Query 015682
Match_columns 402
No_of_seqs 290 out of 1733
Neff 8.0
Searched_HMMs 46136
Date Fri Mar 29 08:35:37 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/015682.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/015682hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4585 Predicted transposase 100.0 3E-43 6.4E-48 339.5 14.0 312 66-394 7-321 (326)
2 PF13359 DDE_Tnp_4: DDE superf 100.0 7.1E-38 1.5E-42 275.0 3.8 152 181-346 1-158 (158)
3 PF04827 Plant_tran: Plant tra 100.0 7.2E-35 1.6E-39 254.0 6.8 198 151-352 2-201 (205)
4 PF13613 HTH_Tnp_4: Helix-turn 98.9 5.4E-10 1.2E-14 79.3 3.2 51 100-150 2-52 (53)
5 PF13612 DDE_Tnp_1_3: Transpos 98.9 6.5E-10 1.4E-14 96.6 3.4 128 175-324 4-150 (155)
6 PF13586 DDE_Tnp_1_2: Transpos 97.4 8.6E-05 1.9E-09 58.4 1.7 52 292-344 34-85 (88)
7 PF01609 DDE_Tnp_1: Transposas 97.3 4.5E-06 9.8E-11 75.3 -7.0 151 176-347 4-213 (213)
8 PF04218 CENP-B_N: CENP-B N-te 95.8 0.0048 1E-07 43.6 1.6 42 97-139 3-44 (53)
9 PF04545 Sigma70_r4: Sigma-70, 95.8 0.0088 1.9E-07 41.5 3.0 45 100-145 4-48 (50)
10 PF13936 HTH_38: Helix-turn-he 95.8 0.0026 5.6E-08 43.1 0.0 41 99-140 3-43 (44)
11 PF02796 HTH_7: Helix-turn-hel 94.8 0.0065 1.4E-07 41.3 -0.4 39 100-139 5-43 (45)
12 smart00351 PAX Paired Box doma 94.6 0.028 6E-07 47.2 2.7 47 96-143 13-59 (125)
13 cd00131 PAX Paired Box domain 94.2 0.038 8.2E-07 46.6 2.8 47 96-143 13-59 (128)
14 PF08281 Sigma70_r4_2: Sigma-7 94.1 0.039 8.5E-07 38.7 2.2 44 100-144 10-53 (54)
15 PF13518 HTH_28: Helix-turn-he 93.7 0.03 6.4E-07 38.8 1.0 37 106-143 2-38 (52)
16 PF13384 HTH_23: Homeodomain-l 93.6 0.012 2.5E-07 40.7 -1.1 37 105-142 6-42 (50)
17 COG3415 Transposase and inacti 92.0 0.07 1.5E-06 45.4 1.2 44 100-143 4-47 (138)
18 cd06571 Bac_DnaA_C C-terminal 91.8 0.16 3.5E-06 39.9 3.0 51 97-147 24-75 (90)
19 PF05225 HTH_psq: helix-turn-h 91.7 0.068 1.5E-06 36.3 0.6 36 104-139 2-38 (45)
20 PRK09413 IS2 repressor TnpA; R 91.5 0.13 2.8E-06 42.9 2.3 46 98-143 10-55 (121)
21 PRK04217 hypothetical protein; 91.5 0.17 3.7E-06 41.3 2.9 49 100-149 42-90 (110)
22 PF01527 HTH_Tnp_1: Transposas 91.3 0.059 1.3E-06 40.6 -0.0 45 98-142 4-48 (76)
23 PF02209 VHP: Villin headpiece 91.3 0.1 2.2E-06 33.5 1.1 23 58-80 2-24 (36)
24 smart00421 HTH_LUXR helix_turn 91.0 0.18 3.8E-06 35.1 2.2 43 101-145 4-46 (58)
25 PF13011 LZ_Tnp_IS481: leucine 90.9 0.17 3.6E-06 39.2 2.2 45 99-143 7-51 (85)
26 PRK00118 putative DNA-binding 90.9 0.21 4.6E-06 40.4 2.8 49 100-149 17-65 (104)
27 smart00153 VHP Villin headpiec 90.6 0.15 3.3E-06 32.8 1.4 22 58-79 2-23 (36)
28 cd06171 Sigma70_r4 Sigma70, re 90.5 0.2 4.3E-06 34.1 2.1 43 101-144 11-53 (55)
29 PF13340 DUF4096: Putative tra 89.8 0.68 1.5E-05 35.0 4.7 46 97-143 21-66 (75)
30 PF12116 SpoIIID: Stage III sp 89.6 0.1 2.2E-06 39.6 0.0 42 106-147 8-49 (82)
31 PRK09639 RNA polymerase sigma 89.5 0.28 6E-06 42.7 2.7 47 101-149 113-159 (166)
32 cd00569 HTH_Hin_like Helix-tur 89.3 0.18 3.9E-06 31.2 1.1 37 100-137 5-41 (42)
33 PRK09652 RNA polymerase sigma 89.1 0.28 6.1E-06 43.0 2.5 49 101-150 129-177 (182)
34 PRK12529 RNA polymerase sigma 89.1 0.33 7E-06 43.0 2.8 49 100-149 127-175 (178)
35 TIGR02960 SigX5 RNA polymerase 88.5 0.61 1.3E-05 45.4 4.6 71 101-172 143-217 (324)
36 PRK12519 RNA polymerase sigma 88.2 0.31 6.7E-06 43.6 2.1 49 101-150 142-190 (194)
37 TIGR00721 tfx DNA-binding prot 87.8 0.83 1.8E-05 38.9 4.3 46 100-147 6-51 (137)
38 TIGR02985 Sig70_bacteroi1 RNA 87.5 0.47 1E-05 40.6 2.8 46 101-147 114-159 (161)
39 PRK06030 hypothetical protein; 87.5 0.43 9.2E-06 39.9 2.3 47 99-145 51-97 (124)
40 PRK08301 sporulation sigma fac 87.5 0.5 1.1E-05 43.9 3.1 50 101-150 179-231 (234)
41 TIGR01321 TrpR trp operon repr 87.2 0.32 7E-06 38.4 1.4 39 101-139 33-77 (94)
42 TIGR02952 Sig70_famx2 RNA poly 87.2 0.5 1.1E-05 41.1 2.8 47 100-147 122-168 (170)
43 PRK07037 extracytoplasmic-func 86.9 0.54 1.2E-05 40.7 2.9 48 101-149 110-157 (163)
44 cd06170 LuxR_C_like C-terminal 86.9 0.57 1.2E-05 32.5 2.5 42 102-145 2-43 (57)
45 PRK12514 RNA polymerase sigma 86.5 0.67 1.4E-05 40.9 3.2 47 101-148 130-176 (179)
46 TIGR03879 near_KaiC_dom probab 86.4 0.31 6.8E-06 36.7 0.9 40 101-140 16-55 (73)
47 PRK05911 RNA polymerase sigma 86.2 0.57 1.2E-05 44.3 2.8 49 101-150 206-254 (257)
48 TIGR02531 yecD_yerC TrpR-relat 86.0 0.28 6.1E-06 38.4 0.5 31 108-138 41-71 (88)
49 TIGR02392 rpoH_proteo alternat 86.0 0.64 1.4E-05 44.3 3.0 48 101-148 219-267 (270)
50 TIGR02937 sigma70-ECF RNA poly 85.9 0.63 1.4E-05 39.0 2.7 46 101-147 111-156 (158)
51 PRK09638 RNA polymerase sigma 85.8 0.41 8.8E-06 42.0 1.5 47 101-148 127-173 (176)
52 PRK12530 RNA polymerase sigma 85.4 0.55 1.2E-05 42.0 2.2 49 100-149 134-182 (189)
53 PRK05803 sporulation sigma fac 84.9 0.79 1.7E-05 42.5 3.0 49 100-148 175-226 (233)
54 PRK12547 RNA polymerase sigma 84.9 0.76 1.6E-05 40.0 2.8 49 100-149 112-160 (164)
55 PRK09415 RNA polymerase factor 84.7 0.72 1.6E-05 40.8 2.6 48 101-149 128-175 (179)
56 TIGR02999 Sig-70_X6 RNA polyme 84.6 0.82 1.8E-05 40.4 2.9 47 101-148 135-181 (183)
57 PRK12511 RNA polymerase sigma 83.9 0.86 1.9E-05 40.6 2.7 50 100-150 111-160 (182)
58 PRK06596 RNA polymerase factor 83.9 0.9 1.9E-05 43.7 3.0 48 101-148 231-279 (284)
59 TIGR02989 Sig-70_gvs1 RNA poly 83.9 0.86 1.9E-05 39.1 2.7 47 100-147 111-157 (159)
60 PRK11923 algU RNA polymerase s 83.9 0.76 1.6E-05 41.1 2.4 51 101-152 139-189 (193)
61 PRK12533 RNA polymerase sigma 83.8 0.81 1.8E-05 42.1 2.6 49 101-150 135-183 (216)
62 PRK09641 RNA polymerase sigma 83.8 0.83 1.8E-05 40.4 2.6 48 101-149 137-184 (187)
63 PRK11924 RNA polymerase sigma 83.8 0.89 1.9E-05 39.6 2.8 48 101-149 126-173 (179)
64 PRK12516 RNA polymerase sigma 83.6 0.92 2E-05 40.6 2.8 49 101-150 117-165 (187)
65 PRK12515 RNA polymerase sigma 83.3 0.92 2E-05 40.4 2.7 49 100-149 131-179 (189)
66 TIGR02939 RpoE_Sigma70 RNA pol 83.3 0.84 1.8E-05 40.5 2.4 49 101-150 139-187 (190)
67 PRK12524 RNA polymerase sigma 83.3 0.95 2.1E-05 40.7 2.8 48 100-148 136-183 (196)
68 PRK09047 RNA polymerase factor 83.1 0.93 2E-05 39.0 2.6 50 100-150 106-155 (161)
69 PRK12512 RNA polymerase sigma 83.1 1 2.2E-05 39.9 2.8 49 100-149 131-179 (184)
70 PRK03975 tfx putative transcri 83.1 0.96 2.1E-05 38.7 2.5 46 100-147 6-51 (141)
71 PHA00675 hypothetical protein 83.1 0.49 1.1E-05 35.7 0.6 39 101-139 23-61 (78)
72 PF13542 HTH_Tnp_ISL3: Helix-t 83.0 0.38 8.3E-06 33.3 0.0 28 114-141 24-51 (52)
73 PRK12537 RNA polymerase sigma 83.0 1.1 2.3E-05 39.7 3.0 47 101-148 134-180 (182)
74 TIGR02983 SigE-fam_strep RNA p 82.9 1 2.2E-05 38.9 2.7 48 101-149 111-158 (162)
75 PRK12534 RNA polymerase sigma 82.8 1.2 2.7E-05 39.4 3.3 48 101-149 138-185 (187)
76 PRK06704 RNA polymerase factor 82.8 1.7 3.7E-05 40.3 4.3 69 101-170 117-186 (228)
77 PRK05572 sporulation sigma fac 82.7 1.1 2.4E-05 42.1 3.1 48 100-148 202-249 (252)
78 PRK13919 putative RNA polymera 82.6 1.2 2.5E-05 39.5 3.1 48 101-149 136-183 (186)
79 PRK05602 RNA polymerase sigma 82.5 1 2.2E-05 40.1 2.6 49 101-150 129-177 (186)
80 TIGR02950 SigM_subfam RNA poly 82.4 0.46 9.9E-06 40.6 0.3 47 101-148 106-152 (154)
81 TIGR02984 Sig-70_plancto1 RNA 82.2 1.2 2.5E-05 39.4 2.9 47 101-148 141-187 (189)
82 PRK07408 RNA polymerase sigma 81.8 1.2 2.5E-05 42.1 2.9 48 101-149 204-251 (256)
83 PRK12532 RNA polymerase sigma 81.6 1.1 2.4E-05 40.1 2.6 48 101-149 137-184 (195)
84 TIGR02846 spore_sigmaK RNA pol 81.4 1.4 2.9E-05 40.8 3.1 48 100-147 174-224 (227)
85 PRK09642 RNA polymerase sigma 81.1 1.3 2.8E-05 38.2 2.7 48 101-149 107-154 (160)
86 PRK09645 RNA polymerase sigma 81.1 1.4 3.1E-05 38.5 3.0 48 101-149 119-166 (173)
87 PRK12531 RNA polymerase sigma 81.0 1.3 2.9E-05 39.6 2.9 49 100-149 141-189 (194)
88 COG1595 RpoE DNA-directed RNA 80.9 1.2 2.7E-05 39.4 2.6 50 100-150 127-176 (182)
89 PRK12528 RNA polymerase sigma 80.9 1.2 2.5E-05 38.6 2.3 46 100-146 113-158 (161)
90 PRK07500 rpoH2 RNA polymerase 80.9 1.4 3E-05 42.5 3.1 51 100-150 227-278 (289)
91 PRK12525 RNA polymerase sigma 80.7 1.4 3.1E-05 38.4 2.8 48 100-148 118-165 (168)
92 TIGR02835 spore_sigmaE RNA pol 80.7 1.5 3.2E-05 40.8 3.1 49 100-148 178-229 (234)
93 TIGR02954 Sig70_famx3 RNA poly 80.6 1.5 3.2E-05 38.2 2.9 48 101-149 120-167 (169)
94 PRK12540 RNA polymerase sigma 80.5 1.3 2.9E-05 39.3 2.7 49 101-150 112-160 (182)
95 PRK09643 RNA polymerase sigma 80.5 1.3 2.9E-05 39.6 2.6 48 101-149 135-182 (192)
96 PF13730 HTH_36: Helix-turn-he 80.5 1 2.3E-05 31.4 1.6 39 104-142 7-50 (55)
97 TIGR02948 SigW_bacill RNA poly 80.5 1.3 2.9E-05 39.1 2.6 49 100-149 136-184 (187)
98 TIGR02980 SigBFG RNA polymeras 80.2 1.5 3.2E-05 40.4 2.9 46 101-147 179-224 (227)
99 PRK12520 RNA polymerase sigma 80.1 1.4 3E-05 39.3 2.6 49 101-150 132-180 (191)
100 PRK12544 RNA polymerase sigma 80.0 1.4 3.1E-05 40.0 2.8 48 101-149 149-196 (206)
101 PRK12522 RNA polymerase sigma 80.0 1.4 3.1E-05 38.6 2.6 52 101-153 120-171 (173)
102 PF12802 MarR_2: MarR family; 79.9 1.1 2.5E-05 31.8 1.6 43 101-143 3-47 (62)
103 TIGR02393 RpoD_Cterm RNA polym 79.8 1.4 3.1E-05 41.0 2.7 48 100-147 176-226 (238)
104 PRK15320 transcriptional activ 79.8 0.86 1.9E-05 41.0 1.1 38 109-146 171-208 (251)
105 PRK12539 RNA polymerase sigma 79.8 1.6 3.4E-05 38.8 2.8 49 100-149 131-179 (184)
106 PRK08583 RNA polymerase sigma 79.7 1.6 3.4E-05 41.2 3.0 47 101-148 206-252 (257)
107 TIGR02885 spore_sigF RNA polym 79.7 1.5 3.3E-05 40.5 2.8 47 100-147 183-229 (231)
108 PRK08215 sporulation sigma fac 79.6 1.6 3.5E-05 41.2 3.0 47 100-147 209-255 (258)
109 PRK12523 RNA polymerase sigma 79.6 1.6 3.5E-05 38.2 2.8 47 100-147 119-165 (172)
110 PRK09637 RNA polymerase sigma 79.4 1.6 3.5E-05 38.8 2.8 49 101-150 107-155 (181)
111 TIGR02394 rpoS_proteo RNA poly 79.3 1.7 3.7E-05 41.7 3.1 51 100-150 222-275 (285)
112 PRK06759 RNA polymerase factor 79.2 1.6 3.5E-05 37.2 2.7 46 100-146 106-151 (154)
113 TIGR03001 Sig-70_gmx1 RNA poly 79.2 1.6 3.4E-05 41.0 2.8 48 101-149 162-209 (244)
114 PRK06986 fliA flagellar biosyn 79.0 1.7 3.7E-05 40.3 3.0 48 101-149 185-232 (236)
115 PRK12546 RNA polymerase sigma 78.9 1.6 3.5E-05 39.1 2.6 50 100-150 113-162 (188)
116 PRK06811 RNA polymerase factor 78.7 1.6 3.4E-05 39.0 2.5 47 100-147 131-177 (189)
117 PHA00542 putative Cro-like pro 78.6 1.6 3.5E-05 33.6 2.2 51 109-170 23-73 (82)
118 PRK12536 RNA polymerase sigma 78.6 1.8 3.8E-05 38.3 2.8 47 101-148 130-176 (181)
119 PRK12535 RNA polymerase sigma 78.6 1.8 3.9E-05 39.0 2.9 52 101-153 134-185 (196)
120 COG2963 Transposase and inacti 78.5 1.7 3.6E-05 35.6 2.4 47 98-144 5-52 (116)
121 PRK06930 positive control sigm 78.4 1.8 4E-05 38.3 2.8 49 100-149 114-162 (170)
122 PRK12545 RNA polymerase sigma 77.9 1.9 4.1E-05 38.9 2.9 48 101-149 140-187 (201)
123 PRK12527 RNA polymerase sigma 77.9 1.9 4.1E-05 37.1 2.7 49 101-150 106-154 (159)
124 PRK09644 RNA polymerase sigma 77.7 1.7 3.7E-05 37.7 2.4 49 100-149 108-156 (165)
125 TIGR02947 SigH_actino RNA poly 77.5 1.1 2.3E-05 40.1 1.1 48 101-149 132-179 (193)
126 PF01371 Trp_repressor: Trp re 77.4 1.2 2.7E-05 34.7 1.2 36 104-139 36-71 (87)
127 TIGR02957 SigX4 RNA polymerase 77.4 3.3 7.1E-05 39.6 4.5 67 101-170 109-175 (281)
128 PRK09649 RNA polymerase sigma 77.2 1.8 3.8E-05 38.6 2.4 47 100-147 130-176 (185)
129 PF13412 HTH_24: Winged helix- 77.2 1.6 3.5E-05 29.5 1.7 37 106-143 7-43 (48)
130 PF04967 HTH_10: HTH DNA bindi 77.2 0.94 2E-05 31.9 0.5 29 117-145 23-51 (53)
131 PF00196 GerE: Bacterial regul 77.2 0.84 1.8E-05 32.4 0.2 43 101-145 4-46 (58)
132 PRK09636 RNA polymerase sigma 77.2 3.6 7.8E-05 39.5 4.7 68 101-171 116-183 (293)
133 PRK12543 RNA polymerase sigma 77.1 2 4.4E-05 37.8 2.7 48 101-149 118-165 (179)
134 PRK08241 RNA polymerase factor 77.0 2.5 5.5E-05 41.4 3.7 72 101-173 154-228 (339)
135 TIGR02943 Sig70_famx1 RNA poly 77.0 1.9 4.2E-05 38.5 2.6 49 101-150 132-180 (188)
136 PF00356 LacI: Bacterial regul 76.8 0.45 9.7E-06 32.5 -1.2 20 120-139 2-21 (46)
137 TIGR02941 Sigma_B RNA polymera 76.8 2.2 4.8E-05 40.1 3.0 47 100-147 205-251 (255)
138 PF00872 Transposase_mut: Tran 76.7 3 6.6E-05 41.8 4.2 86 114-226 111-205 (381)
139 TIGR02850 spore_sigG RNA polym 76.6 2.2 4.8E-05 40.1 3.0 47 100-147 206-252 (254)
140 PRK12542 RNA polymerase sigma 76.6 2.2 4.7E-05 37.9 2.8 49 101-150 123-171 (185)
141 PF07374 DUF1492: Protein of u 76.5 1.7 3.6E-05 34.8 1.8 43 102-145 57-99 (100)
142 TIGR02844 spore_III_D sporulat 76.5 0.96 2.1E-05 34.7 0.4 36 104-139 5-41 (80)
143 PRK12541 RNA polymerase sigma 76.5 2 4.3E-05 37.1 2.4 47 100-147 112-158 (161)
144 TIGR02997 Sig70-cyanoRpoD RNA 76.4 1.8 3.9E-05 41.8 2.4 44 101-144 250-296 (298)
145 PF01047 MarR: MarR family; I 76.1 1.5 3.2E-05 31.0 1.3 30 113-142 13-42 (59)
146 cd00092 HTH_CRP helix_turn_hel 75.9 1.1 2.3E-05 32.5 0.5 26 118-143 26-51 (67)
147 PRK12538 RNA polymerase sigma 75.6 1.9 4.1E-05 40.1 2.2 48 101-149 172-219 (233)
148 PF08299 Bac_DnaA_C: Bacterial 75.5 0.74 1.6E-05 34.4 -0.5 43 99-141 27-70 (70)
149 COG2739 Uncharacterized protei 75.4 2 4.3E-05 34.3 1.9 46 101-147 18-63 (105)
150 PRK12526 RNA polymerase sigma 75.4 2.4 5.3E-05 38.4 2.8 47 101-148 154-200 (206)
151 PRK07670 RNA polymerase sigma 75.2 2.6 5.6E-05 39.6 3.1 47 101-148 202-248 (251)
152 TIGR02959 SigZ RNA polymerase 75.1 2.4 5.2E-05 37.1 2.6 50 100-150 100-149 (170)
153 PRK07405 RNA polymerase sigma 75.0 2.6 5.5E-05 41.2 3.0 48 100-147 256-306 (317)
154 PRK07122 RNA polymerase sigma 74.6 2.6 5.7E-05 40.0 2.9 46 101-147 216-261 (264)
155 PRK09646 RNA polymerase sigma 74.6 2.9 6.3E-05 37.4 3.1 48 101-149 143-190 (194)
156 PRK08295 RNA polymerase factor 74.3 2.4 5.3E-05 38.1 2.6 47 101-149 156-202 (208)
157 TIGR02479 FliA_WhiG RNA polyme 74.2 2.8 6.2E-05 38.5 3.0 46 101-147 176-221 (224)
158 PF01022 HTH_5: Bacterial regu 73.9 1.7 3.6E-05 29.5 1.0 38 106-143 4-41 (47)
159 PRK01381 Trp operon repressor; 73.7 2.2 4.8E-05 34.0 1.8 39 101-139 33-77 (99)
160 PRK12513 RNA polymerase sigma 73.6 1.7 3.6E-05 38.9 1.3 48 101-149 140-187 (194)
161 COG1191 FliA DNA-directed RNA 73.6 2.8 6E-05 39.4 2.7 49 100-149 196-244 (247)
162 PF13551 HTH_29: Winged helix- 73.5 1.4 2.9E-05 35.4 0.6 34 110-143 4-38 (112)
163 PRK09648 RNA polymerase sigma 73.3 2.9 6.4E-05 37.1 2.8 48 100-148 139-186 (189)
164 PRK11922 RNA polymerase sigma 73.1 1.8 3.8E-05 40.1 1.3 49 101-150 150-198 (231)
165 TIGR01636 phage_rinA phage tra 73.1 4.9 0.00011 34.0 3.9 48 101-148 83-131 (134)
166 PRK09651 RNA polymerase sigma 73.0 2.7 5.8E-05 36.8 2.4 47 101-148 120-166 (172)
167 PRK09635 sigI RNA polymerase s 71.8 5.1 0.00011 38.6 4.2 67 101-170 119-185 (290)
168 PF01325 Fe_dep_repress: Iron 71.7 2.5 5.5E-05 30.4 1.6 40 103-142 5-47 (60)
169 PF04297 UPF0122: Putative hel 71.1 3.3 7.2E-05 33.2 2.3 47 100-147 17-63 (101)
170 PF09339 HTH_IclR: IclR helix- 71.0 1.6 3.6E-05 30.2 0.5 27 117-143 18-44 (52)
171 PRK10402 DNA-binding transcrip 70.5 1.9 4.2E-05 39.6 1.0 67 100-166 148-219 (226)
172 PF00292 PAX: 'Paired box' dom 70.2 3.3 7.1E-05 34.6 2.1 46 96-143 13-59 (125)
173 PRK12517 RNA polymerase sigma 70.1 3.6 7.7E-05 36.8 2.6 49 101-150 129-177 (188)
174 PRK15418 transcriptional regul 69.8 3.5 7.7E-05 40.3 2.6 69 109-180 21-89 (318)
175 PRK07406 RNA polymerase sigma 68.9 3.7 8E-05 41.1 2.6 48 100-147 311-361 (373)
176 PRK09647 RNA polymerase sigma 68.5 4.1 8.9E-05 36.9 2.7 48 101-149 139-186 (203)
177 PRK05657 RNA polymerase sigma 68.1 4.7 0.0001 39.5 3.1 50 100-149 262-314 (325)
178 PF13751 DDE_Tnp_1_6: Transpos 67.2 2.6 5.6E-05 34.8 1.0 49 299-349 74-123 (125)
179 smart00342 HTH_ARAC helix_turn 67.1 6.5 0.00014 29.1 3.1 71 60-142 4-76 (84)
180 PRK12518 RNA polymerase sigma 67.0 2.3 5E-05 37.1 0.7 48 101-149 121-168 (175)
181 PRK14086 dnaA chromosomal repl 66.6 5 0.00011 42.7 3.1 51 97-147 549-599 (617)
182 TIGR02859 spore_sigH RNA polym 66.4 3.9 8.4E-05 36.4 2.1 41 105-147 155-195 (198)
183 TIGR03209 P21_Cbot clostridium 66.0 2.7 6E-05 35.4 0.9 35 100-135 107-141 (142)
184 PRK09640 RNA polymerase sigma 66.0 1.9 4.1E-05 38.4 -0.1 48 101-149 135-182 (188)
185 PRK06288 RNA polymerase sigma 65.4 5.3 0.00011 37.9 2.8 48 100-148 212-259 (268)
186 PRK12427 flagellar biosynthesi 65.4 5.2 0.00011 37.1 2.7 46 100-146 183-228 (231)
187 PRK15201 fimbriae regulatory p 65.2 2.8 6.2E-05 37.1 0.8 44 100-145 133-176 (198)
188 PF07638 Sigma70_ECF: ECF sigm 64.3 6 0.00013 35.3 2.8 45 101-146 136-180 (185)
189 PRK07598 RNA polymerase sigma 64.3 5.1 0.00011 40.6 2.6 46 101-146 351-399 (415)
190 PRK09210 RNA polymerase sigma 64.2 5.3 0.00011 39.9 2.7 48 100-147 305-355 (367)
191 COG2390 DeoR Transcriptional r 64.0 5.3 0.00011 39.1 2.6 67 110-180 19-86 (321)
192 PRK05949 RNA polymerase sigma 63.9 6.2 0.00013 38.8 3.0 47 101-147 267-316 (327)
193 PF08279 HTH_11: HTH domain; 63.4 4.3 9.2E-05 28.2 1.3 26 117-142 15-40 (55)
194 PRK00149 dnaA chromosomal repl 63.2 6.5 0.00014 40.3 3.2 51 97-147 382-433 (450)
195 smart00550 Zalpha Z-DNA-bindin 63.0 5.7 0.00012 29.3 2.0 40 102-141 6-46 (68)
196 COG3316 Transposase and inacti 62.6 22 0.00048 32.6 6.1 181 102-349 10-199 (215)
197 PF01381 HTH_3: Helix-turn-hel 62.6 2.5 5.4E-05 29.3 0.0 43 114-168 6-48 (55)
198 TIGR03697 NtcA_cyano global ni 62.4 3.9 8.4E-05 36.2 1.2 44 101-144 113-170 (193)
199 PF01710 HTH_Tnp_IS630: Transp 62.4 2.1 4.5E-05 35.4 -0.5 29 112-140 13-41 (119)
200 smart00346 HTH_ICLR helix_turn 62.4 4.6 0.0001 31.1 1.5 38 106-143 6-46 (91)
201 PF01710 HTH_Tnp_IS630: Transp 61.9 7.9 0.00017 32.0 2.9 72 62-141 23-95 (119)
202 PRK14088 dnaA chromosomal repl 61.3 6.4 0.00014 40.3 2.7 49 97-145 367-415 (440)
203 PRK15411 rcsA colanic acid cap 60.7 4 8.6E-05 37.2 1.0 45 100-146 137-181 (207)
204 PRK05901 RNA polymerase sigma 60.2 9.3 0.0002 39.8 3.7 48 100-147 447-497 (509)
205 PF13545 HTH_Crp_2: Crp-like h 60.2 3.4 7.4E-05 30.7 0.4 27 117-143 28-54 (76)
206 PF13463 HTH_27: Winged helix 58.4 4.2 9.1E-05 29.4 0.6 33 111-143 9-44 (68)
207 PRK13870 transcriptional regul 57.5 4.4 9.6E-05 37.7 0.7 44 100-145 173-216 (234)
208 PRK11753 DNA-binding transcrip 57.2 5.8 0.00012 35.6 1.4 44 100-143 138-194 (211)
209 PF02001 DUF134: Protein of un 57.0 9.8 0.00021 30.9 2.5 46 100-146 41-86 (106)
210 TIGR01610 phage_O_Nterm phage 57.0 6.9 0.00015 30.9 1.7 28 115-142 45-72 (95)
211 PRK13918 CRP/FNR family transc 56.9 3.7 8.1E-05 36.6 0.1 64 101-164 119-197 (202)
212 PRK07921 RNA polymerase sigma 56.9 9.4 0.0002 37.4 2.9 47 101-147 263-312 (324)
213 PF10654 DUF2481: Protein of u 56.8 4.6 0.0001 32.8 0.6 31 116-146 79-109 (126)
214 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 56.8 4.5 9.8E-05 28.1 0.5 41 98-139 2-42 (50)
215 PRK03573 transcriptional regul 56.6 8.1 0.00018 32.7 2.2 43 101-143 29-72 (144)
216 PRK14087 dnaA chromosomal repl 56.3 9.9 0.00022 39.1 3.1 51 97-147 381-432 (450)
217 PF12840 HTH_20: Helix-turn-he 55.6 3.3 7.2E-05 29.6 -0.3 30 114-143 21-50 (61)
218 PF06056 Terminase_5: Putative 55.0 7 0.00015 28.0 1.3 33 106-140 4-36 (58)
219 COG2522 Predicted transcriptio 54.9 5.3 0.00011 33.1 0.7 32 106-139 13-44 (119)
220 PF00126 HTH_1: Bacterial regu 54.4 6.7 0.00014 28.0 1.1 29 118-146 14-42 (60)
221 PRK12422 chromosomal replicati 54.4 11 0.00023 38.8 3.0 50 97-146 377-426 (445)
222 TIGR02337 HpaR homoprotocatech 54.3 18 0.0004 29.4 3.9 42 101-143 26-68 (118)
223 PF13560 HTH_31: Helix-turn-he 54.1 3.2 6.9E-05 30.0 -0.7 28 111-138 8-35 (64)
224 smart00419 HTH_CRP helix_turn_ 53.7 4.6 0.0001 26.8 0.2 27 117-143 8-34 (48)
225 PF00325 Crp: Bacterial regula 53.0 4 8.8E-05 25.5 -0.2 24 119-142 4-27 (32)
226 COG0593 DnaA ATPase involved i 52.8 11 0.00023 38.1 2.6 52 96-147 344-395 (408)
227 PF09862 DUF2089: Protein of u 52.6 9.9 0.00021 31.2 1.9 45 101-146 34-78 (113)
228 cd00090 HTH_ARSR Arsenical Res 52.4 8.6 0.00019 27.7 1.5 27 116-142 19-45 (78)
229 COG3413 Predicted DNA binding 52.3 30 0.00064 31.6 5.3 51 97-147 152-208 (215)
230 PRK13719 conjugal transfer tra 52.1 6.5 0.00014 36.1 0.9 44 100-145 143-186 (217)
231 smart00418 HTH_ARSR helix_turn 51.7 7.1 0.00015 27.2 0.9 29 115-143 8-36 (66)
232 PRK09392 ftrB transcriptional 51.3 7.2 0.00016 35.8 1.1 64 100-163 146-219 (236)
233 smart00345 HTH_GNTR helix_turn 51.1 5.3 0.00011 27.8 0.1 24 119-142 22-45 (60)
234 PRK09191 two-component respons 51.1 18 0.00038 33.5 3.7 51 100-151 88-138 (261)
235 PRK11512 DNA-binding transcrip 50.8 14 0.0003 31.4 2.7 42 101-143 38-80 (144)
236 PF05344 DUF746: Domain of Unk 50.2 9.7 0.00021 27.9 1.4 43 106-148 2-44 (65)
237 smart00347 HTH_MARR helix_turn 49.2 17 0.00037 28.0 2.8 43 101-143 8-50 (101)
238 COG2197 CitB Response regulato 49.0 7.8 0.00017 35.4 0.9 44 100-145 148-191 (211)
239 PF01978 TrmB: Sugar-specific 49.0 6.5 0.00014 28.7 0.3 38 104-142 10-47 (68)
240 PRK10840 transcriptional regul 48.5 7.6 0.00017 35.0 0.8 44 100-145 150-193 (216)
241 PRK11161 fumarate/nitrate redu 47.7 9.7 0.00021 34.9 1.3 42 101-142 154-209 (235)
242 PHA02591 hypothetical protein; 47.5 6.6 0.00014 29.7 0.1 36 105-140 47-82 (83)
243 PRK13413 mpi multiple promoter 46.7 6.4 0.00014 35.5 -0.0 29 111-139 166-194 (200)
244 TIGR03541 reg_near_HchA LuxR f 46.1 14 0.00031 34.1 2.3 46 99-146 170-215 (232)
245 cd01392 HTH_LacI Helix-turn-he 45.3 5.7 0.00012 27.1 -0.5 18 122-139 2-19 (52)
246 PRK11475 DNA-binding transcrip 45.1 8.9 0.00019 34.9 0.7 44 100-145 134-177 (207)
247 PRK09391 fixK transcriptional 44.3 13 0.00029 34.1 1.7 43 101-143 153-205 (230)
248 KOG0930 Guanine nucleotide exc 44.3 61 0.0013 30.9 5.9 83 105-188 94-189 (395)
249 TIGR01889 Staph_reg_Sar staphy 44.1 20 0.00044 28.9 2.5 43 101-143 23-69 (109)
250 PRK10188 DNA-binding transcrip 44.0 10 0.00022 35.5 0.8 44 100-145 179-222 (240)
251 TIGR03020 EpsA transcriptional 43.8 16 0.00035 34.3 2.2 45 99-145 189-233 (247)
252 PHA00738 putative HTH transcri 43.8 7.2 0.00016 31.6 -0.2 38 106-144 14-53 (108)
253 PRK09483 response regulator; P 43.8 9.6 0.00021 33.8 0.7 44 100-145 148-191 (217)
254 PF12964 DUF3853: Protein of u 43.4 7.2 0.00015 30.9 -0.2 69 66-150 10-80 (96)
255 COG2771 CsgD DNA-binding HTH d 42.3 12 0.00026 26.4 0.9 36 110-145 12-47 (65)
256 PF04552 Sigma54_DBD: Sigma-54 42.1 8.5 0.00018 33.7 0.0 22 118-139 50-71 (160)
257 PRK10100 DNA-binding transcrip 41.7 12 0.00025 34.4 0.9 43 101-145 156-198 (216)
258 smart00420 HTH_DEOR helix_turn 41.3 20 0.00043 23.9 1.8 27 117-143 14-40 (53)
259 PF13309 HTH_22: HTH domain 40.9 18 0.00039 26.3 1.6 39 100-138 20-63 (64)
260 smart00352 POU Found in Pit-Oc 40.6 6.5 0.00014 29.7 -0.8 28 112-139 19-52 (75)
261 smart00344 HTH_ASNC helix_turn 40.5 21 0.00046 28.4 2.1 38 105-143 6-43 (108)
262 COG5421 Transposase [DNA repli 40.3 60 0.0013 33.4 5.6 55 206-275 155-209 (480)
263 smart00354 HTH_LACI helix_turn 40.2 6.2 0.00013 29.2 -1.0 21 119-139 2-22 (70)
264 PRK05658 RNA polymerase sigma 39.2 23 0.00051 37.9 2.8 47 100-146 556-605 (619)
265 PRK08558 adenine phosphoribosy 39.0 23 0.00049 33.1 2.4 56 102-169 8-63 (238)
266 PRK10141 DNA-binding transcrip 38.9 13 0.00028 30.8 0.6 43 102-144 14-57 (117)
267 TIGR00180 parB_part ParB-like 38.6 16 0.00034 32.7 1.2 41 99-139 101-142 (187)
268 COG3293 Transposase and inacti 38.4 18 0.00038 29.8 1.4 56 269-325 40-101 (124)
269 PF13744 HTH_37: Helix-turn-he 38.2 6.7 0.00015 29.9 -1.1 34 106-139 18-53 (80)
270 PRK12682 transcriptional regul 38.0 20 0.00043 34.3 1.9 43 105-147 4-46 (309)
271 TIGR02405 trehalos_R_Ecol treh 37.8 13 0.00028 35.6 0.5 21 119-139 3-23 (311)
272 PF05263 DUF722: Protein of un 37.7 23 0.00049 29.9 1.9 45 101-145 82-127 (130)
273 PF05269 Phage_CII: Bacterioph 36.7 19 0.00041 28.4 1.2 30 118-147 24-53 (91)
274 PF00165 HTH_AraC: Bacterial r 36.5 9.7 0.00021 24.9 -0.4 28 114-141 5-32 (42)
275 PF13404 HTH_AsnC-type: AsnC-t 36.4 9.6 0.00021 25.3 -0.4 24 117-140 17-40 (42)
276 COG4496 Uncharacterized protei 36.2 21 0.00045 27.8 1.3 34 104-138 44-77 (100)
277 PRK09492 treR trehalose repres 36.2 17 0.00037 34.7 1.1 23 118-140 5-27 (315)
278 PF13443 HTH_26: Cro/C1-type H 36.0 14 0.00031 26.2 0.4 43 115-168 8-50 (63)
279 TIGR03070 couple_hipB transcri 35.8 11 0.00025 25.8 -0.1 25 114-138 12-36 (58)
280 PHA01976 helix-turn-helix prot 35.5 11 0.00024 27.2 -0.3 44 113-168 11-54 (67)
281 PRK00215 LexA repressor; Valid 34.8 26 0.00056 31.6 2.0 26 118-143 24-50 (205)
282 PRK10360 DNA-binding transcrip 34.6 17 0.00037 31.5 0.8 44 100-145 137-180 (196)
283 PF05043 Mga: Mga helix-turn-h 34.5 23 0.0005 27.1 1.4 34 114-147 27-60 (87)
284 PRK10870 transcriptional repre 33.6 28 0.0006 30.8 1.9 42 101-142 53-96 (176)
285 TIGR00122 birA_repr_reg BirA b 33.5 15 0.00032 26.9 0.2 25 118-142 14-38 (69)
286 cd04762 HTH_MerR-trunc Helix-T 33.1 10 0.00022 24.9 -0.7 22 119-140 2-23 (49)
287 COG4941 Predicted RNA polymera 33.1 38 0.00083 33.3 2.9 49 98-147 118-166 (415)
288 PRK10651 transcriptional regul 32.9 18 0.00039 31.7 0.6 44 100-145 155-198 (216)
289 cd07377 WHTH_GntR Winged helix 32.7 15 0.00033 25.9 0.1 25 119-143 27-51 (66)
290 PRK09958 DNA-binding transcrip 32.5 20 0.00043 31.4 0.8 44 100-145 143-186 (204)
291 PRK10014 DNA-binding transcrip 32.5 10 0.00023 36.6 -1.1 23 118-140 7-29 (342)
292 COG1508 RpoN DNA-directed RNA 32.4 12 0.00026 38.1 -0.7 35 113-157 320-360 (444)
293 PRK12683 transcriptional regul 32.2 28 0.00061 33.4 1.9 43 105-147 4-46 (309)
294 PRK09834 DNA-binding transcrip 32.0 26 0.00055 33.1 1.5 43 101-143 7-52 (263)
295 PRK14987 gluconate operon tran 31.8 11 0.00024 36.4 -1.1 21 119-139 7-27 (331)
296 PRK10163 DNA-binding transcrip 31.8 33 0.00071 32.6 2.2 44 100-143 20-66 (271)
297 PRK09526 lacI lac repressor; R 31.3 11 0.00025 36.3 -1.0 21 119-139 7-27 (342)
298 TIGR02431 pcaR_pcaU beta-ketoa 31.0 29 0.00062 32.3 1.7 43 101-143 5-50 (248)
299 PRK10403 transcriptional regul 30.8 21 0.00046 31.2 0.7 44 100-145 153-196 (215)
300 PRK11303 DNA-binding transcrip 30.6 13 0.00028 35.7 -0.8 22 119-140 2-23 (328)
301 cd00131 PAX Paired Box domain 30.5 1E+02 0.0022 25.7 4.8 79 58-139 34-125 (128)
302 PF04703 FaeA: FaeA-like prote 30.3 18 0.00038 26.4 0.1 37 105-141 3-39 (62)
303 PF00392 GntR: Bacterial regul 30.2 16 0.00034 26.3 -0.2 23 120-142 27-49 (64)
304 PF09607 BrkDBD: Brinker DNA-b 30.1 21 0.00046 25.5 0.5 41 98-138 3-46 (58)
305 PRK10339 DNA-binding transcrip 29.7 13 0.00029 35.8 -0.9 21 119-139 3-23 (327)
306 COG3355 Predicted transcriptio 29.6 31 0.00068 28.9 1.5 29 116-144 41-69 (126)
307 PRK04140 hypothetical protein; 29.6 22 0.00047 34.8 0.6 82 67-168 96-178 (317)
308 PRK13777 transcriptional regul 29.4 45 0.00097 29.9 2.5 41 101-141 43-83 (185)
309 PRK12679 cbl transcriptional r 29.3 35 0.00077 32.8 2.0 42 106-147 5-46 (316)
310 PRK10423 transcriptional repre 29.1 14 0.00031 35.4 -0.8 19 121-139 2-20 (327)
311 PRK11233 nitrogen assimilation 29.1 34 0.00073 32.7 1.8 37 111-147 9-45 (305)
312 PRK10703 DNA-binding transcrip 28.9 14 0.0003 35.8 -0.9 22 119-140 3-24 (341)
313 PRK10401 DNA-binding transcrip 28.9 22 0.00049 34.5 0.6 21 119-139 3-23 (346)
314 PRK15092 DNA-binding transcrip 28.8 23 0.0005 34.1 0.7 51 97-147 5-55 (310)
315 TIGR01764 excise DNA binding d 28.8 13 0.00028 24.5 -0.8 21 119-139 3-23 (49)
316 PRK15369 two component system 28.0 26 0.00057 30.2 0.8 43 101-145 150-192 (211)
317 smart00529 HTH_DTXR Helix-turn 27.9 25 0.00054 27.3 0.6 24 120-143 2-25 (96)
318 PRK11050 manganese transport r 27.8 37 0.00079 29.3 1.7 28 116-143 50-77 (152)
319 PF12728 HTH_17: Helix-turn-he 27.8 15 0.00032 25.0 -0.7 21 119-139 3-23 (51)
320 PF00665 rve: Integrase core d 27.6 1.1E+02 0.0024 24.1 4.5 17 303-319 104-120 (120)
321 PRK11179 DNA-binding transcrip 27.5 50 0.0011 28.3 2.5 43 101-143 7-49 (153)
322 TIGR02607 antidote_HigA addict 27.0 29 0.00064 25.7 0.8 38 101-139 3-40 (78)
323 PF03333 PapB: Adhesin biosynt 27.0 75 0.0016 25.0 3.1 56 68-141 22-77 (91)
324 PRK12684 transcriptional regul 26.0 46 0.00099 31.9 2.2 42 106-147 5-46 (313)
325 TIGR01884 cas_HTH CRISPR locus 26.0 52 0.0011 29.7 2.4 32 111-142 149-182 (203)
326 PRK15090 DNA-binding transcrip 25.5 47 0.001 31.1 2.1 43 101-143 10-54 (257)
327 PRK11569 transcriptional repre 25.1 48 0.001 31.5 2.1 43 101-143 24-69 (274)
328 TIGR02395 rpoN_sigma RNA polym 24.8 23 0.00049 36.2 -0.3 30 118-157 319-348 (429)
329 TIGR00637 ModE_repress ModE mo 24.8 36 0.00077 27.1 0.9 35 113-147 12-46 (99)
330 TIGR02417 fruct_sucro_rep D-fr 24.7 19 0.0004 34.6 -0.9 21 120-140 2-22 (327)
331 TIGR02702 SufR_cyano iron-sulf 24.5 52 0.0011 29.7 2.1 38 104-142 3-40 (203)
332 TIGR01481 ccpA catabolite cont 24.4 18 0.0004 34.7 -0.9 21 119-139 3-23 (329)
333 PRK10072 putative transcriptio 24.4 20 0.00043 28.5 -0.6 26 114-139 43-68 (96)
334 smart00760 Bac_DnaA_C Bacteria 24.1 37 0.00081 24.1 0.9 32 97-128 25-56 (60)
335 COG1846 MarR Transcriptional r 23.6 54 0.0012 26.0 1.9 23 121-143 40-62 (126)
336 PF08220 HTH_DeoR: DeoR-like h 23.3 28 0.0006 24.6 0.1 23 118-140 15-37 (57)
337 PRK10727 DNA-binding transcrip 23.1 20 0.00044 34.7 -1.0 21 119-139 3-23 (343)
338 TIGR01637 phage_arpU phage tra 23.1 96 0.0021 25.7 3.3 49 101-149 80-129 (132)
339 COG2512 Predicted membrane-ass 22.9 59 0.0013 30.8 2.2 44 99-142 191-235 (258)
340 TIGR03830 CxxCG_CxxCG_HTH puta 22.9 25 0.00054 28.9 -0.3 27 113-139 74-100 (127)
341 TIGR03454 partition_RepB plasm 22.8 72 0.0016 31.3 2.8 70 97-169 157-231 (325)
342 PRK09906 DNA-binding transcrip 22.7 48 0.001 31.2 1.6 40 108-147 6-45 (296)
343 PRK11169 leucine-responsive tr 22.5 57 0.0012 28.4 1.9 43 101-143 12-54 (164)
344 PRK09935 transcriptional regul 21.8 38 0.00082 29.5 0.7 44 100-145 149-192 (210)
345 PRK11151 DNA-binding transcrip 21.7 57 0.0012 31.0 1.9 41 106-147 5-45 (305)
346 PF10668 Phage_terminase: Phag 21.7 40 0.00086 24.4 0.6 25 113-137 16-42 (60)
347 COG4565 CitB Response regulato 21.6 80 0.0017 29.0 2.7 23 119-141 175-197 (224)
348 PF08765 Mor: Mor transcriptio 21.6 27 0.00058 28.2 -0.4 31 115-145 70-100 (108)
349 TIGR02944 suf_reg_Xantho FeS a 21.2 43 0.00093 27.7 0.8 26 118-143 26-51 (130)
350 PF14493 HTH_40: Helix-turn-he 21.1 47 0.001 25.8 1.0 59 108-169 4-63 (91)
351 COG3677 Transposase and inacti 21.1 51 0.0011 27.7 1.2 43 105-147 77-119 (129)
352 COG1609 PurR Transcriptional r 21.0 24 0.00052 34.6 -0.9 21 119-139 2-22 (333)
353 COG4974 XerD Site-specific rec 20.5 1.9E+02 0.004 28.0 5.0 100 36-148 187-292 (300)
354 PRK05932 RNA polymerase factor 20.3 31 0.00068 35.5 -0.3 30 118-157 344-373 (455)
355 PRK12469 RNA polymerase factor 20.1 33 0.00071 35.6 -0.2 30 118-157 370-399 (481)
356 PRK13832 plasmid partitioning 20.0 59 0.0013 33.8 1.6 42 97-138 98-139 (520)
No 1
>KOG4585 consensus Predicted transposase [Replication, recombination and repair]
Probab=100.00 E-value=3e-43 Score=339.51 Aligned_cols=312 Identities=38% Similarity=0.573 Sum_probs=254.6
Q ss_pred ccCCCHHHHHHHHHHHhccccCCCCCCCccccCCcCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHH
Q 015682 66 FFRVSKKTFDYICSLVREDLVSRPPSGLINIEGRLLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEAL 145 (402)
Q Consensus 66 ~fRms~~tF~~L~~~l~~~~~~~~~~g~~~~~~~~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al 145 (402)
.|++++.+|++||.........+. ++.+... .+++..++++.++.++++.+.+.++..||...+|+ .+....
T Consensus 7 ~~~~s~~~~~~~~~~~~~~~~~~~-~~~~~~~--~~~~~~~v~~~~~~~~~~~~~~~i~~~fg~~~~~~-----~~~~~~ 78 (326)
T KOG4585|consen 7 EFRKSYTTFDKICSLVQSLNVVKN-SGFMLSS--LLPADTLVAVALWRLKTGESLRTVEKKFGLGQSTC-----KFLEEK 78 (326)
T ss_pred HHHHHHHHHHHHhhhhhhhhhhcc-cchhhhc--cccHHhhhhhhhccccccchHHHHHHHcCCcchhh-----hHHHhh
Confidence 789999999999998766554444 3322222 22288999999999999999999999999999999 666677
Q ss_pred HHhhcccccCCCchhHHHHHHHHHHhhCCCCcccccceeEEEEecCCCCCCCccccCCCceeeeEeeeeCCCceEEeeec
Q 015682 146 EERAKHHLKWPDSNRMEEIKSKFEESFGLLNCCGAIDATHIIMTLPAVQTSDDWCDQENNYSMLVQGIVDHEMRFIDIVT 225 (402)
Q Consensus 146 ~~~~~~~i~~P~~~~~~~i~~~f~~~~~fp~~iGaIDgthI~i~~P~~~~~~~y~~~k~~~s~~~q~vvD~~~rf~~v~~ 225 (402)
...+..++.||....+..+.+.|+. +|+|+|+||+|||++..|+...+ .|.|+ .+++++|+|||.+++|+++.+
T Consensus 79 ~~~~~~~~~~p~~~~~~~i~~~~~~---~~~~~g~~d~~hi~~~~~~~~~~-~~~n~--~~~~Nvlav~n~d~~f~~v~v 152 (326)
T KOG4585|consen 79 EDLAPHFLKWPSRRILYEIRERFES---LPNCVGAIDTTHIPIRVPPKSGS-VYFNK--EQSKNLLAVCNFDMRFIYVDV 152 (326)
T ss_pred hcccchhhcCchhhhhhhhcccccc---ccchhccccccccceecCccccc-ccccc--ccchhhhheecCCceEEEEEc
Confidence 7788999999998788888888875 99999999999999999887554 46666 889999999999999999999
Q ss_pred cCCCcccchhhhhcchhhhhhhhcccCCCCcccCCCccccceEEEeCCCCCCccccccCcccCCCCCchhhhhHhHHHhh
Q 015682 226 GWPGGMNVSRLLKFSGFFKLCEAGQRLNGNVRISSEEVELREYIVGGVGYPLLSWLITPYETNGLSASMPTFNSLHEATR 305 (402)
Q Consensus 226 g~pGs~~D~~v~~~S~l~~~~~~~~~l~~~~~~~~~~~~~~~~llgD~gYpl~~~l~~Py~~~~l~~~~~~fN~~~s~~R 305 (402)
|||||.||+.|++.+.+++....+..+ +..+...|.+...+++|+.+||+.+++|+||.+..++..+..||.+|+.+|
T Consensus 153 g~~Gs~~D~kvl~~~~~~~~~~~~~~~--k~yl~d~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~elFN~rh~~~r 230 (326)
T KOG4585|consen 153 GWPGSAHDTKVLQDSLLYKRNFPHPPL--KYYLVDSGYPLRPGLLGPIGFPLYSLLMFPYGGPQPTNSQELFNKRHSSLR 230 (326)
T ss_pred cCCCCccHHHHHHhhcccccccccCCc--cccccccCcccccccccccccccchhhhcccCCCCCCchHHHHhhhhhhHH
Confidence 999999999999999988877665433 333444566788999999999999999999998878999999999999999
Q ss_pred hHHHHHHHHHhccceeccccccccCCCChhHHHHHHHHHhhhhhccCCCCCCCCccCCCCCCC--Cccc-cccCCCchHH
Q 015682 306 SLAVKAFLQLKGGWRILSKVMWRPDKRKLPSIILVCCLLHNIIIDSGDQLHPDVALSDHHDSG--YGEQ-CCKQVDPMGR 382 (402)
Q Consensus 306 ~~vE~afg~LK~rfriL~~~~~~~~~~~~~~ii~accvLHN~~~~~~~~~~~~~~~~~~~d~~--~~~~-~~~~~~~~~~ 382 (402)
.++|++||+||+||+||.+. +.++..+.+.||.|||+|||||++..+...++......+|.+ .... ...+...-+.
T Consensus 231 ~v~e~~fg~lk~rw~il~~~-~~~~~~~~~~iV~a~caLHN~~~~~~~~~~~~~~~e~~~d~~~~~~~~~~~~~~~~~~~ 309 (326)
T KOG4585|consen 231 SVAERAFGVLKAKWRILQRR-EKYDLKKLPKIVTACCALHNIIRDSDEEDPDDPKWEKFDDYGENVAHLRYAPQQRDYME 309 (326)
T ss_pred HHHHHHHHHhhhhhHHHhhc-ccccccchHHHHHHHHHHHHHHHhhcccccccccccccccccccchhcccchhHHHHHH
Confidence 99999999999999999998 677888999999999999999999887544332112222221 1111 1123456678
Q ss_pred HHHHHHHHHHhh
Q 015682 383 TTRENLEKHLQH 394 (402)
Q Consensus 383 ~~Rd~l~~~~~~ 394 (402)
..|+.|+..+.+
T Consensus 310 ~~r~~l~~~l~~ 321 (326)
T KOG4585|consen 310 KIRDNLLSELWN 321 (326)
T ss_pred HHHHHHHHHHHh
Confidence 889999888875
No 2
>PF13359 DDE_Tnp_4: DDE superfamily endonuclease
Probab=100.00 E-value=7.1e-38 Score=274.95 Aligned_cols=152 Identities=36% Similarity=0.653 Sum_probs=137.4
Q ss_pred cceeEEEEecCCC--CCCCccccCCCceeeeEeeeeCCCceEEeeeccCCCcccchhhhhcchhhhhhhhcccCCCCccc
Q 015682 181 IDATHIIMTLPAV--QTSDDWCDQENNYSMLVQGIVDHEMRFIDIVTGWPGGMNVSRLLKFSGFFKLCEAGQRLNGNVRI 258 (402)
Q Consensus 181 IDgthI~i~~P~~--~~~~~y~~~k~~~s~~~q~vvD~~~rf~~v~~g~pGs~~D~~v~~~S~l~~~~~~~~~l~~~~~~ 258 (402)
||||||+|++|.. .+...|+++|+.|++++|+|||++|+|++++++||||+||+.+|++|.+...++..
T Consensus 1 iDgt~v~i~~P~~~~~~~~~y~~~k~~~~~~~q~v~d~~g~i~~v~~~~~Gs~~D~~i~~~s~~~~~l~~~--------- 71 (158)
T PF13359_consen 1 IDGTHVPIQRPSDKEEQREFYSGKKKNHSLKVQIVCDPDGRIIYVSVGWPGSVHDSTIFRQSGLLDRLEQA--------- 71 (158)
T ss_pred CccEEEEEEeCCccccccccccCCCCcceEeEEEEEeccceeEeeecccccccccccccccccccceeecc---------
Confidence 7999999999986 46678999999999999999999999999999999999999999999888776521
Q ss_pred CCCccccceEEEeCCCCCCccccccCcc---cCCCCCchhhhhHhHHHhhhHHHHHHHHHhccceeccccccccC-CCCh
Q 015682 259 SSEEVELREYIVGGVGYPLLSWLITPYE---TNGLSASMPTFNSLHEATRSLAVKAFLQLKGGWRILSKVMWRPD-KRKL 334 (402)
Q Consensus 259 ~~~~~~~~~~llgD~gYpl~~~l~~Py~---~~~l~~~~~~fN~~~s~~R~~vE~afg~LK~rfriL~~~~~~~~-~~~~ 334 (402)
.+.++++|||+|||+.+++|+||+ +..++.+++.||++|+++|.+||++||+||+||+||...+ +.+ ...+
T Consensus 72 ----~~~~~~~l~D~gy~~~~~~~~P~~~~~~~~l~~~e~~~N~~~s~~R~~vE~~~~~lK~rf~~l~~~~-~~~~~~~~ 146 (158)
T PF13359_consen 72 ----FPPGEYLLGDSGYPLSPYLLTPYKKPKGRELTPEEKEFNRRHSSARIIVERAFGRLKSRFRILRGRL-RLSRPEKA 146 (158)
T ss_pred ----cccCccccccccccccccccccccccccccccccccchhccccceeeeeHHHHHHHHHhcccCCccc-CCCcHhHH
Confidence 123689999999999999999995 5678999999999999999999999999999999998765 344 7789
Q ss_pred hHHHHHHHHHhh
Q 015682 335 PSIILVCCLLHN 346 (402)
Q Consensus 335 ~~ii~accvLHN 346 (402)
..+|.|||+|||
T Consensus 147 ~~ii~~~~~LhN 158 (158)
T PF13359_consen 147 PQIILACCVLHN 158 (158)
T ss_pred HHHHheeEEEEC
Confidence 999999999999
No 3
>PF04827 Plant_tran: Plant transposon protein; InterPro: IPR006912 This entry represents a putative Harbinger transposase-derived nuclease, which is thought to have nuclease activity. However it does not have transposase activity [, ]. ; GO: 0016788 hydrolase activity, acting on ester bonds
Probab=100.00 E-value=7.2e-35 Score=253.96 Aligned_cols=198 Identities=21% Similarity=0.287 Sum_probs=169.6
Q ss_pred ccccCCCchhHHHHHHHHHHhhCCCCcccccceeEEEEe-cCCCCCCCccccCCCceeeeEeeeeCCCceEEeeeccCCC
Q 015682 151 HHLKWPDSNRMEEIKSKFEESFGLLNCCGAIDATHIIMT-LPAVQTSDDWCDQENNYSMLVQGIVDHEMRFIDIVTGWPG 229 (402)
Q Consensus 151 ~~i~~P~~~~~~~i~~~f~~~~~fp~~iGaIDgthI~i~-~P~~~~~~~y~~~k~~~s~~~q~vvD~~~rf~~v~~g~pG 229 (402)
+|++-|+.++++++...++. .||||.+|+|||+|+.+. +|......+..++++..++.++||+|+|.+|+++..|.||
T Consensus 2 ~YLr~P~~~d~~rll~~~e~-rGFpGmlGSIDCmHw~WkncP~aw~g~~~~G~~g~pTiiLEaVAs~dlwIWhaffG~~G 80 (205)
T PF04827_consen 2 EYLRRPTNEDLERLLQIGEA-RGFPGMLGSIDCMHWEWKNCPTAWKGQYTRGKEGVPTIILEAVASHDLWIWHAFFGMPG 80 (205)
T ss_pred cccCCCChhHHHHHHHhhhh-cCCCccccceeEEEeehhcchHHhhhcccCCCCCCCeehhhhhhccchhhhheeeccCC
Confidence 58889999999999977765 499999999999999999 6666555544499999999999999999999999999999
Q ss_pred cccchhhhhcchhhhhhhhcccCCCCcccCCCcccc-ceEEEeCCCCCCccccccCcccCCCCCchhhhhHhHHHhhhHH
Q 015682 230 GMNVSRLLKFSGFFKLCEAGQRLNGNVRISSEEVEL-REYIVGGVGYPLLSWLITPYETNGLSASMPTFNSLHEATRSLA 308 (402)
Q Consensus 230 s~~D~~v~~~S~l~~~~~~~~~l~~~~~~~~~~~~~-~~~llgD~gYpl~~~l~~Py~~~~l~~~~~~fN~~~s~~R~~v 308 (402)
|.+|..|+..|+++..+.+|... +....-+|.+- -.|+|+|..||-+..++...+ .+.++.++.|..+..++|.-|
T Consensus 81 S~NDiNVL~~Splf~~~~~G~ap--~v~f~VNg~~Y~~gYYLaDGiYP~watfvktI~-~p~~~k~k~fa~~QE~~RKDV 157 (205)
T PF04827_consen 81 SNNDINVLDRSPLFDDLLQGQAP--RVQFTVNGHEYNMGYYLADGIYPEWATFVKTIS-LPQGEKRKLFAKHQESARKDV 157 (205)
T ss_pred cccccccccccHHHHHHhcCcCC--ceEEEecCeecccceeeccCcCcchHhHhhhcc-hhhchhhHHHHHhCHHHHHHH
Confidence 99999999999999998888531 11122222211 248899999999999999988 777889999999999999999
Q ss_pred HHHHHHHhccceeccccccccCCCChhHHHHHHHHHhhhhhccC
Q 015682 309 VKAFLQLKGGWRILSKVMWRPDKRKLPSIILVCCLLHNIIIDSG 352 (402)
Q Consensus 309 E~afg~LK~rfriL~~~~~~~~~~~~~~ii~accvLHN~~~~~~ 352 (402)
|+|||+|++||+|++.+....+...+..|+.||++||||+++.+
T Consensus 158 ErAFGVLQaRfaIi~~p~r~w~~~~l~~Im~aCiILHNMIvEDE 201 (205)
T PF04827_consen 158 ERAFGVLQARFAIIRGPARLWDREDLANIMRACIILHNMIVEDE 201 (205)
T ss_pred HHHHHHHHHHHHHhcCchhccCHHHHHHHHHHHHHhhheeEecc
Confidence 99999999999999998755677789999999999999998655
No 4
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=98.94 E-value=5.4e-10 Score=79.33 Aligned_cols=51 Identities=31% Similarity=0.365 Sum_probs=47.9
Q ss_pred cCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhhc
Q 015682 100 LLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERAK 150 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~~ 150 (402)
.+|+++|+.++|.||++|.++.++|..||||+|||+++++++++.|...++
T Consensus 2 kLs~~d~lll~L~~LR~~~~~~~La~~FgIs~stvsri~~~~~~~L~~~l~ 52 (53)
T PF13613_consen 2 KLSLEDQLLLTLMYLRLNLTFQDLAYRFGISQSTVSRIFHEWIPLLYQVLK 52 (53)
T ss_pred CCCHHHHHHHHHHHHHcCCcHhHHhhheeecHHHHHHHHHHHHHHHHHhcC
Confidence 489999999999999999999999999999999999999999999987643
No 5
>PF13612 DDE_Tnp_1_3: Transposase DDE domain
Probab=98.92 E-value=6.5e-10 Score=96.62 Aligned_cols=128 Identities=21% Similarity=0.254 Sum_probs=95.5
Q ss_pred CCcccccceeEEEEecCCCC-CCC--------ccccCCCceeeeEeeeeCCCceEEeeeccCCCcccchhhhhcchhhhh
Q 015682 175 LNCCGAIDATHIIMTLPAVQ-TSD--------DWCDQENNYSMLVQGIVDHEMRFIDIVTGWPGGMNVSRLLKFSGFFKL 245 (402)
Q Consensus 175 p~~iGaIDgthI~i~~P~~~-~~~--------~y~~~k~~~s~~~q~vvD~~~rf~~v~~g~pGs~~D~~v~~~S~l~~~ 245 (402)
+..+.+||.|-||++.+... ... -|+..+-+|+++++++|+..|.++.+.+ .||++||..++..-
T Consensus 4 ~~~i~~iDS~Pi~vC~~~R~~r~k~~~~~a~~G~~a~~~fyGfKlHllv~~~G~i~~~~l-T~an~~D~~~~~~l----- 77 (155)
T PF13612_consen 4 CTGIYIIDSFPIPVCHNIRIKRHKVFKGLAYRGYCAMGWFYGFKLHLLVNDSGEIVAFTL-TPANVHDRKVLEEL----- 77 (155)
T ss_pred ccEEEEEecCChhHhCccchhhhccccCccccceeccceeEeeeeeeEEccCCcEEEEEE-cccccccccccccc-----
Confidence 56788999999999977531 111 2333445699999999999999999876 69999999887321
Q ss_pred hhhcccCCCCcccCCCccccceEEEeCCCCCCcc----------ccccCcccCCCCCchhhhhHhHHHhhhHHHHHHHHH
Q 015682 246 CEAGQRLNGNVRISSEEVELREYIVGGVGYPLLS----------WLITPYETNGLSASMPTFNSLHEATRSLAVKAFLQL 315 (402)
Q Consensus 246 ~~~~~~l~~~~~~~~~~~~~~~~llgD~gYpl~~----------~l~~Py~~~~l~~~~~~fN~~~s~~R~~vE~afg~L 315 (402)
.. .....++||.||--.. .|+||.+.+-.......+++.+.+.|.+||-.|+.|
T Consensus 78 -~~---------------~~~g~l~gDkGYis~~L~~~L~~~gI~L~t~~RkNmk~~~~~~~~~~l~~~R~~IETvfs~L 141 (155)
T PF13612_consen 78 -SE---------------NLKGKLFGDKGYISKELKDELKEQGIKLITPRRKNMKNKLMPLFDKLLLRKRRIIETVFSQL 141 (155)
T ss_pred -cc---------------ccccceecchhhhcchHHhhhhhceEEEeccccccccccccchhhhhhhheeeEeehHHHHH
Confidence 00 0134799999994322 378999844334445678899999999999999999
Q ss_pred hccceeccc
Q 015682 316 KGGWRILSK 324 (402)
Q Consensus 316 K~rfriL~~ 324 (402)
|+.|.+=+.
T Consensus 142 k~~~~ie~~ 150 (155)
T PF13612_consen 142 KNQFNIEHS 150 (155)
T ss_pred HHhhceEee
Confidence 999887554
No 6
>PF13586 DDE_Tnp_1_2: Transposase DDE domain
Probab=97.36 E-value=8.6e-05 Score=58.37 Aligned_cols=52 Identities=19% Similarity=0.206 Sum_probs=38.0
Q ss_pred CchhhhhHhHHHhhhHHHHHHHHHhccceeccccccccCCCChhHHHHHHHHH
Q 015682 292 ASMPTFNSLHEATRSLAVKAFLQLKGGWRILSKVMWRPDKRKLPSIILVCCLL 344 (402)
Q Consensus 292 ~~~~~fN~~~s~~R~~vE~afg~LK~rfriL~~~~~~~~~~~~~~ii~accvL 344 (402)
.....+...+...|.+||++|+.||. |+.|.....+........+.+||+++
T Consensus 34 ~~~~~~d~~~~~~Rw~VEr~f~wlk~-~Rrl~~ryek~~~s~~~~v~la~~~i 85 (88)
T PF13586_consen 34 RRPRKFDFRLYKRRWVVERTFAWLKR-FRRLATRYEKLASSFLAFVHLACIVI 85 (88)
T ss_pred cccCccchhhhccceehhhhhHHHHH-cCccccccccCHHHHHHHHHHHHHHH
Confidence 44678889999999999999999998 89998865433333444555555543
No 7
>PF01609 DDE_Tnp_1: Transposase DDE domain; InterPro: IPR002559 Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element. Transposases have been grouped into various families [, , ]. This family includes the IS4 transposase. 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: 3ECP_A 4DM0_A 1MUS_A 1MUH_A 1MM8_A 1B7E_A.
Probab=97.31 E-value=4.5e-06 Score=75.28 Aligned_cols=151 Identities=16% Similarity=0.125 Sum_probs=81.5
Q ss_pred CcccccceeEEEEecCCCCCCCccccCCCceeeeEeeee-CCCceEEeeeccCCCcccchhhhhcchhhhhhhhcccCCC
Q 015682 176 NCCGAIDATHIIMTLPAVQTSDDWCDQENNYSMLVQGIV-DHEMRFIDIVTGWPGGMNVSRLLKFSGFFKLCEAGQRLNG 254 (402)
Q Consensus 176 ~~iGaIDgthI~i~~P~~~~~~~y~~~k~~~s~~~q~vv-D~~~rf~~v~~g~pGs~~D~~v~~~S~l~~~~~~~~~l~~ 254 (402)
..+-+||+|+|+.. +.......+.+++....+++++++ +..+.++.+.+. +|+.+|...+.. +++..
T Consensus 4 ~~~~~iD~T~i~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~d~~~~~~-----ll~~~----- 71 (213)
T PF01609_consen 4 RRVVAIDGTTIRTP-HDKSARRYKKGKKRGFGYKLHLAVDDNSGLPLSVKVT-PGNVHDSKALPE-----LLERK----- 71 (213)
T ss_dssp EEEEEEETTT--EE-EEEEE-B-SSGGGHSSHGGHHHHHHHHHGGGGGGEEE-EEEGG-HHHHHH-----HHTT------
T ss_pred CeEEEEECcEEEee-cchhhhcccCCCCcCCCEeEEEEEeecccceeeeecc-ccccceeecccc-----ccccc-----
Confidence 35668999999998 111111223345556677888888 566677777776 999999988875 22210
Q ss_pred CcccCCCccccceEEEeCCCCCCccc----------cccCcccCCCC---------------------------------
Q 015682 255 NVRISSEEVELREYIVGGVGYPLLSW----------LITPYETNGLS--------------------------------- 291 (402)
Q Consensus 255 ~~~~~~~~~~~~~~llgD~gYpl~~~----------l~~Py~~~~l~--------------------------------- 291 (402)
....+.++++|+||.-.+. .+.|.+.+...
T Consensus 72 -------~~~~~~~vv~D~gy~s~~~~~~l~~~~~~~vi~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 144 (213)
T PF01609_consen 72 -------PGRKPDLVVADRGYDSAENLEALKERGIHFVIRLKKNRKKKIQKIENKFWKSFDRRSARKKPKQKSKRVRVVI 144 (213)
T ss_dssp -----------EEEEEE-S--BBTTHHHHHHTS---EEEEE--EEEE-TTS-EEEE--EEEEEEEEEEETGGGEEEEEEE
T ss_pred -------ccccccceeecccccceeccccccccccccccccccccccccccchhhccccccccccccccccccccccccc
Confidence 0123579999999964331 23333321110
Q ss_pred -CchhhhhHh--------------HHHhhhHHHHHHHHHhccceeccccccccCCCChhHHHHHHHHHhhh
Q 015682 292 -ASMPTFNSL--------------HEATRSLAVKAFLQLKGGWRILSKVMWRPDKRKLPSIILVCCLLHNI 347 (402)
Q Consensus 292 -~~~~~fN~~--------------~s~~R~~vE~afg~LK~rfriL~~~~~~~~~~~~~~ii~accvLHN~ 347 (402)
......... +.+.|-.||+.|..||..|. |.... ......+...+.++++-.|+
T Consensus 145 ~~~~~~~~~~~~~~~~~~~~~~~~~Y~~Rw~IE~~f~~lK~~~~-l~~~~-~~~~~~~~~~~~~~~la~nl 213 (213)
T PF01609_consen 145 RKEQKKKGYFLVTNITTLPRDTAALYRRRWQIERFFRELKQFLG-LERLR-VRSPERIEAHLFLTLLAYNL 213 (213)
T ss_dssp EEECS--TTS---EEEEEESS--SHHHCGGHHHHHHHHHTTTTT-GGGS---SSHHHHHHHHHHHHHH---
T ss_pred ccccccccccccccccccccccceeecccchhhHHHHHHHhcCC-Cchhc-ccCHHHHHHHHHHHHhhCcC
Confidence 011111222 88999999999999999655 33322 22334566677777777664
No 8
>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=95.83 E-value=0.0048 Score=43.58 Aligned_cols=42 Identities=36% Similarity=0.538 Sum_probs=31.4
Q ss_pred cCCcCCHHHHHHHHhhhccCCCccccccccccccccchhhhHH
Q 015682 97 EGRLLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTW 139 (402)
Q Consensus 97 ~~~~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~ 139 (402)
.+..+++++++.|.-. +..|.+..+||..|||+.|||+.|+.
T Consensus 3 kR~~LTl~eK~~iI~~-~e~g~s~~~ia~~fgv~~sTv~~I~K 44 (53)
T PF04218_consen 3 KRKSLTLEEKLEIIKR-LEEGESKRDIAREFGVSRSTVSTILK 44 (53)
T ss_dssp SSSS--HHHHHHHHHH-HHCTT-HHHHHHHHT--CCHHHHHHH
T ss_pred CCccCCHHHHHHHHHH-HHcCCCHHHHHHHhCCCHHHHHHHHH
Confidence 4567999999987654 67888999999999999999999875
No 9
>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=95.83 E-value=0.0088 Score=41.47 Aligned_cols=45 Identities=24% Similarity=0.334 Sum_probs=38.7
Q ss_pred cCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHH
Q 015682 100 LLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEAL 145 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al 145 (402)
.+|++++-.+.++| -.|.++.++|..+|+|.+||+++..+.+.-|
T Consensus 4 ~L~~~er~vi~~~y-~~~~t~~eIa~~lg~s~~~V~~~~~~al~kL 48 (50)
T PF04545_consen 4 QLPPREREVIRLRY-FEGLTLEEIAERLGISRSTVRRILKRALKKL 48 (50)
T ss_dssp TS-HHHHHHHHHHH-TST-SHHHHHHHHTSCHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHh-cCCCCHHHHHHHHCCcHHHHHHHHHHHHHHh
Confidence 48999999999999 5689999999999999999999999887765
No 10
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=95.75 E-value=0.0026 Score=43.06 Aligned_cols=41 Identities=29% Similarity=0.294 Sum_probs=23.2
Q ss_pred CcCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHH
Q 015682 99 RLLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWR 140 (402)
Q Consensus 99 ~~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~ 140 (402)
+.|+.+++..|.-. +..|.+++.||..+|+|+|||++.+.+
T Consensus 3 ~~Lt~~eR~~I~~l-~~~G~s~~~IA~~lg~s~sTV~relkR 43 (44)
T PF13936_consen 3 KHLTPEERNQIEAL-LEQGMSIREIAKRLGRSRSTVSRELKR 43 (44)
T ss_dssp ---------HHHHH-HCS---HHHHHHHTT--HHHHHHHHHH
T ss_pred cchhhhHHHHHHHH-HHcCCCHHHHHHHHCcCcHHHHHHHhc
Confidence 35778888877744 689999999999999999999998864
No 11
>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=94.79 E-value=0.0065 Score=41.27 Aligned_cols=39 Identities=33% Similarity=0.296 Sum_probs=29.3
Q ss_pred cCCHHHHHHHHhhhccCCCccccccccccccccchhhhHH
Q 015682 100 LLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTW 139 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~ 139 (402)
.++.+ ++.-++..++.|.+..+||..||||++||.+++.
T Consensus 5 ~~~~~-~~~~i~~l~~~G~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 5 KLSKE-QIEEIKELYAEGMSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp SSSHC-CHHHHHHHHHTT--HHHHHHHTTS-HHHHHHHHC
T ss_pred CCCHH-HHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHh
Confidence 34443 5666777889999999999999999999999874
No 12
>smart00351 PAX Paired Box domain.
Probab=94.56 E-value=0.028 Score=47.20 Aligned_cols=47 Identities=23% Similarity=0.321 Sum_probs=41.0
Q ss_pred ccCCcCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHH
Q 015682 96 IEGRLLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIE 143 (402)
Q Consensus 96 ~~~~~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~ 143 (402)
.+++++|.+++.-|.+.+. .|.+.+.|+..||||++||++++.++-+
T Consensus 13 ~~~~~~s~~~R~riv~~~~-~G~s~~~iA~~~gvs~~tV~kwi~r~~~ 59 (125)
T smart00351 13 VNGRPLPDEERQRIVELAQ-NGVRPCDISRQLCVSHGCVSKILGRYYE 59 (125)
T ss_pred cCCCCCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4567799999998887775 7999999999999999999999998754
No 13
>cd00131 PAX Paired Box domain
Probab=94.20 E-value=0.038 Score=46.59 Aligned_cols=47 Identities=23% Similarity=0.297 Sum_probs=41.6
Q ss_pred ccCCcCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHH
Q 015682 96 IEGRLLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIE 143 (402)
Q Consensus 96 ~~~~~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~ 143 (402)
.+++++|.+.+.-|.+.+ +.|.+.+.++..||||++||.+++.++-+
T Consensus 13 ~m~~~lS~d~R~rIv~~~-~~G~s~~~iA~~~~Vs~~tV~r~i~r~~e 59 (128)
T cd00131 13 VNGRPLPDSIRQRIVELA-QSGIRPCDISRQLRVSHGCVSKILNRYYE 59 (128)
T ss_pred cCCCcCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 567889999988888776 68999999999999999999999988765
No 14
>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=94.05 E-value=0.039 Score=38.70 Aligned_cols=44 Identities=23% Similarity=0.273 Sum_probs=33.4
Q ss_pred cCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHH
Q 015682 100 LLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEA 144 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~a 144 (402)
.+|+.++.++.|+|+. |.++.++|..+|+|.+||...+.+....
T Consensus 10 ~L~~~~r~i~~l~~~~-g~s~~eIa~~l~~s~~~v~~~l~ra~~~ 53 (54)
T PF08281_consen 10 QLPERQREIFLLRYFQ-GMSYAEIAEILGISESTVKRRLRRARKK 53 (54)
T ss_dssp CS-HHHHHHHHHHHTS----HHHHHHHCTS-HHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHH-CcCHHHHHHHHCcCHHHHHHHHHHHHhh
Confidence 4888999999988875 8999999999999999999888776543
No 15
>PF13518 HTH_28: Helix-turn-helix domain
Probab=93.67 E-value=0.03 Score=38.81 Aligned_cols=37 Identities=32% Similarity=0.415 Sum_probs=30.9
Q ss_pred HHHHHhhhccCCCccccccccccccccchhhhHHHHHH
Q 015682 106 QVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIE 143 (402)
Q Consensus 106 ~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~ 143 (402)
++.+...++ .|.++..++..||||.+||.+++..+-.
T Consensus 2 r~~iv~~~~-~g~s~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 2 RLQIVELYL-EGESVREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred HHHHHHHHH-cCCCHHHHHHHHCCCHhHHHHHHHHHHh
Confidence 456666677 5779999999999999999999987764
No 16
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=93.63 E-value=0.012 Score=40.70 Aligned_cols=37 Identities=24% Similarity=0.210 Sum_probs=22.4
Q ss_pred HHHHHHhhhccCCCccccccccccccccchhhhHHHHH
Q 015682 105 KQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFI 142 (402)
Q Consensus 105 ~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~ 142 (402)
.++.+...+. .|.+...++..+|||++||++++.++.
T Consensus 6 ~R~~ii~l~~-~G~s~~~ia~~lgvs~~Tv~~w~kr~~ 42 (50)
T PF13384_consen 6 RRAQIIRLLR-EGWSIREIAKRLGVSRSTVYRWIKRYR 42 (50)
T ss_dssp ----HHHHHH-HT--HHHHHHHHTS-HHHHHHHHT---
T ss_pred HHHHHHHHHH-CCCCHHHHHHHHCcCHHHHHHHHHHcc
Confidence 3444444444 499999999999999999999987764
No 17
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=92.03 E-value=0.07 Score=45.41 Aligned_cols=44 Identities=25% Similarity=0.218 Sum_probs=39.6
Q ss_pred cCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHH
Q 015682 100 LLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIE 143 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~ 143 (402)
+.+.+.+.+++..++..|.|.+.++..||||.||+.++++++-+
T Consensus 4 ~~s~~~R~~~~~~~~~~G~S~re~Ak~~gvs~sTvy~wv~r~~e 47 (138)
T COG3415 4 PFSNDLRERVVDAVVGEGLSCREAAKRFGVSISTVYRWVRRYRE 47 (138)
T ss_pred hhhHHHHHHHHHHHHHcCccHHHHHHHhCccHHHHHHHHHHhcc
Confidence 45678889999999999999999999999999999999987754
No 18
>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=91.75 E-value=0.16 Score=39.87 Aligned_cols=51 Identities=33% Similarity=0.444 Sum_probs=45.2
Q ss_pred cCCcCCHHHHHHHHhhhccCCCcccccccccc-ccccchhhhHHHHHHHHHH
Q 015682 97 EGRLLSVEKQVAIALRRLASGESQVSVGVAFG-VGQSTVSQVTWRFIEALEE 147 (402)
Q Consensus 97 ~~~~ls~e~~l~i~L~~La~g~s~~~l~~~fg-vs~sTv~~~i~~v~~al~~ 147 (402)
+.+.+...-++++.|..--+|.++.+||..|| .++|||+..+.++-..+.+
T Consensus 24 R~~~~~~aR~ia~yl~~~~~~~s~~~Ig~~fg~r~hStV~~a~~ri~~~~~~ 75 (90)
T cd06571 24 RKKEIALARQIAMYLARELTGLSLPEIGRAFGGRDHSTVLHAVRKIEELLEE 75 (90)
T ss_pred CCcCcchHHHHHHHHHHHHhCCCHHHHHHHhCCCCHhHHHHHHHHHHHHHHh
Confidence 44567888899999999999999999999999 9999999999998887754
No 19
>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=91.68 E-value=0.068 Score=36.30 Aligned_cols=36 Identities=22% Similarity=0.297 Sum_probs=28.1
Q ss_pred HHHHHHHhhhccCC-CccccccccccccccchhhhHH
Q 015682 104 EKQVAIALRRLASG-ESQVSVGVAFGVGQSTVSQVTW 139 (402)
Q Consensus 104 e~~l~i~L~~La~g-~s~~~l~~~fgvs~sTv~~~i~ 139 (402)
|+.+..+|..+..| .+++..+..|||++||+++.++
T Consensus 2 ee~l~~Ai~~v~~g~~S~r~AA~~ygVp~sTL~~r~~ 38 (45)
T PF05225_consen 2 EEDLQKAIEAVKNGKMSIRKAAKKYGVPRSTLRRRLR 38 (45)
T ss_dssp HHHHHHHHHHHHTTSS-HHHHHHHHT--HHHHHHHHH
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHc
Confidence 56777788888888 9999999999999999987665
No 20
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=91.53 E-value=0.13 Score=42.86 Aligned_cols=46 Identities=20% Similarity=0.233 Sum_probs=42.2
Q ss_pred CCcCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHH
Q 015682 98 GRLLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIE 143 (402)
Q Consensus 98 ~~~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~ 143 (402)
++..|.|.++.++...+..|.+..+++..||||.+|+++++..+..
T Consensus 10 rr~ys~EfK~~aV~~~~~~g~sv~evA~e~gIs~~tl~~W~r~y~~ 55 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFEPGMTVSLVARQHGVAASQLFLWRKQYQE 55 (121)
T ss_pred CCCCCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHhh
Confidence 4568999999999999999999999999999999999999998754
No 21
>PRK04217 hypothetical protein; Provisional
Probab=91.47 E-value=0.17 Score=41.32 Aligned_cols=49 Identities=20% Similarity=0.223 Sum_probs=40.3
Q ss_pred cCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhh
Q 015682 100 LLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERA 149 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~ 149 (402)
.++.+++-++.|+++ .|.++.+||..+|||.+||.+++++....|.+.+
T Consensus 42 ~Lt~eereai~l~~~-eGlS~~EIAk~LGIS~sTV~r~L~RArkkLre~L 90 (110)
T PRK04217 42 FMTYEEFEALRLVDY-EGLTQEEAGKRMGVSRGTVWRALTSARKKVAQML 90 (110)
T ss_pred cCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 578888766655544 6889999999999999999999999888886643
No 22
>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=91.27 E-value=0.059 Score=40.59 Aligned_cols=45 Identities=27% Similarity=0.279 Sum_probs=38.0
Q ss_pred CCcCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHH
Q 015682 98 GRLLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFI 142 (402)
Q Consensus 98 ~~~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~ 142 (402)
++..|++.++.+.-.+|..|.+..+++..+||+.+|+++++.++.
T Consensus 4 r~~ys~e~K~~~v~~~~~~g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 4 RRRYSPEFKLQAVREYLESGESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp S----HHHHHHHHHHHHHHHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHCCCceEeeecccccccccccHHHHHHh
Confidence 456899999999999999999999999999999999999999887
No 23
>PF02209 VHP: Villin headpiece domain; InterPro: IPR003128 Villin is an F-actin bundling protein involved in the maintenance of the microvilli of the absorptive epithelia. The villin-type "headpiece" domain is a modular motif found at the extreme C terminus of larger "core" domains in over 25 cytoskeletal proteins in plants and animals, often in assocation with the Gelsolin repeat. Although the headpiece is classified as an F-actin-binding domain, it has been shown that not all headpiece domains are intrinsically F-actin-binding motifs, surface charge distribution may be an important element for F-actin recognition []. An autonomously folding, 35 residue, thermostable subdomain (HP36) of the full-length 76 amino acid residue villin headpiece, is the smallest known example of a cooperatively folded domain of a naturally occurring protein. The structure of HP36, as determined by NMR spectroscopy, consists of three short helices surrounding a tightly packed hydrophobic core []. ; GO: 0003779 actin binding, 0007010 cytoskeleton organization; PDB: 1ZV6_A 1QZP_A 1UND_A 2PPZ_A 3TJW_B 1YU8_X 2JM0_A 1WY4_A 3MYC_A 1YU5_X ....
Probab=91.25 E-value=0.1 Score=33.54 Aligned_cols=23 Identities=22% Similarity=0.343 Sum_probs=17.5
Q ss_pred CChhhhhcccCCCHHHHHHHHHH
Q 015682 58 DEEEGFKYFFRVSKKTFDYICSL 80 (402)
Q Consensus 58 ~~~~~F~~~fRms~~tF~~L~~~ 80 (402)
++|++|...|+|+++.|..|-..
T Consensus 2 Lsd~dF~~vFgm~~~eF~~lP~W 24 (36)
T PF02209_consen 2 LSDEDFEKVFGMSREEFYKLPKW 24 (36)
T ss_dssp S-HHHHHHHHSS-HHHHHHS-HH
T ss_pred cCHHHHHHHHCCCHHHHHHChHH
Confidence 47899999999999999987543
No 24
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=90.97 E-value=0.18 Score=35.08 Aligned_cols=43 Identities=21% Similarity=0.346 Sum_probs=34.7
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHH
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEAL 145 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al 145 (402)
++..++-++.+ +..|.++.+++..+|+|.+||.+++.+....+
T Consensus 4 l~~~e~~i~~~--~~~g~s~~eia~~l~is~~tv~~~~~~~~~kl 46 (58)
T smart00421 4 LTPREREVLRL--LAEGLTNKEIAERLGISEKTVKTHLSNIMRKL 46 (58)
T ss_pred CCHHHHHHHHH--HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 56666554433 47899999999999999999999999887665
No 25
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=90.92 E-value=0.17 Score=39.24 Aligned_cols=45 Identities=18% Similarity=0.231 Sum_probs=41.8
Q ss_pred CcCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHH
Q 015682 99 RLLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIE 143 (402)
Q Consensus 99 ~~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~ 143 (402)
-.|++..++.++-..+..|.+...++..||||..|+++++.++-.
T Consensus 7 A~Lt~~gR~~lv~~vv~~g~~~a~aA~~~gVS~~Ta~kW~~Ryra 51 (85)
T PF13011_consen 7 ARLTPRGRLRLVRRVVEQGWPVAHAAAEFGVSRRTAYKWLARYRA 51 (85)
T ss_pred CCCCHHHHHHHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 368999999999999999999999999999999999999988774
No 26
>PRK00118 putative DNA-binding protein; Validated
Probab=90.88 E-value=0.21 Score=40.36 Aligned_cols=49 Identities=22% Similarity=0.201 Sum_probs=40.2
Q ss_pred cCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhh
Q 015682 100 LLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERA 149 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~ 149 (402)
.+|..++-++.++++ .|.++..||..+|+|++||++.+.+....+.+..
T Consensus 17 ~L~ekqRevl~L~y~-eg~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~ 65 (104)
T PRK00118 17 LLTEKQRNYMELYYL-DDYSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYE 65 (104)
T ss_pred cCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 467777777766655 5999999999999999999999998887776543
No 27
>smart00153 VHP Villin headpiece domain.
Probab=90.61 E-value=0.15 Score=32.82 Aligned_cols=22 Identities=18% Similarity=0.317 Sum_probs=19.0
Q ss_pred CChhhhhcccCCCHHHHHHHHH
Q 015682 58 DEEEGFKYFFRVSKKTFDYICS 79 (402)
Q Consensus 58 ~~~~~F~~~fRms~~tF~~L~~ 79 (402)
++|++|...|+||++.|..|-.
T Consensus 2 LsdeeF~~vfgmsr~eF~~LP~ 23 (36)
T smart00153 2 LSDEDFEEVFGMTREEFYKLPL 23 (36)
T ss_pred CCHHHHHHHHCCCHHHHHhCcH
Confidence 3689999999999999988743
No 28
>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=90.49 E-value=0.2 Score=34.12 Aligned_cols=43 Identities=28% Similarity=0.292 Sum_probs=35.3
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHH
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEA 144 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~a 144 (402)
++++++-++.+.++ .|.++.+++..+|++.+|+.+++.+....
T Consensus 11 l~~~~~~~~~~~~~-~~~~~~~ia~~~~~s~~~i~~~~~~~~~~ 53 (55)
T cd06171 11 LPEREREVILLRFG-EGLSYEEIAEILGISRSTVRQRLHRALKK 53 (55)
T ss_pred CCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 66777777766665 78999999999999999999998876543
No 29
>PF13340 DUF4096: Putative transposase of IS4/5 family (DUF4096)
Probab=89.80 E-value=0.68 Score=34.97 Aligned_cols=46 Identities=20% Similarity=0.156 Sum_probs=39.5
Q ss_pred cCCcCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHH
Q 015682 97 EGRLLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIE 143 (402)
Q Consensus 97 ~~~~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~ 143 (402)
.++.++..+-+-..|+.|.||+.++.|...|| +.+||++.+.+...
T Consensus 21 ~~~~~~~R~v~~ail~~lrtG~~Wr~LP~~fg-~~~tv~~~f~rW~~ 66 (75)
T PF13340_consen 21 GRPRIDLREVLNAILYVLRTGCPWRDLPEDFG-PWSTVYRRFRRWSR 66 (75)
T ss_pred CCCccchHHHHhcccccceecceecccchhcc-CcCcHHHHHHHHHH
Confidence 45567888889999999999999999999999 88899888876543
No 30
>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=89.64 E-value=0.1 Score=39.58 Aligned_cols=42 Identities=19% Similarity=0.203 Sum_probs=29.7
Q ss_pred HHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHH
Q 015682 106 QVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEE 147 (402)
Q Consensus 106 ~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~ 147 (402)
.+-++-+.+.+..+.+..|..||||+|||++=+.+=+..|..
T Consensus 8 ~i~i~~yIi~~~aTVR~~Ak~FGvSKSTVHkDvteRL~~in~ 49 (82)
T PF12116_consen 8 VIEIANYIIETKATVRQAAKVFGVSKSTVHKDVTERLPKINP 49 (82)
T ss_dssp HHHHHHHHHHH---HHHHHHHHTS-HHHHHHHHTTHHHHH-H
T ss_pred HHHHHHHHHHcccHHHHHHHHHCCcHHHHHHHHHHHHHhcCH
Confidence 455677788899999999999999999999877665555543
No 31
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=89.51 E-value=0.28 Score=42.66 Aligned_cols=47 Identities=21% Similarity=0.258 Sum_probs=42.5
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhh
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERA 149 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~ 149 (402)
+|++++-++.|++ .|.++..||..+|+|.+||...+.+....|.+.+
T Consensus 113 L~~~~r~il~l~~--~g~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l 159 (166)
T PRK09639 113 MTERDRTVLLLRF--SGYSYKEIAEALGIKESSVGTTLARAKKKFRKIY 159 (166)
T ss_pred CCHHHHHHHHHHH--cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 7888999999988 8999999999999999999999999888886654
No 32
>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=89.35 E-value=0.18 Score=31.19 Aligned_cols=37 Identities=30% Similarity=0.323 Sum_probs=28.0
Q ss_pred cCCHHHHHHHHhhhccCCCccccccccccccccchhhh
Q 015682 100 LLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQV 137 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~ 137 (402)
.++.+++..+... +..|.+...++..||++++|++++
T Consensus 5 ~~~~~~~~~i~~~-~~~~~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 5 KLTPEQIEEARRL-LAAGESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred cCCHHHHHHHHHH-HHcCCCHHHHHHHHCCCHHHHHHh
Confidence 4566665555444 446789999999999999999876
No 33
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=89.07 E-value=0.28 Score=43.00 Aligned_cols=49 Identities=31% Similarity=0.365 Sum_probs=42.4
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhhc
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERAK 150 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~~ 150 (402)
+|+.++.++.|+++ .|.++.+||..+|+|.+||...+.+....|.+.+.
T Consensus 129 L~~~~r~vl~l~~~-~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 177 (182)
T PRK09652 129 LPEELRTAITLREI-EGLSYEEIAEIMGCPIGTVRSRIFRAREALRAKLQ 177 (182)
T ss_pred CCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 78888888888887 68999999999999999999999888887766543
No 34
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=89.05 E-value=0.33 Score=43.04 Aligned_cols=49 Identities=16% Similarity=0.128 Sum_probs=42.8
Q ss_pred cCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhh
Q 015682 100 LLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERA 149 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~ 149 (402)
.||++++.++.|+++ .|.++.+||..+|+|.+||...+++-+..+.+.+
T Consensus 127 ~Lp~~~R~v~~L~~~-~g~s~~EIA~~lgis~~tVk~~l~rAl~~~~~~~ 175 (178)
T PRK12529 127 TLRPRVKQAFLMATL-DGMKQKDIAQALDIALPTVKKYIHQAYVTCLSLM 175 (178)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhC
Confidence 388999999999988 7999999999999999999998888777776543
No 35
>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=88.49 E-value=0.61 Score=45.39 Aligned_cols=71 Identities=17% Similarity=0.262 Sum_probs=54.7
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhhccc--cc--CCCchhHHHHHHHHHHhh
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERAKHH--LK--WPDSNRMEEIKSKFEESF 172 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~~~~--i~--~P~~~~~~~i~~~f~~~~ 172 (402)
+|+.++.++.|+++ .|.++..||..+|+|.+||...+.+....|.+.+... -. -|...+..++...|...+
T Consensus 143 Lp~~~R~v~~L~~~-~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~~~~~~~~~~~~~~~~v~~~~~a~ 217 (324)
T TIGR02960 143 LPPRQRAVLLLRDV-LGWRAAETAELLGTSTASVNSALQRARATLDEVGPSARDDQLAQPPSPEEQDLLERYIAAF 217 (324)
T ss_pred CCHHHhhHhhhHHH-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhcccccccccCCCCCHHHHHHHHHHHHHH
Confidence 78889999999887 6899999999999999999999999999998866543 11 133345556666665543
No 36
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=88.15 E-value=0.31 Score=43.63 Aligned_cols=49 Identities=20% Similarity=0.217 Sum_probs=42.7
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhhc
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERAK 150 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~~ 150 (402)
+|++++-++.|+++. |.++.+||..+|+|.+||...+.+....|.+.+.
T Consensus 142 L~~~~~~v~~l~~~~-g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~ 190 (194)
T PRK12519 142 LPESQRQVLELAYYE-GLSQSEIAKRLGIPLGTVKARARQGLLKLRELLQ 190 (194)
T ss_pred CCHHHhhhhhhhhhc-CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 788888888888876 8999999999999999999999998888866543
No 37
>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=87.84 E-value=0.83 Score=38.88 Aligned_cols=46 Identities=24% Similarity=0.351 Sum_probs=39.5
Q ss_pred cCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHH
Q 015682 100 LLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEE 147 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~ 147 (402)
.++..++-++.|+ ..|.++..+|..+|+|++||+.+.++..+.|..
T Consensus 6 ~Lte~qr~VL~Lr--~~GlTq~EIAe~LgiS~stV~~~e~ra~kkLr~ 51 (137)
T TIGR00721 6 FLTERQIKVLELR--EKGLSQKEIAKELKTTRANVSAIEKRAMENIEK 51 (137)
T ss_pred CCCHHHHHHHHHH--HcCCCHHHHHHHHCcCHHHHHHHHHhHHHHHHH
Confidence 4788888888884 699999999999999999999998887777753
No 38
>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=87.55 E-value=0.47 Score=40.57 Aligned_cols=46 Identities=20% Similarity=0.284 Sum_probs=40.3
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHH
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEE 147 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~ 147 (402)
+|+.++-++.|+++ .|.++.+||..+|+|.+||...+.+....|.+
T Consensus 114 L~~~~r~il~l~~~-~~~~~~eIA~~lgis~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 114 LPEQCRKIFILSRF-EGKSYKEIAEELGISVKTVEYHISKALKELRK 159 (161)
T ss_pred CCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 67888999999887 59999999999999999999999988777643
No 39
>PRK06030 hypothetical protein; Provisional
Probab=87.46 E-value=0.43 Score=39.91 Aligned_cols=47 Identities=23% Similarity=0.287 Sum_probs=41.6
Q ss_pred CcCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHH
Q 015682 99 RLLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEAL 145 (402)
Q Consensus 99 ~~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al 145 (402)
+.+...-|+++.|.+--+|.++.+||..||.++|||...++.+-+.+
T Consensus 51 k~i~~aRqIAMYL~r~~~~~sl~~IG~~FGRDHSTV~haikkIe~~~ 97 (124)
T PRK06030 51 REVSRIRQIAMYVAHVSLGWPMNEVALAFGRDRTTVGHACHTVEDLR 97 (124)
T ss_pred cccchHHHHHHHHHHHHcCCCHHHHHHHHCCChhHHHHHHHHHHHHh
Confidence 56888899999999999999999999999999999998888655544
No 40
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=87.46 E-value=0.5 Score=43.85 Aligned_cols=50 Identities=26% Similarity=0.328 Sum_probs=43.7
Q ss_pred CCHHHHHHHHhhhc---cCCCccccccccccccccchhhhHHHHHHHHHHhhc
Q 015682 101 LSVEKQVAIALRRL---ASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERAK 150 (402)
Q Consensus 101 ls~e~~l~i~L~~L---a~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~~ 150 (402)
+|+.++-++.|+|. -.|.++..||..+|||.+||...+++....|.+.+.
T Consensus 179 Lp~~~R~v~~L~y~l~~~eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~l~ 231 (234)
T PRK08301 179 LSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEKRIIKRLKKEIN 231 (234)
T ss_pred CCHHHHHHHHHHhccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 78899999999884 579999999999999999999999998888866443
No 41
>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=87.25 E-value=0.32 Score=38.43 Aligned_cols=39 Identities=21% Similarity=0.245 Sum_probs=31.5
Q ss_pred CCHHHHHHHHhhh------ccCCCccccccccccccccchhhhHH
Q 015682 101 LSVEKQVAIALRR------LASGESQVSVGVAFGVGQSTVSQVTW 139 (402)
Q Consensus 101 ls~e~~l~i~L~~------La~g~s~~~l~~~fgvs~sTv~~~i~ 139 (402)
++++++-++.++| +..|.+|+.|+...|||.+||+|+-+
T Consensus 33 LTp~E~~~l~~R~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~sn 77 (94)
T TIGR01321 33 LTRSEREDLGDRIRIVNELLNGNMSQREIASKLGVSIATITRGSN 77 (94)
T ss_pred CCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHhCCChhhhhHHHh
Confidence 6777777777763 35678999999999999999988754
No 42
>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=87.22 E-value=0.5 Score=41.09 Aligned_cols=47 Identities=26% Similarity=0.299 Sum_probs=41.6
Q ss_pred cCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHH
Q 015682 100 LLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEE 147 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~ 147 (402)
.+|+.++.++.|+|+. |.++.+||..+|+|.+||...+++....|.+
T Consensus 122 ~L~~~~r~vl~l~~~~-g~s~~eIA~~l~is~~tv~~~l~ra~~~Lr~ 168 (170)
T TIGR02952 122 ILTPKQQHVIALRFGQ-NLPIAEVARILGKTEGAVKILQFRAIKKLAR 168 (170)
T ss_pred hCCHHHHHHHHHHHhc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4888999999998875 8999999999999999999999988877754
No 43
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=86.95 E-value=0.54 Score=40.71 Aligned_cols=48 Identities=21% Similarity=0.281 Sum_probs=41.8
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhh
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERA 149 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~ 149 (402)
+|++++-++.|+|+. |.++.+||..+|+|.+||...+.+....|...+
T Consensus 110 L~~~~r~v~~l~~~~-~~s~~EIA~~lgis~~tV~~~l~ra~~~lr~~l 157 (163)
T PRK07037 110 LPARTRYAFEMYRLH-GETQKDIARELGVSPTLVNFMIRDALVHCRKCL 157 (163)
T ss_pred CCHHHHHHHHHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 788888888888776 999999999999999999999888888776544
No 44
>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=86.86 E-value=0.57 Score=32.46 Aligned_cols=42 Identities=19% Similarity=0.359 Sum_probs=32.6
Q ss_pred CHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHH
Q 015682 102 SVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEAL 145 (402)
Q Consensus 102 s~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al 145 (402)
+..++-++.+ +..|.++.++|..+++|.+||...+.+....+
T Consensus 2 ~~~e~~i~~~--~~~~~s~~eia~~l~~s~~tv~~~~~~~~~~l 43 (57)
T cd06170 2 TPREREVLRL--LAEGKTNKEIADILGISEKTVKTHLRNIMRKL 43 (57)
T ss_pred CHHHHHHHHH--HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHh
Confidence 3344444433 45899999999999999999999998877655
No 45
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=86.48 E-value=0.67 Score=40.88 Aligned_cols=47 Identities=21% Similarity=0.156 Sum_probs=41.8
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHh
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEER 148 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~ 148 (402)
+|++++-++.|+++ .|.++..||..+|+|..||...+.+....|.+.
T Consensus 130 L~~~~r~i~~l~~~-~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 176 (179)
T PRK12514 130 LEKDRAAAVRRAYL-EGLSYKELAERHDVPLNTMRTWLRRSLLKLREC 176 (179)
T ss_pred CCHHHHHHHHHHHH-cCCCHHHHHHHHCCChHHHHHHHHHHHHHHHHH
Confidence 78889999999887 689999999999999999999999888887654
No 46
>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=86.36 E-value=0.31 Score=36.66 Aligned_cols=40 Identities=20% Similarity=0.221 Sum_probs=35.4
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHH
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWR 140 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~ 140 (402)
+|...+.+..|.+.-.|.++.+||..+|+|.+||...++.
T Consensus 16 l~~~~r~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 16 VDSLAEAAAALAREEAGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred CCHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 6777888888888889999999999999999999887753
No 47
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=86.18 E-value=0.57 Score=44.30 Aligned_cols=49 Identities=22% Similarity=0.251 Sum_probs=43.0
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhhc
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERAK 150 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~~ 150 (402)
+|+.++.++.|+|+ .|.++..||..+|+|.+||+++..+....|.+.+.
T Consensus 206 L~~~er~vi~l~y~-e~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~l~ 254 (257)
T PRK05911 206 LEEKERKVMALYYY-EELVLKEIGKILGVSESRVSQIHSKALLKLRATLS 254 (257)
T ss_pred CCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 78889999999886 68999999999999999999999998888766543
No 48
>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=86.02 E-value=0.28 Score=38.42 Aligned_cols=31 Identities=19% Similarity=0.312 Sum_probs=27.0
Q ss_pred HHHhhhccCCCccccccccccccccchhhhH
Q 015682 108 AIALRRLASGESQVSVGVAFGVGQSTVSQVT 138 (402)
Q Consensus 108 ~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i 138 (402)
...+.+++.|.+...|+..+|||++||+++.
T Consensus 41 ~~I~~ll~~G~S~~eIA~~LgISrsTIyRi~ 71 (88)
T TIGR02531 41 LQVAKMLKQGKTYSDIEAETGASTATISRVK 71 (88)
T ss_pred HHHHHHHHCCCCHHHHHHHHCcCHHHHHHHH
Confidence 5556678999999999999999999999954
No 49
>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=85.99 E-value=0.64 Score=44.27 Aligned_cols=48 Identities=17% Similarity=0.261 Sum_probs=42.6
Q ss_pred CCHHHHHHHHhhhcc-CCCccccccccccccccchhhhHHHHHHHHHHh
Q 015682 101 LSVEKQVAIALRRLA-SGESQVSVGVAFGVGQSTVSQVTWRFIEALEER 148 (402)
Q Consensus 101 ls~e~~l~i~L~~La-~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~ 148 (402)
+|..++.++.|+|+. .|.++..||..+|||.++|+++..+.+.-|...
T Consensus 219 L~~rer~vl~l~y~~~~~~t~~eIA~~lgvS~~~V~q~~~~Al~kLr~~ 267 (270)
T TIGR02392 219 LDARSRRIIEARWLDDDKLTLQELAAEYGVSAERIRQIEKNAMKKLKAA 267 (270)
T ss_pred CCHHHHHHHHHHhcCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 888999999999985 478999999999999999999999888877553
No 50
>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=85.93 E-value=0.63 Score=39.00 Aligned_cols=46 Identities=26% Similarity=0.306 Sum_probs=38.6
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHH
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEE 147 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~ 147 (402)
+|+.++-++.+.++ .|.++.+||..+|+|.+||++...+....|.+
T Consensus 111 L~~~~~~ii~~~~~-~g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 111 LPEREREVLVLRYL-EGLSYKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred CCHHHHHHHhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 67777777777665 69999999999999999999999998877643
No 51
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=85.85 E-value=0.41 Score=42.05 Aligned_cols=47 Identities=17% Similarity=0.226 Sum_probs=41.7
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHh
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEER 148 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~ 148 (402)
+|+.++.++.|+++ .|.++.+||..+|+|.+||...+.+....|...
T Consensus 127 L~~~~r~v~~l~~~-~g~s~~eIA~~l~is~~~V~~~l~ra~~~l~~~ 173 (176)
T PRK09638 127 LDPEFRAPVILKHY-YGYTYEEIAKMLNIPEGTVKSRVHHGIKQLRKE 173 (176)
T ss_pred CCHHHhheeeehhh-cCCCHHHHHHHHCCChhHHHHHHHHHHHHHHHH
Confidence 78888999999887 599999999999999999999998888877654
No 52
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=85.44 E-value=0.55 Score=42.01 Aligned_cols=49 Identities=12% Similarity=0.117 Sum_probs=43.1
Q ss_pred cCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhh
Q 015682 100 LLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERA 149 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~ 149 (402)
.+|+..+-++.|+++- |.++..||..+|+|.+||...+++....|.+.+
T Consensus 134 ~Lp~~~R~v~~L~~~~-g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l 182 (189)
T PRK12530 134 HLPAQQARVFMMREYL-ELSSEQICQECDISTSNLHVLLYRARLQLQACL 182 (189)
T ss_pred hCCHHHHHHHhHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3788899999999876 999999999999999999999998888876543
No 53
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=84.90 E-value=0.79 Score=42.54 Aligned_cols=49 Identities=22% Similarity=0.327 Sum_probs=42.3
Q ss_pred cCCHHHHHHHHhhhc---cCCCccccccccccccccchhhhHHHHHHHHHHh
Q 015682 100 LLSVEKQVAIALRRL---ASGESQVSVGVAFGVGQSTVSQVTWRFIEALEER 148 (402)
Q Consensus 100 ~ls~e~~l~i~L~~L---a~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~ 148 (402)
.+|+.++.++.|+|+ -.|.++..||..+|+|.+||.+..++....|.+.
T Consensus 175 ~Lp~~~R~i~~l~y~~~~~e~~S~~EIA~~lgis~~tV~~~~~rA~~kLr~~ 226 (233)
T PRK05803 175 ILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKKLFKE 226 (233)
T ss_pred hCCHHHHHHHHHHhCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 488999999999886 4678999999999999999999988877777554
No 54
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=84.90 E-value=0.76 Score=40.00 Aligned_cols=49 Identities=29% Similarity=0.240 Sum_probs=43.1
Q ss_pred cCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhh
Q 015682 100 LLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERA 149 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~ 149 (402)
.+|+.++-++.|+++ .|.++.+||..+|+|.+||...+.+....|.+.+
T Consensus 112 ~L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 160 (164)
T PRK12547 112 LLSADQREAIILIGA-SGFSYEDAAAICGCAVGTIKSRVSRARNRLQELL 160 (164)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 378889999999888 7999999999999999999999999888886543
No 55
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=84.72 E-value=0.72 Score=40.82 Aligned_cols=48 Identities=21% Similarity=0.134 Sum_probs=42.8
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhh
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERA 149 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~ 149 (402)
+|+.++-++.|+++. |.++..+|..+|+|.+||...+.+....|.+.+
T Consensus 128 L~~~~r~v~~l~~~~-g~s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~l 175 (179)
T PRK09415 128 LPIKYREVIYLFYYE-ELSIKEIAEVTGVNENTVKTRLKKAKELLKKGL 175 (179)
T ss_pred CCHHHhhHhHhHHhc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 788899999998886 999999999999999999999999888886644
No 56
>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=84.59 E-value=0.82 Score=40.35 Aligned_cols=47 Identities=19% Similarity=0.157 Sum_probs=41.2
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHh
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEER 148 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~ 148 (402)
+|+.++-++.|+++. |.++.+||..+|+|.+||...+++....|.+.
T Consensus 135 Lp~~~r~v~~l~~~~-g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 181 (183)
T TIGR02999 135 VDPRQAEVVELRFFA-GLTVEEIAELLGVSVRTVERDWRFARAWLADE 181 (183)
T ss_pred CCHHHHHHHHHHHHc-CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 788888888888775 89999999999999999999999988887653
No 57
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=83.93 E-value=0.86 Score=40.59 Aligned_cols=50 Identities=22% Similarity=0.187 Sum_probs=43.1
Q ss_pred cCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhhc
Q 015682 100 LLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERAK 150 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~~ 150 (402)
.+|+..+-++.|+++ .|.++.+||..+|||.+||...+.+....|.+.+.
T Consensus 111 ~Lp~~~R~v~~L~~~-eg~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~~ 160 (182)
T PRK12511 111 DLPEEQRAALHLVAI-EGLSYQEAAAVLGIPIGTLMSRIGRARAALRAFEE 160 (182)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHH
Confidence 378889999999888 59999999999999999999999888887765433
No 58
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=83.91 E-value=0.9 Score=43.67 Aligned_cols=48 Identities=19% Similarity=0.264 Sum_probs=42.7
Q ss_pred CCHHHHHHHHhhhcc-CCCccccccccccccccchhhhHHHHHHHHHHh
Q 015682 101 LSVEKQVAIALRRLA-SGESQVSVGVAFGVGQSTVSQVTWRFIEALEER 148 (402)
Q Consensus 101 ls~e~~l~i~L~~La-~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~ 148 (402)
++..++.++.++|+. .+.++..||..+|||+++|+++..+.+.-|...
T Consensus 231 L~~rEr~VL~lry~~~~~~Tl~EIA~~lgvS~~rVrqi~~~Al~kLR~~ 279 (284)
T PRK06596 231 LDERSRDIIEARWLDDDKSTLQELAAEYGVSAERVRQIEKNAMKKLKAA 279 (284)
T ss_pred CCHHHHHHHHHHhcCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 788999999999986 588999999999999999999999888877553
No 59
>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=83.90 E-value=0.86 Score=39.12 Aligned_cols=47 Identities=19% Similarity=0.200 Sum_probs=41.0
Q ss_pred cCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHH
Q 015682 100 LLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEE 147 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~ 147 (402)
.+|+.++-++.|+++ .|.++..||..+|+|.+||...+++....|.+
T Consensus 111 ~L~~~~r~v~~l~~~-~g~~~~eIA~~l~is~~tv~~~l~Rar~~Lr~ 157 (159)
T TIGR02989 111 KLPERQRELLQLRYQ-RGVSLTALAEQLGRTVNAVYKALSRLRVRLRD 157 (159)
T ss_pred HCCHHHHHHHHHHHh-cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 378889999999776 69999999999999999999999888777644
No 60
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=83.88 E-value=0.76 Score=41.07 Aligned_cols=51 Identities=22% Similarity=0.275 Sum_probs=44.0
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhhccc
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERAKHH 152 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~~~~ 152 (402)
+|++++-++.|+++ .|.++..||..+|+|..||...+.+....|.+.+..+
T Consensus 139 L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~~~ 189 (193)
T PRK11923 139 LPEDLRTALTLREF-DGLSYEDIASVMQCPVGTVRSRIFRAREAIDKALQPL 189 (193)
T ss_pred CCHHHhHHHhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 78888888888887 6999999999999999999999999888887655443
No 61
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=83.84 E-value=0.81 Score=42.08 Aligned_cols=49 Identities=24% Similarity=0.142 Sum_probs=43.3
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhhc
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERAK 150 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~~ 150 (402)
+|+.++-++.|+|+ .|.++..|+..+|||.+||...+++....|.+.+.
T Consensus 135 Lp~~~R~v~~L~y~-eg~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l~ 183 (216)
T PRK12533 135 LPVEYREVLVLREL-EDMSYREIAAIADVPVGTVMSRLARARRRLAALLG 183 (216)
T ss_pred CCHHHHhHhhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHc
Confidence 78889999999888 59999999999999999999999998888866543
No 62
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=83.84 E-value=0.83 Score=40.40 Aligned_cols=48 Identities=21% Similarity=0.177 Sum_probs=42.0
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhh
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERA 149 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~ 149 (402)
+|.+++-++.|.|+ .|.++..+|..+|||.+||...+++....|...+
T Consensus 137 L~~~~r~il~l~~~-~~~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l 184 (187)
T PRK09641 137 LPEKYRTVIVLKYI-EDLSLKEISEILDLPVGTVKTRIHRGREALRKQL 184 (187)
T ss_pred CCHHHHHHhhhHHh-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 78888888888887 6999999999999999999999998888776543
No 63
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=83.78 E-value=0.89 Score=39.63 Aligned_cols=48 Identities=27% Similarity=0.266 Sum_probs=41.4
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhh
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERA 149 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~ 149 (402)
+|+.++-++.|.++ .|.++.+||..+|+|.+||.+.+.+....|.+.+
T Consensus 126 L~~~~r~i~~l~~~-~~~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l 173 (179)
T PRK11924 126 LPVKQREVFLLRYV-EGLSYREIAEILGVPVGTVKSRLRRARQLLRECL 173 (179)
T ss_pred CCHHHHHHhhHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 77788888888877 5999999999999999999999999888776543
No 64
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=83.60 E-value=0.92 Score=40.58 Aligned_cols=49 Identities=22% Similarity=0.172 Sum_probs=43.5
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhhc
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERAK 150 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~~ 150 (402)
+|+.++-++.|+++ .|.++.+||..+|+|.+||...+.+....|.+.+.
T Consensus 117 Lp~~~r~i~~L~~~-~g~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~ 165 (187)
T PRK12516 117 LPDDQREAIILVGA-SGFAYEEAAEICGCAVGTIKSRVNRARQRLQEILQ 165 (187)
T ss_pred CCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 78889999999887 79999999999999999999999998888876544
No 65
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=83.31 E-value=0.92 Score=40.43 Aligned_cols=49 Identities=27% Similarity=0.204 Sum_probs=43.2
Q ss_pred cCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhh
Q 015682 100 LLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERA 149 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~ 149 (402)
.+|++++-++.|+++ .|.++.+||..+|+|.+||...+.+....|.+.+
T Consensus 131 ~L~~~~r~vl~l~~~-~~~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 179 (189)
T PRK12515 131 KLSPAHREIIDLVYY-HEKSVEEVGEIVGIPESTVKTRMFYARKKLAELL 179 (189)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 378889999999888 7999999999999999999999998888876643
No 66
>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=83.31 E-value=0.84 Score=40.50 Aligned_cols=49 Identities=29% Similarity=0.320 Sum_probs=42.3
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhhc
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERAK 150 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~~ 150 (402)
+|++++-++.|+|+ .|.++..||..+|++.+||...+++....|.+.+.
T Consensus 139 L~~~~r~v~~l~~~-~~~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l~ 187 (190)
T TIGR02939 139 LPEDLRTAITLREL-EGLSYEDIARIMDCPVGTVRSRIFRAREAIAIRLR 187 (190)
T ss_pred CCHHHhhhhhhhhh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence 67778888888776 79999999999999999999999999888876554
No 67
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=83.30 E-value=0.95 Score=40.66 Aligned_cols=48 Identities=25% Similarity=0.309 Sum_probs=42.5
Q ss_pred cCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHh
Q 015682 100 LLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEER 148 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~ 148 (402)
.+|++++-++.|+++ .|.++..||..+|||.+||...+++....|...
T Consensus 136 ~L~~~~r~i~~L~~~-~g~s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~ 183 (196)
T PRK12524 136 ALPERQRQAVVLRHI-EGLSNPEIAEVMEIGVEAVESLTARGKRALAAL 183 (196)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 378889989999888 799999999999999999999999988887654
No 68
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=83.14 E-value=0.93 Score=39.01 Aligned_cols=50 Identities=20% Similarity=0.214 Sum_probs=43.5
Q ss_pred cCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhhc
Q 015682 100 LLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERAK 150 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~~ 150 (402)
.+|+.++-++.|+++- |.++..||..+|+|.+||...+.+....|.+.+.
T Consensus 106 ~Lp~~~r~v~~l~~~~-g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 155 (161)
T PRK09047 106 KLPARQREAFLLRYWE-DMDVAETAAAMGCSEGSVKTHCSRATHALAKALE 155 (161)
T ss_pred hCCHHHHHHHHHHHHh-cCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 3888899999998874 9999999999999999999999999888866543
No 69
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=83.13 E-value=1 Score=39.94 Aligned_cols=49 Identities=14% Similarity=0.161 Sum_probs=43.2
Q ss_pred cCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhh
Q 015682 100 LLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERA 149 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~ 149 (402)
.+|++++-++.|+|+. |.++.+||..+|+|.+||...+++....|.+.+
T Consensus 131 ~L~~~~r~v~~l~~~~-g~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12512 131 TLPPRQRDVVQSISVE-GASIKETAAKLSMSEGAVRVALHRGLAALAAKF 179 (184)
T ss_pred hCCHHHHHHHHHHHHc-CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 3788888888888877 999999999999999999999999998887654
No 70
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=83.13 E-value=0.96 Score=38.68 Aligned_cols=46 Identities=24% Similarity=0.359 Sum_probs=38.7
Q ss_pred cCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHH
Q 015682 100 LLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEE 147 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~ 147 (402)
.+|+.++-.+.|+ ..|.++.++|..+|+|++||+.+.......|.+
T Consensus 6 ~Lt~rqreVL~lr--~~GlTq~EIAe~LGiS~~tVs~ie~ra~kkLr~ 51 (141)
T PRK03975 6 FLTERQIEVLRLR--ERGLTQQEIADILGTSRANVSSIEKRARENIEK 51 (141)
T ss_pred CCCHHHHHHHHHH--HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4788888888883 699999999999999999999998876666543
No 71
>PHA00675 hypothetical protein
Probab=83.07 E-value=0.49 Score=35.68 Aligned_cols=39 Identities=13% Similarity=0.129 Sum_probs=28.7
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHH
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTW 139 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~ 139 (402)
|+..+--.|-...-..|.++..||..||||+|||+.|.+
T Consensus 23 Lt~~qV~~IR~l~~r~G~s~~~IA~~fGVsrstV~~I~~ 61 (78)
T PHA00675 23 LTDAEVERIRELHEVEGMSYAVLAEKFEQSKGAIAKICR 61 (78)
T ss_pred cCHHHHHHHHHHHHhcCccHHHHHHHhCCCHHHHHHHHc
Confidence 554444444443336788999999999999999988764
No 72
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=83.04 E-value=0.38 Score=33.26 Aligned_cols=28 Identities=32% Similarity=0.350 Sum_probs=23.5
Q ss_pred ccCCCccccccccccccccchhhhHHHH
Q 015682 114 LASGESQVSVGVAFGVGQSTVSQVTWRF 141 (402)
Q Consensus 114 La~g~s~~~l~~~fgvs~sTv~~~i~~v 141 (402)
|..+.++.++|..+|||.+||.+++.+.
T Consensus 24 ~~~~~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 24 LRESRSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred HhhcCCHHHHHHHHCCCHHHHHHHHHhh
Confidence 3334589999999999999999998764
No 73
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=82.97 E-value=1.1 Score=39.74 Aligned_cols=47 Identities=23% Similarity=0.228 Sum_probs=40.7
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHh
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEER 148 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~ 148 (402)
+|+..+.++.|++ -.|.++.+||..+|||.+||...+++....|.+.
T Consensus 134 L~~~~r~i~~l~~-~~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 180 (182)
T PRK12537 134 LEPARRNCILHAY-VDGCSHAEIAQRLGAPLGTVKAWIKRSLKALREC 180 (182)
T ss_pred CCHHHHHHHHHHH-HcCCCHHHHHHHHCCChhhHHHHHHHHHHHHHHH
Confidence 7888888888875 5699999999999999999999999988887653
No 74
>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=82.88 E-value=1 Score=38.92 Aligned_cols=48 Identities=25% Similarity=0.292 Sum_probs=41.7
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhh
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERA 149 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~ 149 (402)
+|++++.++.|.+ -.|.++.+||..+|+|.+||...+.+....|.+.+
T Consensus 111 L~~~~r~i~~l~~-~~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 158 (162)
T TIGR02983 111 LPARQRAVVVLRY-YEDLSEAQVAEALGISVGTVKSRLSRALARLRELL 158 (162)
T ss_pred CCHHHHHHhhhHH-HhcCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 7788888888887 45999999999999999999999999988886543
No 75
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=82.85 E-value=1.2 Score=39.43 Aligned_cols=48 Identities=15% Similarity=0.043 Sum_probs=40.8
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhh
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERA 149 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~ 149 (402)
+|+.++-++.|+++ .|.++..||..+|+|.+||...+++....|.+.+
T Consensus 138 L~~~~r~i~~l~~~-~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l 185 (187)
T PRK12534 138 LEPPRSELIRTAFF-EGITYEELAARTDTPIGTVKSWIRRGLAKLKACL 185 (187)
T ss_pred CCHHHHHHHHHHHH-cCCCHHHHHHHhCCChhHHHHHHHHHHHHHHHHH
Confidence 67777777777765 7999999999999999999999999888876543
No 76
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=82.83 E-value=1.7 Score=40.35 Aligned_cols=69 Identities=16% Similarity=0.258 Sum_probs=53.3
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhhcccccCCC-chhHHHHHHHHHH
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERAKHHLKWPD-SNRMEEIKSKFEE 170 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~~~~i~~P~-~~~~~~i~~~f~~ 170 (402)
+|+.++.++.|+++- |.++.+||..+|+|.+||...+.+....|.+.+.....-+. ..+...+...|..
T Consensus 117 Lp~~~R~v~lL~~~e-g~S~~EIAe~LgiS~~tVksrL~Rark~Lr~~l~~~~~~~~~~~~~~~~~~~~~~ 186 (228)
T PRK06704 117 LNVQQSAILLLKDVF-QYSIADIAKVCSVSEGAVKASLFRSRNRLKTVSEEGIEIVEFTDDMEVVVTSIRE 186 (228)
T ss_pred CCHHHhhHhhhHHhh-CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhcCCCCCccccHHHHHHHHHh
Confidence 788888888887765 89999999999999999999999999998876655444332 2356666666643
No 77
>PRK05572 sporulation sigma factor SigF; Validated
Probab=82.73 E-value=1.1 Score=42.13 Aligned_cols=48 Identities=21% Similarity=0.397 Sum_probs=42.6
Q ss_pred cCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHh
Q 015682 100 LLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEER 148 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~ 148 (402)
.+|+.++.++.|+|+ .|.++..||..+|+|.+||+++..+.+..|...
T Consensus 202 ~L~~~~~~v~~l~~~-~~~s~~eIA~~lgis~~~V~~~~~ral~kLr~~ 249 (252)
T PRK05572 202 ELDERERLIVYLRYF-KDKTQSEVAKRLGISQVQVSRLEKKILKQMKEK 249 (252)
T ss_pred cCCHHHHHHHHHHHh-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 388899999999886 589999999999999999999999998887654
No 78
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=82.59 E-value=1.2 Score=39.52 Aligned_cols=48 Identities=21% Similarity=0.230 Sum_probs=42.0
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhh
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERA 149 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~ 149 (402)
+|..++.++.|+++ .|.++..||..+|+|.+||...+++....|.+.+
T Consensus 136 L~~~~r~vl~l~~~-~~~s~~eIA~~lgis~~~V~~~l~ra~~~Lr~~l 183 (186)
T PRK13919 136 LSPEERRVIEVLYY-QGYTHREAAQLLGLPLGTLKTRARRALSRLKEVL 183 (186)
T ss_pred CCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 78888888888876 4899999999999999999999999888886543
No 79
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=82.51 E-value=1 Score=40.06 Aligned_cols=49 Identities=18% Similarity=0.226 Sum_probs=43.1
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhhc
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERAK 150 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~~ 150 (402)
+|+.++-++.|+++. |.++..||..+|+|..||...+++....|...+.
T Consensus 129 L~~~~r~i~~l~~~~-g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 177 (186)
T PRK05602 129 LPERQREAIVLQYYQ-GLSNIEAAAVMDISVDALESLLARGRRALRAQLA 177 (186)
T ss_pred CCHHHHHHhhHHHhc-CCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHH
Confidence 788899999998875 9999999999999999999999998888866443
No 80
>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=82.40 E-value=0.46 Score=40.64 Aligned_cols=47 Identities=15% Similarity=0.174 Sum_probs=40.3
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHh
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEER 148 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~ 148 (402)
+|+.++-++.|.++ .|.++.+||..+|+|.+||...+++....|.+.
T Consensus 106 L~~~~r~i~~l~~~-~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~~ 152 (154)
T TIGR02950 106 LPENYRTVLILREF-KEFSYKEIAELLNLSLAKVKSNLFRARKELKKL 152 (154)
T ss_pred CCHhheeeeeehhh-ccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 67777778888777 699999999999999999999999888777553
No 81
>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=82.24 E-value=1.2 Score=39.44 Aligned_cols=47 Identities=26% Similarity=0.234 Sum_probs=41.2
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHh
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEER 148 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~ 148 (402)
+|+.++-++.|+++ .|.++..||..+|||.+||...+++....|.+.
T Consensus 141 L~~~~r~vi~l~~~-~g~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~~ 187 (189)
T TIGR02984 141 LPEDYREVILLRHL-EGLSFAEVAERMDRSEGAVSMLWVRGLARLRQI 187 (189)
T ss_pred CCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 78888888888777 799999999999999999999999888877553
No 82
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=81.83 E-value=1.2 Score=42.13 Aligned_cols=48 Identities=17% Similarity=0.174 Sum_probs=42.5
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhh
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERA 149 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~ 149 (402)
+++.++.++.|+|+ .|.++..||..+|+|.+||++...+....|...+
T Consensus 204 L~~~~r~vl~l~y~-~~~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~l 251 (256)
T PRK07408 204 LEERTREVLEFVFL-HDLTQKEAAERLGISPVTVSRRVKKGLDQLKKLL 251 (256)
T ss_pred CCHHHHHHHHHHHH-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 78889999999986 5899999999999999999999999888876543
No 83
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=81.61 E-value=1.1 Score=40.09 Aligned_cols=48 Identities=19% Similarity=0.230 Sum_probs=42.5
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhh
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERA 149 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~ 149 (402)
+|+.++-++.|+++ .|.++..||..+|+|.+||...+++....|.+.+
T Consensus 137 L~~~~r~i~~L~~~-~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 184 (195)
T PRK12532 137 LPENTARVFTLKEI-LGFSSDEIQQMCGISTSNYHTIMHRARESLRQCL 184 (195)
T ss_pred CCHHHHHHhhhHHH-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 78888888888887 6999999999999999999999999888886654
No 84
>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=81.39 E-value=1.4 Score=40.81 Aligned_cols=48 Identities=21% Similarity=0.275 Sum_probs=42.4
Q ss_pred cCCHHHHHHHHhhhc---cCCCccccccccccccccchhhhHHHHHHHHHH
Q 015682 100 LLSVEKQVAIALRRL---ASGESQVSVGVAFGVGQSTVSQVTWRFIEALEE 147 (402)
Q Consensus 100 ~ls~e~~l~i~L~~L---a~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~ 147 (402)
.+|+.++-++.|+|+ -.|.++..||..+|+|.+||.+.+++....|.+
T Consensus 174 ~L~~~~r~il~l~y~~~~~e~~S~~EIAe~lgis~~tV~~~~~rAl~~Lr~ 224 (227)
T TIGR02846 174 VLDGREREVIEMRYGLGDGRRKTQREIAKILGISRSYVSRIEKRALMKLYK 224 (227)
T ss_pred hCCHHHHHHHHHHHcCCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 378889999999886 478999999999999999999999988887755
No 85
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=81.15 E-value=1.3 Score=38.19 Aligned_cols=48 Identities=13% Similarity=0.075 Sum_probs=41.1
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhh
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERA 149 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~ 149 (402)
+|+.++-++.|+++ .|.++..||..+|+|.+||...+.+....|.+.+
T Consensus 107 Lp~~~r~v~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (160)
T PRK09642 107 LPENYRDVVLAHYL-EEKSYQEIALQEKIEVKTVEMKLYRARKWIKKHW 154 (160)
T ss_pred CCHHHHHHHHHHHH-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 78888888888775 5899999999999999999999988888876644
No 86
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=81.08 E-value=1.4 Score=38.46 Aligned_cols=48 Identities=21% Similarity=0.225 Sum_probs=41.9
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhh
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERA 149 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~ 149 (402)
+|+.++-++.|+++. |.++..||..+|+|.+||...+++....|.+.+
T Consensus 119 L~~~~r~vl~L~~~~-g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 166 (173)
T PRK09645 119 LSPEHRAVLVRSYYR-GWSTAQIAADLGIPEGTVKSRLHYALRALRLAL 166 (173)
T ss_pred CCHHHHHHHHHHHHc-CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 788888888888765 999999999999999999999998888886644
No 87
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=80.97 E-value=1.3 Score=39.60 Aligned_cols=49 Identities=16% Similarity=0.104 Sum_probs=42.1
Q ss_pred cCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhh
Q 015682 100 LLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERA 149 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~ 149 (402)
.+|++.+-++.|+++ .|.++..||..+|||.+||...+++....|...+
T Consensus 141 ~Lp~~~r~v~~l~~~-eg~s~~EIA~~lgis~~tVk~rl~ra~~~Lr~~l 189 (194)
T PRK12531 141 RLPKAQRDVLQAVYL-EELPHQQVAEMFDIPLGTVKSRLRLAVEKLRHSM 189 (194)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHh
Confidence 378888898888887 6999999999999999999998888888776543
No 88
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=80.94 E-value=1.2 Score=39.38 Aligned_cols=50 Identities=26% Similarity=0.281 Sum_probs=43.7
Q ss_pred cCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhhc
Q 015682 100 LLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERAK 150 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~~ 150 (402)
.+|++++-++.|+++. |.||..+|..+|||.+||...+++....+.+.+.
T Consensus 127 ~Lp~~~R~~~~l~~~~-gls~~EIA~~l~i~~~tVks~l~ra~~~l~~~l~ 176 (182)
T COG1595 127 RLPPRQREAFLLRYLE-GLSYEEIAEILGISVGTVKSRLHRARKKLREQLE 176 (182)
T ss_pred hCCHHHhHHhhhHhhc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 3788899999998885 8999999999999999999999999888876543
No 89
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=80.89 E-value=1.2 Score=38.58 Aligned_cols=46 Identities=15% Similarity=0.086 Sum_probs=39.1
Q ss_pred cCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHH
Q 015682 100 LLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALE 146 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~ 146 (402)
.+|++++-++.|+++ .|.++..||..+|+|.+||...+.+....+.
T Consensus 113 ~L~~~~r~v~~L~~~-~g~s~~EIA~~l~is~~tV~~~l~ra~~~~~ 158 (161)
T PRK12528 113 GLPPLVKRAFLLAQV-DGLGYGEIATELGISLATVKRYLNKAAMRCY 158 (161)
T ss_pred HCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 378888888888776 4899999999999999999998888776653
No 90
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=80.88 E-value=1.4 Score=42.47 Aligned_cols=51 Identities=25% Similarity=0.353 Sum_probs=44.6
Q ss_pred cCCHHHHHHHHhhhc-cCCCccccccccccccccchhhhHHHHHHHHHHhhc
Q 015682 100 LLSVEKQVAIALRRL-ASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERAK 150 (402)
Q Consensus 100 ~ls~e~~l~i~L~~L-a~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~~ 150 (402)
.+|+.++.++.|+|+ ..|.++..||..+|||.+||+++.++.+..|...+.
T Consensus 227 ~L~~rer~vl~lr~~~~~~~t~~EIa~~lgvs~~~V~q~~~~Al~kLr~~l~ 278 (289)
T PRK07500 227 TLNERELRIIRERRLREDGATLEALGEELGISKERVRQIEARALEKLRRALL 278 (289)
T ss_pred cCCHHHHHHHHHHhcCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 388999999999986 368999999999999999999999999988866543
No 91
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=80.70 E-value=1.4 Score=38.44 Aligned_cols=48 Identities=23% Similarity=0.260 Sum_probs=40.9
Q ss_pred cCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHh
Q 015682 100 LLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEER 148 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~ 148 (402)
.+|+.++.++.|+++ .|.++..||..+|+|.+||...+.+....+...
T Consensus 118 ~L~~~~r~v~~L~~~-eg~s~~EIA~~l~is~~tV~~~l~ra~~~~~~~ 165 (168)
T PRK12525 118 GLSGKARAAFLMSQL-EGLTYVEIGERLGVSLSRIHQYMVEAFKCCYQG 165 (168)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 378888888888864 689999999999999999999988888777553
No 92
>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=80.67 E-value=1.5 Score=40.76 Aligned_cols=49 Identities=22% Similarity=0.311 Sum_probs=42.9
Q ss_pred cCCHHHHHHHHhhhc---cCCCccccccccccccccchhhhHHHHHHHHHHh
Q 015682 100 LLSVEKQVAIALRRL---ASGESQVSVGVAFGVGQSTVSQVTWRFIEALEER 148 (402)
Q Consensus 100 ~ls~e~~l~i~L~~L---a~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~ 148 (402)
.+|+.++.++.|+++ -.|.++..||...|+|.+||.....+....|.+.
T Consensus 178 ~Lp~~~R~ii~L~~~l~~~eg~s~~EIA~~Lgis~~tV~~~l~ra~~~LR~~ 229 (234)
T TIGR02835 178 KLNDREKKIMELRFGLVGGTEKTQKEVADMLGISQSYISRLEKRILKRLKKE 229 (234)
T ss_pred hCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 388999999999985 3789999999999999999999998888877654
No 93
>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=80.62 E-value=1.5 Score=38.23 Aligned_cols=48 Identities=23% Similarity=0.225 Sum_probs=41.3
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhh
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERA 149 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~ 149 (402)
+|+.++-++.|.++. |.++..+|..+|||.+||...+.+....|.+.+
T Consensus 120 L~~~~r~i~~l~~~~-g~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~~l 167 (169)
T TIGR02954 120 LNDKYQTAIILRYYH-DLTIKEIAEVMNKPEGTVKTYLHRALKKLKKRL 167 (169)
T ss_pred CCHHHhHHHHHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 777888888887776 899999999999999999999999888876543
No 94
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=80.53 E-value=1.3 Score=39.33 Aligned_cols=49 Identities=20% Similarity=0.130 Sum_probs=43.4
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhhc
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERAK 150 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~~ 150 (402)
+|+..+-++.|+++ .|.++.+||..+|+|.+||...+++....|.+.+.
T Consensus 112 Lp~~~R~v~~L~~~-~g~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~ 160 (182)
T PRK12540 112 LPQDQREALILVGA-SGFSYEDAAAICGCAVGTIKSRVNRARSKLSALLY 160 (182)
T ss_pred CCHHHHHHhhHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 78888888888876 79999999999999999999999999988876554
No 95
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=80.50 E-value=1.3 Score=39.64 Aligned_cols=48 Identities=27% Similarity=0.264 Sum_probs=41.0
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhh
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERA 149 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~ 149 (402)
+|++++.++.|+++ .|.++..||..+|+|.+||..-+.+....|.+.+
T Consensus 135 Lp~~~r~i~~l~~~-~g~s~~EIA~~lg~s~~tV~~rl~rar~~Lr~~l 182 (192)
T PRK09643 135 LPVEQRAALVAVDM-QGYSVADAARMLGVAEGTVKSRCARGRARLAELL 182 (192)
T ss_pred CCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 78888888888877 6899999999999999999988888777775543
No 96
>PF13730 HTH_36: Helix-turn-helix domain
Probab=80.46 E-value=1 Score=31.41 Aligned_cols=39 Identities=28% Similarity=0.322 Sum_probs=29.5
Q ss_pred HHHHHHHhhhccC--CC---ccccccccccccccchhhhHHHHH
Q 015682 104 EKQVAIALRRLAS--GE---SQVSVGVAFGVGQSTVSQVTWRFI 142 (402)
Q Consensus 104 e~~l~i~L~~La~--g~---s~~~l~~~fgvs~sTv~~~i~~v~ 142 (402)
+..|.+.|..++. +. |+..|+...|+|+.||.+.+.+..
T Consensus 7 ~~~v~~~l~~~~~~~~~~~pS~~~la~~~g~s~~Tv~~~i~~L~ 50 (55)
T PF13730_consen 7 AKLVYLYLASYANKNGGCFPSQETLAKDLGVSRRTVQRAIKELE 50 (55)
T ss_pred HHHHHHHHHHhcCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 4466667777763 22 668899999999999999887654
No 97
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=80.46 E-value=1.3 Score=39.09 Aligned_cols=49 Identities=20% Similarity=0.177 Sum_probs=42.3
Q ss_pred cCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhh
Q 015682 100 LLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERA 149 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~ 149 (402)
.+|+.++-++.|+++ .|.++..+|..+|+|.+||...+.+....|...+
T Consensus 136 ~L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l 184 (187)
T TIGR02948 136 ALPPKYRMVIVLKYM-EDLSLKEISEILDLPVGTVKTRIHRGREALRKQL 184 (187)
T ss_pred hCCHHHhHHhhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 378888888888877 5899999999999999999999999888876543
No 98
>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=80.23 E-value=1.5 Score=40.45 Aligned_cols=46 Identities=24% Similarity=0.371 Sum_probs=40.7
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHH
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEE 147 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~ 147 (402)
+|+.++-++.|+|+ .|.++.+||..+|+|.+||+..+.+....|..
T Consensus 179 L~~~~r~vl~l~y~-~~~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~ 224 (227)
T TIGR02980 179 LPERERRILLLRFF-EDKTQSEIAERLGISQMHVSRLLRRALKKLRE 224 (227)
T ss_pred CCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 78888888888876 58999999999999999999999998887754
No 99
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=80.13 E-value=1.4 Score=39.34 Aligned_cols=49 Identities=10% Similarity=0.058 Sum_probs=42.7
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhhc
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERAK 150 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~~ 150 (402)
+|+.++-++.|+++- |.++..||..+|+|.+||...+.+....|.+.+.
T Consensus 132 Lp~~~r~v~~l~~~~-g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 180 (191)
T PRK12520 132 LPPRTGRVFMMREWL-ELETEEICQELQITATNAWVLLYRARMRLRECLD 180 (191)
T ss_pred CCHHHHHHHHHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 788899999888875 7999999999999999999999998888866543
No 100
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=80.04 E-value=1.4 Score=40.03 Aligned_cols=48 Identities=15% Similarity=0.124 Sum_probs=43.1
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhh
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERA 149 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~ 149 (402)
+|++++-++.|+++. |.++..||..+|+|.+||...+++....|.+.+
T Consensus 149 L~~~~r~v~~L~~~~-g~s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l 196 (206)
T PRK12544 149 LPAKYARVFMMREFI-ELETNEICHAVDLSVSNLNVLLYRARLRLRECL 196 (206)
T ss_pred CCHHHHHHHHHHHHc-CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 788999999998876 999999999999999999999999988886644
No 101
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=79.98 E-value=1.4 Score=38.56 Aligned_cols=52 Identities=12% Similarity=0.029 Sum_probs=41.8
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhhcccc
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERAKHHL 153 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~~~~i 153 (402)
+|++.+-++.|.|+ .|.++..+|..+|+|.+||...+.+....|...+...|
T Consensus 120 L~~~~r~i~~l~~~-~~~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~~~~ 171 (173)
T PRK12522 120 LNEKYKTVLVLYYY-EQYSYKEMSEILNIPIGTVKYRLNYAKKQMREHLEGFV 171 (173)
T ss_pred CCHHHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHh
Confidence 66666666666555 58999999999999999999999999988877665443
No 102
>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=79.87 E-value=1.1 Score=31.85 Aligned_cols=43 Identities=28% Similarity=0.394 Sum_probs=28.6
Q ss_pred CCHHH-HHHHHhhhccCC-CccccccccccccccchhhhHHHHHH
Q 015682 101 LSVEK-QVAIALRRLASG-ESQVSVGVAFGVGQSTVSQVTWRFIE 143 (402)
Q Consensus 101 ls~e~-~l~i~L~~La~g-~s~~~l~~~fgvs~sTv~~~i~~v~~ 143 (402)
+++.+ .++.+|.....+ .+..+|+..++++++|+++++.+...
T Consensus 3 lt~~q~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~ 47 (62)
T PF12802_consen 3 LTPSQFRVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEK 47 (62)
T ss_dssp STHHHHHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred cCHHHHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 34433 344444443333 68899999999999999998877653
No 103
>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=79.80 E-value=1.4 Score=41.01 Aligned_cols=48 Identities=17% Similarity=0.261 Sum_probs=42.1
Q ss_pred cCCHHHHHHHHhhhc---cCCCccccccccccccccchhhhHHHHHHHHHH
Q 015682 100 LLSVEKQVAIALRRL---ASGESQVSVGVAFGVGQSTVSQVTWRFIEALEE 147 (402)
Q Consensus 100 ~ls~e~~l~i~L~~L---a~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~ 147 (402)
.+|+.++.++.|+|. ..|.++..||..+|||.++|+++..+.+.-|..
T Consensus 176 ~L~~~er~vl~l~ygl~~~~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~ 226 (238)
T TIGR02393 176 TLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRKLRH 226 (238)
T ss_pred hCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence 378889999999985 567899999999999999999999988887754
No 104
>PRK15320 transcriptional activator SprB; Provisional
Probab=79.76 E-value=0.86 Score=40.99 Aligned_cols=38 Identities=29% Similarity=0.388 Sum_probs=34.5
Q ss_pred HHhhhccCCCccccccccccccccchhhhHHHHHHHHH
Q 015682 109 IALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALE 146 (402)
Q Consensus 109 i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~ 146 (402)
-.|..|+.|.+...||..+++|.+||+.+..+..+-+.
T Consensus 171 EVL~LLAkG~SNKEIAekL~LS~KTVSTYKnRLLeKLg 208 (251)
T PRK15320 171 ALLILLSSGHPAIELAKKFGLGTKTVSIYRKKVMYRLG 208 (251)
T ss_pred HHHHHHHcCCCHHHHHHHhccchhhHHHHHHHHHHHcC
Confidence 56788999999999999999999999999998887763
No 105
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=79.76 E-value=1.6 Score=38.80 Aligned_cols=49 Identities=24% Similarity=0.242 Sum_probs=43.2
Q ss_pred cCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhh
Q 015682 100 LLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERA 149 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~ 149 (402)
.+|+..+-++.|+++. |.++.+||..+|+|.+||...+++....|.+.+
T Consensus 131 ~L~~~~r~v~~l~~~~-g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12539 131 RLPEKMRLAIQAVKLE-GLSVAEAATRSGMSESAVKVSVHRGLKALAALI 179 (184)
T ss_pred hCCHHHHHHHHHHHHc-CCcHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 3788888888888885 999999999999999999999999998886643
No 106
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=79.71 E-value=1.6 Score=41.16 Aligned_cols=47 Identities=28% Similarity=0.309 Sum_probs=41.6
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHh
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEER 148 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~ 148 (402)
+|+.++-++.|+|+ .|.++..||..+|||.+||.+..++....|...
T Consensus 206 L~~~~r~vl~l~~~-~g~s~~eIA~~l~is~~tV~~~~~ra~~kLr~~ 252 (257)
T PRK08583 206 LSDREKSIIQCTFI-ENLSQKETGERLGISQMHVSRLQRQAIKKLREA 252 (257)
T ss_pred CCHHHHHHHHHHHh-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 78888888888876 689999999999999999999999988887653
No 107
>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=79.68 E-value=1.5 Score=40.47 Aligned_cols=47 Identities=23% Similarity=0.380 Sum_probs=40.8
Q ss_pred cCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHH
Q 015682 100 LLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEE 147 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~ 147 (402)
.+|..++.++.++|+ .|.++..||..+|+|+++|+++.++.+.-|.+
T Consensus 183 ~L~~~e~~i~~~~~~-~~~t~~eIA~~lgis~~~V~~~~~~al~~Lr~ 229 (231)
T TIGR02885 183 KLDERERQIIMLRYF-KDKTQTEVANMLGISQVQVSRLEKKVLKKMKE 229 (231)
T ss_pred cCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 378888888888875 58899999999999999999999998887754
No 108
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=79.59 E-value=1.6 Score=41.16 Aligned_cols=47 Identities=21% Similarity=0.391 Sum_probs=41.0
Q ss_pred cCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHH
Q 015682 100 LLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEE 147 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~ 147 (402)
.+++.++.++.++|+ .|.++..+|..+|+|.+||+++..+.+..|.+
T Consensus 209 ~L~~~er~vi~~~~~-~~~t~~eIA~~lgis~~~V~~~~~~al~kLr~ 255 (258)
T PRK08215 209 KLNDREKLILNLRFF-QGKTQMEVAEEIGISQAQVSRLEKAALKHMRK 255 (258)
T ss_pred cCCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 378888988888886 58899999999999999999999988877754
No 109
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=79.58 E-value=1.6 Score=38.20 Aligned_cols=47 Identities=23% Similarity=0.209 Sum_probs=40.5
Q ss_pred cCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHH
Q 015682 100 LLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEE 147 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~ 147 (402)
.+|++++-++.|+++. |.++..||..+|+|.+||...+.+.+..+..
T Consensus 119 ~Lp~~~r~v~~L~~~~-g~s~~EIA~~lgis~~tV~~~l~ra~~~~~~ 165 (172)
T PRK12523 119 KLSSKARAAFLYNRLD-GMGHAEIAERLGVSVSRVRQYLAQGLRQCYI 165 (172)
T ss_pred hCCHHHHHHHHHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3788889988888874 8999999999999999999998887777654
No 110
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=79.37 E-value=1.6 Score=38.77 Aligned_cols=49 Identities=24% Similarity=0.195 Sum_probs=41.7
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhhc
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERAK 150 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~~ 150 (402)
+|++++.++.|+++ .|.++.+||..+|+|.+||...+.+....|.+.+.
T Consensus 107 L~~~~r~i~~l~~~-~g~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 155 (181)
T PRK09637 107 LPEKYAEALRLTEL-EGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKELLE 155 (181)
T ss_pred CCHHHHHHHHHHHh-cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 78888888888775 58999999999999999999999888887765443
No 111
>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=79.28 E-value=1.7 Score=41.69 Aligned_cols=51 Identities=18% Similarity=0.187 Sum_probs=44.4
Q ss_pred cCCHHHHHHHHhhh-c--cCCCccccccccccccccchhhhHHHHHHHHHHhhc
Q 015682 100 LLSVEKQVAIALRR-L--ASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERAK 150 (402)
Q Consensus 100 ~ls~e~~l~i~L~~-L--a~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~~ 150 (402)
.||..++.++.|+| | -.|.++..||..+|+|.+||....++....|...+.
T Consensus 222 ~Lp~~~R~Vl~l~ygL~~~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~l~ 275 (285)
T TIGR02394 222 ELNERQREVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQVEALKKLRRILE 275 (285)
T ss_pred cCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 38899999999998 4 568999999999999999999999998888866543
No 112
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=79.25 E-value=1.6 Score=37.25 Aligned_cols=46 Identities=13% Similarity=0.161 Sum_probs=39.7
Q ss_pred cCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHH
Q 015682 100 LLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALE 146 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~ 146 (402)
.+|+.++-++.|+|+. |.++.+||..+|+|.+||...+.+....|-
T Consensus 106 ~L~~~~r~ii~l~~~~-~~s~~EIA~~l~is~~tV~~~~~ra~~~Lr 151 (154)
T PRK06759 106 VLDEKEKYIIFERFFV-GKTMGEIALETEMTYYQVRWIYRQALEKMR 151 (154)
T ss_pred hCCHHHHHHHHHHHhc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHh
Confidence 3788888888888875 899999999999999999999988777663
No 113
>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=79.21 E-value=1.6 Score=41.02 Aligned_cols=48 Identities=31% Similarity=0.308 Sum_probs=42.5
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhh
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERA 149 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~ 149 (402)
+|..++-++.|+++ .|.++.+||..+|||.+||...+.+....|.+.+
T Consensus 162 Lp~~~R~v~~L~~~-eg~S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l 209 (244)
T TIGR03001 162 LSERERHLLRLHFV-DGLSMDRIGAMYQVHRSTVSRWVAQARERLLERT 209 (244)
T ss_pred CCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 78888999999887 7899999999999999999999999888886643
No 114
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=79.04 E-value=1.7 Score=40.32 Aligned_cols=48 Identities=27% Similarity=0.358 Sum_probs=41.9
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhh
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERA 149 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~ 149 (402)
+|+.++-++.|+|+ .|.++..||..+|||.+||...+.+....|...+
T Consensus 185 L~~~~r~vl~l~~~-~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l 232 (236)
T PRK06986 185 LPEREQLVLSLYYQ-EELNLKEIGAVLGVSESRVSQIHSQAIKRLRARL 232 (236)
T ss_pred CCHHHHHHHHhHhc-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 78888888888875 6899999999999999999999999888886644
No 115
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=78.91 E-value=1.6 Score=39.09 Aligned_cols=50 Identities=28% Similarity=0.171 Sum_probs=44.1
Q ss_pred cCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhhc
Q 015682 100 LLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERAK 150 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~~ 150 (402)
.+|++++-++.|+++ .|.++.+||..+|||.+||...+.+....|.+.+.
T Consensus 113 ~Lp~~~r~v~~L~~~-~g~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l~ 162 (188)
T PRK12546 113 QLPDEQREALILVGA-SGFSYEEAAEMCGVAVGTVKSRANRARARLAELLQ 162 (188)
T ss_pred hCCHHHhHHhhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 378899999999988 79999999999999999999999999888866543
No 116
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=78.69 E-value=1.6 Score=39.01 Aligned_cols=47 Identities=19% Similarity=0.159 Sum_probs=41.8
Q ss_pred cCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHH
Q 015682 100 LLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEE 147 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~ 147 (402)
.+|++++-++.|+|+ .|.++..||..+|+|.+||...+.+....|..
T Consensus 131 ~L~~~~r~i~~l~~~-~g~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~ 177 (189)
T PRK06811 131 DLEKLDREIFIRRYL-LGEKIEEIAKKLGLTRSAIDNRLSRGRKKLQK 177 (189)
T ss_pred hCCHHHHHHHHHHHH-ccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 388899999999887 58999999999999999999999988887754
No 117
>PHA00542 putative Cro-like protein
Probab=78.65 E-value=1.6 Score=33.60 Aligned_cols=51 Identities=20% Similarity=0.162 Sum_probs=36.3
Q ss_pred HHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhhcccccCCCchhHHHHHHHHHH
Q 015682 109 IALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERAKHHLKWPDSNRMEEIKSKFEE 170 (402)
Q Consensus 109 i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~~~~i~~P~~~~~~~i~~~f~~ 170 (402)
+...+...|.++.++|..+|||++|++++.+.- ..-|+.+.+..+++.+.+
T Consensus 23 l~~~l~~~glTq~elA~~lgIs~~tIsr~e~g~-----------~~~p~~~~l~ki~~~~~~ 73 (82)
T PHA00542 23 LVCALIRAGWSQEQIADATDVSQPTICRIYSGR-----------HKDPRYSVVEKLRHLVLN 73 (82)
T ss_pred HHHHHHHCCCCHHHHHHHHCcCHHHHHHHHcCC-----------CCCCCHHHHHHHHHHHHH
Confidence 334457789999999999999999999887421 123555566666665554
No 118
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=78.63 E-value=1.8 Score=38.34 Aligned_cols=47 Identities=23% Similarity=0.269 Sum_probs=39.9
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHh
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEER 148 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~ 148 (402)
+|+.++.++.|+++ .|.++.+||..+|+|.+||...+++....|.+.
T Consensus 130 L~~~~r~v~~l~~~-~g~s~~EIA~~l~is~~tV~~~l~rar~~Lr~~ 176 (181)
T PRK12536 130 LPDRQRLPIVHVKL-EGLSVAETAQLTGLSESAVKVGIHRGLKALAAK 176 (181)
T ss_pred CCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 67778877777665 589999999999999999999999988887654
No 119
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=78.56 E-value=1.8 Score=39.03 Aligned_cols=52 Identities=17% Similarity=0.100 Sum_probs=44.8
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhhcccc
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERAKHHL 153 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~~~~i 153 (402)
+|+..+-++.|+++- |.++..||..+|+|.+||...+++....|.+.+..+.
T Consensus 134 Lp~~~r~v~~l~~~~-g~s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~~~~ 185 (196)
T PRK12535 134 LPPERREALILTQVL-GYTYEEAAKIADVRVGTIRSRVARARADLIAATATGQ 185 (196)
T ss_pred CCHHHHHHhhhHHHh-CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhcccc
Confidence 777888888888764 7889999999999999999999999999988776554
No 120
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=78.46 E-value=1.7 Score=35.65 Aligned_cols=47 Identities=15% Similarity=0.217 Sum_probs=41.9
Q ss_pred CCcCCHHHHHHHHhhhccCCCccccccccccc-cccchhhhHHHHHHH
Q 015682 98 GRLLSVEKQVAIALRRLASGESQVSVGVAFGV-GQSTVSQVTWRFIEA 144 (402)
Q Consensus 98 ~~~ls~e~~l~i~L~~La~g~s~~~l~~~fgv-s~sTv~~~i~~v~~a 144 (402)
++..|.|.++-++-.++..|.++..+|..||| +.++.++++.+..+.
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~sv~~vAr~~gv~~~~~l~~W~~~~~~~ 52 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGDTVSEVAREFGIVSATQLYKWRIQLQKG 52 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCccHHHHHHHhCCCChHHHHHHHHHHHHc
Confidence 45689999999999999999999999999996 999999888776654
No 121
>PRK06930 positive control sigma-like factor; Validated
Probab=78.36 E-value=1.8 Score=38.25 Aligned_cols=49 Identities=16% Similarity=0.199 Sum_probs=40.7
Q ss_pred cCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhh
Q 015682 100 LLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERA 149 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~ 149 (402)
.+|+.++-++.|++ ..|.++..||..+|+|.+||...+.+....|.+.+
T Consensus 114 ~L~~rer~V~~L~~-~eg~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l 162 (170)
T PRK06930 114 VLTEREKEVYLMHR-GYGLSYSEIADYLNIKKSTVQSMIERAEKKIARQI 162 (170)
T ss_pred hCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 37777777776654 67999999999999999999999998888876644
No 122
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=77.90 E-value=1.9 Score=38.93 Aligned_cols=48 Identities=10% Similarity=0.058 Sum_probs=42.0
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhh
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERA 149 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~ 149 (402)
+|+..+-++.|+|+ .|.++..||..+|+|.+||...+.+....|.+.+
T Consensus 140 Lp~~~r~v~~L~~~-eg~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l 187 (201)
T PRK12545 140 LPEQIGRVFMMREF-LDFEIDDICTELTLTANHCSVLLYRARTRLRTCL 187 (201)
T ss_pred CCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 78889999999876 4899999999999999999999988888886654
No 123
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=77.87 E-value=1.9 Score=37.11 Aligned_cols=49 Identities=18% Similarity=0.243 Sum_probs=41.4
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhhc
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERAK 150 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~~ 150 (402)
+|++++-++.|++ -.|.++.+||..+|+|.+||...+.+....|.+.+.
T Consensus 106 L~~~~r~v~~l~~-~~~~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l~ 154 (159)
T PRK12527 106 LPPACRDSFLLRK-LEGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVRMR 154 (159)
T ss_pred CCHHHHHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 7788888777766 468999999999999999999999988888866543
No 124
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=77.71 E-value=1.7 Score=37.70 Aligned_cols=49 Identities=16% Similarity=0.066 Sum_probs=41.4
Q ss_pred cCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhh
Q 015682 100 LLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERA 149 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~ 149 (402)
.+|++++-++.|+++ .|.++..||..+|+|.+||...+++....|.+.+
T Consensus 108 ~L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 156 (165)
T PRK09644 108 TLPVIEAQAILLCDV-HELTYEEAASVLDLKLNTYKSHLFRGRKRLKALL 156 (165)
T ss_pred hCCHHHHHHHHhHHH-hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 377888888777765 5899999999999999999999999888886643
No 125
>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=77.48 E-value=1.1 Score=40.14 Aligned_cols=48 Identities=21% Similarity=0.158 Sum_probs=41.0
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhh
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERA 149 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~ 149 (402)
+|+..+-++.|+++ .|.++..||..+|+|.+||...+.+....|.+.+
T Consensus 132 Lp~~~r~i~~L~~~-~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 179 (193)
T TIGR02947 132 LPEEFRQAVYLADV-EGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQL 179 (193)
T ss_pred CCHHHhhheeehhh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 77788888888765 5899999999999999999999998888876544
No 126
>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=77.39 E-value=1.2 Score=34.73 Aligned_cols=36 Identities=22% Similarity=0.309 Sum_probs=29.2
Q ss_pred HHHHHHHhhhccCCCccccccccccccccchhhhHH
Q 015682 104 EKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTW 139 (402)
Q Consensus 104 e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~ 139 (402)
.+++.|+=-.|..|.+|+.|+...|+|..||+|+-+
T Consensus 36 ~~R~~va~~lL~~g~syreIa~~tgvS~aTItRvsr 71 (87)
T PF01371_consen 36 AQRWQVAKELLDEGKSYREIAEETGVSIATITRVSR 71 (87)
T ss_dssp HHHHHHHHHHHHTTSSHHHHHHHHTSTHHHHHHHHH
T ss_pred HHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 345555555788999999999999999999988654
No 127
>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=77.36 E-value=3.3 Score=39.61 Aligned_cols=67 Identities=16% Similarity=0.200 Sum_probs=50.3
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhhcccccCCCchhHHHHHHHHHH
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERAKHHLKWPDSNRMEEIKSKFEE 170 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~~~~i~~P~~~~~~~i~~~f~~ 170 (402)
+|+.++-++.|+++ .|.++.+||..+|+|.+||...+++....|.+..+..- +..++..++.+.|-.
T Consensus 109 L~~~~R~v~~L~~~-~g~s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~~~~~~--~~~~~~~~~~~~f~~ 175 (281)
T TIGR02957 109 LSPLERAVFVLREV-FDYPYEEIASIVGKSEANCRQLVSRARRHLDARRPRFE--VSREESRQLLERFVE 175 (281)
T ss_pred CCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCCCCC--CChHHHHHHHHHHHH
Confidence 78888888888765 48999999999999999999999999999977544321 222344556666643
No 128
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=77.23 E-value=1.8 Score=38.57 Aligned_cols=47 Identities=23% Similarity=0.232 Sum_probs=40.9
Q ss_pred cCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHH
Q 015682 100 LLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEE 147 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~ 147 (402)
.+|++++-++.|+++. |.++..||..+|+|.+||...+.+....|.+
T Consensus 130 ~Lp~~~r~v~~L~~~~-g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 130 DLTTDQREALLLTQLL-GLSYADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred hCCHHHhHHhhhHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 3788888888888775 8899999999999999999999888887754
No 129
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=77.23 E-value=1.6 Score=29.54 Aligned_cols=37 Identities=22% Similarity=0.276 Sum_probs=26.6
Q ss_pred HHHHHhhhccCCCccccccccccccccchhhhHHHHHH
Q 015682 106 QVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIE 143 (402)
Q Consensus 106 ~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~ 143 (402)
+++-.|.. ..+.+..+++..+|+|.+||++++.+..+
T Consensus 7 ~Il~~l~~-~~~~t~~ela~~~~is~~tv~~~l~~L~~ 43 (48)
T PF13412_consen 7 KILNYLRE-NPRITQKELAEKLGISRSTVNRYLKKLEE 43 (48)
T ss_dssp HHHHHHHH-CTTS-HHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHH-cCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 44444444 44588999999999999999999987754
No 130
>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=77.22 E-value=0.94 Score=31.89 Aligned_cols=29 Identities=24% Similarity=0.224 Sum_probs=24.4
Q ss_pred CCccccccccccccccchhhhHHHHHHHH
Q 015682 117 GESQVSVGVAFGVGQSTVSQVTWRFIEAL 145 (402)
Q Consensus 117 g~s~~~l~~~fgvs~sTv~~~i~~v~~al 145 (402)
+.+..+||..+|||++|++..+++...-|
T Consensus 23 ~~tl~elA~~lgis~st~~~~LRrae~kl 51 (53)
T PF04967_consen 23 RITLEELAEELGISKSTVSEHLRRAERKL 51 (53)
T ss_pred cCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 35677899999999999999998876655
No 131
>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=77.19 E-value=0.84 Score=32.43 Aligned_cols=43 Identities=28% Similarity=0.404 Sum_probs=33.6
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHH
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEAL 145 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al 145 (402)
+|..+.- .|..++.|.+...+|...+||.+||.........-+
T Consensus 4 LT~~E~~--vl~~l~~G~~~~eIA~~l~is~~tV~~~~~~i~~Kl 46 (58)
T PF00196_consen 4 LTERELE--VLRLLAQGMSNKEIAEELGISEKTVKSHRRRIMKKL 46 (58)
T ss_dssp S-HHHHH--HHHHHHTTS-HHHHHHHHTSHHHHHHHHHHHHHHHH
T ss_pred cCHHHHH--HHHHHHhcCCcchhHHhcCcchhhHHHHHHHHHHHh
Confidence 4444433 567889999999999999999999999888777665
No 132
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=77.16 E-value=3.6 Score=39.53 Aligned_cols=68 Identities=15% Similarity=0.140 Sum_probs=51.2
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhhcccccCCCchhHHHHHHHHHHh
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERAKHHLKWPDSNRMEEIKSKFEES 171 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~~~~i~~P~~~~~~~i~~~f~~~ 171 (402)
+|++++-++.|+++- |.+|.+||..+|+|.+||...+++....|.+..+..- +..++-.++...|...
T Consensus 116 L~~~~R~v~~L~~~~-g~s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~~~~~~--~~~~~~~~~v~~f~~A 183 (293)
T PRK09636 116 LSPLERAAFLLHDVF-GVPFDEIASTLGRSPAACRQLASRARKHVRAARPRFP--VSDEEGAELVEAFFAA 183 (293)
T ss_pred CCHHHHHHHHHHHHh-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCCCCC--CCchHHHHHHHHHHHH
Confidence 788888888887765 8999999999999999999999999998877554321 2233445566666543
No 133
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=77.08 E-value=2 Score=37.84 Aligned_cols=48 Identities=21% Similarity=0.218 Sum_probs=40.7
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhh
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERA 149 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~ 149 (402)
+|+.++-++.|+++ .|.++..||..+|+|.+||...+.+....|.+.+
T Consensus 118 Lp~~~r~i~~l~~~-e~~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 165 (179)
T PRK12543 118 LPYKLRQVIILRYL-HDYSQEEIAQLLQIPIGTVKSRIHAALKKLRQKE 165 (179)
T ss_pred CCHHHHHHHHHHHH-ccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 78888888888766 4889999999999999999999888888776543
No 134
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=77.00 E-value=2.5 Score=41.42 Aligned_cols=72 Identities=19% Similarity=0.278 Sum_probs=53.7
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhhcccc---cCCCchhHHHHHHHHHHhhC
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERAKHHL---KWPDSNRMEEIKSKFEESFG 173 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~~~~i---~~P~~~~~~~i~~~f~~~~~ 173 (402)
+|+.++-++.|+++ .|.++.+||..+|+|.+||...+.+....|.+..+... .-|..++..++...|...++
T Consensus 154 Lp~~~R~v~~L~~~-~g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~~~~~~~~~~~~~~~~~~~~v~~~~~A~~ 228 (339)
T PRK08241 154 LPPRQRAVLILRDV-LGWSAAEVAELLDTSVAAVNSALQRARATLAERGPSAADTLREPDDPEERALLARYVAAFE 228 (339)
T ss_pred CCHHHhhhhhhHHh-hCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhhcCCCcccccCCCCChHHHHHHHHHHHHHh
Confidence 78888888888775 58999999999999999999999999998877433211 11233456667776665544
No 135
>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=76.97 E-value=1.9 Score=38.48 Aligned_cols=49 Identities=12% Similarity=0.143 Sum_probs=42.3
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhhc
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERAK 150 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~~ 150 (402)
+|+.++-++.|+|+- |.++..||..+|+|.+||...+.+....|.+.+.
T Consensus 132 L~~~~r~v~~l~~~~-g~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l~ 180 (188)
T TIGR02943 132 LPEQTARVFMMREVL-GFESDEICQELEISTSNCHVLLYRARLSLRACLS 180 (188)
T ss_pred CCHHHHHHHHHHHHh-CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 778888888888775 9999999999999999999999998888866543
No 136
>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=76.80 E-value=0.45 Score=32.45 Aligned_cols=20 Identities=35% Similarity=0.308 Sum_probs=17.5
Q ss_pred cccccccccccccchhhhHH
Q 015682 120 QVSVGVAFGVGQSTVSQVTW 139 (402)
Q Consensus 120 ~~~l~~~fgvs~sTv~~~i~ 139 (402)
..+||...|||.+|||++++
T Consensus 2 i~dIA~~agvS~~TVSr~ln 21 (46)
T PF00356_consen 2 IKDIAREAGVSKSTVSRVLN 21 (46)
T ss_dssp HHHHHHHHTSSHHHHHHHHT
T ss_pred HHHHHHHHCcCHHHHHHHHh
Confidence 45789999999999999885
No 137
>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=76.75 E-value=2.2 Score=40.10 Aligned_cols=47 Identities=28% Similarity=0.295 Sum_probs=41.3
Q ss_pred cCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHH
Q 015682 100 LLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEE 147 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~ 147 (402)
.+|+.++-++.|+|+ .|.++..||..+|+|.+||+...++....|..
T Consensus 205 ~L~~~~r~ii~l~~~-~g~s~~eIA~~lgis~~~V~~~~~ra~~~Lr~ 251 (255)
T TIGR02941 205 ILSEREKSIIHCTFE-ENLSQKETGERLGISQMHVSRLQRQAISKLKE 251 (255)
T ss_pred cCCHHHHHHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 378889998888886 58999999999999999999999988887754
No 138
>PF00872 Transposase_mut: Transposase, Mutator family; InterPro: IPR001207 Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element. Transposases have been grouped into various families [, , ]. The mutator family of transposases consists of a number of elements that include, mutator from maize, IsT2 from Thiobacillus ferrooxidans, Is256 from Staphylococcus aureus, Is1201 from Lactobacillus helveticus, Is1081 from Mycobacterium bovis, IsRm3 from Rhizobium meliloti and others. 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
Probab=76.70 E-value=3 Score=41.81 Aligned_cols=86 Identities=21% Similarity=0.147 Sum_probs=51.8
Q ss_pred ccCCCccccccc----ccc---ccccchhhhHHHHHHHHHHhhcccccCCCchhHHHHHHHHHHhhCCCCcccccceeEE
Q 015682 114 LASGESQVSVGV----AFG---VGQSTVSQVTWRFIEALEERAKHHLKWPDSNRMEEIKSKFEESFGLLNCCGAIDATHI 186 (402)
Q Consensus 114 La~g~s~~~l~~----~fg---vs~sTv~~~i~~v~~al~~~~~~~i~~P~~~~~~~i~~~f~~~~~fp~~iGaIDgthI 186 (402)
++.|.|.++++. .+| +|++|||+++.++.+.+.....+- ..+.|-++-.|||+|+
T Consensus 111 y~~G~Str~i~~~l~~l~g~~~~S~s~vSri~~~~~~~~~~w~~R~------------------L~~~~y~~l~iD~~~~ 172 (381)
T PF00872_consen 111 YLKGVSTRDIEEALEELYGEVAVSKSTVSRITKQLDEEVEAWRNRP------------------LESEPYPYLWIDGTYF 172 (381)
T ss_pred hccccccccccchhhhhhcccccCchhhhhhhhhhhhhHHHHhhhc------------------cccccccceeeeeeec
Confidence 567888777665 456 999999999888776654321110 1122345778999999
Q ss_pred EEecCCCCCCCccccCCCceeeeEeeeeCCCce--EEeeecc
Q 015682 187 IMTLPAVQTSDDWCDQENNYSMLVQGIVDHEMR--FIDIVTG 226 (402)
Q Consensus 187 ~i~~P~~~~~~~y~~~k~~~s~~~q~vvD~~~r--f~~v~~g 226 (402)
.+..-. .-..-++.+-.-+|.+|+ ++.+.++
T Consensus 173 kvr~~~---------~~~~~~~~v~iGi~~dG~r~vLg~~~~ 205 (381)
T PF00872_consen 173 KVREDG---------RVVKKAVYVAIGIDEDGRREVLGFWVG 205 (381)
T ss_pred cccccc---------ccccchhhhhhhhhcccccceeeeecc
Confidence 986211 111123333444677774 7777665
No 139
>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=76.60 E-value=2.2 Score=40.12 Aligned_cols=47 Identities=19% Similarity=0.387 Sum_probs=41.0
Q ss_pred cCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHH
Q 015682 100 LLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEE 147 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~ 147 (402)
.+++.++.++.++|+ .|.++..||..+|+|+++|+++..+.+.-|..
T Consensus 206 ~L~~rer~vi~~~~~-~~~t~~eIA~~lgis~~~V~~~~~ral~kLr~ 252 (254)
T TIGR02850 206 RLNEREKMILNMRFF-EGKTQMEVAEEIGISQAQVSRLEKAALKHMRK 252 (254)
T ss_pred cCCHHHHHHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHh
Confidence 478889999999886 58899999999999999999999988877643
No 140
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=76.57 E-value=2.2 Score=37.86 Aligned_cols=49 Identities=8% Similarity=0.110 Sum_probs=41.7
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhhc
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERAK 150 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~~ 150 (402)
+|+..+-++.|+++ .|.++..||..+|+|.+||...+.+....|.+.+.
T Consensus 123 L~~~~r~i~~l~~~-~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~ 171 (185)
T PRK12542 123 LNESNRQVFKYKVF-YNLTYQEISSVMGITEANVRKQFERARKRVQNMIG 171 (185)
T ss_pred CCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHc
Confidence 77788888877766 48999999999999999999999998888866543
No 141
>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=76.52 E-value=1.7 Score=34.84 Aligned_cols=43 Identities=7% Similarity=0.215 Sum_probs=37.1
Q ss_pred CHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHH
Q 015682 102 SVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEAL 145 (402)
Q Consensus 102 s~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al 145 (402)
.++++..+.++|+ .+.++.+++..+++|++|++++-++.+..|
T Consensus 57 d~~~r~iL~~~Yi-~~~~~~~I~~~l~~S~~t~yr~~~~Al~~L 99 (100)
T PF07374_consen 57 DPDERLILRMRYI-NKLTWEQIAEELNISRRTYYRIHKKALKEL 99 (100)
T ss_pred ChhHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHhc
Confidence 4678999999999 578999999999999999999888766544
No 142
>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=76.50 E-value=0.96 Score=34.74 Aligned_cols=36 Identities=22% Similarity=0.210 Sum_probs=26.1
Q ss_pred HHHHHHHhhhccCC-CccccccccccccccchhhhHH
Q 015682 104 EKQVAIALRRLASG-ESQVSVGVAFGVGQSTVSQVTW 139 (402)
Q Consensus 104 e~~l~i~L~~La~g-~s~~~l~~~fgvs~sTv~~~i~ 139 (402)
++++..-+-+|..| .+..+|+..||||.+|||+.++
T Consensus 5 ~~R~~~I~e~l~~~~~ti~dvA~~~gvS~~TVsr~L~ 41 (80)
T TIGR02844 5 EERVLEIGKYIVETKATVRETAKVFGVSKSTVHKDVT 41 (80)
T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHhc
Confidence 44555555555553 4677899999999999999774
No 143
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=76.48 E-value=2 Score=37.10 Aligned_cols=47 Identities=19% Similarity=0.162 Sum_probs=40.6
Q ss_pred cCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHH
Q 015682 100 LLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEE 147 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~ 147 (402)
.+|+.++.++.|+++. |.++..||..+|+|.+||...+++....|.+
T Consensus 112 ~L~~~~r~v~~l~~~~-~~s~~eIA~~lgis~~tv~~~l~Rar~~L~~ 158 (161)
T PRK12541 112 SLPLERRNVLLLRDYY-GFSYKEIAEMTGLSLAKVKIELHRGRKETKS 158 (161)
T ss_pred HCCHHHHHHhhhHHhc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 4888889988888765 8999999999999999999999888877754
No 144
>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=76.39 E-value=1.8 Score=41.83 Aligned_cols=44 Identities=14% Similarity=0.206 Sum_probs=39.1
Q ss_pred CCHHHHHHHHhhhc---cCCCccccccccccccccchhhhHHHHHHH
Q 015682 101 LSVEKQVAIALRRL---ASGESQVSVGVAFGVGQSTVSQVTWRFIEA 144 (402)
Q Consensus 101 ls~e~~l~i~L~~L---a~g~s~~~l~~~fgvs~sTv~~~i~~v~~a 144 (402)
+|+.++.++.|+|. ..+.++..||..+|||+.||.++..+.+..
T Consensus 250 L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVrq~~~rAl~k 296 (298)
T TIGR02997 250 LTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRK 296 (298)
T ss_pred CCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 88899999999985 578999999999999999999998876654
No 145
>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=76.10 E-value=1.5 Score=31.02 Aligned_cols=30 Identities=23% Similarity=0.340 Sum_probs=23.6
Q ss_pred hccCCCccccccccccccccchhhhHHHHH
Q 015682 113 RLASGESQVSVGVAFGVGQSTVSQVTWRFI 142 (402)
Q Consensus 113 ~La~g~s~~~l~~~fgvs~sTv~~~i~~v~ 142 (402)
+=..|.+..+|+..++++++|+++++.+..
T Consensus 13 ~~~~~~~~~~la~~~~~~~~~~t~~i~~L~ 42 (59)
T PF01047_consen 13 YENGGITQSELAEKLGISRSTVTRIIKRLE 42 (59)
T ss_dssp HHHSSEEHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHcCCCCHHHHHHHHCCChhHHHHHHHHHH
Confidence 334457899999999999999999887655
No 146
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=75.93 E-value=1.1 Score=32.46 Aligned_cols=26 Identities=19% Similarity=0.213 Sum_probs=22.1
Q ss_pred CccccccccccccccchhhhHHHHHH
Q 015682 118 ESQVSVGVAFGVGQSTVSQVTWRFIE 143 (402)
Q Consensus 118 ~s~~~l~~~fgvs~sTv~~~i~~v~~ 143 (402)
.+..+|+..+|+|++|+++++....+
T Consensus 26 ~s~~ela~~~g~s~~tv~r~l~~L~~ 51 (67)
T cd00092 26 LTRQEIADYLGLTRETVSRTLKELEE 51 (67)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 56778999999999999988877654
No 147
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=75.65 E-value=1.9 Score=40.12 Aligned_cols=48 Identities=15% Similarity=0.136 Sum_probs=41.1
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhh
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERA 149 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~ 149 (402)
+|..++-++.|+|+ .|.++..||..+|+|.+||...+++....|.+.+
T Consensus 172 Lp~~~R~v~~L~~~-eg~s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l 219 (233)
T PRK12538 172 LPEQQRIAVILSYH-ENMSNGEIAEVMDTTVAAVESLLKRGRQQLRDLL 219 (233)
T ss_pred CCHHHHHHhhhHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 67778888888775 5899999999999999999999999988886644
No 148
>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=75.48 E-value=0.74 Score=34.35 Aligned_cols=43 Identities=33% Similarity=0.394 Sum_probs=33.3
Q ss_pred CcCCHHHHHHHHhhhccCCCcccccccccc-ccccchhhhHHHH
Q 015682 99 RLLSVEKQVAIALRRLASGESQVSVGVAFG-VGQSTVSQVTWRF 141 (402)
Q Consensus 99 ~~ls~e~~l~i~L~~La~g~s~~~l~~~fg-vs~sTv~~~i~~v 141 (402)
+.+.-.-++++.|.+--++.++.+||..|| ..+|||...++++
T Consensus 27 ~~i~~aR~va~yL~r~~~~~sl~~Ig~~fg~rdHstV~~a~~ki 70 (70)
T PF08299_consen 27 RKIVEARQVAMYLARELTGLSLSEIGRYFGGRDHSTVIHAIRKI 70 (70)
T ss_dssp HHHHHHHHHHHHHHHHHS---HHHHHHHCTSSTHHHHHHHHHHH
T ss_pred hhhcchHHHHHHHHHHHhCCCHHHHHHHhCCCCHHHHHHHHHhC
Confidence 345567789998888888999999999999 9999998777653
No 149
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=75.36 E-value=2 Score=34.26 Aligned_cols=46 Identities=20% Similarity=0.218 Sum_probs=36.3
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHH
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEE 147 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~ 147 (402)
++-.++--+-|+|+ -..|+..||..|+||+++|+..|.+++..+..
T Consensus 18 LT~KQ~~Y~~lyy~-dDlSl~EIAee~~VSRqAIyDnIKr~~~~L~~ 63 (105)
T COG2739 18 LTKKQKNYLELYYL-DDLSLSEIAEEFNVSRQAIYDNIKRTEKILED 63 (105)
T ss_pred HhHHHHHHHHHHHH-hhccHHHHHHHhCccHHHHHHHHHHHHHHHHH
Confidence 33345555666554 57899999999999999999999999988864
No 150
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=75.36 E-value=2.4 Score=38.40 Aligned_cols=47 Identities=17% Similarity=0.078 Sum_probs=40.6
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHh
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEER 148 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~ 148 (402)
+|++++.++.|+|+ .|.++..||..+|+|.+||...+++....|.+.
T Consensus 154 L~~~~r~vl~l~~~-~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 200 (206)
T PRK12526 154 LPEAQQTVVKGVYF-QELSQEQLAQQLNVPLGTVKSRLRLALAKLKVQ 200 (206)
T ss_pred CCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 78888888888776 489999999999999999999988888877654
No 151
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=75.23 E-value=2.6 Score=39.56 Aligned_cols=47 Identities=21% Similarity=0.253 Sum_probs=41.3
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHh
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEER 148 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~ 148 (402)
+|+.++-++.|+|+ .|.++..||..+|+|.+||...+++....|...
T Consensus 202 L~~~~r~vl~l~~~-~~~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 248 (251)
T PRK07670 202 LSEKEQLVISLFYK-EELTLTEIGQVLNLSTSRISQIHSKALFKLKKL 248 (251)
T ss_pred CCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 78889999999886 789999999999999999999998888877543
No 152
>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=75.10 E-value=2.4 Score=37.12 Aligned_cols=50 Identities=28% Similarity=0.223 Sum_probs=42.2
Q ss_pred cCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhhc
Q 015682 100 LLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERAK 150 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~~ 150 (402)
.+|+.++.++.|.++ .|.++..||..+|+|.+||...+.+....|...+.
T Consensus 100 ~L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 149 (170)
T TIGR02959 100 ELPDEYREAIRLTEL-EGLSQQEIAEKLGLSLSGAKSRVQRGRKKLKELLE 149 (170)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 378888888888876 48999999999999999999999988887765443
No 153
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=74.97 E-value=2.6 Score=41.24 Aligned_cols=48 Identities=19% Similarity=0.243 Sum_probs=42.5
Q ss_pred cCCHHHHHHHHhhhc---cCCCccccccccccccccchhhhHHHHHHHHHH
Q 015682 100 LLSVEKQVAIALRRL---ASGESQVSVGVAFGVGQSTVSQVTWRFIEALEE 147 (402)
Q Consensus 100 ~ls~e~~l~i~L~~L---a~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~ 147 (402)
.+|+.++..+.|+|. ..+.++..||..+|||+.+|.++..+.+..|..
T Consensus 256 ~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVRqi~~rAl~kLr~ 306 (317)
T PRK07405 256 DLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLRK 306 (317)
T ss_pred cCCHHHHHHHHHHhhcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 388899999999996 467899999999999999999999988888755
No 154
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=74.58 E-value=2.6 Score=39.97 Aligned_cols=46 Identities=20% Similarity=0.329 Sum_probs=40.8
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHH
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEE 147 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~ 147 (402)
+|+.++-++.|+|+ .|.++..||..+|||.+||+++..+....|..
T Consensus 216 L~~rer~vl~l~y~-~~~t~~EIA~~lgis~~~V~~~~~ral~kLr~ 261 (264)
T PRK07122 216 LPERERTVLVLRFF-ESMTQTQIAERVGISQMHVSRLLAKTLARLRD 261 (264)
T ss_pred CCHHHHHHHHHHhc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 78888999999886 58999999999999999999999988877754
No 155
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=74.55 E-value=2.9 Score=37.41 Aligned_cols=48 Identities=17% Similarity=0.115 Sum_probs=41.0
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhh
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERA 149 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~ 149 (402)
||..++-++.|+|+ .|.++..||..+|+|.+||...+.+....|...+
T Consensus 143 L~~~~r~vl~l~~~-~~~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l 190 (194)
T PRK09646 143 LTDTQRESVTLAYY-GGLTYREVAERLAVPLGTVKTRMRDGLIRLRDCL 190 (194)
T ss_pred CCHHHHHHHHHHHH-cCCCHHHHHHHhCCChHhHHHHHHHHHHHHHHHh
Confidence 78888888878775 5799999999999999999999998888886543
No 156
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=74.34 E-value=2.4 Score=38.14 Aligned_cols=47 Identities=19% Similarity=0.205 Sum_probs=40.1
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhh
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERA 149 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~ 149 (402)
+|+.++-++.| ++ .|.++..||..+|+|.+||...+.+....|.+.+
T Consensus 156 L~~~~r~vl~l-~~-e~~s~~EIA~~lgis~~tV~~~l~rar~~Lr~~l 202 (208)
T PRK08295 156 LSELEKEVLEL-YL-DGKSYQEIAEELNRHVKSIDNALQRVKRKLEKYL 202 (208)
T ss_pred CCHHHHHHHHH-HH-ccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 67778888888 65 6999999999999999999999988888776643
No 157
>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=74.22 E-value=2.8 Score=38.47 Aligned_cols=46 Identities=24% Similarity=0.328 Sum_probs=40.5
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHH
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEE 147 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~ 147 (402)
+|+.++-++.|+|+ .|.++.+||..+|+|.+||.+.+++....|.+
T Consensus 176 L~~~~r~il~l~y~-~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~ 221 (224)
T TIGR02479 176 LSEREQLVLSLYYY-EELNLKEIGEVLGLTESRVSQIHSQALKKLRA 221 (224)
T ss_pred CCHHHHHHHHHHHh-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 78888888888885 68899999999999999999999888877754
No 158
>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=73.93 E-value=1.7 Score=29.49 Aligned_cols=38 Identities=21% Similarity=0.148 Sum_probs=26.0
Q ss_pred HHHHHhhhccCCCccccccccccccccchhhhHHHHHH
Q 015682 106 QVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIE 143 (402)
Q Consensus 106 ~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~ 143 (402)
++-|.........+..+|+..+|++++|+++.+....+
T Consensus 4 R~~Il~~L~~~~~~~~el~~~l~~s~~~vs~hL~~L~~ 41 (47)
T PF01022_consen 4 RLRILKLLSEGPLTVSELAEELGLSQSTVSHHLKKLRE 41 (47)
T ss_dssp HHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHhCCCchhhHHHhccccchHHHHHHHHHHH
Confidence 34443333334567889999999999999998876543
No 159
>PRK01381 Trp operon repressor; Provisional
Probab=73.68 E-value=2.2 Score=34.02 Aligned_cols=39 Identities=26% Similarity=0.336 Sum_probs=28.9
Q ss_pred CCHHHHHHHHhhh------ccCCCccccccccccccccchhhhHH
Q 015682 101 LSVEKQVAIALRR------LASGESQVSVGVAFGVGQSTVSQVTW 139 (402)
Q Consensus 101 ls~e~~l~i~L~~------La~g~s~~~l~~~fgvs~sTv~~~i~ 139 (402)
+++.++-+++.++ +..+.+|+.|+..+|||.+||+|.-+
T Consensus 33 lTp~Er~al~~R~~I~~~L~~g~~sQREIa~~lGvSiaTITRgsn 77 (99)
T PRK01381 33 LTPDEREALGTRVRIVEELLRGELSQREIKQELGVGIATITRGSN 77 (99)
T ss_pred CCHHHHHHHHHHHHHHHHHHcCCcCHHHHHHHhCCceeeehhhHH
Confidence 5555655555543 34458999999999999999987654
No 160
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=73.57 E-value=1.7 Score=38.86 Aligned_cols=48 Identities=21% Similarity=0.165 Sum_probs=39.8
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhh
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERA 149 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~ 149 (402)
+|+.++.++.|++ -.|.++..||..+|+|.+||...+.+....|.+.+
T Consensus 140 L~~~~r~i~~l~~-~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 187 (194)
T PRK12513 140 LPDEQREVFLLRE-HGDLELEEIAELTGVPEETVKSRLRYALQKLRELL 187 (194)
T ss_pred CCHhHhhheeeeh-ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 6777777777766 45899999999999999999998888887776543
No 161
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=73.56 E-value=2.8 Score=39.41 Aligned_cols=49 Identities=20% Similarity=0.307 Sum_probs=42.5
Q ss_pred cCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhh
Q 015682 100 LLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERA 149 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~ 149 (402)
.++-.+|+.+.|+|. .+.++..+|...|||+|.||++..+.+..|...+
T Consensus 196 ~L~EREk~Vl~l~y~-eelt~kEI~~~LgISes~VSql~kkai~kLr~~l 244 (247)
T COG1191 196 PLPEREKLVLVLRYK-EELTQKEIAEVLGISESRVSRLHKKAIKKLRKEL 244 (247)
T ss_pred ccCHHHHHHHHHHHH-hccCHHHHHHHhCccHHHHHHHHHHHHHHHHHHh
Confidence 467788999999994 4789999999999999999999999998886543
No 162
>PF13551 HTH_29: Winged helix-turn helix
Probab=73.54 E-value=1.4 Score=35.43 Aligned_cols=34 Identities=29% Similarity=0.337 Sum_probs=29.4
Q ss_pred HhhhccCCCc-cccccccccccccchhhhHHHHHH
Q 015682 110 ALRRLASGES-QVSVGVAFGVGQSTVSQVTWRFIE 143 (402)
Q Consensus 110 ~L~~La~g~s-~~~l~~~fgvs~sTv~~~i~~v~~ 143 (402)
+|..++.|.+ ...++..+|+|.+||++++.++..
T Consensus 4 ~l~l~~~g~~~~~~ia~~lg~s~~Tv~r~~~~~~~ 38 (112)
T PF13551_consen 4 ILLLLAEGVSTIAEIARRLGISRRTVYRWLKRYRE 38 (112)
T ss_pred HHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHc
Confidence 4566888996 999999999999999999988654
No 163
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=73.26 E-value=2.9 Score=37.09 Aligned_cols=48 Identities=21% Similarity=0.239 Sum_probs=40.6
Q ss_pred cCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHh
Q 015682 100 LLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEER 148 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~ 148 (402)
.+|+.++-++.|+|+- |.++..||..+|+|.+||...+.+....|...
T Consensus 139 ~L~~~~r~i~~l~~~~-g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 186 (189)
T PRK09648 139 TLPEKQREILILRVVV-GLSAEETAEAVGSTPGAVRVAQHRALARLRAE 186 (189)
T ss_pred hCCHHHHHHHHHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3778888888887776 89999999999999999999998888777543
No 164
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=73.12 E-value=1.8 Score=40.13 Aligned_cols=49 Identities=22% Similarity=0.167 Sum_probs=42.0
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhhc
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERAK 150 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~~ 150 (402)
+|++++-++.|+++. |.++..||..+|+|.+||...+.+....|.+.+.
T Consensus 150 L~~~~r~i~~l~~~~-g~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l~ 198 (231)
T PRK11922 150 LPDAFRAVFVLRVVE-ELSVEETAQALGLPEETVKTRLHRARRLLRESLA 198 (231)
T ss_pred CCHHHhhhheeehhc-CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 777888888887765 9999999999999999999999988888876554
No 165
>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=73.09 E-value=4.9 Score=34.01 Aligned_cols=48 Identities=19% Similarity=0.171 Sum_probs=40.4
Q ss_pred CCHHHHHHHHhhhccC-CCccccccccccccccchhhhHHHHHHHHHHh
Q 015682 101 LSVEKQVAIALRRLAS-GESQVSVGVAFGVGQSTVSQVTWRFIEALEER 148 (402)
Q Consensus 101 ls~e~~l~i~L~~La~-g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~ 148 (402)
++.+++-.+.++|+.. ..++..|+..+|+|++|++++=.+++..+.+.
T Consensus 83 Ld~~er~II~~rY~~~~~~t~~~Ia~~l~iS~~t~~r~r~~~l~kla~~ 131 (134)
T TIGR01636 83 ADEQTRVIIQELYMKKRPLTLVGLAQQLFISKSTAYRLRNHIIEAVAEE 131 (134)
T ss_pred CCHHHHHHHHHHHccCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 7888999999999743 34899999999999999999988888777653
No 166
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=72.98 E-value=2.7 Score=36.85 Aligned_cols=47 Identities=21% Similarity=0.184 Sum_probs=38.5
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHh
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEER 148 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~ 148 (402)
+|++++-++.|.++ .|.++..||..+|+|.+||...+++....+...
T Consensus 120 L~~~~r~i~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~Ra~~~~~~~ 166 (172)
T PRK09651 120 LNGKTREAFLLSQL-DGLTYSEIAHKLGVSVSSVKKYVAKATEHCLLF 166 (172)
T ss_pred CCHHHhHHhhhhhc-cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 67777777666665 589999999999999999999998888777543
No 167
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=71.83 E-value=5.1 Score=38.60 Aligned_cols=67 Identities=18% Similarity=0.230 Sum_probs=49.7
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhhcccccCCCchhHHHHHHHHHH
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERAKHHLKWPDSNRMEEIKSKFEE 170 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~~~~i~~P~~~~~~~i~~~f~~ 170 (402)
+|+.++-++.|+++- |.++.+||..+|+|.+||...+++....|.+..+.+- +..++..++.+.|-.
T Consensus 119 L~p~~R~vf~L~~~~-g~s~~EIA~~Lgis~~tVr~~l~RAr~~Lr~~~~~~~--~~~~~~~~~~~~f~~ 185 (290)
T PRK09635 119 LGPAERVVFVLHEIF-GLPYQQIATTIGSQASTCRQLAHRARRKINESRIAAS--VEPAQHRVVTRAFIE 185 (290)
T ss_pred CCHHHHHHhhHHHHh-CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhhCCCCC--CChHHHHHHHHHHHH
Confidence 777888887776654 9999999999999999999999999888876543221 233344556666643
No 168
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=71.74 E-value=2.5 Score=30.43 Aligned_cols=40 Identities=20% Similarity=0.253 Sum_probs=28.5
Q ss_pred HHHHHHHHhhhcc---CCCccccccccccccccchhhhHHHHH
Q 015682 103 VEKQVAIALRRLA---SGESQVSVGVAFGVGQSTVSQVTWRFI 142 (402)
Q Consensus 103 ~e~~l~i~L~~La---~g~s~~~l~~~fgvs~sTv~~~i~~v~ 142 (402)
..+.-+-+++.|. ...+-.+||..++||++||+..+.+..
T Consensus 5 ~~e~YL~~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~~L~ 47 (60)
T PF01325_consen 5 SEEDYLKAIYELSEEGGPVRTKDIAERLGVSPPTVTEMLKRLA 47 (60)
T ss_dssp HHHHHHHHHHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHcCCCCccHHHHHHHHCCChHHHHHHHHHHH
Confidence 3455556666665 345667899999999999998887654
No 169
>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=71.14 E-value=3.3 Score=33.25 Aligned_cols=47 Identities=21% Similarity=0.261 Sum_probs=33.8
Q ss_pred cCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHH
Q 015682 100 LLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEE 147 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~ 147 (402)
.++..++-.+-| |+-...|+..||..+|||+.+|+..+.+....|.+
T Consensus 17 LLT~kQ~~~l~l-yy~eDlSlsEIAe~~~iSRqaV~d~ikr~~~~L~~ 63 (101)
T PF04297_consen 17 LLTEKQREILEL-YYEEDLSLSEIAEELGISRQAVYDSIKRAEKKLEE 63 (101)
T ss_dssp GS-HHHHHHHHH-HCTS---HHHHHHHCTS-HHHHHHHHHHHHHHHHH
T ss_pred HCCHHHHHHHHH-HHccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 355556666665 55568999999999999999999999999888854
No 170
>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=71.01 E-value=1.6 Score=30.19 Aligned_cols=27 Identities=22% Similarity=0.306 Sum_probs=21.4
Q ss_pred CCccccccccccccccchhhhHHHHHH
Q 015682 117 GESQVSVGVAFGVGQSTVSQVTWRFIE 143 (402)
Q Consensus 117 g~s~~~l~~~fgvs~sTv~~~i~~v~~ 143 (402)
+.+..+|+...|+++||+++++.....
T Consensus 18 ~~t~~eia~~~gl~~stv~r~L~tL~~ 44 (52)
T PF09339_consen 18 PLTLSEIARALGLPKSTVHRLLQTLVE 44 (52)
T ss_dssp CEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 346889999999999999998876553
No 171
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=70.52 E-value=1.9 Score=39.60 Aligned_cols=67 Identities=15% Similarity=0.210 Sum_probs=48.0
Q ss_pred cCCHHHHHHHHhhhccCC----CccccccccccccccchhhhHHHHHHH-HHHhhcccccCCCchhHHHHHH
Q 015682 100 LLSVEKQVAIALRRLASG----ESQVSVGVAFGVGQSTVSQVTWRFIEA-LEERAKHHLKWPDSNRMEEIKS 166 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g----~s~~~l~~~fgvs~sTv~~~i~~v~~a-l~~~~~~~i~~P~~~~~~~i~~ 166 (402)
..+++++|+-+|..++.+ .+..+||..+|+++.|++|++.++.+. +.+.....|.-++.+.+.+++.
T Consensus 148 ~~~~~~Rla~~L~~~~~~~~~~~t~~~lA~~lG~sretvsR~L~~L~~~G~I~~~~~~i~I~d~~~L~~~~~ 219 (226)
T PRK10402 148 SFPLENRLAAFILLTQEGDLYHEKHTQAAEYLGVSYRHLLYVLAQFIQDGYLKKSKRGYLIKNRKQLSGLAL 219 (226)
T ss_pred cChHHHHHHHHHHhcccCCcccchHHHHHHHHCCcHHHHHHHHHHHHHCCCEEeeCCEEEEeCHHHHHHHHH
Confidence 358899999999877543 355789999999999999999888763 3333334565566555555544
No 172
>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=70.19 E-value=3.3 Score=34.64 Aligned_cols=46 Identities=28% Similarity=0.407 Sum_probs=34.2
Q ss_pred ccCCcCCHHHHHHHH-hhhccCCCccccccccccccccchhhhHHHHHH
Q 015682 96 IEGRLLSVEKQVAIA-LRRLASGESQVSVGVAFGVGQSTVSQVTWRFIE 143 (402)
Q Consensus 96 ~~~~~ls~e~~l~i~-L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~ 143 (402)
.+++++|.+.+.-|. |.. .|.+-.+|+..+.||+++|++|+.++-+
T Consensus 13 ~nGrPLp~~~R~rIvela~--~G~rp~~Isr~l~Vs~gcVsKIl~Ry~e 59 (125)
T PF00292_consen 13 INGRPLPNELRQRIVELAK--EGVRPCDISRQLRVSHGCVSKILSRYRE 59 (125)
T ss_dssp ETTSSS-HHHHHHHHHHHH--TT--HHHHHHHHT--HHHHHHHHHHHHH
T ss_pred eCCccCcHHHHHHHHHHhh--hcCCHHHHHHHHccchhHHHHHHHHHHH
Confidence 568899999887776 543 5999999999999999999999988754
No 173
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=70.08 E-value=3.6 Score=36.75 Aligned_cols=49 Identities=20% Similarity=0.246 Sum_probs=41.2
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhhc
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERAK 150 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~~ 150 (402)
+|...+-++.|+++ .|.++..||..+|+|.+||...+.+....|.+.+.
T Consensus 129 Lp~~~r~v~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 177 (188)
T PRK12517 129 LDPEYREPLLLQVI-GGFSGEEIAEILDLNKNTVMTRLFRARNQLKEALE 177 (188)
T ss_pred CCHHHHHHHHHHHH-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 77778887777665 48999999999999999999999998888866543
No 174
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=69.80 E-value=3.5 Score=40.29 Aligned_cols=69 Identities=16% Similarity=0.139 Sum_probs=47.6
Q ss_pred HHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhhcccccCCCchhHHHHHHHHHHhhCCCCcccc
Q 015682 109 IALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERAKHHLKWPDSNRMEEIKSKFEESFGLLNCCGA 180 (402)
Q Consensus 109 i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~~~~i~~P~~~~~~~i~~~f~~~~~fp~~iGa 180 (402)
++=.|+-.|.++.+||..+|||+++|+|++.+.-+. ....-.|.-|.. ...++...+.+++|+..|+-+
T Consensus 21 vA~lYY~~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~~--GiV~I~I~~~~~-~~~~Le~~L~~~fgLk~~iVv 89 (318)
T PRK15418 21 IAWFYYHDGLTQSEIGERLGLTRLKVSRLLEKGRQS--GIIRVQINSRFE-GCLELENALRQHFSLQHIRVL 89 (318)
T ss_pred HHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHc--CcEEEEEeCCCc-cHHHHHHHHHHHhCCCEEEEE
Confidence 555677789999999999999999999998754321 012334555532 345566677777788777543
No 175
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=68.90 E-value=3.7 Score=41.06 Aligned_cols=48 Identities=19% Similarity=0.251 Sum_probs=41.4
Q ss_pred cCCHHHHHHHHhhhc---cCCCccccccccccccccchhhhHHHHHHHHHH
Q 015682 100 LLSVEKQVAIALRRL---ASGESQVSVGVAFGVGQSTVSQVTWRFIEALEE 147 (402)
Q Consensus 100 ~ls~e~~l~i~L~~L---a~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~ 147 (402)
.+++.++..+.|+|+ ..+.++..||..+|||+.+|+++..+.+.-|..
T Consensus 311 ~L~~rEr~IL~lrygl~~~~~~Tl~EIA~~lgiS~eRVRQie~rAL~KLR~ 361 (373)
T PRK07406 311 TLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRH 361 (373)
T ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence 388899999999886 246799999999999999999999988887743
No 176
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=68.46 E-value=4.1 Score=36.92 Aligned_cols=48 Identities=25% Similarity=0.244 Sum_probs=40.5
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhh
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERA 149 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~ 149 (402)
+|+..+-++.|+++ .|.++..||..+|+|.+||...+.+....|.+.+
T Consensus 139 L~~~~r~v~~L~~~-~g~s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l 186 (203)
T PRK09647 139 LPPEFRAAVVLCDI-EGLSYEEIAATLGVKLGTVRSRIHRGRQQLRAAL 186 (203)
T ss_pred CCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 67777777777764 5899999999999999999999999888886644
No 177
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=68.06 E-value=4.7 Score=39.53 Aligned_cols=50 Identities=20% Similarity=0.204 Sum_probs=43.2
Q ss_pred cCCHHHHHHHHhhh-c--cCCCccccccccccccccchhhhHHHHHHHHHHhh
Q 015682 100 LLSVEKQVAIALRR-L--ASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERA 149 (402)
Q Consensus 100 ~ls~e~~l~i~L~~-L--a~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~ 149 (402)
.+|+.++.++.++| | -.|.++..||..+|||.+||..+.++....|...+
T Consensus 262 ~L~~~~R~vl~lrygL~~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l 314 (325)
T PRK05657 262 ELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLREIL 314 (325)
T ss_pred cCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 38889999999887 4 46789999999999999999999999988886644
No 178
>PF13751 DDE_Tnp_1_6: Transposase DDE domain
Probab=67.24 E-value=2.6 Score=34.85 Aligned_cols=49 Identities=16% Similarity=0.069 Sum_probs=34.8
Q ss_pred HhHHHhhh-HHHHHHHHHhccceeccccccccCCCChhHHHHHHHHHhhhhh
Q 015682 299 SLHEATRS-LAVKAFLQLKGGWRILSKVMWRPDKRKLPSIILVCCLLHNIII 349 (402)
Q Consensus 299 ~~~s~~R~-~vE~afg~LK~rfriL~~~~~~~~~~~~~~ii~accvLHN~~~ 349 (402)
..+.+.|. .||..||.||. +--|..... ....++..-+...|+.|||-.
T Consensus 74 k~~y~~R~~~VE~~fg~~K~-~~g~~r~~~-rG~~kv~~~~~l~a~a~Nl~r 123 (125)
T PF13751_consen 74 KELYKQRSIKVEGVFGTIKR-NHGLRRFRY-RGLEKVRIEFLLAAIAYNLKR 123 (125)
T ss_pred hhhhheeecccccccccchh-ccCCccccc-cchhhhHHHHHHHHHHHHHHH
Confidence 45566777 99999999997 444444432 245567777888888999853
No 179
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=67.11 E-value=6.5 Score=29.06 Aligned_cols=71 Identities=14% Similarity=0.107 Sum_probs=50.4
Q ss_pred hhhhhcccCCCHHHHHHHHHHHhccccCCCCCCCccccCCcCCHHHHHHHHhhhccCC-Cccccccccccc-cccchhhh
Q 015682 60 EEGFKYFFRVSKKTFDYICSLVREDLVSRPPSGLINIEGRLLSVEKQVAIALRRLASG-ESQVSVGVAFGV-GQSTVSQV 137 (402)
Q Consensus 60 ~~~F~~~fRms~~tF~~L~~~l~~~~~~~~~~g~~~~~~~~ls~e~~l~i~L~~La~g-~s~~~l~~~fgv-s~sTv~~~ 137 (402)
-++.-..++++..+|..++......... ..-...++.-++.+|..+ .+..+++..+|+ +.++.++.
T Consensus 4 ~~~la~~~~~s~~~l~~~f~~~~~~s~~------------~~~~~~r~~~a~~~l~~~~~~~~~ia~~~g~~s~~~f~r~ 71 (84)
T smart00342 4 LEDLAEALGMSPRHLQRLFKKETGTTPK------------QYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRA 71 (84)
T ss_pred HHHHHHHhCCCHHHHHHHHHHHhCcCHH------------HHHHHHHHHHHHHHHHcCCCCHHHHHHHhCCCChHHHHHH
Confidence 3456678899999998888754211000 112245677777787776 789999999999 99999988
Q ss_pred HHHHH
Q 015682 138 TWRFI 142 (402)
Q Consensus 138 i~~v~ 142 (402)
+.+..
T Consensus 72 Fk~~~ 76 (84)
T smart00342 72 FKKLF 76 (84)
T ss_pred HHHHH
Confidence 87654
No 180
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=66.97 E-value=2.3 Score=37.15 Aligned_cols=48 Identities=19% Similarity=0.205 Sum_probs=39.8
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhh
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERA 149 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~ 149 (402)
+|..++-++.|+++ .|.++.+||..+|+|.+||...+.+....|.+.+
T Consensus 121 L~~~~r~vl~l~~~-~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l 168 (175)
T PRK12518 121 LSLEHRAVLVLHDL-EDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFL 168 (175)
T ss_pred CCHHHeeeeeehHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 66677777777665 4888999999999999999999999888886644
No 181
>PRK14086 dnaA chromosomal replication initiation protein; Provisional
Probab=66.57 E-value=5 Score=42.66 Aligned_cols=51 Identities=25% Similarity=0.360 Sum_probs=45.5
Q ss_pred cCCcCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHH
Q 015682 97 EGRLLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEE 147 (402)
Q Consensus 97 ~~~~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~ 147 (402)
+.+.+...-+++|.|.+=-++.++..||..||.++|||...++++-+.|.+
T Consensus 549 R~~~i~~aRqiAMYL~r~lt~~Sl~~IG~~FgRdHSTV~~A~~kI~~~~~~ 599 (617)
T PRK14086 549 RSRVLVTARQIAMYLCRELTDLSLPKIGQQFGRDHTTVMHADRKIRALMAE 599 (617)
T ss_pred CCcccchHHHHHHHHHHHHcCCCHHHHHHHhCCChhHHHHHHHHHHHHHHh
Confidence 445677888999999999999999999999999999999999988887755
No 182
>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=66.42 E-value=3.9 Score=36.44 Aligned_cols=41 Identities=15% Similarity=0.180 Sum_probs=32.4
Q ss_pred HHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHH
Q 015682 105 KQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEE 147 (402)
Q Consensus 105 ~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~ 147 (402)
.+.++ +.++ .|.++.+||..+|+|.+||...+++....|..
T Consensus 155 ~~~i~-~~~~-~~~s~~eIA~~l~~s~~tV~~~l~r~r~~L~~ 195 (198)
T TIGR02859 155 EWKVL-QSYL-DGKSYQEIACDLNRHVKSIDNALQRVKRKLEK 195 (198)
T ss_pred HHHHH-HHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 34444 5555 79999999999999999999888887776644
No 183
>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=65.99 E-value=2.7 Score=35.37 Aligned_cols=35 Identities=9% Similarity=0.257 Sum_probs=30.6
Q ss_pred cCCHHHHHHHHhhhccCCCccccccccccccccchh
Q 015682 100 LLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVS 135 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~ 135 (402)
.+|+..+-++.|+++ .|.++.+||..+|+|.+||.
T Consensus 107 ~Lp~~~r~v~~l~~~-~~~s~~EIA~~l~is~~tV~ 141 (142)
T TIGR03209 107 ILPNKQKKIIYMKFF-EDMKEIDIAKKLHISRQSVY 141 (142)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHhhc
Confidence 378888888888776 48999999999999999985
No 184
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=65.97 E-value=1.9 Score=38.36 Aligned_cols=48 Identities=15% Similarity=0.131 Sum_probs=38.4
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhh
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERA 149 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~ 149 (402)
+|++++=++.|+++ .|.++..||..+|||.+||...+.+....|-+.+
T Consensus 135 L~~~~r~v~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 182 (188)
T PRK09640 135 VNPIDREILVLRFV-AELEFQEIADIMHMGLSATKMRYKRALDKLREKF 182 (188)
T ss_pred cChhheeeeeeHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 45555555666655 6899999999999999999999999888886644
No 185
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=65.40 E-value=5.3 Score=37.89 Aligned_cols=48 Identities=19% Similarity=0.261 Sum_probs=40.9
Q ss_pred cCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHh
Q 015682 100 LLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEER 148 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~ 148 (402)
.+|+.++-++.|+|+ .|.++..||..+|+|.+||.+...+....|...
T Consensus 212 ~L~~~~r~vl~l~~~-~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~ 259 (268)
T PRK06288 212 TLPEREKKVLILYYY-EDLTLKEIGKVLGVTESRISQLHTKAVLQLRAK 259 (268)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 378888888888875 589999999999999999998888887777554
No 186
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=65.40 E-value=5.2 Score=37.11 Aligned_cols=46 Identities=11% Similarity=0.198 Sum_probs=39.3
Q ss_pred cCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHH
Q 015682 100 LLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALE 146 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~ 146 (402)
.+++.++-++.|+|. .|.++..+|..+|||+++|+++..+...-|.
T Consensus 183 ~L~~~er~vi~l~~~-~~~t~~EIA~~lgis~~~V~q~~~~~~~kLr 228 (231)
T PRK12427 183 QLDEREQLILHLYYQ-HEMSLKEIALVLDLTEARICQLNKKIAQKIK 228 (231)
T ss_pred cCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 377888888888884 6899999999999999999999888777663
No 187
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=65.20 E-value=2.8 Score=37.13 Aligned_cols=44 Identities=16% Similarity=0.241 Sum_probs=36.8
Q ss_pred cCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHH
Q 015682 100 LLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEAL 145 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al 145 (402)
.+|+.|+ =.|..++.|.+..+||..+++|.+||..++.++..-+
T Consensus 133 ~LSpREr--EVLrLLAqGkTnKEIAe~L~IS~rTVkth~srImkKL 176 (198)
T PRK15201 133 HFSVTER--HLLKLIASGYHLSETAALLSLSEEQTKSLRRSIMRKL 176 (198)
T ss_pred CCCHHHH--HHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 3777654 4566789999999999999999999999988877666
No 188
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=64.32 E-value=6 Score=35.25 Aligned_cols=45 Identities=22% Similarity=0.265 Sum_probs=34.8
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHH
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALE 146 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~ 146 (402)
+++++.=.+.|+++ .|.++..||..+|||.+||.+-....-..+.
T Consensus 136 l~~~~~~~v~l~~~-~Gls~~EIA~~lgiS~~tV~r~l~~aR~~l~ 180 (185)
T PF07638_consen 136 LDPRQRRVVELRFF-EGLSVEEIAERLGISERTVRRRLRRARAWLR 180 (185)
T ss_pred cCHHHHHHHHHHHH-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 45556666667666 6899999999999999999988776655443
No 189
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=64.27 E-value=5.1 Score=40.60 Aligned_cols=46 Identities=22% Similarity=0.276 Sum_probs=40.3
Q ss_pred CCHHHHHHHHhhhc-c--CCCccccccccccccccchhhhHHHHHHHHH
Q 015682 101 LSVEKQVAIALRRL-A--SGESQVSVGVAFGVGQSTVSQVTWRFIEALE 146 (402)
Q Consensus 101 ls~e~~l~i~L~~L-a--~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~ 146 (402)
+++.++-++.|+|. . .+.++..||..+|||.++|.++.++.+..|.
T Consensus 351 L~~reR~VI~LRygl~d~~~~Tl~EIA~~LGvS~erVRqie~rAl~KLR 399 (415)
T PRK07598 351 LTSRERDVIRMRFGLADGHTYSLAEIGRALDLSRERVRQIESKALQKLR 399 (415)
T ss_pred CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHh
Confidence 88899999999985 3 4579999999999999999999998887774
No 190
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=64.18 E-value=5.3 Score=39.90 Aligned_cols=48 Identities=21% Similarity=0.290 Sum_probs=40.4
Q ss_pred cCCHHHHHHHHhhhc-c--CCCccccccccccccccchhhhHHHHHHHHHH
Q 015682 100 LLSVEKQVAIALRRL-A--SGESQVSVGVAFGVGQSTVSQVTWRFIEALEE 147 (402)
Q Consensus 100 ~ls~e~~l~i~L~~L-a--~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~ 147 (402)
.||..++..+.|+|. . .+.++..||..||||+..|+++-.+.+.-|..
T Consensus 305 ~L~~rEr~Vl~lrygl~~~~~~tl~EIa~~lgvs~erVrQi~~~Al~kLr~ 355 (367)
T PRK09210 305 TLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRH 355 (367)
T ss_pred hCCHHHHHHHHHHhccCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhC
Confidence 378899999999985 3 45799999999999999999998887776643
No 191
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=64.03 E-value=5.3 Score=39.10 Aligned_cols=67 Identities=24% Similarity=0.301 Sum_probs=44.6
Q ss_pred HhhhccCCCccccccccccccccchhhhHHHHHHHHHH-hhcccccCCCchhHHHHHHHHHHhhCCCCcccc
Q 015682 110 ALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEE-RAKHHLKWPDSNRMEEIKSKFEESFGLLNCCGA 180 (402)
Q Consensus 110 ~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~-~~~~~i~~P~~~~~~~i~~~f~~~~~fp~~iGa 180 (402)
+=.|+..|.++.+||..+|||+.||++.+.+--+ + ..+-.|..|.. ..-++.+...+++|++.|+-+
T Consensus 19 A~lYY~~gltQ~eIA~~LgiSR~~v~rlL~~Ar~---~GiV~I~i~~~~~-~~~~Le~~L~~~fgL~~a~VV 86 (321)
T COG2390 19 AWLYYVEGLTQSEIAERLGISRATVSRLLAKARE---EGIVKISINSPVE-GCLELEQQLKERFGLKEAIVV 86 (321)
T ss_pred HHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHH---CCeEEEEeCCCCc-chHHHHHHHHHhcCCCeEEEE
Confidence 4456678999999999999999999998764321 1 12334553333 334455666677787777533
No 192
>PRK05949 RNA polymerase sigma factor; Validated
Probab=63.88 E-value=6.2 Score=38.77 Aligned_cols=47 Identities=21% Similarity=0.308 Sum_probs=41.2
Q ss_pred CCHHHHHHHHhhh-cc--CCCccccccccccccccchhhhHHHHHHHHHH
Q 015682 101 LSVEKQVAIALRR-LA--SGESQVSVGVAFGVGQSTVSQVTWRFIEALEE 147 (402)
Q Consensus 101 ls~e~~l~i~L~~-La--~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~ 147 (402)
+++.++-++.|+| |. .+.++..||..+|||+++|..+..+.+..|..
T Consensus 267 L~~rer~Vi~lr~gl~~~e~~Tl~EIa~~lgiS~erVrq~~~rAl~kLr~ 316 (327)
T PRK05949 267 LTPQQREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHLRR 316 (327)
T ss_pred CCHHHHHHHHHHhccCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 7888999999988 43 56899999999999999999999988888755
No 193
>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=63.37 E-value=4.3 Score=28.22 Aligned_cols=26 Identities=12% Similarity=0.124 Sum_probs=20.7
Q ss_pred CCccccccccccccccchhhhHHHHH
Q 015682 117 GESQVSVGVAFGVGQSTVSQVTWRFI 142 (402)
Q Consensus 117 g~s~~~l~~~fgvs~sTv~~~i~~v~ 142 (402)
..+...||..|+||+.||.+.+...-
T Consensus 15 ~it~~eLa~~l~vS~rTi~~~i~~L~ 40 (55)
T PF08279_consen 15 PITAKELAEELGVSRRTIRRDIKELR 40 (55)
T ss_dssp SBEHHHHHHHCTS-HHHHHHHHHHHH
T ss_pred CcCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 36777899999999999998887654
No 194
>PRK00149 dnaA chromosomal replication initiation protein; Reviewed
Probab=63.21 E-value=6.5 Score=40.33 Aligned_cols=51 Identities=27% Similarity=0.352 Sum_probs=45.1
Q ss_pred cCCcCCHHHHHHHHhhhccCCCccccccccc-cccccchhhhHHHHHHHHHH
Q 015682 97 EGRLLSVEKQVAIALRRLASGESQVSVGVAF-GVGQSTVSQVTWRFIEALEE 147 (402)
Q Consensus 97 ~~~~ls~e~~l~i~L~~La~g~s~~~l~~~f-gvs~sTv~~~i~~v~~al~~ 147 (402)
+.+.+...-++|+.|.+--++.++.+||..| |.++|||...++++-+.+.+
T Consensus 382 R~~~~~~aR~iamyl~~~~~~~s~~~Ig~~fg~rdhstV~~a~~~i~~~~~~ 433 (450)
T PRK00149 382 RTRNIARPRQIAMYLAKELTDLSLPEIGRAFGGRDHTTVLHAVRKIEKLLEE 433 (450)
T ss_pred CCcccChHHHHHHHHHHHhcCCCHHHHHHHcCCCCHhHHHHHHHHHHHHHHh
Confidence 4567888899999999999999999999999 69999999999988887743
No 195
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=62.98 E-value=5.7 Score=29.31 Aligned_cols=40 Identities=15% Similarity=0.315 Sum_probs=31.2
Q ss_pred CHHHHHHHHhhhccC-CCccccccccccccccchhhhHHHH
Q 015682 102 SVEKQVAIALRRLAS-GESQVSVGVAFGVGQSTVSQVTWRF 141 (402)
Q Consensus 102 s~e~~l~i~L~~La~-g~s~~~l~~~fgvs~sTv~~~i~~v 141 (402)
+.+++++.+|..-.. |.+..+|+..+|++.++|++++...
T Consensus 6 ~~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L 46 (68)
T smart00550 6 SLEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSL 46 (68)
T ss_pred HHHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence 456777777776654 5888999999999999988776544
No 196
>COG3316 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=62.65 E-value=22 Score=32.58 Aligned_cols=181 Identities=13% Similarity=0.028 Sum_probs=100.5
Q ss_pred CHHHHHHHHhhhccCCCcccccccc-----ccccccchhhhHHHHHHHHHHhhcccccCCCchhHHHHHHHHHHhhCCCC
Q 015682 102 SVEKQVAIALRRLASGESQVSVGVA-----FGVGQSTVSQVTWRFIEALEERAKHHLKWPDSNRMEEIKSKFEESFGLLN 176 (402)
Q Consensus 102 s~e~~l~i~L~~La~g~s~~~l~~~-----fgvs~sTv~~~i~~v~~al~~~~~~~i~~P~~~~~~~i~~~f~~~~~fp~ 176 (402)
+-+.+...+=+||+.+.+|+.|... ..|+.+|+++++.++-..+.+..+..- .-++
T Consensus 10 ~~~vi~~~V~~yl~~~Ls~r~v~e~l~~rgi~v~h~Ti~rwv~k~~~~~~~~~~~r~-------------------~~~~ 70 (215)
T COG3316 10 PRNIIAVAVWLYLRYGLSLRDVEEMLAERGIEVDHETIHRWVQKYGPLLARRLKRRK-------------------RKAG 70 (215)
T ss_pred chhhHHHHHHHHhhcchhhccHHHHHHHcCcchhHHHHHHHHHHHhHHHHHHhhhhc-------------------cccc
Confidence 3334444455567779999998874 355689999999999888876544211 0012
Q ss_pred cccccceeEEEEecCCCCCCCccccCCCceeeeEeeeeCCCceEEeeeccCCCcccchhhhhcchhhhhhhhcccCCCCc
Q 015682 177 CCGAIDATHIIMTLPAVQTSDDWCDQENNYSMLVQGIVDHEMRFIDIVTGWPGGMNVSRLLKFSGFFKLCEAGQRLNGNV 256 (402)
Q Consensus 177 ~iGaIDgthI~i~~P~~~~~~~y~~~k~~~s~~~q~vvD~~~rf~~v~~g~pGs~~D~~v~~~S~l~~~~~~~~~l~~~~ 256 (402)
-.-.||-|.|.|. +...| +-..||.+|..+++..----....+..| +.++++.. +
T Consensus 71 ~~w~vDEt~ikv~-----gkw~y----------lyrAid~~g~~Ld~~L~~rRn~~aAk~F----l~kllk~~----g-- 125 (215)
T COG3316 71 DSWRVDETYIKVN-----GKWHY----------LYRAIDADGLTLDVWLSKRRNALAAKAF----LKKLLKKH----G-- 125 (215)
T ss_pred cceeeeeeEEeec-----cEeee----------hhhhhccCCCeEEEEEEcccCcHHHHHH----HHHHHHhc----C--
Confidence 2235899999884 11111 2246788898888877533334444433 23344432 1
Q ss_pred ccCCCccccceEEEeCCCCCCccc---cccCcccCCCCCchhhhhHhHHHh-hhHHHHHHHHHhccceeccccccccCCC
Q 015682 257 RISSEEVELREYIVGGVGYPLLSW---LITPYETNGLSASMPTFNSLHEAT-RSLAVKAFLQLKGGWRILSKVMWRPDKR 332 (402)
Q Consensus 257 ~~~~~~~~~~~~llgD~gYpl~~~---l~~Py~~~~l~~~~~~fN~~~s~~-R~~vE~afg~LK~rfriL~~~~~~~~~~ 332 (402)
.+..++-|.+=-+... +..+ +-++-+.. .++||+-+..+|.|=+-+..- +...
T Consensus 126 --------~p~v~vtDka~s~~~A~~~l~~~------------~ehr~~~ylnN~iE~dh~~iKrr~~~~~~f---~~~~ 182 (215)
T COG3316 126 --------EPRVFVTDKAPSYTAALRKLGSE------------VEHRTSKYLNNRIEQDHRPIKRRTRPMKRF---KSLS 182 (215)
T ss_pred --------CCceEEecCccchHHHHHhcCcc------------hheecccccccchhhcchhHHHHhcccccC---CChH
Confidence 2457788876332221 1111 11111222 366777777777655543221 2333
Q ss_pred ChhHHHHHHHHHhhhhh
Q 015682 333 KLPSIILVCCLLHNIII 349 (402)
Q Consensus 333 ~~~~ii~accvLHN~~~ 349 (402)
.....+...=.+|++-.
T Consensus 183 sa~~~~~gie~i~~~~~ 199 (215)
T COG3316 183 SAASTISGIESIHMLYK 199 (215)
T ss_pred HHHHHHHhHHHHHHHHh
Confidence 45566677777777754
No 197
>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=62.64 E-value=2.5 Score=29.27 Aligned_cols=43 Identities=21% Similarity=0.344 Sum_probs=31.3
Q ss_pred ccCCCccccccccccccccchhhhHHHHHHHHHHhhcccccCCCchhHHHHHHHH
Q 015682 114 LASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERAKHHLKWPDSNRMEEIKSKF 168 (402)
Q Consensus 114 La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~~~~i~~P~~~~~~~i~~~f 168 (402)
...|.++.++|...|+|++|++++.+. -..|+.+.+..++..|
T Consensus 6 ~~~gls~~~la~~~gis~~~i~~~~~g------------~~~~~~~~~~~ia~~l 48 (55)
T PF01381_consen 6 KEKGLSQKELAEKLGISRSTISRIENG------------KRNPSLDTLKKIAKAL 48 (55)
T ss_dssp HHTTS-HHHHHHHHTS-HHHHHHHHTT------------SSTSBHHHHHHHHHHH
T ss_pred HHcCCCHHHHHHHhCCCcchhHHHhcC------------CCCCCHHHHHHHHHHH
Confidence 367899999999999999999988753 3456666666666655
No 198
>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=62.42 E-value=3.9 Score=36.16 Aligned_cols=44 Identities=14% Similarity=0.129 Sum_probs=35.7
Q ss_pred CCHHHHHHHHhhhccC--------------CCccccccccccccccchhhhHHHHHHH
Q 015682 101 LSVEKQVAIALRRLAS--------------GESQVSVGVAFGVGQSTVSQVTWRFIEA 144 (402)
Q Consensus 101 ls~e~~l~i~L~~La~--------------g~s~~~l~~~fgvs~sTv~~~i~~v~~a 144 (402)
.+++++|+-+|..|+. ..+..+||...|+++.||+++++++.+.
T Consensus 113 ~~~~~Rla~~L~~l~~~~~~~~~~~~~~~~~~t~~~iA~~lG~tretvsR~l~~l~~~ 170 (193)
T TIGR03697 113 RDMGSRLVSFLLILCRDFGVPGQRGVTIDLRLSHQAIAEAIGSTRVTITRLLGDLRKK 170 (193)
T ss_pred CCHHHHHHHHHHHHHHHhCCCCCCeEEecCCCCHHHHHHHhCCcHHHHHHHHHHHHHC
Confidence 5789999999887643 2467789999999999999999877653
No 199
>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=62.37 E-value=2.1 Score=35.42 Aligned_cols=29 Identities=28% Similarity=0.320 Sum_probs=25.4
Q ss_pred hhccCCCccccccccccccccchhhhHHH
Q 015682 112 RRLASGESQVSVGVAFGVGQSTVSQVTWR 140 (402)
Q Consensus 112 ~~La~g~s~~~l~~~fgvs~sTv~~~i~~ 140 (402)
.+...|.+.+.++..|+||.+||.+++.+
T Consensus 13 ~~~~~g~s~~eaa~~F~VS~~Tv~~W~k~ 41 (119)
T PF01710_consen 13 AYIEKGKSIREAAKRFGVSRNTVYRWLKR 41 (119)
T ss_pred HHHHccchHHHHHHHhCcHHHHHHHHHHh
Confidence 46677889999999999999999988873
No 200
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=62.36 E-value=4.6 Score=31.08 Aligned_cols=38 Identities=24% Similarity=0.296 Sum_probs=27.8
Q ss_pred HHHHHhhhccC---CCccccccccccccccchhhhHHHHHH
Q 015682 106 QVAIALRRLAS---GESQVSVGVAFGVGQSTVSQVTWRFIE 143 (402)
Q Consensus 106 ~l~i~L~~La~---g~s~~~l~~~fgvs~sTv~~~i~~v~~ 143 (402)
+..-.|.+|+. +.+..+|+..+|++++||++++.....
T Consensus 6 r~~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~ 46 (91)
T smart00346 6 RGLAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQE 46 (91)
T ss_pred HHHHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 33444445543 467889999999999999999877654
No 201
>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=61.87 E-value=7.9 Score=31.95 Aligned_cols=72 Identities=19% Similarity=0.160 Sum_probs=44.3
Q ss_pred hhhcccCCCHHHHHHHHHHHhc-cccCCCCCCCccccCCcCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHH
Q 015682 62 GFKYFFRVSKKTFDYICSLVRE-DLVSRPPSGLINIEGRLLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWR 140 (402)
Q Consensus 62 ~F~~~fRms~~tF~~L~~~l~~-~~~~~~~~g~~~~~~~~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~ 140 (402)
+=-..|++|+.|....+..... ++..++ ..++.+..+ . +..+.--....+...++..||||.+|+++.+.+
T Consensus 23 eaa~~F~VS~~Tv~~W~k~~~~G~~~~k~------r~~~Kid~~-~-L~~~v~~~pd~tl~Ela~~l~Vs~~ti~~~Lkr 94 (119)
T PF01710_consen 23 EAAKRFGVSRNTVYRWLKRKETGDLEPKP------RGRKKIDRD-E-LKALVEENPDATLRELAERLGVSPSTIWRALKR 94 (119)
T ss_pred HHHHHhCcHHHHHHHHHHhcccccccccc------cccccccHH-H-HHHHHHHCCCcCHHHHHHHcCCCHHHHHHHHHH
Confidence 3446799999999888873332 122221 112255432 2 333333345577789999999999999877654
Q ss_pred H
Q 015682 141 F 141 (402)
Q Consensus 141 v 141 (402)
.
T Consensus 95 l 95 (119)
T PF01710_consen 95 L 95 (119)
T ss_pred c
Confidence 3
No 202
>PRK14088 dnaA chromosomal replication initiation protein; Provisional
Probab=61.34 E-value=6.4 Score=40.34 Aligned_cols=49 Identities=10% Similarity=0.157 Sum_probs=43.7
Q ss_pred cCCcCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHH
Q 015682 97 EGRLLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEAL 145 (402)
Q Consensus 97 ~~~~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al 145 (402)
+.+.+...-++++.|.+=-+|.++..||..||.++|||...+.++-+.+
T Consensus 367 R~~~i~~aR~iamyl~r~~~~~s~~~Ig~~fgr~hstV~~a~~~i~~~~ 415 (440)
T PRK14088 367 RNVKALLARRIGMYVAKNYLGSSLRTIAEKFNRSHPVVVDSVKKVKDSL 415 (440)
T ss_pred CCccccHHHHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 4556788889999999989999999999999999999999998888765
No 203
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=60.73 E-value=4 Score=37.16 Aligned_cols=45 Identities=18% Similarity=0.220 Sum_probs=37.9
Q ss_pred cCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHH
Q 015682 100 LLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALE 146 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~ 146 (402)
.+|+.|+ =.|..++.|.+..+||...++|.+||..++.++..-+.
T Consensus 137 ~LT~RE~--eVL~lla~G~snkeIA~~L~iS~~TVk~h~~~I~~KL~ 181 (207)
T PRK15411 137 SLSRTES--SMLRMWMAGQGTIQISDQMNIKAKTVSSHKGNIKRKIK 181 (207)
T ss_pred cCCHHHH--HHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHHhC
Confidence 3777665 45677999999999999999999999999988877663
No 204
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=60.24 E-value=9.3 Score=39.83 Aligned_cols=48 Identities=19% Similarity=0.274 Sum_probs=41.9
Q ss_pred cCCHHHHHHHHhhhc---cCCCccccccccccccccchhhhHHHHHHHHHH
Q 015682 100 LLSVEKQVAIALRRL---ASGESQVSVGVAFGVGQSTVSQVTWRFIEALEE 147 (402)
Q Consensus 100 ~ls~e~~l~i~L~~L---a~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~ 147 (402)
.|+..++..|.++|. ..+.++..||..||||++.|+++-.+.+.-|..
T Consensus 447 ~L~eREr~VI~lRyGL~~~e~~TL~EIa~~lGVSrERVRQIe~kAL~KLR~ 497 (509)
T PRK05901 447 TLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKLRH 497 (509)
T ss_pred hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 388899999999995 456899999999999999999999988877754
No 205
>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=60.22 E-value=3.4 Score=30.70 Aligned_cols=27 Identities=26% Similarity=0.340 Sum_probs=22.1
Q ss_pred CCccccccccccccccchhhhHHHHHH
Q 015682 117 GESQVSVGVAFGVGQSTVSQVTWRFIE 143 (402)
Q Consensus 117 g~s~~~l~~~fgvs~sTv~~~i~~v~~ 143 (402)
..+..+||...|+|+.||+++++++.+
T Consensus 28 ~lt~~~iA~~~g~sr~tv~r~l~~l~~ 54 (76)
T PF13545_consen 28 PLTQEEIADMLGVSRETVSRILKRLKD 54 (76)
T ss_dssp ESSHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 356778999999999999988877654
No 206
>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=58.40 E-value=4.2 Score=29.40 Aligned_cols=33 Identities=33% Similarity=0.454 Sum_probs=23.2
Q ss_pred hhhcc---CCCccccccccccccccchhhhHHHHHH
Q 015682 111 LRRLA---SGESQVSVGVAFGVGQSTVSQVTWRFIE 143 (402)
Q Consensus 111 L~~La---~g~s~~~l~~~fgvs~sTv~~~i~~v~~ 143 (402)
|++++ ...+..+|+..++++++|+++.+.+.++
T Consensus 9 L~~l~~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~ 44 (68)
T PF13463_consen 9 LRALAHSDGPMTQSDLAERLGISKSTVSRIIKKLEE 44 (68)
T ss_dssp HHHHT--TS-BEHHHHHHHTT--HHHHHHHHHHHHH
T ss_pred HHHHHccCCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 44444 3466788999999999999988877664
No 207
>PRK13870 transcriptional regulator TraR; Provisional
Probab=57.49 E-value=4.4 Score=37.72 Aligned_cols=44 Identities=18% Similarity=0.200 Sum_probs=37.8
Q ss_pred cCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHH
Q 015682 100 LLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEAL 145 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al 145 (402)
.+|+.|+ =+|.|+|.|.+..+||...|||.+||.-.+.....-|
T Consensus 173 ~LT~RE~--E~L~W~A~GKT~~EIa~ILgISe~TV~~Hl~na~~KL 216 (234)
T PRK13870 173 WLDPKEA--TYLRWIAVGKTMEEIADVEGVKYNSVRVKLREAMKRF 216 (234)
T ss_pred CCCHHHH--HHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHc
Confidence 5776654 4688999999999999999999999999998887766
No 208
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=57.24 E-value=5.8 Score=35.64 Aligned_cols=44 Identities=23% Similarity=0.302 Sum_probs=33.8
Q ss_pred cCCHHHHHHHHhhhccC-------------CCccccccccccccccchhhhHHHHHH
Q 015682 100 LLSVEKQVAIALRRLAS-------------GESQVSVGVAFGVGQSTVSQVTWRFIE 143 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~-------------g~s~~~l~~~fgvs~sTv~~~i~~v~~ 143 (402)
..++.++++-+|..|+. ..+..+||..+|+++.|++++++++.+
T Consensus 138 ~~~~~~Rl~~~L~~l~~~~~~~~~~~~~~~~~t~~~lA~~lG~tr~tvsR~l~~l~~ 194 (211)
T PRK11753 138 FLDVTGRIAQTLLDLAKQPDAMTHPDGMQIKITRQEIGRIVGCSREMVGRVLKMLED 194 (211)
T ss_pred hcChhhHHHHHHHHHHHhcCCcCCCCceecCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 46888999998887753 123467899999999999998876653
No 209
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=56.96 E-value=9.8 Score=30.85 Aligned_cols=46 Identities=24% Similarity=0.278 Sum_probs=36.5
Q ss_pred cCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHH
Q 015682 100 LLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALE 146 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~ 146 (402)
.|++++-=++-|..+- |.++.+.|...|||++|+.+++...-.-|.
T Consensus 41 ~L~~dElEAiRL~D~e-gl~QeeaA~~MgVSR~T~~ril~~ARkKiA 86 (106)
T PF02001_consen 41 VLTVDELEAIRLVDYE-GLSQEEAAERMGVSRPTFQRILESARKKIA 86 (106)
T ss_pred EeeHHHHHHHHHHHHc-CCCHHHHHHHcCCcHHHHHHHHHHHHHHHH
Confidence 4677777777777664 689999999999999999999876554443
No 210
>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=56.96 E-value=6.9 Score=30.94 Aligned_cols=28 Identities=11% Similarity=0.133 Sum_probs=22.7
Q ss_pred cCCCccccccccccccccchhhhHHHHH
Q 015682 115 ASGESQVSVGVAFGVGQSTVSQVTWRFI 142 (402)
Q Consensus 115 a~g~s~~~l~~~fgvs~sTv~~~i~~v~ 142 (402)
.-+.+...|+...|++++||++++.+..
T Consensus 45 ~~~is~~eLa~~~g~sr~tVsr~L~~Le 72 (95)
T TIGR01610 45 QDRVTATVIAELTGLSRTHVSDAIKSLA 72 (95)
T ss_pred CCccCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 3456778899999999999998887654
No 211
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=56.92 E-value=3.7 Score=36.63 Aligned_cols=64 Identities=19% Similarity=0.229 Sum_probs=43.2
Q ss_pred CCHHHHHHHHhhhccC--------------CCccccccccccccccchhhhHHHHHHH-HHHhhcccccCCCchhHHHH
Q 015682 101 LSVEKQVAIALRRLAS--------------GESQVSVGVAFGVGQSTVSQVTWRFIEA-LEERAKHHLKWPDSNRMEEI 164 (402)
Q Consensus 101 ls~e~~l~i~L~~La~--------------g~s~~~l~~~fgvs~sTv~~~i~~v~~a-l~~~~~~~i~~P~~~~~~~i 164 (402)
.+++++|+-+|..|+. ..++.+||...|+++.||++++.++.+. +.+.....|..++.+.+.++
T Consensus 119 ~~~~~Rla~~Ll~l~~~~~~~~~~~~~~~~~~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~~~~~i~I~d~~~L~~~ 197 (202)
T PRK13918 119 QRLKNRIAAALLELSDTPLATQEDSGETMIYATHDELAAAVGSVRETVTKVIGELSREGYIRSGYGKIQLLDLKGLEEL 197 (202)
T ss_pred CchHHHHHHHHHHHHHHhCCCCCCCCeEEecCCHHHHHHHhCccHHHHHHHHHHHHHCCCEEcCCCEEEEECHHHHHHH
Confidence 5678999999877653 1256789999999999999999887652 22222334555555444433
No 212
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=56.91 E-value=9.4 Score=37.45 Aligned_cols=47 Identities=23% Similarity=0.323 Sum_probs=40.4
Q ss_pred CCHHHHHHHHhhhc-c--CCCccccccccccccccchhhhHHHHHHHHHH
Q 015682 101 LSVEKQVAIALRRL-A--SGESQVSVGVAFGVGQSTVSQVTWRFIEALEE 147 (402)
Q Consensus 101 ls~e~~l~i~L~~L-a--~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~ 147 (402)
++..++..+.++|. . .+.++..||..||||+..|++|-.+.+.-|..
T Consensus 263 L~eREr~Vl~~rygl~~~~~~Tl~eIa~~lgvS~eRVrQIe~~Al~KLr~ 312 (324)
T PRK07921 263 LDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRN 312 (324)
T ss_pred CCHHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 78889999999885 2 34799999999999999999999888877754
No 213
>PF10654 DUF2481: Protein of unknown function (DUF2481) ; InterPro: IPR018916 This entry is represented by Bacteriophage A500, Gp59. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=56.79 E-value=4.6 Score=32.83 Aligned_cols=31 Identities=19% Similarity=0.141 Sum_probs=25.4
Q ss_pred CCCccccccccccccccchhhhHHHHHHHHH
Q 015682 116 SGESQVSVGVAFGVGQSTVSQVTWRFIEALE 146 (402)
Q Consensus 116 ~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~ 146 (402)
-|.+..+||+.|+||+||+..++.+.-..-.
T Consensus 79 AGlt~~aIAd~F~iS~s~~~nft~~n~~eYy 109 (126)
T PF10654_consen 79 AGLTCYAIADYFKISKSTVFNFTQNNKKEYY 109 (126)
T ss_pred cCCChHHHHHHHhHHHHHHHHHHHHhHHHHH
Confidence 3789999999999999999998866554443
No 214
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=56.76 E-value=4.5 Score=28.08 Aligned_cols=41 Identities=17% Similarity=0.208 Sum_probs=25.1
Q ss_pred CCcCCHHHHHHHHhhhccCCCccccccccccccccchhhhHH
Q 015682 98 GRLLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTW 139 (402)
Q Consensus 98 ~~~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~ 139 (402)
+..|+..||--|-+. ...|.+.+.++...|.|+.+|.+++.
T Consensus 2 G~~Lt~~Eqaqid~m-~qlG~s~~~isr~i~RSr~~Ir~yl~ 42 (50)
T PF11427_consen 2 GKTLTDAEQAQIDVM-HQLGMSLREISRRIGRSRTCIRRYLK 42 (50)
T ss_dssp S----HHHHHHHHHH-HHTT--HHHHHHHHT--HHHHHHHHH
T ss_pred CCcCCHHHHHHHHHH-HHhchhHHHHHHHhCccHHHHHHHhc
Confidence 456787777766553 34589999999999999999887764
No 215
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=56.65 E-value=8.1 Score=32.72 Aligned_cols=43 Identities=19% Similarity=0.278 Sum_probs=31.0
Q ss_pred CCHHH-HHHHHhhhccCCCccccccccccccccchhhhHHHHHH
Q 015682 101 LSVEK-QVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIE 143 (402)
Q Consensus 101 ls~e~-~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~ 143 (402)
+++.+ .++..|.....|.+..+|+..++++++|+++++.+...
T Consensus 29 lt~~q~~vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~v~~Le~ 72 (144)
T PRK03573 29 LTQTHWVTLHNIHQLPPEQSQIQLAKAIGIEQPSLVRTLDQLEE 72 (144)
T ss_pred CCHHHHHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHHH
Confidence 45444 44455554444578899999999999999988876553
No 216
>PRK14087 dnaA chromosomal replication initiation protein; Provisional
Probab=56.33 E-value=9.9 Score=39.07 Aligned_cols=51 Identities=16% Similarity=0.315 Sum_probs=45.1
Q ss_pred cCCcCCHHHHHHHHhhhccCCCcccccccccc-ccccchhhhHHHHHHHHHH
Q 015682 97 EGRLLSVEKQVAIALRRLASGESQVSVGVAFG-VGQSTVSQVTWRFIEALEE 147 (402)
Q Consensus 97 ~~~~ls~e~~l~i~L~~La~g~s~~~l~~~fg-vs~sTv~~~i~~v~~al~~ 147 (402)
+.+.+...-|+||.|.+=-++.++..||..|| .++|||...+.++-..+.+
T Consensus 381 R~~~i~~~RqiamyL~r~~t~~sl~~IG~~FggrdHsTV~~a~~ki~~~~~~ 432 (450)
T PRK14087 381 RSKSIVTARHIAMYLTKEILNHTLAQIGEEFGGRDHTTVINAERKIEKMLKK 432 (450)
T ss_pred CCccccHHHHHHHHHHHHHcCCCHHHHHHHhCCCChHHHHHHHHHHHHHHHh
Confidence 45568888999999999999999999999997 9999999998888877753
No 217
>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=55.63 E-value=3.3 Score=29.63 Aligned_cols=30 Identities=23% Similarity=0.182 Sum_probs=24.6
Q ss_pred ccCCCccccccccccccccchhhhHHHHHH
Q 015682 114 LASGESQVSVGVAFGVGQSTVSQVTWRFIE 143 (402)
Q Consensus 114 La~g~s~~~l~~~fgvs~sTv~~~i~~v~~ 143 (402)
-..+.+..+|+..+|++++|++..+....+
T Consensus 21 ~~~~~t~~ela~~l~~~~~t~s~hL~~L~~ 50 (61)
T PF12840_consen 21 SNGPMTVSELAEELGISQSTVSYHLKKLEE 50 (61)
T ss_dssp HCSTBEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred cCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 567788999999999999999998876544
No 218
>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=55.04 E-value=7 Score=27.99 Aligned_cols=33 Identities=30% Similarity=0.200 Sum_probs=26.7
Q ss_pred HHHHHhhhccCCCccccccccccccccchhhhHHH
Q 015682 106 QVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWR 140 (402)
Q Consensus 106 ~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~ 140 (402)
..|..|+. .|-+...||..+|++.+||+.+..+
T Consensus 4 ~~A~~LY~--~G~~~~eIA~~Lg~~~~TV~~W~~r 36 (58)
T PF06056_consen 4 EQARSLYL--QGWSIKEIAEELGVPRSTVYSWKDR 36 (58)
T ss_pred HHHHHHHH--cCCCHHHHHHHHCCChHHHHHHHHh
Confidence 34566654 5999999999999999999887754
No 219
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=54.93 E-value=5.3 Score=33.11 Aligned_cols=32 Identities=31% Similarity=0.253 Sum_probs=26.5
Q ss_pred HHHHHhhhccCCCccccccccccccccchhhhHH
Q 015682 106 QVAIALRRLASGESQVSVGVAFGVGQSTVSQVTW 139 (402)
Q Consensus 106 ~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~ 139 (402)
.||--|..- |.++..+|...|+|+++||+++.
T Consensus 13 ~lA~~L~ee--G~Sq~~iA~LLGltqaAVS~Yls 44 (119)
T COG2522 13 LLAKELIEE--GLSQYRIAKLLGLTQAAVSQYLS 44 (119)
T ss_pred HHHHHHHHc--CCcHHHHHHHhCCCHHHHHHHHc
Confidence 455555555 99999999999999999999974
No 220
>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=54.42 E-value=6.7 Score=27.95 Aligned_cols=29 Identities=28% Similarity=0.289 Sum_probs=24.8
Q ss_pred CccccccccccccccchhhhHHHHHHHHH
Q 015682 118 ESQVSVGVAFGVGQSTVSQVTWRFIEALE 146 (402)
Q Consensus 118 ~s~~~l~~~fgvs~sTv~~~i~~v~~al~ 146 (402)
.++...|..++||++++++.+.+.-..+.
T Consensus 14 gs~~~AA~~l~is~~~vs~~i~~LE~~lg 42 (60)
T PF00126_consen 14 GSISAAAEELGISQSAVSRQIKQLEEELG 42 (60)
T ss_dssp SSHHHHHHHCTSSHHHHHHHHHHHHHHHT
T ss_pred CCHHHHHHHhhccchHHHHHHHHHHHHhC
Confidence 38889999999999999999988776663
No 221
>PRK12422 chromosomal replication initiation protein; Provisional
Probab=54.37 E-value=11 Score=38.78 Aligned_cols=50 Identities=30% Similarity=0.296 Sum_probs=44.4
Q ss_pred cCCcCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHH
Q 015682 97 EGRLLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALE 146 (402)
Q Consensus 97 ~~~~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~ 146 (402)
+.+.+...-|+||.|.+=-++.|+.+||..||..+|||...+.++-+.+.
T Consensus 377 R~~~i~~~Rqiamyl~r~~t~~s~~~IG~~fgrdHsTV~~a~~ki~~~~~ 426 (445)
T PRK12422 377 QSREYVLPRQVAMYLCRQKLSLSYVKIGDVFSRDHSTVISSIRAISQKLE 426 (445)
T ss_pred CCcccccHHHHHHHHHHHhcCCCHHHHHHHhCCChHHHHHHHHHHHHHHH
Confidence 55567888999999999999999999999999999999988888877773
No 222
>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=54.28 E-value=18 Score=29.40 Aligned_cols=42 Identities=7% Similarity=0.055 Sum_probs=29.5
Q ss_pred CCHHH-HHHHHhhhccCCCccccccccccccccchhhhHHHHHH
Q 015682 101 LSVEK-QVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIE 143 (402)
Q Consensus 101 ls~e~-~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~ 143 (402)
+++.+ .++.+|. -..+.+..+|+..++++++|+++.+.+...
T Consensus 26 lt~~q~~iL~~l~-~~~~~t~~ela~~~~~~~~tvs~~l~~Le~ 68 (118)
T TIGR02337 26 LTEQQWRILRILA-EQGSMEFTQLANQACILRPSLTGILARLER 68 (118)
T ss_pred CCHHHHHHHHHHH-HcCCcCHHHHHHHhCCCchhHHHHHHHHHH
Confidence 44444 3333443 345678899999999999999988876654
No 223
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=54.13 E-value=3.2 Score=29.98 Aligned_cols=28 Identities=39% Similarity=0.426 Sum_probs=21.7
Q ss_pred hhhccCCCccccccccccccccchhhhH
Q 015682 111 LRRLASGESQVSVGVAFGVGQSTVSQVT 138 (402)
Q Consensus 111 L~~La~g~s~~~l~~~fgvs~sTv~~~i 138 (402)
..+-+.|.++.+++...|+|.||++++-
T Consensus 8 ~~R~~~gls~~~lA~~~g~s~s~v~~iE 35 (64)
T PF13560_consen 8 RLRERAGLSQAQLADRLGVSQSTVSRIE 35 (64)
T ss_dssp HHHHCHTS-HHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHcCCCHHHHHHHHCcCHHHHHHHH
Confidence 3455678999999999999999998765
No 224
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=53.72 E-value=4.6 Score=26.80 Aligned_cols=27 Identities=19% Similarity=0.234 Sum_probs=22.2
Q ss_pred CCccccccccccccccchhhhHHHHHH
Q 015682 117 GESQVSVGVAFGVGQSTVSQVTWRFIE 143 (402)
Q Consensus 117 g~s~~~l~~~fgvs~sTv~~~i~~v~~ 143 (402)
..+..+++..+|+|++|+++++..+.+
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~~L~~ 34 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLKRLEK 34 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 456778999999999999888876654
No 225
>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=52.96 E-value=4 Score=25.50 Aligned_cols=24 Identities=17% Similarity=0.299 Sum_probs=18.9
Q ss_pred ccccccccccccccchhhhHHHHH
Q 015682 119 SQVSVGVAFGVGQSTVSQVTWRFI 142 (402)
Q Consensus 119 s~~~l~~~fgvs~sTv~~~i~~v~ 142 (402)
+..+||+..|+++.||||++.++-
T Consensus 4 tr~diA~~lG~t~ETVSR~l~~l~ 27 (32)
T PF00325_consen 4 TRQDIADYLGLTRETVSRILKKLE 27 (32)
T ss_dssp -HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CHHHHHHHhCCcHHHHHHHHHHHH
Confidence 456899999999999999987654
No 226
>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]
Probab=52.78 E-value=11 Score=38.15 Aligned_cols=52 Identities=27% Similarity=0.333 Sum_probs=45.6
Q ss_pred ccCCcCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHH
Q 015682 96 IEGRLLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEE 147 (402)
Q Consensus 96 ~~~~~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~ 147 (402)
.+.+.+...-|+||.|.+--+..|+..||..||-.+|||...+.++-+.+.+
T Consensus 344 ~R~~~i~~~RqiamyL~r~lt~~Slp~IG~~FgrdHtTV~~a~~kI~~~~~~ 395 (408)
T COG0593 344 SRTRNIVRPRQIAMYLARELTNLSLPEIGKAFGRDHTTVLHAVRKIEQLIEE 395 (408)
T ss_pred ccccccchHHHHHHHHHHHHccCcHHHHHHHhCCCccHHHHHHHHHHHHHhc
Confidence 4556677889999999999999999999999999999999888888877754
No 227
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=52.61 E-value=9.9 Score=31.19 Aligned_cols=45 Identities=20% Similarity=0.149 Sum_probs=35.8
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHH
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALE 146 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~ 146 (402)
++.|++- ....|+.+..+...++..+|||=+||..-+.+++.+|.
T Consensus 34 L~~E~~~-Fi~~Fi~~rGnlKe~e~~lgiSYPTvR~rLd~ii~~lg 78 (113)
T PF09862_consen 34 LSPEQLE-FIKLFIKNRGNLKEMEKELGISYPTVRNRLDKIIEKLG 78 (113)
T ss_pred CCHHHHH-HHHHHHHhcCCHHHHHHHHCCCcHHHHHHHHHHHHHhC
Confidence 5655544 44456666778999999999999999999999998884
No 228
>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=52.45 E-value=8.6 Score=27.67 Aligned_cols=27 Identities=22% Similarity=0.193 Sum_probs=22.3
Q ss_pred CCCccccccccccccccchhhhHHHHH
Q 015682 116 SGESQVSVGVAFGVGQSTVSQVTWRFI 142 (402)
Q Consensus 116 ~g~s~~~l~~~fgvs~sTv~~~i~~v~ 142 (402)
.+.+..+++..++++.+|+++.+..+.
T Consensus 19 ~~~~~~ei~~~~~i~~~~i~~~l~~L~ 45 (78)
T cd00090 19 GPLTVSELAERLGLSQSTVSRHLKKLE 45 (78)
T ss_pred CCcCHHHHHHHHCcCHhHHHHHHHHHH
Confidence 348888999999999999988877653
No 229
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=52.29 E-value=30 Score=31.60 Aligned_cols=51 Identities=20% Similarity=0.132 Sum_probs=35.3
Q ss_pred cCCcCCHHHHHHHHhhh----ccC--CCccccccccccccccchhhhHHHHHHHHHH
Q 015682 97 EGRLLSVEKQVAIALRR----LAS--GESQVSVGVAFGVGQSTVSQVTWRFIEALEE 147 (402)
Q Consensus 97 ~~~~ls~e~~l~i~L~~----La~--g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~ 147 (402)
....|+..|.-++.+-| +-. ..+..+||..||||+||++.++++...-|.+
T Consensus 152 ~~~~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLRrAe~Kl~~ 208 (215)
T COG3413 152 GKNDLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLRRAERKLIE 208 (215)
T ss_pred ccccCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 33457776644443332 222 3567789999999999999999988776654
No 230
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=52.09 E-value=6.5 Score=36.06 Aligned_cols=44 Identities=5% Similarity=-0.004 Sum_probs=36.1
Q ss_pred cCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHH
Q 015682 100 LLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEAL 145 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al 145 (402)
.+++.++- .|..++.|.+..+||..+++|.+||..++.++..-+
T Consensus 143 ~LS~RE~e--VL~Lia~G~SnkEIA~~L~IS~~TVk~hvs~I~~KL 186 (217)
T PRK13719 143 KVTKYQND--VFILYSFGFSHEYIAQLLNITVGSSKNKISEILKFF 186 (217)
T ss_pred CCCHHHHH--HHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 46665543 456688999999999999999999999998887766
No 231
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=51.71 E-value=7.1 Score=27.21 Aligned_cols=29 Identities=24% Similarity=0.224 Sum_probs=23.2
Q ss_pred cCCCccccccccccccccchhhhHHHHHH
Q 015682 115 ASGESQVSVGVAFGVGQSTVSQVTWRFIE 143 (402)
Q Consensus 115 a~g~s~~~l~~~fgvs~sTv~~~i~~v~~ 143 (402)
....+..+++..+++|.+|+++++.+..+
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~ 36 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLRE 36 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 34467788999999999999988876553
No 232
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=51.29 E-value=7.2 Score=35.85 Aligned_cols=64 Identities=11% Similarity=0.040 Sum_probs=43.2
Q ss_pred cCCHHHHHHHHhhhccCC----------CccccccccccccccchhhhHHHHHHHHHHhhcccccCCCchhHHH
Q 015682 100 LLSVEKQVAIALRRLASG----------ESQVSVGVAFGVGQSTVSQVTWRFIEALEERAKHHLKWPDSNRMEE 163 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g----------~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~~~~i~~P~~~~~~~ 163 (402)
..+++++++-+|..++.. .+..+||..+|+++.||+++++++.+.=.......|..++.+.+.+
T Consensus 146 ~~~~~~Rla~~Ll~~~~~~~~~~~~~i~~t~~~iA~~lG~tretvsR~l~~L~~~gl~~~~~~i~I~d~~~L~~ 219 (236)
T PRK09392 146 LRSSAERLANYLLKQSLRQGGADVVTLPYEKRVLASYLGMTPENLSRAFAALASHGVHVDGSAVTITDPAGLAR 219 (236)
T ss_pred cCCHHHHHHHHHHHhccccCCCcEEEeeCCHHHHHHHhCCChhHHHHHHHHHHhCCeEeeCCEEEEcCHHHHHH
Confidence 358999999999877652 1235699999999999999988755432222234565565554443
No 233
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=51.08 E-value=5.3 Score=27.76 Aligned_cols=24 Identities=25% Similarity=0.371 Sum_probs=19.6
Q ss_pred ccccccccccccccchhhhHHHHH
Q 015682 119 SQVSVGVAFGVGQSTVSQVTWRFI 142 (402)
Q Consensus 119 s~~~l~~~fgvs~sTv~~~i~~v~ 142 (402)
+..+++..|++|++||.+.+....
T Consensus 22 s~~~la~~~~vs~~tv~~~l~~L~ 45 (60)
T smart00345 22 SERELAAQLGVSRTTVREALSRLE 45 (60)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHH
Confidence 566789999999999988776554
No 234
>PRK09191 two-component response regulator; Provisional
Probab=51.06 E-value=18 Score=33.47 Aligned_cols=51 Identities=16% Similarity=0.083 Sum_probs=42.8
Q ss_pred cCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhhcc
Q 015682 100 LLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERAKH 151 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~~~ 151 (402)
.+|+.++-++.|.++. |.++..+|..+|+|.+||...+.+....+.+.+..
T Consensus 88 ~L~~~~r~v~~l~~~~-~~s~~eIA~~l~~s~~tV~~~l~ra~~~l~~~~~~ 138 (261)
T PRK09191 88 GLTPLPRQAFLLTALE-GFSVEEAAEILGVDPAEAEALLDDARAEIARQVAT 138 (261)
T ss_pred hCCHHHhHHHHHHHHh-cCCHHHHHHHHCCCHHHHHHHHHHHHHHHhccCCC
Confidence 3777888888887764 88999999999999999999999988888765543
No 235
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=50.79 E-value=14 Score=31.38 Aligned_cols=42 Identities=14% Similarity=0.243 Sum_probs=31.2
Q ss_pred CCHHH-HHHHHhhhccCCCccccccccccccccchhhhHHHHHH
Q 015682 101 LSVEK-QVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIE 143 (402)
Q Consensus 101 ls~e~-~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~ 143 (402)
+++.+ .++..|+ -..|.+...|+..++++++|+++++.+..+
T Consensus 38 lt~~q~~vL~~l~-~~~~~t~~eLa~~l~i~~~tvsr~l~~Le~ 80 (144)
T PRK11512 38 ITAAQFKVLCSIR-CAACITPVELKKVLSVDLGALTRMLDRLVC 80 (144)
T ss_pred CCHHHHHHHHHHH-HcCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 55555 3444443 355688999999999999999998876553
No 236
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=50.16 E-value=9.7 Score=27.89 Aligned_cols=43 Identities=19% Similarity=0.130 Sum_probs=37.0
Q ss_pred HHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHh
Q 015682 106 QVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEER 148 (402)
Q Consensus 106 ~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~ 148 (402)
++-.++.+|..-.+..+.++..|+.+.+|.+++..|-..+.++
T Consensus 2 ~~~~fIrlLs~~~s~~~Aa~~lG~~~~~v~~wv~~fR~wll~L 44 (65)
T PF05344_consen 2 KARAFIRLLSQQISVAQAADRLGTDPGTVRRWVRMFRQWLLQL 44 (65)
T ss_pred cHHHHHHHhcccccHHHHHHHHCcCHHHHHHHHHHHHHHHHHc
Confidence 3456788899999999999999999999999999988877653
No 237
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=49.18 E-value=17 Score=27.95 Aligned_cols=43 Identities=21% Similarity=0.187 Sum_probs=29.8
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHH
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIE 143 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~ 143 (402)
++..+..++.+.....+.+...++..++++++|+++.+.+..+
T Consensus 8 l~~~~~~il~~l~~~~~~~~~~la~~~~~s~~~i~~~l~~L~~ 50 (101)
T smart00347 8 LTPTQFLVLRILYEEGPLSVSELAKRLGVSPSTVTRVLDRLEK 50 (101)
T ss_pred CCHHHHHHHHHHHHcCCcCHHHHHHHHCCCchhHHHHHHHHHH
Confidence 4444433333333344578889999999999999988887765
No 238
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=49.05 E-value=7.8 Score=35.39 Aligned_cols=44 Identities=25% Similarity=0.307 Sum_probs=36.6
Q ss_pred cCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHH
Q 015682 100 LLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEAL 145 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al 145 (402)
.+|..+. -.|..|+.|.+...||...++|.+||..++.+...-|
T Consensus 148 ~LT~RE~--eVL~lla~G~snkeIA~~L~iS~~TVk~h~~~i~~KL 191 (211)
T COG2197 148 LLTPREL--EVLRLLAEGLSNKEIAEELNLSEKTVKTHVSNILRKL 191 (211)
T ss_pred CCCHHHH--HHHHHHHCCCCHHHHHHHHCCCHhHHHHHHHHHHHHc
Confidence 4666554 4567799999999999999999999999998877665
No 239
>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=49.02 E-value=6.5 Score=28.71 Aligned_cols=38 Identities=21% Similarity=0.233 Sum_probs=28.1
Q ss_pred HHHHHHHhhhccCCCccccccccccccccchhhhHHHHH
Q 015682 104 EKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFI 142 (402)
Q Consensus 104 e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~ 142 (402)
|.++..+|. -..+.+..+|+...|++++||++++....
T Consensus 10 E~~vy~~Ll-~~~~~t~~eIa~~l~i~~~~v~~~L~~L~ 47 (68)
T PF01978_consen 10 EAKVYLALL-KNGPATAEEIAEELGISRSTVYRALKSLE 47 (68)
T ss_dssp HHHHHHHHH-HHCHEEHHHHHHHHTSSHHHHHHHHHHHH
T ss_pred HHHHHHHHH-HcCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 445555554 23347788999999999999998887654
No 240
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=48.47 E-value=7.6 Score=35.02 Aligned_cols=44 Identities=20% Similarity=0.137 Sum_probs=37.4
Q ss_pred cCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHH
Q 015682 100 LLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEAL 145 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al 145 (402)
.+|+.++ -.|..++.|.+...||...++|.+||..++.+...-+
T Consensus 150 ~Lt~rE~--evl~~~~~G~s~~eIA~~l~iS~~TV~~h~~~i~~Kl 193 (216)
T PRK10840 150 RLSPKES--EVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKL 193 (216)
T ss_pred cCCHHHH--HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHc
Confidence 4787775 5677789999999999999999999999988777655
No 241
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=47.69 E-value=9.7 Score=34.91 Aligned_cols=42 Identities=21% Similarity=0.307 Sum_probs=34.2
Q ss_pred CCHHHHHHHHhhhccC--------------CCccccccccccccccchhhhHHHHH
Q 015682 101 LSVEKQVAIALRRLAS--------------GESQVSVGVAFGVGQSTVSQVTWRFI 142 (402)
Q Consensus 101 ls~e~~l~i~L~~La~--------------g~s~~~l~~~fgvs~sTv~~~i~~v~ 142 (402)
.+++++++-+|..|+. ..+..+||...|+++.|+++++.++-
T Consensus 154 ~~~~~Rla~~L~~l~~~~~~~~~~~~~~~~~lt~~~iA~~lG~sr~tvsR~l~~l~ 209 (235)
T PRK11161 154 KNAEERLAAFIYNLSRRFAQRGFSPREFRLTMTRGDIGNYLGLTVETISRLLGRFQ 209 (235)
T ss_pred CCHHHHHHHHHHHHHHHHhhcCCCCceeEccccHHHHHHHhCCcHHHHHHHHHHHH
Confidence 5789999999998763 13567899999999999999886554
No 242
>PHA02591 hypothetical protein; Provisional
Probab=47.49 E-value=6.6 Score=29.75 Aligned_cols=36 Identities=11% Similarity=0.116 Sum_probs=28.7
Q ss_pred HHHHHHhhhccCCCccccccccccccccchhhhHHH
Q 015682 105 KQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWR 140 (402)
Q Consensus 105 ~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~ 140 (402)
+-+.++=.....|.+...||...|+++.||+++++.
T Consensus 47 d~~~vA~eL~eqGlSqeqIA~~LGVsqetVrKYL~~ 82 (83)
T PHA02591 47 DLISVTHELARKGFTVEKIASLLGVSVRKVRRYLES 82 (83)
T ss_pred hHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHhc
Confidence 344455555677999999999999999999998763
No 243
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=46.65 E-value=6.4 Score=35.52 Aligned_cols=29 Identities=21% Similarity=0.351 Sum_probs=25.6
Q ss_pred hhhccCCCccccccccccccccchhhhHH
Q 015682 111 LRRLASGESQVSVGVAFGVGQSTVSQVTW 139 (402)
Q Consensus 111 L~~La~g~s~~~l~~~fgvs~sTv~~~i~ 139 (402)
..++..|.++..++..+|||++|+++++.
T Consensus 166 ~~~~~~g~s~~~iak~lgis~~Tv~r~~k 194 (200)
T PRK13413 166 KKLLDKGTSKSEIARKLGVSRTTLARFLK 194 (200)
T ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 34568899999999999999999999886
No 244
>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=46.14 E-value=14 Score=34.11 Aligned_cols=46 Identities=22% Similarity=0.268 Sum_probs=38.3
Q ss_pred CcCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHH
Q 015682 99 RLLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALE 146 (402)
Q Consensus 99 ~~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~ 146 (402)
..+|+.++=++.+ .+.|.++.+||..+|||.+||...+.+....+.
T Consensus 170 ~~Lt~re~evl~~--~a~G~t~~eIa~~l~is~~Tv~~~l~~~~~kl~ 215 (232)
T TIGR03541 170 GVLSEREREVLAW--TALGRRQADIAAILGISERTVENHLRSARRKLG 215 (232)
T ss_pred ccCCHHHHHHHHH--HHCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHC
Confidence 3588877666665 589999999999999999999999988877663
No 245
>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=45.31 E-value=5.7 Score=27.06 Aligned_cols=18 Identities=39% Similarity=0.377 Sum_probs=15.5
Q ss_pred cccccccccccchhhhHH
Q 015682 122 SVGVAFGVGQSTVSQVTW 139 (402)
Q Consensus 122 ~l~~~fgvs~sTv~~~i~ 139 (402)
+++...|||++||+++++
T Consensus 2 ~lA~~~gvs~~tvs~~l~ 19 (52)
T cd01392 2 DIARAAGVSVATVSRVLN 19 (52)
T ss_pred cHHHHHCcCHHHHHHHHc
Confidence 578889999999998774
No 246
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=45.14 E-value=8.9 Score=34.95 Aligned_cols=44 Identities=18% Similarity=0.243 Sum_probs=35.9
Q ss_pred cCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHH
Q 015682 100 LLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEAL 145 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al 145 (402)
.+|+.|+ =.|..++.|.+..+||...+||..||..+..+...-+
T Consensus 134 ~LT~RE~--eVL~ll~~G~snkeIA~~L~iS~~TV~~h~~~I~~KL 177 (207)
T PRK11475 134 MLSPTER--EILRFMSRGYSMPQIAEQLERNIKTIRAHKFNVMSKL 177 (207)
T ss_pred CCCHHHH--HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHc
Confidence 3666554 3466788999999999999999999999988776655
No 247
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=44.35 E-value=13 Score=34.10 Aligned_cols=43 Identities=21% Similarity=0.235 Sum_probs=34.8
Q ss_pred CCHHHHHHHHhhhccC--C--------CccccccccccccccchhhhHHHHHH
Q 015682 101 LSVEKQVAIALRRLAS--G--------ESQVSVGVAFGVGQSTVSQVTWRFIE 143 (402)
Q Consensus 101 ls~e~~l~i~L~~La~--g--------~s~~~l~~~fgvs~sTv~~~i~~v~~ 143 (402)
.+++++|+-+|..++. | .+..+||...|+++.|++|++.++-+
T Consensus 153 ~~~~~Rla~~Ll~l~~~~g~~~~i~i~lt~~~IA~~lGisretlsR~L~~L~~ 205 (230)
T PRK09391 153 KTAMERVAAFLLEMDERLGGAGMMALPMSRRDIADYLGLTIETVSRALSQLQD 205 (230)
T ss_pred CCHHHHHHHHHHHHHHHhCCCCEEEecCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 5889999999988754 1 34578999999999999998876653
No 248
>KOG0930 consensus Guanine nucleotide exchange factor Cytohesin, contains PH and Sec7 domains [Intracellular trafficking, secretion, and vesicular transport]
Probab=44.34 E-value=61 Score=30.91 Aligned_cols=83 Identities=16% Similarity=0.311 Sum_probs=56.0
Q ss_pred HHHHHHhhhccCCCccccccccccccccchhhhHHHHHHH-------HHHhhccc---ccCCCch-hHHHHHHHHHHhhC
Q 015682 105 KQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEA-------LEERAKHH---LKWPDSN-RMEEIKSKFEESFG 173 (402)
Q Consensus 105 ~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~a-------l~~~~~~~---i~~P~~~-~~~~i~~~f~~~~~ 173 (402)
+.+|.+| |-+.|.+-..|+..+|=-..-.-.+++.|++. |...+++| .+.|... .+.++++.|...+.
T Consensus 94 q~iA~fl-ykGEGLnKtaIG~yLGer~~~nl~vL~aFv~~Hef~dlnlVqALRQfLwSFRLPGEaQKIdRmmEaFA~rYc 172 (395)
T KOG0930|consen 94 EDIARFL-YKGEGLNKTAIGDYLGERDEFNLQVLHAFVDLHEFTDLNLVQALRQFLWSFRLPGEAQKIDRMMEAFAQRYC 172 (395)
T ss_pred HHHHHHH-HhcCCcchhhHhhhhccCchhHHHHHHHHHHHHHhccchHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHHh
Confidence 4566665 44667788888888887766555555555443 11222333 4678754 78899999988765
Q ss_pred C--CCcccccceeEEEE
Q 015682 174 L--LNCCGAIDATHIIM 188 (402)
Q Consensus 174 f--p~~iGaIDgthI~i 188 (402)
+ ||+++.-|.+|+--
T Consensus 173 lcNPgvfqstDtcyvls 189 (395)
T KOG0930|consen 173 LCNPGVFQSTDTCYVLS 189 (395)
T ss_pred ccCCcccccCceeeeee
Confidence 4 88999999998853
No 249
>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=44.06 E-value=20 Score=28.86 Aligned_cols=43 Identities=16% Similarity=0.166 Sum_probs=30.0
Q ss_pred CCHHH-HHHHHhhhcc---CCCccccccccccccccchhhhHHHHHH
Q 015682 101 LSVEK-QVAIALRRLA---SGESQVSVGVAFGVGQSTVSQVTWRFIE 143 (402)
Q Consensus 101 ls~e~-~l~i~L~~La---~g~s~~~l~~~fgvs~sTv~~~i~~v~~ 143 (402)
+++.+ .++..|..+. .+.+..+|+..++++++|+++++.+..+
T Consensus 23 ls~~q~~vL~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le~ 69 (109)
T TIGR01889 23 LSLEELLILYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKKLSK 69 (109)
T ss_pred CCHHHHHHHHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 44444 3444444222 3588999999999999999998876654
No 250
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=44.01 E-value=10 Score=35.48 Aligned_cols=44 Identities=14% Similarity=0.233 Sum_probs=36.4
Q ss_pred cCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHH
Q 015682 100 LLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEAL 145 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al 145 (402)
.+|+.++= .|.+++.|.+..+||..++||..||...+.++..-+
T Consensus 179 ~LT~rE~e--vl~~~a~G~t~~eIa~~l~is~~TV~~h~~~~~~KL 222 (240)
T PRK10188 179 NFSKREKE--ILKWTAEGKTSAEIAMILSISENTVNFHQKNMQKKF 222 (240)
T ss_pred CCCHHHHH--HHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 57776654 455679999999999999999999999888877665
No 251
>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=43.83 E-value=16 Score=34.33 Aligned_cols=45 Identities=16% Similarity=0.311 Sum_probs=37.9
Q ss_pred CcCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHH
Q 015682 99 RLLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEAL 145 (402)
Q Consensus 99 ~~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al 145 (402)
..+|+.++=++.| ++.|.++.+||..++||..||...+.....-+
T Consensus 189 ~~LT~RE~evl~l--~a~G~s~~eIA~~L~IS~~TVk~hl~~i~~KL 233 (247)
T TIGR03020 189 GLITAREAEILAW--VRDGKTNEEIAAILGISSLTVKNHLQHIFKKL 233 (247)
T ss_pred cCCCHHHHHHHHH--HHCCCCHHHHHHHHCcCHHHHHHHHHHHHHHh
Confidence 3588887777665 57999999999999999999999988877655
No 252
>PHA00738 putative HTH transcription regulator
Probab=43.80 E-value=7.2 Score=31.63 Aligned_cols=38 Identities=16% Similarity=-0.004 Sum_probs=26.4
Q ss_pred HHHHHhhhccCC--CccccccccccccccchhhhHHHHHHH
Q 015682 106 QVAIALRRLASG--ESQVSVGVAFGVGQSTVSQVTWRFIEA 144 (402)
Q Consensus 106 ~l~i~L~~La~g--~s~~~l~~~fgvs~sTv~~~i~~v~~a 144 (402)
++.|.. +|+.| .+-.+|+..|++|++|||+.+...-+|
T Consensus 14 Rr~IL~-lL~~~e~~~V~eLae~l~lSQptVS~HLKvLreA 53 (108)
T PHA00738 14 RRKILE-LIAENYILSASLISHTLLLSYTTVLRHLKILNEQ 53 (108)
T ss_pred HHHHHH-HHHHcCCccHHHHHHhhCCCHHHHHHHHHHHHHC
Confidence 344433 34444 567789999999999999988654433
No 253
>PRK09483 response regulator; Provisional
Probab=43.79 E-value=9.6 Score=33.82 Aligned_cols=44 Identities=16% Similarity=0.257 Sum_probs=35.7
Q ss_pred cCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHH
Q 015682 100 LLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEAL 145 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al 145 (402)
.++..+.-.+ ..++.|.+...||..+++|.+||..++.+...-+
T Consensus 148 ~Lt~rE~~vl--~~~~~G~~~~~Ia~~l~is~~TV~~~~~~i~~Kl 191 (217)
T PRK09483 148 SLSERELQIM--LMITKGQKVNEISEQLNLSPKTVNSYRYRMFSKL 191 (217)
T ss_pred ccCHHHHHHH--HHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHc
Confidence 4777665443 4578999999999999999999999888777655
No 254
>PF12964 DUF3853: Protein of unknown function (DUF3853); InterPro: IPR024363 This entry represents a family of uncharacterised proteins that were found by clustering human gut metagenomic sequences [].
Probab=43.39 E-value=7.2 Score=30.85 Aligned_cols=69 Identities=9% Similarity=0.138 Sum_probs=38.5
Q ss_pred ccCCCHHHHHHHHHHHhccccCCCCCCCccccCCcCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHH--HHH
Q 015682 66 FFRVSKKTFDYICSLVREDLVSRPPSGLINIEGRLLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWR--FIE 143 (402)
Q Consensus 66 ~fRms~~tF~~L~~~l~~~~~~~~~~g~~~~~~~~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~--v~~ 143 (402)
.+-|+-+.|-.|.+.....-..+. .......+.+-. -.+.-||..||+|.||++||... .=+
T Consensus 10 v~qmTg~ell~L~~~~~~~~~~~~-------~~~~~~~~~~yv---------yG~~GlAklfgcSv~Ta~RiK~sG~id~ 73 (96)
T PF12964_consen 10 VWQMTGEELLFLLKEGKTNSEKQT-------SQKAKKDEKKYV---------YGLKGLAKLFGCSVPTANRIKKSGKIDP 73 (96)
T ss_pred HHHhhHHHHHHHHHHHhcCCCccC-------CccccCccccee---------ehHHHHHHHhCCCchhHHHHHhcCCccH
Confidence 456777777777776633322211 011122222211 23557899999999999999753 334
Q ss_pred HHHHhhc
Q 015682 144 ALEERAK 150 (402)
Q Consensus 144 al~~~~~ 150 (402)
||....+
T Consensus 74 AI~Q~Gr 80 (96)
T PF12964_consen 74 AITQIGR 80 (96)
T ss_pred HHHHcCC
Confidence 5544443
No 255
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=42.27 E-value=12 Score=26.45 Aligned_cols=36 Identities=25% Similarity=0.370 Sum_probs=30.0
Q ss_pred HhhhccCCCccccccccccccccchhhhHHHHHHHH
Q 015682 110 ALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEAL 145 (402)
Q Consensus 110 ~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al 145 (402)
.+.+++.|.+...++..+++|..||......+..-+
T Consensus 12 v~~l~~~G~s~~eia~~l~is~~tV~~h~~~i~~Kl 47 (65)
T COG2771 12 ILRLVAQGKSNKEIARILGISEETVKTHLRNIYRKL 47 (65)
T ss_pred HHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 456778899999999999999999988887765544
No 256
>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=42.07 E-value=8.5 Score=33.70 Aligned_cols=22 Identities=23% Similarity=0.249 Sum_probs=0.0
Q ss_pred CccccccccccccccchhhhHH
Q 015682 118 ESQVSVGVAFGVGQSTVSQVTW 139 (402)
Q Consensus 118 ~s~~~l~~~fgvs~sTv~~~i~ 139 (402)
.++.++|...|++.|||||++.
T Consensus 50 Lt~~~iA~~lgl~~STVSRav~ 71 (160)
T PF04552_consen 50 LTMKDIADELGLHESTVSRAVK 71 (160)
T ss_dssp ----------------------
T ss_pred CCHHHHHHHhCCCHhHHHHHHc
Confidence 5678999999999999999885
No 257
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=41.72 E-value=12 Score=34.41 Aligned_cols=43 Identities=16% Similarity=0.306 Sum_probs=34.5
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHH
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEAL 145 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al 145 (402)
+|+.++=. |..++.|.++.+||..+++|..||...+.+.+..+
T Consensus 156 Lt~rE~~V--l~l~~~G~s~~eIA~~L~iS~~TVk~~~~~i~~Kl 198 (216)
T PRK10100 156 LTHREKEI--LNKLRIGASNNEIARSLFISENTVKTHLYNLFKKI 198 (216)
T ss_pred CCHHHHHH--HHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 67655444 34456699999999999999999999998887766
No 258
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=41.26 E-value=20 Score=23.93 Aligned_cols=27 Identities=19% Similarity=0.158 Sum_probs=21.9
Q ss_pred CCccccccccccccccchhhhHHHHHH
Q 015682 117 GESQVSVGVAFGVGQSTVSQVTWRFIE 143 (402)
Q Consensus 117 g~s~~~l~~~fgvs~sTv~~~i~~v~~ 143 (402)
+.+..+++..|+++++|+++.+..+..
T Consensus 14 ~~s~~~l~~~l~~s~~tv~~~l~~L~~ 40 (53)
T smart00420 14 KVSVEELAELLGVSEMTIRRDLNKLEE 40 (53)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 466778999999999999988876543
No 259
>PF13309 HTH_22: HTH domain
Probab=40.88 E-value=18 Score=26.33 Aligned_cols=39 Identities=23% Similarity=0.235 Sum_probs=28.5
Q ss_pred cCCHHHHHHHHhhhccCCC-----ccccccccccccccchhhhH
Q 015682 100 LLSVEKQVAIALRRLASGE-----SQVSVGVAFGVGQSTVSQVT 138 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~-----s~~~l~~~fgvs~sTv~~~i 138 (402)
.++-++++.+.-..-..|. +-..+|..+|||+.||++++
T Consensus 20 ~l~~~~k~~iV~~L~~~G~F~lKgav~~vA~~L~iS~~TVY~YL 63 (64)
T PF13309_consen 20 RLSKEEKKEIVRQLYEKGIFLLKGAVEYVAEKLGISRATVYRYL 63 (64)
T ss_pred hCCHHHHHHHHHHHHHCCCcccCcHHHHHHHHHCCCHHHHHHHc
Confidence 4666777777655555553 44568999999999999876
No 260
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=40.61 E-value=6.5 Score=29.70 Aligned_cols=28 Identities=36% Similarity=0.576 Sum_probs=23.2
Q ss_pred hhccCCCcccccccccc------ccccchhhhHH
Q 015682 112 RRLASGESQVSVGVAFG------VGQSTVSQVTW 139 (402)
Q Consensus 112 ~~La~g~s~~~l~~~fg------vs~sTv~~~i~ 139 (402)
++...|.++.++|...| +|++|||++-.
T Consensus 19 ~R~~lGLTQ~dvA~~lg~~~g~i~SQstISR~Es 52 (75)
T smart00352 19 RRIKLGFTQADVGLALGALYGPDFSQTTICRFEA 52 (75)
T ss_pred HHHHcCCCHHHHHHHhcccccCcCCHHHHHHHHh
Confidence 35667899999999999 59999999754
No 261
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=40.50 E-value=21 Score=28.40 Aligned_cols=38 Identities=21% Similarity=0.258 Sum_probs=27.8
Q ss_pred HHHHHHhhhccCCCccccccccccccccchhhhHHHHHH
Q 015682 105 KQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIE 143 (402)
Q Consensus 105 ~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~ 143 (402)
.+++-.|.. ....++..|+..+|+|++|+++.+.+..+
T Consensus 6 ~~il~~L~~-~~~~~~~~la~~l~~s~~tv~~~l~~L~~ 43 (108)
T smart00344 6 RKILEELQK-DARISLAELAKKVGLSPSTVHNRVKRLEE 43 (108)
T ss_pred HHHHHHHHH-hCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 344444444 23578999999999999999888876654
No 262
>COG5421 Transposase [DNA replication, recombination, and repair]
Probab=40.27 E-value=60 Score=33.38 Aligned_cols=55 Identities=16% Similarity=0.181 Sum_probs=37.7
Q ss_pred eeeeEeeeeCCCceEEeeeccCCCcccchhhhhcchhhhhhhhcccCCCCcccCCCccccceEEEeCCCC
Q 015682 206 YSMLVQGIVDHEMRFIDIVTGWPGGMNVSRLLKFSGFFKLCEAGQRLNGNVRISSEEVELREYIVGGVGY 275 (402)
Q Consensus 206 ~s~~~q~vvD~~~rf~~v~~g~pGs~~D~~v~~~S~l~~~~~~~~~l~~~~~~~~~~~~~~~~llgD~gY 275 (402)
.-+++..++|..|-.+.+.+ ++|+.+|...+... .+.+.+. ++ ..+.++++|+||
T Consensus 155 ~QI~vsMi~~~~gIPl~~~v-~~Gni~D~~~~~~t--i~kl~~~--l~----------~~~~~~V~Dkgf 209 (480)
T COG5421 155 PQINVSMIVNQKGIPLFVRV-YSGNISDKNTLIKT--IQKLKSV--LV----------KDEVYLVADKGF 209 (480)
T ss_pred ceeEEEEEEcCCCCceEEEc-cCCCccchHHHHHH--HHHHHHh--cc----------cceEEEEEcccc
Confidence 56888888888877666666 79999999877542 2222221 11 113799999998
No 263
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=40.16 E-value=6.2 Score=29.18 Aligned_cols=21 Identities=33% Similarity=0.286 Sum_probs=17.2
Q ss_pred ccccccccccccccchhhhHH
Q 015682 119 SQVSVGVAFGVGQSTVSQVTW 139 (402)
Q Consensus 119 s~~~l~~~fgvs~sTv~~~i~ 139 (402)
+..+|+...|||.+|||++++
T Consensus 2 t~~~iA~~~gvS~~TVSr~ln 22 (70)
T smart00354 2 TIKDVARLAGVSKATVSRVLN 22 (70)
T ss_pred CHHHHHHHHCCCHHHHHHHHC
Confidence 356788899999999998763
No 264
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=39.19 E-value=23 Score=37.95 Aligned_cols=47 Identities=17% Similarity=0.250 Sum_probs=40.1
Q ss_pred cCCHHHHHHHHhhhc---cCCCccccccccccccccchhhhHHHHHHHHH
Q 015682 100 LLSVEKQVAIALRRL---ASGESQVSVGVAFGVGQSTVSQVTWRFIEALE 146 (402)
Q Consensus 100 ~ls~e~~l~i~L~~L---a~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~ 146 (402)
.|+..++..+.++|. ..+.++..||..||||++.|+++-.+.+.-|.
T Consensus 556 ~L~~rE~~Vl~~r~g~~~~~~~tl~ei~~~lgvs~eRVrQie~~al~kLr 605 (619)
T PRK05658 556 SLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 605 (619)
T ss_pred cCCHHHHHHHHHhcCCCCCCCccHHHHHHHhCCCHHHHHHHHHHHHHHHh
Confidence 378889999999996 35678999999999999999999888777664
No 265
>PRK08558 adenine phosphoribosyltransferase; Provisional
Probab=39.00 E-value=23 Score=33.12 Aligned_cols=56 Identities=18% Similarity=0.199 Sum_probs=40.9
Q ss_pred CHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHhhcccccCCCchhHHHHHHHHH
Q 015682 102 SVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERAKHHLKWPDSNRMEEIKSKFE 169 (402)
Q Consensus 102 s~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~~~~i~~P~~~~~~~i~~~f~ 169 (402)
-...++.-.|+.|..--+|.+|+..+|++.|.++|+++- -..|+.++..++.+...
T Consensus 8 ~~~~~~v~~lr~lk~~~ty~el~~~~g~p~~~l~RYv~g------------~~~P~~~~a~~~~~~l~ 63 (238)
T PRK08558 8 RLQLRAVRVLRSLKKTYTYEELSSITGLPESVLNRYVNG------------HVLPSVERAREIVEKLG 63 (238)
T ss_pred HHHHHHHHHHHHHhcccCHHHHHHHHCCCHHHHHHHHcC------------CcCCCHHHHHHHHHHHH
Confidence 344566678899999999999999999999999998851 12466665555555443
No 266
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=38.95 E-value=13 Score=30.77 Aligned_cols=43 Identities=21% Similarity=0.114 Sum_probs=30.0
Q ss_pred CHHHHHHHHhhhccC-CCccccccccccccccchhhhHHHHHHH
Q 015682 102 SVEKQVAIALRRLAS-GESQVSVGVAFGVGQSTVSQVTWRFIEA 144 (402)
Q Consensus 102 s~e~~l~i~L~~La~-g~s~~~l~~~fgvs~sTv~~~i~~v~~a 144 (402)
+-+.++.|....+.. +.+..+|+..++++++|||+.+...-++
T Consensus 14 adptRl~IL~~L~~~~~~~v~ela~~l~lsqstvS~HL~~L~~A 57 (117)
T PRK10141 14 SDETRLGIVLLLRESGELCVCDLCTALDQSQPKISRHLALLRES 57 (117)
T ss_pred CCHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 334555555433333 3567789999999999999998766655
No 267
>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=38.63 E-value=16 Score=32.70 Aligned_cols=41 Identities=15% Similarity=0.114 Sum_probs=30.3
Q ss_pred CcCCHHHHHHHHhhhcc-CCCccccccccccccccchhhhHH
Q 015682 99 RLLSVEKQVAIALRRLA-SGESQVSVGVAFGVGQSTVSQVTW 139 (402)
Q Consensus 99 ~~ls~e~~l~i~L~~La-~g~s~~~l~~~fgvs~sTv~~~i~ 139 (402)
..+++-++.......+. .|.+...|+..+|+|+++|++++.
T Consensus 101 ~~lt~~e~a~~~~~l~~~~g~s~~~iA~~lg~s~~~V~r~l~ 142 (187)
T TIGR00180 101 EDLSPIEEAQAYKRLLEKFSMTQEDLAKKIGKSRAHITNLLR 142 (187)
T ss_pred cCCCHHHHHHHHHHHHHHhCCCHHHHHHHHCcCHHHHHHHHH
Confidence 35666665544444443 688999999999999999998764
No 268
>COG3293 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=38.43 E-value=18 Score=29.83 Aligned_cols=56 Identities=18% Similarity=0.170 Sum_probs=39.1
Q ss_pred EEeCCCCCCccccccCcccCC----CC--CchhhhhHhHHHhhhHHHHHHHHHhccceecccc
Q 015682 269 IVGGVGYPLLSWLITPYETNG----LS--ASMPTFNSLHEATRSLAVKAFLQLKGGWRILSKV 325 (402)
Q Consensus 269 llgD~gYpl~~~l~~Py~~~~----l~--~~~~~fN~~~s~~R~~vE~afg~LK~rfriL~~~ 325 (402)
+|.|.+|...+|-+-|-.-.+ .. ..+.-++..+...|..+|+.|+.+|. |+.+...
T Consensus 40 ~i~~~~~~g~~wr~~p~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~f~~~~~-~r~~~~~ 101 (124)
T COG3293 40 GIADLLYTGCAWRALPADFPPATTVIPYRRFRRWFKRGLWKRRNLVERTFGRLKQ-FRRTATR 101 (124)
T ss_pred HHHHHhccchHHHHhHHHhCCCceEeCCCcchhhHHHHHHHHHHHHHHHHHHHhc-ccceecc
Confidence 466777766666554433211 11 13678899999999999999999997 8777754
No 269
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=38.23 E-value=6.7 Score=29.86 Aligned_cols=34 Identities=29% Similarity=0.446 Sum_probs=23.4
Q ss_pred HHHHHhhhc--cCCCccccccccccccccchhhhHH
Q 015682 106 QVAIALRRL--ASGESQVSVGVAFGVGQSTVSQVTW 139 (402)
Q Consensus 106 ~l~i~L~~L--a~g~s~~~l~~~fgvs~sTv~~~i~ 139 (402)
+++..|..+ +.|.++.++|...|+++|+||++.+
T Consensus 18 ~l~~~i~~~~~~~~ltQ~e~A~~lgisq~~vS~l~~ 53 (80)
T PF13744_consen 18 QLMAAIRELREERGLTQAELAERLGISQPRVSRLEN 53 (80)
T ss_dssp HHHHHHHHHHHCCT--HHHHHHHHTS-HHHHHHHHT
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHCCChhHHHHHHc
Confidence 444444443 5678999999999999999998874
No 270
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=38.00 E-value=20 Score=34.31 Aligned_cols=43 Identities=16% Similarity=0.119 Sum_probs=35.7
Q ss_pred HHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHH
Q 015682 105 KQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEE 147 (402)
Q Consensus 105 ~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~ 147 (402)
.+|-.++....+|.+++..|...+||+||||+.+.+.-..+..
T Consensus 4 ~~L~~F~~v~~~~~s~s~AA~~L~isq~avSr~I~~LE~~lg~ 46 (309)
T PRK12682 4 QQLRFVREAVRRNLNLTEAAKALHTSQPGVSKAIIELEEELGI 46 (309)
T ss_pred HHHHHHHHHHHccCCHHHHHHHhcCccHHHHHHHHHHHHHhCC
Confidence 3455566666678899999999999999999999998888854
No 271
>TIGR02405 trehalos_R_Ecol trehalose operon repressor, proteobacterial. This family consists of repressors of the LacI 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 Gammaproteobacteria and does not include the GntR family TreR of Bacillus subtilis
Probab=37.80 E-value=13 Score=35.62 Aligned_cols=21 Identities=38% Similarity=0.397 Sum_probs=18.6
Q ss_pred ccccccccccccccchhhhHH
Q 015682 119 SQVSVGVAFGVGQSTVSQVTW 139 (402)
Q Consensus 119 s~~~l~~~fgvs~sTv~~~i~ 139 (402)
+..+||...|||++|||++++
T Consensus 3 ti~dIA~~agVS~sTVSr~Ln 23 (311)
T TIGR02405 3 TIKDIARLAGVGKSTVSRVLN 23 (311)
T ss_pred cHHHHHHHhCCCHHHHHHHhC
Confidence 456899999999999999985
No 272
>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=37.72 E-value=23 Score=29.87 Aligned_cols=45 Identities=18% Similarity=0.165 Sum_probs=38.1
Q ss_pred CCHHHHHHHHhhhccC-CCccccccccccccccchhhhHHHHHHHH
Q 015682 101 LSVEKQVAIALRRLAS-GESQVSVGVAFGVGQSTVSQVTWRFIEAL 145 (402)
Q Consensus 101 ls~e~~l~i~L~~La~-g~s~~~l~~~fgvs~sTv~~~i~~v~~al 145 (402)
+..+++-.+-|+|-.. +.++..||..+.+|.+|+.++-.+|-..|
T Consensus 82 l~de~k~Ii~lry~~r~~~TW~~IA~~l~i~erta~r~~~~fK~~i 127 (130)
T PF05263_consen 82 LIDEEKRIIKLRYDRRSRRTWYQIAQKLHISERTARRWRDRFKNDI 127 (130)
T ss_pred hCHHHHHHHHHHHcccccchHHHHHHHhCccHHHHHHHHHHHHHHh
Confidence 5667888888888877 79999999999999999999887776544
No 273
>PF05269 Phage_CII: Bacteriophage CII protein; InterPro: IPR007933 The CII protein is a transcription activator, conserved in bacteriophage lambda and related phages, that plays a key role in the decision between lytic or lysogenic phage development. CII is regulated at multiple levels including transcription, translation initiation, mRNA stability, and proteolysis []. Conditions that stabilise cII favour lysogenic development. The lambda CII protein activates three specific promoters, binding to direct repeat sequences rather than the more usual inverted repeats. Structurally, CII is a homotetramer where each monomer is composed of four alpha helices and a disordered C terminus [, ]. The alpha helical region is responsible for DNA binding and multimerisation. The homotetramer has an unusual spatial arrangement that allows recognition of the direct repeat sequences.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1ZS4_C 1ZPQ_C 1XWR_A.
Probab=36.74 E-value=19 Score=28.37 Aligned_cols=30 Identities=37% Similarity=0.418 Sum_probs=23.4
Q ss_pred CccccccccccccccchhhhHHHHHHHHHH
Q 015682 118 ESQVSVGVAFGVGQSTVSQVTWRFIEALEE 147 (402)
Q Consensus 118 ~s~~~l~~~fgvs~sTv~~~i~~v~~al~~ 147 (402)
..+..++...||+.|||||+-..++.-+..
T Consensus 24 ~gq~~vA~~~Gv~eStISR~k~~~~~~~a~ 53 (91)
T PF05269_consen 24 VGQKKVAEAMGVDESTISRWKNDFIEKMAM 53 (91)
T ss_dssp HHHHHHHHHHTSSTTTHHHHHHHHHHHHHH
T ss_pred HhhHHHHHHhCCCHHHHHHHHhhHHHHHHH
Confidence 456789999999999999987665554444
No 274
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=36.53 E-value=9.7 Score=24.87 Aligned_cols=28 Identities=14% Similarity=0.046 Sum_probs=20.1
Q ss_pred ccCCCccccccccccccccchhhhHHHH
Q 015682 114 LASGESQVSVGVAFGVGQSTVSQVTWRF 141 (402)
Q Consensus 114 La~g~s~~~l~~~fgvs~sTv~~~i~~v 141 (402)
|.++.+..+||..+|+|.+..++.+.+.
T Consensus 5 ~~~~~~l~~iA~~~g~S~~~f~r~Fk~~ 32 (42)
T PF00165_consen 5 LQQKLTLEDIAEQAGFSPSYFSRLFKKE 32 (42)
T ss_dssp T-SS--HHHHHHHHTS-HHHHHHHHHHH
T ss_pred ccCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 4566777889999999999999888764
No 275
>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=36.39 E-value=9.6 Score=25.28 Aligned_cols=24 Identities=25% Similarity=0.321 Sum_probs=18.4
Q ss_pred CCccccccccccccccchhhhHHH
Q 015682 117 GESQVSVGVAFGVGQSTVSQVTWR 140 (402)
Q Consensus 117 g~s~~~l~~~fgvs~sTv~~~i~~ 140 (402)
-.+|..||...|+|.+||.+-+.+
T Consensus 17 r~s~~~la~~lglS~~~v~~Ri~r 40 (42)
T PF13404_consen 17 RRSYAELAEELGLSESTVRRRIRR 40 (42)
T ss_dssp TS-HHHHHHHHTS-HHHHHHHHHH
T ss_pred CccHHHHHHHHCcCHHHHHHHHHH
Confidence 467899999999999999876654
No 276
>COG4496 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=36.23 E-value=21 Score=27.82 Aligned_cols=34 Identities=21% Similarity=0.378 Sum_probs=26.8
Q ss_pred HHHHHHHhhhccCCCccccccccccccccchhhhH
Q 015682 104 EKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVT 138 (402)
Q Consensus 104 e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i 138 (402)
++++-|+ ..|..|.+|++|...-|.|-.|+||+-
T Consensus 44 aqRlqVa-~mL~eg~tY~~I~~eTGaStaTIsRVk 77 (100)
T COG4496 44 AQRLQVA-KMLKEGRTYRDIEDETGASTATISRVK 77 (100)
T ss_pred HHHHHHH-HHHHcCCCcchhhhccCcchhhHHHHH
Confidence 3444333 567889999999999999999999864
No 277
>PRK09492 treR trehalose repressor; Provisional
Probab=36.23 E-value=17 Score=34.65 Aligned_cols=23 Identities=35% Similarity=0.319 Sum_probs=20.0
Q ss_pred CccccccccccccccchhhhHHH
Q 015682 118 ESQVSVGVAFGVGQSTVSQVTWR 140 (402)
Q Consensus 118 ~s~~~l~~~fgvs~sTv~~~i~~ 140 (402)
.+..+||...|||.+|||++++.
T Consensus 5 ~ti~dIA~~agVS~~TVSrvLn~ 27 (315)
T PRK09492 5 LTIKDIARLSGVGKSTVSRVLNN 27 (315)
T ss_pred CcHHHHHHHhCCCHHHHhHHhCC
Confidence 35779999999999999999863
No 278
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=36.02 E-value=14 Score=26.17 Aligned_cols=43 Identities=21% Similarity=0.275 Sum_probs=24.8
Q ss_pred cCCCccccccccccccccchhhhHHHHHHHHHHhhcccccCCCchhHHHHHHHH
Q 015682 115 ASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERAKHHLKWPDSNRMEEIKSKF 168 (402)
Q Consensus 115 a~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~~~~i~~P~~~~~~~i~~~f 168 (402)
..|.+..+|+...|||++|++++++.- +..|+.+.+..++..|
T Consensus 8 ~~~it~~~La~~~gis~~tl~~~~~~~-----------~~~~~~~~l~~ia~~l 50 (63)
T PF13443_consen 8 ERGITQKDLARKTGISRSTLSRILNGK-----------PSNPSLDTLEKIAKAL 50 (63)
T ss_dssp HTT--HHHHHHHHT--HHHHHHHHTTT----------------HHHHHHHHHHH
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHhcc-----------cccccHHHHHHHHHHc
Confidence 346788899999999999999887522 2234455566666655
No 279
>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=35.80 E-value=11 Score=25.80 Aligned_cols=25 Identities=28% Similarity=0.300 Sum_probs=21.5
Q ss_pred ccCCCccccccccccccccchhhhH
Q 015682 114 LASGESQVSVGVAFGVGQSTVSQVT 138 (402)
Q Consensus 114 La~g~s~~~l~~~fgvs~sTv~~~i 138 (402)
-..|.++.+++...|+|++|++++.
T Consensus 12 ~~~gltq~~lA~~~gvs~~~vs~~e 36 (58)
T TIGR03070 12 KALGLTQADLADLAGVGLRFIRDVE 36 (58)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHH
Confidence 3468889999999999999998876
No 280
>PHA01976 helix-turn-helix protein
Probab=35.46 E-value=11 Score=27.19 Aligned_cols=44 Identities=16% Similarity=0.155 Sum_probs=31.0
Q ss_pred hccCCCccccccccccccccchhhhHHHHHHHHHHhhcccccCCCchhHHHHHHHH
Q 015682 113 RLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEERAKHHLKWPDSNRMEEIKSKF 168 (402)
Q Consensus 113 ~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~~~~i~~P~~~~~~~i~~~f 168 (402)
+-..|.+..++|...||+++|++++-+. ..-|+.+.+..+++.|
T Consensus 11 R~~~glt~~~lA~~~gvs~~~v~~~e~g------------~~~p~~~~l~~ia~~l 54 (67)
T PHA01976 11 RNARAWSAPELSRRAGVRHSLIYDFEAD------------KRLPNLKTLLRLADAL 54 (67)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHHcC------------CCCCCHHHHHHHHHHH
Confidence 4456889999999999999999876531 1235555566666554
No 281
>PRK00215 LexA repressor; Validated
Probab=34.78 E-value=26 Score=31.63 Aligned_cols=26 Identities=19% Similarity=0.196 Sum_probs=22.1
Q ss_pred Cccccccccccc-cccchhhhHHHHHH
Q 015682 118 ESQVSVGVAFGV-GQSTVSQVTWRFIE 143 (402)
Q Consensus 118 ~s~~~l~~~fgv-s~sTv~~~i~~v~~ 143 (402)
.++.+|+..+|+ +++|+++++....+
T Consensus 24 ~s~~ela~~~~~~~~~tv~~~l~~L~~ 50 (205)
T PRK00215 24 PSRREIADALGLRSPSAVHEHLKALER 50 (205)
T ss_pred CCHHHHHHHhCCCChHHHHHHHHHHHH
Confidence 477899999999 99999988876654
No 282
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=34.64 E-value=17 Score=31.55 Aligned_cols=44 Identities=20% Similarity=0.296 Sum_probs=34.7
Q ss_pred cCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHH
Q 015682 100 LLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEAL 145 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al 145 (402)
.+++.+. -.|..|+.|.+...|+..+++|.+||...+.++..-+
T Consensus 137 ~Lt~~E~--~il~~l~~g~~~~~Ia~~l~~s~~tv~~~~~~l~~Kl 180 (196)
T PRK10360 137 PLTKRER--QVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKL 180 (196)
T ss_pred CCCHHHH--HHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 3555444 3455688899999999999999999999988887655
No 283
>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=34.45 E-value=23 Score=27.08 Aligned_cols=34 Identities=12% Similarity=0.001 Sum_probs=26.8
Q ss_pred ccCCCccccccccccccccchhhhHHHHHHHHHH
Q 015682 114 LASGESQVSVGVAFGVGQSTVSQVTWRFIEALEE 147 (402)
Q Consensus 114 La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~ 147 (402)
...+.+..+++..+.||+||+.+.+.++-+.+..
T Consensus 27 ~~~~~s~~~la~~~~iS~sti~~~i~~l~~~l~~ 60 (87)
T PF05043_consen 27 NNEYVSIEDLAEELFISRSTIYRDIKKLNKYLKK 60 (87)
T ss_dssp H-SEEEHHHHHHHHT--HHHHHHHHHHHHHHHHC
T ss_pred cCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 5667888999999999999999999888877754
No 284
>PRK10870 transcriptional repressor MprA; Provisional
Probab=33.60 E-value=28 Score=30.82 Aligned_cols=42 Identities=10% Similarity=0.160 Sum_probs=29.1
Q ss_pred CCHHH-HHHHHhhhccC-CCccccccccccccccchhhhHHHHH
Q 015682 101 LSVEK-QVAIALRRLAS-GESQVSVGVAFGVGQSTVSQVTWRFI 142 (402)
Q Consensus 101 ls~e~-~l~i~L~~La~-g~s~~~l~~~fgvs~sTv~~~i~~v~ 142 (402)
+++.+ .++..|+.... +.+..+|+..++++++|+++++.+..
T Consensus 53 Lt~~q~~iL~~L~~~~~~~it~~eLa~~l~l~~~tvsr~v~rLe 96 (176)
T PRK10870 53 INETLFMALITLESQENHSIQPSELSCALGSSRTNATRIADELE 96 (176)
T ss_pred CCHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 45443 44445544333 35678999999999999998887655
No 285
>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=33.53 E-value=15 Score=26.86 Aligned_cols=25 Identities=20% Similarity=0.248 Sum_probs=20.3
Q ss_pred CccccccccccccccchhhhHHHHH
Q 015682 118 ESQVSVGVAFGVGQSTVSQVTWRFI 142 (402)
Q Consensus 118 ~s~~~l~~~fgvs~sTv~~~i~~v~ 142 (402)
.+...|+..||+|.+||++.+...-
T Consensus 14 ~~~~eLa~~l~vS~~tv~~~l~~L~ 38 (69)
T TIGR00122 14 FSGEKLGEALGMSRTAVNKHIQTLR 38 (69)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3466899999999999988886653
No 286
>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=33.13 E-value=10 Score=24.87 Aligned_cols=22 Identities=18% Similarity=0.181 Sum_probs=17.7
Q ss_pred ccccccccccccccchhhhHHH
Q 015682 119 SQVSVGVAFGVGQSTVSQVTWR 140 (402)
Q Consensus 119 s~~~l~~~fgvs~sTv~~~i~~ 140 (402)
+..+++..+|||.+|+.+++.+
T Consensus 2 s~~e~a~~lgvs~~tl~~~~~~ 23 (49)
T cd04762 2 TTKEAAELLGVSPSTLRRWVKE 23 (49)
T ss_pred CHHHHHHHHCcCHHHHHHHHHc
Confidence 3456888999999999888764
No 287
>COG4941 Predicted RNA polymerase sigma factor containing a TPR repeat domain [Transcription]
Probab=33.09 E-value=38 Score=33.27 Aligned_cols=49 Identities=27% Similarity=0.329 Sum_probs=40.7
Q ss_pred CCcCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHH
Q 015682 98 GRLLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEE 147 (402)
Q Consensus 98 ~~~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~ 147 (402)
.+.+++++|++++|+.+ +|.+-..|+..|=|+.+|+.+-|-+--..|.+
T Consensus 118 HPal~~~~riALtLR~v-~GLs~~eIArAFLv~e~am~QRivRAK~ri~~ 166 (415)
T COG4941 118 HPALPPEQRIALTLRLV-GGLSTAEIARAFLVPEAAMAQRIVRAKARIRE 166 (415)
T ss_pred CCCCChhhHHHHHHHHH-cCCcHHHHHHHHcCCcHHHHHHHHHHHHHHHh
Confidence 35799999999999766 58999999999999999997766666666654
No 288
>PRK10651 transcriptional regulator NarL; Provisional
Probab=32.91 E-value=18 Score=31.70 Aligned_cols=44 Identities=16% Similarity=0.221 Sum_probs=35.3
Q ss_pred cCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHH
Q 015682 100 LLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEAL 145 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al 145 (402)
.+++.+. =.|.+|+.|.+...++..+++|..||..++.+...-+
T Consensus 155 ~Lt~rE~--~vl~~l~~g~~~~~ia~~l~is~~tV~~~~~~l~~Kl 198 (216)
T PRK10651 155 QLTPRER--DILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKM 198 (216)
T ss_pred cCCHHHH--HHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHHc
Confidence 3776664 3345688999999999999999999999998877655
No 289
>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=32.67 E-value=15 Score=25.88 Aligned_cols=25 Identities=20% Similarity=0.298 Sum_probs=19.6
Q ss_pred ccccccccccccccchhhhHHHHHH
Q 015682 119 SQVSVGVAFGVGQSTVSQVTWRFIE 143 (402)
Q Consensus 119 s~~~l~~~fgvs~sTv~~~i~~v~~ 143 (402)
+..+|+..|++|++||++.+.+..+
T Consensus 27 ~~~~la~~~~is~~~v~~~l~~L~~ 51 (66)
T cd07377 27 SERELAEELGVSRTTVREALRELEA 51 (66)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4567899999999999877765543
No 290
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=32.53 E-value=20 Score=31.39 Aligned_cols=44 Identities=23% Similarity=0.297 Sum_probs=35.8
Q ss_pred cCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHH
Q 015682 100 LLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEAL 145 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al 145 (402)
.++..+. -.|..|+.|.+..+|+..+++|.+||..++.+...-+
T Consensus 143 ~lt~~E~--~vl~~l~~g~~~~~I~~~l~~s~~tv~~~~~~l~~Kl 186 (204)
T PRK09958 143 SLSKQEI--SVMRYILDGKDNNDIAEKMFISNKTVSTYKSRLMEKL 186 (204)
T ss_pred cCCHHHH--HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHc
Confidence 4666554 3667778899999999999999999999988877665
No 291
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=32.51 E-value=10 Score=36.61 Aligned_cols=23 Identities=39% Similarity=0.242 Sum_probs=20.1
Q ss_pred CccccccccccccccchhhhHHH
Q 015682 118 ESQVSVGVAFGVGQSTVSQVTWR 140 (402)
Q Consensus 118 ~s~~~l~~~fgvs~sTv~~~i~~ 140 (402)
.+..+||..+|||.+|||++++.
T Consensus 7 ~Ti~dIA~~agVS~~TVSr~Ln~ 29 (342)
T PRK10014 7 ITIHDVALAAGVSVSTVSLVLSG 29 (342)
T ss_pred CcHHHHHHHhCCCHHHHHHHHCC
Confidence 46789999999999999999853
No 292
>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]
Probab=32.43 E-value=12 Score=38.10 Aligned_cols=35 Identities=23% Similarity=0.226 Sum_probs=27.1
Q ss_pred hccCC------CccccccccccccccchhhhHHHHHHHHHHhhcccccCCC
Q 015682 113 RLASG------ESQVSVGVAFGVGQSTVSQVTWRFIEALEERAKHHLKWPD 157 (402)
Q Consensus 113 ~La~g------~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~~~~i~~P~ 157 (402)
||.+| ...+++|+.+|++.|||||+|. ..|+.-|.
T Consensus 320 Ff~~g~~~l~PL~LrdvA~~i~~HESTISRai~----------nKy~~tpr 360 (444)
T COG1508 320 FFEGGEEALKPLVLRDVADEIGMHESTISRAIT----------NKYLATPR 360 (444)
T ss_pred HHhCCcccCCcccHHHHHHHhCccHHHHHHHHh----------cccccCCc
Confidence 45566 5668999999999999999885 45666663
No 293
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=32.19 E-value=28 Score=33.38 Aligned_cols=43 Identities=21% Similarity=0.114 Sum_probs=36.0
Q ss_pred HHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHH
Q 015682 105 KQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEE 147 (402)
Q Consensus 105 ~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~ 147 (402)
.+|-+++....+|.|+...|..+++|+||||+.+.+.-+.+..
T Consensus 4 ~~L~~F~~v~~~~~S~s~AA~~L~isQpavS~~I~~LE~~lg~ 46 (309)
T PRK12683 4 QQLRIIREAVRQNFNLTEVANALYTSQSGVSKQIKDLEDELGV 46 (309)
T ss_pred HHHHHHHHHHHccCCHHHHHHHhcCCcHHHHHHHHHHHHHhCC
Confidence 3566666667778899999999999999999999988888754
No 294
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=31.98 E-value=26 Score=33.10 Aligned_cols=43 Identities=19% Similarity=0.172 Sum_probs=32.1
Q ss_pred CCHHHHHHHHhhhccC---CCccccccccccccccchhhhHHHHHH
Q 015682 101 LSVEKQVAIALRRLAS---GESQVSVGVAFGVGQSTVSQVTWRFIE 143 (402)
Q Consensus 101 ls~e~~l~i~L~~La~---g~s~~~l~~~fgvs~sTv~~~i~~v~~ 143 (402)
+..-++.+-.|..|+. +.+..+|+..+|+++||+++++.....
T Consensus 7 v~sl~ral~iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~tL~~ 52 (263)
T PRK09834 7 VRGLSRGLMVLRALNRLDGGATVGLLAELTGLHRTTVRRLLETLQE 52 (263)
T ss_pred HHHHHHHHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4444556666666653 367899999999999999999876654
No 295
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=31.78 E-value=11 Score=36.36 Aligned_cols=21 Identities=29% Similarity=0.204 Sum_probs=18.6
Q ss_pred ccccccccccccccchhhhHH
Q 015682 119 SQVSVGVAFGVGQSTVSQVTW 139 (402)
Q Consensus 119 s~~~l~~~fgvs~sTv~~~i~ 139 (402)
+..+||...|||.+|||++++
T Consensus 7 ti~dIA~~agVS~~TVSrvLn 27 (331)
T PRK14987 7 VLQDVADRVGVTKMTVSRFLR 27 (331)
T ss_pred cHHHHHHHhCCCHHHhhhhhC
Confidence 567899999999999999984
No 296
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=31.75 E-value=33 Score=32.57 Aligned_cols=44 Identities=11% Similarity=0.015 Sum_probs=33.5
Q ss_pred cCCHHHHHHHHhhhccC---CCccccccccccccccchhhhHHHHHH
Q 015682 100 LLSVEKQVAIALRRLAS---GESQVSVGVAFGVGQSTVSQVTWRFIE 143 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~---g~s~~~l~~~fgvs~sTv~~~i~~v~~ 143 (402)
.++.-++.+-.|..|+. +.+..+|+...|+++||+++++...+.
T Consensus 20 ~~~sl~r~l~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL~~ 66 (271)
T PRK10163 20 GAQALERGIAILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQA 66 (271)
T ss_pred cchHHHHHHHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 35555666666677754 467889999999999999999876654
No 297
>PRK09526 lacI lac repressor; Reviewed
Probab=31.25 E-value=11 Score=36.32 Aligned_cols=21 Identities=33% Similarity=0.219 Sum_probs=19.0
Q ss_pred ccccccccccccccchhhhHH
Q 015682 119 SQVSVGVAFGVGQSTVSQVTW 139 (402)
Q Consensus 119 s~~~l~~~fgvs~sTv~~~i~ 139 (402)
+..+||...|||.+|||++++
T Consensus 7 ti~dIA~~aGVS~~TVSrvLn 27 (342)
T PRK09526 7 TLYDVARYAGVSYQTVSRVLN 27 (342)
T ss_pred cHHHHHHHhCCCHHHHHHHhc
Confidence 567999999999999999986
No 298
>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=31.01 E-value=29 Score=32.35 Aligned_cols=43 Identities=9% Similarity=0.146 Sum_probs=31.6
Q ss_pred CCHHHHHHHHhhhccC---CCccccccccccccccchhhhHHHHHH
Q 015682 101 LSVEKQVAIALRRLAS---GESQVSVGVAFGVGQSTVSQVTWRFIE 143 (402)
Q Consensus 101 ls~e~~l~i~L~~La~---g~s~~~l~~~fgvs~sTv~~~i~~v~~ 143 (402)
++.-++.+-.|..++. +.+..+|+...|+++||+++++...+.
T Consensus 5 v~sl~ral~IL~~l~~~~~~~~l~eia~~lglpksT~~RlL~tL~~ 50 (248)
T TIGR02431 5 VASLARGLAVIEAFGAERPRLTLTDVAEATGLTRAAARRFLLTLVE 50 (248)
T ss_pred HHHHHHHHHHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3334455556666653 468899999999999999999876654
No 299
>PRK10403 transcriptional regulator NarP; Provisional
Probab=30.80 E-value=21 Score=31.17 Aligned_cols=44 Identities=20% Similarity=0.299 Sum_probs=35.7
Q ss_pred cCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHH
Q 015682 100 LLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEAL 145 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al 145 (402)
.++..+.- .|.+++.|.+...|+...++|..||..++.+...-+
T Consensus 153 ~Lt~~e~~--vl~~~~~g~s~~~ia~~l~~s~~tv~~~~~~i~~kl 196 (215)
T PRK10403 153 VLTERELD--VLHELAQGLSNKQIASVLNISEQTVKVHIRNLLRKL 196 (215)
T ss_pred cCCHHHHH--HHHHHHCCCCHHHHHHHcCCCHHHHHHHHHHHHHHc
Confidence 36665544 356678999999999999999999999998887765
No 300
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=30.58 E-value=13 Score=35.73 Aligned_cols=22 Identities=23% Similarity=0.133 Sum_probs=18.9
Q ss_pred ccccccccccccccchhhhHHH
Q 015682 119 SQVSVGVAFGVGQSTVSQVTWR 140 (402)
Q Consensus 119 s~~~l~~~fgvs~sTv~~~i~~ 140 (402)
+..+||...|||.+|||++++.
T Consensus 2 ti~dIA~~aGVS~~TVSrvLn~ 23 (328)
T PRK11303 2 KLDEIARLAGVSRTTASYVING 23 (328)
T ss_pred CHHHHHHHhCCCHHHHHHHHcC
Confidence 4568999999999999998863
No 301
>cd00131 PAX Paired Box domain
Probab=30.54 E-value=1e+02 Score=25.72 Aligned_cols=79 Identities=15% Similarity=0.083 Sum_probs=44.8
Q ss_pred CChhhhhcccCCCHHHHHHHHHHHhccc--cCCCCCCCccccCCcCCHHH-HHHHHhhhccCCCccccccccc---cc--
Q 015682 58 DEEEGFKYFFRVSKKTFDYICSLVREDL--VSRPPSGLINIEGRLLSVEK-QVAIALRRLASGESQVSVGVAF---GV-- 129 (402)
Q Consensus 58 ~~~~~F~~~fRms~~tF~~L~~~l~~~~--~~~~~~g~~~~~~~~ls~e~-~l~i~L~~La~g~s~~~l~~~f---gv-- 129 (402)
.+..+--..|++|+.|...++...+... ..++..| .+.+.++.+. ...+.+..-.-..+...|+..+ |+
T Consensus 34 ~s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v~pk~~gg---~rpr~~~~~~~~~i~~~v~~~p~~Tl~El~~~L~~~gv~~ 110 (128)
T cd00131 34 IRPCDISRQLRVSHGCVSKILNRYYETGSIRPGAIGG---SKPRVATPEVVKKIEIYKQENPGMFAWEIRDRLLQEGVCD 110 (128)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCCCCCC---CCCCcCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCCcc
Confidence 3556667889999999999998876543 2222111 1122233332 3333333333334555555542 55
Q ss_pred -----cccchhhhHH
Q 015682 130 -----GQSTVSQVTW 139 (402)
Q Consensus 130 -----s~sTv~~~i~ 139 (402)
|.||+++++.
T Consensus 111 ~~~~~s~stI~R~L~ 125 (128)
T cd00131 111 KSNVPSVSSINRILR 125 (128)
T ss_pred cCCCCCHHHHHHHHH
Confidence 8899988764
No 302
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=30.35 E-value=18 Score=26.35 Aligned_cols=37 Identities=5% Similarity=0.041 Sum_probs=26.3
Q ss_pred HHHHHHhhhccCCCccccccccccccccchhhhHHHH
Q 015682 105 KQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRF 141 (402)
Q Consensus 105 ~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v 141 (402)
+++.-+|.....+.+=++||+.+|+|..++..++...
T Consensus 3 e~Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~L 39 (62)
T PF04703_consen 3 EKILEYIKEQNGPLKTREIADALGLSIYQARYYLEKL 39 (62)
T ss_dssp HCHHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 3455556666777888899999999999998777543
No 303
>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=30.21 E-value=16 Score=26.33 Aligned_cols=23 Identities=22% Similarity=0.390 Sum_probs=16.4
Q ss_pred cccccccccccccchhhhHHHHH
Q 015682 120 QVSVGVAFGVGQSTVSQVTWRFI 142 (402)
Q Consensus 120 ~~~l~~~fgvs~sTv~~~i~~v~ 142 (402)
..+|+..|+||++||.+.+....
T Consensus 27 ~~~la~~~~vsr~tvr~al~~L~ 49 (64)
T PF00392_consen 27 ERELAERYGVSRTTVREALRRLE 49 (64)
T ss_dssp HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHHHHHHhccCCcHHHHHHHHHH
Confidence 35678899999999977665443
No 304
>PF09607 BrkDBD: Brinker DNA-binding domain; InterPro: IPR018586 This DNA-binding domain is the first approx. 100 residues of the N-terminal end of Brinker. The structure of this domain in complex with DNA consists of four alpha-helices that contain a helix-turn-helix DNA recognition motif specific for GC-rich DNA. The Brinker nuclear repressor is a major element of the Drosophila Decapentaplegic morphogen signalling pathway []. ; PDB: 2GLO_A.
Probab=30.12 E-value=21 Score=25.53 Aligned_cols=41 Identities=15% Similarity=0.151 Sum_probs=27.9
Q ss_pred CCcCCHHHHHHHHhhhccCCC---ccccccccccccccchhhhH
Q 015682 98 GRLLSVEKQVAIALRRLASGE---SQVSVGVAFGVGQSTVSQVT 138 (402)
Q Consensus 98 ~~~ls~e~~l~i~L~~La~g~---s~~~l~~~fgvs~sTv~~~i 138 (402)
++..+++-+|-+.-++..++. +|+..+..|+|++..|.++.
T Consensus 3 rrsy~~~FKL~Vv~~a~~~~nc~~~~RAaarkf~V~r~~Vr~W~ 46 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEKDNNCKGNQRAAARKFNVSRRQVRKWR 46 (58)
T ss_dssp -----HHHHHHHHHHHHH-TTTTT-HHHHHHHTTS-HHHHHHHH
T ss_pred ccccChHHHHHHHHHHHHccchhhhHHHHHHHhCccHHHHHHHH
Confidence 456788889988888888876 56999999999998876654
No 305
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=29.67 E-value=13 Score=35.75 Aligned_cols=21 Identities=29% Similarity=0.336 Sum_probs=18.6
Q ss_pred ccccccccccccccchhhhHH
Q 015682 119 SQVSVGVAFGVGQSTVSQVTW 139 (402)
Q Consensus 119 s~~~l~~~fgvs~sTv~~~i~ 139 (402)
+..+||...|||++|||++++
T Consensus 3 ti~dIA~~agVS~~TVSrvln 23 (327)
T PRK10339 3 TLKDIAIEAGVSLATVSRVLN 23 (327)
T ss_pred CHHHHHHHhCCCHHhhhhhhc
Confidence 456899999999999999986
No 306
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=29.65 E-value=31 Score=28.87 Aligned_cols=29 Identities=17% Similarity=0.106 Sum_probs=23.9
Q ss_pred CCCccccccccccccccchhhhHHHHHHH
Q 015682 116 SGESQVSVGVAFGVGQSTVSQVTWRFIEA 144 (402)
Q Consensus 116 ~g~s~~~l~~~fgvs~sTv~~~i~~v~~a 144 (402)
.+.+-.+||...++++|||++.+++.+.+
T Consensus 41 ~~~tvdelae~lnr~rStv~rsl~~L~~~ 69 (126)
T COG3355 41 GPLTVDELAEILNRSRSTVYRSLQNLLEA 69 (126)
T ss_pred CCcCHHHHHHHHCccHHHHHHHHHHHHHc
Confidence 34556689999999999999999887765
No 307
>PRK04140 hypothetical protein; Provisional
Probab=29.56 E-value=22 Score=34.77 Aligned_cols=82 Identities=16% Similarity=0.118 Sum_probs=50.9
Q ss_pred cCCCHHH-HHHHHHHHhccccCCCCCCCccccCCcCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHH
Q 015682 67 FRVSKKT-FDYICSLVREDLVSRPPSGLINIEGRLLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEAL 145 (402)
Q Consensus 67 fRms~~t-F~~L~~~l~~~~~~~~~~g~~~~~~~~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al 145 (402)
.-|+.+| |+++++-..|.+.. .+ ++--+...-..+-. .+-..|.++.++|...|+|++|+++|-+.
T Consensus 96 ~~~~~~tl~~~~~~g~~p~v~~-~~------Gg~~v~i~GerLk~-lRe~~GlSq~eLA~~lGVSr~tIskyE~G----- 162 (317)
T PRK04140 96 PALSPDTLYDDFVEGEPPLIYA-AP------GGFYVKIDGDVLRE-AREELGLSLGELASELGVSRRTISKYENG----- 162 (317)
T ss_pred eeecHHHHHHHHhCCCCceEEE-cC------CCeeehhhHHHHHH-HHHHcCCCHHHHHHHhCCCHHHHHHHHcC-----
Confidence 3467888 88877766654332 22 23334333322222 35678999999999999999999887641
Q ss_pred HHhhcccccCCCchhHHHHHHHH
Q 015682 146 EERAKHHLKWPDSNRMEEIKSKF 168 (402)
Q Consensus 146 ~~~~~~~i~~P~~~~~~~i~~~f 168 (402)
-.-|+.+.+..+++-|
T Consensus 163 -------~~~Ps~e~~~kLa~~L 178 (317)
T PRK04140 163 -------GMNASIEVAIKLEEIL 178 (317)
T ss_pred -------CCCCCHHHHHHHHHHh
Confidence 1235555555555554
No 308
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=29.42 E-value=45 Score=29.91 Aligned_cols=41 Identities=12% Similarity=0.055 Sum_probs=29.3
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHH
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRF 141 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v 141 (402)
|++.+-.++...+-..|.++.+|+...++.++|+++++.+.
T Consensus 43 Lt~~q~~iL~~L~~~~~itq~eLa~~l~l~~sTvtr~l~rL 83 (185)
T PRK13777 43 LNINEHHILWIAYHLKGASISEIAKFGVMHVSTAFNFSKKL 83 (185)
T ss_pred CCHHHHHHHHHHHhCCCcCHHHHHHHHCCCHhhHHHHHHHH
Confidence 56555444433344557899999999999999998776543
No 309
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=29.26 E-value=35 Score=32.78 Aligned_cols=42 Identities=19% Similarity=0.066 Sum_probs=35.1
Q ss_pred HHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHH
Q 015682 106 QVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEE 147 (402)
Q Consensus 106 ~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~ 147 (402)
+|-.++.-..+|.++...|...+||+||||+.+.+.-..+..
T Consensus 5 ~l~~f~~v~~~~~s~s~AA~~L~iSQ~avSr~I~~LE~~lg~ 46 (316)
T PRK12679 5 QLKIIREAARQDYNLTEVANMLFTSQSGVSRHIRELEDELGI 46 (316)
T ss_pred HHHHHHHHHHcCCCHHHHHHHhcCCchHHHHHHHHHHHHhCC
Confidence 455566666677899999999999999999999998888854
No 310
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=29.14 E-value=14 Score=35.36 Aligned_cols=19 Identities=42% Similarity=0.323 Sum_probs=17.1
Q ss_pred ccccccccccccchhhhHH
Q 015682 121 VSVGVAFGVGQSTVSQVTW 139 (402)
Q Consensus 121 ~~l~~~fgvs~sTv~~~i~ 139 (402)
.+||...|||.+|||++++
T Consensus 2 ~dIA~~agVS~~TVSrvLn 20 (327)
T PRK10423 2 KDVARLAGVSTSTVSHVIN 20 (327)
T ss_pred hhHHHHhCCcHHHHHHHhC
Confidence 4789999999999999985
No 311
>PRK11233 nitrogen assimilation transcriptional regulator; Provisional
Probab=29.14 E-value=34 Score=32.69 Aligned_cols=37 Identities=14% Similarity=0.135 Sum_probs=30.0
Q ss_pred hhhccCCCccccccccccccccchhhhHHHHHHHHHH
Q 015682 111 LRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEE 147 (402)
Q Consensus 111 L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~ 147 (402)
+..++...++...|...+||+||||+.+.+.-+.+..
T Consensus 9 F~~v~~~~S~s~AA~~L~isQ~avS~~I~~LE~~lg~ 45 (305)
T PRK11233 9 FVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQ 45 (305)
T ss_pred HHHHHHcCCHHHHHHHhCCCchHHHHHHHHHHHHhCC
Confidence 3344445599999999999999999999988887754
No 312
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=28.91 E-value=14 Score=35.77 Aligned_cols=22 Identities=32% Similarity=0.317 Sum_probs=19.2
Q ss_pred ccccccccccccccchhhhHHH
Q 015682 119 SQVSVGVAFGVGQSTVSQVTWR 140 (402)
Q Consensus 119 s~~~l~~~fgvs~sTv~~~i~~ 140 (402)
+..+||...|||++|||++++.
T Consensus 3 Ti~dIA~~agVS~~TVSrvLn~ 24 (341)
T PRK10703 3 TIKDVAKRAGVSTTTVSHVINK 24 (341)
T ss_pred CHHHHHHHhCCCHHHHHHHHcC
Confidence 4678999999999999999863
No 313
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=28.87 E-value=22 Score=34.46 Aligned_cols=21 Identities=33% Similarity=0.249 Sum_probs=18.8
Q ss_pred ccccccccccccccchhhhHH
Q 015682 119 SQVSVGVAFGVGQSTVSQVTW 139 (402)
Q Consensus 119 s~~~l~~~fgvs~sTv~~~i~ 139 (402)
+..+||...|||.+|||++++
T Consensus 3 ti~dIA~~aGVS~~TVSrvLn 23 (346)
T PRK10401 3 TIRDVARQAGVSVATVSRVLN 23 (346)
T ss_pred CHHHHHHHhCCCHHHHHHHHC
Confidence 467899999999999999985
No 314
>PRK15092 DNA-binding transcriptional repressor LrhA; Provisional
Probab=28.81 E-value=23 Score=34.13 Aligned_cols=51 Identities=16% Similarity=0.147 Sum_probs=40.3
Q ss_pred cCCcCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHH
Q 015682 97 EGRLLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEE 147 (402)
Q Consensus 97 ~~~~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~ 147 (402)
.+.+...+.+.+-.+.-++...++...|...+||++|||+-+.+.-+.+..
T Consensus 5 ~~~~~~m~l~~L~~F~~v~e~gs~s~AA~~L~iSQpavS~~I~~LE~~lG~ 55 (310)
T PRK15092 5 NRPIINLDLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGK 55 (310)
T ss_pred hhhhhcCCHHHHHHHHHHHHcCCHHHHHHHhCCChHHHHHHHHHHHHHhCc
Confidence 334445555666667777788899999999999999999999988888754
No 315
>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=28.81 E-value=13 Score=24.49 Aligned_cols=21 Identities=19% Similarity=0.241 Sum_probs=16.8
Q ss_pred ccccccccccccccchhhhHH
Q 015682 119 SQVSVGVAFGVGQSTVSQVTW 139 (402)
Q Consensus 119 s~~~l~~~fgvs~sTv~~~i~ 139 (402)
+..+++..+|||++|+.+++.
T Consensus 3 t~~e~a~~lgis~~ti~~~~~ 23 (49)
T TIGR01764 3 TVEEAAEYLGVSKDTVYRLIH 23 (49)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 345788899999999987764
No 316
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=27.98 E-value=26 Score=30.24 Aligned_cols=43 Identities=14% Similarity=0.268 Sum_probs=34.0
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHH
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEAL 145 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al 145 (402)
+++.++=. |.+++.|.+...++...++|..||...+.+...-+
T Consensus 150 lt~~e~~v--l~l~~~g~~~~~Ia~~l~~s~~tv~~~~~~~~~kl 192 (211)
T PRK15369 150 LTPRERQI--LKLITEGYTNRDIAEQLSISIKTVETHRLNMMRKL 192 (211)
T ss_pred CCHHHHHH--HHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 55544433 44478999999999999999999999988876665
No 317
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=27.87 E-value=25 Score=27.25 Aligned_cols=24 Identities=17% Similarity=0.235 Sum_probs=19.7
Q ss_pred cccccccccccccchhhhHHHHHH
Q 015682 120 QVSVGVAFGVGQSTVSQVTWRFIE 143 (402)
Q Consensus 120 ~~~l~~~fgvs~sTv~~~i~~v~~ 143 (402)
...++..+|++++|+++.+.+...
T Consensus 2 ~~ela~~l~is~stvs~~l~~L~~ 25 (96)
T smart00529 2 TSEIAERLNVSPPTVTQMLKKLEK 25 (96)
T ss_pred HHHHHHHhCCChHHHHHHHHHHHH
Confidence 357889999999999998876654
No 318
>PRK11050 manganese transport regulator MntR; Provisional
Probab=27.83 E-value=37 Score=29.26 Aligned_cols=28 Identities=29% Similarity=0.432 Sum_probs=23.9
Q ss_pred CCCccccccccccccccchhhhHHHHHH
Q 015682 116 SGESQVSVGVAFGVGQSTVSQVTWRFIE 143 (402)
Q Consensus 116 ~g~s~~~l~~~fgvs~sTv~~~i~~v~~ 143 (402)
.+.+..+|+..++|+++||++.+.+...
T Consensus 50 ~~~t~~eLA~~l~is~stVsr~l~~Le~ 77 (152)
T PRK11050 50 GEARQVDIAARLGVSQPTVAKMLKRLAR 77 (152)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4568889999999999999998877654
No 319
>PF12728 HTH_17: Helix-turn-helix domain
Probab=27.77 E-value=15 Score=25.03 Aligned_cols=21 Identities=19% Similarity=0.200 Sum_probs=17.0
Q ss_pred ccccccccccccccchhhhHH
Q 015682 119 SQVSVGVAFGVGQSTVSQVTW 139 (402)
Q Consensus 119 s~~~l~~~fgvs~sTv~~~i~ 139 (402)
+..+++..+|||.+|+.+++.
T Consensus 3 t~~e~a~~l~is~~tv~~~~~ 23 (51)
T PF12728_consen 3 TVKEAAELLGISRSTVYRWIR 23 (51)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 345788899999999988774
No 320
>PF00665 rve: Integrase core domain; InterPro: IPR001584 Integrase comprises three domains capable of folding independently and whose three-dimensional structures are known. However, the manner in which the N-terminal, catalytic, and C-terminal domains interact in the holoenzyme remains obscure. Numerous studies indicate that the enzyme functions as a multimer, minimally a dimer. The integrase proteins from Human immunodeficiency virus 1 (HIV-1) and Avian sarcoma virus (ASV) have been studied most carefully with respect to the structural basis of catalysis. Although the active site of ASV integrase does not undergo significant conformational changes on binding the required metal cofactor, that of HIV-1 does. This active site-mediated conformational change in HIV-1 reorganises the catalytic core and C-terminal domains and appears to promote an interaction that is favourable for catalysis []. Retroviral integrase is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. The presence of retrovirus integrase-related gene sequences in eukaryotes is known. Bacterial transposases involved in the transposition of the insertion sequence also belong to this group. HIV integrase catalyses the incorporation of virally derived DNA into the human genome. This unique step in the virus life cycle provides a variety of points for intervention and hence is an attractive target for the development of new therapeutics for the treatment of AIDS []. Substrate recognition by the retroviral integrase enzyme is critical for retroviral integration. To catalyse this recombination event, integrase must recognise and act on two types of substrates, viral DNA and host DNA, yet the necessary interactions exhibit markedly different degrees of specificity [].; GO: 0015074 DNA integration; PDB: 3AO3_A 3OVN_A 3AO5_A 3AO4_A 3AO1_A 1C6V_D 3HPG_A 3HPH_A 3OYD_A 3OYF_B ....
Probab=27.64 E-value=1.1e+02 Score=24.10 Aligned_cols=17 Identities=12% Similarity=-0.013 Sum_probs=13.5
Q ss_pred HhhhHHHHHHHHHhccc
Q 015682 303 ATRSLAVKAFLQLKGGW 319 (402)
Q Consensus 303 ~~R~~vE~afg~LK~rf 319 (402)
.....||+.++.||.+|
T Consensus 104 ~~ng~vEr~~~~l~~~~ 120 (120)
T PF00665_consen 104 QQNGFVERFNRTLKRRI 120 (120)
T ss_dssp HHHHHHHHHHHHHHHHH
T ss_pred hhccHHHHHHHHHHHhC
Confidence 34568999999999875
No 321
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=27.45 E-value=50 Score=28.32 Aligned_cols=43 Identities=9% Similarity=0.075 Sum_probs=28.9
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHH
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIE 143 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~ 143 (402)
++..++-.+.+..-..-.++..||...|+|++||.+-+.+..+
T Consensus 7 lD~~D~~Il~~Lq~d~R~s~~eiA~~lglS~~tV~~Ri~rL~~ 49 (153)
T PRK11179 7 IDNLDRGILEALMENARTPYAELAKQFGVSPGTIHVRVEKMKQ 49 (153)
T ss_pred cCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3433333333333334588999999999999999887766543
No 322
>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=27.04 E-value=29 Score=25.65 Aligned_cols=38 Identities=21% Similarity=0.167 Sum_probs=27.1
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHH
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTW 139 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~ 139 (402)
.++.+++.-.+ .-..|.+..+++...|+|++|++++.+
T Consensus 3 ~~~g~~i~~~~-~~~~~~t~~~lA~~~gis~~tis~~~~ 40 (78)
T TIGR02607 3 AHPGEILREEF-LEPLGLSIRALAKALGVSRSTLSRIVN 40 (78)
T ss_pred CCHHHHHHHHH-HHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 34455543122 345688999999999999999998753
No 323
>PF03333 PapB: Adhesin biosynthesis transcription regulatory protein; InterPro: IPR004356 P pili, or fimbriae, are ~68A in diameter and 1 micron in length, the bulk of which is a fibre composed of the main structural protein PapA []. At its tip, the pilus is terminated by a fibrillum consisting of repeating units of the PapE protein. This, in turn, is topped by the adhesins, PapF and PapG, both of which are needed for receptor binding. The tip fibrillum is anchored to the main PapA fibre by the PapK pilus-adaptor protein. PapH, an outer membrane protein, then anchors the entire rod in the bacterial envelope []. A cytoplasmic chaperone (PapD) assists in assembling the monomers of the macromolecule in the membrane. All of the functional pap genes are arranged in a cluster (operon) on the Escherichia coli genome. It is believed that selective pressure exerted by the host's urinal and intestinal tract isoreceptors forced the spread of this operon to other strains via lateral transfer []. PapB, encoded within the cluster, acts as a transcriptional regulator of the functional pap genes and is located in the bacterial cytoplasm []. Its mechanism involves differential binding to separate sites in the cluster, suggesting that this protein is both an activator and repressor of pilus-adhesion transcription. The protein shares similarity with other E. coli fimbrial- adhesion transcription regulators, such as AfaA, DaaA and FanB. ; GO: 0006355 regulation of transcription, DNA-dependent; PDB: 3M8J_A.
Probab=27.03 E-value=75 Score=25.03 Aligned_cols=56 Identities=29% Similarity=0.273 Sum_probs=33.8
Q ss_pred CCCHHHHHHHHHHHhccccCCCCCCCccccCCcCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHH
Q 015682 68 RVSKKTFDYICSLVREDLVSRPPSGLINIEGRLLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRF 141 (402)
Q Consensus 68 Rms~~tF~~L~~~l~~~~~~~~~~g~~~~~~~~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v 141 (402)
.|+.+.|.-|+++- +|..+.-++.-=-||-.|.+-..++..+||++|-.+..+.+.
T Consensus 22 ~vs~e~F~lLl~ls------------------~IrS~kiI~AL~dyLV~G~srkeac~~~gV~~syfs~~L~rL 77 (91)
T PF03333_consen 22 KVSEEHFWLLLELS------------------SIRSEKIIAALRDYLVDGLSRKEACERHGVNQSYFSRALNRL 77 (91)
T ss_dssp -S-HHHHHHHHHHS----------------------HHHHHHHHHHHTT---HHHHHHHTT--HHHHHHHHHHH
T ss_pred CcCHHHHHHHHHHC------------------CCCcHHHHHHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHHHH
Confidence 46777888777742 133344444444589999999999999999999999877654
No 324
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=25.97 E-value=46 Score=31.94 Aligned_cols=42 Identities=14% Similarity=0.083 Sum_probs=34.3
Q ss_pred HHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHH
Q 015682 106 QVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEE 147 (402)
Q Consensus 106 ~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~ 147 (402)
+|-+++....+|.|+...|...++|++|||+.+.+.-..+..
T Consensus 5 ~L~~f~~v~~~g~S~s~AA~~L~isQpavS~~ik~LE~~lg~ 46 (313)
T PRK12684 5 QLRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEDELGV 46 (313)
T ss_pred HHHHHHHHHHcCCCHHHHHHHhcCCChHHHHHHHHHHHHhCC
Confidence 455555555666699999999999999999999998888854
No 325
>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=25.96 E-value=52 Score=29.68 Aligned_cols=32 Identities=22% Similarity=0.220 Sum_probs=24.5
Q ss_pred hhhccC--CCccccccccccccccchhhhHHHHH
Q 015682 111 LRRLAS--GESQVSVGVAFGVGQSTVSQVTWRFI 142 (402)
Q Consensus 111 L~~La~--g~s~~~l~~~fgvs~sTv~~~i~~v~ 142 (402)
|.+|.. +.+..+++..+++|++|+++.+.+..
T Consensus 149 L~~l~~~g~~s~~eia~~l~is~stv~r~L~~Le 182 (203)
T TIGR01884 149 LEVLKAEGEKSVKNIAKKLGKSLSTISRHLRELE 182 (203)
T ss_pred HHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 444443 46899999999999999988876643
No 326
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=25.45 E-value=47 Score=31.10 Aligned_cols=43 Identities=16% Similarity=0.036 Sum_probs=31.5
Q ss_pred CCHHHHHHHHhhhccCC--CccccccccccccccchhhhHHHHHH
Q 015682 101 LSVEKQVAIALRRLASG--ESQVSVGVAFGVGQSTVSQVTWRFIE 143 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g--~s~~~l~~~fgvs~sTv~~~i~~v~~ 143 (402)
++.-++.+-.|..|+.. .+..+|+...|+++||+++++...+.
T Consensus 10 v~sl~r~l~IL~~l~~~~~l~l~eia~~lgl~kstv~Rll~tL~~ 54 (257)
T PRK15090 10 VSSVLKVFGILQALGEEREIGITELSQRVMMSKSTVYRFLQTMKT 54 (257)
T ss_pred cHHHHHHHHHHHHhhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 55555666666666543 56788999999999999998876554
No 327
>PRK11569 transcriptional repressor IclR; Provisional
Probab=25.12 E-value=48 Score=31.46 Aligned_cols=43 Identities=12% Similarity=0.068 Sum_probs=32.6
Q ss_pred CCHHHHHHHHhhhccC---CCccccccccccccccchhhhHHHHHH
Q 015682 101 LSVEKQVAIALRRLAS---GESQVSVGVAFGVGQSTVSQVTWRFIE 143 (402)
Q Consensus 101 ls~e~~l~i~L~~La~---g~s~~~l~~~fgvs~sTv~~~i~~v~~ 143 (402)
++.-++.+-.|..|+. +.+..+|+...|+++||+++++...++
T Consensus 24 v~sl~ral~IL~~l~~~~~~~~lseia~~lglpksTv~RlL~tL~~ 69 (274)
T PRK11569 24 VQSLTRGLKLLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQQ 69 (274)
T ss_pred ccHHHHHHHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4455566666666654 468889999999999999998876554
No 328
>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=24.78 E-value=23 Score=36.24 Aligned_cols=30 Identities=23% Similarity=0.267 Sum_probs=24.6
Q ss_pred CccccccccccccccchhhhHHHHHHHHHHhhcccccCCC
Q 015682 118 ESQVSVGVAFGVGQSTVSQVTWRFIEALEERAKHHLKWPD 157 (402)
Q Consensus 118 ~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~~~~i~~P~ 157 (402)
..+.+||...|++.|||||+|+ ..|+..|.
T Consensus 319 LtlkdiA~~lglheSTVSRav~----------~Kyi~tp~ 348 (429)
T TIGR02395 319 LTLREVAEELGLHESTISRAIN----------NKYLQTPR 348 (429)
T ss_pred CcHHHHHHHhCCCccchhhhhc----------CceEecCC
Confidence 5678999999999999999884 55676664
No 329
>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=24.76 E-value=36 Score=27.13 Aligned_cols=35 Identities=11% Similarity=-0.008 Sum_probs=28.4
Q ss_pred hccCCCccccccccccccccchhhhHHHHHHHHHH
Q 015682 113 RLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEE 147 (402)
Q Consensus 113 ~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~ 147 (402)
-++...|++.-|..+|||++|+++.+.+.-+.+..
T Consensus 12 av~~~gSis~AA~~L~iS~stvs~~I~~LE~~lg~ 46 (99)
T TIGR00637 12 AIARMGSISQAAKDAGISYKSAWDYIRAMNNLSGE 46 (99)
T ss_pred HHHHhCCHHHHHHHHCCCHHHHHHHHHHHHHHhCC
Confidence 33445778899999999999999999888777744
No 330
>TIGR02417 fruct_sucro_rep D-fructose-responsive transcription factor. Members of this family belong the lacI helix-turn-helix family (pfam00356) of DNA-binding transcriptional regulators. All members are from the proteobacteria. Characterized members act as positive and negative transcriptional regulators of fructose and sucrose transport and metabolism. Sucrose is a disaccharide composed of fructose and glucose; D-fructose-1-phosphate rather than an intact sucrose moiety has been shown to act as the inducer.
Probab=24.72 E-value=19 Score=34.63 Aligned_cols=21 Identities=24% Similarity=0.177 Sum_probs=18.0
Q ss_pred cccccccccccccchhhhHHH
Q 015682 120 QVSVGVAFGVGQSTVSQVTWR 140 (402)
Q Consensus 120 ~~~l~~~fgvs~sTv~~~i~~ 140 (402)
..+||...|||.+|||++++.
T Consensus 2 i~dIA~~aGVS~~TVSrvLn~ 22 (327)
T TIGR02417 2 LSDIAKLAGVSKTTASYVING 22 (327)
T ss_pred HHHHHHHhCCCHHHHHHHHcC
Confidence 457899999999999998863
No 331
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR. All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.
Probab=24.49 E-value=52 Score=29.68 Aligned_cols=38 Identities=8% Similarity=0.110 Sum_probs=28.2
Q ss_pred HHHHHHHhhhccCCCccccccccccccccchhhhHHHHH
Q 015682 104 EKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFI 142 (402)
Q Consensus 104 e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~ 142 (402)
..+++..|..- .+.+..+|+..+||+.+||++.+.+..
T Consensus 3 r~~IL~~L~~~-~~~t~~eLA~~lgis~~tV~~~L~~Le 40 (203)
T TIGR02702 3 KEDILSYLLKQ-GQATAAALAEALAISPQAVRRHLKDLE 40 (203)
T ss_pred HHHHHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 34555566543 458888999999999999988776543
No 332
>TIGR01481 ccpA catabolite control protein A. Catabolite control protein A is a LacI family global transcriptional regulator found in Gram-positive bacteria. CcpA is involved in repressing carbohydrate utilization genes [ex: alpha-amylase (amyE), acetyl-coenzyme A synthase (acsA)] and in activating genes involved in transporting excess carbon from the cell [ex: acetate kinase (ackA), alpha-acetolactate synthase (alsS)]. Additionally, disruption of CcpA in Bacillus megaterium, Staphylococcus xylosus, Lactobacillus casei and Lactocacillus pentosus also decreases growth rate, which suggests CcpA is involved in the regulation of other metabolic pathways.
Probab=24.40 E-value=18 Score=34.65 Aligned_cols=21 Identities=33% Similarity=0.295 Sum_probs=18.3
Q ss_pred ccccccccccccccchhhhHH
Q 015682 119 SQVSVGVAFGVGQSTVSQVTW 139 (402)
Q Consensus 119 s~~~l~~~fgvs~sTv~~~i~ 139 (402)
+..+||..-|||.+|||++++
T Consensus 3 ti~dIA~~agvS~~TVSrvLn 23 (329)
T TIGR01481 3 TIYDVAREAGVSMATVSRVVN 23 (329)
T ss_pred cHHHHHHHhCCCHHHHHHHhC
Confidence 456899999999999999874
No 333
>PRK10072 putative transcriptional regulator; Provisional
Probab=24.38 E-value=20 Score=28.52 Aligned_cols=26 Identities=15% Similarity=0.115 Sum_probs=22.5
Q ss_pred ccCCCccccccccccccccchhhhHH
Q 015682 114 LASGESQVSVGVAFGVGQSTVSQVTW 139 (402)
Q Consensus 114 La~g~s~~~l~~~fgvs~sTv~~~i~ 139 (402)
-..|.++..+|..+|||.+||+++.+
T Consensus 43 ~~~glTQ~elA~~lGvS~~TVs~WE~ 68 (96)
T PRK10072 43 KGTGLKIDDFARVLGVSVAMVKEWES 68 (96)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 35589999999999999999998764
No 334
>smart00760 Bac_DnaA_C Bacterial dnaA protein helix-turn-helix domain. Could be involved in DNA-binding.
Probab=24.08 E-value=37 Score=24.10 Aligned_cols=32 Identities=28% Similarity=0.404 Sum_probs=28.1
Q ss_pred cCCcCCHHHHHHHHhhhccCCCcccccccccc
Q 015682 97 EGRLLSVEKQVAIALRRLASGESQVSVGVAFG 128 (402)
Q Consensus 97 ~~~~ls~e~~l~i~L~~La~g~s~~~l~~~fg 128 (402)
+.+.++..-++++.|..--+|.++.+||..||
T Consensus 25 R~~~~~~aR~iamyla~~~~~~sl~~Ig~~fg 56 (60)
T smart00760 25 RKREIVLARQIAMYLARELTDLSLPEIGKIFG 56 (60)
T ss_pred CCcchhHHHHHHHHHHHHHHCCCHHHHHHHhC
Confidence 44568888899999999889999999999998
No 335
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=23.56 E-value=54 Score=25.99 Aligned_cols=23 Identities=22% Similarity=0.365 Sum_probs=20.0
Q ss_pred ccccccccccccchhhhHHHHHH
Q 015682 121 VSVGVAFGVGQSTVSQVTWRFIE 143 (402)
Q Consensus 121 ~~l~~~fgvs~sTv~~~i~~v~~ 143 (402)
.+|+...+++++|+++++.+...
T Consensus 40 ~~la~~l~i~~~~vt~~l~~Le~ 62 (126)
T COG1846 40 KELAERLGLDRSTVTRLLKRLED 62 (126)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHH
Confidence 89999999999999988876653
No 336
>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=23.31 E-value=28 Score=24.56 Aligned_cols=23 Identities=22% Similarity=0.251 Sum_probs=18.7
Q ss_pred CccccccccccccccchhhhHHH
Q 015682 118 ESQVSVGVAFGVGQSTVSQVTWR 140 (402)
Q Consensus 118 ~s~~~l~~~fgvs~sTv~~~i~~ 140 (402)
.+..+++..|+||..|+.+-+..
T Consensus 15 ~s~~ela~~~~VS~~TiRRDl~~ 37 (57)
T PF08220_consen 15 VSVKELAEEFGVSEMTIRRDLNK 37 (57)
T ss_pred EEHHHHHHHHCcCHHHHHHHHHH
Confidence 45667999999999999876654
No 337
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=23.12 E-value=20 Score=34.73 Aligned_cols=21 Identities=33% Similarity=0.249 Sum_probs=18.4
Q ss_pred ccccccccccccccchhhhHH
Q 015682 119 SQVSVGVAFGVGQSTVSQVTW 139 (402)
Q Consensus 119 s~~~l~~~fgvs~sTv~~~i~ 139 (402)
+..+||..-|||.+|||++++
T Consensus 3 ti~dIA~~aGVS~~TVSrvLn 23 (343)
T PRK10727 3 TIKDVARLAGVSVATVSRVIN 23 (343)
T ss_pred CHHHHHHHhCCCHHHHHHHhC
Confidence 456899999999999999984
No 338
>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=23.06 E-value=96 Score=25.73 Aligned_cols=49 Identities=8% Similarity=0.051 Sum_probs=38.7
Q ss_pred CCHHHHHHHHhhhcc-CCCccccccccccccccchhhhHHHHHHHHHHhh
Q 015682 101 LSVEKQVAIALRRLA-SGESQVSVGVAFGVGQSTVSQVTWRFIEALEERA 149 (402)
Q Consensus 101 ls~e~~l~i~L~~La-~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~ 149 (402)
++..++-.+..+||. .+.+...++..+|+|++++.++-++.+..+.+.+
T Consensus 80 l~~~~r~Il~~~Yl~~~~~~~~~I~~~l~~s~~~~y~~k~~Al~~fA~~l 129 (132)
T TIGR01637 80 LDEISRQILYDKYLEPDQKYDYQIMMELGYSHRQYYRIKKRALLRFATLY 129 (132)
T ss_pred CCHHHHHHHHHHHcCccccchHHHHHHhCCcHHHHHHHHHHHHHHHHHHh
Confidence 677788888888886 3567778999999999999988777666665543
No 339
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=22.89 E-value=59 Score=30.80 Aligned_cols=44 Identities=25% Similarity=0.326 Sum_probs=35.1
Q ss_pred CcCCHHHHHHHHhhhccCC-CccccccccccccccchhhhHHHHH
Q 015682 99 RLLSVEKQVAIALRRLASG-ESQVSVGVAFGVGQSTVSQVTWRFI 142 (402)
Q Consensus 99 ~~ls~e~~l~i~L~~La~g-~s~~~l~~~fgvs~sTv~~~i~~v~ 142 (402)
..++.+++-.+-+-.=..| ..+.+|....|.|++|+||++++.-
T Consensus 191 ~~L~~~e~~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L~~LE 235 (258)
T COG2512 191 YDLNEDEKEILDLIRERGGRITQAELRRALGLSKTTVSRILRRLE 235 (258)
T ss_pred CCCCHHHHHHHHHHHHhCCEEeHHHHHHhhCCChHHHHHHHHHHH
Confidence 4577778777766666666 6888999999999999999987643
No 340
>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=22.89 E-value=25 Score=28.86 Aligned_cols=27 Identities=26% Similarity=0.217 Sum_probs=23.2
Q ss_pred hccCCCccccccccccccccchhhhHH
Q 015682 113 RLASGESQVSVGVAFGVGQSTVSQVTW 139 (402)
Q Consensus 113 ~La~g~s~~~l~~~fgvs~sTv~~~i~ 139 (402)
+-..|.++.++|..+|+|++|++++-+
T Consensus 74 r~~~gltq~~lA~~lg~~~~tis~~e~ 100 (127)
T TIGR03830 74 RKKLGLSQREAAELLGGGVNAFSRYER 100 (127)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 455699999999999999999988753
No 341
>TIGR03454 partition_RepB plasmid partitioning protein RepB. Members of this family are the RepB protein involved in replicon partitioning. RepB is found, in general, as part of a repABC operon in plasmids and small chromosomes, separate from the main chromosome, in various bacteria. This model describes a rather narrow clade of proteins; it should be noted that additional homologs scoring below the trusted cutoff have very similar functions, although they may be named differently.
Probab=22.78 E-value=72 Score=31.33 Aligned_cols=70 Identities=23% Similarity=0.167 Sum_probs=44.8
Q ss_pred cCCcCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHH---HHHHHHhhcccccCCCc--hhHHHHHHHHH
Q 015682 97 EGRLLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRF---IEALEERAKHHLKWPDS--NRMEEIKSKFE 169 (402)
Q Consensus 97 ~~~~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v---~~al~~~~~~~i~~P~~--~~~~~i~~~f~ 169 (402)
.+..+|.-++.......+..|.+...++..+|+++++|++++.-. -+.|.+... .-|.. ..|.+++..+.
T Consensus 157 ~R~dLS~iE~A~~~~~L~~~G~~~~~ia~~Lg~~ks~vSr~lsl~~~lP~~li~~ig---~ap~~Gr~rw~~La~~l~ 231 (325)
T TIGR03454 157 ARRDLSFIERALFAQRLEDRGFDRDTIMAALSVDKTELSRMISVARRIPEELIEAIG---PAPGIGRPRWMELAELLE 231 (325)
T ss_pred cccCCCHHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHhCCHHHHHHhc---ccccccHHHHHHHHHHHh
Confidence 455677777765555666788888889999999999999987532 122222211 22432 26777766664
No 342
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=22.71 E-value=48 Score=31.22 Aligned_cols=40 Identities=10% Similarity=-0.019 Sum_probs=32.1
Q ss_pred HHHhhhccCCCccccccccccccccchhhhHHHHHHHHHH
Q 015682 108 AIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEE 147 (402)
Q Consensus 108 ~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~ 147 (402)
+-++..++...+++..|...++|+||||+.+.+.-+.+..
T Consensus 6 L~~f~~v~~~gs~s~AA~~L~isQ~avSr~i~~LE~~lg~ 45 (296)
T PRK09906 6 LRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGV 45 (296)
T ss_pred HHHHHHHHhhCCHHHHHHHhCCCCcHHHHHHHHHHHHhCC
Confidence 3344555556699999999999999999999988887743
No 343
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=22.49 E-value=57 Score=28.35 Aligned_cols=43 Identities=12% Similarity=0.074 Sum_probs=29.8
Q ss_pred CCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHH
Q 015682 101 LSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIE 143 (402)
Q Consensus 101 ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~ 143 (402)
+..-++-.+.+..-..-.++.+||...|+|.+||.+-+.+..+
T Consensus 12 lD~~D~~IL~~Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~ 54 (164)
T PRK11169 12 LDRIDRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLER 54 (164)
T ss_pred HHHHHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4433444444444445578999999999999999887766543
No 344
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=21.84 E-value=38 Score=29.52 Aligned_cols=44 Identities=27% Similarity=0.230 Sum_probs=35.2
Q ss_pred cCCHHHHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHH
Q 015682 100 LLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEAL 145 (402)
Q Consensus 100 ~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al 145 (402)
.++..+. -.|.+|+.|.+...|+...++|..||...+.+....+
T Consensus 149 ~lt~re~--~vl~~l~~g~s~~eIa~~l~~s~~tv~~~~~~~~~kl 192 (210)
T PRK09935 149 VLSNREV--TILRYLVSGLSNKEIADQLLLSNKTVSAHKSNIYGKL 192 (210)
T ss_pred cCCHHHH--HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHc
Confidence 3555544 3456799999999999999999999999888877665
No 345
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=21.72 E-value=57 Score=30.96 Aligned_cols=41 Identities=12% Similarity=0.033 Sum_probs=31.9
Q ss_pred HHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHH
Q 015682 106 QVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEE 147 (402)
Q Consensus 106 ~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~ 147 (402)
+|-+++....+| |+...|...+|+++|||+.+++.-+.+..
T Consensus 5 ~L~~f~~v~~~g-S~s~AA~~L~itQpavS~~i~~LE~~lg~ 45 (305)
T PRK11151 5 DLEYLVALAEHR-HFRRAADSCHVSQPTLSGQIRKLEDELGV 45 (305)
T ss_pred HHHHHHHHHHhC-CHHHHHHHhCCCchHHHHHHHHHHHHhCc
Confidence 344444444555 89999999999999999999988887743
No 346
>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=21.67 E-value=40 Score=24.36 Aligned_cols=25 Identities=20% Similarity=0.205 Sum_probs=20.2
Q ss_pred hccCC--Cccccccccccccccchhhh
Q 015682 113 RLASG--ESQVSVGVAFGVGQSTVSQV 137 (402)
Q Consensus 113 ~La~g--~s~~~l~~~fgvs~sTv~~~ 137 (402)
|+.++ ..+.+||..+|||.+||+.+
T Consensus 16 y~~~~g~i~lkdIA~~Lgvs~~tIr~W 42 (60)
T PF10668_consen 16 YKESNGKIKLKDIAEKLGVSESTIRKW 42 (60)
T ss_pred HHHhCCCccHHHHHHHHCCCHHHHHHH
Confidence 45444 67889999999999999754
No 347
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=21.61 E-value=80 Score=29.02 Aligned_cols=23 Identities=13% Similarity=0.188 Sum_probs=18.2
Q ss_pred ccccccccccccccchhhhHHHH
Q 015682 119 SQVSVGVAFGVGQSTVSQVTWRF 141 (402)
Q Consensus 119 s~~~l~~~fgvs~sTv~~~i~~v 141 (402)
+-..+|...|+|+.|+.+++...
T Consensus 175 Taeela~~~giSRvTaRRYLeyl 197 (224)
T COG4565 175 TAEELAQALGISRVTARRYLEYL 197 (224)
T ss_pred CHHHHHHHhCccHHHHHHHHHHH
Confidence 34468899999999999887544
No 348
>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=21.60 E-value=27 Score=28.24 Aligned_cols=31 Identities=10% Similarity=0.187 Sum_probs=21.8
Q ss_pred cCCCccccccccccccccchhhhHHHHHHHH
Q 015682 115 ASGESQVSVGVAFGVGQSTVSQVTWRFIEAL 145 (402)
Q Consensus 115 a~g~s~~~l~~~fgvs~sTv~~~i~~v~~al 145 (402)
-.|.+...|+..||+|..+|.+|+.+.-...
T Consensus 70 f~G~n~~eLA~kyglS~r~I~~Ii~~~~~~~ 100 (108)
T PF08765_consen 70 FNGMNVRELARKYGLSERQIYRIIKRVRRRE 100 (108)
T ss_dssp --SS-HHHHHHHHT--HHHHHHHHHHHHH--
T ss_pred hCCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 3499999999999999999999998775543
No 349
>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=21.18 E-value=43 Score=27.75 Aligned_cols=26 Identities=19% Similarity=0.190 Sum_probs=21.0
Q ss_pred CccccccccccccccchhhhHHHHHH
Q 015682 118 ESQVSVGVAFGVGQSTVSQVTWRFIE 143 (402)
Q Consensus 118 ~s~~~l~~~fgvs~sTv~~~i~~v~~ 143 (402)
.+..+|+..+++|++++++++.....
T Consensus 26 ~s~~eia~~l~is~~~v~~~l~~L~~ 51 (130)
T TIGR02944 26 YSAAEIAEQTGLNAPTVSKILKQLSL 51 (130)
T ss_pred ccHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 46778999999999999888765543
No 350
>PF14493 HTH_40: Helix-turn-helix domain
Probab=21.13 E-value=47 Score=25.76 Aligned_cols=59 Identities=19% Similarity=0.190 Sum_probs=40.5
Q ss_pred HHHhhhccCCCccccccccccccccchhhhHHHHHHHHHHh-hcccccCCCchhHHHHHHHHH
Q 015682 108 AIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEER-AKHHLKWPDSNRMEEIKSKFE 169 (402)
Q Consensus 108 ~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~-~~~~i~~P~~~~~~~i~~~f~ 169 (402)
.+|+..+..|.+..+||..-+++.|||...+-+.+..=... +.++ -+.++...+...+.
T Consensus 4 ~~T~~l~~~G~si~eIA~~R~L~~sTI~~HL~~~~~~g~~~~~~~~---l~~e~~~~I~~~~~ 63 (91)
T PF14493_consen 4 QITYELFQKGLSIEEIAKIRGLKESTIYGHLAELIESGEPLDIEEL---LSEEEIKQIEDAIE 63 (91)
T ss_pred HHHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHhCCCCCHHHh---CCHHHHHHHHHHHH
Confidence 46777788999999999999999999988877666542211 1222 23445566666554
No 351
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=21.12 E-value=51 Score=27.70 Aligned_cols=43 Identities=21% Similarity=0.193 Sum_probs=34.5
Q ss_pred HHHHHHhhhccCCCccccccccccccccchhhhHHHHHHHHHH
Q 015682 105 KQVAIALRRLASGESQVSVGVAFGVGQSTVSQVTWRFIEALEE 147 (402)
Q Consensus 105 ~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i~~v~~al~~ 147 (402)
.....+..++..|.+.++++...||+.+|+.+++.++...+..
T Consensus 77 ~~~~~~~~~~~~~~~i~~~a~~l~i~~~~~~r~~~r~~~~~~~ 119 (129)
T COG3677 77 KIKLQAVTLYMLGLGIRDIARTLGISINTVNRWSKRFGSRVEG 119 (129)
T ss_pred HHHHHHHHHHHcCCCcccHHHHhcccHHHHHHHHHhhcchhhc
Confidence 3444445556667889999999999999999999999888754
No 352
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=21.02 E-value=24 Score=34.58 Aligned_cols=21 Identities=33% Similarity=0.291 Sum_probs=18.0
Q ss_pred ccccccccccccccchhhhHH
Q 015682 119 SQVSVGVAFGVGQSTVSQVTW 139 (402)
Q Consensus 119 s~~~l~~~fgvs~sTv~~~i~ 139 (402)
+..++|..-|||.+|||++++
T Consensus 2 TikDVA~~AGVS~sTVSrvln 22 (333)
T COG1609 2 TIKDVAKLAGVSKATVSRVLN 22 (333)
T ss_pred CHHHHHHHhCCCHHHHHHHHc
Confidence 356889999999999999874
No 353
>COG4974 XerD Site-specific recombinase XerD [DNA replication, recombination, and repair]
Probab=20.52 E-value=1.9e+02 Score=28.03 Aligned_cols=100 Identities=14% Similarity=0.051 Sum_probs=63.1
Q ss_pred ccccccccccccCCCCCCCCCCC--Chhhhhcc--cCCCHHHHHHHHHHHhccccCCCCCCCccccCCcCCHH-HHHHHH
Q 015682 36 DSDWWPSFWAKNSSTPGATIPSD--EEEGFKYF--FRVSKKTFDYICSLVREDLVSRPPSGLINIEGRLLSVE-KQVAIA 110 (402)
Q Consensus 36 ~~~ww~~~~~~~~~~~~~~~~~~--~~~~F~~~--fRms~~tF~~L~~~l~~~~~~~~~~g~~~~~~~~ls~e-~~l~i~ 110 (402)
...|...|+..-+. ..+... +|.-|.+. -+|||..|-++++.+...-.. . ..+||- .+=+.+
T Consensus 187 A~~~l~~Yl~~~R~---~l~~~~~~~~~LF~n~~g~~ltrq~~w~~lk~~a~~Agi---------~-~~isPH~LRHsFA 253 (300)
T COG4974 187 AVEALEKYLEEARP---KLLKGKSSTDALFPNQRGGGLTRQGFWKRLKDYAERAGI---------D-KKISPHTLRHSFA 253 (300)
T ss_pred HHHHHHHHHHHhhH---HHhccCCCCCeeeecCCCCCCCHHHHHHHHHHHHHHhCC---------C-CCcCchhhHHHHH
Confidence 34677777762221 001001 34455553 468999999999876432111 1 234443 367788
Q ss_pred hhhccCCCcccccccccccc-ccchhhhHHHHHHHHHHh
Q 015682 111 LRRLASGESQVSVGVAFGVG-QSTVSQVTWRFIEALEER 148 (402)
Q Consensus 111 L~~La~g~s~~~l~~~fgvs-~sTv~~~i~~v~~al~~~ 148 (402)
-+.|.+|...+.++...|.+ -||...+++-.-+.|.++
T Consensus 254 THLL~~GADlRvVQeLLGHadisTTQIYTHV~~e~L~~~ 292 (300)
T COG4974 254 THLLENGADLRVVQELLGHADISTTQIYTHVTKERLRDL 292 (300)
T ss_pred HHHHhCCccHHHHHHHhCccccchhHHHHHHHHHHHHHH
Confidence 88899999999999999986 577777776555555444
No 354
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=20.26 E-value=31 Score=35.50 Aligned_cols=30 Identities=20% Similarity=0.242 Sum_probs=24.6
Q ss_pred CccccccccccccccchhhhHHHHHHHHHHhhcccccCCC
Q 015682 118 ESQVSVGVAFGVGQSTVSQVTWRFIEALEERAKHHLKWPD 157 (402)
Q Consensus 118 ~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~~~~i~~P~ 157 (402)
..+.+||...|++.|||||+|. ..|+..|.
T Consensus 344 LtlkdvAe~lglheSTVSRav~----------~Kyv~tp~ 373 (455)
T PRK05932 344 LVLKDIAEELGMHESTISRATT----------NKYMATPR 373 (455)
T ss_pred ccHHHHHHHhCCCccchhhhhc----------CceeecCC
Confidence 5678999999999999999884 56676664
No 355
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=20.07 E-value=33 Score=35.59 Aligned_cols=30 Identities=23% Similarity=0.238 Sum_probs=24.7
Q ss_pred CccccccccccccccchhhhHHHHHHHHHHhhcccccCCC
Q 015682 118 ESQVSVGVAFGVGQSTVSQVTWRFIEALEERAKHHLKWPD 157 (402)
Q Consensus 118 ~s~~~l~~~fgvs~sTv~~~i~~v~~al~~~~~~~i~~P~ 157 (402)
..+++||...|++.|||||++. ..|+..|.
T Consensus 370 LtlkdVAe~lglHeSTVSRa~~----------~KY~~tp~ 399 (481)
T PRK12469 370 LVLRDVAEELGLHESTISRATG----------NKYMATPR 399 (481)
T ss_pred CcHHHHHHHhCCCcchhhHHhc----------CceeecCC
Confidence 4678999999999999999884 56776664
No 356
>PRK13832 plasmid partitioning protein; Provisional
Probab=20.02 E-value=59 Score=33.82 Aligned_cols=42 Identities=17% Similarity=0.158 Sum_probs=35.0
Q ss_pred cCCcCCHHHHHHHHhhhccCCCccccccccccccccchhhhH
Q 015682 97 EGRLLSVEKQVAIALRRLASGESQVSVGVAFGVGQSTVSQVT 138 (402)
Q Consensus 97 ~~~~ls~e~~l~i~L~~La~g~s~~~l~~~fgvs~sTv~~~i 138 (402)
.+..+++-++...+-..+..|.+...|+..||+|+++|++..
T Consensus 98 QRedL~PiEea~AfkrLie~G~T~EeIA~~lG~S~~~V~rll 139 (520)
T PRK13832 98 AREPLNPVDQWRAIERLVALGWTEEAIAVALALPVRQIRKLR 139 (520)
T ss_pred CcCCCCHHHHHHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHH
Confidence 345678878877777777899999999999999999999854
Done!