Query 007404
Match_columns 605
No_of_seqs 440 out of 2413
Neff 5.7
Searched_HMMs 46136
Date Thu Mar 28 23:08:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/007404.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/007404hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK07598 RNA polymerase sigma 100.0 5E-64 1.1E-68 539.5 37.9 313 289-603 57-412 (415)
2 PRK07406 RNA polymerase sigma 100.0 6.1E-62 1.3E-66 519.5 38.0 311 290-602 61-372 (373)
3 PRK05949 RNA polymerase sigma 100.0 6.8E-61 1.5E-65 504.9 38.3 310 290-603 16-326 (327)
4 TIGR02997 Sig70-cyanoRpoD RNA 100.0 4E-60 8.7E-65 493.1 35.0 297 292-590 1-298 (298)
5 PRK07405 RNA polymerase sigma 100.0 7.9E-60 1.7E-64 495.1 37.4 309 291-603 7-316 (317)
6 COG0568 RpoD DNA-directed RNA 100.0 3.3E-59 7.2E-64 488.4 30.8 312 291-603 8-342 (342)
7 PRK05901 RNA polymerase sigma 100.0 1.2E-58 2.5E-63 508.8 33.2 301 289-603 208-509 (509)
8 PRK07921 RNA polymerase sigma 100.0 7.4E-58 1.6E-62 481.1 34.7 300 290-603 24-324 (324)
9 PRK09210 RNA polymerase sigma 100.0 4.1E-54 8.9E-59 460.1 33.1 274 289-603 93-367 (367)
10 PRK05658 RNA polymerase sigma 100.0 2.7E-51 5.9E-56 464.6 31.5 270 296-603 349-618 (619)
11 TIGR02393 RpoD_Cterm RNA polym 100.0 3.7E-47 8.1E-52 383.3 26.8 238 366-603 1-238 (238)
12 PRK07500 rpoH2 RNA polymerase 100.0 2.4E-44 5.3E-49 373.5 31.3 262 292-596 6-280 (289)
13 PRK06596 RNA polymerase factor 100.0 4.1E-44 8.9E-49 370.9 31.5 261 290-595 12-282 (284)
14 PRK05657 RNA polymerase sigma 100.0 7.1E-44 1.5E-48 375.6 32.7 269 291-600 52-321 (325)
15 TIGR02392 rpoH_proteo alternat 100.0 1.3E-43 2.8E-48 364.4 30.5 257 293-594 2-269 (270)
16 PRK07122 RNA polymerase sigma 100.0 6.6E-43 1.4E-47 358.4 27.3 221 364-593 39-263 (264)
17 PRK07408 RNA polymerase sigma 100.0 2.5E-41 5.4E-46 345.1 30.1 227 362-595 22-253 (256)
18 TIGR02394 rpoS_proteo RNA poly 100.0 3.6E-40 7.9E-45 341.1 32.9 271 287-598 8-279 (285)
19 TIGR02850 spore_sigG RNA polym 100.0 2.9E-40 6.2E-45 336.5 29.4 242 301-592 10-253 (254)
20 PRK05911 RNA polymerase sigma 100.0 1.3E-39 2.7E-44 332.8 27.7 227 362-595 20-255 (257)
21 PRK08215 sporulation sigma fac 100.0 1.4E-38 3.1E-43 324.5 29.7 243 301-593 13-257 (258)
22 PRK06288 RNA polymerase sigma 100.0 2.1E-37 4.6E-42 317.7 29.8 249 301-595 6-262 (268)
23 COG1191 FliA DNA-directed RNA 100.0 1.9E-37 4.1E-42 313.7 27.6 222 362-594 21-245 (247)
24 TIGR02941 Sigma_B RNA polymera 100.0 1.1E-36 2.5E-41 309.7 30.2 245 304-593 7-253 (255)
25 TIGR02885 spore_sigF RNA polym 100.0 1.4E-36 3E-41 304.3 27.3 223 361-593 7-231 (231)
26 TIGR02980 SigBFG RNA polymeras 100.0 5.8E-36 1.3E-40 298.9 26.9 221 364-593 2-226 (227)
27 PRK07670 RNA polymerase sigma 100.0 1.6E-35 3.5E-40 301.0 29.5 226 362-594 19-250 (251)
28 PRK08583 RNA polymerase sigma 100.0 8.9E-35 1.9E-39 296.1 29.3 248 303-595 6-255 (257)
29 PRK05572 sporulation sigma fac 100.0 2E-34 4.2E-39 293.2 29.3 241 302-594 9-251 (252)
30 TIGR02479 FliA_WhiG RNA polyme 100.0 8.3E-35 1.8E-39 290.5 25.9 217 370-593 1-223 (224)
31 PRK12427 flagellar biosynthesi 100.0 7.2E-34 1.6E-38 286.3 26.6 210 366-592 16-230 (231)
32 PRK06986 fliA flagellar biosyn 100.0 1.8E-33 4E-38 283.1 27.5 224 362-594 5-233 (236)
33 PRK05803 sporulation sigma fac 100.0 4.8E-28 1E-32 243.5 25.1 209 294-596 18-230 (233)
34 TIGR02846 spore_sigmaK RNA pol 99.9 8.7E-25 1.9E-29 219.2 24.4 205 296-593 19-226 (227)
35 PRK08301 sporulation sigma fac 99.9 1.1E-24 2.5E-29 218.7 23.6 180 362-594 49-231 (234)
36 TIGR02835 spore_sigmaE RNA pol 99.9 9.6E-24 2.1E-28 212.6 23.5 180 362-594 49-231 (234)
37 PRK08295 RNA polymerase factor 99.9 5.9E-23 1.3E-27 201.3 21.3 192 354-597 13-206 (208)
38 PRK05602 RNA polymerase sigma 99.9 3E-22 6.4E-27 193.8 20.9 172 354-597 9-180 (186)
39 TIGR02948 SigW_bacill RNA poly 99.9 3.6E-22 7.8E-27 192.2 20.2 181 352-594 5-185 (187)
40 PRK12513 RNA polymerase sigma 99.9 2.3E-22 5E-27 195.8 19.0 180 352-598 13-192 (194)
41 PRK09646 RNA polymerase sigma 99.9 3.6E-22 7.9E-27 195.0 20.4 172 356-595 21-192 (194)
42 PRK09648 RNA polymerase sigma 99.9 1.1E-21 2.5E-26 190.1 22.4 167 359-594 18-188 (189)
43 PRK09641 RNA polymerase sigma 99.9 9.2E-22 2E-26 189.4 20.9 177 356-594 9-185 (187)
44 TIGR02859 spore_sigH RNA polym 99.9 6.6E-22 1.4E-26 192.3 19.9 186 356-593 10-197 (198)
45 PRK11922 RNA polymerase sigma 99.9 1.5E-21 3.2E-26 196.3 20.4 193 302-595 7-199 (231)
46 PRK09652 RNA polymerase sigma 99.9 2E-21 4.3E-26 184.9 20.2 174 359-594 4-177 (182)
47 TIGR02952 Sig70_famx2 RNA poly 99.9 2.8E-21 6E-26 183.0 20.0 166 359-593 5-170 (170)
48 PRK12519 RNA polymerase sigma 99.9 2.3E-21 5E-26 188.5 19.6 171 356-594 20-190 (194)
49 PRK06759 RNA polymerase factor 99.9 1.3E-21 2.9E-26 182.8 16.6 151 364-592 3-153 (154)
50 PRK12514 RNA polymerase sigma 99.9 4E-21 8.6E-26 184.6 20.2 168 357-594 11-178 (179)
51 PRK12524 RNA polymerase sigma 99.9 5.4E-21 1.2E-25 187.0 21.2 174 353-596 14-187 (196)
52 TIGR02939 RpoE_Sigma70 RNA pol 99.9 5.9E-21 1.3E-25 184.2 21.0 178 355-594 10-187 (190)
53 PRK13919 putative RNA polymera 99.9 4E-21 8.6E-26 185.5 19.5 172 355-594 13-184 (186)
54 PRK11923 algU RNA polymerase s 99.9 8.6E-21 1.9E-25 184.4 21.5 177 356-594 11-187 (193)
55 PRK12537 RNA polymerase sigma 99.9 6.6E-21 1.4E-25 184.1 20.3 170 354-593 12-181 (182)
56 PRK12534 RNA polymerase sigma 99.9 5.8E-21 1.2E-25 184.7 19.5 172 355-594 15-186 (187)
57 PRK06811 RNA polymerase factor 99.9 7E-21 1.5E-25 185.2 20.1 171 355-595 8-181 (189)
58 PRK12538 RNA polymerase sigma 99.9 6.7E-21 1.4E-25 192.4 20.4 164 361-596 59-222 (233)
59 PRK12542 RNA polymerase sigma 99.9 3.2E-21 7E-26 186.6 16.8 175 361-602 5-179 (185)
60 PRK11924 RNA polymerase sigma 99.9 2.6E-20 5.6E-25 176.8 21.4 171 358-596 6-176 (179)
61 TIGR02984 Sig-70_plancto1 RNA 99.9 1.7E-20 3.7E-25 180.6 20.3 180 361-593 3-188 (189)
62 PRK12515 RNA polymerase sigma 99.9 2.1E-20 4.5E-25 181.5 20.9 176 352-598 9-184 (189)
63 PRK12526 RNA polymerase sigma 99.9 1.8E-20 3.8E-25 185.2 19.9 173 359-596 32-204 (206)
64 PRK09640 RNA polymerase sigma 99.9 6.3E-21 1.4E-25 185.2 16.4 172 351-594 8-183 (188)
65 PRK12543 RNA polymerase sigma 99.9 2.9E-20 6.3E-25 179.2 19.7 166 361-596 3-168 (179)
66 PRK09643 RNA polymerase sigma 99.9 5.4E-20 1.2E-24 179.7 20.4 169 354-595 16-184 (192)
67 PRK09645 RNA polymerase sigma 99.8 4.1E-20 8.8E-25 176.4 18.9 164 362-596 6-169 (173)
68 PRK12531 RNA polymerase sigma 99.8 4.1E-20 8.9E-25 180.5 18.7 176 356-597 18-193 (194)
69 TIGR02937 sigma70-ECF RNA poly 99.8 8.7E-20 1.9E-24 166.3 18.2 157 366-593 2-158 (158)
70 PRK09415 RNA polymerase factor 99.8 8.2E-20 1.8E-24 176.2 18.8 165 362-595 13-177 (179)
71 PRK09638 RNA polymerase sigma 99.8 5.2E-20 1.1E-24 175.9 17.0 165 357-593 10-174 (176)
72 TIGR03001 Sig-70_gmx1 RNA poly 99.8 1.9E-19 4.1E-24 183.2 21.9 182 351-601 24-217 (244)
73 PRK12520 RNA polymerase sigma 99.8 1.1E-19 2.4E-24 176.7 19.3 181 366-597 3-183 (191)
74 PRK12522 RNA polymerase sigma 99.8 1E-19 2.3E-24 174.0 18.6 167 365-595 3-169 (173)
75 TIGR02985 Sig70_bacteroi1 RNA 99.8 5.3E-20 1.1E-24 171.4 16.1 160 366-593 2-161 (161)
76 TIGR02954 Sig70_famx3 RNA poly 99.8 1.3E-19 2.9E-24 172.4 19.2 163 355-594 6-168 (169)
77 PRK12536 RNA polymerase sigma 99.8 9.3E-20 2E-24 176.0 17.9 168 355-595 11-179 (181)
78 COG1595 RpoE DNA-directed RNA 99.8 2.9E-19 6.4E-24 172.8 20.3 172 357-596 7-178 (182)
79 PRK12539 RNA polymerase sigma 99.8 2.2E-19 4.9E-24 173.8 19.3 166 356-595 12-181 (184)
80 TIGR02999 Sig-70_X6 RNA polyme 99.8 2.4E-19 5.2E-24 172.4 19.2 167 358-593 10-182 (183)
81 PRK12529 RNA polymerase sigma 99.8 1.8E-19 3.9E-24 173.9 18.0 165 361-593 9-175 (178)
82 PRK12533 RNA polymerase sigma 99.8 3.9E-19 8.4E-24 177.8 20.6 170 363-596 16-185 (216)
83 PRK12512 RNA polymerase sigma 99.8 4.1E-19 8.9E-24 171.3 19.4 165 357-596 14-182 (184)
84 PRK12518 RNA polymerase sigma 99.8 2.1E-19 4.6E-24 171.6 17.0 168 358-596 4-171 (175)
85 TIGR02989 Sig-70_gvs1 RNA poly 99.8 1.2E-19 2.6E-24 170.3 15.0 157 366-592 2-158 (159)
86 PRK09649 RNA polymerase sigma 99.8 3.8E-19 8.2E-24 172.8 18.5 167 357-597 16-182 (185)
87 PRK09647 RNA polymerase sigma 99.8 7E-19 1.5E-23 174.0 20.5 165 362-596 25-189 (203)
88 PRK09642 RNA polymerase sigma 99.8 3.1E-19 6.6E-24 168.3 16.9 156 372-596 2-157 (160)
89 TIGR02947 SigH_actino RNA poly 99.8 2.4E-19 5.3E-24 174.6 16.7 173 363-595 9-181 (193)
90 PRK12516 RNA polymerase sigma 99.8 4.1E-19 8.9E-24 173.2 17.7 162 362-597 7-168 (187)
91 PRK12523 RNA polymerase sigma 99.8 5.7E-19 1.2E-23 169.0 17.6 163 362-595 7-169 (172)
92 PRK09639 RNA polymerase sigma 99.8 1E-18 2.2E-23 165.3 18.8 160 364-595 2-161 (166)
93 PRK09644 RNA polymerase sigma 99.8 7.3E-19 1.6E-23 166.9 17.7 157 367-596 3-159 (165)
94 TIGR02983 SigE-fam_strep RNA p 99.8 6.4E-19 1.4E-23 166.2 16.9 157 362-594 3-159 (162)
95 PRK12528 RNA polymerase sigma 99.8 1.1E-18 2.3E-23 165.0 17.9 157 365-592 4-160 (161)
96 TIGR02943 Sig70_famx1 RNA poly 99.8 1.5E-18 3.3E-23 169.1 19.2 178 369-597 6-183 (188)
97 PRK12532 RNA polymerase sigma 99.8 1.6E-18 3.5E-23 169.1 18.8 181 368-598 8-189 (195)
98 PRK12541 RNA polymerase sigma 99.8 1.7E-18 3.7E-23 163.6 18.4 157 363-592 3-159 (161)
99 PRK12530 RNA polymerase sigma 99.8 2.5E-18 5.5E-23 167.6 19.5 176 368-596 10-185 (189)
100 PRK12547 RNA polymerase sigma 99.8 2.5E-18 5.3E-23 163.5 18.8 158 364-595 5-162 (164)
101 PRK12545 RNA polymerase sigma 99.8 2.3E-18 5E-23 169.5 19.2 181 369-598 12-192 (201)
102 TIGR02960 SigX5 RNA polymerase 99.8 1.9E-18 4.1E-23 181.0 19.7 183 362-595 2-192 (324)
103 PRK08241 RNA polymerase factor 99.8 3.3E-18 7.2E-23 180.7 21.5 187 354-591 8-199 (339)
104 PRK12535 RNA polymerase sigma 99.8 4.1E-18 8.9E-23 167.5 19.4 169 357-597 17-185 (196)
105 PRK12544 RNA polymerase sigma 99.8 5.4E-18 1.2E-22 168.1 20.3 179 367-596 20-199 (206)
106 PRK07037 extracytoplasmic-func 99.8 7.6E-18 1.7E-22 159.1 19.1 158 369-595 2-159 (163)
107 PRK12527 RNA polymerase sigma 99.8 6.6E-18 1.4E-22 159.3 17.9 155 371-595 1-155 (159)
108 TIGR02950 SigM_subfam RNA poly 99.8 1.4E-18 3E-23 162.2 13.1 153 371-593 1-153 (154)
109 PRK12517 RNA polymerase sigma 99.8 1E-17 2.2E-22 163.5 19.3 162 360-596 18-179 (188)
110 PRK12540 RNA polymerase sigma 99.8 8.4E-18 1.8E-22 163.3 18.1 160 365-598 5-164 (182)
111 PRK09637 RNA polymerase sigma 99.8 1.2E-17 2.6E-22 162.0 18.4 154 367-595 3-156 (181)
112 PRK09651 RNA polymerase sigma 99.8 1.1E-17 2.4E-22 160.4 17.6 162 363-595 8-169 (172)
113 TIGR02895 spore_sigI RNA polym 99.8 1.6E-17 3.4E-22 166.5 19.1 115 362-477 7-126 (218)
114 PRK12546 RNA polymerase sigma 99.8 2.7E-17 5.9E-22 160.8 18.0 157 364-595 7-163 (188)
115 TIGR02959 SigZ RNA polymerase 99.8 2.4E-17 5.3E-22 157.9 17.2 148 372-594 2-149 (170)
116 PRK12511 RNA polymerase sigma 99.7 3.1E-17 6.8E-22 159.5 16.5 156 367-595 6-161 (182)
117 PRK12525 RNA polymerase sigma 99.7 5.9E-17 1.3E-21 154.6 18.0 159 364-593 8-166 (168)
118 PRK09636 RNA polymerase sigma 99.7 7E-17 1.5E-21 167.9 18.2 160 365-594 4-164 (293)
119 PRK09047 RNA polymerase factor 99.7 1.1E-16 2.3E-21 150.6 15.6 155 387-597 2-158 (161)
120 PRK06704 RNA polymerase factor 99.7 5.7E-16 1.2E-20 156.4 17.8 159 355-595 8-166 (228)
121 TIGR02957 SigX4 RNA polymerase 99.7 5.9E-16 1.3E-20 160.3 18.2 156 369-594 1-157 (281)
122 PRK09635 sigI RNA polymerase s 99.7 1.3E-15 2.8E-20 158.9 18.8 161 365-593 5-166 (290)
123 TIGR03209 P21_Cbot clostridium 99.5 5.8E-14 1.3E-18 130.2 13.4 136 367-579 1-141 (142)
124 PRK09191 two-component respons 99.5 1.1E-13 2.3E-18 139.1 13.9 136 366-594 2-137 (261)
125 PRK08311 putative RNA polymera 99.4 1.3E-11 2.8E-16 125.6 19.4 86 357-442 10-97 (237)
126 PF07638 Sigma70_ECF: ECF sigm 99.4 2.4E-11 5.2E-16 118.7 19.4 173 355-594 7-184 (185)
127 PF04542 Sigma70_r2: Sigma-70 99.2 1.8E-11 3.8E-16 99.6 7.3 70 370-439 1-70 (71)
128 PF04545 Sigma70_r4: Sigma-70, 99.2 3.7E-11 8.1E-16 93.0 7.2 50 538-591 1-50 (50)
129 PF04539 Sigma70_r3: Sigma-70 99.1 2E-10 4.4E-15 96.5 5.6 77 449-525 1-77 (78)
130 PF08281 Sigma70_r4_2: Sigma-7 98.9 3.8E-09 8.3E-14 82.7 7.1 54 532-589 1-54 (54)
131 PRK06930 positive control sigm 98.6 1.5E-07 3.2E-12 91.4 10.1 70 523-596 96-165 (170)
132 PRK00118 putative DNA-binding 98.4 1.1E-06 2.5E-11 78.7 9.3 61 533-597 9-69 (104)
133 cd06171 Sigma70_r4 Sigma70, re 98.3 2.8E-06 6.2E-11 64.3 6.9 54 533-590 2-55 (55)
134 TIGR00721 tfx DNA-binding prot 98.1 1.1E-05 2.5E-10 75.7 7.9 57 541-602 6-62 (137)
135 PRK04217 hypothetical protein; 98.1 9E-06 1.9E-10 73.7 6.7 57 540-600 41-97 (110)
136 PRK03975 tfx putative transcri 98.0 2.1E-05 4.6E-10 74.2 8.1 51 540-595 5-55 (141)
137 PF04297 UPF0122: Putative hel 98.0 3.4E-05 7.4E-10 68.8 8.6 59 534-596 9-68 (101)
138 PF00140 Sigma70_r1_2: Sigma-7 97.9 3.3E-06 7.1E-11 62.0 1.4 31 291-322 1-32 (37)
139 TIGR01636 phage_rinA phage tra 97.9 6.6E-05 1.4E-09 70.2 8.9 62 530-593 71-132 (134)
140 smart00421 HTH_LUXR helix_turn 97.8 6E-05 1.3E-09 58.0 5.7 47 540-591 2-48 (58)
141 TIGR03879 near_KaiC_dom probab 97.6 0.00015 3.4E-09 61.0 6.9 47 534-584 8-55 (73)
142 PF07374 DUF1492: Protein of u 97.6 0.00035 7.6E-09 62.2 8.9 55 531-589 44-99 (100)
143 PRK05658 RNA polymerase sigma 97.6 0.004 8.8E-08 72.0 20.0 32 290-322 102-134 (619)
144 PF04967 HTH_10: HTH DNA bindi 97.5 0.00032 6.9E-09 55.6 7.0 48 542-589 1-51 (53)
145 cd06170 LuxR_C_like C-terminal 97.5 0.00023 5E-09 55.0 6.0 46 542-592 1-46 (57)
146 PF00196 GerE: Bacterial regul 97.4 0.00032 7E-09 55.8 5.9 47 540-591 2-48 (58)
147 PRK13719 conjugal transfer tra 97.1 0.00089 1.9E-08 67.4 6.1 51 536-591 138-188 (217)
148 PRK15411 rcsA colanic acid cap 97.1 0.0009 2E-08 66.7 6.2 46 541-591 137-182 (207)
149 TIGR03541 reg_near_HchA LuxR f 97.1 0.00096 2.1E-08 67.7 6.1 50 539-593 169-218 (232)
150 PRK10840 transcriptional regul 97.1 0.001 2.2E-08 65.5 6.2 46 540-590 149-194 (216)
151 PRK11475 DNA-binding transcrip 97.0 0.0011 2.5E-08 66.2 6.3 46 540-590 133-178 (207)
152 TIGR01321 TrpR trp operon repr 97.0 0.0011 2.4E-08 58.5 5.4 48 533-580 23-74 (94)
153 TIGR03020 EpsA transcriptional 97.0 0.0011 2.4E-08 68.2 6.4 50 539-593 188-237 (247)
154 PRK15201 fimbriae regulatory p 97.0 0.0013 2.9E-08 64.2 6.4 46 541-591 133-178 (198)
155 COG2197 CitB Response regulato 97.0 0.0013 2.8E-08 65.9 5.9 47 540-591 147-193 (211)
156 PRK10100 DNA-binding transcrip 97.0 0.0014 3.1E-08 65.9 6.2 47 540-591 154-200 (216)
157 PRK13870 transcriptional regul 96.9 0.0015 3.2E-08 66.7 6.2 46 541-591 173-218 (234)
158 PRK10188 DNA-binding transcrip 96.9 0.0017 3.7E-08 66.4 6.4 46 541-591 179-224 (240)
159 COG4566 TtrR Response regulato 96.9 0.0052 1.1E-07 60.8 9.0 65 530-599 131-195 (202)
160 PF02001 DUF134: Protein of un 96.9 0.0028 6E-08 57.2 6.5 53 541-597 41-93 (106)
161 PRK15369 two component system 96.7 0.0036 7.9E-08 58.9 6.4 47 540-591 148-194 (211)
162 PF13936 HTH_38: Helix-turn-he 96.7 0.0022 4.7E-08 48.7 3.9 41 540-584 3-43 (44)
163 COG3413 Predicted DNA binding 96.7 0.0042 9E-08 62.4 7.0 53 541-593 155-210 (215)
164 COG2771 CsgD DNA-binding HTH d 96.7 0.0059 1.3E-07 48.6 6.5 51 540-595 3-53 (65)
165 PRK09483 response regulator; P 96.6 0.0033 7.2E-08 60.7 6.0 46 540-590 147-192 (217)
166 TIGR01637 phage_arpU phage tra 96.6 0.014 2.9E-07 54.2 9.3 63 530-594 67-130 (132)
167 COG4941 Predicted RNA polymera 96.6 0.053 1.1E-06 57.9 14.4 159 368-592 8-167 (415)
168 COG2739 Uncharacterized protei 96.5 0.0075 1.6E-07 53.7 6.6 49 540-592 16-64 (105)
169 PRK09390 fixJ response regulat 96.3 0.011 2.3E-07 55.4 7.1 56 534-594 134-189 (202)
170 PRK10651 transcriptional regul 96.2 0.0081 1.8E-07 57.3 5.8 47 540-591 154-200 (216)
171 PRK01381 Trp operon repressor; 96.1 0.0077 1.7E-07 53.6 4.5 51 529-579 19-73 (99)
172 PF00325 Crp: Bacterial regula 96.0 0.0082 1.8E-07 42.8 3.5 27 561-591 2-28 (32)
173 COG1342 Predicted DNA-binding 95.9 0.021 4.5E-07 50.4 6.2 53 541-597 33-85 (99)
174 PRK13558 bacterio-opsin activa 95.3 0.033 7.1E-07 64.3 7.0 54 539-592 605-661 (665)
175 PRK10403 transcriptional regul 95.1 0.041 8.8E-07 52.3 5.8 48 540-592 152-199 (215)
176 PRK09935 transcriptional regul 95.0 0.047 1E-06 52.0 6.1 46 541-591 149-194 (210)
177 PRK15320 transcriptional activ 95.0 0.046 9.9E-07 54.6 5.8 66 520-591 144-209 (251)
178 PRK10360 DNA-binding transcrip 95.0 0.048 1E-06 51.7 5.9 47 540-591 136-182 (196)
179 PF01726 LexA_DNA_bind: LexA D 94.9 0.04 8.6E-07 45.5 4.4 44 539-582 1-47 (65)
180 PF13613 HTH_Tnp_4: Helix-turn 94.8 0.074 1.6E-06 41.8 5.6 49 541-592 2-50 (53)
181 PRK09958 DNA-binding transcrip 94.8 0.06 1.3E-06 51.4 6.1 47 539-590 141-187 (204)
182 COG1356 tfx Transcriptional re 94.6 0.035 7.5E-07 51.4 3.7 49 541-594 8-56 (143)
183 PF13412 HTH_24: Winged helix- 94.6 0.11 2.4E-06 39.6 5.8 39 542-583 1-39 (48)
184 PRK04841 transcriptional regul 94.5 0.06 1.3E-06 64.1 6.4 47 540-591 837-883 (903)
185 PF05263 DUF722: Protein of un 94.5 0.15 3.2E-06 47.9 7.6 52 531-584 71-122 (130)
186 PF12645 HTH_16: Helix-turn-he 94.2 0.19 4.1E-06 41.5 6.8 57 355-411 3-65 (65)
187 PF13384 HTH_23: Homeodomain-l 93.9 0.067 1.5E-06 40.9 3.4 31 549-584 10-40 (50)
188 PF13730 HTH_36: Helix-turn-he 93.7 0.25 5.4E-06 38.5 6.5 47 541-591 2-51 (55)
189 cd00569 HTH_Hin_like Helix-tur 93.3 0.2 4.4E-06 33.7 4.8 36 542-581 6-41 (42)
190 PF06530 Phage_antitermQ: Phag 93.3 0.48 1E-05 43.9 8.6 52 539-594 60-111 (125)
191 PF13404 HTH_AsnC-type: AsnC-t 93.0 0.29 6.4E-06 36.9 5.6 39 542-583 1-39 (42)
192 PRK15418 transcriptional regul 92.9 0.15 3.3E-06 54.5 5.3 36 548-587 20-55 (318)
193 PF10668 Phage_terminase: Phag 92.8 0.21 4.5E-06 40.8 4.8 35 548-584 11-45 (60)
194 TIGR02531 yecD_yerC TrpR-relat 92.7 0.24 5.2E-06 43.4 5.4 38 539-582 34-71 (88)
195 PF08279 HTH_11: HTH domain; 92.6 0.29 6.3E-06 38.1 5.3 42 545-592 1-42 (55)
196 PF02796 HTH_7: Helix-turn-hel 92.3 0.18 3.9E-06 38.3 3.6 32 546-582 11-42 (45)
197 PRK10430 DNA-binding transcrip 92.3 0.29 6.2E-06 49.1 6.2 47 541-587 158-204 (239)
198 PF09862 DUF2089: Protein of u 92.2 0.41 8.9E-06 43.8 6.4 49 539-591 31-79 (113)
199 PHA00675 hypothetical protein 91.4 0.41 9E-06 40.8 5.1 40 540-583 21-61 (78)
200 PF04539 Sigma70_r3: Sigma-70 91.3 0.37 8E-06 40.2 4.9 38 323-360 4-41 (78)
201 PRK09210 RNA polymerase sigma 91.0 2.2 4.9E-05 46.4 11.8 126 324-490 217-347 (367)
202 TIGR02393 RpoD_Cterm RNA polym 90.8 2.8 6.2E-05 42.5 11.7 35 324-358 88-122 (238)
203 PF01325 Fe_dep_repress: Iron 90.8 0.59 1.3E-05 37.9 5.3 46 542-591 2-48 (60)
204 PRK07598 RNA polymerase sigma 90.7 1.2 2.7E-05 49.4 9.5 38 452-489 111-148 (415)
205 PF13518 HTH_28: Helix-turn-he 89.9 0.61 1.3E-05 35.5 4.6 24 562-585 13-36 (52)
206 PRK05901 RNA polymerase sigma 89.9 3.3 7.1E-05 47.3 12.1 35 324-358 359-393 (509)
207 PF06056 Terminase_5: Putative 89.7 0.72 1.6E-05 37.3 4.9 24 562-585 14-37 (58)
208 PRK07921 RNA polymerase sigma 89.5 3.6 7.8E-05 44.2 11.6 35 324-358 174-208 (324)
209 smart00351 PAX Paired Box doma 89.4 0.96 2.1E-05 41.8 6.3 41 542-586 18-58 (125)
210 COG3355 Predicted transcriptio 89.4 1.3 2.8E-05 41.4 7.1 53 533-591 16-68 (126)
211 PF12802 MarR_2: MarR family; 89.4 0.97 2.1E-05 35.6 5.5 41 541-582 2-42 (62)
212 PRK11083 DNA-binding response 89.1 0.56 1.2E-05 45.1 4.8 50 541-591 154-208 (228)
213 PF04218 CENP-B_N: CENP-B N-te 88.9 0.56 1.2E-05 37.0 3.7 40 541-584 6-45 (53)
214 COG2390 DeoR Transcriptional r 88.6 0.61 1.3E-05 50.1 5.0 35 549-587 18-52 (321)
215 PF03444 HrcA_DNA-bdg: Winged 88.5 1.2 2.6E-05 38.3 5.7 41 541-581 1-43 (78)
216 PRK12423 LexA repressor; Provi 88.4 0.85 1.8E-05 45.4 5.6 48 540-591 2-52 (202)
217 PRK15479 transcriptional regul 88.3 0.76 1.6E-05 44.0 5.0 49 541-590 148-201 (221)
218 smart00550 Zalpha Z-DNA-bindin 88.2 1.5 3.3E-05 36.2 6.1 41 546-591 8-48 (68)
219 COG1191 FliA DNA-directed RNA 88.0 5.4 0.00012 41.4 11.2 123 325-490 112-234 (247)
220 TIGR01610 phage_O_Nterm phage 88.0 1.4 3.1E-05 38.7 6.2 49 539-591 20-73 (95)
221 PHA02591 hypothetical protein; 87.9 1.1 2.3E-05 38.4 4.9 22 562-583 60-81 (83)
222 PRK10336 DNA-binding transcrip 87.8 0.77 1.7E-05 44.0 4.7 49 541-590 149-202 (219)
223 PF02650 HTH_WhiA: WhiA C-term 87.8 1.1 2.5E-05 38.9 5.3 42 539-583 35-78 (85)
224 PRK10710 DNA-binding transcrip 87.8 0.83 1.8E-05 44.5 5.0 50 541-591 160-214 (240)
225 PF01978 TrmB: Sugar-specific 87.7 0.63 1.4E-05 38.0 3.5 44 541-591 5-48 (68)
226 cd06571 Bac_DnaA_C C-terminal 87.6 2 4.2E-05 37.4 6.7 42 545-594 32-74 (90)
227 TIGR00498 lexA SOS regulatory 87.6 1 2.2E-05 44.5 5.5 48 540-591 2-52 (199)
228 TIGR03787 marine_sort_RR prote 87.6 0.84 1.8E-05 44.3 4.9 50 541-591 156-207 (227)
229 smart00344 HTH_ASNC helix_turn 87.6 1.5 3.3E-05 38.6 6.2 43 542-591 1-43 (108)
230 smart00345 HTH_GNTR helix_turn 87.1 1 2.3E-05 34.7 4.3 28 560-591 18-46 (60)
231 COG2909 MalT ATP-dependent tra 87.0 0.74 1.6E-05 54.7 4.8 46 542-592 832-877 (894)
232 PF09339 HTH_IclR: IclR helix- 86.7 0.97 2.1E-05 35.1 3.9 35 548-582 5-39 (52)
233 PRK07408 RNA polymerase sigma 86.7 2.2 4.9E-05 43.9 7.7 35 324-358 114-148 (256)
234 PF01047 MarR: MarR family; I 86.4 1.7 3.6E-05 34.1 5.1 39 542-583 1-39 (59)
235 PF13463 HTH_27: Winged helix 85.6 1.5 3.3E-05 35.1 4.7 44 542-591 1-44 (68)
236 TIGR02787 codY_Gpos GTP-sensin 85.2 4.5 9.8E-05 41.8 8.7 56 532-591 167-224 (251)
237 cd00131 PAX Paired Box domain 85.0 2.4 5.2E-05 39.4 6.3 41 542-586 18-58 (128)
238 PRK11179 DNA-binding transcrip 84.4 2.2 4.7E-05 40.6 5.8 38 541-581 6-43 (153)
239 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 84.4 2.5 5.5E-05 33.3 5.1 39 541-583 4-42 (50)
240 PRK10046 dpiA two-component re 84.3 1.1 2.3E-05 44.7 3.8 39 541-583 161-199 (225)
241 PF13022 HTH_Tnp_1_2: Helix-tu 84.0 4.5 9.7E-05 38.5 7.5 67 535-601 4-76 (142)
242 PRK07122 RNA polymerase sigma 84.0 11 0.00023 39.2 11.3 34 325-358 129-162 (264)
243 PRK05911 RNA polymerase sigma 83.7 8.1 0.00017 39.9 10.1 32 327-358 114-145 (257)
244 COG1522 Lrp Transcriptional re 83.4 1.9 4.2E-05 40.2 5.0 40 540-582 4-43 (154)
245 TIGR02154 PhoB phosphate regul 83.3 0.9 1.9E-05 43.6 2.8 50 541-591 154-208 (226)
246 PF01022 HTH_5: Bacterial regu 83.1 3.3 7.1E-05 31.5 5.3 22 561-582 15-36 (47)
247 PRK00215 LexA repressor; Valid 83.1 2.1 4.6E-05 42.3 5.4 42 542-583 2-46 (205)
248 PF13545 HTH_Crp_2: Crp-like h 83.1 1.7 3.6E-05 35.8 3.9 27 561-591 28-54 (76)
249 PF08220 HTH_DeoR: DeoR-like h 83.0 2.7 5.8E-05 33.5 4.9 39 546-591 2-40 (57)
250 PF13011 LZ_Tnp_IS481: leucine 82.9 3.1 6.8E-05 36.3 5.6 43 540-585 7-49 (85)
251 TIGR02147 Fsuc_second hypothet 82.8 18 0.00039 38.1 12.3 100 466-570 135-238 (271)
252 smart00419 HTH_CRP helix_turn_ 82.8 2 4.4E-05 31.8 4.0 27 561-591 8-34 (48)
253 PF12840 HTH_20: Helix-turn-he 82.8 4.8 0.0001 32.1 6.4 41 544-591 10-50 (61)
254 PF12728 HTH_17: Helix-turn-he 82.5 1.4 3E-05 33.8 3.0 23 562-584 2-24 (51)
255 cd00092 HTH_CRP helix_turn_hel 82.4 4 8.7E-05 32.4 5.8 28 560-591 24-51 (67)
256 TIGR02850 spore_sigG RNA polym 82.2 11 0.00025 38.6 10.5 35 325-359 122-156 (254)
257 PHA02547 55 RNA polymerase sig 82.1 4.3 9.3E-05 39.8 6.7 64 372-435 44-110 (179)
258 TIGR03697 NtcA_cyano global ni 82.0 1.6 3.5E-05 41.8 4.0 29 560-592 142-170 (193)
259 PRK05949 RNA polymerase sigma 81.9 14 0.00031 39.7 11.4 34 325-358 180-213 (327)
260 PF00356 LacI: Bacterial regul 81.8 1.4 3.1E-05 33.9 2.8 22 563-584 1-22 (46)
261 PRK11169 leucine-responsive tr 81.7 2.2 4.7E-05 41.1 4.7 37 542-581 12-48 (164)
262 PRK07406 RNA polymerase sigma 81.5 6.8 0.00015 43.0 9.0 37 454-490 96-132 (373)
263 TIGR02885 spore_sigF RNA polym 81.5 4.8 0.0001 40.4 7.3 32 327-358 101-132 (231)
264 PRK06288 RNA polymerase sigma 81.4 21 0.00046 36.8 12.3 34 324-357 119-152 (268)
265 CHL00148 orf27 Ycf27; Reviewed 81.0 2.2 4.8E-05 41.5 4.6 50 541-591 161-217 (240)
266 COG1654 BirA Biotin operon rep 80.9 4.2 9.1E-05 35.0 5.6 32 556-591 14-45 (79)
267 PF01418 HTH_6: Helix-turn-hel 80.9 3 6.5E-05 35.1 4.8 52 531-582 3-55 (77)
268 PF01371 Trp_repressor: Trp re 80.8 5.1 0.00011 35.1 6.2 44 541-587 26-74 (87)
269 PF00046 Homeobox: Homeobox do 80.5 3.9 8.4E-05 31.9 5.0 51 541-591 6-57 (57)
270 TIGR01764 excise DNA binding d 80.5 1.9 4.2E-05 31.8 3.1 24 562-585 2-25 (49)
271 smart00420 HTH_DEOR helix_turn 80.3 5.1 0.00011 29.9 5.5 27 561-591 14-40 (53)
272 PF02954 HTH_8: Bacterial regu 80.3 3.1 6.8E-05 31.0 4.2 36 544-582 4-39 (42)
273 cd07377 WHTH_GntR Winged helix 80.2 3.6 7.9E-05 32.3 4.8 26 562-591 26-51 (66)
274 PF01726 LexA_DNA_bind: LexA D 80.2 3.8 8.3E-05 33.8 5.0 39 452-490 9-48 (65)
275 smart00342 HTH_ARAC helix_turn 80.0 20 0.00043 28.9 9.4 23 468-490 1-23 (84)
276 cd04762 HTH_MerR-trunc Helix-T 79.8 2.2 4.7E-05 31.4 3.2 25 562-586 1-25 (49)
277 COG3415 Transposase and inacti 79.7 3.6 7.8E-05 39.1 5.3 34 549-586 13-46 (138)
278 PRK07670 RNA polymerase sigma 79.2 19 0.00041 36.8 10.9 35 325-359 111-145 (251)
279 PF00392 GntR: Bacterial regul 78.5 2.9 6.4E-05 33.7 3.8 29 559-591 21-50 (64)
280 PF01710 HTH_Tnp_IS630: Transp 78.4 13 0.00029 33.8 8.6 27 562-592 72-98 (119)
281 PRK00423 tfb transcription ini 77.9 34 0.00074 36.5 12.7 84 368-488 119-202 (310)
282 PRK13918 CRP/FNR family transc 77.9 2.5 5.5E-05 40.9 3.9 28 560-591 148-175 (202)
283 PF02082 Rrf2: Transcriptional 77.8 5 0.00011 34.1 5.2 31 557-591 21-51 (83)
284 PRK11564 stationary phase indu 77.8 5.9 0.00013 43.7 7.2 51 541-591 10-60 (426)
285 PF08822 DUF1804: Protein of u 77.7 5.1 0.00011 39.2 5.7 42 543-587 4-45 (165)
286 TIGR02997 Sig70-cyanoRpoD RNA 77.6 26 0.00056 36.9 11.6 34 325-358 163-196 (298)
287 PF08280 HTH_Mga: M protein tr 77.5 4.2 9E-05 32.6 4.4 41 545-592 6-46 (59)
288 PF13542 HTH_Tnp_ISL3: Helix-t 77.4 6 0.00013 30.2 5.1 24 562-585 28-51 (52)
289 COG1510 Predicted transcriptio 77.0 2.7 5.8E-05 41.3 3.7 29 559-591 39-67 (177)
290 cd04761 HTH_MerR-SF Helix-Turn 76.5 2 4.4E-05 32.2 2.2 25 562-586 1-25 (49)
291 PHA00542 putative Cro-like pro 76.3 2.5 5.4E-05 36.2 3.0 24 562-585 32-55 (82)
292 PRK07405 RNA polymerase sigma 76.2 19 0.00041 38.5 10.3 34 324-357 169-202 (317)
293 PF13744 HTH_37: Helix-turn-he 76.1 5.2 0.00011 34.0 4.8 44 549-596 23-71 (80)
294 smart00346 HTH_ICLR helix_turn 76.0 6.6 0.00014 33.2 5.5 24 560-583 19-42 (91)
295 TIGR00122 birA_repr_reg BirA b 75.7 7.1 0.00015 31.9 5.4 27 561-591 13-39 (69)
296 TIGR02479 FliA_WhiG RNA polyme 75.5 31 0.00068 34.4 11.1 35 324-358 84-118 (224)
297 smart00347 HTH_MARR helix_turn 75.2 8.2 0.00018 32.6 5.9 44 541-591 7-50 (101)
298 PHA01976 helix-turn-helix prot 75.0 5.5 0.00012 32.0 4.5 32 549-584 7-38 (67)
299 PRK11753 DNA-binding transcrip 74.7 15 0.00033 35.7 8.4 28 561-592 168-195 (211)
300 PRK10072 putative transcriptio 74.7 4.8 0.0001 35.8 4.4 32 549-584 38-69 (96)
301 PRK07500 rpoH2 RNA polymerase 74.5 20 0.00042 37.8 9.7 24 467-490 244-267 (289)
302 cd00090 HTH_ARSR Arsenical Res 74.1 10 0.00022 29.8 5.9 26 562-591 21-46 (78)
303 PRK11161 fumarate/nitrate redu 74.0 3.6 7.8E-05 41.0 3.9 27 561-591 184-210 (235)
304 PRK06030 hypothetical protein; 73.8 10 0.00022 35.4 6.5 49 544-600 56-104 (124)
305 TIGR02612 mob_myst_A mobile my 73.5 8.1 0.00017 37.2 5.9 48 543-594 24-77 (150)
306 PRK09954 putative kinase; Prov 73.1 6.1 0.00013 42.4 5.6 42 542-586 1-42 (362)
307 TIGR02337 HpaR homoprotocatech 72.8 18 0.00039 32.5 7.8 44 541-591 25-68 (118)
308 PF13560 HTH_31: Helix-turn-he 72.3 5.4 0.00012 32.0 3.9 23 562-584 15-37 (64)
309 PRK13413 mpi multiple promoter 72.2 6.8 0.00015 38.7 5.3 33 546-583 162-194 (200)
310 TIGR03070 couple_hipB transcri 72.0 7.2 0.00016 29.8 4.4 23 562-584 16-38 (58)
311 PF13411 MerR_1: MerR HTH fami 71.9 2.1 4.5E-05 34.6 1.3 25 562-586 1-25 (69)
312 PF01381 HTH_3: Helix-turn-hel 71.7 5.6 0.00012 30.6 3.7 23 562-584 10-32 (55)
313 TIGR02844 spore_III_D sporulat 71.6 7 0.00015 33.7 4.5 35 545-583 7-41 (80)
314 COG1476 Predicted transcriptio 71.6 6.4 0.00014 33.0 4.1 32 549-584 6-37 (68)
315 PF05043 Mga: Mga helix-turn-h 71.3 3.1 6.8E-05 35.4 2.4 35 560-598 29-63 (87)
316 PRK10402 DNA-binding transcrip 71.0 9.3 0.0002 38.1 6.1 47 542-592 149-196 (226)
317 COG2512 Predicted membrane-ass 70.7 6.7 0.00014 41.0 5.0 46 540-591 191-236 (258)
318 PF01527 HTH_Tnp_1: Transposas 70.3 6.5 0.00014 32.3 4.0 40 543-586 8-48 (76)
319 PF12116 SpoIIID: Stage III sp 70.1 7.4 0.00016 33.7 4.2 46 546-593 6-51 (82)
320 PF08765 Mor: Mor transcriptio 69.8 9.9 0.00021 34.2 5.3 42 545-592 62-103 (108)
321 PRK11512 DNA-binding transcrip 69.8 24 0.00053 32.8 8.2 51 533-590 27-79 (144)
322 PRK09391 fixK transcriptional 69.4 5.4 0.00012 40.1 4.0 28 561-592 179-206 (230)
323 PRK11014 transcriptional repre 69.4 11 0.00024 35.2 5.8 30 558-591 22-51 (141)
324 PRK11337 DNA-binding transcrip 69.3 12 0.00027 38.9 6.7 62 531-594 15-83 (292)
325 PRK01905 DNA-binding protein F 69.0 22 0.00047 30.1 6.9 35 545-582 37-71 (77)
326 PRK10870 transcriptional repre 68.6 27 0.00059 34.0 8.6 50 533-583 42-93 (176)
327 TIGR01884 cas_HTH CRISPR locus 68.5 14 0.00031 36.7 6.7 44 538-584 137-180 (203)
328 PF13551 HTH_29: Winged helix- 68.3 45 0.00098 28.9 9.2 22 470-491 14-35 (112)
329 PF00376 MerR: MerR family reg 67.9 3.6 7.8E-05 30.3 1.7 23 563-585 1-23 (38)
330 PRK11302 DNA-binding transcrip 67.9 9.6 0.00021 39.3 5.5 50 532-583 4-56 (284)
331 PRK09413 IS2 repressor TnpA; R 67.8 15 0.00032 33.7 6.1 24 562-585 30-53 (121)
332 PF07750 GcrA: GcrA cell cycle 67.0 7.3 0.00016 37.9 4.2 36 545-584 6-42 (162)
333 cd01104 HTH_MlrA-CarA Helix-Tu 66.9 6.9 0.00015 31.4 3.4 23 562-584 1-23 (68)
334 TIGR02941 Sigma_B RNA polymera 66.9 39 0.00086 34.5 9.8 32 326-357 119-150 (255)
335 PRK03573 transcriptional regul 66.7 20 0.00043 33.3 6.9 52 533-590 18-71 (144)
336 cd00086 homeodomain Homeodomai 66.4 17 0.00037 28.0 5.5 51 541-591 6-57 (59)
337 PF13551 HTH_29: Winged helix- 66.2 9.7 0.00021 33.2 4.5 23 562-584 12-35 (112)
338 PRK08215 sporulation sigma fac 66.2 57 0.0012 33.5 10.8 33 326-358 126-158 (258)
339 smart00418 HTH_ARSR helix_turn 65.9 10 0.00022 28.9 4.1 23 561-583 10-32 (66)
340 TIGR02944 suf_reg_Xantho FeS a 65.1 13 0.00028 34.1 5.2 30 558-591 22-51 (130)
341 PRK09392 ftrB transcriptional 64.7 7 0.00015 39.0 3.7 28 561-592 173-200 (236)
342 PRK10161 transcriptional regul 64.6 7.3 0.00016 37.8 3.7 50 541-591 154-208 (229)
343 TIGR03830 CxxCG_CxxCG_HTH puta 64.5 22 0.00047 32.1 6.6 46 534-585 57-102 (127)
344 PRK05572 sporulation sigma fac 64.3 50 0.0011 33.7 9.9 32 325-356 120-151 (252)
345 PF14502 HTH_41: Helix-turn-he 64.3 12 0.00026 29.3 4.0 30 559-592 4-33 (48)
346 PF14493 HTH_40: Helix-turn-he 64.2 12 0.00027 32.4 4.7 27 562-588 14-40 (91)
347 COG0568 RpoD DNA-directed RNA 64.0 65 0.0014 35.1 11.0 36 321-356 187-222 (342)
348 COG5484 Uncharacterized conser 63.7 9.5 0.00021 39.7 4.4 32 549-584 11-42 (279)
349 cd04764 HTH_MlrA-like_sg1 Heli 63.4 9 0.00019 30.9 3.4 23 562-584 1-23 (67)
350 PRK11050 manganese transport r 63.0 27 0.00059 33.2 7.2 27 561-591 51-77 (152)
351 COG2345 Predicted transcriptio 62.6 13 0.00028 37.9 5.1 24 561-584 25-48 (218)
352 TIGR01387 cztR_silR_copR heavy 61.5 12 0.00027 35.5 4.6 49 541-590 147-200 (218)
353 PF14394 DUF4423: Domain of un 61.3 13 0.00027 36.4 4.7 109 466-594 37-153 (171)
354 PRK04984 fatty acid metabolism 61.2 11 0.00023 38.0 4.3 30 558-591 27-57 (239)
355 PRK09863 putative frv operon r 61.1 40 0.00086 38.9 9.4 103 467-590 16-121 (584)
356 PRK11517 transcriptional regul 60.9 15 0.00032 35.2 5.1 49 541-590 147-200 (223)
357 PRK15482 transcriptional regul 60.9 16 0.00035 38.0 5.7 59 533-593 5-70 (285)
358 TIGR02980 SigBFG RNA polymeras 60.9 59 0.0013 32.4 9.5 30 328-357 95-124 (227)
359 smart00422 HTH_MERR helix_turn 60.4 6.7 0.00014 31.6 2.2 25 562-586 1-25 (70)
360 TIGR03338 phnR_burk phosphonat 60.3 9.9 0.00021 37.5 3.8 37 549-591 24-60 (212)
361 COG0856 Orotate phosphoribosyl 59.7 7.9 0.00017 38.3 2.8 30 562-591 19-48 (203)
362 cd04763 HTH_MlrA-like Helix-Tu 59.7 11 0.00024 30.5 3.4 23 562-584 1-23 (68)
363 PRK03902 manganese transport t 59.6 21 0.00045 33.3 5.7 28 560-591 21-48 (142)
364 TIGR02607 antidote_HigA addict 59.3 20 0.00044 29.4 5.0 23 562-584 19-41 (78)
365 smart00389 HOX Homeodomain. DN 58.9 19 0.0004 27.6 4.4 48 541-588 6-54 (56)
366 PRK06986 fliA flagellar biosyn 58.9 94 0.002 31.3 10.7 32 327-358 99-130 (236)
367 PRK11557 putative DNA-binding 58.8 13 0.00029 38.3 4.6 57 535-593 3-66 (278)
368 TIGR00647 MG103 conserved hypo 58.6 21 0.00046 37.8 6.0 42 539-583 225-272 (279)
369 TIGR02431 pcaR_pcaU beta-ketoa 58.4 18 0.00038 36.9 5.3 38 546-583 9-46 (248)
370 PRK11414 colanic acid/biofilm 58.1 11 0.00024 37.5 3.8 37 549-591 24-60 (221)
371 TIGR00180 parB_part ParB-like 58.0 19 0.0004 35.4 5.2 43 540-584 101-143 (187)
372 PF05225 HTH_psq: helix-turn-h 57.8 16 0.00035 27.9 3.7 22 562-583 17-38 (45)
373 PF13556 HTH_30: PucR C-termin 57.6 31 0.00067 27.5 5.5 33 562-594 13-45 (59)
374 smart00354 HTH_LACI helix_turn 57.6 10 0.00023 31.2 2.9 23 562-584 1-23 (70)
375 PF08784 RPA_C: Replication pr 57.5 19 0.00041 31.7 4.8 41 541-581 44-85 (102)
376 PRK10141 DNA-binding transcrip 57.4 30 0.00065 31.9 6.1 49 536-591 7-56 (117)
377 COG2522 Predicted transcriptio 57.2 18 0.0004 33.5 4.7 22 562-583 23-44 (119)
378 COG1508 RpoN DNA-directed RNA 57.1 54 0.0012 36.9 9.2 47 536-582 293-351 (444)
379 TIGR02812 fadR_gamma fatty aci 56.9 14 0.0003 37.2 4.2 30 558-591 26-56 (235)
380 TIGR00738 rrf2_super rrf2 fami 56.8 26 0.00055 31.9 5.7 30 558-591 22-51 (132)
381 PF12298 Bot1p: Eukaryotic mit 56.6 23 0.00051 34.8 5.6 40 541-583 16-55 (172)
382 PRK09990 DNA-binding transcrip 56.4 14 0.00031 37.5 4.3 37 549-591 20-57 (251)
383 TIGR01889 Staph_reg_Sar staphy 56.3 74 0.0016 28.3 8.4 42 541-582 22-64 (109)
384 COG4367 Uncharacterized protei 56.3 21 0.00045 31.5 4.5 39 456-494 10-49 (97)
385 PRK13239 alkylmercury lyase; P 56.2 20 0.00043 36.3 5.2 28 465-492 33-60 (206)
386 PRK14101 bifunctional glucokin 56.2 20 0.00044 41.9 6.0 62 531-594 343-411 (638)
387 PRK04158 transcriptional repre 56.0 19 0.00041 37.6 5.1 58 530-591 168-227 (256)
388 PRK09464 pdhR transcriptional 55.9 15 0.00032 37.4 4.3 38 548-591 22-60 (254)
389 PRK03837 transcriptional regul 55.9 15 0.00033 36.9 4.3 37 549-591 26-63 (241)
390 PRK11534 DNA-binding transcrip 55.8 15 0.00032 36.7 4.2 38 548-591 19-56 (224)
391 PRK10225 DNA-binding transcrip 55.7 15 0.00032 37.6 4.3 38 548-591 21-59 (257)
392 COG2973 TrpR Trp operon repres 55.1 30 0.00065 31.1 5.4 45 541-590 37-85 (103)
393 PRK09726 antitoxin HipB; Provi 54.9 21 0.00045 30.7 4.4 23 562-584 26-48 (88)
394 PRK10411 DNA-binding transcrip 54.6 23 0.00051 36.3 5.5 41 544-587 4-44 (240)
395 smart00862 Trans_reg_C Transcr 54.5 41 0.00089 27.2 6.0 50 541-591 5-60 (78)
396 PF04703 FaeA: FaeA-like prote 54.4 14 0.00031 30.3 3.1 24 560-583 14-37 (62)
397 PRK10421 DNA-binding transcrip 54.2 16 0.00035 37.2 4.3 38 548-591 14-52 (253)
398 PRK09834 DNA-binding transcrip 53.6 25 0.00055 36.2 5.7 42 546-591 11-52 (263)
399 PRK10434 srlR DNA-bindng trans 53.3 22 0.00047 36.8 5.1 38 544-584 5-42 (256)
400 PF05732 RepL: Firmicute plasm 53.0 41 0.00088 32.8 6.6 53 535-591 46-101 (165)
401 COG2944 Predicted transcriptio 52.9 27 0.00059 31.7 4.9 39 540-584 42-80 (104)
402 PRK10857 DNA-binding transcrip 52.5 38 0.00083 32.9 6.3 31 557-591 21-51 (164)
403 COG1737 RpiR Transcriptional r 52.3 21 0.00046 37.3 4.9 51 531-583 5-58 (281)
404 COG4465 CodY Pleiotropic trans 52.2 53 0.0011 33.7 7.3 55 533-591 174-230 (261)
405 PRK10163 DNA-binding transcrip 52.2 24 0.00051 36.7 5.2 25 558-582 37-61 (271)
406 COG1846 MarR Transcriptional r 52.1 31 0.00067 29.9 5.2 38 542-582 20-57 (126)
407 TIGR02698 CopY_TcrY copper tra 52.0 36 0.00078 31.7 5.8 44 541-587 1-48 (130)
408 PRK10643 DNA-binding transcrip 51.8 16 0.00034 34.9 3.5 49 541-590 149-202 (222)
409 COG1318 Predicted transcriptio 51.7 15 0.00032 36.2 3.2 24 562-585 62-85 (182)
410 PF08535 KorB: KorB domain; I 51.7 13 0.00029 32.3 2.7 22 562-583 4-25 (93)
411 PRK13509 transcriptional repre 51.6 27 0.00059 36.0 5.4 37 545-584 6-42 (251)
412 PRK11569 transcriptional repre 51.1 24 0.00053 36.6 5.1 31 552-582 34-64 (274)
413 PRK09706 transcriptional repre 50.4 25 0.00053 32.6 4.5 23 562-584 19-41 (135)
414 COG1321 TroR Mn-dependent tran 50.3 30 0.00066 33.3 5.2 25 558-582 21-45 (154)
415 PRK06266 transcription initiat 50.1 51 0.0011 32.5 6.8 51 533-591 12-62 (178)
416 KOG0484 Transcription factor P 49.9 29 0.00062 31.6 4.5 52 540-595 27-78 (125)
417 smart00342 HTH_ARAC helix_turn 49.9 33 0.00072 27.5 4.8 25 562-586 2-26 (84)
418 PF09012 FeoC: FeoC like trans 49.9 13 0.00028 30.5 2.3 23 561-583 14-36 (69)
419 PRK09863 putative frv operon r 49.9 32 0.00068 39.7 6.2 46 542-591 2-47 (584)
420 PF08299 Bac_DnaA_C: Bacterial 49.7 38 0.00082 28.1 5.0 33 545-581 33-66 (70)
421 PRK13777 transcriptional regul 49.7 78 0.0017 31.4 8.1 38 541-581 42-79 (185)
422 smart00530 HTH_XRE Helix-turn- 49.7 30 0.00064 24.7 4.0 23 562-584 11-33 (56)
423 cd04768 HTH_BmrR-like Helix-Tu 49.4 12 0.00027 32.8 2.2 25 562-586 1-25 (96)
424 TIGR02395 rpoN_sigma RNA polym 49.3 93 0.002 34.9 9.6 24 467-490 317-340 (429)
425 COG1349 GlpR Transcriptional r 49.2 21 0.00045 37.0 4.1 38 543-583 4-41 (253)
426 COG3877 Uncharacterized protei 49.2 41 0.00088 30.7 5.4 47 539-589 39-85 (122)
427 PRK11523 DNA-binding transcrip 49.1 22 0.00048 36.2 4.3 37 549-591 21-58 (253)
428 PF00165 HTH_AraC: Bacterial r 48.8 26 0.00057 25.6 3.6 24 561-584 8-31 (42)
429 PF00486 Trans_reg_C: Transcri 48.7 44 0.00096 27.1 5.3 51 541-592 5-60 (77)
430 PF08006 DUF1700: Protein of u 48.6 48 0.001 32.3 6.4 57 528-584 3-63 (181)
431 TIGR02010 IscR iron-sulfur clu 48.3 42 0.00091 31.1 5.7 30 558-591 22-51 (135)
432 cd00383 trans_reg_C Effector d 48.3 42 0.00091 28.3 5.3 49 541-590 23-76 (95)
433 PF11662 DUF3263: Protein of u 48.2 67 0.0014 27.7 6.3 44 541-586 2-47 (77)
434 cd01392 HTH_LacI Helix-turn-he 48.0 12 0.00027 28.3 1.7 21 565-585 1-21 (52)
435 PF06971 Put_DNA-bind_N: Putat 47.3 37 0.0008 26.7 4.3 46 443-488 3-48 (50)
436 cd04775 HTH_Cfa-like Helix-Tur 47.2 14 0.00029 32.9 2.1 26 562-587 2-27 (102)
437 PF01710 HTH_Tnp_IS630: Transp 47.1 28 0.00061 31.7 4.2 22 562-583 19-40 (119)
438 PF12844 HTH_19: Helix-turn-he 47.0 33 0.00072 27.1 4.2 23 562-584 13-35 (64)
439 smart00352 POU Found in Pit-Oc 47.0 36 0.00078 29.2 4.5 32 549-584 16-53 (75)
440 PRK00430 fis global DNA-bindin 46.9 82 0.0018 27.9 7.0 36 544-582 54-89 (95)
441 cd00093 HTH_XRE Helix-turn-hel 46.3 42 0.0009 24.0 4.4 23 562-584 13-35 (58)
442 PF06413 Neugrin: Neugrin; In 46.2 33 0.00072 35.2 5.0 42 541-583 10-51 (225)
443 PRK04424 fatty acid biosynthes 45.8 38 0.00081 33.4 5.2 37 544-583 7-43 (185)
444 PRK12469 RNA polymerase factor 45.7 27 0.00058 39.7 4.7 45 538-582 334-390 (481)
445 cd04773 HTH_TioE_rpt2 Second H 45.6 15 0.00033 33.0 2.2 25 562-586 1-25 (108)
446 TIGR02018 his_ut_repres histid 45.5 27 0.00059 35.0 4.3 26 562-591 26-51 (230)
447 PHA00738 putative HTH transcri 45.3 45 0.00097 30.5 5.1 35 545-582 13-47 (108)
448 COG5625 Predicted transcriptio 45.1 36 0.00078 30.8 4.3 54 533-586 8-61 (113)
449 PRK10681 DNA-binding transcrip 45.0 33 0.00072 35.3 4.9 38 544-584 7-44 (252)
450 PRK00082 hrcA heat-inducible t 44.9 35 0.00076 37.0 5.2 44 540-583 2-49 (339)
451 cd01107 HTH_BmrR Helix-Turn-He 44.7 16 0.00035 32.7 2.3 26 562-587 1-26 (108)
452 PRK06424 transcription factor; 44.7 33 0.00072 32.8 4.4 32 549-584 89-120 (144)
453 COG4709 Predicted membrane pro 44.6 59 0.0013 32.6 6.2 59 528-586 3-65 (195)
454 COG3093 VapI Plasmid maintenan 44.6 36 0.00079 30.9 4.4 35 548-584 12-46 (104)
455 PRK05932 RNA polymerase factor 44.5 1.2E+02 0.0027 34.2 9.7 24 467-490 342-365 (455)
456 PF10078 DUF2316: Uncharacteri 44.5 50 0.0011 29.2 5.1 22 562-583 24-45 (89)
457 TIGR02325 C_P_lyase_phnF phosp 44.5 30 0.00065 34.6 4.4 26 562-591 33-58 (238)
458 PRK09764 DNA-binding transcrip 44.5 29 0.00062 35.2 4.3 25 563-591 31-55 (240)
459 TIGR02395 rpoN_sigma RNA polym 44.4 25 0.00055 39.3 4.2 23 560-582 317-339 (429)
460 PRK14999 histidine utilization 44.3 29 0.00063 35.1 4.3 26 562-591 37-62 (241)
461 cd04765 HTH_MlrA-like_sg2 Heli 44.0 26 0.00057 31.1 3.4 23 562-584 1-23 (99)
462 TIGR00373 conserved hypothetic 44.0 77 0.0017 30.6 6.9 42 543-591 13-54 (158)
463 cd01105 HTH_GlnR-like Helix-Tu 44.0 17 0.00036 31.4 2.2 25 562-586 2-26 (88)
464 COG1802 GntR Transcriptional r 44.0 19 0.0004 36.2 2.8 37 549-591 29-65 (230)
465 TIGR00637 ModE_repress ModE mo 43.9 72 0.0016 28.3 6.2 42 543-593 3-44 (99)
466 PRK10955 DNA-binding transcrip 43.8 16 0.00036 35.2 2.4 50 541-591 156-210 (232)
467 PF00126 HTH_1: Bacterial regu 43.6 67 0.0014 25.4 5.4 29 562-594 14-42 (60)
468 PF00292 PAX: 'Paired box' dom 43.5 52 0.0011 30.9 5.4 32 548-584 25-56 (125)
469 PRK11886 bifunctional biotin-- 43.4 40 0.00087 35.8 5.4 39 545-586 5-43 (319)
470 COG4367 Uncharacterized protei 43.3 57 0.0012 28.8 5.2 39 542-583 3-45 (97)
471 cd04782 HTH_BltR Helix-Turn-He 43.2 18 0.00038 31.9 2.2 25 562-586 1-25 (97)
472 PF02787 CPSase_L_D3: Carbamoy 43.0 1.8E+02 0.0039 27.0 8.9 43 534-583 52-94 (123)
473 PF00440 TetR_N: Bacterial reg 43.0 50 0.0011 24.8 4.4 26 553-581 11-36 (47)
474 cd04772 HTH_TioE_rpt1 First He 43.0 18 0.00039 32.0 2.3 25 562-586 1-25 (99)
475 cd04766 HTH_HspR Helix-Turn-He 43.0 17 0.00038 31.4 2.1 25 562-586 2-26 (91)
476 PF04552 Sigma54_DBD: Sigma-54 42.9 46 0.001 32.3 5.2 24 467-490 48-71 (160)
477 TIGR02404 trehalos_R_Bsub treh 42.9 33 0.0007 34.5 4.4 27 561-591 24-50 (233)
478 PRK10906 DNA-binding transcrip 42.8 40 0.00087 34.8 5.1 37 544-583 5-41 (252)
479 cd04789 HTH_Cfa Helix-Turn-Hel 42.5 18 0.0004 32.1 2.2 25 562-586 2-26 (102)
480 PF04552 Sigma54_DBD: Sigma-54 42.4 8.3 0.00018 37.5 0.0 47 534-582 24-70 (160)
481 PRK13705 plasmid-partitioning 42.3 33 0.00071 37.8 4.6 55 532-586 4-64 (388)
482 COG3711 BglG Transcriptional a 42.2 27 0.00059 39.1 4.1 47 544-591 84-130 (491)
483 PF12085 DUF3562: Protein of u 42.1 36 0.00077 28.5 3.6 39 562-603 8-46 (66)
484 cd01279 HTH_HspR-like Helix-Tu 41.9 19 0.00041 31.8 2.2 24 562-585 2-25 (98)
485 cd04774 HTH_YfmP Helix-Turn-He 41.9 18 0.0004 31.8 2.1 25 562-586 1-25 (96)
486 cd04788 HTH_NolA-AlbR Helix-Tu 41.7 19 0.00041 31.6 2.1 25 562-586 1-25 (96)
487 cd04780 HTH_MerR-like_sg5 Heli 41.6 19 0.00042 31.7 2.2 25 562-586 1-25 (95)
488 cd00592 HTH_MerR-like Helix-Tu 41.4 20 0.00043 31.3 2.2 25 562-586 1-25 (100)
489 PRK10079 phosphonate metabolis 41.3 30 0.00065 35.0 3.9 28 560-591 34-61 (241)
490 cd01106 HTH_TipAL-Mta Helix-Tu 41.2 20 0.00042 31.7 2.2 25 562-586 1-25 (103)
491 PRK09943 DNA-binding transcrip 41.2 39 0.00085 32.9 4.5 23 562-584 21-43 (185)
492 cd01109 HTH_YyaN Helix-Turn-He 41.0 20 0.00043 32.3 2.2 25 562-586 1-25 (113)
493 cd01282 HTH_MerR-like_sg3 Heli 41.0 20 0.00043 32.4 2.2 26 562-587 1-26 (112)
494 cd01108 HTH_CueR Helix-Turn-He 40.4 20 0.00043 33.1 2.2 26 562-587 1-26 (127)
495 cd04769 HTH_MerR2 Helix-Turn-H 40.4 20 0.00044 32.4 2.2 26 562-587 1-26 (116)
496 PRK09836 DNA-binding transcrip 40.3 41 0.00088 32.5 4.5 49 541-590 150-203 (227)
497 PRK05932 RNA polymerase factor 40.0 32 0.0007 38.8 4.1 44 539-582 309-364 (455)
498 TIGR02044 CueR Cu(I)-responsiv 39.5 21 0.00045 32.9 2.2 25 562-586 1-25 (127)
499 TIGR00270 conserved hypothetic 39.5 44 0.00095 32.3 4.4 30 551-584 76-105 (154)
500 PRK13890 conjugal transfer pro 39.5 46 0.001 30.6 4.4 23 562-584 19-41 (120)
No 1
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=100.00 E-value=5e-64 Score=539.50 Aligned_cols=313 Identities=39% Similarity=0.696 Sum_probs=295.4
Q ss_pred CCCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHH--------------------HHhHHHHHHhhcCCCCchHHHHH
Q 007404 289 DYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLK--------------------LEGLREVLSERCGGSPTFAQWAA 347 (605)
Q Consensus 289 ~~~d~l~-yL~~i~~~~~lLT~eEE~eL~~~iq~~~~--------------------le~~~~~L~~~~G~~pt~~ewA~ 347 (605)
...|+++ ||++| ++.||||++||++|+++||.+++ |++++..|.+++|++||..+||.
T Consensus 57 ~~~d~v~~yl~~i-gr~~lL~~~eEv~l~~~vq~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~g~~pt~~ewa~ 135 (415)
T PRK07598 57 RSTDLVRLYLQEI-GRVRLLGRDEEVSEAQKVQRYMKLIVLANAAKEGDEVIKPYLRLIEVRERLTSELGHRPSLERWAK 135 (415)
T ss_pred CCCChHHHHHHhc-ccccCCCHHHHHHHHHHHHHHHHHhhhhhhhhcccchhhhHHHHHHHHHHHHHHhCCCCCHHHHHH
Confidence 3479999 99999 99999999999999999999999 89999999999999999999996
Q ss_pred hhcC----------------------CHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHH
Q 007404 348 AAGV----------------------DQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVR 405 (605)
Q Consensus 348 a~g~----------------------d~~~L~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLir 405 (605)
++|+ +.+.|.+.++.|..|+++||.+|+++|++||++|.++|++++||||||++|||+
T Consensus 136 ~~~~~~~~l~~~l~~~~~~~~~~~~l~~~eL~~~l~~G~~A~e~LI~~nlrLVvsiAkky~~~g~~~eDLiQEG~iGL~r 215 (415)
T PRK07598 136 TADISLADLKPTLAEGKRRWAEIAKLTVEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLER 215 (415)
T ss_pred HhCCcHHHHHHhhhhhhhhhhhhccCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHH
Confidence 6555 455555556778899999999999999999999999999999999999999999
Q ss_pred hhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHH
Q 007404 406 GAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRL 485 (605)
Q Consensus 406 A~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V 485 (605)
|+++|||++|++|+||++||||++|.+++.+++++||+|.|+.+.+++++++.+.+.+++||.|+.+|||+.+|+++++|
T Consensus 216 avekFDp~rG~rFSTYa~wwIRqaI~r~i~~~srtIrlP~~i~e~l~~lrk~~r~L~~~lgR~pt~~EiA~~l~is~~~v 295 (415)
T PRK07598 216 AVEKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQV 295 (415)
T ss_pred HHHHcCcccCCCHHHHHHHHHHHHHHHHHHHcCCceehhHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHH
Q 007404 486 HAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQ 565 (605)
Q Consensus 486 ~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~ 565 (605)
+.++.....++|||.+++++++..+.+.+.++ ..+|++.+....+...|..+|..||++||.||.||||++||.++|++
T Consensus 296 r~~l~~~~~~~SLd~~vg~~~d~~l~d~l~~~-~~~pee~~~~~~l~~~L~~~L~~L~~reR~VI~LRygl~d~~~~Tl~ 374 (415)
T PRK07598 296 REVLLRVPRSVSLETKVGKDKDTELGDLLETD-DISPEEMLMRESLQRDLQHLLADLTSRERDVIRMRFGLADGHTYSLA 374 (415)
T ss_pred HHHHHHccCCcccccccCCCccccHHHhccCC-CCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCCCCCCCHH
Confidence 99999889999999999988888888877654 45899999999999999999999999999999999999999999999
Q ss_pred HHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhhHhhhhc
Q 007404 566 EIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAI 603 (605)
Q Consensus 566 EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~yl~ 603 (605)
|||+.||||+++|||++++|++|||+.-....|++|+.
T Consensus 375 EIA~~LGvS~erVRqie~rAl~KLR~~~~~~~l~~y~~ 412 (415)
T PRK07598 375 EIGRALDLSRERVRQIESKALQKLRQPKRRNRIRDYLE 412 (415)
T ss_pred HHHHHHCcCHHHHHHHHHHHHHHHhchhHHHHHHHHHH
Confidence 99999999999999999999999999999999999985
No 2
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=6.1e-62 Score=519.48 Aligned_cols=311 Identities=48% Similarity=0.794 Sum_probs=299.6
Q ss_pred CCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHHHHhccHHHHH
Q 007404 290 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKD 368 (605)
Q Consensus 290 ~~d~l~-yL~~i~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~~l~~g~~A~e 368 (605)
..|++. ||++| +++|+||++||++|+++|++++.+++++.+|++..|+.|+..+||.++|++...|.+++..|..|++
T Consensus 61 ~~d~l~~Yl~~i-~~~~lLt~eEE~~La~~i~~~~~~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~ 139 (373)
T PRK07406 61 TEDSIRVYLQEI-GRIRLLRPDEEIELARKIADLLELEELREQFESELGREPSDKEWAELVDMPLPKFRRRLMLGRRAKE 139 (373)
T ss_pred CCCHHHHHHHHh-cccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccchhhHhhhccccHHHHHHHHhcCHHHHH
Confidence 368899 99999 9999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHH
Q 007404 369 KMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMV 448 (605)
Q Consensus 369 ~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~ 448 (605)
.||..|+++|+++|++|.++|.+++||+|||++|||+++++|||.+|++|+|||+||||++|.++|++++++||+|.|+.
T Consensus 140 ~Li~~~l~lV~~iA~ry~~~~~~~eDLiQEG~igL~~Ai~kFd~~kg~~FsTYA~wWIRqaI~~~I~~~~r~IRlP~~~~ 219 (373)
T PRK07406 140 KMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLY 219 (373)
T ss_pred HHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhcCCceeCCHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHHHHHH
Q 007404 449 EATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIK 528 (605)
Q Consensus 449 ~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~l~~ 528 (605)
..+++++++...|.+++|+.||.+|||+.+|+++++|..++.....++|||.+++++++.++.++++++. .+|++.+..
T Consensus 220 ~~~~~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~~~~~~~~~~~SLd~~i~~~~~~~l~d~l~d~~-~~pee~~~~ 298 (373)
T PRK07406 220 ETISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIEADG-ETPEDDVAK 298 (373)
T ss_pred HHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCcccHHHhcCCCC-CCHHHHHHH
Confidence 9999999999999999999999999999999999999999988889999999998777777888888763 478988999
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhhHhhhh
Q 007404 529 KFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYA 602 (605)
Q Consensus 529 ~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~yl 602 (605)
..+...|..+|..||++||.||.+|||++|++++|++|||+.||||++||||++.+|++|||+......|+.|+
T Consensus 299 ~~~~~~L~~aL~~L~~rEr~IL~lrygl~~~~~~Tl~EIA~~lgiS~eRVRQie~rAL~KLR~~~~~~~l~~~~ 372 (373)
T PRK07406 299 NLLREDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSVLKEYI 372 (373)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHhchhHHHHHHHHh
Confidence 99999999999999999999999999998888899999999999999999999999999999999999999986
No 3
>PRK05949 RNA polymerase sigma factor; Validated
Probab=100.00 E-value=6.8e-61 Score=504.90 Aligned_cols=310 Identities=37% Similarity=0.688 Sum_probs=296.9
Q ss_pred CCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHHHHhccHHHHH
Q 007404 290 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKD 368 (605)
Q Consensus 290 ~~d~l~-yL~~i~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~~l~~g~~A~e 368 (605)
..|++. ||++| +++|+||++||++|+++|+.++.++..+..|....|+.|+..+|+.+++++...|...++.|..|++
T Consensus 16 ~~d~~~~yl~~i-~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~eL~~~~~~g~~A~~ 94 (327)
T PRK05949 16 SADMVRTYLHEI-GRVPLLTHEQEIVYGKQVQQMMSLLEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGKRAKQ 94 (327)
T ss_pred CCCHHHHHHHHc-CCccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCchHHHHHhccCCHHHHHHHHHccHHHHH
Confidence 478999 99999 9999999999999999999999999999999999999999999999999999999999999989999
Q ss_pred HHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHH
Q 007404 369 KMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMV 448 (605)
Q Consensus 369 ~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~ 448 (605)
.||..|+++|+++|++|.+++.+++|||||||+|||+++++|||++|++|+|||+||||++|.+++.+++++||+|.|+.
T Consensus 95 ~Li~~~~~~V~~iA~~y~~~~~~~eDLvQEg~igL~~a~~kfd~~~G~rFsTYa~wwIrq~I~r~i~~~~r~iRlP~~~~ 174 (327)
T PRK05949 95 KMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHIT 174 (327)
T ss_pred HHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHhcCCcCCCChhhhhHHHHHHHHHHHHHHcCCceeCCHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHHHHHH
Q 007404 449 EATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIK 528 (605)
Q Consensus 449 ~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~l~~ 528 (605)
..+++++++.+.+.+++|+.||.+|||+.+|+++++|..++.....++|||.+++++++.++.+.++|+. .+|++.+..
T Consensus 175 ~~~~~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~~~l~d~~-~~pe~~~~~ 253 (327)
T PRK05949 175 EKLNKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMARQPISLDVRVGDNQDTELSELLEDEG-PSPDQYITQ 253 (327)
T ss_pred HHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhccccccCCCcCCCCCccHHhhcCCCC-CCHHHHHHH
Confidence 9999999999999999999999999999999999999999998899999999998777777888888765 589999999
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhhHhhhhc
Q 007404 529 KFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAI 603 (605)
Q Consensus 529 ~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~yl~ 603 (605)
..+...|..+|+.||++||.||.+|||++|++++|++|||+.||||+++|||++.+|++|||+. ...|+.|+.
T Consensus 254 ~~~~~~L~~~L~~L~~rer~Vi~lr~gl~~~e~~Tl~EIa~~lgiS~erVrq~~~rAl~kLr~~--~~~l~~~~~ 326 (327)
T PRK05949 254 ELLRQDLNNLLAELTPQQREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHLRRR--RANVKEYLA 326 (327)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH--HHHHHHHHh
Confidence 9999999999999999999999999999988999999999999999999999999999999994 467888874
No 4
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family. This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).
Probab=100.00 E-value=4e-60 Score=493.10 Aligned_cols=297 Identities=45% Similarity=0.778 Sum_probs=284.2
Q ss_pred CHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHHHHhccHHHHHHH
Q 007404 292 DPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKM 370 (605)
Q Consensus 292 d~l~-yL~~i~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~~l~~g~~A~e~L 370 (605)
|++. ||++| +++|+||++||.+|+++++.++.++.++.+|+++.|++|+..+||+++|++...|...++.|..|++.|
T Consensus 1 ~~~~~yl~~~-~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~L 79 (298)
T TIGR02997 1 DLVRLYLQEI-GRVPLLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQRAKEKM 79 (298)
T ss_pred CcHHHHHHHc-cccCCCCHHHHHHHHHHHHHHhHHHHHHHHHHHhhcCCCcHHHHHHhccCCHHHHHHHHhccHHHHHHH
Confidence 4677 99999 999999999999999999999999999999999999999999999999999999999999899999999
Q ss_pred HHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHHHH
Q 007404 371 ITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEA 450 (605)
Q Consensus 371 I~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~~~ 450 (605)
|.+|+++|++||++|.++|.+++|||||||+|||+|+++|||.+|++|+||++||||++|.+++.+++++||+|.++...
T Consensus 80 v~~~lrlV~~iA~~y~~~~~~~eDLiQEg~igL~~a~~kfd~~~g~rFsTya~~wIr~~I~r~i~~~~r~vr~p~~~~~~ 159 (298)
T TIGR02997 80 IKANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWWIRQGITRAIANQSRTIRLPIHITEK 159 (298)
T ss_pred HHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCccCCCChHHHHHHHHHHHHHHHHHhcCCCeeCcHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHHHHHHHH
Q 007404 451 TYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKF 530 (605)
Q Consensus 451 i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~l~~~e 530 (605)
+++++++.+.+.+.+|+.||.+|||+.+|+++++|..++.....++|||.+++++++.++.+.++++ ..+|++.+...+
T Consensus 160 ~~~~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~~~~~~~~~-~~~pe~~~~~~~ 238 (298)
T TIGR02997 160 LNKIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPVGDEEDTELGDLLEDD-GESPEEQVERES 238 (298)
T ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHcccCcccCCCcCCCCcchHHHhccCC-CCCHHHHHHHHH
Confidence 9999999999999999999999999999999999999999888999999999776666677777764 458999999999
Q ss_pred HHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 007404 531 MKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK 590 (605)
Q Consensus 531 l~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR 590 (605)
+...|..+|+.||++||.||.+|||++|++++|++|||+.||||++||||++++|++|||
T Consensus 239 ~~~~L~~~L~~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVrq~~~rAl~kLr 298 (298)
T TIGR02997 239 LRQDLESLLAELTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRKLR 298 (298)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence 999999999999999999999999998888899999999999999999999999999996
No 5
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=100.00 E-value=7.9e-60 Score=495.12 Aligned_cols=309 Identities=41% Similarity=0.705 Sum_probs=295.4
Q ss_pred CCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHHHHhccHHHHHH
Q 007404 291 SDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDK 369 (605)
Q Consensus 291 ~d~l~-yL~~i~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~~l~~g~~A~e~ 369 (605)
+|++. ||++| +++|+||++||++|+++|++++.+++++..|++++|++|+..+||+++++++..|...+..|..|+++
T Consensus 7 ~~~~~~yl~~i-~~~~lLt~eeE~~La~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~g~~A~~~ 85 (317)
T PRK07405 7 TDLVRTYLREI-GRVPLLTHEEEILYGKQVQRLVALQEIREELAEELGREPTDAEWAKAAKLSEEELRSAIAEGEAAKRK 85 (317)
T ss_pred CcHHHHHHHHc-cccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccchHHHhhhccCCHHHHHHHHhccHHHHHH
Confidence 67899 99999 99999999999999999999999999999999999999999999999999999999999989999999
Q ss_pred HHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHHH
Q 007404 370 MITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVE 449 (605)
Q Consensus 370 LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~~ 449 (605)
||..|+++|+++|++|.+++.+++||+||||+|||+++++|||++|++|+|||+||||++|.++|.+++++||+|.|+..
T Consensus 86 L~~~~~~~V~~~a~~~~~~~~~~eDLvQEg~i~L~~a~~~fd~~~g~rf~tYa~~wIR~~I~~~i~~~~~~ir~p~~~~~ 165 (317)
T PRK07405 86 MVEANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITE 165 (317)
T ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcCCCCChHHHHHHHHHHHHHHHHHhcCCCccCChHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHHHHHHH
Q 007404 450 ATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKK 529 (605)
Q Consensus 450 ~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~l~~~ 529 (605)
.+++++++.+.+.+.+|+.||.+|||+.+|+++++|..++.....++|||.+++++++.++.+.++|+. .+|++.+...
T Consensus 166 ~~~~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~~~~~d~~-~~pe~~~~~~ 244 (317)
T PRK07405 166 KLNKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERARQPLSLDLRVGDNQDTELGELLEDTG-ASPEDFATQS 244 (317)
T ss_pred HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCeeecCCCCCCCCccHHHhhcCCC-CCHHHHHHHH
Confidence 999999999999999999999999999999999999999988888999999998777777788887764 5899999999
Q ss_pred HHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhhHhhhhc
Q 007404 530 FMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAI 603 (605)
Q Consensus 530 el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~yl~ 603 (605)
.+...|..+|+.||++||.||.+|||++|++++|++|||+.||||++||||++.+|++|||+. ...|..|+.
T Consensus 245 ~~~~~l~~al~~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVRqi~~rAl~kLr~~--~~~l~~~~~ 316 (317)
T PRK07405 245 SLQLDLERLMEDLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLRKR--KANIQEYLA 316 (317)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHhhcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH--HHHHHHHHh
Confidence 999999999999999999999999999988999999999999999999999999999999995 467888874
No 6
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=100.00 E-value=3.3e-59 Score=488.37 Aligned_cols=312 Identities=42% Similarity=0.708 Sum_probs=286.6
Q ss_pred CCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHh-hcCCCCchH---------------HHHHhhcCCH
Q 007404 291 SDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSE-RCGGSPTFA---------------QWAAAAGVDQ 353 (605)
Q Consensus 291 ~d~l~-yL~~i~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~L~~-~~G~~pt~~---------------ewA~a~g~d~ 353 (605)
.|.+. |+.++ +..++++.++|..+...++....+..+...|.. ..|..|+.. +|+.....++
T Consensus 8 ~d~~~~~l~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~E 86 (342)
T COG0568 8 ADAVRAYLDEI-GRIPLLVREAEVELAKQLEDEQLLVELGEDLTDLKLGREPSERARRPAGRLSFYIRAIEAAPLLTPEE 86 (342)
T ss_pred hhHHHHHHHHh-cchhhhhHHHHHHHHHHHhHhhhhhHHHHHHHhcccccccchhhhhhhhhHHHHHHHHhhhcccChHH
Confidence 56788 99999 999999999999999999887766666777766 567778876 5555555444
Q ss_pred -HHHHHHHhcc---HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHH
Q 007404 354 -RELRRRLNYG---ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQA 429 (605)
Q Consensus 354 -~~L~~~l~~g---~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqa 429 (605)
..|..++..| ..|+.+||.+|+|||++||++|.|+|+++.||||||+||||+|+++|||++||+|||||+|||||+
T Consensus 87 e~~la~~~~~g~~~~~Ak~klv~snLRlVvsIAk~Y~~rGL~~~DLIQEGniGLmkAVekFdp~rG~kFsTYA~wWIrqa 166 (342)
T COG0568 87 EKALARRLKRGERDLDAKKKLVESNLRLVVSIAKKYTGRGLPFLDLIQEGNIGLMKAVEKFDPEKGFKFSTYATWWIRQA 166 (342)
T ss_pred HHHHHHHHHcCCccHHHHHHHHHHHHHHHHHHHHHhhcCCCcHHHHHhcccHHHHHHHHhcCcccCCcchhHHHHHHHHH
Confidence 5666666655 559999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCC
Q 007404 430 VRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLK 509 (605)
Q Consensus 430 I~r~ir~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~ 509 (605)
|.++|.+++|+||+|+|+.+.++++++..+++.+++|++|+.+|||+.+|+++++|.+++.....++|||.|++++++..
T Consensus 167 I~raI~~q~rtIRipvh~~e~~nkl~r~~r~l~q~~~r~p~~eeia~~l~~~~~~V~~m~~~~~~~~SLd~~ig~ded~~ 246 (342)
T COG0568 167 ITRAIADQARTIRIPVHQVELINKLRRVKRELLQELGREPTPEEIAEELGVSPDKVREMLKRASEPISLDTPIGDDEDSE 246 (342)
T ss_pred HHHHHHHhcchhhHhHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHhCCCHHHHHHHHHhcccCcccCCcCCCCcccH
Confidence 99999999999999999999999999999999999999999999999999999999999999989999999999998889
Q ss_pred CCcccCCCCCCCHHHHHHHHHHHHHHHHHHhc-CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q 007404 510 PSEVIADPEAETAEDLLIKKFMKEDLEKVLDT-LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRK 588 (605)
Q Consensus 510 l~d~l~D~~~~spEe~l~~~el~~~L~~aL~~-L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkK 588 (605)
+.|+++|+...+|++.+....+.+.+...|.. |+++|+.||++|||++|++|.|++|||+.+|||++|||||+.+||+|
T Consensus 247 l~d~leD~~~~~p~~~~~~~~~~~~~~~~L~~~Lt~rE~~Vi~~R~gl~~~~~~TLeevg~~~~isrERvRQIE~kAl~K 326 (342)
T COG0568 247 LGDFLEDDKSVSPEDAVERESLKEDLNEVLAEALTERERRVIRLRFGLDDGEPKTLEELGEEFGISRERVRQIEAKALRK 326 (342)
T ss_pred HHHHhhcCCcCCHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCcchHHHHHHHhCCcHHHHHHHHHHHHHH
Confidence 99999999888999999999999999999999 99999999999999999999999999999999999999999999999
Q ss_pred HH-hHHhhhhHhhhhc
Q 007404 589 LK-NKKRTKHLMQYAI 603 (605)
Q Consensus 589 LR-~~l~~~~L~~yl~ 603 (605)
|| .......+++|++
T Consensus 327 Lr~~~~~~~~~~~~l~ 342 (342)
T COG0568 327 LRRHPERSALLRSYLD 342 (342)
T ss_pred HHHhhhhhhHHHHhhC
Confidence 99 5555666788874
No 7
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=100.00 E-value=1.2e-58 Score=508.81 Aligned_cols=301 Identities=40% Similarity=0.674 Sum_probs=276.0
Q ss_pred CCCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHHHHhccHHHH
Q 007404 289 DYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCK 367 (605)
Q Consensus 289 ~~~d~l~-yL~~i~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~~l~~g~~A~ 367 (605)
...|+++ ||++| +++|+||++||++|+++|+.+..++. .+. ...+|+.. ....|+.+++.|..|+
T Consensus 208 ~~~d~l~~YL~~i-~~~~lLt~eEE~~La~~i~~g~~~~~---~~~-------~~~~~~~~---~~~~l~~~~~~g~~Ar 273 (509)
T PRK05901 208 ATADPVKAYLKQI-GKVKLLNAEEEVELAKRIEAGLYAEE---LLA-------EGEKLDPE---LRRDLQWIGRDGKRAK 273 (509)
T ss_pred ccccHHHHHHHHh-ccCCCCCHHHHHHHHHHHHhCCchhh---hhh-------hcccchhh---hhhhhhhhccchHHHH
Confidence 3578999 99999 99999999999999999987532221 111 11234422 4567888888999999
Q ss_pred HHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccH
Q 007404 368 DKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHM 447 (605)
Q Consensus 368 e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~ 447 (605)
++||.+|+|||++||++|.++|++++||||||+||||+|+++|||++|++|+|||+||||++|.++|++++|+||+|.|+
T Consensus 274 ~~LI~sNLrLVvsIAkrY~~~Gl~~eDLIQEGnIGLikAvekFDp~rG~rFSTYA~wWIRqaI~raI~d~~r~IRvP~~~ 353 (509)
T PRK05901 274 NHLLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHM 353 (509)
T ss_pred HHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCchhhhHHHHHHHHHHHHHHcCCceecCHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHHHHH
Q 007404 448 VEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLI 527 (605)
Q Consensus 448 ~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~l~ 527 (605)
.+.+++++++.+.|.+++||.||.+|||+.+|+++++|..++.....++|||.+++++++..+.+++.|+....|++.+.
T Consensus 354 ~e~i~kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~~p~~~~~ 433 (509)
T PRK05901 354 VETINKLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQKYNREPISLDKTIGKEGDSQFGDFIEDSEAVSPVDAVS 433 (509)
T ss_pred HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccccccccCCcccHHHhccCCCCCCHHHHHH
Confidence 99999999999999999999999999999999999999999998889999999998777778889999887778999999
Q ss_pred HHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhhHhhhhc
Q 007404 528 KKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAI 603 (605)
Q Consensus 528 ~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~yl~ 603 (605)
...++..|..+|..|+++||.||.+|||+++++++|++|||+.||||++|||||+.+||+|||+......|+.|++
T Consensus 434 ~~~l~~~L~~aL~~L~eREr~VI~lRyGL~~~e~~TL~EIa~~lGVSrERVRQIe~kAL~KLR~~~~~~~l~~~l~ 509 (509)
T PRK05901 434 FTLLQDQLQEVLETLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKLRHPSRSQVLRDFLD 509 (509)
T ss_pred HHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 9999999999999999999999999999998899999999999999999999999999999999999999999974
No 8
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=100.00 E-value=7.4e-58 Score=481.11 Aligned_cols=300 Identities=42% Similarity=0.710 Sum_probs=275.1
Q ss_pred CCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHHHHhccHHHHH
Q 007404 290 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKD 368 (605)
Q Consensus 290 ~~d~l~-yL~~i~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~~l~~g~~A~e 368 (605)
.+|++. ||++| +++|+||++||++|+++|+....++.. |+..+|.... ....+...++.|..|++
T Consensus 24 ~~~~~~~Yl~~i-~~~~lLt~eeE~~La~~~~~g~~~~~~-----------~~~~~~~~~~--~~~~l~~~~~~~~~A~~ 89 (324)
T PRK07921 24 AADLVRVYLNGI-GKTALLTAADEVELAKRIEAGLYAEHL-----------LETRKRLSEA--RKRDLAAVVRDGEAARR 89 (324)
T ss_pred CCChHHHHHHHh-cccCCCCHHHHHHHHHHHHhhhhhhhh-----------hccccccchh--HHHHHHHHHhcCHHHHH
Confidence 468899 99999 999999999999999999976544432 2223332111 44578888899999999
Q ss_pred HHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHH
Q 007404 369 KMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMV 448 (605)
Q Consensus 369 ~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~ 448 (605)
+||..|+++|+++|++|.+++.+++||+|||+||||+|+++|||++|++|+|||+||||++|.++|++++++||+|.|+.
T Consensus 90 ~Lv~~~~~lV~~iA~r~~~~~~~~eDLvQEg~igL~~a~~~fdp~~G~rFsTYA~~wIr~aI~~~i~~~~r~vrlP~~~~ 169 (324)
T PRK07921 90 HLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLV 169 (324)
T ss_pred HHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHcCCCccCCHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHHHHHH
Q 007404 449 EATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIK 528 (605)
Q Consensus 449 ~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~l~~ 528 (605)
+.+++++++.+.|.+++|+.||.+|||+.+|+++++|..++.....++|||.+++++++.++.++++|+...+|++.+..
T Consensus 170 ~~~~~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~l~d~~~~~pe~~~~~ 249 (324)
T PRK07921 170 EQVNKLARIKRELHQQLGREATDEELAEESGIPEEKIADLLEHSRDPVSLDMPVGSDEEAPLGDFIEDSEATSAENAVIA 249 (324)
T ss_pred HHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCceecCCCCCCCCchHHHHhcCCCCCCHHHHHHH
Confidence 99999999999999999999999999999999999999999888889999999987777778899988777789999999
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhhHhhhhc
Q 007404 529 KFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAI 603 (605)
Q Consensus 529 ~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~yl~ 603 (605)
.+++..|..+|..|+++|+.||.+|||++|++++|++|||+.||||++|||||+.+||+|||.......|+.|+.
T Consensus 250 ~~~~~~l~~~L~~L~eREr~Vl~~rygl~~~~~~Tl~eIa~~lgvS~eRVrQIe~~Al~KLr~~~~~~~l~~~~~ 324 (324)
T PRK07921 250 GLLHTDIRSVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRNGERADRLRSYAS 324 (324)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHHHHHHHHhhC
Confidence 999999999999999999999999999998899999999999999999999999999999999999999999863
No 9
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=4.1e-54 Score=460.08 Aligned_cols=274 Identities=45% Similarity=0.765 Sum_probs=261.5
Q ss_pred CCCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHHHHhccHHHH
Q 007404 289 DYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCK 367 (605)
Q Consensus 289 ~~~d~l~-yL~~i~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~~l~~g~~A~ 367 (605)
...|+++ ||++| +++|+||++||.+|+++++. |+..|+
T Consensus 93 ~~~d~~~~yl~~i-~~~~~l~~~ee~~L~~~~~~----------------------------------------Gd~~A~ 131 (367)
T PRK09210 93 KINDPVRMYLKEI-GRVPLLTAEEEIELAKRIEE----------------------------------------GDEEAK 131 (367)
T ss_pred ccCcHHHHHHHHh-hccCCCCHHHHHHHHHHHHh----------------------------------------hHHHHH
Confidence 3478999 99999 99999999999999988764 346799
Q ss_pred HHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccH
Q 007404 368 DKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHM 447 (605)
Q Consensus 368 e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~ 447 (605)
+.||..|+++|+++|++|.+++.+++||+||||+|||+|+++|||.+|++|+|||+||||++|.++|++++|++|+|.|+
T Consensus 132 ~~Li~~~~~lV~~iA~~~~~~~~~~eDLiQEg~igL~~a~~~fd~~~g~~FsTyA~~wIr~aI~~~i~~~~r~irip~~~ 211 (367)
T PRK09210 132 QRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHM 211 (367)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHcCCceeccHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHHHHH
Q 007404 448 VEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLI 527 (605)
Q Consensus 448 ~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~l~ 527 (605)
.+.++++.++.+.|.+++||.||.+|||+.+|+++++|..++.....++|||.+++++++..+.++++|+...+|++.+.
T Consensus 212 ~~~~~~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~i~d~~~~~p~~~~~ 291 (367)
T PRK09210 212 VETINKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPADHAA 291 (367)
T ss_pred HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCCcCCCCCCCCcchhhhhccCCCCCCHHHHHH
Confidence 99999999999999999999999999999999999999999998888999999998777778889999887778999999
Q ss_pred HHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhhHhhhhc
Q 007404 528 KKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAI 603 (605)
Q Consensus 528 ~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~yl~ 603 (605)
...++..|..+|..||++||.||.+|||++||+++|++|||+.||||++|||||+.+||+|||+......|+.|++
T Consensus 292 ~~~~~~~l~~~l~~L~~rEr~Vl~lrygl~~~~~~tl~EIa~~lgvs~erVrQi~~~Al~kLr~~~~~~~l~~~~~ 367 (367)
T PRK09210 292 YELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 367 (367)
T ss_pred HHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhChHHHhHHHHhhC
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999974
No 10
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=2.7e-51 Score=464.56 Aligned_cols=270 Identities=40% Similarity=0.667 Sum_probs=252.3
Q ss_pred HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHHHHhccHHHHHHHHHHHH
Q 007404 296 YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNI 375 (605)
Q Consensus 296 yL~~i~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~~l~~g~~A~e~LI~~nl 375 (605)
||+++ ...+.||++|+..++++|+. |.. .+..|+++||.+|+
T Consensus 349 ~L~~i-e~~~~Ls~eElk~l~~~i~~---------------g~~----------------------~~~~a~~~Li~~nl 390 (619)
T PRK05658 349 ELEAI-EEETGLTIEELKEINRQISK---------------GEA----------------------KARRAKKEMVEANL 390 (619)
T ss_pred HHHHH-HHHhCCCHHHHHHHHHHHhc---------------cch----------------------hhhHHHHHHHHHHH
Confidence 67777 77777777777777777664 320 12468999999999
Q ss_pred HHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHHHHHHHHH
Q 007404 376 RLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVK 455 (605)
Q Consensus 376 rLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~~~i~ki~ 455 (605)
|||++||++|.++|++++||||||+||||+|+++|||.+|++|+|||+||||++|.++|++++|+||+|.|+.+.+++++
T Consensus 391 rlV~~iA~ky~~~gl~~~DLiQeG~iGL~~Av~kfd~~~G~~FstYA~~wIr~aI~~~i~~~~r~irip~~~~~~~~k~~ 470 (619)
T PRK05658 391 RLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLN 470 (619)
T ss_pred HHHHHHHHHHhhCCCCHHHHHHHHHHHHHHHHHhcCccCCCchHHHhHHHHHHHHHHHHHHcCCceecCHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHHHHHHHHHHHHH
Q 007404 456 EARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDL 535 (605)
Q Consensus 456 ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~l~~~el~~~L 535 (605)
++.+.+.+++||.||.+|||+.+|+++++|..++.....++|||.|++++++.++.++++|....+|++.+....++..|
T Consensus 471 ~~~~~~~~~~gr~pt~~eiA~~l~~~~~~v~~~~~~~~~~~Sld~~i~~~~~~~l~d~i~d~~~~~p~~~~~~~~~~~~l 550 (619)
T PRK05658 471 RISRQMLQEIGREPTPEELAERLGMPEDKVRKVLKIAKEPISLETPIGDDEDSHLGDFIEDKNAELPIDAAIQESLREAT 550 (619)
T ss_pred HHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCCcCCCCCCCCCCCchhhhcCCCCCCChHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999989999999999888888899999988878899999999999999
Q ss_pred HHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhhHhhhhc
Q 007404 536 EKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAI 603 (605)
Q Consensus 536 ~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~yl~ 603 (605)
..+|..||++|+.||++|||++++.++|++|||+.||||++|||||+.+||+|||+......|+.|++
T Consensus 551 ~~~l~~L~~rE~~Vl~~r~g~~~~~~~tl~ei~~~lgvs~eRVrQie~~al~kLr~~~~~~~l~~~~~ 618 (619)
T PRK05658 551 TDVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSRKLRSFLD 618 (619)
T ss_pred HHHHHcCCHHHHHHHHHhcCCCCCCCccHHHHHHHhCCCHHHHHHHHHHHHHHHhchHHHHHHHHHhc
Confidence 99999999999999999999988899999999999999999999999999999999999999999986
No 11
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain. This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.
Probab=100.00 E-value=3.7e-47 Score=383.33 Aligned_cols=238 Identities=45% Similarity=0.777 Sum_probs=226.6
Q ss_pred HHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccc
Q 007404 366 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPF 445 (605)
Q Consensus 366 A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~ 445 (605)
|+++||..|+++|+++|++|.+++.+++||+|||++||++|+++|||++|++|+|||+||||++|.++++++.+.+|+|.
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 cHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHHH
Q 007404 446 HMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDL 525 (605)
Q Consensus 446 ~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~ 525 (605)
++...++++.++.+.+.+++|+.||.+|||+.+|+++++|..++......+|||.+++++++.++.+.++|+...+|++.
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 99999999999999999999999999999999999999999999887789999999977766677788888877789988
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhhHhhhhc
Q 007404 526 LIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAI 603 (605)
Q Consensus 526 l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~yl~ 603 (605)
+...++...|..+|+.||++||.||.++||+++++++|++|||+.||||+++|+|++.+|++|||+.+....|+.|++
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 888899999999999999999999999999887788999999999999999999999999999999999999999975
No 12
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=100.00 E-value=2.4e-44 Score=373.51 Aligned_cols=262 Identities=26% Similarity=0.418 Sum_probs=225.9
Q ss_pred CHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHHHHhccHHHHHHH
Q 007404 292 DPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKM 370 (605)
Q Consensus 292 d~l~-yL~~i~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~~l~~g~~A~e~L 370 (605)
+..+ ||++| +++|+||+++|.+|+.+++. .||..|+++|
T Consensus 6 ~~~~~y~~~~-~~~~~l~~~~e~~L~~~~~~---------------------------------------~gd~~A~~~L 45 (289)
T PRK07500 6 SADRSMIRSA-MKAPYLEREEEHALAYRWKD---------------------------------------HRDEDALHRI 45 (289)
T ss_pred hHHHHHHHHH-hcCCCCCHHHHHHHHHHHHH---------------------------------------CCCHHHHHHH
Confidence 4556 99999 99999999999999987652 1457899999
Q ss_pred HHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHHH-
Q 007404 371 ITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVE- 449 (605)
Q Consensus 371 I~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~~- 449 (605)
|..|+++|+++|++|.+++.+++||+||||+|||+++++|||.+|.+|+|||+||||++|.++|+++++++|+|.+...
T Consensus 46 v~~~~~lV~~~a~~~~~~~~~~eDLvQeg~i~L~~a~~~fd~~~~~~f~tya~~~Ir~~I~~~lr~~~~~iR~p~~~~~~ 125 (289)
T PRK07500 46 ISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQK 125 (289)
T ss_pred HHHhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHHCCCceecCccHHHH
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999998765
Q ss_pred -HHHHHHHHHHHHHH---HcCCCCCHHHHHHhcCCCHHHHHHHH-hCCCCCCCccccccccCCC--CCCcccCCCCCCCH
Q 007404 450 -ATYRVKEARKQLYS---ENGRHPNNEEVAEATGLSMKRLHAVL-LSPKAPRSLDQKIGINQNL--KPSEVIADPEAETA 522 (605)
Q Consensus 450 -~i~ki~ka~~~L~~---elgr~PT~eEIAe~lgis~e~V~~~l-~~~~~~~SLD~~i~~d~~~--~l~d~l~D~~~~sp 522 (605)
...++++.+..+.+ .+|+.||.+|||+.||+++++|..+. .....++|||.+++++++. ++.+.++|+.. +|
T Consensus 126 ~~~~~~~~~~~~~~~~~~~l~~~pt~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~~~~~~~l~d~i~d~~~-~p 204 (289)
T PRK07500 126 ALFFNLRRLRARLAQADEELTKQEIHREIATALGVSLSDVEMMDARLSGPDASLNAPQSEEDEGRSERMDFLVDDSP-LP 204 (289)
T ss_pred HHHHHHHHHHHHHHhhhcccCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCccccCCCCCCCCCcccHHHhccCCCC-Cc
Confidence 45566666666655 68999999999999999999998875 3455799999998765443 56778877643 56
Q ss_pred HHHHHH----HHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhh
Q 007404 523 EDLLIK----KFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK 596 (605)
Q Consensus 523 Ee~l~~----~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 596 (605)
++.+.. ......|..+|+.||++||.||.+||+.. +++|++|||+.||||++||+|++++|++|||..+...
T Consensus 205 e~~~~~~~~~~~~~~~l~~al~~L~~rer~vl~lr~~~~--~~~t~~EIa~~lgvs~~~V~q~~~~Al~kLr~~l~~~ 280 (289)
T PRK07500 205 DEQVESSIDGERRRRWLTQALQTLNERELRIIRERRLRE--DGATLEALGEELGISKERVRQIEARALEKLRRALLSQ 280 (289)
T ss_pred hHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcCC--CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhc
Confidence 665443 34567799999999999999999999732 2399999999999999999999999999999988753
No 13
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=100.00 E-value=4.1e-44 Score=370.92 Aligned_cols=261 Identities=28% Similarity=0.440 Sum_probs=223.3
Q ss_pred CCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHHHHhccHHHHH
Q 007404 290 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKD 368 (605)
Q Consensus 290 ~~d~l~-yL~~i~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~~l~~g~~A~e 368 (605)
+.+++. |++++ +++|+||.++|.+|+.+++. .|+..|++
T Consensus 12 ~~~~~~~y~~~~-~~~~~l~~~~e~~l~~~~~~---------------------------------------~Gd~~a~~ 51 (284)
T PRK06596 12 PEGNLDAYIQAV-NKIPMLTAEEEYMLAKRLRE---------------------------------------HGDLEAAK 51 (284)
T ss_pred CccHHHHHHHHH-hccCCCCHHHHHHHHHHHHH---------------------------------------cCCHHHHH
Confidence 457888 99999 99999999999999886542 14578999
Q ss_pred HHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHH
Q 007404 369 KMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMV 448 (605)
Q Consensus 369 ~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~ 448 (605)
.||..|+++|+++|++|.+.+.+++||+|||++||++|+++|||++|++|+|||+||||++|.+++++++++||+|.+..
T Consensus 52 ~Lv~~~~~lV~~ia~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~~~FstYA~~~Ir~~i~~~l~~~~~~vr~p~~~~ 131 (284)
T PRK06596 52 QLVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIHEYILRNWRIVKVATTKA 131 (284)
T ss_pred HHHHHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHHcCCeeeccchHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999988999999864
Q ss_pred --HHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHh-CCCCCCCccccccccCC--CCCCcccCCCCCCCHH
Q 007404 449 --EATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLL-SPKAPRSLDQKIGINQN--LKPSEVIADPEAETAE 523 (605)
Q Consensus 449 --~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~-~~~~~~SLD~~i~~d~~--~~l~d~l~D~~~~spE 523 (605)
....++++....+. .+++||.+|||+.||+++++|..++. .....+|||.+++++++ .++.+.++|+. .+|+
T Consensus 132 ~~~~~~~~~~~~~~l~--~~~~~t~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~~~~~~~l~~~l~d~~-~~p~ 208 (284)
T PRK06596 132 QRKLFFNLRKAKKRLG--WLNPEEVEMVAEELGVSEEEVREMESRLSGQDASLDAPIDDDDEESGAPQDYLEDKS-SDPA 208 (284)
T ss_pred HHHHHHHHHHHHHHhc--cCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCcCcCCCCCCCCCCcchHHHHcCCCC-CCch
Confidence 23444555555443 35999999999999999999999875 34578999999865532 34667777763 4677
Q ss_pred HHHHHH----HHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 007404 524 DLLIKK----FMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT 595 (605)
Q Consensus 524 e~l~~~----el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 595 (605)
+.++.. .+...|..+|+.||++||.||.+||+.+ +++|++|||+.||||++||||++.+|++|||..+..
T Consensus 209 ~~~~~~~~~~~~~~~L~~al~~L~~rEr~VL~lry~~~--~~~Tl~EIA~~lgvS~~rVrqi~~~Al~kLR~~l~~ 282 (284)
T PRK06596 209 DVLEEDNWEDQRRALLADALEGLDERSRDIIEARWLDD--DKSTLQELAAEYGVSAERVRQIEKNAMKKLKAAIEA 282 (284)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcCC--CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 766654 3578899999999999999999999753 459999999999999999999999999999998754
No 14
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=100.00 E-value=7.1e-44 Score=375.60 Aligned_cols=269 Identities=36% Similarity=0.568 Sum_probs=250.4
Q ss_pred CCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHHHHhccHHHHHH
Q 007404 291 SDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDK 369 (605)
Q Consensus 291 ~d~l~-yL~~i~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~~l~~g~~A~e~ 369 (605)
.|.++ ||++| +..|+||+++|.+|..+++. |+..|++.
T Consensus 52 ~~~~~~y~~~~-~~~~~l~~~ee~~li~~~~~----------------------------------------Gd~~A~~~ 90 (325)
T PRK05657 52 LDATQLYLNEI-GYSPLLTAEEEVYFARRALR----------------------------------------GDFAARQR 90 (325)
T ss_pred ccHHHHHHHHH-hcCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHH
Confidence 57788 99999 99999999999999887764 45789999
Q ss_pred HHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHHH
Q 007404 370 MITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVE 449 (605)
Q Consensus 370 LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~~ 449 (605)
||..|.++|+++|++|.+++.+++||+||||+|+|+++++||+.+|++|+||++||||.+|.++++++.+.+|+|.++.+
T Consensus 91 Li~~y~~~V~~~a~~~~~~~~~aeDLvQE~fi~l~~ai~~fd~~rg~~Fstyatw~iR~ai~~~i~~~~r~ir~p~~~~~ 170 (325)
T PRK05657 91 MIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPVHVVK 170 (325)
T ss_pred HHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCccCCCHHHHHHHHHHHHHHHHHHHcCCccccCHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHHHHHHH
Q 007404 450 ATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKK 529 (605)
Q Consensus 450 ~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~l~~~ 529 (605)
.++.+.++.+.+.+.+|+.|+.+|||+.+|+++++|..++.......|||.+++.+...++.+.+.++...+|++.+...
T Consensus 171 ~l~~~~R~~~~l~~~l~r~~t~~eiA~~l~~~~~~v~~~l~~~~~~~sld~~~~~~~~~~l~d~l~d~~~~~pe~~~~~~ 250 (325)
T PRK05657 171 ELNVYLRAARELEHKLDHEPSAEEIAELLDKPVDDVSRMLALNERITSLDTPLGGDPEKSLLDILADEQENGPEDTTQDD 250 (325)
T ss_pred HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhccCCcccCCCCCCCCCcchhhhccCCCCCCHHHHHHHH
Confidence 99989999999999999999999999999999999999998888899999998877666777888877667899999888
Q ss_pred HHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhhHhh
Q 007404 530 FMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQ 600 (605)
Q Consensus 530 el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~ 600 (605)
+....|..+|..||+++|.||.+|||+.+.+.+|++|||+.||||++||+++++||+++||+.+...++..
T Consensus 251 e~~~~L~~aL~~L~~~~R~vl~lrygL~~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l~~~~~~~ 321 (325)
T PRK05657 251 DMKQSIVKWLFELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLREILQTQGLSI 321 (325)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhCccch
Confidence 89999999999999999999999998776667999999999999999999999999999999998877653
No 15
>TIGR02392 rpoH_proteo alternative sigma factor RpoH. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.
Probab=100.00 E-value=1.3e-43 Score=364.36 Aligned_cols=257 Identities=29% Similarity=0.489 Sum_probs=216.7
Q ss_pred HHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHHHHhccHHHHHHHH
Q 007404 293 PLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMI 371 (605)
Q Consensus 293 ~l~-yL~~i~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~~l~~g~~A~e~LI 371 (605)
++. ||+++ +++|+|++++|.+|+.++.. .|+..|++.||
T Consensus 2 ~~~~yl~~~-~~~~~l~~~~e~~l~~~~~~---------------------------------------~gd~~a~~~Lv 41 (270)
T TIGR02392 2 SLDAYIRAV-NRIPMLTPEEEYQLAKRLRE---------------------------------------HGDLDAAKKLV 41 (270)
T ss_pred hHHHHHHHH-hcCCCCCHHHHHHHHHHHHH---------------------------------------CCCHHHHHHHH
Confidence 567 99999 99999999999999886432 14578999999
Q ss_pred HHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHH--H
Q 007404 372 TSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMV--E 449 (605)
Q Consensus 372 ~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~--~ 449 (605)
..|+++|+++|++|.+++.+++||+|||++|||+|+++|||++|++|+|||+||||++|.++++++++++|+|.+.. +
T Consensus 42 ~~~~~lV~~~a~~~~~~~~~~eDLvQeg~igl~~a~~~fd~~~~~~FsTYA~~~Ir~~i~~~l~~~~~~ir~p~~~~~~~ 121 (270)
T TIGR02392 42 LSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEYILRNWRLVKVATTKAQRK 121 (270)
T ss_pred HHhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCChHHhhHHHHHHHHHHHHHHcCCceecCchHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999988999998764 3
Q ss_pred HHHHHHHHHHHHHHHcCCCC-CHHHHHHhcCCCHHHHHHHHh-CCCCCCCccccccccCCC--CCCcccCCCCCCCHHHH
Q 007404 450 ATYRVKEARKQLYSENGRHP-NNEEVAEATGLSMKRLHAVLL-SPKAPRSLDQKIGINQNL--KPSEVIADPEAETAEDL 525 (605)
Q Consensus 450 ~i~ki~ka~~~L~~elgr~P-T~eEIAe~lgis~e~V~~~l~-~~~~~~SLD~~i~~d~~~--~l~d~l~D~~~~spEe~ 525 (605)
...++++....+. .++.| +.+|||+.||+++++|..++. .....+|||.+++++++. .+.+.+.|+. .+|++.
T Consensus 122 ~~~~~~~~~~~~~--~~~~~~~~~eiA~~l~~~~~~v~~~~~~~~~~~~Sld~~~~~~~~~~~~~~~~l~d~~-~~pe~~ 198 (270)
T TIGR02392 122 LFFNLRKMKKRLQ--GWLNPEEVEAIAEELGVSEREVREMESRLSGQDMSLNASIDDDEDDGGAPIAYLVDKT-SDPEDT 198 (270)
T ss_pred HHHHHHHHHHHHh--cCCCCCCHHHHHHHhCCCHHHHHHHHHHccCCCccCCCCCCCCCCccccHHHHhcCCC-CChHHH
Confidence 4555555555443 22555 699999999999999999865 334589999998765432 4556677654 367776
Q ss_pred HHHH----HHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404 526 LIKK----FMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR 594 (605)
Q Consensus 526 l~~~----el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 594 (605)
+... .+...|..+|..||++||.||.+||+.+ +++|++|||+.||||+++|+|++.+||+|||+.+.
T Consensus 199 ~~~~~~~~~~~~~L~~al~~L~~rer~vl~l~y~~~--~~~t~~eIA~~lgvS~~~V~q~~~~Al~kLr~~l~ 269 (270)
T TIGR02392 199 LEEEQWEELQRQALANALGSLDARSRRIIEARWLDD--DKLTLQELAAEYGVSAERIRQIEKNAMKKLKAALA 269 (270)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhcCC--CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Confidence 6543 3568899999999999999999999752 34999999999999999999999999999998764
No 16
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=100.00 E-value=6.6e-43 Score=358.40 Aligned_cols=221 Identities=25% Similarity=0.372 Sum_probs=201.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccc
Q 007404 364 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRL 443 (605)
Q Consensus 364 ~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRl 443 (605)
..++++||..|++||++||++|.++|++++||||||+|||++|+++|||++|++|+|||+||||++|.++++++.++||+
T Consensus 39 ~~~r~~Lv~~~l~LV~~iA~~y~~~g~~~~DLiQeG~iGLi~AierFDp~~G~~FsTYA~~~Irg~I~~~lr~~~~~ir~ 118 (264)
T PRK07122 39 QRQRDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGEVRRHFRDNSWSVKV 118 (264)
T ss_pred HHHHHHHHHHhHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHHcCCcccc
Confidence 45899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhC--CCCCCCccccccccCCC--CCCcccCCCCC
Q 007404 444 PFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLS--PKAPRSLDQKIGINQNL--KPSEVIADPEA 519 (605)
Q Consensus 444 P~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~--~~~~~SLD~~i~~d~~~--~l~d~l~D~~~ 519 (605)
|.++.+.+++++++...+.+++|+.||.+|||+.||+++++|.+++.. ...++|||.+++++++. .+.+.++
T Consensus 119 Pr~~~~~~~~i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~~~~~d~~~---- 194 (264)
T PRK07122 119 PRRLKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVVEGLVAGSAYNTLSIDSGGGSGDDDARAIADTLG---- 194 (264)
T ss_pred CHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhhcCCCCcccccccCCCCCcccchhccC----
Confidence 999999999999999999999999999999999999999999998853 45689999998653332 3333333
Q ss_pred CCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 007404 520 ETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 593 (605)
Q Consensus 520 ~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 593 (605)
+++..++..+....|..+|+.||++||.||.++|+.+ +|++|||+.||||.++|++++++|+++||+.+
T Consensus 195 -~~~~~~e~~~~~~~l~~~l~~L~~rer~vl~l~y~~~----~t~~EIA~~lgis~~~V~~~~~ral~kLr~~l 263 (264)
T PRK07122 195 -DVDAGLDQIENREALRPLLAALPERERTVLVLRFFES----MTQTQIAERVGISQMHVSRLLAKTLARLRDQL 263 (264)
T ss_pred -CcHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhcCC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHc
Confidence 3455566677788899999999999999999999876 99999999999999999999999999999875
No 17
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=100.00 E-value=2.5e-41 Score=345.09 Aligned_cols=227 Identities=27% Similarity=0.453 Sum_probs=201.9
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHhhCC-CCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcccc
Q 007404 362 YGILCKDKMITSNIRLVISIAKNYQGA-GMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRT 440 (605)
Q Consensus 362 ~g~~A~e~LI~~nlrLVvsIAkrY~~~-g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~ 440 (605)
++..|+++||..|+++|+++|++|.+. +.+++||+|||+||||+|+++|||++|++|+|||+||||++|.++++++.++
T Consensus 22 gd~~a~~~Lv~~~~~lV~~ia~~~~~~~~~~~eDL~Qeg~igL~~a~~~fd~~~g~~F~tya~~~Ir~~i~~~lr~~~~~ 101 (256)
T PRK07408 22 PSIALRNQLVELNLGLVRKEAHRWSNQCSEPYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLRDKSPT 101 (256)
T ss_pred CCHHHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHHcCCe
Confidence 457899999999999999999999875 6679999999999999999999999999999999999999999999999999
Q ss_pred ccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHh--CCCCCCCccccccccCC--CCCCcccCC
Q 007404 441 IRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLL--SPKAPRSLDQKIGINQN--LKPSEVIAD 516 (605)
Q Consensus 441 IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~--~~~~~~SLD~~i~~d~~--~~l~d~l~D 516 (605)
||+|.++.+.+++++++...|.+++|++||.+|||+.+|+++++|..++. .....+|||.+++++++ ..+.+.+++
T Consensus 102 vr~pr~~~~~~~~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~~~l~d~~~d 181 (256)
T PRK07408 102 VRIPRRWQELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIKLALQNRTPLSLDAPVNQDEDGSTSLGDLLPD 181 (256)
T ss_pred eeeCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHhhccCCccccccCCCCCCCccccccccCC
Confidence 99999999999999999999999999999999999999999999999864 34568899999865433 245666666
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 007404 517 PEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT 595 (605)
Q Consensus 517 ~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 595 (605)
+... +.. ...+....|..+|..||+++|.||.++|+.+ +|++|||+.||+|.++|++++++|++|||+.+..
T Consensus 182 ~~~~-~~~--~~~~~~~~l~~~l~~L~~~~r~vl~l~y~~~----~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~l~~ 253 (256)
T PRK07408 182 PRYR-SFQ--LAQEDRIRLQQALAQLEERTREVLEFVFLHD----LTQKEAAERLGISPVTVSRRVKKGLDQLKKLLQP 253 (256)
T ss_pred cccc-hhh--hhHHHHHHHHHHHHcCCHHHHHHHHHHHHCC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhhc
Confidence 5432 211 2334567799999999999999999999877 9999999999999999999999999999998764
No 18
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).
Probab=100.00 E-value=3.6e-40 Score=341.12 Aligned_cols=271 Identities=37% Similarity=0.561 Sum_probs=246.2
Q ss_pred CCCCCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHHHHhccHH
Q 007404 287 EVDYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGIL 365 (605)
Q Consensus 287 ~~~~~d~l~-yL~~i~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~~l~~g~~ 365 (605)
+...+|.++ ||.+| +.+|.||.++|.+|+.+++. |+..
T Consensus 8 ~~~~~~~~~~~~~~~-~~~~~~~~~~~~~li~~~~~----------------------------------------gd~~ 46 (285)
T TIGR02394 8 ETRVADVTQLYLREI-GFKPLLTAEEEIAYARRALA----------------------------------------GDFE 46 (285)
T ss_pred ccCcchHHHHHHHHH-hccCCCCHHHHHHHHHHHHc----------------------------------------CCHH
Confidence 345688999 99999 99999999999999887664 3478
Q ss_pred HHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccc
Q 007404 366 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPF 445 (605)
Q Consensus 366 A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~ 445 (605)
|++.||..|.++|+++|++|.+++.+++||+||||+|||+++++||+.+|++|+||++|||+.++.+++.++.+.+++|.
T Consensus 47 a~~~L~~~y~~~v~~~a~~~~~~~~~aeDLvQe~~i~l~~a~~~fd~~~g~~f~tya~w~i~~ain~~i~~~~~~~~~p~ 126 (285)
T TIGR02394 47 ARKVMIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVEKFDPERGFRFSTYATWWIRQTIERAIMNQARTIRLPV 126 (285)
T ss_pred HHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCCCCCCcHhhhHHHHHHHHHHHHHHcCCceeCcH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHHH
Q 007404 446 HMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDL 525 (605)
Q Consensus 446 ~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~ 525 (605)
++...++.+.+..+.+.+.+|+.|+.+++|..+|++++++..++......+|+|.++..++...+.+.+.++...+|++.
T Consensus 127 ~~~~~~~~~~r~~~~l~~~~~r~~~~~e~a~~l~~~~~~~~~~~~~~~~~~sld~~~~~~~~~~~~~~~~~~~~~~pe~~ 206 (285)
T TIGR02394 127 HVIKELNVYLRAARQLEKKLGREPSVEEIAELLDKPVEDVSRVLALNERITSLDAPLDDDSSKSLLDTIADEQSIDPESL 206 (285)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhhcCCCcCCCCCCCCCCcchhhhhcCCCCCCHHHH
Confidence 99999999999888888999999999999999999999999999888889999988765555555566666655689999
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhhH
Q 007404 526 LIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHL 598 (605)
Q Consensus 526 l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L 598 (605)
+...+....|..+|..||+++|.||.|+||+.+.+.+|++|||+.||||.++|++++++|+++||+.+...+.
T Consensus 207 ~~~~e~~~~L~~al~~Lp~~~R~Vl~l~ygL~~~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~l~~~~~ 279 (285)
T TIGR02394 207 VQNDDLKQLIEAWLAELNERQREVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQVEALKKLRRILERDGV 279 (285)
T ss_pred HHHHHHHHHHHHHHHcCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 9999999999999999999999999999976544559999999999999999999999999999999876543
No 19
>TIGR02850 spore_sigG RNA polymerase sigma-G factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also desginated stage III sporulation protein G (SpoIIIG). This protein is rather closely related to sigma-F (SpoIIAC), another sporulation sigma factor.
Probab=100.00 E-value=2.9e-40 Score=336.48 Aligned_cols=242 Identities=28% Similarity=0.425 Sum_probs=215.5
Q ss_pred hcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHHHHhccHHHHHHHHHHHHHHHHH
Q 007404 301 TSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVIS 380 (605)
Q Consensus 301 ~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~~l~~g~~A~e~LI~~nlrLVvs 380 (605)
|+++|+||++||.+|+.+++. ++..|++.||..|+++|++
T Consensus 10 ~~~~~~l~~~~~~~li~~~~~----------------------------------------gd~~a~~~L~~~~~~~v~~ 49 (254)
T TIGR02850 10 TSKLPVLKNQEMRELFIRMQS----------------------------------------GDTTAREKLINGNLRLVLS 49 (254)
T ss_pred ccCCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHHHhHHHHHH
Confidence 478999999999999877653 3477999999999999999
Q ss_pred HHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHHHHHHHHHHHHHH
Q 007404 381 IAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQ 460 (605)
Q Consensus 381 IAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~~~i~ki~ka~~~ 460 (605)
+|++|.+++.+++||+||||+|||+++++|||.+|.+|+||++|||++.|.++++++. .+|+|.++.+.++++.++...
T Consensus 50 ~a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~tyl~~~irn~~~~~lr~~~-~ir~p~~~~~~~~~~~~~~~~ 128 (254)
T TIGR02850 50 VIQRFNNRGEYVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVRDK 128 (254)
T ss_pred HHHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHHHHHHhCC-CccCchHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999975 789999999999999999999
Q ss_pred HHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCC--CCCcccCCCCCCCHHHHHHHHHHHHHHHHH
Q 007404 461 LYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNL--KPSEVIADPEAETAEDLLIKKFMKEDLEKV 538 (605)
Q Consensus 461 L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~--~l~d~l~D~~~~spEe~l~~~el~~~L~~a 538 (605)
+.+++|+.||.+|||+.+|+++++|..++.....+.|||.++.++++. ++.+.+.|+.. .++ .......|..+
T Consensus 129 l~~~l~~~pt~~elA~~l~~~~e~v~~~~~~~~~~~Sld~~~~~~~~~~~~~~~~~~d~~~-~~~----~~~~~~~l~~~ 203 (254)
T TIGR02850 129 LISENSKEPTVSEIAKELKVPQEEVVFALDAIQDPVSLFEPIYNDGGDPIYVMDQISDEKN-KDS----QWLEGIALKEA 203 (254)
T ss_pred HHHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCCcccCCCCCCCCCcchhhhhcCCccc-cHH----HHHhHHHHHHH
Confidence 999999999999999999999999999998888889999988544332 35666666432 122 22345578999
Q ss_pred HhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 007404 539 LDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 592 (605)
Q Consensus 539 L~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 592 (605)
|..|++++|.||.++|+.+ +|++|||+.||+|+++|++++.+|++|||+.
T Consensus 204 l~~L~~rer~vi~~~~~~~----~t~~eIA~~lgis~~~V~~~~~ral~kLr~~ 253 (254)
T TIGR02850 204 MKRLNEREKMILNMRFFEG----KTQMEVAEEIGISQAQVSRLEKAALKHMRKY 253 (254)
T ss_pred HHcCCHHHHHHHHHHHcCC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHhh
Confidence 9999999999999999766 9999999999999999999999999999985
No 20
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=100.00 E-value=1.3e-39 Score=332.81 Aligned_cols=227 Identities=30% Similarity=0.422 Sum_probs=205.2
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHhhC---CCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcc
Q 007404 362 YGILCKDKMITSNIRLVISIAKNYQG---AGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQS 438 (605)
Q Consensus 362 ~g~~A~e~LI~~nlrLVvsIAkrY~~---~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~s 438 (605)
++..|+++||..|+++|+++|++|.+ .+.+++||+|||+||||+|+++|||++|++|+||++||||++|.++++++.
T Consensus 20 ~~~~ar~~Li~~~~~lV~~ia~~~~~~~~~~~~~eDL~QeG~igL~~ai~~fd~~~g~~F~tya~~~Ir~~i~~~lr~~~ 99 (257)
T PRK05911 20 QEIEYRDVLIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAIIDDLRKQD 99 (257)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhcC
Confidence 45789999999999999999999862 356899999999999999999999999999999999999999999999987
Q ss_pred ccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCC--CCCCccccccc--cC--CCCCCc
Q 007404 439 RTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPK--APRSLDQKIGI--NQ--NLKPSE 512 (605)
Q Consensus 439 r~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~--~~~SLD~~i~~--d~--~~~l~d 512 (605)
| +|.++.+.++++.++...+.+++|+.|+.+|||+.+|+++++|..++.... .++|||.++.. ++ +.++.+
T Consensus 100 ~---~pr~~~~~~~~l~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~~~Sld~~~~~~~~~~~~~~l~~ 176 (257)
T PRK05911 100 W---VPRSVHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFSSARPALILSLNEEFPCQSDDEAGLALEE 176 (257)
T ss_pred C---CCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHHhhccceeeccccCCCCCCCccccchhh
Confidence 6 899999999999999999999999999999999999999999999986543 46899987643 11 235677
Q ss_pred ccCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 007404 513 VIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 592 (605)
Q Consensus 513 ~l~D~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 592 (605)
.++|+....|++.+...+....|..+|..||++||.||.++|+.+ +|++|||+.||||+++|++++++|+++||+.
T Consensus 177 ~l~d~~~~~~~~~~~~~~~~~~l~~al~~L~~~er~vi~l~y~e~----~t~~EIA~~lgis~~~V~~~~~ral~kLr~~ 252 (257)
T PRK05911 177 RIADERAETGYDVVDKKEFSSILAEAILALEEKERKVMALYYYEE----LVLKEIGKILGVSESRVSQIHSKALLKLRAT 252 (257)
T ss_pred hccCCCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHhcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 888876667888888888999999999999999999999999877 9999999999999999999999999999998
Q ss_pred Hhh
Q 007404 593 KRT 595 (605)
Q Consensus 593 l~~ 595 (605)
+..
T Consensus 253 l~~ 255 (257)
T PRK05911 253 LSA 255 (257)
T ss_pred HHh
Confidence 753
No 21
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=100.00 E-value=1.4e-38 Score=324.51 Aligned_cols=243 Identities=28% Similarity=0.442 Sum_probs=215.0
Q ss_pred hcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHHHHhccHHHHHHHHHHHHHHHHH
Q 007404 301 TSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVIS 380 (605)
Q Consensus 301 ~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~~l~~g~~A~e~LI~~nlrLVvs 380 (605)
+.++|+|+++|+..|+.+++. ++..|++.||..|+++|++
T Consensus 13 ~~~~~~l~~~~~~~l~~~~~~----------------------------------------gd~~a~~~l~~~~~~~v~~ 52 (258)
T PRK08215 13 TSKLPVLKNEEMRELFERMQN----------------------------------------GDKEAREKLINGNLRLVLS 52 (258)
T ss_pred CCCCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHHHHHHHHHH
Confidence 367899999999999877653 3478999999999999999
Q ss_pred HHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHHHHHHHHHHHHHH
Q 007404 381 IAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQ 460 (605)
Q Consensus 381 IAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~~~i~ki~ka~~~ 460 (605)
+|++|.+++.+++||+|||++|||+++++||+.+|.+|+||+++||+++|.++++++. .+|+|.++.....++.++...
T Consensus 53 ~a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~t~l~~~ir~~i~~~lr~~~-~vrip~~~~~~~~~~~~~~~~ 131 (258)
T PRK08215 53 VIQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVREK 131 (258)
T ss_pred HHHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHhCC-ceEecHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999985 789999999999999999999
Q ss_pred HHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCC--CCCcccCCCCCCCHHHHHHHHHHHHHHHHH
Q 007404 461 LYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNL--KPSEVIADPEAETAEDLLIKKFMKEDLEKV 538 (605)
Q Consensus 461 L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~--~l~d~l~D~~~~spEe~l~~~el~~~L~~a 538 (605)
+.+++|+.|+.+|||+.+|+++++|..++.....+.|||.++.++++. ++.+.++++.. .++. ......|..+
T Consensus 132 l~~~~~r~p~~~eia~~l~v~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~~~~~~-~~~~----~~~~~~l~~~ 206 (258)
T PRK08215 132 LINENSKEPTVEEIAKELEVPREEVVFALDAIQDPVSLFEPIYHDGGDPIYVMDQISDEKN-KDEN----WLEEIALKEA 206 (258)
T ss_pred HHHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCccccCCCCCCCCcchhhhhhccCccc-cHHH----HHhHHHHHHH
Confidence 999999999999999999999999999988777888999988654432 34555655432 2222 2334578899
Q ss_pred HhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 007404 539 LDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 593 (605)
Q Consensus 539 L~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 593 (605)
|+.||++|+.||.++|+.+ +|++|||+.||||.++|++++++|++|||+.+
T Consensus 207 l~~L~~~er~vi~~~~~~~----~t~~eIA~~lgis~~~V~~~~~~al~kLr~~l 257 (258)
T PRK08215 207 MKKLNDREKLILNLRFFQG----KTQMEVAEEIGISQAQVSRLEKAALKHMRKYI 257 (258)
T ss_pred HHcCCHHHHHHHHHHHhcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 9999999999999999766 99999999999999999999999999999875
No 22
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=100.00 E-value=2.1e-37 Score=317.72 Aligned_cols=249 Identities=24% Similarity=0.353 Sum_probs=222.0
Q ss_pred hcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHHHHhccHHHHHHHHHHHHHHHHH
Q 007404 301 TSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVIS 380 (605)
Q Consensus 301 ~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~~l~~g~~A~e~LI~~nlrLVvs 380 (605)
+|++|+||.++|.+|+.+++. + ++..+++.|+..|.++|+.
T Consensus 6 ~~~~~~~~~~~e~~l~~~~~~---------------~------------------------~d~~a~~~l~~~y~~lv~~ 46 (268)
T PRK06288 6 SGKIPKYAQQDETELWREYKK---------------T------------------------GDPKIREYLILKYSPLVKY 46 (268)
T ss_pred cCCCccccchHHHHHHHHHHH---------------c------------------------CCHHHHHHHHHHHHHHHHH
Confidence 588999999999999987663 1 3478999999999999999
Q ss_pred HHHHhh-C--CCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHHHHHHHHHHH
Q 007404 381 IAKNYQ-G--AGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEA 457 (605)
Q Consensus 381 IAkrY~-~--~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~~~i~ki~ka 457 (605)
+|++|. + .+.+++||+||||+|||+++++||+.+|++|+||++||||+.|.+++++.. ++|.++....++++++
T Consensus 47 ~a~~~~~~~~~~~~~eDl~Qeg~l~L~~a~~~fd~~~~~~f~ty~~~~ir~~i~d~~R~~~---~~p~~~~~~~~~i~~~ 123 (268)
T PRK06288 47 VAGRIAVGMPQNVEFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAIFDELRSID---WIPRSVRQKARQIERA 123 (268)
T ss_pred HHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhcC---ccCHHHHHHHHHHHHH
Confidence 999986 2 567899999999999999999999999999999999999999999999754 5899999999999999
Q ss_pred HHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCC--CCCCCccccccccC---CCCCCcccCCCCCCCHHHHHHHHHHH
Q 007404 458 RKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSP--KAPRSLDQKIGINQ---NLKPSEVIADPEAETAEDLLIKKFMK 532 (605)
Q Consensus 458 ~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~--~~~~SLD~~i~~d~---~~~l~d~l~D~~~~spEe~l~~~el~ 532 (605)
...|.+++|+.||.+|||+.+|++.+++..++... ...+|||.++..++ ...+.+.++++..++|++.+...+..
T Consensus 124 ~~~l~~~~~~~pt~~eia~~lg~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~l~~~~~~~~~~~pe~~~~~~e~~ 203 (268)
T PRK06288 124 IAMLEARLGRTPSDEEIADELGISLEEYNSLLSKLSGTSVVSLNDLWFGGDEGDEVSLMDTLESPAALNPDEIAEREEIK 203 (268)
T ss_pred HHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhcccccchhhhhccCCCcccchhhhhccCCCCCCHHHHHHHHHHH
Confidence 99999999999999999999999999999987533 45789998764222 23456777777777899988888999
Q ss_pred HHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 007404 533 EDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT 595 (605)
Q Consensus 533 ~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 595 (605)
..|..+|+.||+++|.||.++|+.+ +|++|||+.||+|.++|+++++||+++||+.+..
T Consensus 204 ~~l~~~l~~L~~~~r~vl~l~~~~~----~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l~~ 262 (268)
T PRK06288 204 RVIVEAIKTLPEREKKVLILYYYED----LTLKEIGKVLGVTESRISQLHTKAVLQLRAKLAE 262 (268)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999887 9999999999999999999999999999998864
No 23
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=100.00 E-value=1.9e-37 Score=313.75 Aligned_cols=222 Identities=31% Similarity=0.477 Sum_probs=202.1
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHhhCCCC-CHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcccc
Q 007404 362 YGILCKDKMITSNIRLVISIAKNYQGAGM-NLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRT 440 (605)
Q Consensus 362 ~g~~A~e~LI~~nlrLVvsIAkrY~~~g~-d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~ 440 (605)
++..++ .||+.|+|||.++|++|.+++. +.+||+|-|+|||++|+++|||++|.+|+|||...|+++|.+++|++. .
T Consensus 21 g~~~~~-~Li~~ylpLV~~ia~k~~~r~~~~~dDLiqiG~iGLi~Aieryd~~kg~kF~tyA~~~I~Gei~d~LR~~~-~ 98 (247)
T COG1191 21 GDEEAR-RLIERYLPLVKSIARKFENRGPSEYDDLIQIGMIGLIKAIERYDPSKGTKFSTYAVRRIRGEILDYLRKND-S 98 (247)
T ss_pred cCHHHH-HHHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHHHHcCcccCcchHHHHHHHHHHHHHHHHHhCC-C
Confidence 457788 9999999999999999998887 999999999999999999999999999999999999999999999999 8
Q ss_pred ccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCC--CCCCCccccccccCCCCCCcccCCCC
Q 007404 441 IRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSP--KAPRSLDQKIGINQNLKPSEVIADPE 518 (605)
Q Consensus 441 IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~--~~~~SLD~~i~~d~~~~l~d~l~D~~ 518 (605)
+++|..+.+..+++..+...+.+++||+||.+|||+.+|++.++|..++... ...+|+|..+..+++.. .++.
T Consensus 99 v~vpR~~~~~~~~i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~~~~~~~~sld~~~~~~~d~~-----~~~~ 173 (247)
T COG1191 99 VKVPRSLRELGRRIEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAINGSQLLSLDEDVLKDDDDD-----VDDQ 173 (247)
T ss_pred ccCcHHHHHHHHHHHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHHhccccccchhhhhccccccc-----hhhc
Confidence 9999999999999999999999999999999999999999999999998755 36788887765443333 2223
Q ss_pred CCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404 519 AETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR 594 (605)
Q Consensus 519 ~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 594 (605)
..+|.+.+...+....|.+++..|++|||.||.+||+.+ +|++|||+.||||..+|+|++.+|++|||+.+.
T Consensus 174 ~~~~~~~~~~~~~~~~l~~ai~~L~EREk~Vl~l~y~ee----lt~kEI~~~LgISes~VSql~kkai~kLr~~l~ 245 (247)
T COG1191 174 IENPDDGVEKEELLEILKEAIEPLPEREKLVLVLRYKEE----LTQKEIAEVLGISESRVSRLHKKAIKKLRKELN 245 (247)
T ss_pred cccchhHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHhc----cCHHHHHHHhCccHHHHHHHHHHHHHHHHHHhc
Confidence 346777888888888999999999999999999999988 999999999999999999999999999999775
No 24
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=100.00 E-value=1.1e-36 Score=309.70 Aligned_cols=245 Identities=26% Similarity=0.342 Sum_probs=216.4
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHHHHhccHHHHHHHHHHHHHHHHHHHH
Q 007404 304 SRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAK 383 (605)
Q Consensus 304 ~~lLT~eEE~eL~~~iq~~~~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~~l~~g~~A~e~LI~~nlrLVvsIAk 383 (605)
.|.||+++|.+|..+++. | ++..|+++||..|.++|+.+|+
T Consensus 7 ~~~l~~~~~~~li~~~~~---------------~------------------------gd~~a~~~l~~~y~~~v~~~a~ 47 (255)
T TIGR02941 7 PTNLTKEDVIQWIAEFQQ---------------N------------------------QNGEAQEKLVDHYQNLVYSIAY 47 (255)
T ss_pred CCCCCHHHHHHHHHHHHH---------------C------------------------CCHHHHHHHHHHhHHHHHHHHH
Confidence 367899999988877663 1 3478999999999999999999
Q ss_pred HhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHHHHHHHHHHHHHHHHH
Q 007404 384 NYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYS 463 (605)
Q Consensus 384 rY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~~~i~ki~ka~~~L~~ 463 (605)
+|.+++.+++||+||||+|||+++++||++.|.+|.||+++||++.|.++++++.+.+++|.++....++++++...+.+
T Consensus 48 ~~~~~~~~aeDlvQe~~i~l~~a~~~~~~~~~~~f~tyl~~~i~n~~~~~lr~~~~~iri~~~~~~~~~~~~~~~~~l~~ 127 (255)
T TIGR02941 48 KYSKGGPMHEDLVQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIIGEIKRYLRDKTWSVHVPRRIKELGPKIKKAIDELTD 127 (255)
T ss_pred HHhcCCCCHHHHHHHHHHHHHHHHHHcCCcCCCCcHhHHHHHHHHHHHHHHHHcCCCcCCCHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HcCCCCCHHHHHHhcCCCHHHHHHHHhC--CCCCCCccccccccCCCCCCcccCCCCCCCHHHHHHHHHHHHHHHHHHhc
Q 007404 464 ENGRHPNNEEVAEATGLSMKRLHAVLLS--PKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDT 541 (605)
Q Consensus 464 elgr~PT~eEIAe~lgis~e~V~~~l~~--~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~l~~~el~~~L~~aL~~ 541 (605)
.+|+.|+.+|||+.+|++.+++..++.. .....|||.+++.+++......+ +. ..+|++.+...+....|..+|+.
T Consensus 128 ~~~r~p~~~eia~~l~i~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~-~~-~~~~~~~~~~~e~~~~l~~~l~~ 205 (255)
T TIGR02941 128 HLQRSPKIIEIADHLGLSEEEVLEIMEMGQSYRALSVDDVIEADSDGSTVARL-DS-VGEVEDGYDQTERRMVLEKILPI 205 (255)
T ss_pred HhCCCCCHHHHHHHhCCCHHHHHHHHHHHhccCCccccccccCCCCCcccccc-cc-cCCcchHHHHHHHHHHHHHHHHc
Confidence 9999999999999999999999888754 34678999988765443322222 11 12466667777778889999999
Q ss_pred CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 007404 542 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 593 (605)
Q Consensus 542 L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 593 (605)
||+++|.||.++|+.+ +|++|||+.||+|.++|++++++|+++||+.+
T Consensus 206 L~~~~r~ii~l~~~~g----~s~~eIA~~lgis~~~V~~~~~ra~~~Lr~~~ 253 (255)
T TIGR02941 206 LSEREKSIIHCTFEEN----LSQKETGERLGISQMHVSRLQRQAISKLKEAA 253 (255)
T ss_pred CCHHHHHHHHHHHcCC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 9999999999999877 99999999999999999999999999999865
No 25
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=100.00 E-value=1.4e-36 Score=304.32 Aligned_cols=223 Identities=32% Similarity=0.483 Sum_probs=199.3
Q ss_pred hccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcccc
Q 007404 361 NYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRT 440 (605)
Q Consensus 361 ~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~ 440 (605)
.++..|++.||..|.++|+++|++|.+++.+++||+|||++|||+++++|||.+|.+|+||++|||++.|.++++++. .
T Consensus 7 ~gd~~a~~~l~~~y~~~v~~~a~~~~~~~~~aeDl~Qe~~i~l~~a~~~f~~~~~~~f~tyl~~~i~~~i~~~lr~~~-~ 85 (231)
T TIGR02885 7 NGDKEARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEIKRFLRDDG-I 85 (231)
T ss_pred cCCHHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHhCC-C
Confidence 466889999999999999999999999999999999999999999999999999999999999999999999999986 7
Q ss_pred ccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCC--CCCcccCCCC
Q 007404 441 IRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNL--KPSEVIADPE 518 (605)
Q Consensus 441 IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~--~l~d~l~D~~ 518 (605)
+++|.++...+++++++...+..++|+.||.+|||+.+|+++++|..++.....+.|||.++.++++. ++.+.+.++.
T Consensus 86 i~~p~~~~~~~~~~~~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~d~~~~~~ 165 (231)
T TIGR02885 86 IKVSRSLKELARKIRYMKEELSKELGREPTINELAEALGVSPEEIVMALESARSPQSLYDTVHQDDGDPIYLLDQIADKG 165 (231)
T ss_pred eECCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHHHccCCcCcccCCCCCCCCcchhhhhcCCCC
Confidence 99999999999999999999999999999999999999999999999988777889999988655432 3456665543
Q ss_pred CCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 007404 519 AETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 593 (605)
Q Consensus 519 ~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 593 (605)
. +++. ......|..+++.||++|++||.++|+.+ +|++|||+.||||+++|++++++|++|||..+
T Consensus 166 ~--~~~~---~~~~~~l~~~l~~L~~~e~~i~~~~~~~~----~t~~eIA~~lgis~~~V~~~~~~al~~Lr~~l 231 (231)
T TIGR02885 166 S--EDSD---WLEKIALKEAISKLDERERQIIMLRYFKD----KTQTEVANMLGISQVQVSRLEKKVLKKMKEKL 231 (231)
T ss_pred c--cHHh---HHHHHHHHHHHHcCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHhC
Confidence 2 2222 22356788999999999999999999876 99999999999999999999999999999753
No 26
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily. This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.
Probab=100.00 E-value=5.8e-36 Score=298.87 Aligned_cols=221 Identities=29% Similarity=0.445 Sum_probs=198.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccc
Q 007404 364 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRL 443 (605)
Q Consensus 364 ~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRl 443 (605)
..|++.||..|.++|+++|++|.+++.+.+||+|||++|||+++++||+.+|.+|+||++|||++.|.++++++.+.+++
T Consensus 2 ~~a~~~lv~~y~~~v~~~a~~~~~~~~~~eDl~Qe~~i~l~~a~~~f~~~~~~~F~ty~~~~i~~~~~~~~r~~~~~~ri 81 (227)
T TIGR02980 2 KEAREKLVELNLPLVRSIARRFRNRGEPHEDLVQVGTIGLVKAIDRFDPSYGVKFSTFAVPTIMGEIKRFFRDDTWAVRV 81 (227)
T ss_pred HHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCCcHHHHHHHHHHHHHHHHHHcCCceec
Confidence 56899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCC--CCCccccccccCC--CCCCcccCCCCC
Q 007404 444 PFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKA--PRSLDQKIGINQN--LKPSEVIADPEA 519 (605)
Q Consensus 444 P~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~--~~SLD~~i~~d~~--~~l~d~l~D~~~ 519 (605)
|.++...+++++++...+.+++|+.|+.+|+|+.+|++.+++..++..... ..|||.++.++++ .++.+.+.
T Consensus 82 ~~~~~~~~~~~~~~~~~l~~~~~~~p~~~ela~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~~d~~~---- 157 (227)
T TIGR02980 82 PRRLKELGLKINKATEELTQRLGRSPTIAEIAEELGVSEEEVVEALEAGNSYSALSLDAPIEDDDGDPIALLDTLG---- 157 (227)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCCeeccccCCCCCCCCcccccccC----
Confidence 999999999999999999999999999999999999999999998875544 8999998863222 12333333
Q ss_pred CCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 007404 520 ETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 593 (605)
Q Consensus 520 ~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 593 (605)
++++.+...+....|..+|..||++|++||.++|+.+ +|++|||+.||+|+++|++++++|+++||+.+
T Consensus 158 -~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~y~~~----~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~~l 226 (227)
T TIGR02980 158 -DEDDALETVEDRLALKPLLAALPERERRILLLRFFED----KTQSEIAERLGISQMHVSRLLRRALKKLREQL 226 (227)
T ss_pred -CcchHHHhHHHHHHHHHHHHcCCHHHHHHHHHHHhcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 3344455566778899999999999999999999877 99999999999999999999999999999864
No 27
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=100.00 E-value=1.6e-35 Score=300.97 Aligned_cols=226 Identities=30% Similarity=0.358 Sum_probs=203.1
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHhhC---CCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcc
Q 007404 362 YGILCKDKMITSNIRLVISIAKNYQG---AGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQS 438 (605)
Q Consensus 362 ~g~~A~e~LI~~nlrLVvsIAkrY~~---~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~s 438 (605)
++..|++.||..|.++|+++|++|.+ ++.+.+||+||||+|||+++++||+.+|.+|+||+++||+|.|.++++++.
T Consensus 19 ~d~~a~~~L~~~y~~~v~~~~~~~~~~~~~~~~~eDl~Qe~~i~l~~~~~~f~~~~~~~f~tyl~~~irn~~~d~lR~~~ 98 (251)
T PRK07670 19 RDPDAADELIRRYMPLVHYHVQRISVGLPKSVSKDDLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIRGAIIDGLRKED 98 (251)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhcC
Confidence 35889999999999999999999975 678999999999999999999999999999999999999999999999876
Q ss_pred ccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHh--CCCCCCCccccccccCCC-CCCcccC
Q 007404 439 RTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLL--SPKAPRSLDQKIGINQNL-KPSEVIA 515 (605)
Q Consensus 439 r~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~--~~~~~~SLD~~i~~d~~~-~l~d~l~ 515 (605)
++|.++.+.+++++++.+.+.+.+|+.|+.+|||+.+|+++++|..++. ......|||.++.++++. .+.+.+.
T Consensus 99 ---~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~~~~~ 175 (251)
T PRK07670 99 ---WLPRSMREKTKKVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATMNEGFFANLLSIDEKTHDQDDGENVSVTIR 175 (251)
T ss_pred ---CCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHHHHHHhccCccccCccccCCCCcchhhhhhc
Confidence 5899999999999999999999999999999999999999999999975 456789999988654432 2334445
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404 516 DPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR 594 (605)
Q Consensus 516 D~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 594 (605)
++...++++.+...+....|..+|..||+++|.||.++|+.+ +|++|||+.||+|.++|+++++||+++||..+.
T Consensus 176 ~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~----~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l~ 250 (251)
T PRK07670 176 DDKTPTPEEKLLKEELIEELAEKIKQLSEKEQLVISLFYKEE----LTLTEIGQVLNLSTSRISQIHSKALFKLKKLLE 250 (251)
T ss_pred CcCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence 555567888888888889999999999999999999999877 999999999999999999999999999998764
No 28
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=100.00 E-value=8.9e-35 Score=296.13 Aligned_cols=248 Identities=25% Similarity=0.329 Sum_probs=215.3
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHHHHhccHHHHHHHHHHHHHHHHHHH
Q 007404 303 SSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIA 382 (605)
Q Consensus 303 ~~~lLT~eEE~eL~~~iq~~~~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~~l~~g~~A~e~LI~~nlrLVvsIA 382 (605)
..|+|+++||.+|..+++. .++..|++.||..|.++|+++|
T Consensus 6 ~~~~l~~~e~~~li~~~~~---------------------------------------~gd~~a~~~l~~~~~~~v~~~a 46 (257)
T PRK08583 6 QPTKLTKEEVNKWIAEYQE---------------------------------------NQDEEAQEKLVKHYKNLVESLA 46 (257)
T ss_pred cCCcCChHHHHHHHHHHHH---------------------------------------cCCHHHHHHHHHHHHHHHHHHH
Confidence 3478999999888776653 1347899999999999999999
Q ss_pred HHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHHHHHHHHHHHHHHHH
Q 007404 383 KNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLY 462 (605)
Q Consensus 383 krY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~~~i~ki~ka~~~L~ 462 (605)
++|.+++.+++||+||||++||+++++||+.+|.+|+||+++||+|.|.++++++.+.+++|.+.....++++++...+.
T Consensus 47 ~~~~~~~~~aeDlvQe~~l~l~~~~~~f~~~~~~~f~tyl~~~i~n~~~~~lr~~~~~~~i~r~~~~~~~~~~~~~~~~~ 126 (257)
T PRK08583 47 YKYSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPTIIGEIKRYLRDKTWSVHVPRRIKELGPKIKKAVDELT 126 (257)
T ss_pred HHHhcCCCCHHHHHHHHHHHHHHHHHHcCccCCCChHHHHHHHHHHHHHHHHHhcCCCcCCCHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999989999999999999999999999999999999999999999999999
Q ss_pred HHcCCCCCHHHHHHhcCCCHHHHHHHHhCC--CCCCCccccccccCCCCCCcccCCCCCCCHHHHHHHHHHHHHHHHHHh
Q 007404 463 SENGRHPNNEEVAEATGLSMKRLHAVLLSP--KAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLD 540 (605)
Q Consensus 463 ~elgr~PT~eEIAe~lgis~e~V~~~l~~~--~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~l~~~el~~~L~~aL~ 540 (605)
..+++.|+.+|+++.+|++.+++..+.... ....|+|.+++.+++....... + ...+|++.+...+....|..+|.
T Consensus 127 ~~~~r~~~~~e~a~~~~~~~~~~~~~~~~~~~~~~~sld~~~~~~~~~~~~~~~-~-~~~~~e~~~~~~~~~~~l~~~l~ 204 (257)
T PRK08583 127 TELQRSPKISEIADRLGVSEEEVLEAMEMGKSYQALSVDHSIEADSDGSTVTLL-D-IVGQQEDGYELTEQRMILEKILP 204 (257)
T ss_pred HHhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceecCccccCCCCCccchHh-h-hcCCcchhHHHHHHHHHHHHHHH
Confidence 999999999999999999999998876543 4678999887654332111111 1 11245566666777788999999
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 007404 541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT 595 (605)
Q Consensus 541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 595 (605)
.||+++|+||.++|+.+ +|++|||+.||||.++|++++++|+++||+.+..
T Consensus 205 ~L~~~~r~vl~l~~~~g----~s~~eIA~~l~is~~tV~~~~~ra~~kLr~~l~~ 255 (257)
T PRK08583 205 VLSDREKSIIQCTFIEN----LSQKETGERLGISQMHVSRLQRQAIKKLREAAFL 255 (257)
T ss_pred hCCHHHHHHHHHHHhCC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhcc
Confidence 99999999999999887 9999999999999999999999999999998754
No 29
>PRK05572 sporulation sigma factor SigF; Validated
Probab=100.00 E-value=2e-34 Score=293.19 Aligned_cols=241 Identities=29% Similarity=0.452 Sum_probs=211.2
Q ss_pred cCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHHHHhccHHHHHHHHHHHHHHHHHH
Q 007404 302 SSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISI 381 (605)
Q Consensus 302 ~~~~lLT~eEE~eL~~~iq~~~~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~~l~~g~~A~e~LI~~nlrLVvsI 381 (605)
...|.||.+++.+|..+++. ++..|++.||..|.++|+++
T Consensus 9 ~~~~~l~~~~~~~li~~~~~----------------------------------------gd~~a~~~L~~~y~~~v~~~ 48 (252)
T PRK05572 9 KKKPQLKDEENKELIKKSQD----------------------------------------GDQEARDTLVEKNLRLVWSV 48 (252)
T ss_pred cCCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHHHhHHHHHHH
Confidence 56899999999888765542 34779999999999999999
Q ss_pred HHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHHHHHHHHHHHHHHH
Q 007404 382 AKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQL 461 (605)
Q Consensus 382 AkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~~~i~ki~ka~~~L 461 (605)
|++|.+++.+++||+||||+++|+++++|++.+|.+|.||+++||++.|.+++++.. .+|+|.++....++++++...+
T Consensus 49 a~~~~~~~~~aeDl~Qe~~l~l~~~~~~f~~~~~~~f~twl~~~i~~~i~~~lr~~~-~~r~~~~~~~~~~~~~~~~~~l 127 (252)
T PRK05572 49 VQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSLKETANKIRKDKDEL 127 (252)
T ss_pred HHHHccCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHhCC-CCCCCHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999998889999999999999999999885 7899999999999999999999
Q ss_pred HHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCC--CCCcccCCCCCCCHHHHHHHHHHHHHHHHHH
Q 007404 462 YSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNL--KPSEVIADPEAETAEDLLIKKFMKEDLEKVL 539 (605)
Q Consensus 462 ~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~--~l~d~l~D~~~~spEe~l~~~el~~~L~~aL 539 (605)
..++|+.|+.+|+|+.+|++++++..++.....+.||+.++.+++.. ++.+.+.++.. +. ......|..+|
T Consensus 128 ~~~~~r~p~~~eia~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~d~~~~~~~---~~----~~~~~~l~~~l 200 (252)
T PRK05572 128 SKELGREPTIEELAEYLGVTPEEVVLAQEASRSPQSIHETVHENDGDPITLLDQIADQSE---ED----WFDKIALKEAI 200 (252)
T ss_pred HHHHCcCCCHHHHHHHhCcCHHHHHHHHHhcCCCcCcccCcccCCCCcchhhhhcCCCch---hh----HHHHHHHHHHH
Confidence 99999999999999999999999999888777889999887654332 23344443321 11 23456789999
Q ss_pred hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404 540 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR 594 (605)
Q Consensus 540 ~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 594 (605)
..||+++++||.++|+.+ +|++|||+.+|+|.++|++++++|+++||+.+.
T Consensus 201 ~~L~~~~~~v~~l~~~~~----~s~~eIA~~lgis~~~V~~~~~ral~kLr~~l~ 251 (252)
T PRK05572 201 RELDERERLIVYLRYFKD----KTQSEVAKRLGISQVQVSRLEKKILKQMKEKLD 251 (252)
T ss_pred HcCCHHHHHHHHHHHhCC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhc
Confidence 999999999999999876 999999999999999999999999999998764
No 30
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.
Probab=100.00 E-value=8.3e-35 Score=290.48 Aligned_cols=217 Identities=30% Similarity=0.467 Sum_probs=196.1
Q ss_pred HHHHHHHHHHHHHHHhhC---CCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcccccccccc
Q 007404 370 MITSNIRLVISIAKNYQG---AGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFH 446 (605)
Q Consensus 370 LI~~nlrLVvsIAkrY~~---~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~ 446 (605)
|+..|.++|+++|++|.+ ++.+++||+|||++|||+++++|||++|++|+||+++||++.+.+++++.. ++|.+
T Consensus 1 L~~~~~~lv~~~a~~~~~~~~~~~~~eDl~Qe~~~~l~~a~~~fd~~~~~~f~t~~~~~i~~~~~~~lr~~~---~~p~~ 77 (224)
T TIGR02479 1 LIRRYLPLVKRIAGRLSVGLPSSVELDDLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAMLDELRRLD---WVPRS 77 (224)
T ss_pred CHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHHcC---ccCHH
Confidence 688999999999999986 789999999999999999999999999999999999999999999999875 48999
Q ss_pred HHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHh--CCCCCCCcccccccc-CCCCCCcccCCCCCCCHH
Q 007404 447 MVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLL--SPKAPRSLDQKIGIN-QNLKPSEVIADPEAETAE 523 (605)
Q Consensus 447 ~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~--~~~~~~SLD~~i~~d-~~~~l~d~l~D~~~~spE 523 (605)
+...++++.++..++.+.+|+.|+.+|||+.+|+++++|..++. ......|+|.++.++ +...+.+.++++...+|+
T Consensus 78 ~~~~~~~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~~~~~~~~~ 157 (224)
T TIGR02479 78 LRQKARKLERAIRELEARLGREPTEEEIAEELGMDLKEYRQALNEINALSLVSLDELLESGDDGGSLIDRIEDDKSEDPE 157 (224)
T ss_pred HHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHHHHHHHhcCCccccCCcccCCCccchhhhhccccccCCHH
Confidence 99999999999999999999999999999999999999999985 344567888876543 234555666655666888
Q ss_pred HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 007404 524 DLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 593 (605)
Q Consensus 524 e~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 593 (605)
+.+...+....|..+|+.||+++|+||.++|+.+ +|++|||+.||+|.++|++++++|+++||+.+
T Consensus 158 ~~~~~~~~~~~l~~~l~~L~~~~r~il~l~y~~~----~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l 223 (224)
T TIGR02479 158 EELEREELREALAEAIESLSEREQLVLSLYYYEE----LNLKEIGEVLGLTESRVSQIHSQALKKLRAKL 223 (224)
T ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhCC----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHc
Confidence 8888888899999999999999999999999887 99999999999999999999999999999865
No 31
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=100.00 E-value=7.2e-34 Score=286.30 Aligned_cols=210 Identities=20% Similarity=0.360 Sum_probs=181.5
Q ss_pred HHHHHHHHHHHHHHHHHHHhhC---CCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcccccc
Q 007404 366 CKDKMITSNIRLVISIAKNYQG---AGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIR 442 (605)
Q Consensus 366 A~e~LI~~nlrLVvsIAkrY~~---~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IR 442 (605)
-...|+..|+++|.++|++|.. .+.+.+||+|||++|||+|+++|||.+| +|+||++||||++|.+++++..+
T Consensus 16 ~~~~lv~~y~~lV~~la~~~~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~-~F~tYa~~~Ir~~il~~lr~~~~--- 91 (231)
T PRK12427 16 EEGKYLNAYLPLVKKVVRQLAFQADSVIDREDMEQIALMGLLEALRRYGHPDE-QFAAYAVHRIRGAILDELRELDW--- 91 (231)
T ss_pred hHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHhcCCCCC-ChHHHHHHHHHHHHHHHHHhcCC---
Confidence 3557899999999999999875 4679999999999999999999998666 89999999999999999998765
Q ss_pred ccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhC--CCCCCCccccccccCCCCCCcccCCCCCC
Q 007404 443 LPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLS--PKAPRSLDQKIGINQNLKPSEVIADPEAE 520 (605)
Q Consensus 443 lP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~--~~~~~SLD~~i~~d~~~~l~d~l~D~~~~ 520 (605)
+|.++...+++++++.+.+.+++|+.||.+|||+.+|++.++|.+++.. .....|||.+++++++.. .+++ .
T Consensus 92 ~~r~vr~~~~~i~~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~---~~~~---~ 165 (231)
T PRK12427 92 RPRRLRQKTHKTNDAIREIAKRLGHEPNFEEISAELNLTAEEYQEYLLLENAGTLESLDELLALEAHND---ILQS---R 165 (231)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceeccCcccCCCccc---ccCC---C
Confidence 5778888999999999999999999999999999999999999998753 456899999986554322 2222 1
Q ss_pred CHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 007404 521 TAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 592 (605)
Q Consensus 521 spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 592 (605)
.+++.. .....|..++..||+++|.||.++|+.+ +|++|||+.||||.++|+|++.++++|||..
T Consensus 166 ~~~~~~---~~~~~l~~~l~~L~~~er~vi~l~~~~~----~t~~EIA~~lgis~~~V~q~~~~~~~kLr~~ 230 (231)
T PRK12427 166 DLEENI---IIEDNLKQALSQLDEREQLILHLYYQHE----MSLKEIALVLDLTEARICQLNKKIAQKIKSF 230 (231)
T ss_pred CHHHHH---HHHHHHHHHHHcCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHhh
Confidence 344322 2456789999999999999999999877 9999999999999999999999999999964
No 32
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=100.00 E-value=1.8e-33 Score=283.07 Aligned_cols=224 Identities=30% Similarity=0.437 Sum_probs=198.2
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHhh---CCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcc
Q 007404 362 YGILCKDKMITSNIRLVISIAKNYQ---GAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQS 438 (605)
Q Consensus 362 ~g~~A~e~LI~~nlrLVvsIAkrY~---~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~s 438 (605)
.|.-+++.||..|.++|+++|++|. +++.+++||+||||+|||+++++|||++|.+|+||+++||+|.|.++++++.
T Consensus 5 ~~~~~~~~L~~~~~~~v~~~a~~~~~~~~~~~~aeDlvQe~~i~l~~~~~~f~~~~~~~f~tyl~~~irn~~~~~lR~~~ 84 (236)
T PRK06986 5 EGKMDQDELVEQYAPLVKRIALRLKARLPASVDLDDLIQAGMIGLLEAARRYDGEQGASFETYAGQRIRGAMLDELRSLD 84 (236)
T ss_pred cccccHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhcCcccCCChHHHHHHHHHHHHHHHHHHcC
Confidence 4577899999999999999999997 6789999999999999999999999999999999999999999999999986
Q ss_pred ccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhC--CCCCCCccccccccCCCCCCcccCC
Q 007404 439 RTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLS--PKAPRSLDQKIGINQNLKPSEVIAD 516 (605)
Q Consensus 439 r~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~--~~~~~SLD~~i~~d~~~~l~d~l~D 516 (605)
+ +|.++....+++.++...+.+.+|++|+.+|||+.+|++.++|..++.. .....|++..++++++. +.. ..+
T Consensus 85 ~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ela~~l~i~~~~v~~~~~~~~~~~~~sl~~~~~~~~~~-~~~-~~~ 159 (236)
T PRK06986 85 W---VPRSVRRNAREVAQAIRQLEQELGREPTDTEVAEKLGLSLEEYREMLLDTNISQLFSIDELRGEHGDS-ILV-TED 159 (236)
T ss_pred C---CCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhccCCccccccccCCCcc-ccc-ccC
Confidence 5 6877777888899999999999999999999999999999999998863 34567888887654443 222 223
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404 517 PEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR 594 (605)
Q Consensus 517 ~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 594 (605)
+..++|++.+...+....|..+|+.||+++|.||.++|+.+ +|++|||+.||||.++|+++++||+++||+.+.
T Consensus 160 ~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~g----~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l~ 233 (236)
T PRK06986 160 HQDEDPLQQLEDEELREALVEAIESLPEREQLVLSLYYQEE----LNLKEIGAVLGVSESRVSQIHSQAIKRLRARLG 233 (236)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHhHhccC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 33457888888888889999999999999999999999887 999999999999999999999999999999775
No 33
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=99.96 E-value=4.8e-28 Score=243.50 Aligned_cols=209 Identities=29% Similarity=0.488 Sum_probs=168.4
Q ss_pred HH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHHHHhccHHHHHHHHH
Q 007404 294 LR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMIT 372 (605)
Q Consensus 294 l~-yL~~i~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~~l~~g~~A~e~LI~ 372 (605)
+. |+.++ ++.|+||+++|..|...++. ++..|++.|+.
T Consensus 18 ~~~~~~~~-~~~~~~~~~~e~~l~~~~~~----------------------------------------gd~~a~~~l~~ 56 (233)
T PRK05803 18 LVSYVKNN-SFPQPLSEEEERKYLELMKE----------------------------------------GDEEARNILIE 56 (233)
T ss_pred HHHHHHHh-cccCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHH
Confidence 45 99999 99999999999988766543 34789999999
Q ss_pred HHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHHHHHH
Q 007404 373 SNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATY 452 (605)
Q Consensus 373 ~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~~~i~ 452 (605)
.|.++|++++.+|.+++.+++||+|||++++|+++++||+++|.+|.||+++|+|+.+.+++++..+..+
T Consensus 57 ~y~~~l~~~a~~~~~~~~daeDlvQE~fi~l~~~~~~f~~~~~~~f~~wl~~i~rn~~id~~Rk~~~~~~---------- 126 (233)
T PRK05803 57 RNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYAARCIENEILMHLRNLKKTKK---------- 126 (233)
T ss_pred HhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCChHHHHHHHHHHHHHHHHHHHhcccc----------
Confidence 9999999999999999999999999999999999999999988899999999999999999987643100
Q ss_pred HHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCcccccccc---CCCCCCcccCCCCCCCHHHHHHHH
Q 007404 453 RVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGIN---QNLKPSEVIADPEAETAEDLLIKK 529 (605)
Q Consensus 453 ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d---~~~~l~d~l~D~~~~spEe~l~~~ 529 (605)
..+++.+.+.+ ...++.+.+++. .+++++.+..+
T Consensus 127 ------------------------------------------~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~ 163 (233)
T PRK05803 127 ------------------------------------------EVSLQDPIGVDKEGNEISLIDILGSE-EDDVIEQVELK 163 (233)
T ss_pred ------------------------------------------CCCccccccCCCCcCcccHHHHccCC-CCCHHHHHHHH
Confidence 01111111101 011222233332 23577777777
Q ss_pred HHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhh
Q 007404 530 FMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK 596 (605)
Q Consensus 530 el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 596 (605)
...+.|..+|..||+++|+||.++|++++.+.+|++|||+.||+|.++|+++++||+++||+.+...
T Consensus 164 ~~~~~l~~~l~~Lp~~~R~i~~l~y~~~~~e~~S~~EIA~~lgis~~tV~~~~~rA~~kLr~~l~~~ 230 (233)
T PRK05803 164 MEVEKLYKKIDILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKKLFKELYRA 230 (233)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHhCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHh
Confidence 7888899999999999999999999754444599999999999999999999999999999987653
No 34
>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=99.94 E-value=8.7e-25 Score=219.23 Aligned_cols=205 Identities=28% Similarity=0.487 Sum_probs=157.9
Q ss_pred HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHHHHhccHHHHHHHHHHHH
Q 007404 296 YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNI 375 (605)
Q Consensus 296 yL~~i~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~~l~~g~~A~e~LI~~nl 375 (605)
|.-.--++.+.|++.+|.+|..+++. ++..|++.|+..|.
T Consensus 19 ~~~~~~~~~~~~~~~~~~~li~~~~~----------------------------------------gd~~af~~l~~~y~ 58 (227)
T TIGR02846 19 YVTNNGSFPQPLSEEEEKKYLDRLKE----------------------------------------GDEEARNVLIERNL 58 (227)
T ss_pred HHHHHHhCCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHHHhH
Confidence 54222266788999999888776653 44789999999999
Q ss_pred HHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHHHHHHHHH
Q 007404 376 RLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVK 455 (605)
Q Consensus 376 rLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~~~i~ki~ 455 (605)
++|+++|.+|.++..+++||+||+|+++|+++++|+++++.+|.||+++|++|.+.+++++..+..+
T Consensus 59 ~~v~~~~~~~~~~~~dAEDlvQevfi~l~~~~~~~~~~~~~~f~twl~~i~rN~~~d~~Rk~~r~~~------------- 125 (227)
T TIGR02846 59 RLVAHIVKKFSNTGEDVDDLISIGTIGLIKAIDSFDPDKGTRLATYAARCIENEILMHLRALKKTKG------------- 125 (227)
T ss_pred HHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHhCCcccCCChHHHHHHHHHHHHHHHHHHHhcccc-------------
Confidence 9999999999999999999999999999999999999988899999999999999999988653110
Q ss_pred HHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCcccccccc---CCCCCCcccCCCCCCCHHHHHHHHHHH
Q 007404 456 EARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGIN---QNLKPSEVIADPEAETAEDLLIKKFMK 532 (605)
Q Consensus 456 ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d---~~~~l~d~l~D~~~~spEe~l~~~el~ 532 (605)
..+++...+.+ ....+.+...+ ...++++.....+..
T Consensus 126 ---------------------------------------~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~ 165 (227)
T TIGR02846 126 ---------------------------------------EVSLQDPIGVDKEGNEISLIDILGS-DGDSVIEQVELNLEI 165 (227)
T ss_pred ---------------------------------------ceeccccccCCcccCcccHHHHhcC-CCCChHHHHHHHHHH
Confidence 00111111000 00011112221 123566666666677
Q ss_pred HHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 007404 533 EDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 593 (605)
Q Consensus 533 ~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 593 (605)
+.|..+|+.||+++|+||.++|+++..+.+|++|||++||+|.++|++++++|+++||+.+
T Consensus 166 ~~l~~~i~~L~~~~r~il~l~y~~~~~e~~S~~EIAe~lgis~~tV~~~~~rAl~~Lr~~~ 226 (227)
T TIGR02846 166 KKLYKKLSVLDGREREVIEMRYGLGDGRRKTQREIAKILGISRSYVSRIEKRALMKLYKEL 226 (227)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHcCCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 8899999999999999999999743222399999999999999999999999999999864
No 35
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=99.93 E-value=1.1e-24 Score=218.69 Aligned_cols=180 Identities=28% Similarity=0.498 Sum_probs=137.8
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccc
Q 007404 362 YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI 441 (605)
Q Consensus 362 ~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~I 441 (605)
++..|++.|+..|.++|+.+|++|.+++.+++|++||+|+++|+++++|++..+++|.||+++++||.+.++++++.+..
T Consensus 49 gd~~af~~l~~~y~~~l~~~a~~~~~~~~~AeDlvQevfl~l~~~~~~f~~~~~~~f~twl~~iarn~~~d~lRk~~~~~ 128 (234)
T PRK08301 49 GDEAVRSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEILMYLRRNNKVK 128 (234)
T ss_pred cCHHHHHHHHHHhHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHHHHHHhccc
Confidence 45789999999999999999999999999999999999999999999999988889999999999999999998765410
Q ss_pred cccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccc--cCC-CCCCcccCCCC
Q 007404 442 RLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGI--NQN-LKPSEVIADPE 518 (605)
Q Consensus 442 RlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~--d~~-~~l~d~l~D~~ 518 (605)
. ..+++.+... ++. ..+.+...+.
T Consensus 129 ~----------------------------------------------------~~~~~~~~~~~~~~~~~~~~~~~~~~- 155 (234)
T PRK08301 129 A----------------------------------------------------EVSFDEPLNIDWDGNELLLSDVLGTD- 155 (234)
T ss_pred c----------------------------------------------------ccccccccccccCCCcccHHHhccCc-
Confidence 0 0111111100 000 0011111111
Q ss_pred CCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404 519 AETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR 594 (605)
Q Consensus 519 ~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 594 (605)
...++...........|..+|+.||+++|+||.|+|++...+.+|++|||+.||||.+||+++++||+++||+.+.
T Consensus 156 ~~~~~~~~~~~~~~~~l~~al~~Lp~~~R~v~~L~y~l~~~eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~l~ 231 (234)
T PRK08301 156 NDIIYKDIEDEVDRKLLKKALKKLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEKRIIKRLKKEIN 231 (234)
T ss_pred ccchHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 1233344445556677999999999999999999995211112999999999999999999999999999999764
No 36
>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. As characterized in Bacillus subtilis, this protein is synthesized as a precursor, specifically in the mother cell compartment, and must cleaved by the SpoIIGA protein to be made active.
Probab=99.92 E-value=9.6e-24 Score=212.63 Aligned_cols=180 Identities=30% Similarity=0.513 Sum_probs=139.4
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccc
Q 007404 362 YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI 441 (605)
Q Consensus 362 ~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~I 441 (605)
++..|++.|+..|.+.|+.+|++|.+++.+++||+||+|+++|+++++|++..+++|.||++.+++|.+.++++++.+..
T Consensus 49 ~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~AEDlvQE~fl~l~~~~~~f~~~~~~~f~~wl~~iarN~~~d~~Rk~~r~~ 128 (234)
T TIGR02835 49 GDESAKSTLIERNLRLVVYIARKFENTGIGIEDLVSIGTIGLIKAVNTFNPSKKIKLATYASRCIENEILMYLRRNNKTR 128 (234)
T ss_pred CCHHHHHHHHHHhHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHHhcccc
Confidence 45789999999999999999999999999999999999999999999999988888999999999999999999865411
Q ss_pred cccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccc--cCC-CCCCcccCCCC
Q 007404 442 RLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGI--NQN-LKPSEVIADPE 518 (605)
Q Consensus 442 RlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~--d~~-~~l~d~l~D~~ 518 (605)
.. .+++..+.. +++ ....+. .++.
T Consensus 129 ~~----------------------------------------------------~~~~~~~~~~~~~~~~~~~~~-~~~~ 155 (234)
T TIGR02835 129 SE----------------------------------------------------VSFDEPLNVDWDGNELLLSDV-LGTD 155 (234)
T ss_pred Cc----------------------------------------------------ccccccccCCCCCCcchHHHh-cCCC
Confidence 00 111111100 000 000111 1112
Q ss_pred CCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404 519 AETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR 594 (605)
Q Consensus 519 ~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 594 (605)
...+++.+........|..+|+.||+++|.||.++|++.+++.+|++|||+.||||.++|+++.+||+++||+.+.
T Consensus 156 ~~~~~~~~~~~~~~~~l~~ai~~Lp~~~R~ii~L~~~l~~~eg~s~~EIA~~Lgis~~tV~~~l~ra~~~LR~~l~ 231 (234)
T TIGR02835 156 SDIVYKYLEEEVDRELLRKALAKLNDREKKIMELRFGLVGGTEKTQKEVADMLGISQSYISRLEKRILKRLKKEIN 231 (234)
T ss_pred CCcHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhh
Confidence 2234444555566678999999999999999999996432233999999999999999999999999999999775
No 37
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=99.91 E-value=5.9e-23 Score=201.34 Aligned_cols=192 Identities=23% Similarity=0.303 Sum_probs=147.1
Q ss_pred HHHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHH
Q 007404 354 RELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKS 433 (605)
Q Consensus 354 ~~L~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ 433 (605)
..+.....++..|++.|+..|.++|+.+|++|.++..+++|++||+|++||+++.+||+.++.+|.||++.++++.+.++
T Consensus 13 ~l~~~~~~~d~~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~~~~f~twl~~i~~n~~~d~ 92 (208)
T PRK08295 13 ELVELARSGDKEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAELCITRQIITA 92 (208)
T ss_pred HHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHH
Confidence 33444456778999999999999999999999999999999999999999999999999887899999999999999999
Q ss_pred HhhccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccc-cCCCCCCc
Q 007404 434 LSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGI-NQNLKPSE 512 (605)
Q Consensus 434 ir~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~-d~~~~l~d 512 (605)
+++..+..+.+. ....|++.++.+ +.+..+.+
T Consensus 93 ~r~~~r~~~~~~-----------------------------------------------~~~~s~~~~~~~~~~~~~~~~ 125 (208)
T PRK08295 93 IKTANRQKHIPL-----------------------------------------------NSYVSLDKPIYDEESDRTLLD 125 (208)
T ss_pred HHHhhhhccccc-----------------------------------------------cceeecCCcccCCccchhHHH
Confidence 886543211110 001222322211 11112233
Q ss_pred ccCCCCCCCHHHHHHHHHHHHHH-HHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 513 VIADPEAETAEDLLIKKFMKEDL-EKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 513 ~l~D~~~~spEe~l~~~el~~~L-~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
.+.++...+|++.+...+....+ ..++..||+++|.||.+ |..+ +|++|||+.||+|.++|+..++||+++||+
T Consensus 126 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~L~~~~r~vl~l-~~e~----~s~~EIA~~lgis~~tV~~~l~rar~~Lr~ 200 (208)
T PRK08295 126 VISEAKVTDPEELIISKEELEDIEEKIEELLSELEKEVLEL-YLDG----KSYQEIAEELNRHVKSIDNALQRVKRKLEK 200 (208)
T ss_pred HhcCcccCCHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHH-HHcc----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 33333334677766655555555 45679999999999999 8777 999999999999999999999999999999
Q ss_pred HHhhhh
Q 007404 592 KKRTKH 597 (605)
Q Consensus 592 ~l~~~~ 597 (605)
.+....
T Consensus 201 ~l~~~~ 206 (208)
T PRK08295 201 YLENRE 206 (208)
T ss_pred HHHhhc
Confidence 886543
No 38
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=99.90 E-value=3e-22 Score=193.76 Aligned_cols=172 Identities=16% Similarity=0.235 Sum_probs=141.9
Q ss_pred HHHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHH
Q 007404 354 RELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKS 433 (605)
Q Consensus 354 ~~L~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ 433 (605)
..+.....++..|++.|+..|.++|+.+|++|.+++.+++|++||+|+++|+++.+|++. +.+|.+|++..+++.+.++
T Consensus 9 ~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~f~~wl~~ia~n~~~d~ 87 (186)
T PRK05602 9 ELLARVAAGDPAAFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRPG-EARFDTWLHRVVLNLCYDR 87 (186)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHhhhcCCC-CCcHHHHHHHHHHHHHHHH
Confidence 344455567799999999999999999999999999999999999999999999999986 4579999999999999999
Q ss_pred HhhccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcc
Q 007404 434 LSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEV 513 (605)
Q Consensus 434 ir~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~ 513 (605)
++++... + .+. ..+
T Consensus 88 ~R~~~~~---~-----------------------------------------------------~~~---------~~~- 101 (186)
T PRK05602 88 LRRRREV---P-----------------------------------------------------VED---------APD- 101 (186)
T ss_pred HHhcCCC---C-----------------------------------------------------ccc---------ccc-
Confidence 9875421 0 000 000
Q ss_pred cCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 007404 514 IADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 593 (605)
Q Consensus 514 l~D~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 593 (605)
..+. ...+++.+...+....+..+|..||+++|+||.|+|..+ +|++|||+.||+|..+|+++++||+++||+.+
T Consensus 102 ~~~~-~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 176 (186)
T PRK05602 102 VPDP-APGPDAGLEARQRARRVEQALAALPERQREAIVLQYYQG----LSNIEAAAVMDISVDALESLLARGRRALRAQL 176 (186)
T ss_pred cCCC-CCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhHHHhcC----CCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence 0011 124566666666777899999999999999999999887 99999999999999999999999999999988
Q ss_pred hhhh
Q 007404 594 RTKH 597 (605)
Q Consensus 594 ~~~~ 597 (605)
...+
T Consensus 177 ~~~~ 180 (186)
T PRK05602 177 ADLP 180 (186)
T ss_pred Hhcc
Confidence 7654
No 39
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=99.89 E-value=3.6e-22 Score=192.16 Aligned_cols=181 Identities=15% Similarity=0.229 Sum_probs=144.0
Q ss_pred CHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHH
Q 007404 352 DQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVR 431 (605)
Q Consensus 352 d~~~L~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~ 431 (605)
|...+.....++..|+..|+..|.++|+.+|++|.+++.+++|++||+|+++|+++.+|++.. +|.+|++..++|.+.
T Consensus 5 ~~~li~~~~~gd~~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~~ 82 (187)
T TIGR02948 5 IKKRIKEVRKGDENAFADLVDLYKDKIYQLCYRMLGNVHEAEDVAQEAFIRAYTNIDTYDIQR--KFSTWLYRIATNLTI 82 (187)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCCC--chHHHHHHHHHHHHH
Confidence 344556666778999999999999999999999999999999999999999999999999865 599999999999999
Q ss_pred HHHhhccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCC
Q 007404 432 KSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPS 511 (605)
Q Consensus 432 r~ir~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~ 511 (605)
+++++..+...+ +.....++.....
T Consensus 83 ~~~rk~~~~~~~-------------------------------------------------------~~~~~~~~~~~~~ 107 (187)
T TIGR02948 83 DRLRKRKPDFYL-------------------------------------------------------DDEVQGTDGLTME 107 (187)
T ss_pred HHHHhhcccccc-------------------------------------------------------cccccCccccccc
Confidence 998864421000 0000000011111
Q ss_pred cccCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 512 EVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 512 d~l~D~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
+...+ ..+.|++.+...+....+..+|..||+++|.||.++|..+ +|++|||+.||+|.++|++.++||+++||.
T Consensus 108 ~~~~~-~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g----~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 182 (187)
T TIGR02948 108 SQLAA-DEAPPEDQVISLELRDTIQQEIQALPPKYRMVIVLKYMED----LSLKEISEILDLPVGTVKTRIHRGREALRK 182 (187)
T ss_pred ccccc-CcCCHHHHHHHHHHHHHHHHHHHhCCHHHhHHhhhHHhcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 11111 1235677777777778899999999999999999999887 999999999999999999999999999999
Q ss_pred HHh
Q 007404 592 KKR 594 (605)
Q Consensus 592 ~l~ 594 (605)
.+.
T Consensus 183 ~l~ 185 (187)
T TIGR02948 183 QLR 185 (187)
T ss_pred Hhh
Confidence 775
No 40
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=99.89 E-value=2.3e-22 Score=195.78 Aligned_cols=180 Identities=17% Similarity=0.182 Sum_probs=146.4
Q ss_pred CHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHH
Q 007404 352 DQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVR 431 (605)
Q Consensus 352 d~~~L~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~ 431 (605)
+...+.....++..|++.|+..|.+.|+++|++|.++..+++|++||+|+++|++.++|++. ..|.+|++.++++.++
T Consensus 13 ~~~l~~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~fi~l~~~~~~~~~~--~~f~~wl~~i~~n~~~ 90 (194)
T PRK12513 13 DEALMLRYRAGDAAAFEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRARAQYQPR--ARFRTWLYQIARNLLI 90 (194)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCC--CchHHHHHHHHHHHHH
Confidence 44555566667799999999999999999999999999999999999999999999999975 3699999999999999
Q ss_pred HHHhhccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCC
Q 007404 432 KSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPS 511 (605)
Q Consensus 432 r~ir~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~ 511 (605)
+++++..+....+. ..+. . .
T Consensus 91 ~~~R~~~~~~~~~~---------------------------------------------------~~~~------~--~- 110 (194)
T PRK12513 91 DHWRRHGARQAPSL---------------------------------------------------DADE------Q--L- 110 (194)
T ss_pred HHHHHhcccccccc---------------------------------------------------ccch------h--h-
Confidence 99988765221100 0000 0 0
Q ss_pred cccCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 512 EVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 512 d~l~D~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
....+ ...+|++.+...+....|..+|+.||+++|.||.|+|+.| +|++|||+.||+|.++|+++++||+++||+
T Consensus 111 ~~~~~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g----~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 185 (194)
T PRK12513 111 HALAD-DGAAPEQQLSLFRDRRRLQAALETLPDEQREVFLLREHGD----LELEEIAELTGVPEETVKSRLRYALQKLRE 185 (194)
T ss_pred hhcCC-CCCCHHHHHHHHHHHHHHHHHHHhCCHhHhhheeeehccC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 00111 1235777777777888999999999999999999999887 999999999999999999999999999999
Q ss_pred HHhhhhH
Q 007404 592 KKRTKHL 598 (605)
Q Consensus 592 ~l~~~~L 598 (605)
.+...++
T Consensus 186 ~l~~~~~ 192 (194)
T PRK12513 186 LLAEEVA 192 (194)
T ss_pred HHHHhhc
Confidence 8876543
No 41
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=99.89 E-value=3.6e-22 Score=194.96 Aligned_cols=172 Identities=15% Similarity=0.172 Sum_probs=138.7
Q ss_pred HHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHh
Q 007404 356 LRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLS 435 (605)
Q Consensus 356 L~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir 435 (605)
+.....++..+++.|+..|.++|+++|.+|.++..+++|++||+|+++|+++++||+.+| .|.+|++..++|.++++++
T Consensus 21 i~~~~~g~~~a~~~l~~~y~~~l~~~~~~~~~~~~dAeDivQe~fi~l~~~~~~~~~~~~-~~~~wl~~ia~n~~~d~~r 99 (194)
T PRK09646 21 LRRVARGDQDAFAELYDRTSSRVYGLVRRVLRDPGYSEETTQEVYLEVWRTASRFDPARG-SALAWLLTLAHRRAVDRVR 99 (194)
T ss_pred HHHHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhhcCcccc-cHHHHHHHHHHHHHHHHHH
Confidence 334445668999999999999999999999999999999999999999999999998766 6999999999999999998
Q ss_pred hccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccC
Q 007404 436 DQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIA 515 (605)
Q Consensus 436 ~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~ 515 (605)
++.+..+.- .+ .. . . +.
T Consensus 100 ~~~~~~~~~---------------------------------------------------~~----~~-~--~---~~-- 116 (194)
T PRK09646 100 SEQAASQRE---------------------------------------------------VR----YG-A--R---NV-- 116 (194)
T ss_pred hhccccccc---------------------------------------------------cc----cc-c--c---cc--
Confidence 765311100 00 00 0 0 00
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 007404 516 DPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT 595 (605)
Q Consensus 516 D~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 595 (605)
+.....+++.+...+....|..+|..||+++|.||.|+|..+ +|++|||+.||+|..+|+++++||+++||+.+..
T Consensus 117 ~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~----~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l~~ 192 (194)
T PRK09646 117 DPAFDQVAEEVEARLERERVRDCLDALTDTQRESVTLAYYGG----LTYREVAERLAVPLGTVKTRMRDGLIRLRDCLGV 192 (194)
T ss_pred cccccchHHHHHHHhHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHhCCChHhHHHHHHHHHHHHHHHhcc
Confidence 001113444444456667899999999999999999999888 9999999999999999999999999999998753
No 42
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=99.89 E-value=1.1e-21 Score=190.11 Aligned_cols=167 Identities=16% Similarity=0.274 Sum_probs=137.0
Q ss_pred HHhccHHHHHHHHHHHHHHHHHHHHHhhCC----CCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHH
Q 007404 359 RLNYGILCKDKMITSNIRLVISIAKNYQGA----GMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSL 434 (605)
Q Consensus 359 ~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~----g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~i 434 (605)
...++..|++.|+..|.+.|+.+|.++.++ +.+++|++||+|+++|+++.+|++. +..|.+|++..++|.+.+++
T Consensus 18 ~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~~~~wl~~i~~n~~~d~~ 96 (189)
T PRK09648 18 AVAGDRRALREVLEIIRPLVVRYCRARLGGVERPGLSADDVAQEVCLAVITALPRYRDQ-GRPFLAFVYGIAAHKVADAH 96 (189)
T ss_pred HHcCCHHHHHHHHHHHHHHHHHHHHHHhcccccCCCCHHHHHHHHHHHHHHHHHHHhcc-CCcHHHHHHHHHHHHHHHHH
Confidence 334568999999999999999999998765 3689999999999999999999864 45799999999999999999
Q ss_pred hhccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCccc
Q 007404 435 SDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVI 514 (605)
Q Consensus 435 r~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l 514 (605)
+++.+....+ .+ ...+..
T Consensus 97 r~~~r~~~~~-----------------------------------------------------~~---------~~~~~~ 114 (189)
T PRK09648 97 RAAGRDKAVP-----------------------------------------------------TE---------EVPERP 114 (189)
T ss_pred HHhCCCcccc-----------------------------------------------------cc---------cccccc
Confidence 8865421100 00 000011
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404 515 ADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR 594 (605)
Q Consensus 515 ~D~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 594 (605)
. ...+|++.+...+..+.|..+|..||+++|+||.++|+.| +|++|||+.||+|..+|+++++||+++||+.+.
T Consensus 115 ~--~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g----~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~ 188 (189)
T PRK09648 115 S--DDAGPEERALRSESSNRMRELLDTLPEKQREILILRVVVG----LSAEETAEAVGSTPGAVRVAQHRALARLRAEIE 188 (189)
T ss_pred c--cCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Confidence 1 1135777777777788899999999999999999999988 999999999999999999999999999998763
No 43
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=99.89 E-value=9.2e-22 Score=189.35 Aligned_cols=177 Identities=14% Similarity=0.192 Sum_probs=141.3
Q ss_pred HHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHh
Q 007404 356 LRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLS 435 (605)
Q Consensus 356 L~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir 435 (605)
+.....++..+++.|+..|.++|+++|++|.++..+++|++||++++||+++.+|++.. +|.+|++..+|+.+.++++
T Consensus 9 i~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~~--~~~~wl~~iarn~~~d~~R 86 (187)
T PRK09641 9 IKQVKKGDQNAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINR--KFSTWLYRIATNLTIDRLR 86 (187)
T ss_pred HHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhhCCCc--chhHHHHHHHHHHHHHHHH
Confidence 33444566899999999999999999999999999999999999999999999999853 6999999999999999998
Q ss_pred hccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccC
Q 007404 436 DQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIA 515 (605)
Q Consensus 436 ~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~ 515 (605)
++.+... ++.....++.....+.+.
T Consensus 87 ~~~~~~~-------------------------------------------------------~~~~~~~~~~~~~~~~~~ 111 (187)
T PRK09641 87 KRKPDYY-------------------------------------------------------LDAEVAGTEGLTMYSQLA 111 (187)
T ss_pred hcCcccc-------------------------------------------------------ccccccCCcchhhhcccc
Confidence 7643110 000000011111111122
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404 516 DPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR 594 (605)
Q Consensus 516 D~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 594 (605)
+. ..+|++.+...+....|..+|..||+++++||.++|..+ ++++|||+.||||.++|++.++||+++||+.+.
T Consensus 112 ~~-~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~~~~----~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l~ 185 (187)
T PRK09641 112 AD-DALPEEQVVSLELQETIQEAILQLPEKYRTVIVLKYIED----LSLKEISEILDLPVGTVKTRIHRGREALRKQLR 185 (187)
T ss_pred cC-cCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHHhhC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 21 235777777777778899999999999999999999877 999999999999999999999999999999774
No 44
>TIGR02859 spore_sigH RNA polymerase sigma-H factor. Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs are detected in Listeria, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt.
Probab=99.89 E-value=6.6e-22 Score=192.27 Aligned_cols=186 Identities=20% Similarity=0.259 Sum_probs=139.5
Q ss_pred HHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHh
Q 007404 356 LRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLS 435 (605)
Q Consensus 356 L~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir 435 (605)
+.....++..|++.||..|.+.|+.+|+++.++..+++||+||+|+.+|+++.+|++..+..|.||++.+|++.+.++++
T Consensus 10 ~~~~~~~d~~a~~~l~~~~~~~l~~~a~~~~~~~~~aeDlvQe~fl~~~~~~~~~~~~~~~~f~~wl~~~~~~~~~~~~r 89 (198)
T TIGR02859 10 VELARQGNTHALEYLINKYKNFVRAKARSYFLIGADKEDIIQEGMIGLYKAIRDFRPDKLSSFKAFAELCVTRQIITAIK 89 (198)
T ss_pred HHHHHcCCHHHHHHHHHHHHHHHHHHHHHHccccCcHHHHHHHHHHHHHHHHHHhCcccCCChHHHHHHHHHHHHHHHHH
Confidence 33344556899999999999999999999999999999999999999999999999988779999999999999988887
Q ss_pred hccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccc-cCCCCCCccc
Q 007404 436 DQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGI-NQNLKPSEVI 514 (605)
Q Consensus 436 ~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~-d~~~~l~d~l 514 (605)
...+..+.+. ....|++.+... +++.++.+.+
T Consensus 90 ~~~~~~~~~~-----------------------------------------------~~~~~~~~~~~~~~~~~~~~~~~ 122 (198)
T TIGR02859 90 TATRQKHIPL-----------------------------------------------NSYVSLNKPIYDEESDRTLLDVI 122 (198)
T ss_pred HHHHhcccch-----------------------------------------------hhhcCcccccccccccchHHHHh
Confidence 5432111100 011233322211 1111222222
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHhcC-CHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 007404 515 ADPEAETAEDLLIKKFMKEDLEKVLDTL-NPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 593 (605)
Q Consensus 515 ~D~~~~spEe~l~~~el~~~L~~aL~~L-~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 593 (605)
.+....+|++.+...+....|.++|+.| ++.++.|+ ++|..+ +|++|||+.||+|.++|++.++||+++||+.+
T Consensus 123 ~~~~~~~~e~~~~~~e~~~~l~~~l~~Ll~~~~~~i~-~~~~~~----~s~~eIA~~l~~s~~tV~~~l~r~r~~L~~~l 197 (198)
T TIGR02859 123 SGAKVTDPEELIISQEEYGDIESKMNELLSDLEWKVL-QSYLDG----KSYQEIACDLNRHVKSIDNALQRVKRKLEKYL 197 (198)
T ss_pred hccccCCHHHHHHHHHHHHHHHHHHHHhcCHHHHHHH-HHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhc
Confidence 2222346787777778788899999995 55666665 557666 99999999999999999999999999999865
No 45
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=99.88 E-value=1.5e-21 Score=196.28 Aligned_cols=193 Identities=19% Similarity=0.192 Sum_probs=153.9
Q ss_pred cCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHHHHhccHHHHHHHHHHHHHHHHHH
Q 007404 302 SSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISI 381 (605)
Q Consensus 302 ~~~~lLT~eEE~eL~~~iq~~~~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~~l~~g~~A~e~LI~~nlrLVvsI 381 (605)
.+.|+|++..+.+|...++. ++..|++.|+..|.+.|+++
T Consensus 7 ~~~~~~~~~~~~~l~~~~~~----------------------------------------gd~~a~~~l~~~y~~~l~~~ 46 (231)
T PRK11922 7 SRPPPLSAASDRELVARVLA----------------------------------------GDEAAFEALMRRHNRRLYRT 46 (231)
T ss_pred CCCCCcCcccHHHHHHHHHc----------------------------------------CCHHHHHHHHHHHHHHHHHH
Confidence 56788888888877665543 45789999999999999999
Q ss_pred HHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHHHHHHHHHHHHHHH
Q 007404 382 AKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQL 461 (605)
Q Consensus 382 AkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~~~i~ki~ka~~~L 461 (605)
++++.++..+++||+||+|+++|+++++|++. ..|.+|++..+++.+.+++++..+..+++..
T Consensus 47 a~~~~~~~~~AEDlvQE~fi~l~~~~~~~~~~--~~~~~wL~~iarn~~~d~~Rk~~r~~~~~~~--------------- 109 (231)
T PRK11922 47 ARAILRNDAEAEDVVQEAYLRAFRALGTFRGD--ASLSTWLSRIVLNEALGRLRRRRRLVNLAEM--------------- 109 (231)
T ss_pred HHHHhCChhhHHHHHHHHHHHHHHHHHhcCCC--chhHHHHHHHHHHHHHHHHHhhcccccchhc---------------
Confidence 99999999999999999999999999999986 3799999999999999999886642211000
Q ss_pred HHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHHHHHHHHHHHHHHHHHhc
Q 007404 462 YSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDT 541 (605)
Q Consensus 462 ~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~l~~~el~~~L~~aL~~ 541 (605)
..+. .. .++ ...... ....+|++.+...+..+.|..+|+.
T Consensus 110 -----------------------------------~~~~-~~-~~~--~~~~~~-~~~~~~e~~~~~~e~~~~l~~~l~~ 149 (231)
T PRK11922 110 -----------------------------------VMAS-TI-AGG--ERTPLA-DPAEDPERAAARREIRALLERAIDA 149 (231)
T ss_pred -----------------------------------cccc-cc-ccc--cccccC-cccCChHHHHHHHHHHHHHHHHHHh
Confidence 0000 00 000 000011 1223677777788888899999999
Q ss_pred CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 007404 542 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT 595 (605)
Q Consensus 542 L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 595 (605)
||+++|+||.++|..+ +|++|||+.||+|.++|+++++||+++||+.+..
T Consensus 150 L~~~~r~i~~l~~~~g----~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l~~ 199 (231)
T PRK11922 150 LPDAFRAVFVLRVVEE----LSVEETAQALGLPEETVKTRLHRARRLLRESLAR 199 (231)
T ss_pred CCHHHhhhheeehhcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999887 9999999999999999999999999999998864
No 46
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=99.88 E-value=2e-21 Score=184.87 Aligned_cols=174 Identities=17% Similarity=0.169 Sum_probs=139.8
Q ss_pred HHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcc
Q 007404 359 RLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQS 438 (605)
Q Consensus 359 ~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~s 438 (605)
...++..|++.|+..|.++|+.++++|.+++.+.+|++||++++||+++++|+ .+.+|.+|++.++++.+.+++++..
T Consensus 4 ~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~r~~~ 81 (182)
T PRK09652 4 VQRGDRAAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFR--GGAAFYTWLYRIARNTAINYLRKQG 81 (182)
T ss_pred hhcCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHhcC--CCcchHHHHHHHHHHHHHHHHHccc
Confidence 34567889999999999999999999999999999999999999999999999 3458999999999999999998765
Q ss_pred ccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCC
Q 007404 439 RTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPE 518 (605)
Q Consensus 439 r~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~ 518 (605)
+....+ ..+.+ +.++....+...+
T Consensus 82 ~~~~~~--------------------------------------------------~~~~~----~~~~~~~~~~~~~-- 105 (182)
T PRK09652 82 RRPPAS--------------------------------------------------DVDAE----EAEDFDLADALRD-- 105 (182)
T ss_pred CCCCcc--------------------------------------------------ccccc----ccccccccccccc--
Confidence 421110 00000 0011111111111
Q ss_pred CCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404 519 AETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR 594 (605)
Q Consensus 519 ~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 594 (605)
..+|++.+...+....+..+|..||+++++||.++|+.+ +|++|||+.||+|..+|++.++||+++||+.+.
T Consensus 106 ~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~----~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 177 (182)
T PRK09652 106 ISTPENELLSAELEQRVRAAIESLPEELRTAITLREIEG----LSYEEIAEIMGCPIGTVRSRIFRAREALRAKLQ 177 (182)
T ss_pred ccChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 135777777777788899999999999999999999877 999999999999999999999999999999775
No 47
>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=99.88 E-value=2.8e-21 Score=183.01 Aligned_cols=166 Identities=19% Similarity=0.306 Sum_probs=137.6
Q ss_pred HHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcc
Q 007404 359 RLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQS 438 (605)
Q Consensus 359 ~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~s 438 (605)
...++..|++.|+..|.+.+++++.++.++..+++|++||+|+.+|+.+++|+...+ .|.+|++.++++.+.++++++.
T Consensus 5 ~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~-~~~~wl~~i~~n~~~d~~R~~~ 83 (170)
T TIGR02952 5 AQDREEDAFARIYETYSDRVYRYIYYRVGCKYTAEDLTSEVFERVLRKIDSFKEQKN-SFEAWLFTIARNVVNDYFRGSK 83 (170)
T ss_pred HHccCHHHHHHHHHHHHHHHHHHHHHHHCChhhHHHHHHHHHHHHHHhHHhcccccc-cHHHHHHHHHHHHHHHHHHhcC
Confidence 344678999999999999999999999998899999999999999999999997555 7999999999999999999865
Q ss_pred ccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCC
Q 007404 439 RTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPE 518 (605)
Q Consensus 439 r~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~ 518 (605)
+.... +++.. .+... .
T Consensus 84 ~~~~~-----------------------------------------------------~~~~~---------~~~~~--~ 99 (170)
T TIGR02952 84 RHPLF-----------------------------------------------------SLDVF---------KELLS--N 99 (170)
T ss_pred CCCCC-----------------------------------------------------cHHHH---------hhcCC--C
Confidence 42110 00000 00000 1
Q ss_pred CCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 007404 519 AETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 593 (605)
Q Consensus 519 ~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 593 (605)
..+|++.+...+....+..+|..|||++|+||.++|..| +|++|||+.||||..+|+++++||+++||+.+
T Consensus 100 ~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~g----~s~~eIA~~l~is~~tv~~~l~ra~~~Lr~~l 170 (170)
T TIGR02952 100 EPNPEEAILKEEANEKLLKALKILTPKQQHVIALRFGQN----LPIAEVARILGKTEGAVKILQFRAIKKLARQM 170 (170)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhC
Confidence 125677777777778899999999999999999999887 99999999999999999999999999999853
No 48
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=99.88 E-value=2.3e-21 Score=188.52 Aligned_cols=171 Identities=16% Similarity=0.199 Sum_probs=136.8
Q ss_pred HHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHh
Q 007404 356 LRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLS 435 (605)
Q Consensus 356 L~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir 435 (605)
+.+...++..+++.|+..|.+.|+.+++++.++..+++|++||+|+++|+. ..|++..+ .|.||++.++++.++++++
T Consensus 20 ~~~~~~gd~~a~~~L~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~l~~~-~~~~~~~~-~f~~wl~~iarn~~~d~~R 97 (194)
T PRK12519 20 FSALKAGQSAALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRK-SSYDPKRG-SLSSYLLTLTRSRAIDRLR 97 (194)
T ss_pred HHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHh-cCCCcccc-cHHHHHHHHHHHHHHHHHH
Confidence 344455678999999999999999999999999999999999999999976 67887655 7999999999999999998
Q ss_pred hccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccC
Q 007404 436 DQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIA 515 (605)
Q Consensus 436 ~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~ 515 (605)
++.+..+.. . + .+ .. ...
T Consensus 98 k~~~~~~~~------------------~---------~------------------------~~--------~~---~~~ 115 (194)
T PRK12519 98 SRRSRQRLL------------------E---------R------------------------WQ--------QE---LLG 115 (194)
T ss_pred hcccccchh------------------h---------h------------------------hh--------hh---hcc
Confidence 765411100 0 0 00 00 000
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404 516 DPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR 594 (605)
Q Consensus 516 D~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 594 (605)
+.....+++.+...+....|..+|..||+++++||.|+|..| +|++|||+.||+|.++|+++++||+++||+.+.
T Consensus 116 ~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~~~v~~l~~~~g----~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~ 190 (194)
T PRK12519 116 EASEDTPLEQASLAERSQRVQTALAQLPESQRQVLELAYYEG----LSQSEIAKRLGIPLGTVKARARQGLLKLRELLQ 190 (194)
T ss_pred cccCCCHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhhhhhcC----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 011124556666666677899999999999999999999887 999999999999999999999999999999764
No 49
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=99.88 E-value=1.3e-21 Score=182.80 Aligned_cols=151 Identities=20% Similarity=0.246 Sum_probs=124.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccc
Q 007404 364 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRL 443 (605)
Q Consensus 364 ~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRl 443 (605)
..|++.|++.|.++|+.+++++ +...+++|++||+++++|+++++|++..| .|.+|++..+++.++++++++.+...
T Consensus 3 ~~af~~l~~~y~~~l~~~~~~~-~~~~~aeDi~Qe~~l~l~~~~~~~~~~~~-~f~~wl~~i~~n~~ld~~rk~~~~~~- 79 (154)
T PRK06759 3 PATFTEAVVLYEGLIVNQIKKL-GIYQDYEEYYQCGLIGLWHAYERYDEKKG-SFPAYAVVTVRGYILERLKKEFAVQE- 79 (154)
T ss_pred cccHHHHHHHHHHHHHHHHHHh-CCcccHHHHHHHHHHHHHHHHHHhCccCC-chHHHHHHHHHHHHHHHHHHHHhhcc-
Confidence 5689999999999999999986 55679999999999999999999998776 79999999999999999987632000
Q ss_pred cccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHH
Q 007404 444 PFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAE 523 (605)
Q Consensus 444 P~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spE 523 (605)
. ... + + .|+
T Consensus 80 --------------------~------------------------------~~~-------~---------~-----~~~ 88 (154)
T PRK06759 80 --------------------K------------------------------CVC-------V---------G-----EYE 88 (154)
T ss_pred --------------------c------------------------------ccc-------c---------C-----CCc
Confidence 0 000 0 0 111
Q ss_pred HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 007404 524 DLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 592 (605)
Q Consensus 524 e~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 592 (605)
+.....+....|..+|..||+++|+||.++|+.| +|++|||+.||+|..+|+++++||+++||+.
T Consensus 89 ~~~~~~~~~~~l~~~l~~L~~~~r~ii~l~~~~~----~s~~EIA~~l~is~~tV~~~~~ra~~~Lr~~ 153 (154)
T PRK06759 89 DHFHFEDVEMKVKDFMSVLDEKEKYIIFERFFVG----KTMGEIALETEMTYYQVRWIYRQALEKMRNS 153 (154)
T ss_pred ccccHHHHHHHHHHHHHhCCHHHHHHHHHHHhcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHhhc
Confidence 1222233456799999999999999999999988 9999999999999999999999999999974
No 50
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=99.88 E-value=4e-21 Score=184.58 Aligned_cols=168 Identities=14% Similarity=0.116 Sum_probs=136.6
Q ss_pred HHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhh
Q 007404 357 RRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSD 436 (605)
Q Consensus 357 ~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~ 436 (605)
.....++..++..|+..|.+.|+.+|.+|.++..+++|++||+|+++|+++++|++..+ .|.||++..++|.+.+++++
T Consensus 11 ~~~~~g~~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~fl~~~~~~~~~~~~~~-~~~~wl~~ia~n~~~d~~R~ 89 (179)
T PRK12514 11 VRVSLGDRDAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAVSGL-SPMTWLITIARNHAIDRLRA 89 (179)
T ss_pred HHHHcCCHHHHHHHHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHHHhHHhcCcccc-cHHHHHHHHHHHHHHHHHHh
Confidence 33445668899999999999999999999999999999999999999999999987544 69999999999999999987
Q ss_pred ccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCC
Q 007404 437 QSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIAD 516 (605)
Q Consensus 437 ~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D 516 (605)
+.+. ..+ ++. . .+ ..+
T Consensus 90 ~~~~-~~~-----------------------------------------------------~~~------~---~~-~~~ 105 (179)
T PRK12514 90 RKAV-AVD-----------------------------------------------------IDE------A---HD-LAD 105 (179)
T ss_pred cCCc-ccc-----------------------------------------------------ccc------c---hh-ccc
Confidence 5431 000 000 0 00 001
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404 517 PEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR 594 (605)
Q Consensus 517 ~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 594 (605)
. ..+|++.+...+....|..+|..||+++|+||.++|+.| +|++|||+.||+|..+|++.++||+++||+++.
T Consensus 106 ~-~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 178 (179)
T PRK12514 106 P-SPGPEAEVIAGDEGQRIDACLEELEKDRAAAVRRAYLEG----LSYKELAERHDVPLNTMRTWLRRSLLKLRECLS 178 (179)
T ss_pred c-CCCHHHHHHhHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCCChHHHHHHHHHHHHHHHHHhc
Confidence 1 124666655555556799999999999999999999877 999999999999999999999999999999764
No 51
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=99.87 E-value=5.4e-21 Score=187.00 Aligned_cols=174 Identities=22% Similarity=0.194 Sum_probs=141.5
Q ss_pred HHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHH
Q 007404 353 QRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRK 432 (605)
Q Consensus 353 ~~~L~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r 432 (605)
...+.+...++..|++.|+..|.+.|+.+|.++.++..+++|++||+++.+|+.+.+|++.. ..|.+|++..+++.+.+
T Consensus 14 ~~li~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~~-~~~~~wl~~ia~n~~~d 92 (196)
T PRK12524 14 EALLVLYANGDPAAARALTLRLAPRALAVATRVLGDRAEAEDVTQEAMLRLWRIAPDWRQGE-ARVSTWLYRVVCNLCTD 92 (196)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhcccccc-chHHHHHHHHHHHHHHH
Confidence 34444455567999999999999999999999999999999999999999999999998643 36999999999999999
Q ss_pred HHhhccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCc
Q 007404 433 SLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSE 512 (605)
Q Consensus 433 ~ir~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d 512 (605)
+++++.+.. ..++.. . +
T Consensus 93 ~~Rk~~~~~------------------------------------------------------~~~~~~---~------~ 109 (196)
T PRK12524 93 RLRRRRRAS------------------------------------------------------VDLDDA---P------E 109 (196)
T ss_pred HHHhhcCCC------------------------------------------------------CCcccc---c------c
Confidence 988754300 000000 0 0
Q ss_pred ccCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 007404 513 VIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 592 (605)
Q Consensus 513 ~l~D~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 592 (605)
. .+. ...+++.+...+....|..+|+.||+++|.||.|+|..+ ++++|||+.||||..+|+++++||+++||+.
T Consensus 110 ~-~~~-~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~L~~~~g----~s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~ 183 (196)
T PRK12524 110 P-ADA-APGAEEALIEGDRMRALDAALAALPERQRQAVVLRHIEG----LSNPEIAEVMEIGVEAVESLTARGKRALAAL 183 (196)
T ss_pred c-ccc-CCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 0 111 124566667677778899999999999999999999987 9999999999999999999999999999998
Q ss_pred Hhhh
Q 007404 593 KRTK 596 (605)
Q Consensus 593 l~~~ 596 (605)
+...
T Consensus 184 l~~~ 187 (196)
T PRK12524 184 LAGQ 187 (196)
T ss_pred HHhc
Confidence 8753
No 52
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.
Probab=99.87 E-value=5.9e-21 Score=184.17 Aligned_cols=178 Identities=15% Similarity=0.150 Sum_probs=140.0
Q ss_pred HHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHH
Q 007404 355 ELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSL 434 (605)
Q Consensus 355 ~L~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~i 434 (605)
.+.....++..+++.|+..|.+.|+.+|+++.++..+++|++||+|+++|+++++|++. .+|.+|++..+++.+.+++
T Consensus 10 l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~--~~~~~wl~~iarn~~~~~~ 87 (190)
T TIGR02939 10 LVERVQRGEKQAFDLLVRKYQHKVVALVGRYVRDSSEVEDVAQEAFVKAYRALSSFRGD--SAFYTWLYRIAVNTAKNHL 87 (190)
T ss_pred HHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCC--CccHhHHHHHHHHHHHHHH
Confidence 34444456789999999999999999999999999999999999999999999999975 3699999999999999998
Q ss_pred hhccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCccc
Q 007404 435 SDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVI 514 (605)
Q Consensus 435 r~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l 514 (605)
+++.+..... ..+.+.. ....+..
T Consensus 88 r~~~r~~~~~--------------------------------------------------~~~~~~~------~~~~~~~ 111 (190)
T TIGR02939 88 VAQGRRPPTS--------------------------------------------------DVEIEDA------EHFEGAD 111 (190)
T ss_pred HHhccCCCcc--------------------------------------------------cccccch------hhhcccc
Confidence 7654311100 0000000 0000000
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404 515 ADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR 594 (605)
Q Consensus 515 ~D~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 594 (605)
......+|++.+...+....|..+|..||+++|+||.++|..+ +|++|||+.||+|..+|++.++||+++||+.+.
T Consensus 112 ~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~~----~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l~ 187 (190)
T TIGR02939 112 RLREIDTPERLLLSRELEQTVMRAVEALPEDLRTAITLRELEG----LSYEDIARIMDCPVGTVRSRIFRAREAIAIRLR 187 (190)
T ss_pred cccccCChHHHHHHHHHHHHHHHHHHcCCHHHhhhhhhhhhcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence 0001235677677777788899999999999999999999887 999999999999999999999999999999875
No 53
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=99.87 E-value=4e-21 Score=185.48 Aligned_cols=172 Identities=17% Similarity=0.202 Sum_probs=133.0
Q ss_pred HHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHH
Q 007404 355 ELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSL 434 (605)
Q Consensus 355 ~L~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~i 434 (605)
.+.....++..|++.|+..|.+.|+.++++|.+++.+++|++||+|+.+|+++++|++..+ .|.+|++..++|.+.+++
T Consensus 13 l~~~~~~~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~~i~l~~~~~~~~~~~~-~~~~wl~~ia~n~~~d~~ 91 (186)
T PRK13919 13 LLALVARGEEEALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKKAKEFDPRRG-SARAWLLALAHHAAVDHV 91 (186)
T ss_pred HHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhhhccCcccc-chHHHHHHHHHHHHHHHH
Confidence 3444446678999999999999999999999999999999999999999999999987644 699999999999999999
Q ss_pred hhccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCccc
Q 007404 435 SDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVI 514 (605)
Q Consensus 435 r~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l 514 (605)
++..+..+. .+.+ .......+ .
T Consensus 92 rk~~~~~~~----------------------------------------------------~~~~-----~~~~~~~~-~ 113 (186)
T PRK13919 92 RRRAARPQP----------------------------------------------------LEPD-----EREPEAFD-L 113 (186)
T ss_pred Hhhhccccc----------------------------------------------------cccc-----cccccccc-C
Confidence 876431000 0000 00000000 0
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404 515 ADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR 594 (605)
Q Consensus 515 ~D~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 594 (605)
+++. .. .........|..+|+.||+++|+||.++|..+ +|++|||+.||+|..+|+.+++||+++||+.+.
T Consensus 114 ~~~~--~~---~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~----~s~~eIA~~lgis~~~V~~~l~ra~~~Lr~~l~ 184 (186)
T PRK13919 114 PGPG--LD---EEGHLDRTRLGRALKALSPEERRVIEVLYYQG----YTHREAAQLLGLPLGTLKTRARRALSRLKEVLR 184 (186)
T ss_pred CCcc--cc---HHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhc
Confidence 0111 11 11223346689999999999999999999887 999999999999999999999999999999764
No 54
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=99.87 E-value=8.6e-21 Score=184.37 Aligned_cols=177 Identities=13% Similarity=0.128 Sum_probs=139.6
Q ss_pred HHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHh
Q 007404 356 LRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLS 435 (605)
Q Consensus 356 L~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir 435 (605)
+.....++..+++.|+..|.+.|+.++++|.++..+++|++||+++++|+++.+|++.. .|.+|++..+++.+.++++
T Consensus 11 l~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~~i~l~~~~~~~~~~~--~~~~wl~~ia~n~~~d~~r 88 (193)
T PRK11923 11 VERVQRGDKRAFDLLVLKYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYRALGNFRGDS--AFYTWLYRIAINTAKNHLV 88 (193)
T ss_pred HHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHhCcCCCC--ccHhHHHHHHHHHHHHHHH
Confidence 33444466889999999999999999999999999999999999999999999999874 5999999999999999998
Q ss_pred hccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccC
Q 007404 436 DQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIA 515 (605)
Q Consensus 436 ~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~ 515 (605)
++.+..... ...++......+. +.+.
T Consensus 89 k~~~~~~~~--------------------------------------------------~~~~~~~~~~~~~----~~~~ 114 (193)
T PRK11923 89 SRGRRPPDS--------------------------------------------------DVSSEDAEFYDGD----HALK 114 (193)
T ss_pred HhcCCCccc--------------------------------------------------cccccchhhhccc----cccc
Confidence 755411100 0000000000000 0011
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404 516 DPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR 594 (605)
Q Consensus 516 D~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 594 (605)
...+|++.+...+....|..+|..||+++|.||.++|..| +|++|||+.||+|..+|+++.+||+++||+++.
T Consensus 115 --~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g----~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~ 187 (193)
T PRK11923 115 --DIESPERALLRDEIEGTVHRTIQQLPEDLRTALTLREFDG----LSYEDIASVMQCPVGTVRSRIFRAREAIDKALQ 187 (193)
T ss_pred --CcCCHHHHHHHHHHHHHHHHHHHhCCHHHhHHHhhHHhcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 1235677777777788899999999999999999999877 999999999999999999999999999999875
No 55
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=99.87 E-value=6.6e-21 Score=184.11 Aligned_cols=170 Identities=14% Similarity=0.165 Sum_probs=136.9
Q ss_pred HHHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHH
Q 007404 354 RELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKS 433 (605)
Q Consensus 354 ~~L~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ 433 (605)
..+.....++..|++.|+..|.+.|+.+++++.++..+++|++||+|+.+|+.+++|++..+ .|.+|++..+++.+.++
T Consensus 12 ~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~~-~~~~wL~~iarn~~~d~ 90 (182)
T PRK12537 12 ACLLACARGDRRALQALYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTGAASFDPARG-SARGWIYSVTRHLALNV 90 (182)
T ss_pred HHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhccccCCcccc-cHHHHHHHHHHHHHHHH
Confidence 34455556679999999999999999999999999999999999999999999999986544 69999999999999999
Q ss_pred HhhccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcc
Q 007404 434 LSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEV 513 (605)
Q Consensus 434 ir~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~ 513 (605)
++++.+...+ +. . . .+.
T Consensus 91 ~r~~~~~~~~-------------------------------------------------------~~----~-~---~~~ 107 (182)
T PRK12537 91 LRDTRREVVL-------------------------------------------------------DD----D-A---EET 107 (182)
T ss_pred HHhccccCcc-------------------------------------------------------cc----c-h---hhh
Confidence 9886531100 00 0 0 000
Q ss_pred cCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 007404 514 IADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 593 (605)
Q Consensus 514 l~D~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 593 (605)
..+ ...+++..........|..+|+.||+++|+||.++|..| +|++|||+.||||.++|+++++||+++||+.+
T Consensus 108 ~~~--~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~~----~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 181 (182)
T PRK12537 108 AQT--LHEIIDDFDLWANSGKIHRCLEQLEPARRNCILHAYVDG----CSHAEIAQRLGAPLGTVKAWIKRSLKALRECM 181 (182)
T ss_pred ccc--ccchHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCCChhhHHHHHHHHHHHHHHHh
Confidence 000 112333444445567799999999999999999999888 99999999999999999999999999999875
No 56
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=99.87 E-value=5.8e-21 Score=184.71 Aligned_cols=172 Identities=13% Similarity=0.120 Sum_probs=138.2
Q ss_pred HHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHH
Q 007404 355 ELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSL 434 (605)
Q Consensus 355 ~L~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~i 434 (605)
.+.....++..+++.|+..|.++|+.+|++|.++..+++|++||+|+++|+++++|++.++ .|.+|++..++|.+++++
T Consensus 15 l~~~~~~~~~~~~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~~~~~~~~~~~~~~-~~~~wl~~I~~n~~~d~~ 93 (187)
T PRK12534 15 LLTATAGGDRHAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFDPSRA-RGLTWLAMIARNKAIDHL 93 (187)
T ss_pred HHHHHHcCCHHHHHHHHHHhhHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccCCcccc-cHHHHHHHHHHHHHHHHH
Confidence 4445556778999999999999999999999999999999999999999999999998655 589999999999999999
Q ss_pred hhccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCccc
Q 007404 435 SDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVI 514 (605)
Q Consensus 435 r~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l 514 (605)
+++.+..+. .+++.. .+..
T Consensus 94 R~~~~~~~~----------------------------------------------------~~~~~~---------~~~~ 112 (187)
T PRK12534 94 RANAPQRRN----------------------------------------------------VALDDA---------GELR 112 (187)
T ss_pred Hhccccccc----------------------------------------------------ccccch---------hhhc
Confidence 876431000 000000 0000
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404 515 ADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR 594 (605)
Q Consensus 515 ~D~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 594 (605)
++ ..++++.....+....|..+|..||++++.||.++|..| +|++|||+.||+|.++|+++++||+++||+.+.
T Consensus 113 -~~-~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g----~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l~ 186 (187)
T PRK12534 113 -AA-DASPLERTERASTRRRIDHCLAELEPPRSELIRTAFFEG----ITYEELAARTDTPIGTVKSWIRRGLAKLKACLE 186 (187)
T ss_pred -cc-cCChhhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHhCCChhHHHHHHHHHHHHHHHHHc
Confidence 00 113444445556678899999999999999999999877 999999999999999999999999999999764
No 57
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=99.87 E-value=7e-21 Score=185.17 Aligned_cols=171 Identities=20% Similarity=0.265 Sum_probs=138.8
Q ss_pred HHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCC---CCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHH
Q 007404 355 ELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAG---MNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVR 431 (605)
Q Consensus 355 ~L~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g---~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~ 431 (605)
.+.+...++..|++.|+..|.+.|++++.++.+++ .+++|++||+++++|+++++|++..+ .|.+|++..++|.+.
T Consensus 8 li~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~~~daeDi~Qe~~i~l~~~~~~~~~~~~-~~~~wl~~iarn~~~ 86 (189)
T PRK06811 8 FIKELKKKNEKALEFIVDTYGNLVKKIVHKVLGTVNYSQLIEECVNDIFLSIWNNIDKFDEEKG-SFKKWIAAISKYKAI 86 (189)
T ss_pred HHHHHHccCHHHHHHHHHHHHHHHHHHHHHHHcccCchhHHHHHHHHHHHHHHHhHHHhccccc-cHHHHHHHHHHHHHH
Confidence 34444556689999999999999999999998853 47999999999999999999997655 799999999999999
Q ss_pred HHHhhccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCC
Q 007404 432 KSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPS 511 (605)
Q Consensus 432 r~ir~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~ 511 (605)
++++++.+.... .+.+.
T Consensus 87 d~~rk~~~~~~~----------------------------------------------------~~~~~----------- 103 (189)
T PRK06811 87 DYKRKLTKNNEI----------------------------------------------------DSIDE----------- 103 (189)
T ss_pred HHHHHhcccccc----------------------------------------------------ccchh-----------
Confidence 999886541110 00000
Q ss_pred cccCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 512 EVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 512 d~l~D~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
...+ ..++|++.+...+....|..+|..||+++|.||.|+|..| +|++|||+.||+|..+|+++++||+++||+
T Consensus 104 -~~~~-~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g----~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~ 177 (189)
T PRK06811 104 -FILI-SEESIENEIILKENKEEILKLINDLEKLDREIFIRRYLLG----EKIEEIAKKLGLTRSAIDNRLSRGRKKLQK 177 (189)
T ss_pred -hhhc-ccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcc----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 0000 1125666677777778899999999999999999999877 999999999999999999999999999998
Q ss_pred HHhh
Q 007404 592 KKRT 595 (605)
Q Consensus 592 ~l~~ 595 (605)
..-+
T Consensus 178 ~~~~ 181 (189)
T PRK06811 178 NKLN 181 (189)
T ss_pred cccC
Confidence 6543
No 58
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=99.87 E-value=6.7e-21 Score=192.45 Aligned_cols=164 Identities=16% Similarity=0.208 Sum_probs=135.6
Q ss_pred hccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcccc
Q 007404 361 NYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRT 440 (605)
Q Consensus 361 ~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~ 440 (605)
.|+..|++.|+..|.+.|+.+++++.++..+++|++||+|+.+|+.+++|++..+ .|.+|++..++|.++++++++.+.
T Consensus 59 ~gd~~af~~L~~~y~~~l~~~~~~~~~d~~dAEDivQEvfl~l~~~~~~~~~~~~-~f~~WL~~IarN~~id~~Rk~~~~ 137 (233)
T PRK12538 59 TDDEAAFRLLVERHIDRAYAIALRIVGNRADAEDVVQDTMLKVWTHRGRWQHGRA-KFSTWLYRVVSNRCIDLRRKPRTE 137 (233)
T ss_pred hCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHcccccc-cHHHHHHHHHHHHHHHHHHhhccc
Confidence 4568899999999999999999999999999999999999999999999987554 799999999999999998764210
Q ss_pred ccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCC
Q 007404 441 IRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAE 520 (605)
Q Consensus 441 IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~ 520 (605)
.+ +. . . +.. + ...
T Consensus 138 -~~-------------------------------------------------------~~-~--~------~~~-~-~~~ 150 (233)
T PRK12538 138 -NV-------------------------------------------------------DA-V--P------EVA-D-GKP 150 (233)
T ss_pred -cc-------------------------------------------------------cc-c--c------ccc-c-CCC
Confidence 00 00 0 0 000 0 012
Q ss_pred CHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhh
Q 007404 521 TAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK 596 (605)
Q Consensus 521 spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 596 (605)
.+++.+...+....|..+|..||+++|+||.|+|..| +|++|||+.||+|.++|+++++||+++||+.+...
T Consensus 151 ~~~~~~~~~e~~~~l~~~L~~Lp~~~R~v~~L~~~eg----~s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l~~~ 222 (233)
T PRK12538 151 DAVSVIERNELSDLLEAAMQRLPEQQRIAVILSYHEN----MSNGEIAEVMDTTVAAVESLLKRGRQQLRDLLRRH 222 (233)
T ss_pred CHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHHhcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHh
Confidence 3455555666677899999999999999999999988 99999999999999999999999999999988754
No 59
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=99.87 E-value=3.2e-21 Score=186.56 Aligned_cols=175 Identities=19% Similarity=0.216 Sum_probs=139.8
Q ss_pred hccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcccc
Q 007404 361 NYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRT 440 (605)
Q Consensus 361 ~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~ 440 (605)
.++..|++.|+..|.+.++.+|+++.++..+++|++||+|+.+|+++++|++..+..|.||++..++|.++++++++.+.
T Consensus 5 ~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~~~~~~~~wL~~Iarn~~~d~~Rk~~~~ 84 (185)
T PRK12542 5 NNDYEKMEELYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKNLEKLHSLNTQELKRYILRVAKNKAIDSYRKNKRH 84 (185)
T ss_pred ccCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 35688999999999999999999999999999999999999999999999875445799999999999999999886531
Q ss_pred ccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCC
Q 007404 441 IRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAE 520 (605)
Q Consensus 441 IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~ 520 (605)
... . + +... +.... ..+
T Consensus 85 ~~~------------------~------------------------------------~-----~~~~---~~~~~-~~~ 101 (185)
T PRK12542 85 ETF------------------L------------------------------------E-----EYER---ESIEA-VDE 101 (185)
T ss_pred hhh------------------h------------------------------------h-----hccc---cchhh-hhc
Confidence 000 0 0 0000 00000 011
Q ss_pred CHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhhHhh
Q 007404 521 TAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQ 600 (605)
Q Consensus 521 spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~ 600 (605)
.+++.....+....|..+|..||+++|+||.|+|..+ +|++|||+.||+|.++|+++++||+++||+.+.......
T Consensus 102 ~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g----~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~~~~~ 177 (185)
T PRK12542 102 NIEEWEKRKMSEVQIDTLLKELNESNRQVFKYKVFYN----LTYQEISSVMGITEANVRKQFERARKRVQNMIGGIQHDE 177 (185)
T ss_pred cHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHcccchHH
Confidence 3344344444556799999999999999999999988 999999999999999999999999999999998776666
Q ss_pred hh
Q 007404 601 YA 602 (605)
Q Consensus 601 yl 602 (605)
|+
T Consensus 178 ~~ 179 (185)
T PRK12542 178 FK 179 (185)
T ss_pred HH
Confidence 54
No 60
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=99.86 E-value=2.6e-20 Score=176.78 Aligned_cols=171 Identities=19% Similarity=0.162 Sum_probs=141.9
Q ss_pred HHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhc
Q 007404 358 RRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQ 437 (605)
Q Consensus 358 ~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~ 437 (605)
....++..|++.|++.|.+.|+.+++++.++..+++|++||+++.||++.++|+ .+.+|.+|++..+++.+.+++++.
T Consensus 6 ~~~~~~~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDl~qe~~~~l~~~~~~~~--~~~~~~~~l~~i~~~~~~d~~r~~ 83 (179)
T PRK11924 6 VDATGDKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFN--GKGSARTWLLTIARNVCYDLLRRR 83 (179)
T ss_pred HHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHhhcC--CcchHHHHHHHHHHHHHHHHHHhc
Confidence 344567899999999999999999999999999999999999999999999998 345899999999999999999876
Q ss_pred cccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCC
Q 007404 438 SRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADP 517 (605)
Q Consensus 438 sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~ 517 (605)
.+.... ..+ +. .+...+.
T Consensus 84 ~~~~~~-----------------------------------------------------~~~-----~~----~~~~~~~ 101 (179)
T PRK11924 84 RREKAV-----------------------------------------------------LSD-----DA----LEPEFAE 101 (179)
T ss_pred cccccc-----------------------------------------------------Ccc-----cc----cccccCC
Confidence 541110 000 00 0000000
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhh
Q 007404 518 EAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK 596 (605)
Q Consensus 518 ~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 596 (605)
...+|++.+...+....|..+|..||++++.||.++|..+ +|++|||+.||+|+.+|+++++||+++||+.+...
T Consensus 102 ~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~~----~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l~~~ 176 (179)
T PRK11924 102 TAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEG----LSYREIAEILGVPVGTVKSRLRRARQLLRECLEAQ 176 (179)
T ss_pred ccCCHHHHHhhHHHHHHHHHHHHhCCHHHHHHhhHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 2346888888888889999999999999999999999877 99999999999999999999999999999988754
No 61
>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=99.86 E-value=1.7e-20 Score=180.57 Aligned_cols=180 Identities=14% Similarity=0.152 Sum_probs=138.7
Q ss_pred hccHHHHHHHHHHHHHHHHHHHHHhhC----CCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhh
Q 007404 361 NYGILCKDKMITSNIRLVISIAKNYQG----AGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSD 436 (605)
Q Consensus 361 ~~g~~A~e~LI~~nlrLVvsIAkrY~~----~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~ 436 (605)
.++..|++.|+..|.+.|+.+|++|.+ +..+++|++||+++.+|+++..|++..+.+|.+|++..+++.+.+++++
T Consensus 3 ~~~~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~~~~~~wl~~i~~n~~~d~~r~ 82 (189)
T TIGR02984 3 GGDQEALGELLDRYRNYLRLLARVQLDPRLRRRVDPSDLVQETLLEAHRRFDQFRGKTEGEFAGWLRGILSNVLADALRR 82 (189)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHhhhhcCCccCHHHHHHHHHHHHHHHHHhccCcccchHHHHHHHHHHHHHHHHHHH
Confidence 356889999999999999999999853 5678999999999999999999998666689999999999999999886
Q ss_pred ccc-cccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccC-CCCCCccc
Q 007404 437 QSR-TIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQ-NLKPSEVI 514 (605)
Q Consensus 437 ~sr-~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~-~~~l~d~l 514 (605)
+.+ ..+. + ....+++.....++ ...+.+.+
T Consensus 83 ~~~~~~r~-------------------------~-----------------------~~~~~~~~~~~~~~~~~~~~~~~ 114 (189)
T TIGR02984 83 HLGAQKRD-------------------------I-----------------------RREQSLDAGGRLDESSVRLAAQL 114 (189)
T ss_pred HHHHHhhh-------------------------c-----------------------ccccCCCcccccCCcchhHHHHc
Confidence 521 0000 0 00012221110011 11122222
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 007404 515 ADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 593 (605)
Q Consensus 515 ~D~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 593 (605)
.+ ..++|++.+...+....|..+|..||+++|.||.++|+.+ +|++|||+.||||.++|++.++||+++||+.+
T Consensus 115 ~~-~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~vi~l~~~~g----~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~~l 188 (189)
T TIGR02984 115 AA-DGPSPSQVAARREAAVRLAQALAKLPEDYREVILLRHLEG----LSFAEVAERMDRSEGAVSMLWVRGLARLRQIL 188 (189)
T ss_pred cC-CCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHhcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 22 2336777777777778899999999999999999999877 99999999999999999999999999999875
No 62
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=99.86 E-value=2.1e-20 Score=181.54 Aligned_cols=176 Identities=20% Similarity=0.240 Sum_probs=143.1
Q ss_pred CHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHH
Q 007404 352 DQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVR 431 (605)
Q Consensus 352 d~~~L~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~ 431 (605)
|...+.....++..|++.|+..|.+.|+.+++++.++..+++|++||+|+.+|++.++|++. ..|.+|++..+++.+.
T Consensus 9 ~~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~l~~~~~~~~~~--~~~~~wl~~i~~n~~~ 86 (189)
T PRK12515 9 DEMLLARIAQGDRTAMQTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEGR--SQVSTWLLSIARFKAL 86 (189)
T ss_pred HHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCC--CChHHHHHHHHHHHHH
Confidence 33444555567799999999999999999999999999999999999999999999999974 3799999999999999
Q ss_pred HHHhhccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCC
Q 007404 432 KSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPS 511 (605)
Q Consensus 432 r~ir~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~ 511 (605)
+++++..+. .+ .. + . .
T Consensus 87 d~~r~~~~~-~~-------------------------------------------------------~~----~-~--~- 102 (189)
T PRK12515 87 SALRRRKHE-EI-------------------------------------------------------DD----E-A--A- 102 (189)
T ss_pred HHHHccCCC-CC-------------------------------------------------------cc----c-c--c-
Confidence 999865421 00 00 0 0 0
Q ss_pred cccCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 512 EVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 512 d~l~D~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
....+ ..++|++.....+....+..+|+.||+++|+||.++|..+ +|++|||+.||+|..+|+++++||+++||+
T Consensus 103 ~~~~~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 177 (189)
T PRK12515 103 AAIED-GADTPEVALQKSDTSAALRACLAKLSPAHREIIDLVYYHE----KSVEEVGEIVGIPESTVKTRMFYARKKLAE 177 (189)
T ss_pred cccCC-CCCCHHHHHHhHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 00111 1235666666667778899999999999999999999988 999999999999999999999999999999
Q ss_pred HHhhhhH
Q 007404 592 KKRTKHL 598 (605)
Q Consensus 592 ~l~~~~L 598 (605)
.+...+.
T Consensus 178 ~l~~~~~ 184 (189)
T PRK12515 178 LLKAAGV 184 (189)
T ss_pred HHHHhcc
Confidence 8876543
No 63
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=99.86 E-value=1.8e-20 Score=185.23 Aligned_cols=173 Identities=14% Similarity=0.170 Sum_probs=135.1
Q ss_pred HHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcc
Q 007404 359 RLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQS 438 (605)
Q Consensus 359 ~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~s 438 (605)
...++..+++.|+..|.+.|+.++.++.++..+++|++||+|+.+|++++.|++.++ .|.||++.++||.+.++++++.
T Consensus 32 ~~~~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~~-~~~~wl~~I~rn~~~d~~Rk~~ 110 (206)
T PRK12526 32 AISRDKQAFTHLFQFFAPKIKRFGIKQLGNEAQANELVQETMSNVWRKAHLYNGDKG-AATTWVYTVMRNAAFDMLRKIK 110 (206)
T ss_pred HHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCccc-chhHHHHHHHHHHHHHHHHHhc
Confidence 344678999999999999999999999999899999999999999999999998766 5999999999999999998865
Q ss_pred ccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCC
Q 007404 439 RTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPE 518 (605)
Q Consensus 439 r~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~ 518 (605)
+..... ++ ++.....+.+.+..
T Consensus 111 ~~~~~~-----------------------------------------------------~~-----~~~~~~~~~~~~~~ 132 (206)
T PRK12526 111 AKKEQN-----------------------------------------------------LG-----DDIWPIEQALAESQ 132 (206)
T ss_pred cccccc-----------------------------------------------------cc-----cccchhhhhccccc
Confidence 411000 00 00000000111111
Q ss_pred CCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhh
Q 007404 519 AETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK 596 (605)
Q Consensus 519 ~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 596 (605)
..+. ..........|..+|..||+++|+||.++|+.+ +|++|||+.||+|..+|+.+++||+++||+.+...
T Consensus 133 -~~~~-~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~g----~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~~~ 204 (206)
T PRK12526 133 -SESE-EFSDHLMDKQILSYIEKLPEAQQTVVKGVYFQE----LSQEQLAQQLNVPLGTVKSRLRLALAKLKVQMGEQ 204 (206)
T ss_pred -CchH-HHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhhc
Confidence 1222 222333446789999999999999999999988 99999999999999999999999999999988643
No 64
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=99.86 E-value=6.3e-21 Score=185.17 Aligned_cols=172 Identities=20% Similarity=0.286 Sum_probs=134.0
Q ss_pred CCHHHHHHHHh----ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHH
Q 007404 351 VDQRELRRRLN----YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWI 426 (605)
Q Consensus 351 ~d~~~L~~~l~----~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wI 426 (605)
++.+.|...++ ++..|++.|+..|.+.|+.+|.+|.++..+++|++||+|+.+|+++++|++. ..|.+|++.++
T Consensus 8 ~~~~~li~~~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~f~~l~~~~~~~~~~--~~~~~wl~~ia 85 (188)
T PRK09640 8 LNDEELVARVHVELFHVTRAYEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGK--SKFKTWLYSIT 85 (188)
T ss_pred CCHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHHHhcCC--CcchHHHHHHH
Confidence 44444555544 4799999999999999999999999999999999999999999999999863 47999999999
Q ss_pred HHHHHHHHhhccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccC
Q 007404 427 KQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQ 506 (605)
Q Consensus 427 RqaI~r~ir~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~ 506 (605)
+|.+.+++++..+.... ..+...
T Consensus 86 ~n~~~d~~R~~~~~~~~-----------------------------------------------------~~~~~~---- 108 (188)
T PRK09640 86 YNECITQYRKERRKRRL-----------------------------------------------------MDALSL---- 108 (188)
T ss_pred HHHHHHHHHHhcccccC-----------------------------------------------------cchhhh----
Confidence 99999999875431100 000000
Q ss_pred CCCCCcccCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 007404 507 NLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAF 586 (605)
Q Consensus 507 ~~~l~d~l~D~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RAL 586 (605)
+...++. ++.....+....|..+|+.||+++|+||.|+|..+ +|++|||+.||||..+|+.++.||+
T Consensus 109 -----~~~~~~~----~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g----~s~~EIA~~lgis~~tV~~~l~Ra~ 175 (188)
T PRK09640 109 -----DPLEEAS----EEKAPKPEERGGLDRWLVHVNPIDREILVLRFVAE----LEFQEIADIMHMGLSATKMRYKRAL 175 (188)
T ss_pred -----ccccccc----ccccccHHHHHHHHHHHHhcChhheeeeeeHHhcC----CCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 0000000 00011123446689999999999999999999988 9999999999999999999999999
Q ss_pred HHHHhHHh
Q 007404 587 RKLKNKKR 594 (605)
Q Consensus 587 kKLR~~l~ 594 (605)
++||+.+.
T Consensus 176 ~~Lr~~l~ 183 (188)
T PRK09640 176 DKLREKFA 183 (188)
T ss_pred HHHHHHHH
Confidence 99999764
No 65
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=99.86 E-value=2.9e-20 Score=179.19 Aligned_cols=166 Identities=16% Similarity=0.242 Sum_probs=134.9
Q ss_pred hccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcccc
Q 007404 361 NYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRT 440 (605)
Q Consensus 361 ~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~ 440 (605)
.++..|++.|+..|.+.|+.+++.|.++..+++|++||+|+.+|+++.+|++.. .|.+|++..+++.+.+++++..+.
T Consensus 3 ~~d~~af~~l~~~~~~~l~~~~~~~~~~~~daeDl~Qevfl~l~~~~~~~~~~~--~f~~wl~~iarn~~~~~~r~~~~~ 80 (179)
T PRK12543 3 SGDQEAFSEIYDVTIQEVYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKYDSNR--PFRFWLIGLVIKQIHSWRRKRWRR 80 (179)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHcCCCC--ChHHHHHHHHHHHHHHHHHhhccc
Confidence 356789999999999999999999999999999999999999999999999864 699999999999999988765421
Q ss_pred ccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCC
Q 007404 441 IRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAE 520 (605)
Q Consensus 441 IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~ 520 (605)
.+. ++.. . + ..+. ....
T Consensus 81 ~~~------------------------------------------------------~~~~---~-~--~~~~---~~~~ 97 (179)
T PRK12543 81 FRI------------------------------------------------------FEKA---E-E--QRKP---VSID 97 (179)
T ss_pred ccc------------------------------------------------------cccc---c-c--cccc---cccc
Confidence 000 0000 0 0 0000 0111
Q ss_pred CHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhh
Q 007404 521 TAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK 596 (605)
Q Consensus 521 spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 596 (605)
.|+. +...+....|..+|..||+++|+||.|+|..| +|++|||+.||||..+|+..++||+++||+.+...
T Consensus 98 ~~~~-~~~~~~~~~l~~~l~~Lp~~~r~i~~l~~~e~----~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~ 168 (179)
T PRK12543 98 FSED-VLSKESNQELIELIHKLPYKLRQVIILRYLHD----YSQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQIE 168 (179)
T ss_pred ChHH-HHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcc----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444 55666778899999999999999999999988 99999999999999999999999999999998754
No 66
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=99.85 E-value=5.4e-20 Score=179.71 Aligned_cols=169 Identities=14% Similarity=0.134 Sum_probs=137.1
Q ss_pred HHHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHH
Q 007404 354 RELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKS 433 (605)
Q Consensus 354 ~~L~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ 433 (605)
..+.....++..+++.|++.|.+.|++++.++.++..+++|++||+|+.+|+.+++|++.. .|.+|++..+++.+.++
T Consensus 16 ~l~~~~~~gd~~~~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQEvfl~l~~~~~~~~~~~--~f~~wL~~i~rn~~~d~ 93 (192)
T PRK09643 16 ELLAAHVAGDRYAFGELFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHRAAGSFRGDA--AVSSWLHRIVVNACLDR 93 (192)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCCCC--ccHHHHHHHHHHHHHHH
Confidence 3445555677999999999999999999999999999999999999999999999999753 69999999999999999
Q ss_pred HhhccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcc
Q 007404 434 LSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEV 513 (605)
Q Consensus 434 ir~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~ 513 (605)
+++..+..+. +++. . . +
T Consensus 94 ~Rk~~~~~~~-----------------------------------------------------~~~~----~-~----~- 110 (192)
T PRK09643 94 LRRAKARPTV-----------------------------------------------------PLDD----V-Y----P- 110 (192)
T ss_pred HHccccCCCC-----------------------------------------------------Cccc----c-c----c-
Confidence 9876531100 0000 0 0 0
Q ss_pred cCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 007404 514 IADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 593 (605)
Q Consensus 514 l~D~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 593 (605)
... .+++.+...+....|..+|+.||+++|+||.|+|..+ +|++|||+.||+|..+|+.++.||+++||+.+
T Consensus 111 ~~~----~~~~~~~~~e~~~~l~~~l~~Lp~~~r~i~~l~~~~g----~s~~EIA~~lg~s~~tV~~rl~rar~~Lr~~l 182 (192)
T PRK09643 111 VAQ----LERDPTARVETALAVQRALMRLPVEQRAALVAVDMQG----YSVADAARMLGVAEGTVKSRCARGRARLAELL 182 (192)
T ss_pred ccC----CcccHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 000 1222334445567799999999999999999999987 99999999999999999999999999999988
Q ss_pred hh
Q 007404 594 RT 595 (605)
Q Consensus 594 ~~ 595 (605)
..
T Consensus 183 ~~ 184 (192)
T PRK09643 183 GY 184 (192)
T ss_pred HH
Confidence 64
No 67
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=99.85 E-value=4.1e-20 Score=176.44 Aligned_cols=164 Identities=13% Similarity=0.094 Sum_probs=131.3
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccc
Q 007404 362 YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI 441 (605)
Q Consensus 362 ~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~I 441 (605)
++..+++.|+..|.+.|+.+|.++.++..+++|++||.|+.+|+..++|++.. ..|.+|++..++|.+.++++++.+..
T Consensus 6 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~~~AeD~vQevfl~~~~~~~~~~~~~-~~~~~wL~~iarn~~~d~~Rk~~~~~ 84 (173)
T PRK09645 6 AEAALMRALYDEHAAPLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLADTG-RSARAWLFTVARNLVIDERRSARARP 84 (173)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCccc-ccHHHHHHHHHHHHHHHHHHhhcccc
Confidence 45889999999999999999999999989999999999999999999997533 36999999999999999998764310
Q ss_pred cccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCC
Q 007404 442 RLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAET 521 (605)
Q Consensus 442 RlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~s 521 (605)
.. .. ++.. + .++. .
T Consensus 85 ~~-----------------------------------------------------~~------~~~~---~-~~~~---~ 98 (173)
T PRK09645 85 VE-----------------------------------------------------GG------DDVL---G-VPEQ---S 98 (173)
T ss_pred cc-----------------------------------------------------cc------cccc---c-CCCC---C
Confidence 00 00 0000 0 0011 1
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhh
Q 007404 522 AEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK 596 (605)
Q Consensus 522 pEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 596 (605)
+++..........|..+|+.||+++|+||.|+|+.| +|++|||+.||+|..+|+.+++||+++||+.+...
T Consensus 99 ~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~L~~~~g----~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~ 169 (173)
T PRK09645 99 APDEVDRALDRLLVADALAQLSPEHRAVLVRSYYRG----WSTAQIAADLGIPEGTVKSRLHYALRALRLALQER 169 (173)
T ss_pred CchHHHHHhHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhhcc
Confidence 122233334456789999999999999999999988 99999999999999999999999999999988653
No 68
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=99.85 E-value=4.1e-20 Score=180.51 Aligned_cols=176 Identities=18% Similarity=0.147 Sum_probs=134.9
Q ss_pred HHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHh
Q 007404 356 LRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLS 435 (605)
Q Consensus 356 L~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir 435 (605)
+.+...++..+++.|+..|.+.|+.+|.++.++..+++|++||+|+.+|+..++|++.++ .|.+|++..++|.++++++
T Consensus 18 i~~~~~~d~~af~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQev~l~l~~~~~~~~~~~~-~~~~wL~~iarn~~ld~~R 96 (194)
T PRK12531 18 MEKVKSRDKQAFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKAHLFDGQKS-ALSTWIYTIIRNLCFDLLR 96 (194)
T ss_pred HHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCcccc-hHHHHHHHHHHHHHHHHHH
Confidence 344445678999999999999999999999999899999999999999999999997554 6999999999999999998
Q ss_pred hccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccC
Q 007404 436 DQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIA 515 (605)
Q Consensus 436 ~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~ 515 (605)
+..+.... ...+.... + . .......
T Consensus 97 k~~~~~~~----------------------------------------------------~~~~~~~~-~-~-~~~~~~~ 121 (194)
T PRK12531 97 KQKGKDLH----------------------------------------------------IHADDIWP-S-D-YYPPDLV 121 (194)
T ss_pred Hhcccccc----------------------------------------------------cchhhccc-c-c-ccccccc
Confidence 86531100 00000000 0 0 0000000
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 007404 516 DPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT 595 (605)
Q Consensus 516 D~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 595 (605)
+ ...++.. .....+..+|..||+++|+||.|+|..+ +|++|||+.||||.++|+.+++||+++||+.+..
T Consensus 122 ~--~~~~e~~----~~~~~l~~~l~~Lp~~~r~v~~l~~~eg----~s~~EIA~~lgis~~tVk~rl~ra~~~Lr~~l~~ 191 (194)
T PRK12531 122 D--HYSPEQD----MLKEQVMKFLDRLPKAQRDVLQAVYLEE----LPHQQVAEMFDIPLGTVKSRLRLAVEKLRHSMDA 191 (194)
T ss_pred c--ccCHHHH----HHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHhhh
Confidence 0 1123322 2335688899999999999999999987 9999999999999999999999999999998875
Q ss_pred hh
Q 007404 596 KH 597 (605)
Q Consensus 596 ~~ 597 (605)
..
T Consensus 192 ~~ 193 (194)
T PRK12531 192 ES 193 (194)
T ss_pred cc
Confidence 43
No 69
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=99.84 E-value=8.7e-20 Score=166.28 Aligned_cols=157 Identities=23% Similarity=0.346 Sum_probs=132.5
Q ss_pred HHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccc
Q 007404 366 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPF 445 (605)
Q Consensus 366 A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~ 445 (605)
|++.|+..|.++|+++++++.+++.+.+|++||+++++|++++.|++. .+|.+|+.+++++.+.++++++.+ .+.
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 789999999999999999999999999999999999999999999998 589999999999999999998765 111
Q ss_pred cHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHHH
Q 007404 446 HMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDL 525 (605)
Q Consensus 446 ~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~ 525 (605)
.. ... . ... ...+.+++.
T Consensus 77 ~~---------------------------------------------------~~~---~-------~~~-~~~~~~~~~ 94 (158)
T TIGR02937 77 EL---------------------------------------------------DLL---E-------ELL-DSDPSPEEE 94 (158)
T ss_pred ch---------------------------------------------------hhh---h-------hcc-cccCCHHHH
Confidence 00 000 0 000 112256666
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 007404 526 LIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 593 (605)
Q Consensus 526 l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 593 (605)
.........|..+++.||++++.||.++|..+ +|+.|||+.||+|+.+|+++..++++|||+.+
T Consensus 95 ~~~~~~~~~l~~~l~~L~~~~~~ii~~~~~~g----~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~~l 158 (158)
T TIGR02937 95 LEQEEEREALREALEKLPEREREVLVLRYLEG----LSYKEIAEILGISVGTVKRRLKRARKKLRELL 158 (158)
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHhhHHhcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence 77777788899999999999999999998877 99999999999999999999999999999753
No 70
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=99.84 E-value=8.2e-20 Score=176.22 Aligned_cols=165 Identities=16% Similarity=0.136 Sum_probs=135.6
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccc
Q 007404 362 YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI 441 (605)
Q Consensus 362 ~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~I 441 (605)
.+..|++.|+..|.+.|+++++++.++..+++|++||+|+.+|+++++|++. ..|.+|++..+++.+.+++++..+..
T Consensus 13 ~~~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQd~fl~l~~~~~~~~~~--~~~~awl~~ia~n~~~d~~Rk~~~~~ 90 (179)
T PRK09415 13 DKEDLIDEIMNEYGQEVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYKGK--SSLKTWLYRIAINHCKDYLKSWHNKK 90 (179)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcCCC--cccHHHHHHHHHHHHHHHHHhhcccc
Confidence 3478999999999999999999999999999999999999999999999874 36999999999999999998754311
Q ss_pred cccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCC
Q 007404 442 RLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAET 521 (605)
Q Consensus 442 RlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~s 521 (605)
..+ .+. ...+... ..++
T Consensus 91 ~~~-----------------------------------------------------~~~--------~~~~~~~--~~~~ 107 (179)
T PRK09415 91 VIV-----------------------------------------------------TED--------IFTYMES--QKES 107 (179)
T ss_pred ccc-----------------------------------------------------ccc--------ccccccc--cccC
Confidence 000 000 0000001 1125
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 007404 522 AEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT 595 (605)
Q Consensus 522 pEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 595 (605)
|++.+...+....|..+|..||+++|+||.|+|+.| +|++|||+.||||.++|++++.||+++||+.+..
T Consensus 108 ~e~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g----~s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~l~~ 177 (179)
T PRK09415 108 VEEEVIQNAEDERLASAVMSLPIKYREVIYLFYYEE----LSIKEIAEVTGVNENTVKTRLKKAKELLKKGLEE 177 (179)
T ss_pred cHHHHHHHHHHHHHHHHHHhCCHHHhhHhHhHHhcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 666666677778899999999999999999999988 9999999999999999999999999999997753
No 71
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=99.84 E-value=5.2e-20 Score=175.95 Aligned_cols=165 Identities=15% Similarity=0.140 Sum_probs=131.0
Q ss_pred HHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhh
Q 007404 357 RRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSD 436 (605)
Q Consensus 357 ~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~ 436 (605)
.....++..|++.|+..|.+.|+.+|++|.++..+++|++||+|+++|++++.|++. .+|.+|++..+++.+.+++++
T Consensus 10 ~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~r~ 87 (176)
T PRK09638 10 QKAKKGDDAALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSFQGR--SKFSTWLISIASRLYKDHLRK 87 (176)
T ss_pred HHHHCCCHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHHHHHHHHH
Confidence 444556789999999999999999999999999999999999999999999999874 479999999999999999987
Q ss_pred ccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCC
Q 007404 437 QSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIAD 516 (605)
Q Consensus 437 ~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D 516 (605)
..+..... +.+ .+ ...+
T Consensus 88 ~~~~~~~~---------------------------~~~-----------------------~~-------------~~~~ 104 (176)
T PRK09638 88 QKREKLRL---------------------------QRA-----------------------KE-------------ETLR 104 (176)
T ss_pred hccccchh---------------------------hhc-----------------------cc-------------ccCC
Confidence 65311000 000 00 0000
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 007404 517 PEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 593 (605)
Q Consensus 517 ~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 593 (605)
.. .. +..........|..+|..||+++|+||.++|..| +|++|||+.||+|..+|++.++||+++||+.+
T Consensus 105 ~~--~~-~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g----~s~~eIA~~l~is~~~V~~~l~ra~~~l~~~l 174 (176)
T PRK09638 105 KE--KW-EAAIKGAEWSEMLDALSKLDPEFRAPVILKHYYG----YTYEEIAKMLNIPEGTVKSRVHHGIKQLRKEW 174 (176)
T ss_pred cc--ch-HHHHHhhhHHHHHHHHHcCCHHHhheeeehhhcC----CCHHHHHHHHCCChhHHHHHHHHHHHHHHHHh
Confidence 00 00 1122233445689999999999999999999877 99999999999999999999999999999976
No 72
>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=99.84 E-value=1.9e-19 Score=183.23 Aligned_cols=182 Identities=13% Similarity=0.155 Sum_probs=141.2
Q ss_pred CCHHHHHH-HHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHH-------hhhccCCcCCCcchhHH
Q 007404 351 VDQRELRR-RLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVR-------GAEKFDASKGFKFSTYA 422 (605)
Q Consensus 351 ~d~~~L~~-~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLir-------A~ekFDp~kG~rFSTYA 422 (605)
.++..|.. ...++..|++.|+..|.+.|+.+++++.++..+++|++||+|+.+|. .+.+|++. ..|.||+
T Consensus 24 ~~d~~Li~~~~~gd~~Af~~L~~~y~~~l~~~~~~~~~~~~dAEDivQEvFlkl~~~~~~~~~~~~~~~~~--~~~~tWL 101 (244)
T TIGR03001 24 AADLYLACACAQGEPAALAALERHVLSKVPARLAGLRPPTAFVDEVLQRLRQRLLVPRAERPPRIAEYSGR--GPLLSWV 101 (244)
T ss_pred ccHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhccchhhhhhccCCC--CchHhHH
Confidence 34444444 45566899999999999999999999999999999999999999994 78889864 3699999
Q ss_pred HHHHHHHHHHHHhhccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccc
Q 007404 423 HWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKI 502 (605)
Q Consensus 423 ~~wIRqaI~r~ir~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i 502 (605)
+.+++|.++++++++.+...+ +
T Consensus 102 ~~Ia~N~~id~lRk~~r~~~~-------------------------------------------------------~--- 123 (244)
T TIGR03001 102 RIVATRIALELQAQERRHSPV-------------------------------------------------------E--- 123 (244)
T ss_pred HHHHHHHHHHHHHHhcccCcc-------------------------------------------------------c---
Confidence 999999999999875431100 0
Q ss_pred cccCCCCCCcccCCCCCCCHHHHHHH----HHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHH
Q 007404 503 GINQNLKPSEVIADPEAETAEDLLIK----KFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERI 578 (605)
Q Consensus 503 ~~d~~~~l~d~l~D~~~~spEe~l~~----~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerV 578 (605)
+.+ ...+. .+. ..+|++.+.. .+....|..+|++||+++|+||.|+|..| +|++|||++||||.++|
T Consensus 124 --~~~-~~~~~-~~~-~~~~e~~~~~~e~~~e~~~~l~~aL~~Lp~~~R~v~~L~~~eg----~S~~EIA~~Lgis~~TV 194 (244)
T TIGR03001 124 --EPT-ELAAL-PAP-GSDPELDLLRERYRQDFRQALREALAALSERERHLLRLHFVDG----LSMDRIGAMYQVHRSTV 194 (244)
T ss_pred --ccc-ccccc-cCC-CCCHHHHHHHHhhHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHH
Confidence 000 00000 011 1234444432 23567799999999999999999999988 99999999999999999
Q ss_pred HHHHHHHHHHHHhHHhhhhHhhh
Q 007404 579 RQIESSAFRKLKNKKRTKHLMQY 601 (605)
Q Consensus 579 Rqie~RALkKLR~~l~~~~L~~y 601 (605)
+.+++||+++||+.+.+.....|
T Consensus 195 k~rl~RAr~~Lr~~l~~~~~~~~ 217 (244)
T TIGR03001 195 SRWVAQARERLLERTRRRLAERL 217 (244)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhc
Confidence 99999999999999987765554
No 73
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=99.84 E-value=1.1e-19 Score=176.70 Aligned_cols=181 Identities=15% Similarity=0.162 Sum_probs=137.9
Q ss_pred HHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccc
Q 007404 366 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPF 445 (605)
Q Consensus 366 A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~ 445 (605)
+++.|+..|.+.|+.+|+++.++..+++|++||.|+.+|+.+++|++. .+|.+|++..++|.++++++++.+....+.
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 689999999999999999999999999999999999999999999865 369999999999999999998764221100
Q ss_pred cHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHHH
Q 007404 446 HMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDL 525 (605)
Q Consensus 446 ~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~ 525 (605)
.. .......++ ++... +.+ ......++. ..+|++.
T Consensus 81 ~~------------------~~~~~~~~~-----------------------~~~~~--~~~-~~~~~~~~~-~~~~~~~ 115 (191)
T PRK12520 81 DD------------------ADEQSDDDL-----------------------FDALF--AAD-GHYREPPSD-WGDPDAA 115 (191)
T ss_pred cc------------------cccchhhhh-----------------------hhhhc--ccc-cccccCccc-cCCHHHH
Confidence 00 000000000 00000 000 000011111 2367777
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhh
Q 007404 526 LIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKH 597 (605)
Q Consensus 526 l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~ 597 (605)
+...+....|..+|..||+++|.||.|+|..+ +|++|||+.||+|.++|+++++||+++||+.+....
T Consensus 116 ~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~~~g----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~ 183 (191)
T PRK12520 116 LSRREFFEVLQACVDRLPPRTGRVFMMREWLE----LETEEICQELQITATNAWVLLYRARMRLRECLDLHW 183 (191)
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 77777778899999999999999999999988 999999999999999999999999999999998765
No 74
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=99.84 E-value=1e-19 Score=174.03 Aligned_cols=167 Identities=11% Similarity=0.156 Sum_probs=131.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcccccccc
Q 007404 365 LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLP 444 (605)
Q Consensus 365 ~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP 444 (605)
..+++|+..|.++|+.+|++|.++..+++|++||+++.+|++.++|++.. +|.+|++..++|.+.++++++.+....+
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 35899999999999999999999999999999999999999999999854 7999999999999999998766421100
Q ss_pred ccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHH
Q 007404 445 FHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAED 524 (605)
Q Consensus 445 ~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe 524 (605)
.. . .+. +....+ ...+. ...++.
T Consensus 81 ~~-------------------------------------------------~-~~~----~~~~~~--~~~~~-~~~~~~ 103 (173)
T PRK12522 81 LD-------------------------------------------------L-FHK----EDGGEI--EFADD-VNISEE 103 (173)
T ss_pred cc-------------------------------------------------c-cch----hhhhhh--ccccC-CCChHH
Confidence 00 0 000 000000 00011 112333
Q ss_pred HHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 007404 525 LLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT 595 (605)
Q Consensus 525 ~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 595 (605)
....+..+.|..+|..||+++++||.|+|..| +|++|||+.||+|.++|+.+++||+++||+.+..
T Consensus 104 -~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~~----~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~~ 169 (173)
T PRK12522 104 -FIQKVEAEMIREVIQLLNEKYKTVLVLYYYEQ----YSYKEMSEILNIPIGTVKYRLNYAKKQMREHLEG 169 (173)
T ss_pred -HHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 44456678899999999999999999999988 9999999999999999999999999999997754
No 75
>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=99.84 E-value=5.3e-20 Score=171.43 Aligned_cols=160 Identities=17% Similarity=0.172 Sum_probs=130.1
Q ss_pred HHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccc
Q 007404 366 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPF 445 (605)
Q Consensus 366 A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~ 445 (605)
|+++|+..|.+.|+++++++.++..+.+|++||+++++|+.+.+|++. .+|.+|++.++|+.+.+++++..+....
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 789999999999999999999998999999999999999999999874 3799999999999999999876531000
Q ss_pred cHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHHH
Q 007404 446 HMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDL 525 (605)
Q Consensus 446 ~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~ 525 (605)
.. .+ .+... + ....+++++.
T Consensus 78 ----------------~~---------~~----------------------------~~~~~----~---~~~~~~~~~~ 97 (161)
T TIGR02985 78 ----------------QE---------EI----------------------------LEIEV----D---ELSENDPEEE 97 (161)
T ss_pred ----------------HH---------HH----------------------------Hhhcc----c---ccCCCCcHHH
Confidence 00 00 00000 0 0011245666
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 007404 526 LIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 593 (605)
Q Consensus 526 l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 593 (605)
+...+....|..++..||+++++||.++|..+ +|.+|||+.||+|+++|+++++||+++||+.+
T Consensus 98 ~~~~e~~~~l~~~l~~L~~~~r~il~l~~~~~----~~~~eIA~~lgis~~tv~~~~~ra~~~Lr~~l 161 (161)
T TIGR02985 98 LEAKELQLIIYKAIEKLPEQCRKIFILSRFEG----KSYKEIAEELGISVKTVEYHISKALKELRKEL 161 (161)
T ss_pred HHHHHHHHHHHHHHHHCCHHHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence 66677778899999999999999999999877 99999999999999999999999999999753
No 76
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=99.84 E-value=1.3e-19 Score=172.44 Aligned_cols=163 Identities=20% Similarity=0.236 Sum_probs=130.4
Q ss_pred HHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHH
Q 007404 355 ELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSL 434 (605)
Q Consensus 355 ~L~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~i 434 (605)
.+.....++..|++.|+..|.+.|++++.++.++..+++|++||+|+.+|+..++|++.. +|.+|++..+++.+++++
T Consensus 6 l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~l~~~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~ 83 (169)
T TIGR02954 6 LVKKAKRGNKPAFESLIKKHKEKLYKTAFIYVKNEHDALDVIQETVYKAYLSIDKLKHPK--YFNTWLTRILINECIDLL 83 (169)
T ss_pred HHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhccCcc--ccHHHHHHHHHHHHHHHH
Confidence 334445567899999999999999999999999999999999999999999999999753 699999999999999999
Q ss_pred hhccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCccc
Q 007404 435 SDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVI 514 (605)
Q Consensus 435 r~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l 514 (605)
++..+... ++... . .
T Consensus 84 R~~~~~~~-------------------------------------------------------~~~~~------~----~ 98 (169)
T TIGR02954 84 KKKKKVIP-------------------------------------------------------FDPNT------S----I 98 (169)
T ss_pred HhcCCcCc-------------------------------------------------------ccccc------c----c
Confidence 87643100 00000 0 0
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404 515 ADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR 594 (605)
Q Consensus 515 ~D~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 594 (605)
.+. .++. .. .....|..+|..||+++|+||.++|+.| +|++|||+.||||..+|+.+++||+++||+.+.
T Consensus 99 ~~~---~~~~--~~-~~~~~l~~~l~~L~~~~r~i~~l~~~~g----~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~~l~ 168 (169)
T TIGR02954 99 EKG---ECET--HA-DSRLDLYKAIDTLNDKYQTAIILRYYHD----LTIKEIAEVMNKPEGTVKTYLHRALKKLKKRLE 168 (169)
T ss_pred ccc---hhhh--ch-HHHHHHHHHHHhCCHHHhHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Confidence 000 0110 01 1123688999999999999999999988 999999999999999999999999999999763
No 77
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=99.84 E-value=9.3e-20 Score=175.97 Aligned_cols=168 Identities=20% Similarity=0.201 Sum_probs=131.7
Q ss_pred HHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhC-CCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHH
Q 007404 355 ELRRRLNYGILCKDKMITSNIRLVISIAKNYQG-AGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKS 433 (605)
Q Consensus 355 ~L~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~-~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ 433 (605)
.+.....++..|++.|+..|.+.|+.++.++.+ ...+++|++||+|+.||+.++.|++. ..|.+|++..++|.+.++
T Consensus 11 ~~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~~aeDlvQevfl~l~~~~~~~~~~--~~~~~wl~~iarN~~~d~ 88 (181)
T PRK12536 11 LLLRGLAGDAAAYRQFLSELAAHLRGFLRRRLPQLPDEVEDLVQEILLAVHNARHTYRAD--QPLTAWVHAIARYKLMDF 88 (181)
T ss_pred HHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCChhhHHHHHHHHHHHHHHhHHhcCCC--CchHHHHHHHHHHHHHHH
Confidence 345556678999999999999999999998764 57899999999999999999999974 369999999999999999
Q ss_pred HhhccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcc
Q 007404 434 LSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEV 513 (605)
Q Consensus 434 ir~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~ 513 (605)
++++.+.... ..+++. . .+.
T Consensus 89 ~Rk~~~~~~~---------------------------------------------------~~~~~~----~-----~~~ 108 (181)
T PRK12536 89 LRSRARREAL---------------------------------------------------HDPLDD----E-----SEL 108 (181)
T ss_pred HHHHhccccc---------------------------------------------------cCCccc----h-----hhh
Confidence 9886431000 000000 0 000
Q ss_pred cCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 007404 514 IADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 593 (605)
Q Consensus 514 l~D~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 593 (605)
..+... .+ .+....|..+|+.||+++|.||.++|..| +|++|||+.||+|+++|+.+++||+++||+.+
T Consensus 109 ~~~~~~-~~------~~~~~~l~~~l~~L~~~~r~v~~l~~~~g----~s~~EIA~~l~is~~tV~~~l~rar~~Lr~~l 177 (181)
T PRK12536 109 FATSDD-EA------AEARRDLGKLLEQLPDRQRLPIVHVKLEG----LSVAETAQLTGLSESAVKVGIHRGLKALAAKI 177 (181)
T ss_pred cCCCCc-ch------HHHHHHHHHHHHHCCHHHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 001110 11 12345689999999999999999999888 99999999999999999999999999999987
Q ss_pred hh
Q 007404 594 RT 595 (605)
Q Consensus 594 ~~ 595 (605)
..
T Consensus 178 ~~ 179 (181)
T PRK12536 178 RG 179 (181)
T ss_pred cC
Confidence 64
No 78
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=99.83 E-value=2.9e-19 Score=172.81 Aligned_cols=172 Identities=21% Similarity=0.277 Sum_probs=137.9
Q ss_pred HHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhh
Q 007404 357 RRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSD 436 (605)
Q Consensus 357 ~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~ 436 (605)
.....++..++..++..|.+.++.+++++.++..+++||+||+|+.+|+++..| ... ..|.||++.+++|.+++++++
T Consensus 7 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~dAeDlvQE~~lr~~~~~~~~-~~~-~~~~~wl~~Ia~n~~iD~~R~ 84 (182)
T COG1595 7 AEALRGDRAAFEELLERLRPRLRRLARRLLGDRADAEDLVQETFLRAWRAIDSF-RGR-SSFKAWLYRIARNLAIDRLRK 84 (182)
T ss_pred HHHHhcchHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhc-CCC-CchHHHHHHHHHHHHHHHHHH
Confidence 344556788999999999999999999999988899999999999999999999 433 479999999999999999998
Q ss_pred ccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCC
Q 007404 437 QSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIAD 516 (605)
Q Consensus 437 ~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D 516 (605)
..+..... + +.+. .+...+
T Consensus 85 ~~r~~~~~------------------------------------------------------~-----~~~~--~~~~~~ 103 (182)
T COG1595 85 RKRRRARV------------------------------------------------------E-----EADL--LPEEAD 103 (182)
T ss_pred hccccccc------------------------------------------------------c-----cccc--cccccC
Confidence 76522210 0 0000 000011
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhh
Q 007404 517 PEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK 596 (605)
Q Consensus 517 ~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 596 (605)
...+.. +.+...+....|..+|..||+++|++|.|+|+.| +|++|||+.||||.++|+.+++||+++||+.+...
T Consensus 104 ~~~~~~-~~~~~~~~~~~l~~al~~Lp~~~R~~~~l~~~~g----ls~~EIA~~l~i~~~tVks~l~ra~~~l~~~l~~~ 178 (182)
T COG1595 104 PAPDLA-ELLLAEEELERLRRALARLPPRQREAFLLRYLEG----LSYEEIAEILGISVGTVKSRLHRARKKLREQLEEA 178 (182)
T ss_pred cccccc-hHHHHHHHHHHHHHHHHhCCHHHhHHhhhHhhcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhhc
Confidence 111011 2455667778899999999999999999999988 99999999999999999999999999999988653
No 79
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=99.83 E-value=2.2e-19 Score=173.75 Aligned_cols=166 Identities=13% Similarity=0.109 Sum_probs=130.1
Q ss_pred HHHHHhccHHHHHHHHHHHHHHHHHHHH----HhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHH
Q 007404 356 LRRRLNYGILCKDKMITSNIRLVISIAK----NYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVR 431 (605)
Q Consensus 356 L~~~l~~g~~A~e~LI~~nlrLVvsIAk----rY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~ 431 (605)
+.+...++..|++.|+..|.+.|+.+++ +|.++..+++|++||+++.+|++++.|++.. .|.+|++..++|.+.
T Consensus 12 ~~~~~~gd~~af~~l~~~~~~~l~~~~~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~~--~f~~wl~~i~~n~~~ 89 (184)
T PRK12539 12 MLASLDGDAAAHRALLERLSGHLRAYYKGKLARIGRGAEEAEDLVQEALMAIHTRRHTYDPEQ--PLTPWVYAIARYKLI 89 (184)
T ss_pred HHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHhhcCCCC--ChHHHHHHHHHHHHH
Confidence 3445567789999999999999999987 4557789999999999999999999999753 699999999999999
Q ss_pred HHHhhccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCC
Q 007404 432 KSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPS 511 (605)
Q Consensus 432 r~ir~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~ 511 (605)
+++++..+.. .+ .+++ +..
T Consensus 90 d~~R~~~~~~-~~---------------------------------------------------~~~~------~~~--- 108 (184)
T PRK12539 90 DHLRRTRASL-AD---------------------------------------------------VPID------DAD--- 108 (184)
T ss_pred HHHHHHhccc-cc---------------------------------------------------cChh------hhc---
Confidence 9998754310 00 0000 000
Q ss_pred cccCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 512 EVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 512 d~l~D~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
+.... .+ ....+....|..+|..||+++|+||.|+|..| +|++|||+.||+|..+|+++++||+++||+
T Consensus 109 ~~~~~----~~---~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g----~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 177 (184)
T PRK12539 109 ELVAH----DD---HAAVESTLDLGRLLARLPEKMRLAIQAVKLEG----LSVAEAATRSGMSESAVKVSVHRGLKALAA 177 (184)
T ss_pred cccCC----cH---HhhHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CcHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 00000 01 11223345789999999999999999999887 999999999999999999999999999999
Q ss_pred HHhh
Q 007404 592 KKRT 595 (605)
Q Consensus 592 ~l~~ 595 (605)
.+..
T Consensus 178 ~l~~ 181 (184)
T PRK12539 178 LIGR 181 (184)
T ss_pred HHhh
Confidence 8754
No 80
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=99.83 E-value=2.4e-19 Score=172.42 Aligned_cols=167 Identities=22% Similarity=0.218 Sum_probs=124.1
Q ss_pred HHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCC-----CHHHHHHHHHHHHHH-hhhccCCcCCCcchhHHHHHHHHHHH
Q 007404 358 RRLNYGILCKDKMITSNIRLVISIAKNYQGAGM-----NLQDLVQEGCRGLVR-GAEKFDASKGFKFSTYAHWWIKQAVR 431 (605)
Q Consensus 358 ~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~-----d~eDLIQEG~IGLir-A~ekFDp~kG~rFSTYA~~wIRqaI~ 431 (605)
....++..|++.|+..|.+.|+.+|++|.++.. +++|++||+|+.+|+ ..++|++. ..|.+|++.+++|.+.
T Consensus 10 ~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~AeDlvQevfl~~~~~~~~~~~~~--~~~~~wl~~i~~n~~~ 87 (183)
T TIGR02999 10 QWQNGDAAARDQLFPQLYQELRRIARRQLRRERSGQTLQTTALVHEAYLRLSDQDEQKWDDR--AHFFAAAAKAMRRILV 87 (183)
T ss_pred HHHcCCHHHHHHHHHHHHHHHHHHHHHHhhcccccccchHHHHHHHHHHHHhhcccCCCCch--HHHHHHHHHHHHHHHH
Confidence 334466889999999999999999999998877 899999999999998 78889764 3699999999999999
Q ss_pred HHHhhccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCC
Q 007404 432 KSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPS 511 (605)
Q Consensus 432 r~ir~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~ 511 (605)
++++++.+..+.. ...+.. +.
T Consensus 88 d~~R~~~~~~~~~---------------------------------------------------~~~~~~--------~~ 108 (183)
T TIGR02999 88 DHARRRRAQKRGG---------------------------------------------------GAVRVP--------LD 108 (183)
T ss_pred HHHHHHHHHhccC---------------------------------------------------Cccccc--------cc
Confidence 9998754310000 000000 00
Q ss_pred cccCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 512 EVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 512 d~l~D~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
+..++... ...+ .......+...|+.||+++|+||.|+|..| +|++|||+.||||.++|+.+++||+++||+
T Consensus 109 ~~~~~~~~-~~~~---~~~~l~~~~~~l~~Lp~~~r~v~~l~~~~g----~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 180 (183)
T TIGR02999 109 EVLPDAEA-DLDE---ELLDLDDALDKLAQVDPRQAEVVELRFFAG----LTVEEIAELLGVSVRTVERDWRFARAWLAD 180 (183)
T ss_pred cccCCCCc-cHHH---HHHHHHHHHHHhhcCCHHHHHHHHHHHHcC----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 00001010 1111 111123344456779999999999999988 999999999999999999999999999998
Q ss_pred HH
Q 007404 592 KK 593 (605)
Q Consensus 592 ~l 593 (605)
.+
T Consensus 181 ~l 182 (183)
T TIGR02999 181 EL 182 (183)
T ss_pred Hh
Confidence 75
No 81
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=99.83 E-value=1.8e-19 Score=173.88 Aligned_cols=165 Identities=12% Similarity=0.048 Sum_probs=131.5
Q ss_pred hccHHHHHHHHHHHHHHHHHHHHHhhC--CCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcc
Q 007404 361 NYGILCKDKMITSNIRLVISIAKNYQG--AGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQS 438 (605)
Q Consensus 361 ~~g~~A~e~LI~~nlrLVvsIAkrY~~--~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~s 438 (605)
.++..+|+.|+..|.+.|+.++..+.+ +..+++|++||.|+.+|+..++|++.....|.||++..++|.+.++++++.
T Consensus 9 ~~d~~af~~ly~~~~~~l~~~~~~~~~~~~~~~AeDivQevFl~~~~~~~~~~~~~~~~~~~wL~~ia~n~~~d~~Rk~~ 88 (178)
T PRK12529 9 SADRDKVATLYRENHAWLRNWLAYRLRSWGRGVADDLAHDIFLRILASRDGGQREAIRQPRAYLARIANCVLVSWRRRQS 88 (178)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHhcccccccccccCHHHHHHHHHHHHHHHHHHHHH
Confidence 466889999999999999998766665 457899999999999999999998544457999999999999999887643
Q ss_pred ccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCC
Q 007404 439 RTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPE 518 (605)
Q Consensus 439 r~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~ 518 (605)
+. . .. .+. . . + ..+..
T Consensus 89 ~~--~----------------~~------------------------------------~~~-~--~------~-~~~~~ 104 (178)
T PRK12529 89 LE--L----------------AW------------------------------------LEA-L--A------T-LPEPL 104 (178)
T ss_pred HH--h----------------hh------------------------------------hhH-h--h------h-ccCcC
Confidence 20 0 00 000 0 0 0 00011
Q ss_pred CCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 007404 519 AETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 593 (605)
Q Consensus 519 ~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 593 (605)
.++|++.....+....|..+|.+||+++|.||.|+|..| +|++|||+.||+|.++|+.+++||+.+|++.+
T Consensus 105 ~~~~e~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~~g----~s~~EIA~~lgis~~tVk~~l~rAl~~~~~~~ 175 (178)
T PRK12529 105 HPSPEQQSVILETLHEIDALLDTLRPRVKQAFLMATLDG----MKQKDIAQALDIALPTVKKYIHQAYVTCLSLM 175 (178)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhC
Confidence 135666666666677899999999999999999999987 99999999999999999999999999998864
No 82
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=99.83 E-value=3.9e-19 Score=177.76 Aligned_cols=170 Identities=14% Similarity=0.134 Sum_probs=137.1
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcccccc
Q 007404 363 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIR 442 (605)
Q Consensus 363 g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IR 442 (605)
...++..||..|.+.++.+++++.++..+.+|++||+|+.+|+.+++|++. .|.+|++.+++|.++++++++.+...
T Consensus 16 ~~~~f~~l~~~~~~~l~~~~~~~~~d~~dAEDlvQEvflkl~~~~~~~~~~---~~~aWL~~IarN~~~d~~Rk~~~~~~ 92 (216)
T PRK12533 16 RGERFRQLVLPHLDAAYNLARWLCGNASDADDVVQEACMRALRFFDSFRGD---NARPWLLAIVRHTWYSEWRRRANAHE 92 (216)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCcc---chHhHHHHHHHHHHHHHHHhhccccc
Confidence 467999999999999999999999999999999999999999999999853 49999999999999999987653111
Q ss_pred ccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCH
Q 007404 443 LPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETA 522 (605)
Q Consensus 443 lP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~sp 522 (605)
.. .+..+. + .... +.+. +...+|
T Consensus 93 ~~-----------------------------------------------------~~~~~~-~-~~~~-~~~~-~~~~~~ 115 (216)
T PRK12533 93 VA-----------------------------------------------------APDTLD-D-ADSL-DDWQ-PAGEDP 115 (216)
T ss_pred cc-----------------------------------------------------cccccc-c-cccc-cccc-cCCCCH
Confidence 00 000000 0 0000 0011 112357
Q ss_pred HHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhh
Q 007404 523 EDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK 596 (605)
Q Consensus 523 Ee~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 596 (605)
++.+...+....|..+|..||+++|+||.|+|..+ +|++|||+.||||.++|+++++||+++||+.+...
T Consensus 116 e~~~~~~e~~~~l~~al~~Lp~~~R~v~~L~y~eg----~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l~~~ 185 (216)
T PRK12533 116 LALLLRAEDVRLVNAALAKLPVEYREVLVLRELED----MSYREIAAIADVPVGTVMSRLARARRRLAALLGGA 185 (216)
T ss_pred HHHHHHHHHHHHHHHHHHcCCHHHHhHhhhHHhcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHccc
Confidence 77777778888999999999999999999999987 99999999999999999999999999999998653
No 83
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=99.82 E-value=4.1e-19 Score=171.34 Aligned_cols=165 Identities=17% Similarity=0.215 Sum_probs=129.5
Q ss_pred HHHHhccHHHHHHHHHHHHHHHHHHHHHhhC----CCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHH
Q 007404 357 RRRLNYGILCKDKMITSNIRLVISIAKNYQG----AGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRK 432 (605)
Q Consensus 357 ~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~----~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r 432 (605)
.....++..|++.|+..|.+.|+.+|+++++ ...+++|++||+++.+|+..+.|++. ..|.+|++..+|+.+.+
T Consensus 14 ~~~~~gd~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeDlvQe~fl~l~~~~~~~~~~--~~~~~wl~~i~rn~~~d 91 (184)
T PRK12512 14 RSANAGDAAAYRRLLKAVTPVLRAAARRGLARAGQPADQAEDIVQEILLAVHLKRHTWDPG--APFAPWLFAIARNKLID 91 (184)
T ss_pred HHHHccCHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccHHHHHHHHHHHHHHhHHhcCcc--ccHHHHHHHHHHHHHHH
Confidence 3344567999999999999999999999886 24689999999999999999999874 47999999999999999
Q ss_pred HHhhccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCc
Q 007404 433 SLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSE 512 (605)
Q Consensus 433 ~ir~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d 512 (605)
+++++.+.... +++. ..+
T Consensus 92 ~~Rr~~~~~~~-----------------------------------------------------~~~~---------~~~ 109 (184)
T PRK12512 92 ALRRRGRRVFV-----------------------------------------------------DIDD---------FAE 109 (184)
T ss_pred HHHhhcccccC-----------------------------------------------------Cchh---------ccc
Confidence 99876531111 0000 000
Q ss_pred ccCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 007404 513 VIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 592 (605)
Q Consensus 513 ~l~D~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 592 (605)
.+++.. +.+ ......+..+|+.||+++|+||.++|..+ +|++|||+.||+|..+|+..++||+++||..
T Consensus 110 ~~~~~~---~~~----~~~~~~l~~~l~~L~~~~r~v~~l~~~~g----~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~ 178 (184)
T PRK12512 110 TLPAEP---ATE----TLPAGDVGRHLETLPPRQRDVVQSISVEG----ASIKETAAKLSMSEGAVRVALHRGLAALAAK 178 (184)
T ss_pred cccccc---hhh----HHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 111110 011 12234578899999999999999999887 9999999999999999999999999999998
Q ss_pred Hhhh
Q 007404 593 KRTK 596 (605)
Q Consensus 593 l~~~ 596 (605)
+.+.
T Consensus 179 l~~~ 182 (184)
T PRK12512 179 FRSE 182 (184)
T ss_pred hhcC
Confidence 8653
No 84
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=99.82 E-value=2.1e-19 Score=171.58 Aligned_cols=168 Identities=17% Similarity=0.129 Sum_probs=130.0
Q ss_pred HHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhc
Q 007404 358 RRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQ 437 (605)
Q Consensus 358 ~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~ 437 (605)
....++..+++.|+..|.+.|+.+++++.+ ..+++|++||+|+.+|+.++.|++. ..|.+|++..+++.+.+++++.
T Consensus 4 ~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~-~~~aeDivQe~~l~l~~~~~~~~~~--~~~~~wl~~ia~n~~~d~~R~~ 80 (175)
T PRK12518 4 RCQRGDRQSFRQLYRRYQQKVRSTLYQLCG-RELLDDLVQEVFLRVWKGLPKLRNP--AYFSTWLYRITWNVATDARRQF 80 (175)
T ss_pred HHHcCCHHHHHHHHHHHHHHHHHHHHHHcC-HhHHHHHHHHHHHHHHHhHHhhCCc--ccHHHHHHHHHHHHHHHHHHHh
Confidence 344567899999999999999999999875 4789999999999999999999974 4699999999999999998865
Q ss_pred cccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCC
Q 007404 438 SRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADP 517 (605)
Q Consensus 438 sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~ 517 (605)
.+.-.. ++.. .... . ...
T Consensus 81 ~~~~~~------------------------------------------------------~~~~---~~~~---~-~~~- 98 (175)
T PRK12518 81 AQRPSR------------------------------------------------------IQDD---SLND---Q-PSR- 98 (175)
T ss_pred hccccc------------------------------------------------------hhcc---cccc---c-ccC-
Confidence 321000 0000 0000 0 000
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhh
Q 007404 518 EAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK 596 (605)
Q Consensus 518 ~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 596 (605)
....++ ....+....+..+|+.||+++|.||.|+|+.| +|++|||+.||+|..+|++.++||+++||+.+...
T Consensus 99 ~~~~~~--~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~g----~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l~~~ 171 (175)
T PRK12518 99 PSDTPD--LMQLHYQDLVQQGLQTLSLEHRAVLVLHDLED----LPQKEIAEILNIPVGTVKSRLFYARRQLRKFLQQQ 171 (175)
T ss_pred CCCcHH--HHHHHHHHHHHHHHHhCCHHHeeeeeehHhcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhc
Confidence 011122 22223445688999999999999999999988 99999999999999999999999999999988764
No 85
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=99.82 E-value=1.2e-19 Score=170.25 Aligned_cols=157 Identities=18% Similarity=0.244 Sum_probs=125.3
Q ss_pred HHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccc
Q 007404 366 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPF 445 (605)
Q Consensus 366 A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~ 445 (605)
+++.++..|.+.|+.+|+++.++..+++|++||+++.+|+++++|++.. .|.+|++..+++.++++++++.+.-.. .
T Consensus 2 ~~~~~~~~~~~~l~~~~~~~~~~~~~aEDivQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~r~~~~~~~~-~ 78 (159)
T TIGR02989 2 AFAALLQRHQRSLRAFVRSLVPDRDDADDVLQETFVTAWRKFDEFDPGT--DFGAWARGIARNKVLNHRRKLGRDRLV-F 78 (159)
T ss_pred HHHHHHHHhHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHHhCCCCC--chHHHHHHHHHHHHHHHHHHhcccccc-c
Confidence 7899999999999999999999999999999999999999999999764 599999999999999999987542110 0
Q ss_pred cHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHHH
Q 007404 446 HMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDL 525 (605)
Q Consensus 446 ~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~ 525 (605)
.+++. +.+.+.. ++.+.
T Consensus 79 -------------------------~~~~~------------------------------------~~~~~~~--~~~~~ 95 (159)
T TIGR02989 79 -------------------------DDELL------------------------------------EALAAEA--EATEA 95 (159)
T ss_pred -------------------------CHHHH------------------------------------HHHHhhc--ccchH
Confidence 00000 0000000 01111
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 007404 526 LIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 592 (605)
Q Consensus 526 l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 592 (605)
.........|..+++.||++++.||.++|..| +|++|||+.||||.++|+..++||+++||+.
T Consensus 96 ~~~~~~~~~l~~~i~~L~~~~r~v~~l~~~~g----~~~~eIA~~l~is~~tv~~~l~Rar~~Lr~~ 158 (159)
T TIGR02989 96 DRSEDELQALEGCLEKLPERQRELLQLRYQRG----VSLTALAEQLGRTVNAVYKALSRLRVRLRDC 158 (159)
T ss_pred hhHHHHHHHHHHHHHHCCHHHHHHHHHHHhcC----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHhc
Confidence 22233456789999999999999999999887 9999999999999999999999999999975
No 86
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=99.82 E-value=3.8e-19 Score=172.77 Aligned_cols=167 Identities=13% Similarity=0.066 Sum_probs=128.6
Q ss_pred HHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhh
Q 007404 357 RRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSD 436 (605)
Q Consensus 357 ~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~ 436 (605)
.+...++..|++.||..|.+.++.+++ +.++..+++|++||.|+.+|+..++|++. ..|.+|++.+++|.+.+++++
T Consensus 16 ~~~~~gd~~af~~l~~~~~~~l~~~~~-~~~~~~~AeDivQe~flkl~~~~~~~~~~--~~~~~Wl~~Iarn~~~d~~Rk 92 (185)
T PRK09649 16 LSAAKGNGRALEAFIKATQQDVWRFVA-YLSDVGSADDLTQETFLRAIGAIPRFSAR--SSARTWLLAIARHVVADHIRH 92 (185)
T ss_pred HHHHccCHHHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHhccccCcc--chHHHHHHHHHHHHHHHHHHH
Confidence 344456789999999999999999995 67888899999999999999999999864 369999999999999999987
Q ss_pred ccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCC
Q 007404 437 QSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIAD 516 (605)
Q Consensus 437 ~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D 516 (605)
+.+..+.. .+. . .+...+
T Consensus 93 ~~~~~~~~-----------------------------------------------------~~~----~-----~~~~~~ 110 (185)
T PRK09649 93 VRSRPRTT-----------------------------------------------------RGA----R-----PEHLID 110 (185)
T ss_pred hccccccc-----------------------------------------------------ccc----c-----hhhccC
Confidence 54311100 000 0 000000
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhh
Q 007404 517 PEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK 596 (605)
Q Consensus 517 ~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 596 (605)
. +......+....|..+|..||+++|+||.|+|+.+ +|++|||+.||+|.++|+++++||+++||+.+...
T Consensus 111 ~-----~~~~~~~e~~~~l~~~l~~Lp~~~r~v~~L~~~~g----~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~~~~~ 181 (185)
T PRK09649 111 G-----DRHARGFEDLVEVTTMIADLTTDQREALLLTQLLG----LSYADAAAVCGCPVGTIRSRVARARDALLADAEPD 181 (185)
T ss_pred h-----hhhhhhHHHHHHHHHHHHhCCHHHhHHhhhHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCCcc
Confidence 0 00001112234588899999999999999999988 99999999999999999999999999999966544
Q ss_pred h
Q 007404 597 H 597 (605)
Q Consensus 597 ~ 597 (605)
.
T Consensus 182 ~ 182 (185)
T PRK09649 182 D 182 (185)
T ss_pred c
Confidence 3
No 87
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=99.82 E-value=7e-19 Score=174.05 Aligned_cols=165 Identities=18% Similarity=0.269 Sum_probs=136.8
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccc
Q 007404 362 YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI 441 (605)
Q Consensus 362 ~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~I 441 (605)
++..+++.|+..|.+.++.++.+|.++..+.+|++||+|+.+|+...+|++ + .|.+|++..+|+.+.+++++..+ .
T Consensus 25 ~d~~a~~~l~~~~~~~L~~~~~~~~~~~~~AEDivQEvflkl~~~~~~~~~--~-~~~~wL~~iarn~~~d~~Rk~~~-~ 100 (203)
T PRK09647 25 ATMPSWEELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSLQNYQP--G-TFEGWLHRITTNLFLDMVRRRAR-I 100 (203)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCC--c-ccHHHHHHHHHHHHHHHHHhccc-C
Confidence 357899999999999999999999999999999999999999999999985 3 69999999999999999987643 1
Q ss_pred cccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCC
Q 007404 442 RLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAET 521 (605)
Q Consensus 442 RlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~s 521 (605)
+. ..++ + + . +.... ..++
T Consensus 101 ~~----------------------------------------------------~~~~-----~-~--~-~~~~~-~~~~ 118 (203)
T PRK09647 101 RM----------------------------------------------------EALP-----E-D--Y-DRVPG-DEPN 118 (203)
T ss_pred cc----------------------------------------------------cccc-----c-c--c-cccCC-CCCC
Confidence 10 0000 0 0 0 01111 1235
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhh
Q 007404 522 AEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK 596 (605)
Q Consensus 522 pEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 596 (605)
|+..+...++...|..+|..||++++.||.|+|+.| ++++|||+.||||.++|++.++||+++||+.+...
T Consensus 119 ~~~~~~~~~~~~~l~~~L~~L~~~~r~v~~L~~~~g----~s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l~~~ 189 (203)
T PRK09647 119 PEQIYHDARLDPDLQAALDSLPPEFRAAVVLCDIEG----LSYEEIAATLGVKLGTVRSRIHRGRQQLRAALAAH 189 (203)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 666677777778899999999999999999999888 99999999999999999999999999999988754
No 88
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=99.82 E-value=3.1e-19 Score=168.32 Aligned_cols=156 Identities=17% Similarity=0.123 Sum_probs=126.6
Q ss_pred HHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHHHHH
Q 007404 372 TSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEAT 451 (605)
Q Consensus 372 ~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~~~i 451 (605)
+.|.+.|+.+|+++.++..+++|++||+|+.+|+++++|++. .|.+|++..++|.+.++++++.+..+.
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 578999999999999999999999999999999999999863 499999999999999999876531100
Q ss_pred HHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHHHHHHHHH
Q 007404 452 YRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFM 531 (605)
Q Consensus 452 ~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~l~~~el 531 (605)
..+.. + . .+... ...++++.+...+.
T Consensus 71 --------------------------------------------~~~~~----~-~---~~~~~--~~~~~~~~~~~~e~ 96 (160)
T PRK09642 71 --------------------------------------------LSLCK----E-T---EENIK--SSHNIEDLLLTKEQ 96 (160)
T ss_pred --------------------------------------------cccch----h-h---hhhcc--CCCChHHHHHHHHH
Confidence 00000 0 0 00000 11245666666677
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhh
Q 007404 532 KEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK 596 (605)
Q Consensus 532 ~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 596 (605)
...|..+|+.||+++|.||.|+|..| +|++|||+.||+|.++|+++++||+++||+.+...
T Consensus 97 ~~~l~~~l~~Lp~~~r~v~~l~~~~g----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~ 157 (160)
T PRK09642 97 KLLIAQKLRELPENYRDVVLAHYLEE----KSYQEIALQEKIEVKTVEMKLYRARKWIKKHWKEE 157 (160)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHhC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhhh
Confidence 78899999999999999999999988 99999999999999999999999999999988654
No 89
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.
Probab=99.82 E-value=2.4e-19 Score=174.57 Aligned_cols=173 Identities=13% Similarity=0.135 Sum_probs=132.4
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcccccc
Q 007404 363 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIR 442 (605)
Q Consensus 363 g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IR 442 (605)
+..+|+.|+..|.+.|+.+|+++.++..+++|++||+|+.+|+.+.+|++. ..|.+|++..++|.+.++++++.+...
T Consensus 9 ~~~~f~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQevfl~~~~~~~~~~~~--~~~~~wL~~iarN~~~d~~Rk~~~~~~ 86 (193)
T TIGR02947 9 RAQRFERDALEYLDQLYGAALRMTRNPADAEDLVQEAYAKAFSSFHQFKPG--TNLKAWLYRILTNTYINSYRKAQRRPQ 86 (193)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhcccCCC--CcchHHHHHHHHHHHHHHHHHhcCCcc
Confidence 367999999999999999999999999999999999999999999999864 369999999999999999987654111
Q ss_pred ccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCH
Q 007404 443 LPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETA 522 (605)
Q Consensus 443 lP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~sp 522 (605)
.. ..+++. .. ... + ..+ ........+
T Consensus 87 ~~-------------------------~~~~~~-----------~~------------~~~-~----~~~-~~~~~~~~~ 112 (193)
T TIGR02947 87 QS-------------------------DDDDIE-----------DW------------QLA-K----AAS-HTSNGLRSA 112 (193)
T ss_pred cc-------------------------cchhhh-----------hh------------hhc-c----ccc-cccccccch
Confidence 00 000000 00 000 0 000 000011133
Q ss_pred HHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 007404 523 EDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT 595 (605)
Q Consensus 523 Ee~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 595 (605)
+...........|..+|..||+++|+||.|+|..| +|++|||+.||||.++|+.+++||+++||+.+..
T Consensus 113 e~~~~~~~~~~~l~~~l~~Lp~~~r~i~~L~~~~g----~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~ 181 (193)
T TIGR02947 113 ELEALDGLPDQDIKDALQGLPEEFRQAVYLADVEG----FAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQLVD 181 (193)
T ss_pred hHHHHhhhhHHHHHHHHHhCCHHHhhheeehhhcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 33344444567789999999999999999999888 9999999999999999999999999999998864
No 90
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=99.82 E-value=4.1e-19 Score=173.24 Aligned_cols=162 Identities=14% Similarity=0.155 Sum_probs=129.6
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccc
Q 007404 362 YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI 441 (605)
Q Consensus 362 ~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~I 441 (605)
++..++..|+..|.+.++.+|+++.++..+++|++||.|+.+|+..++|+... .|.+|++..++|.++++++++.+..
T Consensus 7 ~~~~~f~~l~~~~~~~L~~~a~~~~~~~~~AEDivQevfl~~~~~~~~~~~~~--~~~awL~~Ia~n~~~d~~R~~~~~~ 84 (187)
T PRK12516 7 EGTPPFKRELLAALPSLRAFAVSLIGRHDRADDLVQDTIMKAWAKQDHFEVGT--NMKAWLFTILRNEFYSQMRKRGREV 84 (187)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHhhhccCCcc--cHHHHHHHHHHHHHHHHHHhhcCCc
Confidence 35789999999999999999999999999999999999999999999998643 5999999999999999998765411
Q ss_pred cccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCC
Q 007404 442 RLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAET 521 (605)
Q Consensus 442 RlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~s 521 (605)
.. .+.. +.+.... . +.
T Consensus 85 ~~------------------------------------------------------~~~~--------~~~~~~~-~-~~ 100 (187)
T PRK12516 85 QD------------------------------------------------------TDGM--------FTEQLAV-H-PS 100 (187)
T ss_pred cc------------------------------------------------------cccc--------cccccCC-C-cc
Confidence 00 0000 0000000 0 01
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhh
Q 007404 522 AEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKH 597 (605)
Q Consensus 522 pEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~ 597 (605)
.. .......|..+|..||+++|+||.|+|..| +|++|||+.||||.++|+++++||+++||+.+....
T Consensus 101 ~~----~~~~~~~l~~~L~~Lp~~~r~i~~L~~~~g----~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~~~~ 168 (187)
T PRK12516 101 QY----GTLDLQDFRAALDQLPDDQREAIILVGASG----FAYEEAAEICGCAVGTIKSRVNRARQRLQEILQIEG 168 (187)
T ss_pred hh----hHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhc
Confidence 11 112235689999999999999999999988 999999999999999999999999999999987654
No 91
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=99.81 E-value=5.7e-19 Score=168.96 Aligned_cols=163 Identities=13% Similarity=0.092 Sum_probs=129.2
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccc
Q 007404 362 YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI 441 (605)
Q Consensus 362 ~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~I 441 (605)
++..++..|+..|.+.|+.++.++.++..+++|++||+|+.+|+. ..|+.. ..|.+|++.+++|.+.++++++.+..
T Consensus 7 ~~~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQevflk~~~~-~~~~~~--~~~~~wL~~Iarn~~~d~~Rk~~~~~ 83 (172)
T PRK12523 7 PHSELVGALYRDHRGWLLAWLRRNVACRQRAEDLSQDTFVRLLGR-PELPTP--REPRAFLAAVAKGLMFDHFRRAALEQ 83 (172)
T ss_pred CCcHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHcc-cccCcc--hhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 557899999999999999999999999999999999999999987 446543 36999999999999999998764200
Q ss_pred cccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCC
Q 007404 442 RLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAET 521 (605)
Q Consensus 442 RlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~s 521 (605)
... .++ . . .......+
T Consensus 84 ------------------~~~---------~~~------------------------~-----~--------~~~~~~~~ 99 (172)
T PRK12523 84 ------------------AYL---------AEL------------------------A-----L--------VPEAEQPS 99 (172)
T ss_pred ------------------HHH---------HHH------------------------h-----h--------cccccCCC
Confidence 000 000 0 0 00001124
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 007404 522 AEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT 595 (605)
Q Consensus 522 pEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 595 (605)
|++.....+....|..+|..||+++|+||.|+|..| +|++|||+.||+|.++|+++++||+++||..+..
T Consensus 100 ~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~L~~~~g----~s~~EIA~~lgis~~tV~~~l~ra~~~~~~~l~~ 169 (172)
T PRK12523 100 PEEQHLILEDLKAIDRLLGKLSSKARAAFLYNRLDG----MGHAEIAERLGVSVSRVRQYLAQGLRQCYIALYG 169 (172)
T ss_pred hHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhcC
Confidence 555444444556799999999999999999999988 9999999999999999999999999999987753
No 92
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=99.81 E-value=1e-18 Score=165.27 Aligned_cols=160 Identities=18% Similarity=0.180 Sum_probs=130.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccc
Q 007404 364 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRL 443 (605)
Q Consensus 364 ~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRl 443 (605)
..+++.|+..|.+.|+.+|+++.++..+++|++||+|+.+|++ .|+. +..|.+|++..+++.+.+++++..+..+.
T Consensus 2 ~~~f~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fi~~~~~--~~~~--~~~~~~wl~~i~rn~~~d~~rk~~~~~~~ 77 (166)
T PRK09639 2 DETFEDLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLYRS--DFKG--IENEKGWLIKSARNVAYNYLRSEKRRRAR 77 (166)
T ss_pred chHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH--hccc--ccchHHHHHHHHHHHHHHHHHHhcccccc
Confidence 4589999999999999999999999999999999999999999 6764 34799999999999999999876542111
Q ss_pred cccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHH
Q 007404 444 PFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAE 523 (605)
Q Consensus 444 P~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spE 523 (605)
.. ... + ..+. + ....|+
T Consensus 78 ~~------------------------------------------------------~~~--~----~~~~--~-~~~~~e 94 (166)
T PRK09639 78 IL------------------------------------------------------GEF--Q----WQEV--D-NEPSPE 94 (166)
T ss_pred cc------------------------------------------------------chh--h----hhhc--c-CCCChH
Confidence 00 000 0 0000 1 123567
Q ss_pred HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 007404 524 DLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT 595 (605)
Q Consensus 524 e~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 595 (605)
+.....+....|..+|..||+++|.||.++| .| +|++|||+.||+|..+|+..+.||+++||+.+..
T Consensus 95 ~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~-~g----~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l~~ 161 (166)
T PRK09639 95 EIWIRKEEITKVQEVLAKMTERDRTVLLLRF-SG----YSYKEIAEALGIKESSVGTTLARAKKKFRKIYEQ 161 (166)
T ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH-cC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 7777777777899999999999999999999 77 9999999999999999999999999999998864
No 93
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=99.81 E-value=7.3e-19 Score=166.93 Aligned_cols=157 Identities=17% Similarity=0.146 Sum_probs=131.0
Q ss_pred HHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcccccccccc
Q 007404 367 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFH 446 (605)
Q Consensus 367 ~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~ 446 (605)
++.|+..|.+.|+.+|++|.++..+++|++||+|+.+|+.+++|++. .|.+|++..++|.+.+++++..+....
T Consensus 3 ~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~---~~~~wL~~i~~n~~~d~~R~~~~~~~~--- 76 (165)
T PRK09644 3 IEEIYKMYINDVYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDYDNQ---KVKPWLFKVAYHTFIDFVRKEKKVSFV--- 76 (165)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcccc---chHHHHHHHHHHHHHHHHHhhhhcccc---
Confidence 67899999999999999999999999999999999999999999863 599999999999999999886541100
Q ss_pred HHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHHHH
Q 007404 447 MVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLL 526 (605)
Q Consensus 447 ~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~l 526 (605)
+.+++ +.+.+ .+|++.+
T Consensus 77 -----------------------~~~~~-------------------------------------~~~~~---~~~~~~~ 93 (165)
T PRK09644 77 -----------------------GTDEI-------------------------------------EAIQA---ESTEEYV 93 (165)
T ss_pred -----------------------chhHH-------------------------------------hhhcc---cChHHHH
Confidence 00000 00000 2455656
Q ss_pred HHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhh
Q 007404 527 IKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK 596 (605)
Q Consensus 527 ~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 596 (605)
...+....|..+|..||+++|+||.|+|..| +|++|||+.||+|.++|+++++||+++||+.+...
T Consensus 94 ~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g----~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~~~ 159 (165)
T PRK09644 94 VAKNSYEKLIQIIHTLPVIEAQAILLCDVHE----LTYEEAASVLDLKLNTYKSHLFRGRKRLKALLKEE 159 (165)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHHHhHHHhc----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhh
Confidence 6666778899999999999999999999988 99999999999999999999999999999988754
No 94
>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=99.81 E-value=6.4e-19 Score=166.25 Aligned_cols=157 Identities=16% Similarity=0.175 Sum_probs=127.6
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccc
Q 007404 362 YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI 441 (605)
Q Consensus 362 ~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~I 441 (605)
|+..+++.|+..|.+.|+.++..+.++..+++|++||+|+.+|+..++|+. . ..|.+|++..+++.+.++++++.+.
T Consensus 3 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~~~~~~~~~~~-~-~~~~~wl~~i~~n~~~d~~rk~~~~- 79 (162)
T TIGR02983 3 ATEEEFTAFVAARYPRLLRTAYLLTGDPHEAEDLVQEALVRTYVRWDRIRD-P-DAPDAYVRRVLVNLARSRWRRRRLL- 79 (162)
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhcCC-c-ccHHHHHHHHHHHHHHHHHHhhccc-
Confidence 568899999999999999999999999999999999999999999999964 3 4799999999999999998865430
Q ss_pred cccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCC
Q 007404 442 RLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAET 521 (605)
Q Consensus 442 RlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~s 521 (605)
.++ +... .+. +.. .
T Consensus 80 ~~~------------------------------------------------------~~~~--------~~~--~~~--~ 93 (162)
T TIGR02983 80 ELP------------------------------------------------------TREL--------PDA--AAP--D 93 (162)
T ss_pred ccc------------------------------------------------------cccc--------Ccc--cCC--c
Confidence 000 0000 000 000 0
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404 522 AEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR 594 (605)
Q Consensus 522 pEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 594 (605)
........+.|..+|..||+++|+||.|+|..| +|++|||+.||+|.++|++++.||+++||+.+.
T Consensus 94 ---~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g----~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 159 (162)
T TIGR02983 94 ---PAPDVALRAALARALRRLPARQRAVVVLRYYED----LSEAQVAEALGISVGTVKSRLSRALARLRELLE 159 (162)
T ss_pred ---cchhHHHHHHHHHHHHhCCHHHHHHhhhHHHhc----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhc
Confidence 111233456788999999999999999999877 999999999999999999999999999999775
No 95
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=99.81 E-value=1.1e-18 Score=164.96 Aligned_cols=157 Identities=13% Similarity=0.100 Sum_probs=125.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcccccccc
Q 007404 365 LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLP 444 (605)
Q Consensus 365 ~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP 444 (605)
.|++.|+..|.+.|+.++.++.++..+++|++||+|+.+|+..+.|++. .|.+|++.+++|.+.+++++..+..
T Consensus 4 ~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~flk~~~~~~~~~~~---~~~~wl~~i~~n~~~d~~R~~~~~~--- 77 (161)
T PRK12528 4 ATVEGLYSAHHHWLTGWLRRRLGCPQSAADLAQDTFVKVLVARETAQII---EPRAFLTTIAKRVLCNHYRRQDLER--- 77 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHhcccccccc---CHHHHHHHHHHHHHHHHHHHHHHHH---
Confidence 5899999999999999999999999999999999999999999888652 6999999999999999988753200
Q ss_pred ccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHH
Q 007404 445 FHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAED 524 (605)
Q Consensus 445 ~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe 524 (605)
.. ..++ + + .++.....+++
T Consensus 78 ---------------~~---------~~~~------------------------~------------~-~~~~~~~~~~~ 96 (161)
T PRK12528 78 ---------------AY---------LEAL------------------------A------------Q-LPERVAPSEEE 96 (161)
T ss_pred ---------------hh---------HHHh------------------------h------------c-cccccCCCHHH
Confidence 00 0000 0 0 00001123444
Q ss_pred HHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 007404 525 LLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 592 (605)
Q Consensus 525 ~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 592 (605)
.....+....|..+|..||+++|+||.|+|..| +|++|||+.||+|.++|+++++||+++||..
T Consensus 97 ~~~~~~~~~~l~~~l~~L~~~~r~v~~L~~~~g----~s~~EIA~~l~is~~tV~~~l~ra~~~~~~~ 160 (161)
T PRK12528 97 RAIILETLVELDQLLDGLPPLVKRAFLLAQVDG----LGYGEIATELGISLATVKRYLNKAAMRCYFA 160 (161)
T ss_pred HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHhc
Confidence 444444556799999999999999999999988 9999999999999999999999999999964
No 96
>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=99.81 E-value=1.5e-18 Score=169.10 Aligned_cols=178 Identities=16% Similarity=0.103 Sum_probs=134.4
Q ss_pred HHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHH
Q 007404 369 KMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMV 448 (605)
Q Consensus 369 ~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~ 448 (605)
+++..|.+.|+.+++++.++..+++|++||+|+.+|+...+|++. .+|.+|++..++|.++++++++.+....+.-
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 578899999999999999999999999999999999999999875 4799999999999999999877642111000
Q ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHHHHHH
Q 007404 449 EATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIK 528 (605)
Q Consensus 449 ~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~l~~ 528 (605)
.++. . .-.++.... ..+....+..++ ..++|++.+..
T Consensus 82 ----------------------~~~~------~-------------~~~~~~~~~-~~~~~~~~~~~~-~~~~~e~~~~~ 118 (188)
T TIGR02943 82 ----------------------DDEL------D-------------DEAFNALFT-QNGHWAQHGQPQ-HWNTPEKQLEN 118 (188)
T ss_pred ----------------------cccc------c-------------cchhhhhhc-cccchhcccccc-ccCCHHHHHHH
Confidence 0000 0 000000000 000000011111 22367777777
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhh
Q 007404 529 KFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKH 597 (605)
Q Consensus 529 ~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~ 597 (605)
++....|..+|..||+++|+||.|+|..+ +|++|||+.||+|.++|++++.||+++||+.+....
T Consensus 119 ~e~~~~l~~~l~~L~~~~r~v~~l~~~~g----~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l~~~~ 183 (188)
T TIGR02943 119 KEFWEVFEACLYHLPEQTARVFMMREVLG----FESDEICQELEISTSNCHVLLYRARLSLRACLSINW 183 (188)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHHHhC----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHh
Confidence 77788899999999999999999999988 999999999999999999999999999999987553
No 97
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=99.80 E-value=1.6e-18 Score=169.12 Aligned_cols=181 Identities=17% Similarity=0.150 Sum_probs=134.2
Q ss_pred HHHHHHHHHHHHHHHHHhhCCCCC-HHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcccccccccc
Q 007404 368 DKMITSNIRLVISIAKNYQGAGMN-LQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFH 446 (605)
Q Consensus 368 e~LI~~nlrLVvsIAkrY~~~g~d-~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~ 446 (605)
+..+..|.+.|+.+|+++.++..+ ++|++||+|+.+|+++++|++. .+|.+|++..++|.++++++++.+.......
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 457888999999999999998888 9999999999999999999864 3799999999999999999986542111000
Q ss_pred HHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHHHH
Q 007404 447 MVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLL 526 (605)
Q Consensus 447 ~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~l 526 (605)
. ......+.. .+. .. .+.....+..+ ....+|++.+
T Consensus 86 ~-------------------~~~~~~~~~--------------------~~~---~~-~~~~~~~~~~~-~~~~~~e~~~ 121 (195)
T PRK12532 86 L-------------------DDELLDEAF--------------------ESH---FS-QNGHWTPEGQP-QHWNTPEKSL 121 (195)
T ss_pred c-------------------cccccchhh--------------------hhh---hc-cccccccccCc-cccCCHHHHH
Confidence 0 000000000 000 00 00000000011 1123677777
Q ss_pred HHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhhH
Q 007404 527 IKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHL 598 (605)
Q Consensus 527 ~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L 598 (605)
...+....+..+|..||+++|+||.|+|..| +|++|||+.||+|..+|+++++||+++||+.+....+
T Consensus 122 ~~~e~~~~l~~~l~~L~~~~r~i~~L~~~~g----~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~~~ 189 (195)
T PRK12532 122 NNNEFQKILQSCLYNLPENTARVFTLKEILG----FSSDEIQQMCGISTSNYHTIMHRARESLRQCLQIKWF 189 (195)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHhhhHHHhC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 7777888899999999999999999999988 9999999999999999999999999999999876544
No 98
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=99.80 E-value=1.7e-18 Score=163.58 Aligned_cols=157 Identities=13% Similarity=0.158 Sum_probs=125.2
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcccccc
Q 007404 363 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIR 442 (605)
Q Consensus 363 g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IR 442 (605)
+..+++.++..|.+.|+.++.++.++..+++|++||+++.+|+..++|++. .|.||++..++|.+.++++++.+...
T Consensus 3 ~~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDv~Qe~f~~~~~~~~~~~~~---~~~~wl~~i~~n~~~d~~R~~~~~~~ 79 (161)
T PRK12541 3 RKQSLEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYKGE---EIRPWLFTIAYNAFIDWYRKEKKYKT 79 (161)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhHHHccCC---ChHHHHHHHHHHHHHHHHHhcccccc
Confidence 467999999999999999999999999999999999999999999999863 59999999999999999988654110
Q ss_pred ccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCH
Q 007404 443 LPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETA 522 (605)
Q Consensus 443 lP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~sp 522 (605)
+ ..+. .. . +.....+
T Consensus 80 ~-----------------------------------------------------~~~~-------~~---~--~~~~~~~ 94 (161)
T PRK12541 80 T-----------------------------------------------------TIEE-------FH---L--PNVPSTE 94 (161)
T ss_pred c-----------------------------------------------------chhh-------hh---c--cCCCCcH
Confidence 0 0000 00 0 0000112
Q ss_pred HHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 007404 523 EDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 592 (605)
Q Consensus 523 Ee~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 592 (605)
++....++. ..+..+|..||+++|.||.|+|..| +|++|||+.||+|.++|++.++||+++||+.
T Consensus 95 ~~~~~~~~~-~~~~~~l~~L~~~~r~v~~l~~~~~----~s~~eIA~~lgis~~tv~~~l~Rar~~L~~~ 159 (161)
T PRK12541 95 HEYFIKHEI-ASWLDSLSSLPLERRNVLLLRDYYG----FSYKEIAEMTGLSLAKVKIELHRGRKETKSI 159 (161)
T ss_pred HHHHHHhHH-HHHHHHHHHCCHHHHHHhhhHHhcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 222333333 4456789999999999999999988 9999999999999999999999999999974
No 99
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=99.80 E-value=2.5e-18 Score=167.56 Aligned_cols=176 Identities=17% Similarity=0.136 Sum_probs=132.5
Q ss_pred HHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccH
Q 007404 368 DKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHM 447 (605)
Q Consensus 368 e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~ 447 (605)
+..|..|.+.++.+|.+|.++..+++|++||+|+.+|+..++|++.. +|.+|++..++|.+.++++++.+..... ..
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 34678889999999999999999999999999999999999998753 6999999999999999999765421110 00
Q ss_pred HHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHHHHH
Q 007404 448 VEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLI 527 (605)
Q Consensus 448 ~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~l~ 527 (605)
. ++ ........ .......+........+|++.+.
T Consensus 87 ------------------~-----~~-------------------~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~ 120 (189)
T PRK12530 87 ------------------I-----EE-------------------DSPNSFFD----EKGHWKPEYYEPSEWQEVENTVY 120 (189)
T ss_pred ------------------c-----cc-------------------ccchhhhc----ccccccccccCCccccCHHHHHH
Confidence 0 00 00000000 00000000111111235677777
Q ss_pred HHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhh
Q 007404 528 KKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK 596 (605)
Q Consensus 528 ~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 596 (605)
..+....|..+|+.||+++|+||.|+|..| +|++|||+.||+|.++|+.+++||+++||+++...
T Consensus 121 ~~~~~~~l~~~l~~Lp~~~R~v~~L~~~~g----~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~~ 185 (189)
T PRK12530 121 KEEFWLIFEACLNHLPAQQARVFMMREYLE----LSSEQICQECDISTSNLHVLLYRARLQLQACLSKN 185 (189)
T ss_pred HHHHHHHHHHHHHhCCHHHHHHHhHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 777888899999999999999999999988 99999999999999999999999999999988654
No 100
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=99.80 E-value=2.5e-18 Score=163.54 Aligned_cols=158 Identities=11% Similarity=0.140 Sum_probs=126.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccc
Q 007404 364 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRL 443 (605)
Q Consensus 364 ~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRl 443 (605)
...|..++..|.+.|+.+|+++.++..+++|++||+|+.+|+..++|++.. .|.+|++..++|.+.+++++..+....
T Consensus 5 ~~~f~~~~~~~~~~l~~~a~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~R~~~~~~~~ 82 (164)
T PRK12547 5 SKNFKQELLLALPALRAFAVSLSSKHDKAEDLVQDTLMKAWAKQDSFEMGT--NLKAWLFTILRNEFYSQMRKRGREVQD 82 (164)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHhhhhcCCcc--cHHHHHHHHHHHHHHHHHHhhcccccc
Confidence 467999999999999999999999999999999999999999999998643 599999999999999999876431000
Q ss_pred cccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHH
Q 007404 444 PFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAE 523 (605)
Q Consensus 444 P~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spE 523 (605)
. +... .. . .+. .++
T Consensus 83 ----------------------------~--------------------------~~~~--~~-----~--~~~---~~~ 96 (164)
T PRK12547 83 ----------------------------S--------------------------DGVF--TA-----R--VAV---HPA 96 (164)
T ss_pred ----------------------------c--------------------------cccc--cc-----c--CCC---Cch
Confidence 0 0000 00 0 000 111
Q ss_pred HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 007404 524 DLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT 595 (605)
Q Consensus 524 e~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 595 (605)
. ........|..+|..||+++|+||.|+|..| +|++|||+.||||.++|+++++||+++||..+..
T Consensus 97 ~--~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 162 (164)
T PRK12547 97 Q--YGSLDLQDFKKALNLLSADQREAIILIGASG----FSYEDAAAICGCAVGTIKSRVSRARNRLQELLKV 162 (164)
T ss_pred h--hhHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 1 0112245688999999999999999999887 9999999999999999999999999999998754
No 101
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=99.80 E-value=2.3e-18 Score=169.54 Aligned_cols=181 Identities=16% Similarity=0.141 Sum_probs=132.3
Q ss_pred HHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHH
Q 007404 369 KMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMV 448 (605)
Q Consensus 369 ~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~ 448 (605)
.++..|.+.|+.+|+++.++..+++|++||.|+.+|+.+++|++.. .|.+|++.+++|.++++++++.+...++..
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 3589999999999999999999999999999999999999999763 699999999999999999987642111000
Q ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHHHHHH
Q 007404 449 EATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIK 528 (605)
Q Consensus 449 ~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~l~~ 528 (605)
..++.. ...++............+..++ ...++++....
T Consensus 88 ----------------------~~~~~~------------------~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~ 126 (201)
T PRK12545 88 ----------------------DAELDG------------------EALLDRELFKDNGHWAAHAKPR-PWPKPETILQQ 126 (201)
T ss_pred ----------------------ccccch------------------hhhhhhhhhcccccccccccCc-CCCCHHHHHHH
Confidence 000000 0000000000000000001111 12256666666
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhhH
Q 007404 529 KFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHL 598 (605)
Q Consensus 529 ~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L 598 (605)
.+....|..+|..||+++|+||.|+|+.| +|++|||+.||+|.++|++++.||+++||+.+...++
T Consensus 127 ~~~~~~l~~~L~~Lp~~~r~v~~L~~~eg----~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~~~~ 192 (201)
T PRK12545 127 QQFWTLFETCLDHLPEQIGRVFMMREFLD----FEIDDICTELTLTANHCSVLLYRARTRLRTCLSEKGL 192 (201)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 66667899999999999999999999988 9999999999999999999999999999999975443
No 102
>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=99.80 E-value=1.9e-18 Score=181.03 Aligned_cols=183 Identities=18% Similarity=0.155 Sum_probs=135.9
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccc
Q 007404 362 YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI 441 (605)
Q Consensus 362 ~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~I 441 (605)
|+..+++.|+..|.+.|+.+|+++.++..+++|++||.|+.+|+.+++|++. ..|.+|++.+++|.++++++++.+..
T Consensus 2 gd~~af~~l~~~~~~~l~~~a~~~~~~~~~AEDivQe~fl~~~~~~~~~~~~--~~~~~WL~~Ia~n~~~d~~Rk~~~~~ 79 (324)
T TIGR02960 2 VDGAAFTALAEPHRRELLAHCYRMLGSLHEAEDLVQETLLRAWRARDRFEGR--SSVRTWLYRIATNACLDALEARQRRP 79 (324)
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHHHhhhhccCcc--cchHHHHHHHHHHHHHHHHHhccCCc
Confidence 4578999999999999999999999999999999999999999999999864 36999999999999999998765411
Q ss_pred cccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccC------
Q 007404 442 RLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIA------ 515 (605)
Q Consensus 442 RlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~------ 515 (605)
... . ... + .....+.. ..+......+.+.
T Consensus 80 ~~~-~-----------------~~~--~------------------------~~~~~~~~-~~~~~~~~~~~~~~~~~~~ 114 (324)
T TIGR02960 80 RPV-G-----------------LGA--P------------------------SADGTAAA-SEAAEVTWLEPLPDLTLDL 114 (324)
T ss_pred Ccc-c-----------------cCC--C------------------------CCcccccc-cccccccccCCCCcccccc
Confidence 100 0 000 0 00000000 0000000000000
Q ss_pred -CCCCCCHHHHHHHHH-HHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 007404 516 -DPEAETAEDLLIKKF-MKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 593 (605)
Q Consensus 516 -D~~~~spEe~l~~~e-l~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 593 (605)
.....+|++.+...+ +...|..+|.+||+++|.||.|+|..+ +|++|||+.||+|.++|+++++||+++||+.+
T Consensus 115 ~~~~~~~~~~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L~~~~g----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 190 (324)
T TIGR02960 115 DDPAAADPSVAAGSRESVRLAFVAAIQYLPPRQRAVLLLRDVLG----WRAAETAELLGTSTASVNSALQRARATLDEVG 190 (324)
T ss_pred ccCCCCCHHHHHHHHHHHHHHHHHHHHhCCHHHhhHhhhHHHhC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhc
Confidence 111235666655554 456789999999999999999999988 99999999999999999999999999999988
Q ss_pred hh
Q 007404 594 RT 595 (605)
Q Consensus 594 ~~ 595 (605)
..
T Consensus 191 ~~ 192 (324)
T TIGR02960 191 PS 192 (324)
T ss_pred cc
Confidence 74
No 103
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=99.80 E-value=3.3e-18 Score=180.73 Aligned_cols=187 Identities=18% Similarity=0.156 Sum_probs=137.7
Q ss_pred HHHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHH
Q 007404 354 RELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKS 433 (605)
Q Consensus 354 ~~L~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ 433 (605)
+.+.+...++..+++.|+..|.+.|+.+|+++.++..+++|++||.|+.+|+.+++|++. ..|.+|++..++|.++++
T Consensus 8 ~l~~~~~~gd~~af~~l~~~y~~~l~~~~~~~~~~~~dAEDivQevfl~~~~~~~~~~~~--~~~~~wL~~Ia~n~~~d~ 85 (339)
T PRK08241 8 ALLARAAAGDRDAFAALVEPHRRELLAHCYRMLGSVHDAEDAVQETLLRAWRGYDRFEGR--SSLRTWLYRIATNVCLDA 85 (339)
T ss_pred HHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHhhhhccccc--cchHHHHHHHHHHHHHHH
Confidence 345555667789999999999999999999999999999999999999999999999853 369999999999999999
Q ss_pred HhhccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcc
Q 007404 434 LSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEV 513 (605)
Q Consensus 434 ir~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~ 513 (605)
++++.+.... .. ... +. .........+......+.
T Consensus 86 ~Rk~~~~~~~-~~------------------~~~-~~-------------------------~~~~~~~~~~~~~~~~~~ 120 (339)
T PRK08241 86 LEGRARRPLP-TD------------------LGA-PA-------------------------ADPVDELVERPEVPWLEP 120 (339)
T ss_pred HHhhccccCc-cc------------------cCC-Cc-------------------------CcccccccccccccccCC
Confidence 9876541000 00 000 00 000000000000001111
Q ss_pred cCCC----CCCCHHHHHHHHH-HHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q 007404 514 IADP----EAETAEDLLIKKF-MKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRK 588 (605)
Q Consensus 514 l~D~----~~~spEe~l~~~e-l~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkK 588 (605)
+.+. ...+|++.+...+ ....|..+|.+||+++|+||.|+|..+ +|++|||+.||+|.++|+++++||+++
T Consensus 121 ~~~~~~~~~~~~~e~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L~~~~g----~s~~EIA~~lgis~~tVk~~l~RAr~~ 196 (339)
T PRK08241 121 YPDALLDPAAADPAARVVARESVRLAFVAALQHLPPRQRAVLILRDVLG----WSAAEVAELLDTSVAAVNSALQRARAT 196 (339)
T ss_pred CCcccccccCCChHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhhHHhhC----CCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 1111 1235666655544 455689999999999999999999988 999999999999999999999999999
Q ss_pred HHh
Q 007404 589 LKN 591 (605)
Q Consensus 589 LR~ 591 (605)
||+
T Consensus 197 Lr~ 199 (339)
T PRK08241 197 LAE 199 (339)
T ss_pred Hhh
Confidence 999
No 104
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=99.79 E-value=4.1e-18 Score=167.48 Aligned_cols=169 Identities=16% Similarity=0.069 Sum_probs=130.3
Q ss_pred HHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhh
Q 007404 357 RRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSD 436 (605)
Q Consensus 357 ~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~ 436 (605)
.....++..+++.|+..|.+.++.+++ +.++..+++|++||.|+.+|+..++|++. .+|.+|++..+||.+++++++
T Consensus 17 ~~~~~~d~~a~~~l~~~y~~~l~~~~~-~~~~~~~AEDivQevflkl~~~~~~~~~~--~~~~~WL~~Iarn~~id~~Rk 93 (196)
T PRK12535 17 LAAGRGDRAALTEFIRETQDDVWRLLA-HLGGHDIADDLTQETYLRVMSALPRFAAR--SSARTWLLSLARRVWVDNIRH 93 (196)
T ss_pred HHHHcCCHHHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHHhhhcCCc--ccHHHHHHHHHHHHHHHHHHh
Confidence 444456789999999999999999975 67888899999999999999999999864 369999999999999999997
Q ss_pred ccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCC
Q 007404 437 QSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIAD 516 (605)
Q Consensus 437 ~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D 516 (605)
+.+..+. ..+ .. ....+.
T Consensus 94 ~~~~~~~-----------------------------------------------------~~~-~~-----~~~~~~--- 111 (196)
T PRK12535 94 DMARPRK-----------------------------------------------------SAT-EY-----EDAAAT--- 111 (196)
T ss_pred hccCCCc-----------------------------------------------------ccc-cc-----cccccc---
Confidence 6531110 000 00 000000
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhh
Q 007404 517 PEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK 596 (605)
Q Consensus 517 ~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 596 (605)
. ..++.... ......|..+|+.||+++|+||.|+|..| +|++|||+.||+|.++|+++++||+++||+.+...
T Consensus 112 -~-~~~~~~~~-~~~~~~l~~~l~~Lp~~~r~v~~l~~~~g----~s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~~~ 184 (196)
T PRK12535 112 -T-ASNETTGS-WSEWIDVRTLIDALPPERREALILTQVLG----YTYEEAAKIADVRVGTIRSRVARARADLIAATATG 184 (196)
T ss_pred -c-CCcchhHH-HHHHHHHHHHHHcCCHHHHHHhhhHHHhC----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhccc
Confidence 0 01111111 11234689999999999999999999988 99999999999999999999999999999988654
Q ss_pred h
Q 007404 597 H 597 (605)
Q Consensus 597 ~ 597 (605)
.
T Consensus 185 ~ 185 (196)
T PRK12535 185 Q 185 (196)
T ss_pred c
Confidence 3
No 105
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=99.79 E-value=5.4e-18 Score=168.09 Aligned_cols=179 Identities=17% Similarity=0.144 Sum_probs=134.9
Q ss_pred HHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcccccccccc
Q 007404 367 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFH 446 (605)
Q Consensus 367 ~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~ 446 (605)
-..++..|.+.|+.+|+++.++..+++|++||+|+.+|+.+.+|++. .+|.+|++.+++|.+++++++..+....+..
T Consensus 20 ~~~~~~~~~~~l~~~~~~~~~d~~~AEDivQEvfikl~~~~~~~~~~--~~~~~WL~~IarN~~~d~~Rk~~~~~~~~~~ 97 (206)
T PRK12544 20 DPVFLEDLRKQMIKFATLQLSDLHLAEDAVQEALIGALKNADSFAGR--AAFKTWVFAILKNKIIDLLRQKKRHVSASSL 97 (206)
T ss_pred hHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHHHHHHHHhhccccccccc
Confidence 35789999999999999999999999999999999999999999864 4699999999999999999987652211100
Q ss_pred HHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCC-CcccCCCCCCCHHHH
Q 007404 447 MVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKP-SEVIADPEAETAEDL 525 (605)
Q Consensus 447 ~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l-~d~l~D~~~~spEe~ 525 (605)
........ .+..+. +..... .+...+ ...+|++.
T Consensus 98 ------------------~~~~~~~~-----------~~~~~~---------------~~~~~~~~~~~~~-~~~~~e~~ 132 (206)
T PRK12544 98 ------------------LRDEEEEE-----------DFEELF---------------DESGHWQKDERPQ-AWGNPEES 132 (206)
T ss_pred ------------------ccccchhh-----------HHHHhh---------------ccccccccccccc-ccCCHHHH
Confidence 00000000 000000 000000 000111 12367777
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhh
Q 007404 526 LIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK 596 (605)
Q Consensus 526 l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 596 (605)
+...+....+..+|..||+++|+||.|+|+.+ +|++|||+.||+|..+|+++++||+++||+.+...
T Consensus 133 ~~~~e~~~~l~~~L~~L~~~~r~v~~L~~~~g----~s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l~~~ 199 (206)
T PRK12544 133 LEQEQFWRIFEACLDGLPAKYARVFMMREFIE----LETNEICHAVDLSVSNLNVLLYRARLRLRECLENK 199 (206)
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHH
Confidence 77777778899999999999999999999988 99999999999999999999999999999998754
No 106
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=99.79 E-value=7.6e-18 Score=159.07 Aligned_cols=158 Identities=16% Similarity=0.197 Sum_probs=126.6
Q ss_pred HHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHH
Q 007404 369 KMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMV 448 (605)
Q Consensus 369 ~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~ 448 (605)
.++..|.+.++.+|.++.++..+++|++||+++.+|+....|++. .|.+|++..+|+.+.++++++.+....
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 367889999999999999999999999999999999998888763 478999999999999999876531100
Q ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHHHHHH
Q 007404 449 EATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIK 528 (605)
Q Consensus 449 ~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~l~~ 528 (605)
+ + .+.... +. .+. ..+|++.+..
T Consensus 74 ------------------------------------------------~-~-----~~~~~~-~~-~~~-~~~~~~~~~~ 96 (163)
T PRK07037 74 ------------------------------------------------H-G-----DEEDGL-DV-PSP-EASPEAALIN 96 (163)
T ss_pred ------------------------------------------------c-c-----cccccc-cc-CCC-CCCHHHHHHH
Confidence 0 0 000000 00 111 1246666666
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 007404 529 KFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT 595 (605)
Q Consensus 529 ~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 595 (605)
.+..+.|..+|..||+++|.||.++|..+ +|++|||+.||+|.++|++.+.||+++||+.+..
T Consensus 97 ~~~~~~l~~~l~~L~~~~r~v~~l~~~~~----~s~~EIA~~lgis~~tV~~~l~ra~~~lr~~l~~ 159 (163)
T PRK07037 97 RDTLRHVADALSELPARTRYAFEMYRLHG----ETQKDIARELGVSPTLVNFMIRDALVHCRKCLDA 159 (163)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 66678899999999999999999999988 9999999999999999999999999999998764
No 107
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=99.78 E-value=6.6e-18 Score=159.26 Aligned_cols=155 Identities=14% Similarity=0.120 Sum_probs=125.3
Q ss_pred HHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHHHH
Q 007404 371 ITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEA 450 (605)
Q Consensus 371 I~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~~~ 450 (605)
+..|.+.++.++.++.++..+++|++||+|+.+|+..+.|++. +|.||++..++|.++++++++.+....
T Consensus 1 ~~~~~~~l~~~~~~~~~~~~~aeDi~Qevf~~l~~~~~~~~~~---~~~~wL~~ia~n~~~d~~R~~~~~~~~------- 70 (159)
T PRK12527 1 MENYYRELVRFLSARLGNRQAAEDVAHDAYLRVLERSSSAQIE---HPRAFLYRTALNLVVDRHRRHRVRQAE------- 70 (159)
T ss_pred ChhHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHhcccccccc---chHHHHHHHHHHHHHHHHHHHhccccc-------
Confidence 3578899999999999998999999999999999999998752 799999999999999999865421000
Q ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHHHHHHHH
Q 007404 451 TYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKF 530 (605)
Q Consensus 451 i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~l~~~e 530 (605)
+++. .. +. . ....++|++.+..++
T Consensus 71 ----------------------------------------------~~~~-~~-~~-----~---~~~~~~~~~~~~~~~ 94 (159)
T PRK12527 71 ----------------------------------------------PLEV-LD-EE-----E---RLHSPSPQTRLDLGQ 94 (159)
T ss_pred ----------------------------------------------chhh-hh-cc-----c---cccCCCHHHHHHHHH
Confidence 0000 00 00 0 001225677777777
Q ss_pred HHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 007404 531 MKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT 595 (605)
Q Consensus 531 l~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 595 (605)
....|..+|..||+++++||.|+|+.+ +|++|||+.||+|.++|+..+.||+++||+.+..
T Consensus 95 ~~~~l~~~l~~L~~~~r~v~~l~~~~~----~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l~~ 155 (159)
T PRK12527 95 RLALLQRALAELPPACRDSFLLRKLEG----LSHQQIAEHLGISRSLVEKHIVNAMKHCRVRMRQ 155 (159)
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 778899999999999999999999988 9999999999999999999999999999998764
No 108
>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=99.78 E-value=1.4e-18 Score=162.20 Aligned_cols=153 Identities=17% Similarity=0.150 Sum_probs=123.8
Q ss_pred HHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHHHH
Q 007404 371 ITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEA 450 (605)
Q Consensus 371 I~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~~~ 450 (605)
+..|.+.|+.+++++.++..+++|++||+++.+|+.+++|++ .+|.+|++..+++.+.++++++.+....+
T Consensus 1 y~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~l~~~~~~~~~---~~f~~wl~~i~~~~~~d~~r~~~~~~~~~------ 71 (154)
T TIGR02950 1 YREYMHDVFRYLYRLTKDKHLAEDLLQETFLKAYIHLHSFKD---SSIKPWLFRIARNAFIDWYRKDKKIQTID------ 71 (154)
T ss_pred CchHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHhcC---CchHHHHHHHHHHHHHHHHHHhhhhcccc------
Confidence 357899999999999999899999999999999999999997 37999999999999999998765311000
Q ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHHHHHHHH
Q 007404 451 TYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKF 530 (605)
Q Consensus 451 i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~l~~~e 530 (605)
.+. +.+...+ ....|++.+...+
T Consensus 72 --------------------~~~------------------------------------~~~~~~~-~~~~~~~~~~~~~ 94 (154)
T TIGR02950 72 --------------------DDA------------------------------------IGDLEQH-PVESPEHHLLIKI 94 (154)
T ss_pred --------------------Hhh------------------------------------hhhcccc-ccCChhHHHHHHH
Confidence 000 0000001 1124566666666
Q ss_pred HHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 007404 531 MKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 593 (605)
Q Consensus 531 l~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 593 (605)
....|..+|..||+++++||.++|+.| +|++|||+.||+|..+|++..+||+++||+.+
T Consensus 95 ~~~~l~~~l~~L~~~~r~i~~l~~~~g----~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~~l 153 (154)
T TIGR02950 95 EQEEITHHLSRLPENYRTVLILREFKE----FSYKEIAELLNLSLAKVKSNLFRARKELKKLL 153 (154)
T ss_pred HHHHHHHHHHhCCHhheeeeeehhhcc----CcHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 677899999999999999999999877 99999999999999999999999999999865
No 109
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=99.78 E-value=1e-17 Score=163.49 Aligned_cols=162 Identities=14% Similarity=0.100 Sum_probs=127.8
Q ss_pred HhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccc
Q 007404 360 LNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSR 439 (605)
Q Consensus 360 l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr 439 (605)
+..+..+++.++..|.+.|+.+|+++.++..+++|++||+|+.+|+.++.|++. ..|.+|++..+++.+.+.++++.+
T Consensus 18 ~~~~~~~f~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQdvflkl~~~~~~~~~~--~~~~~wL~~Iarn~~~~~~r~~~~ 95 (188)
T PRK12517 18 MLSKQRRYEALVKALHADIYRYAYWLCKDKHIAEDLVQETFLRAWRSLDSLKDE--KAAKAWLITILRRENARRFERKQF 95 (188)
T ss_pred hhccHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhhcCc--cchHHHHHHHHHHHHHHHHHHhcc
Confidence 345688999999999999999999999999999999999999999999999865 369999999999987665543221
Q ss_pred cccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCC
Q 007404 440 TIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEA 519 (605)
Q Consensus 440 ~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~ 519 (605)
. . ...+ .. ...+...
T Consensus 96 ~--~----------------------------------------------------~~~~-------~~----~~~~~~~ 110 (188)
T PRK12517 96 D--L----------------------------------------------------VDIE-------DD----SIEDDAS 110 (188)
T ss_pred C--c----------------------------------------------------cCcc-------cc----cccCccc
Confidence 0 0 0000 00 0111111
Q ss_pred CCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhh
Q 007404 520 ETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK 596 (605)
Q Consensus 520 ~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 596 (605)
.+++.. .....|..+|..||+++|.||.++|..| ++++|||+.||||..+|+.+++||+++||+.+...
T Consensus 111 ~~~e~~----~~~~~l~~~l~~Lp~~~r~v~~l~~~~g----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~ 179 (188)
T PRK12517 111 HSSEEE----MEQEWLRRQIAKLDPEYREPLLLQVIGG----FSGEEIAEILDLNKNTVMTRLFRARNQLKEALEKP 179 (188)
T ss_pred cChhHH----HHHHHHHHHHHhCCHHHHHHHHHHHHhC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 133332 2235689999999999999999999988 99999999999999999999999999999998754
No 110
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=99.78 E-value=8.4e-18 Score=163.34 Aligned_cols=160 Identities=14% Similarity=0.156 Sum_probs=127.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcccccccc
Q 007404 365 LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLP 444 (605)
Q Consensus 365 ~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP 444 (605)
.++..++..|.+.|+.+|.++.++..+++|++||.|+.+|+..++|++.. .|.+|++..++|.++++++++.+....
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 46888999999999999999999999999999999999999999998653 699999999999999999876531100
Q ss_pred ccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHH
Q 007404 445 FHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAED 524 (605)
Q Consensus 445 ~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe 524 (605)
.+. ...+... + .++.
T Consensus 82 -----------------------------------------------------~~~--------~~~~~~~-~---~~~~ 96 (182)
T PRK12540 82 -----------------------------------------------------ADG--------SYAKTLK-S---QPGQ 96 (182)
T ss_pred -----------------------------------------------------ccc--------ccccccc-C---CCch
Confidence 000 0000000 0 1111
Q ss_pred HHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhhH
Q 007404 525 LLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHL 598 (605)
Q Consensus 525 ~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L 598 (605)
.. ......|..+|+.||+++|+||.|+|..+ +|++|||+.||+|..+|+++++||+++||+.+.....
T Consensus 97 ~~--~~~~~~l~~~l~~Lp~~~R~v~~L~~~~g----~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~~~~~ 164 (182)
T PRK12540 97 NA--HLEFEEFRAALDKLPQDQREALILVGASG----FSYEDAAAICGCAVGTIKSRVNRARSKLSALLYVDGA 164 (182)
T ss_pred HH--HHHHHHHHHHHHhCCHHHHHHhhHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhccc
Confidence 11 11234689999999999999999999887 9999999999999999999999999999999886553
No 111
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=99.77 E-value=1.2e-17 Score=162.02 Aligned_cols=154 Identities=14% Similarity=0.120 Sum_probs=127.0
Q ss_pred HHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcccccccccc
Q 007404 367 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFH 446 (605)
Q Consensus 367 ~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~ 446 (605)
++.|++.|.+.|+.++.++.++..+++|++||.++.+|+.+..|++. .+|.+|++..+++.+.++++++.+...++
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 37999999999999999998765411100
Q ss_pred HHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHHHH
Q 007404 447 MVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLL 526 (605)
Q Consensus 447 ~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~l 526 (605)
++. ...+ .+++..
T Consensus 79 ----------------------------------------------------------~~~-----~~~~----~~~~~~ 91 (181)
T PRK09637 79 ----------------------------------------------------------DDL-----LFED----EEREEN 91 (181)
T ss_pred ----------------------------------------------------------hhh-----hccC----CChhHH
Confidence 000 0000 111223
Q ss_pred HHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 007404 527 IKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT 595 (605)
Q Consensus 527 ~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 595 (605)
...+....+..+|+.||+++|.||.|+|..| ++++|||+.||+|..+|+.++.||+++||+.+..
T Consensus 92 ~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g----~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 156 (181)
T PRK09637 92 AKKELAPCLRPFIDALPEKYAEALRLTELEG----LSQKEIAEKLGLSLSGAKSRVQRGRVKLKELLEG 156 (181)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHHHHHHhcC----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 3344567799999999999999999999988 9999999999999999999999999999998764
No 112
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=99.77 E-value=1.1e-17 Score=160.37 Aligned_cols=162 Identities=14% Similarity=0.081 Sum_probs=126.9
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcccccc
Q 007404 363 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIR 442 (605)
Q Consensus 363 g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IR 442 (605)
+..|+..++..|.+.++.++.++.++..+++||+||.|+.+|+. ..|++.. .|.+|++..++|.+.++++++.+...
T Consensus 8 ~~~af~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQe~flkl~~~-~~~~~~~--~~~~wL~~iarn~~~d~~R~~~~~~~ 84 (172)
T PRK09651 8 ASLTFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVS-ETLSTIR--DPRSFLCTIAKRVMVDLFRRNALEKA 84 (172)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhh-ccccccc--CHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 36799999999999999999999999999999999999999998 3565432 58999999999999999986532000
Q ss_pred ccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCH
Q 007404 443 LPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETA 522 (605)
Q Consensus 443 lP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~sp 522 (605)
. ...+ . .+ .+...++|
T Consensus 85 ~---------------------------~~~~------------------------------~---~~----~~~~~~~~ 100 (172)
T PRK09651 85 Y---------------------------LEML------------------------------A---LM----PEGGAPSP 100 (172)
T ss_pred h---------------------------hhHH------------------------------h---hc----cccCCCCh
Confidence 0 0000 0 00 00011134
Q ss_pred HHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 007404 523 EDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT 595 (605)
Q Consensus 523 Ee~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 595 (605)
+......+....|..+|+.||+++|+||.|+|+.+ +|++|||+.||+|.++|+..++||+++|+...-.
T Consensus 101 ~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g----~s~~EIA~~lgis~~tV~~~l~Ra~~~~~~~~~~ 169 (172)
T PRK09651 101 EERESQLETLQLLDSMLDGLNGKTREAFLLSQLDG----LTYSEIAHKLGVSVSSVKKYVAKATEHCLLFRLE 169 (172)
T ss_pred HHHHHHHHHHHHHHHHHHhCCHHHhHHhhhhhccC----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 44444445557799999999999999999999988 9999999999999999999999999999986543
No 113
>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=99.77 E-value=1.6e-17 Score=166.52 Aligned_cols=115 Identities=16% Similarity=0.187 Sum_probs=104.0
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHhhCCC--CCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcc-
Q 007404 362 YGILCKDKMITSNIRLVISIAKNYQGAG--MNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQS- 438 (605)
Q Consensus 362 ~g~~A~e~LI~~nlrLVvsIAkrY~~~g--~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~s- 438 (605)
|+.. +++||..|.++|.++|++|.++. .+.+|++|+|++|||+|+++|||++|.+|.|||.+|||+.|.+++|+..
T Consensus 7 gd~~-~e~LI~~Y~plI~~~a~~~~~~~~~~e~dDlvQ~glial~eAi~~yd~~kg~~F~sya~~~Ir~~i~dylRk~~k 85 (218)
T TIGR02895 7 GNEE-REELIRQYKPFIAKIVSSVCGRYIDTKSDDELSIGLIAFNEAIESYDSNKGKSFLSFAKLIIKRRLIDYIRKNQK 85 (218)
T ss_pred CChH-HHHHHHHhHHHHHHHHHHHHccCCCCChhHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHhccc
Confidence 4455 99999999999999999998764 5899999999999999999999999999999999999999999999887
Q ss_pred --ccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHh
Q 007404 439 --RTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEA 477 (605)
Q Consensus 439 --r~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~ 477 (605)
+.+++|....+....+..+...+..+.++.|+.+||+..
T Consensus 86 ~~~~v~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~eEI~~~ 126 (218)
T TIGR02895 86 YQNLLYLDEDYDENPLEFNKSMEEYRNEIENENRRLEILEY 126 (218)
T ss_pred ccCeeeCCchHHHHHHHHHHHHHHHHHHHccccHHHHHHHH
Confidence 678999776666778888888999999999999999864
No 114
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=99.76 E-value=2.7e-17 Score=160.77 Aligned_cols=157 Identities=12% Similarity=0.137 Sum_probs=122.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccc
Q 007404 364 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRL 443 (605)
Q Consensus 364 ~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRl 443 (605)
..+++.|+. |.+.|+.+|+.+.++..+++|++||.|+.+|+.+..|+.. ..|.+|++..++|.+.++++++.+....
T Consensus 7 ~~~~~~l~~-~~~~l~~~a~~~l~~~~~AEDivQevfl~l~~~~~~~~~~--~~~~awL~~ia~n~~~d~~Rk~~r~~~~ 83 (188)
T PRK12546 7 RDPRDELVE-HLPALRAFAISLTRNVAVADDLVQDTIVKAWTNFDKFQEG--TNLRAWLFTILRNTFYSDRRKHKREVPD 83 (188)
T ss_pred hhHHHHHHH-HHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHhccCCC--cchHHHHHHHHHHHHHHHHHHhcccccC
Confidence 456666766 7799999999999999999999999999999999999864 3699999999999999998876531000
Q ss_pred cccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHH
Q 007404 444 PFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAE 523 (605)
Q Consensus 444 P~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spE 523 (605)
.+. ...+...+.. ..+
T Consensus 84 ------------------------------------------------------~~~--------~~~~~~~~~~--~~~ 99 (188)
T PRK12546 84 ------------------------------------------------------PEG--------VHAASLAVKP--AHD 99 (188)
T ss_pred ------------------------------------------------------ccc--------ccccccccCC--cch
Confidence 000 0000000000 111
Q ss_pred HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 007404 524 DLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT 595 (605)
Q Consensus 524 e~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 595 (605)
. ......|..+|..||+++|+||.|+|..+ +|++|||+.||||..+|+++++||+++||+.+..
T Consensus 100 ~----~~~~~~l~~~L~~Lp~~~r~v~~L~~~~g----~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l~~ 163 (188)
T PRK12546 100 G----RLAMSDFRAAFAQLPDEQREALILVGASG----FSYEEAAEMCGVAVGTVKSRANRARARLAELLQL 163 (188)
T ss_pred h----HHHHHHHHHHHHhCCHHHhHHhhhHHhcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 1 12234688999999999999999999987 9999999999999999999999999999998864
No 115
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=99.76 E-value=2.4e-17 Score=157.89 Aligned_cols=148 Identities=18% Similarity=0.206 Sum_probs=121.5
Q ss_pred HHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHHHHH
Q 007404 372 TSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEAT 451 (605)
Q Consensus 372 ~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~~~i 451 (605)
..|.+.++.+++++.++..+++|++||+|+.+|+++++|++. .+|.+|++..+++.+.+++++..+...++
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 468899999999999999999999999999999999999863 47999999999999999998875411110
Q ss_pred HHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHHHHHHHHH
Q 007404 452 YRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFM 531 (605)
Q Consensus 452 ~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~l~~~el 531 (605)
+ . .... . ++++.....+.
T Consensus 73 -----------------------------------------------~-----~-------~~~~-~--~~~~~~~~~e~ 90 (170)
T TIGR02959 73 -----------------------------------------------E-----S-------LLAA-D--SAREETFVKEL 90 (170)
T ss_pred -----------------------------------------------h-----h-------hccc-C--CccHHHHHHHH
Confidence 0 0 0000 0 11222334445
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404 532 KEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR 594 (605)
Q Consensus 532 ~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 594 (605)
...|..+|..||+++|.||.|+|..+ +|++|||+.||+|..+|+++++||+++||..+.
T Consensus 91 ~~~l~~~l~~L~~~~r~v~~l~~~~g----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 149 (170)
T TIGR02959 91 SQCIPPMIKELPDEYREAIRLTELEG----LSQQEIAEKLGLSLSGAKSRVQRGRKKLKELLE 149 (170)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 66789999999999999999999988 999999999999999999999999999999876
No 116
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=99.75 E-value=3.1e-17 Score=159.46 Aligned_cols=156 Identities=13% Similarity=0.133 Sum_probs=122.6
Q ss_pred HHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcccccccccc
Q 007404 367 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFH 446 (605)
Q Consensus 367 ~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~ 446 (605)
.+..+..+++.|+.++.++.++..+++|++||.|+.+|+....|++. .+|.+|++..+++.+.++++++.+.....
T Consensus 6 ~~~~~~~~~~~l~~~~~~~~~~~~dAEDivQe~flkl~~~~~~~~~~--~~~~~WL~~Iarn~~id~~Rk~~~~~~~~-- 81 (182)
T PRK12511 6 KRFDVLDQLVPLRRYARSLTRDSAEAEDLVHDALVRALERRASFRSG--GNLRTWLMSILHNAFIDELRRRRVEARRA-- 81 (182)
T ss_pred hhhhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCc--cchHHHHHHHHHHHHHHHHHhhccccccc--
Confidence 44568889999999999999999999999999999999999999864 36999999999999999998865411000
Q ss_pred HHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHHHH
Q 007404 447 MVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLL 526 (605)
Q Consensus 447 ~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~l 526 (605)
+++ . +. .+...+.+.+
T Consensus 82 -------------------------~~~------------------------~------------~~-~~~~~~~~~~-- 97 (182)
T PRK12511 82 -------------------------DEL------------------------A------------VL-ADASLPAAQE-- 97 (182)
T ss_pred -------------------------cch------------------------h------------hc-cccCCCcchH--
Confidence 000 0 00 0000001111
Q ss_pred HHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 007404 527 IKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT 595 (605)
Q Consensus 527 ~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 595 (605)
.......|..+|..||+++|+||.|+|..+ +|++|||+.||||.++|+++++||+++||+.+..
T Consensus 98 -~~~~~~~l~~~l~~Lp~~~R~v~~L~~~eg----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~~~ 161 (182)
T PRK12511 98 -HAVRLAQIRDAFFDLPEEQRAALHLVAIEG----LSYQEAAAVLGIPIGTLMSRIGRARAALRAFEEG 161 (182)
T ss_pred -HHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHHh
Confidence 122345688999999999999999999987 9999999999999999999999999999998864
No 117
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=99.75 E-value=5.9e-17 Score=154.63 Aligned_cols=159 Identities=15% Similarity=0.108 Sum_probs=127.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccc
Q 007404 364 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRL 443 (605)
Q Consensus 364 ~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRl 443 (605)
..++.+++..|.+.++.++.+|.++..+++|++||.|+.+|+..+.++. ..|.+|++..++|.+.+++++....
T Consensus 8 ~~~~~~~~~~~~~~l~~~~~~~~~~~~~aeDlvQevf~~l~~~~~~~~~---~~~~~wl~~Iarn~~~d~~Rr~~~~--- 81 (168)
T PRK12525 8 NTLIGQMFQQDYDWLCKKLSRQLGCPHSAEDIASETFLQVLALPDPASI---REPRALLTTIARRLMYEGWRRQDLE--- 81 (168)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCcCcHHHHHHHHHHHHHhCCCcccc---cCHHHHHHHHHHHHHHHHHHHHHHH---
Confidence 4689999999999999999999999999999999999999987665542 2699999999999999988764310
Q ss_pred cccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHH
Q 007404 444 PFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAE 523 (605)
Q Consensus 444 P~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spE 523 (605)
+..... ++ + .+.....+|+
T Consensus 82 ---------------~~~~~~---------------------------------~~-----~--------~~~~~~~~~~ 100 (168)
T PRK12525 82 ---------------RAYLQS---------------------------------LA-----E--------APEAVQPSPE 100 (168)
T ss_pred ---------------HHHHHH---------------------------------Hh-----c--------ccccccCChH
Confidence 000000 00 0 0001113566
Q ss_pred HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 007404 524 DLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 593 (605)
Q Consensus 524 e~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 593 (605)
+.....+....|..+|..||+++|+||.|+|..| +|++|||+.||+|..+|+..+.||+++||..+
T Consensus 101 ~~~~~~~~~~~l~~~l~~L~~~~r~v~~L~~~eg----~s~~EIA~~l~is~~tV~~~l~ra~~~~~~~~ 166 (168)
T PRK12525 101 EQWMVIETLLAIDRLLDGLSGKARAAFLMSQLEG----LTYVEIGERLGVSLSRIHQYMVEAFKCCYQGF 166 (168)
T ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhh
Confidence 6666666678899999999999999999999888 99999999999999999999999999999865
No 118
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=99.74 E-value=7e-17 Score=167.88 Aligned_cols=160 Identities=16% Similarity=0.141 Sum_probs=124.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcccccccc
Q 007404 365 LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLP 444 (605)
Q Consensus 365 ~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP 444 (605)
..+..++..|.+.++.+|+++.++..+++|++||.|+. |.....|+. ..|.+|++..++|.++++++++.+....
T Consensus 4 ~~~~~l~~~~~~~l~~~a~~~~~~~~dAEDlvQe~fl~-~~~~~~~~~---~~~~~WL~~Ia~n~~~d~lR~~~~~~~~- 78 (293)
T PRK09636 4 ADAAAEFEPLRPHLLSVAYRMLGSVADAEDIVQEAWLR-WNNADRAQI---RDPRAWLTRVVTRLCLDRLRSARHRRET- 78 (293)
T ss_pred cHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH-HHhcccccc---cCHHHHHHHHHHHHHHHHHHhhhccccc-
Confidence 34678999999999999999999999999999999999 666677762 4799999999999999999875431000
Q ss_pred ccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHH
Q 007404 445 FHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAED 524 (605)
Q Consensus 445 ~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe 524 (605)
.. + ..+.+...+.. .+|++
T Consensus 79 ----------------------------------------------------~~----~----~~~~e~~~~~~-~~~~~ 97 (293)
T PRK09636 79 ----------------------------------------------------YV----G----PWLPEPVVEEL-DDPLE 97 (293)
T ss_pred ----------------------------------------------------cc----C----CcCCcCCCCCC-CChHH
Confidence 00 0 00000011111 13444
Q ss_pred H-HHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404 525 L-LIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR 594 (605)
Q Consensus 525 ~-l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 594 (605)
. .....+...+..+|+.||+++|.||.|+|..+ +|++|||+.||+|..+|+++++||+++||+...
T Consensus 98 ~~~~~~~~~~~l~~~l~~L~~~~R~v~~L~~~~g----~s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~~~ 164 (293)
T PRK09636 98 AVVAAEDLSLALMLALERLSPLERAAFLLHDVFG----VPFDEIASTLGRSPAACRQLASRARKHVRAARP 164 (293)
T ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCC
Confidence 3 33445566789999999999999999999988 999999999999999999999999999999754
No 119
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=99.72 E-value=1.1e-16 Score=150.56 Aligned_cols=155 Identities=16% Similarity=0.180 Sum_probs=113.0
Q ss_pred CCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHHHHHHHHHHHHHHHHHHcC
Q 007404 387 GAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENG 466 (605)
Q Consensus 387 ~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~~~i~ki~ka~~~L~~elg 466 (605)
++..+++|++||+|+.+|+....+ + +..|.+|++..++|.++++++++.+..+....
T Consensus 2 ~~~~~AeDivQe~fl~~~~~~~~~-~--~~~~~~wl~~ia~n~~~d~~Rk~~~~~~~~~~-------------------- 58 (161)
T PRK09047 2 RDDDAALDIVQDAMIKLAEKYGDR-P--AAEWPPLFQRILQNRIHDWFRRQKVRNTWVSL-------------------- 58 (161)
T ss_pred CCHHHHHHHHHHHHHHHHHHHhhc-c--cCchHHHHHHHHHHHHHHHHHhhccccccccc--------------------
Confidence 344678999999999999998863 3 34799999999999999999876531111000
Q ss_pred CCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCC--CCCHHHHHHHHHHHHHHHHHHhcCCH
Q 007404 467 RHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPE--AETAEDLLIKKFMKEDLEKVLDTLNP 544 (605)
Q Consensus 467 r~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~--~~spEe~l~~~el~~~L~~aL~~L~~ 544 (605)
..++..... +++....+.+.+.. ..+|++.+...+....|..+|..||+
T Consensus 59 ----------------------------~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~ 109 (161)
T PRK09047 59 ----------------------------FSSFSDDDD-DDDFDPLETLDSADEGAESPADKLERAQVLQLIEEAIQKLPA 109 (161)
T ss_pred ----------------------------ccccccccc-cccccHHHHhccccccCCCHHHHHHHHHHHHHHHHHHHhCCH
Confidence 000000000 00011111122111 24677777777888889999999999
Q ss_pred HHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhh
Q 007404 545 RERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKH 597 (605)
Q Consensus 545 rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~ 597 (605)
++|+||.|+|+.| +|++|||+.||||..+|+.+++||+++||+.+...+
T Consensus 110 ~~r~v~~l~~~~g----~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~ 158 (161)
T PRK09047 110 RQREAFLLRYWED----MDVAETAAAMGCSEGSVKTHCSRATHALAKALEAKG 158 (161)
T ss_pred HHHHHHHHHHHhc----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhcC
Confidence 9999999999988 999999999999999999999999999999887654
No 120
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=99.70 E-value=5.7e-16 Score=156.41 Aligned_cols=159 Identities=13% Similarity=0.137 Sum_probs=124.4
Q ss_pred HHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHH
Q 007404 355 ELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSL 434 (605)
Q Consensus 355 ~L~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~i 434 (605)
.|++.+.++..+++.+++.| +.++.++.++.++..+++||+||.|+.+|+. |+.. ..|.+|++.+++|.+++++
T Consensus 8 ~~~~~~~~~~~~~~~l~~~y-~~L~r~~~~~~~d~~dAEDlvQE~flk~~~~---~~~~--~~~~~WL~~IarN~~id~~ 81 (228)
T PRK06704 8 ILKNHIDMNHSNINFLIEQY-GELKRYCTFLTKNKWDGEDLAQETVCKVLQK---YSNK--DICMTLVYKIARNRWLDQI 81 (228)
T ss_pred HHhcccCCCHHHHHHHHHHH-HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH---cCcc--ccHHHHHHHHHHHHHHHHH
Confidence 34555667778898888877 7899999999999999999999999999986 5543 2599999999999999999
Q ss_pred hhccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCccc
Q 007404 435 SDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVI 514 (605)
Q Consensus 435 r~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l 514 (605)
+++.+.-.+ . + ... .
T Consensus 82 Rk~k~~~~~-------------------------------------------------------~-----~-~~~----~ 96 (228)
T PRK06704 82 KSKSVHEKI-------------------------------------------------------R-----D-QIT----F 96 (228)
T ss_pred hcccccccc-------------------------------------------------------c-----c-ccc----c
Confidence 876531000 0 0 000 0
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404 515 ADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR 594 (605)
Q Consensus 515 ~D~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 594 (605)
..+.+.. .+..+.+..+|+.||+++|.||.|+|..+ +|++|||+.||+|.++|+++++||+++||+.+.
T Consensus 97 -----~~~~~~~--~~~~~~l~~~L~~Lp~~~R~v~lL~~~eg----~S~~EIAe~LgiS~~tVksrL~Rark~Lr~~l~ 165 (228)
T PRK06704 97 -----EEPHEKI--ADLHEMVGKVLSSLNVQQSAILLLKDVFQ----YSIADIAKVCSVSEGAVKASLFRSRNRLKTVSE 165 (228)
T ss_pred -----CChHHHH--HHHHHHHHHHHHhCCHHHhhHhhhHHhhC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 0111111 12345688999999999999999999887 999999999999999999999999999999886
Q ss_pred h
Q 007404 595 T 595 (605)
Q Consensus 595 ~ 595 (605)
.
T Consensus 166 ~ 166 (228)
T PRK06704 166 E 166 (228)
T ss_pred h
Confidence 4
No 121
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.
Probab=99.69 E-value=5.9e-16 Score=160.34 Aligned_cols=156 Identities=18% Similarity=0.161 Sum_probs=120.3
Q ss_pred HHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHH
Q 007404 369 KMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMV 448 (605)
Q Consensus 369 ~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~ 448 (605)
+++..|.+.++.+|+++.++..++||++||+|+.+++. .|+.. ..|.+|++.+++|.+++++++..+....
T Consensus 1 ~l~~~~~~~l~~~a~r~lg~~~dAEDvvQE~flk~~~~--~~~~~--~~~~awL~~Ia~n~~ld~lR~~~~~~~~----- 71 (281)
T TIGR02957 1 EEFEALRPLLFSLAYRMLGSVADAEDIVQETFLRWQEA--DRAQI--ENPKAYLTKVVTRRCIDVLRSARARREV----- 71 (281)
T ss_pred ChHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhC--Ccccc--cCHHHHHHHHHHHHHHHHHHHhhhcccc-----
Confidence 37899999999999999999999999999999998775 45432 3699999999999999999875421000
Q ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHHHHHH
Q 007404 449 EATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIK 528 (605)
Q Consensus 449 ~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~l~~ 528 (605)
.. +..+.+...+. ..+|++....
T Consensus 72 -------------------------------------------------~~-------~~~~~e~~~~~-~~~~~~~~~~ 94 (281)
T TIGR02957 72 -------------------------------------------------YV-------GPWLPEPLLTT-SADPAESVEL 94 (281)
T ss_pred -------------------------------------------------cC-------CCCCCcccCCC-CCChHHHHHH
Confidence 00 00000001111 1245554443
Q ss_pred -HHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404 529 -KFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR 594 (605)
Q Consensus 529 -~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 594 (605)
+.+...+..+|++||++||.||.|+|..+ +|++|||+.||+|..+|+++++||+++||+...
T Consensus 95 ~e~~~~~l~~~l~~L~~~~R~v~~L~~~~g----~s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~~~ 157 (281)
T TIGR02957 95 AESLSMAYLLLLERLSPLERAVFVLREVFD----YPYEEIASIVGKSEANCRQLVSRARRHLDARRP 157 (281)
T ss_pred HHHHHHHHHHHHhhCCHHHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCC
Confidence 34556788999999999999999999988 999999999999999999999999999998653
No 122
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=99.68 E-value=1.3e-15 Score=158.91 Aligned_cols=161 Identities=16% Similarity=0.133 Sum_probs=124.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcccccccc
Q 007404 365 LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLP 444 (605)
Q Consensus 365 ~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP 444 (605)
..+..+++.|.+.++.+|+++.++..++||++||.|+.+|++...+ . ..|.+|++...+|.+++++++..+.-..+
T Consensus 5 ~~~~~l~~~~~~~L~~~a~r~lgs~~dAEDvvQE~flr~~~~~~~~-~---~~~~aWL~~Ia~n~~id~lRk~~~rr~~~ 80 (290)
T PRK09635 5 DPVSAAWRAHRAYLVDLAFRMVGDIGVAEDMVQEAFSRLLRAPVGD-I---DDERGWLIVVTSRLCLDHIKSASTRRERP 80 (290)
T ss_pred cHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCccc-c---ccHHHHHHHHHHHHHHHHHhhhhccCcCc
Confidence 4678899999999999999999999999999999999999987653 1 25999999999999999998754210000
Q ss_pred ccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHH
Q 007404 445 FHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAED 524 (605)
Q Consensus 445 ~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe 524 (605)
...+... ..+..++ ..+|++
T Consensus 81 ---------------------------------------------------~~~~~~~-------~~~~~~~--~~~~~~ 100 (290)
T PRK09635 81 ---------------------------------------------------QDIAAWH-------DGDASVS--SVDPAD 100 (290)
T ss_pred ---------------------------------------------------ccccccC-------ccccCCC--CCCcHH
Confidence 0000000 0000111 113333
Q ss_pred -HHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 007404 525 -LLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 593 (605)
Q Consensus 525 -~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 593 (605)
....++....+..+|..|||++|.||.|+|..+ +|++|||+.||+|..+|+++++||+++||+..
T Consensus 101 ~~~~~~e~~~al~~~L~~L~p~~R~vf~L~~~~g----~s~~EIA~~Lgis~~tVr~~l~RAr~~Lr~~~ 166 (290)
T PRK09635 101 RVTLDDEVRLALLIMLERLGPAERVVFVLHEIFG----LPYQQIATTIGSQASTCRQLAHRARRKINESR 166 (290)
T ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHhhHHHHhC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHhhC
Confidence 344556667899999999999999999999998 99999999999999999999999999999854
No 123
>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR. Similarly, tetanus toxin production of Clostridium tetani is regulated by TetR which is a very close relative of BotR. Both BotR and TetR are members of the TIGR02937 subfamily of sigma-70 RNA polymerase sigma factors. Functional complementation experiments have been done for botR and tetR in highly transformable strain of Clostridium perfringens host cells to assess functional interchangeability of sigma factors and it has been confirmed that they are interchangeable in vivo.
Probab=99.55 E-value=5.8e-14 Score=130.16 Aligned_cols=136 Identities=11% Similarity=0.164 Sum_probs=100.9
Q ss_pred HHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhc-----cCCcCCCcchhHHHHHHHHHHHHHHhhccccc
Q 007404 367 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEK-----FDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI 441 (605)
Q Consensus 367 ~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ek-----FDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~I 441 (605)
++.|+..|.++++.++++|... +| +||.++.+|+.+.+ |++. ..|.||++..+||.++++++++.+..
T Consensus 1 f~~~~~~y~~~l~~~~~~~~~~----~~-~qdvf~~~w~~~~~~~~~~~~~~--~~~~~wL~~iarN~~id~~Rk~~~~~ 73 (142)
T TIGR03209 1 FEEIYMNFKNTIDIFTRKYNLY----YD-YNDILYHLWIILKKIDLNKFNTE--NDLEKYISTSLKRYCLDICNKKNRDK 73 (142)
T ss_pred ChHHHHHHHHHHHHHHHHhcch----hh-HHHHHHHHHHHHHHhhhhhcCch--hHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 4679999999999999999762 34 49999999999865 5543 46999999999999999998764310
Q ss_pred cccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCC
Q 007404 442 RLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAET 521 (605)
Q Consensus 442 RlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~s 521 (605)
+. . .. .+ + . +.. ..
T Consensus 74 ~~-----------------~-~~-------~~------------------------~------~----------~~~-~~ 87 (142)
T TIGR03209 74 KI-----------------I-YN-------SE------------------------I------T----------DIK-LS 87 (142)
T ss_pred hh-----------------h-hh-------hh------------------------h------h----------ccc-cc
Confidence 00 0 00 00 0 0 000 01
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHH
Q 007404 522 AEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIR 579 (605)
Q Consensus 522 pEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVR 579 (605)
+.+.....+....|..+|+.||+++|+||.|+|..| +|++|||+.||+|.+||+
T Consensus 88 ~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~~~~----~s~~EIA~~l~is~~tV~ 141 (142)
T TIGR03209 88 LINVYSSNDLEFEFNDLISILPNKQKKIIYMKFFED----MKEIDIAKKLHISRQSVY 141 (142)
T ss_pred hhHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHhhc
Confidence 122333444556789999999999999999999988 999999999999999997
No 124
>PRK09191 two-component response regulator; Provisional
Probab=99.52 E-value=1.1e-13 Score=139.12 Aligned_cols=136 Identities=14% Similarity=0.143 Sum_probs=111.1
Q ss_pred HHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccc
Q 007404 366 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPF 445 (605)
Q Consensus 366 A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~ 445 (605)
++..|+..|.+.|+.+|.++.++..+++|++||+|+.+|+...+|++. ..|.+|++.++++..... .
T Consensus 2 ~~~~l~~~~~~~l~~~~~~~~~~~~~aeDi~qd~~~~~~~~~~~~~~~--~~~~~wl~~~~~~~~~~~----~------- 68 (261)
T PRK09191 2 SLSQRIAPHLPYLRRYARALTGSQSSGDAYVAATLEALLADPSIFPEA--SSPRVGLYRLFHRLWSSA----G------- 68 (261)
T ss_pred chHHHHHHHhHHHHHHHHHhcCChhhHHHHHHHHHHHHHHhHHhcCCC--cchhhHHHHHHHHHhccc----c-------
Confidence 578899999999999999999999999999999999999999999874 358999998775432100 0
Q ss_pred cHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHHH
Q 007404 446 HMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDL 525 (605)
Q Consensus 446 ~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~ 525 (605)
. . .. ... .+..
T Consensus 69 --------------------------------------------------------~--~-~~-------~~~--~~~~- 79 (261)
T PRK09191 69 --------------------------------------------------------A--N-DP-------EPG--SPFE- 79 (261)
T ss_pred --------------------------------------------------------c--c-CC-------CCC--CCch-
Confidence 0 0 00 000 0110
Q ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404 526 LIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR 594 (605)
Q Consensus 526 l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 594 (605)
..+..+|+.||+++|+||.|+|..+ +|++|||+.||+|.++|+.+.+||+++||..+.
T Consensus 80 -------~~l~~~l~~L~~~~r~v~~l~~~~~----~s~~eIA~~l~~s~~tV~~~l~ra~~~l~~~~~ 137 (261)
T PRK09191 80 -------ARAERRLAGLTPLPRQAFLLTALEG----FSVEEAAEILGVDPAEAEALLDDARAEIARQVA 137 (261)
T ss_pred -------HHHHHHHHhCCHHHhHHHHHHHHhc----CCHHHHHHHHCCCHHHHHHHHHHHHHHHhccCC
Confidence 1688999999999999999999888 999999999999999999999999999998664
No 125
>PRK08311 putative RNA polymerase sigma factor SigI; Reviewed
Probab=99.41 E-value=1.3e-11 Score=125.58 Aligned_cols=86 Identities=15% Similarity=0.209 Sum_probs=76.5
Q ss_pred HHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCC--CHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHH
Q 007404 357 RRRLNYGILCKDKMITSNIRLVISIAKNYQGAGM--NLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSL 434 (605)
Q Consensus 357 ~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~--d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~i 434 (605)
.....++..|++.|+..|.++|+++|.+|.++.. +.+|++|||++++|+++++|++++|.+|.+|++.+|++.+.+++
T Consensus 10 ~~~~~gD~~AfeeLi~~Y~p~I~~~a~~~~~~~~~~eaeDlvQe~fi~l~eai~~y~~~kg~sF~awl~~Iirn~~iDyl 89 (237)
T PRK08311 10 EKIKNGDEELREELIEEYKPFIAKVVSSVCGRYIDWENDDELSIGLIAFNEAIDSYDEEKGKSFLSFAELVIKRRLIDYF 89 (237)
T ss_pred HHHHCCCHHHHHHHHHHHHHHHHHHHHHHhcccCCCCchHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHH
Confidence 3344566889999999999999999999998765 58999999999999999999999988899999999999999999
Q ss_pred hhcccccc
Q 007404 435 SDQSRTIR 442 (605)
Q Consensus 435 r~~sr~IR 442 (605)
|++.+...
T Consensus 90 Rk~~~~~~ 97 (237)
T PRK08311 90 RKESKHNL 97 (237)
T ss_pred HHhhcccc
Confidence 98766433
No 126
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=99.39 E-value=2.4e-11 Score=118.66 Aligned_cols=173 Identities=25% Similarity=0.310 Sum_probs=119.7
Q ss_pred HHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCC---CCCHHH--HHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHH
Q 007404 355 ELRRRLNYGILCKDKMITSNIRLVISIAKNYQGA---GMNLQD--LVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQA 429 (605)
Q Consensus 355 ~L~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~---g~d~eD--LIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqa 429 (605)
.|.+...||..|++.|+..|+.-++.+|+++... +.+.+| |++|.|+.+++.-...+.+.-..|-.|+...+++.
T Consensus 7 ll~~~~~GD~~A~~~L~~~~y~~L~~~a~~~l~~~~~~~~~~~~~lv~ea~lrl~~~~~~~~~~~~~~f~~~~~~~~rr~ 86 (185)
T PF07638_consen 7 LLDRWRQGDEAALDQLFERYYPELRRLARRRLRRERRGHDLQDTALVHEAFLRLARRGRFVQFSDRRHFWALLARIMRRK 86 (185)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHhccccCCchhHHHHHHHHHHHHhccccccCCCCHHHHHHHHHHHHHHH
Confidence 3455556779999999999999999999987643 344554 57788888877433323332236888888999999
Q ss_pred HHHHHhhccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCC
Q 007404 430 VRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLK 509 (605)
Q Consensus 430 I~r~ir~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~ 509 (605)
+.++.+++....|- |.. ...+||...
T Consensus 87 lid~~R~~~a~KRg----------------------~~~-------------------------~~~~l~~~~------- 112 (185)
T PF07638_consen 87 LIDHARRRQAQKRG----------------------GDQ-------------------------VRVELDERA------- 112 (185)
T ss_pred HHHHHHHHHHHhcC----------------------CCC-------------------------cccchhhhh-------
Confidence 98888876542221 000 011222111
Q ss_pred CCcccCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 007404 510 PSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKL 589 (605)
Q Consensus 510 l~d~l~D~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKL 589 (605)
.+...+.|++.+. +.+.+..+.. |+|+++++|.++|+.| +|.+|||+.||||..||+.....|..+|
T Consensus 113 -----~~~~~~~~~~~~~---l~e~l~~L~~-l~~~~~~~v~l~~~~G----ls~~EIA~~lgiS~~tV~r~l~~aR~~l 179 (185)
T PF07638_consen 113 -----DSGDEPSPEELLE---LEEALERLLA-LDPRQRRVVELRFFEG----LSVEEIAERLGISERTVRRRLRRARAWL 179 (185)
T ss_pred -----ccccCCCHHHHHH---HHHHHHHHHc-cCHHHHHHHHHHHHCC----CCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 0111235555433 3344555444 9999999999999877 9999999999999999999999999999
Q ss_pred HhHHh
Q 007404 590 KNKKR 594 (605)
Q Consensus 590 R~~l~ 594 (605)
+..+.
T Consensus 180 ~~~l~ 184 (185)
T PF07638_consen 180 RRELR 184 (185)
T ss_pred HHHhc
Confidence 98664
No 127
>PF04542 Sigma70_r2: Sigma-70 region 2 ; InterPro: IPR007627 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core-binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime [, ]. The aromatic residues of the recognition helix, found at the C terminus of this domain are thought to mediate strand separation, thereby allowing transcription initiation [, ].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1OR7_B 1H3L_B 2Z2S_C 2Q1Z_C 2O7G_B 1SMY_F 1IW7_P 2BE5_F 2A6E_F 2CW0_F ....
Probab=99.24 E-value=1.8e-11 Score=99.57 Aligned_cols=70 Identities=23% Similarity=0.377 Sum_probs=67.3
Q ss_pred HHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccc
Q 007404 370 MITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSR 439 (605)
Q Consensus 370 LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr 439 (605)
|++.|.++|++++++|.+++.+.+|++||++++||+++++||++++..|.+|++..+++.+.++++++.|
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 7899999999999999999999999999999999999999999999899999999999999999998765
No 128
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=99.21 E-value=3.7e-11 Score=93.05 Aligned_cols=50 Identities=46% Similarity=0.726 Sum_probs=46.0
Q ss_pred HHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 538 VLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 538 aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
+|+.||++|++||.++|+.+ +|++|||+.||+|+++|++++.+|++|||+
T Consensus 1 Al~~L~~~er~vi~~~y~~~----~t~~eIa~~lg~s~~~V~~~~~~al~kLR~ 50 (50)
T PF04545_consen 1 ALDQLPPREREVIRLRYFEG----LTLEEIAERLGISRSTVRRILKRALKKLRK 50 (50)
T ss_dssp HHCTS-HHHHHHHHHHHTST-----SHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred ChhhCCHHHHHHHHHHhcCC----CCHHHHHHHHCCcHHHHHHHHHHHHHHhcC
Confidence 58899999999999999887 999999999999999999999999999995
No 129
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=99.06 E-value=2e-10 Score=96.51 Aligned_cols=77 Identities=31% Similarity=0.538 Sum_probs=66.3
Q ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHHH
Q 007404 449 EATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDL 525 (605)
Q Consensus 449 ~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~ 525 (605)
+.+++|.+++++|.+++||.||.+|||+.||+++++|..++.....++|||.+++.+++.++.+++.|+...+|++.
T Consensus 1 E~l~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~~~~~~~Sl~~~~~~~~~~~l~~~i~d~~~~~P~e~ 77 (78)
T PF04539_consen 1 EKLRKIERARRELEQELGREPTDEEIAEELGISVEEVRELLQASRRPVSLDLPVGDEDDSTLGDFIEDDDAPSPEEE 77 (78)
T ss_dssp HHHHHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHHHHSCCEESSHCCSSSSSEEGGGSSB-SSS--HHHH
T ss_pred ChHHHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHHhCCCCeEEeeeecCCCCCchhheecCCCCCChhhc
Confidence 36789999999999999999999999999999999999999999999999999998888899999999988888875
No 130
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=98.91 E-value=3.8e-09 Score=82.74 Aligned_cols=54 Identities=28% Similarity=0.465 Sum_probs=46.5
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 007404 532 KEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKL 589 (605)
Q Consensus 532 ~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKL 589 (605)
++.|..+|..||+++|.||.++|..| +|++|||+.+|+|.++|++++.||+++|
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 REALQQALAQLPERQREIFLLRYFQG----MSYAEIAEILGISESTVKRRLRRARKKL 54 (54)
T ss_dssp HHHHHHHHHCS-HHHHHHHHHHHTS-------HHHHHHHCTS-HHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHC----cCHHHHHHHHCcCHHHHHHHHHHHHhhC
Confidence 35789999999999999999999988 9999999999999999999999999987
No 131
>PRK06930 positive control sigma-like factor; Validated
Probab=98.64 E-value=1.5e-07 Score=91.42 Aligned_cols=70 Identities=19% Similarity=0.332 Sum_probs=61.9
Q ss_pred HHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhh
Q 007404 523 EDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK 596 (605)
Q Consensus 523 Ee~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 596 (605)
.+..........|..+|..||+++|+||.|+|+.| +|++|||+.||+|.++|++++.||+++|++.+...
T Consensus 96 ~~~~~~~e~~~~l~~al~~L~~rer~V~~L~~~eg----~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l~~~ 165 (170)
T PRK06930 96 PESVISEWDKIRIEDALSVLTEREKEVYLMHRGYG----LSYSEIADYLNIKKSTVQSMIERAEKKIARQINES 165 (170)
T ss_pred hhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHh
Confidence 33444455677899999999999999999999888 99999999999999999999999999999988654
No 132
>PRK00118 putative DNA-binding protein; Validated
Probab=98.43 E-value=1.1e-06 Score=78.72 Aligned_cols=61 Identities=18% Similarity=0.163 Sum_probs=54.8
Q ss_pred HHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhh
Q 007404 533 EDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKH 597 (605)
Q Consensus 533 ~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~ 597 (605)
..+.-....||+++++||.++|..+ +|++|||+.+|+|+.+|+.++.||+++||+++..-+
T Consensus 9 ~l~d~~~~~L~ekqRevl~L~y~eg----~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~~~~~ 69 (104)
T PRK00118 9 LLFDFYGSLLTEKQRNYMELYYLDD----YSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEEKLH 69 (104)
T ss_pred HHHHHHhccCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHC
Confidence 3445566799999999999999987 999999999999999999999999999999987643
No 133
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=98.27 E-value=2.8e-06 Score=64.28 Aligned_cols=54 Identities=44% Similarity=0.701 Sum_probs=49.4
Q ss_pred HHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 007404 533 EDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK 590 (605)
Q Consensus 533 ~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR 590 (605)
..+..++..|++.++.++.++|..+ +|..+||+.+|+|..+|+++.+++..+||
T Consensus 2 ~~~~~~~~~l~~~~~~~~~~~~~~~----~~~~~ia~~~~~s~~~i~~~~~~~~~~l~ 55 (55)
T cd06171 2 ERLEEALDKLPEREREVILLRFGEG----LSYEEIAEILGISRSTVRQRLHRALKKLR 55 (55)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHhcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence 3577889999999999999999766 99999999999999999999999988875
No 134
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=98.07 E-value=1.1e-05 Score=75.68 Aligned_cols=57 Identities=19% Similarity=0.335 Sum_probs=50.1
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhhHhhhh
Q 007404 541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYA 602 (605)
Q Consensus 541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~yl 602 (605)
-|+++|++||.|++ .| +|++|||+.||+|+.+|++++++|+++||+......+-.++
T Consensus 6 ~Lte~qr~VL~Lr~-~G----lTq~EIAe~LgiS~stV~~~e~ra~kkLr~a~~~~~l~~~~ 62 (137)
T TIGR00721 6 FLTERQIKVLELRE-KG----LSQKEIAKELKTTRANVSAIEKRAMENIEKARNTLDFVKFI 62 (137)
T ss_pred CCCHHHHHHHHHHH-cC----CCHHHHHHHHCcCHHHHHHHHHhHHHHHHHHhhHHHHHHHh
Confidence 59999999999963 44 99999999999999999999999999999877666665554
No 135
>PRK04217 hypothetical protein; Provisional
Probab=98.06 E-value=9e-06 Score=73.68 Aligned_cols=57 Identities=23% Similarity=0.119 Sum_probs=51.5
Q ss_pred hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhhHhh
Q 007404 540 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQ 600 (605)
Q Consensus 540 ~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~ 600 (605)
..|++.|++||.++|..+ +|++|||+.||||+.||++++.+|+++|++.+.......
T Consensus 41 ~~Lt~eereai~l~~~eG----lS~~EIAk~LGIS~sTV~r~L~RArkkLre~L~~~~~~~ 97 (110)
T PRK04217 41 IFMTYEEFEALRLVDYEG----LTQEEAGKRMGVSRGTVWRALTSARKKVAQMLVEGRELI 97 (110)
T ss_pred ccCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhcccee
Confidence 579999999999999887 999999999999999999999999999999987655443
No 136
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=97.99 E-value=2.1e-05 Score=74.24 Aligned_cols=51 Identities=31% Similarity=0.464 Sum_probs=46.3
Q ss_pred hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 007404 540 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT 595 (605)
Q Consensus 540 ~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 595 (605)
..|+++|++||.++ ..+ +|++|||+.||+|+.+|++++++++++||+....
T Consensus 5 ~~Lt~rqreVL~lr-~~G----lTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~t 55 (141)
T PRK03975 5 SFLTERQIEVLRLR-ERG----LTQQEIADILGTSRANVSSIEKRARENIEKARET 55 (141)
T ss_pred cCCCHHHHHHHHHH-HcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 46999999999995 355 9999999999999999999999999999997764
No 137
>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=97.98 E-value=3.4e-05 Score=68.83 Aligned_cols=59 Identities=22% Similarity=0.317 Sum_probs=46.0
Q ss_pred HHHHHHh-cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhh
Q 007404 534 DLEKVLD-TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK 596 (605)
Q Consensus 534 ~L~~aL~-~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~ 596 (605)
.|.+... -|+++|+.++.++|..| +|+.|||+.+|||+..|...+.||.++|...-..-
T Consensus 9 ~L~d~Yg~LLT~kQ~~~l~lyy~eD----lSlsEIAe~~~iSRqaV~d~ikr~~~~L~~yE~kL 68 (101)
T PF04297_consen 9 LLFDFYGELLTEKQREILELYYEED----LSLSEIAEELGISRQAVYDSIKRAEKKLEEYEEKL 68 (101)
T ss_dssp HHHHHHGGGS-HHHHHHHHHHCTS-------HHHHHHHCTS-HHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHCCHHHHHHHHHHHccC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444444 49999999999999888 99999999999999999999999999998765543
No 138
>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=97.95 E-value=3.3e-06 Score=61.96 Aligned_cols=31 Identities=45% Similarity=0.620 Sum_probs=27.8
Q ss_pred CCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHH
Q 007404 291 SDPLR-YLRATTSSSRLLTANEEMQLSAGIQDL 322 (605)
Q Consensus 291 ~d~l~-yL~~i~~~~~lLT~eEE~eL~~~iq~~ 322 (605)
+|+++ ||++| +++||||++||++|+++|+..
T Consensus 1 ~D~l~~Yl~ei-~~~~LLt~eeE~~LA~~i~~g 32 (37)
T PF00140_consen 1 SDSLRLYLKEI-GRYPLLTAEEEIELARRIRKG 32 (37)
T ss_dssp HHHHHHHHHHH-HHS-EETTHHHHHHHHHHHHH
T ss_pred CcHHHHHHHHH-cCCCCCCHHHHHHHHHHHHHh
Confidence 37899 99999 999999999999999999974
No 139
>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=97.86 E-value=6.6e-05 Score=70.21 Aligned_cols=62 Identities=11% Similarity=0.205 Sum_probs=55.5
Q ss_pred HHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 007404 530 FMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 593 (605)
Q Consensus 530 el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 593 (605)
.....|..+|+.|++.+|.||.++|+.. ..+|..+||..||+|+.+|+++..+++.+|+..+
T Consensus 71 ~~~~~I~~~l~~Ld~~er~II~~rY~~~--~~~t~~~Ia~~l~iS~~t~~r~r~~~l~kla~~l 132 (134)
T TIGR01636 71 RNRDAIENCLNEADEQTRVIIQELYMKK--RPLTLVGLAQQLFISKSTAYRLRNHIIEAVAEEL 132 (134)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHccC--CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 4567789999999999999999999754 2379999999999999999999999999999864
No 140
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=97.75 E-value=6e-05 Score=58.05 Aligned_cols=47 Identities=36% Similarity=0.525 Sum_probs=41.1
Q ss_pred hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 540 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 540 ~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
..|+++|+.|+.+ +..+ +|.+|||+.||+|+.+|+++..++++||+-
T Consensus 2 ~~l~~~e~~i~~~-~~~g----~s~~eia~~l~is~~tv~~~~~~~~~kl~~ 48 (58)
T smart00421 2 ASLTPREREVLRL-LAEG----LTNKEIAERLGISEKTVKTHLSNIMRKLGV 48 (58)
T ss_pred CCCCHHHHHHHHH-HHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Confidence 4689999999877 4444 899999999999999999999999998864
No 141
>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=97.65 E-value=0.00015 Score=61.02 Aligned_cols=47 Identities=19% Similarity=0.196 Sum_probs=40.8
Q ss_pred HHHHHHhcCCHHHHHHHHHHH-hcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 007404 534 DLEKVLDTLNPRERQVVRWRF-GLEDGRMKTLQEIGELMGVSRERIRQIESS 584 (605)
Q Consensus 534 ~L~~aL~~L~~rER~VL~LRy-Gl~dg~~~Tl~EIAe~LGISrerVRqie~R 584 (605)
.+.+-|+.||++.+.++.|.+ ..+ +|++|||+.||+|..+|++++++
T Consensus 8 ~~~~~l~~l~~~~r~af~L~R~~eG----lS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 8 KLAERLTWVDSLAEAAAALAREEAG----KTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred hHHHHHhcCCHHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHhc
Confidence 456678999999999999964 455 99999999999999999988775
No 142
>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=97.59 E-value=0.00035 Score=62.15 Aligned_cols=55 Identities=27% Similarity=0.491 Sum_probs=49.6
Q ss_pred HHHHHHHHHhcCC-HHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 007404 531 MKEDLEKVLDTLN-PRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKL 589 (605)
Q Consensus 531 l~~~L~~aL~~L~-~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKL 589 (605)
.+..+..+++.|. +.+|.||.++|..+ ++..+|++.||+|+.++..+..+|++.|
T Consensus 44 ~k~ei~~~I~~l~d~~~r~iL~~~Yi~~----~~~~~I~~~l~~S~~t~yr~~~~Al~~L 99 (100)
T PF07374_consen 44 EKLEIRRAINKLEDPDERLILRMRYINK----LTWEQIAEELNISRRTYYRIHKKALKEL 99 (100)
T ss_pred HHHHHHHHHHHccChhHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHhc
Confidence 4456888888886 79999999999976 9999999999999999999999999876
No 143
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=97.59 E-value=0.004 Score=71.98 Aligned_cols=32 Identities=34% Similarity=0.583 Sum_probs=30.1
Q ss_pred CCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHH
Q 007404 290 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDL 322 (605)
Q Consensus 290 ~~d~l~-yL~~i~~~~~lLT~eEE~eL~~~iq~~ 322 (605)
..||++ ||+++ |..||||+|+|++++++|...
T Consensus 102 t~DPVRMYLREM-G~V~LLTREgEIeIAKRIE~G 134 (619)
T PRK05658 102 TDDPVRMYLREM-GTVELLTREGEIEIAKRIEAG 134 (619)
T ss_pred CCChHHHHHHHh-ccCcCCCcHHHHHHHHHHHHH
Confidence 479999 99999 999999999999999999864
No 144
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=97.54 E-value=0.00032 Score=55.63 Aligned_cols=48 Identities=33% Similarity=0.517 Sum_probs=42.5
Q ss_pred CCHHHHHHHHHHHhcC--C-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 007404 542 LNPRERQVVRWRFGLE--D-GRMKTLQEIGELMGVSRERIRQIESSAFRKL 589 (605)
Q Consensus 542 L~~rER~VL~LRyGl~--d-g~~~Tl~EIAe~LGISrerVRqie~RALkKL 589 (605)
|+++|++||..-|-.| + .+..|+.|||+.||||+.+|..++.+|.+||
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 7899999999887665 2 3468999999999999999999999999987
No 145
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=97.53 E-value=0.00023 Score=54.98 Aligned_cols=46 Identities=37% Similarity=0.571 Sum_probs=40.2
Q ss_pred CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 007404 542 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 592 (605)
Q Consensus 542 L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 592 (605)
|+++|+.|+.+. ..+ +|.+|||+.||+|+.+|+++.++++++|+..
T Consensus 1 l~~~e~~i~~~~-~~~----~s~~eia~~l~~s~~tv~~~~~~~~~~l~~~ 46 (57)
T cd06170 1 LTPREREVLRLL-AEG----KTNKEIADILGISEKTVKTHLRNIMRKLGVK 46 (57)
T ss_pred CCHHHHHHHHHH-HcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHhCCC
Confidence 689999999874 344 8999999999999999999999998888763
No 146
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=97.44 E-value=0.00032 Score=55.83 Aligned_cols=47 Identities=26% Similarity=0.354 Sum_probs=39.5
Q ss_pred hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 540 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 540 ~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
..|+++|.+||.+.. .| ++.+|||+.||||..||+.+..+.++||.-
T Consensus 2 ~~LT~~E~~vl~~l~-~G----~~~~eIA~~l~is~~tV~~~~~~i~~Kl~~ 48 (58)
T PF00196_consen 2 PSLTERELEVLRLLA-QG----MSNKEIAEELGISEKTVKSHRRRIMKKLGV 48 (58)
T ss_dssp GSS-HHHHHHHHHHH-TT----S-HHHHHHHHTSHHHHHHHHHHHHHHHHT-
T ss_pred CccCHHHHHHHHHHH-hc----CCcchhHHhcCcchhhHHHHHHHHHHHhCC
Confidence 479999999998754 44 899999999999999999999999999864
No 147
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=97.09 E-value=0.00089 Score=67.41 Aligned_cols=51 Identities=8% Similarity=0.067 Sum_probs=45.6
Q ss_pred HHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 536 EKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 536 ~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
.++...|+++|++||.+. ..| +|.+|||+.|++|..||+.+..+.++||.-
T Consensus 138 ~~~~~~LS~RE~eVL~Li-a~G----~SnkEIA~~L~IS~~TVk~hvs~I~~KLgv 188 (217)
T PRK13719 138 LEAKNKVTKYQNDVFILY-SFG----FSHEYIAQLLNITVGSSKNKISEILKFFGI 188 (217)
T ss_pred hhccCCCCHHHHHHHHHH-HCC----CCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 556688999999999985 455 999999999999999999999999999964
No 148
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=97.09 E-value=0.0009 Score=66.68 Aligned_cols=46 Identities=17% Similarity=0.258 Sum_probs=41.9
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
.|++||++||.+. ..| +|.+|||+.||||..||+.+..+.++||.-
T Consensus 137 ~LT~RE~eVL~ll-a~G----~snkeIA~~L~iS~~TVk~h~~~I~~KL~v 182 (207)
T PRK15411 137 SLSRTESSMLRMW-MAG----QGTIQISDQMNIKAKTVSSHKGNIKRKIKT 182 (207)
T ss_pred cCCHHHHHHHHHH-HcC----CCHHHHHHHcCCCHHHHHHHHHHHHHHhCC
Confidence 4999999999985 344 999999999999999999999999999974
No 149
>TIGR03541 reg_near_HchA LuxR family transcriptional regulatory, chaperone HchA-associated. Members of this protein family belong to the LuxR transcriptional regulator family, and contain both autoinducer binding (pfam03472) and transcriptional regulator (pfam00196) domains. Members, however, occur only in a few members of the Gammaproteobacteria that have the chaperone/aminopeptidase HchA, and are always encoded by the adjacent gene.
Probab=97.06 E-value=0.00096 Score=67.68 Aligned_cols=50 Identities=30% Similarity=0.501 Sum_probs=44.4
Q ss_pred HhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 007404 539 LDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 593 (605)
Q Consensus 539 L~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 593 (605)
...|+++|++||.+. ..| +|.+|||++||||..||+.++.++++||+..-
T Consensus 169 ~~~Lt~re~evl~~~-a~G----~t~~eIa~~l~is~~Tv~~~l~~~~~kl~~~~ 218 (232)
T TIGR03541 169 AGVLSEREREVLAWT-ALG----RRQADIAAILGISERTVENHLRSARRKLGVAT 218 (232)
T ss_pred hccCCHHHHHHHHHH-HCC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHCCCC
Confidence 347999999999995 444 99999999999999999999999999998543
No 150
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=97.06 E-value=0.001 Score=65.49 Aligned_cols=46 Identities=28% Similarity=0.299 Sum_probs=41.7
Q ss_pred hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 007404 540 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK 590 (605)
Q Consensus 540 ~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR 590 (605)
..|++||++||.+.- .| +|.+|||+.|+||..||+.+..+.++||-
T Consensus 149 ~~Lt~rE~evl~~~~-~G----~s~~eIA~~l~iS~~TV~~h~~~i~~Kl~ 194 (216)
T PRK10840 149 KRLSPKESEVLRLFA-EG----FLVTEIAKKLNRSIKTISSQKKSAMMKLG 194 (216)
T ss_pred ccCCHHHHHHHHHHH-CC----CCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence 359999999999853 44 99999999999999999999999999995
No 151
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=97.04 E-value=0.0011 Score=66.25 Aligned_cols=46 Identities=24% Similarity=0.364 Sum_probs=41.9
Q ss_pred hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 007404 540 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK 590 (605)
Q Consensus 540 ~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR 590 (605)
..|++||++||.+.- .| +|.+|||+.|+||..||+.+..+.++||.
T Consensus 133 ~~LT~RE~eVL~ll~-~G----~snkeIA~~L~iS~~TV~~h~~~I~~KLg 178 (207)
T PRK11475 133 RMLSPTEREILRFMS-RG----YSMPQIAEQLERNIKTIRAHKFNVMSKLG 178 (207)
T ss_pred CCCCHHHHHHHHHHH-CC----CCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence 469999999999853 44 99999999999999999999999999995
No 152
>TIGR01321 TrpR trp operon repressor, proteobacterial. This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis.
Probab=97.03 E-value=0.0011 Score=58.50 Aligned_cols=48 Identities=25% Similarity=0.367 Sum_probs=41.4
Q ss_pred HHHHHHHh-cCCHHHHHHHHHHHhcCC---CCCCCHHHHHHHHCCCHHHHHH
Q 007404 533 EDLEKVLD-TLNPRERQVVRWRFGLED---GRMKTLQEIGELMGVSRERIRQ 580 (605)
Q Consensus 533 ~~L~~aL~-~L~~rER~VL~LRyGl~d---g~~~Tl~EIAe~LGISrerVRq 580 (605)
+.+..+|. -|+|+|+.+|.+||++-+ ..++|++|||+.+|||+.+|..
T Consensus 23 ~~l~~~l~~lLTp~E~~~l~~R~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR 74 (94)
T TIGR01321 23 DDMQLLLELILTRSEREDLGDRIRIVNELLNGNMSQREIASKLGVSIATITR 74 (94)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHhCCChhhhhH
Confidence 45667774 599999999999999876 4569999999999999999984
No 153
>TIGR03020 EpsA transcriptional regulator EpsA. Proteins in this family include a C-terminal LuxR transcriptional regulator domain (pfam00196). These proteins are positioned proximal to either EpsH-containing exopolysaccharide biosynthesis operons of the Methylobacillus type, or the associated PEP-CTERM-containing genes.
Probab=97.03 E-value=0.0011 Score=68.23 Aligned_cols=50 Identities=24% Similarity=0.436 Sum_probs=44.4
Q ss_pred HhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 007404 539 LDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 593 (605)
Q Consensus 539 L~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 593 (605)
+..|+++|++||.+.. .| +|.+|||++||||..||+.+..++++||.-.-
T Consensus 188 ~~~LT~RE~evl~l~a-~G----~s~~eIA~~L~IS~~TVk~hl~~i~~KL~v~n 237 (247)
T TIGR03020 188 AGLITAREAEILAWVR-DG----KTNEEIAAILGISSLTVKNHLQHIFKKLDVRN 237 (247)
T ss_pred ccCCCHHHHHHHHHHH-CC----CCHHHHHHHHCcCHHHHHHHHHHHHHHhCCCC
Confidence 4579999999999854 55 99999999999999999999999999997543
No 154
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=97.03 E-value=0.0013 Score=64.16 Aligned_cols=46 Identities=24% Similarity=0.374 Sum_probs=42.0
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
.|+++|++||.+. ..| +|.+|||+.|++|..||+....++++||.-
T Consensus 133 ~LSpRErEVLrLL-AqG----kTnKEIAe~L~IS~rTVkth~srImkKLgV 178 (198)
T PRK15201 133 HFSVTERHLLKLI-ASG----YHLSETAALLSLSEEQTKSLRRSIMRKLHV 178 (198)
T ss_pred CCCHHHHHHHHHH-HCC----CCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 5999999999985 344 999999999999999999999999999975
No 155
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=96.96 E-value=0.0013 Score=65.94 Aligned_cols=47 Identities=30% Similarity=0.393 Sum_probs=42.3
Q ss_pred hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 540 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 540 ~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
..|++||++|+++- ..| +|.+|||+.|++|..||+.+.++.++||.-
T Consensus 147 ~~LT~RE~eVL~ll-a~G----~snkeIA~~L~iS~~TVk~h~~~i~~KL~v 193 (211)
T COG2197 147 ELLTPRELEVLRLL-AEG----LSNKEIAEELNLSEKTVKTHVSNILRKLGV 193 (211)
T ss_pred CCCCHHHHHHHHHH-HCC----CCHHHHHHHHCCCHhHHHHHHHHHHHHcCC
Confidence 46999999999874 444 999999999999999999999999999964
No 156
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=96.95 E-value=0.0014 Score=65.91 Aligned_cols=47 Identities=17% Similarity=0.189 Sum_probs=43.3
Q ss_pred hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 540 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 540 ~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
..|+++|++||.+... | +|.+|||+.|++|..||+.+..++++||.-
T Consensus 154 ~~Lt~rE~~Vl~l~~~-G----~s~~eIA~~L~iS~~TVk~~~~~i~~Kl~v 200 (216)
T PRK10100 154 ALLTHREKEILNKLRI-G----ASNNEIARSLFISENTVKTHLYNLFKKIAV 200 (216)
T ss_pred CCCCHHHHHHHHHHHc-C----CCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 4699999999999874 4 999999999999999999999999999975
No 157
>PRK13870 transcriptional regulator TraR; Provisional
Probab=96.93 E-value=0.0015 Score=66.66 Aligned_cols=46 Identities=28% Similarity=0.549 Sum_probs=41.4
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
.|++||++||.+- -.| +|..|||.+||||..||..++.+|++||--
T Consensus 173 ~LT~RE~E~L~W~-A~G----KT~~EIa~ILgISe~TV~~Hl~na~~KLga 218 (234)
T PRK13870 173 WLDPKEATYLRWI-AVG----KTMEEIADVEGVKYNSVRVKLREAMKRFDV 218 (234)
T ss_pred CCCHHHHHHHHHH-HcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence 5999999999885 333 999999999999999999999999999954
No 158
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=96.90 E-value=0.0017 Score=66.36 Aligned_cols=46 Identities=20% Similarity=0.453 Sum_probs=42.2
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
.|++||++||.+- ..| +|..|||++||||..||+.++.++++||--
T Consensus 179 ~LT~rE~evl~~~-a~G----~t~~eIa~~l~is~~TV~~h~~~~~~KL~~ 224 (240)
T PRK10188 179 NFSKREKEILKWT-AEG----KTSAEIAMILSISENTVNFHQKNMQKKFNA 224 (240)
T ss_pred CCCHHHHHHHHHH-HcC----CCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 5999999999987 344 999999999999999999999999999964
No 159
>COG4566 TtrR Response regulator [Signal transduction mechanisms]
Probab=96.86 E-value=0.0052 Score=60.75 Aligned_cols=65 Identities=20% Similarity=0.261 Sum_probs=54.8
Q ss_pred HHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhhHh
Q 007404 530 FMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLM 599 (605)
Q Consensus 530 el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~ 599 (605)
.....+...+++|++|||+|+..-- .| +..++||..||||..||..+..+.++||+..-...-++
T Consensus 131 ~~~~~~~~~l~tLT~RERqVl~~vV-~G----~~NKqIA~dLgiS~rTVe~HRanvM~Km~a~SlaeLvr 195 (202)
T COG4566 131 DRQAAIRARLATLTPRERQVLDLVV-RG----LMNKQIAFDLGISERTVELHRANVMEKMQARSLAELVR 195 (202)
T ss_pred HHHHHHHHHHHhcCHHHHHHHHHHH-cC----cccHHHHHHcCCchhhHHHHHHHHHHHHhhccHHHHHH
Confidence 4456788999999999999998764 45 89999999999999999999999999998755444433
No 160
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=96.86 E-value=0.0028 Score=57.24 Aligned_cols=53 Identities=26% Similarity=0.225 Sum_probs=49.0
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhh
Q 007404 541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKH 597 (605)
Q Consensus 541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~ 597 (605)
.|+..|-+.|+|.++++ +|++|-|+.||||+.|+..++..|.+|+-..+....
T Consensus 41 ~L~~dElEAiRL~D~eg----l~QeeaA~~MgVSR~T~~ril~~ARkKiA~ALv~Gk 93 (106)
T PF02001_consen 41 VLTVDELEAIRLVDYEG----LSQEEAAERMGVSRPTFQRILESARKKIADALVEGK 93 (106)
T ss_pred EeeHHHHHHHHHHHHcC----CCHHHHHHHcCCcHHHHHHHHHHHHHHHHHHHHCCC
Confidence 57888999999999988 999999999999999999999999999999887654
No 161
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=96.69 E-value=0.0036 Score=58.90 Aligned_cols=47 Identities=28% Similarity=0.397 Sum_probs=42.2
Q ss_pred hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 540 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 540 ~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
..|+++|++||.+ +..+ ++.+|||+.|++|..||+.+..++++||.-
T Consensus 148 ~~lt~~e~~vl~l-~~~g----~~~~~Ia~~l~~s~~tv~~~~~~~~~kl~~ 194 (211)
T PRK15369 148 PLLTPRERQILKL-ITEG----YTNRDIAEQLSISIKTVETHRLNMMRKLDV 194 (211)
T ss_pred cCCCHHHHHHHHH-HHCC----CCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 4599999999998 5555 899999999999999999999999999963
No 162
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=96.68 E-value=0.0022 Score=48.73 Aligned_cols=41 Identities=22% Similarity=0.337 Sum_probs=23.3
Q ss_pred hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 007404 540 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS 584 (605)
Q Consensus 540 ~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~R 584 (605)
..|++.||..|...+-.+ +|+.+||+.||+|++||...+.|
T Consensus 3 ~~Lt~~eR~~I~~l~~~G----~s~~~IA~~lg~s~sTV~relkR 43 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQG----MSIREIAKRLGRSRSTVSRELKR 43 (44)
T ss_dssp ---------HHHHHHCS-------HHHHHHHTT--HHHHHHHHHH
T ss_pred cchhhhHHHHHHHHHHcC----CCHHHHHHHHCcCcHHHHHHHhc
Confidence 468999999998776555 99999999999999999977665
No 163
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=96.67 E-value=0.0042 Score=62.35 Aligned_cols=53 Identities=25% Similarity=0.398 Sum_probs=46.4
Q ss_pred cCCHHHHHHHHHHHhcC--C-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 007404 541 TLNPRERQVVRWRFGLE--D-GRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 593 (605)
Q Consensus 541 ~L~~rER~VL~LRyGl~--d-g~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 593 (605)
.|+++|++||+.-|-.| | .+..+++|||+.||||+.++.+++.||.+||=...
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 69999999999988765 2 25589999999999999999999999999996644
No 164
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=96.65 E-value=0.0059 Score=48.59 Aligned_cols=51 Identities=33% Similarity=0.573 Sum_probs=43.2
Q ss_pred hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 007404 540 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT 595 (605)
Q Consensus 540 ~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 595 (605)
..|+++|.+|+.+. ..+ ++..|||..+|+|..+|+.+..+.++||.-.-+.
T Consensus 3 ~~Lt~rE~~v~~l~-~~G----~s~~eia~~l~is~~tV~~h~~~i~~Kl~~~~r~ 53 (65)
T COG2771 3 ADLTPREREILRLV-AQG----KSNKEIARILGISEETVKTHLRNIYRKLGVKNRV 53 (65)
T ss_pred ccCCHHHHHHHHHH-HCC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHH
Confidence 36899999999774 333 8999999999999999999999999999764433
No 165
>PRK09483 response regulator; Provisional
Probab=96.65 E-value=0.0033 Score=60.67 Aligned_cols=46 Identities=24% Similarity=0.336 Sum_probs=41.2
Q ss_pred hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 007404 540 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK 590 (605)
Q Consensus 540 ~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR 590 (605)
..|+++|++||.+. ..| +|.+|||+.|++|..||+.+.++.++||-
T Consensus 147 ~~Lt~rE~~vl~~~-~~G----~~~~~Ia~~l~is~~TV~~~~~~i~~Kl~ 192 (217)
T PRK09483 147 ASLSERELQIMLMI-TKG----QKVNEISEQLNLSPKTVNSYRYRMFSKLN 192 (217)
T ss_pred cccCHHHHHHHHHH-HCC----CCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 46999999999874 344 99999999999999999999999999994
No 166
>TIGR01637 phage_arpU phage transcriptional regulator, ArpU family. This model represents a family of phage proteins, including ArpU, called a putative autolysin regulatory protein. ArpU was described as a regulator of cellular muramidase-2 of Enterococcus hirae but appears to have been cloned from a prophage. This family appears related to the RinA family of bacteriophage transcriptional activators and to some sporulation-specific sigma factors. We propose that this is a phage transcriptional activator family.
Probab=96.59 E-value=0.014 Score=54.16 Aligned_cols=63 Identities=16% Similarity=0.142 Sum_probs=54.1
Q ss_pred HHHHHHHHHH-hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404 530 FMKEDLEKVL-DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR 594 (605)
Q Consensus 530 el~~~L~~aL-~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 594 (605)
.....+..++ +.|++.+|+||.++|...++ ++..+|+..||+|+.+...+..+|+.++-..+.
T Consensus 67 ~~~~~i~~ai~~~l~~~~r~Il~~~Yl~~~~--~~~~~I~~~l~~s~~~~y~~k~~Al~~fA~~l~ 130 (132)
T TIGR01637 67 QEARAIVNAIVNQLDEISRQILYDKYLEPDQ--KYDYQIMMELGYSHRQYYRIKKRALLRFATLYG 130 (132)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHHcCccc--cchHHHHHHhCCcHHHHHHHHHHHHHHHHHHhC
Confidence 4455677778 99999999999999987332 899999999999999999999999999877553
No 167
>COG4941 Predicted RNA polymerase sigma factor containing a TPR repeat domain [Transcription]
Probab=96.56 E-value=0.053 Score=57.94 Aligned_cols=159 Identities=11% Similarity=0.058 Sum_probs=99.7
Q ss_pred HHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccH
Q 007404 368 DKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHM 447 (605)
Q Consensus 368 e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~ 447 (605)
+..+..-.+.++.---+|+++-.-.||.+||.|+.-.+.-.+=-|-++ -..|++..-|+.-++.++++.+.-..|.+
T Consensus 8 e~~~r~~~~r~~a~L~r~~rd~dlAEEa~~dA~~~Ale~WPr~G~P~~--PaAWL~~v~R~~aiD~~Rr~~~~~~~~~e- 84 (415)
T COG4941 8 EAAARIERPRAMAALARYLRDLDLAEEALQDAFAAALERWPRAGPPRN--PAAWLIAVGRNRAIDRVRRRARRDAAPPE- 84 (415)
T ss_pred HHHHHHhhhHHHHHHHHHhcccchHHHHHHHHHHHHHHhCcccCCCCC--hHHHHHHHHhhhHHHHHHHHHHhccCChh-
Confidence 334444444444444556676667899999999866655554444333 46788888999999988887653322211
Q ss_pred HHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHHHHH
Q 007404 448 VEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLI 527 (605)
Q Consensus 448 ~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~l~ 527 (605)
+. ++.+ |.+....+...| ...
T Consensus 85 --------------------------l~--------------------~~~e-----~~e~~~a~~~~d--------~~i 105 (415)
T COG4941 85 --------------------------LL--------------------LSDE-----DEEMEEAEALDD--------EHI 105 (415)
T ss_pred --------------------------hc--------------------cccc-----chhhhccccccc--------ccc
Confidence 00 0000 000000011111 111
Q ss_pred HHHHHHHHHHH-HhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 007404 528 KKFMKEDLEKV-LDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 592 (605)
Q Consensus 528 ~~el~~~L~~a-L~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 592 (605)
.++....|.-+ =-.|++.+|--|.||...| +|..|||..|=++..++-|++.||.++|+..
T Consensus 106 ~Dd~LRLiFvccHPal~~~~riALtLR~v~G----Ls~~eIArAFLv~e~am~QRivRAK~ri~~a 167 (415)
T COG4941 106 RDDRLRLIFVCCHPALPPEQRIALTLRLVGG----LSTAEIARAFLVPEAAMAQRIVRAKARIREA 167 (415)
T ss_pred chhhHHhhhhhcCCCCChhhHHHHHHHHHcC----CcHHHHHHHHcCCcHHHHHHHHHHHHHHHhc
Confidence 11122222222 2369999999999998877 9999999999999999999999999999974
No 168
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=96.51 E-value=0.0075 Score=53.66 Aligned_cols=49 Identities=20% Similarity=0.239 Sum_probs=44.0
Q ss_pred hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 007404 540 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 592 (605)
Q Consensus 540 ~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 592 (605)
.-|+.+|+..+.++|..| +|+.|||+.++||+..|...+.|+-+.|-+.
T Consensus 16 sLLT~KQ~~Y~~lyy~dD----lSl~EIAee~~VSRqAIyDnIKr~~~~L~~Y 64 (105)
T COG2739 16 SLLTKKQKNYLELYYLDD----LSLSEIAEEFNVSRQAIYDNIKRTEKILEDY 64 (105)
T ss_pred HHHhHHHHHHHHHHHHhh----ccHHHHHHHhCccHHHHHHHHHHHHHHHHHH
Confidence 348999999999999888 9999999999999999999999987776554
No 169
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=96.31 E-value=0.011 Score=55.38 Aligned_cols=56 Identities=18% Similarity=0.243 Sum_probs=47.6
Q ss_pred HHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404 534 DLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR 594 (605)
Q Consensus 534 ~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 594 (605)
.+...+..|+++|++||.+ +..+ ++.++||+.+|+|..+|+.+..++++||+..-.
T Consensus 134 ~~~~~~~~l~~~e~~vl~~-~~~~----~~~~~ia~~l~~s~~tv~~~~~~~~~kl~~~~~ 189 (202)
T PRK09390 134 DIRARIASLSERERQVMDG-LVAG----LSNKVIARDLDISPRTVEVYRANVMTKMQAGSL 189 (202)
T ss_pred HHHHHHHhhhhhHHHHHHH-HHcc----CchHHHHHHcCCCHHHHHHHHHHHHHHHccccH
Confidence 3556678899999999996 4444 899999999999999999999999999976443
No 170
>PRK10651 transcriptional regulator NarL; Provisional
Probab=96.22 E-value=0.0081 Score=57.27 Aligned_cols=47 Identities=17% Similarity=0.329 Sum_probs=41.7
Q ss_pred hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 540 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 540 ~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
..|+++|++|+.+. ..+ ++.++||+.|++|..||+.+..+.++||.-
T Consensus 154 ~~Lt~rE~~vl~~l-~~g----~~~~~ia~~l~is~~tV~~~~~~l~~Kl~~ 200 (216)
T PRK10651 154 NQLTPRERDILKLI-AQG----LPNKMIARRLDITESTVKVHVKHMLKKMKL 200 (216)
T ss_pred ccCCHHHHHHHHHH-HcC----CCHHHHHHHcCCCHHHHHHHHHHHHHHcCC
Confidence 45999999999984 344 899999999999999999999999999964
No 171
>PRK01381 Trp operon repressor; Provisional
Probab=96.10 E-value=0.0077 Score=53.65 Aligned_cols=51 Identities=24% Similarity=0.298 Sum_probs=41.4
Q ss_pred HHHHHHHHHHHhc-CCHHHHHHHHHHHhcCC---CCCCCHHHHHHHHCCCHHHHH
Q 007404 529 KFMKEDLEKVLDT-LNPRERQVVRWRFGLED---GRMKTLQEIGELMGVSRERIR 579 (605)
Q Consensus 529 ~el~~~L~~aL~~-L~~rER~VL~LRyGl~d---g~~~Tl~EIAe~LGISrerVR 579 (605)
....+.+..+|.. |+|+|+..|..||+.-. ...+|+.||++.+|||..+|.
T Consensus 19 a~~~~~~~~~l~~llTp~Er~al~~R~~I~~~L~~g~~sQREIa~~lGvSiaTIT 73 (99)
T PRK01381 19 AFEEDLHLPLLTLLLTPDEREALGTRVRIVEELLRGELSQREIKQELGVGIATIT 73 (99)
T ss_pred hccHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHcCCcCHHHHHHHhCCceeeeh
Confidence 3334556677765 99999999999998864 335999999999999999887
No 172
>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=96.04 E-value=0.0082 Score=42.83 Aligned_cols=27 Identities=30% Similarity=0.559 Sum_probs=21.7
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 561 MKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 561 ~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
|+|.+|||+.+|+|+|+|. |++++|++
T Consensus 2 ~mtr~diA~~lG~t~ETVS----R~l~~l~~ 28 (32)
T PF00325_consen 2 PMTRQDIADYLGLTRETVS----RILKKLER 28 (32)
T ss_dssp E--HHHHHHHHTS-HHHHH----HHHHHHHH
T ss_pred CcCHHHHHHHhCCcHHHHH----HHHHHHHH
Confidence 4899999999999999999 88888876
No 173
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=95.92 E-value=0.021 Score=50.41 Aligned_cols=53 Identities=23% Similarity=0.166 Sum_probs=47.6
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhh
Q 007404 541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKH 597 (605)
Q Consensus 541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~ 597 (605)
.|+..|-+.|+|...++ ++.+|-|.+||||+.|+-..++.|++|+-..+....
T Consensus 33 ~lt~eElEAlRLvD~~~----l~QeeAA~rMgISr~Tfwr~l~sAR~KvA~aLveGk 85 (99)
T COG1342 33 ILTIEELEALRLVDYEG----LTQEEAALRMGISRQTFWRLLTSARKKVADALVEGK 85 (99)
T ss_pred eecHHHHHHHHHHhHhh----ccHHHHHHHhcccHHHHHHHHHHHHHHHHHHHhcCC
Confidence 46777889999999988 999999999999999999999999999998886543
No 174
>PRK13558 bacterio-opsin activator; Provisional
Probab=95.31 E-value=0.033 Score=64.30 Aligned_cols=54 Identities=26% Similarity=0.221 Sum_probs=46.1
Q ss_pred HhcCCHHHHHHHHHHHhcC---CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 007404 539 LDTLNPRERQVVRWRFGLE---DGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 592 (605)
Q Consensus 539 L~~L~~rER~VL~LRyGl~---dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 592 (605)
...|+++|+++|..-|..| -.+.-|++|||+.||||+.|+.+++.+|.+||=..
T Consensus 605 ~~~lt~~q~e~l~~a~~~gyf~~pr~~~~~e~a~~l~is~~t~~~~lr~a~~~l~~~ 661 (665)
T PRK13558 605 ENDLTDRQLTALQKAYVSGYFEWPRRVEGEELAESMGISRSTFHQHLRAAERKLVGA 661 (665)
T ss_pred hhhCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 4679999999999999876 01223999999999999999999999999998653
No 175
>PRK10403 transcriptional regulator NarP; Provisional
Probab=95.09 E-value=0.041 Score=52.27 Aligned_cols=48 Identities=19% Similarity=0.276 Sum_probs=41.8
Q ss_pred hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 007404 540 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 592 (605)
Q Consensus 540 ~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 592 (605)
..|+++|.+|+.+. ..+ +|.+|||+.+|+|..||+.+..+.++||.-.
T Consensus 152 ~~Lt~~e~~vl~~~-~~g----~s~~~ia~~l~~s~~tv~~~~~~i~~kl~~~ 199 (215)
T PRK10403 152 SVLTERELDVLHEL-AQG----LSNKQIASVLNISEQTVKVHIRNLLRKLNVR 199 (215)
T ss_pred ccCCHHHHHHHHHH-HCC----CCHHHHHHHcCCCHHHHHHHHHHHHHHcCCC
Confidence 35999999999875 344 9999999999999999999999999999543
No 176
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=95.03 E-value=0.047 Score=51.96 Aligned_cols=46 Identities=22% Similarity=0.304 Sum_probs=39.3
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
.|+++|..|+.+ +..+ +|.+|||+.|++|..||+.+..++++||.-
T Consensus 149 ~lt~re~~vl~~-l~~g----~s~~eIa~~l~~s~~tv~~~~~~~~~kl~~ 194 (210)
T PRK09935 149 VLSNREVTILRY-LVSG----LSNKEIADQLLLSNKTVSAHKSNIYGKLGL 194 (210)
T ss_pred cCCHHHHHHHHH-HHcC----CCHHHHHHHhCCCHHHHHHHHHHHHHHcCC
Confidence 488888888865 3344 999999999999999999999999999953
No 177
>PRK15320 transcriptional activator SprB; Provisional
Probab=95.00 E-value=0.046 Score=54.57 Aligned_cols=66 Identities=11% Similarity=0.088 Sum_probs=48.3
Q ss_pred CCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 520 ETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 520 ~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
++||+.+..-.. -....+--.|+++|.+|+.+-- .| +|.+|||+.|++|.+||+....+.+.||.-
T Consensus 144 ~~~~~~~~~~~~-~~~~~~~~~LSdREIEVL~LLA-kG----~SNKEIAekL~LS~KTVSTYKnRLLeKLgA 209 (251)
T PRK15320 144 ETPEEVLFNINQ-YAWWNLPPGVTQAKYALLILLS-SG----HPAIELAKKFGLGTKTVSIYRKKVMYRLGM 209 (251)
T ss_pred CChHHHhhhccc-eeeecCCCCCCHHHHHHHHHHH-cC----CCHHHHHHHhccchhhHHHHHHHHHHHcCC
Confidence 356665443211 1122333579999999998742 33 999999999999999999999999999853
No 178
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=94.98 E-value=0.048 Score=51.67 Aligned_cols=47 Identities=28% Similarity=0.330 Sum_probs=41.6
Q ss_pred hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 540 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 540 ~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
..|+++|++|+.+.. .+ +|.++||+.|++|..+|+.+..+.++||.-
T Consensus 136 ~~Lt~~E~~il~~l~-~g----~~~~~Ia~~l~~s~~tv~~~~~~l~~Kl~~ 182 (196)
T PRK10360 136 DPLTKRERQVAEKLA-QG----MAVKEIAAELGLSPKTVHVHRANLMEKLGV 182 (196)
T ss_pred cCCCHHHHHHHHHHH-CC----CCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 369999999999843 34 899999999999999999999999999864
No 179
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=94.90 E-value=0.04 Score=45.47 Aligned_cols=44 Identities=23% Similarity=0.467 Sum_probs=29.6
Q ss_pred HhcCCHHHHHHHHH--HHhcCCCCCCCHHHHHHHHCCC-HHHHHHHH
Q 007404 539 LDTLNPRERQVVRW--RFGLEDGRMKTLQEIGELMGVS-RERIRQIE 582 (605)
Q Consensus 539 L~~L~~rER~VL~L--RyGl~dg~~~Tl~EIAe~LGIS-rerVRqie 582 (605)
|..|+++|++||.. .|....|-|-|+.|||+.||++ ..+|.+++
T Consensus 1 M~~LT~rQ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L 47 (65)
T PF01726_consen 1 MKELTERQKEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHL 47 (65)
T ss_dssp -----HHHHHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHH
Confidence 45799999999876 4445567778999999999997 99999554
No 180
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=94.85 E-value=0.074 Score=41.82 Aligned_cols=49 Identities=14% Similarity=0.176 Sum_probs=41.8
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 007404 541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 592 (605)
Q Consensus 541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 592 (605)
+|+..++-++.+.|.-.+ .++++||..+|||+++|.++.+..+.-|-..
T Consensus 2 kLs~~d~lll~L~~LR~~---~~~~~La~~FgIs~stvsri~~~~~~~L~~~ 50 (53)
T PF13613_consen 2 KLSLEDQLLLTLMYLRLN---LTFQDLAYRFGISQSTVSRIFHEWIPLLYQV 50 (53)
T ss_pred CCCHHHHHHHHHHHHHcC---CcHhHHhhheeecHHHHHHHHHHHHHHHHHh
Confidence 588889988888776654 8999999999999999999998888777653
No 181
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=94.79 E-value=0.06 Score=51.36 Aligned_cols=47 Identities=30% Similarity=0.398 Sum_probs=41.2
Q ss_pred HhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 007404 539 LDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK 590 (605)
Q Consensus 539 L~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR 590 (605)
+..|+++|++|+.+.. .+ .+.+|||+.+++|..||+.+..+.++||.
T Consensus 141 ~~~lt~~E~~vl~~l~-~g----~~~~~I~~~l~~s~~tv~~~~~~l~~Kl~ 187 (204)
T PRK09958 141 LDSLSKQEISVMRYIL-DG----KDNNDIAEKMFISNKTVSTYKSRLMEKLE 187 (204)
T ss_pred cccCCHHHHHHHHHHH-cC----CCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 3569999999998754 33 79999999999999999999999999994
No 182
>COG1356 tfx Transcriptional regulator [DNA replication, recombination and repair]
Probab=94.65 E-value=0.035 Score=51.40 Aligned_cols=49 Identities=20% Similarity=0.316 Sum_probs=43.2
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404 541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR 594 (605)
Q Consensus 541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 594 (605)
-|+++|-.||.||- .| .|.+|||++||-|+..|+-++.+|+.++.+.-.
T Consensus 8 flte~qikvl~lRe-kG----~tQ~eIA~~L~TTraNvSaIEkrA~enIekarn 56 (143)
T COG1356 8 FLTEQQIKVLVLRE-KG----LTQSEIARILKTTRANVSAIEKRALENIEKARN 56 (143)
T ss_pred eeehhheeeeehhh-cc----ccHHHHHHHHccchhhHHHHHHHHHHHHHHHHH
Confidence 38899999999984 23 899999999999999999999999999987654
No 183
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=94.57 E-value=0.11 Score=39.55 Aligned_cols=39 Identities=21% Similarity=0.351 Sum_probs=27.8
Q ss_pred CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 007404 542 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES 583 (605)
Q Consensus 542 L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~ 583 (605)
|++.++.||..-+-.+ ..|..|||+.+|+|..+|++++.
T Consensus 1 l~~~~~~Il~~l~~~~---~~t~~ela~~~~is~~tv~~~l~ 39 (48)
T PF13412_consen 1 LDETQRKILNYLRENP---RITQKELAEKLGISRSTVNRYLK 39 (48)
T ss_dssp --HHHHHHHHHHHHCT---TS-HHHHHHHHTS-HHHHHHHHH
T ss_pred CCHHHHHHHHHHHHcC---CCCHHHHHHHhCCCHHHHHHHHH
Confidence 5778888987765422 39999999999999999995543
No 184
>PRK04841 transcriptional regulator MalT; Provisional
Probab=94.50 E-value=0.06 Score=64.14 Aligned_cols=47 Identities=21% Similarity=0.257 Sum_probs=42.1
Q ss_pred hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 540 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 540 ~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
..|+++|++|+.+.. .+ +|.+|||+.|+||..||+.++++.++||.-
T Consensus 837 ~~lt~~e~~v~~~~~-~g----~~~~~ia~~l~~s~~tv~~h~~~~~~kl~v 883 (903)
T PRK04841 837 SPLTQREWQVLGLIY-SG----YSNEQIAGELDVAATTIKTHIRNLYQKLGI 883 (903)
T ss_pred CCCCHHHHHHHHHHH-cC----CCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 349999999999854 44 999999999999999999999999999964
No 185
>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=94.49 E-value=0.15 Score=47.87 Aligned_cols=52 Identities=21% Similarity=0.418 Sum_probs=44.0
Q ss_pred HHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 007404 531 MKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS 584 (605)
Q Consensus 531 l~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~R 584 (605)
....|..+++.|.+.++.||.+||+...+ +|..+||..|+||..+++.....
T Consensus 71 ~k~~id~~~~~l~de~k~Ii~lry~~r~~--~TW~~IA~~l~i~erta~r~~~~ 122 (130)
T PF05263_consen 71 QKEAIDRWLETLIDEEKRIIKLRYDRRSR--RTWYQIAQKLHISERTARRWRDR 122 (130)
T ss_pred HHHHHHHHHHhhCHHHHHHHHHHHccccc--chHHHHHHHhCccHHHHHHHHHH
Confidence 34567888899999999999999986633 99999999999999999955443
No 186
>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=94.15 E-value=0.19 Score=41.52 Aligned_cols=57 Identities=14% Similarity=0.119 Sum_probs=46.8
Q ss_pred HHHHHHhccHHHHHHHHHHHHHHHHHHHHHhh----C--CCCCHHHHHHHHHHHHHHhhhccC
Q 007404 355 ELRRRLNYGILCKDKMITSNIRLVISIAKNYQ----G--AGMNLQDLVQEGCRGLVRGAEKFD 411 (605)
Q Consensus 355 ~L~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~----~--~g~d~eDLIQEG~IGLirA~ekFD 411 (605)
.+.++.+||..|.++++..|.+++.+.+.+-. + .+.-=+|+-|+--..|++++.+|+
T Consensus 3 vI~~A~~GD~~A~~~IL~~y~~yI~kls~r~~~d~~g~~~~~vDedl~q~l~~kLi~~I~~F~ 65 (65)
T PF12645_consen 3 VIKAAKQGDPEAMEEILKHYEPYISKLSTRTLYDEYGNVYGYVDEDLKQRLEIKLIEAILKFE 65 (65)
T ss_pred HHHHHHcCCHHHHHHHHHHHHHHHHHHHHhhcccccCCcCceeCHHHHHHHHHHHHHHHHccC
Confidence 45667778899999999999999999988722 1 123338999999999999999996
No 187
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=93.85 E-value=0.067 Score=40.90 Aligned_cols=31 Identities=23% Similarity=0.308 Sum_probs=21.6
Q ss_pred HHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 007404 549 VVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS 584 (605)
Q Consensus 549 VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~R 584 (605)
||.+.. .+ +|..+||+.||||+.||+++.++
T Consensus 10 ii~l~~-~G----~s~~~ia~~lgvs~~Tv~~w~kr 40 (50)
T PF13384_consen 10 IIRLLR-EG----WSIREIAKRLGVSRSTVYRWIKR 40 (50)
T ss_dssp HHHHHH-HT------HHHHHHHHTS-HHHHHHHHT-
T ss_pred HHHHHH-CC----CCHHHHHHHHCcCHHHHHHHHHH
Confidence 555544 34 99999999999999999987665
No 188
>PF13730 HTH_36: Helix-turn-helix domain
Probab=93.73 E-value=0.25 Score=38.47 Aligned_cols=47 Identities=21% Similarity=0.435 Sum_probs=34.1
Q ss_pred cCCHHHHHHHHHHHhc--CCCCC-CCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 541 TLNPRERQVVRWRFGL--EDGRM-KTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 541 ~L~~rER~VL~LRyGl--~dg~~-~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
.|++.++.|+..-... +++.. .|.+.||+.+|+|+.||+ ++++.|.+
T Consensus 2 ~Ls~~~~~v~~~l~~~~~~~~~~~pS~~~la~~~g~s~~Tv~----~~i~~L~~ 51 (55)
T PF13730_consen 2 NLSPTAKLVYLYLASYANKNGGCFPSQETLAKDLGVSRRTVQ----RAIKELEE 51 (55)
T ss_pred CCCHHHHHHHHHHHHhcCCCCCCCcCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence 5888888776543322 22222 389999999999999999 77777765
No 189
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=93.29 E-value=0.2 Score=33.67 Aligned_cols=36 Identities=25% Similarity=0.420 Sum_probs=27.4
Q ss_pred CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHH
Q 007404 542 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQI 581 (605)
Q Consensus 542 L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqi 581 (605)
+++.++..+...|..+ .+..+|++.+|+|+.+|..+
T Consensus 6 ~~~~~~~~i~~~~~~~----~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 6 LTPEQIEEARRLLAAG----ESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred CCHHHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHh
Confidence 4555666565555443 79999999999999999865
No 190
>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=93.27 E-value=0.48 Score=43.92 Aligned_cols=52 Identities=15% Similarity=0.136 Sum_probs=47.5
Q ss_pred HhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404 539 LDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR 594 (605)
Q Consensus 539 L~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 594 (605)
|.+-.+.+-+||.++|..+ +|...||..+++|...||+.+.+|-.-+..++.
T Consensus 60 L~~~~~~~~~ll~~~Yv~g----~s~r~IA~~~~~s~~~ir~~l~~ae~~i~g~l~ 111 (125)
T PF06530_consen 60 LKKRDPEEYDLLILYYVYG----WSKRQIARKLKCSEGKIRKRLQRAEGFIDGCLS 111 (125)
T ss_pred HHccCHHHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHhhhhHhhhhH
Confidence 4557889999999999988 999999999999999999999999999988764
No 191
>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=93.02 E-value=0.29 Score=36.88 Aligned_cols=39 Identities=23% Similarity=0.405 Sum_probs=26.1
Q ss_pred CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 007404 542 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES 583 (605)
Q Consensus 542 L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~ 583 (605)
|++-.+.||..--. | ...|+.+||+.+|+|..+|.+++.
T Consensus 1 lD~~D~~Il~~Lq~--d-~r~s~~~la~~lglS~~~v~~Ri~ 39 (42)
T PF13404_consen 1 LDELDRKILRLLQE--D-GRRSYAELAEELGLSESTVRRRIR 39 (42)
T ss_dssp --HHHHHHHHHHHH----TTS-HHHHHHHHTS-HHHHHHHHH
T ss_pred CCHHHHHHHHHHHH--c-CCccHHHHHHHHCcCHHHHHHHHH
Confidence 34566777776433 2 238999999999999999996554
No 192
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=92.85 E-value=0.15 Score=54.45 Aligned_cols=36 Identities=19% Similarity=0.364 Sum_probs=31.7
Q ss_pred HHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 007404 548 QVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFR 587 (605)
Q Consensus 548 ~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALk 587 (605)
.|=.|||..+ +|.+|||++|||||.+|.+++.+|++
T Consensus 20 ~vA~lYY~~g----~tQ~eIA~~lgiSR~~VsRlL~~Ar~ 55 (318)
T PRK15418 20 RIAWFYYHDG----LTQSEIGERLGLTRLKVSRLLEKGRQ 55 (318)
T ss_pred HHHHHHHhcC----CCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4667777776 99999999999999999999998876
No 193
>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=92.81 E-value=0.21 Score=40.76 Aligned_cols=35 Identities=26% Similarity=0.301 Sum_probs=26.5
Q ss_pred HHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 007404 548 QVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS 584 (605)
Q Consensus 548 ~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~R 584 (605)
..+.++...+|. +++.+||+.||||..+||....+
T Consensus 11 kA~e~y~~~~g~--i~lkdIA~~Lgvs~~tIr~WK~~ 45 (60)
T PF10668_consen 11 KAFEIYKESNGK--IKLKDIAEKLGVSESTIRKWKSR 45 (60)
T ss_pred HHHHHHHHhCCC--ccHHHHHHHHCCCHHHHHHHhhh
Confidence 455555443333 99999999999999999987654
No 194
>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=92.74 E-value=0.24 Score=43.41 Aligned_cols=38 Identities=26% Similarity=0.351 Sum_probs=29.8
Q ss_pred HhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 007404 539 LDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIE 582 (605)
Q Consensus 539 L~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie 582 (605)
++.|++| ..|+.+. ..+ +|..|||+.+|||+.||..+.
T Consensus 34 ~~~Ls~R-~~I~~ll-~~G----~S~~eIA~~LgISrsTIyRi~ 71 (88)
T TIGR02531 34 IQSLAQR-LQVAKML-KQG----KTYSDIEAETGASTATISRVK 71 (88)
T ss_pred HHhhhHH-HHHHHHH-HCC----CCHHHHHHHHCcCHHHHHHHH
Confidence 3468888 7777763 222 899999999999999999733
No 195
>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=92.56 E-value=0.29 Score=38.11 Aligned_cols=42 Identities=29% Similarity=0.461 Sum_probs=29.7
Q ss_pred HHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 007404 545 RERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 592 (605)
Q Consensus 545 rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 592 (605)
|++.||.+-+-. +.+.|.+|||+.||||+.||+ +-++.|+..
T Consensus 1 R~~~il~~L~~~--~~~it~~eLa~~l~vS~rTi~----~~i~~L~~~ 42 (55)
T PF08279_consen 1 RQKQILKLLLES--KEPITAKELAEELGVSRRTIR----RDIKELREW 42 (55)
T ss_dssp HHHHHHHHHHHT--TTSBEHHHHHHHCTS-HHHHH----HHHHHHHHT
T ss_pred CHHHHHHHHHHc--CCCcCHHHHHHHhCCCHHHHH----HHHHHHHHC
Confidence 456777764333 334999999999999999999 555666553
No 196
>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=92.32 E-value=0.18 Score=38.32 Aligned_cols=32 Identities=19% Similarity=0.250 Sum_probs=22.1
Q ss_pred HHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 007404 546 ERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIE 582 (605)
Q Consensus 546 ER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie 582 (605)
..+|+.|+ -.+ +|..+||+.+|||+.||..++
T Consensus 11 ~~~i~~l~-~~G----~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 11 IEEIKELY-AEG----MSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp HHHHHHHH-HTT------HHHHHHHTTS-HHHHHHHH
T ss_pred HHHHHHHH-HCC----CCHHHHHHHHCcCHHHHHHHH
Confidence 34566664 333 999999999999999999664
No 197
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=92.26 E-value=0.29 Score=49.12 Aligned_cols=47 Identities=13% Similarity=0.105 Sum_probs=35.3
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 007404 541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFR 587 (605)
Q Consensus 541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALk 587 (605)
.|+++|.+++........+..+|.+|||+.||+|..||+.+..++..
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 48889987775443221223399999999999999999998887743
No 198
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=92.16 E-value=0.41 Score=43.84 Aligned_cols=49 Identities=20% Similarity=0.337 Sum_probs=41.5
Q ss_pred HhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 539 LDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 539 L~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
+..|++.+..-|... ....| +++|+++.||||-.|||.++.+.+++|..
T Consensus 31 ~~~L~~E~~~Fi~~F-i~~rG---nlKe~e~~lgiSYPTvR~rLd~ii~~lg~ 79 (113)
T PF09862_consen 31 FARLSPEQLEFIKLF-IKNRG---NLKEMEKELGISYPTVRNRLDKIIEKLGY 79 (113)
T ss_pred hhcCCHHHHHHHHHH-HHhcC---CHHHHHHHHCCCcHHHHHHHHHHHHHhCC
Confidence 678998888877664 44433 99999999999999999999999999876
No 199
>PHA00675 hypothetical protein
Probab=91.38 E-value=0.41 Score=40.80 Aligned_cols=40 Identities=18% Similarity=0.085 Sum_probs=32.1
Q ss_pred hcCCHHHHHHHHHHH-hcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 007404 540 DTLNPRERQVVRWRF-GLEDGRMKTLQEIGELMGVSRERIRQIES 583 (605)
Q Consensus 540 ~~L~~rER~VL~LRy-Gl~dg~~~Tl~EIAe~LGISrerVRqie~ 583 (605)
.+|++.+-+.|+.++ -.+ .|+.+||..||||+++|.+|.+
T Consensus 21 AKLt~~qV~~IR~l~~r~G----~s~~~IA~~fGVsrstV~~I~~ 61 (78)
T PHA00675 21 AKLTDAEVERIRELHEVEG----MSYAVLAEKFEQSKGAIAKICR 61 (78)
T ss_pred cccCHHHHHHHHHHHHhcC----ccHHHHHHHhCCCHHHHHHHHc
Confidence 467777777776666 344 7999999999999999998865
No 200
>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=91.33 E-value=0.37 Score=40.18 Aligned_cols=38 Identities=32% Similarity=0.414 Sum_probs=28.9
Q ss_pred HHHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHHHH
Q 007404 323 LKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRL 360 (605)
Q Consensus 323 ~~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~~l 360 (605)
.++.+.+.+|...+|+.||..+.|..+|++.+.+...+
T Consensus 4 ~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l 41 (78)
T PF04539_consen 4 RKIERARRELEQELGREPTDEEIAEELGISVEEVRELL 41 (78)
T ss_dssp HHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHH
Confidence 35667888999999999999999999999987765543
No 201
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=91.04 E-value=2.2 Score=46.44 Aligned_cols=126 Identities=21% Similarity=0.187 Sum_probs=69.6
Q ss_pred HHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHH-HHH
Q 007404 324 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEG-CRG 402 (605)
Q Consensus 324 ~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG-~IG 402 (605)
++.+...+|...+|+.||..+.|...|++.+.+...+... .. ..++++.+.++ -..
T Consensus 217 ~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~~-------------------~~----~~SLd~~~~~~~~~~ 273 (367)
T PRK09210 217 KLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIA-------------------QE----PVSLETPIGEEDDSH 273 (367)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHh-------------------cC----CCCcCCCCCCCCcch
Confidence 3455677788889999999999999999987765432211 00 01111111100 001
Q ss_pred HHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHHHHHHHHHHHHHHHHHHc----CCCCCHHHHHHhc
Q 007404 403 LVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSEN----GRHPNNEEVAEAT 478 (605)
Q Consensus 403 LirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~~~i~ki~ka~~~L~~el----gr~PT~eEIAe~l 478 (605)
|..-+. |+.............++..+.+++.. +|..-. .-+.... |.+-|.+|||+.+
T Consensus 274 l~d~i~--d~~~~~p~~~~~~~~~~~~l~~~l~~------L~~rEr----------~Vl~lrygl~~~~~~tl~EIa~~l 335 (367)
T PRK09210 274 LGDFIE--DQDATSPADHAAYELLKEQLEDVLDT------LTDREE----------NVLRLRFGLDDGRTRTLEEVGKVF 335 (367)
T ss_pred hhhhcc--CCCCCCHHHHHHHHHHHHHHHHHHHh------CCHHHH----------HHHHHHhccCCCCCccHHHHHHHH
Confidence 111111 11112233444555666666666642 222211 1112222 3678999999999
Q ss_pred CCCHHHHHHHHh
Q 007404 479 GLSMKRLHAVLL 490 (605)
Q Consensus 479 gis~e~V~~~l~ 490 (605)
|+|.++|+.+..
T Consensus 336 gvs~erVrQi~~ 347 (367)
T PRK09210 336 GVTRERIRQIEA 347 (367)
T ss_pred CCCHHHHHHHHH
Confidence 999999998853
No 202
>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=90.80 E-value=2.8 Score=42.47 Aligned_cols=35 Identities=26% Similarity=0.353 Sum_probs=28.0
Q ss_pred HHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHH
Q 007404 324 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRR 358 (605)
Q Consensus 324 ~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~ 358 (605)
++.+....|....|++||..+.|...|++.+.+..
T Consensus 88 ~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~ 122 (238)
T TIGR02393 88 KLIKAERQLTQELGREPTDEELAERMGMPAEKVRE 122 (238)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence 34455677778889999999999999999876653
No 203
>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=90.79 E-value=0.59 Score=37.89 Aligned_cols=46 Identities=22% Similarity=0.400 Sum_probs=30.5
Q ss_pred CCHHHHHHHHHHHhcC-CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 542 LNPRERQVVRWRFGLE-DGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 542 L~~rER~VL~LRyGl~-dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
|++....-|..-|.+. ++.+.+..+||+.||+|+.+|. .+++||.+
T Consensus 2 Lt~~~e~YL~~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt----~ml~~L~~ 48 (60)
T PF01325_consen 2 LTESEEDYLKAIYELSEEGGPVRTKDIAERLGVSPPTVT----EMLKRLAE 48 (60)
T ss_dssp CSCHHHHHHHHHHHHHHCTSSBBHHHHHHHHTS-HHHHH----HHHHHHHH
T ss_pred CCcHHHHHHHHHHHHHcCCCCccHHHHHHHHCCChHHHH----HHHHHHHH
Confidence 3343333333333332 5667999999999999999999 66777765
No 204
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=90.69 E-value=1.2 Score=49.39 Aligned_cols=38 Identities=34% Similarity=0.492 Sum_probs=30.4
Q ss_pred HHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHH
Q 007404 452 YRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVL 489 (605)
Q Consensus 452 ~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l 489 (605)
..+.+.+..|..++|+.||.+|.|...|+++..++..+
T Consensus 111 ~~l~~~~~~l~~~~g~~pt~~ewa~~~~~~~~~l~~~l 148 (415)
T PRK07598 111 LRLIEVRERLTSELGHRPSLERWAKTADISLADLKPTL 148 (415)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCCcHHHHHHhh
Confidence 35666778899999999999999988887766666554
No 205
>PF13518 HTH_28: Helix-turn-helix domain
Probab=89.87 E-value=0.61 Score=35.51 Aligned_cols=24 Identities=21% Similarity=0.361 Sum_probs=21.1
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHH
Q 007404 562 KTLQEIGELMGVSRERIRQIESSA 585 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~RA 585 (605)
.|+.+||..+|||+.+|+++..+-
T Consensus 13 ~s~~~~a~~~gis~~tv~~w~~~y 36 (52)
T PF13518_consen 13 ESVREIAREFGISRSTVYRWIKRY 36 (52)
T ss_pred CCHHHHHHHHCCCHhHHHHHHHHH
Confidence 699999999999999999776553
No 206
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=89.85 E-value=3.3 Score=47.25 Aligned_cols=35 Identities=26% Similarity=0.373 Sum_probs=29.2
Q ss_pred HHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHH
Q 007404 324 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRR 358 (605)
Q Consensus 324 ~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~ 358 (605)
++.+.+.+|...+|+.||..+.|+..|++.+.+..
T Consensus 359 kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~ 393 (509)
T PRK05901 359 KLGRIERELLQELGREPTPEELAKEMGFTPEKVRE 393 (509)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence 45567788888899999999999999999876654
No 207
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=89.66 E-value=0.72 Score=37.27 Aligned_cols=24 Identities=25% Similarity=0.392 Sum_probs=22.2
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHH
Q 007404 562 KTLQEIGELMGVSRERIRQIESSA 585 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~RA 585 (605)
++..|||+.||+++.||.+...+-
T Consensus 14 ~~~~eIA~~Lg~~~~TV~~W~~r~ 37 (58)
T PF06056_consen 14 WSIKEIAEELGVPRSTVYSWKDRY 37 (58)
T ss_pred CCHHHHHHHHCCChHHHHHHHHhh
Confidence 999999999999999999988763
No 208
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=89.53 E-value=3.6 Score=44.23 Aligned_cols=35 Identities=20% Similarity=0.368 Sum_probs=28.7
Q ss_pred HHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHH
Q 007404 324 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRR 358 (605)
Q Consensus 324 ~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~ 358 (605)
++.+.+..|...+|++||..+.|+..|++.+.+..
T Consensus 174 ~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~ 208 (324)
T PRK07921 174 KLARIKRELHQQLGREATDEELAEESGIPEEKIAD 208 (324)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHH
Confidence 45566777888889999999999999999876654
No 209
>smart00351 PAX Paired Box domain.
Probab=89.42 E-value=0.96 Score=41.82 Aligned_cols=41 Identities=20% Similarity=0.094 Sum_probs=31.3
Q ss_pred CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 007404 542 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAF 586 (605)
Q Consensus 542 L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RAL 586 (605)
|+..+|.=|...|-.+ .|..+||+.||||+.+|..++.+..
T Consensus 18 ~s~~~R~riv~~~~~G----~s~~~iA~~~gvs~~tV~kwi~r~~ 58 (125)
T smart00351 18 LPDEERQRIVELAQNG----VRPCDISRQLCVSHGCVSKILGRYY 58 (125)
T ss_pred CCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 5555555455555444 8999999999999999998888754
No 210
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=89.40 E-value=1.3 Score=41.38 Aligned_cols=53 Identities=21% Similarity=0.262 Sum_probs=41.8
Q ss_pred HHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 533 EDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 533 ~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
..+..++-.|++.+-+|+..-.-. +.|+|..|||+.||++++||. ||+++|-.
T Consensus 16 ~dvl~c~~GLs~~Dv~v~~~LL~~--~~~~tvdelae~lnr~rStv~----rsl~~L~~ 68 (126)
T COG3355 16 EDVLKCVYGLSELDVEVYKALLEE--NGPLTVDELAEILNRSRSTVY----RSLQNLLE 68 (126)
T ss_pred HHHHHHHhCCcHHHHHHHHHHHhh--cCCcCHHHHHHHHCccHHHHH----HHHHHHHH
Confidence 346677778999999998765422 346999999999999999998 77777754
No 211
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=89.35 E-value=0.97 Score=35.64 Aligned_cols=41 Identities=24% Similarity=0.319 Sum_probs=31.2
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 007404 541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIE 582 (605)
Q Consensus 541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie 582 (605)
.|++.|..||..-+..+ +...|..||++.+++++.+|.+++
T Consensus 2 glt~~q~~vL~~l~~~~-~~~~t~~~la~~l~~~~~~vs~~v 42 (62)
T PF12802_consen 2 GLTPSQFRVLMALARHP-GEELTQSELAERLGISKSTVSRIV 42 (62)
T ss_dssp TSTHHHHHHHHHHHHST-TSGEEHHHHHHHHTS-HHHHHHHH
T ss_pred ccCHHHHHHHHHHHHCC-CCCcCHHHHHHHHCcCHHHHHHHH
Confidence 37788888887766554 334899999999999999999443
No 212
>PRK11083 DNA-binding response regulator CreB; Provisional
Probab=89.10 E-value=0.56 Score=45.15 Aligned_cols=50 Identities=18% Similarity=0.185 Sum_probs=43.1
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCC-----HHHHHHHHHHHHHHHHh
Q 007404 541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVS-----RERIRQIESSAFRKLKN 591 (605)
Q Consensus 541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGIS-----rerVRqie~RALkKLR~ 591 (605)
.|+++|.+||.+.. .+.|..+|.+||++.++.+ ..||+.+..+.++||..
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 59999999998765 3456679999999999996 78999999999999974
No 213
>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=88.86 E-value=0.56 Score=37.04 Aligned_cols=40 Identities=23% Similarity=0.309 Sum_probs=26.4
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 007404 541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS 584 (605)
Q Consensus 541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~R 584 (605)
.|+..|+.=|.-+|-.| .+..+||..|||+++||+.|...
T Consensus 6 ~LTl~eK~~iI~~~e~g----~s~~~ia~~fgv~~sTv~~I~K~ 45 (53)
T PF04218_consen 6 SLTLEEKLEIIKRLEEG----ESKRDIAREFGVSRSTVSTILKN 45 (53)
T ss_dssp S--HHHHHHHHHHHHCT----T-HHHHHHHHT--CCHHHHHHHC
T ss_pred cCCHHHHHHHHHHHHcC----CCHHHHHHHhCCCHHHHHHHHHh
Confidence 46666666444455444 69999999999999999988765
No 214
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=88.62 E-value=0.61 Score=50.09 Aligned_cols=35 Identities=23% Similarity=0.261 Sum_probs=29.8
Q ss_pred HHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 007404 549 VVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFR 587 (605)
Q Consensus 549 VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALk 587 (605)
+-.+||..+ +|..|||++||||+.+|+..+.+|.+
T Consensus 18 ~A~lYY~~g----ltQ~eIA~~LgiSR~~v~rlL~~Ar~ 52 (321)
T COG2390 18 AAWLYYVEG----LTQSEIAERLGISRATVSRLLAKARE 52 (321)
T ss_pred HHHHHHhcC----CCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 556677666 99999999999999999988888765
No 215
>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=88.48 E-value=1.2 Score=38.26 Aligned_cols=41 Identities=27% Similarity=0.344 Sum_probs=33.0
Q ss_pred cCCHHHHHHHHHHH--hcCCCCCCCHHHHHHHHCCCHHHHHHH
Q 007404 541 TLNPRERQVVRWRF--GLEDGRMKTLQEIGELMGVSRERIRQI 581 (605)
Q Consensus 541 ~L~~rER~VL~LRy--Gl~dg~~~Tl~EIAe~LGISrerVRqi 581 (605)
.|+++|++||..-- +...++|..-++||+.+++|..|||+.
T Consensus 1 ~Lt~rq~~IL~alV~~Y~~~~~PVgSk~ia~~l~~s~aTIRN~ 43 (78)
T PF03444_consen 1 MLTERQREILKALVELYIETGEPVGSKTIAEELGRSPATIRNE 43 (78)
T ss_pred CCCHHHHHHHHHHHHHHHhcCCCcCHHHHHHHHCCChHHHHHH
Confidence 38899999876532 233678999999999999999999954
No 216
>PRK12423 LexA repressor; Provisional
Probab=88.44 E-value=0.85 Score=45.45 Aligned_cols=48 Identities=27% Similarity=0.424 Sum_probs=36.6
Q ss_pred hcCCHHHHHHHHHH--HhcCCCCCCCHHHHHHHHC-CCHHHHHHHHHHHHHHHHh
Q 007404 540 DTLNPRERQVVRWR--FGLEDGRMKTLQEIGELMG-VSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 540 ~~L~~rER~VL~LR--yGl~dg~~~Tl~EIAe~LG-ISrerVRqie~RALkKLR~ 591 (605)
..|++++++|+..- |...+|-+-|..|||+.|| .|+.+|+ ++|++|++
T Consensus 2 ~~lt~~q~~il~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~----~~l~~L~~ 52 (202)
T PRK12423 2 DTLTPKRAAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVAR----KHVQALAE 52 (202)
T ss_pred CcCCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHH----HHHHHHHH
Confidence 34899999998753 2233455579999999999 5999999 56777766
No 217
>PRK15479 transcriptional regulatory protein TctD; Provisional
Probab=88.28 E-value=0.76 Score=44.01 Aligned_cols=49 Identities=27% Similarity=0.246 Sum_probs=42.4
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHC-----CCHHHHHHHHHHHHHHHH
Q 007404 541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMG-----VSRERIRQIESSAFRKLK 590 (605)
Q Consensus 541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LG-----ISrerVRqie~RALkKLR 590 (605)
.|+++|.+|+.+.. .+-|.+.|.++|++.+. +|..+|+.+..+.++||.
T Consensus 148 ~Lt~~E~~il~~l~-~~~~~~~~~~~i~~~l~~~~~~~~~~tv~~~i~~ir~kl~ 201 (221)
T PRK15479 148 ALTPREQALLTVLM-YRRTRPVSRQQLFEQVFSLNDEVSPESIELYIHRLRKKLQ 201 (221)
T ss_pred ecCHHHHHHHHHHH-hCCCCcCcHHHHHHHhcCCCCCCCcccHHHHHHHHHHhcC
Confidence 59999999998764 44466789999999996 999999999999999985
No 218
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=88.19 E-value=1.5 Score=36.19 Aligned_cols=41 Identities=10% Similarity=0.278 Sum_probs=28.1
Q ss_pred HHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 546 ERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 546 ER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
+..||.+-. ..++++.|..|||+.+||++.+|+ +.|.+|.+
T Consensus 8 ~~~IL~~L~-~~g~~~~ta~eLa~~lgl~~~~v~----r~L~~L~~ 48 (68)
T smart00550 8 EEKILEFLE-NSGDETSTALQLAKNLGLPKKEVN----RVLYSLEK 48 (68)
T ss_pred HHHHHHHHH-HCCCCCcCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 344554433 223335999999999999999999 55566654
No 219
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=88.02 E-value=5.4 Score=41.43 Aligned_cols=123 Identities=17% Similarity=0.185 Sum_probs=68.5
Q ss_pred HHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHH
Q 007404 325 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLV 404 (605)
Q Consensus 325 le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLi 404 (605)
++.+..+|+..+|++||..+.|...|++.+++.. .+...+-...+++-......+...
T Consensus 112 i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~----------~~~~~~~~~~~sld~~~~~~~d~~------------ 169 (247)
T COG1191 112 IEEAIDELEQELGREPTDEEIAEELGIDKEEYIE----------ALLAINGSQLLSLDEDVLKDDDDD------------ 169 (247)
T ss_pred HHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHH----------HHHHhccccccchhhhhccccccc------------
Confidence 4456778888999999999999999999866543 333333222222222222111110
Q ss_pred HhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHH
Q 007404 405 RGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKR 484 (605)
Q Consensus 405 rA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~ 484 (605)
-+...+..+..+-.|-.++.+..++.. +|..- +.-+.-....+-|..||++.||+|..+
T Consensus 170 -----~~~~~~~~~~~~~~~~~~~~l~~ai~~------L~ERE----------k~Vl~l~y~eelt~kEI~~~LgISes~ 228 (247)
T COG1191 170 -----VDDQIENPDDGVEKEELLEILKEAIEP------LPERE----------KLVLVLRYKEELTQKEIAEVLGISESR 228 (247)
T ss_pred -----hhhccccchhHHHHHHHHHHHHHHHHc------cCHHH----------HHHHHHHHHhccCHHHHHHHhCccHHH
Confidence 011122234445556666666666542 11110 000111123456788999999999999
Q ss_pred HHHHHh
Q 007404 485 LHAVLL 490 (605)
Q Consensus 485 V~~~l~ 490 (605)
|..+..
T Consensus 229 VSql~k 234 (247)
T COG1191 229 VSRLHK 234 (247)
T ss_pred HHHHHH
Confidence 987753
No 220
>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=88.00 E-value=1.4 Score=38.70 Aligned_cols=49 Identities=29% Similarity=0.342 Sum_probs=37.3
Q ss_pred HhcCCHHHHHHHHHH----HhcC-CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 539 LDTLNPRERQVVRWR----FGLE-DGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 539 L~~L~~rER~VL~LR----yGl~-dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
...|++++..+|..- ||.+ ...+.|..|||+.+|+++++|. |++++|.+
T Consensus 20 ~~~l~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~sr~tVs----r~L~~Le~ 73 (95)
T TIGR01610 20 GADLSGREFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLSRTHVS----DAIKSLAR 73 (95)
T ss_pred hCCCCHHHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence 457899999877633 3322 2356999999999999999999 77777765
No 221
>PHA02591 hypothetical protein; Provisional
Probab=87.86 E-value=1.1 Score=38.43 Aligned_cols=22 Identities=32% Similarity=0.527 Sum_probs=20.7
Q ss_pred CCHHHHHHHHCCCHHHHHHHHH
Q 007404 562 KTLQEIGELMGVSRERIRQIES 583 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~ 583 (605)
+|.++||+.||+|.++||+..+
T Consensus 60 lSqeqIA~~LGVsqetVrKYL~ 81 (83)
T PHA02591 60 FTVEKIASLLGVSVRKVRRYLE 81 (83)
T ss_pred CCHHHHHHHhCCCHHHHHHHHh
Confidence 9999999999999999998765
No 222
>PRK10336 DNA-binding transcriptional regulator QseB; Provisional
Probab=87.79 E-value=0.77 Score=44.00 Aligned_cols=49 Identities=24% Similarity=0.230 Sum_probs=42.4
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHC-----CCHHHHHHHHHHHHHHHH
Q 007404 541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMG-----VSRERIRQIESSAFRKLK 590 (605)
Q Consensus 541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LG-----ISrerVRqie~RALkKLR 590 (605)
.|+++|.+||.+. ..+.|..+|.++|++.+. ++..+|+.+..+.++||.
T Consensus 149 ~Lt~~E~~il~~l-~~~~~~~~s~~~i~~~l~~~~~~~~~~tv~~~i~~lr~Kl~ 202 (219)
T PRK10336 149 TLKPKEFALLELL-MRNAGRVLPRKLIEEKLYTWDEEVTSNAVEVHVHHLRRKLG 202 (219)
T ss_pred ecCHHHHHHHHHH-HhCCCccCcHHHHHHHhcCCCCCCCccCHHHHHHHHHHhcC
Confidence 4999999999864 445567799999999996 999999999999999885
No 223
>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=87.77 E-value=1.1 Score=38.94 Aligned_cols=42 Identities=29% Similarity=0.473 Sum_probs=31.4
Q ss_pred HhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHH--CCCHHHHHHHHH
Q 007404 539 LDTLNPRERQVVRWRFGLEDGRMKTLQEIGELM--GVSRERIRQIES 583 (605)
Q Consensus 539 L~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~L--GISrerVRqie~ 583 (605)
++.||+..+++..+|--.-+ .|+.|+|+.| .||++.|.-+..
T Consensus 35 ~~~l~~~l~~~a~lRl~~Pd---~SL~EL~~~~~~~iSKSgvnhrlr 78 (85)
T PF02650_consen 35 LDKLPEKLREFAELRLENPD---ASLKELGELLEPPISKSGVNHRLR 78 (85)
T ss_dssp GGGS-HHHHHHHHHHHH-TT---S-HHHHHHTT--T--HHHHHHHHH
T ss_pred cccCCHHHHHHHHHHHHCcc---ccHHHHHHHHcCcCcHHHHHHHHH
Confidence 57899999999999975544 9999999999 999999985543
No 224
>PRK10710 DNA-binding transcriptional regulator BaeR; Provisional
Probab=87.75 E-value=0.83 Score=44.53 Aligned_cols=50 Identities=20% Similarity=0.226 Sum_probs=44.1
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHC-----CCHHHHHHHHHHHHHHHHh
Q 007404 541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMG-----VSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LG-----ISrerVRqie~RALkKLR~ 591 (605)
.|+++|++|+.+... +.|+..|.++|++.+. ++..+|+.+..+.++||..
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 599999999998664 4567799999999998 9999999999999999963
No 225
>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=87.65 E-value=0.63 Score=37.95 Aligned_cols=44 Identities=27% Similarity=0.323 Sum_probs=33.2
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
.|++.|..|+..-.-.+ +.|..|||+.+|+++.+|+ +++++|.+
T Consensus 5 gLs~~E~~vy~~Ll~~~---~~t~~eIa~~l~i~~~~v~----~~L~~L~~ 48 (68)
T PF01978_consen 5 GLSENEAKVYLALLKNG---PATAEEIAEELGISRSTVY----RALKSLEE 48 (68)
T ss_dssp CHHHHHHHHHHHHHHHC---HEEHHHHHHHHTSSHHHHH----HHHHHHHH
T ss_pred CcCHHHHHHHHHHHHcC---CCCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence 46777888876543222 3999999999999999999 66666654
No 226
>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=87.64 E-value=2 Score=37.38 Aligned_cols=42 Identities=24% Similarity=0.231 Sum_probs=29.1
Q ss_pred HHHHHHHHHHhcCCCCCCCHHHHHHHHC-CCHHHHHHHHHHHHHHHHhHHh
Q 007404 545 RERQVVRWRFGLEDGRMKTLQEIGELMG-VSRERIRQIESSAFRKLKNKKR 594 (605)
Q Consensus 545 rER~VL~LRyGl~dg~~~Tl~EIAe~LG-ISrerVRqie~RALkKLR~~l~ 594 (605)
|+--+...+...+ +|+.+||..|| .+..+|. .|++|+.+.+.
T Consensus 32 R~ia~yl~~~~~~----~s~~~Ig~~fg~r~hStV~----~a~~ri~~~~~ 74 (90)
T cd06571 32 RQIAMYLARELTG----LSLPEIGRAFGGRDHSTVL----HAVRKIEELLE 74 (90)
T ss_pred HHHHHHHHHHHhC----CCHHHHHHHhCCCCHhHHH----HHHHHHHHHHH
Confidence 3333444444455 99999999999 9999999 45555555444
No 227
>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=87.64 E-value=1 Score=44.46 Aligned_cols=48 Identities=17% Similarity=0.305 Sum_probs=37.2
Q ss_pred hcCCHHHHHHHHHHHh--cCCCCCCCHHHHHHHHCCC-HHHHHHHHHHHHHHHHh
Q 007404 540 DTLNPRERQVVRWRFG--LEDGRMKTLQEIGELMGVS-RERIRQIESSAFRKLKN 591 (605)
Q Consensus 540 ~~L~~rER~VL~LRyG--l~dg~~~Tl~EIAe~LGIS-rerVRqie~RALkKLR~ 591 (605)
..|+++|++||..-.- ..++.+.|..|||+.+|++ +.+|+ +.+++|.+
T Consensus 2 ~~lt~~q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~----~~l~~L~~ 52 (199)
T TIGR00498 2 KPLTARQQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAE----EHLKALER 52 (199)
T ss_pred CccCHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHH----HHHHHHHH
Confidence 3589999999887542 3356778999999999998 99999 55555554
No 228
>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=87.55 E-value=0.84 Score=44.29 Aligned_cols=50 Identities=18% Similarity=0.129 Sum_probs=42.6
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHH--HHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 541 TLNPRERQVVRWRFGLEDGRMKTLQEI--GELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 541 ~L~~rER~VL~LRyGl~dg~~~Tl~EI--Ae~LGISrerVRqie~RALkKLR~ 591 (605)
.|+++|.+||.+.. .+-|..+|.++| +..++++..+|+.+..|.++||..
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 444666799999 888999999999999999999963
No 229
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=87.55 E-value=1.5 Score=38.60 Aligned_cols=43 Identities=16% Similarity=0.341 Sum_probs=31.8
Q ss_pred CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 542 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 542 L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
|++.++.||..... + .+.|+.+||+.+|+|+.+|+ +.+++|.+
T Consensus 1 ld~~D~~il~~L~~-~--~~~~~~~la~~l~~s~~tv~----~~l~~L~~ 43 (108)
T smart00344 1 LDEIDRKILEELQK-D--ARISLAELAKKVGLSPSTVH----NRVKRLEE 43 (108)
T ss_pred CCHHHHHHHHHHHH-h--CCCCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence 46678888876543 2 24899999999999999999 44455544
No 230
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=87.07 E-value=1 Score=34.71 Aligned_cols=28 Identities=29% Similarity=0.488 Sum_probs=24.1
Q ss_pred CCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 560 RMK-TLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 560 ~~~-Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
... |..|||+.+|+|+.+|+ +++++|.+
T Consensus 18 ~~l~s~~~la~~~~vs~~tv~----~~l~~L~~ 46 (60)
T smart00345 18 DKLPSERELAAQLGVSRTTVR----EALSRLEA 46 (60)
T ss_pred CcCcCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 345 89999999999999999 77777775
No 231
>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]
Probab=87.05 E-value=0.74 Score=54.72 Aligned_cols=46 Identities=20% Similarity=0.190 Sum_probs=41.8
Q ss_pred CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 007404 542 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 592 (605)
Q Consensus 542 L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 592 (605)
|+.||++|+.+.|- | +|.+|||++|.||-.||+.+.++...||.-.
T Consensus 832 Ls~RE~eVL~Lia~-G----~SN~eIa~~L~isl~TVKtH~rniy~KLgV~ 877 (894)
T COG2909 832 LSQRELEVLGLIAQ-G----LSNEEIAQELFISLTTVKTHIRNIYQKLGVA 877 (894)
T ss_pred ccHHHHHHHHHHHc-c----CCHHHHHHHHHHHHHHHHHHHHHHHHHhCcc
Confidence 89999999999873 3 8999999999999999999999999998643
No 232
>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=86.74 E-value=0.97 Score=35.07 Aligned_cols=35 Identities=20% Similarity=0.265 Sum_probs=25.0
Q ss_pred HHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 007404 548 QVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIE 582 (605)
Q Consensus 548 ~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie 582 (605)
-+-.+.+.-..+.++|+.||++.+|+++.+|..++
T Consensus 5 al~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L 39 (52)
T PF09339_consen 5 ALRILEALAESGGPLTLSEIARALGLPKSTVHRLL 39 (52)
T ss_dssp HHHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHH
Confidence 33344445555666899999999999999999443
No 233
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=86.71 E-value=2.2 Score=43.89 Aligned_cols=35 Identities=23% Similarity=0.315 Sum_probs=28.4
Q ss_pred HHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHH
Q 007404 324 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRR 358 (605)
Q Consensus 324 ~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~ 358 (605)
++.+.+.+|...+|++|+..+.|...|++.+.+..
T Consensus 114 ~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~ 148 (256)
T PRK07408 114 QAKKVRQELRQELGRQPTDQEIAQALDISLEEWQE 148 (256)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHH
Confidence 34556777888899999999999999999876543
No 234
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=86.40 E-value=1.7 Score=34.12 Aligned_cols=39 Identities=26% Similarity=0.434 Sum_probs=29.7
Q ss_pred CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 007404 542 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES 583 (605)
Q Consensus 542 L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~ 583 (605)
|+..|-.||..-+-.++ .|..|||+.+++++.+|.++..
T Consensus 1 lt~~q~~iL~~l~~~~~---~~~~~la~~~~~~~~~~t~~i~ 39 (59)
T PF01047_consen 1 LTPSQFRILRILYENGG---ITQSELAEKLGISRSTVTRIIK 39 (59)
T ss_dssp STHHHHHHHHHHHHHSS---EEHHHHHHHHTS-HHHHHHHHH
T ss_pred CCHHHHHHHHHHHHcCC---CCHHHHHHHHCCChhHHHHHHH
Confidence 56677778877765543 9999999999999999994443
No 235
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=85.56 E-value=1.5 Score=35.09 Aligned_cols=44 Identities=23% Similarity=0.337 Sum_probs=27.4
Q ss_pred CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 542 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 542 L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
|+..|..||..-. ..+.+++..+|++.+++++.+|. +++++|..
T Consensus 1 lt~~q~~vL~~l~--~~~~~~t~~~l~~~~~~~~~~vs----~~i~~L~~ 44 (68)
T PF13463_consen 1 LTRPQWQVLRALA--HSDGPMTQSDLAERLGISKSTVS----RIIKKLEE 44 (68)
T ss_dssp --HHHHHHHHHHT----TS-BEHHHHHHHTT--HHHHH----HHHHHHHH
T ss_pred CCHHHHHHHHHHH--ccCCCcCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence 4566666665443 34456999999999999999999 55555543
No 236
>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=85.17 E-value=4.5 Score=41.83 Aligned_cols=56 Identities=29% Similarity=0.428 Sum_probs=42.9
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHHhcCCC--CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 532 KEDLEKVLDTLNPRERQVVRWRFGLEDG--RMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 532 ~~~L~~aL~~L~~rER~VL~LRyGl~dg--~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
+..++-++.+|+--|.+.+...+-.=++ .-.+..+||+.+|||+..|+ +|+++|..
T Consensus 167 ka~Vq~Ai~tLSySEleAv~~IL~~L~~~egrlse~eLAerlGVSRs~ir----eAlrkLE~ 224 (251)
T TIGR02787 167 KAAVQMAINTLSYSELEAVEHIFEELDGNEGLLVASKIADRVGITRSVIV----NALRKLES 224 (251)
T ss_pred HHHHHHHHHhccHhHHHHHHHHHHHhccccccccHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 4457788999998887766655443222 34899999999999999999 77787765
No 237
>cd00131 PAX Paired Box domain
Probab=84.99 E-value=2.4 Score=39.43 Aligned_cols=41 Identities=17% Similarity=0.054 Sum_probs=30.1
Q ss_pred CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 007404 542 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAF 586 (605)
Q Consensus 542 L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RAL 586 (605)
|+...|.=|...|..+ +|..+||+.||||+.+|..+.++-.
T Consensus 18 lS~d~R~rIv~~~~~G----~s~~~iA~~~~Vs~~tV~r~i~r~~ 58 (128)
T cd00131 18 LPDSIRQRIVELAQSG----IRPCDISRQLRVSHGCVSKILNRYY 58 (128)
T ss_pred CCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 5554555444445444 8999999999999999998877644
No 238
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=84.43 E-value=2.2 Score=40.59 Aligned_cols=38 Identities=16% Similarity=0.253 Sum_probs=30.0
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHH
Q 007404 541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQI 581 (605)
Q Consensus 541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqi 581 (605)
.|++.++.||..--- || ..|+.|||+.+|+|+.+|+.+
T Consensus 6 ~lD~~D~~Il~~Lq~--d~-R~s~~eiA~~lglS~~tV~~R 43 (153)
T PRK11179 6 QIDNLDRGILEALME--NA-RTPYAELAKQFGVSPGTIHVR 43 (153)
T ss_pred ccCHHHHHHHHHHHH--cC-CCCHHHHHHHHCcCHHHHHHH
Confidence 477888888876432 22 389999999999999999943
No 239
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=84.41 E-value=2.5 Score=33.30 Aligned_cols=39 Identities=31% Similarity=0.343 Sum_probs=27.4
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 007404 541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES 583 (605)
Q Consensus 541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~ 583 (605)
.|++-|+--|....-++ +++.|||..+|-|+..|+..+.
T Consensus 4 ~Lt~~Eqaqid~m~qlG----~s~~~isr~i~RSr~~Ir~yl~ 42 (50)
T PF11427_consen 4 TLTDAEQAQIDVMHQLG----MSLREISRRIGRSRTCIRRYLK 42 (50)
T ss_dssp ---HHHHHHHHHHHHTT------HHHHHHHHT--HHHHHHHHH
T ss_pred cCCHHHHHHHHHHHHhc----hhHHHHHHHhCccHHHHHHHhc
Confidence 47888888888877787 9999999999999999996643
No 240
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=84.31 E-value=1.1 Score=44.67 Aligned_cols=39 Identities=21% Similarity=0.232 Sum_probs=28.0
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 007404 541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES 583 (605)
Q Consensus 541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~ 583 (605)
.|+++ +|+.+.- +|...+|.+|||+.||||+.||+.+..
T Consensus 161 ~Lt~r--~Vl~~~~--~g~~g~s~~eIa~~l~iS~~Tv~~~~~ 199 (225)
T PRK10046 161 PLTLN--AVRKLFK--EPGVQHTAETVAQALTISRTTARRYLE 199 (225)
T ss_pred HHHHH--HHHHHHH--cCCCCcCHHHHHHHhCccHHHHHHHHH
Confidence 35554 5665532 222238999999999999999997764
No 241
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=84.02 E-value=4.5 Score=38.50 Aligned_cols=67 Identities=25% Similarity=0.358 Sum_probs=39.5
Q ss_pred HHHHHhcCCHHHHHHHHHH----HhcCCCCCCCHHHHHHHHCCCHHHHHHHHH--HHHHHHHhHHhhhhHhhh
Q 007404 535 LEKVLDTLNPRERQVVRWR----FGLEDGRMKTLQEIGELMGVSRERIRQIES--SAFRKLKNKKRTKHLMQY 601 (605)
Q Consensus 535 L~~aL~~L~~rER~VL~LR----yGl~dg~~~Tl~EIAe~LGISrerVRqie~--RALkKLR~~l~~~~L~~y 601 (605)
+..+=.+|++.|+....+. |...+|+.+|+.|||+.+||++.+.-++.+ +++-...+.+....+.++
T Consensus 4 ~~~le~~L~~~Q~kAa~ll~~ne~~~~~~~r~T~~eiAee~Gis~~tLYrWr~~~~~Fiey~n~la~~~~~~~ 76 (142)
T PF13022_consen 4 LKELEAKLTLQQRKAAQLLVENELMPENGERRTQAEIAEEVGISRSTLYRWRQQNKAFIEYKNELADRFLSSH 76 (142)
T ss_dssp HHHHHTTS-HHHHHHHHHHHHHHHS------S-HHHHHHHHTS-HHHHHHHHHH-HHHHHHHHHHHHHHHHTT
T ss_pred HHHHHHHcCHHHHHHHHHHHHHHHhhhccccchHHHHHHHhCCCHHHHHHHHhcCHHHHHHHHHHHHHHHHHh
Confidence 4455578999988833322 222244669999999999999999999874 455555555555544444
No 242
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=84.00 E-value=11 Score=39.17 Aligned_cols=34 Identities=35% Similarity=0.479 Sum_probs=27.1
Q ss_pred HHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHH
Q 007404 325 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRR 358 (605)
Q Consensus 325 le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~ 358 (605)
+.+...+|...+|+.||..+.|...|++.+.+..
T Consensus 129 i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~ 162 (264)
T PRK07122 129 LGRATAELSQRLGRAPTASELAAELGMDREEVVE 162 (264)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence 3445666777889999999999999999876644
No 243
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=83.69 E-value=8.1 Score=39.88 Aligned_cols=32 Identities=22% Similarity=0.285 Sum_probs=25.3
Q ss_pred hHHHHHHhhcCCCCchHHHHHhhcCCHHHHHH
Q 007404 327 GLREVLSERCGGSPTFAQWAAAAGVDQRELRR 358 (605)
Q Consensus 327 ~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~ 358 (605)
.....|...+|++|+..+.|+..|++.+.+..
T Consensus 114 ~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~ 145 (257)
T PRK05911 114 DAMDSLRQSLGKEPTDGELCEYLNISQQELSG 145 (257)
T ss_pred HHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHH
Confidence 34455667789999999999999999876643
No 244
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=83.36 E-value=1.9 Score=40.19 Aligned_cols=40 Identities=25% Similarity=0.333 Sum_probs=31.7
Q ss_pred hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 007404 540 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIE 582 (605)
Q Consensus 540 ~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie 582 (605)
..|++.++.||...- .|++ .|+.|||+.+|+|+.+|+.+.
T Consensus 4 ~~lD~~D~~IL~~L~--~d~r-~~~~eia~~lglS~~~v~~Ri 43 (154)
T COG1522 4 MKLDDIDRRILRLLQ--EDAR-ISNAELAERVGLSPSTVLRRI 43 (154)
T ss_pred ccccHHHHHHHHHHH--HhCC-CCHHHHHHHHCCCHHHHHHHH
Confidence 457888899988743 3333 999999999999999999443
No 245
>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=83.26 E-value=0.9 Score=43.56 Aligned_cols=50 Identities=14% Similarity=0.212 Sum_probs=42.0
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHH-----HHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 541 TLNPRERQVVRWRFGLEDGRMKTLQEI-----GELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 541 ~L~~rER~VL~LRyGl~dg~~~Tl~EI-----Ae~LGISrerVRqie~RALkKLR~ 591 (605)
.|+++|.+||.+-.. +-|..+|.++| |..+++|..||+.+..+.++||..
T Consensus 154 ~Lt~~E~~il~~l~~-~~~~~~s~~~i~~~~~~~~~~~~~~tv~~~i~~l~~Kl~~ 208 (226)
T TIGR02154 154 SLGPTEFRLLHFFMT-HPERVYSREQLLDRVWGRDVYVEERTVDVHIRRLRKALNP 208 (226)
T ss_pred EcCHHHHHHHHHHHh-CCCceEcHHHHHHHhcCCCCCCCCccHHHHHHHHHHhhcc
Confidence 599999999988654 34556888888 778999999999999999999963
No 246
>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=83.13 E-value=3.3 Score=31.50 Aligned_cols=22 Identities=23% Similarity=0.330 Sum_probs=18.9
Q ss_pred CCCHHHHHHHHCCCHHHHHHHH
Q 007404 561 MKTLQEIGELMGVSRERIRQIE 582 (605)
Q Consensus 561 ~~Tl~EIAe~LGISrerVRqie 582 (605)
+++..||++.+|+|+.+|++++
T Consensus 15 ~~~~~el~~~l~~s~~~vs~hL 36 (47)
T PF01022_consen 15 PLTVSELAEELGLSQSTVSHHL 36 (47)
T ss_dssp SEEHHHHHHHHTS-HHHHHHHH
T ss_pred CCchhhHHHhccccchHHHHHH
Confidence 5999999999999999999654
No 247
>PRK00215 LexA repressor; Validated
Probab=83.11 E-value=2.1 Score=42.31 Aligned_cols=42 Identities=19% Similarity=0.297 Sum_probs=32.8
Q ss_pred CCHHHHHHHHHHH--hcCCCCCCCHHHHHHHHCC-CHHHHHHHHH
Q 007404 542 LNPRERQVVRWRF--GLEDGRMKTLQEIGELMGV-SRERIRQIES 583 (605)
Q Consensus 542 L~~rER~VL~LRy--Gl~dg~~~Tl~EIAe~LGI-SrerVRqie~ 583 (605)
|+++|++||.+-. ...++.+.|+.|||+.+|+ ++.+|..++.
T Consensus 2 lt~~q~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~ 46 (205)
T PRK00215 2 LTKRQQEILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLK 46 (205)
T ss_pred CCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHH
Confidence 7889999986543 2345667899999999999 9999995443
No 248
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=83.06 E-value=1.7 Score=35.76 Aligned_cols=27 Identities=37% Similarity=0.661 Sum_probs=24.0
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 561 MKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 561 ~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
++|.++||..+|+|+++|. +.+++|++
T Consensus 28 ~lt~~~iA~~~g~sr~tv~----r~l~~l~~ 54 (76)
T PF13545_consen 28 PLTQEEIADMLGVSRETVS----RILKRLKD 54 (76)
T ss_dssp ESSHHHHHHHHTSCHHHHH----HHHHHHHH
T ss_pred cCCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 5899999999999999998 77777776
No 249
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=83.04 E-value=2.7 Score=33.51 Aligned_cols=39 Identities=26% Similarity=0.371 Sum_probs=27.2
Q ss_pred HHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 546 ERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 546 ER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
+..|+.+-.- ....|.+|+|+.||||..||| |=|..|.+
T Consensus 2 ~~~Il~~l~~---~~~~s~~ela~~~~VS~~TiR----RDl~~L~~ 40 (57)
T PF08220_consen 2 QQQILELLKE---KGKVSVKELAEEFGVSEMTIR----RDLNKLEK 40 (57)
T ss_pred HHHHHHHHHH---cCCEEHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence 4455555322 234899999999999999999 44555543
No 250
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=82.93 E-value=3.1 Score=36.31 Aligned_cols=43 Identities=21% Similarity=0.177 Sum_probs=36.1
Q ss_pred hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 007404 540 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSA 585 (605)
Q Consensus 540 ~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RA 585 (605)
..|++.-|..|..+...++ .++.++|+.||||+.|++++..|=
T Consensus 7 A~Lt~~gR~~lv~~vv~~g---~~~a~aA~~~gVS~~Ta~kW~~Ry 49 (85)
T PF13011_consen 7 ARLTPRGRLRLVRRVVEQG---WPVAHAAAEFGVSRRTAYKWLARY 49 (85)
T ss_pred CCCCHHHHHHHHHHHHHcC---CcHHHHHHHhCCCHHHHHHHHHHH
Confidence 3589999998888875543 899999999999999999877663
No 251
>TIGR02147 Fsuc_second hypothetical protein, TIGR02147. This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterized.
Probab=82.84 E-value=18 Score=38.06 Aligned_cols=100 Identities=20% Similarity=0.204 Sum_probs=51.9
Q ss_pred CCCCCHHHHHHhcC--CCHHHHHHHHhCCCCCCCccccccccCCCCC-CcccCCCCCCCHHH-HHHHHHHHHHHHHHHhc
Q 007404 466 GRHPNNEEVAEATG--LSMKRLHAVLLSPKAPRSLDQKIGINQNLKP-SEVIADPEAETAED-LLIKKFMKEDLEKVLDT 541 (605)
Q Consensus 466 gr~PT~eEIAe~lg--is~e~V~~~l~~~~~~~SLD~~i~~d~~~~l-~d~l~D~~~~spEe-~l~~~el~~~L~~aL~~ 541 (605)
+..+++++||+.++ ||.++|++.+......-=|. ..+ ++.-.. ...+.......+.. .-...++.+.-.++|+.
T Consensus 135 ~~~~~~~~ia~~l~p~is~~ev~~sL~~L~~~glik-k~~-~g~y~~t~~~l~~~~~~~~~avr~~h~q~l~lA~~al~~ 212 (271)
T TIGR02147 135 PFADDPEELAKRCFPKISAEQVKESLDLLERLGLIK-KNE-DGFYKQTDKAVSTGDEVIPLAVRQYQKQMIDLAKEALDA 212 (271)
T ss_pred CCCCCHHHHHHHhCCCCCHHHHHHHHHHHHHCCCee-ECC-CCcEEeecceeecCCccchHHHHHHHHHHHHHHHHHHHh
Confidence 44567889999998 99999999876322111111 001 110000 11122111111221 11223344455677888
Q ss_pred CCHHHHHHHHHHHhcCCCCCCCHHHHHHH
Q 007404 542 LNPRERQVVRWRFGLEDGRMKTLQEIGEL 570 (605)
Q Consensus 542 L~~rER~VL~LRyGl~dg~~~Tl~EIAe~ 570 (605)
.|+.+|.+=.+-++.+. ..+++|.+.
T Consensus 213 ~p~~eR~~S~lT~~i~~---~~~~~i~~~ 238 (271)
T TIGR02147 213 LPPSERDVSTVTFGISE---EAYKEIVKK 238 (271)
T ss_pred CCccccccceeeEecCH---HHHHHHHHH
Confidence 99999998777666552 455554443
No 252
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=82.80 E-value=2 Score=31.80 Aligned_cols=27 Identities=37% Similarity=0.639 Sum_probs=23.0
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 561 MKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 561 ~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
+.|..|||+.+|+|+.+|+ +.+++|.+
T Consensus 8 ~~s~~~la~~l~~s~~tv~----~~l~~L~~ 34 (48)
T smart00419 8 PLTRQEIAELLGLTRETVS----RTLKRLEK 34 (48)
T ss_pred ccCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 4899999999999999997 66677665
No 253
>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=82.77 E-value=4.8 Score=32.14 Aligned_cols=41 Identities=22% Similarity=0.399 Sum_probs=27.8
Q ss_pred HHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 544 PRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 544 ~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
|.-+.||.+-.. +.++|..|||+.+|++..+|+.+ +++|++
T Consensus 10 p~R~~Il~~L~~---~~~~t~~ela~~l~~~~~t~s~h----L~~L~~ 50 (61)
T PF12840_consen 10 PTRLRILRLLAS---NGPMTVSELAEELGISQSTVSYH----LKKLEE 50 (61)
T ss_dssp HHHHHHHHHHHH---CSTBEHHHHHHHHTS-HHHHHHH----HHHHHH
T ss_pred HHHHHHHHHHhc---CCCCCHHHHHHHHCCCHHHHHHH----HHHHHH
Confidence 555566665422 23599999999999999999944 445543
No 254
>PF12728 HTH_17: Helix-turn-helix domain
Probab=82.49 E-value=1.4 Score=33.77 Aligned_cols=23 Identities=30% Similarity=0.469 Sum_probs=20.9
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q 007404 562 KTLQEIGELMGVSRERIRQIESS 584 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~R 584 (605)
+|.+|+|+.||||+.+|+++..+
T Consensus 2 lt~~e~a~~l~is~~tv~~~~~~ 24 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWIRQ 24 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHc
Confidence 68999999999999999988754
No 255
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=82.44 E-value=4 Score=32.39 Aligned_cols=28 Identities=29% Similarity=0.515 Sum_probs=23.9
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 560 RMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 560 ~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
.++|..|||+.+|+|+.+|+ +.+++|++
T Consensus 24 ~~~s~~ela~~~g~s~~tv~----r~l~~L~~ 51 (67)
T cd00092 24 LPLTRQEIADYLGLTRETVS----RTLKELEE 51 (67)
T ss_pred CCcCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 45899999999999999998 66677765
No 256
>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=82.17 E-value=11 Score=38.55 Aligned_cols=35 Identities=23% Similarity=0.186 Sum_probs=27.3
Q ss_pred HHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHHH
Q 007404 325 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRR 359 (605)
Q Consensus 325 le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~~ 359 (605)
+.+...++...+|++||..+.|+..|++.+.+...
T Consensus 122 ~~~~~~~l~~~l~~~pt~~elA~~l~~~~e~v~~~ 156 (254)
T TIGR02850 122 ALQVRDKLISENSKEPTVSEIAKELKVPQEEVVFA 156 (254)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHH
Confidence 33445667777899999999999999998776543
No 257
>PHA02547 55 RNA polymerase sigma factor; Provisional
Probab=82.05 E-value=4.3 Score=39.75 Aligned_cols=64 Identities=14% Similarity=0.252 Sum_probs=45.6
Q ss_pred HHHHHHHHHHHHHhhCCCCC---HHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHh
Q 007404 372 TSNIRLVISIAKNYQGAGMN---LQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLS 435 (605)
Q Consensus 372 ~~nlrLVvsIAkrY~~~g~d---~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir 435 (605)
.+-+..+..+.++|.-++.. -+|+|.+|.-..++.+..|||++...+-.|++..+-++..+.|.
T Consensus 44 ~~imkIa~glS~r~nF~~Yt~~wKedMI~DgIe~~i~ylhNFD~~k~~Np~aYiT~~~~~AF~~RI~ 110 (179)
T PHA02547 44 LAIMKIAEGLSRRPNFSGYTQTWKEDMIADGIEACIKGLHNFDETKYKNPHAYITQACFNAFVQRIK 110 (179)
T ss_pred HHHHHHHhccccCCccccchHHHHHHHHHHHHHHHHHHhhcCCcccccChHHHHHHHHHHHHHHHHH
Confidence 34445555566665545555 48999999999999999999999877766666666555555443
No 258
>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial. Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.
Probab=81.98 E-value=1.6 Score=41.81 Aligned_cols=29 Identities=28% Similarity=0.346 Sum_probs=25.9
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 007404 560 RMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 592 (605)
Q Consensus 560 ~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 592 (605)
-++|.+|||..+|+|+++|. |++++|++.
T Consensus 142 ~~~t~~~iA~~lG~tretvs----R~l~~l~~~ 170 (193)
T TIGR03697 142 LRLSHQAIAEAIGSTRVTIT----RLLGDLRKK 170 (193)
T ss_pred CCCCHHHHHHHhCCcHHHHH----HHHHHHHHC
Confidence 36899999999999999999 888888874
No 259
>PRK05949 RNA polymerase sigma factor; Validated
Probab=81.88 E-value=14 Score=39.71 Aligned_cols=34 Identities=24% Similarity=0.330 Sum_probs=26.9
Q ss_pred HHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHH
Q 007404 325 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRR 358 (605)
Q Consensus 325 le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~ 358 (605)
+.+.+.++...+|++|+..+.|+..|++.+.+..
T Consensus 180 l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~ 213 (327)
T PRK05949 180 IKKTQRELSQKLGRSATPAEIAKELELEPSQIRE 213 (327)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHH
Confidence 4445566777789999999999999999876544
No 260
>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=81.82 E-value=1.4 Score=33.90 Aligned_cols=22 Identities=23% Similarity=0.483 Sum_probs=19.5
Q ss_pred CHHHHHHHHCCCHHHHHHHHHH
Q 007404 563 TLQEIGELMGVSRERIRQIESS 584 (605)
Q Consensus 563 Tl~EIAe~LGISrerVRqie~R 584 (605)
|++|||+..|+|..||+..++.
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 7899999999999999977653
No 261
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=81.65 E-value=2.2 Score=41.07 Aligned_cols=37 Identities=19% Similarity=0.235 Sum_probs=28.7
Q ss_pred CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHH
Q 007404 542 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQI 581 (605)
Q Consensus 542 L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqi 581 (605)
|++.++.||..- ..|| ..|+.|||+.+|+|+.+|+.+
T Consensus 12 lD~~D~~IL~~L--q~d~-R~s~~eiA~~lglS~~tv~~R 48 (164)
T PRK11169 12 LDRIDRNILNEL--QKDG-RISNVELSKRVGLSPTPCLER 48 (164)
T ss_pred HHHHHHHHHHHh--ccCC-CCCHHHHHHHHCcCHHHHHHH
Confidence 566778888753 2233 399999999999999999944
No 262
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=81.49 E-value=6.8 Score=43.01 Aligned_cols=37 Identities=32% Similarity=0.546 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHh
Q 007404 454 VKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLL 490 (605)
Q Consensus 454 i~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~ 490 (605)
+.+.+.+|..++|+.|+..+.|...|++...+...+.
T Consensus 96 ~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~l~~~~~ 132 (373)
T PRK07406 96 LEELREQFESELGREPSDKEWAELVDMPLPKFRRRLM 132 (373)
T ss_pred HHHHHHHHHHhcccccchhhHhhhccccHHHHHHHHh
Confidence 3455677888899999999999999998877665543
No 263
>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=81.46 E-value=4.8 Score=40.42 Aligned_cols=32 Identities=34% Similarity=0.460 Sum_probs=25.3
Q ss_pred hHHHHHHhhcCCCCchHHHHHhhcCCHHHHHH
Q 007404 327 GLREVLSERCGGSPTFAQWAAAAGVDQRELRR 358 (605)
Q Consensus 327 ~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~ 358 (605)
+....|...+|+.||..+.|+..|++.+.+..
T Consensus 101 ~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~ 132 (231)
T TIGR02885 101 YMKEELSKELGREPTINELAEALGVSPEEIVM 132 (231)
T ss_pred HHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHH
Confidence 34556667789999999999999999876543
No 264
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=81.39 E-value=21 Score=36.84 Aligned_cols=34 Identities=24% Similarity=0.371 Sum_probs=27.4
Q ss_pred HHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHH
Q 007404 324 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELR 357 (605)
Q Consensus 324 ~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~ 357 (605)
.+.+....|+..+|+.||..+.|...|++.+.+.
T Consensus 119 ~i~~~~~~l~~~~~~~pt~~eia~~lg~~~~~v~ 152 (268)
T PRK06288 119 QIERAIAMLEARLGRTPSDEEIADELGISLEEYN 152 (268)
T ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHH
Confidence 4555667778888999999999999999876554
No 265
>CHL00148 orf27 Ycf27; Reviewed
Probab=80.98 E-value=2.2 Score=41.55 Aligned_cols=50 Identities=14% Similarity=0.086 Sum_probs=42.4
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHH-------CCCHHHHHHHHHHHHHHHHh
Q 007404 541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELM-------GVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~L-------GISrerVRqie~RALkKLR~ 591 (605)
.|+++|.+|+.+.. .+.|+.+|.+||++.+ +++..+|+.+..+.++||..
T Consensus 161 ~Lt~~E~~il~~l~-~~~~~~~s~~~i~~~l~~~~~~~~~~~~tv~~~i~~lr~KL~~ 217 (240)
T CHL00148 161 RLTGMEFSLLELLI-SKSGEIFSRATILKEVWGYTPERHIDTRVVDVHISRLRAKLED 217 (240)
T ss_pred EcCHHHHHHHHHHH-HCCCEEEcHHHHHHHhcCCCcccCCCcccHHHHHHHHHHHhcc
Confidence 49999999998754 3345669999999999 48999999999999999974
No 266
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=80.94 E-value=4.2 Score=35.03 Aligned_cols=32 Identities=22% Similarity=0.451 Sum_probs=27.1
Q ss_pred cCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 556 LEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 556 l~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
+.++.+.|-++||+.||+|+.+|- +.+++||+
T Consensus 14 ~~~~~~~SGe~La~~LgiSRtaVw----K~Iq~Lr~ 45 (79)
T COG1654 14 LLTGNFVSGEKLAEELGISRTAVW----KHIQQLRE 45 (79)
T ss_pred HcCCCcccHHHHHHHHCccHHHHH----HHHHHHHH
Confidence 345677999999999999999998 77788886
No 267
>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=80.93 E-value=3 Score=35.14 Aligned_cols=52 Identities=19% Similarity=0.357 Sum_probs=34.4
Q ss_pred HHHHHHHHHhcCCHHHHHHHHHHHhcC-CCCCCCHHHHHHHHCCCHHHHHHHH
Q 007404 531 MKEDLEKVLDTLNPRERQVVRWRFGLE-DGRMKTLQEIGELMGVSRERIRQIE 582 (605)
Q Consensus 531 l~~~L~~aL~~L~~rER~VL~LRyGl~-dg~~~Tl~EIAe~LGISrerVRqie 582 (605)
+...|......|++.|+.|...-.-.- +-..+|..|||+..|+|..+|-...
T Consensus 3 l~~~i~~~~~~ls~~e~~Ia~yil~~~~~~~~~si~elA~~~~vS~sti~Rf~ 55 (77)
T PF01418_consen 3 LLEKIRSQYNSLSPTEKKIADYILENPDEIAFMSISELAEKAGVSPSTIVRFC 55 (77)
T ss_dssp HHHHHHHHGGGS-HHHHHHHHHHHH-HHHHCT--HHHHHHHCTS-HHHHHHHH
T ss_pred HHHHHHHHHhhCCHHHHHHHHHHHhCHHHHHHccHHHHHHHcCCCHHHHHHHH
Confidence 345677778899999999876432211 1134999999999999999998443
No 268
>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=80.82 E-value=5.1 Score=35.14 Aligned_cols=44 Identities=30% Similarity=0.445 Sum_probs=29.9
Q ss_pred cCCHHHHHHHHHHHhc-----CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 007404 541 TLNPRERQVVRWRFGL-----EDGRMKTLQEIGELMGVSRERIRQIESSAFR 587 (605)
Q Consensus 541 ~L~~rER~VL~LRyGl-----~dg~~~Tl~EIAe~LGISrerVRqie~RALk 587 (605)
-|+|.|+.-|..|+-. .+| +|+.||++.+|+|..||. +.+|+|+
T Consensus 26 L~T~~E~~~l~~R~~va~~lL~~g--~syreIa~~tgvS~aTIt-Rvsr~Lk 74 (87)
T PF01371_consen 26 LCTPDELEALAQRWQVAKELLDEG--KSYREIAEETGVSIATIT-RVSRCLK 74 (87)
T ss_dssp HSSHHHHHHHHHHHHHHHHHHHTT--SSHHHHHHHHTSTHHHHH-HHHHHHH
T ss_pred hCCHHHHHHHHHHHHHHHHHHHCC--CCHHHHHHHhCCCHHHHH-HHHHHHH
Confidence 3677777655554422 233 999999999999999997 2334443
No 269
>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=80.53 E-value=3.9 Score=31.89 Aligned_cols=51 Identities=14% Similarity=0.188 Sum_probs=40.9
Q ss_pred cCCHHHHHHHHHHHhcCCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 541 TLNPRERQVVRWRFGLEDG-RMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 541 ~L~~rER~VL~LRyGl~dg-~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
.+++.+..+|.-.|..+.. .....++||..+||+...|.....+-..+.|+
T Consensus 6 ~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 6 RFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence 4788889999999887532 12467899999999999999999887777663
No 270
>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=80.46 E-value=1.9 Score=31.84 Aligned_cols=24 Identities=25% Similarity=0.479 Sum_probs=21.5
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHH
Q 007404 562 KTLQEIGELMGVSRERIRQIESSA 585 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~RA 585 (605)
+|.+|+|+.||||+.+|+++....
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~~g 25 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIHEG 25 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHcC
Confidence 689999999999999999887654
No 271
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=80.29 E-value=5.1 Score=29.93 Aligned_cols=27 Identities=37% Similarity=0.631 Sum_probs=22.0
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 561 MKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 561 ~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
+.|..+|++.+|+|+.+|++ .++.|.+
T Consensus 14 ~~s~~~l~~~l~~s~~tv~~----~l~~L~~ 40 (53)
T smart00420 14 KVSVEELAELLGVSEMTIRR----DLNKLEE 40 (53)
T ss_pred CcCHHHHHHHHCCCHHHHHH----HHHHHHH
Confidence 48999999999999999984 4455543
No 272
>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=80.26 E-value=3.1 Score=31.02 Aligned_cols=36 Identities=19% Similarity=0.294 Sum_probs=24.5
Q ss_pred HHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 007404 544 PRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIE 582 (605)
Q Consensus 544 ~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie 582 (605)
+-|+.+|.-..-..+ -...+.|+.||||+.+++..+
T Consensus 4 ~~E~~~i~~aL~~~~---gn~~~aA~~Lgisr~tL~~kl 39 (42)
T PF02954_consen 4 EFEKQLIRQALERCG---GNVSKAARLLGISRRTLYRKL 39 (42)
T ss_dssp HHHHHHHHHHHHHTT---T-HHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHHHHHHhC---CCHHHHHHHHCCCHHHHHHHH
Confidence 446666665554444 378999999999999998443
No 273
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=80.18 E-value=3.6 Score=32.26 Aligned_cols=26 Identities=38% Similarity=0.640 Sum_probs=22.6
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 562 KTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
.|..+||+.+|+|+++|+ +++++|.+
T Consensus 26 ~~~~~la~~~~is~~~v~----~~l~~L~~ 51 (66)
T cd07377 26 PSERELAEELGVSRTTVR----EALRELEA 51 (66)
T ss_pred CCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 469999999999999999 77777765
No 274
>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=80.16 E-value=3.8 Score=33.76 Aligned_cols=39 Identities=33% Similarity=0.393 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHHHcCCCCCHHHHHHhcCCC-HHHHHHHHh
Q 007404 452 YRVKEARKQLYSENGRHPNNEEVAEATGLS-MKRLHAVLL 490 (605)
Q Consensus 452 ~ki~ka~~~L~~elgr~PT~eEIAe~lgis-~e~V~~~l~ 490 (605)
.++-.....+..++|..||..|||+.+|++ ...|...+.
T Consensus 9 ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~ 48 (65)
T PF01726_consen 9 KEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLK 48 (65)
T ss_dssp HHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHH
T ss_pred HHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHH
Confidence 344555566778899999999999999997 888877764
No 275
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=80.01 E-value=20 Score=28.86 Aligned_cols=23 Identities=30% Similarity=0.408 Sum_probs=19.6
Q ss_pred CCCHHHHHHhcCCCHHHHHHHHh
Q 007404 468 HPNNEEVAEATGLSMKRLHAVLL 490 (605)
Q Consensus 468 ~PT~eEIAe~lgis~e~V~~~l~ 490 (605)
+++.++||+.+|++...+..+..
T Consensus 1 ~~~~~~la~~~~~s~~~l~~~f~ 23 (84)
T smart00342 1 PLTLEDLAEALGMSPRHLQRLFK 23 (84)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHH
Confidence 36889999999999999888765
No 276
>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=79.82 E-value=2.2 Score=31.37 Aligned_cols=25 Identities=32% Similarity=0.380 Sum_probs=22.1
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 007404 562 KTLQEIGELMGVSRERIRQIESSAF 586 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~RAL 586 (605)
+|..|+|+.||||+.+|+.......
T Consensus 1 ~s~~e~a~~lgvs~~tl~~~~~~g~ 25 (49)
T cd04762 1 LTTKEAAELLGVSPSTLRRWVKEGK 25 (49)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCC
Confidence 5889999999999999999887653
No 277
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=79.67 E-value=3.6 Score=39.08 Aligned_cols=34 Identities=21% Similarity=0.104 Sum_probs=27.1
Q ss_pred HHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 007404 549 VVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAF 586 (605)
Q Consensus 549 VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RAL 586 (605)
++...++.| +|..|||++||||..||...+.+--
T Consensus 13 ~~~~~~~~G----~S~re~Ak~~gvs~sTvy~wv~r~~ 46 (138)
T COG3415 13 VVDAVVGEG----LSCREAAKRFGVSISTVYRWVRRYR 46 (138)
T ss_pred HHHHHHHcC----ccHHHHHHHhCccHHHHHHHHHHhc
Confidence 444455555 9999999999999999998877643
No 278
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=79.25 E-value=19 Score=36.83 Aligned_cols=35 Identities=26% Similarity=0.242 Sum_probs=27.3
Q ss_pred HHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHHH
Q 007404 325 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRR 359 (605)
Q Consensus 325 le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~~ 359 (605)
+.+....+...+|+.|+..++|...|++.+.+...
T Consensus 111 ~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~ 145 (251)
T PRK07670 111 VEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEAT 145 (251)
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHH
Confidence 34455667777899999999999999998766543
No 279
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=78.53 E-value=2.9 Score=33.67 Aligned_cols=29 Identities=38% Similarity=0.599 Sum_probs=23.0
Q ss_pred CCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 559 GRMK-TLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 559 g~~~-Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
|..+ |..+||+.||+|+.+|| +|+..|..
T Consensus 21 g~~lps~~~la~~~~vsr~tvr----~al~~L~~ 50 (64)
T PF00392_consen 21 GDRLPSERELAERYGVSRTTVR----EALRRLEA 50 (64)
T ss_dssp TSBE--HHHHHHHHTS-HHHHH----HHHHHHHH
T ss_pred CCEeCCHHHHHHHhccCCcHHH----HHHHHHHH
Confidence 4457 99999999999999999 78887765
No 280
>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=78.41 E-value=13 Score=33.83 Aligned_cols=27 Identities=37% Similarity=0.522 Sum_probs=22.8
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 007404 562 KTLQEIGELMGVSRERIRQIESSAFRKLKNK 592 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 592 (605)
.|+.|||+.||||..+|. ++|++|.-.
T Consensus 72 ~tl~Ela~~l~Vs~~ti~----~~Lkrlg~t 98 (119)
T PF01710_consen 72 ATLRELAERLGVSPSTIW----RALKRLGIT 98 (119)
T ss_pred cCHHHHHHHcCCCHHHHH----HHHHHcCch
Confidence 899999999999999998 667666543
No 281
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=77.88 E-value=34 Score=36.47 Aligned_cols=84 Identities=17% Similarity=0.121 Sum_probs=49.8
Q ss_pred HHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccH
Q 007404 368 DKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHM 447 (605)
Q Consensus 368 e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~ 447 (605)
++-+...+..+-.++.... + -+-+.|.-..+++.+.....-+|.+...++.-.|--+++ .+
T Consensus 119 er~l~~a~~~I~~~~~~L~---L--p~~v~e~A~~iyk~~~~~~~~rgrs~~~i~AAclYiACR----~~---------- 179 (310)
T PRK00423 119 ERNLAFALSELDRIASQLG---L--PRSVREEAAVIYRKAVEKGLIRGRSIEGVVAAALYAACR----RC---------- 179 (310)
T ss_pred hHHHHHHHHHHHHHHHHcC---C--CHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHH----Hc----------
Confidence 3344445566666666653 2 256777777777777666667887665555444444332 22
Q ss_pred HHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHH
Q 007404 448 VEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAV 488 (605)
Q Consensus 448 ~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~ 488 (605)
+-+-|..||+..++++..++...
T Consensus 180 ------------------~~prtl~eI~~~~~v~~k~i~~~ 202 (310)
T PRK00423 180 ------------------KVPRTLDEIAEVSRVSRKEIGRC 202 (310)
T ss_pred ------------------CCCcCHHHHHHHhCCCHHHHHHH
Confidence 22335667777777777766544
No 282
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=77.87 E-value=2.5 Score=40.92 Aligned_cols=28 Identities=21% Similarity=0.325 Sum_probs=25.1
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 560 RMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 560 ~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
-+.|.++||..+|+|+++|. |.|++|++
T Consensus 148 ~~~t~~~iA~~lG~tretvs----R~l~~l~~ 175 (202)
T PRK13918 148 IYATHDELAAAVGSVRETVT----KVIGELSR 175 (202)
T ss_pred ecCCHHHHHHHhCccHHHHH----HHHHHHHH
Confidence 35899999999999999999 88888886
No 283
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=77.77 E-value=5 Score=34.08 Aligned_cols=31 Identities=35% Similarity=0.591 Sum_probs=22.9
Q ss_pred CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 557 EDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 557 ~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
+++.+.|.+|||+.+|+|+..|++ .+++|++
T Consensus 21 ~~~~~~s~~eiA~~~~i~~~~l~k----il~~L~~ 51 (83)
T PF02082_consen 21 PDGKPVSSKEIAERLGISPSYLRK----ILQKLKK 51 (83)
T ss_dssp TTSC-BEHHHHHHHHTS-HHHHHH----HHHHHHH
T ss_pred CCCCCCCHHHHHHHHCcCHHHHHH----HHHHHhh
Confidence 344569999999999999999994 4556654
No 284
>PRK11564 stationary phase inducible protein CsiE; Provisional
Probab=77.75 E-value=5.9 Score=43.66 Aligned_cols=51 Identities=22% Similarity=0.268 Sum_probs=39.5
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
.+++.||..+.+.+.+....+.|+.++|+.|+||+.|+.+-+.+.-+.|.+
T Consensus 10 ~~s~~ER~~~il~~LL~~~~~v~l~~Lae~l~VSrsTi~~DLk~l~~~L~~ 60 (426)
T PRK11564 10 VLSAPQRRCQILLMLFQPGLTVTLETFSQLNGVDDDTARQDIAETGREIQR 60 (426)
T ss_pred CCCHHHHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 477888887777766666778999999999999999999655544444443
No 285
>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=77.66 E-value=5.1 Score=39.15 Aligned_cols=42 Identities=21% Similarity=0.272 Sum_probs=34.7
Q ss_pred CHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 007404 543 NPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFR 587 (605)
Q Consensus 543 ~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALk 587 (605)
|+.-|.-++..|..++ +|++.+|..+|||..|+|.+..+|..
T Consensus 4 ~~e~R~~~R~~YV~~~---~sLe~aA~~~gVs~~TarrWK~~Ak~ 45 (165)
T PF08822_consen 4 PQETRDAVRRAYVFDR---LSLEQAAAKCGVSYATARRWKREAKA 45 (165)
T ss_pred cHHHHHHHHHHHHhCC---CCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4455667777777554 99999999999999999999998864
No 286
>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=77.55 E-value=26 Score=36.94 Aligned_cols=34 Identities=24% Similarity=0.437 Sum_probs=26.9
Q ss_pred HHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHH
Q 007404 325 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRR 358 (605)
Q Consensus 325 le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~ 358 (605)
+.+.+..+...+|+.|+..+.|...|++.+.+..
T Consensus 163 ~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~ 196 (298)
T TIGR02997 163 IKKVQRELSQKLGRTPSEAEIAEALELEPEQVRE 196 (298)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence 4445566777789999999999999999876654
No 287
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=77.47 E-value=4.2 Score=32.59 Aligned_cols=41 Identities=17% Similarity=0.353 Sum_probs=29.0
Q ss_pred HHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 007404 545 RERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 592 (605)
Q Consensus 545 rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 592 (605)
|+-.+|.+-+. + ..+|+.|||+.+|+|..+|++ -+..|+..
T Consensus 6 rq~~Ll~~L~~-~--~~~~~~ela~~l~~S~rti~~----~i~~L~~~ 46 (59)
T PF08280_consen 6 RQLKLLELLLK-N--KWITLKELAKKLNISERTIKN----DINELNEF 46 (59)
T ss_dssp HHHHHHHHHHH-H--TSBBHHHHHHHCTS-HHHHHH----HHHHHHTT
T ss_pred HHHHHHHHHHc-C--CCCcHHHHHHHHCCCHHHHHH----HHHHHHHH
Confidence 45567776665 2 349999999999999999994 44555543
No 288
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=77.41 E-value=6 Score=30.22 Aligned_cols=24 Identities=21% Similarity=0.452 Sum_probs=21.6
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHH
Q 007404 562 KTLQEIGELMGVSRERIRQIESSA 585 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~RA 585 (605)
.|+++||+.+|||..+|+.+..+.
T Consensus 28 ~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 28 RSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHhh
Confidence 599999999999999999887653
No 289
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=77.03 E-value=2.7 Score=41.27 Aligned_cols=29 Identities=31% Similarity=0.565 Sum_probs=25.4
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 559 GRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 559 g~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
.+|+|+.||++.+|+|+++|+ -++++|..
T Consensus 39 ~~Pmtl~Ei~E~lg~Sks~vS----~~lkkL~~ 67 (177)
T COG1510 39 RKPLTLDEIAEALGMSKSNVS----MGLKKLQD 67 (177)
T ss_pred CCCccHHHHHHHHCCCcchHH----HHHHHHHh
Confidence 478999999999999999999 67777765
No 290
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=76.46 E-value=2 Score=32.16 Aligned_cols=25 Identities=32% Similarity=0.457 Sum_probs=22.4
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 007404 562 KTLQEIGELMGVSRERIRQIESSAF 586 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~RAL 586 (605)
+|..|+|+.+|||..+|+..+.+.+
T Consensus 1 ~~~~e~a~~~gv~~~tlr~~~~~g~ 25 (49)
T cd04761 1 YTIGELAKLTGVSPSTLRYYERIGL 25 (49)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999999987765
No 291
>PHA00542 putative Cro-like protein
Probab=76.35 E-value=2.5 Score=36.21 Aligned_cols=24 Identities=25% Similarity=0.256 Sum_probs=22.2
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHH
Q 007404 562 KTLQEIGELMGVSRERIRQIESSA 585 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~RA 585 (605)
+|..|+|+.+|||+.+|.+++...
T Consensus 32 lTq~elA~~lgIs~~tIsr~e~g~ 55 (82)
T PHA00542 32 WSQEQIADATDVSQPTICRIYSGR 55 (82)
T ss_pred CCHHHHHHHHCcCHHHHHHHHcCC
Confidence 999999999999999999998654
No 292
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=76.17 E-value=19 Score=38.47 Aligned_cols=34 Identities=21% Similarity=0.375 Sum_probs=27.0
Q ss_pred HHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHH
Q 007404 324 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELR 357 (605)
Q Consensus 324 ~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~ 357 (605)
++.+.+..+...+|+.||..+.|.+.|++.+.+.
T Consensus 169 ~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~ 202 (317)
T PRK07405 169 KIKKAQRQLSQQLGRAATIGELAEELELTPKQVR 202 (317)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHH
Confidence 3455666777788999999999999999876554
No 293
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=76.14 E-value=5.2 Score=33.95 Aligned_cols=44 Identities=20% Similarity=0.258 Sum_probs=28.4
Q ss_pred HHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH-----HHHHHHHhHHhhh
Q 007404 549 VVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES-----SAFRKLKNKKRTK 596 (605)
Q Consensus 549 VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~-----RALkKLR~~l~~~ 596 (605)
|..++--.+ +|..|+|+.+|+|+.+|.++++ -.+.+|.+.+..-
T Consensus 23 i~~~~~~~~----ltQ~e~A~~lgisq~~vS~l~~g~~~~~sl~~L~~~l~aL 71 (80)
T PF13744_consen 23 IRELREERG----LTQAELAERLGISQPRVSRLENGKIDDFSLDTLLRYLEAL 71 (80)
T ss_dssp HHHHHHCCT------HHHHHHHHTS-HHHHHHHHTT-GCC--HHHHHHHHHHT
T ss_pred HHHHHHHcC----CCHHHHHHHHCCChhHHHHHHcCcccCCCHHHHHHHHHHc
Confidence 444444444 9999999999999999999884 2466666655543
No 294
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=75.97 E-value=6.6 Score=33.22 Aligned_cols=24 Identities=25% Similarity=0.367 Sum_probs=20.7
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
Q 007404 560 RMKTLQEIGELMGVSRERIRQIES 583 (605)
Q Consensus 560 ~~~Tl~EIAe~LGISrerVRqie~ 583 (605)
.+.|..|||+.+|+++.+|+.++.
T Consensus 19 ~~~t~~~ia~~l~i~~~tv~r~l~ 42 (91)
T smart00346 19 GGLTLAELAERLGLSKSTAHRLLN 42 (91)
T ss_pred CCcCHHHHHHHhCCCHHHHHHHHH
Confidence 469999999999999999995443
No 295
>TIGR00122 birA_repr_reg BirA biotin operon repressor domain. This model may recognize some other putative repressor proteins, such as DnrO of Streptomyces peucetius with scores below the noise cutoff but with significance shown by low E-value.
Probab=75.70 E-value=7.1 Score=31.86 Aligned_cols=27 Identities=22% Similarity=0.448 Sum_probs=22.1
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 561 MKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 561 ~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
+.+..|||+.+|+|+.+|+ +.+++|+.
T Consensus 13 ~~~~~eLa~~l~vS~~tv~----~~l~~L~~ 39 (69)
T TIGR00122 13 PFSGEKLGEALGMSRTAVN----KHIQTLRE 39 (69)
T ss_pred CcCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 3789999999999999999 55555654
No 296
>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=75.46 E-value=31 Score=34.43 Aligned_cols=35 Identities=37% Similarity=0.468 Sum_probs=27.8
Q ss_pred HHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHH
Q 007404 324 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRR 358 (605)
Q Consensus 324 ~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~ 358 (605)
++.+...+|...+|++|+..+.|+..|++.+.+..
T Consensus 84 ~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~ 118 (224)
T TIGR02479 84 KLERAIRELEARLGREPTEEEIAEELGMDLKEYRQ 118 (224)
T ss_pred HHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHH
Confidence 45556677777889999999999999998766544
No 297
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=75.21 E-value=8.2 Score=32.60 Aligned_cols=44 Identities=20% Similarity=0.354 Sum_probs=34.4
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
.|+..+..||.+-+..+ ++|..+|++.+++|+.+|. +++++|.+
T Consensus 7 ~l~~~~~~il~~l~~~~---~~~~~~la~~~~~s~~~i~----~~l~~L~~ 50 (101)
T smart00347 7 GLTPTQFLVLRILYEEG---PLSVSELAKRLGVSPSTVT----RVLDRLEK 50 (101)
T ss_pred CCCHHHHHHHHHHHHcC---CcCHHHHHHHHCCCchhHH----HHHHHHHH
Confidence 46777888887766533 4899999999999999988 66666655
No 298
>PHA01976 helix-turn-helix protein
Probab=75.01 E-value=5.5 Score=31.97 Aligned_cols=32 Identities=19% Similarity=0.236 Sum_probs=25.9
Q ss_pred HHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 007404 549 VVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS 584 (605)
Q Consensus 549 VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~R 584 (605)
+-.+|-..+ +|.+|+|+.+|+|+.+|.++++.
T Consensus 7 l~~~R~~~g----lt~~~lA~~~gvs~~~v~~~e~g 38 (67)
T PHA01976 7 LIKARNARA----WSAPELSRRAGVRHSLIYDFEAD 38 (67)
T ss_pred HHHHHHHcC----CCHHHHHHHhCCCHHHHHHHHcC
Confidence 344454455 99999999999999999999864
No 299
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=74.71 E-value=15 Score=35.67 Aligned_cols=28 Identities=36% Similarity=0.573 Sum_probs=24.8
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 007404 561 MKTLQEIGELMGVSRERIRQIESSAFRKLKNK 592 (605)
Q Consensus 561 ~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 592 (605)
+.|.++||..+|+|+++|. |++++|++.
T Consensus 168 ~~t~~~lA~~lG~tr~tvs----R~l~~l~~~ 195 (211)
T PRK11753 168 KITRQEIGRIVGCSREMVG----RVLKMLEDQ 195 (211)
T ss_pred CCCHHHHHHHhCCCHHHHH----HHHHHHHHC
Confidence 6899999999999999999 778888763
No 300
>PRK10072 putative transcriptional regulator; Provisional
Probab=74.69 E-value=4.8 Score=35.83 Aligned_cols=32 Identities=22% Similarity=0.372 Sum_probs=27.9
Q ss_pred HHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 007404 549 VVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS 584 (605)
Q Consensus 549 VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~R 584 (605)
|-.+|...+ +|..|+|+.+|||..+|+++++.
T Consensus 38 ik~LR~~~g----lTQ~elA~~lGvS~~TVs~WE~G 69 (96)
T PRK10072 38 FEQLRKGTG----LKIDDFARVLGVSVAMVKEWESR 69 (96)
T ss_pred HHHHHHHcC----CCHHHHHHHhCCCHHHHHHHHcC
Confidence 556677777 99999999999999999999863
No 301
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=74.55 E-value=20 Score=37.82 Aligned_cols=24 Identities=21% Similarity=0.303 Sum_probs=21.1
Q ss_pred CCCCHHHHHHhcCCCHHHHHHHHh
Q 007404 467 RHPNNEEVAEATGLSMKRLHAVLL 490 (605)
Q Consensus 467 r~PT~eEIAe~lgis~e~V~~~l~ 490 (605)
..-|..|||+.+|+|.++|..++.
T Consensus 244 ~~~t~~EIa~~lgvs~~~V~q~~~ 267 (289)
T PRK07500 244 DGATLEALGEELGISKERVRQIEA 267 (289)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
Confidence 566999999999999999988764
No 302
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=74.11 E-value=10 Score=29.83 Aligned_cols=26 Identities=27% Similarity=0.533 Sum_probs=21.6
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 562 KTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
.+..||++.+|+++.+|+ ++++.|..
T Consensus 21 ~~~~ei~~~~~i~~~~i~----~~l~~L~~ 46 (78)
T cd00090 21 LTVSELAERLGLSQSTVS----RHLKKLEE 46 (78)
T ss_pred cCHHHHHHHHCcCHhHHH----HHHHHHHH
Confidence 899999999999999998 55555543
No 303
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=73.96 E-value=3.6 Score=41.00 Aligned_cols=27 Identities=22% Similarity=0.445 Sum_probs=24.1
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 561 MKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 561 ~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
++|.++||..+|+|+++|. |.+++|++
T Consensus 184 ~lt~~~iA~~lG~sr~tvs----R~l~~l~~ 210 (235)
T PRK11161 184 TMTRGDIGNYLGLTVETIS----RLLGRFQK 210 (235)
T ss_pred cccHHHHHHHhCCcHHHHH----HHHHHHHH
Confidence 5899999999999999999 77778776
No 304
>PRK06030 hypothetical protein; Provisional
Probab=73.81 E-value=10 Score=35.38 Aligned_cols=49 Identities=10% Similarity=0.120 Sum_probs=33.0
Q ss_pred HHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhhHhh
Q 007404 544 PRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQ 600 (605)
Q Consensus 544 ~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~ 600 (605)
+|+--+...+-..+ +|+.+||+.||.+..||-.-.. ++++.+.+..++.
T Consensus 56 aRqIAMYL~r~~~~----~sl~~IG~~FGRDHSTV~haik----kIe~~~~d~~lk~ 104 (124)
T PRK06030 56 IRQIAMYVAHVSLG----WPMNEVALAFGRDRTTVGHACH----TVEDLRDDAAFDA 104 (124)
T ss_pred HHHHHHHHHHHHcC----CCHHHHHHHHCCChhHHHHHHH----HHHHHhhCHHHHH
Confidence 45545555555555 9999999999999999995544 4444444444443
No 305
>TIGR02612 mob_myst_A mobile mystery protein A. Members of this protein family are found in mobization-related contexts more often than not, including within a CRISPR-associated gene region in Geobacter sulfurreducens PCA, and on plasmids in Agrobacterium tumefaciens and Coxiella burnetii, always together with mobile mystery protein B, a member of the Fic protein family (pfam02661). This protein is encoded by the upstream member of the gene pair and belongs to a family of helix-turn-helix DNA binding proteins (pfam01381).
Probab=73.46 E-value=8.1 Score=37.16 Aligned_cols=48 Identities=23% Similarity=0.387 Sum_probs=36.4
Q ss_pred CHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH------HHHHHHhHHh
Q 007404 543 NPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS------AFRKLKNKKR 594 (605)
Q Consensus 543 ~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~R------ALkKLR~~l~ 594 (605)
+|..-.|=.+|-..| +|..|+|+.+|||+.+|.++++. .+..|.+...
T Consensus 24 ~p~~~~Ir~~R~~lG----mTq~eLAerlGVS~~tIs~iE~G~~~~~psl~~L~kIA~ 77 (150)
T TIGR02612 24 TPKEGWVRAIRKALG----MSGAQLAGRLGVTPQRVEALEKSELSGTVTLKTLRAAAE 77 (150)
T ss_pred cCcHHHHHHHHHHcC----CCHHHHHHHhCCCHHHHHHHHcCCCCCCCCHHHHHHHHH
Confidence 444445666777777 99999999999999999999985 3445555443
No 306
>PRK09954 putative kinase; Provisional
Probab=73.09 E-value=6.1 Score=42.43 Aligned_cols=42 Identities=19% Similarity=0.352 Sum_probs=33.0
Q ss_pred CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 007404 542 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAF 586 (605)
Q Consensus 542 L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RAL 586 (605)
|+++++.||.+.. .+ ...|..|||+.||||+.+|+.++.+=.
T Consensus 1 ~~~~~~~il~~l~--~~-~~~s~~~la~~l~~s~~~v~~~i~~L~ 42 (362)
T PRK09954 1 MNNREKEILAILR--RN-PLIQQNEIADILQISRSRVAAHIMDLM 42 (362)
T ss_pred CChHHHHHHHHHH--HC-CCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4667777876654 22 369999999999999999999988643
No 307
>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR. This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.
Probab=72.82 E-value=18 Score=32.47 Aligned_cols=44 Identities=9% Similarity=0.179 Sum_probs=33.9
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
.|++.+..||..-+.. .+.|..|||+.+|+++.+|. +.+++|-+
T Consensus 25 ~lt~~q~~iL~~l~~~---~~~t~~ela~~~~~~~~tvs----~~l~~Le~ 68 (118)
T TIGR02337 25 GLTEQQWRILRILAEQ---GSMEFTQLANQACILRPSLT----GILARLER 68 (118)
T ss_pred CCCHHHHHHHHHHHHc---CCcCHHHHHHHhCCCchhHH----HHHHHHHH
Confidence 6899998888765432 24899999999999999998 55555543
No 308
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=72.34 E-value=5.4 Score=31.98 Aligned_cols=23 Identities=22% Similarity=0.462 Sum_probs=19.7
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q 007404 562 KTLQEIGELMGVSRERIRQIESS 584 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~R 584 (605)
+|..++|+.+|+|..+|+++++-
T Consensus 15 ls~~~lA~~~g~s~s~v~~iE~G 37 (64)
T PF13560_consen 15 LSQAQLADRLGVSQSTVSRIERG 37 (64)
T ss_dssp S-HHHHHHHHTS-HHHHHHHHTT
T ss_pred CCHHHHHHHHCcCHHHHHHHHCC
Confidence 99999999999999999999864
No 309
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=72.16 E-value=6.8 Score=38.68 Aligned_cols=33 Identities=21% Similarity=0.319 Sum_probs=25.5
Q ss_pred HHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 007404 546 ERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES 583 (605)
Q Consensus 546 ER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~ 583 (605)
++.|..++ ..+ +|+.+||+.||||+.||.++..
T Consensus 162 ~~~i~~~~-~~g----~s~~~iak~lgis~~Tv~r~~k 194 (200)
T PRK13413 162 EEKIKKLL-DKG----TSKSEIARKLGVSRTTLARFLK 194 (200)
T ss_pred HHHHHHHH-HCC----CCHHHHHHHHCCCHHHHHHHHH
Confidence 34566553 333 8999999999999999997765
No 310
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=72.05 E-value=7.2 Score=29.75 Aligned_cols=23 Identities=30% Similarity=0.488 Sum_probs=21.6
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q 007404 562 KTLQEIGELMGVSRERIRQIESS 584 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~R 584 (605)
+|..++|+.+|+|+.+|+.+++.
T Consensus 16 ltq~~lA~~~gvs~~~vs~~e~g 38 (58)
T TIGR03070 16 LTQADLADLAGVGLRFIRDVENG 38 (58)
T ss_pred CCHHHHHHHhCCCHHHHHHHHCC
Confidence 99999999999999999999864
No 311
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=71.88 E-value=2.1 Score=34.64 Aligned_cols=25 Identities=32% Similarity=0.566 Sum_probs=22.4
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 007404 562 KTLQEIGELMGVSRERIRQIESSAF 586 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~RAL 586 (605)
||..|+|+.+|||..+||..+.+.+
T Consensus 1 yti~eva~~~gvs~~tlr~y~~~gl 25 (69)
T PF13411_consen 1 YTIKEVAKLLGVSPSTLRYYEREGL 25 (69)
T ss_dssp EEHHHHHHHTTTTHHHHHHHHHTTS
T ss_pred CcHHHHHHHHCcCHHHHHHHHHhcC
Confidence 5789999999999999999987665
No 312
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=71.70 E-value=5.6 Score=30.56 Aligned_cols=23 Identities=35% Similarity=0.599 Sum_probs=19.8
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q 007404 562 KTLQEIGELMGVSRERIRQIESS 584 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~R 584 (605)
+|.+|+|+.+|+|+.+|..+++.
T Consensus 10 ls~~~la~~~gis~~~i~~~~~g 32 (55)
T PF01381_consen 10 LSQKELAEKLGISRSTISRIENG 32 (55)
T ss_dssp S-HHHHHHHHTS-HHHHHHHHTT
T ss_pred CCHHHHHHHhCCCcchhHHHhcC
Confidence 99999999999999999998876
No 313
>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID. Members of this protein are the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if and only if the species is capable of endospore formation as occurs in the model species Bacillus subtilis. SpoIIID is a DNA binding protein that, in B. subtilis, downregulates many genes but also turns on ten genes.
Probab=71.64 E-value=7 Score=33.75 Aligned_cols=35 Identities=20% Similarity=0.379 Sum_probs=25.5
Q ss_pred HHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 007404 545 RERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES 583 (605)
Q Consensus 545 rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~ 583 (605)
|..+|+.+- .. ...|+++||+.+|||+.||+..+.
T Consensus 7 R~~~I~e~l--~~--~~~ti~dvA~~~gvS~~TVsr~L~ 41 (80)
T TIGR02844 7 RVLEIGKYI--VE--TKATVRETAKVFGVSKSTVHKDVT 41 (80)
T ss_pred HHHHHHHHH--HH--CCCCHHHHHHHhCCCHHHHHHHhc
Confidence 444555443 22 237999999999999999997554
No 314
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=71.57 E-value=6.4 Score=33.02 Aligned_cols=32 Identities=38% Similarity=0.487 Sum_probs=26.2
Q ss_pred HHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 007404 549 VVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS 584 (605)
Q Consensus 549 VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~R 584 (605)
+-.+|-..+ +|.+|.|+.+|||+.||-.+++.
T Consensus 6 ~k~~R~~~~----ltQ~elA~~vgVsRQTi~~iEkg 37 (68)
T COG1476 6 LKELRAELG----LTQEELAKLVGVSRQTIIAIEKG 37 (68)
T ss_pred HHHHHHHhC----cCHHHHHHHcCcCHHHHHHHHcC
Confidence 444555555 99999999999999999998864
No 315
>PF05043 Mga: Mga helix-turn-helix domain; InterPro: IPR007737 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions []. The family also contains VirR like proteins which match only at the C terminus of the alignment.; PDB: 3SQN_A.
Probab=71.32 E-value=3.1 Score=35.42 Aligned_cols=35 Identities=20% Similarity=0.308 Sum_probs=24.0
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhhH
Q 007404 560 RMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHL 598 (605)
Q Consensus 560 ~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L 598 (605)
++.|+.++|+.++||+.++. +-+++|++.+...++
T Consensus 29 ~~~s~~~la~~~~iS~sti~----~~i~~l~~~l~~~~l 63 (87)
T PF05043_consen 29 EYVSIEDLAEELFISRSTIY----RDIKKLNKYLKKYGL 63 (87)
T ss_dssp SEEEHHHHHHHHT--HHHHH----HHHHHHHHHHHCCT-
T ss_pred CCcCHHHHHHHHCCCHHHHH----HHHHHHHHHHHHcCe
Confidence 34899999999999999999 555556655554433
No 316
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=71.04 E-value=9.3 Score=38.14 Aligned_cols=47 Identities=13% Similarity=0.096 Sum_probs=33.5
Q ss_pred CCHHHHHHHHHHHhc-CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 007404 542 LNPRERQVVRWRFGL-EDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 592 (605)
Q Consensus 542 L~~rER~VL~LRyGl-~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 592 (605)
++.++|-+-.+.... ++..+.|.+|||+.+|+|+++|. |.|++|++.
T Consensus 149 ~~~~~Rla~~L~~~~~~~~~~~t~~~lA~~lG~sretvs----R~L~~L~~~ 196 (226)
T PRK10402 149 FPLENRLAAFILLTQEGDLYHEKHTQAAEYLGVSYRHLL----YVLAQFIQD 196 (226)
T ss_pred ChHHHHHHHHHHhcccCCcccchHHHHHHHHCCcHHHHH----HHHHHHHHC
Confidence 366666655444222 12345799999999999999999 888888873
No 317
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=70.69 E-value=6.7 Score=40.99 Aligned_cols=46 Identities=20% Similarity=0.307 Sum_probs=37.5
Q ss_pred hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 540 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 540 ~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
..|++.|++||.+--+.+|- .++.||-+.+|+|+.||. |.+++|-+
T Consensus 191 ~~L~~~e~~il~~i~~~GGr--i~Q~eL~r~lglsktTvs----R~L~~LEk 236 (258)
T COG2512 191 YDLNEDEKEILDLIRERGGR--ITQAELRRALGLSKTTVS----RILRRLEK 236 (258)
T ss_pred CCCCHHHHHHHHHHHHhCCE--EeHHHHHHhhCCChHHHH----HHHHHHHh
Confidence 46899999999887665543 899999999999999999 66666644
No 318
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=70.31 E-value=6.5 Score=32.25 Aligned_cols=40 Identities=15% Similarity=0.185 Sum_probs=28.1
Q ss_pred CHHHHH-HHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 007404 543 NPRERQ-VVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAF 586 (605)
Q Consensus 543 ~~rER~-VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RAL 586 (605)
|+.++. ||....-.+ .|+.+||..+||++.+++++.....
T Consensus 8 s~e~K~~~v~~~~~~g----~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 8 SPEFKLQAVREYLESG----ESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp -HHHHHHHHHHHHHHH----CHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHCC----CceEeeecccccccccccHHHHHHh
Confidence 444444 444442333 8999999999999999999988775
No 319
>PF12116 SpoIIID: Stage III sporulation protein D; InterPro: IPR014208 Members of this entry represent the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if, and only if, the species is capable of endospore formation. In Bacillus subtilis SpoIIID is a DNA binding protein that is involved in gene repression as well as activation [].; PDB: 2L0K_A.
Probab=70.08 E-value=7.4 Score=33.66 Aligned_cols=46 Identities=17% Similarity=0.300 Sum_probs=30.0
Q ss_pred HHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 007404 546 ERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 593 (605)
Q Consensus 546 ER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 593 (605)
||-|-.-.|..+.. .|..+.|..||||++||..-...=|.++-..+
T Consensus 6 eR~i~i~~yIi~~~--aTVR~~Ak~FGvSKSTVHkDvteRL~~in~~L 51 (82)
T PF12116_consen 6 ERVIEIANYIIETK--ATVRQAAKVFGVSKSTVHKDVTERLPKINPEL 51 (82)
T ss_dssp HHHHHHHHHHHHH-----HHHHHHHHTS-HHHHHHHHTTHHHHH-HHH
T ss_pred HHHHHHHHHHHHcc--cHHHHHHHHHCCcHHHHHHHHHHHHHhcCHHH
Confidence 45555556666532 89999999999999999987766666554443
No 320
>PF08765 Mor: Mor transcription activator family; InterPro: IPR014875 Mor (Middle operon regulator) is a sequence specific DNA binding protein. It mediates transcription activation through its interactions with the C-terminal domains of the alpha and sigma subunits of bacterial RNA polymerase. The N-terminal region of Mor is the dimerisation region, and the C-terminal contains a helix-turn-helix motif which binds DNA []. ; PDB: 1RR7_A.
Probab=69.81 E-value=9.9 Score=34.20 Aligned_cols=42 Identities=21% Similarity=0.309 Sum_probs=26.5
Q ss_pred HHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 007404 545 RERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 592 (605)
Q Consensus 545 rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 592 (605)
+.++|...+- + ++..|+|..+|+|..+|++|+.+..++-++.
T Consensus 62 R~~~I~~~f~--G----~n~~eLA~kyglS~r~I~~Ii~~~~~~~~~~ 103 (108)
T PF08765_consen 62 RNREIRREFN--G----MNVRELARKYGLSERQIYRIIKRVRRRERRR 103 (108)
T ss_dssp HHHHHHHH----S----S-HHHHHHHHT--HHHHHHHHHHHHH-----
T ss_pred HHHHHHHHhC--C----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHh
Confidence 4556666432 3 8999999999999999999998887776553
No 321
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=69.76 E-value=24 Score=32.82 Aligned_cols=51 Identities=14% Similarity=0.105 Sum_probs=37.3
Q ss_pred HHHHHHHh--cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 007404 533 EDLEKVLD--TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK 590 (605)
Q Consensus 533 ~~L~~aL~--~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR 590 (605)
..+...+. .|++-|..||..-+..+ +.|..|||+.+|+++.+|. +.+++|-
T Consensus 27 ~~~~~~l~~~glt~~q~~vL~~l~~~~---~~t~~eLa~~l~i~~~tvs----r~l~~Le 79 (144)
T PRK11512 27 RLLNEYLSPLDITAAQFKVLCSIRCAA---CITPVELKKVLSVDLGALT----RMLDRLV 79 (144)
T ss_pred HHHHHHhcccCCCHHHHHHHHHHHHcC---CCCHHHHHHHHCCCHHHHH----HHHHHHH
Confidence 33444443 58999998888765322 3999999999999999999 5555554
No 322
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=69.45 E-value=5.4 Score=40.08 Aligned_cols=28 Identities=18% Similarity=0.470 Sum_probs=24.8
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 007404 561 MKTLQEIGELMGVSRERIRQIESSAFRKLKNK 592 (605)
Q Consensus 561 ~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 592 (605)
+.|.++||..+|+|+++|. |++++|++.
T Consensus 179 ~lt~~~IA~~lGisretls----R~L~~L~~~ 206 (230)
T PRK09391 179 PMSRRDIADYLGLTIETVS----RALSQLQDR 206 (230)
T ss_pred cCCHHHHHHHHCCCHHHHH----HHHHHHHHC
Confidence 5899999999999999999 788888863
No 323
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=69.40 E-value=11 Score=35.22 Aligned_cols=30 Identities=33% Similarity=0.657 Sum_probs=25.8
Q ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 558 DGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 558 dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
+|++.|..|||+.+|||+..|| +++.+|++
T Consensus 22 ~g~~~s~~~ia~~~~is~~~vr----k~l~~L~~ 51 (141)
T PRK11014 22 EGRMTSISEVTEVYGVSRNHMV----KIINQLSR 51 (141)
T ss_pred CCCccCHHHHHHHHCcCHHHHH----HHHHHHHh
Confidence 4567899999999999999999 77777776
No 324
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=69.28 E-value=12 Score=38.87 Aligned_cols=62 Identities=27% Similarity=0.495 Sum_probs=45.5
Q ss_pred HHHHHHHHHhcCCHHHHHHHHHHHhcCCC---CCCCHHHHHHHHCCCHHHHHHHHHH----HHHHHHhHHh
Q 007404 531 MKEDLEKVLDTLNPRERQVVRWRFGLEDG---RMKTLQEIGELMGVSRERIRQIESS----AFRKLKNKKR 594 (605)
Q Consensus 531 l~~~L~~aL~~L~~rER~VL~LRyGl~dg---~~~Tl~EIAe~LGISrerVRqie~R----ALkKLR~~l~ 594 (605)
+...|+..+..|++.|+.|.... +++. ..+|..+||+..|+|..+|-..-++ ....||..+.
T Consensus 15 i~~~i~~~~~~Lt~~e~~Ia~yi--l~~~~~v~~~si~~lA~~~~vS~aTi~Rf~kkLGf~gf~efk~~l~ 83 (292)
T PRK11337 15 LGPYIRMKQEGLTPLESRVVEWL--LKPGDLSEATALKDIAEALAVSEAMIVKVAKKLGFSGFRNLRSALE 83 (292)
T ss_pred HHHHHHHHHhhcCHHHHHHHHHH--HhCHHHHHhcCHHHHHHHhCCChHHHHHHHHHcCCCCHHHHHHHHH
Confidence 44578888999999999998754 3322 2389999999999999999855443 4455555443
No 325
>PRK01905 DNA-binding protein Fis; Provisional
Probab=69.02 E-value=22 Score=30.12 Aligned_cols=35 Identities=14% Similarity=0.232 Sum_probs=24.8
Q ss_pred HHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 007404 545 RERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIE 582 (605)
Q Consensus 545 rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie 582 (605)
-|+.+|...+-..+ -+..+.|+.||||+.+++...
T Consensus 37 ~E~~~i~~aL~~~~---gn~s~aAr~LGIsrstL~rkl 71 (77)
T PRK01905 37 VEKPLLEVVMEQAG---GNQSLAAEYLGINRNTLRKKL 71 (77)
T ss_pred HHHHHHHHHHHHcC---CCHHHHHHHHCCCHHHHHHHH
Confidence 45666655444433 378999999999999988443
No 326
>PRK10870 transcriptional repressor MprA; Provisional
Probab=68.60 E-value=27 Score=34.00 Aligned_cols=50 Identities=18% Similarity=0.145 Sum_probs=35.7
Q ss_pred HHHHHHHh--cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 007404 533 EDLEKVLD--TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES 583 (605)
Q Consensus 533 ~~L~~aL~--~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~ 583 (605)
..+...+. .|++-+-.||..-+.. ++.+.|..|||+.+|+++.+|.++..
T Consensus 42 ~~~~~~l~~~gLt~~q~~iL~~L~~~-~~~~it~~eLa~~l~l~~~tvsr~v~ 93 (176)
T PRK10870 42 ENRNKMLKAQGINETLFMALITLESQ-ENHSIQPSELSCALGSSRTNATRIAD 93 (176)
T ss_pred HHHHHHHHHCCCCHHHHHHHHHHhcC-CCCCcCHHHHHHHHCCCHHHHHHHHH
Confidence 34455554 4888887777766532 33458999999999999999984433
No 327
>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein. Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity.
Probab=68.51 E-value=14 Score=36.65 Aligned_cols=44 Identities=20% Similarity=0.188 Sum_probs=33.8
Q ss_pred HHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 007404 538 VLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS 584 (605)
Q Consensus 538 aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~R 584 (605)
....|++++..||.+-...+ +.+..|||+.+|+|+.+|++++.+
T Consensus 137 ~~~~ls~~~~~IL~~l~~~g---~~s~~eia~~l~is~stv~r~L~~ 180 (203)
T TIGR01884 137 LLAGLSREELKVLEVLKAEG---EKSVKNIAKKLGKSLSTISRHLRE 180 (203)
T ss_pred hhcCCCHHHHHHHHHHHHcC---CcCHHHHHHHHCcCHHHHHHHHHH
Confidence 35679999988887654322 389999999999999999954443
No 328
>PF13551 HTH_29: Winged helix-turn helix
Probab=68.30 E-value=45 Score=28.90 Aligned_cols=22 Identities=23% Similarity=0.241 Sum_probs=20.2
Q ss_pred CHHHHHHhcCCCHHHHHHHHhC
Q 007404 470 NNEEVAEATGLSMKRLHAVLLS 491 (605)
Q Consensus 470 T~eEIAe~lgis~e~V~~~l~~ 491 (605)
+..+||..+|++...|..+++.
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~ 35 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKR 35 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHH
Confidence 7999999999999999999864
No 329
>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....
Probab=67.91 E-value=3.6 Score=30.34 Aligned_cols=23 Identities=35% Similarity=0.583 Sum_probs=19.2
Q ss_pred CHHHHHHHHCCCHHHHHHHHHHH
Q 007404 563 TLQEIGELMGVSRERIRQIESSA 585 (605)
Q Consensus 563 Tl~EIAe~LGISrerVRqie~RA 585 (605)
|..|+|+.+|||..++|..+...
T Consensus 1 ti~e~A~~~gvs~~tlR~ye~~G 23 (38)
T PF00376_consen 1 TIGEVAKLLGVSPRTLRYYEREG 23 (38)
T ss_dssp EHHHHHHHHTS-HHHHHHHHHTT
T ss_pred CHHHHHHHHCCCHHHHHHHHHCC
Confidence 46799999999999999888764
No 330
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=67.87 E-value=9.6 Score=39.29 Aligned_cols=50 Identities=18% Similarity=0.282 Sum_probs=39.3
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHHhcCCC---CCCCHHHHHHHHCCCHHHHHHHHH
Q 007404 532 KEDLEKVLDTLNPRERQVVRWRFGLEDG---RMKTLQEIGELMGVSRERIRQIES 583 (605)
Q Consensus 532 ~~~L~~aL~~L~~rER~VL~LRyGl~dg---~~~Tl~EIAe~LGISrerVRqie~ 583 (605)
...|...+..|++.|+.|..+- +++. ..+|..|||+..|+|..||-..-+
T Consensus 4 ~~~i~~~~~~Lt~~e~~Ia~yi--l~n~~~v~~~si~~lA~~~~vS~aTv~Rf~k 56 (284)
T PRK11302 4 LEKIQSRLEHLSKSERKVAEVI--LASPQTAIHSSIATLAKMANVSEPTVNRFCR 56 (284)
T ss_pred HHHHHHHHhhCCHHHHHHHHHH--HhCHHHHHhcCHHHHHHHhCCCHHHHHHHHH
Confidence 3567888899999999998653 4332 238999999999999999985544
No 331
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=67.84 E-value=15 Score=33.66 Aligned_cols=24 Identities=13% Similarity=0.117 Sum_probs=22.2
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHH
Q 007404 562 KTLQEIGELMGVSRERIRQIESSA 585 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~RA 585 (605)
.|+.+||..+|||..++.++....
T Consensus 30 ~sv~evA~e~gIs~~tl~~W~r~y 53 (121)
T PRK09413 30 MTVSLVARQHGVAASQLFLWRKQY 53 (121)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHH
Confidence 899999999999999999997764
No 332
>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].
Probab=67.03 E-value=7.3 Score=37.86 Aligned_cols=36 Identities=17% Similarity=0.191 Sum_probs=27.7
Q ss_pred HHHHHHHHHHhcCCCCCCCHHHHHHHHC-CCHHHHHHHHHH
Q 007404 545 RERQVVRWRFGLEDGRMKTLQEIGELMG-VSRERIRQIESS 584 (605)
Q Consensus 545 rER~VL~LRyGl~dg~~~Tl~EIAe~LG-ISrerVRqie~R 584 (605)
..-+.|.-.+..| +|..|||+.|| +|++.|--..+|
T Consensus 6 e~~~~L~~lw~~G----~SasqIA~~lg~vsRnAViGk~hR 42 (162)
T PF07750_consen 6 ERVERLRKLWAEG----LSASQIARQLGGVSRNAVIGKAHR 42 (162)
T ss_pred HHHHHHHHHHHcC----CCHHHHHHHhCCcchhhhhhhhhc
Confidence 3344455455554 99999999999 999999987776
No 333
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=66.95 E-value=6.9 Score=31.42 Aligned_cols=23 Identities=30% Similarity=0.466 Sum_probs=20.8
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q 007404 562 KTLQEIGELMGVSRERIRQIESS 584 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~R 584 (605)
+|..|+|+.+|||..++|.++.+
T Consensus 1 ~s~~eva~~~gvs~~tlr~w~~~ 23 (68)
T cd01104 1 YTIGAVARLTGVSPDTLRAWERR 23 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHh
Confidence 57899999999999999998865
No 334
>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=66.88 E-value=39 Score=34.45 Aligned_cols=32 Identities=19% Similarity=0.282 Sum_probs=24.8
Q ss_pred HhHHHHHHhhcCCCCchHHHHHhhcCCHHHHH
Q 007404 326 EGLREVLSERCGGSPTFAQWAAAAGVDQRELR 357 (605)
Q Consensus 326 e~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~ 357 (605)
......+....|+.|+..+.|...|++.+.+.
T Consensus 119 ~~~~~~l~~~~~r~p~~~eia~~l~i~~~~~~ 150 (255)
T TIGR02941 119 KKAIDELTDHLQRSPKIIEIADHLGLSEEEVL 150 (255)
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHH
Confidence 34456666777999999999999999876543
No 335
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=66.70 E-value=20 Score=33.27 Aligned_cols=52 Identities=10% Similarity=0.189 Sum_probs=36.3
Q ss_pred HHHHHHHh--cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 007404 533 EDLEKVLD--TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK 590 (605)
Q Consensus 533 ~~L~~aL~--~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR 590 (605)
..+...+. .|++.|..||..-+..+ .+.|..|||+.+|+++.+|. +.+++|-
T Consensus 18 ~~~~~~l~~~glt~~q~~vL~~l~~~~--~~~t~~eLa~~l~~~~~tvt----~~v~~Le 71 (144)
T PRK03573 18 ALIDHRLKPLELTQTHWVTLHNIHQLP--PEQSQIQLAKAIGIEQPSLV----RTLDQLE 71 (144)
T ss_pred HHHHHHHHhcCCCHHHHHHHHHHHHcC--CCCCHHHHHHHhCCChhhHH----HHHHHHH
Confidence 33444443 58888888776654332 23899999999999999999 4455554
No 336
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=66.37 E-value=17 Score=27.95 Aligned_cols=51 Identities=14% Similarity=0.221 Sum_probs=39.9
Q ss_pred cCCHHHHHHHHHHHhcCCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 541 TLNPRERQVVRWRFGLEDG-RMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 541 ~L~~rER~VL~LRyGl~dg-~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
.+++.+..+|.-.|..+.. ......+||..+|++...|+.....-..+.+.
T Consensus 6 ~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~ 57 (59)
T cd00086 6 RFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKR 57 (59)
T ss_pred cCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence 4677888888888877532 22468899999999999999998887776654
No 337
>PF13551 HTH_29: Winged helix-turn helix
Probab=66.22 E-value=9.7 Score=33.19 Aligned_cols=23 Identities=26% Similarity=0.398 Sum_probs=20.7
Q ss_pred C-CHHHHHHHHCCCHHHHHHHHHH
Q 007404 562 K-TLQEIGELMGVSRERIRQIESS 584 (605)
Q Consensus 562 ~-Tl~EIAe~LGISrerVRqie~R 584 (605)
. |..+||+.+|+|+.||..++++
T Consensus 12 ~~~~~~ia~~lg~s~~Tv~r~~~~ 35 (112)
T PF13551_consen 12 VSTIAEIARRLGISRRTVYRWLKR 35 (112)
T ss_pred CCcHHHHHHHHCcCHHHHHHHHHH
Confidence 5 6999999999999999977766
No 338
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=66.16 E-value=57 Score=33.45 Aligned_cols=33 Identities=24% Similarity=0.211 Sum_probs=26.3
Q ss_pred HhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHH
Q 007404 326 EGLREVLSERCGGSPTFAQWAAAAGVDQRELRR 358 (605)
Q Consensus 326 e~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~ 358 (605)
.+....+....|++|+..+.|...|++.+.+..
T Consensus 126 ~~~~~~l~~~~~r~p~~~eia~~l~v~~~~v~~ 158 (258)
T PRK08215 126 LQVREKLINENSKEPTVEEIAKELEVPREEVVF 158 (258)
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHH
Confidence 344556777789999999999999999877653
No 339
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=65.91 E-value=10 Score=28.94 Aligned_cols=23 Identities=17% Similarity=0.323 Sum_probs=19.9
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHH
Q 007404 561 MKTLQEIGELMGVSRERIRQIES 583 (605)
Q Consensus 561 ~~Tl~EIAe~LGISrerVRqie~ 583 (605)
+.|..+|++.+|+|+.+|+.+++
T Consensus 10 ~~~~~~i~~~l~is~~~v~~~l~ 32 (66)
T smart00418 10 ELCVCELAEILGLSQSTVSHHLK 32 (66)
T ss_pred CccHHHHHHHHCCCHHHHHHHHH
Confidence 48999999999999999995443
No 340
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial. The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.
Probab=65.11 E-value=13 Score=34.13 Aligned_cols=30 Identities=20% Similarity=0.326 Sum_probs=24.4
Q ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 558 DGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 558 dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
++.+.|..|||+.+|+|+.+|+ +.+++|++
T Consensus 22 ~~~~~s~~eia~~l~is~~~v~----~~l~~L~~ 51 (130)
T TIGR02944 22 DSQPYSAAEIAEQTGLNAPTVS----KILKQLSL 51 (130)
T ss_pred CCCCccHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence 4567999999999999999999 45556654
No 341
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=64.73 E-value=7 Score=39.03 Aligned_cols=28 Identities=18% Similarity=0.332 Sum_probs=24.0
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 007404 561 MKTLQEIGELMGVSRERIRQIESSAFRKLKNK 592 (605)
Q Consensus 561 ~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 592 (605)
++|.++||..+|+++++|. |++++|++.
T Consensus 173 ~~t~~~iA~~lG~tretvs----R~l~~L~~~ 200 (236)
T PRK09392 173 PYEKRVLASYLGMTPENLS----RAFAALASH 200 (236)
T ss_pred eCCHHHHHHHhCCChhHHH----HHHHHHHhC
Confidence 4778999999999999998 777777763
No 342
>PRK10161 transcriptional regulator PhoB; Provisional
Probab=64.64 E-value=7.3 Score=37.81 Aligned_cols=50 Identities=10% Similarity=0.127 Sum_probs=40.0
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHH-----HHCCCHHHHHHHHHHHHHHHHh
Q 007404 541 TLNPRERQVVRWRFGLEDGRMKTLQEIGE-----LMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe-----~LGISrerVRqie~RALkKLR~ 591 (605)
.|+++|.+||.+.. .+-|+..|.++|.. .++++..+|+.+..|.++||..
T Consensus 154 ~Lt~~E~~ll~~l~-~~~~~~~s~~~l~~~~~~~~~~~~~~tv~~~i~rlr~Kl~~ 208 (229)
T PRK10161 154 EMGPTEFKLLHFFM-THPERVYSREQLLNHVWGTNVYVEDRTVDVHIRRLRKALEP 208 (229)
T ss_pred EcCHHHHHHHHHHH-hCCCceEcHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhcc
Confidence 59999999997654 44566688777644 6688999999999999999963
No 343
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=64.51 E-value=22 Score=32.13 Aligned_cols=46 Identities=26% Similarity=0.290 Sum_probs=32.9
Q ss_pred HHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 007404 534 DLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSA 585 (605)
Q Consensus 534 ~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RA 585 (605)
.+...-..+.+.+-.-++.. .+ +|..++|+.+|+|+.+|+++++..
T Consensus 57 ~~~~~~~~~~~~~i~~~r~~--~g----ltq~~lA~~lg~~~~tis~~e~g~ 102 (127)
T TIGR03830 57 FYRKVDGLLTPPEIRRIRKK--LG----LSQREAAELLGGGVNAFSRYERGE 102 (127)
T ss_pred HHHHccCCcCHHHHHHHHHH--cC----CCHHHHHHHhCCCHHHHHHHHCCC
Confidence 33333355777654444443 45 899999999999999999988743
No 344
>PRK05572 sporulation sigma factor SigF; Validated
Probab=64.29 E-value=50 Score=33.71 Aligned_cols=32 Identities=28% Similarity=0.422 Sum_probs=24.5
Q ss_pred HHhHHHHHHhhcCCCCchHHHHHhhcCCHHHH
Q 007404 325 LEGLREVLSERCGGSPTFAQWAAAAGVDQREL 356 (605)
Q Consensus 325 le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L 356 (605)
+.+....+....|+.|+..+.|+..|++.+.+
T Consensus 120 ~~~~~~~l~~~~~r~p~~~eia~~l~~~~~~v 151 (252)
T PRK05572 120 IRKDKDELSKELGREPTIEELAEYLGVTPEEV 151 (252)
T ss_pred HHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHH
Confidence 34455666667799999999999999887654
No 345
>PF14502 HTH_41: Helix-turn-helix domain
Probab=64.26 E-value=12 Score=29.35 Aligned_cols=30 Identities=37% Similarity=0.574 Sum_probs=25.9
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 007404 559 GRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 592 (605)
Q Consensus 559 g~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~ 592 (605)
.+-.|..|.++.|++|+.+|. .||+.|.+.
T Consensus 4 dRi~tI~e~~~~~~vs~GtiQ----~Alk~Le~~ 33 (48)
T PF14502_consen 4 DRIPTISEYSEKFGVSRGTIQ----NALKFLEEN 33 (48)
T ss_pred cccCCHHHHHHHhCcchhHHH----HHHHHHHHC
Confidence 355799999999999999998 889888763
No 346
>PF14493 HTH_40: Helix-turn-helix domain
Probab=64.25 E-value=12 Score=32.35 Aligned_cols=27 Identities=15% Similarity=0.261 Sum_probs=24.9
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHH
Q 007404 562 KTLQEIGELMGVSRERIRQIESSAFRK 588 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~RALkK 588 (605)
+|+.|||+.-|++.+||..++.++...
T Consensus 14 ~si~eIA~~R~L~~sTI~~HL~~~~~~ 40 (91)
T PF14493_consen 14 LSIEEIAKIRGLKESTIYGHLAELIES 40 (91)
T ss_pred CCHHHHHHHcCCCHHHHHHHHHHHHHh
Confidence 999999999999999999998887765
No 347
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=64.02 E-value=65 Score=35.14 Aligned_cols=36 Identities=25% Similarity=0.317 Sum_probs=29.6
Q ss_pred HHHHHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHH
Q 007404 321 DLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQREL 356 (605)
Q Consensus 321 ~~~~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L 356 (605)
.+.++.+++.+|....|++|+..+.|+..|+....+
T Consensus 187 ~~nkl~r~~r~l~q~~~r~p~~eeia~~l~~~~~~V 222 (342)
T COG0568 187 LINKLRRVKRELLQELGREPTPEEIAEELGVSPDKV 222 (342)
T ss_pred HHHHHHHHHHHHHHHhcCCCCHHHHHHHhCCCHHHH
Confidence 345667788888888999999999999999987543
No 348
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=63.70 E-value=9.5 Score=39.67 Aligned_cols=32 Identities=22% Similarity=0.350 Sum_probs=26.0
Q ss_pred HHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 007404 549 VVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS 584 (605)
Q Consensus 549 VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~R 584 (605)
+..--|..+ |.+.+||+.||||+.+|+.+..|
T Consensus 11 ~Akk~yl~g----mk~~dIAeklGvspntiksWKrr 42 (279)
T COG5484 11 IAKKDYLKG----MKLKDIAEKLGVSPNTIKSWKRR 42 (279)
T ss_pred HHHHHHHhh----ccHHHHHHHhCCChHHHHHHHHh
Confidence 444445554 99999999999999999998876
No 349
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=63.41 E-value=9 Score=30.95 Aligned_cols=23 Identities=30% Similarity=0.567 Sum_probs=20.9
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q 007404 562 KTLQEIGELMGVSRERIRQIESS 584 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~R 584 (605)
+|..|+|+.+|||..++|.++.+
T Consensus 1 ~~i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 1 YTIKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHh
Confidence 57899999999999999998775
No 350
>PRK11050 manganese transport regulator MntR; Provisional
Probab=62.96 E-value=27 Score=33.21 Aligned_cols=27 Identities=19% Similarity=0.351 Sum_probs=22.7
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 561 MKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 561 ~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
+.+..|||+.||||+.+|+ +++++|.+
T Consensus 51 ~~t~~eLA~~l~is~stVs----r~l~~Le~ 77 (152)
T PRK11050 51 EARQVDIAARLGVSQPTVA----KMLKRLAR 77 (152)
T ss_pred CCCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 4899999999999999999 55666654
No 351
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=62.57 E-value=13 Score=37.94 Aligned_cols=24 Identities=21% Similarity=0.297 Sum_probs=21.2
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHH
Q 007404 561 MKTLQEIGELMGVSRERIRQIESS 584 (605)
Q Consensus 561 ~~Tl~EIAe~LGISrerVRqie~R 584 (605)
|+|..|||++||||..+||+++..
T Consensus 25 ~~sa~elA~~Lgis~~avR~HL~~ 48 (218)
T COG2345 25 PVSADELAEELGISPMAVRRHLDD 48 (218)
T ss_pred CccHHHHHHHhCCCHHHHHHHHHH
Confidence 499999999999999999977543
No 352
>TIGR01387 cztR_silR_copR heavy metal response regulator. Members of this family contain a response regulator receiver domain (Pfam:PF00072) and an associated transcriptional regulatory region (Pfam:PF00486). This group is separated phylogenetically from related proteins with similar architecture and contains a number of proteins associated with heavy metal resistance efflux systems for copper, silver, cadmium, and/or zinc. Most members encoded by genes adjacent to genes for encoding a member of the heavy metal sensor histidine kinase family (TIGRFAMs:TIGR01386), its partner in the two-component response regulator system.
Probab=61.46 E-value=12 Score=35.49 Aligned_cols=49 Identities=16% Similarity=0.137 Sum_probs=41.3
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHH-----CCCHHHHHHHHHHHHHHHH
Q 007404 541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELM-----GVSRERIRQIESSAFRKLK 590 (605)
Q Consensus 541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~L-----GISrerVRqie~RALkKLR 590 (605)
.|+++|.+||.+-. .+.|+..|.++|.+.+ ..+..+|..++.|-++||.
T Consensus 147 ~Lt~~E~~il~~l~-~~~~~~~sr~~i~~~~~~~~~~~~~~~~~~~i~~lr~kl~ 200 (218)
T TIGR01387 147 TLTRKEFQLLWLLM-RRTGEVLPRTVIASLVWGMNFDSDTNVVDVAIRRLRAKVD 200 (218)
T ss_pred eCCHHHHHHHHHHH-hCCCeeEcHHHHHHHhcCCCCCCCcCCHHHHHHHHHHhhc
Confidence 59999999998755 4567889999999999 4567899988888888886
No 353
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=61.29 E-value=13 Score=36.44 Aligned_cols=109 Identities=14% Similarity=0.142 Sum_probs=56.9
Q ss_pred CCCCCHHHHHHhc--CCCHHHHHHHHhCCCCCCCccccccccCCCCC---CcccCCCCCCCHHHHHHHH---HHHHHHHH
Q 007404 466 GRHPNNEEVAEAT--GLSMKRLHAVLLSPKAPRSLDQKIGINQNLKP---SEVIADPEAETAEDLLIKK---FMKEDLEK 537 (605)
Q Consensus 466 gr~PT~eEIAe~l--gis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l---~d~l~D~~~~spEe~l~~~---el~~~L~~ 537 (605)
+-.+++.+||+.+ ++|.+++++.+......-=+. .+++..+ ...+..+.. .+. ...+. .+.+.=.+
T Consensus 37 ~~~~d~~~iak~l~p~is~~ev~~sL~~L~~~gli~----k~~~g~y~~t~~~l~~~~~-~~~-~avr~~h~q~~~lA~~ 110 (171)
T PF14394_consen 37 PFAPDPEWIAKRLRPKISAEEVRDSLEFLEKLGLIK----KDGDGKYVQTDKSLTTSSE-IPS-EAVRSYHKQMLELAQE 110 (171)
T ss_pred CCCCCHHHHHHHhcCCCCHHHHHHHHHHHHHCCCeE----ECCCCcEEEecceeeCCCC-CcH-HHHHHHHHHHHHHHHH
Confidence 4466899999999 999999999875321111110 0111111 111211111 121 22233 33334456
Q ss_pred HHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404 538 VLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR 594 (605)
Q Consensus 538 aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 594 (605)
+|+..|+.+|.+=.+-++.+. .++++| +..+....+++.....
T Consensus 111 al~~~p~~~R~~s~~T~~vs~---~~~~ki-----------~~~i~~fRk~i~~i~~ 153 (171)
T PF14394_consen 111 ALDRVPPEERDFSGLTMSVSR---EDYEKI-----------KKEIREFRKKIIAIAE 153 (171)
T ss_pred HHHhCCccccceeeeEEEeCH---HHHHHH-----------HHHHHHHHHHHHHHHh
Confidence 677788888887776665542 344443 4444555555555444
No 354
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=61.22 E-value=11 Score=38.05 Aligned_cols=30 Identities=30% Similarity=0.624 Sum_probs=25.9
Q ss_pred CCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 558 DGRMK-TLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 558 dg~~~-Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
.|..+ |-.|+++.||||+.+|| .||++|..
T Consensus 27 pG~~LPsE~eLae~~gVSRt~VR----eAL~~L~~ 57 (239)
T PRK04984 27 PGSILPAERELSELIGVTRTTLR----EVLQRLAR 57 (239)
T ss_pred CCCcCCCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 34567 79999999999999999 88888875
No 355
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=61.13 E-value=40 Score=38.94 Aligned_cols=103 Identities=12% Similarity=0.176 Sum_probs=55.2
Q ss_pred CCCCHHHHHHhcCCCHHHHHHHHhCCCCC---CCccccccccCCCCCCcccCCCCCCCHHHHHHHHHHHHHHHHHHhcCC
Q 007404 467 RHPNNEEVAEATGLSMKRLHAVLLSPKAP---RSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLN 543 (605)
Q Consensus 467 r~PT~eEIAe~lgis~e~V~~~l~~~~~~---~SLD~~i~~d~~~~l~d~l~D~~~~spEe~l~~~el~~~L~~aL~~L~ 543 (605)
...|..+||+.+|+|...|+.-+..-... ..+. .+....+ -.+... ++. .+...+..-+
T Consensus 16 ~~~t~~~LA~~l~VS~RTIr~dI~~in~~l~~~~~~-~i~~~~G----y~l~~~---~~~----------~~~~~~~~~~ 77 (584)
T PRK09863 16 QDRSGGELAQQLGVSRRTIVRDIAYINFTLNGKAIG-SISGSAK----YHLEIL---NRR----------SLFQLLQKSD 77 (584)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhcchh-heecCCc----eEEEeC---CHH----------HHHHHHhcCC
Confidence 45689999999999999887655421100 0000 0000011 111100 111 1111222223
Q ss_pred HHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 007404 544 PRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK 590 (605)
Q Consensus 544 ~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR 590 (605)
+ |+..+.++...+ .+.++.++|+.|.||+.||.+-+.+.-+.|.
T Consensus 78 ~-e~~~il~~Ll~~--~~~~~~~La~~l~vS~sTi~~dl~~v~~~l~ 121 (584)
T PRK09863 78 N-EDRLLLLRLLLN--TFTPMAQLASALNLSRTWVAERLPRLNQRYE 121 (584)
T ss_pred H-HHHHHHHHHHHc--CCccHHHHHHHhCCCHHHHHHHHHHHHHhhh
Confidence 3 443344444443 4699999999999999999966655555444
No 356
>PRK11517 transcriptional regulatory protein YedW; Provisional
Probab=60.92 E-value=15 Score=35.20 Aligned_cols=49 Identities=14% Similarity=0.087 Sum_probs=40.8
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHH-----CCCHHHHHHHHHHHHHHHH
Q 007404 541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELM-----GVSRERIRQIESSAFRKLK 590 (605)
Q Consensus 541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~L-----GISrerVRqie~RALkKLR 590 (605)
.|+++|.+||.+-. .+-|+..|.++|.+.+ ..+..+|+.++.|-++||.
T Consensus 147 ~Lt~~E~~il~~l~-~~~g~~~s~~~i~~~~w~~~~~~~~~tv~~~i~rlr~Kl~ 200 (223)
T PRK11517 147 TLTRKEFQLLWLLA-SRAGEIIPRTVIASEIWGINFDSDTNTVDVAIRRLRAKVD 200 (223)
T ss_pred eCCHHHHHHHHHHH-hCCCccCCHHHHHHHhcCCCCCCCcCCHHHHHHHHHHhhc
Confidence 59999999998754 4557789999999997 4578899999888888885
No 357
>PRK15482 transcriptional regulator MurR; Provisional
Probab=60.90 E-value=16 Score=37.99 Aligned_cols=59 Identities=10% Similarity=0.272 Sum_probs=43.6
Q ss_pred HHHHHHHhcCCHHHHHHHHHHHhcCCC---CCCCHHHHHHHHCCCHHHHHHHHHH----HHHHHHhHH
Q 007404 533 EDLEKVLDTLNPRERQVVRWRFGLEDG---RMKTLQEIGELMGVSRERIRQIESS----AFRKLKNKK 593 (605)
Q Consensus 533 ~~L~~aL~~L~~rER~VL~LRyGl~dg---~~~Tl~EIAe~LGISrerVRqie~R----ALkKLR~~l 593 (605)
..|......|++.|+.|..+- +++. .-+|..|||+..|+|..||-..-++ ....||..+
T Consensus 5 ~~i~~~~~~Lt~~e~~Ia~yI--l~n~~~v~~~si~elA~~~~vS~aTv~Rf~kkLGf~Gf~efk~~l 70 (285)
T PRK15482 5 TKIRNAESEFTENEQKIADFL--RANVSELKSVSSRKMAKQLGISQSSIVKFAQKLGAQGFTELRMAL 70 (285)
T ss_pred HHHHHHHhhcCHHHHHHHHHH--HhCHHHHHhcCHHHHHHHhCCCHHHHHHHHHHhCCCCHHHHHHHH
Confidence 567788899999999998653 4432 2389999999999999999755443 444555444
No 358
>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=60.90 E-value=59 Score=32.42 Aligned_cols=30 Identities=40% Similarity=0.546 Sum_probs=23.9
Q ss_pred HHHHHHhhcCCCCchHHHHHhhcCCHHHHH
Q 007404 328 LREVLSERCGGSPTFAQWAAAAGVDQRELR 357 (605)
Q Consensus 328 ~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~ 357 (605)
....+....|+.|+..+.|...|++.+.+.
T Consensus 95 ~~~~l~~~~~~~p~~~ela~~l~~~~~~v~ 124 (227)
T TIGR02980 95 ATEELTQRLGRSPTIAEIAEELGVSEEEVV 124 (227)
T ss_pred HHHHHHHHHCCCCCHHHHHHHhCCCHHHHH
Confidence 445666677999999999999999876553
No 359
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=60.42 E-value=6.7 Score=31.58 Aligned_cols=25 Identities=32% Similarity=0.448 Sum_probs=21.6
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 007404 562 KTLQEIGELMGVSRERIRQIESSAF 586 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~RAL 586 (605)
+|..|+|+.+|||..++|.++...+
T Consensus 1 ~s~~eva~~~gvs~~tlr~~~~~gl 25 (70)
T smart00422 1 YTIGEVAKLAGVSVRTLRYYERIGL 25 (70)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999998876544
No 360
>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Polaromonas, Burkholderia, Ralstonia and Verminephrobacter.
Probab=60.27 E-value=9.9 Score=37.45 Aligned_cols=37 Identities=30% Similarity=0.469 Sum_probs=28.9
Q ss_pred HHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 549 VVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 549 VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
|+.-.|. .|..++-.++|+.||||+..|| .||+.|..
T Consensus 24 I~~g~l~--pG~~L~e~~La~~lgVSRtpVR----eAL~~L~~ 60 (212)
T TIGR03338 24 ILSGELP--PGAKLNESDIAARLGVSRGPVR----EAFRALEE 60 (212)
T ss_pred HHcCCCC--CCCEecHHHHHHHhCCChHHHH----HHHHHHHH
Confidence 4444332 3455899999999999999999 88888875
No 361
>COG0856 Orotate phosphoribosyltransferase homologs [Nucleotide transport and metabolism]
Probab=59.69 E-value=7.9 Score=38.30 Aligned_cols=30 Identities=33% Similarity=0.346 Sum_probs=27.2
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 562 KTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
+|-.|||+.||+|++|++-+..|+.++...
T Consensus 19 lt~gEIAdELNvSreTa~WL~~r~~~~~~~ 48 (203)
T COG0856 19 LTTGEIADELNVSRETATWLLTRAFKKESV 48 (203)
T ss_pred CcHHHhhhhhhhhHHHHHHHHhhhhhccCC
Confidence 999999999999999999999998876543
No 362
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=59.66 E-value=11 Score=30.53 Aligned_cols=23 Identities=26% Similarity=0.384 Sum_probs=20.6
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q 007404 562 KTLQEIGELMGVSRERIRQIESS 584 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~R 584 (605)
+|..|+|+.+|||..++|.++..
T Consensus 1 ~~i~e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 1 YTIGEVALLTGIKPHVLRAWERE 23 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHh
Confidence 47889999999999999988765
No 363
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=59.61 E-value=21 Score=33.34 Aligned_cols=28 Identities=18% Similarity=0.331 Sum_probs=22.4
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 560 RMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 560 ~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
.+.+..+||+.||+|+.+|+ +++++|.+
T Consensus 21 ~~~~~~ela~~l~vs~~svs----~~l~~L~~ 48 (142)
T PRK03902 21 GYARVSDIAEALSVHPSSVT----KMVQKLDK 48 (142)
T ss_pred CCcCHHHHHHHhCCChhHHH----HHHHHHHH
Confidence 34799999999999999999 45555544
No 364
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair.
Probab=59.29 E-value=20 Score=29.44 Aligned_cols=23 Identities=22% Similarity=0.497 Sum_probs=21.4
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q 007404 562 KTLQEIGELMGVSRERIRQIESS 584 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~R 584 (605)
+|..++|+.+|+|+.+|.++++.
T Consensus 19 ~t~~~lA~~~gis~~tis~~~~g 41 (78)
T TIGR02607 19 LSIRALAKALGVSRSTLSRIVNG 41 (78)
T ss_pred CCHHHHHHHhCCCHHHHHHHHcC
Confidence 89999999999999999998863
No 365
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=58.94 E-value=19 Score=27.62 Aligned_cols=48 Identities=13% Similarity=0.198 Sum_probs=37.4
Q ss_pred cCCHHHHHHHHHHHhcCCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q 007404 541 TLNPRERQVVRWRFGLEDG-RMKTLQEIGELMGVSRERIRQIESSAFRK 588 (605)
Q Consensus 541 ~L~~rER~VL~LRyGl~dg-~~~Tl~EIAe~LGISrerVRqie~RALkK 588 (605)
.+++.+..+|.-.|..+.. ......+||..+|++...|.........+
T Consensus 6 ~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~ 54 (56)
T smart00389 6 SFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAK 54 (56)
T ss_pred cCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhc
Confidence 3788888999888876632 22468899999999999999887766554
No 366
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=58.92 E-value=94 Score=31.30 Aligned_cols=32 Identities=25% Similarity=0.287 Sum_probs=24.7
Q ss_pred hHHHHHHhhcCCCCchHHHHHhhcCCHHHHHH
Q 007404 327 GLREVLSERCGGSPTFAQWAAAAGVDQRELRR 358 (605)
Q Consensus 327 ~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~ 358 (605)
+....+....|++|+..++|+..|++.+.+..
T Consensus 99 ~~~~~~~~~~~~~~~~~ela~~l~i~~~~v~~ 130 (236)
T PRK06986 99 QAIRQLEQELGREPTDTEVAEKLGLSLEEYRE 130 (236)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHH
Confidence 34455666779999999999999999866543
No 367
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=58.84 E-value=13 Score=38.28 Aligned_cols=57 Identities=19% Similarity=0.285 Sum_probs=41.4
Q ss_pred HHHHHhcCCHHHHHHHHHHHhcCCC---CCCCHHHHHHHHCCCHHHHHHHHHH----HHHHHHhHH
Q 007404 535 LEKVLDTLNPRERQVVRWRFGLEDG---RMKTLQEIGELMGVSRERIRQIESS----AFRKLKNKK 593 (605)
Q Consensus 535 L~~aL~~L~~rER~VL~LRyGl~dg---~~~Tl~EIAe~LGISrerVRqie~R----ALkKLR~~l 593 (605)
|......|++.|+.|..+- +++. ..+|..|+|+..|+|..||-..-++ ...-+|..+
T Consensus 3 i~~~~~~Lt~~e~~ia~yi--l~n~~~v~~~si~elA~~~~vS~aTv~Rf~kklG~~Gf~efk~~l 66 (278)
T PRK11557 3 IRQRYPGLAQSDRKLADYL--LLQPDTARHLSSQQLANEAGVSQSSVVKFAQKLGYKGFPALKLAL 66 (278)
T ss_pred hhHhhhhCCHHHHHHHHHH--HhCHHHHHhcCHHHHHHHhCCCHHHHHHHHHHcCCCCHHHHHHHH
Confidence 5667788999999998654 4322 2399999999999999999865543 344444444
No 368
>TIGR00647 MG103 conserved hypothetical protein.
Probab=58.61 E-value=21 Score=37.78 Aligned_cols=42 Identities=17% Similarity=0.253 Sum_probs=35.1
Q ss_pred HhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHC------CCHHHHHHHHH
Q 007404 539 LDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMG------VSRERIRQIES 583 (605)
Q Consensus 539 L~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LG------ISrerVRqie~ 583 (605)
++.||+..+++..+|--.- ..|++|+|+.|. ||++.|.-+..
T Consensus 225 l~~Lp~~L~~~a~lRl~~P---d~SL~ELgell~~~~~~~isKSgvnhRlr 272 (279)
T TIGR00647 225 FEKLPLNFQRICLLKIDHP---DWSLEQIAEFFASKYKVKISRSGIQHRLR 272 (279)
T ss_pred cccCCHHHHHHHHHHHhCc---ccCHHHHHHHhccCCCCCcCHHHHHHHHH
Confidence 5789999999999997443 499999999994 99999985543
No 369
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family. Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.
Probab=58.39 E-value=18 Score=36.93 Aligned_cols=38 Identities=18% Similarity=0.155 Sum_probs=27.6
Q ss_pred HHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 007404 546 ERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES 583 (605)
Q Consensus 546 ER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~ 583 (605)
+|-+-.|.++-....++|+.|||+.+|+++.||..++.
T Consensus 9 ~ral~IL~~l~~~~~~~~l~eia~~lglpksT~~RlL~ 46 (248)
T TIGR02431 9 ARGLAVIEAFGAERPRLTLTDVAEATGLTRAAARRFLL 46 (248)
T ss_pred HHHHHHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 34444444444445679999999999999999995543
No 370
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=58.12 E-value=11 Score=37.53 Aligned_cols=37 Identities=19% Similarity=0.253 Sum_probs=29.0
Q ss_pred HHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 549 VVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 549 VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
|+...|. .|..++-.+||+.||||+..|| .||+.|..
T Consensus 24 I~~g~l~--pG~~L~e~~La~~lgVSRtpVR----EAL~~L~~ 60 (221)
T PRK11414 24 LSIGALK--PGARLITKNLAEQLGMSITPVR----EALLRLVS 60 (221)
T ss_pred HHhCCCC--CCCccCHHHHHHHHCCCchhHH----HHHHHHHH
Confidence 4444432 4456888999999999999999 88988865
No 371
>TIGR00180 parB_part ParB-like partition proteins. This model represents the most well-conserved core of a set of chromosomal and plasmid partition proteins related to ParB, including Spo0J, RepB, and SopB. Spo0J has been shown to bind a specific DNA sequence that, when introduced into a plasmid, can serve as partition site. Study of RepB, which has nicking-closing activity, suggests that it forms a transient protein-DNA covalent intermediate during the strand transfer reaction.
Probab=57.95 E-value=19 Score=35.42 Aligned_cols=43 Identities=21% Similarity=0.234 Sum_probs=31.6
Q ss_pred hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 007404 540 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS 584 (605)
Q Consensus 540 ~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~R 584 (605)
..|++-|+.....+.....| +|.++||+.+|+|+.+|++++.-
T Consensus 101 ~~lt~~e~a~~~~~l~~~~g--~s~~~iA~~lg~s~~~V~r~l~l 143 (187)
T TIGR00180 101 EDLSPIEEAQAYKRLLEKFS--MTQEDLAKKIGKSRAHITNLLRL 143 (187)
T ss_pred cCCCHHHHHHHHHHHHHHhC--CCHHHHHHHHCcCHHHHHHHHHH
Confidence 46888887665554332212 89999999999999999976643
No 372
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []. In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.
Probab=57.82 E-value=16 Score=27.86 Aligned_cols=22 Identities=18% Similarity=0.348 Sum_probs=16.7
Q ss_pred CCHHHHHHHHCCCHHHHHHHHH
Q 007404 562 KTLQEIGELMGVSRERIRQIES 583 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~ 583 (605)
+|+.+.|+.+||++.|++.+..
T Consensus 17 ~S~r~AA~~ygVp~sTL~~r~~ 38 (45)
T PF05225_consen 17 MSIRKAAKKYGVPRSTLRRRLR 38 (45)
T ss_dssp S-HHHHHHHHT--HHHHHHHHH
T ss_pred CCHHHHHHHHCcCHHHHHHHHc
Confidence 9999999999999999995544
No 373
>PF13556 HTH_30: PucR C-terminal helix-turn-helix domain; PDB: 3ONQ_B.
Probab=57.59 E-value=31 Score=27.51 Aligned_cols=33 Identities=9% Similarity=0.051 Sum_probs=24.5
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404 562 KTLQEIGELMGVSRERIRQIESSAFRKLKNKKR 594 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 594 (605)
.+..+.|+.|+|.+.||+.++.|.-+.+--.+.
T Consensus 13 ~n~~~tA~~L~iHrNTl~yRl~ki~~l~g~dl~ 45 (59)
T PF13556_consen 13 GNISKTARALHIHRNTLRYRLKKIEELLGLDLD 45 (59)
T ss_dssp T-HHHHHHHHTS-HHHHHHHHHHHHHHHS--TT
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHCcCCC
Confidence 799999999999999999888877766654443
No 374
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=57.59 E-value=10 Score=31.20 Aligned_cols=23 Identities=22% Similarity=0.538 Sum_probs=19.7
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q 007404 562 KTLQEIGELMGVSRERIRQIESS 584 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~R 584 (605)
.|+.|||+.+|||+.||+..++.
T Consensus 1 ~t~~~iA~~~gvS~~TVSr~ln~ 23 (70)
T smart00354 1 ATIKDVARLAGVSKATVSRVLNG 23 (70)
T ss_pred CCHHHHHHHHCCCHHHHHHHHCC
Confidence 37899999999999999977654
No 375
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=57.46 E-value=19 Score=31.65 Aligned_cols=41 Identities=20% Similarity=0.343 Sum_probs=28.0
Q ss_pred cCCHHHHHHHHHHHh-cCCCCCCCHHHHHHHHCCCHHHHHHH
Q 007404 541 TLNPRERQVVRWRFG-LEDGRMKTLQEIGELMGVSRERIRQI 581 (605)
Q Consensus 541 ~L~~rER~VL~LRyG-l~dg~~~Tl~EIAe~LGISrerVRqi 581 (605)
.|++.+++||.+.-. ....+..++.+|++.|+++...||+.
T Consensus 44 ~~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~a 85 (102)
T PF08784_consen 44 GLSPLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKA 85 (102)
T ss_dssp -S-HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHH
T ss_pred CCCHHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHH
Confidence 677778888776544 22234599999999999999999944
No 376
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=57.38 E-value=30 Score=31.92 Aligned_cols=49 Identities=12% Similarity=0.173 Sum_probs=33.9
Q ss_pred HHHHhcCCHHHH-HHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 536 EKVLDTLNPRER-QVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 536 ~~aL~~L~~rER-~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
.+.+..|.+.-| .||.+-. ++.+++..||++.+|+|+.+|.++ |+.|++
T Consensus 7 ~~~fkaLadptRl~IL~~L~---~~~~~~v~ela~~l~lsqstvS~H----L~~L~~ 56 (117)
T PRK10141 7 LQLFKILSDETRLGIVLLLR---ESGELCVCDLCTALDQSQPKISRH----LALLRE 56 (117)
T ss_pred HHHHHHhCCHHHHHHHHHHH---HcCCcCHHHHHHHHCcCHHHHHHH----HHHHHH
Confidence 456667776655 4555432 122499999999999999999965 445554
No 377
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=57.19 E-value=18 Score=33.52 Aligned_cols=22 Identities=23% Similarity=0.366 Sum_probs=21.0
Q ss_pred CCHHHHHHHHCCCHHHHHHHHH
Q 007404 562 KTLQEIGELMGVSRERIRQIES 583 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~ 583 (605)
+|..+||+.||+|+..|+|.++
T Consensus 23 ~Sq~~iA~LLGltqaAVS~Yls 44 (119)
T COG2522 23 LSQYRIAKLLGLTQAAVSQYLS 44 (119)
T ss_pred CcHHHHHHHhCCCHHHHHHHHc
Confidence 9999999999999999999875
No 378
>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]
Probab=57.14 E-value=54 Score=36.91 Aligned_cols=47 Identities=15% Similarity=0.263 Sum_probs=32.5
Q ss_pred HHHHhcCCHHHHHHHHH---------HHhcC---CCCCCCHHHHHHHHCCCHHHHHHHH
Q 007404 536 EKVLDTLNPRERQVVRW---------RFGLE---DGRMKTLQEIGELMGVSRERIRQIE 582 (605)
Q Consensus 536 ~~aL~~L~~rER~VL~L---------RyGl~---dg~~~Tl~EIAe~LGISrerVRqie 582 (605)
..++..|..|++.++.. -|+.+ --.|+++++||+.+|++.+||+...
T Consensus 293 ~wLiksL~qR~~TLlkV~~~Iv~~Q~~Ff~~g~~~l~PL~LrdvA~~i~~HESTISRai 351 (444)
T COG1508 293 KWLIKSLEQREETLLKVAEEIVEYQKAFFEGGEEALKPLVLRDVADEIGMHESTISRAI 351 (444)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccCCcccHHHHHHHhCccHHHHHHHH
Confidence 33456677777766542 12222 2378999999999999999999544
No 379
>TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR. Members of this family are FadR, a transcriptional regulator of fatty acid metabolism, including both biosynthesis and beta-oxidation. It is found exclusively in a subset of Gammaproteobacteria, with strictly one copy per genome. It has an N-terminal DNA-binding domain and a less well conserved C-terminal long chain acyl-CoA-binding domain. FadR from this family heterologously expressed in Escherichia coli show differences in regulatory response and fatty acid binding profiles. The family is nevertheless designated equivalog, as all member proteins have at least nominally the same function.
Probab=56.87 E-value=14 Score=37.15 Aligned_cols=30 Identities=30% Similarity=0.624 Sum_probs=26.1
Q ss_pred CCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 558 DGRMK-TLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 558 dg~~~-Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
.|..+ |-.++++.||||+..|| .||.+|..
T Consensus 26 pG~~LpsE~~La~~lgVSRtpVR----EAL~~Le~ 56 (235)
T TIGR02812 26 PGSILPAERELSELIGVTRTTLR----EVLQRLAR 56 (235)
T ss_pred CCCcCcCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence 34558 79999999999999999 89998875
No 380
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=56.81 E-value=26 Score=31.93 Aligned_cols=30 Identities=30% Similarity=0.483 Sum_probs=24.2
Q ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 558 DGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 558 dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
++.+.|.+|||+.+|+++..|+ +.+.+|++
T Consensus 22 ~~~~~s~~eia~~~~i~~~~v~----~il~~L~~ 51 (132)
T TIGR00738 22 DEGPVSVKEIAERQGISRSYLE----KILRTLRR 51 (132)
T ss_pred CCCcCcHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence 3458999999999999999999 45555554
No 381
>PF12298 Bot1p: Eukaryotic mitochondrial regulator protein ; InterPro: IPR021036 This entry represents Ribosomal protein S35, which localises to the mitochondria in live cells and co-fractionates with purified mitochondrial ribosomes. This group of proteins have a novel function in the control of cell respiration by acting on the mitochondrial protein synthesis machinery and a role in mitochondrial integrity. Observations also indicate that in Schizosaccharomyces pombe (Fission yeast), alterations of mitochondrial function are linked to changes in cell cycle and cell morphology control mechanisms [].
Probab=56.62 E-value=23 Score=34.83 Aligned_cols=40 Identities=18% Similarity=0.292 Sum_probs=31.1
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 007404 541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES 583 (605)
Q Consensus 541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~ 583 (605)
.|++.-|.-|.-.+..++ +|+++||..+||+..||.-|+.
T Consensus 16 ~lse~~r~~Iy~~~~~~~---~sv~~vS~~ygi~~~RV~AIvr 55 (172)
T PF12298_consen 16 VLSEELREQIYEDVMQDG---KSVREVSQKYGIKIQRVEAIVR 55 (172)
T ss_pred cCCHHHHHHHHHHHHhCC---CCHHHHHHHhCCCHHHHHHHHH
Confidence 366677776766665553 7999999999999999986654
No 382
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=56.40 E-value=14 Score=37.46 Aligned_cols=37 Identities=22% Similarity=0.342 Sum_probs=29.1
Q ss_pred HHHHHHhcCCCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 549 VVRWRFGLEDGRMK-TLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 549 VL~LRyGl~dg~~~-Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
|+.-.|- .|..+ +-.+||+.||||+..|| .||++|..
T Consensus 20 I~~g~l~--pG~~LPsE~eLa~~~gVSRtpVR----EAL~~L~~ 57 (251)
T PRK09990 20 IVDGVLK--VGQALPSERRLCEKLGFSRSALR----EGLTVLRG 57 (251)
T ss_pred HHcCCCC--CCCcCcCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 4444443 44568 89999999999999999 88988875
No 383
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=56.33 E-value=74 Score=28.30 Aligned_cols=42 Identities=17% Similarity=0.101 Sum_probs=32.2
Q ss_pred cCCHHHHHHHHHHHh-cCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 007404 541 TLNPRERQVVRWRFG-LEDGRMKTLQEIGELMGVSRERIRQIE 582 (605)
Q Consensus 541 ~L~~rER~VL~LRyG-l~dg~~~Tl~EIAe~LGISrerVRqie 582 (605)
.|+..|-.||..-+. ...+.+.|..|||+.+++++.+|...+
T Consensus 22 ~ls~~q~~vL~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i 64 (109)
T TIGR01889 22 NLSLEELLILYYLGKLENNEGKLTLKEIIKEILIKQSALVKII 64 (109)
T ss_pred CCCHHHHHHHHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHH
Confidence 689999988876551 112335999999999999999999443
No 384
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=56.28 E-value=21 Score=31.48 Aligned_cols=39 Identities=18% Similarity=0.243 Sum_probs=28.4
Q ss_pred HHHHHHHHHcCC-CCCHHHHHHhcCCCHHHHHHHHhCCCC
Q 007404 456 EARKQLYSENGR-HPNNEEVAEATGLSMKRLHAVLLSPKA 494 (605)
Q Consensus 456 ka~~~L~~elgr-~PT~eEIAe~lgis~e~V~~~l~~~~~ 494 (605)
..+.+|.....- .-+++|||..|++++.+++.++...++
T Consensus 10 ~Tk~elqan~el~~LS~~~iA~~Ln~t~~~lekil~~tqr 49 (97)
T COG4367 10 RTKQELQANFELCPLSDEEIATALNWTEVKLEKILQVTQR 49 (97)
T ss_pred HHHHHHHHhhhhccccHHHHHHHhCCCHHHHHHHHHHhhc
Confidence 344455444443 348999999999999999999976544
No 385
>PRK13239 alkylmercury lyase; Provisional
Probab=56.25 E-value=20 Score=36.32 Aligned_cols=28 Identities=29% Similarity=0.363 Sum_probs=25.4
Q ss_pred cCCCCCHHHHHHhcCCCHHHHHHHHhCC
Q 007404 465 NGRHPNNEEVAEATGLSMKRLHAVLLSP 492 (605)
Q Consensus 465 lgr~PT~eEIAe~lgis~e~V~~~l~~~ 492 (605)
.|+.||.++||+.+|+++++|+.+|...
T Consensus 33 ~G~pvt~~~lA~~~~~~~~~v~~~L~~l 60 (206)
T PRK13239 33 KGRPVSVTTLAAALGWPVEEVEAVLEAM 60 (206)
T ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHhC
Confidence 5899999999999999999999998753
No 386
>PRK14101 bifunctional glucokinase/RpiR family transcriptional regulator; Provisional
Probab=56.22 E-value=20 Score=41.86 Aligned_cols=62 Identities=23% Similarity=0.293 Sum_probs=45.4
Q ss_pred HHHHHHHHHhcCCHHHHHHHHHHHhcCCC---CCCCHHHHHHHHCCCHHHHHHHHHH----HHHHHHhHHh
Q 007404 531 MKEDLEKVLDTLNPRERQVVRWRFGLEDG---RMKTLQEIGELMGVSRERIRQIESS----AFRKLKNKKR 594 (605)
Q Consensus 531 l~~~L~~aL~~L~~rER~VL~LRyGl~dg---~~~Tl~EIAe~LGISrerVRqie~R----ALkKLR~~l~ 594 (605)
+.+.|...+..|++.||.|..+. +++. ..+|..|||+..|+|..||-..-++ .+.-||..+.
T Consensus 343 l~~~I~~~~~~Lt~~E~~IA~yI--l~n~~~v~~~si~eLA~~~~vS~aTV~Rf~kkLGf~Gf~efK~~L~ 411 (638)
T PRK14101 343 VFERIRQMRDALTPAERRVADLA--LNHPRSIINDPIVDIARKADVSQPTVIRFCRSLGCQGLSDFKLKLA 411 (638)
T ss_pred HHHHHHHHHhhcCHHHHHHHHHH--HhCHHHHHhccHHHHHHHhCCCHHHHHHHHHHhCCCCHHHHHHHHH
Confidence 45678888999999999998653 3322 2389999999999999999755443 4445555443
No 387
>PRK04158 transcriptional repressor CodY; Validated
Probab=56.04 E-value=19 Score=37.62 Aligned_cols=58 Identities=28% Similarity=0.380 Sum_probs=46.2
Q ss_pred HHHHHHHHHHhcCCHHHHHHHHHHHhcCCCC--CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 530 FMKEDLEKVLDTLNPRERQVVRWRFGLEDGR--MKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 530 el~~~L~~aL~~L~~rER~VL~LRyGl~dg~--~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
.-+..++.++.+|+--|.+-+.+-|..=||. -+.-..||++.||||+-|= .||+||-.
T Consensus 168 Rk~~~V~~Ai~tLSySEleAv~hIf~eL~g~EG~lvASkiADrvgITRSVIV----NALRK~ES 227 (256)
T PRK04158 168 RKKAVVQMAINTLSYSELEAVEHIFEELDGNEGLLVASKIADRVGITRSVIV----NALRKLES 227 (256)
T ss_pred HHHHHHHHHHHhcCHhHHHHHHHHHHhcCCCcceEEeeecccccCCchhhhh----hhhhhhhc
Confidence 3445688899999999999999998775552 3677899999999977665 88888754
No 388
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=55.91 E-value=15 Score=37.43 Aligned_cols=38 Identities=21% Similarity=0.353 Sum_probs=29.2
Q ss_pred HHHHHHHhcCCCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 548 QVVRWRFGLEDGRMK-TLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 548 ~VL~LRyGl~dg~~~-Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
.|+.-.|. .|..+ |-.++|+.||||+..|| .||+.|..
T Consensus 22 ~I~~g~l~--pG~~LpsE~eLa~~lgVSRtpVR----EAL~~L~~ 60 (254)
T PRK09464 22 LILEGTLR--PGEKLPPERELAKQFDVSRPSLR----EAIQRLEA 60 (254)
T ss_pred HHHcCCCC--CCCcCCCHHHHHHHhCCCHHHHH----HHHHHHHH
Confidence 34444443 34557 89999999999999999 88888875
No 389
>PRK03837 transcriptional regulator NanR; Provisional
Probab=55.88 E-value=15 Score=36.86 Aligned_cols=37 Identities=30% Similarity=0.497 Sum_probs=28.6
Q ss_pred HHHHHHhcCCCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 549 VVRWRFGLEDGRMK-TLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 549 VL~LRyGl~dg~~~-Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
|+.-.|. .|..+ +..+||+.||||+.+|| .||..|..
T Consensus 26 I~~g~l~--pG~~Lp~E~~Lae~~gVSRt~VR----EAL~~L~~ 63 (241)
T PRK03837 26 IRSGEFG--PGDQLPSERELMAFFGVGRPAVR----EALQALKR 63 (241)
T ss_pred HHhCCCC--CCCCCCCHHHHHHHhCCCHHHHH----HHHHHHHH
Confidence 4444433 34557 89999999999999999 88888874
No 390
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=55.80 E-value=15 Score=36.66 Aligned_cols=38 Identities=13% Similarity=0.215 Sum_probs=29.7
Q ss_pred HHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 548 QVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 548 ~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
.|+.-.|- .|..++..++|+.||||+..|| .||.+|..
T Consensus 19 ~I~~g~l~--pG~~L~e~eLae~lgVSRtpVR----EAL~~L~~ 56 (224)
T PRK11534 19 DIIRGNFQ--PDEKLRMSLLTSRYALGVGPLR----EALSQLVA 56 (224)
T ss_pred HHHhCCCC--CCCcCCHHHHHHHHCCChHHHH----HHHHHHHH
Confidence 45555443 3456899999999999999999 88888865
No 391
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=55.74 E-value=15 Score=37.57 Aligned_cols=38 Identities=24% Similarity=0.401 Sum_probs=29.3
Q ss_pred HHHHHHHhcCCCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 548 QVVRWRFGLEDGRMK-TLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 548 ~VL~LRyGl~dg~~~-Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
.|+.-.|. -|..+ |-.++|+.||||+..|| .||++|..
T Consensus 21 ~I~~g~l~--pG~~LpsE~eLa~~~gVSRtpVR----EAL~~L~~ 59 (257)
T PRK10225 21 LIIKTPYN--PGERLPPEREIAEMLDVTRTVVR----EALIMLEI 59 (257)
T ss_pred HHHhCCCC--CCCcCcCHHHHHHHhCCCHHHHH----HHHHHHHH
Confidence 35544443 34558 69999999999999999 88988875
No 392
>COG2973 TrpR Trp operon repressor [Transcription]
Probab=55.07 E-value=30 Score=31.11 Aligned_cols=45 Identities=31% Similarity=0.410 Sum_probs=32.5
Q ss_pred cCCHHHHHHHHHHHhcC----CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 007404 541 TLNPRERQVVRWRFGLE----DGRMKTLQEIGELMGVSRERIRQIESSAFRKLK 590 (605)
Q Consensus 541 ~L~~rER~VL~LRyGl~----dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR 590 (605)
-|++.||+-+..|+-.- +| .+|.+||++.||+|-.+|- |+=.-|+
T Consensus 37 lLTpdEReal~~Rv~Iv~eLL~g-e~sQREi~~~LgvsiAtIT----RGSN~LK 85 (103)
T COG2973 37 LLTPDEREALGTRVRIVEELLRG-ELSQREIAQKLGVSIATIT----RGSNSLK 85 (103)
T ss_pred HcCHhHHHHHHHHHHHHHHHHhc-cccHHHHHHHhCcchhhhc----cchhhhc
Confidence 37888888776666431 12 2999999999999998886 5544444
No 393
>PRK09726 antitoxin HipB; Provisional
Probab=54.95 E-value=21 Score=30.75 Aligned_cols=23 Identities=22% Similarity=0.409 Sum_probs=21.9
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q 007404 562 KTLQEIGELMGVSRERIRQIESS 584 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~R 584 (605)
+|..|+|+.+|||+.+|+++++.
T Consensus 26 ltq~elA~~~gvs~~tis~~e~g 48 (88)
T PRK09726 26 WTQSELAKKIGIKQATISNFENN 48 (88)
T ss_pred CCHHHHHHHHCcCHHHHHHHHCC
Confidence 99999999999999999999884
No 394
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=54.62 E-value=23 Score=36.28 Aligned_cols=41 Identities=22% Similarity=0.265 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 007404 544 PRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFR 587 (605)
Q Consensus 544 ~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALk 587 (605)
+|++.|+.+-.. ....+.+||++.||||..|||..+..--.
T Consensus 4 ~R~~~Il~~l~~---~~~~~~~eLa~~l~VS~~TiRRdL~~L~~ 44 (240)
T PRK10411 4 ARQQAIVDLLLN---HTSLTTEALAEQLNVSKETIRRDLNELQT 44 (240)
T ss_pred HHHHHHHHHHHH---cCCCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 566667665432 23599999999999999999988876433
No 395
>smart00862 Trans_reg_C Transcriptional regulatory protein, C terminal. This domain is almost always found associated with the response regulator receiver domain. It may play a role in DNA binding.
Probab=54.51 E-value=41 Score=27.22 Aligned_cols=50 Identities=22% Similarity=0.276 Sum_probs=36.0
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHH------CCCHHHHHHHHHHHHHHHHh
Q 007404 541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELM------GVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~L------GISrerVRqie~RALkKLR~ 591 (605)
.|+++|..+|.+- ....|...|.++|.+.+ ..+..+|++...+-.++|..
T Consensus 5 ~Lt~~e~~lL~~L-~~~~~~~vs~~~l~~~lw~~~~~~~~~~~l~~~i~~LR~~l~~ 60 (78)
T smart00862 5 KLTPKEFRLLELL-LRNPGRVVSREELLEAVWGDDDDDVDDNTLDVHISRLRKKLED 60 (78)
T ss_pred ecCHHHHHHHHHH-HhCCCCccCHHHHHHHHcCCCCCCCccchHHHHHHHHHHHHhc
Confidence 4789999977654 34456689999999986 35667777666666666654
No 396
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=54.43 E-value=14 Score=30.31 Aligned_cols=24 Identities=21% Similarity=0.184 Sum_probs=19.1
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
Q 007404 560 RMKTLQEIGELMGVSRERIRQIES 583 (605)
Q Consensus 560 ~~~Tl~EIAe~LGISrerVRqie~ 583 (605)
.|.|-.|||+.+|+|..+||.++.
T Consensus 14 ~p~~T~eiA~~~gls~~~aR~yL~ 37 (62)
T PF04703_consen 14 GPLKTREIADALGLSIYQARYYLE 37 (62)
T ss_dssp S-EEHHHHHHHHTS-HHHHHHHHH
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Confidence 459999999999999999996543
No 397
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=54.24 E-value=16 Score=37.22 Aligned_cols=38 Identities=24% Similarity=0.336 Sum_probs=29.3
Q ss_pred HHHHHHHhcCCCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 548 QVVRWRFGLEDGRMK-TLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 548 ~VL~LRyGl~dg~~~-Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
.|+.-.|. .|..+ +-.|+|+.||||+..|| .||+.|..
T Consensus 14 ~I~~g~l~--pG~~LpsE~eLae~~gVSRtpVR----EAL~~Le~ 52 (253)
T PRK10421 14 LIEEKNLE--AGMKLPAERQLAMQLGVSRNSLR----EALAKLVS 52 (253)
T ss_pred HHHcCCCC--CCCcCCCHHHHHHHhCCCHHHHH----HHHHHHHH
Confidence 35544443 34557 68999999999999999 88988875
No 398
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=53.64 E-value=25 Score=36.22 Aligned_cols=42 Identities=21% Similarity=0.239 Sum_probs=29.3
Q ss_pred HHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 546 ERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 546 ER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
+|-+-.|.+.-+.+.+.|+.||++.+|+++.+|. |.++.|.+
T Consensus 11 ~ral~iL~~l~~~~~~ls~~eia~~lgl~kstv~----RlL~tL~~ 52 (263)
T PRK09834 11 SRGLMVLRALNRLDGGATVGLLAELTGLHRTTVR----RLLETLQE 52 (263)
T ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence 4444445544444456999999999999999999 44555543
No 399
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=53.30 E-value=22 Score=36.79 Aligned_cols=38 Identities=11% Similarity=0.189 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 007404 544 PRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS 584 (605)
Q Consensus 544 ~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~R 584 (605)
+|++.|+.+---. ...+..|+|+.||||+.|||+-+..
T Consensus 5 eR~~~Il~~L~~~---~~v~v~eLa~~l~VS~~TIRRDL~~ 42 (256)
T PRK10434 5 QRQAAILEYLQKQ---GKTSVEELAQYFDTTGTTIRKDLVI 42 (256)
T ss_pred HHHHHHHHHHHHc---CCEEHHHHHHHHCCCHHHHHHHHHH
Confidence 4666666654322 2489999999999999999988776
No 400
>PF05732 RepL: Firmicute plasmid replication protein (RepL); InterPro: IPR008813 This entry consists of proteins thought to be involved in plasmid replication. ; GO: 0006260 DNA replication, 0006276 plasmid maintenance
Probab=53.00 E-value=41 Score=32.81 Aligned_cols=53 Identities=26% Similarity=0.429 Sum_probs=35.3
Q ss_pred HHHHHhcCCHHHHHHHHHHHhcCC---CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 535 LEKVLDTLNPRERQVVRWRFGLED---GRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 535 L~~aL~~L~~rER~VL~LRyGl~d---g~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
+...++-+..+.-.||.+-...-| --.+|+++||+.+|+|+.||. |+++.|.+
T Consensus 46 i~~~l~l~g~k~~~Vl~~il~~~d~~N~v~~t~~~ia~~l~iS~~Tv~----r~ik~L~e 101 (165)
T PF05732_consen 46 IIKVLDLIGNKAFRVLMYILENMDKDNAVVATQKEIAEKLGISKPTVS----RAIKELEE 101 (165)
T ss_pred HHHHhhhhchhHHHHHHHHHHhcCCCCeEEeeHHHHHHHhCCCHHHHH----HHHHHHHh
Confidence 334445455555555544322111 234799999999999999998 89999886
No 401
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=52.94 E-value=27 Score=31.70 Aligned_cols=39 Identities=28% Similarity=0.427 Sum_probs=32.9
Q ss_pred hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 007404 540 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS 584 (605)
Q Consensus 540 ~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~R 584 (605)
..|++.|-..|+-. ++ +|..+-|..||+|.++|+.++..
T Consensus 42 ~~ls~~eIk~iRe~--~~----lSQ~vFA~~L~vs~~Tv~~WEqG 80 (104)
T COG2944 42 KTLSPTEIKAIREK--LG----LSQPVFARYLGVSVSTVRKWEQG 80 (104)
T ss_pred CCCCHHHHHHHHHH--hC----CCHHHHHHHHCCCHHHHHHHHcC
Confidence 56898886666655 44 89999999999999999999975
No 402
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=52.55 E-value=38 Score=32.86 Aligned_cols=31 Identities=23% Similarity=0.399 Sum_probs=24.9
Q ss_pred CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 557 EDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 557 ~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
.++.+.|.++||+.+|+|..-+. +.+.+|++
T Consensus 21 ~~~~~vs~~eIA~~~~ip~~~l~----kIl~~L~~ 51 (164)
T PRK10857 21 SEAGPVPLADISERQGISLSYLE----QLFSRLRK 51 (164)
T ss_pred CCCCcCcHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence 35568999999999999999888 44556655
No 403
>COG1737 RpiR Transcriptional regulators [Transcription]
Probab=52.33 E-value=21 Score=37.30 Aligned_cols=51 Identities=22% Similarity=0.404 Sum_probs=39.8
Q ss_pred HHHHHHHHHhcCCHHHHHHHHHHHhcCCC---CCCCHHHHHHHHCCCHHHHHHHHH
Q 007404 531 MKEDLEKVLDTLNPRERQVVRWRFGLEDG---RMKTLQEIGELMGVSRERIRQIES 583 (605)
Q Consensus 531 l~~~L~~aL~~L~~rER~VL~LRyGl~dg---~~~Tl~EIAe~LGISrerVRqie~ 583 (605)
+...|......|++.||.|-.+- +++. .-+|.+|||+..|||+.||-.--+
T Consensus 5 l~~~I~~~~~~Lt~~er~iA~yi--l~~~~~~~~~si~elA~~a~VS~aTv~Rf~~ 58 (281)
T COG1737 5 LLERIRERYDSLTKSERKIADYI--LANPDEVALLSIAELAERAGVSPATVVRFAR 58 (281)
T ss_pred HHHHHHHHHhcCCHHHHHHHHHH--HhCHHHHHHHHHHHHHHHhCCCHHHHHHHHH
Confidence 45678888999999999998653 4322 238999999999999999974433
No 404
>COG4465 CodY Pleiotropic transcriptional repressor [Transcription]
Probab=52.22 E-value=53 Score=33.69 Aligned_cols=55 Identities=27% Similarity=0.398 Sum_probs=44.3
Q ss_pred HHHHHHHhcCCHHHHHHHHHHHhcCCCC--CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 533 EDLEKVLDTLNPRERQVVRWRFGLEDGR--MKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 533 ~~L~~aL~~L~~rER~VL~LRyGl~dg~--~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
..+.-+++.|+--|.+.+...|+.-||. -+.-.-||++.||+++-|= .||+||-.
T Consensus 174 t~V~mAi~tLSYSEleAve~I~eELdG~EG~lvASkiADrvGITRSVIV----NALRKlES 230 (261)
T COG4465 174 TVVQMAISTLSYSELEAVEHIFEELDGNEGLLVASKIADRVGITRSVIV----NALRKLES 230 (261)
T ss_pred HHHHHHHhhccHHHHHHHHHHHHhcCCccceeeehhhhhhhCchHHHHH----HHHHHhhh
Confidence 3456678899999999999999876653 3688899999999976655 88888864
No 405
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=52.17 E-value=24 Score=36.70 Aligned_cols=25 Identities=8% Similarity=0.138 Sum_probs=21.2
Q ss_pred CCCCCCHHHHHHHHCCCHHHHHHHH
Q 007404 558 DGRMKTLQEIGELMGVSRERIRQIE 582 (605)
Q Consensus 558 dg~~~Tl~EIAe~LGISrerVRqie 582 (605)
.+.++|+.|||+.+|+++.+|..++
T Consensus 37 ~~~~~tl~eIa~~lglpkStv~RlL 61 (271)
T PRK10163 37 SGGSSSVSDISLNLDLPLSTTFRLL 61 (271)
T ss_pred CCCCcCHHHHHHHHCcCHHHHHHHH
Confidence 4456999999999999999999544
No 406
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=52.06 E-value=31 Score=29.92 Aligned_cols=38 Identities=24% Similarity=0.406 Sum_probs=31.0
Q ss_pred CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 007404 542 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIE 582 (605)
Q Consensus 542 L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie 582 (605)
|++.|..||...+..++ .+..+||+.+++++.+|.+++
T Consensus 20 lt~~q~~~L~~l~~~~~---~~~~~la~~l~i~~~~vt~~l 57 (126)
T COG1846 20 LTPPQYQVLLALYEAGG---ITVKELAERLGLDRSTVTRLL 57 (126)
T ss_pred CCHHHHHHHHHHHHhCC---CcHHHHHHHHCCCHHHHHHHH
Confidence 99999999988776653 233999999999999999443
No 407
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.
Probab=52.03 E-value=36 Score=31.68 Aligned_cols=44 Identities=18% Similarity=0.240 Sum_probs=33.1
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHH----CCCHHHHHHHHHHHHH
Q 007404 541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELM----GVSRERIRQIESSAFR 587 (605)
Q Consensus 541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~L----GISrerVRqie~RALk 587 (605)
.|++.|.+|+..-+..+ +.|..||.+.| |++..||...+.|-.+
T Consensus 1 ~Lt~~E~~VM~vlW~~~---~~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~ 48 (130)
T TIGR02698 1 SISDAEWEVMRVVWTLG---ETTSRDIIRILAEKKDWSDSTIKTLLGRLVD 48 (130)
T ss_pred CCCHHHHHHHHHHHcCC---CCCHHHHHHHHhhccCCcHHHHHHHHHHHHH
Confidence 37899999987765332 48999977776 7999999976665443
No 408
>PRK10643 DNA-binding transcriptional regulator BasR; Provisional
Probab=51.78 E-value=16 Score=34.91 Aligned_cols=49 Identities=12% Similarity=0.011 Sum_probs=36.2
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHH-----HCCCHHHHHHHHHHHHHHHH
Q 007404 541 TLNPRERQVVRWRFGLEDGRMKTLQEIGEL-----MGVSRERIRQIESSAFRKLK 590 (605)
Q Consensus 541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~-----LGISrerVRqie~RALkKLR 590 (605)
.|+++|.+|+.+..- .-|...+.++|.+. ++++..+|+.+.++.++||.
T Consensus 149 ~Lt~~E~~il~~l~~-~~g~~~~~~~~~~~~~~~~~~~~~~tv~~~i~~lr~Kl~ 202 (222)
T PRK10643 149 ILTPKEFALLSRLML-KAGSPVHREILYQDIYNWDDEPSSNTLEVHIHNLRDKVG 202 (222)
T ss_pred ecCHHHHHHHHHHHh-CCCceEcHHHHHHHhcCCCCCCCcCCHHHHHHHHHHhCC
Confidence 599999999987543 23433455555543 58999999999999999985
No 409
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=51.75 E-value=15 Score=36.25 Aligned_cols=24 Identities=25% Similarity=0.387 Sum_probs=21.8
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHH
Q 007404 562 KTLQEIGELMGVSRERIRQIESSA 585 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~RA 585 (605)
||..|||+.+|.|+.|||+++.-.
T Consensus 62 ~Ti~EIAeelG~TeqTir~hlkge 85 (182)
T COG1318 62 MTISEIAEELGRTEQTVRNHLKGE 85 (182)
T ss_pred CcHHHHHHHhCCCHHHHHHHHhcc
Confidence 999999999999999999887643
No 410
>PF08535 KorB: KorB domain; InterPro: IPR013741 This entry contains several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon []. This domain includes the DNA-binding HTH motif []. ; PDB: 1R71_C.
Probab=51.69 E-value=13 Score=32.29 Aligned_cols=22 Identities=27% Similarity=0.291 Sum_probs=16.4
Q ss_pred CCHHHHHHHHCCCHHHHHHHHH
Q 007404 562 KTLQEIGELMGVSRERIRQIES 583 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~ 583 (605)
+|..|||+.+|.|+..|.+++.
T Consensus 4 ~tq~eIA~~lGks~s~Vs~~l~ 25 (93)
T PF08535_consen 4 WTQEEIAKRLGKSRSWVSNHLA 25 (93)
T ss_dssp --HHHHHHHTT--HHHHHHHHG
T ss_pred CCHHHHHHHHCCCHHHHHHHHH
Confidence 8999999999999999997764
No 411
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=51.61 E-value=27 Score=36.00 Aligned_cols=37 Identities=16% Similarity=0.176 Sum_probs=27.3
Q ss_pred HHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 007404 545 RERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS 584 (605)
Q Consensus 545 rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~R 584 (605)
|++.|+.+ ... ....+.+||++.||||..|||..+..
T Consensus 6 R~~~Il~~--l~~-~~~~~~~ela~~l~vS~~TirRdL~~ 42 (251)
T PRK13509 6 RHQILLEL--LAQ-LGFVTVEKVIERLGISPATARRDINK 42 (251)
T ss_pred HHHHHHHH--HHH-cCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 44445443 332 23489999999999999999988775
No 412
>PRK11569 transcriptional repressor IclR; Provisional
Probab=51.14 E-value=24 Score=36.62 Aligned_cols=31 Identities=13% Similarity=0.212 Sum_probs=23.9
Q ss_pred HHHhcCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 007404 552 WRFGLEDGRMKTLQEIGELMGVSRERIRQIE 582 (605)
Q Consensus 552 LRyGl~dg~~~Tl~EIAe~LGISrerVRqie 582 (605)
|.++-..+.++|+.|||+.+|+++.||..++
T Consensus 34 L~~l~~~~~~~~lseia~~lglpksTv~RlL 64 (274)
T PRK11569 34 LEWIAESNGSVALTELAQQAGLPNSTTHRLL 64 (274)
T ss_pred HHHHHhCCCCcCHHHHHHHHCcCHHHHHHHH
Confidence 3333344567999999999999999999544
No 413
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=50.37 E-value=25 Score=32.58 Aligned_cols=23 Identities=22% Similarity=0.234 Sum_probs=21.7
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q 007404 562 KTLQEIGELMGVSRERIRQIESS 584 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~R 584 (605)
+|..++|+.+|||+.+|+++++.
T Consensus 19 ltq~~lA~~~gvs~~~is~~E~g 41 (135)
T PRK09706 19 LSQRSLAKAVKVSHVSISQWERD 41 (135)
T ss_pred CCHHHHHHHhCCCHHHHHHHHcC
Confidence 99999999999999999999865
No 414
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=50.31 E-value=30 Score=33.30 Aligned_cols=25 Identities=16% Similarity=0.274 Sum_probs=20.9
Q ss_pred CCCCCCHHHHHHHHCCCHHHHHHHH
Q 007404 558 DGRMKTLQEIGELMGVSRERIRQIE 582 (605)
Q Consensus 558 dg~~~Tl~EIAe~LGISrerVRqie 582 (605)
++.+....+||+.|||++.+|.+.+
T Consensus 21 ~~~~~~~~diA~~L~Vsp~sVt~ml 45 (154)
T COG1321 21 EKGFARTKDIAERLKVSPPSVTEML 45 (154)
T ss_pred ccCcccHHHHHHHhCCCcHHHHHHH
Confidence 4456899999999999999998443
No 415
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=50.13 E-value=51 Score=32.55 Aligned_cols=51 Identities=24% Similarity=0.314 Sum_probs=32.2
Q ss_pred HHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 533 EDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 533 ~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
..+..++. -++....||..-.- .| +.|-+|||+.|||+...||++ |.+|..
T Consensus 12 ~~l~~~~~-~~~~~~~Vl~~L~~--~g-~~tdeeLA~~Lgi~~~~VRk~----L~~L~e 62 (178)
T PRK06266 12 KVLFEIME-GDEEGFEVLKALIK--KG-EVTDEEIAEQTGIKLNTVRKI----LYKLYD 62 (178)
T ss_pred HHHHHHhc-CCccHhHHHHHHHH--cC-CcCHHHHHHHHCCCHHHHHHH----HHHHHH
Confidence 34444443 24444555554332 22 499999999999999999954 555543
No 416
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=49.94 E-value=29 Score=31.61 Aligned_cols=52 Identities=17% Similarity=0.181 Sum_probs=43.9
Q ss_pred hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 007404 540 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT 595 (605)
Q Consensus 540 ~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~ 595 (605)
.+|.+-||-...-+|-.= +|-+|||-.+.++..+|..+...-..|.|+.-+.
T Consensus 27 ~QLkELErvF~ETHYPDI----YTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~ 78 (125)
T KOG0484|consen 27 AQLKELERVFAETHYPDI----YTREEIALKIDLTEARVQVWFQNRRAKFRKQERA 78 (125)
T ss_pred HHHHHHHHHHHhhcCCcc----hhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHH
Confidence 467778887777777544 9999999999999999999999999999986553
No 417
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=49.92 E-value=33 Score=27.48 Aligned_cols=25 Identities=20% Similarity=0.408 Sum_probs=22.2
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 007404 562 KTLQEIGELMGVSRERIRQIESSAF 586 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~RAL 586 (605)
.|+++||+.+|+|...+.++..+..
T Consensus 2 ~~~~~la~~~~~s~~~l~~~f~~~~ 26 (84)
T smart00342 2 LTLEDLAEALGMSPRHLQRLFKKET 26 (84)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHh
Confidence 7899999999999999998887655
No 418
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=49.92 E-value=13 Score=30.52 Aligned_cols=23 Identities=22% Similarity=0.367 Sum_probs=18.4
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHH
Q 007404 561 MKTLQEIGELMGVSRERIRQIES 583 (605)
Q Consensus 561 ~~Tl~EIAe~LGISrerVRqie~ 583 (605)
..|+.|||..||+|++.|+.++.
T Consensus 14 ~~S~~eLa~~~~~s~~~ve~mL~ 36 (69)
T PF09012_consen 14 RVSLAELAREFGISPEAVEAMLE 36 (69)
T ss_dssp SEEHHHHHHHTT--HHHHHHHHH
T ss_pred CcCHHHHHHHHCcCHHHHHHHHH
Confidence 48999999999999999996654
No 419
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=49.88 E-value=32 Score=39.74 Aligned_cols=46 Identities=26% Similarity=0.260 Sum_probs=35.4
Q ss_pred CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 542 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 542 L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
|++|+++||.+- .+ .+.|.+++|+.||||..|||.-+..-=.-|++
T Consensus 2 l~~R~~~iL~~L--~~--~~~t~~~LA~~l~VS~RTIr~dI~~in~~l~~ 47 (584)
T PRK09863 2 LNERELKIVDLL--EQ--QDRSGGELAQQLGVSRRTIVRDIAYINFTLNG 47 (584)
T ss_pred hHHHHHHHHHHH--Hc--CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 578888988764 22 35999999999999999999876655444554
No 420
>PF08299 Bac_DnaA_C: Bacterial dnaA protein helix-turn-helix; InterPro: IPR013159 This entry represents the C-terminal domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication. DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) [].; GO: 0005524 ATP binding, 0043565 sequence-specific DNA binding, 0006270 DNA-dependent DNA replication initiation, 0006275 regulation of DNA replication; PDB: 2HCB_B 3R8F_C 1L8Q_A 3PVP_B 3PVV_A 1J1V_A.
Probab=49.73 E-value=38 Score=28.11 Aligned_cols=33 Identities=21% Similarity=0.202 Sum_probs=21.9
Q ss_pred HHHHHHHHHHhcCCCCCCCHHHHHHHHC-CCHHHHHHH
Q 007404 545 RERQVVRWRFGLEDGRMKTLQEIGELMG-VSRERIRQI 581 (605)
Q Consensus 545 rER~VL~LRyGl~dg~~~Tl~EIAe~LG-ISrerVRqi 581 (605)
|+--+...+-..+ +|+.|||+.|| ....+|..-
T Consensus 33 R~va~yL~r~~~~----~sl~~Ig~~fg~rdHstV~~a 66 (70)
T PF08299_consen 33 RQVAMYLARELTG----LSLSEIGRYFGGRDHSTVIHA 66 (70)
T ss_dssp HHHHHHHHHHHS-------HHHHHHHCTSSTHHHHHHH
T ss_pred HHHHHHHHHHHhC----CCHHHHHHHhCCCCHHHHHHH
Confidence 4434444454455 99999999999 999999843
No 421
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=49.71 E-value=78 Score=31.44 Aligned_cols=38 Identities=16% Similarity=0.203 Sum_probs=31.7
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHH
Q 007404 541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQI 581 (605)
Q Consensus 541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqi 581 (605)
.|++.|..||..-+..+ +.|..+||+.+++++.+|..+
T Consensus 42 gLt~~q~~iL~~L~~~~---~itq~eLa~~l~l~~sTvtr~ 79 (185)
T PRK13777 42 DLNINEHHILWIAYHLK---GASISEIAKFGVMHVSTAFNF 79 (185)
T ss_pred CCCHHHHHHHHHHHhCC---CcCHHHHHHHHCCCHhhHHHH
Confidence 69999999997766543 399999999999999998843
No 422
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=49.69 E-value=30 Score=24.66 Aligned_cols=23 Identities=39% Similarity=0.603 Sum_probs=21.0
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q 007404 562 KTLQEIGELMGVSRERIRQIESS 584 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~R 584 (605)
+|..++|+.+|++..+|.+++..
T Consensus 11 ~s~~~la~~~~i~~~~i~~~~~~ 33 (56)
T smart00530 11 LTQEELAEKLGVSRSTLSRIENG 33 (56)
T ss_pred CCHHHHHHHhCCCHHHHHHHHCC
Confidence 89999999999999999987764
No 423
>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=49.37 E-value=12 Score=32.77 Aligned_cols=25 Identities=28% Similarity=0.450 Sum_probs=22.1
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 007404 562 KTLQEIGELMGVSRERIRQIESSAF 586 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~RAL 586 (605)
+|..|+|+.+|||..|+|-.+...+
T Consensus 1 ~ti~eva~~~gvs~~tLRyye~~Gl 25 (96)
T cd04768 1 LTIGEFAKLAGVSIRTLRHYDDIGL 25 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999999887744
No 424
>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., PubMed:15231786). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations
Probab=49.30 E-value=93 Score=34.89 Aligned_cols=24 Identities=25% Similarity=0.267 Sum_probs=21.1
Q ss_pred CCCCHHHHHHhcCCCHHHHHHHHh
Q 007404 467 RHPNNEEVAEATGLSMKRLHAVLL 490 (605)
Q Consensus 467 r~PT~eEIAe~lgis~e~V~~~l~ 490 (605)
++-|..+||+.+|+.+.+|..+..
T Consensus 317 kPLtlkdiA~~lglheSTVSRav~ 340 (429)
T TIGR02395 317 KPLTLREVAEELGLHESTISRAIN 340 (429)
T ss_pred cCCcHHHHHHHhCCCccchhhhhc
Confidence 455999999999999999998874
No 425
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=49.20 E-value=21 Score=36.98 Aligned_cols=38 Identities=24% Similarity=0.324 Sum_probs=29.3
Q ss_pred CHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 007404 543 NPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES 583 (605)
Q Consensus 543 ~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~ 583 (605)
.+|.+.|+.+---.+ ..+.+|+++.||||..|||.=+.
T Consensus 4 ~eR~~~Il~~l~~~g---~v~v~eLa~~~~VS~~TIRRDL~ 41 (253)
T COG1349 4 EERHQKILELLKEKG---KVSVEELAELFGVSEMTIRRDLN 41 (253)
T ss_pred HHHHHHHHHHHHHcC---cEEHHHHHHHhCCCHHHHHHhHH
Confidence 357777887754332 38999999999999999997443
No 426
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=49.19 E-value=41 Score=30.71 Aligned_cols=47 Identities=17% Similarity=0.299 Sum_probs=38.1
Q ss_pred HhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 007404 539 LDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKL 589 (605)
Q Consensus 539 L~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKL 589 (605)
++.|++.|-+.+++++--- =+++||-..+|+|--+||..+...|++|
T Consensus 39 F~~Lt~d~LeFv~lf~r~R----GnlKEvEr~lg~sYptvR~kld~vlram 85 (122)
T COG3877 39 FEYLTSDQLEFVELFLRCR----GNLKEVERELGISYPTVRTKLDEVLRAM 85 (122)
T ss_pred ccccCHhHhHHHHHHHHHc----cCHHHHHHHHCCccHHHHHHHHHHHHHc
Confidence 3567888878777766554 3899999999999999998888777765
No 427
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=49.13 E-value=22 Score=36.21 Aligned_cols=37 Identities=22% Similarity=0.136 Sum_probs=28.4
Q ss_pred HHHHHHhcCCCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 549 VVRWRFGLEDGRMK-TLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 549 VL~LRyGl~dg~~~-Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
|+...|. .|..+ |-.+||+.||||+..|| .||+.|..
T Consensus 21 I~~g~l~--pG~~LpsE~eLae~~gVSRtpVR----EAL~~L~~ 58 (253)
T PRK11523 21 IEQGVYL--VGDKLPAERFIADEKNVSRTVVR----EAIIMLEV 58 (253)
T ss_pred HHcCCCC--CCCCCCCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 4444443 34557 58899999999999999 88888865
No 428
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=48.76 E-value=26 Score=25.65 Aligned_cols=24 Identities=25% Similarity=0.293 Sum_probs=17.1
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHH
Q 007404 561 MKTLQEIGELMGVSRERIRQIESS 584 (605)
Q Consensus 561 ~~Tl~EIAe~LGISrerVRqie~R 584 (605)
+.|+.+||+.+|+|+...+++.++
T Consensus 8 ~~~l~~iA~~~g~S~~~f~r~Fk~ 31 (42)
T PF00165_consen 8 KLTLEDIAEQAGFSPSYFSRLFKK 31 (42)
T ss_dssp S--HHHHHHHHTS-HHHHHHHHHH
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHH
Confidence 499999999999999988855443
No 429
>PF00486 Trans_reg_C: Transcriptional regulatory protein, C terminal; InterPro: IPR001867 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. This entry represents a domain that is almost always found associated with the response regulator receiver domain (see IPR001789 from INTERPRO). It may play a role in DNA binding [].; GO: 0000156 two-component response regulator activity, 0003677 DNA binding, 0000160 two-component signal transduction system (phosphorelay), 0006355 regulation of transcription, DNA-dependent; PDB: 2K4J_A 2JPB_A 1ODD_A 1OPC_A 1KGS_A 2PMU_E 2JZY_A 1GXP_B 1QQI_A 2Z33_A ....
Probab=48.65 E-value=44 Score=27.06 Aligned_cols=51 Identities=24% Similarity=0.301 Sum_probs=39.7
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHC-----CCHHHHHHHHHHHHHHHHhH
Q 007404 541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMG-----VSRERIRQIESSAFRKLKNK 592 (605)
Q Consensus 541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LG-----ISrerVRqie~RALkKLR~~ 592 (605)
.|+++|..+|.+-. ...+++.|.++|.+.+- .+..+|++.+.+-.+||+..
T Consensus 5 ~Lt~~e~~lL~~L~-~~~~~~vs~~~l~~~~w~~~~~~~~~~l~~~I~rLR~kL~~~ 60 (77)
T PF00486_consen 5 KLTPKEFRLLELLL-RNPGRVVSREELIEALWGDEEDVSDNSLDVHISRLRKKLEDA 60 (77)
T ss_dssp ESSHHHHHHHHHHH-HTTTSEEEHHHHHHHHTSSSSTTCTHHHHHHHHHHHHHHHSS
T ss_pred ecCHHHHHHHHHHH-hCCCCCCCHHHhCChhhhcccccchhhHHHHHHHHHHHHhhc
Confidence 48999999998654 45678899999999774 67788887777777777653
No 430
>PF08006 DUF1700: Protein of unknown function (DUF1700); InterPro: IPR012963 This family contains many hypothetical bacterial proteins and two putative membrane proteins (Q6GFD0 from SWISSPROT and Q6G806 from SWISSPROT).
Probab=48.59 E-value=48 Score=32.27 Aligned_cols=57 Identities=26% Similarity=0.283 Sum_probs=43.4
Q ss_pred HHHHHHHHHHHHhcCCHHHHHHHHHHHhc---CC-CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 007404 528 KKFMKEDLEKVLDTLNPRERQVVRWRFGL---ED-GRMKTLQEIGELMGVSRERIRQIESS 584 (605)
Q Consensus 528 ~~el~~~L~~aL~~L~~rER~VL~LRyGl---~d-g~~~Tl~EIAe~LGISrerVRqie~R 584 (605)
+++..+.|+..|..||+.|++=+.-+|-. +. .+.+|-+||-+.||=+++-++++...
T Consensus 3 k~efL~~L~~~L~~lp~~e~~e~l~~Y~e~f~d~~~~G~sEeeii~~LG~P~~iA~~i~~~ 63 (181)
T PF08006_consen 3 KNEFLNELEKYLKKLPEEEREEILEYYEEYFDDAGEEGKSEEEIIAELGSPKEIAREILAE 63 (181)
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhCCCCHHHHHHHcCCHHHHHHHHHHh
Confidence 34556778899999999998866554433 21 23489999999999999999988754
No 431
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.
Probab=48.34 E-value=42 Score=31.13 Aligned_cols=30 Identities=33% Similarity=0.448 Sum_probs=24.4
Q ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 558 DGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 558 dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
++++.|.+|||+.++||..-|++ .+.+|++
T Consensus 22 ~~~~~s~~~ia~~~~ip~~~l~k----il~~L~~ 51 (135)
T TIGR02010 22 ETGPVTLADISERQGISLSYLEQ----LFAKLRK 51 (135)
T ss_pred CCCcCcHHHHHHHHCcCHHHHHH----HHHHHHH
Confidence 45689999999999999999994 4556655
No 432
>cd00383 trans_reg_C Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and a response regulator. The former autophosphorylates in a histidine residue on detecting an external stimulus. The phosphate is then transferred to an invariant aspartate residue in a highly conserved receiver domain of the response regulator. Phosphorylation activates a variable effector domain of the response regulator, which triggers the cellular response. The C-terminal effector domain contains DNA and RNA polymerase binding sites. Several dimers or monomers bind head to tail to small tandem repeats upstream of the genes. The RNA polymerase binding sites interact with the alpha or sigma subunite of RNA polymerase.
Probab=48.28 E-value=42 Score=28.27 Aligned_cols=49 Identities=20% Similarity=0.236 Sum_probs=35.9
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHC-----CCHHHHHHHHHHHHHHHH
Q 007404 541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMG-----VSRERIRQIESSAFRKLK 590 (605)
Q Consensus 541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LG-----ISrerVRqie~RALkKLR 590 (605)
.|+++|..+|.+-. ..-|+..|.++|.+.+. .+..++++.+.+-.+||.
T Consensus 23 ~Lt~~e~~lL~~L~-~~~~~~vs~~~l~~~lw~~~~~~~~~~l~~~I~rLRkkl~ 76 (95)
T cd00383 23 ELTPKEFELLELLA-RNPGRVLSREQLLEAVWGDDYDVDDRTVDVHISRLRKKLE 76 (95)
T ss_pred EeCHHHHHHHHHHH-hCCCCcCCHHHHHHHhcCCCCCCCcccHHHHHHHHHHHhc
Confidence 48999999998754 44678899999999884 566667666555555554
No 433
>PF11662 DUF3263: Protein of unknown function (DUF3263); InterPro: IPR021678 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=48.23 E-value=67 Score=27.69 Aligned_cols=44 Identities=23% Similarity=0.329 Sum_probs=34.1
Q ss_pred cCCHHHHHHHHHH--HhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 007404 541 TLNPRERQVVRWR--FGLEDGRMKTLQEIGELMGVSRERIRQIESSAF 586 (605)
Q Consensus 541 ~L~~rER~VL~LR--yGl~dg~~~Tl~EIAe~LGISrerVRqie~RAL 586 (605)
.|+++++.||.+- ..-.+| -+-+.|-+.||+|.-+--|+++.-+
T Consensus 2 ~Ls~~d~~iL~fE~~ww~~~G--aKe~aIre~fGls~~rYyq~Ln~Li 47 (77)
T PF11662_consen 2 GLSDRDRAILDFERRWWRHGG--AKEEAIREEFGLSPTRYYQRLNALI 47 (77)
T ss_pred CCCHHHHHHHHHHHHhCcCCC--CcHHHHHHHHCCCHHHHHHHHHHHh
Confidence 5899999998752 222222 5788999999999999999988765
No 434
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=47.97 E-value=12 Score=28.31 Aligned_cols=21 Identities=19% Similarity=0.363 Sum_probs=18.2
Q ss_pred HHHHHHHCCCHHHHHHHHHHH
Q 007404 565 QEIGELMGVSRERIRQIESSA 585 (605)
Q Consensus 565 ~EIAe~LGISrerVRqie~RA 585 (605)
++||+.+|||+.+|+++++.-
T Consensus 1 ~~lA~~~gvs~~tvs~~l~g~ 21 (52)
T cd01392 1 KDIARAAGVSVATVSRVLNGK 21 (52)
T ss_pred CcHHHHHCcCHHHHHHHHcCC
Confidence 379999999999999988754
No 435
>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=47.28 E-value=37 Score=26.75 Aligned_cols=46 Identities=20% Similarity=0.186 Sum_probs=27.8
Q ss_pred ccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHH
Q 007404 443 LPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAV 488 (605)
Q Consensus 443 lP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~ 488 (605)
||....+.+-...+.-..|..+.-..-+..+||+.+|+++.+|+.=
T Consensus 3 Ip~~ti~RL~~Y~r~L~~l~~~G~~~vSS~~La~~~gi~~~qVRKD 48 (50)
T PF06971_consen 3 IPKATIRRLPLYLRYLEQLKEEGVERVSSQELAEALGITPAQVRKD 48 (50)
T ss_dssp -SHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHTS-HHHHHHH
T ss_pred CCHHHHHHHHHHHHHHHHHHHcCCeeECHHHHHHHHCCCHHHhccc
Confidence 3444444444444555555555445668899999999999999763
No 436
>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimil
Probab=47.22 E-value=14 Score=32.88 Aligned_cols=26 Identities=27% Similarity=0.333 Sum_probs=23.3
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH
Q 007404 562 KTLQEIGELMGVSRERIRQIESSAFR 587 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~RALk 587 (605)
+|..|+|+.+|||..++|-++...+-
T Consensus 2 ~~i~eva~~~gvs~~tLR~ye~~Gll 27 (102)
T cd04775 2 YTIGQMSRKFGVSRSTLLYYESIGLI 27 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 78999999999999999999887654
No 437
>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=47.06 E-value=28 Score=31.74 Aligned_cols=22 Identities=27% Similarity=0.437 Sum_probs=20.5
Q ss_pred CCHHHHHHHHCCCHHHHHHHHH
Q 007404 562 KTLQEIGELMGVSRERIRQIES 583 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~ 583 (605)
.|..|+|..|+||+.||..+..
T Consensus 19 ~s~~eaa~~F~VS~~Tv~~W~k 40 (119)
T PF01710_consen 19 KSIREAAKRFGVSRNTVYRWLK 40 (119)
T ss_pred chHHHHHHHhCcHHHHHHHHHH
Confidence 7999999999999999998866
No 438
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=47.02 E-value=33 Score=27.08 Aligned_cols=23 Identities=35% Similarity=0.601 Sum_probs=18.8
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q 007404 562 KTLQEIGELMGVSRERIRQIESS 584 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~R 584 (605)
+|+.++|+.+|+++.++.++++.
T Consensus 13 lt~~~~a~~~~i~~~~i~~~e~g 35 (64)
T PF12844_consen 13 LTQKDLAEKLGISRSTISKIENG 35 (64)
T ss_dssp --HHHHHHHHTS-HHHHHHHHTT
T ss_pred CCHHHHHHHHCcCHHHHHHHHCC
Confidence 99999999999999999999865
No 439
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=46.99 E-value=36 Score=29.16 Aligned_cols=32 Identities=25% Similarity=0.332 Sum_probs=26.6
Q ss_pred HHHHHHhcCCCCCCCHHHHHHHHC------CCHHHHHHHHHH
Q 007404 549 VVRWRFGLEDGRMKTLQEIGELMG------VSRERIRQIESS 584 (605)
Q Consensus 549 VL~LRyGl~dg~~~Tl~EIAe~LG------ISrerVRqie~R 584 (605)
+...|--.+ +|..++|+.+| +|..+|.++++-
T Consensus 16 lk~~R~~lG----LTQ~dvA~~lg~~~g~i~SQstISR~Es~ 53 (75)
T smart00352 16 FKQRRIKLG----FTQADVGLALGALYGPDFSQTTICRFEAL 53 (75)
T ss_pred HHHHHHHcC----CCHHHHHHHhcccccCcCCHHHHHHHHhc
Confidence 555666676 99999999999 599999998863
No 440
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=46.92 E-value=82 Score=27.91 Aligned_cols=36 Identities=11% Similarity=0.186 Sum_probs=25.6
Q ss_pred HHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 007404 544 PRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIE 582 (605)
Q Consensus 544 ~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie 582 (605)
+-|+.+|...+-..+ -...+.|+.||||+.+++..+
T Consensus 54 ~~Er~~i~~aL~~~~---gn~s~AAr~LGIsRsTL~rKL 89 (95)
T PRK00430 54 EVEAPLLDMVMQYTR---GNQTRAALMLGINRGTLRKKL 89 (95)
T ss_pred HHHHHHHHHHHHHcC---CCHHHHHHHhCCCHHHHHHHH
Confidence 346666665554433 478899999999999988443
No 441
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
Probab=46.26 E-value=42 Score=24.04 Aligned_cols=23 Identities=43% Similarity=0.621 Sum_probs=21.0
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q 007404 562 KTLQEIGELMGVSRERIRQIESS 584 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~R 584 (605)
+|..++|..+|+|+.+|.+++..
T Consensus 13 ~s~~~~a~~~~~~~~~v~~~~~g 35 (58)
T cd00093 13 LTQEELAEKLGVSRSTISRIENG 35 (58)
T ss_pred CCHHHHHHHHCCCHHHHHHHHcC
Confidence 89999999999999999987764
No 442
>PF06413 Neugrin: Neugrin; InterPro: IPR010487 This family contains mouse and human neugrin proteins. Neugrin and m-neugrin are mainly expressed in neurons in the nervous system, and are thought to play an important role in the process of neuronal differentiation []. Homologues of neugrin are found in fungi suggesting they have a alternative role or more than one function.
Probab=46.17 E-value=33 Score=35.21 Aligned_cols=42 Identities=24% Similarity=0.284 Sum_probs=33.4
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 007404 541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES 583 (605)
Q Consensus 541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~ 583 (605)
.|+..+.+-|++-+-.+ .+.+|...+|+.|+||++.||.|+.
T Consensus 10 ~Ls~~~~~~ir~L~~~~-p~~~t~~~Lae~F~vspe~irrILk 51 (225)
T PF06413_consen 10 KLSREAMEQIRYLHKED-PEEWTVERLAESFKVSPEAIRRILK 51 (225)
T ss_pred CCCHHHHHHHHHHHHhC-ccccCHHHHHhhCCCCHHHHHHHHh
Confidence 57777777777665443 3458999999999999999998875
No 443
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=45.76 E-value=38 Score=33.43 Aligned_cols=37 Identities=24% Similarity=0.219 Sum_probs=26.4
Q ss_pred HHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 007404 544 PRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES 583 (605)
Q Consensus 544 ~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~ 583 (605)
+|++.|+.+--- ....+..++++.||+|..|||.-+.
T Consensus 7 ~R~~~Il~~l~~---~~~~~~~~La~~~~vS~~TiRRDl~ 43 (185)
T PRK04424 7 ERQKALQELIEE---NPFITDEELAEKFGVSIQTIRLDRM 43 (185)
T ss_pred HHHHHHHHHHHH---CCCEEHHHHHHHHCcCHHHHHHHHH
Confidence 355556554332 2348999999999999999996543
No 444
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=45.69 E-value=27 Score=39.75 Aligned_cols=45 Identities=16% Similarity=0.230 Sum_probs=32.0
Q ss_pred HHhcCCHHHHHHHHH---------HHhcCCC---CCCCHHHHHHHHCCCHHHHHHHH
Q 007404 538 VLDTLNPRERQVVRW---------RFGLEDG---RMKTLQEIGELMGVSRERIRQIE 582 (605)
Q Consensus 538 aL~~L~~rER~VL~L---------RyGl~dg---~~~Tl~EIAe~LGISrerVRqie 582 (605)
++..|..|.+.|++. -|+..|. +|+|+++||+.+|+..+||+...
T Consensus 334 li~si~qR~~TllkV~~~Iv~~Q~~Ff~~G~~~LkPLtlkdVAe~lglHeSTVSRa~ 390 (481)
T PRK12469 334 LIRNAQQRFDTIQRVAECIVARQRDFFRYGEIALKPLVLRDVAEELGLHESTISRAT 390 (481)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccCcCCcHHHHHHHhCCCcchhhHHh
Confidence 345566666665542 3443333 89999999999999999999544
No 445
>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.
Probab=45.56 E-value=15 Score=32.98 Aligned_cols=25 Identities=28% Similarity=0.531 Sum_probs=22.5
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 007404 562 KTLQEIGELMGVSRERIRQIESSAF 586 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~RAL 586 (605)
+|..|+|+.+|||..++|..+...+
T Consensus 1 ~~i~eva~~~gvs~~tlR~ye~~Gl 25 (108)
T cd04773 1 MTIGELAHLLGVPPSTLRHWEKEGL 25 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5889999999999999999988765
No 446
>TIGR02018 his_ut_repres histidine utilization repressor, proteobacterial. This model represents a proteobacterial histidine utilization repressor. It is usually found clustered with the enzymes HutUHIG so that it can regulate its own expression as well. A number of species have several paralogs and may fine-tune the regulation according to levels of degradation intermediates such as urocanate. This family belongs to the larger GntR family of transcriptional regulators.
Probab=45.51 E-value=27 Score=35.03 Aligned_cols=26 Identities=27% Similarity=0.408 Sum_probs=23.3
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 562 KTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
-|-.|+|+.+|||+.||| +||..|.+
T Consensus 26 PsE~eLa~~~~VSR~TVR----~Al~~L~~ 51 (230)
T TIGR02018 26 PSEHELVAQYGCSRMTVN----RALRELTD 51 (230)
T ss_pred cCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 389999999999999999 88888865
No 447
>PHA00738 putative HTH transcription regulator
Probab=45.28 E-value=45 Score=30.53 Aligned_cols=35 Identities=9% Similarity=0.049 Sum_probs=25.3
Q ss_pred HHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 007404 545 RERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIE 582 (605)
Q Consensus 545 rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie 582 (605)
.=+.||.+-. .+++++..||++.+++|+.+|++++
T Consensus 13 tRr~IL~lL~---~~e~~~V~eLae~l~lSQptVS~HL 47 (108)
T PHA00738 13 LRRKILELIA---ENYILSASLISHTLLLSYTTVLRHL 47 (108)
T ss_pred HHHHHHHHHH---HcCCccHHHHHHhhCCCHHHHHHHH
Confidence 3345555432 2334999999999999999999664
No 448
>COG5625 Predicted transcription regulator containing HTH domain [Transcription]
Probab=45.09 E-value=36 Score=30.83 Aligned_cols=54 Identities=20% Similarity=0.393 Sum_probs=37.2
Q ss_pred HHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 007404 533 EDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAF 586 (605)
Q Consensus 533 ~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RAL 586 (605)
..+..+|..++-+--+|+.+.+...-+..+-..||+..||||.-+||-...--+
T Consensus 8 ~~l~~~L~~~glk~~eI~IY~lLve~~~~mri~ei~rEl~is~rtvr~~v~~l~ 61 (113)
T COG5625 8 RKLGKALEAIGLKKNEIRIYSLLVEKGRGMRIREIQRELGISERTVRAAVAVLL 61 (113)
T ss_pred HHHHHHHHHcCCCcchhhhhhHHHHhcCCchHHHHHHHHhHHHHHHHHHHHHHH
Confidence 446666766554444455555544444459999999999999999997666555
No 449
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=45.03 E-value=33 Score=35.32 Aligned_cols=38 Identities=24% Similarity=0.246 Sum_probs=27.6
Q ss_pred HHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 007404 544 PRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS 584 (605)
Q Consensus 544 ~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~R 584 (605)
+|+..|+.+- .. ....+..|+|+.||||..|||.=+..
T Consensus 7 eR~~~I~~~l--~~-~~~v~v~eLa~~~~VS~~TIRRDL~~ 44 (252)
T PRK10681 7 ERIGQLLQAL--KR-SDKLHLKDAAALLGVSEMTIRRDLNA 44 (252)
T ss_pred HHHHHHHHHH--HH-cCCCcHHHHHHHhCCCHHHHHHHHHH
Confidence 4555566553 22 22489999999999999999976654
No 450
>PRK00082 hrcA heat-inducible transcription repressor; Provisional
Probab=44.89 E-value=35 Score=36.98 Aligned_cols=44 Identities=23% Similarity=0.317 Sum_probs=33.6
Q ss_pred hcCCHHHHHHHHH--HHhcCCCCCCCHHHHHHH--HCCCHHHHHHHHH
Q 007404 540 DTLNPRERQVVRW--RFGLEDGRMKTLQEIGEL--MGVSRERIRQIES 583 (605)
Q Consensus 540 ~~L~~rER~VL~L--RyGl~dg~~~Tl~EIAe~--LGISrerVRqie~ 583 (605)
..|++|+++|+.. ..+...++|.+.+++++. +|+|..|||....
T Consensus 2 ~~l~~R~~~Il~~IV~~yi~~~~pv~s~~l~~~~~l~~S~aTIR~dm~ 49 (339)
T PRK00082 2 SMLDERQREILRAIVEDYIATGEPVGSKTLSKRYGLGVSSATIRNDMA 49 (339)
T ss_pred CccCHHHHHHHHHHHHHHHhcCCCcCHHHHHHHhCCCCChHHHHHHHH
Confidence 3588999999862 122335788999999977 9999999995443
No 451
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=44.75 E-value=16 Score=32.67 Aligned_cols=26 Identities=19% Similarity=0.244 Sum_probs=22.9
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH
Q 007404 562 KTLQEIGELMGVSRERIRQIESSAFR 587 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~RALk 587 (605)
++..|+|+.+|||..++|-++..++=
T Consensus 1 ~~i~eva~~~gis~~tlR~ye~~GLi 26 (108)
T cd01107 1 FTIGEFAKLSNLSIKALRYYDKIGLL 26 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCC
Confidence 57899999999999999999987653
No 452
>PRK06424 transcription factor; Provisional
Probab=44.68 E-value=33 Score=32.79 Aligned_cols=32 Identities=19% Similarity=0.135 Sum_probs=26.0
Q ss_pred HHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 007404 549 VVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS 584 (605)
Q Consensus 549 VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~R 584 (605)
|-.+|--.+ +|.+|+|+.+|+++.+|+++++.
T Consensus 89 Ir~lRe~~G----LSQ~eLA~~iGvs~stIskiE~G 120 (144)
T PRK06424 89 VKNARERLS----MSQADLAAKIFERKNVIASIERG 120 (144)
T ss_pred HHHHHHHcC----CCHHHHHHHhCCCHHHHHHHHCC
Confidence 333454455 99999999999999999999973
No 453
>COG4709 Predicted membrane protein [Function unknown]
Probab=44.57 E-value=59 Score=32.60 Aligned_cols=59 Identities=24% Similarity=0.268 Sum_probs=44.7
Q ss_pred HHHHHHHHHHHHhcCCHHHHHHHHHHHhc----CCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 007404 528 KKFMKEDLEKVLDTLNPRERQVVRWRFGL----EDGRMKTLQEIGELMGVSRERIRQIESSAF 586 (605)
Q Consensus 528 ~~el~~~L~~aL~~L~~rER~VL~LRyGl----~dg~~~Tl~EIAe~LGISrerVRqie~RAL 586 (605)
+.+...+|++.|+.||+.+|.=+...|-. .+...+|-+||+..||-+.+-.+++..+..
T Consensus 3 k~efL~eL~~yL~~Lp~~~r~e~m~dyeehF~~a~~~GksE~EI~~~LG~P~eiA~ei~s~~~ 65 (195)
T COG4709 3 KTEFLNELEQYLEGLPREERREIMYDYEEHFREAQEAGKSEEEIAKDLGDPKEIAAEILSERG 65 (195)
T ss_pred HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhhhhcCCCHHHHHHHhCCHHHHHHHHHHHcc
Confidence 34556778999999999998766554432 122448999999999999999998877653
No 454
>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]
Probab=44.55 E-value=36 Score=30.90 Aligned_cols=35 Identities=29% Similarity=0.420 Sum_probs=27.3
Q ss_pred HHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 007404 548 QVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS 584 (605)
Q Consensus 548 ~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~R 584 (605)
+||.-.|...-| +|..+.|+.|||++.+|..+++.
T Consensus 12 EiL~eeflep~g--lt~~~lA~~lgV~r~~is~ling 46 (104)
T COG3093 12 EILREEFLEPLG--LTQTELAEALGVTRNTISELING 46 (104)
T ss_pred HHHHHHHhcccc--CCHHHHHHHhCCCHHHHHHHHcC
Confidence 466666655312 99999999999999999988764
No 455
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=44.54 E-value=1.2e+02 Score=34.20 Aligned_cols=24 Identities=13% Similarity=0.174 Sum_probs=21.0
Q ss_pred CCCCHHHHHHhcCCCHHHHHHHHh
Q 007404 467 RHPNNEEVAEATGLSMKRLHAVLL 490 (605)
Q Consensus 467 r~PT~eEIAe~lgis~e~V~~~l~ 490 (605)
++-|..+||+.+|+.+.+|..+..
T Consensus 342 kPLtlkdvAe~lglheSTVSRav~ 365 (455)
T PRK05932 342 KPLVLKDIAEELGMHESTISRATT 365 (455)
T ss_pred cCccHHHHHHHhCCCccchhhhhc
Confidence 455899999999999999998874
No 456
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=44.54 E-value=50 Score=29.23 Aligned_cols=22 Identities=27% Similarity=0.445 Sum_probs=20.3
Q ss_pred CCHHHHHHHHCCCHHHHHHHHH
Q 007404 562 KTLQEIGELMGVSRERIRQIES 583 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~ 583 (605)
+|.++||..||+|.+.|.+++.
T Consensus 24 ls~~~ia~dL~~s~~~le~vL~ 45 (89)
T PF10078_consen 24 LSLEQIAADLGTSPEHLEQVLN 45 (89)
T ss_pred CCHHHHHHHhCCCHHHHHHHHc
Confidence 9999999999999999997764
No 457
>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF. All members of the seed alignment for this family are predicted helix-turn-helix transcriptional regulatory proteins of the broader gntR and are found associated with genes for the import and degradation of phosphonates and/or related compounds (e.g. phosphonites) with a direct C-P bond.
Probab=44.46 E-value=30 Score=34.60 Aligned_cols=26 Identities=27% Similarity=0.427 Sum_probs=23.6
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 562 KTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
-|-.|+|+.+|||+.||| +||..|.+
T Consensus 33 PsE~eLa~~~~VSR~TvR----~Al~~L~~ 58 (238)
T TIGR02325 33 PAEMQLAERFGVNRHTVR----RAIAALVE 58 (238)
T ss_pred cCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 488999999999999999 88888875
No 458
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=44.46 E-value=29 Score=35.17 Aligned_cols=25 Identities=36% Similarity=0.494 Sum_probs=22.8
Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 563 TLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 563 Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
|-.|+++.+|||+.||| +||..|..
T Consensus 31 sE~eL~~~~~VSR~TvR----~Al~~L~~ 55 (240)
T PRK09764 31 TESALQTEFGVSRVTVR----QALRQLVE 55 (240)
T ss_pred CHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 88999999999999999 88888865
No 459
>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., PubMed:15231786). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations
Probab=44.42 E-value=25 Score=39.32 Aligned_cols=23 Identities=26% Similarity=0.398 Sum_probs=21.0
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHH
Q 007404 560 RMKTLQEIGELMGVSRERIRQIE 582 (605)
Q Consensus 560 ~~~Tl~EIAe~LGISrerVRqie 582 (605)
+|+|+++||+.+|++.+||+...
T Consensus 317 kPLtlkdiA~~lglheSTVSRav 339 (429)
T TIGR02395 317 KPLTLREVAEELGLHESTISRAI 339 (429)
T ss_pred cCCcHHHHHHHhCCCccchhhhh
Confidence 79999999999999999999543
No 460
>PRK14999 histidine utilization repressor; Provisional
Probab=44.35 E-value=29 Score=35.11 Aligned_cols=26 Identities=31% Similarity=0.402 Sum_probs=23.1
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 562 KTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
-|-.|+|+.+|||+.||| +||..|..
T Consensus 37 PsE~eLa~~~gVSR~TVR----~Al~~L~~ 62 (241)
T PRK14999 37 PSEAELVAQYGFSRMTIN----RALRELTD 62 (241)
T ss_pred CCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 389999999999999999 88888765
No 461
>cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=44.05 E-value=26 Score=31.07 Aligned_cols=23 Identities=22% Similarity=0.465 Sum_probs=20.9
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q 007404 562 KTLQEIGELMGVSRERIRQIESS 584 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~R 584 (605)
+|..|+|+.+|||..++|.++..
T Consensus 1 yti~EvA~~~gVs~~tLR~ye~~ 23 (99)
T cd04765 1 FSIGEVAEILGLPPHVLRYWETE 23 (99)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHH
Confidence 57899999999999999998766
No 462
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=44.05 E-value=77 Score=30.59 Aligned_cols=42 Identities=21% Similarity=0.123 Sum_probs=29.5
Q ss_pred CHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 543 NPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 543 ~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
.+....||..-+ ..| .+|-+|||+.|||+...|| +.+.+|..
T Consensus 13 g~~~v~Vl~aL~--~~~-~~tdEeLa~~Lgi~~~~VR----k~L~~L~e 54 (158)
T TIGR00373 13 EEEVGLVLFSLG--IKG-EFTDEEISLELGIKLNEVR----KALYALYD 54 (158)
T ss_pred ChhHHHHHHHHh--ccC-CCCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 344455555433 222 4999999999999999999 66666665
No 463
>cd01105 HTH_GlnR-like Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=44.03 E-value=17 Score=31.43 Aligned_cols=25 Identities=28% Similarity=0.453 Sum_probs=22.5
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 007404 562 KTLQEIGELMGVSRERIRQIESSAF 586 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~RAL 586 (605)
+|..|+|+.+|||..++|.++.+.+
T Consensus 2 ~ti~evA~~~gvs~~tLR~ye~~Gl 26 (88)
T cd01105 2 IGIGEVSKLTGVSPRQLRYWEEKGL 26 (88)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 7899999999999999999987654
No 464
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=43.96 E-value=19 Score=36.19 Aligned_cols=37 Identities=30% Similarity=0.520 Sum_probs=29.9
Q ss_pred HHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 549 VVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 549 VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
|+..++- -|..++..+||+.||||+.-|| .||.+|-.
T Consensus 29 Il~g~l~--pG~~l~e~~La~~~gvSrtPVR----eAL~rL~~ 65 (230)
T COG1802 29 ILSGELA--PGERLSEEELAEELGVSRTPVR----EALRRLEA 65 (230)
T ss_pred HHhCCCC--CCCCccHHHHHHHhCCCCccHH----HHHHHHHH
Confidence 5555543 4567999999999999999999 88888865
No 465
>TIGR00637 ModE_repress ModE molybdate transport repressor domain. ModE is a molybdate-activated repressor of the molybdate transport operon in E. coli. It consists of the domain represented by this model and two tandem copies of mop-like domain, where Mop proteins are a family of 68-residue molybdenum-pterin binding proteins of Clostridium pasteurianum. This model also represents the full length of a pair of archaeal proteins that lack Mop-like domains. PSI-BLAST analysis shows similarity to helix-turn-helix regulatory proteins.
Probab=43.93 E-value=72 Score=28.33 Aligned_cols=42 Identities=14% Similarity=0.252 Sum_probs=29.8
Q ss_pred CHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 007404 543 NPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 593 (605)
Q Consensus 543 ~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l 593 (605)
+.++-.+|....-. -|+..-|+.||||..+|. +.+++|.+.+
T Consensus 3 ~~~~l~~~~av~~~-----gSis~AA~~L~iS~stvs----~~I~~LE~~l 44 (99)
T TIGR00637 3 DPRRVALLKAIARM-----GSISQAAKDAGISYKSAW----DYIRAMNNLS 44 (99)
T ss_pred CHHHHHHHHHHHHh-----CCHHHHHHHHCCCHHHHH----HHHHHHHHHh
Confidence 44455555555443 499999999999999999 5556665544
No 466
>PRK10955 DNA-binding transcriptional regulator CpxR; Provisional
Probab=43.83 E-value=16 Score=35.15 Aligned_cols=50 Identities=18% Similarity=0.116 Sum_probs=37.8
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCC-----HHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 541 TLNPRERQVVRWRFGLEDGRMKT-----LQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 541 ~L~~rER~VL~LRyGl~dg~~~T-----l~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
.|+++|.+||.+.. .+-|...| ..+||..++++..+|+.+..+.++||..
T Consensus 156 ~Lt~~E~~~l~~l~-~~~~~v~sr~~l~~~~~~~~~~~~~~tv~~~i~~lr~Kl~~ 210 (232)
T PRK10955 156 ELTGTEFTLLYLLA-QHLGQVVSREHLSQEVLGKRLTPFDRAIDMHISNLRRKLPD 210 (232)
T ss_pred cCCHHHHHHHHHHH-hCCCceEcHHHHHHHHhCCCCCCCCcCHHHHHHHHHHhccc
Confidence 59999999998754 33232223 4567777889999999999999999963
No 467
>PF00126 HTH_1: Bacterial regulatory helix-turn-helix protein, lysR family; InterPro: IPR000847 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, the lysR family, groups together a range of proteins, including ampR, catM, catR, cynR, cysB, gltC, iciA, ilvY, irgB, lysR, metR, mkaC, mleR, nahR, nhaR, nodD, nolR, oxyR, pssR, rbcR, syrM, tcbR, tfdS and trpI [, , , , ]. The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-termini.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3T1B_D 3SZP_A 1O7L_C 1B9N_A 1B9M_A 3FZJ_J 3FXR_B 3FXQ_A 3FXU_A 2IJL_B ....
Probab=43.59 E-value=67 Score=25.43 Aligned_cols=29 Identities=14% Similarity=0.365 Sum_probs=23.5
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404 562 KTLQEIGELMGVSRERIRQIESSAFRKLKNKKR 594 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~ 594 (605)
.++...|+.||||..+|+ +.+++|.+.+.
T Consensus 14 gs~~~AA~~l~is~~~vs----~~i~~LE~~lg 42 (60)
T PF00126_consen 14 GSISAAAEELGISQSAVS----RQIKQLEEELG 42 (60)
T ss_dssp SSHHHHHHHCTSSHHHHH----HHHHHHHHHHT
T ss_pred CCHHHHHHHhhccchHHH----HHHHHHHHHhC
Confidence 499999999999999999 56666665543
No 468
>PF00292 PAX: 'Paired box' domain; InterPro: IPR001523 The paired box is a conserved 124 amino acid N-terminal domain of unknown function that usually, but not always, precedes a homeobox domain (see IPR001356 from INTERPRO) [, ]. Paired box genes are expressed in alternate segments of the developing fruit fly, the observed grouping of segments into pairs depending on the position of the segment in the segmental array, and not on the identity of the segment as in the case of homeotic genes. This implies that the genes affect different processes from those altered by homeotic genes.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 6PAX_A 1K78_E 1MDM_A 2K27_A 1PDN_C.
Probab=43.49 E-value=52 Score=30.86 Aligned_cols=32 Identities=19% Similarity=0.128 Sum_probs=22.3
Q ss_pred HHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 007404 548 QVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS 584 (605)
Q Consensus 548 ~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~R 584 (605)
.||.|.. .+ ..-.+||..|+||...|++++.|
T Consensus 25 rIvela~-~G----~rp~~Isr~l~Vs~gcVsKIl~R 56 (125)
T PF00292_consen 25 RIVELAK-EG----VRPCDISRQLRVSHGCVSKILSR 56 (125)
T ss_dssp HHHHHHH-TT------HHHHHHHHT--HHHHHHHHHH
T ss_pred HHHHHhh-hc----CCHHHHHHHHccchhHHHHHHHH
Confidence 4666654 34 89999999999999999987765
No 469
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=43.41 E-value=40 Score=35.79 Aligned_cols=39 Identities=23% Similarity=0.284 Sum_probs=29.8
Q ss_pred HHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 007404 545 RERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAF 586 (605)
Q Consensus 545 rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RAL 586 (605)
+.++||.+.. ++...+..|||+.+|||+.+|++.+.+-.
T Consensus 5 r~~~il~~L~---~~~~~s~~~LA~~lgvsr~tV~~~l~~L~ 43 (319)
T PRK11886 5 VMLQLLSLLA---DGDFHSGEQLGEELGISRAAIWKHIQTLE 43 (319)
T ss_pred HHHHHHHHHH---cCCCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4556666543 34568999999999999999998876644
No 470
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=43.26 E-value=57 Score=28.84 Aligned_cols=39 Identities=23% Similarity=0.335 Sum_probs=27.4
Q ss_pred CCHHHHHH----HHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 007404 542 LNPRERQV----VRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES 583 (605)
Q Consensus 542 L~~rER~V----L~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~ 583 (605)
|++.|+++ |.-.|-+- ++|.++||..||+|...|..++.
T Consensus 3 Ln~eq~~~Tk~elqan~el~---~LS~~~iA~~Ln~t~~~lekil~ 45 (97)
T COG4367 3 LNPEQKQRTKQELQANFELC---PLSDEEIATALNWTEVKLEKILQ 45 (97)
T ss_pred CCHHHHHHHHHHHHHhhhhc---cccHHHHHHHhCCCHHHHHHHHH
Confidence 55555444 33334333 59999999999999999887764
No 471
>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=43.24 E-value=18 Score=31.86 Aligned_cols=25 Identities=20% Similarity=0.348 Sum_probs=22.3
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 007404 562 KTLQEIGELMGVSRERIRQIESSAF 586 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~RAL 586 (605)
+|..|+|+.+|||..++|-.+..++
T Consensus 1 ~~i~eva~~~gvs~~tlR~ye~~Gl 25 (97)
T cd04782 1 FTTGEFAKLCGISKQTLFHYDKIGL 25 (97)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5788999999999999999988765
No 472
>PF02787 CPSase_L_D3: Carbamoyl-phosphate synthetase large chain, oligomerisation domain; InterPro: IPR005480 Carbamoyl phosphate synthase (CPSase) is a heterodimeric enzyme composed of a small and a large subunit (with the exception of CPSase III, see below). CPSase catalyses the synthesis of carbamoyl phosphate from biocarbonate, ATP and glutamine (6.3.5.5 from EC) or ammonia (6.3.4.16 from EC), and represents the first committed step in pyrimidine and arginine biosynthesis in prokaryotes and eukaryotes, and in the urea cycle in most terrestrial vertebrates [, ]. CPSase has three active sites, one in the small subunit and two in the large subunit. The small subunit contains the glutamine binding site and catalyses the hydrolysis of glutamine to glutamate and ammonia. The large subunit has two homologous carboxy phosphate domains, both of which have ATP-binding sites; however, the N-terminal carboxy phosphate domain catalyses the phosphorylation of biocarbonate, while the C-terminal domain catalyses the phosphorylation of the carbamate intermediate []. The carboxy phosphate domain found duplicated in the large subunit of CPSase is also present as a single copy in the biotin-dependent enzymes acetyl-CoA carboxylase (6.4.1.2 from EC) (ACC), propionyl-CoA carboxylase (6.4.1.3 from EC) (PCCase), pyruvate carboxylase (6.4.1.1 from EC) (PC) and urea carboxylase (6.3.4.6 from EC). Most prokaryotes carry one form of CPSase that participates in both arginine and pyrimidine biosynthesis, however certain bacteria can have separate forms. The large subunit in bacterial CPSase has four structural domains: the carboxy phosphate domain 1, the oligomerisation domain, the carbamoyl phosphate domain 2 and the allosteric domain []. CPSase heterodimers from Escherichia coli contain two molecular tunnels: an ammonia tunnel and a carbamate tunnel. These inter-domain tunnels connect the three distinct active sites, and function as conduits for the transport of unstable reaction intermediates (ammonia and carbamate) between successive active sites []. The catalytic mechanism of CPSase involves the diffusion of carbamate through the interior of the enzyme from the site of synthesis within the N-terminal domain of the large subunit to the site of phosphorylation within the C-terminal domain. Eukaryotes have two distinct forms of CPSase: a mitochondrial enzyme (CPSase I) that participates in both arginine biosynthesis and the urea cycle; and a cytosolic enzyme (CPSase II) involved in pyrimidine biosynthesis. CPSase II occurs as part of a multi-enzyme complex along with aspartate transcarbamoylase and dihydroorotase; this complex is referred to as the CAD protein []. The hepatic expression of CPSase is transcriptionally regulated by glucocorticoids and/or cAMP []. There is a third form of the enzyme, CPSase III, found in fish, which uses glutamine as a nitrogen source instead of ammonia []. CPSase III is closely related to CPSase I, and is composed of a single polypeptide that may have arisen from gene fusion of the glutaminase and synthetase domains []. This entry represents the oligomerisation domain found in the large subunit of carbamoyl phosphate synthases as well as in certain other carboxy phsophate domain-containing enzymes.; GO: 0006807 nitrogen compound metabolic process; PDB: 1M6V_C 1CS0_C 1C30_E 1C3O_G 1BXR_A 1T36_E 1A9X_A 1KEE_G 1CE8_A 1JDB_H ....
Probab=43.02 E-value=1.8e+02 Score=26.95 Aligned_cols=43 Identities=30% Similarity=0.513 Sum_probs=24.5
Q ss_pred HHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 007404 534 DLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES 583 (605)
Q Consensus 534 ~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~ 583 (605)
.|......|++. .|.---..| .|-.+||..+|++.+-||++..
T Consensus 52 ~L~~~~~~~~~~---~L~~aK~~G----FsD~~IA~l~~~~e~~vr~~R~ 94 (123)
T PF02787_consen 52 ELKEYLNELDPE---LLRKAKRLG----FSDRQIARLWGVSEEEVRELRK 94 (123)
T ss_dssp HHHHHGGG--HH---HHHHHHHTT------HHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHhhccchHH---HHHHHHHcC----CCHHHHHhccCCCHHHHHHHHH
Confidence 344434455554 333333344 8999999999999999996543
No 473
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....
Probab=43.02 E-value=50 Score=24.83 Aligned_cols=26 Identities=23% Similarity=0.377 Sum_probs=21.3
Q ss_pred HHhcCCCCCCCHHHHHHHHCCCHHHHHHH
Q 007404 553 RFGLEDGRMKTLQEIGELMGVSRERIRQI 581 (605)
Q Consensus 553 RyGl~dg~~~Tl~EIAe~LGISrerVRqi 581 (605)
..|.. ..|+.+|++..|+|+.++.+.
T Consensus 11 ~~G~~---~~s~~~Ia~~~gvs~~~~y~~ 36 (47)
T PF00440_consen 11 EKGYE---AVSIRDIARRAGVSKGSFYRY 36 (47)
T ss_dssp HHHTT---TSSHHHHHHHHTSCHHHHHHH
T ss_pred HhCHH---hCCHHHHHHHHccchhhHHHH
Confidence 44554 399999999999999999864
No 474
>cd04772 HTH_TioE_rpt1 First Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD contains the N-terminal or first repeat (rpt1) of these tandem MerR-like domain proteins.
Probab=42.99 E-value=18 Score=31.96 Aligned_cols=25 Identities=20% Similarity=0.372 Sum_probs=21.7
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 007404 562 KTLQEIGELMGVSRERIRQIESSAF 586 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~RAL 586 (605)
++..|+|+.+|||..|+|..+...+
T Consensus 1 y~i~e~A~~~gvs~~tlR~Ye~~Gl 25 (99)
T cd04772 1 YRTVDLARAIGLSPQTVRNYESLGL 25 (99)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCC
Confidence 4788999999999999998877554
No 475
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=42.98 E-value=17 Score=31.36 Aligned_cols=25 Identities=20% Similarity=0.302 Sum_probs=22.2
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 007404 562 KTLQEIGELMGVSRERIRQIESSAF 586 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~RAL 586 (605)
+|..|+|+.+|||..++|.++...+
T Consensus 2 ~~i~e~A~~~gvs~~tLr~ye~~Gl 26 (91)
T cd04766 2 YVISVAAELSGMHPQTLRLYERLGL 26 (91)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 7899999999999999999987544
No 476
>PF04552 Sigma54_DBD: Sigma-54, DNA binding domain; InterPro: IPR007634 This DNA-binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore, this region contains a putative helix-turn-helix motif. At the C terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins [].; PDB: 2AHQ_A 2O9L_A 2O8K_A.
Probab=42.93 E-value=46 Score=32.35 Aligned_cols=24 Identities=13% Similarity=0.245 Sum_probs=0.0
Q ss_pred CCCCHHHHHHhcCCCHHHHHHHHh
Q 007404 467 RHPNNEEVAEATGLSMKRLHAVLL 490 (605)
Q Consensus 467 r~PT~eEIAe~lgis~e~V~~~l~ 490 (605)
++-|..+||+.+|+++..|..++.
T Consensus 48 ~PLt~~~iA~~lgl~~STVSRav~ 71 (160)
T PF04552_consen 48 KPLTMKDIADELGLHESTVSRAVK 71 (160)
T ss_dssp ------------------------
T ss_pred cCCCHHHHHHHhCCCHhHHHHHHc
Confidence 344889999999999999988764
No 477
>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B. subtilis-type. This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from E. coli.
Probab=42.92 E-value=33 Score=34.47 Aligned_cols=27 Identities=30% Similarity=0.475 Sum_probs=23.8
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 561 MKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 561 ~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
--|-.|+++.+|||+.||| +|+..|..
T Consensus 24 LPsE~eLa~~~gVSR~TVR----~Al~~L~~ 50 (233)
T TIGR02404 24 LPSEHELMDQYGASRETVR----KALNLLTE 50 (233)
T ss_pred CcCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 3589999999999999999 88888865
No 478
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=42.77 E-value=40 Score=34.81 Aligned_cols=37 Identities=19% Similarity=0.195 Sum_probs=27.4
Q ss_pred HHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 007404 544 PRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES 583 (605)
Q Consensus 544 ~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~ 583 (605)
+|.+.|+.+-- .....+..||++.||||..|||+-+.
T Consensus 5 ~R~~~Il~~l~---~~~~~~~~ela~~l~vS~~TiRRdL~ 41 (252)
T PRK10906 5 QRHDAIIELVK---QQGYVSTEELVEHFSVSPQTIRRDLN 41 (252)
T ss_pred HHHHHHHHHHH---HcCCEeHHHHHHHhCCCHHHHHHHHH
Confidence 45666666542 22348999999999999999997543
No 479
>cd04789 HTH_Cfa Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator. Putative helix-turn-helix (HTH) MerR-like transcription regulator; the N-terminal domain of Cfa, a cyclopropane fatty acid synthase and other related methyltransferases. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=42.48 E-value=18 Score=32.09 Aligned_cols=25 Identities=28% Similarity=0.401 Sum_probs=22.4
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 007404 562 KTLQEIGELMGVSRERIRQIESSAF 586 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~RAL 586 (605)
+|..|+|+.+|||..|+|-++...+
T Consensus 2 ~~i~eva~~~gvs~~tlR~ye~~Gl 26 (102)
T cd04789 2 YTISELAEKAGISRSTLLYYEKLGL 26 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 7899999999999999998887654
No 480
>PF04552 Sigma54_DBD: Sigma-54, DNA binding domain; InterPro: IPR007634 This DNA-binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore, this region contains a putative helix-turn-helix motif. At the C terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins [].; PDB: 2AHQ_A 2O9L_A 2O8K_A.
Probab=42.38 E-value=8.3 Score=37.45 Aligned_cols=47 Identities=15% Similarity=0.246 Sum_probs=0.0
Q ss_pred HHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 007404 534 DLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIE 582 (605)
Q Consensus 534 ~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie 582 (605)
.|..+...|=..|+.-|. .|.+.-.|+|+++||+.+|++.+||+...
T Consensus 24 TL~~v~~~iv~~Q~~ff~--~g~~~l~PLt~~~iA~~lgl~~STVSRav 70 (160)
T PF04552_consen 24 TLLRVAQAIVERQKDFFL--GGPGALKPLTMKDIADELGLHESTVSRAV 70 (160)
T ss_dssp -------------------------------------------------
T ss_pred HHHHHHHHHHHHHHHHHh--cCcccCcCCCHHHHHHHhCCCHhHHHHHH
Confidence 344555556666665443 23333478999999999999999999544
No 481
>PRK13705 plasmid-partitioning protein SopA; Provisional
Probab=42.34 E-value=33 Score=37.77 Aligned_cols=55 Identities=22% Similarity=0.313 Sum_probs=40.1
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHHhcC---CC---CCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 007404 532 KEDLEKVLDTLNPRERQVVRWRFGLE---DG---RMKTLQEIGELMGVSRERIRQIESSAF 586 (605)
Q Consensus 532 ~~~L~~aL~~L~~rER~VL~LRyGl~---dg---~~~Tl~EIAe~LGISrerVRqie~RAL 586 (605)
.+.+..+++.+..-.+.+...-|+.+ .. ..++..|+|+.+|||..+||..+...+
T Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~k~~r~~~i~e~A~~~gvs~~tiR~ye~~gl 64 (388)
T PRK13705 4 METLNQCINAGHEMTKAIAIAQFNDDSPEARKITRRWRIGEAADLVGVSSQAIRDAEKAGR 64 (388)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCcCCCccccccCCCCHHHHHHHHCcCHHHHHHHHHcCC
Confidence 45677777777777777777666221 11 347889999999999999998866544
No 482
>COG3711 BglG Transcriptional antiterminator [Transcription]
Probab=42.24 E-value=27 Score=39.05 Aligned_cols=47 Identities=21% Similarity=0.139 Sum_probs=37.4
Q ss_pred HHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 544 PRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 544 ~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
..||.++.+.+...+ .+.++.++|..|++|+.||.+-......+++.
T Consensus 84 ~~er~~~~ll~~~~~-~~~~l~~La~~l~vs~~ti~~dl~~v~~~l~~ 130 (491)
T COG3711 84 KDERIIIILLLLLLS-ELLSLHELADELFVSKSTIINDLKDVRLKLLL 130 (491)
T ss_pred hHHHHHHHHHHHHhc-ChhhHHHHHHHHHhHHHHHHHHHHHHHHHHHh
Confidence 677777777776654 67999999999999999999888775555543
No 483
>PF12085 DUF3562: Protein of unknown function (DUF3562); InterPro: IPR021945 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 62 to 84 amino acids in length. This protein has two completely conserved residues (A and Y) that may be functionally important.
Probab=42.07 E-value=36 Score=28.50 Aligned_cols=39 Identities=21% Similarity=0.411 Sum_probs=31.4
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhhHhhhhc
Q 007404 562 KTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAI 603 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~yl~ 603 (605)
-.+++||+..|++.+.|++.....+..|+.-. ...+|+.
T Consensus 8 e~i~~iA~~t~~P~e~V~~my~dt~~~l~~~A---RV~DYl~ 46 (66)
T PF12085_consen 8 EVIRSIAEETGTPAETVRRMYDDTMRELSSGA---RVHDYLP 46 (66)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHHHHHHHcCC---chhhhHH
Confidence 36789999999999999999999998887644 3445543
No 484
>cd01279 HTH_HspR-like Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator HspR and related proteins, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=41.95 E-value=19 Score=31.81 Aligned_cols=24 Identities=17% Similarity=0.356 Sum_probs=21.5
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHH
Q 007404 562 KTLQEIGELMGVSRERIRQIESSA 585 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~RA 585 (605)
+|+.|+|+.+|||..++|.++...
T Consensus 2 ~~i~eva~~~gVs~~tLR~ye~~G 25 (98)
T cd01279 2 YPISVAAELLGIHPQTLRVYDRLG 25 (98)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHCC
Confidence 789999999999999999987654
No 485
>cd04774 HTH_YfmP Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator. Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=41.93 E-value=18 Score=31.81 Aligned_cols=25 Identities=12% Similarity=0.402 Sum_probs=21.8
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 007404 562 KTLQEIGELMGVSRERIRQIESSAF 586 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~RAL 586 (605)
++..|+|+.+|||..++|.++...+
T Consensus 1 ~~I~e~a~~~gvs~~tLR~ye~~Gl 25 (96)
T cd04774 1 YKVDEVAKRLGLTKRTLKYYEEIGL 25 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999999987644
No 486
>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR. Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=41.69 E-value=19 Score=31.61 Aligned_cols=25 Identities=12% Similarity=0.252 Sum_probs=22.1
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 007404 562 KTLQEIGELMGVSRERIRQIESSAF 586 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~RAL 586 (605)
|+..|+|+.+|||..++|.++...+
T Consensus 1 m~i~eva~~~gvs~~tlR~ye~~Gl 25 (96)
T cd04788 1 WKIGELARRTGLSVRTLHHYDHIGL 25 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5788999999999999999887654
No 487
>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=41.60 E-value=19 Score=31.67 Aligned_cols=25 Identities=20% Similarity=0.266 Sum_probs=21.9
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 007404 562 KTLQEIGELMGVSRERIRQIESSAF 586 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~RAL 586 (605)
|+..|+|+.+|||..+||-.+...+
T Consensus 1 m~I~eva~~~gvs~~tlR~Ye~~GL 25 (95)
T cd04780 1 MRMSELSKRSGVSVATIKYYLREGL 25 (95)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999998887655
No 488
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=41.38 E-value=20 Score=31.25 Aligned_cols=25 Identities=32% Similarity=0.525 Sum_probs=22.1
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 007404 562 KTLQEIGELMGVSRERIRQIESSAF 586 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~RAL 586 (605)
+|..|+|+.+||++.+|+.++...+
T Consensus 1 ~~~~eva~~~gi~~~tlr~~~~~Gl 25 (100)
T cd00592 1 YTIGEVAKLLGVSVRTLRYYEEKGL 25 (100)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999999887654
No 489
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=41.30 E-value=30 Score=35.00 Aligned_cols=28 Identities=21% Similarity=0.323 Sum_probs=24.2
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404 560 RMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591 (605)
Q Consensus 560 ~~~Tl~EIAe~LGISrerVRqie~RALkKLR~ 591 (605)
.--|-.|+|+.+|||+.||| +|+..|..
T Consensus 34 ~LPsE~eLa~~~~VSR~TVR----~Al~~L~~ 61 (241)
T PRK10079 34 YLPAEQQLAARYEVNRHTLR----RAIDQLVE 61 (241)
T ss_pred cCCCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 33588999999999999999 88888865
No 490
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=41.22 E-value=20 Score=31.74 Aligned_cols=25 Identities=24% Similarity=0.375 Sum_probs=22.1
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 007404 562 KTLQEIGELMGVSRERIRQIESSAF 586 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~RAL 586 (605)
+|..|+|+.+|||..++|..+...+
T Consensus 1 ~ti~eva~~~gvs~~tlR~ye~~Gl 25 (103)
T cd01106 1 YTVGEVAKLTGVSVRTLHYYDEIGL 25 (103)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999998887655
No 491
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=41.19 E-value=39 Score=32.87 Aligned_cols=23 Identities=26% Similarity=0.404 Sum_probs=21.8
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q 007404 562 KTLQEIGELMGVSRERIRQIESS 584 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~R 584 (605)
+|++|+|+.+|||+.+|+++++.
T Consensus 21 lt~~elA~~~gis~~~is~~E~g 43 (185)
T PRK09943 21 LSQRRAAELSGLTHSAISTIEQD 43 (185)
T ss_pred CCHHHHHHHHCCCHHHHHHHHcC
Confidence 99999999999999999999974
No 492
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=40.99 E-value=20 Score=32.25 Aligned_cols=25 Identities=28% Similarity=0.492 Sum_probs=22.4
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 007404 562 KTLQEIGELMGVSRERIRQIESSAF 586 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~RAL 586 (605)
+|..|+|+.+|||..++|-.+...+
T Consensus 1 ~~i~e~a~~~gvs~~tlr~ye~~gl 25 (113)
T cd01109 1 YTIKEVAEKTGLSADTLRYYEKEGL 25 (113)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999999888765
No 493
>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=40.95 E-value=20 Score=32.37 Aligned_cols=26 Identities=23% Similarity=0.310 Sum_probs=22.8
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH
Q 007404 562 KTLQEIGELMGVSRERIRQIESSAFR 587 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~RALk 587 (605)
|+..|+|+.+|||..++|-.+...|=
T Consensus 1 m~i~eva~~~gvs~~tlR~Ye~~GLl 26 (112)
T cd01282 1 MRIGELAARTGVSVRSLRYYEEQGLL 26 (112)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCC
Confidence 57889999999999999999887553
No 494
>cd01108 HTH_CueR Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators. Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements
Probab=40.37 E-value=20 Score=33.08 Aligned_cols=26 Identities=27% Similarity=0.344 Sum_probs=22.8
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH
Q 007404 562 KTLQEIGELMGVSRERIRQIESSAFR 587 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~RALk 587 (605)
||..|+|+.+|||..++|-++...|-
T Consensus 1 m~I~e~a~~~gvs~~tlRyYe~~GLl 26 (127)
T cd01108 1 MNIGEAAKLTGLSAKMIRYYEEIGLI 26 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 58899999999999999998877654
No 495
>cd04769 HTH_MerR2 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=40.36 E-value=20 Score=32.43 Aligned_cols=26 Identities=23% Similarity=0.324 Sum_probs=23.0
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH
Q 007404 562 KTLQEIGELMGVSRERIRQIESSAFR 587 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~RALk 587 (605)
||..|+|+.+|||..|+|-.+..+|=
T Consensus 1 ~~ige~a~~~gvs~~tLryYe~~GLi 26 (116)
T cd04769 1 MYIGELAQQTGVTIKAIRLYEEKGLL 26 (116)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 58899999999999999998887654
No 496
>PRK09836 DNA-binding transcriptional activator CusR; Provisional
Probab=40.34 E-value=41 Score=32.50 Aligned_cols=49 Identities=14% Similarity=0.156 Sum_probs=40.0
Q ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHH-----CCCHHHHHHHHHHHHHHHH
Q 007404 541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELM-----GVSRERIRQIESSAFRKLK 590 (605)
Q Consensus 541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~L-----GISrerVRqie~RALkKLR 590 (605)
.|+++|.+|+.+.. .+-|...|.++|.+.+ ..+..+|+.++.|-.+||.
T Consensus 150 ~Lt~~E~~ll~~l~-~~~g~~~sr~~l~~~~w~~~~~~~~~~v~~~i~~lR~Kl~ 203 (227)
T PRK09836 150 TLTSKEFTLLEFFL-RHQGEVLPRSLIASQVWDMNFDSDTNAIDVAVKRLRGKID 203 (227)
T ss_pred ecCHHHHHHHHHHH-hCCCeeEcHHHHHHHHcCCCCCCCcCCHHHHHHHHHHHhC
Confidence 49999999998755 4456779999999998 4677889988888888884
No 497
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=40.00 E-value=32 Score=38.83 Aligned_cols=44 Identities=18% Similarity=0.344 Sum_probs=30.6
Q ss_pred HhcCCHHHHHHHHH---------HHhcCCC---CCCCHHHHHHHHCCCHHHHHHHH
Q 007404 539 LDTLNPRERQVVRW---------RFGLEDG---RMKTLQEIGELMGVSRERIRQIE 582 (605)
Q Consensus 539 L~~L~~rER~VL~L---------RyGl~dg---~~~Tl~EIAe~LGISrerVRqie 582 (605)
+..|..|.+.++.. -|+..|. +|+|+++||+.+|+..+||+...
T Consensus 309 i~~i~~R~~TL~~v~~~Iv~~Q~~Ff~~G~~~LkPLtlkdvAe~lglheSTVSRav 364 (455)
T PRK05932 309 IKSLEQRKETLLKVARCIVEQQRDFFEHGEEALKPLVLKDIAEELGMHESTISRAT 364 (455)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccCcCccHHHHHHHhCCCccchhhhh
Confidence 34566666555432 2443332 79999999999999999999543
No 498
>TIGR02044 CueR Cu(I)-responsive transcriptional regulator. This model represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue.
Probab=39.55 E-value=21 Score=32.90 Aligned_cols=25 Identities=24% Similarity=0.446 Sum_probs=22.3
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Q 007404 562 KTLQEIGELMGVSRERIRQIESSAF 586 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~RAL 586 (605)
|+..|+|+.+|||..++|-.+...+
T Consensus 1 m~I~e~a~~~gvs~~tlRyYe~~GL 25 (127)
T TIGR02044 1 MNIGQVAKLTGLSSKMIRYYEEKGL 25 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999999887655
No 499
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=39.53 E-value=44 Score=32.28 Aligned_cols=30 Identities=17% Similarity=0.171 Sum_probs=25.1
Q ss_pred HHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 007404 551 RWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS 584 (605)
Q Consensus 551 ~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~R 584 (605)
.+|--.+ +|++++|+.+|+++.+|+++++-
T Consensus 76 ~~Re~~g----lSqeeLA~~lgvs~s~IsriE~G 105 (154)
T TIGR00270 76 REREKRG----WSQEQLAKKIQEKESLIKKIENA 105 (154)
T ss_pred HHHHHcC----CCHHHHHHHhCCCHHHHHHHHCC
Confidence 3454455 99999999999999999999963
No 500
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=39.51 E-value=46 Score=30.58 Aligned_cols=23 Identities=26% Similarity=0.323 Sum_probs=21.5
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Q 007404 562 KTLQEIGELMGVSRERIRQIESS 584 (605)
Q Consensus 562 ~Tl~EIAe~LGISrerVRqie~R 584 (605)
+|.+|+|+.+|||+.+|.++++.
T Consensus 19 lsq~eLA~~~Gis~~~is~iE~g 41 (120)
T PRK13890 19 MTKKELSERSGVSISFLSDLTTG 41 (120)
T ss_pred CCHHHHHHHHCcCHHHHHHHHcC
Confidence 99999999999999999999864
Done!