--ccchHHHHHHHHHH
Confidence 45788999999998 99999999999999999999999999999999999999999999984 34799999999999
Q ss_pred HHHHHHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCC--
Q psy15215 464 AITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDE-- 541 (1432)
Q Consensus 464 ~i~~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~-- 541 (1432)
.+.+++|++.+.. .+ .....+..++.
T Consensus 81 ~~~d~~Rk~~~~~-~~---------------------------------------------------~~~~~~~~~~~~~ 108 (339)
T PRK08241 81 VCLDALEGRARRP-LP---------------------------------------------------TDLGAPAADPVDE 108 (339)
T ss_pred HHHHHHHhhcccc-Cc---------------------------------------------------cccCCCcCccccc
Confidence 9999999876410 00 00000000000
Q ss_pred -----CCCcCcccccC----CCCChHHHHHHHH-HHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchh
Q psy15215 542 -----DSHLGDFIEDE----NMLAPSDAALNAS-MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRE 611 (1432)
Q Consensus 542 -----~~~~~~~i~d~----~~~~p~~~~~~~~-~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~ 611 (1432)
...+.+.+.+. ...+|++.+...+ ....+..+|.+||+++|.||.|+|..|+ |++|||+.||+|.+
T Consensus 109 ~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L~~~~g~----s~~EIA~~lgis~~ 184 (339)
T PRK08241 109 LVERPEVPWLEPYPDALLDPAAADPAARVVARESVRLAFVAALQHLPPRQRAVLILRDVLGW----SAAEVAELLDTSVA 184 (339)
T ss_pred ccccccccccCCCCcccccccCCChHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhhHHhhCC----CHHHHHHHhCCCHH
Confidence 00011111110 1346776666554 4557899999999999999999999999 99999999999999
Q ss_pred HHHHHHHHHHHHHHH
Q psy15215 612 RIRQIEAKALRKLRP 626 (1432)
Q Consensus 612 ~v~~~~~rAl~kLr~ 626 (1432)
+|+++.+||+++|++
T Consensus 185 tVk~~l~RAr~~Lr~ 199 (339)
T PRK08241 185 AVNSALQRARATLAE 199 (339)
T ss_pred HHHHHHHHHHHHHhh
Confidence 999999999999998
No 213
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=99.64 E-value=3.1e-15 Score=158.90 Aligned_cols=158 Identities=18% Similarity=0.192 Sum_probs=126.6
Q ss_pred HHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHHHHHHhcccccccccHH
Q psy15215 1194 EMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 1273 (1432)
Q Consensus 1194 ~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~~~~ 1273 (1432)
.++..|.+.|+++|.+++++..+++|++||+++.+|+....|++. +|.+|++.+++|.+.+++|++.+....
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 367889999999999999999999999999999999988877643 588999999999999999987641100
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHHHHH
Q psy15215 1274 ETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALN 1353 (1432)
Q Consensus 1274 ~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~~d~i~d~~~~~p~~~~~~ 1353 (1432)
+ +.+.... .. .. ...+|+.....
T Consensus 74 ------------------------------------------------~------~~~~~~~-~~-~~-~~~~~~~~~~~ 96 (163)
T PRK07037 74 ------------------------------------------------H------GDEEDGL-DV-PS-PEASPEAALIN 96 (163)
T ss_pred ------------------------------------------------c------ccccccc-cc-CC-CCCCHHHHHHH
Confidence 0 0000000 00 01 12356666666
Q ss_pred HHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchhh
Q psy15215 1354 ASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRY 1420 (1432)
Q Consensus 1354 ~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~~ 1420 (1432)
.+....+..+|+.|||++|.||.++|+.|+ |.+|||+.||+|.++|++.+.||+++||..+..
T Consensus 97 ~~~~~~l~~~l~~L~~~~r~v~~l~~~~~~----s~~EIA~~lgis~~tV~~~l~ra~~~lr~~l~~ 159 (163)
T PRK07037 97 RDTLRHVADALSELPARTRYAFEMYRLHGE----TQKDIARELGVSPTLVNFMIRDALVHCRKCLDA 159 (163)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 677788999999999999999999999998 999999999999999999999999999986543
No 214
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=99.64 E-value=4.2e-15 Score=161.81 Aligned_cols=174 Identities=16% Similarity=0.194 Sum_probs=132.0
Q ss_pred HHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHHHHHHhccccccchhHH
Q psy15215 404 EMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 483 (1432)
Q Consensus 404 ~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~~~~ 483 (1432)
..+..|.+.|+.+|.+++++..+++|++||+|+.+|+..++|++. .+|.+|++..++|.+.+++|++.+....+ ..
T Consensus 11 ~~~~~~~~~l~~~~~~~~~d~~~AeDivQe~flk~~~~~~~~~~~--~~~~~wL~~Ia~n~~~d~~Rk~~~~~~~~-~~- 86 (189)
T PRK12530 11 LEIEEIRLQMLKFATLQLKDADLAEDVVQEALVSAYKNADSFKGQ--SALKTWIFAILKNKIIDLIRYRKRFVNES-EL- 86 (189)
T ss_pred HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHhchhccCC--ccHHHHHHHHHHHHHHHHHHhhccCCCcc-cc-
Confidence 557889999999999999998999999999999999999999864 37999999999999999999876521110 00
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHHHHH
Q psy15215 484 ETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALN 563 (1432)
Q Consensus 484 ~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~i~d~~~~~p~~~~~~ 563 (1432)
..+. .+.... +.......+........+|.+....
T Consensus 87 -----------------~~~~------------------------~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~ 121 (189)
T PRK12530 87 -----------------IEED------------------------SPNSFF----DEKGHWKPEYYEPSEWQEVENTVYK 121 (189)
T ss_pred -----------------cccc------------------------cchhhh----cccccccccccCCccccCHHHHHHH
Confidence 0000 000000 0000000000001112356777777
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHHHH
Q psy15215 564 ASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLAHD 630 (1432)
Q Consensus 564 ~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l~~ 630 (1432)
.+....+..+|++||+++|.||.|+|..|+ |++|||+.||+|+++|+.+.+||+++|++++..
T Consensus 122 ~~~~~~l~~~l~~Lp~~~R~v~~L~~~~g~----s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~ 184 (189)
T PRK12530 122 EEFWLIFEACLNHLPAQQARVFMMREYLEL----SSEQICQECDISTSNLHVLLYRARLQLQACLSK 184 (189)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHhHHHHcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 788889999999999999999999999999 999999999999999999999999999998864
No 215
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=99.64 E-value=2.7e-15 Score=160.84 Aligned_cols=158 Identities=9% Similarity=0.099 Sum_probs=125.4
Q ss_pred hhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHHHHHHhcccccc
Q psy15215 1189 RKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI 1268 (1432)
Q Consensus 1189 ~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~~i~~~~r~iri 1268 (1432)
..|+..++..|.+.++.++.+++++..+++|++||+|+.+|+. ..|..- .+|.+|++.+++|.+.+++|++.+...
T Consensus 9 ~~af~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQe~flkl~~~-~~~~~~--~~~~~wL~~iarn~~~d~~R~~~~~~~- 84 (172)
T PRK09651 9 SLTFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVS-ETLSTI--RDPRSFLCTIAKRVMVDLFRRNALEKA- 84 (172)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhh-cccccc--cCHHHHHHHHHHHHHHHHHHHHHHHhh-
Confidence 4599999999999999999999999999999999999999998 345433 268999999999999999997653100
Q ss_pred cccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChH
Q psy15215 1269 PVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPS 1348 (1432)
Q Consensus 1269 p~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~~d~i~d~~~~~p~ 1348 (1432)
. .+ .+. .+ .+....+|.
T Consensus 85 --~---------------------------------------------------~~-~~~-----~~----~~~~~~~~~ 101 (172)
T PRK09651 85 --Y---------------------------------------------------LE-MLA-----LM----PEGGAPSPE 101 (172)
T ss_pred --h---------------------------------------------------hh-HHh-----hc----cccCCCChH
Confidence 0 00 000 00 000112344
Q ss_pred HHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCc
Q psy15215 1349 DAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417 (1432)
Q Consensus 1349 ~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~ 1417 (1432)
......+....+..+|..|||++|.|+.|+|+.|. |++|||+.||+|.++|+..++||+++|+..
T Consensus 102 ~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~----s~~EIA~~lgis~~tV~~~l~Ra~~~~~~~ 166 (172)
T PRK09651 102 ERESQLETLQLLDSMLDGLNGKTREAFLLSQLDGL----TYSEIAHKLGVSVSSVKKYVAKATEHCLLF 166 (172)
T ss_pred HHHHHHHHHHHHHHHHHhCCHHHhHHhhhhhccCC----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 44445556678999999999999999999999988 999999999999999999999999999873
No 216
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=99.64 E-value=3.4e-15 Score=163.52 Aligned_cols=183 Identities=13% Similarity=0.146 Sum_probs=135.9
Q ss_pred HHHHHHHHHHHHHHHHhcccCCCC-hhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHHHHHHhccccccchh
Q psy15215 403 REMTEANLRLVISIAKKYTDRGLQ-FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 481 (1432)
Q Consensus 403 ~~li~~~~~lV~~ia~ky~~~~~~-~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~~ 481 (1432)
++.+..|.+.|+.+|.+++++..+ ++|++||+|+.+|++.++|+.. .+|.+|++.+++|.+.+++|++.+.......
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 367888999999999999998888 9999999999999999999863 4799999999999999999987652111000
Q ss_pred HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHHH
Q psy15215 482 MIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAA 561 (1432)
Q Consensus 482 ~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~i~d~~~~~p~~~~ 561 (1432)
. ..+.+ ... ..+.. ..+ .....+..+ ....+|+..+
T Consensus 86 ~----------------------~~~~~-----------~~~------~~~~~---~~~-~~~~~~~~~-~~~~~~e~~~ 121 (195)
T PRK12532 86 L----------------------DDELL-----------DEA------FESHF---SQN-GHWTPEGQP-QHWNTPEKSL 121 (195)
T ss_pred c----------------------ccccc-----------chh------hhhhh---ccc-cccccccCc-cccCCHHHHH
Confidence 0 00000 000 00000 000 000000000 1124688888
Q ss_pred HHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHHHHHHHHh
Q psy15215 562 LNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLAHDWLEQR 635 (1432)
Q Consensus 562 ~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l~~~~~~~ 635 (1432)
...+....+..+|.+||++++.||.|+|..|+ |++|||+.||+|.++|+++.+||+++|++.+...+..+
T Consensus 122 ~~~e~~~~l~~~l~~L~~~~r~i~~L~~~~g~----s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~~~~~ 191 (195)
T PRK12532 122 NNNEFQKILQSCLYNLPENTARVFTLKEILGF----SSDEIQQMCGISTSNYHTIMHRARESLRQCLQIKWFNQ 191 (195)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHhhhHHHhCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhccc
Confidence 87788889999999999999999999999998 99999999999999999999999999999997655443
No 217
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=99.64 E-value=2.6e-15 Score=159.12 Aligned_cols=157 Identities=10% Similarity=0.097 Sum_probs=125.6
Q ss_pred HhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHHHHHHhccccccc
Q psy15215 400 KAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 479 (1432)
Q Consensus 400 ~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip 479 (1432)
.|+..|+..|.+.|+++|.++++...+++|++||+|+.+|+..+.|++ .+|.+|++.+++|.+.+++|++.+...
T Consensus 4 ~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~flk~~~~~~~~~~---~~~~~wl~~i~~n~~~d~~R~~~~~~~-- 78 (161)
T PRK12528 4 ATVEGLYSAHHHWLTGWLRRRLGCPQSAADLAQDTFVKVLVARETAQI---IEPRAFLTTIAKRVLCNHYRRQDLERA-- 78 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHhccccccc---cCHHHHHHHHHHHHHHHHHHHHHHHHh--
Confidence 389999999999999999999999999999999999999999888764 369999999999999999987653100
Q ss_pred hhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHH
Q psy15215 480 VHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 559 (1432)
Q Consensus 480 ~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~i~d~~~~~p~~ 559 (1432)
. . + .+. + . ++....+++.
T Consensus 79 -~---------------~---------~------------------------~~~----~-----~----~~~~~~~~~~ 96 (161)
T PRK12528 79 -Y---------------L---------E------------------------ALA----Q-----L----PERVAPSEEE 96 (161)
T ss_pred -h---------------H---------H------------------------Hhh----c-----c----ccccCCCHHH
Confidence 0 0 0 000 0 0 0001123333
Q ss_pred HHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHH
Q psy15215 560 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPL 627 (1432)
Q Consensus 560 ~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~ 627 (1432)
.....+....+..+|.+||++++.||.|+|..|+ |++|||+.+|+|.++|+.+.++|+++|+..
T Consensus 97 ~~~~~~~~~~l~~~l~~L~~~~r~v~~L~~~~g~----s~~EIA~~l~is~~tV~~~l~ra~~~~~~~ 160 (161)
T PRK12528 97 RAIILETLVELDQLLDGLPPLVKRAFLLAQVDGL----GYGEIATELGISLATVKRYLNKAAMRCYFA 160 (161)
T ss_pred HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHhc
Confidence 4444455678999999999999999999999999 999999999999999999999999999854
No 218
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=99.64 E-value=3.4e-15 Score=159.00 Aligned_cols=156 Identities=13% Similarity=0.124 Sum_probs=130.6
Q ss_pred HHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHHHHHHhccccccchh
Q psy15215 402 KREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 481 (1432)
Q Consensus 402 ~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~~ 481 (1432)
++.|+..|.+.|+++|++++++..+++|++||+++.+|+++++|++ .+|.+|++..++|.+.+++|+..+....
T Consensus 3 ~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~---~~~~~wL~~i~~n~~~d~~R~~~~~~~~--- 76 (165)
T PRK09644 3 IEEIYKMYINDVYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDYDN---QKVKPWLFKVAYHTFIDFVRKEKKVSFV--- 76 (165)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhccc---cchHHHHHHHHHHHHHHHHHhhhhcccc---
Confidence 6789999999999999999999999999999999999999999985 2699999999999999999987642100
Q ss_pred HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHHH
Q psy15215 482 MIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAA 561 (1432)
Q Consensus 482 ~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~i~d~~~~~p~~~~ 561 (1432)
+.+++ +.+. ..+|++..
T Consensus 77 -----------------------~~~~~-------------------------------------~~~~---~~~~~~~~ 93 (165)
T PRK09644 77 -----------------------GTDEI-------------------------------------EAIQ---AESTEEYV 93 (165)
T ss_pred -----------------------chhHH-------------------------------------hhhc---ccChHHHH
Confidence 00000 0000 12455666
Q ss_pred HHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHHHH
Q psy15215 562 LNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLAHD 630 (1432)
Q Consensus 562 ~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l~~ 630 (1432)
...+....+..+|..||+++++|+.|+|..|+ |++|||+.||+|.++|+.+.+||+++|++.+..
T Consensus 94 ~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~----s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~~ 158 (165)
T PRK09644 94 VAKNSYEKLIQIIHTLPVIEAQAILLCDVHEL----TYEEAASVLDLKLNTYKSHLFRGRKRLKALLKE 158 (165)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHHHhHHHhcC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 66677788999999999999999999999998 999999999999999999999999999988753
No 219
>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=99.64 E-value=9e-16 Score=161.42 Aligned_cols=152 Identities=15% Similarity=0.158 Sum_probs=124.1
Q ss_pred HHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHH
Q psy15215 1196 TEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIET 1275 (1432)
Q Consensus 1196 i~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~~~~~~ 1275 (1432)
+..|.+.|+.+|.+++++..+++|++||+|+.+|+++++|++ .+|.||++..+++.+.++++++.+....+.
T Consensus 1 y~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~l~~~~~~~~~---~~f~~wl~~i~~~~~~d~~r~~~~~~~~~~----- 72 (154)
T TIGR02950 1 YREYMHDVFRYLYRLTKDKHLAEDLLQETFLKAYIHLHSFKD---SSIKPWLFRIARNAFIDWYRKDKKIQTIDD----- 72 (154)
T ss_pred CchHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHhcC---CchHHHHHHHHHHHHHHHHHHhhhhccccH-----
Confidence 357899999999999999899999999999999999999997 379999999999999999998764110000
Q ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHHHHHHH
Q psy15215 1276 INKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNAS 1355 (1432)
Q Consensus 1276 ~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~~d~i~d~~~~~p~~~~~~~~ 1355 (1432)
.. +.+... ....+|++.....+
T Consensus 73 -------------------------------------------------~~--------~~~~~~-~~~~~~~~~~~~~~ 94 (154)
T TIGR02950 73 -------------------------------------------------DA--------IGDLEQ-HPVESPEHHLLIKI 94 (154)
T ss_pred -------------------------------------------------hh--------hhhccc-cccCChhHHHHHHH
Confidence 00 000000 01124666666666
Q ss_pred HHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCc
Q psy15215 1356 MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417 (1432)
Q Consensus 1356 ~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~ 1417 (1432)
....+..+|+.||++++.|+.|+|+.|+ |++|||+.||+|..+|++.++||+++||+.
T Consensus 95 ~~~~l~~~l~~L~~~~r~i~~l~~~~g~----s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~~ 152 (154)
T TIGR02950 95 EQEEITHHLSRLPENYRTVLILREFKEF----SYKEIAELLNLSLAKVKSNLFRARKELKKL 152 (154)
T ss_pred HHHHHHHHHHhCCHhheeeeeehhhccC----cHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 7788999999999999999999998888 999999999999999999999999999974
No 220
>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=99.64 E-value=4.8e-15 Score=162.00 Aligned_cols=119 Identities=14% Similarity=0.196 Sum_probs=107.1
Q ss_pred HHHHHhHHHHHHhHHHHHHHHHHHHHHHHHhcccCC--CChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHH
Q psy15215 389 RKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRG--LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 466 (1432)
Q Consensus 389 ~~i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~--~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~ 466 (1432)
..++.||.. +++|+..|.|+|.++|.+|.++. .+.+|++|+|+||||+|+++||+.+|.+|+|||.+||++.+.
T Consensus 2 ~~~~~gd~~----~e~LI~~Y~plI~~~a~~~~~~~~~~e~dDlvQ~glial~eAi~~yd~~kg~~F~sya~~~Ir~~i~ 77 (218)
T TIGR02895 2 QPIQPGNEE----REELIRQYKPFIAKIVSSVCGRYIDTKSDDELSIGLIAFNEAIESYDSNKGKSFLSFAKLIIKRRLI 77 (218)
T ss_pred chhhcCChH----HHHHHHHhHHHHHHHHHHHHccCCCCChhHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHH
Confidence 356778764 99999999999999999998775 589999999999999999999999999999999999999999
Q ss_pred HHHHHhc---cccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHH
Q psy15215 467 RSIADQA---RTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAI 511 (1432)
Q Consensus 467 ~~i~~~~---r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~ 511 (1432)
+++|+.. +.+++|....+....+..+..++.++.++.|+.+||+.
T Consensus 78 dylRk~~k~~~~v~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~eEI~~ 125 (218)
T TIGR02895 78 DYIRKNQKYQNLLYLDEDYDENPLEFNKSMEEYRNEIENENRRLEILE 125 (218)
T ss_pred HHHHhcccccCeeeCCchHHHHHHHHHHHHHHHHHHHccccHHHHHHH
Confidence 9999988 67789987777777788888899999999999999985
No 221
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=99.64 E-value=4.3e-15 Score=161.19 Aligned_cols=156 Identities=12% Similarity=0.096 Sum_probs=126.0
Q ss_pred hHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHHHHHHhccccccch
Q psy15215 401 AKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 480 (1432)
Q Consensus 401 A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~ 480 (1432)
|+..++..|.+.|+.+|.+++++..+++|++||+|+.+|+..++|+.. .+|.+|++.+++|.+.++++++.+....
T Consensus 11 ~f~~l~~~~~~~L~~~a~~~~~~~~~AEDivQevfl~~~~~~~~~~~~--~~~~awL~~Ia~n~~~d~~R~~~~~~~~-- 86 (187)
T PRK12516 11 PFKRELLAALPSLRAFAVSLIGRHDRADDLVQDTIMKAWAKQDHFEVG--TNMKAWLFTILRNEFYSQMRKRGREVQD-- 86 (187)
T ss_pred HHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHhhhccCCc--ccHHHHHHHHHHHHHHHHHHhhcCCccc--
Confidence 999999999999999999999999999999999999999999999854 3699999999999999999987642000
Q ss_pred hHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHH
Q psy15215 481 HMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 560 (1432)
Q Consensus 481 ~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~i~d~~~~~p~~~ 560 (1432)
.+... .+.... .+++.
T Consensus 87 ----------------------------------------------------~~~~~--------~~~~~~--~~~~~-- 102 (187)
T PRK12516 87 ----------------------------------------------------TDGMF--------TEQLAV--HPSQY-- 102 (187)
T ss_pred ----------------------------------------------------ccccc--------ccccCC--Ccchh--
Confidence 00000 000000 00111
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHHHH
Q psy15215 561 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLAHD 630 (1432)
Q Consensus 561 ~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l~~ 630 (1432)
.......+..+|..||+++|.||.|+|..|+ |++|||+.||+|.++|+.+.++|+++|++.+..
T Consensus 103 --~~~~~~~l~~~L~~Lp~~~r~i~~L~~~~g~----s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~~ 166 (187)
T PRK12516 103 --GTLDLQDFRAALDQLPDDQREAIILVGASGF----AYEEAAEICGCAVGTIKSRVNRARQRLQEILQI 166 (187)
T ss_pred --hHHHHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 1122356899999999999999999999999 999999999999999999999999999998864
No 222
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=99.64 E-value=2.2e-15 Score=162.62 Aligned_cols=156 Identities=13% Similarity=0.118 Sum_probs=123.1
Q ss_pred hHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHHHHHHhcccccccc
Q psy15215 1191 AKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 1270 (1432)
Q Consensus 1191 A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~ 1270 (1432)
.....+..+++.|+.+|.+++++..+++|++||+|+.+|+...+|++. .+|.||++.+++|.+.+++|++.+....+.
T Consensus 5 ~~~~~~~~~~~~l~~~~~~~~~~~~dAEDivQe~flkl~~~~~~~~~~--~~~~~WL~~Iarn~~id~~Rk~~~~~~~~~ 82 (182)
T PRK12511 5 SKRFDVLDQLVPLRRYARSLTRDSAEAEDLVHDALVRALERRASFRSG--GNLRTWLMSILHNAFIDELRRRRVEARRAD 82 (182)
T ss_pred chhhhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCc--cchHHHHHHHHHHHHHHHHHhhcccccccc
Confidence 455678899999999999999999999999999999999999999864 379999999999999999998765210000
Q ss_pred cHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHH
Q psy15215 1271 HMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 1350 (1432)
Q Consensus 1271 ~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~~d~i~d~~~~~p~~~ 1350 (1432)
.+. +. .+.....+..
T Consensus 83 ---------------------------------------------------~~~----~~---------~~~~~~~~~~- 97 (182)
T PRK12511 83 ---------------------------------------------------ELA----VL---------ADASLPAAQE- 97 (182)
T ss_pred ---------------------------------------------------chh----hc---------cccCCCcchH-
Confidence 000 00 0000001111
Q ss_pred HHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchh
Q psy15215 1351 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 1419 (1432)
Q Consensus 1351 ~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~ 1419 (1432)
.......+..+|..||+++|.||.|+|..|+ |++|||+.||+|.++|+++++||+++||....
T Consensus 98 --~~~~~~~l~~~l~~Lp~~~R~v~~L~~~eg~----s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~~ 160 (182)
T PRK12511 98 --HAVRLAQIRDAFFDLPEEQRAALHLVAIEGL----SYQEAAAVLGIPIGTLMSRIGRARAALRAFEE 160 (182)
T ss_pred --HHHHHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHH
Confidence 1223467889999999999999999999998 99999999999999999999999999998554
No 223
>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=99.64 E-value=5.1e-15 Score=160.93 Aligned_cols=176 Identities=15% Similarity=0.168 Sum_probs=134.0
Q ss_pred HHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHHHHHHhccccccchhHH
Q psy15215 404 EMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 483 (1432)
Q Consensus 404 ~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~~~~ 483 (1432)
+.+..|.+.|+.+|.+++++..+++|++||+|+.+|+...+|+.. .+|.+|++.+++|.+.++++++.+....+.-
T Consensus 6 ~~~~~~~~~l~~~~~~~~~~~~dAeDivQevfl~l~~~~~~~~~~--~~~~~wL~~iarn~~~d~~R~~~r~~~~~~~-- 81 (188)
T TIGR02943 6 QELEQLRRDLLRFARLQLRDRDLAEDAVQETLLAALSHRDSFAGR--SALKTWLFAILKNKIIDALRAKGREVKVSDL-- 81 (188)
T ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhccc--cHHHHHHHHHHHHHHHHHHHhhcccCCcccc--
Confidence 678899999999999999999999999999999999999999864 4899999999999999999987652111100
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHHHHH
Q psy15215 484 ETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALN 563 (1432)
Q Consensus 484 ~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~i~d~~~~~p~~~~~~ 563 (1432)
..++.. -.+.......+. +.........++|+..+..
T Consensus 82 -----------------~~~~~~------------------------~~~~~~~~~~~~--~~~~~~~~~~~~~e~~~~~ 118 (188)
T TIGR02943 82 -----------------DDELDD------------------------EAFNALFTQNGH--WAQHGQPQHWNTPEKQLEN 118 (188)
T ss_pred -----------------cccccc------------------------chhhhhhccccc--hhccccccccCCHHHHHHH
Confidence 000000 000000000000 0000111122467777888
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHHHH
Q psy15215 564 ASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLAHD 630 (1432)
Q Consensus 564 ~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l~~ 630 (1432)
.+....+..+|.+||+++++||.|+|..|+ |++|||+.||+|.++|+++.+||+++|++.+..
T Consensus 119 ~e~~~~l~~~l~~L~~~~r~v~~l~~~~g~----s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l~~ 181 (188)
T TIGR02943 119 KEFWEVFEACLYHLPEQTARVFMMREVLGF----ESDEICQELEISTSNCHVLLYRARLSLRACLSI 181 (188)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHHHhCC----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 888889999999999999999999999999 999999999999999999999999999998864
No 224
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=99.64 E-value=2.9e-15 Score=162.76 Aligned_cols=157 Identities=15% Similarity=0.161 Sum_probs=125.4
Q ss_pred hhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q psy15215 1190 KAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 1269 (1432)
Q Consensus 1190 ~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip 1269 (1432)
.+++.++..|.+.|+.+|.+++++..+++|++||+|+.+|+..++|.+. ..|.+|++.+++|.+.+..++..+. .
T Consensus 23 ~~f~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQdvflkl~~~~~~~~~~--~~~~~wL~~Iarn~~~~~~r~~~~~--~- 97 (188)
T PRK12517 23 RRYEALVKALHADIYRYAYWLCKDKHIAEDLVQETFLRAWRSLDSLKDE--KAAKAWLITILRRENARRFERKQFD--L- 97 (188)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhhcCc--cchHHHHHHHHHHHHHHHHHHhccC--c-
Confidence 3899999999999999999999999999999999999999999999864 3799999999999887766543320 0
Q ss_pred ccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHH
Q psy15215 1270 VHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349 (1432)
Q Consensus 1270 ~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~~d~i~d~~~~~p~~ 1349 (1432)
.+.+ +. ...+....+|+.
T Consensus 98 ---------------------------------------------------~~~~----~~-------~~~~~~~~~~e~ 115 (188)
T PRK12517 98 ---------------------------------------------------VDIE----DD-------SIEDDASHSSEE 115 (188)
T ss_pred ---------------------------------------------------cCcc----cc-------cccCccccChhH
Confidence 0000 00 001111123333
Q ss_pred HHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchhhh
Q psy15215 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYY 1421 (1432)
Q Consensus 1350 ~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~~~ 1421 (1432)
.. ....|..+|..||+++|.|+.|+|+.|+ |++|||+.+|+|.++|+.+++||+++||......
T Consensus 116 ~~----~~~~l~~~l~~Lp~~~r~v~~l~~~~g~----s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~ 179 (188)
T PRK12517 116 EM----EQEWLRRQIAKLDPEYREPLLLQVIGGF----SGEEIAEILDLNKNTVMTRLFRARNQLKEALEKP 179 (188)
T ss_pred HH----HHHHHHHHHHhCCHHHHHHHHHHHHhCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 22 2357899999999999999999999998 9999999999999999999999999999977643
No 225
>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=99.63 E-value=3e-15 Score=158.87 Aligned_cols=158 Identities=16% Similarity=0.207 Sum_probs=128.7
Q ss_pred HhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHHHHHHh
Q psy15215 393 AGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQ 472 (1432)
Q Consensus 393 ~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~~i~~~ 472 (1432)
+|+.. |+..++..|.+.|+++|.+++++..+++|++||+|+.+|+..++|+. ..+|.+|++..++|.+.++++++
T Consensus 2 ~~~~~---~~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~~~~~~~~~~~--~~~~~~wl~~i~~n~~~d~~rk~ 76 (162)
T TIGR02983 2 SATEE---EFTAFVAARYPRLLRTAYLLTGDPHEAEDLVQEALVRTYVRWDRIRD--PDAPDAYVRRVLVNLARSRWRRR 76 (162)
T ss_pred CCcHH---HHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhcCC--cccHHHHHHHHHHHHHHHHHHhh
Confidence 47777 99999999999999999999999999999999999999999999964 34899999999999999999876
Q ss_pred ccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccC
Q psy15215 473 ARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDE 552 (1432)
Q Consensus 473 ~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~i~d~ 552 (1432)
.+. ..+ .....+. .
T Consensus 77 ~~~-~~~------------------------------------------------------~~~~~~~---~-------- 90 (162)
T TIGR02983 77 RLL-ELP------------------------------------------------------TRELPDA---A-------- 90 (162)
T ss_pred ccc-ccc------------------------------------------------------ccccCcc---c--------
Confidence 531 000 0000000 0
Q ss_pred CCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHHH
Q psy15215 553 NMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLAH 629 (1432)
Q Consensus 553 ~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l~ 629 (1432)
+.+..........|..+|..||++++.|+.|+|..|+ |.+|||+.||+|.++|+++.++|+.+|++.+.
T Consensus 91 ----~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~----s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 159 (162)
T TIGR02983 91 ----APDPAPDVALRAALARALRRLPARQRAVVVLRYYEDL----SEAQVAEALGISVGTVKSRLSRALARLRELLE 159 (162)
T ss_pred ----CCccchhHHHHHHHHHHHHhCCHHHHHHhhhHHHhcC----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhc
Confidence 0001112344567889999999999999999999888 99999999999999999999999999998763
No 226
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=99.63 E-value=4.8e-15 Score=160.79 Aligned_cols=155 Identities=15% Similarity=0.139 Sum_probs=120.9
Q ss_pred hHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHHHHHHhcccccccc
Q psy15215 1191 AKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 1270 (1432)
Q Consensus 1191 A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~ 1270 (1432)
+++.|.. |.+.|+++|.+++++..+++|++||+|+.+|++.++|+.. ..|.+|++.+++|.+.+++|++.+.. .
T Consensus 9 ~~~~l~~-~~~~l~~~a~~~l~~~~~AEDivQevfl~l~~~~~~~~~~--~~~~awL~~ia~n~~~d~~Rk~~r~~---~ 82 (188)
T PRK12546 9 PRDELVE-HLPALRAFAISLTRNVAVADDLVQDTIVKAWTNFDKFQEG--TNLRAWLFTILRNTFYSDRRKHKREV---P 82 (188)
T ss_pred HHHHHHH-HHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHhccCCC--cchHHHHHHHHHHHHHHHHHHhcccc---c
Confidence 4555555 7899999999999999999999999999999999999864 37999999999999999999876410 0
Q ss_pred cHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHH
Q psy15215 1271 HMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 1350 (1432)
Q Consensus 1271 ~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~~d~i~d~~~~~p~~~ 1350 (1432)
. .+. ...+...+ .|..
T Consensus 83 ~---------------------------------------------------~~~--------~~~~~~~~----~~~~- 98 (188)
T PRK12546 83 D---------------------------------------------------PEG--------VHAASLAV----KPAH- 98 (188)
T ss_pred C---------------------------------------------------ccc--------cccccccc----CCcc-
Confidence 0 000 00000000 0100
Q ss_pred HHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchhh
Q psy15215 1351 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRY 1420 (1432)
Q Consensus 1351 ~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~~ 1420 (1432)
........+..+|+.|||+++.||.|+|..|+ |.+|||+.||+|..+|+++++||+++||+....
T Consensus 99 -~~~~~~~~l~~~L~~Lp~~~r~v~~L~~~~g~----s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l~~ 163 (188)
T PRK12546 99 -DGRLAMSDFRAAFAQLPDEQREALILVGASGF----SYEEAAEMCGVAVGTVKSRANRARARLAELLQL 163 (188)
T ss_pred -hhHHHHHHHHHHHHhCCHHHhHHhhhHHhcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 01122346889999999999999999999888 999999999999999999999999999986543
No 227
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=99.62 E-value=7.3e-15 Score=161.70 Aligned_cols=178 Identities=18% Similarity=0.199 Sum_probs=134.0
Q ss_pred HHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHHHHHHhccccccchhH
Q psy15215 403 REMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 482 (1432)
Q Consensus 403 ~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~~~ 482 (1432)
..++..|.+.|+++|.++++...+++|++||+|+.+|+.+.+|+.. .+|++|++.+++|.+.+++|++.+....+..
T Consensus 21 ~~~~~~~~~~l~~~~~~~~~d~~~AEDivQEvfikl~~~~~~~~~~--~~~~~WL~~IarN~~~d~~Rk~~~~~~~~~~- 97 (206)
T PRK12544 21 PVFLEDLRKQMIKFATLQLSDLHLAEDAVQEALIGALKNADSFAGR--AAFKTWVFAILKNKIIDLLRQKKRHVSASSL- 97 (206)
T ss_pred HHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHHHHHHHHhhccccccccc-
Confidence 3688999999999999999999999999999999999999999854 4799999999999999999987652111100
Q ss_pred HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHHHH
Q psy15215 483 IETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAAL 562 (1432)
Q Consensus 483 ~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~i~d~~~~~p~~~~~ 562 (1432)
.+...+...+ ..+ .+..........+ ....+|+..+.
T Consensus 98 -----------------~~~~~~~~~~-----------~~~--------------~~~~~~~~~~~~~-~~~~~~e~~~~ 134 (206)
T PRK12544 98 -----------------LRDEEEEEDF-----------EEL--------------FDESGHWQKDERP-QAWGNPEESLE 134 (206)
T ss_pred -----------------ccccchhhHH-----------HHh--------------hcccccccccccc-cccCCHHHHHH
Confidence 0000000000 000 0000000000001 11236777777
Q ss_pred HHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHHHH
Q psy15215 563 NASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLAHD 630 (1432)
Q Consensus 563 ~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l~~ 630 (1432)
..+....+..+|.+|||++|.||.|+|+.|+ |++|||+.||+|.++|+++.+||+++|++.+..
T Consensus 135 ~~e~~~~l~~~L~~L~~~~r~v~~L~~~~g~----s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l~~ 198 (206)
T PRK12544 135 QEQFWRIFEACLDGLPAKYARVFMMREFIEL----ETNEICHAVDLSVSNLNVLLYRARLRLRECLEN 198 (206)
T ss_pred HHHHHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 7777788999999999999999999999999 999999999999999999999999999998864
No 228
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=99.62 E-value=1e-14 Score=155.06 Aligned_cols=156 Identities=13% Similarity=0.137 Sum_probs=125.1
Q ss_pred HhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHHHHHHhccccccc
Q psy15215 400 KAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 479 (1432)
Q Consensus 400 ~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip 479 (1432)
+.+..++..|.+.|+.+|++++++..+++|++||+++.+|+...+|+.. .+|.+|++..++|.+.+++|++.+....
T Consensus 6 ~~f~~~~~~~~~~l~~~a~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~R~~~~~~~~- 82 (164)
T PRK12547 6 KNFKQELLLALPALRAFAVSLSSKHDKAEDLVQDTLMKAWAKQDSFEMG--TNLKAWLFTILRNEFYSQMRKRGREVQD- 82 (164)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHhhhhcCCc--ccHHHHHHHHHHHHHHHHHHhhcccccc-
Confidence 3799999999999999999999999999999999999999999999753 3799999999999999999987541000
Q ss_pred hhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHH
Q psy15215 480 VHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 559 (1432)
Q Consensus 480 ~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~i~d~~~~~p~~ 559 (1432)
.......+ . + ..+..
T Consensus 83 -------------------------------------------------~~~~~~~~------~-------~---~~~~~ 97 (164)
T PRK12547 83 -------------------------------------------------SDGVFTAR------V-------A---VHPAQ 97 (164)
T ss_pred -------------------------------------------------cccccccc------C-------C---CCchh
Confidence 00000000 0 0 01111
Q ss_pred HHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHHH
Q psy15215 560 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLAH 629 (1432)
Q Consensus 560 ~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l~ 629 (1432)
. .......+..+|+.||++++.|+.|+|..|+ |++|||+.||+|+++|+++.+||+++|+..+.
T Consensus 98 ~--~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~----s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 161 (164)
T PRK12547 98 Y--GSLDLQDFKKALNLLSADQREAIILIGASGF----SYEDAAAICGCAVGTIKSRVSRARNRLQELLK 161 (164)
T ss_pred h--hHHHHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHh
Confidence 1 1122457889999999999999999999998 99999999999999999999999999998763
No 229
>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=99.62 E-value=5.6e-15 Score=158.00 Aligned_cols=148 Identities=11% Similarity=0.181 Sum_probs=121.7
Q ss_pred HHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHH
Q psy15215 1197 EANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 1276 (1432)
Q Consensus 1197 ~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~~~~~~~ 1276 (1432)
..|.+.|+.++.+++++..+++|++||+|+.+|+++++|+.. .+|.+|++.+++|.+.+++++..+...++
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 468899999999999999999999999999999999999963 48999999999999999999876421100
Q ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHHHHHHHH
Q psy15215 1277 NKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 1356 (1432)
Q Consensus 1277 ~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~~d~i~d~~~~~p~~~~~~~~~ 1356 (1432)
+.. ... .+|.+.....+.
T Consensus 73 ----------------------------------------------------~~~-------~~~---~~~~~~~~~~e~ 90 (170)
T TIGR02959 73 ----------------------------------------------------ESL-------LAA---DSAREETFVKEL 90 (170)
T ss_pred ----------------------------------------------------hhh-------ccc---CCccHHHHHHHH
Confidence 000 000 012223334455
Q ss_pred HHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchh
Q psy15215 1357 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 1419 (1432)
Q Consensus 1357 ~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~ 1419 (1432)
...+..+|..||+++|.||.|+|..|+ |++|||+.||+|..+|+++++||+++||....
T Consensus 91 ~~~l~~~l~~L~~~~r~v~~l~~~~g~----s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 149 (170)
T TIGR02959 91 SQCIPPMIKELPDEYREAIRLTELEGL----SQQEIAEKLGLSLSGAKSRVQRGRKKLKELLE 149 (170)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 678999999999999999999999888 99999999999999999999999999999654
No 230
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=99.62 E-value=8.1e-15 Score=155.41 Aligned_cols=154 Identities=12% Similarity=0.132 Sum_probs=123.1
Q ss_pred hHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHHHHHHhccccccch
Q psy15215 401 AKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 480 (1432)
Q Consensus 401 A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~ 480 (1432)
|+..++..|.+.|+.+|.+++++..+++|++||+++.+|+..++|++. +|.||++..++|.+.++++++.+....
T Consensus 6 a~~~l~~~~~~~l~~~~~~~~~~~~~AeDv~Qe~f~~~~~~~~~~~~~---~~~~wl~~i~~n~~~d~~R~~~~~~~~-- 80 (161)
T PRK12541 6 SLEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYKGE---EIRPWLFTIAYNAFIDWYRKEKKYKTT-- 80 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhHHHccCC---ChHHHHHHHHHHHHHHHHHhccccccc--
Confidence 999999999999999999999999999999999999999999999852 699999999999999999987652000
Q ss_pred hHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHH
Q psy15215 481 HMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 560 (1432)
Q Consensus 481 ~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~i~d~~~~~p~~~ 560 (1432)
..+ + ... ......+...
T Consensus 81 ---------------------------------------------------~~~-----~--~~~-----~~~~~~~~~~ 97 (161)
T PRK12541 81 ---------------------------------------------------TIE-----E--FHL-----PNVPSTEHEY 97 (161)
T ss_pred ---------------------------------------------------chh-----h--hhc-----cCCCCcHHHH
Confidence 000 0 000 0000112222
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHH
Q psy15215 561 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPL 627 (1432)
Q Consensus 561 ~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~ 627 (1432)
....+. ..+..+|..||++++.||.|+|..|. |++|||+.||+|+++|+++.+||+.+|++.
T Consensus 98 ~~~~~~-~~~~~~l~~L~~~~r~v~~l~~~~~~----s~~eIA~~lgis~~tv~~~l~Rar~~L~~~ 159 (161)
T PRK12541 98 FIKHEI-ASWLDSLSSLPLERRNVLLLRDYYGF----SYKEIAEMTGLSLAKVKIELHRGRKETKSI 159 (161)
T ss_pred HHHhHH-HHHHHHHHHCCHHHHHHhhhHHhcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 333333 34557899999999999999999998 999999999999999999999999999864
No 231
>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=99.62 E-value=8.1e-15 Score=173.79 Aligned_cols=184 Identities=18% Similarity=0.162 Sum_probs=137.3
Q ss_pred hHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHHHHHHhc
Q psy15215 394 GEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA 473 (1432)
Q Consensus 394 gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~~i~~~~ 473 (1432)
||.. |+..|+..|.+.|+++|.+++++..+++|++||.|+.+|+.+++|+.. .+|.+|++.+++|.|.+++|++.
T Consensus 2 gd~~---af~~l~~~~~~~l~~~a~~~~~~~~~AEDivQe~fl~~~~~~~~~~~~--~~~~~WL~~Ia~n~~~d~~Rk~~ 76 (324)
T TIGR02960 2 VDGA---AFTALAEPHRRELLAHCYRMLGSLHEAEDLVQETLLRAWRARDRFEGR--SSVRTWLYRIATNACLDALEARQ 76 (324)
T ss_pred CcHH---HHHHHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHHHhhhhccCcc--cchHHHHHHHHHHHHHHHHHhcc
Confidence 6666 999999999999999999999999999999999999999999999863 47999999999999999999876
Q ss_pred cccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccc---
Q psy15215 474 RTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIE--- 550 (1432)
Q Consensus 474 r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~i~--- 550 (1432)
+.... .. ... + ........ +++....+.+.+.
T Consensus 77 ~~~~~-~~-----------------~~~--~------------------------~~~~~~~~-~~~~~~~~~~~~~~~~ 111 (324)
T TIGR02960 77 RRPRP-VG-----------------LGA--P------------------------SADGTAAA-SEAAEVTWLEPLPDLT 111 (324)
T ss_pred CCcCc-cc-----------------cCC--C------------------------CCcccccc-cccccccccCCCCccc
Confidence 42100 00 000 0 00000000 0000000000000
Q ss_pred ----cCCCCChHHHHHHHH-HHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHH
Q psy15215 551 ----DENMLAPSDAALNAS-MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625 (1432)
Q Consensus 551 ----d~~~~~p~~~~~~~~-~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr 625 (1432)
.....+|++.....+ +...+..+|.+|||++|.||.|+|..|+ |++|||+.||+|+++|+++.+||+++|+
T Consensus 112 ~~~~~~~~~~~~~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L~~~~g~----s~~EIA~~lgis~~tV~~~l~Rar~~Lr 187 (324)
T TIGR02960 112 LDLDDPAAADPSVAAGSRESVRLAFVAAIQYLPPRQRAVLLLRDVLGW----RAAETAELLGTSTASVNSALQRARATLD 187 (324)
T ss_pred cccccCCCCCHHHHHHHHHHHHHHHHHHHHhCCHHHhhHhhhHHHhCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 111246777666554 4567899999999999999999999999 9999999999999999999999999999
Q ss_pred HHHHHH
Q psy15215 626 PLAHDW 631 (1432)
Q Consensus 626 ~~l~~~ 631 (1432)
+.+...
T Consensus 188 ~~l~~~ 193 (324)
T TIGR02960 188 EVGPSA 193 (324)
T ss_pred Hhcccc
Confidence 988643
No 232
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=99.62 E-value=1e-14 Score=160.34 Aligned_cols=178 Identities=11% Similarity=0.144 Sum_probs=131.2
Q ss_pred HHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHHHHHHhccccccchhHH
Q psy15215 404 EMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 483 (1432)
Q Consensus 404 ~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~~~~ 483 (1432)
.++..|.+.|+.+|.+++++..+++|++||+|+.+|+..++|++. .+|.+|++.+++|.+.++++++.+...++..
T Consensus 12 ~~~~~~~~~l~~~~~~~~~d~~~AEDivQe~fl~~~~~~~~~~~~--~~~~~WL~~IarN~~~d~~Rk~~r~~~~~~~-- 87 (201)
T PRK12545 12 AYLAQLRHDLLRFARLQLRDADAAEDAVQEALAAAWSQAGRFAGQ--SAHKTWVFGILRNKLIDTLRARQRTVNLSAL-- 87 (201)
T ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhcccc--chHHHHHHHHHHHHHHHHHHhhccccccccc--
Confidence 568999999999999999999999999999999999999999864 3699999999999999999987652111100
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHHHHH
Q psy15215 484 ETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALN 563 (1432)
Q Consensus 484 ~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~i~d~~~~~p~~~~~~ 563 (1432)
..++. ....++............+..++ ...+|.+....
T Consensus 88 ----------------------~~~~~------------------~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~ 126 (201)
T PRK12545 88 ----------------------DAELD------------------GEALLDRELFKDNGHWAAHAKPR-PWPKPETILQQ 126 (201)
T ss_pred ----------------------ccccc------------------hhhhhhhhhhcccccccccccCc-CCCCHHHHHHH
Confidence 00000 00000000000000000000001 12356666666
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHHHH
Q psy15215 564 ASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLAHD 630 (1432)
Q Consensus 564 ~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l~~ 630 (1432)
.+....+..+|.+|||++|.||.|+|+.|+ |++|||+.+|+|+++|+.+.+||+++||+.+..
T Consensus 127 ~~~~~~l~~~L~~Lp~~~r~v~~L~~~eg~----s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~ 189 (201)
T PRK12545 127 QQFWTLFETCLDHLPEQIGRVFMMREFLDF----EIDDICTELTLTANHCSVLLYRARTRLRTCLSE 189 (201)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 666778999999999999999999999999 999999999999999999999999999998853
No 233
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=99.62 E-value=6.5e-15 Score=157.24 Aligned_cols=158 Identities=15% Similarity=0.122 Sum_probs=127.4
Q ss_pred hhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q psy15215 1190 KAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 1269 (1432)
Q Consensus 1190 ~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip 1269 (1432)
.++..++..|.+.++++|.+++++..+++|++||+|+.+|+....+.. .+|.+|++++++|.+.+++++.... +
T Consensus 9 ~~~~~~~~~~~~~l~~~~~~~~~~~~~aeDlvQevf~~l~~~~~~~~~---~~~~~wl~~Iarn~~~d~~Rr~~~~-~-- 82 (168)
T PRK12525 9 TLIGQMFQQDYDWLCKKLSRQLGCPHSAEDIASETFLQVLALPDPASI---REPRALLTTIARRLMYEGWRRQDLE-R-- 82 (168)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCcCcHHHHHHHHHHHHHhCCCcccc---cCHHHHHHHHHHHHHHHHHHHHHHH-H--
Confidence 379999999999999999999999999999999999999986555542 3799999999999999999875420 0
Q ss_pred ccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHH
Q psy15215 1270 VHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349 (1432)
Q Consensus 1270 ~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~~d~i~d~~~~~p~~ 1349 (1432)
.... +.. + .......+|++
T Consensus 83 ---------------~~~~---------------------------------~~~----~---------~~~~~~~~~~~ 101 (168)
T PRK12525 83 ---------------AYLQ---------------------------------SLA----E---------APEAVQPSPEE 101 (168)
T ss_pred ---------------HHHH---------------------------------HHh----c---------ccccccCChHH
Confidence 0000 000 0 00011135666
Q ss_pred HHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCch
Q psy15215 1350 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418 (1432)
Q Consensus 1350 ~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~ 1418 (1432)
..........+..+|+.|||++|.||.|+|..|+ |++|||+.||+|.++|+..+.+|+++||...
T Consensus 102 ~~~~~~~~~~l~~~l~~L~~~~r~v~~L~~~eg~----s~~EIA~~l~is~~tV~~~l~ra~~~~~~~~ 166 (168)
T PRK12525 102 QWMVIETLLAIDRLLDGLSGKARAAFLMSQLEGL----TYVEIGERLGVSLSRIHQYMVEAFKCCYQGF 166 (168)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHhh
Confidence 6666677789999999999999999999999998 9999999999999999999999999999743
No 234
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=99.60 E-value=2e-14 Score=155.24 Aligned_cols=159 Identities=11% Similarity=0.133 Sum_probs=130.3
Q ss_pred HHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHHHHHHhccccccchh
Q psy15215 402 KREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 481 (1432)
Q Consensus 402 ~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~~ 481 (1432)
++.+++.|.+.|+++|.++++...+++|++||+++.+|+.+.+|++ +.+|.+|++..++|.+.+++|++.+....+
T Consensus 3 ~~~l~~~y~~~l~~~~~~~~~~~~~aeDi~QEvflkl~~~~~~~~~--~~~~~~wL~~i~~n~~~d~~Rk~~~~~~~~-- 78 (181)
T PRK09637 3 LESIWSEYKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLKD--GSSIKSWLYQIANNTIIDFYRKKNRSEELP-- 78 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHhHHHhcc--ccchHHHHHHHHHHHHHHHHHhccccCCcc--
Confidence 6789999999999999999999999999999999999999999985 348999999999999999999776521100
Q ss_pred HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHHH
Q psy15215 482 MIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAA 561 (1432)
Q Consensus 482 ~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~i~d~~~~~p~~~~ 561 (1432)
.++ . .+ .++.+..
T Consensus 79 --------------------------------------------------------~~~-~------~~----~~~~~~~ 91 (181)
T PRK09637 79 --------------------------------------------------------DDL-L------FE----DEEREEN 91 (181)
T ss_pred --------------------------------------------------------hhh-h------cc----CCChhHH
Confidence 000 0 00 0112233
Q ss_pred HHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHHHHHHHHh
Q psy15215 562 LNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLAHDWLEQR 635 (1432)
Q Consensus 562 ~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l~~~~~~~ 635 (1432)
...+....+..+|..||++++.||.|+|..|+ +.+|||+.||+|.++|+.+.++|+++|++.+.....-+
T Consensus 92 ~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~----~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~~~~ 161 (181)
T PRK09637 92 AKKELAPCLRPFIDALPEKYAEALRLTELEGL----SQKEIAEKLGLSLSGAKSRVQRGRVKLKELLEGCCDFE 161 (181)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCC----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHccCce
Confidence 44456778999999999999999999999999 99999999999999999999999999999887654333
No 235
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=99.60 E-value=1.4e-14 Score=153.16 Aligned_cols=154 Identities=9% Similarity=0.106 Sum_probs=125.9
Q ss_pred HHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHHHHHHhccccccchhHHHHH
Q psy15215 407 EANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 486 (1432)
Q Consensus 407 ~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~~~~~~~ 486 (1432)
..|.+.++.+|.++++...+++|++||+++.+|+..+.|++ .+|.||++..++|.+.++++++.+....
T Consensus 2 ~~~~~~l~~~~~~~~~~~~~aeDi~Qevf~~l~~~~~~~~~---~~~~~wL~~ia~n~~~d~~R~~~~~~~~-------- 70 (159)
T PRK12527 2 ENYYRELVRFLSARLGNRQAAEDVAHDAYLRVLERSSSAQI---EHPRAFLYRTALNLVVDRHRRHRVRQAE-------- 70 (159)
T ss_pred hhHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHhccccccc---cchHHHHHHHHHHHHHHHHHHHhccccc--------
Confidence 57889999999999999899999999999999999999864 3799999999999999999976431000
Q ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHHHHHHHH
Q psy15215 487 NKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 566 (1432)
Q Consensus 487 ~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~i~d~~~~~p~~~~~~~~~ 566 (1432)
+++. . ++.. ....++|.+.+...+.
T Consensus 71 ---------------------------------------------~~~~-~-~~~~--------~~~~~~~~~~~~~~~~ 95 (159)
T PRK12527 71 ---------------------------------------------PLEV-L-DEEE--------RLHSPSPQTRLDLGQR 95 (159)
T ss_pred ---------------------------------------------chhh-h-hccc--------cccCCCHHHHHHHHHH
Confidence 0000 0 0000 0012357777777777
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHHHH
Q psy15215 567 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLAHD 630 (1432)
Q Consensus 567 ~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l~~ 630 (1432)
...+..+|.+|||+++.||.|+|+.|+ |++|||+.||+|.++|+.+..+|+++|+..+..
T Consensus 96 ~~~l~~~l~~L~~~~r~v~~l~~~~~~----s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l~~ 155 (159)
T PRK12527 96 LALLQRALAELPPACRDSFLLRKLEGL----SHQQIAEHLGISRSLVEKHIVNAMKHCRVRMRQ 155 (159)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 788999999999999999999999999 999999999999999999999999999998764
No 236
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=99.59 E-value=2.2e-14 Score=154.96 Aligned_cols=159 Identities=14% Similarity=0.134 Sum_probs=126.6
Q ss_pred HhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHHHHHHhccccccc
Q psy15215 400 KAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 479 (1432)
Q Consensus 400 ~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip 479 (1432)
+++..++..|.+.|+++|.+++++..+++|++||+|+.+|+..++|++. .+|.+|++.+++|.+.++++++.+....
T Consensus 5 ~~~~~~~~~~~~~l~~~~~~~~~~~~~AEDivQevflkl~~~~~~~~~~--~~~~~WL~~Ia~n~~~d~~Rk~~~~~~~- 81 (182)
T PRK12540 5 DSLRDDILAAVPSLRAFAISLSGNGDRADDLVQETLLRALANIDSFQPG--SNLPAWLFTILRNLFRSDYRKRRREVED- 81 (182)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCC--chHHHHHHHHHHHHHHHHHHhccccccc-
Confidence 4788999999999999999999999999999999999999999999864 3699999999999999999887641000
Q ss_pred hhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHH
Q psy15215 480 VHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 559 (1432)
Q Consensus 480 ~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~i~d~~~~~p~~ 559 (1432)
. +.. ..+... .+|..
T Consensus 82 ----------------------------------------------------~-~~~--------~~~~~~----~~~~~ 96 (182)
T PRK12540 82 ----------------------------------------------------A-DGS--------YAKTLK----SQPGQ 96 (182)
T ss_pred ----------------------------------------------------c-ccc--------cccccc----CCCch
Confidence 0 000 000000 01111
Q ss_pred HHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHHHHHH
Q psy15215 560 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLAHDWL 632 (1432)
Q Consensus 560 ~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l~~~~ 632 (1432)
.. ......+..+|++||++++.||.|+|..|+ |++|||+.||+|.++|+++.+||+++|++.+....
T Consensus 97 ~~--~~~~~~l~~~l~~Lp~~~R~v~~L~~~~g~----s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~~~~ 163 (182)
T PRK12540 97 NA--HLEFEEFRAALDKLPQDQREALILVGASGF----SYEDAAAICGCAVGTIKSRVNRARSKLSALLYVDG 163 (182)
T ss_pred HH--HHHHHHHHHHHHhCCHHHHHHhhHHHHcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhcc
Confidence 11 112346899999999999999999999888 99999999999999999999999999999886543
No 237
>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=99.58 E-value=7.8e-15 Score=154.29 Aligned_cols=152 Identities=16% Similarity=0.171 Sum_probs=124.1
Q ss_pred HHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHHHHHHhccccccchhHHHHH
Q psy15215 407 EANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 486 (1432)
Q Consensus 407 ~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~~~~~~~ 486 (1432)
..|.+.|+.+|.+++++..+++|++||+++.+|+++++|++ .+|.||++..+++.+.++++++.+....+.
T Consensus 2 ~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~l~~~~~~~~~---~~f~~wl~~i~~~~~~d~~r~~~~~~~~~~------ 72 (154)
T TIGR02950 2 REYMHDVFRYLYRLTKDKHLAEDLLQETFLKAYIHLHSFKD---SSIKPWLFRIARNAFIDWYRKDKKIQTIDD------ 72 (154)
T ss_pred chHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHhcC---CchHHHHHHHHHHHHHHHHHHhhhhccccH------
Confidence 57899999999999999899999999999999999999987 379999999999999999987764110000
Q ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHHHHHHHH
Q psy15215 487 NKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 566 (1432)
Q Consensus 487 ~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~i~d~~~~~p~~~~~~~~~ 566 (1432)
.. +.+... ....+|++.....+.
T Consensus 73 ------------------------------------------------~~--------~~~~~~-~~~~~~~~~~~~~~~ 95 (154)
T TIGR02950 73 ------------------------------------------------DA--------IGDLEQ-HPVESPEHHLLIKIE 95 (154)
T ss_pred ------------------------------------------------hh--------hhhccc-cccCChhHHHHHHHH
Confidence 00 000000 011246666666666
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHH
Q psy15215 567 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLA 628 (1432)
Q Consensus 567 ~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l 628 (1432)
...+..+|..||++++.|+.|+|+.|+ |++|||+.||+|+++|+++.++|+.+|++.+
T Consensus 96 ~~~l~~~l~~L~~~~r~i~~l~~~~g~----s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~~l 153 (154)
T TIGR02950 96 QEEITHHLSRLPENYRTVLILREFKEF----SYKEIAELLNLSLAKVKSNLFRARKELKKLL 153 (154)
T ss_pred HHHHHHHHHhCCHhheeeeeehhhccC----cHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 778999999999999999999998888 9999999999999999999999999999764
No 238
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=99.58 E-value=2.8e-14 Score=152.90 Aligned_cols=160 Identities=9% Similarity=0.107 Sum_probs=126.1
Q ss_pred HhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHHHHHHhccccccc
Q psy15215 400 KAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 479 (1432)
Q Consensus 400 ~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip 479 (1432)
.|+..++..|.+.++.++.+++++..+++||+||.++.+|+. ..|... .+|.+|++..++|.+.++++++.+...
T Consensus 10 ~af~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQe~flkl~~~-~~~~~~--~~~~~wL~~iarn~~~d~~R~~~~~~~-- 84 (172)
T PRK09651 10 LTFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVS-ETLSTI--RDPRSFLCTIAKRVMVDLFRRNALEKA-- 84 (172)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhh-cccccc--cCHHHHHHHHHHHHHHHHHHHHHHHhh--
Confidence 499999999999999999999999999999999999999998 355432 268999999999999999987643100
Q ss_pred hhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHH
Q psy15215 480 VHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 559 (1432)
Q Consensus 480 ~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~i~d~~~~~p~~ 559 (1432)
. . + .+. .+ .+....+|..
T Consensus 85 -~-------------------------------------------------~--~-~~~-----~~----~~~~~~~~~~ 102 (172)
T PRK09651 85 -Y-------------------------------------------------L--E-MLA-----LM----PEGGAPSPEE 102 (172)
T ss_pred -h-------------------------------------------------h--h-HHh-----hc----cccCCCChHH
Confidence 0 0 0 000 00 0001123444
Q ss_pred HHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHHHH
Q psy15215 560 AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLAHD 630 (1432)
Q Consensus 560 ~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l~~ 630 (1432)
.....+....+..+|..|||+++.|+.|+|+.|+ |++|||+.||+|.++|+.+.++|+.+|+...-+
T Consensus 103 ~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~----s~~EIA~~lgis~~tV~~~l~Ra~~~~~~~~~~ 169 (172)
T PRK09651 103 RESQLETLQLLDSMLDGLNGKTREAFLLSQLDGL----TYSEIAHKLGVSVSSVKKYVAKATEHCLLFRLE 169 (172)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHhHHhhhhhccCC----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 4444555678999999999999999999999998 999999999999999999999999999876543
No 239
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=99.58 E-value=3.7e-14 Score=150.68 Aligned_cols=158 Identities=18% Similarity=0.197 Sum_probs=127.0
Q ss_pred HHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHHHHHHhccccccchhHH
Q psy15215 404 EMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 483 (1432)
Q Consensus 404 ~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~~~~ 483 (1432)
.++..|.+.|+++|.+++++..+++|++||+++.+|+....|++. +|.+|++..++|.+.+++|++.+....
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 367788999999999999999999999999999999988877642 588999999999999999987641100
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHHHHH
Q psy15215 484 ETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALN 563 (1432)
Q Consensus 484 ~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~i~d~~~~~p~~~~~~ 563 (1432)
+ +.+..... ... ...+|......
T Consensus 74 ------------------------------------------------~------~~~~~~~~--~~~-~~~~~~~~~~~ 96 (163)
T PRK07037 74 ------------------------------------------------H------GDEEDGLD--VPS-PEASPEAALIN 96 (163)
T ss_pred ------------------------------------------------c------cccccccc--cCC-CCCCHHHHHHH
Confidence 0 00000000 001 12356666666
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHHHH
Q psy15215 564 ASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLAHD 630 (1432)
Q Consensus 564 ~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l~~ 630 (1432)
.+..+.+..+|++|||+++.||.|+|..|+ |++|||+.+|+|.++|+....+|+++||..+..
T Consensus 97 ~~~~~~l~~~l~~L~~~~r~v~~l~~~~~~----s~~EIA~~lgis~~tV~~~l~ra~~~lr~~l~~ 159 (163)
T PRK07037 97 RDTLRHVADALSELPARTRYAFEMYRLHGE----TQKDIARELGVSPTLVNFMIRDALVHCRKCLDA 159 (163)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 677788999999999999999999999998 999999999999999999999999999988754
No 240
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=99.58 E-value=3e-14 Score=154.78 Aligned_cols=157 Identities=15% Similarity=0.150 Sum_probs=125.2
Q ss_pred hHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHHHHHHhccccccch
Q psy15215 401 AKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 480 (1432)
Q Consensus 401 A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~ 480 (1432)
|+..++..|.+.|+.+|.+++++..+++|++||+|+.+|+...+|.+. .+|.+|++.+++|.+.+.+++..+. .
T Consensus 24 ~f~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQdvflkl~~~~~~~~~~--~~~~~wL~~Iarn~~~~~~r~~~~~--~-- 97 (188)
T PRK12517 24 RYEALVKALHADIYRYAYWLCKDKHIAEDLVQETFLRAWRSLDSLKDE--KAAKAWLITILRRENARRFERKQFD--L-- 97 (188)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhhcCc--cchHHHHHHHHHHHHHHHHHHhccC--c--
Confidence 999999999999999999999999999999999999999999999864 3799999999999877665543220 0
Q ss_pred hHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHH
Q psy15215 481 HMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 560 (1432)
Q Consensus 481 ~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~i~d~~~~~p~~~ 560 (1432)
.+.+ +. . ..+....+|+..
T Consensus 98 --------------------------------------------------~~~~----~~---~----~~~~~~~~~e~~ 116 (188)
T PRK12517 98 --------------------------------------------------VDIE----DD---S----IEDDASHSSEEE 116 (188)
T ss_pred --------------------------------------------------cCcc----cc---c----ccCccccChhHH
Confidence 0000 00 0 011111233322
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHHHHHH
Q psy15215 561 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLAHDWL 632 (1432)
Q Consensus 561 ~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l~~~~ 632 (1432)
. ....|..+|..||++++.|+.|+|+.|+ |++|||..+|+|.++|+.+.+||+++|+..+...-
T Consensus 117 ~----~~~~l~~~l~~Lp~~~r~v~~l~~~~g~----s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~ 180 (188)
T PRK12517 117 M----EQEWLRRQIAKLDPEYREPLLLQVIGGF----SGEEIAEILDLNKNTVMTRLFRARNQLKEALEKPD 180 (188)
T ss_pred H----HHHHHHHHHHhCCHHHHHHHHHHHHhCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 2 2357899999999999999999999998 99999999999999999999999999999987543
No 241
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=99.57 E-value=3.1e-14 Score=165.88 Aligned_cols=159 Identities=14% Similarity=0.164 Sum_probs=124.2
Q ss_pred hHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHHHHHHhcccccccc
Q psy15215 1191 AKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 1270 (1432)
Q Consensus 1191 A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~ 1270 (1432)
.+.+++..|.+.++.+|++++++..+++|++||+|+. |.....|+ ...|.+|++.+++|.|.+++|++.+. + ..
T Consensus 5 ~~~~l~~~~~~~l~~~a~~~~~~~~dAEDlvQe~fl~-~~~~~~~~---~~~~~~WL~~Ia~n~~~d~lR~~~~~-~-~~ 78 (293)
T PRK09636 5 DAAAEFEPLRPHLLSVAYRMLGSVADAEDIVQEAWLR-WNNADRAQ---IRDPRAWLTRVVTRLCLDRLRSARHR-R-ET 78 (293)
T ss_pred HHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH-HHhccccc---ccCHHHHHHHHHHHHHHHHHHhhhcc-c-cc
Confidence 5778999999999999999999999999999999999 65667775 24799999999999999999986541 0 00
Q ss_pred cHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHH
Q psy15215 1271 HMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 1350 (1432)
Q Consensus 1271 ~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~~d~i~d~~~~~p~~~ 1350 (1432)
. .. ..+..+. .+. ..+|.+.
T Consensus 79 ~---------------------------------------------~~--~~~~e~~------------~~~-~~~~~~~ 98 (293)
T PRK09636 79 Y---------------------------------------------VG--PWLPEPV------------VEE-LDDPLEA 98 (293)
T ss_pred c---------------------------------------------cC--CcCCcCC------------CCC-CCChHHH
Confidence 0 00 0000000 000 1134443
Q ss_pred H-HHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchh
Q psy15215 1351 A-LNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 1419 (1432)
Q Consensus 1351 ~-~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~ 1419 (1432)
. ....+...+..+|++|||++|.|+.|+|..|+ |++|||+.||+|.++|+++++||+++||+...
T Consensus 99 ~~~~~~~~~~l~~~l~~L~~~~R~v~~L~~~~g~----s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~~~ 164 (293)
T PRK09636 99 VVAAEDLSLALMLALERLSPLERAAFLLHDVFGV----PFDEIASTLGRSPAACRQLASRARKHVRAARP 164 (293)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCC
Confidence 3 34455677999999999999999999999988 99999999999999999999999999998543
No 242
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=99.57 E-value=2.9e-14 Score=153.97 Aligned_cols=156 Identities=13% Similarity=0.134 Sum_probs=123.2
Q ss_pred hHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHHHHHHhccccccch
Q psy15215 401 AKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 480 (1432)
Q Consensus 401 A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~ 480 (1432)
..+..+..+++.|+.+|.+++++..+++|++||.|+.+|+...+|+.. .+|.+|++.+++|.+.++++++.+....+
T Consensus 5 ~~~~~~~~~~~~l~~~~~~~~~~~~dAEDivQe~flkl~~~~~~~~~~--~~~~~WL~~Iarn~~id~~Rk~~~~~~~~- 81 (182)
T PRK12511 5 SKRFDVLDQLVPLRRYARSLTRDSAEAEDLVHDALVRALERRASFRSG--GNLRTWLMSILHNAFIDELRRRRVEARRA- 81 (182)
T ss_pred chhhhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCc--cchHHHHHHHHHHHHHHHHHhhccccccc-
Confidence 345668899999999999999999999999999999999999999863 37999999999999999999876521000
Q ss_pred hHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHH
Q psy15215 481 HMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 560 (1432)
Q Consensus 481 ~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~i~d~~~~~p~~~ 560 (1432)
++ + .+. . +.....+..
T Consensus 82 --------------------------~~------------------------~----~~~----~-----~~~~~~~~~- 97 (182)
T PRK12511 82 --------------------------DE------------------------L----AVL----A-----DASLPAAQE- 97 (182)
T ss_pred --------------------------cc------------------------h----hhc----c-----ccCCCcchH-
Confidence 00 0 000 0 000001111
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHHH
Q psy15215 561 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLAH 629 (1432)
Q Consensus 561 ~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l~ 629 (1432)
.......+..+|.+||++++.||.|+|..|+ |++|||+.||+|.++|+++.++|+.+|+..+.
T Consensus 98 --~~~~~~~l~~~l~~Lp~~~R~v~~L~~~eg~----s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~~ 160 (182)
T PRK12511 98 --HAVRLAQIRDAFFDLPEEQRAALHLVAIEGL----SYQEAAAVLGIPIGTLMSRIGRARAALRAFEE 160 (182)
T ss_pred --HHHHHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHH
Confidence 1223467889999999999999999999998 99999999999999999999999999998776
No 243
>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=99.57 E-value=4.6e-14 Score=150.94 Aligned_cols=149 Identities=12% Similarity=0.210 Sum_probs=122.5
Q ss_pred HHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHHHHHHhccccccchhHHHHH
Q psy15215 407 EANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETI 486 (1432)
Q Consensus 407 ~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~~~~~~~ 486 (1432)
..|.+.|+.++.++++...+++|++||+++.+|+++++|+. +.+|.+|++..++|.+.+++++..+...++
T Consensus 2 ~~~~~~l~~~~~~~~~~~~~AeDlvQe~fl~l~~~~~~~~~--~~~f~~wl~~iarn~~~d~~Rk~~~~~~~~------- 72 (170)
T TIGR02959 2 DEFRSELKAFIKSRVSDASDVEDLLQEVFIKIHRNLPSLKD--GQKIQSWLYQIARNTIIDFYRSKSRSVELP------- 72 (170)
T ss_pred chHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCC--cccHHHHHHHHHHHHHHHHHHhccCccccc-------
Confidence 46889999999999999999999999999999999999986 358999999999999999999876521110
Q ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHHHHHHHH
Q psy15215 487 NKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALNASM 566 (1432)
Q Consensus 487 ~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~i~d~~~~~p~~~~~~~~~ 566 (1432)
+.. ... .+|.+.....+.
T Consensus 73 ----------------------------------------------------~~~-------~~~---~~~~~~~~~~e~ 90 (170)
T TIGR02959 73 ----------------------------------------------------ESL-------LAA---DSAREETFVKEL 90 (170)
T ss_pred ----------------------------------------------------hhh-------ccc---CCccHHHHHHHH
Confidence 000 000 012223334455
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHHHH
Q psy15215 567 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLAHD 630 (1432)
Q Consensus 567 ~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l~~ 630 (1432)
...+..+|..||++++.||.|+|..|+ |++|||+.||+|+.+|+++.+||+++|+..+..
T Consensus 91 ~~~l~~~l~~L~~~~r~v~~l~~~~g~----s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 150 (170)
T TIGR02959 91 SQCIPPMIKELPDEYREAIRLTELEGL----SQQEIAEKLGLSLSGAKSRVQRGRKKLKELLET 150 (170)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 678999999999999999999999888 999999999999999999999999999998764
No 244
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=99.57 E-value=4.9e-14 Score=152.91 Aligned_cols=156 Identities=15% Similarity=0.135 Sum_probs=121.6
Q ss_pred hHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHHHHHHhccccccch
Q psy15215 401 AKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 480 (1432)
Q Consensus 401 A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~ 480 (1432)
+++.|+. |.+.|+++|.+++++..+++|++||.|+.+|+.+.+|+.. .+|.+|++..++|.+.++++++.+...
T Consensus 9 ~~~~l~~-~~~~l~~~a~~~l~~~~~AEDivQevfl~l~~~~~~~~~~--~~~~awL~~ia~n~~~d~~Rk~~r~~~--- 82 (188)
T PRK12546 9 PRDELVE-HLPALRAFAISLTRNVAVADDLVQDTIVKAWTNFDKFQEG--TNLRAWLFTILRNTFYSDRRKHKREVP--- 82 (188)
T ss_pred HHHHHHH-HHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHhccCCC--cchHHHHHHHHHHHHHHHHHHhccccc---
Confidence 5555555 7799999999999999999999999999999999999863 479999999999999999988764100
Q ss_pred hHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHH
Q psy15215 481 HMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 560 (1432)
Q Consensus 481 ~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~i~d~~~~~p~~~ 560 (1432)
. .+. ...+...+ .|..
T Consensus 83 ~---------------------------------------------------~~~--------~~~~~~~~----~~~~- 98 (188)
T PRK12546 83 D---------------------------------------------------PEG--------VHAASLAV----KPAH- 98 (188)
T ss_pred C---------------------------------------------------ccc--------cccccccc----CCcc-
Confidence 0 000 00000000 0100
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHHHHH
Q psy15215 561 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLAHDW 631 (1432)
Q Consensus 561 ~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l~~~ 631 (1432)
........+..+|++|||+++.||.|+|..|+ |++|||+.||+|+.+|+++.+||+++|++.+...
T Consensus 99 -~~~~~~~~l~~~L~~Lp~~~r~v~~L~~~~g~----s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l~~~ 164 (188)
T PRK12546 99 -DGRLAMSDFRAAFAQLPDEQREALILVGASGF----SYEEAAEMCGVAVGTVKSRANRARARLAELLQLE 164 (188)
T ss_pred -hhHHHHHHHHHHHHhCCHHHhHHhhhHHhcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhcc
Confidence 01122346889999999999999999999998 9999999999999999999999999999887543
No 245
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=99.56 E-value=2.8e-14 Score=151.28 Aligned_cols=154 Identities=14% Similarity=0.168 Sum_probs=113.1
Q ss_pred CCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHHhC
Q psy15215 1212 DRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETG 1291 (1432)
Q Consensus 1212 ~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g 1291 (1432)
++..+++|++||+|+.+|+..+.+ .+..|++|++.+++|.|.+++|++.+..+....
T Consensus 2 ~~~~~AeDivQe~fl~~~~~~~~~---~~~~~~~wl~~ia~n~~~d~~Rk~~~~~~~~~~-------------------- 58 (161)
T PRK09047 2 RDDDAALDIVQDAMIKLAEKYGDR---PAAEWPPLFQRILQNRIHDWFRRQKVRNTWVSL-------------------- 58 (161)
T ss_pred CCHHHHHHHHHHHHHHHHHHHhhc---ccCchHHHHHHHHHHHHHHHHHhhccccccccc--------------------
Confidence 345679999999999999998863 245799999999999999999987642110000
Q ss_pred CCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCC--CCChHHHHHHHHHHHHHHHHHccCCH
Q psy15215 1292 SEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDEN--MLAPSDAALNASMRSVVKDILNSLTP 1369 (1432)
Q Consensus 1292 ~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~~d~i~d~~--~~~p~~~~~~~~~~~~l~~~L~~L~~ 1369 (1432)
..++.... +.++....+.+.+.. ..+|++.....+....+..+|..||+
T Consensus 59 ----------------------------~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~ 109 (161)
T PRK09047 59 ----------------------------FSSFSDDD-DDDDFDPLETLDSADEGAESPADKLERAQVLQLIEEAIQKLPA 109 (161)
T ss_pred ----------------------------cccccccc-ccccccHHHHhccccccCCCHHHHHHHHHHHHHHHHHHHhCCH
Confidence 00000000 000011111111111 24688888888888999999999999
Q ss_pred HHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchhhh
Q psy15215 1370 RESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYY 1421 (1432)
Q Consensus 1370 rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~~~ 1421 (1432)
++|.||.|+|+.|+ |++|||+.||+|.++|+++++||+++||......
T Consensus 110 ~~r~v~~l~~~~g~----s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~ 157 (161)
T PRK09047 110 RQREAFLLRYWEDM----DVAETAAAMGCSEGSVKTHCSRATHALAKALEAK 157 (161)
T ss_pred HHHHHHHHHHHhcC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhc
Confidence 99999999999988 9999999999999999999999999999876543
No 246
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=99.56 E-value=4.4e-14 Score=156.37 Aligned_cols=159 Identities=16% Similarity=0.162 Sum_probs=124.9
Q ss_pred HHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHH
Q psy15215 1177 INRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 1256 (1432)
Q Consensus 1177 l~~~~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~ 1256 (1432)
++++...++.. ++..+++.| +.|+++|.+++++..+++||+||+|+.+|+. |+.. ..|.+|++.+++|.+.
T Consensus 8 ~~~~~~~~~~~---~~~~l~~~y-~~L~r~~~~~~~d~~dAEDlvQE~flk~~~~---~~~~--~~~~~WL~~IarN~~i 78 (228)
T PRK06704 8 ILKNHIDMNHS---NINFLIEQY-GELKRYCTFLTKNKWDGEDLAQETVCKVLQK---YSNK--DICMTLVYKIARNRWL 78 (228)
T ss_pred HHhcccCCCHH---HHHHHHHHH-HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH---cCcc--ccHHHHHHHHHHHHHH
Confidence 45566677777 888777777 7899999999999999999999999999986 4432 3599999999999999
Q ss_pred HHHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcC
Q psy15215 1257 RSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLG 1336 (1432)
Q Consensus 1257 ~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~~ 1336 (1432)
+++|++.+.-.+ . ++ ...
T Consensus 79 d~~Rk~k~~~~~-------------------------------------------------------~----~~--~~~- 96 (228)
T PRK06704 79 DQIKSKSVHEKI-------------------------------------------------------R----DQ--ITF- 96 (228)
T ss_pred HHHhcccccccc-------------------------------------------------------c----cc--ccc-
Confidence 999987641000 0 00 000
Q ss_pred cccccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhC
Q psy15215 1337 DFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 1416 (1432)
Q Consensus 1337 d~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~ 1416 (1432)
.+|.... ......+..+|+.||+++|.|+.|+|+.|+ |++|||+.+|+|.++|+++++||+++||.
T Consensus 97 --------~~~~~~~--~~~~~~l~~~L~~Lp~~~R~v~lL~~~eg~----S~~EIAe~LgiS~~tVksrL~Rark~Lr~ 162 (228)
T PRK06704 97 --------EEPHEKI--ADLHEMVGKVLSSLNVQQSAILLLKDVFQY----SIADIAKVCSVSEGAVKASLFRSRNRLKT 162 (228)
T ss_pred --------CChHHHH--HHHHHHHHHHHHhCCHHHhhHhhhHHhhCC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 0111111 233467899999999999999999999888 99999999999999999999999999998
Q ss_pred chhh
Q psy15215 1417 PSRY 1420 (1432)
Q Consensus 1417 ~~~~ 1420 (1432)
....
T Consensus 163 ~l~~ 166 (228)
T PRK06704 163 VSEE 166 (228)
T ss_pred HHHh
Confidence 6643
No 247
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=99.55 E-value=5.4e-14 Score=150.16 Aligned_cols=158 Identities=15% Similarity=0.115 Sum_probs=127.3
Q ss_pred hHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHHHHHHhccccccch
Q psy15215 401 AKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 480 (1432)
Q Consensus 401 A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~ 480 (1432)
++.+++..|.+.++++|.+++++..+++|++||.|+.+|+....+.. .+|.+|+++.++|.+.+++++..+. +
T Consensus 10 ~~~~~~~~~~~~l~~~~~~~~~~~~~aeDlvQevf~~l~~~~~~~~~---~~~~~wl~~Iarn~~~d~~Rr~~~~-~--- 82 (168)
T PRK12525 10 LIGQMFQQDYDWLCKKLSRQLGCPHSAEDIASETFLQVLALPDPASI---REPRALLTTIARRLMYEGWRRQDLE-R--- 82 (168)
T ss_pred HHHHHHHHHHHHHHHHHHHHcCCcCcHHHHHHHHHHHHHhCCCcccc---cCHHHHHHHHHHHHHHHHHHHHHHH-H---
Confidence 79999999999999999999999999999999999999986554432 3799999999999999998865320 0
Q ss_pred hHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHH
Q psy15215 481 HMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 560 (1432)
Q Consensus 481 ~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~i~d~~~~~p~~~ 560 (1432)
. ... +.. + .+.....+|.+.
T Consensus 83 -----------~---~~~---------------------------------~~~----~---------~~~~~~~~~~~~ 102 (168)
T PRK12525 83 -----------A---YLQ---------------------------------SLA----E---------APEAVQPSPEEQ 102 (168)
T ss_pred -----------H---HHH---------------------------------HHh----c---------ccccccCChHHH
Confidence 0 000 000 0 000011356666
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHHH
Q psy15215 561 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLAH 629 (1432)
Q Consensus 561 ~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l~ 629 (1432)
....+....+..+++.|||+++.||.|+|..|+ |++|||+.||+|+++|+.+..+|++.++..+.
T Consensus 103 ~~~~~~~~~l~~~l~~L~~~~r~v~~L~~~eg~----s~~EIA~~l~is~~tV~~~l~ra~~~~~~~~~ 167 (168)
T PRK12525 103 WMVIETLLAIDRLLDGLSGKARAAFLMSQLEGL----TYVEIGERLGVSLSRIHQYMVEAFKCCYQGFQ 167 (168)
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHhhc
Confidence 666677789999999999999999999999998 99999999999999999999999999997653
No 248
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=99.55 E-value=6.9e-14 Score=161.48 Aligned_cols=160 Identities=16% Similarity=0.153 Sum_probs=124.8
Q ss_pred hhHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q psy15215 1190 KAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 1269 (1432)
Q Consensus 1190 ~A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip 1269 (1432)
+.+..+++.|.+.++++|++++++..+++|++||+|+.+|++...+ . ..|.+|++.+++|.|.+++|+..+. +-
T Consensus 5 ~~~~~l~~~~~~~L~~~a~r~lgs~~dAEDvvQE~flr~~~~~~~~---~-~~~~aWL~~Ia~n~~id~lRk~~~r-r~- 78 (290)
T PRK09635 5 DPVSAAWRAHRAYLVDLAFRMVGDIGVAEDMVQEAFSRLLRAPVGD---I-DDERGWLIVVTSRLCLDHIKSASTR-RE- 78 (290)
T ss_pred cHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCccc---c-ccHHHHHHHHHHHHHHHHHhhhhcc-Cc-
Confidence 3788999999999999999999999999999999999999986543 1 3699999999999999999976531 00
Q ss_pred ccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHH
Q psy15215 1270 VHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 1349 (1432)
Q Consensus 1270 ~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~~d~i~d~~~~~p~~ 1349 (1432)
........ ..+ +... ...+|++
T Consensus 79 -------------------------------------------------~~~~~~~~-~~~------~~~~--~~~~~~~ 100 (290)
T PRK09635 79 -------------------------------------------------RPQDIAAW-HDG------DASV--SSVDPAD 100 (290)
T ss_pred -------------------------------------------------Cccccccc-Ccc------ccCC--CCCCcHH
Confidence 00000000 000 0000 1123443
Q ss_pred -HHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCc
Q psy15215 1350 -AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417 (1432)
Q Consensus 1350 -~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~ 1417 (1432)
.....+....+..+|.+|||++|.|+.|+|+.|+ |++|||+.+|+|..+|+++++||+++||..
T Consensus 101 ~~~~~~e~~~al~~~L~~L~p~~R~vf~L~~~~g~----s~~EIA~~Lgis~~tVr~~l~RAr~~Lr~~ 165 (290)
T PRK09635 101 RVTLDDEVRLALLIMLERLGPAERVVFVLHEIFGL----PYQQIATTIGSQASTCRQLAHRARRKINES 165 (290)
T ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHhhHHHHhCC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHhh
Confidence 3345566778999999999999999999999998 999999999999999999999999999974
No 249
>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=99.53 E-value=1.3e-13 Score=159.36 Aligned_cols=155 Identities=19% Similarity=0.178 Sum_probs=120.8
Q ss_pred HHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHHHHHHhcccccccccHH
Q psy15215 1194 EMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 1273 (1432)
Q Consensus 1194 ~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~~~~ 1273 (1432)
+++..|.+.|+++|++++++..+++|++||+|+.+++. +|... ..|.+|++.+++|.|.+++|++.+.-...
T Consensus 1 ~l~~~~~~~l~~~a~r~lg~~~dAEDvvQE~flk~~~~--~~~~~--~~~~awL~~Ia~n~~ld~lR~~~~~~~~~---- 72 (281)
T TIGR02957 1 EEFEALRPLLFSLAYRMLGSVADAEDIVQETFLRWQEA--DRAQI--ENPKAYLTKVVTRRCIDVLRSARARREVY---- 72 (281)
T ss_pred ChHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhC--Ccccc--cCHHHHHHHHHHHHHHHHHHHhhhccccc----
Confidence 37899999999999999999999999999999998775 55432 37999999999999999999765310000
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHHHHH
Q psy15215 1274 ETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALN 1353 (1432)
Q Consensus 1274 ~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~~d~i~d~~~~~p~~~~~~ 1353 (1432)
..+ -+..|. .+ ...+|++....
T Consensus 73 --------------------------------------------~~~-~~~e~~------------~~-~~~~~~~~~~~ 94 (281)
T TIGR02957 73 --------------------------------------------VGP-WLPEPL------------LT-TSADPAESVEL 94 (281)
T ss_pred --------------------------------------------CCC-CCCccc------------CC-CCCChHHHHHH
Confidence 000 000010 00 01246555443
Q ss_pred H-HHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCch
Q psy15215 1354 A-SMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418 (1432)
Q Consensus 1354 ~-~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~ 1418 (1432)
. .+...+..+|++|||+||.||.|+|..|+ |++|||+.||+|..+|+++++||+++||+..
T Consensus 95 ~e~~~~~l~~~l~~L~~~~R~v~~L~~~~g~----s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~~ 156 (281)
T TIGR02957 95 AESLSMAYLLLLERLSPLERAVFVLREVFDY----PYEEIASIVGKSEANCRQLVSRARRHLDARR 156 (281)
T ss_pred HHHHHHHHHHHHhhCCHHHHHHHHHHHHcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence 3 45667889999999999999999999888 9999999999999999999999999999854
No 250
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=99.49 E-value=3.4e-13 Score=142.95 Aligned_cols=152 Identities=14% Similarity=0.173 Sum_probs=112.4
Q ss_pred CCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHHHHHHhccccccchhHHHHHHHHHHHHHHHHHHhCC
Q psy15215 423 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGS 502 (1432)
Q Consensus 423 ~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~ 502 (1432)
+..+++|++||+|+.+|+..+.+ .+.+|.+|++.+++|.|.+++|++.+..+...
T Consensus 3 ~~~~AeDivQe~fl~~~~~~~~~---~~~~~~~wl~~ia~n~~~d~~Rk~~~~~~~~~---------------------- 57 (161)
T PRK09047 3 DDDAALDIVQDAMIKLAEKYGDR---PAAEWPPLFQRILQNRIHDWFRRQKVRNTWVS---------------------- 57 (161)
T ss_pred CHHHHHHHHHHHHHHHHHHHhhc---ccCchHHHHHHHHHHHHHHHHHhhcccccccc----------------------
Confidence 44578999999999999998863 24579999999999999999998764211000
Q ss_pred CCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCC--CCChHHHHHHHHHHHHHHHHHhcCCHH
Q psy15215 503 EPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDEN--MLAPSDAALNASMRSVVKDILNSLTPR 580 (1432)
Q Consensus 503 ~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~i~d~~--~~~p~~~~~~~~~~~~l~~~L~~L~~r 580 (1432)
...++.... +.++....+.+.+.. ..+|.+.+...+....+..+|.+||++
T Consensus 58 --------------------------~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~ 110 (161)
T PRK09047 58 --------------------------LFSSFSDDD-DDDDFDPLETLDSADEGAESPADKLERAQVLQLIEEAIQKLPAR 110 (161)
T ss_pred --------------------------ccccccccc-ccccccHHHHhccccccCCCHHHHHHHHHHHHHHHHHHHhCCHH
Confidence 000000000 000011111111111 246888888888889999999999999
Q ss_pred HHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHHHH
Q psy15215 581 ESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLAHD 630 (1432)
Q Consensus 581 er~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l~~ 630 (1432)
+|.||.|+|+.|+ |++|||+.||+|.++|+.+.++|+++|+..+..
T Consensus 111 ~r~v~~l~~~~g~----s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~ 156 (161)
T PRK09047 111 QREAFLLRYWEDM----DVAETAAAMGCSEGSVKTHCSRATHALAKALEA 156 (161)
T ss_pred HHHHHHHHHHhcC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 9999999999998 999999999999999999999999999998864
No 251
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=99.49 E-value=4e-13 Score=156.60 Aligned_cols=158 Identities=13% Similarity=0.151 Sum_probs=123.6
Q ss_pred hHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHHHHHHhccccccch
Q psy15215 401 AKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 480 (1432)
Q Consensus 401 A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~ 480 (1432)
.+.+++..|.+.++.+|++++++..+++|++||+++. |.....|+ ..+|.+|++.+++|.|.+++|++.+....
T Consensus 5 ~~~~l~~~~~~~l~~~a~~~~~~~~dAEDlvQe~fl~-~~~~~~~~---~~~~~~WL~~Ia~n~~~d~lR~~~~~~~~-- 78 (293)
T PRK09636 5 DAAAEFEPLRPHLLSVAYRMLGSVADAEDIVQEAWLR-WNNADRAQ---IRDPRAWLTRVVTRLCLDRLRSARHRRET-- 78 (293)
T ss_pred HHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH-HHhccccc---ccCHHHHHHHHHHHHHHHHHHhhhccccc--
Confidence 5778999999999999999999999999999999999 55667775 34799999999999999999976531000
Q ss_pred hHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHH
Q psy15215 481 HMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 560 (1432)
Q Consensus 481 ~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~i~d~~~~~p~~~ 560 (1432)
. . . ..+..+ ..+. ..+|.+.
T Consensus 79 ~---------------------------------------------~-~-~~~~e~------------~~~~-~~~~~~~ 98 (293)
T PRK09636 79 Y---------------------------------------------V-G-PWLPEP------------VVEE-LDDPLEA 98 (293)
T ss_pred c---------------------------------------------c-C-CcCCcC------------CCCC-CCChHHH
Confidence 0 0 0 000000 0000 1134444
Q ss_pred H-HHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHH
Q psy15215 561 A-LNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLA 628 (1432)
Q Consensus 561 ~-~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l 628 (1432)
. ....+...+..+|++|||++|.|+.|+|..|+ |++|||+.+|+|.++|+++.+||+++|++..
T Consensus 99 ~~~~~~~~~~l~~~l~~L~~~~R~v~~L~~~~g~----s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~~ 163 (293)
T PRK09636 99 VVAAEDLSLALMLALERLSPLERAAFLLHDVFGV----PFDEIASTLGRSPAACRQLASRARKHVRAAR 163 (293)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence 3 34455677899999999999999999999998 9999999999999999999999999999864
No 252
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=99.49 E-value=4.2e-13 Score=148.62 Aligned_cols=159 Identities=15% Similarity=0.171 Sum_probs=125.3
Q ss_pred HHHHHHHHhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHH
Q psy15215 386 DINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 465 (1432)
Q Consensus 386 ~l~~~i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i 465 (1432)
.+++++..|+.. ++..+++.| +.|+++|.+++++..+++||+||.|+.+|+. |+.. ..|.+|++.+++|.+
T Consensus 7 ~~~~~~~~~~~~---~~~~l~~~y-~~L~r~~~~~~~d~~dAEDlvQE~flk~~~~---~~~~--~~~~~WL~~IarN~~ 77 (228)
T PRK06704 7 HILKNHIDMNHS---NINFLIEQY-GELKRYCTFLTKNKWDGEDLAQETVCKVLQK---YSNK--DICMTLVYKIARNRW 77 (228)
T ss_pred HHHhcccCCCHH---HHHHHHHHH-HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH---cCcc--ccHHHHHHHHHHHHH
Confidence 345667778887 888888777 7899999999999999999999999999986 4432 359999999999999
Q ss_pred HHHHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCc
Q psy15215 466 TRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHL 545 (1432)
Q Consensus 466 ~~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~ 545 (1432)
.+.+|++.+.-.+ .++ ...
T Consensus 78 id~~Rk~k~~~~~-----------------------------------------------------------~~~--~~~ 96 (228)
T PRK06704 78 LDQIKSKSVHEKI-----------------------------------------------------------RDQ--ITF 96 (228)
T ss_pred HHHHhcccccccc-----------------------------------------------------------ccc--ccc
Confidence 9999976541000 000 000
Q ss_pred CcccccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHH
Q psy15215 546 GDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625 (1432)
Q Consensus 546 ~~~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr 625 (1432)
.+|.... .+....+..+|++||+++|.|+.|+|..|+ |++|||+.+|+|.++|+++.+||+++|+
T Consensus 97 ---------~~~~~~~--~~~~~~l~~~L~~Lp~~~R~v~lL~~~eg~----S~~EIAe~LgiS~~tVksrL~Rark~Lr 161 (228)
T PRK06704 97 ---------EEPHEKI--ADLHEMVGKVLSSLNVQQSAILLLKDVFQY----SIADIAKVCSVSEGAVKASLFRSRNRLK 161 (228)
T ss_pred ---------CChHHHH--HHHHHHHHHHHHhCCHHHhhHhhhHHhhCC----CHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 0111111 223467899999999999999999999888 9999999999999999999999999999
Q ss_pred HHHH
Q psy15215 626 PLAH 629 (1432)
Q Consensus 626 ~~l~ 629 (1432)
+.+.
T Consensus 162 ~~l~ 165 (228)
T PRK06704 162 TVSE 165 (228)
T ss_pred HHHH
Confidence 8764
No 253
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=99.46 E-value=8.2e-13 Score=152.59 Aligned_cols=161 Identities=17% Similarity=0.156 Sum_probs=125.0
Q ss_pred HhHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHHHHHHhccccccc
Q psy15215 400 KAKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 479 (1432)
Q Consensus 400 ~A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip 479 (1432)
..+..+++.|.+.++++|++++++..+++|++||.|+.+|++...+ ..+|.+|++..++|.|.++++++.+. +.
T Consensus 5 ~~~~~l~~~~~~~L~~~a~r~lgs~~dAEDvvQE~flr~~~~~~~~----~~~~~aWL~~Ia~n~~id~lRk~~~r-r~- 78 (290)
T PRK09635 5 DPVSAAWRAHRAYLVDLAFRMVGDIGVAEDMVQEAFSRLLRAPVGD----IDDERGWLIVVTSRLCLDHIKSASTR-RE- 78 (290)
T ss_pred cHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCccc----cccHHHHHHHHHHHHHHHHHhhhhcc-Cc-
Confidence 3788999999999999999999999999999999999999987543 13699999999999999999976431 00
Q ss_pred hhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHH
Q psy15215 480 VHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSD 559 (1432)
Q Consensus 480 ~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~i~d~~~~~p~~ 559 (1432)
.... ++.... .+... ...+|.+
T Consensus 79 -------------------------------------------------~~~~----~~~~~~---~~~~~--~~~~~~~ 100 (290)
T PRK09635 79 -------------------------------------------------RPQD----IAAWHD---GDASV--SSVDPAD 100 (290)
T ss_pred -------------------------------------------------Cccc----ccccCc---cccCC--CCCCcHH
Confidence 0000 000000 00000 1123443
Q ss_pred -HHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHH
Q psy15215 560 -AALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLA 628 (1432)
Q Consensus 560 -~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l 628 (1432)
.....+....+..+|.+|||++|.|+.|+|..|+ |++|||+.+|+|+.+|+++.+||+++|+...
T Consensus 101 ~~~~~~e~~~al~~~L~~L~p~~R~vf~L~~~~g~----s~~EIA~~Lgis~~tVr~~l~RAr~~Lr~~~ 166 (290)
T PRK09635 101 RVTLDDEVRLALLIMLERLGPAERVVFVLHEIFGL----PYQQIATTIGSQASTCRQLAHRARRKINESR 166 (290)
T ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHhhHHHHhCC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHhhC
Confidence 3445566778999999999999999999999998 9999999999999999999999999998753
No 254
>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=99.44 E-value=1.4e-12 Score=150.86 Aligned_cols=155 Identities=19% Similarity=0.170 Sum_probs=120.5
Q ss_pred HHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHHHHHHhccccccchhHH
Q psy15215 404 EMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 483 (1432)
Q Consensus 404 ~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~~~~ 483 (1432)
+++..|.+.|+++|++++++..+++|++||+++.+++. +|.. ...|.+|++.+++|.|.++++++.+.-..
T Consensus 1 ~l~~~~~~~l~~~a~r~lg~~~dAEDvvQE~flk~~~~--~~~~--~~~~~awL~~Ia~n~~ld~lR~~~~~~~~----- 71 (281)
T TIGR02957 1 EEFEALRPLLFSLAYRMLGSVADAEDIVQETFLRWQEA--DRAQ--IENPKAYLTKVVTRRCIDVLRSARARREV----- 71 (281)
T ss_pred ChHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhC--Cccc--ccCHHHHHHHHHHHHHHHHHHHhhhcccc-----
Confidence 36899999999999999999999999999999998775 4543 34799999999999999999976531000
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHHHHH
Q psy15215 484 ETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALN 563 (1432)
Q Consensus 484 ~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~i~d~~~~~p~~~~~~ 563 (1432)
...+ .+.+.... ...+|++....
T Consensus 72 -------------------------------------------------~~~~-------~~~e~~~~-~~~~~~~~~~~ 94 (281)
T TIGR02957 72 -------------------------------------------------YVGP-------WLPEPLLT-TSADPAESVEL 94 (281)
T ss_pred -------------------------------------------------cCCC-------CCCcccCC-CCCChHHHHHH
Confidence 0000 00000000 01246555543
Q ss_pred H-HHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHH
Q psy15215 564 A-SMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLA 628 (1432)
Q Consensus 564 ~-~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l 628 (1432)
. .+...+..+|++|||++|.||.|+|..|+ |++|||+.||+|..+|+++.+||+++|++..
T Consensus 95 ~e~~~~~l~~~l~~L~~~~R~v~~L~~~~g~----s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~~ 156 (281)
T TIGR02957 95 AESLSMAYLLLLERLSPLERAVFVLREVFDY----PYEEIASIVGKSEANCRQLVSRARRHLDARR 156 (281)
T ss_pred HHHHHHHHHHHHhhCCHHHHHHHHHHHHcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence 3 45567889999999999999999999998 9999999999999999999999999999764
No 255
>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=99.39 E-value=2.6e-12 Score=133.24 Aligned_cols=138 Identities=14% Similarity=0.171 Sum_probs=101.9
Q ss_pred HHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhcc---ccCCCcchhHHHHHHHHHHHHHHHHhcccccc
Q psy15215 1192 KREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE---YRRGYKFSTYATWWIRQAITRSIADQARTIRI 1268 (1432)
Q Consensus 1192 ~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd---~~~g~~Fstya~~~ir~~i~~~i~~~~r~iri 1268 (1432)
|+.++..|.+.++.+|++|... +.+||+|+.+|+.+.+|+ .....+|.||++.+++|.+.+++|++.+..+.
T Consensus 1 f~~~~~~y~~~l~~~~~~~~~~-----~~~qdvf~~~w~~~~~~~~~~~~~~~~~~~wL~~iarN~~id~~Rk~~~~~~~ 75 (142)
T TIGR03209 1 FEEIYMNFKNTIDIFTRKYNLY-----YDYNDILYHLWIILKKIDLNKFNTENDLEKYISTSLKRYCLDICNKKNRDKKI 75 (142)
T ss_pred ChHHHHHHHHHHHHHHHHhcch-----hhHHHHHHHHHHHHHHhhhhhcCchhHHHHHHHHHHHHHHHHHHHHHhhhhhh
Confidence 4679999999999999999662 235999999999987642 12234799999999999999999987641000
Q ss_pred cccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChH
Q psy15215 1269 PVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPS 1348 (1432)
Q Consensus 1269 p~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~~d~i~d~~~~~p~ 1348 (1432)
. . +....+. ..++.
T Consensus 76 ~----------------------------------------------------~-~~~~~~~-------------~~~~~ 89 (142)
T TIGR03209 76 I----------------------------------------------------Y-NSEITDI-------------KLSLI 89 (142)
T ss_pred h----------------------------------------------------h-hhhhhcc-------------ccchh
Confidence 0 0 0000000 00122
Q ss_pred HHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHH
Q psy15215 1349 DAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIR 1404 (1432)
Q Consensus 1349 ~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vr 1404 (1432)
+.....+....+..+|+.|||++|.|+.|+|..|+ |++|||+.||+|.+||+
T Consensus 90 ~~~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~~~~~----s~~EIA~~l~is~~tV~ 141 (142)
T TIGR03209 90 NVYSSNDLEFEFNDLISILPNKQKKIIYMKFFEDM----KEIDIAKKLHISRQSVY 141 (142)
T ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHHCcCHHhhc
Confidence 33334445567899999999999999999999999 99999999999999997
No 256
>PF03979 Sigma70_r1_1: Sigma-70 factor, region 1.1; InterPro: IPR007127 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 [, ]. This entry represents Region 1.1 which modulates DNA binding by region 2 and 4 when sigma is unbound by the core RNA polymerase [, ]. Region 1.1 is also involved in promoter binding.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2K6X_A.
Probab=99.33 E-value=9.4e-13 Score=121.63 Aligned_cols=63 Identities=44% Similarity=0.635 Sum_probs=42.6
Q ss_pred HHHHHHHHHHhccccCcccHHHHHhhCCCCCCCHHHHHHHHHHHhhCCCcccccCCchhhhhc
Q psy15215 39 LRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 101 (1432)
Q Consensus 39 ~~~~l~~Li~~Gke~G~lTy~EInd~LP~~~~~~d~id~ii~~L~~~gI~v~d~~~~~~~~~~ 101 (1432)
....|+.||.+||++|||||+|||++||+..++|++||+|+.+|.++||+|++..++.+.+.+
T Consensus 5 ~~~~i~~Li~~gK~~G~lT~~eI~~~L~~~~~~~e~id~i~~~L~~~gI~Vvd~~~~~~~~~~ 67 (82)
T PF03979_consen 5 YEEAIKKLIEKGKKKGYLTYDEINDALPEDDLDPEQIDEIYDTLEDEGIEVVDEEEDEEELAL 67 (82)
T ss_dssp HHHHHHHHHHHHHHHSS-BHHHHHHH-S-S---HHHHHHHHHHHHTT----B--S--S-SS--
T ss_pred hHHHHHHHHHHHhhcCcCCHHHHHHHcCccCCCHHHHHHHHHHHHHCCCEEecCCCchhhhcc
Confidence 467899999999999999999999999999999999999999999999999997766554433
No 257
>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=99.31 E-value=1.5e-11 Score=127.43 Aligned_cols=138 Identities=14% Similarity=0.216 Sum_probs=101.9
Q ss_pred HHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhcc---ccCCCccHHHHHHHHHHHHHHHHHHhcccccc
Q psy15215 402 KREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFE---YRRGYKFSTYATWWIRQAITRSIADQARTIRI 478 (1432)
Q Consensus 402 ~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd---~~~g~~Fstya~~~ir~~i~~~i~~~~r~iri 478 (1432)
++.++..|.+.++.+|++|.. .++ +||.++.+|+.+.+|+ .+...+|.||++..++|.+.+++|++.+..+.
T Consensus 1 f~~~~~~y~~~l~~~~~~~~~----~~~-~qdvf~~~w~~~~~~~~~~~~~~~~~~~wL~~iarN~~id~~Rk~~~~~~~ 75 (142)
T TIGR03209 1 FEEIYMNFKNTIDIFTRKYNL----YYD-YNDILYHLWIILKKIDLNKFNTENDLEKYISTSLKRYCLDICNKKNRDKKI 75 (142)
T ss_pred ChHHHHHHHHHHHHHHHHhcc----hhh-HHHHHHHHHHHHHHhhhhhcCchhHHHHHHHHHHHHHHHHHHHHHhhhhhh
Confidence 467999999999999999966 234 4999999999987643 22235799999999999999999977541000
Q ss_pred chhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChH
Q psy15215 479 PVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPS 558 (1432)
Q Consensus 479 p~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~i~d~~~~~p~ 558 (1432)
. . +....+. ..++.
T Consensus 76 --~--------------------------------------------------~-~~~~~~~-------------~~~~~ 89 (142)
T TIGR03209 76 --I--------------------------------------------------Y-NSEITDI-------------KLSLI 89 (142)
T ss_pred --h--------------------------------------------------h-hhhhhcc-------------ccchh
Confidence 0 0 0000000 00122
Q ss_pred HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHH
Q psy15215 559 DAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIR 614 (1432)
Q Consensus 559 ~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~ 614 (1432)
+.....+....+..+|+.|||++|.|+.|+|..|+ |++|||+.||+|+++|+
T Consensus 90 ~~~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~~~~~----s~~EIA~~l~is~~tV~ 141 (142)
T TIGR03209 90 NVYSSNDLEFEFNDLISILPNKQKKIIYMKFFEDM----KEIDIAKKLHISRQSVY 141 (142)
T ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHHCcCHHhhc
Confidence 33334445567899999999999999999999999 99999999999999986
No 258
>PRK08311 putative RNA polymerase sigma factor SigI; Reviewed
Probab=99.30 E-value=6.6e-11 Score=131.84 Aligned_cols=93 Identities=18% Similarity=0.327 Sum_probs=84.4
Q ss_pred hHHHHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHhccCCCC--ChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHH
Q psy15215 1173 DLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGL--QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 1250 (1432)
Q Consensus 1173 e~~~l~~~~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~~~--~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ 1250 (1432)
++..++.+++.|+.. |++.|+..|.|+|+++|.+++++.. ..+|++|+|++++|+++++|++.+|.+|.+|+.++
T Consensus 4 ~~~~Li~~~~~gD~~---AfeeLi~~Y~p~I~~~a~~~~~~~~~~eaeDlvQe~fi~l~eai~~y~~~kg~sF~awl~~I 80 (237)
T PRK08311 4 SLEDILEKIKNGDEE---LREELIEEYKPFIAKVVSSVCGRYIDWENDDELSIGLIAFNEAIDSYDEEKGKSFLSFAELV 80 (237)
T ss_pred cHHHHHHHHHCCCHH---HHHHHHHHHHHHHHHHHHHHhcccCCCCchHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHH
Confidence 466788899999988 9999999999999999999998865 59999999999999999999999887899999999
Q ss_pred HHHHHHHHHHHhcccccc
Q psy15215 1251 IRQAITRSIADQARTIRI 1268 (1432)
Q Consensus 1251 ir~~i~~~i~~~~r~iri 1268 (1432)
++|.+.+++|++.+...+
T Consensus 81 irn~~iDylRk~~~~~~~ 98 (237)
T PRK08311 81 IKRRLIDYFRKESKHNLV 98 (237)
T ss_pred HHHHHHHHHHHhhccccc
Confidence 999999999998764443
No 259
>PRK09191 two-component response regulator; Provisional
Probab=99.29 E-value=1.6e-11 Score=140.98 Aligned_cols=136 Identities=11% Similarity=0.063 Sum_probs=111.7
Q ss_pred hHHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHHHHHHhcccccccc
Q psy15215 1191 AKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 1270 (1432)
Q Consensus 1191 A~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~ 1270 (1432)
++..++..|.+.|+++|.+++++...++|++||+|+.+|+...+|++. ..|.||++.++++...+ ...
T Consensus 2 ~~~~l~~~~~~~l~~~~~~~~~~~~~aeDi~qd~~~~~~~~~~~~~~~--~~~~~wl~~~~~~~~~~----~~~------ 69 (261)
T PRK09191 2 SLSQRIAPHLPYLRRYARALTGSQSSGDAYVAATLEALLADPSIFPEA--SSPRVGLYRLFHRLWSS----AGA------ 69 (261)
T ss_pred chHHHHHHHhHHHHHHHHHhcCChhhHHHHHHHHHHHHHHhHHhcCCC--cchhhHHHHHHHHHhcc----ccc------
Confidence 688999999999999999999999999999999999999999999864 36999999887653210 000
Q ss_pred cHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHH
Q psy15215 1271 HMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 1350 (1432)
Q Consensus 1271 ~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~~d~i~d~~~~~p~~~ 1350 (1432)
..+ .. ..+..
T Consensus 70 -----------------------------------------------------~~~--~~--------------~~~~~- 79 (261)
T PRK09191 70 -----------------------------------------------------NDP--EP--------------GSPFE- 79 (261)
T ss_pred -----------------------------------------------------cCC--CC--------------CCCch-
Confidence 000 00 00111
Q ss_pred HHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchh
Q psy15215 1351 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 1419 (1432)
Q Consensus 1351 ~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~ 1419 (1432)
..+..+|++||+++|.|+.|+|..|+ |++|||+.+|+|.++|+.+.++|+++||....
T Consensus 80 -------~~l~~~l~~L~~~~r~v~~l~~~~~~----s~~eIA~~l~~s~~tV~~~l~ra~~~l~~~~~ 137 (261)
T PRK09191 80 -------ARAERRLAGLTPLPRQAFLLTALEGF----SVEEAAEILGVDPAEAEALLDDARAEIARQVA 137 (261)
T ss_pred -------HHHHHHHHhCCHHHhHHHHHHHHhcC----CHHHHHHHHCCCHHHHHHHHHHHHHHHhccCC
Confidence 16888999999999999999999998 99999999999999999999999999997654
No 260
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=99.25 E-value=1.3e-10 Score=125.77 Aligned_cols=176 Identities=15% Similarity=0.270 Sum_probs=126.7
Q ss_pred hHHHHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHhccCC---CCChh--HHHHHHHHHHHHHHHhccccCCCcchhHH
Q psy15215 1173 DLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDR---GLQFL--DLIQEGNIGLMKAVDKFEYRRGYKFSTYA 1247 (1432)
Q Consensus 1173 e~~~l~~~~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~~~---~~~~~--DLiQEg~igl~kav~kfd~~~g~~Fstya 1247 (1432)
++-.|+.++++||.. |.+.|+..|++.++.+|++++.+ +.+.+ +|++|+|+.+...-...++..-..|-.|+
T Consensus 3 ~it~ll~~~~~GD~~---A~~~L~~~~y~~L~~~a~~~l~~~~~~~~~~~~~lv~ea~lrl~~~~~~~~~~~~~~f~~~~ 79 (185)
T PF07638_consen 3 EITELLDRWRQGDEA---ALDQLFERYYPELRRLARRRLRRERRGHDLQDTALVHEAFLRLARRGRFVQFSDRRHFWALL 79 (185)
T ss_pred hHHHHHHHHHCCCHH---HHHHHHHHHHHHHHHHHHHHHhccccCCchhHHHHHHHHHHHHhccccccCCCCHHHHHHHH
Confidence 567899999999999 99999999999999999987643 23344 45778888777633322332223689999
Q ss_pred HHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCC
Q psy15215 1248 TWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPV 1327 (1432)
Q Consensus 1248 ~~~ir~~i~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~ 1327 (1432)
...+++.+.++.|++....|-+.. ...+|+...
T Consensus 80 ~~~~rr~lid~~R~~~a~KRg~~~-----------------------------------------------~~~~l~~~~ 112 (185)
T PF07638_consen 80 ARIMRRKLIDHARRRQAQKRGGDQ-----------------------------------------------VRVELDERA 112 (185)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCCC-----------------------------------------------cccchhhhh
Confidence 999999999999887653221100 011222111
Q ss_pred CCCCCCCcCcccccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHH
Q psy15215 1328 GDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 1407 (1432)
Q Consensus 1328 ~~~~~~~~~d~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~ 1407 (1432)
. +...++|...+ .+.+.+..+.. |+|++++++.++|+.|+ |.+|||+.+|||+.||+..+
T Consensus 113 ~------------~~~~~~~~~~~---~l~e~l~~L~~-l~~~~~~~v~l~~~~Gl----s~~EIA~~lgiS~~tV~r~l 172 (185)
T PF07638_consen 113 D------------SGDEPSPEELL---ELEEALERLLA-LDPRQRRVVELRFFEGL----SVEEIAERLGISERTVRRRL 172 (185)
T ss_pred c------------cccCCCHHHHH---HHHHHHHHHHc-cCHHHHHHHHHHHHCCC----CHHHHHHHHCcCHHHHHHHH
Confidence 0 01113455544 34556666555 99999999999999888 99999999999999999999
Q ss_pred HHHHHHhhCch
Q psy15215 1408 AKALRKLRHPS 1418 (1432)
Q Consensus 1408 ~rAl~kLr~~~ 1418 (1432)
..|..+|+..+
T Consensus 173 ~~aR~~l~~~l 183 (185)
T PF07638_consen 173 RRARAWLRREL 183 (185)
T ss_pred HHHHHHHHHHh
Confidence 99999998743
No 261
>PRK08311 putative RNA polymerase sigma factor SigI; Reviewed
Probab=99.20 E-value=4.1e-10 Score=125.55 Aligned_cols=92 Identities=18% Similarity=0.319 Sum_probs=84.1
Q ss_pred hHHHHHHHHHHhHHHHHHhHHHHHHHHHHHHHHHHHhcccCCC--ChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHH
Q psy15215 383 DLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDRGL--QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 460 (1432)
Q Consensus 383 e~~~l~~~i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~~~--~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ 460 (1432)
++..++..++.||.. |++.|+..|.|+|+++|.+++++.. ..+|++|+|++++|+++++|++.+|.+|.+|+.++
T Consensus 4 ~~~~Li~~~~~gD~~---AfeeLi~~Y~p~I~~~a~~~~~~~~~~eaeDlvQe~fi~l~eai~~y~~~kg~sF~awl~~I 80 (237)
T PRK08311 4 SLEDILEKIKNGDEE---LREELIEEYKPFIAKVVSSVCGRYIDWENDDELSIGLIAFNEAIDSYDEEKGKSFLSFAELV 80 (237)
T ss_pred cHHHHHHHHHCCCHH---HHHHHHHHHHHHHHHHHHHHhcccCCCCchHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHH
Confidence 466788899999998 9999999999999999999998865 58999999999999999999998888999999999
Q ss_pred HHHHHHHHHHHhccccc
Q psy15215 461 IRQAITRSIADQARTIR 477 (1432)
Q Consensus 461 ir~~i~~~i~~~~r~ir 477 (1432)
++|.+.+++|++.+...
T Consensus 81 irn~~iDylRk~~~~~~ 97 (237)
T PRK08311 81 IKRRLIDYFRKESKHNL 97 (237)
T ss_pred HHHHHHHHHHHhhcccc
Confidence 99999999998876433
No 262
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=99.20 E-value=3.9e-10 Score=122.20 Aligned_cols=177 Identities=15% Similarity=0.264 Sum_probs=124.9
Q ss_pred hHHHHHHHHHHhHHHHHHhHHHHHHHHHHHHHHHHHhcccC---CCChh--hHHHHHHHHHHHHHhhccccCCCccHHHH
Q psy15215 383 DLRDINRKMIAGEMKARKAKREMTEANLRLVISIAKKYTDR---GLQFL--DLIQEGNIGLMKAVDKFEYRRGYKFSTYA 457 (1432)
Q Consensus 383 e~~~l~~~i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~~~---~~~~~--DLiQEg~igL~kav~~fd~~~g~~Fstya 457 (1432)
++-.|+.++++||.. |.+.|+..|++.++.+|++++.. +.+.+ +||+|.|+.+...-...++..-..|..|+
T Consensus 3 ~it~ll~~~~~GD~~---A~~~L~~~~y~~L~~~a~~~l~~~~~~~~~~~~~lv~ea~lrl~~~~~~~~~~~~~~f~~~~ 79 (185)
T PF07638_consen 3 EITELLDRWRQGDEA---ALDQLFERYYPELRRLARRRLRRERRGHDLQDTALVHEAFLRLARRGRFVQFSDRRHFWALL 79 (185)
T ss_pred hHHHHHHHHHCCCHH---HHHHHHHHHHHHHHHHHHHHHhccccCCchhHHHHHHHHHHHHhccccccCCCCHHHHHHHH
Confidence 567889999999999 99999999999999999987643 23344 45777777776633222332224689999
Q ss_pred HHHHHHHHHHHHHHhccccccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCC
Q psy15215 458 TWWIRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPV 537 (1432)
Q Consensus 458 ~~~ir~~i~~~i~~~~r~irip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~ 537 (1432)
...+++.+.+++|.+....|-+.. ...+++...
T Consensus 80 ~~~~rr~lid~~R~~~a~KRg~~~-----------------------------------------------~~~~l~~~~ 112 (185)
T PF07638_consen 80 ARIMRRKLIDHARRRQAQKRGGDQ-----------------------------------------------VRVELDERA 112 (185)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCCC-----------------------------------------------cccchhhhh
Confidence 999999999998877653221100 001111111
Q ss_pred CCCCCCCcCcccccCCCCChHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHH
Q psy15215 538 GDDEDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 617 (1432)
Q Consensus 538 ~~~~~~~~~~~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~ 617 (1432)
.+ ...++|...+ ++.+.+..+.. |+|++++++.++|..|+ |.+|||+.+|+|+.+|++..
T Consensus 113 ~~------------~~~~~~~~~~---~l~e~l~~L~~-l~~~~~~~v~l~~~~Gl----s~~EIA~~lgiS~~tV~r~l 172 (185)
T PF07638_consen 113 DS------------GDEPSPEELL---ELEEALERLLA-LDPRQRRVVELRFFEGL----SVEEIAERLGISERTVRRRL 172 (185)
T ss_pred cc------------ccCCCHHHHH---HHHHHHHHHHc-cCHHHHHHHHHHHHCCC----CHHHHHHHHCcCHHHHHHHH
Confidence 00 0113455443 34555555555 99999999999999888 99999999999999999999
Q ss_pred HHHHHHHHHHHH
Q psy15215 618 AKALRKLRPLAH 629 (1432)
Q Consensus 618 ~rAl~kLr~~l~ 629 (1432)
+.|..+|+..++
T Consensus 173 ~~aR~~l~~~l~ 184 (185)
T PF07638_consen 173 RRARAWLRRELR 184 (185)
T ss_pred HHHHHHHHHHhc
Confidence 999888877653
No 263
>PRK09191 two-component response regulator; Provisional
Probab=99.15 E-value=1.8e-10 Score=132.30 Aligned_cols=135 Identities=12% Similarity=0.052 Sum_probs=110.3
Q ss_pred hHHHHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHHHHHHhccccccch
Q psy15215 401 AKREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 480 (1432)
Q Consensus 401 A~~~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~ 480 (1432)
++..++..|.+.|+++|.+++++...++|++||+|+.+|+...+|++. .+|.+|++.++++.... ...
T Consensus 2 ~~~~l~~~~~~~l~~~~~~~~~~~~~aeDi~qd~~~~~~~~~~~~~~~--~~~~~wl~~~~~~~~~~----~~~------ 69 (261)
T PRK09191 2 SLSQRIAPHLPYLRRYARALTGSQSSGDAYVAATLEALLADPSIFPEA--SSPRVGLYRLFHRLWSS----AGA------ 69 (261)
T ss_pred chHHHHHHHhHHHHHHHHHhcCChhhHHHHHHHHHHHHHHhHHhcCCC--cchhhHHHHHHHHHhcc----ccc------
Confidence 688999999999999999999999999999999999999999999863 46999999877653210 000
Q ss_pred hHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHH
Q psy15215 481 HMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDA 560 (1432)
Q Consensus 481 ~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~i~d~~~~~p~~~ 560 (1432)
.... . ..+..
T Consensus 70 ---------------------------------------------------------~~~~---------~---~~~~~- 79 (261)
T PRK09191 70 ---------------------------------------------------------NDPE---------P---GSPFE- 79 (261)
T ss_pred ---------------------------------------------------------cCCC---------C---CCCch-
Confidence 0000 0 01111
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHH
Q psy15215 561 ALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLA 628 (1432)
Q Consensus 561 ~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l 628 (1432)
..+..+|++||+++|.|+.|+|..|+ |++|||+.+|+|.++|+.+.++|+++|+..+
T Consensus 80 -------~~l~~~l~~L~~~~r~v~~l~~~~~~----s~~eIA~~l~~s~~tV~~~l~ra~~~l~~~~ 136 (261)
T PRK09191 80 -------ARAERRLAGLTPLPRQAFLLTALEGF----SVEEAAEILGVDPAEAEALLDDARAEIARQV 136 (261)
T ss_pred -------HHHHHHHHhCCHHHhHHHHHHHHhcC----CHHHHHHHHCCCHHHHHHHHHHHHHHHhccC
Confidence 16889999999999999999999999 9999999999999999999999999998554
No 264
>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=99.02 E-value=5.9e-10 Score=100.57 Aligned_cols=70 Identities=27% Similarity=0.382 Sum_probs=67.4
Q ss_pred HHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHHHHHHhcc
Q psy15215 1195 MTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR 1264 (1432)
Q Consensus 1195 Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~~i~~~~r 1264 (1432)
|++.|.++|+++|++|++++.+++|++||++++||+++++|++..+.+|++|++.++++.+.+.++++.|
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 6899999999999999999999999999999999999999999999899999999999999999998775
No 265
>PF13155 Toprim_2: Toprim-like
Probab=99.02 E-value=4.6e-10 Score=108.01 Aligned_cols=68 Identities=25% Similarity=0.309 Sum_probs=59.7
Q ss_pred EEEecchhHHHHhhhCC----------------------------CCCeEEEEecCcHHHHHHHHHHHHHhhhhcCCCce
Q psy15215 733 LITEGYMDVIGLSQFGF----------------------------FANSSYTCFDGDQAGRRAARRALEVCLLYATDDKI 784 (1432)
Q Consensus 733 ~~vEG~~D~ia~~~~g~----------------------------~~~~i~~~~D~D~aG~~a~~~~~~~~~~~~~~~~~ 784 (1432)
|||||++|+||++|.+. ..++|++|||||.||++|+.+....+...+.....
T Consensus 1 ~v~Eg~iDaLS~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~l~~~~~~~i~l~~DnD~aG~~~~~~~~~~l~~~~~~~~~ 80 (96)
T PF13155_consen 1 VVFEGPIDALSYYQLGKENIKDNSLSLAGGGTLSEKQQIKFLKENPYKKIVLAFDNDEAGRKAAEKLQKELKEEGFPNIK 80 (96)
T ss_pred cEEeCHHHHHHHHHhCchhcCCceEEEECCchHHHHHHHHHHHhCCCCcEEEEeCCCHHHHHHHHHHHHHHHhhCCCcce
Confidence 68999999999999876 23689999999999999999999988877755666
Q ss_pred EEEecCCCCCCHHHHH
Q psy15215 785 IKFLFLPDKYDPDSYI 800 (1432)
Q Consensus 785 ~~~~~lp~~~Dpde~~ 800 (1432)
+.+..+|++||++|+|
T Consensus 81 ~~~~~~~~~KD~Nd~L 96 (96)
T PF13155_consen 81 VRIEDPPDGKDWNDYL 96 (96)
T ss_pred eeecCCCCCcCchhhC
Confidence 8888899999999985
No 266
>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI. This protein is a component of the relaxosome complex. In the process of conjugative plasmid transfer the realaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein.
Probab=99.02 E-value=7.9e-10 Score=154.92 Aligned_cols=164 Identities=13% Similarity=0.083 Sum_probs=121.8
Q ss_pred HHHHHHHHHHHHhhh-hhhhhH-hh-cC--CCcccccccccCCCCCchhhHHHHHHHHHHhhhccEEEEee-----eeee
Q psy15215 623 KLRPLAHDWLEQRTH-QNEKII-AC-SS--DSSNHNEHVTNNNFPPGFNIFHKLLRILQEYLESFLISFFL-----RNHG 692 (1432)
Q Consensus 623 kLr~~l~~~~~~~l~-~~~~~~-~l-~~--l~~~~~~~f~~Gyap~~~~~l~~~~~~~~~~~~~fri~fpi-----r~ig 692 (1432)
.+...++.+|..... .+..|. || +. |+. +..|.|||+|..|.. ....|+. ++|||| +++|
T Consensus 1667 ~~~~~A~rl~~~a~pi~gt~A~~YL~~~RGI~~--~~~~~LrfhP~~y~~------~~~~~~P--aliapv~D~~G~i~g 1736 (1960)
T TIGR02760 1667 QLEKRAKSLFQGSQELKGTLAEKYLKQHRGLAS--IDNDDIRFHPTVYSS------DKKNKHP--ALIAAARNEKGEITG 1736 (1960)
T ss_pred hHHHHHHHHHHhcCCCCCHHHHHHHHhcCCCCC--CCccceEECcccccC------CCCCcCC--eEEEEEECCCCCEEE
Confidence 344556677766542 244444 99 66 543 578999999987641 1123444 499999 6999
Q ss_pred eeeeeeCC---CCC----CCCCCCcccCccccCchHhHHhhccCCeEEEEecchhHHHHhhhCC----------------
Q psy15215 693 ISGFLLTT---PDP----VHETPLFHKSNELYGLFEAKNAIGKSGYVLITEGYMDVIGLSQFGF---------------- 749 (1432)
Q Consensus 693 f~gR~~~~---~~~----s~et~~f~K~~~Ly~~~~a~~~~~~~~~~~~vEG~~D~ia~~~~g~---------------- 749 (1432)
|.++.|++ +++ +|.+.+|+|+..+|+++.+. ..+.++|||||+|++|+++++.
T Consensus 1737 v~rt~L~p~~g~~~k~l~~~kr~~G~k~g~~v~l~~~~----~~~~liiaEGiEtaLS~~~a~~~~~~vvA~lg~~~l~~ 1812 (1960)
T TIGR02760 1737 IQITYLDKDDANKDKDMDNNKRVKGSISGQFVVINKGM----QGDRSYIAEGIETGLSIALANPKATVVIAVGGKNNLSP 1812 (1960)
T ss_pred EEEEEccCCCCCCCccCCCcccccccccCcEEEecCCC----CCCeEEEEcCHHHHHHHHHhCCCCccEEEECCcccccc
Confidence 99999983 223 89999999999999998653 3578999999999999999862
Q ss_pred -----CCCeEEEEecCc--HH-HHHHHHHHHHHhhhhcCCCceEEEecCCCCCCHHHHHHHhChhhhhh
Q psy15215 750 -----FANSSYTCFDGD--QA-GRRAARRALEVCLLYATDDKIIKFLFLPDKYDPDSYIRKFGYKIFSK 810 (1432)
Q Consensus 750 -----~~~~i~~~~D~D--~a-G~~a~~~~~~~~~~~~~~~~~~~~~~lp~~~Dpde~~~~~g~~~~~~ 810 (1432)
...+||+|+|+| .| |++|+.+++..+...|+. |.|+ +|+ |.+++ |.++|.+
T Consensus 1813 i~~~~~~~~viI~~D~D~~~a~G~~Aa~k~~~~l~~~G~~---v~i~-~P~--Dfnd~----g~~~~~~ 1871 (1960)
T TIGR02760 1813 IIPKFIPKNVVIVLDNDGEEAKSQRAIEKIINKFKQDNIS---ARIV-FPD--DWNDI----GEEELQK 1871 (1960)
T ss_pred ccCCCCCceEEEEeCCCCcccchHHHHHHHHHHHHhCCCe---eEEe-CCc--hhhhh----hHHHHHH
Confidence 358899999999 55 999999999999887766 7776 664 44333 6556554
No 267
>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=98.99 E-value=7.2e-10 Score=92.59 Aligned_cols=50 Identities=40% Similarity=0.733 Sum_probs=46.0
Q ss_pred HHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhC
Q psy15215 1363 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 1416 (1432)
Q Consensus 1363 ~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~ 1416 (1432)
+|++|||+|+.||.++|+.++ |++|||+.||+|+++|+++..+|++|||+
T Consensus 1 Al~~L~~~er~vi~~~y~~~~----t~~eIa~~lg~s~~~V~~~~~~al~kLR~ 50 (50)
T PF04545_consen 1 ALDQLPPREREVIRLRYFEGL----TLEEIAERLGISRSTVRRILKRALKKLRK 50 (50)
T ss_dssp HHCTS-HHHHHHHHHHHTST-----SHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred ChhhCCHHHHHHHHHHhcCCC----CHHHHHHHHCCcHHHHHHHHHHHHHHhcC
Confidence 589999999999999998888 99999999999999999999999999984
No 268
>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=98.99 E-value=7.8e-10 Score=101.96 Aligned_cols=78 Identities=40% Similarity=0.751 Sum_probs=67.6
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHHH
Q psy15215 1274 ETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAA 1351 (1432)
Q Consensus 1274 ~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~~d~i~d~~~~~p~~~~ 1351 (1432)
+.++++.++.+++.+++||+||++|||+.|||++++|+.++.....++||+.+++.+++..+++++.|....+|++.+
T Consensus 1 E~l~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~~~~~~~Sl~~~~~~~~~~~l~~~i~d~~~~~P~e~~ 78 (78)
T PF04539_consen 1 EKLRKIERARRELEQELGREPTDEEIAEELGISVEEVRELLQASRRPVSLDLPVGDEDDSTLGDFIEDDDAPSPEEEV 78 (78)
T ss_dssp HHHHHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHHHHSCCEESSHCCSSSSSEEGGGSSB-SSS--HHHH-
T ss_pred ChHHHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHHhCCCCeEEeeeecCCCCCchhheecCCCCCChhhcc
Confidence 468999999999999999999999999999999999999999999999999999999889999999999888998753
No 269
>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=98.98 E-value=9.5e-10 Score=99.23 Aligned_cols=70 Identities=27% Similarity=0.382 Sum_probs=67.3
Q ss_pred HHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHHHHHHhcc
Q psy15215 405 MTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR 474 (1432)
Q Consensus 405 li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~~i~~~~r 474 (1432)
|++.|.++|+++|.+|++++.+.+|++||++++||+++++|++..+.+|++|++.++++.+.+.++++.|
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 6899999999999999999999999999999999999999999998899999999999999999998875
No 270
>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=98.97 E-value=1.1e-09 Score=101.08 Aligned_cols=78 Identities=40% Similarity=0.751 Sum_probs=67.3
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHHH
Q psy15215 484 ETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAA 561 (1432)
Q Consensus 484 ~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~i~d~~~~~p~~~~ 561 (1432)
+.++++.++.++|.+++||+||.+|||+.|||++++|+.++..+..++||+.+++.+++.+++++++|....+|++.+
T Consensus 1 E~l~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~~~~~~~Sl~~~~~~~~~~~l~~~i~d~~~~~P~e~~ 78 (78)
T PF04539_consen 1 EKLRKIERARRELEQELGREPTDEEIAEELGISVEEVRELLQASRRPVSLDLPVGDEDDSTLGDFIEDDDAPSPEEEV 78 (78)
T ss_dssp HHHHHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHHHHSCCEESSHCCSSSSSEEGGGSSB-SSS--HHHH-
T ss_pred ChHHHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHHhCCCCeEEeeeecCCCCCchhheecCCCCCChhhcc
Confidence 468999999999999999999999999999999999999999999999999999998888999999999888998753
No 271
>PF03979 Sigma70_r1_1: Sigma-70 factor, region 1.1; InterPro: IPR007127 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 [, ]. This entry represents Region 1.1 which modulates DNA binding by region 2 and 4 when sigma is unbound by the core RNA polymerase [, ]. Region 1.1 is also involved in promoter binding.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2K6X_A.
Probab=98.95 E-value=5.9e-10 Score=103.09 Aligned_cols=64 Identities=44% Similarity=0.629 Sum_probs=42.7
Q ss_pred HHHHHHHHHHHhccccCccchHHHhhhCCCCCCCHHHHHHHHHHHHhcCccccccccchhhhhc
Q psy15215 828 NLRKKFKILIKLGKERGYLTFSEINDFLPEDIIDHEIIESIIKTFRYMDISVSEHVLDTETLML 891 (1432)
Q Consensus 828 ~~~~~~~~Li~~gk~~g~lT~~ei~~~lp~~~~~~e~ie~i~~~l~~~gI~v~e~~~~~e~~~~ 891 (1432)
.....++.|+..||++|||||++||++||+..+++++++.++..|.+.||+|++..++.+.+.+
T Consensus 4 ~~~~~i~~Li~~gK~~G~lT~~eI~~~L~~~~~~~e~id~i~~~L~~~gI~Vvd~~~~~~~~~~ 67 (82)
T PF03979_consen 4 QYEEAIKKLIEKGKKKGYLTYDEINDALPEDDLDPEQIDEIYDTLEDEGIEVVDEEEDEEELAL 67 (82)
T ss_dssp HHHHHHHHHHHHHHHHSS-BHHHHHHH-S-S---HHHHHHHHHHHHTT----B--S--S-SS--
T ss_pred hhHHHHHHHHHHHhhcCcCCHHHHHHHcCccCCCHHHHHHHHHHHHHCCCEEecCCCchhhhcc
Confidence 3466789999999999999999999999999999999999999999999999997766654433
No 272
>PRK04031 DNA primase; Provisional
Probab=98.93 E-value=1.2e-09 Score=125.76 Aligned_cols=85 Identities=22% Similarity=0.314 Sum_probs=69.7
Q ss_pred hHhHHhhccCCeEEEEecchhHHHHhhhCC-------------------CCCeEEEEecCcHHHHHHHHHHHHHhhhhcC
Q psy15215 720 FEAKNAIGKSGYVLITEGYMDVIGLSQFGF-------------------FANSSYTCFDGDQAGRRAARRALEVCLLYAT 780 (1432)
Q Consensus 720 ~~a~~~~~~~~~~~~vEG~~D~ia~~~~g~-------------------~~~~i~~~~D~D~aG~~a~~~~~~~~~~~~~ 780 (1432)
-.|.+.+++.+.+||||||+||++|+++|+ ...+|++|||||.||..+..+..+ .+.
T Consensus 160 L~Agp~i~k~~~iIVVEG~~DVi~L~~aGi~nvVAt~GT~l~~~i~~l~k~~~Vil~~DgD~aGe~I~k~l~~----v~~ 235 (408)
T PRK04031 160 LPAGPNVDDSDAIIVVEGRADVLNLLRYGIKNAIAVEGTNVPETIIELSKKKTVTAFLDGDRGGELILKELLQ----VAD 235 (408)
T ss_pred cccCcccccCCeEEEEeCHHHHHHHHhcccceEEEeCCcccHHHHHHHhcCCCEEEEECCCHHHHHHHHHHHh----hcc
Confidence 367788888999999999999999999999 578999999999999888665544 222
Q ss_pred CCceEEEecCCCCCCHHHHHHHhChhhhhhc
Q psy15215 781 DDKIIKFLFLPDKYDPDSYIRKFGYKIFSKK 811 (1432)
Q Consensus 781 ~~~~~~~~~lp~~~Dpde~~~~~g~~~~~~~ 811 (1432)
..+|+.+|+|+||+++-.+.-..++.++
T Consensus 236 ---~d~VaraP~G~dVE~ls~eeI~kAL~~~ 263 (408)
T PRK04031 236 ---IDYVARAPPGKEVEELTKKEIAKALRNK 263 (408)
T ss_pred ---eeEEecCCCCCChhhCCHHHHHHHHHhc
Confidence 4778899999999999766666666554
No 273
>PHA02415 DNA primase domain-containing protein
Probab=98.88 E-value=5.2e-09 Score=127.66 Aligned_cols=172 Identities=12% Similarity=0.084 Sum_probs=107.1
Q ss_pred hhhhhH-hhcC--CCcccccc-cccCCCC-CchhhHHHHHHHHHHhhhcc-EEEEee----eeeeeeeeeeCCCCCCCCC
Q psy15215 638 QNEKII-ACSS--DSSNHNEH-VTNNNFP-PGFNIFHKLLRILQEYLESF-LISFFL----RNHGISGFLLTTPDPVHET 707 (1432)
Q Consensus 638 ~~~~~~-~l~~--l~~~~~~~-f~~Gyap-~~~~~l~~~~~~~~~~~~~f-ri~fpi----r~igf~gR~~~~~~~s~et 707 (1432)
.+..+. ||+. ||+++|.. |+.|=.- +.|..-.-..+.. .+.... -++||- .++.-.-|.+...-+....
T Consensus 120 d~rrA~AYLK~RGIS~EVI~~cIk~GlIg~~~W~s~rv~agd~-gygg~nAAFIVpf~rdGtvv~v~~Rg~d~afkG~vK 198 (930)
T PHA02415 120 ERERVREYLGGRGISAAAIDAAFAARSLGFNTWTSSKVAAGEV-GHAGPAAAFIVREPADGRVVAVDMRYVDPALNGGVK 198 (930)
T ss_pred chHHHHHHHHhcCCCHHHHHHHHHcCccccccccccccccccc-ccCCCceEEEecccCCceEEEeeeccccccccCCcc
Confidence 466677 9977 99999996 7776331 1221111010000 110110 135665 4666665654321111111
Q ss_pred CCcccCccccCchHhHHhhccCCeEEEEecchhHHHHhhhCC----------------------CCCeEEEEecCcHH--
Q psy15215 708 PLFHKSNELYGLFEAKNAIGKSGYVLITEGYMDVIGLSQFGF----------------------FANSSYTCFDGDQA-- 763 (1432)
Q Consensus 708 ~~f~K~~~Ly~~~~a~~~~~~~~~~~~vEG~~D~ia~~~~g~----------------------~~~~i~~~~D~D~a-- 763 (1432)
.=|.-+...|++..-.......+.|+||||.||+||++++|+ ..++|++|+|||.|
T Consensus 199 anf~Gs~~G~gW~~p~~~L~~a~eVwIvEGiIDAISL~q~Gi~avAaVAL~GLan~~~iD~~~l~~KrVvlcLDNDea~~ 278 (930)
T PHA02415 199 TQTQGDKAGYGWTADARRLDKAKRVFIVESAINALSIDTCAMPGAAALALRGLANVDAIDFSSLRGKQVVICLDNDEPFE 278 (930)
T ss_pred ccCCCCCCCCccCCCccccCCCCEEEEEechHhHHHHHHcCchhHHHHHHcCcCCCchhhchhhcCceEEEEecCCcccc
Confidence 122223344555432222445678999999999999999998 25699999999998
Q ss_pred ----------HHHHHHHHHHHhhhhcCCCceEEEecCCC-------CC----CHHHHHHHhChhhhhh
Q psy15215 764 ----------GRRAARRALEVCLLYATDDKIIKFLFLPD-------KY----DPDSYIRKFGYKIFSK 810 (1432)
Q Consensus 764 ----------G~~a~~~~~~~~~~~~~~~~~~~~~~lp~-------~~----Dpde~~~~~g~~~~~~ 810 (1432)
|++||.+..+.+...++..+-|.-...-. |. |.+||++.+|++.+..
T Consensus 279 ~~~~~~g~rpG~eAA~~l~e~lta~~i~~~lvd~~~w~~~~~~~~~~~~~~~d~nd~l~~~g~~~~~~ 346 (930)
T PHA02415 279 DGHPRAGHRPGPEAAWALYERLASLNISAVLVDQAGWLADLADGETKQQPINDVNDYLQLRGPEELAR 346 (930)
T ss_pred ccCcccccCccHHHHHHHHHHHhhcCCceEEeehhhhhhhcccccccccccccHHHHHHHhCHHHHHH
Confidence 99999999999998888744333222222 44 9999999999998765
No 274
>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=98.85 E-value=9.2e-10 Score=84.76 Aligned_cols=35 Identities=40% Similarity=0.785 Sum_probs=31.9
Q ss_pred CChHHHHHHhcCCccCCCchHHHHHHHHHHHHHHH
Q psy15215 129 KDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKD 163 (1432)
Q Consensus 129 ~DPVRmYLREMG~V~LLTREgEIeIAKRIE~G~~~ 163 (1432)
+|||++||++||++||||+++|+++|++|+.|-..
T Consensus 1 ~D~l~~Yl~ei~~~~LLt~eeE~~LA~~i~~g~~~ 35 (37)
T PF00140_consen 1 SDSLRLYLKEIGRYPLLTAEEEIELARRIRKGDEA 35 (37)
T ss_dssp HHHHHHHHHHHHHS-EETTHHHHHHHHHHHHHHHH
T ss_pred CcHHHHHHHHHcCCCCCCHHHHHHHHHHHHHhHHh
Confidence 48999999999999999999999999999999753
No 275
>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=98.83 E-value=9.2e-10 Score=84.76 Aligned_cols=35 Identities=40% Similarity=0.785 Sum_probs=31.9
Q ss_pred CChHHHHHHccCCccCCCchHHHHHHHHHHHhHHH
Q psy15215 919 KDPIKMYMREMGSVELLTRDGEIEIAKRIEEGLKD 953 (1432)
Q Consensus 919 ~DPVRmYLREMG~v~LLTREgEIeIAKRIE~G~~~ 953 (1432)
+|||++||++||++||||+++|+++|++|+.|-..
T Consensus 1 ~D~l~~Yl~ei~~~~LLt~eeE~~LA~~i~~g~~~ 35 (37)
T PF00140_consen 1 SDSLRLYLKEIGRYPLLTAEEEIELARRIRKGDEA 35 (37)
T ss_dssp HHHHHHHHHHHHHS-EETTHHHHHHHHHHHHHHHH
T ss_pred CcHHHHHHHHHcCCCCCCHHHHHHHHHHHHHhHHh
Confidence 48999999999999999999999999999999753
No 276
>cd03364 TOPRIM_DnaG_primases TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of proteins similar to Escherichia coli DnaG. Primases synthesize RNA primers for the initiation of DNA replication. DnaG type primases are often closely associated with DNA helicases in primosome assemblies. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. E. coli DnaG is a single subunit enzyme.
Probab=98.80 E-value=1.1e-08 Score=94.46 Aligned_cols=57 Identities=46% Similarity=0.713 Sum_probs=50.0
Q ss_pred CeEEEEecchhHHHHhhhCC---------------------CCCeEEEEecCcHHHHHHHHHHHHHhhhhcCCCceEEEe
Q psy15215 730 GYVLITEGYMDVIGLSQFGF---------------------FANSSYTCFDGDQAGRRAARRALEVCLLYATDDKIIKFL 788 (1432)
Q Consensus 730 ~~~~~vEG~~D~ia~~~~g~---------------------~~~~i~~~~D~D~aG~~a~~~~~~~~~~~~~~~~~~~~~ 788 (1432)
+.++||||++|++++++.|+ +..+|++|||||.||++|+.+....+.+.|.. ++++
T Consensus 1 ~~v~i~EG~~D~ls~~~~g~~~~va~~G~~~~~~~~~~L~~~~~~vii~~D~D~aG~~a~~~~~~~l~~~g~~---~~~~ 77 (79)
T cd03364 1 KKVILVEGYMDVIALHQAGIKNVVASLGTALTEEQAELLKRLAKEVILAFDGDEAGQKAALRALELLLKLGLN---VRVL 77 (79)
T ss_pred CeEEEEeCHHHHHHHHHcCCCCEEECCCccCcHHHHHHHHhcCCeEEEEECCCHHHHHHHHHHHHHHHHCCCe---EEEE
Confidence 46899999999999999987 24899999999999999999999999988765 7665
Q ss_pred c
Q psy15215 789 F 789 (1432)
Q Consensus 789 ~ 789 (1432)
.
T Consensus 78 ~ 78 (79)
T cd03364 78 T 78 (79)
T ss_pred e
Confidence 4
No 277
>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=98.79 E-value=1e-08 Score=85.58 Aligned_cols=50 Identities=40% Similarity=0.725 Sum_probs=46.0
Q ss_pred HHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHH
Q psy15215 573 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRP 626 (1432)
Q Consensus 573 ~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~ 626 (1432)
||++|||+|+.||.++|+.++ |++|||+.+|+|.++|+++.++|+.+||+
T Consensus 1 Al~~L~~~er~vi~~~y~~~~----t~~eIa~~lg~s~~~V~~~~~~al~kLR~ 50 (50)
T PF04545_consen 1 ALDQLPPREREVIRLRYFEGL----TLEEIAERLGISRSTVRRILKRALKKLRK 50 (50)
T ss_dssp HHCTS-HHHHHHHHHHHTST-----SHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred ChhhCCHHHHHHHHHHhcCCC----CHHHHHHHHCCcHHHHHHHHHHHHHHhcC
Confidence 689999999999999998888 99999999999999999999999999985
No 278
>PF13662 Toprim_4: Toprim domain; PDB: 1EQN_E 1DD9_A 3B39_B 1DDE_A.
Probab=98.72 E-value=1.4e-08 Score=94.30 Aligned_cols=52 Identities=33% Similarity=0.470 Sum_probs=41.2
Q ss_pred CeEEEEecchhHHHHhhhCC----------------------C--CCeEEEEecCcHHHHHHHHHHHHHhhhhcCC
Q psy15215 730 GYVLITEGYMDVIGLSQFGF----------------------F--ANSSYTCFDGDQAGRRAARRALEVCLLYATD 781 (1432)
Q Consensus 730 ~~~~~vEG~~D~ia~~~~g~----------------------~--~~~i~~~~D~D~aG~~a~~~~~~~~~~~~~~ 781 (1432)
+.+|||||++||++++++|+ . ..+||+|||+|.||++++.+..+.|...|+.
T Consensus 1 k~viIvEG~~D~~~l~~~g~~~~v~~~g~~~~~~~~~~~~~~~~~~~~Vii~~D~D~~G~~~a~~i~~~l~~~gi~ 76 (81)
T PF13662_consen 1 KEVIIVEGEFDAIALEQAGYKNVVAVLGGNLSPLDQILREKLEKKVKEVIIAFDNDKAGEKAAQKIAKKLLPLGIR 76 (81)
T ss_dssp --EEEESSHHHHHHHHHTT-TTEEEESSSS---HHHHHHHHHH---SEEEEEEESSHHHHHHHHHHHHHHG-----
T ss_pred CEEEEECCHHHHHHHHHhCCCeEEEECCCCCChHHHhChHhhhccCceEEEEeCcCHHHHHHHHHHHHHHHhhccc
Confidence 46899999999999999999 2 4899999999999999999999988877765
No 279
>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=98.67 E-value=5.6e-08 Score=82.67 Aligned_cols=54 Identities=19% Similarity=0.400 Sum_probs=46.5
Q ss_pred HHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Q psy15215 1357 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 1414 (1432)
Q Consensus 1357 ~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kL 1414 (1432)
++.|.++|+.|||++|.|+.++|+.|+ |+.|||+.+|+|.++|++++++|+++|
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 REALQQALAQLPERQREIFLLRYFQGM----SYAEIAEILGISESTVKRRLRRARKKL 54 (54)
T ss_dssp HHHHHHHHHCS-HHHHHHHHHHHTS-------HHHHHHHCTS-HHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCc----CHHHHHHHHCcCHHHHHHHHHHHHhhC
Confidence 357889999999999999999999999 999999999999999999999999987
No 280
>PF13362 Toprim_3: Toprim domain
Probab=98.50 E-value=3e-07 Score=88.37 Aligned_cols=73 Identities=21% Similarity=0.233 Sum_probs=62.6
Q ss_pred eEEEEecchhHHHH-hhhCC-------------------CCCeEEEEecCcHH--HHHHHHHHHHHhhhhcCCCceEEEe
Q psy15215 731 YVLITEGYMDVIGL-SQFGF-------------------FANSSYTCFDGDQA--GRRAARRALEVCLLYATDDKIIKFL 788 (1432)
Q Consensus 731 ~~~~vEG~~D~ia~-~~~g~-------------------~~~~i~~~~D~D~a--G~~a~~~~~~~~~~~~~~~~~~~~~ 788 (1432)
.++||||+.|++|+ ++.+- ...+|+++.|+|.+ |++++.++...+...|.. +.++
T Consensus 1 tl~i~EG~etals~~~~~~~~~~~a~~~~~nl~~~~~~~~~~~vii~~D~D~~~~G~~~a~~~~~~~~~~g~~---~~~~ 77 (96)
T PF13362_consen 1 TLIIAEGIETALSIAQQATGVPVVAALGAGNLKNVAIPEPGRRVIIAADNDKANEGQKAAEKAAERLEAAGIA---VSIV 77 (96)
T ss_pred CEEEEEhHHHHHHHHHhcCCCeEEEEEChhhhhhhcCCCCCCeEEEEECCCCchhhHHHHHHHHHHHHhCCCe---EEEE
Confidence 37999999999999 44322 56789999999999 999999999999887776 7777
Q ss_pred cC-CCCCCHHHHHHHhChh
Q psy15215 789 FL-PDKYDPDSYIRKFGYK 806 (1432)
Q Consensus 789 ~l-p~~~Dpde~~~~~g~~ 806 (1432)
.. |.|+|.+|+++.+|++
T Consensus 78 ~p~~~g~D~ND~l~~~G~e 96 (96)
T PF13362_consen 78 EPGPEGKDWNDLLQARGKE 96 (96)
T ss_pred CCCCCCchHHHHHHhhCCC
Confidence 77 6789999999999974
No 281
>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=98.47 E-value=3.9e-07 Score=77.51 Aligned_cols=54 Identities=19% Similarity=0.400 Sum_probs=46.2
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHH
Q psy15215 567 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 624 (1432)
Q Consensus 567 ~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kL 624 (1432)
++.|.++|++|||+++.|+.++|..|+ |+.|||+.+|+|+++|+++.++|+++|
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 REALQQALAQLPERQREIFLLRYFQGM----SYAEIAEILGISESTVKRRLRRARKKL 54 (54)
T ss_dssp HHHHHHHHHCS-HHHHHHHHHHHTS-------HHHHHHHCTS-HHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCc----CHHHHHHHHCcCHHHHHHHHHHHHhhC
Confidence 357889999999999999999999999 999999999999999999999999886
No 282
>cd01027 TOPRIM_RNase_M5_like TOPRIM_ RNase M5_like: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain found in Ribonuclease M5: (RNase M5) and other small primase-like proteins from bacteria and archaea. RNase M5 catalyzes the maturation of 5S rRNA in low G+C Gram-positive bacteria. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=98.42 E-value=3.8e-07 Score=83.98 Aligned_cols=48 Identities=25% Similarity=0.290 Sum_probs=43.6
Q ss_pred CeEEEEecchhHHHHhhhCC----------------------CCCeEEEEecCcHHHHHHHHHHHHHhhh
Q psy15215 730 GYVLITEGYMDVIGLSQFGF----------------------FANSSYTCFDGDQAGRRAARRALEVCLL 777 (1432)
Q Consensus 730 ~~~~~vEG~~D~ia~~~~g~----------------------~~~~i~~~~D~D~aG~~a~~~~~~~~~~ 777 (1432)
+.+|||||++|+++++++|+ ....||+++|+|.||.+++.+..+.+..
T Consensus 2 ~~vIiVEG~~D~~~l~~~g~~~~~i~t~Gt~~~~~~~~~l~~~~~~VIiltD~D~aG~~i~~~~~~~l~~ 71 (81)
T cd01027 2 GEVIIVEGKNDTESLKKLGIEAEIIETNGSIINKETIELIKKAYRGVIILTDPDRKGEKIRKKLSEYLSG 71 (81)
T ss_pred CeEEEEEchHHHHHHHHhCCCccEEEECCCcCCHHHHHHHHHhCCEEEEEECCCHHHHHHHHHHHHHhcc
Confidence 56899999999999999998 3588999999999999999999997754
No 283
>cd01029 TOPRIM_primases TOPRIM_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of bacterial DnaG-type primases and their homologs. Primases synthesize RNA primers for the initiation of DNA replication. DnaG type primases are often closely associated with DNA helicases in primosome assemblies. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. The prototypical bacterial primase. Escherichia coli DnaG is a single subunit enzyme.
Probab=98.40 E-value=6.5e-07 Score=82.73 Aligned_cols=52 Identities=46% Similarity=0.677 Sum_probs=45.8
Q ss_pred CeEEEEecchhHHHHhhhCC--------------------C-CCeEEEEecCcHHHHHHHHHHHHHhhhhcCC
Q psy15215 730 GYVLITEGYMDVIGLSQFGF--------------------F-ANSSYTCFDGDQAGRRAARRALEVCLLYATD 781 (1432)
Q Consensus 730 ~~~~~vEG~~D~ia~~~~g~--------------------~-~~~i~~~~D~D~aG~~a~~~~~~~~~~~~~~ 781 (1432)
+.++||||++|++++++.|+ . ..+|++|+|||.||++++.++.+.+...+..
T Consensus 1 ~~v~i~EG~~Dals~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~vii~~D~D~~G~~~~~~~~~~~~~~~~~ 73 (79)
T cd01029 1 DEVIIVEGYMDVLALHQAGIKNVVAALGTANTEEQLRLLKRFARTVILAFDNDEAGKKAAARALELLLALGGR 73 (79)
T ss_pred CEEEEEeCHHHHHHHHHcCCCCEEECCCccCcHHHHHHHHhcCCEEEEEECCCHHHHHHHHHHHHHHHHCCCE
Confidence 36899999999999999997 2 3899999999999999999999988876543
No 284
>PRK06930 positive control sigma-like factor; Validated
Probab=98.26 E-value=2.4e-06 Score=90.51 Aligned_cols=71 Identities=17% Similarity=0.310 Sum_probs=62.2
Q ss_pred hHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchhhh
Q psy15215 1347 PSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYY 1421 (1432)
Q Consensus 1347 p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~~~ 1421 (1432)
|.+..........+..+++.|||+++.||.|+|+.|+ |++|||+.||+|.++|++++++|+++|+......
T Consensus 95 ~~~~~~~~e~~~~l~~al~~L~~rer~V~~L~~~eg~----s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l~~~ 165 (170)
T PRK06930 95 EPESVISEWDKIRIEDALSVLTEREKEVYLMHRGYGL----SYSEIADYLNIKKSTVQSMIERAEKKIARQINES 165 (170)
T ss_pred ChhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHh
Confidence 3344455566788999999999999999999999888 9999999999999999999999999999866543
No 285
>PRK06930 positive control sigma-like factor; Validated
Probab=98.11 E-value=1e-05 Score=85.85 Aligned_cols=70 Identities=17% Similarity=0.344 Sum_probs=62.2
Q ss_pred hHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHHHH
Q psy15215 557 PSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLAHD 630 (1432)
Q Consensus 557 p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l~~ 630 (1432)
|.+..........+..+++.|||+++.||.|+|+.|+ |++|||+.||+|+++|+.+.++|+++|+..+..
T Consensus 95 ~~~~~~~~e~~~~l~~al~~L~~rer~V~~L~~~eg~----s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l~~ 164 (170)
T PRK06930 95 EPESVISEWDKIRIEDALSVLTEREKEVYLMHRGYGL----SYSEIADYLNIKKSTVQSMIERAEKKIARQINE 164 (170)
T ss_pred ChhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 3444455566788999999999999999999999888 999999999999999999999999999988764
No 286
>PRK00118 putative DNA-binding protein; Validated
Probab=98.08 E-value=1.1e-05 Score=77.27 Aligned_cols=63 Identities=14% Similarity=0.216 Sum_probs=55.9
Q ss_pred HHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchhhhh
Q psy15215 1356 MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYK 1422 (1432)
Q Consensus 1356 ~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~~~~ 1422 (1432)
+...+....+.||++++.|+.++|+.|+ |..|||+.+|+|++||++++.+|+++||+....-+
T Consensus 7 ~~~l~d~~~~~L~ekqRevl~L~y~eg~----S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~~~~~ 69 (104)
T PRK00118 7 MNLLFDFYGSLLTEKQRNYMELYYLDDY----SLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEEKLH 69 (104)
T ss_pred HHHHHHHHhccCCHHHHHHHHHHHHcCC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHC
Confidence 3455666778999999999999999888 99999999999999999999999999999766543
No 287
>smart00493 TOPRIM topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins.
Probab=98.08 E-value=6e-06 Score=75.61 Aligned_cols=49 Identities=27% Similarity=0.280 Sum_probs=42.3
Q ss_pred CeEEEEecchhHHHHhhhCC-----------------------CC--CeEEEEecCcHHHHHHHHHHHHHhhhh
Q psy15215 730 GYVLITEGYMDVIGLSQFGF-----------------------FA--NSSYTCFDGDQAGRRAARRALEVCLLY 778 (1432)
Q Consensus 730 ~~~~~vEG~~D~ia~~~~g~-----------------------~~--~~i~~~~D~D~aG~~a~~~~~~~~~~~ 778 (1432)
+.++||||++|+++++++|+ .. .+|++|+|+|.+|++++.++.+.+...
T Consensus 1 ~~l~ivEg~~da~~~~~~~~~~~~~~~~~G~~~~~~~~~~l~~~~~~~~Iii~~D~D~~G~~~~~~i~~~l~~~ 74 (76)
T smart00493 1 KVLIIVEGPADAIALEKAGGFGGNVVALGGHLLKKEIIKLLKRLAKKKEVILATDPDREGEAIAWKLAELLKPA 74 (76)
T ss_pred CEEEEEcCHHHHHHHHHhcCCCEEEEEEeeeecHHHHHHHHHHHhcCCEEEEEcCCChhHHHHHHHHHHHhhhh
Confidence 46899999999999999986 12 569999999999999999998877653
No 288
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=97.87 E-value=3.7e-05 Score=64.83 Aligned_cols=54 Identities=33% Similarity=0.605 Sum_probs=50.0
Q ss_pred HHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhh
Q psy15215 1358 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 1415 (1432)
Q Consensus 1358 ~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr 1415 (1432)
..+..++..||+.++.++.++|..|+ |..+||+.+|+|..+|+++++++..+||
T Consensus 2 ~~~~~~~~~l~~~~~~~~~~~~~~~~----~~~~ia~~~~~s~~~i~~~~~~~~~~l~ 55 (55)
T cd06171 2 ERLEEALDKLPEREREVILLRFGEGL----SYEEIAEILGISRSTVRQRLHRALKKLR 55 (55)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHhcCC----CHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence 45778899999999999999998787 9999999999999999999999998875
No 289
>PRK00118 putative DNA-binding protein; Validated
Probab=97.85 E-value=8.7e-05 Score=71.22 Aligned_cols=66 Identities=15% Similarity=0.232 Sum_probs=57.7
Q ss_pred HHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHHHH--HHHHh
Q psy15215 566 MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLAHD--WLEQR 635 (1432)
Q Consensus 566 ~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l~~--~~~~~ 635 (1432)
+...+..+-..||++++.++.++|..|+ |..|||+.+|+|+++|.++.++++.+|++++.. +|+..
T Consensus 7 ~~~l~d~~~~~L~ekqRevl~L~y~eg~----S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~~~~~~~~~~ 74 (104)
T PRK00118 7 MNLLFDFYGSLLTEKQRNYMELYYLDDY----SLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEEKLHLYEKF 74 (104)
T ss_pred HHHHHHHHhccCCHHHHHHHHHHHHcCC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHChHHHH
Confidence 3455666778999999999999999888 999999999999999999999999999998875 45543
No 290
>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=97.64 E-value=9.5e-05 Score=74.64 Aligned_cols=58 Identities=26% Similarity=0.454 Sum_probs=49.8
Q ss_pred ccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchhhhhHHhhh
Q psy15215 1365 NSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFL 1427 (1432)
Q Consensus 1365 ~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~~~~l~~~~ 1427 (1432)
.-||++|++|+.|+ ..|+ |++|||+.||+|+++|++++++|+++||.....-.+-.++
T Consensus 5 ~~Lte~qr~VL~Lr-~~Gl----Tq~EIAe~LgiS~stV~~~e~ra~kkLr~a~~~~~l~~~~ 62 (137)
T TIGR00721 5 TFLTERQIKVLELR-EKGL----SQKEIAKELKTTRANVSAIEKRAMENIEKARNTLDFVKFI 62 (137)
T ss_pred CCCCHHHHHHHHHH-HcCC----CHHHHHHHHCcCHHHHHHHHHhHHHHHHHHhhHHHHHHHh
Confidence 35999999999996 4666 9999999999999999999999999999866555555555
No 291
>PRK04217 hypothetical protein; Provisional
Probab=97.61 E-value=8.4e-05 Score=72.07 Aligned_cols=61 Identities=25% Similarity=0.158 Sum_probs=54.1
Q ss_pred HccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchhhhhHHhhhc
Q psy15215 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLE 1428 (1432)
Q Consensus 1364 L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~~~~l~~~~~ 1428 (1432)
...|++.++.++.++|..+. |++|||+.+|||++||++++++|+++|+..+.......++.
T Consensus 40 ~~~Lt~eereai~l~~~eGl----S~~EIAk~LGIS~sTV~r~L~RArkkLre~L~~~~~~~~~~ 100 (110)
T PRK04217 40 PIFMTYEEFEALRLVDYEGL----TQEEAGKRMGVSRGTVWRALTSARKKVAQMLVEGRELIILP 100 (110)
T ss_pred cccCCHHHHHHHHHHHHcCC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhccceeEec
Confidence 46699999999999998888 99999999999999999999999999999887766555543
No 292
>PRK07078 hypothetical protein; Validated
Probab=97.60 E-value=0.00014 Score=93.81 Aligned_cols=86 Identities=21% Similarity=0.193 Sum_probs=70.2
Q ss_pred cCccccCchHhHHhhccCCeEEEEecchhHHHHhhhCC---------------------CCCeEEEEecCcHHHHHHHHH
Q psy15215 712 KSNELYGLFEAKNAIGKSGYVLITEGYMDVIGLSQFGF---------------------FANSSYTCFDGDQAGRRAARR 770 (1432)
Q Consensus 712 K~~~Ly~~~~a~~~~~~~~~~~~vEG~~D~ia~~~~g~---------------------~~~~i~~~~D~D~aG~~a~~~ 770 (1432)
+..-|||+..... ...|+||||.-||.++...|+ ...+||+++|+|.+|.+.|.+
T Consensus 177 ~~~pLy~lp~l~~----a~~V~lvEGEk~adal~~~g~~att~~~Ga~~~~~~~d~~~L~g~~VvI~pD~D~~G~~~a~~ 252 (759)
T PRK07078 177 EPRPLYNQPGLLS----AEQVVLVEGEKCAQALIDAGVVATTAMHGANAPVDKTDWSPLAGKAVLIWPDRDKPGWEYADR 252 (759)
T ss_pred CCcCCcCchhhhc----CCeEEEEeChHHHHHHHhcCCeEEecCCCCCCCcccccccccCCCEEEEEcCCChHHHHHHHH
Confidence 4456899976543 368999999999999999999 135799999999999999999
Q ss_pred HHHHhhhhcCCCceEEEec-----CCCCCCHHHHHHHhC
Q psy15215 771 ALEVCLLYATDDKIIKFLF-----LPDKYDPDSYIRKFG 804 (1432)
Q Consensus 771 ~~~~~~~~~~~~~~~~~~~-----lp~~~Dpde~~~~~g 804 (1432)
+...|...|.. +.++. +|.|.|..|++..+.
T Consensus 253 va~~l~~~g~~---~~~v~~p~~~~~~~~D~aD~~~~G~ 288 (759)
T PRK07078 253 AAQAILSAGAS---SCAVLLPPEDLPEGWDAADAIAEGF 288 (759)
T ss_pred HHHHHHhcCCe---EEEEEecCcccCcCCCHHHHHHcCC
Confidence 99999988876 33333 456899999998753
No 293
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=97.59 E-value=0.00013 Score=74.08 Aligned_cols=51 Identities=25% Similarity=0.407 Sum_probs=45.3
Q ss_pred ccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchhh
Q psy15215 1365 NSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRY 1420 (1432)
Q Consensus 1365 ~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~~ 1420 (1432)
..|||+|++||.++ ..|+ |++|||+.||+|+++|++++++|+++||+....
T Consensus 5 ~~Lt~rqreVL~lr-~~Gl----Tq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~t 55 (141)
T PRK03975 5 SFLTERQIEVLRLR-ERGL----TQQEIADILGTSRANVSSIEKRARENIEKARET 55 (141)
T ss_pred cCCCHHHHHHHHHH-HcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 46999999999995 4566 999999999999999999999999999985543
No 294
>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=97.56 E-value=0.00028 Score=67.04 Aligned_cols=48 Identities=19% Similarity=0.421 Sum_probs=40.3
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCc
Q psy15215 1366 SLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417 (1432)
Q Consensus 1366 ~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~ 1417 (1432)
-||++|+.++.++|..++ |+.|||+.+||||.+|...+.||.++|...
T Consensus 17 LLT~kQ~~~l~lyy~eDl----SlsEIAe~~~iSRqaV~d~ikr~~~~L~~y 64 (101)
T PF04297_consen 17 LLTEKQREILELYYEEDL----SLSEIAEELGISRQAVYDSIKRAEKKLEEY 64 (101)
T ss_dssp GS-HHHHHHHHHHCTS-------HHHHHHHCTS-HHHHHHHHHHHHHHHHHH
T ss_pred HCCHHHHHHHHHHHccCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 499999999999998888 999999999999999999999999998653
No 295
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=97.51 E-value=0.00022 Score=59.98 Aligned_cols=54 Identities=33% Similarity=0.605 Sum_probs=48.9
Q ss_pred HHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHH
Q psy15215 568 SVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625 (1432)
Q Consensus 568 ~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr 625 (1432)
+.+..++..||+.++.++.++|..|+ |..+||..+|+|..+|.++.+++..+|+
T Consensus 2 ~~~~~~~~~l~~~~~~~~~~~~~~~~----~~~~ia~~~~~s~~~i~~~~~~~~~~l~ 55 (55)
T cd06171 2 ERLEEALDKLPEREREVILLRFGEGL----SYEEIAEILGISRSTVRQRLHRALKKLR 55 (55)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHhcCC----CHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence 45778899999999999999998777 9999999999999999999999887764
No 296
>PF12965 DUF3854: Domain of unknown function (DUF3854); InterPro: IPR024385 This is a family of uncharacterised proteins, found by clustering human gut metagenomic sequences [].
Probab=97.50 E-value=0.00031 Score=71.01 Aligned_cols=76 Identities=25% Similarity=0.299 Sum_probs=63.6
Q ss_pred CeEEEEecchhHHHHhhhCC------------------------------------CCCeEEEEecCc------HHHHHH
Q psy15215 730 GYVLITEGYMDVIGLSQFGF------------------------------------FANSSYTCFDGD------QAGRRA 767 (1432)
Q Consensus 730 ~~~~~vEG~~D~ia~~~~g~------------------------------------~~~~i~~~~D~D------~aG~~a 767 (1432)
-.++|+||.+=+.++.+.|+ ...+|++|||.| ..-.+|
T Consensus 11 ~pi~ItEG~kKA~al~s~G~~aIalpGV~~~~~~~~~~~~~~~~~~L~p~L~~~~~~gr~v~iaFD~D~~~~Tn~~V~~a 90 (130)
T PF12965_consen 11 IPIWITEGAKKAGALLSQGYPAIALPGVNNGYRWPKDEGDKIGKRRLIPELAKLAKPGREVYIAFDADTKPKTNKNVRRA 90 (130)
T ss_pred ccEEEEechHHHHHHHcCCceEEEeCceeccccccccccccccchhcchhHHHhccCCceEEEEecCCCccchhHHHHHH
Confidence 46999999999999999988 135799999999 556677
Q ss_pred HHHHHHHhhhhcCCCceEEEecCC--CCCCHHHHHHHhChhhh
Q psy15215 768 ARRALEVCLLYATDDKIIKFLFLP--DKYDPDSYIRKFGYKIF 808 (1432)
Q Consensus 768 ~~~~~~~~~~~~~~~~~~~~~~lp--~~~Dpde~~~~~g~~~~ 808 (1432)
..+...+|...|.. |+++.+| .+|=.|||+.++|+++|
T Consensus 91 ~~~l~~~L~~~G~~---v~~~~w~~~~~KGiDD~l~~~G~~~f 130 (130)
T PF12965_consen 91 IKRLGKLLKEAGCK---VKIITWPPGEGKGIDDLLAAKGPDAF 130 (130)
T ss_pred HHHHHHHHHHCCCE---EEEEEeCCCCCCCHhHHHHhcCcccC
Confidence 77777777776665 9999999 56899999999999987
No 297
>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=97.41 E-value=0.00047 Score=57.58 Aligned_cols=48 Identities=25% Similarity=0.444 Sum_probs=44.1
Q ss_pred CCHHHHHHHHHHhcccCC---CCCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Q psy15215 1367 LTPRESKVLRMRFGIEMS---SDHTLEEVGKQFDVTRERIRQIEAKALRKL 1414 (1432)
Q Consensus 1367 L~~rer~Vl~lr~~~~~~---~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kL 1414 (1432)
||++|+++|..-|-.|.. ...|++|+|+.||||.+++.+++.+|.+||
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 799999999998887753 578999999999999999999999999987
No 298
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=97.25 E-value=0.0007 Score=57.83 Aligned_cols=51 Identities=31% Similarity=0.513 Sum_probs=44.3
Q ss_pred ccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchhh
Q psy15215 1365 NSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRY 1420 (1432)
Q Consensus 1365 ~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~~ 1420 (1432)
..||++|+.++.+ +..|+ |..|||+.+|+|+.+|+++.++++++|+-..+.
T Consensus 2 ~~l~~~e~~i~~~-~~~g~----s~~eia~~l~is~~tv~~~~~~~~~kl~~~~~~ 52 (58)
T smart00421 2 ASLTPREREVLRL-LAEGL----TNKEIAERLGISEKTVKTHLSNIMRKLGVRSRT 52 (58)
T ss_pred CCCCHHHHHHHHH-HHcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHH
Confidence 5699999999877 55555 999999999999999999999999999865553
No 299
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=97.20 E-value=0.00076 Score=68.57 Aligned_cols=51 Identities=25% Similarity=0.399 Sum_probs=45.7
Q ss_pred hcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHHHH
Q psy15215 575 NSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLAHD 630 (1432)
Q Consensus 575 ~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l~~ 630 (1432)
..|||+|++||.++ ..|+ |++|||+.||+|+++|++++++++++|++....
T Consensus 5 ~~Lt~rqreVL~lr-~~Gl----Tq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~t 55 (141)
T PRK03975 5 SFLTERQIEVLRLR-ERGL----TQQEIADILGTSRANVSSIEKRARENIEKARET 55 (141)
T ss_pred cCCCHHHHHHHHHH-HcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 45999999999995 4555 999999999999999999999999999988765
No 300
>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=97.20 E-value=0.00098 Score=68.11 Aligned_cols=61 Identities=10% Similarity=0.189 Sum_probs=55.0
Q ss_pred HHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCc
Q psy15215 1355 SMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417 (1432)
Q Consensus 1355 ~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~ 1417 (1432)
.....|..+|+.|++.++.||.++|+.+. .+|..+||..||+|+.+|.++..+|+.+|+..
T Consensus 71 ~~~~~I~~~l~~Ld~~er~II~~rY~~~~--~~t~~~Ia~~l~iS~~t~~r~r~~~l~kla~~ 131 (134)
T TIGR01636 71 RNRDAIENCLNEADEQTRVIIQELYMKKR--PLTLVGLAQQLFISKSTAYRLRNHIIEAVAEE 131 (134)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHccCC--CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 45688999999999999999999997554 37999999999999999999999999999863
No 301
>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=97.19 E-value=0.00072 Score=60.24 Aligned_cols=47 Identities=11% Similarity=0.087 Sum_probs=41.5
Q ss_pred HHHHHHccCCHHHHHHHHHH-hcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q psy15215 1359 VVKDILNSLTPRESKVLRMR-FGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409 (1432)
Q Consensus 1359 ~l~~~L~~L~~rer~Vl~lr-~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~r 1409 (1432)
.+.+-|+.||++.+.++.|. |..|+ |++|||+.+|+|+.+|++++++
T Consensus 8 ~~~~~l~~l~~~~r~af~L~R~~eGl----S~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 8 KLAERLTWVDSLAEAAAALAREEAGK----TASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred hHHHHHhcCCHHHHHHHHHHHHHcCC----CHHHHHHHHCcCHHHHHHHHhc
Confidence 45667899999999999994 56777 9999999999999999998874
No 302
>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=97.18 E-value=0.0016 Score=61.89 Aligned_cols=54 Identities=19% Similarity=0.416 Sum_probs=42.2
Q ss_pred HHHHHh-cCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHH
Q psy15215 570 VKDILN-SLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPL 627 (1432)
Q Consensus 570 l~~~L~-~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~ 627 (1432)
+-.... -||++|+.++.++|..++ |+.|||+.+|||+..|....+||..+|...
T Consensus 10 L~d~Yg~LLT~kQ~~~l~lyy~eDl----SlsEIAe~~~iSRqaV~d~ikr~~~~L~~y 64 (101)
T PF04297_consen 10 LFDFYGELLTEKQREILELYYEEDL----SLSEIAEELGISRQAVYDSIKRAEKKLEEY 64 (101)
T ss_dssp HHHHHGGGS-HHHHHHHHHHCTS-------HHHHHHHCTS-HHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHCCHHHHHHHHHHHccCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 333444 499999999999998888 999999999999999999999999888654
No 303
>PRK04217 hypothetical protein; Provisional
Probab=97.17 E-value=0.00087 Score=65.13 Aligned_cols=55 Identities=24% Similarity=0.185 Sum_probs=49.8
Q ss_pred HhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHHHHHH
Q psy15215 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLAHDWL 632 (1432)
Q Consensus 574 L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l~~~~ 632 (1432)
...|++.++.++.++|..++ |++|||+.+|+|+++|+++.++|.++|++.+....
T Consensus 40 ~~~Lt~eereai~l~~~eGl----S~~EIAk~LGIS~sTV~r~L~RArkkLre~L~~~~ 94 (110)
T PRK04217 40 PIFMTYEEFEALRLVDYEGL----TQEEAGKRMGVSRGTVWRALTSARKKVAQMLVEGR 94 (110)
T ss_pred cccCCHHHHHHHHHHHHcCC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhcc
Confidence 34599999999999998888 99999999999999999999999999998886443
No 304
>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=97.01 E-value=0.0024 Score=61.67 Aligned_cols=55 Identities=29% Similarity=0.552 Sum_probs=50.0
Q ss_pred HHHHHHHHHccCC-HHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Q psy15215 1356 MRSVVKDILNSLT-PRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 1414 (1432)
Q Consensus 1356 ~~~~l~~~L~~L~-~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kL 1414 (1432)
.+..+..++++|+ +.+|.||.++|..++ +..+|+..||+|+.++-.+..+|++.|
T Consensus 44 ~k~ei~~~I~~l~d~~~r~iL~~~Yi~~~----~~~~I~~~l~~S~~t~yr~~~~Al~~L 99 (100)
T PF07374_consen 44 EKLEIRRAINKLEDPDERLILRMRYINKL----TWEQIAEELNISRRTYYRIHKKALKEL 99 (100)
T ss_pred HHHHHHHHHHHccChhHHHHHHHHHHcCC----CHHHHHHHHCCCHHHHHHHHHHHHHhc
Confidence 4566888889986 899999999999888 999999999999999999999999886
No 305
>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=97.01 E-value=0.0023 Score=65.45 Aligned_cols=62 Identities=10% Similarity=0.163 Sum_probs=55.2
Q ss_pred HHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHH
Q psy15215 565 SMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLA 628 (1432)
Q Consensus 565 ~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l 628 (1432)
...+.|..+|+.|++.++.||.++|+.+. .+|..+||..+|+|..++.++..+++.+|...+
T Consensus 71 ~~~~~I~~~l~~Ld~~er~II~~rY~~~~--~~t~~~Ia~~l~iS~~t~~r~r~~~l~kla~~l 132 (134)
T TIGR01636 71 RNRDAIENCLNEADEQTRVIIQELYMKKR--PLTLVGLAQQLFISKSTAYRLRNHIIEAVAEEL 132 (134)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHccCC--CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 45678999999999999999999997554 379999999999999999999999999998754
No 306
>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=96.99 E-value=0.0022 Score=54.67 Aligned_cols=50 Identities=30% Similarity=0.407 Sum_probs=43.6
Q ss_pred CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchhhh
Q psy15215 1367 LTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYY 1421 (1432)
Q Consensus 1367 L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~~~ 1421 (1432)
||++++.++.+. ..|+ |.++||+.+|+|+.+|+++.++++++|+-.....
T Consensus 1 l~~~e~~i~~~~-~~~~----s~~eia~~l~~s~~tv~~~~~~~~~~l~~~~~~~ 50 (57)
T cd06170 1 LTPREREVLRLL-AEGK----TNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQ 50 (57)
T ss_pred CCHHHHHHHHHH-HcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHhCCCCHHH
Confidence 689999999874 4555 9999999999999999999999999999876543
No 307
>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=96.94 E-value=0.0014 Score=61.20 Aligned_cols=68 Identities=19% Similarity=0.284 Sum_probs=54.1
Q ss_pred HHHHHHHHhc-CCHHHHHHHHHHhhccc---CCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHHHHHHHHh
Q psy15215 567 RSVVKDILNS-LTPRESKVLRMRFGIEM---SSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLAHDWLEQR 635 (1432)
Q Consensus 567 ~~~l~~~L~~-L~~rer~Vl~lr~~~~~---~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l~~~~~~~ 635 (1432)
.+.+...|.. |||+|+.++.+||++-. ..++|++|||+.+|||+.+|. +-.++++..-.....|++++
T Consensus 22 ~~~l~~~l~~lLTp~E~~~l~~R~~i~~~Ll~~~~tQrEIa~~lGiS~atIs-R~sn~lk~~~~~~~~~l~~~ 93 (94)
T TIGR01321 22 EDDMQLLLELILTRSEREDLGDRIRIVNELLNGNMSQREIASKLGVSIATIT-RGSNNLKTMDPNFKQFLRKK 93 (94)
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHhCCChhhhh-HHHhhcccCCHHHHHHHHhh
Confidence 4567777855 99999999999999865 578899999999999999997 45566665556666676654
No 308
>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=96.94 E-value=0.0016 Score=65.89 Aligned_cols=48 Identities=29% Similarity=0.476 Sum_probs=43.5
Q ss_pred cCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHH
Q psy15215 576 SLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLA 628 (1432)
Q Consensus 576 ~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l 628 (1432)
.||++|++|+.|+ ..|+ |++|||+.+|+|+++|++++++|+++|+...
T Consensus 6 ~Lte~qr~VL~Lr-~~Gl----Tq~EIAe~LgiS~stV~~~e~ra~kkLr~a~ 53 (137)
T TIGR00721 6 FLTERQIKVLELR-EKGL----SQKEIAKELKTTRANVSAIEKRAMENIEKAR 53 (137)
T ss_pred CCCHHHHHHHHHH-HcCC----CHHHHHHHHCcCHHHHHHHHHhHHHHHHHHh
Confidence 4999999999996 4555 9999999999999999999999999999754
No 309
>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=96.85 E-value=0.0028 Score=54.70 Aligned_cols=53 Identities=25% Similarity=0.365 Sum_probs=43.3
Q ss_pred ccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchhhhh
Q psy15215 1365 NSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYK 1422 (1432)
Q Consensus 1365 ~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~~~~ 1422 (1432)
..||++|..|+.+-. .|+ |.+|||..+|+|..||++...++++||.-..+..-
T Consensus 2 ~~LT~~E~~vl~~l~-~G~----~~~eIA~~l~is~~tV~~~~~~i~~Kl~~~~~~~l 54 (58)
T PF00196_consen 2 PSLTERELEVLRLLA-QGM----SNKEIAEELGISEKTVKSHRRRIMKKLGVKNRAEL 54 (58)
T ss_dssp GSS-HHHHHHHHHHH-TTS-----HHHHHHHHTSHHHHHHHHHHHHHHHHT-SSHHHH
T ss_pred CccCHHHHHHHHHHH-hcC----CcchhHHhcCcchhhHHHHHHHHHHHhCCCCHHHH
Confidence 579999999998753 444 99999999999999999999999999987766653
No 310
>cd00188 TOPRIM Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from bacterial and archaea, and bacterial DNA repair proteins of the RecR/M family. This domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases and in strand joining in topoisomerases and, as a general acid in strand cleavage by topisomerases and nucleases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=96.79 E-value=0.0036 Score=57.37 Aligned_cols=48 Identities=31% Similarity=0.321 Sum_probs=40.8
Q ss_pred CeEEEEecchhHHHHhhhCC-------------------------CCCeEEEEecCcHHHHHHHHHHHHHhhh
Q psy15215 730 GYVLITEGYMDVIGLSQFGF-------------------------FANSSYTCFDGDQAGRRAARRALEVCLL 777 (1432)
Q Consensus 730 ~~~~~vEG~~D~ia~~~~g~-------------------------~~~~i~~~~D~D~aG~~a~~~~~~~~~~ 777 (1432)
+.++||||..|++++++.|. ...+|++++|+|.+|..++......+..
T Consensus 1 ~~viivEg~~d~~~l~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~~v~i~~D~D~~g~~~~~~~~~~~~~ 73 (83)
T cd00188 1 KKLIIVEGPSDALALAQAGGYGGAVVALGGHALNKTRELLKRLLGEAKEVIIATDADREGEAIALRLLELLKS 73 (83)
T ss_pred CEEEEEecHHHHHHHHHHcCCCEEEEEEccEEcHHHHHHHHHHhcCCCEEEEEcCCChhHHHHHHHHHHHHHh
Confidence 36899999999999999876 2389999999999999888877776654
No 311
>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=96.75 E-value=0.004 Score=52.14 Aligned_cols=49 Identities=24% Similarity=0.441 Sum_probs=44.2
Q ss_pred CCHHHHHHHHHHhhccc---CCCCcHHHHHhhcccchhHHHHHHHHHHHHHH
Q psy15215 577 LTPRESKVLRMRFGIEM---SSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625 (1432)
Q Consensus 577 L~~rer~Vl~lr~~~~~---~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr 625 (1432)
||++|+++|..-|-.|. ....|+.|+|+.||||.+++..+.++|.++|-
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~LRrae~kli 52 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSEHLRRAERKLI 52 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Confidence 79999999999988775 34689999999999999999999999999874
No 312
>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=96.72 E-value=0.0028 Score=56.54 Aligned_cols=47 Identities=11% Similarity=0.087 Sum_probs=40.8
Q ss_pred HHHHHHhcCCHHHHHHHHHH-hhcccCCCCcHHHHHhhcccchhHHHHHHHH
Q psy15215 569 VVKDILNSLTPRESKVLRMR-FGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 619 (1432)
Q Consensus 569 ~l~~~L~~L~~rer~Vl~lr-~~~~~~~~~t~~EIa~~l~is~~~v~~~~~r 619 (1432)
.+..-|+.||++.+.++.|. |..|+ |++|||+.+|+|+.+|+++.++
T Consensus 8 ~~~~~l~~l~~~~r~af~L~R~~eGl----S~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 8 KLAERLTWVDSLAEAAAALAREEAGK----TASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred hHHHHHhcCCHHHHHHHHHHHHHcCC----CHHHHHHHHCcCHHHHHHHHhc
Confidence 45667899999999999995 56777 9999999999999999987663
No 313
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=96.68 E-value=0.0039 Score=64.46 Aligned_cols=53 Identities=17% Similarity=0.285 Sum_probs=46.6
Q ss_pred ccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchhhhh
Q psy15215 1365 NSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYK 1422 (1432)
Q Consensus 1365 ~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~~~~ 1422 (1432)
+.|||||++||.+- .+|+|.+|||+.|++|..||+....++++||.-..+...
T Consensus 132 ~~LSpRErEVLrLL-----AqGkTnKEIAe~L~IS~rTVkth~srImkKLgV~SRaEL 184 (198)
T PRK15201 132 RHFSVTERHLLKLI-----ASGYHLSETAALLSLSEEQTKSLRRSIMRKLHVKTEQQF 184 (198)
T ss_pred CCCCHHHHHHHHHH-----HCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCHHHH
Confidence 34999999999985 345599999999999999999999999999998777664
No 314
>COG4941 Predicted RNA polymerase sigma factor containing a TPR repeat domain [Transcription]
Probab=96.68 E-value=0.034 Score=63.04 Aligned_cols=161 Identities=14% Similarity=0.151 Sum_probs=108.9
Q ss_pred HHHHHHHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHHHHHHhccccccccc
Q psy15215 1192 KREMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 1271 (1432)
Q Consensus 1192 ~~~Li~~~~~lV~~ia~~y~~~~~~~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~~ 1271 (1432)
.+..+..-.+.++.---+|+.+-...++.+||.|+...+.-.+=-+.+ .-..|++..-|+.-.|.+|+.++.-+.|.+
T Consensus 7 ie~~~r~~~~r~~a~L~r~~rd~dlAEEa~~dA~~~Ale~WPr~G~P~--~PaAWL~~v~R~~aiD~~Rr~~~~~~~~~e 84 (415)
T COG4941 7 IEAAARIERPRAMAALARYLRDLDLAEEALQDAFAAALERWPRAGPPR--NPAAWLIAVGRNRAIDRVRRRARRDAAPPE 84 (415)
T ss_pred HHHHHHHhhhHHHHHHHHHhcccchHHHHHHHHHHHHHHhCcccCCCC--ChHHHHHHHHhhhHHHHHHHHHHhccCChh
Confidence 344555555666666667777777899999999996666555444433 357899999999999999998863332221
Q ss_pred HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHHH
Q psy15215 1272 MIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAA 1351 (1432)
Q Consensus 1272 ~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~~d~i~d~~~~~p~~~~ 1351 (1432)
. .+|.+ ++.....+...| +.+
T Consensus 85 l-----------------------------------------------~~~~e-----~~e~~~a~~~~d-------~~i 105 (415)
T COG4941 85 L-----------------------------------------------LLSDE-----DEEMEEAEALDD-------EHI 105 (415)
T ss_pred h-----------------------------------------------ccccc-----chhhhccccccc-------ccc
Confidence 0 01110 011101110111 111
Q ss_pred HHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCc
Q psy15215 1352 LNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417 (1432)
Q Consensus 1352 ~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~ 1417 (1432)
....++-.+-.|---|||.+|--|.||...|. |..|||.-|=|+..++-|++.||.++++..
T Consensus 106 ~Dd~LRLiFvccHPal~~~~riALtLR~v~GL----s~~eIArAFLv~e~am~QRivRAK~ri~~a 167 (415)
T COG4941 106 RDDRLRLIFVCCHPALPPEQRIALTLRLVGGL----STAEIARAFLVPEAAMAQRIVRAKARIREA 167 (415)
T ss_pred chhhHHhhhhhcCCCCChhhHHHHHHHHHcCC----cHHHHHHHHcCCcHHHHHHHHHHHHHHHhc
Confidence 22234444555555699999999999999999 999999999999999999999999999863
No 315
>COG4566 TtrR Response regulator [Signal transduction mechanisms]
Probab=96.66 E-value=0.0073 Score=63.42 Aligned_cols=69 Identities=19% Similarity=0.317 Sum_probs=59.1
Q ss_pred HHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchhhhhHHhhh
Q psy15215 1354 ASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFL 1427 (1432)
Q Consensus 1354 ~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~~~~l~~~~ 1427 (1432)
......+...+++||||||+|+..-- .|. ..++||..||+|..||....++.++||+..+-+..++-++
T Consensus 130 ~~~~~~~~~~l~tLT~RERqVl~~vV-~G~----~NKqIA~dLgiS~rTVe~HRanvM~Km~a~SlaeLvr~a~ 198 (202)
T COG4566 130 ADRQAAIRARLATLTPRERQVLDLVV-RGL----MNKQIAFDLGISERTVELHRANVMEKMQARSLAELVRMAL 198 (202)
T ss_pred HHHHHHHHHHHHhcCHHHHHHHHHHH-cCc----ccHHHHHHcCCchhhHHHHHHHHHHHHhhccHHHHHHHHH
Confidence 34567889999999999999998764 444 9999999999999999999999999999887777666554
No 316
>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=96.62 E-value=0.0068 Score=58.59 Aligned_cols=55 Identities=29% Similarity=0.552 Sum_probs=49.6
Q ss_pred HHHHHHHHHhcCC-HHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHH
Q psy15215 566 MRSVVKDILNSLT-PRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKL 624 (1432)
Q Consensus 566 ~~~~l~~~L~~L~-~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kL 624 (1432)
.+..+..++++|+ +.+|.||.|+|..++ +..+|+..||+|..++...+.+|++.|
T Consensus 44 ~k~ei~~~I~~l~d~~~r~iL~~~Yi~~~----~~~~I~~~l~~S~~t~yr~~~~Al~~L 99 (100)
T PF07374_consen 44 EKLEIRRAINKLEDPDERLILRMRYINKL----TWEQIAEELNISRRTYYRIHKKALKEL 99 (100)
T ss_pred HHHHHHHHHHHccChhHHHHHHHHHHcCC----CHHHHHHHHCCCHHHHHHHHHHHHHhc
Confidence 3456888899986 899999999999888 999999999999999999999999876
No 317
>PRK01381 Trp operon repressor; Provisional
Probab=96.54 E-value=0.0042 Score=58.47 Aligned_cols=75 Identities=24% Similarity=0.341 Sum_probs=60.3
Q ss_pred HHHHHHHHHHHHhc-CCHHHHHHHHHHhhccc---CCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q psy15215 563 NASMRSVVKDILNS-LTPRESKVLRMRFGIEM---SSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLAHDWLEQRTHQ 638 (1432)
Q Consensus 563 ~~~~~~~l~~~L~~-L~~rer~Vl~lr~~~~~---~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l~~~~~~~l~~ 638 (1432)
...-.+.+...|.. |||+|+..|..||++-. ..++|+.|||+.+|+|..+|. +-+++|+..-.....|+++.+..
T Consensus 18 ~a~~~~~~~~~l~~llTp~Er~al~~R~~I~~~L~~g~~sQREIa~~lGvSiaTIT-Rgsn~Lk~~~~~~k~~l~~~l~~ 96 (99)
T PRK01381 18 QAFEEDLHLPLLTLLLTPDEREALGTRVRIVEELLRGELSQREIKQELGVGIATIT-RGSNSLKTAPPEFKEWLEQQLLK 96 (99)
T ss_pred HhccHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHcCCcCHHHHHHHhCCceeeeh-hhHHHhccCCHHHHHHHHHHhcc
Confidence 33445667777877 99999999999999754 446899999999999999986 56777887777788888887654
No 318
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=96.53 E-value=0.0044 Score=52.79 Aligned_cols=46 Identities=30% Similarity=0.554 Sum_probs=40.4
Q ss_pred hcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHH
Q psy15215 575 NSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625 (1432)
Q Consensus 575 ~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr 625 (1432)
..||++|+.++.+ +..|+ |..|||+.+|+|+.+|+++..+++.+|.
T Consensus 2 ~~l~~~e~~i~~~-~~~g~----s~~eia~~l~is~~tv~~~~~~~~~kl~ 47 (58)
T smart00421 2 ASLTPREREVLRL-LAEGL----TNKEIAERLGISEKTVKTHLSNIMRKLG 47 (58)
T ss_pred CCCCHHHHHHHHH-HHcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHC
Confidence 4699999999877 54555 9999999999999999999999988885
No 319
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=96.45 E-value=0.0064 Score=65.95 Aligned_cols=59 Identities=15% Similarity=0.147 Sum_probs=51.0
Q ss_pred HHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchhhhhHH
Q psy15215 1361 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLK 1424 (1432)
Q Consensus 1361 ~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~~~~l~ 1424 (1432)
.++...|||||++||.+. ..|+ |.+|||+.|++|..||+....+.++||--..+...+.
T Consensus 138 ~~~~~~LS~RE~eVL~Li-a~G~----SnkEIA~~L~IS~~TVk~hvs~I~~KLgv~sR~eLv~ 196 (217)
T PRK13719 138 LEAKNKVTKYQNDVFILY-SFGF----SHEYIAQLLNITVGSSKNKISEILKFFGISSRDELLI 196 (217)
T ss_pred hhccCCCCHHHHHHHHHH-HCCC----CHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCHHHHHH
Confidence 456788999999999985 3455 9999999999999999999999999999887777543
No 320
>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=96.42 E-value=0.0061 Score=52.60 Aligned_cols=46 Identities=24% Similarity=0.430 Sum_probs=39.2
Q ss_pred hcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHH
Q psy15215 575 NSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625 (1432)
Q Consensus 575 ~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr 625 (1432)
..||++|..||.+-. .|+|.+|||..+|+|+.+|+.+..++++||.
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 579999999998753 4559999999999999999999999999986
No 321
>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=96.31 E-value=0.0059 Score=57.18 Aligned_cols=55 Identities=20% Similarity=0.239 Sum_probs=44.4
Q ss_pred HHHHHHHHcc-CCHHHHHHHHHHhcccC---CCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q psy15215 1357 RSVVKDILNS-LTPRESKVLRMRFGIEM---SSDHTLEEVGKQFDVTRERIRQIEAKALR 1412 (1432)
Q Consensus 1357 ~~~l~~~L~~-L~~rer~Vl~lr~~~~~---~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~ 1412 (1432)
.+.+...|.. |||+|+.++.+||++-. ..++|++|||+.+|||+.+|.+. +++++
T Consensus 22 ~~~l~~~l~~lLTp~E~~~l~~R~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~-sn~lk 80 (94)
T TIGR01321 22 EDDMQLLLELILTRSEREDLGDRIRIVNELLNGNMSQREIASKLGVSIATITRG-SNNLK 80 (94)
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHhCCChhhhhHH-Hhhcc
Confidence 4556667754 99999999999999875 57889999999999999999853 34433
No 322
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=96.24 E-value=0.007 Score=62.63 Aligned_cols=46 Identities=20% Similarity=0.366 Sum_probs=41.6
Q ss_pred cCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHH
Q psy15215 576 SLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRP 626 (1432)
Q Consensus 576 ~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~ 626 (1432)
.|||||++||.+. ..|+|.+|||+.|++|+.+|+....++++||.-
T Consensus 133 ~LSpRErEVLrLL-----AqGkTnKEIAe~L~IS~rTVkth~srImkKLgV 178 (198)
T PRK15201 133 HFSVTERHLLKLI-----ASGYHLSETAALLSLSEEQTKSLRRSIMRKLHV 178 (198)
T ss_pred CCCHHHHHHHHHH-----HCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 4999999999986 456699999999999999999999999999963
No 323
>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=96.14 E-value=0.01 Score=66.99 Aligned_cols=54 Identities=19% Similarity=0.188 Sum_probs=48.4
Q ss_pred HccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchhhhh
Q psy15215 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYK 1422 (1432)
Q Consensus 1364 L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~~~~ 1422 (1432)
+..||++|++|+.+.. .|+ |..|||+.||||..||+..+.++++||.-..+...
T Consensus 188 ~~~LT~RE~evl~l~a-~G~----s~~eIA~~L~IS~~TVk~hl~~i~~KL~v~nr~qA 241 (247)
T TIGR03020 188 AGLITAREAEILAWVR-DGK----TNEEIAAILGISSLTVKNHLQHIFKKLDVRNRAQA 241 (247)
T ss_pred ccCCCHHHHHHHHHHH-CCC----CHHHHHHHHCcCHHHHHHHHHHHHHHhCCCCHHHH
Confidence 4579999999999954 555 99999999999999999999999999998877764
No 324
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=96.13 E-value=0.0085 Score=66.33 Aligned_cols=51 Identities=20% Similarity=0.318 Sum_probs=45.0
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchhhh
Q psy15215 1366 SLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYY 1421 (1432)
Q Consensus 1366 ~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~~~ 1421 (1432)
.|||||++||.+. . +|+|.+|||++||+|..||+...++.++||.-..|..
T Consensus 137 ~LT~RE~eVL~ll-a----~G~snkeIA~~L~iS~~TVk~h~~~I~~KL~v~nr~~ 187 (207)
T PRK15411 137 SLSRTESSMLRMW-M----AGQGTIQISDQMNIKAKTVSSHKGNIKRKIKTHNKQV 187 (207)
T ss_pred cCCHHHHHHHHHH-H----cCCCHHHHHHHcCCCHHHHHHHHHHHHHHhCCCcHHH
Confidence 4999999999885 3 4559999999999999999999999999998766643
No 325
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=96.10 E-value=0.0081 Score=48.60 Aligned_cols=41 Identities=20% Similarity=0.367 Sum_probs=24.5
Q ss_pred ccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q psy15215 1365 NSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409 (1432)
Q Consensus 1365 ~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~r 1409 (1432)
.+|++.||..|...+-.|+ |..+||+.||+|++||...+.|
T Consensus 3 ~~Lt~~eR~~I~~l~~~G~----s~~~IA~~lg~s~sTV~relkR 43 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQGM----SIREIAKRLGRSRSTVSRELKR 43 (44)
T ss_dssp ---------HHHHHHCS-------HHHHHHHTT--HHHHHHHHHH
T ss_pred cchhhhHHHHHHHHHHcCC----CHHHHHHHHCcCcHHHHHHHhc
Confidence 4699999999988886666 9999999999999999998876
No 326
>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=96.07 E-value=0.01 Score=66.92 Aligned_cols=54 Identities=17% Similarity=0.209 Sum_probs=48.1
Q ss_pred HccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchhhhh
Q psy15215 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYK 1422 (1432)
Q Consensus 1364 L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~~~~ 1422 (1432)
...||++|++||.+. ..|+ |..|||+.||+|..||+..+.++++||+-..+...
T Consensus 169 ~~~Lt~re~evl~~~-a~G~----t~~eIa~~l~is~~Tv~~~l~~~~~kl~~~~~~~a 222 (232)
T TIGR03541 169 AGVLSEREREVLAWT-ALGR----RQADIAAILGISERTVENHLRSARRKLGVATTAQA 222 (232)
T ss_pred hccCCHHHHHHHHHH-HCCC----CHHHHHHHHCcCHHHHHHHHHHHHHHHCCCCHHHH
Confidence 357999999999995 4565 99999999999999999999999999998777664
No 327
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=95.98 E-value=0.013 Score=64.77 Aligned_cols=55 Identities=22% Similarity=0.271 Sum_probs=47.1
Q ss_pred HccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchhhhhH
Q psy15215 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKL 1423 (1432)
Q Consensus 1364 L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~~~~l 1423 (1432)
...||+||++||.+-- . |+|.+|||++|++|..||+...++.++||--..+....
T Consensus 132 ~~~LT~RE~eVL~ll~-~----G~snkeIA~~L~iS~~TV~~h~~~I~~KLgv~n~~eLv 186 (207)
T PRK11475 132 SRMLSPTEREILRFMS-R----GYSMPQIAEQLERNIKTIRAHKFNVMSKLGVSSDAGLL 186 (207)
T ss_pred cCCCCHHHHHHHHHHH-C----CCCHHHHHHHHCCCHHHHHHHHHHHHHHcCCCCHHHHH
Confidence 3469999999998853 4 45999999999999999999999999999876666543
No 328
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=95.97 E-value=0.014 Score=64.88 Aligned_cols=55 Identities=15% Similarity=0.165 Sum_probs=48.8
Q ss_pred HccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchhhhhH
Q psy15215 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKL 1423 (1432)
Q Consensus 1364 L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~~~~l 1423 (1432)
+..||++|++|+.+... |. |.+|||+.|++|..||+...+++++||.-..|.+..
T Consensus 153 ~~~Lt~rE~~Vl~l~~~-G~----s~~eIA~~L~iS~~TVk~~~~~i~~Kl~v~nr~elv 207 (216)
T PRK10100 153 SALLTHREKEILNKLRI-GA----SNNEIARSLFISENTVKTHLYNLFKKIAVKNRTQAV 207 (216)
T ss_pred cCCCCHHHHHHHHHHHc-CC----CHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCHHHHH
Confidence 34699999999999874 55 999999999999999999999999999987777754
No 329
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=95.97 E-value=0.014 Score=56.27 Aligned_cols=49 Identities=22% Similarity=0.264 Sum_probs=45.6
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCch
Q psy15215 1366 SLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418 (1432)
Q Consensus 1366 ~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~ 1418 (1432)
.|+..|-+.|+|.++.|+ |++|-|+++||||.|+..++..|++|+-...
T Consensus 41 ~L~~dElEAiRL~D~egl----~QeeaA~~MgVSR~T~~ril~~ARkKiA~AL 89 (106)
T PF02001_consen 41 VLTVDELEAIRLVDYEGL----SQEEAAERMGVSRPTFQRILESARKKIADAL 89 (106)
T ss_pred EeeHHHHHHHHHHHHcCC----CHHHHHHHcCCcHHHHHHHHHHHHHHHHHHH
Confidence 388999999999999999 9999999999999999999999999997644
No 330
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=95.95 E-value=0.013 Score=54.75 Aligned_cols=46 Identities=22% Similarity=0.394 Sum_probs=42.0
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhh
Q psy15215 1366 SLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 1415 (1432)
Q Consensus 1366 ~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr 1415 (1432)
-||.+|+..+.++|..+. |+.|||+.++|||++|...+.|+-..|-
T Consensus 17 LLT~KQ~~Y~~lyy~dDl----Sl~EIAee~~VSRqAIyDnIKr~~~~L~ 62 (105)
T COG2739 17 LLTKKQKNYLELYYLDDL----SLSEIAEEFNVSRQAIYDNIKRTEKILE 62 (105)
T ss_pred HHhHHHHHHHHHHHHhhc----cHHHHHHHhCccHHHHHHHHHHHHHHHH
Confidence 489999999999998888 9999999999999999999999876653
No 331
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=95.95 E-value=0.01 Score=64.42 Aligned_cols=50 Identities=14% Similarity=0.159 Sum_probs=44.6
Q ss_pred HHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHH
Q psy15215 571 KDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625 (1432)
Q Consensus 571 ~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr 625 (1432)
..+...|||||++||+|. ..|+|.+|||+.|++|+.||+.+..+.++||.
T Consensus 138 ~~~~~~LS~RE~eVL~Li-----a~G~SnkEIA~~L~IS~~TVk~hvs~I~~KLg 187 (217)
T PRK13719 138 LEAKNKVTKYQNDVFILY-----SFGFSHEYIAQLLNITVGSSKNKISEILKFFG 187 (217)
T ss_pred hhccCCCCHHHHHHHHHH-----HCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 456788999999999985 34559999999999999999999999999995
No 332
>COG4566 TtrR Response regulator [Signal transduction mechanisms]
Probab=95.94 E-value=0.024 Score=59.64 Aligned_cols=59 Identities=19% Similarity=0.351 Sum_probs=50.8
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHH
Q psy15215 564 ASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPL 627 (1432)
Q Consensus 564 ~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~ 627 (1432)
......+...+++||||||+||..-- .|+..++||..||+|+-||..+.++.++|++..
T Consensus 130 ~~~~~~~~~~l~tLT~RERqVl~~vV-----~G~~NKqIA~dLgiS~rTVe~HRanvM~Km~a~ 188 (202)
T COG4566 130 ADRQAAIRARLATLTPRERQVLDLVV-----RGLMNKQIAFDLGISERTVELHRANVMEKMQAR 188 (202)
T ss_pred HHHHHHHHHHHHhcCHHHHHHHHHHH-----cCcccHHHHHHcCCchhhHHHHHHHHHHHHhhc
Confidence 34567888999999999999998764 455999999999999999999999999998743
No 333
>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=95.91 E-value=0.015 Score=49.44 Aligned_cols=45 Identities=29% Similarity=0.434 Sum_probs=39.1
Q ss_pred CCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHH
Q psy15215 577 LTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRP 626 (1432)
Q Consensus 577 L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~ 626 (1432)
||++++.++.+. ..|+ |.++||+.+|+|+.+|+.+.+++++++..
T Consensus 1 l~~~e~~i~~~~-~~~~----s~~eia~~l~~s~~tv~~~~~~~~~~l~~ 45 (57)
T cd06170 1 LTPREREVLRLL-AEGK----TNKEIADILGISEKTVKTHLRNIMRKLGV 45 (57)
T ss_pred CCHHHHHHHHHH-HcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHhCC
Confidence 689999999874 4555 99999999999999999999999888764
No 334
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=95.89 E-value=0.025 Score=49.64 Aligned_cols=57 Identities=23% Similarity=0.370 Sum_probs=48.7
Q ss_pred ccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchhhhhHHhh
Q psy15215 1365 NSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIF 1426 (1432)
Q Consensus 1365 ~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~~~~l~~~ 1426 (1432)
..|+++|.+|+.+.- .++|..|||..+++|+.+|+....++.+||.-..+...+..+
T Consensus 3 ~~Lt~rE~~v~~l~~-----~G~s~~eia~~l~is~~tV~~h~~~i~~Kl~~~~r~~~~~~~ 59 (65)
T COG2771 3 ADLTPREREILRLVA-----QGKSNKEIARILGISEETVKTHLRNIYRKLGVKNRVELVALA 59 (65)
T ss_pred ccCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHH
Confidence 469999999997753 335999999999999999999999999999998887765544
No 335
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=95.85 E-value=0.015 Score=64.65 Aligned_cols=51 Identities=24% Similarity=0.414 Sum_probs=46.4
Q ss_pred cCCHHHHHHHHHHhcccCC---CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhC
Q psy15215 1366 SLTPRESKVLRMRFGIEMS---SDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 1416 (1432)
Q Consensus 1366 ~L~~rer~Vl~lr~~~~~~---~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~ 1416 (1432)
.||++|++||+.-|-.|.. ...|++|||+.||||.+++.++++||.+||=.
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLRrAe~Kl~~ 208 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLRRAERKLIE 208 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 6999999999999987753 67899999999999999999999999999844
No 336
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=95.81 E-value=0.012 Score=65.15 Aligned_cols=45 Identities=22% Similarity=0.380 Sum_probs=41.6
Q ss_pred cCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHH
Q psy15215 576 SLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625 (1432)
Q Consensus 576 ~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr 625 (1432)
.|||||++||.|. ..|+|.+|||++||+|..||+.+..+.++||.
T Consensus 137 ~LT~RE~eVL~ll-----a~G~snkeIA~~L~iS~~TVk~h~~~I~~KL~ 181 (207)
T PRK15411 137 SLSRTESSMLRMW-----MAGQGTIQISDQMNIKAKTVSSHKGNIKRKIK 181 (207)
T ss_pred cCCHHHHHHHHHH-----HcCCCHHHHHHHcCCCHHHHHHHHHHHHHHhC
Confidence 4999999999986 46669999999999999999999999999997
No 337
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=95.79 E-value=0.017 Score=64.03 Aligned_cols=56 Identities=25% Similarity=0.360 Sum_probs=48.5
Q ss_pred ccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchhhhhHHh
Q psy15215 1365 NSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKI 1425 (1432)
Q Consensus 1365 ~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~~~~l~~ 1425 (1432)
..||+||++||++- . .|+|.+|||++|++|..||+...++.++||.-..|......
T Consensus 147 ~~LT~RE~eVL~ll-a----~G~snkeIA~~L~iS~~TVk~h~~~i~~KL~v~~Rtea~~~ 202 (211)
T COG2197 147 ELLTPRELEVLRLL-A----EGLSNKEIAEELNLSEKTVKTHVSNILRKLGVRNRTEAAIR 202 (211)
T ss_pred CCCCHHHHHHHHHH-H----CCCCHHHHHHHHCCCHhHHHHHHHHHHHHcCCCCHHHHHHH
Confidence 56999999999884 3 44599999999999999999999999999998887765443
No 338
>PRK01381 Trp operon repressor; Provisional
Probab=95.74 E-value=0.017 Score=54.47 Aligned_cols=61 Identities=21% Similarity=0.255 Sum_probs=46.2
Q ss_pred HHHHHHHHHHHHHcc-CCHHHHHHHHHHhcccC---CCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q psy15215 1352 LNASMRSVVKDILNS-LTPRESKVLRMRFGIEM---SSDHTLEEVGKQFDVTRERIRQIEAKALRK 1413 (1432)
Q Consensus 1352 ~~~~~~~~l~~~L~~-L~~rer~Vl~lr~~~~~---~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~k 1413 (1432)
......+.+...|.. |||+|+..|..||++-. ..++|+.|||+.+|||+.+|. +-+++|+.
T Consensus 17 ~~a~~~~~~~~~l~~llTp~Er~al~~R~~I~~~L~~g~~sQREIa~~lGvSiaTIT-Rgsn~Lk~ 81 (99)
T PRK01381 17 KQAFEEDLHLPLLTLLLTPDEREALGTRVRIVEELLRGELSQREIKQELGVGIATIT-RGSNSLKT 81 (99)
T ss_pred HHhccHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHcCCcCHHHHHHHhCCceeeeh-hhHHHhcc
Confidence 334445666677776 99999999999998764 456899999999999999987 23444443
No 339
>COG4941 Predicted RNA polymerase sigma factor containing a TPR repeat domain [Transcription]
Probab=95.69 E-value=0.22 Score=56.82 Aligned_cols=187 Identities=13% Similarity=0.113 Sum_probs=119.1
Q ss_pred HHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHHHHHHhccccccchhHH
Q psy15215 404 EMTEANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMI 483 (1432)
Q Consensus 404 ~li~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~~i~~~~r~irip~~~~ 483 (1432)
..+..-.+.++.---+|+..-.-.++..|+.|+...+.-.+=-+- -.-..|++..-|+.-.+.+|++.+.-+.|.+
T Consensus 9 ~~~r~~~~r~~a~L~r~~rd~dlAEEa~~dA~~~Ale~WPr~G~P--~~PaAWL~~v~R~~aiD~~Rr~~~~~~~~~e-- 84 (415)
T COG4941 9 AAARIERPRAMAALARYLRDLDLAEEALQDAFAAALERWPRAGPP--RNPAAWLIAVGRNRAIDRVRRRARRDAAPPE-- 84 (415)
T ss_pred HHHHHhhhHHHHHHHHHhcccchHHHHHHHHHHHHHHhCcccCCC--CChHHHHHHHHhhhHHHHHHHHHHhccCChh--
Confidence 344444455555555677776779999999998644433322222 2457899999999999999988763222221
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccccCCCCChHHHHHH
Q psy15215 484 ETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIEDENMLAPSDAALN 563 (1432)
Q Consensus 484 ~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~i~d~~~~~p~~~~~~ 563 (1432)
+ .+|. +++.....+-..|. .+.+
T Consensus 85 -------------------------l--------------------~~~~-----e~~e~~~a~~~~d~-------~i~D 107 (415)
T COG4941 85 -------------------------L--------------------LLSD-----EDEEMEEAEALDDE-------HIRD 107 (415)
T ss_pred -------------------------h--------------------cccc-----cchhhhcccccccc-------ccch
Confidence 0 0111 01111111101111 1111
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHHHH-------HHHHhh
Q psy15215 564 ASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLAHD-------WLEQRT 636 (1432)
Q Consensus 564 ~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l~~-------~~~~~l 636 (1432)
..++-..-.+=--|||.+|--|.||...|. |..|||.-|=++..+..|+..||..+++..--. -+.+++
T Consensus 108 d~LRLiFvccHPal~~~~riALtLR~v~GL----s~~eIArAFLv~e~am~QRivRAK~ri~~agiPfevP~~~e~~ERl 183 (415)
T COG4941 108 DRLRLIFVCCHPALPPEQRIALTLRLVGGL----STAEIARAFLVPEAAMAQRIVRAKARIREAGIPFEVPGPQELPERL 183 (415)
T ss_pred hhHHhhhhhcCCCCChhhHHHHHHHHHcCC----cHHHHHHHHcCCcHHHHHHHHHHHHHHHhcCCCCcCCChhhHHHHH
Confidence 122222233334599999999999999999 999999999999999999999999999875432 355667
Q ss_pred hhhhhhHhhcCCCcccccccccCCCCCc
Q psy15215 637 HQNEKIIACSSDSSNHNEHVTNNNFPPG 664 (1432)
Q Consensus 637 ~~~~~~~~l~~l~~~~~~~f~~Gyap~~ 664 (1432)
...-+++|| -|.=||+..+
T Consensus 184 aaVl~~iYl---------iFneGysa~~ 202 (415)
T COG4941 184 AAVLQVIYL---------IFNEGYSATA 202 (415)
T ss_pred HHHHHHHHH---------HHhccccccC
Confidence 667777785 5777887663
No 340
>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=95.67 E-value=0.087 Score=53.82 Aligned_cols=63 Identities=11% Similarity=0.129 Sum_probs=52.9
Q ss_pred HHHHHHHHHH-hcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHHH
Q psy15215 565 SMRSVVKDIL-NSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLAH 629 (1432)
Q Consensus 565 ~~~~~l~~~L-~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l~ 629 (1432)
.....+..++ ..|++.+|.||.++|.... .++..+|+..+|+|..+......+|+.++...+.
T Consensus 67 ~~~~~i~~ai~~~l~~~~r~Il~~~Yl~~~--~~~~~~I~~~l~~s~~~~y~~k~~Al~~fA~~l~ 130 (132)
T TIGR01637 67 QEARAIVNAIVNQLDEISRQILYDKYLEPD--QKYDYQIMMELGYSHRQYYRIKKRALLRFATLYG 130 (132)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHHcCcc--ccchHHHHHHhCCcHHHHHHHHHHHHHHHHHHhC
Confidence 3455677777 9999999999999998721 3489999999999999999999999999876653
No 341
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=95.67 E-value=0.019 Score=63.82 Aligned_cols=54 Identities=26% Similarity=0.356 Sum_probs=46.7
Q ss_pred ccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchhhhhH
Q psy15215 1365 NSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKL 1423 (1432)
Q Consensus 1365 ~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~~~~l 1423 (1432)
..||+||++||.+-- .|+|.+|||+.|++|..||+.+.++.++||--..+...+
T Consensus 149 ~~Lt~rE~evl~~~~-----~G~s~~eIA~~l~iS~~TV~~h~~~i~~Kl~v~~~~~l~ 202 (216)
T PRK10840 149 KRLSPKESEVLRLFA-----EGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVENDIALL 202 (216)
T ss_pred ccCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCCCCHHHHH
Confidence 359999999998863 445999999999999999999999999999876666543
No 342
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=95.66 E-value=0.025 Score=54.54 Aligned_cols=48 Identities=23% Similarity=0.264 Sum_probs=45.6
Q ss_pred CCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHH
Q psy15215 577 LTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLA 628 (1432)
Q Consensus 577 L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l 628 (1432)
|+..|-+.|+|.+.+|+ |++|.|+.||||+.|+..+...|.+|+...+
T Consensus 42 L~~dElEAiRL~D~egl----~QeeaA~~MgVSR~T~~ril~~ARkKiA~AL 89 (106)
T PF02001_consen 42 LTVDELEAIRLVDYEGL----SQEEAAERMGVSRPTFQRILESARKKIADAL 89 (106)
T ss_pred eeHHHHHHHHHHHHcCC----CHHHHHHHcCCcHHHHHHHHHHHHHHHHHHH
Confidence 89999999999999999 9999999999999999999999999998776
No 343
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=95.58 E-value=0.016 Score=64.09 Aligned_cols=47 Identities=23% Similarity=0.396 Sum_probs=42.0
Q ss_pred HhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHH
Q psy15215 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625 (1432)
Q Consensus 574 L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr 625 (1432)
...||+||++||.+. ..|+|.+|||+.|++|..||+.+..+.++||.
T Consensus 132 ~~~LT~RE~eVL~ll-----~~G~snkeIA~~L~iS~~TV~~h~~~I~~KLg 178 (207)
T PRK11475 132 SRMLSPTEREILRFM-----SRGYSMPQIAEQLERNIKTIRAHKFNVMSKLG 178 (207)
T ss_pred cCCCCHHHHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence 346999999999986 35569999999999999999999999999995
No 344
>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=95.55 E-value=0.095 Score=53.55 Aligned_cols=61 Identities=10% Similarity=0.116 Sum_probs=51.2
Q ss_pred HHHHHHHHHH-ccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCc
Q psy15215 1355 SMRSVVKDIL-NSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417 (1432)
Q Consensus 1355 ~~~~~l~~~L-~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~ 1417 (1432)
.....+..++ +.|++.+|.||.++|.... ..+..+|+..+|+|+.+...+..+|+.++-..
T Consensus 67 ~~~~~i~~ai~~~l~~~~r~Il~~~Yl~~~--~~~~~~I~~~l~~s~~~~y~~k~~Al~~fA~~ 128 (132)
T TIGR01637 67 QEARAIVNAIVNQLDEISRQILYDKYLEPD--QKYDYQIMMELGYSHRQYYRIKKRALLRFATL 128 (132)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHHcCcc--ccchHHHHHHhCCcHHHHHHHHHHHHHHHHHH
Confidence 3445667777 8999999999999998721 34899999999999999999999999988653
No 345
>PRK13870 transcriptional regulator TraR; Provisional
Probab=95.50 E-value=0.024 Score=63.93 Aligned_cols=52 Identities=23% Similarity=0.286 Sum_probs=46.5
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchhhhh
Q psy15215 1366 SLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYK 1422 (1432)
Q Consensus 1366 ~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~~~~ 1422 (1432)
.||+||++||.+- ..|+|..|||.+||||..||...+..|++||--..|...
T Consensus 173 ~LT~RE~E~L~W~-----A~GKT~~EIa~ILgISe~TV~~Hl~na~~KLga~nr~qA 224 (234)
T PRK13870 173 WLDPKEATYLRWI-----AVGKTMEEIADVEGVKYNSVRVKLREAMKRFDVRSKAHL 224 (234)
T ss_pred CCCHHHHHHHHHH-----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCCCCHHHH
Confidence 5999999999886 356699999999999999999999999999988777664
No 346
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=95.30 E-value=0.032 Score=63.16 Aligned_cols=52 Identities=13% Similarity=0.280 Sum_probs=46.6
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchhhhh
Q psy15215 1366 SLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYK 1422 (1432)
Q Consensus 1366 ~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~~~~ 1422 (1432)
.||+||++||.+- ..| +|..|||.+||||..||+..+.++++||--..+...
T Consensus 179 ~LT~rE~evl~~~-a~G----~t~~eIa~~l~is~~TV~~h~~~~~~KL~~~nr~q~ 230 (240)
T PRK10188 179 NFSKREKEILKWT-AEG----KTSAEIAMILSISENTVNFHQKNMQKKFNAPNKTQI 230 (240)
T ss_pred CCCHHHHHHHHHH-HcC----CCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCHHHH
Confidence 5999999999997 344 499999999999999999999999999987777665
No 347
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=95.24 E-value=0.023 Score=63.09 Aligned_cols=46 Identities=28% Similarity=0.500 Sum_probs=41.9
Q ss_pred hcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHH
Q psy15215 575 NSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625 (1432)
Q Consensus 575 ~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr 625 (1432)
..||+||+.||+|- ..|+|.+|||..|++|..||+.+.++.++||.
T Consensus 147 ~~LT~RE~eVL~ll-----a~G~snkeIA~~L~iS~~TVk~h~~~i~~KL~ 192 (211)
T COG2197 147 ELLTPRELEVLRLL-----AEGLSNKEIAEELNLSEKTVKTHVSNILRKLG 192 (211)
T ss_pred CCCCHHHHHHHHHH-----HCCCCHHHHHHHHCCCHhHHHHHHHHHHHHcC
Confidence 56999999999985 45669999999999999999999999999995
No 348
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=95.19 E-value=0.025 Score=62.95 Aligned_cols=46 Identities=28% Similarity=0.463 Sum_probs=41.6
Q ss_pred hcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHH
Q psy15215 575 NSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625 (1432)
Q Consensus 575 ~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr 625 (1432)
..||+||++||.+. ..|+|.+|||+.+++|..||+.+..+.++||.
T Consensus 149 ~~Lt~rE~evl~~~-----~~G~s~~eIA~~l~iS~~TV~~h~~~i~~Kl~ 194 (216)
T PRK10840 149 KRLSPKESEVLRLF-----AEGFLVTEIAKKLNRSIKTISSQKKSAMMKLG 194 (216)
T ss_pred ccCCHHHHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence 35999999999986 35669999999999999999999999999994
No 349
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=95.11 E-value=0.026 Score=45.71 Aligned_cols=41 Identities=20% Similarity=0.367 Sum_probs=23.6
Q ss_pred hcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHH
Q psy15215 575 NSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 619 (1432)
Q Consensus 575 ~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~r 619 (1432)
..|++.|+..|...+-.|+ |..+||..||+++++|....+|
T Consensus 3 ~~Lt~~eR~~I~~l~~~G~----s~~~IA~~lg~s~sTV~relkR 43 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQGM----SIREIAKRLGRSRSTVSRELKR 43 (44)
T ss_dssp ---------HHHHHHCS-------HHHHHHHTT--HHHHHHHHHH
T ss_pred cchhhhHHHHHHHHHHcCC----CHHHHHHHHCcCcHHHHHHHhc
Confidence 4699999999988876565 9999999999999999977665
No 350
>COG1356 tfx Transcriptional regulator [DNA replication, recombination and repair]
Probab=95.11 E-value=0.014 Score=56.39 Aligned_cols=49 Identities=29% Similarity=0.406 Sum_probs=43.8
Q ss_pred CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchhh
Q psy15215 1367 LTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRY 1420 (1432)
Q Consensus 1367 L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~~ 1420 (1432)
|+++|-+||.||- +|.|.+|||+.||-|+..|+-++.+|+.++.+....
T Consensus 9 lte~qikvl~lRe-----kG~tQ~eIA~~L~TTraNvSaIEkrA~enIekarnT 57 (143)
T COG1356 9 LTEQQIKVLVLRE-----KGLTQSEIARILKTTRANVSAIEKRALENIEKARNT 57 (143)
T ss_pred eehhheeeeehhh-----ccccHHHHHHHHccchhhHHHHHHHHHHHHHHHHHH
Confidence 8999999999994 566999999999999999999999999999875443
No 351
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=95.05 E-value=0.048 Score=59.22 Aligned_cols=55 Identities=22% Similarity=0.323 Sum_probs=47.6
Q ss_pred ccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchhhhhHH
Q psy15215 1365 NSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLK 1424 (1432)
Q Consensus 1365 ~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~~~~l~ 1424 (1432)
..||++|++||.+ +..|. |.+|||+.+++|..||+.+..++++||.-..+...+.
T Consensus 148 ~~lt~~e~~vl~l-~~~g~----~~~~Ia~~l~~s~~tv~~~~~~~~~kl~~~~~~~l~~ 202 (211)
T PRK15369 148 PLLTPRERQILKL-ITEGY----TNRDIAEQLSISIKTVETHRLNMMRKLDVHKVAELLN 202 (211)
T ss_pred cCCCHHHHHHHHH-HHCCC----CHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCHHHHHH
Confidence 4599999999998 55555 9999999999999999999999999998777655444
No 352
>PRK13870 transcriptional regulator TraR; Provisional
Probab=94.88 E-value=0.035 Score=62.59 Aligned_cols=46 Identities=24% Similarity=0.342 Sum_probs=42.2
Q ss_pred cCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHH
Q psy15215 576 SLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRP 626 (1432)
Q Consensus 576 ~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~ 626 (1432)
.||+||++||++- ..|+|..|||.+||||..||..+...|.+||--
T Consensus 173 ~LT~RE~E~L~W~-----A~GKT~~EIa~ILgISe~TV~~Hl~na~~KLga 218 (234)
T PRK13870 173 WLDPKEATYLRWI-----AVGKTMEEIADVEGVKYNSVRVKLREAMKRFDV 218 (234)
T ss_pred CCCHHHHHHHHHH-----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence 5999999999986 567799999999999999999999999999953
No 353
>TIGR03020 EpsA transcriptional regulator EpsA. Proteins in this family include a C-terminal LuxR transcriptional regulator domain (pfam00196). These proteins are positioned proximal to either EpsH-containing exopolysaccharide biosynthesis operons of the Methylobacillus type, or the associated PEP-CTERM-containing genes.
Probab=94.80 E-value=0.042 Score=62.09 Aligned_cols=47 Identities=19% Similarity=0.227 Sum_probs=42.4
Q ss_pred HhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHH
Q psy15215 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625 (1432)
Q Consensus 574 L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr 625 (1432)
+..||++|++|+.+.. .|+ |..|||+.||+|+.+|+.+..++++||.
T Consensus 188 ~~~LT~RE~evl~l~a-~G~----s~~eIA~~L~IS~~TVk~hl~~i~~KL~ 234 (247)
T TIGR03020 188 AGLITAREAEILAWVR-DGK----TNEEIAAILGISSLTVKNHLQHIFKKLD 234 (247)
T ss_pred ccCCCHHHHHHHHHHH-CCC----CHHHHHHHHCcCHHHHHHHHHHHHHHhC
Confidence 4579999999999853 555 9999999999999999999999999986
No 354
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=94.80 E-value=0.041 Score=61.23 Aligned_cols=47 Identities=15% Similarity=0.187 Sum_probs=42.2
Q ss_pred HhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHH
Q psy15215 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625 (1432)
Q Consensus 574 L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr 625 (1432)
+..||+||++||.+... |+ |.+|||+.|++|..+|+.+..++++||.
T Consensus 153 ~~~Lt~rE~~Vl~l~~~-G~----s~~eIA~~L~iS~~TVk~~~~~i~~Kl~ 199 (216)
T PRK10100 153 SALLTHREKEILNKLRI-GA----SNNEIARSLFISENTVKTHLYNLFKKIA 199 (216)
T ss_pred cCCCCHHHHHHHHHHHc-CC----CHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 34599999999999863 44 9999999999999999999999999995
No 355
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=94.62 E-value=0.069 Score=46.86 Aligned_cols=48 Identities=25% Similarity=0.443 Sum_probs=41.6
Q ss_pred hcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHH
Q psy15215 575 NSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPL 627 (1432)
Q Consensus 575 ~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~ 627 (1432)
..|+++|.+|+.+. ..|+|..|||..+++|+.+|+....++..|+.-.
T Consensus 3 ~~Lt~rE~~v~~l~-----~~G~s~~eia~~l~is~~tV~~h~~~i~~Kl~~~ 50 (65)
T COG2771 3 ADLTPREREILRLV-----AQGKSNKEIARILGISEETVKTHLRNIYRKLGVK 50 (65)
T ss_pred ccCCHHHHHHHHHH-----HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
Confidence 45999999999875 3456999999999999999999999999998643
No 356
>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=94.57 E-value=0.048 Score=61.49 Aligned_cols=48 Identities=19% Similarity=0.255 Sum_probs=42.9
Q ss_pred HhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHH
Q psy15215 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRP 626 (1432)
Q Consensus 574 L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~ 626 (1432)
...||++|++||.+. ..|+ |..|||+.||+|..+|+.+..++++||.-
T Consensus 169 ~~~Lt~re~evl~~~-a~G~----t~~eIa~~l~is~~Tv~~~l~~~~~kl~~ 216 (232)
T TIGR03541 169 AGVLSEREREVLAWT-ALGR----RQADIAAILGISERTVENHLRSARRKLGV 216 (232)
T ss_pred hccCCHHHHHHHHHH-HCCC----CHHHHHHHHCcCHHHHHHHHHHHHHHHCC
Confidence 347999999999995 4555 99999999999999999999999999973
No 357
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=94.52 E-value=0.091 Score=56.69 Aligned_cols=61 Identities=15% Similarity=0.263 Sum_probs=52.1
Q ss_pred HHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchhhhhHH
Q psy15215 1359 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLK 1424 (1432)
Q Consensus 1359 ~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~~~~l~ 1424 (1432)
.+...+..|++++++|+.+ +..|. +.++||+.+|+|..+|+...+++++||+...+....+
T Consensus 134 ~~~~~~~~l~~~e~~vl~~-~~~~~----~~~~ia~~l~~s~~tv~~~~~~~~~kl~~~~~~~~~~ 194 (202)
T PRK09390 134 DIRARIASLSERERQVMDG-LVAGL----SNKVIARDLDISPRTVEVYRANVMTKMQAGSLSELVR 194 (202)
T ss_pred HHHHHHHhhhhhHHHHHHH-HHccC----chHHHHHHcCCCHHHHHHHHHHHHHHHccccHHHHHH
Confidence 3455678899999999986 54555 9999999999999999999999999999888877544
No 358
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=94.42 E-value=0.091 Score=48.73 Aligned_cols=48 Identities=23% Similarity=0.237 Sum_probs=44.9
Q ss_pred CCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHH
Q psy15215 577 LTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLA 628 (1432)
Q Consensus 577 L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l 628 (1432)
|+..|-+.|+|...+++ |++|-|.+||||+.++.+....|+.|+-.++
T Consensus 34 lt~eElEAlRLvD~~~l----~QeeAA~rMgISr~Tfwr~l~sAR~KvA~aL 81 (99)
T COG1342 34 LTIEELEALRLVDYEGL----TQEEAALRMGISRQTFWRLLTSARKKVADAL 81 (99)
T ss_pred ecHHHHHHHHHHhHhhc----cHHHHHHHhcccHHHHHHHHHHHHHHHHHHH
Confidence 88899999999999999 9999999999999999999999999987766
No 359
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=94.39 E-value=0.081 Score=58.93 Aligned_cols=53 Identities=23% Similarity=0.392 Sum_probs=47.8
Q ss_pred cCCHHHHHHHHHHhhccc---CCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHH
Q psy15215 576 SLTPRESKVLRMRFGIEM---SSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLA 628 (1432)
Q Consensus 576 ~L~~rer~Vl~lr~~~~~---~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l 628 (1432)
.||++|++||+.-|-.|. .+..|++|+|+.||||.+++.+++++|.+||-..+
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 599999999999998875 35689999999999999999999999999997654
No 360
>PRK04017 hypothetical protein; Provisional
Probab=94.38 E-value=0.078 Score=53.25 Aligned_cols=53 Identities=26% Similarity=0.309 Sum_probs=44.3
Q ss_pred cCCeEEEEecchhHHHHhhhCC---------------------CCCeEEEEecCcHHHHHHHHHHHHHhhhhcC
Q psy15215 728 KSGYVLITEGYMDVIGLSQFGF---------------------FANSSYTCFDGDQAGRRAARRALEVCLLYAT 780 (1432)
Q Consensus 728 ~~~~~~~vEG~~D~ia~~~~g~---------------------~~~~i~~~~D~D~aG~~a~~~~~~~~~~~~~ 780 (1432)
..+.+|||||=-|.-++.++|+ ....||+..|.|.+|.+-+.+..+.+...|.
T Consensus 21 ~~g~vIVVEGk~D~~~L~~lGv~~~iI~t~g~~~~~~~e~ia~~~r~VIILTD~D~~GekIr~~l~~~l~~~G~ 94 (132)
T PRK04017 21 EAGAPIIVEGKRDVESLRKLGVEGEIIKVSRTPLAEIAELIASRGKEVIILTDFDRKGEELAKKLSEYLQGYGI 94 (132)
T ss_pred CCCCEEEEeCccHHHHHHHcCCCccEEEECCeecchHHHHHHhcCCeEEEEECCCcchHHHHHHHHHHHHhCCC
Confidence 3468999999999999999988 4577999999999999888888777665554
No 361
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=94.36 E-value=0.082 Score=49.00 Aligned_cols=48 Identities=23% Similarity=0.248 Sum_probs=44.7
Q ss_pred CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCch
Q psy15215 1367 LTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418 (1432)
Q Consensus 1367 L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~ 1418 (1432)
|+..|-+.|+|..+.++ |++|-|.++|||+.|+-+.+..|++|.-.+.
T Consensus 34 lt~eElEAlRLvD~~~l----~QeeAA~rMgISr~Tfwr~l~sAR~KvA~aL 81 (99)
T COG1342 34 LTIEELEALRLVDYEGL----TQEEAALRMGISRQTFWRLLTSARKKVADAL 81 (99)
T ss_pred ecHHHHHHHHHHhHhhc----cHHHHHHHhcccHHHHHHHHHHHHHHHHHHH
Confidence 78889999999999999 9999999999999999999999999987644
No 362
>COG1356 tfx Transcriptional regulator [DNA replication, recombination and repair]
Probab=94.34 E-value=0.029 Score=54.28 Aligned_cols=49 Identities=29% Similarity=0.432 Sum_probs=44.8
Q ss_pred CCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHHHH
Q psy15215 577 LTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLAHD 630 (1432)
Q Consensus 577 L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l~~ 630 (1432)
|+++|-+||.|| .+|.|++|||++||-|+..|+-++++|+.++.+.-+.
T Consensus 9 lte~qikvl~lR-----ekG~tQ~eIA~~L~TTraNvSaIEkrA~enIekarnT 57 (143)
T COG1356 9 LTEQQIKVLVLR-----EKGLTQSEIARILKTTRANVSAIEKRALENIEKARNT 57 (143)
T ss_pred eehhheeeeehh-----hccccHHHHHHHHccchhhHHHHHHHHHHHHHHHHHH
Confidence 899999999999 4777999999999999999999999999999876654
No 363
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=94.26 E-value=0.09 Score=49.28 Aligned_cols=47 Identities=21% Similarity=0.381 Sum_probs=41.8
Q ss_pred cCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHH
Q psy15215 576 SLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRP 626 (1432)
Q Consensus 576 ~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~ 626 (1432)
-||.+|+..+.++|..+. |+.|||+.++||+..|.....|.-..|-.
T Consensus 17 LLT~KQ~~Y~~lyy~dDl----Sl~EIAee~~VSRqAIyDnIKr~~~~L~~ 63 (105)
T COG2739 17 LLTKKQKNYLELYYLDDL----SLSEIAEEFNVSRQAIYDNIKRTEKILED 63 (105)
T ss_pred HHhHHHHHHHHHHHHhhc----cHHHHHHHhCccHHHHHHHHHHHHHHHHH
Confidence 389999999999998888 99999999999999999888887666543
No 364
>PRK10651 transcriptional regulator NarL; Provisional
Probab=94.23 E-value=0.09 Score=57.63 Aligned_cols=55 Identities=24% Similarity=0.405 Sum_probs=47.1
Q ss_pred ccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchhhhhHH
Q psy15215 1365 NSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLK 1424 (1432)
Q Consensus 1365 ~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~~~~l~ 1424 (1432)
..||++|++|+.+. ..|. |.++||+.+++|..||+...++.++||.-..+.+...
T Consensus 154 ~~Lt~rE~~vl~~l-~~g~----~~~~ia~~l~is~~tV~~~~~~l~~Kl~~~~~~~~~~ 208 (216)
T PRK10651 154 NQLTPRERDILKLI-AQGL----PNKMIARRLDITESTVKVHVKHMLKKMKLKSRVEAAV 208 (216)
T ss_pred ccCCHHHHHHHHHH-HcCC----CHHHHHHHcCCCHHHHHHHHHHHHHHcCCCCHHHHHH
Confidence 45999999999984 3454 9999999999999999999999999998777666533
No 365
>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=94.22 E-value=0.13 Score=45.33 Aligned_cols=58 Identities=22% Similarity=0.272 Sum_probs=49.2
Q ss_pred HHHHHHHHhHHHHHHhHHHHHHHHHHHHHHHHHhcc-----c-CCCChhhHHHHHHHHHHHHHhhcc
Q psy15215 386 DINRKMIAGEMKARKAKREMTEANLRLVISIAKKYT-----D-RGLQFLDLIQEGNIGLMKAVDKFE 446 (1432)
Q Consensus 386 ~l~~~i~~gd~~~~~A~~~li~~~~~lV~~ia~ky~-----~-~~~~~~DLiQEg~igL~kav~~fd 446 (1432)
+++.++++||.. |.++++..|.|++.+.+.+-+ + .+.--+|+-|+-...|++++-+|+
T Consensus 2 ~vI~~A~~GD~~---A~~~IL~~y~~yI~kls~r~~~d~~g~~~~~vDedl~q~l~~kLi~~I~~F~ 65 (65)
T PF12645_consen 2 EVIKAAKQGDPE---AMEEILKHYEPYISKLSTRTLYDEYGNVYGYVDEDLKQRLEIKLIEAILKFE 65 (65)
T ss_pred HHHHHHHcCCHH---HHHHHHHHHHHHHHHHHHhhcccccCCcCceeCHHHHHHHHHHHHHHHHccC
Confidence 467889999999 999999999999999987621 1 134459999999999999999985
No 366
>PRK09483 response regulator; Provisional
Probab=94.17 E-value=0.079 Score=58.47 Aligned_cols=53 Identities=17% Similarity=0.276 Sum_probs=45.3
Q ss_pred ccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchhhhh
Q psy15215 1365 NSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYK 1422 (1432)
Q Consensus 1365 ~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~~~~ 1422 (1432)
..||++|++||.+. ..| +|.+|||+.|++|..||+...++.++||--..+...
T Consensus 147 ~~Lt~rE~~vl~~~-~~G----~~~~~Ia~~l~is~~TV~~~~~~i~~Kl~v~~~~~l 199 (217)
T PRK09483 147 ASLSERELQIMLMI-TKG----QKVNEISEQLNLSPKTVNSYRYRMFSKLNISGDVEL 199 (217)
T ss_pred cccCHHHHHHHHHH-HCC----CCHHHHHHHhCCCHHHHHHHHHHHHHHcCCCCHHHH
Confidence 46999999999874 344 499999999999999999999999999976665553
No 367
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=94.03 E-value=0.077 Score=60.11 Aligned_cols=46 Identities=13% Similarity=0.312 Sum_probs=41.6
Q ss_pred cCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHH
Q psy15215 576 SLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRP 626 (1432)
Q Consensus 576 ~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~ 626 (1432)
.||+||++||++- . .|+|..|||++||+|..+|+.+..++++||.-
T Consensus 179 ~LT~rE~evl~~~-a----~G~t~~eIa~~l~is~~TV~~h~~~~~~KL~~ 224 (240)
T PRK10188 179 NFSKREKEILKWT-A----EGKTSAEIAMILSISENTVNFHQKNMQKKFNA 224 (240)
T ss_pred CCCHHHHHHHHHH-H----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 5999999999997 3 45599999999999999999999999999963
No 368
>PRK15320 transcriptional activator SprB; Provisional
Probab=93.92 E-value=0.098 Score=55.05 Aligned_cols=50 Identities=20% Similarity=0.272 Sum_probs=43.3
Q ss_pred HHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCc
Q psy15215 1363 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 1417 (1432)
Q Consensus 1363 ~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~ 1417 (1432)
+--.||.+|.+|+.+- .+|+|.+|||++|++|.+||+...++.+.||.-.
T Consensus 161 ~~~~LSdREIEVL~LL-----AkG~SNKEIAekL~LS~KTVSTYKnRLLeKLgAk 210 (251)
T PRK15320 161 LPPGVTQAKYALLILL-----SSGHPAIELAKKFGLGTKTVSIYRKKVMYRLGMD 210 (251)
T ss_pred CCCCCCHHHHHHHHHH-----HcCCCHHHHHHHhccchhhHHHHHHHHHHHcCCC
Confidence 3357999999999885 3556999999999999999999999999999753
No 369
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=93.91 E-value=0.13 Score=55.76 Aligned_cols=60 Identities=17% Similarity=0.253 Sum_probs=52.3
Q ss_pred ccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchhhhhHHhhhcc
Q psy15215 1365 NSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429 (1432)
Q Consensus 1365 ~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~~~~l~~~~~~ 1429 (1432)
..|+++|.+|+.+-. .| +|.++||+.+++|..||+.+..+.++||.-..+.....-|+++
T Consensus 136 ~~Lt~~E~~il~~l~-~g----~~~~~Ia~~l~~s~~tv~~~~~~l~~Kl~~~~~~~l~~~~~~~ 195 (196)
T PRK10360 136 DPLTKRERQVAEKLA-QG----MAVKEIAAELGLSPKTVHVHRANLMEKLGVSNDVELARRMFDG 195 (196)
T ss_pred cCCCHHHHHHHHHHH-CC----CCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCHHHHHHHHHhc
Confidence 369999999998844 44 4999999999999999999999999999988888877777664
No 370
>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=93.52 E-value=0.23 Score=43.88 Aligned_cols=58 Identities=22% Similarity=0.260 Sum_probs=49.5
Q ss_pred HHHHHHHhhhhhhhhhHHHHHHHHHHHHHHHHHhcc----C--CCCChhHHHHHHHHHHHHHHHhcc
Q psy15215 1176 DINRKMIAGEMKARKAKREMTEANLRLVISIAKKYT----D--RGLQFLDLIQEGNIGLMKAVDKFE 1236 (1432)
Q Consensus 1176 ~l~~~~~~g~~~~~~A~~~Li~~~~~lV~~ia~~y~----~--~~~~~~DLiQEg~igl~kav~kfd 1236 (1432)
+++.++++||.. |.++++..|.|++.+.+.+-. + .+.-=+|+-|+--..|++++-+|+
T Consensus 2 ~vI~~A~~GD~~---A~~~IL~~y~~yI~kls~r~~~d~~g~~~~~vDedl~q~l~~kLi~~I~~F~ 65 (65)
T PF12645_consen 2 EVIKAAKQGDPE---AMEEILKHYEPYISKLSTRTLYDEYGNVYGYVDEDLKQRLEIKLIEAILKFE 65 (65)
T ss_pred HHHHHHHcCCHH---HHHHHHHHHHHHHHHHHHhhcccccCCcCceeCHHHHHHHHHHHHHHHHccC
Confidence 467889999999 999999999999999988722 1 244568999999999999999995
No 371
>PRK09483 response regulator; Provisional
Probab=93.27 E-value=0.11 Score=57.29 Aligned_cols=46 Identities=20% Similarity=0.395 Sum_probs=40.6
Q ss_pred hcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHH
Q psy15215 575 NSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625 (1432)
Q Consensus 575 ~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr 625 (1432)
..||++|++||.+. . .|+|.+|||+.+++|..+|+.+.++.++||.
T Consensus 147 ~~Lt~rE~~vl~~~-~----~G~~~~~Ia~~l~is~~TV~~~~~~i~~Kl~ 192 (217)
T PRK09483 147 ASLSERELQIMLMI-T----KGQKVNEISEQLNLSPKTVNSYRYRMFSKLN 192 (217)
T ss_pred cccCHHHHHHHHHH-H----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 45999999999875 3 4559999999999999999999999999984
No 372
>PF01751 Toprim: Toprim domain; InterPro: IPR006171 This is a conserved region from DNA primase. This corresponds to the Toprim (topoisomerase-primase) domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR/M DNA repair proteins []. Both DnaG motifs IV and V are present in the alignment, the DxD (V) motif may be involved in Mg2+ binding and mutations to the conserved glutamate (IV) completely abolish DnaG type primase activity. DNA primase 2.7.7.6 from EC is a nucleotidyltransferase it synthesizes the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork; it can also prime the leading stand and has been implicated in cell division []. This family also includes the atypical archaeal A subunit from type II DNA topoisomerases []. Type II DNA topoisomerases catalyse the relaxation of DNA supercoiling by causing transient double strand breaks.; PDB: 2ZJT_A 3IG0_A 3M4I_A 3NUH_B 1GKU_B 1GL9_C 3PWT_A 1CY4_A 1ECL_A 1CY7_A ....
Probab=93.06 E-value=0.24 Score=47.97 Aligned_cols=49 Identities=18% Similarity=0.067 Sum_probs=41.2
Q ss_pred eEEEEecchhHHHHhhhCC---------------------------------------CCCeEEEEecCcHHHHHHHHHH
Q psy15215 731 YVLITEGYMDVIGLSQFGF---------------------------------------FANSSYTCFDGDQAGRRAARRA 771 (1432)
Q Consensus 731 ~~~~vEG~~D~ia~~~~g~---------------------------------------~~~~i~~~~D~D~aG~~a~~~~ 771 (1432)
.+|||||..|+.++.++.. ...+||+|.|+|..|...+...
T Consensus 1 ~liIvE~ps~a~~i~~~l~~~~~~v~~~~Ghl~~~~~~~~~~~~~~~~~i~~l~~~~~~~~~iiiatD~D~EGe~Ia~~i 80 (100)
T PF01751_consen 1 ELIIVEKPSDAKAIAKALGGEEYIVIATSGHLLELAKPEDYDPKDKKKQIKNLKKLLKKADEIIIATDPDREGELIAWEI 80 (100)
T ss_dssp EEEEESSHHHHHHHHHHSSTTTEEEEEESSSSEESTTSSHHHCHTTHHHHHHHHHHHHSCSEEEEEC-SSHHHHHHHHHH
T ss_pred CEEEEeCHHHHHHHHHHcCCCCEEEEEeCCcccccccccccccccccccchhhHHHhhhccEeeecCCCChHHHHHHHHH
Confidence 4789999999999888744 2579999999999999999999
Q ss_pred HHHhhhhc
Q psy15215 772 LEVCLLYA 779 (1432)
Q Consensus 772 ~~~~~~~~ 779 (1432)
+..+...+
T Consensus 81 ~~~~~~~~ 88 (100)
T PF01751_consen 81 IELLGKNN 88 (100)
T ss_dssp HHHHHHHS
T ss_pred HHHHhHhC
Confidence 99887765
No 373
>PRK15320 transcriptional activator SprB; Provisional
Probab=93.00 E-value=0.15 Score=53.77 Aligned_cols=47 Identities=21% Similarity=0.284 Sum_probs=42.1
Q ss_pred HhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHH
Q psy15215 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625 (1432)
Q Consensus 574 L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr 625 (1432)
--.|+++|..|+.+- ..|+|.+|||+.|++|.++|+.+..+.+.||.
T Consensus 162 ~~~LSdREIEVL~LL-----AkG~SNKEIAekL~LS~KTVSTYKnRLLeKLg 208 (251)
T PRK15320 162 PPGVTQAKYALLILL-----SSGHPAIELAKKFGLGTKTVSIYRKKVMYRLG 208 (251)
T ss_pred CCCCCHHHHHHHHHH-----HcCCCHHHHHHHhccchhhHHHHHHHHHHHcC
Confidence 356999999999885 56779999999999999999999999999986
No 374
>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=92.94 E-value=0.33 Score=48.85 Aligned_cols=58 Identities=12% Similarity=0.346 Sum_probs=48.5
Q ss_pred HHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhh
Q psy15215 1356 MRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 1415 (1432)
Q Consensus 1356 ~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr 1415 (1432)
....+...++.|++.++.||.|||+.. .+.|..+||..+++|..+++.+...-...++
T Consensus 71 ~k~~id~~~~~l~de~k~Ii~lry~~r--~~~TW~~IA~~l~i~erta~r~~~~fK~~i~ 128 (130)
T PF05263_consen 71 QKEAIDRWLETLIDEEKRIIKLRYDRR--SRRTWYQIAQKLHISERTARRWRDRFKNDIY 128 (130)
T ss_pred HHHHHHHHHHhhCHHHHHHHHHHHccc--ccchHHHHHHHhCccHHHHHHHHHHHHHHhc
Confidence 457788889999999999999999876 2459999999999999999988766554443
No 375
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=92.62 E-value=0.26 Score=48.10 Aligned_cols=50 Identities=18% Similarity=0.301 Sum_probs=44.6
Q ss_pred HHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhC
Q psy15215 1363 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 1416 (1432)
Q Consensus 1363 ~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~ 1416 (1432)
.+..|++.+..-+....-... +++|+++.+|||-.|||.++.+.+++|-.
T Consensus 30 ~~~~L~~E~~~Fi~~Fi~~rG----nlKe~e~~lgiSYPTvR~rLd~ii~~lg~ 79 (113)
T PF09862_consen 30 WFARLSPEQLEFIKLFIKNRG----NLKEMEKELGISYPTVRNRLDKIIEKLGY 79 (113)
T ss_pred hhhcCCHHHHHHHHHHHHhcC----CHHHHHHHHCCCcHHHHHHHHHHHHHhCC
Confidence 377899999998877665555 99999999999999999999999999987
No 376
>PRK10403 transcriptional regulator NarP; Provisional
Probab=92.60 E-value=0.25 Score=53.97 Aligned_cols=60 Identities=23% Similarity=0.278 Sum_probs=51.2
Q ss_pred ccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchhhhhHHhhhcc
Q psy15215 1365 NSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLKIFLEG 1429 (1432)
Q Consensus 1365 ~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~~~~l~~~~~~ 1429 (1432)
..||++|.+|+.+.. .| +|.++||+.+++|..||+...++.++||.-..+.....-|+..
T Consensus 152 ~~Lt~~e~~vl~~~~-~g----~s~~~ia~~l~~s~~tv~~~~~~i~~kl~~~~~~~~~~~~~~~ 211 (215)
T PRK10403 152 SVLTERELDVLHELA-QG----LSNKQIASVLNISEQTVKVHIRNLLRKLNVRSRVAATILFLQQ 211 (215)
T ss_pred ccCCHHHHHHHHHHH-CC----CCHHHHHHHcCCCHHHHHHHHHHHHHHcCCCCHHHHHHHHHHh
Confidence 359999999998753 44 5999999999999999999999999999988888876666543
No 377
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=92.48 E-value=0.19 Score=54.52 Aligned_cols=46 Identities=24% Similarity=0.438 Sum_probs=41.3
Q ss_pred hcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHH
Q psy15215 575 NSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625 (1432)
Q Consensus 575 ~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr 625 (1432)
..||++|++||.+ +..|. |.+|||+.+++|..+|+.+..++++||.
T Consensus 148 ~~lt~~e~~vl~l-~~~g~----~~~~Ia~~l~~s~~tv~~~~~~~~~kl~ 193 (211)
T PRK15369 148 PLLTPRERQILKL-ITEGY----TNRDIAEQLSISIKTVETHRLNMMRKLD 193 (211)
T ss_pred cCCCHHHHHHHHH-HHCCC----CHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 4599999999998 55555 9999999999999999999999999995
No 378
>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=92.42 E-value=0.2 Score=44.24 Aligned_cols=45 Identities=18% Similarity=0.303 Sum_probs=30.7
Q ss_pred HccCCHHHHHHHHH--HhcccCCCCCCHHHHHHHhCCC-HHHHHHHHH
Q psy15215 1364 LNSLTPRESKVLRM--RFGIEMSSDHTLEEVGKQFDVT-RERIRQIEA 1408 (1432)
Q Consensus 1364 L~~L~~rer~Vl~l--r~~~~~~~~~t~~EIa~~l~vs-~~~Vrq~~~ 1408 (1432)
+..||++|++||.. .|....|.+-|..|||+.||++ .++|.+.+.
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 35799999999876 5556667777999999999996 999987654
No 379
>PRK13558 bacterio-opsin activator; Provisional
Probab=91.80 E-value=0.27 Score=64.61 Aligned_cols=53 Identities=25% Similarity=0.234 Sum_probs=47.2
Q ss_pred HHccCCHHHHHHHHHHhcccCC---CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhh
Q psy15215 1363 ILNSLTPRESKVLRMRFGIEMS---SDHTLEEVGKQFDVTRERIRQIEAKALRKLR 1415 (1432)
Q Consensus 1363 ~L~~L~~rer~Vl~lr~~~~~~---~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr 1415 (1432)
....||++|+++|..-|..|.. .+.|.+|||+.||||++|+.+++++|.+||=
T Consensus 604 ~~~~lt~~q~e~l~~a~~~gyf~~pr~~~~~e~a~~l~is~~t~~~~lr~a~~~l~ 659 (665)
T PRK13558 604 LENDLTDRQLTALQKAYVSGYFEWPRRVEGEELAESMGISRSTFHQHLRAAERKLV 659 (665)
T ss_pred hhhhCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 3567999999999999987763 5679999999999999999999999999984
No 380
>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=91.74 E-value=0.29 Score=45.93 Aligned_cols=42 Identities=19% Similarity=0.316 Sum_probs=32.2
Q ss_pred HccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q psy15215 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALR 1412 (1432)
Q Consensus 1364 L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~ 1412 (1432)
+++|++| ..|+.+. . .++|..+||+.+|+|+.||.. +.|+++
T Consensus 34 ~~~Ls~R-~~I~~ll-~----~G~S~~eIA~~LgISrsTIyR-i~R~~n 75 (88)
T TIGR02531 34 IQSLAQR-LQVAKML-K----QGKTYSDIEAETGASTATISR-VKRCLN 75 (88)
T ss_pred HHhhhHH-HHHHHHH-H----CCCCHHHHHHHHCcCHHHHHH-HHHhcc
Confidence 4568999 7777764 2 345999999999999999998 445433
No 381
>PRK10651 transcriptional regulator NarL; Provisional
Probab=91.11 E-value=0.28 Score=53.69 Aligned_cols=46 Identities=24% Similarity=0.470 Sum_probs=40.6
Q ss_pred hcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHH
Q psy15215 575 NSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625 (1432)
Q Consensus 575 ~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr 625 (1432)
..||++|++|+.+. ..| ++.++||+.+++|..+|+.+.++.++||.
T Consensus 154 ~~Lt~rE~~vl~~l-~~g----~~~~~ia~~l~is~~tV~~~~~~l~~Kl~ 199 (216)
T PRK10651 154 NQLTPRERDILKLI-AQG----LPNKMIARRLDITESTVKVHVKHMLKKMK 199 (216)
T ss_pred ccCCHHHHHHHHHH-HcC----CCHHHHHHHcCCCHHHHHHHHHHHHHHcC
Confidence 45999999999984 344 49999999999999999999999999985
No 382
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=91.07 E-value=0.26 Score=58.20 Aligned_cols=37 Identities=16% Similarity=0.373 Sum_probs=34.2
Q ss_pred HHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q psy15215 1372 SKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALR 1412 (1432)
Q Consensus 1372 r~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~ 1412 (1432)
-+|-+|||..|+ |..|||++||+||.+|++.+++|++
T Consensus 19 ~~vA~lYY~~g~----tQ~eIA~~lgiSR~~VsRlL~~Ar~ 55 (318)
T PRK15418 19 ARIAWFYYHDGL----TQSEIGERLGLTRLKVSRLLEKGRQ 55 (318)
T ss_pred HHHHHHHHhcCC----CHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 357889999888 9999999999999999999999986
No 383
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=90.85 E-value=0.56 Score=39.62 Aligned_cols=47 Identities=13% Similarity=0.333 Sum_probs=39.6
Q ss_pred cCCHHHHHHHHHHhc-ccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhC
Q psy15215 1366 SLTPRESKVLRMRFG-IEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 1416 (1432)
Q Consensus 1366 ~L~~rer~Vl~lr~~-~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~ 1416 (1432)
+||..++-++.+.|. .+. |.+.+|..||||+++|+++.+..+.-|..
T Consensus 2 kLs~~d~lll~L~~LR~~~----~~~~La~~FgIs~stvsri~~~~~~~L~~ 49 (53)
T PF13613_consen 2 KLSLEDQLLLTLMYLRLNL----TFQDLAYRFGISQSTVSRIFHEWIPLLYQ 49 (53)
T ss_pred CCCHHHHHHHHHHHHHcCC----cHhHHhhheeecHHHHHHHHHHHHHHHHH
Confidence 688889988777654 444 99999999999999999999998877754
No 384
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=90.71 E-value=0.22 Score=41.30 Aligned_cols=32 Identities=16% Similarity=0.316 Sum_probs=22.2
Q ss_pred HHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q psy15215 1374 VLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 1410 (1432)
Q Consensus 1374 Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rA 1410 (1432)
++.++. .|. |..+||+.||||+.||+++.++-
T Consensus 10 ii~l~~-~G~----s~~~ia~~lgvs~~Tv~~w~kr~ 41 (50)
T PF13384_consen 10 IIRLLR-EGW----SIREIAKRLGVSRSTVYRWIKRY 41 (50)
T ss_dssp HHHHHH-HT------HHHHHHHHTS-HHHHHHHHT--
T ss_pred HHHHHH-CCC----CHHHHHHHHCcCHHHHHHHHHHc
Confidence 555544 355 99999999999999999997763
No 385
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=90.54 E-value=0.54 Score=45.97 Aligned_cols=50 Identities=18% Similarity=0.295 Sum_probs=42.6
Q ss_pred HHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHH
Q psy15215 573 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRP 626 (1432)
Q Consensus 573 ~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~ 626 (1432)
.+..|++.+..-+....--.. +++|+++.+|||.+|||.+..+.+.+|--
T Consensus 30 ~~~~L~~E~~~Fi~~Fi~~rG----nlKe~e~~lgiSYPTvR~rLd~ii~~lg~ 79 (113)
T PF09862_consen 30 WFARLSPEQLEFIKLFIKNRG----NLKEMEKELGISYPTVRNRLDKIIEKLGY 79 (113)
T ss_pred hhhcCCHHHHHHHHHHHHhcC----CHHHHHHHHCCCcHHHHHHHHHHHHHhCC
Confidence 377899999988876555555 99999999999999999999998888864
No 386
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=90.31 E-value=0.54 Score=51.26 Aligned_cols=53 Identities=19% Similarity=0.228 Sum_probs=44.6
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchhhhhH
Q psy15215 1366 SLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKL 1423 (1432)
Q Consensus 1366 ~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~~~~l 1423 (1432)
.|+++|..|+.+ +..|. |.+|||+.+++|..||+....++++||.-..+....
T Consensus 149 ~lt~re~~vl~~-l~~g~----s~~eIa~~l~~s~~tv~~~~~~~~~kl~~~~~~~l~ 201 (210)
T PRK09935 149 VLSNREVTILRY-LVSGL----SNKEIADQLLLSNKTVSAHKSNIYGKLGLHSIVELI 201 (210)
T ss_pred cCCHHHHHHHHH-HHcCC----CHHHHHHHhCCCHHHHHHHHHHHHHHcCCCCHHHHH
Confidence 389999999875 43555 999999999999999999999999999876655543
No 387
>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=90.26 E-value=0.83 Score=46.03 Aligned_cols=51 Identities=14% Similarity=0.417 Sum_probs=43.3
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHH
Q psy15215 567 RSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 619 (1432)
Q Consensus 567 ~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~r 619 (1432)
...+...++.|++.++.||.|||+.. .+.|..+||..+++|..+++.....
T Consensus 72 k~~id~~~~~l~de~k~Ii~lry~~r--~~~TW~~IA~~l~i~erta~r~~~~ 122 (130)
T PF05263_consen 72 KEAIDRWLETLIDEEKRIIKLRYDRR--SRRTWYQIAQKLHISERTARRWRDR 122 (130)
T ss_pred HHHHHHHHHhhCHHHHHHHHHHHccc--ccchHHHHHHHhCccHHHHHHHHHH
Confidence 46778889999999999999999876 2459999999999999998865443
No 388
>COG1658 Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair]
Probab=90.24 E-value=0.5 Score=47.32 Aligned_cols=47 Identities=23% Similarity=0.246 Sum_probs=39.4
Q ss_pred CCeEEEEecchhHHHHhhhCC------------------------CCCeEEEEecCcHHHHHHHHHHHHHh
Q psy15215 729 SGYVLITEGYMDVIGLSQFGF------------------------FANSSYTCFDGDQAGRRAARRALEVC 775 (1432)
Q Consensus 729 ~~~~~~vEG~~D~ia~~~~g~------------------------~~~~i~~~~D~D~aG~~a~~~~~~~~ 775 (1432)
.+.+|||||=-|..++.+.|+ +.+.|++..|.|.+|.+-..+..+.+
T Consensus 9 ~~~vIVVEGK~D~~~l~~~~~~~~i~~~g~~i~~~~~ie~i~~~~~~k~VIILTD~D~~Ge~Irk~l~~~l 79 (127)
T COG1658 9 LKEVIVVEGKDDTASLKRLGDAGVIITNGSAINSLETIELIKKAQKYKGVIILTDPDRKGERIRKKLKEYL 79 (127)
T ss_pred cCceEEEeCCcHHHHHHHhcCCceEEEcCCccchHHHHHHHHHhhccCCEEEEeCCCcchHHHHHHHHHHh
Confidence 478999999999999999988 46779999999999987765555543
No 389
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=90.18 E-value=0.59 Score=50.27 Aligned_cols=53 Identities=15% Similarity=0.333 Sum_probs=45.3
Q ss_pred HHHHHHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHH
Q psy15215 569 VVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRP 626 (1432)
Q Consensus 569 ~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~ 626 (1432)
.+...+..|+++++.|+.+ +..|. +.++||+.+|+|..+|+.+..+++.||..
T Consensus 134 ~~~~~~~~l~~~e~~vl~~-~~~~~----~~~~ia~~l~~s~~tv~~~~~~~~~kl~~ 186 (202)
T PRK09390 134 DIRARIASLSERERQVMDG-LVAGL----SNKVIARDLDISPRTVEVYRANVMTKMQA 186 (202)
T ss_pred HHHHHHHhhhhhHHHHHHH-HHccC----chHHHHHHcCCCHHHHHHHHHHHHHHHcc
Confidence 3455678899999999996 54455 99999999999999999999999999963
No 390
>PHA00675 hypothetical protein
Probab=90.05 E-value=0.57 Score=41.91 Aligned_cols=40 Identities=20% Similarity=0.238 Sum_probs=34.4
Q ss_pred ccCCHHHHHHHHHHh-cccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q psy15215 1365 NSLTPRESKVLRMRF-GIEMSSDHTLEEVGKQFDVTRERIRQIEA 1408 (1432)
Q Consensus 1365 ~~L~~rer~Vl~lr~-~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~ 1408 (1432)
.+|++.+-+.|+..+ -.|. |+.+||..||||+++|.+|.+
T Consensus 21 AKLt~~qV~~IR~l~~r~G~----s~~~IA~~fGVsrstV~~I~~ 61 (78)
T PHA00675 21 AKLTDAEVERIRELHEVEGM----SYAVLAEKFEQSKGAIAKICR 61 (78)
T ss_pred cccCHHHHHHHHHHHHhcCc----cHHHHHHHhCCCHHHHHHHHc
Confidence 568888888787777 6676 999999999999999999865
No 391
>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=89.87 E-value=0.37 Score=35.97 Aligned_cols=23 Identities=26% Similarity=0.417 Sum_probs=17.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q psy15215 1387 HTLEEVGKQFDVTRERIRQIEAK 1409 (1432)
Q Consensus 1387 ~t~~EIa~~l~vs~~~Vrq~~~r 1409 (1432)
.|.+|||..+|+|+++|+..+.+
T Consensus 3 mtr~diA~~lG~t~ETVSR~l~~ 25 (32)
T PF00325_consen 3 MTRQDIADYLGLTRETVSRILKK 25 (32)
T ss_dssp --HHHHHHHHTS-HHHHHHHHHH
T ss_pred cCHHHHHHHhCCcHHHHHHHHHH
Confidence 48999999999999999854443
No 392
>PRK14719 bifunctional RNAse/5-amino-6-(5-phosphoribosylamino)uracil reductase; Provisional
Probab=89.87 E-value=0.33 Score=58.03 Aligned_cols=54 Identities=22% Similarity=0.264 Sum_probs=47.7
Q ss_pred cCCeEEEEecchhHHHHhhhCC----------------------CCCeEEEEecCcHHHHHHHHHHHHHhhhhcCC
Q psy15215 728 KSGYVLITEGYMDVIGLSQFGF----------------------FANSSYTCFDGDQAGRRAARRALEVCLLYATD 781 (1432)
Q Consensus 728 ~~~~~~~vEG~~D~ia~~~~g~----------------------~~~~i~~~~D~D~aG~~a~~~~~~~~~~~~~~ 781 (1432)
+.+.+|||||--|+.||...|| +.++||+++|.|.+|+..+.+.++.|...|+.
T Consensus 22 ~~~~~ilveg~~d~~~l~~lgi~g~~i~~s~~p~~~cad~ii~~gi~rVVi~~D~d~~G~~~~~~~~~~L~~aGi~ 97 (360)
T PRK14719 22 EKGIPILVEGPNDILSLKNLKINANFITVSNTPVFQIADDLIAENISEVILLTDFDRAGRVYAKNIMEEFQSRGIK 97 (360)
T ss_pred hCCCEEEEEcchHHHHHHHcCCCCcEEEEeCCchHHHHHHHHHcCCCEEEEEECCCCCCCccchHHHHHHHHCCCE
Confidence 4468999999999999999999 45788888899999999888889999888875
No 393
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=89.44 E-value=0.77 Score=49.94 Aligned_cols=54 Identities=17% Similarity=0.271 Sum_probs=45.3
Q ss_pred HccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchhhhh
Q psy15215 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYK 1422 (1432)
Q Consensus 1364 L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~~~~ 1422 (1432)
+..|+++|.+|+.+-. . ++|.++||+.+++|..||+...++.++||.-..+...
T Consensus 141 ~~~lt~~E~~vl~~l~-~----g~~~~~I~~~l~~s~~tv~~~~~~l~~Kl~~~~~~~l 194 (204)
T PRK09958 141 LDSLSKQEISVMRYIL-D----GKDNNDIAEKMFISNKTVSTYKSRLMEKLECKSLMDL 194 (204)
T ss_pred cccCCHHHHHHHHHHH-c----CCCHHHHHHHhCCCHHHHHHHHHHHHHHcCCCCHHHH
Confidence 3569999999998854 3 4499999999999999999999999999976555543
No 394
>PRK04841 transcriptional regulator MalT; Provisional
Probab=89.01 E-value=0.6 Score=63.80 Aligned_cols=55 Identities=24% Similarity=0.253 Sum_probs=47.7
Q ss_pred ccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchhhhhHH
Q psy15215 1365 NSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYKLK 1424 (1432)
Q Consensus 1365 ~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~~~~l~ 1424 (1432)
..||++|.+|+.+. ..|. |++|||..|+||..||+..+++..+||.-..|.....
T Consensus 837 ~~lt~~e~~v~~~~-~~g~----~~~~ia~~l~~s~~tv~~h~~~~~~kl~v~~r~~~~~ 891 (903)
T PRK04841 837 SPLTQREWQVLGLI-YSGY----SNEQIAGELDVAATTIKTHIRNLYQKLGIAHRQEAVQ 891 (903)
T ss_pred CCCCHHHHHHHHHH-HcCC----CHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCHHHHHH
Confidence 45999999999994 3555 9999999999999999999999999999877766543
No 395
>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=88.51 E-value=0.52 Score=38.32 Aligned_cols=33 Identities=18% Similarity=0.303 Sum_probs=22.9
Q ss_pred HHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q psy15215 1371 ESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEA 1408 (1432)
Q Consensus 1371 er~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~ 1408 (1432)
...|+.|+ -.| +|..+||+.||||+.||..++.
T Consensus 11 ~~~i~~l~-~~G----~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 11 IEEIKELY-AEG----MSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp HHHHHHHH-HTT------HHHHHHHTTS-HHHHHHHHC
T ss_pred HHHHHHHH-HCC----CCHHHHHHHHCcCHHHHHHHHh
Confidence 44566664 333 4999999999999999998763
No 396
>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=88.11 E-value=0.55 Score=39.70 Aligned_cols=40 Identities=23% Similarity=0.315 Sum_probs=28.8
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q psy15215 1366 SLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409 (1432)
Q Consensus 1366 ~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~r 1409 (1432)
.||..++.=+.-+|-.|. +..+||..|||+++||++|+..
T Consensus 6 ~LTl~eK~~iI~~~e~g~----s~~~ia~~fgv~~sTv~~I~K~ 45 (53)
T PF04218_consen 6 SLTLEEKLEIIKRLEEGE----SKRDIAREFGVSRSTVSTILKN 45 (53)
T ss_dssp S--HHHHHHHHHHHHCTT-----HHHHHHHHT--CCHHHHHHHC
T ss_pred cCCHHHHHHHHHHHHcCC----CHHHHHHHhCCCHHHHHHHHHh
Confidence 578788776656676666 9999999999999999999876
No 397
>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=87.64 E-value=0.77 Score=43.15 Aligned_cols=36 Identities=19% Similarity=0.331 Sum_probs=29.5
Q ss_pred HhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHH
Q psy15215 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQ 615 (1432)
Q Consensus 574 L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~ 615 (1432)
+++|++| ..|+.+. ..|+|..+||+.+|+|+.+|..
T Consensus 34 ~~~Ls~R-~~I~~ll-----~~G~S~~eIA~~LgISrsTIyR 69 (88)
T TIGR02531 34 IQSLAQR-LQVAKML-----KQGKTYSDIEAETGASTATISR 69 (88)
T ss_pred HHhhhHH-HHHHHHH-----HCCCCHHHHHHHHCcCHHHHHH
Confidence 4568999 7777764 3456999999999999999987
No 398
>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=87.54 E-value=1 Score=33.91 Aligned_cols=36 Identities=19% Similarity=0.375 Sum_probs=27.9
Q ss_pred CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHH
Q psy15215 1367 LTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQI 1406 (1432)
Q Consensus 1367 L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~ 1406 (1432)
+++.++..+...|..+. |..+||+.+|+|+.+|..+
T Consensus 6 ~~~~~~~~i~~~~~~~~----s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 6 LTPEQIEEARRLLAAGE----SVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred CCHHHHHHHHHHHHcCC----CHHHHHHHHCCCHHHHHHh
Confidence 56666666655565454 9999999999999999875
No 399
>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=87.31 E-value=1.4 Score=36.15 Aligned_cols=41 Identities=17% Similarity=0.269 Sum_probs=29.3
Q ss_pred CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q psy15215 1367 LTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 1410 (1432)
Q Consensus 1367 L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rA 1410 (1432)
|++.++.||..-+- ..+.|..|||+.+|+|+.+|++++.+-
T Consensus 1 l~~~~~~Il~~l~~---~~~~t~~ela~~~~is~~tv~~~l~~L 41 (48)
T PF13412_consen 1 LDETQRKILNYLRE---NPRITQKELAEKLGISRSTVNRYLKKL 41 (48)
T ss_dssp --HHHHHHHHHHHH---CTTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHH---cCCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 56788888866554 234699999999999999999877654
No 400
>PRK13558 bacterio-opsin activator; Provisional
Probab=86.53 E-value=1.2 Score=58.49 Aligned_cols=56 Identities=23% Similarity=0.211 Sum_probs=48.6
Q ss_pred HHhcCCHHHHHHHHHHhhccc---CCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHH
Q psy15215 573 ILNSLTPRESKVLRMRFGIEM---SSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLA 628 (1432)
Q Consensus 573 ~L~~L~~rer~Vl~lr~~~~~---~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l 628 (1432)
....||++|+++|..-|..|. ..+.|.+|||..||||++++.+++++|.+||-..+
T Consensus 604 ~~~~lt~~q~e~l~~a~~~gyf~~pr~~~~~e~a~~l~is~~t~~~~lr~a~~~l~~~~ 662 (665)
T PRK13558 604 LENDLTDRQLTALQKAYVSGYFEWPRRVEGEELAESMGISRSTFHQHLRAAERKLVGAF 662 (665)
T ss_pred hhhhCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 346799999999999998776 34579999999999999999999999999996543
No 401
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=86.47 E-value=1.5 Score=37.02 Aligned_cols=48 Identities=13% Similarity=0.242 Sum_probs=38.5
Q ss_pred cCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHH
Q psy15215 576 SLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRP 626 (1432)
Q Consensus 576 ~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~ 626 (1432)
+||..++-++.|.|.- .+.|++.+|..||||+++|.++.+....-|..
T Consensus 2 kLs~~d~lll~L~~LR---~~~~~~~La~~FgIs~stvsri~~~~~~~L~~ 49 (53)
T PF13613_consen 2 KLSLEDQLLLTLMYLR---LNLTFQDLAYRFGISQSTVSRIFHEWIPLLYQ 49 (53)
T ss_pred CCCHHHHHHHHHHHHH---cCCcHhHHhhheeecHHHHHHHHHHHHHHHHH
Confidence 5888999888777652 23499999999999999999888877666654
No 402
>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=86.41 E-value=1.1 Score=38.70 Aligned_cols=24 Identities=17% Similarity=0.465 Sum_probs=21.5
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHH
Q psy15215 1386 DHTLEEVGKQFDVTRERIRQIEAK 1409 (1432)
Q Consensus 1386 ~~t~~EIa~~l~vs~~~Vrq~~~r 1409 (1432)
..++.+||++||||..+||.+.++
T Consensus 22 ~i~lkdIA~~Lgvs~~tIr~WK~~ 45 (60)
T PF10668_consen 22 KIKLKDIAEKLGVSESTIRKWKSR 45 (60)
T ss_pred CccHHHHHHHHCCCHHHHHHHhhh
Confidence 459999999999999999998765
No 403
>PHA02547 55 RNA polymerase sigma factor; Provisional
Probab=86.24 E-value=3.6 Score=42.71 Aligned_cols=70 Identities=16% Similarity=0.208 Sum_probs=57.4
Q ss_pred HHHHHHHHHHHHHHhccCCCCC---hhHHHHHHHHHHHHHHHhccccCCCcchhHHHHHHHHHHHHHHHHhcc
Q psy15215 1195 MTEANLRLVISIAKKYTDRGLQ---FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR 1264 (1432)
Q Consensus 1195 Li~~~~~lV~~ia~~y~~~~~~---~~DLiQEg~igl~kav~kfd~~~g~~Fstya~~~ir~~i~~~i~~~~r 1264 (1432)
+=.+-+..+..++++|.-++.. -+|+|.+|.-.+++.+.+||+.+...+-.|.|..+-++..+.|....+
T Consensus 42 ig~~imkIa~glS~r~nF~~Yt~~wKedMI~DgIe~~i~ylhNFD~~k~~Np~aYiT~~~~~AF~~RI~kEkk 114 (179)
T PHA02547 42 IGLAIMKIAEGLSRRPNFSGYTQTWKEDMIADGIEACIKGLHNFDETKYKNPHAYITQACFNAFVQRIKKEKK 114 (179)
T ss_pred HHHHHHHHHhccccCCccccchHHHHHHHHHHHHHHHHHHhhcCCcccccChHHHHHHHHHHHHHHHHHHHHH
Confidence 4445555566666777666666 689999999999999999999999889999999999999988887664
No 404
>TIGR00334 5S_RNA_mat_M5 ribonuclease M5. This family of orthologous proteins shows a weak but significant similarity to the central region of the DnaG-type DNA primase. The region of similarity is termed the Toprim (topoisomerase-primase) domain and is also shared by RecR, OLD family nucleases, and type IA and II topoisomerases.
Probab=85.74 E-value=1.4 Score=46.64 Aligned_cols=38 Identities=18% Similarity=0.100 Sum_probs=31.4
Q ss_pred CeEEEEecchhHHHHhhhCC-----------------------CCCeEEEEecCcHHHHHH
Q psy15215 730 GYVLITEGYMDVIGLSQFGF-----------------------FANSSYTCFDGDQAGRRA 767 (1432)
Q Consensus 730 ~~~~~vEG~~D~ia~~~~g~-----------------------~~~~i~~~~D~D~aG~~a 767 (1432)
+.||||||=.|+.++.++.- ...-||++.|+|.||.+=
T Consensus 3 kevIVVEGK~D~~~lk~~~d~~~I~T~Gs~i~~~~i~~i~~~~~~rgVIIfTDpD~~GekI 63 (174)
T TIGR00334 3 KEIIVVEGKDDQARIKQAFDVDVIETNGSALKDETINLIKKAQKKQGVIILTDPDFPGEKI 63 (174)
T ss_pred CeEEEEecchHHHHHHHhcCceEEEECCCccCHHHHHHHHHHhhcCCEEEEeCCCCchHHH
Confidence 57999999999999988742 467789999999999654
No 405
>PRK10403 transcriptional regulator NarP; Provisional
Probab=85.70 E-value=1.1 Score=48.72 Aligned_cols=46 Identities=22% Similarity=0.280 Sum_probs=40.3
Q ss_pred hcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHH
Q psy15215 575 NSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625 (1432)
Q Consensus 575 ~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr 625 (1432)
..|+++|..|+.+.. .| +|.++||+.+++|+.+|+.+.++.++||.
T Consensus 152 ~~Lt~~e~~vl~~~~-~g----~s~~~ia~~l~~s~~tv~~~~~~i~~kl~ 197 (215)
T PRK10403 152 SVLTERELDVLHELA-QG----LSNKQIASVLNISEQTVKVHIRNLLRKLN 197 (215)
T ss_pred ccCCHHHHHHHHHHH-CC----CCHHHHHHHcCCCHHHHHHHHHHHHHHcC
Confidence 359999999998753 34 59999999999999999999999999985
No 406
>PHA02547 55 RNA polymerase sigma factor; Provisional
Probab=85.62 E-value=4.4 Score=42.11 Aligned_cols=67 Identities=16% Similarity=0.224 Sum_probs=52.4
Q ss_pred HHHHHHHHHHHhcccCCCC---hhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHHHHHHHHhcc
Q psy15215 408 ANLRLVISIAKKYTDRGLQ---FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR 474 (1432)
Q Consensus 408 ~~~~lV~~ia~ky~~~~~~---~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i~~~i~~~~r 474 (1432)
+-+..+..++++|-=+|.. -+|.|.+|.-.+++.+..||+.+...+.+|+|..+-++..+.|....+
T Consensus 45 ~imkIa~glS~r~nF~~Yt~~wKedMI~DgIe~~i~ylhNFD~~k~~Np~aYiT~~~~~AF~~RI~kEkk 114 (179)
T PHA02547 45 AIMKIAEGLSRRPNFSGYTQTWKEDMIADGIEACIKGLHNFDETKYKNPHAYITQACFNAFVQRIKKEKK 114 (179)
T ss_pred HHHHHHhccccCCccccchHHHHHHHHHHHHHHHHHHhhcCCcccccChHHHHHHHHHHHHHHHHHHHHH
Confidence 3344444444555444554 789999999999999999999999899999999999999888876654
No 407
>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=85.33 E-value=2.1 Score=34.29 Aligned_cols=39 Identities=13% Similarity=0.269 Sum_probs=26.3
Q ss_pred CHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q psy15215 1368 TPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409 (1432)
Q Consensus 1368 ~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~r 1409 (1432)
.+-.+.||..--.. ...|+.+||+.+|+|.++|.+++.+
T Consensus 2 D~~D~~Il~~Lq~d---~r~s~~~la~~lglS~~~v~~Ri~r 40 (42)
T PF13404_consen 2 DELDRKILRLLQED---GRRSYAELAEELGLSESTVRRRIRR 40 (42)
T ss_dssp -HHHHHHHHHHHH----TTS-HHHHHHHHTS-HHHHHHHHHH
T ss_pred CHHHHHHHHHHHHc---CCccHHHHHHHHCcCHHHHHHHHHH
Confidence 34456666554332 3469999999999999999988764
No 408
>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=84.86 E-value=3.5 Score=41.68 Aligned_cols=52 Identities=13% Similarity=0.185 Sum_probs=46.3
Q ss_pred HHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCch
Q psy15215 1363 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 1418 (1432)
Q Consensus 1363 ~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~ 1418 (1432)
.|.+-.|.+-.+|.++|..+. |...||..+++|...|++.+.+|-.-+..+.
T Consensus 59 ~L~~~~~~~~~ll~~~Yv~g~----s~r~IA~~~~~s~~~ir~~l~~ae~~i~g~l 110 (125)
T PF06530_consen 59 RLKKRDPEEYDLLILYYVYGW----SKRQIARKLKCSEGKIRKRLQRAEGFIDGCL 110 (125)
T ss_pred HHHccCHHHHHHHHHHHHcCC----CHHHHHHHHCCCHHHHHHHHHHhhhhHhhhh
Confidence 345578999999999999888 9999999999999999999999988887753
No 409
>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=84.81 E-value=1.1 Score=33.50 Aligned_cols=26 Identities=27% Similarity=0.494 Sum_probs=19.0
Q ss_pred CcHHHHHhhcccchhHHHHHHHHHHHHHHH
Q psy15215 597 HTLEEVGKQFDVTRERIRQIEAKALRKLRP 626 (1432)
Q Consensus 597 ~t~~EIa~~l~is~~~v~~~~~rAl~kLr~ 626 (1432)
.|.+|||..+|+|+++|+ |++.+|++
T Consensus 3 mtr~diA~~lG~t~ETVS----R~l~~l~~ 28 (32)
T PF00325_consen 3 MTRQDIADYLGLTRETVS----RILKKLER 28 (32)
T ss_dssp --HHHHHHHHTS-HHHHH----HHHHHHHH
T ss_pred cCHHHHHHHhCCcHHHHH----HHHHHHHH
Confidence 389999999999999998 55555543
No 410
>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=84.79 E-value=2.2 Score=37.74 Aligned_cols=41 Identities=17% Similarity=0.340 Sum_probs=31.2
Q ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHcCCC-HHHHHHHHHHc
Q psy15215 1277 NKISRISRQILQETGSEPDPSVIAIKMEMP-EEKIRKIMKIA 1317 (1432)
Q Consensus 1277 ~k~~~~~~~~~~~~g~~pt~~eia~~~~~~-~~~v~~~~~~~ 1317 (1432)
.++..+..+...+.|.+||..|||+.+|++ +..|...++..
T Consensus 9 ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~L 50 (65)
T PF01726_consen 9 KEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKAL 50 (65)
T ss_dssp HHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHH
Confidence 455666677788999999999999999997 99988888643
No 411
>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=84.70 E-value=2 Score=39.10 Aligned_cols=43 Identities=21% Similarity=0.264 Sum_probs=35.0
Q ss_pred cCCHHHHHHHHHH--hcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q psy15215 1366 SLTPRESKVLRMR--FGIEMSSDHTLEEVGKQFDVTRERIRQIEA 1408 (1432)
Q Consensus 1366 ~L~~rer~Vl~lr--~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~ 1408 (1432)
.|++||++||..- -+...+.+..-++||+.+++|..|||+.+.
T Consensus 1 ~Lt~rq~~IL~alV~~Y~~~~~PVgSk~ia~~l~~s~aTIRN~M~ 45 (78)
T PF03444_consen 1 MLTERQREILKALVELYIETGEPVGSKTIAEELGRSPATIRNEMA 45 (78)
T ss_pred CCCHHHHHHHHHHHHHHHhcCCCcCHHHHHHHHCCChHHHHHHHH
Confidence 3899999988752 233446889999999999999999998764
No 412
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=84.67 E-value=1.5 Score=47.26 Aligned_cols=46 Identities=20% Similarity=0.293 Sum_probs=40.2
Q ss_pred hcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHH
Q psy15215 575 NSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625 (1432)
Q Consensus 575 ~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr 625 (1432)
..|+++|..|+.+-. .| +|.++||+.+++|..+|+.+..+.++||.
T Consensus 136 ~~Lt~~E~~il~~l~-~g----~~~~~Ia~~l~~s~~tv~~~~~~l~~Kl~ 181 (196)
T PRK10360 136 DPLTKRERQVAEKLA-QG----MAVKEIAAELGLSPKTVHVHRANLMEKLG 181 (196)
T ss_pred cCCCHHHHHHHHHHH-CC----CCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 359999999999843 34 49999999999999999999999988885
No 413
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=84.66 E-value=1.4 Score=48.04 Aligned_cols=45 Identities=20% Similarity=0.314 Sum_probs=39.2
Q ss_pred cCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHH
Q psy15215 576 SLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625 (1432)
Q Consensus 576 ~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr 625 (1432)
.|+++|..|+.+ +..|. |.+|||+.+++|..+|+.+..++++||.
T Consensus 149 ~lt~re~~vl~~-l~~g~----s~~eIa~~l~~s~~tv~~~~~~~~~kl~ 193 (210)
T PRK09935 149 VLSNREVTILRY-LVSGL----SNKEIADQLLLSNKTVSAHKSNIYGKLG 193 (210)
T ss_pred cCCHHHHHHHHH-HHcCC----CHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 389999999975 43455 9999999999999999999999999985
No 414
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=84.61 E-value=1.1 Score=52.56 Aligned_cols=36 Identities=17% Similarity=0.325 Sum_probs=32.8
Q ss_pred HHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q psy15215 1373 KVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALR 1412 (1432)
Q Consensus 1373 ~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~ 1412 (1432)
++-.+||..|+ |..|||++||+||.+|+..+.+|++
T Consensus 17 ~~A~lYY~~gl----tQ~eIA~~LgiSR~~v~rlL~~Ar~ 52 (321)
T COG2390 17 RAAWLYYVEGL----TQSEIAERLGISRATVSRLLAKARE 52 (321)
T ss_pred HHHHHHHhcCC----CHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 46678998888 9999999999999999999999975
No 415
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=84.60 E-value=1 Score=53.15 Aligned_cols=37 Identities=16% Similarity=0.373 Sum_probs=32.2
Q ss_pred HHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHH
Q psy15215 582 SKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALR 622 (1432)
Q Consensus 582 r~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~ 622 (1432)
-+|-.|+|..|+ |+.|||++||+|+.+|.+.+.+|..
T Consensus 19 ~~vA~lYY~~g~----tQ~eIA~~lgiSR~~VsRlL~~Ar~ 55 (318)
T PRK15418 19 ARIAWFYYHDGL----TQSEIGERLGLTRLKVSRLLEKGRQ 55 (318)
T ss_pred HHHHHHHHhcCC----CHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 357789999898 9999999999999999987777654
No 416
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=84.19 E-value=1.6 Score=47.44 Aligned_cols=47 Identities=17% Similarity=0.391 Sum_probs=40.9
Q ss_pred HhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHH
Q psy15215 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625 (1432)
Q Consensus 574 L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr 625 (1432)
+..|+++|.+||.+-. .++|.++||+.+++|..+|+.+..+.++||.
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 3569999999998764 4459999999999999999999999999984
No 417
>PF13518 HTH_28: Helix-turn-helix domain
Probab=84.12 E-value=1.5 Score=36.42 Aligned_cols=33 Identities=9% Similarity=0.312 Sum_probs=26.0
Q ss_pred HHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q psy15215 1374 VLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKAL 1411 (1432)
Q Consensus 1374 Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl 1411 (1432)
|+.+.. .|. |+.+||..||||+.+|++++.+-.
T Consensus 5 iv~~~~-~g~----s~~~~a~~~gis~~tv~~w~~~y~ 37 (52)
T PF13518_consen 5 IVELYL-EGE----SVREIAREFGISRSTVYRWIKRYR 37 (52)
T ss_pred HHHHHH-cCC----CHHHHHHHHCCCHhHHHHHHHHHH
Confidence 454443 454 999999999999999999887654
No 418
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=83.74 E-value=1.8 Score=48.84 Aligned_cols=47 Identities=15% Similarity=0.241 Sum_probs=36.5
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q psy15215 1366 SLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALR 1412 (1432)
Q Consensus 1366 ~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~ 1412 (1432)
.|++++.+++..........++|.+|||+.||+|..||+....++..
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 48999987775443222345569999999999999999999988754
No 419
>COG4026 Uncharacterized protein containing TOPRIM domain, potential nuclease [General function prediction only]
Probab=83.09 E-value=4.8 Score=43.22 Aligned_cols=78 Identities=24% Similarity=0.213 Sum_probs=56.3
Q ss_pred CeEEEEecchhHHHHhhh------CC-----------------------CCCeEEEEecCcHHHHHHHHHHHHHhhhhcC
Q psy15215 730 GYVLITEGYMDVIGLSQF------GF-----------------------FANSSYTCFDGDQAGRRAARRALEVCLLYAT 780 (1432)
Q Consensus 730 ~~~~~vEG~~D~ia~~~~------g~-----------------------~~~~i~~~~D~D~aG~~a~~~~~~~~~~~~~ 780 (1432)
+.=|||||.-||=++.++ |- +++=|+++-|.|..|++-|.|..+-+....-
T Consensus 8 DVRIiVEGAsDvE~iSkalQr~aLG~eYnITisSIiPTT~~eIA~raaeGADlvlIATDaD~~GReLA~kf~eeLrg~VG 87 (290)
T COG4026 8 DVRIIVEGASDVEVISKALQRLALGSEYNITISSIIPTTNVEIAKRAAEGADLVLIATDADRVGRELAEKFFEELRGMVG 87 (290)
T ss_pred eEEEEeeccchHHHHHHHHHHhhhcccceeEEEeeccCchHHHHHHhhccCCEEEEeecCcchhHHHHHHHHHHHHHhhh
Confidence 345899999999877665 21 5777899999999999999999998775543
Q ss_pred CCceEEEecCCCCCCHH----HHHHHhChhhhhh
Q psy15215 781 DDKIIKFLFLPDKYDPD----SYIRKFGYKIFSK 810 (1432)
Q Consensus 781 ~~~~~~~~~lp~~~Dpd----e~~~~~g~~~~~~ 810 (1432)
. +.-+.+|-|.|.. +++++.-..++.+
T Consensus 88 h---iERmK~PiGHDvEhiD~elvrkEl~nAlvR 118 (290)
T COG4026 88 H---IERMKIPIGHDVEHIDVELVRKELKNALVR 118 (290)
T ss_pred h---hheeccCCCCCccccCHHHHHHHHHHHHHH
Confidence 3 5556789887542 3455544444433
No 420
>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=82.95 E-value=2.8 Score=39.29 Aligned_cols=58 Identities=17% Similarity=0.255 Sum_probs=40.2
Q ss_pred HHHHHHhc-CCHHHHHHHHHHhhcc---cCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHH
Q psy15215 569 VVKDILNS-LTPRESKVLRMRFGIE---MSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPL 627 (1432)
Q Consensus 569 ~l~~~L~~-L~~rer~Vl~lr~~~~---~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~ 627 (1432)
.+...+.. |||.|+.-+..|+-.- +..++|+.||++.+|+|..+|. +-+++|+..-..
T Consensus 18 e~~~f~~dL~T~~E~~~l~~R~~va~~lL~~g~syreIa~~tgvS~aTIt-Rvsr~Lk~~~~~ 79 (87)
T PF01371_consen 18 ECYDFFEDLCTPDELEALAQRWQVAKELLDEGKSYREIAEETGVSIATIT-RVSRCLKYGDDG 79 (87)
T ss_dssp CHHHHHHHHSSHHHHHHHHHHHHHHHHHHHTTSSHHHHHHHHTSTHHHHH-HHHHHHHHSHCH
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHH-HHHHHHHcCCHH
Confidence 34445543 8899988887776542 2356799999999999999987 444555544333
No 421
>PRK04841 transcriptional regulator MalT; Provisional
Probab=82.94 E-value=1.5 Score=60.03 Aligned_cols=46 Identities=26% Similarity=0.286 Sum_probs=41.0
Q ss_pred hcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHH
Q psy15215 575 NSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625 (1432)
Q Consensus 575 ~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr 625 (1432)
..||++|.+|+++. .. |+|++|||..++||.+||+.+.++.+.||.
T Consensus 837 ~~lt~~e~~v~~~~-~~----g~~~~~ia~~l~~s~~tv~~h~~~~~~kl~ 882 (903)
T PRK04841 837 SPLTQREWQVLGLI-YS----GYSNEQIAGELDVAATTIKTHIRNLYQKLG 882 (903)
T ss_pred CCCCHHHHHHHHHH-Hc----CCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 34999999999985 34 459999999999999999999999999995
No 422
>PHA00675 hypothetical protein
Probab=82.63 E-value=2.1 Score=38.44 Aligned_cols=40 Identities=20% Similarity=0.238 Sum_probs=33.7
Q ss_pred hcCCHHHHHHHHHHh-hcccCCCCcHHHHHhhcccchhHHHHHHH
Q psy15215 575 NSLTPRESKVLRMRF-GIEMSSDHTLEEVGKQFDVTRERIRQIEA 618 (1432)
Q Consensus 575 ~~L~~rer~Vl~lr~-~~~~~~~~t~~EIa~~l~is~~~v~~~~~ 618 (1432)
++|++.+-+.|+.++ -.|. |+.+||+.||+|+++|.++..
T Consensus 21 AKLt~~qV~~IR~l~~r~G~----s~~~IA~~fGVsrstV~~I~~ 61 (78)
T PHA00675 21 AKLTDAEVERIRELHEVEGM----SYAVLAEKFEQSKGAIAKICR 61 (78)
T ss_pred cccCHHHHHHHHHHHHhcCc----cHHHHHHHhCCCHHHHHHHHc
Confidence 468888888888777 5666 999999999999999998754
No 423
>smart00351 PAX Paired Box domain.
Probab=82.50 E-value=2.7 Score=42.45 Aligned_cols=42 Identities=12% Similarity=0.101 Sum_probs=32.9
Q ss_pred CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q psy15215 1367 LTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALR 1412 (1432)
Q Consensus 1367 L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~ 1412 (1432)
+|..+|.=+...|-.|. |..+||++||||+.+|..++++...
T Consensus 18 ~s~~~R~riv~~~~~G~----s~~~iA~~~gvs~~tV~kwi~r~~~ 59 (125)
T smart00351 18 LPDEERQRIVELAQNGV----RPCDISRQLCVSHGCVSKILGRYYE 59 (125)
T ss_pred CCHHHHHHHHHHHHcCC----CHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 56655554445554566 9999999999999999999998754
No 424
>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=82.47 E-value=2.3 Score=35.99 Aligned_cols=39 Identities=21% Similarity=0.367 Sum_probs=27.5
Q ss_pred HHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q psy15215 1370 RESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 1410 (1432)
Q Consensus 1370 rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rA 1410 (1432)
|++.||.+-+-.+ .+.|.+|||+.||||+.||++.+..-
T Consensus 1 R~~~il~~L~~~~--~~it~~eLa~~l~vS~rTi~~~i~~L 39 (55)
T PF08279_consen 1 RQKQILKLLLESK--EPITAKELAEELGVSRRTIRRDIKEL 39 (55)
T ss_dssp HHHHHHHHHHHTT--TSBEHHHHHHHCTS-HHHHHHHHHHH
T ss_pred CHHHHHHHHHHcC--CCcCHHHHHHHhCCCHHHHHHHHHHH
Confidence 4566666533222 34899999999999999999876654
No 425
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=81.16 E-value=1.4 Score=36.57 Aligned_cols=31 Identities=16% Similarity=0.350 Sum_probs=21.4
Q ss_pred HHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHH
Q psy15215 584 VLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 619 (1432)
Q Consensus 584 Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~r 619 (1432)
++.+.. .|. |..+||+.+|+|+.+|.++..+
T Consensus 10 ii~l~~-~G~----s~~~ia~~lgvs~~Tv~~w~kr 40 (50)
T PF13384_consen 10 IIRLLR-EGW----SIREIAKRLGVSRSTVYRWIKR 40 (50)
T ss_dssp HHHHHH-HT------HHHHHHHHTS-HHHHHHHHT-
T ss_pred HHHHHH-CCC----CHHHHHHHHCcCHHHHHHHHHH
Confidence 555554 254 9999999999999999987654
No 426
>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=81.03 E-value=2.8 Score=36.19 Aligned_cols=26 Identities=12% Similarity=0.312 Sum_probs=22.9
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHH
Q psy15215 1386 DHTLEEVGKQFDVTRERIRQIEAKAL 1411 (1432)
Q Consensus 1386 ~~t~~EIa~~l~vs~~~Vrq~~~rAl 1411 (1432)
+++..|||+.||+++.||.++..+.-
T Consensus 13 G~~~~eIA~~Lg~~~~TV~~W~~r~~ 38 (58)
T PF06056_consen 13 GWSIKEIAEELGVPRSTVYSWKDRYK 38 (58)
T ss_pred CCCHHHHHHHHCCChHHHHHHHHhhC
Confidence 34999999999999999999988753
No 427
>PF13730 HTH_36: Helix-turn-helix domain
Probab=80.46 E-value=4.7 Score=34.10 Aligned_cols=47 Identities=19% Similarity=0.374 Sum_probs=32.0
Q ss_pred cCCHHHHHHHHH--HhcccCCCC-CCHHHHHHHhCCCHHHHHHHHHHHHHHhhC
Q psy15215 1366 SLTPRESKVLRM--RFGIEMSSD-HTLEEVGKQFDVTRERIRQIEAKALRKLRH 1416 (1432)
Q Consensus 1366 ~L~~rer~Vl~l--r~~~~~~~~-~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~ 1416 (1432)
.|+|.++.|+.. +|..+.+.. .|.+.||+.+|+|+.||++ +++.|..
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 588888887654 332222222 3899999999999999985 5555543
No 428
>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=80.10 E-value=2.1 Score=34.79 Aligned_cols=36 Identities=19% Similarity=0.375 Sum_probs=23.8
Q ss_pred CCH-HHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHH
Q psy15215 577 LTP-RESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 617 (1432)
Q Consensus 577 L~~-rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~ 617 (1432)
+++ ....|+.|+ - .|+|..+||+.+|||+.+|....
T Consensus 6 ~~~~~~~~i~~l~-~----~G~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 6 LSKEQIEEIKELY-A----EGMSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp SSHCCHHHHHHHH-H----TT--HHHHHHHTTS-HHHHHHHH
T ss_pred CCHHHHHHHHHHH-H----CCCCHHHHHHHHCcCHHHHHHHH
Confidence 444 345566665 3 34599999999999999998654
No 429
>PHA02591 hypothetical protein; Provisional
Probab=80.00 E-value=2 Score=38.42 Aligned_cols=23 Identities=17% Similarity=0.365 Sum_probs=20.6
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHH
Q psy15215 1386 DHTLEEVGKQFDVTRERIRQIEA 1408 (1432)
Q Consensus 1386 ~~t~~EIa~~l~vs~~~Vrq~~~ 1408 (1432)
|+|.++||..||+|+++||+.++
T Consensus 59 GlSqeqIA~~LGVsqetVrKYL~ 81 (83)
T PHA02591 59 GFTVEKIASLLGVSVRKVRRYLE 81 (83)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHh
Confidence 33999999999999999999875
No 430
>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]
Probab=79.24 E-value=2.5 Score=54.58 Aligned_cols=52 Identities=19% Similarity=0.232 Sum_probs=46.6
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhCchhhhh
Q psy15215 1366 SLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRYYK 1422 (1432)
Q Consensus 1366 ~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~~~~~~~ 1422 (1432)
-||.||.+||.+-| .|+|.+|||+++.||-.||+..++.--.||.-..|...
T Consensus 831 ~Ls~RE~eVL~Lia-----~G~SN~eIa~~L~isl~TVKtH~rniy~KLgV~~RtqA 882 (894)
T COG2909 831 PLSQRELEVLGLIA-----QGLSNEEIAQELFISLTTVKTHIRNIYQKLGVANRTQA 882 (894)
T ss_pred CccHHHHHHHHHHH-----ccCCHHHHHHHHHHHHHHHHHHHHHHHHHhCcchHHHH
Confidence 59999999999987 45599999999999999999999999999987766554
No 431
>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=78.76 E-value=2.9 Score=35.32 Aligned_cols=40 Identities=23% Similarity=0.315 Sum_probs=27.3
Q ss_pred cCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHH
Q psy15215 576 SLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 619 (1432)
Q Consensus 576 ~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~r 619 (1432)
.||..++.=+.-+|-.|. +..+||+.|||+.++|+.+...
T Consensus 6 ~LTl~eK~~iI~~~e~g~----s~~~ia~~fgv~~sTv~~I~K~ 45 (53)
T PF04218_consen 6 SLTLEEKLEIIKRLEEGE----SKRDIAREFGVSRSTVSTILKN 45 (53)
T ss_dssp S--HHHHHHHHHHHHCTT-----HHHHHHHHT--CCHHHHHHHC
T ss_pred cCCHHHHHHHHHHHHcCC----CHHHHHHHhCCCHHHHHHHHHh
Confidence 477777775555676665 9999999999999999987653
No 432
>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=78.05 E-value=9.5 Score=38.58 Aligned_cols=51 Identities=14% Similarity=0.219 Sum_probs=44.7
Q ss_pred HhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHH
Q psy15215 574 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLA 628 (1432)
Q Consensus 574 L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l 628 (1432)
|.+-.|.+-.+|.++|..+. |...||..+++|...+++...+|-..+..++
T Consensus 60 L~~~~~~~~~ll~~~Yv~g~----s~r~IA~~~~~s~~~ir~~l~~ae~~i~g~l 110 (125)
T PF06530_consen 60 LKKRDPEEYDLLILYYVYGW----SKRQIARKLKCSEGKIRKRLQRAEGFIDGCL 110 (125)
T ss_pred HHccCHHHHHHHHHHHHcCC----CHHHHHHHHCCCHHHHHHHHHHhhhhHhhhh
Confidence 45578999999999998887 9999999999999999999988877776654
No 433
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=77.80 E-value=4.7 Score=33.56 Aligned_cols=38 Identities=24% Similarity=0.379 Sum_probs=27.8
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHH
Q psy15215 1366 SLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 1407 (1432)
Q Consensus 1366 ~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~ 1407 (1432)
.|++-||.-|-..+-.|. ++.|||.++|-|+..|+..+
T Consensus 4 ~Lt~~Eqaqid~m~qlG~----s~~~isr~i~RSr~~Ir~yl 41 (50)
T PF11427_consen 4 TLTDAEQAQIDVMHQLGM----SLREISRRIGRSRTCIRRYL 41 (50)
T ss_dssp ---HHHHHHHHHHHHTT------HHHHHHHHT--HHHHHHHH
T ss_pred cCCHHHHHHHHHHHHhch----hHHHHHHHhCccHHHHHHHh
Confidence 588889988888888888 99999999999999999764
No 434
>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=77.76 E-value=5.1 Score=32.84 Aligned_cols=40 Identities=18% Similarity=0.286 Sum_probs=27.8
Q ss_pred CCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHH
Q psy15215 577 LTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 619 (1432)
Q Consensus 577 L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~r 619 (1432)
|++.+++||..-+- ..+.|..|||+.+|+|.++|+++..+
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 56778888866554 23479999999999999999865543
No 435
>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]
Probab=77.76 E-value=2.6 Score=54.39 Aligned_cols=47 Identities=19% Similarity=0.236 Sum_probs=41.9
Q ss_pred cCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHH
Q psy15215 576 SLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPL 627 (1432)
Q Consensus 576 ~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~ 627 (1432)
-||.||.+||.+.| .|+|++|||+++.||..||+.+.+....||.-.
T Consensus 831 ~Ls~RE~eVL~Lia-----~G~SN~eIa~~L~isl~TVKtH~rniy~KLgV~ 877 (894)
T COG2909 831 PLSQRELEVLGLIA-----QGLSNEEIAQELFISLTTVKTHIRNIYQKLGVA 877 (894)
T ss_pred CccHHHHHHHHHHH-----ccCCHHHHHHHHHHHHHHHHHHHHHHHHHhCcc
Confidence 38999999999987 566999999999999999999999988888543
No 436
>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=76.91 E-value=4.5 Score=30.12 Aligned_cols=36 Identities=19% Similarity=0.375 Sum_probs=27.0
Q ss_pred CCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHH
Q psy15215 577 LTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQI 616 (1432)
Q Consensus 577 L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~ 616 (1432)
+++.++..+...|..+. |..+||+.+|++..+|..+
T Consensus 6 ~~~~~~~~i~~~~~~~~----s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 6 LTPEQIEEARRLLAAGE----SVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred CCHHHHHHHHHHHHcCC----CHHHHHHHHCCCHHHHHHh
Confidence 55666665555564444 9999999999999998764
No 437
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=76.34 E-value=4.1 Score=46.02 Aligned_cols=47 Identities=15% Similarity=0.241 Sum_probs=35.0
Q ss_pred cCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHHH
Q psy15215 576 SLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALR 622 (1432)
Q Consensus 576 ~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl~ 622 (1432)
.|++++.+++........+.|+|.+|||..+|+|+.||+....+...
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 48999987765443322345669999999999999999987765533
No 438
>cd00131 PAX Paired Box domain
Probab=75.93 E-value=5.8 Score=40.28 Aligned_cols=42 Identities=10% Similarity=0.078 Sum_probs=31.9
Q ss_pred CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q psy15215 1367 LTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALR 1412 (1432)
Q Consensus 1367 L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~ 1412 (1432)
||...|.-+..-|-.|. |..+||++||||+++|..+.++-..
T Consensus 18 lS~d~R~rIv~~~~~G~----s~~~iA~~~~Vs~~tV~r~i~r~~e 59 (128)
T cd00131 18 LPDSIRQRIVELAQSGI----RPCDISRQLRVSHGCVSKILNRYYE 59 (128)
T ss_pred CCHHHHHHHHHHHHcCC----CHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 55545543334455666 9999999999999999999998653
No 439
>PF13730 HTH_36: Helix-turn-helix domain
Probab=75.86 E-value=7.4 Score=32.85 Aligned_cols=46 Identities=20% Similarity=0.351 Sum_probs=31.5
Q ss_pred cCCHHHHHHHHHHhhcccCCC---CcHHHHHhhcccchhHHHHHHHHHHHHHH
Q psy15215 576 SLTPRESKVLRMRFGIEMSSD---HTLEEVGKQFDVTRERIRQIEAKALRKLR 625 (1432)
Q Consensus 576 ~L~~rer~Vl~lr~~~~~~~~---~t~~EIa~~l~is~~~v~~~~~rAl~kLr 625 (1432)
.|+|.++.|+..-...-.+.+ .|.+.||+.+|+|+.+|. ++++.|.
T Consensus 2 ~Ls~~~~~v~~~l~~~~~~~~~~~pS~~~la~~~g~s~~Tv~----~~i~~L~ 50 (55)
T PF13730_consen 2 NLSPTAKLVYLYLASYANKNGGCFPSQETLAKDLGVSRRTVQ----RAIKELE 50 (55)
T ss_pred CCCHHHHHHHHHHHHhcCCCCCCCcCHHHHHHHHCcCHHHHH----HHHHHHH
Confidence 588888887654332221122 389999999999999998 5555554
No 440
>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=75.75 E-value=4.9 Score=37.70 Aligned_cols=48 Identities=19% Similarity=0.278 Sum_probs=35.5
Q ss_pred CCHHHHHHHHHHhcccC---CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhh
Q psy15215 1367 LTPRESKVLRMRFGIEM---SSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 1415 (1432)
Q Consensus 1367 L~~rer~Vl~lr~~~~~---~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr 1415 (1432)
|||.|+.-+..|+-.-. ..++|+.||++.+|+|..||. +.+|+++..-
T Consensus 27 ~T~~E~~~l~~R~~va~~lL~~g~syreIa~~tgvS~aTIt-Rvsr~Lk~~~ 77 (87)
T PF01371_consen 27 CTPDELEALAQRWQVAKELLDEGKSYREIAEETGVSIATIT-RVSRCLKYGD 77 (87)
T ss_dssp SSHHHHHHHHHHHHHHHHHHHTTSSHHHHHHHHTSTHHHHH-HHHHHHHHSH
T ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHH-HHHHHHHcCC
Confidence 78888877766664321 256799999999999999997 4566666543
No 441
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=75.19 E-value=31 Score=31.11 Aligned_cols=25 Identities=12% Similarity=0.189 Sum_probs=21.7
Q ss_pred CCCHHHHHHHcCCCHHHHHHHHHHc
Q psy15215 1293 EPDPSVIAIKMEMPEEKIRKIMKIA 1317 (1432)
Q Consensus 1293 ~pt~~eia~~~~~~~~~v~~~~~~~ 1317 (1432)
++|+++||+.+|+++..+..+++..
T Consensus 1 ~~~~~~la~~~~~s~~~l~~~f~~~ 25 (84)
T smart00342 1 PLTLEDLAEALGMSPRHLQRLFKKE 25 (84)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 4789999999999999999987643
No 442
>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=74.81 E-value=4.4 Score=35.09 Aligned_cols=37 Identities=14% Similarity=0.330 Sum_probs=26.0
Q ss_pred HHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHH
Q psy15215 581 ESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 619 (1432)
Q Consensus 581 er~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~r 619 (1432)
--..+.++.- .+...++.+||+.||||..+|+....+
T Consensus 9 rdkA~e~y~~--~~g~i~lkdIA~~Lgvs~~tIr~WK~~ 45 (60)
T PF10668_consen 9 RDKAFEIYKE--SNGKIKLKDIAEKLGVSESTIRKWKSR 45 (60)
T ss_pred HHHHHHHHHH--hCCCccHHHHHHHHCCCHHHHHHHhhh
Confidence 3344444432 223559999999999999999987654
No 443
>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=74.76 E-value=7.1 Score=36.50 Aligned_cols=45 Identities=18% Similarity=0.363 Sum_probs=34.2
Q ss_pred HccCCHHHHHHHHHHhcccCCCCCCHHHHHHHh--CCCHHHHHHHHHHHH
Q psy15215 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQF--DVTRERIRQIEAKAL 1411 (1432)
Q Consensus 1364 L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l--~vs~~~Vrq~~~rAl 1411 (1432)
++.||+..+.+..+|.- ..+.|+.|+|+.+ .+|.+.|..++.|-.
T Consensus 35 ~~~l~~~l~~~a~lRl~---~Pd~SL~EL~~~~~~~iSKSgvnhrlrKl~ 81 (85)
T PF02650_consen 35 LDKLPEKLREFAELRLE---NPDASLKELGELLEPPISKSGVNHRLRKLK 81 (85)
T ss_dssp GGGS-HHHHHHHHHHHH----TTS-HHHHHHTT--T--HHHHHHHHHHHH
T ss_pred cccCCHHHHHHHHHHHH---CccccHHHHHHHHcCcCcHHHHHHHHHHHH
Confidence 57899999999999974 3557999999999 899999998877643
No 444
>PRK12423 LexA repressor; Provisional
Probab=74.21 E-value=4.7 Score=44.41 Aligned_cols=48 Identities=21% Similarity=0.387 Sum_probs=33.7
Q ss_pred ccCCHHHHHHHHHH--hcccCCCCCCHHHHHHHhC-CCHHHHHHHHHHHHHHhhC
Q psy15215 1365 NSLTPRESKVLRMR--FGIEMSSDHTLEEVGKQFD-VTRERIRQIEAKALRKLRH 1416 (1432)
Q Consensus 1365 ~~L~~rer~Vl~lr--~~~~~~~~~t~~EIa~~l~-vs~~~Vrq~~~rAl~kLr~ 1416 (1432)
..||+++++|+..- +....+.+-|..|||+.|| +|+++|+. ++++|++
T Consensus 2 ~~lt~~q~~il~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~~----~l~~L~~ 52 (202)
T PRK12423 2 DTLTPKRAAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARK----HVQALAE 52 (202)
T ss_pred CcCCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHH----HHHHHHH
Confidence 35899999998752 2222233459999999999 59999995 4444443
No 445
>PRK11083 DNA-binding response regulator CreB; Provisional
Probab=73.63 E-value=3.9 Score=45.10 Aligned_cols=50 Identities=14% Similarity=0.047 Sum_probs=43.3
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCC-----HHHHHHHHHHHHHHhhC
Q psy15215 1366 SLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVT-----RERIRQIEAKALRKLRH 1416 (1432)
Q Consensus 1366 ~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs-----~~~Vrq~~~rAl~kLr~ 1416 (1432)
.||++|.+||.+-. .+.|...|.++|++.++.+ ..||+...++.++||..
T Consensus 154 ~Lt~~E~~il~~l~-~~~~~~~s~~~i~~~l~~~~~~~~~~tv~~~i~~l~~Kl~~ 208 (228)
T PRK11083 154 TLTRYEFLLLKTLL-LSPGRVFSRQQLMDIVWEDAQDSYDRTVDTHIKTLRAKLRA 208 (228)
T ss_pred ecCHHHHHHHHHHH-hCCCceECHHHHHHHhcCCCCCCCccCHHHHHHHHHHHhcc
Confidence 59999999998754 4555678999999999986 78999999999999974
No 446
>cd01025 TOPRIM_recR TOPRIM_recR: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in Escherichia coli RecR. RecR participates in the RecFOR pathway of homologous recombinational repair in prokaryotes. This pathway provides a single-stranded DNA molecule coated with RecA to allow invasion of a homologous molecule. The RecFOR system directs the loading of RecA onto gapped DNA coated with SSB protein. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). In RecR sequences this glutamate in the first turn of the TOPRIM domain is semiconserved, the DXD motif is not conserved.
Probab=73.53 E-value=11 Score=37.14 Aligned_cols=62 Identities=11% Similarity=0.127 Sum_probs=46.6
Q ss_pred CeEEEEecchhHHHHhhhCC-----------------------------------CCCeEEEEecCcHHHHHHHHHHHHH
Q psy15215 730 GYVLITEGYMDVIGLSQFGF-----------------------------------FANSSYTCFDGDQAGRRAARRALEV 774 (1432)
Q Consensus 730 ~~~~~vEG~~D~ia~~~~g~-----------------------------------~~~~i~~~~D~D~aG~~a~~~~~~~ 774 (1432)
+.++|||-.-|++++.+.|. ..++|||++|.+.-|..-|.-..+.
T Consensus 1 ~~lcVVE~~~Dv~~iE~~~~y~G~Y~VL~G~ispl~gi~p~~l~i~~L~~ri~~~~i~EVIlA~~pt~EGe~Ta~yi~~~ 80 (112)
T cd01025 1 NKLCVVEEPRDVLAIEESGEYRGLYHVLGGLISPLDGIGPDDLNIDKLLERIAKGQVKEVILATNPTVEGEATALYIAKL 80 (112)
T ss_pred CEEEEECCHHHHHHHHhhCccceEEEEeCCCcCCCCCCCccccCHHHHHHHHhcCCCcEEEEecCCCchHHHHHHHHHHH
Confidence 35889999999999999885 3578999999999998888777777
Q ss_pred hhhhcCCCceEEEec-CCCC
Q psy15215 775 CLLYATDDKIIKFLF-LPDK 793 (1432)
Q Consensus 775 ~~~~~~~~~~~~~~~-lp~~ 793 (1432)
+...+.. ..+++. +|-|
T Consensus 81 l~~~~~k--vsRlA~GiP~G 98 (112)
T cd01025 81 LKDFGVK--VTRLAQGIPVG 98 (112)
T ss_pred HhHcCCC--eEEEEEcCCCC
Confidence 6654433 233333 6655
No 447
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=73.49 E-value=7.5 Score=36.17 Aligned_cols=45 Identities=22% Similarity=0.215 Sum_probs=36.9
Q ss_pred ccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q psy15215 1365 NSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALR 1412 (1432)
Q Consensus 1365 ~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~ 1412 (1432)
..|||.-|..|..+...+ +.+..++|+.||||+.|++.+..|-..
T Consensus 7 A~Lt~~gR~~lv~~vv~~---g~~~a~aA~~~gVS~~Ta~kW~~Ryra 51 (85)
T PF13011_consen 7 ARLTPRGRLRLVRRVVEQ---GWPVAHAAAEFGVSRRTAYKWLARYRA 51 (85)
T ss_pred CCCCHHHHHHHHHHHHHc---CCcHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 359999999888877532 349999999999999999999987553
No 448
>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=73.20 E-value=8 Score=31.01 Aligned_cols=38 Identities=13% Similarity=0.276 Sum_probs=24.9
Q ss_pred HHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHH
Q psy15215 579 PRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 619 (1432)
Q Consensus 579 ~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~r 619 (1432)
+-.+.||..--.. ...|+.+||+.+|+|+++|.++..+
T Consensus 3 ~~D~~Il~~Lq~d---~r~s~~~la~~lglS~~~v~~Ri~r 40 (42)
T PF13404_consen 3 ELDRKILRLLQED---GRRSYAELAEELGLSESTVRRRIRR 40 (42)
T ss_dssp HHHHHHHHHHHH----TTS-HHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHc---CCccHHHHHHHHCcCHHHHHHHHHH
Confidence 3455566544332 3469999999999999999876553
No 449
>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=72.73 E-value=8.3 Score=35.31 Aligned_cols=53 Identities=17% Similarity=0.214 Sum_probs=35.9
Q ss_pred HHHHHHHHHccCCHHHHHHHHHHhccc-CCCCCCHHHHHHHhCCCHHHHHHHHH
Q psy15215 1356 MRSVVKDILNSLTPRESKVLRMRFGIE-MSSDHTLEEVGKQFDVTRERIRQIEA 1408 (1432)
Q Consensus 1356 ~~~~l~~~L~~L~~rer~Vl~lr~~~~-~~~~~t~~EIa~~l~vs~~~Vrq~~~ 1408 (1432)
+...|.....+||+.|+.|...-.-.- .-...|..|||+..|||..+|-+.-+
T Consensus 3 l~~~i~~~~~~ls~~e~~Ia~yil~~~~~~~~~si~elA~~~~vS~sti~Rf~k 56 (77)
T PF01418_consen 3 LLEKIRSQYNSLSPTEKKIADYILENPDEIAFMSISELAEKAGVSPSTIVRFCK 56 (77)
T ss_dssp HHHHHHHHGGGS-HHHHHHHHHHHH-HHHHCT--HHHHHHHCTS-HHHHHHHHH
T ss_pred HHHHHHHHHhhCCHHHHHHHHHHHhCHHHHHHccHHHHHHHcCCCHHHHHHHHH
Confidence 456778888999999999876533211 11456999999999999999986543
No 450
>PRK15479 transcriptional regulatory protein TctD; Provisional
Probab=72.03 E-value=5 Score=43.97 Aligned_cols=50 Identities=24% Similarity=0.238 Sum_probs=43.5
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHhhC
Q psy15215 1366 SLTPRESKVLRMRFGIEMSSDHTLEEVGKQFD-----VTRERIRQIEAKALRKLRH 1416 (1432)
Q Consensus 1366 ~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~-----vs~~~Vrq~~~rAl~kLr~ 1416 (1432)
.||++|.+|+.+. ..+.|...|.++|++.+. +|..+|+...++.++||..
T Consensus 148 ~Lt~~E~~il~~l-~~~~~~~~~~~~i~~~l~~~~~~~~~~tv~~~i~~ir~kl~~ 202 (221)
T PRK15479 148 ALTPREQALLTVL-MYRRTRPVSRQQLFEQVFSLNDEVSPESIELYIHRLRKKLQG 202 (221)
T ss_pred ecCHHHHHHHHHH-HhCCCCcCcHHHHHHHhcCCCCCCCcccHHHHHHHHHHhcCC
Confidence 5999999999775 555567789999999986 9999999999999999964
No 451
>PRK10336 DNA-binding transcriptional regulator QseB; Provisional
Probab=72.03 E-value=4.5 Score=44.27 Aligned_cols=50 Identities=18% Similarity=0.192 Sum_probs=43.4
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHhhC
Q psy15215 1366 SLTPRESKVLRMRFGIEMSSDHTLEEVGKQFD-----VTRERIRQIEAKALRKLRH 1416 (1432)
Q Consensus 1366 ~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~-----vs~~~Vrq~~~rAl~kLr~ 1416 (1432)
.||++|.+||.+ +..+.|..+|.++|++.+. +|..+|+...++.++||..
T Consensus 149 ~Lt~~E~~il~~-l~~~~~~~~s~~~i~~~l~~~~~~~~~~tv~~~i~~lr~Kl~~ 203 (219)
T PRK10336 149 TLKPKEFALLEL-LMRNAGRVLPRKLIEEKLYTWDEEVTSNAVEVHVHHLRRKLGS 203 (219)
T ss_pred ecCHHHHHHHHH-HHhCCCccCcHHHHHHHhcCCCCCCCccCHHHHHHHHHHhcCC
Confidence 499999999976 4456567789999999996 9999999999999999963
No 452
>COG3593 Predicted ATP-dependent endonuclease of the OLD family [DNA replication, recombination, and repair]
Probab=71.98 E-value=3.6 Score=51.89 Aligned_cols=80 Identities=21% Similarity=0.173 Sum_probs=59.4
Q ss_pred eeeeeeeeeeCCCCCCCCCCCcccCccccCchHhHHhhccCCeEEEEecchhHHHHh----hhCC---------------
Q psy15215 689 RNHGISGFLLTTPDPVHETPLFHKSNELYGLFEAKNAIGKSGYVLITEGYMDVIGLS----QFGF--------------- 749 (1432)
Q Consensus 689 r~igf~gR~~~~~~~s~et~~f~K~~~Ly~~~~a~~~~~~~~~~~~vEG~~D~ia~~----~~g~--------------- 749 (1432)
++.+|+....+- +.+. .|....|.++.++..+-=.+.+|+|||..++|-+. +.|+
T Consensus 362 ~v~~~~~~~~~~---~~~~---~~r~i~r~l~~trs~~lFAr~vIlVEG~aE~ill~~la~~~~~~L~~~gi~VI~~~gs 435 (581)
T COG3593 362 RVAAFQLGPNNF---SKEE---DKRRIKRHLDATRSSLLFARGVILVEGEAEVILLPELARQCGIDLEKEGIIVIEFAGS 435 (581)
T ss_pred ceeeeccCcccc---cccc---chhhhhhhcccccchhhhhceeEEEeccchhhhHHHHHHHhccccccCcEEEEeeccc
Confidence 455655443332 2333 67888889988888776678899999999999876 4555
Q ss_pred -----------CCCeEEEEecCcHHHHHHHHHHHHH
Q psy15215 750 -----------FANSSYTCFDGDQAGRRAARRALEV 774 (1432)
Q Consensus 750 -----------~~~~i~~~~D~D~aG~~a~~~~~~~ 774 (1432)
...++.+..|+|.||.++..++-.+
T Consensus 436 ~~k~f~kf~~~~gI~~~vitD~D~~g~~~~~~~~~l 471 (581)
T COG3593 436 GLKPFIKFAEAMGIRVHVITDGDEAGKKYEATVRDL 471 (581)
T ss_pred CcHHHHHHhhccCceEEEEecCCcccchhhhhhhhc
Confidence 3458899999999999998777643
No 453
>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=71.94 E-value=7.5 Score=33.57 Aligned_cols=44 Identities=18% Similarity=0.281 Sum_probs=32.9
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q psy15215 1366 SLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 1410 (1432)
Q Consensus 1366 ~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rA 1410 (1432)
.|++.+..||..-+..+. .+.|..|||+.+++++++|.+++++-
T Consensus 2 glt~~q~~vL~~l~~~~~-~~~t~~~la~~l~~~~~~vs~~v~~L 45 (62)
T PF12802_consen 2 GLTPSQFRVLMALARHPG-EELTQSELAERLGISKSTVSRIVKRL 45 (62)
T ss_dssp TSTHHHHHHHHHHHHSTT-SGEEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHHCCC-CCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 478888888876554442 23699999999999999998776553
No 454
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=71.73 E-value=6.4 Score=40.32 Aligned_cols=36 Identities=17% Similarity=0.250 Sum_probs=30.2
Q ss_pred HHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q psy15215 1372 SKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKAL 1411 (1432)
Q Consensus 1372 r~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl 1411 (1432)
+.++...++.|+ |..|||++||||.+||..++++..
T Consensus 11 ~~~~~~~~~~G~----S~re~Ak~~gvs~sTvy~wv~r~~ 46 (138)
T COG3415 11 ERVVDAVVGEGL----SCREAAKRFGVSISTVYRWVRRYR 46 (138)
T ss_pred HHHHHHHHHcCc----cHHHHHHHhCccHHHHHHHHHHhc
Confidence 345666677777 999999999999999999988765
No 455
>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=71.43 E-value=6.4 Score=34.24 Aligned_cols=46 Identities=15% Similarity=0.343 Sum_probs=31.1
Q ss_pred CCHHHHHHHHHHhccc-CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhC
Q psy15215 1367 LTPRESKVLRMRFGIE-MSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 1416 (1432)
Q Consensus 1367 L~~rer~Vl~lr~~~~-~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~ 1416 (1432)
|++....-|..-|.+. .+...+..+||+.||||+++|.. ++++|.+
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 5555555555544433 45678999999999999999985 4455543
No 456
>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=71.39 E-value=29 Score=34.68 Aligned_cols=88 Identities=15% Similarity=0.220 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCC
Q psy15215 1251 IRQAITRSIADQARTIRIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDD 1330 (1432)
Q Consensus 1251 ir~~i~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~ 1330 (1432)
+|+.+.+++..-. +..++|...+|+...|..+++..
T Consensus 7 lR~rVl~~~~~g~-------------------------------s~~eaa~~F~VS~~Tv~~W~k~~------------- 42 (119)
T PF01710_consen 7 LRQRVLAYIEKGK-------------------------------SIREAAKRFGVSRNTVYRWLKRK------------- 42 (119)
T ss_pred HHHHHHHHHHccc-------------------------------hHHHHHHHhCcHHHHHHHHHHhc-------------
Q ss_pred CCCCcCcccccCCCCChHHHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q psy15215 1331 EDSHLGDFIEDENMLAPSDAALNASMRSVVKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409 (1432)
Q Consensus 1331 ~~~~~~d~i~d~~~~~p~~~~~~~~~~~~l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~r 1409 (1432)
..+++-+.+.... .+....+...|.. .-+. |+.|+|+.||||.++|...+.+
T Consensus 43 ---~~G~~~~k~r~~~---Kid~~~L~~~v~~-----------------~pd~----tl~Ela~~l~Vs~~ti~~~Lkr 94 (119)
T PF01710_consen 43 ---ETGDLEPKPRGRK---KIDRDELKALVEE-----------------NPDA----TLRELAERLGVSPSTIWRALKR 94 (119)
T ss_pred ---ccccccccccccc---cccHHHHHHHHHH-----------------CCCc----CHHHHHHHcCCCHHHHHHHHHH
No 457
>COG2973 TrpR Trp operon repressor [Transcription]
Probab=71.10 E-value=13 Score=34.97 Aligned_cols=60 Identities=25% Similarity=0.426 Sum_probs=42.5
Q ss_pred CCHHHHHHHHHHhhcc---cCCCCcHHHHHhhcccchhHHHHHHHHHHHHHHHHHHHHHHHhhh
Q psy15215 577 LTPRESKVLRMRFGIE---MSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRPLAHDWLEQRTH 637 (1432)
Q Consensus 577 L~~rer~Vl~lr~~~~---~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr~~l~~~~~~~l~ 637 (1432)
|||.||+-+-.|+-+- +....|..||++.+|+|..++- +-+..++-+-..+..|+++.+.
T Consensus 38 LTpdEReal~~Rv~Iv~eLL~ge~sQREi~~~LgvsiAtIT-RGSN~LK~~~~~~k~~L~~~l~ 100 (103)
T COG2973 38 LTPDEREALGTRVRIVEELLRGELSQREIAQKLGVSIATIT-RGSNSLKTADPEFKQWLEKVLL 100 (103)
T ss_pred cCHhHHHHHHHHHHHHHHHHhccccHHHHHHHhCcchhhhc-cchhhhccCCHHHHHHHHHHhc
Confidence 7888888777776541 2345699999999999999885 3344555555667778877653
No 458
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=71.06 E-value=4.5 Score=47.59 Aligned_cols=35 Identities=17% Similarity=0.330 Sum_probs=29.7
Q ss_pred HHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHHH
Q psy15215 583 KVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKAL 621 (1432)
Q Consensus 583 ~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rAl 621 (1432)
++-.|+|..|+ |+.|||++||+|+.+|++...+|.
T Consensus 17 ~~A~lYY~~gl----tQ~eIA~~LgiSR~~v~rlL~~Ar 51 (321)
T COG2390 17 RAAWLYYVEGL----TQSEIAERLGISRATVSRLLAKAR 51 (321)
T ss_pred HHHHHHHhcCC----CHHHHHHHhCCCHHHHHHHHHHHH
Confidence 46678998888 999999999999999997666554
No 459
>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=70.63 E-value=4.1 Score=33.37 Aligned_cols=22 Identities=9% Similarity=0.394 Sum_probs=19.7
Q ss_pred CHHHHHHHhCCCHHHHHHHHHH
Q psy15215 1388 TLEEVGKQFDVTRERIRQIEAK 1409 (1432)
Q Consensus 1388 t~~EIa~~l~vs~~~Vrq~~~r 1409 (1432)
|+++||+..|||..||+..++.
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 7899999999999999987764
No 460
>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=70.43 E-value=8.2 Score=33.58 Aligned_cols=45 Identities=16% Similarity=0.348 Sum_probs=31.3
Q ss_pred CCHHHHHHHHHHhhcc-cCCCCcHHHHHhhcccchhHHHHHHHHHHHHHH
Q psy15215 577 LTPRESKVLRMRFGIE-MSSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625 (1432)
Q Consensus 577 L~~rer~Vl~lr~~~~-~~~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr 625 (1432)
|++....-|...|... .+...+..+||+.||+|+++|.. ++++|.
T Consensus 2 Lt~~~e~YL~~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~----ml~~L~ 47 (60)
T PF01325_consen 2 LTESEEDYLKAIYELSEEGGPVRTKDIAERLGVSPPTVTE----MLKRLA 47 (60)
T ss_dssp CSCHHHHHHHHHHHHHHCTSSBBHHHHHHHHTS-HHHHHH----HHHHHH
T ss_pred CCcHHHHHHHHHHHHHcCCCCccHHHHHHHHCCChHHHHH----HHHHHH
Confidence 5666666666555544 34678999999999999999984 455553
No 461
>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=69.14 E-value=9.5 Score=31.22 Aligned_cols=37 Identities=14% Similarity=0.318 Sum_probs=26.1
Q ss_pred HHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q psy15215 1369 PRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409 (1432)
Q Consensus 1369 ~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~r 1409 (1432)
|.-..|+.+-.. .+++..||++.+|+|+++|++.+..
T Consensus 2 ~~R~~Il~~L~~----~~~~~~el~~~l~~s~~~vs~hL~~ 38 (47)
T PF01022_consen 2 PTRLRILKLLSE----GPLTVSELAEELGLSQSTVSHHLKK 38 (47)
T ss_dssp HHHHHHHHHHTT----SSEEHHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHHHHHHh----CCCchhhHHHhccccchHHHHHHHH
Confidence 344455555442 4569999999999999999987654
No 462
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=69.11 E-value=9.5 Score=34.05 Aligned_cols=24 Identities=8% Similarity=0.246 Sum_probs=20.7
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHH
Q psy15215 1386 DHTLEEVGKQFDVTRERIRQIEAK 1409 (1432)
Q Consensus 1386 ~~t~~EIa~~l~vs~~~Vrq~~~r 1409 (1432)
+.|..|||+.+|+++.+|++++.+
T Consensus 22 ~~ta~eLa~~lgl~~~~v~r~L~~ 45 (68)
T smart00550 22 TSTALQLAKNLGLPKKEVNRVLYS 45 (68)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHH
Confidence 479999999999999999876553
No 463
>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=68.92 E-value=15 Score=31.91 Aligned_cols=42 Identities=14% Similarity=0.290 Sum_probs=29.2
Q ss_pred HHHHccCCHHHHHHHHHH-hcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q psy15215 1361 KDILNSLTPRESKVLRMR-FGIEMSSDHTLEEVGKQFDVTRERIRQIEA 1408 (1432)
Q Consensus 1361 ~~~L~~L~~rer~Vl~lr-~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~ 1408 (1432)
-++|++ |.-+.||.+- - +.+.|..|||+.+|+|.++|++.+.
T Consensus 4 ~~aL~~--p~R~~Il~~L~~----~~~~t~~ela~~l~~~~~t~s~hL~ 46 (61)
T PF12840_consen 4 FKALSD--PTRLRILRLLAS----NGPMTVSELAEELGISQSTVSYHLK 46 (61)
T ss_dssp HHHHTS--HHHHHHHHHHHH----CSTBEHHHHHHHHTS-HHHHHHHHH
T ss_pred HHHhCC--HHHHHHHHHHhc----CCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 345554 5556666655 3 3456999999999999999987654
No 464
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=68.51 E-value=17 Score=33.00 Aligned_cols=49 Identities=29% Similarity=0.519 Sum_probs=39.3
Q ss_pred HHHHHHHhhcccCCCCcHHHHHhhcc------cchhHHHHHH-----HHHHHHHHHHHHHHHHH
Q psy15215 582 SKVLRMRFGIEMSSDHTLEEVGKQFD------VTRERIRQIE-----AKALRKLRPLAHDWLEQ 634 (1432)
Q Consensus 582 r~Vl~lr~~~~~~~~~t~~EIa~~l~------is~~~v~~~~-----~rAl~kLr~~l~~~~~~ 634 (1432)
..+...|--.|+ |+.++|+.+| +|.++|.+.+ .+...+|+-.+..|+++
T Consensus 14 ~~lk~~R~~lGL----TQ~dvA~~lg~~~g~i~SQstISR~Es~~ls~~n~~kl~p~l~~wl~~ 73 (75)
T smart00352 14 KTFKQRRIKLGF----TQADVGLALGALYGPDFSQTTICRFEALQLSFKNMCKLKPLLEKWLEE 73 (75)
T ss_pred HHHHHHHHHcCC----CHHHHHHHhcccccCcCCHHHHHHHHhcCccHHHHHHHHHHHHHHHHh
Confidence 344556766677 9999999999 5999999876 47788888888888765
No 465
>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=68.14 E-value=12 Score=31.47 Aligned_cols=36 Identities=22% Similarity=0.391 Sum_probs=24.8
Q ss_pred HHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHH
Q psy15215 580 RESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 617 (1432)
Q Consensus 580 rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~ 617 (1432)
|+..||.+-+-. ..+.|.+|+|+.||||+.+|++..
T Consensus 1 R~~~il~~L~~~--~~~it~~eLa~~l~vS~rTi~~~i 36 (55)
T PF08279_consen 1 RQKQILKLLLES--KEPITAKELAEELGVSRRTIRRDI 36 (55)
T ss_dssp HHHHHHHHHHHT--TTSBEHHHHHHHCTS-HHHHHHHH
T ss_pred CHHHHHHHHHHc--CCCcCHHHHHHHhCCCHHHHHHHH
Confidence 456666653222 234899999999999999998543
No 466
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=67.55 E-value=10 Score=31.60 Aligned_cols=38 Identities=24% Similarity=0.379 Sum_probs=27.4
Q ss_pred cCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHH
Q psy15215 576 SLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIE 617 (1432)
Q Consensus 576 ~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~ 617 (1432)
.|++.|+--|...+-.|. ++.|||..+|.|+..|+...
T Consensus 4 ~Lt~~Eqaqid~m~qlG~----s~~~isr~i~RSr~~Ir~yl 41 (50)
T PF11427_consen 4 TLTDAEQAQIDVMHQLGM----SLREISRRIGRSRTCIRRYL 41 (50)
T ss_dssp ---HHHHHHHHHHHHTT------HHHHHHHHT--HHHHHHHH
T ss_pred cCCHHHHHHHHHHHHhch----hHHHHHHHhCccHHHHHHHh
Confidence 588899998888888888 99999999999999888653
No 467
>PRK10710 DNA-binding transcriptional regulator BaeR; Provisional
Probab=67.52 E-value=6.7 Score=43.69 Aligned_cols=50 Identities=26% Similarity=0.234 Sum_probs=44.2
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHhhC
Q psy15215 1366 SLTPRESKVLRMRFGIEMSSDHTLEEVGKQFD-----VTRERIRQIEAKALRKLRH 1416 (1432)
Q Consensus 1366 ~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~-----vs~~~Vrq~~~rAl~kLr~ 1416 (1432)
.||++|.+|+.+-.. +.+.+.|.++|++.+. +|..||+...++.++||..
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 599999999987654 5567789999999998 9999999999999999974
No 468
>PF13518 HTH_28: Helix-turn-helix domain
Probab=67.05 E-value=7.6 Score=32.17 Aligned_cols=22 Identities=14% Similarity=0.490 Sum_probs=19.4
Q ss_pred cHHHHHhhcccchhHHHHHHHH
Q psy15215 598 TLEEVGKQFDVTRERIRQIEAK 619 (1432)
Q Consensus 598 t~~EIa~~l~is~~~v~~~~~r 619 (1432)
|+.+||..+|||+.+|.++..+
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~ 35 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKR 35 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHH
Confidence 9999999999999999876543
No 469
>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=66.97 E-value=3.4 Score=45.39 Aligned_cols=52 Identities=17% Similarity=0.192 Sum_probs=43.6
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHH-----HHHhCCCHHHHHHHHHHHHHHhhCch
Q psy15215 1366 SLTPRESKVLRMRFGIEMSSDHTLEEV-----GKQFDVTRERIRQIEAKALRKLRHPS 1418 (1432)
Q Consensus 1366 ~L~~rer~Vl~lr~~~~~~~~~t~~EI-----a~~l~vs~~~Vrq~~~rAl~kLr~~~ 1418 (1432)
.||++|.+||.+-. .+.|.+.|.++| |..+++|..||+...++.++||....
T Consensus 154 ~Lt~~E~~il~~l~-~~~~~~~s~~~i~~~~~~~~~~~~~~tv~~~i~~l~~Kl~~~~ 210 (226)
T TIGR02154 154 SLGPTEFRLLHFFM-THPERVYSREQLLDRVWGRDVYVEERTVDVHIRRLRKALNPFG 210 (226)
T ss_pred EcCHHHHHHHHHHH-hCCCceEcHHHHHHHhcCCCCCCCCccHHHHHHHHHHhhccCC
Confidence 59999999997755 355566788888 88899999999999999999997543
No 470
>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=66.75 E-value=9 Score=33.08 Aligned_cols=25 Identities=12% Similarity=0.352 Sum_probs=21.4
Q ss_pred CCcHHHHHhhcccchhHHHHHHHHH
Q psy15215 596 DHTLEEVGKQFDVTRERIRQIEAKA 620 (1432)
Q Consensus 596 ~~t~~EIa~~l~is~~~v~~~~~rA 620 (1432)
|++..|||+.||+++.+|.+...+.
T Consensus 13 G~~~~eIA~~Lg~~~~TV~~W~~r~ 37 (58)
T PF06056_consen 13 GWSIKEIAEELGVPRSTVYSWKDRY 37 (58)
T ss_pred CCCHHHHHHHHCCChHHHHHHHHhh
Confidence 4499999999999999999876553
No 471
>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=66.61 E-value=5.2 Score=32.34 Aligned_cols=25 Identities=16% Similarity=0.201 Sum_probs=22.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q psy15215 1387 HTLEEVGKQFDVTRERIRQIEAKAL 1411 (1432)
Q Consensus 1387 ~t~~EIa~~l~vs~~~Vrq~~~rAl 1411 (1432)
+|..|+|+.||||+.+|+++..++.
T Consensus 1 ~s~~e~a~~lgvs~~tl~~~~~~g~ 25 (49)
T cd04762 1 LTTKEAAELLGVSPSTLRRWVKEGK 25 (49)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCC
Confidence 4899999999999999999988764
No 472
>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=66.55 E-value=20 Score=39.91 Aligned_cols=56 Identities=23% Similarity=0.262 Sum_probs=41.9
Q ss_pred HHHHHHHHHccCCHHHHHHHHHHhcccCC--CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhh
Q psy15215 1356 MRSVVKDILNSLTPRESKVLRMRFGIEMS--SDHTLEEVGKQFDVTRERIRQIEAKALRKLR 1415 (1432)
Q Consensus 1356 ~~~~l~~~L~~L~~rer~Vl~lr~~~~~~--~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr 1415 (1432)
-+..++-++++||-.|.+-+...+-.-.+ ...+..+||+++||||+.|+. |+++|.
T Consensus 166 kka~Vq~Ai~tLSySEleAv~~IL~~L~~~egrlse~eLAerlGVSRs~ire----AlrkLE 223 (251)
T TIGR02787 166 KKAAVQMAINTLSYSELEAVEHIFEELDGNEGLLVASKIADRVGITRSVIVN----ALRKLE 223 (251)
T ss_pred HHHHHHHHHHhccHhHHHHHHHHHHHhccccccccHHHHHHHHCCCHHHHHH----HHHHHH
Confidence 45677888999999988766655443332 467999999999999999885 555554
No 473
>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=66.01 E-value=8.9 Score=42.06 Aligned_cols=44 Identities=14% Similarity=0.154 Sum_probs=33.9
Q ss_pred ccCCHHHHHHHHHHh--cccCCCCCCHHHHHHHhCCC-HHHHHHHHH
Q psy15215 1365 NSLTPRESKVLRMRF--GIEMSSDHTLEEVGKQFDVT-RERIRQIEA 1408 (1432)
Q Consensus 1365 ~~L~~rer~Vl~lr~--~~~~~~~~t~~EIa~~l~vs-~~~Vrq~~~ 1408 (1432)
..|+++|+.||..-. ....+.+-|..|||+.+|++ +++|+.++.
T Consensus 2 ~~lt~~q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~ 48 (199)
T TIGR00498 2 KPLTARQQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLK 48 (199)
T ss_pred CccCHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHH
Confidence 458999999987754 22234566999999999998 999986554
No 474
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=65.60 E-value=1.2e+02 Score=35.97 Aligned_cols=32 Identities=25% Similarity=0.215 Sum_probs=26.6
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhh
Q psy15215 1384 SSDHTLEEVGKQFDVTRERIRQIEAKALRKLR 1415 (1432)
Q Consensus 1384 ~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr 1415 (1432)
|.+.|++|||...|||..+|++....-.+.|.
T Consensus 274 g~~~t~keIa~v~~Vs~~tI~~~ykel~~~l~ 305 (310)
T PRK00423 274 GERRTQREVAEVAGVTEVTVRNRYKELAEKLD 305 (310)
T ss_pred CCCCCHHHHHHHcCCCHHHHHHHHHHHHHHhC
Confidence 35679999999999999999988777666553
No 475
>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=65.38 E-value=14 Score=35.40 Aligned_cols=49 Identities=20% Similarity=0.291 Sum_probs=35.3
Q ss_pred HccCCHHHHHHHHHH----hccc-CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhC
Q psy15215 1364 LNSLTPRESKVLRMR----FGIE-MSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 1416 (1432)
Q Consensus 1364 L~~L~~rer~Vl~lr----~~~~-~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~ 1416 (1432)
...|++++..+|..- ||.+ ...+.|..|||+.+|+|+++|+. ++++|.+
T Consensus 20 ~~~l~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~sr~tVsr----~L~~Le~ 73 (95)
T TIGR01610 20 GADLSGREFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLSRTHVSD----AIKSLAR 73 (95)
T ss_pred hCCCCHHHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcCHHHHHH----HHHHHHH
Confidence 456999999977632 3322 23567999999999999999875 5555543
No 476
>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=65.33 E-value=7.8 Score=42.81 Aligned_cols=50 Identities=12% Similarity=0.064 Sum_probs=42.4
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHH--HHHhCCCHHHHHHHHHHHHHHhhC
Q psy15215 1366 SLTPRESKVLRMRFGIEMSSDHTLEEV--GKQFDVTRERIRQIEAKALRKLRH 1416 (1432)
Q Consensus 1366 ~L~~rer~Vl~lr~~~~~~~~~t~~EI--a~~l~vs~~~Vrq~~~rAl~kLr~ 1416 (1432)
.||++|..||.+-. .+.|...|.++| |..++++..||+....+.++||..
T Consensus 156 ~Lt~~E~~il~~l~-~~~g~v~s~~~i~~~~~~~~~~~tv~~~v~rlr~Kl~~ 207 (227)
T TIGR03787 156 DLTVTEFWMVHALA-KHPGHVKSRQQLMDAAKIVVDDSTITSHIKRIRKKFQA 207 (227)
T ss_pred cCCHHHHHHHHHHH-hCCCccccHHHHHHHhhhcCCccCHHHHHHHHHHHhcc
Confidence 49999999998754 333445699999 888999999999999999999974
No 477
>PF12728 HTH_17: Helix-turn-helix domain
Probab=65.16 E-value=6.4 Score=32.70 Aligned_cols=24 Identities=13% Similarity=0.259 Sum_probs=21.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHH
Q psy15215 1387 HTLEEVGKQFDVTRERIRQIEAKA 1410 (1432)
Q Consensus 1387 ~t~~EIa~~l~vs~~~Vrq~~~rA 1410 (1432)
+|.+|+|+.||||+.+|+++.++.
T Consensus 2 lt~~e~a~~l~is~~tv~~~~~~g 25 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWIRQG 25 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcC
Confidence 389999999999999999998765
No 478
>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=64.47 E-value=9.2 Score=32.03 Aligned_cols=37 Identities=11% Similarity=0.189 Sum_probs=26.9
Q ss_pred HHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q psy15215 1372 SKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEA 1408 (1432)
Q Consensus 1372 r~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~ 1408 (1432)
|-+-.+.++...+.+.|+.|||+.+|+++++|..++.
T Consensus 4 ral~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~ 40 (52)
T PF09339_consen 4 RALRILEALAESGGPLTLSEIARALGLPKSTVHRLLQ 40 (52)
T ss_dssp HHHHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3344455555556677999999999999999987654
No 479
>smart00351 PAX Paired Box domain.
Probab=64.31 E-value=13 Score=37.61 Aligned_cols=40 Identities=13% Similarity=0.102 Sum_probs=30.2
Q ss_pred CCHHHHHHHHHHhhcccCCCCcHHHHHhhcccchhHHHHHHHHH
Q psy15215 577 LTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 620 (1432)
Q Consensus 577 L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is~~~v~~~~~rA 620 (1432)
+|..+|.-+...|-.|. |..+||+.||||+.+|..+.++.
T Consensus 18 ~s~~~R~riv~~~~~G~----s~~~iA~~~gvs~~tV~kwi~r~ 57 (125)
T smart00351 18 LPDEERQRIVELAQNGV----RPCDISRQLCVSHGCVSKILGRY 57 (125)
T ss_pred CCHHHHHHHHHHHHcCC----CHHHHHHHHCcCHHHHHHHHHHH
Confidence 55555554445554555 99999999999999999877664
No 480
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=64.07 E-value=1.4e+02 Score=35.27 Aligned_cols=54 Identities=13% Similarity=0.030 Sum_probs=35.3
Q ss_pred HHHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHhhccccCCCccHHHHHHHHHHHH
Q psy15215 407 EANLRLVISIAKKYTDRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 465 (1432)
Q Consensus 407 ~~~~~lV~~ia~ky~~~~~~~~DLiQEg~igL~kav~~fd~~~g~~Fstya~~~ir~~i 465 (1432)
...+..+..++.+. ...+-|.|.-..+++.+.....-+|.+..+++.-.+.-+|
T Consensus 123 ~~a~~~I~~~~~~L-----~Lp~~v~e~A~~iyk~~~~~~~~rgrs~~~i~AAclYiAC 176 (310)
T PRK00423 123 AFALSELDRIASQL-----GLPRSVREEAAVIYRKAVEKGLIRGRSIEGVVAAALYAAC 176 (310)
T ss_pred HHHHHHHHHHHHHc-----CCCHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHH
Confidence 33445555565554 3346677777778887766666678777777777766666
No 481
>PF13551 HTH_29: Winged helix-turn helix
Probab=63.61 E-value=14 Score=36.03 Aligned_cols=103 Identities=20% Similarity=0.301 Sum_probs=0.0
Q ss_pred HHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHccCCCCCCCCCCCCCCCCcCcccc-cCCCCChHHHHHHHHHHHH
Q psy15215 1281 RISRQILQETGSEPDPSVIAIKMEMPEEKIRKIMKIAKEPVSMESPVGDDEDSHLGDFIE-DENMLAPSDAALNASMRSV 1359 (1432)
Q Consensus 1281 ~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~~~~~~~~Sl~~~~~~~~~~~~~d~i~-d~~~~~p~~~~~~~~~~~~ 1359 (1432)
|..--+....|.. |+.++|..+|++..+|.++++.. ....+..+.. ......|... ...+....
T Consensus 1 R~~~l~l~~~g~~-~~~~ia~~lg~s~~Tv~r~~~~~-------------~~~G~~~l~~~~~~~g~~~~~-l~~~~~~~ 65 (112)
T PF13551_consen 1 RAQILLLLAEGVS-TIAEIARRLGISRRTVYRWLKRY-------------REGGIEGLLPRKPRGGRPRKR-LSEEQRAQ 65 (112)
T ss_pred CHHHHHHHHcCCC-cHHHHHHHHCcCHHHHHHHHHHH-------------HcccHHHHHhccccCCCCCCC-CCHHHHHH
Q ss_pred HHHHHccCCHHHHHHHHHHhcccCCCCCCHHHHHHHh-------CCCHHHHHHHHHHH
Q psy15215 1360 VKDILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQF-------DVTRERIRQIEAKA 1410 (1432)
Q Consensus 1360 l~~~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l-------~vs~~~Vrq~~~rA 1410 (1432)
|.+.+..-|+... ... |..+|++.+ .+|.++|+++++++
T Consensus 66 l~~~~~~~p~~g~--------~~~----t~~~l~~~l~~~~~~~~~s~~ti~r~L~~~ 111 (112)
T PF13551_consen 66 LIELLRENPPEGR--------SRW----TLEELAEWLIEEEFGIDVSPSTIRRILKRA 111 (112)
T ss_pred HHHHHHHCCCCCC--------Ccc----cHHHHHHHHHHhccCccCCHHHHHHHHHHC
No 482
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=62.99 E-value=6.8 Score=43.76 Aligned_cols=40 Identities=23% Similarity=0.276 Sum_probs=29.1
Q ss_pred ccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q psy15215 1365 NSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEA 1408 (1432)
Q Consensus 1365 ~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~ 1408 (1432)
+.||++ +|+.+-- .| ..++|.+|||+.||+|+.||+....
T Consensus 160 ~~Lt~r--~Vl~~~~-~g-~~g~s~~eIa~~l~iS~~Tv~~~~~ 199 (225)
T PRK10046 160 DPLTLN--AVRKLFK-EP-GVQHTAETVAQALTISRTTARRYLE 199 (225)
T ss_pred CHHHHH--HHHHHHH-cC-CCCcCHHHHHHHhCccHHHHHHHHH
Confidence 346665 5665532 22 1356999999999999999998875
No 483
>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=62.74 E-value=6.7 Score=31.80 Aligned_cols=24 Identities=17% Similarity=0.358 Sum_probs=21.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHH
Q psy15215 1387 HTLEEVGKQFDVTRERIRQIEAKA 1410 (1432)
Q Consensus 1387 ~t~~EIa~~l~vs~~~Vrq~~~rA 1410 (1432)
+|.+|+|+.||||+.+|.++.+.+
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~~g 25 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIHEG 25 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHcC
Confidence 389999999999999999998765
No 484
>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=62.51 E-value=10 Score=32.28 Aligned_cols=50 Identities=24% Similarity=0.276 Sum_probs=40.2
Q ss_pred cCCHHHHHHHHHHhcccCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhh
Q psy15215 1366 SLTPRESKVLRMRFGIEMS-SDHTLEEVGKQFDVTRERIRQIEAKALRKLR 1415 (1432)
Q Consensus 1366 ~L~~rer~Vl~lr~~~~~~-~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr 1415 (1432)
.+++.+..+|...|..+.. .....++||..+|||...|..+...-..+.|
T Consensus 6 ~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~k 56 (57)
T PF00046_consen 6 RFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEK 56 (57)
T ss_dssp SSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhC
Confidence 4788899999998876431 2245789999999999999999988777765
No 485
>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=62.50 E-value=5.5 Score=32.56 Aligned_cols=25 Identities=28% Similarity=0.297 Sum_probs=22.9
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q psy15215 1387 HTLEEVGKQFDVTRERIRQIEAKAL 1411 (1432)
Q Consensus 1387 ~t~~EIa~~l~vs~~~Vrq~~~rAl 1411 (1432)
+|..|+|+.+|||+.+|+.+..+++
T Consensus 1 ~~~~e~a~~~gv~~~tlr~~~~~g~ 25 (49)
T cd04761 1 YTIGELAKLTGVSPSTLRYYERIGL 25 (49)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHCCC
Confidence 3889999999999999999988875
No 486
>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=62.19 E-value=15 Score=38.59 Aligned_cols=41 Identities=15% Similarity=0.212 Sum_probs=33.2
Q ss_pred CHHHHHHHHHHhc-ccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q psy15215 1368 TPRESKVLRMRFG-IEMSSDHTLEEVGKQFDVTRERIRQIEAKALR 1412 (1432)
Q Consensus 1368 ~~rer~Vl~lr~~-~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~ 1412 (1432)
|+.-|.-++..|. .++ |++.+|..+|||..|+|++..+|..
T Consensus 4 ~~e~R~~~R~~YV~~~~----sLe~aA~~~gVs~~TarrWK~~Ak~ 45 (165)
T PF08822_consen 4 PQETRDAVRRAYVFDRL----SLEQAAAKCGVSYATARRWKREAKA 45 (165)
T ss_pred cHHHHHHHHHHHHhCCC----CHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 3445666777776 446 9999999999999999999998863
No 487
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=62.18 E-value=71 Score=28.68 Aligned_cols=24 Identities=13% Similarity=0.196 Sum_probs=20.8
Q ss_pred CCCHHHHHHHcCCCHHHHHHHHHH
Q psy15215 503 EPDPSVIAIKMEMPEEKIRKIMKI 526 (1432)
Q Consensus 503 ~pt~~eia~~~~~~~~~v~~~~~~ 526 (1432)
++|.++||+.+|++...+..+...
T Consensus 1 ~~~~~~la~~~~~s~~~l~~~f~~ 24 (84)
T smart00342 1 PLTLEDLAEALGMSPRHLQRLFKK 24 (84)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHH
Confidence 478899999999999999988654
No 488
>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=62.06 E-value=15 Score=30.67 Aligned_cols=48 Identities=19% Similarity=0.243 Sum_probs=35.2
Q ss_pred cccccHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHH
Q psy15215 1267 RIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIM 1314 (1432)
Q Consensus 1267 rip~~~~~~~~k~~~~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~ 1314 (1432)
.||..+++.+-...|....+..+.-.--+-.+||+.+|+++..|++=+
T Consensus 2 ~Ip~~ti~RL~~Y~r~L~~l~~~G~~~vSS~~La~~~gi~~~qVRKDl 49 (50)
T PF06971_consen 2 KIPKATIRRLPLYLRYLEQLKEEGVERVSSQELAEALGITPAQVRKDL 49 (50)
T ss_dssp S-SHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHTS-HHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHHHHHHcCCeeECHHHHHHHHCCCHHHhcccC
Confidence 467777777777788888777654456789999999999999998743
No 489
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=61.63 E-value=17 Score=30.17 Aligned_cols=23 Identities=17% Similarity=0.446 Sum_probs=21.4
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHH
Q psy15215 1388 TLEEVGKQFDVTRERIRQIEAKA 1410 (1432)
Q Consensus 1388 t~~EIa~~l~vs~~~Vrq~~~rA 1410 (1432)
|.++||+.+|||-.+|+.+..+.
T Consensus 29 s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 29 SFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred CHHHHHHHHCCCHHHHHHHHHhh
Confidence 99999999999999999998764
No 490
>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=61.31 E-value=18 Score=33.88 Aligned_cols=44 Identities=18% Similarity=0.334 Sum_probs=31.5
Q ss_pred HHhcCCHHHHHHHHHHhhcccCCCCcHHHHHhhc--ccchhHHHHHHHH
Q psy15215 573 ILNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQF--DVTRERIRQIEAK 619 (1432)
Q Consensus 573 ~L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l--~is~~~v~~~~~r 619 (1432)
.+..||+..+.+..+|--. ...|+.|+|+.+ .+|.+.|..+.++
T Consensus 34 ~~~~l~~~l~~~a~lRl~~---Pd~SL~EL~~~~~~~iSKSgvnhrlrK 79 (85)
T PF02650_consen 34 GLDKLPEKLREFAELRLEN---PDASLKELGELLEPPISKSGVNHRLRK 79 (85)
T ss_dssp -GGGS-HHHHHHHHHHHH----TTS-HHHHHHTT--T--HHHHHHHHHH
T ss_pred ccccCCHHHHHHHHHHHHC---ccccHHHHHHHHcCcCcHHHHHHHHHH
Confidence 3578999999999999743 456999999999 8899988765544
No 491
>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=61.26 E-value=15 Score=32.33 Aligned_cols=42 Identities=19% Similarity=0.279 Sum_probs=26.5
Q ss_pred CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q psy15215 1367 LTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKA 1410 (1432)
Q Consensus 1367 L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rA 1410 (1432)
|++.|..||..-. ..+.+.|..+|++.++++..+|+..+++-
T Consensus 1 lt~~q~~vL~~l~--~~~~~~t~~~l~~~~~~~~~~vs~~i~~L 42 (68)
T PF13463_consen 1 LTRPQWQVLRALA--HSDGPMTQSDLAERLGISKSTVSRIIKKL 42 (68)
T ss_dssp --HHHHHHHHHHT----TS-BEHHHHHHHTT--HHHHHHHHHHH
T ss_pred CCHHHHHHHHHHH--ccCCCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 5667777765544 33456799999999999999998655544
No 492
>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=61.11 E-value=31 Score=38.51 Aligned_cols=55 Identities=24% Similarity=0.276 Sum_probs=42.7
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHhhcccC--CCCcHHHHHhhcccchhHHHHHHHHHHHHHH
Q psy15215 567 RSVVKDILNSLTPRESKVLRMRFGIEMS--SDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625 (1432)
Q Consensus 567 ~~~l~~~L~~L~~rer~Vl~lr~~~~~~--~~~t~~EIa~~l~is~~~v~~~~~rAl~kLr 625 (1432)
+..++-|+++||-.|.+.+.-.+-.=.+ .-.+..++|+++|+|++.++ +|+++|.
T Consensus 167 ka~Vq~Ai~tLSySEleAv~~IL~~L~~~egrlse~eLAerlGVSRs~ir----eAlrkLE 223 (251)
T TIGR02787 167 KAAVQMAINTLSYSELEAVEHIFEELDGNEGLLVASKIADRVGITRSVIV----NALRKLE 223 (251)
T ss_pred HHHHHHHHHhccHhHHHHHHHHHHHhccccccccHHHHHHHHCCCHHHHH----HHHHHHH
Confidence 4567889999999988877766654433 35799999999999999887 5666664
No 493
>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=61.00 E-value=12 Score=29.83 Aligned_cols=38 Identities=11% Similarity=0.155 Sum_probs=24.4
Q ss_pred HHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q psy15215 1369 PRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409 (1432)
Q Consensus 1369 ~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~r 1409 (1432)
.-|+.+|.-..-... .+..+.|+.||||+.++...+.+
T Consensus 4 ~~E~~~i~~aL~~~~---gn~~~aA~~Lgisr~tL~~klkk 41 (42)
T PF02954_consen 4 EFEKQLIRQALERCG---GNVSKAARLLGISRRTLYRKLKK 41 (42)
T ss_dssp HHHHHHHHHHHHHTT---T-HHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHHhC---CCHHHHHHHHCCCHHHHHHHHHh
Confidence 345555554443222 27899999999999999876653
No 494
>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=60.84 E-value=27 Score=31.95 Aligned_cols=51 Identities=18% Similarity=0.244 Sum_probs=34.8
Q ss_pred HHHHHHHHHhcCCHHHHHHHHHHhhcc-cCCCCcHHHHHhhcccchhHHHHH
Q psy15215 566 MRSVVKDILNSLTPRESKVLRMRFGIE-MSSDHTLEEVGKQFDVTRERIRQI 616 (1432)
Q Consensus 566 ~~~~l~~~L~~L~~rer~Vl~lr~~~~-~~~~~t~~EIa~~l~is~~~v~~~ 616 (1432)
+...|.....+||+.|+.|...-.-.- .-...|..|||+..|+|+.+|.+.
T Consensus 3 l~~~i~~~~~~ls~~e~~Ia~yil~~~~~~~~~si~elA~~~~vS~sti~Rf 54 (77)
T PF01418_consen 3 LLEKIRSQYNSLSPTEKKIADYILENPDEIAFMSISELAEKAGVSPSTIVRF 54 (77)
T ss_dssp HHHHHHHHGGGS-HHHHHHHHHHHH-HHHHCT--HHHHHHHCTS-HHHHHHH
T ss_pred HHHHHHHHHhhCCHHHHHHHHHHHhCHHHHHHccHHHHHHHcCCCHHHHHHH
Confidence 456788888999999999886443211 113469999999999999998753
No 495
>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=60.74 E-value=19 Score=30.13 Aligned_cols=48 Identities=19% Similarity=0.243 Sum_probs=33.4
Q ss_pred ccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHH
Q psy15215 477 RIPVHMIETINKISRISRQILQETGSEPDPSVIAIKMEMPEEKIRKIM 524 (1432)
Q Consensus 477 rip~~~~~~~~k~~r~~~~~~~~~g~~pt~~eia~~~~~~~~~v~~~~ 524 (1432)
.||..+++.+-...|.-..+..+.-.-.+..+||+.+|+++..|++-+
T Consensus 2 ~Ip~~ti~RL~~Y~r~L~~l~~~G~~~vSS~~La~~~gi~~~qVRKDl 49 (50)
T PF06971_consen 2 KIPKATIRRLPLYLRYLEQLKEEGVERVSSQELAEALGITPAQVRKDL 49 (50)
T ss_dssp S-SHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHTS-HHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHHHHHHcCCeeECHHHHHHHHCCCHHHhcccC
Confidence 467777777766677766666554456789999999999999999743
No 496
>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=60.46 E-value=21 Score=33.79 Aligned_cols=44 Identities=18% Similarity=0.221 Sum_probs=34.7
Q ss_pred HHHHHHHHHHhcccCCCCCCHHHHHHHhC-CCHHHHHHHHHHHHHHhhC
Q psy15215 1369 PRESKVLRMRFGIEMSSDHTLEEVGKQFD-VTRERIRQIEAKALRKLRH 1416 (1432)
Q Consensus 1369 ~rer~Vl~lr~~~~~~~~~t~~EIa~~l~-vs~~~Vrq~~~rAl~kLr~ 1416 (1432)
+|+-.+..++...|+ |+.+||+.|| .+.++|.....+.-+++..
T Consensus 31 aR~ia~yl~~~~~~~----s~~~Ig~~fg~r~hStV~~a~~ri~~~~~~ 75 (90)
T cd06571 31 ARQIAMYLARELTGL----SLPEIGRAFGGRDHSTVLHAVRKIEELLEE 75 (90)
T ss_pred HHHHHHHHHHHHhCC----CHHHHHHHhCCCCHhHHHHHHHHHHHHHHh
Confidence 455555556665566 9999999999 9999999888887777765
No 497
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=60.35 E-value=13 Score=33.16 Aligned_cols=33 Identities=33% Similarity=0.438 Sum_probs=26.7
Q ss_pred HHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q psy15215 1373 KVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409 (1432)
Q Consensus 1373 ~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~r 1409 (1432)
.+-.+|=..|+ |.+|.|+.+||||.||-.+++-
T Consensus 5 k~k~~R~~~~l----tQ~elA~~vgVsRQTi~~iEkg 37 (68)
T COG1476 5 KLKELRAELGL----TQEELAKLVGVSRQTIIAIEKG 37 (68)
T ss_pred HHHHHHHHhCc----CHHHHHHHcCcCHHHHHHHHcC
Confidence 34455665667 9999999999999999998763
No 498
>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=60.31 E-value=8.9 Score=34.03 Aligned_cols=41 Identities=20% Similarity=0.280 Sum_probs=30.3
Q ss_pred cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q psy15215 1366 SLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAK 1409 (1432)
Q Consensus 1366 ~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~r 1409 (1432)
.|++.|.+|+..-.-. .+.|..|||+.+|+++++|...+.+
T Consensus 5 gLs~~E~~vy~~Ll~~---~~~t~~eIa~~l~i~~~~v~~~L~~ 45 (68)
T PF01978_consen 5 GLSENEAKVYLALLKN---GPATAEEIAEELGISRSTVYRALKS 45 (68)
T ss_dssp CHHHHHHHHHHHHHHH---CHEEHHHHHHHHTSSHHHHHHHHHH
T ss_pred CcCHHHHHHHHHHHHc---CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 3778888887554311 2459999999999999999865543
No 499
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=60.22 E-value=19 Score=34.35 Aligned_cols=49 Identities=16% Similarity=0.270 Sum_probs=42.5
Q ss_pred HccCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhhC
Q psy15215 1364 LNSLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 1416 (1432)
Q Consensus 1364 L~~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~vs~~~Vrq~~~rAl~kLr~ 1416 (1432)
.+.|++.+-+-+.+++--.. +++||-+.+|+|-.+||..+...+++|--
T Consensus 39 F~~Lt~d~LeFv~lf~r~RG----nlKEvEr~lg~sYptvR~kld~vlramgy 87 (122)
T COG3877 39 FEYLTSDQLEFVELFLRCRG----NLKEVERELGISYPTVRTKLDEVLRAMGY 87 (122)
T ss_pred ccccCHhHhHHHHHHHHHcc----CHHHHHHHHCCccHHHHHHHHHHHHHcCC
Confidence 45688888888888876666 99999999999999999999999998853
No 500
>PRK11083 DNA-binding response regulator CreB; Provisional
Probab=60.20 E-value=11 Score=41.54 Aligned_cols=49 Identities=14% Similarity=0.053 Sum_probs=40.3
Q ss_pred cCCHHHHHHHHHHhhcccCCCCcHHHHHhhcccc-----hhHHHHHHHHHHHHHH
Q psy15215 576 SLTPRESKVLRMRFGIEMSSDHTLEEVGKQFDVT-----RERIRQIEAKALRKLR 625 (1432)
Q Consensus 576 ~L~~rer~Vl~lr~~~~~~~~~t~~EIa~~l~is-----~~~v~~~~~rAl~kLr 625 (1432)
.||++|.+||.+-. .+.|.+.|.++|++.++.+ ..+|+.+.++.++||.
T Consensus 154 ~Lt~~E~~il~~l~-~~~~~~~s~~~i~~~l~~~~~~~~~~tv~~~i~~l~~Kl~ 207 (228)
T PRK11083 154 TLTRYEFLLLKTLL-LSPGRVFSRQQLMDIVWEDAQDSYDRTVDTHIKTLRAKLR 207 (228)
T ss_pred ecCHHHHHHHHHHH-hCCCceECHHHHHHHhcCCCCCCCccCHHHHHHHHHHHhc
Confidence 49999999998754 4556678999999999986 6788888888777775
Done!